# 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/Crenarchaeota/Fervidicoccus_fontis_Kam940_uid162201/NC_017461.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/Crenarchaeota/Fervidicoccus_fontis_Kam940_uid162201/NC_017461.PFam32-A
# per-seq hits tabular output:     /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Crenarchaeota/Fervidicoccus_fontis_Kam940_uid162201/NC_017461.PFam32-A.tblout
# number of worker threads:        20
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       gi|385805052|ref|YP_005841450.1|  [L=599]
Description: hypothetical protein FFONT_0001 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score 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   12.2   0.0       0.89    9.8   0.0    2.2  2  AAA_22    AAA domain


Domain annotation for each model (and alignments):
>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.38   6.7e+03      92     117 ..     143     177 ..     103     198 .. 0.54
   2 ?    9.8   0.0     5e-05      0.89       8      27 ..     309     328 ..     307     340 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.38
                            AAA_22  92 ielliiDEaqh.lrs.........eealeeLrslln 117
                                        e+  iDE+   + s         +++l+eL ++++
  gi|385805052|ref|YP_005841450.1| 143 SEFASIDEIAGkV-SeilgekfypARLLSELYTRWD 177
                                       4444455554444.2222233444555555555555 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 5e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlle 27 
                                       l+++Ge+GtGKT+  + +  
  gi|385805052|ref|YP_005841450.1| 309 LALFGEPGTGKTFASKDMIL 328
                                       789**********9887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (599 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); 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: 0.72u 0.31s 00:00:01.03 Elapsed: 00:00:00.55
# Mc/sec: 3282.43
//
Query:       gi|385805053|ref|YP_005841451.1|  [L=41]
Description: hypothetical protein FFONT_0002 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.32s 00:00:00.77 Elapsed: 00:00:00.51
# Mc/sec: 239.99
//
Query:       gi|385805054|ref|YP_005841452.1|  [L=42]
Description: hypothetical protein FFONT_0004 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.46
# Mc/sec: 274.70
//
Query:       gi|385805055|ref|YP_005841453.1|  [L=146]
Description: hypothetical protein FFONT_0005 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score 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   15.2  11.1      0.011   15.0  11.1    1.0  1  ABC2_membrane_2  ABC-2 family transporter protein
        2.4    8.6   8.4       0.28   11.6   0.6    2.3  2  DUF983           Protein of unknown function (DUF983)


Domain annotation for each model (and alignments):
>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0  11.1   1.2e-06     0.011     159     286 ..      11     135 ..       1     136 [. 0.77

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.2e-06
                   ABC2_membrane_2 159 edllllvvasvlllllv.vflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqeindfls 234
                                       e+ l lvv+s+l+++++ +f a+  ll +v++s ++a   + ++ ++l++l+  +l  +++l+a  ++         
  gi|385805055|ref|YP_005841453.1|  11 ENTLGLVVSSLLSAVFLyAFSAFLSLLMIVLKSPKSA-SFVTAVPLMLSFLSYSSL--WLNLKA--SA--------- 73 
                                       5678899******999988888888999999955555.555566666666666666..666666..44......... PP

                   ABC2_membrane_2 235 llsptsayntllneilagsdlna..........lgstatnllilllllavllvlgyvlFkrk 286
                                       ++sp++ + +l+   ++g +  +          l+  + ++++l+++++++l+l++ l++++
  gi|385805055|ref|YP_005841453.1|  74 YISPFNCISALFYYYFSGNEPATggyftsggkeLMNVTLTAFSLIGWTIIMLILAIILLRKM 135
                                       66999999999999999996555999999***65555667888999**********999886 PP

>> DUF983  Protein of unknown function (DUF983)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   1.7     0.073   6.5e+02      32      67 ..      28      58 ..      13      71 .. 0.52
   2 ?   11.6   0.6   3.1e-05      0.28      56      81 ..     115     140 ..     106     143 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.073
                            DUF983 32 ilivghlvvplallvevayepplwvhlliwlpltll 67
                                      + + ++l      l+ + ++ p   ++++ +pl+l 
  gi|385805055|ref|YP_005841453.1| 28 YAFSAFL-----SLLMIVLKSPKSASFVTAVPLMLS 58
                                      3333333.....333344444444555555555443 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 3.1e-05
                            DUF983  56 vhlliwlpltlllsllllrplKGalv 81 
                                       ++l+ w++++l+l+++llr ++G+ +
  gi|385805055|ref|YP_005841453.1| 115 FSLIGWTIIMLILAIILLRKMRGVSI 140
                                       67899******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       855  (0.0476881); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 871.37
//
Query:       gi|385805056|ref|YP_005841454.1|  [L=54]
Description: hypothetical protein FFONT_0006 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       190  (0.0105974); 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: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 368.60
//
Query:       gi|385805057|ref|YP_005841455.1|  [L=372]
Description: hypothetical protein FFONT_0007 [Fervidicoccus fontis Kam940]
Scores for complete 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-97  326.5   0.0    1.8e-97  326.3   0.0    1.0  1  DUF917    Protein of unknown function (DUF917)
  ------ inclusion threshold ------
      0.037   13.7   0.0      0.067   12.9   0.0    1.3  1  DUF4807   Domain of unknown function (DUF4807)


Domain annotation for each model (and alignments):
>> DUF917  Protein of unknown function (DUF917)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  326.3   0.0    2e-101   1.8e-97       2     350 .]      10     362 ..       9     362 .. 0.95

  Alignments for each domain:
  == domain 1  score: 326.3 bits;  conditional E-value: 2e-101
                                       GHHHHHHHHHHTTTT-SS-HHHHHHHHTT-SBTT.--EEEE-GGG--SEE..EEEEEEE-HHHHTT-SS-...HH.. CS
                            DUF917   2 dlealatGaavLGtGGGGspysgylllrqaleeg.ksvrvvsldelpddalvvvvgamGsptvieeklps...gdel 74 
                                       d+e l++Ga+vLGtGGGG+p++gy  l  +l+e+ k +++ +l++lp d ++vv++++Gs++++ ++  +   +d +
  gi|385805057|ref|YP_005841455.1|  10 DVERLVIGATVLGTGGGGDPKEGYKALSGVLKEKeKPIKIADLESLPSDGVIVVPYYVGSIAPGLKQKKPvviKDPI 86 
                                       89******************************99549*************************998877552225699 PP

                                       ..HHHHHHHHHT--EEEEE-SSSSCCHHHHHHHHHHHHT-EEESB-SSSS--SSGGGSHHHHTT----SEEEE-SSS CS
                            DUF917  75 leavealekllgrkidavislEiGGlNglvallaaaklglpvvDaDgmGRAfPelqqttfavagisltPlaladekg 151
                                        ea+e lek lg+k++av++ E+GG+N+ +al ++a+ +lp +D+D+ GRA Pel+q+t+ ++g s++P+al++e+g
  gi|385805057|ref|YP_005841455.1|  87 SEAFEILEKELGKKVNAVVASEMGGSNTSIALSIGARRDLPAIDGDLLGRAAPELHQCTVLIFGYSMAPSALVTETG 163
                                       ***************************************************************************** PP

                                       -EEEEEE.---HHHHHHHHHHCTTTTTEEEEEEEEE-HHHHHH--SBSHHHHHHHHHHHHHTT--......-SHHHH CS
                            DUF917 152 nvvllkkaqsdkavErllRaalvemgsfagvaaypmtgaelkraavpgtlslalriGravaearea.k...dvveai 224
                                       +vv++k+a  d  +E ++R + v  g+f++v++ p+t++ +++a+v+gt+sla+++G  + +a+++ +    ++e++
  gi|385805057|ref|YP_005841455.1| 164 DVVVVKNAYID-DYEAIARYISVLGGGFVAVVDTPLTKEMAENAVVKGTMSLAYKLGDEILSAKARgErgnITAERV 239
                                       *******6555.8***************************************************8773575677999 PP

                                       HHHHHH-EEEEEEEEE--------------EEEET.......EEEEEEESSSEEEEE..ET-SEETTSEEEEEHHB- CS
                            DUF917 225 lealgggakvlfkGkivdverrteggfdvgevtiegldedegrelkiefqNEnllaeedgevlatvPDlIsvldaet 301
                                       ++ l+ g++ +f+G ++++++r+e+gf +ge++++g ++++gr+l+ +++NE+++++ ++e l++ PD+ ++l +++
  gi|385805057|ref|YP_005841455.1| 240 ADLLR-GWV-VFEGIVSKYSWRDERGFLRGEAELRGKGDYAGRKLRSWIMNEHIMVWINDESLVMPPDIFTLL-SSD 313
                                       99999.688.***************************************************************.899 PP

                                       SSSSB-TTTT.TS-EEEEEE---GGGS..SHHHH-S-....-....--- CS
                            DUF917 302 gepigteelryGlrVtVlalpasekwrteeglelvgPkaFGydleykpl 350
                                       g+p+++ +l++G++V  +a p ++ wrte+glel+gPk+FG++ley p+
  gi|385805057|ref|YP_005841455.1| 314 GNPVTNTDLKEGMEVIAVAAPSPKVWRTERGLELFGPKHFGFNLEYIPV 362
                                       **********************************************997 PP

>> DUF4807  Domain of unknown function (DUF4807)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   7.5e-06     0.067      22      73 ..     177     228 ..     164     228 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.5e-06
                           DUF4807  22 eeamawLstLggafsaLgdkfeeaaevAgkislqQlklAlklgdPlllarck 73 
                                       e +  ++s Lgg+f a+ d           +    ++lA klgd +l a+++
  gi|385805057|ref|YP_005841455.1| 177 EAIARYISVLGGGFVAVVDTPLTKEMAENAVVKGTMSLAYKLGDEILSAKAR 228
                                       6677789************9766544445566678**************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); 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: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2535.91
//
Query:       gi|385805058|ref|YP_005841456.1|  [L=259]
Description: putative permease [Fervidicoccus fontis Kam940]
Scores for complete 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-54  182.6  38.1      1e-53  182.4  38.1    1.0  1  TauE          Sulfite exporter TauE/SafE
  ------ inclusion threshold ------
       0.17   11.9   7.0        1.9    8.5   0.1    3.0  2  DUF1422       Protein of unknown function (DUF1422)


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 !  182.4  38.1   1.1e-57     1e-53       2     236 .]      13     250 ..      11     250 .. 0.96

  Alignments for each domain:
  == domain 1  score: 182.4 bits;  conditional E-value: 1.1e-57
                              TauE   2 llagllaGfvagllGiGggliavPlLlll..l.ppavavatsllavvatslsgalahrrrgnvdwrlllllllgsli 75 
                                       ++ gl++Gf  gl+G+Gg+++a+PlLl++  + +p+++++t++lav ++++ +++ h r++nv++r ++l+++++++
  gi|385805058|ref|YP_005841456.1|  13 IISGLIVGFSLGLIGGGGSILAIPLLLYFvgFnHPHMVIGTTALAVSINAFLNLIPHARKKNVNFRKGILFSIPGVA 89 
                                       789*************************73549******************************************** PP

                              TauE  76 GallGallllllpsellkllfgvlllllallmllrkkrsrakgrerrptaillvligglvGllsGllGiGgGfllvp 152
                                       G+l+Ga l ll+p++ l++lf++l+++++++ml rk  ++a + +++++ + l+ ig+lvG++sG++GiGgGfl+vp
  gi|385805058|ref|YP_005841456.1|  90 GVLIGAELGLLTPGKKLLFLFAILMIIIGIYMLKRKCVNAAAEPKHEESIAKLLSIGFLVGFASGYFGIGGGFLIVP 166
                                       ********************************997776666667888889999999999****************** PP

                              TauE 153 llllllglplkkavatslllilvislagalgyalagavdwpllllllpgallGallGarlarrlsertlrrlfalll 229
                                        l++   l++ +av+tsl+ + +++l++a+ ya++g++++ + + +++g+++G+++Ga++a+++s+r l ++fa+++
  gi|385805058|ref|YP_005841456.1| 167 GLIYSAALNILQAVGTSLISVGLFGLVTAIRYAISGDLNLIISASYILGGIFGGWIGAYFASKVSKRLLTKIFAIII 243
                                       *****************************************9999******************************** PP

                              TauE 230 lvlgvkl 236
                                       +++++++
  gi|385805058|ref|YP_005841456.1| 244 IIVAIYM 250
                                       *****98 PP

>> DUF1422  Protein of unknown function (DUF1422)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1   0.00022       1.9       8      73 ..      79     150 ..      72     157 .. 0.77
   2 ?    5.1   1.6    0.0025        23      19      51 ..     221     253 ..     207     257 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00022
                           DUF1422   8 ktllLal..iaGlslngtlsalfsslvpfsifplialvlavyclyqrYlnksle....eglPllalacfllG 73 
                                       k +l ++  +aG+ + + l  l+       +f+++ +++ +y+l ++ +n + e    e + +l    fl+G
  gi|385805058|ref|YP_005841456.1|  79 KGILFSIpgVAGVLIGAELGLLTPGKKLLFLFAILMIIIGIYMLKRKCVNAAAEpkheESIAKLLSIGFLVG 150
                                       555555555899999999*****9999999*****************9987654111156667777777777 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0025
                           DUF1422  19 slngtlsalfsslvpfsifplialvlavyclyq 51 
                                        + + ++  +s  +   if++i +++a+y+l+ 
  gi|385805058|ref|YP_005841456.1| 221 WIGAYFASKVSKRLLTKIFAIIIIIVAIYMLFM 253
                                       45555666666666778**************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1175  (0.0655363); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 1808.13
//
Query:       gi|385805059|ref|YP_005841457.1|  [L=47]
Description: hypothetical protein FFONT_0009 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); 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: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 298.73
//
Query:       gi|385805060|ref|YP_005841458.1|  [L=453]
Description: putative transporter component [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-23   83.3  20.1    2.3e-23   83.3  20.1    1.7  2  Sulf_transp     Sulphur transport
  ------ inclusion threshold ------
        1.6    8.8   9.5       0.58   10.1   0.2    3.8  4  UCR_UQCRX_QCR9  Ubiquinol-cytochrome C reductase, UQCRX/QCR9 


Domain annotation for each model (and alignments):
>> Sulf_transp  Sulphur transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   1.0      0.93   8.3e+03      38      46 ..      20      28 ..       7      51 .. 0.39
   2 !   83.3  20.1   2.5e-27   2.3e-23      11     310 .]      66     437 ..      58     437 .. 0.63

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 0.93
                       Sulf_transp 38 llaaaglid 46
                                      ll  +g i 
  gi|385805060|ref|YP_005841458.1| 20 LLMLFGGIY 28
                                      222222222 PP

  == domain 2  score: 83.3 bits;  conditional E-value: 2.5e-27
                       Sulf_transp  11 rdivvekdgrllralllaiavaavgfqllaaa.glidlpksafpvvglivGGllFGvGMalaGgCasgtlyrvGeGs 86 
                                        +++ ++d  l+  + +ai+  a+++ +l+    + ++  ++f v g+i+GG++FG+G  +aG  ++++++ +G+G+
  gi|385805060|ref|YP_005841458.1|  66 YRVMAFQDRFLMVCFGFAIGFGAILLYALNLIvPSPNFGIKSFFVPGVIIGGIIFGIGVGIAGYFPGTVWIALGQGR 142
                                       5789999999999999****9998877776551566677789999******************************** PP

                       Sulf_transp  87 lralitllffilgava...lltgilsswleqllestvskeslyetlg.lspllliall..lliallllvkelrkek. 156
                                         a+++ll+  lga+    +   + ++++++l   ++++ ++ ++++ +++  + +++  +li l l++ +    + 
  gi|385805060|ref|YP_005841458.1| 143 RDAIWALLGGLLGAFTwslIFGYAKPFFWDTLNYGPITWADILGKTSkIGMFEVSLIFgtVLILLFLILPRYPG-Ek 218
                                       *************9862222333344666677777888887754444244433322221122222222212222.13 PP

                       Sulf_transp 157 .............................lqeaeklektslakklfrkpwslvlgavllgllavlawllsaktgrsf 204
                                                                    + +a++  +  + ++ ++++  +++ +  + ++av++++l + +g s+
  gi|385805060|ref|YP_005841458.1| 219 ikdscgahilglsksviqfndlineekekYPHARPFITRITNESSIKNARYILILGAEFTITAVAVIILHQIFGEST 295
                                       45567777777777777777765433333333332222233344444444444555555666666666665566655 PP

                       Sulf_transp 205 glg........ft..vpgakilqyl..........vlgtskf..lnwgvvlvlGiilGaflaall.sgef.kle..a 255
                                       +++        +    ++a+ l+++          v  ++ f  + w+ +++lG +lG +++a l s++f +++  +
  gi|385805060|ref|YP_005841458.1| 296 TYSwigaqlsyLLnpMWAASNLYFQlfggmhlvngVPVNNPFseIGWEPLSDLGTFLGGLISATLiSKRFmAFKplV 372
                                       4321111111111112333333333334433333222233443345899************9976266662333213 PP

                       Sulf_transp 256 pk.a.........rellaallGGllMGfGarlAgGCniGaglsgiaslslsgwlalvflllGavl 310
                                       pk +         ++++ +++G +l+ fGar+A+GC +G++lsg  ++++s+++++v++ll a++
  gi|385805060|ref|YP_005841458.1| 373 PKvWerrfgpsetKRAIGSFIGTFLVLFGARMANGCASGHILSGNIQMAVSSFVFMVTVLLSAWI 437
                                       33225555555555***********************************************9996 PP

>> UCR_UQCRX_QCR9  Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.3     0.021   1.8e+02      12      30 ..     107     125 ..     105     128 .. 0.88
   2 ?   10.1   0.2   6.5e-05      0.58      19      49 ..     153     184 ..     142     187 .. 0.85
   3 ?   -2.7   0.0      0.67   6.1e+03      27      39 ..     366     378 ..     350     379 .. 0.63
   4 ?   -1.1   0.4       0.2   1.8e+03      12      24 ..     425     437 ..     423     441 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.021
                                       HHHHHHHHHHHHHHHHHHH CS
                    UCR_UQCRX_QCR9  12 stfvltifagAfvferafD 30 
                                       s fv  +++g+++f +++ 
  gi|385805060|ref|YP_005841458.1| 107 SFFVPGVIIGGIIFGIGVG 125
                                       789***********99986 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 6.5e-05
                                       HHHHHHHHHHHHHHHHHHHHHHTTTT.SHHHH CS
                    UCR_UQCRX_QCR9  19 fagAfvferafDsatdkiWdsiNkGK.lWkDI 49 
                                       + gAf+++  f +a   +Wd++N G   W DI
  gi|385805060|ref|YP_005841458.1| 153 LLGAFTWSLIFGYAKPFFWDTLNYGPiTWADI 184
                                       68*********************996247777 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 0.67
                                       HHHHHHHHHHHHH CS
                    UCR_UQCRX_QCR9  27 rafDsatdkiWds 39 
                                       +af  ++ k+W++
  gi|385805060|ref|YP_005841458.1| 366 MAFKPLVPKVWER 378
                                       4677788888986 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 0.2
                                       HHHHHHHHHHHHH CS
                    UCR_UQCRX_QCR9  12 stfvltifagAfv 24 
                                        +f++t++ +A +
  gi|385805060|ref|YP_005841458.1| 425 FVFMVTVLLSAWI 437
                                       69******99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       710  (0.0396006); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 2855.24
//
Query:       gi|385805061|ref|YP_005841459.1|  [L=64]
Description: hypothetical protein FFONT_0011 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       412  (0.0229795); 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:                         0  (0); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 441.65
//
Query:       gi|385805062|ref|YP_005841460.1|  [L=43]
Description: hypothetical protein FFONT_0012 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       207  (0.0115455); expected 358.6 (0.02)
Passed bias filter:                      173  (0.00964917); 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: 0.43u 0.32s 00:00:00.75 Elapsed: 00:00:00.49
# Mc/sec: 265.16
//
Query:       gi|385805063|ref|YP_005841461.1|  [L=71]
Description: hypothetical protein FFONT_0013 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00062   19.6   1.4       0.21   11.5   0.1    2.4  2  zinc_ribbon_4   zinc-ribbon domain
     0.0039   17.1   1.2       0.34   10.9   0.0    2.2  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
     0.0063   16.5   0.6       0.46   10.6   0.0    2.1  2  zf-Sec23_Sec24  Sec23/Sec24 zinc finger
  ------ inclusion threshold ------
      0.011   15.8   0.2       0.82    9.7   0.0    2.0  2  CpXC            CpXC protein
      0.026   14.8   1.4        2.4    8.5   0.0    2.3  2  zf-C6H2         zf-MYND-like zinc finger, mRNA-binding
      0.036   13.5   0.5        6.2    6.4   0.3    2.2  2  Mu-like_Com     Mu-like prophage protein Com
      0.037   13.4   3.0       0.31   10.4   3.1    2.0  1  zf-TFIIB        Transcription factor zinc-finger
      0.038   13.7   2.8       0.16   11.8   0.1    2.2  2  Zn_Tnp_IS1      InsA N-terminal domain
      0.056   12.9   3.5       0.51    9.8   0.4    2.2  2  zf-ribbon_3     zinc-ribbon domain
      0.059   13.8   2.8        1.2    9.7   0.6    2.4  2  zf-H2C2_2       Zinc-finger double domain
      0.064   13.2   3.3       0.14   12.2   0.2    2.2  2  ADK_lid         Adenylate kinase, active site lid
      0.079   13.0   0.3       0.11   12.5   0.3    1.3  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.12   12.2   1.1        4.5    7.1   0.1    2.3  2  PADR1           PADR1 (NUC008) domain
       0.13   12.2   2.2       0.89    9.6   0.2    2.4  2  zf_CopZ         Zinc binding domain
       0.15   11.6   1.8        2.7    7.6   0.2    2.2  2  TF_Zn_Ribbon    TFIIB zinc-binding
       0.16   11.9   2.1       0.55   10.2   1.8    1.9  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.17   11.8   3.3        1.9    8.5   0.1    2.3  2  Nudix_N_2       Nudix N-terminal
       0.18   12.5   1.7       0.52   11.0   0.3    2.0  2  FYDLN_acid      Protein of unknown function (FYDLN_acid)
       0.19   11.5   2.5         25    4.8   0.0    3.0  3  Cys_rich_KTR    Cysteine-rich KTR
       0.29   11.0   2.8        8.1    6.4   0.4    2.2  2  TFIIS_C         Transcription factor S-II (TFIIS)
       0.29   11.1   5.1        1.5    8.8   0.3    2.2  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
        0.3   11.1   2.2        1.1    9.4   0.2    2.1  2  zf-BED          BED zinc finger
        0.4   10.3   2.6        2.5    7.7   2.6    1.9  1  TackOD1         Thaumarchaeal output domain 1
       0.43   10.7   5.4       0.96    9.6   0.3    2.2  2  UPF0547         Uncharacterised protein family UPF0547
       0.62    9.8   3.8         12    5.7   0.8    2.3  2  A2L_zn_ribbon   A2L zinc ribbon domain
          1    9.2   6.9          3    7.7   1.3    2.3  2  zinc_ribbon_2   zinc-ribbon domain
        1.2    9.3   5.7         22    5.3   5.7    2.2  1  Zn-ribbon_8     Zinc ribbon domain
        7.9    6.6   9.4        2.4    8.3   1.9    2.3  2  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai


Domain annotation for each model (and alignments):
>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.1    0.0075       4.8      25      33 ..       1       9 [.       1      10 [. 0.89
   2 !   11.5   0.1   0.00033      0.21       3      13 ..      33      43 ..      28      54 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0075
                     zinc_ribbon_4 25 kvrCskCgh 33
                                      +++C+ Cgh
  gi|385805063|ref|YP_005841461.1|  1 MIKCPVCGH 9 
                                      689****99 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00033
                     zinc_ribbon_4  3 itCpsCkakye 13
                                       +Cp+C+a ++
  gi|385805063|ref|YP_005841461.1| 33 LECPKCHAIFN 43
                                      57888888876 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.3      0.03        19      22      28 ..       4      10 ..       1      10 [. 0.85
   2 !   10.9   0.0   0.00054      0.34       5      16 ..      35      46 ..      34      62 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.03
                    PhnA_Zn_Ribbon 22 CpeCahE 28
                                      Cp C+hE
  gi|385805063|ref|YP_005841461.1|  4 CPVCGHE 10
                                      9999998 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00054
                    PhnA_Zn_Ribbon  5 CplCaSeytYed 16
                                      Cp+C ++++Y  
  gi|385805063|ref|YP_005841461.1| 35 CPKCHAIFNYYS 46
                                      **********44 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 ?    4.6   0.1     0.054        34      25      32 ..       3      10 ..       1      13 [. 0.82
   2 !   10.6   0.0   0.00073      0.46       3      22 ..      34      53 ..      33      56 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.054
                    zf-Sec23_Sec24 25 iCnfCnhk 32
                                      +C+ C+h+
  gi|385805063|ref|YP_005841461.1|  3 KCPVCGHE 10
                                      8*****97 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00073
                    zf-Sec23_Sec24  3 rCrrCraylNpfckidfggk 22
                                       C +C+a+ N ++     g+
  gi|385805063|ref|YP_005841461.1| 34 ECPKCHAIFNYYSGTSPKGR 53
                                      5***********97766665 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1     0.042        27       1       9 [.       2      10 ..       1      21 [. 0.67
   2 ?    9.7   0.0    0.0013      0.82      36      74 ..      31      69 ..      24      71 .] 0.87

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.042
                              CpXC  1 ltCpaCgke 9 
                                      ++Cp Cg+e
  gi|385805063|ref|YP_005841461.1|  2 IKCPVCGHE 10
                                      455555554 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0013
                              CpXC 36 featCpkCgatakleapllyhdpekellillvpeserse 74
                                       + +CpkC+a + +   +  + ++ e++i + p + ++ 
  gi|385805063|ref|YP_005841461.1| 31 KRLECPKCHAIFNYYSGTSPKGRKSEFVIKVKPREVKRV 69
                                      6789***************99999****99999988765 PP

>> zf-C6H2  zf-MYND-like zinc finger, mRNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.3     0.038        24      13      26 ..       2      15 ..       1      25 [. 0.79
   2 ?    8.5   0.0    0.0037       2.4      11      20 ..      31      40 ..      28      44 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.038
                           zf-C6H2 13 LqCptClklgikes 26
                                      ++Cp+C   g +++
  gi|385805063|ref|YP_005841461.1|  2 IKCPVCGHEGNEGE 15
                                      59****99987764 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0037
                           zf-C6H2 11 ssLqCptClk 20
                                      ++L+Cp+C+ 
  gi|385805063|ref|YP_005841461.1| 31 KRLECPKCHA 40
                                      57******85 PP

>> Mu-like_Com  Mu-like prophage protein Com
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.3    0.0096       6.2      25      31 ..       2       8 ..       1      11 [. 0.90
   2 ?    5.5   0.0     0.017        11      24      42 ..      32      51 ..      24      57 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0096
                       Mu-like_Com 25 iKCPRCG 31
                                      iKCP CG
  gi|385805063|ref|YP_005841461.1|  2 IKCPVCG 8 
                                      9*****9 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.017
                       Mu-like_Com 24 tiKCPRCGt.LnHlkaesld 42
                                      ++ CP+C    n   + s++
  gi|385805063|ref|YP_005841461.1| 32 RLECPKCHAiFNYYSGTSPK 51
                                      57899997625888888875 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   3.1   0.00049      0.31       1      26 [.       3      39 ..       3      42 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00049
                          zf-TFIIB  1 kCPkCqdele...........eserggveidyCpqCr 26
                                      kCP+C++e +           ++++ +v+   Cp+C+
  gi|385805063|ref|YP_005841461.1|  3 KCPVCGHEGNegefklfkepwKFRFYDVKRLECPKCH 39
                                      8*******99555555555555555999999999997 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 ?    2.3   0.3      0.23   1.5e+02       6      11 ..       2       7 ..       1      10 [. 0.85
   2 ?   11.8   0.1   0.00024      0.16       7      25 ..      34      52 ..      31      55 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.23
                        Zn_Tnp_IS1  6 ihCPrC 11
                                      i CP C
  gi|385805063|ref|YP_005841461.1|  2 IKCPVC 7 
                                      89**** PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00024
                        Zn_Tnp_IS1  7 hCPrCsstdVyRhGkstag 25
                                       CP+C++   y  G s++g
  gi|385805063|ref|YP_005841461.1| 34 ECPKCHAIFNYYSGTSPKG 52
                                      7****************98 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.4   0.00079      0.51       2      10 ..       1       9 [.       1      11 [. 0.88
   2 ?    4.0   0.2     0.056        36       4       8 ..      34      38 ..      33      42 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00079
                       zf-ribbon_3  2 tvrCPnCGa 10
                                      +++CP CG+
  gi|385805063|ref|YP_005841461.1|  1 MIKCPVCGH 9 
                                      789999997 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.056
                       zf-ribbon_3  4 rCPnC 8 
                                      +CP+C
  gi|385805063|ref|YP_005841461.1| 34 ECPKC 38
                                      69999 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1      0.09        58      16      21 ..       3       8 ..       1      12 [. 0.85
   2 ?    9.7   0.6    0.0019       1.2      13      25 ..      31      43 ..      14      44 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.09
                         zf-H2C2_2 16 eCplCd 21
                                      +Cp+C+
  gi|385805063|ref|YP_005841461.1|  3 KCPVCG 8 
                                      8****7 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0019
                         zf-H2C2_2 13 kpyeCplCdkaFk 25
                                      k++eCp+C+  F+
  gi|385805063|ref|YP_005841461.1| 31 KRLECPKCHAIFN 43
                                      678*****97665 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 ?    1.9   0.3      0.35   2.2e+02      23      29 ..       3       9 ..       2      10 .. 0.67
   2 ?   12.2   0.2   0.00022      0.14       1      19 [.      32      51 ..      32      65 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.35
                                      B-TTT-- CS
                           ADK_lid 23 lCDkCGe 29
                                      +C +CG 
  gi|385805063|ref|YP_005841461.1|  3 KCPVCGH 9 
                                      5777775 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00022
                                      EEE-TTT--EEETTT.B--S CS
                           ADK_lid  1 RrvCpkCGrsYhvvf.npPk 19
                                      R+ CpkC +++++     Pk
  gi|385805063|ref|YP_005841461.1| 32 RLECPKCHAIFNYYSgTSPK 51
                                      788*********66466666 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 ?   12.5   0.3   0.00017      0.11      71      94 ..       2      40 ..       1      51 [. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00017
                                      EEETTTS-EEECHHHHH...............S-TTTSS CS
                              HypA 71 vrCreCgkefeleekal...............rCpkCgs 94
                                      ++C +Cg+e+++ e +l               +CpkC++
  gi|385805063|ref|YP_005841461.1|  2 IKCPVCGHEGNEGEFKLfkepwkfrfydvkrlECPKCHA 40
                                      79*********876333577999**************97 PP

>> PADR1  PADR1 (NUC008) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1     0.057        36      14      21 ..       2       9 ..       1      24 [. 0.78
   2 ?    7.1   0.1     0.007       4.5      15      28 ..      34      47 ..      31      58 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.057
                             PADR1 14 ekCpeCke 21
                                       kCp C++
  gi|385805063|ref|YP_005841461.1|  2 IKCPVCGH 9 
                                      69****85 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.007
                             PADR1 15 kCpeCkegqlvfds 28
                                      +Cp+C+    ++++
  gi|385805063|ref|YP_005841461.1| 34 ECPKCHAIFNYYSG 47
                                      7*****76666665 PP

>> zf_CopZ  Zinc binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.2    0.0014      0.89       3      12 ..       3      12 ..       1      16 [. 0.90
   2 ?    2.2   0.2      0.27   1.8e+02       3       9 ..      34      40 ..      32      43 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0014
                                      B-TTT--B-E CS
                           zf_CopZ  3 kCPvCgkkGk 12
                                      kCPvCg++G+
  gi|385805063|ref|YP_005841461.1|  3 KCPVCGHEGN 12
                                      7********8 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.27
                                      B-TTT-- CS
                           zf_CopZ  3 kCPvCgk 9 
                                      +CP+C++
  gi|385805063|ref|YP_005841461.1| 34 ECPKCHA 40
                                      7****95 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   0.2    0.0042       2.7       2       9 ..       3      10 ..       2      16 .. 0.86
   2 ?    3.7   0.1     0.069        44       2      12 ..      34      41 ..      33      49 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0042
                                      EETTTTCE CS
                      TF_Zn_Ribbon  2 kCPnCgst 9 
                                      kCP+Cg++
  gi|385805063|ref|YP_005841461.1|  3 KCPVCGHE 10
                                      9*****85 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.069
                                      EETTTTCEECH CS
                      TF_Zn_Ribbon  2 kCPnCgstnlv 12
                                       CP+C+    +
  gi|385805063|ref|YP_005841461.1| 34 ECPKCHA---I 41
                                      5****96...4 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.8   0.00085      0.55      30      56 ..       3      42 ..       2      44 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00085
                    OrfB_Zn_ribbon 30 tCseCgsknke.............alsgrtfkCpnCgfea 56
                                      +C++Cg++++e               + ++++Cp+C + +
  gi|385805063|ref|YP_005841461.1|  3 KCPVCGHEGNEgefklfkepwkfrFYDVKRLECPKCHAIF 42
                                      7**********99999999888877888999999998765 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.7     0.093        60       3       9 ..       4      10 ..       4      14 .. 0.82
   2 ?    8.5   0.1     0.003       1.9      21      32 ..      31      42 ..      29      44 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.093
                                      -TTT--B CS
                         Nudix_N_2  3 CsqCGtp 9 
                                      C+ CG++
  gi|385805063|ref|YP_005841461.1|  4 CPVCGHE 10
                                      8888885 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.003
                                      -EEEETTTTEEE CS
                         Nudix_N_2 21 eRlvCpaCgtih 32
                                       Rl Cp+C++i+
  gi|385805063|ref|YP_005841461.1| 31 KRLECPKCHAIF 42
                                      5999*****996 PP

>> FYDLN_acid  Protein of unknown function (FYDLN_acid)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1      0.87   5.6e+02      27      38 ..       2      13 ..       2      22 .. 0.75
   2 ?   11.0   0.3   0.00081      0.52      18      42 ..      26      48 ..      21      71 .] 0.73

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.87
                        FYDLN_acid 27 ivcpkcgeefep 38
                                      i cp cg+e + 
  gi|385805063|ref|YP_005841461.1|  2 IKCPVCGHEGNE 13
                                      679999998665 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00081
                        FYDLN_acid 18 kFYDLnkdPivcpkcgeefepeevl 42
                                      +FYD ++    cpkc++ f+  + +
  gi|385805063|ref|YP_005841461.1| 26 RFYDVKR--LECPKCHAIFNYYSGT 48
                                      9****99..79*******9987773 PP

>> Cys_rich_KTR  Cysteine-rich KTR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.038        25       4      11 ..       2       9 ..       1      19 [. 0.87
   2 ?    3.8   0.2      0.08        51      29      34 ..      34      39 ..      29      43 .. 0.81
   3 ?    2.1   0.0      0.27   1.7e+02      34      50 ..      54      70 ..      47      71 .] 0.78

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.038
                      Cys_rich_KTR  4 vlcPvCgn 11
                                      + cPvCg 
  gi|385805063|ref|YP_005841461.1|  2 IKCPVCGH 9 
                                      78****96 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.08
                      Cys_rich_KTR 29 fCPKCk 34
                                       CPKC 
  gi|385805063|ref|YP_005841461.1| 34 ECPKCH 39
                                      599997 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.27
                      Cys_rich_KTR 34 kqetlinvkqlkievik 50
                                      k e +i+vk  +++ +k
  gi|385805063|ref|YP_005841461.1| 54 KSEFVIKVKPREVKRVK 70
                                      56899****99999887 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 ?    6.4   0.4     0.013       8.1       1       9 [.       2      10 ..       2      12 .. 0.85
   2 ?    5.0   0.1     0.035        22       2       8 ..      34      40 ..      33      46 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.013
                           TFIIS_C  1 akCpkCgsr 9 
                                      +kCp Cg++
  gi|385805063|ref|YP_005841461.1|  2 IKCPVCGHE 10
                                      68****997 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.035
                           TFIIS_C  2 kCpkCgs 8 
                                      +CpkC+ 
  gi|385805063|ref|YP_005841461.1| 34 ECPKCHA 40
                                      7****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 ?    5.2   5.6     0.032        21      20      44 ..       3      39 ..       1      40 [. 0.74
   2 ?    8.8   0.3    0.0024       1.5      19      34 ..      33      49 ..      18      55 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.032
                     Zn_Tnp_IS1595 20 vCPhCgsr.kayrikt...........rglfqCkeCr 44
                                       CP Cg++    ++k             ++++C +C+
  gi|385805063|ref|YP_005841461.1|  3 KCPVCGHEgNEGEFKLfkepwkfrfydVKRLECPKCH 39
                                      5999999994444444445888888999999999998 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0024
                     Zn_Tnp_IS1595 19 fvCPhCgsr.kayrikt 34
                                        CP+C+    +y+ ++
  gi|385805063|ref|YP_005841461.1| 33 LECPKCHAIfNYYSGTS 49
                                      57****98888887665 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1      0.36   2.3e+02      16      29 ..       1      14 [.       1      21 [. 0.81
   2 ?    9.4   0.2    0.0017       1.1      14      33 ..      30      49 ..      20      50 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.36
                                      --EETTTTEE---- CS
                            zf-BED 16 kavCryCgkilsrg 29
                                      +++C  Cg + + g
  gi|385805063|ref|YP_005841461.1|  1 MIKCPVCGHEGNEG 14
                                      689*****988766 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0017
                                      SS--EETTTTEE----SSTH CS
                            zf-BED 14 eqkavCryCgkilsrgggtt 33
                                       ++ +C  C++i+++ +gt+
  gi|385805063|ref|YP_005841461.1| 30 VKRLECPKCHAIFNYYSGTS 49
                                      4699***********99997 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   2.6     0.004       2.5     104     132 ..       2      41 ..       1      46 [. 0.64

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.004
                           TackOD1 104 ihhftCgnvgpeeef...........lkegkleCpkCktk 132
                                       i++  Cg+ g+e ef            + ++leCpkC+  
  gi|385805063|ref|YP_005841461.1|   2 IKCPVCGHEGNEGEFklfkepwkfrfYDVKRLECPKCHAI 41 
                                       7788888888887764322222222246689******975 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.3    0.0015      0.96      14      23 ..       1      10 [.       1      10 [. 0.88
   2 ?    3.2   0.7      0.14        93       2       8 ..      34      40 ..      34      41 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0015
                           UPF0547 14 aqfCphCGyv 23
                                      + +Cp CG++
  gi|385805063|ref|YP_005841461.1|  1 MIKCPVCGHE 10
                                      689******7 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.14
                           UPF0547  2 vCPeCea 8 
                                      +CP C a
  gi|385805063|ref|YP_005841461.1| 34 ECPKCHA 40
                                      5999976 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.8     0.019        12       4      13 ..       2      11 ..       1      12 [. 0.89
   2 ?    5.1   0.1     0.031        20      24      33 .]      35      44 ..      32      44 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.019
                     A2L_zn_ribbon  4 kvCsvCggng 13
                                      ++C vCg++g
  gi|385805063|ref|YP_005841461.1|  2 IKCPVCGHEG 11
                                      69******97 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.031
                     A2L_zn_ribbon 24 CieCgasfpy 33
                                      C++C a+f y
  gi|385805063|ref|YP_005841461.1| 35 CPKCHAIFNY 44
                                      ******9976 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   1.3    0.0046         3       1       8 [.       3      10 ..       3      15 .. 0.64
   2 ?    4.6   0.4     0.042        27       2       7 ..      35      40 ..      34      41 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0046
                     zinc_ribbon_2  1 fCpnCGae 8 
                                      +Cp CG+e
  gi|385805063|ref|YP_005841461.1|  3 KCPVCGHE 10
                                      56666666 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.042
                     zinc_ribbon_2  2 CpnCGa 7 
                                      Cp+C+a
  gi|385805063|ref|YP_005841461.1| 35 CPKCHA 40
                                      777765 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   5.7     0.034        22       7      34 ..       3      40 ..       2      44 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.034
                       Zn-ribbon_8  7 rCeeCghefe.........vlqsis.dapltaCPeCgs 34
                                      +C  Cghe +         ++   + d +  +CP+C++
  gi|385805063|ref|YP_005841461.1|  3 KCPVCGHEGNegefklfkePWKFRFyDVKRLECPKCHA 40
                                      79999998888867677774444444555667****86 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 ?    8.3   1.9    0.0037       2.4       1       7 [.       3       9 ..       3      10 .. 0.85
   2 ?    2.7   1.0      0.21   1.3e+02       1       6 [.      34      39 ..      34      40 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0037
                    DNA_ligase_ZBD 1 hCPvCGs 7
                                     +CPvCG+
  gi|385805063|ref|YP_005841461.1| 3 KCPVCGH 9
                                     6*****7 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.21
                    DNA_ligase_ZBD  1 hCPvCG 6 
                                      +CP C+
  gi|385805063|ref|YP_005841461.1| 34 ECPKCH 39
                                      5****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); 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: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.49
# Mc/sec: 435.02
//
Query:       gi|385805064|ref|YP_005841462.1|  [L=310]
Description: hypothetical protein FFONT_0014 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00061   19.7   0.0     0.0018   18.1   0.0    1.8  1  RMMBL     Zn-dependent metallo-hydrolase RNA specificity doma


Domain annotation for each model (and alignments):
>> 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 !   18.1   0.0     1e-07    0.0018       7      41 ..     263     297 ..     259     302 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1e-07
                             RMMBL   7 rieeidfSgHadknellelirklkprnvilvHGee 41 
                                       +++ + +SgH +  +  +li  l+p+ ++++H e 
  gi|385805064|ref|YP_005841462.1| 263 EVYRLRLSGHYYPHQFSDLIGILRPKEIVPIHTEN 297
                                       688899**************************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 2110.89
//
Query:       gi|385805065|ref|YP_005841463.1|  [L=100]
Description: PilT protein domain-containing protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-06   28.6   0.1    1.8e-06   28.4   0.1    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 !   28.4   0.1     1e-10   1.8e-06      40     120 ..       3      88 ..       1      90 [. 0.74

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 1e-10
                                       HHHHHHHS.....SCHCHHHHHHHHHHHHHHHTSEEEE.BCHHHHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE. CS
                               PIN  40 Ellyvlar.....rkskrekaaelvelllllsalkilp.idaeiaeeaaeialkygllpnDaliaAtAkehgiklia 110
                                       E+l+ + r     +  +++ a +l+e ll + ++++l     +   +  eialk g +++Dal +A+A e +++li 
  gi|385805065|ref|YP_005841463.1|   3 EVLNTIWRdysvrKTISIDQAVRLREILLSMIGINVLIePEGKYISKGFEIALKTGTTVYDALYIALAAEKNLPLI- 78 
                                       6666666666644455556666666666665556655525555667889***************************. PP

                                       ESSTHHHHHH CS
                               PIN 111 tfDedfrrva 120
                                       t D++ ++++
  gi|385805065|ref|YP_005841463.1|  79 TLDKKQAKAS 88 
                                       *****99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 674.89
//
Query:       gi|385805066|ref|YP_005841464.1|  [L=76]
Description: hypothetical protein FFONT_0016 [Fervidicoccus fontis Kam940]
Scores for complete 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   18.3   0.9     0.0036   17.8   0.9    1.2  1  YtxH      YtxH-like protein
  ------ inclusion threshold ------
      0.011   16.3   4.3      0.013   16.0   4.3    1.1  1  AAA_23    AAA domain
      0.016   15.4   0.2      0.019   15.2   0.2    1.0  1  DUF1779   TATA-box binding
       0.14   11.8   0.3       0.34   10.6   0.0    1.7  2  DUF3755   Protein of unknown function (DUF3755)


Domain annotation for each model (and alignments):
>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.9     8e-07    0.0036      25      70 ..       7      53 ..       6      57 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 8e-07
                              YtxH 25 etRkdlkekaddlkekakelleeakeka.........kekaedlkekvkekadel 70
                                      ++R+d+kek++ +k+k+ +++ee+++           +       +++k+ ++el
  gi|385805066|ref|YP_005841464.1|  7 KLRRDIKEKMNRYKDKV-NWAEEIRKFIeeklrtleaE-------DNIKKIVEEL 53
                                      79***************.88899999996655554444.......4444444444 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.0   4.3   2.9e-06     0.013     145     195 ..       6      56 ..       2      59 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.9e-06
                            AAA_23 145 efelkdkkerleelekeleeledekkllekleqekekekeleeleeeleei 195
                                        +++ d ke+++ ++++ + +e+++k++e++++ +e e++++++ eel +i
  gi|385805066|ref|YP_005841464.1|   6 LKLRRDIKEKMNRYKDKVNWAEEIRKFIEEKLRTLEAEDNIKKIVEELSQI 56 
                                       567899******************************************997 PP

>> DUF1779  TATA-box binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.2   4.2e-06     0.019      94     157 ..       7      69 ..       5      70 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.2e-06
                                       .HHHHHHHHHHHHHSS---EEEEEEEEE---HHHH.HHHHHHHHHHHH---------BTTEEEE CS
                           DUF1779  94 elkekvektlkklfsekpeifsclkGefegklseeelekkaekilkeldAkkvEslkeenfvSv 157
                                       +l++ ++++++++ + k+  +  ++  +e+kl+  e e++++ki++el+  ++Es + ++  Sv
  gi|385805066|ref|YP_005841464.1|   7 KLRRDIKEKMNRY-KDKVNWAEEIRKFIEEKLRTLEAEDNIKKIVEELSQIPIESPRGSSTSSV 69 
                                       67899********.****************************************9888777765 PP

>> DUF3755  Protein of unknown function (DUF3755)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1      0.67     3e+03      20      26 ..      11      17 ..      10      18 .. 0.78
   2 ?   10.6   0.0   7.5e-05      0.34      16      29 ..      44      57 ..      41      57 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.67
                           DUF3755 20 aIlndMs 26
                                      +I ++M+
  gi|385805066|ref|YP_005841464.1| 11 DIKEKMN 17
                                      6888997 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 7.5e-05
                           DUF3755 16 dNImaIlndMsdmp 29
                                      dNI++I +++s+ p
  gi|385805066|ref|YP_005841464.1| 44 DNIKKIVEELSQIP 57
                                      9***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1744  (0.0972726); expected 358.6 (0.02)
Passed bias filter:                      860  (0.047967); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.31s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 455.76
//
Query:       gi|385805067|ref|YP_005841465.1|  [L=50]
Description: hypothetical protein FFONT_0017 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       523  (0.0291706); 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:                         0  (0); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 380.14
//
Query:       gi|385805068|ref|YP_005841466.1|  [L=38]
Description: hypothetical protein FFONT_0018 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.30s 00:00:00.64 Elapsed: 00:00:00.45
# Mc/sec: 252.50
//
Query:       gi|385805069|ref|YP_005841467.1|  [L=43]
Description: hypothetical protein FFONT_0019 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       219  (0.0122148); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.44
# Mc/sec: 295.45
//
Query:       gi|385805070|ref|YP_005841468.1|  [L=57]
Description: hypothetical protein FFONT_0020 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score 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   12.9   0.0      0.093   12.5   0.0    1.3  1  Cecropin  Cecropin family


Domain annotation for each model (and alignments):
>> Cecropin  Cecropin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.2e-06     0.093       6      21 ..      31      46 ..      28      47 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.2e-06
                          Cecropin  6 LEnaGkrirdAaIkgg 21
                                      LE++Gk+i+d aI ++
  gi|385805070|ref|YP_005841468.1| 31 LEKMGKNISDLAIFAI 46
                                      9********9777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); 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 0.28s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 386.86
//
Query:       gi|385805071|ref|YP_005841469.1|  [L=439]
Description: hypothetical protein FFONT_0021 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.044   14.1   0.2          1    9.6   0.2    2.4  1  PIN_4         PIN domain
      0.088   13.1   0.2       0.51   10.7   0.1    2.2  2  PG_binding_2  Putative peptidoglycan binding domain


Domain annotation for each model (and alignments):
>> PIN_4  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.2   0.00011         1      74     117 ..     304     348 ..     248     354 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00011
                             PIN_4  74 aeelpee.e..seseknDnrIlavalelkeekpdrkvvLvskDinlr 117
                                       a+ l+++ +  ++ ++ D++I++   ++k+ek   kv+++s D+ l 
  gi|385805071|ref|YP_005841469.1| 304 AAALNNSvPamRDYRRGDQEIINSLKNMKNEK--MKVCFMSSDRRLS 348
                                       3334433223234679**************98..9********9875 PP

>> PG_binding_2  Putative peptidoglycan binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   5.7e-05      0.51      40      68 ..     215     244 ..     205     247 .. 0.90
   2 ?   -1.3   0.0      0.32   2.9e+03       4      37 ..     363     394 ..     360     400 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 5.7e-05
                      PG_binding_2  40 realrdALrafiaveNFEnraradge.idr 68 
                                       +ea+ +AL++f+++eN  + a+++++ id+
  gi|385805071|ref|YP_005841469.1| 215 EEAFDEALKSFLEIENRDEAAEKAKKcIDE 244
                                       6899*************9999999999996 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.32
                      PG_binding_2   4 erkpeeervlaedvaeevqaaLsrLGyydgeagg 37 
                                       e+  +e r+   + aeev+  + +L +y  e ++
  gi|385805071|ref|YP_005841469.1| 363 ES--PELREESRTCAEEVAGFMMNLAFYCNEGKL 394
                                       44..667788889999999999999998766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 2799.77
//
Query:       gi|385805072|ref|YP_005841470.1|  [L=38]
Description: hypothetical protein FFONT_0022 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       223  (0.0124379); 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: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 269.69
//
Query:       gi|385805073|ref|YP_005841471.1|  [L=237]
Description: hypothetical protein FFONT_0023 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-38  132.8   0.0    2.2e-38  132.5   0.0    1.0  1  DUF72     Protein of unknown function DUF72


Domain annotation for each model (and alignments):
>> DUF72  Protein of unknown function DUF72
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.5   0.0   1.2e-42   2.2e-38      10     204 ..      23     219 ..      17     233 .. 0.85

  Alignments for each domain:
  == domain 1  score: 132.5 bits;  conditional E-value: 1.2e-42
                                       HHHHHCCT..-SEEEE-HHCCSSS-HHHHHHHHCTS-TT-EEEEE--CCCCCS....G-SCHHHHHHHHHH.CHHHC CS
                             DUF72  10 rLeyYarh..fntVEinstFYalpspetvakwaaqtpedFrFavKapraither...nedaeealerflesalepLg 81 
                                        L+ Ya+   +n+VE+n++FY++p p++v  w+++  e  r++vK++r+ith r   +  +e+ +e+f + +++pL 
  gi|385805073|ref|YP_005841471.1|  23 DLRWYAESsgLNAVELNASFYRFPFPSQVLGWRKRG-ERLRWSVKVHRSITHLRkmgK-GSEKIWEKFRR-LFSPLD 96 
                                       6999**9999************************98.89*************753322.58899999999.6***** PP

                                       T-EEEEEEE--TT--S.HHHHHHHHHH..TTTS-S.EEEE--BGGGH.H.HHHHHHHTT-E.EEEE--SSC------ CS
                             DUF72  82 eklgpllfQlppsfkfdeenlerLeaf..laalpl.lavEvRhrswf.e.llellrehgva.vvldepkkpklpled 152
                                       + +  +lfQlppsf++ ee ++++e+f   ++l   +avE+R++s f e l ++ +++g++ v +d   ++   +  
  gi|385805073|ref|YP_005841471.1|  97 DIVDFYLFQLPPSFSCREEMMKKIEDFesSSKLGErMAVEFRSSSCFrEeLSSWGERLGITlVSVDS--PEG--TWV 169
                                       ****************999********875566655***********955***********555592..222..234 PP

                                       --SSTEEEEEE--SHHTTB----HHHHHHHHHHHHHHHTCSSEEEEEE-SBC CS
                             DUF72 153 vttadfvyvRlhgreeryayrYseeelaewaerikawaaegrevyvffnnda 204
                                       ++ ++  y+Rlhgr e+y y+Ys+eel e++e+  +++   +++y+ffnnd+
  gi|385805073|ref|YP_005841471.1| 170 AKSSSSLYLRLHGRGEWYFYNYSREELVELIEKSISLKP--EKIYIFFNNDH 219
                                       444599*******999*****************999988..79*******75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); 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 0.31s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1471.38
//
Query:       gi|385805074|ref|YP_005841472.1|  [L=153]
Description: ATP-binding protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-16   61.1   0.2    1.3e-16   60.8   0.2    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 !   60.8   0.2   7.3e-21   1.3e-16      67     169 ..      19     119 ..      12     126 .. 0.92

  Alignments for each domain:
  == domain 1  score: 60.8 bits;  conditional E-value: 7.3e-21
                   Diphthami_syn_2  67 aGeeekevedLkgtlkkldveavviGaieseyqksriervCrelGlksvaPLWkkdpeelleeiveekfevivvavk 143
                                       + ++ ke e+ ++ l+kl++e ++ G+++ e + +++er+ +e+G k+v  LW+ dpeell e+++ + + +vv+ +
  gi|385805074|ref|YP_005841472.1|  19 KLNKGKEFEETADVLRKLGAEEIIAGDVYVEDHLKYMERLGEEVGAKLVESLWGIDPEELLHEEIASGIRTLVVGCE 95 
                                       55678999*******************************************************************98 PP

                   Diphthami_syn_2 144 aegldeslLGrridkklidelkklse 169
                                             ++LGr i  + +++  + ++
  gi|385805074|ref|YP_005841472.1|  96 YSMS--NWLGREISSESVENFLRDAK 119
                                       7776..9************9887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1191.97
//
Query:       gi|385805075|ref|YP_005841473.1|  [L=37]
Description: hypothetical protein FFONT_0025 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       153  (0.00853366); expected 358.6 (0.02)
Passed bias filter:                      149  (0.00831056); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 248.50
//
Query:       gi|385805076|ref|YP_005841474.1|  [L=319]
Description: cobalamin biosynthesis protein CobD [Fervidicoccus fontis Kam940]
Scores for complete 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-71  240.2   0.1      3e-71  239.9   0.1    1.0  1  CobD_Cbib  CobD/Cbib protein
  ------ inclusion threshold ------
      0.016   14.4   3.8      0.027   13.7   3.8    1.3  1  Photo_RC   Photosynthetic reaction centre protein
       0.19   11.0   0.1        1.6    7.9   0.0    2.0  2  TAtT       TRAP transporter T-component


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 !  239.9   0.1     5e-75     3e-71       1     275 [.      18     296 ..      18     297 .. 0.91

  Alignments for each domain:
  == domain 1  score: 239.9 bits;  conditional E-value: 5e-75
                         CobD_Cbib   1 lllAlllDlllgdprrl...lhPvvligklisalekrlrkakkerlaGvllalllvllallvalllllla..laall 72 
                                       ll AlllD+++ +++ +   +hPv+    l+ +l++rl k   +++aGv+++++ v++ l+++ l+++++  +++l+
  gi|385805076|ref|YP_005841474.1|  18 LLSALLLDWMYPKHEGFlyyMHPVHTSYALALFLHRRLPK---SKAAGVAIWICSVGIHLVAYGLAMFILrpVSQLV 91 
                                       578**********99988889***************8864...578**************99999999887544444 PP

                         CobD_Cbib  73 glvlealllkltlalrsLleevrkvakalk.gdleaaReavsmiVgRdtseldeeeiarAavEsvaENlsDgvvaPl 148
                                        ++l+++++k+++++r L++ vr+  + lk gd+++aRe+ s iV+Rd s+l e  ia+A +Es+ E+++Dg+++Pl
  gi|385805076|ref|YP_005841474.1|  92 WMILSIYIMKVSISQRLLIDYVREASDCLKrGDIQCARESASNIVRRDLSRLGEGYIASAGIESLFESMVDGFISPL 168
                                       679**************************659********************************************* PP

                         CobD_Cbib 149 fyflllglpgalaykavnTlDsmvGYkneryedfGwaaArlDDllnyiPARltalllala.........aalriarr 216
                                       f++lllg++gal+++++nT+Ds +GYk++++++ Gwa+A++D++ln+iPAR+  l+++l          +a++++r+
  gi|385805076|ref|YP_005841474.1| 169 FFYLLLGPLGALLQRLANTMDSALGYKDDEFREKGWASAKMDTILNFIPARIGSLITVLLcpcvggkvkEAWAAFRK 245
                                       *****************************************************999999545566666688****** PP

                         CobD_Cbib 217 darkhpSpNsgwpeaalAgalgvrLggpnvY.lgkleekptlgdkkrpleaedieralrl 275
                                       +++ ++S N+g p++a+ g+l+++L++  +Y  g  +e p        ++++d+eralrl
  gi|385805076|ref|YP_005841474.1| 246 YRNCTESINAGNPMSAASGCLRIKLEKHMHYtIG--KEFPL-------PSYHDLERALRL 296
                                       *******************************877..44444.......367788888876 PP

>> Photo_RC  Photosynthetic reaction centre protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   3.8   4.6e-06     0.027      58     123 ..      27      92 ..      17      98 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.6e-06
                                       SS-GGGTHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-TSHHHHHHHHHHHHHHHHHTHHHHHHTSG CS
                          Photo_RC  58 laplkeGglwqlitlhlliaiiswllRevelarklgigphiaiAFsaaiaaylsvvlirPilmGsw 123
                                       ++p +eG+l+ +  +h   a+ ++l R    +++ g+  +i+      +a  l+++++rP+ +  w
  gi|385805076|ref|YP_005841474.1|  27 MYPKHEGFLYYMHPVHTSYALALFLHRRLPKSKAAGVAIWICSVGIHLVAYGLAMFILRPVSQLVW 92 
                                       58999*************************************9999999999*********99777 PP

>> TAtT  TRAP transporter T-component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1     0.051   3.1e+02      20      47 ..      20      49 ..      13      60 .. 0.78
   2 ?    7.9   0.0   0.00027       1.6     178     223 ..     230     275 ..     223     280 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.051
                                      HHHHH..HSTT-HHHHHHHHHHHHHHHHHH CS
                              TAtT 20 ealle..edpahegLllaaaslftaYanaF 47
                                       all+  ++p+heg+l  +    t Ya+a+
  gi|385805076|ref|YP_005841474.1| 20 SALLLdwMYPKHEGFLYYMHPVHTSYALAL 49
                                      555541257******************996 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00027
                                       GGGT--HHHHHHHHHHHHHHS-TT-SHHHHHHHHHTTTTTT-HHHH CS
                              TAtT 178 eslGGnpekaeahferalelskgkslgakvlyAesyavpaqdrelF 223
                                       + +GG+ ++a a+f++ ++ ++  ++g  ++ A   ++ + ++ ++
  gi|385805076|ref|YP_005841474.1| 230 PCVGGKVKEAWAAFRKYRNCTESINAGNPMSAASGCLRIKLEKHMH 275
                                       789***********************************99999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); 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: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1996.84
//
Query:       gi|385805077|ref|YP_005841475.1|  [L=256]
Description: cobalamin 5'-phosphate synthase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.3e-33  114.3   3.3    9.6e-33  114.1   3.3    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 !  114.1   3.3   5.3e-37   9.6e-33       2     203 ..       8     245 ..       7     246 .. 0.77

  Alignments for each domain:
  == domain 1  score: 114.1 bits;  conditional E-value: 5.3e-37
                              CobS   2 lsflTrlPvp...elar......alaffPlvGlllGlll.llallllllll...llaallavaalvlltgglHlDGl 65 
                                       lsflT +Pvp   +  +      +++++P++Gll G+++ ++a++ll l+    +l a+ +va+ ++++g+lH DG+
  gi|385805077|ref|YP_005841475.1|   8 LSFLTPIPVPrkyR--EgglsfgSVYLLPIIGLLRGGIAiIPAAVLLSLKIklvPLIAFSIVALHFIMQGFLHADGF 82 
                                       89*******95331..24566789999************9999999998889765555555777788********** PP

                              CobS  66 aDtaDglgsgrdrerrleImkDsrvGafGvlalvlvlllkvaalaala.........lllapvlsRlaallaiallp 133
                                       +D+  +l +gr   ++ +++kD+  G+++++++ ++ l+ +++l+++           + a+v+s  +++l+  l+ 
  gi|385805077|ref|YP_005841475.1|  83 IDFTEALLAGRFGVDAKKVLKDKYRGSYAIASFSVFTLWLYSSLSSFQepgyalilfPISAEVWSPSSMILTSLLSG 159
                                       *******9999******************************998555556666545545779999988888888877 PP

                              CobS 134 yaeeglgalfaeaqkk......lvllal..............avlllll.alllaallvalllrrlarrklggvtGD 189
                                        ++eg+g+ f ++++       l    l              +  l+++ + l  +ll  ll +++ ++ lg  +GD
  gi|385805077|ref|YP_005841475.1| 160 EPPEGMGREFKRSSSPsslaasL----LisfpftlmlsfslkL-SLIITaLSLSSLLLSSLLSYYMGKKALGYANGD 231
                                       778*******9855555544331....1344555555666531.222221344555667778889************ PP

                              CobS 190 vlGavieltellvl 203
                                       vlG+++el+ +l+l
  gi|385805077|ref|YP_005841475.1| 232 VLGFSNELCYALLL 245
                                       *********99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1545.14
//
Query:       gi|385805078|ref|YP_005841476.1|  [L=327]
Description: threonine-phosphate decarboxylase [Fervidicoccus fontis Kam940]
Scores for complete 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-40  139.2   0.0    2.3e-40  138.9   0.0    1.0  1  Aminotran_1_2  Aminotransferase class I and II
    0.00026   20.1   0.0     0.0024   16.9   0.0    2.2  2  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 !  138.9   0.0   2.5e-44   2.3e-40      34     363 .]      17     320 ..       9     323 .. 0.89

  Alignments for each domain:
  == domain 1  score: 138.9 bits;  conditional E-value: 2.5e-44
                                       HTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHH CS
                     Aminotran_1_2  34 ggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknil 110
                                       +g l +y+++  + +l+ a+ +f+g        re  +v +sGag++i+++if+lk  p+  i+v +p+y++y+   
  gi|385805078|ref|YP_005841476.1|  17 SGVLERYPDYN-YEKLKRAISSFYG-------CREEDIVPTSGAGEAINLAIFALK--PK-WIYVLEPSYGEYEVLS 82 
                                       567889*****.*************.......6777*******************7..55.8*************** PP

                                       HHTTSEEEEEEBEET.TTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEE CS
                     Aminotran_1_2 111 rlsggevvryplyse.edfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfv 186
                                       ++ g+   ++ ++++ + f+l++ +leea  +      +  +i++++p+NP G  + + e+ + l+ +   +++++ 
  gi|385805078|ref|YP_005841476.1|  83 KALGISYKPVFYRKSgDVFSLNFSDLEEACGR------EDSLIVITNPSNPLGIYIERGEIIEKLSRC---RARVLM 150
                                       ******999999999799************99......7789****************9975553444...58**** PP

                                       EETTTTCBSSSSHTHHHHGGSTTSTT..EEEEEESSSTTSSGGG-EEEEEE.EHHHHHHHHHHHHHHTSSHHHHHHH CS
                     Aminotran_1_2 187 DeaYagfvfgsldavatranveeepn..llivgslsKafGlaGeRvGyilg.naavvsqlrklsrpflsssllqaav 260
                                       DeaY+++++  +       ++  ++    l+v+s+ K ++l+G+R+G++++ + +v++ +  + +p+++ sl+  ++
  gi|385805078|ref|YP_005841476.1| 151 DEAYSELCSR-C-----AIELGSGIPenFLLVRSMTKWLSLPGIRLGFLFSsSREVLEKIDAVRQPWNVGSLADCFA 221
                                       *********9.4.....45555555558***********************777*********************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEEEEETHHCHHHHHHHHHHTCTEEEEEGGG CS
                     Aminotran_1_2 261 aaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmflltdlsaetakelskkLleevgvyvtpgts 337
                                        + ls +++ ++++  +r+ ++ +rk++ +eL++lglk ++s ++++l+   + +   +ls  Ll+ +g++v+ + s
  gi|385805078|ref|YP_005841476.1| 222 RELLSRKDEAREFIMRSRRYIEGERKRMLNELKSLGLKPYDSSANFILVESPRGL---DLSF-LLKGEGIHVRSCAS 294
                                       ******************************************************9...5555.55555********* PP

                                       GTS..TTEEEEECTTS-HHHHHHHHHHH CS
                     Aminotran_1_2 338 ftv..pgrlRitvAglteeeleelveal 363
                                       f    ++++Ri +   ++ e +el++al
  gi|385805078|ref|YP_005841476.1| 295 FKGlgSSFIRIGI--RKPHEDDELINAL 320
                                       *999*********..5555555555543 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.6e-07    0.0024      44     177 ..      27     153 ..      16     159 .. 0.76
   2 ?   -3.4   0.0       0.4   3.6e+03     322     337 ..     276     291 ..     259     307 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.6e-07
                                       HHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEE...EE CS
                       Aminotran_5  44 aveearekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgak...vk 117
                                        +e+ +  +  +++ ++ e+i+ tsG++eainl++ +l+++       +++     ++    + l+k+ g+    v 
  gi|385805078|ref|YP_005841476.1|  27 NYEKLKRAISSFYGCRE-EDIVPTSGAGEAINLAIFALKPK------WIYVLEPSYGEY---EVLSKALGISykpVF 93 
                                       68999***********6.*******************9443......333333333333...334444444400144 PP

                                       EEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-T CS
                       Aminotran_5 118 vipldeegeldldelekllnektklvaithvsnvtGtiqpveeigklakkkgalvlvDaa 177
                                       + +  +  +l+ ++le++   + +l+ it  sn +G+  +  ei++ + +  a vl+D a
  gi|385805078|ref|YP_005841476.1|  94 YRKSGDVFSLNFSDLEEACGREDSLIVITNPSNPLGIYIERGEIIEKLSRCRARVLMDEA 153
                                       555555567789999999999999999999999999999999999999999999999976 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.4
                                       HHHHHHHHHTTEEEEE CS
                       Aminotran_5 322 edvatlLdeegIavrs 337
                                        d+  lL+ egI+vrs
  gi|385805078|ref|YP_005841476.1| 276 LDLSFLLKGEGIHVRS 291
                                       5778889999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); 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: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 2054.71
//
Query:       gi|385805079|ref|YP_005841477.1|  [L=176]
Description: nucleoside triphosphate:adenosylcobinamide-phosphate guanylyltransferase [Fervidicoccus fontis Kam940]
Scores for complete 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-18   66.0   0.0    5.8e-18   65.8   0.0    1.1  1  NTP_transf_3     MobA-like NTP transferase domain
  ------ inclusion threshold ------
      0.015   14.9   0.0        3.5    7.1   0.0    2.1  2  NTP_transferase  Nucleotidyl transferase
       0.02   14.1   0.1      0.072   12.3   0.0    1.8  2  CofC             Guanylyl transferase CofC like
      0.036   14.0   0.0      0.067   13.1   0.0    1.4  1  PB1              PB1 domain
      0.059   13.1   0.0      0.089   12.5   0.0    1.6  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
        0.1   12.5   0.0        3.4    7.5   0.0    2.3  3  CTP_transf_3     Cytidylyltransferase
       0.16   12.0   0.6       0.38   10.8   0.2    1.8  2  BMC              BMC domain


Domain annotation for each model (and alignments):
>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.8   0.0   2.3e-21   5.8e-18       4     122 ..       1     117 [.       1     138 [. 0.94

  Alignments for each domain:
  == domain 1  score: 65.8 bits;  conditional E-value: 2.3e-21
                                       EEESS-TTTTT.THHHHCCCCCCHHHHHHHHHCTT..-CEEEEECSHCHHHHHHTTCTS-EEE-TTSS-SHHHHHHH CS
                      NTP_transf_3   4 LAGGrSsRmgg.dKallplggkpllervldalraa.gvdevvvvggdeevlaalarlgvrvvededpgkgplaslaa 78 
                                       +AGGr+ R+gg  K++l ++gk+l++ ++da++++ g ++v+v+++ e++ +   r gv+ ve +  g g ++ l  
  gi|385805079|ref|YP_005841477.1|   1 MAGGRGERLGGlKKPFLIICGKRLIDVSIDAAEKVrGNGKVYVCVRGEDLGKVEGREGVQAVECP--GLGYVEDLSL 75 
                                       59*********************************7689*********9998777889******7..9********* PP

                                       HHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEE CS
                      NTP_transf_3  79 alraaadadavlvlacDmPlltpelverllaaaaasgadvvvpt 122
                                        l+++  + ++l+l++DmP+l++e++er+l++a +s+advv ++
  gi|385805079|ref|YP_005841477.1|  76 ILKRV--TFPALILPGDMPFLSREALERFLDKALNSKADVVTLV 117
                                       ***98..8*******************************99876 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0    0.0014       3.5       5      53 ..       1      44 [.       1      54 [. 0.81
   2 ?    6.0   0.0     0.003       7.8     105     148 ..      83     127 ..      69     142 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0014
                                      E--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEE CS
                   NTP_transferase  5 LaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvl 53
                                      +aGG+G+RL  L     k+ + + gk rli+  + ++ + + +  ++v+
  gi|385805079|ref|YP_005841477.1|  1 MAGGRGERLGGL----KKPFLIICGK-RLIDVSIDAAEKVRGNGKVYVC 44
                                      8********876....7888888888.*****99998886555556666 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.003
                                       EEEEETTEE..EESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTS CS
                   NTP_transferase 105 lvlvLggDh..likdayeeavkkaiekaakgtvtfgivpveeatey 148
                                        +l+L+gD+  l ++a+e++++ka +++a+  vt++ ++   a+e 
  gi|385805079|ref|YP_005841477.1|  83 PALILPGDMpfLSREALERFLDKALNSKAD-VVTLVKMRSGSAEET 127
                                       579*****8335566**************6.555555555444444 PP

>> CofC  Guanylyl transferase CofC like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.8e-05     0.072      90     120 ..      83     115 ..      22     126 .. 0.74
   2 ?   -0.5   0.0      0.23   5.9e+02     171     181 ..     151     161 ..     143     172 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.8e-05
                              CofC  90 eviiipsdiPlikkedvkdllele..kradvvi 120
                                       + +i+p d+P++++e ++++l+++  ++advv 
  gi|385805079|ref|YP_005841477.1|  83 PALILPGDMPFLSREALERFLDKAlnSKADVVT 115
                                       56799****************975337799985 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.23
                              CofC 171 vdinteedlge 181
                                       +di+t+edl  
  gi|385805079|ref|YP_005841477.1| 151 LDIDTPEDLKK 161
                                       79******975 PP

>> PB1  PB1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.6e-05     0.067      46      72 ..     143     169 ..     130     175 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.6e-05
                                       EEETTSSEEEESSHHHHHHHHHHHHHT CS
                               PB1  46 YpdedgdlVtitsDeDLeealeearsl 72 
                                       Y +ed dl+ i + eDL++a+e + s+
  gi|385805079|ref|YP_005841477.1| 143 YFNEDRDLLDIDTPEDLKKAVELCGST 169
                                       789*********************886 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 ?   12.5   0.0   3.5e-05     0.089       7      60 ..       2      54 ..       1     120 [. 0.92

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.5e-05
                                      CTTSSCTT-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHH CS
                              IspD  7 AAGsGkRmkaglpKqflelkgqtllehtvdallaskavdkivvvvseddteefe 60
                                      A G+G+R++ gl K fl + g+ l+  ++da+ + +  +k+ v v+ +d +++e
  gi|385805079|ref|YP_005841477.1|  2 AGGRGERLG-GLKKPFLIICGKRLIDVSIDAAEKVRGNGKVYVCVRGEDLGKVE 54
                                      88*****97.89*********************************999977654 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.043   1.1e+02      15      43 ..      13      41 ..       7      48 .. 0.83
   2 ?    7.5   0.0    0.0013       3.4      96     130 ..      87     120 ..      75     135 .. 0.87
   3 ?   -3.2   0.0       2.5   6.4e+03     193     210 ..     151     166 ..     138     169 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.043
                                      TGGGSEETTEEHHHHHHHHHHHTTTTSEE CS
                      CTP_transf_3 15 gKnlldlggkpliayvleaalkskafekv 43
                                       K+ l + gk+li+  ++aa k     kv
  gi|385805079|ref|YP_005841477.1| 13 KKPFLIICGKRLIDVSIDAAEKVRGNGKV 41
                                      599999*************9986655555 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0013
                                       E-TT-TT--HHHHHHHHHHHHHSTTSSEEEEEEET CS
                      CTP_transf_3  96 lqGdnPllqeevikkaietlkenqedylstlvkkv 130
                                       l Gd P+l+ e++++ +++ ++++  +++tlvk+ 
  gi|385805079|ref|YP_005841477.1|  87 LPGDMPFLSREALERFLDKALNSKA-DVVTLVKMR 120
                                       569********************65.999999885 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 2.5
                                       HHHSHHHHHSHHHHHT-T CS
                      CTP_transf_3 193 lvidtptseilekiekle 210
                                       l+idtp++  l+k+ +l+
  gi|385805079|ref|YP_005841477.1| 151 LDIDTPED--LKKAVELC 166
                                       67788888..88888775 PP

>> BMC  BMC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   0.00015      0.38      25      51 ..      26      54 ..      26      71 .. 0.86
   2 ?   -2.3   0.0       1.7   4.4e+03      22      34 ..     110     122 ..      98     129 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00015
                                      SEEEEEEEECTT.TCEEEEEEE.SHHHHH CS
                               BMC 25 nVelvgvekvgg.gkvtviitG.dvaaVk 51
                                      +V++  +ekv+g gkv+v+++G d++ V+
  gi|385805079|ref|YP_005841477.1| 26 DVSIDAAEKVRGnGKVYVCVRGeDLGKVE 54
                                      6888899*****99************996 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.7
                                       HHSSEEEEEEEEC CS
                               BMC  22 KaAnVelvgvekv 34 
                                       Ka  V+lv++++ 
  gi|385805079|ref|YP_005841477.1| 110 KADVVTLVKMRSG 122
                                       4555678877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); 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:                         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 0.28s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 1147.92
//
Query:       gi|385805080|ref|YP_005841478.1|  [L=302]
Description: CbiZ domain containing protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-24   87.3   0.0    1.7e-24   87.0   0.0    1.1  1  CbiZ      Adenosylcobinamide amidohydrolase
    8.3e-05   22.6   0.0    0.00015   21.8   0.0    1.4  1  PgpA      Phosphatidylglycerophosphatase A


Domain annotation for each model (and alignments):
>> CbiZ  Adenosylcobinamide amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.0   0.0   1.9e-28   1.7e-24      50     191 ..       2     136 ..       1     137 [. 0.91

  Alignments for each domain:
  == domain 1  score: 87.0 bits;  conditional E-value: 1.9e-28
                              CbiZ  50 glppektvgllTaadmenaaiaeeefedlevtavvTaGvesnavragdedeeaekpGTINiivlinaaLtdaalvra 126
                                       g++ e+++ +lTa+d+++++  +++++++e++a+vT Gv   + + + +  e+ k GTIN++v+++++L+d  l+++
  gi|385805080|ref|YP_005841478.1|   2 GIDIEESAIFLTAVDLKKYSRGSSSYKGVEAEAFVTYGV-DSPSCFEGA--ERGKFGTINVAVIVDEPLSDVGLLDL 75 
                                       67889**********************************.777777764..6899********************** PP

                              CbiZ 127 litatEAKtaalqdlgvrsrysegatGTgTDaiavaadkegeeeltyaGkhtklGeliaraVyeA 191
                                       + t+ E K   +  lg + +ys+   GT +Da++va++  ge   ++aG++t++G   + aV +A
  gi|385805080|ref|YP_005841478.1|  76 FRTVSEVKGMIM-SLGGPMCYSSSYVGTPSDATMVASPFGGE---RFAGSATDVGISASLAVLRA 136
                                       ********9866.57777788888**************7776...6*************999988 PP

>> PgpA  Phosphatidylglycerophosphatase A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   1.7e-08   0.00015      63     141 ..     226     295 ..     200     297 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.7e-08
                                       S-HHT-TT--HHHHTTHHHHH........TTHHHHHHHHHHHHS--THHHHTSSS.-S---TTHHHHHHHHHHHHHH CS
                              PgpA  63 lgekDpgeiviDEvvgqwiallllpatllalllafilFrlfDivKpgpigwldrklkgglgvmlDDllAgiaaalvl 139
                                         ++D ++i+ DEv+g +ia       +l  + +++ + ++D +K g     d    +gl  m+DD++++i++++++
  gi|385805080|ref|YP_005841478.1| 226 EYSSDSSGIIADEVMGKAIAE------YLNGFKGLLAYYWIDRIKEGDKDLEDL---SGLPLMTDDVVGAIVGGVLS 293
                                       4468*****************......3455899************98777666...59***************999 PP

                                       HH CS
                              PgpA 140 al 141
                                       ++
  gi|385805080|ref|YP_005841478.1| 294 RI 295
                                       87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); 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: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1919.25
//
Query:       gi|385805081|ref|YP_005841479.1|  [L=351]
Description: nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-06   27.3   0.1    2.9e-06   26.7   0.1    1.2  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 !   26.7   0.1   1.6e-10   2.9e-06      96     260 ..      86     251 ..      74     257 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 1.6e-10
                                       TEEEEEEEEE..-S.--T.EE--SSSSB--TTTS-SS-HHHHHHHHHHHHHHHHHHHCTTECEEEEEEE-TTCHHHH CS
                           DBI_PRT  96 gaelrvvDvg..va.dle.vdrkvrrgtaniakepAmtreeaeaaleaGieladeladagadllalGemGigNttaa 168
                                       +a   vv+ g  v+ +l+ +    rr  ++i+ke+A+ r + ++ ++ + ++ +   ++  d++++Ge   g tt+a
  gi|385805081|ref|YP_005841479.1|  86 NAPFIVVNSGsyVEpKLPaLTLPSRRVGGRIDKEEALPRGTSKRLFSEAKTAGKT-FSSLSDVVLIGESMPGGTTTA 161
                                       566677777732224444543367888999**************99998877766.6778****************9 PP

                                       HHHHHHHHT--HHHH---TTT--HHHHHHHHHHHHHHHHCH-TT..HHHHHHHHS-HHHHHHHHHHHHHHHTT--EE CS
                           DBI_PRT 169 aallaallglepeevvGrGtglddeglarKiavieqalarhaek.dplevLakvGGleiaalaGailgAaarripvv 244
                                         +l    gl + ++    +  + + +  K +v+e+al+r++   dp+e+   +G      +aG+ +gA + +  v+
  gi|385805081|ref|YP_005841479.1| 162 LSILK---GLGMGDCSSVSSSSNVNPIDIKKSVVEAALKRAEGMdDPFEINDVLGDPLHISIAGIAIGALSGGSHVI 235
                                       87765...555666666668889999***************7444******************************** PP

                                       E-SHHHHHHHHHHHHH CS
                           DBI_PRT 245 lDGfistaAalvAvrl 260
                                       l G   + Aal+ +r 
  gi|385805081|ref|YP_005841479.1| 236 LAGGTQMLAALALMRA 251
                                       ***********98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 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:                        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 0.29s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 2209.61
//
Query:       gi|385805082|ref|YP_005841480.1|  [L=107]
Description: hypothetical protein FFONT_0032 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-19   68.7   0.5    1.3e-18   66.9   0.1    1.9  2  DUF167    Uncharacterised ACR, YggU family COG1872


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 ?    0.2   0.0     0.046   8.3e+02      55      66 ..       6      17 ..       4      20 .. 0.89
   2 !   66.9   0.1   7.2e-23   1.3e-18       3      76 ..      20      88 ..      18      89 .. 0.96

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.046
                                      S...SEEEE-S- CS
                            DUF167 55 gvpksdveivsG 66
                                      gv+ks+++i  G
  gi|385805082|ref|YP_005841480.1|  6 GVAKSSIQIGNG 17
                                      899*****9887 PP

  == domain 2  score: 66.9 bits;  conditional E-value: 7.2e-23
                                      EEEEES---SSS----...--TTTT-------TTIIIIIHHHHHHHHHHHHHS...SEEEE-S-GGGSEEEEEE CS
                            DUF167  3 ilavrvkPgakkdaigleedaegrealkvrvaappvdGkANkalikfLakalgvpksdveivsGeksreKvvri 76
                                       l ++vkP++k + i       +r++l ++ ++pp++Gk N+ likfL+k+ g++ +++ei +Gek r K+vri
  gi|385805082|ref|YP_005841480.1| 20 DLIIYVKPKSKDTGII-----SERGELIFHSTQPPERGKVNASLIKFLSKLTGISSNKIEINRGEKDRVKTVRI 88
                                      5789************.....57899***********************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); 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 0.27s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 772.48
//
Query:       gi|385805083|ref|YP_005841481.1|  [L=48]
Description: hypothetical protein FFONT_0033 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.0   0.0       0.16   11.6   0.0    1.3  1  DUF594    Protein of unknown function, DUF594


Domain annotation for each model (and alignments):
>> DUF594  Protein of unknown function, DUF594
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   8.8e-06      0.16      24      41 ..       5      22 ..       1      26 [. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.8e-06
                            DUF594 24 ApscrakaHakqLarGGE 41
                                       ps++a++H+ qL +GGE
  gi|385805083|ref|YP_005841481.1|  5 RPSSGAASHKMQLDEGGE 22
                                      5899*************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       143  (0.0079759); expected 358.6 (0.02)
Passed bias filter:                      128  (0.00713927); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 317.37
//
Query:       gi|385805084|ref|YP_005841482.1|  [L=414]
Description: PUA domain containing protein [Fervidicoccus fontis Kam940]
Scores for complete 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   0.0    1.7e-31  109.5   0.0    1.2  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
    1.4e-09   37.8   1.0      3e-09   36.7   0.4    2.0  2  PUA              PUA domain
    0.00029   20.7   0.0     0.0011   18.7   0.0    2.0  1  Methyltransf_31  Methyltransferase domain
  ------ inclusion threshold ------
      0.011   16.0   0.0      0.021   15.1   0.0    1.5  1  UPF0113          UPF0113 PUA domain


Domain annotation for each model (and alignments):
>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.5   0.0   3.7e-35   1.7e-31       5     200 .]     223     412 ..     219     412 .. 0.90

  Alignments for each domain:
  == domain 1  score: 109.5 bits;  conditional E-value: 3.7e-35
                                       ---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC..EE CS
                   Methyltr_RsmB-F   5 apqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfD 81 
                                        p+e++ i Dl a+PGgK +h  e+ + k++ +A d+ + ++++v+e+++rLg +n++v +aD r   k        
  gi|385805084|ref|YP_005841482.1| 223 SPREGDVIADLTASPGGKISHAYEFTRGKAEYYAFDHTNAKVEKVEETMRRLGHENVKVYKADSRSLGKEFPWLSPS 299
                                       69***************************************************************998876655556 PP

                                       EEEEEE--CCGGGTTT-TCHHHH--HHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEES--STTTTHHHHHHHHHH-T CS
                   Methyltr_RsmB-F  82 riLlDaPCsgtgvirrdpdvklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaLkkre 158
                                         ++D PC+g+g    +p + ++ +e++   l +lqk+lls ai  + +gG +vYsTC+++veEne v+e aLk+ +
  gi|385805084|ref|YP_005841482.1| 300 FTIVDPPCTGLG---NRPRLSFSFEEEEQEVLIRLQKALLSEAIRITSPGGKIVYSTCTLTVEENEGVVEWALKNFP 373
                                       689*******99...5677888899999999*********************************************9 PP

                                       TEEEESSBSTTSTTSSECEECTSEEE-TTTTSS-SEEEEEEE CS
                   Methyltr_RsmB-F 159 dvelvetelsepkglklgeeagtlrllPhtenkdgffiaklk 200
                                         + +++      ++kl+      r+lP+ ++  gff a lk
  gi|385805084|ref|YP_005841482.1| 374 VCAEEPLA--PYPRTKLSDFP-FARFLPGYHKYPGFFFAVLK 412
                                       99999883..33355565555.799**************885 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0       3.5   1.6e+04      15      29 ..      13      27 ..      10      29 .. 0.71
   2 !   36.7   0.4   6.7e-13     3e-09       2      72 ..     120     189 ..     119     191 .. 0.95

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 3.5
                                      TT-EEEGGGEEEEET CS
                               PUA 15 sgasLlapGvveveg 29
                                      +g+s l  G vev++
  gi|385805084|ref|YP_005841482.1| 13 RGRSFLSGGAVEVRC 27
                                      477888888888876 PP

  == domain 2  score: 36.7 bits;  conditional E-value: 6.7e-13
                                       EEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEE CS
                               PUA   2 rvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveier 72 
                                       +v+ d  A++ ++ g++L+ pG ++v    ++g++Va+v+e+g +v+ G+   + +e+   k+g++v+ier
  gi|385805084|ref|YP_005841482.1| 120 YVIADIKAAERVMLGSDLFMPGALKVVN-GKRGEEVAVVSENGYVVGSGILDIDPSEVNPKKRGIAVRIER 189
                                       588999*******************987.7***************************************98 PP

>> Methyltransf_31  Methyltransferase 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    0.0011       4     115 ..     227     357 ..     224     381 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.5e-07
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieelekl..ledekfDli 78 
                                       g ++ Dl +  G ++  ++e  + kae++ +D +   +e+ +e  ++lg +nv++ ++d  +l k   +   +f + 
  gi|385805084|ref|YP_005841482.1| 227 GDVIADLTASPGGKISHAYEFTRGKAEYYAFDHTNAKVEKVEETMRRLGHENVKVYKADSRSLGKEfpWLSPSFTI- 302
                                       6678899999999999999877889*************************************88662333344444. PP

                   Methyltransf_31  79 lsn.....................evlnaladpdkileeiervlkpggilliedprll 115
                                         +                     e   ++  +++ l e++r  +pgg ++ +++ l 
  gi|385805084|ref|YP_005841482.1| 303 -VDppctglgnrprlsfsfeeeeqE--VLIRLQKALLSEAIRITSPGGKIVYSTCTLT 357
                                       .223455555555555455555444..5599999999999999999999999999833 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   4.6e-06     0.021       1      61 [.     120     180 ..     120     192 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.6e-06
                           UPF0113   1 kvvvkekaeklFLYGrdvlkesilkitesvkenqvvvVlnengeplGiGkirkdtk.aspgk 61 
                                       +v+ + ka+++++ G d++  + lk+  +++ ++ v+V++eng ++G G++ +d +  +p+k
  gi|385805084|ref|YP_005841482.1| 120 YVIADIKAAERVMLGSDLFMPGALKVVNGKR-GEEVAVVSENGYVVGSGILDIDPSeVNPKK 180
                                       6788899********************9999.7888888************88773344444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); 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: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2792.29
//
Query:       gi|385805085|ref|YP_005841483.1|  [L=285]
Description: stomatin [Fervidicoccus fontis Kam940]
Scores for complete 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-29  101.0   2.2      1e-28  100.5   2.2    1.1  1  Band_7    SPFH domain / Band 7 family
     0.0004   20.1   0.3     0.0011   18.8   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 !  100.5   2.2   1.1e-32     1e-28      13     177 ..      41     200 ..      30     201 .. 0.96

  Alignments for each domain:
  == domain 1  score: 100.5 bits;  conditional E-value: 1.1e-32
                            Band_7  13 rfGklsrvlepGlhfilPfgrsvt.vvsvrvqtldvsvsltvptkDglpvtidvtviyrvpddapklvaaveresan 88 
                                         G+ +++++pG+ +i+P++++v  v+s+r qt  ++   +++tkD++pv++d++++++   d  k+v++v    ++
  gi|385805085|ref|YP_005841483.1|  41 VLGRFRGFKGPGIVYIVPLISKVPfVISTRLQTQAFKT-EQTLTKDNVPVNVDAVMYFQP-VDLEKVVLNV----ED 111
                                       3699*******************99*************.9999*****************.**********....9* PP

                            Band_7  89 ldnlirrvlesalrevisemtleellsnreelaeelknelneqlrkyGvevldvritdidpppevaqalaakqaaea 165
                                       +    + +++ +lrevi+  tl+ell++re++   ++n + ++ + +G+ v++v i+d+ +p ++++a+ + +aae+
  gi|385805085|ref|YP_005841483.1| 112 YILATTLAAQTTLREVIGGITLDELLAEREKIGTIARNIIDQKTEAWGIKVTSVEIRDVLIPTALQEAMSRQAAAER 188
                                       99*************************************************************************** PP

                            Band_7 166 eaqaeiaraeae 177
                                       e++a++  a+ae
  gi|385805085|ref|YP_005841483.1| 189 ERRARVTLAQAE 200
                                       *********998 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 !   18.8   0.1   1.2e-07    0.0011     153     209 ..     130     186 ..      98     188 .. 0.87
   2 ?   -2.2   0.0      0.32   2.9e+03     160     190 ..     198     228 ..     189     233 .. 0.64

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.2e-07
                          Band_7_1 153 kipvldlaakseelaeklkealkeelaeyGlelekleienislpeevekaldkrasm 209
                                       +i++ +l a+ e+++   ++ ++++ ++ G++++++ei+++ +p  +++a++++a++
  gi|385805085|ref|YP_005841483.1| 130 GITLDELLAEREKIGTIARNIIDQKTEAWGIKVTSVEIRDVLIPTALQEAMSRQAAA 186
                                       6888899*********************************************99976 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.32
                          Band_7_1 160 aakseelaeklkealkeelaeyGleleklei 190
                                       +a++e+ a++++ a   e ++yGlel  ++i
  gi|385805085|ref|YP_005841483.1| 198 QAEYEAAAKMIEAAKLYESSKYGLELRWMNI 228
                                       5666666666666666666777777765554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       735  (0.040995); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); 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 0.31s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 1665.02
//
Query:       gi|385805086|ref|YP_005841484.1|  [L=430]
Description: membrane-bound serine peptidase Nfed [Fervidicoccus fontis Kam940]
Scores for complete 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   66.1   1.8    1.5e-17   63.7   0.8    2.5  2  NfeD           NfeD-like C-terminal, partner-binding
    6.9e-07   29.3   1.5    1.9e-06   27.9   1.5    1.6  1  CLP_protease   Clp protease
    0.00064   18.8   0.1      0.001   18.1   0.1    1.2  1  SDH_sah        Serine dehydrogenase proteinase
      0.003   17.5   1.4     0.0086   16.0   0.8    2.1  2  Peptidase_S49  Peptidase family S49


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 ?   -0.5   0.0      0.37   1.7e+03       3      21 ..       8      26 ..       7      40 .. 0.79
   2 !   63.7   0.8   3.3e-21   1.5e-17       4      84 .]     333     417 ..     330     417 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.37
                                      XXXXXXXXXXXXXXS---S CS
                              NfeD  3 avvsvlllvllrplllkkl 21
                                      + +s+++++ll+pll +++
  gi|385805086|ref|YP_005841484.1|  8 IFISAAVIILLFPLLANAQ 26
                                      5689999999999988766 PP

  == domain 2  score: 63.7 bits;  conditional E-value: 3.3e-21
                                       XXXXXXXXXXX..XXS---SSS--S.S---GGTTSEEEEEE-BS.-EEEEETTEEEEEE-.SS..B-TT-EEEEEEE CS
                              NfeD   4 vvsvlllvllr..plllkklkkkekktnaealiGkegvvledig.tGrvkvdGeeWsarsege..iekgerVrVvev 75 
                                       +++ l +++ +   +++k+++ k+k  + e+liGk+g++++d++ +G+v+v+G +W+ars+++  i++g++VrVv++
  gi|385805086|ref|YP_005841484.1| 333 IIAGLGIIAAYylNWIRKTFRVKPK-AGPESLIGKKGIAVKDLDpEGEVRVEGIIWRARSKNGerISAGSEVRVVAR 408
                                       445544444443589***9988666.9999*************658**************86669************ PP

                                       -SSSEEEEE CS
                              NfeD  76 eGltliVep 84 
                                       e l liVe+
  gi|385805086|ref|YP_005841484.1| 409 EELILIVEE 417
                                       *******95 PP

>> CLP_protease  Clp protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   1.5   4.2e-10   1.9e-06      23     180 ..      38     192 ..      28     193 .. 0.70

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 4.2e-10
                                       S-BSHHHHHHHHHHHHHHHHH-SSS-EEEEEEE--B-HHHHHHHHHHHHHSSS-EEEEEE.....EEEETHHHHHHH CS
                      CLP_protease  23 seiddevankiiaqLllLeaedpdkdillyinspGGsvtaglaIydtmqyikpdvsticl.....GlaaSmgsllla 94 
                                        ++d    + + +   ++e ++ +  + + +n+pGG ++++++I ++    + + +t+++     G+aaS+gs +++
  gi|385805086|ref|YP_005841484.1|  38 MQVDPGAVSLFQRSFSYAE-SNRIPYVIIEMNTPGGYLDSMMSIVNMTLQAEQKNITVVTfvppgGMAASAGSYIAV 113
                                       5555555555555566663.45566788999***************8766665555555446688************ PP

                                       TS-TTGEEEETTEEEEES-TEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHCSTEEEEHHHHHH CS
                      CLP_protease  95 agekgkRfalpnarimihqPlggaqgqasdieieaeellkikerlneilakhtgqslekiekdldrdtflsaeeAve 171
                                       a +k     + n  + i      ++g   + e +a+  + + + ++++ a+  g+++  +++ + ++t  sa eA +
  gi|385805086|ref|YP_005841484.1| 114 ASDKI---YMSNGTF-IGPSTPIVEG--GNAEEQAHVKNAMLAWMVSL-AQLHGRNVTAVKAMVLNNTAYSAGEAYQ 183
                                       **998...4455444.3333334444..23445555555555556554.4455899999****************** PP

                                       HTSSSEE-S CS
                      CLP_protease 172 yGLidevie 180
                                       y Lid + +
  gi|385805086|ref|YP_005841484.1| 184 YHLIDGIAN 192
                                       *****9975 PP

>> SDH_sah  Serine dehydrogenase proteinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   2.3e-07     0.001      98     159 ..      67     133 ..      53     147 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.3e-07
                           SDH_sah  98 ihtpGGlvlaatqiak.alkehkaktrvi..vph..yamsGGtlialaadeiildenavlGpvdpql 159
                                       + tpGG   +   i + +l++ + +++v+  vp    a s G+ ia+a+d+i + + + +Gp  p +
  gi|385805086|ref|YP_005841484.1|  67 MNTPGGYLDSMMSIVNmTLQAEQKNITVVtfVPPggMAASAGSYIAVASDKIYMSNGTFIGPSTPIV 133
                                       579***98888777652688887777776447752367799*********************99976 PP

>> Peptidase_S49  Peptidase family S49
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.8   1.9e-06    0.0086      13      40 ..     100     127 ..      86     148 .. 0.83
   2 ?   -1.5   0.0      0.47   2.1e+03     113     140 ..     165     193 ..     137     203 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.9e-06
                                       EEEEEETHHHHHHTTSSEEEE-TT-EEE CS
                     Peptidase_S49  13 aenvaaSggYylasaadkivanpstivg 40 
                                        +++aaS+g y+a+a+dki+++  t++g
  gi|385805086|ref|YP_005841484.1| 100 PGGMAASAGSYIAVASDKIYMSNGTFIG 127
                                       389***********************99 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.47
                                       HHHCHHCC.HEEEHHHHHHTTSSSEETSH CS
                     Peptidase_S49 113 qvdkiAeg.rvltgqqAlklgLvdelgtv 140
                                       +v+++  +   +++ +A +  L+d + ++
  gi|385805086|ref|YP_005841484.1| 165 AVKAMVLNnTAYSAGEAYQYHLIDGIANS 193
                                       44444333378999999999999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); 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):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 2784.83
//
Query:       gi|385805087|ref|YP_005841485.1|  [L=178]
Description: hypothetical protein FFONT_0037 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-29  101.6   0.0    5.3e-29  100.9   0.0    1.3  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 !  100.9   0.0   2.9e-33   5.3e-29      11     114 ..      26     135 ..      21     139 .. 0.85

  Alignments for each domain:
  == domain 1  score: 100.9 bits;  conditional E-value: 2.9e-33
                                       .-EEEEEE-HHH..HGGGTTGGG-SEEEEEEE-TTS....-.SS--E-TT-........SS-E.EGGGS--S-SSS- CS
                              TrmO  11 eaeaeielepeynseealegleefshlwllfvfhen.aekklkakvrpprl.......ggnervGvfatRsphRpnp 79 
                                        +e+eie+ pey  ee+l+g+e+fsh++l+ ++h    ek+   kv+p+rl       ++  +vGvf++ sphRpnp
  gi|385805087|ref|YP_005841485.1|  26 GVEGEIEILPEY--EEGLKGIEGFSHIILIAYLHLVeGEKRRVLKVKPRRLrnfgisiDDLPEVGVFSSDSPHRPNP 100
                                       5789********..********************65233333566667766444444466799************** PP

                                       EEEEEEEEEEEETTEEEEES----TT-EEEEEEE- CS
                              TrmO  80 iglsvvklekvegnvlevsgvDlldgtpvlDiKPY 114
                                       i++s+vkl+ v+g+vlev+g+Dl  gtp+lDiKPY
  gi|385805087|ref|YP_005841485.1| 101 IAISIVKLKGVQGRVLEVEGLDLYSGTPILDIKPY 135
                                       *********************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1234.29
//
Query:       gi|385805088|ref|YP_005841486.1|  [L=414]
Description: hypothetical protein FFONT_0038 [Fervidicoccus fontis Kam940]
Scores for complete 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-07   29.5   3.3    0.00063   19.8   0.1    2.2  2  Laminin_II       Laminin Domain II
     0.0001   22.6   5.7      0.042   14.3   0.1    2.6  2  ZapB             Cell division protein ZapB
    0.00014   20.0   0.6    0.00019   19.5   0.6    1.1  1  V_ATPase_I       V-type ATPase 116kDa subunit family
     0.0015   18.1   2.9      0.002   17.6   2.9    1.1  1  HMMR_N           Hyaluronan mediated motility receptor N-term
     0.0017   17.4   9.7     0.0088   15.1   7.0    2.0  2  IFT57            Intra-flagellar transport protein 57
     0.0031   17.8   1.8     0.0059   16.8   1.6    1.5  1  Jnk-SapK_ap_N    JNK_SAPK-associated protein-1
     0.0039   15.4  11.0      0.016   13.4   1.8    2.2  2  EzrA             Septation ring formation regulator, EzrA
     0.0047   15.8   4.2      0.011   14.7   4.3    1.5  1  Spc7             Spc7 kinetochore protein
     0.0073   16.1   1.7      0.013   15.3   1.5    1.5  1  DUF4201          Domain of unknown function (DUF4201)
     0.0074   16.4   0.6       0.14   12.4   0.1    2.4  2  JIP_LZII         JNK-interacting protein  leucine zipper II
     0.0088   15.2   1.3      0.013   14.7   1.3    1.1  1  AIP3             Actin interacting protein 3
  ------ inclusion threshold ------
      0.011   16.2   5.6       0.07   13.7   1.5    2.2  2  APG6_N           Apg6 coiled-coil region
      0.013   13.0   0.7      0.016   12.7   0.7    1.0  1  DUF3584          Protein of unknown function (DUF3584)
      0.016   15.2   3.2      0.018   15.1   1.9    1.5  1  Rootletin        Ciliary rootlet component, centrosome cohesi
      0.018   14.8   2.5      0.034   14.0   2.1    1.5  1  TACC_C           Transforming acidic coiled-coil-containing p
      0.019   15.0   4.4       0.39   10.7   1.5    2.3  2  LOH1CR12         Tumour suppressor protein
      0.019   14.3   3.4       0.19   11.0   3.1    2.0  2  GAS              Growth-arrest specific micro-tubule binding
      0.032   14.3  19.7       0.52   10.3  10.5    2.4  2  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
      0.036   13.8  13.3      0.042   13.6   5.5    2.4  2  LXG              LXG domain of WXG superfamily
      0.037   14.3   8.8        2.7    8.3   3.0    2.6  2  DUF5082          Domain of unknown function (DUF5082)
      0.046   13.1   0.7      0.077   12.3   0.7    1.4  1  DUF4407          Domain of unknown function (DUF4407)
      0.051   13.4   6.3       0.34   10.7   6.5    1.9  1  KASH_CCD         Coiled-coil region of CCDC155 or KASH
      0.052   13.6   1.2       0.34   10.9   0.9    2.1  2  DUF1664          Protein of unknown function (DUF1664)
      0.055   13.7   9.1       0.44   10.7   1.9    2.1  2  ATG16            Autophagy protein 16 (ATG16)
      0.061   12.2   3.8       0.18   10.6   3.8    1.6  1  DUF812           Protein of unknown function (DUF812)
      0.087   13.2   3.4       0.21   12.0   1.1    2.3  2  Csm1_N           Csm1 N-terminal domain
        0.1   11.7   8.6       0.24   10.5   6.7    1.9  2  APG17            Autophagy protein Apg17
       0.12   13.0   2.4       0.41   11.3   1.0    2.3  1  SlyX             SlyX
       0.12   12.6   0.1       0.19   12.0   0.1    1.3  1  zf-C4H2          Zinc finger-containing protein
       0.13   12.2   4.2       0.24   11.3   4.2    1.4  1  PhaP_Bmeg        Polyhydroxyalkanoic acid inclusion protein (
       0.14   12.4  16.0       0.38   11.1   2.9    3.9  3  BLOC1_2          Biogenesis of lysosome-related organelles co
       0.15   10.7   4.2       0.36    9.4   4.2    1.6  1  FapA             Flagellar Assembly Protein A
       0.16   11.5   6.6       0.14   11.7   3.1    1.8  2  Filament         Intermediate filament protein
       0.17   10.1   1.9       0.22    9.7   1.9    1.1  1  Cast             RIM-binding protein of the cytomatrix active
       0.18   11.9   9.3       0.09   12.8   4.7    2.1  2  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
       0.18   12.5   2.7       0.51   11.1   1.8    2.1  2  DUF4472          Domain of unknown function (DUF4472)
       0.21   11.3   4.7       0.21   11.2   1.6    2.0  2  Lebercilin       Ciliary protein causing Leber congenital ama
       0.21   11.6   0.8       0.93    9.6   0.2    1.9  2  DHR10            Designed helical repeat protein 10 domain
       0.22   11.3   2.8         17    5.3   0.6    2.8  2  DivIC            Septum formation initiator
       0.23   11.7   6.1       0.19   12.0   2.8    2.2  2  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
       0.24   11.1  14.4       0.42   10.3  14.4    1.3  1  SHE3             SWI5-dependent HO expression protein 3
       0.27   11.6   4.8       0.36   11.2   2.4    2.1  2  Muted            Organelle biogenesis, Muted-like protein
       0.27   11.3  12.9        1.1    9.4  12.0    2.2  1  Mod_r            Modifier of rudimentary (Mod(r)) protein
       0.28   12.1   6.1       0.69   10.8   6.1    1.7  1  DUF4744          Domain of unknown function (DUF4744)
       0.29   11.2   4.2        0.6   10.1   1.8    2.1  1  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
       0.29    9.0   8.8       0.26    9.2   4.7    1.5  2  Prominin         Prominin
       0.34   11.0   8.7       0.41   10.7   1.2    2.3  2  ADIP             Afadin- and alpha -actinin-Binding
       0.37   10.3   5.3       0.57    9.7   5.3    1.3  1  Exonuc_VII_L     Exonuclease VII, large subunit
       0.38   11.1   2.3        1.1    9.6   0.3    2.2  2  Gp-FAR-1         Nematode fatty acid retinoid binding protein
       0.39   10.1   6.1       0.76    9.1   2.3    1.9  2  Rab5-bind        Rabaptin-like protein
       0.39   11.0   1.7        4.3    7.7   0.9    2.7  2  DUF948           Bacterial protein of unknown function (DUF94
       0.53   10.6   5.6          1    9.7   2.5    2.6  3  KxDL             Uncharacterized conserved protein
        0.6    9.4  11.2        1.5    8.0   0.5    2.1  2  DUF3450          Protein of unknown function (DUF3450)
       0.64   10.7   5.3        6.8    7.4   1.2    2.7  2  YabA             Initiation control protein YabA
       0.85    9.1  13.3       0.34   10.4   7.3    2.1  2  HAUS-augmin3     HAUS augmin-like complex subunit 3
       0.86    9.8   7.1        6.1    7.0   1.5    2.7  2  HR1              Hr1 repeat
       0.92    9.3   4.3        3.5    7.5   4.1    2.1  1  CdvA             CdvA-like coiled-coil domain
        1.2    9.3   9.6        5.6    7.1   0.3    3.3  3  bZIP_1           bZIP transcription factor
        1.4    9.0   8.3        2.6    8.1   0.7    3.0  3  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding
        1.5    8.1  11.8      0.066   12.5   3.8    2.4  3  CorA             CorA-like Mg2+ transporter protein
        2.2    8.7   7.2        9.5    6.7   0.8    3.4  3  CLZ              C-terminal leucine zipper domain of cyclic n
        2.4    8.5   9.0       0.15   12.3   1.4    2.8  3  HALZ             Homeobox associated leucine zipper
        2.4    8.0  11.3       0.42   10.4   1.4    3.1  3  DASH_Duo1        DASH complex subunit Duo1
        3.2    7.3   5.1         61    3.1   0.8    2.2  2  DUF4795          Domain of unknown function (DUF4795)
        3.8    7.7  12.0        6.5    6.9   5.5    2.2  2  Fib_alpha        Fibrinogen alpha/beta chain family
        4.2    7.6   6.1          2    8.6   0.7    2.2  2  Cortex-I_coil    Cortexillin I, coiled coil
        4.5    7.9  11.6      6e+02    1.1  11.7    2.7  1  AATF-Che1        Apoptosis antagonizing transcription factor


Domain annotation for each model (and alignments):
>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.8    0.0024      0.64       7      55 ..      52     100 ..      36     108 .. 0.83
   2 !   19.8   0.1   2.4e-06   0.00063       4      87 ..     116     199 ..     113     206 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0024
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II   7 eanetakevleqlaplsqnlentkeklseinrsveetnekvkdankair 55 
                                       ++++++++ l+ + +l+q+l   +++ls++n++  et ++++++n+ + 
  gi|385805088|ref|YP_005841486.1|  52 SVQQSLENALRTISDLQQKLFYYNSSLSQLNQTYIETIAQLQQMNQNLT 100
                                       6678888888899999999999999999999998888888888888765 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 2.4e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHH CS
                        Laminin_II   4 laaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkq 80 
                                       ++++ net ++ l+   +l ++ + +++++s+++++  +   k++++n++   A ++ + L+    +Ll++l+++ q
  gi|385805088|ref|YP_005841486.1| 116 NLSSLNETYSSLLSSYSQLMNEYSSLNASYSSLKANYSQLLTKMSELNETYSYAISELSSLNTSYANLLSQLSTISQ 192
                                       68899************************************************************************ PP

                                       HHHH... CS
                        Laminin_II  81 leeasss 87 
                                       l+ ++++
  gi|385805088|ref|YP_005841486.1| 193 LSFERGN 199
                                       9987665 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   1.5    0.0038         1      10      56 ..      54     104 ..      51     113 .. 0.76
   2 !   14.3   0.1   0.00016     0.042       5      55 ..     116     166 ..     114     189 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0038
                              ZapB  10 EskiqkaidtitlLqme....ieeLkeeneelkeenreleeeneqlkeere 56 
                                       +++ ++a+ ti+ Lq++    ++ L + n+++ e +++l++ n++l  + e
  gi|385805088|ref|YP_005841486.1|  54 QQSLENALRTISDLQQKlfyyNSSLSQLNQTYIETIAQLQQMNQNLTSTIE 104
                                       678899**********95555678888888888888888888888876555 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 0.00016
                              ZapB   5 lLeqLEskiqkaidtitlLqmeieeLkeeneelkeenreleeeneqlkeer 55 
                                       +L+ L + +++++  +++L +e++ L +  ++lk +  +l  + ++l e+ 
  gi|385805088|ref|YP_005841486.1| 116 NLSSLNETYSSLLSSYSQLMNEYSSLNASYSSLKANYSQLLTKMSELNETY 166
                                       688999999999999999999999999999999999999998888887554 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.6   7.2e-07   0.00019      18     129 ..      50     161 ..      43     201 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 7.2e-07
                        V_ATPase_I  18 vnafqrkfvkevrrcdemerklrfleeeieklekavikeeeaeesleapeekeldeleeelekleeelkelnenlek 94 
                                        +++q++  + +r + ++++kl + ++ +++l+++ i++  + ++++++ +++++ l+++l + + +l++lne++++
  gi|385805088|ref|YP_005841486.1|  50 SSSVQQSLENALRTISDLQQKLFYYNSSLSQLNQTYIETIAQLQQMNQNLTSTIEILNSSLASCNGNLSSLNETYSS 126
                                       578899999******************************************************************** PP

                        V_ATPase_I  95 lkkelnelvelkavlekakefleeeeeeeeeeese 129
                                       l +++++l+++ + l+   + l+++ ++  ++ se
  gi|385805088|ref|YP_005841486.1| 127 LLSSYSQLMNEYSSLNASYSSLKANYSQLLTKMSE 161
                                       **********9999999999998773333333332 PP

>> HMMR_N  Hyaluronan mediated motility receptor N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   2.9   7.6e-06     0.002     186     317 ..      45     173 ..      37     181 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 7.6e-06
                            HMMR_N 186 dmeaklqvtqknLeeskakvaqLkeklvslekekieekseteklleyieelsnvseqlekykldiaqleellkeknd 262
                                       ++ +   ++q+ Le++  +++ L++kl   +       + ++  +e i++l+++ ++l      i+ l++ l++ n 
  gi|385805088|ref|YP_005841486.1|  45 NTSGGSSSVQQSLENALRTISDLQQKLFYYNSS---LSQLNQTYIETIAQLQQMNQNL---TSTIEILNSSLASCNG 115
                                       555666799*****************9544443...3344577899999999999999...9999999999999999 PP

                            HMMR_N 263 eiesLk...ssLeekeqelskqvkdlnekckllekekeelvreeeekeqtlsaEleel 317
                                       +++sL    ssL  +  +l ++ ++ln+ ++ l ++  +l+++  e ++t+s  + el
  gi|385805088|ref|YP_005841486.1| 116 NLSSLNetySSLLSSYSQLMNEYSSLNASYSSLKANYSQLLTKMSELNETYSYAISEL 173
                                       99999833346777777899999*************************9999777665 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   7.0   3.3e-05    0.0088     226     329 ..      57     160 ..      51     161 .. 0.89
   2 !   10.0   0.3    0.0011       0.3     267     326 ..     140     199 ..     139     202 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.3e-05
                             IFT57 226 leqmkkhkksieeslpetksqlkklhedisktlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegvse 302
                                       le+  +  + ++++l  ++s+l++l +   +t+ ++++  ++l+s +e l + + +++ +ls+++e y+ l ++ s+
  gi|385805088|ref|YP_005841486.1|  57 LENALRTISDLQQKLFYYNSSLSQLNQTYIETIAQLQQMNQNLTSTIEILNSSLASCNGNLSSLNETYSSLLSSYSQ 133
                                       555566667889999999*********************************************************** PP

                             IFT57 303 ltrelaeiseelekvkqemeergssmt 329
                                       l +e+++++  ++++k +  +  ++m+
  gi|385805088|ref|YP_005841486.1| 134 LMNEYSSLNASYSSLKANYSQLLTKMS 160
                                       **********99999998887777776 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0011
                             IFT57 267 ylnsqleellqeyreaqeelsevkekykqlsegvseltrelaeiseelekvkqemeergs 326
                                        ln ++++l ++y+++ +++se++e y+ + +++s+l++ +a++  +l++++q   erg+
  gi|385805088|ref|YP_005841486.1| 140 SLNASYSSLKANYSQLLTKMSELNETYSYAISELSSLNTSYANLLSQLSTISQLSFERGN 199
                                       5899***********************************************998888876 PP

>> Jnk-SapK_ap_N  JNK_SAPK-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   1.6   2.2e-05    0.0059      49     150 ..      54     162 ..      48     167 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.2e-05
                     Jnk-SapK_ap_N  49 eaeleelreeleqLeteyerekelrkraeeeleeiedqweeerkelqekveqleeenrelelkaknaadqlsrleek 125
                                       ++ le+  +++++L++++   ++   + +++++e+  q+++ +++l + +e l++     +  ++++++  s+l ++
  gi|385805088|ref|YP_005841486.1|  54 QQSLENALRTISDLQQKLFYYNSSLSQLNQTYIETIAQLQQMNQNLTSTIEILNSSLASCNGNLSSLNETYSSLLSS 130
                                       67788888888888888888888888888999999999999999999999999999988888888999999999999 PP

                     Jnk-SapK_ap_N 126 eaelkkeysklhe.......retellkklkel 150
                                        ++l++eys+l+        ++++ll k+ el
  gi|385805088|ref|YP_005841486.1| 131 YSQLMNEYSSLNAsysslkaNYSQLLTKMSEL 162
                                       99999999999885555655666666666665 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   2.1    0.0066       1.8     372     428 ..      48     104 ..      34     112 .. 0.86
   2 !   13.4   1.8   5.9e-05     0.016     346     420 ..     117     191 ..     111     194 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0066
                                       ---STTGGGTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              EzrA 372 vaYSelqeeleeleekleeieekqeeileslkslrkdEkrAreqldeikkelkeikr 428
                                          S++q+ le++ ++++++++k+ +++ sl++l +   +   ql+++++ l ++  
  gi|385805088|ref|YP_005841486.1|  48 GGSSSVQQSLENALRTISDLQQKLFYYNSSLSQLNQTYIETIAQLQQMNQNLTSTIE 104
                                       55699*********************************************9988765 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 5.9e-05
                                       HHHHHHHHHHHHHHHHHHHHHHS-SS---STTGGGTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              EzrA 346 lrelekelkelekdyeeleekleekkvaYSelqeeleeleekleeieekqeeileslkslrkdEkrAreqldeik 420
                                       l +l++  ++l ++y +l ++ ++ +++YS+l+ ++ +l  k++e++e   +   +l+sl  + ++   ql++i+
  gi|385805088|ref|YP_005841486.1| 117 LSSLNETYSSLLSSYSQLMNEYSSLNASYSSLKANYSQLLTKMSELNETYSYAISELSSLNTSYANLLSQLSTIS 191
                                       678999999**************************************************9988877777777765 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   4.3     4e-05     0.011     150     278 ..      56     183 ..      40     197 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4e-05
                              Spc7 150 gleedkelLekqeeeldellpeleeekaeleeeleklqeaaeeles...idkeeLeelreelaelkaeieekkkela 223
                                       +le+  +++++ +++l  +  +l++  ++  e++++lq+++++l+s   i + +L+++  +l++l+++++++   ++
  gi|385805088|ref|YP_005841486.1|  56 SLENALRTISDLQQKLFYYNSSLSQLNQTYIETIAQLQQMNQNLTStieILNSSLASCNGNLSSLNETYSSLLSSYS 132
                                       34444444444444444444444444444444444444444444443334566777777777777777777777777 PP

                              Spc7 224 elqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkal 278
                                       +l ++  +l+++ ++lk+++s+l ++++e ++++        se+s+l++++ +l
  gi|385805088|ref|YP_005841486.1| 133 QLMNEYSSLNASYSSLKANYSQLLTKMSELNETYS----YAISELSSLNTSYANL 183
                                       77777777777777777777777777665554443....5555555555555444 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   1.5   4.7e-05     0.013      69     176 ..      54     160 ..      51     168 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.7e-05
                           DUF4201  69 kkkttktvhalthlkeklhmleselselkkelkekeerlaklrkel.ykvklerdklrkqneklkqqggllrvPaLl 144
                                       +++  + + ++++l++kl  ++s ls+l++ + e  ++l+++ ++l +  +  ++ l   n +l++ ++   + +Ll
  gi|385805088|ref|YP_005841486.1|  54 QQSLENALRTISDLQQKLFYYNSSLSQLNQTYIETIAQLQQMNQNLtSTIEILNSSLASCNGNLSSLNET--YSSLL 128
                                       5667789999******************9999888888888877761567999999********999998..77888 PP

                           DUF4201 145 kDYdktkekveekrksvkkLrrkvkilemrlk 176
                                         Y + ++++ ++ +s  +L+  + +l  +++
  gi|385805088|ref|YP_005841486.1| 129 SSYSQLMNEYSSLNASYSSLKANYSQLLTKMS 160
                                       88999999999988888888888888766655 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 ?    1.9   0.1      0.94   2.5e+02      37      61 ..      98     122 ..      79     130 .. 0.65
   2 !   12.4   0.1   0.00051      0.14       8      66 ..     132     190 ..     125     193 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.94
                          JIP_LZII  37 eLtsereiLreEleslqkakerles 61 
                                       +Lts  eiL++ l s++ ++++l++
  gi|385805088|ref|YP_005841486.1|  98 NLTSTIEILNSSLASCNGNLSSLNE 122
                                       4566666666666666666666655 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00051
                          JIP_LZII   8 enLikENteLletknaLnvvkddLIarvdeLtsereiLreEleslqkakerlesrikel 66 
                                        +L++E++ L +    L      L+++  eL++ ++   +El+sl+++ + l s+++ +
  gi|385805088|ref|YP_005841486.1| 132 SQLMNEYSSLNASYSSLKANYSQLLTKMSELNETYSYAISELSSLNTSYANLLSQLSTI 190
                                       579*********************************************99999998765 PP

>> AIP3  Actin interacting protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   1.3   4.7e-05     0.013     100     212 ..      55     164 ..      23     168 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.7e-05
                                       ...XXXXXXXXXXXXXXXXXXXXXXXX........................XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              AIP3 100 esqkaslqevserqeeaakekasesla...............kkelkaqlkevqslrrdLavlrqlysefkseikes 161
                                       +s +++l+++s                               +++  + ++++q+++++L+++ ++ +++  +++ +
  gi|385805088|ref|YP_005841486.1|  55 QSLENALRTIS---------------DlqqklfyynsslsqlNQTYIETIAQLQQMNQNLTSTIEILNSSLASCNGN 116
                                       12222222233...............1444466666666555788889999************************** PP

                                       XXXXXXXXXXXXXXXX.XXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              AIP3 162 lselrekakkvkeaslastkkssnrayiekgkkkLseesdklvtkvddLqD 212
                                       ls+l+e+ +++   s   ++  ++ + ++++ ++L+++ ++l+tk+ +L+ 
  gi|385805088|ref|YP_005841486.1| 117 LSSLNETYSSLL--SS-YSQLMNEYSSLNASYSSLKANYSQLLTKMSELNE 164
                                       **********99..33.46779999***********************986 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.5   0.00026      0.07      30     128 ..      31     147 ..      27     152 .. 0.73
   2 ?   13.1   3.1    0.0004      0.11      25     133 .]      82     187 ..      73     192 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00026
                            APG6_N  30 eflkklkkekkeeek..............qdeeleeleee....leklekeeeelleeLkelekereeleaelaale 88 
                                       ++l +l+++++++++                  + +l+++     + l++  ++ +e +++l++ +++l + ++ l 
  gi|385805088|ref|YP_005841486.1|  31 SYLYQLTSSSQTPQNtsggsssvqqslenALRTISDLQQKlfyyNSSLSQLNQTYIETIAQLQQMNQNLTSTIEILN 107
                                       66777777766665566665444444333222333333335554667999999999999999999999999999999 PP

                            APG6_N  89 eelealeeeeerfwreynelqlelleleeeldsleaqyeh 128
                                       + l+  + +     + y++l    ++l +e  sl+a+y  
  gi|385805088|ref|YP_005841486.1| 108 SSLASCNGNLSSLNETYSSLLSSYSQLMNEYSSLNASYSS 147
                                       9999999999999999999999999999999999999976 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.0004
                            APG6_N  25 rdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerf 101
                                        ++Y e  ++l++ +++     + +e l+ +l+  +   ++l e    l +  ++l +e ++l +  + l+++  + 
  gi|385805088|ref|YP_005841486.1|  82 NQTYIETIAQLQQMNQNL---TSTIEILNSSLASCNGNLSSLNETYSSLLSSYSQLMNEYSSLNASYSSLKANYSQL 155
                                       467888888888885554...46777777777777777777777777777777777777777777777777777777 PP

                            APG6_N 102 wreynelqlelleleeeldsleaqyehaqnql 133
                                       +++ +el+ + +    el sl+++y+  ++ql
  gi|385805088|ref|YP_005841486.1| 156 LTKMSELNETYSYAISELSSLNTSYANLLSQL 187
                                       77777777777777777777777777777665 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.7   6.1e-05     0.016     781     885 ..      56     167 ..      40     222 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.1e-05
                           DUF3584 781 eLekkieriekrreevreYra...flqetwlk.vdslaeerpalkeqveelesaaeeleqeltrliedtkl...erk 850
                                       +Le+ + +i++ ++++  Y++    l++t+ + + +l++ +++l ++ e l+s+++  + +l+ l+e +       +
  gi|385805088|ref|YP_005841486.1|  56 SLENALRTISDLQQKLFYYNSslsQLNQTYIEtIAQLQQMNQNLTSTIEILNSSLASCNGNLSSLNETYSSllsSYS 132
                                       56666666666666666666411134666654134566667777777777777777777777776666654111345 PP

                           DUF3584 851 klekerkalekqldqldenlrklrdllsklaelkl 885
                                       +l++e ++l++  + l++n ++l + +s+l+e   
  gi|385805088|ref|YP_005841486.1| 133 QLMNEYSSLNASYSSLKANYSQLLTKMSELNETYS 167
                                       67777777777777777777777777777755432 PP

>> Rootletin  Ciliary rootlet component, centrosome cohesion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   1.9   6.7e-05     0.018      62     144 ..      50     136 ..      29     142 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6.7e-05
                         Rootletin  62 eeeesadleealakLeeErqr....seklaqvnslLreqleearqaneaLtedlqkltkdwerlreeleqkekewre 134
                                       +++ +++le+al+   + +q+    +++l+q+n+++ e + + +q n++Lt+ ++ l++ + +++ +l + ++++ +
  gi|385805088|ref|YP_005841486.1|  50 SSSVQQSLENALRTISDLQQKlfyyNSSLSQLNQTYIETIAQLQQMNQNLTSTIEILNSSLASCNGNLSSLNETYSS 126
                                       456677888888888888887555589************************************99999999888888 PP

                         Rootletin 135 eeeafneyls 144
                                          ++++ ++
  gi|385805088|ref|YP_005841486.1| 127 LLSSYSQLMN 136
                                       7777777665 PP

>> TACC_C  Transforming acidic coiled-coil-containing protein (TACC), C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   2.1   0.00013     0.034      23     133 ..      63     166 ..      42     168 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.00013
                            TACC_C  23 eiqelkkkveelkkenqemkkivaefektiaqlieekqkqkelakkeiqkvleekeqlladlnsveksfsdlfkrye 99 
                                        i       ++l+++    +  +++  +t  ++i++ q+ +++   +i+ + +     + +l+s++ ++s l++ y 
  gi|385805088|ref|YP_005841486.1|  63 TI-------SDLQQKLFYYNSSLSQLNQTYIETIAQLQQMNQNLTSTIEILNSSLASCNGNLSSLNETYSSLLSSYS 132
                                       33.......3333333333344444444444555555677788889999999999********************** PP

                            TACC_C 100 kqkevlegykkneeslkkcaeeylarvkkeeqRY 133
                                       ++ +  + + +   slk+  +++l+++ + ++ Y
  gi|385805088|ref|YP_005841486.1| 133 QLMNEYSSLNASYSSLKANYSQLLTKMSELNETY 166
                                       *999999999999999999999999988877766 PP

>> LOH1CR12  Tumour suppressor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.5    0.0015      0.39      49     109 ..      52     112 ..      32     124 .. 0.77
   2 ?    4.8   0.1       0.1        27      45      93 ..     146     194 ..     125     197 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0015
                          LOH1CR12  49 adqaklverikevdakiitllaelrekqkqyasyaealskvnelsdqlsriqiiledivpl 109
                                       + q+ l +  ++++   ++l+       +  + y+e+++++++++++l++   il+  +++
  gi|385805088|ref|YP_005841486.1|  52 SVQQSLENALRTISDLQQKLFYYNSSLSQLNQTYIETIAQLQQMNQNLTSTIEILNSSLAS 112
                                       4577777777777777778888888888888888888888888888888888888877665 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.1
                          LOH1CR12  45 kavAadqaklverikevdakiitllaelrekqkqyasyaealskvnels 93 
                                       +   a+  +l  ++ e+++  + +++el   +  ya+   +ls + +ls
  gi|385805088|ref|YP_005841486.1| 146 SSLKANYSQLLTKMSELNETYSYAISELSSLNTSYANLLSQLSTISQLS 194
                                       3344566677777778888888888888888888888888888777776 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.8    0.0026      0.69      55     138 ..      49     133 ..      35     136 .. 0.86
   2 ?   11.0   3.1   0.00071      0.19      43     136 ..      83     173 ..      57     197 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0026
                               GAS  55 enkrlkepLkkaeeeveeLrkqlknyekdkqslknlk.arlkelekelkdlkwehevleqrfekvekerdelykkfe 130
                                         ++ ++ L++a + +  L+++l  y++  ++l+++  + + +l++  ++l+   e+l+  +++       l++++ 
  gi|385805088|ref|YP_005841486.1|  49 GSSSVQQSLENALRTISDLQQKLFYYNSSLSQLNQTYiETIAQLQQMNQNLTSTIEILNSSLASCNGNLSSLNETYS 125
                                       56778999********************9999998863678899999999**********99999999999999999 PP

                               GAS 131 aaiqevqq 138
                                       + +  ++q
  gi|385805088|ref|YP_005841486.1| 126 SLLSSYSQ 133
                                       98888877 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00071
                               GAS  43 ernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekve 119
                                       +     +++++q n++l+ +++ ++  ++  + +l   ++    + +l + +++l +e+++l  ++ +l+  ++++ 
  gi|385805088|ref|YP_005841486.1|  83 QTYIETIAQLQQMNQNLTSTIEILNSSLASCNGNLSSLNE---TYSSLLSSYSQLMNEYSSLNASYSSLKANYSQLL 156
                                       3334455666666666666666666666655555555444...3333344455555566666666666666666666 PP

                               GAS 120 kerdelykkfeaaiqev 136
                                        +  el++++  ai e+
  gi|385805088|ref|YP_005841486.1| 157 TKMSELNETYSYAISEL 173
                                       66666666665555554 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 ?   10.3  10.5     0.002      0.52      36     116 ..      53     132 ..      44     141 .. 0.70
   2 ?    8.7   2.1    0.0063       1.7      60     105 ..     143     191 ..     131     193 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.002
                      Baculo_PEP_C  36 latlldaietqLnalsedlksllaeldt...rldtlltnLtdalnalqdtlrneLtnlnsiltnLlssvtNinstLn 109
                                       +++ l++  +++++l+++l       ++   +l+++  +  ++l++++++l++ ++ lns l++ + ++  +n+t +
  gi|385805088|ref|YP_005841486.1|  53 VQQSLENALRTISDLQQKLFY----YNSslsQLNQTYIETIAQLQQMNQNLTSTIEILNSSLASCNGNLSSLNETYS 125
                                       444444444445555554444....44412256666666666666666***************************** PP

                      Baculo_PEP_C 110 nllqaln 116
                                       +ll++  
  gi|385805088|ref|YP_005841486.1| 126 SLLSSYS 132
                                       **98765 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0063
                      Baculo_PEP_C  60 eldtrldtlltnLtdalnalq...dtlrneLtnlnsiltnLlssvtNin 105
                                       +  + l+++ ++L +++ +l+       +eL +ln+  +nLls++  i 
  gi|385805088|ref|YP_005841486.1| 143 ASYSSLKANYSQLLTKMSELNetySYAISELSSLNTSYANLLSQLSTIS 191
                                       33447899999999999999943344568999************98876 PP

>> LXG  LXG domain of WXG superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   5.5   0.00016     0.042     118     195 ..      53     126 ..      33     133 .. 0.79
   2 ?    4.4   1.1       0.1        27     140     190 ..     138     188 ..     128     194 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00016
                               LXG 118 lkdeinkilasvsdivslpelddsevkdslqkakkkvqetiekledfdqeqksalanlesdlkalktyvseLeemts 194
                                        +++++++l+++sd+    + ++ ++++sl++ +++  eti +l++++q+++s  + l+s l++ +  +s+L+e++s
  gi|385805088|ref|YP_005841486.1|  53 VQQSLENALRTISDL----QQKLFYYNSSLSQLNQTYIETIAQLQQMNQNLTSTIEILNSSLASCNGNLSSLNETYS 125
                                       344555555555655....6677778899999999999999999999999999999999999999999999999998 PP

                               LXG 195 k 195
                                       +
  gi|385805088|ref|YP_005841486.1| 126 S 126
                                       6 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.1
                               LXG 140 dsevkdslqkakkkvqetiekledfdqeqksalanlesdlkalktyvseLe 190
                                       +s++++s+++ k + ++ ++k+ ++++  ++a ++l s  ++ ++++s+L+
  gi|385805088|ref|YP_005841486.1| 138 YSSLNASYSSLKANYSQLLTKMSELNETYSYAISELSSLNTSYANLLSQLS 188
                                       667777777777777777777777777777777777777666666666665 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   3.0      0.01       2.7      68     121 ..      74     127 ..      68     129 .. 0.92
   2 ?    8.2   0.1     0.011       2.9       3      54 ..     136     187 ..     134     194 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.01
                           DUF5082  68 ydgirsnlessyqtyvdkldelidaieeEIerLenqiseaqgvldtlqsqlnsl 121
                                       y++ +s+l + y + + +l ++ +++ + Ie L +++ ++ g+l++l++  +sl
  gi|385805088|ref|YP_005841486.1|  74 YNSSLSQLNQTYIETIAQLQQMNQNLTSTIEILNSSLASCNGNLSSLNETYSSL 127
                                       788899****************************************99887766 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.011
                           DUF5082   3 tkisklqaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklekpl 54 
                                       ++ s+l+a +++l+++ ++l  k ++L e+++   +e +sl ++  +l  +l
  gi|385805088|ref|YP_005841486.1| 136 NEYSSLNASYSSLKANYSQLLTKMSELNETYSYAISELSSLNTSYANLLSQL 187
                                       677999**************************99999999998877776555 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.7   0.00029     0.077     110     229 ..      79     190 ..      38     206 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00029
                           DUF4407 110 aelaeeqqeeakelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaak 186
                                       ++l++++ e++++l +q++++lt++++ l++ +a+ ++++++++++++ l   + + ++   +          +++ 
  gi|385805088|ref|YP_005841486.1|  79 SQLNQTYIETIAQL-QQMNQNLTSTIEILNSSLASCNGNLSSLNETYSSLLSSYSQLMNEY-S-S------LNASYS 146
                                       57888888888888.7778899999999999999999999999999999999998777652.2.2......245677 PP

                           DUF4407 187 ekkaqldaaqaelaelkakld.atarlaalraelaeleaerake 229
                                       + ka++ ++ +++ el+++ + a ++l++l++ +a l ++++++
  gi|385805088|ref|YP_005841486.1| 147 SLKANYSQLLTKMSELNETYSyAISELSSLNTSYANLLSQLSTI 190
                                       77777777777777777776667777777777777777776654 PP

>> KASH_CCD  Coiled-coil region of CCDC155 or KASH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   6.5    0.0013      0.34       8     133 ..      62     188 ..      51     199 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0013
                          KASH_CCD   8 stvadLqln....NkkLaeenskLkkavetaeetnakLteeieeLkkklkstQqalqkaklleeEleelkalvkele 80 
                                        t+ dLq+     N +L++ n+   +++ + +  n+ Lt  ie L   l s         +l+e    l  + ++l 
  gi|385805088|ref|YP_005841486.1|  62 RTISDLQQKlfyyNSSLSQLNQTYIETIAQLQQMNQNLTSTIEILNSSLASCNGN---LSSLNETYSSLLSSYSQLM 135
                                       4566666422222444444444444444444444444444444444444443332...3456666666666666666 PP

                          KASH_CCD  81 EkrarlkaqnkqlekenqsLiakiesLqeenikllaekdelkkklkeLlkeka 133
                                        +  +l+a  + l+ +  +L +k+ +L+e      +e + l++  ++Ll++ +
  gi|385805088|ref|YP_005841486.1| 136 NEYSSLNASYSSLKANYSQLLTKMSELNETYSYAISELSSLNTSYANLLSQLS 188
                                       66666667667776666666677777777666666666666666666665544 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.9    0.0013      0.34      47     121 ..      89     163 ..      40     166 .. 0.79
   2 ?    5.7   0.0     0.053        14      48     121 ..     118     191 ..     109     193 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0013
                           DUF1664  47 skqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                         ql+q+ ++l++t + L+s +++ + +l + +e+ +++ +  +++ ++ s+++   +s+k+  ++l +k+++++
  gi|385805088|ref|YP_005841486.1|  89 IAQLQQMNQNLTSTIEILNSSLASCNGNLSSLNETYSSLLSSYSQLMNEYSSLNASYSSLKANYSQLLTKMSELN 163
                                       457888888888888888888888888888888888888888888888888888888888888888888888776 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.053
                           DUF1664  48 kqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                       ++l++ ++sl +   +L+++  +++++  + k+  +++  +++e++e  s   ++++s+++   +l s+l++i+
  gi|385805088|ref|YP_005841486.1| 118 SSLNETYSSLLSSYSQLMNEYSSLNASYSSLKANYSQLLTKMSELNETYSYAISELSSLNTSYANLLSQLSTIS 191
                                       46888889999999999999999999999999999999999999999999999999999999888888888876 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.9    0.0016      0.44      73     139 ..      40     103 ..      33     114 .. 0.77
   2 ?    6.4   0.9     0.035       9.5      16     150 ..     123     163 ..     114     196 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0016
                             ATG16  73 sakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletkl 139
                                       s++ q+++   +++++ l++++++ ++l+q+l   n++l++l+++  e   ++a+l++++++l+  +
  gi|385805088|ref|YP_005841486.1|  40 SQTPQNTSGGSSSVQQSLENALRTISDLQQKLFYYNSSLSQLNQTYIE---TIAQLQQMNQNLTSTI 103
                                       4566777778889999999****************9999999987765...5666666666666555 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.035
                             ATG16  16 afaeliqaynrLldrtsaleaenaklekaaasakssksskksakekeasasqsnskqsakiqsleqklaqlreelae 92 
                                        +++l + y++L++  s+l+a  ++l+++ ++  +                                          
  gi|385805088|ref|YP_005841486.1| 123 TYSSLLSSYSQLMNEYSSLNASYSSLKANYSQLLT------------------------------------------ 157
                                       45566666666666666666666666444333332.......................................... PP

                             ATG16  93 lyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelreke 150
                                                                                           ++ e++
  gi|385805088|ref|YP_005841486.1| 158 ----------------------------------------------------KMSELN 163
                                       ....................................................222222 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   3.8   0.00068      0.18     333     482 ..      51     190 ..      29     194 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00068
                            DUF812 333 eelqeqieeleskieeleeeikklessikqveeeleeekeeneelekevklkkktlellpdaeeniekLqalveasa 409
                                       +++q+ +e++ ++i+ l++++  ++ss++q+++++ e+    ++l++ +++ + t+e+l          ++ + + +
  gi|385805088|ref|YP_005841486.1|  51 SSVQQSLENALRTISDLQQKLFYYNSSLSQLNQTYIETI---AQLQQMNQNLTSTIEIL----------NSSLASCN 114
                                       455555555555555555555555555555555444333...33333333333444444..........33333333 PP

                            DUF812 410 qrlvelakqWe...khRvplieeyrelkesksekekeaerkleeikklrekmkevaeelrqkeellkqLvaelekl 482
                                        +l +l + +    +  ++l++ey +l  s s+ ++++++ l+++ +l e+   +++el + + ++ +L+++l ++
  gi|385805088|ref|YP_005841486.1| 115 GNLSSLNETYSsllSSYSQLMNEYSSLNASYSSLKANYSQLLTKMSELNETYSYAISELSSLNTSYANLLSQLSTI 190
                                       3333333333311134466888888888888888888888888888888888888888888888888888877665 PP

>> Csm1_N  Csm1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.1   0.00077      0.21       9      59 ..      51     105 ..      50     116 .. 0.84
   2 ?    0.8   0.0       2.4   6.4e+02      24      56 ..     133     165 ..     125     179 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00077
                            Csm1_N   9 esVqerldsAdllvs....klvhENsvLsqkletkdqeiesLkeqlaeleekvke 59 
                                        sVq+ l++A   +s    kl + Ns Lsq ++t+ + i +L++  ++l + ++ 
  gi|385805088|ref|YP_005841486.1|  51 SSVQQSLENALRTISdlqqKLFYYNSSLSQLNQTYIETIAQLQQMNQNLTSTIEI 105
                                       59********99885444489999*******************998888877665 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 2.4
                            Csm1_N  24 klvhENsvLsqkletkdqeiesLkeqlaeleek 56 
                                       +l +E s L+   ++ +   ++L  ++ el+e 
  gi|385805088|ref|YP_005841486.1| 133 QLMNEYSSLNASYSSLKANYSQLLTKMSELNET 165
                                       566666666666666666666666666666665 PP

>> APG17  Autophagy protein Apg17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   6.7    0.0009      0.24     257     367 ..      53     164 ..      41     167 .. 0.60
   2 ?    4.2   0.3     0.071        19     246     297 ..     140     191 ..     138     207 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0009
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHHHHHHHH CS
                             APG17 257 akkllsekkeeiekllsalkkaleeleevgkklpeylaifkaeeeflerw.eeekekieekleeleeLrefYegFls 332
                                       ++++l++  ++i  l+++l    + l+++++++ e++a +++ ++ l+ + e  ++++++   +l++L e Y + ls
  gi|385805088|ref|YP_005841486.1|  53 VQQSLENALRTISDLQQKLFYYNSSLSQLNQTYIETIAQLQQMNQNLTSTiEILNSSLASCNGNLSSLNETYSSLLS 129
                                       34444444444444444444444444444334444444333333333333266666777777788888889999999 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             APG17 333 aYdklllEveRRraveekmekilkkarekLeklqe 367
                                       +Y +l+ E++  +a++   ++  +++  k+ +l+e
  gi|385805088|ref|YP_005841486.1| 130 SYSQLMNEYSSLNASYSSLKANYSQLLTKMSELNE 164
                                       99999999888888888877777777777777665 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.071
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHH CS
                             APG17 246 elqerleemekakkllsekkeeiekllsalkkaleeleevgkklpeylaifk 297
                                       +l+++++++++ +++l +k++e+++++s   + l+ l++  ++l + l++++
  gi|385805088|ref|YP_005841486.1| 140 SLNASYSSLKANYSQLLTKMSELNETYSYAISELSSLNTSYANLLSQLSTIS 191
                                       6899999999999999999999999999999999999976666666666444 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.0    0.0015      0.41       5      47 ..      64     106 ..      62     119 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0015
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT- CS
                              SlyX   5 leeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerl 47 
                                       + +L+ kl +    + +Ln++ +e   q++++ + l    e l
  gi|385805088|ref|YP_005841486.1|  64 ISDLQQKLFYYNSSLSQLNQTYIETIAQLQQMNQNLTSTIEIL 106
                                       889******************9998888888877776655555 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00072      0.19      13     102 ..      51     144 ..      44     224 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00072
                           zf-C4H2  13 eklknklakevealekeekcleeykkelelLeqEkmaHveeLrlIhaDinalEsvikeaeeekekslekakkly... 86 
                                       +++++ l +++ ++++ ++ l  y++ l++L+q   + + +L+++++ + +  ++++++  + + +l++ +++y   
  gi|385805088|ref|YP_005841486.1|  51 SSVQQSLENALRTISDLQQKLFYYNSSLSQLNQTYIETIAQLQQMNQNLTSTIEILNSSLASCNGNLSSLNETYssl 127
                                       578899****************************************9988777777777777666666665555111 PP

                           zf-C4H2  87 .eeykklkeevnelrse 102
                                        + y++l++e  +l  +
  gi|385805088|ref|YP_005841486.1| 128 lSSYSQLMNEYSSLNAS 144
                                       14444444444433333 PP

>> PhaP_Bmeg  Polyhydroxyalkanoic acid inclusion protein (PhaP_Bmeg)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   4.2   0.00088      0.24      21     115 ..      71     170 ..      51     210 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00088
                         PhaP_Bmeg  21 lerfaslskqvEqltLkalkqqqdlvkeltkalselekeskqltael...edqlqktvenlrs..kaGnkvednieE 92 
                                       l  ++s   q+ q++++++ q q+++++lt+ ++ l+      + +l   ++ + + ++   +  +   +++ +++ 
  gi|385805088|ref|YP_005841486.1|  71 LFYYNSSLSQLNQTYIETIAQLQQMNQNLTSTIEILNSSLASCNGNLsslNETYSSLLSSYSQlmNEYSSLNASYSS 147
                                       55567778899999******************999999999988655111555655555443211334567889999 PP

                         PhaP_Bmeg  93 wtdkleevsakleklalspsKss 115
                                       ++  + ++++k+ +l+ + s + 
  gi|385805088|ref|YP_005841486.1| 148 LKANYSQLLTKMSELNETYSYAI 170
                                       99999999999988876666554 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   1.5      0.29        77      30      69 ..      58      97 ..      36      98 .. 0.83
   2 ?   11.1   2.9    0.0014      0.38      19      67 ..      86     134 ..      76     137 .. 0.84
   3 ?    6.7   7.7     0.034       9.1       4      69 ..      99     164 ..      96     196 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.29
                           BLOC1_2 30 eaasekykklkdvaaslekkleklnekyeelqpylqqidq 69
                                      e+a + + +l++++   +++l++ln++y e   +lqq++q
  gi|385805088|ref|YP_005841486.1| 58 ENALRTISDLQQKLFYYNSSLSQLNQTYIETIAQLQQMNQ 97
                                      5666777888888888999999999999999999999876 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0014
                           BLOC1_2  19 vedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqi 67 
                                        e +  L+++N++ ++ ++ l++++as + +l+ lne+y +l +  +q+
  gi|385805088|ref|YP_005841486.1|  86 IETIAQLQQMNQNLTSTIEILNSSLASCNGNLSSLNETYSSLLSSYSQL 134
                                       5667889999999999999999999999999999999999988877776 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.034
                           BLOC1_2   4 fekvskyleaeleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidq 69 
                                       ++++ ++l++ l++ + +++ L++   +  + y +l ++ +sl+++ + l++ y +l  +++++++
  gi|385805088|ref|YP_005841486.1|  99 LTSTIEILNSSLASCNGNLSSLNETYSSLLSSYSQLMNEYSSLNASYSSLKANYSQLLTKMSELNE 164
                                       78999999999*****************************************99999999998876 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   4.2    0.0014      0.36     340     432 ..      65     153 ..      38     196 .. 0.54

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0014
                              FapA 340 keleeeleeleeeleklkkk.ikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeeleskkeea 415
                                       ++l+++l  ++++l +l+++ i+ + +    +q++++  ++++ l  ++ + + +l++l+e + +l ++  +   ++
  gi|385805088|ref|YP_005841486.1|  65 SDLQQKLFYYNSSLSQLNQTyIETIAQ---LQQMNQNLTSTIEILNSSLASCNGNLSSLNETYSSLLSSYSQL--MN 136
                                       455555555555555555553222222...3334445555555555555555555555555555444444444..22 PP

                              FapA 416 kikvnkeiypgvkikig 432
                                       +++  +  y++ k ++ 
  gi|385805088|ref|YP_005841486.1| 137 EYSSLNASYSSLKANYS 153
                                       23333333333222222 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   3.1   0.00053      0.14     204     290 ..      50     136 ..      31     143 .. 0.78
   2 ?    1.6   0.2      0.61   1.6e+02     226     264 ..     139     177 ..     129     198 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00053
                                       XXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 204 aeknsealrsakeeitelrrqiqsleieleslkkqkasleaqlaeleerleaeleklqeklseleeelaeireemar 280
                                       +++ +++l++a + i++l++++   ++ l++l ++   + aql+ ++++l + +e l+++l++ + +l+++ e+   
  gi|385805088|ref|YP_005841486.1|  50 SSSVQQSLENALRTISDLQQKLFYYNSSLSQLNQTYIETIAQLQQMNQNLTSTIEILNSSLASCNGNLSSLNETYSS 126
                                       45556777888888888888888888888888888888888888888888888888888888888888888888888 PP

                                       HHHHHHHHHH CS
                          Filament 281 qlreYqeLLd 290
                                        l+ Y++L++
  gi|385805088|ref|YP_005841486.1| 127 LLSSYSQLMN 136
                                       8888888887 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.61
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 226 qsleieleslkkqkasleaqlaeleerleaeleklqekl 264
                                        sl++  +slk++ ++l ++++el+e+++ ++++l +  
  gi|385805088|ref|YP_005841486.1| 139 SSLNASYSSLKANYSQLLTKMSELNETYSYAISELSSLN 177
                                       556666666666666677777777777666655544433 PP

>> Cast  RIM-binding protein of the cytomatrix active zone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.9   0.00082      0.22     460     544 ..      79     163 ..      34     192 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00082
                              Cast 460 eredrerleeleslkkenkelkeklsalqaeltekesslldlkekasslassglkkdsklksleiavekkkeecskl 536
                                       ++ +++  e +++l++ n++l  ++++l+++l++ +  l++l+e  ssl ss  + +++  sl+ + +  k + s+l
  gi|385805088|ref|YP_005841486.1|  79 SQLNQTYIETIAQLQQMNQNLTSTIEILNSSLASCNGNLSSLNETYSSLLSSYSQLMNEYSSLNASYSSLKANYSQL 155
                                       566788999********************************************************999999999999 PP

                              Cast 537 eaqlkkaq 544
                                        ++++  +
  gi|385805088|ref|YP_005841486.1| 156 LTKMSELN 163
                                       88877544 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 ?    7.8   1.6     0.012       3.2      54     123 ..      59     128 ..      41     130 .. 0.86
   2 ?   12.8   4.7   0.00034      0.09       9     100 ..      88     179 ..      84     193 .. 0.55

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.012
                        TPR_MLP1_2  54 edvkelqalreelnelkaeiaelkaeaesakaeleeseesweeqkeelekelselekriedlneqNklLh 123
                                       ++++++++l ++l  +++ +++l++   ++ a+l++  ++++++ e l + l++++  +  lne  + L+
  gi|385805088|ref|YP_005841486.1|  59 NALRTISDLQQKLFYYNSSLSQLNQTYIETIAQLQQMNQNLTSTIEILNSSLASCNGNLSSLNETYSSLL 128
                                       5678899999999999999999999999999999999999999999999999999999999998877776 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00034
                        TPR_MLP1_2   9 eikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesaka 85 
                                       +i++l++ +++++++++ l + l +    ++  ++ Y++ l   ++ ++e ++l++ +++lka +++l ++  ++++
  gi|385805088|ref|YP_005841486.1|  88 TIAQLQQMNQNLTSTIEILNSSLASCNGNLSSLNETYSSLLSSYSQLMNEYSSLNASYSSLKANYSQLLTKMSELNE 164
                                       45555666666666666666666666666666666666666666666666666666666666666666666655555 PP

                        TPR_MLP1_2  86 eleeseesweeqkee 100
                                       + + + +++++  ++
  gi|385805088|ref|YP_005841486.1| 165 TYSYAISELSSLNTS 179
                                       555444444333333 PP

>> DUF4472  Domain of unknown function (DUF4472)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.5      0.54   1.4e+02      48      93 ..      54      99 ..      44     104 .. 0.50
   2 ?   11.1   1.8    0.0019      0.51      21     104 ..      80     163 ..      66     173 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.54
                           DUF4472 48 elerekaaeeiqslrerlaeleeekkeleeeyvvlkknyqalekef 93
                                      +   e+a + i++l+++l   +++ ++l++ y+ +  ++q++++++
  gi|385805088|ref|YP_005841486.1| 54 QQSLENALRTISDLQQKLFYYNSSLSQLNQTYIETIAQLQQMNQNL 99
                                      3334444444444444444444444445444444444444444443 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0019
                           DUF4472  21 klreqheaekfelknkvlalenrvlelelerekaaeeiqslrerlaeleeekkeleeeyvvlkknyqalekefekek 97 
                                       +l + + +++ +l+ +  +l +++  l++  +  + + +sl+e +  l ++ ++l +ey++l+ +y +l++++ +  
  gi|385805088|ref|YP_005841486.1|  80 QLNQTYIETIAQLQQMNQNLTSTIEILNSSLASCNGNLSSLNETYSSLLSSYSQLMNEYSSLNASYSSLKANYSQLL 156
                                       56677777777888877788887777777777888888888888888888888888888888888888888888887 PP

                           DUF4472  98 kkqqels 104
                                       +k  el+
  gi|385805088|ref|YP_005841486.1| 157 TKMSELN 163
                                       7777765 PP

>> Lebercilin  Ciliary protein causing Leber congenital amaurosis disease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.6    0.0008      0.21     128     187 ..      52     111 ..      51     117 .. 0.95
   2 ?    0.9   0.1       1.2   3.1e+02      55      99 ..     124     168 ..     114     195 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0008
                        Lebercilin 128 eleakleekeekikeLerkleleeksfrrqlaaekkktkeaqeevkalqeeierlkqklk 187
                                       ++++ le++ ++i++L++kl   ++s ++  ++  + + ++q+ +++l+++ie l+++l+
  gi|385805088|ref|YP_005841486.1|  52 SVQQSLENALRTISDLQQKLFYYNSSLSQLNQTYIETIAQLQQMNQNLTSTIEILNSSLA 111
                                       6899****************************************************9986 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 1.2
                        Lebercilin  55 eaeLpqllarhneEvrvlrerlRksqekerelekklkekeaellr 99 
                                        ++L +  ++ ++E   l++ +  +++++++l  k+ e ++    
  gi|385805088|ref|YP_005841486.1| 124 YSSLLSSYSQLMNEYSSLNASYSSLKANYSQLLTKMSELNETYSY 168
                                       455555555556666666666666666666666666555554443 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.4     0.021       5.5      30      99 ..      52     122 ..      37     140 .. 0.72
   2 ?    9.6   0.2    0.0035      0.93       9      98 ..      87     177 ..      79     183 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.021
                             DHR10  30 vvekdlrsciklleeieaelakleeakkklkel.rdaleekeielrelerkeerlqrqlenaeeklerlre 99 
                                        v++ l+++++ + +++++l  ++++ ++l+++  ++++++++  + l++++e l+  l++ +  l+ l e
  gi|385805088|ref|YP_005841486.1|  52 SVQQSLENALRTISDLQQKLFYYNSSLSQLNQTyIETIAQLQQMNQNLTSTIEILNSSLASCNGNLSSLNE 122
                                       56777777777777777777777777777765525777777777777777777777777777777776666 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0035
                             DHR10   9 eelaelErkarelqakidalqvvekdlrscikllee.ieaelakleeakkklkelrdaleekeielrelerkeerlq 84 
                                       e++a+l++ +++l+ +i+ l+   + ++  +  l+e  ++ l ++ + + + ++l++ +++++++ ++l +k + l+
  gi|385805088|ref|YP_005841486.1|  87 ETIAQLQQMNQNLTSTIEILNSSLASCNGNLSSLNEtYSSLLSSYSQLMNEYSSLNASYSSLKANYSQLLTKMSELN 163
                                       78999***************999999998887777746778899999999999999999999999999999999999 PP

                             DHR10  85 rqlenaeeklerlr 98 
                                          + a  +l+ l 
  gi|385805088|ref|YP_005841486.1| 164 ETYSYAISELSSLN 177
                                       98888887777765 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.6     0.064        17      31      52 ..      87     108 ..      56     112 .. 0.81
   2 ?    5.1   0.1      0.07        19      16      55 ..     128     167 ..     122     172 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.064
                                       HHHHHHHHHHHHHHHHHCC-XX CS
                             DivIC  31 aelaklkaeneeLeaevkdLks 52 
                                       +++a+l++ n++L++ ++ L+s
  gi|385805088|ref|YP_005841486.1|  87 ETIAQLQQMNQNLTSTIEILNS 108
                                       5789999999999999998854 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.07
                                       XXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXX CS
                             DivIC  16 llaykqlkqeiaalqaelaklkaeneeLeaevkdLksded 55 
                                       l++y+ql +e+  l+a + +lka   +L  + ++L+ +++
  gi|385805088|ref|YP_005841486.1| 128 LSSYSQLMNEYSSLNASYSSLKANYSQLLTKMSELNETYS 167
                                       6789999999999999999999999999888888865555 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   1.5     0.023       6.2       5      83 ..      55     134 ..      41     136 .. 0.82
   2 ?   12.0   2.8    0.0007      0.19       6      81 ..      95     167 ..      89     198 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.023
                       TMF_TATA_bd   5 ssagpsvqlverlsseirrlEgElaslkeelerleaerdeareeivklm.keneelkelkkeleelekeleelqery 80 
                                       +s ++  ++++ l++++    + l++l++++ +  a+ +++++ + + +   n +l++ +++l++l++ +++l + y
  gi|385805088|ref|YP_005841486.1|  55 QSLENALRTISDLQQKLFYYNSSLSQLNQTYIETIAQLQQMNQNLTSTIeILNSSLASCNGNLSSLNETYSSLLSSY 131
                                       45567778899999999999999999999999999999999999998883467888888999999998888887777 PP

                       TMF_TATA_bd  81 etl 83 
                                       ++l
  gi|385805088|ref|YP_005841486.1| 132 SQL 134
                                       665 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.0007
                       TMF_TATA_bd   6 sagpsvqlverlsseirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqerye 81 
                                        +++ ++++e l+s++ +  g l+sl+e++++l ++ +++ +e  +l     + ++lk+++++l ++++el+e y+
  gi|385805088|ref|YP_005841486.1|  95 MNQNLTSTIEILNSSLASCNGNLSSLNETYSSLLSSYSQLMNEYSSLN---ASYSSLKANYSQLLTKMSELNETYS 167
                                       456667778888888888888888888888888888888888877765...5556667777777778888877776 PP

>> SHE3  SWI5-dependent HO expression protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3  14.4    0.0016      0.42      21     140 ..      63     175 ..      53     194 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0016
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              SHE3  21 qLtqqsqeLleklelaqkkeskflenlaslkhENdnLsslLkRKerrlkdlekelselkesveelklekkqlkkrle 97 
                                       ++   +q+L    ++  + ++ ++e++a+l++ N+nL+s ++  +  l   + +ls+l+e + +l  +  ql ++  
  gi|385805088|ref|YP_005841486.1|  63 TISDLQQKLFYYNSSLSQLNQTYIETIAQLQQMNQNLTSTIEILNSSLASCNGNLSSLNETYSSLLSSYSQLMNEY- 138
                                       5555667788888888889999999999999999999998888888888888888888888877777777665544. PP

                                       HCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              SHE3  98 nssaseteleeelerlkvqYdalvdsqkeYkehYqqeieeLke 140
                                             ++l++ ++ lk++Y  l+   +e  e Y+  i+eL+ 
  gi|385805088|ref|YP_005841486.1| 139 ------SSLNASYSSLKANYSQLLTKMSELNETYSYAISELSS 175
                                       ......4566677888888888888888888888876666653 PP

>> Muted  Organelle biogenesis, Muted-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.2       2.6   6.9e+02      69      87 ..      52      70 ..      35      91 .. 0.59
   2 ?   11.2   2.4    0.0013      0.36      39     124 ..      90     166 ..      75     189 .. 0.53

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 2.6
                             Muted 69 elnkkleaalekverllqk 87
                                      ++++ le+al ++++l+qk
  gi|385805088|ref|YP_005841486.1| 52 SVQQSLENALRTISDLQQK 70
                                      4555555555555555555 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0013
                             Muted  39 elLenikklvnelkeqllpkclesmkenLselnkkleaalekverllqkeleeekrkseqlqekeeerkaeweeflk 115
                                        +L++++++++++ e         ++++L + n +l  ++e+ + ll+   ++ +++ + l+++   +ka+ +++l+
  gi|385805088|ref|YP_005841486.1|  90 AQLQQMNQNLTSTIEI--------LNSSLASCNGNLSSLNETYSSLLSS-YSQLMNEYSSLNASYSSLKANYSQLLT 157
                                       3444444444444444........5555555555555555555555555.333334556666666666666666655 PP

                             Muted 116 elqekkeev 124
                                       +++e +e+ 
  gi|385805088|ref|YP_005841486.1| 158 KMSELNETY 166
                                       555554443 PP

>> Mod_r  Modifier of rudimentary (Mod(r)) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4  12.0     0.004       1.1      18      93 ..      82     161 ..      63     198 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.004
                             Mod_r  18 lealvktlpevkqlkeekeella.enesla..eknlsl.epeleelrselqekleelkelekefeekeqeldellqk 90 
                                        + +++t+ +++q+++++++ ++  n sla  + nls+ ++++  l s+ ++ ++e+ +l++++  +++++++ll k
  gi|385805088|ref|YP_005841486.1|  82 NQTYIETIAQLQQMNQNLTSTIEiLNSSLAscNGNLSSlNETYSSLLSSYSQLMNEYSSLNASYSSLKANYSQLLTK 158
                                       34566666777888777776543123333344666666666666666666666666666666666666666666655 PP

                             Mod_r  91 fsp 93 
                                       +s+
  gi|385805088|ref|YP_005841486.1| 159 MSE 161
                                       554 PP

>> DUF4744  Domain of unknown function (DUF4744)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   6.1    0.0026      0.69       3      54 ..     120     171 ..     118     180 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0026
                           DUF4744   3 qTesypsiteeyssqteaYpsqteayssqteayslaesepnkpsssFdlaid 54 
                                       + e+y+s+ ++ys+  ++Y+s  ++yss    ys   ++ ++   +++ ai 
  gi|385805088|ref|YP_005841486.1| 120 LNETYSSLLSSYSQLMNEYSSLNASYSSLKANYSQLLTKMSELNETYSYAIS 171
                                       6699********************************************9996 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.8    0.0023       0.6      14     112 ..      91     186 ..      83     189 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0023
                    CENP-F_leu_zip  14 eserkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelq 90 
                                       + ++ + +L   +e L++ l   + n++++     +     ++l +e   l+++ + l+++ ++l     eL++   
  gi|385805088|ref|YP_005841486.1|  91 QLQQMNQNLTSTIEILNSSLASCNGNLSSLNETYSSLLSSYSQLMNEYSSLNASYSSLKANYSQLLTKMSELNE--- 164
                                       45666777888888888888888888888877777777777777777777777777777777777777777754... PP

                    CENP-F_leu_zip  91 kkqervseLeslnsslenllee 112
                                       +    +seL sln s  nll++
  gi|385805088|ref|YP_005841486.1| 165 TYSYAISELSSLNTSYANLLSQ 186
                                       4456799999999999999986 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   4.7   0.00097      0.26     630     710 ..      30     119 ..      15     140 .. 0.68
   2 ?    7.7   8.6    0.0028      0.76     231     352 ..      54     168 ..      50     197 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00097
                          Prominin 630 aekleelanelsngk......knlkqslkneaqdlraiqqe...lvlplessvkklkksvkkldeensdlqesikkl 697
                                       a+ l++l ++ ++ +      ++++qsl+n+ ++++++qq+   ++  l+++ ++  +++ +l++ n++l+++i++l
  gi|385805088|ref|YP_005841486.1|  30 ASYLYQLTSSSQTPQntsggsSSVQQSLENALRTISDLQQKlfyYNSSLSQLNQTYIETIAQLQQMNQNLTSTIEIL 106
                                       55555555554444445666688888888888888888887222345577777777888888888888888888888 PP

                          Prominin 698 laaveraenflkk 710
                                        +++ + +  l  
  gi|385805088|ref|YP_005841486.1| 107 NSSLASCNGNLSS 119
                                       8888777666544 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0028
                          Prominin 231 esnvlpaLaelerllenlkeakeqLeqvnklekeLrksgsqLrdglrgvkrdlnqalsnlCqseeCskilssleiek 307
                                       ++++ +aL ++  l ++l   + +L+q+n++  e   + +q++++l++  + ln++l++ C+  + s+++++++   
  gi|385805088|ref|YP_005841486.1|  54 QQSLENALRTISDLQQKLFYYNSSLSQLNQTYIETIAQLQQMNQNLTSTIEILNSSLAS-CN-GNLSSLNETYSSLL 128
                                       4556678**************************************************99.88.55555555555533 PP

                          Prominin 308 ldtskcldqlpnvdevlealeevletnlssivkeglarlneipek 352
                                         +    +ql n  + l+a  + l++n+s++   ++++lne  + 
  gi|385805088|ref|YP_005841486.1| 129 SSY----SQLMNEYSSLNASYSSLKANYSQLL-TKMSELNETYSY 168
                                       333....3444444444444444444444444.233334433333 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   3.0      0.24        65      58     123 ..      39     104 ..      31     117 .. 0.63
   2 ?   10.7   1.2    0.0015      0.41      35     119 ..     100     181 ..      95     193 .. 0.54

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.24
                              ADIP  58 lnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlkn 123
                                       +++t ++ +  +++ q++ e   +  ++l+++l  +++ + ql++++ +++++l++  + l+ +  
  gi|385805088|ref|YP_005841486.1|  39 SSQTPQNTSGGSSSVQQSLENALRTISDLQQKLFYYNSSLSQLNQTYIETIAQLQQMNQNLTSTIE 104
                                       555555555555666666666666677777777777777777777777777777776666654444 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0015
                              ADIP  35 aaiinviysLlqardrdleqreslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqkl 111
                                        ++i +++s l++   +l    slnet ++l +++++l++++++l +++++l+   +++  k  +l+ ++  +++ l
  gi|385805088|ref|YP_005841486.1| 100 TSTIEILNSSLASCNGNL---SSLNETYSSLLSSYSQLMNEYSSLNASYSSLKANYSQLLTKMSELNETYSYAISEL 173
                                       555555555555555444...45666666666666666666666666666666666666666666665555555555 PP

                              ADIP 112 knekeelq 119
                                        ++  + +
  gi|385805088|ref|YP_005841486.1| 174 SSLNTSYA 181
                                       55444444 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   5.3    0.0021      0.57     175     287 ..      54     163 ..      29     198 .. 0.37

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0021
                      Exonuc_VII_L 175 asrlkspeellerkrqrldeleerleralkkqlkkkrerleelkerlkekleekkerlkklkerlelleekkerlee 251
                                       +++l+++ + +++ +q+l  ++++l++ l++++ +  ++l++++++l++++e  +++l++ + +l++l+e+ ++l  
  gi|385805088|ref|YP_005841486.1|  54 QQSLENALRTISDLQQKLFYYNSSLSQ-LNQTYIETIAQLQQMNQNLTSTIEILNSSLASCNGNLSSLNETYSSL-- 127
                                       333333333333333333333333333.33332233333333333332222222222222222222111111111.. PP

                      Exonuc_VII_L 252 leeklealsplkvLkrGyaivrkedgkvvtsakdlk 287
                                       l++  ++++  + L+  y+ ++ +  +++t++++l+
  gi|385805088|ref|YP_005841486.1| 128 LSSYSQLMNEYSSLNASYSSLKANYSQLLTKMSELN 163
                                       111111122222222222222222222222222222 PP

>> Gp-FAR-1  Nematode fatty acid retinoid binding protein (Gp-FAR-1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1       1.5   4.1e+02      33      64 ..      79     110 ..      51     129 .. 0.67
   2 ?    9.6   0.3    0.0042       1.1      29      83 ..     131     185 ..     111     206 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 1.5
                          Gp-FAR-1  33 ykgyknedellaalKkkspaLyekaeklqakl 64 
                                       ++ ++++ e +a l + + +L +++e l++ l
  gi|385805088|ref|YP_005841486.1|  79 SQLNQTYIETIAQLQQMNQNLTSTIEILNSSL 110
                                       34477777778888888777777777776665 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0042
                          Gp-FAR-1  29 vvknykgyknedellaalKkkspaLyekaeklqaklkekvdkLspeakeFvkkli 83 
                                         + +++y + ++  + lK+ + +L +k+++l++++   + +Ls     +++ l+
  gi|385805088|ref|YP_005841486.1| 131 YSQLMNEYSSLNASYSSLKANYSQLLTKMSELNETYSYAISELSSLNTSYANLLS 185
                                       444467799999999****************************999888888665 PP

>> Rab5-bind  Rabaptin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   2.3    0.0028      0.76      50     128 ..      50     135 ..      34     140 .. 0.78
   2 ?    2.4   0.2      0.31        82     207     253 ..     143     189 ..     132     198 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0028
                         Rab5-bind  50 edslkelseetskqvselakrvkksEllleeLqqafskak.......rniqeqlavlvksreqvedelvrLqkdyes 119
                                        +s++++ e++++ +s+l+++    +  l++L+q++ + +       +n++  +++l +s+   + +l+ L++ y s
  gi|385805088|ref|YP_005841486.1|  50 SSSVQQSLENALRTISDLQQKLFYYNSSLSQLNQTYIETIaqlqqmnQNLTSTIEILNSSLASCNGNLSSLNETYSS 126
                                       57899***************9999999999999998665511101115556677888899999999*********** PP

                         Rab5-bind 120 LlGkhrkhv 128
                                       Ll + ++ +
  gi|385805088|ref|YP_005841486.1| 127 LLSSYSQLM 135
                                       999888765 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.31
                         Rab5-bind 207 asisslkveleeikvekeslekslaektrqldklqtikselEeqlke 253
                                       as sslk++ ++++    +l+++ + ++++l +l+t   +l +ql  
  gi|385805088|ref|YP_005841486.1| 143 ASYSSLKANYSQLLTKMSELNETYSYAISELSSLNTSYANLLSQLST 189
                                       56667777777777777777777777777777777777776666654 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.9     0.016       4.3      26      73 ..      76     123 ..      14     142 .. 0.80
   2 ?    0.2   0.0       3.4   9.1e+02      34      86 ..     137     189 ..     123     192 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.016
                            DUF948  26 ktldeaaatieelekqvdpilkevedllakvnelledvneklekvdpl 73 
                                       + l+++++t  e+  q++++ ++++ +++  n  l+ +n+ l ++++ 
  gi|385805088|ref|YP_005841486.1|  76 SSLSQLNQTYIETIAQLQQMNQNLTSTIEILNSSLASCNGNLSSLNET 123
                                       455666666666667777777777777777777777777777777665 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 3.4
                            DUF948  34 tieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvse 86 
                                          +l+    ++  +  +ll+k+ el e  +  + ++ +l ++ a+l  ++s+
  gi|385805088|ref|YP_005841486.1| 137 EYSSLNASYSSLKANYSQLLTKMSELNETYSYAISELSSLNTSYANLLSQLST 189
                                       45566677777778888888888887777777777777766666666655555 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1       1.3   3.4e+02      57      78 ..      50      71 ..      35      77 .. 0.81
   2 ?    9.7   2.5    0.0038         1       9      79 ..      55     125 ..      50     131 .. 0.87
   3 ?    0.1   0.1       3.7     1e+03      32      76 ..     134     178 ..     122     184 .. 0.66

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 1.3
                              KxDL 57 lkevkkdLesifkkirslkakl 78
                                      +++v++ Le+  ++i+ l++kl
  gi|385805088|ref|YP_005841486.1| 50 SSSVQQSLENALRTISDLQQKL 71
                                      5789999999999999999987 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0038
                              KxDL   9 edldeilalQaqtsgrlnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLesifkkirslkakla 79 
                                       + l+++l++ +++ ++l   n  L++ln+   e  a+l++  ++ t ++  +++ L s++ +++sl+++++
  gi|385805088|ref|YP_005841486.1|  55 QSLENALRTISDLQQKLFYYNSSLSQLNQTYIETIAQLQQMNQNLTSTIEILNSSLASCNGNLSSLNETYS 125
                                       56777777777777888888999*******************************************98765 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 3.7
                              KxDL  32 LlelnalsqerlaklrarfkqgtkllkevkkdLesifkkirslka 76 
                                       L++    +++ +++l+a++ q  + ++e+++   +  + ++sl++
  gi|385805088|ref|YP_005841486.1| 134 LMNEYSSLNASYSSLKANYSQLLTKMSELNETYSYAISELSSLNT 178
                                       555555666777777777777777777777766666666666665 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   4.9     0.043        12      30      94 ..      38     102 ..      26     111 .. 0.85
   2 ?    8.0   0.5    0.0058       1.5      13      94 ..     112     193 ..     104     196 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.043
                           DUF3450  30 aaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieei 94 
                                       ++++  q+    ++  +q+l++ +r++++ +++l  yn+ l++l ++  ++ia+l++  ++++ +
  gi|385805088|ref|YP_005841486.1|  38 SSSQTPQNTSGGSSSVQQSLENALRTISDLQQKLFYYNSSLSQLNQTYIETIAQLQQMNQNLTST 102
                                       55566666666777889****************************************99998876 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0058
                           DUF3450  13 alaatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqie 89 
                                       +++ +l++++++ ++  ++ +q  +++++l+   ++l+a+y +l ++ ++l+   ++  + ++s++++ a+l  q++
  gi|385805088|ref|YP_005841486.1| 112 SCNGNLSSLNETYSSLLSSYSQLMNEYSSLNASYSSLKANYSQLLTKMSELNETYSYAISELSSLNTSYANLLSQLS 188
                                       44667888888888888888888888888888888888888888888888888888888888888888888888888 PP

                           DUF3450  90 eieei 94 
                                        i+++
  gi|385805088|ref|YP_005841486.1| 189 TISQL 193
                                       88775 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.9      0.12        31       8      48 ..      76     117 ..      50     133 .. 0.56
   2 ?    7.4   1.2     0.026       6.8       6      62 ..      99     155 ..      95     206 .. 0.56

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.12
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHH CS
                              YabA   8 dkleeleeqleelleeleelkeelaelle.enaeLelenekl 48 
                                       ++l++l+++  e+ ++l++++++l++++e  n++L   n +l
  gi|385805088|ref|YP_005841486.1|  76 SSLSQLNQTYIETIAQLQQMNQNLTSTIEiLNSSLASCNGNL 117
                                       345555555555555555555555555442344454444444 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.026
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXX CS
                              YabA   6 lfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekek 62 
                                       l++++e l+++l++++ +l++l+e+ ++ll   ++L  e ++l    ++ +++ ++ 
  gi|385805088|ref|YP_005841486.1|  99 LTSTIEILNSSLASCNGNLSSLNETYSSLLSSYSQLMNEYSSLNASYSSLKANYSQL 155
                                       555555566666666666666666665555555555555555555542222222222 PP

>> HAUS-augmin3  HAUS augmin-like complex subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   5.2     0.035       9.4      62     157 ..      39     134 ..      30     136 .. 0.64
   2 ?   10.4   7.3    0.0013      0.34      53     160 ..      92     195 ..      87     212 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.035
                      HAUS-augmin3  62 kqedvellevileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqelrkleeeekeakkklkeaqeelra 138
                                       ++++++ ++   +  ++sle+  + +++Lq+     ++ l++L+ +  +   +l++++++ +++ + l+ + ++ + 
  gi|385805088|ref|YP_005841486.1|  39 SSQTPQNTSGGSSSVQQSLENALRTISDLQQKLFYYNSSLSQLNQTYIETIAQLQQMNQNLTSTIEILNSSLASCNG 115
                                       44677777777777777777777777777777777777777776666666666666666666666666666666666 PP

                      HAUS-augmin3 139 enaetnavLqqlteeakql 157
                                       + + +n+ +++l+++ +ql
  gi|385805088|ref|YP_005841486.1| 116 NLSSLNETYSSLLSSYSQL 134
                                       6666666666666665555 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0013
                      HAUS-augmin3  53 LktiepsdlkqedvellevileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqelrkleeeekeakkkl 129
                                       L++++  ++ +++ e l+++l+  + +l  L++  + L +    + ++++ L++  +sl+ + ++l ++ +e ++  
  gi|385805088|ref|YP_005841486.1|  92 LQQMN--QNLTSTIEILNSSLASCNGNLSSLNETYSSLLSSYSQLMNEYSSLNASYSSLKANYSQLLTKMSELNETY 166
                                       45555..22235789999999999999************************************************** PP

                      HAUS-augmin3 130 keaqeelraenaetnavLqqlteeakqlaey 160
                                         a +el++ n    ++L+ql+    ++ ++
  gi|385805088|ref|YP_005841486.1| 167 SYAISELSSLNTSYANLLSQLST--ISQLSF 195
                                       ********************998..334444 PP

>> HR1  Hr1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   1.5     0.023       6.1      28      63 ..      47      83 ..      28      88 .. 0.77
   2 ?    4.8   0.4      0.11        30      37      63 ..      89     115 ..      87     119 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.023
                               HR1 28 sk.ktqnkkvrqeaeselsesnskielLreqLeelqa 63
                                      s+ ++  +++++ a  ++s+ ++k+ + +++L++l++
  gi|385805088|ref|YP_005841486.1| 47 SGgSSSVQQSLENALRTISDLQQKLFYYNSSLSQLNQ 83
                                      4446666779999999999999999999999999998 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.11
                               HR1  37 rqeaeselsesnskielLreqLeelqa 63 
                                       +++ +++ +   s ie+L+++L+ +++
  gi|385805088|ref|YP_005841486.1|  89 IAQLQQMNQNLTSTIEILNSSLASCNG 115
                                       57899******************9997 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   4.1     0.013       3.5       8     113 ..      66     178 ..      59     183 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.013
                              CdvA   8 eLvsegdipkstyeeikekleealkklkekakel...keklkkrlkeledqikslekalanlkisyas..GEid..E 77 
                                       +L ++   + s  +++++ + e++++l++  ++l   +e l+++l++++ +++sl++++ +l  sy +  +E +   
  gi|385805088|ref|YP_005841486.1|  66 DLQQKLFYYNSSLSQLNQTYIETIAQLQQMNQNLtstIEILNSSLASCNGNLSSLNETYSSLLSSYSQlmNEYSslN 142
                                       555555566666777777777777777666666622268899********************999965336665334 PP

                              CdvA  78 eaYksaieairellesaleekeeikklleklsklel 113
                                        +Y s +  +++ll++++e  e  + ++++ls+l++
  gi|385805088|ref|YP_005841486.1| 143 ASYSSLKANYSQLLTKMSELNETYSYAISELSSLNT 178
                                       678888888888888887777777777777777765 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.3     0.021       5.6      36      62 ..      76     102 ..      63     104 .. 0.86
   2 ?    1.3   0.2       1.4   3.8e+02      40      56 ..     122     138 ..     100     151 .. 0.54
   3 ?    5.5   0.7     0.069        18      25      63 ..     149     187 ..     147     188 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.021
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  36 kaLekeNksLkseleelkkevekLksk 62 
                                       + L++ N+++++++ +l+ ++++L s 
  gi|385805088|ref|YP_005841486.1|  76 SSLSQLNQTYIETIAQLQQMNQNLTST 102
                                       5799*******************9876 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 1.4
                                       HHHHHHHHHHHHHHHHH CS
                            bZIP_1  40 keNksLkseleelkkev 56 
                                       +  +sL s  ++l++e+
  gi|385805088|ref|YP_005841486.1| 122 ETYSSLLSSYSQLMNEY 138
                                       22223333333333333 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.069
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  25 qaeieeLerrvkaLekeNksLkseleelkkevekLkskv 63 
                                       +a  ++L +++++L++  +  +sel++l+  +++L+s++
  gi|385805088|ref|YP_005841486.1| 149 KANYSQLLTKMSELNETYSYAISELSSLNTSYANLLSQL 187
                                       567789999999**9999999**************9986 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1      0.75     2e+02      40      70 ..      55      85 ..      51      88 .. 0.82
   2 ?    8.1   0.7    0.0095       2.6      24      71 ..      78     125 ..      76     127 .. 0.87
   3 ?    3.4   0.5      0.28        74      16      69 ..     133     186 ..     131     191 .. 0.66

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.75
                        TMF_DNA_bd 40 kknkelekeikelkkkleklekeleeleerl 70
                                      + ++++  +i++l++kl  ++++l++l++ +
  gi|385805088|ref|YP_005841486.1| 55 QSLENALRTISDLQQKLFYYNSSLSQLNQTY 85
                                      6677777899999999999999999999876 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0095
                        TMF_DNA_bd  24 LskkelklnntikkLrkknkelekeikelkkkleklekeleeleerlk 71 
                                       Ls  ++   +ti +L++ n++l+++i+ l++ l++ + +l++l+e ++
  gi|385805088|ref|YP_005841486.1|  78 LSQLNQTYIETIAQLQQMNQNLTSTIEILNSSLASCNGNLSSLNETYS 125
                                       5566666679********************************998775 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.28
                        TMF_DNA_bd  16 qLmeEGekLskkelklnntikkLrkknkelekeikelkkkleklekeleeleer 69 
                                       qLm E   L ++   l++  ++L  k++el+++ +   ++l++l+ + ++l + 
  gi|385805088|ref|YP_005841486.1| 133 QLMNEYSSLNASYSSLKANYSQLLTKMSELNETYSYAISELSSLNTSYANLLSQ 186
                                       677777777777777777777777777777776666667777777766666555 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   3.8   0.00025     0.066     125     228 ..      31     137 ..       6     142 .. 0.79
   2 ?   -0.0   0.2       1.7   4.4e+02     189     228 ..     147     186 ..     138     188 .. 0.85
   3 ?   -2.1   0.0         7   1.9e+03     204     234 ..     278     308 ..     260     308 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00025
                              CorA 125 ellekleeeldeledel.....edstkkeilrelaqlrrrlvklrralapnrevlkrllakaddkllddedkeylrd 196
                                        +l +l +  +  +++       +++ ++ lr++++l+++l ++ ++l+++ +++ + +a     ++++     ++ 
  gi|385805088|ref|YP_005841486.1|  31 SYLYQLTSSSQTPQNTSggsssVQQSLENALRTISDLQQKLFYYNSSLSQLNQTYIETIA--QLQQMNQNLTSTIEI 105
                                       555555555555555555555456666789********************9999977777..899999999999999 PP

                              CorA 197 lldelerllemlealrerleslqdtyssllse 228
                                       l + l++    l++l e  +sl ++ys+l++e
  gi|385805088|ref|YP_005841486.1| 106 LNSSLASCNGNLSSLNETYSSLLSSYSQLMNE 137
                                       99999999999999999999999999999987 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.7
                              CorA 189 edkeylrdlldelerllemlealrerleslqdtyssllse 228
                                         k ++++ll +++ l e+ +   + l+sl+ +y++lls+
  gi|385805088|ref|YP_005841486.1| 147 SLKANYSQLLTKMSELNETYSYAISELSSLNTSYANLLSQ 186
                                       5667799999999999999999999999999999999987 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 7
                              CorA 204 llemlealrerleslqdtyssllserlNrvm 234
                                       l +     ++++  l+ +y+s ls+ lN+ m
  gi|385805088|ref|YP_005841486.1| 278 LNNGYGDAKDQALLLSTLYASYLSNYLNTSM 308
                                       5555556678899999999999999999877 PP

>> CLZ  C-terminal leucine zipper domain of cyclic nucleotide-gated channels
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.8     0.036       9.5      21      69 ..      59     107 ..      53     109 .. 0.86
   2 ?    1.0   0.1       2.1   5.5e+02      33      58 ..     117     142 ..     111     160 .. 0.72
   3 ?    2.5   0.2      0.72   1.9e+02      38      56 ..     171     189 ..     149     194 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.036
                               CLZ  21 kagaeqkeleekverLessLeaLqtrlarLlaeyessqrkLkqRitkLE 69 
                                       +a  +  +l++k+   +ssL +L++ +  ++a+++++++ L++ i+ L 
  gi|385805088|ref|YP_005841486.1|  59 NALRTISDLQQKLFYYNSSLSQLNQTYIETIAQLQQMNQNLTSTIEILN 107
                                       5556667899999999***************************999886 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 2.1
                               CLZ  33 verLessLeaLqtrlarLlaeyessq 58 
                                       +++L+++  +L   + +L++ey+s +
  gi|385805088|ref|YP_005841486.1| 117 LSSLNETYSSLLSSYSQLMNEYSSLN 142
                                       56677777777777888888887755 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.72
                               CLZ  38 ssLeaLqtrlarLlaeyes 56 
                                       s+L +L+t +a Ll+++++
  gi|385805088|ref|YP_005841486.1| 171 SELSSLNTSYANLLSQLST 189
                                       5677777777777777665 PP

>> HALZ  Homeobox associated leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       9.6   2.6e+03      24      40 ..      92     108 ..      89     111 .. 0.76
   2 ?    3.0   0.1      0.46   1.2e+02      11      32 ..     121     142 ..     118     143 .. 0.66
   3 ?   12.3   1.4   0.00056      0.15       2      26 ..     133     157 ..     130     165 .. 0.62

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 9.6
                              HALZ  24 LkkenekLkaelqeLke 40 
                                       L++ n++L + ++ L++
  gi|385805088|ref|YP_005841486.1|  92 LQQMNQNLTSTIEILNS 108
                                       78889999988877765 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.46
                              HALZ  11 KasYdaLksdydsLkkenekLk 32 
                                          Y +L s+y +L +e  +L 
  gi|385805088|ref|YP_005841486.1| 121 NETYSSLLSSYSQLMNEYSSLN 142
                                       5567777777777777766664 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.00056
                              HALZ   2 QLErDYdvLKasYdaLksdydsLkk 26 
                                       QL  +Y +L asY +Lk++y +L+ 
  gi|385805088|ref|YP_005841486.1| 133 QLMNEYSSLNASYSSLKANYSQLLT 157
                                       4445677777777777777777664 PP

>> DASH_Duo1  DASH complex subunit Duo1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.2       1.7   4.6e+02       2      33 ..      57      89 ..      51      97 .. 0.52
   2 ?   10.4   1.4    0.0016      0.42      10      52 ..      97     136 ..      87     144 .. 0.64
   3 ?    1.9   1.3      0.74     2e+02      20      60 ..     153     193 ..     134     196 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1.7
                         DASH_Duo1  2 LekEleqLrkinevienviesLkkak.snierv 33
                                      Le+ l+++ ++ + +  +++sL + + ++ie++
  gi|385805088|ref|YP_005841486.1| 57 LENALRTISDLQQKLFYYNSSLSQLNqTYIETI 89
                                      444444455555555555555555544444444 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0016
                         DASH_Duo1  10 rkinevienviesLkkaksniervketvestntLLdkWirIls 52 
                                       +++ ++ie +++sL ++++n+++++et +   +LL +++++++
  gi|385805088|ref|YP_005841486.1|  97 QNLTSTIEILNSSLASCNGNLSSLNETYS---SLLSSYSQLMN 136
                                       34556889999999999999999998864...34444444443 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.74
                         DASH_Duo1  20 iesLkkaksniervketvestntLLdkWirIlsqtehtqrl 60 
                                        + L k+++ +e+ + ++++ ++L  ++ ++lsq + +++l
  gi|385805088|ref|YP_005841486.1| 153 SQLLTKMSELNETYSYAISELSSLNTSYANLLSQLSTISQL 193
                                       455667777788888899999*************9888876 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.8      0.23        61     106     154 ..      52     101 ..      34     105 .. 0.76
   2 ?    2.6   5.3      0.32        86      99     122 ..      87     110 ..      53     192 .. 0.42

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.23
                           DUF4795 106 eqeealkkaldtLqeelkekld..rlelepLkeqleerlkelqkelqeame 154
                                       +++++l+ al t++ +l++kl     +l++L +   e++ +lq++ q+ ++
  gi|385805088|ref|YP_005841486.1|  52 SVQQSLENALRTIS-DLQQKLFyyNSSLSQLNQTYIETIAQLQQMNQNLTS 101
                                       56777888888888.888888877888888888877888888877776555 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.32
                           DUF4795  99 ellekleeqeealkkaldtLqeel 122
                                       e + +l++  ++l++ ++ L+++l
  gi|385805088|ref|YP_005841486.1|  87 ETIAQLQQMNQNLTSTIEILNSSL 110
                                       333333333333333333322211 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   3.1     0.038        10      57     126 ..      32     100 ..      27     104 .. 0.79
   2 ?    6.9   5.5     0.024       6.5      26     123 ..      92     192 ..      90     197 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.038
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  57 lvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvlesneqkiqkLeqdid 126
                                       +  ++++s +  q+++ ++++v +++++ l+  i++l++++    s++ +L +++ +   ++q+++q+ +
  gi|385805088|ref|YP_005841486.1|  32 YLYQLTSSSQTPQNTSGGSSSVQQSLENALR-TISDLQQKLFYYNSSLSQLNQTYIETIAQLQQMNQNLT 100
                                       5566677777777777777888888888888.99999999999999999999999999999999888765 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.024
                                       CCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHCCCHHHHHHH CS
                         Fib_alpha  26 llkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdn....dnvikksskeleeeilrlketid 98 
                                       l++++++++ ++e l+++l++ + + ++ +e+ +++ +s+ +  ++++      +++  ++s+ l  ++++l+et +
  gi|385805088|ref|YP_005841486.1|  92 LQQMNQNLTSTIEILNSSLASCNGNLSSLNETYSSLLSSYSQLMNEYSSLnasySSLKANYSQLLT-KMSELNETYS 167
                                       88999****************999999999998888888887777776651222333344444454.8888888888 PP

                                       CCHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  99 aqesnirvLqnvlesneqkiqkLeq 123
                                         +s++  L + + ++ ++++ + q
  gi|385805088|ref|YP_005841486.1| 168 YAISELSSLNTSYANLLSQLSTISQ 192
                                       8889999998888888887776665 PP

>> Cortex-I_coil  Cortexillin I, coiled coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.4       1.6   4.2e+02      20      71 ..      52     103 ..      39     114 .. 0.69
   2 ?    8.6   0.7    0.0076         2       5      67 ..     125     187 ..     121     197 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 1.6
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Cortex-I_coil  20 glenslesekvsreelikqkdelesllasleseaaerekrlreleakldeal 71 
                                       ++++sle    +  +l ++    +s+l+ l++   e   +l++++  l  ++
  gi|385805088|ref|YP_005841486.1|  52 SVQQSLENALRTISDLQQKLFYYNSSLSQLNQTYIETIAQLQQMNQNLTSTI 103
                                       6677777776666677666667777777777777666666666666665555 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0076
                                       XXXXXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Cortex-I_coil   5 erleasknelanklaglenslesekvsreelikqkdelesllasleseaaerekrlreleakl 67 
                                         l +s ++l n  ++l+ s  s k    +l+ +  el+++ +   se    +   ++l ++l
  gi|385805088|ref|YP_005841486.1| 125 SSLLSSYSQLMNEYSSLNASYSSLKANYSQLLTKMSELNETYSYAISELSSLNTSYANLLSQL 187
                                       578899**********************************98887777777777777776666 PP

>> AATF-Che1  Apoptosis antagonizing transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1  11.7       2.2     6e+02      48      87 ..      43     125 ..      29     206 .. 0.67

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 2.2
                         AATF-Che1  48 seefeealeeaekalkklleslleLreelleqne.ikkla..................................... 86 
                                        ++++  +++++++l++ l+++ +L+++l+  n+ +++l+                                     
  gi|385805088|ref|YP_005841486.1|  43 PQNTSGGSSSVQQSLENALRTISDLQQKLFYYNSsLSQLNqtyietiaqlqqmnqnltstieilnsslascngnlss 119
                                       445666678999999**************999998888887787777777776666666666665444333333322 PP

                         AATF-Che1  87 .....e 87 
                                            +
  gi|385805088|ref|YP_005841486.1| 120 lnetyS 125
                                       222220 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1809  (0.100898); expected 358.6 (0.02)
Passed bias filter:                      947  (0.0528195); expected 358.6 (0.02)
Passed Vit filter:                       182  (0.0101512); expected 17.9 (0.001)
Passed Fwd filter:                        75  (0.00418317); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              67  [number of targets reported over threshold]
# CPU time: 1.11u 0.37s 00:00:01.48 Elapsed: 00:00:00.50
# Mc/sec: 2472.73
//
Query:       gi|385805089|ref|YP_005841487.1|  [L=329]
Description: hypothetical protein FFONT_0039 [Fervidicoccus fontis Kam940]
Scores for complete 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-81  274.4   0.0    1.4e-81  274.2   0.0    1.0  1  DUF4392   Domain of unknown function (DUF4392)


Domain annotation for each model (and alignments):
>> DUF4392  Domain of unknown function (DUF4392)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  274.2   0.0   7.7e-86   1.4e-81       1     294 [.      11     324 ..      11     325 .. 0.98

  Alignments for each domain:
  == domain 1  score: 274.2 bits;  conditional E-value: 7.7e-86
                           DUF4392   1 Leeliardpggrgikkllkkgellkaaeslshak...........ksvlItTGFpvhpahsppeEtDGplGAialar 66 
                                       L++li++d++grg+ k l++++++ka+e+l  ++           + vlI+TGF ++p +   +EtDGplGA+++ r
  gi|385805089|ref|YP_005841487.1|  11 LDQLINSDSNGRGVAKKLYPYAFEKAGEPLVYKAarelvensdkgSPVLIMTGFRTPPLY--VQETDGPLGAASISR 85 
                                       89*****************************9999************************9..9************** PP

                           DUF4392  67 aL.qalgkkvvivtd..elnekiveaaveq.gvlktevpllelqdrsaeaaivfltkdgdkkeaeaeelleklkpdh 139
                                       a+   l++k++i+t+  e + +iv+aave  g+++++++ l   d++ +a++v +t++++ +e++a++l+++++p +
  gi|385805089|ref|YP_005841487.1|  86 AFsICLNAKPIILTEqdERSLRIVRAAVEGaGLKISPLEDLLRGDQDLSASVVGFTHSEEYAEEDAKRLIDEVNPRA 162
                                       **************988999**********9*999998888888999****************************** PP

                           DUF4392 140 liaiErpGraadGnyynmrgeniselvaplddlfeaakeigiptigiGDgGNElGmGkvkeavkkhvpngek..... 211
                                       +ia+ ++Gr+ +G y++m g n+s+++a++++++++a+++gi tig GDgGNE+GmG++++av+khvp+g+      
  gi|385805089|ref|YP_005841487.1| 163 VIAVKKAGRNFKGVYHSMSGLNVSKYHAKVEYIVDEARKKGILTIGTGDGGNEVGMGAIEDAVRKHVPYGDVcrcpc 239
                                       ***************************************************************************** PP

                           DUF4392 212 ...iacavaadflivagvSNWggyalaaalallsskevsllpsvekeeevlealveagvvdGvtgeremsVDglele 285
                                          ia++ ++d+li++++SNWggyal  +++ + +k+ + ++++e+ee + + ++++g+vdG++g+++ s Dgl++e
  gi|385805089|ref|YP_005841487.1| 240 rggIASSSKVDVLITSSISNWGGYALSGMISKILEKP-NGIHDPEAEELMFSLVAKEGAVDGIKGKAGKSADGLGVE 315
                                       ************************************9.*************************************** PP

                           DUF4392 286 ehaeilkeL 294
                                        h+++l  +
  gi|385805089|ref|YP_005841487.1| 316 AHKSVLMLI 324
                                       **9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 2126.57
//
Query:       gi|385805090|ref|YP_005841488.1|  [L=220]
Description: ParB-like nuclease [Fervidicoccus fontis Kam940]
Scores for complete 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   0.4    4.7e-10   39.6   0.4    1.7  1  ParBc     ParB-like nuclease domain
  ------ inclusion threshold ------
      0.038   14.2   0.1      0.081   13.1   0.1    1.6  1  PLDc      Phospholipase D Active site motif
      0.052   13.6   0.1       0.11   12.6   0.0    1.5  1  ParBc_2   Putative ParB-like nuclease


Domain annotation for each model (and alignments):
>> ParBc  ParB-like nuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.4   7.8e-14   4.7e-10      12      77 ..      16      80 ..       6      86 .. 0.86

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 7.8e-14
                             ParBc 12 plqprkd.spekieelvasIkkkGll.qPiivrktrqgryeiiaGerRlrAakrlglkevpvivleid 77
                                      +  p  d ++ +++ l as+++k++l  Piiv++ +   + +i+G++RlrA++  g+k vpvi+ +  
  gi|385805090|ref|YP_005841488.1| 16 EIIPAEDiEEPRLKYLLASLREKKVLhRPIIVEHRK---MLVIDGHHRLRALEASGAKLVPVILADYR 80
                                      44466667899***************99*******9...************************98876 PP

>> PLDc  Phospholipase D Active site motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   1.4e-05     0.081       5      26 ..      48      99 ..      45     101 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.4e-05
                                      E---EEEETTT..............................EEEEE---SSH CS
                              PLDc  5 hHqKivivDdr..............................vafvGgaNLcd 26
                                       H+K++++D++                              ++++G+ ++++
  gi|385805090|ref|YP_005841488.1| 48 EHRKMLVIDGHhrlraleasgaklvpviladyrsdvrsvgrWMYIGSWSIDR 99
                                      5*********************************************999887 PP

>> ParBc_2  Putative ParB-like nuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.8e-05      0.11      45      79 ..      43      72 ..      18      95 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.8e-05
                                      EEEEE-STT-EEE-S-HHHHHHHHHTT-....-EE CS
                           ParBc_2 45 vpvVigpdgelYliDhHHllrallesgvggaekkv 79
                                       p+++ ++ ++ +iD+HH lral  sg+    k v
  gi|385805090|ref|YP_005841488.1| 43 RPIIV-EHRKMLVIDGHHRLRALEASGA----KLV 72
                                      57777.667999***********99776....323 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1576.68
//
Query:       gi|385805091|ref|YP_005841489.1|  [L=207]
Description: n-type ATP pyrophosphatase superfamily [Fervidicoccus fontis Kam940]
Scores for complete 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   80.2   0.0    2.7e-22   79.4   0.0    1.4  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 !   79.4   0.0   1.5e-26   2.7e-22       4     205 ..       3     197 ..       1     206 [. 0.85

  Alignments for each domain:
  == domain 1  score: 79.4 bits;  conditional E-value: 1.5e-26
                   Diphthami_syn_2   4 avlysGGkDsilaLykalkeseve.sLvsvisenkesymfhvvnvhlvellaesvGiplikletaGeeekevedLkg 79 
                                       +++ sGGkDs +a y+    +++  +Lv  ++        h +n+     +    G p ++ +    + ke e+   
  gi|385805091|ref|YP_005841489.1|   3 VAFLSGGKDSYYAAYRSSSGFDIGlFLVYDFPRPSP----HFLNLGKSIETILLTGKPAVVAKLD--KGKEFEETVS 73 
                                       4678******************96367777777666....5556543333333458888887777..899999**** PP

                   Diphthami_syn_2  80 tlkkldveavviGaieseyqksriervCrelGlksvaPLWkkdpeelleeiveekfevivvavkaegldeslLGrri 156
                                       +lk+l++  ++ G+++ e + +++e++ re+G  ++  LW+ d+ee+l +++e + + +v++        +++Gr +
  gi|385805091|ref|YP_005841489.1|  74 ILKRLGASEIIAGDVYIEDHLKYMESLARESGAALIESLWGLDSEEVLRKEMEDGIRGLVLGSISSID--KWIGREL 148
                                       *************************************************************9887765..8****** PP

                   Diphthami_syn_2 157 dkklidelkklsekygidkagegGeaetlvlDaPlfkkrlevkelekkw 205
                                       +   +d   + +++ g d+ ge+Ge++t+v  +P+++  l    + ++ 
  gi|385805091|ref|YP_005841489.1| 149 NAGSVDSFIEDAKRAGADPLGENGEYHTIVTFGPMHRAPLSYSRVSIED 197
                                       ************************************9877766655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 1494.02
//
Query:       gi|385805092|ref|YP_005841490.1|  [L=259]
Description: putative asparagine synthetase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-20   73.8   0.0    7.4e-12   45.6   0.0    2.1  2  Asn_synthase  Asparagine synthase
  ------ inclusion threshold ------
      0.032   13.7   0.0      0.046   13.2   0.0    1.2  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 !   45.6   0.0   8.3e-16   7.4e-12      22     143 ..      30     159 ..      28     185 .. 0.83
   2 !   26.4   0.0   5.6e-10     5e-06     237     303 ..     188     256 ..     179     259 .] 0.85

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 8.3e-16
                      Asn_synthase  22 alLSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgtehtelvlteeelldalpdviyhlee. 97 
                                       + LSGG+DSS++ a a  +   + + ++  + +   +++++  ++++ +++e   + ++ ++++ + + +++++ e 
  gi|385805092|ref|YP_005841490.1|  30 IALSGGIDSSTVLAAAISEGI-KPRGYASVYRNGLPKDIAFLNYISKLFNLEVKYVFIDDQDIEGLRKSIVECIGEe 105
                                       67*************999997.78888888878999****************9999999999999999999844444 PP

                      Asn_synthase  98 .........pfadrsaiplyllsrlakrkgvkvvLsGeGaDElfgGYpyfykaal 143
                                                 +  r +   y + r+ak++g+k++ +G G+DE+f+GY+ f   ++
  gi|385805092|ref|YP_005841490.1| 106 klnshedggCIEFRNDAVFYSVIRKAKEDGCKCIYTGSGGDEIFAGYS-FLLSKE 159
                                       555555546555677889******************************.655443 PP

  == domain 2  score: 26.4 bits;  conditional E-value: 5.6e-10
                      Asn_synthase 237 aRvPflDhrlvevalrlppe.lklrggieKyiLRealegylPeeileRpKegfsapvgewklk.gelre 303
                                       a  PflD+rl  +al++p++ l+ ++ ++K +LRe+l+g+  + i+eR K+++  ++g+ ++   +l e
  gi|385805092|ref|YP_005841490.1| 188 AIAPFLDNRLRSFALSIPVNcLRSNEMKGKDVLREILRGVGLKLIAERAKVPAESGSGTRSMCtSPLDE 256
                                       678****************9456666***************************9999988776566665 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   5.1e-06     0.046       4     120 ..      30     142 ..      28     152 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.1e-06
                                       EE--SSHHHHHHHHHHHHH-SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-GGGGGGSCGGG------.- CS
                              QueC   4 vllSGGlDSttvlalakkegkevealtfdYgqrhkkeleaakkiakelgveehkildldllkelggsaLtdeeie.v 79 
                                       + lSGG+DS+tvla a +eg +       Y +   k++   + i+k +++ e k + +d   +   + L ++ +e +
  gi|385805092|ref|YP_005841490.1|  30 IALSGGIDSSTVLAAAISEGIKPRGYASVYRNGLPKDIAFLNYISKLFNL-EVKYVFID---DQDIEGLRKSIVEcI 102
                                       569****************9998888888888888888888888888887.44444333...444444544444434 PP

                                       ----...--------TTHH.HHHHHHHHHHHHHHT-SEEEE- CS
                              QueC  80 pkeeleeeelpntfVpaRN.liflslaasyaealgaeaiiiG 120
                                        + e+ +++     + +RN ++f+s+    a++ g++ i++G
  gi|385805092|ref|YP_005841490.1| 103 GE-EKLNSHEDGGCIEFRNdAVFYSV-IRKAKEDGCKCIYTG 142
                                       44.33334445566667763344444.444666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 1642.38
//
Query:       gi|385805093|ref|YP_005841491.1|  [L=66]
Description: hypothetical protein FFONT_0043 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.019   14.2   0.1      0.019   14.2   0.1    1.0  1  Baculo_ME53      Baculoviridae ME53
      0.028   14.6   0.3      0.038   14.2   0.3    1.3  1  Spindle_Spc25    Chromosome segregation protein Spc25
        0.1   12.8   0.0       0.12   12.6   0.0    1.1  1  Lig_chan-Glu_bd  Ligated ion channel L-glutamate- and glycine


Domain annotation for each model (and alignments):
>> Baculo_ME53  Baculoviridae ME53
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   3.2e-06     0.019     114     152 ..      11      50 ..       2      63 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.2e-06
                       Baculo_ME53 114 yPslklvdlkklarervlrkyifnvsldttvevk.elrid 152
                                        Ps+ l dlkkl  +r ++ +++n+ ++ +v  k ++ +d
  gi|385805093|ref|YP_005841491.1|  11 NPSIFLSDLKKLNGNRNFQTFLLNLRKELSVHKKlKYSMD 50 
                                       69**************************999876445554 PP

>> Spindle_Spc25  Chromosome segregation protein Spc25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.3   6.3e-06     0.038      52      72 ..      19      39 ..       4      40 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.3e-06
                     Spindle_Spc25 52 leeLnetndlgkFlkevRkaF 72
                                      l++Ln ++++ +Fl ++Rk++
  gi|385805093|ref|YP_005841491.1| 19 LKKLNGNRNFQTFLLNLRKEL 39
                                      799****************86 PP

>> Lig_chan-Glu_bd  Ligated ion channel L-glutamate- and glycine-binding site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0     2e-05      0.12      10      50 ..      10      50 ..       5      56 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2e-05
                                      BTTTBEES..S---GGGGEESHHHHHHHHHHHHHT-EEEEE CS
                   Lig_chan-Glu_bd 10 eePyvmlkkeeelegneryeGfcidLlkelakklgfkYelk 50
                                      ++P + l++ ++l+gn++++ f ++L kel+ + ++kY++ 
  gi|385805093|ref|YP_005841491.1| 10 QNPSIFLSDLKKLNGNRNFQTFLLNLRKELSVHKKLKYSMD 50
                                      67888888999***************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); 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: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 428.46
//
Query:       gi|385805094|ref|YP_005841492.1|  [L=151]
Description: hypothetical protein FFONT_0044 [Fervidicoccus fontis Kam940]
Scores for 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   98.6   1.1    2.5e-28   98.3   1.1    1.1  1  DGC       DGC domain
     0.0033   17.4   0.0     0.0081   16.1   0.0    1.6  2  BAAT_C    BAAT / Acyl-CoA thioester hydrolase C terminal


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 !   98.3   1.1   2.7e-32   2.5e-28       1     105 [.      24     130 ..      24     131 .. 0.97

  Alignments for each domain:
  == domain 1  score: 98.3 bits;  conditional E-value: 2.7e-32
                               DGC   1 lvvsCsGasnvGqlaneaavklake.ge.akmiclagvgagveelvelaksarkiiaidGCpleCakkilekagvkp 75 
                                       +v +C+Gas++Gq+ ne+a+ l+k+ ++ ++m+cl++v+ g++ + +++k+ar +iai+GC+l Ca+++l+++g++p
  gi|385805094|ref|YP_005841492.1|  24 IVATCDGASSTGQIGNEVARMLTKTfPDkVRMCCLSAVASGSKLHLDIFKKARAVIAINGCQLMCASNVLKQKGIQP 100
                                       699**********************9555************************************************ PP

                               DGC  76 dehlvvtdlgikkeekldlseeeiekvvea 105
                                       + +++v++ gi+k  +ld++ee+++k++++
  gi|385805094|ref|YP_005841492.1| 101 TYEITVAKEGINKLPTLDFDEEDVRKIANK 130
                                       **************************9987 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 ?    0.0   0.0     0.076   6.8e+02     109     152 ..      12      54 ..       3      60 .. 0.66
   2 !   16.1   0.0   9.1e-07    0.0081      20      91 ..      49     133 ..      43     150 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.076
                                       --GGG--SEEEEEEETT-SSS-HHHHHHHHHHHHHCTT--.--E CS
                            BAAT_C 109 ipvekakgpillvvgedDknwpSkesaekaserLkkagkkvevq 152
                                       +p   + ++ l++v++ D    + +  ++++++L+k+  + +v+
  gi|385805094|ref|YP_005841492.1|  12 LPSCSTYAEGLIIVATCDGASSTGQIGNEVARMLTKTFPD-KVR 54 
                                       5555566667788888888888888888887777776544.444 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 9.1e-07
                                       --SSEEEEEETHHHHHHHHHHHHSSSEEEEEEES--SB--SSEEEETTE...............EE----B-GGG-E CS
                            BAAT_C  20 kkdkigllGiSkGgelalllasflkkisavvlingsavvvegklvykdes.............kvlpelklsmeklk 83 
                                         dk+ ++ +S  +    l   ++kk +av++ing++ +++ + ++++ +             + lp l++++e++ 
  gi|385805094|ref|YP_005841492.1|  49 FPDKVRMCCLSAVASGSKLHLDIFKKARAVIAINGCQLMCASNVLKQKGIqptyeitvakegiNKLPTLDFDEEDVR 125
                                       55677777777777777777778*****************8888888777777777777777777777777777777 PP

                                       E-TTS-EE CS
                            BAAT_C  84 vnknglld 91 
                                       + +n+  +
  gi|385805094|ref|YP_005841492.1| 126 KIANKITE 133
                                       66666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1000.90
//
Query:       gi|385805095|ref|YP_005841493.1|  [L=169]
Description: transposase, IS605 OrfB family [Fervidicoccus fontis Kam940]
Scores for complete 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   66.3   0.0    2.4e-18   65.8   0.0    1.2  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 !   65.8   0.0   1.3e-22   2.4e-18       1      68 [.      42     109 ..      42     110 .. 0.94

  Alignments for each domain:
  == domain 1  score: 65.8 bits;  conditional E-value: 1.3e-22
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                       fr +++ +e+ka+e+G +v++vnp++TS  C+ + s+  +++ +r+ +C++ g  ++rDv+A++N+lk
  gi|385805095|ref|YP_005841493.1|  42 FRGMQKAIEEKAREHGLPVVYVNPRNTSRLCPIHCSEIAYENGSRLGRCTKGGEAWHRDVVAVWNLLK 109
                                       7889****************************977777777*************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1070.27
//
Query:       gi|385805096|ref|YP_005841494.1|  [L=88]
Description: hypothetical protein FFONT_0047 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.049   13.5   0.2      0.057   13.3   0.2    1.1  1  CEP63     Centrosomal protein of 63 kDa


Domain annotation for each model (and alignments):
>> CEP63  Centrosomal protein of 63 kDa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   3.2e-06     0.057     192     247 ..      29      84 ..      21      87 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.2e-06
                             CEP63 192 qseiqrLrskleraqdtleaqelelerLrllveelgkskrvlleekqeleeelres 247
                                       + e++rL+s+l+ra++ l ++ l ++r++ + e  ++ +    +  ++ ++el+e+
  gi|385805096|ref|YP_005841494.1|  29 EDEMKRLESRLKRAEKLLGSHKLPMNRIKNIIETSVDWRVCSPDTIRRISKELKEA 84 
                                       5699*****************************99997766666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); 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: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 599.37
//
Query:       gi|385805097|ref|YP_005841495.1|  [L=172]
Description: hypothetical protein FFONT_0048 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00094   19.2   0.5     0.0089   16.0   0.0    2.3  2  HTH_29        Winged helix-turn helix
     0.0016   18.1   0.4       0.06   13.2   0.1    2.3  2  HTH_23        Homeodomain-like domain
  ------ inclusion threshold ------
      0.024   14.1   0.1      0.043   13.2   0.1    1.4  1  HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family I
      0.028   14.5   0.0      0.068   13.3   0.0    1.7  1  HTH_28        Helix-turn-helix domain
      0.055   13.7   0.3      0.088   13.0   0.3    1.3  1  TetR_C_16     Tetracyclin repressor-like, C-terminal domain
      0.073   13.2   1.0       0.39   10.9   0.1    2.3  2  AbiEi_4       Transcriptional regulator, AbiEi antitoxin
      0.078   12.5   1.6       0.13   11.7   1.6    1.4  1  TF_Zn_Ribbon  TFIIB zinc-binding


Domain annotation for each model (and alignments):
>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.19   4.9e+02      21      41 ..      54      74 ..      46      87 .. 0.83
   2 !   16.0   0.0   3.5e-06    0.0089       5      39 ..     137     170 ..     131     171 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.19
                            HTH_29 21 llglsrrtvyrwlkrfeegGl 41
                                       l+ s+r  +r lk    +Gl
  gi|385805097|ref|YP_005841495.1| 54 DLQRSYRAYFRLLKKAKRKGL 74
                                      578899999999998888884 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 3.5e-06
                            HTH_29   5 llllaeGvstvsqiAkllglsrrtvyrwlkrfeeg 39 
                                        + la    ++++iA+++gls+ ++ r +k+  e+
  gi|385805097|ref|YP_005841495.1| 137 AMILASSD-SIARIAEVTGLSPEHIARLRKLLKED 170
                                       33333333.5********************98876 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.039     1e+02      27      46 ..      55      74 ..      53      77 .. 0.88
   2 !   13.2   0.1   2.4e-05      0.06      10      43 ..     138     169 ..     128     172 .] 0.74

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.039
                            HTH_23 27 LgvsrrTvyrwlkryreeGl 46
                                      L +s+r + r lk+ +++Gl
  gi|385805097|ref|YP_005841495.1| 55 LQRSYRAYFRLLKKAKRKGL 74
                                      899***********988985 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 2.4e-05
                            HTH_23  10 illllaeGlsvreIAreLgvsrrTvyrwlkryre 43 
                                       ++l+    +s+++IA+  g s+ ++ r +k  +e
  gi|385805097|ref|YP_005841495.1| 138 MILAS--SDSIARIAEVTGLSPEHIARLRKLLKE 169
                                       33333..68********************98755 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   1.7e-05     0.043       8      42 ..     124     158 ..     123     163 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.7e-05
                      HTH_Tnp_ISL3   8 rrsriTlrleayilelllesrsvkavArqlgvSwt 42 
                                       r s+ Tlr++a++++ l +s s++ +A+ +g+S+ 
  gi|385805097|ref|YP_005841495.1| 124 RFSGRTLRAKAAAAMILASSDSIARIAEVTGLSPE 158
                                       66899****************************86 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.6e-05     0.068       2      38 ..     131     169 ..     130     172 .] 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.6e-05
                            HTH_28   2 Rleiiklla..aGhsvreaArelgisrrtvyrWikryee 38 
                                       R+++  +++  + +s++ +A+  g+s++++ r++k + e
  gi|385805097|ref|YP_005841495.1| 131 RAKAAAAMIlaSSDSIARIAEVTGLSPEHIARLRKLLKE 169
                                       55566555443678********************98776 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 ?   13.0   0.3   3.4e-05     0.088      31      98 ..      94     163 ..      89     165 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.4e-05
                                       -------HHHHHHHHHHHHHHCTTTS-ST....THHHHHHHHHHHHHHHHHHHHTS--TTCCCS-HHHHHHH CS
                         TetR_C_16  31 lsseeaaellrefleeqvlaplaarlggp....daelRaalvasqllGlalaRyvlrleplasasreelval 98 
                                        s++++  l+r ++e++++++  +r++ +     ++lRa+ +a+++  la   +++r+ +++ +s+e++++l
  gi|385805097|ref|YP_005841495.1|  94 FSHPKTPSLMRFIMENEIIRRAFERVSRDprfsGRTLRAKAAAAMI--LASSDSIARIAEVTGLSPEHIARL 163
                                       5899999*********************99998899*********9..699999999999999999999986 PP

>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.32   8.1e+02      25      39 ..      58      76 ..      53      76 .. 0.78
   2 ?   10.9   0.1   0.00015      0.39       6      34 ..     140     165 ..     136     166 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.32
                           AbiEi_4 25 spsa....lrrLvrkGwLv 39
                                      s++a    l ++ rkG+L+
  gi|385805097|ref|YP_005841495.1| 58 SYRAyfrlLKKAKRKGLLI 76
                                      5555677799999***996 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00015
                           AbiEi_4   6 lasrqvGlfttreleaaGispsalrrLvr 34 
                                       las++  +++ +e+   G+sp +++rL++
  gi|385805097|ref|YP_005841495.1| 140 LASSD-SIARIAEV--TGLSPEHIARLRK 165
                                       55555.59******..***********98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.6   5.3e-05      0.13       5      28 ..       3      27 ..       2      37 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.3e-05
                                      TTTC.EECHEETSTTCEEESSSSBE CS
                      TF_Zn_Ribbon  5 nCgs.tnlveDpergelvCtdCGlV 28
                                      +C++ ++l++D+ +g+++C++ G++
  gi|385805097|ref|YP_005841495.1|  3 ECSGcKELIWDYRTGDIICSESGEI 27
                                      6777566************986665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); 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: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1047.40
//
Query:       gi|385805098|ref|YP_005841496.1|  [L=100]
Description: hypothetical protein FFONT_0049 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 608.93
//
Query:       gi|385805099|ref|YP_005841497.1|  [L=695]
Description: hypothetical protein FFONT_0050 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (695 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.67u 0.25s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 4503.30
//
Query:       gi|385805100|ref|YP_005841498.1|  [L=42]
Description: hypothetical protein FFONT_0051 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       143  (0.0079759); expected 358.6 (0.02)
Passed bias filter:                      110  (0.00613531); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 271.64
//
Query:       gi|385805101|ref|YP_005841499.1|  [L=635]
Description: anaerobic ribonucleoside triphosphate reductase [Fervidicoccus fontis Kam940]
Scores for complete 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-147  491.3   0.0   5.1e-147  491.0   0.0    1.0  1  NRDD           Anaerobic ribonucleoside-triphosphate reductas
     0.0054   16.4   0.0     0.0094   15.6   0.0    1.3  1  TackOD1        Thaumarchaeal output domain 1
  ------ inclusion threshold ------
      0.042   13.9   1.1      0.051   13.6   0.1    1.6  2  HypA           Hydrogenase/urease nickel incorporation, metal
        3.4    7.5   5.5        3.2    7.6   0.6    2.5  2  zinc_ribbon_2  zinc-ribbon domain


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 !  491.0   0.0  1.1e-150  5.1e-147       1     561 []      30     633 ..      30     633 .. 0.91

  Alignments for each domain:
  == domain 1  score: 491.0 bits;  conditional E-value: 1.1e-150
                                       .XHTTHHHHHHHHHHHHHHHHHHHH-H..HHHHHHHHHHHTTSEEETTGGGTTT.S--EEE--SHHHHHH-CTT-SS CS
                              NRDD   1 enanvdskslsglrlklasevskeyalkkllpkevaeaheegdiHiHDldylallttyClgidlkdlleeGlktgng 77 
                                       enan     ++g+ ++l + ++k+  l  l+p++v + h eg i+iH+l + +++++yC g+++++lle+Gl+t   
  gi|385805101|ref|YP_005841499.1|  30 ENANR-YIGPTGFFSYLLEDYMKRELL-GLMPNRVLRSHSEGLIYIHKLPH-SIYIPYCSGHSISRLLEKGLETFTV 103
                                       89999.99*****************99.6********************88.577*******************999 PP

                                       S-B---SHHHHHHHHHHHHHHHHTSSSS-EEETTHHHHHHHHHHHHHHTTSS-GHHHHHHHHHHHHHHHTTS-S..S CS
                              NRDD  78 vsrppkhietalalavnilqtlqneqaGgqaissfdtylapfvrkdyekklkkltkkeikqamqefvynlntlpsrr 154
                                       vsrp+kh++t++++++n+l+t+q+ ++G+qa+ss+++y+ pf+r+d      +l+ +e+kq++q++++nln +p+r 
  gi|385805101|ref|YP_005841499.1| 104 VSRPAKHFDTFVDHVANYLITMQHYFTGAQAFSSVEWYAGPFIRND------GLDSREVKQHIQRLLFNLN-YPTRV 173
                                       9*********************************************......*******************.***** PP

                                       SSS---EEEEEE.-HH................................HHHHHTTTTS-HCH----SEEEEEEEEET CS
                              NRDD 155 GaQvpFtninlgldtp.................tegrfee..kliikallevmleGdgnkgtpftFPilifklkedf 212
                                       G+Q+pFtn+++++d                   + g +e+  k ++ka++e ++eGd+  g+pftFPi++++ +  +
  gi|385805101|ref|YP_005841499.1| 174 GMQTPFTNFTVTMDAArkalegdsavydgkklnPLGAYEDeaKTFFKAMVELLMEGDAL-GQPFTFPIPTLMTTASW 249
                                       *********************************777777667*****************.***************** PP

                                       ETTH.....HHHHHHHHHHTTT--EEE.......EEES--GGGTT--------........................ CS
                              NRDD 213 nleeedpnydlfklalevtakrgfpyffnlledlepedekevasmgCRlrldege...................... 267
                                        +e+     +l +l+++ +ak+g+ y+ n+       d+  + +m+CR+ +d++e                      
  gi|385805101|ref|YP_005841499.1| 250 LWED----PELHELIFRAAAKKGSFYWLNTRV----VDPDASFAMCCRIAIDRSEltyalsgkgkpglgslkmrdle 318
                                       ****....9******************99964....3334489*********5223344545555666666666666 PP

                                       ..........S---............EEEEEEEEEEHHHHHH..HH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              NRDD 268 ..........rlgg............rgslgvvtiNlprlaleakgdeekffelLdellelakealeerrkilekll 322
                                                 +               +gs++v  +Nlpr+al a+++e+kf+el++e+l l++ea++  r++  kl+
  gi|385805101|ref|YP_005841499.1| 319 evqneywkkmE--RqsfggiwampdiTGSVNVADVNLPRVALDAQSEESKFWELYEERLMLVREAVDWFRQRYVKLM 393
                                       66555555550..055556************************************************9999988988 PP

                                       HTT-HHH.HTTSS-GE.............EEEEEEE-HHHHHHHT........TEEEE..-HHHHHHHHHHHHHHHH CS
                              NRDD 323 akglpflmgkgylksrkkkdeveevlkngtltiGfiGlaEalkal........tgkkigeseeakefalkvlkhmre 391
                                       ++ +p l+  g++      + + e+ +++++tiG++Gl Ea++++        +g++  ++  a +++ k++++  +
  gi|385805101|ref|YP_005841499.1| 394 KQ-YPSLY--GMIL-----KYMPEFPSSHFNTIGLVGLPEAAAIFmadpklwfEGSRS-NKMSAADLMRKMVEFATK 461
                                       77.88864..4443.....14668****************************888887.9999************** PP

                                       HHHHHHHHHSS-EEEEE---TTHHHHHHHHH..HH................HHG-SSSS-TTSSB-HHHHHHHHHHH CS
                              NRDD 392 kadelkeetglnfsleatPaEslsgrfakldkkkfgeipgvdke......pyYtNsfhvpvdekislfekikleaef 462
                                       +a+e+++e+g+ +++e++PaEs+s ++a +d k + ++ +          p+Y++s+ +++++ i+l e+i++ea++
  gi|385805101|ref|YP_005841499.1| 462 HAREWMRESGVPWNVEEVPAESASPKMASMDLKLYPHLSE---YlpdpsePVYSTSIAPYYGS-IELPERIEIEARV 534
                                       ***********************************55555...34557899*****9876666.************* PP

                                       TGGGTT-S-EEEEBSS--SSHHHHHHHHHHHHHTT--EEEEE--EEEETT.--..EESSSB-TTT--BE.EEEEEES CS
                              NRDD 463 qklttGGailyieldeekknpealeklvkiakktgigYfsinpkidvCnecgy..kgeiekCpkCgseeevevirRi 537
                                       qk++tGG++++i+l+ee  +pe+l+kl k +++++++Y+s++p +++C++c +  +g+++kCp+Cg+e+ ve+++Ri
  gi|385805101|ref|YP_005841499.1| 535 QKFFTGGVMMHIFLGEE-AEPESLAKLAKRMMEMDLVYWSFTPSLTYCPSCRRtfTGLHTKCPVCGNEN-VEIWSRI 609
                                       ***************99.89*********99999*******************99***********888.******* PP

                                       SSSEEEHHHHHHHHHHHSGG---B CS
                              NRDD 538 tGYlrpvsswnkgkkaElkdRvkh 561
                                       +GY+rp ++wn+ +++E+++R+++
  gi|385805101|ref|YP_005841499.1| 610 IGYYRPLKNWNPQRRKEFWTRKHY 633
                                       **********************88 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   2.1e-06    0.0094      48     100 ..     553     605 ..     526     612 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.1e-06
                           TackOD1  48 ekeeseelleelvkrglleeelvdrirlCpsCksghlnvrevCpkCkSidiee 100
                                       e e+  +l++++ + +l+  ++  ++  CpsC+     ++  Cp C+  ++e 
  gi|385805101|ref|YP_005841499.1| 553 EPESLAKLAKRMMEMDLVYWSFTPSLTYCPSCRRTFTGLHTKCPVCGNENVEI 605
                                       4457889999*************************************999875 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 ?   -3.7   0.1       2.6   1.2e+04       4      20 ..     449     465 ..     446     470 .. 0.77
   2 ?   13.6   0.1   1.1e-05     0.051      65      99 ..     573     605 ..     550     608 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 2.6
                                       HHHHHHHHHHHHHHHCC CS
                              HypA   4 lsiaesivevveeeake 20 
                                       + +++++ve ++++a+e
  gi|385805101|ref|YP_005841499.1| 449 ADLMRKMVEFATKHARE 465
                                       67899999999999966 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 1.1e-05
                                       EEE--EEEETTTS-EEECHHHHHS-TTTSSS-EEE CS
                              HypA  65 eevpvkvrCreCgkefeleekalrCpkCgsadvei 99 
                                       + +p  ++C +C+++f+    +++Cp Cg+++vei
  gi|385805101|ref|YP_005841499.1| 573 SFTPSLTYCPSCRRTFTGL--HTKCPVCGNENVEI 605
                                       55678899********954..358*********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 ?    1.6   0.4     0.055   2.5e+02      15      19 ..     580     584 ..     579     587 .. 0.57
   2 ?    7.6   0.6   0.00071       3.2       1      10 [.     594     603 ..     594     605 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.055
                     zinc_ribbon_2  15 FCpyC 19 
                                       +Cp C
  gi|385805101|ref|YP_005841499.1| 580 YCPSC 584
                                       55555 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00071
                     zinc_ribbon_2   1 fCpnCGaelq 10 
                                       +Cp CG+e+ 
  gi|385805101|ref|YP_005841499.1| 594 KCPVCGNENV 603
                                       8*******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (635 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      568  (0.0316805); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
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: 0.74u 0.32s 00:00:01.06 Elapsed: 00:00:00.54
# Mc/sec: 3529.93
//
Query:       gi|385805102|ref|YP_005841500.1|  [L=253]
Description: anaerobic ribonucleoside-triphosphate reductase activating protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      2e-13   51.1   0.0    6.6e-13   49.4   0.0    1.7  2  Radical_SAM  Radical SAM superfamily
    3.8e-10   39.9   0.0    6.9e-10   39.1   0.0    1.4  1  Fer4_14      4Fe-4S single cluster domain
    2.9e-09   37.3   0.0    5.2e-09   36.5   0.0    1.4  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 !   49.4   0.0   1.1e-16   6.6e-13       5     165 ..      30     187 ..      26     189 .. 0.90
   2 ?   -0.8   0.0       0.3   1.8e+03      26      45 ..     226     245 ..     212     253 .] 0.64

  Alignments for each domain:
  == domain 1  score: 49.4 bits;  conditional E-value: 1.1e-16
                                       SEESS--TTTSCCTT.HHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGS.TTHHHHHHHHHHTCCCTE CS
                                       xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   5 rgCnlrCsfCarpet.vrregrgrslsveeileevkelkaekg.vkevilgggeplly.pdfvellerlaklavpgi 78 
                                        gCnl C+fC++++  + + +r  +l+ +++le v++ +   g +++++++ggepl++  ++ +ll+ l++    gi
  gi|385805102|ref|YP_005841500.1|  30 CGCNLSCPFCHNWKLaGNNPERCDFLDNRRLLEDVEASR---GlIDFLHVTGGEPLVQyIELGKLLRTLKES--YGI 101
                                       69***********99999999999999999999999887...88*************867888888999888..7** PP

                                       EEEEEECSSCHGHHHHHHHHHTT.-SEEEEEEBSSSHH..HHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEB CS
                                       xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  79 ritvetngtlpdeeklerllelg.vdrvslgleaadde..kvlklmnrghtfeevlealeklreagikrvvdrivgl 152
                                       ++++ tn tl     l r+ e   vd+++ + + + d+      l+  ++ ++++ e+l + ++++++    ri++ 
  gi|385805102|ref|YP_005841500.1| 102 EVSLNTNLTL--TSPLSRIIEEDlVDHLATDFKVPPDKmfGLSSLL-AQKLWQKYEEGLSLVADHQLP-LELRIPIA 174
                                       **********..589******99***************76666666.99*******************.9****999 PP

                                       TTTSHHHHHHHHH CS
                                       xxxxxxxxxxxxx RF
                       Radical_SAM 153 pGendeeleelle 165
                                       +  + e l e+l+
  gi|385805102|ref|YP_005841500.1| 175 KFTTPELLGEYLR 187
                                       9998887777766 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.3
                                       HHHHHHHHHHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  26 grslsveeileevkelkaek 45 
                                       + +  ++ei+e vk+l +e 
  gi|385805102|ref|YP_005841500.1| 226 PSNDRLDEIAESVKKLGFEV 245
                                       45556666666666666444 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 !   39.1   0.0   1.2e-13   6.9e-10       5      94 ..      29     114 ..      25     132 .. 0.81

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 1.2e-13
                           Fer4_14   5 lsgCnlsCkgCdnketwkselgkpqteelle..qilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeyp 79 
                                       l gCnlsC++C n +      ++p+  + l+  + l+d+++s+  i++l +tGGePL   +  el kl++ lke+y 
  gi|385805102|ref|YP_005841500.1|  29 LCGCNLSCPFCHNWK---LAGNNPERCDFLDnrRLLEDVEASRGLIDFLHVTGGEPL--VQYIELGKLLRTLKESY- 99 
                                       689********9855...555555555555411668899****9*************..7799*************. PP

                           Fer4_14  80 ekkiwletngtleie 94 
                                        +++ l+tn tl   
  gi|385805102|ref|YP_005841500.1| 100 GIEVSLNTNLTLTSP 114
                                       *********999755 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 !   36.5   0.0   8.7e-13   5.2e-09       6      92 ..      23     108 ..      20     135 .. 0.77

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 8.7e-13
                           Fer4_12   6 vrlslfvsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesi..egltllGGEPllpenaeallelvkevk 80 
                                       v +++++ gCnlsC++C+n ++   ++ +  ++   ++++ed++ ++   + l ++GGEPl+  ++ +l +l++ +k
  gi|385805102|ref|YP_005841500.1|  23 VTFTVWLCGCNLSCPFCHNWKLA-GNNPERCDFLDNRRLLEDVEASRGliDFLHVTGGEPLV--QYIELGKLLRTLK 96 
                                       5679**************87654.4445556788888999999876655599**********..************* PP

                           Fer4_12  81 eekpekdiwlyt 92 
                                       e +  ++ + ++
  gi|385805102|ref|YP_005841500.1|  97 ESYGIEVSLNTN 108
                                       *99833444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1588.42
//
Query:       gi|385805103|ref|YP_005841501.1|  [L=215]
Description: CbiZ domain containing protein [Fervidicoccus fontis Kam940]
Scores for complete 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-31  108.4   0.0    5.3e-31  108.2   0.0    1.0  1  CbiZ      Adenosylcobinamide amidohydrolase


Domain annotation for each model (and alignments):
>> CbiZ  Adenosylcobinamide amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.2   0.0   2.9e-35   5.3e-31       2     191 ..      16     197 ..      15     198 .. 0.93

  Alignments for each domain:
  == domain 1  score: 108.2 bits;  conditional E-value: 2.9e-35
                              CbiZ   2 feeprrvlssavlngGlrelravlnhqvpegyeredpeeyleeyleelglppektvgllTaadmenaaiaeeefedl 78 
                                       +e++  +ls++ + + ++++r++++ +vp+g+e+ d +ey++e+ ++lg++ e+t++++Ta+d++n++  + +++++
  gi|385805103|ref|YP_005841501.1|  16 LEGELMSLSTSGCPKVYERARYLAFKRVPKGFEHVDLDEYCREVSRSLGVDIEETALFFTAVDLRNYSKGSYSHRGV 92 
                                       5778899******999999********************************************************** PP

                              CbiZ  79 evtavvTaGvesnavragdedeeaekpGTINiivlinaaLtdaalvralitatEAKtaalqdlgvrsrysegatGTg 155
                                       +++a+vT Gv   + + +++   ++++GTIN++v+++++++   l++++ t+ E K   ++  g  + +++   GT+
  gi|385805103|ref|YP_005841501.1|  93 KAEAFVTYGV-DSPSCFEER---RREIGTINVAVIVEKPMSRVGLLDLFRTVSEIKGMSISLGGPMCPSHS-SVGTA 164
                                       **********.99****995...89*********************************9987777766665.9**** PP

                              CbiZ 156 TDaiavaadkegeeeltyaGkhtklGeliaraVyeA 191
                                       +Da++va++ +g+  ++++G +t++G   + a  eA
  gi|385805103|ref|YP_005841501.1| 165 SDATMVASP-QGD--ESFGGIATDVGISASLALLEA 197
                                       *********.777..59*********9988887777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       227  (0.0126611); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1342.36
//
Query:       gi|385805104|ref|YP_005841502.1|  [L=279]
Description: hypothetical protein FFONT_0056 [Fervidicoccus fontis Kam940]
Scores for complete 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   24.5   0.0    6.1e-05   23.6   0.0    1.6  1  CRISPR_Cas6  CRISPR-associated endoribonuclease Cas6


Domain annotation for each model (and alignments):
>> CRISPR_Cas6  CRISPR-associated endoribonuclease Cas6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   3.4e-09   6.1e-05      18      85 ..     194     274 ..     149     275 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 3.4e-09
                                       -HHHHHHH......HHHHHHHHTSS...EECHHH...HH.HEEEEEEEE....--..HHHECCCHHHHHHHH-SSST CS
                       CRISPR_Cas6  18 sprlvfss......llrrwnalaglkgkptveee...le.gGfvGevky....sg..eleelekllrfaeylgvGkk 78 
                                       + +lv+ss      l+++w ++++l+  p + ++    +   + G+++y    ++  ele ++k l++ae++g+G++
  gi|385805104|ref|YP_005841502.1| 194 TESLVVSSfptigkLVETWYSIKTLR--P-IAIFfkgKKqVNLAGSITYliqnENakELEMVQKTLAVAELAGIGRS 267
                                       44445555666666888888888887..3.33333442223899*****998622569999999************* PP

                                       GGGTTT- CS
                       CRISPR_Cas6  79 tafGlGk 85 
                                       +  G+G 
  gi|385805104|ref|YP_005841502.1| 268 RQNGFGT 274
                                       ******6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); 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 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1784.23
//
Query:       gi|385805105|ref|YP_005841503.1|  [L=299]
Description: hypothetical protein FFONT_0057 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.7e-15   56.3   0.0    8.1e-15   55.2   0.0    1.6  1  CRISPR_Cas6  CRISPR-associated endoribonuclease Cas6
    5.8e-05   23.3   0.0    9.8e-05   22.6   0.0    1.4  1  Cas6_N       Cas6 N-terminal domain
  ------ inclusion threshold ------
       0.17   11.2   0.0        1.1    8.6   0.1    1.8  2  Cas_Cmr3     CRISPR-associated protein (Cas_Cmr3)


Domain annotation for each model (and alignments):
>> CRISPR_Cas6  CRISPR-associated endoribonuclease Cas6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.2   0.0   1.4e-18   8.1e-15       1      86 []     153     293 ..     153     293 .. 0.77

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 1.4e-18
                                       EEEEEEE-EE.................TEEESS--HHHHHHHHHHHHHHHTSS........................ CS
                       CRISPR_Cas6   1 lrfltPtrfk.................krkgllpsprlvfssllrrwnalaglkgk..................... 39 
                                       +rfltPt +                  + ++llp+p+l+++s+l+ + +  g+ gk                     
  gi|385805105|ref|YP_005841503.1| 153 VRFLTPTILSkkiatppwlskrasalkDSYSLLPTPGLLAGSVLKNLLEHLGEIGKkdqrvpymalrffdlfveevd 229
                                       79******************9999999899999*********99886665555555576677777777776664433 PP

                                       EECHHH................HH.HEEEEEEEE....--HHHECCCHHHHHHHH-SSSTGGGTTT-E CS
                       CRISPR_Cas6  40 ptveee................le.gGfvGevky....sgeleelekllrfaeylgvGkktafGlGkv 86 
                                            e                ++  G++G+++y    +g+  ++ +ll++ae++gvGk++++GlG++
  gi|385805105|ref|YP_005841503.1| 230 H----ElkpvtvllgkddkgnmRRgRGIIGWINYramnEGVAGAFVRLLKIAEIVGVGKSRGIGLGEI 293
                                       0....244555555555555643444********766444999999********************85 PP

>> Cas6_N  Cas6 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   1.6e-08   9.8e-05       3     113 ..      21     139 ..      19     140 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.6e-08
                                       EEEEEEESS-EE--SSTTHHHHHHHHT...SSGGGHHHHH---TT-SEEE-.--BS.TTSB--.S------EE-SSS CS
                            Cas6_N   3 atfevtpkrDvilppltSKvskyills...lspslsklvesrekyKplris.vlkd.ngrrly.aegkkkvrlkage 73 
                                       ++++v+  + ++lppl+S ++k  ++s   l +  +   es+++ K l     l   +gr +  + +k ++++  ++
  gi|385805105|ref|YP_005841503.1|  21 ISYRVKSRDFIMLPPLSSNLLKAAVASsedLHNIWEMYAESKRPRKVLYKAlRLPGsGGRLVAlEGKKGLLHMDPDK 97 
                                       8999**9999***************9945444444445679999888864314544366666667778899****** PP

                                       SEEEEEEE.ESSSCCTTTTGSEEE.EEETTEEEEEEEEEEEE CS
                            Cas6_N  74 rlsfslsf.aledvveeivekegv.vktvygefsveLkeikv 113
                                        +++ + + ++++   + + k++v vkt+yge ++e+++i +
  gi|385805105|ref|YP_005841503.1|  98 FYEAEIVLiSDSNALMSYLPKPYVsVKTPYGEVELEVTTIDI 139
                                       ***9877515677777899999873689***********998 PP

>> Cas_Cmr3  CRISPR-associated protein (Cas_Cmr3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1   0.00018       1.1     246     287 ..     133     175 ..     122     195 .. 0.78
   2 ?    1.1   0.0     0.035   2.1e+02      27      54 ..     182     208 ..     172     237 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00018
                          Cas_Cmr3 246 elesvpeeveaaiaeggrlrlvLlTPaifakgw.rpgwldkek 287
                                       e+ +++   e++ + +g +r+ +lTP+i+ k+   p wl+k +
  gi|385805105|ref|YP_005841503.1| 133 EVTTIDIIREVPASTAGSVRVRFLTPTILSKKIaTPPWLSKRA 175
                                       455555556777779******************9****99875 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.035
                          Cas_Cmr3  27 sllfPlPsTlaGavrtalgekagldfgk 54 
                                       ++l+P P  laG v   l+e++g ++gk
  gi|385805105|ref|YP_005841503.1| 182 YSLLPTPGLLAGSVLKNLLEHLG-EIGK 208
                                       7899*****************99.5544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1824.05
//
Query:       gi|385805106|ref|YP_005841504.1|  [L=231]
Description: HTH_ARSR domain containing protein [Fervidicoccus fontis Kam940]
Scores for complete 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   29.9   0.2      7e-07   29.0   0.2    1.4  1  MarR_2           MarR family
    1.1e-06   28.3   0.1    2.2e-06   27.4   0.1    1.4  1  HTH_IclR         IclR helix-turn-helix domain
    1.9e-06   27.6   0.3    4.4e-06   26.4   0.3    1.5  1  HTH_5            Bacterial regulatory protein, arsR family
    4.9e-06   26.0   1.6    5.8e-06   25.8   0.4    1.8  1  HTH_24           Winged helix-turn-helix DNA-binding
    9.6e-06   25.4   0.0      2e-05   24.4   0.0    1.6  1  TrmB             Sugar-specific transcriptional regulator Trm
    2.9e-05   24.0   0.1    6.5e-05   22.9   0.1    1.6  1  HTH_20           Helix-turn-helix domain
    0.00011   22.1   0.0     0.0002   21.3   0.0    1.4  1  HTH_29           Winged helix-turn helix
    0.00022   21.1   0.1    0.00042   20.2   0.1    1.4  1  MarR             MarR family
    0.00034   20.5   0.1    0.00069   19.5   0.1    1.5  1  HTH_36           Helix-turn-helix domain
    0.00066   19.6   0.0     0.0011   18.9   0.0    1.3  1  Dimerisation2    Dimerisation domain
     0.0016   18.9   0.2     0.0041   17.6   0.1    1.8  1  HTH_27           Winged helix DNA-binding domain
     0.0025   17.4   1.1     0.0032   17.1   1.1    1.2  1  Cas_DxTHG        CRISPR-associated (Cas) DxTHG family
      0.008   15.9   0.1      0.076   12.8   0.0    2.3  2  DUF4364          Domain of unknown function (DUF4364)
     0.0085   16.3   0.0      0.019   15.1   0.0    1.6  1  PaaX             PaaX-like protein
  ------ inclusion threshold ------
      0.011   15.7   0.1      0.032   14.2   0.1    1.7  1  HTH_Crp_2        Crp-like helix-turn-helix domain
      0.019   14.7   0.0      0.037   13.8   0.0    1.4  1  HTH_23           Homeodomain-like domain
       0.02   14.8   1.5      0.028   14.4   0.2    1.9  2  HTH_11           HTH domain
      0.031   13.1   0.0      0.048   12.5   0.0    1.2  1  Cas_Cas02710     CRISPR-associated protein (Cas_Cas02710)
      0.036   14.2   0.0      0.085   13.1   0.0    1.6  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
      0.051   12.1   0.1      0.063   11.8   0.1    1.1  1  PaRep2b          PaRep2b protein
      0.072   12.9   0.0       0.16   11.8   0.0    1.5  1  HTH_38           Helix-turn-helix domain
      0.072   12.9   0.1        2.8    7.8   0.1    2.5  2  HTH_DeoR         DeoR-like helix-turn-helix domain
      0.086   13.2   0.0       0.19   12.1   0.0    1.6  1  Rrf2             Transcriptional regulator
       0.15   12.4   0.0       0.27   11.6   0.0    1.4  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 !   29.0   0.2   9.3e-10     7e-07       8      54 ..     149     193 ..     144     200 .. 0.89

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 9.3e-10
                                       HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2   8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54 
                                       +rvL  + r +   lt  ++ r+lg sk++v r +k L + GL++ +
  gi|385805106|ref|YP_005841504.1| 149 LRVLDLISRKEA--LTLDDISRELGKSKPTVFRSVKLLRQLGLITPE 193
                                       79*********9..******************************877 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 !   27.4   0.1   2.9e-09   2.2e-06       6      49 ..     149     191 ..     148     193 .. 0.95

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 2.9e-09
                                       HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR   6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49 
                                       l++Ld++++    ltl +++r++g +k+tv+R ++ L +lG+++
  gi|385805106|ref|YP_005841504.1| 149 LRVLDLISRKEA-LTLDDISRELGKSKPTVFRSVKLLRQLGLIT 191
                                       89*******999.9***************************986 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.3   5.9e-09   4.4e-06       5      46 ..     149     191 ..     146     191 .. 0.95

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 5.9e-09
                                       HHHHHHHTTSS.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5   5 lkILklLaege.lcvcelaeelglsqstvShHLkkLreaGLVe 46 
                                       l++L l +++e l+  ++++elg+s++tv +  k Lr++GL++
  gi|385805106|ref|YP_005841504.1| 149 LRVLDLISRKEaLTLDDISRELGKSKPTVFRSVKLLRQLGLIT 191
                                       789******888*****************************95 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.4   7.7e-09   5.8e-06       4      48 .]     147     191 ..     144     191 .. 0.95

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 7.7e-09
                            HTH_24   4 tdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                       + +++L l+ ++  ++  +++++lg S++tv r +k L + GlI+
  gi|385805106|ref|YP_005841504.1| 147 LSLRVLDLISRKEALTLDDISRELGKSKPTVFRSVKLLRQLGLIT 191
                                       5799***************************************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 !   24.4   0.0   2.6e-08     2e-05      18      66 ..     155     205 ..     144     207 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 2.6e-08
                                       H.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES.STTTEEEE-- CS
                              TrmB  18 l.klgpatadeiaeelgvprskvYevLrsLedkGlVerek.grpklYravd 66 
                                       + +++ +t d+i++elg ++++v ++++ L + Gl++ ek gr+ lY+ ++
  gi|385805106|ref|YP_005841504.1| 155 IsRKEALTLDDISRELGKSKPTVFRSVKLLRQLGLITPEKrGRKDLYKLTP 205
                                       4478899*********************************44466999876 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.1   8.7e-08   6.5e-05       9      61 .]     145     197 ..     139     197 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 8.7e-08
                                       -HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                            HTH_20   9 hPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvregr 61 
                                       +   +r+l++++r+e+lt+ ++ ++l+ sk t+ + ++ L++ gL++ ++ gr
  gi|385805106|ref|YP_005841504.1| 145 SSLSLRVLDLISRKEALTLDDISRELGKSKPTVFRSVKLLRQLGLITPEKRGR 197
                                       66789*******************************************99987 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   2.7e-07    0.0002       5      59 ..     152     205 ..     149     206 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.7e-07
                            HTH_29   5 llllaeGvs.tvsqiAkllglsrrtvyrwlkrfeegGlaalld.rrrsgrprn.rlse 59 
                                       l l+++ +  t  +i + lg s++tv+r +k+ ++ Gl   +   +r gr    +l++
  gi|385805106|ref|YP_005841504.1| 152 LDLISRKEAlTLDDISRELGKSKPTVFRSVKLLRQLGL---ITpEKR-GRKDLyKLTP 205
                                       55566665569**************************6...333444.4444445665 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.1   5.6e-07   0.00042       1      48 [.     144     191 ..     144     195 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 5.6e-07
                                       --HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR   1 ltltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlie 48 
                                       l+   +++L +++++++l++ ++ + lg sk+tv r ++ L + Gli+
  gi|385805106|ref|YP_005841504.1| 144 LSSLSLRVLDLISRKEALTLDDISRELGKSKPTVFRSVKLLRQLGLIT 191
                                       5667899***************************************97 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1   9.2e-07   0.00069      27      55 .]     162     190 ..     152     190 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 9.2e-07
                            HTH_36  27 sqetlakrlglsknTvsraikeLeqlGyi 55 
                                       + +++++ lg+sk Tv r +k+L+qlG+i
  gi|385805106|ref|YP_005841504.1| 162 TLDDISRELGKSKPTVFRSVKLLRQLGLI 190
                                       5799***********************98 PP

>> Dimerisation2  Dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.5e-06    0.0011      10      78 ..     138     205 ..     133     209 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.5e-06
                     Dimerisation2  10 laSkaLftAceLgvFdlLkeeeplsaeevaeelgasvkGterLldacvaLgLLerekkeekkalYsnte 78 
                                          k   ++ +L+v dl+  +e l+++++++elg s   + r ++ +  LgL + ek+ + k+lY+ t+
  gi|385805106|ref|YP_005841504.1| 138 ITVKPFLSSLSLRVLDLISRKEALTLDDISRELGKSKPTVFRSVKLLRQLGLITPEKRGR-KDLYKLTP 205
                                       5667788999********************************************775555.7****997 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   5.5e-06    0.0041       8      68 .]     151     207 ..     144     207 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 5.5e-06
                            HTH_27   8 vLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68 
                                       vL li  r +  +l d+++ l  ++ ++  s+k L   GL+   + e+ +r  +++lT+kG
  gi|385805106|ref|YP_005841504.1| 151 VLDLIS-RKEALTLDDISRELGKSKPTVFRSVKLLRQLGLI---TPEKRGRKDLYKLTPKG 207
                                       455666.999999****************************...44466899********9 PP

>> Cas_DxTHG  CRISPR-associated (Cas) DxTHG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   1.1   4.3e-06    0.0032      49     136 ..      29     116 ..       9     203 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.3e-06
                         Cas_DxTHG  49 villtdtladkeaeek.....eeaak.lkeeleelleiekvdveiipg.ggteee.lweifekllekleendeiilD 117
                                        i +       + +ek     +e+   +ke++e        +ve+      +++e + ei ++ll+   e+++ii+D
  gi|385805106|ref|YP_005841504.1|  29 FIAVIN----NDKNEKvlkalDEITTfIKEYVE-------RSVEVWEIdFSSPHEaFHEISKRLLDL--EESSIIID 92 
                                       333333....24444466666666666666664.......223333320344466688899999997..8899**** PP

                         Cas_DxTHG 118 iThGfrylPvla.....llalayl 136
                                       +++G+r + +++     +++  y 
  gi|385805106|ref|YP_005841504.1|  93 VSSGMRLIGIITlgaaiASVDPYR 116
                                       ********9999655554444444 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.97   7.3e+02      71     106 ..      27      62 ..      25      69 .. 0.83
   2 !   12.8   0.0    0.0001     0.076      43      80 ..     184     221 ..     176     228 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.97
                           DUF4364  71 elfenripksirekideylkenkeelkkesevkady 106
                                       +lf   i ++  ek+ ++l+e  + +k+ +e ++++
  gi|385805106|ref|YP_005841504.1|  27 DLFIAVINNDKNEKVLKALDEITTFIKEYVERSVEV 62 
                                       678888999999999999999999999988777765 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.0001
                           DUF4364  43 LvesglieeeekenktlykiTekGketlelfenripks 80 
                                       L + gli+ e++  k+lyk+T+kG  + + f n +p++
  gi|385805106|ref|YP_005841504.1| 184 LRQLGLITPEKRGRKDLYKLTPKGMVISRAFRNVLPSE 221
                                       66779******************************987 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.6e-05     0.019      29      70 .]     166     207 ..     157     207 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.6e-05
                              PaaX  29 llaelGiseslvRaalsRlakaGwlvrekegrrsfYrLsdkg 70 
                                       +  elG s  +v  ++  l + G++++ek gr+ +Y+L+ kg
  gi|385805106|ref|YP_005841504.1| 166 ISRELGKSKPTVFRSVKLLRQLGLITPEKRGRKDLYKLTPKG 207
                                       678999999***9*************************9775 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   4.3e-05     0.032      21      54 ..     160     195 ..     143     205 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.3e-05
                                       EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE..ET CS
                         HTH_Crp_2  21 pltqeelAsmlGltretvsrilseLkreglis..rg 54 
                                        lt +++++ lG +  tv r  + L++ gli+  ++
  gi|385805106|ref|YP_005841504.1| 160 ALTLDDISRELGKSKPTVFRSVKLLRQLGLITpeKR 195
                                       58999***************************7423 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0     5e-05     0.037      13      45 ..     154     188 ..     149     191 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5e-05
                            HTH_23  13 llae..GlsvreIAreLgvsrrTvyrwlkryreeG 45 
                                       l  +   l+  +I+reLg s+ Tv r +k  r+ G
  gi|385805106|ref|YP_005841504.1| 154 LISRkeALTLDDISRELGKSKPTVFRSVKLLRQLG 188
                                       55544478999***************999887766 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       4.4   3.2e+03      32      51 ..      77      96 ..      77     102 .. 0.79
   2 ?   14.4   0.2   3.7e-05     0.028       8      44 ..     154     189 ..     148     201 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 4.4
                            HTH_11 32 vrrdIkaLeelgvpIesepg 51
                                      + +++ +Lee+ + I+ ++g
  gi|385805106|ref|YP_005841504.1| 77 ISKRLLDLEESSIIIDVSSG 96
                                      56788899999999987766 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 3.7e-05
                            HTH_11   8 lLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44 
                                       l ++ ++ ++ +++++eL+ S+ tv r +k L+ lg+
  gi|385805106|ref|YP_005841504.1| 154 L-ISRKEALTLDDISRELGKSKPTVFRSVKLLRQLGL 189
                                       4.477888***************************94 PP

>> Cas_Cas02710  CRISPR-associated protein (Cas_Cas02710)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.4e-05     0.048      24      85 ..      42     103 ..      29     118 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.4e-05
                                       GGGHHHHHHHH-S-...EEEE.E--TT-HHHHHHHHHHHHHHS.TTS-EEEE-SSS-HHHHHH CS
                      Cas_Cas02710  24 ekkleevkealgkklkqevll.dedandllelykkikevlekaleeeevivDlTgGtkeMtag 85 
                                        k l+e+  ++++ ++ +v++ ++d +++ e++++i + l    ee ++i+D+++G +   ++
  gi|385805106|ref|YP_005841504.1|  42 LKALDEITTFIKEYVERSVEVwEIDFSSPHEAFHEISKRLLDL-EESSIIIDVSSGMRLIGII 103
                                       567788888888888887765378************9999998.9***********9865443 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00011     0.085      16      57 ..     154     195 ..     150     197 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00011
                                       HHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                    Fe_dep_repress  16 lseekkvvktkdlaerLnvspssVsemlkkLekdGyveyeky 57 
                                       l   k+  +  d++++L+ s+++V  ++k L++ G++  ek+
  gi|385805106|ref|YP_005841504.1| 154 LISRKEALTLDDISRELGKSKPTVFRSVKLLRQLGLITPEKR 195
                                       555566677789***********************9987765 PP

>> PaRep2b  PaRep2b protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   8.5e-05     0.063      44      75 ..      35      66 ..      17      93 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.5e-05
                           PaRep2b 44 dvrnesffkkleeivtmvedyvyrnvavergl 75
                                      + +ne++ k l+ei t++ +yv+r v+v ++ 
  gi|385805106|ref|YP_005841504.1| 35 NDKNEKVLKALDEITTFIKEYVERSVEVWEID 66
                                      5689********************77775544 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00021      0.16      17      42 ..     157     182 ..     146     182 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00021
                            HTH_38  17 laeGlslreIArrLgrspsTIsRElk 42 
                                       ++e l+l +I r+Lg+s+ T+ R +k
  gi|385805106|ref|YP_005841504.1| 157 RKEALTLDDISRELGKSKPTVFRSVK 182
                                       678899***************99876 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 ?    7.8   0.1    0.0037       2.8       6      45 ..     152     191 ..     150     193 .. 0.90
   2 ?    2.1   0.0      0.22   1.6e+02      32      46 ..     197     212 ..     197     214 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0037
                          HTH_DeoR   6 lellkqqgklsveelvellgvSeaTiRRDLneLeeqgllt 45 
                                       l+l+ ++  l++++++ +lg S+ T+ R  + L + gl+t
  gi|385805106|ref|YP_005841504.1| 152 LDLISRKEALTLDDISRELGKSKPTVFRSVKLLRQLGLIT 191
                                       899***********************99888888888875 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.22
                          HTH_DeoR  32 RRDLneLeeqgl.ltR 46 
                                       R+DL +L+ +g+ + R
  gi|385805106|ref|YP_005841504.1| 197 RKDLYKLTPKGMvISR 212
                                       9**********95555 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00025      0.19      17      67 ..     152     203 ..     144     212 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00025
                                       HHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE.EETTT-TCEEE CS
                              Rrf2  17 LakeeeeepvsseeiaerqnispsylekilakLrkaglvk.svrGkgGGyrL 67 
                                       L + +++e +++++i+++ + s++ + + ++ Lr+ gl++  +rG++  y+L
  gi|385805106|ref|YP_005841504.1| 152 LDLISRKEALTLDDISRELGKSKPTVFRSVKLLRQLGLITpEKRGRKDLYKL 203
                                       4444455569*****************************8346788766666 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00036      0.27       2      63 ..     145     202 ..     144     220 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00036
                                       --S-SHHHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE CS
                   Penicillinase_R   2 gelEaevmeilwekgeatvkevveeleeekelaysTVktllrrLvkKgllsrekegrafiYs 63 
                                       ++l + v++++ +k+ +t +++  el +     + TV   ++ L + gl++ ek gr+ +Y 
  gi|385805106|ref|YP_005841504.1| 145 SSLSLRVLDLISRKEALTLDDISRELGKS----KPTVFRSVKLLRQLGLITPEKRGRKDLYK 202
                                       677889*********************99....99999999*****************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); 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: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1433.66
//
Query:       gi|385805107|ref|YP_005841505.1|  [L=261]
Description: hypothetical protein FFONT_0059 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.16   12.1   0.0        0.3   11.2   0.0    1.4  1  WW        WW domain
       0.26   11.5   2.9        2.3    8.4   0.1    2.9  3  DUF2666   Protein of unknown function (DUF2666)


Domain annotation for each model (and alignments):
>> WW  WW domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.4e-05       0.3      14      25 ..      60      71 ..      55      72 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.4e-05
                                      T-EEEEETTT-- CS
                                WW 14 GrvYYyNheTge 25
                                      G+++Y+N+eT+e
  gi|385805107|ref|YP_005841505.1| 60 GKIFYHNPETKE 71
                                      9**********9 PP

>> DUF2666  Protein of unknown function (DUF2666)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1     0.026   2.3e+02      67      94 ..       6      33 ..       3      63 .. 0.73
   2 ?   -1.3   0.0      0.26   2.3e+03     100     124 ..      77     101 ..      59     108 .. 0.75
   3 ?    8.4   0.1   0.00025       2.3      65     121 ..     173     228 ..     141     242 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.026
                                      -S....HHHHHHHHHHHHT-........ CS
                           DUF2666 67 kkgrvkeedisevleklkspattkklnk 94
                                      +kg++ +e i++++  +++    +k ++
  gi|385805107|ref|YP_005841505.1|  6 RKGQMLDEHIKKMIDFYEKCYKRRKYTA 33
                                      7999999*****9999998877777654 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.26
                                       ---HHHHHHHHHHHHHTTT--SS-- CS
                           DUF2666 100 egkeilkvilarivLerlGiktkve 124
                                        g+eil  ++ +i+ ++l +k +++
  gi|385805107|ref|YP_005841505.1|  77 AGHEILSSLVMHIASKKLELKKNMK 101
                                       5778888888888888888877665 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.00025
                                       S--S....HHHHHHHHHHHHT-..............---HHHHHHHHHHHHHTTT--S CS
                           DUF2666  65 kkkkgrvkeedisevleklkspattkkln.kitdskegkeilkvilarivLerlGikt 121
                                       + +  +v++e+++ ++e +k++ t + l+ +i + +e k+  + ++a+ +L+ l +  
  gi|385805107|ref|YP_005841505.1| 173 EMRE-KVEDEELKGLIETYKEF-TERYLAwNIFEMHEPKAAKVSMMAQHILKVLIMSD 228
                                       4444.8****************.5555643899******9999999999998776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       789  (0.0440069); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); 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: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1501.71
//
Query:       gi|385805108|ref|YP_005841506.1|  [L=552]
Description: ATP-dependent RNA helicase related protein [Fervidicoccus fontis Kam940]
Scores for complete 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   39.4   0.0    1.7e-09   38.0   0.0    1.8  1  Helicase_C  Helicase conserved C-terminal domain
    5.9e-08   32.9   0.0    5.5e-07   29.8   0.0    2.2  2  ResIII      Type III restriction enzyme, res subunit
    3.2e-07   30.3   0.0    7.7e-06   25.8   0.0    2.5  2  DEAD        DEAD/DEAH box 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 !   38.0   0.0   2.9e-13   1.7e-09       9     109 ..     253     355 ..     245     357 .. 0.81

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 2.9e-13
                                       H.HHHTTTTSEEEEEESSHHHHHH..HHHHHHHTTSTEEEESTTSTHHHHH....HHHHHHHTTSSSEEEESGGGTS CS
                        Helicase_C   9 l.lkleeeggkilifvntidrlek..vklllekkgikvavlhgelpqnere....eileqfnkgesdvLiatdvaer 78 
                                       l +k+++eg+++li++nt++++ k   kll  + g + + lhg l++n+re    e l+ +++ges + +at+v+e 
  gi|385805108|ref|YP_005841506.1| 253 LaIKRKREGKRVLIILNTRETVLKaqRKLL--ELGERPILLHGLLSKNDREertsELLDMYKRGESYIALATSVVEA 327
                                       324999**************7755644444..5578888************77777888888*************** PP

                                       SSTSTTESEEEESSSSSSHHHHHHHHTTSSS CS
                        Helicase_C  79 GidipkvnlVinfdlprnvtsyiqriGRtgR 109
                                       Gidi +  +V  +++     s+iqr+GR  R
  gi|385805108|ref|YP_005841506.1| 328 GIDISSDFMVAELSPL---PSLIQRAGRLLR 355
                                       ****877666666665...679******998 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0   9.2e-11   5.5e-07      27     169 ..      20     179 ..       4     181 .. 0.78
   2 ?    0.3   0.0       0.1     6e+02      85     135 ..     219     264 ..     190     311 .. 0.62

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 9.2e-11
                                       EEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--....... CS
                            ResIII  27 glikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseaykeigkkvsgdkkka.kekdst 102
                                       g++ ++TG GKT + ++++e   + g++e+++ + p ++l e +++++++  ++ +++   ++  +++++ +e+   
  gi|385805108|ref|YP_005841506.1|  20 GVLRLPTGYGKTELFLQFAEMTCN-GNIERAVYVSPLRTLNEDLYRKLAERVPCLREN--SDILAREYMErRESPFF 93 
                                       6799**************999988.7889************************99854..33333333333555579 PP

                                       .-SEEEEEHHHHHHTH........................HHHTTT-S...............EEEEETGGGTTS.T CS
                            ResIII 103 nkkilvttiqsldadseee................eeeseellrdrfd...............viiiDEaHrlgakk 148
                                       +kk++vtti+++  ++++                                             +++iDE H +  +k
  gi|385805108|ref|YP_005841506.1|  94 HKKVIVTTIDTIGMHLHKIpipelkallrgffkkdF-----------StrghypvsrsnvsesLVFIDEPHLMVLEK 159
                                       9***************66698877666666555551...........1444444555556678**********9999 PP

                                       TTHHHHHT---SEEEEEESS- CS
                            ResIII 149 swreilekfkeavllglTATp 169
                                        +++ + ++  ++llg  AT 
  gi|385805108|ref|YP_005841506.1| 160 GMKQ-MFYNTLYYLLGTGATV 179
                                       9999.4555778999988885 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.1
                                       GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SE CS
                            ResIII  85 igkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdv 135
                                       ++++ +g+ +++ e+++  k++ ++  +sld +++       + +r+ + v
  gi|385805108|ref|YP_005841506.1| 219 KCGEADGRDEDF-EEKALAKRVSISMSESLDDSLS----LAIKRKREGKRV 264
                                       666666666666.6667777777777777776662....222222222222 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   1.3e-09   7.7e-06      19     171 ..      22     189 ..      15     194 .. 0.72
   2 ?    1.3   0.0     0.041   2.5e+02      43      93 ..     257     306 ..     234     325 .. 0.71

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 1.3e-09
                                       EEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSH.HHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                              DEAD  19 vaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaa.rdqlskl 94 
                                       ++ +TG+GKT+ fl  +  +     + +  +a++v+P+r L e+ +++l ++     lr+++ i   ++ ++  s +
  gi|385805108|ref|YP_005841506.1|  22 LRLPTGYGKTELFLQFAEMTC----NGNIERAVYVSPLRTLNEDLYRKLAERVPC--LRENSDILAREYmERRESPF 92 
                                       5689*********99888666....45666***********************96..78885555444414444444 PP

                                       HTTCSEEEEEHHHHHHHH.....................HCTS..SHCTTE..EEEEEETHHHHHHT.TTHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxx.....................xxxx..xxxxxx..xxxxxxxxxxxxxx.xxxxxxxxx RF
                              DEAD  95 dngvdivvgtpgrlddll.....................stgk..lnlsqv..rflVlDEadrlldq.gfsdfinri 145
                                         + +++v+t + +  +l                     ++g+  ++ s+v  +++ +DE + +  + g+++   + 
  gi|385805108|ref|YP_005841506.1|  93 -FHKKVIVTTIDTIGMHLhkipipelkallrgffkkdfsTRGHypVSRSNVseSLVFIDEPHLMVLEkGMKQMFYNT 168
                                       .678888888877777666778888888888888888864555333356666567889****987664666655555 PP

                                       HHHSHHHCTTST.TTSEEEEEESSBS.H CS
                                       xxxxxxxxxxxx.xxxxxxxxxxxxx.x RF
                              DEAD 146 lnqlpqitcdgk.lqrqvivlSATlp.k 171
                                       l  l      g  +  +v++ SAT+p +
  gi|385805108|ref|YP_005841506.1| 169 LYYL-----LGTgA--TVVLASATIPgS 189
                                       5555.....23323..49999**99855 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.041
                                       TTSTS-EEEEEESSHHHHHHHHHHHHHHTTT.STSEEEEEETTSSHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                              DEAD  43 kgktgpkalivePtreLaeqtlnnlkkfkky.idlrvlliiggvaardqlsk 93 
                                       ++++g+++li+  tre + +  ++l ++++  i   ++ +++++++++  s+
  gi|385805108|ref|YP_005841506.1| 257 RKREGKRVLIILNTRETVLKAQRKLLELGERpI--LLHGLLSKNDREERTSE 306
                                       688999**********99999999999999533..23333444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (552 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 3438.92
//
Query:       gi|385805109|ref|YP_005841507.1|  [L=404]
Description: hypothetical protein FFONT_0061 [Fervidicoccus fontis Kam940]
Scores for complete 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   18.1   0.0     0.0019   17.5   0.0    1.2  1  Cas_Csx9  CRISPR-associated protein (Cas_Csx9)


Domain annotation for each model (and alignments):
>> Cas_Csx9  CRISPR-associated protein (Cas_Csx9)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.1e-07    0.0019      52     164 ..     103     211 ..      73     223 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.1e-07
                          Cas_Csx9  52 kawfgrsapetygelfelvvtet.ikllrdgnidpgeslstiktdkngtylgiayngeqailpaiikqpeyyerqsg 127
                                       k  f  s  +t   +f+ vv    + + r gni     l +i+   +  ylg     + a l   + + e ye    
  gi|385805109|ref|YP_005841507.1| 103 KLGFSISDDDTICSFFKKVVDSMpMYISRIGNIALETELKSINLSGDTLYLGGDMA-DFAQLQ--VLKLEKYEYGRN 176
                                       3445667789999***999976427889***********************96554.445554..345688999999 PP

                          Cas_Csx9 128 flspttgqkaqirmdplwfsfmalgfftsfagfiggk 164
                                       +ls     k ++++ plw+ ++  g+++sf+g+ g  
  gi|385805109|ref|YP_005841507.1| 177 YLSLK--FKGDMKISPLWYGILGGGWLASFSGYFGDT 211
                                       99965..69999*********************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); 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: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2604.94
//
Query:       gi|385805110|ref|YP_005841508.1|  [L=243]
Description: hypothetical protein FFONT_0062 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1473.97
//
Query:       gi|385805111|ref|YP_005841509.1|  [L=369]
Description: DevR family CRISPR-associated autoregulator [Fervidicoccus fontis Kam940]
Scores for complete 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-65  218.9   2.2      1e-64  218.2   2.2    1.4  1  DevR      CRISPR-associated negative auto-regulator DevR/Csa2
  ------ inclusion threshold ------
       0.14   12.4   1.1        0.3   11.3   1.1    1.5  1  E7        E7 protein, Early protein


Domain annotation for each model (and alignments):
>> DevR  CRISPR-associated negative auto-regulator DevR/Csa2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.2   2.2   1.2e-68     1e-64       1     268 [.       6     311 ..       6     312 .. 0.91

  Alignments for each domain:
  == domain 1  score: 218.2 bits;  conditional E-value: 1.2e-68
                                       EEEEEE-------------------EEEEEE--T..T--EEEEEE-THHHHHHHHHHHHHHHHTS..TTSSBH.HHH CS
                              DevR   1 isgrvvvnveaLNmdesvGNytehrkvpvvlkee..ykvrtvpaiSgeslkHayfetlvklaken..nlpvce.lck 72 
                                       isgrv++n+eaLNm e++GN+ +hr+vp+++k++  y+v +vpaiSgesl Ha++ +lv+ ak    + +++    +
  gi|385805111|ref|YP_005841509.1|   6 ISGRVIANAEALNMTETIGNVSKHRRVPYIMKTSegYRVIYVPAISGESLGHAFQSNLVEAAKLIyeKEKINPpPID 82 
                                       79******************************99*************************998754323333321356 PP

                                       TT------TT--EEEBTTS.....................EESS-HHHHHHH-HHHHHH-EEEGGGT..EEE--SEE CS
                              DevR  73 rvegdggvikfatekklke.....................kelkvekeiikecvveDvfGfLitekeksvkRkspvk 128
                                       +  + +++ikf+++k+ ++                      + ++e+ +ike+ v+D++Gf+++e+  +++R+s ++
  gi|385805111|ref|YP_005841509.1|  83 QWAMRNEMIKFSDKKHITDslkeileqaksnkgskktvedFQHEFERVAIKESLVADIGGFMLAEEL-PIRRTSLFY 158
                                       77788*******99999999*****************9988999*******************9666.5******** PP

                                       E--BEE-TTTTTTT.-----------............------------------HHHHHSSEEEEEEEEEGGGTT CS
                              DevR 129 fsyavpveesekav.vdaqfharydl............lenrarkkgeeeekqnifqvEehsalYalsfvlDldriG 192
                                       ++ya p+e+++ ++ ++aq+h+r                +++++k++++ ++q+i++vE++s++Y++sf+lD+++iG
  gi|385805111|ref|YP_005841509.1| 159 VGYATPIEDAVAESvIEAQMHTRQIAskeeieekteeeIKEKTEKEERKRKSQMIYYVEVASTVYGISFFLDVSNIG 235
                                       ***********9989********877799****998874444555556899************************** PP

                                       S-TTS--EE---S-HHHHHHHHHHHHHTHHHHHH--.------------EEEEEEEE--S.SS------TTTTHHHH CS
                              DevR 193 kpevkkskieyvleeeerkkRikaalkallnlLsgs.fgakrarllPvfeveslvaavsk.kpfpvfpirledyvee 267
                                       k+++   ++e v+++ e+ +R+k+al al +++  + fgakr+r++P++ veslv +vs  +p+   p++++ y+ee
  gi|385805111|ref|YP_005841509.1| 236 KTSM--IRKEDVVDNAEKLRRVKTALLALSLTFGAQqFGAKRSRFNPILSVESLVGVVSHpVPIAPVPPQKKRYIEE 310
                                       ****..9***************************999*****************99999988888888********9 PP

                                       H CS
                              DevR 268 e 268
                                       +
  gi|385805111|ref|YP_005841509.1| 311 T 311
                                       7 PP

>> E7  E7 protein, Early protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.1   3.4e-05       0.3       5      56 ..     168     219 ..     165     232 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.4e-05
                                       XXXXXXXXXXXXXX--S------XXXXXXXXXXXXXXXXXXXXEE.EEEEEE CS
                                E7   5 tlkdlvLeeqpevldllceeelesedeeeeeedeptlkdktprrpgYaveva 56 
                                       ++++ v+e q ++ ++ ++ee e+++eee +e++++++ k++ +  Y veva
  gi|385805111|ref|YP_005841509.1| 168 AVAESVIEAQMHTRQIASKEEIEEKTEEEIKEKTEKEERKRKSQMIYYVEVA 219
                                       578889999999999*********9999988887777888888888999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2142  (0.119471); expected 358.6 (0.02)
Passed bias filter:                      829  (0.0462379); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.32s 00:00:00.95 Elapsed: 00:00:00.47
# Mc/sec: 2382.12
//
Query:       gi|385805112|ref|YP_005841510.1|  [L=110]
Description: hypothetical protein FFONT_0064 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.15   12.0   1.8        6.7    6.7   0.3    2.8  3  RHH_4     Ribbon-helix-helix domain


Domain annotation for each model (and alignments):
>> RHH_4  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.3   0.00037       6.7      16      33 ..       4      21 ..       3      26 .. 0.86
   2 ?    0.2   0.0      0.04   7.2e+02      17      33 ..      24      40 ..      21      45 .. 0.85
   3 ?    2.9   0.1    0.0055        99      20      32 ..      47      59 ..      43      64 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.00037
                                      EEEHHHHHHHHHHHHHTT CS
                             RHH_4 16 rLEpafWdaLeeiArreg 33
                                      +LEp+ W aL+++A++ +
  gi|385805112|ref|YP_005841510.1|  4 KLEPSEWWALRRVATALN 21
                                      69************8765 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.04
                                      EEHHHHHHHHHHHHHTT CS
                             RHH_4 17 LEpafWdaLeeiArreg 33
                                      +E++ +++++ iA +++
  gi|385805112|ref|YP_005841510.1| 24 IENKAYNTIDVIADSQK 40
                                      69999********9986 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.0055
                                      HHHHHHHHHHHHT CS
                             RHH_4 20 afWdaLeeiArre 32
                                      + W+aL+ iA+++
  gi|385805112|ref|YP_005841510.1| 47 SLWRALRMIASED 59
                                      57********986 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:                      254  (0.014167); 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 0.25s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 749.13
//
Query:       gi|385805113|ref|YP_005841511.1|  [L=79]
Description: hypothetical protein FFONT_0065 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       252  (0.0140554); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); 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: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 539.65
//
Query:       gi|385805114|ref|YP_005841512.1|  [L=299]
Description: CRISPR-associated protein, Csa1 family [Fervidicoccus fontis Kam940]
Scores for complete 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-58  198.6   0.0    1.8e-58  198.2   0.0    1.0  1  Csa1      CRISPR-associated exonuclease Csa1
      3e-05   24.1   0.0    4.2e-05   23.6   0.0    1.2  1  PDDEXK_1  PD-(D/E)XK nuclease superfamily


Domain annotation for each model (and alignments):
>> Csa1  CRISPR-associated exonuclease Csa1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.2   0.0     2e-62   1.8e-58       2     291 ..       3     295 ..       2     297 .. 0.87

  Alignments for each domain:
  == domain 1  score: 198.2 bits;  conditional E-value: 2e-62
                              Csa1   2 fstleevrlL.krlkklsaskeveeElRGWnwnePPvkprslvklslsdvvsgyCetkRdvYLkrvlgvrge..eek 75 
                                        + ++ v+   krl  l+++++v+e+lRGW +++ Pv+pr++ +l +s+v+++yCet Rd++++r + vrge  e+ 
  gi|385805114|ref|YP_005841512.1|   3 QMLFSLVKDVpKRLYWLRSNDPVPEDLRGWSYHTYPVRPRAYFGLGVSEVAYKYCETFRDLWMRRKEYVRGEvlESS 79 
                                       566677888889999999*****************************************************944578 PP

                              Csa1  76 klllGaaiHeavakaleelkkliysgekldsslerllvadeiv.alledvie.kakelykylasrvsaelsevrskf 150
                                       +l +G++iH  +  a++++ ++++ +  +   le + +a+e+  +  +++++ + ++ ++++++ v++ +s++  + 
  gi|385805114|ref|YP_005841512.1|  80 PLYMGKLIHSLMNYAFRDASEIVSRNLGP---LESIRRAQELSrKRASELTKsYYRKAMEFYMTMVLSAISTLWIQ- 152
                                       9******************9996555444...44445666777433344444477777888899999999997776. PP

                              Csa1 151 ekatedsvaarviPvlvefkvdGsllGlsslvrvDafililplvvelkvgs....ykeehelalaGYalalEsqlei 223
                                       +++t+d ++   i + +ef +dG ++Gls+++rvDa     ++++e k g+     +e+h + laGYala+Es l+i
  gi|385805114|ref|YP_005841512.1| 153 QSLTNDPLSY--ISIKTEFVIDGTPVGLSNTLRVDA-YHEGGVIIEYKLGNpdplLTERHSVGLAGYALAIESSLDI 226
                                       8889999888..999*********************.45667********85555689******************* PP

                              Csa1 224 PvDfGvlisv.tvngevklkaelvaisdslRkefleeRdraidivekesDPGlakkCsskClflevCkg 291
                                       P+D+G+++++  +     +k+ +v+is   Rk+fle+Rd+ai+++ + + P  + +C + C+f + C+g
  gi|385805114|ref|YP_005841512.1| 227 PIDYGAIVYIsELSRRPSIKVFPVYISSLYRKKFLENRDEAIEVLMRATPPPRSGNCYQYCPFFKACNG 295
                                       **********8888888**************************************************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 !   23.6   0.0   4.6e-09   4.2e-05      32     255 .]      78     294 ..      56     294 .. 0.60

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 4.6e-09
                          PDDEXK_1  32 eap.dlGtlvHaaleefye......wkkldkedleelleeaveelwpellleeeilessarlrylaeklkevleklv 101
                                       ++p  +G l+H++++  ++       ++l + +  + ++e+ ++ ++e       l++s   + +   +  vl++  
  gi|385805114|ref|YP_005841512.1|  78 SSPlYMGKLIHSLMNYAFRdaseivSRNLGPLESIRRAQELSRKRASE-------LTKSYYRKAMEFYMTMVLSAIS 147
                                       344489*********888866555533333333333332222333333.......2222333444444455555554 PP

                          PDDEXK_1 102 erlaeeleakrgfrpvalelefg..gekvrLkGriDrvd.dkegelriiDyKtgsappkskelaelkeglQlllYll 175
                                         + ++   ++++++++++ ef   g+ v L   + rvd  +eg  +ii+yK g++   ++     ++++ l+ Y+l
  gi|385805114|ref|YP_005841512.1| 148 TLWIQQSLTNDPLSYISIKTEFVidGTPVGLSNTL-RVDaYHEG-GVIIEYKLGNPD--PLL--TERHSVGLAGYAL 218
                                       45666555566667777776666656888888777.99974444.6*******9933..222..458888******* PP

                          PDDEXK_1 176 alaegeelkeegepagalylrl.ee.pkvkdeevvkkmalteeeleallqeleelaeeilagefparpskkC.eyCp 249
                                       a++    l  + + + ++y++   + p++k  +v+ +  l ++++ + ++e+ e++ ++     p+  s +C +yCp
  gi|385805114|ref|YP_005841512.1| 219 AIESS--LDIPIDYGAIVYISElSRrPSIKVFPVYISS-LYRKKFLENRDEAIEVLMRAT----PPPRSGNCyQYCP 288
                                       ****9..5555556666666652334666666666555.556666555555555533333....4555556****** PP

                          PDDEXK_1 250 yksvCr 255
                                       + + C+
  gi|385805114|ref|YP_005841512.1| 289 FFKACN 294
                                       **9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2071.93
//
Query:       gi|385805115|ref|YP_005841513.1|  [L=327]
Description: CRISPR-associated protein Cas1 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-55  188.9   0.0    1.4e-55  188.5   0.0    1.2  1  Cas_Cas1  CRISPR associated protein Cas1
  ------ inclusion threshold ------
        3.5    7.6   5.6        9.8    6.1   5.6    1.8  1  RF-1      RF-1 domain


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 !  188.5   0.0   1.5e-59   1.4e-55       1     276 [.       4     275 ..       4     282 .. 0.92

  Alignments for each domain:
  == domain 1  score: 188.5 bits;  conditional E-value: 1.5e-59
                                       EEEESTEEEEEEETTEEEEEESSEEEEEEECCCEEEEEEEST.EEEEHHHHHHHHHTT-EEEEE-TTS-EEEEEEES CS
                          Cas_Cas1   1 lyvteqgaylrkkgerlvvekegeekkeiplediesivifge.vslstkalrllaekgipvvflsengkylgrlepe 76 
                                       l++t +g++l+++g+ +++e++++ + ++   diesivi ++ vs++++a++l++  gip+ ++  +g+++      
  gi|385805115|ref|YP_005841513.1|   4 LVITGYGKRLSVEGKVFKIEDRNKSSSKVNPADIESIVIESSgVSITSAAIELASMAGIPIFIIRGRGSPTVISPIY 80 
                                       789**************************************99***************************988777* PP

                                       SSSTHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHCCHHCTTHHHHCHCHHHHHHHHHHHH-....HSHH CS
                          Cas_Cas1  77 esgnvelrraQyraaddeekrlelakkivagklenqrkvlrrlkrdreeeeleeaieeleellekleka....esle 149
                                       + +++e+rr+Qy a + ++ ++ lak++v++k++nq++ lr+l+r+ ++e++++++e+l+e  ++++++    +  +
  gi|385805115|ref|YP_005841513.1|  81 SVKTAETRRKQYSATTGKS-GCTLAKSLVRSKISNQAECLRNLNRYFNDEDVRKEVEKLRENSKRAQELqcseNWSS 156
                                       **************98877.***************************99**************9999999999999* PP

                                       HHHHHHHHHHHHHHHHHHHHCSCGGS-SS-SSSS-SSHHHHHHHHHHHHHHHHHHHHHHTSS--TT--SSS--TTSS CS
                          Cas_Cas1 150 eLrgiEGeaakaYfeafdkllkeefefegRsrrppkDpvNalLsfgYtllysevlsaieavgLdPyiGfLHedrpgr 226
                                       +Lr+iE +aa+aY++ ++ +l+e++ f+gR      D +N+ L+++Y+llyse+++++  +gLdPy G++H d+ gr
  gi|385805115|ref|YP_005841513.1| 157 QLRQIESSAARAYWGSLAVFLPESIGFDGRDVDS-GDAFNCSLNYIYALLYSECFKKLSIAGLDPYGGIYHVDKAGR 232
                                       ******************************9998.9***************************************** PP

                                       -HHHHHHHHHHHHHHCHHHHHHHHHTTSS-GGGEEEETTEEEE-HHHHHH CS
                          Cas_Cas1 227 psLalDLmEefRpllvDrlvlslinkrqlkekdFekeengvlLteegrkk 276
                                        sL++D+ ++ +p + D    sl ++rql     + + +  +L+e++rk+
  gi|385805115|ref|YP_005841513.1| 233 MSLVYDFSDPVKP-FLDY---SLTKERQLL---LNIKVSDGVLDEDARKN 275
                                       *************.5564...455555555...44445555555555555 PP

>> RF-1  RF-1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   5.6    0.0011       9.8      41     102 ..      81     159 ..      26     168 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0011
                                       T..................TEEEEEEECSSSHHHHHHHHHHHHHHHHHHHHHHHCCC..CCHTTTTT-.S.-S---S CS
                              RF-1  41 t..................gvivvecqeeRsqekNrekAlerLkaklkekeleeeke..eekkrrvkkekkkigtgs 97 
                                       +                  g  + + +  Rs+++N++++l+ L+   +++++++e e  +e+++r+++   +  +++
  gi|385805115|ref|YP_005841513.1|  81 SvktaetrrkqysattgksG-CTLAKSLVRSKISNQAECLRNLNRYFNDEDVRKEVEklRENSKRAQE--LQC-SEN 153
                                       05555555555555555546.47778889******************884444444300444444344..222.222 PP

                                       .--ECE CS
                              RF-1  98 .sekiR 102
                                        s++ R
  gi|385805115|ref|YP_005841513.1| 154 wSSQLR 159
                                       233444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       988  (0.0551063); expected 358.6 (0.02)
Passed bias filter:                      673  (0.037537); 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: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 2037.79
//
Query:       gi|385805116|ref|YP_005841514.1|  [L=96]
Description: CRISPR-associated protein Cas2 [Fervidicoccus fontis Kam940]
Scores for complete 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   59.1   0.3      4e-16   58.9   0.3    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 !   58.9   0.3   2.3e-20     4e-16       2      75 ..       3      75 ..       1      76 [. 0.97

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 2.3e-20
                                      EEEEEEECHCHHHHHHHHHHHHHHTTEEEEETTEEEEEESHHHHHHHHHHHHHHSHTTTCEEEEEEEETCHHHT CS
                       CRISPR_Cas2  2 lvlvvYDikedrkrrrkvakilkkyGfqrvQySVFegelseaqleklkkrlkkiidpeedsiriykltekqfek 75
                                      ++++vYDi  d+ +r++v +il+k G+ r+Q S F+g ++e ++++++++++  id e+d + i+++++k +++
  gi|385805116|ref|YP_005841514.1|  3 FYIIVYDI-GDQGKRQRVVEILEKWGLRRIQRSAFVGYVQEGRAKDIAREIEMTIDLEKDVVHIVQIERKEWNR 75
                                      79******.*************************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.32s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 573.66
//
Query:       gi|385805117|ref|YP_005841515.1|  [L=193]
Description: hypothetical protein FFONT_0069 [Fervidicoccus fontis Kam940]
Scores for 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-09   35.6   0.0    5.2e-08   33.2   0.0    1.9  1  Cas_Cas4  Domain of unknown function DUF83
    1.7e-06   28.1   0.0    2.2e-06   27.8   0.0    1.2  1  PDDEXK_1  PD-(D/E)XK nuclease superfamily
  ------ inclusion threshold ------
       0.17   12.0   0.0       0.24   11.5   0.0    1.2  1  XisH      XisH protein


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 !   33.2   0.0   8.7e-12   5.2e-08       3     161 ..      11     184 ..       9     185 .. 0.68

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 8.7e-12
                          Cas_Cas4   3 tkiqyyliCkrklwlish.eitleensetvelGkllhe...........esyerekkevelse.........sikiD 58 
                                       + i+ + +C+r +w+  +  i+     +++      h                   + +++++          ++ D
  gi|385805117|ref|YP_005841515.1|  11 SLIRNLPYCERMVWFKLNsDIEEPPTPSMIL-SSERHRdlkriaeslmlP------QPMQFNKklchpqipvCGSPD 80 
                                       6677777888888877663444333333332.222222222222233330......33333113444444558999* PP

                          Cas_Cas4  59 vvekekeklvvvEvKkskkk...eeaaklQllyYlllLe.kkgveikeGvleypkekkreevelteelreelekaik 131
                                       +++  +e+ ++vE+K+ ++     ++ ++Qll Y +l++  +g   k   + ++  +   e e++ el+ ++++ ++
  gi|385805117|ref|YP_005841515.1|  81 IIS-GEERKIIVEYKHFSRErgdFQDFRAQLLTYGWLVQeVEGRVWK--LVLMVGREVVWEQEYSYELHISARHLVE 154
                                       ***.99999*******999833234559***********66666666..44444445555689************** PP

                          Cas_Cas4 132 eieeiissekppkvkkkkiCkkCayaelCl 161
                                       ++ +i++s +pp++++  +C+ C ++++C 
  gi|385805117|ref|YP_005841515.1| 155 RLLKILDSPTPPSASYGGKCSYCFFKSVCS 184
                                       *****************************5 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 !   27.8   0.0   3.7e-10   2.2e-06     115     254 ..      60     183 ..      14     184 .. 0.66

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 3.7e-10
                          PDDEXK_1 115 rpvalelefg....gekvrLkGriDrvd.dkegelriiDyKtgsappkskelaelkeglQlllYllalaegeelkee 186
                                       +p+++    +      ++ + G  D +  ++     i++yK  s++  +++      + Qll+Y ++++e       
  gi|385805117|ref|YP_005841515.1|  60 QPMQF----NkklcHPQIPVCGSPDIISgEER--KIIVEYKHFSRERGDFQ----DFRAQLLTYGWLVQEV------ 120
                                       33444....144445678899999*9974444..69*****8775555555....3345************...... PP

                          PDDEXK_1 187 gepagalylrleepkvkdeevvkkmalteeeleallqeleelaeeilagefparpskk..CeyCpyksvC 254
                                         ++++  l l   +v+ e v+++    + el+  +++l e++ +il+   p++ s    C+yC +ksvC
  gi|385805117|ref|YP_005841515.1| 121 --EGRVWKLVL---MVGREVVWEQE--YSYELHISARHLVERLLKILDSPTPPSASYGgkCSYCFFKSVC 183
                                       ..444444444...33455555555..667777888899999999997777777765589********** PP

>> XisH  XisH protein
   #    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      51     102 ..      85     135 ..      78     160 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4e-05
                              XisH  51 eeekiavEiksFlgksaisdfeealGqyllYrllLeeeepe.relyLAvseei 102
                                       ee+ki+vE k F ++    df++   q l+Y +l++e+e   ++l L v +e+
  gi|385805117|ref|YP_005841515.1|  85 EERKIIVEYKHFSRER--GDFQDFRAQLLTYGWLVQEVEGRvWKLVLMVGREV 135
                                       689*********8754..57888888**********99865479999987664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.52
# Mc/sec: 1108.65
//
Query:       gi|385805118|ref|YP_005841516.1|  [L=62]
Description: hypothetical protein FFONT_0070 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.9e-05   23.2   0.0      7e-05   22.7   0.0    1.3  1  HTH_36         Helix-turn-helix domain
     0.0017   18.3   0.0     0.0023   17.8   0.0    1.3  1  HTH_11         HTH domain
      0.002   17.5   0.0     0.0031   16.9   0.0    1.4  1  HTH_Tnp_ISL3   Helix-turn-helix domain of transposase family 
     0.0027   17.8   0.1     0.0047   17.0   0.0    1.6  2  Mrr_N          Mrr N-terminal domain
     0.0054   16.4   0.2      0.052   13.2   0.0    2.0  2  Sigma70_r4_2   Sigma-70, region 4
      0.006   16.2   0.0      0.006   16.2   0.0    1.2  1  HrcA_DNA-bdg   Winged helix-turn-helix transcription represso
     0.0071   16.2   0.0      0.011   15.7   0.0    1.3  1  TrmB           Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.011   15.7   0.0      0.017   15.1   0.0    1.3  1  HTH_Mga        M protein trans-acting positive regulator (MGA
      0.013   15.3   0.0       0.02   14.8   0.0    1.3  1  HTH_5          Bacterial regulatory protein, arsR family
      0.014   15.9   0.0      0.018   15.5   0.0    1.3  1  HTH_27         Winged helix DNA-binding domain
      0.015   15.2   0.0      0.022   14.6   0.0    1.3  1  MarR_2         MarR family
      0.019   14.5   0.0      0.027   14.0   0.0    1.3  1  GerE           Bacterial regulatory proteins, luxR family
      0.022   14.5   0.0      0.022   14.5   0.0    1.1  1  DUF4423        Domain of unknown function (DUF4423)
      0.022   14.7   0.0      0.031   14.2   0.0    1.3  1  HTH_Crp_2      Crp-like helix-turn-helix domain
      0.024   14.7   0.1      0.042   13.9   0.1    1.6  1  HTH_29         Winged helix-turn helix
      0.026   14.4   0.0      0.049   13.5   0.0    1.5  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain
      0.028   14.5   0.0      0.031   14.4   0.0    1.2  1  DUF2250        Uncharacterized protein conserved in archaea (
       0.13   12.2   0.0        0.2   11.6   0.0    1.3  1  MarR           MarR family


Domain annotation for each model (and alignments):
>> HTH_36  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     7e-08     7e-05      27      55 .]       2      30 ..       1      30 [. 0.96

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 7e-08
                            HTH_36 27 sqetlakrlglsknTvsraikeLeqlGyi 55
                                      s++++ak++g+ ++Tv++ i  L +lG++
  gi|385805118|ref|YP_005841516.1|  2 SVKDIAKATGCGEKTVVNRISYLKKLGLV 30
                                      89*************************85 PP

>> HTH_11  HTH 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    0.0023      17      43 ..       2      28 ..       1      40 [. 0.90

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.3e-06
                            HTH_11 17 sgeeLAeeLnvSrrtvrrdIkaLeelg 43
                                      s +++A+ +++ ++tv+++I  L++lg
  gi|385805118|ref|YP_005841516.1|  2 SVKDIAKATGCGEKTVVNRISYLKKLG 28
                                      899***********************9 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   3.1e-06    0.0031      27      50 ..       1      23 [.       1      25 [. 0.91

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.1e-06
                      HTH_Tnp_ISL3 27 srsvkavArqlgvSwtTVwrildr 50
                                      + svk++A+ +g++++TV +++ +
  gi|385805118|ref|YP_005841516.1|  1 M-SVKDIAKATGCGEKTVVNRISY 23
                                      5.******************9865 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   4.7e-06    0.0047      58      84 ..      21      47 ..       2      52 .. 0.88
   2 ?   -0.9   0.0       1.8   1.8e+03      33      42 ..      50      59 ..      45      62 .] 0.58

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.7e-06
                             Mrr_N 58 rtyLkkagllespkrgvwkiTekGrev 84
                                      ++yLkk gl+e+  r+ +k+T+ G ++
  gi|385805118|ref|YP_005841516.1| 21 ISYLKKLGLVERKGRSPLKLTPWGEAA 47
                                      58********************99876 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.8
                             Mrr_N 33 lseeeraell 42
                                      lsee r+ l 
  gi|385805118|ref|YP_005841516.1| 50 LSEESRELLE 59
                                      5666666555 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   5.3e-05     0.052      27      48 ..       1      22 [.       1      26 [. 0.93
   2 ?    1.3   0.0      0.28   2.8e+02       6      20 ..      45      59 ..      42      61 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.3e-05
                                      --HHHHHHHHT--HHHHHHHHH CS
                      Sigma70_r4_2 27 lsykEIAellgisegtVksrls 48
                                      +s k+IA+ +g+ e+tV +r+s
  gi|385805118|ref|YP_005841516.1|  1 MSVKDIAKATGCGEKTVVNRIS 22
                                      89***************99986 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.28
                                      HHHTTS-HHHHHHHH CS
                      Sigma70_r4_2  6 ealaeLperqreifl 20
                                      ea a L+e+ re ++
  gi|385805118|ref|YP_005841516.1| 45 EAAALLSEESRELLE 59
                                      677889999999987 PP

>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0     6e-06     0.006      27      56 ..       4      33 ..       1      56 [. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6e-06
                      HrcA_DNA-bdg 27 eeiAevlkrneGtvRNqlqsLkalgLvegv 56
                                      ++iA++ +  e tv N ++ Lk lgLve +
  gi|385805118|ref|YP_005841516.1|  4 KDIAKATGCGEKTVVNRISYLKKLGLVERK 33
                                      79*************************976 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.1e-05     0.011      24      61 ..       2      39 ..       1      43 [. 0.91

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.1e-05
                                      HHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTE CS
                              TrmB 24 tadeiaeelgvprskvYevLrsLedkGlVerekgrpkl 61
                                      ++++ia+++g  + +v + ++ L++ GlVer+ ++p +
  gi|385805118|ref|YP_005841516.1|  2 SVKDIAKATGCGEKTVVNRISYLKKLGLVERKGRSPLK 39
                                      799*****************************998876 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   1.7e-05     0.017      21      47 ..       1      27 [.       1      33 [. 0.93

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.7e-05
                           HTH_Mga 21 ltldelakeLglseltlqsdiseLnel 47
                                      ++++++ak++g+ e+t+ ++is L+ l
  gi|385805118|ref|YP_005841516.1|  1 MSVKDIAKATGCGEKTVVNRISYLKKL 27
                                      899*******************99965 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0     2e-05      0.02      16      46 ..       1      31 [.       1      32 [. 0.96

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2e-05
                                      EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5 16 lcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      ++v ++a+++g  + tv    + L+++GLVe
  gi|385805118|ref|YP_005841516.1|  1 MSVKDIAKATGCGEKTVVNRISYLKKLGLVE 31
                                      79****************************8 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.0   1.8e-05     0.018      21      53 ..       3      35 ..       1      44 [. 0.82

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.8e-05
                            HTH_27 21 ladlcgrlnvedshisyslkkLtekGLvertgd 53
                                       +d+++++ ++  ++++ ++ L + GLver+g 
  gi|385805118|ref|YP_005841516.1|  3 VKDIAKATGCGEKTVVNRISYLKKLGLVERKGR 35
                                      579*************************77665 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   2.2e-05     0.022      23      55 ..       2      35 ..       1      39 [. 0.91

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.2e-05
                                      EHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE.E CS
                            MarR_2 23 tvgelarrlglsksavsrilkrLvaaGLverr.p 55
                                      +v+++a+++g    +v +++  L + GLver+ +
  gi|385805118|ref|YP_005841516.1|  2 SVKDIAKATGCGEKTVVNRISYLKKLGLVERKgR 35
                                      89****************************9844 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.7e-05     0.027      18      46 ..       1      28 [.       1      33 [. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.7e-05
                                      S-HHHHHHHHTS-HHHHHHHHHHHHHHHT CS
                              GerE 18 ksnkeIAeelniSekTVkvhksnimkKLn 46
                                      +s+k+IA++ ++ ekTV + +s  +kKL+
  gi|385805118|ref|YP_005841516.1|  1 MSVKDIAKATGCGEKTVVNRIS-YLKKLG 28
                                      689**************77765.456766 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   2.2e-05     0.022      39      73 ..       3      35 ..       1      58 [. 0.91

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.2e-05
                           DUF4423 39 peelakrlrpkisaeevekalefLlklgllkkded 73
                                      ++ +ak+++  + ++ v + +++L+klgl+++++ 
  gi|385805118|ref|YP_005841516.1|  3 VKDIAKATG--CGEKTVVNRISYLKKLGLVERKGR 35
                                      789******..*********************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 ?   14.2   0.0   3.2e-05     0.031      22      55 ..       1      35 [.       1      43 [. 0.87

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.2e-05
                                      HHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ETE CS
                         HTH_Crp_2 22 ltqeelAsmlGltretvsrilseLkreglis.rgr 55
                                      ++ +++A   G    tv   +s Lk+ gl++ +gr
  gi|385805118|ref|YP_005841516.1|  1 MSVKDIAKATGCGEKTVVNRISYLKKLGLVErKGR 35
                                      6789***************************4455 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   4.2e-05     0.042      12      52 ..       1      35 [.       1      56 [. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.2e-05
                            HTH_29 12 vstvsqiAkllglsrrtvyrwlkrfeegGlaalldrrrsgr 52
                                      +s v++iAk++g+ ++tv + +    + G   l +r+  gr
  gi|385805118|ref|YP_005841516.1|  1 MS-VKDIAKATGCGEKTVVNRISYLKKLG---LVERK--GR 35
                                      55.9**************99888888888...66655..33 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   4.9e-05     0.049      18      41 ..       1      24 [.       1      25 [. 0.93

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.9e-05
                     HTH_AsnC-type 18 isyaeLAervGlSestvlrRvrrL 41
                                      +s++++A+++G+ e tv +R+  L
  gi|385805118|ref|YP_005841516.1|  1 MSVKDIAKATGCGEKTVVNRISYL 24
                                      699******************887 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   3.1e-05     0.031      26      63 ..       4      41 ..       3      58 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.1e-05
                           DUF2250 26 ksiakeleipleevrellkkLeelGLlervegktikrt 63
                                      k iak +    + v + +  L++lGL+er+ ++ +k t
  gi|385805118|ref|YP_005841516.1|  4 KDIAKATGCGEKTVVNRISYLKKLGLVERKGRSPLKLT 41
                                      789999************************99988865 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0002       0.2      18      50 ..       1      33 [.       1      36 [. 0.96

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0002
                                      EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR 18 lsvseLakklgvskstvtrvldrLekkGlieRs 50
                                      +sv+++ak+ g+   tv + +  L k Gl+eR+
  gi|385805118|ref|YP_005841516.1|  1 MSVKDIAKATGCGEKTVVNRISYLKKLGLVERK 33
                                      799*****************************6 PP



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:                      353  (0.0196888); 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):              18  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 439.89
//
Query:       gi|385805119|ref|YP_005841517.1|  [L=177]
Description: hypothetical protein FFONT_0071 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.14   10.9   0.0       0.16   10.7   0.0    1.1  1  Cas_Cas02710  CRISPR-associated protein (Cas_Cas02710)


Domain annotation for each model (and alignments):
>> Cas_Cas02710  CRISPR-associated protein (Cas_Cas02710)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   9.2e-06      0.16      41     101 ..      71     131 ..      34     143 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 9.2e-06
                                       EEEEE--TT-HHHHHHHHHHHHHHS.TTS-EEEE-SSS-HHHHHHHHHHHHHHTEEEEEEE CS
                      Cas_Cas02710  41 evlldedandllelykkikevlekaleeeevivDlTgGtkeMtaglalagillrvklsyVg 101
                                         +l +d+ ++ +    i + ++ +  ++ ++v++ gG +  t+ l+la + ++ ++s+ +
  gi|385805119|ref|YP_005841517.1|  71 MQTLRIDPAEPWKGIPAIAQKIREVCGDRRIVVEAGGGLRGITVMLMLALFSMKRSFSVET 131
                                       4444444444444444444444455899**************************9999755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       255  (0.0142228); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1080.45
//
Query:       gi|385805120|ref|YP_005841518.1|  [L=439]
Description: hypothetical protein FFONT_0072 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score 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   15.4   0.2      0.043   14.2   0.2    1.6  1  DUF5613   Domain of unknown function (DUF5613)


Domain annotation for each model (and alignments):
>> DUF5613  Domain of unknown function (DUF5613)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2   2.4e-06     0.043      40      92 ..     134     186 ..     105     188 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.4e-06
                           DUF5613  40 kmPtleefkedeeylkefhkkkgqkhlkfifPeneklseeleeylkkegyelg 92 
                                         P+l+ +k d+++lke+h +  q+hl+ ++Pe  +   +l +   +++++++
  gi|385805120|ref|YP_005841518.1| 134 LYPELNLLKLDASKLKEVHISDPQEHLQKVAPETIQAIVNLYSQSGANEFSIE 186
                                       36*******************************99998888888888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.50
# Mc/sec: 2666.27
//
Query:       gi|385805121|ref|YP_005841519.1|  [L=40]
Description: hypothetical protein FFONT_0073 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      171  (0.00953762); 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 0.29s 00:00:00.65 Elapsed: 00:00:00.45
# Mc/sec: 269.27
//
Query:       gi|385805122|ref|YP_005841520.1|  [L=247]
Description: putative CRISPR-associated protein, APE2256 family [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-31  109.3   0.6      2e-31  108.7   0.6    1.3  1  Cas_APE2256      CRISPR-associated protein (Cas_APE2256)
    8.2e-05   21.5   0.4      0.001   17.8   0.1    2.0  2  DUF1887          Domain of unknown function (DUF1887)
  ------ inclusion threshold ------
      0.028   15.0   0.7        2.4    8.8   0.2    2.2  2  DUF3502          Domain of unknown function (DUF3502)
       0.12   11.6   0.0       0.18   11.1   0.0    1.2  1  Beta_elim_lyase  Beta-eliminating lyase


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 !  108.7   0.6   4.5e-35     2e-31       2     136 .]      51     181 ..      50     181 .. 0.96

  Alignments for each domain:
  == domain 1  score: 108.7 bits;  conditional E-value: 4.5e-35
                       Cas_APE2256   2 kasAElnallkllekkkkeqkeelvllssdTaaGklvaeilkeyleeegaevevveieklsdlgreeFreglrnLve 78 
                                       k+sAE+n++ ++l++k+++ + ++ ll+sdT++Gk++ae+l+ ++e + ++ ev+    +++lg+  F+ g +nL++
  gi|385805122|ref|YP_005841520.1|  51 KVSAEVNSMRTYLNEKERKIA-SVTLLASDTDEGKVCAEALRSFFEDREIKAEVMV---VEKLGKA-FEVGTSNLMD 122
                                       78***************9975.*************************999999977...8999998.********** PP

                       Cas_APE2256  79 klarevknkkregekvlinaTgGfKpeiavltlvall.ladevyYihEsfsevvelPkl 136
                                       ++a++v ++++eg ++++n+TgG+K+e+a++++ all   d+v YihE+ +  velP l
  gi|385805122|ref|YP_005841520.1| 123 AIAKAVATARKEGLEIILNLTGGYKAESAIAYVSALLlSVDKVLYIHETLRVPVELPAL 181
                                       *************************************8899****************75 PP

>> DUF1887  Domain of unknown function (DUF1887)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   2.3e-07     0.001      20     116 ..      63     168 ..      52     189 .. 0.75
   2 ?    1.9   0.0     0.016        73     220     242 ..     213     234 ..     189     240 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.3e-07
                           DUF1887  20 lldkelkpehlvlivteaq..kekanrlekvlkekgidveifeled.....evdlee.leeslkglleelkaaeevv 88 
                                       l +ke k   + l+ +++   k  a+ l++ ++ ++i+ e++ +e+     ev +++ ++  +k++++  k   e++
  gi|385805122|ref|YP_005841520.1|  63 LNEKERKIASVTLLASDTDegKVCAEALRSFFEDREIKAEVMVVEKlgkafEVGTSNlMDAIAKAVATARKEGLEII 139
                                       4566667777778877777578889**************9987775333335666662455567888888889**** PP

                           DUF1887  89 lNvtgGtklm.algayevfRskhkrIfyv 116
                                       lN+tgG k   a++   ++   + +++y+
  gi|385805122|ref|YP_005841520.1| 140 LNLTGGYKAEsAIAYVSALLLSVDKVLYI 168
                                       ********752677777777666666677 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.016
                           DUF1887 220 lnllledladekllkleggivtf 242
                                       ++ + edl+d++l++++gg  ++
  gi|385805122|ref|YP_005841520.1| 213 VREI-EDLVDKGLVEMDGGKCKV 234
                                       4566.9*************8655 PP

>> DUF3502  Domain of unknown function (DUF3502)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0    0.0035        16      64      92 ..      43      71 ..       4      83 .. 0.78
   2 ?    8.8   0.2   0.00054       2.4      35     118 ..      59     140 ..      57     142 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0035
                           DUF3502 64 lgFtfDsspvkteiaalsnvveeykkale 92
                                       + +fD+s+v++e++ +++ ++e ++++ 
  gi|385805122|ref|YP_005841520.1| 43 KKLNFDPSKVSAEVNSMRTYLNEKERKIA 71
                                      5679***************9999887765 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00054
                           DUF3502  35 firyllegepe.dkwekvkefneeaka.spalgFtfDsspvkteiaalsnvveeykkaletGlvDpeetlpkfnekl 109
                                       + +yl e+e +   ++ + + ++e k    al   f++ ++k+e+     vve+  ka+e+G+ +  ++++k  + +
  gi|385805122|ref|YP_005841520.1|  59 MRTYLNEKERKiASVTLLASDTDEGKVcAEALRSFFEDREIKAEV----MVVEKLGKAFEVGTSNLMDAIAKAVATA 131
                                       555655555553333334444444444477777777777777776....6999************************ PP

                           DUF3502 110 kaaGidkvi 118
                                       ++ G++ ++
  gi|385805122|ref|YP_005841520.1| 132 RKEGLEIIL 140
                                       *****9886 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   3.9e-05      0.18      89     166 ..      66     140 ..      44     145 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.9e-05
                                       HHHHCC--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEE..EESSBTTTTTB---HHHHHHHHHHHHHCT-E CS
                   Beta_elim_lyase  89 aiaelagvklrdlknkeaGkmdlekleaaikevgaheekiklis..ltvTnntagGqvvsleelrevaaiakkygip 163
                                           +a+v+l   +++e Gk+ +e+l++  +++++  +   +++  l  + ++  G+   ++ ++++ a+a+k+g++
  gi|385805122|ref|YP_005841520.1|  66 KERKIASVTLLASDTDE-GKVCAEALRSFFEDREI--KAEVMVVekLGKAFEV--GTSNLMDAIAKAVATARKEGLE 137
                                       55667899999999999.**************999..4444554125566776..********************99 PP

                                       EEE CS
                   Beta_elim_lyase 164 lhl 166
                                       ++l
  gi|385805122|ref|YP_005841520.1| 138 IIL 140
                                       865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       830  (0.0462937); expected 358.6 (0.02)
Passed bias filter:                      676  (0.0377043); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 1648.62
//
Query:       gi|385805123|ref|YP_005841521.1|  [L=301]
Description: Cmr6 family CRISPR-associated RAMP protein [Fervidicoccus fontis Kam940]
Scores for complete 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-13   49.4   0.0    1.1e-12   48.4   0.0    1.5  1  RAMPs        RAMP superfamily
  ------ inclusion threshold ------
      0.055   14.0   0.2         13    6.3   0.0    2.4  2  Pox_D5       Poxvirus D5 protein-like
      0.077   13.0   0.3       0.34   10.9   0.3    2.0  1  NADH_u_ox_C  C-terminal of NADH-ubiquinone oxidoreductase 21 


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 !   48.4   0.0   1.9e-16   1.1e-12      24     213 .]     132     293 ..     126     293 .. 0.69

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 1.9e-16
                                       ....---S----HHHHHHHHHHHHHHHHH.HHHTT-HHHHH.H.........HHHHHH--S.....SS--SEEEEE. CS
                             RAMPs  24 efrdkgglPyIPGSSlkGalRsalekllgsekkekkdeysrkkekqrvkkgdleeaiFGne..eeskiagrvffeDa 98 
                                       +++  +++P+IP+SSl+GalR  l         +++d+  +            ++ +FG+   ee k++g + + Da
  gi|385805123|ref|YP_005841521.1| 132 AIDPYMNVPFIPASSLRGALRMQLS---L----NNNDISHN-----------NISLLFGKSegEEGKHPGILSIFDA 190
                                       5677899**************5553...2....22233333...........99*********************** PP

                                       ......................EEEEEEEEEEEEEEEEE--SSS-EEEEEE...-TT-EEEEEEEESS......... CS
                             RAMPs  99 rpvkipgqileeskqikstpspklsgselrelldhsterrtrvaidrktktngkkkgglftleaipae...rikfsg 172
                                       +pvk ++  +e             ++   ++  +++ e+ +++  ++++       +++    ++p +   r+  ++
  gi|385805123|ref|YP_005841521.1| 191 YPVKAQNGLFEADV--------ITPHYRESDHKIGKREVDYGIGEHESK-------PNPILFLTVPSGvtfRAFSAV 252
                                       *****988776532........223333333333344444444444433.......333444455555555555555 PP

                                       ........HHHHHHHHHHHHHH.HHH---STTTTBTTT-EE CS
                             RAMPs 173 rirlenlsdeelgallklLdlldlhflglGggkplGfGsve 213
                                          l+++ +++l ++  +++ + ++ lglG+++  G+G ve
  gi|385805123|ref|YP_005841521.1| 253 CDELDEQEKQALTKFVGAFKNFREFPLGLGAKTMTGYGVVE 293
                                       55599999999999999999999999************886 PP

>> Pox_D5  Poxvirus D5 protein-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.2     0.005        30      30      79 ..      49      94 ..      17      97 .. 0.81
   2 ?    6.3   0.0    0.0023        13      21      54 ..     239     272 ..     232     277 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.005
                            Pox_D5 30 aYkafcekngykpvlskrtFqkrlkkileegfekkkkkkgqqpneyleyi 79
                                       Y    ek+g ++   +++F+ ++ k++++  ++++k++ +  neyl+++
  gi|385805123|ref|YP_005841521.1| 49 YYEVTSEKSGEVE---LTQFYGKIVKHIQQ-LKSREKTDLNLVNEYLKDV 94
                                      4555555555555...9***********76.9999999999999999986 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0023
                            Pox_D5  21 rvpsdvlYeaYkafcekngykpvlskrtFqkrlk 54 
                                       +vps v+++a+ a c + + +++  +++F   +k
  gi|385805123|ref|YP_005841521.1| 239 TVPSGVTFRAFSAVCDELDEQEKQALTKFVGAFK 272
                                       69*****************999999999987776 PP

>> NADH_u_ox_C  C-terminal of NADH-ubiquinone oxidoreductase 21 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.3   5.6e-05      0.34      19      65 ..      23      68 ..      11      93 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.6e-05
                       NADH_u_ox_C 19 esvLddrlkdvanRnsqysalllailPWFnlayhpyhgvdlkkYYen 65
                                      +  L++r k + nRn  ys+++  il ++ ++  ++ +v+l+++Y +
  gi|385805123|ref|YP_005841521.1| 23 HDILNERFKSLVNRN-LYSSIVRSILEYYEVTSEKSGEVELTQFYGK 68
                                      5689**********9.69**************************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 2051.45
//
Query:       gi|385805124|ref|YP_005841522.1|  [L=417]
Description: Cmr1 family CRISPR-associated RAMP protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00042   20.4   0.5    0.00042   20.4   0.5    2.6  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 !   20.4   0.5   2.4e-08   0.00042      34     212 ..      31     204 ..      29     205 .. 0.62
   2 ?   -2.1   1.1      0.18   3.2e+03     167     167 ..     296     296 ..     206     374 .. 0.55

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.4e-08
                                       --HHHHHHHHHHHHHHHHH.HHHTT-HHHHH.H.........HHHHHH--S..............SS--SEEEEE.. CS
                             RAMPs  34 IPGSSlkGalRsalekllgsekkekkdeysrkkekqrvkkgdleeaiFGne...........eeskiagrvffeDar 99 
                                       ++++ lkG +R+++++ +++ +   + + +             + +i G++            +s  +++ ++++ +
  gi|385805124|ref|YP_005841522.1|  31 LRPTELKGIWRWWARAFACGVLYDRGCNPLPS----------DLVKIVGKDlglgyagvnigGKSAMPSKYIIRVNE 97 
                                       689************88885543333322221..........34445566666666677777667777777777776 PP

                                       .....................EEEEEEEEEEEEEEEEE--SSS-EEEEEE........-TT-E.EEEEEEESS.... CS
                             RAMPs 100 pvkipgqileeskqikstpspklsgselrelldhsterrtrvaidrktktngk.....kkggl.ftleaipae.rik 169
                                        ++  + +   ++          ++ +l+el +  +  + r    ++++ ++      +kgg   tle++ +  r+ 
  gi|385805124|ref|YP_005841522.1|  98 TFEPTNFK---KA--------SINKTDLKELQRIVLLLGGRPESLEPNNAEKVilkrrGKGGVeRTLELYLPQsRFY 163
                                       65544432...22........22333333333333333333333322222222443554555545566666666999 PP

                                       ...........HHHHHHHHHHHHHH.HHH---STTTTBTTT-E CS
                             RAMPs 170 fsgrirlenlsdeelgallklLdlldlhflglGggkplGfGsv 212
                                         +++  e +s+++  a+l  L+++  + +g+G g ++G+Gs+
  gi|385805124|ref|YP_005841522.1| 164 TISLFSTESDSNKKAAAVLSFLSAI--MLMGIGKGGRRGLGSL 204
                                       99999999*****************..**************97 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.18
                                       . CS
                             RAMPs 167 r 167
                                        
  gi|385805124|ref|YP_005841522.1| 296 L 296
                                       1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 2454.27
//
Query:       gi|385805125|ref|YP_005841523.1|  [L=182]
Description: hypothetical protein FFONT_0077 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-06   27.8   0.0    1.7e-05   25.1   0.0    2.0  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 !   25.1   0.0   9.4e-10   1.7e-05      10     121 ..      28     172 ..      23     173 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 9.4e-10
                                       HHHHHHHHHHT.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC............................... CS
                          Cas_Cmr5  10 yekvkelkeks.kkkekkykslvkklPalIltnGLgqalAfllskg............................... 54 
                                       ++kv+e k+k+ k+  k ++s+++++P+ I t+GL+ +   +l+k+                               
  gi|385805125|ref|YP_005841523.1|  28 LSKVAESKDKDvKEYLKALRSRARDAPTEIFTSGLALFTVTYLAKSkdcfpkmanelskspdrdillknlekklivt 104
                                       7899999999899*****************************************99999999999999999999999 PP

                                       .......SSCCCHHHHHHHHHHHHHHHHCTSS...STTTCHHHHHHHHSTHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Cas_Cmr5  55 .......kkkkedahkkllehlaewlkkeksaskkkkgendllkelleadlseymratreaLallnWlkRfAea 121
                                               ++ +  +   l  l++ lk++     + +gen+ lk +l++  s y  ++++aL + + +kRf+ea
  gi|385805125|ref|YP_005841523.1| 105 ddgqekkCESPDFGYGSYLLILMYLLKRQ-----RIVGENTNLKDFLKMA-SSYPPLSEKALIISELIKRFSEA 172
                                       88876543333445666677777777777.....8888888888888876.78999999999999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1126.03
//
Query:       gi|385805126|ref|YP_005841524.1|  [L=305]
Description: Cmr4 family CRISPR-associated RAMP protein [Fervidicoccus fontis Kam940]
Scores for complete 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  106.5   2.2    2.5e-30  106.1   2.2    1.1  1  RAMPs     RAMP superfamily
  ------ inclusion threshold ------
      0.024   14.6   0.5       0.95    9.5   0.0    2.4  2  XPA_C     XPA protein C-terminus


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 !  106.1   2.2   2.8e-34   2.5e-30       2     211 ..      15     297 ..      14     299 .. 0.98

  Alignments for each domain:
  == domain 1  score: 106.1 bits;  conditional E-value: 2.8e-34
                                       EEESS-EE----..............---S----HHHHHHHHHHHHHHHHH.HHHTT-HHHHH.H.........HHH CS
                             RAMPs   2 letltPlhiGdgkisdekeespefrdkgglPyIPGSSlkGalRsalekllgsekkekkdeysrkkekqrvkkgdlee 78 
                                       + ++tPlh+G g  ++e++++ ++rd++g P+I+G+SlkGa++s + +++g+ +k                   +++
  gi|385805126|ref|YP_005841524.1|  15 IRAITPLHVGVG--EGEHVDLSVQRDEFGFPIIWGTSLKGAIKSQFNRIYGKDEK-------------------FIK 70 
                                       789*********..*************************************7776...................*** PP

                                       HHH--S...SS--SEEEEE.......................................................... CS
                             RAMPs  79 aiFGneeeskiagrvffeDarpvkipgqileeskqikstpsp................................... 120
                                       ++FG++     ++++++ Dar++ ip+++ ++++ +++++                                     
  gi|385805126|ref|YP_005841524.1|  71 ELFGDD---EKPSKLRVLDARLFLIPARTYKKVWTYVTSKQVierlepyaelagfkldtgveskgsstvgnagahep 144
                                       ******...*********************999999999999*********************************** PP

                                       .....................................................................EEEEEEEE CS
                             RAMPs 121 .....................................................................klsgselr 128
                                                                                                             +++s+ r
  gi|385805126|ref|YP_005841524.1| 145 iekvdvivnkdylledgkitlneifdltaksnptefnmintlinkissiknekieklikrieergiclvTDEESKSR 221
                                       ***************************************************************************** PP

                                       EEEEEEEEE--SSS-EEEEEE...-TT-EEEEEEEESS..............HHHHHHHHHHHHHH.HHH---STTT CS
                             RAMPs 129 elldhsterrtrvaidrktktngkkkgglftleaipaerikfsgrirlenlsdeelgallklLdlldlhflglGggk 205
                                        ++++s  +++r+++    k +++  ggl+++e++p e             ++++l +l++l ++   ++l++Gg++
  gi|385805126|ref|YP_005841524.1| 222 AIINKSIVIQYRIRLKGDEKVVKE--GGLWSEELLPSE----TLMLSALVVNESDLSKLKNLVEKN-PFYLFIGGKE 291
                                       **********************99..************....999999999***************.********** PP

                                       TBTTT- CS
                             RAMPs 206 plGfGs 211
                                       ++G G+
  gi|385805126|ref|YP_005841524.1| 292 SVGRGL 297
                                       ****97 PP

>> XPA_C  XPA protein C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00011      0.95      11      36 ..     153     178 ..     151     182 .. 0.92
   2 ?    2.9   0.1     0.012   1.1e+02      16      35 ..     266     282 ..     258     284 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00011
                             XPA_C  11 kedYLLtdedLkdrelLkflkkkNPh 36 
                                        +dYLL+d  +  +e++    k NP 
  gi|385805126|ref|YP_005841524.1| 153 NKDYLLEDGKITLNEIFDLTAKSNPT 178
                                       68***********************6 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.012
                             XPA_C  16 LtdedLkdrelLkflkkkNP 35 
                                        +++dL++   Lk l  kNP
  gi|385805126|ref|YP_005841524.1| 266 VNESDLSK---LKNLVEKNP 282
                                       6899****...********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       847  (0.0472419); expected 358.6 (0.02)
Passed bias filter:                      588  (0.032796); 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: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 1855.97
//
Query:       gi|385805127|ref|YP_005841525.1|  [L=341]
Description: hypothetical protein FFONT_0079 [Fervidicoccus fontis Kam940]
Scores for 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-05   22.1   0.0      0.046   13.2   0.0    2.2  2  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 !   13.2   0.0   2.5e-06     0.046      14      93 ..      15      99 ..       4     114 .. 0.71
   2 !    6.9   0.0   0.00021       3.7     170     332 ..     124     306 ..     104     322 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.5e-06
                          Cas_Cmr3 14 grpFedgeear.aasllfPlPsTlaGavrtalgekagldf.gklleeekar.......dgealgeiavrGpllvrepdg 83
                                       rpF++ +         +P+P+T+aG++  alg +   +  +kll  +k         +     +++++Gpll+     
  gi|385805127|ref|YP_005841525.1| 15 RRPFSSPDYIAsHSVWEIPPPTTVAGTLGDALGITIPTNEsSKLLGLDKLSeklneklTEPCGIPFSITGPLLET---- 89
                                      589997775322455578**************9877654434444444433555543444444578899******.... PP

                          Cas_Cmr3 84 keellfPaPa 93
                                      ++++++P++ 
  gi|385805127|ref|YP_005841525.1| 90 EGRYFVPIGE 99
                                      *******976 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.00021
                          Cas_Cmr3 170 dlltkeeRigialdpetrtaeegalyqteglrlk.................edvrlallvelddpaeeeklepailr 229
                                        +  +e+R+g++l+++ +++ee    +  ++r                     v    ++++++ +++    +++ r
  gi|385805127|ref|YP_005841525.1| 124 LIHGTERRVGVSLKRGYNQSEEKVGRSGMHYRYLvsvyemvenekkrpvlpNYVYKLTGCQGSGNIQQ----KRAIR 196
                                       37889999999999999999887654444444443333333666555555333333334444444443....9**** PP

                          Cas_Cmr3 230 LGGerrlalvee.elseelesvpeeveaaiaeggrlrlvLlTPaifakgw.rpgwldkekeleleelsaelvaaav. 303
                                       +GGe+  a++e  +++ee   ++++++  ++ ++ + l L +P ++ ++   +++ ++   le  ++++++   +  
  gi|385805127|ref|YP_005841525.1| 197 FGGEGGIAFLEInRSKEEDSIFSAMFSPLSNLEQGCYLAL-SPIPLIPKHgNSSHISEVTGLEPFGGPSSVRGICDe 272
                                       ***********96666666666666677767777777765.565555554466666665533333333445555543 PP

                          Cas_Cmr3 304 ....krpvavS.gwdlarkkpkptrravPaGsVy 332
                                            + v+ + g++ + k+++p   a P+G+ +
  gi|385805127|ref|YP_005841525.1| 273 rsckVKVVRMGlGFSEVYKSRRPQILALPQGTLL 306
                                       3333344466677777777777777778888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       248  (0.0138323); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.49
# Mc/sec: 2089.03
//
Query:       gi|385805128|ref|YP_005841526.1|  [L=1137]
Description: Crm2 family CRISPR-associated protein [Fervidicoccus fontis Kam940]
Scores for 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-30  103.7   0.1    1.9e-29  102.1   0.1    1.9  1  DUF3692       CRISPR-associated protein
  ------ inclusion threshold ------
      0.016   15.0   1.1       0.95    9.3   0.0    3.5  3  Nsp1_C        Nsp1-like C-terminal region
          4    7.5  12.9          2    8.5   2.1    4.0  4  Spore_III_AB  Stage III sporulation protein AB (spore_III_AB)


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 !  102.1   0.1   3.1e-33   1.9e-29       2     110 ..     207     368 ..     206     369 .. 0.82

  Alignments for each domain:
  == domain 1  score: 102.1 bits;  conditional E-value: 3.1e-33
                                       EEEEEEESHHHHHS-SSHHHHHHHHHHHHHHHHHHHHHHHHHT-GGGEEES--TT-HHHHHHTS-............ CS
                           DUF3692   2 lvvsigpVqefIaaaRktrDlWagSyllSylawkaikelvekyGpdvliyPslrgnplvdawlle............ 66 
                                       ++v+i++Vq+fI+++Rk++D+Wa+S+++S+l+w++++++++++Gpdvli+Ps+r np++   l++            
  gi|385805128|ref|YP_005841526.1| 207 VSVDIPGVQSFISHSRKLGDFWAASWIISNLSWRTVWRAIKAFGPDVLISPSPRLNPYLLVSLSNeaeklgkqdlkk 283
                                       899*************************************************************9666666666555 PP

                                       --GG..............................GGGSB---SEEEEEEE.TT.............THHHHHHHHHH CS
                           DUF3692  67 klee..............................eletalipnrfvlilpkee.............eaeelaeevee 100
                                       k  +                              ++ t++ip+++ +ilpk                +e++a+ v+ 
  gi|385805128|ref|YP_005841526.1| 284 K--NlvdilkkstnelmkmispyesfsgndlfelAEITPMIPEKIRFILPKMFyiedkdgsvkyieREEDVADLVKV 358
                                       0..055555555666667777777777777777799**************998988777666655333366666*** PP

                                       HHHHHHHHHH CS
                           DUF3692 101 alkeawkeia 110
                                        ++eawkei+
  gi|385805128|ref|YP_005841526.1| 359 WFREAWKEIL 368
                                       ********97 PP

>> Nsp1_C  Nsp1-like C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00016      0.95      16      34 ..     112     130 ..     102     133 .. 0.87
   2 ?    2.0   0.1     0.029   1.7e+02      13      40 ..     279     306 ..     267     310 .. 0.67
   3 ?   -3.1   0.0       1.1   6.5e+03      69      92 ..     522     545 ..     496     546 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00016
                            Nsp1_C  16 knktldelinkWtteLeeq 34 
                                       + kt+del+++W++eL+++
  gi|385805128|ref|YP_005841526.1| 112 DRKTMDELVQRWAEELNKA 130
                                       579*************986 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.029
                            Nsp1_C  13 aslknktldelinkWtteLeeqekeFee 40 
                                       + lk+k+l ++++k t+eL +  + +e+
  gi|385805128|ref|YP_005841526.1| 279 QDLKKKNLVDILKKSTNELMKMISPYES 306
                                       3477777777777777777776666655 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 1.1
                            Nsp1_C  69 aeqeqnkidqeLeyiesqqdeLes 92 
                                       a+ +++ +++ Le+   +++eLe+
  gi|385805128|ref|YP_005841526.1| 522 AKYKEEDLEKILEITGVSRSELED 545
                                       677888899999999999999986 PP

>> Spore_III_AB  Stage III sporulation protein AB (spore_III_AB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1     0.023   1.4e+02      85     116 ..     360     394 ..     342     398 .. 0.82
   2 ?    8.5   2.1   0.00034         2      81     144 ..     622     683 ..     595     690 .. 0.80
   3 ?   -2.0   0.0      0.57   3.4e+03      54      80 ..     694     720 ..     684     745 .. 0.55
   4 ?    0.7   0.1     0.084     5e+02      26      87 ..     742     804 ..     737     828 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.023
                                       HHHHHHHHHHHH...GGGS---HHHHHHHHHHHHH CS
                      Spore_III_AB  85 feeaweeavekl...lkklaLkkedkeilkelges 116
                                       f+eaw+e +e+     +   +kk+ +e++k++ge+
  gi|385805128|ref|YP_005841526.1| 360 FREAWKEILEEAgfySNGDRMKKALREMIKQFGEK 394
                                       89999999999876556688889999999999986 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00034
                                       TSS-HHHHHHHHHHHHGGGS---HHHHHHHHHHHHHHT--SHHHHHHHHHHHHHHHHHHHHHHH CS
                      Spore_III_AB  81 egesfeeaweeavekllkklaLkkedkeilkelgeslgysdregqlkalelaleeleeeieear 144
                                       +++ ++ea++  ++++   ++L ke  e + + +++lg  + e+ ++ le al++l+ee+++ +
  gi|385805128|ref|YP_005841526.1| 622 DNDKIREALSLVFSET--FSHLGKERYEGFEKAANKLGIDEEEKFINMLEDALRNLKEELKKEK 683
                                       6667777777777776..488**************************************99865 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.57
                                       HHHHHHHCS-TTHHHHHHHHHHHHH.S CS
                      Spore_III_AB  54 aleklaeksesplseffeevaerleek 80 
                                       + e ++++ +++l+++fee  +r e+k
  gi|385805128|ref|YP_005841526.1| 694 LAEMVSKHFGKDLGRLFEEYLNREENK 720
                                       334444444444444444444443332 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.084
                                       HHHHHHHHHHHHHHHHHHHHH-SS-H.HHHHHHHHHCS-TTHHHHHHHHHHHHH.STSS-HHH CS
                      Spore_III_AB  26 rlkeleelkralellegeirygatpL.pealeklaeksesplseffeevaerleekegesfee 87 
                                       rl++  +++r+   + g+i  g+ pL  e++   ++  + +lse+++++++ ++++  ++ + 
  gi|385805128|ref|YP_005841526.1| 742 RLRRYYAILRMDGDFIGRIVSGKLPLySEMFTDDGKMRTMKLSEYVKMLYDSMKKNASGEQRV 804
                                       666777777777778889999999998899999999999999******999999852222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       964  (0.0537676); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); 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: 0.89u 0.30s 00:00:01.19 Elapsed: 00:00:00.47
# Mc/sec: 7225.47
//
Query:       gi|385805129|ref|YP_005841527.1|  [L=515]
Description: CRISPR-associated protein [Fervidicoccus fontis Kam940]
Scores for complete 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-33  115.0   1.0    6.6e-33  114.8   1.0    1.0  1  Cas_DxTHG  CRISPR-associated (Cas) DxTHG family


Domain annotation for each model (and alignments):
>> Cas_DxTHG  CRISPR-associated (Cas) DxTHG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.8   1.0   3.7e-37   6.6e-33       2     359 .]      19     482 ..      18     482 .. 0.76

  Alignments for each domain:
  == domain 1  score: 114.8 bits;  conditional E-value: 3.7e-37
                         Cas_DxTHG   2 lisflGt.gnykevkYelkeeeeeeketsfvqeallellaekedpdkvvilltdtlad................... 58 
                                       +i+++G    ++++kY+l+ee+     +s+ +++ +  la+k++++kv+i+++d+l+d                   
  gi|385805129|ref|YP_005841527.1|  19 IIATWGApWVWRKTKYVLHEEGVS---ESVESCSSVFALAKKHKNAKVIIVGADSLLDyeqrqngrgddqicrdify 92 
                                       8******666*******5543333...3333333333346678889************8888887777777777776 PP

                         Cas_DxTHG  59 ...........keaeek............eeaak.lkeeleelle....iekvdveiipgggteee.lwe....... 99 
                                                       k             +a+k + e  ++++     +++ +++i+p+ g+++e +++       
  gi|385805129|ref|YP_005841527.1|  93 evadklgieplS----KsmekyssyeeiiLDAKKlISETAKRMSPeglmLNNMEAIIMPMLGKPSEvTFNggprdpf 165
                                       666666665552....044446677556644555444444444449*9666666**********9999999****99 PP

                         Cas_DxTHG 100 ..ifekllekleen..deiilDiThGfrylPvlallalaylrnvknltikgiyYgafkeeeedPildlteflelsdw 172
                                         ++ +l+++ ++    +i+lD+++G++y+P l l+a+  l +++           f     dP +d+++++e++  
  gi|385805129|ref|YP_005841527.1| 166 svLLFELFKITKDSsfGKIYLDLSQGVNYMPSLLLQAAKMLASLSL----------F-----DPSIDTKDVVEIK-- 225
                                       974447777777776788**************************82..........5.....*************.. PP

                         Cas_DxTHG 173 ltaverflktg....daeklaellre...kkek.....kkek....................lkklkklkeklkkel 217
                                            +f+++     ++  l+e+++e   ++++        +                     + lkk++ek++k  
  gi|385805129|ref|YP_005841527.1| 226 -----AFNSEParklSEIALHEIYWEnvgTIQVplglgD--SreikvldrrieikgddgekaVDSLKKFNEKYDKIK 295
                                       .....8888886666777777777777764444656441..155679999999********999999********** PP

                         Cas_DxTHG 218 eefskalelirp..lell.e..kaekleke...........ivek..lk...eeleei.esleeeesakplel.... 268
                                        ++sk l+ +r   ++ll    ++ +  +e           ++e+  ++   +++e+  e +++  ++++l++    
  gi|385805129|ref|YP_005841527.1| 296 GSVSKVLKSLRYpvPLLLrYscSTIEDYREflnalddafslWKENtvINsdgKRIERRlELNYWGLYSYSLSYkacs 372
                                       ***********55533333334444444445666666666655555522357999999999999999999999*999 PP

                         Cas_DxTHG 269 ........................lldeikkklekflkkqikwclekgliqqaltllreliislllegedilnkkkr 321
                                                                lde++kk+++           ++++++a+   + +i      +++++n++k+
  gi|385805129|ref|YP_005841527.1| 373 qikdsvrqnadgstkpqnsndvimYLDEFDKKIARK---------IYRRVSRAF---EPII------TNEVSNIDKK 431
                                       988888888888888888888877788888887777.........677777777...5666......8999****** PP

                         Cas_DxTHG 322 reeieeelknlskvekksseekeek.............lsniRNdiaHaGl 359
                                       +ee +e l++ +++e ++  eke +              +++R  iaHaGl
  gi|385805129|ref|YP_005841527.1| 432 IEEKGEVLNKGECLELDELFEKEGDseekgssaskgtrEPDRRIVIAHAGL 482
                                       *****************999988889**********999***********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (515 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      576  (0.0321267); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 3479.77
//
Query:       gi|385805130|ref|YP_005841528.1|  [L=160]
Description: hypothetical protein FFONT_0082 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.093   12.5   0.8       0.19   11.5   0.8    1.5  1  FixS      Cytochrome oxidase maturation protein cbb3-type


Domain annotation for each model (and alignments):
>> FixS  Cytochrome oxidase maturation protein cbb3-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.8     1e-05      0.19       8      25 ..      25      42 ..      23      45 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1e-05
                              FixS  8 plSlllgllalaaFlWav 25
                                       + l+l ll+++aFlW+ 
  gi|385805130|ref|YP_005841528.1| 25 SILLILMLLFIGAFLWSY 42
                                      566999**********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); 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: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1052.99
//
Query:       gi|385805131|ref|YP_005841529.1|  [L=269]
Description: hypothetical protein FFONT_0083 [Fervidicoccus fontis Kam940]
Scores for complete 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   20.1   0.3    0.00053   20.1   0.3    3.8  3  DUF4234          Domain of unknown function (DUF4234)
  ------ inclusion threshold ------
      0.082   13.4   0.1         26    5.3   0.0    2.6  2  DUF202           Domain of unknown function (DUF202)
       0.15   12.6   0.2       0.15   12.6   0.2    2.1  2  DUF2418          Protein of unknown function (DUF2418)
        1.2    8.1   8.5          1    8.3   0.8    2.3  2  DUF973           Protein of unknown function (DUF973)
        1.4    8.9   5.2          3    7.8   1.5    3.0  3  UcrQ             UcrQ family
        4.4    6.0  14.0       0.64    8.7   4.6    3.0  2  DUF2207          Predicted membrane protein (DUF2207)
        7.8    6.5   6.9        8.8    6.3   0.1    3.2  3  TRIQK            Triple QxxK/R motif-containing protein famil


Domain annotation for each model (and alignments):
>> DUF4234  Domain of unknown function (DUF4234)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   4.6      0.99   2.5e+03      31      51 ..      17      75 ..      10     111 .. 0.46
   2 ?    3.0   0.1     0.043   1.1e+02      23      65 ..     135     175 ..     133     180 .. 0.57
   3 !   20.1   0.3   2.1e-07   0.00053       1      35 [.     216     250 ..     216     262 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.99
                           DUF4234 31 rlsgrkkttslllv..........flllsl................................i 51
                                      ++sg++k t+++++          +    +                                 
  gi|385805131|ref|YP_005841529.1| 17 EISGESKRTDYKMPiilpfipailA----ViamilmlfgffyyfpnpghiyyavsiyqdippN 75
                                      5566666677777733333333220....1232222222344444444444444444444440 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.043
                           DUF4234  23 ykltrelnrlsgrkkttslllvflllslitcgiysivwayklg 65 
                                       y++ + +n+l++  ++t+ +++     li++++y +++++ l+
  gi|385805131|ref|YP_005841529.1| 135 YSIKSRFNELKEVDSNTKSAIAN--AILIIVPFYIFYVFHFLN 175
                                       55555556655552223333331..235888999888887655 PP

  == domain 3  score: 20.1 bits;  conditional E-value: 2.1e-07
                           DUF4234   1 rslavvilLsivTlGIYslyWlykltrelnrlsgr 35 
                                       rs+ ++i+L ++  G++++yW+y+lt++ n++ + 
  gi|385805131|ref|YP_005841529.1| 216 RSTFLYIILYLISSGLFGIYWVYTLTNDPNKHFES 250
                                       7999************************9998766 PP

>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0      0.01        26      45      63 ..      38      56 ..      15      58 .. 0.88
   2 ?    5.3   0.0      0.01        27      43      67 ..      85     109 ..      68     110 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.01
                            DUF202 45 lilivlgiltllvglvryl 63
                                      +il+v++++++l+g++ y+
  gi|385805131|ref|YP_005841529.1| 38 AILAVIAMILMLFGFFYYF 56
                                      589************9997 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.01
                            DUF202  43 lglilivlgiltllvglvrylrrqr 67 
                                       +g++++++++l+ +++++ +++r++
  gi|385805131|ref|YP_005841529.1|  85 IGYGILLIAVLMYFYVVYKWIKRRN 109
                                       6999****************99875 PP

>> DUF2418  Protein of unknown function (DUF2418)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.5       1.3   3.3e+03      24      34 ..      59      69 ..      35     114 .. 0.52
   2 ?   12.6   0.2   5.7e-05      0.15      41      87 ..     160     204 ..     134     212 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.3
                           DUF2418 24 Plhvlllvlll 34
                                      P+h+   v++ 
  gi|385805131|ref|YP_005841529.1| 59 PGHIYYAVSIY 69
                                      44444444433 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 5.7e-05
                           DUF2418  41 tlllvvllslqlylliskfeqqikDkkiiqkevleEYnekfVkPrln 87 
                                       ++++ + + +++++l++ f + ++ +k++ +e+++E++ek+  P  +
  gi|385805131|ref|YP_005841529.1| 160 LIIVPFYIFYVFHFLNKDFYKHSEKEKLLLSELFDEIKEKI--PSFT 204
                                       455677888999***************************98..6555 PP

>> DUF973  Protein of unknown function (DUF973)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   5.8      0.21   5.3e+02     101     124 ..      31      63 ..      19     105 .. 0.61
   2 ?    8.3   0.8   0.00041         1      71     111 ..     128     168 ..      89     175 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.21
                            DUF973 101 ltliligaiiiiigvilaivsll.........s 124
                                       ++l  i ai+++i++il++++++         +
  gi|385805131|ref|YP_005841529.1|  31 IILPFIPAILAVIAMILMLFGFFyyfpnpghiY 63 
                                       444455666666666666666665555544440 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00041
                            DUF973  71 vllilgllkirsgfsiLsstgrdvgiGitgltliligaiii 111
                                       +l +   ++i+s f++L++  ++++  i+ ++li++   i 
  gi|385805131|ref|YP_005841529.1| 128 ILKFKRAYSIKSRFNELKEVDSNTKSAIANAILIIVPFYIF 168
                                       66777789************************999876654 PP

>> UcrQ  UcrQ family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   1.5    0.0012         3      10      68 ..      58     111 ..      49     114 .. 0.76
   2 ?    0.7   0.0       0.2   5.1e+02      43      58 ..     156     171 ..     148     185 .. 0.76
   3 ?   -2.4   0.0       1.9   4.8e+03      52      67 ..     231     246 ..     218     251 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0012
                                       -BSEEEEEE-GGGB-SSTTTTTTSSSSTTCTTTTTHHHHHHHHHHHHHHHHHHHHHHHH CS
                              UcrQ  10 qkgiitYslSPfeqkafagalskaifntlrRtksqvlyvlppfiiayliykwakeeney 68 
                                         g i+Y++S ++  + +g     ++  +r +   +l +++ ++ +y++ykw k++n+ 
  gi|385805131|ref|YP_005841529.1|  58 NPGHIYYAVSIYQDIPPNG----MVIYPFREIGYGILLIAV-LMYFYVVYKWIKRRNDH 111
                                       5577888888888888888....567788888888888876.6789**********986 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.2
                                       TTHHHHHHHHHHHHHH CS
                              UcrQ  43 sqvlyvlppfiiayli 58 
                                       ++++ +++pf i+y+ 
  gi|385805131|ref|YP_005841529.1| 156 ANAILIIVPFYIFYVF 171
                                       4567788899998874 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.9
                                       HHHHHHHHHHHHHHHH CS
                              UcrQ  52 fiiayliykwakeene 67 
                                       ++ +y +y+ +++ n+
  gi|385805131|ref|YP_005841529.1| 231 LFGIYWVYTLTNDPNK 246
                                       4556777777777666 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   4.6   0.00025      0.64     369     464 ..      16     134 ..       1     140 [. 0.68
   2 ?    0.6   0.5     0.073   1.9e+02     316     339 ..     182     206 ..     170     241 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00025
                           DUF2207 369 rgyfdkkgkkklkklsalglgliilglilillallllvll.....................lvfllilllillliai 424
                                       ++   + +++ +k  ++l ++ +il++i+++l l+++++                      +v++ +  ++ ++++i
  gi|385805131|ref|YP_005841529.1|  16 EEISGESKRTDYKMPIILPFIPAILAVIAMILMLFGFFYYfpnpghiyyavsiyqdippngMVIYPFREIGYGILLI 92 
                                       33444444555566666666666666666666666555557888899999999999999996666666677777777 PP

                           DUF2207 425 ivlllfsrllgrrteeGaellakwkgFkkyLe...Dfsefker 464
                                       +vl++f ++++++ +  ++  a++++F + ++   D+++fk++
  gi|385805131|ref|YP_005841529.1|  93 AVLMYF-YVVYKWIKRRNDHFARTLSFYENIAeaaDILKFKRA 134
                                       777776.678888888888888888888888888888888765 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.073
                           DUF2207 316 dpyEkalldlLfdkseeg.kslkei 339
                                       ++ Ek ll+ Lfd+++e+  s+ + 
  gi|385805131|ref|YP_005841529.1| 182 SEKEKLLLSELFDEIKEKiPSFTRK 206
                                       6667777777776666655553222 PP

>> TRIQK  Triple QxxK/R motif-containing protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1    0.0034       8.8      55      71 ..      39      55 ..      13      58 .. 0.85
   2 ?    0.4   0.7      0.24   6.1e+02      53      67 ..      89     103 ..      79     106 .. 0.76
   3 ?    1.0   0.0      0.15   3.9e+02      48      72 ..     155     175 ..     130     185 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0034
                             TRIQK 55 lvailvlllalYalffl 71
                                      ++a+++++l l+++f++
  gi|385805131|ref|YP_005841529.1| 39 ILAVIAMILMLFGFFYY 55
                                      89999**********98 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.24
                             TRIQK  53 lvlvailvlllalYa 67 
                                       ++l+a+l++  ++Y 
  gi|385805131|ref|YP_005841529.1|  89 ILLIAVLMYFYVVYK 103
                                       468999999999986 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.15
                             TRIQK  48 ikevllvlvailvlllalYalffln 72 
                                       i +++l++v        +Y + fln
  gi|385805131|ref|YP_005841529.1| 155 IANAILIIVP----FYIFYVFHFLN 175
                                       3333333333....34455555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       981  (0.0547158); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.64u 0.36s 00:00:01.00 Elapsed: 00:00:00.56
# Mc/sec: 1452.96
//
Query:       gi|385805132|ref|YP_005841530.1|  [L=486]
Description: hypothetical protein FFONT_0085 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        2.5    8.1   4.7         15    5.6   0.2    3.7  4  L27_1     L27_1


Domain annotation for each model (and alignments):
>> L27_1  L27_1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1     0.026   4.7e+02      29      47 ..      25      43 ..       4      47 .. 0.62
   2 ?    5.6   0.2   0.00085        15       9      50 ..     156     206 ..     154     208 .. 0.89
   3 ?   -1.0   0.0       0.1   1.8e+03       4      14 ..     270     280 ..     268     282 .. 0.86
   4 ?   -0.8   0.1     0.086   1.5e+03      23      46 ..     402     425 ..     395     429 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.026
                             L27_1 29 LrqalerviniFksqLfqA 47
                                       r+a + v  +F s+Lf++
  gi|385805132|ref|YP_005841530.1| 25 YRNARKEVGLTFYSSLFSS 43
                                      34677788899******85 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.00085
                             L27_1   9 rALelLeeyrakLsk.........eedeeLrqalerviniFksqLfqALLD 50 
                                       rA +lL+ey ++Ls+         + ++ +++a   + +  +s+ + ALL 
  gi|385805132|ref|YP_005841530.1| 156 RARQLLNEYASSLSSgtalymlrdRANDMVKNAQVELEKSIQSRIMLALLL 206
                                       7889***********999999999888889999999999999999999995 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.1
                             L27_1   4 kkDaerALelL 14 
                                       +kD erAL+l+
  gi|385805132|ref|YP_005841530.1| 270 RKDVERALNLI 280
                                       6899****997 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 0.086
                             L27_1  23 keedeeLrqalerviniFksqLfq 46 
                                       +e++++L++  + +  +F  +Lf+
  gi|385805132|ref|YP_005841530.1| 402 HESERSLKKFTQVLAIVFGTSLFS 425
                                       6788999999999999******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (486 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.56
# Mc/sec: 2623.88
//
Query:       gi|385805133|ref|YP_005841531.1|  [L=487]
Description: type II secretion system protein E [Fervidicoccus fontis Kam940]
Scores for complete 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-35  120.3   0.0    1.4e-34  119.4   0.0    1.3  1  T2SSE            Type II/IV secretion system protein
    9.8e-05   22.8   0.0    0.00023   21.6   0.0    1.6  1  AAA_16           AAA ATPase domain
    0.00014   21.5   0.0      0.002   17.7   0.0    2.2  2  AAA_7            P-loop containing dynein motor region
    0.00026   20.6   0.0     0.0008   19.0   0.0    1.7  2  AAA_25           AAA domain
    0.00048   20.4   0.1     0.0022   18.3   0.1    2.1  2  AAA_22           AAA domain
     0.0012   18.4   0.0     0.0025   17.5   0.0    1.4  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
     0.0037   17.0   0.3       0.01   15.5   0.0    1.8  2  AAA_30           AAA domain
     0.0041   17.6   0.0      0.011   16.2   0.0    1.8  1  AAA_18           AAA domain
      0.006   16.8   0.1      0.023   14.9   0.0    2.0  2  AAA_33           AAA domain
     0.0072   16.7   0.1      0.054   13.9   0.0    2.4  2  AAA              ATPase family associated with various cellul
  ------ inclusion threshold ------
      0.013   15.3   0.3      0.036   13.9   0.0    1.8  2  AAA_11           AAA domain
      0.021   14.8   0.0      0.068   13.2   0.0    1.9  1  AAA_5            AAA domain (dynein-related subfamily)
      0.027   14.8   0.1      0.075   13.4   0.1    1.7  1  AAA_19           AAA domain
      0.033   13.5   0.0      0.085   12.2   0.0    1.7  2  FtsK_SpoIIIE     FtsK/SpoIIIE family
      0.036   14.2   0.4        1.4    9.0   0.0    2.9  2  Trans_reg_C      Transcriptional regulatory protein, C termin
      0.039   13.7   0.0      0.062   13.0   0.0    1.3  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.048   13.1   0.0       0.11   11.9   0.0    1.6  1  SRPRB            Signal recognition particle receptor beta su
       0.05   13.4   0.0        0.1   12.4   0.0    1.4  1  AAA_29           P-loop containing region of AAA domain
       0.06   13.1   0.0       0.12   12.1   0.0    1.4  1  IstB_IS21        IstB-like ATP binding protein
      0.063   12.6   0.0       0.27   10.5   0.0    1.9  2  Zeta_toxin       Zeta toxin
      0.065   13.0   0.0       0.12   12.1   0.0    1.4  1  ATP_bind_1       Conserved hypothetical ATP binding protein
      0.081   12.7   0.0       0.16   11.7   0.0    1.5  1  DEAD             DEAD/DEAH box helicase
       0.11   12.4   0.0       0.32   10.9   0.0    1.7  1  NACHT            NACHT domain
       0.14   11.9   0.0       0.28   10.9   0.0    1.4  1  AAA_24           AAA domain
       0.16   12.2   0.0       0.32   11.2   0.0    1.5  1  AAA_28           AAA domain
       0.39   11.2   2.3          3    8.3   0.0    2.8  3  AAA_23           AAA domain
       0.44   10.0   0.0       0.44   10.0   0.0    1.9  3  UvrD-helicase    UvrD/REP helicase N-terminal 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 !  119.4   0.0   2.1e-37   1.4e-34       5     244 ..     126     379 ..     123     391 .. 0.88

  Alignments for each domain:
  == domain 1  score: 119.4 bits;  conditional E-value: 2.1e-37
                             T2SSE   5 leallddekvsdihvekpervkvrervdg.......ielreveelekaalerlisriaalakldiseerplqdarlp 74 
                                       l+a+ldd+ + d+ ve p++++vr  + +        +  ++ + +++++ ++ + ia+  +  is+++p++d +lp
  gi|385805133|ref|YP_005841531.1| 126 LQAILDDPYILDLSVEGPGQIWVRHSLVEmlrpeqdFVPTNIIFNSNEEIVMMQQVIATKCNTFISTSNPILDSQLP 202
                                       689********************99876633333345667777889999999999********************** PP

                             T2SSE  75 ..ekgvrlrvvllPvvag.ealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllya 148
                                         ++g+r+++v++ v+++ +++viRk+ ++  ++++++ ++ +  ++ae+lr  +++rg+++v+G+ gsGKtt++ +
  gi|385805133|ref|YP_005841531.1| 203 pkDGGHRVHLVFPTVSHQrPEIVIRKRLPMPPSIEQYIEMKVMPRAVAELLRLVLNARGSVIVAGPPGSGKTTVMRS 279
                                       9999********99999999*******************************************************88 PP

                             T2SSE 149 llkeinksderivtvEDpvEiql.eganqvqlnak...kakvtfadllraaLRlrPDr.imvGEiRdketleilkAv 220
                                       ll     ++ +++++ED+ Ei++ +g   ++  +    ++kv++ dl +a+LR    r i+vGE R++e+  + +A+
  gi|385805133|ref|YP_005841531.1| 280 LLYHSVPKTWKVMVIEDTGEIDPpQGSPWTRYTTFelgSVKVDLFDLAKASLRASGTRlIVVGETRGQEARVLAQAM 356
                                       876554455*************94455555555547789**************998764889*************** PP

                             T2SSE 221 nTGHlgslsTlHansaagalerLe 244
                                       + G  g+l++ H  s+ ++ +rL 
  gi|385805133|ref|YP_005841531.1| 357 MVGL-GALTSFHGSSPEEVSTRLM 379
                                       ***5.55***************96 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   3.5e-07   0.00023      12      61 ..     249     299 ..     246     360 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 3.5e-07
                            AAA_16  12 LlsalervrsgrpelvllsGesGvGKsslvrellralekd..ggiflrgkcd 61 
                                       ++++l+ v   r ++v++ G++G+GK++++r+ll +   +  ++ +++ + +
  gi|385805133|ref|YP_005841531.1| 249 VAELLRLVLNAR-GSVIVAGPPGSGKTTVMRSLLYHSVPKtwKVMVIEDTGE 299
                                       566666666555.79***************9999766666343444555554 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 ?    1.0   0.0      0.38   2.5e+02      54      86 ..     153     186 ..     141     189 .. 0.81
   2 !   17.7   0.0     3e-06     0.002      24      67 ..     251     294 ..     244     302 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.38
                             AAA_7  54 lkkld.kekylsltinfsaqtsanqlqdiieskl 86 
                                       ++ l  ++++++++i f+++ +  ++q++i  k 
  gi|385805133|ref|YP_005841531.1| 153 VEMLRpEQDFVPTNIIFNSNEEIVMMQQVIATKC 186
                                       555543789*********************9886 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 3e-06
                             AAA_7  24 yllelllknkkpvllvGptGtGKtviikdllkkldkekylslti 67 
                                        ll+l+l+++ +v++ Gp G+GKt+++++ll +  ++++++++i
  gi|385805133|ref|YP_005841531.1| 251 ELLRLVLNARGSVIVAGPPGSGKTTVMRSLLYHSVPKTWKVMVI 294
                                       589999***********************776666699988877 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.2e-06    0.0008      13      56 ..     240     283 ..     228     295 .. 0.86
   2 ?   -2.8   0.0       5.9   3.9e+03      71      96 ..     334     359 ..     326     379 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.2e-06
                            AAA_25  13 adlaapppprrwlvkgllpagelallaGapgtGKttlaldlala 56 
                                        + ++ p+ +  l++ +l a + +++aG+pg+GKtt+  +l ++
  gi|385805133|ref|YP_005841531.1| 240 IEMKVMPRAVAELLRLVLNARGSVIVAGPPGSGKTTVMRSLLYH 283
                                       567789999****************************9988876 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 5.9
                            AAA_25  71 qgkVlyvsaEdsedelrrRlravgea 96 
                                        g+ l+v++E + +e r  ++a++  
  gi|385805133|ref|YP_005841531.1| 334 SGTRLIVVGETRGQEARVLAQAMMVG 359
                                       57778888888886666655555544 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       5.3   3.5e+03      71      87 ..      67      83 ..       8      90 .. 0.62
   2 !   18.3   0.1   3.3e-06    0.0022       5      29 ..     260     284 ..     257     344 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 5.3
                            AAA_22 71 erlsseellealeqalr 87
                                      + ++ e+l++++e+ l+
  gi|385805133|ref|YP_005841531.1| 67 PLKNVEDLRQRIEEKLE 83
                                      44455555555555554 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 3.3e-06
                            AAA_22   5 agilvvtGesGtGKTtllrrlleql 29 
                                       +g+++v G++G+GKTt++r ll+  
  gi|385805133|ref|YP_005841531.1| 260 RGSVIVAGPPGSGKTTVMRSLLYHS 284
                                       799*****************99865 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 !   17.5   0.0   3.7e-06    0.0025       3      35 ..     263     296 ..     262     305 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.7e-06
                                       EEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS CS
                              cobW   3 tvltGflGsGKTtLlnhll..enraglklavivNe 35 
                                       ++++G++GsGKTt++++ll  +  +  k+ vi+ +
  gi|385805133|ref|YP_005841531.1| 263 VIVAGPPGSGKTTVMRSLLyhSVPKTWKVMVIE-D 296
                                       689****************55445555555554.4 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.6e-05      0.01      11      38 ..     254     280 ..     249     299 .. 0.77
   2 ?   -1.9   0.1       3.5   2.3e+03     110     126 ..     329     345 ..     315     359 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.6e-05
                            AAA_30  11 ealltsgdrvavltGpAGtGKttalkal 38 
                                       + +l+ +   +++ Gp+G+GKtt++++l
  gi|385805133|ref|YP_005841531.1| 254 RLVLNAR-GSVIVAGPPGSGKTTVMRSL 280
                                       5455555.5899*************987 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.5
                            AAA_30 110 kaaekagakvilvGDer 126
                                       ++++++g+++i+vG +r
  gi|385805133|ref|YP_005841531.1| 329 ASLRASGTRLIVVGETR 345
                                       44566678888888765 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   1.7e-05     0.011       1      18 [.     263     280 ..     263     302 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.7e-05
                            AAA_18   1 IlltGtpGvGKttlakeL 18 
                                       ++++G+pG+GKtt+ + L
  gi|385805133|ref|YP_005841531.1| 263 VIVAGPPGSGKTTVMRSL 280
                                       79************9988 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   3.5e-05     0.023       2      20 ..     263     281 ..     263     342 .. 0.89
   2 ?   -1.7   0.0       4.5     3e+03      19      46 ..     411     438 ..     409     464 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.5e-05
                            AAA_33   2 vllvGlpGsGKstlaerll 20 
                                       v++ G+pGsGK+t+ ++ll
  gi|385805133|ref|YP_005841531.1| 263 VIVAGPPGSGKTTVMRSLL 281
                                       7899************997 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4.5
                            AAA_33  19 llkklgavllssdtlrrrlfgtdqqskt 46 
                                       ll++l++  ls++++++++  +d++  +
  gi|385805133|ref|YP_005841531.1| 411 LLAELKYDPLSQNVVSKTIWDRDKDGME 438
                                       7789999999999999999998887554 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       2.1   1.4e+03      30      63 ..      57      88 ..      11      99 .. 0.75
   2 !   13.9   0.0   8.2e-05     0.054       1      21 [.     263     283 ..     263     356 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 2.1
                                      ETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEE CS
                               AAA 30 sgsellskyvgesekkirelfkeakekakpsilf 63
                                      sgs++   yv +  k++++l ++++ek +  il+
  gi|385805133|ref|YP_005841531.1| 57 SGSNFA--YVVKPLKNVEDLRQRIEEKLEEIILL 88
                                      333333..89999999999999999988435554 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 8.2e-05
                                       EEEESSTTSSHHHHHHHHHHH CS
                               AAA   1 vllyGppGtGKTllakavake 21 
                                       v++ GppG GKT++++++  +
  gi|385805133|ref|YP_005841531.1| 263 VIVAGPPGSGKTTVMRSLLYH 283
                                       6899************99766 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   5.4e-05     0.036      11      42 ..     254     285 ..     247     338 .. 0.85
   2 ?   -1.9   0.2       3.5   2.3e+03     150     187 ..     438     475 ..     405     484 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.4e-05
                            AAA_11  11 ksalseseitliqGPPGtgKTktivellsqll 42 
                                       + +l+ ++ +++ GPPG+gKT++  +ll + +
  gi|385805133|ref|YP_005841531.1| 254 RLVLNARGSVIVAGPPGSGKTTVMRSLLYHSV 285
                                       6678888889**************99998775 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.5
                            AAA_11 150 eklkkskekskskleqerrklkkerkelskeleeaees 187
                                       e+++++   +++k e+ +  l+k  + l+++++ +ees
  gi|385805133|ref|YP_005841531.1| 438 EISLETLISRSEKIEELEMRLEKPFQALNRKVKDEEES 475
                                       55555555566666666666666666666666555544 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0    0.0001     0.068       2      30 ..     263     292 ..     262     301 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.0001
                                       EEEE--SSSSHHHHHHHGGGGB.S--EEEE CS
                             AAA_5   2 vlLvGppGtgKselaerlaaal.nreveyv 30 
                                       v++ GppG+gK++++++l+     +++ ++
  gi|385805133|ref|YP_005841531.1| 263 VIVAGPPGSGKTTVMRSLLYHSvPKTWKVM 292
                                       899***************988843333333 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   0.00011     0.075      10      34 ..     260     284 ..     254     294 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00011
                            AAA_19  10 ekvllvtaGpGtGKTrvlkhivall 34 
                                       ++ ++v ++pG+GKT+v++  + + 
  gi|385805133|ref|YP_005841531.1| 260 RGSVIVAGPPGSGKTTVMRSLLYHS 284
                                       567899999*********9887765 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       7.4   4.9e+03     155     174 ..      70      93 ..      55     100 .. 0.66
   2 ?   12.2   0.0   0.00013     0.085      38      61 ..     258     282 ..     231     295 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 7.4
                                       ........................ CS
                      FtsK_SpoIIIE 155 nyddlaaene....ritsLsnqgp 174
                                       n +dl+++ e    +i++L+++g 
  gi|385805133|ref|YP_005841531.1|  70 NVEDLRQRIEekleEIILLMKRGN 93 
                                       555555555555568888888875 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00013
                                       S-..SEEEE--TTSSHHHHHHHHHH CS
                      FtsK_SpoIIIE  38 ma.shllvaGatgsGKStalntLil 61 
                                       +a + ++vaG +gsGK+t++++L+ 
  gi|385805133|ref|YP_005841531.1| 258 NArGSVIVAGPPGSGKTTVMRSLLY 282
                                       336789*************999874 PP

>> Trans_reg_C  Transcriptional regulatory protein, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.38   2.5e+02      18      46 ..     140     168 ..     134     170 .. 0.87
   2 ?    9.0   0.0    0.0021       1.4      12      52 ..     407     447 ..     401     454 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.38
                                       HHTTTSEEEHHHHHHHHTTTTSTSHTHHH CS
                       Trans_reg_C  18 lenpgrvvsreeLleevwgededvddrtv 46 
                                       +e pg+++ r  L+e + +e+++v ++ +
  gi|385805133|ref|YP_005841531.1| 140 VEGPGQIWVRHSLVEMLRPEQDFVPTNII 168
                                       6789******************9999875 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0021
                                       HHHHHHHHTTTSEEEHHHHHHHHTTTTSTSHTHHHHHHHHH CS
                       Trans_reg_C  12 klLelLlenpgrvvsreeLleevwgededvddrtvdvhisr 52 
                                       + L+lL+e +  ++s++   + +w++d+d+ + ++++ isr
  gi|385805133|ref|YP_005841531.1| 407 RQLKLLAELKYDPLSQNVVSKTIWDRDKDGMEISLETLISR 447
                                       5699***********************************98 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   9.4e-05     0.062       2      22 ..     264     284 ..     263     325 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.4e-05
                   Viral_helicase1   2 vvhGvpGcGKStlirkllrts 22 
                                       +v+G pG+GK+t+ r+ll +s
  gi|385805133|ref|YP_005841531.1| 264 IVAGPPGSGKTTVMRSLLYHS 284
                                       89****************883 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 ?   11.9   0.0   0.00017      0.11       3      33 ..     260     290 ..     258     306 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00017
                                       --EEEEE-STTSSHHHHHHHHHHSS---B-- CS
                             SRPRB   3 kpavllvGlsdsGKTslftrLttdsvkktvt 33 
                                       + +v+++G+  sGKT+++  L+  sv kt  
  gi|385805133|ref|YP_005841531.1| 260 RGSVIVAGPPGSGKTTVMRSLLYHSVPKTWK 290
                                       5689*******************99999865 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00015       0.1      19      50 ..     257     288 ..     251     292 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00015
                            AAA_29  19 idlkgatlltGpsGsGKSTllDAiqalLvpak 50 
                                       ++ +g+++++Gp GsGK+T++ ++ +  vp++
  gi|385805133|ref|YP_005841531.1| 257 LNARGSVIVAGPPGSGKTTVMRSLLYHSVPKT 288
                                       5667899*************977776666665 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 ?   12.1   0.0   0.00018      0.12      28      79 ..     242     292 ..     227     297 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00018
                         IstB_IS21  28 rsldkrkvkeLatlsfiekkenivllGpsGvGKshlaialgveavraglsvl 79 
                                        ++ +r+v+eL  l  ++++ ++++ Gp+G GK+ +  +l ++ v + ++v+
  gi|385805133|ref|YP_005841531.1| 242 MKVMPRAVAELLRLV-LNARGSVIVAGPPGSGKTTVMRSLLYHSVPKTWKVM 292
                                       467788888888774.688899******************999999999997 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0    0.0004      0.27      18      38 ..     262     282 ..     259     297 .. 0.79
   2 ?   -1.2   0.0       1.5     1e+03     112     168 ..     427     483 ..     421     484 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0004
                        Zeta_toxin  18 lillgGqpGAGKselaellkd 38 
                                       +++++G pG+GK+++++ l  
  gi|385805133|ref|YP_005841531.1| 262 SVIVAGPPGSGKTTVMRSLLY 282
                                       589************998765 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.5
                        Zeta_toxin 112 klaealkkaGYevevvvvavkkelSrlgvldRyeeevae.gRlvpkeehdeafeglre 168
                                       k++ +  k+G e+ +  ++ ++e  +++++ R e+  ++ +R+v+ ee  ++fe+l e
  gi|385805133|ref|YP_005841531.1| 427 KTIWDRDKDGMEISLETLISRSEK-IEELEMRLEKPFQAlNRKVKDEEESKMFENLLE 483
                                       555555556666666666655554.677788888886675699999999999999875 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 ?   12.1   0.0   0.00018      0.12       1      23 [.     265     287 ..     265     296 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00018
                        ATP_bind_1   1 vvGpaGsGKttfvgalseilelr 23 
                                       v+Gp+GsGKtt +++l  +   +
  gi|385805133|ref|YP_005841531.1| 265 VAGPPGSGKTTVMRSLLYHSVPK 287
                                       89*************98876555 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00024      0.16       6      54 ..     251     295 ..     247     345 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00024
                                       HHHHHHH.TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEE CS
                                       xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   6 eaiplil.gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalive 54 
                                       e + l+l   g+v+va++ GsGKT+++   ++++v      ++ k++++e
  gi|385805133|ref|YP_005841531.1| 251 ELLRLVLnARGSVIVAGPPGSGKTTVMRSLLYHSV-----PKTWKVMVIE 295
                                       55667774557***************877777666.....4444555555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00048      0.32       3      21 ..     263     281 ..     262     286 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00048
                                       EEEEC-TTTCHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqkla 21 
                                       vi+ G++GsGKTt +++l 
  gi|385805133|ref|YP_005841531.1| 263 VIVAGPPGSGKTTVMRSLL 281
                                       89**************986 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00042      0.28       5      22 ..     263     280 ..     260     305 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00042
                            AAA_24   5 iliyGpsgiGKTtlakel 22 
                                       +++ Gp+g+GKTt++++l
  gi|385805133|ref|YP_005841531.1| 263 VIVAGPPGSGKTTVMRSL 280
                                       789************998 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00048      0.32       2      22 ..     263     283 ..     262     300 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00048
                            AAA_28   2 ivitGgestGKTtlleaLaar 22 
                                       +++ G++++GKTt+++ L  +
  gi|385805133|ref|YP_005841531.1| 263 VIVAGPPGSGKTTVMRSLLYH 283
                                       7899*************9866 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0       1.1   7.2e+02     152     174 ..      68      90 ..       4     115 .. 0.60
   2 ?    8.3   0.0    0.0044         3      19      41 ..     260     282 ..     252     283 .. 0.87
   3 ?   -1.0   0.9       3.2   2.1e+03     136     156 ..     446     466 ..     402     484 .. 0.49

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 1.1
                            AAA_23 152 kerleelekeleeledekkllek 174
                                       ++ +e+l++ +ee+ +e+ ll k
  gi|385805133|ref|YP_005841531.1|  68 LKNVEDLRQRIEEKLEEIILLMK 90 
                                       33566666666666666555554 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0044
                            AAA_23  19 kgltlItGpNGaGKTTildAikl 41 
                                       +g +++ Gp G+GKTT+++ + +
  gi|385805133|ref|YP_005841531.1| 260 RGSVIVAGPPGSGKTTVMRSLLY 282
                                       5778999***********98865 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 3.2
                            AAA_23 136 lflgqerfeefelkdkkerle 156
                                       +   + ++ e++l++++++l+
  gi|385805133|ref|YP_005841531.1| 446 SRSEKIEELEMRLEKPFQALN 466
                                       111122222222222222222 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 ?   -3.3   0.0       7.7   5.1e+03      59     259 ..      72      84 ..      61     104 .. 0.68
   2 ?   10.0   0.0   0.00067      0.44      10      38 ..     257     285 ..     249     293 .. 0.81
   3 ?   -2.5   0.2       4.4   2.9e+03     187     203 ..     449     465 ..     407     483 .. 0.52

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 7.7
                                       HHHHHHHHHHHHHCCHHCTT-HHHHHHHHHCTTSEEEEHHHHHHHHHHHHHGGTTSHTTTEEECHHHHHHCCHHHHH CS
                     UvrD-helicase  59 eElkeRieealkkaeqessdderlrlalqnlseanisTlHsfcqkilkkeanrigldpnfrildeedeedlkqqell 135
                                       e l++Riee+l+                                                                 
  gi|385805133|ref|YP_005841531.1|  72 EDLRQRIEEKLE----------------------------------------------------------------- 83 
                                       445555555444................................................................. PP

                                       HHHHSCHSHTTTTHHHHHHHHHHHHHHCCCCCHHHHCCCHHHHHCHHHHHHHHHHHTTCCTTHHCHSSTSCSHHHHH CS
                     UvrD-helicase 136 kelleksaddslnldkkkleklikelsksrnikkeelslskskaeelrelvskakekqlspkelkkafekasdlqkk 212
                                                                                                                    
  gi|385805133|ref|YP_005841531.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                                       HHHHHHHHHHHHHHHTCEEHHHHHHHHHHHHHHCHHHHHHHHHHSSE CS
                     UvrD-helicase 213 iaeflkeyqeqkkeenalDfsdllhallelleeneelaealreryke 259
                                                                                     e
  gi|385805133|ref|YP_005841531.1|  84 ----------------------------------------------E 84 
                                       ..............................................3 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00067
                                       HS-SSEEEEEE-TTSSHHHHHHHHHHHHH CS
                     UvrD-helicase  10 aslggpilveAsAGsGKTfvlaerilrli 38 
                                        + +g+++v+  +GsGKT+v+ ++  + +
  gi|385805133|ref|YP_005841531.1| 257 LNARGSVIVAGPPGSGKTTVMRSLLYHSV 285
                                       5567888899999********99988877 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 4.4
                                       HHHHHTTCCTTHHCHSS CS
                     UvrD-helicase 187 skakekqlspkelkkaf 203
                                       +k++e +++ ++  +a 
  gi|385805133|ref|YP_005841531.1| 449 EKIEELEMRLEKPFQAL 465
                                       44444444444443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (487 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       815  (0.0454571); expected 358.6 (0.02)
Passed bias filter:                      665  (0.0370907); expected 358.6 (0.02)
Passed Vit filter:                       119  (0.00663729); 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: 0.73u 0.36s 00:00:01.08 Elapsed: 00:00:00.53
# Mc/sec: 2783.61
//
Query:       gi|385805134|ref|YP_005841532.1|  [L=163]
Description: hypothetical protein FFONT_0087 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.28   11.0   2.7       0.14   11.9   0.7    1.6  2  DUF4307   Domain of unknown function (DUF4307)


Domain annotation for each model (and alignments):
>> DUF4307  Domain of unknown function (DUF4307)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.7   8.1e-06      0.14       6      55 ..      32      83 ..      29     108 .. 0.82
   2 ?   -2.8   0.0      0.32   5.7e+03      16      28 ..     133     146 ..     126     154 .. 0.42

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.1e-06
                           DUF4307  6 villvvlvvvalalvawigysq.gsadvsaevvgfevvdd.stvevtfeVtr 55
                                      ++ll+++vv++ al +w+ ++q + ++++  +++++v++  s   ++++V+ 
  gi|385805134|ref|YP_005841532.1| 32 MALLLIAVVAVFALRGWLSTQQsRMTNIDMATASYSVQTTfSGYVISLDVRN 83
                                      678899999999999*******9*************9864144556666665 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.32
                           DUF4307  16 alalvawigysq.g 28 
                                       a+ +va+  ++   
  gi|385805134|ref|YP_005841532.1| 133 AGSGVAVKQINVrV 146
                                       33333333333323 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1093  (0.0609627); expected 358.6 (0.02)
Passed bias filter:                      634  (0.0353617); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 994.86
//
Query:       gi|385805135|ref|YP_005841533.1|  [L=108]
Description: hypothetical protein FFONT_0088 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
        1.6    8.8   9.4        1.4    8.9   7.6    1.9  2  Gly-zipper_Omp  Glycine zipper
        5.3    7.3   7.2        1.9    8.7   0.1    2.3  2  XhlA            Haemolysin XhlA


Domain annotation for each model (and alignments):
>> Gly-zipper_Omp  Glycine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.51   4.6e+03      19      28 ..      12      21 ..       6      24 .. 0.64
   2 ?    8.9   7.6   0.00016       1.4       7      34 ..      62      95 ..      62     105 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.51
                    Gly-zipper_Omp 19 grgtGaliGA 28
                                      g g+ a+i+ 
  gi|385805135|ref|YP_005841533.1| 12 GKGIYAFIAS 21
                                      5677777765 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00016
                    Gly-zipper_Omp  7 AaaGaliGgavg......grgtGaliGAavGaav 34
                                      A+aG+ i+ga         +g+  liGA++Ga++
  gi|385805135|ref|YP_005841533.1| 62 AVAGGFIAGAIHfvlgntESGKKLLIGAIIGALI 95
                                      556666666533344444569***********97 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   3.2     0.085   7.6e+02      50      66 ..      57      74 ..      46      75 .. 0.63
   2 ?    8.7   0.1   0.00021       1.9      49      65 ..      84     100 ..      76     102 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.085
                              XhlA 50 Wl.irtiiGalisaviyl 66
                                      Wl + +++G++i+++i +
  gi|385805135|ref|YP_005841533.1| 57 WLgWIAVAGGFIAGAIHF 74
                                      442556889999998866 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00021
                              XhlA  49 kWlirtiiGalisaviy 65 
                                       k li++iiGali a+ +
  gi|385805135|ref|YP_005841533.1|  84 KLLIGAIIGALIMAFYS 100
                                       55789999999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 671.74
//
Query:       gi|385805136|ref|YP_005841534.1|  [L=167]
Description: 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase [Fervidicoccus fontis Kam940]
Scores for complete 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-39  133.5   0.0      1e-38  133.2   0.0    1.0  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
    1.8e-38  132.0   0.1    2.1e-38  131.7   0.1    1.0  1  adh_short     short chain dehydrogenase


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.2   0.0   1.2e-42     1e-38      52     203 ..       4     161 ..       3     164 .. 0.89

  Alignments for each domain:
  == domain 1  score: 133.2 bits;  conditional E-value: 1.2e-42
                                       SHHHHHHHHHHHHHHHSSEEEEEE-----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC..CEEEEE CS
                      adh_short_C2  52 deeqvealveevvekfgklDilvnnagiapklkgpfletsreefdraldvnlyslfllakaalplmkeg..gsivnl 126
                                       +ee+v++  e++ e +g++D+lvnnagi p+ ++++l+++ ee+dr+ldvnl++++l++k+ +p+m+++  gsi+n+
  gi|385805136|ref|YP_005841534.1|   4 NEESVKRGLEKAIEVVGGIDVLVNNAGIEPP-NKSLLDLTSEEYDRVLDVNLKGVWLITKYTVPHMAKRggGSIINI 79 
                                       689****************************.********************************7776669****** PP

                                       EEGGGTSBSTTTTHHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEE--BHCTGGGGSTT.....HHHHHHHHHHHSTT CS
                      adh_short_C2 127 ssvgaervvpnynaygaaKaalealtrylAvelgpkgiRvNavspgpikTlaasgikg.....fdelleelearapl 198
                                       +s+++ ++    +ay+++Ka+++ +t   A elg+ +iRvNa++pg+++T++ +++++      +e+++   +r  l
  gi|385805136|ref|YP_005841534.1|  80 ASMAGLKTAGWSDAYSVSKAGVIMFTMVSAIELGKLKIRVNAIAPGWVDTPMIERAAKnlmmtPEEFKKLNSQRVVL 156
                                       ****************************************************7777653554445566666666666 PP

                                       SS-B- CS
                      adh_short_C2 199 grlgt 203
                                        r+ t
  gi|385805136|ref|YP_005841534.1| 157 ARFRT 161
                                       66555 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.7   0.1   2.4e-42   2.1e-38      61     191 ..       5     136 ..       1     139 [. 0.96

  Alignments for each domain:
  == domain 1  score: 131.7 bits;  conditional E-value: 2.4e-42
                                       HHHHHHHHHHHHHHHSSESEEEE---S.S--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEE CS
                         adh_short  61 reevealvekavkklgkldvLvnNAGi.tgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsS 136
                                       +e+v++ +eka++ +g++dvLvnNAGi   +++  +l++ee++rv++vNl+gv l+t+  +p+m k+ +G+I+n++S
  gi|385805136|ref|YP_005841534.1|   5 EESVKRGLEKAIEVVGGIDVLVNNAGIePPNKSLLDLTSEEYDRVLDVNLKGVWLITKYTVPHMAKRGGGSIINIAS 81 
                                       7899***********************87889999****************************************** PP

                                       GGGTSB-TTBHHHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHHC CS
                         adh_short 137 vagkvpvagvaaYsAsKaavagltrslakelaptgirvnavaPGlvdTdmakelr 191
                                       +ag++   +  aYs sKa+v+++t+  a el + +irvna+aPG vdT+m +++ 
  gi|385805136|ref|YP_005841534.1|  82 MAGLKTAGWSDAYSVSKAGVIMFTMVSAIELGKLKIRVNAIAPGWVDTPMIERAA 136
                                       **************************************************88765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.49
# Mc/sec: 1029.43
//
Query:       gi|385805137|ref|YP_005841535.1|  [L=65]
Description: short chain dehydrogenase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-13   51.1   0.1    1.2e-13   50.9   0.1    1.0  1  adh_short        short chain dehydrogenase
    1.6e-07   31.2   0.1    1.7e-07   31.1   0.1    1.0  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    0.00014   21.8   0.1    0.00016   21.6   0.1    1.0  1  KR               KR domain
    0.00094   18.4   0.2      0.001   18.3   0.2    1.0  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
     0.0032   16.8   0.1     0.0032   16.8   0.1    1.1  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
     0.0032   17.0   0.0     0.0034   16.9   0.0    1.0  1  Epimerase        NAD dependent epimerase/dehydratase family
  ------ inclusion threshold ------
      0.014   15.3   0.0      0.016   15.2   0.0    1.0  1  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
      0.015   15.1   0.0      0.024   14.4   0.0    1.3  1  NOG1             Nucleolar GTP-binding protein 1 (NOG1)
      0.024   15.4   0.0      0.026   15.2   0.0    1.1  1  Methyltransf_25  Methyltransferase domain
      0.032   14.5   0.0      0.036   14.3   0.0    1.1  1  TrkA_N           TrkA-N domain
      0.084   12.8   0.2      0.096   12.6   0.2    1.1  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
      0.091   11.7   0.2      0.094   11.7   0.2    1.0  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
       0.13   11.7   0.1       0.13   11.6   0.1    1.0  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.9   0.1   8.8e-17   1.2e-13       1      59 [.       6      64 ..       6      65 .] 0.97

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 8.8e-17
                                      SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTT CS
                         adh_short  1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvt 59
                                      k+ lvtG++sGIG+aia++l ++G +v+++d se+    vak++++eg +a++++vDv+
  gi|385805137|ref|YP_005841535.1|  6 KISLVTGGGSGIGKAIAEKLSSMGSTVIIFDVSEQSGSSVAKQINDEGGNAHFFKVDVS 64
                                      5679******************************************************8 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.1   1.2e-10   1.7e-07       4      52 ..      15      65 .]      10      65 .] 0.91

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 1.2e-10
                                      TSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSE.EEE--TTS CS
                      adh_short_C2  4 sgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgae.vlecDVtd 52
                                      sgIG+aiA++l + G +v++ d++e++  + ++++ +e+g++ ++++DV++
  gi|385805137|ref|YP_005841535.1| 15 SGIGKAIAEKLSSMGSTVIIFDVSEQSgSSVAKQINDEGGNAhFFKVDVSQ 65
                                      8**************************89999999999997758*****85 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.1   1.2e-07   0.00016       4      64 ..       9      65 .]       7      65 .] 0.84

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.2e-07
                                      EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT- CS
                                KR  4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsd 64
                                      l+tGG  g+G+++a+ l + g + +++   + +   + ++  +++++ g + +++++Dvs+
  gi|385805137|ref|YP_005841535.1|  9 LVTGGGSGIGKAIAEKLSSMGSTVIIFDVSE-Q---SGSSVAKQINDEGGNAHFFKVDVSQ 65
                                      9********************9988886555.2...3334678999*************95 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.2   7.5e-07     0.001       2      50 ..       9      56 ..       8      64 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 7.5e-07
                                      EEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-T CS
                   Polysacc_synt_2  2 lvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkk 50
                                      lvtG+g  iG+++ +++ ++  +++i+++ +E++  +++k++++e  + 
  gi|385805137|ref|YP_005841535.1|  9 LVTGGGSGIGKAIAEKLSSMG-STVIIFDVSEQSGSSVAKQINDEGGNA 56
                                      8************99988775.6899**************987766554 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   0.1   2.3e-06    0.0032      35      74 ..       4      44 ..       1      61 [. 0.78

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.3e-06
                                      TTSEEEEES-SH.HHHHHHHHHHHTT-EEEEESSSHHHHHC CS
                      2-Hacid_dh_C 35 sgktvGiiGlGr.IGqavakrlkafgmkviaydrskkkeee 74
                                      ++k   + G G+ IG+a+a++l+++g  vi++d+s+++ ++
  gi|385805137|ref|YP_005841535.1|  4 KNKISLVTGGGSgIGKAIAEKLSSMGSTVIIFDVSEQSGSS 44
                                      5555566666644**********************997763 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.4e-06    0.0034       2      50 ..       9      63 ..       8      65 .] 0.79

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.4e-06
                                      EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.......EEEE--T CS
                         Epimerase  2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl.......elveldl 50
                                      lVtG+   iG+a++++l + g +vi +d  ++++ + +++ +       ++ ++d+
  gi|385805137|ref|YP_005841535.1|  9 LVTGGGSGIGKAIAEKLSSMGSTVIIFDVSEQSGSSVAKQ-IndeggnaHFFKVDV 63
                                      8**************************9996666654443.236677777777776 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   1.1e-05     0.016       4      49 ..      10      60 ..       6      64 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.1e-05
                                      EE--SH.HHHHHHHHHHTTT--EEEE-S-H....HHHHHHHHHSSBTTTBT CS
                    NAD_Gly3P_dh_N  4 vlGaGs.wGtalAkvlaenghevrlwvree....elieeineehenvkyLp 49
                                      v G+Gs  G a+A  l++ g++v ++  +e     ++++in+e  n ++++
  gi|385805137|ref|YP_005841535.1| 10 VTGGGSgIGKAIAEKLSSMGSTVIIFDVSEqsgsSVAKQINDEGGNAHFFK 60
                                      45777657********************99999999********9999876 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 ?   14.4   0.0   1.7e-05     0.024      18      36 ..      32      50 ..      23      50 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.7e-05
                              NOG1 18 lFllDpseecgysleeQls 36
                                      + ++D+se++g s+++Q++
  gi|385805137|ref|YP_005841535.1| 32 VIIFDVSEQSGSSVAKQIN 50
                                      5699*************86 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   1.9e-05     0.026       5      56 ..      14      64 ..       9      65 .] 0.79

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.9e-05
                                      T-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCC CS
                   Methyltransf_25  5 GcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdae 56
                                      G G G+ +++ +  +g ++v+ +D+se+    +++++++eg n++f + d++
  gi|385805137|ref|YP_005841535.1| 14 GSGIGKAIAEKLSSMG-STVIIFDVSEQSGSSVAKQINDEGGNAHFFKVDVS 64
                                      5566654444444446.*****************************999986 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   2.6e-05     0.036       5      50 ..      13      64 ..       9      65 .] 0.77

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.6e-05
                                      S-SHHHHHHHHHHHH.TTEEEEEEESSHHH....HHHHHHTT..SEEEES-TT CS
                            TrkA_N  5 GlGrvGrslaeeLse.ggkdvvvidkdeer....veelreeg..levvvgdat 50
                                      G + +G+++ae+Ls+ g+  v++ d +e+     ++++ +eg  +++++ d++
  gi|385805137|ref|YP_005841535.1| 13 GGSGIGKAIAEKLSSmGS-TVIIFDVSEQSgssvAKQINDEGgnAHFFKVDVS 64
                                      6778***********666.6*******96544448888888866667777765 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   0.2     7e-05     0.096       5      44 ..      11      51 ..       8      61 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7e-05
                                      E--SC.CHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHH CS
                           3HCDH_N  5 iGaGt.mGagiaavfasagleVvlvdiseealekalekiek 44
                                       G G  +G+ ia+ + s g +V ++d+se++  +++++i++
  gi|385805137|ref|YP_005841535.1| 11 TGGGSgIGKAIAEKLSSMGSTVIIFDVSEQSGSSVAKQIND 51
                                      5665449***********************99999999987 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   6.8e-05     0.094       1      54 [.       9      63 ..       9      65 .] 0.73

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.8e-05
                         3Beta_HSD  1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkk....viegDv 54
                                      +vtGg+  +G+a+ ++L ++++  +v ++D+ e++   + ++++n +     + ++Dv
  gi|385805137|ref|YP_005841535.1|  9 LVTGGGSGIGKAIAEKLSSMGS--TVIIFDVSEQSGS-SVAKQINDEGgnahFFKVDV 63
                                      69*******************6..9*****9987654.33333333223334777777 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   9.6e-05      0.13       1      61 [.       9      63 ..       9      65 .] 0.75

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.6e-05
                                      EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--T CS
                     GDP_Man_Dehyd  1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDl 61
                                      L+TG+   iG  +ae+L + g +v++++  ++s +  ++++  +d      +n +++k+D+
  gi|385805137|ref|YP_005841535.1|  9 LVTGGGSGIGKAIAEKLSSMGSTVIIFDVSEQSGS--SVAKQIND----EGGNAHFFKVDV 63
                                      8****999****************99877766654..33333332....246788888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 413.67
//
Query:       gi|385805138|ref|YP_005841536.1|  [L=38]
Description: hypothetical protein FFONT_0091 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 256.38
//
Query:       gi|385805139|ref|YP_005841537.1|  [L=47]
Description: hypothetical protein FFONT_0092 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 333.59
//
Query:       gi|385805140|ref|YP_005841538.1|  [L=536]
Description: potassium-transporting ATPase subunit A [Fervidicoccus fontis Kam940]
Scores for complete 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-146  488.5  34.2   2.5e-146  488.1  34.2    1.1  1  KdpA      Potassium-transporting ATPase A subunit


Domain annotation for each model (and alignments):
>> KdpA  Potassium-transporting ATPase A subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  488.1  34.2  1.4e-150  2.5e-146       3     543 ..      12     532 ..      10     534 .. 0.95

  Alignments for each domain:
  == domain 1  score: 488.1 bits;  conditional E-value: 1.4e-150
                                       HHHHHHHHHHHHHHHHHHHHTT-...--SS-SHHHHHHHHHHT---.----HHHHHHHHHHHHHHHHHHHHHHHHTT CS
                              KdpA   3 llllllllalplgkylakvfegektlldkllkpverllyrllgvdeeeemtwkeYalalllfnlvlllllylllrlq 79 
                                       +++++ ll + l++ l+k++ + +    kllk+v ++ + ++g+ +++e+++ +Y++  +l+n++l+++ +++l+ q
  gi|385805140|ref|YP_005841538.1|  12 IFIAVSLLGYELSRLLKKMVLEWNFEPPKLLKKVFDV-LDIIGLGSSSEKSFLKYIADAFLLNFILIAIDTIMLMKQ 87 
                                       6788889999999999998888887778888888765.6899*********************************** PP

                                       TTSS--SS------HHHHHHHHHHHHTT-----S-HHHH--HHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHS-S-S CS
                              KdpA  80 gvlplnpeglealspdlafntavSFvtntnlQhYsgestlsylsqmlgltvlnFvsaatGlavavalirglarketk 156
                                       ++++      + l +dla+ntavSFvtntnlQhY+ge +l++++q++++ +++F+++atG+av +a++r+l++ +  
  gi|385805140|ref|YP_005841538.1|  88 SLFFGG----PDLPWDLALNTAVSFVTNTNLQHYAGEISLTNMAQCVVIGTTMFIAPATGIAVSLAFMRSLKGLQ-- 158
                                       988766....679**********************************************************9887.. PP

                                       ----HHHHHHHHHHHTHHHHHHHHHHHHHHHT--------EEEE-SSS-EEEE--SSHHHHHHHHHHTT----SSSS CS
                              KdpA 157 elGnfyvdlvrailrvLLPlslvvalllvaqGvpqtlsgkaevttlegakqtialGpvAsleaIkqlGtnGGGffga 233
                                         Gnfy dlv +++++LLP+s+++a++l + Gvpqt++++++++     +  ++lGp+As+eaIk lGtnGGGffga
  gi|385805140|ref|YP_005841538.1| 159 -AGNFYRDLVMVTFFLLLPISIIAAVILASLGVPQTFEDHVAFENPYAGSFIMRLGPIASFEAIKLLGTNGGGFFGA 234
                                       .9*******************************************999***************************** PP

                                       TTTSTTTS-SHHHHHHHHHHHHHHHHHHHHHHHHHTS-THHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHH..-- CS
                              KdpA 234 NsahpfenptaltnlleilaillipaalvftfGrmvkdkrqglailavmlvlflvllvvvvvaeaagnpalaeeqag 310
                                       Nsahpfenp+ l+n++e +++llip++l+ftfGr++++kr gl ++a+ ++l+++++ v+v++ +   pal+     
  gi|385805140|ref|YP_005841538.1| 235 NSAHPFENPNGLSNFIESVLMLLIPTSLLFTFGRIFGKKR-GLSMFAIAYALAFMIIGVAVMNRV---PALSY---- 303
                                       *************************************988.999999999999999999988765...55554.... PP

                                       ---TTB-SSS-HHHHHHHHHHHHHTT----SS-GGGS-HHHHHHHHHHHHTS-TT-TTTHHHHHHHHHHHHHHHHHH CS
                              KdpA 311 gnmeGkEvrfGiaasalfavvttatstGavnamhdsltplgglvpllnmmlevvfGGvGvGllnllvfvilavFiag 387
                                             E r+G++ +  f++++    tGa  +++ ++ p ++++ l++m+++ v+G+ GvGll+llv++++ +Fi +
  gi|385805140|ref|YP_005841538.1| 304 ----LAEPRLGYEGALAFNTASLLSDTGATASSLFAMRPSAIASFLIAMFIQSVPGADGVGLLYLLVYIFIIIFIGS 376
                                       ....4589********************************************************************* PP

                                       HHHTS--EETTEE--HHHHHHHHHHHHHHHHHHHHHHHHHTTSHHHTT.--S-THHHHHHHHHHHHHHHTT-----S CS
                              KdpA 388 LmvGrtPeylgkkiearevklaalaiLvhpllilvgtalalalpalas.lsnpgahglsevLYeftSaaanNGSafe 463
                                       Lm+G+tP++l+  i+ + vk++++++L+hp++ilv+ta+al++++  s  s  +++ ++ vLYeftSaaanNGS++ 
  gi|385805140|ref|YP_005841538.1| 377 LMIGKTPKFLNMGISPKVVKYSTIVFLIHPTIILVPTAIALLTKQYLSfASSLNPQVYTMVLYEFTSAAANNGSGYL 453
                                       ********************************************6666589999*********************** PP

                                       -S---SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS------TT---SSHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                              KdpA 464 GlgdntvfwnltlglamllgRflpiiavlaiAgslaakkkvpesagtlktdtplFvvllvgvilivgaLtFlPalaL 540
                                       G   nt fwn++++++m+lgR+lp+ + l+iA+ l++ k+     + +kt++ lF+v+ v++i+i++aLtF+P++++
  gi|385805140|ref|YP_005841538.1| 454 GTMGNTAFWNVSTAIVMFLGRYLPLGLFLLIAQDLHRCKRG-VADEPVKTQGGLFIVFSVVMIIILTALTFFPFIVI 529
                                       *************************************9997.67889****************************** PP

                                       THH CS
                              KdpA 541 GPi 543
                                       GP+
  gi|385805140|ref|YP_005841538.1| 530 GPM 532
                                       **8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (536 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       955  (0.0532657); 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:                         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: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 3617.61
//
Query:       gi|385805141|ref|YP_005841539.1|  [L=704]
Description: K+-transporting ATPase subunit B [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.3e-37  127.1   1.4    5.3e-37  127.1   1.4    2.7  3  E1-E2_ATPase  E1-E2 ATPase
    1.3e-28  100.7   0.4    2.3e-28   99.9   0.4    1.4  1  Hydrolase     haloacid dehalogenase-like hydrolase
    2.1e-07   31.0   1.2    1.9e-05   24.6   0.3    2.5  2  Hydrolase_3   haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.017   15.0   0.0        0.2   11.5   0.0    2.2  2  Aminotran_4   Amino-transferase class IV


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1      0.65   2.9e+03     120     135 ..      57      73 ..      51      85 .. 0.48
   2 !  127.1   1.4   1.2e-40   5.3e-37       8     181 .]     102     273 ..      97     273 .. 0.95
   3 !    5.8   2.3     0.002       9.1     113     167 ..     597     654 ..     571     659 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.65
                                       HH.HHHHHHHHHHHHHH CS
                      E1-E2_ATPase 120 kv.lvpvvlliallvfl 135
                                       ++ + +v ++++++v++
  gi|385805141|ref|YP_005841539.1|  57 AWfYLAVFIILFMTVWF 73 
                                       44122233333333333 PP

  == domain 2  score: 127.1 bits;  conditional E-value: 1.2e-40
                                       EEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEEE-EEEEE CS
                      E1-E2_ATPase   8 kvirdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvvsgeakav 84 
                                       +++ +++ ++++++el++GD+v++++++++p Dg +veg+a+vdes+LTGEs+pv k kgd+v+sGt vv+g+++++
  gi|385805141|ref|YP_005841539.1| 102 HKLVGEKRVDVRSSELKMGDYVVVEQNEVIPQDGFVVEGEASVDESMLTGESEPVFKGKGDKVISGTKVVAGRIVVE 178
                                       5566778899******************************************************************* PP

                                       EEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHHHS-T CS
                      E1-E2_ATPase  85 VtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallralallvaaiPc 161
                                       V a   +++l+k+++l++ ak+++ + + +l+ l   l+++ l+++  +++i+ + g  +      +++llva +P 
  gi|385805141|ref|YP_005841539.1| 179 VAAEPGKSYLDKMIALIAGAKRSRMQSEVMLSILLLGLSLIFLIVVSSLYFILGSFGSYP--ESSLMISLLVALMPT 253
                                       ****************************************************99999987..556689********* PP

                                       THHHHHHHHHHHHHHHHHHT CS
                      E1-E2_ATPase 162 aLplavplalalgarrlakk 181
                                        ++ ++p + + g+ rla++
  gi|385805141|ref|YP_005841539.1| 254 TIGGLLPAIGISGVLRLAEH 273
                                       *****************986 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.002
                                       HHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTT...HHHHHHHHHHHHHS-TTHHHHH CS
                      E1-E2_ATPase 113 kkldklgkvlvpvvlliallvflialllgksla...eallralallvaaiPcaLplav 167
                                        +++ ++k+++++ ++i+ ++  + +l++ +l    +a+l ++ +  ++iP  +pla+
  gi|385805141|ref|YP_005841539.1| 597 SIMNDIAKYFTILPFIISTIMPGVSFLNFLNLYntvTAVLATMIFNAIIIPMLIPLAL 654
                                       3567777777777777777777777766666664458888888888899999999886 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.9   0.4   5.2e-32   2.3e-28       2     210 .]     290     548 ..     289     548 .. 0.83

  Alignments for each domain:
  == domain 1  score: 99.9 bits;  conditional E-value: 5.2e-32
                                       SEEEEESBTTTBCHHHHHHHHHHHH.....CHHHHHHHHHH.......HHCHHHHHHHHHHHHH..........HHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxx.......xxxxxxxxxxxxxxxx..........xxx RF
                         Hydrolase   2 ktvvfDkdGTLttgepsvedvivsa.....alalaaaletg.......sehpigkalvaaakar..........sga 56 
                                       ++v+fDk+GT+t+g++s +++i+       +     +  ++       s+h     +   a++           +  
  gi|385805141|ref|YP_005841539.1| 290 DVVIFDKTGTITEGSRSAVEFIPLDgfterD-----VAIVAylsaigdSTHEAKSII-QLAEEKggipakflmeE-- 358
                                       68******************99999665332.....222223336685555555555.44444423443332220.. PP

                                       HHHHHHETTTE...................................................HHHHTHHHHHHHH.. CS
                                       xxxxxxxxxxx...................................................xxxxxxxxxxxxx.. RF
                         Hydrolase  57 ltgfatfigrg...................................................ayaigkpewltal.. 80 
                                           a+                                                        ++ +g p+ + +l  
  gi|385805141|ref|YP_005841539.1| 359 ----AK----VaskvlytpsrryssitlswkgsknqlspqeisslsriekkmlvmrdfgedvTIIKGAPDAVLKLln 427
                                       ....22....1334466666667888888888889999999999999999999999999***************9*9 PP

                                       .HCHHHHHHHHHHHHHHCHHHHHH..TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHH CS
                                       .xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  81 .dippdlgaaigsaqsqgrtvall..qaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanq 154
                                        d  p +++ i    ++g t +l   ++r+ +   + d+  +k++++e +++L+ +gi+++++tgdnp ta  +an+
  gi|385805141|ref|YP_005841539.1| 428 iDRDPVVEDIIKRVGARGDTPILIalNDRLIGFAVLRDK--LKKGIKERIRELNLMGIKTIMITGDNPYTAANVANE 502
                                       999******************9998899999999999**..************************************ PP

                                       TTGGGESEEEEHHCES.STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 155 lGddyfdaviasdiet.vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                       +G           ie+  a ++pe+k+ ++++ + ++  va+ GDg nDa+ala+A+
  gi|385805141|ref|YP_005841539.1| 503 AG-----------IEGfYAQAKPEDKLMLVEKEKKQGFVVAVMGDGTNDAPALARAD 548
                                       **...........******************************************98 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.7   0.0    0.0048        21      15      58 ..     466     509 ..     463     513 .. 0.90
   2 !   24.6   0.3   4.2e-09   1.9e-05     206     244 ..     531     569 ..     520     580 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0048
                                       ---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEE CS
                       Hydrolase_3  15 kisektkeaikklkekgikvviATGRslravlpvleelgldlpv 58 
                                       k+++ +ke i++l   gik +  TG +++++ +v++e g++ ++
  gi|385805141|ref|YP_005841539.1| 466 KLKKGIKERIRELNLMGIKTIMITGDNPYTAANVANEAGIEGFY 509
                                       567889999******************************99766 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 4.2e-09
                                       EEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE- CS
                       Hydrolase_3 206 viafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtk 244
                                       v+++GDg ND + L +a++gvAm+ ++  +k+aA+++  
  gi|385805141|ref|YP_005841539.1| 531 VAVMGDGTNDAPALARADVGVAMHTGTAPAKEAANMIDL 569
                                       789********************************9855 PP

>> Aminotran_4  Amino-transferase class IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   4.4e-05       0.2     130     159 ..     283     313 ..     275     323 .. 0.84
   2 ?    0.5   0.0       0.1   4.5e+02      30      77 ..     457     501 ..     452     521 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.4e-05
                       Aminotran_4 130 akergadevllvdedgnvtEgstsNv.fivk 159
                                        +++g  +v+++d+ g +tEgs+s v fi  
  gi|385805141|ref|YP_005841539.1| 283 VEAAGDADVVIFDKTGTITEGSRSAVeFIPL 313
                                       4556666*******************99865 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.1
                       Aminotran_4  30 lglelpfdeeelrkileelleannsengrlrllvsrgggglgaatsep 77 
                                       l +++ + ++ l+k ++e ++++n     ++ +++ g++ ++aa++++
  gi|385805141|ref|YP_005841539.1| 457 L-IGFAVLRDKLKKGIKERIRELNLMG--IKTIMITGDNPYTAANVAN 501
                                       5.7889999**************9986..9999999998877555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (704 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); 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:                         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: 0.69u 0.33s 00:00:01.02 Elapsed: 00:00:00.50
# Mc/sec: 4252.63
//
Query:       gi|385805142|ref|YP_005841540.1|  [L=161]
Description: hypothetical protein FFONT_0095 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-20   73.8   0.1    5.7e-10   39.3   0.0    2.0  2  KdpC      K+-transporting ATPase, c chain
  ------ inclusion threshold ------
      0.021   14.3   0.5      0.029   13.8   0.5    1.2  1  ASFV_360  African swine fever virus multigene family 360 prot


Domain annotation for each model (and alignments):
>> KdpC  K+-transporting ATPase, c chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   0.0   6.4e-14   5.7e-10       4      65 ..      18      79 ..      15      84 .. 0.91
   2 !   33.1   0.0     5e-12   4.5e-08     119     180 ..      84     150 ..      81     152 .. 0.83

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 6.4e-14
                                      HHHHHHHHHHHHHTHHHHHHHHHHHHH-HHHHTT-EEE.ETEEEEETTT------SSS---- CS
                              KdpC  4 alrlllvltvllgliYplavtgiaqllfpeqAnGslieadgkvvGseligqeftsdkYfhgR 65
                                      a++lll+++ +lgl+Yp++v+gi++l+ p++A Gsl ++ gkv+ s li    +s+  fh+ 
  gi|385805142|ref|YP_005841540.1| 18 AALLLLAMIAFLGLLYPALVWGISSLVSPWRAGGSLYTSCGKVISSDLISVYNESSPLFHPF 79
                                      678999********************************99**********999888888875 PP

  == domain 2  score: 33.1 bits;  conditional E-value: 5e-12
                                       BSSS---EE-HHHHHHTHHHHHHHHT--HHHHHHHHHHTEE--...SSTTT..---EEEHHHHHHHH CS
                              KdpC 119 SgSGLDPhIspeaAelQvarvakarglseeeveklvaentegr...llgil..GeprVnVlklNlaL 180
                                         SG+DP I +e A  Qv+rv+k++g++ e++ +l+ +n   +    l ++  G + VnV ++N+++
  gi|385805142|ref|YP_005841540.1|  84 TSSGVDPYIPLEEAMKQVERVSKETGIPREKLVDLLMSNAAYNdmiDLHVFspGYSIVNVEEVNMQI 150
                                       579*******************************99976654411156677667889*******986 PP

>> ASFV_360  African swine fever virus multigene family 360 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.5   3.3e-06     0.029     118     149 ..     121     158 ..     115     161 .] 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.3e-06
                          ASFV_360 118 calsfnnvfdlh......eiyrtekvnmdidemmelac 149
                                          ++n++ dlh       i+++e vnm+i emm+++c
  gi|385805142|ref|YP_005841540.1| 121 SNAAYNDMIDLHvfspgySIVNVEEVNMQIMEMMNVTC 158
                                       56789******9666665689***************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); 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: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1113.90
//
Query:       gi|385805143|ref|YP_005841541.1|  [L=39]
Description: hypothetical protein FFONT_0096 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); 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: 0.43u 0.32s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 242.04
//
Query:       gi|385805144|ref|YP_005841542.1|  [L=620]
Description: hypothetical protein FFONT_0097 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (620 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.69u 0.28s 00:00:00.97 Elapsed: 00:00:00.49
# Mc/sec: 3787.31
//
Query:       gi|385805145|ref|YP_005841543.1|  [L=144]
Description: hypothetical protein FFONT_0098 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       809  (0.0451224); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.30s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 946.59
//
Query:       gi|385805146|ref|YP_005841544.1|  [L=126]
Description: hypothetical protein FFONT_0099 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0069   15.3   0.2     0.0079   15.1   0.2    1.2  1  LptF_LptG     Lipopolysaccharide export system permease LptF/
  ------ inclusion threshold ------
      0.014   15.1   1.2      0.025   14.3   1.2    1.4  1  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> LptF_LptG  Lipopolysaccharide export system permease LptF/LptG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.2   8.8e-07    0.0079      98     138 ..       8      48 ..       6     100 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 8.8e-07
                         LptF_LptG  98 ililalllsvlsfllnnyvvPwankkaesllseirqkspsl 138
                                        ++++++ls+++++  +yv+Pw + ++e+  s+i+ +sp+ 
  gi|385805146|ref|YP_005841544.1|   8 TIVVGIALSLVLIATALYVIPWLEIQSERAQSSISPSSPTI 48 
                                       799***********************************987 PP

>> 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 ?   14.3   1.2   2.8e-06     0.025      32     132 ..       8     124 ..       4     126 .] 0.77

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.8e-06
                      BPD_transp_1  32 sfvlaillvlvf................vilsilghlilpviillllsaapyvrlirraalrslpkdlveaaralGa 92 
                                       ++v++i l lv+                  +s++  +   + + ++++++ y +++++ +++s+pk ++ + ++ Ga
  gi|385805146|ref|YP_005841544.1|   8 TIVVGIALSLVLiatalyvipwleiqseRAQSSISPSSPTISAFAFYYNGNYQVIVYNYGIKSIPKAYIIYNTTSGA 84 
                                       555444444444446666666778776633333333444456667788999************************** PP

                      BPD_transp_1  93 srwqifrkvvlPnalppiitglilafggllggavlleflg 132
                                       +    + ++   + ++ +i+g ++a   +lg+++ +e + 
  gi|385805146|ref|YP_005841544.1|  85 NAMYSLGYIPAGSYVIATIPGCPIAYSDNLGNTFGVEVVN 124
                                       *********************************9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       722  (0.04027); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.37
# Mc/sec: 1028.92
//
Query:       gi|385805147|ref|YP_005841545.1|  [L=203]
Description: hypothetical protein FFONT_0100 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00017   20.7  15.7    0.00021   20.3  15.7    1.1  1  MFS_1        Major Facilitator Superfamily
  ------ inclusion threshold ------
      0.086   11.2   4.5        0.1   10.9   4.5    1.1  1  MFS_3        Transmembrane secretion effector
       0.11   11.9   0.9       0.15   11.5   0.9    1.1  1  Nicastrin    Nicastrin


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 !   20.3  15.7   3.5e-08   0.00021       4     112 ..      22     134 ..      19     144 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 3.5e-08
                             MFS_1   4 aaflsalarsilgpalplalaedlg.ispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalglll 78 
                                       +++ + l r++ ++++   l  +++ is+  +g++ + y+l+ a++ +++G + + +G+ r +ll + llfa+ +++
  gi|385805147|ref|YP_005841545.1|  22 IYVSIVLIRAANASFIV-SLVAAFHsISAYMQGIIQASYSLTEAIFGIFAGIIYEYLGSFRsILLSSSLLFASYAAM 97 
                                       45555555555555555.5666666488888***************************8777999999999999677 PP

                             MFS_1  79 llfa...sslwlllvlrvlqGlgagalfpagaaliad 112
                                        +f+    +  +++v  +l+Gl a++l++++ a+i++
  gi|385805147|ref|YP_005841545.1|  98 VVFSsieVGPQAFAVPSALAGLSASFLLTSSFAVISE 134
                                       778455544347**********************997 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   4.5   1.7e-05       0.1      28      96 ..      29     102 ..      20     135 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 1.7e-05
                             MFS_3  28 iqevaasWlmtdi....sasplmvAlvqaaatLPifllsilaGalaDnf.drRkvllavqlllalvsvlltvla 96 
                                       i++  as++++ +    s s +m  ++qa+ +L   ++ i+aG++ + + + R +ll   ll a+ +++++ ++
  gi|385805147|ref|YP_005841545.1|  29 IRAANASFIVSLVaafhSISAYMQGIIQASYSLTEAIFGIFAGIIYEYLgSFRSILLSSSLLFASYAAMVVFSS 102
                                       55555665554441112569999***********************9983568888888888887777766544 PP

>> Nicastrin  Nicastrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.9   2.6e-05      0.15      24      72 ..      35      83 ..      29     102 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.6e-05
                         Nicastrin 24 ssvsslvallaaaealskllkdisnlkrnvlFvffnGEsydYiGSqrfv 72
                                      s ++slva  + ++a  +   + s +  + +F +f G  y+Y+GS r +
  gi|385805147|ref|YP_005841545.1| 35 SFIVSLVAAFHSISAYMQGIIQASYSLTEAIFGIFAGIIYEYLGSFRSI 83
                                      56777777777666666666678888999****************9865 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:                      292  (0.0162865); 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):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1365.14
//
Query:       gi|385805148|ref|YP_005841546.1|  [L=619]
Description: putative TrbE protein [Fervidicoccus fontis Kam940]
Scores for complete 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-14   51.3   0.1    5.2e-07   28.9   0.0    2.2  2  AAA_10           AAA-like domain
    4.1e-10   40.1   0.0    7.4e-10   39.3   0.0    1.4  1  DUF87            Helicase HerA, central domain
    0.00036   19.6   0.0      0.072   12.0   0.0    2.2  2  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
    0.00087   19.6   0.0      0.028   14.7   0.0    2.6  2  AAA_22           AAA domain
     0.0028   17.1   0.0     0.0059   16.0   0.0    1.5  1  FtsK_SpoIIIE     FtsK/SpoIIIE family
     0.0098   15.0   0.0      0.017   14.2   0.0    1.3  1  T2SSE            Type II/IV secretion system protein
  ------ inclusion threshold ------
      0.011   14.7   0.0      0.024   13.7   0.0    1.4  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
      0.018   14.6   0.0      0.031   13.8   0.0    1.3  1  AAA_7            P-loop containing dynein motor region
      0.056   14.0   0.0       0.12   12.9   0.0    1.6  1  ABC_tran         ABC transporter
      0.097   12.1   0.0       0.16   11.4   0.0    1.3  1  Fer4_NifH        4Fe-4S iron sulfur cluster binding proteins,
       0.11   12.2   0.5       0.37   10.4   0.0    2.1  2  Thymidylate_kin  Thymidylate kinase
       0.11   12.9   0.0       0.52   10.7   0.0    2.2  2  AAA_16           AAA ATPase domain


Domain annotation for each model (and alignments):
>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   1.7e-07   0.00026      21     115 ..     309     398 ..     305     406 .. 0.80
   2 !   28.9   0.0   3.5e-10   5.2e-07     237     303 ..     490     560 ..     464     579 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.7e-07
                            AAA_10  21 asasliiGdlGnGKSvlakllvlyisllg..gkaliiDpkkerekfketlpeiakkinvvtLdseeenegvLdPlvl 95 
                                       +++ +i+G +G GKS++ak+    ++  +    ++ iDp  e  +   ++ +     + v+++  e++   LdPl l
  gi|385805148|ref|YP_005841546.1| 309 NLNFVIVGITGSGKSMTAKVFLKRLREKDasIPIVGIDPESEYTEIASKFGA-----QAVEIK--ERESLGLDPLKL 378
                                       77889***************99999888844667889*****6666666655.....889998..566678****** PP

                            AAA_10  96 lkeekeaeslaedilelllg 115
                                       + e    +    d+l+ ++ 
  gi|385805148|ref|YP_005841546.1| 379 MREGAMEIGQVSDVLSEIYS 398
                                       **887777777888877665 PP

  == domain 2  score: 28.9 bits;  conditional E-value: 3.5e-10
                            AAA_10 237 dkkefkvvifDEawiftssaeGkkllkelvRiGRsynaavylvtqsadDvlkee....lknniglklaFre 303
                                        + +  + ++DEaw f +++    l +++ R GR++ +a + ++q a+D+  ++    + ++ g+++  r+
  gi|385805148|ref|YP_005841546.1| 490 TRAQKSAFFVDEAWLFMETPSILSLFENIARRGRKHGTAFLYISQRAEDLARSKegrtILEQAGTVFLMRQ 560
                                       4556667899****************************************666633555566788888884 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   0.0     5e-13   7.4e-10       8      82 ..     294     368 ..     288     395 .. 0.77

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 5e-13
                             DUF87   8 sgsevpvyldlnklvtrHlAilgsTGsGKSntvavLleelle.kkgatililDpHGEYgkalekllsekvkvitps 82 
                                       sg++ pv ldl +  +  + i+g TGsGKS t++v l++l e + +++i+ +Dp +EY  +  +++  +++ i+ +
  gi|385805148|ref|YP_005841546.1| 294 SGTGSPVLLDLWSKPNLNFVIVGITGSGKSMTAKVFLKRLREkDASIPIVGIDPESEYTEIA-SKFGAQAVEIKER 368
                                       788999*****777799************************744445**************9.4444444444433 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   4.8e-05     0.072      15      57 ..     309     353 ..     304     365 .. 0.80
   2 !    5.3   0.0    0.0052       7.7     216     311 ..     469     562 ..     450     580 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.8e-05
                     TrwB_AAD_bind  15 tqhilivGttGsGKtqalekllrairargdraiv..lDltGafvs 57 
                                       +  ++ivG tGsGK+ +++ +l+ +r++   + +  +D++ ++++
  gi|385805148|ref|YP_005841546.1| 309 NLNFVIVGITGSGKSMTAKVFLKRLREKDASIPIvgIDPESEYTE 353
                                       56799**********************997763313688887775 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0052
                     TrwB_AAD_bind 216 rallrpllsawld.laikallslpesrerrlWfflDE......lpaLgrleelksllaegRkfGgavvlglqsiaql 285
                                       ++ l+ l+sa+++  a ++ll++     ++  ff+DE       p++  l+ +++++ +gRk+G a+    q  + l
  gi|385805148|ref|YP_005841546.1| 469 SKKLKLLISALISsYAYNKLLTR----AQKSAFFVDEawlfmeTPSI--LSLFENIARRGRKHGTAFLYISQRAEDL 539
                                       45555666665532466666654....44444555552221004443..5567889999*********999999999 PP

                     TrwB_AAD_bind 286 revYGedaaqsilslvntklilrvsd 311
                                            +++ ++il+ ++t +++r ++
  gi|385805148|ref|YP_005841546.1| 540 AR---SKEGRTILEQAGTVFLMRQEP 562
                                       87...578899999999999998664 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   1.9e-05     0.028       8      47 ..     312     347 ..     307     385 .. 0.72
   2 ?    1.8   0.0      0.18   2.6e+02      79     128 ..     480     532 ..     450     539 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.9e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtl 47 
                                        v++G +G+GK+++++ +l++l e      ++ ++v +++
  gi|385805148|ref|YP_005841546.1| 312 FVIVGITGSGKSMTAKVFLKRLREKD----ASIPIVGIDP 347
                                       69*******************95432....2333333333 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.18
                            AAA_22  79 l.ealeqalraravielliiDEaqhlr...s.eealeeLrsllnlsrkgvqliLv 128
                                       + ++ ++ l +ra ++++ +DEa  ++   s   ++e++ ++    ++g++++++
  gi|385805148|ref|YP_005841546.1| 480 IsSYAYNKLLTRAQKSAFFVDEAWLFMetpSiLSLFENIARRGR--KHGTAFLYI 532
                                       4455555555555569*******998765336777777777777..888888876 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   3.9e-06    0.0059      18      60 ..     287     330 ..     281     348 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.9e-06
                                       TEEEEEEETTS-EEEEEGGGS-..SEEEE--TTSSHHHHHHHHH CS
                      FtsK_SpoIIIE  18 lpvalgkeisgnplvldlkkma.shllvaGatgsGKStalntLi 60 
                                       + v lg  ++g+p+ ldl + +  + +++G tgsGKS + ++++
  gi|385805148|ref|YP_005841546.1| 287 NGVFLGMSGTGSPVLLDLWSKPnLNFVIVGITGSGKSMTAKVFL 330
                                       556788889*************889************9987765 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   1.1e-05     0.017     110     163 ..     293     343 ..     287     377 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.1e-05
                             T2SSE 110 aeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderivtv 163
                                       ++++ ++ + ++ +k+   + ++++ G TgsGK+ ++ + lk + ++d  i +v
  gi|385805148|ref|YP_005841546.1| 293 MSGTGSPVLLDLWSKP---NLNFVIVGITGSGKSMTAKVFLKRLREKDASIPIV 343
                                       5556666666677777...99*************************98877555 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 ?   13.7   0.0   1.6e-05     0.024      34      72 ..     314     352 ..     305     359 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.6e-05
                                       EEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE------- CS
                              MeaB  34 ltGvPGaGkstlvealglelrrrGkrvavlavDPsspft 72 
                                       + G+ G+Gks + + +  +lr++   + ++ +DP s++t
  gi|385805148|ref|YP_005841546.1| 314 IVGITGSGKSMTAKVFLKRLREKDASIPIVGIDPESEYT 352
                                       679999******************************997 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.1e-05     0.031      24      63 ..     300     339 ..     296     355 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.1e-05
                             AAA_7  24 yllelllknkkpvllvGptGtGKtviikdllkkldkekyl 63 
                                       +ll+l  k + ++++vG tG+GK++++k +lk+l +++ +
  gi|385805148|ref|YP_005841546.1| 300 VLLDLWSKPNLNFVIVGITGSGKSMTAKVFLKRLREKDAS 339
                                       5889999999************************976654 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   7.9e-05      0.12      13      51 ..     311     349 ..     301     420 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.9e-05
                                       EEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  13 kvaivGenGaGKStLlkllagllkpteGeilldgkdlke 51 
                                         +ivG +G+GKS  +k++++ l+ +  +i + g d ++
  gi|385805148|ref|YP_005841546.1| 311 NFVIVGITGSGKSMTAKVFLKRLREKDASIPIVGIDPES 349
                                       678********************9999999777666655 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 ?   11.4   0.0    0.0001      0.16       3      45 ..     312     354 ..     310     377 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0001
                         Fer4_NifH   3 iaiyGkGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrl 45 
                                       + i G  G+Gks+t++  ++ l e+   + ivG DP ++ t +
  gi|385805148|ref|YP_005841546.1| 312 FVIVGITGSGKSMTAKVFLKRLREKDASIPIVGIDPESEYTEI 354
                                       5788999*******************************99965 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       1.5   2.2e+03      41     168 ..      66      94 ..      48     105 .. 0.54
   2 ?   10.4   0.0   0.00025      0.37       3      47 ..     316     363 ..     314     373 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.5
                                       HHHHHHHTCS---HHHHHHHHHHHHHHTTHHHHHHHHHTT-EEEEES-HHHHHHHHHTTTTTTCHHHHHHGGGTTSE CS
                   Thymidylate_kin  41 kirelllkeeeleeqteallfaadriehleekikpalkqgktvivdRylfSslaYqgakegvdldlvlslnedvllk 117
                                       k +                                                                          
  gi|385805148|ref|YP_005841546.1|  66 KTQ-------------------------------------------------------------------------- 68 
                                       332.......................................................................... PP

                                       -SEEEEEESSHHHHHTSCCTTSSTTTSHHHHHHHHHHHHHHHHHHHHTTST CS
                   Thymidylate_kin 118 PdltflldvdpevalkRlakrdeldeeeeeqldflrkvrerylelakeder 168
                                                                +e + + ++++++++ ++ +a++d +
  gi|385805148|ref|YP_005841546.1|  69 -------------------------REFQYSSHIFQSFETEFFLAARADAQ 94 
                                       .........................33344444555555555544444444 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00025
                                       ESTTSSHHHHHHHHHHHHHHTTE....EEEESSSTTSHHHHHHHHHHH CS
                   Thymidylate_kin   3 GlDGaGKttqaellkerlkeegik...vvltrepggteiGekirelll 47 
                                       G+ G+GK+  a+ + +rl+e+  +   v + +e++ tei++k+ ++  
  gi|385805148|ref|YP_005841546.1| 316 GITGSGKSMTAKVFLKRLREKDASipiVGIDPESEYTEIASKFGAQAV 363
                                       999****************99887767778999999999999877655 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0         6     9e+03      54      88 ..      62      93 ..      46     116 .. 0.58
   2 ?   10.7   0.0   0.00035      0.52      25      88 ..     310     369 ..     300     428 .. 0.69

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 6
                            AAA_16 54 iflrgkcdqlesaipysa.laqalareellrqllde 88
                                      i++r + ++      ys  + q +++e +l++ +d+
  gi|385805148|ref|YP_005841546.1| 62 ILARKTQRE----FQYSShIFQSFETEFFLAARADA 93
                                      333333333....36655577777665555544444 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00035
                            AAA_16  25 elvllsGesGvGKsslvrellralekdggif.lrgkcdqlesaipysalaqalareellrqllde 88 
                                        + +++G  G+GKs  ++ +l++l+++++   + g   ++    +y  +a+ + + + ++  ++e
  gi|385805148|ref|YP_005841546.1| 310 LNFVIVGITGSGKSMTAKVFLKRLREKDASIpIVGIDPES----EYTEIASKFGA-QAVEIKERE 369
                                       6788***********************8555455544444....67778888844.776666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (619 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.72u 0.30s 00:00:01.02 Elapsed: 00:00:00.50
# Mc/sec: 3757.85
//
Query:       gi|385805149|ref|YP_005841547.1|  [L=79]
Description: hypothetical protein FFONT_0102 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score 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   15.8   3.4      0.016   15.4   2.8    1.4  1  SpoIIIAC  Stage III sporulation protein AC/AD protein family


Domain annotation for each model (and alignments):
>> SpoIIIAC  Stage III sporulation protein AC/AD protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   2.8     9e-07     0.016      10      46 ..      41      77 ..      40      78 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 9e-07
                          SpoIIIAC 10 iaalladilkdageeeiAslielagkiiilllalpll 46
                                      +a+l+ ++++  ++ ++Asli l g ++i ll+++ +
  gi|385805149|ref|YP_005841547.1| 41 LATLSVLLCRLIRKLAYASLIALWGIALISLLIIGAI 77
                                      689999***************************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       808  (0.0450667); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); 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 0.31s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 470.77
//
Query:       gi|385805150|ref|YP_005841548.1|  [L=683]
Description: hypothetical protein FFONT_0103 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (683 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       806  (0.0449551); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); 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):               0  [number of targets reported over threshold]
# CPU time: 0.68u 0.29s 00:00:00.97 Elapsed: 00:00:00.50
# Mc/sec: 4118.28
//
Query:       gi|385805151|ref|YP_005841549.1|  [L=190]
Description: hypothetical protein FFONT_0104 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); 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: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1324.88
//
Query:       gi|385805152|ref|YP_005841550.1|  [L=639]
Description: vird-like protein [Fervidicoccus fontis Kam940]
Scores for complete 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   56.4   0.3    1.6e-14   53.7   0.3    1.9  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
    1.8e-13   51.1   0.1    2.7e-13   50.5   0.1    1.3  1  DUF87            Helicase HerA, central domain
    5.5e-09   36.1   0.0    1.1e-08   35.1   0.0    1.5  1  TraG-D_C         TraM recognition site of TraD and TraG
    1.6e-07   30.6   0.0    4.9e-05   22.3   0.0    2.1  2  T4SS-DNA_transf  Type IV secretory system Conjugative DNA tra
    3.3e-07   30.7   0.1     0.0037   17.5   0.0    3.0  3  AAA_22           AAA domain
    5.9e-05   22.2   0.0    0.00012   21.1   0.0    1.6  1  AAA_10           AAA-like domain
    0.00043   20.1   0.0      0.018   14.8   0.0    2.3  2  AAA_30           AAA domain
    0.00066   18.4   0.0     0.0026   16.4   0.0    1.8  2  DUF853           Bacterial protein of unknown function (DUF85
      0.001   19.0   0.0       0.16   11.9   0.0    2.2  2  ATPase_2         ATPase domain predominantly from Archaea
     0.0046   17.3   0.5      0.038   14.3   0.5    2.1  1  AAA_19           AAA domain
     0.0048   17.3   0.6       0.98    9.8   0.6    2.8  1  AAA_16           AAA ATPase domain
     0.0061   15.7   0.0      0.016   14.3   0.0    1.6  1  T2SSE            Type II/IV secretion system protein
     0.0085   16.6   0.0      0.019   15.5   0.0    1.5  1  ABC_tran         ABC transporter
  ------ inclusion threshold ------
      0.027   14.0   0.1      0.065   12.7   0.0    1.6  2  Pox_A32          Poxvirus A32 protein
      0.032   13.6   0.0       0.32   10.3   0.0    2.1  2  FtsK_SpoIIIE     FtsK/SpoIIIE family
      0.042   13.6   0.0       0.13   12.0   0.0    1.8  1  ATP_bind_1       Conserved hypothetical ATP binding protein
      0.045   13.6   0.0       0.36   10.7   0.0    2.4  2  NTPase_1         NTPase
      0.063   13.7   0.0        1.5    9.2   0.0    2.7  2  RNA_helicase     RNA helicase
      0.069   13.1   0.0        0.2   11.6   0.0    1.8  1  NACHT            NACHT domain
      0.087   12.1   0.0       0.19   11.0   0.0    1.5  1  Zeta_toxin       Zeta toxin
       0.13   11.4   0.1        1.2    8.2   0.0    2.1  2  G-alpha          G-protein alpha subunit
       0.15   11.8   0.0        0.3   10.9   0.0    1.4  1  AAA_29           P-loop containing region of AAA domain
       0.16   11.8   0.0        1.7    8.5   0.0    2.2  2  RsgA_GTPase      RsgA GTPase


Domain annotation for each model (and alignments):
>> 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 !   53.7   0.3     2e-17   1.6e-14      12     309 ..     281     585 ..     276     610 .. 0.78

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 2e-17
                     TrwB_AAD_bind  12 eretqhilivGttGsGKtqalekllrairargd.raivlDltGafvsrfydegk.dillnPlDaR.saaWsvfaeik 85 
                                       e+  +h+ ++G tGsGKt+ l+ l++ i + g+  +iv+D++G+++ +  +e      + P  a  s +   +  ++
  gi|385805152|ref|YP_005841550.1| 281 EDLYRHAYLIGQTGSGKTTFLKLLVHRIHEIGEaSVIVIDPHGDMTVELKREIPhAKFFHPTRAPfSMNPLELPRAE 357
                                       55679*************************996258899***********965437889888664355666667788 PP

                     TrwB_AAD_bind  86 eksdfaeiAaalipedggs..sdpfWaeaartvlaetlrelvrekkksn.aallralltadlee....Lkellagte 155
                                       +  ++ ++A  ++ +  ++  +   +a + + +l+ +lr l +ek++ + a+l++a+l     +    +k++  +++
  gi|385805152|ref|YP_005841550.1| 358 SRDHAITLATDILLKVFKEvlNLTDYAVNVKYMLQVILRTLYQEKEEPTmADLYHAILGLYEGTyvldVKDIRWKQS 434
                                       88899999999988864431145568888899999999999887766555******987554440000444444444 PP

                     TrwB_AAD_bind 156 aaalvaeeaertaasiratlatnle..vlelLaekgerFSireWleeedesgwlfltskaeqrallrpllsa.wldl 229
                                       ++al     e+t+ s ++ l+ +++  +l+ L  k +   i e ++ +   +   l++++  ++++r   s+ +++l
  gi|385805152|ref|YP_005841550.1| 435 VEALQ-RMREQTFISALSRLEAYANdpLLQKLTGKTS-INIEEIMKPGS-LSLFSLPKAELGENVTRLTASTiVMKL 508
                                       44443.57788************98557888888777.88999887774.566668888878888887766526888 PP

                     TrwB_AAD_bind 230 aikallslpesrerr.lWfflDElpaLgrleelksllaegRkfGgavvlglqsiaqlrevYGedaaqsilslvntkl 305
                                         +al + + +++r  +++++DE++ +  l+ ++++l e+Rk+G  ++++ q+++q+ +    d  qsil +++ k+
  gi|385805152|ref|YP_005841550.1| 509 WFEALARARLQKKRTpVFLMIDEFQFVADLPIIETILSEARKYGLHLIVAHQHTKQIPD----DLLQSILTNCGVKV 581
                                       8888888777666667****************************************975....88889999999998 PP

                     TrwB_AAD_bind 306 ilrv 309
                                        + v
  gi|385805152|ref|YP_005841550.1| 582 AFVV 585
                                       8765 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.5   0.1   3.5e-16   2.7e-13       2     210 ..     266     489 ..     265     508 .. 0.69

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 3.5e-16
                             DUF87   2 eiGrllsgsevpvyldlnklvtrHlAilgsTGsGKSntvavLleellekkgatililDpHGEYgkalekllsekvkv 78 
                                       +iG+l   ++ + +l ++ l  rH   +g+TGsGK+++ ++L++++ e   a+++++DpHG+    l k+  +++k 
  gi|385805152|ref|YP_005841550.1| 266 RIGKLE--DGREFRLSVEDL-YRHAYLIGQTGSGKTTFLKLLVHRIHEIGEASVIVIDPHGDMTVEL-KREIPHAKF 338
                                       799994..444699999666.**************************98999***********9999.788888999 PP

                             DUF87  79 itpspsa.kdkelkinpwsldpeelldllee........ddkpaaav.qrsvleealdqakakeekeklssdepvek 145
                                       + p +++ ++++l+++ ++ + + +    ++         + +++av  + +l+ +l+++   +eke+ + +++   
  gi|385805152|ref|YP_005841550.1| 339 FHPTRAPfSMNPLELPRAESRDHAITLATDIllkvfkevLNLTDYAVnVKYMLQVILRTLY--QEKEEPTMADLYHA 413
                                       9999888955555555444444444333333333333354444555549999999999999..89999999999999 PP

                             DUF87 146 lleelk.............kekeelrklknqaiarlldkledllrkggsf...snsstdliallleklekegkitii 206
                                       +l  ++             +++e l+++++q+  + l++le   +++ +    +++s ++++       k+g+++ +
  gi|385805152|ref|YP_005841550.1| 414 ILGLYEgtyvldvkdirwkQSVEALQRMREQTFISALSRLEAYANDPLLQkltGKTSINIEEI-----MKPGSLSLF 485
                                       999999999999999955555555555555555555555555555555445544444444444.....488888877 PP

                             DUF87 207 dlsg 210
                                        l +
  gi|385805152|ref|YP_005841550.1| 486 SLPK 489
                                       7765 PP

>> TraG-D_C  TraM recognition site of TraD and TraG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.0   1.4e-11   1.1e-08       1      65 [.     524     584 ..     524     617 .. 0.89

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 1.4e-11
                          TraG-D_C   1 pvlfllDEfanlgkipdleellstgrsrgislvlilQsiaqleelYgkegaetilgncdvklflg 65 
                                       pv +++DEf+ ++ +p +e++ls++r++g++l+++ Q  +q+ +       ++il nc vk+++ 
  gi|385805152|ref|YP_005841550.1| 524 PVFLMIDEFQFVADLPIIETILSEARKYGLHLIVAHQHTKQIPDDL----LQSILTNCGVKVAFV 584
                                       799***************************************9776....69**********774 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 !    6.1   0.0    0.0053       4.2      31      82 ..     264     325 ..     251     352 .. 0.74
   2 !   22.3   0.0   6.3e-08   4.9e-05     231     347 ..     449     567 ..     426     592 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0053
                   T4SS-DNA_transf  31 alyaggllntdGdf........ehvlvvAptrsgKgvgv..viPnllkwkq.siVvlDpkgEl 82 
                                       ++  g+l ++  +f         h+ +++ t+sgK++ +   +  +   ++ s++v+Dp g++
  gi|385805152|ref|YP_005841550.1| 264 SFRIGKLEDGR-EFrlsvedlyRHAYLIGQTGSGKTTFLklLVHRIHEIGEaSVIVIDPHGDM 325
                                       45555533333.45777777789*************96521667777777789******9985 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 6.3e-08
                   T4SS-DNA_transf 231 akselaly.adplvrnatSksdFdlrdlr.rkkvsvyvivnpk..dlevvapllrlffnmvvellkrklpnkderpk 303
                                       a s l+ y +dpl +++t k + ++++++  +  s++   +++  ++ +    + +++ +  e+l+r+  +k+++  
  gi|385805152|ref|YP_005841550.1| 449 ALSRLEAYaNDPLLQKLTGKTSINIEEIMkPGSLSLFSLPKAElgENVTRLTASTIVMKLWFEALARARLQKKRT-- 523
                                       455677773468888888888888888874577888876555411333333445566666777788777777777.. PP

                   T4SS-DNA_transf 304 evlflLDEfpslGkleileealatiagYgirltlIiQsisqlke 347
                                        v +++DEf+ +  l+i+e+ l   ++Yg+ l++  Q ++q+ +
  gi|385805152|ref|YP_005841550.1| 524 PVFLMIDEFQFVADLPIIETILSEARKYGLHLIVAHQHTKQIPD 567
                                       79**************************************9865 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   4.8e-06    0.0037       6      51 ..     285     325 ..     281     340 .. 0.81
   2 ?   -1.2   0.0       2.8   2.2e+03      44      66 ..     398     420 ..     372     450 .. 0.66
   3 !    9.3   0.0    0.0017       1.3      81     128 ..     512     558 ..     478     564 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.8e-06
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst 51 
                                       ++ +++G++G+GKTt l+ l+++ +e       +++v+ +++ +++
  gi|385805152|ref|YP_005841550.1| 285 RHAYLIGQTGSGKTTFLKLLVHRIHEI-----GEASVIVIDPHGDM 325
                                       6889******************98643.....46777777766666 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.8
                            AAA_22  44 fvtlpsstsskdllrellralgl 66 
                                       +++ +++ + +dl++++l  ++ 
  gi|385805152|ref|YP_005841550.1| 398 LYQEKEEPTMADLYHAILGLYEG 420
                                       44555555788888888888774 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0017
                            AAA_22  81 aleqalrarav.ielliiDEaqhlrseealeeLrsllnlsrkgvqliLv 128
                                       al++a  ++++ +++l+iDE+q++    ++e++ s +   ++g++li++
  gi|385805152|ref|YP_005841550.1| 512 ALARARLQKKRtPVFLMIDEFQFVADLPIIETILSEAR--KYGLHLIVA 558
                                       3444333333369**********956999999977777..999999886 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   1.6e-07   0.00012      23     109 ..     286     369 ..     281     592 .. 0.62

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.6e-07
                            AAA_10  23 asliiGdlGnGKSvlakllvlyisllg.gkaliiDpkke.rekfketlpe....iakkinvvtLdseeenegvLdPl 93 
                                       ++ +iG++G GK  + kllv+ i  +g   +++iDp  + + + k+++p+                 +++  +++Pl
  gi|385805152|ref|YP_005841550.1| 286 HAYLIGQTGSGKTTFLKLLVHRIHEIGeASVIVIDPHGDmTVELKREIPHakffH-----------PTRAPFSMNPL 351
                                       7789*******************99983567789*****7778999998733220...........22333344444 PP

                            AAA_10  94 vllk..eekeaeslaedi 109
                                        l    +  +a++la di
  gi|385805152|ref|YP_005841550.1| 352 ELPRaeSRDHAITLATDI 369
                                       443321222333333333 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   2.3e-05     0.018      20      66 ..     286     333 ..     276     344 .. 0.85
   2 ?    2.6   0.0      0.12        94      68     121 ..     499     557 ..     486     566 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.3e-05
                            AAA_30  20 vavltGpAGtGKttalkalreaweaa.ggrviglAptgkaAkvLaeel 66 
                                        a l G  G+GKtt lk l++ +++  + +vi++ p g +  +L++e+
  gi|385805152|ref|YP_005841550.1| 286 HAYLIGQTGSGKTTFLKLLVHRIHEIgEASVIVIDPHGDMTVELKREI 333
                                       56799**************7777777379**********999999875 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.12
                            AAA_30  68 ieastiakllkrlk....grarlepg.tllivDEagmv.dtkqlaallkaaekagakvil 121
                                       ++asti   l + +    +r + ++    l++DE   v d   ++++l++a+k+g ++i+
  gi|385805152|ref|YP_005841550.1| 499 LTASTIVMKL-WFEalarARLQKKRTpVFLMIDEFQFVaDLPIIETILSEARKYGLHLIV 557
                                       5677776666.3334755334444445789*****99879999**********9988876 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 !   16.4   0.0   3.3e-06    0.0026       8      62 ..     271     326 ..     265     337 .. 0.88
   2 ?   -1.3   0.0      0.79   6.1e+02     346     369 ..     603     626 ..     561     635 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.3e-06
                            DUF853   8 eaeqelalalklanrhGliaGatGtGktvtLqvlaeslseaG.vpvfladvkGdLs 62 
                                       e+ +e +l+++   rh  + G tG Gkt  L++l + + e+G  +v++ d  Gd++
  gi|385805152|ref|YP_005841550.1| 271 EDGREFRLSVEDLYRHAYLIGQTGSGKTTFLKLLVHRIHEIGeASVIVIDPHGDMT 326
                                       66778889999999****************************4469999*****97 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.79
                            DUF853 346 dveeaiteLgvGealvsvLdekGa 369
                                       ++ +a+t L vG+a+v +    G+
  gi|385805152|ref|YP_005841550.1| 603 SLSKALTGLRVGKAVVKMTARAGE 626
                                       577899999999999999877775 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0    0.0002      0.16      23     120 ..     287     405 ..     278     424 .. 0.69
   2 ?    4.9   0.0     0.027        21      51     133 ..     444     538 ..     418     560 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0002
                          ATPase_2  23 yfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie...................eeeekkklek 80 
                                        ++ G  gsGKt++lk ++ + ++ ++  + +i+ +++ + +l++ i                              
  gi|385805152|ref|YP_005841550.1| 287 AYLIGQTGSGKTTFLKLLVHRIHEIGEASVIVIDPHGDMTVELKREIPhakffhptrapfsmnplelP--------- 354
                                       5678***********************99999999999999999885555555455444444444441......... PP

                          ATPase_2  81 al..........giavpkaeleeilk..eksklvfkaielllekikkkgkki 120
                                                   ++++  + ++e+l+  +   +v+  ++ +l+ + +++ ++
  gi|385805152|ref|YP_005841550.1| 355 -RaesrdhaitlATDILLKVFKEVLNltDYAVNVKYMLQVILRTLYQEKEEP 405
                                       .044444433333444444444555555667777777777777777776665 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.027
                          ATPase_2  51 viyyialreesiskldefie..eeeekkklekal......giavpkaeleeilk..eksklvfkaielllekikkkg 117
                                         +++al++ +    d  ++  + + + ++e+ +      +  +pkael e +   + s+ v k + ++l+  + ++
  gi|385805152|ref|YP_005841550.1| 444 QTFISALSRLEAYANDPLLQklTGKTSINIEEIMkpgslsLFSLPKAELGENVTrlTASTIVMKLWFEALARARLQK 520
                                       44444444444444444444443333333344337777777778888888877755555566666655555544444 PP

                          ATPase_2 118 kk..iiiiiDelqklidl 133
                                       k+  + ++iDe+q + dl
  gi|385805152|ref|YP_005841550.1| 521 KRtpVFLMIDEFQFVADL 538
                                       446699*******88866 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.5   4.8e-05     0.038      12     127 ..     286     550 ..     280     559 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.8e-05
                            AAA_19  12 vllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgaeatTiHrlal........... 77 
                                       +  +++  G+GKT+ lk  v+ + e+g+   ++++++ + g  + el+ ++     +a+ +H               
  gi|385805152|ref|YP_005841550.1| 286 HAYLIGQTGSGKTTFLKLLVHRIHEIGE---ASVIVIDPHGDMTVELKREI----PHAKFFHPTRApfsmnplelpr 355
                                       56899**********************6...58999*****9999999999....4455555432344558888888 PP

                            AAA_19  78 ............................................................................. 77 
                                                                                                                    
  gi|385805152|ref|YP_005841550.1| 356 aesrdhaitlatdillkvfkevlnltdyavnvkymlqvilrtlyqekeeptmadlyhailglyegtyvldvkdirwk 432
                                       88888888888899999999999999999999999999999999999999999999999999999999999999999 PP

                            AAA_19  78 ...................................................................ldfddlltea 87 
                                                                                                           + +  ++ +
  gi|385805152|ref|YP_005841550.1| 433 qsvealqrmreqtfisalsrleayandpllqkltgktsinieeimkpgslslfslpkaelgenvtrlTASTIVMKLW 509
                                       99999999999999999999999999999999999999999999999999999999999988877753333344455 PP

                            AAA_19  88 lelleeaeeekklqeeellivDEfqdvd..elqyrLlkallg 127
                                       +e+l + ++ +k +    l++DEfq v   + + ++l++  +
  gi|385805152|ref|YP_005841550.1| 510 FEALAR-ARLQKKRTPVFLMIDEFQFVAdlPIIETILSEARK 550
                                       555553.33333324459999999988645666666666655 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   0.6    0.0013      0.98      26      56 ..     286     319 ..     274     558 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0013
                            AAA_16  26 lvllsGesGvGKsslvrellralekd...ggifl 56 
                                         +l+G+ G+GK++ ++ l +++ +     +i++
  gi|385805152|ref|YP_005841550.1| 286 HAYLIGQTGSGKTTFLKLLVHRIHEIgeaSVIVI 319
                                       6789999999999999999987766532233333 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0     2e-05     0.016     135     166 ..     290     321 ..     262     337 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2e-05
                             T2SSE 135 sGgTgsGKttllyallkeinksderivtvEDp 166
                                        G TgsGKtt+l  l++ i++  e  v+v Dp
  gi|385805152|ref|YP_005841550.1| 290 IGQTGSGKTTFLKLLVHRIHEIGEASVIVIDP 321
                                       59*******************97777777676 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.4e-05     0.019      14      37 ..     287     310 ..     278     359 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.4e-05
                                       EEEEESTTSSHHHHHHHHTTSS-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  14 vaivGenGaGKStLlkllagllkp 37 
                                         ++G++G+GK+t+lkll +  + 
  gi|385805152|ref|YP_005841550.1| 287 AYLIGQTGSGKTTFLKLLVHRIHE 310
                                       579***************998875 PP

>> Pox_A32  Poxvirus A32 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   8.3e-05     0.065      17      37 ..     288     308 ..     275     313 .. 0.81
   2 ?   -2.9   0.0       4.6   3.6e+03      88     155 ..     514     579 ..     499     584 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.3e-05
                           Pox_A32  17 alvGgsGsGktvyLlsLlrtl 37 
                                        l+G++GsGkt++L+ L++++
  gi|385805152|ref|YP_005841550.1| 288 YLIGQTGSGKTTFLKLLVHRI 308
                                       48*************998876 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.6
                           Pox_A32  88 akkeknqkeaerfLlilDDlGdkqtksktLlellnvgRhlnvsiilLcqtykhvpvngrasithlvci 155
                                       a+ ++ qk+ + + l++D++        ++ ++l  +R   + +i+  q  k +p    +si   + +
  gi|385805152|ref|YP_005841550.1| 514 AR-ARLQKKRTPVFLMIDEFQF-VADLPIIETILSEARKYGLHLIVAHQHTKQIPDDLLQSILTNCGV 579
                                       44.3444444444444555432.333344555566666666666677777777777777777666655 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00041      0.32      40      61 ..     285     306 ..     259     336 .. 0.80
   2 ?    0.4   0.0      0.43   3.4e+02     165     191 ..     540     566 ..     512     575 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00041
                                       .SEEEE--TTSSHHHHHHHHHH CS
                      FtsK_SpoIIIE  40 shllvaGatgsGKStalntLil 61 
                                        h  ++G tgsGK+t+l+ L+ 
  gi|385805152|ref|YP_005841550.1| 285 RHAYLIGQTGSGKTTFLKLLVH 306
                                       477899***********99875 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.43
                                       ...........-----------B---- CS
                      FtsK_SpoIIIE 165 ritsLsnqgpsygvhvlvtagrelekr 191
                                        i  + ++  +yg h++v+ +   +++
  gi|385805152|ref|YP_005841550.1| 540 IIETILSEARKYGLHLIVAHQHTKQIP 566
                                       444555555555666665555555555 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 ?   12.0   0.0   0.00017      0.13       2      34 ..     290     321 ..     289     327 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00017
                        ATP_bind_1   2 vGpaGsGKttfvgalseilelrgrsvavvNLDP 34 
                                       +G  GsGKttf + l+  ++++g    v+ +DP
  gi|385805152|ref|YP_005841550.1| 290 IGQTGSGKTTFLKLLVHRIHEIGE-ASVIVIDP 321
                                       89********************55.55555777 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00046      0.36      46     110 ..     264     328 ..     257     334 .. 0.87
   2 ?   -1.4   0.0       2.4   1.9e+03      63      95 ..     373     404 ..     363     409 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00046
                                       EEEEEET.T--EEEEEETT.---SSEETTEEE-HHHHHHHHHHHHHHHHHHH-EEEE---STTGGG CS
                          NTPase_1  46 gFkivdlasgeegiLarve.akreprvgkyvvdvesfeelalealrkalseadviviDEiGkmElk 110
                                        F+i +l++g+e  L+ ++  ++ + +g+     + f +l ++ +++ + ea viviD  G m ++
  gi|385805152|ref|YP_005841550.1| 264 SFRIGKLEDGREFRLSVEDlYRHAYLIGQTGSGKTTFLKLLVHRIHE-IGEASVIVIDPHGDMTVE 328
                                       699999999***9**999988889999***999999****9*99987.68999*****99999554 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.4
                                       TT---SSEETTEEE-HHHHHHHHHHHHHHHHHH CS
                          NTPase_1  63 veakreprvgkyvvdvesfeelalealrkalse 95 
                                       v  k+  ++  y v+v+ + +++l+ l ++ +e
  gi|385805152|ref|YP_005841550.1| 373 VF-KEVLNLTDYAVNVKYMLQVILRTLYQEKEE 404
                                       44.66778889***********99999876654 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0    0.0019       1.5       2      23 ..     288     309 ..     287     332 .. 0.79
   2 ?    1.1   0.0      0.66   5.2e+02      35     103 ..     438     506 ..     417     507 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0019
                      RNA_helicase   2 wlyGpsgeGKStlakeLakall 23 
                                       +l G++g GK+t+ k L++++ 
  gi|385805152|ref|YP_005841550.1| 288 YLIGQTGSGKTTFLKLLVHRIH 309
                                       899*************999887 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.66
                      RNA_helicase  35 ysrnpeddfwdgYtgqevvvidDfgqvkdeenps.dlaelirlvsstpyplnmasleekgtlftSkvviv 103
                                         r  e++f +  ++ e+   d + q+ ++ + s  ++e+++  s   + l++a+l e  t  t++ +++
  gi|385805152|ref|YP_005841550.1| 438 LQRMREQTFISALSRLEAYANDPLLQKLTG-KTSiNIEEIMKPGSLSLFSLPKAELGENVTRLTASTIVM 506
                                       347888999999999999999999999988.6666999******************99998887777764 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   0.00025       0.2       4      25 ..     288     309 ..     285     316 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00025
                                       EEEC-TTTCHHHHHHHHHHHHC CS
                             NACHT   4 ilqGeaGsGKTtLlqklalawa 25 
                                        l G+ GsGKTt+l+ l++ + 
  gi|385805152|ref|YP_005841550.1| 288 YLIGQTGSGKTTFLKLLVHRIH 309
                                       689************9998765 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00024      0.19      21      51 ..     289     321 ..     279     343 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00024
                        Zeta_toxin  21 lgGqpGAGKselaellkdele..rqgnvvrldp 51 
                                       l Gq+G+GK++ ++ll  +++   + +v+++dp
  gi|385805152|ref|YP_005841550.1| 289 LIGQTGSGKTTFLKLLVHRIHeiGEASVIVIDP 321
                                       559*************99998666778888887 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0015       1.2      27      43 ..     288     304 ..     277     316 .. 0.85
   2 ?    0.3   0.0      0.39     3e+02      90     148 ..     442     511 ..     385     579 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0015
                                       EEEESTTSSHHHHHHHH CS
                           G-alpha  27 lllGqseSGKsTilkql 43 
                                       +l+Gq +SGK+T+lk l
  gi|385805152|ref|YP_005841550.1| 288 YLIGQTGSGKTTFLKLL 304
                                       89************976 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.39
                                       HHHC-SS-SCCCS-HC.HHHH..........HHCCHHC.........-HCHHHHHHHHCCSHHHHHH.HC CS
                           G-alpha  90 elqelkerldplkkve.asliaklssateeeqeiefnp.........raevgedikaLwndpgiqel.ye 148
                                        +q+   +l++l ++  + l +kl+++t+++ e+ ++p         +ae+ge++ +L  + ++ +l +e
  gi|385805152|ref|YP_005841550.1| 442 REQTFISALSRLEAYAnDPLLQKLTGKTSINIEEIMKPgslslfslpKAELGENVTRLTASTIVMKLwFE 511
                                       4444444555554433033456777777777777777788888888889999999999888888777344 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00038       0.3      16      39 ..     275     301 ..     268     305 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00038
                            AAA_29  16 tieidlkg...atlltGpsGsGKSTll 39 
                                       ++++++++      l+G++GsGK+T+l
  gi|385805152|ref|YP_005841550.1| 275 EFRLSVEDlyrHAYLIGQTGSGKTTFL 301
                                       555555555556789**********97 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0    0.0022       1.7     101     122 ..     286     307 ..     271     320 .. 0.82
   2 ?    0.3   0.0      0.73   5.7e+02      43      97 ..     519     573 ..     505     587 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0022
                                       EEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase 101 tsvlvGqSGvGKStLinallpe 122
                                        + l+Gq+G GK+t+++ l+ +
  gi|385805152|ref|YP_005841550.1| 286 HAYLIGQTGSGKTTFLKLLVHR 307
                                       5689*************99876 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.73
                                       HHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHC CS
                       RsgA_GTPase  43 eekgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkell 97 
                                       ++k+ ++ +++     + +   +e++ +e +++g+++++ +++tk+  ++l + +
  gi|385805152|ref|YP_005841550.1| 519 QKKRTPVFLMIDEFQFVADLPIIETILSEARKYGLHLIVAHQHTKQIPDDLLQSI 573
                                       6777888889999999999999999*************99999998777766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (639 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); 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: 0.71u 0.30s 00:00:01.01 Elapsed: 00:00:00.49
# Mc/sec: 3945.06
//
Query:       gi|385805153|ref|YP_005841551.1|  [L=144]
Description: hypothetical protein FFONT_0106 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00071   19.4   1.4     0.0012   18.6   1.4    1.4  1  Rick_17kDa_Anti  Glycine zipper 2TM domain
     0.0022   17.9   0.4     0.0038   17.2   0.4    1.3  1  Gly-zipper_Omp   Glycine zipper
     0.0044   16.7   0.3     0.0069   16.1   0.3    1.2  1  Gly-zipper_YMGG  YMGG-like Gly-zipper
  ------ inclusion threshold ------
      0.019   15.1   0.3      0.029   14.5   0.3    1.2  1  DUF3792          Protein of unknown function (DUF3792)
        5.5    7.3   5.3        5.7    7.3   0.2    2.1  2  DUF1269          Protein of unknown function (DUF1269)


Domain annotation for each model (and alignments):
>> Rick_17kDa_Anti  Glycine zipper 2TM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   1.4   3.4e-07    0.0012       4      36 ..      99     130 ..      96     133 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 3.4e-07
                   Rick_17kDa_Anti   4 liGAaaGgvaGaaigggggrvlGavvGAaaGav 36 
                                       ++GA++Gg++G   ++ g+++ G + GA++G +
  gi|385805153|ref|YP_005841551.1|  99 ALGAIVGGLLGKSSSK-GDKTEGFLCGALIGLL 130
                                       79************99.9*************66 PP

>> Gly-zipper_Omp  Glycine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.4   1.1e-06    0.0038       4      33 ..      99     130 ..      98     133 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.1e-06
                    Gly-zipper_Omp   4 aiGAaaGaliGgavg..grgtGaliGAavGaa 33 
                                       a+GA++G+l+G+ ++  +   G l+GA +G +
  gi|385805153|ref|YP_005841551.1|  99 ALGAIVGGLLGKSSSkgDKTEGFLCGALIGLL 130
                                       68**********76543778**********65 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 !   16.1   0.3   1.9e-06    0.0069       8      39 ..      99     131 ..      96     135 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.9e-06
                                       XXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXX CS
                   Gly-zipper_YMGG   8 aiGAaaGAvvGaliG.sgggkGAaiGAaaGala 39 
                                       a GA++G ++G  +  ++   G + GA +G l 
  gi|385805153|ref|YP_005841551.1|  99 ALGAIVGGLLGKSSSkGDKTEGFLCGALIGLLL 131
                                       44555555555555566666799*******986 PP

>> DUF3792  Protein of unknown function (DUF3792)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.3   8.2e-06     0.029      44      82 ..      97     137 ..      93     141 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 8.2e-06
                           DUF3792  44 ililsvfigGfl...agkkakkkgllnGllvGllyflillll 82 
                                        l+l++++gG+l   ++k  k+ g+l G+l+Gll++ i +l+
  gi|385805153|ref|YP_005841551.1|  97 ALALGAIVGGLLgksSSKGDKTEGFLCGALIGLLLTSI-FLV 137
                                       45666666655422278888999***********9999.555 PP

>> DUF1269  Protein of unknown function (DUF1269)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.2    0.0016       5.7      14      38 ..      90     114 ..      86     119 .. 0.82
   2 ?    2.3   0.8     0.055     2e+02       3      16 ..     119     132 ..     117     139 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0016
                           DUF1269  14 lflnPllGaavGAaaGAlvgalsdv 38 
                                       +  +P + +a+GA +G+l g+ s  
  gi|385805153|ref|YP_005841551.1|  90 IYDSPRIALALGAIVGGLLGKSSSK 114
                                       556899**************98765 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.055
                           DUF1269   3 sGalwGllvGllfl 16 
                                       +G l+G+l+Gll+ 
  gi|385805153|ref|YP_005841551.1| 119 EGFLCGALIGLLLT 132
                                       57777777777653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.51
# Mc/sec: 849.77
//
Query:       gi|385805154|ref|YP_005841552.1|  [L=82]
Description: putative DNA methylase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      0.003   17.2   0.0     0.0031   17.2   0.0    1.1  1  Cons_hypoth95  Conserved hypothetical protein 95
     0.0067   16.1   0.0     0.0067   16.1   0.0    1.1  1  UPF0020        Putative RNA methylase family UPF0020
  ------ inclusion threshold ------
       0.16   11.7   0.0       0.18   11.5   0.0    1.1  1  Met_10         Met-10+ like-protein


Domain annotation for each model (and alignments):
>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   5.2e-07    0.0031      38      91 ..       2      54 ..       1      78 [. 0.77

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5.2e-07
                                      CCHCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--T CS
                     Cons_hypoth95 38 aeiegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelklee 91
                                      +e+eg ++LD faG G++ lE + R  ++a++ve  ++a+  lk ++   + e+
  gi|385805154|ref|YP_005841552.1|  2 EELEGRKLLDPFAGFGSIPLEGM-RFGSNATAVELLPTAYVFLKGDVGISGSEA 54
                                      5789999***************8.6669***************99988777554 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.1e-06    0.0067      28      58 ..       5      35 ..       2      77 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.1e-06
                                      TTS-EEETT-TTSHHHHHHHHHHTT--TTTT CS
                           UPF0020 28 pgepllDPmCGsGtilIEaallganiapgll 58
                                      +g++llDP+ G G+i++E+   g+n+ +  l
  gi|385805154|ref|YP_005841552.1|  5 EGRKLLDPFAGFGSIPLEGMRFGSNATAVEL 35
                                      6899***************999999886554 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     3e-05      0.18     100     163 ..       5      66 ..       2      78 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3e-05
                                       TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG- CS
                            Met_10 100 egevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrev 163
                                       eg   +d fAG G  ++   +++  +   a++l P+++ +lk  +     e +   i+  +r +
  gi|385805154|ref|YP_005841552.1|   5 EGRKLLDPFAGFGSIPLEGMRFG--SNATAVELLPTAYVFLKGDVGISGSEAKQLEIEDIVRSF 66 
                                       5778899******7777777755..5559*************8886654444443444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); 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:                         3  (0.000167327); expected 0.2 (1e-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 0.29s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 550.25
//
Query:       gi|385805155|ref|YP_005841553.1|  [L=878]
Description: ATP dependent helicase [Fervidicoccus fontis Kam940]
Scores for complete 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  179.6   0.1    1.1e-52  178.7   0.1    1.5  1  DEAD_assoc  DEAD/H associated
      1e-29  103.5   0.0    3.7e-29  101.7   0.0    2.0  2  DEAD        DEAD/DEAH box helicase
    1.5e-17   63.9   0.1    2.6e-15   56.7   0.0    2.7  2  Helicase_C  Helicase conserved C-terminal domain
    3.3e-09   37.0   0.0      2e-08   34.4   0.0    2.3  2  ResIII      Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
       0.03   14.1   0.0       0.21   11.3   0.0    2.3  2  AAA_11      AAA domain
      0.031   14.3   0.0      0.088   12.9   0.0    1.7  1  DUF4130     Domain of unknown function (DUF4130
      0.038   13.4   0.0       0.11   12.0   0.0    1.7  1  PhoH        PhoH-like protein
      0.073   13.5   1.7        3.9    7.9   1.7    2.8  1  AAA         ATPase family associated with various cellular ac
      0.095   13.0   0.0       0.82   10.0   0.0    2.5  2  AAA_19      AAA domain
       0.15   10.7   0.0       0.39    9.4   0.0    1.7  2  SNF2_N      SNF2 family N-terminal domain


Domain annotation for each model (and alignments):
>> DEAD_assoc  DEAD/H associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.7   0.1   5.9e-56   1.1e-52       2     191 .]     644     831 ..     643     831 .. 0.96

  Alignments for each domain:
  == domain 1  score: 178.7 bits;  conditional E-value: 5.9e-56
                        DEAD_assoc   2 PtdrtllvErfrdelgdwrlvvhspfGrrvnealalllaarlsrrfgidvqvaanDdgivlllpleerlpllldell 78 
                                        +dr + +E ++de  ++++++hs+fGr++n+al++++a+ ls++ g+ v+v+++D++++l+lp + +++  + +l+
  gi|385805155|ref|YP_005841553.1| 644 ASDRLVHIEIYDDER-GRNIIFHSLFGRKANDALSRAYAYALSEQSGTAVRVTVSDNAFMLTLPGRPEVD--VSTLV 717
                                       6799999****9998.67*******************************************996666654..67899 PP

                        DEAD_assoc  79 ellspdeleedleaalnaselfkrrFrevAaralllprrypgkrkplwqqrlraaqLldvareypdfpllleavrev 155
                                       ++++++++e++l++++ ++e++kr Fr++A+r+++++r+y+g +k++++ +l+a+ +ld+++e  ++p+++e+vre+
  gi|385805155|ref|YP_005841553.1| 718 KSVNSKNVEDLLTKSIYNTEMMKRIFRQCAQRSFMILRNYRGWEKSPNKLQLSAQTILDALKEDSENPVVKETVREI 794
                                       **************************************************************999************ PP

                        DEAD_assoc 156 ledqlDlerlaellrriaageirvveve.tprpSpfA 191
                                       ++d +D+++++e+l+ri++gei+v+ +  ++ pSpfA
  gi|385805155|ref|YP_005841553.1| 795 IHDHMDVDAAKEVLKRIEDGEIEVEITGpSEVPSPFA 831
                                       *************************988999*****9 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.7   0.0   2.1e-32   3.7e-29       1     170 [.      26     211 ..      26     216 .. 0.82
   2 ?   -3.5   0.0       4.2   7.5e+03      48      75 ..     278     305 ..     266     342 .. 0.65

  Alignments for each domain:
  == domain 1  score: 101.7 bits;  conditional E-value: 2.1e-32
                                       -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHS....TTSTS-EEEEEESSHHHHHHHHHHHHHHTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyet....kgktgpkalivePtreLaeqtlnnlkkfkky 73 
                                       t+ Q++aipli +g++vl++ +TG+GKTla+++ +++++y      k +++  +l+v+P+r+L +++ +nl + ++ 
  gi|385805155|ref|YP_005841553.1|  26 TEPQKRAIPLIKRGENVLISSPTGTGKTLAAFLGIIDALYALseekKLENEIYVLYVSPLRALNNDIRRNLIEPLEG 102
                                       578************************************999999999***************************98 PP

                                       ST.............SEEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHH...HCTSSH..CTTEEEEEEETHHH CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxx..xxxxxxxxxxxxxx RF
                              DEAD  74 id.............lrvlliiggvaardqlskldngvdivvgtpgrlddll...stgkln..lsqvrflVlDEadr 132
                                       i+             ++++  ++++++++ +  l++ ++i+++tp+ l+ +l   +   ++  l+++r++++DE+++
  gi|385805155|ref|YP_005841553.1| 103 IKkiarekygveledIKASIRTSDTPQNERQIMLRKPPHILITTPESLALILvapK---FRerLRSIRWVIIDEIHE 176
                                       7766666666555444444334444444444455566*************884541...4444************** PP

                                       HHHTTTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 133 lldqgfsdfinrilnqlpqitcdgklqrqvivlSATlp 170
                                       + +++++  ++ +l++l++  +    + q i lSAT++
  gi|385805155|ref|YP_005841553.1| 177 IASSKRGSNLSILLERLQELAE---REVQRIGLSATIS 211
                                       *****************54444...3467*******97 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4.2
                                       -EEEEEESSHHHHHHHHHHHHHHTTTST CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  48 pkalivePtreLaeqtlnnlkkfkkyid 75 
                                       + +li + tr+ +e ++ +lkk++ + +
  gi|385805155|ref|YP_005841553.1| 278 KSTLIFTNTRSATERVVFKLKKVLAEKN 305
                                       5677888888888888888888777433 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 ?    4.1   0.0     0.032        58      25      63 ..     102     140 ..      62     158 .. 0.77
   2 !   56.7   0.0   1.5e-18   2.6e-15      11     108 ..     272     377 ..     264     379 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.032
                                       SHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHH CS
                        Helicase_C  25 tidrlekvklllekkgikvavlhgelpqnereeileqfn 63 
                                        i+++ + k+  e ++ik+ + ++++pqner+ +l++  
  gi|385805155|ref|YP_005841553.1| 102 GIKKIAREKYGVELEDIKASIRTSDTPQNERQIMLRKPP 140
                                       4444444555556669****************9998874 PP

  == domain 2  score: 56.7 bits;  conditional E-value: 1.5e-18
                                       HHTTTTSEEEEEESSHHHHHH.....HHHHHHHT...TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSS CS
                        Helicase_C  11 kleeeggkilifvntidrlek.....vklllekk...gikvavlhgelpqnereeileqfnkgesdvLiatdvaerG 79 
                                       +l  +++ +lif+nt++  e+      k+l ek+      + ++h++l+ + r+++ e+ ++ge +v+++++ +e G
  gi|385805155|ref|YP_005841553.1| 272 ELVLSHKSTLIFTNTRSATERvvfklKKVLAEKNlvgLDDIGAHHSSLSRDIRLDVEERLKRGELRVVVSSTSLELG 348
                                       4458999**********66555556668888888996578999********************************** PP

                                       STSTTESEEEESSSSSSHHHHHHHHTTSS CS
                        Helicase_C  80 idipkvnlVinfdlprnvtsyiqriGRtg 108
                                       idi  ++lV  ++ p++v+++ qr+GR+g
  gi|385805155|ref|YP_005841553.1| 349 IDIGYIDLVLLLSSPKSVSRLLQRVGRAG 377
                                       ****************************8 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.0   1.1e-11     2e-08      22     169 ..      37     210 ..       9     212 .. 0.69
   2 ?   -1.7   0.0       1.4   2.6e+03      60      96 ..     614     650 ..     614     682 .. 0.79

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 1.1e-11
                                       .TTSEEEEEESTTSTHHHHH.HHHHHHH-S...........-EEEEESSHHHHHHHHHHGGGGTGG........... CS
                            ResIII  22 krdkrglikmaTGtGKTlva.aklierllkkgkee......kflflvprkslleqtleefkkflseayke....... 84 
                                       kr +++li  +TGtGKTl a + +i++l+   +e+       +l + p ++l +  ++++ + l+  +k        
  gi|385805155|ref|YP_005841553.1|  37 KRGENVLISSPTGTGKTLAAfLGIIDALYALSEEKkleneiYVLYVSPLRALNNDIRRNLIEPLEGIKKIarekygv 113
                                       68899***************9999999998877778999999***************88855555444442222222 PP

                                       ....GEEEESSS-B--....................-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGT CS
                            ResIII  85 ....igkkvsgdkkka.............kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrl 144
                                           i          +             +   ++  +il+tt +sl  ++      + + +  ++  +iiDE H +
  gi|385805155|ref|YP_005841553.1| 114 eledI----------KasirtsdtpqnerQIMLRKPPHILITTPESLALIL---VAPKFRERLRSIRWVIIDEIHEI 177
                                       44331..........022333233333333345667789999999999999...6666666677777********** PP

                                       TS.T.......TTHHHHHT---.....SEEEEEESS- CS
                            ResIII 145 gakk.......swreilekfke.....avllglTATp 169
                                       +++k            le ++e       ++gl+AT+
  gi|385805155|ref|YP_005841553.1| 178 ASSKrgsnlsiL----LERLQElaereVQRIGLSATI 210
                                       **9644433331....4444333334499*******7 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.4
                                       EESSHHHHHHHHHHGGGGTGG....GEEEESSS-B-- CS
                            ResIII  60 lvprkslleqtleefkkflseaykeigkkvsgdkkka 96 
                                       ++++  l e + +e+++++se+y++++++v +d+  +
  gi|385805155|ref|YP_005841553.1| 614 IADEMMLDEDAAREVARYISEQYAFTSGIVASDRLVH 650
                                       5788889999999*********999888888887766 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00012      0.21       3      81 ..      26     106 ..      24     147 .. 0.79
   2 ?   -0.5   0.0      0.47   8.5e+02     208     225 ..     156     173 ..     104     174 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
                            AAA_11   3 ndsqreaiksalseseitliqGPPGtgKT.ktivellsqllsrrkseeeksakpriLvCapSNaAvDellerllr.. 76 
                                        + q++ai  + + ++ +li+ P GtgKT  + ++++ +l+   ++e++ +++  +L+ +p  a  +++   l++  
  gi|385805155|ref|YP_005841553.1|  26 TEPQKRAIPLIKRGEN-VLISSPTGTGKTlAAFLGIIDALYA-LSEEKKLENEIYVLYVSPLRALNNDIRRNLIEpl 100
                                       6789999999888888.9***********9999999999942.3457788888888998888877777777777755 PP

                            AAA_11  77 .gllds 81 
                                        g+++ 
  gi|385805155|ref|YP_005841553.1| 101 eGIKKI 106
                                       555544 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.47
                            AAA_11 208 sklleklakkfdvviIDE 225
                                       ++++++  + +++viIDE
  gi|385805155|ref|YP_005841553.1| 156 APKFRERLRSIRWVIIDE 173
                                       56677776799******9 PP

>> DUF4130  Domain of unknown function (DUF4130
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   4.9e-05     0.088      65     102 ..     145     182 ..      97     210 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.9e-05
                           DUF4130  65 iePkhnvlellaehFadRfadekwlIldekrklalvyd 102
                                         P+   l l+a+ F++R+++ +w+I+de +++a   +
  gi|385805155|ref|YP_005841553.1| 145 TTPESLALILVAPKFRERLRSIRWVIIDEIHEIASSKR 182
                                       679999999*******************9999987665 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   5.9e-05      0.11       6      45 ..      26      65 ..      24      79 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.9e-05
                                      SHHHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHH CS
                              PhoH  6 tkeQkeylealkkndivfaiGpaGtGKtylavalavealk 45
                                      t+ Qk+++  +k+ + v +  p+GtGKt+ a    ++al 
  gi|385805155|ref|YP_005841553.1| 26 TEPQKRAIPLIKRGENVLISSPTGTGKTLAAFLGIIDALY 65
                                      678*************************988776666654 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 ?    7.9   1.7    0.0022       3.9       2     114 ..      43     212 ..      42     221 .. 0.56

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0022
                                       EEESSTTSSHHHHHHH.HHHHH...........THEEEEEETTTCSSS............................. CS
                               AAA   2 llyGppGtGKTllaka.vakel...........gvefleisgsellsk............................. 37 
                                       l++ p GtGKTl+a   ++  l           ++++l +s  + l++                             
  gi|385805155|ref|YP_005841553.1|  43 LISSPTGTGKTLAAFLgIIDALyalseekklenEIYVLYVSPLRALNNdirrnlieplegikkiarekygveledik 119
                                       56666677777666431444433333333322224444444444443345555566666666666666666666666 PP

                                       ......................STTHHHHHHHHHHHHHHHTS...TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHH CS
                               AAA  38 ......................yvgesekkirelfkeakeka...kpsilfiDEidalaksrsgseseeeervvnqL 89 
                                                             ++  ++++++ ++ + k  +   +   ++iDEi+++a+s+       + + ++ L
  gi|385805155|ref|YP_005841553.1| 120 asirtsdtpqnerqimlrkpphILITTPESLALILVAPKFRErlrSIRWVIIDEIHEIASSK-------RGSNLSIL 189
                                       666666666666666666666644444444444443322222234457899*******9999.......77779999 PP

                                       HHHHHHTTTSSSTEEEEEEESSGGG CS
                               AAA  90 lteldgvkkkeskvivigatnrpdk 114
                                       l+ l+++ ++  +v  ig + +++ 
  gi|385805155|ref|YP_005841553.1| 190 LERLQELAER--EVQRIGLSATISP 212
                                       9999988884..5777777666554 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00046      0.82       1     115 [.      29     178 ..      29     197 .. 0.66
   2 ?   -0.7   0.0      0.89   1.6e+03      41      69 ..     276     312 ..     265     436 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00046
                            AAA_19   1 qreave.alkekvllvtaGpGtGKTrv.lkhivallvelggvkp....eeillvaftgrAakelrerlaalgaeatT 71 
                                       q++a+    + +++l+  + GtGKT     +i+  l +l ++k       +l v++ +   + +r +l    ++ + 
  gi|385805155|ref|YP_005841553.1|  29 QKRAIPlIKRGENVLISSPTGTGKTLAaFLGIIDALYALSEEKKleneIYVLYVSPLRALNNDIRRNL---IEPLEG 102
                                       7788876778889999999******7424455555544444433332255666777777778888888...888888 PP

                            AAA_19  72 iHrlal..................................ldfddlltealelle...........eaeeekklqee 103
                                       i ++a                                   l                           + ++ l++ 
  gi|385805155|ref|YP_005841553.1| 103 IKKIARekygveledikasirtsdtpqnerqimlrkpphiL-------------IttpeslalilvAPKFRERLRSI 166
                                       88887777788888888887776666666666666666542.............03333333334455788899677 PP

                            AAA_19 104 ellivDEfqdvd 115
                                        ++i+DE+ ++ 
  gi|385805155|ref|YP_005841553.1| 167 RWVIIDEIHEIA 178
                                       799***999887 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.89
                            AAA_19  41 kpeeillvaftgrAakelrerlaalgae........a 69 
                                       + ++ l+ + t+ A++++  +l++++ae        +
  gi|385805155|ref|YP_005841553.1| 276 SHKSTLIFTNTRSATERVVFKLKKVLAEknlvglddI 312
                                       3478899999999999988888777766555555543 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 ?    9.4   0.0   0.00022      0.39     148     214 ..     138     209 ..      30     214 .. 0.82
   2 ?   -3.1   0.0       1.4   2.4e+03     220     259 ..     457     499 ..     452     507 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00022
                                       ----EEEE-HHHHHHHT......TTS-S-S-SEEEES-GGGT--TT..SHHHHHHHH--.....-S-EEEE-S- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxx.....xxxxxxxxxx RF
                            SNF2_N 148 adydvvittYdvlsreaelqkkrsvlkqvewkrvvlDEghtlknst..skaaeavskLs.....tsnrwiltGT 214
                                       +  +++itt + l+     +k r+ l +++w  v++DE h + +s+  s+++  +++L+       +r+ l++T
  gi|385805155|ref|YP_005841553.1| 138 KPPHILITTPESLALILVAPKFRERLRSIRW--VIIDEIHEIASSKrgSNLSILLERLQelaerEVQRIGLSAT 209
                                       45689*********999888********999..9***********64544444443333221335566666665 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.4
                                       HHHHHHHHHHH-..TTTT--HHHHHHHTHHHHH.HHHHHHHHH CS
                                       xxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                            SNF2_N 220 ledlygLlkfLr..eepfgekqtfdkllqrpie.aqaekgrsr 259
                                        ed+ + +kfL+  e+ ++e+++++k  ++p e a  +k++ r
  gi|385805155|ref|YP_005841553.1| 457 YEDFLSVVKFLGgdEKRLEEQKVYRKIWYDPEEnAFGKKRSTR 499
                                       6899999****74466788899999999999885444554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (878 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.77u 0.32s 00:00:01.09 Elapsed: 00:00:00.47
# Mc/sec: 5567.89
//
Query:       gi|385805156|ref|YP_005841554.1|  [L=140]
Description: putative signal transduction protein [Fervidicoccus fontis Kam940]
Scores for 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-36  122.9   3.7    2.6e-18   66.2   0.1    2.1  2  CBS       CBS domain
     0.0015   18.8   0.1       0.25   11.6   0.0    2.4  2  IF3_N     Translation initiation factor IF-3, N-terminal doma
  ------ inclusion threshold ------
        0.1   12.3   0.0       0.22   11.3   0.0    1.5  1  NETI      NETI 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 !   58.0   0.5   1.6e-19   9.7e-16       2      54 ..      11      63 ..      10      66 .. 0.92
   2 !   66.2   0.1   4.3e-22   2.6e-18       3      55 ..      79     131 ..      73     133 .. 0.93

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 1.6e-19
                                      HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS  2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54
                                      ++im++++v+v+ +t+++ea+++m ++++++++VV++dg+l+Gi+t+rDl+ +
  gi|385805156|ref|YP_005841554.1| 11 ESIMSSPPVVVHKETSVHEAARIMFNNRIGSVLVVEDDGRLIGILTERDLVYL 63
                                      689********************65888**********************865 PP

  == domain 2  score: 66.2 bits;  conditional E-value: 4.3e-22
                                       HHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   3 dimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       ++mt++++tv+ ++t+++al +m+e ++++lPVV+++gk++Giv++rD+l+++
  gi|385805156|ref|YP_005841554.1|  79 HLMTENPITVKANETIGDALSKMKEVNIRHLPVVNDEGKPIGIVSMRDILDYI 131
                                       57*********************77779***********************98 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 !    4.9   0.0    0.0053        32       8      34 ..      40      66 ..      35      71 .. 0.79
   2 !   11.6   0.0   4.2e-05      0.25       4      30 ..     103     129 ..      91     133 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0053
                                      SEEEEE-SSS-EEEEEEHHHHHHHHHH CS
                             IF3_N  8 revrlvdedGeqlGvistreAlrlaee 34
                                        v +v++dG  +G+++ r+ + l  +
  gi|385805156|ref|YP_005841554.1| 40 GSVLVVEDDGRLIGILTERDLVYLVAS 66
                                      6799*************9998776655 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 4.2e-05
                                       S--SSEEEEE-SSS-EEEEEEHHHHHH CS
                             IF3_N   4 qIrarevrlvdedGeqlGvistreAlr 30 
                                       +++ r+  +v+++G+ +G++s+r++l+
  gi|385805156|ref|YP_005841554.1| 103 EVNIRHLPVVNDEGKPIGIVSMRDILD 129
                                       56789999****************997 PP

>> NETI  NETI protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   3.7e-05      0.22       3      19 ..      87     103 ..      86     107 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.7e-05
                              NETI   3 eVeeneTIedcLeRmkk 19 
                                       +V+ neTI d L++mk+
  gi|385805156|ref|YP_005841554.1|  87 TVKANETIGDALSKMKE 103
                                       699************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); 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: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 906.43
//
Query:       gi|385805157|ref|YP_005841555.1|  [L=335]
Description: NADPH glutamate synthase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-22   79.3   0.3    1.4e-21   77.0   0.3    2.0  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    1.6e-07   31.5   0.6    1.1e-06   28.8   0.1    2.2  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    1.4e-05   25.6   0.1      0.037   14.6   0.1    2.6  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    3.3e-05   23.3   0.3       0.38   10.0   0.0    3.0  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
     0.0023   17.2   0.1      0.029   13.6   0.1    2.3  3  Thi4           Thi4 family
     0.0042   16.4   0.1       0.11   11.8   0.0    2.2  2  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
      0.005   16.1   0.1     0.0087   15.3   0.1    1.3  1  FAD_binding_3  FAD binding domain
  ------ inclusion threshold ------
      0.017   14.0   0.0      0.024   13.4   0.0    1.2  1  MCRA           MCRA family
      0.018   13.8   0.1       0.03   13.0   0.1    1.3  1  HI0933_like    HI0933-like protein
       0.03   13.7   0.1        8.6    5.7   0.0    2.6  3  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
      0.036   13.1   0.2       0.85    8.6   0.1    2.2  2  FAD_binding_2  FAD binding domain
      0.045   12.8   2.1        1.3    8.0   0.5    2.8  3  GIDA           Glucose inhibited division protein A
       0.08   12.8   0.2       0.54   10.1   0.0    2.2  2  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
       0.15   11.1   0.0       0.24   10.4   0.0    1.3  1  Emaravirus_P4  P4 movement protein of Emaravirus, and the 30K
       0.18   11.1   0.1       0.26   10.6   0.1    1.2  1  FAD_oxidored   FAD dependent oxidoreductase
       0.27   10.7   1.0       0.53    9.8   1.0    1.4  1  DAO            FAD dependent oxidoreductase
       0.43   10.5   2.2       0.38   10.7   0.2    1.9  3  NAD_binding_9  FAD-NAD(P)-binding


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.0   0.3   1.3e-24   1.4e-21       3     294 .]      19     321 ..      17     321 .. 0.74

  Alignments for each domain:
  == domain 1  score: 77.0 bits;  conditional E-value: 1.3e-24
                                       EEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHHHHHHCHHHHCCCCHCCTCEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2   3 vvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeiasevvkklnqgielllgeevvkid 79 
                                       v +iGgGpAGl+aa +l  +g++++++   + ++  g l+   + + + +++ +++       g++ l     +++ 
  gi|385805157|ref|YP_005841555.1|  19 VSIIGGGPAGLSAAGYLVCKGYEIHVY---DVHPELGGLMMFGIPEERLKKDGIRN-------GVKELIS---TGMV 82 
                                       67*************************...77888888886777777777765554.......6666666...3333 PP

                                       ESC.EEEEETEEECTCEEEEEESEEEE---E.EE-BCTCTTC..TTBEECCSECHHHHHHCCSS-T........... CS
                                       xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx........... RF
                       Pyr_redox_2  80 pgk.kkvklekkkegdeekiaydklvlAtGs.sprdlgipGv.aenvgklvrtldsaealklkllp........... 142
                                       +++ k+++ ek    +e     d+ ++ tG  +++++++  + aenv+ +      +e l +  l+           
  gi|385805157|ref|YP_005841555.1|  83 RAHlKTMVGEKVP-LKEIIRSSDATLISTGTlKTKRMNVRCEnAENVYPS------VEWLIDYHLEkfgyqklfnir 152
                                       4443445553332.34444456********55999998884424666444......444444444444455588899 PP

                                       ....SEEEEES-SHHHHHHHHHHHHH.T-..................EEEEEESSSSSSTTS-HHHHHHHHHHHHHT CS
                                       ....xxxxxxxxxxxxxxxxxxxxxx.xx..................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 143 ....krivvvGgGyiGvElAaalakl.gk..................evtlveardrllraldkelsaaleealeke 196
                                           + + v+G+G+++ + A   + + ++                  ++ ++e r  l     + ls +  e+l k+
  gi|385805157|ref|YP_005841555.1| 153 tyvkEPVGVIGAGFTAADAAFISSTAfKAktfifyrrtkkdapmganDIKMLEERGVLF---YELLSPR--EVLCKN 224
                                       9999999*************995444133445555555555555554466666665554...4555555..899999 PP

                                       TEEEEESCEEEEEEETTEEEE..EEETTSCEEEESEEEE-S-EEES-HHCS.HCCT-EEEETTEEE--TTSBESSTT CS
                                       xxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 197 Gvevklgtsvkeidgngekle..vvledgeeidadlvvvavGvrpstelle.eklglelderggivvdeflrtnvpg 270
                                       Gv+  +   v+e++g g+++e  v++++ +++   +++ a+G  p +++ +  ++g++l+++g i  +e+ +t+v+g
  gi|385805157|ref|YP_005841555.1| 225 GVAEGMSFYVTEMRGSGRSAEliVHEDKVQTYYLNTIINAIGPIPTPPI-DvGEAGIKLNSNGTIAANEKFETSVKG 300
                                       9999999999999999995556488888888****************99.77************************* PP

                                       EEE-GGGCTECCSS--HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 271 iyaiGDvaggkggpelaqaAvqqG 294
                                       ++a+GDv    +gp ++  Av++G
  gi|385805157|ref|YP_005841555.1| 301 VFAAGDVK---HGPSQIGPAVKSG 321
                                       ********...8888888888766 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 !   28.8   0.1     1e-09   1.1e-06       1      35 [.      21      55 ..      21      70 .. 0.95
   2 ?    0.5   0.0      0.69   7.3e+02       1      16 [.     161     176 ..     161     190 .. 0.77

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 1e-09
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGra 35
                                      I+G+G +Gl+aA +L  +g+++++++ ++ lGG +
  gi|385805157|ref|YP_005841555.1| 21 IIGGGPAGLSAAGYLVCKGYEIHVYDVHPELGGLM 55
                                      9********************************76 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.69
                                       EE--SHHHHHHHHHHH CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLa 16 
                                       ++GaG++++ aA   +
  gi|385805157|ref|YP_005841555.1| 161 VIGAGFTAADAAFISS 176
                                       8*****9998887655 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   3.5e-05     0.037       3      55 ..      20      69 ..      18      76 .. 0.86
   2 !    8.3   0.0    0.0033       3.4       2      57 ..     159     211 ..     158     227 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.5e-05
                                      EEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTE CS
                         Pyr_redox  3 vvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngi 55
                                       ++GgG  gl +Ag+l   g +++v + +++l    + ++  i +e+l+k gi
  gi|385805157|ref|YP_005841555.1| 20 SIIGGGPAGLSAAGYLVCKGYEIHVYDVHPELG---GLMMFGIPEERLKKDGI 69
                                      69****************************999...66666666777777776 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0033
                                       EEEECSSHHHHHHHHHH.HHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEE CS
                         Pyr_redox   2 vvvvGgGyiglElAgal.aelgkkVtvversdkllrllDeeaskilqeklekngiev 57 
                                       v v+G+G+++ ++A +  +++++k+ ++ r+ k     D+ ++++  + le++g+ +
  gi|385805157|ref|YP_005841555.1| 159 VGVIGAGFTAADAAFISsTAFKAKTFIFYRRTK----KDAPMGANDIKMLEERGVLF 211
                                       67************8884669999999999855....35677777777777777755 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00036      0.38     167     196 ..      19      48 ..       3     113 .. 0.67
   2 !    9.5   0.1   0.00049      0.52     153     305 .]     145     305 ..     135     305 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00036
                       Pyr_redox_3 167 vvViGgknSavDaAlelvrkgaeVtvvtrg 196
                                       v +iGg+  +  aA  lv kg e++v++ +
  gi|385805157|ref|YP_005841555.1|  19 VSIIGGGPAGLSAAGYLVCKGYEIHVYDVH 48 
                                       555555555555555555555555555555 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00049
                       Pyr_redox_3 153 yskvkefhkyagqkvvViGgknSavDaAlelvrk.gaeVtvvtrgseiekee..sdpsyslkpdienrleelvke.. 224
                                       y+k  +++ y ++ v ViG++ +a+DaA+    +  a+  +++r+++ ++    +d+++ l+ +    + el++   
  gi|385805157|ref|YP_005841555.1| 145 YQKLFNIRTYVKEPVGVIGAGFTAADAAFISSTAfKAKTFIFYRRTKKDAPMgaNDIKM-LEERGVL-FYELLSPre 219
                                       6677788899999999**********997655554788888888876555431122222.2222221.222222123 PP

                       Pyr_redox_3 225 ....ekikvlfnaevkeikekeeeykvktedgkkvev..kddvvlatGykpdlsf.lkkslfeldedgrpvlteete 294
                                           + +       v+e++ + ++ ++  ++ k v++   + ++ a+G  p+  + + +++++l+++g+++ +e + 
  gi|385805157|ref|YP_005841555.1| 220 vlckNGVAEGMSFYVTEMRGSGRSAELIVHEDK-VQTyyLNTIINAIGPIPTPPIdVGEAGIKLNSNGTIAANE-KF 294
                                       344333444445558888888877776655533.3332246777889988776554555999999999888775.57 PP

                       Pyr_redox_3 295 etnvpglflaG 305
                                       et v+g+f aG
  gi|385805157|ref|YP_005841555.1| 295 ETSVKGVFAAG 305
                                       89999999998 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.1   2.8e-05     0.029      11      57 ..      10      55 ..       2      60 .. 0.79
   2 ?   -3.4   0.0       4.4   4.7e+03     207     224 ..      68      85 ..      61      88 .. 0.78
   3 ?    0.6   0.0      0.25   2.7e+02      12      49 ..     151     188 ..     145     196 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.8e-05
                                      HHHHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTT CS
                              Thi4 11 dllkyaesDvvivGaGssGLtaayylakkpdlkvailersvspGGGa 57
                                      ++ k  +  v i+G+G++GL+aa yl  k + ++ + + +  +GG +
  gi|385805157|ref|YP_005841555.1| 10 EIAKEKNKIVSIIGGGPAGLSAAGYLVCK-GYEIHVYDVHPELGGLM 55
                                      55555666688**************9999.99999998888888865 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 4.4
                                       HECEEETTEEE-THHHHH CS
                              Thi4 207 ktrevvpnlyvaGmevae 224
                                       + r+ v++l+ +Gm  a 
  gi|385805157|ref|YP_005841555.1|  68 GIRNGVKELISTGMVRAH 85 
                                       568899999999998776 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.25
                                       HHHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                              Thi4  12 llkyaesDvvivGaGssGLtaayylakkpdlkvailer 49 
                                       + +y++  v ++GaG +   aa++ +++ + k+ i+ r
  gi|385805157|ref|YP_005841555.1| 151 IRTYVKEPVGVIGAGFTAADAAFISSTAFKAKTFIFYR 188
                                       67899999********9999999988887788877765 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   0.0   0.00011      0.11      31      62 ..      19      50 ..       6      54 .. 0.90
   2 ?    2.4   0.0     0.077        81      31      64 ..     159     193 ..     150     262 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                                      EEEESTSHHHHHHHHHHHHTT-EEEEEESSHH CS
                       AlaDh_PNT_C 31 vlviGgGvaGlqAiatakglgakVtvlDvrpa 62
                                      v +iGgG aGl+A+   +  g ++ v+Dv p+
  gi|385805157|ref|YP_005841555.1| 19 VSIIGGGPAGLSAAGYLVCKGYEIHVYDVHPE 50
                                      88**************************9986 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.077
                                       EEEESTSHHHHHHHHH.HHHTT-EEEEEESSHHHH CS
                       AlaDh_PNT_C  31 vlviGgGvaGlqAiat.akglgakVtvlDvrparl 64 
                                       v viG+G     A+ + +++++ak+ ++  r+++ 
  gi|385805157|ref|YP_005841555.1| 159 VGVIGAGFTAADAAFIsSTAFKAKTFIFYRRTKKD 193
                                       67899998777777551567788888887666554 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   8.2e-06    0.0087       4      31 ..      19      46 ..      16      51 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 8.2e-06
                                      EEEE--SHHHHHHHHHHHHTTHHEEEEE CS
                     FAD_binding_3  4 VlIVGaGpaGlmlallLseaGvrvvlve 31
                                      V I+G+GpaGl++a  L  +G + ++ +
  gi|385805157|ref|YP_005841555.1| 19 VSIIGGGPAGLSAAGYLVCKGYEIHVYD 46
                                      78****************9999887765 PP

>> MCRA  MCRA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.3e-05     0.024       4      44 ..      19      55 ..      16      72 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.3e-05
                                      EEEE--SHHHHHHHHHHHHTT---GGGEEEE-SS------- CS
                              MCRA  4 aylvGsGiasLaaAvyLirdakvpgenihileelkvaggsl 44
                                      + ++G+G a+L+aA yL+     +g +ih+++ ++ +gg +
  gi|385805157|ref|YP_005841555.1| 19 VSIIGGGPAGLSAAGYLV----CKGYEIHVYDVHPELGGLM 55
                                      569**************9....5789*********999976 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   2.8e-05      0.03       3      36 ..      19      52 ..      17      57 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.8e-05
                                      EEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                       HI0933_like  3 viviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                      v +iGgG+AGl aA  +  +g ++ +++  ++lg
  gi|385805157|ref|YP_005841555.1| 19 VSIIGGGPAGLSAAGYLVCKGYEIHVYDVHPELG 52
                                      679*************************998887 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 ?    5.0   0.0     0.013        14      34      70 ..      14      50 ..       4      66 .. 0.89
   2 ?   -1.9   0.0       1.7   1.8e+03      76      98 ..      87     109 ..      76     120 .. 0.72
   3 ?    5.7   0.0    0.0082       8.6      26      73 ..     146     194 ..     131     214 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.013
                                      GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHH CS
                      2-Hacid_dh_C 34 lsgktvGiiGlGrIGqavakrlkafgmkviaydrskk 70
                                       ++k v iiG G  G ++a +l   g ++ +yd++++
  gi|385805157|ref|YP_005841555.1| 14 EKNKIVSIIGGGPAGLSAAGYLVCKGYEIHVYDVHPE 50
                                      57899****************************9875 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.7
                                       HHHTCEECSHHHHHHH-SEEEE- CS
                      2-Hacid_dh_C  76 eelgvelvsleellaesDivslh 98 
                                       +++  e+v l+e++++sD   + 
  gi|385805157|ref|YP_005841555.1|  87 KTMVGEKVPLKEIIRSSDATLIS 109
                                       55556889999999999986554 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.0082
                                       TCCGSBS-GTTSEEEEES-SHHHHHHHHHHH.HTT-EEEEESSSHHHHH CS
                      2-Hacid_dh_C  26 ekallgkelsgktvGiiGlGrIGqavakrlk.afgmkviaydrskkkee 73 
                                       +k + +++  ++ vG+iG+G  +  +a + + af++k +++ r+ kk++
  gi|385805157|ref|YP_005841555.1| 146 QKLFNIRTYVKEPVGVIGAGFTAADAAFISStAFKAKTFIFYRRTKKDA 194
                                       5566677777889****************999****7766655555443 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1   0.00081      0.85       4      36 ..      21      53 ..      19      63 .. 0.85
   2 ?    2.3   0.0     0.066        70     375     402 ..     279     308 ..     244     315 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00081
                                      EE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                     FAD_binding_2  4 ViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36
                                      +iG+G AGL+AA  +  +G ++ v +  +e gg
  gi|385805157|ref|YP_005841555.1| 21 IIGGGPAGLSAAGYLVCKGYEIHVYDVHPELGG 53
                                      9***********999999988888877776665 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.066
                                       EEEBETTSBE..STTEEESSBTEEE-STCE CS
                     FAD_binding_2 375 Gvetdengrv..ldadgqpipGLYAaGeva 402
                                       G++ + ng     ++ ++ ++G +AaG v 
  gi|385805157|ref|YP_005841555.1| 279 GIKLNSNGTIaaNEKFETSVKGVFAAGDVK 308
                                       6666666665444444569********997 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.5    0.0013       1.3       2      28 ..      19      45 ..      18      71 .. 0.86
   2 ?   -2.7   0.0       2.2   2.3e+03     136     155 ..      97     116 ..      69     126 .. 0.61
   3 ?    3.2   0.0     0.035        37       2      58 ..     159     216 ..     158     265 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0013
                                      EEEE-SSHHHHHHHHHHHHTT--EEEE CS
                              GIDA  2 viViGgGhAGceAAlaaarlGakvlLi 28
                                      v +iGgG AG+ AA  +  +G+++  +
  gi|385805157|ref|YP_005841555.1| 19 VSIIGGGPAGLSAAGYLVCKGYEIHVY 45
                                      78************9999999888776 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.2
                                       S-EEEEC.EEEE--TT-BT-E CS
                              GIDA 136 getikak.avviatGtflkgk 155
                                       +e+i+++ a+ i+tGt lk k
  gi|385805157|ref|YP_005841555.1|  97 KEIIRSSdATLISTGT-LKTK 116
                                       4444444489999999.4433 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.035
                                       EEEE-SSHHHHHHHHHHHH.TT--EEEEES-GGGTT--SSSSEEE-TTHHHHHHHHHH CS
                              GIDA   2 viViGgGhAGceAAlaaar.lGakvlLithkldtiaelsCnpsiggiakgllvrEida 58 
                                       v ViG+G     AA+ ++    ak+ ++  ++++ a ++ n+    + +g l  E+  
  gi|385805157|ref|YP_005841555.1| 159 VGVIGAGFTAADAAFISSTaFKAKTFIFYRRTKKDAPMGANDIKMLEERGVLFYELLS 216
                                       78************87765169999999999999888888887777777777777655 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 ?   10.1   0.0   0.00051      0.54       2      34 ..      19      51 ..      18     100 .. 0.81
   2 ?    0.1   0.0       0.6   6.3e+02       2      20 ..     159     177 ..     158     205 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00051
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseea 34
                                      v +iG G  G + a  ++ +g+e++++d+++e 
  gi|385805157|ref|YP_005841555.1| 19 VSIIGGGPAGLSAAGYLVCKGYEIHVYDVHPEL 51
                                      78***************************9875 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.6
                                       EEEE--SCCHHHHHHHHHH CS
                           3HCDH_N   2 vaviGaGtmGagiaavfas 20 
                                       v+viGaG   a  a +   
  gi|385805157|ref|YP_005841555.1| 159 VGVIGAGFTAADAAFISST 177
                                       89*****998888876654 PP

>> Emaravirus_P4  P4 movement protein of Emaravirus, and the 30K superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00023      0.24     101     136 ..      61      96 ..      48     110 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00023
                     Emaravirus_P4 101 derfkddgikagkkellktgklnldlvgtvitavpf 136
                                       +er+k dgi++g kel++tg +   l   v   vp+
  gi|385805157|ref|YP_005841555.1|  61 EERLKKDGIRNGVKELISTGMVRAHLKTMVGEKVPL 96 
                                       79********************99998877777775 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00024      0.26       2      42 ..      19      59 ..      19     109 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00024
                      FAD_oxidored  2 vvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsgl 42
                                      v ++GGgpaG+ AA     +G +  + + ++ lGGl+  g+
  gi|385805157|ref|YP_005841555.1| 19 VSIIGGGPAGLSAAGYLVCKGYEIHVYDVHPELGGLMMFGI 59
                                      679*********************************98766 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   1.0    0.0005      0.53       3      33 ..      20      52 ..      19      54 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0005
                                      EEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                               DAO  3 viiGGGiiGlstAyeLarrg..Vtllekgdiag 33
                                       iiGGG +Gls+A +L  +g  + +++ ++++g
  gi|385805157|ref|YP_005841555.1| 20 SIIGGGPAGLSAAGYLVCKGyeIHVYDVHPELG 52
                                      59**************999999**999988877 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   0.00036      0.38       2      39 ..      21      53 ..      20      62 .. 0.86
   2 ?   -2.4   0.2         4   4.3e+03       2      11 ..     161     170 ..     160     173 .. 0.81
   3 ?   -3.6   0.0       9.3   9.8e+03      39      61 ..     245     267 ..     221     273 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00036
                     NAD_binding_9  2 ivGaGprGlavlerLlarakkkspleitlfdpsep.gag 39
                                      i+G+Gp+Gl+++  L+ +       ei+++d ++  g g
  gi|385805157|ref|YP_005841555.1| 21 IIGGGPAGLSAAGYLVCK-----GYEIHVYDVHPElG-G 53
                                      9***************99.....59999999988744.4 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4
                     NAD_binding_9   2 ivGaGprGla 11 
                                       ++GaG++++ 
  gi|385805157|ref|YP_005841555.1| 161 VIGAGFTAAD 170
                                       8*****9975 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 9.3
                     NAD_binding_9  39 grvwrtdqseelllNvpasemsl 61 
                                       + + ++d+ +++ lN+  +++ +
  gi|385805157|ref|YP_005841555.1| 245 ELIVHEDKVQTYYLNTIINAIGP 267
                                       33444444555556665555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.65u 0.34s 00:00:00.99 Elapsed: 00:00:00.52
# Mc/sec: 1937.48
//
Query:       gi|385805158|ref|YP_005841556.1|  [L=84]
Description: hypothetical protein FFONT_0112 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       222  (0.0123822); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); 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 0.29s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 535.18
//
Query:       gi|385805159|ref|YP_005841557.1|  [L=159]
Description: Endonuclease III [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-23   82.2   0.0    3.6e-23   81.9   0.0    1.1  1  DUF123    Domain of unknown function DUF123
  ------ inclusion threshold ------
      0.084   12.7   0.1       0.95    9.3   0.0    2.1  2  DUF3189   Protein of unknown function (DUF3189)


Domain annotation for each model (and alignments):
>> DUF123  Domain of unknown function DUF123
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.9   0.0   4.1e-27   3.6e-23       2      93 ..      49     140 ..      48     141 .. 0.88

  Alignments for each domain:
  == domain 1  score: 81.9 bits;  conditional E-value: 4.1e-27
                            DUF123   2 elkkgvylYvGsalgsgglasRvkrHaslskkkekklhWhiDyLleseeaelaevvv.a.seerlEcalaealeaea 76 
                                        +k+g+y+Y+Gs++ +gg+++R+++H++++    kk++WhiD+L+++e++++a +++ + +++ lE++laea e+ +
  gi|385805159|ref|YP_005841557.1|  49 YFKRGYYAYIGSSFIRGGIQARLRHHLKKK----KKKFWHIDFLTSNESFTIAGYIClSsQKRGLEAELAEAAEEYC 121
                                       699***********************4433....689********************7448889*********4332 PP

                            DUF123  77 ..pvagfGasDckcesHLl 93 
                                         +++gfGa+D+k+  HL+
  gi|385805159|ref|YP_005841557.1| 122 epYIKGFGATDTKDAGHLF 140
                                       469***************8 PP

>> DUF3189  Protein of unknown function (DUF3189)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0     0.036   3.2e+02      80     137 ..      15      73 ..       4      82 .. 0.76
   2 ?    9.3   0.0   0.00011      0.95      38      60 ..     125     147 ..     114     150 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.036
                           DUF3189  80 lkdlleilgieeeelllvdtlptvnllmk.iggflsrrlglvklGrplvvkgikkaykk 137
                                       l++ l+ +g +   +l+  +++ vn+ +k  g f  +r     +G  ++  gi+ ++++
  gi|385805159|ref|YP_005841557.1|  15 LRSPLNTCGEKGYYVLFLKCTRDVNVKIKdRGEFYFKRGYYAYIGSSFIRGGIQARLRH 73 
                                       55666667777777889999999999887357788899999999999999999988765 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00011
                           DUF3189  38 lpyfdklekeeiGkliyiGkDel 60 
                                       ++ f ++++++ G+l++iG+D +
  gi|385805159|ref|YP_005841557.1| 125 IKGFGATDTKDAGHLFFIGEDVF 147
                                       567999***************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 957.40
//
Query:       gi|385805160|ref|YP_005841558.1|  [L=198]
Description: haloacid dehalogenase-like (HAD) hydrolase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.2e-14   52.7   0.1    6.3e-14   52.4   0.1    1.1  1  HAD_2           Haloacid dehalogenase-like hydrolase
    1.6e-07   31.9   0.0    1.5e-06   28.6   0.0    2.0  1  Hydrolase       haloacid dehalogenase-like hydrolase
    4.2e-05   23.4   0.2       0.24   11.1   0.0    3.1  3  Hydrolase_3     haloacid dehalogenase-like hydrolase
    0.00026   21.5   0.1     0.0039   17.6   0.1    2.1  1  HAD             haloacid dehalogenase-like hydrolase
     0.0009   19.3   0.0     0.0015   18.5   0.0    1.3  1  Hydrolase_like  HAD-hyrolase-like
  ------ inclusion threshold ------
       0.11   12.3   0.0       0.51   10.2   0.0    1.9  2  Acid_PPase      Acid Phosphatase
       0.13   12.4   0.0         24    5.1   0.0    2.4  2  Hydrolase_6     Haloacid dehalogenase-like hydrolase
        0.2   11.1   0.0        0.4   10.2   0.0    1.5  2  S6PP            Sucrose-6F-phosphate phosphohydrolase


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 !   52.4   0.1   2.8e-17   6.3e-14       1     176 [.       5     176 ..       5     178 .. 0.78

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 2.8e-17
                             HAD_2   1 iiFDlDgTlldteeliiqafnelleey.gls.elseeelrkliglslrellrklgeseeeeekieellrkyneekkk 75 
                                       ++FD+DgT +dt + ++  + e++ee  g++ e  ++ + +  g+s +e l+ +g++     k ee++r++ e k  
  gi|385805160|ref|YP_005841558.1|   5 VMFDFDGTVIDTMNEYAGLASEIIEEIaGIDrEKAKSLYLSTAGMSFKEQLKIMGIEGG---KAEEIYRRFIEGKMV 78 
                                       79**********************99823334444444455555555555555555544...777777888887777 PP

                             HAD_2  76 ..kevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpeviekaleklkl 150
                                         k+ ++ ++v+ l+ +Lke+g    i++s s+++  + +  ++  + Fd +++ +     K +p  ++ ++ek++l
  gi|385805160|ref|YP_005841558.1|  79 ilKSKRISPHVEILIGNLKERG----IISSLSTNNECSVVYLIEGIRAFDEVLCFNGSDSYKGEPH-LKFLMEKYGL 150
                                       677889999*********9975....566666666666778889999*******999999995554.68899***** PP

                             HAD_2 151 kkeeviyvGDsptDieaakkagikvi 176
                                        kee++++GDs +Di +   +gik+i
  gi|385805160|ref|YP_005841558.1| 151 RKEEIVFIGDSDYDIRTYSVLGIKSI 176
                                       *****************999999987 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   6.9e-10   1.5e-06       1     203 [.       2     165 ..       2     169 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 6.9e-10
                                       SSEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHH..HHHHHHHHHETTTEHHHHTHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase   1 iktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakar..sgaltgfatfigrgayaigkpe 75 
                                       i++v+fD+dGT++++ ++   +  ++                    +++  ++  + a + +       ++ +  +e
  gi|385805160|ref|YP_005841558.1|   2 IRAVMFDFDGTVIDTMNEYAGLASEI--------------------IEEIAGIdrEKAKSLYLS-----TAGMSFKE 53 
                                       79**************9998888888....................444444433777788888.....99999999 PP

                                       HHHHHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  76 wltaldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraa 152
                                        l+ +          g + +++++ +     + +   i  ++++ p ++ ++  Lk++gi +  l+ +n+  +  ++
  gi|385805160|ref|YP_005841558.1|  54 QLKIM----------GIEGGKAEEIYRR--FIEGKMVILKSKRISPHVEILIGNLKERGI-ISSLSTNNECSVVYLI 117
                                       99999..........7777777777777..7777777777778*****************.*********9999999 PP

                                       HHTTGGGESEEEEHHCES..STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHH CS
                                       xxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 153 nqlGddyfdaviasdiet..vakpspegkvaaireLqgkpeevamVGDgvnDa 203
                                       + +   +fd v++   +    ++p   +++ ++++++ ++ee++++GD+  D+
  gi|385805160|ref|YP_005841558.1| 118 EGIR--AFDEVLCFNGSDsyKGEP---HLKFLMEKYGLRKEEIVFIGDSDYDI 165
                                       9866..888888877777446666...88999****************99998 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.033        73       1      27 [.       5      31 ..       5      47 .. 0.80
   2 !    6.2   0.0    0.0034       7.6      12      64 ..      81     132 ..      78     139 .. 0.85
   3 !   11.1   0.0   0.00011      0.24     192     217 ..     141     166 ..     133     174 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.033
                                      EEEEIIIIIS-TTS---HHHHHHHHHH CS
                       Hydrolase_3  1 ialDlDGTLlnsdkkisektkeaikkl 27
                                      +++D DGT+++  +++   + e+i+++
  gi|385805160|ref|YP_005841558.1|  5 VMFDFDGTVIDTMNEYAGLASEIIEEI 31
                                      689*******99888877777766665 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0034
                                       TTS---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEEEGGGT CS
                       Hydrolase_3  12 sdkkisektkeaikklkekgikvviATGRslravlpvleelgldlpvialNGa 64 
                                       + k+is++    i +lke+gi   ++T ++  +v +++e +     v+++NG+
  gi|385805160|ref|YP_005841558.1|  81 KSKRISPHVEILIGNLKERGIISSLSTNNE-CSVVYLIEGIRAFDEVLCFNGS 132
                                       5789***********************765.567778887776679*****97 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00011
                                       HHHHHHHCT--GGGEEEEESSGGGHH CS
                       Hydrolase_3 192 lkklakelnisleeviafGDgeNDie 217
                                       lk+l++++++ +ee++ +GD++ Di 
  gi|385805160|ref|YP_005841558.1| 141 LKFLMEKYGLRKEEIVFIGDSDYDIR 166
                                       899*********************96 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   1.7e-06    0.0039       1     185 [.       5     166 ..       5     168 .. 0.44

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.7e-06
                               HAD   1 alfDfDgTLldg.dsle....lllrfllrrgaprlwralreklllalfrellrldraglaelleallaglseelaae 72 
                                       + fDfDgT +d+ + +     ++++ +        +   re                 +a+ l+   ag+s  ++++
  gi|385805160|ref|YP_005841558.1|   5 VMFDFDGTVIDTmNEYAglasEIIEEI--------AGIDRE-----------------KAKSLYLSTAGMS--FKEQ 54 
                                       67**********222222222222222........222233.................3333333344444..3333 PP

                               HAD  73 lerfv.................aevirpklldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatel 132
                                       l+ ++                   + + k + p++  l+   +++G+   + +++   +v  +    g    +    
  gi|385805160|ref|YP_005841558.1|  55 LKIMGieggkaeeiyrrfiegkMVILKSKRISPHVEILIGNLKERGIISSLSTNNECSVVYLIE---G----IR--- 121
                                       3333300000000000000111112222224455555555666666666666666555555555...3....22... PP

                               HAD 133 evddrltgelglegkpvrgegkvaalrewlaaegegidleevvayGDspsDlp 185
                                            ++  l   g+++++     +   +  +e++g++ ee+v++GDs  D+ 
  gi|385805160|ref|YP_005841558.1| 122 ----AFDEVLCFNGSDSYK----GEPHLKFLMEKYGLRKEEIVFIGDSDYDIR 166
                                       ....344444444444444....222223356689999999**********96 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   6.8e-07    0.0015       9      58 ..     140     187 ..     137     194 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 6.8e-07
                                       HHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-TTTH CS
                    Hydrolase_like   9 mydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrpedl 58 
                                        ++f +e++g+ +ee+++iGD+ + Di+     G+ks+ + +G++++e++
  gi|385805160|ref|YP_005841558.1| 140 HLKFLMEKYGLRKEEIVFIGDS-DYDIRTYSVLGIKSIKT-RGIFSEEER 187
                                       5789******************.******99999999976.566666664 PP

>> Acid_PPase  Acid Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.37   8.3e+02       4      14 ..       3      13 ..       1      44 [. 0.83
   2 ?   10.2   0.0   0.00023      0.51     110     159 ..     138     187 ..     116     196 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.37
                                      SEEEE-STTTS CS
                        Acid_PPase  4 klivFDLDyTL 14
                                      ++++FD D T+
  gi|385805160|ref|YP_005841558.1|  3 RAVMFDFDGTV 13
                                      67999999998 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00023
                                       HHHHHHHHHHH---GGGEEEEES-HHHHHHHHTTT-EEEE-SSS--HHHH CS
                        Acid_PPase 110 tkhfeklkkktgieyedmlfFDdesrnievesrlgvtfvlvpdGltreef 159
                                         h++ l +k g++ e+++f  d + +i+  s lg++++ ++   ++ee 
  gi|385805160|ref|YP_005841558.1| 138 EPHLKFLMEKYGLRKEEIVFIGDSDYDIRTYSVLGIKSIKTRGIFSEEER 187
                                       469999********************************999654455554 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.012        27       1      26 [.       5      31 ..       5      69 .. 0.68
   2 ?    5.1   0.0     0.011        24       8      40 ..      78     110 ..      74     117 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.012
                                      EEEESTTTSEETTEE-TT.HHHHHHHH CS
                       Hydrolase_6  1 flfDidGvLwrgdkaipg.aaealnal 26
                                      ++fD dG++++ ++ + g a e+++ +
  gi|385805160|ref|YP_005841558.1|  5 VMFDFDGTVIDTMNEYAGlASEIIEEI 31
                                      68*********9998887455666655 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.011
                                       TSEETTEE-TTHHHHHHHHHHTT-EEEEEE--- CS
                       Hydrolase_6   8 vLwrgdkaipgaaealnalraagkpvvllTNns 40 
                                       v+++ +++ p+++ ++  l+++g+   l TNn 
  gi|385805160|ref|YP_005841558.1|  78 VILKSKRISPHVEILIGNLKERGIISSLSTNNE 110
                                       78899999***********************96 PP

>> S6PP  Sucrose-6F-phosphate phosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.3   2.8e+03       5      19 ..       5      19 ..       3      58 .. 0.54
   2 ?   10.2   0.0   0.00018       0.4     169     198 ..     140     170 ..     106     193 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.3
                                      EEE-TBTTTB.S-HH CS
                              S6PP  5 lvsdLDntlvdgdne 19
                                      ++ d D+t++d  ne
  gi|385805160|ref|YP_005841558.1|  5 VMFDFDGTVIDTMNE 19
                                      567888888843332 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00018
                                       HHHHHHHHHT--GGGEEEEE-SGGGHHHH.T CS
                              S6PP 169 AlryLakkleleleqilvcGdsgnDeell.i 198
                                        l++L++k++l  e+i++ Gds  D+  + +
  gi|385805160|ref|YP_005841558.1| 140 HLKFLMEKYGLRKEEIVFIGDSDYDIRTYsV 170
                                       489**********************987644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 1269.39
//
Query:       gi|385805161|ref|YP_005841559.1|  [L=387]
Description: DNA primase large subunit [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-30  106.0   0.0    3.3e-30  105.4   0.0    1.2  1  DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large s


Domain annotation for each model (and alignments):
>> DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.4   0.0   1.9e-34   3.3e-30       7     205 ..     161     353 ..     156     386 .. 0.78

  Alignments for each domain:
  == domain 1  score: 105.4 bits;  conditional E-value: 1.9e-34
                                       HHHHHHHTT-G.........GS-EETTEEEE-HHHHHHHHHHHHHHHHHH..........HHGGGSSS---HHHHHH CS
                   DNA_primase_lrg   7 fedvldlvkrr.........rvllkkGyaylpkeeleslllekfrkrlekalestkeslpeleeeikederekleel 74 
                                       + d+++l kr          ++l+  G++y+++ el++l++e++  ++ ++l++++++ +++          +l+++
  gi|385805161|ref|YP_005841559.1| 161 IFDYMRLGKRLegdekwrfsNQLISGGMVYIQRAELQRLMEEAVYYKVLDKLKRISNDISDI----SILPP-QLKDI 232
                                       5555555552244556777799**************************************98....22222.46666 PP

                                       HCT--.............TTSSTTG..GSHHHHTT--HHHHCCHHHHCCCSS--CHHHHHHHHHHHHCT--CHHHHC CS
                   DNA_primase_lrg  75 lealsesyvaedvqeeedskisakn..idklakesfPpCmrelleglkknghlkhegrlqltlFlkdiglsldeile 149
                                         +++++  ++ +++  +s+i+ +     + + e+fPpC++++l++   +++l+h++r+q+++Fl ++ +s d++le
  gi|385805161|ref|YP_005841559.1| 233 AVEVQSQVAKRRISFYGESQIGGEGggAIAYKPELFPPCIKNILRKASNGENLSHQERFQIATFLLNLNISIDDVLE 309
                                       6666644444455555555555555332466789******************************************* PP

                                       CCHCHST..HHHHHH.HTHCHCHHHCC-STT--------HHHHHHS....TT---S.- CS
                   DNA_primase_lrg 150 lwkeaftrteekFdk.eyrynirhnyGkegkrtnyspysCekiltkpppgkgdahg.C 205
                                       ++k++     +++++   ry+++h +Gk g++++y+py+Cek          +a g C
  gi|385805161|ref|YP_005841559.1| 310 VFKQL-----PDYNEkIARYQVEHLAGKRGSGIKYKPYDCEKS---------KAIGlC 353
                                       ****9.....*****8888***********************9.........555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.35s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 2278.09
//
Query:       gi|385805162|ref|YP_005841560.1|  [L=318]
Description: putative ATP-fructose-6-phosphate kinase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-33  115.7   0.0      4e-33  115.0   0.0    1.2  1  PfkB      pfkB family carbohydrate kinase
  ------ inclusion threshold ------
      0.031   14.0   0.0      0.069   12.8   0.0    1.6  1  DUF1331   Protein of unknown function (DUF1331)


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 !  115.0   0.0   4.4e-37     4e-33       5     298 ..      17     302 ..      16     305 .. 0.89

  Alignments for each domain:
  == domain 1  score: 115.0 bits;  conditional E-value: 4.4e-37
                                       EEEEEEEEEEEEECSSH..TTSEEEESEEEEEEESHHHHHHHHHHHTT-EEEEEEEEESSHHHHHHHHHHHHTTEEE CS
                              PfkB   5 vviGealidliavsekl..egelvevktveksaGGagaNvAvalarlgadvafigavGdDnfGeflleelkkegvdt 79 
                                       v++G ++id+i  + +l  e+++v++k++  +aGG ++N  va++r g+ +++ig     + +  + ++l ++gv++
  gi|385805162|ref|YP_005841560.1|  17 VSVGNLNIDIISSVPELpaEDDSVKAKSLFIGAGGGALNYSVAASRFGHTSYLIGITTPIFSSLGFFRYLIENGVKI 93 
                                       799***************888888*************************************9*************** PP

                                       TTEEEESSSEEEEEEEEETTTSEEEEEEEEGGGGGHHHHHHHHHHHHHGCTSEEEEESEECTTSHHHHHHHHHHHHH CS
                              PfkB  80 dyvkidedtrtglalivvdedgertivfnrgaaadltkeeleededlleeadllyisgllsselpeavleelaeaak 156
                                       d vki+e+ ++g+  i+   +++r i+ +rg ++ l+++    ++++++++d++++s+    + ++ +l +++++++
  gi|385805162|ref|YP_005841560.1|  94 DNVKIVEEGSPGVSNIIHLPNEQRRIISYRGVNNLLDDDYIARSVEKINSVDVVHFSS----VKSSVALSAIKKIKE 166
                                       *************999999999****************9999***************9....666788888888888 PP

                                       HTTEEEEEECESSSHH...HHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEEGGG CS
                              PfkB 157 nggtfdpnlldplgaq...fkeallellaladllkpneeElealtgekledieealaalhklkakgaktvvvtlGke 230
                                       +     p+++ + g +   + +++ e+  l+d+l++ne+ ++ ++g      ++ l    +     ++ v  +lG++
  gi|385805162|ref|YP_005841560.1| 167 KRVLKSPIFSLDPGTEsreYEKVIGEFTGLVDVLFLNEKFARNVWGYG---FADFLYDMSW-----KTIVALKLGER 235
                                       888844444433333337999**************************9...3444444444.....689******** PP

                                       EEEEEE.TTEEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHTSSSSSTC CS
                              PfkB 231 Galvve.kdgelkvpavpkvkvvDttGAGDsfvggflaallegksleealrfanavAalvvqkkgaias 298
                                       Ga ++  ++ ++++ +  kv+ vDttGAGD+f + f  al e  s+ee+l++a++++al  ++ ga++s
  gi|385805162|ref|YP_005841560.1| 236 GAEAFYeGKRTSRILK--KVEYVDTTGAGDAFDAVFNCALIETRSVEESLELAVTAGALKSRNIGASSS 302
                                       **88875777777777..8*****************************************999999874 PP

>> DUF1331  Protein of unknown function (DUF1331)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   7.7e-06     0.069      12      33 ..     156     177 ..     151     178 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.7e-06
                           DUF1331  12 VaLTVYPKVRERRvLKmPFFLl 33 
                                       VaL    K++E+RvLK P F l
  gi|385805162|ref|YP_005841560.1| 156 VALSAIKKIKEKRVLKSPIFSL 177
                                       8999999***********9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1951.65
//
Query:       gi|385805163|ref|YP_005841561.1|  [L=287]
Description: uridine phosphorylase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.3e-41  140.7   0.0    5.1e-41  140.4   0.0    1.0  1  PNP_UDP_1  Phosphorylase superfamily
  ------ inclusion threshold ------
      0.087   13.2   0.0       0.16   12.3   0.0    1.4  1  DUF4465    Domain of unknown function (DUF4465)


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 !  140.4   0.0   5.7e-45   5.1e-41       1     218 [.      33     242 ..      33     262 .. 0.88

  Alignments for each domain:
  == domain 1  score: 140.4 bits;  conditional E-value: 5.7e-45
                                       CEEEEESSHHHHHHHHHHEEEEEEEEEE.TTEEEEEEEETTEEEEEEE--SSHHHHHHHHHHHHHHHC--SEEEEEE CS
                         PNP_UDP_1   1 kiaiivgspgevellaespleetpfgregrgfkfvtGtlkgkpvvivstGiGkpnaavvaeirllkefgvkaiiriG 77 
                                       +++++ g+p++ el+a++  +e +f  ++r++ ++ G++kg +++++stGiG p+aa +a+ +ll ++ ++++ir+G
  gi|385805163|ref|YP_005841561.1|  33 RYVLLPGDPERSELIAKT-WDEWRFVARHREYVTYSGKYKGAEISVTSTGIGGPSAA-IAVEELLRAG-ADTFIRVG 106
                                       5799**************.**************************************.********77.******** PP

                                       EEEESSTTT-TT-EEEEEEEEESSSCCGCCTHHCCTCCCCTTSSEE--HHHHHHHHHCHHTTTTTEEEEEEEEESES CS
                         PNP_UDP_1  78 taGglnpdlkvGDvvipddainfdgrsplygpkeegqyfpdsydapadpelrallkeaaealgikvhrGvvatadgf 154
                                       t G+++ ++++GD++i++ a+++dg+s+        qy++++y+a  + e + +l+eaae l+ ++ +G++a++d+f
  gi|385805163|ref|YP_005841561.1| 107 TTGAIKGEIEIGDLIISSGAVRLDGTSK--------QYAIPEYPAVSSYEVLLALVEAAESLNKRYWVGITASTDSF 175
                                       ****************************........***************************************** PP

                                       S-CH.............HHHHHHHHHTC-CEEESSHHHHHHHHHHTT--EEEEEEEEETTTBETTCTCH.HCCCHHH CS
                         PNP_UDP_1 155 yaet.............eaelrllrrlgadaveMEtaavaqlArelgipfaairvvsdlaaggadaeatheeveefa 218
                                       y  +             +  ++ l++l++ + eME++ ++++A+ +g+++ +i++v  +  +         ++e++ 
  gi|385805163|ref|YP_005841561.1| 176 YLGQgrpgyknfmnswaKSIISELKSLNVLNFEMEASTIFTMANIYGARASSICAVIAN--R--------VTNEFVP 242
                                       ******9999999887666666999999**************************99432..2........2222222 PP

>> DUF4465  Domain of unknown function (DUF4465)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.8e-05      0.16     119     166 ..     170     214 ..     163     227 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.8e-05
                           DUF4465 119 tgsvefyLadyrsknsakskivdtWkwvDLssLgevkklkfnlessds 166
                                        ++ +fyL + r +    ++++++W +  +s+L++ + l+f++e s  
  gi|385805163|ref|YP_005841561.1| 170 ASTDSFYLGQGRPG---YKNFMNSWAKSIISELKSLNVLNFEMEASTI 214
                                       45667999999977...9**************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1881.78
//
Query:       gi|385805164|ref|YP_005841562.1|  [L=109]
Description: hypothetical protein FFONT_0118 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); 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: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 765.41
//
Query:       gi|385805165|ref|YP_005841563.1|  [L=212]
Description: haloacid dehalogenase-like (HAD) hydrolase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-15   58.0   0.2    1.5e-15   57.7   0.2    1.1  1  HAD_2           Haloacid dehalogenase-like hydrolase
    4.4e-06   27.2   0.0    7.2e-06   26.5   0.0    1.3  1  HAD             haloacid dehalogenase-like hydrolase
    6.2e-05   23.4   0.0     0.0001   22.7   0.0    1.5  1  Hydrolase       haloacid dehalogenase-like hydrolase
    7.8e-05   22.7   0.0    0.00028   20.9   0.0    1.8  2  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 !   57.7   0.2   3.4e-19   1.5e-15       2     177 ..       7     178 ..       6     179 .. 0.88

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 3.4e-19
                             HAD_2   2 iFDlDgTlldteeliiqafnelleeyglselseeelrkliglslrellrklgeseeeeekieellrkyneekkkkev 78 
                                       i DlD Tl+d+ ++ + ++ +ll++y  +++s e++ +++  ++ + ++++ ++      ++++ + y+++    e+
  gi|385805165|ref|YP_005841563.1|   7 ILDLDMTLIDSLKVFYRVYSQLLKKYFNEDISFEDFYEKFCTNSLDNYKNYPKD-----FWKDFKEMYYAKDRS-EI 77 
                                       89************************8889999999888888886777777775.....889998888888888.** PP

                             HAD_2  79 kpydgvkelLeeLkeagyklgivTsk.sreaveekleqlgiesyFdvivtsedvekkKP..dpeviekaleklklkk 152
                                       kp+dg++elL  L+e+g+ + +   + + ++v ++le + + +y + ++t +     KP  + + ++k++++ +   
  gi|385805165|ref|YP_005841563.1|  78 KPIDGAEELLRFLNERGIVVVLSGRGvDGDEVLKELEYFSLSKYVSEVYTLKIYDSDKPflKDDAVRKIINN-HRGF 153
                                       ******************998888888999****************************84445667776655.6677 PP

                             HAD_2 153 eeviyvGDsptDieaakkagikvia 177
                                       +++i vGD   D+ a+ k g+ +i+
  gi|385805165|ref|YP_005841563.1| 154 SKCILVGDYVDDVSAGPKNGCISIG 178
                                       89***************99998776 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   0.0   1.6e-09   7.2e-06       2     186 ..       7     168 ..       6     169 .. 0.70

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1.6e-09
                               HAD   2 lfDfDgTLldgdslelllrfllrrgaprlwralreklllalfrellrldraglaelleallaglseelaaelerfv. 77 
                                       ++D+D TL+d+   ++ +            ++l+ ++ +++    ++++++++  +    ++ ++ ++ +++++++ 
  gi|385805165|ref|YP_005841563.1|   7 ILDLDMTLIDSLKVFYRVY----------SQLLKKYFNEDI---SFEDFYEKFCTNSLDNYKNYPKDFWKDFKEMYy 70 
                                       68*********44443333..........566666666666...5666677777788889****************7 PP

                               HAD  78 ...aevirpklldpgalellaahraaGdrvvvvSgg...lrplvepllaelgadevlatelevddrltgelglegkp 148
                                          +++i+p     ga ell+   ++G+ vvv+Sg     ++++++l   +     +++      ++t ++  ++kp
  gi|385805165|ref|YP_005841563.1|  71 akdRSEIKPI---DGAEELLRFLNERGI-VVVLSGRgvdGDEVLKELE-YFSLSKYVSE------VYTLKIYDSDKP 136
                                       6666666665...48888888888***9.99*****555556666655.6663333344......777775566666 PP

                               HAD 149 vrgegkvaalrewlaaegegidleevvayGDspsDlpl 186
                                         +++ v+++        ++  +++++ +GD++ D+ +
  gi|385805165|ref|YP_005841563.1| 137 FLKDDAVRKIIN------NHRGFSKCILVGDYVDDVSA 168
                                       666666666666......55567789*******99975 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   2.2e-08    0.0001     114     206 ..      74     169 ..       4     173 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 2.2e-08
                                       HHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT....GGGESEEEEHHCESSTTTSHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 114 adplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG....ddyfdaviasdietvakpspegkvaaireL 186
                                         ++k+ ++a+e+++ L+++gi vv+l+g      e ++++l      +y++ v++  i      +p  k  a+r++
  gi|385805165|ref|YP_005841563.1|  74 RSEIKPIDGAEELLRFLNERGI-VVVLSGRGVDGDE-VLKELEyfslSKYVSEVYTLKIYDSD--KPFLKDDAVRKI 146
                                       45677889**************.*****99986666.99999954433333444444444444..555555555555 PP

                                       ..T.STGGGEEEEESSHHHHHHH CS
                                       ..x.xxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 187 ..q.gkpeevamVGDgvnDaaal 206
                                         +    ++++ VGD v D++a+
  gi|385805165|ref|YP_005841563.1| 147 inNhRGFSKCILVGDYVDDVSAG 169
                                       321244778***********997 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.46   2.1e+03      42      62 ..      94     114 ..      91     128 .. 0.67
   2 !   20.9   0.0   6.2e-08   0.00028      11      74 ..     140     204 ..     131     205 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.46
                                       T-EEEEESSSSS-TTTHHHHH CS
                    Hydrolase_like  42 GwksvLVltGvtrpedleepe 62 
                                       G+  vL  +Gv ++e l+e e
  gi|385805165|ref|YP_005841563.1|  94 GIVVVLSGRGVDGDEVLKELE 114
                                       777788888898888888766 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 6.2e-08
                                       HHHHHHH...---GGGEEEEES-TTTHHHHHHHCT-EEEEESS.SSS-TTTHHHHHHHHT---SEEES CS
                    Hydrolase_like  11 dfalevl...gsdpeevlmiGDrlatDiagAnnaGwksvLVlt.Gvtrpedleepehkptyvaddlae 74 
                                       d a++++   +  +++++++GD   +D+ ++ + G+ s+ ++  G ++ e+l    ++++yv++dl e
  gi|385805165|ref|YP_005841563.1| 140 DDAVRKIinnHRGFSKCILVGDY-VDDVSAGPKNGCISIGITInGCKSGEEL--LRAGADYVVEDLFE 204
                                       55555554435559*********.****************998466666664..5789*******966 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       819  (0.0456802); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); 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: 0.60u 0.36s 00:00:00.96 Elapsed: 00:00:00.56
# Mc/sec: 1145.63
//
Query:       gi|385805166|ref|YP_005841564.1|  [L=91]
Description: hypothetical protein FFONT_0120 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score 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      0.015   15.2   0.0    1.0  1  dNK       Deoxynucleoside kinase


Domain annotation for each model (and alignments):
>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   8.2e-07     0.015     109     180 ..      16      89 ..       3      90 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8.2e-07
                                       HHHHHHHHHHHCCH.-SEEEEEE--HHHHHHHHHHCTTCCCT.TS-HHHHHHHHHHHHHHHTSGGCS-EEEEET CS
                               dNK 109 ykelldnlleelak.pdlliYLkasletclerikkRgreeek.kieldYlekLhekyeewlkklnevpvlvidv 180
                                        +++ +++++ ++k  +l  Y + ++++c+ r+ k ++ + k  +   ++e L +ky e+++k +  pv ++d+
  gi|385805166|ref|YP_005841564.1|  16 KDKWIQKMIKSAKKhHKLCPYFDKKTQKCFIRLGKTCDRDGKfDMCPTFMEFLSSKYDEYVSKNKPLPVDFMDI 89 
                                       57899999977777577788***************999888889999******************99*998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       803  (0.0447878); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); 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: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 550.53
//
Query:       gi|385805167|ref|YP_005841565.1|  [L=116]
Description: hypothetical protein FFONT_0121 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); 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: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 740.02
//
Query:       gi|385805168|ref|YP_005841566.1|  [L=128]
Description: hypothetical protein FFONT_0122 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score 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   12.6   1.4        9.6    6.9   0.4    2.4  2  MCM_N     MCM N-terminal domain


Domain annotation for each model (and alignments):
>> MCM_N  MCM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.002        37      56      83 ..      13      40 ..       5      44 .. 0.83
   2 ?    6.9   0.4   0.00054       9.6      37      83 ..      43      94 ..      38     126 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.002
                             MCM_N 56 ailenpkeylplleealkevvkklepsy 83
                                      +i+ +   yl+lle+alk+v +k  +s 
  gi|385805168|ref|YP_005841566.1| 13 KIEAKIDYYLDLLENALKNVEPKASRSV 40
                                      57778889************99977765 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.00054
                             MCM_N 37 ttLevdlddLaafde...eLaeailenpkeylpl..leealkevvkklepsy 83
                                      +++ v+ + L ++     +++++++ ++ke+l +  +++al+e++k    s+
  gi|385805168|ref|YP_005841566.1| 43 DSIFVNSKELLDVAImklNIVKNLVVKTKEMLAIyaMQDALNELMKLRVYSS 94
                                      678888888888855556999**********987779********6544333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1079  (0.0601818); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.50
# Mc/sec: 762.90
//
Query:       gi|385805169|ref|YP_005841567.1|  [L=755]
Description: Oligosaccharyl transferase, STT3 subunit [Fervidicoccus fontis Kam940]
Scores for complete 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-32  113.7  43.8    1.7e-32  113.0  43.8    1.3  1  STT3      Oligosaccharyl transferase STT3 subunit
    4.4e-05   23.8  13.0    4.4e-05   23.8  13.0    4.1  5  PMT_2     Dolichyl-phosphate-mannose-protein mannosyltransfer
  ------ inclusion threshold ------
        5.8    6.9   6.4         19    5.2   0.1    3.2  3  ODV-E18   Occlusion-derived virus envelope protein ODV-E18


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 !  113.0  43.8   2.9e-36   1.7e-32       2     486 ..      29     555 ..      28     557 .. 0.83

  Alignments for each domain:
  == domain 1  score: 113.0 bits;  conditional E-value: 2.9e-36
                                       HHHHHHHHHCCCCCHCC.CCCCCCT--S--SSCHHHHHHHCCCHHHT-C.....CCHHSSEETTSSTTT-EEESTT. CS
                              STT3   2 lilvifalialvavasrdlFtdedglsylsefDpYYnyRltenllnnGfpGdvvikkknwfdhsqyyPpGsrvdyg. 77 
                                       ++l+i+++i  +a++ r +  ++++  +l e Dp+  y +t++++++G+       + n+ ++  +yP G+ ++y  
  gi|385805169|ref|YP_005841567.1|  29 ISLAIVIAISAAAFYIR-MLRVFKYGYMLDEADPFIAYYATNYMVQHGISSWYSLTQSNPAMQIFWYPWGRDLAYSd 104
                                       67788888999999999.99*****************************8878888889999999**********75 PP

                                       .CCHCCC.CHHHHHHCCHHCHHHHHHHHCCHHHHHHHHCHHHHHHHHHHS-CCCHHHHHHHCCC-CCCCCTTSTT-- CS
                              STT3  78 .plivlLamlasaiinhsldvsirevclwlpallgsLlaIpiyflvrelksdiaGllAAlllaiaPgYlsrtvaGfy 153
                                        pl ++La l  + i   +  s+++ +++ p++ g L+a   y+lvre+++++aG+++A+++a+ Pg l rt+aGf+
  gi|385805169|ref|YP_005841567.1| 105 yPLFMMLAAL-TYPIGKLFGLSVMQWVVIQPPIAGALIALFSYLLVREVTGEMAGIISAFMAAVLPGMLDRTIAGFF 180
                                       5888888544.4556666668******************************************************** PP

                                       STCCCCHHHHHHHHHHHHHHHHCCS..TTCHHHHHHHHHHHHHHTTSCCGGHHHHCCHHHHHHHHHCTTTS-CCHHH CS
                              STT3 154 Dtdmfeivlllfvlffflkaiktks..nkislaviaaliiflivlaWggyailiyallllfilalLiigrfelklki 228
                                          +++  l+++++ f++ + k+++  +ki +  i+++++ l+   Wggy++  +++  + +++ L        ++ 
  gi|385805169|ref|YP_005841567.1| 181 VKLGMVQPLIVLAFLFLVLMFKEGElkRKIIYTIISGVLVGLVAWDWGGYQVVDLVIGTFLVFYPLAKEPEIREFYS 257
                                       ***************************************************99999999999999987777777777 PP

                                       HHHHHHHHHHHH..CCCCCCCTTCHHH..STTTCHHCCCCHHHHHHHHCCCHHC..CCCCCHHCCCHHTT.HHHHTT CS
                              STT3 229 avtfsviiaflviaiivllflgfqvva..vseiigalgifgllqlvafgsvvvlvaelkfyqfislfqpgilsevlg 303
                                         +f  ++++++   ++ +++g+ +++  ++  i   gi++++ ++++  + ++ a lk y+ +++  ++    ++ 
  gi|385805169|ref|YP_005841567.1| 258 IWLFTAVTLIVQ---LLSPPVGLMSIIkgSGLFIIGGGIAYTFSFLLLRYSKKI-ALLKKYSWRKIYSGF----LVF 326
                                       778888888888...999999999988654445555578888877766555555.99********99999....444 PP

                                       --GGGHHHHHHHHHHHHCCCCCCTS-----TTHHHHHHHHHS---S--CCHHHCCSSST.TTTCCCHH.HCHHCCHH CS
                              STT3 304 ligevvtalavlglialwlgilyslldleyaklkikiiilvsvwlpvgllaltkglrfl.iftvPlgi.ifvgllle 378
                                       l   vv+++++      ++g+ y +++   ++ +  ++++vs+++ ++l+ l+ ++ +  i+tv   +  +  +  +
  gi|385805169|ref|YP_005841567.1| 327 L--AVVAVIMLYFNFFDISGRAYYFIG---LNTNNALVASVSEHQEMTLSGLISEVGLSfILTVFYIVyGLFQSRKQ 398
                                       4..455666666667778999*****8...889999****************9988877566665555356666677 PP

                                       CTCHHHHHHHHHHHHHCCC-SCHCCCCCHHHHHHHCCCHHHHHHHHC.CHHHHHHHHH....HHHHH.......... CS
                              STT3 379 flavfvkiysvsqilfsgvvvillmltllpvlallaavkiskifsty.kdekeakikv....aakav.......... 440
                                        l++f++  +v +i++    + llm  ++  +++  +++++ i ++  k++  +++kv    +  +           
  gi|385805169|ref|YP_005841567.1| 399 PLHMFFIVLAVYSIIMGFKASYLLM-FVATSFSITGGIVVNLISDNLvKAFGLKELKVerkkK--SQkvnrdsigit 472
                                       89******99776666666666444.4566677777777776666652344556666655332..224467777888 PP

                                       ....................................HHHHCT.TTTTHHH.TTHHHCHHHHHHHHHHHHHHHHHHHH CS
                              STT3 441 ....................................aptksnglkeslew.kantnrdsvvitwwdyghilaveadr 480
                                                                           +  +++ +   l+  k+ t+ +sv+ twwdyg+ + v+  r
  gi|385805169|ref|YP_005841567.1| 473 iwsaalivivvigfiqmsttiayaqtpplilsggigMARENDAWIYTLDYiKNDTPANSVILTWWDYGYWIPVMTGR 549
                                       8888999999**************************99999********99************************** PP

                                       HHHHHC CS
                              STT3 481 pVtfdg 486
                                        +++dg
  gi|385805169|ref|YP_005841567.1| 550 ATVADG 555
                                       *****9 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 ?   -3.1   0.3       1.3   7.8e+03     100     117 ..      30      47 ..      19      55 .. 0.59
   2 !   23.8  13.0   7.3e-09   4.4e-05       8     153 ..     113     271 ..     103     276 .. 0.68
   3 ?   -5.0   7.5         3   1.8e+04     108     156 ..     275     332 ..     235     336 .. 0.70
   4 ?    2.3   1.1      0.03   1.8e+02      79     124 ..     379     426 ..     354     438 .. 0.64
   5 ?   -3.7   0.3         2   1.2e+04      55      66 ..     476     487 ..     468     497 .. 0.51

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.3
                             PMT_2 100 ywllagvlfGlgflsKyt 117
                                        ++++ ++ +++f++++ 
  gi|385805169|ref|YP_005841567.1|  30 SLAIVIAISAAAFYIRML 47 
                                       345555555555555554 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 7.3e-09
                             PMT_2   8 wllalftklfgf.selairlvsalagvltilllyllarrlfgkraallaalllavvplfvalsa.....lftpdapl 78 
                                        l+  + klfg   ++++ + + +ag+l +l+ yll+r+++g++a++++a+++av+p ++  +      ++ +  pl
  gi|385805169|ref|YP_005841567.1| 113 ALTYPIGKLFGLsVMQWVVIQPPIAGALIALFSYLLVREVTGEMAGIISAFMAAVLPGMLDRTIagffvKLGMVQPL 189
                                       3444455899976999999**************************************99988777764555666666 PP

                             PMT_2  79 vllwalalylllrale.knklkywllagvlfGlgfl..sKytaalllia.all.yllis..arrilkekkpylalll 148
                                       ++l  l+l l+++  e k+k+ y +++gvl+Gl       y ++ l+i+ +l+ y l++  + r + + +++ a++l
  gi|385805169|ref|YP_005841567.1| 190 IVLAFLFLVLMFKEGElKRKIIYTIISGVLVGLVAWdwGGYQVVDLVIGtFLVfYPLAKepEIREFYSIWLFTAVTL 266
                                       666666666666655567779999********976422344444444431333555555333333333444445555 PP

                             PMT_2 149 alllf 153
                                       ++ l 
  gi|385805169|ref|YP_005841567.1| 267 IVQLL 271
                                       55555 PP

  == domain 3  score: -5.0 bits;  conditional E-value: 3
                             PMT_2 108 fGlgflsKytaallliaall....yllis.arr.ilke..kkpyl.alllalllfspv 156
                                       +Gl+  +K   ++++ + ++    +ll++  ++  l +  ++  +  ++l++l++++v
  gi|385805169|ref|YP_005841567.1| 275 VGLMSIIKGSGLFIIGGGIAytfsFLLLRySKKiALLKkySWRKIySGFLVFLAVVAV 332
                                       7888888888888887755557788888884444555525333333444444444444 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.03
                             PMT_2  79 vllwalalylllraleknk..lkywllagvlfGlgflsKytaalllia 124
                                       + +++ + y+++ + +++k  l  ++++ ++  +++ +K   +l+ +a
  gi|385805169|ref|YP_005841567.1| 379 LSFILTVFYIVYGLFQSRKqpLHMFFIVLAVYSIIMGFKASYLLMFVA 426
                                       455555566666666533323555566666666666666655555553 PP

  == domain 5  score: -3.7 bits;  conditional E-value: 2
                             PMT_2  55 aalllavvplfv 66 
                                       aal++ vv+ f+
  gi|385805169|ref|YP_005841567.1| 476 AALIVIVVIGFI 487
                                       233333333333 PP

>> ODV-E18  Occlusion-derived virus envelope protein ODV-E18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1    0.0033        19      27      62 ..     323     358 ..     314     364 .. 0.88
   2 ?   -2.8   0.1      0.97   5.8e+03      25      38 ..     401     414 ..     397     430 .. 0.75
   3 ?    3.5   0.3     0.011        65      26      49 ..     469     492 ..     461     499 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0033
                           ODV-E18  27 lltilvvlviiillvllvqssstGsdssssnannar 62 
                                       +l  l+v+ +i+l   +++ s       + n+nna 
  gi|385805169|ref|YP_005841567.1| 323 FLVFLAVVAVIMLYFNFFDISGRAYYFIGLNTNNAL 358
                                       8999*****************999899999999985 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.97
                           ODV-E18  25 sllltilvvlviii 38 
                                        +++ +l+v  ii+
  gi|385805169|ref|YP_005841567.1| 401 HMFFIVLAVYSIIM 414
                                       58999999999885 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.011
                           ODV-E18  26 llltilvvlviiillvllvqssst 49 
                                       + +ti    +i+i+++ ++q+s+t
  gi|385805169|ref|YP_005841567.1| 469 IGITIWSAALIVIVVIGFIQMSTT 492
                                       5689999999************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (755 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1026  (0.0572257); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.79u 0.33s 00:00:01.12 Elapsed: 00:00:00.53
# Mc/sec: 4324.42
//
Query:       gi|385805170|ref|YP_005841568.1|  [L=280]
Description: NAD(+) kinase [Fervidicoccus fontis Kam940]
Scores for complete 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   75.5   0.0    7.5e-21   74.6   0.0    1.5  1  NAD_kinase  ATP-NAD kinase
     0.0032   17.1   0.0     0.0059   16.2   0.0    1.4  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 !   74.6   0.0   8.4e-25   7.5e-21      82     280 ..      71     256 ..      12     268 .. 0.82

  Alignments for each domain:
  == domain 1  score: 74.6 bits;  conditional E-value: 8.4e-25
                                       EEEEE-HHHHHHHHHHHHHCT-EEEEEESSS--SS-SEEGGGHHHHHHHHHHT-SEEEEEEEEEEEEEETTE..... CS
                        NAD_kinase  82 iivvGGDGTaldvarllqkaeiPvlgvnaGvkgfltefepeaaaellekllegeirvekrevldavimrskgeedia 158
                                       +i+vGGDGT l + +  ++++  +++v  G+ +f+ + +  + +++l++ll+g +  +k   l+  + r+k      
  gi|385805170|ref|YP_005841568.1|  71 LIIVGGDGTLLNALQDETNHDAIIATVAGGRRNFYYDASSIQGRSILKRLLNGAYVEQKVWGLKLEMGRRKH----- 142
                                       5779************************************************88877776677766666666..... PP

                                       .EEEEEEESSEEEEEESSSSS-EEEEEEETTEEEEEEEESEEEEE-TGGGGTHHHHTT--EE-TT---EEEEEESES CS
                        NAD_kinase 159 diviensvlnevviirgpgstlielelyvdtelleadqldglivstPtGstayslsaGgplisPgvlailivpicPh 235
                                                n+ vi   +  ++iel++ ++++ l ++  dg+i+st  Gs ay +s Ggpl++ + + il++p++  
  gi|385805170|ref|YP_005841568.1| 143 ------FFFNDAVIA-SNHMKVIELNVFINGRKLYEVAGDGIIISTSSGSSAYNISCGGPLVDFSHPSILLSPLNST 212
                                       ......457777665.56678999***************************************************** PP

                                       SS----EEE-TT-EEEEEE-.SS--EEEEETTTEEEEE-TT-EEEE CS
                        NAD_kinase 236 slssrpiVvssssklrirva.srseallaldGseelelspgdevrv 280
                                       +l +rp+V++  s+++i+++ + +   ++ldG + l+ +  + +++
  gi|385805170|ref|YP_005841568.1| 213 ILWNRPVVLDYLSSVDIEIErNIEYSKVILDGTKVLDPE--EKIKI 256
                                       ********************8888899******999865..44555 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   6.6e-07    0.0059      50      99 ..      62     108 ..      19     125 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6.6e-07
                                       HHHHCC-SEEEEEESHHHHHHHHHHHCTHHCTTSEEEEEE-SS--HHHHH CS
                          DAGK_cat  50 eakeegvdlivvaGGDGtvsevlnglleelatkpplgiiPlGtgNdlara 99 
                                       ++++++  +++++GGDGt+ ++l+   +e++++  ++++ +G  N    a
  gi|385805170|ref|YP_005841568.1|  62 KVESKKPCRLIIVGGDGTLLNALQ---DETNHDAIIATVAGGRRNFYYDA 108
                                       56667889**********865555...55559999**9999998866555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); 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: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1801.94
//
Query:       gi|385805171|ref|YP_005841569.1|  [L=129]
Description: hypothetical protein FFONT_0125 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-06   28.6   0.1    4.5e-06   27.1   0.1    1.7  1  PIN_6     PIN domain of ribonuclease
  ------ inclusion threshold ------
      0.011   15.3   0.3      0.013   15.0   0.3    1.1  1  CTV_P23   Citrus tristeza virus (CTV) P23 protein
       0.08   13.1   0.0       0.11   12.7   0.0    1.2  1  Pox_A28   Poxvirus A28 family
       0.11   12.8   1.6       0.32   11.3   1.6    1.7  1  MbeB_N    MbeB-like, N-term conserved region


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 !   27.1   0.1     1e-09   4.5e-06       2      87 ..      12      90 ..      11      91 .. 0.77

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 1e-09
                             PIN_6  2 VlDagaliknslsslqnlaeklyttpeVvaEirdkkarerlellp..lelevrePspesvkkvtefakktGDlsvLSkt 78
                                      ++D+ga+++    +l ++  ++yt++eVv+E++d +++++le +    ++ ++e +++  +  ++ +      + LSk+
  gi|385805171|ref|YP_005841569.1| 12 IFDTGAFLTG--LHL-SFPFQIYTVKEVVDEVKDFENKSKLEYTLsaNRIIIEEVEDDLRSLNKKLS------KALSKA 81
                                      79******99..665.7899**********************9884336666666655444444443......468999 PP

                             PIN_6 79 DievlALty 87
                                      D +++ L++
  gi|385805171|ref|YP_005841569.1| 82 DRKLINLAL 90
                                      999988886 PP

>> CTV_P23  Citrus tristeza virus (CTV) P23 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.3     3e-06     0.013      76     138 ..      38     100 ..      32     112 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3e-06
                           CTV_P23  76 dkalkterkckvnntqsqnevahmlmhdpvkylnkrkarafsnaelfaidlvlytkerqlavd 138
                                       d     e k k++ t s n +    + d ++ lnk+ ++a+s+a+   i+l l  k   + v 
  gi|385805171|ref|YP_005841569.1|  38 DEVKDFENKSKLEYTLSANRIIIEEVEDDLRSLNKKLSKALSKADRKLINLALKKKGEGFNVV 100
                                       55566799*********************************************9998776665 PP

>> Pox_A28  Poxvirus A28 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.4e-05      0.11      19      56 ..      26      62 ..      12      80 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.4e-05
                           Pox_A28 19 lllqlyaiyenydnikefndahsaleysksigvlalDr 56
                                      + +q+y++ e  d++k+f + +s+ley+ s++ + ++ 
  gi|385805171|ref|YP_005841569.1| 26 FPFQIYTVKEVVDEVKDFEN-KSKLEYTLSANRIIIEE 62
                                      569***************76.589******99887754 PP

>> MbeB_N  MbeB-like, N-term conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.6   7.1e-05      0.32       9      48 ..      41      85 ..      40      87 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.1e-05
                            MbeB_N  9 ktFeqkskeq.....aeSteemvksafekheksvkeaLkesekki 48
                                      k+Fe ksk +       ++ e v  +++ + k++++aL+++ +k+
  gi|385805171|ref|YP_005841569.1| 41 KDFENKSKLEytlsaNRIIIEEVEDDLRSLNKKLSKALSKADRKL 85
                                      79999*997733333578999********************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1382  (0.0770818); expected 358.6 (0.02)
Passed bias filter:                      826  (0.0460706); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.30s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 847.20
//
Query:       gi|385805172|ref|YP_005841570.1|  [L=38]
Description: hypothetical protein FFONT_0126 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       108  (0.00602376); expected 358.6 (0.02)
Passed bias filter:                       99  (0.00552178); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.47
# Mc/sec: 243.54
//
Query:       gi|385805173|ref|YP_005841571.1|  [L=156]
Description: single-strand DNA-binding protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-08   34.6   0.7    2.1e-08   34.0   0.7    1.2  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
    3.5e-05   23.6   1.5    4.7e-05   23.2   1.5    1.2  1  REPA_OB_2        Replication protein A OB 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 !   34.0   0.7   2.4e-12   2.1e-08       1      70 [.      26      98 ..      26     103 .. 0.95

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 2.4e-12
                                      EEEEEEEEEEE.......EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEE CS
                   tRNA_anti-codon  1 VtvaGrvtsis.......drsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrrpggelelkv 70
                                      V++++rv  +        +++++ ++ ++l D+tgri+++++     + a +++eG+ v+v+G ++++ +g+++l+v
  gi|385805173|ref|YP_005841571.1| 26 VSIKARVLETGdtktietKKGTRTISEAILGDDTGRIKATFWG----DKAGSVQEGQAVEVKGAWTTSFRGKVQLNV 98
                                      89***************99999*********************....*********************8888*9988 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 !   23.2   1.5   5.2e-09   4.7e-05      10      95 ..      23     104 ..      14     107 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 5.2e-09
                         REPA_OB_2  10 dsivDvigvvksveevseitskstekelkkreltlvDesgasvevtlWgkeaekfesseepvvalkgvkvsdFgg.r 85 
                                       +s v + + v +++++++i +k+++++++  e  l D++g+ ++ t+Wg++a +++  e + v +kg+  + F g  
  gi|385805173|ref|YP_005841571.1|  23 ESSVSIKARVLETGDTKTIETKKGTRTIS--EAILGDDTGR-IKATFWGDKAGSVQ--EGQAVEVKGAWTTSFRGkV 94 
                                       55667777788999**********97766..56789**996.9**********965..8889*************55 PP

                         REPA_OB_2  86 slsllssstl 95 
                                       +l++ sss++
  gi|385805173|ref|YP_005841571.1|  95 QLNVGSSSEV 104
                                       8999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); 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: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 934.07
//
Query:       gi|385805174|ref|YP_005841572.1|  [L=93]
Description: hypothetical protein FFONT_0128 [Fervidicoccus fontis Kam940]
Scores for complete 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-08   32.8   0.2    7.1e-08   32.6   0.2    1.1  1  PqqD      Coenzyme PQQ synthesis protein D (PqqD)
  ------ inclusion threshold ------
      0.021   15.2   1.0      0.027   14.8   0.1    1.6  2  Jag_N     Jag N-terminus
      0.082   12.8   0.0       0.13   12.1   0.0    1.4  1  DUF3283   Protein of unknown function (DUF3283)


Domain annotation for each model (and alignments):
>> PqqD  Coenzyme PQQ synthesis protein D (PqqD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.2   1.2e-11   7.1e-08       9      67 .]      31      89 ..      16      89 .. 0.91

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 1.2e-11
                                      -..EEE--CHHHHHHHH-SSSS-HHHHHHHHHHHCT--HHHHHHHHHHHHHHHHCTT-- CS
                              PqqD  9 tgkyisLnetgafiWklldgersveeivaalaeeydvdeeeaeadvlafldqLrekgli 67
                                      +  +++++   ++iWk  dg++s+eeiv++ +ee +++ +e+e+ ++  +++L+e +l+
  gi|385805174|ref|YP_005841572.1| 31 NQVTYEMSAAVYYIWKVSDGTKSLEEIVKQASEELNIPVNELEEPIAMIITKLLESNLL 89
                                      34568**************************************************9986 PP

>> Jag_N  Jag N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       1.7     1e+04      20      27 ..      29      36 ..      27      36 .. 0.77
   2 ?   14.8   0.1   4.5e-06     0.027       4      25 ..      52      73 ..      51      76 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.7
                             Jag_N 20 srdeveie 27
                                      ++++v++e
  gi|385805174|ref|YP_005841572.1| 29 DENQVTYE 36
                                      67889998 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 4.5e-06
                             Jag_N  4 kTveeAiekAlkeLgvsrdeve 25
                                      k++ee +++A++eL+++++e+e
  gi|385805174|ref|YP_005841572.1| 52 KSLEEIVKQASEELNIPVNELE 73
                                      89*****************997 PP

>> DUF3283  Protein of unknown function (DUF3283)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.1e-05      0.13      18      42 ..      39      63 ..      26      70 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.1e-05
                           DUF3283 18 qAsFlvwklkqakagpeaiteqlek 42
                                       A +++wk+  + +  e+i++q+++
  gi|385805174|ref|YP_005841572.1| 39 AAVYYIWKVSDGTKSLEEIVKQASE 63
                                      356******************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 604.86
//
Query:       gi|385805175|ref|YP_005841573.1|  [L=168]
Description: hypothetical protein FFONT_0129 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.039   14.3   0.2      0.059   13.7   0.2    1.3  1  LRAT      Lecithin retinol acyltransferase


Domain annotation for each model (and alignments):
>> LRAT  Lecithin retinol acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   3.3e-06     0.059      57     121 ..      80     148 ..      63     154 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.3e-06
                                       B--EEEEEEEHHHHHTTSEEEE--HHH....HCT----HHHHHHHHHHHTT-E-SCGHHCHHHHHHHHH CS
                              LRAT  57 lkkagVrkssleefaagdklrvneksd....skaeslpneeviqrAeelvGeveYsllsnNCEhFvtyc 121
                                       lkk+++ ++ +++ ++g k  + +  +    ++ + + +++++   +       Ys+l++NCE++   +
  gi|385805175|ref|YP_005841573.1|  80 LKKSEISVKYVNCEVRGVKKDLCKELEekikKEIKFDRKSDIVLHIQGIKDYYGYSVLKRNCENYSKLL 148
                                       5556666666666666655443333331211445578889999999999999************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1190  (0.0663729); expected 358.6 (0.02)
Passed bias filter:                      612  (0.0341346); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1109.25
//
Query:       gi|385805176|ref|YP_005841574.1|  [L=225]
Description: HhH-GPD family protein [Fervidicoccus fontis Kam940]
Scores for 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   58.2   0.0    1.3e-15   57.7   0.0    1.2  1  HhH-GPD        HhH-GPD superfamily base excision DNA repair p
    0.00038   20.2   0.0      0.001   18.8   0.0    1.7  1  HHH            Helix-hairpin-helix motif
     0.0004   20.9   0.5     0.0013   19.3   0.5    1.8  2  HHH_5          Helix-hairpin-helix domain
  ------ inclusion threshold ------
       0.02   15.2   0.0      0.089   13.2   0.0    2.2  1  IMS_HHH        IMS family HHH motif
      0.036   14.4   6.0      0.069   13.5   6.0    1.5  1  EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III
      0.083   13.3   0.0       0.27   11.6   0.0    1.8  1  HHH_8          Helix-hairpin-helix domain


Domain annotation for each model (and alignments):
>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.7   0.0   4.5e-19   1.3e-15       1     103 [.      45     181 ..      45     186 .. 0.92

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 4.5e-19
                                       HHHHHHTTS-HHHHHHHHHHHHHHHSHCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH........... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........... RF
                           HhH-GPD   1 vsailsqqtsderanriierlferfgfptpedladadeekLrelirelGfyrrKakyikelArilv........... 66 
                                       +s+ilsq+t+d +a +++ +l+er  ++++ +l +++  +L+e+ir  G+y++Ka+ ik lA  l            
  gi|385805176|ref|YP_005841574.1|  45 ISIILSQNTTDRNAIEAFLNLVER--GLDFRKLNSMSLGELEEIIRISGLYKSKAETIKRLAGFLSkdelflknlck 119
                                       799*********************..79************************************************* PP

                                       .............................S-SSS--TTSHHHHHHHHHHTTSSSSTTHHHHHHHHH CS
                                       .............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           HhH-GPD  67 .............................gkpdvlivvDvhvrrilkrlrsikekktkkkvekkle 103
                                                                    +   +l++vD h++r+ +rl   k +  +++v +  +
  gi|385805176|ref|YP_005841574.1| 120 kppeearreltsikgigkktadlflsvycN--MPLFPVDRHIKRVTERLLDKKMD--YEEVSQFWR 181
                                       **************************9654..69**************9766654..777776655 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   3.5e-07     0.001      12      29 ..     128     145 ..     125     146 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3.5e-07
                                       HHHTSTT-SHHHHHHHHH CS
                               HHH  12 eLlalPGVGpktAeaIls 29 
                                       eL++++G+G+ktA+ +ls
  gi|385805176|ref|YP_005841574.1| 128 ELTSIKGIGKKTADLFLS 145
                                       9*************9998 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   0.1      0.13     4e+02      33      52 ..      82     101 ..      63     104 .. 0.75
   2 !   19.3   0.5   4.3e-07    0.0013       2      49 ..      84     141 ..      83     143 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.13
                                       -HHHHHTSTTS-HHHHHHHH CS
                             HHH_5  33 dveeLakipGiGkktAerii 52 
                                       + ee+ +i G+ k +Ae i+
  gi|385805176|ref|YP_005841574.1|  82 ELEEIIRISGLYKSKAETIK 101
                                       57899999999999999885 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 4.3e-07
                                       HHHHTSTT--HHHHHHHHTT.T--SHHHH.....HHS....-HHHHHTSTTS-HHHHH CS
                             HHH_5   2 eeLlsvsGiGpktAlallsa.Giesvedl.....aaa....dveeLakipGiGkktAe 49 
                                       ee++++sG+ ++ A ++ +  G+ s ++l     +++    ++ eL++i+GiGkktA+
  gi|385805176|ref|YP_005841574.1|  84 EEIIRISGLYKSKAETIKRLaGFLSKDELflknlCKKppeeARRELTSIKGIGKKTAD 141
                                       678999999999999999999999988774322244433334556************7 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0     3e-05     0.089      11      28 ..     127     145 ..     125     147 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3e-05
                           IMS_HHH  11 lpitkipGiGgklgek.Le 28 
                                       +++t+i GiG+k+++  L 
  gi|385805176|ref|YP_005841574.1| 127 RELTSIKGIGKKTADLfLS 145
                                       689***********99776 PP

>> EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   6.0   2.3e-05     0.069       7      17 .]     210     220 ..     204     220 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.3e-05
                     EndIII_4Fe-2S   7 kCeaCPLaDlC 17 
                                       kC+ CPLaD+C
  gi|385805176|ref|YP_005841574.1| 210 KCDLCPLADIC 220
                                       9********** PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0     9e-05      0.27      43      61 ..     123     141 ..     114     145 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9e-05
                                       HHH.TTHCTTSTT--HHHHH CS
                             HHH_8  43 tsl.eeeltklpgiGkkiaa 61 
                                       +++ +e lt+++giGkk+a+
  gi|385805176|ref|YP_005841574.1| 123 EEArRE-LTSIKGIGKKTAD 141
                                       555345.***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1496.07
//
Query:       gi|385805177|ref|YP_005841575.1|  [L=79]
Description: hypothetical protein FFONT_0131 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score 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   15.1   0.1      0.025   14.1   0.1    1.4  1  Sigma70_r4     Sigma-70, region 4
       0.14   12.0   0.0       0.22   11.4   0.0    1.3  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain


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 ?   14.1   0.1   2.8e-06     0.025       6      32 ..      24      50 ..      23      51 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.8e-06
                                      -HHHHHHHHHHHTTT--HHHHHHHHTS CS
                        Sigma70_r4  6 pererevlelrfgeglTleEIgerlgi 32
                                      +er  +vl+ + +  +TleE++++ g+
  gi|385805177|ref|YP_005841575.1| 24 DERLLKVLRKYVYTQMTLEELAKEIGL 50
                                      577789999999***********9996 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 ?   11.4   0.0   2.4e-05      0.22       4      29 ..      23      50 ..      22      52 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.4e-05
                     HTH_AsnC-type  4 iDrkILeaLqed..aRisyaeLAervGl 29
                                      iD ++L+ L++     ++ +eLA+++Gl
  gi|385805177|ref|YP_005841575.1| 23 IDERLLKVLRKYvyTQMTLEELAKEIGL 50
                                      9**************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); 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: 0.43u 0.31s 00:00:00.74 Elapsed: 00:00:00.49
# Mc/sec: 486.24
//
Query:       gi|385805178|ref|YP_005841576.1|  [L=222]
Description: hypothetical protein FFONT_0132 [Fervidicoccus fontis Kam940]
Scores for complete 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   19.9   0.7    0.00075   19.1   0.7    1.5  1  Snf7      Snf7


Domain annotation for each model (and alignments):
>> Snf7  Snf7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.7   4.2e-08   0.00075       5     101 ..      43     139 ..      40     215 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 4.2e-08
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              Snf7   5 sLrkaerkldkkqeslekkikkleaelkklakkgnkdralllLKqkkryekqldqldnqlanleqvslaienlksnk 81 
                                       ++r +++kl+    +l+++ + l +++ + + k++ +ra  ++++  + +k  + + ++ + le + l +e+  +  
  gi|385805178|ref|YP_005841576.1|  43 KIRIEKNKLEYTLNKLQERANGLFEKVVDAQVKKDSERAAMYANEVAEVRKVAKTIMSSIFALERIGLRLETVRDVG 119
                                       67888999999999*************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHCT CS
                              Snf7  82 evlnamkqgakamkamnkkv 101
                                       +++ am+ +  + k++++++
  gi|385805178|ref|YP_005841576.1| 120 DLVSAMGPVVGVVKEVRNNL 139
                                       *************9998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       924  (0.0515366); expected 358.6 (0.02)
Passed bias filter:                      582  (0.0324614); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1414.20
//
Query:       gi|385805179|ref|YP_005841577.1|  [L=430]
Description: enolase [Fervidicoccus fontis Kam940]
Scores for complete 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-100  336.6   0.0   1.4e-100  336.3   0.0    1.1  1  Enolase_C  Enolase, C-terminal TIM barrel domain
    6.2e-45  152.6   0.1    9.3e-45  152.0   0.1    1.3  1  Enolase_N  Enolase, N-terminal domain
    2.9e-07   30.3   0.0    4.1e-07   29.8   0.0    1.2  1  MR_MLE_C   Enolase C-terminal domain-like


Domain annotation for each model (and alignments):
>> Enolase_C  Enolase, C-terminal TIM barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  336.3   0.0  2.4e-104  1.4e-100       2     292 ..     143     428 ..     142     430 .] 0.98

  Alignments for each domain:
  == domain 1  score: 336.3 bits;  conditional E-value: 2.4e-104
                                       -EE-EE-EEEEE-GGGSSSS--SSEEEEE-TT-SSHHHHHHHHHHHHHHHHHHHHHCC.GGGG-B-TTS-B----SS CS
                         Enolase_C   2 lvlPvPalnvinGGshagnklalqefmilPvgassfkealrlGaevyhklksvlkkkygksatnvGdeGGfaPnlqs 78 
                                       ++lPvP+ln+inGG+ha + l++qefmi+Pvg ++fk+a+   +evyhklk+++k+kyg   t+vGdeGGf+P +++
  gi|385805179|ref|YP_005841577.1| 143 FILPVPFLNIINGGKHASSGLDFQEFMIVPVGFDTFKDAIWASSEVYHKLKEIIKEKYGGIHTSVGDEGGFTPPIRD 219
                                       79*************************************************************************** PP

                                       HHHHHHHHHHHHHHCT-TC..TBEEEEE--GGGCEETCTTEEECTTTTTT..GGCEEEHHHHHHHHHHHHHHS-EEE CS
                         Enolase_C  79 nkealdliveaiekaGykg..kvkialdvassefykekdkkydldfkeeesdkskkltseqladlykelvkkyPivs 153
                                       ++ a+ l+ +ai+++Gy    +  ia+d+ass+fy+e+++ y +++k+          +++l ++y +l++ +P+ s
  gi|385805179|ref|YP_005841577.1| 220 PEAAVILLEDAIKASGYAVgdNFYIAIDAASSNFYNEEKGVYTVNGKN--------YRKDELLEFYLKLIDAHPVKS 288
                                       *****************97779*************************9........7789***************** PP

                                       EES-S-TT-HHHHHHHHHHHTTT.SEEEESTTTTT-HHHHHHHHHCT--SEEEE-HHHH-SHHHHHHHHHHHHHTT- CS
                         Enolase_C 154 iedpldeddweawkklteelgdk.vqivGddltvtnpkrlkeaiekkaanalllkvnqiGsltesleavklakeagy 229
                                       iedp+ e+d+e++++l ++l +k v +vGddl+ tnpkrl++a+ek++   +++k nqiG+lte++   ++a ++g 
  gi|385805179|ref|YP_005841577.1| 289 IEDPFYEEDFESFSELNSKLRKKgVLVVGDDLLTTNPKRLEKALEKGSVSGVIVKPNQIGTLTETIRFSEMAMHSGI 365
                                       ******************998876999************************************************** PP

                                       EEEEE--SC--S--HHHHHHHHCT-SEEE---S-SHHHHHHHHHHHHHHHHHGCC-EE-GGGC CS
                         Enolase_C 230 gvvvshrsGetedttiadlavglsaGqiktGaparserlakynqllrieeelgekakyaGkkv 292
                                        ++vshrsGet+d +iadl+v+l+ G ik+Gap+r er +kyn+l+ ie  l+  +++aG+++
  gi|385805179|ref|YP_005841577.1| 366 KAIVSHRSGETDDPFIADLSVALRNGAIKAGAPCRGERTSKYNRLIEIESLLSGYSEFAGRRF 428
                                       ************************************************************987 PP

>> Enolase_N  Enolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.0   0.1   1.6e-48   9.3e-45       1     131 []       9     137 ..       9     137 .. 0.98

  Alignments for each domain:
  == domain 1  score: 152.0 bits;  conditional E-value: 1.6e-48
                                       EEEEEEEEEE-TTS-EEEEEEEEETTC-EEEEE--B-BSSSSSS-B----SSTTSGGGT--HHHHHHHHHTHHHHHT CS
                         Enolase_N   1 IkkvkareildSrGnpTvevevttedgalgraavpsGaStgekealelrDgdkkrylgkgvekavenvnekiapali 77 
                                       I+++ a+eildSrG pT++v v t+ +a g a vpsG S+g++e+ elrDg   + +gkgv+kave+v++ i +al+
  gi|385805179|ref|YP_005841577.1|   9 ITEISAYEILDSRGDPTLRVCVSTK-KARGCANVPSGLSKGKHEVAELRDG-IGKLGGKGVSKAVETVKDYILQALV 83 
                                       899*********************8.5689********************9.899********************** PP

                                       TSBTT-HHHHHHHHHHHH-STT-TTT-HHHHHHHHHHHHHHHHHHHTS-HHHHH CS
                         Enolase_N  78 gldvtdqeeiDkllielDgtenksklGaNailavSlAvakaaAkakelplyryl 131
                                       g dv++q++iD+++++lDgte+ksklG+N++l+vSlAva+ aA   +++ly+yl
  gi|385805179|ref|YP_005841577.1|  84 GEDVREQQKIDRIMMSLDGTEDKSKLGGNTMLGVSLAVARTAAILTSQELYSYL 137
                                       *****************************************************7 PP

>> MR_MLE_C  Enolase C-terminal domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0   6.9e-11   4.1e-07      41     156 ..     238     371 ..     190     404 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 6.9e-11
                                       HTTTSTSEEEEE-TTT..S..............BHHHHHHHHHHHGG.GTESEEESSSSTTTHHHHHHHHHH..HH. CS
                          MR_MLE_C  41 vgpgddvdlmvDanqa..w..............dlatAirvarelee.ldllwlEEPvppeddleglaelra..ra. 97 
                                       v  gd++ +++Da  +  +                ++ +++  +l + + +  +E+P+   +d e+  el +  r+ 
  gi|385805179|ref|YP_005841577.1| 238 V--GDNFYIAIDAASSnfYneekgvytvngknyRKDELLEFYLKLIDaHPVKSIEDPFYE-EDFESFSELNSklRKk 311
                                       4..44556666666664314444444444444477888888888866466*********9.57*********99667 PP

                                       SSEEEESTTSSS.HHHHHHHHHHTSESEEEEBHHHHTSHHHHHHHHHHHHHTT-EEEEBS CS
                          MR_MLE_C  98 sipiaagEslys.radfrelleagavdivqpdvsrvgGitearkvaalaeafgvpvapHs 156
                                       ++ ++++  l++ +++++++le+g v  v ++++++g +te++++ ++a + g++ ++ +
  gi|385805179|ref|YP_005841577.1| 312 GVLVVGDDLLTTnPKRLEKALEKGSVSGVIVKPNQIGTLTETIRFSEMAMHSGIKAIVSH 371
                                       9*******99998*****************************************965544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 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:                        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 0.30s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 2593.70
//
Query:       gi|385805180|ref|YP_005841578.1|  [L=108]
Description: hypothetical protein FFONT_0134 [Fervidicoccus fontis Kam940]
Scores for complete 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   24.1   0.1    3.7e-05   23.7   0.1    1.2  1  DZR             Double zinc ribbon
    3.9e-05   23.6   6.1      0.015   15.4   0.4    2.2  2  UPF0547         Uncharacterised protein family UPF0547
    0.00078   19.1   0.4      0.027   14.2   0.0    2.2  2  zinc_ribbon_5   zinc-ribbon domain
     0.0017   18.0   6.7        0.1   12.3   0.3    2.3  2  zinc_ribbon_2   zinc-ribbon domain
     0.0022   18.6   1.6        1.3    9.8   0.3    2.2  2  FYDLN_acid      Protein of unknown function (FYDLN_acid)
     0.0038   17.3   1.6        1.2    9.3   0.3    2.3  2  Zn-ribbon_8     Zinc ribbon domain
     0.0038   17.3   0.0     0.0067   16.5   0.0    1.3  1  CpXC            CpXC protein
     0.0053   16.3   1.4       0.31   10.7   0.1    2.3  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
     0.0061   16.9   1.2      0.035   14.5   0.0    2.2  2  DUF4379         Probable Zinc-ribbon domain
     0.0062   16.5   3.2      0.077   13.0   3.9    2.0  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
     0.0092   16.4   0.5      0.031   14.7   0.5    1.9  1  zf-IS66         zinc-finger binding domain of transposase IS6
  ------ inclusion threshold ------
      0.012   14.9   0.3        2.6    7.4   0.0    2.4  2  zf-TFIIB        Transcription factor zinc-finger
      0.016   15.1   1.0        1.2    9.1   0.0    2.5  2  zinc_ribbon_4   zinc-ribbon domain
      0.021   14.4   3.8        2.7    7.7   0.1    2.2  2  zf-tcix         Putative treble-clef, zinc-finger, Zn-binding
      0.024   14.6   0.2          2    8.4   0.0    2.2  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
      0.038   14.6   0.3        5.5    7.7   0.1    2.4  2  zf-ISL3         zinc-finger of transposase IS204/IS1001/IS109
      0.044   14.5   1.3        0.1   13.3   0.1    2.0  2  zf-3CxxC_2      Zinc-binding domain
      0.045   13.2   7.0        1.8    8.1   1.3    2.4  2  zf-ribbon_3     zinc-ribbon domain
      0.065   12.8   5.3        3.5    7.2   1.1    2.6  2  TF_Zn_Ribbon    TFIIB zinc-binding
      0.066   13.0   1.0        6.2    6.7   0.1    2.3  2  A2L_zn_ribbon   A2L zinc ribbon domain
      0.083   13.2   0.6         11    6.3   0.1    2.4  2  zinc_ribbon_9   zinc-ribbon
        0.1   12.5   5.2       0.51   10.3   0.6    2.2  2  zf-HIT          HIT zinc finger
       0.11   12.5   0.1       0.25   11.4   0.1    1.7  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.14   12.1   3.8       0.88    9.5   0.2    2.4  2  zf-FPG_IleRS    Zinc finger found in FPG and IleRS
       0.14   12.1   1.6        7.1    6.7   0.1    2.2  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
       0.14   11.8   2.9        2.3    7.9   0.2    2.3  2  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
       0.14   11.6   2.3        3.9    7.0   0.5    2.3  2  Mu-like_Com     Mu-like prophage protein Com
       0.14   12.0   3.7       0.46   10.4   0.3    2.1  2  TFIIS_C         Transcription factor S-II (TFIIS)
       0.22   11.7   3.5        2.8    8.1   0.0    2.6  3  zf-Mss51        Zinc-finger of mitochondrial splicing suppres
       0.51   10.3   6.3        1.2    9.2   1.1    2.3  2  DUF1610         Domain of unknown function (DUF1610)
       0.77    9.7   5.7        7.3    6.6   0.9    2.2  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
        1.1    8.9   3.7         18    5.0   0.1    2.4  2  zf_C2H2_10      C2H2 type zinc-finger
        2.1    9.0   4.0        8.4    7.1   0.4    2.2  2  zf-C2H2         Zinc finger, C2H2 type


Domain annotation for each model (and alignments):
>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.1   6.7e-08   3.7e-05       9      38 ..       5      55 ..       1      60 [. 0.90

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 6.7e-08
                               DZR  9 ppdarfCseCgtklkavaa.....................edrCpsCgekv 38
                                      +++ ++C++Cgt+++++++                     +++Cp+Cg++ 
  gi|385805180|ref|YP_005841578.1|  5 EKKPNVCPRCGTEVPNPTKtwnfvsplpddkgrititvmgSYKCPNCGYSW 55
                                      567899********988889****************************986 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.8   0.00058      0.31       2      11 ..      10      19 ..       9      23 .. 0.92
   2 !   15.4   0.4   2.7e-05     0.015      16      26 .]      47      57 ..      45      57 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00058
                           UPF0547  2 vCPeCeakvP 11
                                      vCP+C ++vP
  gi|385805180|ref|YP_005841578.1| 10 VCPRCGTEVP 19
                                      7********9 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 2.7e-05
                           UPF0547 16 fCphCGyvFqa 26
                                      +Cp CGy+++a
  gi|385805180|ref|YP_005841578.1| 47 KCPNCGYSWKA 57
                                      7********97 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.2      0.18        98       5      10 ..      11      16 ..       9      18 .. 0.88
   2 !   14.2   0.0   4.9e-05     0.027       4      26 ..      47      69 ..      46      70 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.18
                     zinc_ribbon_5  5 CpdCdt 10
                                      Cp C+t
  gi|385805180|ref|YP_005841578.1| 11 CPRCGT 16
                                      *****9 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 4.9e-05
                     zinc_ribbon_5  4 rCpdCdtkFklvdsklKksgkkV 26
                                      +Cp+C+   k + sklK+ g+ V
  gi|385805180|ref|YP_005841578.1| 47 KCPNCGYSWKAAISKLKVGGGEV 69
                                      7*******************988 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.3   0.00019       0.1       2      11 ..      11      20 ..      10      24 .. 0.83
   2 !    8.3   1.5    0.0035       1.9       1       7 [.      47      53 ..      46      54 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00019
                     zinc_ribbon_2  2 CpnCGaelqd 11
                                      Cp+CG+e+++
  gi|385805180|ref|YP_005841578.1| 11 CPRCGTEVPN 20
                                      9999999987 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0035
                     zinc_ribbon_2  1 fCpnCGa 7 
                                      +CpnCG+
  gi|385805180|ref|YP_005841578.1| 47 KCPNCGY 53
                                      6888885 PP

>> FYDLN_acid  Protein of unknown function (FYDLN_acid)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.3    0.0023       1.3      23      38 ..       5      20 ..       4      34 .. 0.87
   2 !    8.2   0.0    0.0072       3.9      28      88 ..      47     104 ..      46     108 .] 0.42

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0023
                        FYDLN_acid 23 nkdPivcpkcgeefep 38
                                      +k+P vcp cg+e++ 
  gi|385805180|ref|YP_005841578.1|  5 EKKPNVCPRCGTEVPN 20
                                      589**********986 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0072
                        FYDLN_acid  28 vcpkcgeefepeevlksraaaaeaeeakkkkeeeedeedeeeeedvsdedadeeeeedddd 88 
                                        cp+cg +++ +   k +    e e ++  ke++ + e+ +  ++ ++ + d e+  ++dd
  gi|385805180|ref|YP_005841578.1|  47 KCPNCGYSWKAAIS-KLKVGGGEVEIDAGGKEKKIAGEAPK--QKPEEIELDLEDIINEDD 104
                                       5*********9988.44444333333322222222222221..222222222222223333 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   0.3    0.0022       1.2      23      36 ..       5      18 ..       1      20 [. 0.68
   2 ?    7.2   0.0      0.01       5.6       6      14 ..      46      54 ..      45      63 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0022
                       Zn-ribbon_8 23 dapltaCPeCgsev 36
                                      ++++ +CP+Cg ev
  gi|385805180|ref|YP_005841578.1|  5 EKKPNVCPRCGTEV 18
                                      444455*****976 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.01
                       Zn-ribbon_8  6 YrCeeCghe 14
                                      Y+C +Cg  
  gi|385805180|ref|YP_005841578.1| 46 YKCPNCGYS 54
                                      999999965 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.2e-05    0.0067       3      50 ..      11      58 ..      10      65 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.2e-05
                              CpXC  3 CpaCgkefeaeiwtsidadedpelkeklldgslfeatCpkCgatakle 50
                                      Cp+Cg+e   ++ t   ++  p+ k ++    + +++Cp+Cg++ k+ 
  gi|385805180|ref|YP_005841578.1| 11 CPRCGTEVPNPTKTWNFVSPLPDDKGRITITVMGSYKCPNCGYSWKAA 58
                                      ******998776666666667*********************998765 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.1   0.00058      0.31       4      15 ..      10      21 ..       8      24 .. 0.85
   2 ?    4.7   0.1     0.041        22       2       9 ..      45      52 ..      44      57 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00058
                            zf_UBZ  4 lCerCgkeipes 15
                                      +C+rCg+e+p +
  gi|385805180|ref|YP_005841578.1| 10 VCPRCGTEVPNP 21
                                      8********976 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.041
                            zf_UBZ  2 tylCerCg 9 
                                      +y C+ Cg
  gi|385805180|ref|YP_005841578.1| 45 SYKCPNCG 52
                                      79*****9 PP

>> DUF4379  Probable Zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.3       1.1   6.1e+02      52      56 .]       7      14 ..       1      17 [. 0.62
   2 !   14.5   0.0   6.4e-05     0.035      30      45 ..      46      61 ..      34      68 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 1.1
                           DUF4379 52 k...CpkC 56
                                      k   Cp C
  gi|385805180|ref|YP_005841578.1|  7 KpnvCPRC 14
                                      23458888 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 6.4e-05
                           DUF4379 30 WkCakCgheWeasvsn 45
                                       kC++Cg++W+a++s+
  gi|385805180|ref|YP_005841578.1| 46 YKCPNCGYSWKAAISK 61
                                      69***********987 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   3.9   0.00014     0.077      19      45 ..       9      53 ..       5      54 .. 0.88
   2 !    7.3   0.2    0.0087       4.7      20      28 ..      47      56 ..      43      63 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00014
                     Zn_Tnp_IS1595 19 fvCPhCgsrkayrikt..................rglfqCkeCrk 45
                                       vCP+Cg + +  +kt                   g ++C  C++
  gi|385805180|ref|YP_005841578.1|  9 NVCPRCGTEVPNPTKTwnfvsplpddkgrititvMGSYKCPNCGY 53
                                      58*******777777777*************************98 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0087
                     Zn_Tnp_IS1595 20 vCPhCgsr.k 28
                                       CP+Cg++ k
  gi|385805180|ref|YP_005841578.1| 47 KCPNCGYSwK 56
                                      6*****9864 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 !   14.7   0.5   5.7e-05     0.031       2      46 .]       9      52 ..       8      52 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.7e-05
                           zf-IS66  2 rtCpcCGgllkpigedrvreeldipPakfrViehirpkyaCpcCe 46
                                       +Cp CG++ +p +++ +  +  +p  k r++ ++   y+Cp+C+
  gi|385805180|ref|YP_005841578.1|  9 NVCPRCGTE-VPNPTKTWNFVSPLPDDKGRITITVMGSYKCPNCG 52
                                      68******9.6888888***************************7 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.2     0.024        13       2       8 ..      11      17 ..      10      27 .. 0.78
   2 ?    7.4   0.0    0.0049       2.6       1      20 [.      47      72 ..      47      73 .. 0.66

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.024
                          zf-TFIIB  2 CPkCqde 8 
                                      CP+C++e
  gi|385805180|ref|YP_005841578.1| 11 CPRCGTE 17
                                      9999986 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0049
                          zf-TFIIB  1 kCPkCqdele..eser....ggveid 20
                                      kCP+C+ + +  +s++    g+veid
  gi|385805180|ref|YP_005841578.1| 47 KCPNCGYSWKaaISKLkvggGEVEID 72
                                      8****988775533335565667777 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.3     0.083        45       5      10 ..      11      16 ..      10      17 .. 0.73
   2 ?    9.1   0.0    0.0022       1.2      26      36 .]      46      56 ..      31      56 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.083
                     zinc_ribbon_4  5 CpsCka 10
                                      Cp+C++
  gi|385805180|ref|YP_005841578.1| 11 CPRCGT 16
                                      888887 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0022
                     zinc_ribbon_4 26 vrCskCghvFr 36
                                       +C++Cg +++
  gi|385805180|ref|YP_005841578.1| 46 YKCPNCGYSWK 56
                                      59******995 PP

>> zf-tcix  Putative treble-clef, zinc-finger, Zn-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.8    0.0059       3.2      13      21 ..      11      19 ..       9      24 .. 0.81
   2 ?    7.7   0.1     0.005       2.7       6      17 ..      41      52 ..      39      54 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0059
                           zf-tcix 13 CpkCGtyNG 21
                                      Cp+CGt+ +
  gi|385805180|ref|YP_005841578.1| 11 CPRCGTEVP 19
                                      ******855 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.005
                           zf-tcix  6 tlRGvrkCpkCG 17
                                      t+ G  kCp+CG
  gi|385805180|ref|YP_005841578.1| 41 TVMGSYKCPNCG 52
                                      666777****** PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.064        35      30      40 ..      10      20 ..       2      30 .. 0.71
   2 ?    8.4   0.0    0.0038         2      46      58 ..      45      57 ..      36      64 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.064
                    OrfB_Zn_ribbon 30 tCseCgsknke 40
                                       C++Cg ++ +
  gi|385805180|ref|YP_005841578.1| 10 VCPRCGTEVPN 20
                                      47777777665 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0038
                    OrfB_Zn_ribbon 46 tfkCpnCgfeadr 58
                                       +kCpnCg+++ +
  gi|385805180|ref|YP_005841578.1| 45 SYKCPNCGYSWKA 57
                                      5677777777665 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1      0.01       5.5       2      11 ..       8      17 ..       7      43 .. 0.81
   2 ?    5.3   0.0     0.059        32       4      10 ..      47      53 ..      45      81 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.01
                           zf-ISL3  2 phrCPnCgsk 11
                                      p +CP+Cg  
  gi|385805180|ref|YP_005841578.1|  8 PNVCPRCGTE 17
                                      789*****87 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.059
                           zf-ISL3  4 rCPnCgs 10
                                      +CPnCg 
  gi|385805180|ref|YP_005841578.1| 47 KCPNCGY 53
                                      699*996 PP

>> zf-3CxxC_2  Zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1       4.5   2.4e+03      30      37 ..      11      18 ..       4      27 .. 0.73
   2 ?   13.3   0.1   0.00019       0.1       5      22 ..      43      60 ..      40      64 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 4.5
                        zf-3CxxC_2 30 CkkCkekv 37
                                      C +C+++v
  gi|385805180|ref|YP_005841578.1| 11 CPRCGTEV 18
                                      77777776 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00019
                        zf-3CxxC_2  5 fGefkCekCgkeWsSana 22
                                       G++kC++Cg +W  a +
  gi|385805180|ref|YP_005841578.1| 43 MGSYKCPNCGYSWKAAIS 60
                                      69***********99865 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   0.4    0.0035       1.9       4      10 ..      10      16 ..       8      24 .. 0.65
   2 ?    8.1   1.3    0.0033       1.8       4      23 ..      47      52 ..      44      54 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0035
                       zf-ribbon_3  4 rCPnCGa 10
                                       CP+CG+
  gi|385805180|ref|YP_005841578.1| 10 VCPRCGT 16
                                      3555555 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0033
                       zf-ribbon_3  4 rCPnCGaplssddnvCpyCG 23
                                      +              Cp+CG
  gi|385805180|ref|YP_005841578.1| 47 K--------------CPNCG 52
                                      4..............55555 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.2    0.0081       4.4      21      28 ..      10      17 ..       8      25 .. 0.69
   2 ?    7.2   1.1    0.0065       3.5       1       7 [.      46      52 ..      46      54 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0081
                                      EESSSSBE CS
                      TF_Zn_Ribbon 21 vCtdCGlV 28
                                      vC++CG+ 
  gi|385805180|ref|YP_005841578.1| 10 VCPRCGTE 17
                                      56666654 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0065
                                      EEETTTT CS
                      TF_Zn_Ribbon  1 ykCPnCg 7 
                                      ykCPnCg
  gi|385805180|ref|YP_005841578.1| 46 YKCPNCG 52
                                      89****9 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.046        25       4      30 ..       9      17 ..       4      19 .. 0.59
   2 ?    6.7   0.1     0.011       6.2      22      30 ..      46      54 ..      40      55 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.046
                     A2L_zn_ribbon  4 kvCsvCggngilnseqgylvCieCgas 30
                                      +                  vC+ Cg++
  gi|385805180|ref|YP_005841578.1|  9 N------------------VCPRCGTE 17
                                      4..................56666553 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.011
                     A2L_zn_ribbon 22 lvCieCgas 30
                                      + C++Cg+s
  gi|385805180|ref|YP_005841578.1| 46 YKCPNCGYS 54
                                      77*****97 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1     0.021        11      18      28 ..       6      15 ..       2      17 .. 0.74
   2 ?    5.0   0.0     0.056        30      21      28 ..      37      52 ..      26      54 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.021
                     zinc_ribbon_9 18 edsdvlCPhCg 28
                                      + ++v CP+Cg
  gi|385805180|ref|YP_005841578.1|  6 KKPNV-CPRCG 15
                                      56678.****8 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.056
                     zinc_ribbon_9 21 d.........vlCPhCg 28
                                                + CP+Cg
  gi|385805180|ref|YP_005841578.1| 37 RititvmgsyK-CPNCG 52
                                      34455444336.****8 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.3     0.064        35      16      21 ..      11      16 ..       8      18 .. 0.88
   2 ?   10.3   0.6   0.00093      0.51      12      20 ..      44      52 ..      42      54 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.064
                                      -TTT-- CS
                            zf-HIT 16 CpkCnt 21
                                      Cp+C+t
  gi|385805180|ref|YP_005841578.1| 11 CPRCGT 16
                                      ****98 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00093
                                      -SEE-TTT- CS
                            zf-HIT 12 akYkCpkCn 20
                                      + YkCp+C+
  gi|385805180|ref|YP_005841578.1| 44 GSYKCPNCG 52
                                      68******8 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00046      0.25      66      95 ..       4      54 ..       1      80 [. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00046
                                      EE--EEEETTTS-EEECHHH..HH...................S-TTTSSS CS
                              HypA 66 evpvkvrCreCgkefeleek..al...................rCpkCgsa 95
                                      +++    C +Cg+e+   +k  ++                   +Cp+Cg +
  gi|385805180|ref|YP_005841578.1|  4 KEKKPNVCPRCGTEVPNPTKtwNFvsplpddkgrititvmgsyKCPNCGYS 54
                                      555667899***99996654234488999999**********9*****965 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 ?    9.5   0.2    0.0016      0.88       3       9 ..      10      16 ..       2      20 .. 0.75
   2 ?    3.2   0.3      0.15        84       3       8 ..      47      52 ..      46      52 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0016
                                      B-TTT-- CS
                      zf-FPG_IleRS  3 pCpRCwr 9 
                                      +CpRC++
  gi|385805180|ref|YP_005841578.1| 10 VCPRCGT 16
                                      5777777 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.15
                                      B-TTT- CS
                      zf-FPG_IleRS  3 pCpRCw 8 
                                      +Cp C+
  gi|385805180|ref|YP_005841578.1| 47 KCPNCG 52
                                      899997 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.056        31      21      28 ..      10      17 ..       9      19 .. 0.81
   2 ?    6.7   0.1     0.013       7.1      22      29 ..      48      55 ..      44      56 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.056
                    PhnA_Zn_Ribbon 21 vCpeCahE 28
                                      vCp C+ E
  gi|385805180|ref|YP_005841578.1| 10 VCPRCGTE 17
                                      79999877 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.013
                    PhnA_Zn_Ribbon 22 CpeCahEw 29
                                      Cp+C++ w
  gi|385805180|ref|YP_005841578.1| 48 CPNCGYSW 55
                                      89998887 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.2    0.0043       2.3       6      12 ..      11      17 ..       9      18 .. 0.71
   2 ?    4.0   0.2      0.07        38      24      29 ..      48      53 ..      46      54 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0043
                     zf-NADH-PPase  6 CgrCGap 12
                                      C+rCG++
  gi|385805180|ref|YP_005841578.1| 11 CPRCGTE 17
                                      8888875 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.07
                     zf-NADH-PPase 24 CpaCgl 29
                                      Cp+Cg+
  gi|385805180|ref|YP_005841578.1| 48 CPNCGY 53
                                      999986 PP

>> Mu-like_Com  Mu-like prophage protein Com
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.5    0.0071       3.9      27      32 ..      11      16 ..       9      20 .. 0.93
   2 ?    4.0   0.1     0.061        33      26      31 ..      47      52 ..      41      55 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0071
                       Mu-like_Com 27 CPRCGt 32
                                      CPRCGt
  gi|385805180|ref|YP_005841578.1| 11 CPRCGT 16
                                      *****9 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.061
                       Mu-like_Com 26 KCPRCG 31
                                      KCP CG
  gi|385805180|ref|YP_005841578.1| 47 KCPNCG 52
                                      9****9 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.2      0.22   1.2e+02       3       8 ..      11      16 ..       9      18 .. 0.79
   2 ?   10.4   0.3   0.00084      0.46      29      39 .]      46      56 ..      43      56 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.22
                           TFIIS_C  3 CpkCgs 8 
                                      Cp+Cg 
  gi|385805180|ref|YP_005841578.1| 11 CPRCGT 16
                                      999986 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00084
                           TFIIS_C 29 ykCtkCghrWr 39
                                      ykC +Cg+ W+
  gi|385805180|ref|YP_005841578.1| 46 YKCPNCGYSWK 56
                                      9*********7 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.077        42      17      27 ..       9      19 ..       2      27 .. 0.70
   2 ?    8.1   0.0    0.0052       2.8      16      25 ..      45      54 ..      32      61 .. 0.88
   3 ?   -2.4   0.1       9.8   5.3e+03      47      54 ..      96     104 ..      86     104 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.077
                          zf-Mss51 17 feCpdCGipty 27
                                        Cp+CG  + 
  gi|385805180|ref|YP_005841578.1|  9 NVCPRCGTEVP 19
                                      57*****8665 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0052
                          zf-Mss51 16 dfeCpdCGip 25
                                      +++Cp+CG++
  gi|385805180|ref|YP_005841578.1| 45 SYKCPNCGYS 54
                                      69******97 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 9.8
                          zf-Mss51  47 Lrq.vnede 54 
                                       L   +ned+
  gi|385805180|ref|YP_005841578.1|  96 LEDiINEDD 104
                                       555589987 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.3      0.11        59      19      23 ..      11      15 ..      10      16 .. 0.90
   2 ?    9.2   1.1    0.0022       1.2      17      23 ..      46      52 ..      44      53 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.11
                           DUF1610 19 CPNCG 23
                                      CP CG
  gi|385805180|ref|YP_005841578.1| 11 CPRCG 15
                                      ****9 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0022
                           DUF1610 17 FpCPNCG 23
                                      + CPNCG
  gi|385805180|ref|YP_005841578.1| 46 YKCPNCG 52
                                      67****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 ?    5.7   0.3     0.026        14       6      15 ..      10      19 ..      10      23 .. 0.83
   2 ?    6.6   0.9     0.013       7.3       5      11 ..      46      52 ..      45      57 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.026
                    Zn_ribbon_SprT  6 rCtgCgreyt 15
                                      +C++Cg+e++
  gi|385805180|ref|YP_005841578.1| 10 VCPRCGTEVP 19
                                      6*****9865 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.013
                    Zn_ribbon_SprT  5 YrCtgCg 11
                                      Y+C++Cg
  gi|385805180|ref|YP_005841578.1| 46 YKCPNCG 52
                                      9*****9 PP

>> zf_C2H2_10  C2H2 type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1     0.033        18       5      13 ..      11      19 ..       9      20 .. 0.88
   2 ?    4.4   0.5     0.051        27       3      10 ..      46      53 ..      45      55 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.033
                        zf_C2H2_10  5 CPKCqeklP 13
                                      CP+C+  +P
  gi|385805180|ref|YP_005841578.1| 11 CPRCGTEVP 19
                                      *****9988 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.051
                        zf_C2H2_10  3 fsCPKCqe 10
                                      + CP C++
  gi|385805180|ref|YP_005841578.1| 46 YKCPNCGY 53
                                      67*****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 ?    3.1   0.2      0.29   1.6e+02       2      13 ..      10      21 ..      10      24 .. 0.81
   2 ?    7.1   0.4     0.015       8.4       1       9 [.      46      54 ..      46      57 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.29
                                      EETTTTEEESSH CS
                           zf-C2H2  2 kCpdCgksFkrk 13
                                      +Cp Cg   +++
  gi|385805180|ref|YP_005841578.1| 10 VCPRCGTEVPNP 21
                                      6*****887766 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.015
                                      EEETTTTEE CS
                           zf-C2H2  1 ykCpdCgks 9 
                                      ykCp Cg+s
  gi|385805180|ref|YP_005841578.1| 46 YKCPNCGYS 54
                                      9******86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); 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: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 656.57
//
Query:       gi|385805181|ref|YP_005841579.1|  [L=108]
Description: hypothetical protein FFONT_0135 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       287  (0.0160076); 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:                         0  (0); expected 0.2 (1e-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: 704.65
//
Query:       gi|385805182|ref|YP_005841580.1|  [L=364]
Description: translation initiation factor 2B subunit I family (IF-2BI) [Fervidicoccus fontis Kam940]
Scores for complete 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-85  286.5   0.9    2.2e-85  286.3   0.9    1.0  1  IF-2B     Initiation factor 2 subunit family
  ------ inclusion threshold ------
      0.084   12.2   0.0       0.12   11.7   0.0    1.2  1  DUF3810   Protein of unknown function (DUF3810)
      0.097   12.6   0.3       0.16   11.8   0.3    1.3  1  DUF4435   Protein of unknown function (DUF4435)


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 !  286.3   0.9   3.6e-89   2.2e-85       1     281 [.      64     352 ..      64     353 .. 0.95

  Alignments for each domain:
  == domain 1  score: 286.3 bits;  conditional E-value: 3.6e-89
                                       SS-SHHHHHHHHHHHHHHHHHHCCCSTHHHHHHHHHHHHHHHHTSSTS-HHHHHHHHHHHHHHHCCTTTSSHHHHHH CS
                             IF-2B   1 kvrGspaiaiaalevllevikdaktskvaeLkeelrkaidlLkkarPtavslgnairrllkeiselksssdvkeakk 77 
                                       ++rG+pai+++++ ++++v+ ++  ++ +e++++++ka++ L  +rPta +l++a++ ++k     + + + +e+k+
  gi|385805182|ref|YP_005841580.1|  64 EIRGAPAIGVTTALAVAMVAYNSP-NNKDEMMKNIEKAVEILSHTRPTAYNLFWALNIMKK-TFYESIDLSPQEIKE 138
                                       58***************9998887.99**********************************.344466677789*** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHTTC-TTEEEEEES--SH........HHHHHHHHHHTTEEEEEEEEEXTTTTH CS
                             IF-2B  78 sliekikelikeieeadekigdiaaelikdgdtilTicnskt........vlevlraaakekkkfkVivvEsrPrlq 146
                                       +l++k+ +++ e+ +++ k+g+i+++li+dgdtilT+cn+++        +l+v+++a+k++kk+kVi++E+rP lq
  gi|385805182|ref|YP_005841580.1| 139 KLLSKALKIQIEDIKNNLKMGEIGEKLIQDGDTILTHCNTGSlataghgtALGVIKTAWKNGKKIKVIATETRPLLQ 215
                                       ***************************************************************************** PP

                                       H.HTHHHHHHHTTXEEEEEEGGGHHHHHHC.TESEEEEEXSEEETTSEEEEETTHHHHHHHHHHTTXEEEEEXXGGG CS
                             IF-2B 147 G.rltakeLvqagipvtlitdsavayvmse.evdkvivGAdrilenGaiankiGTsslAvlAkefnipvlvvaeslk 221
                                       G rlta+eL+++gip++litd++v++vm + +v kv+vGAdril+ G ++nkiGT+ +AvlA  ++ip+++va++++
  gi|385805182|ref|YP_005841580.1| 216 GaRLTAWELKKEGIPFKLITDNMVGIVMMKeMVHKVFVGADRILRTGHVINKIGTYGIAVLASYHKIPFYAVAPTST 292
                                       ***************************9999********************************************** PP

                                       BESTSSSGGGSSXXBEXTHHHHEE.TTEESSTTTEEEEEBSEEEEEGGGXSEEEETTEEEX CS
                             IF-2B 222 fservqldedifieerdpeellni.tgeriaeeelkvvnpafDvtPpelItliITevGvlp 281
                                       f+  +   ed++ie rd+ e++ + ++ ria+e +  +n afD+tPpel+++i+Te+G+++
  gi|385805182|ref|YP_005841580.1| 293 FDLTT-SPEDVIIENRDESEVTTVlNKLRIAPEGTSAYNFAFDMTPPELVSGIVTEKGIVE 352
                                       **995.5666888******9986527789*****************************986 PP

>> DUF3810  Protein of unknown function (DUF3810)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0     2e-05      0.12      36     117 ..      74     155 ..      64     203 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2e-05
                           DUF3810  36 vilylvlaiklkkrkkkkkrllkvllrvllvllvv.yflftllwglnYyreplserlglkkeeyseeelaelaeklv 111
                                       ++++ v ++   +  ++k +++k + +++++l+    + + l+w+ln  +++++e+++l+++e +e+ l + ++  +
  gi|385805182|ref|YP_005841580.1|  74 TTALAVAMV-AYNSPNNKDEMMKNIEKAVEILSHTrPTAYNLFWALNIMKKTFYESIDLSPQEIKEKLLSKALKIQI 149
                                       333344444.3345566677788888888888866157889****************************99999999 PP

                           DUF3810 112 eklnel 117
                                       e++++ 
  gi|385805182|ref|YP_005841580.1| 150 EDIKNN 155
                                       888765 PP

>> DUF4435  Protein of unknown function (DUF4435)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.3   2.7e-05      0.16     106     181 ..      89     164 ..      74     177 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.7e-05
                           DUF4435 106 ndrd.yktifdlfeqfleelseiiiplflwnvlfyrkklekdikls.lslqevdlssiekitleeikvenkieelke 180
                                       n+++ +k i +  +++l++++ ++++lf      ++k  +++i+ls  +++e+ ls+ +ki+ e ik + k+ e+ e
  gi|385805182|ref|YP_005841580.1|  89 NKDEmMKNIEK-AVEILSHTRPTAYNLFWAL-NIMKKTFYESIDLSpQEIKEKLLSKALKIQIEDIKNNLKMGEIGE 163
                                       33465677777.999*************844.444777899999998899***********9999998877777666 PP

                           DUF4435 181 e 181
                                       +
  gi|385805182|ref|YP_005841580.1| 164 K 164
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); 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: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 2341.63
//
Query:       gi|385805183|ref|YP_005841581.1|  [L=434]
Description: cationic amino acid transporter-like protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-27   95.9  57.7      3e-27   95.5  57.7    1.0  1  AA_permease_2  Amino acid permease
    1.2e-20   73.6  57.4      3e-20   72.3  57.4    1.7  1  AA_permease    Amino acid permease
  ------ inclusion threshold ------
      0.028   13.4  32.2      0.013   14.6  29.9    1.6  1  Trp_Tyr_perm   Tryptophan/tyrosine permease family


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 !   95.5  57.7     5e-31     3e-27       1     420 [.       5     425 ..       5     431 .. 0.78

  Alignments for each domain:
  == domain 1  score: 95.5 bits;  conditional E-value: 5e-31
                     AA_permease_2   1 lsllsafalvigsvigsgifvkn.laas..ggpalilwvwiavligslavllvyaElssalprsgGiyvytkaaf.. 72 
                                       ++ll a++l ig ++g+gifv + +++    g  ++ w++++++  ++av+lvy  +ssa++ +gG  vy  ++f  
  gi|385805183|ref|YP_005841581.1|   5 ITLLEAIMLGIGGMYGVGIFVFPgSTGRlnDGLDFLAWLITGIM--MIAVGLVYSDMSSAFEVDGGPAVYPFEVFkk 79 
                                       67999***************998855552144444444444444..48*********999**********9777744 PP

                     AA_permease_2  73 ...gkkvaflsawfnwfayvpvlasilsvaasyllnalgp.dlqgntwltyliaiaililvalinirgikesakiqn 145
                                          +k++ f s+  +++++ +++ +i+++   y+l+ + p +l+     +++   +++ + +l+ i+g+k s+k++ 
  gi|385805183|ref|YP_005841581.1|  80 ralSKFLSFYSGAGFFVGWTIAI-TICAITSPYYLYYILPiSLN----YSIVTSLILIFFATLLVIFGVKLSGKVNQ 151
                                       44477777888888899999865.99999999999998773442....2444455666677889************* PP

                     AA_permease_2 146 ilgilkillpliiliilglitvdgggfsslstetdtffpngwpgvllgllivlwsfdGfesaanvsee..vkkkdvp 220
                                       il+ + + ++l++ i++  + + + + s       +  +   + +l++++i++ +++++ s+ +v +   ++kk+vp
  gi|385805183|ref|YP_005841581.1| 152 ILTFILLAITLAFTIAVFSYSGLPIHLS-------NNYKFDISKFLASIGIIIGAYGAWASIPSVYSSveNPKKNVP 221
                                       *999999999999997777776553332.......3455566669******************99999445569*** PP

                     AA_permease_2 221 kaifigllivlvlyllvniaflgvvpddeianlsn.lgsv...aalffeav.ggkvvaiivvilialsllgaintav 292
                                       +   i++l v+ +y+l+ +++   +p +e+ n+ +   s+   a++ +e++ g k++++++++ + l+++  ++  +
  gi|385805183|ref|YP_005841581.1| 222 LSVAISILSVAAIYVLMVMSLHSLIPYNEFLNNPEvAYSPfsyASIQLEKLtGTKIFTYLFSLSALLAIFTTMIVGF 298
                                       *****************************95544413333555666665551567********************** PP

                     AA_permease_2 293 igssrvlealardgvlPrffakvn.kfgspiraiiltaivslillllfllassaaynfllsvsslgliisyllliig 368
                                       ++ sr ++a+++ g++P  + +++ k+g++i +++++ + s++++ lf   +   y f++   ++g +i+y++++i+
  gi|385805183|ref|YP_005841581.1| 299 LSLSRAVYAMSEKGIIPQKIYDIDsKNGRYILSTVIISLTSSLFS-LF---PQYFYKFMVIGLVVGTNIPYAINLIS 371
                                       *****************88888888****9999999988886654.44...5669********************** PP

                     AA_permease_2 369 alilrkkrphl...krpgkilvaiigalfllfllvalffppkgpatqssliytii 420
                                       +++ +  +p     +r+g i ++i+++ ++++  +al +  +++++   +i+ ++
  gi|385805183|ref|YP_005841581.1| 372 YIYFKHSSPSGflsRRIG-IFLGIMSFSIIIVSSYALSLQEVKASAIALSILFVA 425
                                       *******99553444454.667777777777777777766555555555554444 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.3  57.4   4.9e-24     3e-20       2     370 ..      10     386 ..       9     433 .. 0.72

  Alignments for each domain:
  == domain 1  score: 72.3 bits;  conditional E-value: 4.9e-24
                       AA_permease   2 vlvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksgg.....fytyasrflgpe 73 
                                       +++  +gg+ G+g+fv  g++ +   +   +la+l++g+++++v+l  + +++++ + gg     f ++ +r l++ 
  gi|385805183|ref|YP_005841581.1|  10 AIMLGIGGMYGVGIFVFPGSTGRLNDG-LDFLAWLITGIMMIAVGLVYSDMSSAFEVDGGpavypFEVFKKRALSKF 85 
                                       689****************99998888.558*************************66663444477889******* PP

                       AA_permease  74 lGfviGlnylfswitvlaleltaasiliqfwelvtdlpkawvtgavflvvlliinlvgvkvygeaefilalikiiai 150
                                       l+f+ G+ +++ w +++++  +++ +++ ++  ++ l++ +vt+++++++ +++ ++gvk++g++  il++i++ + 
  gi|385805183|ref|YP_005841581.1|  86 LSFYSGAGFFVGWTIAITICAITSPYYLYYILPIS-LNYSIVTSLILIFFATLLVIFGVKLSGKVNQILTFILLAIT 161
                                       *******************************5555.555*************************9999888887777 PP

                       AA_permease 151 iafiivgiillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkd 227
                                       +af i  ++++   ++  +                l++++    ++ ++ f++ + i++ a+    +++ + + v++
  gi|385805183|ref|YP_005841581.1| 162 LAFTIAVFSYS---GLPIH----------------LSNNY----KFDISKFLASIGIIIGAYGAWASIPSVYSSVEN 215
                                       77777664333...33333................22222....2225556666666666666666666666789** PP

                       AA_permease 228 PeksiPkailqvviritifYvlsllligllvprndlgllndsasaaspfvifi....kesgvsvlaplinaviltaa 300
                                       P+k++P ++   ++ ++ +Yvl+++++ +l+p+n   +ln   +a+spf ++     k +g +++  l+ +  l+a+
  gi|385805183|ref|YP_005841581.1| 216 PKKNVPLSVAISILSVAAIYVLMVMSLHSLIPYNE--FLNNPEVAYSPFSYASiqleKLTGTKIFTYLFSLSALLAI 290
                                       ***********************************..7776666799*98763222267778888888888888888 PP

                       AA_permease 301 lssansslysasRvlyslakdglaP.kvlkkvskrgvPlraillsmiisllal........................ 352
                                       + +++ +  s sR++y++++ g++P k+ +  sk+g+ + + ++ +++s l+                         
  gi|385805183|ref|YP_005841581.1| 291 FTTMIVGFLSLSRAVYAMSEKGIIPqKIYDIDSKNGRYILSTVIISLTSSLFSlfpqyfykfmviglvvgtnipyai 367
                                       8888888899***************************9988666666655555244444444444444444444444 PP

                       AA_permease 353 .llaslnlaapivfnflla 370
                                        l+++++++  + + fl+ 
  gi|385805183|ref|YP_005841581.1| 368 nLISYIYFKHSSPSGFLSR 386
                                       4444444444444444433 PP

>> Trp_Tyr_perm  Tryptophan/tyrosine permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6  29.9   2.2e-06     0.013       4     307 ..       6     308 ..       3     355 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.2e-06
                      Trp_Tyr_perm   4 sllggvlliagtviGaGmlalPvatagagfipsllllilswvlmlasgllllEvllaake.....easfttlakkll 75 
                                        ll +++l +g + G G++  P +t +       l+ +++ ++m+a gl++ ++++a +         f+ + k+ l
  gi|385805183|ref|YP_005841581.1|   6 TLLEAIMLGIGGMYGVGIFVFPGSTGRLNDGLDFLAWLITGIMMIAVGLVYSDMSSAFEVdggpaVYPFEVFKKRAL 82 
                                       678999***************************************************99977765566888899999 PP

                      Trp_Tyr_perm  76 GkkgniivalvllfllyiLlvAyisggGs..ilselleeasgialsarlavliftlvlga.lvvlstkavdrinrvl 149
                                        k   +  ++ + f+ + + +  i+++ s   l+ +l+ +     +  +++ ++ +++++ lv+++ k+  ++n++l
  gi|385805183|ref|YP_005841581.1|  83 SKFLSFYSGAGF-FVGWTIAI-TICAITSpyYLYYILPISL----NYSIVTSLILIFFATlLVIFGVKLSGKVNQIL 153
                                       888887777654.44444333.3444333114455555444....44444444444444405566667888999999 PP

                      Trp_Tyr_perm 150 lflklvafvlllalllskvksdvLlsaksdtskvslvlsalPvlllsfGFhgivpslvkyldknvkkvkkailiGtl 226
                                        f++l a++l++++ +++ ++  +  +++   ++s  l ++ +++ ++G   ++ps+++ +++ +k+v  ++ i  l
  gi|385805183|ref|YP_005841581.1| 154 TFILL-AITLAFTIAVFSYSGLPIHLSNNYKFDISKFLASIGIIIGAYGAWASIPSVYSSVENPKKNVPLSVAISIL 229
                                       88765.444444444444444433333567889999**************************************999 PP

                      Trp_Tyr_perm 227 iaLvlyllWelivlGnlpreelariiakggnldtlveallelleskslelavelFsflAlatSflGvalglfdylad 303
                                          ++y+l  ++ +  +p +e+++  + +   + +  a+ +l + +  +++  lFs +Al++ f  + +g++     
  gi|385805183|ref|YP_005841581.1| 230 SVAAIYVLMVMSLHSLIPYNEFLNNPEVA--YSPFSYASIQLEKLTGTKIFTYLFSLSALLAIFTTMIVGFLSLSRA 304
                                       9999******************9866655..8889999999999999999999999999999999999998876666 PP

                      Trp_Tyr_perm 304 lfkl 307
                                       ++ +
  gi|385805183|ref|YP_005841581.1| 305 VYAM 308
                                       6655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       998  (0.055664); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); 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):               3  [number of targets reported over threshold]
# CPU time: 0.75u 0.34s 00:00:01.09 Elapsed: 00:00:00.55
# Mc/sec: 2360.79
//
Query:       gi|385805184|ref|YP_005841582.1|  [L=506]
Description: nonphosphorylating glyceraldehyde-3-phosphate dehydrogenase [Fervidicoccus fontis Kam940]
Scores for complete 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-123  412.9   0.0   1.5e-123  412.7   0.0    1.0  1  Aldedh    Aldehyde dehydrogenase family


Domain annotation for each model (and alignments):
>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  412.7   0.0  8.4e-128  1.5e-123       9     462 .]      37     492 ..      30     492 .. 0.95

  Alignments for each domain:
  == domain 1  score: 412.7 bits;  conditional E-value: 8.4e-128
                                       EEEEETTTCEEEEEEE-B-HHHHHHHHHHHHHHHH.HHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH---HH CS
                            Aldedh   9 ievinPatgeviakvpaataedvdaavaaAkeafk.awaklpaeeRaeiLrkaadlleerkeelaeletletGkpla 84 
                                        + ++P++ ++i+++p+ t +d++  +++  e  k + +++p ++R e+L+k+a+l+ee++e+++e +++ +Gk+  
  gi|385805184|ref|YP_005841582.1|  37 EQIFSPIDTNTIGTIPKLTYDDIEPYIKELYESGKwKIRNTPGYKRIEYLEKMAKLIEEHREDFIESLMIGAGKTRD 113
                                       5789**************************9977769**************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHSEEEEEEC.....TTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT-E CS
                            Aldedh  85 earaeveeaidvlryyaelaeklegevlpss.....egklalvrrePlGvvgaItPWNfPlllaawklapalaaGNt 156
                                       +a++ev+ +i+ l+ ++  ++k++ge +p +      ++++lvr+eP+G+v+aI+P+N+Pl+ ++ k+   ++aGN+
  gi|385805184|ref|YP_005841582.1| 114 QAAGEVNASINRLKSAMLDLRKVYGEYIPGDwdqttLESESLVRKEPYGIVLAISPFNYPLFDTVAKFTYSVVAGNA 190
                                       ****************************99766776778899*********************************** PP

                                       EEEEE-TTSHHHHHHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTTSEEE CS
                            Aldedh 157 vvlKPaeetplsalllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknlkrvt 233
                                       v++KP +++p+ +l++a+++e  g+Pk+ l v+t +gse+ + +v++p++ ++s+tGs+e+g+k++ka +  +kr +
  gi|385805184|ref|YP_005841582.1| 191 VIIKPPTQVPVPSLMFARIAEVSGFPKESLMVLTVPGSEMEK-VVSDPRIGVISLTGSSETGKKVLKAGG--IKRYI 264
                                       *************************************99866.6788********************988..9**** PP

                                       EEE---EEEEE-TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT-SB-- CS
                            Aldedh 234 lElGGknplivledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpldedtdvGP 310
                                       +ElGG +p+ivl+daD+d+a + i +g++++aGQ+C a++ ++ ++s+ de+ +k+ve ++k+kvgdp+d++t++GP
  gi|385805184|ref|YP_005841582.1| 265 MELGGGDPAIVLDDADIDEASRLISTGIYSYAGQRCDAIKMIIAHHSVKDELKKKIVENLAKVKVGDPRDPNTTMGP 341
                                       ***************************************************************************** PP

                                       -SSHHHHHHHHHHHHHHHHTTSEEEE-TTE.SB-SSSTTEE--EEEES-TTTSH.....HHHS---SSEEEEEEESS CS
                            Aldedh 311 liseaqlekvekyveeakeegaklllGgereeaglekgyfvePtvlanvtpdmr.....iaqeEiFGPVlsvikfkd 382
                                       lis++++e+++k +++a+e+g k+l+Gg     ++ +g++vePt+++ +++ ++     +++eE+F+PV+ ++ + +
  gi|385805184|ref|YP_005841582.1| 342 LISKKAVEEMMKGIQDAVEKGGKILYGG-----RRLNGNYVEPTLIEITDK-SKlnsllLYKEEVFAPVAIIFNYAN 412
                                       ****************************.....458**********96554.331222379**************** PP

                                       HHHHHHHHHSSSEESEEEEE-SBHHHHHHHHHHS-SSEEEESSSST--TTTSEB--CGGGEES-BSHHHHHHHTEEE CS
                            Aldedh 383 eeeaieiaNdteyGLaagvftkdleraervaerleaGnvyiNdsttgaaealpfgGvkqSglGreggkegleeytev 459
                                       e+ea+ +aN+ +yGL a++f+kd++r++++++ le+G +yiNd  ++ +   p+gG k+Sg+Gre+ ++++ee++ +
  gi|385805184|ref|YP_005841582.1| 413 EDEAVMLANNRKYGLDASIFAKDINRIRKIIRYLEYGAIYINDIPRHGIGYYPYGGRKESGIGRESIAYSIEEVMAI 489
                                       ****************************************************************************9 PP

                                       EEE CS
                            Aldedh 460 ktv 462
                                       k++
  gi|385805184|ref|YP_005841582.1| 490 KAI 492
                                       986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (506 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); 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: 0.71u 0.30s 00:00:01.01 Elapsed: 00:00:00.51
# Mc/sec: 2956.89
//
Query:       gi|385805185|ref|YP_005841583.1|  [L=311]
Description: N-acetyltransferase GCN5 [Fervidicoccus fontis Kam940]
Scores for 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-20   71.0   0.5    2.8e-17   63.0   0.2    2.2  2  Acetyltransf_1   Acetyltransferase (GNAT) family
    4.5e-16   58.9   0.1    3.2e-13   49.7   0.1    2.3  2  Acetyltransf_10  Acetyltransferase (GNAT) domain
    4.8e-13   49.3   2.1    5.4e-13   49.2   0.9    1.7  2  Acetyltransf_7   Acetyltransferase (GNAT) domain
    5.8e-07   29.8   1.0    5.8e-07   29.8   1.0    1.7  2  Acetyltransf_4   Acetyltransferase (GNAT) domain
    8.5e-06   26.5   0.0    1.4e-05   25.8   0.0    1.4  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
    0.00018   21.2   0.0    0.00029   20.6   0.0    1.2  1  DUF4821          Domain of unknown function (DUF4821)
     0.0045   17.1   0.0      0.034   14.2   0.0    2.2  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
     0.0067   16.4   0.1      0.012   15.6   0.1    1.4  1  FR47             FR47-like protein
  ------ inclusion threshold ------
      0.018   14.7   0.0      0.043   13.5   0.0    1.6  2  PanZ             Acetyltransferase (GNAT) domain, PanZ
      0.035   14.3   0.0      0.057   13.6   0.0    1.3  1  Acetyltransf_6   Acetyltransferase (GNAT) domain
      0.045   13.9   0.0      0.092   12.9   0.0    1.5  1  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 !   63.0   0.2   1.7e-20   2.8e-17      15     117 .]      42     143 ..      27     143 .. 0.79
   2 !    6.3   0.0    0.0069        11      26      67 ..     208     243 ..     180     248 .. 0.73

  Alignments for each domain:
  == domain 1  score: 63.0 bits;  conditional E-value: 1.7e-20
                                       HHHHHHHHHHHHHHHSTTC...EEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHH CS
                    Acetyltransf_1  15 pnedaseeefeesfsleae...gllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeer 88 
                                       ++ d++   + +s ++  +   +++va++  +l+Gfi ++k+      +ayi+ +aV++ yrg G+G++Ll+ +e+ 
  gi|385805185|ref|YP_005841583.1|  42 EYLDEESKNWLKSIIKKKSrraRIYVALKRKKLVGFIIFYKKRK----EAYIDAFAVDSRYRGLGIGRKLLNCIEQT 114
                                       33444444433442222222359999***********9999999....8***************************9 PP

                                       HHHTTESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  89 areegikkivlaveedndaairlYeklGF 117
                                       ++ eg+k+i+l v + n+ a +lY k G+
  gi|385805185|ref|YP_005841583.1| 115 LELEGVKRIYLSVKNGNNNALGLYLKNGY 143
                                       9999********************99997 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0069
                                       HHHHSTTC.EEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEE CS
                    Acetyltransf_1  26 esfsleae.gllvaeedgeliGfisllkipdekggvayiesla 67 
                                       +  s  +e +++ ++ + +liG ++++++ +    +++ie+la
  gi|385805185|ref|YP_005841583.1| 208 I--S-KEEaTYITIYSGKRLIGVARAHIDKN----KVVIERLA 243
                                       2..3.44436666999999*********988....88888877 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7   0.1   1.9e-16   3.2e-13      27     110 ..      57     147 ..      37     156 .. 0.82
   2 !    6.7   0.0    0.0039       6.3      25      58 ..     207     243 ..     198     247 .. 0.80

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 1.9e-16
                   Acetyltransf_10  27 e..egealllvaeeggkivGviel.rdgs..hisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.y 96 
                                       +  + +a ++va + +k+vG+i   ++++  +i  ++Vd+ yrg Gig++Ll+ +e+ +e +g k   l+v+  + +
  gi|385805185|ref|YP_005841583.1|  57 KkkSRRARIYVALKRKKLVGFIIFyKKRKeaYIDAFAVDSRYRGLGIGRKLLNCIEQTLELEGVKRiYLSVKNGNnN 133
                                       2235667789999*********775555578****************************************99999* PP

                   Acetyltransf_10  97 avpfYeklGFkavg 110
                                       a ++Y k G+k+++
  gi|385805185|ref|YP_005841583.1| 134 ALGLYLKNGYKVTN 147
                                       ***********985 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0039
                   Acetyltransf_10  25 rieegealllvaeeggkivGviel.rdgs..hisllf 58 
                                       +i+++ea+++  + g++++Gv++   d++   i++l+
  gi|385805185|ref|YP_005841583.1| 207 KISKEEATYITIYSGKRLIGVARAhIDKNkvVIERLA 243
                                       35699*****************877666656777776 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   0.9   3.3e-16   5.4e-13       2      75 ..      62     144 ..      61     145 .. 0.79
   2 ?   -3.0   0.0       6.5   1.1e+04      10      24 ..     220     234 ..     212     248 .. 0.56

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 3.3e-16
                                       TEEEEEEEETTEEEEEEEEEEES..TCTEEEEE-GGGTTSSHHHHHHHHTT.....SEEEEEEEEE.....THHHHH CS
                    Acetyltransf_7   2 kgevfVaeddgkivGfialslld..aeitrlaVdpeyrgkGiGraLleaae.....kgiileqlel.....naekai 66 
                                       +++++Va + +k vGfi+++     a+i  +aVd  yrg GiGr+Ll+++e     +g++ +  +l     n ++a+
  gi|385805185|ref|YP_005841583.1|  62 RARIYVALKRKKLVGFIIFYKKRkeAYIDAFAVDSRYRGLGIGRKLLNCIEqtlelEGVKRI--YLsvkngN-NNAL 135
                                       6799**************999999999999******************73334556665423..44333332.289* PP

                                       HHHHHTTEE CS
                    Acetyltransf_7  67 kfYeklGFe 75 
                                       ++Y k+G++
  gi|385805185|ref|YP_005841583.1| 136 GLYLKNGYK 144
                                       ********8 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6.5
                                       ETTEEEEEEEEEEES CS
                    Acetyltransf_7  10 ddgkivGfialslld 24 
                                        +++ +G +++++++
  gi|385805185|ref|YP_005841583.1| 220 SGKRLIGVARAHIDK 234
                                       445556655555443 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   1.0   3.6e-10   5.8e-07       1     139 [.      22     148 ..      22     151 .. 0.87
   2 ?   -1.4   0.0       1.4   2.3e+03      83      83 ..     247     247 ..     201     305 .. 0.45

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 3.6e-10
                    Acetyltransf_4   1 iraateeDakeilaiyaeyvvntaitfeyevssveefekflealdsekeyvflvaesdrivGyaylgqfkkrakdwk 77 
                                       +r a+ +D ++i +iy+e+ +      + +++s+ +++ ++++  s   +++ +++  ++vG        k  k+++
  gi|385805185|ref|YP_005841583.1|  22 VRKARISDVDRIFKIYSENIE------YLDEESKNWLKSIIKKK-SRRARIYVALKRKKLVGFIIFY---K--KRKE 86 
                                       689999***********8333......445679**********7.*****************99876...3..4555 PP

                    Acetyltransf_4  78 aelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGFelvgi 139
                                       a +  + ++   +  g+gr+l++ +eq l   ++++++ ++   n n+  ++ + G++++ i
  gi|385805185|ref|YP_005841583.1|  87 AYIDAFAVDSRYRGLGIGRKLLNCIEQTLELEGVKRIYLSVKNGNNNALGLYLKNGYKVTNI 148
                                       66666655688999********************************************9876 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.4
                    Acetyltransf_4  83 y 83 
                                       y
  gi|385805185|ref|YP_005841583.1| 247 Y 247
                                       2 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   8.5e-09   1.4e-05       2     138 .]      20     144 ..      19     144 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 8.5e-09
                    Acetyltransf_3   2 LlLrplteeDlealfelrsdpevmrylpepltleeaeewlerawaeeseeegygwaivlkdtgviGsvglrdleeed 78 
                                       +++r+++ +D++++f+++s+  ++      + +ee++ wl+++ +++s++    ++  ++++  +G++ +++  +e 
  gi|385805185|ref|YP_005841583.1|  20 VIVRKARISDVDRIFKIYSE-NIE------YLDEESKNWLKSIIKKKSRRAR-IYVALKRKK-LVGFIIFYKKRKE- 86 
                                       688999**********9993.444......45799******98766544444.444434555.8*******88887. PP

                    Acetyltransf_3  79 eeaelg.ymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGfe 138
                                         a ++ + +++ ++g G+++  ++++ + + e +g++r++  ++  N +   ++ k G++
  gi|385805185|ref|YP_005841583.1|  87 --AYIDaFAVDSRYRGLGIGRKLLNCIEQTL-ELEGVKRIYLSVKNGNNNALGLYLKNGYK 144
                                       ..78883555566*************99999.9999**********************985 PP

>> DUF4821  Domain of unknown function (DUF4821)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   1.8e-07   0.00029     169     240 ..      11      81 ..       6      92 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.8e-07
                           DUF4821 169 ckreallpklhiRkArvEDhDDlveiferqseelreefGdyflaelieaqdeenkaiVaevegkavGllsls 240
                                       +k+e+ ++++ +RkAr  D D + +i  ++ e l+ee +++ l  +i+++ ++ ++ Va  ++k vG++   
  gi|385805185|ref|YP_005841583.1|  11 SKKENSMKNVIVRKARISDVDRIFKIYSENIEYLDEESKNW-LKSIIKKKSRRARIYVALKRKKLVGFIIFY 81 
                                       7899*********************************9997.7899**999999999***********9865 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   2.1e-05     0.034       2     125 ..      22     143 ..      21     146 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.1e-05
                                       EEEE-GGGHHHHHHHHHHHTT----H....HHHHHHHHHHTTSEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEE CS
                    Acetyltransf_9   2 irelteedldevlellkyaFqdeespl..eeireyfrklleesrvlgaedngelvgqlallplelnvpGktlkaagv 76 
                                       +r+++ +d+d ++++ ++  ++ +++   + ++   +k+  ++r+++a +  +lvg + +++        + k a++
  gi|385805185|ref|YP_005841583.1|  22 VRKARISDVDRIFKIYSENIEYLDEESknW-LKSIIKKKSRRARIYVALKRKKLVGFIIFYK--------KRKEAYI 89 
                                       6999*************9998888886222.445555555578***************9995........7788999 PP

                                       EEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--.....SSHHHHHTTT- CS
                    Acetyltransf_9  77 tgVavapehrgrgvlskLlaraleemreegqplsllfP.....ssipiYrrfGy 125
                                        + av+  +rg g+ +kLl+   + ++ eg++ ++l        + ++Y + Gy
  gi|385805185|ref|YP_005841583.1|  90 DAFAVDSRYRGLGIGRKLLNCIEQTLELEGVKRIYLSVkngnnNALGLYLKNGY 143
                                       ******************999999999999888888765555444566666665 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   7.3e-06     0.012      19      80 ..      84     146 ..      67     151 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 7.3e-06
                                       -TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-.S-EEEEEETT-HHHHHHHHHHT-EEE CS
                              FR47  19 kdggelgalqvlpehrrrGlgsrlvkalakeiaerg.ktvllvvvasNtpsirlyeklGfeki 80 
                                       ++  ++ a  v+   r+ G g++l + + + +  +g k + l v+ +N+++  ly k G+++ 
  gi|385805185|ref|YP_005841583.1|  84 RKEAYIDAFAVDSRYRGLGIGRKLLNCIEQTLELEGvKRIYLSVKNGNNNALGLYLKNGYKVT 146
                                       455889999***********************99884678999****************9875 PP

>> PanZ  Acetyltransferase (GNAT) domain, PanZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.6e-05     0.043      17     104 ..      29     131 ..      18     143 .. 0.74
   2 ?   -3.0   0.0       3.4   5.6e+03      39      64 ..     214     239 ..     185     243 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.6e-05
                              PanZ  17 DLakIy..........paqsaealea...alteegalfaarFNdRlLgAvkveledkeaelsdlcVRevTRrRGVgs 80 
                                       D  +I+          +++s++ l++   +  ++ ++++a   ++l g +    + kea ++ + V    R  G+g+
  gi|385805185|ref|YP_005841583.1|  29 DVDRIFkiysenieylDEESKNWLKSiikKKSRRARIYVALKRKKLVGFIIFYKKRKEAYIDAFAVDSRYRGLGIGR 105
                                       444444444999999866665555550005556789***************************************** PP

                              PanZ  81 yLl...eearrqaPevkswvlaeedvk 104
                                       +Ll   e++++    vk+ +l+ ++++
  gi|385805185|ref|YP_005841583.1| 106 KLLnciEQTLELE-GVKRIYLSVKNGN 131
                                       ***4444554444.7777777777655 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.4
                              PanZ  39 alfaarFNdRlLgAvkveledkeael 64 
                                       + +     +Rl+g ++ ++++++  +
  gi|385805185|ref|YP_005841583.1| 214 TYITIYSGKRLIGVARAHIDKNKVVI 239
                                       33333334566777776666666555 PP

>> Acetyltransf_6  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.5e-05     0.057      55     133 ..      49     125 ..      29     138 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.5e-05
                    Acetyltransf_6  55 raflrdllaalaargalrlyvlrldgrpvAvalglrsgdrlyywlggydpelaklspgllllweliedaae.eGlrr 130
                                         +l+++++    + ++r+yv+    ++v++++ +++++ +y    ++d ++++l++g+ ll  +ie+  e eG++r
  gi|385805185|ref|YP_005841583.1|  49 KNWLKSIIKKK--SRRARIYVALKRKKLVGFIIFYKKRKEAYIDAFAVDSRYRGLGIGRKLLN-CIEQTLElEGVKR 122
                                       55566666665..789*******************************************9875.5555555378887 PP

                    Acetyltransf_6 131 fdl 133
                                       + l
  gi|385805185|ref|YP_005841583.1| 123 IYL 125
                                       766 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 ?   12.9   0.0   5.7e-05     0.092       4      47 ..      67     109 ..      64     123 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.7e-05
                   Acetyltransf_CG   4 ltldegeevafleYevrkegvldfthTeVpeelrGkGiAkkLvk 47 
                                       + l+ ++ v+f+ +  +k ++  ++   V+ ++rG Gi++kL +
  gi|385805185|ref|YP_005841583.1|  67 VALKRKKLVGFIIFY-KKRKEAYIDAFAVDSRYRGLGIGRKLLN 109
                                       445557899**9996.677799********************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       857  (0.0477997); 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:                        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 0.29s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2065.24
//
Query:       gi|385805186|ref|YP_005841584.1|  [L=256]
Description: Threonyl/alanyl tRNA synthetase, SAD [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-11   42.9   0.1    3.9e-11   42.2   0.0    1.4  2  tRNA-synt_2c     tRNA synthetases class II (A)
    1.2e-07   31.7   0.3    3.2e-07   30.3   0.3    1.7  1  tRNA_SAD         Threonyl and Alanyl tRNA synthetase second a
  ------ inclusion threshold ------
      0.014   15.5   0.1      0.063   13.4   0.1    1.9  1  GramPos_pilinD1  Gram-positive pilin subunit D1, N-terminal d


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 !   42.2   0.0   6.5e-15   3.9e-11     478     552 .]      35     111 ..       2     111 .. 0.82
   2 ?   -3.0   0.0      0.32   1.9e+03      93     108 ..     146     161 ..     141     237 .. 0.62

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 6.5e-15
                                       EEEEEETTEEEESEEXXXXSSSSCSXXXEEEEESSEEEEESEEEEETTEEEEEXSS.XSX..XXTTSEEEEEEXHHH CS
                      tRNA-synt_2c 478 eveegeevgvvLdrTpfYaesGGqigDeGliekegaefrvkdvqkakgvvlhkgkleegk..lkvgdkvkaevdeer 552
                                        +e+ +++++v+d+T f + sGGq++D+G+i +++  f+vk+v +++gv +h +++++++   ++g+  ++++d+er
  gi|385805186|ref|YP_005841584.1|  35 LMESKNKAYLVFDKTIFHPKSGGQESDTGTIYDNERLFEVKKVLEVDGVAFHYANIQKNSgiQEKGEIFRLKLDWER 111
                                       466788999*******************************************9988654433789999999999875 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.32
                                       ESSSS-HHHHHHHHHH CS
                      tRNA-synt_2c  93 sfgdYfkeeaiefawe 108
                                       s+g Y k e i++++ 
  gi|385805186|ref|YP_005841584.1| 146 SIGSYIKYEHINLSHI 161
                                       5666666666666543 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 !   30.3   0.3   5.3e-11   3.2e-07       2      36 ..     210     246 ..     209     250 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 5.3e-11
                                       EEEEETT.EEEEESS---SBGGGC-SEEEE..CCECC CS
                          tRNA_SAD   2 rvvsiGdisvelCgGtHvpnTgeIgafkil..seesi 36 
                                       r+v+i +i   +C GtHv+nT+eI+ +ki   +ee +
  gi|385805186|ref|YP_005841584.1| 210 RIVEIQNINSIPCSGTHVKNTSEINYIKIKgvKEEDD 246
                                       8999999999*******************96666554 PP

>> GramPos_pilinD1  Gram-positive pilin subunit D1, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   1.1e-05     0.063      11     125 ..      44     215 ..      42     220 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.1e-05
                   GramPos_pilinD1  11 ilmdkdtfpkfteetnggegteedgnkit.gksskelaGVtFa.................................. 52 
                                       +++dk+ f  +  ++++ +gt +d++     k+  e++GV+F+                                  
  gi|385805186|ref|YP_005841584.1|  44 LVFDKTIFHPKSGGQESDTGTIYDNERLFeVKKVLEVDGVAFHyaniqknsgiqekgeifrlkldwerrykimrsht 120
                                       5899******************99877779999**********5555555555555555555555555555555555 PP

                   GramPos_pilinD1  53 ........vydvtdeydgvetedldsndeeatkklkeaakakagddakeaklskatak................... 102
                                               v +vt ++  v+                                     +                   
  gi|385805186|ref|YP_005841584.1| 121 aghildyaVMKVTGKK--VN-------------------------------------Tieanhasigsyikyehinl 158
                                       5555544444444433..11.....................................12222222222222222222 PP

                   GramPos_pilinD1 103 ................................eG.ianftklkk.grdgvYlivEtk 125
                                                                       e  ++n+ +l+     g Y+ivE++
  gi|385805186|ref|YP_005841584.1| 159 shiqlemiektaneavkagisvnvryvkreelEKfVFNAPNLERlPDVGIYRIVEIQ 215
                                       222222222222223333455555556666663336666666665555777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 1458.11
//
Query:       gi|385805187|ref|YP_005841585.1|  [L=227]
Description: isochorismatase hydrolase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      6e-38  130.8   0.0    7.1e-38  130.5   0.0    1.1  1  Isochorismatase  Isochorismatase family
  ------ inclusion threshold ------
       0.14   11.5   0.2        0.2   11.0   0.2    1.2  1  DUF1776          Fungal family of unknown function (DUF1776)


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 !  130.5   0.0     8e-42   7.1e-38       2     175 .]      34     221 ..      33     221 .. 0.96

  Alignments for each domain:
  == domain 1  score: 130.5 bits;  conditional E-value: 8e-42
                   Isochorismatase   2 alvviDmqndfv..........eegvkeseeisavveninkllkaarkagipviftrdvhe....leevkgdlderk 64 
                                       alv++D+q++f+          ++++  +  ++ +++ni+kll+ +r++++pv++           ++   + ++++
  gi|385805187|ref|YP_005841585.1|  34 ALVIVDVQKGFLeeakmikekhGHAYLYDRLVQVTIPNIKKLLDFFRENKLPVVHAVIGSYrtdgKDRSPVQSRPGW 110
                                       9*******************************************************999998887777777777788 PP

                   Isochorismatase  65 aaphfkpgttgaelvpelaplegdvvvdKtrfsafagtdldeiLkelgiktivlaGiatdvCVeatardaldlGyev 141
                                       +    + gt+ +e v+el+pl++++vv Kt+ sa +gt+l  iL+  gi+++v++Gi td CV  t+rd++d G+ v
  gi|385805187|ref|YP_005841585.1| 111 NYSLQIIGTSSQEEVDELRPLKDEIVVYKTTDSALNGTSLGHILRWMGIEHVVVTGIVTDQCVAGTVRDLADWGFIV 187
                                       8888899********************************************************************** PP

                   Isochorismatase 142 vvvsDAvaalspelhdaalkrlkqafatvitted 175
                                       +vv+DA+aa+s+e h++ l+ ++q  a+v++te+
  gi|385805187|ref|YP_005841585.1| 188 YVVEDATAAISQEYHEMELRIINQIYAKVVSTEE 221
                                       *******************************996 PP

>> DUF1776  Fungal family of unknown function (DUF1776)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2   2.2e-05       0.2       5      47 ..     161     202 ..     159     227 .] 0.65

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 2.2e-05
                           DUF1776   5 vvlvlGsptePltRsialDLerrGFiVfvtvesaeeeklvese 47 
                                        v+v G +t+  +   + DL   GFiV+v+    + ++  e +
  gi|385805187|ref|YP_005841585.1| 161 HVVVTGIVTDQCVAGTVRDLADWGFIVYVVEDATA-AISQEYH 202
                                       6999*************************865443.2222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1548.37
//
Query:       gi|385805188|ref|YP_005841586.1|  [L=463]
Description: ethanolamine transporter [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-38  132.3  61.2    2.8e-38  131.8  61.2    1.2  1  AA_permease_2  Amino acid permease
    2.7e-32  112.0  52.4    3.5e-32  111.6  52.4    1.1  1  AA_permease    Amino acid permease
  ------ inclusion threshold ------
        8.6    7.0  12.4        1.6    9.3   3.4    3.0  2  Phage_holin_1  Bacteriophage holin


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 !  131.8  61.2   4.8e-42   2.8e-38       1     404 [.      17     425 ..      17     459 .. 0.83

  Alignments for each domain:
  == domain 1  score: 131.8 bits;  conditional E-value: 4.8e-42
                     AA_permease_2   1 lsllsafalvigsvigsgifvkn..laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkk 75 
                                       ls++   ++++g+v+g gif  +  ++as+g ++i+ ++ia + + +a++l + El   +p+ gG + ++k++ g+k
  gi|385805188|ref|YP_005841586.1|  17 LSFWMIWGIAVGAVVGDGIFTFTgyAVASAGSSVIIAYLIAGITQ-MALMLSFGELVVWKPSAGGPSIWVKELLGEK 92 
                                       79999***********88865445899*************99999.7*********7779***************** PP

                     AA_permease_2  76 vaflsawfnwfayvpvlasilsvaasyl...lnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgi 149
                                       +  +s+ ++ ++++++  s+  + + y    l  +g +l + t  + ++ai++ +++a++ni+g+ + ak+q i+++
  gi|385805188|ref|YP_005841586.1|  93 WELVSSVSYSIGWIIAGGSTGLATGTYVywlLDYAGIHLGNITLWVTVFAILFNVIFAIMNILGVDIAAKAQLIMVL 169
                                       ***************8866655555554222333456888889899999**************************** PP

                     AA_permease_2 150 lkillpliiliilglitvdgggfsslstetdtffpngwpgvllgllivlwsfdGfesaanvseevkk.kdvpkaifi 225
                                       + +  +  ++  ++++t +++ +      +++f+png  g+l++++i ++++ G ++++   ee+k+  d+++a+f+
  gi|385805188|ref|YP_005841586.1| 170 FLVA-I--MVAYAAFATPHINFSY----FKENFMPNGFFGFLAAIPIGVYAYMGASTIIFSGEEAKRpIDISRALFW 239
                                       9995.4..4556777777776665....3679***********************************77******** PP

                     AA_permease_2 226 gllivlvlyllvniaflgvvpddeianlsnlgsvaalffeavggkvvaiivvilialsllgaintavigs.srvlea 301
                                       + l+ ++ly    + ++g +p +e+ +  + +  ++  +e+++g+++  i+ ++++l+++ +i++ ++++ +r l++
  gi|385805188|ref|YP_005841586.1| 240 SSLTFIILYSWDLVCAVGTIPYNEVVVFYQAL--YSTSAERLWGPAGGLIITFGAWLAAATCILMGTMYQpPRNLYD 314
                                       *************************9888754..89999******************999988776666528***** PP

                     AA_permease_2 302 lardgvlP.rffakvn.kfgspiraiiltaivslillllfllas.saaynfllsvsslgliisyllliigalilrkk 375
                                       l+r g+   +++   + k+++p++a+ +++++s+il++l ++a  ++ y +l    +++  +s+++++++a+ lrkk
  gi|385805188|ref|YP_005841586.1| 315 LSRRGYKVpKWWGYLHpKYKTPTYATLFVLVISIILIILGAMAGqTTVYAMLGYSLVWAWAVSWIFTLAAAIQLRKK 391
                                       ******777************************9998888888867777777777799******************* PP

                     AA_permease_2 376 rphl.kr.pgk...ilvaiigalfllfllvalff 404
                                        ++  ++ p+k   ++++  +a+++l l++++++
  gi|385805188|ref|YP_005841586.1| 392 HKDViEKlPWKvplWPLTPAFAVISLGLIFFAMI 425
                                       **88644666657755555444444444444332 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.6  52.4   5.9e-36   3.5e-32       5     469 ..      25     458 ..      22     463 .] 0.87

  Alignments for each domain:
  == domain 1  score: 111.6 bits;  conditional E-value: 5.9e-36
                       AA_permease   5 ialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGln 81 
                                       ia+g v+G g+f+ +g+++++aG  ++++ayl+ag+  ++ mls+ge+++ +p++gg + ++++ lg+++  v + +
  gi|385805188|ref|YP_005841586.1|  25 IAVGAVVGDGIFTFTGYAVASAGS-SVIIAYLIAGITQMALMLSFGELVVWKPSAGGPSIWVKELLGEKWELVSSVS 100
                                       899*********************.*******************************************999999999 PP

                       AA_permease  82 ylfswitvlaleltaasi....liqfwelvtdlpkawvt..gavflvvlliinlvgvkvygeaefilalikiiaiia 152
                                       y + wi++ +    a +     l+ +++    ++++wvt  +++f v++ i+n++gv   ++a++i+ l+++ +++a
  gi|385805188|ref|YP_005841586.1| 101 YSIGWIIAGGSTGLATGTyvywLLDYAGIHLGNITLWVTvfAILFNVIFAIMNILGVDIAAKAQLIMVLFLVAIMVA 177
                                       9899988876654444440001455555555555566669999********************************** PP

                       AA_permease 153 fiivg.iillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkdP 228
                                       +  +  +++                 n s fk+n+ p+        f +f+++++i v a++G + ++  ++E+k P
  gi|385805188|ref|YP_005841586.1| 178 YAAFAtPHI-----------------NFSYFKENFMPN-------GFFGFLAAIPIGVYAYMGASTIIFSGEEAKRP 230
                                       **9992222.................334455666666.......4******************************* PP

                       AA_permease 229 eksiPkailqvviritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinavi.ltaalssa 304
                                         +i +a     ++ +i+Y   l++++ ++p+n   ++ ++     ++ +  + +  ++ + +i+++  l+aa+ ++
  gi|385805188|ref|YP_005841586.1| 231 I-DISRALFWSSLTFIILYSWDLVCAVGTIPYNEVVVFYQA-----LYSTSAERLWGPAGGLIITFGAwLAAATCIL 301
                                       8.7*********************************99933.....6778889999999999999975278888899 PP

                       AA_permease 305 nsslysasRvlyslakdgl.aP.kvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaligliv 379
                                       ++ +y  +R ly l+++g+  P +++  + k++ P  a l++++is ++++l +++ + ++v+++l  +   +  + 
  gi|385805188|ref|YP_005841586.1| 302 MGTMYQPPRNLYDLSRRGYkVPkWWGYLHPKYKTPTYATLFVLVISIILIILGAMAGQ-TTVYAMLGYSLVWAWAVS 377
                                       ******************846777777789********************99999999.****************** PP

                       AA_permease 380 wlliilsylrfRkalkyqgrsieelgfkaallplgvilvlaaliiillilalyayltvkkgpkdwgaasfaaayliv 456
                                       w++++++ + +Rk+   ++  ie+l+ k +l pl++ +++++l +i+ ++ l  +l ++        + f+    ++
  gi|385805188|ref|YP_005841586.1| 378 WIFTLAAAIQLRKK---HKDVIEKLPWKVPLWPLTPAFAVISLGLIFFAMILDMFLSYG------ALTAFVTILGNL 445
                                       **************...9999********************************999933......333555555566 PP

                       AA_permease 457 llfliilvgvklh 469
                                        ++++++++ k++
  gi|385805188|ref|YP_005841586.1| 446 TWTILLIIATKYI 458
                                       7777777777665 PP

>> Phage_holin_1  Bacteriophage holin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   3.4   0.00027       1.6       7      54 ..     131     176 ..     128     183 .. 0.79
   2 ?    1.4   1.7     0.079   4.7e+02      13      57 ..     338     385 ..     332     388 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00027
                     Phage_holin_1   7 lknkafwvalisavlllilavlglfgldltvaklaeqllqivsavlsl 54 
                                       l n + wv+++++++ +i+a++++ g+d+  +  a+ ++ ++ +++++
  gi|385805188|ref|YP_005841586.1| 131 LGNITLWVTVFAILFNVIFAIMNILGVDIAAK--AQLIMVLFLVAIMV 176
                                       568899************************99..55555555544444 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.079
                     Phage_holin_1  13 wvalisavlllilavlglfgldltva.klaeqllq..ivsavlsllaa 57 
                                       +++l+ +v+++il +lg+++ ++tv+  l+  l+   +vs +++l aa
  gi|385805188|ref|YP_005841586.1| 338 YATLFVLVISIILIILGAMAGQTTVYaMLGYSLVWawAVSWIFTLAAA 385
                                       678889999999999999999999996666666541134466666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1123  (0.062636); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.73u 0.31s 00:00:01.04 Elapsed: 00:00:00.49
# Mc/sec: 2869.86
//
Query:       gi|385805189|ref|YP_005841587.1|  [L=966]
Description: hypothetical protein FFONT_0143 [Fervidicoccus fontis Kam940]
Scores for complete 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   23.2   8.7     0.0062   15.9   0.5    3.6  3  TRAP_beta        Translocon-associated protein beta (TRAPB)
    0.00013   22.1   0.7        4.2    7.7   0.0    5.3  7  NPCBM_assoc      NPCBM-associated, NEW3 domain of alpha-galac
    0.00071   19.8  20.1     0.0017   18.5   0.6    6.0  6  CARDB            CARDB
  ------ inclusion threshold ------
      0.021   15.0   0.6       0.23   11.6   0.0    2.8  3  Staufen_C        Staufen C-terminal domain
      0.065   13.5  28.9       0.91    9.9   0.7    6.7  7  DUF11            Domain of unknown function DUF11
       0.57    9.5   6.8       0.54    9.6   0.5    3.4  3  DUF5305          Family of unknown function (DUF5305)
        1.4    9.7  11.5       0.43   11.3   0.6    4.5  4  Sec23_BS         Sec23/Sec24 beta-sandwich domain


Domain annotation for each model (and alignments):
>> TRAP_beta  Translocon-associated protein beta (TRAPB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       2.5   6.4e+03      72     110 ..     624     663 ..     621     681 .. 0.69
   2 !   15.9   0.5   2.4e-06    0.0062      37     110 ..     702     789 ..     690     811 .. 0.70
   3 !   10.2   0.6   0.00014      0.37      34      58 ..     827     851 ..     822     955 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.5
                         TRAP_beta  72 slsakwerlapgenvshsfvvepkk.sgsfngtaavvtYr 110
                                       ++s++   ++ g+++++sf +   + s+ ++ + a++++ 
  gi|385805189|ref|YP_005841587.1| 624 QSSTQQSGIQKGSTITFSFPLNINVnSTGIYTANATLSFV 663
                                       5666667788899999999886554256677777777774 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 2.4e-06
                         TRAP_beta  37 ltveytiyNvGssaAldVslvD...dsf.peeaFevvsgsls.akwerlapgenvsh..sfvvepkksgsfngtaav 106
                                        ++++ i+N Gss+A++V ++      + +  + +++  + s + ++ ++p++nvs+  +f   p   +sf+g++++
  gi|385805189|ref|YP_005841587.1| 702 TNMTVVICNYGSSPAYNVYVTLsppSTItSGASSSLLLATPSvFYIKEIPPNSNVSFpvTFAFNPLGAQSFSGASTI 778
                                       57899************8766422334444444555555555156799********84467789************* PP

                         TRAP_beta 107 vtY.......r 110
                                       ++Y       +
  gi|385805189|ref|YP_005841587.1| 779 INYgvaplniQ 789
                                       ***44333331 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00014
                         TRAP_beta  34 gedltveytiyNvGssaAldVslvD 58 
                                        +d+ v+ t++N Gss+A+ V++v 
  gi|385805189|ref|YP_005841587.1| 827 SNDIKVTGTLINYGSSTAYRVEVVG 851
                                       5799******************986 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 ?   -1.3   0.0       1.1   2.7e+03      57      79 .]     115     137 ..     100     137 .. 0.80
   2 !    7.0   0.0    0.0027         7       5      71 ..     178     244 ..     175     251 .. 0.71
   3 ?   -3.0   0.0       3.6   9.2e+03       7      24 ..     305     322 ..     303     323 .. 0.81
   4 ?   -1.3   0.0         1   2.6e+03       8      35 ..     555     582 ..     554     609 .. 0.77
   5 ?   -3.6   0.0       5.4   1.4e+04      42      77 ..     627     661 ..     623     662 .. 0.72
   6 !    7.7   0.0    0.0016       4.2       7      32 ..     702     727 ..     698     737 .. 0.91
   7 ?   -2.1   0.0       1.9   4.8e+03      17      43 ..     782     806 ..     775     812 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.1
                       NPCBM_assoc  57 vkVtppagaaaGdyevtakarlt 79 
                                         + ++++  +G+y++ +++++t
  gi|385805189|ref|YP_005841587.1| 115 YYLNVNSDVSPGTYPIGFSLSYT 137
                                       5567889999******9999986 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0027
                       NPCBM_assoc   5 etvtltltvtndgtaaatnvslslslPeGWtvvevspasaaslapGetveatvk.VtppagaaaGdye 71 
                                       + ++l++t+ ndg++++ +   slslP+G    +    ++ +l+ + +++  +  + + ++  +G y+
  gi|385805189|ref|YP_005841587.1| 178 QNTQLQITIENDGNSTINSAVASLSLPSGFV-YTGGSIQIGTLQSNSRTTISFSgINIDKSLSPGNYT 244
                                       457899***********************87.333444444777777777766446666666666665 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 3.6
                       NPCBM_assoc   7 vtltltvtndgtaaatnv 24 
                                       v+l +t+ n+g+ ++ +v
  gi|385805189|ref|YP_005841587.1| 305 VQLSATFLNTGQYPIFSV 322
                                       678899*****9998666 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 1
                       NPCBM_assoc   8 tltltvtndgtaaatnvslslslPeGWt 35 
                                       +++lt+ n g +++    l++ lP+G t
  gi|385805189|ref|YP_005841587.1| 555 QFRLTIRNLGYDSMNYPVLTVNLPPGIT 582
                                       5899999999999999999999999966 PP

  == domain 5  score: -3.6 bits;  conditional E-value: 5.4
                       NPCBM_assoc  42 asaaslapGetveatvkVtppagaaaGdyevtakar 77 
                                       ++ + ++ G t ++ + + ++ +   G y+  a+++
  gi|385805189|ref|YP_005841587.1| 627 TQQSGIQKGSTITFSFPLNINVNST-GIYTANATLS 661
                                       5556788888888888888887776.7777777766 PP

  == domain 6  score: 7.7 bits;  conditional E-value: 0.0016
                       NPCBM_assoc   7 vtltltvtndgtaaatnvslslslPe 32 
                                       +++t+++ n g+++a nv+++ls P+
  gi|385805189|ref|YP_005841587.1| 702 TNMTVVICNYGSSPAYNVYVTLSPPS 727
                                       68999********************7 PP

  == domain 7  score: -2.1 bits;  conditional E-value: 1.9
                       NPCBM_assoc  17 gtaaatnvslslslPeGWtvvevspas 43 
                                       g  a  n+++s + P+G + +++++  
  gi|385805189|ref|YP_005841587.1| 782 GV-APLNIQISYEDPQGNS-KSFTTSL 806
                                       44.45799****9999977.6666555 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.6   6.8e-07    0.0017       4      82 ..     160     247 ..     157     251 .. 0.81
   2 ?    3.7   0.1     0.029        75      35      82 ..     347     391 ..     324     395 .. 0.87
   3 ?   -3.5   0.0         5   1.3e+04      22      33 ..     555     566 ..     554     570 .. 0.84
   4 ?    1.2   0.2      0.17   4.3e+02      44      82 ..     619     658 ..     607     670 .. 0.80
   5 ?   -1.2   0.0      0.96   2.4e+03      21      43 ..     702     724 ..     697     765 .. 0.77
   6 ?    4.3   2.1     0.018        47      11      72 ..     820     880 ..     812     924 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 6.8e-07
                                       EEE....EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE...EEEEESEE-CTEEEEEEEEEE-S.. CS
                             CARDB   4 Ltv...tntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelv...gtvtvpsLaagesttvsftwtte.. 72 
                                       L+v   ++++np+     ++ ++++t++N G+ +  +  ++l l    v   g++++  L++++ tt+sf+   +  
  gi|385805189|ref|YP_005841587.1| 160 LMVkvvSSQWNPAGYPGTQNTQLQITIENDGNSTINSAVASLSLPSGFVytgGSIQIGTLQSNSRTTISFSGINIdk 236
                                       5555534455555555555667********************999999999********************999888 PP

                                       .-S-CEEEEEE CS
                             CARDB  73 .ategevtltv 82 
                                        +++g++t+++
  gi|385805189|ref|YP_005841587.1| 237 sLSPGNYTFSI 247
                                       88889999765 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.029
                                       EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S-S-CEEEEEE CS
                             CARDB  35 sgatkvalyldgelvgtvtvpsLaagesttvsftwtteategevtltv 82 
                                        g++++++y d ++   +++++L +++++ v f++ ++++ g+ +++v
  gi|385805189|ref|YP_005841587.1| 347 GGTFTLSFYFDINS---TSLSQLLSQNEVPVHFNVSYMINLGNNAYIV 391
                                       46788999999888...67*******************9999998877 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 5
                                       EEEEEEEE-SSS CS
                             CARDB  22 titvtvkNqGta 33 
                                       ++++t++N G +
  gi|385805189|ref|YP_005841587.1| 555 QFRLTIRNLGYD 566
                                       6899*****976 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.17
                                       ETTEEEEEEEESEE-CTEEEEEEEEEE-S.-S-CEEEEEE CS
                             CARDB  44 ldgelvgtvtvpsLaagesttvsftwtte.ategevtltv 82 
                                       l+ +++++++ ++++ g+++t sf   ++  ++g +t ++
  gi|385805189|ref|YP_005841587.1| 619 LSSSQQSSTQQSGIQKGSTITFSFPLNINvNSTGIYTANA 658
                                       455556778889************9999977888888766 PP

  == domain 5  score: -1.2 bits;  conditional E-value: 0.96
                                       EEEEEEEEE-SSS-EEEEEEEEE CS
                             CARDB  21 ntitvtvkNqGtaasgatkvaly 43 
                                        ++tv + N G+  ++++ v+l 
  gi|385805189|ref|YP_005841587.1| 702 TNMTVVICNYGSSPAYNVYVTLS 724
                                       57899999999988888777664 PP

  == domain 6  score: 4.3 bits;  conditional E-value: 0.018
                                       C-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S CS
                             CARDB  11 npseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtte 72 
                                       + ++ +  +++++t t+ N G+ +++ ++v     +++ ++  v  +++++++  ++ ++++
  gi|385805189|ref|YP_005841587.1| 820 GGQAIYSSNDIKVTGTLINYGSSTAYRVEVVGSTGKQT-SSYFVGDIDPSSQYAFRVDIPAS 880
                                       5678899999******************9976666666.99*************99999987 PP

>> Staufen_C  Staufen C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       0.8   2.1e+03      65      87 ..     141     164 ..     130     170 .. 0.68
   2 ?   -1.2   0.0      0.87   2.2e+03      68      92 ..     714     737 ..     710     739 .. 0.83
   3 ?   11.6   0.0     9e-05      0.23      54      83 ..     786     814 ..     769     837 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.8
                                       --TTS-EEE.EEEE-SSS-EEEEE CS
                         Staufen_C  65 kgnkkefls.lvtlstePvqllhG 87 
                                          + ++ + +vt+s  P+++++ 
  gi|385805189|ref|YP_005841587.1| 141 TTRETDYFTiYVTVSQYPPLMVKV 164
                                       455666666379*******99875 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.87
                                       TS-EEEEEEE-SSS-EEEEEEESSH CS
                         Staufen_C  68 kkeflslvtlstePvqllhGiGssl 92 
                                          +  +vtls  P+ ++ G+ ssl
  gi|385805189|ref|YP_005841587.1| 714 SPAYNVYVTLS-PPSTITSGASSSL 737
                                       5678899***9.8899999999886 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 9e-05
                                       H---EEEEEE---TTS-EEEEEEE-SSS-E CS
                         Staufen_C  54 qgfqveysDfPkgnkkeflslvtlstePvq 83 
                                       + +q+ y+D P+gn k f + + ls eP  
  gi|385805189|ref|YP_005841587.1| 786 LNIQISYED-PQGNSKSFTTSLALSIEPFI 814
                                       5789*****.*****************964 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       2.4   6.2e+03      47      84 ..      43      70 ..      23      76 .. 0.58
   2 ?    9.9   0.7   0.00035      0.91      13      80 ..     177     253 ..     161     278 .. 0.70
   3 ?   -1.4   0.0       1.2   3.1e+03      44      86 ..     303     366 ..     295     372 .. 0.68
   4 ?    5.5   0.1    0.0082        21      12      67 ..     430     497 ..     423     522 .. 0.66
   5 ?    8.9   0.9    0.0007       1.8      13      52 ..     553     612 ..     538     658 .. 0.68
   6 ?    5.1   0.3     0.011        27      17      49 ..     703     735 ..     699     773 .. 0.68
   7 ?    0.5   0.3      0.29   7.4e+02      13      35 ..     827     849 ..     799     924 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.4
                             DUF11 47 svsasqgtasaltsvgsL.eagesatlsftvrvtrtaas 84
                                      s++            + + + ++ a+l+++v  ++ a++
  gi|385805189|ref|YP_005841587.1| 43 SSQN-----------TPVyPGSKNAQLRIEVLFNVNASN 70
                                      3222...........333144456777777777766664 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00035
                             DUF11  13 GdtvtytltvtNtgpasangvvvtDtlPaglayvsvsas....qgtasaltsv......gsLeagesatlsftvrvt 79 
                                       +++++  +t  N g+++ n +v +  lP+g+ y  +s +    q++ +++ s+      +sL +g+  t+s+t+++ 
  gi|385805189|ref|YP_005841587.1| 177 TQNTQLQITIENDGNSTINSAVASLSLPSGFVYTGGSIQigtlQSNSRTTISFsginidKSLSPGN-YTFSITLNAL 252
                                       3578899********************************666633333333336656666665554.3445555444 PP

                             DUF11  80 r 80 
                                        
  gi|385805189|ref|YP_005841587.1| 253 M 253
                                       4 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.2
                             DUF11  44 ayvsvsas............qgtasaltsv.........gsLeagesatlsftvrvtrtaasga 86 
                                       +yv+ sa+            +gta+ ++ +         gs+  g++ tlsf    + t+ s++
  gi|385805189|ref|YP_005841587.1| 303 RYVQLSATflntgqypifsvNGTANSEYFIpisnidsyyGSISTGGTFTLSFYFDINSTSLSQL 366
                                       5666666666666666666666666666666655666678889999999999888877777665 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.0082
                             DUF11  12 pGdtvtytltvtNtgpasangvvvtDtlP.....aglayvsvsas.......qgtasaltsvgsLeag 67 
                                        +d+  yt+   N+ p s ng+  t  lP      g +y s+  +       ++t + +++vg++++g
  gi|385805189|ref|YP_005841587.1| 430 NTDNAIYTVQIANRLPFSINGINATLFLPsgfesNGCNYASAYYGtilqsysSSTLQFKFNVGNIPPG 497
                                       578999**********************9444443333333333344444333344444444666665 PP

  == domain 5  score: 8.9 bits;  conditional E-value: 0.0007
                             DUF11  13 GdtvtytltvtNtgpasangvvvtDtlPaglayvsvsas......................q 52 
                                       Gd+  + lt +N g +s n  v+t  lP+g +y    +s                      q
  gi|385805189|ref|YP_005841587.1| 553 GDQ--FRLTIRNLGYDSMNYPVLTVNLPPGITYSNTNTSvfsilpytpsvslpsqltvqslQ 612
                                       554..77999***********************99999966666665444444443333331 PP

  == domain 6  score: 5.1 bits;  conditional E-value: 0.011
                             DUF11  17 tytltvtNtgpasangvvvtDtlPaglayvsvs 49 
                                       + t++  N+g ++a++v vt  +P+  +   +s
  gi|385805189|ref|YP_005841587.1| 703 NMTVVICNYGSSPAYNVYVTLSPPSTITSGASS 735
                                       5699***************98777655433332 PP

  == domain 7  score: 0.5 bits;  conditional E-value: 0.29
                             DUF11  13 GdtvtytltvtNtgpasangvvv 35 
                                          +++t t+ N+g ++a++v v
  gi|385805189|ref|YP_005841587.1| 827 SNDIKVTGTLINYGSSTAYRVEV 849
                                       45677888888888888888876 PP

>> DUF5305  Family of unknown function (DUF5305)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1      0.51   1.3e+03     119     149 ..       7      37 ..       3      41 .. 0.76
   2 ?    2.5   0.3     0.032        82      26      53 ..     886     913 ..     880     914 .. 0.89
   3 ?    9.6   0.5   0.00021      0.54      97     143 ..     914     958 ..     901     964 .. 0.60

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.51
                           DUF5305 119 liilgllaliglvvlirriiftsskaekyel 149
                                       +++l+++++++ +++i++   ts +++ + +
  gi|385805189|ref|YP_005841587.1|   7 FYLLSIIIIAASFAIIVSEAQTSEPTNTQIN 37 
                                       6788888888888888888888888777665 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.032
                           DUF5305  26 vsinlseyndrieeieeelglsvgtsel 53 
                                       v+i +s yn++ e+i+++l+lsv + ++
  gi|385805189|ref|YP_005841587.1| 886 VNITISYYNAFNENINRTLQLSVINQQV 913
                                       79*******************9977665 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00021
                           DUF5305  97 engeitetvtvkespslae.gilliilgllaliglvvlirriiftssk 143
                                       ++  + +t+t++ s+++ e +i+l+i++++  +g+ ++i+r+++t +k
  gi|385805189|ref|YP_005841587.1| 914 NE--TSATTTTSTSEMPEEyIIALFIVAIFL-LGAGYIIYRMYKTHQK 958
                                       33..334444444444444456666666665.7889999999999887 PP

>> Sec23_BS  Sec23/Sec24 beta-sandwich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.26   6.6e+02       3      85 ..      55     144 ..      53     155 .. 0.53
   2 ?   -0.5   0.1      0.81   2.1e+03      52      63 ..     351     366 ..     335     401 .. 0.57
   3 ?    0.5   0.2      0.41     1e+03      27      65 ..     612     650 ..     574     680 .. 0.77
   4 ?   11.3   0.6   0.00017      0.43       8      60 ..     824     882 ..     819     923 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.26
                                       EEEEEEEE-TTEEEEEEESSSEEC......STBESS..EESECSES..EEEEEEEETT--EEEEEEESSBTCTTSEE CS
                          Sec23_BS   3 natlevrtSkelkvsgliGncvsl......snvsek..eiGeggts..ewklcsldpdstlavyfdideklksgkqa 69 
                                       na+l++ +  +++ s++iGn +sl      s  s++       ++   ++ + + +    +  y++++++++   + 
  gi|385805189|ref|YP_005841587.1|  55 NAQLRIEVLFNVNASNAIGNLSSLppgfspS--SNSgySSAARDLYgnQVYFINASDVVYFEYYLNVNSDVS-PGTY 128
                                       7899999999999999999999997776541..222112222333200222333333333333333343333.3555 PP

                                       EEEEEEEEEETTSEEE CS
                          Sec23_BS  70 yiQfatlYthssgerr 85 
                                        i f ++Yt +s +r 
  gi|385805189|ref|YP_005841587.1| 129 PIGFSLSYTINSTTRE 144
                                       5666666666666665 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.81
                                       -EEEEEEE....SSBT CS
                          Sec23_BS  52 tlavyfdi....dekl 63 
                                       tl++yfdi     ++l
  gi|385805189|ref|YP_005841587.1| 351 TLSFYFDInstsLSQL 366
                                       5566666632221122 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.41
                                       STBESSEESECSESEEEEEEEETT--EEEEEEESSBTCT CS
                          Sec23_BS  27 snvsekeiGeggtsewklcsldpdstlavyfdideklks 65 
                                       +++ ++++  ++ s+++ + +++ st+++ f  + +++s
  gi|385805189|ref|YP_005841587.1| 612 QAYYQQVLSSSQQSSTQQSGIQKGSTITFSFPLNINVNS 650
                                       445556677788888999999999999999977655544 PP

  == domain 4  score: 11.3 bits;  conditional E-value: 0.00017
                                       EEE-TTEEEEEEESSSEECSTBESSEESECS..ESEEEEEEEETT--EEEEEEE....S CS
                          Sec23_BS   8 vrtSkelkvsgliGncvslsnvsekeiGegg..tsewklcsldpdstlavyfdi....d 60 
                                       +  S+++kv+g + n+ s ++++ +++G +g  ts++ ++ +dp+s +a+ +di     
  gi|385805189|ref|YP_005841587.1| 824 IYSSNDIKVTGTLINYGSSTAYRVEVVGSTGkqTSSYFVGDIDPSSQYAFRVDIpasqY 882
                                       678****************99999***997522778999**************944330 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (966 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       769  (0.0428914); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); 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):               7  [number of targets reported over threshold]
# CPU time: 0.79u 0.32s 00:00:01.11 Elapsed: 00:00:00.47
# Mc/sec: 6134.97
//
Query:       gi|385805190|ref|YP_005841588.1|  [L=411]
Description: putative ABC transporter [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-17   62.8   4.5    5.4e-17   62.8   4.5    2.2  2  MacB_PCD  MacB-like periplasmic core domain
    9.1e-11   42.1   8.2    9.1e-11   42.1   8.2    3.3  3  FtsX      FtsX-like permease family
  ------ inclusion threshold ------
       0.35   10.6   8.0       0.42   10.3   5.9    2.2  2  DUF21     Cyclin M transmembrane N-terminal domain


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 !   62.8   4.5     9e-21   5.4e-17       1     192 [.      28     246 ..      28     249 .. 0.76
   2 ?   -3.7   5.5       2.1   1.3e+04      13      68 ..     280     311 ..     254     401 .. 0.37

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 9e-21
                          MacB_PCD   1 slltvLGiaiGvaaviaivslgeglqasvlsqisdlgnlvtvtpgkgsgeslsdpdvealrrevp.veavapvv... 73 
                                       s+lt+LGi+iG a+++++++++ g ++++l q+++lg+++ ++++++s  +l+ +d++ ++ +++ v++++p++   
  gi|385805190|ref|YP_005841588.1|  28 SILTILGIIIGPAVIVMMGAVVGGYSQYILNQVTSLGQNN-IMITPSSDYTLTSSDLSYFK-SFSyVVNAVPYYltq 102
                                       79********************************998744.44555667778888897664.5778999***98787 PP

                          MacB_PCD  74 .tvrgggsgeeevtvvgvdpdyfk..vfglklaeGrffteadlrggpnvvvigeelaerlf.....pvGdtirl... 139
                                        tv+ g+s +e++ ++ +d ++    + gl+++eG+  ++ d+      ++ig+++a +        vGd++ l   
  gi|385805190|ref|YP_005841588.1| 103 aTVTVGNS-QEQIYIYCTDVNFVLhaIGGLEIEEGSAPSQGDVL----DALIGHKVAYDQNgnleyGVGDVVPLkvf 174
                                       75667764.44466666887776677889988999766666666....49*******7733566799*****88899 PP

                          MacB_PCD 140 ............kpftVvGvledppgsgsalg.ddavylp......lttl...qrrsitvrlkdgadleaaaael 192
                                                   +++ V+Gvl+++ g++  ++ d+ ++l+      l  l   + + i+v+++d+  ++++   +
  gi|385805190|ref|YP_005841588.1| 175 tkitngipqyktVNVIVSGVLKEY-GGALIFSpDQTIFLDtdagqkL--LglnSWSGILVQVSDPIYVKDFVSTV 246
                                       999***99998888*******888.5554545599999996654331..13323455****99998777766655 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 2.1
                          MacB_PCD  13 aaviaivslgeglqasvlsqisdlgnlvtvtpgkgsgeslsdpdvealrrevpvea 68 
                                       a+++a+ + ++g++a++  ++ +                           e++v +
  gi|385805190|ref|YP_005841588.1| 280 ASLSAFAVAIAGTTATMVTSVIERTK------------------------EIGVMK 311
                                       33333333333333333333221111........................112111 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.3      0.01        60      28      65 ..      30      71 ..      14     116 .. 0.62
   2 ?   -0.9   3.4       0.4   2.4e+03      40      90 ..     251     302 ..     222     305 .. 0.75
   3 !   42.1   8.2   1.5e-14   9.1e-11       2      96 .]     305     404 ..     304     404 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.01
                              FtsX 28 itlvalviGlgl....gllaaqllsdvllssvfsselkisid 65
                                      +t+++++iG ++    g+++  +++  l+++ + ++  i+i 
  gi|385805190|ref|YP_005841588.1| 30 LTILGIIIGPAVivmmGAVVGGYSQYILNQVTSLGQNNIMIT 71
                                      455555555222112244444443333333322233333333 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.4
                              FtsX  40 gllaaqllsdvllssvfs.selkisidlitvliiivlllllallagllsisk 90 
                                       g++++ ++++ +  +v+s + +  +i++ + l ++++++  ++++++ s++ 
  gi|385805190|ref|YP_005841588.1| 251 GNKVSVISFSAIADIVSSiTGAVNYINYVASLSAFAVAIAGTTATMVTSVIE 302
                                       5555566666666666666777888888888888888888888888887765 PP

  == domain 3  score: 42.1 bits;  conditional E-value: 1.5e-14
                              FtsX   2 reigilralGmkkkqvlllllteillitlvalviGlglgllaaql...lsdvllssvfs.....selkisidlitvl 70 
                                       +eig+++++G+++++++ ++l+e+ l +++a+v+G +lg++ + +   +   + +   +     ++ ++ ++   ++
  gi|385805190|ref|YP_005841588.1| 305 KEIGVMKSIGYTNREIIIMILSESTLMSFIAAVAGSLLGVAGSFVlggSGMTIRA---GtntvvINSHPLFSAHLFI 378
                                       8**********************************77755554441113333333...133466************* PP

                              FtsX  71 iiivlllllallagllsiskilkkep 96 
                                       + i+l +l+ ++ g+l+++ ++++ p
  gi|385805190|ref|YP_005841588.1| 379 TSIGLTILVGVVGGILPAYMASRIPP 404
                                       **********************9976 PP

>> DUF21  Cyclin M transmembrane N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   2.7      0.48   2.9e+03      68      97 ..     260     298 ..     246     337 .. 0.51
   2 ?   10.3   5.9     7e-05      0.42      46     119 ..     301     409 ..     279     410 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.48
                             DUF21  68 salatalfvellae..........galavviatvivtlli 97 
                                       sa+a+ + +++ ++          +a+av+ia +  t+++
  gi|385805190|ref|YP_005841588.1| 260 SAIADIV-SSITGAvnyinyvaslSAFAVAIAGTTATMVT 298
                                       4444333.22222223333343354444444443223322 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 7e-05
                             DUF21  46 lknperlLstlligntlvnillsalatalfvellae...................................galavv 87 
                                       +++ ++  +   ig t  +i++ +l ++++++++a+                                    ++ ++
  gi|385805190|ref|YP_005841588.1| 301 IERTKEIGVMKSIGYTNREIIIMILSESTLMSFIAAvagsllgvagsfvlggsgmtiragtntvvinshplFSAHLF 377
                                       44444444445555555555555555555555555555555556666677889999999999999999998777899 PP

                             DUF21  88 iatvivtllilvfgEilPkslalkyaekiala 119
                                       i+ + +t+l+ v+g ilP  +a + + ++al+
  gi|385805190|ref|YP_005841588.1| 378 ITSIGLTILVGVVGGILPAYMASRIPPAVALR 409
                                       99999*************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       894  (0.0498633); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.72u 0.28s 00:00:01.00 Elapsed: 00:00:00.54
# Mc/sec: 2279.04
//
Query:       gi|385805191|ref|YP_005841589.1|  [L=164]
Description: putative transcription regulator, encoded next to RecA superfamily ATPase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0011   18.9   0.2     0.0036   17.2   0.0    1.9  2  HTH_11    HTH domain
  ------ inclusion threshold ------
      0.032   13.2   1.0      0.043   12.8   1.0    1.1  1  Vps53_N   Vps53-like, N-terminal
      0.048   14.1   2.2      0.078   13.4   1.0    2.0  2  HTH_40    Helix-turn-helix domain
      0.063   13.1   0.1       0.15   11.9   0.1    1.6  1  HTH_23    Homeodomain-like domain


Domain annotation for each model (and alignments):
>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.3   5.7e+03       3      17 ..      51      65 ..      50      65 .. 0.74
   2 !   17.2   0.0     8e-07    0.0036      12      36 ..      80     104 ..      74     106 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.3
                            HTH_11  3 lqilelLleargpis 17
                                      +++l++ le++++++
  gi|385805191|ref|YP_005841589.1| 51 EDVLQQALETKDKLT 65
                                      678899778887765 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 8e-07
                            HTH_11  12 argpisgeeLAeeLnvSrrtvrrdI 36 
                                       +r  i+++++AeeL+++++t+r+++
  gi|385805191|ref|YP_005841589.1|  80 ERAGIPASRIAEELERTEATIRNHL 104
                                       44459******************98 PP

>> Vps53_N  Vps53-like, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.0   9.5e-06     0.043      10      97 ..      54     162 ..      50     163 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.5e-06
                           Vps53_N  10 inellpteqslanideli...............kklqeeikklddeiksvvraqanvgekgkealeeaqkaieelfq 71 
                                       +++ l t+  l+ +d+li                ++ ee+++ ++ i+++  ++++ g+  ke  e++ k+  +l++
  gi|385805191|ref|YP_005841589.1|  54 LQQALETKDKLTWLDSLIvaagalareragipaSRIAEELERTEATIRNHLSGKTDAGKMVKETYEQLVKSGGSLSN 130
                                       6788999999999***999*************9*******************************9999999888888 PP

                           Vps53_N  72 kikeikdkaekse......emvkeitrdIkqL 97 
                                        + ei  k+ + e      e vk+  ++Ik+L
  gi|385805191|ref|YP_005841589.1| 131 IVPEILVKSSEEEkckerlELVKQKIEEIKKL 162
                                       88887655554441112225677778888876 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.2   5.6e+03      51      51 ..      33      33 ..       6      60 .. 0.61
   2 ?   13.4   1.0   1.7e-05     0.078      12      61 ..      83     135 ..      77     164 .] 0.62

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.2
                            HTH_40 51 e 51
                                      +
  gi|385805191|ref|YP_005841589.1| 33 K 33
                                      1 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1.7e-05
                            HTH_40  12 glsieeIAkerglkesTIegHLaelieegeeidl..erlvse.eeekeIeeai 61 
                                       g     IA+e + +e+TI +HL     +g+ ++   e+lv++    ++I   i
  gi|385805191|ref|YP_005841589.1|  83 GIPASRIAEELERTEATIRNHLSGKTDAGKMVKEtyEQLVKSgGSLSNIVPEI 135
                                       556678*****************999999744434466664434444444333 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   3.4e-05      0.15      14      36 ..      78     102 ..      71     106 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.4e-05
                            HTH_23  14 lae..GlsvreIAreLgvsrrTvyr 36 
                                       ++e  G++ ++IA+eL +++ T+++
  gi|385805191|ref|YP_005841589.1|  78 AREraGIPASRIAEELERTEATIRN 102
                                       34457******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1330  (0.0741815); expected 358.6 (0.02)
Passed bias filter:                      691  (0.0385409); 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: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1019.09
//
Query:       gi|385805192|ref|YP_005841590.1|  [L=77]
Description: hypothetical protein FFONT_0146 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score 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   15.5   0.5      0.028   15.2   0.5    1.3  1  VAPB_antitox    Putative antitoxin
      0.028   14.3   0.0      0.031   14.1   0.0    1.2  1  5-FTHF_cyc-lig  5-formyltetrahydrofolate cyclo-ligase family
      0.056   13.8   0.0      0.056   13.8   0.0    1.1  1  DUF2663         Protein of unknown function (DUF2663)


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 ?   15.2   0.5   4.7e-06     0.028      32      69 .]      38      75 ..      19      75 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.7e-06
                      VAPB_antitox 32 ekkkkgkkkellelfgilseeeadeiekaskelrkefk 69
                                      e k+++ +++  +l++i s+e++  ie++s+e+r+ fk
  gi|385805192|ref|YP_005841590.1| 38 EAKRSKAEEAFNKLRKIISSEDLGGIERSSREFREGFK 75
                                      34555667899************************886 PP

>> 5-FTHF_cyc-lig  5-formyltetrahydrofolate cyclo-ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   5.2e-06     0.031      58      96 ..       1      39 [.       1      60 [. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.2e-06
                                      HHHHHHHTTEEEEEEEECSSCTEECEEEEEECCCCCCCC CS
                    5-FTHF_cyc-lig 58 likklleegkevllPrvrlesgslkvvrlttlkeedsle 96
                                      +++++leegk +l+P +rl++g++ +  ++++k+ ++ +
  gi|385805192|ref|YP_005841590.1|  1 MRQRALEEGKMLLIPSPRLKTGFMLLNPSEIQKKLYREA 39
                                      6899**********************9999988776654 PP

>> DUF2663  Protein of unknown function (DUF2663)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   9.4e-06     0.056      60     101 ..      23      62 ..       8      76 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.4e-06
                           DUF2663  60 llllvallyvavkllkkKaeKaEkefhaLrceiiekSkdlwk 101
                                       ++ll  + +    + + K+ KaE+ f++Lr+ i   S+dl  
  gi|385805192|ref|YP_005841590.1|  23 FMLLNPSEIQKKLYREAKRSKAEEAFNKLRKII--SSEDLGG 62 
                                       55556666666778899*************833..5667655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       789  (0.0440069); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); 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: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 469.90
//
Query:       gi|385805193|ref|YP_005841591.1|  [L=117]
Description: PilT domain-containing protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.6e-11   43.0   3.8    1.7e-10   41.5   3.8    1.7  1  PIN          PIN domain
     0.0076   16.0   0.1      0.091   12.5   0.1    2.1  2  DUF5615      Domain of unknown function (DUF5615)
  ------ inclusion threshold ------
      0.013   15.9   0.5      0.018   15.5   0.5    1.2  1  Terminase_4  Phage terminase, small subunit


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 !   41.5   3.8   2.8e-14   1.7e-10       3     118 ..       4     105 ..       2     109 .. 0.83

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 2.8e-14
                                       E-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHHHHH CS
                               PIN   3 lDTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidaeiae 79 
                                       +DTsvli+    ++     +  +   ee ++s+++l+E+l+++a        ++++   +ll ++ ++ ++d e+ +
  gi|385805193|ref|YP_005841591.1|   4 IDTSVLIE----DV----KKGVY---EEGAISSITLIEVLRGIAP-------EKRVMVKELLEKSYELKSLDNEAIL 62 
                                       67777771....11....13334...899****************.......55555555558889999999***** PP

                                       HHHHHHHHHH.....SBHHHHHHHHHHHHHT-EEE.ESSTHHHH CS
                               PIN  80 eaaeialkyg.....llpnDaliaAtAkehgikliatfDedfrr 118
                                       ++ e+++ ++     ++ +D+lia++A++ +++l  t+D+df+r
  gi|385805193|ref|YP_005841591.1|  63 KYCELYDALKekenlIRDADLLIASVAIAKNLELM-TKDKDFER 105
                                       ********************************999.******98 PP

>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.043   2.6e+02      31      47 ..      52      68 ..      39      71 .. 0.81
   2 !   12.5   0.1   1.5e-05     0.091      36      60 ..      81     105 ..      70     113 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.043
                           DUF5615 31 glegasDeeileyAkee 47
                                      +l++ ++e+il+y++  
  gi|385805193|ref|YP_005841591.1| 52 ELKSLDNEAILKYCELY 68
                                      46778999*****9865 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 1.5e-05
                           DUF5615  36 sDeeileyAkeedriivTkDkDFge 60 
                                        D  i ++A+++++ ++TkDkDF +
  gi|385805193|ref|YP_005841591.1|  81 ADLLIASVAIAKNLELMTKDKDFER 105
                                       5778999****************75 PP

>> Terminase_4  Phage terminase, small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.5     3e-06     0.018       9      73 ..      43     105 ..      39     113 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3e-06
                       Terminase_4   9 ike.LdelgilseldseaLaayceayaryreaekkiekeGvtittaegegakkknpavtilnsaek 73 
                                       +ke L++   l+ ld ea+ +yce+y+  +e e+ i+ + + i +       k+  ++t+ ++ e+
  gi|385805193|ref|YP_005841591.1|  43 VKElLEKSYELKSLDNEAILKYCELYDALKEKENLIRDADLLIASVAI---AKNLELMTKDKDFER 105
                                       5552566666*********************99999888888875553...556666666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 867.63
//
Query:       gi|385805194|ref|YP_005841592.1|  [L=653]
Description: arginyl-tRNA synthetase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-33  116.6   2.6      1e-19   70.7   0.7    2.2  2  tRNA-synt_1d  tRNA synthetases class I (R)
    4.6e-24   84.9   1.1    2.7e-23   82.4   0.0    2.8  3  DALR_1        DALR anticodon binding domain
  ------ inclusion threshold ------
      0.057   11.7   0.0       0.15   10.3   0.0    1.7  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 !   45.7   0.1   6.7e-16     4e-12      14      86 ..     121     193 ..     114     254 .. 0.81
   2 !   70.7   0.7   1.7e-23     1e-19      83     335 ..     243     509 ..     237     517 .. 0.86

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 6.7e-16
                                       ---SST-EEEEE----BTTS--BHHHHHHHHHHHHHHHHHHHCT-EEEEEE--B-SSTCHHHHHHHHHHHTTT CS
                      tRNA-synt_1d  14 kksrekkkvvvdfssPniakemhvGhLrstiiGdavsrlleflGydvirlnhvGDWGtqfGlLiaylekkqde 86 
                                        ++ +k ++vv+++s n   ++h+Gh r   +Gd++srll f G ++ r  ++ D G+q+ lLi ++ k +++
  gi|385805194|ref|YP_005841592.1| 121 GQAVKKLNIVVEHTSANPLHPLHIGHARNSCLGDTISRLLKFYGMNIERRFYIDDMGRQMALLIYGILKLNED 193
                                       56778889********************************************************987776655 PP

  == domain 2  score: 70.7 bits;  conditional E-value: 1.7e-23
                                       HTTTTTTS-----SCC.CHHHHHHHHCCCSHCCCHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHCT--- CS
                      tRNA-synt_1d  83 kqdekllqeqelqdLe.afykeakkdydeeeifaerarnyvvkLqsgdedirklwkllvditrtelqklydrldvtl 158
                                       +qde ++++  + d   +++     +  ++e  +++  +   + ++ de++ k+++ +++++   ++++  +l +  
  gi|385805194|ref|YP_005841592.1| 243 QQDELVAESARIRDRSpEIFDVLAEKIMKDEDPEKEISQLSLRYEQHDENVVKIFREVIELVIGGFKETLGKLGIEF 319
                                       56666666666666542455556667788899999999999999*************99999999999999999999 PP

                                       EC.--CC..CCCCCHHHHHHHHHCTT-EEECTTCEEEEECCC.............TSSC.CEECC-TTS-B-HHHHH CS
                      tRNA-synt_1d 159 ie.rGes..lykeslneivkelkkkglvkesdGalvvfldef.............gkrl.gvvvqksDGgylytttD 218
                                        +   es  ++   ++ei+ + ++ ++     Ga  +  +                  + ++++++sDG++lytt+D
  gi|385805194|ref|YP_005841592.1| 320 DKwDYESdlVWSGLVDEILRKARESQVFTIYKGAEALSYETIlndslkeklfipkEMDIpPLILKRSDGTTLYTTRD 396
                                       877667776899999*******************99887777788889999996533442459999*********** PP

                                       HHHHHHHHHTT--SEEEEEEECCCHHHHHHHHHHHHCTTSSTTTSEEEEEEE--EE-TTSSBSBCSSSTC-BHHHHH CS
                      tRNA-synt_1d 219 iaaakerkeelkadkvlyvidsrqslhlqqiflilkkigyvpeskdlehanfGmvlgkdkkkfktrkGetvkLadlL 295
                                       ia  +++ +e +ad v+ vi ++q l   q+ l+l  +gy   + +l h ++ mv    + k++ r+G  v L++l+
  gi|385805194|ref|YP_005841592.1| 397 IAYSIKKFKEFNADYVINVIAKEQTLPQAQLRLALYSLGYREYAERLIHYSYEMV-NLPGYKMSGRRGRFVSLDELI 472
                                       ****************************************888************.899****************** PP

                                       HHHHHHHHHHHCCCCCCTS-CCCCHCHHHHHHHHHHHHCC CS
                      tRNA-synt_1d 296 dealeralqlikeknkdkvlqadelekvaeavgvgaikya 335
                                       + + + a+q +  +   k   a++ e+v +avg +a++y 
  gi|385805194|ref|YP_005841592.1| 473 EMSENAAKQELLKR---KGQVAEDVEQVYKAVGRSAVRYS 509
                                       99998888855544...44589****************97 PP

>> DALR_1  DALR anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1      0.76   4.5e+03      74      74 ..     260     260 ..     213     295 .. 0.55
   2 ?   -1.0   0.1      0.32   1.9e+03      29      97 ..     355     432 ..     334     434 .. 0.45
   3 !   82.4   0.0   4.5e-27   2.7e-23       1     119 []     537     653 .]     537     653 .] 0.94

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.76
                                       H CS
                            DALR_1  74 k 74 
                                       +
  gi|385805194|ref|YP_005841592.1| 260 E 260
                                       1 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.32
                                       C......S-SH.HHHHHHHHHHTHHHHHHHHHHHT-THHHHHHHHHH..HHHHHHHHHHCTSTTSCTHHH.HHHHHH CS
                            DALR_1  29 l......leee.eekeLlkalaqfpevleeaaeelephklaeylyeL..aatfhkfYnkervlkeeeeelaaaRLaL 96 
                                              l++  +ek  + +  ++p ++ +  +  ++ +  + +y++   ++f++ Y  + + ke+   +a+ RLaL
  gi|385805194|ref|YP_005841592.1| 355 AlsyetiLNDSlKEKLFIPKEMDIPPLILKRSDGTTLYTTRDIAYSIkkFKEFNADYVINVIAKEQTLPQAQLRLAL 431
                                       33455544444455555555555555555555544333333333332003445555544444444444446667776 PP

                                       H CS
                            DALR_1  97 v 97 
                                        
  gi|385805194|ref|YP_005841592.1| 432 Y 432
                                       5 PP

  == domain 3  score: 82.4 bits;  conditional E-value: 4.5e-27
                                       HHHHHHHHHHHHHHTTCTTCCCCHCCHCCS-SHHHHHHHHHHHTHHHHHHHHHHHT-THHHHHHHHHHHHHHHHHHH CS
                            DALR_1   1 vqyahaRiksilrkaeeegekleeealalleeeeekeLlkalaqfpevleeaaeelephklaeylyeLaatfhkfYn 77 
                                       vqy++aR+ s+l ka+  +  +e +     ++++  +L+++l +fp v+ ++  el+p+ ++ yl +++++f+++Y+
  gi|385805194|ref|YP_005841592.1| 537 VQYTYARAFSLLAKAGSYERPTEFDIIE--KDDQTYKLIRSLSKFPWVIHKSTTELKPELIVAYLGDISQKFNSWYD 611
                                       8**************9877665555444..599******************************************** PP

                                       HCTSTTSCTHHH.HHHHHHHHHHHHHHHHHHHHTT----S-- CS
                            DALR_1  78 kervlkeeeeelaaaRLaLvkavrqvLangLdlLGieapekm 119
                                       +++vl+e++e  +a ++a v+av++++ ++L+++G+ ++ekm
  gi|385805194|ref|YP_005841592.1| 612 NVPVLGEKDERYRALKIATVNAVKSIIGSALNIVGVVTLEKM 653
                                       *****************************************9 PP

>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   2.5e-05      0.15      38      74 ..     142     178 ..     136     217 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 2.5e-05
                       tRNA-synt_1  38 lHiGhalaktlkdivirykrmkGkevlyvpGwDhaGl 74 
                                       lHiGha ++ l d++ r  ++ G + ++++ +D  G 
  gi|385805194|ref|YP_005841592.1| 142 LHIGHARNSCLGDTISRLLKFYGMNIERRFYIDDMGR 178
                                       8*****************************9998885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (653 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       973  (0.0542696); expected 358.6 (0.02)
Passed bias filter:                      663  (0.0369792); 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: 0.73u 0.31s 00:00:01.04 Elapsed: 00:00:00.49
# Mc/sec: 3988.39
//
Query:       gi|385805195|ref|YP_005841593.1|  [L=221]
Description: putative SAM-dependent methyl transferase [Fervidicoccus fontis Kam940]
Scores for 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-15   55.0   0.0    1.5e-14   54.4   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    1.9e-09   37.6   0.0    2.7e-09   37.1   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    7.8e-09   36.1   0.0    1.4e-08   35.3   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    2.7e-06   26.9   0.0    5.5e-05   22.6   0.0    2.3  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    1.3e-05   25.9   0.0    2.2e-05   25.1   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
    1.4e-05   24.9   0.0    2.2e-05   24.3   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
  ------ inclusion threshold ------
      0.055   13.1   0.0      0.081   12.5   0.0    1.2  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 !   54.4   0.0   5.8e-18   1.5e-14       1      95 [.      51     135 ..      51     136 .. 0.94

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 5.8e-18
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCH CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedp 77 
                                       L++G+GtGr+a++l       +g+D+s   lk++ ek+      +e+++a+ae lp++d+sf   ++  +l++vedp
  gi|385805195|ref|YP_005841593.1|  51 LEIGVGTGRFAKPLN----VEFGIDPSVSSLKISAEKG------IEVIRATAEYLPLRDESFNTAYLIVTLCFVEDP 117
                                       89*************....789*********8886555......6779***************************** PP

                                       HHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  78 ekalkeiaRvLkpgGllv 95 
                                       +++l e+ R+Lkp+G+lv
  gi|385805195|ref|YP_005841593.1| 118 NRTLLEAFRILKPEGKLV 135
                                       ****************98 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.0     1e-12   2.7e-09      25     160 ..      49     181 ..      17     185 .. 0.72

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 1e-12
                   Methyltransf_23  25 rvLdiGcGtGillevlrengfsvt.gvDlspeaveiae..kakkaqkdqfdeqeaae..........pqgkfdlIvl 88 
                                        +L+iG GtG++++ l     +v+ g+D+s    +i +  + +             +           +++f++++l
  gi|385805195|ref|YP_005841593.1|  49 PCLEIGVGTGRFAKPL-----NVEfGIDPSVSSLKISAekG-IE------------VirataeylplRDESFNTAYL 107
                                       69************77.....66669999965444432221.11............12222233444777******* PP

                   Methyltransf_23  89 revlehvpdppellrqiatllkpgGylllse.plasl....kedrllldwlylvpagrhisffsarslkelleeaGl 160
                                       + +l+ v+dp ++l  ++++lkp+G l+ ++ pl s+    +e+++ ++ ++  ++     ff+ +++ke+  +aG+
  gi|385805195|ref|YP_005841593.1| 108 IVTLCFVEDPNRTLLEAFRILKPEGKLVTCVvPLDSQwgsfYEEKKKKEETFFYKE---AVFFTKKEIKEMISNAGF 181
                                       ****************************9994444446765444444443333322...468899999999999998 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.0   5.4e-12   1.4e-08       2      97 .]      51     132 ..      50     132 .. 0.94

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 5.4e-12
                                       EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSS CS
                   Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhls 78 
                                       L++G GtGr+++ l  ++      g+D+s + l++ +e+       +e++++ ae lp+ d+sf+  +++ +l++++
  gi|385805195|ref|YP_005841593.1|  51 LEIGVGTGRFAKPLNVEF------GIDPSVSSLKISAEKG------IEVIRATAEYLPLRDESFNTAYLIVTLCFVE 115
                                       89*************997......9**********99999......***********************87799998 PP

                                       HHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  79 dedlekalkeiarvLkpgG 97 
                                       d++  ++l e++r+Lkp+G
  gi|385805195|ref|YP_005841593.1| 116 DPN--RTLLEAFRILKPEG 132
                                       665..89**********99 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   2.2e-08   5.5e-05      94     151 ..      79     136 ..      70     140 .. 0.91
   2 ?    1.8   0.0      0.05   1.3e+02     198     215 ..     166     183 ..     143     190 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 2.2e-08
                                       HHTSSTEEEEE--TTT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEE CS
                   Ubie_methyltran  94 eegkinieflqanaeeLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvv 151
                                        ++ + ie + a ae Lp  d+sf++  +   l  v D +++L ea+r+lkp G+lv 
  gi|385805195|ref|YP_005841593.1|  79 ISAEKGIEVIRATAEYLPLRDESFNTAYLIVTLCFVEDPNRTLLEAFRILKPEGKLVT 136
                                       5567789********************999************************9874 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.05
                                       S--HHHHHHHHHHTTEEE CS
                   Ubie_methyltran 198 fPdqetlkeliedaGfks 215
                                       f  ++++ke+i +aGf  
  gi|385805195|ref|YP_005841593.1| 166 FFTKKEIKEMISNAGFIL 183
                                       667899*********975 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   8.8e-09   2.2e-05       1      99 []      51     134 ..      51     134 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 8.8e-09
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       LeiG GtG+++++l  +       g+D+s s++     k++++++   ++++ +a+ l  +d+  sf + +++ +l+
  gi|385805195|ref|YP_005841593.1|  51 LEIGVGTGRFAKPLNVE------FGIDPSVSSL-----KISAEKG--IEVIRATAEYLPLRDE--SFNTAYLIVTLC 112
                                       8*************999......9*********.....5555554..3344444444444443..9*********** PP

                   Methyltransf_12  78 hlkdirevldnirklLkpgGrl 99 
                                        ++d++++l ++ + Lkp+G+l
  gi|385805195|ref|YP_005841593.1| 113 FVEDPNRTLLEAFRILKPEGKL 134
                                       ********************97 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   8.7e-09   2.2e-05       7     149 ..      50     177 ..      48     185 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 8.7e-09
                   Methyltransf_31   7 vlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnev 83 
                                        l++G GtG++++ l+ e       +GiD s  +++ + e       + +e+ ++ +e l+  l de+f+      +
  gi|385805195|ref|YP_005841593.1|  50 CLEIGVGTGRFAKPLNVE-------FGIDPSVSSLKISAE-------KGIEVIRATAEYLP--LRDESFNTAYLIVT 110
                                       5899************44.......7*************9.......5889**********..99************ PP

                   Methyltransf_31  84 lnaladpdkileeiervlkpggilliedprllaelpakveeeskay........evvegakigt..qkdelyelle 149
                                       l+ + dp+ +l e++r lkp+g l+++ +  l+ + ++++ee k++        +           +k+e++e++ 
  gi|385805195|ref|YP_005841593.1| 111 LCFVEDPNRTLLEAFRILKPEGKLVTCVVP-LDSQWGSFYEEKKKKeetffykeA--------VffTKKEIKEMIS 177
                                       *************************87777.555556666666644431122211........1235556666555 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.2e-05     0.081      14     102 ..      47     128 ..      38     138 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.2e-05
                              MetW  14 gsrvldlGcGdGellellkeekqvdgrGleldeegvaecvakGlsviqgdldkdlenfedksfdyvvlsqtlqatrn 90 
                                        s  l++G G G + + l+        G++ + ++++ + +kG++vi+  ++      +d+sf+ + l  tl  + +
  gi|385805195|ref|YP_005841593.1|  47 ISPCLEIGVGTGRFAKPLNV-----EFGIDPSVSSLKISAEKGIEVIRATAE--YLPLRDESFNTAYLIVTLCFVED 116
                                       57789999999999999844.....57999*****************98876..45679****************** PP

                              MetW  91 pkevldellrig 102
                                       p++ l e +ri 
  gi|385805195|ref|YP_005841593.1| 117 PNRTLLEAFRIL 128
                                       **********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); 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: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1433.21
//
Query:       gi|385805196|ref|YP_005841594.1|  [L=273]
Description: putative signal transduction protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-22   78.7   4.0    5.1e-08   33.2   0.1    4.2  4  CBS       CBS domain
  ------ inclusion threshold ------
      0.054   13.4   0.1       0.11   12.4   0.1    1.5  1  DUF502    Protein of unknown function (DUF502)


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 !   24.3   0.1   3.5e-09   3.1e-05      16      55 ..      20      59 ..       5      61 .. 0.77
   2 !   33.2   0.1   5.7e-12   5.1e-08       6      56 ..      88     137 ..      83     138 .. 0.93
   3 !    8.6   0.0   0.00029       2.6       3      55 ..     146     197 ..     145     199 .. 0.86
   4 !   11.5   0.0   3.5e-05      0.31       8      56 ..     224     270 ..     214     271 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 3.5e-09
                                      SBHHHHHHHHHHHT.SSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS 16 ttleealelmrekg.vsrlPVVdedgklvGivtlrDllral 55
                                      ++l  + ++m +++  +++ +Vd++g+  G+v+ rD+++a+
  gi|385805196|ref|YP_005841594.1| 20 DSLLAVSREMLKRNrNHSI-IVDDSGRAWGVVSIRDIAKAI 59
                                      6777777887644434599.*******************98 PP

  == domain 2  score: 33.2 bits;  conditional E-value: 5.7e-12
                                       BSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   6 trdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                       ++++++++ +++l ++++l+++k+++ +PV+ e++++ G + +r ll+a++
  gi|385805196|ref|YP_005841594.1|  88 SSPIISLNIESSLDDVIDLLVNKNIGFVPVI-ENNEIMGAIDERNLLKAIP 137
                                       789**********************999***.8999*************97 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.00029
                                       HHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   3 dimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       +++ +++ +v+ d+ +  a+ lm ++gv +l+V+   +++ G+ +l  +l ++
  gi|385805196|ref|YP_005841594.1| 146 EVPAPEPQSVDFDEEILVAVGLMLSTGVKQLLVMK-GEEIYGMTSLLKILYYV 197
                                       577889999999999****************9995.445***99999998776 PP

  == domain 4  score: 11.5 bits;  conditional E-value: 3.5e-05
                                       SCEEEETTSBHHHHHHHHHHHTSSEEEE.EETTTBEEEEEEHHHHHHHHH CS
                               CBS   8 dvvtvppdttleealelmrekgvsrlPV.VdedgklvGivtlrDllrall 56 
                                       ++  ++ + +l+ea+ l+  +++++++V +  +g  v i+++rDll++ll
  gi|385805196|ref|YP_005841594.1| 224 NPWQIDCTYSLKEAASLIYFERLGAVLVrI--NG-SVKIISDRDLLKVLL 270
                                       5556777889*******9634488886655..89.9***********986 PP

>> DUF502  Protein of unknown function (DUF502)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   1.2e-05      0.11       7      62 ..     162     218 ..     160     228 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.2e-05
                            DUF502   7 illvGllasnligrkllklgerllkriPlvksiYsalkq.vvetfsseekksfrevv 62 
                                       +++vGl++s+ + + l+  ge++   + l+k +Y +l +  v+++++ ++k ++e+v
  gi|385805196|ref|YP_005841594.1| 162 LVAVGLMLSTGVKQLLVMKGEEIYGMTSLLKILYYVLSEhSVDLLLKGSRKPVEEMV 218
                                       789*******************************99876367888888888888866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        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 0.28s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1672.44
//
Query:       gi|385805197|ref|YP_005841595.1|  [L=253]
Description: beta-lactamase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-23   83.0   0.0    2.3e-23   82.8   0.0    1.1  1  Lactamase_B_2  Beta-lactamase superfamily domain
    4.9e-12   46.3   0.1      8e-12   45.6   0.0    1.5  2  Lactamase_B    Metallo-beta-lactamase superfamily
  ------ inclusion threshold ------
      0.035   13.2   0.0      0.067   12.3   0.0    1.4  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 !   82.8   0.0   3.8e-27   2.3e-23       3     201 .]      32     219 ..      30     219 .. 0.87

  Alignments for each domain:
  == domain 1  score: 82.8 bits;  conditional E-value: 3.8e-27
                                       EEES--TTHHHH.HTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC.....C--EE..EEEEEEHHHHHHCC CS
                     Lactamase_B_2   3 iLiDagpdlrqq.alralqPvelrdelppidaVllthaHyDHlaglltlre.....lrpkk..lplyapkgvlavle 71 
                                       +LiD+g +      +r          l++ida+++th H+DH+ gl+ l        r  +  l++++p g+ + ++
  gi|385805197|ref|YP_005841595.1|  32 LLIDCGVGCHYRlGER--------GLLKEIDAIFITHYHMDHFLGLPELLFqahieKR--SkpLKIIGPNGIESMIR 98 
                                       79******54332234........44899*******************9987775433..3469************* PP

                                       TTCGHHHCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEE.CTTEEEEEESS-S--- CS
                     Lactamase_B_2  72 anfvylaleeepavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlrie.gggkrvyyigDtgyip 147
                                       +  + l+++  +  +v++++ +e+ +l+  +  +t++pa+  +         + +Gl i  + g+++ ++ Dt +  
  gi|385805197|ref|YP_005841595.1|  99 TAAPHLFSNISFSFSVETVKVHETYKLN--D--LTLIPAPACHTI-------ESYGLKILdKRGNSLGFSSDTSEPC 164
                                       ***************************9..4..777888887777.......77***998799***********999 PP

                                       HHHHHHHCT-SEEEEE-S-SSTTHHHH...HHT---STSHHHHCTTSSSSEEEEESB CS
                     Lactamase_B_2 148 eeigerlggadllllditayeddemir...hmgHltpeeaveaaadlgakrlvliHi 201
                                       e++   l+g++ l++++t+ e ++  +   + gH+t+ ea+eaa+++ga++l+l Hi
  gi|385805197|ref|YP_005841595.1| 165 ESLISVLKGVKYLVHEATCDERNK--DlchKYGHSTVLEAIEAAKAIGAEKLILNHI 219
                                       9999*************9777655..35689*************************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 !   45.6   0.0   1.3e-15     8e-12       8      78 ..      22      86 ..      19     182 .. 0.88
   2 ?   -3.6   0.0       1.6   9.5e+03      64      87 ..     190     213 ..     186     220 .. 0.56

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 1.3e-15
                                      EEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHH CS
                       Lactamase_B  8 syliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaee 78
                                      s ++  +++++LiD+G++  + +       ++  +k++da+++TH+H DH+ gl++l  ++ + ++  +++
  gi|385805197|ref|YP_005841595.1| 22 SSVVFSEETALLIDCGVGCHYRLG------ERGLLKEIDAIFITHYHMDHFLGLPELLFQAHIEKRSKPLK 86
                                      557779*****************9......79*************************99998887776665 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.6
                                       CTTHHCCEETCCEHHHHCCHCHHH CS
                       Lactamase_B  64 lveatdvpvgavaeeapalfmeea 87 
                                       l+++++  ++ +a+ea++ ++ e+
  gi|385805197|ref|YP_005841595.1| 190 LCHKYGHSTVLEAIEAAKAIGAEK 213
                                       555556555555555555544443 PP

>> PDEase_II  cAMP phosphodiesterases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.1e-05     0.067      79     131 ..      51     107 ..      44     135 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.1e-05
                                       HTEEEEE-S---GGGTHHH..HHHGGGGGS-S.--.EEE..EE-HHHHHHHHHHTBSS CS
                         PDEase_II  79 nniksylItHsHLDHvsgl..vinSaefykaqlkk.kti..vGlpytInalqkhlFNn 131
                                       ++i   +ItH H+DH  gl  ++  a+++k  +k+ k+i   G ++ I +   hlF n
  gi|385805197|ref|YP_005841595.1|  51 KEIDAIFITHYHMDHFLGLpeLLFQAHIEKR-SKPlKIIgpNGIESMIRTAAPHLFSN 107
                                       578899************9778999999998.55526664447888999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1574.93
//
Query:       gi|385805198|ref|YP_005841596.1|  [L=490]
Description: ABC-type carbohydrate transport system, substrate-binding component [Fervidicoccus fontis Kam940]
Scores for complete 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-26   92.1   6.1      1e-25   91.3   6.1    1.3  1  SBP_bac_1   Bacterial extracellular solute-binding protein
    7.4e-24   85.0   6.1      1e-23   84.6   6.1    1.2  1  SBP_bac_8   Bacterial extracellular solute-binding protein
     0.0015   18.3   0.0        1.5    8.5   0.0    2.2  2  SBP_bac_11  Bacterial extracellular solute-binding protein


Domain annotation for each model (and alignments):
>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.3   6.1   1.8e-29     1e-25      10     312 ..      66     391 ..      60     394 .. 0.84

  Alignments for each domain:
  == domain 1  score: 91.3 bits;  conditional E-value: 1.8e-29
                                       HHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEECGGHHHHHHHTTSBECCHHHHHHTTECTT CS
                         SBP_bac_1  10 lqalvakafekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviavdndwiarlakaglllpldpyvkaylapgv 86 
                                       + ++va++f+ ++pg+++++++v++g+l     + + + ++ +D+i+  +++ ++l  + +ll++ py+ +   +  
  gi|385805198|ref|YP_005841596.1|  66 YVQMVANDFMSKNPGVTIQVQPVPFGQLVSTALTSLRNQNPSPDLIIYYPSQASTL--GPYLLDVRPYFTKGVFNLS 140
                                       45677799********************************999*****88888876..79************99998 PP

                                       CCTEEEEHHHHTHHHHCE.EE...ES.EEEE.E.EEEEEEETTTHH..........CTTGGG....SHBHHHHHHHH CS
                         SBP_bac_1  87 kdaadklsssvlpkilds.kv...ly.vPly.a.argliYNkdlfe..........kagldp....pwtWdelveaa 142
                                       +   + l     ++ lds ++   +  vP++    ++liY k++fe          k+g d     + tWd l++ a
  gi|385805198|ref|YP_005841596.1| 141 DIPPSTL---LPAYLLDSqGGvvkISgVPFQqVfGYVLIYQKSIFEnqtlanefksKYGFDFdptkWDTWDKLIDGA 214
                                       8877776...4455566655589*******************************99666666777777********* PP

                                       HHHHHHCTCTHCCHCCEEHHHHHHHHHHHHHHHHTGGGEECCCT........................HHCSHHHHS CS
                         SBP_bac_1 143 kklkekgkkpiggarggsasgtayyfalalakslggkvfdkdgg........................gldnpegvt 195
                                       + +  ++ ++       +a+   + +++ +++++ + +++   +                          +n + v 
  gi|385805198|ref|YP_005841596.1| 215 QFIQSQNITK-------YALLFPDGLTQSIFNGYVSIFYTYAINdpctqvpqssqqgipvqgywaffkL-VNKTIVP 283
                                       **********.......5555555556666666666666666666777777777777777777767962.4444444 PP

                                       ...HHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHHHHHTTSCSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEE CS
                         SBP_bac_1 196 ...aatylvklyavanltkelkgkgaenkdgaaalalfeaGeaamaivglwaalaamkvapkvafaadkekpkeelg 269
                                           ++ +++l+ ++ l + +++ + +    +++++lf +G+ am  ++++         +    +a+ +k+ +++g
  gi|385805198|ref|YP_005841596.1| 284 tinCTAGVQALETYKQLIQFQPPIDQQAMEYDQLRDLFLTGDYAMVAAWTSF--------IPIYNNASLSKVAGNIG 352
                                       4666666666666677779**************************9999887........899************** PP

                                       EECEEBETTTTSEEEEEEEEEEBTTCSTHHHHHHHHHHHTSHH CS
                         SBP_bac_1 270 vaplPagkggkpgilgayglaipkgsknpeaAkkFldfllspe 312
                                       +aplP + +g         ++i+ +sknp+ A +F++f+++++
  gi|385805198|ref|YP_005841596.1| 353 IAPLPSVATGQ----APTFIGINPNSKNPDLAADFIAFMTTAQ 391
                                       **********8....7899*********************987 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 !   84.6   6.1   1.7e-27     1e-23       2     265 ..      70     406 ..      69     425 .. 0.72

  Alignments for each domain:
  == domain 1  score: 84.6 bits;  conditional E-value: 1.7e-27
                                       HHHHHHHH-.TEEEEEEE--SSSHHHHHHHHHHTT---SEE.EEE-HHHHHHHHHTTSB--GG.....GSTTHHH-H CS
                         SBP_bac_8   2 lakefekkt.gvkvnvvtaasndleqklkaalaagtapdidvvwanedalatlaeeglladls.....dldnlddlt 72 
                                       +a++f  k+ gv+++v++++ ++l++++ ++l   + p++d+++ + ++++tl    +l d+       + nl d++
  gi|385805198|ref|YP_005841596.1|  70 VANDFMSKNpGVTIQVQPVPFGQLVSTALTSLRNQN-PSPDLIIYYPSQASTLGP--YLLDVRpyftkGVFNLSDIP 143
                                       6899****************************8666.899*************97..77777666665445555543 PP

                                       H..HHHTT.....--TS.----EEEEEEE-EEEEEHHHHHH...S..............---BHHHHHHHHHHH... CS
                         SBP_bac_8  73 d..alaav.....gydgklygvPyasetpyvliynkdllek...a.............edpktwdellaaakkl... 123
                                       +   l a+     g+  k+ gvP+++  +yvliy k+++e    a              +++twd+l + a+ +   
  gi|385805198|ref|YP_005841596.1| 144 PstLLPAYlldsqGGVVKISGVPFQQVFGYVLIYQKSIFENqtlAnefkskygfdfdpTKWDTWDKLIDGAQFIqsq 220
                                       333333333322255556*********************98666267778899998888999999999955533332 PP

                                       .HHH-......SEGG---G..GGGGGTHH..................ETTEE---H..HHH..........HHHHHH CS
                         SBP_bac_8 124 .kgkf......glpdpasg..wlqaalla..................kdgksldddggkdgl.........kealel 164
                                          k+      gl+++  +  + +++ +a                  ++++ + + + ++++         ++ale 
  gi|385805198|ref|YP_005841596.1| 221 nITKYallfpdGLTQSIFNgyVSIFYTYAindpctqvpqssqqgipvQGYWAFFKLV-NKTIvptinctagVQALET 296
                                       125557767775555553333336666667777777777776666665777776664.3344677788555555555 PP

                                       HHHHHHTT-....EE-S..--SSTTTTTSBSEEEE-TTHHHHHH.....-TTTSEEEE--S-.-EEEEEEEEEEBTT CS
                         SBP_bac_8 165 lkklkdngk....tydtgadavsefanGevaftingswdiaaaq.....kagkklgaivpkq.gsfaggkglavpkn 231
                                       +k+l +       +   ++++ ++f +G++a++ ++++ i  ++     k   ++g++++++ ++ +  +++ ++ n
  gi|385805198|ref|YP_005841596.1| 297 YKQLIQFQPpidqQAMEYDQLRDLFLTGDYAMVAAWTSFIPIYNnaslsKVAGNIGIAPLPSvATGQAPTFIGINPN 373
                                       5555422222223446789****************998766555333666678*****765414555556799**** PP

                                       S-HHHHHHHHHHHHHTTSHHHHHHHHHH---BS- CS
                         SBP_bac_8 232 aknedlaAldFlkwltspenqaalaektgyipvn 265
                                       +kn+dl A+dF+ ++t+++  ++ ae +g+ p++
  gi|385805198|ref|YP_005841596.1| 374 SKNPDL-AADFIAFMTTAQEYKKGAELYGFMPAT 406
                                       *****9.**********************98865 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 !    8.5   0.0   0.00025       1.5      12      52 ..      66     112 ..      59     120 .. 0.77
   2 !    7.6   0.1   0.00048       2.9     105     219 ..     279     391 ..     216     402 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00025
                                       HHHHHHHHH.HHHH---EEEEESSHHHHHHHH....HHH...-SEEE CS
                        SBP_bac_11  12 alrelaaaF.eahtgvkvevsaggsgklarqi....adga.rpDvwi 52 
                                        ++ +a++F ++++gv+++v+ ++ g+l+++     ++++  pD++i
  gi|385805198|ref|YP_005841596.1|  66 YVQMVANDFmSKNPGVTIQVQPVPFGQLVSTAltslRNQNpSPDLII 112
                                       56679****8889***************9976444333336788766 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00048
                                       -EEEE--T-TTTTHH.HHHHGGG--HHHHHHHHHTEEEEESSHHHHHHHHHTTT-SEEEEEHHHH......H..HST CS
                        SBP_bac_11 105 klavadPttspsGlaalalleaagaqellkalekkvvklgessrqlltaveageadagivyesea......kaaeng 175
                                       k +v++  + ++G +al++++++       +++  + +++  ++ql + + +g+++++ ++ s +       + + +
  gi|385805198|ref|YP_005841596.1| 279 KTIVPTI-NCTAGVQALETYKQLI------QFQPPIDQQAMEYDQLRDLFLTGDYAMVAAWTSFIpiynnaSLSKVA 348
                                       4444443.3355555555555543......34444445555667888889999999999996655544332445778 PP

                                       TSSEEEE--TTT--...EEEEEEEE-TT--HHHHHHHHHTTSHH CS
                        SBP_bac_11 176 dkleavylpeglnldpldypaavlkkaakreaAraFlafLrspe 219
                                       +++ + +lp       ++  +++  +++++  A++F+af+++++
  gi|385805198|ref|YP_005841596.1| 349 GNIGIAPLPSVATG-QAPTFIGINPNSKNPDLAADFIAFMTTAQ 391
                                       88888888888887.5666677788899************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (490 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       747  (0.0416643); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.46
# Mc/sec: 3187.41
//
Query:       gi|385805199|ref|YP_005841597.1|  [L=563]
Description: ABC-type carbohydrate transport system, permease component [Fervidicoccus fontis Kam940]
Scores for complete 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-22   77.9  47.0      3e-14   53.2  17.7    4.7  4  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.2     0.024   4.4e+02     106     146 ..      12      50 ..       4      58 .. 0.59
   2 !   39.0  21.3   3.8e-14   6.8e-10      13     176 ..      67     263 ..      59     266 .. 0.86
   3 ?   -4.4  10.6      0.76   1.4e+04      23     174 ..     297     363 ..     288     367 .. 0.52
   4 !   53.2  17.7   1.7e-18     3e-14       3     174 ..     368     547 ..     366     555 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.024
                      BPD_transp_1 106 alppiitglilafggllggavlleflgswpGlgtllleail 146
                                       +lp i+  li+++  ++ +++l +++  +p lg+l+ + ++
  gi|385805199|ref|YP_005841597.1|  12 SLPAIAYILIFTIYPIVSNFILSLYTQ-DP-LGRLIYTGLE 50 
                                       455666666666666666665555555.33.6666665555 PP

  == domain 2  score: 39.0 bits;  conditional E-value: 3.8e-14
                      BPD_transp_1  13 nkkldkllrpliivllslPsfv.........laillvlvf.......................vilsilghlilpvi 57 
                                       n  l  + +p+i++++++P  v         l+++++ +f                         ++ l ++i+ v+
  gi|385805199|ref|YP_005841597.1|  67 NTLLYMFATPIIDIIFAIPLAValkrvgskwLFLIMLPAFippvtaasmwylminpffgvayyLTKTNLASSIWTVV 143
                                       566778888899999999999988998888755555555578888888888888999*****999999********* PP

                      BPD_transp_1  58 illllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgsw 134
                                       ++ ++ ++p+++li++++l s+pk+   aa  +G+   ++f+ + lP++ p i+t ++l ++  l  +  +++ +s+
  gi|385805199|ref|YP_005841597.1| 144 LIDVWRSLPMATLIIYSGLVSIPKEIQHAASSDGLAGAKRFFMIDLPLISPQILTAFVLMMITGLFTFDPIYIGTSQ 220
                                       *********************************************************************99999988 PP

                      BPD_transp_1 135 pGlgtllleailgydyseis...nggvlalviavlllnlvadilq 176
                                          g ++l+ + +y +++ +    g+++a+++++ ll++++ i++
  gi|385805199|ref|YP_005841597.1| 221 --AGPRILDNLAYYAFDQFYsgvPGYAAAIIVLMSLLSTALAIIY 263
                                       ..5777777777777765556777888888888888888888876 PP

  == domain 3  score: -4.4 bits;  conditional E-value: 0.76
                      BPD_transp_1  23 liivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrslpkdlveaaralGasrwqifr 99 
                                       ++ +                                                                         
  gi|385805199|ref|YP_005841597.1| 297 IYLA------------------------------------------------------------------------- 300
                                       3344......................................................................... PP

                      BPD_transp_1 100 kvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseisnggvlalviavlllnlvadi 174
                                                  + ++++ +++++   + +e++   p+l +++  +  ++d+ +++  +++++++av+ +n+++ +
  gi|385805199|ref|YP_005841597.1| 301 -----------FFLIPMYWIINIALKTPIELIS-IPPLLYPRSVTFANFDLMFTQGLPYIITTLAVASINTLITL 363
                                       ...........4444444444444444444444.55566666666666666666666666666666666666655 PP

  == domain 4  score: 53.2 bits;  conditional E-value: 1.7e-18
                      BPD_transp_1   3 llGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrsl 79 
                                       +l++ +a  ++k++   l+++i  l ++P+++ +i+++++++il ++ ++++++i+++ ++++p++++i++++    
  gi|385805199|ref|YP_005841597.1| 368 PLAYSMA--SHKFGGSKLLIYILYLNATPTLIYIIPIFAFLKIL-GIINTWWALILTYPIMTIPITTWIMYNYYLKF 441
                                       6777888..9999999999*************999988655555.6668**************************** PP

                      BPD_transp_1  80 pkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG.........lgtllleailg 147
                                       pk+ +eaa ++G++r ++f+k vlP++ + +   +i+af +++g+ ++++ ++ +++                   g
  gi|385805199|ref|YP_005841597.1| 442 PKQIEEAAQMDGMNRLKVFYKMVLPLSRSGLSVAAIYAFLYSWGALIFPLAFT-YSPydlskplsfS---------G 508
                                       *************************************************9999.5553433333331.........3 PP

                      BPD_transp_1 148 ydyseis............nggvlalviavlllnlvadi 174
                                        ++ +i              g+++a+vi+ ++ ++++++
  gi|385805199|ref|YP_005841597.1| 509 AQTFSIFigllmspvsmsyGGVAAAGVISSIPSLVLLYF 547
                                       333333345566666677455555555555555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (563 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      184  (0.0102627); 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):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.53
# Mc/sec: 3205.84
//
Query:       gi|385805200|ref|YP_005841598.1|  [L=329]
Description: ABC-type carbohydrate transport system, ATPase component [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-33  115.6   0.0    4.9e-32  111.3   0.0    2.2  2  ABC_tran       ABC transporter
    1.8e-09   37.7   0.0    4.1e-09   36.5   0.0    1.7  1  TOBE_2         TOBE domain
    7.9e-07   29.2   0.3      0.019   14.8   0.0    2.5  2  AAA_21         AAA domain, putative AbiEii toxin, Type IV TA 
    4.5e-06   26.3   0.1     0.0011   18.5   0.1    2.3  2  SMC_N          RecF/RecN/SMC N terminal domain
     0.0018   17.0   0.0      0.022   13.4   0.0    2.1  2  AAA_13         AAA domain
  ------ inclusion threshold ------
      0.044   13.5   0.0       0.11   12.2   0.0    1.6  2  AAA_30         AAA domain
      0.049   14.1   0.2       0.14   12.6   0.0    1.8  2  AAA_23         AAA domain
       0.12   11.4   0.0       0.17   10.9   0.0    1.1  1  Lycopene_cycl  Lycopene cyclase protein
       0.15   12.5   0.7        2.1    8.8   0.7    2.4  1  AAA            ATPase family associated with various cellular
       0.15   12.3   0.5       0.49   10.7   0.5    2.1  1  AAA_22         AAA domain
       0.16   11.6   0.0        0.3   10.7   0.0    1.3  1  AAA_27         AAA domain
       0.16   11.7   0.0       0.32   10.8   0.0    1.4  1  AAA_29         P-loop containing region of AAA domain
       0.25   11.6   0.5        4.2    7.7   0.1    2.7  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 !  111.3   0.0   3.6e-35   4.9e-32       7     136 ..      23     159 ..      18     160 .. 0.90
   2 ?    1.6   0.0      0.26   3.6e+02      98     125 ..     291     319 ..     274     322 .. 0.74

  Alignments for each domain:
  == domain 1  score: 111.3 bits;  conditional E-value: 3.6e-35
                                       EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.... RF
                          ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.... 79 
                                       ++ke +  +++G++G+GK+t l+l+agl+ p+eG+i ldg d+++   + +++ ig ++q+  l p+lt++en    
  gi|385805200|ref|YP_005841598.1|  23 TFKEKSYNVVLGSSGSGKTTTLRLIAGLELPDEGKIILDGVDITN--VPAWKRDIGLVFQNYALYPHLTAYENisvp 97 
                                       788899999***********************************9..****************************** PP

                                       .........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       .........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  80 .........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                + de+++++++ lg++      +++ p++LSgGq+qrva+aral+k+pk+lllDEp 
  gi|385805200|ref|YP_005841598.1|  98 lkikkldrkTIDEKVKNVAEILGISS----ELHKYPHQLSGGQQQRVAIARALVKEPKILLLDEPL 159
                                       ***98666666666777777777766....555566*****************************7 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.26
                                       TCBGESTTS.GGS-HHHHHHHHHHHHHHH CS
                                       xxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  98 kdtvvkssp.ssLSgGqkqrvalarallk 125
                                       +  +v+  p +++S+Gqk+ +++ r l+ 
  gi|385805200|ref|YP_005841598.1| 291 HSVIVRVLPsEEISEGQKVGISIPRDLML 319
                                       444555555789**********9998876 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.0     3e-12   4.1e-09       1      72 [.     251     317 ..     251     321 .. 0.91

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 3e-12
                            TOBE_2   1 laiRPEklrlaaagg.anglsGtVedveylGsstryvvelaggqlvvvrqpnadrdsalapGdtVelswdpdd 72 
                                       ++ RPE+ ++      ++ +sG Ve+++ylG++ ++ +++++   v+vr+ +++    + +G++V++s++ d 
  gi|385805200|ref|YP_005841598.1| 251 VGFRPEDAEI---VNtDGDISGLVEEIQYLGAYKLLEISIDEKHSVIVRVLPSE---EISEGQKVGISIPRDL 317
                                       678*******...553679***********************************...9**********98875 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   8.2e-05      0.11       2      22 ..      30      50 ..      29      74 .. 0.79
   2 !   14.8   0.0   1.4e-05     0.019     234     299 ..     129     192 ..      98     197 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.2e-05
                            AAA_21  2 nvliGpNgsGKSnLLdaldll 22
                                      nv+ G  gsGK++ L+++ +l
  gi|385805200|ref|YP_005841598.1| 30 NVVLGSSGSGKTTTLRLIAGL 50
                                      9*****************999 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.4e-05
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSp 299
                                       +++lS G+++  a++ al   +   ++ll+DEp ++L+ +l  ++  +lkel+r  +  vi +TH+ 
  gi|385805200|ref|YP_005841598.1| 129 PHQLSGGQQQRVAIARALVKEP---KILLLDEPLSNLDARLRLEVRVFLKELQRkLNMTVIHVTHDQ 192
                                       5788999999978888888777...9*************9999999999999998999999999985 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.0    0.0074        10      23      40 ..      26      43 ..       7      49 .. 0.85
   2 !   18.5   0.1     8e-07    0.0011      97     205 ..      94     196 ..      66     211 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0074
                                      TSSEEEEEESTTSSHHHH CS
                                      xxxxxxxxxxxxxxxxxx RF
                             SMC_N 23 sksftaivGpNGSGKsnl 40
                                      +ks ++++G+ GSGK+  
  gi|385805200|ref|YP_005841598.1| 26 EKSYNVVLGSSGSGKTTT 43
                                      6789***********975 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 8e-07
                                       EEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  97 vsisrrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDe 173
                                       +s+  ++k+ +  + +i++k  + +e+  + ++ + ++++LSgG+++ va+a       vk   + llDe  ++LD+
  gi|385805200|ref|YP_005841598.1|  94 ISVPLKIKKLD--RKTIDEKVKNVAEILGISSELHKYPHQLSGGQQQRVAIARA----LVKEPKILLLDEPLSNLDA 164
                                       44444444444..36799999999999999999999999********9998754....46777799*********** PP

                                       HHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 174 knvkkvaellkeksknaQfivislreemleka 205
                                       + + +v  +lke + +  + vi +++++ e +
  gi|385805200|ref|YP_005841598.1| 165 RLRLEVRVFLKELQRKLNMTVIHVTHDQEEAM 196
                                       ***********998886666655544443333 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   1.6e-05     0.022      16      42 ..      27      53 ..      11      83 .. 0.83
   2 ?    1.2   0.0      0.08   1.1e+02     524     569 ..     147     190 ..     139     204 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.6e-05
                            AAA_13 16 kriNliYGwNGaGKTtLSrllrslelg 42
                                      k +N++ G+ G+GKTt  rl++ lel 
  gi|385805200|ref|YP_005841598.1| 27 KSYNVVLGSSGSGKTTTLRLIAGLELP 53
                                      78*********************9874 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.08
                            AAA_13 524 igkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTH 569
                                       +++ ki  +D P S LD+     v +++k+    +k    ++  TH
  gi|385805200|ref|YP_005841598.1| 147 VKEPKILLLDEPLSNLDARLRLEVRVFLKELQ--RKLNMTVIHVTH 190
                                       56899**************9999999999986..344444555566 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   7.8e-05      0.11      12      40 ..      21      49 ..      14      64 .. 0.82
   2 ?   -2.5   0.0       2.6   3.6e+03      79      96 ..     131     157 ..     111     196 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.8e-05
                            AAA_30 12 alltsgdrvavltGpAGtGKttalkalre 40
                                      + + +++ + v+ G  G+GKtt+l+ ++ 
  gi|385805200|ref|YP_005841598.1| 21 EYTFKEKSYNVVLGSSGSGKTTTLRLIAG 49
                                      5556677899***************9976 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.6
                            AAA_30  79 rlk.........grarlepgtllivDE 96 
                                       +l          +ra +++ ++l+ DE
  gi|385805200|ref|YP_005841598.1| 131 QLSggqqqrvaiARALVKEPKILLLDE 157
                                       444555555554434444445555555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0    0.0001      0.14       2      39 ..       3      47 ..       2      50 .. 0.74
   2 ?   -1.3   0.0       1.9   2.6e+03     115     131 ..     109     127 ..      83     194 .. 0.49

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0001
                            AAA_23  2 Lkienfrsf.rdqeidF......skgltlItGpNGaGKTTildAi 39
                                      L++en+r+  + +e+        +k  +++ G  G+GKTT l+ i
  gi|385805200|ref|YP_005841598.1|  3 LRLENLRKRyGQFELRIeeytfkEKSYNVVLGSSGSGKTTTLRLI 47
                                      67777776534445444445559999***************9987 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.9
                            AAA_23 115 deleqfisellgskki..i 131
                                       de+ +++ e+lg++ +   
  gi|385805200|ref|YP_005841598.1| 109 DEKVKNVAEILGISSElhK 127
                                       3333333333333322221 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   0.0   0.00012      0.17      99     181 ..     175     257 ..     159     267 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00012
                     Lycopene_cycl  99 engvklleakvesveeeeageslvvleggrki..rarlvvdarglaslkkarrlglQtfyGvevevdnppfdldkmv 173
                                       ++  + l+ +v +v+++++    ++++++  i   +++v d++++   +k++++ + tf G+   + ++ f++d ++
  gi|385805200|ref|YP_005841598.1| 175 KELQRKLNMTVIHVTHDQE--EAMAIADNIVIlnSGKIVQDGSPAEIYRKPKNTFIFTFIGLSNLLPASFFGIDDAD 249
                                       455667899********99..55566666655335789******99999**************************** PP

                     Lycopene_cycl 174 lMDfrveq 181
                                       l  fr e+
  gi|385805200|ref|YP_005841598.1| 250 LVGFRPED 257
                                       *9999554 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.7    0.0015       2.1       3      74 ..      32     165 ..      31     199 .. 0.50

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0015
                                       EESSTTSSHHHHHHHHHHH............HTHE..............................EEEEETTTCSSS CS
                               AAA   3 lyGppGtGKTllakavake............lgve..............................fleisgsellsk 37 
                                       + G  G GKT++ + +a              +  +                                          
  gi|385805200|ref|YP_005841598.1|  32 VLGSSGSGKTTTLRLIAGLelpdegkiildgV--DitnvpawkrdiglvfqnyalyphltayeniS----------V 96 
                                       67999***********9975444333333220..12233344444444444444444555534431..........0 PP

                                       ...............................STTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHH CS
                               AAA  38 ...............................yvgesekkirelfkeakeka.kpsilfiDEidalaksr 74 
                                                                      y  + +   ++ ++ a++   +p+il++DE  +   +r
  gi|385805200|ref|YP_005841598.1|  97 plkikkldrktidekvknvaeilgisselhkYPHQLSGGQQQRVAIARALVkEPKILLLDEPLSNLDAR 165
                                       333333444444444555555555555555544444444444443333333457888888855555555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.5   0.00036      0.49       8      28 ..      30      50 ..      22     193 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00036
                            AAA_22  8 lvvtGesGtGKTtllrrlleq 28
                                       vv G sG+GKTt+lr ++  
  gi|385805200|ref|YP_005841598.1| 30 NVVLGSSGSGKTTTLRLIAGL 50
                                      5899***********988754 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   0.00022       0.3       3      47 ..       5      48 ..       2      51 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00022
                            AAA_27  3 lerLdLeryGkftdrsldfsaeeadlhliyGpNEAGKstalrAis 47
                                      le+L+ +ryG+f+ r  ++  +e++  +++G+  +GK+t+lr i 
  gi|385805200|ref|YP_005841598.1|  5 LENLR-KRYGQFELRIEEYTFKEKSYNVVLGSSGSGKTTTLRLIA 48
                                      55554.79*****998888888*******************9765 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   0.00023      0.32      16      39 ..      21      44 ..      13      55 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00023
                            AAA_29 16 tieidlkgatlltGpsGsGKSTll 39
                                      ++++++k+  ++ G sGsGK+T l
  gi|385805200|ref|YP_005841598.1| 21 EYTFKEKSYNVVLGSSGSGKTTTL 44
                                      567887888999*********976 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       2.1   2.8e+03       9      43 ..      12      45 ..       6      51 .. 0.59
   2 ?    7.7   0.1     0.003       4.2      31      81 ..     130     167 ..     105     176 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.1
                           SbcCD_C  9 ylsfevevrdedgkekelsrssgtlSGGekqflay 43
                                      y +fe+++++ + ke + ++ + + SG  k +++ 
  gi|385805200|ref|YP_005841598.1| 12 YGQFELRIEEYTFKE-KSYNVVLGSSGSGKTTTLR 45
                                      556777777556555.4466777777766644443 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.003
                           SbcCD_C  31 gtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesi 81 
                                        +lSGG++q    +a+a a   l        + +++++LDE  s+lD++ +
  gi|385805200|ref|YP_005841598.1| 130 HQLSGGQQQR---VAIARA---L-------VKEPKILLLDEPLSNLDARLR 167
                                       5666666632...233322...2.......2358999*********99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       751  (0.0418874); expected 358.6 (0.02)
Passed bias filter:                      631  (0.0351944); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); 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: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2146.90
//
Query:       gi|385805201|ref|YP_005841599.1|  [L=332]
Description: phosphoesterase, DHHA1 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-07   31.5   0.0    4.7e-07   30.3   0.0    1.6  1  DHHA1     DHHA1 domain
       0.01   16.1   0.2      0.038   14.2   0.1    1.9  2  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 !   30.3   0.0   5.2e-11   4.7e-07      19     120 ..     200     287 ..     185     301 .. 0.69

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 5.2e-11
                                       HHHHHHHHHHHHHHTCEEEC....TCEEEEEECHCCHHHHHHHHHHHHHHTHGBT.TCEEEEEEEECTEEEEEEEES CS
                             DHHA1  19 kealaklkaeellekaeevk....gvkvlvaevgeewdagalgiaadklksklkk.pvivfvakeegdkvkvsarsk 90 
                                        ++++ + +  + ekae+++    + +++++   ++  +     +a +l s   +   iv+v+ +   + k  +rsk
  gi|385805201|ref|YP_005841599.1| 200 DREIELMGF--YREKAEDINiegiKLTFVFKSH-NDLSTS---MLAQYLMS--VRnSDIVVVVDK---RGKYEFRSK 265
                                       555555554..5566777777633333444444.444444...44666666..553777777766...55999**** PP

                                       SHSS-HHHHHHHHHHHTTCCEEEETCEEEE CS
                             DHHA1  91 kdgvdagelakeaaaklgggGGGHdlAaGa 120
                                         + +++e+a +      +gGGGH+ A+Ga
  gi|385805201|ref|YP_005841599.1| 266 --KCNVREIAFK------LGGGGHPEASGA 287
                                       ..9*********......***********8 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.1   4.3e-06     0.038       5      82 ..       7     128 ..       3     146 .. 0.69
   2 ?    1.3   0.1     0.044   3.9e+02       7      25 ..     125     198 ..     121     275 .. 0.52

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.3e-06
                                       E-ECSSSHHHHHH.HHHHHH.................................CECS--TCGGCGCCH.......HC CS
                                       xxxxxxxxxxxxx.xxxxxx.................................xxxxxxxxxxxxxxx.......xx RF
                               DHH   5 vghknpDtDsigS.aialan.................................llvDhneksqavege.......ak 40 
                                       + + + D+D++gS ++ ++n                                 ++ D + ++ + ++         +
  gi|385805201|ref|YP_005841599.1|   7 ISITHTDLDGVGSsSLYIRNtkpesykvifvepyqllkavksiaksdesfdelVITDIGPNASTIKEVeralekiSR 83 
                                       67899********5566666888888888888888887777777777777777566766666655554566777679 PP

                                       CCSEEEEEEE-S---S.....S---SS--EEEE-SSS-HHHHHHHHH CS
                                       xxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DHH  41 eeaedviiiDHHrlge.....efetlapilflnepvgstaeivaell 82 
                                       e++ ++   DHH  ++      +++   + ++  +  ++ e+v++ l
  gi|385805201|ref|YP_005841599.1|  84 EKGARIRWFDHHIWNNewkddLIKQG--VDLRVDENHCATEVVYRNL 128
                                       99999999999999886776533333..3334445557777777655 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.044
                                       ECSSSHHHHHHHHHHHHC.......................................................E CS
                                       xxxxxxxxxxxxxxxxxx.......................................................x RF
                               DHH   7 hknpDtDsigSaialanl.......................................................l 25 
                                       ++n  tD+i S+++ + +                                                       +
  gi|385805201|ref|YP_005841599.1| 125 YRNLNTDDIFSYMLSKSVcsadlwifndwaapflvrfvgngrgkkwleyvhsifvkspsfetlieasknkaveV 198
                                       78999999999888877433333333444444444444444444444444444444444444444444443330 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 2127.50
//
Query:       gi|385805202|ref|YP_005841600.1|  [L=100]
Description: hypothetical protein FFONT_0156 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 714.38
//
Query:       gi|385805203|ref|YP_005841601.1|  [L=102]
Description: methylated-DNA--protein-cysteine methyltransferase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.3e-22   77.5   0.0      8e-22   77.2   0.0    1.1  1  DNA_binding_1  6-O-methylguanine DNA methyltransferase, DNA b


Domain annotation for each model (and alignments):
>> DNA_binding_1  6-O-methylguanine DNA methyltransferase, DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.2   0.0   4.4e-26     8e-22       9      81 .]      10      82 ..       5      82 .. 0.94

  Alignments for each domain:
  == domain 1  score: 77.2 bits;  conditional E-value: 4.4e-26
                                      HHTTS-TT-BEEHHHHHHHTT.TSCHHHHHHHHHTSSBTTTSGGGGEEBTTSBCCTT..TTCHHHHHHHHHHTTS CS
                     DNA_binding_1  9 llrqIpyGkvttYgeiAkllgkpkaaraVgqalaanplailvPcHRVvgadgklggy..agglerkralLeaEgv 81
                                      ll+ Ip+Gkvt+Y+e++k  g   ++r Vg++l +n  +ilvPcHRVv ++g+lggy   +g e kr+lLe Egv
  gi|385805203|ref|YP_005841601.1| 10 LLQLIPPGKVTSYSELSKITG--WSPRSVGKILSKNDEPILVPCHRVVMKNGNLGGYsaFSGKEFKRRLLELEGV 82
                                      7899*****************..**********************************6656************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 732.72
//
Query:       gi|385805204|ref|YP_005841602.1|  [L=300]
Description: MRP protein-like protein [Fervidicoccus fontis Kam940]
Scores for complete 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-75  252.5   0.0    4.9e-75  252.2   0.0    1.1  1  ParA         NUBPL iron-transfer P-loop NTPase
    3.5e-15   56.2   0.0    1.9e-14   53.8   0.0    2.1  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    7.7e-10   39.0   0.1    1.4e-08   34.9   0.1    2.2  1  AAA_31       AAA domain
    1.4e-07   31.0   0.6    1.4e-07   31.0   0.6    2.2  3  ArsA_ATPase  Anion-transporting ATPase
    1.9e-06   27.5   0.1      0.048   13.1   0.0    2.3  2  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
    0.00015   21.6   0.1      0.069   13.0   0.1    2.3  2  AAA_26       AAA domain
    0.00092   18.6   0.0     0.0018   17.6   0.0    1.5  1  MipZ         ATPase MipZ
     0.0048   16.6   0.0     0.0079   15.9   0.0    1.3  1  IstB_IS21    IstB-like ATP binding protein
     0.0084   15.3   0.1      0.016   14.4   0.1    1.4  1  NB-ARC       NB-ARC domain
     0.0095   15.6   0.1      0.019   14.6   0.1    1.4  1  SRP54        SRP54-type protein, GTPase domain
  ------ inclusion threshold ------
      0.011   15.2   0.1      0.021   14.3   0.1    1.4  1  PhoH         PhoH-like protein
      0.031   14.3   0.1      0.064   13.3   0.1    1.5  1  ResIII       Type III restriction enzyme, res subunit
      0.057   13.3   0.0      0.089   12.7   0.0    1.3  1  APS_kinase   Adenylylsulphate kinase
      0.074   13.4   0.0       0.15   12.4   0.0    1.5  2  AAA_16       AAA ATPase domain
      0.077   13.4   0.0       0.17   12.3   0.0    1.6  1  AAA          ATPase family associated with various cellular a
       0.15   12.0   0.0       0.48   10.3   0.0    1.8  2  RsgA_GTPase  RsgA GTPase
       0.18   11.4   0.2       0.35   10.4   0.2    1.7  1  AAA_25       AAA domain


Domain annotation for each model (and alignments):
>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  252.2   0.0   4.6e-78   4.9e-75       1     245 [.      45     291 ..      45     292 .. 0.96

  Alignments for each domain:
  == domain 1  score: 252.2 bits;  conditional E-value: 4.6e-78
                              ParA   1 kvkkviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqs..ekkliPveakgikv 75 
                                       k+k+ i++ SgKGGVGK+ +a+++A+ L+k+g+kvg+ DaD +G  ip +lg +++++ ++  + +liP + kgi+v
  gi|385805204|ref|YP_005841602.1|  45 KIKNRIMIFSGKGGVGKTFIAASIAMYLSKMGYKVGVYDADETGSVIPFVLGNSDAEIYMEesSGELIPANIKGIQV 121
                                       589****************************************************99988754556*********** PP

                              ParA  76 mSigfllesedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqkl.plagaviVttpqevala 151
                                       mS++++l+++d++++w+G++ +k+i q l+ ++w++lD+Li D+PPGtgDe++t+ q + + + a+iV++p +++  
  gi|385805204|ref|YP_005841602.1| 122 MSLELMLKEKDSPLIWQGALRTKFILQTLALTRWEDLDFLIFDMPPGTGDEAITISQYVpSPKYAIIVSSPGKLSEG 198
                                       ***********************************************************545789************ PP

                              ParA 152 dvkkaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdegkplvlk 228
                                       +v+ka+ ++kk+++++lG+veNms+++c++ g+k+e+fgk+  e++a+++g++ lg+ipld++ire++d+g p+++ 
  gi|385805204|ref|YP_005841602.1| 199 VVRKAVVFLKKMEIPILGIVENMSHYTCDD-GSKIEVFGKSYIEEIARDHGIEALGKIPLDERIRESQDKGVPIYEL 274
                                       ****************************97.8999****************************************** PP

                              ParA 229 epeseaakaleeiaekv 245
                                       ++ se+ ++le +a+k+
  gi|385805204|ref|YP_005841602.1| 275 ASGSEIDRSLELLAKKI 291
                                       *********99999987 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 !   53.8   0.0   1.8e-17   1.9e-14       1     128 []      50     271 ..      50     271 .. 0.86

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 1.8e-17
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep....................... 54 
                                       i+i s+kGGvGKT++aa++a +l++ g++V ++DaD  ++     + l n  ++                       
  gi|385805204|ref|YP_005841602.1|  50 IMIFSGKGGVGKTFIAASIAMYLSKMGYKVGVYDADETGSVIP--FVLGNSDAEiymeessgelipanikgiqvmsl 124
                                       89***************************************98..666666666678999***************** PP

                                       .........................................................................CCHC CS
                                       .........................................................................xxxx RF
                              CbiA  55 .........................................................................dlkr 58 
                                                                                                                +   
  gi|385805204|ref|YP_005841602.1| 125 elmlkekdspliwqgalrtkfilqtlaltrwedldflifdmppgtgdeaitisqyvpspkyaiivsspgklseG--- 198
                                       ***************************************************************98886543331... PP

                                       CCHHHHHHCHCHHHH.......EEEEEEEEE.....SS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHT CS
                                       xxxxxxxxxxxxxxx.....xxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  59 llellealgkkkall.....lkiagvvlnrv.....dgeneetllkealeelkqrygvpvlgviprdeavaeaparg 125
                                          ++++ +     +     + i+g+v n+      dg++ e   k+ +ee+ +++g++ lg+ip de++ e+  +g
  gi|385805204|ref|YP_005841602.1| 199 ---VVRKAVV----FlkkmeIPILGIVENMShytcdDGSKIEVFGKSYIEEIARDHGIEALGKIPLDERIRESQDKG 268
                                       ...3333222....12223589*****99974455456666777788888888888*****************9999 PP

                                       S-H CS
                                       xxx RF
                              CbiA 126 epv 128
                                        p+
  gi|385805204|ref|YP_005841602.1| 269 VPI 271
                                       886 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.1   1.3e-11   1.4e-08       4     156 ..      50     199 ..      47     214 .. 0.73

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 1.3e-11
                            AAA_31   4 IaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekneiektlyevlieeknikeaiiktkven 80 
                                       I i   KGGvGKT  +  +a+ l+k+g+kv + D+D  ++    +     + + ++y      ++  e+i  ++++ 
  gi|385805204|ref|YP_005841602.1|  50 IMIFSGKGGVGKTFIAASIAMYLSKMGYKVGVYDADETGSVIPFV---LGNSDAEIYME----ESSGELIP-ANIKG 118
                                       788999******************************988876533...34555666643....34445544.67889 PP

                            AAA_31  81 ldlipssidLaeaeielvelekk..eeilkellekvkdeYDyiiiDcpPsLg..lltenaLvas.dsviipvqaeay 152
                                       ++++  ++ L e +  l+       + il++l  +  ++ D+ i+D+pP  g   +t++  v s  + ii+  + ++
  gi|385805204|ref|YP_005841602.1| 119 IQVMSLELMLKEKDSPLIWQGALrtKFILQTLALTRWEDLDFLIFDMPPGTGdeAITISQYVPSpKYAIIVSSPGKL 195
                                       999999999999999998655442267787777777889**********9863345555555552455666666666 PP

                            AAA_31 153 aleG 156
                                       +   
  gi|385805204|ref|YP_005841602.1| 196 SEGV 199
                                       6555 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.2   1.3e+03     174     195 ..      26      47 ..       8      51 .. 0.62
   2 !   31.0   0.6   1.3e-10   1.4e-07       2      34 ..      49      81 ..      48      90 .. 0.90
   3 ?   -1.8   0.0       1.3   1.4e+03     121     136 ..     154     170 ..     145     177 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.2
                                       HCHHHHHHHHHHHHHHHHHHHH CS
                       ArsA_ATPase 174 glggvsieealeeleetkeeik 195
                                       + ++ +i+++++ +++++e+ik
  gi|385805204|ref|YP_005841602.1|  26 KKAAEEIDQYISMMQKKFEKIK 47 
                                       3445566677777777777776 PP

  == domain 2  score: 31.0 bits;  conditional E-value: 1.3e-10
                                      EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEE CS
                       ArsA_ATPase  2 kvilvgGKGGVGKttvsaatavklsekgkkvll 34
                                      ++++++GKGGVGKt ++a++a++ls++g+kv +
  gi|385805204|ref|YP_005841602.1| 49 RIMIFSGKGGVGKTFIAASIAMYLSKMGYKVGV 81
                                      799**************************9966 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.3
                                       HCSSSSEEEEESBS.CC CS
                       ArsA_ATPase 121 keeeydvvvlDtaP.TG 136
                                       + e+ d +++D +P TG
  gi|385805204|ref|YP_005841602.1| 154 RWEDLDFLIFDMPPgTG 170
                                       56789*******99566 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 !   13.1   0.0   4.6e-05     0.048       3      40 ..      51      88 ..      49     117 .. 0.82
   2 !   12.4   0.0   7.4e-05     0.079     189     247 ..     236     294 ..     152     298 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.6e-05
                         Fer4_NifH  3 iaiyGkGGiGksttsqnlsaalaemgkkvlivGCDPka 40
                                      + + GkGG+Gk++ ++ +++ l++mg kv +   D   
  gi|385805204|ref|YP_005841602.1| 51 MIFSGKGGVGKTFIAASIAMYLSKMGYKVGVYDADETG 88
                                      5677************************9888777655 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 7.4e-05
                         Fer4_NifH 189 ereliekfaeelgtkvlevvPrdeivrkaelrkktvieyapeseqakeyrelarkilen 247
                                       ++  ie++a++ g++ l ++P+de +r+++ +   + e a+ se+    + la+ki+e+
  gi|385805204|ref|YP_005841602.1| 236 GKSYIEEIARDHGIEALGKIPLDERIRESQDKGVPIYELASGSEIDRSLELLAKKIIEK 294
                                       356789999999********************************************986 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.1   6.6e-05     0.069       2      35 ..      49      82 ..      48      92 .. 0.94
   2 !    6.6   0.0    0.0059       6.3     149     196 ..     204     263 ..     184     265 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.6e-05
                            AAA_26  2 tifvtgtdtgvGKTvvslgLvralkrkgvkvgyf 35
                                      +i++ +   gvGKT++++ ++ +l++ g+kvg++
  gi|385805204|ref|YP_005841602.1| 49 RIMIFSGKGGVGKTFIAASIAMYLSKMGYKVGVY 82
                                      79*****************************985 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0059
                            AAA_26 149 iealrqknvrvlGvilNkvrnp...e..........nvetlekksgipvlGvvPylpdlea 196
                                       + +l++ ++++lG++ N   +    +           +e++   +gi+ lG +P ++++++
  gi|385805204|ref|YP_005841602.1| 204 VVFLKKMEIPILGIVENM-SHYtcdDgskievfgksYIEEIARDHGIEALGKIPLDERIRE 263
                                       445688899********8.444354145566677779*****************9998775 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.7e-06    0.0018       3     108 ..      50     166 ..      48     180 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.7e-06
                                       EEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHHHHHHHH..HHHHT------EE.........E CS
                              MipZ   3 ivlgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlarylenraat..aerkglsLplpea.........l 68 
                                       i++   kGG Gk+ +a  +a+ L+k+G +v++ d d     +   l+n  a   +e++  +L  +++         l
  gi|385805204|ref|YP_005841602.1|  50 IMIFSGKGGVGKTFIAASIAMYLSKMGYKVGVYDADETGSVIPFVLGNSDAEiyMEESSGELIPANIkgiqvmsleL 126
                                       666678******************************99888777777766541122222233222220000000002 PP

                                       -SSS-HHHHTTS-HHHHHHHHHHHHHHHHHH-SEEEEE-- CS
                              MipZ  69 alseaeeaeveeeeeaevaeleelvadleaeldfividtP 108
                                       +l+e+++  + +++  +   l++l+    ++ldf+++d P
  gi|385805204|ref|YP_005841602.1| 127 MLKEKDSPLIWQGALRTKFILQTLALTRWEDLDFLIFDMP 166
                                       4455555555566655656666776677778888888875 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 !   15.9   0.0   7.5e-06    0.0079      37      79 ..      37      80 ..       5      89 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7.5e-06
                         IstB_IS21 37 eLatlsfiekken.ivllGpsGvGKshlaialgveavraglsvl 79
                                      ++++ +f + k+  +++ G  GvGK+++a+++++   + g++v 
  gi|385805204|ref|YP_005841602.1| 37 SMMQKKFEKIKNRiMIFSGKGGVGKTFIAASIAMYLSKMGYKVG 80
                                      445556655554415667**********************9995 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   1.5e-05     0.016      15      43 ..      43      71 ..      29      83 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.5e-05
                                      TTTSCSEEEEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC 15 kdelqslvvalvGmgGvGKttlakqilnk 43
                                       ++++  ++ ++G+gGvGKt +a++i   
  gi|385805204|ref|YP_005841602.1| 43 FEKIKNRIMIFSGKGGVGKTFIAASIAMY 71
                                      3567778*****************99765 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   1.8e-05     0.019       3      38 ..      50      85 ..      48      87 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.8e-05
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                      ++++ G  G+GKT  +a +a +l+k+g+kv +  aD
  gi|385805204|ref|YP_005841602.1| 50 IMIFSGKGGVGKTFIAASIAMYLSKMGYKVGVYDAD 85
                                      67899*************************998887 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1     2e-05     0.021      11      43 ..      34      72 ..      26      79 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2e-05
                                      HHHHHHH......H-SEEEEE--TTSSTTHHHHHHHHHH CS
                              PhoH 11 eylealk......kndivfaiGpaGtGKtylavalavea 43
                                      +y+++++      kn i++  G+ G GKt++a ++a+ +
  gi|385805204|ref|YP_005841602.1| 34 QYISMMQkkfekiKNRIMIFSGKGGVGKTFIAASIAMYL 72
                                      6677776666666888******************99866 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1     6e-05     0.064      12      53 ..      36      77 ..      25      86 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6e-05
                                      HHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S... CS
                            ResIII 12 ienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgk 53
                                      i  + +k+++ +++ +++    G+GKT++aa+++ +l+k g+
  gi|385805204|ref|YP_005841602.1| 36 ISMMQKKFEKIKNRIMIFSGKGGVGKTFIAASIAMYLSKMGY 77
                                      444556777566667779******************999776 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   8.4e-05     0.089       4      41 ..      50      87 ..      47     105 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.4e-05
                                      EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHH CS
                        APS_kinase  4 vvwltGlsgsGKstianalekkLvekgisvylLdGdnv 41
                                      ++ ++G  g GK+ ia  ++ +L ++g++v + d d+ 
  gi|385805204|ref|YP_005841602.1| 50 IMIFSGKGGVGKTFIAASIAMYLSKMGYKVGVYDADET 87
                                      7889****************************999975 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00014      0.15      22      53 ..      45      77 ..      29     115 .. 0.72
   2 ?   -3.1   0.0       8.4   8.8e+03     108     108 ..     271     271 ..     232     298 .. 0.42

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
                            AAA_16 22 grp.elvllsGesGvGKsslvrellralekdgg 53
                                          +++++sG  GvGK+ ++ +++ +l+k g 
  gi|385805204|ref|YP_005841602.1| 45 KIKnRIMIFSGKGGVGKTFIAASIAMYLSKMGY 77
                                      333489******************998888744 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 8.4
                            AAA_16 108 v 108
                                       +
  gi|385805204|ref|YP_005841602.1| 271 I 271
                                       1 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00016      0.17       1      23 [.      51      73 ..      51     122 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00016
                                      EEEESSTTSSHHHHHHHHHHHHT CS
                               AAA  1 vllyGppGtGKTllakavakelg 23
                                      ++++G  G+GKT +a ++a  l+
  gi|385805204|ref|YP_005841602.1| 51 MIFSGKGGVGKTFIAASIAMYLS 73
                                      799****************9874 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   0.00046      0.48      91     119 ..      40      68 ..       8      85 .. 0.79
   2 ?   -1.9   0.0       2.6   2.7e+03      21      50 ..     187     215 ..     182     235 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00046
                                       HHHHHHCTTSEEEEECSTTSSHHHHHHHH CS
                       RsgA_GTPase  91 eelkellkdktsvlvGqSGvGKStLinal 119
                                       ++  e++k++++++ G+ GvGK+ +  ++
  gi|385805204|ref|YP_005841602.1|  40 QKKFEKIKNRIMIFSGKGGVGKTFIAASI 68 
                                       444578999*************9776555 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.6
                                       EEEESTTTT--HHHHHHHHHHHHHTT-EEE CS
                       RsgA_GTPase  21 ivvslkepelslnlldrfLvlaeekgiepv 50 
                                       i+vs    +ls+  + +++v++++ +i+++
  gi|385805204|ref|YP_005841602.1| 187 IIVSSP-GKLSEGVVRKAVVFLKKMEIPIL 215
                                       444444.58999999999999999988765 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   0.00033      0.35      33      57 ..      48      72 ..      44     165 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00033
                            AAA_25 33 gelallaGapgtGKttlaldlalav 57
                                      + + ++ G +g+GKt++a ++a  +
  gi|385805204|ref|YP_005841602.1| 48 NRIMIFSGKGGVGKTFIAASIAMYL 72
                                      567899*************999755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       866  (0.0483016); expected 358.6 (0.02)
Passed bias filter:                      759  (0.0423336); expected 358.6 (0.02)
Passed Vit filter:                       119  (0.00663729); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.65u 0.34s 00:00:00.99 Elapsed: 00:00:00.51
# Mc/sec: 1784.98
//
Query:       gi|385805205|ref|YP_005841603.1|  [L=369]
Description: peptidase M50 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-16   59.5   9.2    1.8e-15   56.9   9.2    2.2  1  Peptidase_M50  Peptidase family M50
    7.7e-06   26.1   0.0    1.6e-05   25.1   0.0    1.5  1  PDZ_2          PDZ domain
    8.9e-06   25.5   0.0    1.6e-05   24.7   0.0    1.4  1  PDZ_6          PDZ domain
    0.00097   19.4   0.5     0.0025   18.1   0.1    1.8  2  PDZ            PDZ domain
  ------ inclusion threshold ------
      0.034   14.1   0.0      0.065   13.2   0.0    1.4  1  Tricorn_PDZ    Tricorn protease PDZ domain
      0.063   13.3   0.0       0.11   12.5   0.0    1.3  1  7TMR-DISMED2   7TMR-DISM extracellular 2


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 !   56.9   9.2     6e-19   1.8e-15       1     247 [.     113     356 ..     113     360 .. 0.71

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 6e-19
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50   1 afilllgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallpLGGyVkmageepeeelseeeak 77 
                                       ++++ +gi  ++HEl H+++ + +++ v++  +gf   +          a+ ++p  ++V+ ++e            
  gi|385805205|ref|YP_005841603.1| 113 YILISIGIAALIHELSHAFASRVAHIPVKN--VGF---I---------LAV-FIP-AAFVEPDEEA----------- 162
                                       57899***********************99..667...2.........133.455.69*****999........... PP

                                       .XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...............-EEECECTTTSCEE-SEEEC-.......... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...............xxxxxxxxxxxxxxxxxxxxx.......... RF
                     Peptidase_M50  78 aflkkspwqrllivlAGplanfilailvfvv...............pkkskeseeekrgviGvspkp.......... 129
                                        f+k+s   ++ i+ AGp  n+i+a++++++                     ++ +  ++ G++p +          
  gi|385805205|ref|YP_005841603.1| 163 -FKKASFKDKIKILSAGPSSNLIIAFIFLILillmtvnavgatvvsV-----ESGSPAQIYGIKPGYtileingtki 233
                                       .***************************9998888877776443330.....4455556667777778888887777 PP

                                       ............XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXX...X CS
                                       ............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx...x RF
                     Peptidase_M50 130 ............vkkegllealkegvektlkvvvltvkalgklitg.klslktlggpisiaqlaseaaeagls...s 190
                                                   ++++g+   +++   +           l+ l++    +++++g++i  a+  ++  ++      +
  gi|385805205|ref|YP_005841603.1| 234 gspydigpiienYTNSGVWFNITYRSPSSE--------NLSWLLVYkPSNVSKIGITIEQAKGIQSLPDSVYFpmlE 302
                                       554444444333444444444444444443........66666666466677888888888877544444333455* PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50 191 flqllalisvnLgilNLlPipvLDGghllfalleairrkplserkeevanlvglall 247
                                       f+ ++++i+++L+i+N+ Pi++ DGg++++++++        ++ +++  +++ ++l
  gi|385805205|ref|YP_005841603.1| 303 FFTFMYVINFSLAIINAAPIFITDGGRIISEIISLKI---PGNKGKALNFFIQTFTL 356
                                       *******************************987433...44444444444444444 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   5.3e-09   1.6e-05      14      49 ..     201     236 ..     190     257 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 5.3e-09
                                       .-EEEEEE-TTSGGGGT.--TT-EEEEETTB--SSH CS
                             PDZ_2  14 ggvlvvsVkeggPaakaglkagDvilkvdgkkvksl 49 
                                        g++vvsV++g+Pa+  g+k+g +il+++g+k+ s 
  gi|385805205|ref|YP_005841603.1| 201 VGATVVSVESGSPAQIYGIKPGYTILEINGTKIGSP 236
                                       59*******************************875 PP

>> PDZ_6  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   5.3e-09   1.6e-05       2      48 ..     205     249 ..     204     255 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 5.3e-09
                             PDZ_6   2 VtaVdpgsPAdrAGlrvGDiilsvNGqpveglsladvaallrgsage 48 
                                       V +V+ gsPA   G+++G +il++NG+ +  +s+ d+  ++++ +++
  gi|385805205|ref|YP_005841603.1| 205 VVSVESGSPAQIYGIKPGYTILEINGTKI--GSPYDIGPIIENYTNS 249
                                       89***************************..*****99999876655 PP

>> PDZ  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   8.3e-07    0.0025      26      58 ..     201     233 ..     193     235 .. 0.92
   2 ?   -3.1   0.0       3.4     1e+04      14      42 ..     312     344 ..     310     348 .. 0.61

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 8.3e-07
                                       SSEEEEEECTTSHHHHHTSSTTEEEEEETTEET CS
                               PDZ  26 kgifvsevlpggaaeadglkvGDkIlsvNgvdv 58 
                                        g+ v +v+ g++a+  g+k+G  Il++Ng+++
  gi|385805205|ref|YP_005841603.1| 201 VGATVVSVESGSPAQIYGIKPGYTILEINGTKI 233
                                       58999*************************997 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.4
                                       EEEEEETTSS...SSSSEEEEEECTT.SHHHHH CS
                               PDZ  14 fslkggsdqr...gdkgifvsevlpg.gaaead 42 
                                       fsl+  +++    +d g ++se+     + +++
  gi|385805205|ref|YP_005841603.1| 312 FSLAIINAAPifiTDGGRIISEIISLkIPGNKG 344
                                       666666666566667777777777665666655 PP

>> Tricorn_PDZ  Tricorn protease PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.2e-05     0.065      26      76 ..     207     255 ..     199     265 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.2e-05
                                       SSS-B-GGGGGS---.TT-EEEEETTEE-BTTB-HHHHHHTTTTSEEEEEE CS
                       Tricorn_PDZ  26 deearSPLaepGvnvreGdlilavdgepvskekgiaelLvgkagkeveLtv 76 
                                       + e  SP + +G++   G++il+++g ++++  +i +++++ +++ v  ++
  gi|385805205|ref|YP_005841603.1| 207 SVESGSPAQIYGIK--PGYTILEINGTKIGSPYDIGPIIENYTNSGVWFNI 255
                                       5677899999***9..8***********************99998876555 PP

>> 7TMR-DISMED2  7TMR-DISM extracellular 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.7e-05      0.11      39      72 ..     246     279 ..     242     292 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.7e-05
                                       SECEEEEEEEEE-.--SS-EE..EEEE-TT-SEE CS
                      7TMR-DISMED2  39 ytssayWlrftlenptdaprrwllelayplldev 72 
                                       yt+s +W+ +t + p++++ +wll+  ++ + ++
  gi|385805205|ref|YP_005841603.1| 246 YTNSGVWFNITYRSPSSENLSWLLVYKPSNVSKI 279
                                       9***********************9999888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       800  (0.0446204); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); 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):               6  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2327.83
//
Query:       gi|385805206|ref|YP_005841604.1|  [L=237]
Description: glutaredoxin-like domain-containing protein [Fervidicoccus fontis Kam940]
Scores for complete 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-29  101.0   1.1    4.5e-15   55.4   0.3    2.3  2  Thioredoxin_3   Thioredoxin domain
    2.9e-09   37.0   1.5    0.00059   20.0   0.1    2.8  2  Glutaredoxin    Glutaredoxin
    3.5e-06   27.0   0.1     0.0025   17.7   0.0    2.5  2  TraF            F plasmid transfer operon protein
    2.1e-05   24.5   0.1      0.032   14.2   0.1    2.2  2  Thioredoxin     Thioredoxin
    0.00051   19.6   0.6      0.021   14.3   0.1    2.1  2  ABC_transp_aux  ABC-type uncharacterized transport system
     0.0011   19.3   6.4      0.037   14.5   0.8    3.5  2  Thioredoxin_2   Thioredoxin-like domain
     0.0018   18.5   4.4       0.47   10.6   0.0    3.5  4  Thioredoxin_4   Thioredoxin
     0.0062   16.9   0.1        1.9    9.0   0.0    2.5  2  DUF836          Glutaredoxin-like domain (DUF836)
  ------ inclusion threshold ------
      0.038   13.8   0.2       0.72    9.6   0.1    2.2  2  Thioredoxin_9   Thioredoxin


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 !   44.2   0.0   7.5e-15   1.5e-11       4      76 .]      44     125 ..      41     125 .. 0.82
   2 !   55.4   0.3   2.3e-18   4.5e-15       3      73 ..     154     231 ..     152     234 .. 0.82

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 7.5e-15
                                       EE.ESSSSTTCH...HHHHHHHHHCHCCTCEC.......EEECCTTHHHHHHCT-SSSSEE.ECTTCEEEESS---C CS
                     Thioredoxin_3   4 kv.lgpgCakCp...klekavkeaaaekgika.......evekvtdfeeiekygVmsvPal.vidgkvvvsGkvpse 68 
                                       ++ ++ +C +C+   kl + ++e  ++ +           ++k +d+e++++yg+ ++P++ +++g+++++G +ps+
  gi|385805206|ref|YP_005841604.1|  44 EIfVKESCYYCQetiKLLSYFREKSPSVN--GkklfdfvVYDKEKDVEKFKQYGISRTPTVtLVEGRIRYTG-IPSG 117
                                       6878999*****66666666666666654..3335999777788*****************9**********.**** PP

                                       CHHHHHHH CS
                     Thioredoxin_3  69 eeirklle 76 
                                       eeir+l+e
  gi|385805206|ref|YP_005841604.1| 118 EEIRSLVE 125
                                       *****986 PP

  == domain 2  score: 55.4 bits;  conditional E-value: 2.3e-18
                                       EEE.ESSSSTTCH...HHHHHHHHHCHCCT.CEC..EEECCTTHHHH.HHCT-SSSSEEECTTCEEEESS---CCHH CS
                     Thioredoxin_3   3 ikv.lgpgCakCp...klekavkeaaaekg.ika..evekvtdfeei.ekygVmsvPalvidgkvvvsGkvpseeei 71 
                                       i+v ++p+C++Cp    l+++++ +  ++g  ++  + ++++++++i +ky+VmsvP ++i+g+v ++G +p e ++
  gi|385805206|ref|YP_005841604.1| 154 IEViITPSCPYCPyaaLLANMIAFESYKSGnKSViaDTVEAYENPDIaDKYNVMSVPVIAINGEVAFVG-LPYEVDF 229
                                       89989*********988888888888888434444499999****************************.7776654 PP

                                       HH CS
                     Thioredoxin_3  72 rk 73 
                                        +
  gi|385805206|ref|YP_005841604.1| 230 VE 231
                                       44 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.2   9.1e-06     0.018       2      54 ..      44     103 ..      43     109 .. 0.77
   2 !   20.0   0.1   2.9e-07   0.00059       1      59 [.     154     218 ..     154     219 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 9.1e-06
                                       EEEESTSSHHHHHHHHHHHHTT.....GG....EEEEEGCCSHHHHHHHHHHHTSSSSSEEE CS
                      Glutaredoxin   2 vlftkptCpyCkkakrlLkelg.....vk....feeidvdkdeeireelkelsgvrtvPqvf 54 
                                       ++f+k  C yC+ +++lL +++     v+    f+++  dk+ +  e+ k++ g++  P+v 
  gi|385805206|ref|YP_005841604.1|  44 EIFVKESCYYCQETIKLLSYFRekspsVNgkklFDFVVYDKE-KDVEKFKQY-GISRTPTVT 103
                                       79****************666644445335567888877776.888999999.889888885 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 2.9e-07
                                       EEEEESTSSHHHHHHHHHH.....HHTT.....GGEEEEEGCCSHHHHHHHHHHHTSSSSSEEEETTEE CS
                      Glutaredoxin   1 vvlftkptCpyCkkakrlL.....kelg.....vkfeeidvdkdeeireelkelsgvrtvPqvfidgkh 59 
                                       +++  +p CpyC+ a  l+     ++++     v  ++++  ++++i ++     +v++vP++ i+g++
  gi|385805206|ref|YP_005841604.1| 154 IEVIITPSCPYCPYAALLAnmiafESYKsgnksVIADTVEAYENPDIADKY----NVMSVPVIAINGEV 218
                                       678899*********999877777333344556889999999999999999....************96 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.3e-06    0.0025     121     200 ..      31     106 ..      21     117 .. 0.82
   2 !    6.8   0.0    0.0027       5.3     116     156 ..     137     177 ..     128     216 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.3e-06
                              TraF 121 eaalkklakeygLlfFyrgkcpyceaqapilqafadkyglevraVsvdgrplpe..lpnarvdkgqaarlgvkrtPa 195
                                       e+al+++a+ +   +F++++c yc++ ++ l+ f++k        sv+g+ l +  + ++++d ++ +++g++rtP+
  gi|385805206|ref|YP_005841604.1|  31 EEALRDMASPVIAEIFVKESCYYCQETIKLLSYFREKSP------SVNGKKLFDfvVYDKEKDVEKFKQYGISRTPT 101
                                       677777777777779*********************975......66666665533566788888999********* PP

                              TraF 196 lvlvd 200
                                       + lv+
  gi|385805206|ref|YP_005841604.1| 102 VTLVE 106
                                       ***97 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0027
                              TraF 116 rkeekeaalkklakeygLlfFyrgkcpyceaqapilqafad 156
                                        +e  ++++k++  ++ + ++  ++cpyc  +a   +++a 
  gi|385805206|ref|YP_005841604.1| 137 LEESSKQTIKSINRKVYIEVIITPSCPYCPYAALLANMIAF 177
                                       567889***********************988877777764 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0012       2.4       8      81 ..      28     107 ..      22     128 .. 0.72
   2 !   14.2   0.1   1.6e-05     0.032      20      78 ..     155     214 ..     137     222 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0012
                                       HHHHHHHTTTSSEEEEE.EE-TTSHHHHCHHHHHHHHHHHCTT.....TSEEEEEETTTSHHHHHHTT-SSSSEEEE CS
                       Thioredoxin   8 enFeeevakekklvlve.FyApwCghCkalaPeleklaeelkd.....kvklakvdvdenedlakkyevegiPtlkl 78 
                                       e+ ee++++ +++v+ e F  + C  C++    l  + e+         + ++  d ++  +  k+y+++  Pt+ l
  gi|385805206|ref|YP_005841604.1|  28 EALEEALRDMASPVIAEiFVKESCYYCQETIKLLSYFREKSPSvngkkLFDFVVYDKEKDVEKFKQYGISRTPTVTL 104
                                       5667888888888888845667899999766555555555544444767888999999999999***********99 PP

                                       EET CS
                       Thioredoxin  79 fkn 81 
                                       ++ 
  gi|385805206|ref|YP_005841604.1| 105 VEG 107
                                       865 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 1.6e-05
                                       EEEEEEE-TTSHHHHCHHHHHHHHHHHCTT...TSEEEEEETTTSHHHHHHTT-SSSSEEEE CS
                       Thioredoxin  20 lvlveFyApwCghCkalaPeleklaeelkd...kvklakvdvdenedlakkyevegiPtlkl 78 
                                       +v++    p+C+    la +++  + +       v    v++ en+d+a+ky+v ++P + +
  gi|385805206|ref|YP_005841604.1| 155 EVIITPSCPYCPYAALLANMIAFESYK--SgnkSVIADTVEAYENPDIADKYNVMSVPVIAI 214
                                       455555666777777777766543333..3445888889*******************9976 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 ?    4.3   0.1     0.012        23      17      99 ..      31     108 ..      22     138 .. 0.71
   2 !   14.3   0.1     1e-05     0.021      12      94 ..     137     213 ..     131     226 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.012
                    ABC_transp_aux  17 kellknleepvtikvylsenlalppelkalekevkdlLeeyaaysg...gkisvefidpspneeeeeeaeaygitpv 90 
                                       +e+l+++ +pv  +++++e+      +  + +e+ +lL  +++ s+   gk  ++f+ ++++ ++ e+ ++ygi+ +
  gi|385805206|ref|YP_005841604.1|  31 EEALRDMASPVIAEIFVKESC-----Y--YCQETIKLLSYFREKSPsvnGKKLFDFVVYDKE-KDVEKFKQYGISRT 99 
                                       577889999***********5.....3..789999999999988862223555777777644.47788889999998 PP

                    ABC_transp_aux  91 qisveekde 99 
                                       +  +  +++
  gi|385805206|ref|YP_005841604.1| 100 PTVTLVEGR 108
                                       876665455 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 1e-05
                    ABC_transp_aux  12 LsdatkellknleepvtikvylsenlalppelkalekevkdlLeeyaaysggkisvefidpspneeeeeeaeaygit 88 
                                       L + +k+++k+++++v+i+v+++++   + ++ al  ++   +e+y++ ++  +  + +++++n+   + a +y + 
  gi|385805206|ref|YP_005841604.1| 137 LEESSKQTIKSINRKVYIEVIITPSCP-YCPYAALLANM-IAFESYKSGNK-SVIADTVEAYENP---DIADKYNVM 207
                                       8899*********************74.34554443333.359*****877.9999999999888...666677777 PP

                    ABC_transp_aux  89 pvqisv 94 
                                       +v++  
  gi|385805206|ref|YP_005841604.1| 208 SVPVIA 213
                                       776544 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.8   1.9e-05     0.037      11     107 ..      45     122 ..      38     124 .. 0.65
   2 ?    4.8   0.5     0.019        38       6      84 ..     151     212 ..     146     222 .. 0.52

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.9e-05
                     Thioredoxin_2  11 vftdpdCpyCkklkkelkelddvtvrvllfp.lkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPtivf 86 
                                       +f +++C+yC+   k    l+ ++++    p ++ +  + +v  ++           e+ ve  ++yg++ tPt+ +
  gi|385805206|ref|YP_005841604.1|  45 IFVKESCYYCQETIK---LLSYFREK---SPsVNGKKLFDFVVYDK-----------EKDVEKFKQYGISRTPTVTL 104
                                       566777888877333...33223333...33444443333333333...........445689999*********** PP

                     Thioredoxin_2  87 ldgkeivarlpGyvpaeelea 107
                                        +g+ i  r++G  + ee++ 
  gi|385805206|ref|YP_005841604.1| 105 VEGR-I--RYTGIPSGEEIRS 122
                                       ****.4..9999988888765 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.019
                     Thioredoxin_2   6 kpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtP 82 
                                       k  + v+ +p+CpyC    + l ++ +++++      + + + +a  +   +++           + a+ky+v ++P
  gi|385805206|ref|YP_005841604.1| 151 KVYIEVIITPSCPYCPY-AALLANMIAFESY-----KSGNKSVIADTVEAYENP-----------DIADKYNVMSVP 210
                                       55566777888888854.2222222222222.....222323333333333333...........466666666666 PP

                     Thioredoxin_2  83 ti 84 
                                        i
  gi|385805206|ref|YP_005841604.1| 211 VI 212
                                       65 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.68   1.4e+03      13      31 ..      39      57 ..      36      69 .. 0.81
   2 !   10.6   0.0   0.00024      0.47     127     165 ..      85     125 ..      78     126 .. 0.87
   3 ?    0.3   0.3      0.36   7.1e+02      18      51 ..     155     188 ..     148     198 .. 0.64
   4 !    6.7   0.0    0.0037       7.3     129     151 ..     197     219 ..     177     234 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.68
                                      -SEEEEEEE-TT-HHHHHH CS
                     Thioredoxin_4 13 ApvtvieyedlrCphCakf 31
                                       pv  ++++  +C +C + 
  gi|385805206|ref|YP_005841604.1| 39 SPVIAEIFVKESCYYCQET 57
                                      6888999*********986 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00024
                                       HHHHHHHHHHT--SS-EEEE.TTEE.E-TT--HHHHHHHHT CS
                     Thioredoxin_4 127 eaeskeakkagiestPtfii.ngek.veepqtyeelkalid 165
                                       e++++++k+ gi+ tPt+ +  g++ +++ ++ ee+++l++
  gi|385805206|ref|YP_005841604.1|  85 EKDVEKFKQYGISRTPTVTLvEGRIrYTGIPSGEEIRSLVE 125
                                       68999*************86588877899999999999987 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.36
                                       EEEE-TT-HHHHHHHHHHHHHHHHHHHTTSEEEE CS
                     Thioredoxin_4  18 ieyedlrCphCakfeeeveklleeyidtGkvkfi 51 
                                       ++    +Cp+C   +   + +  e  ++G+ ++i
  gi|385805206|ref|YP_005841604.1| 155 EVIITPSCPYCPYAALLANMIAFESYKSGNKSVI 188
                                       5556679****88777776433333366665555 PP

  == domain 4  score: 6.7 bits;  conditional E-value: 0.0037
                                       HHHHHHHHT--SS-EEEETTEEE CS
                     Thioredoxin_4 129 eskeakkagiestPtfiingekv 151
                                       +   a+k ++ s+P + inge+ 
  gi|385805206|ref|YP_005841604.1| 197 NPDIADKYNVMSVPVIAINGEVA 219
                                       445789**************984 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0   0.00095       1.9       4      56 ..      45     105 ..      43     146 .. 0.83
   2 !    5.8   0.0    0.0095        19       6      57 ..     158     216 ..     153     232 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00095
                                       EEE-TT-HHHHHHHHHHHHHCCCTT.......EEEEEEETTT-CCCHCCCC.TTTTEEEEC CS
                            DUF836   4 LyskpgChlCeqakekLkelkleeg.......leleviDIakdeeleakYg.leipvlale 56 
                                       +++k+ C  C++  ++L+ +++++        ++ +v D +kd e +++Yg  ++p + l+
  gi|385805206|ref|YP_005841604.1|  45 IFVKESCYYCQETIKLLSYFREKSPsvngkklFDFVVYDKEKDVEKFKQYGiSRTPTVTLV 105
                                       89****************9666666777777799999999999998888873356666655 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0095
                                       E-TT-HHHHHHHHHHHH.HCCCTT......EEEEEEETTT-CCCHCCCCTT.TTEEEECT CS
                            DUF836   6 skpgChlCeqakekLke.lkleeg......leleviDIakdeeleakYgle.ipvlaleg 57 
                                        +p C+ C  a  +L++ ++ e+       +  +++  +++++  +kY+++ +pv+a++g
  gi|385805206|ref|YP_005841604.1| 158 ITPSCPYCPYAA-LLANmIAFESYksgnksVIADTVEAYENPDIADKYNVMsVPVIAING 216
                                       678888887443.333323333323344446667777779999******8548****998 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.077   1.5e+02      30     103 ..      28     104 ..      18     126 .. 0.72
   2 ?    9.6   0.1   0.00036      0.72      27      90 ..     136     204 ..     124     219 .. 0.69

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.077
                                       ---HHHHHT--S-EEEEEE--TT-HHHHHHHHHHHHHHHH-TTEE....EEEE-HHHHHHHTTTTTT-SS--SSEEE CS
                     Thioredoxin_9  30 eeteekiksiekklkilvltedwCgDaavnvPvlakiaelnpnie....vkillrdenlelmdqyltngaraiPtli 102
                                       e  ee+++    ++   ++ ++ C  +++++  l  + e +p ++    +++++ d+++++ +++++ g  ++Pt+ 
  gi|385805206|ref|YP_005841604.1|  28 EALEEALRDMASPVIAEIFVKESCYYCQETIKLLSYFREKSPSVNgkklFDFVVYDKEKDV-EKFKQYGISRTPTVT 103
                                       3444566777777777788889999999999999999999999983333456666666654.557776777777776 PP

                                       E CS
                     Thioredoxin_9 103 i 103
                                       +
  gi|385805206|ref|YP_005841604.1| 104 L 104
                                       5 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00036
                                       HHH---HHHHHT--S-EEEEEE--TT-HHH.....HHHHHHHHHHHHH-TTEEEEEE-HHHHHHHTTTT CS
                     Thioredoxin_9  27 elseeteekiksiekklkilvltedwCgDa.....avnvPvlakiaelnpnievkillrdenlelmdqy 90 
                                        l+e  ++ iksi++k+ i v+ ++ C+ +      +n+ +++  ++ n+ +  + +   en+++ d+y
  gi|385805206|ref|YP_005841604.1| 136 GLEESSKQTIKSINRKVYIEVIITPSCPYCpyaalLANMIAFESYKSGNKSVIADTVEAYENPDIADKY 204
                                       57889999****************999977332222344444444455556666666666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       762  (0.042501); expected 358.6 (0.02)
Passed bias filter:                      631  (0.0351944); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1604.12
//
Query:       gi|385805207|ref|YP_005841605.1|  [L=182]
Description: ATP:cobalamin adenosyltransferase [Fervidicoccus fontis Kam940]
Scores for complete 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-35  122.0   0.0    2.9e-35  121.8   0.0    1.0  1  Cob_adeno_trans  Cobalamin adenosyltransferase
  ------ inclusion threshold ------
      0.014   15.5   0.0      0.035   14.2   0.0    1.7  2  DUF1940          Domain of unknown function (DUF1940)


Domain annotation for each model (and alignments):
>> Cob_adeno_trans  Cobalamin adenosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.8   0.0   3.2e-39   2.9e-35       2     161 ..       4     160 ..       3     163 .. 0.93

  Alignments for each domain:
  == domain 1  score: 121.8 bits;  conditional E-value: 3.2e-39
                                       XXXXXXXXXXXXX.XX.XXXTTHHHHHHHHHHHHHHHHHHHHHHHCTTTTHHHHHHHHHHHHHHHHHHHHHHT.-BT CS
                   Cob_adeno_trans   2 yTrtGDkGtTslv.ggervsKddprveayGtvDelnsaiglarallaeeeeelkeaLeeiqneLfdlgaelatpekk 77 
                                       y ++GD+G+T ++   e v+K++p ve++G++De+++ +gla +l+++e +e+k+++ +iq+ Lf++g ++a     
  gi|385805207|ref|YP_005841605.1|   4 YSKKGDEGSTFCMkYLEMVPKNHPFVEFVGELDEAEASLGLASSLIPDELKEIKSEVDWIQTLLFRIGFTIA----- 75 
                                       99**********85789******************************************************9..... PP

                                       CCG-S--HHHHHHHHHHHHHHHHHS--EESEEES-SSHHHHHHHHHHHHHHHHHHHHHHHHHHS.....HHHHHHHH CS
                   Cob_adeno_trans  78 kekkkiteeeveelekeideleaelpplksfilpggspaaaalhvaRtvcRraERavvelaeee....veeevlkyl 150
                                         k  i+ee+++ le+  d+++   +pl  f+l+gg+paaaa+++ R+++Rr+ER++++l +++     e+ vl++l
  gi|385805207|ref|YP_005841605.1|  76 -GKDCISEEDLKVLESIADKYSIYAKPL--FLLNGGHPAAAAVSLSRAIVRRVERRLIDLISRKevinKEKLVLSIL 149
                                       .456799999************999987..******************************99777865579999*** PP

                                       HHHHHHHHHHH CS
                   Cob_adeno_trans 151 NRLSDlLfvla 161
                                       NR S+ L+ ++
  gi|385805207|ref|YP_005841605.1| 150 NRASSALYGIQ 160
                                       *******9765 PP

>> DUF1940  Domain of unknown function (DUF1940)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   3.9e-06     0.035       1      52 [.      14      66 ..      14      96 .. 0.84
   2 ?   -1.5   0.0      0.28   2.5e+03     113     140 ..     124     151 ..     102     154 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.9e-06
                                      EETTTTEEEETT-HHHHHHHHHHHHHHHHHHHHHT.-SSHHHHHHHHHHHHHH CS
                           DUF1940  1 yCdvlddeldaespyfkyrseiklaeaslGlaise.GikvqatrelldilDtl 52
                                      +C    +++++++p+ ++  e++ aeaslGla s     +++++  +d + tl
  gi|385805207|ref|YP_005841605.1| 14 FCMKYLEMVPKNHPFVEFVGELDEAEASLGLASSLiPDELKEIKSEVDWIQTL 66
                                      68788899************************874134667777666766665 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.28
                                       HTSTTTTTT--HHHHHHHHHHHHHHHHH CS
                           DUF1940 113 kedeefkeivkdylikyllklsvfiyre 140
                                       + + ++ ++++ + +   +kl++ i++ 
  gi|385805207|ref|YP_005841605.1| 124 RVERRLIDLISRKEVINKEKLVLSILNR 151
                                       3445666667666666667777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 1136.15
//
Query:       gi|385805208|ref|YP_005841606.1|  [L=96]
Description: hypothetical protein FFONT_0162 [Fervidicoccus fontis Kam940]
Scores for 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-29  102.5   6.3    1.1e-29  102.4   6.3    1.0  1  DUF211    Uncharacterized ArCR, COG1888
  ------ inclusion threshold ------
      0.041   13.7   4.9      0.066   13.0   4.9    1.3  1  YabP      YabP family


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 !  102.4   6.3   1.2e-33   1.1e-29       2      86 ..       3      88 ..       2      91 .. 0.98

  Alignments for each domain:
  == domain 1  score: 102.4 bits;  conditional E-value: 1.2e-33
                                      EEEEEEEEEEE.SSS-HHHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHCTT-EEEEEEEEE CS
                            DUF211  2 irrlvLDvlkp.hepsivelakklaelegvdgvnitvkevDketenlkitieGenidyeeieeaieelggvihSiDevv 79
                                      i r vLDvl+p +++ i el+  l++++gv+gvnitvke+D+ete++ i+ieG++id++e+e+++ ++ggvihSiD+v+
  gi|385805208|ref|YP_005841606.1|  3 ILRAVLDVLIPiKGIGIDELSLVLERVRGVEGVNITVKEIDVETESILIVIEGRDIDLKEVERELLNYGGVIHSIDQVI 81
                                      789**************************************************************************** PP

                                      EESS--- CS
                            DUF211 80 aGkkive 86
                                       Gkkive
  gi|385805208|ref|YP_005841606.1| 82 SGKKIVE 88
                                      ******9 PP

>> YabP  YabP family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   4.9   7.4e-06     0.066      10      62 ..      23      77 ..      18      78 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.4e-06
                              YabP 10 elliegvkgvl..sfdeeeirletkkgkltIkGenLhikklskgelkieGkIdsl 62
                                      +l++e v+gv+  + + +ei +et++  ++I+G++  +k+   + l   G I+s+
  gi|385805208|ref|YP_005841606.1| 23 SLVLERVRGVEgvNITVKEIDVETESILIVIEGRDIDLKEVERELLNYGGVIHSI 77
                                      578888888863367899********************************99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); 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 0.33s 00:00:00.83 Elapsed: 00:00:00.53
# Mc/sec: 543.82
//
Query:       gi|385805209|ref|YP_005841607.1|  [L=352]
Description: hypothetical protein FFONT_0163 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.063   13.6   0.2        6.1    7.2   0.0    2.8  2  Synapsin  Synapsin, N-terminal domain


Domain annotation for each model (and alignments):
>> Synapsin  Synapsin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0   0.00034       6.1      36      74 ..      51      89 ..      43     104 .. 0.89
   2 ?    3.5   0.2    0.0048        87      10      32 ..     140     162 ..     130     256 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00034
                          Synapsin 36 aefselnlvaysdkglvvdlkvsrngtkvvrsfkpdfvl 74
                                      a +s l++ a  dk+ +v+ +    g +v+++fkp+f+l
  gi|385805209|ref|YP_005841607.1| 51 ATLSLLEIGAIFDKQESVKWRIWFDGISVSKQFKPNFIL 89
                                      78889999999999*******999**************9 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.0048
                          Synapsin  10 ddqktdwskyfrgkklsGeydir 32 
                                       ++++t+w+ky+ g  +  + +i+
  gi|385805209|ref|YP_005841607.1| 140 NSDTTNWIKYYTGGAIIKSQEIK 162
                                       35689******999887666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.49
# Mc/sec: 2151.54
//
Query:       gi|385805210|ref|YP_005841608.1|  [L=198]
Description: hypothetical protein FFONT_0164 [Fervidicoccus fontis Kam940]
Scores for 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-36  123.2   9.3    1.1e-35  122.9   9.3    1.0  1  Lys_export  Lysine exporter LysO
  ------ inclusion threshold ------
       0.62   10.4   8.7        3.2    8.1   0.2    2.5  2  DUF4149     Domain of unknown function (DUF4149)
        0.7    9.6   0.1        0.7    9.6   0.1    2.8  3  FeoB_C      Ferrous iron transport protein B C terminus
        4.2    5.6  11.3        5.7    5.1  11.3    1.2  1  DUF2070     Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> Lys_export  Lysine exporter LysO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.9   9.3   2.5e-39   1.1e-35       1     188 [.       9     191 ..       9     193 .. 0.88

  Alignments for each domain:
  == domain 1  score: 122.9 bits;  conditional E-value: 2.5e-39
                        Lys_export   1 llaliaGillGllllleaelleeelseylLylLlflvGislgss.kelleklkklnlkllllplatilgsllgglla 76 
                                       +la+iaG+++G l+++e+   +  + + +L++L+f+  i+ + + +e +++++k  l +  + l+ ilgsl++gll+
  gi|385805210|ref|YP_005841608.1|   9 ILAFIAGFIAGKLFRPENV--SLLMENSFLVMLVFFASIEASLRiRE-IKSFRKAFLGV-RTLLFGILGSLITGLLF 81 
                                       579**********999984..55678999********9999999444.33333333322.2346679********** PP

                        Lys_export  77 alllglslkeslavasGfGwYSLsgilitelkgaelGtiallanllREllalllipllakrfgklaaisvaGatsmD 153
                                       +++lg   k s+  ++G+GwY+++g++++ l+g++lGti++++nl REl+ ++ +p + k+fg++ a+++aG    D
  gi|385805210|ref|YP_005841608.1|  82 FFVLG---KGSIPACMGLGWYTFTGPYLSALGGSTLGTIGFFSNLSRELFGIIAFPSIQKYFGDFGAVTYAGDPVYD 155
                                       ****8...58899999************************************************************* PP

                        Lys_export 154 ttLPiitkssg.kevvvlaivhGvilsllvPilvsl 188
                                       +++P++ k+++ ++ v++a+v+G+++ ++vPi+v+l
  gi|385805210|ref|YP_005841608.1| 156 VLFPFVLKYCKsEDSVIAAFVQGFLTGFVVPIIVPL 191
                                       **********7478999*****************98 PP

>> DUF4149  Domain of unknown function (DUF4149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   3.8    0.0095        42      14      90 ..      11      86 ..       5      89 .. 0.77
   2 ?    8.1   0.2   0.00071       3.2      11      44 ..      97     143 ..      94     150 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0095
                           DUF4149 14 tfvvapvlfrsLprhqfgelqsklFplyfglglalsvlllltevavgseklaseellqlllllvvllltllnafyle 90
                                       f++++++ +   ++  + l+++ F ++ ++ + + + l + e++++ +k +   +++l ++l +l+++ll++f+l+
  gi|385805210|ref|YP_005841608.1| 11 AFIAGFIAGKLFRPENVSLLMENSFLVMLVFFASIEASLRIREIKSF-RKAFLGVRTLLFGILGSLITGLLFFFVLG 86
                                      56666666666644557788888888888888888888888888777.777888899999***************97 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00071
                           DUF4149  11 lwvtfvv............apvlfrsLprhqfgelqsklFplyfg.l 44 
                                       +w+tf              +++ f++L+r+ fg ++    ++yfg +
  gi|385805210|ref|YP_005841608.1|  97 GWYTFTGpylsalggstlgTIGFFSNLSRELFGIIAFPSIQKYFGdF 143
                                       5666666666666677776999**************99999999844 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 ?    9.6   0.1   0.00016       0.7       9      34 ..       8      32 ..       5      32 .. 0.94
   2 ?    2.2   0.8     0.032   1.5e+02       6      21 ..      68      83 ..      66      99 .. 0.77
   3 ?   -3.2   0.4       1.6   7.1e+03      13      18 ..     179     184 ..     171     189 .. 0.45

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00016
                            FeoB_C  9 ilvallvalllkkttlkgepspfvmE 34
                                      +++a+++++++ k+ ++ e+ +++mE
  gi|385805210|ref|YP_005841608.1|  8 VILAFIAGFIAGKL-FRPENVSLLME 32
                                      789**********8.**********9 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.032
                            FeoB_C  6 llgilvallvalllkk 21
                                      l+gil  l+++ll+  
  gi|385805210|ref|YP_005841608.1| 68 LFGILGSLITGLLFFF 83
                                      79**********9955 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 1.6
                            FeoB_C  13 llvall 18 
                                       +l++++
  gi|385805210|ref|YP_005841608.1| 179 FLTGFV 184
                                       333332 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1  11.3    0.0013       5.7      21     149 ..       7     166 ..       3     197 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0013
                           DUF2070  21 iillalligllaflssk.lfgillfglpalvaflltlpvlrilggr.ltykrslflalltelivviisllaillsal 95 
                                       +++la+++g++a   +   + +ll+  ++lv ++++  +  +l++r +++ r++fl + t+l+ ++ sl+  ll+++
  gi|385805210|ref|YP_005841608.1|   7 AVILAFIAGFIAGKLFRpENVSLLMENSFLVMLVFFASIEASLRIReIKSFRKAFLGVRTLLFGILGSLITGLLFFF 83 
                                       5788888888887777663344444445666666666666666666689************************9998 PP

                           DUF2070  96 l..qalvllalvls..........lalvfalrllvlvavsdesllkavlpaliqpllailllvly............ 148
                                       +  + +++ ++ l+                l ++ +++  +++l+ +++  +iq +++ + +v y            
  gi|385805210|ref|YP_005841608.1|  84 VlgKGSIPACMGLGwytftgpylsALGGSTLGTIGFFSNLSRELFGIIAFPSIQKYFGDFGAVTYagdpvydvlfpf 160
                                       89988888888888888888865544444555566666677778888888888998888888888777766666666 PP

                           DUF2070 149 .....f 149
                                             
  gi|385805210|ref|YP_005841608.1| 161 vlkycK 166
                                       655541 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1207.86
//
Query:       gi|385805211|ref|YP_005841609.1|  [L=95]
Description: hypothetical protein FFONT_0165 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 621.50
//
Query:       gi|385805212|ref|YP_005841610.1|  [L=330]
Description: PP-loop domain-containing protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.5e-11   42.8   0.0    9.5e-11   41.8   0.0    1.6  1  ATP_bind_3     PP-loop family
  ------ inclusion threshold ------
       0.17   12.2   1.8       0.29   11.5   0.2    2.2  2  DUF2175        Uncharacterized protein conserved in archaea (
       0.19   11.7   0.2       0.19   11.7   0.2    2.6  2  DUF4428        Domain of unknown function (DUF4428)


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 !   41.8   0.0   1.6e-14   9.5e-11       2     130 ..      50     191 ..      49     246 .. 0.81

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 1.6e-14
                                       EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSS.TCHHHHHHHHHHHHHHTT-EEEEEE--H......... CS
                        ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglr.eeskeeaelvkelckklnikleiekvdv......... 68 
                                       +l+A+SgG DS +Ll ++ + +   ++k++a+ +  g+   + +e  e +k++ k+ +i+ +i++++          
  gi|385805212|ref|YP_005841610.1|  50 LLLAISGGKDSFVLLDAVSHFHP--SSKIIALSIVEGIPgYNRQEYIERIKKYTKERGIDTVITSIKEfvgyslgei 124
                                       689******************77..5688999999999867999999********************9999999888 PP

                                       .HHCTTSTCC....CHHHHHHHHHHHHCHHCCT.CEEE---BHHHHHHHHHHHHCCT--CCHHH-S- CS
                        ATP_bind_3  69 .akkkgknle....eaARelRYevlkealkkegievlllAhhadDqaEtfllrlargsglaglagik 130
                                        +k+++ ++e    +    lR ++++ ++++ g++  l+Ah+ dD + t+++++ rg   + l   +
  gi|385805212|ref|YP_005841610.1| 125 vEKSREMGIElspcTYCGSLRRRIINVYARELGADRTLTAHNLDDEVQTVFMNILRGDPERLLRQHP 191
                                       85555666662233456789*************************************9987776544 PP

>> DUF2175  Uncharacterized protein conserved in archaea (DUF2175)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   4.8e-05      0.29       4      52 ..       2      48 ..       1      57 [. 0.80
   2 ?   -1.9   0.1      0.71   4.2e+03       4      13 ..     285     294 ..     285     298 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.8e-05
                           DUF2175  4 kCyiCgkeivegekFTftkkgvvHyeClvekarkklkes.edaaaLlele 52
                                      kC++Cg e v  + FT   +     eC+ e++rk++ ++ +d+ +++e +
  gi|385805212|ref|YP_005841610.1|  2 KCSLCGREAVFYQAFT---NKYLCRECFIEDVRKRIANEvKDKRMFSERD 48
                                      8*************99...456788************9966665555544 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.71
                           DUF2175   4 kCyiCgkeiv 13 
                                       +C iCg+   
  gi|385805212|ref|YP_005841610.1| 285 TCRICGEPTS 294
                                       6*****9765 PP

>> DUF4428  Domain of unknown function (DUF4428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   3.1e-05      0.19       1      29 [.       2      28 ..       2      47 .. 0.90
   2 ?   -0.5   1.6      0.19   1.2e+03       2      10 ..     286     294 ..     285     309 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.1e-05
                           DUF4428  1 iCaiCgkKigllkrlkleDgyvCkdClkK 29
                                      +C++Cg +   +   ++ + y+C +C+ +
  gi|385805212|ref|YP_005841610.1|  2 KCSLCGREAVFYQ--AFTNKYLCRECFIE 28
                                      7***********9..9**********976 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.19
                           DUF4428   2 CaiCgkKig 10 
                                       C iCg+ ++
  gi|385805212|ref|YP_005841610.1| 286 CRICGEPTS 294
                                       999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       824  (0.0459591); expected 358.6 (0.02)
Passed bias filter:                      708  (0.0394891); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); 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):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 2248.24
//
Query:       gi|385805213|ref|YP_005841611.1|  [L=340]
Description: phosphoesterase, DHH family [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00012   22.5   1.0    0.00039   20.9   1.0    1.8  2  DHHA1          DHHA1 domain
  ------ inclusion threshold ------
      0.072   12.9   0.1        2.4    8.0   0.0    2.5  2  RNA_pol_A_CTD  Bacterial RNA polymerase, alpha chain C termin
        0.2   12.0   1.4       0.64   10.4   0.4    2.1  2  kleA_kleC      Uncharacterized KorC regulated protein A


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 ?   -2.2   0.0      0.88   5.3e+03      39      65 ..      95     121 ..      79     132 .. 0.64
   2 !   20.9   1.0   6.5e-08   0.00039       8     123 ..     212     321 ..     209     340 .] 0.76

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.88
                                       TCEEEEEECHCCHHHHHHHHHHHHHHT CS
                             DHHA1  39 gvkvlvaevgeewdagalgiaadklks 65 
                                       +v ++ +++++  +  +l+  +dk++ 
  gi|385805213|ref|YP_005841611.1|  95 QVIYVDHHFSTIDNVEVLRKFIDKFRL 121
                                       666667777444444888888887765 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 6.5e-08
                                       HHHHHHHHHCHHHHHHHHHHHHHHHTCEEECTCEEEEEECHCCHHHHHHHHHHHHHHTHGBTTCEEEEEEEECTEEE CS
                             DHHA1   8 rkelekeleelkealaklkaeellekaeevkgvkvlvaevgeewdagalgiaadklksklkkpvivfvakeegdkvk 84 
                                       ++++e+e++ +++++ +++ e+l  +a++v g   +v +  ++w+++ + ++a++l  k+k pv++++ +++g +  
  gi|385805213|ref|YP_005841611.1| 212 LNKVEEEIK-KRDEELEKAVEDLAISARRV-GCFRFVDAR-KKWKRRGVSSLATRLARKFKAPVALLAKVKDG-E-I 283
                                       578999995.66666667777777788777.555555555.9****************************999.4.4 PP

                                       EEEEESSHSS-HHHHHHH.HHHHTTCCEEEETCEEEEEEE CS
                             DHHA1  85 vsarskkdgvdagelake.aaaklgggGGGHdlAaGagip 123
                                       +++r+k  +  a ++a e  a  +  + GGH++ +  +++
  gi|385805213|ref|YP_005841611.1| 284 LVIRTK--NATAKKIADElYAIGMAVNTGGHRNISIVRLK 321
                                       667888..89999999995556789999***877766665 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 ?    1.9   0.0     0.032   1.9e+02      53      65 ..     158     170 ..     155     171 .. 0.89
   2 ?    8.0   0.0   0.00039       2.4       2      28 ..     217     243 ..     216     247 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.032
                                       -SSHHHHHHHHHH CS
                     RNA_pol_A_CTD  53 lGkKSleEIkekL 65 
                                       lG+K  +EIke++
  gi|385805213|ref|YP_005841611.1| 158 LGRKPSDEIKETV 170
                                       9*********986 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00039
                                       ...XXXXXXX--BHHHHT--HHHHHHH CS
                     RNA_pol_A_CTD   2 eeeeeelkklsisIeeLeLSvRslNcL 28 
                                       ee +++ ++l++++e+L +S+R   c 
  gi|385805213|ref|YP_005841611.1| 217 EEIKKRDEELEKAVEDLAISARRVGCF 243
                                       56778899**************98885 PP

>> kleA_kleC  Uncharacterized KorC regulated protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.4   0.00011      0.64      29      72 ..     219     262 ..     191     266 .. 0.85
   2 ?   -0.0   0.0      0.19   1.1e+03       3      36 ..     266     300 ..     264     304 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00011
                         kleA_kleC  29 klaeAeeLvrqaeeLRakvyeesaaLedrakkrWtleeveqAka 72 
                                         ++ eeL++ +e+L + +++ ++    +a+k+W    v   ++
  gi|385805213|ref|YP_005841611.1| 219 IKKRDEELEKAVEDLAISARRVGCFRFVDARKKWKRRGVSSLAT 262
                                       456789****************************9887766555 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.19
                         kleA_kleC   3 eKimpWiDeLpeva.tdlvarRdkiAaklaeAeeL 36 
                                        K+ + + +L +v+  +++  R k A   + A+eL
  gi|385805213|ref|YP_005841611.1| 266 RKFKAPVALLAKVKdGEILVIRTKNATAKKIADEL 300
                                       58888899999999889999999999999999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       752  (0.0419432); expected 358.6 (0.02)
Passed bias filter:                      580  (0.0323498); 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: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2204.69
//
Query:       gi|385805214|ref|YP_005841612.1|  [L=247]
Description: circadian clock protein KaiC [Fervidicoccus fontis Kam940]
Scores for complete 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-86  287.8   0.3    5.8e-86  287.6   0.3    1.0  1  ATPase     KaiC
    6.4e-08   31.7   0.0    8.6e-08   31.2   0.0    1.0  1  GvpD       GvpD gas vesicle protein
    5.9e-07   29.2   0.0    9.5e-07   28.6   0.0    1.4  1  AAA_25     AAA domain
      4e-05   23.0   0.3    0.00035   19.9   0.1    1.9  2  DUF2075    Uncharacterized conserved protein (DUF2075)
    0.00014   21.3   0.0    0.00021   20.7   0.0    1.3  1  DnaB_C     DnaB-like helicase C terminal domain
    0.00024   21.1   0.0    0.00049   20.1   0.0    1.6  1  AAA_14     AAA domain
    0.00039   20.2   0.1     0.0019   18.0   0.1    2.0  2  AAA_24     AAA domain
     0.0006   19.2   0.4     0.0086   15.4   0.4    2.1  1  Rad51      Rad51
     0.0015   18.0   0.1      0.064   12.7   0.0    2.1  2  RecA       recA bacterial DNA recombination protein
     0.0019   18.2   0.0     0.0025   17.8   0.0    1.2  1  ATPase_2   ATPase domain predominantly from Archaea
      0.002   18.4   0.2     0.0048   17.2   0.1    1.6  2  AAA_19     AAA domain
     0.0052   16.5   0.0     0.0099   15.6   0.0    1.5  1  IstB_IS21  IstB-like ATP binding protein
     0.0071   15.4   0.0      0.012   14.7   0.0    1.4  1  T2SSE      Type II/IV secretion system protein
     0.0083   16.0   1.5      0.016   15.1   1.5    1.4  1  NTPase_1   NTPase
  ------ inclusion threshold ------
      0.019   15.4   0.0      0.027   14.9   0.0    1.3  1  AAA_16     AAA ATPase domain
      0.021   14.7   0.0      0.033   14.0   0.0    1.4  1  MEDS       MEDS: MEthanogen/methylotroph, DcmR Sensory domain
      0.021   15.1   0.0      0.039   14.2   0.0    1.5  1  AAA_28     AAA domain
      0.023   13.8   0.0      0.081   12.1   0.0    1.7  2  PAXNEB     PAXNEB protein
       0.03   14.6   0.1      0.049   13.9   0.1    1.5  1  AAA_22     AAA domain
       0.04   12.7   0.0      0.058   12.2   0.0    1.2  1  PPV_E1_C   Papillomavirus helicase
      0.059   13.1   0.1       0.13   12.0   0.1    1.5  1  AAA_30     AAA domain
      0.069   12.2   0.0       0.17   10.9   0.0    1.6  2  Parvo_NS1  Parvovirus non-structural protein NS1
      0.095   12.6   0.1       0.18   11.7   0.1    1.5  1  NACHT      NACHT domain
       0.13   11.7   0.1       0.32   10.5   0.0    1.6  2  AAA_7      P-loop containing dynein motor region


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 !  287.6   0.3   7.7e-89   5.8e-86       1     230 [.       8     240 ..       8     241 .. 0.99

  Alignments for each domain:
  == domain 1  score: 287.6 bits;  conditional E-value: 7.7e-89
                            ATPase   1 vktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekl 77 
                                       vkt I+glDe+l+gGip+++vv itG+pGtGKti++++Fl++g+++ ge+ v+v++ee+++++r+ ++++Gwd++k+
  gi|385805214|ref|YP_005841612.1|   8 VKTWIPGLDELLNGGIPKRNVVIITGGPGTGKTILSQHFLYNGLVR-GEASVYVSLEEHPVQVRRAMATFGWDVKKF 83 
                                       79********************************************.****************************** PP

                            ATPase  78 eeegklaiidasesaeesaee......kdkedleelieelaeaikeikakrvviDsitglayeekeavaReilrqlv 148
                                       eeegk+ai+da++s++++a++      k+ +d+ eli+ ++ aike++a+rvviDs+++l y +k+a aR++++ql+
  gi|385805214|ref|YP_005841612.1|  84 EEEGKFAIVDAFTSGIGEAAKrekyvvKSVDDVGELIDVIRMAIKETNAQRVVIDSVSTL-YMTKPAIARNTVMQLK 159
                                       *****************9999999*9999*******************************.**************** PP

                            ATPase 149 rvlkklgvTailvsekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIteegik 225
                                       r+l++lg+T+ l+s++s++e+++gg+gve+ ++dg+i+Ldl+e++++l R+++++kmRgt+h++++hpf+It++gi 
  gi|385805214|ref|YP_005841612.1| 160 RILSGLGTTSFLISQVSVTERGFGGPGVEH-AADGIIRLDLDEYDGQLLRSIIVWKMRGTAHDMRRHPFDITDKGII 235
                                       ******************************.********************************************** PP

                            ATPase 226 vleek 230
                                       ++++k
  gi|385805214|ref|YP_005841612.1| 236 IYHDK 240
                                       *9876 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   1.1e-10   8.6e-08      12     207 ..      28     231 ..      23     238 .. 0.71

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 1.1e-10
                              GvpD  12 tllikGaPGtGktlftlrgl.dvlrresdvlyvstrvddetvseay......fsgeaeldktalldllkdpleldld 81 
                                        ++i G PGtGkt++  ++l + l r +  +yvs       v  a       ++   e  k a++d +  +++   +
  gi|385805214|ref|YP_005841612.1|  28 VVIITGGPGTGKTILSQHFLyNGLVRGEASVYVSLEEHPVQVRRAMatfgwdVKKFEEEGKFAIVDAFTSGIGEAAK 104
                                       5799***************955799999999****9999999988878787744444445889*********98877 PP

                              GvpD  82 vdvPiekldlesllefvdeia...aiatkliialdswelvyeylaerydsPed.....iktvkndlvvlares.gvr 149
                                       ++  +    ++ + e +d i    + ++   + +ds       +++ y + +      +  +k  l  l   s  + 
  gi|385805214|ref|YP_005841612.1| 105 REKYV-VKSVDDVGELIDVIRmaiKETNAQRVVIDS-------VSTLYMTKPAiarntVMQLKRILSGLGTTSfLIS 173
                                       76555.445666666666443000334444455555.......4444444333111123444444444444331577 PP

                              GvpD 150 lvlvletaan.srleyivdGvvtlnvkeddrgrlrrdlrleklrGvrignrlqPftlad 207
                                        v+v+e       +e+ +dG++ l++ e   g+l r++ + k+rG   + r +Pf ++d
  gi|385805214|ref|YP_005841612.1| 174 QVSVTERGFGgPGVEHAADGIIRLDLDEY-DGQLLRSIIVWKMRGTAHDMRRHPFDITD 231
                                       88888876551469************998.7************************9887 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   1.3e-09   9.5e-07      12     156 ..       5     145 ..       1     179 [. 0.72

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1.3e-09
                            AAA_25  12 vadlaapppprrwlvkgllpagelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsedelr 87 
                                       ++++++ +p ++ l+ g +p+  +++++G pgtGKt l  +  +  + +G+           + +yvs+E+   ++r
  gi|385805214|ref|YP_005841612.1|   5 IERVKTWIPGLDELLNGGIPKRNVVIITGGPGTGKTILSQHFLYNGLvRGE-----------ASVYVSLEEHPVQVR 70 
                                       5667888999*********************************99997777...........78*********9999 PP

                            AAA_25  88 rRlravgeal.....................rddarllvldlagveslpLfakdrggtlltadvdaleaaieevegv 143
                                       r ++  g ++                     +++++ +v++                  + + +d ++ ai+e  ++
  gi|385805214|ref|YP_005841612.1|  71 RAMATFGWDVkkfeeegkfaivdaftsgigeAAKREKYVVKS--------------VDDVGELIDVIRMAIKE-TNA 132
                                       999998877777755444444444444443322222222221..............12256778889999999.56* PP

                            AAA_25 144 rlvviDplsralg 156
                                       + vviD++s ++ 
  gi|385805214|ref|YP_005841612.1| 133 QRVVIDSVSTLYM 145
                                       ********99875 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1   4.6e-07   0.00035       2      46 ..      27      69 ..      26      86 .. 0.86
   2 ?    1.1   0.0      0.24   1.8e+02     180     229 ..      92     137 ..      79     148 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 4.6e-07
                           DUF2075  2 avvlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlv 46
                                      +vv++tG++GtGKt++  ++l++     +++ +vy+s  +  v+v
  gi|385805214|ref|YP_005841612.1| 27 NVVIITGGPGTGKTILSQHFLYNG--LVRGEASVYVSLEEHPVQV 69
                                      79*******************998..8999999999888877776 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.24
                           DUF2075 180 vdalldgkkekakplssqenfdirvfddleelkkalkeknkesgrsrlva 229
                                       vda+++g  e+ak    +e++ ++ +dd+ el + ++   ke++  r+v 
  gi|385805214|ref|YP_005841612.1|  92 VDAFTSGIGEAAK----REKYVVKSVDDVGELIDVIRMAIKETNAQRVVI 137
                                       5555544444433....679*****************9999999999986 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 !   20.7   0.0   2.8e-07   0.00021       7     145 ..      13     147 ..       8     175 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.8e-07
                                       HHHHHHCT.SBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHHHHHHHHTXXHHHH.HH CS
                                       xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                            DnaB_C   7 kdLDklts.GlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqRllsseaeidskkl.rt 81 
                                         LD+l++ G+ k +++ii + p++Gkt l  ++  n  v+ +   +++sle +  q+ + + +   +   kk+ ++
  gi|385805214|ref|YP_005841612.1|  13 PGLDELLNgGIPKRNVVIITGGPGTGKTILSQHFLYNGLVRGE-ASVYVSLEEHPVQVRRAMATFGWD--VKKFeEE 86 
                                       56898775268999***********************998666.56678***9999976555554445..5555245 PP

                                       TTSXHHHHHHHHHHHHHHHHSEEEEEEXSSXCHHHHHHHHHHHHHHTTEEEEEEEEGGGTBTSC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  82 gklkeedweklteaieelseaklfiddtpaltvseirskarrlkkekglgliviDyLqlmegse 145
                                       gk+    ++ +t+ i+e ++ + ++ ++ +  v e+   +r   ke++ + +viD +  +  ++
  gi|385805214|ref|YP_005841612.1|  87 GKFAI--VDAFTSGIGEAAKREKYVVKSVD-DVGELIDVIRMAIKETNAQRVVIDSVSTLYMTK 147
                                       77765..67788888888888877777665.688888888888888899999999988776433 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   6.6e-07   0.00049       2      90 ..      26     130 ..      25     159 .. 0.60

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 6.6e-07
                            AAA_14   2 rkilvitGaRrvGKTtllkqlikellvkkesilyinldderd.............kkladpe.....kllelilekl 60 
                                       r++++itG   +GKT l ++++++ lv+ e  +y++l++++              kk+   e      + +++ + +
  gi|385805214|ref|YP_005841612.1|  26 RNVVIITGGPGTGKTILSQHFLYNGLVRGEASVYVSLEEHPVqvrramatfgwdvKKF---EeegkfAIVDAFTSGI 99 
                                       789************************************9994443333333322111...0112222333333332 PP

                            AAA_14  61 ke..ekktylflDEiqevpewekalkslvdeg 90 
                                        e  ++++  +   +  v e+ ++++  ++e+
  gi|385805214|ref|YP_005841612.1| 100 GEaaKREK-YVVKSVDDVGELIDVIRMAIKET 130
                                       22322222.23344444455555555555555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   2.5e-06    0.0019       3      79 ..      27     145 ..      25     156 .. 0.69
   2 ?   -2.9   0.0       6.2   4.6e+03     158     176 ..     185     203 ..     174     223 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.5e-06
                            AAA_24   3 lkiliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdie........swedfldevvel..... 59 
                                       + ++i+G +g+GKT l  ++       g+  +++ +e+  + +++++                              
  gi|385805214|ref|YP_005841612.1|  27 NVVIITGGPGTGKTILSQHFlynglvrGEASVYVSLEE--HPVQVRRAMATFgwdvkkfeE----------Egkfai 91 
                                       5789****************999999988888888888..788888877666443333330..........233336 PP

                            AAA_24  60 ..................................aaeladyktlviDtidelee 79 
                                                                         a ++ + + +viD+++ l+ 
  gi|385805214|ref|YP_005841612.1|  92 vdaftsgigeaakrekyvvksvddvgelidvirmAIKETNAQRVVIDSVSTLYM 145
                                       666666666655555555555555555566668877777788888888888765 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.2
                            AAA_24 158 nelkeevDlvlranlkred 176
                                       + +++ +D ++r++l+++d
  gi|385805214|ref|YP_005841612.1| 185 PGVEHAADGIIRLDLDEYD 203
                                       5688999999999998776 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.4   1.2e-05    0.0086      20     146 ..       9     145 ..       3     169 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.2e-05
                                       --S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEESSS---GGGGHHHHHHTT CS
                             Rad51  20 ttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyidtegtfrperlveiaeryk 96 
                                        t    lDelL+GGi+  ++  i G  ++Gkt l++ +     +        ++ vy++ e    p ++ +    ++
  gi|385805214|ref|YP_005841612.1|   9 KTWIPGLDELLNGGIPKRNVVIITGGPGTGKTILSQHFLYNGLV------RGEASVYVSLEEH--PVQVRRAMATFG 77 
                                       5666679*************************998765332221......2234556665542..333333333343 PP

                                       --HHHHGG..GEEEEE--ST................THHHHHHHHTHHHHHHS-EEEEEEETTTGGGC CS
                             Rad51  97 ldkeevle..nvayaRayti................ehqeellqqaaallaedkfallivDsvtalyR 146
                                        d ++  e  + a+  a+t+                ++  el++ + + ++e++ + +++Dsv +ly 
  gi|385805214|ref|YP_005841612.1|  78 WDVKKFEEegKFAIVDAFTSgigeaakrekyvvksvDDVGELIDVIRMAIKETNAQRVVIDSVSTLYM 145
                                       33333333112333344444445555555555555566667777777777777777777777777765 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   8.6e-05     0.064      32      98 ..       6      72 ..       2      84 .. 0.79
   2 ?    3.3   0.1     0.064        48     109     144 ..     109     144 ..      88     159 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.6e-05
                                      -EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEES.S----HHHH CS
                              RecA 32 etissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafida.ehaldpkya 98
                                      e + +   +ld  l  GG+pk  ++ i G   +Gkt l+ h + +   +g  ++++   eh ++++ a
  gi|385805214|ref|YP_005841612.1|  6 ERVKTWIPGLDELLN-GGIPKRNVVIITGGPGTGKTILSQHFLYNGLVRGEASVYVSLeEHPVQVRRA 72
                                      555555667777776.***********************************99999862587777665 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.064
                                       EEE--SSHHHHHHHHHHHHTTT--SEEEEE-TTT-- CS
                              RecA 109 lvsqpdtGeqaleiadalvrsgaidlivvdsvaalv 144
                                       +v   d   + ++++ + ++ +  + +v+dsv++l 
  gi|385805214|ref|YP_005841612.1| 109 VVKSVDDVGELIDVIRMAIKETNAQRVVIDSVSTLY 144
                                       55555555557999******************9984 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   3.3e-06    0.0025      19     131 ..      25     144 ..      12     185 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.3e-06
                          ATPase_2  19 pneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie.........eeeekkklekalgiav 86 
                                       +++++ i+G  g GKt L ++++ n +  ++  +y++ l+e+  +  + + +         eee k  + +a+ + +
  gi|385805214|ref|YP_005841612.1|  25 KRNVVIITGGPGTGKTILSQHFLYNGLVRGEASVYVS-LEEHPVQVRRAM-AtfgwdvkkfEEEGKFAIVDAFTSGI 99 
                                       5799************************9*9999985.555544433333.33669999999999999999999999 PP

                          ATPase_2  87 pkaeleeilk.eksklvfkaielllekikkkgkkiiiiiDelqkli 131
                                       ++a+  e +  +   +v + i+ + ++ik++  + ++ iD +  l 
  gi|385805214|ref|YP_005841612.1| 100 GEAAKREKYVvKSVDDVGELIDVIRMAIKETNAQRVV-IDSVSTLY 144
                                       99999888888********************998654.57766665 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   6.4e-06    0.0048       9      31 ..      25      47 ..      22      77 .. 0.85
   2 ?   -2.0   0.0       5.5   4.1e+03     102     117 ..     131     146 ..      80     163 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 6.4e-06
                            AAA_19  9 kekvllvtaGpGtGKTrvlkhiv 31
                                      k++v+++t+GpGtGKT + +h +
  gi|385805214|ref|YP_005841612.1| 25 KRNVVIITGGPGTGKTILSQHFL 47
                                      5789************9877765 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 5.5
                            AAA_19 102 eeellivDEfqdvdel 117
                                       +++ +++D ++ ++ +
  gi|385805214|ref|YP_005841612.1| 131 NAQRVVIDSVSTLYMT 146
                                       2335566666655544 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.3e-05    0.0099      45      93 ..      24      72 ..      17     110 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.3e-05
                         IstB_IS21 45 ekkenivllGpsGvGKshlaialgveavraglsvlfvrvedLveelkra 93
                                       k++ ++++G++G+GK+ l+  + +++  +g + ++v++e+   +++ra
  gi|385805214|ref|YP_005841612.1| 24 PKRNVVIITGGPGTGKTILSQHFLYNGLVRGEASVYVSLEEHPVQVRRA 72
                                      5778899**********************999999**999877777766 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.6e-05     0.012     117     148 ..      14      45 ..       4      69 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.6e-05
                             T2SSE 117 kiaevlrkavrerglilvsGgTgsGKttllya 148
                                        ++e+l+  + +r +++++Gg g+GKt+l   
  gi|385805214|ref|YP_005841612.1|  14 GLDELLNGGIPKRNVVIITGGPGTGKTILSQH 45 
                                       578999999******************98754 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   1.5   2.1e-05     0.016       2     107 ..      29     143 ..      28     167 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.1e-05
                                       EEEE--TTSSHHHHHHH.HHHHH...GGGEEEEEEEE....E-------EEEEEET.T--EEEEEETT.....---S CS
                          NTPase_1   2 vfiTGppGvGKtTlvkk.vlellkssgvkvgGfytee....vreggrrigFkivdlasgeegiLarve.....akre 68 
                                       v+iTG pG+GKt l +  +++ l + + +v  +  ee    vr+     g+++ +   +eeg +a v+       + 
  gi|385805214|ref|YP_005841612.1|  29 VIITGGPGTGKTILSQHfLYNGLVRGEASVY-VSLEEhpvqVRRAMATFGWDVKKF--EEEGKFAIVDaftsgIGEA 102
                                       89************87625667776666665.555551222667777789****99..8888888888888877788 PP

                                       SEETTEEE-.HHHHHHHHHHHHHHHH..HHH-EEEE---STT CS
                          NTPase_1  69 prvgkyvvd.vesfeelalealrkal..seadviviDEiGkm 107
                                       ++ +kyvv+ v+++ e  ++++r a+  ++a+ +viD +  +
  gi|385805214|ref|YP_005841612.1| 103 AKREKYVVKsVDDVGE-LIDVIRMAIkeTNAQRVVIDSVSTL 143
                                       8999999982445555.4999999995455669999988665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   3.6e-05     0.027      24      66 ..      24      72 ..      15     169 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.6e-05
                            AAA_16 24 p..elvllsGesGvGKsslvrellr..alekd.ggif.lrgkcdqlesa 66
                                      p  ++v+++G +G+GK+ l +++l    ++++  +++ l+++ +q ++a
  gi|385805214|ref|YP_005841612.1| 24 PkrNVVIITGGPGTGKTILSQHFLYngLVRGEaSVYVsLEEHPVQVRRA 72
                                      34499****************9995332222223555677777776444 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 ?   14.0   0.0   4.4e-05     0.033      20      68 ..      46      94 ..      42     144 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.4e-05
                              MEDS 20 fikaglargekvlyvasastldelrealrkagldvdaalesgqleilda 68
                                      f+ +gl rge+ +yv  +++  ++r+a++  g dv +++e+g++ i+da
  gi|385805214|ref|YP_005841612.1| 46 FLYNGLVRGEASVYVSLEEHPVQVRRAMATFGWDVKKFEEEGKFAIVDA 94
                                      8889**********999***************************99997 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   5.2e-05     0.039       2      19 ..      29      46 ..      28      76 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.2e-05
                            AAA_28  2 ivitGgestGKTtlleaL 19
                                      ++itGg++tGKT l++++
  gi|385805214|ref|YP_005841612.1| 29 VIITGGPGTGKTILSQHF 46
                                      89************9876 PP

>> PAXNEB  PAXNEB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00011     0.081      23      85 ..      12      73 ..       8      90 .. 0.88
   2 ?   -1.0   0.0         1   7.5e+02     188     237 ..     120     158 ..      96     180 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
                            PAXNEB 23 tpsLDklLgGGLplGsillieEdgttdfakvLlkyFlAeGvvqkhevlvlsldddpeewlreL 85
                                      +p LD+lL GG+p  ++++i   g  + +++L + Fl +G+v +   +++sl+++p ++ r +
  gi|385805214|ref|YP_005841612.1| 12 IPGLDELLNGGIPKRNVVIITG-GPGTGKTILSQHFLYNGLVRGEASVYVSLEEHPVQVRRAM 73
                                      689**************99985.677889***************************9998865 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1
                            PAXNEB 188 lnqiqqllkkesfsaptkknvlRivipsLlspllydyppeeskpedllkF 237
                                       ++ i+ ++k+        +n  R+vi s     +++  p +   ++++++
  gi|385805214|ref|YP_005841612.1| 120 IDVIRMAIKE--------TNAQRVVIDSVSTLYMTK--P-AIARNTVMQL 158
                                       3333333333........357788888876666633..3.3334444444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   6.5e-05     0.049       5      31 ..      26      52 ..      24     175 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.5e-05
                            AAA_22  5 agilvvtGesGtGKTtllrrlleqlde 31
                                      ++++++tG +GtGKT l + +l++   
  gi|385805214|ref|YP_005841612.1| 26 RNVVIITGGPGTGKTILSQHFLYNGLV 52
                                      6789***************99987554 PP

>> PPV_E1_C  Papillomavirus helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   7.8e-05     0.058     252     294 ..      15      60 ..       4      66 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.8e-05
                          PPV_E1_C 252 lkefLk.gvPkknclvllGppntGkslfamsli..kfLkGkvlsfv 294
                                       l e+L+ g+Pk+n+++++G p tGk+++++ ++   +++G+   +v
  gi|385805214|ref|YP_005841612.1|  15 LDELLNgGIPKRNVVIITGGPGTGKTILSQHFLynGLVRGEASVYV 60 
                                       556665269*****************99887641135566655555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00017      0.13      18      35 ..      26      43 ..      22      54 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00017
                            AAA_30 18 drvavltGpAGtGKttal 35
                                      + v+++tG++GtGKt + 
  gi|385805214|ref|YP_005841612.1| 26 RNVVIITGGPGTGKTILS 43
                                      569************875 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 ?   10.9   0.0   0.00023      0.17     111     133 ..      23      45 ..      15      98 .. 0.77
   2 ?   -1.5   0.0       1.4   1.1e+03      89     118 ..     127     156 ..     104     177 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00023
                         Parvo_NS1 111 lgkrntvwfyGpantGktnlaea 133
                                       + krn v ++G + tGkt+l + 
  gi|385805214|ref|YP_005841612.1|  23 IPKRNVVIITGGPGTGKTILSQH 45 
                                       679*****************983 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.4
                         Parvo_NS1  89 lslngynpvevgqvllawlskqlgkrntvw 118
                                       +++++++ v++ +v+   ++k    rntv+
  gi|385805214|ref|YP_005841612.1| 127 IKETNAQRVVIDSVSTLYMTKPAIARNTVM 156
                                       566777777777777777888878888775 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00025      0.18       2      21 ..      28      47 ..      27      56 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00025
                                      CEEEEC-TTTCHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqkla 21
                                      +vi++G +G GKT+L q++ 
  gi|385805214|ref|YP_005841612.1| 28 VVIITGGPGTGKTILSQHFL 47
                                      79**************9986 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00043      0.32      29      55 ..      22      48 ..      14      64 .. 0.79
   2 ?   -2.7   0.0       4.9   3.6e+03     144     166 ..     134     156 ..     127     164 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00043
                             AAA_7 29 llknkkpvllvGptGtGKtviikdllk 55
                                       + +++ v+++G  GtGKt++ +++l 
  gi|385805214|ref|YP_005841612.1| 22 GIPKRNVVIITGGPGTGKTILSQHFLY 48
                                      56778899***************9553 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.9
                             AAA_7 144 keikdvqlvaamgppgggrneit 166
                                       + ++d + +  m++p+  rn++ 
  gi|385805214|ref|YP_005841612.1| 134 RVVIDSVSTLYMTKPAIARNTVM 156
                                       45667777777788888877775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); 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: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.52
# Mc/sec: 1436.55
//
Query:       gi|385805215|ref|YP_005841613.1|  [L=525]
Description: metal-dependent hydrolase [Fervidicoccus fontis Kam940]
Scores for complete 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-118  396.6   0.0   3.1e-118  396.3   0.0    1.0  1  Amidohydro_3  Amidohydrolase family
    8.8e-16   58.1   0.0    2.1e-11   43.7   0.0    2.5  2  Amidohydro_1  Amidohydrolase family


Domain annotation for each model (and alignments):
>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  396.3   0.0  3.4e-122  3.1e-118       2     469 ..      54     521 ..      53     524 .. 0.96

  Alignments for each domain:
  == domain 1  score: 396.3 bits;  conditional E-value: 3.4e-122
                      Amidohydro_3   2 viDakGrlvlPGFvDsHtHlagggvnlrllrlpdarvtslegvltavrdqagttpkgrwivgeGwdeaqfaeerfpy 78 
                                       + D++Gr+vlPGF+DsH+Hl++ g+ l++l+l++  v+s+e+++ ++r+++ +   + wi+g+Gwd+ ++  er+p 
  gi|385805215|ref|YP_005841613.1|  54 ILDLNGRVVLPGFIDSHMHLDELGMFLNMLDLRE--VKSVEEMKSMLREYVRK-ARNSWILGHGWDQEKM--ERWP- 124
                                       78**********************999*******..***************99.9***********9985..7899. PP

                      Amidohydro_3  79 alaeldevledapvllaaldtHaavrnsaaldlagiteatpdpaggeilrdangegatgllregafhlvldla.pl. 153
                                       ++++ldev+++ pv+l +++ Haav+n++a++l+g+  +++ p   ++++d+ng  +tg+++e++f+ ++ ++ ++ 
  gi|385805215|ref|YP_005841613.1| 125 TRHDLDEVVKEKPVMLTRICMHAAVLNTKAMELTGLI-NSDLP---GVMKDENGI-PTGVVKEESFEVARRKFsESl 196
                                       ********************************96665.44444...7********.******************555 PP

                      Amidohydro_3 154 areaeaaavaaalaalasyGitsveagggnvsslddleplfeltaeeklplrvi.......ikelldaaerlglpls 223
                                       +++++ ++++ a+  + s+G+t+v   g  ++sl+++++l ++++e+++ +rv          el d ++ lgl+++
  gi|385805215|ref|YP_005841613.1| 197 TIDDYSKFLEDAMNYTSSQGVTTV---GFVSCSLKAFKALMKIKDEGRMKVRVRaylnyqeAMELFDFFKSLGLKRG 270
                                       ************************...**********************************99************** PP

                      Amidohydro_3 224 pgseeltigavklfadgvlgsrtalltepyf.....tgwpdfedealaelvaaadergldvaihaigdaavddvlda 295
                                        g++ l++ ++k++adg+lg rta+l+ py+     +g  ++++++l e+v+aade gl++a+h igd a+d+++ a
  gi|385805215|ref|YP_005841613.1| 271 VGDDMLKLMGIKIIADGSLGARTAWLSSPYSddpenSGHSNIDEQVLMEIVKAADELGLQIAVHGIGDRAIDMIISA 347
                                       ***************************************************************************** PP

                      Amidohydro_3 296 feaa.aekngnqdrrrlehaegvtesqiervaalqvaagvqpvfnfedelldsrlgperargstpvkellnagvkva 371
                                       +e+  + k+ ++   r+eha++++++q+e++a+l++a+++qp+f++ d+++++r+g+er r+ +p+k+++++g+k+ 
  gi|385805215|ref|YP_005841613.1| 348 YEKLgNLKEKRH---RIEHASILRPDQLEKIAELGIAISLQPRFVISDWWIKNRVGEERIRLAYPFKSMIKKGIKLG 421
                                       ****55555555...9************************************************************* PP

                      Amidohydro_3 372 lgsDapvgpfdpwprigaavmrktrrgg..evlrpdeelsleealalyTrgpAkalgledrkGtLevGadADlvvld 446
                                       +++D+pv++++pw ++++ ++r ++++   + ++ de++ lee l  yT+g+A++l++e   G+Le+G++AD++v +
  gi|385805215|ref|YP_005841613.1| 422 FSTDSPVESLNPWETVYSSITRGKYENLpiYEFTKDERINLEESLYFYTEGSAYLLFEESSLGSLEEGKYADFIVVN 498
                                       *************************999************************************************* PP

                      Amidohydro_3 447 adpldvdppelaearvrltvvdG 469
                                       ++p+++d+ e++++++++t+ +G
  gi|385805215|ref|YP_005841613.1| 499 RNPFELDEREIRDVKIEETYLSG 521
                                       *********************99 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   1.4e-05      0.13       1      16 [.      61      75 ..      61     108 .. 0.63
   2 !   43.7   0.0   2.4e-15   2.1e-11     132     330 ..     315     506 ..     280     515 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.4e-05
                                      EEEE-EEEEEEECETT CS
                      Amidohydro_1  1 ivlPGlIDaHvHleqs 16
                                      +vlPG+ID+H Hl   
  gi|385805215|ref|YP_005841613.1| 61 VVLPGFIDSHMHLD-E 75
                                      69***********4.2 PP

  == domain 2  score: 43.7 bits;  conditional E-value: 2.4e-15
                                       HHHHHHHHHHHHHTTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHHH CS
                      Amidohydro_1 132 eelkealkeakkrdlpvaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpteaellke 208
                                         l e++k+a++ +l++a+H  +++++  +++ a+    + g + e ++           ++h   l p+ +e ++e
  gi|385805215|ref|YP_005841613.1| 315 QVLMEIVKAADELGLQIAVHGIGDRAID-MIISAYE---KLGNLKEKRHR----------IEHASILRPDQLEKIAE 377
                                       47899****************9988887.9999999...99889999777..........67777777666666666 PP

                                       HHHHHCEE............HHHHHHHHSEHHHHHHHHHHHHTSCEEEEEECTTSSCCG.....GHHHHHHHHHHHH CS
                      Amidohydro_1 209 rlkeagva............hcpfsnsilrsgrealrkaldeGvkvglgtDgaasgnsl.....nlleelrlalklq 268
                                          ++ ++              +  ++++r    +++ ++++G+k g++tD+     ++     + ++++++     
  gi|385805215|ref|YP_005841613.1| 378 L--GIAISlqprfvisdwwiKNRVGEERIRLAY-PFKSMIKKGIKLGFSTDSPVESLNPwetvySSITRGKYEN--- 448
                                       6..333435566666655556666677777666.9****************77443333344444555566666... PP

                                       HHCCTT.TTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECCCTCGGGTTTCT CS
                      Amidohydro_1 269 rgllye.deegglslkealrmaTingAkalglddkvGsievGkdADlvvvdldilaafvglkk 330
                                        +  ye  ++  + l+e l+++T + A  l  ++ +Gs+e+Gk+AD++vv    + + ++l +
  gi|385805215|ref|YP_005841613.1| 449 -LPIYEfTKDERINLEESLYFYTEGSAYLLFEESSLGSLEEGKYADFIVV----NRNPFELDE 506
                                       .88999988888***************999999*****************....766666644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (525 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 3457.97
//
Query:       gi|385805216|ref|YP_005841614.1|  [L=258]
Description: short-chain dehydrogenase/reductase SDR [Fervidicoccus fontis Kam940]
Scores for complete 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-79  265.5   0.1    4.4e-79  265.3   0.1    1.0  1  adh_short_C2   Enoyl-(Acyl carrier protein) reductase
    5.1e-61  205.5   0.4      6e-61  205.3   0.4    1.1  1  adh_short      short chain dehydrogenase
      3e-13   50.1   0.0    4.6e-13   49.5   0.0    1.1  1  KR             KR domain
    5.8e-05   22.7   0.2    8.6e-05   22.1   0.2    1.4  1  Epimerase      NAD dependent epimerase/dehydratase family
     0.0068   16.3   0.2      0.011   15.7   0.2    1.3  1  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
  ------ inclusion threshold ------
       0.01   15.3   0.1      0.015   14.7   0.1    1.2  1  GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
      0.037   13.3   0.0      0.059   12.6   0.0    1.2  1  ABC_sub_bind   ABC transporter substrate binding protein
      0.052   13.7   0.0        1.5    8.9   0.0    2.2  2  DUF5012        Domain of unknown function (DUF5012)
       0.12   11.7   0.1       0.17   11.2   0.1    1.1  1  YPEB           YpeB sporulation


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 !  265.3   0.1   2.2e-82   4.4e-79       1     234 []      14     256 ..      14     256 .. 0.95

  Alignments for each domain:
  == domain 1  score: 265.3 bits;  conditional E-value: 2.2e-82
                                       TTTTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSE.E..EE--TTSHHHHHHHHHHHHHHHSSEEEE CS
                      adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgae.v..lecDVtdeeqvealveevvekfgklDil 73 
                                       Gaa+gIG+a+A ++a+eGa+v+++d+ e++ kk++ee+++ +g++ v  +++DVt+e++v++++e++ +++g + +l
  gi|385805216|ref|YP_005841614.1|  14 GAARGIGYATAMLAAKEGAKVAVCDVLEDEgKKAAEEIKRTTGNQnVkfYRLDVTNEDEVKRTFEQISKDLGDVYGL 90 
                                       9*****************************9***********9776667**************************** PP

                                       EE-----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSC.CEEEEEEEGGGTSBSTTTTHHHHHHHHH CS
                      adh_short_C2  74 vnnagiapklkgpfletsreefdraldvnlyslfllakaalp.lmkeg.gsivnlssvgaervvpnynaygaaKaal 148
                                       vnnagia   ++p++e++ ee++++++vnl+++fl++k+a+p ++k++ gsivnlss+ + ++ p+   y+a+K+a+
  gi|385805216|ref|YP_005841614.1|  91 VNNAGIAGV-SKPTHEITLEEWNKVINVNLNGVFLCTKHAVPyMIKNNrGSIVNLSSIYGIVGAPDVPPYHASKGAV 166
                                       ********8.********************************5445448**************************** PP

                                       HHHHHHHHHHHGGGTEEEEEEEE--BHCTGGGGSTT....HHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT CS
                      adh_short_C2 149 ealtrylAvelgpkgiRvNavspgpikTlaasgikg....fdelleelearaplgrlgtpeevaeaalfLasdeasy 221
                                         +t+  A  +++++iRvN+v+pg+i+T++++g+++     d+++e+l++ +plgrlg+pee+a++++fL+sde+s+
  gi|385805216|ref|YP_005841614.1| 167 RIMTKVDALFYAKYNIRVNSVHPGFIDTPMVRGYAEgtgnRDAVYEALKKLHPLGRLGRPEEIASVIVFLLSDESSF 243
                                       ******************************8777665555889********************************** PP

                                       --SEEEEESTTGG CS
                      adh_short_C2 222 itGqtlvvDgGlt 234
                                       +tG+++vvDgG+t
  gi|385805216|ref|YP_005841614.1| 244 MTGSEVVVDGGYT 256
                                       ************8 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.3   0.4     3e-64     6e-61       2     191 ..       9     201 ..       8     205 .. 0.98

  Alignments for each domain:
  == domain 1  score: 205.3 bits;  conditional E-value: 3e-64
                                       EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT..TSEEEEEE-TTTSHHHHHHHHHHHHHHHS CS
                         adh_short   2 vvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee..gakalaiqvDvtdreevealvekavkklg 76 
                                       vv++tGa++GIG+a+a   akeGakv+v+d  e++ +++a+e+k++  ++++ ++++Dvt+++ev++++e++ k+lg
  gi|385805216|ref|YP_005841614.1|   9 VVVITGAARGIGYATAMLAAKEGAKVAVCDVLEDEGKKAAEEIKRTtgNQNVKFYRLDVTNEDEVKRTFEQISKDLG 85 
                                       9*********************************************98899************************** PP

                                       SESEEEE---S.S--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHH CS
                         adh_short  77 kldvLvnNAGi.tgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAs 152
                                        +  LvnNAGi   s+p++e++ eew++vi+vNl+gvfl+t++++p+m+k+++G+Ivn sS+ g v+ + v++Y As
  gi|385805216|ref|YP_005841614.1|  86 DVYGLVNNAGIaGVSKPTHEITLEEWNKVINVNLNGVFLCTKHAVPYMIKNNRGSIVNLSSIYGIVGAPDVPPYHAS 162
                                       ***********88899************************************************************* PP

                                       HHHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHHC CS
                         adh_short 153 KaavagltrslakelaptgirvnavaPGlvdTdmakelr 191
                                       K+av+ +t+  a  +a+++irvn+v+PG++dT+m++   
  gi|385805216|ref|YP_005841614.1| 163 KGAVRIMTKVDALFYAKYNIRVNSVHPGFIDTPMVRGYA 201
                                       **********************************98765 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5   0.0   2.3e-16   4.6e-13       3     152 ..      10     162 ..       9     171 .. 0.84

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 2.3e-16
                                       EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHS CS
                                KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaee 79 
                                       ++itG++ g+G ++a   a++ga+  v+   +  + ++++++i++ +  + +v+++++Dv+++d+v++++e+i+++ 
  gi|385805216|ref|YP_005841614.1|  10 VVITGAARGIGYATAMLAAKEGAKVAVCDVLE-DEGKKAAEEIKRTTG-NQNVKFYRLDVTNEDEVKRTFEQISKDL 84 
                                       79************999999998866655555.455555555554443.569************************* PP

                                       S---EEEE------.---TTT--HHHHHHHHTTTTHHHHHHHHHTTT....S--SEEEEEEEHHHHH--TT-HHHHH CS
                                KR  80 ppikGvihaAgvlr.dklleemtaedleqvlapKvkGawnLhelled....esldffvlfSSiagllgsagqanYaa 151
                                       + + G ++ Ag++   k+  e t e++++v++  ++G+    +   +    ++   +v +SSi g++g++    Y a
  gi|385805216|ref|YP_005841614.1|  85 GDVYGLVNNAGIAGvSKPTHEITLEEWNKVINVNLNGVFLCTKHAVPymikNNRGSIVNLSSIYGIVGAPDVPPYHA 161
                                       ************997899*******************9877654443366589999**************9999988 PP

                                       H CS
                                KR 152 a 152
                                        
  gi|385805216|ref|YP_005841614.1| 162 S 162
                                       5 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.2   4.3e-08   8.6e-05       1      66 [.      10      83 ..      10     171 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 4.3e-08
                                      EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC........EEEE--TT-HHHHHHHHHHHT-S CS
                         Epimerase  1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl........elveldltdrsalerlfkeeqpd 66
                                      +++tGa+  iG a++   +++g +v + d l++++++a++e +        ++++ld+t++++++r f++   d
  gi|385805216|ref|YP_005841614.1| 10 VVITGAARGIGYATAMLAAKEGAKVAVCDVLEDEGKKAAEEIKrttgnqnvKFYRLDVTNEDEVKRTFEQISKD 83
                                      68*****************************99999888877799***********************987544 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 !   15.7   0.2   5.4e-06     0.011      10      68 ..      19      81 ..       9      91 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.4e-06
                                      CHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHH.HCCTTTTSS-...HHHHCCCHHCEE CS
                           3HCDH_N 10 mGagiaavfasagleVvlvdiseealekalekieksl.eklvekgklk...eeeveaalaris 68
                                      +G   a+++a++g +V ++d+ e+  +ka+e+i++++ ++ v+  +l+   e+ev++++++is
  gi|385805216|ref|YP_005841614.1| 19 IGYATAMLAAKEGAKVAVCDVLEDEGKKAAEEIKRTTgNQNVKFYRLDvtnEDEVKRTFEQIS 81
                                      79999*****************************95413444444444444888888887776 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 ?   14.7   0.1   7.5e-06     0.015       2      76 ..      12      82 ..      11      97 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 7.5e-06
                                      EETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT- CS
                     GDP_Man_Dehyd  2 iTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqp 76
                                      iTG a  iG  +a l  ++g +v + + ++++ + +  e++++      ++n+k+++ D+t++++++r ++++  
  gi|385805216|ref|YP_005841614.1| 12 ITGAARGIGYATAMLAAKEGAKVAVCDVLEDEGK-KAAEEIKRTT---GNQNVKFYRLDVTNEDEVKRTFEQISK 82
                                      9999999******999*******99988888766.5667776543...5789******************99864 PP

>> ABC_sub_bind  ABC transporter substrate binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0     3e-05     0.059     137     194 ..      36      93 ..      30     104 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3e-05
                                       EE-TT-HHHHHHHHHHHHHHHHTT-EEEEEE-SSGGGHHHHHHHHHTT-SEEEE-S-H CS
                      ABC_sub_bind 137 lyspgeansvslveelkklakkaglkvveaavknvndvesavsslaekvdaiyiltdn 194
                                       ++   e+  ++++ee+k++  ++++k + + v n  +v+ + +++ ++   +y l +n
  gi|385805216|ref|YP_005841614.1|  36 VCDVLEDEGKKAAEEIKRTTGNQNVKFYRLDVTNEDEVKRTFEQISKDLGDVYGLVNN 93 
                                       6777799999*************************************99999988877 PP

>> DUF5012  Domain of unknown function (DUF5012)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.082   1.6e+02      13      55 ..      46      89 ..      38     119 .. 0.77
   2 ?    8.9   0.0   0.00077       1.5      12      45 ..     159     193 ..     154     214 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.082
                                      EE-SSEEEEE.SS-EEE---EEEEE.EEETTEEEES-TTTTTTT CS
                           DUF5012 13 tvaeGskrlsggavveyagyevtie.kiaPGlfyisdflGGyyd 55
                                      ++ae  kr++g++ v++ + +vt e +++  + +is  lG  y 
  gi|385805216|ref|YP_005841614.1| 46 KAAEEIKRTTGNQNVKFYRLDVTNEdEVKRTFEQISKDLGDVYG 89
                                      56677899999999***99*99986257888889**99999986 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00077
                                       EEE-SSEEEEE..SS-EEE---EEEEEEEETTEEE CS
                           DUF5012  12 ytvaeGskrlsg.gavveyagyevtiekiaPGlfy 45 
                                       y++ +G+ r  +      ya+y++ ++ + PG+  
  gi|385805216|ref|YP_005841614.1| 159 YHASKGAVRIMTkVDALFYAKYNIRVNSVHPGFID 193
                                       888899999876466778**************975 PP

>> YPEB  YpeB sporulation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   8.3e-05      0.17     209     273 ..      29      93 ..      22     106 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 8.3e-05
                              YPEB 209 eeeakkiakkflgkk.kaekvevvesekkgkipaYsvevkdkkakkeeitvdvskkGGhviwllne 273
                                       +e ak  + ++l+++ k+++ e + ++ ++++++Y++ v+++++ k+ +  ++sk  G+v+ l+n+
  gi|385805216|ref|YP_005841614.1|  29 KEGAKVAVCDVLEDEgKKAAEEIKRTTGNQNVKFYRLDVTNEDEVKR-TFEQISKDLGDVYGLVNN 93 
                                       56788888899999989999999999***************998887.999********9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       768  (0.0428356); expected 358.6 (0.02)
Passed bias filter:                      678  (0.0378158); 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: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1630.61
//
Query:       gi|385805217|ref|YP_005841615.1|  [L=38]
Description: hypothetical protein FFONT_0171 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); 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 0.25s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 263.19
//
Query:       gi|385805218|ref|YP_005841616.1|  [L=56]
Description: hypothetical protein FFONT_0172 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       212  (0.0118244); 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:                         0  (0); expected 0.2 (1e-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 0.34s 00:00:00.79 Elapsed: 00:00:00.53
# Mc/sec: 318.45
//
Query:       gi|385805219|ref|YP_005841617.1|  [L=51]
Description: hypothetical protein FFONT_0173 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       116  (0.00646996); expected 358.6 (0.02)
Passed bias filter:                      106  (0.00591221); 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: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.52
# Mc/sec: 294.64
//
Query:       gi|385805220|ref|YP_005841618.1|  [L=358]
Description: ATPase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-15   58.2   0.3    1.1e-15   58.2   0.3    1.9  2  ATPase_2  ATPase domain predominantly from Archaea
    6.2e-10   39.2   0.1    0.00081   19.4   0.0    2.8  3  AAA_14    AAA domain
    4.2e-06   27.1   0.1    1.3e-05   25.5   0.0    1.8  2  AAA_22    AAA domain
     0.0032   17.9   0.0     0.0093   16.4   0.0    1.8  1  AAA_16    AAA ATPase domain
  ------ inclusion threshold ------
       0.11   12.5   0.0       0.28   11.1   0.0    1.8  1  PUB       PUB domain
       0.12   12.4   0.0       0.26   11.4   0.0    1.5  1  BTB_3     BTB/POZ domain
       0.13   12.7   0.0       0.43   11.0   0.0    1.9  1  AAA       ATPase family associated with various cellular acti
       0.14   12.4   1.0         16    5.9   0.1    3.1  3  BLOC1_2   Biogenesis of lysosome-related organelles complex-1


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 !   58.2   0.3   4.9e-19   1.1e-15       5     228 ..      18     249 ..      14     254 .. 0.76
   2 ?   -2.8   0.0       2.1   4.8e+03     212     222 ..     261     271 ..     256     283 .. 0.85

  Alignments for each domain:
  == domain 1  score: 58.2 bits;  conditional E-value: 4.9e-19
                          ATPase_2   5 ekelkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdk.yviyyi....alreesiskldefie...... 70 
                                       eke + l++ + +   + +++ G ++ GKt+L+   ++ +   d  yv++ +    + r++  + l+   e      
  gi|385805220|ref|YP_005841618.1|  18 EKEFEFLKKNIGE---PLLVVSGLRRTGKTSLILSTLNDS---DIpYVFFDMrsmpNSRRDLYHLLS---Egltdfl 85 
                                       6667777766666...8899*************9999888...331555533111122333333333...2444666 PP

                          ATPase_2  71 .....eeeekkklekal........giavpkaeleeilk..eksklvfkaielllekikkkgkkiiiiiDelqklid 132
                                            +    +k+ k l        gi v  +e+   l+  + ++ + + + +l e+  + g k +i++Delq++  
  gi|385805220|ref|YP_005841618.1|  86 trisnK----EKFYKSLtkmlklirGISVDGFEVS--LSwgKDRASLVEILRALDESCVEHGIKAVIVFDELQRVT- 155
                                       654432....3333333555688777777777774..445699999******************************. PP

                          ATPase_2 133 lglngaellvkeLlnliesltke.khlcvviclsSeglfiervyn.eselegrhky.ilvddldketalnflkegfk 206
                                             ++l  eL+n+i + + + ++l +++ +s+ g++ +  ++ +++l+gr+   ++ + ldke++ +flk+gf+
  gi|385805220|ref|YP_005841618.1| 156 ------GKLSVELANAIAYSYDHlRNLSFIVSGSEMGVLYRFFDEpNAPLYGRAYLeVKTRRLDKEKSIDFLKRGFE 226
                                       ......6899999**99999988357889999********9665439*******999******************** PP

                          ATPase_2 207 el.eelskedfeeiyryvGGkPk 228
                                       e  +  ++e++e +++ ++G+ +
  gi|385805220|ref|YP_005841618.1| 227 ESkIRVNDEELEAAVDKLDGIIG 249
                                       **7778**********9999865 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.1
                          ATPase_2 212 skedfeeiyry 222
                                       ++ dfe i+r 
  gi|385805220|ref|YP_005841618.1| 261 QNRDFESIWRE 271
                                       7899****996 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   2.7e-06    0.0061       3      57 ..      31      78 ..      29     103 .. 0.64
   2 !   19.4   0.0   3.6e-07   0.00081      53     107 ..     130     190 ..     111     207 .. 0.79
   3 ?   -1.8   0.0       1.3     3e+03      78     118 ..     279     322 ..     274     341 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.7e-06
                            AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelil 57
                                      ++lv++G+Rr+GKT l+   ++++      i y+ +d  +  +++    l++l+ 
  gi|385805220|ref|YP_005841618.1| 31 PLLVVSGLRRTGKTSLILSTLNDSD-----IPYVFFDMRSMPNSRRD--LYHLLS 78
                                      5799************999986665.....66666665555333322..333333 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 3.6e-07
                            AAA_14  53 lelilek.lkeekktylflDEiqev.....pewekalkslvdegknldvivtGSnskllsk 107
                                       l+++ e+ +++  k ++++DE q+v      e+ +a+ + +d+ +nl +iv+GS  ++l++
  gi|385805220|ref|YP_005841618.1| 130 LRALDEScVEHGIKAVIVFDELQRVtgklsVELANAIAYSYDHLRNLSFIVSGSEMGVLYR 190
                                       4444444333346789*********8888889***********************999976 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.3
                            AAA_14  78 ewekalkslvdeg...knldvivtGSnskllskeiatslagrva 118
                                       e+e++lk+ v  +     l++++ G      +k+  ++l grv 
  gi|385805220|ref|YP_005841618.1| 279 ELENFLKNRVSAEryrAVLKFLANGEREWKELKKKMEDLEGRVL 322
                                       55666666666331223356667776666666777777777765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   5.7e-09   1.3e-05       6     131 ..      31     184 ..      28     191 .. 0.91
   2 ?   -2.4   0.0       2.4   5.3e+03      39      58 ..     293     312 ..     274     346 .. 0.56

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 5.7e-09
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllrellralglelka........... 70 
                                        +lvv G   tGKT l+   l+           + ++vf+++ s   s++dl++ l + l++ l +           
  gi|385805220|ref|YP_005841618.1|  31 PLLVVSGLRRTGKTSLILSTLNDS---------DIPYVFFDMRSMPnSRRDLYHLLSEGLTDFLTRisnkekfyksl 98 
                                       5799**************999998.........9**********9999*************9888899********* PP

                            AAA_22  71 .......................erlsseellealeqalraravielliiDEaqhlr...seealeeLrsllnlsrk 121
                                                               r+s+ e+l+al + + +++ +++++ DE q+++   s e+ + +   ++ +  
  gi|385805220|ref|YP_005841618.1|  99 tkmlklirgisvdgfevslswgkDRASLVEILRALDESCVEHGIKAVIVFDELQRVTgklSVELANAIAYSYD-HLR 174
                                       ********************************************************77666888888877777.899 PP

                            AAA_22 122 gvqliLvGtp 131
                                       ++++i+ G +
  gi|385805220|ref|YP_005841618.1| 175 NLSFIVSGSE 184
                                       9999999976 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.4
                            AAA_22  39 rpevvfvtlpsstsskdllr 58 
                                        + v+++ ++++ ++k+l +
  gi|385805220|ref|YP_005841618.1| 293 YRAVLKFLANGEREWKELKK 312
                                       33333444444444444433 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   4.2e-06    0.0093      22     147 ..      29     154 ..      18     179 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.2e-06
                            AAA_16  22 grpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawr 98 
                                       g+ +l+++sG + +GK+sl+ + l+     +++f   +   +++   y  l + l + ++l+ + ++      e + 
  gi|385805220|ref|YP_005841618.1|  29 GE-PLLVVSGLRRTGKTSLILSTLNDSDIPYVFF-DMRSMPNSRRDLYHLLSEGL-T-DFLTRISNK------EKFY 95 
                                       44.7999*************88888777665444.44444442222233355555.3.333333333......3333 PP

                            AAA_16  99 ekleeala..........avpelagaeasrllellkrllallsrderplvlvlDdlqwa 147
                                       + l++ l+          +v+   g+++ +l e l++l + + +++ + v+v+D+lq++
  gi|385805220|ref|YP_005841618.1|  96 KSLTKMLKlirgisvdgfEVSLSWGKDRASLVEILRALDESCVEHGIKAVIVFDELQRV 154
                                       3344444444455344444444444444888888877777777666679******9976 PP

>> PUB  PUB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00013      0.28      29      66 ..     229     265 ..     209     285 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00013
                               PUB  29 rIrleNkafkekvlplegavelLealGFeekneeeeef 66 
                                       +Ir++++ +++ v++l+g++ +L+ +G+ ++  ++ +f
  gi|385805220|ref|YP_005841618.1| 229 KIRVNDEELEAAVDKLDGIIGWLTYYGYSRTM-QNRDF 265
                                       79**************************8764.45543 PP

>> BTB_3  BTB/POZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00011      0.26       6      68 ..     241     303 ..     236     308 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                             BTB_3   6 vdetrfvvdkelfrahPdtllgrmfgsslesnltkpnekGeyevaegisaevfraildyykkG 68 
                                       vd+   ++   ++  +  t+  r f s   + +t + ++ e  +++ +sae +ra+l++  +G
  gi|385805220|ref|YP_005841618.1| 241 VDKLDGIIGWLTYYGYSRTMQNRDFESIWREAVTMARQELENFLKNRVSAERYRAVLKFLANG 303
                                       566666677777778899*********999999999999999*****************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 ?   11.0   0.0   0.00019      0.43       2      74 ..      34     158 ..      33     188 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00019
                                       EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS......................................... CS
                               AAA   2 llyGppGtGKTllakavakelgvefleisgsellsk......................................... 37 
                                       +++G   tGKT+l+ +  ++++++++ +++ ++ ++                                         
  gi|385805220|ref|YP_005841618.1|  34 VVSGLRRTGKTSLILSTLNDSDIPYVFFDMRSMPNSrrdlyhllsegltdfltrisnkekfyksltkmlklirgisv 110
                                       5788889**************99988888888776667888888888888888888888888899999999999999 PP

                                       .......STTHHHHHHHHHHHHHHHTS....TSEEEEEETGGGHHHHH CS
                               AAA  38 .......yvgesekkirelfkeakeka....kpsilfiDEidalaksr 74 
                                               +g+  +++ e+++++ e+      + ++++DE+ +++++ 
  gi|385805220|ref|YP_005841618.1| 111 dgfevslSWGKDRASLVEILRALDESCvehgIKAVIVFDELQRVTGKL 158
                                       9999999999999999999999877768885449*******9998876 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.94   2.1e+03      37      70 ..      75     108 ..      64     111 .. 0.69
   2 ?    3.1   0.0     0.054   1.2e+02      73      88 ..     233     248 ..     226     252 .. 0.80
   3 ?    5.9   0.1     0.007        16      29      61 ..     286     318 ..     271     322 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.94
                           BLOC1_2  37 kklkdvaaslekkleklnekyeelqpylqqidqi 70 
                                       + l++ + ++ + +++ ++ y++l ++l+ i  i
  gi|385805220|ref|YP_005841618.1|  75 HLLSEGLTDFLTRISNKEKFYKSLTKMLKLIRGI 108
                                       5555666666667777777788888888877766 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.054
                           BLOC1_2  73 qvteLeeavseLDeys 88 
                                       + +eLe+av++LD ++
  gi|385805220|ref|YP_005841618.1| 233 NDEELEAAVDKLDGII 248
                                       5589*********987 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.007
                           BLOC1_2  29 Neaasekykklkdvaaslekkleklnekyeelq 61 
                                       N++++e+y ++ + +a+ e++ ++l++k e l+
  gi|385805220|ref|YP_005841618.1| 286 NRVSAERYRAVLKFLANGEREWKELKKKMEDLE 318
                                       999*************************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       824  (0.0459591); expected 358.6 (0.02)
Passed bias filter:                      633  (0.0353059); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.68u 0.33s 00:00:01.01 Elapsed: 00:00:00.53
# Mc/sec: 2023.95
//
Query:       gi|385805221|ref|YP_005841619.1|  [L=166]
Description: hypothetical protein FFONT_0176 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-06   27.3   2.3      0.017   15.5   0.2    2.2  1  Rubrerythrin     Rubrerythrin
     0.0038   17.4   0.0     0.0055   16.9   0.0    1.2  1  RuBisCO_large_N  Ribulose bisphosphate carboxylase large chai
  ------ inclusion threshold ------
        0.2   11.8   0.8       0.62   10.3   0.2    2.0  2  CHCH             CHCH 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 !   15.5   0.2   2.8e-06     0.017      18      54 ..     124     157 ..     115     166 .] 0.83

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.8e-06
                                       HHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Rubrerythrin  18 kelaekakegypqiaelFeelAeeEreHakilnklle 54 
                                       ++l e++k   + i+++Fe + e+E++H+k+l +ll 
  gi|385805221|ref|YP_005841619.1| 124 RILGENLK---GGIKKIFELIEEDEKKHEKLLMDLLI 157
                                       56788888...899*****************999875 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 !   16.9   0.0   9.1e-07    0.0055      47     101 ..      73     130 ..      58     144 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 9.1e-07
                   RuBisCO_large_N  47 vsttkdellkklkakvyeieevee....ekelvkiAYplelFeegsipqllssiaGnif 101
                                       ++ ++ + +k+lka v++i+++++    e   + + Y+  ++ee  ++++++ i+G ++
  gi|385805221|ref|YP_005841619.1|  73 LFMDSLNSIKQLKASVFKIDKISDeqiyEIISMLVNYEGGVYEE-ALSSIITRILGENL 130
                                       566777899************98744444455777888888876.57888888888776 PP

>> CHCH  CHCH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.2    0.0001      0.62       3      14 ..       2      13 ..       2      18 .. 0.88
   2 ?   -1.1   0.0      0.37   2.2e+03      15      24 ..      60      68 ..      58      70 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0001
                                      HHHHHHHHHHHH CS
                              CHCH  3 eefkeylkClkd 14
                                      eefkeylkCl+d
  gi|385805221|ref|YP_005841619.1|  2 EEFKEYLKCLRD 13
                                      7*********97 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.37
                                      CTSSTTTTHH CS
                              CHCH 15 nsdefskCrk 24
                                      +sd  ++Cr+
  gi|385805221|ref|YP_005841619.1| 60 SSD-EDLCRD 68
                                      555.999*97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       973  (0.0542696); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); 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: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1010.82
//
Query:       gi|385805222|ref|YP_005841620.1|  [L=440]
Description: 4-aminobutyrate aminotransferase-related aminotransferase [Fervidicoccus fontis Kam940]
Scores for complete 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-117  390.9   0.0   6.5e-117  390.6   0.0    1.0  1  Aminotran_3  Aminotransferase class-III
  ------ inclusion threshold ------
      0.057   12.8   0.0      0.095   12.1   0.0    1.3  1  DUF4159      Domain of unknown function (DUF4159)


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 !  390.6   0.0  7.3e-121  6.5e-117      10     404 ..      26     431 ..      18     433 .. 0.96

  Alignments for each domain:
  == domain 1  score: 390.6 bits;  conditional E-value: 7.3e-121
                                       CEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT-. CS
                       Aminotran_3  10 llvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapkg 86 
                                       ++ + ++e+++l d +gk+y+D++s+i v+ lGha+P++++a+ eq+ kl+h+s+ +l++ ++++la+k+ ++ p++
  gi|385805222|ref|YP_005841620.1|  26 PITVIRGENAFLFDTEGKKYIDFTSGIGVTSLGHANPELIDAAVEQLRKLWHISIMNLNYPSYVELAKKISEVSPGK 102
                                       58899**********************************************************************96 PP

                                       .S.EEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHH..HHHHSS--TTTTTTCTTB-TSEEEE CS
                       Aminotran_3  87 ld.kvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlg..alsvtgskkkyktlfgpflpevvrl 160
                                          +v + nsGseA+ +A+K+ar+      at ++ i+af++afHGr  +  al++tg+ ++yk+ ++pf+ +v  l
  gi|385805222|ref|YP_005841620.1| 103 EKkRVAFWNSGSEAIDNAIKVARQ------ATGRHVIVAFENAFHGRGTYgpALAATGKYMPYKESMEPFSQGVELL 173
                                       5569********************......*****************765468************************ PP

                                       -TTBGGGTB-HHHHHHHHHHHHHHHH......CHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEE CS
                       Aminotran_3 161 kypdeevlkeneeeeaalleeleale......kkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvlliv 231
                                       +yp+++++++++e  ++ l +l  ++      +   + +aA+++E iqgegG+vv+++e++++l+++ + +++lli 
  gi|385805222|ref|YP_005841620.1| 174 PYPYCYRCPFRHEYPECGLACLDYMKkwfthaRYPPNRIAAFLMEMIQGEGGFVVPPKEYVKELKSFLESNGILLID 250
                                       *****************99999999988898778899**************************************** PP

                                       E-TTTTTTTTSSSSGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTSB--TTTT-HHHHHHHHHHHHHH CS
                       Aminotran_3 232 DEvqtGfGrTGklfAlehagvspDlmtlaKaltgGlplsavlataevmqalapgshgsTfgGnplacavalavleii 308
                                       DEvq Gf+rTGk++A+eh++v+pD+m++aKa+++Glpls +++++ +++ ++ gs g+TfgGnp+ cav l+vlei+
  gi|385805222|ref|YP_005841620.1| 251 DEVQAGFARTGKMWAVEHFDVEPDIMAFAKAVANGLPLSGIAVRESIAEKVHLGSLGGTFGGNPVSCAVGLKVLEIM 327
                                       ***************************************************************************** PP

                                       HHTTHHHHHHHHHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTC......HHHHHHHHHCTEE-EEETT CS
                       Aminotran_3 309 eeekllenaqelgaalkegLeelqkkyevikevRgkGlmiaielkeeaevke......keilkkakekGvlilsaGd 379
                                       ++++l  +a+ lg++++++Lee+ +kye i++vRg+G m aie+++++++ke      k+i++ a+e G+l+l aG 
  gi|385805222|ref|YP_005841620.1| 328 KRDNLPARAEMLGRIIRKRLEEMYEKYEIIGDVRGLGIMQAIEIVKDRKTKEpdeditKKIINTARERGLLLLIAGL 404
                                       *************************************************9999*****99***********999998 PP

                                       ..TEEEE---TT--HHHHHHHHHHHHH CS
                       Aminotran_3 380 ..nvirllppliitdeeidelleilkk 404
                                         nvirl ppl+i+++ ++ +l+il +
  gi|385805222|ref|YP_005841620.1| 405 ysNVIRLHPPLTIEEDVLKRGLDILDE 431
                                       88*********************9976 PP

>> DUF4159  Domain of unknown function (DUF4159)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.1e-05     0.095      61      95 ..     225     258 ..     219     299 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.1e-05
                                       S------HHHHHHHHHHHTT-EEEEEE-SSSSHHH CS
                           DUF4159  61 gnvkfssaeakaLraYlrkGGfLliDdrgygaaea 95 
                                       g v ++++ +k+L+++l++ G+LliDd   +a++a
  gi|385805222|ref|YP_005841620.1| 225 GFVVPPKEYVKELKSFLESNGILLIDDE-VQAGFA 258
                                       445566699******************5.554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.31s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 2661.07
//
Query:       gi|385805223|ref|YP_005841621.1|  [L=820]
Description: Thermopsin, endopeptidase A5 [Fervidicoccus fontis Kam940]
Scores for complete 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-87  291.2  17.5    6.8e-87  291.2  17.5    2.5  4  Thermopsin     Thermopsin
    5.2e-08   33.4   1.0      0.098   13.3   0.0    5.3  7  Ig_3           Immunoglobulin domain
    1.6e-06   28.6   4.0     0.0068   16.9   0.1    4.3  4  Cadherin-like  Cadherin-like beta sandwich domain
    2.9e-05   24.0   0.0      0.025   14.6   0.0    2.9  3  BiPBP_C        Penicillin-Binding Protein C-terminus Family
    5.2e-05   22.9   0.3       0.12   12.1   0.0    3.4  3  PKD_3          PKD-like domain
     0.0064   16.1   0.1        2.1    8.0   0.0    2.8  3  ChitinaseA_N   Chitinase A, N-terminal domain
  ------ inclusion threshold ------
      0.059   13.7   4.9        1.3    9.5   0.1    4.4  5  Ig_2           Immunoglobulin domain
       0.79    9.7   0.0       0.79    9.7   0.0    2.8  4  L51_S25_CI-B8  Mitochondrial ribosomal protein L51 / S25 / CI
        1.8    8.4  33.4       0.34   10.7   1.4    5.8  6  SprB           SprB repeat


Domain annotation for each model (and alignments):
>> Thermopsin  Thermopsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.8       2.8   5.6e+03     132     165 ..      49      81 ..      22     135 .. 0.61
   2 !  291.2  17.5   3.4e-90   6.8e-87       3     259 ..     146     407 ..     144     408 .. 0.98
   3 ?   -2.3   0.2       1.3   2.5e+03     130     171 ..     552     592 ..     545     628 .. 0.74
   4 ?   -2.5   0.1       1.4   2.8e+03     156     195 ..     645     684 ..     592     700 .. 0.66

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.8
                        Thermopsin 132 YyayateylelslPltlkLvinvsltsngvpevs 165
                                       Y +++++y+ l +P++++  +n +   n +++v+
  gi|385805223|ref|YP_005841621.1|  49 YVSIQPNYF-LYYPIQVESGMNITFEVNSSEIVD 81 
                                       455555532.334444444444444433332332 PP

  == domain 2  score: 291.2 bits;  conditional E-value: 3.4e-90
                        Thermopsin   3 vnvlslyssepaPmGiadyGiknnsgkltpysyntssvlGevnisslsaynsssn...spesaslQLNvvlevvtgg 76 
                                       ++v+s+y+s paP+GiadyG+ n+sg l+py++ +++ +G +ni+s++ayns+s    s+++aslQLNvvl+v+t+ 
  gi|385805223|ref|YP_005841621.1| 146 IDVYSYYNSLPAPIGIADYGVVNSSGVLIPYELLYKEAIGIANIYSIEAYNSTSPsgvSEYGASLQLNVVLQVNTTY 222
                                       689***************************************************999999***************** PP

                        Thermopsin  77 ktysywvQnVvsfnttekqltfidNiWNftspsanlsnsaisGnGtvyasskgefYyayateylelslPltlkLvin 153
                                       ++y+ywvQnV +f t++++l f+dN+WNfts+ + l+n++++GnG+vy ++ ge Yyay+te+ +++lPl+lkL+++
  gi|385805223|ref|YP_005841621.1| 223 GSYTYWVQNVPNFWTNNNTLFFVDNVWNFTSHFSFLTNQSVKGNGYVYVDNVGEDYYAYSTEMRKYTLPLNLKLAVS 299
                                       ***************************************************************************** PP

                        Thermopsin 154 vsltsngvpevsFgYsid..ggvvtYDnvtinstgkasaeilvngssltpsgllyDaeLvlgGpgngekttfnslna 228
                                       ++ +sn+v ++sFgYs+   +++++YD+v+i +tg +sa+++++g+s+tpsg++yD+eLv+gG+gn e+t+f+++na
  gi|385805223|ref|YP_005841621.1| 300 ENFSSNAV-YISFGYSLGesEEITWYDKVIIPQTGITSASFIISGFSQTPSGHFYDSELVFGGEGNREITNFTKMNA 375
                                       ****9999.*******889999******************************************************* PP

                        Thermopsin 229 tlsLyY.lngtnyqpvknaydfGsdTaEtaen 259
                                       +l+L+Y l++++++ + ++y fGsdTaE+a++
  gi|385805223|ref|YP_005841621.1| 376 QLMLKYvLENETIVLPMSLYGFGSDTAEGADD 407
                                       ******888888*****************987 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1.3
                        Thermopsin 130 efYyayateylelslPltlkLvinvsltsngvpevsFgYsid 171
                                       +fY+  +t ++++s+ ++ +L+ + s  ++g+ +v+ +Y  +
  gi|385805223|ref|YP_005841621.1| 552 SFYAFNGTPQYTYSIYANGSLIDSGSILQQGS-KVNVTYAPS 592
                                       57777777779999999999999999999997.999999855 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 1.4
                        Thermopsin 156 ltsngvpevsFgYsidggvvtYDnvtinstgkasaeilvn 195
                                       ++s+g p  +++++i+g+ v + + +   + +   +++v+
  gi|385805223|ref|YP_005841621.1| 645 NVSSGTPPFMYIWMINGTPVAFNTSQYILNATYPGSYYVK 684
                                       2245555666666666667777666666666555566655 PP

>> Ig_3  Immunoglobulin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       2.7   5.4e+03      57      79 .]     106     128 ..      61     128 .. 0.55
   2 ?   -3.8   0.1         9   1.8e+04      54      74 ..     204     226 ..     196     231 .. 0.45
   3 ?   -1.7   0.0       2.3   4.6e+03      31      72 ..     319     351 ..     314     353 .. 0.67
   4 ?   -0.5   0.0         1     2e+03      14      44 ..     452     483 ..     442     522 .. 0.69
   5 ?    1.0   0.0      0.34   6.8e+02       8      50 ..     538     581 ..     532     612 .. 0.68
   6 !   11.6   0.0   0.00017      0.34       1      67 [.     622     688 ..     622     695 .. 0.71
   7 !   13.3   0.0   4.9e-05     0.098       7      49 ..     716     758 ..     707     790 .. 0.66

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.7
                                       CTEEEESS--GGG-EEEEEEEEE CS
                              Ig_3  57 sssLtisnvtksdsGtYtCvAsN 79 
                                        +  +  n+ + + GtY+ v+ N
  gi|385805223|ref|YP_005841621.1| 106 RGYNISANIGPMHYGTYYLVVYN 128
                                       33333445777888888877766 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 9
                                       ECCCTEEEESS--..GGG-EEEE CS
                              Ig_3  54 egssssLtisnvt..ksdsGtYt 74 
                                       +++++sL+++ v    +  G+Yt
  gi|385805223|ref|YP_005841621.1| 204 SEYGASLQLNVVLqvNTTYGSYT 226
                                       34444444444321133366666 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2.3
                                       -EEEEEETTS...TTCSEEESSEECCCTEEEESS--GGG-EE CS
                              Ig_3  31 ptitWykngeklssnstsssissegssssLtisnvtksdsGt 72 
                                        +itWy +     +       +++ +s+s++is  +++ sG 
  gi|385805223|ref|YP_005841621.1| 319 EEITWYDKVI--IP-------QTGITSASFIISGFSQTPSGH 351
                                       4789998766..34.......246777888888877777766 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 1
                                       ETTS-EEEEEEEEEES--.EEEEEETTS...T CS
                              Ig_3  14 tegesvtLtCeaegnppp.titWykngeklss 44 
                                         g +++++ ++ g+ pp t+  y +g+++ +
  gi|385805223|ref|YP_005841621.1| 452 DVGFPIEISSQIIGGLPPyTYIIYVDGSPIYQ 483
                                       6788888888997777777********97333 PP

  == domain 5  score: 1.0 bits;  conditional E-value: 0.34
                                       CSCEEEETTS-EEEEEEE.EEES--EEEEEETTS...TTCSEEE CS
                              Ig_3   8 psstvvtegesvtLtCea.egnppptitWykngeklssnstsss 50 
                                        + t+   g +++++  a  g+p+ t++ y ng+ ++s+s  ++
  gi|385805223|ref|YP_005841621.1| 538 ANATETDVGVPISISFYAfNGTPQYTYSIYANGSLIDSGSILQQ 581
                                       4444457888888888886777777*********9777665543 PP

  == domain 6  score: 11.6 bits;  conditional E-value: 0.00017
                                       EEEEECCCSCEEEETTS-EEEEEEEEEES--.EEEEEETTS......TTCSEEESSEECCCTEEEESS--G CS
                              Ig_3   1 kPvItvppsstvvtegesvtLtCeaegnppp.titWykngek...lssnstsssissegssssLtisnvtk 67 
                                       +P I++    +    g ++ +t +++++ pp  + W+ ng++   +    ts+ i ++++ +s++++ + k
  gi|385805223|ref|YP_005841621.1| 622 PPAISLDYARSNSDVGVPIAFTVNVSSGTPPfMYIWMINGTPvafN----TSQYILNATYPGSYYVKAIAK 688
                                       788886666666689**********9999999*********85322....222245666666666666544 PP

  == domain 7  score: 13.3 bits;  conditional E-value: 4.9e-05
                                       CCSCEEEETTS-EEEEEEEEEES--.EEEEEETTS...TTCSEE CS
                              Ig_3   7 ppsstvvtegesvtLtCeaegnppp.titWykngeklssnstss 49 
                                       ++ss  + e+++v++  ++  + pp  +tWy ng+ +s+ s+++
  gi|385805223|ref|YP_005841621.1| 716 SSSSNFLFENNKVEVFVSVNNGTPPyIYTWYLNGKIVST-SSEP 758
                                       334444899**********7777777*********6333.2222 PP

>> Cadherin-like  Cadherin-like beta sandwich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.1         9   1.8e+04      20      35 ..     135     150 ..     129     158 .. 0.76
   2 !    6.3   0.0    0.0068        14      40      88 ..     472     529 ..     442     530 .. 0.74
   3 ?    3.4   0.1     0.056   1.1e+02      18      64 ..     543     590 ..     532     613 .. 0.69
   4 !   16.9   0.1   3.4e-06    0.0068      29      77 ..     728     780 ..     723     790 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 9
                     Cadherin-like  20 vdVdedvdsvtitata 35 
                                       ++V+++v+++ i++  
  gi|385805223|ref|YP_005841621.1| 135 AYVSYQVSTIPIDVYS 150
                                       5788888888887765 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0068
                     Cadherin-like  40 atvtvngvaveeg.......stetkdvsLneGrnkieikvtaedgst..trtYtltvt 88 
                                       + ++v+g+++ +        +   +  +LneG  +i i+v ++ g++  +++Yt++v+
  gi|385805223|ref|YP_005841621.1| 472 YIIYVDGSPIYQLtsysdklNFLAFVQPLNEGGHYIVIEVNDSLGNSffSNSYTINVN 529
                                       55666666666532222222222333466699999**********9989999****96 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.056
                     Cadherin-like  18 YtvdVdedvdsvtitataedsvatvtvngvaveeg..stetkdvsLneG 64 
                                        +v V+ +++   ++ t++ ++++++ ng+ +++g   ++ ++v+++++
  gi|385805223|ref|YP_005841621.1| 543 TDVGVPISISFYAFNGTPQ-YTYSIYANGSLIDSGsiLQQGSKVNVTYA 590
                                       5555555555566666666.99***********9988555666666554 PP

  == domain 4  score: 16.9 bits;  conditional E-value: 3.4e-06
                     Cadherin-like  29 vtitatae....dsvatvtvngvaveegstetkdvsLneGrnkieikvtaedg 77 
                                       v + ++ +     + +t ++ng+ v ++s+ ++++sL  G nki++kvt++ g
  gi|385805223|ref|YP_005841621.1| 728 VEVFVSVNngtpPYIYTWYLNGKIVSTSSEPEYTFSLANGLNKIQVKVTDSAG 780
                                       5555555545556789**********************************988 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 ?   -2.8   0.0       3.3   6.6e+03      48      61 ..     474     487 ..     461     517 .. 0.63
   2 !    5.9   0.0    0.0065        13      35      82 ..     640     692 ..     626     701 .. 0.69
   3 !   14.6   0.0   1.2e-05     0.025      31      84 ..     726     782 ..     713     787 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.3
                           BiPBP_C  48 Wlldgeplaetkrg 61 
                                       +++dg+p+ + ++ 
  gi|385805223|ref|YP_005841621.1| 474 IYVDGSPIYQLTSY 487
                                       68888888554443 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0065
                           BiPBP_C  35 lqlkarggea....plrWlldgeplaetkrgrelawqp.epGrhrLtv..vDaaG 82 
                                       +++++  + +     + W+++g+p+  + + ++  +    pG + + +   D aG
  gi|385805223|ref|YP_005841621.1| 640 IAFTVNVSSGtppfMYIWMINGTPV--AFNTSQYILNAtYPGSYYVKAiaKDSAG 692
                                       55555555333567778********..6666666666679999999983335555 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 1.2e-05
                           BiPBP_C  31 krqrlqlkarggea..plrWlldgeplaetkrgrelawqpepG..rhrLtvvDaaGrv 84 
                                       ++ ++ +++ +g++   ++W+l+g+ + +t+++ e ++++ +G  + ++ v+D aG +
  gi|385805223|ref|YP_005841621.1| 726 NKVEVFVSVNNGTPpyIYTWYLNGKIV-STSSEPEYTFSLANGlnKIQVKVTDSAGFS 782
                                       567788888999666889*********.88888888888877733777788***9965 PP

>> PKD_3  PKD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.0    0.0032       6.4       1      63 [.     622     684 ..     622     689 .. 0.79
   2 ?   -0.9   0.0      0.73   1.4e+03       8      26 ..     688     706 ..     685     710 .. 0.88
   3 !   12.1   0.0     6e-05      0.12      35      53 ..     743     763 ..     733     775 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0032
                             PKD_3   1 pPvIsLdletegykvkvgreltiaPtvenaenaa.faWtieGk.ivsteptytfteeelgsyevt 63 
                                       pP IsLd   ++  v  g ++ ++ +v++      + W+i+G+ +  +  +y  + +  gsy+v+
  gi|385805223|ref|YP_005841621.1| 622 PPAISLDYARSNSDV--GVPIAFTVNVSSGTPPFmYIWMINGTpVAFNTSQYILNATYPGSYYVK 684
                                       788888777776654..788888888887666667********55557789************97 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.73
                             PKD_3   8 letegykvkvgreltiaPt 26 
                                        +++gy+v ++ ++ ++P+
  gi|385805223|ref|YP_005841621.1| 688 KDSAGYEVSKEIKVDVNPD 706
                                       5789*********999997 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 6e-05
                             PKD_3  35 faWtieGkivst..eptytft 53 
                                       + W+++Gkivst  ep+ytf+
  gi|385805223|ref|YP_005841621.1| 743 YTWYLNGKIVSTssEPEYTFS 763
                                       99*******875449999997 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 !    8.0   0.0    0.0011       2.1      37      79 ..     546     589 ..     526     621 .. 0.80
   2 ?   -3.2   0.0         3   6.1e+03      38      88 ..     638     684 ..     633     703 .. 0.61
   3 !    4.9   0.0    0.0099        20      37     106 ..     725     790 ..     716     795 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0011
                      ChitinaseA_N  37 eaevsvewnvWsGeagdkakvlldgvkvaegaasakesa.tfkv 79 
                                        +++s+++  ++G+   ++ ++ +g  + +g++ +++s+ ++++
  gi|385805223|ref|YP_005841621.1| 546 GVPISISFYAFNGTPQYTYSIYANGSLIDSGSILQQGSKvNVTY 589
                                       689*****************************997776643333 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3
                      ChitinaseA_N  38 aevsvewnvWsGeagdkakvlldgvkvaegaasakesatfkvkkgGryqle 88 
                                       +++  + nv sG+ +  +  +++g+ va  +++      ++ +  G y ++
  gi|385805223|ref|YP_005841621.1| 638 VPIAFTVNVSSGTPPFMYIWMINGTPVAFNTSQ----YILNATYPGSYYVK 684
                                       566677788888888888888888887765554....33333344555555 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.0099
                      ChitinaseA_N  37 eaevsvewnvWsGeagdkakvlldgvkvaegaasakesatfkvkkgGryqlevelCdaeGCsksapkeiv 106
                                       + +v+v  +v +G+ +  ++ +l+g+ v +++     + tf++   G  +++v++ d+ G s  ++   +
  gi|385805223|ref|YP_005841621.1| 725 NNKVEVFVSVNNGTPPYIYTWYLNGKIVSTSSE---PEYTFSLA-NGLNKIQVKVTDSAGFSVYSSIINI 790
                                       446666677779**************9987554...46677765.58999********998876655444 PP

>> Ig_2  Immunoglobulin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       1.2   2.3e+03      47      67 ..     110     130 ..      93     138 .. 0.80
   2 ?   -3.7   0.0         8   1.6e+04      27      42 ..     468     485 ..     464     506 .. 0.64
   3 ?   -0.2   0.0      0.65   1.3e+03      23      44 ..     556     577 ..     535     595 .. 0.72
   4 ?    1.8   0.0      0.15     3e+02      24      77 ..     648     701 ..     624     703 .. 0.68
   5 ?    9.5   0.1   0.00063       1.3      11      46 ..     722     762 ..     713     782 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.2
                              Ig_2  47 finavsaedsgtYtCrarntk 67 
                                       ++ ++ + ++gtY  ++ n+ 
  gi|385805223|ref|YP_005841621.1| 110 ISANIGPMHYGTYYLVVYNDA 130
                                       55789999******9999876 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 8
                              Ig_2  27 pppkvqwykggevin..s 42 
                                       pp+++  y +g++i   +
  gi|385805223|ref|YP_005841621.1| 468 PPYTYIIYVDGSPIYqlT 485
                                       788899999998887441 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.65
                              Ig_2  23 apgnpppkvqwykggevinssp 44 
                                       ++g p ++++ y +g+ i s+ 
  gi|385805223|ref|YP_005841621.1| 556 FNGTPQYTYSIYANGSLIDSGS 577
                                       45889999*******9998554 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.15
                              Ig_2  24 pgnpppkvqwykggevin..sspnffinavsaedsgtYtCrarntkggevsrpvel 77 
                                       +g pp  + w  +g+++   +s+  +i++++   s   + +a+ + g evs+ + +
  gi|385805223|ref|YP_005841621.1| 648 SGTPPFMYIWMINGTPVAfnTSQ--YILNATYPGSYYVKAIAKDSAGYEVSKEIKV 701
                                       4789999*******999984444..5666655555555555566666677776666 PP

  == domain 5  score: 9.5 bits;  conditional E-value: 0.00063
                              Ig_2  11 vtegepvtLtCsap.gnpppkvqwykggevinsspn....f 46 
                                       ++e+++v++  s++ g pp+ ++wy +g+++++s +    f
  gi|385805223|ref|YP_005841621.1| 722 LFENNKVEVFVSVNnGTPPYIYTWYLNGKIVSTSSEpeytF 762
                                       666666666667775788899***********776655532 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 ?   -4.2   1.1       8.7   1.7e+04       5      21 ..     228     244 ..     227     245 .. 0.63
   2 ?   -3.0   0.0       3.6   7.2e+03      31      40 ..     469     478 ..     455     528 .. 0.67
   3 ?   -1.6   0.0       1.3   2.6e+03      19      40 ..     640     661 ..     640     703 .. 0.73
   4 ?    9.7   0.0    0.0004      0.79      14      47 ..     723     764 ..     720     767 .. 0.80

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 8.7
                                       HTTTTHHHHTT-TTSEE CS
                     L51_S25_CI-B8   5 wrknLprlkykNPavpi 21 
                                       w +n+p +   N ++ +
  gi|385805223|ref|YP_005841621.1| 228 WVQNVPNFWTNNNTLFF 244
                                       67777777666666655 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.6
                                       -EEEEE-SS- CS
                     L51_S25_CI-B8  31 PallaiYfng 40 
                                       P+++ iY +g
  gi|385805223|ref|YP_005841621.1| 469 PYTYIIYVDG 478
                                       8999999888 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.3
                                       SEEEEEESS-SS-EEEEE-SS- CS
                     L51_S25_CI-B8  19 vpivvrrrsgdgPallaiYfng 40 
                                       + ++v+ +sg+ P+++    ng
  gi|385805223|ref|YP_005841621.1| 640 IAFTVNVSSGTPPFMYIWMING 661
                                       5799999******988666665 PP

  == domain 4  score: 9.7 bits;  conditional E-value: 0.0004
                                       TT-TTSEEEEEESS-SS-EEEEE-SS-........-B--EE- CS
                     L51_S25_CI-B8  14 ykNPavpivvrrrsgdgPallaiYfng........rektidl 47 
                                       ++N +v++ v+ ++g+ P++++ Y ng        +e+t +l
  gi|385805223|ref|YP_005841621.1| 723 FENNKVEVFVSVNNGTPPYIYTWYLNGkivstssePEYTFSL 764
                                       78999**********************666666555555555 PP

>> SprB  SprB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.4   1.9         9   1.8e+04      25      30 ..     222     227 ..     220     233 .. 0.79
   2 ?    4.0   0.3     0.021        42      23      30 ..     465     472 ..     458     475 .. 0.89
   3 ?    4.8   3.1     0.012        25      16      34 ..     550     568 ..     550     571 .. 0.83
   4 ?    9.1   0.1   0.00055       1.1      18      32 ..     643     657 ..     643     661 .. 0.95
   5 ?   10.7   1.4   0.00017      0.34      19      33 ..     732     746 ..     729     749 .. 0.91
   6 ?   -1.6   0.0       1.2   2.3e+03      26      35 ..     758     767 ..     755     769 .. 0.85

  Alignments for each domain:
  == domain 1  score: -4.4 bits;  conditional E-value: 9
                              SprB  25 tapYtY 30 
                                       +++YtY
  gi|385805223|ref|YP_005841621.1| 222 YGSYTY 227
                                       589*** PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.021
                              SprB  23 GGtapYtY 30 
                                       GG +pYtY
  gi|385805223|ref|YP_005841621.1| 465 GGLPPYTY 472
                                       9******* PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.012
                              SprB  16 sItvtvsGGtapYtYswng 34 
                                       sI+  + +Gt+ YtYs+  
  gi|385805223|ref|YP_005841621.1| 550 SISFYAFNGTPQYTYSIYA 568
                                       67778899********975 PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.00055
                              SprB  18 tvtvsGGtapYtYsw 32 
                                       tv+vs Gt+p+ Y w
  gi|385805223|ref|YP_005841621.1| 643 TVNVSSGTPPFMYIW 657
                                       9************87 PP

  == domain 5  score: 10.7 bits;  conditional E-value: 0.00017
                              SprB  19 vtvsGGtapYtYswn 33 
                                       v+v++Gt+pY Y+w 
  gi|385805223|ref|YP_005841621.1| 732 VSVNNGTPPYIYTWY 746
                                       89************5 PP

  == domain 6  score: -1.6 bits;  conditional E-value: 1.2
                              SprB  26 apYtYswngg 35 
                                       + Yt+s+ +g
  gi|385805223|ref|YP_005841621.1| 758 PEYTFSLANG 767
                                       56******99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (820 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.75u 0.29s 00:00:01.04 Elapsed: 00:00:00.48
# Mc/sec: 5098.50
//
Query:       gi|385805224|ref|YP_005841622.1|  [L=227]
Description: natural resistance-associated macrophage protein [Fervidicoccus fontis Kam940]
Scores for complete 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-52  177.1  10.4      6e-52  176.8  10.4    1.0  1  Nramp     Natural resistance-associated macrophage protein
  ------ inclusion threshold ------
      0.053   13.4   0.1        9.6    6.0   0.0    2.2  2  PSI_PsaF  Photosystem I reaction centre subunit III


Domain annotation for each model (and alignments):
>> Nramp  Natural resistance-associated macrophage protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.8  10.4   6.7e-56     6e-52       2     188 ..      31     216 ..      30     225 .. 0.96

  Alignments for each domain:
  == domain 1  score: 176.8 bits;  conditional E-value: 6.7e-56
                             Nramp   2 atdlqaGaqfGykLlwvlllstllaillqelsarLGlvTgkglaelirerlpkkvsillwilaelaiiatdlaeviG 78 
                                        t+++aG+++G +Llwv+ ls  +ai++q++s + G+vT+kgl ++  ++l+k  + l+++ +++ai+atd+ae++G
  gi|385805224|ref|YP_005841622.1|  31 GTNIEAGSKYGLTLLWVVWLSGAMAIMFQYISGKVGIVTEKGLLDVSMAKLRKNEKKLYFFGLFIAILATDMAEFVG 107
                                       69*************************************************************************** PP

                             Nramp  79 aAialnllfgipllvgvlitavlvllllflekggyrklEaliialvlvialsFiaelflvkpdwgevlkglvvPslp 155
                                       +A++++l++gipl +++ + +v+vlll++  + +  ++E +i++lv++++ls+++el++v+ + +e+l + ++P l+
  gi|385805224|ref|YP_005841622.1| 108 MAVGFHLILGIPLSISAGLSVVDVLLLFL-LTEDLGRMEIVIAGLVGIVGLSYLIELVIVHANPEEILMHSFIPYLS 183
                                       ***********************998877.6889******************************************* PP

                             Nramp 156 gkeslllavgilGatvmphnlflhsslvqerki 188
                                       g+e++l+a++i+Gat+mph++ lhs+l +e+  
  gi|385805224|ref|YP_005841622.1| 184 GSEMILTATSIIGATIMPHAIILHSYLSAEKSA 216
                                       *****************************9984 PP

>> PSI_PsaF  Photosystem I reaction centre subunit III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1     0.002        18     106     131 ..      55      80 ..      52      98 .. 0.83
   2 ?    6.0   0.0    0.0011       9.6     110     128 ..     146     164 ..     138     180 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.002
                          PSI_PsaF 106 gllflyiaGwiGwvGrsylravrkek 131
                                       +++f yi+G +G v  + l  v+  k
  gi|385805224|ref|YP_005841622.1|  55 AIMFQYISGKVGIVTEKGLLDVSMAK 80 
                                       69*************99999988663 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0011
                          PSI_PsaF 110 lyiaGwiGwvGrsylravr 128
                                       + iaG +G vG syl+ + 
  gi|385805224|ref|YP_005841622.1| 146 IVIAGLVGIVGLSYLIELV 164
                                       789************9753 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); 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: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1383.77
//
Query:       gi|385805225|ref|YP_005841623.1|  [L=156]
Description: NRAMP family Mn2+/Fe2+ transporter [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-28   98.5   4.6    3.8e-28   98.5   4.6    1.5  2  Nramp     Natural resistance-associated macrophage protein


Domain annotation for each model (and alignments):
>> Nramp  Natural resistance-associated macrophage protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.5   4.6   2.1e-32   3.8e-28     227     357 ..       5     132 ..       1     133 [. 0.97
   2 ?   -4.9   3.5      0.59   1.1e+04     207     222 ..     140     155 ..     137     156 .] 0.72

  Alignments for each domain:
  == domain 1  score: 98.5 bits;  conditional E-value: 2.1e-32
                             Nramp 227 vly.sggkdvesledaaeaLepllGskaasvlFaigLlaaGlsStitgtlagqyvmegflglrislwlrrlitrala 302
                                       ++y +g ++++sle+a+ +L pl+G ++as++Fai L+++GlsS+++  +ag  ++e ++g   ++w+ rl+ r++ 
  gi|385805225|ref|YP_005841623.1|   5 AFYlKGLTNITSLESAYYTLAPLFG-ALASWIFAISLFSSGLSSSMVSVIAGVKILESYFGTPTKQWKVRLMLRLIN 80 
                                       79999********************.7************************************************** PP

                             Nramp 303 fvpalivilligaelelvkllvlsqvllslllPfaliplllltsskklMGefkns 357
                                       +vp li++ l+ + ++   +lv++q++ls+ lP++l+pl+ + ++ +lMG +k+s
  gi|385805225|ref|YP_005841623.1|  81 MVPFLIAVYLGVDMMS---ILVYTQAILSFSLPLVLFPLINISKDGNLMGGYKIS 132
                                       **************99...*********************************998 PP

  == domain 2  score: -4.9 bits;  conditional E-value: 0.59
                             Nramp 207 iialivaflinlaili 222
                                       +++ +++ lin+a+++
  gi|385805225|ref|YP_005841623.1| 140 LVSTVFIVLINIAMFV 155
                                       5677888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       778  (0.0433934); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 980.69
//
Query:       gi|385805226|ref|YP_005841624.1|  [L=101]
Description: DNA polymerase, beta domain-containing protein region [Fervidicoccus fontis Kam940]
Scores for complete 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   43.6   0.9    3.6e-11   43.2   0.9    1.1  1  NTP_transf_2    Nucleotidyltransferase domain
      8e-09   35.5   0.8    1.1e-08   35.0   0.8    1.3  1  Polbeta         Polymerase beta, Nucleotidyltransferase
    0.00015   21.9   0.0    0.00018   21.7   0.0    1.1  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 !   43.2   0.9   6.1e-15   3.6e-11       2      92 ..      16      98 ..      16     101 .] 0.82

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 6.1e-15
                                      HHHHHHHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEECEEECC CS
                      NTP_transf_2  2 kklleelkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlvtrekle 80
                                      +k++e++ + +p+ak+++fGS+++G++   SDiD+l+++++        +++   + + + +    ++e +++tre++ 
  gi|385805226|ref|YP_005841624.1| 16 RKIKEIVNSFDPNAKLYIFGSAVKGKNVASSDIDILIITEKIEL-----KYEIMVKVFKSID---EPIELHIITREIFD 86
                                      69****************************************43.....2333333333333...369*********** PP

                                      CCTEEEEEECEE CS
                      NTP_transf_2 81 dpllvksileer 92
                                      +++++ +  ee 
  gi|385805226|ref|YP_005841624.1| 87 KWYRRFIPIEEL 98
                                      999998888876 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.8   1.9e-12   1.1e-08       2      56 ..      17      72 ..      16      86 .. 0.81

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 1.9e-12
                                      STTTTHHHHHHHHSTTEEEEEE-S------EEEEEEEESS-.--HHHHHHHHHHHH CS
                           Polbeta  2 kikeilekekeielaylFGSrakgkareeSDiDlavllkek.ldleeelelaaele 56
                                      kikei+++ +  + +y+FGS +kgk   +SDiD+ +++++  l++e  +++ + ++
  gi|385805226|ref|YP_005841624.1| 17 KIKEIVNSFDPNAKLYIFGSAVKGKNVASSDIDILIITEKIeLKYEIMVKVFKSID 72
                                      899*****999999*************************99555555555554444 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 !   21.7   0.0   2.9e-08   0.00018       9      66 ..      13      71 ..       9      92 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.9e-08
                                      HHHHHHHHHHHHH-TT-EEEE-HHHHTT-S.EESSEEEEEEBTTBSTTSS--HHHHHHH CS
                    DNA_pol_B_palm  9 alealvkkaakeldpevevivcGSYRRgae.ssGDvDvlitkkdakseskklkkllekl 66
                                      ++ + +k+ ++++dp++++++ GS  +g++  s D+D+li  ++ + + +   k+++++
  gi|385805226|ref|YP_005841624.1| 13 EIGRKIKEIVNSFDPNAKLYIFGSAVKGKNvASSDIDILIITEKIELKYEIMVKVFKSI 71
                                      5778899********************9984689**********999877776766654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); 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: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 691.86
//
Query:       gi|385805227|ref|YP_005841625.1|  [L=81]
Description: HEPN domain-containing protein [Fervidicoccus fontis Kam940]
Scores for 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-11   41.8   0.4      1e-10   41.7   0.4    1.0  1  HEPN      HEPN domain
  ------ inclusion threshold ------
      0.015   15.7   0.1       0.33   11.4   0.0    2.1  2  DUF3644   Protein of unknown function (DUF3644)


Domain annotation for each model (and alignments):
>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.7   0.4   1.2e-14     1e-10      45     114 ..       3      76 ..       1      81 [] 0.85

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 1.2e-14
                                       HTT--.SSCCHHHHHHCCHHHT.........-HHHHHHHHHHHCCCHHCCCTSS--S--HHHHHHHHHHHHHHHHH CS
                              HEPN  45 kkggeppkthdlreLleelkkelke......seelreeleeLekayiesrYpdakeeyteedaeealkdaeevlel 114
                                        + g++p+th++r+L++ l k   +       e+   ++ +Le+ay+ srY ++ +  +e++  +++k+++ev++ 
  gi|385805227|ref|YP_005841625.1|   3 VHFGTYPRTHSIRRLIKDLTKINTKlrsfieDEDKLHYIARLEEAYVASRYFPYTY--EEKETISLFKFVKEVFKP 76 
                                       57899************7766666667777777777778****************9..9**************986 PP

>> DUF3644  Protein of unknown function (DUF3644)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.015   1.4e+02      38      53 ..       9      24 ..       5      38 .. 0.79
   2 ?   11.4   0.0   3.7e-05      0.33      19      54 ..      47      77 ..      28      81 .] 0.72

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.015
                           DUF3644 38 pktisLeeclkkvdke 53
                                      p+t+s+++++k+++k 
  gi|385805227|ref|YP_005841625.1|  9 PRTHSIRRLIKDLTKI 24
                                      89*********99883 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 3.7e-05
                           DUF3644 19 kgiksiykkkrykknrdGnpktisLeeclkkvdkek 54
                                      + + s+y    +  +   +++tisL++++k+v+k+ 
  gi|385805227|ref|YP_005841625.1| 47 AYVASRY----FPYT-YEEKETISLFKFVKEVFKPI 77
                                      2355666....7777.67799************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       832  (0.0464053); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.31s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 542.10
//
Query:       gi|385805228|ref|YP_005841626.1|  [L=368]
Description: PflX-like protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-10   42.0   0.3    3.3e-10   40.6   0.0    1.9  2  Radical_SAM  Radical SAM superfamily
    1.9e-09   37.9   0.0    4.1e-09   36.8   0.0    1.5  1  Fer4_12      4Fe-4S single cluster domain
    0.00013   22.1   0.4    0.00034   20.7   0.0    1.8  2  Fer4_14      4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.088   13.2   0.1        1.5    9.2   0.1    2.5  2  DUF1064      Protein of unknown function (DUF1064)


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.5       2.1   9.3e+03      10      17 ..     106     113 ..     105     125 .. 0.81
   2 !   40.6   0.0   7.3e-14   3.3e-10       2     115 ..     153     261 ..     152     301 .. 0.71

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.1
                                       --TTTSCC CS
                                       xxxxxxxx RF
                       Radical_SAM  10 rCsfCarp 17 
                                       +C +C r+
  gi|385805228|ref|YP_005841626.1| 106 NCEYCERK 113
                                       8****987 PP

  == domain 2  score: 40.6 bits;  conditional E-value: 7.3e-14
                                       EEESEESS--TTTSCCTT.HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCT CS
                                       xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpet.vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpg 77 
                                       +++ gCnlrC++C+++e  ++   +g+++ +++++++ ++l ++ g+k++  +ggep+ y + +++ +++ k    +
  gi|385805228|ref|YP_005841626.1| 153 IFYSGCNLRCVYCQNYEIsQSFPLKGKVVAPQQLAAIQDKL-VKEGAKNINHVGGEPTPYTHAIVESFKYLKT---N 225
                                       6899**************9999*******************.999******************9999999887...4 PP

                                       EEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  78 iritvetngtlpdeeklerllelgvdrvslgleaadde 115
                                             +n ++  e+   +l++l  d    + + +dd 
  gi|385805228|ref|YP_005841626.1| 226 TPQIWNSNFYMS-EKLTILLRDLI-DLWLPDFKYWDDS 261
                                       444444444443.44444444444.5555555555555 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 !   36.8   0.0   9.2e-13   4.1e-09       9     100 ..     152     241 ..     142     251 .. 0.89

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 9.2e-13
                           Fer4_12   9 slfvsgCnlsCkgCfnketwsfk..sgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeek 83 
                                       ++f sgCnl+C +C n e+ +    +gk +  + l+ i ++l ke  + +  +GGEP     + a++e +k++k++ 
  gi|385805228|ref|YP_005841626.1| 152 TIFYSGCNLRCVYCQNYEISQSFplKGKVVAPQQLAAIQDKLVKEGAKNINHVGGEPTP--YTHAIVESFKYLKTNT 226
                                       69***************998544349999999999***********************9..8889999999999999 PP

                           Fer4_12  84 pekdiwlytgytleels 100
                                       p  +iw ++ y+ e+l+
  gi|385805228|ref|YP_005841626.1| 227 P--QIWNSNFYMSEKLT 241
                                       9..7*******999886 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 ?   -3.5   0.1       2.4   1.1e+04      20      39 ..      64      83 ..      59      96 .. 0.61
   2 !   20.7   0.0   7.7e-08   0.00034       2      84 ..     154     230 ..     153     244 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.4
                           Fer4_14 20 twkselgkpqteelleqilk 39
                                      ++++e +k +++ + ++ ++
  gi|385805228|ref|YP_005841626.1| 64 EFEKEFHKLSNDIMKDESIE 83
                                      45666666666666666553 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 7.7e-08
                           Fer4_14   2 fvrlsgCnlsCkgCdnketwks..elgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlke 76 
                                       f   sgCnl C+ C n e  +s    gk+ + ++l +i ++l k+   ++++  +GGeP  y  ++++++  k+lk+
  gi|385805228|ref|YP_005841626.1| 154 FY--SGCNLRCVYCQNYEISQSfpLKGKVVAPQQLAAIQDKLVKEG--AKNINHVGGEPTPY--THAIVESFKYLKT 224
                                       55..9**********8875554453455555566655553333333..466999******77..999*********9 PP

                           Fer4_14  77 eypekkiw 84 
                                       ++   +iw
  gi|385805228|ref|YP_005841626.1| 225 NT--PQIW 230
                                       99..5566 PP

>> DUF1064  Protein of unknown function (DUF1064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1   0.00034       1.5      25      58 ..      38      71 ..      32     132 .. 0.84
   2 ?    1.3   0.0     0.093   4.2e+02      44      91 ..     166     213 ..     159     240 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00034
                           DUF1064 25 YqeLkllkaagkilkleLqpkfeLqekfkknGkk 58
                                      Y+  ++l+++ k+++l Lq+ + L+e+f+k+  k
  gi|385805228|ref|YP_005841626.1| 38 YKIARSLEVDVKLTSLSLQELWSLHEEFEKEFHK 71
                                      77789999*********************98554 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.093
                           DUF1064  44 pkfeLqekfkknGkkyrkikYvaDFliykedgkveviDvkGmatkdak 91 
                                       +++e+ ++f  +Gk + + + +a     +++g  ++  v G  t  ++
  gi|385805228|ref|YP_005841626.1| 166 QNYEISQSFPLKGKVVAPQQLAAIQDKLVKEGAKNINHVGGEPTPYTH 213
                                       57999*********8877666665555578888888888888776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2283.95
//
Query:       gi|385805229|ref|YP_005841627.1|  [L=335]
Description: MarR family transcriptional regulator [Fervidicoccus fontis Kam940]
Scores for complete 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   19.3   0.1     0.0018   18.3   0.1    1.5  1  z-alpha         Adenosine deaminase z-alpha domain
     0.0013   18.6   0.1     0.0025   17.7   0.1    1.4  1  MarR            MarR family
     0.0054   16.6   0.0      0.014   15.3   0.0    1.7  1  TBPIP           TBPIP/Hop2 winged helix domain
  ------ inclusion threshold ------
      0.013   15.3   0.0      0.023   14.5   0.0    1.4  1  HTH_IclR        IclR helix-turn-helix domain
      0.014   15.3   0.1      0.038   13.9   0.1    1.7  1  TrmB            Sugar-specific transcriptional regulator TrmB
      0.016   15.5   0.1      0.045   14.1   0.1    1.8  1  Rrf2            Transcriptional regulator
      0.021   14.8   0.3      0.076   13.0   0.3    2.0  1  HTH_46          Winged helix-turn-helix DNA binding
       0.03   14.6   0.0       0.19   12.0   0.0    2.5  2  Mnd1            Mnd1 HTH domain
      0.056   13.3   0.0      0.096   12.6   0.0    1.3  1  MarR_2          MarR family
      0.057   13.3   0.5        0.2   11.6   0.0    2.1  3  PAX             'Paired box' domain
      0.081   13.5   0.0       0.15   12.6   0.0    1.5  1  MRFAP1          MORF4 family-associated protein1
      0.086   12.8   0.0       0.19   11.8   0.0    1.5  1  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.099   12.3   0.0        2.7    7.6   0.0    2.1  2  NMT1_2          NMT1-like family
       0.15   11.7   0.3       0.31   10.6   0.3    1.5  1  HTH_24          Winged helix-turn-helix DNA-binding
       0.26   10.6   0.0       0.37   10.1   0.0    1.2  1  LysR_substrate  LysR substrate binding domain


Domain annotation for each model (and alignments):
>> z-alpha  Adenosine deaminase z-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   1.5e-06    0.0018       4      53 ..       5      53 ..       2      56 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.5e-06
                                      HHHHHHHHHHHHC-TTCECCHHHHHHHHCC-HHHHHHHHHHHHHTTSEEE CS
                           z-alpha  4 eqaekilelLeelgekkaatalalergLstpkreiNrvLydlerkgkvyr 53
                                      e +ekilelL +   +++  +    r +s  k  +  +Ly+ler+g + r
  gi|385805229|ref|YP_005841627.1|  5 ELKEKILELLANFQ-GESIPQSYIHRSISASKSRVSEILYELEREGLIKR 53
                                      679***********.******************************98877 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   2.1e-06    0.0025       8      51 ..      10      55 ..       9      60 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.1e-06
                                      HHHHHHHSTT..EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR  8 iLrilyeqgp..lsvseLakklgvskstvtrvldrLekkGlieRsk 51
                                      iL++l++ ++  + +s + + ++ sks v+++l +Le++Gli+R++
  gi|385805229|ref|YP_005841627.1| 10 ILELLANFQGesIPQSYIHRSISASKSRVSEILYELEREGLIKRKQ 55
                                      5666666554459999****************************98 PP

>> TBPIP  TBPIP/Hop2 winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.2e-05     0.014      26      59 ..      27      63 ..      24      66 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.2e-05
                             TBPIP 26 lqk..klgKtavqkaLdeLvdegkiieKeyGKq.kiY 59
                                      +++    +K  v ++L eL+ eg+i+ K++G +  iY
  gi|385805229|ref|YP_005841627.1| 27 IHRsiSASKSRVSEILYELEREGLIKRKQIGRSkFIY 63
                                      56655679************************94477 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0     2e-05     0.023       8      50 ..      10      53 ..       9      55 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2e-05
                                      HHCT-CTTBSS-.BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  8 iLdalaeapqel.tlselArrtglpkStvhRlLqtLvelGyveq 50
                                      iL++la  ++e    s ++r +  +kS v+ +L  L+++G++++
  gi|385805229|ref|YP_005841627.1| 10 ILELLANFQGESiPQSYIHRSISASKSRVSEILYELEREGLIKR 53
                                      8999999888855999**************************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 ?   13.9   0.1   3.2e-05     0.038      28      62 ..      27      63 ..      19      68 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.2e-05
                                      HCCCTTSSCHCHHHHHHHHHHCTSEEEESST..TTEE CS
                              TrmB 28 iaeelgvprskvYevLrsLedkGlVerekgr..pklY 62
                                      i++ +  ++s+v e+L +Le+ Gl++r++    + +Y
  gi|385805229|ref|YP_005841627.1| 27 IHRSISASKSRVSEILYELEREGLIKRKQIGrsKFIY 63
                                      7888899*********************954234455 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   3.7e-05     0.045      12      57 ..       9      53 ..       1      57 [. 0.88

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.7e-05
                                      HHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              Rrf2 12 hallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvks 57
                                      ++l  La+ ++e+ +  + i+++ + s+s ++ il +L+++gl+k 
  gi|385805229|ref|YP_005841627.1|  9 KILELLANFQGES-IPQSYIHRSISASKSRVSEILYELEREGLIKR 53
                                      7888899999988.******************************85 PP

>> HTH_46  Winged helix-turn-helix DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.3   6.3e-05     0.076      26      57 ..      24      55 ..       8      64 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.3e-05
                            HTH_46 26 lkyIqkrtnLSrSsimkvLseLkkggyIeier 57
                                       +yI++    S+S++ ++L eL ++g I+ ++
  gi|385805229|ref|YP_005841627.1| 24 QSYIHRSISASKSRVSEILYELEREGLIKRKQ 55
                                      57*************************98776 PP

>> Mnd1  Mnd1 HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00016      0.19      28      59 ..      34      65 ..      24      66 .. 0.87
   2 ?   -3.0   0.0       8.1   9.7e+03      26      41 ..     251     266 ..     246     269 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
                              Mnd1 28 vsqsVkdvlqsLvdDglveveKiGssnvyWsF 59
                                      ++  V ++l +L  +gl++ + iG s++ +++
  gi|385805229|ref|YP_005841627.1| 34 SKSRVSEILYELEREGLIKRKQIGRSKFIYAY 65
                                      45789***********************9987 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 8.1
                              Mnd1  26 givsqsVkdvlqsLvd 41 
                                       +iv+ sV++ ++ +  
  gi|385805229|ref|YP_005841627.1| 251 NIVAESVREKITWMYR 266
                                       6888899988876655 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0     8e-05     0.096      10      54 ..      10      54 ..       9      59 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8e-05
                                      HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      +L  L++  g+ + ++ + r    sks+vs il +L++ GL+ r+
  gi|385805229|ref|YP_005841627.1| 10 ILELLANFQGESIPQSYIHRSISASKSRVSEILYELEREGLIKRK 54
                                      5777888888889999999***********************986 PP

>> PAX  'Paired box' domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00016       0.2      23      86 ..       7      74 ..       3      89 .. 0.79
   2 ?   -3.2   0.0       6.5   7.8e+03      99     118 ..     180     199 ..     173     205 .. 0.66
   3 ?   -2.2   0.0         3   3.6e+03      32      63 ..     255     285 ..     243     289 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00016
                               PAX 23 rqkivelah....sgvrpcvisrqlrvshgcvskilgryqetgsirpgviggskpkvatpevvkkiee 86
                                      ++ki+el +    + +    i r +  s+  vs il   +  g i+ + ig sk   a   +++k +e
  gi|385805229|ref|YP_005841627.1|  7 KEKILELLAnfqgESIPQSYIHRSISASKSRVSEILYELEREGLIKRKQIGRSKFIYAYTGIKEKAHE 74
                                      55666654312114567788**********************************99998888888766 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 6.5
                               PAX  99 irdkllkegvcdndtvpsvs 118
                                       ir   +k+g++d ++    s
  gi|385805229|ref|YP_005841627.1| 180 IRSLSIKNGIIDAENTVYYS 199
                                       56666777777766655555 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 3
                               PAX  32 sgvrpcvisrqlrvshgcvskilgryqetgsi 63 
                                       + vr  +i+ + r s    sk  +ry e  si
  gi|385805229|ref|YP_005841627.1| 255 ESVRE-KITWMYRESLEAYSKDRSRYLELYSI 285
                                       44443.45555566666667777777776666 PP

>> MRFAP1  MORF4 family-associated protein1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00013      0.15      23      60 ..     253     290 ..     235     316 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00013
                            MRFAP1  23 vlrevrediaalereharaylrarrklleidslldeik 60 
                                       v + vre+i+ + re   ay + r++ le+ s++  i 
  gi|385805229|ref|YP_005841627.1| 253 VAESVREKITWMYRESLEAYSKDRSRYLELYSIITGID 290
                                       56789***************************998876 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00016      0.19      30      55 ..      30      55 ..      12      62 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00016
                                      HTTSSHHHHHHHHHHHHHTTSEEETE CS
                         HTH_Crp_2 30 mlGltretvsrilseLkreglisrgr 55
                                       + ++ + vs il eL+regli+r++
  gi|385805229|ref|YP_005841627.1| 30 SISASKSRVSEILYELEREGLIKRKQ 55
                                      5778999****************753 PP

>> NMT1_2  NMT1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0023       2.7       8      63 ..      80     134 ..      71     143 .. 0.70
   2 ?    2.5   0.0     0.081        97     189     234 ..     226     271 ..     217     274 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0023
                            NMT1_2   8 lklGfialtdaapl.vvakekglfakeGltvelekqaswaelrdkllagelDaahv.l 63 
                                       +++G ++ +++  l    k+++ +++   +v+++ ++ + e++d+l+ g++D+a+   
  gi|385805229|ref|YP_005841627.1|  80 MTIGIVYSSEYLFLgYFLKKMNEMKH---KVNVKVFSDGLEALDALVHGRIDLAISpF 134
                                       45555555555555444445554444...49***********************9744 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.081
                            NMT1_2 189 egiGvtaltsqelwkdhPekvlgvredfveknpntaralvkalleA 234
                                       e +G++++ ++ + ++  ++ l++++ ++e+ ++    + +  leA
  gi|385805229|ref|YP_005841627.1| 226 ESMGFKVVKDAGIMENELCCSLAISNIVAESVREKITWMYRESLEA 271
                                       678***************************9999888877777776 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.3   0.00026      0.31       5      48 .]       7      52 ..       5      52 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00026
                            HTH_24  5 drkILelLqk.npr.isqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      + kILelL   ++  i+q+ + + +  S+s v++ l +Le+eGlIk
  gi|385805229|ref|YP_005841627.1|  7 KEKILELLANfQGEsIPQSYIHRSISASKSRVSEILYELEREGLIK 52
                                      679*******95556******************************8 PP

>> LysR_substrate  LysR substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00031      0.37       4      60 ..      76     131 ..      73     134 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00031
                                       SCEEEEEEEECCCHHHHHHHHHHHHHHHSTTEEEEEEEESHHHHHHHHHTTSSSEEE CS
                    LysR_substrate   4 lrgrLrigapptlaryllppllarfraryPevelelvegdseelldllaegelDlai 60 
                                       ++ r +ig++ +    +l  +l++  +   +v + + ++   e ld+l +g++Dlai
  gi|385805229|ref|YP_005841627.1|  76 DEMRMTIGIVYSSEYLFLGYFLKKMNEMKHKVNVKVFSDG-LEALDALVHGRIDLAI 131
                                       567889*******************************888.999999*********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); 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 0.27s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2320.11
//
Query:       gi|385805230|ref|YP_005841628.1|  [L=51]
Description: hypothetical protein FFONT_0185 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.29s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 359.71
//
Query:       gi|385805231|ref|YP_005841629.1|  [L=471]
Description: pantothenate permease (panF-3) [Fervidicoccus fontis Kam940]
Scores for complete 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   80.9  37.9    1.3e-22   80.2  37.9    1.4  1  SSF            Sodium:solute symporter family
  ------ inclusion threshold ------
      0.051   13.5   0.0       0.12   12.3   0.0    1.6  1  BPL_LplA_LipB  Biotin/lipoate A/B protein ligase 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 !   80.2  37.9   1.5e-26   1.3e-22       1     355 [.      33     375 ..      33     425 .. 0.81

  Alignments for each domain:
  == domain 1  score: 80.2 bits;  conditional E-value: 1.5e-26
                               SSF   1 yflagrsltgfvlglslaasnisaasfvGlaGavaasGlavvllelgalllvllllllla.erlr...nagalTlpd 73 
                                       y+++gr+++g+  g++ aa+  sa  ++Gl G+++  G++++ +el  ll  + +l  ++ e++r   +   +   +
  gi|385805231|ref|YP_005841629.1|  33 YYIGGRKIGGILAGATYAATTYSAFMMIGLVGMAYSTGVGTLGFELSYLLSTVAILSTVGyEIWRiskERQWISPSQ 109
                                       9**********************************************99987777766652666688788889999* PP

                               SSF  74 ylskRfkgkrilvylsalslllvitlklsvdlvggaklielalGlnyetavlllaaltalYtviGGllAvvytdtiq 150
                                       +l   +++  + ++++ l ++++ + ++++++ g +++++ + G++ye +v++ a+++al+++i G+ +v  td  q
  gi|385805231|ref|YP_005841629.1| 110 MLGDLYGSIFLSKFIALLYIFAM-IPYIAAQIQGLGVIFQ-IGGMSYESGVVAAAVIVALWIAIAGMWSVATTDLYQ 184
                                       ********998888888877765.579******9999886.78********************************** PP

                               SSF 151 avlmlvgalilliivllevGgleslveklkeaapkv.vdlltpdslkllrdpltalslwlglvlGvaglphilvRfl 226
                                       a+lml g ++ l +v++ +  +   ++ +   a ++   ++   s   +  +l+ +   l +++  +  p ++ R++
  gi|385805231|ref|YP_005841629.1| 185 AILMLGGGILFLYVVISMILPFGGSLRAIEVLASSGyLGIMPFWS---FPVFLSYT---LPWIFFAITNPQVISRLF 255
                                       ********9999998888776665555555555544244444444...44455555...557888899999****** PP

                               SSF 227 aakdakailkgvlkltivlilvligmisiilfaiklagavpkavgtevgvsniaypeLvvkllpnllaGlllavmlA 303
                                          d k+   +v     + +l  +++++i+lfa  la      ++++    n++ p +  kl   + aG++   ++A
  gi|385805231|ref|YP_005841629.1| 256 IQRDEKSYKMSVTFFAAFGLLYTLLAVMIGLFARYLAIN---GIIPSGLGGNYVTPAILSKLS-AIAAGFIGISIIA 328
                                       *******99999998888888888999******999876...78999999***********85.7999***9999** PP

                               SSF 304 aimstltslllsassaftkDlYkkirrkasakekelvgvsriivlvvislai 355
                                       a +st ++++ls ssa+ kDl     +k      el+  + +++ vv+s++ 
  gi|385805231|ref|YP_005841629.1| 329 AAISTADGIILSVSSAIFKDLLGLKDKKV-----ELIATIDVVLTVVASILA 375
                                       ********************975433333.....455555555555555443 PP

>> BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.3e-05      0.12      91     129 ..      23      61 ..       6      62 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.3e-05
                                       TTEEEETTTEEEETTEEEEEEEEEEEETTS-EEEEEEEE CS
                     BPL_LplA_LipB  91 ipvfikwpnDlyvngrKlaGiavtstrgktlhhivigvg 129
                                         v ik+  D y++grK++Gi+   t+ +t++   +++g
  gi|385805231|ref|YP_005841629.1|  23 KRVGIKSARDYYIGGRKIGGILAGATYAATTYSAFMMIG 61 
                                       56899*******************999999988777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       924  (0.0515366); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 2925.03
//
Query:       gi|385805232|ref|YP_005841630.1|  [L=411]
Description: alcohol dehydrogenase [Fervidicoccus fontis Kam940]
Scores for complete 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-92  309.5   0.1    3.1e-92  309.2   0.1    1.0  1  Fe-ADH    Iron-containing alcohol dehydrogenase
    6.2e-14   52.3   0.2    4.9e-10   39.5   0.0    2.1  2  Fe-ADH_2  Iron-containing alcohol dehydrogenase
  ------ inclusion threshold ------
      0.017   15.2   0.0       0.11   12.6   0.0    2.2  2  KH_8      Krr1 KH1 domain


Domain annotation for each model (and alignments):
>> Fe-ADH  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  309.2   0.1   5.2e-96   3.1e-92       4     362 ..      29     397 ..      27     399 .. 0.93

  Alignments for each domain:
  == domain 1  score: 309.2 bits;  conditional E-value: 5.2e-96
                                       EEEETTGGGGHHHHHTTT...-..EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HHHHHHHHTTS CS
                            Fe-ADH   4 ivfgkgaleelgellkkl...gakralivtdkgslkksglldkvlesleeagievtvfdgvepnptleeveeaaala 77 
                                       ++fg ga++++ e  k+l   g++ra+ivtd+ +++++++ + ++ +lee+gie+t++d+v+pnpt+++++e+a++a
  gi|385805232|ref|YP_005841630.1|  29 TYFGVGAIRMISEISKNLkskGIDRAIIVTDPIVWQSTKVEQYIKPALEENGIEFTIYDKVRPNPTYASCDELANIA 105
                                       689****99998888888443667***************************************************** PP

                                       -TT.--EEEEEESHHHHHHHHHHHHHTT....................--EEEEESS-S-S-TT-SEEEEE.-TTSE CS
                            Fe-ADH  78 reegadvviavGGGsviDtAKaialllanpe..vedylgegkakkkkalpliaiPTtaGtGsevtplavitdeeege 152
                                       re++a v+i vGGGs  DtAK +a+ll+np+   +d++ e+   +++a+p++ i Tt GtGse  ++av   ++ g 
  gi|385805232|ref|YP_005841630.1| 106 REFNAKVFITVGGGSHNDTAKTAAALLKNPGktAKDLY-EKIILINEAIPVVSINTTHGTGSELDKYAVAQ-SDGGY 180
                                       *****************************955766666.666789999***********************.9999* PP

                                       EEEE-..SS--SEEEEEHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHT---TTSSB--HHHHHHHHHHHHHHHHHHH CS
                            Fe-ADH 153 klsifdpellPdlaivDpeltltlPkrvtaatglDalahalEayvskkanplsdalaleairliaknleravadged 229
                                       k +i+ p l+P +ai Dp+ltltlPkr+t +t+lDa+ h +Ea ++k++np+s  l++ airliak+l+ a +++++
  gi|385805232|ref|YP_005841630.1| 181 KPAIAGPGLYPVFAIEDPALTLTLPKRQTLSTALDAFHHSFEAATTKTRNPYSTLLSKTAIRLIAKWLPVAANEPNN 257
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHSS---HHHHHHHHHHC.C.GGGGGS-HHHHHHHHH..........HHHHHHT...... CS
                            Fe-ADH 230 leareqmllastlaglafsnaglgavHalahalgalf.giphglanaillpavlrfnaeaaperlaqlaralgge.. 303
                                       ++ar  +++as +ag++f  a+l+++H l+h+++al  ++phg+++  ++pavl+++++  pe  a+l   +  +  
  gi|385805232|ref|YP_005841630.1| 258 IAARYWLMYASAIAGISFDIASLHLTHTLEHPMSALNpKTPHGIGLTAIFPAVLNVTYKIFPELSADLLSSIIPDlk 334
                                       ***********************************8789*******************7779999999999877799 PP

                                       ...T--HHHHHHHHHHHHHTT---SHHHHT-TT-HHHHHHHHHT-T....SGGGGSSS---HH CS
                            Fe-ADH 304 sdeeaaeeliealrellkelglptsLselgvdeedldklaeaalkd....rslannpreltae 362
                                           +ae + ++++++++++g+p++L +lg++++d+d+l+e+a+++       a+ p+e+t+e
  gi|385805232|ref|YP_005841630.1| 335 GVPGEAEYAEREIEKWFASIGVPDKLTDLGFTDKDVDRLVENAITSpmtpLMAATSPVEVTKE 397
                                       8899999999********************9999*********88854323445677777776 PP

>> Fe-ADH_2  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.0   8.3e-14   4.9e-10       6      99 ..      38     133 ..      30     138 .. 0.89
   2 !   11.0   0.1   4.2e-05      0.25      92     246 ..     145     300 ..     136     303 .. 0.91

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 8.3e-14
                          Fe-ADH_2   6 aleklgellkelelkkvllvadentkka..agekveeslkeagikvevveeveeeadleeveklvealreketdlvv 80 
                                       +++++++ lk+++++++++v+d  +++   +++ ++ +l+e+gi+ +++++v+++++  +  +l++ +re ++++++
  gi|385805232|ref|YP_005841630.1|  38 MISEISKNLKSKGIDRAIIVTDPIVWQStkVEQYIKPALEENGIEFTIYDKVRPNPTYASCDELANIAREFNAKVFI 114
                                       356677778888899*********9987558899******************************************* PP

                          Fe-ADH_2  81 avGgGtiiDiakyvsakln 99 
                                        vGgG+ +D+ak ++a l+
  gi|385805232|ref|YP_005841630.1| 115 TVGGGSHNDTAKTAAALLK 133
                                       ***************9876 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 4.2e-05
                          Fe-ADH_2  92 kyvsaklnvpyvsvpTaaSvDGfaspgaslvvd.gkkrtv.akaaaPlaviaDldvlaeAPrrllasGvGDllgkyt 166
                                       k++  ++ +p+vs+ T+    +  + +a    d g k  +  +  +P+  i D  +  + P+r ++s   D+   + 
  gi|385805232|ref|YP_005841630.1| 145 KIILINEAIPVVSINTTHGTGSELDKYAVAQSDgGYKPAIaGPGLYPVFAIEDPALTLTLPKRQTLSTALDAFHHSF 221
                                       788888899999999999999999999999999888989989999******************************** PP

                          Fe-ADH_2 167 aladwklanevseplaklsaamvqeaaeklvedkketealeellealalsgigisrpaSGsEHliSHaldmlalkqa 243
                                         a+ k  n +s  l+k++++ + + +  ++++++++ a   l+ a+a++gi++  +     H + H + +l   ++
  gi|385805232|ref|YP_005841630.1| 222 EAATTKTRNPYSTLLSKTAIRLIAKWLPVAANEPNNIAARYWLMYASAIAGISFDIASLHLTHTLEHPMSALN-PKT 297
                                       ******************************************************9988888888888887777.666 PP

                          Fe-ADH_2 244 lHG 246
                                        HG
  gi|385805232|ref|YP_005841630.1| 298 PHG 300
                                       777 PP

>> KH_8  Krr1 KH1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.36   2.2e+03      17      35 ..      67      85 ..      65      89 .. 0.85
   2 ?   12.6   0.0   1.8e-05      0.11      27      72 ..     206     250 ..     196     255 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.36
                              KH_8 17 eveekikklleekklklev 35
                                      +ve++ik +lee+ +++++
  gi|385805232|ref|YP_005841630.1| 67 KVEQYIKPALEENGIEFTI 85
                                      6789999999999999887 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 1.8e-05
                              KH_8  27 eekklklevdlkerslkvsTtekTrDPyiilkardlikLisrgvpl 72 
                                       ++++l++++d   +s++  Tt kTr Py  l ++  i+Li++  p+
  gi|385805232|ref|YP_005841630.1| 206 KRQTLSTALDAFHHSFEAATT-KTRNPYSTLLSKTAIRLIAKWLPV 250
                                       67899999********99887.7******************97776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); 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: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 2727.27
//
Query:       gi|385805233|ref|YP_005841631.1|  [L=427]
Description: hydroxymethylglutaryl-CoA reductase, degradative [Fervidicoccus fontis Kam940]
Scores for complete 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-109  366.5   7.3   1.7e-109  366.2   7.3    1.1  1  HMG-CoA_red  Hydroxymethylglutaryl-coenzyme A reductase
  ------ inclusion threshold ------
      0.088   12.5   0.2        3.4    7.4   0.0    3.0  3  RecO_N_2     RecO N terminal


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 !  366.2   7.3  1.9e-113  1.7e-109       2     367 .]      19     384 ..      18     384 .. 0.96

  Alignments for each domain:
  == domain 1  score: 366.2 bits;  conditional E-value: 1.9e-113
                                       HHHHHHHHHH...S-HHHHHHH.TT----HHHHHHHSSS---------EEEEEEEETTEEEEEEE---STTHHHHHH CS
                       HMG-CoA_red   2 veeRrkllee...lteeeleel.keesldeevadkmiEnviGyvqlPlGvagpllingkeylvPmAteEgslvAsas 74 
                                       +ee++k+++e   l++ee++ l + +sld+++a++m+Env+G+++lP++va++++ing++yl+Pm++eE+s+vA+as
  gi|385805233|ref|YP_005841631.1|  19 FEEKLKIVKEfsnLSDEEVNLLkSMGSLDRKIAETMVENVVGVMPLPFSVAPNFRINGRDYLIPMVIEEASVVAAAS 95 
                                       689999999988899999999955599************************************************** PP

                                       HHHHHHHHTT-B.EEEE----EEEEEEEE.--S-HHHHHHHH.HTHHHHHHHHHHCSHH..CCT-EEEEEEE.EE-. CS
                       HMG-CoA_red  75 rgakainesgGvkttvlkdgmtraqvvllesvedaaelkkwi.ekkeeleelanaaest..srggglkdiev.vla. 146
                                       ++a+++++++G+   +++d+++++q++++  v++++ +++ i e+k+e+ +lan++++   + ggg+kd+ev +++ 
  gi|385805233|ref|YP_005841631.1|  96 NAARFMRDGNGI-ISIATDSIMIGQIYIY-GVKNISFASQIIyENKDEILKLANETDKYlvNIGGGAKDVEVrAIDt 170
                                       ************.9999999*********.****************************999***********99999 PP

                                       ...SSEEEEEEEEE-TTC--HHHHHHHHHHHHHHHHHHHTSEEEEEEE-S--GGGEEEEEEEEEHHHH..-SSTTHH CS
                       HMG-CoA_red 147 ...grlvvlrlkvdtgDAmGaNmvnkateaaaelieeefgeeellsilsNlctdkkasainaiegrgksvvaeatig 220
                                          g++++++l vd++DAmGaN+vn+++e++a++ie+ ++++++l+ilsNl++++++++++ ++++ +        g
  gi|385805233|ref|YP_005841631.1| 171 rnyGKVLCVHLLVDVKDAMGANTVNTMAEKVAPFIEKLTEGRAILRILSNLADRRIVRTRAIVKKEML--------G 239
                                       99999****************************************************99998888777........* PP

                                       HHHHHHHHHHHHHHHH-HHHH..HHHHHHH.......HHHHHHHHHHTT--HHHHHHHHHHHTT.......SEEE.. CS
                       HMG-CoA_red 221 eevvekilkasaealvdlnranigtankGiggfnahaaNgiaAvflAtGqDlaaveesshaiaa.......leev.. 288
                                       ee ve i+ as++a+ d++ra  +t+nkGi       +Ng+ Av+lAtGqD +a+e+++h +aa       l+ +  
  gi|385805233|ref|YP_005841631.1| 240 EEAVELIAMASEIAASDPYRA--ATHNKGI-------MNGVIAVALATGQDHRAIEAGAHSYAArtgryttLSFWek 307
                                       *********************..*******.......*******************************999777765 PP

                                       .TTTEEEEEEEEE.----SBSHHHHH-HHHHHH.HHTT---HH...HHHHHHHHHHHHHHHHHHHHHT-----HHHH CS
                       HMG-CoA_red 289 .edgdlygsvtlPsleVGtvGGgtklppqaell.kllgvkgaknakeLaeiiaavgLAqelsalrALaaeglqkgHm 363
                                        ++g+l+g++++P l+VG+vGG++k++p  +++ k+l++++ak   +Laei+ avgLAq+++alrAL++eg+qkgHm
  gi|385805233|ref|YP_005841631.1| 308 dREGNLVGTLEMP-LAVGIVGGSIKVHPITKIAlKILNISTAK---QLAEIMGAVGLAQNFAALRALTTEGIQKGHM 380
                                       46677********.*****************************...******************************* PP

                                       HHHH CS
                       HMG-CoA_red 364 klhr 367
                                       +lh+
  gi|385805233|ref|YP_005841631.1| 381 RLHA 384
                                       **96 PP

>> RecO_N_2  RecO N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0     0.034     3e+02      34      51 ..       5      22 ..       4      36 .. 0.82
   2 ?    7.4   0.0   0.00038       3.4      11      37 ..     101     127 ..      97     147 .. 0.83
   3 ?   -1.9   0.0      0.31   2.8e+03       9      31 ..     393     415 ..     389     417 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.034
                          RecO_N_2 34 Garhsliqlgtkidfele 51
                                      G + s iq ++k+ fe++
  gi|385805233|ref|YP_005841631.1|  5 GEKSSRIQDFHKMSFEEK 22
                                      8899***********986 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00038
                          RecO_N_2  11 vkdedlivtiltkeklktlyrfyGarh 37 
                                       ++d++ i++i t + ++    +yG++ 
  gi|385805233|ref|YP_005841631.1| 101 MRDGNGIISIATDSIMIGQIYIYGVKN 127
                                       79***********************96 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.31
                          RecO_N_2   9 qkvkdedlivtiltkeklktlyr 31 
                                        ++ + ++i +i+ +ek ++ yr
  gi|385805233|ref|YP_005841631.1| 393 ASYEEAEKIAEIMVNEKNISFYR 415
                                       5688899999******9999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       857  (0.0477997); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); 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: 0.57u 0.34s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 2597.02
//
Query:       gi|385805234|ref|YP_005841632.1|  [L=514]
Description: gamma-glutamyltransferase [Fervidicoccus fontis Kam940]
Scores for 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-107  357.9   0.0   1.1e-106  357.7   0.0    1.0  1  G_glu_transpept  Gamma-glutamyltranspeptidase


Domain annotation for each model (and alignments):
>> G_glu_transpept  Gamma-glutamyltranspeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  357.7   0.0    6e-111  1.1e-106       2     512 .]      26     508 ..      25     508 .. 0.93

  Alignments for each domain:
  == domain 1  score: 357.7 bits;  conditional E-value: 6e-111
                                       HHHHTT--HHHHHHHHHHHHHHHSTTT-STTSEEEEEEEETTSCEEEEEEE--BB-TT--TTTTTSCBCCHHHHSSG CS
                   G_glu_transpept   2 evLrkGGnAvDAavAaalclgvvepqssGiGGGgfllvydaktkkvealdaretAPaaatkdmfdkegdsklsktga 78 
                                       +vL+ GGnA+DA vA++l+l+vv p+  GiGG++f+l++d ++k +  + +++ AP+ ++ ++ +++g +k+++ g+
  gi|385805234|ref|YP_005841632.1|  26 KVLDLGGNAIDASVATSLTLSVVLPHLGGIGGDFFALIADPSEKVH-YISGSGWAPKRLSIEYMKSRGFNKMPNEGP 101
                                       79****************************************9977.7***************************** PP

                                       GG-BB--HHHHHHHHHHHH-SS-HHHHHHHHHHHHHH-EE--HHHHHHHHHCHHHHHTSHHHHHHHEETTSE--TTS CS
                   G_glu_transpept  79 lavgVPGevagleeahkkyGklpwadllepaiklareGfpvsealaralaeaeerlkkdpelaklFlpegevlkage 155
                                       +++ VPG v+gl  +++k+G+++w++l+   ++  ++Gfp+s+  a+al++++e+l +dp+++k++++++e + ag+
  gi|385805234|ref|YP_005841632.1| 102 HSIVVPGLVDGLRVMWEKFGTMEWKKLVSIVVDSLKDGFPISNSFASALNSSKEKLLEDPGSKKTYFSNKESYTAGD 178
                                       ***************************************************************************** PP

                                       EE--HHHHHHHHHHHHHTTHHHHSSHHHHHHHHHHHHTT-S--HHHHHH---EEES-EEEEETTCEEEEE-TTCSHH CS
                   G_glu_transpept 156 llkqpalAktLerlaeeGaeaFYkGelAeklvaelqkagGiltaeDLanykvevreplsadyrggytvyepppssgg 232
                                       ++k   l + L +++++ +++FY+G +Aek v+ l+  gG+ +++D++++k+++ +p+s+++ g++t+ye+pp+++g
  gi|385805234|ref|YP_005841632.1| 179 IFKYDGLINALILISQD-PREFYEGPIAEKAVEYLNSLGGAFELSDFKEFKAHIGKPISIEL-GDNTIYEMPPNTQG 253
                                       ***********999875.789*****************************************.************** PP

                                       HHHHHHHHHHCTTTGGGCTTTCHHHHHHHHHHHHHHHHHHHHH-SSTTTSSSGHCHHHHHT-HHHHHHHHTT.BTTB CS
                   G_glu_transpept 233 ivllqiLnilegfdlkslssnsaetlhllvEamklayadRsrylgDpdfvknptelveellskeyakeraklIkdka 309
                                       i++lq L++le + ++ ++s+s e++   +      ya R++y+gDp+++k+   +veells+e++++  k++k ++
  gi|385805234|ref|YP_005841632.1| 254 ITTLQLLKLLEYLGMS-YNSTSRERVLSHLRLYEPIYAVRDAYIGDPEYMKT---TVEELLSQEFLNNAIKSMKYRN 326
                                       **************55.5555677777778888999**************95...5*******************99 PP

                                       ..SGGGCSCGGCSCG.TTEEEEEEEEETTS-EEEEEEEESSTTTTSEBETTTTEBE--GGGGSBSTS..TTSCSTTS CS
                   G_glu_transpept 310 atpsseyykaaeaaeesggTthlsvvDregnaVSltstinllFGsgvvvpgtGilLnnemddfstgvenafgldpsp 386
                                       +             +++++Tt++s++D++g +VS ++++ +++Gs v+ p   i++n + ++f         l   +
  gi|385805234|ref|YP_005841632.1| 327 TLS-----------TQGSDTTFFSIIDESGYVVSGIQSLFTGWGSYVTEPTFEITFNKRASSFN--------LIDGH 384
                                       998...........46************************************************........***** PP

                                       TTB--TT----B----EEEEETTEEEEEEEEESGGGHHHHHHHHHHHHHTT-S-HHHHHHS--EEESSSSTEEEEST CS
                   G_glu_transpept 387 anaiePgkRplssmaPtivlkdgkpvlvlGaaGGsriisavlqvlvnvldlgldlqeavdaprihhqllpdkvevEe 463
                                       +na+ P+kRp+++++ +i+   ++ v+ lG +G+   ++ ++q+  n++ +++++qea++ pr++++   + ve+Ee
  gi|385805234|ref|YP_005841632.1| 385 PNALGPRKRPFHTLSAMIIK-GKERVMSLGLSGAHYRPQLHAQLYENIFRFKMNPQEALEHPRFVWDPENNLVEYEE 460
                                       **************987765.58999****************************************866789***** PP

                                       TS.HHHHHHHHHTTSEEEESSSTCCCEEEEEEEETTTEEEEEE-TTTTT CS
                   G_glu_transpept 464 gfseevveeLearGhkvkevedsssvvaavavakekgvleaasDprkdg 512
                                       g++   ++eL+      +  +  ++v aa+a + e+gv  a sD r+dg
  gi|385805234|ref|YP_005841632.1| 461 GIDMPSANELNGKKIIKRGYPSRIGV-AAIAEILENGVKAAYSDIRGDG 508
                                       **********9655443444444444.4444444************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (514 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 3100.59
//
Query:       gi|385805235|ref|YP_005841633.1|  [L=1055]
Description: DEAD/DEAH box helicase [Fervidicoccus fontis Kam940]
Scores for complete 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   61.8   0.0    1.3e-16   60.8   0.0    1.5  1  DEAD             DEAD/DEAH box helicase
    2.4e-15   56.8   0.1    1.7e-14   54.1   0.1    2.4  2  Helicase_C       Helicase conserved C-terminal domain
    9.5e-06   25.7   0.1    2.4e-05   24.4   0.1    1.7  1  ResIII           Type III restriction enzyme, res subunit
      0.009   16.0   0.0        1.6    8.7   0.0    2.4  2  Flavi_DEAD       Flavivirus DEAD domain
  ------ inclusion threshold ------
       0.11   11.5   0.0       0.22   10.6   0.0    1.4  1  T2SSE            Type II/IV secretion system protein
        1.2    9.5   6.6       0.33   11.3   0.4    2.8  3  Siah-Interact_N  Siah interacting protein, N terminal


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.8   0.0   4.4e-20   1.3e-16       2     171 ..      59     237 ..      58     241 .. 0.80

  Alignments for each domain:
  == domain 1  score: 60.8 bits;  conditional E-value: 4.4e-20
                                       HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrv 78 
                                       + Q +a++++ +g++++++  TGsGKT+a+++ +l++ +   + ++ +++ + Pt +L ++++++++ + k  ++ v
  gi|385805235|ref|YP_005841633.1|  59 SHQLKAMKALEEGKNIIIKSGTGSGKTEAWALYALKKAS---THENFRTIAIYPTLALSNDQVSRIEAYSKAFSVPV 132
                                       5799*******************************9995...79999************************988666 PP

                                       EEE..ETTSSHHHHHHHHH..TT...CSEEEEEHHHHHHHH.......HCTSSH..CTTEEEEEEETHHHHHHTTTH CS
                                       xxx..xxxxxxxxxxxxxx..xx...xxxxxxxxxxxxxxx.......xxxxxx..xxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  79 lli..iggvaardqlskld..ng...vdivvgtpgrlddll.......stgkln..lsqvrflVlDEadrlldqgfs 139
                                       + +   +++a+r+++ +l+  ++    +i++++p  l+  l       +t  ++  + +  ++V+DE d +      
  gi|385805235|ref|YP_005841633.1| 133 MQLdsPSKEAYRKEHGTLSlrKKiisSKILITNPAFLLTDLkkfftkqNTSIFQdfYFNPGLIVIDELDFYDPR-SI 208
                                       644224477889998888532447889*******9999866688865434444466666688********9998.66 PP

                                       HHHHHHHHHSHHHCTTSTTTSEEEEEESSBSH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 140 dfinrilnqlpqitcdgklqrqvivlSATlpk 171
                                         i  il+ +++ +++++   qv +l+ATl++
  gi|385805235|ref|YP_005841633.1| 209 SLILGILELISKVSQRKP---QVAILTATLSN 237
                                       777788888866555544...5********83 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.1   0.1   5.7e-18   1.7e-14      13     110 ..     342     441 ..     333     442 .. 0.89
   2 ?   -1.0   0.0      0.75   2.3e+03      55      81 ..     914     940 ..     896     945 .. 0.76

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 5.7e-18
                                       TTTTSEEEEEESSHHHHHH.HHHHHHHT.TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESE CS
                        Helicase_C  13 eeeggkilifvntidrlek.vklllekk.gikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnl 87 
                                        +++g +++f+  i+r+e+ ++ l+ k  + kva++h   +++er++i +  ++g+++++++ + +++Gidi +v  
  gi|385805235|ref|YP_005841633.1| 342 LQDDGLTIVFTSGINRAEEiARKLKIKVgEDKVATHHHLVSKSERKKIEDWAKEGKIKIIVSPRTLSQGIDIGSVVR 418
                                       378999***********97766664444789********************************************** PP

                                       EEESSSSSSHHHHHHHHTTSSST CS
                        Helicase_C  88 VinfdlprnvtsyiqriGRtgRa 110
                                       +++++lp++++++ qr GR gR 
  gi|385805235|ref|YP_005841633.1| 419 IVHIGLPDSLREFLQREGRKGRR 441
                                       *********************95 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.75
                                       HHHHHHHHHTTSSSEEEESGGGTSSST CS
                        Helicase_C  55 reeileqfnkgesdvLiatdvaerGid 81 
                                         ei +    +e+++Li+++ ++++i 
  gi|385805235|ref|YP_005841633.1| 914 ESEIDDLAEYEEYNILISSKEVAKSIS 940
                                       4444445556899*******9999985 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 !   24.4   0.1   8.1e-09   2.4e-05       5     140 ..      58     199 ..      39     234 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 8.1e-09
                                       -HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHH...HHGGGGT CS
                            ResIII   5 reyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtl...eefkkfl 78 
                                        ++Q +a+++l      ++ k+++ik  TG+GKT   a  + + ++ +++ +++ + p+++l +      e+++k +
  gi|385805235|ref|YP_005841633.1|  58 FSHQLKAMKAL------EEGKNIIIKSGTGSGKTEAWALYALKKASTHENFRTIAIYPTLALSNDQVsriEAYSKAF 128
                                       33444444444......68899***************99999999999999***********999984555555555 PP

                                       GG.........GEEEESSS-B--............-SEEEEEHHHHHHTH.........HHHTTT-S...EEEEET CS
                            ResIII  79 seayke.....igkkvsgdkkka.....kekdstnkkilvttiqsldadseee.eeeseellrdrfd...viiiDE 140
                                       s ++++     + + +++    +      +k++ ++kil+t+   l  d+++  ++++++  +d++    +i+iDE
  gi|385805235|ref|YP_005841633.1| 129 SVPVMQldspsK-EAYRK----EhgtlsLRKKIISSKILITNPAFLLTDLKKFfTKQNTSIFQDFYFnpgLIVIDE 199
                                       555555655431.22111....123334666777999*****9999999944463333333333333699999999 PP

>> Flavi_DEAD  Flavivirus DEAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.8   0.0    0.0086        26       3      47 ..      70     115 ..      68     147 .. 0.76
   2 !    8.7   0.0   0.00054       1.6      94     135 ..     190     234 ..     170     240 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0086
                                       X--EEEEE--TTS-TTTTH.HHHHHHHHHHTT--EEEEESSHHHHH CS
                        Flavi_DEAD   3 kkkltvldlhPGaGktrkv.lpelvkeaierrlrtlvLaPtrvvla 47 
                                       ++k  +++   G+Gkt    l  l k++++++ rt+ + Pt    +
  gi|385805235|ref|YP_005841633.1|  70 EGKNIIIKSGTGSGKTEAWaLYALKKASTHENFRTIAIYPTLALSN 115
                                       56777888999*****9862566666678899********976655 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00054
                                       ---SEEEEETTT--SHHHHH.HHHHHH..HHHHTTS-EEEEEESS CS
                        Flavi_DEAD  94 knyeliimDeahflDPasia.arGyle..tkaeegeaalilltat 135
                                        n  li++De  f DP si+   G+le  +k+++++ ++ +ltat
  gi|385805235|ref|YP_005841633.1| 190 FNPGLIVIDELDFYDPRSISlILGILEliSKVSQRKPQVAILTAT 234
                                       56679**************83579987446778888899999998 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   7.3e-05      0.22     121     164 ..      64     106 ..      24     134 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 7.3e-05
                             T2SSE 121 vlrkavrerglilvsGgTgsGKttll.yallkeinksderivtvE 164
                                       ++ ka++e ++i++  gTgsGKt      +lk+  ++ e++ t+ 
  gi|385805235|ref|YP_005841633.1|  64 AM-KALEEGKNIIIKSGTGSGKTEAWaLYALKKASTH-ENFRTIA 106
                                       44.3558999*************75423445556666.6666664 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 ?    0.3   0.1       0.3     9e+02      15      36 ..     379     400 ..     378     409 .. 0.85
   2 ?   -3.1   0.1       3.4     1e+04      34      45 ..     911     922 ..     910     937 .. 0.78
   3 ?   11.3   0.4   0.00011      0.33       9      40 ..     994    1025 ..     991    1031 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.3
                   Siah-Interact_N  15 kLlekAtRkrVkdlLsaeirKl 36 
                                        L++k++Rk++ d  +  + K+
  gi|385805235|ref|YP_005841633.1| 379 HLVSKSERKKIEDWAKEGKIKI 400
                                       5999*********988888887 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.4
                   Siah-Interact_N  34 rKleteilklke 45 
                                        K+e+ei  l e
  gi|385805235|ref|YP_005841633.1| 911 KKIESEIDDLAE 922
                                       699***977665 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.00011
                   Siah-Interact_N    9 DlEElkkLlekAtRkrVkdlLsaeirKletei 40  
                                        D+EE++ +++  + +  k+lL  e+ K+e+ i
  gi|385805235|ref|YP_005841633.1|  994 DIEEINMIIKRMKSQGYKQLLDSEKKKIESYI 1025
                                        *****************************977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1055 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       869  (0.048469); expected 358.6 (0.02)
Passed bias filter:                      644  (0.0359195); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.90u 0.33s 00:00:01.23 Elapsed: 00:00:00.53
# Mc/sec: 6042.66
//
Query:       gi|385805236|ref|YP_005841634.1|  [L=164]
Description: molybdenum cofactor synthesis domain-containing protein [Fervidicoccus fontis Kam940]
Scores for complete 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-28   98.0   0.0    4.5e-28   97.7   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 !   97.7   0.0   2.5e-32   4.5e-28       2     141 ..       4     141 ..       3     146 .. 0.92

  Alignments for each domain:
  == domain 1  score: 97.7 bits;  conditional E-value: 2.5e-32
                                       EEEE-HHHHTTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSSTT--HHHHH CS
                     MoCF_biosynth   2 vitvGdellsgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGtGptpdDvtpeal 78 
                                       +++v+d++++g++eD++g+l++ ll++ g++v  + +vp d++ei + l+++ ++  + i++GGtGp+p+D+t ++l
  gi|385805236|ref|YP_005841634.1|   4 IVVVSDRVFKGEAEDESGKLMKGLLESKGFKVDYIFTVPNDPKEILRVLRKS-NS-KAFIFIGGTGPSPRDITLDTL 78 
                                       89***********************************************777.56.8999***************** PP

                                       HHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EE......TTEEEEE-SSHHHHHHHHHHHHHGG CS
                     MoCF_biosynth  79 aklfekelegfeeafrrvslkpgkpvgvapgailsrav......gktiigLPGspkavkealeeillpa 141
                                       +++  ++++gf+eafr+ s ++     v+++  +sr++      g+  +++PGs  avk+++e+i   +
  gi|385805236|ref|YP_005841634.1|  79 EEVAWRKIPGFGEAFRMKSFEK-----VGAAGLISRSEmfllydGRVSVVIPGSLDAVKTGFELIA-GI 141
                                       *********************7.....888888999999****65557899************998.54 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1278.13
//
Query:       gi|385805237|ref|YP_005841635.1|  [L=655]
Description: molybdenum cofactor synthesis domain-containing protein [Fervidicoccus fontis Kam940]
Scores for complete 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  164.8   0.0    2.2e-48  164.0   0.0    1.4  1  PBP_like        PBP superfamily domain
    1.7e-37  128.6   0.0      3e-37  127.8   0.0    1.4  1  MoeA_N          MoeA N-terminal region (domain I and II)
    2.4e-24   85.6   0.0    3.9e-24   84.9   0.0    1.4  1  MoCF_biosynth   Probable molybdopterin binding domain
    3.2e-12   46.4   0.0    7.3e-12   45.3   0.0    1.7  1  MoeA_C          MoeA C-terminal region (domain IV)
    3.6e-05   23.6   0.0    6.1e-05   22.9   0.0    1.2  1  SBP_bac_11      Bacterial extracellular solute-binding protei
     0.0023   17.5   0.0     0.0041   16.7   0.0    1.3  1  Phosphonate-bd  ABC transporter, phosphonate, periplasmic sub


Domain annotation for each model (and alignments):
>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.0   0.0   7.4e-52   2.2e-48      10     192 ..     440     628 ..     433     629 .. 0.94

  Alignments for each domain:
  == domain 1  score: 164.0 bits;  conditional E-value: 7.4e-52
                                       TCEEEEEES-HHHHHHHHHTTS-SEEEESS---CCCHHCCCCCEEE.EEEEEEEEE-CC-HCHCCCCHCCHHHS--B CS
                          PBP_like  10 gvrvavanvGsggGlkalrageadiagshlldketeeynapalrka.ldgievvlvnlarreqglvvakgnpkkitn 85 
                                       + +++++ vGs+ Gl+ +++g +dia +hl+d+ t++ynap+l k  + +  + lv++++r+  l +++g   ++++
  gi|385805237|ref|YP_005841635.1| 440 EAKLSYIPVGSYLGLELVKRGFIDIAPIHLFDENTGTYNAPFLNKDpVLKSSALLVRGYSRKLVLAFREG--TNLRG 514
                                       67899**************************************6543555589*****************..679** PP

                                       GGGC-S-B-EEEEE-TTSHHHHHHHHHHC-CEECT........E-SSTTSEEESSHHHHHCCHCCETTCCECCCGG- CS
                          PBP_like  86 wkdladaplrlvnRetGSGtrdlfdellkkegisk........ssikgyaqearshlavaaaVaagradvgvgieav 154
                                       ++d+ +++lr++nR++GSGtr++ d+llk+  ++k         ++kgy+    sh++vaaa+++grad+gv+ie +
  gi|385805237|ref|YP_005841635.1| 515 LEDVLESGLRFANRNKGSGTRMYVDYLLKRISAEKgvdfkkitRELKGYEYNLPSHNSVAAAISQGRADAGVCIEHA 591
                                       ****************************998888899**************************************** PP

                                       HCCCCCCECTTCE-EEEEEEEECTCCCSHHHHHHHHHH CS
                          PBP_like 155 aeelkgldfvplaeerydlvvrkealddpevqaflefl 192
                                       a +++gl ++pl+ee+yd++v+++ l++ +v+ f+++l
  gi|385805237|ref|YP_005841635.1| 592 A-RIYGLRYIPLTEEHYDFAVNRKSLEKNAVKTFIDYL 628
                                       *.79********************************98 PP

>> 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 !  127.8   0.0     1e-40     3e-37       2     157 .]      14     180 ..      13     180 .. 0.88

  Alignments for each domain:
  == domain 1  score: 127.8 bits;  conditional E-value: 1e-40
                                       -HHHHHHHHHHH-HH...-EEEEEGGCG-TT-BBSS-EE-SS-BSSS-EESSSEEEEEEBTTB--............ CS
                            MoeA_N   2 sveealaiilaalel...eeeevplaaealgrvlaedvvApedvPpfdnSamDGYAvraeagsgaseeep....... 68 
                                       svee l+ ++++  l     eev+l ++al rvla+d++Ap+d+Ppfd+S +DGYAv++++ ++a+e +p       
  gi|385805237|ref|YP_005841635.1|  14 SVEEGLEVLEEEQLLnplGIEEVNL-QKALYRVLADDIYAPIDYPPFDRSEVDGYAVNIKSVENADELNPavlkiag 89 
                                       7888888665554235656666***.99************************************************* PP

                                       .......-S---TT-.EEEE-TTSB--TT--EEEEGGGE..E....EETTE.S--STTTTEE-TTSSB-TTSEEE-T CS
                            MoeA_N  69 .saageeperllpgg.avrimTGaplPegadaVvpvEdte.eeeaketvev.kavkpgenvrraGedikaGevllra 141
                                        ++ ge p+ ++ ++ av+i TGa++P+g+  +v+ E+t+ +  ++e vev ++v  gen+  aG+di++Ge+l+++
  gi|385805237|ref|YP_005841635.1|  90 kVRIGEFPKIEVDEKnAVEIDTGAMIPRGTSGIVMEEYTKrK--ENEYVEVyRSVYTGENISFAGSDIAKGELLFSR 164
                                       *889999999888888***********************642..3344444799*********************** PP

                                       TBB--CCCHHHHHHCT CS
                            MoeA_N 142 gtrltpaeigllasvG 157
                                       g++l+  +ig+l s+G
  gi|385805237|ref|YP_005841635.1| 165 GRVLDHIDIGILSSMG 180
                                       **************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 !   84.9   0.0   1.3e-27   3.9e-24       1     143 [.     193     329 ..     193     330 .. 0.94

  Alignments for each domain:
  == domain 1  score: 84.9 bits;  conditional E-value: 1.3e-27
                                       EEEEE-HHHH.......TTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSST CS
                     MoCF_biosynth   1 avitvGdell.......sgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGtGptp 70 
                                       a++++G+el+        gki+D n++++++llk++g+e    ++v+D+e+ ++e +++ l+++d+iit+GGt+++ 
  gi|385805237|ref|YP_005841635.1| 193 AILSTGNELVppgsdlsIGKIYDVNAYMIYSLLKAHGIESDMFGIVQDKEDILEERIRELLKSYDIIITSGGTSAGI 269
                                       79*******************************************************9999999************* PP

                                       T--HHHHHHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EETTEEEEE-SSHHHHHHHHHHHHHGGHH CS
                     MoCF_biosynth  71 dDvtpealaklfekelegfeeafrrvslkpgkpvgvapgailsravgktiigLPGspkavkealeeillpale 143
                                       dDv++++  +++e       +++++ +lkpgkp+++a+    +r+    +igLPG+p ++ +   +illpal 
  gi|385805237|ref|YP_005841635.1| 270 DDVVYRVFDRVGE-------VLIHGFKLKPGKPTVLARS---GRK---LLIGLPGFPFSSLANSLLILLPALF 329
                                       *************.......8************999999...665...799******9988888888879885 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 !   45.3   0.0   2.4e-15   7.3e-12       1      72 []     342     412 ..     342     412 .. 0.96

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 2.4e-15
                                       EEEESS-EE--SSS-EEEEEEEES-S-EEEEEE-S---TT-GGGCTT--EEEEE-TT--EE-TT-EEEEEE- CS
                            MoeA_C   1 karlaedlksdpgrreflRvilteedgeyvaeptgkqgSglLsslaeAnglivipegtegleaGeeVevill 72 
                                       ka +a ++++d grr +++v l + d +++a p+ +++Sg ++  a+A+g++ + e+++ +e+G eV+v ++
  gi|385805237|ref|YP_005841635.1| 342 KASIAVSFRKDIGRRWLVPVLLNSIDKKIYAIPF-STSSGSIMMVARADGIALLSENKDVIEEGSEVDVVVF 412
                                       577899****************************.**********************************986 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 !   22.9   0.0     2e-08   6.1e-05      78     227 ..     499     640 ..     488     642 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 2e-08
                                       EEEEEEEESTT-TT---SHHHHHHSS--EEEE--T-TTTTHH.HHHHGGG--......HHHHHHHHHTEEEEESSHH CS
                        SBP_bac_11  78 ssplviavpkgnpkkikgwadLlkpglklavadPttspsGlaalalleaaga......qellkalekkvvklgessr 148
                                       s +lv+a ++g+  + +g++d+l  gl++a  +   s++  ++  ll++  a      +++ ++l+ +   + +s  
  gi|385805237|ref|YP_005841635.1| 499 SRKLVLAFREGT--NLRGLEDVLESGLRFANRNK-GSGTRMYVDYLLKRISAekgvdfKKITRELK-GYEYNLPSHN 571
                                       678*********..****************9994.5555556667777554444678878888877.566688999* PP

                                       HHHHHHHTTT-SEEEEEHHHHH..HSTTSSEEEE--TTT--...EEEEEEEE-TT--HHHHHHHHHTTSHHHHHHHH CS
                        SBP_bac_11 149 qlltaveageadagivyeseakaaengdkleavylpeglnldpldypaavlkkaakreaAraFlafLrspeaqailr 225
                                       ++++a+ +g+adag+  e++a       +l++++l e+ +       +av +k+ +++a + F+++L   + ++i++
  gi|385805237|ref|YP_005841635.1| 572 SVAAAISQGRADAGVCIEHAAR----IYGLRYIPLTEEHY------DFAVNRKSLEKNAVKTFIDYLEFNKIKKIAE 638
                                       *********************9....89*********977......6899999***************999999999 PP

                                       HT CS
                        SBP_bac_11 226 ky 227
                                       +y
  gi|385805237|ref|YP_005841635.1| 639 RY 640
                                       87 PP

>> Phosphonate-bd  ABC transporter, phosphonate, periplasmic substrate-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.4e-06    0.0041      86     171 ..     501     595 ..     477     633 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.4e-06
                                       EEEEEEETTSS--SHHHHGG-EEEE--TT-TTTTHHHHHHT....CCCCT--HH....HHSSEE.EE--HHHHHHHH CS
                    Phosphonate-bd  86 rsviivradsdiqsledLkgktiafvspsStsGylvpaalL....vkeagldpe....ddfsev.fsgshdaavlav 153
                                       + v++ r++ +++ led+    + f+ ++  sG+ +   +L    ++e+g+d +    ++ +++    sh+++++a+
  gi|385805237|ref|YP_005841635.1| 501 KLVLAFREGTNLRGLEDVLESGLRFANRNKGSGTRMYVDYLlkriSAEKGVDFKkitrELKGYEyNLPSHNSVAAAI 577
                                       56788899999*******77777778888888888777777344444577766644443556665678********* PP

                                       HTTSSSEEEEEHHHHHHH CS
                    Phosphonate-bd 154 lsgdadaaavsadaledl 171
                                        +g+ada++  ++a++ +
  gi|385805237|ref|YP_005841635.1| 578 SQGRADAGVCIEHAARIY 595
                                       *********877776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (655 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); 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: 0.70u 0.29s 00:00:00.99 Elapsed: 00:00:00.47
# Mc/sec: 4187.49
//
Query:       gi|385805238|ref|YP_005841636.1|  [L=406]
Description: molybdenum cofactor synthesis domain-containing protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-32  111.1   0.0    6.1e-32  110.5   0.0    1.3  1  MoeA_N           MoeA N-terminal region (domain I and II)
    1.2e-23   83.4   0.0    1.8e-23   82.8   0.0    1.3  1  MoCF_biosynth    Probable molybdopterin binding domain
    3.8e-14   52.6   0.0      8e-14   51.6   0.0    1.6  1  MoeA_C           MoeA C-terminal region (domain IV)
      0.001   18.2   0.0     0.0017   17.4   0.0    1.3  1  T2SSE            Type II/IV secretion system protein
  ------ inclusion threshold ------
      0.013   15.4   0.2        3.3    7.6   0.1    2.4  2  Intein_splicing  Intein splicing domain


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 !  110.5   0.0   1.7e-35   6.1e-32       2     157 .]      11     168 ..      10     168 .. 0.84

  Alignments for each domain:
  == domain 1  score: 110.5 bits;  conditional E-value: 1.7e-35
                                       -HHHHHHHHHHH-HH.-EEE.EEGGCG-TT-BBSS-EE-SS-BSSS-EESSSEEEEEEBTTB--............. CS
                            MoeA_N   2 sveealaiilaalel.eeee.vplaaealgrvlaedvvApedvPpfdnSamDGYAvraeagsgaseeep..saagee 74 
                                       ++e+a++i+l+++++ +     ++ +e++g++l e +v+p+dvP++++Sa+DG+Av++++ s as ++p   a +++
  gi|385805238|ref|YP_005841636.1|  11 PIEDAIKILLESVKIrKGGFkTHI-NESIGMILNESIVSPVDVPEVNRSAVDGFAVCSDEVSLASFNNPiiLALKKN 86 
                                       6899********977533334677.899*************************************999995555555 PP

                                       -S---TT-EEEE-TTSB--TT--EEEEGGGE...E....EETTE.S--STTTTEE-TTSSB-TTSEEE-TTBB--CC CS
                            MoeA_N  75 perllpggavrimTGaplPegadaVvpvEdte..eeeaketvev.kavkpgenvrraGedikaGevllragtrltpa 148
                                        e    + +v+++TG p+P+ +d Vv+ Ed++  e    ++v++ k+v +  nv ++Ged+k+G++++++g++l+p+
  gi|385805238|ref|YP_005841636.1|  87 GEGFDCSSTVQVNTGMPIPSPYDSVVMKEDARiyE----HSVHIlKSVPKYGNVSKKGEDLKKGDIIAEKGQILKPW 159
                                       55555555**********************96522....2233356666666************************* PP

                                       CHHHHHHCT CS
                            MoeA_N 149 eigllasvG 157
                                       +i+l asvG
  gi|385805238|ref|YP_005841636.1| 160 HISLFASVG 168
                                       ********9 PP

>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.8   0.0   5.2e-27   1.8e-23       1     143 [.     181     321 ..     181     322 .. 0.92

  Alignments for each domain:
  == domain 1  score: 82.8 bits;  conditional E-value: 5.2e-27
                                       EEEEE-HHHH.........TTSSGBHHHHHHHHHHHTTSE.EEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-S CS
                     MoCF_biosynth   1 avitvGdell.........sgkieDtngpllaellkelgv.evskytvvpDdeeeikeallaaleeadviittGGtG 67 
                                       ++i++G+e++         +  + D+++ l+++ l e+ + ++ +y+vv D++e+i+e l++alee+d++ittGGtG
  gi|385805238|ref|YP_005841636.1| 181 GIIATGSEVVdinnthkkgEFYVFDSTSRLIYASLIEHNFlQLTHYGVVEDEKEKIVEVLKKALEENDIVITTGGTG 257
                                       699*******99988875555569************99998*******************9999************* PP

                                       SSTT--HHHHHHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EETTEEEEE-SSHHHHHHHHHHHHHGGHH CS
                     MoCF_biosynth  68 ptpdDvtpealaklfekelegfeeafrrvslkpgkpvgvapgailsravgktiigLPGspkavkealeeillpale 143
                                       p+++D+t +a+ +l ++      ++ r+++++pg+p+++a +   ++   k+i+   G+p+a+ +al++i lp+l 
  gi|385805238|ref|YP_005841636.1| 258 PGERDLTFDAILNLNGQ------ILSRGIAMRPGRPTTIALI---EG---KPIFLFSGYPVASFVALRFIFLPFLS 321
                                       ****************8......************9888877...54...59*******************99986 PP

>> MoeA_C  MoeA C-terminal region (domain IV)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.6   0.0   2.2e-17     8e-14       2      71 ..     336     405 ..     335     406 .] 0.97

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 2.2e-17
                                       EEESS-EE--SSS-EEEEEEEES-S-EEEEEE-S---TT-GGGCTT--EEEEE-TT--EE-TT-EEEEEE CS
                            MoeA_C   2 arlaedlksdpgrreflRvilteedgeyvaeptgkqgSglLsslaeAnglivipegtegleaGeeVevil 71 
                                       a+l+++++   g  +f+Rv++  ++ e+ aep+  +gSg+Lssl ++n++++ip+++eg+e+Ge+V v+l
  gi|385805238|ref|YP_005841636.1| 336 AKLTKRVTGGIGYDTFIRVNVFRCGDELCAEPVMLRGSGILSSLLKTNAFMIIPRNVEGFEEGETVWVHL 405
                                       899***************************************************************9987 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 !   17.4   0.0   4.8e-07    0.0017     101     146 ..     219     264 ..     215     277 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.8e-07
                             T2SSE 101 keltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttll 146
                                       + l+l ++g+ e+ keki evl+ka++e+ +++ +GgTg G   l+
  gi|385805238|ref|YP_005841636.1| 219 NFLQLTHYGVVEDEKEKIVEVLKKALEENDIVITTGGTGPGERDLT 264
                                       6799***********************************9976555 PP

>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1   0.00093       3.3      55     117 ..     114     204 ..      93     219 .. 0.74
   2 ?    6.0   0.0     0.003        11      70     102 ..     229     268 ..     207     403 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00093
                                       TTS-EEEEETT-EEEECCTTEEEEEECCC--TT-EEEEE............................HSCEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................xxxxxxxxxx RF
                   Intein_splicing  55 esgrkikaTpeHkllvvrdegivEkradeLkegdliavp............................dadvvwdkvk 103
                                       ++  +i+  + H l +v + g v k++++Lk+gd+ia                                 ++  +v+
  gi|385805238|ref|YP_005841636.1| 114 KEDARIYEHSVHILKSVPKYGNVSKKGEDLKKGDIIAEKgqilkpwhislfasvgikevevlekikiGIIATGSEVV 190
                                       556677777778888886688889*************8888888888888888888888888877663334445777 PP

                                       EEEEEECEEEEEEE CS
                                       xxxxxxxxxxxxxx RF
                   Intein_splicing 104 sievedeeeyVYdl 117
                                       +i+++++++++Y +
  gi|385805238|ref|YP_005841636.1| 191 DINNTHKKGEFYVF 204
                                       77777776666654 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.003
                                       ECCT.TEEEEEECCC--TT-EEEEE......HSCEEEEEE CS
                                       xxxx.xxxxxxxxxxxxxxxxxxxx......xxxxxxxxx RF
                   Intein_splicing  70 vvrd.egivEkradeLkegdliavp......dadvvwdkv 102
                                       v ++ e+ivE+  + L+e+d++++       ++d+++d +
  gi|385805238|ref|YP_005841636.1| 229 VEDEkEKIVEVLKKALEENDIVITTggtgpgERDLTFDAI 268
                                       4444799***************998788887666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); 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: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 2488.14
//
Query:       gi|385805239|ref|YP_005841637.1|  [L=282]
Description: radical SAM protein [Fervidicoccus fontis Kam940]
Scores for complete 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   57.4   0.0    1.9e-15   56.9   0.0    1.3  1  Mob_synth_C  Molybdenum Cofactor Synthesis C
      1e-14   55.3   0.0    2.7e-14   53.9   0.0    1.7  2  Radical_SAM  Radical SAM superfamily
     0.0047   17.2   0.0      0.011   15.9   0.0    1.6  1  Fer4_12      4Fe-4S single cluster domain
     0.0071   16.5   0.0      0.018   15.1   0.0    1.7  1  Fer4_14      4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.047   13.8   0.0      0.076   13.1   0.0    1.3  1  PDU_like     Putative propanediol utilisation
      0.078   13.3   0.0        0.2   12.0   0.0    1.7  1  YcgL         YcgL domain


Domain annotation for each model (and alignments):
>> Mob_synth_C  Molybdenum Cofactor Synthesis C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.9   0.0   6.5e-19   1.9e-15       2     127 ..     148     271 ..     147     272 .. 0.92

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 6.5e-19
                                       EEEEEE---B-TTSSB--SSB--HHHHHHHHHHHS-EEEE--SST-SSEEEEETTT--EEEEE-TTTS-.-GGG--E CS
                       Mob_synth_C   2 elrfIElmpvgegeewrekkvvsadeilerieerlalleakketkgpakrykikdgkgeiglIapvsep.FCasCnR 77 
                                       +l +IEl p+g+ ++  e+++++ ++ +e +e+   ++ +  ++ +++++y +++g  e+ +I  + +p  C++C+R
  gi|385805239|ref|YP_005841637.1| 148 NLNLIELIPLGTPKNVYEREHFQVKSGFEYLEKVSVKKYI--REFQNRPVYVLPNGV-EVTVIIGYGNPyLCSKCSR 221
                                       799****************************998877777..56899*******999.8**********99****** PP

                                       EEE-TTSEEESSSS-SS-.EEHHHHHHTT--HHHHHHHHHHHHHT----HH CS
                       Mob_synth_C  78 lRltadGklktCLfaeee.idlrdllregaseeeLkelikealarkkekhk 127
                                       lRlt +G++ktC+f e++ +d+ + +++++ e+ ++e +++a+  +++++k
  gi|385805239|ref|YP_005841637.1| 222 LRLTPEGRIKTCIFVEDKyVDILKEIKNRD-EDGVAEGLRKAVLLREPYFK 271
                                       ******************9**********7.567*********99999876 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   0.0   8.9e-18   2.7e-14      43     166 ..      23     141 ..       7     142 .. 0.93
   2 ?   -1.6   0.0       1.1   3.2e+03      49      60 ..     205     216 ..     174     263 .. 0.61

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 8.9e-18
                                       HHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  43 aekgvkevilgggepllypdfvellerlaklavpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlk 119
                                       ++ g+ +  l+ggepl+++d +e++++l ++   g+++t++tng+ + +ek + l e+g+ r +++l++++  ++  
  gi|385805239|ref|YP_005841637.1|  23 KKFGIVNYKLTGGEPLVRKDAHEIVRALNEN---GLHVTMSTNGYFL-KEKSKDLSEAGLERANVSLHSLNLGTFSY 95 
                                       46679999**********************9...*************.*************************9999 PP

                                       HHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHHHH CS
                                       xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 120 lmn.rghtfeevlealeklreagikrvvdrivglpGendeeleellel 166
                                       l++  g+ +e+v+e++  + ++gi+ ++ + +++   n+ el+ ++++
  gi|385805239|ref|YP_005841637.1|  96 LTGtNGKYLEKVIEGINEALSYGID-IKLNFILMN-SNKNELKSIVDF 141
                                       999999*******************.899999988.888889988887 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.1
                                       EEEEESSTGGGS CS
                                       xxxxxxxxxxxx RF
                       Radical_SAM  49 evilgggeplly 60 
                                       +vi+g g+p l 
  gi|385805239|ref|YP_005841637.1| 205 TVIIGYGNPYLC 216
                                       455555555554 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   3.8e-06     0.011      57     106 ..      31      76 ..      20      87 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.8e-06
                           Fer4_12  57 tllGGEPllpenaeallelvkevkeekpekdiwlytgytleelskkekee 106
                                        l+GGEPl+   +++  e+v+ + e+++  + ++++gy l+e sk+ +e 
  gi|385805239|ref|YP_005841637.1|  31 KLTGGEPLV---RKDAHEIVRALNENGL-HVTMSTNGYFLKEKSKDLSEA 76 
                                       69*******...9999************.69**********998764444 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 !   15.1   0.0   6.2e-06     0.018      48      94 ..      27      68 ..      16      88 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6.2e-06
                           Fer4_14 48 iqglvltGGePLhyenkkellklvkrlkeeypekkiwletngtleie 94
                                      i +  ltGGePL     k+  ++v+ l e++  +++++ tng + +e
  gi|385805239|ref|YP_005841637.1| 27 IVNYKLTGGEPLVR---KDAHEIVRALNENG--LHVTMSTNGYFLKE 68
                                      445579******55...888999********..********987644 PP

>> PDU_like  Putative propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.5e-05     0.076      36      92 ..      78     136 ..      58     145 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.5e-05
                          PDU_like  36 lqhakvrltqvdlelleeLaelrae..ealvkwileaiayg..vklqlslnqqllpalpvk 92 
                                       l+ a+v l   +l   ++L++ + +  e++++ i+ea++yg  +kl++ l +   +  + k
  gi|385805239|ref|YP_005841637.1|  78 LERANVSLHSLNLGTFSYLTGTNGKylEKVIEGINEALSYGidIKLNFILMNSNKN--ELK 136
                                       799****************9976543399************666777777766666..444 PP

>> YcgL  YcgL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   6.8e-05       0.2      39      71 ..      27      59 ..      15      67 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.8e-05
                              YcgL 39 vmeleLskerkLaradaekVlaaLeeqGfylql 71
                                      +++ +L+  + L+r+da+++ +aL+e+G ++ +
  gi|385805239|ref|YP_005841637.1| 27 IVNYKLTGGEPLVRKDAHEIVRALNENGLHVTM 59
                                      67889*************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1831.13
//
Query:       gi|385805240|ref|YP_005841638.1|  [L=145]
Description: molybdenum cofactor biosynthesis protein C [Fervidicoccus fontis Kam940]
Scores for complete 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-44  151.2   0.7    2.1e-44  150.9   0.7    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 !  150.9   0.7   1.2e-48   2.1e-44       1     134 [.       5     143 ..       5     144 .. 0.98

  Alignments for each domain:
  == domain 1  score: 150.9 bits;  conditional E-value: 1.2e-48
                                       E---TTS--EEEEEEEEEEEEE-HHHHHHHHTTSSTTB-HHHHHHHHHHHHHHHHHHHSTT-----EEEEEEEEEEE CS
                              MoaC   1 mvdvsekeetkrtAvAegrvklseetlelikekklkkGdvlavariagimaaKktseliplcHplpltkvevelele 77 
                                       mvd+seke++ r+A+A+g++kl++etlel+k+++++kGdv++v+ i++i+++Kkt+el+pl+H++p+t+v++++e e
  gi|385805240|ref|YP_005841638.1|   5 MVDISEKESVYREAMATGFIKLKKETLELMKSGRVEKGDVFSVSTISSIIGVKKTPELLPLTHNIPITNVDTKYEFE 81 
                                       9***********************************************************************99876 PP

                                       TTTTEEEEEEEEEEEESS--HHHHHHHHHHHHHHHHHHHTTTHTT.......-EEEEEEEEEEE CS
                              MoaC  78 eeeesveieatvktegktGvemEALtavsvaaltvyDmvKavdke.......mvieevrlveKs 134
                                         e+ +++ +tv+  +ktGvemEAL++v+ a+l+++DmvK+++k+       ++i+e+++v+K 
  gi|385805240|ref|YP_005841638.1|  82 --EDGIRVYVTVRSVSKTGVEMEALVGVASALLNIWDMVKKYEKDengqyptTEIREIKVVKKI 143
                                       ..89****************************************99****************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); 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 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 978.88
//
Query:       gi|385805241|ref|YP_005841639.1|  [L=605]
Description: aldehyde:ferredoxin oxidoreductase [Fervidicoccus fontis Kam940]
Scores for 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-143  475.7   0.0   1.2e-142  475.4   0.0    1.1  1  AFOR_C    Aldehyde ferredoxin oxidoreductase, domains 2 & 3
    1.9e-84  282.4   0.2      3e-84  281.8   0.2    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 !  475.4   0.0  1.4e-146  1.2e-142       3     382 .]     221     601 ..     219     601 .. 0.97

  Alignments for each domain:
  == domain 1  score: 475.4 bits;  conditional E-value: 1.4e-146
                                       HHHHHHHHHHSH.HHHHHHHH-GGGHHHHHHHTT---BTTTTBS--TTGGGGSHHHHHHHTEEEE.E-TT-SS--EE CS
                            AFOR_C   3 gkkiqkeiksspqvtaelrkyGTaelvnianetgalptknfqegtfekaekisgealeekylvknegCfsCpiaCgr 79 
                                       +++  ++i+++p+  ++l+kyGTa+lvni+ne+g++pt+nfq+g+f+ a++ sgeal+ekylv+n+ Cf+Cpi Cgr
  gi|385805241|ref|YP_005841639.1| 221 VREKVNKIRNDPVGGGGLPKYGTAVLVNIINENGLYPTRNFQTGVFQYAYEQSGEALAEKYLVRNNPCFACPIGCGR 297
                                       6677899*****8888*************************************************99********** PP

                                       EEE......ETEE---HHHHHHHTGGGT---HHHHHHHHHHHHHHTB-HHHHHHHHHHHHHHHHTTSS-HHHH.TS- CS
                            AFOR_C  80 evkveegkkvkvegpeyetlaalGsnlgiddleailklnelcdelGlDtisaGntiafamelyekGllkkedt.dgl 155
                                       ++k ++  +  +egpeyet++alGs+lgi+dl++i++ n+l+de+GlDtis+G+tia amelyekG++k+ed+ +g 
  gi|385805241|ref|YP_005841639.1| 298 VTKLPTVGQ--TEGPEYETIYALGSTLGINDLATIVETNHLADEYGLDTISLGGTIATAMELYEKGYIKEEDLqKGP 372
                                       ***877765..99***********************************************************98899 PP

                                       ---TT-THHHHHHHHHHHTT-TTHHHHTT-HHHHHHCTT-GGG--EETTEE--SS-GGG-HHHHHHHHH-TTSS-SG CS
                            AFOR_C 156 elefgdaeallellekiAkregigdllAeGvkrlaeklgaeelamhvkGlelpaydprgakgmalaYatsnrGacHl 232
                                       +l++g++e l   +eki k+eg+g++lAeG +rla+k++ae++ m vk+lelpaydprga g++l+Yat+nrG+cH+
  gi|385805241|ref|YP_005841639.1| 373 PLRWGNTEVLHYYIEKIVKKEGFGKELAEGGYRLAKKYNAEQYFMGVKKLELPAYDPRGAEGHGLGYATNNRGGCHV 449
                                       ***************************************************************************** PP

                                       GG-THHHH.....S---TT--.HHHHHHHHHHHHHHHHHHHHT--GGGG-HHH......HHHHHHHHHT----HHHH CS
                            AFOR_C 233 rayliale.....ekvdplet.egkaelvkwfqdltalvdslglCkftseaeerldlelyakllsavtGidvteeel 303
                                       ++y+i++e      k+dp++  ++k +++  fq+lta++ds+glC+ft+     l  ++y++ll+a+ G+++++e+ 
  gi|385805241|ref|YP_005841639.1| 450 KNYMISPEilgypYKMDPHDIsDAKINMLLLFQHLTAIIDSAGLCLFTT---FGLGADDYTDLLNAALGWNLKTEDY 523
                                       *************999*****89**************************...5678899****************** PP

                                       HHHHHHHHHHHHHHHHHHT--H.HHS---HHHHHS---SSTTTT---..-HHHHHHHHHHHHT--TTS---HHHHHH CS
                            AFOR_C 304 lkaGeRiynleRlfnlreGltr.kddtlperlleeplkegpakgkvledeleemldeyYelrGWdetGvPtketlkr 379
                                       lk+GeRi+n eRlfnl++Gl++ k+dtlp+r+leep++egp+kg+v+  +l+eml++yY++rGW+e+G++ +e+lk+
  gi|385805241|ref|YP_005841639.1| 524 LKIGERIWNAERLFNLKAGLDPlKEDTLPKRFLEEPMPEGPNKGRVV--RLKEMLPRYYKMRGWTEDGRIPREKLKE 598
                                       **********************************************9..9*************************** PP

                                       CT- CS
                            AFOR_C 380 LgL 382
                                       L+L
  gi|385805241|ref|YP_005841639.1| 599 LEL 601
                                       *97 PP

>> AFOR_N  Aldehyde ferredoxin oxidoreductase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  281.8   0.2   3.3e-88     3e-84       1     197 [.       6     205 ..       6     206 .. 0.98

  Alignments for each domain:
  == domain 1  score: 281.8 bits;  conditional E-value: 3.3e-88
                                       SEEEEEETTTTEEEEEE--HHHHHHH-SCHHHHHHHHHHHS-TTS-TTSTTS-EEEEE-TTTTSSSTTB-EEEEEEE CS
                            AFOR_N   1 gkilrvdLstgkieveelpeelaekylGgrglaakllldevppgvdplspenplvfatGpltgtpapgsgrlvvvak 77 
                                       gkilrv+L++++i+v +++ee+a+k+lG rgl+++lll+e++p+vdpl+pen+l++a+Gpltgtpap+ gr++v++k
  gi|385805241|ref|YP_005841639.1|   6 GKILRVNLTEKEIKVDTYEEEVARKWLGSRGLGIYLLLKEMDPKVDPLGPENKLIIAAGPLTGTPAPTGGRYNVITK 82 
                                       79*************************************************************************** PP

                                       -TTTSSEEEEEEETCHHHHHHHCT-SEEEEES--SS-EEEEEETTEEEEEE-TTTTTS-HHHHHHHHHHHHTS...E CS
                            AFOR_N  78 sPltgtlgesnaGgrfgaelkraGydaivieGkaekpvylvieddkveiedaedlwgldtyettealkeelgd...k 151
                                       sPltg ++ sn+Gg+fgaelk+aGydaiv+eG+++kpvyl+i+d++ve++da++lwg++++et++ +k+el++   +
  gi|385805241|ref|YP_005841639.1|  83 SPLTGYITFSNSGGYFGAELKKAGYDAIVVEGASDKPVYLYINDEHVELRDASHLWGKKMSETEAIIKKELNEehlR 159
                                       *********************************************************************99888899 PP

                                       EEEE-HHHHTT-TTB-E.EETTEEE-SSSHHHHHHHTTEEEEEEE- CS
                            AFOR_N 152 vaviGpaGenlvrfAsisvddgraagrgGlGavmgsKnlkaivvrg 197
                                       va iGpaGenlvrfA+i+ d +raagrgG GavmgsK+lkai+v+g
  gi|385805241|ref|YP_005841639.1| 160 VAGIGPAGENLVRFANIMNDVHRAAGRGGPGAVMGSKKLKAIAVKG 205
                                       99***************666999*********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (605 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 3643.15
//
Query:       gi|385805242|ref|YP_005841640.1|  [L=83]
Description: molybdopterin converting factor subunit 1 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-17   64.2   0.1    1.4e-17   64.1   0.1    1.0  1  ThiS           ThiS family
  ------ inclusion threshold ------
      0.016   15.5   0.5      0.029   14.7   0.5    1.4  1  Urm1           Urm1 (Ubiquitin related modifier)
      0.022   15.1   0.0      0.027   14.8   0.0    1.1  1  Lambda_tail_I  Bacteriophage lambda tail assembly protein I


Domain annotation for each model (and alignments):
>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.1   0.1   2.3e-21   1.4e-17       1      77 []       4      83 .]       4      83 .] 0.98

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 2.3e-21
                                      EEETTCCHHHHTCEEEEESSTSBHHHHHHHHHHHTCHHG..TTTTEEEEETTEEEGC.CTTTSB--TTCEEEEEESTTC CS
                              ThiS  1 vllfaelrelageeelelaegstvaelleaLgerypela..lerrvavavNgeivpr.lwldtelkdgDevailppVaG 76
                                      v+lfa l+el++++ele++++ tv+e++e+L+ +yp+ +  le++  ++vNg ++ + + ldt+++d D+v+i+p V+G
  gi|385805242|ref|YP_005841640.1|  4 VRLFAMLYELTNKKELEVENANTVREIIEKLDSMYPGFKgfLEKGYLILVNGINIVHlNDLDTKVNDTDVVSIFPKVGG 82
                                      89***************************************99**************88******************** PP

                                      - CS
                              ThiS 77 G 77
                                      G
  gi|385805242|ref|YP_005841640.1| 83 G 83
                                      9 PP

>> Urm1  Urm1 (Ubiquitin related modifier)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.5   4.9e-06     0.029      41      96 .]      27      83 .]       8      83 .] 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.9e-06
                                      CCCC-SSGHHHCBS.TTSB-TTEEEEETTCEHHHCTCCCSB--TTEEEEEEETTT-- CS
                              Urm1 41 kknlikerkevFle.kdkvrPGilvLindaDwellgekdyelkdkDkivFistlhGG 96
                                      ++++i++ ++++   k+ +  G l+L+n +++  l+++d++++d+D+++    + GG
  gi|385805242|ref|YP_005841640.1| 27 VREIIEKLDSMYPGfKGFLEKGYLILVNGINIVHLNDLDTKVNDTDVVSIFPKVGGG 83
                                      567899999999988999******************************988888776 PP

>> Lambda_tail_I  Bacteriophage lambda tail assembly protein I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   4.5e-06     0.027      20      86 .]      21      83 .]      15      83 .] 0.89

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.5e-06
                     Lambda_tail_I 20 veavktleeairalssqldafkellqrskfavrvagvdVgesvpvdryaetlkdgkvvtivpvpaGg 86
                                      ve  +t  e+i  l s  ++fk  l+++ + + v g+++ +      +  ++ d  vv i p + Gg
  gi|385805242|ref|YP_005841640.1| 21 VENANTVREIIEKLDSMYPGFKGFLEKG-YLILVNGINIVHLND---LDTKVNDTDVVSIFPKVGGG 83
                                      67789*******************9988.679999999666666...99*************99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); 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: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 517.94
//
Query:       gi|385805243|ref|YP_005841641.1|  [L=384]
Description: putative metallocofactor modifying protein, radical SAM superfamily [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.3e-16   59.6   0.6    3.3e-16   59.6   0.6    2.3  3  SPASM        Iron-sulfur cluster-binding domain
      4e-14   53.3   0.1    2.9e-11   44.0   0.0    2.2  2  Radical_SAM  Radical SAM superfamily
      2e-07   31.1   0.0    5.2e-07   29.8   0.0    1.7  1  Fer4_14      4Fe-4S single cluster domain
    2.7e-07   31.0   0.1    8.2e-07   29.4   0.1    1.8  2  Fer4_12      4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.044   13.9   0.2         16    5.7   0.0    2.7  2  PAH          Paired amphipathic helix repeat


Domain annotation for each model (and alignments):
>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.8     1e+04      64      67 ..      44      47 ..      14      70 .. 0.64
   2 !   59.6   0.6   9.1e-20   3.3e-16       1      68 []     261     339 ..     261     339 .. 0.82
   3 ?   -5.1   1.3         5   1.8e+04      61      67 ..     358     364 ..     354     364 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.8
                             SPASM 64 CrnC 67
                                      C+ C
  gi|385805243|ref|YP_005841641.1| 44 CKMC 47
                                      3333 PP

  == domain 2  score: 59.6 bits;  conditional E-value: 9.1e-20
                             SPASM   1 C.fapsrslfInsdGdVvpCcvd..........kktyveelklGnireesleeIwnseeyqefrkskkfplielCrn 66 
                                       C f + ++++I++dG+V+pC+            +k+ v+ +++Gn+++ sl++Iw +++y +fr   k+ ++++C++
  gi|385805243|ref|YP_005841641.1| 261 CeFDENNAVVIRWDGEVSPCYRFlhtyyeyifgRKKKVNAYSFGNVKNRSLKDIWLDPKYSKFRFVMKNYMYPSCTD 337
                                       87889999************33366666677773334445************************44488899***** PP

                             SPASM  67 Cp 68 
                                       Cp
  gi|385805243|ref|YP_005841641.1| 338 CP 339
                                       *7 PP

  == domain 3  score: -5.1 bits;  conditional E-value: 5
                             SPASM  61 ielCrnC 67 
                                       +++C++C
  gi|385805243|ref|YP_005841641.1| 358 EPSCADC 364
                                       4679999 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.0   8.1e-15   2.9e-11       2     120 ..      35     148 ..      34     172 .. 0.84
   2 !    8.5   0.1   0.00068       2.4      65     159 ..     163     262 ..     142     266 .. 0.76

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 8.1e-15
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEES.STGGGSTTHHHHHHHHHHTCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgg.gepllypdfvellerlaklavp 76 
                                       + t  Cnl+C+ C   +   +e+++ +++    l+++    +e   +k ++lgg gep++yp+f++++++++ +   
  gi|385805243|ref|YP_005841641.1|  35 ELTTRCNLKCKMCFKQY---WEDKEGDMDYNLFLKILNDT-QEFPsIKMIFLGGiGEPTVYPKFTDAVKEIKDR--- 104
                                       7899************8...*****************999.67777999999966******************8... PP

                                       TEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  77 giritvetngtlpdeeklerllelgvdrvslgleaaddekvlkl 120
                                       g+ + ++tngtl+++  ++ l +  vd ++++ +a+     + +
  gi|385805243|ref|YP_005841641.1| 105 GYALGLSTNGTLLNKSLIDFLINEQVDLIYFSMDALPVQSNQVR 148
                                       ***********************99*********9887744444 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00068
                                       HHHHHHHHTCCCTEEEEEEECSSCHG....HHHHHHHHHTT-SEEEEE.EBSSSHHHHHHHHT.CTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx.xxxxxxxxxxxxx RF
                       Radical_SAM  65 ellerlaklavpgiritvetngtlpd....eeklerllelgvdrvslg.leaaddekvlklmn.rghtfeevleale 135
                                       +++e+ +++  p+ +i+ve+ +t+ +    +e+++ l elgvd + ++ l   ++e+v +++  ++ + +++++ le
  gi|385805243|ref|YP_005841641.1| 163 KIIEEKKRRVLPKPSISVEVVATKENykqlPEMAKYLNELGVDSMLISnLLPMTEEQVNDIVYdGKVDMSKIVDELE 239
                                       333333333369999999999999889999***********9999986466666668999999999999******** PP

                                       HHHHTTSETEEEEEEEBTTTSHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 136 klreagikrvvdrivglpGendee 159
                                       k+ ++gi  +++ ++ l+ e + e
  gi|385805243|ref|YP_005841641.1| 240 KISSYGIY-IKIPYFELKTERRCE 262
                                       *****998.777766666665555 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 !   29.8   0.0   1.4e-10   5.2e-07       5      92 ..      37     117 ..      32     140 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 1.4e-10
                           Fer4_14   5 lsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltG.GePLhyenkkellklvkrlkeeype 80 
                                       + +Cnl+Ck+C+++  w+++ g  + +  l +il+d+++   +i+ + l G GeP  y   +++ + vk++k+++  
  gi|385805243|ref|YP_005841641.1|  37 TTRCNLKCKMCFKQY-WEDKEGDMDYNLFL-KILNDTQEFP-SIKMIFLGGiGEPTVY---PKFTDAVKEIKDRG-- 105
                                       679*********999.****9999887777.9995554444.477677777*****99...**************.. PP

                           Fer4_14  81 kkiwletngtle 92 
                                       +   l tngtl 
  gi|385805243|ref|YP_005841641.1| 106 YALGLSTNGTLL 117
                                       9*******9975 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.1   2.3e-10   8.2e-07      12     102 ..      37     123 ..      29     165 .. 0.77
   2 ?   -1.6   0.0      0.85   3.1e+03      89     123 ..     154     188 ..     143     200 .. 0.74

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 2.3e-10
                           Fer4_12  12 vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllG..GEPllpenaeallelvkevkeekpek 86 
                                       +++Cnl+Ck Cf k+ w+ k+g +++ +l  +i++d+++   +++++lG  GEP +   ++++++ vke+k +++  
  gi|385805243|ref|YP_005841641.1|  37 TTRCNLKCKMCF-KQYWEDKEG-DMDYNLFLKILNDTQEFPSIKMIFLGgiGEPTV---YPKFTDAVKEIKDRGY-A 107
                                       689*********.788887766.57888999******995555556666377****...99*************9.5 PP

                           Fer4_12  87 diwlytgytleelskk 102
                                         ++++g+ l++ + +
  gi|385805243|ref|YP_005841641.1| 108 LGLSTNGTLLNKSLID 123
                                       8999999999876644 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.85
                           Fer4_12  89 wlytgytleelskkekeellkeidvlvdGkfeesl 123
                                        + tg  ++++ +++k+++l +  + v +   +++
  gi|385805243|ref|YP_005841641.1| 154 SEITGANIKKIIEEKKRRVLPKPSISVEVVATKEN 188
                                       56788888888888888888888877777665554 PP

>> PAH  Paired amphipathic helix repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1    0.0059        21       3      15 ..      61      73 ..      60     107 .. 0.85
   2 ?    5.7   0.0    0.0045        16       2      15 ..     319     332 ..     318     346 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0059
                               PAH  3 YkeFLdiLhdyqk 15
                                      Y+ FL+iL+d q+
  gi|385805243|ref|YP_005841641.1| 61 YNLFLKILNDTQE 73
                                      999*******995 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0045
                               PAH   2 vYkeFLdiLhdyqk 15 
                                       +Y++F  ++++y++
  gi|385805243|ref|YP_005841641.1| 319 KYSKFRFVMKNYMY 332
                                       7***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.25s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 2598.38
//
Query:       gi|385805244|ref|YP_005841642.1|  [L=647]
Description: peptidase, family S9c [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-55  187.1   0.2    4.1e-55  186.5   0.2    1.3  1  Peptidase_S9   Prolyl oligopeptidase family
    5.8e-17   61.1   0.9    0.00048   20.0   0.0    5.0  4  PD40           WD40-like Beta Propeller Repeat
    5.5e-09   35.2   0.1      0.016   14.0   0.0    3.7  3  DPPIV_N        Dipeptidyl peptidase IV (DPP IV) N-terminal re
    3.8e-08   33.3   0.1     0.0033   17.1   0.0    2.2  2  Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
    5.3e-08   31.9   0.4    1.1e-05   24.3   0.1    2.8  2  AXE1           Acetyl xylan esterase (AXE1)
    1.7e-07   31.1   0.3    0.00015   21.5   0.5    2.4  2  Abhydrolase_1  alpha/beta hydrolase fold
    9.4e-07   28.3   0.5      0.024   13.9   0.0    2.3  2  Hydrolase_4    Serine aminopeptidase, S33
    1.2e-05   25.0   0.0    4.9e-05   23.0   0.0    2.0  2  DLH            Dienelactone hydrolase family
     0.0045   16.2   0.1      0.068   12.3   0.0    2.1  2  DUF2920        Protein of unknown function (DUF2920)
     0.0073   16.6   0.5         26    5.3   0.0    4.9  6  Kelch_6        Kelch motif
  ------ inclusion threshold ------
      0.044   12.4   0.0      0.068   11.8   0.0    1.2  1  PhoPQ_related  PhoPQ-activated pathogenicity-related protein
      0.088   12.7   0.0       0.69    9.7   0.0    2.2  1  Abhydrolase_3  alpha/beta hydrolase fold


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 !  186.5   0.2   2.7e-58   4.1e-55       2     209 ..     432     647 .]     431     647 .] 0.95

  Alignments for each domain:
  == domain 1  score: 186.5 bits;  conditional E-value: 2.7e-58
                                       ---HHHHHHHCCT-EEEEE--TTSSTTHCHHHHTTSGGGGHHHHHHHHHHHHHHHHTT.S--GGGEEEEEETHHHHH CS
                      Peptidase_S9   2 sfsselqlladrGyvvvvanirGsggyGeafhdagkrklgqnefdDfiaaaealakeg.yvdserlaitGgSyGGyl 77 
                                       sf++e+++l+d+G++v++ n+rGs+gy e+f+d +++k+g+++++D+++++++++k++ ++d++rl++ GgSyGG++
  gi|385805244|ref|YP_005841642.1| 432 SFMHEFHVLSDAGFAVIYFNPRGSAGYTEDFKD-MRGKYGTRDYQDLMEGLDYAIKNFsFIDENRLGVAGGSYGGFM 507
                                       799******************************.9****************************************** PP

                                       HHHHHHH-GGG-SEEEEESE---CCCHHCSTTS...THH.HCCCC--TTT.....CHHHHHHHHHH-CGGG-----E CS
                      Peptidase_S9  78 tgaalnqrpdlFkaavaevpvvdvlrydsdtdl...lte.eymewgnpee.....neegykelspyspldnvkaypp 145
                                       t+++++ ++++Fkaav +++++++++++ ++d+   ++e +  +   + +       e y+++sp+++++n  +++p
  gi|385805244|ref|YP_005841642.1| 508 TNWIIG-HTNRFKAAVTQRSISNWISFYGTSDIgyyFAEdQIGGDLGK-DlwtgnLIEVYWDRSPLKYVNN--VKTP 580
                                       ******.****************************9999776665443.2356657899************..99** PP

                                       EEEEEETT-SSS-THHHHHHHHHHH--S-SEEEEEETTS-S...STTSSHHHHHHHHHHHHHHHHHC CS
                      Peptidase_S9 146 lLlihGlaDdrvppaealklvaaLqkkgknvlllifpdegH...gvgkprakveelarllaFlkeal 209
                                       +L++h+++D+r+ + +a++l++aL+ kg++++l+ifp+e+H   + gkp+++ve+l+++++++k++l
  gi|385805244|ref|YP_005841642.1| 581 TLILHSDEDYRCWIDQAYQLFTALKLKGVETKLVIFPGENHelsRKGKPKNRVERLNQIVSWFKKYL 647
                                       *****************************************9988899****************986 PP

>> PD40  WD40-like Beta Propeller Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.2   1.9e-05     0.028      13      36 ..      19      47 ..      15      50 .. 0.78
   2 !   20.0   0.0   3.2e-07   0.00048       4      38 .]      60      97 ..      59      97 .. 0.92
   3 !   14.2   0.0   2.2e-05     0.032       2      27 ..     175     200 ..     174     207 .. 0.89
   4 !    7.0   0.0    0.0038       5.7       2      25 ..     223     246 ..     222     249 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.9e-05
                                      EEEE-TTSSEEEEEEECT....TCEE..E CS
                              PD40 13 aPsfSPDGkrlaFsSdRg...sGkpd..I 36
                                      +P +SPDGk+ aF+ +++   + k+   +
  gi|385805244|ref|YP_005841642.1| 19 DPKISPDGKKVAFVTTKPsisDNKYYskL 47
                                      699************99976655554554 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 3.2e-07
                                      --SSSS.EEEEEE-TTSSEEEEEEECT.....TCEEEEE CS
                              PD40  4 ltntpgnegaPsfSPDGkrlaFsSdRg....sGkpdIyv 38
                                      +tn+p+ +++P++  D +++ F S+R+    + + +++v
  gi|385805244|ref|YP_005841642.1| 60 VTNGPS-DFSPFWAGDSNKILFLSRRSikenEEGLELWV 97
                                      89****.********************998888888886 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 2.2e-05
                                       EE--SSSS.EEEEEE-TTSSEEEEEE CS
                              PD40   2 krltntpgnegaPsfSPDGkrlaFsS 27 
                                       ++lt +++++g   +SPDGk++a+ S
  gi|385805244|ref|YP_005841642.1| 175 EKLTEGNEEIGFAQISPDGKKIAYIS 200
                                       68999999999999**********98 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.0038
                                       EE--SSSS.EEEEEE-TTSSEEEE CS
                              PD40   2 krltntpgnegaPsfSPDGkrlaF 25 
                                       ++lt +++ +++ +++P+ +++aF
  gi|385805244|ref|YP_005841642.1| 223 TKLTQGQFSIEDLAWDPNSSKIAF 246
                                       789999*****************9 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 !    8.3   0.1   0.00058      0.86       1      61 [.      23      82 ..      23     111 .. 0.90
   2 !   14.0   0.0   1.1e-05     0.016      23      63 ..     162     202 ..     156     204 .. 0.91
   3 !    8.2   0.0   0.00062      0.93     263     327 ..     213     277 ..     207     289 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00058
                                      TTTSSEEEEEECEEEESSSEETTEEEEEETTTEECEEEETTTT.BSEEEEESSTTEEEEEE CS
                           DPPIV_N  1 spdgkflllatnaeknwRhsytaeyyiydletneveelspgeeklqlakwSPagdklafvr 61
                                      spdgk++ + t++ ++  ++y+ +++iyd+e++e  ++++g      + w+ +++k+ f  
  gi|385805244|ref|YP_005841642.1| 23 SPDGKKVAFVTTKPSISDNKYYSKLWIYDIEKDEYYHVTNG-PSDFSPFWAGDSNKILFLS 82
                                      79***************************************.8889999999999999965 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 1.1e-05
                                       TEEEEEETTTEECEEEETTTT.BSEEEEESSTTEEEEEETT CS
                           DPPIV_N  23 aeyyiydletneveelspgeeklqlakwSPagdklafvrnn 63 
                                       + +y  dl+++++e+l++g+e++ +a++SP+g+k+a++   
  gi|385805244|ref|YP_005841642.1| 162 NALYFLDLNNGNLEKLTEGNEEIGFAQISPDGKKIAYISAE 202
                                       567899*******************************9866 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.00062
                                       EEEESSS-C.EEESS-SSS-EEEEEEEETTTTEEEEEESS.SE..TTEBEEEEEESSCTTEEEESSTT CS
                           DPPIV_N 263 ylfdldgkseikqlTsGeweVtsilavdekrdlvyFtatk.ds..PlerhlYsvslesggeltrltde 327
                                        l++l++++  ++lT+G++ + + la+d +++++ F a++  +      +l+  +l+ +g+++++t +
  gi|385805244|ref|YP_005841642.1| 213 KLINLQTGE-VTKLTQGQFSI-EDLAWDPNSSKIAFRASDfTHglNSHIKLWIMDLS-SGQIKKITLS 277
                                       566777777.88999999999.77899999999999999954433444558999999.9999998855 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 !   17.1   0.0   2.2e-06    0.0033      10     140 ..     404     532 ..     395     555 .. 0.76
   2 !   14.0   0.0   1.9e-05     0.028     214     265 ..     565     618 ..     551     621 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.2e-06
                                       EEE...TTSSSEEEEEEEESS-CCT.CCCCHTTCHHCCHGGGHHHHHTT-EEEEEE-TTSTTS-S---TT....TTT CS
                     Peptidase_S15  10 yrP.etkskeklPvlltrtPYgkndelasdkalaleelelqdkvfvarGYavVvqdvrGtggSeGeftvg....dsd 81 
                                       + P + k++ek+P++l       + +  s  +  +        v+ + G+av++ + rG++g + +f+ +    +++
  gi|385805244|ref|YP_005841642.1| 404 LKPtTFKEGEKYPAILYIHGGPATAYGESFMHEFH--------VLSDAGFAVIYFNPRGSAGYTEDFKDMrgkyGTR 472
                                       55655566666666665432222221222222222........37799***********998888888878999999 PP

                                       HHHHHHHHHHHHHHC..TTEEEEEEEEEECHHHHHHHHHCTT--TTEEEEEEECE-S-TCC CS
                     Peptidase_S15  82 eaedgadvidWlakq..pwsnGkVgmtGiSYlGttqllaaatgvpalkaivpeaaisdlyd 140
                                       + +d  + +d + k+     + + g+ G SY+G++ + +   ++ + ka+v + +is++  
  gi|385805244|ref|YP_005841642.1| 473 DYQDLMEGLDYAIKNfsFIDENRLGVAGGSYGGFMTNWIIG-HTNRFKAAVTQRSISNWIS 532
                                       99999999999999883456789*************99999.999************9987 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 1.9e-05
                                       HHHTT-HHHHHCT--S-EEEEEECCSSTTC.CHHHHHHHHHCCTT-..EEEEECE CS
                     Peptidase_S15 214 fWkdrnlsedadkvkapvllvgGwnDwnvk.ngaiklyealkapgv..klilgpw 265
                                       +W dr++ + +++vk+p+l++++  D     ++a++l+ alk +gv  kl++ p+
  gi|385805244|ref|YP_005841642.1| 565 YW-DRSPLKYVNNVKTPTLILHSDEDYRCWiDQAYQLFTALKLKGVetKLVIFPG 618
                                       56.5666779****************99999**************99***99987 PP

>> AXE1  Acetyl xylan esterase (AXE1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.42   6.3e+02      12      30 ..      55      73 ..      49      90 .. 0.84
   2 !   24.3   0.1   7.3e-09   1.1e-05      56     203 ..     388     523 ..     352     528 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.42
                                      TT--------TTHHHHHHH CS
                              AXE1 12 keYrgekeapeDFdefWdk 30
                                       eY   ++ p DF+ fW  
  gi|385805244|ref|YP_005841642.1| 55 DEYYHVTNGPSDFSPFWAG 73
                                      578888899********76 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 7.3e-09
                                       EEEEEEEEGGGEEEEEEEEEES...SSSSEEEEEEEE-TT--...GGGHHHHHHHHHTT-EEEEEE-TTTS..SSB- CS
                              AXE1  56 vydltfegvrgarikaklvlPke..keeklPavvefhGYegs...rgeihdllnyaaaGyavvvmdvRGqggesedk 127
                                            f+++ g+ i +++++P++  + ek Pa++  hG  ++   +  +h+    + aG+av+  + RG  g++ed 
  gi|385805244|ref|YP_005841642.1| 388 Y--FRFTASDGNIIDGWVLKPTTfkEGEKYPAILYIHGGPATaygESFMHEFHVLSDAGFAVIYFNPRGSAGYTEDF 462
                                       3..458999************96225579*********8665333677899999999*******************8 PP

                                       SSCCSS-SSSSTTTTTTSTTT-HHHHHHHHHHHHHH.HHHTSTTEEEEEEEEEEETHHHHHHHHHHHH-SS-SEEEE CS
                              AXE1 128 vgskgnkakGfiirGlldkeklyyrrvflDavrlve.ivaslpevDeeRvavlGasqGGalalavaalekrikavva 203
                                       + + g+    +   G          r + D ++ ++ ++++++++De+R++v+G+s GG ++  + +  +r ka+v+
  gi|385805244|ref|YP_005841642.1| 463 KDMRGK----Y---GT---------RDYQDLMEGLDyAIKNFSFIDENRLGVAGGSYGGFMTNWIIGHTNRFKAAVT 523
                                       776622....2...22.........225566655543799*******************999888887777777765 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.5     1e-07   0.00015       1     111 [.     416     531 ..     416     534 .. 0.79
   2 !    8.9   0.0   0.00068         1     182     250 ..     524     621 ..     515     624 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1e-07
                                       SEEEEE-STTTCGGG..GTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHH....HH.HHHC CS
                     Abhydrolase_1   1 pvlvilhGlpgssdv..waerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddld....ri.ldal 70 
                                       p+++++hG+p++++   ++    +  L+++gf vi +++rG++  +         ygt +++d ++    +i   ++
  gi|385805244|ref|YP_005841642.1| 416 PAILYIHGGPATAYGesFMH--EFHVLSDAGFAVIYFNPRGSAGYTEDFKDMRGKYGTRDYQDLMEgldyAIkNFSF 490
                                       79*********665544888..9999**************9865555554444999********9999976665677 PP

                                       TTSSEE.EEEETHHHHHHHHHHHHHGGGEEEEEEESECSSCC CS
                     Abhydrolase_1  71 gddklt.lvGhSmGGmialayaaeyperVkalvllgaidpaa 111
                                        d++   + G+S+GG++ +++   + +r ka v+  +i++++
  gi|385805244|ref|YP_005841642.1| 491 IDENRLgVAGGSYGGFM-TNWIIGHTNRFKAAVTQRSISNWI 531
                                       7888888********86.555556899999999888866655 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00068
                                       HHHHHHHHHHHHHCCHHHHHHHHHC.........................THHHHSEEEEEEETTCSSSCH.HHHHH CS
                     Abhydrolase_1 182 atgalksieqwpttdsaklllrlre.........................lknvlaptlvisgtsDplvpp.kaled 232
                                       ++  +++i+ + t d ++++ ++++                         ++nv+ ptl++++++D    + +a+  
  gi|385805244|ref|YP_005841642.1| 524 QRSISNWISFYGTSDIGYYFAEDQIggdlgkdlwtgnlievywdrsplkyVNNVKTPTLILHSDEDYRCWIdQAYQL 600
                                       5677889999999999999999999999999999999999**************************98888777777 PP

                                       HHHC.HTS..EEEEEEETCSS CS
                     Abhydrolase_1 233 laql.lpk..krlvvisdagH 250
                                       +++l l++   +lv+++++ H
  gi|385805244|ref|YP_005841642.1| 601 FTALkLKGveTKLVIFPGENH 621
                                       777755558777777777777 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.4   5.5e-05     0.082       6     105 ..     417     522 ..     412     525 .. 0.82
   2 !   13.9   0.0   1.6e-05     0.024     187     234 ..     574     623 ..     570     626 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.5e-05
                       Hydrolase_4   6 vvvlvHGl..aehsgryaelaeaLaaqGfavyalDhrGh.Grse......gkrghvpsfddyvdDlaafvekvkeeh 73 
                                       +++ +HG   + + + + + ++ L ++Gfav+ ++ rG  G +e      gk g  ++++d+++ l+ +++++    
  gi|385805244|ref|YP_005841642.1| 417 AILYIHGGpaTAYGESFMHEFHVLSDAGFAVIYFNPRGSaGYTEdfkdmrGKYG-TRDYQDLMEGLDYAIKNFSFID 492
                                       566777752245667899999*****************637777***9988888.9*****************9777 PP

                       Hydrolase_4  74 pelplfllGhSmGGliallyllrypdkvagli 105
                                       +++ l + G S GG++ ++++  + +++++++
  gi|385805244|ref|YP_005841642.1| 493 ENR-LGVAGGSYGGFM-TNWIIGHTNRFKAAV 522
                                       766.99********98.567777777688776 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 1.6e-05
                       Hydrolase_4 187 aakitlPllllhGeaDkvvdpeasrelyerlgsk..dktlklypglyHel 234
                                       ++++++P+l+lh+++D  ++ +++ +l+ +l+ k  + +l ++pg  Hel
  gi|385805244|ref|YP_005841642.1| 574 VNNVKTPTLILHSDEDYRCWIDQAYQLFTALKLKgvETKLVIFPGENHEL 623
                                       57899***************************99777888899****998 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0         4   5.9e+03     134     158 ..     374     398 ..     371     402 .. 0.82
   2 !   23.0   0.0   3.3e-08   4.9e-05      66     216 ..     465     646 ..     410     647 .] 0.77

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 4
                               DLH 134 ekeleeaakikapilalfgeeDefi 158
                                       + e++e aki+ap ++ f   D  i
  gi|385805244|ref|YP_005841642.1| 374 NDEVIEKAKIQAPEYFRFTASDGNI 398
                                       678899999****999999998665 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 3.3e-08
                               DLH  66 ldelvskvaeekvlddlkaavaylksvpevstkkvgvvGfCmGGalalllaaevpevdaav.........afYG... 130
                                       ++++   ++ +++++ l+ a++        +++++gv G   GG ++  ++ + ++++aav         +fYG   
  gi|385805244|ref|YP_005841642.1| 465 MRGKYGTRDYQDLMEGLDYAIKNFSF---IDENRLGVAGGSYGGFMTNWIIGHTNRFKAAVtqrsisnwiSFYGtsd 538
                                       55555555555566666555554444...447888888888888888888888877887753333333336888999 PP

                               DLH 131 ..........................lspekeleeaakikapilalfgeeDefipadevekleealkaanvdlelkv 181
                                                                     ++l++++++k+p l+l+ +eD     d++ +l  alk ++v+ +l++
  gi|385805244|ref|YP_005841642.1| 539 igyyfaedqiggdlgkdlwtgnlievYWDRSPLKYVNNVKTPTLILHSDEDYRCWIDQAYQLFTALKLKGVETKLVI 615
                                       9999999999999999999998888777789********************************************** PP

                               DLH 182 YpgagHaFandsresyneeaaedawervlelfkqv 216
                                       +pg  H   ++ +++ +     +  ++++++fk++
  gi|385805244|ref|YP_005841642.1| 616 FPGENHELSRKGKPKNR----VERLNQIVSWFKKY 646
                                       ******87777665433....34456677888876 PP

>> DUF2920  Protein of unknown function (DUF2920)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   4.5e-05     0.068     155     197 ..     469     511 ..     462     534 .. 0.86
   2 ?    1.4   0.0     0.094   1.4e+02     285     325 ..     578     619 ..     567     622 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.5e-05
                           DUF2920 155 fGimaAlDiinalkdlvkrfpkeadlpviliGgsyGGYlalLi 197
                                       +G    +D++  l++++k f++  ++ + + GgsyGG++++ i
  gi|385805244|ref|YP_005841642.1| 469 YGTRDYQDLMEGLDYAIKNFSFIDENRLGVAGGSYGGFMTNWI 511
                                       6777789****************999999**********9877 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.094
                           DUF2920 285 ntiyvsyHsekDklapaeeKiqlakilkklgfdveleli.de 325
                                       +t  +++Hs++D    +++  ql ++lk +g + +l ++  e
  gi|385805244|ref|YP_005841642.1| 578 KTPTLILHSDEDYRCWIDQAYQLFTALKLKGVETKLVIFpGE 619
                                       477899****************************99988544 PP

>> Kelch_6  Kelch motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.017        26      24      40 ..      41      57 ..      23      65 .. 0.81
   2 ?   -3.1   0.0       7.6   1.1e+04      29      39 ..      94     104 ..      93     104 .. 0.86
   3 ?    0.4   0.0      0.61   9.2e+02       9      43 ..     190     225 ..     186     229 .. 0.82
   4 ?   -2.4   0.0       4.6   6.8e+03      25      43 ..     256     274 ..     251     278 .. 0.81
   5 ?   -1.0   0.1       1.7   2.5e+03       9      23 ..     491     505 ..     487     512 .. 0.78
   6 ?    3.3   0.0     0.073   1.1e+02      12      35 ..     611     638 ..     608     641 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.017
                           Kelch_6 24 spylnkvwvydpetksW 40
                                      ++y++k+w+yd+e +  
  gi|385805244|ref|YP_005841642.1| 41 NKYYSKLWIYDIEKDEY 57
                                      79**********98765 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 7.6
                           Kelch_6  29 kvwvydpetks 39 
                                        +wv+d+++k+
  gi|385805244|ref|YP_005841642.1|  94 ELWVLDLKNKT 104
                                       58******986 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.61
                           Kelch_6   9 svgg.kiYifGGytdsspylnkvwvydpetksWeql 43 
                                       s++g ki +++  ++  py  ++ +++++t+  ++l
  gi|385805244|ref|YP_005841642.1| 190 SPDGkKIAYISAEDHMRPYKTDIKLINLQTGEVTKL 225
                                       5555489899999999999999999****9998876 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 4.6
                           Kelch_6  25 pylnkvwvydpetksWeql 43 
                                       +++ k+w+ d++++ ++++
  gi|385805244|ref|YP_005841642.1| 256 NSHIKLWIMDLSSGQIKKI 274
                                       56899******99998876 PP

  == domain 5  score: -1.0 bits;  conditional E-value: 1.7
                           Kelch_6   9 svggkiYifGGytds 23 
                                       +  +++ ++GG++++
  gi|385805244|ref|YP_005841642.1| 491 IDENRLGVAGGSYGG 505
                                       567899*****9985 PP

  == domain 6  score: 3.3 bits;  conditional E-value: 0.073
                           Kelch_6  12 gkiYifGGytds....spylnkvwvydp 35 
                                        k++if G ++     +++ n+v++++ 
  gi|385805244|ref|YP_005841642.1| 611 TKLVIFPGENHElsrkGKPKNRVERLNQ 638
                                       589**********************996 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 ?   11.8   0.0   4.6e-05     0.068     252     308 ..     569     628 ..     532     645 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.6e-05
                     PhoPQ_related 252 DplsYlerltipkyiinasgDdffvpdstkfyfekLk..g.ekalrivPnssHglsnkev 308
                                        pl+Y+++++ p +i+ + +D    +d++ + f++Lk  g e++l i P ++H+ls+k  
  gi|385805244|ref|YP_005841642.1| 569 SPLKYVNNVKTPTLILHSDEDYRCWIDQAYQLFTALKlkGvETKLVIFPGENHELSRKGK 628
                                       69***************999999999**999999765225799***********998543 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00046      0.69      50     208 ..     475     622 ..     471     625 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00046
                                       HHHHHHHHHHHHTHHHHT.ETTCEEEEEEETHHHHHHHHHH...HHHHHTT.---EEEEEEESE-SST.SSTTSHHH CS
                     Abhydrolase_3  50 edalaalrwlaeqawelg.adpsrivlaGdSaGGnlaaava...lrardeg.epkvagqvliyPvtdl.ertesesi 120
                                       +d ++ l ++ ++   ++ +d++r+ +aG S GG ++  +     r++++  + +++  + +y   d  + + +++i
  gi|385805244|ref|YP_005841642.1| 475 QDLMEGLDYAIKN---FSfIDENRLGVAGGSYGGFMTNWIIghtNRFKAAVtQRSISNWISFYGTSDIgYYFAEDQI 548
                                       5666666666666...566999************9999887543444444323336666666665555444433444 PP

                                       HHCHHTTTSSSSCHHHHHHHHHHHSSGGGGGSTTTSGGGC.S-SST---EEEEEETT-T..THHHHHHHHHHHHHTT CS
                     Abhydrolase_3 121 kkaeeladgplltraaldlfwrlylpeadrddplasplla.edlsglpptlvvvaefDp..lrdegeayaerlraag 194
                                           +l +  l+t + ++ +w+             spl   ++++   ptl++  ++D     d++ ++  +l+ +g
  gi|385805244|ref|YP_005841642.1| 549 --GGDLGK-DLWTGNLIEVYWDR------------SPLKYvNNVK--TPTLILHSDEDYrcWIDQAYQLFTALKLKG 608
                                       ..222322.34555555544433............3343323565..799999999886336799999999999999 PP

                                       --EEEEEETTEETT CS
                     Abhydrolase_3 195 vevelieyegmvHg 208
                                       ve++l+ ++g+ H+
  gi|385805244|ref|YP_005841642.1| 609 VETKLVIFPGENHE 622
                                       99999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (647 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); 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:                        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: 0.72u 0.30s 00:00:01.02 Elapsed: 00:00:00.47
# Mc/sec: 4146.93
//
Query:       gi|385805245|ref|YP_005841643.1|  [L=302]
Description: Arginine transporter [Fervidicoccus fontis Kam940]
Scores for complete 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   40.2  35.0    3.6e-06   25.6  12.1    2.1  2  Mem_trans  Membrane transport protein


Domain annotation for each model (and alignments):
>> Mem_trans  Membrane transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6  15.0   6.8e-09   0.00012       2     139 ..       8     142 ..       7     147 .. 0.74
   2 !   25.6  12.1     2e-10   3.6e-06     238     386 ..     150     296 ..     145     297 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 6.8e-09
                         Mem_trans   2 vleavvplyvimllgYgsvkw.vki.ftpdqcsginrfVvlfavPllifhfisqnnpyemllrfiladvlvklivli 76 
                                       vle+++ l+ im+ g++ ++  +++   p++++++ ++V  + +Pl++++++s++  +     +i+  v + ++vli
  gi|385805245|ref|YP_005841643.1|   8 VLESIALLFAIMFAGFFYKRLfINYnWYPATAKILFNIVYWVLTPLTFINNFSESGIMS---VLIFPFVAITTFVLI 81 
                                       8999***********77666513332469********************9999944443...333434444444444 PP

                         Mem_trans  77 llllgallskifkgslewtitlfslstlpNtlvlgipllkalygeygvslmv.qvvvlqciiiy 139
                                         ++ +++s     ++e++ +++++s+ +N l++g+p+l + +++ ++sl   +++ +++i+i 
  gi|385805245|ref|YP_005841643.1|  82 AGVIICKMSF---KDKETKYVVLINSVNQNNLFIGYPVLYSAFRNATMSLYFgLISFIYAILIP 142
                                       4455555555...7899999999**********************9888643267777777765 PP

  == domain 2  score: 25.6 bits;  conditional E-value: 2e-10
                         Mem_trans 238 mvlrklirnPntyssllglilslvsfkwnvimpkiiqksisilgdaglpmalfslGlfLalqpkkiacgnsvatfa. 313
                                       ++ ++ i+nP +++ ++g +++  ++ +     + i   +    +a + + +f++G  L  +   +   +++a +  
  gi|385805245|ref|YP_005841643.1| 150 VLSKRIILNPVILGFFMGNVIHYATPYIA----SNIPILLFWAPKALVYLSIFVMGMQLTFGTDVFRGSFRKAFYVm 222
                                       55677888888888888888888888877....5555556666788888999********99887777776665445 PP

                         Mem_trans 314 lavRlilgPlvmlvavlavgLrgslllvaivqaAlPqgivlfviAkeynvhere.lstllifgmlialpitlvy 386
                                       +++R++l P+v l+ ++++++   +  + i+   +P++++ +++A +yn h++  +s+ li++++  ++ t+++
  gi|385805245|ref|YP_005841643.1| 223 AFMRFVLNPIVYLPYIYIFHISQLYRYETILLGIMPPATLNTIMALKYNWHPNFtASSTLILTIISLILATILI 296
                                       89**********************88888888********************9615666777777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       999  (0.0557198); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); 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 0.27s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1868.54
//
Query:       gi|385805246|ref|YP_005841644.1|  [L=297]
Description: Agmatinase (agmatine ureohydrolase) (speB-1) [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-66  224.9   0.0    1.6e-66  224.7   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 !  224.7   0.0   8.8e-71   1.6e-66       2     276 ..      23     285 ..      22     289 .. 0.94

  Alignments for each domain:
  == domain 1  score: 224.7 bits;  conditional E-value: 8.8e-71
                                       EEEEEEEE--TTTSSSGGGGGHHHHHHHHHHTSBTHCHEET.TTTESCCSEEEEEEEEE--SSCHHHHHHHHHHHHH CS
                          Arginase   2 dvallGvPfdaagsgrpGarfGPraireasarleealeynl.elgvleelkivdlgdvavtpvdneevleqieeava 77 
                                       +++l+G+P+d+++s+ pG+  +P+air+  + le+   y+l ++g+++e  i+d gd+ + p++ +e ++ i+e++ 
  gi|385805246|ref|YP_005841644.1|  23 KISLIGAPLDLTNSHAPGTYLAPEAIRRIAESLEW---YSLlYEGDFSENGIYDEGDLVLFPGKVRENIDLISESLL 96 
                                       689**************************999998...4440445599***************************** PP

                                       HHHHTTCEEEEEESSGGGHHHHHHHHHHHHSTTEEEEEESSS----SSCTTTBSSSTTSHHHHHHHHTSECGCEEEE CS
                          Arginase  78 eilkagklpivlGGDHsialgilralaekygkplgvihfDAHaDlrtpetegsgnshGtpfrraaeegllkpkklvq 154
                                       +i +++++p +lGG+H+++l++ + l e    +  ++ fDAH+Dlr+++  +s+++h+t++rr++  +  +pk+l++
  gi|385805246|ref|YP_005841644.1|  97 DIKEEKRIPFMLGGEHTVTLASSKLLDE----DTLLVVFDAHFDLRDEY-LNSNITHATVMRRIV--DNFEPKNLLF 166
                                       *********************9887776....5799*************.89*************..78999***** PP

                                       EEE-STCSHHHHHHHHTTSEEEEHHHHHHHHHHHHHHHHHHHHTCTTSEEEEEEEGGGBBTTTSTSSSS-BSS-B-H CS
                          Arginase 155 iGirsvdneeyelakelgirvitmreidelglkavveeilervgaeedpvylSfDiDvlDpavaPGtGtpepgGltl 231
                                       iG r+v++ee +++k+ +i++it r i+ +g+++ +++i+++++ + +++y+S+DiD++Dp +aPG++tpep G+++
  gi|385805246|ref|YP_005841644.1| 167 IGTRAVSQEELDFVKKNQIEYITSRRIWLYGISEFARNIERKLE-KFGKIYVSIDIDAVDPGYAPGVSTPEPLGIDP 242
                                       *******************************************6.779***************************** PP

                                       HHHHHHHHHHHCHSEEEEEEEE-B-GGGSSTTTHHHHHHHHHHHH CS
                          Arginase 232 rellallrelaeklnlvgaDvvEvnPaldteaeqtarlaarlvre 276
                                       + ++ ll+ l + ++l+g+D+vEvnP  d  +e t++laa++v e
  gi|385805246|ref|YP_005841644.1| 243 HMFFGLLDPLVN-EKLIGLDIVEVNPIRDA-GEATSALAAKIVIE 285
                                       *********988.89**************9.88*********988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1827.10
//
Query:       gi|385805247|ref|YP_005841645.1|  [L=62]
Description: hypothetical protein FFONT_0202 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-06   26.2   7.0    1.5e-05   24.6   7.0    1.8  1  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
     0.0032   17.1   1.6          1    9.2   0.1    2.2  2  zinc_ribbon_2    zinc-ribbon domain
     0.0051   16.8   0.1     0.0066   16.4   0.1    1.2  1  DZR              Double zinc ribbon
  ------ inclusion threshold ------
      0.023   15.2   0.7        5.7    7.5   0.1    2.1  2  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
      0.043   13.6   0.2       0.86    9.4   0.0    2.1  2  zinc_ribbon_10   Predicted integral membrane zinc-ribbon meta
      0.049   14.0   0.2        3.1    8.1   0.1    2.0  2  DUF3268          zinc-finger-containing domain
      0.062   12.9   2.0      0.093   12.3   0.1    2.0  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
      0.072   12.8   1.6        3.7    7.4   0.5    2.2  2  A2L_zn_ribbon    A2L zinc ribbon domain
      0.091   12.1   0.7       0.12   11.7   0.7    1.2  1  zf-TFIIB         Transcription factor zinc-finger
        2.5    8.2   5.5        1.5    8.9   1.5    2.0  2  zf-BED           BED zinc finger


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 !   24.6   7.0   8.1e-09   1.5e-05       1      32 []      18      52 ..      18      52 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 8.1e-09
                                      -B-SSS--B--...--SSS----SSS-----B--- CS
                    DNA_RNApol_7kD  1 YiCgeCgaevs...lkkgdpiRCkeCGhRilYKkR 32
                                      YiC++Cg e +    +   +i+C +CG++i+YK R
  gi|385805247|ref|YP_005841645.1| 18 YICARCGRELKphdFELLHSIKCIYCGSKIIYKVR 52
                                      *******8765332555568*************88 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.1   0.00057         1       2      12 ..      20      30 ..      19      31 .. 0.83
   2 !    7.4   0.1    0.0021       3.7      16      22 ..      40      46 ..      36      47 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00057
                     zinc_ribbon_2  2 CpnCGaelqdn 12
                                      C +CG+el++ 
  gi|385805247|ref|YP_005841645.1| 20 CARCGRELKPH 30
                                      999***99875 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0021
                     zinc_ribbon_2 16 CpyCGtp 22
                                      C yCG++
  gi|385805247|ref|YP_005841645.1| 40 CIYCGSK 46
                                      9999987 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   3.7e-06    0.0066      14      39 ..      19      48 ..      10      53 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.7e-06
                               DZR 14 fCseCgtklkavaa......edrCpsCgekvd 39
                                       C +Cg +lk+  +      +++C  Cg+k+ 
  gi|385805247|ref|YP_005841645.1| 19 ICARCGRELKP--HdfellhSIKCIYCGSKII 48
                                      7********94..4479999********9875 PP

>> Zn_ribbon_recom  Recombinase zinc beta ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1    0.0067        12       7      18 ..      19      30 ..      15      31 .. 0.82
   2 ?    7.5   0.1    0.0032       5.7       6      21 ..      38      53 ..      34      61 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0067
                   Zn_ribbon_recom  7 rCgeCGspmtrr 18
                                      +C++CG+ ++ +
  gi|385805247|ref|YP_005841645.1| 19 ICARCGRELKPH 30
                                      8*****998765 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0032
                   Zn_ribbon_recom  6 lrCgeCGspmtrrkrk 21
                                      ++C +CGs+ +++ rk
  gi|385805247|ref|YP_005841645.1| 38 IKCIYCGSKIIYKVRK 53
                                      89*******8876554 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00048      0.86      38      51 ..      11      24 ..       7      27 .. 0.85
   2 ?    2.6   0.1     0.063   1.1e+02      46      53 ..      39      46 ..      29      47 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00048
                    zinc_ribbon_10 38 eeleevkyrCpkCg 51
                                      e le + y+C+ Cg
  gi|385805247|ref|YP_005841645.1| 11 EGLESIIYICARCG 24
                                      567899*******9 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.063
                    zinc_ribbon_10 46 rCpkCgal 53
                                      +C +Cg++
  gi|385805247|ref|YP_005841645.1| 39 KCIYCGSK 46
                                      7****997 PP

>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.025        45      26      41 ..      13      28 ..       5      33 .. 0.77
   2 ?    8.1   0.1    0.0017       3.1       2      15 ..      37      50 ..      36      59 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.025
                           DUF3268 26 kgkllylCpkCdayvg 41
                                       ++++y+C +C+   +
  gi|385805247|ref|YP_005841645.1| 13 LESIIYICARCGRELK 28
                                      56789******97665 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0017
                           DUF3268  2 ttrCpyCGekvilv 15
                                      +++C yCG+k+i++
  gi|385805247|ref|YP_005841645.1| 37 SIKCIYCGSKIIYK 50
                                      579********986 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   5.2e-05     0.093       3      17 ..      18      32 ..      17      33 .. 0.91
   2 ?   -0.0   0.2      0.39   6.9e+02       3      12 ..      38      47 ..      36      49 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.2e-05
                            zf_UBZ  3 ylCerCgkeipesel 17
                                      y+C+rCg+e+ ++++
  gi|385805247|ref|YP_005841645.1| 18 YICARCGRELKPHDF 32
                                      99********99987 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.39
                            zf_UBZ  3 ylCerCgkei 12
                                      + C  Cg++i
  gi|385805247|ref|YP_005841645.1| 38 IKCIYCGSKI 47
                                      67889*9998 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.016        28       2      12 ..      16      26 ..      15      27 .. 0.71
   2 ?    7.4   0.5    0.0021       3.7       4      15 ..      38      49 ..      36      52 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.016
                     A2L_zn_ribbon  2 nlkvCsvCggn 12
                                      ++++C  Cg++
  gi|385805247|ref|YP_005841645.1| 16 IIYICARCGRE 26
                                      67888888876 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0021
                     A2L_zn_ribbon  4 kvCsvCggngil 15
                                      ++C++Cg+  i+
  gi|385805247|ref|YP_005841645.1| 38 IKCIYCGSKIIY 49
                                      69*****98776 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.7   6.8e-05      0.12       2      22 ..      20      43 ..      19      45 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.8e-05
                          zf-TFIIB  2 CPkCqdeleeser...ggveidyC 22
                                      C +C+ el+++++   + +++ yC
  gi|385805247|ref|YP_005841645.1| 20 CARCGRELKPHDFellHSIKCIYC 43
                                      *************55555555555 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1      0.14   2.6e+02      18      28 ..      19      29 ..      11      38 .. 0.82
   2 ?    8.9   1.5   0.00086       1.5      16      28 ..      37      49 ..      33      60 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.14
                                      EETTTTEE--- CS
                            zf-BED 18 vCryCgkilsr 28
                                      +C  Cg++l+ 
  gi|385805247|ref|YP_005841645.1| 19 ICARCGRELKP 29
                                      8999**99975 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00086
                                      --EETTTTEE--- CS
                            zf-BED 16 kavCryCgkilsr 28
                                      +++C+yCg ++ +
  gi|385805247|ref|YP_005841645.1| 37 SIKCIYCGSKIIY 49
                                      689*****99866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); 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: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 411.87
//
Query:       gi|385805248|ref|YP_005841646.1|  [L=229]
Description: protein-L-isoaspartate O-methyltransferase [Fervidicoccus fontis Kam940]
Scores for complete 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  216.4   0.0    4.3e-64  216.1   0.0    1.0  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    1.3e-09   38.0   0.0    1.7e-09   37.6   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    1.7e-05   24.6   0.0    2.6e-05   24.0   0.0    1.3  1  GCD14            tRNA methyltransferase complex GCD14 subunit
      2e-05   25.6   0.0      3e-05   25.0   0.0    1.4  1  Methyltransf_24  Methyltransferase domain
    6.7e-05   22.1   0.0    8.9e-05   21.8   0.0    1.2  1  Methyltransf_3   O-methyltransferase
    0.00036   21.2   0.0    0.00056   20.6   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
     0.0023   18.5   0.0      0.004   17.8   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
      0.003   17.5   0.0     0.0055   16.6   0.0    1.4  1  Methyltransf_18  Methyltransferase domain
  ------ inclusion threshold ------
       0.03   14.0   0.0      0.071   12.7   0.0    1.6  2  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
      0.041   12.9   0.0      0.065   12.3   0.0    1.4  1  RrnaAD           Ribosomal RNA adenine dimethylase
      0.089   12.8   0.0       0.12   12.4   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
       0.12   12.2   0.0       0.48   10.2   0.0    1.8  2  DUF3540          Protein of unknown function (DUF3540)


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 !  216.1   0.0   2.9e-67   4.3e-64       2     209 ..       9     224 ..       7     225 .. 0.95

  Alignments for each domain:
  == domain 1  score: 216.1 bits;  conditional E-value: 2.9e-67
                                       HHHHHHHHHHHTTS---HHHHHHHHHS-GGGGSSCGGGGGTTSSS-EEEETTEEE--HHHHHHHHHHTT--TT-EEE CS
                              PCMT   2 kkealieelkkkgviksdkvaealeevdReefvpesfkekaYedaplsigynatiSaphmvalalellelkkgarvL 78 
                                       +ke +i++l+++g+   +kv+ a+++vdR+ fvp++++++a  d+pl+igy++tiSa hmv +++ ll+ + g++vL
  gi|385805248|ref|YP_005841646.1|   9 EKEWVIKNLESEGFRIPEKVRRAFLKVDRKLFVPQQYEDMANADTPLPIGYGQTISAMHMVLIMTTLLDPEVGDKVL 85 
                                       47789************************************************************************ PP

                                       EES-TTSHHHHHHHHHHCTTC.......EEEEEESBHHHHHHHHHHHHHCTTC.SEEEEES-GGGTTGGG-SEEEEE CS
                              PCMT  79 evGsGsGyltavlarlvgekg.......rvvsierikelveeakrnlkkldle.nvivvvgDGrkGyeekaPYdaih 147
                                       evG+GsGy++a+la++v ++        +v ++erikel+e ak+nlkk ++  +v+v vgDG +G +e++PYd+i+
  gi|385805248|ref|YP_005841646.1|  86 EVGTGSGYQAAILAEIVAPSNteikksgHVYTVERIKELAEFAKENLKKAGYCdRVTVFVGDGSQGLKEFSPYDRII 162
                                       ****************9655444444449*********************9866*********************** PP

                                       ESSBBSS--HHHHHTEEEEEEEEEEESBSSSEEEEEEEEETTTEEEEEEEEEE---B-BCCC CS
                              PCMT 148 vgaaapeiPealidQLkeGGrlvvPvgeeeeQvlklvdkkadgkvvikkleevrfvpltdke 209
                                       v+aa+p++Pe+l dQLk GG lv+P+g+ e Q l +++k+++++++ikk  +++fvpl +ke
  gi|385805248|ref|YP_005841646.1| 163 VTAASPKVPESLKDQLKVGGTLVIPIGSIEFQSLYVIRKNSEKTFNIKKSISCVFVPLIGKE 224
                                       **********************************************************9987 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.0   1.1e-12   1.7e-09       4     113 ..      81     190 ..      78     223 .. 0.86

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 1.1e-12
                   Methyltransf_31   4 glrvlDlGCGtGeltfelae.......elgpkaevvGiDiseeaielArenaqklgld.nveFeqgdiee.leklle 71 
                                       g +vl++G+G+G+ +  lae       e+ + ++v+ +++ +e  e+A+en++k g+  +v++ +gd  + l++ + 
  gi|385805248|ref|YP_005841646.1|  81 GDKVLEVGTGSGYQAAILAEivapsntEIKKSGHVYTVERIKELAEFAKENLKKAGYCdRVTVFVGDGSQgLKE-F- 155
                                       679*****************99999888888999***********************77***********9997.4. PP

                   Methyltransf_31  72 dekfDlilsnevlnaladpdkileeiervlkpggilliedpr 113
                                        +++D i+       +a+++k+ e++++ lk gg l+i   +
  gi|385805248|ref|YP_005841646.1| 156 -SPYDRIIV------TAASPKVPESLKDQLKVGGTLVIPIGS 190
                                       .68***999......79999***************9986555 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   1.7e-08   2.6e-05      32     100 ..      72     147 ..      57     181 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.7e-08
                             GCD14  32 iimkLelkpGsvvvesGtGsgslshaiartvaP.......tGhlftfefheqraekareefrehelsqlvtvthrD 100
                                       +++ L+ + G +v+e GtGsg  +  +a  vaP        Gh++t+e  ++ ae+a+e++++ +  + vtv + D
  gi|385805248|ref|YP_005841646.1|  72 MTTLLDPEVGDKVLEVGTGSGYQAAILAEIVAPsnteikkSGHVYTVERIKELAEFAKENLKKAGYCDRVTVFVGD 147
                                       234456778**************999999999955444445***************************99998776 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0     2e-08     3e-05       1      75 [.      85     163 ..      85     186 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 2e-08
                   Methyltransf_24   1 vEiGvysGvstlwllralrrnga.....grlvavdhdpg.aeeaaalareaglddrvrlikadseealaslaagsiD 71 
                                       +E+G+ sG+ +++l++ +   ++     g++++v+  ++ ae a++++++ag+ drv++ ++d ++ l++++  ++D
  gi|385805248|ref|YP_005841646.1|  85 LEVGTGSGYQAAILAEIVAPSNTeikksGHVYTVERIKElAEFAKENLKKAGYCDRVTVFVGDGSQGLKEFS--PYD 159
                                       7*****************999999************88556667888888*******************999..777 PP

                   Methyltransf_24  72 llfi 75 
                                        +++
  gi|385805248|ref|YP_005841646.1| 160 RIIV 163
                                       6665 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0     6e-08   8.9e-05      48     116 ..      81     156 ..      61     186 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 6e-08
                                       --EEEEE--TTSHHHHHHH.......TTS-TT-EEEEEES-HHHHHHHHHHHHHTT-GGGEEEEES-HHHHHHHHH CS
                    Methyltransf_3  48 akrvleiGvftGyslLata.......lalPeDGkilaididreayeialkfiqkagvaekieliegdalkvLeelv 116
                                         +vle+G+  Gy +  +a        ++ + G++ +++  +e +e a++ ++kag+ +++ + +gd+ + L+e+ 
  gi|385805248|ref|YP_005841646.1|  81 GDKVLEVGTGSGYQAAILAeivapsnTEIKKSGHVYTVERIKELAEFAKENLKKAGYCDRVTVFVGDGSQGLKEFS 156
                                       568**********9877772222222356678*************************************9999885 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   3.7e-07   0.00056       1      72 [.      84     165 ..      84     182 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.7e-07
                                       EEEET-TTSHHHHHHHCTS.......T.SSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrl.......g.kakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDl 67 
                                       vL++G+G+G  ++ la+ +       + +++v+ v+  +e+ e a+e+++++g+  +v++ +gd ++   e + +D 
  gi|385805248|ref|YP_005841646.1|  84 VLEVGTGSGYQAAILAEIVapsnteiKkSGHVYTVERIKELAEFAKENLKKAGYcdRVTVFVGDGSQGLKEFSPYDR 160
                                       9***************9977665544269**********************999***********886666679999 PP

                                       EEEES CS
                   Methyltransf_25  68 vvssg 72 
                                       ++++ 
  gi|385805248|ref|YP_005841646.1| 161 IIVTA 165
                                       99854 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.7e-06     0.004       1      67 [.      85     163 ..      85     186 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.7e-06
                                       EEET-TTSHHHHHHH..........HTTSEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-T.T-EEE CS
                   Methyltransf_11   1 LdvGcGtGrlaeala..........krgarvvgvDlskemlklakekaseegl..kvefvvadaeklpfed.nsfDl 64 
                                       L+vG+G+G+ a+ la          k+ ++v++v+  ke+ + ake+ +++g   +v++ v+d ++  +++ + +D 
  gi|385805248|ref|YP_005841646.1|  85 LEVGTGSGYQAAILAeivapsnteiKKSGHVYTVERIKELAEFAKENLKKAGYcdRVTVFVGDGSQ-GLKEfSPYDR 160
                                       89*************88887765544449**************************9999***9998.4444334555 PP

                                       EEE CS
                   Methyltransf_11  65 vvs 67 
                                       +++
  gi|385805248|ref|YP_005841646.1| 161 IIV 163
                                       555 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   3.7e-06    0.0055      16      88 ..      82     163 ..      73     166 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.7e-06
                   Methyltransf_18  16 srvaDiGtDHgylpiylv........kegkakkviasDinegplekakeniekagledkievrlsdGleklkeee.v 83 
                                       ++v+ +Gt  gy ++ l+        + +k  +v+ ++  ++  e aken++kag+ d+++v ++dG + lke + +
  gi|385805248|ref|YP_005841646.1|  82 DKVLEVGTGSGYQAAILAeivapsntEIKKSGHVYTVERIKELAEFAKENLKKAGYCDRVTVFVGDGSQGLKEFSpY 158
                                       566667777666665555222332224578889**************************************988778 PP

                   Methyltransf_18  84 dtvvi 88 
                                       d +++
  gi|385805248|ref|YP_005841646.1| 159 DRIIV 163
                                       88876 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.7e-05     0.071       2      87 ..      74     165 ..      73     171 .. 0.86
   2 ?   -2.3   0.0         2     3e+03     123     141 ..     173     191 ..     166     195 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.7e-05
                                       HHH---TT-EEEESS-TTSHHHHHHHHHT.......TTTSEEEEEESSCCCHHHHHHHHHHTT--.SEEEEES-CTC CS
                   Methyltr_RsmB-F   2 llLapqeeetilDlcaaPGgKTthiaelm.......knkgtvvAvdankeRlkrvaenlkrLgvt.ntivleaDark 70 
                                       +lL+p+ ++++l++ ++ G + + +ae++       k++g+v+ v++ ke ++  +enlk+ g    ++v+ +D+++
  gi|385805248|ref|YP_005841646.1|  74 TLLDPEVGDKVLEVGTGSGYQAAILAEIVapsnteiKKSGHVYTVERIKELAEFAKENLKKAGYCdRVTVFVGDGSQ 150
                                       689************************96233333356789*********************965489********* PP

                                       CHHHHCC..EEEEEEEE CS
                   Methyltr_RsmB-F  71 idkvlggelfDriLlDa 87 
                                         k  +   +Dri++ a
  gi|385805248|ref|YP_005841646.1| 151 GLKEFSP--YDRIIVTA 165
                                       9998886..9***9876 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2
                                       HHCCCEEEEEEEEEEES-- CS
                   Methyltr_RsmB-F 123 aaidllkkgGvlvYsTCsv 141
                                       ++ d+lk gG+lv    s+
  gi|385805248|ref|YP_005841646.1| 173 SLKDQLKVGGTLVIPIGSI 191
                                       677899*****99766555 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.3e-05     0.065      27      73 ..      77     133 ..      62     185 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.3e-05
                                       -GGTTSEEEEES-TTTCCHHHHHCC-..........SEEEEE-S-HHHHHHHHCHTT CS
                            RrnaAD  27 nleekltvleigpGkGilTeeLakra..........kqvvvlElderLakllqkkls 73 
                                       ++e  ++vle+g+G G + ++La+++           +v  +E  ++La++ +++l+
  gi|385805248|ref|YP_005841646.1|  77 DPEVGDKVLEVGTGSGYQAAILAEIVapsnteikksGHVYTVERIKELAEFAKENLK 133
                                       556689******************987655554322235556666666666666666 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0     8e-05      0.12      22      78 ..      77     137 ..      62     176 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8e-05
                   Methyltransf_32  22 kesgaltvvDvGaGkgYLsfvlal......kekeyklkvvgidakeelvekaekraeklgkkf 78 
                                       + +   +v++vG G gY + +la       +e +++ +v+ ++  +el+e a++  +k g  +
  gi|385805248|ref|YP_005841646.1|  77 DPEVGDKVLEVGTGSGYQAAILAEivapsnTEIKKSGHVYTVERIKELAEFAKENLKKAG--Y 137
                                       45666799**************99999865555799**************9999988887..3 PP

>> DUF3540  Protein of unknown function (DUF3540)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00032      0.48      29      70 ..      75     115 ..      72     123 .. 0.81
   2 ?   -1.0   0.0      0.89   1.3e+03      11      35 ..     197     222 ..     190     224 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00032
                           DUF3540  29 LlePevgDkVLisasdagevYiLAvLera.eaaeaklsveGdl 70 
                                       Ll+PevgDkVL ++++  + Y  A+L+   + ++++++ +G++
  gi|385805248|ref|YP_005841646.1|  75 LLDPEVGDKVLEVGTG--SGYQAAILAEIvAPSNTEIKKSGHV 115
                                       9**********99988..7888888887666677777776665 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.89
                           DUF3540  11 llvese.ggalrarrAaSCLlePevg 35 
                                       ++++ + ++ ++ ++  SC   P +g
  gi|385805248|ref|YP_005841646.1| 197 YVIRKNsEKTFNIKKSISCVFVPLIG 222
                                       5555440455999*******999888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1708.36
//
Query:       gi|385805249|ref|YP_005841647.1|  [L=153]
Description: hypothetical protein FFONT_0204 [Fervidicoccus fontis Kam940]
Scores for 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-48  161.8   0.5    9.2e-48  161.6   0.5    1.0  1  DUF371    Domain of unknown function (DUF371)


Domain annotation for each model (and alignments):
>> DUF371  Domain of unknown function (DUF371)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.6   0.5   5.1e-52   9.2e-48       1     132 [.      16     147 ..      16     148 .. 0.98

  Alignments for each domain:
  == domain 1  score: 161.6 bits;  conditional E-value: 5.1e-52
                                       EEEE--TT-----SSEEEEES-S---TT-TTEEEBS-S--GGGS-HHHHHHHS----EEEEEEE-SS-EEEEEEE-- CS
                            DUF371   1 ikarGHenvkaehksTleitkddeltprgdCIigveadkaaadlseelkealkeeeatitvtlevgeledeitgrGs 77 
                                       i a+GH nv a+h++T+eitkd++lt+rg+CIig++++k+++dlse++k++l++++++++++l v++++d++t++G+
  gi|385805249|ref|YP_005841647.1|  16 IVAYGHYNVLATHRTTFEITKDNYLTKRGNCIIGIKSSKSLKDLSEDMKNNLRNSNTIVRLILYVDGKSDAVTCMGN 92 
                                       689************************************************************************** PP

                                       TT-----SSEEEEESSS---TTEEEBS-S--GGGS-HHHHHHHHTT-EEEEEEEE CS
                            DUF371  78 pkltlenerdlvvRkSdyvddrTllvkadkaaadldrelveaLkkgaeltvelev 132
                                       ++l l+++++++vRkS y+d++Tl+++adk++++l+re+v++L++g+++t+ l+v
  gi|385805249|ref|YP_005841647.1|  93 ENLILNSDSKIIVRKSGYIDGSTLCINADKSSNELSREVVKKLREGKKVTLGLIV 147
                                       **************************************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       729  (0.0406604); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1042.78
//
Query:       gi|385805250|ref|YP_005841648.1|  [L=268]
Description: methyltransferase [Fervidicoccus fontis Kam940]
Scores for complete 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  157.1   1.0    6.4e-46  156.6   1.0    1.2  1  Met_10           Met-10+ like-protein
    9.6e-07   28.5   0.0    1.5e-06   27.8   0.0    1.4  1  DNA_methylase    C-5 cytosine-specific DNA methylase
    1.1e-05   25.1   0.0    1.8e-05   24.3   0.0    1.5  1  MTS              Methyltransferase small domain
    1.9e-05   24.0   0.8    4.4e-05   22.8   0.8    1.6  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
    0.00024   20.9   0.4    0.00065   19.5   0.1    1.8  2  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran
      0.001   18.7   0.0     0.0015   18.2   0.0    1.2  1  Cons_hypoth95    Conserved hypothetical protein 95
     0.0012   18.3   1.3     0.0017   17.8   1.3    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
     0.0012   19.5   0.0     0.0029   18.3   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
     0.0014   18.3   0.0     0.0023   17.6   0.0    1.4  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
     0.0038   17.0   0.1     0.0054   16.5   0.1    1.2  1  Methyltransf_16  Lysine methyltransferase
     0.0046   16.8   0.2      0.014   15.2   0.2    1.9  2  Methyltransf_31  Methyltransferase domain
  ------ inclusion threshold ------
      0.013   15.1   0.1      0.029   14.0   0.1    1.5  1  Methyltransf_15  RNA cap guanine-N2 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 !  156.6   1.0   4.3e-49   6.4e-46       2     198 ..      17     219 ..      16     221 .. 0.90

  Alignments for each domain:
  == domain 1  score: 156.6 bits;  conditional E-value: 4.3e-49
                                       EEEEETTEEEEEB-TTSS.HHHHHHHHHHHHHS.S-SCEEEE-S-SBTTTTB--EEEEEES-.SEEEEEETTEEEEE CS
                            Met_10   2 kfeiiGdvvilnlreelk.eykkvigevildkt.kvktvlrkvsevegefRtfelevlaGsdstetihkEngcrfkl 76 
                                       +f +iGd++++nl++e + +  k+++e il ++  +k+v+ k ++ egefR++++ +l G+++teti kE+g  f +
  gi|385805250|ref|YP_005841648.1|  17 SFLVIGDIALVNLKNENEiDRGKELAEKILRVNkYIKSVYGKIGT-EGEFRVPKIIHLLGEKKTETIAKEYGLLFYV 92 
                                       6999********998765267899*********99**********.******************************* PP

                                       ETTTS---GGGHHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT...-T CS
                            Met_10  77 DvskvyfsskleaErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNk...ve 150
                                       D+skvy++++l++E++ + ++ e+gevV+d+f GiG f+i +a  +k  +v+a+d+nP+++k+l+  + lNk   + 
  gi|385805250|ref|YP_005841648.1|  93 DISKVYYNPRLAEEHHYISQISEDGEVVLDLFSGIGGFSIHLAA-AKRAIVFANDINPYAIKFLNASVLLNKkkiIG 168
                                       *******************************************7.9999**********************944445 PP

                                       TCEEEEES-GGG---...TT-EEEEEE--TTTGGGGHHHHHHHEEEEEEEE CS
                            Met_10 151 kvvkpileDgrevir...eqladrvvmnlpksaieFldkvlaalkdggvih 198
                                       +v+ + le ++ ++    + ++dr++mn p+  + Fl++v a++k g   h
  gi|385805250|ref|YP_005841648.1| 169 EVIASNLEANKLLLMmskKAKFDRIIMNNPTMIEGFLQNVNAVVKTGTTLH 219
                                       5665555555554446778999********************999986554 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 !   27.8   0.0     1e-09   1.5e-06       3      48 ..     120     168 ..     119     198 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 1e-09
                                       EEEES-TT-HHHHHHHHTT-EEEEEEE--TTTHHHHHHH-....-SEEE CS
                     DNA_methylase   3 fidLfaGiGGfrlgleaagfecvaaseidkkaaktYeanfk...kvsig 48 
                                       ++dLf+GiGGf++ l+aa+  +v+a++i+++a+k+++a      k++ig
  gi|385805250|ref|YP_005841648.1| 120 VLDLFSGIGGFSIHLAAAKRAIVFANDINPYAIKFLNASVLlnkKKIIG 168
                                       68*********************************99987655555555 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   1.2e-08   1.8e-05      29     106 ..     115     198 ..      84     214 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1.2e-08
                                       CCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTT......STTS- CS
                               MTS  29 kelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvlee......veekk 97 
                                       +   + vlDl +G+G  +++la+++    v + d++ +A+++ ++ +  nk +  +ev+as++ ++       +++k
  gi|385805250|ref|YP_005841648.1| 115 E-DGEVVLDLFSGIGGFSIHLAAAKRA-IVFANDINPYAIKFLNASVLLNKKKiiGEVIASNLEANklllmmSKKAK 189
                                       4.45679***************97655.799*****************9999999999999987763332224689* PP

                                       EEEEEE--- CS
                               MTS  98 fdlivsNPP 106
                                       fd i++N P
  gi|385805250|ref|YP_005841648.1| 190 FDRIIMNNP 198
                                       ****99977 PP

>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.8     3e-08   4.4e-05      52     150 ..     119     219 ..      75     223 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 3e-08
                                       EEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHHHHHTT--...GGEEEE-S-HHHHHC..--SS-EEE CS
                               TRM  52 kvldaLsasGlRaiRfalEvpgvkevlaNDisekAvelikeNvklneve...eivvineddAnvlla..ekkkrfdv 123
                                        vld +s+ G  +i  a    +   v+aNDi++ A++ ++  v ln+ +   e++ +n  +An ll   +kk +fd 
  gi|385805250|ref|YP_005841648.1| 119 VVLDLFSGIGGFSIHLAAA--KRAIVFANDINPYAIKFLNASVLLNKKKiigEVIASNL-EANKLLLmmSKKAKFDR 192
                                       4788888877777777765..8899*********************9888867665555.8886544349999***9 PP

                                       EEE--SS--GGGHHHHHHHEEEEEEEE CS
                               TRM 124 iDlDPfGspapfldsavqsvkekglLl 150
                                       i +        fl+++ + vk++  L 
  gi|385805250|ref|YP_005841648.1| 193 IIMNNPTMIEGFLQNVNAVVKTGTTLH 219
                                       988776777777777777776666665 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 ?   -1.7   0.0       1.3   1.9e+03     102     137 ..      34      70 ..       5      90 .. 0.63
   2 !   19.5   0.1   4.3e-07   0.00065      15      75 ..     112     172 ..     107     202 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.3
                                       HH-HHHH.HHHHHHHHCCBGGG---B-TTS-B---B- CS
                   MethyltransfD12 102 aireaee.aidflylnrllfsglervnkkgnfnvpyg 137
                                       +i+  +e a ++l+ n+   s+   + ++g+f vp  
  gi|385805250|ref|YP_005841648.1|  34 EIDRGKElAEKILRVNKYIKSVYGKIGTEGEFRVPKI 70 
                                       3333333455677777777777777788888877765 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 4.3e-07
                                       CS-..--SEEEETT-TTSCCHHCS....SSCEEEEES-HHHHHHHHHHCCHSHHHHHHHHH. CS
                   MethyltransfD12  15 lipkdkgktfvepFaGggaVffeakk.qgkkvlinDinedlinlykaliknnveelikelek 75 
                                       +i++ +g+++ ++F+G g +++++   +   v +nDin++ i + +a +  n++++i e+ +
  gi|385805250|ref|YP_005841648.1| 112 QISE-DGEVVLDLFSGIGGFSIHLAAaKRAIVFANDINPYAIKFLNASVLLNKKKIIGEVIA 172
                                       6676.999******99988888887656677889************9999999999987764 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0     1e-06    0.0015      41     154 ..     116     230 ..     107     253 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1e-06
                                       CC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--T..TTEEEEES-HHHHCTS--SS-EEE CS
                     Cons_hypoth95  41 egarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelklee..etaelkedaleallklakkkeefd 115
                                       +g+ vLDlf+G G+ ++  +  + + + + + ++ a+k l++ +   k +   e+ + + +a + ll   +kk++fd
  gi|385805250|ref|YP_005841648.1| 116 DGEVVLDLFSGIGGFSIHLAAAKRAIVFANDINPYAIKFLNASVLLNKKKIigEVIASNLEANKLLLM-MSKKAKFD 191
                                       56789**********99988777678888899999999999998766644333444444444444544.58899*** PP

                                       EEEE--SSSTTCH.HHHHHHHHHTT-EEEEEEEEEEEEC CS
                     Cons_hypoth95 116 ivflDPPyakellieevlelleekkllkenalvvvetek 154
                                        + ++ P + e ++++v + +++   l+  al+v ++ +
  gi|385805250|ref|YP_005841648.1| 192 RIIMNNPTMIEGFLQNVNAVVKTGTTLHIYALIVKDKLE 230
                                       ***********999*999999999999999999876643 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   1.3   1.2e-06    0.0017     155     266 ..     110     229 ..     108     249 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.2e-06
                              PrmA 155 leklvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklev...alseell.....k 223
                                       + ++ + ge vlD+  G G  +i  a    + v+a Di++ A+k  ++ + lNk +   ev   +l+++ l     k
  gi|385805250|ref|YP_005841648.1| 110 ISQISEDGEVVLDLFSGIGGFSIHLAAAKRAIVFANDINPYAIKFLNASVLLNKKKIIGEViasNLEANKLllmmsK 186
                                       567889999**************9999999***********************877766662222333322344445 PP

                              PrmA 224 eekadvivaNILaevlielaedikklvkeggll.ilSGilkeka 266
                                       ++k+d i+ N   +++  ++++++++vk+g++l i   i+k+k 
  gi|385805250|ref|YP_005841648.1| 187 KAKFDRIIMNN-PTMIEGFLQNVNAVVKTGTTLhIYALIVKDKL 229
                                       89*****9996.678999***********998724455556664 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.9e-06    0.0029       1      96 [.     120     215 ..     120     215 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.9e-06
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCG..BS...SSTTTEEEEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaed..lp...fedgsfDlvvs 70 
                                       vLdl  G G ++++la++ ++a v + Di++ +++  ++ +  ++     e++  ++e+  l     ++++fD +++
  gi|385805250|ref|YP_005841648.1| 120 VLDLFSGIGGFSIHLAAA-KRAIVFANDINPYAIKFLNASVLLNKKkiIGEVIASNLEAnkLLlmmSKKAKFDRIIM 195
                                       9***************99.68**************99987755443334455555554422333335899******9 PP

                                       ESTGGGSSHHHHHHHHHHHHHHEEEE CS
                   Methyltransf_25  71 sgalhhlsdedlekalkeiarvLkpg 96 
                                       + +     +  +e +l+++  v+k g
  gi|385805250|ref|YP_005841648.1| 196 N-N-----PTMIEGFLQNVNAVVKTG 215
                                       5.3.....345678888888888865 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 !   17.6   0.0   1.5e-06    0.0023       7     101 ..     115     211 ..     111     245 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.5e-06
                                       -TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHH....HHHHTT--SEEEEES-CTCCHHHHCC.. CS
                   Methyltr_RsmB-F   7 qeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvae....nlkrLgvtntivleaDarkidkvlgg.e 78 
                                       +++e +lDl ++ Gg   h+a+   +++ v+A+d+n   +k +++    n k++   ++i ++ +a+k   ++++ +
  gi|385805250|ref|YP_005841648.1| 115 EDGEVVLDLFSGIGGFSIHLAAA--KRAIVFANDINPYAIKFLNAsvllNKKKIIG-EVIASNLEANKLLLMMSKkA 188
                                       6899*****************97..99**********9999776511114444444.47888888888888887779 PP

                                       .EEEEEEEE--CCGGGTTT-TCH CS
                   Methyltr_RsmB-F  79 lfDriLlDaPCsgtgvirrdpdv 101
                                       +fDri++  P    g ++  ++v
  gi|385805250|ref|YP_005841648.1| 189 KFDRIIMNNPTMIEGFLQNVNAV 211
                                       9*********9998888876666 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   3.6e-06    0.0054      43     142 ..     113     211 ..      92     239 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.6e-06
                   Methyltransf_16  43 nelsklsvlELGsGtGlvGlavaellpeakviltDlee.llellkknielnknalkskvkvevLdWgeeleedllek 118
                                        +  +  vl+L sG G + + +a++ ++a v+  D++  ++++l+ ++ lnk+++  +v ++ L+ ++ l   + +k
  gi|385805250|ref|YP_005841648.1| 113 ISEDGEVVLDLFSGIGGFSIHLAAA-KRAIVFANDINPyAIKFLNASVLLNKKKIIGEVIASNLEANK-LLLMMSKK 187
                                       455677899*****99999998888.9999******9989*************************866.55888899 PP

                   Methyltransf_16 119 eevDlilaaDcvYledslelLvkv 142
                                        ++D i++   +  e  l+   +v
  gi|385805250|ref|YP_005841648.1| 188 AKFDRIIMNNPTMIEGFLQNVNAV 211
                                       99*****98776666665555555 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       2.7   4.1e+03     116     136 ..      39      59 ..      14      83 .. 0.67
   2 !   15.2   0.2   9.7e-06     0.014       2     107 ..     115     218 ..     114     254 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.7
                   Methyltransf_31 116 aelpakveeeskayevvegak 136
                                       +el++k+ + +k+ ++v+g++
  gi|385805250|ref|YP_005841648.1|  39 KELAEKILRVNKYIKSVYGKI 59 
                                       456667777777666666665 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 9.7e-06
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielAre..naqklgld.nveFeqgdiee.leklledek 74 
                                       ++g +vlDl +G G +++ la  + ++a v+  Di++ ai++ ++   + k+++  +v  +  ++++ l +  +++k
  gi|385805250|ref|YP_005841648.1| 115 EDGEVVLDLFSGIGGFSIHLA--AAKRAIVFANDINPYAIKFLNAsvLLNKKKIIgEVIASNLEANKlLLMMSKKAK 189
                                       67899****************..667889************9777666777777768888889999955554666** PP

                   Methyltransf_31  75 fDlilsnevlnaladpdkileeiervlkpggil 107
                                       fD i+ n++       + +l+++  v+k+g+ l
  gi|385805250|ref|YP_005841648.1| 190 FDRIIMNNPT----MIEGFLQNVNAVVKTGTTL 218
                                       ******9665....3444455555555555544 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 ?   14.0   0.1   1.9e-05     0.029       2      44 ..     118     159 ..     117     199 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.9e-05
                   Methyltransf_15   2 rvilDlfsGaGGnviqfalv.fekviaieinleklacaqhNaev 44 
                                       +v+lDlfsG GG +i++a      v+a +in+  ++    Na v
  gi|385805250|ref|YP_005841648.1| 118 EVVLDLFSGIGGFSIHLAAAkRAIVFANDINPYAIKFL--NASV 159
                                       689**************997344577888888777654..5544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       752  (0.0419432); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); 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: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 1658.89
//
Query:       gi|385805251|ref|YP_005841649.1|  [L=309]
Description: metallophosphoesterase [Fervidicoccus fontis Kam940]
Scores for complete 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   89.3   1.3    7.4e-25   88.7   1.3    1.2  1  Metallophos    Calcineurin-like phosphoesterase
     0.0042   17.3   0.0     0.0062   16.8   0.0    1.4  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.7   1.3   8.2e-29   7.4e-25       2     201 ..      52     255 ..      51     257 .. 0.81

  Alignments for each domain:
  == domain 1  score: 88.7 bits;  conditional E-value: 8.2e-29
                                       EEEEEESBTBTTCCTHHHHHHHHHHHH..HHHTTE.SEEEEESTSSSSSHHHHHHHHH.HHHHHHHTSEEEEEC-TT CS
                       Metallophos   2 rilvigDlHlalgggqlddllkllddl..lreekp.dlvllaGDlvdrgdlekellel.laalvkypipvylllGNH 74 
                                       r+ +igDlH     g++++l+++l+++  ++ ek    ++++GD+vdrg +++e+l   l+   +yp  +++l+GNH
  gi|385805251|ref|YP_005841649.1|  52 RVFFIGDLH-----GDFETLKNILSKIdyNSLEKGdLKIIFLGDYVDRGLYQTETLLSvLELESMYPEEIFVLRGNH 123
                                       899******.....*************884444551556677****************99999999*********** PP

                                       S..........CHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESECEEE.THHHHHHHHHHHS CS
                       Metallophos  75 e..........gfeeellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGgspel.lvsldklgslnle 140
                                       e           f  el ++yg+     ++++++++ +++l  a + ++  +++ lhGg p     +++++  + l 
  gi|385805251|ref|YP_005841649.1| 124 EllkhappyphDFPTELYSRYGFTRG-IRIYNTFVSLVDYLDAAIILNK--NIIALHGGLPVTtFQKVSNIYEYLLG 197
                                       *9999987766444466666664333.6888888888899999999999..********444443556666666666 PP

                                       CHHHHCC....HHHHHHHHHHTTCSEEEEEESSESSCSSSCSCCHHHHHHHHHHTTESEEEEESS CS
                       Metallophos 141 leapepg....dewlkdlekrekadwvivlgHsplyrgsgylfgdealedllkkygvdlvisGHt 201
                                       ++++e+     +++++d       ++   +   p yrg+gyl+g +++  + +++g+++vi+GH+
  gi|385805251|ref|YP_005841649.1| 198 RNESEKInvitEILWND-------PIEENIDKLPSYRGIGYLWGKQVTNWVADNFGIKMVIRGHE 255
                                       66555558888999999.......999999999999*************77*************8 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 !   16.8   0.0   6.9e-07    0.0062       3      82 ..      53     137 ..      52     202 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6.9e-07
                     Metallophos_2   3 laiiSDlHsnldaleavlealkevgvd....aiihaGDl.....eeeepe...vleellela.....pvlaVrGNnD 62 
                                       + +i DlH+ ++ l+++l++++  +++    +ii++GD+     +  + e   ++ el   +     ++ + rGN++
  gi|385805251|ref|YP_005841649.1|  53 VFFIGDLHGDFETLKNILSKIDYNSLEkgdlKIIFLGDYvdrglY--QTEtllSVLEL---EsmypeEIFVLRGNHE 124
                                       6789*************999988777633346******8544222..22211244444...3566************ PP

                     Metallophos_2  63 eevveedvlreaaelgtdlp 82 
                                              +l++a ++ +d+p
  gi|385805251|ref|YP_005841649.1| 125 -------LLKHAPPYPHDFP 137
                                       .......4444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.50
# Mc/sec: 1842.83
//
Query:       gi|385805252|ref|YP_005841650.1|  [L=111]
Description: hypothetical protein FFONT_0207 [Fervidicoccus fontis Kam940]
Scores for complete 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-28   96.4   0.3    8.1e-28   96.4   0.3    1.4  2  DUF2258   Uncharacterized protein conserved in archaea (DUF22


Domain annotation for each model (and alignments):
>> DUF2258  Uncharacterized protein conserved in archaea (DUF2258)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.4   0.3   4.5e-32   8.1e-28       1      77 [.       5      81 ..       5      82 .. 0.98
   2 ?   -2.5   0.0      0.33   5.9e+03      59      63 ..      92      96 ..      84     107 .. 0.59

  Alignments for each domain:
  == domain 1  score: 96.4 bits;  conditional E-value: 4.5e-32
                                      EEEECEEGGGHHHHHHHHHHHHTCCCCHTTSS.HHHHHHHHHHHHHHHHHHHHCCTT--TTSEEEEEEEEEEETTEE CS
                           DUF2258  1 lsTGlviaaaYAdKlRrvlfaalsklvkkkkeekkeiaraiaeLNkklYevlveklkidKldvvrirveyeveekkl 77
                                      l+TG+v++++YA KlRr+++aal+kl+++kk+e+k+ ++++++LNk+lY++l++k++i+K++v++i++  ++++++l
  gi|385805252|ref|YP_005841650.1|  5 LKTGPVRMSGYALKLRRATNAALRKLYQEKKIEPKIANQMLTDLNKSLYDILINKYNIPKDAVINIELVLDISDSNL 81
                                      89***********************************************************************9987 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.33
                                      -TTSE CS
                           DUF2258 59 dKldv 63
                                      dK+d+
  gi|385805252|ref|YP_005841650.1| 92 DKDDI 96
                                      44444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       778  (0.0433934); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); 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 0.32s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 702.46
//
Query:       gi|385805253|ref|YP_005841651.1|  [L=181]
Description: hypothetical protein FFONT_0208 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score 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   12.3   3.4        0.2   12.0   1.6    2.0  3  SWIRM     SWIRM domain


Domain annotation for each model (and alignments):
>> SWIRM  SWIRM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.25   4.6e+03      10      25 ..      26      38 ..      20      66 .. 0.53
   2 ?   -1.9   0.0      0.25   4.5e+03      47      65 ..      83     101 ..      75     113 .. 0.65
   3 ?   12.0   1.6   1.1e-05       0.2      12      49 ..     117     156 ..     107     174 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.25
                             SWIRM 10 slhpiEkellselfng 25
                                      +l+ iE   ls +f++
  gi|385805253|ref|YP_005841651.1| 26 ELSNIE---LSAIFEK 38
                                      555555...3333322 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.25
                             SWIRM  47 npkeyltvteaqkalkrrr 65 
                                       n   ++tv+++ +++ +++
  gi|385805253|ref|YP_005841651.1|  83 NDLLEFTVEDIIQSVGEEK 101
                                       5556688888877766333 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 1.1e-05
                             SWIRM  12 hpiEkellself..ngkdktpeeYlkiRnkiialyrenpk 49 
                                       ++iE  +++ +   +++d+ +e+Y +++n +i++y ++ +
  gi|385805253|ref|YP_005841651.1| 117 EEIEAIIFEMVKnfSNNDEVIEKYHEVKNALIRKYEKEKS 156
                                       566666555554113448******************9743 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1382  (0.0770818); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.52
# Mc/sec: 1055.22
//
Query:       gi|385805254|ref|YP_005841652.1|  [L=105]
Description: hypothetical protein FFONT_0209 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score 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   14.0   0.3       0.12   13.3   0.3    1.4  1  zf-C2H2_4  C2H2-type zinc finger


Domain annotation for each model (and alignments):
>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3   6.8e-06      0.12       1      24 []      58      81 ..      58      81 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.8e-06
                         zf-C2H2_4  1 fkCpiC.gksFsskkaLlrHlkthH 24
                                      f+C iC +++F skk+++ Hl+++H
  gi|385805254|ref|YP_005841652.1| 58 FYCGICsKGPF-SKKGIKLHLLRVH 81
                                      89****999**.****999****99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 670.37
//
Query:       gi|385805255|ref|YP_005841653.1|  [L=486]
Description: radical SAM protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.5e-16   60.5   0.5      5e-16   59.5   0.2    1.7  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 ?   -3.5   0.0      0.67   1.2e+04     125     143 ..     110     130 ..      99     137 .. 0.59
   2 !   59.5   0.2   2.8e-20     5e-16       1     167 []     207     391 ..     207     391 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 0.67
                                       SHHHHHHH..HHHHHHHTTSE CS
                                       xxxxxxxx..xxxxxxxxxxx RF
                       Radical_SAM 125 htfeevle..aleklreagik 143
                                       ++f +++e  a++k+r++g+k
  gi|385805255|ref|YP_005841653.1| 110 KSFRRLMEspAVKKMRRRGVK 130
                                       444444443356777777766 PP

  == domain 2  score: 59.5 bits;  conditional E-value: 2.8e-20
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS........TTHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxx RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly........pdfveller 69 
                                       ++++rgC+++C+fC+++      ++ r++++e+i+eev  + +++gv   ++++ + lly        pd v +l  
  gi|385805255|ref|YP_005841653.1| 207 IEIMRGCPRGCKFCSVT-----LRPLRYIPLEKIEEEVLVN-VRNGVTRGLIHSEDILLYgadgvkprPDPVLKLHD 277
                                       689**************.....69*****************.9***9999999999******999777333333333 PP

                                       HHHTC...CCTEEEEEEECSSCHG.....HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHH........HH CS
                                       xxxxx...xxxxxxxxxxxxxxxx.....xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx........xx RF
                       Radical_SAM  70 lakla...vpgiritvetngtlpd.....eeklerllelg.vdrvslgleaaddekvlklmnrghtf........ee 129
                                        + ++    ++ + ++ +  +  +      +++e+++e      v++g+e++ +e   k++++ ++         e 
  gi|385805255|ref|YP_005841653.1| 278 TVLKHvksLAWSHASLAAIKYAEEehkliTKVMEKIREKQdYIGVEVGVETGGYE-LAKKIMPAKSApykpekwhEV 353
                                       3333366667888888888888779999988888888877899************.6666667777778999999** PP

                                       HHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 130 vlealeklreagikrvvdrivglpGendeeleellell 167
                                       v +a+++++e++i +  + i+glp e+++++ e++el+
  gi|385805255|ref|YP_005841653.1| 354 VEDAFRIMHENNIIPAATLIIGLPEETEKDVMETIELI 391
                                       ***********************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (486 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 3564.88
//
Query:       gi|385805256|ref|YP_005841654.1|  [L=104]
Description: hypothetical protein FFONT_0211 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); 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: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 683.09
//
Query:       gi|385805257|ref|YP_005841655.1|  [L=128]
Description: hypothetical protein FFONT_0212 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-05   25.0   0.0    2.7e-05   23.9   0.0    1.5  1  TrmB          Sugar-specific transcriptional regulator TrmB
    3.5e-05   23.6   0.0      6e-05   22.9   0.0    1.4  1  MarR_2        MarR family
    4.5e-05   23.3   0.0    9.2e-05   22.3   0.0    1.5  1  MarR          MarR family
     0.0013   18.5   0.0      0.005   16.6   0.0    1.9  2  HTH_IclR      IclR helix-turn-helix domain
     0.0037   17.3   0.1     0.0078   16.2   0.0    1.6  2  HTH_20        Helix-turn-helix domain
  ------ inclusion threshold ------
      0.021   14.7   0.0        0.1   12.5   0.0    2.1  2  HTH_5         Bacterial regulatory protein, arsR family
      0.028   14.9   0.0       0.11   13.0   0.0    1.8  2  HTH_27        Winged helix DNA-binding domain
      0.049   13.3   0.0        0.3   10.8   0.0    1.9  2  HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor
      0.055   13.2   0.2       0.49   10.1   0.2    1.9  1  DUF4423       Domain of unknown function (DUF4423)
      0.071   12.9   0.1       0.25   11.1   0.0    1.7  1  COR           C-terminal of Roc, COR, domain
      0.095   12.4   1.7        0.2   11.4   0.1    2.4  2  PLN_propep    Protealysin propeptide


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 !   23.9   0.0   1.7e-08   2.7e-05      19      65 ..      29      75 ..      17      78 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.7e-08
                                      HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE- CS
                              TrmB 19 klgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYrav 65
                                      + +p++ +e+ e++g  +  v ++L+ Le+  lVer+++r+k+Y ++
  gi|385805257|ref|YP_005841655.1| 29 NGKPMSFKELVEKSGYTKGHVSNILKLLESFNLVERIPERKKVYFVA 75
                                      567999*************************************9876 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   3.7e-08     6e-05       8      55 ..      19      66 ..      12      70 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 3.7e-08
                                      HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                      a vL+ +    g++++ +el+++ g++k+ vs+ilk L++  Lver p
  gi|385805257|ref|YP_005841655.1| 19 ACVLFSILFYNGKPMSFKELVEKSGYTKGHVSNILKLLESFNLVERIP 66
                                      67999999999999*******************************986 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   5.6e-08   9.2e-05      13      51 ..      28      66 ..      18      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 5.6e-08
                                      HHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR 13 yeqgplsvseLakklgvskstvtrvldrLekkGlieRsk 51
                                      y+  p+s +eL +k+g +k++v+++l+ Le  +l+eR +
  gi|385805257|ref|YP_005841655.1| 28 YNGKPMSFKELVEKSGYTKGHVSNILKLLESFNLVERIP 66
                                      55567********************************76 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       1.2     2e+03      22      33 ..       7      18 ..       2      19 .. 0.69
   2 !   16.6   0.0   3.1e-06     0.005      17      50 ..      31      64 ..      26      66 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.2
                                      HHHHHHHTS-HH CS
                          HTH_IclR 22 selArrtglpkS 33
                                        l   tglp S
  gi|385805257|ref|YP_005841655.1|  7 IKLLLLTGLPLS 18
                                      555667999988 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 3.1e-06
                                      SS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 17 qeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                       +++++el +++g +k  v+++L+ L+   +ve+
  gi|385805257|ref|YP_005841655.1| 31 KPMSFKELVEKSGYTKGHVSNILKLLESFNLVER 64
                                      68******************************98 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   4.8e-06    0.0078      14      60 ..      21      68 ..       9      69 .. 0.91
   2 ?   -2.9   0.1       4.5   7.4e+03      43      50 ..      86      93 ..      82      94 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.8e-06
                                      HHHHHH.STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                            HTH_20 14 rilraL.araegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                                       +++ L   +++++++el e  + +k  +s+ L+ Le+  Lve+  e+
  gi|385805257|ref|YP_005841655.1| 21 VLFSILfYNGKPMSFKELVEKSGYTKGHVSNILKLLESFNLVERIPER 68
                                      5667778889**********************************9998 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.5
                                      HHHHHHHH CS
                            HTH_20 43 yHLrvLee 50
                                       HL+ L+e
  gi|385805257|ref|YP_005841655.1| 86 MHLKSLQE 93
                                      59999987 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.2e-05       0.1      14      46 ..      31      63 ..      23      64 .. 0.92
   2 ?   -1.0   0.0         1   1.7e+03      34      41 ..      86      93 ..      84      94 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.2e-05
                                      SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5 14 gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      +++++ el+e+ g +++ vS  Lk L+  +LVe
  gi|385805257|ref|YP_005841655.1| 31 KPMSFKELVEKSGYTKGHVSNILKLLESFNLVE 63
                                      79**************************99997 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1
                                      HHHHHHHH CS
                             HTH_5 34 hHLkkLre 41
                                      +HLk L e
  gi|385805257|ref|YP_005841655.1| 86 MHLKSLQE 93
                                      79*99976 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   6.7e-05      0.11       5      54 ..      18      68 ..      16      75 .. 0.84
   2 ?   -1.1   0.0       1.7   2.8e+03       9      18 ..      99     108 ..      91     116 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.7e-05
                            HTH_27  5 qalvLhlir.hrrrrkkladlcgrlnvedshisyslkkLtekGLvertgde 54
                                       a+vL++i   ++ +++ ++l+++  +++ h+s++lk L+   Lver + +
  gi|385805257|ref|YP_005841655.1| 18 SACVLFSILfYNGKPMSFKELVEKSGYTKGHVSNILKLLESFNLVERIPER 68
                                      589999999677777777***************************887665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.7
                            HTH_27   9 Lhlirhrrrr 18 
                                       ++++ + +r+
  gi|385805257|ref|YP_005841655.1|  99 INNLDEKDRK 108
                                       4444433333 PP

>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00018       0.3      22      57 ..      31      66 ..      21      73 .. 0.82
   2 ?    0.1   0.0      0.39   6.3e+02      33      51 ..      74      92 ..      69      99 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00018
                      HrcA_DNA-bdg 22 ravKgeeiAevlkrneGtvRNqlqsLkalgLvegvp 57
                                      +++  +e+ e+ +  +G v N+l+ L +++Lve +p
  gi|385805257|ref|YP_005841655.1| 31 KPMSFKELVEKSGYTKGHVSNILKLLESFNLVERIP 66
                                      5556678888889999*****************988 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.39
                      HrcA_DNA-bdg 33 lkrneGtvRNqlqsLkalg 51
                                      + ++eG    +++ Lk+l+
  gi|385805257|ref|YP_005841655.1| 74 VAKKEGIYNHVVMHLKSLQ 92
                                      6788999999999999996 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.2    0.0003      0.49      44     120 ..      40     125 ..      19     127 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0003
                           DUF4423  44 krlrpkisaeevekalefLlklgllkk...........dedgkyrqtekslttssevkseavrsyhkqmlelAieal 109
                                       ++ +   ++  v+++l++L++ +l+++           +++g y+  + +l++ +e  s  ++++  +  ++A++ l
  gi|385805257|ref|YP_005841655.1|  40 EKSG--YTKGHVSNILKLLESFNLVERiperkkvyfvaKKEGIYNHVVMHLKSLQENLSSIINNLDEKDRKKAQTFL 114
                                       5555..66777777777777777777633333333333455788888999999999999999999999999999999 PP

                           DUF4423 110 ervpkeeRdis 120
                                         ++   R++s
  gi|385805257|ref|YP_005841655.1| 115 SDLDLMLRRVS 125
                                       98888888887 PP

>> COR  C-terminal of Roc, COR, domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00015      0.25      98     140 ..      34      76 ..      31      78 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00015
                               COR  98 dlekiwkekeypaeehdlllelmekfelcyeleeeedtylvpq 140
                                       +++++ +++ y++ + + +l+l+e+f+l+ +++e+++ y+v++
  gi|385805257|ref|YP_005841655.1|  34 SFKELVEKSGYTKGHVSNILKLLESFNLVERIPERKKVYFVAK 76 
                                       5788999999************************999999875 PP

>> PLN_propep  Protealysin propeptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       1.2     2e+03      29      36 ..      86      93 ..      85      94 .. 0.84
   2 ?   11.4   0.1   0.00012       0.2       9      28 ..      95     114 ..      95     128 .] 0.82

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.2
                        PLN_propep 29 eHVqslma 36
                                      +H++sl+ 
  gi|385805257|ref|YP_005841655.1| 86 MHLKSLQE 93
                                      7****997 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00012
                        PLN_propep   9 LrrIidngdeeqRacArrtL 28 
                                       L  Ii+n de++R++A+  L
  gi|385805257|ref|YP_005841655.1|  95 LSSIINNLDEKDRKKAQTFL 114
                                       678*************9766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1344  (0.0749624); expected 358.6 (0.02)
Passed bias filter:                      821  (0.0457917); 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: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 822.07
//
Query:       gi|385805258|ref|YP_005841656.1|  [L=287]
Description: putative PP-loop superfamily ATPase [Fervidicoccus fontis Kam940]
Scores for complete 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-40  136.9   0.2    9.3e-40  136.4   0.2    1.2  1  QueC      Queuosine biosynthesis protein QueC
    6.1e-05   22.7   0.0     0.0001   22.0   0.0    1.3  1  ThiI      Thiamine biosynthesis protein (ThiI)
  ------ inclusion threshold ------
       0.13   11.2   0.2        0.2   10.6   0.2    1.2  1  CRT-like  CRT-like, chloroquine-resistance transporter-like


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 !  136.4   0.2   1.6e-43   9.3e-40       2     209 ..      17     244 ..      16     245 .. 0.88

  Alignments for each domain:
  == domain 1  score: 136.4 bits;  conditional E-value: 1.6e-43
                                       EEEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-TTSHHHHHHHHHHHHT-........-.-EEEEE-GGGGGGS.C CS
                              QueC   2 avvllSGGlDSttvlalakkegkevealtfdYgqrhkkeleaakkiakelg........veehkildldllkelg.g 69 
                                       +v ++SGG DS   ++   keg  +++ltf+Ygq++++e+e+ kk+ ++l+        + ehkild++++k+l  +
  gi|385805258|ref|YP_005841656.1|  17 VVSIFSGGPDSFCYTLKWIKEGCDLHLLTFNYGQKASREVEVSKKLYEKLKefagesirI-EHKILDISFMKDLWnK 92 
                                       589******************************************************988.***********98637 PP

                                       GGG-----------...--------TTHHHHHHHHHHHHHHHHT-SE......EEE---S-STT........--GGG CS
                              QueC  70 saLtdeeievpkeeleeeelpntfVpaRNliflslaasyaealgaea......iiiGvneedfs........gYPDc 132
                                       + L+d+++e+++     e   +  Vp RN+++ls+a++ya++l  e+      +i+G+++ d+s         YPDc
  gi|385805258|ref|YP_005841656.1|  93 TQLIDKSKELSS-----EYETSIVVPIRNVVMLSIASAYAYSLISEDeslnayVIYGAHSDDASisekaggpKYPDC 164
                                       789999876666.....6677899****************987654333334499*******98555555555**** PP

                                       SHHHHHHHHHHHHHH...HTS--EEE-TTTT.--HHHHHHHHHHTT.HHHHH-B-STTS.-BTTTTSSSHHHHHHHH CS
                              QueC 133 rdefvkalnkalnlg...edkkieieaPlid.lsKaeivklgkelg.vpleetlsCYegeeegkaCgeCdaCalRkk 204
                                       ++e +++l++  ++    +d+++ei  P+ + +sKae ++   ++   ++ et+sCY++++   +Cg+C++C+ R+k
  gi|385805258|ref|YP_005841656.1| 165 SSECIESLQASFRIChfpKDRRLEIWSPIREgMSKAENIRKCYDIAeNIIYETWSCYRDGD--FHCGKCESCINRHK 239
                                       ***********99999999**********8559****999998887688999*******55..5************* PP

                                       HHHHH CS
                              QueC 205 gfeea 209
                                       +f +a
  gi|385805258|ref|YP_005841656.1| 240 AFLKA 244
                                       **875 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   1.7e-08    0.0001       6     104 ..      17     127 ..      14     137 .. 0.71

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.7e-08
                              ThiI   6 vlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaellaeyqts...levklvvvdfkevl... 76 
                                       v+++ SgG DS   +   +k Gc  +l+++ n+  ++ ++ e+ +kl e+l e+ +    +e k+  ++f + l   
  gi|385805258|ref|YP_005841656.1|  17 VVSIFSGGPDSFCYTLKWIKEGCDLHLLTF-NYGQKASREVEVSKKLYEKLKEFAGEsirIEHKILDISFMKDLwnk 92 
                                       899***************************.8999999****************87322245566667776654121 PP

                              ThiI  77 keilekv......kekltiv.llkrkmlriAekva 104
                                       +++++k+       e + +v +    ml iA+ +a
  gi|385805258|ref|YP_005841656.1|  93 TQLIDKSkelsseYETSIVVpIRNVVMLSIASAYA 127
                                       33444444444322222333123456777777766 PP

>> CRT-like  CRT-like, chloroquine-resistance transporter-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2   3.4e-05       0.2     224     270 ..     200     246 ..     180     252 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 3.4e-05
                          CRT-like 224 lkdGlaCllgkntiveevlscgldeqkscDdCekawivvllyllvNi 270
                                        ++  +C+   ++i+ e+ sc  d +++c +Ce+      ++l +Ni
  gi|385805258|ref|YP_005841656.1| 200 AENIRKCYDIAENIIYETWSCYRDGDFHCGKCESCINRHKAFLKANI 246
                                       444568**888888887779***************999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1916.26
//
Query:       gi|385805259|ref|YP_005841657.1|  [L=245]
Description: hypothetical protein FFONT_0214 [Fervidicoccus fontis Kam940]
Scores for complete 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-28   98.0  21.2    2.3e-21   76.6  11.2    2.0  2  ECF-ribofla_trS  ECF-type riboflavin transporter, S component
  ------ inclusion threshold ------
       0.37    9.5   7.0       0.57    8.9   7.0    1.4  1  DUF2207          Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> 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 !   76.6  11.2   2.5e-25   2.3e-21       6     127 ..       4     124 ..       2     136 .. 0.91
   2 !   27.2   2.9   3.7e-10   3.3e-06      70     172 .]     135     228 ..     121     228 .. 0.70

  Alignments for each domain:
  == domain 1  score: 76.6 bits;  conditional E-value: 2.5e-25
                                       HHHHHHHHHHHHHHHHHH---B-S.SS-B--TTHHHHHHHHHHSS--STHHHHHHHHHHHHHHHSS-GGGHHHHHHH CS
                   ECF-ribofla_trS   6 kvvatailaAlvvvltlfisIplpantegsinlgdavlalaallfGpvvGflvGaiGsalaDllsgYgiwapftlii 82 
                                       ++v  a+++Alv+v+t++++   p  t+g++nlg+a +++ al+  p++ +l+G+iGsalaD+ +gYgi+ap tl+i
  gi|385805259|ref|YP_005841657.1|   4 NIVRFAVFTALVYVFTVVVQFAQP-FTGGYFNLGEAAIYVCALISDPLTTGLAGGIGSALADATTGYGIFAPATLLI 79 
                                       68999******************9.9999************************************************ PP

                                       HHHHHHHHHHH--S-S-SSH...HHHHHHHHHHHHHHHHHHHHHH CS
                   ECF-ribofla_trS  83 kgliGlivGliakklkknkengvfkilalvlfaivmvigyviaeg 127
                                       k+++G++++l++kk+++++++  + +++l++f+++  ig   + g
  gi|385805259|ref|YP_005841657.1|  80 KFTEGYVASLLFKKMGRSNSSIANWLVSLIYFVAISAIGIKFFSG 124
                                       ***************999997777778899999998888766555 PP

  == domain 2  score: 27.2 bits;  conditional E-value: 3.7e-10
                                       SS-GGGHHHHHHHHHHHHHHHHHH--S-S-SSH...HHHHHHHHHHHHHHHHHHHHHHHH..........S-HHHHH CS
                   ECF-ribofla_trS  70 sgYgiwapftliikgliGlivGliakklkknkengvfkilalvlfaivmvigyviaegllpildiiiysepaekval 146
                                         + i + f +++ ++i +i+ +i ++ +k      ++ ++l+l++++mv+gy++ e+++            + +a+
  gi|385805259|ref|YP_005841657.1| 135 FSFNIPWEFWVLVGAII-MIIPFIIERRTKA----GARYASLLLAGMIMVTGYFLYEFFI----SNPLTGRPSIAAV 202
                                       44665555524444444.4555555555233....357889*******************....2333445567888 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   ECF-ribofla_trS 147 qsipaniiqavvgaiialpLlkalak 172
                                        ++p n+ qa+vga +a+p++  l+k
  gi|385805259|ref|YP_005841657.1| 203 FEVPVNFGQALVGAAVAIPVYSFLRK 228
                                       9*******************998876 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   7.0   6.4e-05      0.57     372     446 ..      91     170 ..      65     190 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 6.4e-05
                           DUF2207 372 fdkkgkkklkklsalglgliilglilillallllvll.........lvfllilllillliaiivlllfsrllgrrte 439
                                       f+k+g+++    s++++++ ++++++i ++ + ++++         ++ ++i+  +++l+++i+++++  +++rrt+
  gi|385805259|ref|YP_005841657.1|  91 FKKMGRSNS---SIANWLVSLIYFVAISAIGIKFFSGnltlslssySFSFNIPWEFWVLVGAIIMIIP-FIIERRTK 163
                                       444444443...44444444444444444444444447778999*98888899999999999999998.7899**** PP

                           DUF2207 440 eGaella 446
                                        Ga++++
  gi|385805259|ref|YP_005841657.1| 164 AGARYAS 170
                                       ***9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       823  (0.0459033); 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: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1468.43
//
Query:       gi|385805260|ref|YP_005841658.1|  [L=428]
Description: ABC transporter [Fervidicoccus fontis Kam940]
Scores for 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-41  139.6   2.0    7.7e-23   81.5   0.0    3.5  2  ABC_tran         ABC transporter
    5.4e-17   62.6  17.1    8.3e-09   35.7   0.4    4.2  4  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    2.6e-10   40.1   1.7    2.8e-05   23.7   0.0    4.0  3  SMC_N            RecF/RecN/SMC N terminal domain
    4.1e-10   39.9   7.0      0.017   14.9   0.4    4.1  4  AAA_15           AAA ATPase domain
    5.5e-08   32.2   1.1     0.0052   15.9   0.1    2.6  2  T2SSE            Type II/IV secretion system protein
    6.4e-07   29.4   0.4    0.00042   20.3   0.2    2.7  2  RsgA_GTPase      RsgA GTPase
    8.3e-07   29.7  14.8    0.00031   21.3   1.6    3.3  3  AAA_23           AAA domain
    8.8e-07   29.5   0.1      0.053   13.9   0.0    2.6  2  AAA_16           AAA ATPase domain
    2.4e-06   27.9   0.0      0.027   14.7   0.0    2.5  2  AAA_22           AAA domain
      8e-06   25.5   6.8     0.0051   16.5   0.1    3.0  2  AAA_29           P-loop containing region of AAA domain
    1.8e-05   25.2   4.1      0.096   13.1   0.1    3.3  2  AAA              ATPase family associated with various cellul
      2e-05   24.0   0.2       0.46    9.8   0.0    3.1  3  Mg_chelatase     Magnesium chelatase, subunit ChlI
    4.6e-05   23.2   0.0        0.4   10.4   0.0    2.6  2  AAA_30           AAA domain
    0.00011   22.8   1.2        0.3   11.6   0.3    3.7  3  AAA_18           AAA domain
    0.00014   21.9   1.7       0.36   10.8   0.1    2.7  2  AAA_5            AAA domain (dynein-related subfamily)
    0.00019   21.4   0.2       0.14   12.1   0.0    2.7  2  Rad17            Rad17 P-loop domain
    0.00021   21.0   0.9       0.93    9.2   0.1    3.2  3  AAA_24           AAA domain
    0.00025   21.0   1.2       0.51   10.4   0.0    2.9  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    0.00037   20.0   0.2      0.038   13.5   0.0    2.6  2  AAA_7            P-loop containing dynein motor region
    0.00099   19.1   3.1       0.15   12.0   0.1    3.2  3  NACHT            NACHT domain
     0.0011   18.3   0.1        1.2    8.2   0.0    2.5  2  PIF1             PIF1-like helicase
     0.0011   18.5   0.3       0.32   10.5   0.0    2.7  2  AAA_25           AAA domain
     0.0022   17.3   0.1        0.6    9.4   0.0    2.5  2  Zeta_toxin       Zeta toxin
     0.0026   17.9   1.3       0.59   10.3   0.1    2.7  2  AAA_33           AAA domain
     0.0026   17.4   1.0        0.4   10.3   0.0    2.4  2  SRP54            SRP54-type protein, GTPase domain
     0.0046   16.7   0.2        1.3    8.8   0.1    2.4  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
     0.0053   17.0   0.3        4.3    7.6   0.0    3.7  2  SbcCD_C          Putative exonuclease SbcCD, C subunit
     0.0068   15.9   0.1       0.28   10.6   0.0    2.3  2  PhoH             PhoH-like protein
     0.0071   16.2   0.1        2.5    7.8   0.0    2.3  2  AAA_11           AAA domain
     0.0072   16.4   2.6        1.9    8.5   0.6    3.9  3  AAA_14           AAA domain
     0.0077   15.7   0.2        4.3    6.7   0.1    2.4  2  SRPRB            Signal recognition particle receptor beta su
     0.0086   16.0   0.0        5.6    6.8   0.0    2.4  2  dNK              Deoxynucleoside kinase
     0.0089   16.4   0.7        2.7    8.3   0.1    2.7  2  AAA_19           AAA domain
     0.0092   16.4   0.1        3.8    7.9   0.0    2.6  2  RNA_helicase     RNA helicase
  ------ inclusion threshold ------
      0.013   15.5   0.1        2.4    8.2   0.0    2.6  2  ResIII           Type III restriction enzyme, res subunit
      0.022   14.4   0.0          3    7.5   0.0    2.4  2  Sigma54_activat  Sigma-54 interaction domain
      0.027   13.8   0.3        2.2    7.6   0.0    2.3  2  FtsK_SpoIIIE     FtsK/SpoIIIE family
      0.033   13.4   0.2        2.9    7.0   0.0    2.5  2  G-alpha          G-protein alpha subunit
      0.033   13.4   0.1        1.1    8.5   0.0    2.7  3  KAP_NTPase       KAP family P-loop domain
      0.041   13.9   0.1        3.5    7.7   0.0    2.3  2  Dynamin_N        Dynamin family
      0.051   13.8   1.0          1    9.6   0.1    2.6  2  Roc              Ras of Complex, Roc, domain of DAPkinase
      0.085   12.4   0.2        1.2    8.6   0.0    2.2  2  AAA_27           AAA domain
      0.088   12.2   1.0        4.5    6.7   0.1    2.3  2  Pox_A32          Poxvirus A32 protein
      0.098   12.9   1.7         10    6.3   0.1    2.4  2  AAA_28           AAA domain
      0.098   12.4   0.2         16    5.2   0.0    2.5  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
       0.14   12.3   5.2       0.37   10.9   0.5    3.0  2  MMR_HSR1         50S ribosome-binding GTPase
       0.14   11.9   0.2         20    4.9   0.0    3.1  3  DEAD             DEAD/DEAH box helicase
       0.14   11.9   1.6        7.4    6.3   0.0    3.3  3  IstB_IS21        IstB-like ATP binding protein
       0.14   10.9   0.3        2.6    6.8   0.0    2.2  2  DLIC             Dynein light intermediate chain (DLIC)
       0.14   11.7   2.9          3    7.4   0.3    2.4  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
       0.16   11.1   0.1        1.6    7.9   0.1    2.1  2  DUF815           Protein of unknown function (DUF815)
       0.32   10.9   7.5        6.2    6.7   0.1    3.8  4  NTPase_1         NTPase
       0.39   10.4   2.7        8.9    5.9   0.0    3.6  4  Thymidylate_kin  Thymidylate kinase
       0.48    9.7   3.2        2.6    7.3   0.1    2.6  2  Gtr1_RagA        Gtr1/RagA G protein conserved region
       0.65    8.6   2.5        3.2    6.3   0.1    2.7  3  AAA_13           AAA domain
       0.77    9.1   2.8         17    4.7   0.0    3.1  4  ATPase           KaiC
        8.8    6.3   7.9         27    4.8   0.1    3.6  3  DUF87            Helicase HerA, central 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 !   81.5   0.0   2.4e-25   7.7e-23       1     136 [.      23     168 ..      23     169 .. 0.93
   2 !   53.4   0.3   1.2e-16   3.6e-14       2     136 ..     257     378 ..     256     379 .. 0.79

  Alignments for each domain:
  == domain 1  score: 81.5 bits;  conditional E-value: 2.4e-25
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--.....SEEEEEETTCEGGGB-HHHCCHCEEEE-SS..--S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp.....teGeilldgkdlkeqeleslrkeigvlpqe..pql 70 
                                       +kn++++l+ege++ ++G++G+GK+++l++lag++        eG+++++g d ++ + e+l +++g +pqe  + +
  gi|385805260|ref|YP_005841658.1|  23 VKNINFSLNEGELLLLIGKTGTGKTSILNVLAGNTPRlikakVEGNVRINGIDPRDSPSEVLLRNVGLVPQEpsDGV 99 
                                       58********************************988999999*****************************65455 PP

                                       -TTSBHHHH........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  71 fpeltvren........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                         ++ v+++        ++d+++e +l+ ++l+ l +++      +LS G+ q++a+   +l ++ +ll+DEpt
  gi|385805260|ref|YP_005841658.1| 100 IGDT-VEDEvllslmfrNDDADVEGWLRLFNLERLYERTT----FTLSAGETQKLAILSRVLLNAHVLLFDEPT 168
                                       5555.88889************************999998....*****************************9 PP

  == domain 2  score: 53.4 bits;  conditional E-value: 1.2e-16
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       kn++l++    ++ + G+nG+GK+t+lkll+g ++p+ G+i     ++++ +  +   +   ++ +p+ ++el++  
  gi|385805260|ref|YP_005841658.1| 257 KNINLSFDGPGIILLKGPNGSGKTTFLKLLSGIVRPKRGKI-----EMSH-SALFIPDNPLLYFSKPTPKEELELFA 327
                                       899**************************************.....4444.44456666667777778888887544 PP

                                       HHHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 nesdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                        + ++e ++ l k+++     +++    ++LS G+++ ++l  a l++ +++l+DEpt
  gi|385805260|ref|YP_005841658.1| 328 GNLKKEEKERLLKIKIFA---KKM----KELSSGERRLISLISASLSHHPIILMDEPT 378
                                       444444444444455444...444....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 !    8.4   1.3    0.0052       1.6       3      21 ..      37      55 ..      35     125 .. 0.78
   2 ?    7.2   0.2     0.012       3.8     224     273 ..     128     174 ..     104     202 .. 0.76
   3 !   21.0   0.2   7.8e-07   0.00025       2      26 ..     269     302 ..     268     335 .. 0.68
   4 !   35.7   0.4   2.6e-11   8.3e-09     236     299 ..     350     410 ..     345     413 .. 0.94

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0052
                            AAA_21  3 vliGpNgsGKSnLLdaldl 21
                                      +liG+ g+GK+++L  l +
  gi|385805260|ref|YP_005841658.1| 37 LLIGKTGTGKTSILNVLAG 55
                                      8*************99954 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.012
                            AAA_21 224 lengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPk 273
                                       +  ++ +e++ + lS G  + la+l+ +l  +    +ll+DEp + L+ +
  gi|385805260|ref|YP_005841658.1| 128 FNLERLYERTTFTLSAGETQKLAILSRVLLNA---HVLLFDEPTTYLDEE 174
                                       55567788888999999999999999999999...89********99855 PP

  == domain 3  score: 21.0 bits;  conditional E-value: 7.8e-07
                            AAA_21   2 nvliGpNgsGKSnLLdaldllarl.........d 26 
                                        +l GpNgsGK+++L++l+++ r           
  gi|385805260|ref|YP_005841658.1| 269 ILLKGPNGSGKTTFLKLLSGIVRPkrgkiemshS 302
                                       6899**************9985545444444443 PP

  == domain 4  score: 35.7 bits;  conditional E-value: 2.6e-11
                            AAA_21 236 elSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSp 299
                                       elS+G +rl+ l++a l+ +   +++l DEp  gL+P+  +++l+++k+ls+ g  +i+++H+ 
  gi|385805260|ref|YP_005841658.1| 350 ELSSGERRLISLISASLSHH---PIILMDEPTVGLDPEYKSTVLDIFKKLSDSGRLLIISSHDR 410
                                       89****************99...*****************************99999*****95 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0      0.09        28     101     101 ..      59      59 ..      14     220 .. 0.53
   2 !    7.8   0.2    0.0064         2      24      41 ..     266     283 ..     253     288 .. 0.78
   3 !   23.7   0.0   8.8e-08   2.8e-05     121     213 ..     333     424 ..     318     428 .] 0.75

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.09
                                       E CS
                                       x RF
                             SMC_N 101 r 101
                                       r
  gi|385805260|ref|YP_005841658.1|  59 R 59 
                                       2 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0064
                                       SSEEEEEESTTSSHHHHH CS
                                       xxxxxxxxxxxxxxxxxx RF
                             SMC_N  24 ksftaivGpNGSGKsnll 41 
                                       +++  + GpNGSGK+ +l
  gi|385805260|ref|YP_005841658.1| 266 PGIILLKGPNGSGKTTFL 283
                                       6788899********987 PP

  == domain 3  score: 23.7 bits;  conditional E-value: 8.8e-08
                                       HHHHHHHHCTT-..STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE CS
                                       xxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 121 kevsellesagi..skelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivi 195
                                       +e ++ll+ + +  ++++LS Ge+ L++  L+    + + +p+ l+De    LD ++ + v +++k+ s++  +++i
  gi|385805260|ref|YP_005841658.1| 333 EEKERLLKIKIFakKMKELSSGERRLIS--LI--SASLSHHPIILMDEPTVGLDPEYKSTVLDIFKKLSDSGRLLII 405
                                       444455544444223568********76..56..4578899******************************888777 PP

                                       -SSH.HHCCC-SCEEEEEE CS
                                       xxxx.xxxxxxxxxxxxxx RF
                             SMC_N 196 slre.emlekadklvgvtk 213
                                       s ++ e+ + a ++v v k
  gi|385805260|ref|YP_005841658.1| 406 SSHDrEVEKVATEVVEVNK 424
                                       6555055555688888876 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   1.1   0.00084      0.26      20      43 ..      27      53 ..      15      56 .. 0.81
   2 ?    2.5   0.0      0.31        98     324     364 ..     159     198 ..     153     202 .. 0.94
   3 !   14.9   0.4   5.4e-05     0.017      14      55 ..     256     313 ..     255     348 .. 0.65
   4 !   12.0   0.1   0.00041      0.13     293     365 ..     347     409 ..     321     412 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00084
                            AAA_15 20 dlsee...ltvliGkNnsGKSsileal 43
                                      ++s +   l +liGk ++GK+sil++l
  gi|385805260|ref|YP_005841658.1| 27 NFSLNegeLLLLIGKTGTGKTSILNVL 53
                                      33333447****************998 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.31
                            AAA_15 324 nvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                        ++ll++EP ++L  +  + + +   +l++ +k  viit H
  gi|385805260|ref|YP_005841658.1| 159 AHVLLFDEPTTYLDEESREGFKEVVFSLLKAGK-TVIITGH 198
                                       589*****************************9.9****99 PP

  == domain 3  score: 14.9 bits;  conditional E-value: 5.4e-05
                            AAA_15  14 lkdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekkn...............k 55 
                                       +k++ ++++   + +l G+N+sGK+++l++l  +   k+ k                +
  gi|385805260|ref|YP_005841658.1| 256 FKNINLSFDGPgIILLKGPNGSGKTTFLKLLSGIVRPKRGKIemshsalfipdnpllY 313
                                       677667777668999****************998888844435664444444444440 PP

  == domain 4  score: 12.0 bits;  conditional E-value: 0.00041
                            AAA_15 293 plnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                       ++++ +sG +rl++li   l+ +          i+l++EP + L p+ ++ + + +k+l+++++  +ii++H 
  gi|385805260|ref|YP_005841658.1| 347 KMKELSSGERRLISLISASLSHHP---------IILMDEPTVGLDPEYKSTVLDIFKKLSDSGR-LLIISSHD 409
                                       678899******999988777665.........5*****************************9.9******7 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   1.6e-05    0.0052     102     151 ..       6      55 ..       2      66 .. 0.90
   2 !   14.1   0.1   5.9e-05     0.018     129     157 ..     266     294 ..     245     299 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.6e-05
                             T2SSE 102 eltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallk 151
                                       ++ +d+l+++ +++e+i + ++ +++e  l+l+ G Tg+GKt +l++l  
  gi|385805260|ref|YP_005841658.1|   6 KVFVDNLSISYKNDEQIVKNINFSLNEGELLLLIGKTGTGKTSILNVLAG 55 
                                       56689999**************************************9865 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 5.9e-05
                             T2SSE 129 rglilvsGgTgsGKttllyallkeinksd 157
                                        g+il+ G+ gsGKtt+l  l  ++  + 
  gi|385805260|ref|YP_005841658.1| 266 PGIILLKGPNGSGKTTFLKLLSGIVRPKR 294
                                       589***************99999887765 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.2   1.3e-06   0.00042      81     123 ..      13      57 ..       2      74 .. 0.79
   2 ?    6.4   0.0     0.024       7.5      92     130 ..     258     297 ..     222     303 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.3e-06
                                       E--TT.THTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT- CS
                       RsgA_GTPase  81 lvsak.tkegleelkellkd.ktsvlvGqSGvGKStLinallpel 123
                                        +s k +++ +++++  l++ ++ +l+G++G GK++++n+l++++
  gi|385805260|ref|YP_005841658.1|  13 SISYKnDEQIVKNINFSLNEgELLLLIGKTGTGKTSILNVLAGNT 57 
                                       4554414566789*****999*********************985 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.024
                                       HHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                       RsgA_GTPase  92 elkellkd.ktsvlvGqSGvGKStLinallpelelktgev 130
                                       +++  +++  +++l G+ G GK+t+++ l +  + k g++
  gi|385805260|ref|YP_005841658.1| 258 NINLSFDGpGIILLKGPNGSGKTTFLKLLSGIVRPKRGKI 297
                                       55556666678999*************9998766666655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.4   6.1e-05     0.019      14      39 ..      25      53 ..      13      62 .. 0.81
   2 !   21.3   1.6   9.8e-07   0.00031      10      39 ..     256     286 ..     252     290 .. 0.89
   3 ?    0.6   0.7       2.2   6.8e+02     137     176 ..     305     346 ..     293     364 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.1e-05
                            AAA_23 14 eidF...skgltlItGpNGaGKTTildAi 39
                                      +i+F   +  l l++G++G+GKT+il+ +
  gi|385805260|ref|YP_005841658.1| 25 NINFslnEGELLLLIGKTGTGKTSILNVL 53
                                      4777776668****************976 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 9.8e-07
                            AAA_23  10 frdqeidF.skgltlItGpNGaGKTTildAi 39 
                                       f++ ++ F ++g+ l+ GpNG+GKTT+l  +
  gi|385805260|ref|YP_005841658.1| 256 FKNINLSFdGPGIILLKGPNGSGKTTFLKLL 286
                                       78888999999****************9765 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 2.2
                            AAA_23 137 flgqerfeefelkdkkerleelekeleeledekkllekl..e 176
                                       f+++    +f++ ++ke+le +   l+++e+e+ l  k   +
  gi|385805260|ref|YP_005841658.1| 305 FIPDNPLLYFSKPTPKEELELFAGNLKKEEKERLLKIKIfaK 346
                                       555555677888888999999888888888877543333332 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   0.00017     0.053      23      45 ..      32      54 ..      20     125 .. 0.85
   2 !   13.1   0.1   0.00029      0.09      23      51 ..     265     293 ..     259     405 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00017
                            AAA_16 23 rpelvllsGesGvGKsslvrell 45
                                      ++el+ll+G  G+GK+s+++ l+
  gi|385805260|ref|YP_005841658.1| 32 EGELLLLIGKTGTGKTSILNVLA 54
                                      5599***************9887 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00029
                            AAA_16  23 rpelvllsGesGvGKsslvrellralekd 51 
                                       +p+++ll G+ G+GK++ ++ l   ++ +
  gi|385805260|ref|YP_005841658.1| 265 GPGIILLKGPNGSGKTTFLKLLSGIVRPK 293
                                       579****************9988655555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0    0.0017      0.55       6      33 ..      34      61 ..      30      95 .. 0.79
   2 !   14.7   0.0   8.7e-05     0.027       4      99 ..     265     376 ..     262     408 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0017
                            AAA_22  6 gilvvtGesGtGKTtllrrlleqldeea 33
                                       +l+++G +GtGKT  l+ l+ + ++ +
  gi|385805260|ref|YP_005841658.1| 34 ELLLLIGKTGTGKTSILNVLAGNTPRLI 61
                                      6899***********9998887765554 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 8.7e-05
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee..........erpevvfvtlpsstsskdllrellralglelka 70 
                                       + gi+++ G+ G+GKTt l+ l       +k  +          ++ +++++  +++ ++k+ l+ ++ +l+ e k+
  gi|385805260|ref|YP_005841658.1| 265 GPGIILLKGPNGSGKTTFLKLLSGIVR--PKRGKiemshsalfiPDNPLLYF--SKP-TPKEELELFAGNLKKEEKE 336
                                       579*****************9988763..33333446755555522222222..222.2334444444444444444 PP

                            AAA_22  71 ..............erlsseellealeqalraravielliiDE 99 
                                                         +++l++++   l+++   ++++ DE
  gi|385805260|ref|YP_005841658.1| 337 rllkikifakkmkeLSSGERRLISLISASLSHH---PIILMDE 376
                                       122244444444322223344444444444444...3466665 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.1   0.00042      0.13      17      39 ..      28      50 ..      18      59 .. 0.76
   2 !   16.5   0.1   1.6e-05    0.0051      14      40 ..     258     284 ..     255     303 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00042
                            AAA_29 17 ieidlkgatlltGpsGsGKSTll 39
                                      +++++ +  ll+G++G+GK+++l
  gi|385805260|ref|YP_005841658.1| 28 FSLNEGELLLLIGKTGTGKTSIL 50
                                      445544499************99 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1.6e-05
                            AAA_29  14 ghtieidlkgatlltGpsGsGKSTllD 40 
                                       +  +++d  g++ll Gp+GsGK+T+l 
  gi|385805260|ref|YP_005841658.1| 258 NINLSFDGPGIILLKGPNGSGKTTFLK 284
                                       55567776679*************985 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.1    0.0003     0.096       1      22 [.      36      57 ..      36     223 .. 0.80
   2 !   11.7   0.8   0.00083      0.26       1      66 [.     269     376 ..     269     379 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.0003
                                      EEEESSTTSSHHHHHHHHHHHH CS
                               AAA  1 vllyGppGtGKTllakavakel 22
                                      +ll+G  GtGKT++ + +a ++
  gi|385805260|ref|YP_005841658.1| 36 LLLIGKTGTGKTSILNVLAGNT 57
                                      69*****************995 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00083
                                       EEEESSTTSSHHHHHHHHHHHH..THEEEEEETTTCS.SS..................................... CS
                               AAA   1 vllyGppGtGKTllakavakel..gvefleisgsell.sk..................................... 37 
                                       +ll Gp G GKT++ k +   +  ++  +e+s s l+  +                                     
  gi|385805260|ref|YP_005841658.1| 269 ILLKGPNGSGKTTFLKLLSGIVrpKRGKIEMSHSALFiPDnpllyfskptpkeelelfagnlkkeekerllkikifa 345
                                       699***************99984434456666666553224555555555555555555555444444444444444 PP

                                       ....STTHHHHHHHHHHHHHHHTSTSEEEEEET CS
                               AAA  38 ....yvgesekkirelfkeakekakpsilfiDE 66 
                                            ++ +e+++  l+++  +  ++ i+++DE
  gi|385805260|ref|YP_005841658.1| 346 kkmkELSSGERRLISLISASLS--HHPIILMDE 376
                                       4333444555555555543222..247777776 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0    0.0039       1.2      22      63 ..      33      74 ..      16      88 .. 0.78
   2 !    9.8   0.0    0.0015      0.46      19      50 ..     263     294 ..     256     305 .. 0.79
   3 ?    1.9   0.0       0.4   1.2e+02     102     140 ..     364     407 ..     348     421 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0039
                      Mg_chelatase 22 gHnlllvGppGsGKtmlakrlpsllpplseeealevakiasv 63
                                      g  lll+G  G+GKt + + l++  p+l ++++    +i+ +
  gi|385805260|ref|YP_005841658.1| 33 GELLLLIGKTGTGKTSILNVLAGNTPRLIKAKVEGNVRINGI 74
                                      56799****************999999988887777666665 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0015
                      Mg_chelatase  19 aaGgHnlllvGppGsGKtmlakrlpsllppls 50 
                                         G   +ll Gp GsGKt   k l++++ p  
  gi|385805260|ref|YP_005841658.1| 263 FDGPGIILLKGPNGSGKTTFLKLLSGIVRPKR 294
                                       5566679*******************997654 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.4
                      Mg_chelatase 102 islahnGvLfLDEl.....pefkrkvlevLRePledgevtisra 140
                                        sl+h+ ++++DE      pe+k++vl+++++  ++g++ i  +
  gi|385805260|ref|YP_005841658.1| 364 ASLSHHPIILMDEPtvgldPEYKSTVLDIFKKLSDSGRLLIISS 407
                                       589**********5444458********9999888888766544 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0    0.0017      0.53      16      40 ..      31      55 ..      18      89 .. 0.82
   2 !   10.4   0.0    0.0013       0.4      20      47 ..     268     295 ..     260     302 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0017
                            AAA_30 16 sgdrvavltGpAGtGKttalkalre 40
                                      ++  + +l G  GtGKt +l++l+ 
  gi|385805260|ref|YP_005841658.1| 31 NEGELLLLIGKTGTGKTSILNVLAG 55
                                      3445999*************99875 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0013
                            AAA_30  20 vavltGpAGtGKttalkalreaweaagg 47 
                                       + +l+Gp G+GKtt lk l  +++ + g
  gi|385805260|ref|YP_005841658.1| 268 IILLKGPNGSGKTTFLKLLSGIVRPKRG 295
                                       6789*************99988876644 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0     0.025       7.8       2      20 ..      37      55 ..      36     120 .. 0.85
   2 ?   -0.9   0.0       7.4   2.3e+03      51      87 ..     174     203 ..     145     236 .. 0.71
   3 !   11.6   0.3   0.00097       0.3       1      19 [.     269     287 ..     269     420 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.025
                            AAA_18  2 lltGtpGvGKttlakeLsk 20
                                      ll G+ G+GKt++ + L+ 
  gi|385805260|ref|YP_005841658.1| 37 LLIGKTGTGKTSILNVLAG 55
                                      689***********99964 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 7.4
                            AAA_18  51 rldedkldklldaleenssaleegknlvidghlaele 87 
                                       + +e++ ++++++l++       gk+++i gh a + 
  gi|385805260|ref|YP_005841658.1| 174 ESREGFKEVVFSLLKA-------GKTVIITGHGATFW 203
                                       4444444445555555.......78899999987665 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00097
                            AAA_18   1 IlltGtpGvGKttlakeLs 19 
                                       Ill G+ G+GKtt+ k Ls
  gi|385805260|ref|YP_005841658.1| 269 ILLKGPNGSGKTTFLKLLS 287
                                       899**************95 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   0.2    0.0028      0.87       2      22 ..      36      56 ..      35      66 .. 0.85
   2 !   10.8   0.1    0.0011      0.36       2      24 ..     269     292 ..     268     304 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0028
                                      EEEE--SSSSHHHHHHHGGGG CS
                             AAA_5  2 vlLvGppGtgKselaerlaaa 22
                                      +lL+G++GtgK+++   la  
  gi|385805260|ref|YP_005841658.1| 36 LLLIGKTGTGKTSILNVLAGN 56
                                      79************9998865 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0011
                                       EEEE--SSSSHHHHHHHGGGGB.S CS
                             AAA_5   2 vlLvGppGtgKselaerlaaal.n 24 
                                       +lL+Gp G+gK+++ + l+  +  
  gi|385805260|ref|YP_005841658.1| 269 ILLKGPNGSGKTTFLKLLSGIVrP 292
                                       79***************9988753 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.024       7.6      44      68 ..      32      56 ..      10      78 .. 0.81
   2 !   12.1   0.0   0.00044      0.14      47      71 ..     268     292 ..     257     305 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.024
                             Rad17 44 kkriLLisGPsGCgkstvvkvLske 68
                                      + ++LL+ G +G gk+ +++vL+ +
  gi|385805260|ref|YP_005841658.1| 32 EGELLLLIGKTGTGKTSILNVLAGN 56
                                      3469******************965 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00044
                             Rad17  47 iLLisGPsGCgkstvvkvLskelgi 71 
                                       i+L+ GP G gk+t +k Ls +  +
  gi|385805260|ref|YP_005841658.1| 268 IILLKGPNGSGKTTFLKLLSGIVRP 292
                                       89******************88765 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     0.013       4.1       5      26 ..      36      58 ..      33      81 .. 0.80
   2 ?    1.4   0.0       0.7   2.2e+02     109     139 ..     177     207 ..     173     232 .. 0.82
   3 !    9.2   0.1    0.0029      0.93       5      22 ..     269     286 ..     267     307 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.013
                            AAA_24  5 iliyGpsgiGKTtlakel.gpkp 26
                                      +l++G+ g+GKT++++ l g++p
  gi|385805260|ref|YP_005841658.1| 36 LLLIGKTGTGKTSILNVLaGNTP 58
                                      689***********998864444 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.7
                            AAA_24 109 eefrrllkklqelrknvifiahektrkdedp 139
                                       e f++++  l +++k+vi+++h  t +d  p
  gi|385805260|ref|YP_005841658.1| 177 EGFKEVVFSLLKAGKTVIITGHGATFWDNIP 207
                                       66889999999***********888777655 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0029
                            AAA_24   5 iliyGpsgiGKTtlakel 22 
                                       il+ Gp+g+GKTt++k l
  gi|385805260|ref|YP_005841658.1| 269 ILLKGPNGSGKTTFLKLL 286
                                       7899***********987 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0    0.0066       2.1       8      40 ..      24      54 ..      15      65 .. 0.73
   2 !   10.4   0.0    0.0016      0.51      21      39 ..     268     286 ..     251     297 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0066
                                      HHHHHHHHHCH..TEEEEEEESTTSSHHHHHHHHH CS
                              TsaE  8 ealgkklakal..gdvilLeGdLGaGKTtlvrgla 40
                                      +++  +    l  g+++lL G+ G+GKT +   la
  gi|385805260|ref|YP_005841658.1| 24 KNINFS----LneGELLLLIGKTGTGKTSILNVLA 54
                                      333333....344889************9988776 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0016
                                       EEEEEESTTSSHHHHHHHH CS
                              TsaE  21 vilLeGdLGaGKTtlvrgl 39 
                                       +ilL+G+ G+GKTt+ + l
  gi|385805260|ref|YP_005841658.1| 268 IILLKGPNGSGKTTFLKLL 286
                                       69*************9976 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   0.00012     0.038      10      56 ..      10      56 ..       1      67 [. 0.74
   2 ?    4.0   0.0       0.1        32      36      52 ..     269     285 ..     259     303 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00012
                             AAA_7 10 seilVptvdtvrysyllelllknkkpvllvGptGtGKtviikdllkk 56
                                      +++ +   +  ++   ++  l+++  +ll+G+tGtGKt+i++ l  +
  gi|385805260|ref|YP_005841658.1| 10 DNLSISYKNDEQIVKNINFSLNEGELLLLIGKTGTGKTSILNVLAGN 56
                                      55555555556666667788899999**************9876655 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.1
                             AAA_7  36 vllvGptGtGKtviikd 52 
                                       +ll Gp G+GKt+ +k 
  gi|385805260|ref|YP_005841658.1| 269 ILLKGPNGSGKTTFLKL 285
                                       7999********99875 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.4     0.042        13       2      21 ..      35      54 ..      34      57 .. 0.87
   2 !   12.0   0.1   0.00047      0.15       3      20 ..     269     286 ..     267     306 .. 0.83
   3 ?   -1.0   0.0       4.6   1.4e+03     112     152 ..     392     427 ..     375     428 .] 0.63

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.042
                                      CEEEEC-TTTCHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqkla 21
                                      l++l G+ G GKT  l  la
  gi|385805260|ref|YP_005841658.1| 35 LLLLIGKTGTGKTSILNVLA 54
                                      6899**********998765 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00047
                                       EEEEC-TTTCHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqkl 20 
                                       ++l+G++GsGKTt+l+ l
  gi|385805260|ref|YP_005841658.1| 269 ILLKGPNGSGKTTFLKLL 286
                                       899************866 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 4.6
                                       HHCTTTTT--EEEEEEECCCHHHHCTTSSCE..EEEE--TC CS
                             NACHT 112 lirkkllpeasllltvrpralrdleeqleeaivlevegfse 152
                                       +++k l  + +ll++++ ++     e+++++ v+ev+ +se
  gi|385805260|ref|YP_005841658.1| 392 IFKK-LSDSGRLLIISSHDRE---VEKVATE-VVEVNKLSE 427
                                       5555.4444444444444444...4777777.788888887 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0039       1.2       7      44 ..      20      55 ..      16      69 .. 0.81
   2 !    7.4   0.0     0.007       2.2      10      51 ..     256     295 ..     251     303 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0039
                                      HHHHHHH......HCTS-EEEEESTTSSCHHHHHHHHH CS
                              PIF1  7 kkvfdaiieavlnekgklfFvtGsgGtgKtflwkallk 44
                                      ++++++i    + ++g+l+ + G  GtgKt +++ l  
  gi|385805260|ref|YP_005841658.1| 20 EQIVKNI--NFSLNEGELLLLIGKTGTGKTSILNVLAG 55
                                      5566666..455699*****************998865 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.007
                                       HHHH......HCTS-EEEEESTTSSCHHHHHHHHHHCHCTCC CS
                              PIF1  10 fdaiieavlnekgklfFvtGsgGtgKtflwkallkklrsegk 51 
                                       f++i   ++ + ++++ ++G  G+gKt ++k l+ ++r+++ 
  gi|385805260|ref|YP_005841658.1| 256 FKNI--NLSFDGPGIILLKGPNGSGKTTFLKLLSGIVRPKRG 295
                                       5666..566678999**********************99754 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0     0.001      0.32      30      54 ..      30      54 ..       7      57 .. 0.84
   2 ?    5.1   0.0     0.047        15      35      50 ..     268     283 ..     263     295 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.001
                            AAA_25 30 lpagelallaGapgtGKttlaldla 54
                                      l +gel ll+G +gtGKt ++  la
  gi|385805260|ref|YP_005841658.1| 30 LNEGELLLLIGKTGTGKTSILNVLA 54
                                      789***************9987766 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.047
                            AAA_25  35 lallaGapgtGKttla 50 
                                       ++ll G+ g+GKtt++
  gi|385805260|ref|YP_005841658.1| 268 IILLKGPNGSGKTTFL 283
                                       7899**********98 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.032        10      17      40 ..      34      57 ..      19      75 .. 0.81
   2 !    9.4   0.0    0.0019       0.6       5      40 ..     256     290 ..     253     302 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.032
                        Zeta_toxin 17 klillgGqpGAGKselaellkdel 40
                                       l+ll G +G GK+++++ l+ ++
  gi|385805260|ref|YP_005841658.1| 34 ELLLLIGKTGTGKTSILNVLAGNT 57
                                      678999************998765 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0019
                        Zeta_toxin   5 lkdkkypsqerPklillgGqpGAGKselaellkdel 40 
                                       +k+++  s + P +ill G  G+GK++ ++ll   +
  gi|385805260|ref|YP_005841658.1| 256 FKNIN-LSFDGPGIILLKGPNGSGKTTFLKLLSGIV 290
                                       55555.77899*****************99987655 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.2     0.033        10       1      24 [.      35      58 ..      35     222 .. 0.88
   2 !   10.3   0.1    0.0019      0.59       2      18 ..     269     285 ..     268     292 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.033
                            AAA_33  1 lvllvGlpGsGKstlaerllkklg 24
                                      l+ll+G  G+GK+  +  l+ +++
  gi|385805260|ref|YP_005841658.1| 35 LLLLIGKTGTGKTSILNVLAGNTP 58
                                      6899*********99988876554 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0019
                            AAA_33   2 vllvGlpGsGKstlaer 18 
                                       +ll G++GsGK+t+++ 
  gi|385805260|ref|YP_005841658.1| 269 ILLKGPNGSGKTTFLKL 285
                                       7899**********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 ?    5.3   0.2     0.043        14       4      23 ..      36      55 ..      34      66 .. 0.85
   2 !   10.3   0.0    0.0013       0.4       3      29 ..     268     294 ..     266     304 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.043
                                      EEEEESTTSSHHHHHHHHHH CS
                             SRP54  4 illvGlqGaGKTttlaKLaa 23
                                      +ll+G +G+GKT+ l  La 
  gi|385805260|ref|YP_005841658.1| 36 LLLIGKTGTGKTSILNVLAG 55
                                      79***********9999885 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0013
                                       EEEEEESTTSSHHHHHHHHHHHHHHTT CS
                             SRP54   3 villvGlqGaGKTttlaKLaallkkeg 29 
                                       +ill G++G+GKTt l  L+ +++ + 
  gi|385805260|ref|YP_005841658.1| 268 IILLKGPNGSGKTTFLKLLSGIVRPKR 294
                                       89************9988887776664 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.1     0.004       1.3       4      24 ..      36      56 ..      34      75 .. 0.88
   2 ?    5.4   0.0     0.046        14       4      23 ..     269     288 ..     267     312 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.004
                         PduV-EutP  4 illiGkvgsGKttLtqalkge 24
                                      +lliGk+g+GKt++ + l g+
  gi|385805260|ref|YP_005841658.1| 36 LLLIGKTGTGKTSILNVLAGN 56
                                      689***********9999886 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.046
                         PduV-EutP   4 illiGkvgsGKttLtqalkg 23 
                                       ill G+ gsGKtt  + l+g
  gi|385805260|ref|YP_005841658.1| 269 ILLKGPNGSGKTTFLKLLSG 288
                                       8999**********999986 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1      0.28        87      27      45 ..     135     153 ..     129     183 .. 0.73
   2 ?    7.6   0.0     0.014       4.3      27      89 ..     345     394 ..     329     395 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.28
                           SbcCD_C  27 srssgtlSGGekqflayla 45 
                                       +r + tlS Ge+q+la l 
  gi|385805260|ref|YP_005841658.1| 135 ERTTFTLSAGETQKLAILS 153
                                       5667788889988887664 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.014
                           SbcCD_C  27 srssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                        +++++lS Ge+  l++l+ a      +s+         ++++DE   +lD+e+ +t+l++++
  gi|385805260|ref|YP_005841658.1| 345 AKKMKELSSGER-RLISLISA-----SLSH-------HPIILMDEPTVGLDPEYKSTVLDIFK 394
                                       667777777777.66666554.....2223.......248999**********9999999987 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00089      0.28       7      38 ..      19      52 ..      13      65 .. 0.71
   2 ?    2.6   0.0      0.25        78      21      43 ..     268     291 ..     256     299 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00089
                                      HHHHHHHHHHH....H-SEEEEE--TTSSTTHHHHH CS
                              PhoH  7 keQkeylealk....kndivfaiGpaGtGKtylava 38
                                       e  +++++++    + +++  iG++GtGKt +  +
  gi|385805260|ref|YP_005841658.1| 19 DE--QIVKNINfslnEGELLLLIGKTGTGKTSILNV 52
                                      44..44455444444889*************87554 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.25
                                       EEEEE--TTSSTT.HHHHHHHHHH CS
                              PhoH  21 ivfaiGpaGtGKt.ylavalavea 43 
                                       i+   Gp G+GKt +l +  ++  
  gi|385805260|ref|YP_005841658.1| 268 IILLKGPNGSGKTtFLKLLSGIVR 291
                                       78899*******736777777655 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0     0.008       2.5       7      37 ..      23      53 ..      17      77 .. 0.81
   2 ?    6.2   0.0     0.025       7.7      13      36 ..     262     284 ..     256     359 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.008
                            AAA_11  7 reaiksalseseitliqGPPGtgKTktivel 37
                                       ++i++ l+e e+ l+ G+ GtgKT+ +  l
  gi|385805260|ref|YP_005841658.1| 23 VKNINFSLNEGELLLLIGKTGTGKTSILNVL 53
                                      478899*******************876554 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.025
                            AAA_11  13 alseseitliqGPPGtgKTktive 36 
                                           ++i l++GP G+gKT+++ +
  gi|385805260|ref|YP_005841658.1| 262 SFDGPGIILLKGPNGSGKTTFL-K 284
                                       56677899***********875.3 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.48   1.5e+02       3      42 ..      34      77 ..      32      90 .. 0.74
   2 ?    1.6   0.0      0.85   2.7e+02      55      99 ..     150     197 ..     113     230 .. 0.71
   3 !    8.5   0.6    0.0062       1.9       4      22 ..     268     286 ..     266     423 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.48
                            AAA_14  3 kilvitGaRrvGKTtllkqlikell....vkkesilyinldder 42
                                      ++l++ G   +GKT +l+ l+ +      +k e  + in  d+r
  gi|385805260|ref|YP_005841658.1| 34 ELLLLIGKTGTGKTSILNVLAGNTPrlikAKVEGNVRINGIDPR 77
                                      578999999********999877666655555556666665555 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.85
                            AAA_14  55 lileklkeekktylflDEiqev......pewekalkslvdegknldvivtG 99 
                                       +il+++   + ++l++DE   +      +++++++ sl++ g +  vi+tG
  gi|385805260|ref|YP_005841658.1| 150 AILSRVLL-NAHVLLFDEPTTYldeesrEGFKEVVFSLLKAG-K-TVIITG 197
                                       33443222.467889999888888888899999999999988.3.688888 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0062
                            AAA_14   4 ilvitGaRrvGKTtllkql 22 
                                       i++++G+  +GKTt+lk l
  gi|385805260|ref|YP_005841658.1| 268 IILLKGPNGSGKTTFLKLL 286
                                       899************9876 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 ?    6.7   0.1     0.014       4.3       5      27 ..      35      57 ..      31      72 .. 0.83
   2 ?    6.5   0.0     0.016         5       5      26 ..     268     288 ..     266     308 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.014
                                      EEEEE-STTSSHHHHHHHHHHSS CS
                             SRPRB  5 avllvGlsdsGKTslftrLttds 27
                                       +ll+G + +GKTs+++ L  ++
  gi|385805260|ref|YP_005841658.1| 35 LLLLIGKTGTGKTSILNVLAGNT 57
                                      579**************998765 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.016
                                       EEEEE-STTSSHHHHHHHHHHS CS
                             SRPRB   5 avllvGlsdsGKTslftrLttd 26 
                                       ++ll G+  sGKT+++++L+ +
  gi|385805260|ref|YP_005841658.1| 268 IILLKGPNGSGKTTFLKLLS-G 288
                                       58999*********887765.4 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0     0.018       5.6       5      89 ..      40     161 ..      36     195 .. 0.84
   2 ?    6.7   0.1     0.019       5.9       1      19 [.     269     287 ..     269     293 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.018
                                       ESTTSSHHHHHHHHHCCSTCEEEE-HHHHCCSSSS..................................HHHHHHHH CS
                               dNK   5 GnIgaGKstlvklLskklgvkvfeEpvdkwtnvqk..................................nlLekfYk 47 
                                       G+ g GK++++++L+ ++    ++  v+ ++ +++                                   lL+++++
  gi|385805260|ref|YP_005841658.1|  40 GKTGTGKTSILNVLAGNT-PRLIKAKVEGNVRINGidprdspsevllrnvglvpqepsdgvigdtvedeVLLSLMFR 115
                                       899*************99.7888999999988888999999999999999999999999999999999888999997 PP

                                       S....HHHHHHHHHHHHHHHHHHHHHCHHSSS-EEEEES-HHHHHH CS
                               dNK  48 d....psrwsfalqtyvllsrlkqqlealatkqvvvleRsiysdry 89 
                                       +    +++w   ++ + l +r+  +l+a +t++  +l R   +++ 
  gi|385805260|ref|YP_005841658.1| 116 NddadVEGWLRLFNLERLYERTTFTLSAGETQKLAILSRVLLNAHV 161
                                       5333278899999999999999999999999999999998887774 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.019
                                       EEEEESTTSSHHHHHHHHH CS
                               dNK   1 ivveGnIgaGKstlvklLs 19 
                                       i + G+ g+GK+t++klLs
  gi|385805260|ref|YP_005841658.1| 269 ILLKGPNGSGKTTFLKLLS 287
                                       668899***********98 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.1    0.0087       2.7       9      30 ..      32      53 ..      24      68 .. 0.83
   2 ?    5.5   0.1     0.064        20      11      29 ..     267     285 ..     262     300 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0087
                            AAA_19  9 kekvllvtaGpGtGKTrvlkhi 30
                                      + ++ll+++  GtGKT +l+  
  gi|385805260|ref|YP_005841658.1| 32 EGELLLLIGKTGTGKTSILNVL 53
                                      467899************9875 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.064
                            AAA_19  11 kvllvtaGpGtGKTrvlkh 29 
                                       +++l+ ++ G+GKT+ lk 
  gi|385805260|ref|YP_005841658.1| 267 GIILLKGPNGSGKTTFLKL 285
                                       568899999******9986 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.055        17       2      21 ..      37      56 ..      36      75 .. 0.80
   2 ?    7.9   0.0     0.012       3.8       1      20 [.     269     288 ..     269     310 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.055
                      RNA_helicase  2 wlyGpsgeGKStlakeLaka 21
                                      +l G++g+GK+++ + La +
  gi|385805260|ref|YP_005841658.1| 37 LLIGKTGTGKTSILNVLAGN 56
                                      689************99865 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.012
                      RNA_helicase   1 iwlyGpsgeGKStlakeLak 20 
                                       i+l Gp+g GK+t+ k L+ 
  gi|385805260|ref|YP_005841658.1| 269 ILLKGPNGSGKTTFLKLLSG 288
                                       6899***********99764 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 ?    8.2   0.0    0.0075       2.4       8      42 ..      19      51 ..       5      63 .. 0.82
   2 ?    4.6   0.0     0.095        30      15      66 ..     259     312 ..     245     394 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0075
                                      HHHHHHHHT......TTSEEEEEESTTSTHHHHHH CS
                            ResIII  8 QeeaienlleklkskrdkrglikmaTGtGKTlvaa 42
                                       e++++n+  +l  ++ + +l+   TGtGKT ++ 
  gi|385805260|ref|YP_005841658.1| 19 DEQIVKNINFSL--NEGELLLLIGKTGTGKTSILN 51
                                      577788887777..6888899**********9875 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.095
                                       HT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.........-EEEEESSHHH CS
                            ResIII  15 lleklkskrdkrglikmaTGtGKTlvaaklierllkkgkee....kflflvprksl 66 
                                       +  ++  ++   +l+k + G+GKT  +  l   ++ k+++      +lf+ ++  l
  gi|385805260|ref|YP_005841658.1| 259 INLSF--DGPGIILLKGPNGSGKTTFLKLLSGIVRPKRGKIemshSALFIPDNPLL 312
                                       55555..36667899*********88766655555554433566444444444444 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0095         3      10      47 ..      21      58 ..      13      72 .. 0.77
   2 ?    4.3   0.0     0.092        29      18      43 ..     262     287 ..     250     308 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0095
                                      HHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHST CS
                   Sigma54_activat 10 elleqikkvaktdlsvlitGesGtGKellaraiheask 47
                                      +++++i+   +    +l+ G++GtGK+ + + +  +++
  gi|385805260|ref|YP_005841658.1| 21 QIVKNINFSLNEGELLLLIGKTGTGKTSILNVLAGNTP 58
                                      66777777777778899**********99887766555 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.092
                                       HCTSSS-EEEECSTTSSHHHHHHHHH CS
                   Sigma54_activat  18 vaktdlsvlitGesGtGKellaraih 43 
                                         + +  +l++G +G+GK+++ +++ 
  gi|385805260|ref|YP_005841658.1| 262 SFDGPGIILLKGPNGSGKTTFLKLLS 287
                                       55566679***********9988775 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0069       2.2      33      59 ..      28      53 ..       8      56 .. 0.80
   2 ?    3.9   0.1      0.09        28      42      58 ..     269     285 ..     252     288 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0069
                                      EEGGGS-.SEEEE--TTSSHHHHHHHH CS
                      FtsK_SpoIIIE 33 ldlkkmashllvaGatgsGKStalntL 59
                                      + l++ +  ll++G tg+GK+  ln+L
  gi|385805260|ref|YP_005841658.1| 28 FSLNEGE-LLLLIGKTGTGKTSILNVL 53
                                      5555555.6899*************98 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.09
                                       EEEE--TTSSHHHHHHH CS
                      FtsK_SpoIIIE  42 llvaGatgsGKStalnt 58 
                                       +l+ G  gsGK+t+l+ 
  gi|385805260|ref|YP_005841658.1| 269 ILLKGPNGSGKTTFLKL 285
                                       68899*********985 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1     0.084        26       7      42 ..      18      52 ..      12      63 .. 0.75
   2 ?    7.0   0.0    0.0092       2.9      26      48 ..     269     291 ..     257     311 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.084
                                      XXXXXXXXXXXXXE..EEEEEEEESTTSSHHHHHHH CS
                           G-alpha  7 idkslkaerkarkkkrevkllllGqseSGKsTilkq 42
                                       d+++ ++ +   ++ e  lll+G+ + GK++il+ 
  gi|385805260|ref|YP_005841658.1| 18 NDEQIVKNINFSLNEGE-LLLLIGKTGTGKTSILNV 52
                                      56667777555555344.499************986 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0092
                                       EEEEESTTSSHHHHHHHHHHHCS CS
                           G-alpha  26 llllGqseSGKsTilkqlkllyk 48 
                                       +ll G ++SGK+T+lk l  + +
  gi|385805260|ref|YP_005841658.1| 269 ILLKGPNGSGKTTFLKLLSGIVR 291
                                       8999************8876555 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 ?    1.6   0.0      0.41   1.3e+02      17      40 ..      30      53 ..      19      58 .. 0.78
   2 ?   -1.3   0.0       3.1   9.8e+02     130     175 ..     148     193 ..     119     196 .. 0.72
   3 ?    8.5   0.0    0.0034       1.1      22      45 ..     268     291 ..     258     405 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.41
                        KAP_NTPase 17 latpivvgLygkWGsGKssllnkl 40
                                      l ++  + L gk G+GK+s+ln l
  gi|385805260|ref|YP_005841658.1| 30 LNEGELLLLIGKTGTGKTSILNVL 53
                                      5666678889999*********87 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.1
                        KAP_NTPase 130 egasllavlsraaklkeeaplkklqteveelladmektLdalqkrl 175
                                       + a l+ vl +a+ l++++p + l +e  e +++ + +L ++ k++
  gi|385805260|ref|YP_005841658.1| 148 KLAILSRVLLNAHVLLFDEPTTYLDEESREGFKEVVFSLLKAGKTV 193
                                       444466677799*********9999999998888765555533333 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0034
                        KAP_NTPase  22 vvgLygkWGsGKssllnkledelk 45 
                                       ++ L+g+ GsGK+++l++l    +
  gi|385805260|ref|YP_005841658.1| 268 IILLKGPNGSGKTTFLKLLSGIVR 291
                                       689***************976555 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0     0.011       3.5       2      22 ..      37      57 ..      36      81 .. 0.90
   2 ?    4.1   0.0      0.13        42       2      59 ..     270     330 ..     269     416 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.011
                                      EEEEBTTTTHHHHHHHHHTS- CS
                         Dynamin_N  2 avvGsqSsGKSSvlnaLlged 22
                                      +++G++  GK+S+ln L g  
  gi|385805260|ref|YP_005841658.1| 37 LLIGKTGTGKTSILNVLAGNT 57
                                      689**************9975 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.13
                                       EEEEBTTTTHHHHHHHHHTS--S---SSS---S-EEEEECCT---CCS...SSEEEE...T CS
                         Dynamin_N   2 avvGsqSsGKSSvlnaLlgedilprgpnptTrrplelqlgeeeeaseravkeelkek...e 59 
                                       ++ G   sGK+++l  L g     rg++ ++   l +  +   + s+ + keel+ +    
  gi|385805260|ref|YP_005841658.1| 270 LLKGPNGSGKTTFLKLLSGIVRPKRGKIEMSHSALFIPDNPLLYFSKPTPKEELELFagnL 330
                                       5668889**********99887778888888777777776655555555555555554432 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 ?    9.6   0.1    0.0032         1       2      23 ..      36      57 ..      35      71 .. 0.87
   2 ?    2.1   0.1      0.66   2.1e+02       2      18 ..     269     285 ..     268     298 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0032
                                      EEEESSTTSSHHHHHHCHCT-C CS
                               Roc  2 vvlvGdsgvGKtsllkrfvedk 23
                                      ++l+G++g+GKts+l+ +  ++
  gi|385805260|ref|YP_005841658.1| 36 LLLIGKTGTGKTSILNVLAGNT 57
                                      689************9988765 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.66
                                       EEEESSTTSSHHHHHHC CS
                               Roc   2 vvlvGdsgvGKtsllkr 18 
                                       ++l G +g+GKt++lk 
  gi|385805260|ref|YP_005841658.1| 269 ILLKGPNGSGKTTFLKL 285
                                       5677*********9975 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1      0.74   2.3e+02      18      45 ..      25      52 ..      23      55 .. 0.89
   2 ?    8.6   0.0    0.0039       1.2      14      45 ..     256     285 ..     253     293 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.74
                            AAA_27 18 sldfsaeeadlhliyGpNEAGKstalrA 45
                                      +++fs +e +l l++G   +GK+++l+ 
  gi|385805260|ref|YP_005841658.1| 25 NINFSLNEGELLLLIGKTGTGKTSILNV 52
                                      688999999***************9975 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0039
                            AAA_27  14 ftdrsldfsaeeadlhliyGpNEAGKstalrA 45 
                                       f++ +l+f+   +++ l+ GpN +GK+t l+ 
  gi|385805260|ref|YP_005841658.1| 256 FKNINLSFD--GPGIILLKGPNGSGKTTFLKL 285
                                       566667776..9****************9975 PP

>> Pox_A32  Poxvirus A32 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1       0.1        32      16      33 ..      36      53 ..      26      58 .. 0.84
   2 ?    6.7   0.1     0.014       4.5      17      38 ..     270     290 ..     256     297 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.1
                           Pox_A32 16 lalvGgsGsGktvyLlsL 33
                                      l l+G++G Gkt  L  L
  gi|385805260|ref|YP_005841658.1| 36 LLLIGKTGTGKTSILNVL 53
                                      679*********988655 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.014
                           Pox_A32  17 alvGgsGsGktvyLlsLlrtlv 38 
                                        l G  GsGkt++L+ Ll+ +v
  gi|385805260|ref|YP_005841658.1| 270 LLKGPNGSGKTTFLK-LLSGIV 290
                                       567999*******97.666666 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.3     0.061        19       3      22 ..      37      56 ..      35      67 .. 0.83
   2 ?    6.3   0.1     0.033        10       2      20 ..     269     287 ..     268     302 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.061
                            AAA_28  3 vitGgestGKTtlleaLaar 22
                                       ++G  +tGKT++l+ La +
  gi|385805260|ref|YP_005841658.1| 37 LLIGKTGTGKTSILNVLAGN 56
                                      58999***********9965 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.033
                            AAA_28   2 ivitGgestGKTtlleaLa 20 
                                       i + G+ ++GKTt l+ L+
  gi|385805260|ref|YP_005841658.1| 269 ILLKGPNGSGKTTFLKLLS 287
                                       6788************997 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 ?    5.2   0.0      0.05        16      35      57 ..      35      57 ..       3      70 .. 0.80
   2 ?    4.5   0.1     0.085        27      36      54 ..     269     287 ..     262     297 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.05
                            RuvB_N 35 hvllyGpPGlGkttlakiiakel 57
                                       +ll+G  G Gkt++ +++a + 
  gi|385805260|ref|YP_005841658.1| 35 LLLLIGKTGTGKTSILNVLAGNT 57
                                      5799***************9775 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.085
                            RuvB_N  36 vllyGpPGlGkttlakiia 54 
                                       +ll Gp G Gktt+ k+++
  gi|385805260|ref|YP_005841658.1| 269 ILLKGPNGSGKTTFLKLLS 287
                                       89***********987765 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.5    0.0012      0.37       3      27 ..      37      63 ..      35      74 .. 0.79
   2 ?    2.2   0.1       0.6   1.9e+02       3      22 ..     270     289 ..     268     304 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0012
                                      EEEESTTSSHHHHHHHHHTS..TEEES CS
                          MMR_HSR1  3 aivGrpNvGKStLinaltge..kaivs 27
                                      +++G++ +GK++++n l g+  + i +
  gi|385805260|ref|YP_005841658.1| 37 LLIGKTGTGKTSILNVLAGNtpRLIKA 63
                                      68****************985533333 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.6
                                       EEEESTTSSHHHHHHHHHTS CS
                          MMR_HSR1   3 aivGrpNvGKStLinaltge 22 
                                       ++ G   +GK+t+++ l+g 
  gi|385805260|ref|YP_005841658.1| 270 LLKGPNGSGKTTFLKLLSGI 289
                                       6678999********99983 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.063        20      13      30 ..      32      49 ..      18      66 .. 0.80
   2 ?   -1.8   0.0         7   2.2e+03     119     149 ..     156     186 ..     129     204 .. 0.67
   3 ?    3.2   0.1      0.22        68      16      30 ..     268     282 ..     256     418 .. 0.64

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.063
                                      TTCEEEEEESTTSSHHHH CS
                                      xxxxxxxxxxxxxxxxxx RF
                              DEAD 13 gggdvlvaaeTGsGKTla 30
                                      +g+ +l+ ++TG+GKT +
  gi|385805260|ref|YP_005841658.1| 32 EGELLLLIGKTGTGKTSI 49
                                      7788999*********87 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 7
                                       CTTEEEEEEETHHHHHHTTTHHHHHHHHHHS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 119 lsqvrflVlDEadrlldqgfsdfinrilnql 149
                                       l +  +l +DE  ++ld++ ++  ++++ +l
  gi|385805260|ref|YP_005841658.1| 156 LLNAHVLLFDEPTTYLDEESREGFKEVVFSL 186
                                       4455678888888888886666666655444 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.22
                                       EEEEEESTTSSHHHH CS
                                       xxxxxxxxxxxxxxx RF
                              DEAD  16 dvlvaaeTGsGKTla 30 
                                        +l++++ GsGKT+ 
  gi|385805260|ref|YP_005841658.1| 268 IILLKGPNGSGKTTF 282
                                       567889999999975 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.023       7.4      44      66 ..      30      52 ..       9      61 .. 0.80
   2 ?    1.5   0.0      0.66   2.1e+02      96     155 ..     146     204 ..     126     210 .. 0.75
   3 ?    0.2   0.2       1.7   5.2e+02      50      63 ..     269     282 ..     264     288 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.023
                         IstB_IS21 44 iekkenivllGpsGvGKshlaia 66
                                      +++ e ++l+G +G+GK+ +   
  gi|385805260|ref|YP_005841658.1| 30 LNEGELLLLIGKTGTGKTSILNV 52
                                      56778899*********987655 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.66
                         IstB_IS21  96 dgklaralkrllkvdllilDdlgllpldqaeaellfeviekryerrsiiitsnlpfaewd 155
                                        +kla   + ll++++l+ D+   + ld++++e + ev+ +  +   ++i +      wd
  gi|385805260|ref|YP_005841658.1| 146 TQKLAILSRVLLNAHVLLFDEPT-TYLDEESREGFKEVVFSLLKAGKTVIITGHGATFWD 204
                                       55666677788899999999965.568999999999999888887777766666666666 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 1.7
                         IstB_IS21  50 ivllGpsGvGKshl 63 
                                       i+l Gp G GK+ +
  gi|385805260|ref|YP_005841658.1| 269 ILLKGPNGSGKTTF 282
                                       6789*******965 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1      0.28        89      23      47 ..      31      55 ..      22      64 .. 0.86
   2 ?    6.8   0.0    0.0081       2.6      28      55 ..     269     296 ..     263     305 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.28
                              DLIC 23 PsgksvlvlGedgsGkttliaklqG 47
                                        g  +l++G+ g+Gkt+++  l G
  gi|385805260|ref|YP_005841658.1| 31 NEGELLLLIGKTGTGKTSILNVLAG 55
                                      5567789************999887 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0081
                              DLIC  28 vlvlGedgsGkttliaklqGveeekkGr 55 
                                       +l+ G +gsGktt++  l G+  +k+G+
  gi|385805260|ref|YP_005841658.1| 269 ILLKGPNGSGKTTFLKLLSGIVRPKRGK 296
                                       6888*********************997 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 ?    4.3   0.1     0.088        28       3      25 ..      36      58 ..      34      77 .. 0.76
   2 ?    7.4   0.3    0.0097         3       3      19 ..     269     285 ..     267     297 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.088
                                      EEEEESTTCCHHHHHHHHHCT-- CS
                              cobW  3 tvltGflGsGKTtLlnhllenra 25
                                      ++l G  G+GKT++ln l  n+ 
  gi|385805260|ref|YP_005841658.1| 36 LLLIGKTGTGKTSILNVLAGNTP 58
                                      578899**********9885554 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0097
                                       EEEEESTTCCHHHHHHH CS
                              cobW   3 tvltGflGsGKTtLlnh 19 
                                       ++l G+ GsGKTt+l+ 
  gi|385805260|ref|YP_005841658.1| 269 ILLKGPNGSGKTTFLKL 285
                                       7899*********9975 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1     0.005       1.6      27      74 ..       9      54 ..       2      66 .. 0.76
   2 ?    0.8   0.0      0.73   2.3e+02      56      74 ..     269     287 ..     224     301 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.005
                            DUF815 27 lddLvgidkqkealventeqfleglpannvLLwGarGtGKSslvkall 74
                                      +d+L    k+ e++v+n++  l+  + + +LL+G+ GtGK s++  l 
  gi|385805260|ref|YP_005841658.1|  9 VDNLSISYKNDEQIVKNINFSLN--EGELLLLIGKTGTGKTSILNVLA 54
                                      56666666777888888876665..46779************987665 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.73
                            DUF815  56 vLLwGarGtGKSslvkall 74 
                                       +LL G  G+GK + +k l 
  gi|385805260|ref|YP_005841658.1| 269 ILLKGPNGSGKTTFLKLLS 287
                                       89**********9999765 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.2       1.8   5.5e+02       3      20 ..      37      54 ..      36      74 .. 0.79
   2 ?    5.1   0.0     0.061        19      83     155 ..     146     225 ..     120     238 .. 0.69
   3 ?    6.7   0.1      0.02       6.2       2      23 ..     269     290 ..     268     298 .. 0.83
   4 ?   -0.3   0.1       2.8   8.8e+02      78     105 ..     351     380 ..     327     426 .. 0.59

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.8
                                      EEE--TTSSHHHHHHHHH CS
                          NTPase_1  3 fiTGppGvGKtTlvkkvl 20
                                      ++ G+ G+GKt +++ ++
  gi|385805260|ref|YP_005841658.1| 37 LLIGKTGTGKTSILNVLA 54
                                      5779*******9998665 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.061
                                       HHHHHHHHHHHHHH-EEEE---STT..GGG-HHHHHHHHHHHTTTSEEEEE--SS-.....-SHHHHHHHT-TT-EE CS
                          NTPase_1  83 elalealrkalseadviviDEiGkm..ElkskkfkeaveevLksekpvlavihrrk.....dlalveeirerkdvkv 152
                                       +  l++l++ l +a v++ DE      E + + fke v  +Lk +k v+++ h ++     ++++ve  r+ ++v+v
  gi|385805260|ref|YP_005841658.1| 146 TQKLAILSRVLLNAHVLLFDEPTTYldEESREGFKEVVFSLLKAGKTVIITGHGATfwdniPKKIVELPRKAEEVNV 222
                                       555666666667777777777554334677789********************998865555566666565555554 PP

                                       EE- CS
                          NTPase_1 153 fev 155
                                        e 
  gi|385805260|ref|YP_005841658.1| 223 EEF 225
                                       443 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.02
                                       EEEE--TTSSHHHHHHHHHHHH CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlell 23 
                                       +++ Gp G+GKtT++k ++  +
  gi|385805260|ref|YP_005841658.1| 269 ILLKGPNGSGKTTFLKLLSGIV 290
                                       6789**********99887665 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 2.8
                                       HHHHHHHHHHHHHHHHHHH-EEEE--..-S CS
                          NTPase_1  78 vesfeelalealrkalseadviviDE..iG 105
                                       + s e+  ++ ++ +ls+  +i++DE  +G
  gi|385805260|ref|YP_005841658.1| 351 LSSGERRLISLISASLSHHPIILMDEptVG 380
                                       344677788888888888889999985444 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       5.7   1.8e+03       6      17 ..      43      54 ..      40      60 .. 0.84
   2 ?    1.3   0.0      0.74   2.3e+02      30      91 ..      92     158 ..      83     195 .. 0.80
   3 ?    5.9   0.0     0.028       8.9       3      19 ..     273     289 ..     271     303 .. 0.84
   4 ?   -0.0   0.1       1.9   5.9e+02     137     176 ..     328     366 ..     305     370 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 5.7
                                      TSSHHHHHHHHH CS
                   Thymidylate_kin  6 GaGKttqaellk 17
                                      G+GKt++++ l+
  gi|385805260|ref|YP_005841658.1| 43 GTGKTSILNVLA 54
                                      9******99987 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.74
                                       ESSSTTSHHHHHHHHHHH.....TCS---HHHHHHHHHHHHHHTTHHHHHHHHHTT-EEEEES-HHH CS
                   Thymidylate_kin  30 trepggteiGekirelll.....keeeleeqteallfaadriehleekikpalkqgktvivdRylfS 91 
                                        +ep+++ iG+++ + +l     ++ + + +  + lf  +r ++ ++    a + +k+ i++R l++
  gi|385805260|ref|YP_005841658.1|  92 PQEPSDGVIGDTVEDEVLlslmfRNDDADVEGWLRLFNLERLYERTTFTLSAGETQKLAILSRVLLN 158
                                       5799999999998764444777555555555599999999999999999999999999999998876 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.028
                                       ESTTSSHHHHHHHHHHH CS
                   Thymidylate_kin   3 GlDGaGKttqaellker 19 
                                       G +G+GKtt+++ll   
  gi|385805260|ref|YP_005841658.1| 273 GPNGSGKTTFLKLLSGI 289
                                       99**********99765 PP

  == domain 4  score: -0.0 bits;  conditional E-value: 1.9
                                       TTSSTTTSHHHHHHHHHHHHHHHHHHHH.TTSTEEEEETTS CS
                   Thymidylate_kin 137 krdeldeeeeeqldflrkvrerylelak.ederiliidask 176
                                        +   ++ee+e+l + + + ++++el   e+  i  i+as 
  gi|385805260|ref|YP_005841658.1| 328 GNL--KKEEKERLLKIKIFAKKMKELSSgERRLISLISASL 366
                                       333..48889999999999999****996666666777765 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 ?    7.3   0.1    0.0083       2.6       2      19 ..      36      53 ..      35      63 .. 0.88
   2 ?    2.4   0.1      0.27        84       2      17 ..     269     284 ..     268     293 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0083
                         Gtr1_RagA  2 vLLmGksgsGKtsmrsii 19
                                      +LL+Gk g GKts+ +++
  gi|385805260|ref|YP_005841658.1| 36 LLLIGKTGTGKTSILNVL 53
                                      89************9886 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.27
                         Gtr1_RagA   2 vLLmGksgsGKtsmrs 17 
                                       +LL G++gsGKt+  +
  gi|385805260|ref|YP_005841658.1| 269 ILLKGPNGSGKTTFLK 284
                                       79**********9766 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      0.98   3.1e+02      22      45 ..      39      62 ..      30      79 .. 0.77
   2 ?    6.3   0.1      0.01       3.2      23      41 ..     273     291 ..     250     326 .. 0.82
   3 ?    0.3   0.1      0.64     2e+02     476     511 ..     329     362 ..     318     416 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.98
                            AAA_13 22 YGwNGaGKTtLSrllrslelgete 45
                                       G+ G+GKT++ ++l+  + + ++
  gi|385805260|ref|YP_005841658.1| 39 IGKTGTGKTSILNVLAGNTPRLIK 62
                                      5999*******9999986555444 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.01
                            AAA_13  23 GwNGaGKTtLSrllrslel 41 
                                       G NG+GKTt+ +ll+ + +
  gi|385805260|ref|YP_005841658.1| 273 GPNGSGKTTFLKLLSGIVR 291
                                       99*********99998743 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.64
                            AAA_13 476 eLkfeeekkgYrivrkggsqaaetLSeGEktaIafl 511
                                       +Lk+ee++   +i +   +++ ++LS GE+ +I ++
  gi|385805260|ref|YP_005841658.1| 329 NLKKEEKERLLKIKIF--AKKMKELSSGERRLISLI 362
                                       5777777777777774..568899*******99875 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.053        17      16      33 ..      30      47 ..      20      52 .. 0.88
   2 ?   -2.4   0.0       7.8   2.5e+03     139     163 ..     174     198 ..     161     232 .. 0.75
   3 ?    2.7   0.2      0.21        66      21      35 ..     268     282 ..     261     289 .. 0.91
   4 ?   -1.7   0.0       4.8   1.5e+03      56     101 ..     374     419 ..     371     428 .] 0.66

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.053
                            ATPase 16 ipegrvvlitGepGtGKt 33
                                      + eg+  l+ G++GtGKt
  gi|385805260|ref|YP_005841658.1| 30 LNEGELLLLIGKTGTGKT 47
                                      678999***********9 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 7.8
                            ATPase 139 vaReilrqlvrvlkklgvTailvse 163
                                       + Re ++++v  l k g T i++  
  gi|385805260|ref|YP_005841658.1| 174 ESREGFKEVVFSLLKAGKTVIITGH 198
                                       5677777777777777888777754 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.21
                            ATPase  21 vvlitGepGtGKtif 35 
                                       ++l+ G  G+GKt+f
  gi|385805260|ref|YP_005841658.1| 268 IILLKGPNGSGKTTF 282
                                       799**********99 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 4.8
                            ATPase  56 veepaedlrenakslGwd.lekleeegklaiidasesaeesaeekdk 101
                                       ++ep + l  + ks   d ++kl ++g+l ii     + e+ + ++ 
  gi|385805260|ref|YP_005841658.1| 374 MDEPTVGLDPEYKSTVLDiFKKLSDSGRLLIISSHDREVEKVA-TEV 419
                                       6777777777777777774589999999999987766655433.444 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1     0.086        27      27      44 ..      37      54 ..      30      66 .. 0.88
   2 ?    0.4   0.2       1.8   5.7e+02      33      43 ..     276     286 ..     271     300 .. 0.80
   3 ?    3.2   0.1      0.26        82     122     210 ..     324     407 ..     302     422 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.086
                             DUF87 27 AilgsTGsGKSntvavLl 44
                                      + +g+TG+GK+    vL 
  gi|385805260|ref|YP_005841658.1| 37 LLIGKTGTGKTSILNVLA 54
                                      578********9999985 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.8
                             DUF87  33 GsGKSntvavL 43 
                                       GsGK+++ ++L
  gi|385805260|ref|YP_005841658.1| 276 GSGKTTFLKLL 286
                                       9******9987 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.26
                             DUF87 122 eealdqakakeekeklssdepveklleelkkekeelrklknqaiarlldkledllrkggsf.snsstdlialllekl 197
                                       e +  ++k++e++  l+++ + +k++e       ++r+l + + a+l+++   l++++    + + ++++ ++++kl
  gi|385805260|ref|YP_005841658.1| 324 ELFAGNLKKEEKERLLKIKIFAKKMKELSS----GERRLISLISASLSHHPIILMDEPTVGlDPEYKSTVLDIFKKL 396
                                       555556777777788888888888888777....9999999999999999999999999998999999999****** PP

                             DUF87 198 ekegkitiidlsg 210
                                       +++g++ ii  s+
  gi|385805260|ref|YP_005841658.1| 397 SDSGRLLII--SS 407
                                       ******996..44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      616  (0.0343577); expected 358.6 (0.02)
Passed Vit filter:                       113  (0.00630264); 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: 0.85u 0.39s 00:00:01.24 Elapsed: 00:00:00.56
# Mc/sec: 2311.71
//
Query:       gi|385805261|ref|YP_005841659.1|  [L=238]
Description: hypothetical protein FFONT_0216 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       980  (0.05466); 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:                         0  (0); expected 0.2 (1e-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 0.28s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1433.42
//
Query:       gi|385805262|ref|YP_005841660.1|  [L=320]
Description: radical SAM protein [Fervidicoccus fontis Kam940]
Scores for complete 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-12   46.4   0.0    7.7e-12   45.9   0.0    1.3  1  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.9   0.0   4.3e-16   7.7e-12       3     159 ..      26     185 ..      24     195 .. 0.80

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 4.3e-16
                                       EESEESS--TTTSCCTT.....HHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEE.SSTGGGSTTHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpet.....vrregrgrslsveeileevkelkaekg.vkevilg.ggepllypdfvellerlak 72 
                                       +++ C++ C++C+ ++t     +rre +     v ++++ v el   +g v++++++  gepll++++  ++ +++k
  gi|385805262|ref|YP_005841660.1|  26 PYKTCSYSCIYCQLGRTenfsiERREFYNWKEIVNDVERTVNEL---NGkVDYITFVpDGEPLLDKNIGIEISEIKK 99 
                                       6789**************65555555555555555555555555...566*******99****************** PP

                                       TCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT...CTSHHHHHHHHHHHHHHTTSETEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  73 lavpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn...rghtfeevlealeklreagikrvv 146
                                       +     +++v+tn  l++ e ++  l    d  s+ ++a+ ++ v +++n   ++ +++ +l++++ + +    + +
  gi|385805262|ref|YP_005841660.1| 100 R--VSPKVAVITNSSLLYLEGARSDLSES-DLASVKVDATRED-VWRRINrphPKLSLSSILDGIKEFSKTYRGKLI 172
                                       *..8*************877777777756.*************.55555533377778************977779* PP

                                       EEEEEBTTTSHHH CS
                                       xxxxxxxxxxxxx RF
                       Radical_SAM 147 drivglpGendee 159
                                       + ++++ G+n e+
  gi|385805262|ref|YP_005841660.1| 173 TETMLVDGVNSET 185
                                       ********99864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2166.15
//
Query:       gi|385805263|ref|YP_005841661.1|  [L=230]
Description: hypothetical protein FFONT_0218 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1492.12
//
Query:       gi|385805264|ref|YP_005841662.1|  [L=499]
Description: hypothetical protein FFONT_0219 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (499 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 3186.69
//
Query:       gi|385805265|ref|YP_005841663.1|  [L=511]
Description: hypothetical protein FFONT_0220 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-18   66.6  14.8    2.1e-18   66.6  14.8    2.0  2  ABC2_membrane_2  ABC-2 family transporter protein
  ------ inclusion threshold ------
      0.069   12.8   1.7       0.16   11.6   0.9    2.2  1  DUF2715          Domain of unknown function (DUF2715)
       0.14   11.7  24.5      0.045   13.3  17.6    2.5  2  ABC2_membrane_5  ABC-2 family transporter protein
       0.37   10.7  21.7       0.14   12.1  13.2    3.0  3  ABC2_membrane_4  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.4     0.019        83     160     189 ..      11      40 ..       9      95 .. 0.81
   2 !   66.6  14.8   4.6e-22   2.1e-18      76     287 ..     271     508 ..     105     509 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.019
                   ABC2_membrane_2 160 dllllvvasvlllllvvflalglllSsvar 189
                                       ++l+ + ++ l++++++ ++l+++lS+++ 
  gi|385805265|ref|YP_005841663.1|  11 SFLRPATLIALIVFILAGIGLSYMLSATLS 40 
                                       577777777777777788899999998775 PP

  == domain 2  score: 66.6 bits;  conditional E-value: 4.6e-22
                   ABC2_membrane_2  76 v.....................vstimavlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaig 131
                                                             +  ++a ++p+i + + + +ia+ +  g l++lL++Pv+R++i+     +g++  
  gi|385805265|ref|YP_005841663.1| 271 PveqytpgsvqrtvtslalgasGISLFAEFFPIIVLYIVYALIAKPRGMGALEFLLARPVTRWDIYYTRYAAGVLTT 347
                                       155555555566666666666656678899*********************************************97 PP

                   ABC2_membrane_2 132 la.iavallatvllalaiilalgivlaledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlai 207
                                       +  +av ++      l+ i+  g+ l++++++ll++ ++  l+  +f +l +++S+va  s + +al+++l++++ i
  gi|385805265|ref|YP_005841663.1| 348 ITsTAVFFTSF---VLGSIALIGYTLRAGQMVLLFLGVTGALV--AFYSLCYFISTVAS-SGRYLALSVFLYIFFTI 418
                                       76666666666...56677888999999999999888885555..88***********9.***************** PP

                   ABC2_membrane_2 208 lvpivlygvaellagpavp.....qeindflsllsptsayntllneilagsdlna.....lgstatnllilllllav 274
                                       + +i+++ va  l g +       q+++  l+++sp    +++   ++ + +l        +  a  +++ +l++av
  gi|385805265|ref|YP_005841663.1| 419 ILSIIASVVAFELYGTSGNlfdmlQKLRYELDYFSPLGLTEFASYFVSRSLSLAPsvassVINPALVIASGILWIAV 495
                                       ******875544443333377777*******************99999999877799995555566778899***** PP

                   ABC2_membrane_2 275 llvlgyvlFkrkD 287
                                       ++v g+++Fk++ 
  gi|385805265|ref|YP_005841663.1| 496 PFVAGWFIFKKAN 508
                                       **********975 PP

>> DUF2715  Domain of unknown function (DUF2715)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.9   3.5e-05      0.16      50      90 ..     346     380 ..      89     427 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.5e-05
                           DUF2715  50 fminadaAiggki......ltalvlsaqlLiGYtfrvgekfyltpai 90 
                                        +          i      +t++vl + +LiGYt+r g+ + l + +
  gi|385805265|ref|YP_005841663.1| 346 TT----------ItstavfFTSFVLGSIALIGYTLRAGQ-MVL-LFL 380
                                       33..........13333337*******************.332.223 PP

>> ABC2_membrane_5  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.6     0.032   1.4e+02     181     202 ..      16      37 ..       5      49 .. 0.69
   2 ?   13.3  17.6     1e-05     0.045      34     170 ..     291     429 ..     282     472 .. 0.62

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.032
                   ABC2_membrane_5 181 illiillviillliivSyfiSi 202
                                       + li l+v+il+ i +Sy++S+
  gi|385805265|ref|YP_005841663.1|  16 ATLIALIVFILAGIGLSYMLSA 37 
                                       5556666666777777777665 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 1e-05
                   ABC2_membrane_5  34 dsvllifsilslvisiililttlsyDekskwnkylltLPvtrkeiVksKYlfvlililiailitlllliiavlikgn 110
                                        s++ +f+ ++++i+ +++  ++++ +  +   +ll  Pvtr++i   +Y  +++ ++ ++ +++  ++++++    
  gi|385805265|ref|YP_005841663.1| 291 ASGISLFAEFFPIIVLYIVYALIAKPRGMGALEFLLARPVTRWDIYYTRYAAGVLTTITSTAVFFTSFVLGSIALIG 367
                                       444545555555555555889************************************99999999998888887777 PP

                   ABC2_membrane_5 111 vtise..vllsiliglvialiflaivlPlyfkfgvekgrivliiiifgiif..llvaifslskl 170
                                       +t++   ++l +l + +  ++f+++++ +    +   gr++++ +++ i+f  +l+ i s+  +
  gi|385805265|ref|YP_005841663.1| 368 YTLRAgqMVLLFLGVTGALVAFYSLCYFISTVAS--SGRYLALSVFLYIFFtiILSIIASVVAF 429
                                       6654411555555555555555555555555554..6776555555555443233333333222 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 ?    2.8   0.2     0.022        99      99     146 ..      18      65 ..       9      72 .. 0.80
   2 ?   12.1  13.2   3.1e-05      0.14      58     177 ..     299     418 ..     272     421 .. 0.77
   3 ?    2.6   1.4     0.026   1.2e+02      15      72 ..     411     465 ..     408     467 .. 0.62

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.022
                   ABC2_membrane_4  99 livllllsvllmlvtflitvlfallsgfvgfsvklvlellkkclelgl 146
                                       li+l++++++ + +++++++ +++ sg v+f++ + l++   +l + l
  gi|385805265|ref|YP_005841663.1|  18 LIALIVFILAGIGLSYMLSATLSMSSGTVSFDGYGSLNISSSVLNVQL 65 
                                       677888888888889999999999999999999888877776666555 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 3.1e-05
                   ABC2_membrane_4  58 lllplilgiiasylifrEeqndtlknLltiPvsrtklllaKlivllllsvllmlvtflitvlfallsgfvgfsvklv 134
                                        ++p+i+  i   li + +  + l  Ll +Pv+r  ++   +++ +l+++  + v+f++ vl ++ + +  + ++++
  gi|385805265|ref|YP_005841663.1| 299 EFFPIIVLYIVYALIAKPRGMGALEFLLARPVTRWDIYYTRYAAGVLTTITSTAVFFTSFVLGSIALIGYTLRAGQM 375
                                       4788888889999*************************************************998888887887776 PP

                   ABC2_membrane_4 135 lellkkclelgllvffavlpiia..lvllkksyvlpliltlvyti 177
                                       + l+    ++g+lv+f +l  ++  +++  +  +l++ l +++ti
  gi|385805265|ref|YP_005841663.1| 376 VLLFLG--VTGALVAFYSLCYFIstVASSGRYLALSVFLYIFFTI 418
                                       554442..4566666666654431144455556888888888887 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.026
                   ABC2_membrane_4  15 vwllvlaallvpllallyfnllgktgldpaefyslsvfgftlllllplilgiiasyli 72 
                                       ++ +++ ++l  +  +++f+l g   ++ + f +l+ + + l  + pl l+ +asy +
  gi|385805265|ref|YP_005841663.1| 411 FLYIFFTIILSIIASVVAFELYG---TSGNLFDMLQKLRYELDYFSPLGLTEFASYFV 465
                                       34445555555555566666544...44467777777888888888888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (511 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       960  (0.0535445); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.70u 0.36s 00:00:01.06 Elapsed: 00:00:00.54
# Mc/sec: 2865.51
//
Query:       gi|385805266|ref|YP_005841664.1|  [L=301]
Description: ABC transporter [Fervidicoccus fontis Kam940]
Scores for complete 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   81.5   0.0    2.8e-22   79.7   0.0    1.8  2  ABC_tran  ABC transporter
    2.7e-07   30.7   0.1    0.00012   22.0   0.0    2.2  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
  ------ inclusion threshold ------
      0.068   13.2   1.4        1.6    8.8   0.1    2.9  3  TRAM      TRAM domain
       0.12   12.1   0.0       0.43   10.3   0.0    1.8  2  AAA_30    AAA domain
       0.25   11.8   2.4       0.22   12.0   0.6    1.7  2  AAA_23    AAA domain
       0.35   10.3   3.1        1.8    8.0   0.0    2.4  3  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 !   79.7   0.0   9.5e-26   2.8e-22       2     136 ..      18     160 ..      17     161 .. 0.94
   2 ?   -0.7   0.0      0.61   1.8e+03      80     118 ..     233     271 ..     182     276 .. 0.71

  Alignments for each domain:
  == domain 1  score: 79.7 bits;  conditional E-value: 9.5e-26
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       +nvs+++++ge+v+ vG nGaGK+t +++  g l p++G++ +dg ++++ ++++++++ig++p+ p +  + ++ +
  gi|385805266|ref|YP_005841664.1|  18 ENVSFNVSNGEIVGYVGLNGAGKTTTIRVAVGVLPPDSGDVSIDGFSITR-DKRKASEKIGWVPELPIFETDFKALD 93 
                                       79************************************************.88889999*******99999998888 PP

                                       H.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                     e+++  +++l+++gl++  + ++    s +S+G+k+r ala +++++p+ +++DE  
  gi|385805266|ref|YP_005841664.1|  94 YfvylagyyglsssEAKKMGKEMLERFGLENALNMKL----SAFSQGMKKRFALAVSMINDPPNFIFDEVL 160
                                       89********9977677779999*****999999999....****************************75 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.61
                                       HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  80 esdeeiekalsklglkelkdtvvksspssLSgGqkqrva 118
                                       + d++  ++l+k+g + ++ + v  s  s+S G+ ++v 
  gi|385805266|ref|YP_005841664.1| 233 KIDDNTVNLLEKYGKVSKQGEYVVISSPSVSSGEVVKVL 271
                                       666777788888888888888888888888999888775 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   0.1    0.0025       7.4       5      47 ..      33      62 ..      33      86 .. 0.69
   2 !   22.0   0.0     4e-08   0.00012     229     297 ..     125     190 ..      81     194 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0025
                            AAA_21  5 iGpNgsGKSnLLdaldllarldrdvegltdelsggggirkips 47
                                      +G Ng+GK++ ++   ++              ++ +g  +i++
  gi|385805266|ref|YP_005841664.1| 33 VGLNGAGKTTTIRVAVGVL-------------PPDSGDVSIDG 62
                                      799*********9987763.............33334444444 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 4e-08
                            AAA_21 229 gqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                         +  ++ +S+G+k+ +al+++++ +++    +++DE+ ngL+P+ ++ + ++  + ++++  +++++H
  gi|385805266|ref|YP_005841664.1| 125 ALNMKLSAFSQGMKKRFALAVSMINDPPN---FIFDEVLNGLDPQGIAFFRDMAVDFKKRKKAILFSSH 190
                                       456667789******************66...*****************999998888889999****9 PP

>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.62   1.8e+03      17      27 ..      24      34 ..      16      51 .. 0.69
   2 ?    1.6   0.0     0.091   2.7e+02      20      42 ..     189     212 ..     183     219 .. 0.85
   3 ?    8.8   0.1   0.00054       1.6      23      52 ..     245     275 ..     239     277 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.62
                                      .TTSEEEEEET CS
                              TRAM 17 ksegegiGrtd 27
                                       s+ge++G++ 
  gi|385805266|ref|YP_005841664.1| 24 VSNGEIVGYVG 34
                                      57888888876 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.091
                                       SEEEEEET...TEEEEETT--T..T CS
                              TRAM  20 gegiGrtdn..gkvvfvpgdlpgIG 42 
                                       ++++G ++n  ++vvf+++++  IG
  gi|385805266|ref|YP_005841664.1| 189 SHILGEVQNiaDRVVFIHKGKV-IG 212
                                       67889999999*******9877.77 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.00054
                                       EEEET..TEEEEETT-..-T..TEEEEEEEEEE CS
                              TRAM  23 iGrtdn.gkvvfvpgd..lpgIGdfVeVkItkv 52 
                                       +G++ + g +v+++ +  ++  G++V+V ++k 
  gi|385805266|ref|YP_005841664.1| 245 YGKVSKqGEYVVISSPsvSS--GEVVKVLVEKG 275
                                       58888899*******97788..*********95 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00014      0.43      16      44 ..      25      53 ..      16      75 .. 0.80
   2 ?   -1.3   0.0      0.52   1.6e+03     129     152 ..     260     282 ..     259     287 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00014
                            AAA_30 16 sgdrvavltGpAGtGKttalkalreawea 44
                                      s+  ++  +G  G+GKtt++++++ ++  
  gi|385805266|ref|YP_005841664.1| 25 SNGEIVGYVGLNGAGKTTTIRVAVGVLPP 53
                                      445588899************99887655 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.52
                            AAA_30 129 asVeaGgvlrdlveaagigtaeLt 152
                                       +sV+ G+v++ lve +g ++ e++
  gi|385805266|ref|YP_005841664.1| 260 PSVSSGEVVKVLVE-KGLNVLEIK 282
                                       79**********95.788887775 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.6   7.4e-05      0.22       2      36 ..       2      44 ..       1      47 [. 0.77
   2 ?   -1.8   0.0       1.2   3.6e+03      70      84 ..     222     236 ..     173     293 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.4e-05
                            AAA_23  2 Lkienfrsf.......rdqeidFsk.gltlItGpNGaGKTTil 36
                                      ++i+n+ ++       ++++++ s+  ++  +G NGaGKTT +
  gi|385805266|ref|YP_005841664.1|  2 IEINNISKYfgnvkaiENVSFNVSNgEIVGYVGLNGAGKTTTI 44
                                      6788888888776555666666655279999**********87 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.2
                            AAA_23  70 kvkayveltfenkdg 84 
                                       +vk+++ +++ ++d+
  gi|385805266|ref|YP_005841664.1| 222 TVKPSIVIKLDKIDD 236
                                       333333333333222 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 ?    2.4   0.5      0.03        91      25      40 ..      28      43 ..       2      51 .. 0.69
   2 ?    8.0   0.0    0.0006       1.8     136     193 ..     132     185 ..     102     211 .. 0.73
   3 ?   -3.0   0.0       1.3     4e+03     104     130 ..     249     274 ..     220     278 .. 0.52

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.03
                                      SEEEEEESTTSSHHHH CS
                                      xxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnl 40
                                      ++   vG NG+GK+  
  gi|385805266|ref|YP_005841664.1| 28 EIVGYVGLNGAGKTTT 43
                                      3555799******975 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0006
                                       CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfi 193
                                       ++S G k+     + +A+ +++  p +++De+   LD + ++ + ++    +k+   i
  gi|385805266|ref|YP_005841664.1| 132 AFSQGMKKR----FALAVSMINDPPNFIFDEVLNGLDPQGIAFFRDMAVDFKKRKKAI 185
                                       556666654....4567889******************99998888876555554444 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 1.3
                                       ETTSEEEEEETTEEE-HHHHHHHHHCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 104 krkgeseykingkevtkkevsellesa 130
                                       +++g   + i   +v++ ev ++l ++
  gi|385805266|ref|YP_005841664.1| 249 SKQG-EYVVISSPSVSSGEVVKVLVEK 274
                                       2222.2444555555555665555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
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 0.27s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1869.15
//
Query:       gi|385805267|ref|YP_005841665.1|  [L=519]
Description: N-methylhydantoinase B [Fervidicoccus fontis Kam940]
Scores for 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-180  601.6   0.1   1.2e-180  601.4   0.1    1.0  1  Hydantoinase_B  Hydantoinase B/oxoprolinase


Domain annotation for each model (and alignments):
>> Hydantoinase_B  Hydantoinase B/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  601.4   0.1  6.7e-185  1.2e-180       4     513 ..       3     515 ..       1     517 [. 0.96

  Alignments for each domain:
  == domain 1  score: 601.4 bits;  conditional E-value: 6.7e-185
                    Hydantoinase_B   4 tlevfrnrlmsiaeemgrtlqrtaiSpnikerlDfscalfdadgelvaqaphipvhlgsmseavkavlekf..eg.e 77 
                                         e++ +  + iaeemg  l+r+a+Spni+er+D sca+ ++dg++vaqa+hipvhlgs+   ++++l  +  +g  
  gi|385805267|ref|YP_005841665.1|   3 AWELIYKTTSYIAEEMGISLKRSAFSPNIRERMDHSCAVANEDGKIVAQAEHIPVHLGSFRVGLEKLLFFIqqNGiA 79 
                                       5688889999********************************************************99544432367 PP

                    Hydantoinase_B  78 lkpGDvlltNdPyaggtHlpDitvitPvfhegelvffvasraHhaDiGGitpGsmppdateifeEGlrippvklvee 154
                                       +++GD++++NdPy  gtHl+Di++++Pvfh+g+l+++v+++aHh+D+GG +pGs++pda++i+eEGl+ipp+klv++
  gi|385805267|ref|YP_005841665.1|  80 IEEGDIIAVNDPYISGTHLNDIMLLAPVFHHGRLIGYVVNKAHHVDVGGPVPGSINPDAKSIYEEGLIIPPIKLVKK 156
                                       ***************************************************************************** PP

                    Hydantoinase_B 155 geleedvlelllanvRtpednlgDlkAqiaanqvgerrlkelieeyGldtveaamdeildnaeravraalaelpdgt 231
                                       g+ + + l+++++nvRtp+ +++Dl+Aqiaa  vg  r+ke+ie+yG+++v++ +++ +++++    +++ ++++g+
  gi|385805267|ref|YP_005841665.1| 157 GKIDGEALRFIAENVRTPQSVIADLHAQIAADLVGTVRVKEMIEKYGVENVQNSWEKSIEYSRILSLKQIDSWKKGE 233
                                       ***************************************************************************** PP

                    Hydantoinase_B 232 yeaedyl..dd.gipikvtvtidgdeatvDftgtspqvkgniNaplavtlsaviyvlrclvdediplNeGclrpiev 305
                                        +aed +  dd +i i+ +v+i+   + +Df+g+s+qv+ ++Na++ vt +a  y +r+l++ed+p+NeG+++ ++v
  gi|385805267|ref|YP_005841665.1| 234 ASAEDCVelDDrDIAIRANVSISSRGVDIDFSGSSKQVAAPLNAVFGVTFAASSYSVRALLEEDVPTNEGFYSIVNV 310
                                       *****76667768**************************************************************** PP

                    Hydantoinase_B 306 klpegsllnpsepaavvggnvetsqrvvdvvlkalaqalpervaAasqgtmnnltfggvderggeffgyyetiagGa 382
                                       +++egs+lnp++pa+v+ggn etsqr+vd+v+kal+ +lpe+++Aa++gtm n+++gg+ e gg+ ++yyeti+gG+
  gi|385805267|ref|YP_005841665.1| 311 RAEEGSVLNPRKPAPVSGGNLETSQRIVDTVFKALSYILPEKIPAAGSGTMMNVMLGGYIE-GGRSWAYYETIGGGT 386
                                       **********************************************************987.88899********** PP

                    Hydantoinase_B 383 GArpgkdGasavhvhmtntrntdvEilErryPvlverfelrpdsgGaGkyrGGdGvvreieflepevtvsilserrv 459
                                       GArpgkdG+s+vhv+mtnt nt++Ei Er yP++++++++r++sgG+GkyrGGdG++r +++lep + ++i+++r +
  gi|385805267|ref|YP_005841665.1| 387 GARPGKDGVSGVHVNMTNTMNTPIEIAERSYPIIFTEYRIREGSGGKGKYRGGDGIIRAFRVLEP-AYLAIIGDRFK 462
                                       ****************************************************************9.*********** PP

                    Hydantoinase_B 460 fapwGlaGGepGargrvvlnllvr..geeenlggkatvelkagdvlvietpGGGGy 513
                                         p+Gl GG++G++ rv +   vr  g++e+ g+k +  l +gd ++ietpGGGG 
  gi|385805267|ref|YP_005841665.1| 463 RGPYGLWGGGSGKPARVQV---VRksGKIEENGSKFKEMLGEGDEVIIETPGGGGM 515
                                       ****************554...3345888888999999*****************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (519 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); 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: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 3162.94
//
Query:       gi|385805268|ref|YP_005841666.1|  [L=656]
Description: 5-oxoprolinase [Fervidicoccus fontis Kam940]
Scores for 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-99  330.3   3.5    2.1e-97  325.9   0.1    3.1  4  Hydantoinase_A  Hydantoinase/oxoprolinase
    1.3e-46  158.6   0.0    3.4e-45  153.9   0.0    2.4  2  Hydant_A_N      Hydantoinase/oxoprolinase N-terminal region


Domain annotation for each model (and alignments):
>> Hydantoinase_A  Hydantoinase/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.6   0.8    0.0072        65      80      98 ..       3      21 ..       1      26 [. 0.89
   2 ?   -3.0   0.0      0.39   3.5e+03     176     223 ..     133     178 ..     128     180 .. 0.45
   3 !  325.9   0.1  2.4e-101   2.1e-97       1     290 [.     195     486 ..     195     487 .. 0.99
   4 ?   -0.6   0.0     0.071   6.3e+02     241     284 ..     517     560 ..     494     563 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.0072
                    Hydantoinase_A 80 kvItfDmGGTstDvslikd 98
                                      kv+++D+GGT tD   ikd
  gi|385805268|ref|YP_005841666.1|  3 KVVGIDTGGTFTDFVYIKD 21
                                      799***********99986 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.39
                    Hydantoinase_A 176 qpedfls.gpdgdqkldvelarraf.eelakelnlkveevAegilsvave 223
                                        +e+    g     kl++  +   + + l   +n + e++Ae+ils+ ve
  gi|385805268|ref|YP_005841666.1| 133 REEQIEEiG----SKLKEAGVSSVAiSFLHSYINPSHEKTAERILSKYVE 178
                                       444333111....2333333322222444455555577888888777665 PP

  == domain 3  score: 325.9 bits;  conditional E-value: 2.4e-101
                    Hydantoinase_A   1 rtetavvnAylspilreylesvekslekrgakarlmvmqsdGglvsadearkkpvetilSGPaaGvvgaaatsklag 77 
                                       rt++a+vnA+l+pi+++y+e+++k+l++ ++ ++l+vm+s+Gg+v+a+ea+k+pv++++SGPaaGvv+ a++ ++ g
  gi|385805268|ref|YP_005841666.1| 195 RTSSALVNAALMPIISKYIERLNKRLKELNV-KELLVMSSSGGIVDAEEASKRPVQLVESGPAAGVVATAELCRMMG 270
                                       89**************************887.99******************************************* PP

                    Hydantoinase_A  78 ekkvItfDmGGTstDvslikdgevevsletei............agvkvrlpaldirtvgagGgsilvvdeggklrv 142
                                        +k+I fDmGGT++++ +i + e+e+++e+e+            +g+ vr+p++d+++v+agGg+i+++d++g+lr+
  gi|385805268|ref|YP_005841666.1| 271 INKAISFDMGGTTAKAGTIVNYEFEITSEYEVggesnhgrmikgSGYSVRFPFIDLAEVSAGGGTIIWRDDAGALRI 347
                                       ***************************************************************************** PP

                    Hydantoinase_A 143 gpesagadpgpacyrkGgteltvTDanlvLGrlqpedflsgpdgdqkldvelarrafeelakelnlkveevAegils 219
                                       gp+sagadpgpacy++Gg+ +t+TDanlvLGr+ ++ +l   +g++k++++la +a++ l++++     e+A++ ++
  gi|385805268|ref|YP_005841666.1| 348 GPKSAGADPGPACYDRGGKYPTLTDANLVLGRIGES-LL---GGKMKIRKDLAIKALSSLGEPV-----EIANRSIK 415
                                       ***********************************9.89...9********************9.....******** PP

                    Hydantoinase_A 220 vavenmanavrklsvergldpkeltlvvfGGaGaqhaaalaeelgvkkvivppyagvlsalGmalAdvree 290
                                       +a  +ma+a+r ++verg dp+e++l++fGGaG+q+aa+la+e+g+kk+++pp++gv+salG+++Ad+r e
  gi|385805268|ref|YP_005841666.1| 416 LADLEMARAIRLVTVERGIDPEEFVLFAFGGAGPQFAAELANEIGIKKIVIPPHPGVFSALGLLMADWRFE 486
                                       *******************************************************************9975 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 0.071
                    Hydantoinase_A 241 keltlvvfGGaGaqhaaalaeelgvkkvivppyagvlsalGmal 284
                                        +++ v + G G  ++  +   +++k++  +  ++ +s++G++l
  gi|385805268|ref|YP_005841666.1| 517 IRYADVRYVGQGWELTVPVGSPVDIKEIKKTFNKKHFSTYGFML 560
                                       4577788889999999999999*******************976 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 !  153.9   0.0   3.8e-49   3.4e-45       2     177 ..       5     176 ..       4     177 .. 0.95
   2 ?    2.0   0.0     0.017   1.5e+02      86     142 ..     490     548 ..     488     552 .. 0.86

  Alignments for each domain:
  == domain 1  score: 153.9 bits;  conditional E-value: 3.8e-49
                        Hydant_A_N   2 igIDvGGTfTDavaldekeeevavlKllstpdavaegirealeevleesiprtskidvvrmGTTvatNallerkg.. 76 
                                       +gID+GGTfTD+v+++++ +++  +K lstp+ ++ +++e l+ +        +  ++v+++TT+ tNa+  + g  
  gi|385805268|ref|YP_005841666.1|   5 VGIDTGGTFTDFVYIKDD-GSIGFFKSLSTPKSPEDAVIEGLKAL--------GSGETVIHATTLGTNAIRGQFGie 72 
                                       8***************77.*************************8........34589******************* PP

                        Hydant_A_N  77 .ervaLittkgfrdlleigrqnrpdlfelrik..kplvlyeevvevderveadgevlkpldeeevrealkalkaagv 150
                                        ++++L+tt+gf+ ++eigrqnrp+l++  ++  kplv ++ ++e++er++a g+vl++++ee+++e+ ++lk+agv
  gi|385805268|ref|YP_005841666.1|  73 iPKLSLVTTRGFKGVIEIGRQNRPKLYDIFFEkpKPLVERDFIFEANERIDAFGRVLEKIREEQIEEIGSKLKEAGV 149
                                       ***************************9555588999**************************************** PP

                        Hydant_A_N 151 esiavvllhSylnpehElrvaeiarei 177
                                       +s+a+++lhSy+np+hE+ +++i++++
  gi|385805268|ref|YP_005841666.1| 150 SSVAISFLHSYINPSHEKTAERILSKY 176
                                       ***********************9886 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.017
                        Hydant_A_N  86 gfrdlleigrqnrpdlfelrik..kplvlyeevvevderveadgevlkpldeeevreal 142
                                        f++++e+++ n ++   +++   +  + y +v  v ++ e+++ v +p+d +e++++ 
  gi|385805268|ref|YP_005841666.1| 490 AFPKDIEMAYRNMEEKLLKKVGrvDYFIRYADVRYVGQGWELTVPVGSPVDIKEIKKTF 548
                                       689999999999888766666568999****************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (656 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      597  (0.033298); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.70u 0.35s 00:00:01.04 Elapsed: 00:00:00.49
# Mc/sec: 4020.81
//
Query:       gi|385805269|ref|YP_005841667.1|  [L=139]
Description: hypothetical protein FFONT_0224 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.27    9.4   0.1       0.33    9.2   0.1    1.0  1  Red1      Rec10 / Red1


Domain annotation for each model (and alignments):
>> Red1  Rec10 / Red1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1   1.8e-05      0.33      94     160 ..      14      86 ..      11      91 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 1.8e-05
                              Red1  94 vtkliwelfg.svkknigsiklvkyitelgesellnlslssleydesi..yiqviyek...lyLwlgegfflk 160
                                       ++ + w+ ++ sv++ni ++  +  + +++   +++ s   l+y   +  y+ ++y++   +y+w+g+ f  +
  gi|385805269|ref|YP_005841667.1|  14 ICAFAWSYYKmSVLSNIANLNYSESLESNKALAIPSMSYVTLNYTLPYagYLKISYSStsaIYIWIGSNFSQQ 86 
                                       68899999877***************************99999998666699999987666*******98655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.32s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 879.65
//
Query:       gi|385805270|ref|YP_005841668.1|  [L=301]
Description: dihydrodipicolinate synthase [Fervidicoccus fontis Kam940]
Scores for complete 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-69  233.9   0.0    1.7e-69  233.8   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 !  233.8   0.0   9.3e-74   1.7e-69       1     287 [.       4     295 ..       4     297 .. 0.97

  Alignments for each domain:
  == domain 1  score: 233.8 bits;  conditional E-value: 9.3e-74
                                       --SEEEEE----B-TTSSB-HHHHHHHHHHHHHCT-SEEEESSCCCTGGGS-HHHHHHHHHHHHHHHTTSSEEEEE- CS
                             DHDPS   1 kfsgiitalvtpfdedgkldkealrklieflinkgvdglvvaGttGEsatlsteekeqlveiaveaakgripviagv 77 
                                       kf g+it+ +tpf+ed  ld  ++r l++++ + gv g++   ttGE+  ls ee ++l  ++ e+++g++ +i g+
  gi|385805270|ref|YP_005841668.1|   4 KFYGVITPFITPFKEDLSLDLDSARWLARYQAEGGVHGIFPNSTTGEFVHLSKEEAVKLTGTVLEEVGGKVWIIPGI 80 
                                       588************************************************************************** PP

                                       --SSHHHHHHHHHCCCCCT-SEEEEE---SS---HHHHHHHHHHHHHCHSS-EEEEE-HHHHSHHHHHHHHHHHHT. CS
                             DHDPS  78 GsnstseaiklakkaeeaGadgvlavtPYYnkpsqeglyqhfkaiieatdlpvilYnvpsrtgadlspetvkrLae. 153
                                        +nst+++i+l++ ++++G+ g ++ +P++ k+s e l+ hf  ++e  dlp+i+Yn+ps tg ++ +    +L+e 
  gi|385805270|ref|YP_005841668.1|  81 SANSTEDSISLGRIFKNMGVSGTIITPPFFFKVSGERLKLHFSMVAERVDLPIIIYNIPSATGINIPISLYRELSEe 157
                                       ***************************************************************************99 PP

                                       STTEEEEEE-SS-C...THHHHHHCCCSTTSEEEES-GGGHHHHHHTT-SEEEESCHHCHHHHHHHHHHHHHTT-HH CS
                             DHDPS 154 lenivgvKeavgdl...eevikikkevgkdlviysGddelllsalslGadGvisvtsniagermrqlikalkeGdla 227
                                       ++nivg K + +++   + +i+ +k+v++d++i+ G+d++ll+ l +G+dG i + +n a+++ r++++ ++eG ++
  gi|385805270|ref|YP_005841668.1| 158 YSNIVGAKVTYENFtylRGLIQEVKSVREDFSILVGFDDMLLPNLMMGGDGGIMALANAAPKIHRNVYDFWREGSFE 234
                                       *************95555678889999************************************************** PP

                                       HHHHHHHHHHHHHHHCCCC.SCCHHHHHHHHCTTSSSBB.--TTS--S-HHHHHHHHHHHH CS
                             DHDPS 228 eaaelnekllplikilfae.pnvilvktalellGlvveatlrkPltpleeeekeeleallk 287
                                       +a e  +kll+l k +    +++  vkt l ++G +v++++r+Pltp  +e  ++++++++
  gi|385805270|ref|YP_005841668.1| 235 KALEWWKKLLELTKVYDIStSFPTAVKTLLSVMGSPVKPYVRPPLTPERDEVVQKVRKIAE 295
                                       ***************96655************************************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); 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: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1935.35
//
Query:       gi|385805271|ref|YP_005841669.1|  [L=612]
Description: aldehyde:ferredoxin oxidoreductase [Fervidicoccus fontis Kam940]
Scores for complete 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-117  392.2   0.0     3e-117  391.9   0.0    1.1  1  AFOR_C    Aldehyde ferredoxin oxidoreductase, domains 2 & 3
    2.2e-77  259.4   0.1    3.5e-77  258.8   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 !  391.9   0.0  3.4e-121    3e-117       5     382 .]     223     603 ..     219     603 .. 0.95

  Alignments for each domain:
  == domain 1  score: 391.9 bits;  conditional E-value: 3.4e-121
                                       HHHHHHHHSH.HHHHHHHH-GGGHHHHHHHTT---BTTTTBS--TTGGGGSHHHHHHHTEEEE.E-TT-SS--EEEE CS
                            AFOR_C   5 kiqkeiksspqvtaelrkyGTaelvnianetgalptknfqegtfekaekisgealeekylvknegCfsCpiaCgrev 81 
                                       k+  ei+s+p +t+  r yGT  +v +  ++g +ptk++q++ f+ a+k++g+al+eky vk  +C++CpiaCg+e+
  gi|385805271|ref|YP_005841669.1| 223 KAIAEIESNP-TTHMSRLYGTLDYVAAGMSYGDVPTKYYQDSIFP-AYKLNGKALREKYYVKPIACTGCPIACGKEI 297
                                       677899****.777******************************9.*****************99************ PP

                                       E.......ET.EE---HHHHHHHTGGGT---HHHHHHHHHHHHHHTB-HHHHHHHHHHHHHHHHTTSS-HHHHTS-- CS
                            AFOR_C  82 kveegkk.vk.vegpeyetlaalGsnlgiddleailklnelcdelGlDtisaGntiafamelyekGllkkedtdgle 156
                                       ++  gk+  +  +  eyet+aa+G+ +giddl+a +++n+lc+ +G+DtisaG+ +afam +yekG l+ke+++gle
  gi|385805271|ref|YP_005841669.1| 298 EF--GKYgLEkADTLEYETAAAFGPLCGIDDLDALIYINYLCNAYGMDTISAGASVAFAMNAYEKGKLTKEKLGGLE 372
                                       *8..5554457999*************************************************************** PP

                                       --TT-THHHHHHHHHHHTT-TTHHHHTT-HHHHHHCTT.-GGG--EETTEE--SS-GGG-HHHHHHHHH-TTSS-SG CS
                            AFOR_C 157 lefgdaeallellekiAkregigdllAeGvkrlaeklg.aeelamhvkGlelpaydprgakgmalaYatsnrGacHl 232
                                        ++gd++ ++el+++iA+r++ig +lAeG+k +a klg +   ++ vkGle+p++dpr+   +al+Yats+rGacH+
  gi|385805271|ref|YP_005841669.1| 373 AKWGDKDVAIELVHMIANRKSIGGILAEGTKVAASKLGiEDGEVAVVKGLEIPMHDPRAFSMQALTYATSTRGACHM 449
                                       **************************************544459999****************************** PP

                                       GG-THHHH..........S---TT--.HHHHHHHHHHHHHHHHHHHHT--GGGG-HHH......HHHHHHHHHT--- CS
                            AFOR_C 233 rayliale..........ekvdplet.egkaelvkwfqdltalvdslglCkftseaeerldlelyakllsavtGidv 298
                                       r   +++e          +++d+++   +k+e ++ fq++++++dsl+lCkf++      +l+ ++k++sa+tG++v
  gi|385805271|ref|YP_005841669.1| 450 RPDYFTVEigqeipelgiRQTDRFASnPEKVESFIKFQNVREVYDSLILCKFSA-----NSLTTISKFYSAITGVKV 521
                                       *777777789********99****9977**************************.....57999************* PP

                                       -HHHHHHHHHHHHHHHHHHHHHHT--HHHS---HHHHHS---SSTTTT---..-HHHHHHHHHHHHT--T.TS---H CS
                            AFOR_C 299 teeellkaGeRiynleRlfnlreGltrkddtlperlleeplkegpakgkvledeleemldeyYelrGWde.tGvPtk 374
                                       +++e+   GeRiyn++R +nlr+G++++d +lp+ +l   +k g  +g+v+  ++eeml+ yY++r  d+ tG+P k
  gi|385805271|ref|YP_005841669.1| 522 EPKEFNVLGERIYNIKRSINLRLGMRKEDEKLPKIIL-RSIKRGGTQGNVP--NIEEMLRHYYAMRKIDPvTGKPMK 595
                                       *************************************.78999*******9..8*********************** PP

                                       HHHHHCT- CS
                            AFOR_C 375 etlkrLgL 382
                                       e+l++LgL
  gi|385805271|ref|YP_005841669.1| 596 EKLEELGL 603
                                       *******8 PP

>> AFOR_N  Aldehyde ferredoxin oxidoreductase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  258.8   0.1   3.9e-81   3.5e-77       1     197 [.       7     205 ..       7     206 .. 0.98

  Alignments for each domain:
  == domain 1  score: 258.8 bits;  conditional E-value: 3.9e-81
                                       SEEEEEETTTTEEEEEE--HHHHHHH-SCHHHHHHHHHHHS-TTS-TTSTTS-EEEEE-TTTTSSSTTB-EEEEEEE CS
                            AFOR_N   1 gkilrvdLstgkieveelpeelaekylGgrglaakllldevppgvdplspenplvfatGpltgtpapgsgrlvvvak 77 
                                       gkil+vdLstg+i++ el+ee+a++++Gg+glaa+ll+d +++++dplsp+ pl+f tG +tg+++p+s+r++++ak
  gi|385805271|ref|YP_005841669.1|   7 GKILKVDLSTGTIKTLELSEEMAKSFVGGSGLAAALLYDILTRDLDPLSPDSPLLFITGSFTGSKVPSSSRYAICAK 83 
                                       79*************************************************************************** PP

                                       -TTTSSEEEEEEETCHHHHHHHCT-SEEEEES--SS-EEEEEETTEEEEEE-TTTTTS-HHHHHHHHHHHHTS..EE CS
                            AFOR_N  78 sPltgtlgesnaGgrfgaelkraGydaivieGkaekpvylvieddkveiedaedlwgldtyettealkeelgd..kv 152
                                       sPltg +ges+aGg+f a lk +Gyd+i + G+++kpvyl+++++++ei+da+dlwgl+tyet+ea+++elg+  kv
  gi|385805271|ref|YP_005841669.1|  84 SPLTGLWGESTAGGHFPASLKLSGYDGILFVGRSSKPVYLFVHNGEAEIKDASDLWGLTTYETQEAIRDELGRdvKV 160
                                       *************************************************************************9999 PP

                                       EEE-HHHHTT-TTB-E.EETTEEE-SSSHHHHHHHTTEEEEEEE- CS
                            AFOR_N 153 aviGpaGenlvrfAsisvddgraagrgGlGavmgsKnlkaivvrg 197
                                       a+iGpaGen+v+fA+++ d+g+aagr+G+GavmgsKnlka++v g
  gi|385805271|ref|YP_005841669.1| 161 ASIGPAGENMVKFAAVINDEGKAAGRTGMGAVMGSKNLKAVAVYG 205
                                       9***************666999*********************98 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:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 3962.74
//
Query:       gi|385805272|ref|YP_005841670.1|  [L=413]
Description: iron-containing alcohol dehydrogenase [Fervidicoccus fontis Kam940]
Scores for complete 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-97  324.7   0.0    6.6e-97  324.6   0.0    1.0  1  Fe-ADH    Iron-containing alcohol dehydrogenase
    7.7e-17   61.8   0.0    2.3e-07   30.8   0.5    2.1  2  Fe-ADH_2  Iron-containing alcohol dehydrogenase


Domain annotation for each model (and alignments):
>> Fe-ADH  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  324.6   0.0  7.4e-101   6.6e-97       3     364 .]      34     399 ..      32     399 .. 0.90

  Alignments for each domain:
  == domain 1  score: 324.6 bits;  conditional E-value: 7.4e-101
                                       EEEEETTGGGGHHHHHTTT.-..EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HHHHHHHHTTS- CS
                            Fe-ADH   3 rivfgkgaleelgellkkl.gakralivtdkgslkksglldkvlesleeagievtvfdgvepnptleeveeaaalar 78 
                                       ri++g  a+ + ++ ++++ + kra+ivtd+ +    +++  v + l++ g++ tv+d+v p+p++++++ +a++++
  gi|385805272|ref|YP_005841670.1|  34 RIFMGLAATPMFASSVSSAlKKKRAFIVTDPYIK---PMAFGVGRVLQSFGFNTTVWDKVVPEPPISTLKPCAQAME 107
                                       56666666666666665443678*********77...4555566666666*************************** PP

                                       TT.--EEEEEESHHHHHHHHHHHHHTT.......................--EEEEESS-S-S-TT-SEEEEE.-TT CS
                            Fe-ADH  79 eegadvviavGGGsviDtAKaialllanpe.....vedylgegkakkkkalpliaiPTtaGtGsevtplavitdeee 150
                                       +++ad+++avGGGs+iDt K++++l+++p+     ++ +    +   ++++ + aiPTt+GtGse+t++avitde+ 
  gi|385805272|ref|YP_005841670.1| 108 QFDADLIVAVGGGSAIDTSKVAWALYERPDidfklINPMA---PLGLRNKALFAAIPTTSGTGSEATSAAVITDESY 181
                                       ***************************9876544333333...333455689*********************8777 PP

                                       S..EEEEE-..SS--SEEEEEHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHT---TTSSB--HHHHHHHHHHHHHHH CS
                            Fe-ADH 151 g..eklsifdpellPdlaivDpeltltlPkrvtaatglDalahalEayvskkanplsdalaleairliaknlerava 225
                                          +k+s+++pel+Pd+a++Dp ++++lP+++t  t+lDa+aha+++y++  + +++d la  ai+li+++l+r++ 
  gi|385805272|ref|YP_005841670.1| 182 SppRKFSVVHPELVPDFAVLDPSFVVGLPPKLTLGTALDAFAHAVDSYLTHSSFEMTDFLAIGAIKLIMRWLPRVLS 258
                                       667************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHSS---HHHHHHHHHHC.CGGGGGS-HHHHHHHHH..........HHHHHHT... CS
                            Fe-ADH 226 dgedleareqmllastlaglafsnaglgavHalahalgalfgiphglanaillpavlrfnaeaaperlaqlaralgg 302
                                       + +d+ear ++++a+t+aglafsn+g++++H+l+h+lg+ f i+hg+a++++ p+v+ f+a +  +++ +la++lg 
  gi|385805272|ref|YP_005841670.1| 259 HSDDIEARLKIHEAATMAGLAFSNGGIALTHSLGHSLGKVFSIHHGFAVGVFIPYVIGFYA-EVSDKYTELAKELGV 334
                                       ************************************************************9.446*********988 PP

                                       ....T--HHHHHHHHHHHHHTT---SHHHHT-TT-....HHHHHHHHHT-TSGGGGSSS---HHHH CS
                            Fe-ADH 303 esdeeaaeeliealrellkelglptsLselgvdee....dldklaeaalkdrslannpreltaedv 364
                                       + +e  +++l+ ++ +++k++++p +L++lgvde+    +ld lae a++d ++   pr+++ e+v
  gi|385805272|ref|YP_005841670.1| 335 N-EEPLQKALVLKFLDFFKQVKAPLTLKDLGVDEAklreKLDVLAEYAYEDICTPMSPRPISIEEV 399
                                       7.99******************************7366666*********************9986 PP

>> Fe-ADH_2  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   1.3e-10   1.1e-06      15      96 ..      51     131 ..      43     140 .. 0.88
   2 !   30.8   0.5   2.6e-11   2.3e-07      97     250 .]     152     308 ..     149     308 .. 0.91

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.3e-10
                          Fe-ADH_2  15 kelelkkvllvadentkkaagekveeslkeagikvevveeveeeadleeveklvealreketdlvvavGgGtiiDia 91 
                                       + l+ k++++v+d  +k +a   v + l++ g +++v+++v +e+ +++ +  ++a+++ ++dl+vavGgG++iD++
  gi|385805272|ref|YP_005841670.1|  51 SALKKKRAFIVTDPYIKPMAF-GVGRVLQSFGFNTTVWDKVVPEPPISTLKPCAQAMEQFDADLIVAVGGGSAIDTS 126
                                       456778999999999987765.59999************************************************** PP

                          Fe-ADH_2  92 kyvsa 96 
                                       k++ a
  gi|385805272|ref|YP_005841670.1| 127 KVAWA 131
                                       *9855 PP

  == domain 2  score: 30.8 bits;  conditional E-value: 2.6e-11
                          Fe-ADH_2  97 klnvpyvsvpTaaSvDGfaspgaslvvd....gkkrtv.akaaaPlaviaDldvlaeAPrrllasGvGDllgkytal 168
                                       +++  ++++pT+    + a + a ++ +     +k +v ++  +P   ++D +++   P +l++    D+ +  +  
  gi|385805272|ref|YP_005841670.1| 152 RNKALFAAIPTTSGTGSEATSAAVITDEsyspPRKFSVvHPELVPDFAVLDPSFVVGLPPKLTLGTALDAFAHAVDS 228
                                       5677799999987777777777777666555557899999999**9999***************9999********* PP

                          Fe-ADH_2 169 adwklanevseplaklsaamvqeaaeklvedkketealeellealalsgigisrpaSGsEHliSHaldmlalkqalH 245
                                       +  + + e++++la  +++ ++  + +++++ +++ea  ++ ea +++g+++s+ +    H + H l +++  +  H
  gi|385805272|ref|YP_005841670.1| 229 YLTHSSFEMTDFLAIGAIKLIMRWLPRVLSHSDDIEARLKIHEAATMAGLAFSNGGIALTHSLGHSLGKVF--SIHH 303
                                       ***********************************************************************..999* PP

                          Fe-ADH_2 246 GeqVG 250
                                       G  VG
  gi|385805272|ref|YP_005841670.1| 304 GFAVG 308
                                       **998 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:                      438  (0.0244297); 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: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.55
# Mc/sec: 2272.16
//
Query:       gi|385805273|ref|YP_005841671.1|  [L=954]
Description: hypothetical protein FFONT_0228 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (954 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       699  (0.0389871); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.69u 0.28s 00:00:00.97 Elapsed: 00:00:00.44
# Mc/sec: 6515.44
//
Query:       gi|385805274|ref|YP_005841672.1|  [L=192]
Description: beta-lactamase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-20   73.5   0.0    2.7e-20   73.2   0.0    1.1  1  Lactamase_B    Metallo-beta-lactamase superfamily
    6.8e-07   29.0   0.0    9.7e-07   28.5   0.0    1.2  1  Lactamase_B_2  Beta-lactamase superfamily domain
    1.1e-05   25.1   0.1     0.0052   16.3   0.1    2.1  2  Lactamase_B_5  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 !   73.2   0.0   4.6e-24   2.7e-20       6     197 .]      10     185 ..       6     185 .. 0.90

  Alignments for each domain:
  == domain 1  score: 73.2 bits;  conditional E-value: 4.6e-24
                                       SEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCC CS
                       Lactamase_B   6 vnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapal 82 
                                       +n+yl     + iLiD+G  ++  ++      ++  +  +++v++TH+H+DHi  + +++e+t+++v+a ++ea   
  gi|385805274|ref|YP_005841672.1|  10 CNTYL---TSEGILIDAGAKPSDVLLI-----AKEHGISIKYVLITHYHYDHIKYASEIAERTKAKVVAPEAEADII 78 
                                       66666...4689**************9.....8******************************************** PP

                                       HCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCC CS
                       Lactamase_B  83 fmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetgr 159
                                       ++ ++ + +s     l++ s ++ + +  ++    +g++  ++    ++gh++g+  y +g++ f+GDa+ + +   
  gi|385805274|ref|YP_005841672.1|  79 EGSARPKFPSLS---LRIMSLFATIKPVKVDIKVKDGDEVAGMKAVAAPGHTPGSTAYVSGDIMFSGDAIESDNGKP 152
                                       *****6665555...699*****************************************************555555 PP

                                       CCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                       Lactamase_B 160 idltlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                         +     +  ++ d+  + +s++kl +l++++++pgH
  gi|385805274|ref|YP_005841672.1| 153 SLP-----PRKFTLDQIMAEKSMKKLLELRPKIIYPGH 185
                                       555.....6888888888888889999*********** 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 !   28.5   0.0   1.6e-10   9.7e-07       3     116 ..      19     129 ..      18     151 .. 0.78

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.6e-10
                                       EEES--TT....HHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCG CS
                     Lactamase_B_2   3 iLiDagpd....lrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfv 75 
                                       iLiDag      l    l       ++++  +i+ Vl+th HyDH++ +  ++e++  k++++ap+  ++++e +  
  gi|385805274|ref|YP_005841672.1|  19 ILIDAGAKpsdvL----L------IAKEHGISIKYVLITHYHYDHIKYASEIAERT--KAKVVAPEAEADIIEGSAR 83 
                                       5666666622211....1......12233458***************99*****54..478**********999999 PP

                                       HHHCHTT.....TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--C CS
                     Lactamase_B_2  76 ylaleee.....pavnvheldwgesfelgdggleitatparhksgr 116
                                       + +          + ++++++ + +++ gd+   ++a++a++ ++ 
  gi|385805274|ref|YP_005841672.1|  84 PKFPSLSlrimsLFATIKPVKVDIKVKDGDEVAGMKAVAAPGHTPG 129
                                       9988888888888899999999999999999889999999998886 PP

>> Lactamase_B_5  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   8.8e-07    0.0052      56      90 ..      41      77 ..      15      82 .. 0.83
   2 !    6.9   0.0   0.00064       3.8      92     144 ..     102     150 ..      97     181 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 8.8e-07
                     Lactamase_B_5 56 vawivltn..sdhlraakeiaeltyakiagpaaeket 90
                                      ++++++t    dh++ a eiae+t ak+ +p ae ++
  gi|385805274|ref|YP_005841672.1| 41 IKYVLITHyhYDHIKYASEIAERTKAKVVAPEAEADI 77
                                      456777752269**********************986 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.00064
                     Lactamase_B_5  92 piacdrwlsdgdelvsglkvlelkgsktpgelallleettlitgdlvrakkag 144
                                       p++ d  ++dgde v+g+k ++  g +tpg  a  + +  + +gd + + + g
  gi|385805274|ref|YP_005841672.1| 102 PVKVDIKVKDGDE-VAGMKAVAAPG-HTPGSTAY-VSGDIMFSGDAIESDN-G 150
                                       99***********.68*****9988.69999886.5677889999988754.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1303.04
//
Query:       gi|385805275|ref|YP_005841673.1|  [L=171]
Description: peptidase, family C56 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      3e-50  170.3   0.0    3.3e-50  170.1   0.0    1.0  1  DJ-1_PfpI      DJ-1/PfpI family
    0.00025   20.7   0.0    0.00033   20.3   0.0    1.1  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
    0.00048   19.9   0.0     0.0049   16.6   0.0    2.3  3  ThiJ_like      ThiJ/PfpI family-like
     0.0037   17.1   0.0     0.0041   16.9   0.0    1.2  1  GATase         Glutamine amidotransferase class-I
  ------ inclusion threshold ------
       0.06   13.0   0.0      0.069   12.8   0.0    1.2  1  Catalase_C     C-terminal domain found in long catalases
       0.13   12.0   0.0       0.17   11.6   0.0    1.3  1  Peptidase_C26  Peptidase C26


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 !  170.1   0.0   1.1e-53   3.3e-50       1     164 [.       3     166 ..       3     167 .. 0.97

  Alignments for each domain:
  == domain 1  score: 170.1 bits;  conditional E-value: 1.1e-53
                                       EEEEEEEETTBEHHHHHHHHHHHHHTTEEEEEEESSTSEEEETTSEEEE-SEEGGGCTCCG-SEEEE--BHHHHHHH CS
                         DJ-1_PfpI   1 kkvlvlladgvedvElivpvdvlkragikvdvvsvdkeevkgsrGlkvtvdaslddvkaaeyDalvlpGGragperl 77 
                                       +k+l+l++ ++ed+E+ +p+ +l +ag++v+v+ + ++ev+g++G+++   a ++d++++++D+lvlpGGr  per+
  gi|385805275|ref|YP_005841673.1|   3 RKALILIGPEFEDIEALYPYYRLIEAGFDVTVAAPFSGEVEGKHGYRMNSKA-IKDINPDDFDILVLPGGRG-PERI 77 
                                       699*********************************************9987.9*****************9.**99 PP

                                       HTSH..HHHHHHHHHHHTT-EEEEETTTHHHHHHTTTTTTSEE--SGGGHHHHHHTTSEE-SSSEEEETTEEEESSG CS
                         DJ-1_PfpI  78 rene..kvvelvkefaekgklvaaICagpqlLaaagvlkgrrvTsypavkdklekagakyvdkrvvvdgnlvTsrgp 152
                                       r ++   +v +vk+f+++gk++aaIC+gpqlL++ag++k  ++Tsyp++ d+l+++ga+++ ++vvv gn++Tsr p
  gi|385805275|ref|YP_005841673.1|  78 RVSArdDAVRIVKSFYDSGKPIAAICHGPQLLLSAGIVKDIKLTSYPGIADDLKAGGAEWLNEKVVVHGNIITSRLP 154
                                       8765448********************************************************************** PP

                                       GGHHHHHHHHHH CS
                         DJ-1_PfpI 153 gaaiefalelle 164
                                       ++++ ++++ll+
  gi|385805275|ref|YP_005841673.1| 155 EDLPYWMEALLK 166
                                       *********998 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 !   20.3   0.0   1.1e-07   0.00033      33      89 ..      56     110 ..      42     132 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.1e-07
                          GATase_3  33 kdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLG 89 
                                       kd +  +d d+++lpGg+  ++   ++r+ +  + +k+++ +g+p+ +iC G q+L 
  gi|385805275|ref|YP_005841673.1|  56 KDINP-DDFDILVLPGGRGPERIRVSARD-DAVRIVKSFYDSGKPIAAICHGPQLLL 110
                                       33333.78**********98887777777.88899******************9984 PP

>> ThiJ_like  ThiJ/PfpI family-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.12   3.7e+02      10      31 ..      17      38 ..      12      59 .. 0.80
   2 !   16.6   0.0   1.6e-06    0.0049      83     158 ..      61     129 ..      45     148 .. 0.87
   3 ?   -3.4   0.0       2.2   6.5e+03     152     158 ..     157     163 ..     155     165 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.12
                         ThiJ_like 10 evaipwkvlkdagfsveFvtek 31
                                      e+  p+  l +agf v+ +++ 
  gi|385805275|ref|YP_005841673.1| 17 EALYPYYRLIEAGFDVTVAAPF 38
                                      67789999*******9998875 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1.6e-06
                         ThiJ_like  83 eeydlvllpGGsdkavrelleserlhsllveylklvkrekepskvlgaicqgvlalafakpeldlktttlPlwmer 158
                                       +++d++ lpGG+++    +   +   + ++ +        +  k ++aic+g   l  a    d+k t+ P   + 
  gi|385805275|ref|YP_005841673.1|  61 DDFDILVLPGGRGPERIRVSARDDAVRIVKSFY-------DSGKPIAAICHGPQLLLSAGIVKDIKLTSYPGIADD 129
                                       68***********98777777777788899999.......56899*************************988765 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 2.2
                         ThiJ_like 152 lPlwmer 158
                                       lP+wme+
  gi|385805275|ref|YP_005841673.1| 157 LPYWMEA 163
                                       8****96 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.4e-06    0.0041      39      87 ..      59     112 ..      24     147 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.4e-06
                                       THHSTSEEEEEEESSCTT.....TTTHHHHHHHHCTSTS-EEEETHHHHHHHHH CS
                            GATase  39 llknpdgilvsgGpgspg.....vegkieaikearenkiPiLGICLGmQllaie 87 
                                       + +++d ++++gG g        ++ +++++k + ++++Pi  IC G Qll+ +
  gi|385805275|ref|YP_005841673.1|  59 NPDDFDILVLPGGRGPERirvsaRDDAVRIVKSFYDSGKPIAAICHGPQLLLSA 112
                                       3578999999999888888899999*************************9865 PP

>> Catalase_C  C-terminal domain found in long catalases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.3e-05     0.069      84     119 ..      81     116 ..      23     131 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.3e-05
                        Catalase_C  84 pagrplqllldayrhgKpigalGsgaealkaagisa 119
                                         ++++++++  y  gKpi+a+ +g ++l +agi +
  gi|385805275|ref|YP_005841673.1|  81 ARDDAVRIVKSFYDSGKPIAAICHGPQLLLSAGIVK 116
                                       5677899********************999998865 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.9e-05      0.17      95     119 ..      86     110 ..      61     133 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.9e-05
                     Peptidase_C26  95 laLiraalergvPilgiCrGlqlln 119
                                       + ++++ +++g+Pi +iC G qll 
  gi|385805275|ref|YP_005841673.1|  86 VRIVKSFYDSGKPIAAICHGPQLLL 110
                                       56889999***************93 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       218  (0.0121591); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); 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: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1064.39
//
Query:       gi|385805276|ref|YP_005841674.1|  [L=272]
Description: hypothetical protein FFONT_0231 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-08   33.9   0.4    2.5e-08   33.9   0.4    4.1  3  DUF4234         Domain of unknown function (DUF4234)
     0.0069   15.2   4.8      0.015   14.1   0.6    2.2  2  DUF2207         Predicted membrane protein (DUF2207)
  ------ inclusion threshold ------
      0.012   15.8   3.9      0.098   12.9   1.0    2.5  2  DUF4064         Protein of unknown function (DUF4064)
      0.045   13.7   1.3       0.66    9.9   0.0    3.0  3  UcrQ            UcrQ family
       0.05   13.2   0.5       0.05   13.2   0.5    2.3  3  Virul_fac_BrkB  Virulence factor BrkB
       0.68    9.6   2.9        2.4    7.8   0.0    2.3  2  DUF4131         Domain of unknown function (DUF4131)
        0.7    9.6   5.1       0.56    9.9   1.2    2.4  3  Tetraspanin     Tetraspanin family
       0.89    8.5  14.6       0.78    8.7   0.8    2.5  3  DUF973          Protein of unknown function (DUF973)
        1.4    8.8   6.1       0.87    9.5   0.8    2.4  2  DUF3611         Protein of unknown function (DUF3611)
        1.4    9.5   5.7       0.47   11.0   0.2    2.5  3  DUF2418         Protein of unknown function (DUF2418)
        3.2    7.8  11.2      0.048   13.8   2.7    2.3  3  UPF0242         Uncharacterised protein family (UPF0242) N-te


Domain annotation for each model (and alignments):
>> DUF4234  Domain of unknown function (DUF4234)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   6.3      0.36   5.9e+02      50      67 ..      50     110 ..      10     113 .. 0.49
   2 ?    3.2   0.2      0.06        98      23      65 ..     138     178 ..     137     183 .. 0.61
   3 !   33.9   0.4   1.5e-11   2.5e-08       1      35 [.     219     253 ..     219     268 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.36
                           DUF4234  50 l...........................................itcgiysivwayklgkr 67 
                                       +                                           i++ +++++++yk  kr
  gi|385805276|ref|YP_005841674.1|  50 IgmlysspsieypyssysylqesshsfndsvfssllilfgflviIISIFINFYVIYKWVKR 110
                                       2444444444444444444444444444444444454445466544444466666665544 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.06
                           DUF4234  23 ykltrelnrlsgrkkttslllvflllslitcgiysivwayklg 65 
                                       y++ + ln+l+  +++ + ++v     li++++y +++++ ++
  gi|385805276|ref|YP_005841674.1| 138 YSIKSRLNELKDINNNIKSAIV--NSILIIVPFYILYVYHFIN 178
                                       5555555666555333444444..2445899999999998665 PP

  == domain 3  score: 33.9 bits;  conditional E-value: 1.5e-11
                           DUF4234   1 rslavvilLsivTlGIYslyWlykltrelnrlsgr 35 
                                       rs++++++L ++T+G++++yW+y+lt++ nr+ + 
  gi|385805276|ref|YP_005841674.1| 219 RSTLLYVILYFITCGLFGIYWVYTLTNDPNRHFES 253
                                       899***************************98776 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.6   8.9e-06     0.015     361     449 ..       9     119 ..       1     136 [. 0.59
   2 ?    3.5   0.4     0.015        25     352     426 ..     120     238 ..     112     249 .. 0.49

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.9e-06
                           DUF2207 361 ksavkkkergyfdkkgkkklkklsalglgliilglilillallllvll..........................lvf 411
                                       +  +kk  ++  ++ +k+ +k   +l ++ +il++++++l+++++ +                           +  
  gi|385805276|ref|YP_005841674.1|   9 EALLKK-VEEISQESKKSDYKMPVILPFLPAILYFVAVILLAIGMLYSspsieypyssysylqesshsfndsvfS-- 82 
                                       333333.44455555566666666666666777777776666666666999********************8542.. PP

                           DUF2207 412 llilllillliaiivlllfsrllgrrteeGaellakwk 449
                                        l++l+++l+i ii +++  ++++++ +  ++   + +
  gi|385805276|ref|YP_005841674.1|  83 SLLILFGFLVI-IISIFINFYVIYKWVKRRNDHFLRNM 119
                                       22222222222.22222223456666555555555555 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.015
                           DUF2207 352 kfkkalkkwksavkk.......kergyfdkkgkkklkklsalglgliilglilillallllvll............. 408
                                       +f+++++++++ +k        ++ + +++  ++++k+ ++ ++++i+ ++il ++ ++                  
  gi|385805276|ref|YP_005841674.1| 120 SFYENIAEITNLLKFkrvysikSRLNELKDI-NNNIKSAIVNSILIIVPFYILYVYHFIN---Kdfvkhsqkerlll 192
                                       5555555555555554444443122222221.2333333344444444444443333332...13446677777777 PP

                           DUF2207 409 ............................lvfllilllillliaiiv 426
                                                                     +++il +i   ++ i+
  gi|385805276|ref|YP_005841674.1| 193 sevideirekvplftrrieefaevpdrsTLLYVILYFITCGLFGIY 238
                                       7777777777777777777777777766333333333333333333 PP

>> DUF4064  Protein of unknown function (DUF4064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.0     6e-05     0.098       6      80 ..      31     104 ..      26     112 .. 0.69
   2 ?    3.1   0.1     0.068   1.1e+02      59      86 ..     220     247 ..     156     253 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6e-05
                           DUF4064   6 iiLglIGgilgillglllllflfllssgefsqelteeqalsgedasavleflstllivlgvialiaivlgivgal 80 
                                        iL ++ +il++++++ll++   l ss++ +  ++  + l+++ +s   +++s+lli++g++++i+++++ + ++
  gi|385805276|ref|YP_005841674.1|  31 VILPFLPAILYFVAVILLAIG-MLYSSPSIEYPYSSYSYLQESSHSFNDSVFSSLLILFGFLVIIISIFINFYVI 104
                                       566667777777777776666.45555555555555477777777888899999999999999998888766555 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.068
                           DUF4064  59 tllivlgvialiaivlgivgalllkknk 86 
                                       ++l++ +++++ ++++gi  ++ l +++
  gi|385805276|ref|YP_005841674.1| 220 STLLYVILYFITCGLFGIYWVYTLTNDP 247
                                       4666788889999999998888887776 PP

>> UcrQ  UcrQ family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0    0.0004      0.66      43      68 ..      89     114 ..      65     118 .. 0.78
   2 ?    0.4   0.0      0.38   6.1e+02      44      60 ..     160     175 ..     147     188 .. 0.58
   3 ?   -1.0   0.0       1.1   1.7e+03      46      66 ..     228     248 ..     219     253 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0004
                                       TTHHHHHHHHHHHHHHHHHHHHHHHH CS
                              UcrQ  43 sqvlyvlppfiiayliykwakeeney 68 
                                       + +++++  fi +y+iykw k++n+ 
  gi|385805276|ref|YP_005841674.1|  89 GFLVIIISIFINFYVIYKWVKRRNDH 114
                                       556788889**************986 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.38
                                       THHHHHHHHHHHHHHHH CS
                              UcrQ  44 qvlyvlppfiiayliyk 60 
                                       + + +++pf i y+ y+
  gi|385805276|ref|YP_005841674.1| 160 NSILIIVPFYILYV-YH 175
                                       44556777777664.44 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHHHHHHHHH CS
                              UcrQ  46 lyvlppfiiayliykwakeen 66 
                                       +++   ++ +y +y+ +++ n
  gi|385805276|ref|YP_005841674.1| 228 YFITCGLFGIYWVYTLTNDPN 248
                                       233334445677777666655 PP

>> Virul_fac_BrkB  Virulence factor BrkB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.5   3.1e-05      0.05     113     186 ..      39     112 ..       8     118 .. 0.64
   2 ?   -2.5   0.0       1.9   3.2e+03     164     181 ..     157     174 ..     137     183 .. 0.65
   3 ?    0.4   0.0      0.25   4.1e+02     166     184 ..     225     243 ..     196     251 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.1e-05
                    Virul_fac_BrkB 113 llsllllllllvllllslvlsvflqslllasa....pllglglelsell..llqllrwlvallllvlafallYrvlp 183
                                       +l++++++ll++ +l s   + +        +     +   +++   ++  ll l+++lv+++ +++ f+++Y+++ 
  gi|385805276|ref|YP_005841674.1|  39 ILYFVAVILLAIGMLYSSPSIEYPY------SsysyLQESSHSFNDSVFssLLILFGFLVIIISIFINFYVIYKWVK 109
                                       3444444444444444444444443......23333222223333333467999****9****************98 PP

                    Virul_fac_BrkB 184 nvk 186
                                       ++ 
  gi|385805276|ref|YP_005841674.1| 110 RRN 112
                                       775 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.9
                    Virul_fac_BrkB 164 wlvallllvlafallYrv 181
                                        +v  +l+++ f++lY +
  gi|385805276|ref|YP_005841674.1| 157 AIVNSILIIVPFYILYVY 174
                                       344455555667777655 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.25
                    Virul_fac_BrkB 166 vallllvlafallYrvlpn 184
                                       v+l ++++ ++ +Y+v + 
  gi|385805276|ref|YP_005841674.1| 225 VILYFITCGLFGIYWVYTL 243
                                       5567888899999988765 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   1.6      0.24   3.8e+02       9      36 ..      39      90 ..      30     113 .. 0.44
   2 ?    7.8   0.0    0.0015       2.4      26      65 ..     206     254 ..     156     270 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.24
                           DUF4131  9 llalllllllllllllrr........................rprrrvllll 36
                                      +l +++++ll++++l+ +                          +  +l+++
  gi|385805276|ref|YP_005841674.1| 39 ILYFVAVILLAIGMLYSSpsieypyssysylqesshsfndsvFSSLLILFGF 90
                                      3333333333333333335666655555555544443322221122222222 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0015
                           DUF4131  26 r.........rprrrvllllllllllallgfalrapqpnandlsqlles 65 
                                       +          p r +ll ++l++++++l+  +++++ + ++  ++ + 
  gi|385805276|ref|YP_005841674.1| 206 FtrrieefaeVPDRSTLLYVILYFITCGLFGIYWVYTLTNDPNRHFESH 254
                                       0444566666889999************************999999863 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.2   0.00034      0.56       9      66 ..      37      98 ..      31     112 .. 0.65
   2 ?   -1.7   0.0       1.1   1.9e+03      43      59 ..     153     169 ..     137     189 .. 0.58
   3 ?   -0.1   0.0      0.38   6.2e+02      85     117 ..     224     259 ..     220     271 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00034
                                      XXXXXXXXXXXXXXXXXXXX......XXX.....................XXXXXXXXXXXXXX CS
                                      xxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Tetraspanin  9 nllfwligivllavGvwlrl......khaeaalacllsesaedpailaillivvGvllfllgfl 66
                                        ++  ++++lla+G+ + +        + +  + ++s+++ + ++ + lli++G+l+++++++
  gi|385805276|ref|YP_005841674.1| 37 PAILYFVAVILLAIGMLYSSpsieypY-S-SYSYLQESSHSFNDSVFSSLLILFGFLVIIISIF 98
                                      556666777777777444346777542.2.33334444555555555588**********9997 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.1
                                       ..........XXXXXXX CS
                                       xxxxxxxxxxxxxxxxx RF
                       Tetraspanin  43 aedpailaillivvGvl 59 
                                       + ++ai+  +li+v + 
  gi|385805276|ref|YP_005841674.1| 153 NIKSAIVNSILIIVPFY 169
                                       23333333333333332 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.38
                                       XXXXXXXXXXXXXX.XXX--HHH..........HHH CS
                                       xxxxxxxxxxxxxx.xxxxxxxxxxxxx..xxxxxx RF
                       Tetraspanin  85 lllvlfllelaagi.lgfvfsdkargkv..seiinn 117
                                       ++++ f+++  +gi ++++++++ ++ +  ++ii++
  gi|385805276|ref|YP_005841674.1| 224 YVILYFITCGLFGIyWVYTLTNDPNRHFesHQIIEK 259
                                       456667777777777888888875555432334555 PP

>> DUF973  Protein of unknown function (DUF973)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   3.9    0.0017       2.8      54     122 ..      29     104 ..       8     120 .. 0.67
   2 ?    8.7   0.8   0.00048      0.78      68     113 ..     128     173 ..     122     199 .. 0.80
   3 ?   -4.0   0.1       3.5   5.7e+03      24      33 ..     226     235 ..     220     269 .. 0.40

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0017
                            DUF973  54 svlllli.aaii..liiiasvllilgll.kir...sgfsiLsstgrdvgiGitgltliligaiiiiigvilaivsl 122
                                       + ++l++ +ai+  +++i + + +l+   +i    s +s L++ +   +  + +++lil g  +iii++ ++  ++
  gi|385805276|ref|YP_005841674.1|  29 MPVILPFlPAILyfVAVILLAIGMLYSSpSIEypySSYSYLQESSHSFNDSVFSSLLILFGFLVIIISIFINFYVI 104
                                       4444443044445555555555555544555422278889999999999999999999999999999988776554 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00048
                            DUF973  68 iasvllilgllkirsgfsiLsstgrdvgiGitgltliligaiiiii 113
                                       i+ +l +  +++i+s +++L+ ++++++  i+ ++li++   i+ +
  gi|385805276|ref|YP_005841674.1| 128 ITNLLKFKRVYSIKSRLNELKDINNNIKSAIVNSILIIVPFYILYV 173
                                       56677777889*********************99999886666544 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 3.5
                            DUF973  24 iliilvlvvl 33 
                                       il +++  ++
  gi|385805276|ref|YP_005841674.1| 226 ILYFITCGLF 235
                                       2222222222 PP

>> DUF3611  Protein of unknown function (DUF3611)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.8   0.00053      0.87      23      74 ..      38     103 ..      31     114 .. 0.77
   2 ?    1.3   0.3      0.17   2.8e+02      48      76 ..     217     245 ..     202     256 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00053
                           DUF3611  23 lvLgvvsalillfallgrsl..............aeetnaglgfglflavlglvvllfsifwafry 74 
                                       ++L +v++++l + +l +s               ++++ + + f+ +l ++g++v ++sif++f +
  gi|385805276|ref|YP_005841674.1|  38 AILYFVAVILLAIGMLYSSPsieypyssysylqeSSHSFNDSVFSSLLILFGFLVIIISIFINFYV 103
                                       57889999999999998887778887776664321133444478889*****************86 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.17
                           DUF3611  48 aglgfglflavlglvvllfsifwafrytr 76 
                                       +  +  l++ ++ + + lf+i+w + +t+
  gi|385805276|ref|YP_005841674.1| 217 PDRSTLLYVILYFITCGLFGIYWVYTLTN 245
                                       455666788888899999*****999875 PP

>> DUF2418  Protein of unknown function (DUF2418)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.3       0.4   6.6e+02      37      60 ..      79     108 ..      27     129 .. 0.61
   2 ?   11.0   0.2   0.00029      0.47      41      81 ..     163     203 ..     131     214 .. 0.77
   3 ?   -2.8   0.0       5.8   9.5e+03      49      73 ..     237     261 ..     221     265 .. 0.56

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.4
                           DUF2418  37 svlktll.....lvvllslqlylli.skfe 60 
                                       sv++ ll     lv+++s+ +++ +  k+ 
  gi|385805276|ref|YP_005841674.1|  79 SVFSSLLilfgfLVIIISIFINFYViYKWV 108
                                       333333333344556666555544435554 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00029
                           DUF2418  41 tlllvvllslqlylliskfeqqikDkkiiqkevleEYnekf 81 
                                       ++++ + + ++ +++++ f + ++ ++++ +ev++E+ ek+
  gi|385805276|ref|YP_005841674.1| 163 LIIVPFYILYVYHFINKDFVKHSQKERLLLSEVIDEIREKV 203
                                       2334445555556667*********************9997 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 5.8
                           DUF2418  49 slqlylliskfeqqikDkkiiqkev 73 
                                        + +y+l++  ++  + ++ii ke+
  gi|385805276|ref|YP_005841674.1| 237 IYWVYTLTNDPNRHFESHQIIEKEL 261
                                       3444555555556666667777665 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.4       4.7   7.6e+03     121     132 ..      10      21 ..       2      28 .. 0.39
   2 ?   13.8   2.7     3e-05     0.048       4     103 ..      46     156 ..      39     215 .. 0.72
   3 ?   -0.9   0.0      0.95   1.6e+03      39      74 ..     226     260 ..     203     271 .. 0.64

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 4.7
                           UPF0242 121 qLqekleaiaed 132
                                        L +k e+i+++
  gi|385805276|ref|YP_005841674.1|  10 ALLKKVEEISQE 21 
                                       222233333332 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 3e-05
                           UPF0242   4 llisiiflYllPllllaiysiqllseq.ksWs.......llsiGlllaaaGsLlllllllkwekalkekl.ekskle 71 
                                       +l++i +lY+ P +  + +s  +l e+ +s +       l+ +G l++++   + +++++kw k  + ++  +  + 
  gi|385805276|ref|YP_005841674.1|  46 ILLAIGMLYSSPSIEYPYSSYSYLQESsHSFNdsvfsslLILFGFLVIIISIFINFYVIYKWVKRRNDHFlRNMSFY 122
                                       466777899999999999999999854134559999999889********************999999888777778 PP

                           UPF0242  72 ekeaklteld..eglktkeealeelqeeeeeLke 103
                                       e++a +t+l   + +  ++  l+el++ +++ k 
  gi|385805276|ref|YP_005841674.1| 123 ENIAEITNLLkfKRVYSIKSRLNELKDINNNIKS 156
                                       8888888877453344444555555555555444 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.95
                           UPF0242  39 GlllaaaGsLlllllllkwekalkeklekskleeke 74 
                                        l  + +G  + ++ ++++ ++ + ++e++++ eke
  gi|385805276|ref|YP_005841674.1| 226 ILYFITCGL-FGIYWVYTLTNDPNRHFESHQIIEKE 260
                                       344444443.35566666666666667666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1356  (0.0756317); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.51
# Mc/sec: 1606.49
//
Query:       gi|385805277|ref|YP_005841675.1|  [L=104]
Description: hypothetical protein FFONT_0232 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score 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   5.5        1.5    9.1   5.5    1.9  1  SCAMP     SCAMP family
       0.19   12.0   9.5       0.28   11.4   9.5    1.3  1  EI24      Etoposide-induced protein 2.4 (EI24)
       0.21   11.8   1.5       0.32   11.3   0.2    1.7  2  DUF2530   Protein of unknown function (DUF2530)
          1    9.5   8.0        1.8    8.7   8.0    1.3  1  DUF4870   Domain of unknown function (DUF4870)


Domain annotation for each model (and alignments):
>> SCAMP  SCAMP family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   5.5   0.00032       1.5      40      96 ..       9      83 ..       5      91 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00032
                             SCAMP 40 vlvltlvlNiiavlallisgsse.......k.kflglaily..........lllftpasfvlwyrplYkafrsds 96
                                      +++++++l ++++++++i+++++       + + ++l il            +l+  + f++w + +Y af+++s
  gi|385805277|ref|YP_005841675.1|  9 WYIFAYILTWLSGIIVFITEGQKdkrlkfhSlQSIFLGILGtiidlvfffiPFLGPFLLFLVWLYGMYIAFKAYS 83
                                      5789999999*********99998888665234444444433333322211234444567788888888888766 PP

>> EI24  Etoposide-induced protein 2.4 (EI24)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   9.5   6.2e-05      0.28      89     125 ..      36      79 ..       7      94 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.2e-05
                                       H.HHHHHHHHHHHHHHHHHHH.HHTTHHH....HHHHH.....H CS
                              EI24  89 a.eslkslllllllllvllpl.liPvvglilsplllsw.....l 125
                                         +sl+s++l +l +++ l++ +iP++g++l +l++++     +
  gi|385805277|ref|YP_005841675.1|  36 KfHSLQSIFLGILGTIIDLVFfFIPFLGPFLLFLVWLYgmyiaF 79 
                                       139******************666******99999998433333 PP

>> DUF2530  Protein of unknown function (DUF2530)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2     7e-05      0.32      17      58 ..      11      52 ..       6      56 .. 0.89
   2 ?   -0.8   0.1       0.4   1.8e+03      21      40 ..      68      87 ..      64      92 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7e-05
                           DUF2530 17 ivvgtllWlvalvvllvvgdaleswlpvclaGlvvGllGlai 58
                                      i + +l Wl +++v+++ g++ +++   +l  + +G+lG+ i
  gi|385805277|ref|YP_005841675.1| 11 IFAYILTWLSGIIVFITEGQKDKRLKFHSLQSIFLGILGTII 52
                                      5677899*********99999999999************987 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.4
                           DUF2530 21 tllWlvalvvllvvgdales 40
                                       l+Wl ++ +++ + + ++ 
  gi|385805277|ref|YP_005841675.1| 68 FLVWLYGMYIAFKAYSGVDV 87
                                      57899999988877666555 PP

>> DUF4870  Domain of unknown function (DUF4870)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   8.0   0.00041       1.8      14     103 ..       9      89 ..       6      93 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00041
                           DUF4870  14 sklliplgniilPlviwllkkdksefvdeqgkealNFqislliysiilivlsllvligflllllllllllnlvlvii 90 
                                       + +++ ++ ++  +++++++ +k++ ++ ++ +++   i  +i+ +++++   + ++g   +ll+l++l+     ++
  gi|385805277|ref|YP_005841675.1|   9 WYIFAYILTWLSGIIVFITEGQKDKRLKFHSLQSIFLGILGTIIDLVFFF---IPFLGP--FLLFLVWLYG----MY 76 
                                       56677788899999999999999999999999998777776666544444...355554..4444444444....34 PP

                           DUF4870  91 aaikanegeeyry 103
                                        a ka++g  ++ 
  gi|385805277|ref|YP_005841675.1|  77 IAFKAYSGVDVKV 89 
                                       4455555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       789  (0.0440069); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 667.10
//
Query:       gi|385805278|ref|YP_005841676.1|  [L=181]
Description: hypothetical protein FFONT_0233 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); 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: 00:00:00.43
# Mc/sec: 1272.84
//
Query:       gi|385805279|ref|YP_005841677.1|  [L=47]
Description: hypothetical protein FFONT_0234 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); 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: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 317.93
//
Query:       gi|385805280|ref|YP_005841678.1|  [L=321]
Description: tRNA pseudouridine synthase D [Fervidicoccus fontis Kam940]
Scores for complete 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   76.0   0.2    1.9e-17   63.2   0.0    3.0  3  TruD      tRNA pseudouridine synthase D (TruD)


Domain annotation for each model (and alignments):
>> TruD  tRNA pseudouridine synthase D (TruD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.2   0.0     1e-21   1.9e-17       2     186 ..       6     177 ..       5     181 .. 0.90
   2 !    3.4   0.1    0.0016        28     265     278 ..     192     205 ..     188     216 .. 0.84
   3 !    6.0   0.0   0.00025       4.4     379     416 .]     265     302 ..     254     302 .. 0.86

  Alignments for each domain:
  == domain 1  score: 63.2 bits;  conditional E-value: 1e-21
                              TruD   2 lgielyvtdtegig.GrlrespeDFiVeEieefsgeeeadegeylvlrvekrnwdtldlvrelaralgisrkrvgfa 77 
                                       +gi++++t++egi+ G + e+  DFiV E   f    +++eg+++ + + k++  t ++v+ +     i++ +  + 
  gi|385805280|ref|YP_005841678.1|   6 IGINVFLTNSEGIEaGDFLERCSDFIVIER-SFPP--TNNEGKFYAYFLVKSGLSTESAVKIILT--LIHKGKAFYY 77 
                                       89***********659*************9.4433..3689********************9975..4677888899 PP

                              TruD  78 GtKDkrAvTtQlisirkvepeelealeikdvelevvgrarrklrlGdLaGNkFeirvrdvaeeeeaakraeeileel 154
                                       G+KD +++++Q i +++   ++l      +++l   g+++   + G    N F+i+  d         +ae++lee+
  gi|385805280|ref|YP_005841678.1|  78 GLKDSNSLSVQNIVLTEFVGKNLC--FGGKARLIYQGKTDFIPKKGGFNSNIFAIKFPDSI-------DAEKTLEEI 145
                                       ***************999988887..34899********9999****************42.......588999999 PP

                              TruD 155 eekggvPNyfGvQRFGsrrpvthlvGkaivkg 186
                                       ++ +++PN+fG+QRFG   p +h+++ +++k+
  gi|385805280|ref|YP_005841678.1| 146 KKLKAFPNFFGHQRFGFHEPFNHEIAIKLLKD 177
                                       99999*********************999985 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.0016
                              TruD 265 hAyqSylFNrvlse 278
                                       ++ qSy+FN +ls+
  gi|385805280|ref|YP_005841678.1| 192 ESLQSYIFNVCLSR 205
                                       689*********95 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.00025
                              TruD 379 RaillrvedlelsaeedeltleFsLpkGsYATvvlrEi 416
                                       R+++++   +++ +++++l+   ++p+GsYA  ++rE+
  gi|385805280|ref|YP_005841678.1| 265 RPLFIKNPLIKYYKSKEKLIAIAKMPPGSYASLIIREV 302
                                       77777777778888899999999**************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 2346.57
//
Query:       gi|385805281|ref|YP_005841679.1|  [L=50]
Description: hypothetical protein FFONT_0236 [Fervidicoccus fontis Kam940]
Scores for complete 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   19.3   0.1    0.00058   19.2   0.1    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 !   19.2   0.1   3.2e-08   0.00058     159     194 ..      11      45 ..       3      47 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 3.2e-08
                                       XEEEEEEGGGHHHHHHCTESEEEEEXSEEETTSEEE CS
                             IF-2B 159 ipvtlitdsavayvmseevdkvivGAdrilenGaia 194
                                       ++  +i+ s+v y++ + v+++  GAd+i + G++ 
  gi|385805281|ref|YP_005841679.1|  11 VDAEVILHSSVHYFIGK-VNAIATGADGIYASGDVL 45 
                                       7899*************.***************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 328.57
//
Query:       gi|385805282|ref|YP_005841680.1|  [L=171]
Description: hypothetical protein FFONT_0237 [Fervidicoccus fontis Kam940]
Scores for complete 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-09   37.3  24.5    3.3e-08   33.7  24.5    1.9  1  AmiS_UreI     AmiS/UreI family transporter
  ------ inclusion threshold ------
       0.27   11.1   5.8       0.65    9.8   5.8    1.6  1  DUF4668       Domain of unknown function (DUF4668)
        1.6    8.5  10.1       0.11   12.3   1.3    2.3  2  Trp_oprn_chp  Tryptophan-associated transmembrane protein (Tr


Domain annotation for each model (and alignments):
>> AmiS_UreI  AmiS/UreI family transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7  24.5   5.6e-12   3.3e-08       2     165 ..      11     169 ..      10     170 .. 0.89

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 5.6e-12
                         AmiS_UreI   2 lgvvLLyvgavLilnGlvllg.kvdaksaavinlfvGalsliinlvlivqaaadaasiyaaalglLFgftYLyvain 77 
                                       +g++L + ga +++ G+ l+  k d ks +v+   +++++++++l++++      +   +a   l Fg+ +  ++i+
  gi|385805282|ref|YP_005841680.1|  11 VGMILYLFGANFFVLGMSLMSnKPDLKSSGVFCEAAAIFNVVAALYAATAL----NLGTTATFALTFGVIWVALGII 83 
                                       57889999*********9997256779999999998888888888887777....56666777788*********** PP

                         AmiS_UreI  78 rllgldgrglGwfslfVainavpvallslasaadlvlaliWlaWavLwllfflllalkkkkleklvgwlaivegilT 154
                                        ++g+  +++G +sl+ ai ++ + ++ +a  +++ +a   +++++ ++ +fl++  k +   k++gwl iv gi+ 
  gi|385805282|ref|YP_005841680.1|  84 LIKGYGLTPVGDYSLYAAIGMIWFLYAFIALVHNYLFAYATTLYIITFIAIFLMTRGKVS--LKALGWLLIVFGIIG 158
                                       **********************99999999999********************9888866..69************* PP

                         AmiS_UreI 155 awiPalllltg 165
                                        ++Pal+l++g
  gi|385805282|ref|YP_005841680.1| 159 VLVPALMLFMG 169
                                       ********997 PP

>> DUF4668  Domain of unknown function (DUF4668)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   5.8   0.00011      0.65      99     148 ..     118     168 ..     103     170 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00011
                           DUF4668  99 flllyvslvyslviiqlffktdqgislerlsq.lfqlqlnailitlllayl 148
                                       +l++y+  +y ++ i +f++t+  +sl+ l + l+++ +  +l  +l+ ++
  gi|385805282|ref|YP_005841680.1| 118 YLFAYATTLYIITFIAIFLMTRGKVSLKALGWlLIVFGIIGVLVPALMLFM 168
                                       6899***************************97889999999999988876 PP

>> Trp_oprn_chp  Tryptophan-associated transmembrane protein (Trp_oprn_chp)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.3   1.8e-05      0.11      64     137 ..       5      85 ..       1     115 [. 0.83
   2 ?    1.2   2.0     0.046   2.8e+02      59      85 ..     143     169 ..     120     171 .] 0.66

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.8e-05
                      Trp_oprn_chp  64 glgrrvvgvllalagagaavaalslltdpadaaraaa.aaatgvasaaaave.lta.....wpvlalaggvllllag 133
                                       +++  +vg++l l ga   v ++sl+++++d++ + +  +a+++ + +aa   +ta      + +al  gv+ ++ g
  gi|385805282|ref|YP_005841680.1|   5 QWVESLVGMILYLFGANFFVLGMSLMSNKPDLKSSGVfCEAAAIFNVVAALYaATAlnlgtTATFALTFGVIWVALG 81 
                                       79999****************************99998776666555555553444666668888888888888888 PP

                      Trp_oprn_chp 134 vlll 137
                                       ++l+
  gi|385805282|ref|YP_005841680.1|  82 IILI 85 
                                       8876 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.046
                      Trp_oprn_chp  59 vlavrglgrrvvgvllalagagaavaa 85 
                                        l + g++++v+g++ +l+ a++++ +
  gi|385805282|ref|YP_005841680.1| 143 SLKALGWLLIVFGIIGVLVPALMLFMG 169
                                       444557777777777777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1002  (0.0558871); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.34s 00:00:01.00 Elapsed: 00:00:00.56
# Mc/sec: 919.41
//
Query:       gi|385805283|ref|YP_005841681.1|  [L=241]
Description: peptidase, family S54 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-34  118.5  18.2    2.5e-34  118.5  18.2    1.4  2  Rhomboid  Rhomboid family
      7e-07   29.7   1.4      7e-07   29.7   1.4    2.8  3  DUF1751   Eukaryotic integral membrane protein (DUF1751)
  ------ inclusion threshold ------
        1.1    8.5   3.2        2.2    7.6   3.2    1.4  1  CcmH      Cytochrome C biogenesis protein
        3.2    7.7   4.3          8    6.4   4.3    1.6  1  SLATT_1   SMODS and SLOG-associating 2TM effector domain 1


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 ?   -3.3   0.1       1.8     8e+03     102     110 ..      28      36 ..      13      45 .. 0.50
   2 !  118.5  18.2   5.5e-38   2.5e-34       4     147 ..      62     234 ..      59     236 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.8
                                       HC...CCCC CS
                          Rhomboid 102 iallllllf 110
                                       + +++++++
  gi|385805283|ref|YP_005841681.1|  28 FVVTYFFPW 36 
                                       113333333 PP

  == domain 2  score: 118.5 bits;  conditional E-value: 5.5e-38
                                       CC-TTHHHHGGG--SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-S............. CS
                          Rhomboid   4 rgelwrlltsmflHagwlHllfNmlallvfGsplerrlGslrflllyllsglagsllsllfsaeses.......... 70 
                                        ++lw+++t+mf+H +++H+l+Nml+l++fG ++e  lG++++ll+y+lsg++++l+++     ++           
  gi|385805283|ref|YP_005841681.1|  62 GERLWTIFTAMFIHTDIVHVLGNMLFLYIFGDSIEIALGKVKYLLFYFLSGTGAALFYVTSITLVHVpetssiisqm 138
                                       689**************************************************9999988888877788999***** PP

                                       ......-EESSHHHHHHHHHHHHHHHHCCCCGS----HC............CCCCCCCCCCHHHCTSS....STTTH CS
                          Rhomboid  71 ......plvGaSGaifgllgallvlvprnrkllrkliia.........llllllfillnlvlgllpra....ggvsn 128
                                             p+vGaSGai+g+lga+++l p++  +  +l+++         +++++++++++lvl++l+ +    +g+++
  gi|385805283|ref|YP_005841681.1| 139 nnpwliPAVGASGAISGVLGAYIMLYPSSMVKTLTLWFWapvvinfpaIIFIVIWFIYQLVLAVLTTFsavyTGIAF 215
                                       *************************************999**************************99********* PP

                                       HHHHHHHHHHHHHHHHHCC CS
                          Rhomboid 129 lAHlgGllaGlllgllllr 147
                                       +AH+gG+l+G++++ ++ r
  gi|385805283|ref|YP_005841681.1| 216 WAHVGGFLTGIAVIPFFAR 234
                                       ************9988776 PP

>> DUF1751  Eukaryotic integral membrane protein (DUF1751)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1         1   4.6e+03       4      11 ..      31      38 ..      17      50 .. 0.59
   2 !   29.7   1.4   1.6e-10     7e-07       7      71 ..      64     128 ..      56     161 .. 0.81
   3 ?    0.6   1.8       0.2   8.8e+02      59      77 ..     190     208 ..     169     230 .. 0.49

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1
                           DUF1751  4 llpypwtl 11
                                      + ++pw++
  gi|385805283|ref|YP_005841681.1| 31 TYFFPWVI 38
                                      22344444 PP

  == domain 2  score: 29.7 bits;  conditional E-value: 1.6e-10
                           DUF1751   7 ypwtlltasfveqnvwkvlvslltlllggkylErlWgskEllkFilvvnvitnllvvlltlllyl 71 
                                         wt++ta+f+ + +++vl ++l l+++g  +E + g+  +l F ++ +++++l  v   +l+ +
  gi|385805283|ref|YP_005841681.1|  64 RLWTIFTAMFIHTDIVHVLGNMLFLYIFGDSIEIALGKVKYLLFYFLSGTGAALFYVTSITLVHV 128
                                       78**************************************************9998887776654 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.2
                           DUF1751  59 nllvvlltlllylvtksee 77 
                                        ++ ++++l+l+++t+ + 
  gi|385805283|ref|YP_005841681.1| 190 IVIWFIYQLVLAVLTTFSA 208
                                       2333333333333333332 PP

>> CcmH  Cytochrome C biogenesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   3.2   0.00049       2.2      83     116 ..     158     191 ..     153     199 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00049
                                       TTT-EE---XXXXXXXXXXXXXXXXXXXXXXXXX CS
                              CcmH  83 GdfVlykPpvkastllLWlgPllllllgllvlll 116
                                       G ++++ P    +tl LW+  ++++ + ++++++
  gi|385805283|ref|YP_005841681.1| 158 GAYIMLYPSSMVKTLTLWFWAPVVINFPAIIFIV 191
                                       99****************9988887766544433 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 ?    6.4   4.3    0.0018         8      22      71 ..     170     219 ..     166     226 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0018
                           SLATT_1  22 raakrwrlllillellalllaalrafgelsvdlvgvlaavaaallaWlel 71 
                                       ++ + w+++ +++++ a++++++  + +l ++++ +++av + ++ W+++
  gi|385805283|ref|YP_005841681.1| 170 KTLTLWFWAPVVINFPAIIFIVIWFIYQLVLAVLTTFSAVYTGIAFWAHV 219
                                       67899*******************88888889***************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       878  (0.0489709); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.35s 00:00:00.96 Elapsed: 00:00:00.55
# Mc/sec: 1321.04
//
Query:       gi|385805284|ref|YP_005841682.1|  [L=226]
Description: Transcription regulator of a riboflavin/FAD biosynthetic operon [Fervidicoccus fontis Kam940]
Scores for complete 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  134.2   0.0    3.5e-39  133.6   0.0    1.2  1  CTP-dep_RFKase  Domain of unknown function DUF120
    6.1e-08   32.1   0.5    1.4e-07   30.9   0.5    1.6  1  HTH_24          Winged helix-turn-helix DNA-binding
    6.5e-07   29.1   0.1    1.1e-06   28.4   0.1    1.3  1  MarR_2          MarR family
    1.1e-06   28.4   0.9    2.1e-06   27.6   0.2    1.8  2  HTH_Crp_2       Crp-like helix-turn-helix domain
    9.2e-06   25.5   0.4    1.7e-05   24.7   0.4    1.3  1  MarR            MarR family
    0.00013   21.8   0.2    0.00022   21.0   0.2    1.3  1  HxlR            HxlR-like helix-turn-helix
    0.00044   20.1   0.0    0.00088   19.1   0.0    1.5  1  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00046   20.2   0.5     0.0011   19.0   0.5    1.6  1  HTH_3           Helix-turn-helix
     0.0018   18.3   0.1     0.0031   17.5   0.1    1.4  1  HTH_45          Winged helix-turn-helix
     0.0034   17.3   0.4     0.0069   16.3   0.4    1.5  1  HTH_11          HTH domain
     0.0035   17.3   0.2      0.006   16.5   0.2    1.4  1  HTH_36          Helix-turn-helix domain
     0.0036   17.4   0.1     0.0077   16.3   0.1    1.5  1  HTH_28          Helix-turn-helix domain
     0.0039   17.0   0.2     0.0057   16.4   0.2    1.2  1  DUF4364         Domain of unknown function (DUF4364)
     0.0064   17.0   0.3      0.015   15.8   0.1    1.7  1  HTH_27          Winged helix DNA-binding domain
     0.0073   16.6   0.1      0.012   15.9   0.1    1.3  1  Rrf2            Transcriptional regulator
  ------ inclusion threshold ------
      0.014   14.9   0.2      0.028   14.0   0.2    1.4  1  HTH_CodY        CodY helix-turn-helix domain
      0.015   15.1   0.1      0.035   13.9   0.1    1.8  1  RQC             RQC domain
      0.016   15.2   0.1      0.031   14.2   0.1    1.5  1  Cdc6_C          CDC6, C terminal winged helix domain
      0.019   14.6   0.3      0.027   14.1   0.3    1.2  1  DDRGK           DDRGK domain
      0.061   13.1   0.0       0.11   12.3   0.0    1.4  1  HTH_IclR        IclR helix-turn-helix domain
      0.066   13.1   0.0       0.12   12.2   0.0    1.4  1  HTH_5           Bacterial regulatory protein, arsR family
      0.067   13.0   0.4       0.25   11.1   0.1    2.0  2  HTH_DeoR        DeoR-like helix-turn-helix domain
      0.068   13.0   0.1       0.13   12.1   0.1    1.4  1  HTH_10          HTH DNA binding domain
      0.081   13.6   0.1       0.13   12.9   0.1    1.3  1  RPA_C           Replication protein A C terminal
      0.083   12.7   0.1       0.18   11.7   0.1    1.6  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
      0.086   12.9   0.0       0.14   12.2   0.0    1.4  1  HTH_20          Helix-turn-helix domain
        0.2   11.6   0.4       0.49   10.4   0.4    1.7  1  HTH_1           Bacterial regulatory helix-turn-helix protein


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 !  133.6   0.0   5.3e-42   3.5e-39       1     121 []      98     219 ..      98     219 .. 0.98

  Alignments for each domain:
  == domain 1  score: 133.6 bits;  conditional E-value: 5.3e-42
                                       EE--SSHHHHHHCSHHHHHHHHHHHSS---SS-EEEEESCCGHHHHCHHHHS--EEE--EEETTEEE--EEEEEEEE CS
                    CTP-dep_RFKase   1 VvsGlgeGkyyvslegykeqfeeklgfepypGTLNvkldeeslelrkaleklkgieiegfedeertfgavkvypaki 77 
                                       +v+GlgeG++y++l++y+++++e +gf pypGTLNv+l+ es+ +r+ l+  kg++iegf++eer +g+++++p+k+
  gi|385805284|ref|YP_005841682.1|  98 IVEGLGEGRFYIKLPYYSKKIQELVGFVPYPGTLNVRLKGESVLKRAFLNPEKGLRIEGFRNEERYYGGATLFPVKV 174
                                       699************************************************************************** PP

                                       CCE.EEEEEEESS-SS.TTEEEEE-SS-HHHHTT--TT-EEEEEE CS
                    CTP-dep_RFKase  78 eki.kaavvvperthyeedvlEiiapekLReklelkdgdevevev 121
                                       +++ +aa+++p+rt++e+d++Ei+ap+ LR +l+lk+g++v +e+
  gi|385805284|ref|YP_005841682.1| 175 NGYeRAAIIIPDRTSHEKDIIEIVAPDYLRGELGLKNGSKVVLEI 219
                                       *886899**********************************9986 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.5   2.1e-10   1.4e-07      17      47 ..      23      53 ..      19      54 .. 0.96

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 2.1e-10
                            HTH_24 17 risqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      r++q+ L+e++glS++ ++r l++Le +G+I
  gi|385805284|ref|YP_005841682.1| 23 RTTQKALSEKIGLSQQSISRILRELEAQGII 53
                                      89****************************9 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.1   1.6e-09   1.1e-06      12      53 ..      13      55 ..       6      61 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 1.6e-09
                                      HHHHCTTTS.EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2 12 aaLgrrpgr.dltvgelarrlglsksavsrilkrLvaaGLver 53
                                        + ++  r + t+++l ++ gls++++sril++L+a+G + r
  gi|385805284|ref|YP_005841682.1| 13 ILIFDGKKRtRTTQKALSEKIGLSQQSISRILRELEAQGIIYR 55
                                      445555555778****************************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 !   27.6   0.2   3.2e-09   2.1e-06      20      53 ..      22      55 ..       7      69 .. 0.81
   2 ?   -2.5   0.0       8.1   5.4e+03      55      66 ..     192     204 ..     178     204 .. 0.55

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 3.2e-09
                                      EEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEE CS
                         HTH_Crp_2 20 lpltqeelAsmlGltretvsrilseLkreglisr 53
                                       + tq+ l++ +Gl+++++sril+eL+ +g+i r
  gi|385805284|ref|YP_005841682.1| 22 TRTTQKALSEKIGLSQQSISRILRELEAQGIIYR 55
                                      578*****************************83 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 8.1
                                       EE.EEES-HHHHH CS
                         HTH_Crp_2  55 rr.irildleaLr 66 
                                       ++ i+i  +++Lr
  gi|385805284|ref|YP_005841682.1| 192 KDiIEIVAPDYLR 204
                                       3356777777765 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.4   2.5e-08   1.7e-05      18      49 ..      24      55 ..      19      56 .. 0.93

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 2.5e-08
                                      EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              MarR 18 lsvseLakklgvskstvtrvldrLekkGlieR 49
                                       +++ L +k+g+s+ +++r+l++Le +G i+R
  gi|385805284|ref|YP_005841682.1| 24 TTQKALSEKIGLSQQSISRILRELEAQGIIYR 55
                                      6899***************************9 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.2   3.3e-07   0.00022       9      76 ..      10      77 ..       5      86 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3.3e-07
                                      HHHHHHTTS-EEHHHHHHHST...TS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEE.EE-TCGGGGHHHH CS
                              HxlR  9 lilvellkgkkRfselkralp...kisqkmLaqrLreLeqdglierevypevPpkveY.sltekGrslepvl 76
                                      ++l+ +++gkkR+   ++al    ++sq+ +++ LreLe++g+i r v  +     eY ++tekG +l + l
  gi|385805284|ref|YP_005841682.1| 10 MLLILIFDGKKRTRTTQKALSekiGLSQQSISRILRELEAQGIIYRIVEGK----GEYlEITEKGLKLVETL 77
                                      56677899999998777766532269******************9998754....45536888888887665 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.3e-06   0.00088      21      59 ..      22      60 ..      11      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.3e-06
                                      CCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTT CS
                              TrmB 21 gpatadeiaeelgvprskvYevLrsLedkGlVerekgrp 59
                                       + t + ++e++g++++++ ++Lr+Le  G+++r+ + +
  gi|385805284|ref|YP_005841682.1| 22 TRTTQKALSEKIGLSQQSISRILRELEAQGIIYRIVEGK 60
                                      5678899**************************997765 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.5   1.6e-06    0.0011      10      31 ..      24      45 ..      20      50 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.6e-06
                                      HHHHHHHHHHTSSHHHHHHHHT CS
                             HTH_3 10 lsqeeLAeklGvsrstisriEn 31
                                       +q+ L+ek+G+s+++isri +
  gi|385805284|ref|YP_005841682.1| 24 TTQKALSEKIGLSQQSISRILR 45
                                      59******************88 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   4.7e-06    0.0031      21      69 ..      25      77 ..      12      84 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.7e-06
                            HTH_45 21 kkTkimykanLsykllnkYLdmLvekgli....kkskekYvlTekGlellekl 69
                                      ++ ++  k  Ls + +++ L  L  +g+i    + ++e  ++TekGl+l+e+l
  gi|385805284|ref|YP_005841682.1| 25 TQKALSEKIGLSQQSISRILRELEAQGIIyrivEGKGEYLEITEKGLKLVETL 77
                                      4556778899******************8888444555569********9987 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.4     1e-05    0.0069      12      47 ..      20      57 ..      11      63 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1e-05
                            HTH_11 12 argpisgeeLAeeLnvSrrtvrrdIkaLeelg..vpIe 47
                                      +r   + + L+e++++S + + r +++Le++g  ++I+
  gi|385805284|ref|YP_005841682.1| 20 KRTRTTQKALSEKIGLSQQSISRILRELEAQGiiYRIV 57
                                      455599**************************776554 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.2     9e-06     0.006      27      55 .]      25      53 ..      11      53 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 9e-06
                            HTH_36 27 sqetlakrlglsknTvsraikeLeqlGyi 55
                                      +q+ l+++ gls +++sr+++eLe  G+i
  gi|385805284|ref|YP_005841682.1| 25 TQKALSEKIGLSQQSISRILRELEAQGII 53
                                      6899***********************98 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   1.2e-05    0.0077      12      41 ..      22      52 ..      17      55 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.2e-05
                            HTH_28 12 Gh.svreaArelgisrrtvyrWikryeegGi 41
                                       + ++++++++ g+s+++++r ++ +e++Gi
  gi|385805284|ref|YP_005841682.1| 22 TRtTQKALSEKIGLSQQSISRILRELEAQGI 52
                                      4569**************************8 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.2   8.6e-06    0.0057      33      86 ..      37      90 ..      21      98 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 8.6e-06
                           DUF4364 33 YfdlqqalseLvesglieeeekenktlykiTekGketlelfenripksirekid 86
                                        +++ +l eL+ +g i    + + ++++iTekG + +e++ ++  + ++e+ d
  gi|385805284|ref|YP_005841682.1| 37 QQSISRILRELEAQGIIYRIVEGKGEYLEITEKGLKLVETLWSKAESIVKEEKD 90
                                      5678899*************99*******************9999999998766 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   2.2e-05     0.015      14      68 .]      19      70 ..      10      70 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.2e-05
                            HTH_27 14 hrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                        r r ++++l+++  +++++is +l++L+++G + r     +++   +++T+kG
  gi|385805284|ref|YP_005841682.1| 19 KKRTRTTQKALSEKIGLSQQSISRILRELEAQGIIYRI---VEGKGEYLEITEKG 70
                                      45667788***************************665...56789999999999 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   1.9e-05     0.012      15      61 ..      13      60 ..       4      65 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.9e-05
                                      HHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSE.EEETTT CS
                              Rrf2 15 lyLakeeeeepvsseeiaerqnispsylekilakLrkaglv.ksvrGk 61
                                      + +   ++++  + ++++e+ ++s++ +++il++L+ +g++ + v+Gk
  gi|385805284|ref|YP_005841682.1| 13 ILIFDGKKRTRTTQKALSEKIGLSQQSISRILRELEAQGIIyRIVEGK 60
                                      3334444555599***************************93345565 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 ?   14.0   0.2   4.2e-05     0.028       6      51 ..      25      69 ..      21      77 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.2e-05
                          HTH_CodY  6 taskiaDriGitrsvivnaLrkLesaGiiesrsLGmkGtYlkvlne 51
                                      t   ++++iG+ +  i   Lr Le+ Gii  r +  kG Yl +  +
  gi|385805284|ref|YP_005841682.1| 25 TQKALSEKIGLSQQSISRILRELEAQGIIY-RIVEGKGEYLEITEK 69
                                      5567889**********************5.88888****998655 PP

>> RQC  RQC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   5.3e-05     0.035      58      96 ..      34      73 ..       5      90 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.3e-05
                                      TS-HHHHHHHHHHHHHTTSEEEE..SSS.BEEE-CCGHHH CS
                               RQC 58 dlskkewrrlirqLiaegyLeedveeyg.vlkltekarev 96
                                      +ls++ + r++r+L a+g++   ve+ g +l++tek+ ++
  gi|385805284|ref|YP_005841682.1| 34 GLSQQSISRILRELEAQGIIYRIVEGKGeYLEITEKGLKL 73
                                      5799****************888887777*******9766 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 ?   14.2   0.1   4.7e-05     0.031      37      69 ..      35      63 ..      19      71 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.7e-05
                                      --HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EE CS
                            Cdc6_C 37 ltqrevsdllseLemlgileleksskGrregrt 69
                                      l+q+++s++l+eLe++gi+ + +++kG     +
  gi|385805284|ref|YP_005841682.1| 35 LSQQSISRILRELEAQGIIYRIVEGKG----EY 63
                                      89**********************555....44 PP

>> DDRGK  DDRGK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.3   4.1e-05     0.027     117     164 ..      27      74 ..      14      88 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.1e-05
                                       HHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE---XXXXXX CS
                             DDRGK 117 eelavkfklktqevierikeLeeqgsltGvlDdrGkyiyitdeEleav 164
                                       + l+ k++l+ q +   ++eLe+qg +  ++  +G y+ it++ l+ v
  gi|385805284|ref|YP_005841682.1|  27 KALSEKIGLSQQSISRILRELEAQGIIYRIVEGKGEYLEITEKGLKLV 74 
                                       56999**********99************************9988766 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 ?   12.3   0.0   0.00017      0.11      18      50 ..      23      55 ..      10      56 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00017
                                      S-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 18 eltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      + t + l++++gl+  + +R+L+ L+ +G++ +
  gi|385805284|ref|YP_005841682.1| 23 RTTQKALSEKIGLSQQSISRILRELEAQGIIYR 55
                                      457899***********************9875 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00019      0.12      21      46 ..      29      54 ..      23      55 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00019
                                      HHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5 21 laeelglsqstvShHLkkLreaGLVe 46
                                      l+e++glsq  +S+ L+ L+ +G+++
  gi|385805284|ref|YP_005841682.1| 29 LSEKIGLSQQSISRILRELEAQGIIY 54
                                      99**********************96 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00038      0.25      16      47 ..      25      56 ..      18      61 .. 0.85
   2 ?   -1.6   0.0       3.4   2.3e+03      46      53 ..     162     169 ..     161     170 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00038
                          HTH_DeoR 16 sveelvellgvSeaTiRRDLneLeeqglltRt 47
                                      + + l+e  g S++ i R L+eLe+qg++ R+
  gi|385805284|ref|YP_005841682.1| 25 TQKALSEKIGLSQQSISRILRELEAQGIIYRI 56
                                      456899***********************997 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.4
                          HTH_DeoR  46 RthGGavs 53 
                                       R +GGa++
  gi|385805284|ref|YP_005841682.1| 162 RYYGGATL 169
                                       99***986 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00019      0.13      23      48 ..      23      48 ..      16      51 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00019
                            HTH_10 23 rvtlkeLAkelGIskstlsehLrkae 48
                                      r+t k+L++++G+s++++s +Lr+ e
  gi|385805284|ref|YP_005841682.1| 23 RTTQKALSEKIGLSQQSISRILRELE 48
                                      567899*****************977 PP

>> RPA_C  Replication protein A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1    0.0002      0.13      72      99 ..      28      55 ..      25      58 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.0002
                                      HHHHHSTSXHHHHHHHHHHHHHTTSEEE CS
                             RPA_C 72 eiaqklrlsvndvkqavdeLsneGiiYs 99
                                       +++k++ls +++ ++++eL+ +GiiY 
  gi|385805284|ref|YP_005841682.1| 28 ALSEKIGLSQQSISRILRELEAQGIIYR 55
                                      578899*********************6 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 ?   11.7   0.1   0.00027      0.18      16      42 .]      22      48 ..      11      48 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00027
                     HTH_AsnC-type 16 aRisyaeLAervGlSestvlrRvrrLe 42
                                       R++ ++L+e++GlS++ + r +r Le
  gi|385805284|ref|YP_005841682.1| 22 TRTTQKALSEKIGLSQQSISRILRELE 48
                                      79****************999777776 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00021      0.14      14      60 ..       9      59 ..       4      60 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00021
                                      HHHHHH....STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                            HTH_20 14 rilraL....araegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                                      ++l  L    + +   t ++l e ++ls++++s+ Lr+Le  g++ +  eg
  gi|385805284|ref|YP_005841682.1|  9 GMLLILifdgKKRTRTTQKALSEKIGLSQQSISRILRELEAQGIIYRIVEG 59
                                      55555566655666677789999*********************9777666 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 ?   10.4   0.4   0.00074      0.49      21      40 ..      31      50 ..      20      71 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00074
                                      HHHTS-HHHHHHHHHHHHHH CS
                             HTH_1 21 eeLglsqpavsrqikrLEee 40
                                      e+ glsq ++sr +++LE++
  gi|385805284|ref|YP_005841682.1| 31 EKIGLSQQSISRILRELEAQ 50
                                      789***************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); 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: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 1276.16
//
Query:       gi|385805285|ref|YP_005841683.1|  [L=222]
Description: Endonuclease V [Fervidicoccus fontis Kam940]
Scores for complete 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-43  148.3   0.0    2.7e-43  148.0   0.0    1.1  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 !  148.0   0.0   1.5e-47   2.7e-43      18     197 .]      40     212 ..      25     212 .. 0.88

  Alignments for each domain:
  == domain 1  score: 148.0 bits;  conditional E-value: 1.5e-47
                                       SEEEEEEEEEEECTCEEEEEEEEEEETTTTEEEEEEEEEEE--S-SSTT-CHHHCHHHHHHHHCC-SS..--SEEEE CS
                    Endonuclease_5  18 klvaGvDvsfvkeekkeavaalvvldlpslevvekavavvklsfpYipgfLaFRElpvllkaleklkq..kpdvllv 92 
                                         +a+vD++f+k ++   +a++v ++ ++ + +  a  + k+++pYipgfL FRE+pv+ +a++ l+   + d+llv
  gi|385805285|ref|YP_005841683.1|  40 INIAAVDCAFTKGKEI--IASAVAYRREENDAFFVA-IRDKIRIPYIPGFLGFREVPVAAAAVSILRDfvDIDLLLV 113
                                       469*******776665..9******98888876655.578***************************97669***** PP

                                       EC-SSSSTTS--HHHHHHHHHTS-EEEEESS-SSSBE----SSTTEEEEEEETTEEEEEEEESSTTS--EEEEEECS CS
                    Endonuclease_5  93 DGnGiaHprrlGlAshlGvlldlptiGvaKsllvgkveepekekgsvvplvsegevigaalrtkknvkpiyvSvGhr 169
                                       DG+GiaHpr  G A+hlG++ld+ptiGvaKsllv    ++ +e+g++   + +g  ig +l   +n++++y+S+G +
  gi|385805285|ref|YP_005841683.1| 114 DGHGIAHPRFSGSATHLGLALDIPTIGVAKSLLVY---DKIDEEGNF---FYKGILIGKILSYPENARKLYISPGYK 184
                                       *********************************96...233344433...44699********************** PP

                                       S-HHHHHHHHHHCS-T-SS-HHHHHHHH CS
                    Endonuclease_5 170 isletalelvlallkkyrlPepirqAdl 197
                                       i le+a+e+v++l kk  lP p+  Ad+
  gi|385805285|ref|YP_005841683.1| 185 IPLEKAFEIVKNLRKKPGLPFPLNYADK 212
                                       **************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 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:                        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 0.27s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1463.72
//
Query:       gi|385805286|ref|YP_005841684.1|  [L=199]
Description: 20S proteasome, Alpha and Beta subunits [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-47  161.8   0.4    1.4e-47  161.7   0.4    1.0  1  Proteasome  Proteasome subunit
  ------ inclusion threshold ------
       0.16   12.1   0.1       0.28   11.3   0.1    1.3  1  DUF1192     Protein of unknown function (DUF1192)
       0.19   12.2   0.0       0.37   11.2   0.0    1.5  1  DUF4216     Domain of unknown function (DUF4216)


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 !  161.7   0.4   2.3e-51   1.4e-47       3     190 .]       6     186 ..       4     186 .. 0.94

  Alignments for each domain:
  == domain 1  score: 161.7 bits;  conditional E-value: 2.3e-51
                                       HS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGT CS
                        Proteasome   3 kGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrpi 79 
                                       +G tvvG+k+++g+v+a++ r+t+   ++s++ ++K++ i++++g+++aGl +D+++++r++r+e++ y+ + + ++
  gi|385805286|ref|YP_005841684.1|   6 QGATVVGLKFSNGAVIAGEERMTYRTFIMSSQ-AKKVYLINERLGAGTAGLMGDTQNIIRIFREEIRYYETEIKSKM 81 
                                       8***********************99996666.8******************************************* PP

                                       CHHHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHHST CS
                        Proteasome  80 pverlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekeyke 156
                                       +++    ++a++l++ +++++  p++ ++++ag+d+++ p L  +dp+Gs++e++ ++aiG+g  +a+++le++y++
  gi|385805286|ref|YP_005841684.1|  82 STK----SAAKLLSNILYSYRGFPLYGEFILAGIDDKK-PTLVVLDPAGSVLEDE-YMAIGTGGPVAIGVLEELYQQ 152
                                       ***....6666666666777779************665.***************6.********************* PP

                                       TBSHHHHHHHHHHHHHHHHHHBTTSCSSEEEEEE CS
                        Proteasome 157 dltleeavelavkalkealerdklsgknievavi 190
                                       +++++ a++la++a+k++++rd++sg+ i+ +vi
  gi|385805286|ref|YP_005841684.1| 153 NIDEKTAIDLAIRAVKQGVRRDAMSGGSIDYVVI 186
                                       *****************************99987 PP

>> DUF1192  Protein of unknown function (DUF1192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   4.6e-05      0.28      27      54 ..      61      88 ..      57      90 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.6e-05
                           DUF1192 27 erIalLeaEIaRleaaiakkkasraAAe 54
                                      + I  +++EI   e++i++k ++++AA+
  gi|385805286|ref|YP_005841684.1| 61 NIIRIFREEIRYYETEIKSKMSTKSAAK 88
                                      568899*********************7 PP

>> DUF4216  Domain of unknown function (DUF4216)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   6.3e-05      0.37      45      63 ..      28      46 ..       8      50 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.3e-05
                           DUF4216 45 kkdpfilasqAkqvfYvkd 63
                                      ++  fi++sqAk+v+ +++
  gi|385805286|ref|YP_005841684.1| 28 TYRTFIMSSQAKKVYLINE 46
                                      5678***********9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.48
# Mc/sec: 1245.73
//
Query:       gi|385805287|ref|YP_005841685.1|  [L=347]
Description: glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) [Fervidicoccus fontis Kam940]
Scores for complete 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-13   49.8   0.0    5.9e-13   48.7   0.0    1.6  1  Gp_dh_C          Glyceraldehyde 3-phosphate dehydrogenase, C-
    1.4e-07   31.6   4.0    2.3e-07   31.0   2.8    2.0  2  DapB_N           Dihydrodipicolinate reductase, N-terminus
     0.0012   19.2   1.0       0.01   16.1   1.0    2.7  1  Gp_dh_N          Glyceraldehyde 3-phosphate dehydrogenase, NA
     0.0019   17.6   1.3       0.41   10.0   0.1    2.3  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
     0.0056   17.5   0.0      0.012   16.4   0.0    1.6  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
     0.0097   16.2   0.6      0.021   15.1   0.6    1.6  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
  ------ inclusion threshold ------
      0.039   13.5   1.0       0.11   12.1   1.0    1.7  1  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
      0.059   14.0   1.0       0.25   12.0   1.0    2.0  1  NAD_binding_3    Homoserine dehydrogenase, NAD binding domain
       0.24   11.7   1.7       0.24   11.7   0.4    1.7  2  TrkA_N           TrkA-N domain


Domain annotation for each model (and alignments):
>> Gp_dh_C  Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.7   0.0     3e-16   5.9e-13       3     155 ..     153     302 ..     151     305 .. 0.89

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 3e-16
                                       HHHHHHHHHHEEEEEEEEEEEECTTTSBSSSS--.SSTTTTSBTT.CSSEEEE-THHHHHHHHSGGGTTTEEEEEEE CS
                           Gp_dh_C   3 plakvlndkfgikkglmttvhaytndQkllDgpskkdlrraraaa.eniiptstgaakavglVlpelkgkldglAvr 78 
                                       +++  l++k+gikk+++ +++++++          +   ++ +++      ++++++++v++V+++   ++ ++A++
  gi|385805287|ref|YP_005841685.1| 153 RVIGGLHEKIGIKKARVSIIRRAVDV---W-----ESHSTGIMNTvVPESSIPSHHGPDVKTVVKN--LNIVTMAFK 219
                                       677789*****************998...2.....3345666666544445679***********5..789****** PP

                                       ESSSSEEEEEEEEEESSTS-HHHHHHHHHHHHH....TTTTTTEEEEHSHHHGGGGTTGCS..SEEEEGGGCEEETT CS
                           Gp_dh_C  79 VPtpnvsvvdlvvelekevtveevnaalkeaae....galkgilsyteeelvssDlvgdph..ssifdaketivvee 149
                                             ++++  +e++++ +++ev ++l+++++     + +g+++ ++  + s+Dl++ +   +++ +++  ++ve+
  gi|385805287|ref|YP_005841685.1| 220 GSHNLFHMHSGFIEFNRPISKDEVLNVLNAEPRvsliAYKDGLMGLNSVFELSRDLNRPRGdlYEVPVWSDLMKVED 296
                                       **********************************99999******************999889************** PP

                                       TEEEEE CS
                           Gp_dh_C 150 nlvkvv 155
                                       n+++++
  gi|385805287|ref|YP_005841685.1| 297 NELYLI 302
                                       *99876 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   2.8   1.1e-10   2.3e-07       2      96 ..       6     113 ..       5     132 .. 0.81
   2 ?   -2.8   0.0       3.2   6.3e+03      45      87 ..     205     247 ..     187     256 .. 0.63

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 1.1e-10
                                       EEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTC..STTTTTBHH............HHSSSS--S-BEBSSHHHH CS
                            DapB_N   2 kvavvGasGrmGkevvkaveeaedlelvaavdrke..selegkdag............ellglgklgvavtddleev 64 
                                       +v+v+G+ G +Gk+v++av  ++d++lv++ d ++       k a                +++k+g++v+d++e++
  gi|385805287|ref|YP_005841685.1|   6 RVLVMGY-GVIGKRVADAVVLQDDMKLVGVGDVSSdwR---IKLAQkkginvyavgndAKEKMEKSGIKVEDTVESL 78 
                                       89*****.**********************99988442...32222334678888887666778************* PP

                                       HHH..-SEEEE-S-HHHHHHHHHHHHHT.T-EEEE CS
                            DapB_N  65 lek..advliDFTtpeavlenlklalek.gvklVi 96 
                                       l++  +d+++D T  +    n +++++k gv++++
  gi|385805287|ref|YP_005841685.1|  79 LKSgaVDIVVDATPKDIGARNKETLYKKyGVNAIF 113
                                       *************9999999999999888999998 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.2
                                       HHHSSSS--S-BEBSSHHHHHHH-SEEEE-S-HHHHHHHHHHH CS
                            DapB_N  45 gellglgklgvavtddleevlekadvliDFTtpeavlenlkla 87 
                                        ++++  ++  + ++  ++++      i+F +p +  e+l+++
  gi|385805287|ref|YP_005841685.1| 205 KTVVKNLNIVTMAFKGSHNLFHMHSGFIEFNRPISKDEVLNVL 247
                                       4444444444555555666666677778887777777766665 PP

>> Gp_dh_N  Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   1.0   5.2e-06      0.01       2      37 ..       6      42 ..       5     114 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.2e-06
                                      EEEEESTSHHHHHHHHHHHHHTTCEEEEEE-.TS-HH CS
                           Gp_dh_N  2 kvainGfGRIGrlvlralleekelevvaind.ltdle 37
                                      +v + G+G IG+ v+ a++ ++++++v + d + d++
  gi|385805287|ref|YP_005841685.1|  6 RVLVMGYGVIGKRVADAVVLQDDMKLVGVGDvSSDWR 42
                                      7999***************************445544 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.3    0.0011       2.2      38      64 ..       6      33 ..       3      40 .. 0.79
   2 !   10.0   0.1   0.00021      0.41      40     115 ..      30     104 ..      22     113 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0011
                                      EEEEES-SHHHHHHHHHHH.HTT-EEEE CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlk.afgmkvia 64
                                      +v ++G+G IG++va+ +  + +mk+++
  gi|385805287|ref|YP_005841685.1|  6 RVLVMGYGVIGKRVADAVVlQDDMKLVG 33
                                      799************9876566666665 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00021
                                       EEES-SHHHHHH.HHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHH CS
                      2-Hacid_dh_C  40 GiiGlGrIGqav.akrlkafgmkviaydrskkkeeeeeelgvelvsleellaesDivslhlpltpetrhlinaeela 115
                                        ++G+G++ +   +k++++ g++v+a+    k  e++e+ g+++++  e l +s  v +++ +tp+  +  n+e+l 
  gi|385805287|ref|YP_005841685.1|  30 KLVGVGDVSSDWrIKLAQKKGINVYAVGNDAK--EKMEKSGIKVEDTVESLLKSGAVDIVVDATPKDIGARNKETLY 104
                                       579999999987368888*********99977..447899**99999999999************999999999885 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 !   16.4   0.0   6.2e-06     0.012       2      76 ..       6      97 ..       5     115 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.2e-06
                                      EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESS..................HHHHHTCTT CS
                      GFO_IDH_MocA  2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysd..................leelladpe 62
                                      rv++ G+G ig++ + ++  + ++ ++v++ d ++    ++a++ g+++y+                   +e ll++ +
  gi|385805287|ref|YP_005841685.1|  6 RVLVMGYGVIGKRVADAVVLQ-DDMKLVGVGDVSSDWRIKLAQKKGINVYAVgndakekmeksgikvedtVESLLKSGA 83
                                      89*************666666.**************************99988899999*******999999****99* PP

                                      ESEEEE-S-GGGHH CS
                      GFO_IDH_MocA 63 idavivatpngthe 76
                                      +d+v+ atp + ++
  gi|385805287|ref|YP_005841685.1| 84 VDIVVDATPKDIGA 97
                                      ****9999986554 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.6   1.1e-05     0.021       1      78 [.       7      92 ..       7      98 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.1e-05
                                      EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH..........TTTCEEEEE--TTTHHHHHHHHHTT CS
                   Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka..........lgvrfeaialdaenyeavLaallke 69
                                      vl+ G+G +G+ va+ ++ ++d++  + v d s +   +la+k+          +++++e+  +    +e+++++llk+
  gi|385805287|ref|YP_005841685.1|  7 VLVMGYGVIGKRVADAVVLQDDMK-LVGVGDVSSDWRIKLAQKKginvyavgndAKEKMEKSGIK---VEDTVESLLKS 81
                                      89********************95.8889999998888888777888877754444444444444...45567799999 PP

                                      S..SEEEE-SS CS
                   Sacchrp_dh_NADP 70 g..dlvvnlsp 78
                                      g  d+vv+++p
  gi|385805287|ref|YP_005841685.1| 82 GavDIVVDATP 92
                                      999*****988 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.0   5.3e-05      0.11       6      60 ..       6      62 ..       3     141 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.3e-05
                                      -EEEES-SHHHH..HHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT CS
                              IlvN  6 kiaviGyGsqGh..aqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkk 60
                                      ++ v+GyG  G+  a a  l+d    v vg  +++  +k A+++g++v+ v + +k+
  gi|385805287|ref|YP_005841685.1|  6 RVLVMGYGVIGKrvADAVVLQDDMKLVGVGDVSSDWRIKLAQKKGINVYAVGNDAKE 62
                                      689******9985577889****99************************99754443 PP

>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.0   0.00013      0.25       1      70 [.      11      94 ..      11      99 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                                      --SHHHHHHHHHHHH---S...................SEEEEEEEEESSEEE-TTHHHHHT--CB---HHHHHHHHS- CS
                     NAD_binding_3  1 GlGaiGsavleqlkrqqse...................ielelvavadrdsllskdrkallasealtldlddliahldp 60
                                      G+G+iG++v++++  q +                     +++++av ++   ++k         ++ + +++l++  ++
  gi|385805287|ref|YP_005841685.1| 11 GYGVIGKRVADAVVLQDDMklvgvgdvssdwriklaqkKGINVYAVGNDA--KEKME---KSGIKVEDTVESLLKSGAV 84
                                      77888888887776666543455555555555555555567777777777..33333...444455555666666557* PP

                                      EEEEE-S--H CS
                     NAD_binding_3 61 dvvVEcasse 70
                                      d+vV++++++
  gi|385805287|ref|YP_005841685.1| 85 DIVVDATPKD 94
                                      ******9875 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.4   0.00012      0.24       1      79 [.       7      88 ..       7     105 .. 0.81
   2 ?   -4.0   0.0       8.9   1.8e+04      56      68 ..     160     172 ..     160     177 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                                      EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHH..HHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHH CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeer..veelreeglevvvgdatdeevLeeagiekadaviaatgddean 76
                                      ++++G+G +G+++a+ +   + ++ v++ +  +   ++ ++++g++v+      +e +e+ gi+  d+v  ++++ ++ 
  gi|385805287|ref|YP_005841685.1|  7 VLVMGYGVIGKRVADAVVLqDDMKLVGVGDVSSDwrIKLAQKKGINVYAVGNDAKEKMEKSGIKVEDTVESLLKSGAVD 85
                                      68**************9995667799997655433399999*****999888889999999999888888888777777 PP

                                      HHH CS
                            TrkA_N 77 ila 79
                                      i++
  gi|385805287|ref|YP_005841685.1| 86 IVV 88
                                      766 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 8.9
                                       HHTTGGGESEEEE CS
                            TrkA_N  56 eeagiekadavia 68 
                                       e++gi+ka++ i+
  gi|385805287|ref|YP_005841685.1| 160 EKIGIKKARVSII 172
                                       5789999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 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:                        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: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2196.16
//
Query:       gi|385805288|ref|YP_005841686.1|  [L=311]
Description: hypothetical protein FFONT_0243 [Fervidicoccus fontis Kam940]
Scores for complete 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   17.9   0.1     0.0075   16.7   0.1    1.6  1  SopA      SopA-like central domain


Domain annotation for each model (and alignments):
>> SopA  SopA-like central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   4.2e-07    0.0075       9      57 ..      97     148 ..      92     164 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.2e-07
                                       HHHHH---HHHHGGGHHH...HHHHHTSTTTTC-HHHHHHHHHHHHHHHH-- CS
                              SopA   9 lvksLklteislksvaes...llkilshaPYidepliaewlqeveerffaaf 57 
                                       ++ sLk  +   +   +s   l+  l   PYid+p+i++w++e ++  ++a 
  gi|385805288|ref|YP_005841686.1|  97 IMASLKERNQFARLASSSsvmLVPSLFLIPYIDDPVISRWINEENSIEIDAR 148
                                       77888777776665555422256667789**************999888854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); 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 0.27s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2028.00
//
Query:       gi|385805289|ref|YP_005841687.1|  [L=279]
Description: methylthioadenosine phosphorylase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.2e-50  172.0   0.0    1.3e-50  171.8   0.0    1.0  1  PNP_UDP_1  Phosphorylase superfamily


Domain annotation for each model (and alignments):
>> PNP_UDP_1  Phosphorylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.8   0.0   7.4e-55   1.3e-50       1     233 [.      17     255 ..      17     256 .. 0.93

  Alignments for each domain:
  == domain 1  score: 171.8 bits;  conditional E-value: 7.4e-55
                                       CEEEEESSH....HHHHHHHHH...EEEEEEEEEE.TTEEEEEEEETTEEE.EEEE--....SSHHHHHHHHHHHHH CS
                         PNP_UDP_1   1 kiaiivgsp....gevellaes...pleetpfgregrgfkfvtGtlkgkpv.vivstG....iGkpnaavvaeirll 65 
                                       +iaii+gs+    +    ++e+    l +tp+g +  +  f++Gtlkgk+v ++ ++G    i ++ ++++a+i+++
  gi|385805289|ref|YP_005841687.1|  17 DIAIIGGSGlysaE----FLEDakeLLINTPYGAP--SDAFTIGTLKGKKVaFLPRHGkghrIPPHKINYRANIWAI 87 
                                       69*******74433....33333667*********..*********7777769************************ PP

                                       HHC--SEEEEEEEEEESSTTT-TT-EEEEEEEEESSSCCGCCTHHCCTCCCCTTSSEE--HHHHHHHHHCHHTTTTT CS
                         PNP_UDP_1  66 kefgvkaiiriGtaGglnpdlkvGDvvipddainfdgrsplygpkeegqyfpdsydapadpelrallkeaaealgik 142
                                       k++g+k +++++++G+l+ d+k+GD+++pd++i+f+  + +++++ + + ++ ++++ ++++lr++++e a++l+i+
  gi|385805289|ref|YP_005841687.1|  88 KQLGAKWVLSVSAVGSLRTDVKPGDFIVPDQFIDFTKSREYTFFDGPRVAHVSMAYP-FCESLRRKVVETARKLNIN 163
                                       **********************************************97777777777.******************* PP

                                       EEE.EEEEEESESS-CHHHHHH.HHHHTC-CEEESSHHHHHHHHHHTT--EEEEEEEEETTTBETTCTCH.HCCCHH CS
                         PNP_UDP_1 143 vhr.Gvvatadgfyaeteaelr.llrrlgadaveMEtaavaqlArelgipfaairvvsdlaaggadaeatheeveef 217
                                       +h+ G++++ +g++++t ae+r + + + ad+v+M+ ++++ lA e+++++a++++++d ++ +a+++ t +eve +
  gi|385805289|ref|YP_005841687.1| 164 IHTkGTYVCIEGPRFSTFAESRiWKEVFKADIVGMTLVPEVNLACEMELCYATLAMITD-YDVWAERPVTADEVERV 239
                                       **********************8888888******************************.899************** PP

                                       HHHHHHHHHHHHHHHH CS
                         PNP_UDP_1 218 aqeaaknaaalllall 233
                                       + e++k+a ++l  l+
  gi|385805289|ref|YP_005841687.1| 240 MSENVKKAREILYNLI 255
                                       *********9997766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1675.50
//
Query:       gi|385805290|ref|YP_005841688.1|  [L=224]
Description: purine phosphoribosyltransferase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      7e-18   64.6   0.0      1e-17   64.1   0.0    1.2  1  Pribosyltran  Phosphoribosyl transferase domain
    0.00031   20.3   0.1    0.00042   19.8   0.1    1.1  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 !   64.1   0.0   1.1e-21     1e-17      15     149 ..      18     148 ..       9     159 .. 0.78

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 1.1e-21
                                       EEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----TTSEEE CS
                      Pribosyltran  15 varlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlledpagkkVl 91 
                                        ++la++i+++ +++pdv+++iargGv+ a il d+L+  l+ ++++  +   +  +++++++  +  +d+  k+Vl
  gi|385805290|ref|YP_005841688.1|  18 SRDLARKIIDS-GYQPDVIIAIARGGVVTARILCDYLG-VLDLLSIKIEHWIETAAHTENATVKYSFNTDLSSKRVL 92 
                                       589********.*************************9.4555555555555555555566666689********** PP

                                       EE-SEESSSHHHHHHHH.HHHCC-BSEEEEEEEE.E-HHHHHHHHHH-TTS.....EEEE CS
                      Pribosyltran  92 iVDDildtGgTllaale.lLkekgpeevriavlv.dkpateeevdknakrvfslspdnfv 149
                                       +VDDi+dtG+++  a e + ++ +p e+++a+     +  + ++d++ + v+    d+++
  gi|385805290|ref|YP_005841688.1|  93 LVDDICDTGKSIVVAKEhITEKSRPLEIKTATMQyISSVAKYKPDYYIDDVK----DWIW 148
                                       *****************666777899******98534444455555555555....5554 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.1   4.6e-08   0.00042      70     148 ..      34     115 ..      23     133 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 4.6e-08
                           UPRTase  70 alVpilRaGegmeealrellpearvghlglqreeet....lepveyynkLPkkiaertvlllDpviaTGgsaaaaiq 142
                                       ++++i R+G   ++ l + l    ++ ++++   et     ++      + +++++++vll+D ++ TG+s++ a +
  gi|385805290|ref|YP_005841688.1|  34 VIIAIARGGVVTARILCDYLGVLDLLSIKIEHWIETaahtENATVK-YSFNTDLSSKRVLLVDDICDTGKSIVVAKE 109
                                       689999***9999999999999999999888755552221333333.3578888*********************** PP

                           UPRTase 143 lLkerg 148
                                       +++e+ 
  gi|385805290|ref|YP_005841688.1| 110 HITEKS 115
                                       **9964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1416.50
//
Query:       gi|385805291|ref|YP_005841689.1|  [L=322]
Description: biotin--acetyl-CoA-carboxylase ligase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-12   47.5   0.2    1.2e-12   47.5   0.2    2.1  3  BPL_C          Biotin protein ligase C terminal domain
    4.1e-12   46.2   0.0    6.8e-12   45.4   0.0    1.4  1  BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family
    0.00057   19.7   0.0      0.001   18.9   0.0    1.4  1  TrmB           Sugar-specific transcriptional regulator TrmB
    0.00079   19.2   0.0      0.003   17.4   0.0    1.9  2  HTH_5          Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
      0.014   14.9   0.0      0.033   13.7   0.0    1.6  1  HTH_24         Winged helix-turn-helix DNA-binding
       0.11   12.5   0.0       0.25   11.3   0.0    1.5  1  HTH_11         HTH domain
       0.17   12.1   0.0       0.33   11.2   0.0    1.4  1  HTH_34         Winged helix DNA-binding domain
        0.2   11.8   0.0       0.42   10.7   0.0    1.5  1  HTH_20         Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> 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 ?   -2.9   0.0       3.1   6.9e+03      33      47 ..      55      69 ..      50      69 .. 0.74
   2 ?   -2.4   0.1       2.1   4.8e+03      14      24 ..     255     266 ..     253     266 .. 0.76
   3 !   47.5   0.2   5.6e-16   1.2e-12       1      47 [.     273     319 ..     273     320 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.1
                                      TTE.EEEESSCCEEE CS
                             BPL_C 33 ddglqpdinsGdisl 47
                                      +d++ + ++s d+sl
  gi|385805291|ref|YP_005841689.1| 55 EDNKFKIPSSSDFSL 69
                                      555578899999997 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.1
                                       EEEEEEEEE.-T CS
                             BPL_C  14 kveGiavGI.dd 24 
                                       ++eG+++ I +d
  gi|385805291|ref|YP_005841689.1| 255 IIEGRVEAIiSD 266
                                       679999999665 PP

  == domain 3  score: 47.5 bits;  conditional E-value: 5.6e-16
                                       STTSEEEEEETSCEEEEEEEEE-TTSEEEEEETTE.EEEESSCCEEE CS
                             BPL_C   1 hsGqeVtlededgkveGiavGIdddGaLllktddglqpdinsGdisl 47 
                                       ++G+ V++e +d++v+G+av+Id dG L++ +++g+++++++Gd+++
  gi|385805291|ref|YP_005841689.1| 273 TIGRKVRIENRDEIVYGTAVDIDTDGSLVVNLENGKIEKFYAGDVFH 319
                                       69********************************************8 PP

>> BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   0.0     3e-15   6.8e-12      21     131 .]     106     211 ..      91     211 .. 0.79

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 3e-15
                                       --TT-EEEEEE..ESS-B..-B--B-TTSEEEEEEEEESS...-CCGTHHHHHHHHHHHHHHH......HHTT-TTE CS
                     BPL_LplA_LipB  21 lesgglvvvrr..qtgGr..nvwhspkgeltyslllspeqktfqnrvlelyvsllvlavlealgyrdskpgiegipv 93 
                                        e g+lv+ ++  +  Gr  + wh pkg++++sl+l+p             ++l++la+  ++  +  +    +i+ 
  gi|385805291|ref|YP_005841689.1| 106 AEEGNLVLCEEikNARGRfgRKWHAPKGGIWFSLILRPPS----LEW----INLISLAMGASV--SIAIEDVLNIKS 172
                                       55555555554336679999*****************874....333....555555555555..44558999**** PP

                                       EEETTTEEEETTEEEEEEEEEEEE.TTS-EEEEEEEEEE CS
                     BPL_LplA_LipB  94 fikwpnDlyvngrKlaGiavtstr.gktlhhivigvgvn 131
                                         kwpnD+++n +K+ Gi+ + +    +l ++++gvg+n
  gi|385805291|ref|YP_005841689.1| 173 GLKWPNDVLINEKKICGILSEAKItDDRLDYVIVGVGLN 211
                                       *********************9998999*********98 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   4.6e-07     0.001       9      58 ..       8      57 ..       6      63 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 4.6e-07
                                      HCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB  9 yEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                      yE++++++L ++g+a++de++    +p s++ e +++L + Gl   ++ +
  gi|385805291|ref|YP_005841689.1|  8 YEVSIFKYLAEKGEASIDELSDVFSLPPSNIIEKIKKLNEIGLFINSEDN 57
                                      9*****************************************98777666 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 !   17.4   0.0   1.3e-06     0.003       7      44 ..      12      50 ..      10      52 .. 0.95
   2 ?   -1.9   0.0       1.4   3.1e+03      14      28 ..     183     197 ..     180     199 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.3e-06
                                      HHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                             HTH_5  7 ILklLae.gelcvcelaeelglsqstvShHLkkLreaGL 44
                                      I k+Lae ge+++ el++ + l++s++ +  kkL e GL
  gi|385805291|ref|YP_005841689.1| 12 IFKYLAEkGEASIDELSDVFSLPPSNIIEKIKKLNEIGL 50
                                      7799********************************998 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.4
                                       SSEEHHHHHHHHTS- CS
                             HTH_5  14 gelcvcelaeelgls 28 
                                       +e+++c +  e +++
  gi|385805291|ref|YP_005841689.1| 183 NEKKICGILSEAKIT 197
                                       789999999988876 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.5e-05     0.033       7      46 ..      11      50 ..       7      51 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.5e-05
                            HTH_24  7 kILelLqknprisqreLAerlglSpstvnrrlkrLeeeGl 46
                                       I ++L +++  s+ eL++   l+ps++ + +k+L e Gl
  gi|385805291|ref|YP_005841689.1| 11 SIFKYLAEKGEASIDELSDVFSLPPSNIIEKIKKLNEIGL 50
                                      5889*******************************99886 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00011      0.25       5      51 ..      12      57 ..      10      58 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                            HTH_11  5 ilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpIesepg 51
                                      i + L +++g  s++eL++ +++  + +   Ik+L+e+g+ I se +
  gi|385805291|ref|YP_005841689.1| 12 IFKYL-AEKGEASIDELSDVFSLPPSNIIEKIKKLNEIGLFINSEDN 57
                                      66778.88888********************************9866 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00015      0.33       4      42 ..      11      49 ..       9      64 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00015
                            HTH_34  4 avlsyLasvdeadfvelkealeatdgnLsvhlkkLekag 42
                                      +++ yLa++ ea+  el++  ++  +n+  ++kkL++ g
  gi|385805291|ref|YP_005841689.1| 11 SIFKYLAEKGEASIDELSDVFSLPPSNIIEKIKKLNEIG 49
                                      79*********************************9988 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00019      0.42      14      54 ..      11      52 ..       9      57 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00019
                                      HHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTT.E CS
                            HTH_20 14 rilraLaraegltaselaerldlskntlsyHLrvLeeagL.v 54
                                       i+++La++++++  el + ++l+++++   +++L e gL +
  gi|385805291|ref|YP_005841689.1| 11 SIFKYLAEKGEASIDELSDVFSLPPSNIIEKIKKLNEIGLfI 52
                                      599**********************************99856 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); 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: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2216.78
//
Query:       gi|385805292|ref|YP_005841690.1|  [L=77]
Description: hypothetical protein FFONT_0247 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-12   47.9   0.0    1.9e-12   47.7   0.0    1.0  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 !   47.7   0.0   1.1e-16   1.9e-12       1      76 []       1      75 [.       1      75 [. 0.94

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 1.1e-16
                            MJ1316  1 MrtaqdvlnRirWdkeldkskfvvgyldR.fkgikevpleeiswied..flleeeegelaIPlHRiryikrkgevvWdR 76
                                      M+++  ++++ + +ke  k+k+v + ldR +++++e++++ei+++++  fl+  + +   IP+HRir+i+ kgev+ +R
  gi|385805292|ref|YP_005841690.1|  1 MNNIYSIVKKALLSKE--KKKYVFYALDRkKSTLREIRGNEITDVNEfgFLILLDGS--QIPIHRIRKITFKGEVILER 75
                                      99*************9..9****************************9977777774..5****************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 531.75
//
Query:       gi|385805293|ref|YP_005841691.1|  [L=283]
Description: hypothetical protein FFONT_0248 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.014   15.0   0.3      0.046   13.4   0.0    1.9  2  DUF5314         Family of unknown function (DUF5314)
       0.12   12.4   1.1        1.2    9.2   0.0    2.8  3  CpXC            CpXC protein
       0.16   11.7   0.3       0.16   11.7   0.3    2.3  2  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit


Domain annotation for each model (and alignments):
>> DUF5314  Family of unknown function (DUF5314)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   7.8e-06     0.046      86     170 ..      20     104 ..      14     120 .. 0.85
   2 ?   -1.5   0.1      0.28   1.7e+03      83      94 ..     185     196 ..     134     227 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.8e-06
                           DUF5314  86 svske.vkikieeyfqnhkkkketslelLeyLkskYgrkkvsstaeifselqsmsnkslkekelwakklvktildda 161
                                       s+s++ v+i i++y +++k   +    + + +k++   + v  +a+ ++    m+n s+  k++w+ ++++ i + +
  gi|385805293|ref|YP_005841691.1|  20 SISQRvVEILIDDYEETEK-GRNLPWSMFSKIKDELTSEEVGNLARRYNPRLIMFNGSNPLKHEWILRSIEPIKKMN 95 
                                       7777626899999999999.55556899***********************************************99 PP

                           DUF5314 162 eelelsdkl 170
                                        +  +s++ 
  gi|385805293|ref|YP_005841691.1|  96 IDVGISYSC 104
                                       998888766 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.28
                           DUF5314  83 Ilksvskevkik 94 
                                       I + + +e+++ 
  gi|385805293|ref|YP_005841691.1| 185 IDEMSKEEINKI 196
                                       333333333333 PP

>> CpXC  CpXC protein
   #    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      99     117 ..      11      29 ..       8      30 .. 0.90
   2 ?    0.2   0.2      0.12   7.1e+02      34      46 ..     214     226 ..     186     232 .. 0.77
   3 ?    9.2   0.0   0.00021       1.2      27      54 ..     232     259 ..     228     272 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.38
                              CpXC  99 aEkilileagldDravell 117
                                        Ek ++++  +  r+ve+l
  gi|385805293|ref|YP_005841691.1|  11 NEKAGLFHYSISQRVVEIL 29 
                                       59**************985 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.12
                              CpXC  34 slfeatCpkCgat 46 
                                       ++f ++C+kC + 
  gi|385805293|ref|YP_005841691.1| 214 NYFATRCQKCRNV 226
                                       4677888888665 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.00021
                              CpXC  27 keklldgslfeatCpkCgatakleapll 54 
                                       +e+l++++l+   Cp Cg+++ ++ pl 
  gi|385805293|ref|YP_005841691.1| 232 EENLMKNNLNGENCPFCGYKILYKSPLK 259
                                       799*******************999986 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.6      0.14   8.1e+02      19      23 ..     219     223 ..     217     230 .. 0.87
   2 ?   11.7   0.3   2.6e-05      0.16      20      30 ..     245     255 ..     243     256 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.14
                                       --SSS CS
                    DNA_RNApol_7kD  19 RCkeC 23 
                                       RC++C
  gi|385805293|ref|YP_005841691.1| 219 RCQKC 223
                                       99999 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 2.6e-05
                                       -SSS-----B- CS
                    DNA_RNApol_7kD  20 CkeCGhRilYK 30 
                                       C  CG++ilYK
  gi|385805293|ref|YP_005841691.1| 245 CPFCGYKILYK 255
                                       999******** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       863  (0.0481343); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); 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: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1959.67
//
Query:       gi|385805294|ref|YP_005841692.1|  [L=354]
Description: radical SAM protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.2e-17   62.3   0.9    2.2e-16   60.7   0.0    2.1  3  Radical_SAM    Radical SAM superfamily
    0.00031   21.0   0.0    0.00066   20.0   0.0    1.5  1  Fer4_12        4Fe-4S single cluster domain
     0.0039   16.5   3.1       0.17   11.3   0.1    2.8  2  zf-ribbon_3    zinc-ribbon domain
  ------ inclusion threshold ------
      0.067   13.2   0.2      0.067   13.2   0.2    2.7  3  DZR            Double zinc ribbon
        8.4    6.5   9.7        6.1    7.0   1.0    3.4  3  zf-BED         BED zinc finger


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 !   60.7   0.0   6.1e-20   2.2e-16       3     166 ..      94     254 ..      92     255 .. 0.90
   2 ?   -3.3   0.0       2.9     1e+04     133     144 ..     290     301 ..     279     311 .. 0.48
   3 ?   -1.1   0.5       0.6   2.2e+03       9      17 ..     341     349 ..     340     351 .. 0.82

  Alignments for each domain:
  == domain 1  score: 60.7 bits;  conditional E-value: 6.1e-20
                                       EESEESS--TTTSCCTT....HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCC CS
                                       xxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpet....vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklav 75 
                                        t gCn+ C fC+++e      + + +g +  +eei++++ +++    ++++  +  ep++ +++  +++++ak   
  gi|385805294|ref|YP_005841692.1|  94 STVGCNFFCQFCQNWEIsqsrLEEGLYGNYYEPEEIVNIALSNR----ADGISYTYNEPTVFYEYMYDVAKIAKQ-- 164
                                       689*****************99999******************9....***************************.. PP

                                       CTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHH.HHHHHHTCTSHHHHHHHHHHHHHHTTSET.EEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                       Radical_SAM  76 pgiritvetngtlpdeeklerllelgvdrvslgleaadde.kvlklmnrghtfeevlealeklreagikr.vvdriv 150
                                       + + +t++tng+   e  le++  +  d  +++ +   ++  ++k+m + ++++ + ++l +++e+ i+  ++d +v
  gi|385805294|ref|YP_005841692.1| 165 KALFNTMVTNGYIS-EYALEEISSYM-DAATVDFKGSGNKeFYQKYM-GVPDPSPIFDTLTLMKEKKIHIeITDLVV 238
                                       7************8.*********99.********999995566666.99*******************66666666 PP

                                       EBTTTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxx RF
                       Radical_SAM 151 glpGendeeleellel 166
                                          G  +e++++l ++
  gi|385805294|ref|YP_005841692.1| 239 PKIGDREEDIDKLTKW 254
                                       6666666777776665 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.9
                                       HHHHHHHTTSET CS
                                       xxxxxxxxxxxx RF
                       Radical_SAM 133 aleklreagikr 144
                                         e+++++g+k 
  gi|385805294|ref|YP_005841692.1| 290 FAEIAKNNGLKY 301
                                       233333333332 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.6
                                       S--TTTSCC CS
                                       xxxxxxxxx RF
                       Radical_SAM   9 lrCsfCarp 17 
                                       +rC++C  +
  gi|385805294|ref|YP_005841692.1| 341 GRCKYCGYK 349
                                       69****976 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   1.8e-07   0.00066       8     116 ..      91     195 ..      85     207 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.8e-07
                           Fer4_12   8 lslfvsgCnlsCkgCfnketwsfk.....sgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkev 79 
                                       ls+ + gCn+ C++C n e+ + +     +g+ ++ e + +    +  ++ +g++++  EP +   +e +++++k  
  gi|385805294|ref|YP_005841692.1|  91 LSISTVGCNFFCQFCQNWEISQSRleeglYGNYYEPEEIVN---IALSNRADGISYTYNEPTV--FYEYMYDVAKIA 162
                                       567788*************9987754444555555555555...4568999************..9999******99 PP

                           Fer4_12  80 keekpekdiwlytgytleelskkekeellkeidv.lvd 116
                                       k++++  + ++++gy+ e  ++    e+ +++d  +vd
  gi|385805294|ref|YP_005841692.1| 163 KQKAL-FNTMVTNGYISEYALE----EISSYMDAaTVD 195
                                       99999.689*******999985....566666643555 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.1   4.9e-05      0.17       2      12 ..     314     325 ..     313     328 .. 0.75
   2 !    4.7   0.5    0.0058        21      19      25 ..     343     349 ..     339     350 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.9e-05
                       zf-ribbon_3   2 tvrCPnCGa.pl 12 
                                        ++CP+CG+ ++
  gi|385805294|ref|YP_005841692.1| 314 NTYCPSCGKvLI 325
                                       579999999555 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0058
                       zf-ribbon_3  19 CpyCGtk 25 
                                       C+yCG+k
  gi|385805294|ref|YP_005841692.1| 343 CKYCGYK 349
                                       *****98 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.5      0.15   5.3e+02      28      49 .]      30      51 ..       6      51 .. 0.72
   2 ?   -2.3   0.9       1.3   4.8e+03      14      19 ..     101     106 ..      96     111 .. 0.69
   3 ?   13.2   0.2   1.9e-05     0.067      12      38 ..     314     350 ..     310     352 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.15
                               DZR 28 edrCpsCgekvdpearfCpeCG 49
                                        +C  C++ ++   +  ++CG
  gi|385805294|ref|YP_005841692.1| 30 TVKCKLCKRYCEISNNSYGACG 51
                                      7889999999888888777776 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.3
                               DZR  14 fCseCg 19 
                                       fC+ C+
  gi|385805294|ref|YP_005841692.1| 101 FCQFCQ 106
                                       555554 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 1.9e-05
                               DZR  12 arfCseCgtklkavaa..........edrCpsCgekv 38 
                                       + +C+ Cg+ l + +             rC  Cg+k+
  gi|385805294|ref|YP_005841692.1| 314 NTYCPSCGKVLIEREGfyiekinlteDGRCKYCGYKT 350
                                       689*******9976669999***99999*****9985 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   1.0    0.0017       6.1       5      28 ..      19      42 ..      16      48 .. 0.79
   2 ?    0.4   0.0      0.19   6.7e+02      15      26 ..     313     324 ..     301     329 .. 0.82
   3 ?    2.2   0.6     0.051   1.8e+02      18      26 ..     342     350 ..     340     352 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0017
                                      SSS----GGSS--EETTTTEE--- CS
                            zf-BED  5 kyftpvslkeqkavCryCgkilsr 28
                                      k+ + v+ ke+ ++C+ C++    
  gi|385805294|ref|YP_005841692.1| 19 KFWDQVEGKEKTVKCKLCKRYCEI 42
                                      5678899***********976555 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.19
                                       S--EETTTTEE- CS
                            zf-BED  15 qkavCryCgkil 26 
                                        +++C  Cgk+l
  gi|385805294|ref|YP_005841692.1| 313 ENTYCPSCGKVL 324
                                       5789******97 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.051
                                       EETTTTEE- CS
                            zf-BED  18 vCryCgkil 26 
                                       +C+yCg ++
  gi|385805294|ref|YP_005841692.1| 342 RCKYCGYKT 350
                                       7****9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       723  (0.0403257); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); 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):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2172.04
//
Query:       gi|385805295|ref|YP_005841693.1|  [L=256]
Description: putative ATP binding protein [Fervidicoccus fontis Kam940]
Scores for complete 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-60  203.4   0.0    5.3e-60  203.2   0.0    1.0  1  ATP_bind_1       Conserved hypothetical ATP binding protein
    0.00021   21.2   0.0       0.46   10.4   0.0    3.1  3  RsgA_GTPase      RsgA GTPase
    0.00056   19.7   0.0      0.063   13.0   0.0    2.7  3  PduV-EutP        Ethanolamine utilisation - propanediol utili
    0.00083   18.9   0.0      0.093   12.3   0.0    2.5  2  GTP_EFTU         Elongation factor Tu GTP binding domain
    0.00092   19.5   0.0     0.0039   17.5   0.0    2.0  2  AAA_22           AAA domain
     0.0016   17.7   0.0     0.0037   16.5   0.0    1.6  1  ArsA_ATPase      Anion-transporting ATPase
     0.0018   18.7   0.0     0.0072   16.7   0.0    2.0  2  AAA_16           AAA ATPase domain
     0.0056   16.7   0.0       0.97    9.5   0.0    2.4  2  MMR_HSR1_Xtn     C-terminal region of MMR_HSR1 domain
  ------ inclusion threshold ------
      0.014   15.1   0.0      0.027   14.1   0.0    1.5  1  SRP54            SRP54-type protein, GTPase domain
      0.016   15.1   0.0      0.036   14.0   0.0    1.6  1  NACHT            NACHT domain
      0.017   15.5   0.2       0.92    9.9   0.0    2.7  2  NBD94            Nucleotide-Binding Domain 94 of RH
      0.018   14.4   0.0      0.067   12.5   0.0    2.0  1  Gtr1_RagA        Gtr1/RagA G protein conserved region
      0.024   14.7   0.0      0.028   14.5   0.0    1.3  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
      0.032   14.3   0.0       0.44   10.7   0.0    2.2  1  MMR_HSR1         50S ribosome-binding GTPase
      0.051   14.1   0.0      0.092   13.3   0.0    1.4  1  ABC_tran         ABC transporter
      0.054   13.2   0.0      0.098   12.4   0.0    1.4  1  PRK              Phosphoribulokinase / Uridine kinase family
      0.057   13.3   0.4        5.1    7.0   0.0    2.9  3  AAA_31           AAA domain
      0.073   12.6   0.0       0.12   11.9   0.0    1.3  1  AAA_7            P-loop containing dynein motor region
      0.075   13.3   0.0       0.19   12.0   0.0    1.7  1  AAA_28           AAA domain
      0.078   12.7   0.0       0.13   12.0   0.0    1.2  1  AAA_30           AAA domain
      0.091   12.9   0.0       0.29   11.3   0.0    1.8  2  AAA_33           AAA domain
      0.099   11.7   0.0       0.14   11.2   0.0    1.2  1  T2SSE            Type II/IV secretion system protein
       0.11   12.2   0.0       0.16   11.7   0.0    1.4  1  AAA_24           AAA domain
       0.14   11.4   0.0       0.73    9.0   0.0    2.0  2  NB-ARC           NB-ARC domain
       0.15   11.6   0.0        3.8    7.0   0.0    2.7  3  FeoB_N           Ferrous iron transport protein B
       0.16   10.8   0.0       0.23   10.3   0.0    1.2  1  Polyoma_lg_T_C   Polyomavirus large T antigen C-terminus
       0.17   11.4   0.0       0.29   10.6   0.0    1.4  1  PhoH             PhoH-like protein
       0.17   11.5   0.0       0.32   10.6   0.0    1.4  1  Thymidylate_kin  Thymidylate kinase
       0.22   11.9   0.0       0.56   10.6   0.0    1.7  1  Ribosomal_L18p   Ribosomal L18 of archaea, bacteria, mitoch. 


Domain annotation for each model (and alignments):
>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.2   0.0   8.6e-63   5.3e-60       2     239 ..       9     246 ..       8     248 .. 0.92

  Alignments for each domain:
  == domain 1  score: 203.2 bits;  conditional E-value: 8.6e-63
                        ATP_bind_1   2 vGpaGsGKttfvgalseilelrgrsvavvNLDPAaeelpYeaavdirelitledvmedlglgpngalvvaleflres 78 
                                       +GpaGsGKtt++ ++s++l+++g +   vNLDPA+e lpY++++d+r++++ ++v +++ lgpngal  ++++l  +
  gi|385805295|ref|YP_005841693.1|   9 MGPAGSGKTTLTATFSDWLSSQGIDNVKVNLDPAVEYLPYDPDIDVRNYVDAREVAKKYSLGPNGALLASMDLLYGK 85 
                                       8**************************************************************************** PP

                        ATP_bind_1  79 ldwldeelekeeddyllfDtPGQielfthseslakiveeLesefalvvvyLvDsqrltdptkfisgllsalsamlrl 155
                                       l+++++el + e +y+l+D+PGQ+elf +++ +  iv++L+s+ ++ vv+L+D+++ +++ +f+s l+++ s+ +r+
  gi|385805295|ref|YP_005841693.1|  86 LEDIKKELMEIEGEYVLIDMPGQLELFSFRSTGPLIVDRLSSKNRTAVVFLMDANFTASVENFLSILMLSHSIRIRH 162
                                       ********77799**************************************************************** PP

                        ATP_bind_1 156 elPhvvvlnkfDllkek.lekeleffedvealsl.llekeeekykklaeaiaelleefalvlrflplssekeesied 230
                                         P++++++k+Dll+ + le+ l   e +e l++ +++k + ky++  ++ia++l e ++   f+p+ss ++e++++
  gi|385805295|ref|YP_005841693.1| 163 YFPQINAISKIDLLSPElLEELLTLKESPELLKEkVIDKGDPKYHDYINSIADFLIEEGID--FIPVSSTTGEGLDE 237
                                       ***************9955555555555555543144555599************999987..************** PP

                        ATP_bind_1 231 llslideal 239
                                       l++ i++++
  gi|385805295|ref|YP_005841693.1| 238 LFASIQNLI 246
                                       *****9876 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   0.00075      0.46     100     120 ..       4      24 ..       1      40 [. 0.80
   2 ?    1.0   0.0      0.55   3.4e+02     143     161 ..      90     108 ..      78     113 .. 0.84
   3 ?    5.9   0.0     0.017        11      30     101 ..     176     246 ..     164     249 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00075
                                       SEEEEECSTTSSHHHHHHHHC CS
                       RsgA_GTPase 100 ktsvlvGqSGvGKStLinall 120
                                       k +v++G+ G GK+tL  ++ 
  gi|385805295|ref|YP_005841693.1|   4 KYVVFMGPAGSGKTTLTATFS 24 
                                       789*************98766 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.55
                                       SEEEEEETTTEEEESS-SS CS
                       RsgA_GTPase 143 avellelaegglliDtPGf 161
                                       + el+e++ + +liD PG 
  gi|385805295|ref|YP_005841693.1|  90 KKELMEIEGEYVLIDMPGQ 108
                                       6799****999******95 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.017
                                       --HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTTSE CS
                       RsgA_GTPase  30 lslnlldrfLvlaeekgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkellkdkt 101
                                       ls++ll+ +L+l e+ ++    v+ K D   ++  ++++++ l + g++++ vs++t+egl+el + +++ +
  gi|385805295|ref|YP_005841693.1| 176 LSPELLEELLTLKESPELLKEKVIDKGDPKYHDY-INSIADFLIEEGIDFIPVSSTTGEGLDELFASIQNLI 246
                                       6788999999999999999999999999998888.*****************************99998755 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0    0.0001     0.063       2      23 ..       4      25 ..       3      48 .. 0.82
   2 ?   -2.7   0.0       7.4   4.6e+03      35      46 ..      97     108 ..      86     115 .. 0.72
   3 ?    3.7   0.0     0.078        48     104     142 ..     206     243 ..     197     244 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.0001
                         PduV-EutP  2 kkilliGkvgsGKttLtqalkg 23
                                      k ++++G+ gsGKttLt ++++
  gi|385805295|ref|YP_005841693.1|  4 KYVVFMGPAGSGKTTLTATFSD 25
                                      679**************88765 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7.4
                         PduV-EutP  35 efsdeviDtPGe 46 
                                       e +  +iD PG+
  gi|385805295|ref|YP_005841693.1|  97 EGEYVLIDMPGQ 108
                                       444556888887 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.078
                         PduV-EutP 104 deenieaveelLksaGaekifevsavekegieellkyle 142
                                        ++ i+   ++L + G++  + vs+++ eg++el++ ++
  gi|385805295|ref|YP_005841693.1| 206 YHDYINSIADFLIEEGIDF-IPVSSTTGEGLDELFASIQ 243
                                       5667888888999999875.58*************9887 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 ?    4.1   0.0     0.046        29       6      22 ..       6      22 ..       2      37 .. 0.88
   2 !   12.3   0.0   0.00015     0.093     123     192 ..     164     246 ..      89     248 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.046
                                      EEEEESTTSSHHHHHHH CS
                          GTP_EFTU  6 igiighvDhGKtTLtdr 22
                                      ++++g   +GKtTLt +
  gi|385805295|ref|YP_005841693.1|  6 VVFMGPAGSGKTTLTAT 22
                                      7899**********976 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00015
                                       TEEEEEEESCGST.......HHHHHHHHHHHHHHHHHH........HHHHHHHHHTTT........TTEEEEEEBTT CS
                          GTP_EFTU 123 vpiivfiNKmDrl.......kaelkeiveevkqklsrk........eeklekygekge........kevpvvfgSal 176
                                        p i +i K+D l         +lke++e +k+k+ +k                   +        + + ++++S+ 
  gi|385805295|ref|YP_005841693.1| 164 FPQINAISKIDLLspelleeLLTLKESPELLKEKVIDKgdpkyhdyI----------NsiadflieEGIDFIPVSST 230
                                       458999*******5554444333444444444444222555554443..........04455555567********* PP

                                       TTBTHHHHHHHHHHHS CS
                          GTP_EFTU 177 kgegvktllealvell 192
                                       +geg+++l+  + +l+
  gi|385805295|ref|YP_005841693.1| 231 TGEGLDELFASIQNLI 246
                                       ********99988776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   6.3e-06    0.0039       6      41 ..       4      33 ..       1      97 [. 0.79
   2 ?   -0.7   0.0       2.7   1.6e+03      93     116 ..     166     188 ..     143     199 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 6.3e-06
                            AAA_22  6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpe 41
                                      + +v +G++G+GKTtl +++ ++l  +      + +
  gi|385805295|ref|YP_005841693.1|  4 KYVVFMGPAGSGKTTLTATFSDWLSSQ------GID 33
                                      567899*****************9654......333 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.7
                            AAA_22  93 elliiDEaqhlrseealeeLrsll 116
                                       ++  i  ++ l s+e+leeL +l 
  gi|385805295|ref|YP_005841693.1| 166 QINAISKIDLL-SPELLEELLTLK 188
                                       55556667889.999999998775 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0     6e-06    0.0037       2      40 ..       4      42 ..       3      45 .. 0.96

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6e-06
                                      EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STT CS
                       ArsA_ATPase  2 kvilvgGKGGVGKttvsaatavklsekgkkvllistDPA 40
                                      k++++ G  G GKtt+ a+++ +ls +g + + + +DPA
  gi|385805295|ref|YP_005841693.1|  4 KYVVFMGPAGSGKTTLTATFSDWLSSQGIDNVKVNLDPA 42
                                      8999**********************************9 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.2e-05    0.0072      25      84 ..       4      66 ..       2     199 .. 0.65
   2 ?    0.6   0.0         1   6.3e+02      75     128 ..     175     247 ..     121     254 .. 0.59

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.2e-05
                            AAA_16 25 elvllsGesGvGKsslvrellralekd...ggiflrgkcdqlesaipy..sa.laqalareellrq 84
                                       +v++ G++G+GK++l  ++ + l+ +   ++ +    ++++   +py  ++ + ++ +++e+ ++
  gi|385805295|ref|YP_005841693.1|  4 KYVVFMGPAGSGKTTLTATFSDWLSSQgidNVKVNLDPAVEY---LPYdpDIdVRNYVDAREVAKK 66
                                      6799****************9877777443344444444444...777553335555555555555 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1
                            AAA_16  75 alareellrqlldeaesaeleawrekleeala....................avpelagaeasrllellkrlla 128
                                       +l+  ell++ll+ +es el   +   ++  +                    +v++ +g++   l++ +++l++
  gi|385805295|ref|YP_005841693.1| 175 LLSP-ELLEELLTLKESPELLKEKVIDKGDPKyhdyinsiadflieegidfiPVSSTTGEGLDELFASIQNLIS 247
                                       3323.444444444444333333333333333666666666666666666777777777777777777777764 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 !    9.5   0.0    0.0016      0.97      53      79 ..     161     187 ..     131     198 .. 0.81
   2 ?    4.9   0.0     0.042        26      62     100 ..     199     242 ..     194     247 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0016
                      MMR_HSR1_Xtn  53 rvYipclyvlNKiDlisleeldelare 79 
                                       r Y p + ++ KiDl+s e l+el + 
  gi|385805295|ref|YP_005841693.1| 161 RHYFPQINAISKIDLLSPELLEELLTL 187
                                       69****************999998664 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.042
                      MMR_HSR1_Xtn  62 lNKiDlisleeldelare.....pnsvviSaekelnldeLkeki 100
                                       + K D    ++++++a        + +++S+ ++ +ldeL   i
  gi|385805295|ref|YP_005841693.1| 199 IDKGDPKYHDYINSIADFlieegIDFIPVSSTTGEGLDELFASI 242
                                       56666666666666666334444599**************9887 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   4.4e-05     0.027       2      32 ..       4      34 ..       3      41 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.4e-05
                                      EEEEEEESTTSSHHHHHHHHHHHHHHTTS-E CS
                             SRP54  2 nvillvGlqGaGKTttlaKLaallkkegkkv 32
                                      ++++++G+ G+GKTt +a  +++l+++g + 
  gi|385805295|ref|YP_005841693.1|  4 KYVVFMGPAGSGKTTLTATFSDWLSSQGIDN 34
                                      5799********************9997654 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   5.8e-05     0.036       2      31 ..       5      34 ..       4      40 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.8e-05
                                      CEEEEC-TTTCHHHHHHHHHHHHCTS-SCC CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalawaegklpq 31
                                      +v+  G+aGsGKTtL + + + + ++  ++
  gi|385805295|ref|YP_005841693.1|  5 YVVFMGPAGSGKTTLTATFSDWLSSQGIDN 34
                                      68999************9999888777666 PP

>> NBD94  Nucleotide-Binding Domain 94 of RH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0    0.0015      0.92      16      70 ..      81     135 ..      76     152 .. 0.88
   2 ?    2.6   0.0       0.3   1.8e+02      16      34 ..     237     255 ..     229     256 .] 0.67

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0015
                             NBD94  16 kiyeniekllnEleeiekektsleevknielsYgrsLikllvqkIdeekkkaenl 70 
                                        +y ++e++ +El eie e + ++   ++el   rs + l+v+++  +++ a   
  gi|385805295|ref|YP_005841693.1|  81 LLYGKLEDIKKELMEIEGEYVLIDMPGQLELFSFRSTGPLIVDRLSSKNRTAVVF 135
                                       5799******************************************999988655 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.3
                             NBD94  16 kiyeniekllnEleeieke 34 
                                       +++  i++l++ l+eie++
  gi|385805295|ref|YP_005841693.1| 237 ELFASIQNLISNLDEIETN 255
                                       5566677777777777654 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00011     0.067       2     136 ..       6     188 ..       5     256 .] 0.70

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                         Gtr1_RagA   2 vLLmGksgsGKtsmrsiiFdnylardtlrlgati........................................... 35 
                                       v++mG+ gsGKt++     d ++ + + ++++                                             
  gi|385805295|ref|YP_005841693.1|   6 VVFMGPAGSGKTTLTATFSDWLSSQGIDNVKVNLdpaveylpydpdidvrnyvdarevakkyslgpngallasmdll 82 
                                       789***********998888888888888888888899*************************************** PP

                         Gtr1_RagA  36 .....dveksevrflgnltlnlwDcgGqeafveeyls..sqkeeif.rnvgvliyVfDvesr.eleedletlk.eil 102
                                            d++k+ +++ g+ +  l+D++Gq +++    +     +++  +n  ++++++D++ + ++e+ l+ l  +  
  gi|385805295|ref|YP_005841693.1|  83 ygkleDIKKELMEIEGEYV--LIDMPGQLELFSFRSTgpLIVDRLSsKNRTAVVFLMDANFTaSVENFLSILMlSHS 157
                                       9999999999998888876..69******99976432113344443145569*******955236655555431223 PP

                         Gtr1_RagA 103 ealrqyspeakvfvlihKmDliqedereeifeer 136
                                        ++r+y p+++    i K+Dl++ +  ee+++ +
  gi|385805295|ref|YP_005841693.1| 158 IRIRHYFPQINA---ISKIDLLSPELLEELLTLK 188
                                       357778888774...8999999988777765433 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 ?   14.5   0.0   4.6e-05     0.028       8      55 ..      12      93 ..       5     245 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.6e-05
                                      TTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH...HTTEB-HHHH............................. CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxx............................. RF
                              CbiA  8 GGvGKTtlaanLaralarrglrVllvDaDpqannlai...leglendiep............................. 54
                                       G+GKTtl+a++   l+ +g + + v +Dp  + l +   +     d                                
  gi|385805295|ref|YP_005841693.1| 12 AGSGKTTLTATFSDWLSSQGIDNVKVNLDPAVEYLPYdpdI-----D--Vrnyvdarevakkyslgpngallasmdlly 83
                                      69****************************98877743321.....2..122444556677777777777777444444 PP

                                      .........C CS
                                      .........x RF
                              CbiA 55 .........d 55
                                                
  gi|385805295|ref|YP_005841693.1| 84 gkledikkeL 93
                                      4444444440 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   0.00071      0.44       3      87 ..       7     142 ..       5     174 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00071
                                       EEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEEETTEE............................... CS
                          MMR_HSR1   3 aivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvklkgke............................... 47 
                                       +++G   +GK+tL  + ++   ++  d   + +d+  + + ++  +                               
  gi|385805295|ref|YP_005841693.1|   7 VFMGPAGSGKTTLTATFSDWlSSQGIDNVKVNLDPAVEYLPYDP-Didvrnyvdarevakkyslgpngallasmdll 82 
                                       56666666666666666654333334444444444444443221.12233333444444555555555555555555 PP

                                       .................EEEEECGGCSS...HHHHHHHHHHHHHHHHCTSEEEEEEETT.T CS
                          MMR_HSR1  48 .................ielvDtpGlie...gaseekglgkaflaleeadlillvvdas.e 87 
                                                        ++l+D+pG +e     s++  + +++ + ++  ++++++da+ +
  gi|385805295|ref|YP_005841693.1|  83 ygkledikkelmeiegeYVLIDMPGQLElfsFRSTGPLIVDRLSS-KNRTAVVFLMDANfT 142
                                       55555555555555555********76544233334445555554.444899999996641 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   0.00015     0.092      13      35 ..       5      27 ..       2      57 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00015
                                      EEEEEESTTSSHHHHHHHHTTSS CS
                                      xxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 13 kvaivGenGaGKStLlkllagll 35
                                       v+++G+ G+GK+tL ++++  l
  gi|385805295|ref|YP_005841693.1|  5 YVVFMGPAGSGKTTLTATFSDWL 27
                                      6899************9998765 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00016     0.098       5      70 ..       9      75 ..       6      95 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00016
                               PRK  5 agsSGaGkttvarklekifgrekvkaaeiegdsflrldraekdleleerkrake..kevsflspeand 70
                                       g+ G+Gktt+++++ + +  +++  +++++d  +++   + d+ +++  +a e  k++  l+p+   
  gi|385805295|ref|YP_005841693.1|  9 MGPAGSGKTTLTATFSDWLSSQGIDNVKVNLDPAVEYLPYDPDIDVRNYVDAREvaKKY-SLGPNGAL 75
                                      5899*************************999999998888888877765554411333.35555543 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0082       5.1      12      40 ..      13      41 ..       6      45 .. 0.92
   2 ?    3.1   0.0      0.13        81     105     133 ..      87     113 ..      53     117 .. 0.79
   3 ?   -0.7   0.1       1.8   1.1e+03      86     118 ..     171     206 ..     120     244 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0082
                            AAA_31 12 GvGKTTtsvnlaaalaklgkkvLlvDlDp 40
                                      G GKTT +  ++ +l+++g     v+lDp
  gi|385805295|ref|YP_005841693.1| 13 GSGKTTLTATFSDWLSSQGIDNVKVNLDP 41
                                      99*****************9999999998 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.13
                            AAA_31 105 eilkellekvkdeYDyiiiDcpPsLgllt 133
                                       e +k+ l +++ e  y++iD+p +L+l+ 
  gi|385805295|ref|YP_005841693.1|  87 EDIKKELMEIEGE--YVLIDMPGQLELFS 113
                                       4457777778777..5********99875 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.8
                            AAA_31  86 ssidLaeae..ielvelekkeeil.kellekvkdeY 118
                                       s+idL + e   el++l+++ e l +++++k + +Y
  gi|385805295|ref|YP_005841693.1| 171 SKIDLLSPEllEELLTLKESPELLkEKVIDKGDPKY 206
                                       555554433114566666665555334445544444 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00019      0.12      34      69 ..       4      39 ..       1      45 [. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00019
                             AAA_7 34 kpvllvGptGtGKtviikdllkkldkekylsltinf 69
                                      k v+++Gp+G+GKt+++ ++ + l+++ +  +++n+
  gi|385805295|ref|YP_005841693.1|  4 KYVVFMGPAGSGKTTLTATFSDWLSSQGIDNVKVNL 39
                                      6799****************9999999999998887 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00031      0.19       2      21 ..       6      25 ..       5      63 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00031
                            AAA_28  2 ivitGgestGKTtlleaLaa 21
                                      +v++G+ ++GKTtl++ +++
  gi|385805295|ref|YP_005841693.1|  6 VVFMGPAGSGKTTLTATFSD 25
                                      89*************98874 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00021      0.13      20      46 ..       5      31 ..       2      42 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00021
                            AAA_30 20 vavltGpAGtGKttalkalreaweaag 46
                                      ++v  GpAG+GKtt+ ++  + + ++g
  gi|385805295|ref|YP_005841693.1|  5 YVVFMGPAGSGKTTLTATFSDWLSSQG 31
                                      67899**********999988887776 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00047      0.29       2      17 ..       6      21 ..       6      63 .. 0.92
   2 ?   -1.2   0.0       3.2     2e+03      99     122 ..     182     205 ..     115     211 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00047
                            AAA_33  2 vllvGlpGsGKstlae 17
                                      v++ G++GsGK+tl  
  gi|385805295|ref|YP_005841693.1|  6 VVFMGPAGSGKTTLTA 21
                                      799**********976 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.2
                            AAA_33  99 vrivvvetdeetlkeRlakRaang 122
                                       +++++++ ++e+lke++  + +++
  gi|385805295|ref|YP_005841693.1| 182 EELLTLKESPELLKEKVIDKGDPK 205
                                       566777778888888887777765 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00023      0.14     131     157 ..       5      32 ..       1      58 [. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00023
                             T2SSE 131 lilvsGgTgsGKttllyallkeinks.d 157
                                        +++ G+ gsGKttl+ +   ++ ++  
  gi|385805295|ref|YP_005841693.1|   5 YVVFMGPAGSGKTTLTATFSDWLSSQgI 32 
                                       67899*************9999988742 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00026      0.16       5      25 ..       6      25 ..       2     100 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00026
                            AAA_24  5 iliyGpsgiGKTtlakelgpk 25
                                      ++ +Gp+g+GKTtl +++  +
  gi|385805295|ref|YP_005841693.1|  6 VVFMGPAGSGKTTLTATF-SD 25
                                      7889*************9.44 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0    0.0012      0.73      22      38 ..       5      21 ..       1      30 [. 0.84
   2 ?   -0.3   0.0       0.8   4.9e+02     156     189 ..     182     216 ..     168     244 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0012
                                      EEEEEESTTSSHHHHHH CS
                            NB-ARC 22 vvalvGmgGvGKttlak 38
                                       v ++G +G+GKttl +
  gi|385805295|ref|YP_005841693.1|  5 YVVFMGPAGSGKTTLTA 21
                                      68899**********87 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.8
                                       ESS--HHHHHHHHHHCCTS-GGCHH...CHHHHHH CS
                            NB-ARC 156 velLekdeawellenkvfekkleekes.leevake 189
                                       +elL+ +e+ ell++kv++k + + ++ ++ +a  
  gi|385805295|ref|YP_005841693.1| 182 EELLTLKESPELLKEKVIDKGDPKYHDyINSIADF 216
                                       67899999999999999988776554445555555 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 ?   -0.4   0.0       1.2   7.5e+02       3      20 ..       6      23 ..       4      31 .. 0.83
   2 ?    7.0   0.0    0.0061       3.8      45      89 ..      96     140 ..      84     175 .. 0.84
   3 ?    0.6   0.0      0.57   3.5e+02     135     155 ..     221     241 ..     211     242 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.2
                                      EEEEESTTSSHHHHHHHH CS
                            FeoB_N  3 valvGnpnvGkttlfnal 20
                                      v+++G   +Gkttl  + 
  gi|385805295|ref|YP_005841693.1|  6 VVFMGPAGSGKTTLTATF 23
                                      789999*******97665 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0061
                                       TTEEEEEEE----SSSSSSSHHHHHHHHHHHCTSSSEEEEEEEGG CS
                            FeoB_N  45 kgkeveivDlPGiYslsayseeekvardflleeepdvvvnvvdat 89 
                                        + e+ ++D+PG  +l ++ +   +  d l +++  +vv ++da+
  gi|385805295|ref|YP_005841693.1|  96 IEGEYVLIDMPGQLELFSFRSTGPLIVDRLSSKNRTAVVFLMDAN 140
                                       456899**********99999999999***************996 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.57
                                       TS-EEEEBTTTTBTHHHHHHH CS
                            FeoB_N 135 gvpvvktsakkkegieellka 155
                                       g++ +++s++++eg++el ++
  gi|385805295|ref|YP_005841693.1| 221 GIDFIPVSSTTGEGLDELFAS 241
                                       7899*************9876 PP

>> Polyoma_lg_T_C  Polyomavirus large T antigen C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00037      0.23     156     191 ..       4      40 ..       2      89 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00037
                    Polyoma_lg_T_C 156 rywlfkgpidsgkttlaaalldlcggkal.nvnlple 191
                                       +y +f gp  sgkttl+a++ d    + + nv++ l+
  gi|385805295|ref|YP_005841693.1|   4 KYVVFMGPAGSGKTTLTATFSDWLSSQGIdNVKVNLD 40 
                                       799****************998766554434555444 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00047      0.29      20      39 ..       4      23 ..       1      45 [. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00047
                                      SEEEEE--TTSSTTHHHHHH CS
                              PhoH 20 divfaiGpaGtGKtylaval 39
                                      + v+ +GpaG+GKt l+ + 
  gi|385805295|ref|YP_005841693.1|  4 KYVVFMGPAGSGKTTLTATF 23
                                      568999**********9875 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00052      0.32       3      28 ..      10      36 ..       8      42 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00052
                                      ESTTSSHHHHHHHHHHHHHHTTE..EE CS
                   Thymidylate_kin  3 GlDGaGKttqaellkerlkeegik.vv 28
                                      G  G+GKtt ++++ ++l+++gi  v 
  gi|385805295|ref|YP_005841693.1| 10 GPAGSGKTTLTATFSDWLSSQGIDnVK 36
                                      777*******************98655 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 ?   10.6   0.0   0.00091      0.56      86     116 .]     194     224 ..     174     224 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00091
                                       HTC-EE--TTSSS-CHHHHHHHHHHCTSSB- CS
                    Ribosomal_L18p  86 iekvvfDrggykYhGrvaalAdaaReaGlkf 116
                                       +++ v D+g  kYh  ++++Ad + e+G++f
  gi|385805295|ref|YP_005841693.1| 194 LKEKVIDKGDPKYHDYINSIADFLIEEGIDF 224
                                       677899**********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              29  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.54
# Mc/sec: 1428.62
//
Query:       gi|385805296|ref|YP_005841694.1|  [L=137]
Description: metallopeptidase-like protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score 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   0.0      0.022   14.6   0.0    1.3  1  SprT-like      SprT-like family
      0.031   14.1   0.0      0.042   13.6   0.0    1.2  1  Peptidase_M48  Peptidase family M48
       0.13   12.0   0.0       0.17   11.6   0.0    1.2  1  BSP            Peptidase of plants and bacteria


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 ?   14.6   0.0   3.7e-06     0.022      48      90 ..      64     104 ..      59     121 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.7e-06
                         SprT-like  48 sIeLseklldsrsedrllntLaHElcHlalfvisgvrnnpHGa 90 
                                       +Ie+  + ++s +e+++  +L+HE+ H+   +  g   +pHG+
  gi|385805296|ref|YP_005841694.1|  64 TIEFLCNKIKSLNEREITGVLIHEFLHIPYNMSGG--LRPHGN 104
                                       577777789999****************9999999..99**97 PP

>> Peptidase_M48  Peptidase family M48
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0     7e-06     0.042      20      75 ..      23      91 ..       5      96 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7e-06
                                      -....-EEEEEEE-GGGT-EEEEESSS-EEEEEEHHHH...........-SSB-HHHHHHHHHHHHHHH CS
                                      x..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48 20 l..pkpltkvyvvnspkrNAFalgggknkrivltdgLl...........kqllseeelaaVlGHElGHi 75
                                      l  +  ++ ++v ++ k NA+a   g +k i +   L             + l+e+e+ +Vl HE  Hi
  gi|385805296|ref|YP_005841694.1| 23 LkiNFNNIAFVVSHGAKSNAYARIYGLSKAIQIGHVLPplytieflcnkIKSLNEREITGVLIHEFLHI 91
                                      332447788899999999****9999889888887776778*******9999**************998 PP

>> BSP  Peptidase of plants and bacteria
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.9e-05      0.17      92     120 ..      74     103 ..      52     116 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.9e-05
                               BSP  92 kdakaevtgvLthelvhv.yqweaegrapg 120
                                       +  ++e+tgvL+he  h+ y++++  r++g
  gi|385805296|ref|YP_005841694.1|  74 SLNEREITGVLIHEFLHIpYNMSGGLRPHG 103
                                       34459************8676666445555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 862.41
//
Query:       gi|385805297|ref|YP_005841695.1|  [L=290]
Description: polyprenyl synthetase [Fervidicoccus fontis Kam940]
Scores for 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  129.8   0.1    1.3e-37  129.3   0.1    1.1  1  polyprenyl_synt  Polyprenyl synthetase


Domain annotation for each model (and alignments):
>> polyprenyl_synt  Polyprenyl synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.3   0.1   7.3e-42   1.3e-37       7     198 ..      31     205 ..      26     216 .. 0.92

  Alignments for each domain:
  == domain 1  score: 129.3 bits;  conditional E-value: 7.3e-42
                                       HHHHHHHSSS--HHHHHHHHHHHHHSCGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEETTEE-HHHCTCHHHH CS
                   polyprenyl_synt   7 aleylveagGKrlRpllvllaaealkeeeeelekaavlawivellhaasLvhDDimDdsetRRGqpcahrlvGnklA 83 
                                       +++y+v  gGKrlR+ll+l +  +l   + ++++a ++a+++el+h++sL +DDi+D++  RRG+p++  + G +++
  gi|385805297|ref|YP_005841695.1|  31 VSKYIV-EGGKRLRGLLTLFITDVLV--N-DYNRAVRAAVALELVHSCSLAIDDIIDQDVKRRGRPSVWVAKGISKT 103
                                       78999*.*******************..4.689******************************************** PP

                                       HHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHTTTTTCCC.SHHHHHHHHHHHTHHHCHHHHH CS
                   polyprenyl_synt  84 indgdfllarafellaklfekslellelfsevllqtveGqlldleeekdddlskfsleeyleivkyKTaylfalpva 160
                                       ++++++l  +a + ++ l  ++  +++ + e+ l++ +G+++d+ +e   +      + yl+ ++yKT++lf l++ 
  gi|385805297|ref|YP_005841695.1| 104 VLVSNLLIPIAIKEVSYL--GT-SAVKKVIETWLKVTMGEIYDVFDE---S------SSYLKTIEYKTSSLFQLSLD 168
                                       ****************99..65.99*******************333...3......46****************** PP

                                       HHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS CS
                   polyprenyl_synt 161 laallagasdeelealkdiglelGlaFQiqDDylDlfg 198
                                       la+++++  ++ ++ ++++gl+lG+++Qi DD++D  +
  gi|385805297|ref|YP_005841695.1| 169 LAVIASNR-EDLINVFERYGLYLGYLYQISDDLVDAKK 205
                                       *******6.7889**********************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1659.13
//
Query:       gi|385805298|ref|YP_005841696.1|  [L=345]
Description: dehydrogenase, FixC domain protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00011   22.4   0.1     0.0002   21.5   0.1    1.4  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
     0.0016   17.7   0.0     0.0033   16.7   0.0    1.4  1  FAD_binding_3  FAD binding domain
     0.0037   16.6   0.0     0.0068   15.7   0.0    1.5  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
     0.0051   16.4   0.0       0.02   14.5   0.0    1.7  2  DAO            FAD dependent oxidoreductase
  ------ inclusion threshold ------
      0.083   12.1   0.0       0.17   11.1   0.0    1.5  1  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
      0.086   11.9   0.0       0.23   10.5   0.0    1.9  1  GIDA           Glucose inhibited division protein A


Domain annotation for each model (and alignments):
>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.1   6.7e-08    0.0002       1      32 [.       8      40 ..       8      47 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 6.7e-08
                                      EE--SHHHHHHHHHHHCCTE.EEEEE-SSSSSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagf.dvlllekrdrlG 32
                                      I+GaG +G+++A +L+  g+ +++++e++  lG
  gi|385805298|ref|YP_005841696.1|  8 IIGAGPAGASLAFFLSSLGYsNITVYESSKVLG 40
                                      9*******************66******99888 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.1e-06    0.0033       5      30 ..       7      32 ..       4      42 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.1e-06
                                      EEE--SHHHHHHHHHHHHTTHHEEEE CS
                     FAD_binding_3  5 lIVGaGpaGlmlallLseaGvrvvlv 30
                                       I+GaGpaG++la +Ls+ G +++ v
  gi|385805298|ref|YP_005841696.1|  7 NIIGAGPAGASLAFFLSSLGYSNITV 32
                                      5*******************998877 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.3e-06    0.0068       2      40 ..       5      43 ..       4     147 .. 0.68
   2 ?   -3.3   0.0       1.4   4.2e+03     267     278 ..     235     246 ..     226     258 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.3e-06
                                      SEEEE--SHHHHHHHHHHHHHTS.-EEEEETTHCHHHCSH CS
                                      xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqaga.kvtlvelegtclnggc 40
                                      ++ +iG+GpAG ++a +l+  g+ ++t++e    +l+ ++
  gi|385805298|ref|YP_005841696.1|  5 RINIIGAGPAGASLAFFLSSLGYsNITVYE-SSKVLGSKP 43
                                      567999999999999999997661455553.333444433 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.4
                                       SSTTEEE-GGGC CS
                                       xxxxxxxxxxxx RF
                       Pyr_redox_2 267 nvpgiyaiGDva 278
                                         ++++aiG  +
  gi|385805298|ref|YP_005841696.1| 235 PAENVFAIGEGV 246
                                       478999999755 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   6.5e-06      0.02       2      33 ..       6      40 ..       5      47 .. 0.90
   2 ?   -0.6   0.0      0.27   7.9e+02     195     265 ..     125     185 ..      96     276 .. 0.54

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.5e-06
                                      EEEECTSHHHHHHHHHHHHTT...EEEEESSSSTT CS
                               DAO  2 vviiGGGiiGlstAyeLarrg...Vtllekgdiag 33
                                      + iiG+G +G+s A++L+  g   +t++e+++ +g
  gi|385805298|ref|YP_005841696.1|  6 INIIGAGPAGASLAFFLSSLGysnITVYESSKVLG 40
                                      569**************999999******997776 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.27
                                       E.EEE--GGGHHHHHTTCTTTSEEEEEEEEEEEEEECCTHSTGSGCSEEEEEEEETTTTEEEEEETTSEEEE CS
                               DAO 195 a.vVnaaGawsdllgllkeldlpispvrgqvlvlkplseklvspaailpvpetdddgrgvyvtprkdgrvlv 265
                                          V+aaG++ + +   ++   ++ +v ++v v+ +++e    p  i  ++  +   +++ ++p  + +v +
  gi|385805298|ref|YP_005841696.1| 125 ElYVIAAGIYWNGS---PKE--RLNAVEATVNVY-NWNE----PSIIQIWF-DTKLMGYYWAFPHSEKKVNI 185
                                       24888888884433...333..456666666666.5544....21222222.33333444555554444444 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 ?   11.1   0.0   5.6e-05      0.17       2      32 ..       8      38 ..       7      42 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.6e-05
                       Pyr_redox_3  2 IiGaGPaGlaaaielkkagledylilEkgni 32
                                      IiGaGPaG + a  l  +g +++++ E  ++
  gi|385805298|ref|YP_005841696.1|  8 IIGAGPAGASLAFFLSSLGYSNITVYESSKV 38
                                      9************************998765 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   7.8e-05      0.23       2      50 ..       6      54 ..       5     149 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 7.8e-05
                                      EEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT--SSSSEEE-TTHH CS
                              GIDA  2 viViGgGhAGceAAlaaarlGakvlLithkldtiaelsCnpsiggiakg 50
                                      +++iG+G AG   A+ ++ lG++ + + ++ + +++ +C  ++ +  k 
  gi|385805298|ref|YP_005841696.1|  6 INIIGAGPAGASLAFFLSSLGYSNITVYESSKVLGSKPCGMAVPASIKD 54
                                      79*********************99999*******99998887666444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 2133.43
//
Query:       gi|385805299|ref|YP_005841697.1|  [L=186]
Description: putative Fe-S oxidoreductase [Fervidicoccus fontis Kam940]
Scores for complete 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-10   39.3   0.2    1.2e-09   38.7   0.2    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 !   38.7   0.2   6.9e-14   1.2e-09       1      84 [.      13     118 ..      13     119 .. 0.85

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 6.9e-14
                          CxxCxxCC   1 eCkeCgaCCk.elkvklteedlerlkaaevaeeeeeskkiak...............adgrCvfldeetk...lCki 58 
                                       +C++C  CC    +v++t  d+ r++++  ++  ++ k +++                 grC fl  +++    Cki
  gi|385805299|ref|YP_005841697.1|  13 KCTRCTLCCGtGPNVSITVFDVIRMSKYLDVNPIQFLKIFTNviiadlipvialkgdIAGRCEFLGFDSNgktFCKI 89 
                                       6********96788999999*****999998888888888889**********************866555679*** PP

                          CxxCxxCC  59 YeeRpkicrlfpas...ekeellaraetC 84 
                                       Y+ Rp+ crl+p      k++  ++++ C
  gi|385805299|ref|YP_005841697.1|  90 YKYRPLKCRLYPVKlisPKSNHVYLDTDC 118
                                       ************97666555555666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1434.04
//
Query:       gi|385805300|ref|YP_005841698.1|  [L=100]
Description: hypothetical protein FFONT_0255 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score 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   14.6   0.1      0.031   14.0   0.1    1.2  1  DUF4423   Domain of unknown function (DUF4423)


Domain annotation for each model (and alignments):
>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   1.7e-06     0.031      25      82 ..      35      92 ..      31      99 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.7e-06
                           DUF4423 25 virellplkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqteks 82
                                      +i+el + + +  +++el + l++ +s+e+++k++   +k +++  +  gky+ ++ +
  gi|385805300|ref|YP_005841698.1| 35 IILELFKNNCKGFTIKELHELLKGLASEEKIRKTVYKFKKEKIIVLNDGGKYVLNTNN 92
                                      799999999999****************************************988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1053  (0.0587317); expected 358.6 (0.02)
Passed bias filter:                      611  (0.0340789); 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: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 643.45
//
Query:       gi|385805301|ref|YP_005841699.1|  [L=552]
Description: phenylalanyl-tRNA synthetase subunit beta [Fervidicoccus fontis Kam940]
Scores for complete 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-31  107.7   0.0    7.9e-31  107.2   0.0    1.3  1  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
    2.2e-22   79.1   3.3    2.4e-17   63.0   0.4    3.4  3  B5               tRNA synthetase B5 domain
    8.7e-12   45.1   0.1    1.6e-11   44.2   0.1    1.4  1  B3_4             B3/4 domain
    4.3e-08   33.3   1.0    3.2e-05   24.1   0.0    3.4  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 !  107.2   0.0   1.8e-34   7.9e-31      16     213 ..     363     542 ..     349     543 .. 0.93

  Alignments for each domain:
  == domain 1  score: 107.2 bits;  conditional E-value: 1.8e-34
                   tRNA_synthFbeta  16 nkeqklrrklrdllagaGlnEvitysfvsekeldklleddderkavelanPlsedqsvlRtsLlpglLevlarNlar 92 
                                       ++   +++ +r++ +g+G++E++ + +  ++  + +    +++++++++nP++e ++++R+s++p+lL ++++ ++ 
  gi|385805301|ref|YP_005841699.1| 363 SDLTVVEKIIREVSTGLGFQEILGFILSGDDASKFI---GENEEVIRVKNPVTETMKIIRPSIIPSLLYAIKESQHL 436
                                       5666788999*****************999887777...999*********************************** PP

                   tRNA_synthFbeta  93 gnedvrlFEigkvflkdseeelpeeerhlaivltgkreeeswsekaravdfydlkgivealleslgiekvefepaeh 169
                                       +++ +++FEig++  +   +  p  e++ + +++++            ++f+++   + +lle l++ k   +++e+
  gi|385805301|ref|YP_005841699.1| 437 QLP-IKIFEIGECGYAS--GGIPITENKAGYAIVNEG-----------ASFEEMQSHIYSLLEILKL-KPISKREEK 498
                                       ***.*************..899***************...........*******************.777899*** PP

                   tRNA_synthFbeta 170 palhpgrsAeikvdgkevGvlGelhpevleafdlkqrvyvfEld 213
                                       ++l +grsA++ ++++++G++Ge+hp++le f++k++v+v+El 
  gi|385805301|ref|YP_005841699.1| 499 SFLIKGRSASLFIEKERIGYIGEVHPRILEMFGVKYPVVVAELC 542
                                       ******************************************95 PP

>> B5  tRNA synthetase B5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   6.8e-06     0.031       6      53 ..       9      56 ..       5      60 .. 0.92
   2 ?   -1.3   0.0      0.64   2.9e+03       9      26 ..     100     117 ..      98     152 .. 0.84
   3 !   63.0   0.4   5.3e-21   2.4e-17       2      67 .]     281     346 ..     280     346 .. 0.97

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.8e-06
                                      HHHHHHHTS---HHHHHHHHHHTT-E.EESSTTCEEEE--TT-TT--S CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                B5  6 ekinkllGidlseeeiikiLkrlgceriekdkdlllVtvPswRsDler 53
                                      +++ k +  ++seee  ++L +l+ e  + d++ll+V+v s R+Dl  
  gi|385805301|ref|YP_005841699.1|  9 KRLAKFIEKEFSEEELSNLLFNLKSESRTIDNQLLEVEVNSDRPDLYI 56
                                      578899999************************************965 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.64
                                       HHHHTS---HHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxx RF
                                B5   9 nkllGidlseeeiikiLk 26 
                                         + Gi+l++e+i+++ +
  gi|385805301|ref|YP_005841699.1| 100 ATIRGISLDDEDIKELIQ 117
                                       567799999999888765 PP

  == domain 3  score: 63.0 bits;  conditional E-value: 5.3e-21
                                       EEEHHHHHHHHTS---HHHHHHHHHHTT-E.EESSTTCEEEE--TT-TT--SHHHHHHHHHHHH-G CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                B5   2 slrvekinkllGidlseeeiikiLkrlgceriekdkdlllVtvPswRsDlereeDliEEvaRlyGY 67 
                                       +++ e+i k lG +ls ++i+++L+++ +++ +  +d ++V vP +R D+++++Dl+E++a++yGY
  gi|385805301|ref|YP_005841699.1| 281 RIETEYIIKNLGFELSLNDITELLEKMRFKVASVSEDSINVIVPEYRMDILHKVDLVEDIAMAYGY 346
                                       578899***********************************************************9 PP

>> B3_4  B3/4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.1   3.6e-15   1.6e-11      17     133 ..     109     236 ..      93     245 .. 0.87

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 3.6e-15
                                       ----HHHHHHHHHTT-----HHHHHHHHHHHHHT-.....-EEEEEGGGTBT.EEEEEE--TTEEEEBTT.S-EEEE CS
                              B3_4  17 apspewlqrrLrragirpinnvVDitNyvmlelgq.....PlhafDldkiqg.divvrlakegeklvtld.gkerel 86 
                                        +                i+ ++  +++++l +g+     +++++Dldki + +i+ +la  +ek+ +l+ g++ e+
  gi|385805301|ref|YP_005841699.1| 109 DED---------------IKELIQFQEKLHLTVGRkrkkmAIGIHDLDKIPDrKITYKLASLNEKMRPLFiGRNMEI 170
                                       444...............8999****************************988****************62457777 PP

                                       -T...................TSEEEETEEEEEEETTTEEBTTTB--TT--EEEEEEEE--HHHHH CS
                              B3_4  87 de...................edlviadsekpvslagvmggeeskvsedTknvfleaaafdpvsir 133
                                       +e                   + + i+ +++++sl++v++++ ++++  Tkn ++ +++ d  +i 
  gi|385805301|ref|YP_005841699.1| 171 REvlksteqgisygelslyngSHPAIYSGNEIISLPPVINSDITRIEPGTKNLLIDITGNDFYTIS 236
                                       778999**************************************************9996665555 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 !   24.1   0.0   7.2e-09   3.2e-05       1      82 [.       1      69 [.       1      70 [. 0.90
   2 !    4.6   0.2    0.0085        38       9      77 ..     269     340 ..     266     345 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 7.2e-09
                         PhetRS_B1  1 MPtisvkkeaLfkalgkelteeeledllfefGlElDeiveeeekkkadkkseeviykidipAnryDLLcleglaralkv 79
                                      MP++ + k++L+k ++ke++eeel++llf++        +e+       + +++++ +++ + r+DL   egl ra+k 
  gi|385805301|ref|YP_005841699.1|  1 MPVLQIYKKRLAKFIEKEFSEEELSNLLFNL-------KSESR------TIDNQLLEVEVNSDRPDLYISEGLGRAIKG 66
                                      9****************************85.......55555......67899***********************97 PP

                         PhetRS_B1 80 Flg 82
                                       lg
  gi|385805301|ref|YP_005841699.1| 67 LLG 69
                                      666 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0085
                         PhetRS_B1   9 eaLfkalgkelteeeledllfefGlEl..Deiveeeekkk.adkkseeviykidipAnryDLLcleglaral 77 
                                       + L+ +l+++    e e ++ ++G El   +i+e  ek + +  + +e  + + +p  r D+L    l++ +
  gi|385805301|ref|YP_005841699.1| 269 KVLTPTLERKQIRIETEYIIKNLGFELslNDITELLEKMRfKVASVSEDSINVIVPEYRMDILHKVDLVEDI 340
                                       566677777777777788888888775337888877755435566778888999999999999887777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (552 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); 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: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 3774.24
//
Query:       gi|385805302|ref|YP_005841700.1|  [L=499]
Description: phenylalanyl-tRNA synthetase subunit alpha [Fervidicoccus fontis Kam940]
Scores for complete 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-78  263.0   0.1    3.8e-78  262.3   0.1    1.3  1  tRNA-synt_2d     tRNA synthetases class II core domain (F)
      3e-08   33.4   0.0    4.3e-07   29.6   0.0    2.2  1  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
    1.1e-06   28.4   0.5    1.1e-06   28.4   0.5    2.5  3  TrmB             Sugar-specific transcriptional regulator Trm
    3.6e-06   26.3   0.2      0.028   13.5   0.1    2.5  2  tRNA-synt_2      tRNA synthetases class II (D, K and N)
     0.0005   19.9   0.1     0.0036   17.1   0.0    2.3  2  MarR_2           MarR family
  ------ inclusion threshold ------
      0.014   15.3   5.0      0.017   15.1   0.0    3.1  3  HTH_45           Winged helix-turn-helix
      0.017   14.8   1.5      0.036   13.8   0.2    2.1  2  DUF4364          Domain of unknown function (DUF4364)
      0.058   13.0   0.0      0.058   13.0   0.0    3.3  4  HTH_24           Winged helix-turn-helix DNA-binding
      0.083   13.2   1.6       0.14   12.5   0.1    2.2  2  PheRS_DBD3       PheRS DNA binding domain 3
      0.087   12.6   3.1        0.3   10.9   0.0    2.9  3  RQC              RQC domain
      0.097   13.0   0.2       0.48   10.8   0.0    2.1  2  Rrf2             Transcriptional regulator
       0.18   11.8   1.3       0.35   10.9   0.1    2.1  2  HTH_6            Helix-turn-helix domain, rpiR family


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 !  262.3   0.1   2.6e-81   3.8e-78       2     244 ..     218     488 ..     217     489 .. 0.98

  Alignments for each domain:
  == domain 1  score: 262.3 bits;  conditional E-value: 2.6e-81
                                       .-TSSCTSCTSHSB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-.. CS
                      tRNA-synt_2d   2 idvtlpgkrieagklhpltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpeka.. 76 
                                       ++v+++ +++++g +h ++k++e+ik i+lelgf+ev g+ +e+ef+nfd+L++ qdhp R+++dtF+++k+ k+  
  gi|385805302|ref|YP_005841700.1| 218 YNVEAEPPKVYPGIQHFYSKFIEKIKMILLELGFKEVYGSIIEQEFWNFDVLFQAQDHPSREIHDTFWIDKEVKEif 294
                                       8********************************************************************999888** PP

                                       ...............................ECESEEE-SSTHHHHHHHH.TTS-SSEEEEEEEEEEBSST-SSSB- CS
                      tRNA-synt_2d  77 ...............................veekllLRthttavqirtl.ekkkppikiisigrvfRrdavDathl 121
                                                                      v+++l+LRt+tt v+ rtl  ++++p+++++ig+vfR d +Da+hl
  gi|385805302|ref|YP_005841700.1| 295 arkeliektrevheyggktgsigwrykwdqeVAKRLILRTQTTVVSGRTLsLSPEAPFRFFTIGKVFRPDVIDARHL 371
                                       *******************************999****************999************************ PP

                                       SEEEEEEEEEEETT--HHHHHHHHHHHHHHHCTSTEEEEEEECEETTEEEEEEEEEEECCSSSSEEEEEEEEEE-HH CS
                      tRNA-synt_2d 122 aeFhqveglvvdenvsladlkgvleellkklfgaevkvrfrpsyfpftePsaevdvylvekkkkwlEllgaGmvrpe 198
                                       +eF+q + ++ ++++s+++ +g+l+ ++kk+ g+e ++ f+p+yfpftePs+e  v +   + +++E++gaGm+rpe
  gi|385805302|ref|YP_005841700.1| 372 PEFYQFDAIISEKDMSFSKFLGMLKLFFKKM-GFE-ELIFKPAYFPFTEPSVEGYVKI--GNLGYVEVFGAGMFRPE 444
                                       *******************************.***.********************99..***************** PP

                                       HHHHTT-.TTSEEEEEEEEHHHHHHHHHT-SSGHHHHTT.HHHHGG CS
                      tRNA-synt_2d 199 vleavgideevsgfafGlGveRlamlkygieDiRelvendlrflrq 244
                                       vle ++i  + ++ a+G+G++Rlam  ++++DiR l++++l+ lr+
  gi|385805302|ref|YP_005841700.1| 445 VLEIFDI--KHPVGAWGMGLDRLAMALLNLSDIRMLYDRNLENLRN 488
                                       *******..*******************************998875 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 !   29.6   0.0   2.9e-10   4.3e-07      17     209 ..     234     457 ..     222     462 .. 0.80

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 2.9e-10
                   tRNA_synthFbeta  17 keqklrrklrdllagaGlnEvitysfvsekeldkll...eddderk............................... 59 
                                          k+ +k++ +l ++G+ Ev+ +   +e ++ ++l   +d++ r+                               
  gi|385805302|ref|YP_005841700.1| 234 FYSKFIEKIKMILLELGFKEVYGSIIEQEFWNFDVLfqaQDHPSREihdtfwidkevkeifarkeliektrevheyg 310
                                       56678888888888888888888877777777777764333344448888888888888888888888888888888 PP

                   tRNA_synthFbeta  60 ..avelanPlsedqsvlRtsLlpglLevlarNl...argnedvrlFEigkvflkd.seeelpeeerhlaivltgkre 130
                                         +  +    + dq+v  + +l +   v++      + + + +r+F igkvf++d  + +   e  ++ ++++ k+ 
  gi|385805302|ref|YP_005841700.1| 311 gkTGSIGWRYKWDQEVAKRLILRTQTTVVSGRTlslSPEAP-FRFFTIGKVFRPDvIDARHLPEFYQFDAIISEKD- 385
                                       88888888888888888887777777777543312144445.*************977788999************. PP

                   tRNA_synthFbeta 131 eeswsekaravdfydlkgivealleslgiekvefepaehpalhpgrsAeikvdgk...evGvlGelhpevleafdlk 204
                                                 ++f ++ g+++ +++++g+e++ f+pa  p+ +p     +k+++    ev  +G + pevle fd+k
  gi|385805302|ref|YP_005841700.1| 386 ----------MSFSKFLGMLKLFFKKMGFEELIFKPAYFPFTEPSVEGYVKIGNLgyvEVFGAGMFRPEVLEIFDIK 452
                                       ..........****************************************9976444488889************** PP

                   tRNA_synthFbeta 205 qrvyv 209
                                       ++v +
  gi|385805302|ref|YP_005841700.1| 453 HPVGA 457
                                       *9865 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.5   7.5e-10   1.1e-06       2      63 ..       2      65 ..       1      68 [. 0.91
   2 ?   -2.0   0.0       2.4   3.5e+03      44      55 ..     161     172 ..     158     184 .. 0.76
   3 ?   -2.6   0.0       3.6   5.3e+03      15      30 ..     187     202 ..     180     208 .. 0.56

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 7.5e-10
                                      H.HCHHHHHCCCHCHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEE CS
                              TrmB  2 q.klGLseyEakvYlaLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYr 63
                                      + k+ Ls++E kv + L  k++  +++e+a+  ++p s+++ v++ L++kGlV+ e   +  Y+
  gi|385805302|ref|YP_005841700.1|  2 EsKYELSDNEQKVVKFLAdKNEVFSIEELASGCNIPISTANAVVELLKSKGLVREEVNYKIQYK 65
                                      559**************************************************99866555776 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.4
                                       HHHHHCTSEEEE CS
                              TrmB  44 rsLedkGlVere 55 
                                       + L+++Gl+e++
  gi|385805302|ref|YP_005841700.1| 161 EILIKRGLIEKK 172
                                       569999**9986 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 3.6
                                       HHHHHHCCCHHCHHCC CS
                              TrmB  15 laLlklgpatadeiae 30 
                                       + +l++g++ +++i +
  gi|385805302|ref|YP_005841700.1| 187 KEVLEKGESVVSKITS 202
                                       3455666666665554 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 !   13.5   0.1   1.9e-05     0.028      93     123 ..     353     382 ..     350     405 .. 0.80
   2 !   10.1   0.0    0.0002       0.3     282     306 ..     453     477 ..     444     480 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.9e-05
                                       EEEEEEEEE--S--BTTB-S-CEEEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  93 rvfqiaraFRaEdsrtdrhlaEFtqieaems 123
                                       r f+i+++FR   +++++ + EF+q++a +s
  gi|385805302|ref|YP_005841700.1| 353 RFFTIGKVFRPDVIDARHLP-EFYQFDAIIS 382
                                       78*************98888.******9654 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0002
                                       -SEEEEEEEHHHHHHHHCT-SSGGG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 282 pphgGlglGldRlvmlllgsesIrd 306
                                        p g +g+GldRl m ll++++Ir 
  gi|385805302|ref|YP_005841700.1| 453 HPVGAWGMGLDRLAMALLNLSDIRM 477
                                       57899******************96 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   2.4e-06    0.0036      11      54 ..      15      57 ..       6      59 .. 0.86
   2 ?   -1.1   0.1       1.2   1.7e+03      42      54 ..     160     172 ..     158     178 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.4e-06
                                      HHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2 11 LaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                        +L++  +  +++ ela  ++++ s+++ +++ L ++GLv+++
  gi|385805302|ref|YP_005841700.1| 15 VKFLADKNEV-FSIEELASGCNIPISTANAVVELLKSKGLVREE 57
                                      5577777775.7*****************************987 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.2
                                       HHHHHHTTSEEEE CS
                            MarR_2  42 lkrLvaaGLverr 54 
                                       ++ L ++GL+e++
  gi|385805302|ref|YP_005841700.1| 160 IEILIKRGLIEKK 172
                                       67799*****985 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   1.1e-05     0.017      28      68 ..      33      76 ..      22      78 .. 0.89
   2 ?    1.0   0.1      0.28   4.2e+02      36      52 ..     156     172 ..     142     202 .. 0.78
   3 ?   -2.6   0.5       3.7   5.5e+03      32      42 ..     489     499 .]     475     499 .] 0.66

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.1e-05
                            HTH_45 28 kanLsykllnkYLdmLvekgli...kkskekYvlTekGlellek 68
                                        n+  +++n  ++ L +kgl+    + k +Y+lTe+G+++lek
  gi|385805302|ref|YP_005841700.1| 33 GCNIPISTANAVVELLKSKGLVreeVNYKIQYKLTEEGKKVLEK 76
                                      568888999999**********88778999***********997 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.28
                            HTH_45  36 lnkYLdmLvekglikks 52 
                                       +++ +++L+++gli+k+
  gi|385805302|ref|YP_005841700.1| 156 FKERIEILIKRGLIEKK 172
                                       66779999*****9664 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 3.7
                            HTH_45  32 sykllnkYLdm 42 
                                       sy+++ kYL++
  gi|385805302|ref|YP_005841700.1| 489 SYSNALKYLNY 499
                                       69999999985 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   2.4e-05     0.036      38      99 ..      42     105 ..      38     118 .. 0.82
   2 ?   -1.4   0.1       1.2   1.8e+03      46      76 ..     171     203 ..     156     211 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.4e-05
                           DUF4364  38 qalseLvesglieeeekenktlykiTekGketle..lfenripksirekideylkenkeelkke 99 
                                       +a+ eL++s+ +  ee + k +yk+Te+Gk++le  + e+ + +++rek +  +ke+++++ ++
  gi|385805302|ref|YP_005841700.1|  42 NAVVELLKSKGLVREEVNYKIQYKLTEEGKKVLEkgFPEEALLDALREKQEIDMKELEKNIDRK 105
                                       55666666666666688****************9445789999999999999999999998876 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.2
                           DUF4364  46 sglieeeek..enktlykiTekGketlelfenr 76 
                                       ++ ++e++   e k++ ++ ekG+ +++ + ++
  gi|385805302|ref|YP_005841700.1| 171 KKILKERKIkpEAKKIKEVLEKGESVVSKITSS 203
                                       444443322224444445555555555555544 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.9e-05     0.058       3      48 .]       9      55 ..       7      55 .. 0.82
   2 ?   -1.1   0.1      0.93   1.4e+03       7      23 ..      82      98 ..      80      98 .. 0.89
   3 ?   -3.3   0.1       4.8   7.2e+03       4       9 ..     102     107 ..     100     109 .. 0.89
   4 ?    0.9   0.1      0.22   3.3e+02      34      48 .]     156     170 ..     152     170 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.9e-05
                            HTH_24  3 etdrkILelLqk.nprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      +++ k+ + L + n   s+ eLA  +++++st n+ ++ L+++Gl++
  gi|385805302|ref|YP_005841700.1|  9 DNEQKVVKFLADkNEVFSIEELASGCNIPISTANAVVELLKSKGLVR 55
                                      56666666666634447999*************************96 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.93
                            HTH_24  7 kILelLqknprisqreL 23
                                      ++L +L+++  i ++eL
  gi|385805302|ref|YP_005841700.1| 82 ALLDALREKQEIDMKEL 98
                                      5799**********998 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 4.8
                            HTH_24   4 tdrkIL 9  
                                       +drkIL
  gi|385805302|ref|YP_005841700.1| 102 IDRKIL 107
                                       8****9 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.22
                            HTH_24  34 vnrrlkrLeeeGlIk 48 
                                        ++r++ L++ GlI+
  gi|385805302|ref|YP_005841700.1| 156 FKERIEILIKRGLIE 170
                                       678***********7 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 ?   12.5   0.1   9.2e-05      0.14       3      55 ..      80     133 ..      79     137 .. 0.78
   2 ?   -3.3   0.1       7.8   1.2e+04      18      31 ..     186     199 ..     178     204 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.2e-05
                        PheRS_DBD3   3 Earvfaavpp.eggisqkelkklggdpvakiGfskAmknkWikkdkgdg.kvvrk 55 
                                       E  +  a+++ ++ i +kel+k+ + ++  i+++   k + i +++g+  ++  k
  gi|385805302|ref|YP_005841700.1|  80 EEALLDALREkQE-IDMKELEKNIDRKILPIALAAGKKRGLIDIKNGKVkLIPEK 133
                                       6667889977444.******9999********************44554444455 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 7.8
                        PheRS_DBD3  18 qkelkklggdpvak 31 
                                       +ke+ ++g++ v k
  gi|385805302|ref|YP_005841700.1| 186 IKEVLEKGESVVSK 199
                                       45554444444433 PP

>> RQC  RQC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0    0.0002       0.3      38      99 ..      10      76 ..       7      92 .. 0.86
   2 ?   -0.7   0.1      0.79   1.2e+03      85     112 ..     125     152 ..     115     154 .. 0.83
   3 ?    0.5   0.2      0.34   5.1e+02      65     106 ..     157     199 ..     147     203 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0002
                                      --CCCCCTTGGGSTTTTT.....TTTS-HHHHHHHHHHHHHTTSEEEE..SSSBEEE-CCGHHHHTS CS
                               RQC 38 ktkkirqlghdklstfGi.....gkdlskkewrrlirqLiaegyLeedveeygvlkltekarevlkg 99
                                      +++k+ ++  dk+++f+i     g +++ ++ +++++ L ++g+++e+v++   +klte++++vl +
  gi|385805302|ref|YP_005841700.1| 10 NEQKVVKFLADKNEVFSIeelasGCNIPISTANAVVELLKSKGLVREEVNYKIQYKLTEEGKKVLEK 76
                                      57899999999999998755555889999*******************99555***********985 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.79
                                       SBEEE-CCGHHHHTSSS--EEESHHHXS CS
                               RQC  85 gvlkltekarevlkgeekvklreekkks 112
                                       g +kl ++  e lk+++++ l++e+++s
  gi|385805302|ref|YP_005841700.1| 125 GKVKLIPEKVEELKKDKEILLKIERSES 152
                                       468999999999*********9999875 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.34
                                       HHHHHHHHHTTSEEEE..SSSBEEE-CC.GHHHHTSSS--EEE CS
                               RQC  65 rrlirqLiaegyLeedveeygvlkltek.arevlkgeekvklr 106
                                       ++ i+ Li++g++e+++ + + +k   k  +evl + e+v  +
  gi|385805302|ref|YP_005841700.1| 157 KERIEILIKRGLIEKKILKERKIKPEAKkIKEVLEKGESVVSK 199
                                       5567889999999999999998888777469999988887655 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00032      0.48      21      56 ..      20      55 ..      13      70 .. 0.89
   2 ?   -1.4   0.0         2   3.1e+03      25      61 ..      92     126 ..      82     127 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00032
                                      STCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 21 eeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                      +++e +s+ee+a+  ni+ s +  +++ L+ +glv+
  gi|385805302|ref|YP_005841700.1| 20 DKNEVFSIEELASGCNIPISTANAVVELLKSKGLVR 55
                                      345579*****************************8 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2
                                       -B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT CS
                              Rrf2  25 pvsseeiaerqnispsylekilakLrkaglvksvrGk 61 
                                        + ++e+    ni +++l   la  +k gl+  + Gk
  gi|385805302|ref|YP_005841700.1|  92 EIDMKELE--KNIDRKILPIALAAGKKRGLIDIKNGK 126
                                       46666664..477888888888888999999988886 PP

>> HTH_6  Helix-turn-helix domain, rpiR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00023      0.35      11      58 ..       4      48 ..       1      54 [. 0.75
   2 ?   -2.5   0.1       3.4   5.1e+03      15      39 ..     180     204 ..     172     208 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00023
                                      -----HHHHHHHHHHHH-S---TT--HHHHHHHTT--HHHHHHHH--- CS
                             HTH_6 11 kekltksekkiaeyilaspdkaielsikalAkaaavSeativrfakkL 58
                                      k +l+++e+k+++++  +++    +si++lA  +++  +t + +   L
  gi|385805302|ref|YP_005841700.1|  4 KYELSDNEQKVVKFLA-DKN--EVFSIEELASGCNIPISTANAVVELL 48
                                      668**********985.344..4589********99877766555555 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.4
                                       -HHHHHHHHHHHH-S---TT--HHH CS
                             HTH_6  15 tksekkiaeyilaspdkaielsika 39 
                                        +  kki e++ +  + +++++++ 
  gi|385805302|ref|YP_005841700.1| 180 KPEAKKIKEVLEKGESVVSKITSSI 204
                                       4555666666666666555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (499 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       918  (0.051202); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); 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):              12  [number of targets reported over threshold]
# CPU time: 0.68u 0.31s 00:00:00.99 Elapsed: 00:00:00.53
# Mc/sec: 2823.00
//
Query:       gi|385805303|ref|YP_005841701.1|  [L=318]
Description: putative dehydrogenase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.7e-18   66.1   0.0    7.4e-18   65.5   0.0    1.3  1  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
    8.7e-05   23.0   0.0    0.00015   22.2   0.0    1.4  1  Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domai
    0.00055   20.6   0.1    0.00087   20.0   0.1    1.3  1  G6PD_N          Glucose-6-phosphate dehydrogenase, NAD bindin
     0.0015   19.1   0.0     0.0034   17.9   0.0    1.6  2  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
       0.03   15.0   0.0      0.058   14.1   0.0    1.4  1  CoA_binding     CoA binding domain
      0.063   13.3   0.0       0.13   12.3   0.0    1.5  1  GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta 


Domain annotation for each model (and alignments):
>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.5   0.0   2.5e-21   7.4e-18       3     113 ..       8     121 ..       6     129 .. 0.91

  Alignments for each domain:
  == domain 1  score: 65.5 bits;  conditional E-value: 2.5e-21
                                       EEEETTSHHHHHHHHHHHHTTTTE..EEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHHH CS
                      GFO_IDH_MocA   3 vaiiGaGkigskhlrplnesqrle..evvalldpdaeraeavaesfgveaysdleelladpeidavivatpngthee 77 
                                       ++iiGaG++g+ h+r l e  +++  +++ +++pd ++  ++++++++  y+ l+e  +++e  +++v +p++th +
  gi|385805303|ref|YP_005841701.1|   8 IGIIGAGYMGQAHIRVLSEIAKKYslKITFVVEPDINKGMDISAKYQLRYYQTLSEAIKNEENFIAFVSSPTSTHLD 84 
                                       8*******************999999*************************************************** PP

                                       HHHHHHHTT-.EEEEESSS-SSHHHHHHHHHHHHHHT CS
                      GFO_IDH_MocA  78 lakaaleagk.hvllEKPlattveeakelvelaekkg 113
                                       ++ ++l +g+  +++EKPl  +++ ake+ ++  ++ 
  gi|385805303|ref|YP_005841701.1|  85 YIDELLSNGIeYIFVEKPLGSDINRAKEIFKKYGRNV 121
                                       *******************999999999887665554 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   5.1e-08   0.00015       2      94 ..       8      97 ..       7      99 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 5.1e-08
                                      EEEETTTSHHHHHHHHHHHC...TSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGCTT-SEEEE-SCHH CS
                    Semialdhyde_dh  2 vaivGatGyvGqellrlLee...hpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeelkevdivflalpag 77
                                      ++i+G  Gy+Gq+ +r+L+e   + ++++++++  + ++G  ++++++ l+++++l+    +ee++    i+f + p +
  gi|385805303|ref|YP_005841701.1|  8 IGIIG-AGYMGQAHIRVLSEiakKYSLKITFVVEPDINKGMDISAKYQ-LRYYQTLSEAIKNEENF----IAFVSSPTS 80
                                      79***.8*************963334555555555559*******988.67776666555556666....********* PP

                                      HHHHHHHHHHHTTSEEE CS
                    Semialdhyde_dh 78 vskelapklaeagvkvi 94
                                      ++ ++ ++l+++g+  i
  gi|385805303|ref|YP_005841701.1| 81 THLDYIDELLSNGIEYI 97
                                      *************9654 PP

>> G6PD_N  Glucose-6-phosphate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   2.9e-07   0.00087      86     160 ..      56     123 ..      27     131 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.9e-07
                            G6PD_N  86 eeyekLkekleeleanrlfYlavppslfeevaeklkkaglakeeewkrvvvEKPfGkdlesarelneelkkvfke 160
                                       + y++L+e++++ e+n + +++ p s+  + +++l ++      + + + vEKP+G+d++ a+e+ ++ ++ + e
  gi|385805303|ref|YP_005841701.1|  56 RYYQTLSEAIKN-EENFIAFVSSPTSTHLDYIDELLSN------GIEYIFVEKPLGSDINRAKEIFKKYGRNVLE 123
                                       45899*****98.99***************99999997......4567*****************9988776655 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.1e-06    0.0034       2      82 ..       8      90 ..       7      99 .. 0.85
   2 ?   -3.7   0.0         6   1.8e+04      37      51 ..     108     122 ..     105     127 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.1e-06
                                      EEEETTSHHHHHHHHHHHHTTS.-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHH..H-SEEEE-S-HHHHHHH CS
                     F420_oxidored  2 igiiGaGnmgealasgllaaga.qpheivvansrnpekaeelaeelgvkvtavdneeaae..eadvvvlavkpedveev 77
                                      igiiGaG mg+a ++ l++  +    +i+++ +++ +k   + ++++ +  + + +ea++  e+ + +++ +++ + + 
  gi|385805303|ref|YP_005841701.1|  8 IGIIGAGYMGQAHIRVLSEIAKkYSLKITFVVEPDINKGMDISAKYQLRYYQ-TLSEAIKneENFIAFVSSPTSTHLDY 85
                                      9*************999987666777888889***************99999.9*****95444478999999999888 PP

                                      HHHCG CS
                     F420_oxidored 78 lsela 82
                                      ++el 
  gi|385805303|ref|YP_005841701.1| 86 IDELL 90
                                      88884 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 6
                                       CCHHHHHHHHC-EEE CS
                     F420_oxidored  37 ekaeelaeelgvkvt 51 
                                       ++a+e+ +++g++v 
  gi|385805303|ref|YP_005841701.1| 108 NRAKEIFKKYGRNVL 122
                                       688899999998775 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.9e-05     0.058       5      91 ..       7      98 ..       5     102 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.9e-05
                                      EEEEETTTSHHHHHH.HHHHHHHHECEEEEEEC-TT.TTTCEET...TEEEESCHHHHHHHCTTTEEEEES..-HHHHH CS
                       CoA_binding  5 kviviGagglgiagl.yhfkeklkygikavfgvnpr.kvgtevl...glpvyksvdeleektevdvavitv..Paesaq 76
                                       +++iGag +g+a   + ++  +ky++k+ f v p+   g +++    l  y++++e++++  ++  + +v  P     
  gi|385805303|ref|YP_005841701.1|  7 GIGIIGAGYMGQAHIrVLSEIAKKYSLKITFVVEPDiNKGMDISakyQLRYYQTLSEAIKN--EENFIAFVssPTSTHL 83
                                      689***********9999999999999999999999767777778999*************..8999999966778888 PP

                                      HHHHHHHHTT-SEEE CS
                       CoA_binding 77 eavdelveagikgiv 91
                                      + +del+ +gi+ i 
  gi|385805303|ref|YP_005841701.1| 84 DYIDELLSNGIEYIF 98
                                      99*********9886 PP

>> GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.2e-05      0.13      38      64 ..     169     195 ..     143     221 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.2e-05
                                       CSTSHHHHTCHHHHHHHHHHHTSEEEE CS
                    GFO_IDH_MocA_C  38 ksgGvlgdlgiHdiDllqwLfGqppsv 64 
                                       ++ Gv  dl+iHdiDl   Lf  +p  
  gi|385805303|ref|YP_005841701.1| 169 RDTGVILDLAIHDIDLSLSLFDNEPKG 195
                                       578******************888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.54
# Mc/sec: 1782.65
//
Query:       gi|385805304|ref|YP_005841702.1|  [L=318]
Description: aldo/keto reductase [Fervidicoccus fontis Kam940]
Scores for complete 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-60  205.2   0.0    1.5e-60  204.9   0.0    1.0  1  Aldo_ket_red  Aldo/keto reductase family


Domain annotation for each model (and alignments):
>> Aldo_ket_red  Aldo/keto reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.9   0.0   8.4e-65   1.5e-60       2     290 ..      16     302 ..      15     305 .. 0.94

  Alignments for each domain:
  == domain 1  score: 204.9 bits;  conditional E-value: 8.4e-65
                                       EEEE-SSS-ST..TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE--SSSTT CS
                      Aldo_ket_red   2 lglGtwqlgsk.eeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKvdlrdaei 77 
                                       + lG+wq++   +  + e   +++ +a+++Gin++DtA +Yg+g+se+++G+al++  + +e+v++atK+      +
  gi|385805304|ref|YP_005841702.1|  16 VSLGAWQFSESwGLLDYEMIKKIISTAVDNGINMIDTAIAYGRGKSEDFVGRALEE-LNLKEKVFVATKI------P 85 
                                       679******99999******************************************.99***********......9 PP

                                       SSSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-..HHHHHHHHHHHHHTTSEEEEEEES--HHHHHHH.HHT CS
                      Aldo_ket_red  78 ksglskeniresleeslkrLgtdyvDllllHrpdpslp.sieevldaleelvkeGkiraiGvSnfsveqleka.kkk 152
                                        + l   ++ ++++ sl+rL+ + +Dll++H p  +     +e ++ale+lv +G++r+iGvSnf+   +e+a    
  gi|385805304|ref|YP_005841702.1|  86 GEMLGYHDVLRAVRGSLRRLRKESIDLLQVHSPPLWNNiPTCEYMRALEKLVIQGLVRYIGVSNFPSILVEEAnFCL 162
                                       9999999***************************9876559********************************8677 PP

                                       TT--EEEEE-B-BTT-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC-------...TS-HHHH CS
                      Aldo_ket_red 153 kkvkivavqveynllreleeegllelckkkgvpliaysplggGlltgkyqseedkedkeprkdlkrd...ertsknl 226
                                       +  ++v++qv+ynl ++++e+++++ + ++++ +ia+spl++G+l+gky+ e+ ++ ++  ++++     e+++  +
  gi|385805304|ref|YP_005841702.1| 163 SREEVVSNQVRYNLIERDAEKEIIPHALQNDMSIIAWSPLAKGALSGKYTAENLPK-FSDVRQNEPIfypENFKNIM 238
                                       77789*********************************************777765.55555554448********* PP

                                       HHHHHHHHHHHHTT--HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHGGGG----HHHHHHHH CS
                      Aldo_ket_red 227 daaeelselakehgvslaqlalryalsqpavgivipgasnieqlednldalelklseeevaeld 290
                                        +++ ++ +a+++g+ ++q++l+++l ++ ++ivipga+n+eq+ +n++a ++k+s +++  l+
  gi|385805304|ref|YP_005841702.1| 239 PLIDLVKGIAEKYGKIPSQVSLNWLLTSYDNVIVIPGAKNPEQVIENVGAADWKMSYDDWLLLE 302
                                       *******************************************************999987776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2043.17
//
Query:       gi|385805305|ref|YP_005841703.1|  [L=459]
Description: phosphomethylpyrimidine kinase [Fervidicoccus fontis Kam940]
Scores for complete 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-96  320.7   3.1    7.2e-96  320.3   3.1    1.1  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase
    4.9e-58  195.4   0.8    9.3e-57  191.2   0.0    2.6  3  ThiP_synth    Thiamine-phosphate synthase
      8e-11   41.8   0.5    2.3e-10   40.3   0.5    1.6  1  PfkB          pfkB family carbohydrate kinase
    0.00077   19.0   1.8     0.0012   18.3   1.8    1.3  1  Carb_kinase   Carbohydrate kinase


Domain annotation for each model (and alignments):
>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  320.3   3.1   1.6e-99   7.2e-96       1     246 []      20     265 ..      20     265 .. 0.99

  Alignments for each domain:
  == domain 1  score: 320.3 bits;  conditional E-value: 1.6e-99
                                       ETTSSSHHHHHHHHHHHTTEEEEEEEEEEEEEETTCEEEEEE--HHHHHHHHHHHHHTS--SEEEE-S--SHHHHHH CS
                      Phos_pyr_kin   1 DssGGAGiqADlktfsalgvygmsvitaltaqntkgvkevhplpaelveaqleavledvkvdavKiGmlasaeiiev 77 
                                       Ds+GGAGiqADlktf+ +gvygm +it++taqntk+v++++++++e+v++q+eav +d++vda+K+Gml+++eii++
  gi|385805305|ref|YP_005841703.1|  20 DSGGGAGIQADLKTFTVHGVYGMVAITSITAQNTKEVRAIYDVSPEVVASQIEAVSDDIGVDAAKTGMLSNKEIIHA 96 
                                       9**************************************************************************** PP

                                       HHHHHHHTTSSEEEE---SSCTSSSBSSHHHHHHHHHHTGGG-SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHH. CS
                      Phos_pyr_kin  78 vaeklkkykvpvVlDPVmvaksgselleeeavealkeeLlplatvitPNlpEaeaLlgekikteedmkeaakkllk. 153
                                       v  +lkky++p+V+DPVmvaksg++ll+++a+ealk+eLlp+a+++tPN  Eae L++eki+t +d+ +aakk+ k 
  gi|385805305|ref|YP_005841703.1|  97 VSGVLKKYDFPLVIDPVMVAKSGAKLLKDDAIEALKNELLPRAKIVTPNRMEAEILSNEKIQTIDDAIKAAKKIKKe 173
                                       ****************************************************************************9 PP

                                       TT-SEEEEEEGGS-SSSEEEEEEEETSSEEEEEEEE----S--BTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHH CS
                      Phos_pyr_kin 154 lgakaVlikGghlegeeavvtdvlydgeeveeleaerietknthGtGCtlssaiaaelakgesleeAvkkAkeyvte 230
                                       +  +aV++kGgh+++++++++dvly +++ + le+er++   thGtGC++s++iaa+la g+++ eAvk+Ake++t+
  gi|385805305|ref|YP_005841703.1| 174 YVPEAVVVKGGHISEDSKYAVDVLYVEDHAILLEGERVN-GCTHGTGCSFSASIAANLAWGYDIIEAVKNAKEFITH 249
                                       9**************************************.************************************* PP

                                       HHHCG-BSTSSS-B-- CS
                      Phos_pyr_kin 231 aikealelgkgagpvn 246
                                       +ik +++ g+g+ pvn
  gi|385805305|ref|YP_005841703.1| 250 SIKTGINYGSGHCPVN 265
                                       **************97 PP

>> ThiP_synth  Thiamine-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1     0.036   1.6e+02      91     143 ..     125     185 ..     116     192 .. 0.62
   2 ?   -2.9   0.0         1   4.6e+03      82     100 ..     225     243 ..     223     249 .. 0.80
   3 !  191.2   0.0   2.1e-60   9.3e-57       1     164 [.     282     453 ..     282     454 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.036
                                       HHHHHHHCCTTSEEEE--.CCCS-CCC.....T-HHHHHHHHH..HHCCS-ECEEEE--BC CS
                        ThiP_synth  91 ekilealeelglkvvefd.reeepeev.....gstmewgvaea..ieelevpdviydeGgv 143
                                       ++ +eal++  l  +++  +++ + e+      +t++ ++++a  i+++ vp++++ +Gg 
  gi|385805305|ref|YP_005841703.1| 125 DDAIEALKNELLPRAKIVtPNRMEAEIlsnekIQTIDDAIKAAkkIKKEYVPEAVVVKGGH 185
                                       4556666665555555440444444447755566777777666333333699999999986 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1
                                       -EEEEEE--HHHHHHHCCT CS
                        ThiP_synth  82 raainirydekilealeel 100
                                         a+n+++  +i+ea++++
  gi|385805305|ref|YP_005841703.1| 225 SIAANLAWGYDIIEAVKNA 243
                                       5789999999999998875 PP

  == domain 3  score: 191.2 bits;  conditional E-value: 2.1e-60
                                       HHHHHHHHHHCC--..GCC--TT-B-EEEE-S..T--SGGGEEEETT-EEE-TSSEEE-S-EEETS-CHHHHHHHHH CS
                        ThiP_synth   1 eleralelleeeee.fakliPevgsNiayalp..dAksieDvaavpGRIvrvkgrvkvvgepefgasshvarvllaa 74 
                                       +le+a++ll++++e f k+ Pevg N+a++lp  + k+++Dva++pGRI+r++++++++ +pefgas+hva+ ++a+
  gi|385805305|ref|YP_005841703.1| 282 NLEQAVSLLVDNSEeFVKYYPEVGINLAMSLPswYVKDENDVAGIPGRIIRIGKKLEACYKPEFGASKHVAKSIIAI 358
                                       589******999988************************************************************** PP

                                       HCC-TT--EEEEEE--HHHHHHHCCTTSEEEE--CCCS-CCC....T-HHHHHHHHHHHCC.S-ECEEEE--BCTB- CS
                        ThiP_synth  75 mkfdpevraainirydekilealeelglkvvefdreeepeev....gstmewgvaeaieel.evpdviydeGgvGkE 146
                                       +k+dp++raa+n+ yde +le++e+lg+ ++ fdr+ epe+v    g+t +wg++ ai++  +vpd+iyd G+ GkE
  gi|385805305|ref|YP_005841703.1| 359 QKHDPSIRAAMNLVYDESFLENAERLGYIISGFDRKFEPEDVkkteGATTPWGIDFAIKKIgKVPDIIYDVGEPGKE 435
                                       *************************************************************99************** PP

                                       -EEEEEESSHHHHHHHHH CS
                        ThiP_synth 147 pmiyvlgkdaeevvekvl 164
                                       + ++++g++a++vvek+l
  gi|385805305|ref|YP_005841703.1| 436 ALVFIFGQSAKDVVEKAL 453
                                       ****************86 PP

>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.5     5e-14   2.3e-10     161     282 ..     110     243 ..      88     246 .. 0.76

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 5e-14
                                       EEEEECESSSHH.....HHHHHH.HHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTS.SEEEEEEG.. CS
                              PfkB 161 fdpnlldplgaq.....fkeall.ellaladllkpneeElealtgekledieealaalhklkakga.ktvvvtlG.. 228
                                        dp++++++ga+     + eal+ ell+ a +++pn+ E+e+l++ek+++i++a++a++k+k++++ + vvv+ G  
  gi|385805305|ref|YP_005841703.1| 110 IDPVMVAKSGAKllkddAIEALKnELLPRAKIVTPNRMEAEILSNEKIQTIDDAIKAAKKIKKEYVpEAVVVKGGhi 186
                                       577777777777776665555542678***************************************99999999855 PP

                                       .GGEEEEEE....TTEEEEEEE.SSSS-SB..GTTHHHHHHHHHHHHHHTTHHHHHHHHHH CS
                              PfkB 229 .keGalvve....kdgelkvpavpkvkvvD..ttGAGDsfvggflaallegksleealrfa 282
                                        ++  ++v+    +     +  + + + v+  t G+G sf ++++a+l+ g ++ ea++ a
  gi|385805305|ref|YP_005841703.1| 187 sEDSKYAVDvlyvE----DHAILLEGERVNgcTHGTGCSFSASIAANLAWGYDIIEAVKNA 243
                                       44666666654332....3333344444544499***********************9977 PP

>> Carb_kinase  Carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   1.8   2.8e-07    0.0012       3     215 ..      15     244 ..      13     252 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.8e-07
                                       EEE-BTTCHHHHHHHHHHHHCTT..-SEEEEEESS....TTTCCCCTTTTTCEECCTTHTTTS...--SSS-SEEEE CS
                       Carb_kinase   3 vigGsedytGAallaalaalrlg..aglvsvates....eaiavlksylpevivhplledeqakileklerldavvi 73 
                                        i+Gs+   GA++ a l +  +    g+v +        +++ ++   +pev++++++        +  + + + + 
  gi|385805305|ref|YP_005841703.1|  15 TIAGSDSGGGAGIQADLKTFTVHgvYGMVAITSITaqntKEVRAIYDVSPEVVASQIE--------AVSDDIGVDAA 83 
                                       5999999999999999987765334899988653300003444444555555555555........33444555555 PP

                                       -TT-SSSHCHHHHCHHHCCCCS.-EEEE.....GGGGGSGGGG.......TTTTSSEEEE--HHHHHHHCTTTCHHC CS
                       Carb_kinase  74 GpGLgrdekikklleevlekde.plviD.....AdgLnllaqkne....lserkaeviLTPhkkEfkrLlkaivkke 140
                                         G+ ++++i +++  vl+k++ plviD      +g +ll+++            + i TP+  E + L++  ++  
  gi|385805305|ref|YP_005841703.1|  84 KTGMLSNKEIIHAVSGVLKKYDfPLVIDpvmvaKSGAKLLKDDAIealkNELLPRAKIVTPNRMEAEILSNEKIQTI 160
                                       566667777778888888876537888844443234444443322366555666789*****************9** PP

                                       CSHHHHHHHHHHHH.TTEEEEESTT.....SEEEEC...TTEEEEE----GGG-STTHHHHHHHHHHHHHHCTSSHH CS
                       Carb_kinase 141 ddrlelarelaqkl.navvllkgek.....dvivsp...egevlinstgssalakGGsGDvLaGligalLaqneasy 208
                                       dd  ++a+++ +++ +  v++kg +     +  v+    e+  ++++ + ++  + G+G   + +i+a La+ ++  
  gi|385805305|ref|YP_005841703.1| 161 DDAIKAAKKIKKEYvPEAVVVKGGHisedsKYAVDVlyvEDHAILLEGERVNGCTHGTGCSFSASIAANLAWGYDII 237
                                       **********9886468888998642332223322233388999999999999999****************99999 PP

                                       HHHHHHH CS
                       Carb_kinase 209 eaaiaaa 215
                                       ea+ +a 
  gi|385805305|ref|YP_005841703.1| 238 EAVKNAK 244
                                       9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); 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:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 2956.15
//
Query:       gi|385805306|ref|YP_005841704.1|  [L=227]
Description: Zn-dependent hydrolase of the metallo-beta-lactamase superfamily protein [Fervidicoccus fontis Kam940]
Scores for complete 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-35  122.3   0.0    2.1e-35  122.0   0.0    1.1  1  Lactamase_B_3  Beta-lactamase superfamily domain
    2.5e-10   40.2   0.0     0.0004   19.9   0.0    2.2  2  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.022   14.8   0.7       0.13   12.3   1.1    2.0  2  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 !  122.0   0.0   3.6e-39   2.1e-35       2     163 .]       7     174 ..       6     174 .. 0.93

  Alignments for each domain:
  == domain 1  score: 122.0 bits;  conditional E-value: 3.6e-39
                     Lactamase_B_3   2 ltwlghnsflletagarilvDPfka.nlgyeppaeeaDlvlisqaledHahletlkqlaenvkvlee.....gesle 72 
                                       + ++gh++f ++t+  +il DP  + ++g++p + +aD+vli++++ dH++ e++ +  en++vl++       +++
  gi|385805306|ref|YP_005841704.1|   7 IFYHGHSCFEVKTGSNSILFDPHPGeSIGLKPIETKADIVLITHEHFDHNAKENVVK--ENTQVLSSyfgekRLNAN 81 
                                       78*********************999*************************999988..8******98854334478 PP

                     Lactamase_B_3  73 vggleiravatshdavggsergenngflleqdgltiyhlGhlahelsseelke..lgrvDvvltPvggpltlgqeea 147
                                       ++++ +++++  hd++gg++rg   ++l++ ++ +++hlG+l+ ++s+e l+e   +r+D +++Pvgg +t+g++ea
  gi|385805306|ref|YP_005841704.1|  82 AEEIFVKGFKLPHDNQGGRKRGFVAAYLVKIRNFKLLHLGDLGSDISNELLNEvkKERIDFLFIPVGGYYTIGPQEA 158
                                       89*********************************************9998651157******************** PP

                     Lactamase_B_3 148 lelakrLkpklvlPmh 163
                                        e+ k+++p++++Pmh
  gi|385805306|ref|YP_005841704.1| 159 WEISKKINPEYIVPMH 174
                                       ***************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 !   19.7   0.1     8e-08   0.00048       3      78 ..      24      90 ..      22      94 .. 0.68
   2 !   19.9   0.0   6.8e-08    0.0004     104     201 .]      86     175 ..      75     175 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 8e-08
                                      EEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEE.EEHHHHHHCCTTCGHHH CS
                     Lactamase_B_2  3 iLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklply.apkgvlavleanfvyla 78
                                      iL+D+ p+  +  +  l+P    ++  + d Vl+th+H+DH a    ++e ++  l  y + k++ a+ e+ fv  +
  gi|385805306|ref|YP_005841704.1| 24 ILFDPHPG--E--SIGLKP---IET--KADIVLITHEHFDHNAKENVVKENTQ-VLSSYfGEKRLNANAEEIFVKGF 90
                                      89999999..2..233344...347..99************998888888332.25544477777777776666555 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 6.8e-08
                                       EEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S.---HHHHHHHCT..-SEEEEE-S-SSTTHHHHHHT CS
                     Lactamase_B_2 104 eitatparhksgrrldrnagdtlGlriegggkrvyyigDtg.yipeeigerlgg..adllllditayeddemirhmg 177
                                        ++ + ++h+ +   +r++g +++++++  + +++++gD+g  i+ e+ +++++  +d l+++++         + +
  gi|385805306|ref|YP_005841704.1|  86 FVKGFKLPHDNQG--GRKRGFVAAYLVKIRNFKLLHLGDLGsDISNELLNEVKKerIDFLFIPVG---------GYY 151
                                       5778888999888..99************************667799999999889*********.........778 PP

                                       ---STSHHHHCTTSSSSEEEEESB CS
                     Lactamase_B_2 178 HltpeeaveaaadlgakrlvliHi 201
                                       ++ p+ea+e+ ++++++  v++H+
  gi|385805306|ref|YP_005841704.1| 152 TIGPQEAWEISKKINPEYIVPMHY 175
                                       8**********************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 ?   12.3   1.1   2.1e-05      0.13       7      58 ..      13      56 ..       9      84 .. 0.75
   2 ?   -0.9   0.0      0.24   1.4e+03     144     197 .]     116     174 ..     106     174 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.1e-05
                                      EEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHH CS
                       Lactamase_B  7 nsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHi 58
                                      +++ + ++   iL+D+  +++ +++            + d v++TH H+DH 
  gi|385805306|ref|YP_005841704.1| 13 SCFEVKTGSNSILFDPHPGESIGLKP--------IETKADIVLITHEHFDHN 56
                                      56666666666777776666666654........3556699**********5 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.24
                                       CEEEECTTTSSHHCCCCCC............TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                       Lactamase_B 144 kvlftGDallagetgridl...........tlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                       k+l  GD++   +++++ +           + +g +++ p++a++        ++ ++e++vp H
  gi|385805306|ref|YP_005841704.1| 116 KLLHLGDLGSDISNELLNEvkkeridflfiPVGGYYTIGPQEAWEIS------KKINPEYIVPMH 174
                                       56777777776666666666777777788866666666666655555......367777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1508.62
//
Query:       gi|385805307|ref|YP_005841705.1|  [L=58]
Description: hypothetical protein FFONT_0263 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-11   43.0   0.3    3.8e-11   42.5   0.3    1.2  1  RHH_1            Ribbon-helix-helix protein, copG family
    4.1e-07   29.9   0.7    5.1e-07   29.6   0.7    1.2  1  RHH_3            Ribbon-helix-helix domain
     0.0021   18.2   0.0     0.0022   18.2   0.0    1.1  1  RHH_8            Ribbon-Helix-Helix transcriptional regulator
     0.0023   16.7   0.0     0.0025   16.6   0.0    1.0  1  Condensation     Condensation domain
     0.0086   16.6   0.1      0.011   16.2   0.1    1.2  1  CopG_antitoxin   CopG antitoxin of type II toxin-antitoxin sy
  ------ inclusion threshold ------
      0.042   14.0   0.0      0.072   13.2   0.0    1.4  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit
      0.064   14.0   0.1      0.072   13.9   0.1    1.1  1  PSK_trans_fac    Rv0623-like transcription factor


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   0.3   1.5e-14   3.8e-11       2      37 ..       4      39 ..       4      41 .. 0.97

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 1.5e-14
                                      EEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHH CS
                             RHH_1  2 vsirldeellerLdelarrrgrSrSelIReAlreyl 37
                                      ++++ldeeller+d la ++g +rS++IR A+ +yl
  gi|385805307|ref|YP_005841705.1|  4 ITFKLDEELLERIDMLAQESGTNRSDIIRKAIIMYL 39
                                      79*********************************8 PP

>> RHH_3  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.7     2e-10   5.1e-07       5      42 ..       4      41 ..       2      43 .. 0.96

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 2e-10
                             RHH_3  5 ttvsidpelaekLkaLSekTrIprSklldeAiellLek 42
                                      +t+ +d+el+e+ + L ++ + +rS+++++Ai ++L k
  gi|385805307|ref|YP_005841705.1|  4 ITFKLDEELLERIDMLAQESGTNRSDIIRKAIIMYLSK 41
                                      6999********************************76 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 !   18.2   0.0   8.5e-07    0.0022       6      48 ..       4      45 ..       1      55 [. 0.82

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 8.5e-07
                             RHH_8  6 vtinlgvvDLgqiDlLveeGfYsnRtDlirtairaqLakhdda 48
                                      +t  l+   L +iD+L +e   +nR+D+ir+ai   L+k +++
  gi|385805307|ref|YP_005841705.1|  4 ITFKLDEELLERIDMLAQES-GTNRSDIIRKAIIMYLSKAEKE 45
                                      6888888889******9996.59**********9999876654 PP

>> Condensation  Condensation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   9.8e-07    0.0025     227     270 ..       3      46 ..       1      49 [. 0.92

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 9.8e-07
                                       EEEEEEEE-S-HHHHHHHHSTSS-HHHHHHHHHHHHHHHHHT-S CS
                      Condensation 227 rlsikldeeteeklrklakeqgvtlndvllaalgllLskytgqd 270
                                        +++kldee+ e++  la+e+g++  d+   a  ++Lsk  +++
  gi|385805307|ref|YP_005841705.1|   3 IITFKLDEELLERIDMLAQESGTNRSDIIRKAIIMYLSKAEKES 46 
                                       689************************************88765 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 !   16.2   0.1   4.4e-06     0.011      43      75 ..       2      34 ..       1      38 [. 0.90

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.4e-06
                    CopG_antitoxin 43 ksislrlpedlLealkekAnkrdvpyqslikel 75
                                      k i+++l+e+lLe++ + A++ + + +  i+++
  gi|385805307|ref|YP_005841705.1|  2 KIITFKLDEELLERIDMLAQESGTNRSDIIRKA 34
                                      6799*******************9999999876 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 ?   13.2   0.0   2.8e-05     0.072      95     121 ..       7      33 ..       2      35 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.8e-05
                   HicB_lk_antitox  95 tlpervlkriDaavkaagesRSgflak 121
                                        l e++l+riD +++++g++RS  + k
  gi|385805307|ref|YP_005841705.1|   7 KLDEELLERIDMLAQESGTNRSDIIRK 33 
                                       57899*****************99977 PP

>> PSK_trans_fac  Rv0623-like transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   2.8e-05     0.072      12      44 ..      14      48 ..       8      57 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.8e-05
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..X CS
                     PSK_trans_fac 12 rlareLarltgeskteAvrrAleerlerlrre..r 44
                                      + ++ La+  g++  +++r+A+ ++l++ ++e   
  gi|385805307|ref|YP_005841705.1| 14 ERIDMLAQESGTNRSDIIRKAIIMYLSKAEKEsaV 48
                                      66788***********************9976532 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); 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:                         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 0.30s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 373.88
//
Query:       gi|385805308|ref|YP_005841706.1|  [L=141]
Description: hypothetical protein FFONT_0264 [Fervidicoccus fontis Kam940]
Scores for complete 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   20.5   1.8     0.0023   17.9   1.9    2.1  2  Noelin-1         Neurogenesis glycoprotein
    0.00082   19.6   6.2    0.00082   19.6   6.2    1.6  2  BLOC1_2          Biogenesis of lysosome-related organelles co
     0.0024   17.6   7.1      0.021   14.6   0.8    2.5  2  TRAF_BIRC3_bd    TNF receptor-associated factor BIRC3 binding
     0.0028   16.0   5.0     0.0029   15.9   5.0    1.0  1  FPP              Filament-like plant protein, long coiled-coi
     0.0035   18.3   3.0     0.0055   17.7   3.0    1.3  1  DUF4927          Domain of unknown function (DUF4927)
     0.0038   17.7   0.4      0.044   14.3   0.0    2.3  2  CopG_antitoxin   CopG antitoxin of type II toxin-antitoxin sy
     0.0047   17.1   2.2      0.008   16.3   2.2    1.4  1  Med2             Mediator complex subunit 2
     0.0069   16.1   9.0     0.0083   15.8   8.9    1.2  1  Lebercilin       Ciliary protein causing Leber congenital ama
     0.0084   16.1   0.8       0.07   13.1   0.1    2.5  2  RHH_3            Ribbon-helix-helix domain
     0.0099   14.8   7.1      0.019   13.9   6.6    1.6  2  Spc7             Spc7 kinetochore protein
  ------ inclusion threshold ------
      0.013   15.4   2.1      0.016   15.0   2.1    1.2  1  Spc29            Spindle Pole Component 29
      0.024   14.6   2.6      0.037   14.1   2.6    1.3  1  Laminin_II       Laminin Domain II
      0.051   13.3   0.2       0.13   12.1   0.2    1.7  1  RFX5_N           RFX5 N-terminal domain
       0.07   13.6   4.1       0.77   10.3   4.1    2.2  1  NPV_P10          Nucleopolyhedrovirus P10 protein
       0.12   12.3   0.1       0.33   10.9   0.0    1.7  2  RHH_4            Ribbon-helix-helix domain
       0.18   12.1   0.0       0.29   11.4   0.0    1.3  1  DUF4031          Protein of unknown function (DUF4031)
       0.19   11.9   5.2       0.28   11.4   5.2    1.4  1  Fib_alpha        Fibrinogen alpha/beta chain family
        0.2   11.7   7.4       0.79    9.8   7.4    2.0  1  DUF1664          Protein of unknown function (DUF1664)
       0.23   11.0   1.8       0.25   10.8   1.8    1.1  1  Allexi_40kDa     Allexivirus 40kDa protein
       0.28   11.3   3.2        0.6   10.2   3.2    1.6  1  Cob_adeno_trans  Cobalamin adenosyltransferase
       0.34   11.6   4.6        1.2    9.8   0.3    2.3  2  AKNA             AT-hook-containing transcription factor
       0.61   10.1   9.7        1.4    9.0   7.1    2.1  2  FlxA             FlxA-like protein
        0.8    9.6   4.1       0.64    9.9   0.8    2.4  2  MtrG             Tetrahydromethanopterin S-methyltransferase,
        0.9   10.4   5.4        5.6    7.9   0.0    2.5  2  Histone_HNS      H-NS histone family
       0.93    9.3   3.1        3.7    7.4   0.4    2.5  2  DASH_Dam1        DASH complex subunit Dam1
        1.7    9.3  11.6         23    5.7  10.0    2.6  2  SlyX             SlyX
        1.7    8.7   9.0        1.7    8.7   7.5    1.7  2  DUF848           Gammaherpesvirus protein of unknown function
        1.7    9.1  11.1        7.3    7.1   4.4    2.9  2  FlaC_arch        Flagella accessory protein C (FlaC)
        1.7    9.1   9.0         19    5.8   9.0    2.3  1  DUF16            Protein of unknown function DUF16
        1.9    8.7  10.8        3.2    8.0   4.7    2.6  3  XhlA             Haemolysin XhlA
        2.6    8.2   9.6        5.2    7.2   0.6    2.9  3  Swi5             Swi5
        3.7    6.5   5.2        4.2    6.3   5.2    1.0  1  eIF-4B           Plant specific eukaryotic initiation factor 
        3.8    7.0   4.3         23    4.4   0.4    2.2  2  BRI3BP           Negative regulator of p53/TP53
        6.1    7.2  10.9        1.2    9.5   2.3    2.5  2  Osmo_CC          Osmosensory transporter coiled coil
        6.4    6.9   8.7         13    5.9   1.4    2.6  3  PspB             Phage shock protein B


Domain annotation for each model (and alignments):
>> Noelin-1  Neurogenesis glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       6.9   3.5e+03      30      48 ..      23      41 ..      18      60 .. 0.62
   2 !   17.9   1.9   4.4e-06    0.0023      35      87 ..      69     118 ..      56     131 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 6.9
                          Noelin-1 30 dvCsrDarsrqlrqllekv 48
                                      ++   D  + +lr++ e+ 
  gi|385805308|ref|YP_005841706.1| 23 HLSISDKLYDELREIAEEY 41
                                      5556677777788877653 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 4.4e-06
                          Noelin-1  35 DarsrqlrqllekvqnlsqsievldlRtsrdlqyvrktetllktlesklkvve 87 
                                       +  +++l +l+ek++ +s +i +l++ t+r+l+ +++  +++k le+k++++e
  gi|385805308|ref|YP_005841706.1|  69 NEDTEKLEELEEKIEQISSQIIQLNKFTERQLK-IQN--SMIKALEEKVSNLE 118
                                       445789**************************9.544..34556665555544 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       9.1   4.7e+03      36      47 ..      31      42 ..      25      60 .. 0.63
   2 !   19.6   6.2   1.6e-06   0.00082      31      86 ..      70     126 ..      65     130 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 9.1
                           BLOC1_2 36 ykklkdvaasle 47
                                      y++l+++a++  
  gi|385805308|ref|YP_005841706.1| 31 YDELREIAEEYG 42
                                      555555555544 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 1.6e-06
                           BLOC1_2  31 aasekykklkdvaaslekkleklnekye.elqpylqqidqiekqvteLeeavseLDe 86 
                                       + +ek ++l+++++++++++ +ln+  e +l+ + + i+++e++v+ Le +++eL+e
  gi|385805308|ref|YP_005841706.1|  70 EDTEKLEELEEKIEQISSQIIQLNKFTErQLKIQNSMIKALEEKVSNLELIIDELEE 126
                                       66899********************9999**************************98 PP

>> TRAF_BIRC3_bd  TNF receptor-associated factor BIRC3 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.8     0.014       7.2      42      59 ..      69      86 ..      55      92 .. 0.85
   2 !   14.6   0.8   4.1e-05     0.021      37      62 ..      96     121 ..      85     122 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.014
                     TRAF_BIRC3_bd 42 rldqekieaLekKvrqLe 59
                                      ++d ek e Le+K++q  
  gi|385805308|ref|YP_005841706.1| 69 NEDTEKLEELEEKIEQIS 86
                                      6899***********986 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 4.1e-05
                     TRAF_BIRC3_bd  37 verqrrldqekieaLekKvrqLerti 62 
                                        erq +    +i+aLe+Kv +Le +i
  gi|385805308|ref|YP_005841706.1|  96 TERQLKIQNSMIKALEEKVSNLELII 121
                                       48********************9776 PP

>> FPP  Filament-like plant protein, long coiled-coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   5.0   5.6e-06    0.0029     717     783 ..      68     130 ..      17     137 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.6e-06
                               FPP 717 nleslkaqlqesEqllaelkseLeslkeskslaetqlkcmkesyesletrateleaelnelkqkiea 783
                                       ++e    +l+e E++++++ s++ +   +++ +e qlk ++ + + le + ++le  + el++k+++
  gi|385805308|ref|YP_005841706.1|  68 DNED-TEKLEELEEKIEQISSQIIQ---LNKFTERQLKIQNSMIKALEEKVSNLELIIDELEEKMDN 130
                                       4444.569*************9976...6889*******************************9875 PP

>> DUF4927  Domain of unknown function (DUF4927)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   3.0   1.1e-05    0.0055      34      87 ..      72     125 ..      61     127 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.1e-05
                           DUF4927  34 kPKlEeldskveqgsssklatsksekeeskiktedqdelpgdednLdeILgdLq 87 
                                       + KlEel+ k+eq ss+ ++  k  +++ ki+++  + l+ + +nL+ I+++L+
  gi|385805308|ref|YP_005841706.1|  72 TEKLEELEEKIEQISSQIIQLNKFTERQLKIQNSMIKALEEKVSNLELIIDELE 125
                                       56*********************999**********99*9999********997 PP

>> CopG_antitoxin  CopG antitoxin of type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   8.6e-05     0.044      40      78 ..      17      55 ..      12      56 .. 0.93
   2 ?    1.1   0.3       1.2   5.9e+02      40      60 ..      94     113 ..      67     124 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.6e-05
                    CopG_antitoxin 40 kktksislrlpedlLealkekAnkrdvpyqslikellee 78
                                      k++ ++ l ++ +l ++l+e A++ ++ ++ lik+++++
  gi|385805308|ref|YP_005841706.1| 17 KTMPTVHLSISDKLYDELREIAEEYGIQITDLIKVFIKN 55
                                      67889******************************9986 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 1.2
                    CopG_antitoxin  40 kktksislrlpedlLealkek 60 
                                       k t++  l++ +++++al ek
  gi|385805308|ref|YP_005841706.1|  94 KFTER-QLKIQNSMIKALEEK 113
                                       32222.255556665555555 PP

>> Med2  Mediator complex subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   2.2   1.6e-05     0.008       4      73 ..      73     136 ..      70     141 .] 0.80

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.6e-05
                              Med2   4 nkLtqclddiLkvsgemlvqeqlktiqldsnvvtGfnnqlqksLkekikkFhsiLDdleiklndaksyve 73 
                                       +kL++  + i ++s++++  +  k  +++ ++    +n+++k L+ek+++ + i+D+le k+ + k y+e
  gi|385805308|ref|YP_005841706.1|  73 EKLEELEEKIEQISSQII--QLNKFTERQLKI----QNSMIKALEEKVSNLELIIDELEEKMDNEKPYIE 136
                                       677777777888888888..666666666655....566799**************************98 PP

>> Lebercilin  Ciliary protein causing Leber congenital amaurosis disease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   8.9   1.6e-05    0.0083     130     187 ..      72     129 ..      43     132 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.6e-05
                        Lebercilin 130 eakleekeekikeLerkleleeksfrrqlaaekkktkeaqeevkalqeeierlkqklk 187
                                       ++klee eeki++ + ++ +++k  +rql+ +++++k+++e+v++l+  i++l++k+ 
  gi|385805308|ref|YP_005841706.1|  72 TEKLEELEEKIEQISSQIIQLNKFTERQLKIQNSMIKALEEKVSNLELIIDELEEKMD 129
                                       689***************************************************9985 PP

>> RHH_3  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.1   0.00014      0.07       6      32 ..      23      49 ..      21      50 .. 0.93
   2 ?    0.4   0.1       1.2   6.3e+02      10      23 ..      68      81 ..      61      86 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00014
                             RHH_3  6 tvsidpelaekLkaLSekTrIprSkll 32
                                      + si ++l+++L+++ e+ +I +++l+
  gi|385805308|ref|YP_005841706.1| 23 HLSISDKLYDELREIAEEYGIQITDLI 49
                                      779*********************998 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.2
                             RHH_3 10 dpelaekLkaLSek 23
                                      d+e  ekL++L ek
  gi|385805308|ref|YP_005841706.1| 68 DNEDTEKLEELEEK 81
                                      56667888888777 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.8   9.1e+02     270     290 ..      29      49 ..      27      66 .. 0.74
   2 !   13.9   6.6   3.6e-05     0.019     231     281 ..      70     120 ..      55     136 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.8
                              Spc7 270 rlkeevkaleeltgwkivsls 290
                                       +l +e++++ e++g++i+ l 
  gi|385805308|ref|YP_005841706.1|  29 KLYDELREIAEEYGIQITDLI 49 
                                       678888888899999888774 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 3.6e-05
                              Spc7 231 eleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkaleel 281
                                       e +ek+eel+e+++++ ++i + ++++e++ ++++s +++l+e+v++le +
  gi|385805308|ref|YP_005841706.1|  70 EDTEKLEELEEKIEQISSQIIQLNKFTERQLKIQNSMIKALEEKVSNLELI 120
                                       67899******************************************9976 PP

>> Spc29  Spindle Pole Component 29
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   2.1   3.2e-05     0.016     105     165 ..      61     125 ..      17     134 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.2e-05
                             Spc29 105 desrldsiyssvkkivelekklddqkleIkeL....kreleqqrtvnseLqekvaeleeevkrla 165
                                        ++ l    ++++k +ele k+++   +I +L    +r+l+ q+ ++++L ekv +le  +++l+
  gi|385805308|ref|YP_005841706.1|  61 RRGTLSPDNEDTEKLEELEEKIEQISSQIIQLnkftERQLKIQNSMIKALEEKVSNLELIIDELE 125
                                       55555555667777777777666555555555222357777788888888888888887777765 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   2.6   7.2e-05     0.037      17      76 ..      73     129 ..      53     135 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.2e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHH CS
                        Laminin_II  17 eqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklk 76 
                                       e+l++l++++e++++++ ++n+    t+ ++k  n +i+  +++v++Le  +++L++k+ 
  gi|385805308|ref|YP_005841706.1|  73 EKLEELEEKIEQISSQIIQLNKF---TERQLKIQNSMIKALEEKVSNLELIIDELEEKMD 129
                                       67899999999999999999999...9999999999*********************975 PP

>> RFX5_N  RFX5 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   0.00025      0.13       4      37 ..      99     135 ..      89     136 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00025
                            RFX5_N   4 qqkiknsicKavqsKv...dgiLqdveKFtDleKLYL 37 
                                       q ki+ns+ Ka  +Kv   + i+ + e   D+eK Y+
  gi|385805308|ref|YP_005841706.1|  99 QLKIQNSMIKALEEKVsnlELIIDELEEKMDNEKPYI 135
                                       78*************9555679************985 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   4.1    0.0015      0.77      18      66 ..      73     122 ..      67     139 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0015
                           NPV_P10  18 dkVdalqqqvddvqenlpdvtelne.kLdaqsaqLaeletkvenIqdiLn 66 
                                       +k++ l+++++++++++ ++++ +e +L  q+  +++le+kv+n + i  
  gi|385805308|ref|YP_005841706.1|  73 EKLEELEEKIEQISSQIIQLNKFTErQLKIQNSMIKALEEKVSNLELIID 122
                                       6888899999999998888888765379999999999999*999988876 PP

>> RHH_4  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00064      0.33      17      42 ..      26      51 ..      23      66 .. 0.83
   2 ?   -2.5   0.0       9.4   4.8e+03      23      36 ..     108     121 ..      99     133 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00064
                                      EEHHHHHHHHHHHHHTT--HHHHHHH CS
                             RHH_4 17 LEpafWdaLeeiArregltvnaLiae 42
                                      + ++ +d+L+eiA++ g+++ +Li+ 
  gi|385805308|ref|YP_005841706.1| 26 ISDKLYDELREIAEEYGIQITDLIKV 51
                                      56789******************975 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 9.4
                                       HHHHHHHHHTT--H CS
                             RHH_4  23 daLeeiArregltv 36 
                                       +aLee  ++ +l +
  gi|385805308|ref|YP_005841706.1| 108 KALEEKVSNLELII 121
                                       45554444444444 PP

>> DUF4031  Protein of unknown function (DUF4031)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00057      0.29       7      36 ..      13      44 ..       7      50 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00057
                           DUF4031  7 rwpargrlwsHl.vaD.sleELhafAarlGvp 36
                                      +w+ + +   Hl ++D  ++EL ++A++ G++
  gi|385805308|ref|YP_005841706.1| 13 SWKGKTMPTVHLsISDkLYDELREIAEEYGIQ 44
                                      5777788889*967**99************97 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   5.2   0.00055      0.28      40     131 ..      30     127 ..      17     139 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00055
                                       CCCCCCCCCCHHH.HHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHC....CHHHHHHHHHH CS
                         Fib_alpha  40 leneleeisnstk.eaeelvk.eikdslrekqkskkdndnvikksskeleeeilrlketida....qesnirvLqnv 110
                                       l +el+ei++++  ++ +l+k  ik+ l+++ + +   dn  ++  +elee+i+++  +i++    +e++++   ++
  gi|385805308|ref|YP_005841706.1|  30 LYDELREIAEEYGiQITDLIKvFIKNNLKAARRGTLSPDNEDTEKLEELEEKIEQISSQIIQlnkfTERQLKIQNSM 106
                                       55566666555431233333213555555555544444555555556666666666666654222233566666667 PP

                                       HHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 111 lesneqkiqkLeqdidqkerk 131
                                       ++++e+k+++Le  id++e+k
  gi|385805308|ref|YP_005841706.1| 107 IKALEEKVSNLELIIDELEEK 127
                                       777777777777777766654 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   7.4    0.0015      0.79      12     123 ..       3     127 ..       1     131 [. 0.65

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0015
                           DUF1664  12 vvgavgYgyvwwkGwklsdlmfvTkrslsdavesvsk....qleqvs.....eslaatkrhLssridrvdkkldeqk 79 
                                       ++  + + y+ wkG +++ +       l d + ++++    q++++      ++l+a++r   s  ++  +kl+e +
  gi|385805308|ref|YP_005841706.1|   3 ILYILVFQYFSWKGKTMPTVHLSISDKLYDELREIAEeygiQITDLIkvfikNNLKAARRGTLSPDNEDTEKLEELE 79 
                                       55567788999999777766666555555554444331111555544444557888888877777677778999999 PP

                           DUF1664  80 eiskeikeevtevredls....eigedvesvkeaveglesklerieek 123
                                       e +++i++++ ++++ ++      ++ +++++e v++le  ++++eek
  gi|385805308|ref|YP_005841706.1|  80 EKIEQISSQIIQLNKFTErqlkIQNSMIKALEEKVSNLELIIDELEEK 127
                                       999999999988876444111033445677888888888888888876 PP

>> Allexi_40kDa  Allexivirus 40kDa protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.8    0.0005      0.25      63     144 ..      47     131 ..      21     139 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0005
                      Allexi_40kDa  63 siinklnpvslls.qttlLselrdalrtltklldklksvekklelsae.tasdskllk.klesietsleelhaklde 136
                                        +i+ + +++l + +  +Ls   ++ ++l++l +k++++++++ + ++ t+ + k+++  ++++e+++ +l   +de
  gi|385805308|ref|YP_005841706.1|  47 DLIKVFIKNNLKAaRRGTLSPDNEDTEKLEELEEKIEQISSQIIQLNKfTERQLKIQNsMIKALEEKVSNLELIIDE 123
                                       45555555555442667788888888888887777777766654332213333444441578999999999999999 PP

                      Allexi_40kDa 137 lsssetse 144
                                       l +++++e
  gi|385805308|ref|YP_005841706.1| 124 LEEKMDNE 131
                                       98877665 PP

>> Cob_adeno_trans  Cobalamin adenosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   3.2    0.0012       0.6      49     111 ..      72     137 ..      19     140 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0012
                                       T..THHHHHHHHHHHHHHHHHHHHHHT..-BTCCG-S--HHHHHHHHHHHHHHHHHS--EESEEES CS
                   Cob_adeno_trans  49 e..eeelkeaLeeiqneLfdlgaelatp.ekkkekkkiteeeveelekeideleaelpplksfilp 111
                                       +   eel+e++e+i +++++l +    + + ++++ k  ee+v++le  idele+++++ k +i p
  gi|385805308|ref|YP_005841706.1|  72 TekLEELEEKIEQISSQIIQLNKFTERQlKIQNSMIKALEEKVSNLELIIDELEEKMDNEKPYIEP 137
                                       033456666666666666666655543342222222233556888888899999888887777655 PP

>> AKNA  AT-hook-containing transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.6      0.25   1.3e+02      54      76 ..      74      89 ..      54     106 .. 0.60
   2 ?    9.8   0.3    0.0023       1.2      42      70 ..     108     136 ..     101     138 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.25
                              AKNA 54 rleeLkdqtdqlkqkveefskdi 76
                                      +leeL ++++q+       s++i
  gi|385805308|ref|YP_005841706.1| 74 KLEELEEKIEQI-------SSQI 89
                                      344444444444.......3333 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0023
                              AKNA  42 releaeIyqlgqrleeLkdqtdqlkqkve 70 
                                       + le++++ l+  ++eL +++d+ k  +e
  gi|385805308|ref|YP_005841706.1| 108 KALEEKVSNLELIIDELEEKMDNEKPYIE 136
                                       579********************998766 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   7.1    0.0027       1.4      31      77 ..      55     101 ..      44     116 .. 0.69
   2 ?    2.7   0.8      0.25   1.3e+02      16      40 ..     104     129 ..      96     136 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0027
                              FlxA  31 kqLkelsesdeltkeekkkqqqliqaQIqqlqaQIaqlqqqqaekaq 77 
                                       + Lk     +  +++e  ++ ++++++I+q+ +QI ql +  +++ +
  gi|385805308|ref|YP_005841706.1|  55 NNLKAARRGTLSPDNEDTEKLEELEEKIEQISSQIIQLNKFTERQLK 101
                                       55555555655566777899***************998764443333 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.25
                              FlxA  16 asqiasLqkQiknlqkqLkelses.d 40 
                                       +s i++L++ ++nl+  ++el e+ d
  gi|385805308|ref|YP_005841706.1| 104 NSMIKALEEKVSNLELIIDELEEKmD 129
                                       57899999999999999999988742 PP

>> MtrG  Tetrahydromethanopterin S-methyltransferase, subunit G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.8    0.0012      0.64      16      35 ..      72      91 ..      68     102 .. 0.90
   2 ?   -0.4   0.1       2.1   1.1e+03      19      28 ..     121     130 ..     109     136 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0012
                              MtrG 16 kkrLdeieekvefvnsEiaq 35
                                      +++L+e+eek+e ++s i+q
  gi|385805308|ref|YP_005841706.1| 72 TEKLEELEEKIEQISSQIIQ 91
                                      68***************998 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2.1
                              MtrG  19 Ldeieekvef 28 
                                       +de+eek+++
  gi|385805308|ref|YP_005841706.1| 121 IDELEEKMDN 130
                                       6889999887 PP

>> Histone_HNS  H-NS histone family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0     0.011       5.6      23      45 ..      29      51 ..      25      67 .. 0.77
   2 ?    2.0   3.3      0.75   3.8e+02       1      42 [.      77     124 ..      67     137 .. 0.53

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.011
                                      XXXXXXXXXXXXXX----SSS-- CS
                       Histone_HNS 23 ealaeirelaaeyGltleelaae 45
                                      ++ +e+re+a+eyG+++ +l + 
  gi|385805308|ref|YP_005841706.1| 29 KLYDELREIAEEYGIQITDLIKV 51
                                      67899**************9765 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.75
                                       XXXXXXXXXXXXXXX......XXXXXXXXXXXXXXXXXXXXX----SS CS
                       Histone_HNS   1 eLkalieelekqeea......leaeerkealaeirelaaeyGltleel 42 
                                       eL+++ie++  q+ +      ++ + ++ ++++++e++++  l ++el
  gi|385805308|ref|YP_005841706.1|  77 ELEEKIEQISSQIIQlnkfteRQLKIQNSMIKALEEKVSNLELIIDEL 124
                                       455555555555555433321222222335555555555555666666 PP

>> DASH_Dam1  DASH complex subunit Dam1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.4    0.0072       3.7       3      27 ..      73      97 ..      72     105 .. 0.88
   2 ?    1.7   0.2      0.43   2.2e+02      12      30 ..     107     125 ..      99     131 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0072
                         DASH_Dam1  3 pafaeLaDsletLdknledLqqihe 27
                                      ++++eL++++e++++++ +L++ +e
  gi|385805308|ref|YP_005841706.1| 73 EKLEELEEKIEQISSQIIQLNKFTE 97
                                      7899****************99876 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.43
                         DASH_Dam1  12 letLdknledLqqihesLs 30 
                                       +++L++++++L+ i ++L+
  gi|385805308|ref|YP_005841706.1| 107 IKALEEKVSNLELIIDELE 125
                                       4566777777776666665 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0         6   3.1e+03      16      30 ..      28      42 ..      22      62 .. 0.63
   2 ?    5.7  10.0     0.045        23       3      55 ..      73     129 ..      71     133 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 6
                                      HHHHHHHHHHHHHHH CS
                              SlyX 16 edtieeLndvvaeqq 30
                                      +++ +eL ++  e  
  gi|385805308|ref|YP_005841706.1| 28 DKLYDELREIAEEYG 42
                                      444444444444444 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.045
                                       HHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHHHHHT-XXXXXXXX CS
                              SlyX   3 erleeLEiklafqedtieeLnd....vvaeqqqqidrlqrqlrllaerlkeleessg 55 
                                       e+leeLE+k+     +i +Ln+    ++  q+  i++l++++  l+  + elee++ 
  gi|385805308|ref|YP_005841706.1|  73 EKLEELEEKIEQISSQIIQLNKfterQLKIQNSMIKALEEKVSNLELIIDELEEKMD 129
                                       799******************822224555677888888888888888888888764 PP

>> DUF848  Gammaherpesvirus protein of unknown function (DUF848)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       2.6   1.3e+03      87     109 ..      24      46 ..      17      51 .. 0.78
   2 ?    8.7   7.5    0.0034       1.7      48     118 ..      61     131 ..      37     139 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 2.6
                            DUF848  87 varveeLtdkvlelkeevsleld 109
                                       + + ++L d+  e+ ee  +++ 
  gi|385805308|ref|YP_005841706.1|  24 LSISDKLYDELREIAEEYGIQIT 46 
                                       66779999999999999887775 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0034
                            DUF848  48 sleqlkrtkeikalveavdteieakkkelslLkklnrkkvarveeLtdkvlelkeevsleldsleeaqeey 118
                                       +  +l+  +e  +++e ++++ie+   ++ +L+k+  +++++ + +  + +e   +++l +d+lee+ ++ 
  gi|385805308|ref|YP_005841706.1|  61 RRGTLSPDNEDTEKLEELEEKIEQISSQIIQLNKFTERQLKIQNSMIKALEEKVSNLELIIDELEEKMDNE 131
                                       555666677788999**************************************************987765 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 ?    7.1   4.4     0.014       7.3       1      38 [.      74     115 ..      74     117 .. 0.64
   2 ?    5.1   2.6      0.06        31       2      24 ..     107     129 ..     106     136 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.014
                         FlaC_arch   1 ridelEnklsklst...eletvkkeneelsks.veelkenVk 38 
                                       +++elE+k++++s+   +l+   + + ++++s ++ l+e+V 
  gi|385805308|ref|YP_005841706.1|  74 KLEELEEKIEQISSqiiQLNKFTERQLKIQNSmIKALEEKVS 115
                                       799***********5555555444444444432666777765 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.06
                         FlaC_arch   2 idelEnklsklsteletvkkene 24 
                                       i+ lE+k+s+l+  ++ ++++++
  gi|385805308|ref|YP_005841706.1| 107 IKALEEKVSNLELIIDELEEKMD 129
                                       78899999999999999998876 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   9.0     0.037        19      35      69 ..      74     126 ..      15     137 .. 0.57

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.037
                                       HHHHHHHHHH.....................HHHHHHHHHHHHHHHHHHHHHH CS
                             DUF16  35 rLkkieakvd..................klgeqinkleqkvekqgekikelkv 69 
                                       +L+++e+k++                   ++  i++le+kv++++  i+el++
  gi|385805308|ref|YP_005841706.1|  74 KLEELEEKIEqissqiiqlnkfterqlkIQNSMIKALEEKVSNLELIIDELEE 126
                                       44444444443332222222211111112222233333333333333333322 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       7.2   3.7e+03      44      49 ..      53      58 ..      25      63 .. 0.57
   2 ?    8.0   4.7    0.0063       3.2       4      44 ..      73     117 ..      70     118 .. 0.70
   3 ?    6.1   2.6     0.024        12      16      42 ..     103     129 ..      92     136 .. 0.58

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 7.2
                              XhlA 44 lesnqk 49
                                      +++n+k
  gi|385805308|ref|YP_005841706.1| 53 IKNNLK 58
                                      455555 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0063
                              XhlA   4 erlerietkldnleervdkleekaaeae....ekiknleedlkkl 44 
                                       e+le++e+k++ +++++ +l++  ++++    + ik lee++++l
  gi|385805308|ref|YP_005841706.1|  73 EKLEELEEKIEQISSQIIQLNKFTERQLkiqnSMIKALEEKVSNL 117
                                       89*************888876666665511115677777776666 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.024
                              XhlA  16 leervdkleekaaeaeekiknleedlk 42 
                                        ++ ++ leek ++ e  i++lee+++
  gi|385805308|ref|YP_005841706.1| 103 QNSMIKALEEKVSNLELIIDELEEKMD 129
                                       444555555555555555555555554 PP

>> Swi5  Swi5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0         2     1e+03      69      77 ..      35      43 ..      26      53 .. 0.61
   2 ?    4.8   2.0     0.059        30       3      29 ..      73      99 ..      71     108 .. 0.77
   3 ?    7.2   0.6      0.01       5.2       4      30 ..     106     132 ..     103     140 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 2
                                      GGGHHHCT- CS
                              Swi5 69 kevfeefGv 77
                                      +e+ ee+G+
  gi|385805308|ref|YP_005841706.1| 35 REIAEEYGI 43
                                      344444444 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.059
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              Swi5  3 aeikeleeqleelekelaelkeelkek 29
                                      ++++elee++e++ +++ +l++  + +
  gi|385805308|ref|YP_005841706.1| 73 EKLEELEEKIEQISSQIIQLNKFTERQ 99
                                      689999999999999999998876654 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.01
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              Swi5   4 eikeleeqleelekelaelkeelkekk 30 
                                        ik+lee++++le  ++el+e+++++k
  gi|385805308|ref|YP_005841706.1| 106 MIKALEEKVSNLELIIDELEEKMDNEK 132
                                       699*******************99865 PP

>> eIF-4B  Plant specific eukaryotic initiation factor 4B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   5.2    0.0081       4.2     373     434 ..      72     129 ..      46     137 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0081
                            eIF-4B 373 teeekllkeeieelkkelekeaa...enkesqqessedqnslkelisekekdlellirelddkvr 434
                                       t       e++eel +++e+ ++   + +  ++ + + qns+ + ++ek  +lel+i el++k+ 
  gi|385805308|ref|YP_005841706.1|  72 T-------EKLEELEEKIEQISSqiiQLNKFTERQLKIQNSMIKALEEKVSNLELIIDELEEKMD 129
                                       3.......4444444444444332223333444455568999999*****************985 PP

>> BRI3BP  Negative regulator of p53/TP53
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.3     0.049        25     152     177 ..      69      94 ..      48      97 .. 0.76
   2 ?    4.4   0.4     0.045        23     157     178 ..     106     127 ..      95     129 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.049
                            BRI3BP 152 ksseesgasleakvrsLerqvrelnk 177
                                       ++++e+ ++le+k++++ +q+ +lnk
  gi|385805308|ref|YP_005841706.1|  69 NEDTEKLEELEEKIEQISSQIIQLNK 94 
                                       45566777888888888888888876 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.045
                            BRI3BP 157 sgasleakvrsLerqvrelnkr 178
                                         + le+kv +Le  + el+ +
  gi|385805308|ref|YP_005841706.1| 106 MIKALEEKVSNLELIIDELEEK 127
                                       567899*******999999976 PP

>> Osmo_CC  Osmosensory transporter coiled coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   2.3    0.0023       1.2      12      36 ..      73      99 ..      72     105 .. 0.83
   2 ?    2.0   1.5      0.48   2.4e+02      17      35 ..     110     128 ..     106     132 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0023
                                      XXXTHHHHHHHHHHHHHHHHHH..HHH CS
                           Osmo_CC 12 ehYdnIEqkvedideeIaaLee..kRq 36
                                      e+ ++ E+k+e+i  +I +L++   Rq
  gi|385805308|ref|YP_005841706.1| 73 EKLEELEEKIEQISSQIIQLNKftERQ 99
                                      667899**************9977555 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.48
                                       HHHHHHHHHHHHHHHHHHH CS
                           Osmo_CC  17 IEqkvedideeIaaLeekR 35 
                                        E+kv +++  I +Leek 
  gi|385805308|ref|YP_005841706.1| 110 LEEKVSNLELIIDELEEKM 128
                                       5899999999999999985 PP

>> PspB  Phage shock protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0         4   2.1e+03      21      37 ..       7      24 ..       2      59 .. 0.61
   2 ?    5.3   0.8      0.04        21      36      62 ..      68      94 ..      48     100 .. 0.79
   3 ?    5.9   1.4     0.026        13      39      69 ..     103     133 ..      90     135 .. 0.64

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 4
                              PspB 21 LiLHYrs.kkkrskglsa 37
                                      L++ Y s k k++ ++  
  gi|385805308|ref|YP_005841706.1|  7 LVFQYFSwKGKTMPTVHL 24
                                      566666645555544433 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.04
                              PspB 36 saedekrLeellekAekleeRietLEr 62
                                      ++ed+++Leel ek e++++ i  L +
  gi|385805308|ref|YP_005841706.1| 68 DNEDTEKLEELEEKIEQISSQIIQLNK 94
                                      46799************9999987765 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.026
                              PspB  39 dekrLeellekAekleeRietLEriLdaesp 69 
                                       +++++++l ek ++le  i+ LE+ +d+e+p
  gi|385805308|ref|YP_005841706.1| 103 QNSMIKALEEKVSNLELIIDELEEKMDNEKP 133
                                       3456666777777777777777777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2323  (0.129567); expected 358.6 (0.02)
Passed bias filter:                      973  (0.0542696); expected 358.6 (0.02)
Passed Vit filter:                       166  (0.00925874); 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):              35  [number of targets reported over threshold]
# CPU time: 0.69u 0.37s 00:00:01.06 Elapsed: 00:00:00.53
# Mc/sec: 801.50
//
Query:       gi|385805309|ref|YP_005841707.1|  [L=315]
Description: ABC transporter [Fervidicoccus fontis Kam940]
Scores for complete 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-26   91.5   0.0    2.4e-25   89.6   0.0    1.8  2  ABC_tran     ABC transporter
    2.9e-11   43.7   1.2    2.9e-05   24.0   0.0    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    3.3e-05   23.8   0.1     0.0094   15.7   0.6    2.3  2  AAA_15       AAA ATPase domain
     0.0019   17.9   0.3     0.0043   16.8   0.3    1.6  1  AAA_29       P-loop containing region of AAA domain
     0.0036   17.8   0.9     0.0069   16.9   0.9    1.4  1  AAA_23       AAA domain
  ------ inclusion threshold ------
      0.011   15.5   0.1      0.018   14.9   0.1    1.2  1  MukB         MukB N-terminal
      0.013   15.5   0.1      0.029   14.4   0.1    1.5  1  TsaE         Threonylcarbamoyl adenosine biosynthesis protein
      0.043   13.7   0.2        0.1   12.5   0.2    1.6  1  NACHT        NACHT domain
      0.048   13.9   0.2          1    9.6   0.0    2.6  3  Roc          Ras of Complex, Roc, domain of DAPkinase
      0.053   13.6   0.4          8    6.5   0.1    2.6  3  AAA_14       AAA domain
      0.066   13.1   0.1       0.13   12.2   0.1    1.4  1  RsgA_GTPase  RsgA GTPase
       0.07   12.4   0.0       0.16   11.2   0.0    1.5  1  Zeta_toxin   Zeta toxin
      0.074   13.5   0.1       0.59   10.6   0.0    2.2  2  AAA          ATPase family associated with various cellular a
      0.094   12.1   0.0        4.5    6.7   0.0    2.2  2  SMC_N        RecF/RecN/SMC N terminal domain
        0.1   12.3   0.4        1.3    8.7   0.0    2.2  2  AAA_24       AAA domain
       0.13   12.5   0.6       0.76   10.1   0.1    2.2  3  AAA_22       AAA domain
       0.15   11.8   0.1       0.35   10.6   0.1    1.5  1  AAA_30       AAA domain
       0.28   11.0   1.8        6.1    6.6   0.0    2.6  2  dNK          Deoxynucleoside kinase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.6   0.0   2.4e-28   2.4e-25       1     136 [.      30     174 ..      30     175 .. 0.88
   2 ?   -0.8   0.0       2.1   2.1e+03      23      67 ..     196     249 ..     194     293 .. 0.53

  Alignments for each domain:
  == domain 1  score: 89.6 bits;  conditional E-value: 2.4e-28
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS..--S-TTSB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe..pqlfpelt 75 
                                       l+ ++l++k+g+++ ++G+nGaGK+t+l+++a +l pt+G+i + g d+ + +  + r++i+v+pq+  p lfp   
  gi|385805309|ref|YP_005841707.1|  30 LRGLNLEIKKGTITTLLGKNGAGKTTFLRIIATQLIPTKGNISVLGYDVIK-DVWKIREKIAVIPQDakPLLFPSPL 105
                                       5789*****************************************999998.899************9888888763 PP

                                       HHHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  76 vren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                         e              ++++++++ ls+l+++e   + +++ +  LSgG ++r+ la++++++++l+llDEp+
  gi|385805309|ref|YP_005841707.1| 106 --EFissflvmrgysfsDARKRAKETLSELEIPE---EYWNRAAWDLSGGYQRRLLLAAVMASDSELILLDEPS 174
                                       ..334568*****987777777888888888777...66666679****************************6 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.1
                                       SHHHHHHHHTTSS--.........SEEEEEETTCEGGGB-HHHCCHCEEEE-SS CS
                                       xxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  23 GKStLlkllagllkp.........teGeilldgkdlkeqeleslrkeigvlpqe 67 
                                       GK+ Ll + + ++           ++G+  l+g++ + ++  +++++i+vl + 
  gi|385805309|ref|YP_005841707.1| 196 GKTVLLTTHYMEEAEmlsdhviiiDKGKKILEGNPKELINSFKWKHKIEVLDEC 249
                                       666666665555554432222222333333333333336666777777776664 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.6   1.9e-06    0.0019       1      20 [.      42      61 ..      42      93 .. 0.81
   2 !   24.0   0.0   2.9e-08   2.9e-05     231     297 ..     141     204 ..     109     208 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.9e-06
                            AAA_21  1 lnvliGpNgsGKSnLLdald 20
                                      ++ l G+Ng+GK+++L+++ 
  gi|385805309|ref|YP_005841707.1| 42 ITTLLGKNGAGKTTFLRIIA 61
                                      799****************3 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 2.9e-08
                            AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                       ++ a++lS G +r l l++ ++++     l+l+DEp  gL+P +  +l++ + +l++ g  v+ltTH
  gi|385805309|ref|YP_005841707.1| 141 NRAAWDLSGGYQRRLLLAAVMASDS---ELILLDEPSVGLDPIARMELWGKITLLKKMGKTVLLTTH 204
                                       67899********956666666655...9*************8888888555555555679****** PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.6   9.5e-06    0.0094      18      43 ..      34      60 ..      29      93 .. 0.84
   2 ?    5.0   0.0     0.017        17     315     364 ..     163     204 ..     146     205 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 9.5e-06
                            AAA_15 18 eidlsee.ltvliGkNnsGKSsileal 43
                                       +++++  +t+l GkN++GK+++l+++
  gi|385805309|ref|YP_005841707.1| 34 NLEIKKGtITTLLGKNGAGKTTFLRII 60
                                      56777778*****************99 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.017
                            AAA_15 315 ekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                       +       ++ ++l++EP + L p a ++l+ ++  l + +k  v++tTH
  gi|385805309|ref|YP_005841707.1| 163 S-------DSELILLDEPSVGLDPIARMELWGKITLLKKMGK-TVLLTTH 204
                                       3.......4478**********************99999999.9****** 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 !   16.8   0.3   4.3e-06    0.0043      16      50 ..      34      68 ..      29      72 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.3e-06
                            AAA_29 16 tieidlkg.atlltGpsGsGKSTllDAiqalLvpak 50
                                       +ei+ kg +t l G++G+GK+T+l  i++ L+p+k
  gi|385805309|ref|YP_005841707.1| 34 NLEIK-KGtITTLLGKNGAGKTTFLRIIATQLIPTK 68
                                      56787.5569***************99999999887 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.9   6.9e-06    0.0069      12      41 ..      32      62 ..      22      74 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.9e-06
                            AAA_23 12 dqeidFsk.gltlItGpNGaGKTTildAikl 41
                                      + +++ +k  +t + G+NGaGKTT+l+ i  
  gi|385805309|ref|YP_005841707.1| 32 GLNLEIKKgTITTLLGKNGAGKTTFLRIIAT 62
                                      555666552699**************99875 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1   1.8e-05     0.018      27      54 ..      41      68 ..      33      76 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.8e-05
                                      HHHHHHS--SHHHHHHHHHHHHHHS--T CS
                              MukB 27 lvttlsGgnGaGksttmaafvtaliPdl 54
                                       +ttl G nGaGk+t +  + t liP  
  gi|385805309|ref|YP_005841707.1| 41 TITTLLGKNGAGKTTFLRIIATQLIPTK 68
                                      68************************75 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   2.9e-05     0.029      16      44 ..      39      65 ..      20      82 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.9e-05
                                      HCHTEEEEEEESTTSSHHHHHHHHHHHTT CS
                              TsaE 16 kalgdvilLeGdLGaGKTtlvrglakalg 44
                                      k  g++ +L G+ GaGKTt+ r +a +l 
  gi|385805309|ref|YP_005841707.1| 39 K--GTITTLLGKNGAGKTTFLRIIATQLI 65
                                      2..78899****************99984 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2    0.0001       0.1       4      24 ..      44      64 ..      41      71 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0001
                                      EEEC-TTTCHHHHHHHHHHHH CS
                             NACHT  4 ilqGeaGsGKTtLlqklalaw 24
                                       l G++G GKTt+l+ +a+++
  gi|385805309|ref|YP_005841707.1| 44 TLLGKNGAGKTTFLRIIATQL 64
                                      689**************9876 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 ?    9.6   0.0     0.001         1       4      45 ..      45      86 ..      43      95 .. 0.79
   2 ?   -1.7   0.0       3.2   3.2e+03      57      71 ..     141     155 ..     118     174 .. 0.64
   3 ?    0.9   0.0      0.51   5.1e+02       9      38 ..     194     223 ..     188     247 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.001
                                      EESSTTSSHHHHHHCHCT-CCC.-EEETTTTEEEEEEECGGSG CS
                               Roc  4 lvGdsgvGKtsllkrfvedkfs.ekekstigvdfltkevtkik 45
                                      l+G++g+GKt++l+ + ++ +  + + s +g+d+++ +v+ki+
  gi|385805309|ref|YP_005841707.1| 45 LLGKNGAGKTTFLRIIATQLIPtKGNISVLGYDVIK-DVWKIR 86
                                      89***********99999888515578999999986.466665 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.2
                                       EEEEEEE-SGGCTTT CS
                               Roc  57 klniWDtaGqerfrs 71 
                                       + + WD++G  + r 
  gi|385805309|ref|YP_005841707.1| 141 NRAAWDLSGGYQRRL 155
                                       557899999766555 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.51
                                       TSSHHHHHHCHCT-CCC-EEETTTTEEEEE CS
                               Roc   9 gvGKtsllkrfvedkfsekekstigvdflt 38 
                                       ++GKt ll+ +  ++ +  ++  i +d  +
  gi|385805309|ref|YP_005841707.1| 194 KMGKTVLLTTHYMEEAEMLSDHVIIIDKGK 223
                                       78****999988888877777776666554 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1    0.0081         8       3      35 ..      41      73 ..      39      97 .. 0.76
   2 ?   -3.4   0.0       9.1   9.1e+03      58      72 ..     158     172 ..     144     173 .. 0.71
   3 ?    4.6   0.0     0.031        30      11      72 ..     193     248 ..     189     282 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0081
                            AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesily 35
                                       i ++ G   +GKTt+l+ ++ +l+ +k +i  
  gi|385805309|ref|YP_005841707.1| 41 TITTLLGKNGAGKTTFLRIIATQLIPTKGNISV 73
                                      68899999*********9998887755555555 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 9.1
                            AAA_14  58 eklkeekktylflDE 72 
                                       + +++++ ++++lDE
  gi|385805309|ref|YP_005841707.1| 158 AAVMASDSELILLDE 172
                                       333445678999998 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.031
                            AAA_14  11 RrvGKTtllkqlikell.vkkesilyinldderdkkladpekllelileklkeekktylflDE 72 
                                       +++GKT+ll + + e+  + +++++ i+  ++ ++   +p++l++ ++      k+++ +lDE
  gi|385805309|ref|YP_005841707.1| 193 KKMGKTVLLTTHYMEEAeMLSDHVIIIDKGKKILEG--NPKELINSFKW-----KHKIEVLDE 248
                                       689******999888887888888888876655533..44323333332.....445556666 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00013      0.13      91     130 ..      31      71 ..      10      75 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                                       HHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                       RsgA_GTPase  91 eelkellkd.ktsvlvGqSGvGKStLinallpelelktgev 130
                                       + l+ ++k+  +++l+G+ G+GK+t++  ++ +l    g++
  gi|385805309|ref|YP_005841707.1|  31 RGLNLEIKKgTITTLLGKNGAGKTTFLRIIATQLIPTKGNI 71 
                                       556666766699***************99998876655555 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00016      0.16      18      57 ..      42      82 ..      32      99 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00016
                        Zeta_toxin 18 lillgGqpGAGKselaellkdele.rqgnvvrldpDdlRel 57
                                      +  l G  GAGK++ ++ ++++l  ++gn+ +l  D ++  
  gi|385805309|ref|YP_005841707.1| 42 ITTLLGKNGAGKTTFLRIIATQLIpTKGNISVLGYDVIKDV 82
                                      566789*****************989999999999998875 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   0.0   0.00059      0.59       3      35 ..      45      79 ..      43     108 .. 0.70
   2 ?    0.3   0.0      0.91     9e+02      38      68 ..     194     223 ..     179     256 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00059
                                      EESSTTSSHHHHHHHHHHHH..THEEEEEETTTCS CS
                               AAA  3 lyGppGtGKTllakavakel..gvefleisgsell 35
                                      l G  G GKT++ + +a++l      +++ g +++
  gi|385805309|ref|YP_005841707.1| 45 LLGKNGAGKTTFLRIIATQLipTKGNISVLGYDVI 79
                                      89****************98542223444444444 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.91
                                       STTHHHHHHHHHHHHHHHTSTSEEEEEETGG CS
                               AAA  38 yvgesekkirelfkeakekakpsilfiDEid 68 
                                        +g++   + ++++ea+  +  ++++iD   
  gi|385805309|ref|YP_005841707.1| 194 KMGKTVLLTTHYMEEAEMLS-DHVIIIDKGK 223
                                       45666666777777877776.7888888554 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   0.0    0.0045       4.5      25      42 ..      41      58 ..      31      65 .. 0.82
   2 ?    3.2   0.0     0.049        49     137     197 ..     147     204 ..     115     225 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0045
                                      SEEEEEESTTSSHHHHHH CS
                                      xxxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnlld 42
                                       +t ++G+NG+GK+ +l 
  gi|385805309|ref|YP_005841707.1| 41 TITTLLGKNGAGKTTFLR 58
                                      5799**********9876 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.049
                                       S-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                             SMC_N 137 LSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivisl 197
                                       LSgG +      Ll+A  +++ + l llDe    LD   + ++   +   +k    ++ +++
  gi|385805309|ref|YP_005841707.1| 147 LSGGYQR----RLLLAAVMASDSELILLDEPSVGLDPIARMELWGKITLLKKMgKTVLLTTH 204
                                       5555443....688888999999*************99998887777766655244455554 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0    0.0013       1.3       5      22 ..      43      60 ..      39     110 .. 0.79
   2 ?    1.7   0.1      0.18   1.8e+02     110     137 ..     184     211 ..     181     248 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0013
                            AAA_24  5 iliyGpsgiGKTtlakel 22
                                        + G++g+GKTt+++ +
  gi|385805309|ref|YP_005841707.1| 43 TTLLGKNGAGKTTFLRII 60
                                      5789**********9877 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.18
                            AAA_24 110 efrrllkklqelrknvifiahektrkde 137
                                       e++  ++ l++++k+v ++ h  ++   
  gi|385805309|ref|YP_005841707.1| 184 ELWGKITLLKKMGKTVLLTTHYMEEAEM 211
                                       5666677888888888888887776554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00076      0.76       4      29 ..      39      64 ..      35      91 .. 0.87
   2 ?   -1.8   0.0       3.5   3.5e+03      93      99 ..     166     172 ..     116     212 .. 0.66
   3 ?    0.1   0.1      0.93   9.3e+02      75      99 ..     198     221 ..     151     253 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00076
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleql 29
                                      + +i+++ G  G+GKTt lr ++ ql
  gi|385805309|ref|YP_005841707.1| 39 KGTITTLLGKNGAGKTTFLRIIATQL 64
                                      7899****************999887 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.5
                            AAA_22  93 elliiDE 99 
                                       el+++DE
  gi|385805309|ref|YP_005841707.1| 166 ELILLDE 172
                                       4444444 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.93
                            AAA_22  75 seellealeqalraravielliiDE 99 
                                       +  l ++  + ++  ++ +++iiD 
  gi|385805309|ref|YP_005841707.1| 198 TVLLTTHYMEEAEMLSD-HVIIIDK 221
                                       33333555566666666.7777775 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00035      0.35      18      46 ..      40      69 ..      34      80 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00035
                            AAA_30 18 drvavltGpAGtGKttalkal.reaweaag 46
                                        +++l G  G+GKtt l+ + ++++ ++g
  gi|385805309|ref|YP_005841707.1| 40 GTITTLLGKNGAGKTTFLRIIaTQLIPTKG 69
                                      358999**************9555665554 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1     0.061        61       5      22 ..      47      64 ..      44      73 .. 0.87
   2 ?    6.6   0.0    0.0062       6.1     109     144 ..     254     286 ..     187     298 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.061
                                      ESTTSSHHHHHHHHHCCS CS
                               dNK  5 GnIgaGKstlvklLskkl 22
                                      G+ gaGK+t++ +++ +l
  gi|385805309|ref|YP_005841707.1| 47 GKNGAGKTTFLRIIATQL 64
                                      7779********999876 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0062
                                       HHHHHHHHHHHCCH.....-SEEEEEE--HHHHHHHHHHCT CS
                               dNK 109 ykelldnlleelak.....pdlliYLkasletclerikkRg 144
                                       +k++               p ++iYL+ s++++le ++  g
  gi|385805309|ref|YP_005841707.1| 254 MKKMG--------VlfgsrPPFVIYLNSSIDSVLEELNSNG 286
                                       22222........1333459***************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); 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: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 1805.50
//
Query:       gi|385805310|ref|YP_005841708.1|  [L=244]
Description: ABC transporter [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.1e-09   35.2  32.1    7.9e-09   35.1  32.1    1.0  1  ABC2_membrane_3  ABC-2 family transporter protein
    3.3e-06   26.7  26.9    4.7e-06   26.2  26.9    1.2  1  ABC2_membrane    ABC-2 type transporter


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 !   35.1  32.1   8.9e-13   7.9e-09     143     340 ..      31     232 ..       6     237 .. 0.82

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 8.9e-13
                   ABC2_membrane_3 143 aninvestqleeel.snvasflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyl 218
                                        +i++ ++ +   + + v++ l+g +++i+++  +  +   +   +e +   +++ s+++p +y+++ +l+ ++ ++
  gi|385805310|ref|YP_005841708.1|  31 PPITFLILMKIYARpEMVEYALIGGFIMIIASNAIGLMGDTVFYKREVKFQDMIVASPMTPVAYMFGLVLSGAFFSI 107
                                       555666666644441556667888888888888888788889999999*********************99999999 PP

                   ABC2_membrane_3 219 lqlllilll..afglgipfgnlglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledl 293
                                         + l+l+l  +++  ++f  +g+++l ++l + a++ l++ l +++k ++ +  l +i+++l+s++  + +p   l
  gi|385805310|ref|YP_005841708.1| 108 PGITLFLILmaYYH-LLSFVAFGVIILSSILSLVALSGLAFTLATFVKEPRFVWPLSGILSFLISVLPPVYYPWILL 183
                                       99888888744444.89999***********************************************9999**8899 PP

                   ABC2_membrane_3 294 psalkwifsiiPffapglgllrli..tgdplweillsliilalfavvyl 340
                                       +++l++i+++iP+++ + ++ + +  t   +++ l  +iil+++++++l
  gi|385805310|ref|YP_005841708.1| 184 NKWLAVISMFIPSSSAAALFQKHLglTSSLPMNELFIWIILIVESLLLL 232
                                       ********************99987644433344566777777776665 PP

>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2  26.9   5.2e-10   4.7e-06      13     204 ..      17     202 ..       7     207 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 5.2e-10
                     ABC2_membrane  13 qrwrdpslgllwrliqplllalvfgtvfgnlgnsedgl.nr..pgllffsvlflafsaltsvapvferergvlerel 86 
                                        + r+p l ++++li p+ ++l+++ ++ +      ++ ++  +g +++++  +a ++l++  +++ re ++ +   
  gi|385805310|ref|YP_005841708.1|  17 AARRNP-LWIISNLIPPI-TFLILMKIYAR-----PEMvEYalIGGFIMIIASNA-IGLMGDTVFYKREVKFQDMIV 85 
                                       455666.77799999995.56666777774.....33423355666666666666.566666344444444447778 PP

                     ABC2_membrane  87 vsplyslsayvlakvlvelpvsllqalifll.ivyf.lvgldlsrfflflllllltalaasslgllisalapsfeda 161
                                       +sp+ ++ ay+++ vl+ + +s+  +++fl+ ++y+ l+++    f+ ++l  +l+++a+s+l++ ++++++  + +
  gi|385805310|ref|YP_005841708.1|  86 ASPM-TPVAYMFGLVLSGAFFSIPGITLFLIlMAYYhLLSFVA--FGVIILSSILSLVALSGLAFTLATFVKEPRFV 159
                                       8888.*******************9999999555553446666..9******************************* PP

                     ABC2_membrane 162 sqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavea 204
                                         l++++ +++ +l ++++p   + kwl  i+ + P + a  +
  gi|385805310|ref|YP_005841708.1| 160 WPLSGILSFLISVLPPVYYPWILLNKWLAVISMFIPSSSAAAL 202
                                       ********************999977**********8877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); 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: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1555.34
//
Query:       gi|385805311|ref|YP_005841709.1|  [L=144]
Description: ribonuclease H [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-20   72.4   0.0    3.1e-20   72.2   0.0    1.0  1  RVT_3     Reverse transcriptase-like
    1.2e-09   38.5   0.0    1.7e-09   38.0   0.0    1.2  1  RNase_H   RNase H
  ------ inclusion threshold ------
      0.024   14.5   0.2       0.24   11.2   0.0    2.1  2  HPD       Homeo-prospero domain


Domain annotation for each model (and alignments):
>> RVT_3  Reverse transcriptase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.2   0.0   5.2e-24   3.1e-20       2     124 .]      12     140 ..      11     140 .. 0.90

  Alignments for each domain:
  == domain 1  score: 72.2 bits;  conditional E-value: 5.2e-24
                             RVT_3   2 fdgaf..kkksgaggagvvirdsnGevllagaek..lqgkasveeAElqALlrGLqlalklgirr..lvvegDsktv 72 
                                       fdg +  k+++g+g+ + vi  ++ +++  + +    +g+ ++  AE+ AL  +L+ + ++g++   +++ gDs+ v
  gi|385805311|ref|YP_005841709.1|  12 FDGLYvkKDEEGIGTYAFVIYRNKEKIYEEMGKVsrKEGRVTNNAAEYIALEKALRWIIERGLNDekVIILGDSQLV 88 
                                       78866324778888******99999999887766567999***********************7555********** PP

                             RVT_3  73 vqllngrekvksselanlldeirkllksfesvsvehipReqNrvAdalAkra 124
                                       +++lng+ k+ks++l  l  +i++ll++f+ v++++ipRe+N+ Ad l k+a
  gi|385805311|ref|YP_005841709.1|  89 IRQLNGEYKIKSENLYPLFLQIKNLLNKFKDVEISWIPREENQEADFLTKKA 140
                                       **********************************************999876 PP

>> RNase_H  RNase H
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.0   2.9e-13   1.7e-09       4     142 ..       8     141 ..       5     142 .. 0.73

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 2.9e-13
                                       EEEEEEEEEECTTTCE..EEEEEECTT......E.EEEEEECCCCHHHHHHHHHHHHHHH.TT.SC...SEEEEEES CS
                           RNase_H   4 vvvYtDGsclgnpgeg..gagavlykeg....ar.nisapleeaqtnnraELsAvieaLk.alksd...ekvniytD 69 
                                       + v+ DG + ++ +eg  ++++v+y+++    ++  + ++ e++ tnn aE +A+ +aL+   +++   ekv i  D
  gi|385805311|ref|YP_005841709.1|   8 IKVFFDGLYVKKDEEGigTYAFVIYRNKekiyEEmGKVSRKEGRVTNNAAEYIALEKALRwIIERGlndEKVIILGD 84 
                                       5699******9966665599**999888555422333344448*****************776665778******** PP

                                       -HHHHHHHHCCCHHHHHTTSSSETTSSBHTTHHHHHHHHHCHCSSEEEEEE-SCCSSSTHHHHHHHHHHHHHH CS
                           RNase_H  70 SkYvvkgitqwvhrwkknawkttseqkpvknkdlaellkelakkkkvqlkwvkgHaGvpkgNemaDrlAkeaa 142
                                       S+ v+  ++       + + k ++   p++  ++ +ll    k k+v+++w++      ++N++aD l+k+a+
  gi|385805311|ref|YP_005841709.1|  85 SQLVIRQLNG------EYKIKSENLY-PLFL-QIKNLL---NKFKDVEISWIP----R-EENQEADFLTKKAL 141
                                       ******6665......2233222233.4554.555566...56678******9....4.79********9986 PP

>> HPD  Homeo-prospero domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.043   2.6e+02     107     141 ..       4      40 ..       1      52 [. 0.70
   2 ?   11.2   0.0   4.1e-05      0.24      54      99 ..      59     104 ..      54     125 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.043
                               HPD 107 veltlreffeaikagkdadp..sWkkaiykviaklds 141
                                       +++t++ ff+ +  +kd++   ++   iy+   k+ +
  gi|385805311|ref|YP_005841709.1|   4 SKITIKVFFDGLYVKKDEEGigTYAFVIYRNKEKIYE 40 
                                       6789999999999999998522566666666555555 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 4.1e-05
                               HPD  54 yiqiekfarqalaegvkeaeelkvsrdselfralnlhynknndlev 99 
                                       yi +ek  r  +  g+++++ + ++  + ++r ln  y  +++   
  gi|385805311|ref|YP_005841709.1|  59 YIALEKALRWIIERGLNDEKVIILGDSQLVIRQLNGEYKIKSENLY 104
                                       9************************9999*********87666544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 934.33
//
Query:       gi|385805312|ref|YP_005841710.1|  [L=47]
Description: hypothetical protein FFONT_0268 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 298.16
//
Query:       gi|385805313|ref|YP_005841711.1|  [L=80]
Description: ferredoxin [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-15   56.1   1.4    5.6e-15   55.8   1.4    1.1  1  Fer4_15   4Fe-4S single cluster domain
    1.3e-12   48.0   1.2    1.8e-12   47.6   1.2    1.2  1  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
  ------ inclusion threshold ------
      0.036   14.5   0.1      0.038   14.5   0.1    1.2  1  OsmC      OsmC-like protein
       0.04   13.7   2.3        1.7    8.6   0.4    2.5  2  Fer4      4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.8   1.4   1.2e-18   5.6e-15       1      66 []       6      77 ..       6      77 .. 0.94

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 1.2e-18
                           Fer4_15  1 VvvDrdaCigcglCvaeapevfelded.glasvl......lddgeiaegevpddeeeaaqeAaraCPvdAIrv 66
                                      V vDr +Ci cg+  ++++e+f+l +d g+++v+      l ++ei+ege+p+++ e+a++A ++CPv AI+v
  gi|385805313|ref|YP_005841711.1|  6 VIVDRRTCIACGVAPTVCSEIFQLGSDnGKNRVIdkysmkL-TDEISEGEIPEELYECAKRAEESCPVVAIHV 77
                                      78***********************9669999999***975.4699*************************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 !   47.6   1.2   3.9e-16   1.8e-12       1      58 []       8      77 ..       8      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 3.9e-16
                           Fer4_13  1 VDrdtCiacgaCvelaPdvFeeddeggasvvae............qptseeekadaeeAadaCPvesIgv 58
                                      VDr tCiacg+   ++ ++F+   + g+ +v +            ++ +ee++++a++A ++CPv +I+v
  gi|385805313|ref|YP_005841711.1|  8 VDRRTCIACGVAPTVCSEIFQLGSDNGKNRVIDkysmkltdeiseGEIPEELYECAKRAEESCPVVAIHV 77
                                      9********************************5555555544444445********************7 PP

>> OsmC  OsmC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   8.4e-06     0.038      48      88 ..      33      73 ..       6      79 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 8.4e-06
                                      CCECTCEEEEEEEEEEE-SS-H..HHHHHHHHHHHHHSHHH CS
                              OsmC 48 pegakgiteirlkvevkipgadseeklkkllekaekrCpvs 88
                                      + + ++i++  +k++ +i++ + +e+l + +++ae+ Cpv 
  gi|385805313|ref|YP_005841711.1| 33 NGKNRVIDKYSMKLTDEISEGEIPEELYECAKRAEESCPVV 73
                                      444446888888888888887778***************97 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.4   0.00038       1.7       1      12 [.       6      17 ..       6      18 .. 0.88
   2 ?    4.8   0.1    0.0059        27      16      23 ..      68      75 ..      67      76 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00038
                                      EEEETTTSSS-T CS
                              Fer4  1 vvideekCigCG 12
                                      v++d   Ci+CG
  gi|385805313|ref|YP_005841711.1|  6 VIVDRRTCIACG 17
                                      68999******9 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0059
                                      HHSTTTEE CS
                              Fer4 16 evCPvgAI 23
                                      e CPv AI
  gi|385805313|ref|YP_005841711.1| 68 ESCPVVAI 75
                                      78*****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); 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:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 511.32
//
Query:       gi|385805314|ref|YP_005841712.1|  [L=206]
Description: multiple antibiotic resistance (MarC)-like protein [Fervidicoccus fontis Kam940]
Scores for complete 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  105.9  16.4    2.1e-30  105.6  16.4    1.1  1  MarC        MarC family integral membrane protein


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 !  105.6  16.4   1.2e-34   2.1e-30       3     201 ..      11     196 ..       9     198 .. 0.93

  Alignments for each domain:
  == domain 1  score: 105.6 bits;  conditional E-value: 1.2e-34
                              MarC   3 aiikafvsLlaiinplgnvpvflslleevskeerkrialkasilallillvfllfGelilklfgisidalkiaGgil 79 
                                       +ii + + L+a++npl ++p f  l+e+ + e    i+ k  +  l++ ++f+l+G +il++fgis  +lkiaGgi+
  gi|385805314|ref|YP_005841712.1|  11 EIIVLSLQLYAVMNPLVAIPKFTDLVESNQREGFFSITNKVFLTILFLSTIFVLAGGYILSFFGISYYSLKIAGGII 87 
                                       67888999********************************************************************* PP

                              MarC  80 lfliaidmlkakqkkekkkkseeeeseekdeiavvPLAlPliaGPgaittvlvlaseassivekvavvlaillaali 156
                                       l+++aid l   +k     ++e e    + + +vvP+A+Pli GPg++t++++  + +      + ++la  l++++
  gi|385805314|ref|YP_005841712.1|  88 LLTVAIDTLTTGHK-----PKEVE----TGDLIVVPIATPLIIGPGTMTSLIIFGELHGI----INTLLAAYLSCFF 151
                                       *******9988777.....34444....57899********************9998877....5889999999*** PP

                              MarC 157 tllilllsslilrllgktginaleRlmGllLvalavqlivdGike 201
                                       ++l+l++s ++lrllg t in l + m l+++  a+q+++ G  +
  gi|385805314|ref|YP_005841712.1| 152 VYLTLIVSIALLRLLGPTFINGLGKFMSLIIASFAIQMLLSGFYG 196
                                       ****************************************99866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       820  (0.045736); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.35s 00:00:00.91 Elapsed: 00:00:00.52
# Mc/sec: 1189.52
//
Query:       gi|385805315|ref|YP_005841713.1|  [L=282]
Description: glutamine amidotransferase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-06   27.6   0.0    7.1e-06   26.2   0.0    1.6  2  GATase_6  Glutamine amidotransferase domain
  ------ inclusion threshold ------
       0.12   11.2   0.1       0.27   10.1   0.1    1.5  1  GATase_4  Glutamine amidotransferases class-II


Domain annotation for each model (and alignments):
>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0     8e-10   7.1e-06      14      81 ..      93     165 ..      76     198 .. 0.83
   2 ?   -2.7   0.0       0.7   6.3e+03      39      54 ..     248     263 ..     246     275 .. 0.77

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 8e-10
                          GATase_6  14 valaHvRlaivglaeeega.qPf...psedgrlllvhNGeiynykelreelpalkgla..frsrsDtevllall 81 
                                       v + H+R  ++  +++  + qPf   +++ +rl+++hNG +++ k l     +++ ++  f+++sDt+v+ + l
  gi|385805315|ref|YP_005841713.1|  93 VKIFHARATSEKSTVNILNvQPFefmTTSGSRLIIAHNGAVDKQK-LIGMIDEKESYKkiFEKYSDTYVMGKYL 165
                                       6799*******************998899999***********95.7777777777777899*******97755 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.7
                          GATase_6  39 dgrlllvhNGeiynyk 54 
                                       ++++ +  NG+ y+++
  gi|385805315|ref|YP_005841713.1| 248 NSGWFTLNNGDFYKFE 263
                                       67888999***99996 PP

>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   3.1e-05      0.27      72     113 ..      92     135 ..      34     154 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 3.1e-05
                          GATase_4  72 knvvaHiRkat.qGevklenthpFv.RelwgrewifAHnGdlke 113
                                       ++ + H R  + + +v+  n +pF      g + i+AHnG +++
  gi|385805315|ref|YP_005841713.1|  92 AVKIFHARATSeKSTVNILNVQPFEfMTTSGSRLIIAHNGAVDK 135
                                       45589999765267899*******72467899********9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1817.65
//
Query:       gi|385805316|ref|YP_005841714.1|  [L=164]
Description: hypothetical protein FFONT_0272 [Fervidicoccus fontis Kam940]
Scores for complete 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   40.1   0.0    0.00049   19.4   0.0    2.2  2  Hydrolase_4    Serine aminopeptidase, S33
    8.3e-08   32.2   0.0     0.0061   16.2   0.0    2.0  2  Abhydrolase_1  alpha/beta hydrolase fold
    5.3e-06   26.1   0.0    6.3e-06   25.9   0.0    1.1  1  DLH            Dienelactone hydrolase family
    1.3e-05   25.9   0.0    5.5e-05   23.9   0.0    1.6  2  Abhydrolase_6  Alpha/beta hydrolase family
    0.00075   19.3   0.0      0.001   18.9   0.0    1.1  1  Abhydrolase_5  Alpha/beta hydrolase family
     0.0041   16.8   0.0     0.0066   16.1   0.0    1.5  1  FSH1           Serine hydrolase (FSH1)
     0.0055   16.8   0.0      0.013   15.6   0.0    1.6  2  Abhydrolase_4  TAP-like protein
  ------ inclusion threshold ------
      0.026   14.5   0.0      0.068   13.1   0.0    1.6  2  UPF0227        Uncharacterised protein family (UPF0227)
      0.027   14.1   0.0       0.04   13.5   0.0    1.4  1  Esterase       Putative esterase
      0.033   14.0   0.0      0.041   13.7   0.0    1.1  1  Abhydrolase_2  Phospholipase/Carboxylesterase
      0.044   12.8   0.0      0.074   12.1   0.0    1.4  1  DUF1057        Alpha/beta hydrolase of unknown function (DUF1
      0.054   12.7   0.0      0.082   12.1   0.0    1.2  1  DUF2920        Protein of unknown function (DUF2920)
        0.1   12.1   0.0        4.3    6.8   0.0    2.1  2  Peptidase_S9   Prolyl oligopeptidase family


Domain annotation for each model (and alignments):
>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   4.9e-07   0.00067      69     111 ..      45      86 ..      29      93 .. 0.78
   2 !   19.4   0.0   3.6e-07   0.00049     183     232 ..      92     139 ..      89     146 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 4.9e-07
                       Hydrolase_4  69 vkeehpel.plfllGhSmGGliallyllrypdkvaglilsaPal 111
                                       +k+ +++l p  l+G SmGG++ally + +p   +gl l++P+ 
  gi|385805316|ref|YP_005841714.1|  45 LKKIKKDLkPPLLVGASMGGYLALLYSASNPV--SGLLLIGPVG 86 
                                       33444444699*****************9999..********85 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 3.6e-07
                       Hydrolase_4 183 leeraakitlPllllhGeaDkvvdpeasrelyerlgskdktlklypglyH 232
                                       ++++ +k+++P+ +++Ge+D+++d +  ++++e+l+  + +lk+y+   H
  gi|385805316|ref|YP_005841714.1|  92 VLSSLNKYNFPVCVIIGEKDTIIDFDSVKKFVESLP--NGKLKVYESSGH 139
                                       66788999****************************..7*******9988 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   4.4e-06    0.0061      52     109 ..      32      89 ..       2      99 .. 0.65
   2 !   15.5   0.0   7.6e-06      0.01     198     256 ..      93     145 ..      84     146 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.4e-06
                                       CHHSHHHHHHHHH.HH.HHHCTTSSEEEEEETHHHHHHHHHHHHHGGGEEEEEEESE..CSS CS
                     Abhydrolase_1  52 ddygtasvaddld.ri.ldalgddkltlvGhSmGGmialayaaeyperVkalvllga..idp 109
                                       +d++    +++l+ ++ + + +++++ lvG SmGG +al y a   ++V++l l+g+   d+
  gi|385805316|ref|YP_005841714.1|  32 TDMHK--NEAFLEeALkKIKKDLKPPLLVGASMGGYLALLYSA--SNPVSGLLLIGPvgTDD 89 
                                       55554..455555444222334556669***************..58899999999965554 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 7.6e-06
                                       HHHHHHHHCTHHHHSEEEEEEETTCSSSCHHHHHHHHHCHTSEEEEEEETCSSSHHHHS CS
                     Abhydrolase_1 198 aklllrlrelknvlaptlvisgtsDplvppkaledlaqllpkkrlvvisdagHlafleg 256
                                        ++l++++       p+ vi+g++D +++ ++  ++ + lp+ +l+v++ +gH a+l +
  gi|385805316|ref|YP_005841714.1|  93 LSSLNKYNF------PVCVIIGEKDTIIDFDSVKKFVESLPNGKLKVYESSGHPAYLYK 145
                                       455555665......***************9999999999999************9865 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   4.6e-09   6.3e-06      98     193 ..      53     146 ..      25     163 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 4.6e-09
                               DLH  98 kkvgvvGfCmGGalalllaaevpevdaavafYG..lspekeleeaakikapilalfgeeDefipadevekleealka 172
                                       k   +vG  mGG lall++a +p v + +   +  +     l+  +k + p+ +++ge+D++i++d+v+k+ e l  
  gi|385805316|ref|YP_005841714.1|  53 KPPLLVGASMGGYLALLYSASNP-VSGLLLIGPvgTDDTYVLSSLNKYNFPVCVIIGEKDTIIDFDSVKKFVESL-- 126
                                       555689999*************8.9998777663366666789999*********************99999999.. PP

                               DLH 173 anvdlelkvYpgagH.aFands 193
                                         ++ +lkvY+  gH a++ ++
  gi|385805316|ref|YP_005841714.1| 127 --PNGKLKVYESSGHpAYLYKK 146
                                       ..88999*****9995555555 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0     4e-08   5.5e-05      52      99 ..      39      86 ..       9     102 .. 0.70
   2 ?   -0.7   0.0       1.3   1.7e+03     173     211 ..     105     143 ..      99     152 .. 0.60

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 4e-08
                                      HH.HHHHCCTT..TTSEEEEEETCHHHHHHHHHHCC..EE.EEES-..-- CS
                     Abhydrolase_6 52 dl.aalldelaagggpvvlvGHSlGGalalaaaplalvvg.vlldpppta 99
                                      ++ +++l +++++ +p+ lvG S+GG+lal++ ++ +v+g +l+ p  ++
  gi|385805316|ref|YP_005841714.1| 39 AFlEEALKKIKKDLKPPLLVGASMGGYLALLYSASNPVSGlLLIGP--VG 86
                                      33345555555599*****************8888899**787777..33 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.3
                                       CEEECTT-CHHHHCHHCCCH..STTEEETCE...SSS-HHH CS
                     Abhydrolase_6 173 llvlggeDplvprllerlla..qagarlpvvlpgaGHlphl 211
                                       + ++g++D ++     +  +  ++  +l +v++ +GH  +l
  gi|385805316|ref|YP_005841714.1| 105 V-IIGEKDTIIDFDSVKKFVesLPNGKL-KVYESSGHPAYL 143
                                       3.55778887773322333335566666.999999995444 PP

>> Abhydrolase_5  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   7.3e-07     0.001      55     129 ..      51     129 ..      34     142 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 7.3e-07
                     Abhydrolase_5  55 klekfvvgGhslGGvvasrfaaeeekiegvvflasYPekd.....elselskkvlsivgteDgvlnvkslekakkfl 126
                                       +l+  ++ G s+GG +a  ++a++  + g+++++   ++d     +l++ +++v  i+g++D +++++s++k  + l
  gi|385805316|ref|YP_005841714.1|  51 DLKPPLLVGASMGGYLALLYSASNP-VSGLLLIGPVGTDDtyvlsSLNKYNFPVCVIIGEKDTIIDFDSVKKFVESL 126
                                       444557889***********99886.589*9999877765333336889999********************99999 PP

                     Abhydrolase_5 127 pkd 129
                                       p+ 
  gi|385805316|ref|YP_005841714.1| 127 PNG 129
                                       964 PP

>> FSH1  Serine hydrolase (FSH1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   4.8e-06    0.0066     151     195 ..      87     135 ..      29     140 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.8e-06
                              FSH1 151 yeeyy...eedkiqtptLhvlGelDtvvdeerseaLaeafkns.skvlk 195
                                        +++y   + +k ++p+  ++Ge+Dt++d +  ++++e+  n   kv++
  gi|385805316|ref|YP_005841714.1|  87 TDDTYvlsSLNKYNFPVCVIIGEKDTIIDFDSVKKFVESLPNGkLKVYE 135
                                       4555657677889**************************9996444444 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0         3   4.2e+03      31      42 ..      49      60 ..      33      62 .. 0.70
   2 !   15.6   0.0   9.6e-06     0.013      31      90 ..      97     157 ..      77     159 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3
                     Abhydrolase_4 31 akgaapvLllqn 42
                                      +k+ +p+Ll+++
  gi|385805316|ref|YP_005841714.1| 49 KKDLKPPLLVGA 60
                                      345589999986 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 9.6e-06
                     Abhydrolase_4  31 akgaapvLllqnerDpaTPyegakklakalggavlvtvegeGHgala.agntCvdkavdaY 90 
                                       +k ++pv ++ +e D +  + + kk+ + l++++l ++e++GH a+  ++++ +++ +++Y
  gi|385805316|ref|YP_005841714.1|  97 NKYNFPVCVIIGEKDTIIDFDSVKKFVESLPNGKLKVYESSGHPAYLyKKDRFIEDVLSTY 157
                                       34579*****************************************988888888877777 PP

>> UPF0227  Uncharacterised protein family (UPF0227)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.9e-05     0.068      42      73 ..      34      67 ..      18      84 .. 0.74
   2 ?   -1.4   0.0       1.4   1.9e+03     136     170 ..     102     139 ..      88     142 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.9e-05
                           UPF0227 42 pqqalkeleklvaelgddn..illvGssLGGyya 73
                                      +++  + le++++++++d   +llvG s+GGy+a
  gi|385805316|ref|YP_005841714.1| 34 MHKNEAFLEEALKKIKKDLkpPLLVGASMGGYLA 67
                                      4444445556666666555569**********99 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.4
                           UPF0227 136 rilvllskqDevldy...rravaefraaaeiveddgdH 170
                                       ++ v+ + +D ++d    ++ v+ + + +  v + + H
  gi|385805316|ref|YP_005841714.1| 102 PVCVIIGEKDTIIDFdsvKKFVESLPNGKLKVYESSGH 139
                                       56788888999998765566667776666666666655 PP

>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.9e-05      0.04     117     137 ..      55      75 ..       8      77 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.9e-05
                                       EEEEEETHHHHHHHHHHHCST CS
                          Esterase 117 ravaGqSmGGlgALilalkhp 137
                                         ++G+SmGG+ AL++ + +p
  gi|385805316|ref|YP_005841714.1|  55 PLLVGASMGGYLALLYSASNP 75 
                                       589************999988 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0     3e-05     0.041     108     199 ..      56     139 ..      29     156 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3e-05
                                       EEEEETHHHHHHHHHHHT-SS--SEEEEES---TTGGGTTTTS-GGGGG-EEEEEEETT-SSS-HHHHHHHHHHHHT CS
                     Abhydrolase_2 108 iigGFSqGaalalylaltlpkklggivafsgalplsqklessatavtkklpilqiHgeeDpvvplalgkaakevlkk 184
                                       +++G S+G+ lal   ++ +++++g + ++ +    + + ss ++ +   p++ i ge+D ++++   k++ e    
  gi|385805316|ref|YP_005841714.1|  56 LLVGASMGGYLAL--LYSASNPVSGLLLIGPVGTDDTYVLSSLNKYN--FPVCVIIGEKDTIIDFDSVKKFVES--- 125
                                       6889999999987..57788899******************999999..****************887766654... PP

                                       TS-GEEEEEETT--S CS
                     Abhydrolase_2 185 llkkvelksyeglaH 199
                                        l +++lk+ye+++H
  gi|385805316|ref|YP_005841714.1| 126 -LPNGKLKVYESSGH 139
                                       .44578888888888 PP

>> DUF1057  Alpha/beta hydrolase of unknown function (DUF1057)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   5.4e-05     0.074      57     139 ..       6      88 ..       3     116 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.4e-05
                           DUF1057  57 kleelkiRligvnyP.Gfefvtgylgqk.ytnaeRnsyskalleelelk.gklillghsRGcenaLqlavtleahGl 130
                                        ++e+ki +i+++ P G ++  + ++ + + n   + + +  l++++ + +  +l+g s G+  aL  +++ ++ Gl
  gi|385805316|ref|YP_005841714.1|   6 IFDEKKIPYIALDMPyGIKNSCEPKDTDmHKN---EAFLEEALKKIKKDlKPPLLVGASMGGYLALLYSASNPVSGL 79 
                                       69************966776665544330333...468888888888774556889********************* PP

                           DUF1057 131 vlinptGlr 139
                                        li p G  
  gi|385805316|ref|YP_005841714.1|  80 LLIGPVGTD 88 
                                       *****9965 PP

>> DUF2920  Protein of unknown function (DUF2920)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     6e-05     0.082     167     200 ..      41      73 ..      37      80 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6e-05
                           DUF2920 167 lkdlvkrfpkeadlpviliGgsyGGYlalLiaKi 200
                                       l++++k+  k+  +p +l+G+s GGYlalL +  
  gi|385805316|ref|YP_005841714.1|  41 LEEALKKIKKDL-KPPLLVGASMGGYLALLYSAS 73 
                                       678899999999.999*************97755 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.031        43      68      81 ..      57      70 ..      29      76 .. 0.80
   2 ?    6.8   0.0    0.0031       4.3     142     186 ..      99     139 ..      86     158 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.031
                                      EEEETHHHHHHHHH CS
                      Peptidase_S9 68 itGgSyGGyltgaa 81
                                      + G+S GGyl++  
  gi|385805316|ref|YP_005841714.1| 57 LVGASMGGYLALLY 70
                                      78********9865 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0031
                                       ---EEEEEEETT-SSS-THHHHHHHHHHH--S-SEEEEEETTS-S CS
                      Peptidase_S9 142 aypplLlihGlaDdrvppaealklvaaLqkkgknvlllifpdegH 186
                                        + p+++i G++D+ + + +  k+v+ L +     +l+++  +gH
  gi|385805316|ref|YP_005841714.1|  99 YNFPVCVIIGEKDTIIDFDSVKKFVESLPN----GKLKVYESSGH 139
                                       45699**********************985....45777778887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      632  (0.0352502); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 967.01
//
Query:       gi|385805317|ref|YP_005841715.1|  [L=127]
Description: hydrogenase nickel incorporation protein [Fervidicoccus fontis Kam940]
Scores for complete 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   73.4   1.2    1.6e-20   73.2   1.2    1.0  1  HypA             Hydrogenase/urease nickel incorporation, met
     0.0085   16.1   2.3       0.75    9.8   0.4    2.2  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
  ------ inclusion threshold ------
       0.01   15.8   1.6        2.4    8.2   0.2    2.4  2  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
      0.012   15.3   2.5       0.16   11.7   0.1    2.2  2  Zn_Tnp_IS1       InsA N-terminal domain
      0.014   15.3   0.1          8    6.5   0.0    2.5  2  zinc_ribbon_4    zinc-ribbon domain
      0.021   14.9   0.1      0.024   14.7   0.1    1.2  1  Mut7-C           Mut7-C RNAse domain
      0.022   14.3   0.9       0.41   10.2   0.2    2.2  2  TF_Zn_Ribbon     TFIIB zinc-binding
      0.046   13.8   1.1        1.9    8.6   0.0    2.0  2  Elf1             Transcription elongation factor Elf1 like
      0.064   13.1   0.9        1.7    8.5   0.0    2.3  2  eIF-5_eIF-2B     Domain found in IF2B/IF5
      0.065   13.2   0.1        3.7    7.5   0.0    2.5  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
       0.07   13.2   1.9       0.56   10.3   0.1    2.3  2  UPF0547          Uncharacterised protein family UPF0547
      0.093   12.6   4.3       0.94    9.4   1.1    2.3  2  TFIIS_C          Transcription factor S-II (TFIIS)
       0.11   12.9   0.5       0.82   10.1   0.8    1.9  2  Lar_restr_allev  Restriction alleviation protein Lar
       0.15   12.2   3.6       0.83    9.8   3.6    2.0  1  Zn-ribbon_8      Zinc ribbon domain
       0.32   10.5   4.4        1.2    8.6   0.2    2.2  2  zf-ribbon_3      zinc-ribbon domain
       0.44   10.6   2.7        1.5    8.9   1.1    2.3  2  CpXC             CpXC protein
        2.1    8.2   7.4        3.4    7.5   0.8    2.2  2  Rubredoxin_2     Rubredoxin metal binding domain


Domain annotation for each model (and alignments):
>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.2   1.2   1.5e-23   1.6e-20       1     106 [.       3     123 ..       3     126 .. 0.89

  Alignments for each domain:
  == domain 1  score: 73.2 bits;  conditional E-value: 1.5e-23
                                       XCHHHHHHHHHHHHHHHHCCTT..EEEEEEEEEETTCT--HHHHHHHHHHHHCC.TTTT-EEEEEEE--EEEETTTS CS
                              HypA   1 MHElsiaesivevveeeakeaaarkvtkvkvevGelsgvepeaLefafellaegtvlegaeLeieevpvkvrCreCg 77 
                                       MHE++ia+ i+e+++e+a +   +k+++vkv +Gel++++ +++  + ++  e+  ++  +L++e  +++++C++Cg
  gi|385805317|ref|YP_005841715.1|   3 MHEIAIAQGIIEAIKEKAFH---EKISEVKVLFGELQNIDINIVMNYVTMTLESLNIK-VKLSYEIREARFKCNKCG 75 
                                       ******************32...49*****************9988877776665566.****************** PP

                                       -EEECHHHHH...................S-TTTSSS-EEEEESSSEE CS
                              HypA  78 kefeleekal...................rCpkCgsadveivsGeell 106
                                       +e++l++ +l                   +Cp+C+s+d+e+++G++++
  gi|385805317|ref|YP_005841715.1|  76 YEWSLSDVSLsederemihfmpeavhtvvSCPNCKSSDFEVLDGKNVM 123
                                       ****8863334578999****************************986 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.4   0.00071      0.75      29      45 ..      61      76 ..      57      77 .. 0.85
   2 ?    6.0   0.1     0.011        12      20      27 ..     104     112 ..      97     120 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00071
                     Zn_Tnp_IS1595 29 ayriktrglfqCkeCrk 45
                                      +y+i+   +f+C++C++
  gi|385805317|ref|YP_005841715.1| 61 SYEIRE-ARFKCNKCGY 76
                                      689998.9*******98 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.011
                     Zn_Tnp_IS1595  20 v.CPhCgsr 27 
                                       v CP+C+s+
  gi|385805317|ref|YP_005841715.1| 104 VsCPNCKSS 112
                                       45****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 ?    8.2   0.2    0.0023       2.4      22      30 .]      71      79 ..      66      79 .. 0.89
   2 ?    6.7   0.1    0.0064       6.8       5      10 ..     106     111 ..      81     115 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0023
                    PhnA_Zn_Ribbon 22 CpeCahEwe 30
                                      C +C++Ew+
  gi|385805317|ref|YP_005841715.1| 71 CNKCGYEWS 79
                                      ********7 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0064
                    PhnA_Zn_Ribbon   5 CplCaS 10 
                                       Cp+C+S
  gi|385805317|ref|YP_005841715.1| 106 CPNCKS 111
                                       666655 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 ?    3.5   0.3     0.057        61      27      34 ..      67      74 ..      64      75 .. 0.86
   2 ?   11.7   0.1   0.00015      0.16       6      22 ..     104     121 ..     100     123 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.057
                        Zn_Tnp_IS1 27 eRfrCrdC 34
                                       Rf+C +C
  gi|385805317|ref|YP_005841715.1| 67 ARFKCNKC 74
                                      6******* PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00015
                        Zn_Tnp_IS1   6 ihCPrCsstd.VyRhGks 22 
                                       ++CP C+s d  + +Gk+
  gi|385805317|ref|YP_005841715.1| 104 VSCPNCKSSDfEVLDGKN 121
                                       8********987778887 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0    0.0076         8      25      35 ..      68      78 ..      60      91 .. 0.81
   2 ?    6.5   0.0    0.0076       8.1       3      10 ..     104     111 ..     103     120 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0076
                     zinc_ribbon_4 25 kvrCskCghvF 35
                                      + +C kCg  +
  gi|385805317|ref|YP_005841715.1| 68 RFKCNKCGYEW 78
                                      56888888766 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0076
                     zinc_ribbon_4   3 itCpsCka 10 
                                       ++Cp+Ck+
  gi|385805317|ref|YP_005841715.1| 104 VSCPNCKS 111
                                       79999986 PP

>> Mut7-C  Mut7-C RNAse 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     0.024      67     130 ..      45     110 ..       3     112 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.3e-05
                            Mut7-C  67 rdveeqlreviarlglklslkpelsrCvaCng..eleevekeevkervpekvyeeadeftrCekCr 130
                                       + v   l+ +  +++l++++++   +C +C     l+ v+ +e ++++ + ++e  ++++ C++C+
  gi|385805317|ref|YP_005841715.1|  45 NYVTMTLESLNIKVKLSYEIREARFKCNKCGYewSLSDVSLSEDEREMIHFMPEAVHTVVSCPNCK 110
                                       55667788888899999*****99******986789********9********************7 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.088        93      20      29 ..      69      78 ..      61      91 .. 0.76
   2 ?   10.2   0.2   0.00038      0.41       3      12 ..     106     116 ..     104     123 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.088
                                      EEESSSSBEE CS
                      TF_Zn_Ribbon 20 lvCtdCGlVl 29
                                      + C +CG+ +
  gi|385805317|ref|YP_005841715.1| 69 FKCNKCGYEW 78
                                      5589999765 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00038
                                       ETTTTCEEC.H CS
                      TF_Zn_Ribbon   3 CPnCgstnl.v 12 
                                       CPnC+s+++ v
  gi|385805317|ref|YP_005841715.1| 106 CPNCKSSDFeV 116
                                       ******99734 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0    0.0018       1.9      33      58 ..      56      81 ..      51      89 .. 0.76
   2 ?    3.4   0.2     0.074        78      18      30 ..     100     112 ..      88     117 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0018
                              Elf1 33 vevkldkkekiaevsCkvCgesfetk 58
                                      ++vkl+ + + a+ +C++Cg + +++
  gi|385805317|ref|YP_005841715.1| 56 IKVKLSYEIREARFKCNKCGYEWSLS 81
                                      67888888889999999999887755 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.074
                              Elf1  18 lptkFdCpfCnhe 30 
                                       + t+ +Cp+C+++
  gi|385805317|ref|YP_005841715.1| 100 VHTVVSCPNCKSS 112
                                       5666777777765 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 ?    3.1   0.2     0.078        82      95     116 ..      55      76 ..      27      77 .. 0.73
   2 ?    8.5   0.0    0.0016       1.7      78     108 ..      94     124 ..      83     126 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.078
                                       STCEEECCSSSCEEEEESSSTC CS
                      eIF-5_eIF-2B  95 spetelekeerllvlkCkaCga 116
                                       +  ++l+ e r   +kC++Cg 
  gi|385805317|ref|YP_005841715.1|  55 NIKVKLSYEIREARFKCNKCGY 76 
                                       4555666676667789****96 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0016
                                       HHHHHHHHHHTSTSSSTSTCEEECCSSSCEE CS
                      eIF-5_eIF-2B  78 klldkyieeyVlCkeCkspetelekeerllv 108
                                       + + + +++ V C++Cks + e+   +++++
  gi|385805317|ref|YP_005841715.1|  94 HFMPEAVHTVVSCPNCKSSDFEVLDGKNVMM 124
                                       5566668889***********9998777765 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0035       3.7      42      56 ..      64      78 ..      52      83 .. 0.82
   2 ?    3.3   0.0     0.074        78      26      37 ..     100     112 ..      86     122 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0035
                    OrfB_Zn_ribbon 42 lsgrtfkCpnCgfea 56
                                        + +fkC++Cg+e+
  gi|385805317|ref|YP_005841715.1| 64 IREARFKCNKCGYEW 78
                                      56789*******996 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.074
                    OrfB_Zn_ribbon  26 y.TSktCseCgsk 37 
                                         T  +C++C s 
  gi|385805317|ref|YP_005841715.1| 100 VhTVVSCPNCKSS 112
                                       3477778888765 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00053      0.56      16      25 ..      70      79 ..      62      80 .. 0.84
   2 ?    2.0   0.2      0.22   2.3e+02       3       6 ..     106     109 ..     103     112 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00053
                           UPF0547 16 fCphCGyvFq 25
                                      +C  CGy+++
  gi|385805317|ref|YP_005841715.1| 70 KCNKCGYEWS 79
                                      8********7 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.22
                           UPF0547   3 CPeC 6  
                                       CP C
  gi|385805317|ref|YP_005841715.1| 106 CPNC 109
                                       7777 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   1.1    0.0009      0.94      29      38 ..      69      78 ..      66      79 .. 0.89
   2 ?    4.1   0.1     0.039        41       2       9 ..     105     112 ..      98     115 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0009
                           TFIIS_C 29 ykCtkCghrW 38
                                      +kC+kCg++W
  gi|385805317|ref|YP_005841715.1| 69 FKCNKCGYEW 78
                                      8********* PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.039
                           TFIIS_C   2 kCpkCgsr 9  
                                        Cp+C+s 
  gi|385805317|ref|YP_005841715.1| 105 SCPNCKSS 112
                                       58888765 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 ?    6.4   0.0     0.011        11      27      52 ..      66      90 ..      44      95 .. 0.64
   2 ?   10.1   0.8   0.00078      0.82       6      40 ..      71     115 ..      70     123 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.011
                   Lar_restr_allev 27 q.cvyCadCgastpwfkiaedeaeaek 52
                                      +  + C +Cg+   w   +    e+e 
  gi|385805317|ref|YP_005841715.1| 66 EaRFKCNKCGY--EWSLSDVSLSEDER 90
                                      23899******..44444444444444 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00078
                   Lar_restr_allev   6 CPfCggravlersqrvvaeigq..........cvyCadCgastpw 40 
                                       C+ Cg +  l    +   e+++          +v+C +C+ s  +
  gi|385805317|ref|YP_005841715.1|  71 CNKCGYEWSLSDVSLSEDEREMihfmpeavhtVVSCPNCKSSDFE 115
                                       9*********99999999999899***************995444 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   3.6   0.00079      0.83       6      35 ..      69     113 ..      68     117 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00079
                       Zn-ribbon_8   6 YrCeeCghefe...........vlqsis.dap.lta.CPeCgs.e 35 
                                       ++C++Cg e             ++  ++ +a   ++ CP+C+s +
  gi|385805317|ref|YP_005841715.1|  69 FKCNKCGYEWSlsdvslsederEMIHFMpEAVhTVVsCPNCKSsD 113
                                       9******999998777777766333333355554558****9966 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.7     0.067        70       4       9 ..      70      75 ..      69      77 .. 0.57
   2 ?    8.6   0.2    0.0011       1.2       3      11 ..     104     112 ..     103     116 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.067
                       zf-ribbon_3  4 rCPnCG 9 
                                      +C++CG
  gi|385805317|ref|YP_005841715.1| 70 KCNKCG 75
                                      455555 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0011
                       zf-ribbon_3   3 vrCPnCGap 11 
                                       v+CPnC++ 
  gi|385805317|ref|YP_005841715.1| 104 VSCPNCKSS 112
                                       79****985 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   1.1    0.0014       1.5      37      72 ..      68     101 ..      44     115 .. 0.85
   2 ?    0.9   0.3      0.43   4.6e+02       1       8 [.     104     111 ..     104     121 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0014
                              CpXC  37 eatCpkCgatakleapllyhdpekellillvpeser 72 
                                       +++C kCg++ +l+   l  d  ++ +i ++pe   
  gi|385805317|ref|YP_005841715.1|  68 RFKCNKCGYEWSLSDVSLSED--EREMIHFMPEAVH 101
                                       689**********99999888..7889999998765 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.43
                              CpXC   1 ltCpaCgk 8  
                                       ++Cp+C++
  gi|385805317|ref|YP_005841715.1| 104 VSCPNCKS 111
                                       56777765 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.8    0.0032       3.4       1       9 [.      69      77 ..      69      79 .. 0.90
   2 ?    4.4   0.8      0.03        32      17      23 ..     106     112 ..     105     113 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0032
                      Rubredoxin_2  1 YvCsqCGfe 9 
                                      + C++CG+e
  gi|385805317|ref|YP_005841715.1| 69 FKCNKCGYE 77
                                      89*****97 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.03
                      Rubredoxin_2  17 CpsCgsW 23 
                                       Cp+C+s 
  gi|385805317|ref|YP_005841715.1| 106 CPNCKSS 112
                                       ****986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1054  (0.0587874); expected 358.6 (0.02)
Passed bias filter:                      677  (0.0377601); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.42
# Mc/sec: 907.69
//
Query:       gi|385805318|ref|YP_005841716.1|  [L=254]
Description: nucleotide-binding protein, mrp/nbp35 family [Fervidicoccus fontis Kam940]
Scores for 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-44  151.3   0.1    3.5e-44  151.1   0.1    1.1  1  ParA         NUBPL iron-transfer P-loop NTPase
    1.1e-21   77.2   0.2    1.4e-21   76.9   0.2    1.1  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    1.6e-12   47.7   3.6    4.1e-11   43.1   3.6    2.2  1  AAA_31       AAA domain
    3.5e-08   33.0   1.4    0.00015   21.0   0.0    2.9  3  ArsA_ATPase  Anion-transporting ATPase
    6.7e-07   28.9   0.0    1.4e-06   27.8   0.0    1.5  1  MipZ         ATPase MipZ
    1.7e-05   24.7   1.5      0.011   15.6   0.0    2.3  2  AAA_26       AAA domain
     0.0034   16.9   0.0      0.011   15.2   0.0    1.8  2  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
  ------ inclusion threshold ------
        0.1   12.4   0.3       0.62    9.8   0.1    2.1  2  CLP1_P       mRNA cleavage and polyadenylation factor CLP1 P-


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 !  151.1   0.1   1.6e-47   3.5e-44       1     192 [.      19     208 ..      19     235 .. 0.93

  Alignments for each domain:
  == domain 1  score: 151.1 bits;  conditional E-value: 1.6e-47
                              ParA   1 kvkkviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqsekkliPveakgikvmS 77 
                                       +vk++i ++S+KGGVGK+t+++ lA+aL++ glk+gllD+D++ p+   +lg++ +   ++e+++ Pv  ++ik  S
  gi|385805318|ref|YP_005841716.1|  19 NVKNIIGIVSSKGGVGKTTISTLLAIALNELGLKTGLLDLDLTNPNTHLILGADMKINFEEENGIKPVIINEIKYFS 95 
                                       69****************************************************9866777889************* PP

                              ParA  78 igfllesedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqklplagaviVttpqevaladvk 154
                                         +l+e   +    rG  +++a+k+ll+  +wg+lD+LiiD+PPG +De   +++ lp  + ++V++p +++l+ +k
  gi|385805318|ref|YP_005841716.1|  96 PVILTE--GRISPLRGREIDSALKELLSILDWGSLDFLIIDTPPGMSDELYDLIELLPQIKLILVSSPDKLSLESIK 170
                                       *99999..555567*************************************************************** PP

                              ParA 155 kaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkg 192
                                         i+ ++k ++k+lG+v N+   + +  ++++e+++kg
  gi|385805318|ref|YP_005841716.1| 171 NMIKNLEKENAKILGIVVNLYRTTFDAYKNHKELLNKG 208
                                       ***********************999999999998776 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 !   76.9   0.2     6e-25   1.4e-21       2     122 ..      25     225 ..      24     231 .. 0.96

  Alignments for each domain:
  == domain 1  score: 76.9 bits;  conditional E-value: 6e-25
                                       EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH........................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................ RF
                              CbiA   2 aiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep........................ 54 
                                        i+s kGGvGKTt+++ La+al++ gl++ l+D+D   +n++++ g  ++i+                         
  gi|385805318|ref|YP_005841716.1|  25 GIVSSKGGVGKTTISTLLAIALNELGLKTGLLDLDLTNPNTHLILGADMKINFeeengikpviineikyfspvilte 101
                                       699****************************************88888888888889******************** PP

                                       ...............................................................CCHCCCHHHHHHCH CS
                                       ...............................................................xxxxxxxxxxxxxx RF
                              CbiA  55 ...............................................................dlkrllellealgk 68 
                                                                                                      +l+++++++++l k
  gi|385805318|ref|YP_005841716.1| 102 grisplrgreidsalkellsildwgsldfliidtppgmsdelydliellpqiklilvsspdklSLESIKNMIKNLEK 178
                                       ****************************************************************************9 PP

                                       CHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  69 kkalllkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaeap 122
                                       ++    ki+g+v+n ++    + + k++ e l++  g++ l++i++d+ ++++ 
  gi|385805318|ref|YP_005841716.1| 179 EN---AKILGIVVNLYRTT--FDAYKNHKELLNK--GLKMLKLISYDDTFIFSL 225
                                       96...69**********99..9*99999999999..*************99876 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   3.6   1.8e-14   4.1e-11       2     170 ..      22     182 ..      21     190 .. 0.79

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 1.8e-14
                            AAA_31   2 kvIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanatt.glgiekneiektlyevlieeknikeaiiktk 77 
                                        +I i+  KGGvGKTT s+ la al +lg k+ l DlD  +  t   lg    +   +++    ee+ ik +ii ++
  gi|385805318|ref|YP_005841716.1|  22 NIIGIVSSKGGVGKTTISTLLAIALNELGLKTGLLDLDLTNPNTHlILG---AD--MKINF--EEENGIKPVII-NE 90 
                                       589***********************************87766661333...22..23332..37889999999.33 PP

                            AAA_31  78 venldlipssidLaeaeielvelekkeeilkellekvk.deYDyiiiDcpPsLg..lltenaLvasdsviipvqaea 151
                                       ++      s + L e  i+ ++ ++  ++lkell+ ++  + D+ iiD+pP ++  l+    L+   ++i +  +++
  gi|385805318|ref|YP_005841716.1|  91 IKY----FSPVILTEGRISPLRGREIDSALKELLSILDwGSLDFLIIDTPPGMSdeLYDLIELLPQIKLILVSSPDK 163
                                       222....3555566666666666777888999999998357**********98543888999999999999****** PP

                            AAA_31 152 yaleGleqllktieevkkk 170
                                       ++le +++++k++e+ + k
  gi|385805318|ref|YP_005841716.1| 164 LSLESIKNMIKNLEKENAK 182
                                       ***********99987665 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   6.9e-08   0.00015       5      38 ..      26      59 ..      22      79 .. 0.91
   2 ?    0.1   0.0      0.16   3.7e+02     112     134 ..     115     137 ..     105     151 .. 0.86
   3 !    9.1   0.2   0.00029      0.64     209     244 ..     155     190 ..     139     224 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 6.9e-08
                                      EEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                       ArsA_ATPase  5 lvgGKGGVGKttvsaatavklsekgkkvllistD 38
                                      +v+ KGGVGKtt+s+ +a+ l e g k+ l+ +D
  gi|385805318|ref|YP_005841716.1| 26 IVSSKGGVGKTTISTLLAIALNELGLKTGLLDLD 59
                                      6899**********************99888776 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.16
                                       HHHHHHHHHHCSSSSEEEEESBS CS
                       ArsA_ATPase 112 sfeellkyvkeeeydvvvlDtaP 134
                                       +++ell  ++    d +++Dt+P
  gi|385805318|ref|YP_005841716.1| 115 ALKELLSILDWGSLDFLIIDTPP 137
                                       67888889999999*******99 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.00029
                                       EEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEEE CS
                       ArsA_ATPase 209 frlVvipEklslkEteRaikeLkkygikvdavivNk 244
                                       ++lV+ p+klsl+ ++ +ik+L+k + k+  ++vN 
  gi|385805318|ref|YP_005841716.1| 155 LILVSSPDKLSLESIKNMIKNLEKENAKILGIVVNL 190
                                       789********************************5 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   6.4e-10   1.4e-06       3     111 ..      24     140 ..      22     148 .. 0.68

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 6.4e-10
                                       EEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHHHH..HHHHHHHHT-----.-EEE-.....SS CS
                              MipZ   3 ivlgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlarylen..raataerkglsLpl.peala.....ls 71 
                                       i +   kGG Gk+t++  +a+aL + G++ + +dldl     +  l+   + +++e++g++  +  e+       l+
  gi|385805318|ref|YP_005841716.1|  24 IGIVSSKGGVGKTTISTLLAIALNELGLKTGLLDLDLTNPNTHLILGAdmKINFEEENGIKPVIiNEIKYfspviLT 100
                                       566788*********************************99999987622556778888864330333320111033 PP

                                       S-HHHHTTS-HHHHHHHHHHHHHHHH.HH-SEEEEE--.SS- CS
                              MipZ  72 eaeeaeveeeeeaevaeleelvadle.aeldfividtP.Gsd 111
                                       e+  + + ++ e++ ++l+el++ l   +ldf++idtP G  
  gi|385805318|ref|YP_005841716.1| 101 EGRISPL-RGREID-SALKELLSILDwGSLDFLIIDTPpGMS 140
                                       3333333.444444.688888888863578*******72544 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.7    0.0012       2.6       5      32 ..      26      53 ..      22      56 .. 0.84
   2 !   15.6   0.0   4.7e-06     0.011     121     170 ..     144     194 ..     133     232 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0012
                            AAA_26  5 vtgtdtgvGKTvvslgLvralkrkgvkv 32
                                      +++   gvGKT++s++L+ al++ g k+
  gi|385805318|ref|YP_005841716.1| 26 IVSSKGGVGKTTISTLLAIALNELGLKT 53
                                      889999************9998777665 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 4.7e-06
                            AAA_26 121 adiaknl.gapvilVargglgtinqllltiealrqknvrvlGvilNkvrnp 170
                                       +d+++ l +++ ilV ++++ +++ +  +i+ l ++n ++lG+++N  r  
  gi|385805318|ref|YP_005841716.1| 144 YDLIELLpQIKLILVSSPDKLSLESIKNMIKNLEKENAKILGIVVNLYRTT 194
                                       67777776899***********************************75544 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   4.9e-06     0.011       4      42 ..      24      62 ..      21      94 .. 0.70
   2 ?   -1.4   0.0      0.59   1.3e+03     106     137 ..     117     149 ..     108     178 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.9e-06
                          CBP_BcsQ  4 lalqGvRGGvGttsllaaLawalhelgesvlviDlspdn 42
                                      + +   +GGvG+t++++ La+al+elg +  ++Dl   n
  gi|385805318|ref|YP_005841716.1| 24 IGIVSSKGGVGKTTISTLLAIALNELGLKTGLLDLDLTN 62
                                      5666679*******************9887777653332 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.59
                          CBP_BcsQ 106 laalkelk.eqyrwillDlpagasaltrellal 137
                                       ++ l+ l  ++ +++++D p g+s+   +l++l
  gi|385805318|ref|YP_005841716.1| 117 KELLSILDwGSLDFLIIDTPPGMSDELYDLIEL 149
                                       444455556778899999999888776666554 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00027      0.62       4      35 ..      32      63 ..      30      68 .. 0.91
   2 ?   -0.0   0.0       0.3   6.6e+02     133     166 ..     155     187 ..     110     204 .. 0.52

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00027
                            CLP1_P  4 dsGKSTlarlLlNyalrkgrkpvyvDlDvGqs 35
                                       +GK+T+++lL+  + + g k+ ++DlD+  +
  gi|385805318|ref|YP_005841716.1| 32 GVGKTTISTLLAIALNELGLKTGLLDLDLTNP 63
                                      59**************************8765 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.3
                            CLP1_P 133 vvvvldqeellnelkrdlplskvkvvklpkspgv 166
                                       +++v + ++l  e  +++  ++++ ++ + ++ v
  gi|385805318|ref|YP_005841716.1| 155 LILVSSPDKLSLESIKNMI-KNLEKENAKILGIV 187
                                       3333333444333333333.34444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       844  (0.0470746); expected 358.6 (0.02)
Passed bias filter:                      617  (0.0344135); 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: 0.64u 0.36s 00:00:01.00 Elapsed: 00:00:00.57
# Mc/sec: 1350.39
//
Query:       gi|385805319|ref|YP_005841717.1|  [L=176]
Description: hypothetical protein FFONT_0275 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-31  109.9  15.2    1.4e-31  109.7  15.2    1.0  1  QueT      QueT transporter
  ------ inclusion threshold ------
       0.71   10.1   3.9        3.4    7.9   1.5    2.5  2  S1FA      DNA binding protein S1FA


Domain annotation for each model (and alignments):
>> QueT  QueT transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.7  15.2   1.6e-35   1.4e-31       2     139 .]       7     158 ..       6     158 .. 0.87

  Alignments for each domain:
  == domain 1  score: 109.7 bits;  conditional E-value: 1.6e-35
                              QueT   2 vraaviaAlYvvltlvlapisfgaiqvRiseaLtlLpv...ftpaailGltiGcliaNllsplgllDvifGslatli 75 
                                       + +aviaA Y+ lt+++api++g+iqvRis+++++Lp+   f+ +ai+GltiG++iaNl sp++++D+i+G+ a++i
  gi|385805319|ref|YP_005841717.1|   7 LYIAVIAAGYAGLTVLIAPIAYGPIQVRISDIFLVLPFnkkFGTKAIWGLTIGTFIANLNSPYNPYDLILGTTASFI 83 
                                       679***********************************8888899******************************** PP

                              QueT  76 aalltyllkkkr......llaa.lppvlvnalivgavl....lelpflltvltvglgelivlyvlGlpllkalek 139
                                       +al++yl+ k        l+a   ++++++ ++++++l    +++p+ +++l v++g++i++ + G++l + lek
  gi|385805319|ref|YP_005841717.1|  84 SALAIYLCGKYIknrkvgLIAGiAASIVIVDFFIAFLLlnyiFKVPLGISMLGVTIGQIISVGIGGYLLAIGLEK 158
                                       ********8777888766344325666666677775534556999**********************99998876 PP

>> S1FA  DNA binding protein S1FA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   1.5   0.00037       3.4       5      31 ..     100     126 ..      96     130 .. 0.88
   2 ?    1.9   0.1     0.029   2.6e+02      11      41 ..     132     162 ..     128     170 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00037
                              S1FA   5 kGlnPGlivllvvggllllflvgnyvl 31 
                                        Gl  G+   +v++ +++ fl+ ny++
  gi|385805319|ref|YP_005841717.1| 100 VGLIAGIAASIVIVDFFIAFLLLNYIF 126
                                       599999*******************97 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.029
                              S1FA  11 livllvvggllllflvgnyvlyvyaqktlPp 41 
                                       + +l v  g ++   +g y+l +   k++P+
  gi|385805319|ref|YP_005841717.1| 132 ISMLGVTIGQIISVGIGGYLLAIGLEKKFPE 162
                                       5556677788888888888888888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.55
# Mc/sec: 957.28
//
Query:       gi|385805320|ref|YP_005841718.1|  [L=240]
Description: ABC transporter [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.7e-22   78.7   0.0      8e-22   78.2   0.0    1.2  1  ABC_tran     ABC transporter
    3.5e-11   42.9   0.1    3.5e-06   26.6   0.0    2.0  2  SMC_N        RecF/RecN/SMC N terminal domain
    6.3e-07   29.5   1.9    2.8e-05   24.1   0.3    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    3.4e-06   27.7   0.1    9.3e-06   26.3   0.0    1.8  1  AAA_23       AAA domain
      3e-05   23.7   0.0    4.8e-05   23.1   0.0    1.3  1  AAA_27       AAA domain
    3.2e-05   23.8   0.1    4.4e-05   23.4   0.1    1.4  1  AAA_15       AAA ATPase domain
    9.9e-05   22.0   0.0    0.00018   21.2   0.0    1.4  1  AAA_29       P-loop containing region of AAA domain
     0.0012   18.8   0.2     0.0053   16.7   0.1    2.0  1  ATPase_2     ATPase domain predominantly from Archaea
     0.0017   17.2   0.0     0.0029   16.5   0.0    1.3  1  ABC_ATPase   Predicted ATPase of the ABC class
  ------ inclusion threshold ------
      0.087   13.1   0.0       0.14   12.4   0.0    1.3  1  AAA_28       AAA domain
        0.1   12.6   0.1       0.23   11.5   0.0    2.0  1  AAA_14       AAA domain
       0.12   12.2   0.0       0.26   11.2   0.0    1.4  1  RsgA_GTPase  RsgA GTPase
        0.2   12.0   0.0       0.28   11.6   0.0    1.3  1  AAA_16       AAA ATPase domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.2   0.0   5.8e-25     8e-22       1     137 []      21     160 ..      21     160 .. 0.86

  Alignments for each domain:
  == domain 1  score: 78.2 bits;  conditional E-value: 5.8e-25
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS..--S-TTSB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe..pqlfpelt 75 
                                       l++++l+l +g ++ai+G+n +GKStLlk++a l   ++Ge+ +dg ++++ + ++  + +g++ q+  + +f+++ 
  gi|385805320|ref|YP_005841718.1|  21 LEDITLELPPG-VHAILGPNSSGKSTLLKAIASLIPIKKGEVIYDGISISKLPPKKRAQIVGYCWQNpyQGFFEDS- 95 
                                       67889999998.789****************************************************865666666. PP

                                       HHHH.......HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  76 vren.......esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       v+++       +  +  e++l+ lg ++l +++       LSgG+ +rv++a +++ +++++llDEp++
  gi|385805320|ref|YP_005841718.1|  96 VKREiefilknTNAKASEEVLEILGVNKLYEKNP----FRLSGGEARRVSIASIVVADQPIILLDEPFN 160
                                       5555688766455555778888888777666665....*****************************86 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   2.5e-09   3.5e-06       2      45 ..       8      51 ..       7      64 .. 0.93
   2 !   14.5   0.0   1.3e-05     0.018     108     205 ..      99     196 ..      89     210 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 2.5e-09
                                      EEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  2 lkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAil 45
                                      +++l++e Fk  a + ++l++ +++ ai+GpN SGKs ll Ai 
  gi|385805320|ref|YP_005841718.1|  8 VSNLTVEFFKKVALEDITLELPPGVHAILGPNSSGKSTLLKAIA 51
                                      7899**************************************96 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 1.3e-05
                                       EEEEEETTEEE-H.HHHHHHHHCTT-STT...CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHH CS
                                       xxxxxxxxxxxxx.xxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 108 eseykingkevtk.kevsellesagiske...lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkva 180
                                       e e+ +++++++  +ev e+l   +++++    LSgGe   v++a +     v  +p+ llDe    +D      ++
  gi|385805320|ref|YP_005841718.1|  99 EIEFILKNTNAKAsEEVLEILGVNKLYEKnpfRLSGGEARRVSIASI----VVADQPIILLDEPFNDMDLDGYLSIV 171
                                       556777777777658899999999998874446*****999998877....57899*******99999999999*** PP

                                       HHHHHHCTTSEEEEE-SSHHHCCC- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 181 ellkeksknaQfivislreemleka 205
                                       +ll   +k+   ++i+l++ m  + 
  gi|385805320|ref|YP_005841718.1| 172 NLLSFFRKRNKTVIIALNNSMHLNL 196
                                       *******************997665 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 !   24.1   0.3     2e-08   2.8e-05       2      24 ..      33      55 ..      32      76 .. 0.76
   2 ?    5.0   0.1     0.014        19     233     272 ..     128     164 ..      90     187 .. 0.71

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 2e-08
                            AAA_21  2 nvliGpNgsGKSnLLdaldllar 24
                                       ++ GpN+sGKS+LL+a+  l  
  gi|385805320|ref|YP_005841718.1| 33 HAILGPNSSGKSTLLKAIASLIP 55
                                      689***************99953 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.014
                            AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHP 272
                                       +++ lS G  r   +++++ ++    +++l+DEp n ++ 
  gi|385805320|ref|YP_005841718.1| 128 NPFRLSGGEARRVSIASIVVADQ---PIILLDEPFNDMDL 164
                                       55666666666656666666555...9*******998875 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   6.8e-09   9.3e-06       5      40 ..      14      51 ..      10     129 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 6.8e-09
                            AAA_23  5 enfrsf..rdqeidFskgltlItGpNGaGKTTildAik 40
                                      e f++   +d ++++ +g+ +I GpN +GK+T+l Ai 
  gi|385805320|ref|YP_005841718.1| 14 EFFKKValEDITLELPPGVHAILGPNSSGKSTLLKAIA 51
                                      556666668899999*********************96 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   3.5e-08   4.8e-05       3      49 ..       8      53 ..       6      55 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 3.5e-08
                            AAA_27  3 lerLdLeryGkftdrsldfsaeeadlhliyGpNEAGKstalrAisdl 49
                                      +++L++e + k++ + ++++   +++h i+GpN +GKst+l+Ai +l
  gi|385805320|ref|YP_005841718.1|  8 VSNLTVEFFKKVALEDITLE-LPPGVHAILGPNSSGKSTLLKAIASL 53
                                      56666666766655555555.469********************988 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   0.1   3.2e-08   4.4e-05       4      55 ..       9      93 ..       7     238 .. 0.66

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 3.2e-08
                            AAA_15  4 kkikikNFR..slkdveidlseeltvliGkNnsGKSsilealdlFlnnkekkn.......................... 54
                                      ++++++ F+  +l+d++++l + +  + G+N+sGKS++l+a+  ++  k   +                          
  gi|385805320|ref|YP_005841718.1|  9 SNLTVEFFKkvALEDITLELPPGVHAILGPNSSGKSTLLKAIASLIPIK---Kgeviydgisisklppkkraqivgycw 84
                                      55666666622478899999999*******************9999977...233566666677777755555555555 PP

                            AAA_15 55 ........k 55
                                              +
  gi|385805320|ref|YP_005841718.1| 85 qnpyqgffE 93
                                      555555442 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   1.3e-07   0.00018      22      46 ..      30      54 ..      19      67 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.3e-07
                            AAA_29 22 kgatlltGpsGsGKSTllDAiqalL 46
                                       g++ + Gp+ sGKSTll Ai+ l+
  gi|385805320|ref|YP_005841718.1| 30 PGVHAILGPNSSGKSTLLKAIASLI 54
                                      45899****************9986 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   3.8e-06    0.0053      17     136 ..      27     165 ..      19     198 .. 0.54

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.8e-06
                          ATPase_2  17 repneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie............eeeekkkleka 81 
                                       + p  +  i Gp +sGK++Llk i++    k+ +viy     ++   k++  i             e ++k+++e  
  gi|385805320|ref|YP_005841718.1|  27 ELPPGVHAILGPNSSGKSTLLKAIASLIPIKKGEVIYDGISISKLPPKKRAQIVgycwqnpyqgffEDSVKREIEFI 103
                                       55677889******************998877788884333333333333333347777777777655555555554 PP

                          ATPase_2  82 l........giavpkaeleeilk.eksklvfkaielllekikkkgkkiiiiiDelqklidlgln 136
                                       l         ++++   ++++++ +  +l      ++  +    + ++ii++De ++     l+
  gi|385805320|ref|YP_005841718.1| 104 LkntnakasEEVLEILGVNKLYEkNPFRLSGGEARRVSIASIVVADQPIILLDEPFNDM--DLD 165
                                       43333333222222222222222222222222333333333334455777777777654..566 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 !   16.5   0.0   2.1e-06    0.0029     240     265 ..      26      51 ..      10      54 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.1e-06
                                       EEE-SSEEEEEE-TTSSHHHHHHHHH CS
                        ABC_ATPase 240 mgipkGvtlIvGggfhGKsTLLeAle 265
                                       + +p Gv +I G++  GKsTLL+A++
  gi|385805320|ref|YP_005841718.1|  26 LELPPGVHAILGPNSSGKSTLLKAIA 51 
                                       56899*******************97 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0    0.0001      0.14       3      21 ..      34      52 ..      32      64 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0001
                            AAA_28  3 vitGgestGKTtlleaLaa 21
                                      +i+G+ s+GK+tll+a+a+
  gi|385805320|ref|YP_005841718.1| 34 AILGPNSSGKSTLLKAIAS 52
                                      79**************995 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   0.00017      0.23       5      35 ..      33      63 ..      30     198 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00017
                            AAA_14  5 lvitGaRrvGKTtllkqlikell.vkkesily 35
                                       +i G+  +GK+tllk ++ +l+ +kk +++y
  gi|385805320|ref|YP_005841718.1| 33 HAILGPNSSGKSTLLKAIA-SLIpIKKGEVIY 63
                                      6899***********9998.555688888887 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00018      0.26      82     130 ..      13      61 ..       3      64 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00018
                                       --TTTHTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                       RsgA_GTPase  82 vsaktkegleelkellkdktsvlvGqSGvGKStLinallpelelktgev 130
                                       v+  +k +le+++ +l   + +++G+   GKStL++a+++   +k gev
  gi|385805320|ref|YP_005841718.1|  13 VEFFKKVALEDITLELPPGVHAILGPNSSGKSTLLKAIASLIPIKKGEV 61 
                                       44446678999999***********************998777776665 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   0.0    0.0002      0.28      28      91 ..      34     109 ..      20     190 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0002
                            AAA_16  28 llsGesGvGKsslvrellralekd.................ggiflrgkcdqlesaipysalaqalareellrqlld 87 
                                        + G+  +GKs+l+++++  +  +                 +   + g c q+    py+ + +   + + ++ +l 
  gi|385805320|ref|YP_005841718.1|  34 AILGPNSSGKSTLLKAIASLIPIKkgeviydgisisklppkKRAQIVGYCWQN----PYQGFFEDSVK-REIEFILK 105
                                       689***************97777744555555555544443233355555555....77665554434.55566666 PP

                            AAA_16  88 eaes 91 
                                       ++++
  gi|385805320|ref|YP_005841718.1| 106 NTNA 109
                                       6444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 1439.77
//
Query:       gi|385805321|ref|YP_005841719.1|  [L=193]
Description: hypothetical protein FFONT_0277 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score 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   14.5   0.4      0.079   13.6   0.4    1.6  1  T_Ag_DNA_bind  Origin of replication binding protein


Domain annotation for each model (and alignments):
>> T_Ag_DNA_bind  Origin of replication binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.4   4.4e-06     0.079      10      67 ..      94     154 ..      78     173 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.4e-06
                     T_Ag_DNA_bind  10 ylsaaifsnktleafliyttkeKlkeLykkll...ekfkvkfkllakyeekavlllitakk 67 
                                        +  ai++ +t+ +f ++t+++K +++++k++     ++ +f++ a ye ++++    ++ 
  gi|385805321|ref|YP_005841719.1|  94 LIFLAIYTLSTVLSFFLFTSTTKNETIEEKIKikvLIYSFNFIYYAIYELQEIINSFKVRG 154
                                       456799*************************965556889999988888887766555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       932  (0.0519828); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1248.05
//
Query:       gi|385805322|ref|YP_005841720.1|  [L=610]
Description: amino acid transporter [Fervidicoccus fontis Kam940]
Scores for complete 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-43  148.1  62.2    3.3e-43  148.1  62.2    3.0  3  AA_permease_2  Amino acid permease
    9.1e-32  110.3  62.2    9.1e-32  110.3  62.2    2.5  2  AA_permease    Amino acid permease


Domain annotation for each model (and alignments):
>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.1  62.2   3.7e-47   3.3e-43       1     423 [.      27     488 ..      27     490 .. 0.82
   2 ?   -4.5   8.4      0.76   6.8e+03       7      52 ..     488     531 ..     474     542 .. 0.71
   3 ?   -1.9   5.5      0.12   1.1e+03       8      55 ..     544     592 ..     538     597 .. 0.73

  Alignments for each domain:
  == domain 1  score: 148.1 bits;  conditional E-value: 3.7e-47
                     AA_permease_2   1 lsllsafalvigsvigsgifvkn..laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkk 75 
                                       l++ + f+++++ +igs+ +++   +++++gpa+il++++a++++ + ++ ++aEl++++p sgGi  y +++ g+ 
  gi|385805322|ref|YP_005841720.1|  27 LTFTDIFLVSLTGMIGSAWLFSAlgALNYMGPAAILSWIVAAILF-VFMIVTFAELGGLFPYSGGIARYNHYTHGPI 102
                                       5678899*********9999888877778***************9.68999******99****************99 PP

                     AA_permease_2  76 vaflsawfnwfayvpvlasilsvaasyllnalgpdlqgn....twltyliaiaililvalinirgikesakiqnilg 148
                                         f+ +w+++++ + + ++ ++++++y   +l+  ++++    t   +++a++++i++++i+++g++++ +++ i++
  gi|385805322|ref|YP_005841720.1| 103 SNFFLSWAYLISSITTSPVEAVAIVEYSSAWLKWAWNPEknvlTPEGMGLAALLIIFFFIIQYIGVSTYQWFNRIIT 179
                                       99*****************9999999998888766666555555577****************************** PP

                     AA_permease_2 149 ilkillpliiliilglitvdgggfsslstetdtffpngwpg..vllgllivlwsfdGfesaanvseevkk..kdvpk 221
                                        lk+++p++++i++   ++dg+ f       + ffp g  +  + + +++v++++ Gfe    ++ e+k+  +dvp+
  gi|385805322|ref|YP_005841720.1| 180 ALKFVIPVLTIILIFTMYFDGRNFMG---LPGGFFPFGAASilTGSIISGVVFAYEGFEEGLMYAGEAKNpqRDVPL 253
                                       *******************9999973...344589998887335778999*****************888779**** PP

                     AA_permease_2 222 aifigllivlvlyllvniaflgvvpddei........anlsnlgsv.....aalffeavg...gk...vvaiivvil 279
                                       +i+ +l +v+ +y+l+++a++g+++++                  +      ++f+  +     +    +a+i++i 
  gi|385805322|ref|YP_005841720.1| 254 GIITALFVVAAIYILLQVAYIGGINWSAArvspgdwtG-------LynawgSSPFYYELVstgVPllvGFAVIIAID 323
                                       **************************998644444431.......33445434444433322222444667777799 PP

                     AA_permease_2 280 ialsllgaintavigssrvlealardgvlPrffakvn.kfgspiraiiltaivslillllfllassaaynfllsvss 355
                                       ++ls +g   ++v +++r+++a+a+ g+lP+ f +++ k+ +p++a+i++ i+++i+l+ f +      + ++svs+
  gi|385805322|ref|YP_005841720.1| 324 AILSPAGTFAAYVGSTARQIFAMAKIGYLPEIFGSIHkKYRTPWVALIFSTIIAIIFLMPFPT-----WYSIMSVSV 395
                                       999**********************************9****************999888876.....59******* PP

                     AA_permease_2 356 lgliisyllliigalilrkkrphlkrpgk.......................ilvaiigalfllfllvalf...... 403
                                        +++ sy+   i+a  l+k  p+lkrp+k                       +             +v+ +      
  gi|385805322|ref|YP_005841720.1| 396 SAAVYSYMTGGITAHALKKLVPDLKRPYKtpfwqlfypaafvvaslfvywsgW------------SVVNVIievlli 460
                                       **************************887777777877765555555554443............333333333333 PP

                     AA_permease_2 404 .......fp.pkgpatqssliytiiltv 423
                                               p +k++++++s+iy+i l+v
  gi|385805322|ref|YP_005841720.1| 461 glpllflGPyGKKLSVSRSFIYAISLFV 488
                                       3333323443677789999999976655 PP

  == domain 2  score: -4.5 bits;  conditional E-value: 0.76
                     AA_permease_2   7 falvigsvigsgifvknlaasggpalilwvwiavligslavllvya 52 
                                       +++ +gs+ig++++v    + g+  +i+++ +++li++++++l+ +
  gi|385805322|ref|YP_005841720.1| 488 VWIGTGSAIGLYYYVL--DGMGIQGFIIYWSLVSLIQIITLSLIWL 531
                                       4666677788888877..3334455677777888888788888876 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.12
                     AA_permease_2   8 alvigsvigsgifvkn.laasggpalilwvwiavligslavllvyaEls 55 
                                       ++++++vig+ +++ + +a+s   + + + +i+++i+sl v ++ + ++
  gi|385805322|ref|YP_005841720.1| 544 LIIYNIVIGIVSYIGSlGALSSPLLPVPYDIIVMIIVSLLVYYIGLKVA 592
                                       6889999**9999998655555555777788888888777777666655 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.3  62.2     1e-35   9.1e-32       2     462 ..      32     493 ..      31     504 .. 0.80
   2 ?   -5.5   6.4       1.3   1.1e+04     119     126 ..     546     553 ..     492     596 .. 0.49

  Alignments for each domain:
  == domain 1  score: 110.3 bits;  conditional E-value: 1e-35
                       AA_permease   2 vlvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfvi 78 
                                       +++ +l g+iG + +++   +l+  Gp +a+l++++a + +++++++++e+  ++p sgg++ y + ++gp   f+ 
  gi|385805322|ref|YP_005841720.1|  32 IFLVSLTGMIGSAWLFSALGALNYMGP-AAILSWIVAAILFVFMIVTFAELGGLFPYSGGIARYNHYTHGPISNFFL 107
                                       678999*********************.888********************************************** PP

                       AA_permease  79 Glnylfswitvlaleltaasiliqfwelvtdlpkawvt..............gavflvvlliinlvgvkvygeaefi 141
                                       ++ yl+s+it+ ++e +a++ + + w      + +w++              +a+++++++ii+++gv  y  +  i
  gi|385805322|ref|YP_005841720.1| 108 SWAYLISSITTSPVEAVAIVEYSSAW------L-KWAWnpeknvltpegmglAALLIIFFFIIQYIGVSTYQWFNRI 177
                                       ***************66655555555......4.78888888888*******99*********************** PP

                       AA_permease 142 lalikiiaiiafiivgiillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielv 218
                                       ++ +k+++ + +ii+ + + ++g++        +g +g+    ++p g a++ +       s+++ vvfa+ G+e +
  gi|385805322|ref|YP_005841720.1| 178 ITALKFVIPVLTIILIFTMYFDGRNF-------MGLPGG----FFPFGAASILT------GSIISGVVFAYEGFEEG 237
                                       ***********************954.......558888....77777223322......35667799********* PP

                       AA_permease 219 aiiagEvkdPeksiPkailqvviritifYvlsllligllvprndlgllndsasa......aspfvifikesgvs... 286
                                        + agE+k+P++++P +i+ +++ ++ +Y+l+ ++++ ++++++  +  +  ++      +spf + ++++gv+   
  gi|385805322|ref|YP_005841720.1| 238 LMYAGEAKNPQRDVPLGIITALFVVAAIYILLQVAYIGGINWSAARVSPGDWTGlynawgSSPFYYELVSTGVPllv 314
                                       ********************************************88888777779*****************98222 PP

                       AA_permease 287 vlaplinaviltaalssansslysasRvlyslakdglaP.kvlkkvskrgvPlraillsmiisllalllaslnlaap 362
                                       ++a++i++  +++  ++  +++ s+ R+++++ak g++P  +++ ++k++ P++a+++s+ii+ ++l+     ++  
  gi|385805322|ref|YP_005841720.1| 315 GFAVIIAIDAILSPAGTFAAYVGSTARQIFAMAKIGYLPeIFGSIHKKYRTPWVALIFSTIIAIIFLMP----FP-- 385
                                       45667777777777778899999****************7777888999******************32....22.. PP

                       AA_permease 363 ivfnfllaisaliglivwlliilsyl......rfRkalkyqgrsi...eelgfkaallplgvilvlaaliiillila 430
                                       + + +++ ++ ++  +  +  i++++       +++ +k+  +++   + + + + ++ +  ++v+ ++i +lli  
  gi|385805322|ref|YP_005841720.1| 386 TWYSIMSVSVSAAVYSYMTGGITAHAlkklvpDLKRPYKTPFWQLfypAAFVVASLFVYWSGWSVVNVIIEVLLIGL 462
                                       22333333333333333333333333221122566666666554322133444444444555666667777777766 PP

                       AA_permease 431 lyayltvkkgpkdwgaasfaaaylivllflii 462
                                         ++l  + g k + + sf++a++ ++++   
  gi|385805322|ref|YP_005841720.1| 463 PLLFLG-PYGKKLSVSRSFIYAISLFVWIGTG 493
                                       666666.8999999999999999999998765 PP

  == domain 2  score: -5.5 bits;  conditional E-value: 1.3
                       AA_permease 119 vflvvlli 126
                                       +  +v+ i
  gi|385805322|ref|YP_005841720.1| 546 IYNIVIGI 553
                                       22222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (610 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1035  (0.0577277); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); 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):               2  [number of targets reported over threshold]
# CPU time: 0.86u 0.34s 00:00:01.20 Elapsed: 00:00:00.51
# Mc/sec: 3570.18
//
Query:       gi|385805323|ref|YP_005841721.1|  [L=308]
Description: Dihydroorotate dehydrogenase [Fervidicoccus fontis Kam940]
Scores for 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-54  184.2   3.7    3.4e-54  184.1   3.7    1.0  1  DHO_dh        Dihydroorotate dehydrogenase
      5e-10   39.0   0.2      4e-07   29.4   0.0    2.1  2  Dus           Dihydrouridine synthase (Dus)
    4.2e-06   26.4   0.6     0.0085   15.5   0.0    2.5  3  NMO           Nitronate monooxygenase
      1e-05   25.2   1.0     0.0023   17.4   0.0    2.9  3  His_biosynth  Histidine biosynthesis protein
    0.00056   19.2   0.2      0.024   13.8   0.0    2.3  2  IGPS          Indole-3-glycerol phosphate synthase
     0.0012   17.9   1.5     0.0039   16.3   0.0    2.3  3  IMPDH         IMP dehydrogenase / GMP reductase domain
     0.0033   16.9   0.7       0.17   11.3   0.1    3.3  4  G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
     0.0096   15.1   3.4       0.25   10.5   0.5    2.9  3  DUF561        Protein of unknown function (DUF561)
  ------ inclusion threshold ------
      0.052   12.2   0.8       0.29    9.8   0.1    2.0  2  DHDPS         Dihydrodipicolinate synthetase family
      0.088   12.4   0.0        1.3    8.6   0.0    2.3  3  DeoC          DeoC/LacD family aldolase
       0.13   12.1   0.0       0.29   10.9   0.0    1.5  1  Ligase_CoA    CoA-ligase
        1.3    8.3   3.5         12    5.2   0.0    2.9  3  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 !  184.1   3.7   2.3e-57   3.4e-54       2     281 ..       7     274 ..       6     290 .. 0.88

  Alignments for each domain:
  == domain 1  score: 184.1 bits;  conditional E-value: 2.3e-57
                                       G-EEETTEEESSSEEE-TTSSTTS.SSHHHHHCTTSSEEEEEEE-SS-B--S-S--EEEETTCTEEEE---S-BS-H CS
                            DHO_dh   2 latkvlglkfknpiglAaGfdkeg.eeilkllklgfgaieigsvtpkpqeGnpkPrvfrlkedrsvlNslGlnneGl 77 
                                       l+ +++g+ +knp+++A+G+ ++  e+i++l++ gfga+  +++tp p+ Gn+ P +++l+++  ++N++Gl+n+G 
  gi|385805323|ref|YP_005841721.1|   7 LNIELAGIILKNPLMNASGILGQNkEAIKRLYEYGFGAVVSKTITPMPRIGNKPPIILSLPNG-GLINAVGLENPGK 82 
                                       67889999************987615678899*******************************.************9 PP

                                       HHHHHHHHHHHHHHHCC.CEEEEEEE-TTSS.HHHHHHHHHHHHG.GGESEEEEES-SCTCC.TSCCCGCHHHHHHH CS
                            DHO_dh  78 davlekllkrrkeqeekkelginlskakktenavddyvevvrkig.pfadilelNvSsPntp.glrdlqekeelkai 152
                                        ++ e +++ ++      +++i++s+ +++   +d++ ev+++ +   a+++elN+S+P+t+ ++ ++++++    +
  gi|385805323|ref|YP_005841721.1|  83 GTIKELVEEAKE-----LNIPIIVSVGGTN---EDEFSEVAKEAEiSGANAIELNLSCPHTKgYGLEIGADPRNVFN 151
                                       998876665553.....369*********9...************999**************8899*********** PP

                                       HHHHHHHHHSSEEEEEE-SSSSHHHHHHHHHHHHHHTECEEEE...BSEE--CTTCCGCCCCTTSSEEEEEGGGHHH CS
                            DHO_dh 153 llkvvkevskvpvlvKlaPdltdeekkdiadvllelkldgiivtNttvqrlaidlkseknvkanktGGlsGkalkdi 229
                                       ++k v+ + k+pv++Kl  + +  e   +a ++ +  l  i+    tv+   id+ + k+v  n  GGlsG+++ +i
  gi|385805323|ref|YP_005841721.1| 152 VVKNVSSIIKIPVIAKLGLNDKIVEASGKALEAGAKALGLIN----TVKAIYIDVYTLKPVLSNIHGGLSGPPIHPI 224
                                       *****************9876666666677777777777777....666667************************* PP

                                       HHHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGT CS
                            DHO_dh 230 alkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegp 281
                                       a++vi+++y++ +    iIg+GG++  +Da e i aGA ++q+++al+ ++ 
  gi|385805323|ref|YP_005841721.1| 225 AVRVIYDVYREYR--AEIIGSGGVKDWKDAAEFISAGAKAIQIGSALISNDD 274
                                       ***********99..899*****************************98763 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   2.7e-10     4e-07      40     154 ..      81     188 ..      69     191 .. 0.81
   2 !    7.6   0.0    0.0012       1.8     173     218 ..     227     271 ..     220     279 .. 0.89

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 2.7e-10
                                       HHHHHHH-GGGGGT..SCEEEEEE-S-HHHHHHHHHHHHHTT-SCEEEEESSTTEEETTEEEGGGGGGSHHHHHHHH CS
                               Dus  40 ekvrirmlseeeee..tplavQlggsdpallaeaAklvadlgadeIdlNvGCPskkvtrggaGaaLlrkpdlvaqiv 114
                                        k +i++l ee +e   p++v +gg + ++  e Ak ++ +ga++I+lN+ CP  k  + ++Ga    +p+ v ++v
  gi|385805323|ref|YP_005841721.1|  81 GKGTIKELVEEAKElnIPIIVSVGGTNEDEFSEVAKEAEISGANAIELNLSCPHTKGYGLEIGA----DPRNVFNVV 153
                                       566677777776666789***********************************99988888886....9******** PP

                                       HHHHCCSSS-EEEEEESESSTTTC.HHHHHHHHHHCT-SE CS
                               Dus 115 kavvkaveiPvtvkirigiddeeenalelakiveaaGaqa 154
                                       k+v + ++iPv +k  +  +     ++e+  ++ +aGa+a
  gi|385805323|ref|YP_005841721.1| 154 KNVSSIIKIPVIAKLGLNDK-----IVEASGKALEAGAKA 188
                                       ************99877655.....455555555555555 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0012
                                       HHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCC CS
                               Dus 173 eaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgalg 218
                                       + I++v ++ +  +i+ G++kd++da + ++  Ga+++ ig +  +
  gi|385805323|ref|YP_005841721.1| 227 RVIYDVYREYRAEIIGSGGVKDWKDAAEFISA-GAKAIQIGSALIS 271
                                       67999*************************99.******9988765 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.5   2.3e+03     180     203 ..      81     107 ..      68     128 .. 0.64
   2 !    8.5   0.1   0.00076       1.1     178     218 ..     145     188 ..     131     193 .. 0.77
   3 !   15.5   0.0   5.7e-06    0.0085     193     230 ..     237     274 ..     211     281 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.5
                               NMO 180 glfaLvpqvldavd..iPviA.aGGii 203
                                       g  ++ + v +a +  iP+i   GG +
  gi|385805323|ref|YP_005841721.1|  81 GKGTIKELVEEAKElnIPIIVsVGGTN 107
                                       444555666666666688764146654 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00076
                               NMO 178 d.kglfaLvpqvldavdiPviAaGGiidrrgvaa...aLalGAsg 218
                                       d ++ f++v++v + ++iPviA  G++d+  v+a   aL +GA++
  gi|385805323|ref|YP_005841721.1| 145 DpRNVFNVVKNVSSIIKIPVIAKLGLNDKI-VEAsgkALEAGAKA 188
                                       257899********************9963.44333477777776 PP

  == domain 3  score: 15.5 bits;  conditional E-value: 5.7e-06
                               NMO 193 diPviAaGGiidrrgvaaaLalGAsgvqigtrfLltke 230
                                          +i  GG+ d ++ a  +++GA+++qig++++  ++
  gi|385805323|ref|YP_005841721.1| 237 RAEIIGSGGVKDWKDAAEFISAGAKAIQIGSALISNDD 274
                                       46699***************************997665 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.012        18     183     216 ..      89     122 ..      72     126 .. 0.78
   2 ?   -0.8   0.0      0.57   8.4e+02      63      83 ..     151     171 ..     143     198 .. 0.57
   3 !   17.4   0.0   1.6e-06    0.0023      61     110 ..     225     274 ..     216     285 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.012
                                       HHHHHHHHSSEEEEESS--SHHHHHHHHHTTC.SE CS
                      His_biosynth 183 tkelaeavkipviasGGvgsledlkelksegv.da 216
                                       + e a++++ip+i+s G ++ +++ e+++e   ++
  gi|385805323|ref|YP_005841721.1|  89 V-EEAKELNIPIIVSVGGTNEDEFSEVAKEAEiSG 122
                                       3.446899******************996654366 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.57
                                       HHHHHHHHH-SSEEEEESSSS CS
                      His_biosynth  63 dlveeiaeevfipvqvGGGIr 83 
                                       ++v+++ + ++ipv    G +
  gi|385805323|ref|YP_005841721.1| 151 NVVKNVSSIIKIPVIAKLGLN 171
                                       445555555555555555543 PP

  == domain 3  score: 17.4 bits;  conditional E-value: 1.6e-06
                                       HHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-TH CS
                      His_biosynth  61 nldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknpe 110
                                          ++  + +e ++++   GG+++ +d++e ++aga+ + ig+a ++n +
  gi|385805323|ref|YP_005841721.1| 225 AVRVIYDVYREYRAEIIGSGGVKDWKDAAEFISAGAKAIQIGSALISNDD 274
                                       56788888888888888889999999999999999999999999888765 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.2     0.036        54     146     188 ..      84     127 ..      78     130 .. 0.79
   2 !   13.8   0.0   1.6e-05     0.024     210     253 ..     238     281 ..     226     282 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.036
                                       HHHHHHHHHCCTT-EEEEEESSHHHHHHHH.HTT-SEEEEESEE CS
                              IGPS 146 eleelaeaakslglevLvEvhdeeeleral.klgakiiGvNnRn 188
                                       +++el+e+ak+l++ ++v v  ++e e    + +a+i G N  +
  gi|385805323|ref|YP_005841721.1|  84 TIKELVEEAKELNIPIIVSVGGTNEDEFSEvAKEAEISGANAIE 127
                                       5799****************876666654337788888888655 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.6e-05
                                       SEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC-TTHHHHHHH CS
                              IGPS 210 vllvaeSGiktredveklkeegvnafLvGeslmrqedvekaire 253
                                       + ++   G+k+ +d+ ++ ++g++a+ +G++l++++d +++i++
  gi|385805323|ref|YP_005841721.1| 238 AEIIGSGGVKDWKDAAEFISAGAKAIQIGSALISNDDPKHTIKS 281
                                       5678889********************************99986 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   0.0      0.78   1.2e+03     194     216 ..      83     106 ..      73     126 .. 0.64
   2 ?   -0.8   0.1      0.41   6.1e+02     197     232 ..     150     188 ..     144     193 .. 0.71
   3 !   16.3   0.0   2.6e-06    0.0039     195     242 ..     225     272 ..     215     284 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.78
                                       HHHHHHHHHHCTCT-EEE.EES-- CS
                                       xxxxxxxxxxxxxxxxxx.xxxxx RF
                             IMPDH 194 tAvaevaeaakkagvpvi.aDGGi 216
                                         + e +e ak+ ++p+i + GG 
  gi|385805323|ref|YP_005841721.1|  83 GTIKELVEEAKELNIPIIvSVGGT 106
                                       556677777777777766233444 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.41
                                       HHHHH.HHCTCT-EEEEES---S..HHHHHHHHHTT-SE CS
                                       xxxxx.xxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx RF
                             IMPDH 197 aevae.aakkagvpviaDGGiky..sgdivkAlaaGada 232
                                       ++v++ + +  ++pvia  G++    +   kAl aGa+a
  gi|385805323|ref|YP_005841721.1| 150 FNVVKnVSSIIKIPVIAKLGLNDkiVEASGKALEAGAKA 188
                                       555552445558999999998651156778999999987 PP

  == domain 3  score: 16.3 bits;  conditional E-value: 2.6e-06
                                       HHHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCCCTTB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 195 AvaevaeaakkagvpviaDGGikysgdivkAlaaGadavmlGsllagt 242
                                       Av  ++++ +++  ++i  GG+k  +d +  ++aGa+a+ +Gs l + 
  gi|385805323|ref|YP_005841721.1| 225 AVRVIYDVYREYRAEIIGSGGVKDWKDAAEFISAGAKAIQIGSALISN 272
                                       788889999**********************************99765 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 ?   -1.4   0.0      0.88   1.3e+03      72     165 ..      23      45 ..      16      50 .. 0.56
   2 ?    0.3   0.0      0.27   4.1e+02      79     122 ..      85     128 ..      83     130 .. 0.82
   3 ?    1.1   0.1      0.15   2.3e+02     124     164 ..     146     188 ..     142     198 .. 0.77
   4 !   11.3   0.1   0.00011      0.17      86     168 ..     186     266 ..     174     270 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.88
                                       -SEEEES-HHHHHHHHHTT--EEEEEE--SHHHHHHHHHHHHHHT-SEEEEESGGGHHHHCTSTTS...EEEEESS- CS
                      G3P_antiterm  72 vdGiistksslikkakklglltiqrlfliDssalekalkqiekskpdavevlPglvpkvikeikkelkipiiaGGLi 148
                                       ++Gi+  +++ ik+  + g+                                                         
  gi|385805323|ref|YP_005841721.1|  23 ASGILGQNKEAIKRLYEYGF--------------------------------------------------------- 42 
                                       55555555555555555554......................................................... PP

                                       -SHHHHHHHCTT.SSEE CS
                      G3P_antiterm 149 etkedveealkaGaiav 165
                                                      av
  gi|385805323|ref|YP_005841721.1|  43 --------------GAV 45 
                                       ..............444 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.27
                                       -HHHHHHHHHTT--EEEEEE--SHHHHHHHHHHHHHHT-SEEEE CS
                      G3P_antiterm  79 ksslikkakklglltiqrlfliDssalekalkqiekskpdavev 122
                                        ++l+++ak+l++  i  +  +  + ++++ k +e s ++a+e+
  gi|385805323|ref|YP_005841721.1|  85 IKELVEEAKELNIPIIVSVGGTNEDEFSEVAKEAEISGANAIEL 128
                                       56789999999999999998888888888888888888888886 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.15
                                       SGGGHHHHCTSTTS...EEEEE.SS--SH.HHHHHHCTT.SSE CS
                      G3P_antiterm 124 PglvpkvikeikkelkipiiaG.GLietk.edveealkaGaia 164
                                       P  v +v+k++++ +kip+ia  GL ++  e   +al+aGa a
  gi|385805323|ref|YP_005841721.1| 146 PRNVFNVVKNVSSIIKIPVIAKlGLNDKIvEASGKALEAGAKA 188
                                       5566789999**********96577766414445788888877 PP

  == domain 4  score: 11.3 bits;  conditional E-value: 0.00011
                                       HHHTT--EEEEEE--SHHHHHHHHHHHHHHT-SEEEEESGGGHHHHCTSTTS...EEEEESS--SHHHHHHHCTT.S CS
                      G3P_antiterm  86 akklglltiqrlfliDssalekalkqiekskpdavevlPglvpkvikeikkelkipiiaGGLietkedveealkaGa 162
                                       ak lgl+   +   iD  +l+ +l++i+        + P    +vi ++ +e + +ii +G +++ +d  e ++aGa
  gi|385805323|ref|YP_005841721.1| 186 AKALGLINTVKAIYIDVYTLKPVLSNIHG-GLSGPPIHPIA-VRVIYDVYREYRAEIIGSGGVKDWKDAAEFISAGA 260
                                       55566666666666666666666666653.33333455544.58899999999************************ PP

                                       SEEEE- CS
                      G3P_antiterm 163 iavsts 168
                                        a+  +
  gi|385805323|ref|YP_005841721.1| 261 KAIQIG 266
                                       **9865 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.14   2.2e+02      52      99 ..      88     139 ..      84     154 .. 0.60
   2 !   10.5   0.5   0.00017      0.25     175     221 ..     150     199 ..     144     219 .. 0.79
   3 ?    2.6   0.0     0.042        63     177     226 ..     228     278 ..     220     291 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.14
                            DUF561  52 lvkkvksvsniPiCvs..aveaklll....eavkaGadlveiGnfdslYeqgrk 99 
                                       lv++ k+  niPi vs  + +  ++     ea  +Ga+ +e+ n  + +++g+ 
  gi|385805323|ref|YP_005841721.1|  88 LVEEAKE-LNIPIIVSvgGTNEDEFSevakEAEISGANAIEL-NLSCPHTKGYG 139
                                       5555554.4777777633344444431111456678888776.66666666665 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00017
                            DUF561 175 lastyeiskkvslPvicasGlsdvtvpl...alslgasGiGigsavskln 221
                                       +  + ++s+ +++Pvi+  Gl+d  v+    al++ga  +G+ ++v+ ++
  gi|385805323|ref|YP_005841721.1| 150 FNVVKNVSSIIKIPVIAKLGLNDKIVEAsgkALEAGAKALGLINTVKAIY 199
                                       5667899***************98877544489*********99998765 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.042
                            DUF561 177 styeiskkvslPvicasGlsdvtvpla.lslgasGiGigsavsklndeeem 226
                                        +y + ++ +  +i + G++d       +s+ga  i igsa+ + +d ++ 
  gi|385805323|ref|YP_005841721.1| 228 VIYDVYREYRAEIIGSGGVKDWKDAAEfISAGAKAIQIGSALISNDDPKHT 278
                                       679999999999********98766552689*********98777665554 PP

>> DHDPS  Dihydrodipicolinate synthetase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00019      0.29      62     100 ..      88     126 ..      80     129 .. 0.83
   2 ?    0.4   0.1      0.15   2.2e+02      70     103 ..     161     192 ..     146     194 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00019
                                       HHHHHHTTSSEEEEE---SSHHHHHHHHHCCCCCT-SEE CS
                             DHDPS  62 iaveaakgripviagvGsnstseaiklakkaeeaGadgv 100
                                        + ea + +ip+i  vG+ + +e  ++ak+ae +Ga+++
  gi|385805323|ref|YP_005841721.1|  88 LVEEAKELNIPIIVSVGGTNEDEFSEVAKEAEISGANAI 126
                                       334444559***************************987 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.15
                                       SSEEEEE---SSHHHHHHHHHCCCCCT-SEEEEE CS
                             DHDPS  70 ripviagvGsnstseaiklakkaeeaGadgvlav 103
                                       +ipvia+ G n  +  ++++ ka eaGa+++ ++
  gi|385805323|ref|YP_005841721.1| 161 KIPVIAKLGLN--DKIVEASGKALEAGAKALGLI 192
                                       89*******95..678999999999999987655 PP

>> DeoC  DeoC/LacD family aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0   0.00085       1.3     178     223 ..      79     123 ..      29     145 .. 0.77
   2 ?   -3.5   0.0       4.2   6.3e+03     152     166 ..     173     187 ..     169     213 .. 0.73
   3 ?    1.2   0.0      0.16   2.4e+02     184     218 ..     226     263 ..     215     280 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00085
                                       B.HHHHHHHHHHHHHCHSSTEEEEETTSSHHHHHHHHHHHHHHHTH CS
                              DeoC 178 nateedaevfkdvikaapvpgvvlsGGvseedfletvedAvkeaga 223
                                       n +++ +++  + +k+ ++p +v  GG +e +f+e++++A   +ga
  gi|385805323|ref|YP_005841721.1|  79 NPGKGTIKELVEEAKELNIPIIVSVGGTNEDEFSEVAKEAE-ISGA 123
                                       5566677777778889999988888999************9.7877 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4.2
                                       HHHHHHHHHTCCT-S CS
                              DeoC 152 lvaeAarvsaelGaD 166
                                       ++ eA+  + e+Ga+
  gi|385805323|ref|YP_005841721.1| 173 KIVEASGKALEAGAK 187
                                       566666666666654 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.16
                                       HHHHHHHHHCHSSTEEEEETTS....SHHHHHHHHHHHH CS
                              DeoC 184 aevfkdvikaapvpgvvlsGGv....seedfletvedAv 218
                                       ++v+ dv ++ + + ++ sGGv    ++++f ++  +A+
  gi|385805323|ref|YP_005841721.1| 226 VRVIYDVYREYRAE-IIGSGGVkdwkDAAEFISAGAKAI 263
                                       56677777777777.888888854444444444444443 PP

>> Ligase_CoA  CoA-ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0    0.0002      0.29      92     137 ..      85     123 ..      73     135 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0002
                                       HHHHHHHHHHTT...--S-EEEEEECTTHH.....HHHHHHHTTTS CS
                        Ligase_CoA  92 aaellkaikeakaegrelpvvarvaGteadpqelseqakaleeagv 137
                                       ++el++++ke+     ++p++++v Gt++d  e se ak  e +g+
  gi|385805323|ref|YP_005841721.1|  85 IKELVEEAKEL-----NIPIIVSVGGTNED--EFSEVAKEAEISGA 123
                                       45566666666.....6*************..55555555555554 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.23   3.5e+02     166     187 ..      84     108 ..      66     136 .. 0.60
   2 ?    1.7   0.5     0.087   1.3e+02     167     206 ..     153     195 ..     113     204 .. 0.72
   3 ?    5.2   0.0    0.0078        12     172     216 ..     234     278 ..     200     287 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.23
                                       HHHHHHHH-...SS-BEEES---SH CS
                              ThiG 166 alkiiieea...kvPvivDAGigsp 187
                                       ++k ++eea   ++P+iv  G  + 
  gi|385805323|ref|YP_005841721.1|  84 TIKELVEEAkelNIPIIVSVGGTNE 108
                                       46666655433389****9985443 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.087
                                       HHHHHHH-SS-BEEES---SH..HHHHHHHHTT-SEE.EESHH CS
                              ThiG 167 lkiiieeakvPvivDAGigsp..sdaaqamelGadav.llnta 206
                                       +k + + +k+Pvi   G+     +   +a+e Ga+a+ l+nt 
  gi|385805323|ref|YP_005841721.1| 153 VKNVSSIIKIPVIAKLGLNDKivEASGKALEAGAKALgLINTV 195
                                       444555669****9999976421445689*****998678875 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.0078
                                       HH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHH CS
                              ThiG 172 eeakvPvivDAGigspsdaaqamelGadavllntavaeakdpvam 216
                                       +e +  +i   G+   +daa+ +  Ga+a+ + +a+ + +dp + 
  gi|385805323|ref|YP_005841721.1| 234 REYRAEIIGSGGVKDWKDAAEFISAGAKAIQIGSALISNDDPKHT 278
                                       455677888899****************************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 1775.92
//
Query:       gi|385805324|ref|YP_005841722.1|  [L=418]
Description: dihydroorotase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-15   57.5   0.0    1.1e-14   54.6   0.0    2.1  1  Amidohydro_1  Amidohydrolase family
    1.1e-05   25.1   0.0        0.1   12.1   0.0    2.1  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 !   54.6   0.0   1.2e-18   1.1e-14       1     344 []      47     402 ..      47     402 .. 0.67

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 1.2e-18
                                       EEEE-EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTH.....HHHHHHHHHHT CS
                      Amidohydro_1   1 ivlPGlIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattst.....giealleaaee 72 
                                       i lPG+ID+H Hl+               +  ++e  esg+k+a ++G+t + dm++t ++     ++++ ++++ e
  gi|385805324|ref|YP_005841722.1|  47 IALPGFIDLHAHLR-------------GLELSYKEDEESGTKAAARGGFTGIVDMPNTKPKidntkSLNLKIKSLYE 110
                                       579**********8.............3456799***********************99999977766666665555 PP

                                       .SSSEEEEEEESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEE.EEEEECGTCCSHHHHHHHHHHHHHHHTTE CS
                      Amidohydro_1  73 .lplglrilggkvsldrgsaetskasreklkagaaetikgkadgvvk.valapheapafsdeelkealkeakkrdlp 147
                                        + ++++i +         ++   + +e lka           +vv+  +l p+e+  ++  e+ + + +a  + +p
  gi|385805324|ref|YP_005841722.1| 111 kAYVNFGISVT-------IGKDVDDFIEMLKAK----------EVVSvGELFPEEHERLP--EILKSF-VANGIEKP 167
                                       44444444433.......223334455555444..........47787889999888886..565666.6******* PP

                                       EEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCC....HHTTTHCCEE.EHCTCEEEHHHHHHHHHHHHHHCEE... CS
                      Amidohydro_1 148 vaiHaletkgevedaeaafgetiehgthlevaes....lglldeikli.lahgvhltpteaellkerlkeagva... 216
                                       + iH+ + ++   ++ ++      +  + + +      + +l+++++    h++h+t +   ++ e +k+ + +   
  gi|385805324|ref|YP_005841722.1| 168 IIIHLEHKDALG-ECGKGKR--WACRPIESEMLAlkeiGYMLESARIKaKLHITHVTNK---YVYEMAKKYKFTtdt 238
                                       *****8877777.4444444..3333344443333333223333222125566666644...333444444444555 PP

                                       ....HHHHHHHH..............SEHHHHHHHHHHHHTSCEEEEEECT...............TSSCCGGHHHH CS
                      Amidohydro_1 217 ....hcpfsnsi..............lrsgrealrkaldeGvkvglgtDga...............asgnslnllee 260
                                           ++ +s++                r+    l  +l    + +++tD+a               +          
  gi|385805324|ref|YP_005841722.1| 239 cphyLYLSSEDEekfgclakvnpplrTRDIAKELIGLLPH--FDAISTDHAphsieekslpfekcpS---------- 303
                                       6887555555557788888877666433333333444443..689****999997777766665553.......... PP

                                       HHHHHHHHHHCCTT.TTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECCCT..............C CS
                      Amidohydro_1 261 lrlalklqrgllye.deegglslkealrmaTingAkalglddkvGsievGkdADlvvvdldi..............l 322
                                       ++  ++++ +l  + + +g l l++++++ ++++ k+l++    G ++ G +A+ +vvdld+               
  gi|385805324|ref|YP_005841722.1| 304 GIASIEIAVPLMINlVNKGILNLEDLIQLLSMGPHKILNMKPGWGCFDIGCKANYTVVDLDKewkidsskfytkarF 380
                                       33333333333334456899****************************************44455588999999999 PP

                                       GGGTTTCTSEEEEEEEETTEEE CS
                      Amidohydro_1 323 aafvglkkdgnvkkvivkGklv 344
                                       +++ gl  +g v ++i++G++v
  gi|385805324|ref|YP_005841722.1| 381 SPYDGLIIKGDVSSTIINGTVV 402
                                       99999999999999999*9887 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   1.1e-05       0.1       3      25 ..      40      63 ..      38      87 .. 0.70
   2 !   11.1   0.0   2.2e-05       0.2     408     473 .]     324     403 ..     320     403 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.1e-05
                      Amidohydro_3  3 iDakGr.lvlPGFvDsHtHlaggg 25
                                      iD++ + + lPGF+D H+Hl g  
  gi|385805324|ref|YP_005841722.1| 40 IDLREKgIALPGFIDLHAHLRGLE 63
                                      5665532789*********65533 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 2.2e-05
                      Amidohydro_3 408 lsleealalyTrgpAkalgledrkGtLevGadADlvvld.adpldvdppelaear.............vrltvvdGr 470
                                       l le++++l++ gp+k+l++    G   +G++A+++v d ++  ++d ++ +++              v+ t+++G 
  gi|385805324|ref|YP_005841722.1| 324 LNLEDLIQLLSMGPHKILNMKPGWGCFDIGCKANYTVVDlDKEWKIDSSKFYTKArfspydgliikgdVSSTIINGT 400
                                       6799******************9****************99999999998888779********************* PP

                      Amidohydro_3 471 vvy 473
                                       vvy
  gi|385805324|ref|YP_005841722.1| 401 VVY 403
                                       **8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); 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: 0.68u 0.33s 00:00:01.01 Elapsed: 00:00:00.54
# Mc/sec: 2333.98
//
Query:       gi|385805325|ref|YP_005841723.1|  [L=268]
Description: oxidoreductase FAD/NAD(P)-binding domain-containing protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.9e-09   35.4   4.3    6.9e-09   35.4   4.3    1.9  2  DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydr
  ------ inclusion threshold ------
      0.081   12.4   0.0       0.24   10.8   0.0    1.7  2  ANAPC4           Anaphase-promoting complex, cyclosome, subun
       0.93    9.5   9.8        2.1    8.4   5.4    2.4  2  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   0.3      0.55   3.3e+03       6      12 ..     175     181 ..     174     182 .. 0.86
   2 !   35.4   4.3   1.2e-12   6.9e-09       5      41 ..     229     259 ..     225     260 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.55
                                       SSSSSS- CS
                   DHODB_Fe-S_bind   6 CGvGaCl 12 
                                       C +G C+
  gi|385805325|ref|YP_005841723.1| 175 CSYGKCG 181
                                       999***8 PP

  == domain 2  score: 35.4 bits;  conditional E-value: 1.2e-12
                                       SSSSSSS-TTEEEETTCTT.CEEETTTT-CEEECCCB CS
                   DHODB_Fe-S_bind   5 aCGvGaClgCvvktkggdggeykrvCkdGPvFdadev 41 
                                       +CG+G+C++C +k +      +k +C+dGPvF+ +ev
  gi|385805325|ref|YP_005841723.1| 229 KCGMGICGSCYIKGT------TKLMCSDGPVFECSEV 259
                                       8*************7......589*********9998 PP

>> ANAPC4  Anaphase-promoting complex, cyclosome, subunit 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   4.1e-05      0.24     137     194 ..       2      57 ..       1      60 [. 0.95
   2 ?   -1.7   0.0      0.29   1.7e+03      14      45 ..     149     180 ..     144     196 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 4.1e-05
                            ANAPC4 137 seLrGlakweeryeslgldeeeidelletakslllkaeellqviseelkqfkaFinWl 194
                                       + LrG+ k+e+++  +++ + +i++  e a+++ l +   l+++s e k f+ F+ W+
  gi|385805325|ref|YP_005841723.1|   2 QNLRGIGKMEKKK--FEIKPVKIERNEEVAENTFLISFLPLEDLSLEVKPFNFFMVWI 57 
                                       679********97..******************************************8 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.29
                            ANAPC4  14 kkelvelarkssqlqslleyinetlkeiseew 45 
                                       + el e+ + + ++++l ++i  t ++   ++
  gi|385805325|ref|YP_005841723.1| 149 GSELFEVTKIYGKMNNLKNFIIYTEDCSYGKC 180
                                       67889999999999999998877666655555 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 ?    2.6   0.1     0.022   1.3e+02      41      59 ..     164     182 ..     150     188 .. 0.83
   2 ?    8.4   5.4   0.00035       2.1      49      73 ..     227     249 ..     199     253 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.022
                            Fer2_3  41 evdptlafrasCregiCGs 59 
                                       ++++ + +  +C+ g CG+
  gi|385805325|ref|YP_005841723.1| 164 NLKNFIIYTEDCSYGKCGK 182
                                       4578899***********7 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00035
                            Fer2_3  49 rasCregiCGscavainGkptlaCt 73 
                                         +C+ giCGsc   i G+++l+C+
  gi|385805325|ref|YP_005841723.1| 227 LTKCGMGICGSC--YIKGTTKLMCS 249
                                       479*********..689*******7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); 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: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1631.04
//
Query:       gi|385805326|ref|YP_005841724.1|  [L=161]
Description: aspartate carbamoyltransferase regulatory subunit [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-34  117.4   2.9    2.6e-34  117.4   2.9    1.6  2  PyrI      Aspartate carbamoyltransferase regulatory chain, al
    1.3e-17   63.4   1.3    1.3e-17   63.4   1.3    1.7  2  PyrI_C    Aspartate carbamoyltransferase regulatory chain, me
  ------ inclusion threshold ------
       0.11   12.6   0.2       0.11   12.6   0.2    1.8  2  zf-ACC    Acetyl-coA carboxylase zinc finger domain


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 !  117.4   2.9   4.3e-38   2.6e-34       2      93 ..       8      98 ..       7      99 .. 0.96
   2 ?   -2.1   0.1      0.78   4.6e+03      50      57 ..     148     155 ..     116     160 .. 0.60

  Alignments for each domain:
  == domain 1  score: 117.4 bits;  conditional E-value: 4.3e-38
                                      -----SCEEEEEEEETT-HHHHHHHCT--T...TS-EEEEEEEEETTTEEEEEEEEET----HHHHHHHCCC-TT-EEE CS
                              PyrI  2 kvkkienGiViDHIkagkalkvlklLkldklkseekvaiiknvkskklgkKdiikiegkelseeeldklaliapnatin 80
                                       v+ki++G+ViDHI+agka+++l++L++++ ++++++aii+nv+s+klgkKdiikiegk l+ +++d+++liap+at+n
  gi|385805326|ref|YP_005841724.1|  8 VVSKIKHGTVIDHIPAGKAMNILSVLGIRG-EKGDRIAIIMNVESEKLGKKDIIKIEGKWLEPRDFDVISLIAPSATVN 85
                                      69***************************9.5566******************************************** PP

                                      EEETTEEEEEE-- CS
                              PyrI 81 iIkdgevveKkkv 93
                                      i++++evv+K+kv
  gi|385805326|ref|YP_005841724.1| 86 IVENFEVVKKYKV 98
                                      ***********98 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.78
                                       EEEEEEEE CS
                              PyrI  50 gkKdiiki 57 
                                        k di+k+
  gi|385805326|ref|YP_005841724.1| 148 YKDDIVKL 155
                                       23455555 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 ?   -1.8   0.1       0.5     3e+03      19      32 ..      85      98 ..      81     100 .. 0.74
   2 !   63.4   1.3   2.2e-21   1.3e-17       1      48 []     103     152 ..     103     152 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.5
                                      S-.-EEEEEETTTT CS
                            PyrI_C 19 pveskFkvedkekv 32
                                      ++ ++F+v++k kv
  gi|385805326|ref|YP_005841724.1| 85 NIVENFEVVKKYKV 98
                                      67889999888776 PP

  == domain 2  score: 63.4 bits;  conditional E-value: 2.2e-21
                                       EEESSS--S-TTBGGGT..TS-.-EEEEEETTTTEEEETTT--EEEHHHH CS
                            PyrI_C   1 eiegvlkCpNpnCItnn..epveskFkvedkekvklkCkYCekeiseeei 48 
                                       ++eg+lkCpN +CItn+  e +++kFkv +++++kl+C+YC+++i +++i
  gi|385805326|ref|YP_005841724.1| 103 RVEGLLKCPNMTCITNErnESIKTKFKVLSRDPLKLQCEYCGTIIYKDDI 152
                                       69***************999***************************998 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.4       1.9   1.1e+04       3       5 ..     109     111 ..     109     112 .. 0.61
   2 ?   12.6   0.2   1.8e-05      0.11       3      17 ..     139     153 ..     138     154 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.9
                            zf-ACC   3 KCp 5  
                                       KCp
  gi|385805326|ref|YP_005841724.1| 109 KCP 111
                                       676 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 1.8e-05
                            zf-ACC   3 KCpsCgemlykkeLe 17 
                                       +C+ Cg+++yk ++ 
  gi|385805326|ref|YP_005841724.1| 139 QCEYCGTIIYKDDIV 153
                                       8**********9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1012.16
//
Query:       gi|385805327|ref|YP_005841725.1|  [L=319]
Description: aspartate carbamoyltransferase catalytic subunit [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-44  151.5   0.0    2.3e-44  151.0   0.0    1.3  1  OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl
    5.4e-27   94.8   0.0    3.4e-26   92.2   0.0    2.0  2  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 !  151.0   0.0   2.6e-48   2.3e-44       2     148 .]      18     157 ..      17     157 .. 0.92

  Alignments for each domain:
  == domain 1  score: 151.0 bits;  conditional E-value: 2.6e-48
                                       -BSSGGGS-HHHHHHHHHHHHHHHHHHHTTT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTTTSC CS
                          OTCace_N   2 hllsledlskeeieelldlaaelkekvkkekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseaediq 78 
                                       +++s++++++e++e+l++ a++ k++++  kk +llk+k+++l F+epStRTr+SfevAakrlG++v+ +s +e   
  gi|385805327|ref|YP_005841725.1|  18 DVISIQQFTREDLETLFEYADRAKKHKD--KKLELLKDKVVMLAFFEPSTRTRFSFEVAAKRLGADVVGFSGEE--- 89 
                                       789*********************8865..9****************************************663... PP

                                       TTTGGSTTSSCHHHHHHHHHHHTSEEEEEES..SHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHHHHHH CS
                          OTCace_N  79 lssvskgrkEsleDtarvlsryvdaiviRhp..gaeeleelakyasvpviNagdgdgeHPtQaLaDlltire 148
                                        +s+skg  E+++Dt+r+l++y+++iviRh+  ga  ++   + a+ pviNagdg+++HPtQa++Dl+tire
  gi|385805327|ref|YP_005841725.1|  90 GTSISKG--ENFTDTIRMLDSYSNLIVIRHKleGA--AKYASEIAENPVINAGDGKQHHPTQAMIDLYTIRE 157
                                       4667899..**********************8766..6666666799***********************98 PP

>> OTCace  Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.08   7.2e+02      14      87 ..      66     141 ..      54     157 .. 0.71
   2 !   92.2   0.0   3.8e-30   3.4e-26       2     156 ..     164     313 ..     163     314 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.08
                                       HHHHHHHHHHHHCT-EEEEES-TT...SSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEEE--SSETTCCG CS
                            OTCace  14 nvanslikllarlgmdvvlvaPkg...lepdkevleeakknakksggsititedleeavkgaDvvytdvwvsmgeek 87 
                                       ++  s   ++ rlg+dvv ++ ++   +++ +++ + +    +++++ i i ++le a+k a  +  + ++  g+ k
  gi|385805327|ref|YP_005841725.1|  66 RTRFSFEVAAKRLGADVVGFSGEEgtsISKGENFTDTI-RMLDSYSNLIVIRHKLEGAAKYASEIAENPVINAGDGK 141
                                       55566677888999999988888877655555555555.44678889999999999999998888777777666644 PP

  == domain 2  score: 92.2 bits;  conditional E-value: 3.8e-30
                                       C.EEEEESS.TTSHHHHHHHHHHHHCT-E.EEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEE CS
                            OTCace   2 glkiafvGd.kknnvanslikllarlgmd.vvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvy 76 
                                       +l++a vGd  +++   s i++l +++ + ++lv+P++l   +ev++      k++g  ++   +lee +++ Dv+y
  gi|385805327|ref|YP_005841725.1| 164 ELTYAVVGDlRYGRASTSFIYGLLIYNPKkLYLVSPPNLGAREEVISY----LKEKGVAFEEIRNLEEIIDEIDVLY 236
                                       7899**********************9998***********9999955....55579******************** PP

                                       E--SSETTCCGGHH...HHHHHHCC.CSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHHH CS
                            OTCace  77 tdvwvsmgeekere...erlkklkd.yqvteellklakkdaivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlht 149
                                       t +++     ker+   ++++k k+ y++t +llk+akk ++++H+LP  + +E+++e+++ + +++f+qa+N++ +
  gi|385805327|ref|YP_005841725.1| 237 TIRLQ-----KERFpdiTEYEKAKGsYKITLDLLKNAKKGLKIMHPLP--KLDEIDKEIDSTEYAAYFQQAKNGVPV 306
                                       *****.....8888888999999999**********************..99************************* PP

                                       HHHHHHH CS
                            OTCace 150 ikAllvl 156
                                       ++All l
  gi|385805327|ref|YP_005841725.1| 307 RMALLSL 313
                                       ****987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       740  (0.0412739); expected 358.6 (0.02)
Passed bias filter:                      572  (0.0319036); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 1980.33
//
Query:       gi|385805328|ref|YP_005841726.1|  [L=194]
Description: orotate phosphoribosyltransferase [Fervidicoccus fontis Kam940]
Scores for complete 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   61.4   0.4    9.8e-17   60.9   0.4    1.2  1  Pribosyltran  Phosphoribosyl transferase domain
    0.00058   19.4   0.0    0.00071   19.1   0.0    1.2  1  UPRTase       Uracil phosphoribosyltransferase
  ------ inclusion threshold ------
      0.094   13.0   0.0       0.15   12.3   0.0    1.4  1  Mur_ligase_C  Mur ligase family, glutamate ligase domain
       0.13   11.7   0.1       0.34   10.4   0.1    1.7  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 !   60.9   0.4   2.2e-20   9.8e-17      28     135 ..      57     154 ..      39     173 .. 0.90

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 2.2e-20
                                       GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----TTSEEEEE-SEESSSHHHH CS
                      Pribosyltran  28 gkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlledpagkkVliVDDildtGgTll 104
                                        + dv+vgia+ G+ +a+ +  + + p+ayvr  +++++++            l++++++kk ++VDD+ +tGg+l+
  gi|385805328|ref|YP_005841726.1|  57 DQADVIVGIATSGIALASFIGCKTGKPIAYVRLDRKEHGTQAL----------LEGEVRNKKAVVVDDVATTGGSLE 123
                                       4789********************************9987665..........579********************* PP

                                       HHHHHHHCC-BSEEEEEEEEE-HHHHHHHHH CS
                      Pribosyltran 105 aalelLkekgpeevriavlvdkpateeevdk 135
                                       +a+ ++ke g  ++ ++v+vd+ ++++e+ k
  gi|385805328|ref|YP_005841726.1| 124 HAISAVKEMGGNVMFSVVVVDREQGAREKLK 154
                                       *************************999976 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.6e-07   0.00071     113     169 ..      98     152 ..      45     172 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.6e-07
                           UPRTase 113 nkLPkkiaertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegvkrl 169
                                         L  ++++++++++D v  TGgs+ +ai+ +ke g   + ++ + v+  e+g+++ 
  gi|385805328|ref|YP_005841726.1|  98 ALLEGEVRNKKAVVVDDVATTGGSLEHAISAVKEMGG--NVMFSVVVVDREQGAREK 152
                                       45778889999***********************765..344556666777787654 PP

>> Mur_ligase_C  Mur ligase family, glutamate ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.4e-05      0.15      11      56 ..     106     145 ..      96     170 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.4e-05
                                       TTTEEEEEET--SHHHHHHHHHHHHHHSSSSEEEEEEEESTT.CCS CS
                      Mur_ligase_C  11 adgvtvidDyahnpdslsaalkalreiapdkrlilvfgpggelger 56 
                                       +++ +v+dD a++ +sl++a++a++e+   +  + v+    +   r
  gi|385805328|ref|YP_005841726.1| 106 NKKAVVVDDVATTGGSLEHAISAVKEMGG-NVMFSVVVV--D---R 145
                                       678899********************954.333333333..3...3 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       0.2   9.2e+02      51      86 ..      56      91 ..      38     103 .. 0.65
   2 ?   10.4   0.1   7.6e-05      0.34     120     162 ..     105     146 ..      89     171 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.2
                          PRTase_2 51 lpepvlvigfAEtAtaLghgvadaleeealylhtTR 86
                                      +++  +++g+A   +aL+  +  ++ + + y+   R
  gi|385805328|ref|YP_005841726.1| 56 TDQADVIVGIATSGIALASFIGCKTGKPIAYVRLDR 91
                                      455668899999999998877666655666665555 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 7.6e-05
                          PRTase_2 120 aakelvLvDDEistGktalnliralqeklprkryvvvslvdwr 162
                                       ++k+ v+vDD ++tG ++ + i+a++e   +  + v  +vd  
  gi|385805328|ref|YP_005841726.1| 105 RNKKAVVVDDVATTGGSLEHAISAVKEMGGNVMFSV-VVVDRE 146
                                       3467899*****************998765544433.345544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       795  (0.0443416); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); 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: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1220.03
//
Query:       gi|385805329|ref|YP_005841727.1|  [L=229]
Description: orotidine 5'-phosphate decarboxylase [Fervidicoccus fontis Kam940]
Scores for complete 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-22   78.4   0.1    7.4e-22   78.0   0.1    1.2  1  OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS famil
     0.0058   15.7   0.3       0.01   14.9   0.2    1.4  2  FMN_dh     FMN-dependent dehydrogenase


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 !   78.0   0.1   8.3e-26   7.4e-22       4     224 ..       6     213 ..       3     214 .. 0.82

  Alignments for each domain:
  == domain 1  score: 78.0 bits;  conditional E-value: 8.3e-26
                                       EEEE-SSSH....HHHHHHHHHHGGGSSEEEEEHHHHHHHTHH.HHTHHHHHHHHHTSEEEEEEEE-S-HHHHHHHH CS
                         OMPdecase   4 clalDvata....relleladkvgpsivvlKthydlvegwgfegtgaklaalarkhgflifeDrKfaDIGntvekqa 76 
                                       ++alD++      + +     ++   +  +K++++ v + g    +++  + +++ + l+++D+K+aDIG+++++ a
  gi|385805329|ref|YP_005841727.1|   6 IIALDPPPNvdevEWIENRFYELNGLVSGFKIGLPAVLKNG----LESYKRIFKDYKGLLIADFKLADIGDIMSMSA 78 
                                       667777666333333334455677778899***********....889999999999******************** PP

                                       HSTCHHHHTTESEEEEEGTGH.HHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHHHSHHHHHHHHHHHHHHHTTE CS
                         OMPdecase  77 tagsarikewadivtvhavaG.kasvkalaeaaekwgnrgllilaqmsskgnlmlqekgytqacveaarehkaedfv 152
                                       +   +  + + +++++h ++G + ++ +l ++a+  g  +l++++ ms++g+ +  + g   + ++ a +++     
  gi|385805329|ref|YP_005841727.1|  79 E---IIKSYGFNAMIAHSFVGySNAIDKLSKKAKDLG-LKLILVVSMSHEGSKEYID-GHLNDFLQIAVKAN----A 146
                                       9...7899*************889************7.**************99999.88888888888877....4 PP

                                       SEEECCCHTH....HHHHH.TTCSCEEEHHHTTEEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSSSHHHHHHH CS
                         OMPdecase 153 mGfvaqetln....ateed.addfihltpgigleqggdgkgqqyntpekligiagadiiivGRgIlkagdpveeaer 224
                                       +G+va +t+     + + + ++d+++l pg+g+         q  ++  +i  +gad+ i+GR+I++a++ +e+a +
  gi|385805329|ref|YP_005841727.1| 147 WGVVAPATRVdvirNVRSKvGKDIKILSPGVGA---------QGADFGSAIC-NGADYEIIGRSITGAENIKEKATQ 213
                                       7*******9976643333367777777777776.........4445566677.79****************999976 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0      0.58   5.2e+03     122     142 ..      98     118 ..      78     120 .. 0.71
   2 !   14.9   0.2   1.1e-06      0.01     258     307 ..     156     205 ..     149     224 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 0.58
                                       HHHHHHHHHHHHHCTESEEEE CS
                            FMN_dh 122 relteellkraeaagykalvl 142
                                       ++ +++l k+a+++g+k +++
  gi|385805329|ref|YP_005841727.1|  98 SNAIDKLSKKAKDLGLKLILV 118
                                       556677777778877777765 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.1e-06
                                       HHCHHHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHHHHH CS
                            FMN_dh 258 idvLpeiveavggrievlvDgGirrGsDvlkAlalGAdavllGRpflygl 307
                                       +dv+ +++ +vg++i++l  g   +G+D   A++ GAd  ++GR +  + 
  gi|385805329|ref|YP_005841727.1| 156 VDVIRNVRSKVGKDIKILSPGVGAQGADFGSAICNGADYEIIGRSITGAE 205
                                       79999***************999*********************995544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); 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:                         2  (0.000111551); expected 0.2 (1e-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: 1502.19
//
Query:       gi|385805330|ref|YP_005841728.1|  [L=245]
Description: ABC transporter [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.8e-28   97.9   0.0    1.2e-27   97.1   0.0    1.4  1  ABC_tran     ABC transporter
    4.5e-11   43.1   0.5    0.00027   20.9   0.0    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    0.00019   21.4   0.1    0.00035   20.5   0.1    1.4  1  RsgA_GTPase  RsgA GTPase
    0.00038   21.0   0.4    0.00055   20.5   0.4    1.3  1  AAA_23       AAA domain
     0.0011   19.4   0.1      0.015   15.7   0.0    2.2  1  AAA          ATPase family associated with various cellular a
     0.0013   18.7   0.0     0.0022   17.9   0.0    1.3  1  ATPase_2     ATPase domain predominantly from Archaea
     0.0021   18.5   0.0     0.0026   18.2   0.0    1.2  1  AAA_16       AAA ATPase domain
     0.0028   17.6   0.0     0.0082   16.1   0.0    1.7  2  Rad17        Rad17 P-loop domain
     0.0051   16.5   0.0     0.0098   15.6   0.0    1.4  1  AAA_29       P-loop containing region of AAA domain
     0.0066   16.2   0.4      0.054   13.2   0.2    2.0  2  AAA_15       AAA ATPase domain
  ------ inclusion threshold ------
      0.012   14.5   0.1      0.016   14.0   0.1    1.2  1  Adeno_IVa2   Adenovirus IVa2 protein
      0.012   15.1   0.5       0.16   11.4   0.2    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
      0.017   15.4   0.1      0.048   13.9   0.1    1.9  1  AAA_22       AAA domain
      0.033   14.3   0.0      0.042   13.9   0.0    1.6  1  MMR_HSR1     50S ribosome-binding GTPase
      0.053   12.3   0.1        5.4    5.7   0.0    2.2  2  ABC_ATPase   Predicted ATPase of the ABC class
      0.062   13.5   0.1        0.1   12.9   0.1    1.3  1  AAA_28       AAA domain
      0.073   13.0   0.0       0.13   12.2   0.0    1.4  1  NACHT        NACHT domain
       0.21   11.9   0.0       0.41   10.9   0.0    1.5  1  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 !   97.1   0.0   1.2e-30   1.2e-27       2     136 ..      25     158 ..      24     159 .. 0.93

  Alignments for each domain:
  == domain 1  score: 97.1 bits;  conditional E-value: 1.2e-30
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       +n+sl+++ +e  +i+G++G+GKStLl+++ag  kpt+G+i ++         +    ++g+++q p+l p +tv e
  gi|385805330|ref|YP_005841728.1|  25 DNISLDIY-NEFFVILGPSGCGKSTLLRIIAGVDKPTSGNIIFQ---------TGKPPRFGFVFQFPSLIPWITVLE 91 
                                       78899986.68999***************************666.........5567789***************** PP

                                       H.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       n             e++e ++k+ls +gl+++++       ++LSgG++qrv laral  +p++ll+DEp+
  gi|385805330|ref|YP_005841728.1|  92 NvaivlknmgipknEAEESAKKYLSIVGLSGFENVYP----YELSGGMRQRVNLARALSVQPEILLMDEPF 158
                                       ************9888888************998887....*****************************7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.1   3.2e-07   0.00032       1      63 [.      35      81 ..      35      85 .. 0.81
   2 !   20.9   0.0   2.7e-07   0.00027     228     298 ..     122     193 ..      91     196 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.2e-07
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeie 63
                                      + v+ Gp g+GKS+LL+++ ++                 +++++ + +++++ p+  f+f+++
  gi|385805330|ref|YP_005841728.1| 35 FFVILGPSGCGKSTLLRIIAGVD----------------KPTSGNIIFQTGKPPRFGFVFQFP 81
                                      68*****************9883................377777777777777777777765 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 2.7e-07
                            AAA_21 228 dgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrll.ell....kelsrngaQviltTHS 298
                                       +  ++ ++elS G+++   l+ al  ++    +ll DEp ++L+P   + l  e+l    ++ +     +i++THS
  gi|385805330|ref|YP_005841728.1| 122 GFENVYPYELSGGMRQRVNLARALSVQP---EILLMDEPFSNLDPLTAENLRaEILdiwlSNITP-MKAIIMVTHS 193
                                       557899********************99...9*************77766666666655644444.57899***99 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   3.5e-07   0.00035      82     126 ..      16      60 ..       6      70 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 3.5e-07
                                       --TTTHTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT---- CS
                       RsgA_GTPase  82 vsaktkegleelkellkdktsvlvGqSGvGKStLinallpelelk 126
                                        ++ + + +++++  + +++ v++G+SG GKStL+  +++ ++  
  gi|385805330|ref|YP_005841728.1|  16 SNSGEIKVIDNISLDIYNEFFVILGPSGCGKSTLLRIIAGVDKPT 60 
                                       55566678899999999*******************999876655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.4   5.6e-07   0.00055      11      39 ..      25      53 ..       5      56 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 5.6e-07
                            AAA_23 11 rdqeidFskgltlItGpNGaGKTTildAi 39
                                      ++ ++d  + +++I Gp G+GK+T+l+ i
  gi|385805330|ref|YP_005841728.1| 25 DNISLDIYNEFFVILGPSGCGKSTLLRII 53
                                      5666777999****************988 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.5e-05     0.015       3      66 ..      38     156 ..      36     196 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.5e-05
                                       EESSTTSSHHHHHHHHHHH.....HTHE................................................. CS
                               AAA   3 lyGppGtGKTllakavake.....lgve................................................. 25 
                                       + Gp G+GK++l + +a          +                                                 
  gi|385805330|ref|YP_005841728.1|  38 ILGPSGCGKSTLLRIIAGVdkptsG--Niifqtgkpprfgfvfqfpslipwitvlenvaivlknmgipkneaeesak 112
                                       78***************99555440..13444455566666666667777777777777776666666666666666 PP

                                       .EEEEETTTCS.SSSTTHHHHHHHHHHHHHHHTS.TSEEEEEET CS
                               AAA  26 .fleisgsell.skyvgesekkirelfkeakeka.kpsilfiDE 66 
                                        +l+i g + + + y  e +  +r+ ++ a++ + +p il++DE
  gi|385805330|ref|YP_005841728.1| 113 kYLSIVGLSGFeNVYPYELSGGMRQRVNLARALSvQPEILLMDE 156
                                       63333333333244999999999999999999999999999999 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   2.2e-06    0.0022       7      45 ..      20      58 ..      17      69 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.2e-06
                          ATPase_2  7 elkeleeilerepneiyfiYGpegsGKtaLlkeiienle 45
                                      e+k + +i     ne+ +i Gp g+GK++Ll+ i+   +
  gi|385805330|ref|YP_005841728.1| 20 EIKVIDNISLDIYNEFFVILGPSGCGKSTLLRIIAGVDK 58
                                      88888899888899*****************98876655 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   2.6e-06    0.0026      26      76 ..      35      90 ..      28     179 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.6e-06
                            AAA_16 26 lvllsGesGvGKsslvrellralekd...ggiflrgkcdqlesa...ipysalaqal 76
                                        ++ G+sG+GKs+l+r ++  + k    ++if +gk  +++      ++++++++l
  gi|385805330|ref|YP_005841728.1| 35 FFVILGPSGCGKSTLLRIIA-GVDKPtsgNIIFQTGKPPRFGFVfqfPSLIPWITVL 90
                                      5789************9999.455556745999999999993222212224466666 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   8.2e-06    0.0082      46      66 ..      34      54 ..      15      65 .. 0.84
   2 ?   -1.7   0.0       2.4   2.4e+03     150     166 ..     167     184 ..     109     197 .. 0.58

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.2e-06
                             Rad17 46 riLLisGPsGCgkstvvkvLs 66
                                      +  +i GPsGCgkst +++++
  gi|385805330|ref|YP_005841728.1| 34 EFFVILGPSGCGKSTLLRIIA 54
                                      567899************997 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.4
                             Rad17 150 dalr.evirkylrsseal 166
                                       ++lr e++  +l    ++
  gi|385805330|ref|YP_005841728.1| 167 ENLRaEILDIWLSNITPM 184
                                       334323444555555555 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   9.9e-06    0.0098      17      39 ..      27      50 ..      16      56 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 9.9e-06
                            AAA_29 17 ieidlkg.atlltGpsGsGKSTll 39
                                      i++d  + ++++ GpsG GKSTll
  gi|385805330|ref|YP_005841728.1| 27 ISLDIYNeFFVILGPSGCGKSTLL 50
                                      44554455899************8 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.2   5.4e-05     0.054      14      43 ..      24      53 ..      22     114 .. 0.91
   2 ?    1.5   0.0       0.2     2e+02     323     365 ..     148     193 ..      89     195 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.4e-05
                            AAA_15 14 lkdveidlseeltvliGkNnsGKSsileal 43
                                      ++++++d+ +e+ v+ G+ ++GKS++l+++
  gi|385805330|ref|YP_005841728.1| 24 IDNISLDIYNEFFVILGPSGCGKSTLLRII 53
                                      78999***********************99 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.2
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnkt...QviitTHS 365
                                       ++ ill++EP  +L p   + l   ++++  +n t    +i+ THS
  gi|385805330|ref|YP_005841728.1| 148 QPEILLMDEPFSNLDPLTAENLRAEILDIWLSNITpmkAIIMVTHS 193
                                       568999****999999999**********9999999999999***9 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   1.6e-05     0.016      63     122 ..       6      66 ..       1      72 [. 0.68

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.6e-05
                        Adeno_IVa2  63 diekldakllrddGelssl.nygl..qPviGviyGPtGsGksqllrnlissklisPiPetvif 122
                                       +i++l++ + ++ Ge+  + n+ l       vi GP G+Gks llr +    + +P+   +if
  gi|385805330|ref|YP_005841728.1|   6 SIKNLSKSFKSNSGEIKVIdNISLdiYNEFFVILGPSGCGKSTLLRIIAG--VDKPTSGNIIF 66 
                                       56778888888888887663333300344679**************6543..34566666666 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 ?   11.4   0.2   0.00016      0.16      16      42 ..      25      51 ..       7      56 .. 0.80
   2 ?    2.0   0.0      0.12   1.2e+02     135     179 ..     105     169 ..      88     215 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00016
                                      EEEEEETTSSEEEEEESTTSSHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 16 ktvilpfsksftaivGpNGSGKsnlld 42
                                      ++++l++ ++f +i+Gp G+GKs ll 
  gi|385805330|ref|YP_005841728.1| 25 DNISLDIYNEFFVILGPSGCGKSTLLR 51
                                      467889999**************9986 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.12
                                       T........................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHH CS
                                       x........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 135 e........................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkv 179
                                       +                        +LSgG ++ v la  +++q   p+ + l+De  ++LD    +++
  gi|385805330|ref|YP_005841728.1| 105 NeaeesakkylsivglsgfenvypyELSGGMRQRVNLARALSVQ---PE-ILLMDEPFSNLDPLTAENL 169
                                       45555555555555555555555559999999999999887765...33.6678888888887666555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   4.8e-05     0.048       7      25 ..      35      53 ..      31     198 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.8e-05
                            AAA_22  7 ilvvtGesGtGKTtllrrl 25
                                      + v+ G+sG+GK+tllr +
  gi|385805330|ref|YP_005841728.1| 35 FFVILGPSGCGKSTLLRII 53
                                      789************9965 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   0.0   4.3e-05     0.042       2      38 ..      36      73 ..      35     202 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.3e-05
                                      EEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEE CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltge.kaivsdkpgtTrdine 38
                                      ++i+G +  GKStL++ + g  k   +++ + T ++ +
  gi|385805330|ref|YP_005841728.1| 36 FVILGPSGCGKSTLLRIIAGVdKPTSGNIIFQTGKPPR 73
                                      589****************9757888999999988754 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 ?    4.7   0.0     0.011        11     242     268 ..      31      56 ..      14      63 .. 0.83
   2 ?    5.7   0.0    0.0054       5.4     324     380 ..     132     188 ..     125     207 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.011
                                       E-SSEEEEEE-TTSSHHHHHHHHHHCC CS
                        ABC_ATPase 242 ipkGvtlIvGggfhGKsTLLeAlekGv 268
                                       i +  ++I G+   GKsTLL+ ++ Gv
  gi|385805330|ref|YP_005841728.1|  31 IYNEFFVILGPSGCGKSTLLRIIA-GV 56 
                                       5566799*************9764.55 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0054
                                       -HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS-GGG--B--HHHCH CS
                        ABC_ATPase 324 SGStsqAanimealeagakllLiDEDtsAtNlmirDermqelvskekepitplvdrv 380
                                       SG + q +n+++al ++ ++lL+DE  s    +   ++ +e++  +   itp+   +
  gi|385805330|ref|YP_005841728.1| 132 SGGMRQRVNLARALSVQPEILLMDEPFSNLDPLTAENLRAEILDIWLSNITPMKAII 188
                                       9************************99998888888888888888888888876665 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1    0.0001       0.1       2      20 ..      36      54 ..      35      64 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.0001
                            AAA_28  2 ivitGgestGKTtlleaLa 20
                                      +vi+G++++GK+tll+ +a
  gi|385805330|ref|YP_005841728.1| 36 FVILGPSGCGKSTLLRIIA 54
                                      79*************9887 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00013      0.13       3      21 ..      36      54 ..      34      80 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                                      EEEEC-TTTCHHHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqkla 21
                                       ++ G++G+GK+tLl+ +a
  gi|385805330|ref|YP_005841728.1| 36 FVILGPSGCGKSTLLRIIA 54
                                      5899***********9886 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00042      0.41      47      83 ..     132     168 ..     102     173 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00042
                           SbcCD_C  47 aaalaalyssaegrepalrlvfLDEAFsklDeesiat 83 
                                         ++++ ++ a++ + +++++++DE Fs+lD+ ++++
  gi|385805330|ref|YP_005841728.1| 132 SGGMRQRVNLARALSVQPEILLMDEPFSNLDPLTAEN 168
                                       44577777777666788**************977665 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:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); 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: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.52
# Mc/sec: 1407.48
//
Query:       gi|385805331|ref|YP_005841729.1|  [L=38]
Description: hypothetical protein FFONT_0287 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.051   13.5   0.6      0.051   13.5   0.6    1.4  2  PsbI      Photosystem II reaction centre I protein (PSII 4.8 


Domain annotation for each model (and alignments):
>> PsbI  Photosystem II reaction centre I protein (PSII 4.8 kDa protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.6   2.8e-06     0.051       7      26 ..       2      21 ..       1      26 [. 0.90
   2 ?   -2.5   0.1      0.29   5.1e+03       3       6 ..      33      36 ..      32      37 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.8e-06
                              PsbI  7 vVyivViffvslFvFGfLsn 26
                                      +V i ++ f +lF F f sn
  gi|385805331|ref|YP_005841729.1|  2 LVRIYITIFLLLFAFLFVSN 21
                                      799****************9 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.29
                              PsbI  3 tLKi 6 
                                      +LKi
  gi|385805331|ref|YP_005841729.1| 33 ILKI 36
                                      7998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       787  (0.0438954); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 249.22
//
Query:       gi|385805332|ref|YP_005841730.1|  [L=204]
Description: Small-conductance mechanosensitive channel-like protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.7e-18   65.0   5.9    6.7e-18   65.0   5.9    1.6  2  MS_channel  Mechanosensitive ion channel


Domain annotation for each model (and alignments):
>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.2      0.14   2.5e+03       7     203 ..      20      45 ..      11      48 .. 0.48
   2 !   65.0   5.9   3.7e-22   6.7e-18      10     106 ..      97     196 ..      91     197 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHHHTTT--SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEEEEE-SSE CS
                        MS_channel   7 liivvgilivlsllgvnvsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveigdieGtVediglrt 83 
                                       ++++ +                                                                       
  gi|385805332|ref|YP_005841730.1|  20 TLWIAA----------------------------------------------------------------------- 25 
                                       333333....................................................................... PP

                                       EEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-TTS-EEEEE CS
                        MS_channel  84 tkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlkdkellvvl 160
                                                                                                                    
  gi|385805332|ref|YP_005841730.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                                       EEE-SSSEEEEEEEEEET...TTHHHHHHHHHHHHHHHHHHHT CS
                        MS_channel 161 defgdsslnfevrvfvktvvpeeylsvqseinlrikkileeeg 203
                                                              y  + + in  ++k l e++
  gi|385805332|ref|YP_005841730.1|  26 -----------------------YIIISALINGYVFKLLAEHN 45 
                                       .......................44444444445555555555 PP

  == domain 2  score: 65.0 bits;  conditional E-value: 3.7e-22
                                       HHHHHHHHHTTT--...SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEEEEE-SSE CS
                        MS_channel  10 vvgilivlsllgvn...vsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveigdieGtVediglrt 83 
                                       ++gi ++ls++       +a +a+ G+lgl++g+a+++++ + ++G++ll+ +pfkiGD v+i + +G+V dig  +
  gi|385805332|ref|YP_005841730.1|  97 IIGIGAILSSIAGGvagGTAGVALGGFLGLVVGYASQQVLGQAISGLFLLTIRPFKIGDKVNIVGEDGEVLDIGVMF 173
                                       4444444444443311335679999**************************************************** PP

                                       EEEEETTSEEEEEEHHHHHTS-E CS
                        MS_channel  84 tkirtfdgrivtiPnsslvtsni 106
                                       + +++ d+++v+iPn+s+++++i
  gi|385805332|ref|YP_005841730.1| 174 ILLKKSDNTLVYIPNNSVISQKI 196
                                       *******************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       852  (0.0475208); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1269.36
//
Query:       gi|385805333|ref|YP_005841731.1|  [L=89]
Description: Like-Sm ribonucleoprotein, core [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-17   62.9   0.1      2e-17   62.6   0.1    1.1  1  LSM       LSM domain
    0.00023   21.3   0.0    0.00027   21.0   0.0    1.2  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 !   62.6   0.1   2.2e-21     2e-17       2      67 .]      18      84 ..      17      84 .. 0.94

  Alignments for each domain:
  == domain 1  score: 62.6 bits;  conditional E-value: 2.2e-21
                                      HHHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTET.EEEEEEEEEEEGGGEEEEEE CS
                               LSM  2 flkklinkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkk.ekrklglvliRGnnivlisl 67
                                       l++ ++++v+v+lk+g e++G L   D  mN++L++++e+++ +   k+k+g++liRG++i++isl
  gi|385805333|ref|YP_005841731.1| 18 YLQDAKGNNVLVKLKDGGEYIGELDFSDSTMNVILKNCTEVKERTGePKAKYGTILIRGSQILFISL 84
                                      6999************************************99776579*****************85 PP

>> SM-ATX  Ataxin 2 SM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0     3e-08   0.00027      11      58 ..      22      67 ..      16      85 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3e-08
                                      TTTSEEEEEETTS-EEEEEEEEE-T..T--EEEEEEEETTS....... CS
                            SM-ATX 11 lvGkevevtvknGevyeGifstvslekdfsvvLkmarkvkkansksss 58
                                        G++v v++k+G  y G ++ +++   ++v+Lk+  +vk+  ++++ 
  gi|385805333|ref|YP_005841731.1| 22 AKGNNVLVKLKDGGEYIGELDFSDS--TMNVILKNCTEVKERTGEPKA 67
                                      56***********************..**************2222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); 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: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 599.11
//
Query:       gi|385805334|ref|YP_005841732.1|  [L=278]
Description: hypothetical protein FFONT_0290 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-05   25.3   0.0    2.9e-05   24.1   0.0    1.4  1  Lactamase_B    Metallo-beta-lactamase superfamily
    0.00029   20.4   0.0     0.0004   19.9   0.0    1.2  1  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.015   15.2   0.0      0.025   14.5   0.0    1.4  1  Lactamase_B_3  Beta-lactamase superfamily domain
      0.096   12.6   0.3      0.096   12.6   0.3    1.8  2  Herpes_IE2_3   Herpes virus intermediate/early protein 2/3
       0.11   12.7   0.1       0.26   11.5   0.1    1.6  1  DUF1945        Domain of unknown function (DUF1945)


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 !   24.1   0.0   8.2e-09   2.9e-05      33     157 ..      27     166 ..       2     173 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 8.2e-09
                                       H............HHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHHCCHH CS
                       Lactamase_B  33 l............elaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeaddaasrkgll 97 
                                       l             + ++ ++++d   +++TH+H DH+  +++ +ea+++++++ ++ +   ++  +++a ++ +  
  gi|385805334|ref|YP_005841732.1|  27 LppheielnelekSIEKICKNLNDSNLIVITHFHRDHYLSNDYCIEAFKNKTIIMKHPEIDINYSQKMRAKEFIKKT 103
                                       555555555555555556666677778***********************************999999999999888 PP

                                       ....TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHC CS
                       Lactamase_B  98 ....lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallaget 157
                                           + +++   + v+e +   + ++ + + +  +p+   +++ ++++++++lf+ D+  +g+ 
  gi|385805334|ref|YP_005841732.1| 104 kdisKLIFTNGEDFVFEGIKMKISFPLWHGSQN-TPLGKVLVILIDDEEQRYLFASDTQGPGDD 166
                                       777766677777777777777777777666654.778888888899999999999999877765 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 !   19.9   0.0   1.1e-07    0.0004      25     150 ..      45     167 ..      11     174 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.1e-07
                                       S--..SEEEEE-SS--HHHHGGGGCCCC.C--EEEEEEEEHHHHHHCCTTCGHHHCHTT.TTEEEEEE-TTSEEEEC CS
                     Lactamase_B_2  25 rdelppidaVllthaHyDHlaglltlre.lrpkklplyapkgvlavleanfvylaleee.pavnvheldwgesfelg 99 
                                        ++l++ +++++th H DH+   + + e +++k   ++ ++++  + ++++ +  + ++ + ++   ++ ge f ++
  gi|385805334|ref|YP_005841732.1|  45 CKNLNDSNLIVITHFHRDHYLSNDYCIEaFKNK-TIIMKHPEIDINYSQKMRAKEFIKKtKDISKLIFTNGEDFVFE 120
                                       567788899***********7777777756664.335699**********99999999965666666779******9 PP

                                       STTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HHH CS
                     Lactamase_B_2 100 dggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipeei 150
                                       + +++i  +p+ h+s++   +  g++l  +i+++++r +++ Dt+   ++ 
  gi|385805334|ref|YP_005841732.1| 121 GIKMKIS-FPLWHGSQN---TPLGKVLVILIDDEEQRYLFASDTQGPGDDE 167
                                       6666655.477777777...88899*******************9665544 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 ?   14.5   0.0   6.8e-06     0.025      12      68 ..       5      83 ..       2     129 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.8e-06
                     Lactamase_B_3 12 letagarilvDPfka..nlgyeppa...................eeaDlvlisqaledHahlet..lkqlaenvkvlee 67
                                      +e +g +i +DP+ a     y+ p+                    + +l++i++ + dH+  +   +++ ++n +++ +
  gi|385805334|ref|YP_005841732.1|  5 VEAKGFKIFIDPGAAlaPYRYGLPPheielneleksiekicknlNDSNLIVITHFHRDHYLSNDycIEA-FKNKTIIMK 82
                                      6889*********7644445555558899999999999999999***************9766411333.666666655 PP

                     Lactamase_B_3 68 g 68
                                       
  gi|385805334|ref|YP_005841732.1| 83 H 83
                                      4 PP

>> Herpes_IE2_3  Herpes virus intermediate/early protein 2/3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.3   2.7e-05     0.096       9      76 ..      35     106 ..      29     119 .. 0.82
   2 ?   -0.9   0.1      0.37   1.3e+03      15      48 ..     206     239 ..     200     254 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.7e-05
                      Herpes_IE2_3   9 nvleeaiyrlckledsnakqiqifytRskevkn..aidalrek..LlslpNltvsapfqleitepvthepdv 76 
                                       n le++i ++ck+ + ++  ++  + R + + n   i+a ++k  +++ p + ++  +++   e ++ ++d+
  gi|385805334|ref|YP_005841732.1|  35 NELEKSIEKICKNLNDSNLIVITHFHRDHYLSNdyCIEAFKNKtiIMKHPEIDINYSQKMRAKEFIKKTKDI 106
                                       6799*************9999999*****9998445899988744788899*********776666666664 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.37
                      Herpes_IE2_3  15 iyrlckledsnakqiqifytRskevknaidalre 48 
                                       + ++++ ++ n+  i   ++R k+  n ++ lr 
  gi|385805334|ref|YP_005841732.1| 206 LEKIFSINTLNTIIIDHHFAREKNYVNRLERLRI 239
                                       5577888888888888899999988787777764 PP

>> DUF1945  Domain of unknown function (DUF1945)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   7.1e-05      0.26      31      43 ..     113     125 ..     106     127 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.1e-05
                                       SSS-EEETTEEE- CS
                           DUF1945  31 sGeevvfeGvkmk 43 
                                        Ge+ vfeG+kmk
  gi|385805334|ref|YP_005841732.1| 113 NGEDFVFEGIKMK 125
                                       49**********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); 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 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1711.42
//
Query:       gi|385805335|ref|YP_005841733.1|  [L=187]
Description: putative methyltransferase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-10   42.0   0.0    2.6e-10   40.9   0.0    1.6  2  Methyltransf_25  Methyltransferase domain
    3.1e-10   40.5   0.0    4.9e-10   39.9   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    2.8e-07   30.4   0.3    4.3e-07   29.8   0.3    1.2  1  Methyltransf_31  Methyltransferase domain
    1.2e-05   24.8   0.5    1.5e-05   24.5   0.5    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
     0.0024   17.8   0.0     0.0029   17.4   0.0    1.3  1  Methyltransf_23  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 !   40.9   0.0   7.2e-14   2.6e-10       1      95 [.      44     139 ..      44     140 .. 0.89
   2 ?   -2.6   0.0       2.6   9.4e+03      35      42 ..     156     163 ..     150     185 .. 0.50

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 7.2e-14
                                       EEEET-TTSHHHHHHHCTS...TSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrl...gkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgal 74 
                                       +Ld+G GtG + ++l +++   +   ++g+Dis +ml++  ++ +  + ++e+v+gd+   pf ++ fD+ +s+ +l
  gi|385805335|ref|YP_005841733.1|  44 ILDAGIGTGLFEEYLFRNGkmiNFDLIVGIDISIKMLDELIKKRDFLKEKIELVNGDIAFAPFREKIFDYTFSFTSL 120
                                       8*****************865558999************9999977667************************8666 PP

                                       GGSSHHHHHHHHHHHHHHEEE CS
                   Methyltransf_25  75 hhlsdedlekalkeiarvLkp 95 
                                        +  ++d+e+ l+e+ rv+k+
  gi|385805335|ref|YP_005841733.1| 121 FL--NNDYENELNELERVTKK 139
                                       55..4688999*******996 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.6
                                       HHHHHHHH CS
                   Methyltransf_25  35 eaarerae 42 
                                       e+ +++++
  gi|385805335|ref|YP_005841733.1| 156 EILQHHNA 163
                                       44443332 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.0   1.4e-13   4.9e-10       1      90 [.      45     139 ..      45     145 .. 0.89

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 1.4e-13
                                       EEET-TTSHHHHHHHHTT.....SEEEEEES-HHHHHHH.HHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-C CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg.....arvvgvDlskemlkla.kekaseeglkvefvvadaeklpfednsfDlvvssevl 71 
                                       Ld+G GtG++ e+l ++g       +vg+D+s +ml+   k++   ++ k+e+v +d+   pf+++ fD  +s+ +l
  gi|385805335|ref|YP_005841733.1|  45 LDAGIGTGLFEEYLFRNGkminfDLIVGIDISIKMLDELiKKRDFLKE-KIELVNGDIAFAPFREKIFDYTFSFTSL 120
                                       8**************9999999999***********554144444444.8*********99**************** PP

                                       CC-CCHHHHHHHHHHHEEE CS
                   Methyltransf_11  72 hhvedpekalkeiaRvLkp 90 
                                       +  +d e  l+e+ Rv k+
  gi|385805335|ref|YP_005841733.1| 121 FLNNDYENELNELERVTKK 139
                                       *****************97 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.3   1.2e-10   4.3e-07       6     127 ..      43     163 ..      39     185 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 1.2e-10
                   Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkae...vvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDli 78 
                                       ++lD+G GtG +   l+ + g++++   +vGiDis +++    ++++  +l+  +e+  gdi  ++  + ++ fD+ 
  gi|385805335|ref|YP_005841733.1|  43 KILDAGIGTGLFEEYLF-RNGKMINfdlIVGIDISIKMLDELIKKRD--FLKeKIELVNGDIAFAP--FREKIFDYT 114
                                       79***************.6677777778***********99999755..44447************..99******* PP

                   Methyltransf_31  79 lsnevlnaladpdkileeiervlkpggilliedprllaelpakveeesk 127
                                       +s+  l + +d ++ l+e+erv k+  +l i    l +++++++++++ 
  gi|385805335|ref|YP_005841733.1| 115 FSFTSLFLNNDYENELNELERVTKKSIVLSILKKGLKEKMLEILQHHNA 163
                                       ******9999999999999999998888888877766777777777766 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.5   4.2e-09   1.5e-05      14     152 ..       9     146 ..       2     164 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 4.2e-09
                                       X-HHHHHHHHHHHHHTTTHHHHHHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHH..EEEEEES-HHHHHHH CS
                   Ubie_methyltran  14 esvaskyDlmndvlslgihrlWkkfveklvavkrgakvlDvagGtgDlafklsdsvgekg..kvvvlDinenmLkvg 88 
                                       ++    yD+   +  +++ +++  ++++   ++   k+lD   Gtg +   l ++ +      +v++Di+ +mL++ 
  gi|385805335|ref|YP_005841733.1|   9 QKYNITYDTYEMLYKIEQEEKY--KLIDKLIDQIRGKILDAGIGTGLFEEYLFRNGKMINfdLIVGIDISIKMLDEL 83 
                                       4444556666655555555555..4455555555558*********98888777655433347899*********98 PP

                                       HHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES-.GGG-S-HHHHHHHHHHHEEEEEEEEEE CS
                   Ubie_methyltran  89 ekklkeegkinieflqanaeeLpfeddsfDvvtvsfG.lrnvtDklkaLkeayrvlkpGGrlvvl 152
                                        kk ++  k +ie+++++    pf ++ fD +t sf  l    D+++ L+e+ rv k    l +l
  gi|385805335|ref|YP_005841733.1|  84 IKK-RDFLKEKIELVNGDIAFAPFREKIFD-YTFSFTsLFLNNDYENELNELERVTKKSIVLSIL 146
                                       766.678889********************.689996367778*************987777666 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   8.2e-07    0.0029      10      60 ..      30      83 ..      20     174 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 8.2e-07
                   Methyltransf_23 10 sdklerllpklraggrvLdiGcGtGillevlrengf.....svtgvDlspeaveia 60
                                       +++++l   ++ +g++Ld G GtG + e+l +ng+      ++g+D+s ++ +++
  gi|385805335|ref|YP_005841733.1| 30 YKLIDKLI--DQIRGKILDAGIGTGLFEEYLFRNGKminfdLIVGIDISIKMLDEL 83
                                      46667776..68899****************8877545444588*****8877664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1120  (0.0624686); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); 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 0.25s 00:00:00.64 Elapsed: 00:00:00.53
# Mc/sec: 1056.92
//
Query:       gi|385805336|ref|YP_005841734.1|  [L=629]
Description: putative RNA-binding protein, eukaryotic snRNP-like protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-34  119.1  11.7    3.2e-34  118.5  11.7    1.3  1  FbpA           Fibronectin-binding protein A N-terminus (FbpA
    2.1e-22   79.8   0.1    4.7e-22   78.7   0.1    1.6  1  NFACT-R_1      NFACT protein RNA binding domain
    5.6e-05   23.3   0.0    0.00021   21.4   0.0    2.0  1  NFACT-R_2      NFACT protein RNA binding domain
     0.0062   16.8   9.2      0.051   13.9   2.3    3.5  2  BLOC1_2        Biogenesis of lysosome-related organelles comp
  ------ inclusion threshold ------
      0.019   13.6   0.4      0.038   12.7   0.1    1.5  2  Tweety         Tweety
      0.028   14.4   1.2        9.3    6.3   0.0    2.5  2  Laminin_II     Laminin Domain II
       0.11   12.6   7.3       0.42   10.7   1.2    2.4  2  DHR10          Designed helical repeat protein 10 domain
       0.21   11.9   9.3       0.18   12.1   2.0    2.5  2  DUF5082        Domain of unknown function (DUF5082)
       0.24   11.0   4.9         11    5.6   2.7    2.4  2  DUF4795        Domain of unknown function (DUF4795)
       0.37   10.9  13.7       0.72   10.0   5.8    2.5  2  Tropomyosin_1  Tropomyosin like
       0.84   10.0   8.1        3.2    8.2   2.1    2.6  2  Csm1_N         Csm1 N-terminal domain
        1.3    9.5   6.8        4.1    7.9   0.3    3.1  2  FlaC_arch      Flagella accessory protein C (FlaC)
          2    8.1  12.4       0.53   10.1   4.0    2.2  2  She9_MDM33     She9 / Mdm33 family
        2.8    8.0  16.4          4    7.5   0.6    3.2  3  DUF4315        Domain of unknown function (DUF4315)
        3.5    7.5  12.0        2.3    8.1   1.0    2.8  2  DivIC          Septum formation initiator
        3.6    6.4  15.1       0.91    8.3   0.9    2.2  2  Spc7           Spc7 kinetochore protein
        7.8    6.8  13.5        7.2    6.9   0.5    3.7  3  XhlA           Haemolysin XhlA


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 !  118.5  11.7   3.1e-37   3.2e-34       2     422 ..       9     411 ..       8     429 .. 0.83

  Alignments for each domain:
  == domain 1  score: 118.5 bits;  conditional E-value: 3.1e-37
                                       HHHHHHHHHHHHHHHTTXEEEEEEE.EETTEEEEEEEETTEEEE.EEEEXXTTTXEEEEXXXXXXXXSSXXHHHHHH CS
                              FbpA   2 glvlaavvaELqkellggridkiyq.pekdelvltlranrgrhk.LllsahpsyarihltekpkenpkeppnFcmlL 76 
                                        ++l a ++EL+ke ++ ++++iy  p+ + + ++l+  +   k L+ +a    ++i++++++ + p++p+ F+  L
  gi|385805336|ref|YP_005841734.1|   9 VIDLIAFLRELEKEKINLKVSNIYHiPQTKRILIKLK--DPYFKfLVAEA---SKKIYFSKYSLPTPEKPSIFALSL 80 
                                       58999******************96477888999999..445556*****...************************ PP

                                       HHHHTTXEEEEEEEXTTSSEEEEEEEEEXTTSXEEEEEEEEEXXGGGXEEEEEETTTEEEEESSXBXXXSSXSXXBS CS
                              FbpA  77 RkyLkgarivsieqlgfdRivelsiekrdElgdeeeytLivEimgrhSNiiLvdeenkIidaikhvspkqsrvReil 153
                                       RkyL+  +i+si+q+gfdRi++l++++         y L++E++ r + iiL+d+ ++Ii a     +k+ r+R+i 
  gi|385805336|ref|YP_005841734.1|  81 RKYLNERVITSIKQIGFDRILKLEFDND--------YALYIELLPR-GEIILTDPTERIIHASS---FKKMRDRKIE 145
                                       ****************************........**********.************98765...55556***** PP

                                       TTXBXXXSXXXSXBXTTSXXH.HHHHHHHHHS.XXXHHHHHHHBTTXXHHHHHHHHTTXSSSH.............. CS
                              FbpA 154 pgekYelPpsqdklnPleaeeleefkellskkekdlvkaLvkafqGlspllaeelleragldketsakelseedler 230
                                         ++Y+lPp  +k    e      +++l    + + +k L+k++ Gl  +l  e++ ++g           e+ +e+
  gi|385805336|ref|YP_005841734.1| 146 RNSQYILPPIFEKRPTAEMC----IEAL----SSEGKKGLIKKL-GLPHELIDEAIGEVGC----------ENCFEK 203
                                       **********7666433333....3344....3556899****9.***************3..........446899 PP

                                       .HHHHHHHHTXXX....XX.EE.....XSSSEESSX...XTTXX.SSXXXXSXHHHHHHHHTTTXXX--SHHHHHHH CS
                              FbpA 231 lyealqelleeleeekfep.qlvlkeekpeefsvvp...lkslselekesfdslsealdeyYakkaerdrveqkrsd 303
                                       + ++++e++ +l    +    +v ++++  +f++++   +++  + + e+++++++ald+y+   +    v  + ++
  gi|385805336|ref|YP_005841734.1| 204 ICNKIEEIMGSLG---IDGgYIVHQDDTLIAFYPFNpsvIHK--NSKIEKTEKFNDALDKYFYSIDVLRPVALEDEE 275
                                       9999999999998...33325666777999999998554333..567799*************99999999988888 PP

                                       HHHH...HHHHHHHHHHHHHHHHHHHHCCGGHHHHH.CCHH-----------------------..--......... CS
                              FbpA 304 lekr...veneleklekklkklekelekaekaenyr.ligelltaylyaikkgmsevelenyyde.ge......... 366
                                       ++++   + +++e  ek  +k ++  e a+  +++   i+e +++ + +++k++ + ++++     ++         
  gi|385805336|ref|YP_005841734.1| 276 ISRTkasIDKIREDIEKGEQKVKELYEVANRLASFSsYIEEKIKCAR-EVQKKYGWEKVKERCPGiQKvfqnsgeft 351
                                       88887787777777777777777777777766666514688898877.999*****999988776555899999999 PP

                                       ....---------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                              FbpA 367 ....evtIpLdprkspsenAqkyfkkykKlkraveaveeqieetkeeleylesveaaleq 422
                                           + + + ++  ++  +  k f+++kKlk++ve+++  +e  + +l+ l+ ++++ e+
  gi|385805336|ref|YP_005841734.1| 352 ldleGKEYKFNIFEDAFTQIGKIFDEAKKLKKKVENAKANLETLELKLKELNLKKHEKER 411
                                       99998889999999*************************************999988883 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 !   78.7   0.1   4.5e-25   4.7e-22       1     109 []     425     537 ..     422     537 .. 0.92

  Alignments for each domain:
  == domain 1  score: 78.7 bits;  conditional E-value: 4.5e-25
                         NFACT-R_1   1 kvfwFkssdgylvimGkDkqeneelikkyleesd..vwfhvdkessahvylrlsegeleeipeelleeaaqlakanS 75 
                                       k++w  + ++ l+i+G+D+q+ne ++kkyl ++   ++fh++++++++++l   e+e  +i+ee + +   +a+++S
  gi|385805336|ref|YP_005841734.1| 425 KYIWSFTRNRLLIIAGRDAQQNEAIVKKYLMKNKksLYFHAEIHGAPSTILL-AENE--DIKEEDIYDTSVIAASYS 498
                                       5677779999*******************7665456***************9.4545..8***************** PP

                         NFACT-R_1  76 ia.gnklssvdvvyvpasnlsktap....ldtGsvgfkg 109
                                       +a ++ l+ vdv++v+ +++skt+p    l++Gs++++g
  gi|385805336|ref|YP_005841734.1| 499 KAwKASLKVVDVFWVHSDQVSKTPPageyLEKGSFMIYG 537
                                       ************************************986 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 !   21.4   0.0     2e-07   0.00021       9      78 ..     434     509 ..     430     526 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2e-07
                         NFACT-R_2   9 kaklIvgReeeEnkfl.kgll..kkdfvslrakshkGplvli.d..gelseedlelaarivarYskgkeeeevevk 78 
                                       +  +I gR+++ n+ + k++l  +k+ + ++a+ h +p +++    ++++eed+  ++ i+a Ysk+ +++   v+
  gi|385805336|ref|YP_005841734.1| 434 RLLIIAGRDAQQNEAIvKKYLmkNKKSLYFHAEIHGAPSTILlAenEDIKEEDIYDTSVIAASYSKAWKASLKVVD 509
                                       56799********998456656666677799999*999999864446899****************8766544443 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   2.3   4.9e-05     0.051      49      96 .]     272     319 ..     243     319 .. 0.87
   2 ?    5.0   0.7     0.029        30      60      96 .]     364     400 ..     332     418 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.9e-05
                           BLOC1_2  49 kleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLEakfk 96 
                                       + e+++++++++++  + i++ e++v+eL e++++L ++s+ +E+k+k
  gi|385805336|ref|YP_005841734.1| 272 EDEEISRTKASIDKIREDIEKGEQKVKELYEVANRLASFSSYIEEKIK 319
                                       5578899999************************************97 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.029
                           BLOC1_2  60 lqpylqqidqiekqvteLeeavseLDeyskeLEakfk 96 
                                       ++  ++qi +i ++ ++L++ v+   +    LE k+k
  gi|385805336|ref|YP_005841734.1| 364 FEDAFTQIGKIFDEAKKLKKKVENAKANLETLELKLK 400
                                       4444444444444444444444444444444444432 PP

>> Tweety  Tweety
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0         2   2.1e+03     285     314 ..     276     305 ..     245     321 .. 0.61
   2 ?   12.7   0.1   3.6e-05     0.038     124     189 ..     365     431 ..     339     439 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2
                            Tweety 285 Ltesqkaltemqeqveellriavelfptae 314
                                       ++ ++ ++++++e++e+ ++   el++ a+
  gi|385805336|ref|YP_005841734.1| 276 ISRTKASIDKIREDIEKGEQKVKELYEVAN 305
                                       444455555555555555555555555443 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 3.6e-05
                            Tweety 124 eeeLtkleeifakrtdlletlrlvqeqveevvqqlselp.flkkkdvsltelaeqvelvelyRWlay 189
                                       e+  t++ +if++ ++l + +++++ ++e++  +l+el+   ++k+ +++++a++ + +e+y W  +
  gi|385805336|ref|YP_005841734.1| 365 EDAFTQIGKIFDEAKKLKKKVENAKANLETLELKLKELNlKKHEKEREVKAIARKRDWYEKYIWSFT 431
                                       6678999********************************55557799*****************754 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0    0.0088       9.3      21      55 ..     271     305 ..     251     321 .. 0.75
   2 ?    6.2   0.3    0.0094       9.9       8      54 ..     367     413 ..     361     422 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0088
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II  21 plsqnlentkeklseinrsveetnekvkdankair 55 
                                         ++++++tk+++ +i++++e+ ++kvk++ ++ +
  gi|385805336|ref|YP_005841734.1| 271 LEDEEISRTKASIDKIREDIEKGEQKVKELYEVAN 305
                                       45678999999999999999999999997666543 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0094
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II   8 anetakevleqlaplsqnlentkeklseinrsveetnekvkdankai 54 
                                       a  ++ ++ +  ++l++++en k++l++++ +++e n k +++ + +
  gi|385805336|ref|YP_005841734.1| 367 AFTQIGKIFDEAKKLKKKVENAKANLETLELKLKELNLKKHEKEREV 413
                                       55556667777888999999999999999999998888777665554 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.5     0.026        27      39      99 ..     263     323 ..     246     328 .. 0.82
   2 ?   10.7   1.2    0.0004      0.42      15      81 ..     355     421 ..     349     431 .. 0.59

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.026
                             DHR10  39 iklleeieaelakleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlre 99 
                                       i++l  ++ e ++   +k+ +++ r+ +e+ e++++el     rl    +  eek+  +re
  gi|385805336|ref|YP_005841734.1| 263 IDVLRPVALEDEEISRTKASIDKIREDIEKGEQKVKELYEVANRLASFSSYIEEKIKCARE 323
                                       677788888888999999999****************999999998888888888877776 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0004
                             DHR10  15 Erkarelqakidalqvvekdlrsciklleeieaelakleeakkklkelrdaleekeielrelerkee 81 
                                       E k  +  +  da++++ k + ++ kl +++e+  a le+ + klkel+ + +eke+e++ + rk++
  gi|385805336|ref|YP_005841734.1| 355 EGKEYKFNIFEDAFTQIGKIFDEAKKLKKKVENAKANLETLELKLKELNLKKHEKEREVKAIARKRD 421
                                       5555555555556666666666666666666666666666666666666666666666666666555 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   2.0   0.00017      0.18       3      52 ..     274     323 ..     273     336 .. 0.89
   2 ?    3.4   0.9     0.081        85       6      53 ..     379     426 ..     371     431 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00017
                           DUF5082   3 tkisklqaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklek 52 
                                       ++is+ +a i++ r++i++ e+k+++L+e+  +l + ++ +++k+k  ++
  gi|385805336|ref|YP_005841734.1| 274 EEISRTKASIDKIREDIEKGEQKVKELYEVANRLASFSSYIEEKIKCARE 323
                                       58**********************************99999999887666 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.081
                           DUF5082   6 sklqaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklekp 53 
                                       +kl+++++ +++++++le k+++L   k + + e +++  k+ + ek+
  gi|385805336|ref|YP_005841734.1| 379 KKLKKKVENAKANLETLELKLKELNLKKHEKEREVKAIARKRDWYEKY 426
                                       577888888888888888888888877777766666666666666665 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.015        15     106     167 ..     278     342 ..     195     348 .. 0.67
   2 ?    5.6   2.7      0.01        11      22      71 ..     370     419 ..     360     422 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.015
                           DUF4795 106 eqeealkkaldtLq...eelkekld.rlelepLkeqleerlkelqkelqeamekedkedeaaglrk 167
                                          ++++k+ ++++   +++ke  + ++ l ++++++ee++k  ++ +q++   e+ +++ +g++k
  gi|385805336|ref|YP_005841734.1| 278 RTKASIDKIREDIEkgeQKVKELYEvANRLASFSSYIEEKIKCARE-VQKKYGWEKVKERCPGIQK 342
                                       4444455555555555566666666777788888888888877773.3433344433456777766 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.01
                           DUF4795  22 elekleekvkelekrledkekklealkkqieelekvkadkeeveeelaek 71 
                                       ++ k+ +++k+l+k+ e+ + +le+l+ +++el+ +k +ke   +++a k
  gi|385805336|ref|YP_005841734.1| 370 QIGKIFDEAKKLKKKVENAKANLETLELKLKELNLKKHEKEREVKAIARK 419
                                       56677888999999999999999999999999999999999877777666 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   1.0     0.023        24      33      76 ..     272     315 ..     266     327 .. 0.82
   2 ?   10.0   5.8   0.00068      0.72       4      48 ..     380     424 ..     376     430 .. 0.58

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.023
                     Tropomyosin_1  33 keqeiksLtkknqqleeevekleeklkeakekaeesekkktnne 76 
                                       +++ei+  +  ++++ e++ek e+k+ke  e a+  ++ ++  e
  gi|385805336|ref|YP_005841734.1| 272 EDEEISRTKASIDKIREDIEKGEQKVKELYEVANRLASFSSYIE 315
                                       57899999999*****************9999887776666555 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00068
                     Tropomyosin_1   4 sLkleaeeaqekaeeleekvKeleqenlekeqeiksLtkknqqle 48 
                                       +Lk   e+a++  e le k+Kel+ ++ eke e+k + +k +  e
  gi|385805336|ref|YP_005841734.1| 380 KLKKKVENAKANLETLELKLKELNLKKHEKEREVKAIARKRDWYE 424
                                       455555666666666666666666666666666666555554433 PP

>> Csm1_N  Csm1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.4     0.041        44      37      67 ..     270     300 ..     266     303 .. 0.83
   2 ?    8.2   2.1     0.003       3.2      18      63 ..     367     412 ..     359     417 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.041
                            Csm1_N  37 etkdqeiesLkeqlaeleekvkeleerrkkq 67 
                                          d+ei++ k+ +++++e++++ e++ k+ 
  gi|385805336|ref|YP_005841734.1| 270 ALEDEEISRTKASIDKIREDIEKGEQKVKEL 300
                                       5679999999999999999999999887765 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.003
                            Csm1_N  18 AdllvsklvhENsvLsqkletkdqeiesLkeqlaeleekvkeleer 63 
                                       A   + k+  E   L++k+e+ +  +e+L+ +l+el+ k +e e +
  gi|385805336|ref|YP_005841734.1| 367 AFTQIGKIFDEAKKLKKKVENAKANLETLELKLKELNLKKHEKERE 412
                                       5556889999**************************9988877654 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 ?    7.9   0.3    0.0039       4.1      15      45 ..     275     302 ..     268     306 .. 0.76
   2 ?    2.8   1.5      0.15   1.6e+02       3      29 ..     379     405 ..     370     416 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0039
                         FlaC_arch  15 eletvkkeneelsksveelkenVkdllsLYE 45 
                                       e++  k++++++++++e+ +++Vk+l   YE
  gi|385805336|ref|YP_005841734.1| 275 EISRTKASIDKIREDIEKGEQKVKEL---YE 302
                                       67778888888888888888888875...44 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.15
                         FlaC_arch   3 delEnklsklsteletvkkeneelsks 29 
                                       ++l +k+++ + +let++ +++el+ +
  gi|385805336|ref|YP_005841734.1| 379 KKLKKKVENAKANLETLELKLKELNLK 405
                                       457777888888888888777777655 PP

>> She9_MDM33  She9 / Mdm33 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   1.2     0.086        91      31      76 ..     282     326 ..     274     332 .. 0.85
   2 ?   10.1   4.0    0.0005      0.53      29      94 ..     368     432 ..     362     461 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.086
                        She9_MDM33  31 eieklkksieeleeeleeakeevreakeayeeaiekrsksqrevne 76 
                                       +i+k++++ie+ e++++e  e v +  +++++ ie++ k  rev++
  gi|385805336|ref|YP_005841734.1| 282 SIDKIREDIEKGEQKVKELYE-VANRLASFSSYIEEKIKCAREVQK 326
                                       7999*********99999876.555668899999999999999975 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0005
                        She9_MDM33  29 YseieklkksieeleeeleeakeevreakeayeeaiekrsksqrevneLLqRkssWspedlerfte 94 
                                       +++i k+ ++ ++l++++e+ak++++++  + +e + k+++  rev++ ++Rk  W ++ +  ft+
  gi|385805336|ref|YP_005841734.1| 368 FTQIGKIFDEAKKLKKKVENAKANLETLELKLKELNLKKHEKEREVKA-IARKRDWYEKYIWSFTR 432
                                       6789999999************************************97.69*************96 PP

>> DUF4315  Domain of unknown function (DUF4315)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       5.9   6.3e+03      47      64 ..       7      24 ..       6      31 .. 0.63
   2 ?    7.5   0.6    0.0038         4       2      19 ..     283     300 ..     276     318 .. 0.83
   3 ?    5.2   7.3      0.02        21       2      34 ..     371     410 ..     370     413 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 5.9
                           DUF4315 47 lspeeLaallkamkegaa 64
                                      ++  +L a+l+++ ++++
  gi|385805336|ref|YP_005841734.1|  7 MTVIDLIAFLRELEKEKI 24
                                      666667777776666554 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0038
                           DUF4315   2 lekieaeieKakeKisel 19 
                                       ++ki+++ieK ++K++el
  gi|385805336|ref|YP_005841734.1| 283 IDKIREDIEKGEQKVKEL 300
                                       789999999999999886 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.02
                           DUF4315   2 lekieaeieKakeKiselqa.......rlkelekqktEaE 34 
                                       + ki  e +K+k+K+++++a       +lkel+ +k+E+E
  gi|385805336|ref|YP_005841734.1| 371 IGKIFDEAKKLKKKVENAKAnletlelKLKELNLKKHEKE 410
                                       568889999999999999998899999***********99 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   1.0    0.0022       2.3      19      60 ..     276     317 ..     271     322 .. 0.53
   2 ?    3.0   4.0      0.08        85      22      64 ..     374     420 ..     362     425 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0022
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXXX CS
                             DivIC  19 ykqlkqeiaalqaelaklkaeneeLeaevkdLksdedyieer 60 
                                       ++++k+ i+++ ++++k  ++ +eL +  ++L s  +yiee+
  gi|385805336|ref|YP_005841734.1| 276 ISRTKASIDKIREDIEKGEQKVKELYEVANRLASFSSYIEEK 317
                                       334445555555555555555555555555555566666665 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.08
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCC-XX.....XXXXXXXXXXXX CS
                             DivIC  22 lkqeiaalqaelaklkaeneeLeaevkdLks.....dedyieerARse 64 
                                       +  e ++l++++++ ka  e Le ++k+L +      e  ++++AR++
  gi|385805336|ref|YP_005841734.1| 374 IFDEAKKLKKKVENAKANLETLELKLKEL-NlkkheKEREVKAIARKR 420
                                       55788999999999999999999999999.778898899999999975 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.9   0.00087      0.91     176     259 ..     243     327 ..     198     340 .. 0.63
   2 ?    2.9   7.1     0.038        40     200     248 ..     377     425 ..     354     434 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00087
                              Spc7 176 kaeleeeleklqeaaeelesid.keeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeia 251
                                        +++e++ +   +  + + sid    ++   ee+++ ka i++ ++++++ +++++el e  + l++  s +ee+i+
  gi|385805336|ref|YP_005841734.1| 243 NSKIEKTEKFNDALDKYFYSIDvLRPVALEDEEISRTKASIDKIREDIEKGEQKVKELYEVANRLASFSSYIEEKIK 319
                                       55555554444444445555554444444557888888888888888888888888888888888888888888888 PP

                              Spc7 252 eaervlee 259
                                        a++v+++
  gi|385805336|ref|YP_005841734.1| 320 CAREVQKK 327
                                       77666653 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.038
                              Spc7 200 eLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkselee 248
                                       e ++l+++++++ka++e ++ +l+el+ ++ e+e ++++++ +++ +e+
  gi|385805336|ref|YP_005841734.1| 377 EAKKLKKKVENAKANLETLELKLKELNLKKHEKEREVKAIARKRDWYEK 425
                                       4567788888888888888888888888888888888887777665555 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.5    0.0068       7.2       4      33 ..     274     303 ..     273     322 .. 0.81
   2 ?    3.9   3.8      0.06        63      19      44 ..     377     402 ..     369     419 .. 0.76
   3 ?   -0.4   0.0       1.3   1.3e+03      23      38 ..     588     603 ..     585     614 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0068
                              XhlA   4 erlerietkldnleervdkleekaaeaeek 33 
                                       e++ r+++ +d++ e+++k e+k  e +e 
  gi|385805336|ref|YP_005841734.1| 274 EEISRTKASIDKIREDIEKGEQKVKELYEV 303
                                       789999999999999999999998887765 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.06
                              XhlA  19 rvdkleekaaeaeekiknleedlkkl 44 
                                       + +kl++k ++a+++++ le +lk+l
  gi|385805336|ref|YP_005841734.1| 377 EAKKLKKKVENAKANLETLELKLKEL 402
                                       56788888888888888888888877 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.3
                              XhlA  23 leekaaeaeekiknle 38 
                                        +e a++ ++ iknl+
  gi|385805336|ref|YP_005841734.1| 588 AQEVANKIYQYIKNLN 603
                                       56999*********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (629 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1649  (0.0919739); expected 358.6 (0.02)
Passed bias filter:                      730  (0.0407162); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); 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):              17  [number of targets reported over threshold]
# CPU time: 0.78u 0.34s 00:00:01.12 Elapsed: 00:00:00.56
# Mc/sec: 3388.38
//
Query:       gi|385805337|ref|YP_005841735.1|  [L=142]
Description: inosine-5'-monophosphate dehydrogenase-like protein V [Fervidicoccus fontis Kam940]
Scores for complete 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  109.4   6.2    8.2e-16   58.2   1.5    2.1  2  CBS         CBS domain
  ------ inclusion threshold ------
      0.053   13.6   0.0       0.56   10.3   0.0    2.2  2  AhpC-TSA_2  AhpC/TSA antioxidant enzyme


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 !   58.2   1.5   9.2e-20   8.2e-16       1      55 [.      10      64 ..      10      66 .. 0.95
   2 !   54.0   0.2   1.9e-18   1.7e-14       1      53 [.      76     127 ..      76     131 .. 0.95

  Alignments for each domain:
  == domain 1  score: 58.2 bits;  conditional E-value: 9.2e-20
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55
                                      V+d+m+ +vvtv+p+t+l ea+++m e++++++ VV+e g l+Gi+t++Dl+ ++
  gi|385805337|ref|YP_005841735.1| 10 VKDLMSFNVVTVDPNTSLDEAVRIMLENNIGSVVVVNEKGVLIGILTEKDLITKV 64
                                      89*******************************889***************9875 PP

  == domain 2  score: 54.0 bits;  conditional E-value: 1.9e-18
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53 
                                       V+dim+ +vv+v pdt+l ea+ lm +k++++lPVV ++g++vGi+   D+++
  gi|385805337|ref|YP_005841735.1|  76 VKDIMSAPVVYVEPDTPLYEAVALMQSKKIGHLPVV-KNGRVVGIIATGDIIS 127
                                       89***********************9999*******.9*************97 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 ?    0.8   0.0     0.057   5.1e+02      27      51 ..       6      31 ..       2      43 .. 0.80
   2 ?   10.3   0.0   6.3e-05      0.56      19      63 ..      64     109 ..      51     124 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.057
                        AhpC-TSA_2 27 kkFvkltgfpfe.lyvDpsaklyqal 51
                                      k++     ++f+ + vDp+ +l +a+
  gi|385805337|ref|YP_005841735.1|  6 KEYSVKDLMSFNvVTVDPNTSLDEAV 31
                                      566667778999999****9997776 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 6.3e-05
                        AhpC-TSA_2  19 igigdpsakkFvkltgfpfe.lyvDpsaklyqalglkrglklklap 63 
                                       +++g+ ++k++     ++++ +yv+p+  ly+a+ l ++ k++  p
  gi|385805337|ref|YP_005841735.1|  64 VIKGKLDLKDLKVKDIMSAPvVYVEPDTPLYEAVALMQSKKIGHLP 109
                                       7888999999999999********************9999887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 876.08
//
Query:       gi|385805338|ref|YP_005841736.1|  [L=405]
Description: S-adenosylmethionine synthetase [Fervidicoccus fontis Kam940]
Scores for 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-169  563.6   3.8   2.3e-169  563.4   3.8    1.0  1  AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synt


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 !  563.4   3.8  1.3e-173  2.3e-169       1     395 [.       3     400 ..       3     401 .. 0.98

  Alignments for each domain:
  == domain 1  score: 563.4 bits;  conditional E-value: 1.3e-173
                                       --EEEEE-TTS-GTTSSEEEEEEE-TTSHHHHHHHHHHHHHHHHHHHHHHHHSS---EEEEEEEEE--EEEEETTEE CS
                   AdoMet_Synthase   1 rnivveelkkkpveeqevEivErKGiGHPDsiaDgiaeavsralskeylekfgailhhniDkvllvaGesepkfgGG 77 
                                       +ni vee++ +  +++e+E+vErKGiGHPD+iaD+++e+vs  ls++y+e++g+ilhhn+Dkvl+v+G+s+pkf+GG
  gi|385805338|ref|YP_005841736.1|   3 KNIYVEEVEWQLPQDMEIELVERKGIGHPDYIADSASEEVSIGLSNYYIEHYGRILHHNVDKVLIVGGQSDPKFRGG 79 
                                       69*************************************************************************** PP

                                       EEEE-EEEEEEEEEEEEE.....EEE--HHHHHHHHHHHHHHHH-SS--TTTSEEEEEEEEEEEEHHHHHHCH-SS. CS
                   AdoMet_Synthase  78 eviepieillsgratkev....egekipveeialeaakeylkenlraldlekdvivdvklgkgsadLkdvferkkke 150
                                       +v++pi+il+sgrat++v    + e++p+++i+++++k+++k+n+r+ld+e++vivd+k+gkgs+dL+++f+r  + 
  gi|385805338|ref|YP_005841736.1|  80 RVLHPIYILVSGRATTTVktddGIENVPIGTIIMSSVKKWIKNNMRYLDPEEHVIVDYKIGKGSEDLTGIFDRGLS- 155
                                       ******************76666688***********************************************655. PP

                                       .-BESSSEEEEEEES--HHHHHHHHHHHHHTSHHHHHH-TTEEEEEEEEEEEETTEEEEEEEEEEEGGG--SHHHHH CS
                   AdoMet_Synthase 151 vplaNDtSfgvgyaplseleklvleterllnskelkkklpevGeDiKvmglRekkkielTvavalvdrlvkdleeYl 227
                                       vp+aNDtSfg+g++p+s+le++v++ter+lns e+kkk+pe+GeDiKvmglR+kk+i+lT+a a++++lv+d+++Y+
  gi|385805338|ref|YP_005841736.1| 156 VPHANDTSFGIGFYPYSTLENVVYQTERFLNSPEMKKKIPELGEDIKVMGLRNKKEIDLTIAGAMISKLVDDKDHYI 232
                                       9**************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHSTTSEEEEEE-TT-BGGGTB--EESSSSGGGTT--EETTSS--TTSSB-TTS----S--T CS
                   AdoMet_Synthase 228 evkeeikeeveelakkltkerevevevNtaDkkeeesvyltvtGtsaEegDdGsvGRGNRvnGlitpnrpmslEAaa 304
                                       ++ke++ eev +++++l+ e+e+++++Nt D++e++++yltvtGtsaE+gDdG++GRGNR+nGlitp+rpmslEA+a
  gi|385805338|ref|YP_005841736.1| 233 NIKEKVVEEVYKYTERLAPEYEIKIFFNTGDSPEKNIFYLTVTGTSAEHGDDGATGRGNRANGLITPMRPMSLEATA 309
                                       ***************************************************************************** PP

                                       TS-TTT-HHHHHHHHHHHHHHHHHHH-TTEEEEEEEEEE-TTSBTTS-SEEEEEEEESSS---HHSHHHHHHHHHHH CS
                   AdoMet_Synthase 305 GKNPvsHvGKiYnvlaneiakeiveevegvkevyvrllsqiGkpidePlvasvqvilekgvsleevekeveeiidee 381
                                       GKNPv+HvGKiYn++a+  +k+i+ee+++ ++v v++lsqiG+pid+Pl+ s++++ +++  ++++++e+++ii++e
  gi|385805338|ref|YP_005841736.1| 310 GKNPVNHVGKIYNIIAMLASKKIYEELHEEAHVIVQILSQIGRPIDDPLATSIKLTSKTKPITNDMKEEARNIIEQE 386
                                       ***************************************************************************** PP

                                       HT-HHHHHHHHTTT CS
                   AdoMet_Synthase 382 lekieeiteelieg 395
                                       l++i++ t+ ++e+
  gi|385805338|ref|YP_005841736.1| 387 LKEITKYTKLILEK 400
                                       *********99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       876  (0.0488594); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.52
# Mc/sec: 2335.97
//
Query:       gi|385805339|ref|YP_005841737.1|  [L=639]
Description: hypothetical protein FFONT_0295 [Fervidicoccus fontis Kam940]
Scores for complete 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  151.3   0.3    3.3e-44  150.0   0.0    1.8  2  DUF460       Protein of unknown function (DUF460)
  ------ inclusion threshold ------
      0.012   16.1   7.1       0.55   10.7   0.4    4.2  3  MitMem_reg   Maintenance of mitochondrial structure and funct
      0.026   14.3   0.0        3.3    7.6   0.0    2.6  2  DRTGG        DRTGG domain
        2.2    9.0   7.1        2.8    8.6   0.2    2.9  3  SlyX         SlyX


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 !  150.0   0.0   7.3e-48   3.3e-44       3     141 .]     201     338 ..     199     338 .. 0.95
   2 ?   -3.3   0.0       1.4   6.4e+03      66      79 ..     568     581 ..     558     633 .. 0.58

  Alignments for each domain:
  == domain 1  score: 150.0 bits;  conditional E-value: 7.3e-48
                            DUF460   3 kskdvkvevesvekdkiefeplkkkrkkklivGiDPGittgiavldldgevlalkssreldreevieliselGkpvi 79 
                                       +++ v++e+++    ++ f+++ kk++k++ivGiDPG+++gia+ld++g++l+l ++r+ dreevieli+++G+pvi
  gi|385805339|ref|YP_005841737.1| 201 QGTSVSIEIKNDLVISFAFKKE-KKEDKPIIVGIDPGLNFGIAILDIEGNLLYLGTKRSGDREEVIELIQSYGSPVI 276
                                       67899**************877.9***************************************************** PP

                            DUF460  80 vAtDvspppetvkklarslkavlyvPeedlsveeKeelaeklseke.kvkykddHeRDalaAA 141
                                       +A+Dv+p+p+tvkk+a++++a+l++Pee+lsve K+e+a ++ + + ++   d+H+RDa +AA
  gi|385805339|ref|YP_005841737.1| 277 IAADVKPVPDTVKKIASKFNAELFIPEESLSVEVKREMAFNALSGTsDI-SLDSHMRDAYSAA 338
                                       ***************************************9988888455.88**********8 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.4
                            DUF460  66 evieliselGkpvi 79 
                                        + +l++e G pv+
  gi|385805339|ref|YP_005841737.1| 568 GIYNLLKENGIPVV 581
                                       55666666666665 PP

>> MitMem_reg  Maintenance of mitochondrial structure and function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.068   3.1e+02      35      86 ..      23      70 ..       5      87 .. 0.76
   2 ?    2.8   1.5     0.034   1.5e+02      20      49 ..     329     358 ..     311     462 .. 0.79
   3 ?   10.7   0.4   0.00012      0.55      10      56 ..     467     512 ..     459     536 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.068
                        MitMem_reg 35 ilqerldlikdYl.kkveegelpvnheilrnlqkllnllPhleteelekefnv 86
                                      +l+++++l+ dY+ kkv+++++   +  +r+l+ +++l P  ++      ++v
  gi|385805339|ref|YP_005841737.1| 23 GLEKIIRLAWDYNvKKVATDNIFELAPNVRELKRIISLFPENTE-----FIQV 70
                                      58999999999976999999754445577777777777795444.....2334 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.034
                        MitMem_reg  20 stlstglnrqyyslkilqerldlikdYlkk 49 
                                       s +    ++ y++ k l++ l+++ +Yl +
  gi|385805339|ref|YP_005841737.1| 329 SHMRDAYSAAYNAFKTLSKKLKEVDEYLLR 358
                                       6667777888999999*******9999854 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00012
                        MitMem_reg  10 llkpsiqdasstlstglnrqyyslkilqerldlikdYlkkveege...lp 56 
                                       +lk+si+    +l ++l+++   +k+l+er+++ +d l+k+++ge   +p
  gi|385805339|ref|YP_005841737.1| 467 VLKESIS----ELNKQLEAKNLDIKMLEERVKEYEDILDKLVKGEyipVP 512
                                       5666777....*******************************99965533 PP

>> DRTGG  DRTGG domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.011        50      47      84 ..     258     294 ..     257     308 .. 0.73
   2 ?    7.6   0.0   0.00073       3.3      52      91 ..     544     583 ..     533     594 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.011
                                       ETT-HHHHHHHTT-TEEEEEEETT----HHHHHHHHHH CS
                             DRTGG  47 pGDRediqlaaleagiaalilTgglepseevlklaeea 84 
                                       +GDRe++++ + + g + +i++ +++p ++ +k ++ +
  gi|385805339|ref|YP_005841737.1| 258 SGDREEVIELIQSYG-SPVIIAADVKPVPDTVKKIASK 294
                                       69*******999999.7777777777665555444433 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00073
                                       HHHHHHTT-TEEEEEEETT----HHHHHHHHHHT--EEE- CS
                             DRTGG  52 diqlaaleagiaalilTgglepseevlklaeeaglpvlsv 91 
                                       di + + +++i+++++  ++  ++ +++l++e+g+pv+s+
  gi|385805339|ref|YP_005841737.1| 544 DIGILLKNKNIRGILISYQYSENSGIYNLLKENGIPVVSI 583
                                       6666666677***************************997 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.3     0.027   1.2e+02      20      52 ..     411     443 ..     404     452 .. 0.84
   2 ?    8.6   0.2   0.00063       2.8       9      46 ..     462     499 ..     459     509 .. 0.60
   3 ?   -3.0   0.1       2.7   1.2e+04      41      48 ..     606     613 ..     591     623 .. 0.54

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.027
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXX CS
                              SlyX  20 eeLndvvaeqqqqidrlqrqlrllaerlkelee 52 
                                       ++Ln+++ +  ++   l++++++l+e+lk+ ++
  gi|385805339|ref|YP_005841737.1| 411 KKLNEELEKIKKENILLKAKINKLYEELKNKDK 443
                                       689999999999999**********99987654 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00063
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                              SlyX   9 EiklafqedtieeLndvvaeqqqqidrlqrqlrllaer 46 
                                       E  ++ + + i eLn+++ + + +i+ l++++++ ++ 
  gi|385805339|ref|YP_005841737.1| 462 ERTMSVLKESISELNKQLEAKNLDIKMLEERVKEYEDI 499
                                       55555566666666666666666666666666555544 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 2.7
                                       HHHHHT-X CS
                              SlyX  41 rllaerlk 48 
                                       ++ +e+lk
  gi|385805339|ref|YP_005841737.1| 606 KEAEEKLK 613
                                       22222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (639 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2409  (0.134363); expected 358.6 (0.02)
Passed bias filter:                      647  (0.0360868); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.91u 0.35s 00:00:01.26 Elapsed: 00:00:00.51
# Mc/sec: 3747.55
//
Query:       gi|385805340|ref|YP_005841738.1|  [L=295]
Description: RIO-like serine/threonine kinase [Fervidicoccus fontis Kam940]
Scores for complete 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-43  148.1   0.5    2.8e-43  147.7   0.5    1.1  1  RIO1            RIO1 family
    1.4e-16   60.4   0.1    3.6e-16   59.2   0.1    1.7  1  Rio2_N          Rio2, N-terminal
    0.00026   21.0   0.2      0.018   14.9   0.1    2.1  2  APH             Phosphotransferase enzyme family
    0.00029   19.7   0.0    0.00034   19.5   0.0    1.1  1  Pkinase_fungal  Fungal protein kinase
     0.0062   16.8   0.2      0.013   15.8   0.2    1.5  1  Rrf2            Transcriptional regulator
  ------ inclusion threshold ------
      0.031   13.6   0.1      0.045   13.1   0.1    1.2  1  Pkinase         Protein kinase domain
      0.033   13.8   0.2          1    8.9   0.1    2.1  2  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 !  147.7   0.5   1.1e-46   2.8e-43       2     186 ..     109     286 ..     108     288 .. 0.94

  Alignments for each domain:
  == domain 1  score: 147.7 bits;  conditional E-value: 1.1e-46
                                       EEEEEETTTEEEEEEEE-S---SS-HHHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEEE CS
                              RIO1   2 VyhavsedgkevaiKiyktstteFkkrkkyvsgekrfkdrksktnprklvklwaekEfrnLkrleeagvpvPkpiel 78 
                                       +y+a+   +  +a+K++ +++++Fkk ++ +s+  +    + ++n+ + +k++a++E+++L  l++    v +++ +
  gi|385805340|ref|YP_005841738.1| 109 IYEAIGPGNLRLALKFHMVGRRSFKKTERLRSYVLE----QRTSNWFDESKISAQREYKALDILSKYTKYVSEVVGY 181
                                       89999999999***********************99....4589********************************* PP

                                       ETTEEEEE--EETTEEGGBHHHCG-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEE..TTEEEE--GTTEE CS
                              RIO1  79 krhvlvmefigedgvaapklkdveeeeeaeelyeevleemrklykeaglvHaDLSeyNvlvd..edkvviIDvsQav 153
                                       +r+ +vm++++  gv+++k+k+++   + e+++ ++le + ++y+++g+vH+DLSeyN++++  ++ +v+ID++Q+ 
  gi|385805340|ref|YP_005841738.1| 182 NRNLVVMKYVE--GVELYKIKELK---NPETVFLKILEVIDIAYNKVGIVHGDLSEYNIIIKlpDEIPVLIDWPQYF 253
                                       ***********..***********...999******************************98434589********* PP

                                       ETTSTTHHHHHHHHHHHHHHHHHTTC-----HH CS
                              RIO1 154 eldhpnalefLerDveniikfFrrkgvekvdee 186
                                       +++hpna ++L+rD+ n+++fF++k+ ++++ e
  gi|385805340|ref|YP_005841738.1| 254 DKNHPNANSYLKRDIYNVCTFFNKKYNSQLNCE 286
                                       *************************99977655 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.2   0.1   1.4e-19   3.6e-16       4      81 ..      13      90 ..      10      91 .. 0.96

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 1.4e-19
                            Rio2_N  4 LskedfrvLtavEmgmrnhevVptelieeisrlkeeevkkrlsrllkaklisrktakydGYkLtyeGyDyLALktlvk 81
                                      + +e fr+L a+E g  ++e+Vp + i++ +r+++e++++ l+ l   kli+r+  ++ GYkLty G+ +++L+++v+
  gi|385805340|ref|YP_005841738.1| 13 IPNEGFRILIAIESGLHKYEYVPISYIHQKARISSEKMNSILNLLSSLKLIRRQIGSIVGYKLTYLGLNMISLSAIVR 90
                                      66899********************************************************************99886 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.015        38      17      84 ..     134     198 ..     121     208 .. 0.78
   2 !   14.9   0.1   7.2e-06     0.018     167     193 ..     224     249 ..     217     258 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.015
                                       EETT.--EEEEEE-TT...S-HHHHHHHHHHHHHHHHTT-B--B-CTTBS-EEETTEEEEEEE----EE-SS CS
                               APH  17 ttpa.gryvlrrnppa...raaeeirrevallrlLakagvpvPevlagdtddeeigllfalieyvpgrsllr 84 
                                       +t++ ++yvl +       +++ +++re++ l+ L+k  ++v ev+ +        +  +++ yv+g  l+ 
  gi|385805340|ref|YP_005841738.1| 134 KTERlRSYVLEQRTSNwfdESKISAQREYKALDILSKYTKYVSEVVGY-------NRNLVVMKYVEGVELYK 198
                                       5677788999887777555677788999999999999999******94.......33468888888887776 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 7.2e-06
                                       EEE-SS-SGGGEEEC...TTEEEEE--- CS
                               APH 167 vllHgDlhpgNllvd.pddgrvtGviDf 193
                                       +++HgDl+  N++++ pd+ +v  +iD+
  gi|385805340|ref|YP_005841738.1| 224 GIVHGDLSEYNIIIKlPDEIPV--LIDW 249
                                       79**************999***..**** PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.3e-07   0.00034     285     366 ..     183     259 ..      90     273 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.3e-07
                    Pkinase_fungal 285 rvhrrlvispv.GkpiekaespkellealrDaIkghrsLflkagiLHrDiSenNilitdskkegerkglLiDLDlak 360
                                       r    +v++ v G++++k ++ k+  +++   ++     ++k gi+H D Se+Ni+i      +++  +LiD   + 
  gi|385805340|ref|YP_005841738.1| 183 RN--LVVMKYVeGVELYKIKELKNPETVFLKILEVIDIAYNKVGIVHGDLSEYNIIIK----LPDEIPVLIDWPQYF 253
                                       32..2444433499999999999999999999999999*******************9....667778888876666 PP

                    Pkinase_fungal 361 elsdds 366
                                       + ++++
  gi|385805340|ref|YP_005841738.1| 254 DKNHPN 259
                                       666555 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.2     5e-06     0.013      11      81 ..      18      90 ..      15      91 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5e-06
                                      HHHHHHHHH..SSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCEEESS.HCCCSBHHHHHH CS
                              Rrf2 11 lhallyLak..eeeeepvsseeiaerqnispsylekilakLrkaglvksvrGkgGGyrLak.ppeeItlldvvr 81
                                      +++l+ +++  ++ e  v ++ i+++  is + +  il+ L+  +l++ + G   Gy+L+   ++ I+l  +vr
  gi|385805340|ref|YP_005841738.1| 18 FRILIAIESglHKYE-YVPISYIHQKARISSEKMNSILNLLSSLKLIRRQIGSIVGYKLTYlGLNMISLSAIVR 90
                                      678888865314444.4******************************************862578888888887 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   1.8e-05     0.045      43     141 ..     156     248 ..     113     256 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.8e-05
                                       HHHHHHHHHHHHHS..CTTB--EEEEEEESSEEEEEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHH.H CS
                           Pkinase  43 kkvlrEikilkklk..hpnivrlyevfeekdelylvleyveggeladllerkgslseeeakkiakqilegleylH.s 116
                                        +++rE k l  l+   +++ ++++     ++ ++v+ yveg el ++ e       ++ + ++ +ile ++  + +
  gi|385805340|ref|YP_005841738.1| 156 ISAQREYKALDILSkyTKYVSEVVG----YNRNLVVMKYVEGVELYKIKE------LKNPETVFLKILEVIDIAYnK 222
                                       4455555555555433333333333....3445679*******9999886......456678999**********55 PP

                                       TTEE-SS-SGGGEEEE.TTTEEEE-S CS
                           Pkinase 117 kgiiHrDlKpeNiLid.ekgelKitD 141
                                        gi+H Dl   Ni+i+  ++   ++D
  gi|385805340|ref|YP_005841738.1| 223 VGIVHGDLSEYNIIIKlPDEIPVLID 248
                                       68*************95555555666 PP

>> Choline_kinase  Choline/ethanolamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0    0.0093        24      15      67 ..     153     207 ..     138     210 .. 0.86
   2 ?    8.9   0.1   0.00039         1     124     171 ..     202     249 ..     191     257 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0093
                                       TTCCHHHHHHHHHHHHHHT.TSSS-EEEEETTEEEEE--TCEE-.-TTGGGCHHH CS
                    Choline_kinase  15 eelidretElvvfallser.glgpklygifenGrieefiesrtl.stedlrepei 67 
                                       e+ i+ ++E + + +ls++ ++  +++g   n  + +++e+ +l + ++l++pe+
  gi|385805340|ref|YP_005841738.1| 153 ESKISAQREYKALDILSKYtKYVSEVVGYNRNLVVMKYVEGVELyKIKELKNPET 207
                                       677999***********98468999**************9998846789999886 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00039
                                       HHHHHHHHHTHHHHHHCHGG-EEEE-S--SGGGEEE.-CTTEEEE--G CS
                    Choline_kinase 124 ledlekelekleklleelespvvfcHnDlqegNillnkeekklvlIDF 171
                                       l++ e  + k+ ++++  +++v   H Dl e Ni+ +  ++  vlID+
  gi|385805340|ref|YP_005841738.1| 202 LKNPETVFLKILEVIDIAYNKVGIVHGDLSEYNIIIKLPDEIPVLIDW 249
                                       444445566667777788999***************999999999*99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); 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: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 1710.30
//
Query:       gi|385805341|ref|YP_005841739.1|  [L=271]
Description: FOG CBS domain protein [Fervidicoccus fontis Kam940]
Scores for 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-33  113.6   1.3    5.5e-12   45.9   0.2    4.1  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 !   10.9   0.0   2.6e-05      0.47       7      53 ..      16      64 ..       6      67 .. 0.80
   2 !   25.4   0.0   8.2e-10   1.5e-05       1      54 [.      74     127 ..      74     130 .. 0.92
   3 !   27.7   0.0   1.5e-10   2.7e-06       3      53 ..     141     191 ..     138     193 .. 0.90
   4 !   45.9   0.2   3.1e-16   5.5e-12       1      56 [.     210     265 ..     210     266 .. 0.96

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 2.6e-05
                                      SSCEEEETTSBHHHHHHHHHHHTSSEEEEE..ETTTBEEEEEEHHHHHH CS
                               CBS  7 rdvvtvppdttleealelmrekgvsrlPVV..dedgklvGivtlrDllr 53
                                      ++++++ p +  + a el+re++++ l V   +++ k+vG++ +  +l+
  gi|385805341|ref|YP_005841739.1| 16 KKFPYLLPYDKASHARELIREYKIRVLAVAnsPNNPKIVGLIKRVNILN 64
                                      68899****************99*5556766554559*****9988875 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 8.2e-10
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHT..SSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS   1 Vgdimtrdvvtvppdttleealelmrekg..vsrlPVVdedgklvGivtlrDllra 54 
                                       V dim  ++  +++d+ +  +l+ + +++  + ++ V++++g++ Giv l+D++++
  gi|385805341|ref|YP_005841739.1|  74 VNDIMEQPIAIIREDDEVDVILNALLKNNewY-GI-VTNSSGEYKGIVGLEDVINY 127
                                       679*********************77777788.**.******************98 PP

  == domain 3  score: 27.7 bits;  conditional E-value: 1.5e-10
                                       HHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                               CBS   3 dimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53 
                                       ++ ++++ ++++d+ +++a  +m e+++ ++PVV  d k+vG +t++Dl++
  gi|385805341|ref|YP_005841739.1| 141 SVLSKKLEYLYEDDEISKAWYKMLEHDYAGFPVVKRDLKVVGSLTQHDLIS 191
                                       688999****************************5555***********97 PP

  == domain 4  score: 45.9 bits;  conditional E-value: 3.1e-16
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                       V++ m+ ++++++ ++ +  a+++m++k+v+r++++d+ gk+ Gi+ ++D++r++ 
  gi|385805341|ref|YP_005841739.1| 210 VKEAMNVPPICIKQSDKVTNAVDEMVNKNVGRVFIIDDGGKIKGIIDRSDIARLIF 265
                                       7899********************************9999*************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.31s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 1582.84
//
Query:       gi|385805342|ref|YP_005841740.1|  [L=310]
Description: putative signal transduction protein [Fervidicoccus fontis Kam940]
Scores for complete 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-19   67.7   4.9    3.6e-08   33.7   0.2    4.0  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 !   15.2   0.0   1.2e-06     0.022       9      55 ..      43      89 ..      33      91 .. 0.81
   2 !   33.7   0.2     2e-12   3.6e-08       1      56 [.     114     169 ..     114     170 .. 0.89
   3 ?    0.2   0.0     0.059   1.1e+03       2      52 ..     178     227 ..     177     230 .. 0.76
   4 !   17.6   0.2   2.2e-07     0.004       1      55 [.     252     306 ..     252     308 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.2e-06
                                      CEEEETTSBHHHHHHHHHHHT..SSEEEEE.ETTTBEEEEEEHHHHHHHH CS
                               CBS  9 vvtvppdttleealelmrekg..vsrlPVV.dedgklvGivtlrDllral 55
                                      +v+v+ ++++ +a+e+m  +     +l+V+   + ++ G+vt + ++++l
  gi|385805342|ref|YP_005841740.1| 43 FVSVSQTSPVLDAIEKM--YTfqEEQLLVLhG-ESNFSGLVTSENVIDYL 89
                                      79***************..553235**99955.555***********998 PP

  == domain 2  score: 33.7 bits;  conditional E-value: 2e-12
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEE.ETTTBEEEEEEHHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVV.dedgklvGivtlrDllrall 56 
                                       V+ im ++ ++v+ ++ l +++  m++++ ++lPV+   d+ + Gi+t+rD++ +l+
  gi|385805342|ref|YP_005841740.1| 114 VKTIMIKESPFVYINEKLPDVISSMIKNKTRALPVLyK-DNTVYGIITQRDIVMLLA 169
                                       7889***99****************99999*****745.55599********99886 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.059
                                       HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHH CS
                               CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDll 52 
                                       g+i+ +++++v+  ++l   +++++++ +++++V +e ++++G +  + ++
  gi|385805342|ref|YP_005841740.1| 178 GEIC-SPIISVNSLDPLIVGMKMLVQTSLDSIYVKNEMDQIIGTLDSSGIV 227
                                       5665.5688999999999999999888899998866677888887766665 PP

  == domain 4  score: 17.6 bits;  conditional E-value: 2.2e-07
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       ++d+m  ++  v+ + ++++++ +m +k++  ++V+de+++ +G++t  D + +l
  gi|385805342|ref|YP_005841740.1| 252 IKDVMQFNIERVYKQVDMGDVISKMFNKKLKTVLVTDENDEDIGMITFDDAFFVL 306
                                       5899999*****************65888*9999***************988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       725  (0.0404373); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 2085.62
//
Query:       gi|385805343|ref|YP_005841741.1|  [L=281]
Description: inosine-5'-monophosphate dehydrogenase-like protein II [Fervidicoccus fontis Kam940]
Scores for complete 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-54  180.3  10.4    2.2e-14   53.6   0.3    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 !   48.9   0.2   3.8e-17   6.8e-13       3      56 ..       7      59 ..       5      60 .. 0.94
   2 !   53.6   0.3   1.2e-18   2.2e-14       1      56 [.      73     128 ..      73     129 .. 0.94
   3 !   39.5   0.1   3.2e-14   5.7e-10       1      54 [.     137     189 ..     137     192 .. 0.90
   4 !   43.2   0.1   2.2e-15     4e-11       1      56 [.     223     279 ..     223     280 .. 0.89

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 3.8e-17
                                      HHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS  3 dimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56
                                      d+ +++v++v p++tl+ a +lm ++++srl+V+ ++gklvGi+t +Dll+al+
  gi|385805343|ref|YP_005841741.1|  7 DYISSPVISVLPSDTLAYARNLMLRHEISRLLVI-DEGKLVGILTSSDLLKALS 59
                                      7889******************************.6***************995 PP

  == domain 2  score: 53.6 bits;  conditional E-value: 1.2e-18
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                       V+d+m+++v+t++ ++++++a+ lm+++ +++l V+d++g +vG++t++Dl++a +
  gi|385805343|ref|YP_005841741.1|  73 VRDVMSKNVITIKINSSISDAAALMKKYMIGSLAVIDNNGDVVGLITRTDLIKAYA 128
                                       89***********************6666***********************9975 PP

  == domain 3  score: 39.5 bits;  conditional E-value: 3.2e-14
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                                       V+d+m ++++t++p  ++  ++++++ek +  + +V ++gk+vGi+t++D++ +
  gi|385805343|ref|YP_005841741.1| 137 VKDYMDKNPPTISPFHPITSVFDKIEEKPYYKVIIV-DSGKPVGIITKKDIIFL 189
                                       89***********************87776588799.6*************976 PP

  == domain 4  score: 43.2 bits;  conditional E-value: 2.2e-15
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEE.ETTTBEEEEEEHHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVV.dedgklvGivtlrDllrall 56 
                                       ++dim++++vtv+pd+ l ea++ m+++++++l V+ +++g l+G++t+  +++a++
  gi|385805343|ref|YP_005841741.1| 223 ASDIMSTNLVTVYPDEKLPEAAKVMIKNKIGSLVVIsESNGLLLGLLTKNEIIDAIS 279
                                       58************************999****55566666566**********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); 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: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1746.52
//
Query:       gi|385805344|ref|YP_005841742.1|  [L=274]
Description: hypothetical protein FFONT_0300 [Fervidicoccus fontis Kam940]
Scores for complete 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-33  113.4   7.8    4.2e-10   39.9   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 !   39.9   0.1   2.4e-14   4.2e-10       5      56 ..      20      70 ..      15      71 .. 0.93
   2 !   28.5   0.1   8.8e-11   1.6e-06       1      50 [.      84     132 ..      84     138 .. 0.89
   3 !   16.2   0.0     6e-07     0.011      20      56 ..     164     200 ..     145     201 .. 0.78
   4 !   30.9   0.4   1.5e-11   2.7e-07       1      55 [.     220     273 ..     220     274 .] 0.92

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 2.4e-14
                                      SBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS  5 mtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56
                                       ++d++t++ ++tl +a++lm++++++r+ VV e++ ++Gi t++D+l++l+
  gi|385805344|ref|YP_005841742.1| 20 LRTDFPTIDKNQTLTQAFKLMEKYRIDRV-VVTENKIPIGIMTKKDVLNKLM 70
                                      6899*****************9999****.9989999***********9986 PP

  == domain 2  score: 28.5 bits;  conditional E-value: 8.8e-11
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrD 50 
                                       V+++ t+++  v++ +t+++a ++m+ek++s++ V+ +d  lvGiv ++D
  gi|385805344|ref|YP_005841742.1|  84 VSSFYTPNLYHVDERSTVADAGREMKEKKISSVAVMKDDA-LVGIVIRMD 132
                                       6788899******************9999*******6555.*****8888 PP

  == domain 3  score: 16.2 bits;  conditional E-value: 6e-07
                                       HHHHHHHHHT.SSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS  20 ealelmrekg.vsrlPVVdedgklvGivtlrDllrall 56 
                                        + e++ +++ v  lPVVd ++ l G++t   +++all
  gi|385805344|ref|YP_005841742.1| 164 SLREIFLKEDvV-YLPVVDPNNYLAGYITVNNIADALL 200
                                       444555578856.*****9999999*********9986 PP

  == domain 4  score: 30.9 bits;  conditional E-value: 1.5e-11
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       V+++m+r++++v+ ++++++a +l++e+  +++ V+++d  l+Gi+ + D+lr +
  gi|385805344|ref|YP_005841742.1| 220 VEEVMSRPPLFVYSSDPISKASKLIIEHQSRGVSVIEKDL-LIGIIDDNDILRNI 273
                                       89**********************99*9999*****5555.99*********965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1733.55
//
Query:       gi|385805345|ref|YP_005841743.1|  [L=159]
Description: hypothetical protein FFONT_0301 [Fervidicoccus fontis Kam940]
Scores for complete 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-33  113.5   0.0      1e-32  113.3   0.0    1.1  1  Mut7-C        Mut7-C RNAse domain
    1.4e-05   24.8   0.1    2.6e-05   23.9   0.1    1.4  1  DUF5615       Domain of unknown function (DUF5615)
      0.003   17.2   0.1      0.005   16.5   0.1    1.3  1  DUF188        Uncharacterized BCR, YaiI/YqxD family COG1671
  ------ inclusion threshold ------
       0.02   14.6   1.1      0.051   13.2   1.1    1.6  1  TackOD1       Thaumarchaeal output domain 1
      0.038   14.2   0.9      0.099   12.9   0.9    1.7  1  DUF2197       Uncharacterized protein conserved in bacteria (
       0.04   13.9   0.1      0.059   13.4   0.1    1.3  1  Ogr_Delta     Ogr/Delta-like zinc finger
      0.061   13.6   0.1      0.087   13.1   0.1    1.3  1  DUF3268       zinc-finger-containing domain
      0.076   12.5   1.4       0.34   10.5   1.4    2.1  1  TF_Zn_Ribbon  TFIIB zinc-binding
       0.11   12.5   0.4        4.7    7.3   0.1    2.3  2  ADK_lid       Adenylate kinase, active site lid
       0.74    9.6   3.0        7.4    6.4   1.3    2.2  2  zf-RRN7       Zinc-finger of RNA-polymerase I-specific TFIIB,


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 !  113.3   0.0   5.6e-36     1e-32       1     145 [.       3     148 ..       3     149 .. 0.88

  Alignments for each domain:
  == domain 1  score: 113.3 bits;  conditional E-value: 5.6e-36
                            Mut7-C   1 krfllDamlgklakyLRllGydalyasdvedeellalaakekrillTrdreLlkraklkkg..vll..tsrdveeql 73 
                                       krf++D mlg++a+yLR+lGyd+ly+ d +d+e++++a+ke+ri++T+d  L k+a    +  +l+  + +++++ l
  gi|385805345|ref|YP_005841743.1|   3 KRFIVDCMLGNVARYLRILGYDTLYEIDISDDEIIEKAKKEDRIIITKDNLLWKKALSDGAnaFLVkkSYSNTKDIL 79 
                                       69****************************************************998776677444336789999** PP

                            Mut7-C  74 reviarlglklslkpelsrCvaCngeleevekeevkervpekvyeeadeftrCekCrkvfWkGshwerveel 145
                                       +e+ ++  ++l+++p+ srC  Cng+l    ++     ++ + ++e + ++ C++C+ ++W G h++++ ++
  gi|385805345|ref|YP_005841743.1|  80 CELKKNGLISLKFSPHNSRCPLCNGKLMISINQPL---LKIHKNSEMRVYFVCQSCGNIYWIGKHFKNILKT 148
                                       ***999999******************87766666...4444555566689*****************9876 PP

>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.1   1.5e-08   2.6e-05      13      55 ..      14      51 ..       4      57 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.5e-08
                           DUF5615 13 lvellreaghdvlhvrelglegasDeeileyAkeedriivTkD 55
                                      +++ lr +g+d+l+        +sD+ei+e Ak+edrii+TkD
  gi|385805345|ref|YP_005841743.1| 14 VARYLRILGYDTLYE-----IDISDDEIIEKAKKEDRIIITKD 51
                                      556666666655443.....3489******************* 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 !   16.5   0.1   2.8e-06     0.005      38      74 ..      29      66 ..      24      82 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.8e-06
                            DUF188 38 adaaDdaIveraeagD.lvvTqDipLAarvlekgaaal 74
                                       d  Dd+I+e+a+++D +++T+D  L +++l+ ga a 
  gi|385805345|ref|YP_005841743.1| 29 IDISDDEIIEKAKKEDrIIITKDNLLWKKALSDGANAF 66
                                      6899**********99899***************9986 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.1   2.9e-05     0.051      12     112 ..      35     135 ..      26     144 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.9e-05
                           TackOD1  12 kllayllsrdeeklepvldpkskelysypllealskeke.eseelleelvkrglleeelvdrirlCpsCksghlnvr 87 
                                       ++++  +++d +++  + +   k++ s     +l k++  +++++l el+k+gl+  ++  +   Cp C+++ +  +
  gi|385805345|ref|YP_005841743.1|  35 EIIEKAKKED-RIIITKDNLLWKKALSDGANAFLVKKSYsNTKDILCELKKNGLISLKFSPHNSRCPLCNGKLMISI 110
                                       5555555555.444444444444444444444555656669******************************999988 PP

                           TackOD1  88 evCpkCkSidieeqelihhftCgnv 112
                                       +        + e + ++ + +Cgn+
  gi|385805345|ref|YP_005841743.1| 111 NQPLLKIHKNSEMRVYFVCQSCGNI 135
                                       8877777777888888888888887 PP

>> DUF2197  Uncharacterized protein conserved in bacteria (DUF2197)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.9   5.5e-05     0.099       3      38 ..      97     133 ..      95     135 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.5e-05
                           DUF2197   3 vkCvlCdkveeiddesllaKrLrNrpihtY.mCkeCe 38 
                                        +C lC+ + +i  +++l K  +N  +++Y +C++C 
  gi|385805345|ref|YP_005841743.1|  97 SRCPLCNGKLMISINQPLLKIHKNSEMRVYfVCQSCG 133
                                       69**************************9846****5 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 ?   13.4   0.1   3.3e-05     0.059       1      34 [.      98     133 ..      98     146 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.3e-05
                         Ogr_Delta   1 rCPhCgapaaartsrnlskdvre....ryyqCsnfeCg 34 
                                       rCP+C  +  ++  ++l+k  ++    +y++C+   Cg
  gi|385805345|ref|YP_005841743.1|  98 RCPLCNGKLMISINQPLLKIHKNsemrVYFVCQS--CG 133
                                       7*********************9*********98..76 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   0.1   4.9e-05     0.087       3      53 ..      97     149 ..      95     159 .] 0.69

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.9e-05
                           DUF3268   3 trCpyCGekvilvsaseiYkers..kgkllylCpkCdayvgvhkgtkiplGtl 53 
                                        rCp C +k ++  ++ + k ++  + +++++C++C+    + k+ k  l tl
  gi|385805345|ref|YP_005841743.1|  97 SRCPLCNGKLMISINQPLLKIHKnsEMRVYFVCQSCGNIYWIGKHFKNILKTL 149
                                       69****9999999999877655521566788*****98665555555555555 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.4   0.00019      0.34       2      27 ..      98     134 ..      97     136 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00019
                                       EETTTTCEE.C..........HEETSTTCEEESSSSB CS
                      TF_Zn_Ribbon   2 kCPnCgstn.l..........veDpergelvCtdCGl 27 
                                       +CP C+++  +           + ++r  +vC +CG+
  gi|385805345|ref|YP_005841743.1|  98 RCPLCNGKLmIsinqpllkihKNSEMRVYFVCQSCGN 134
                                       5999999885588888888866669***********8 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 ?    3.3   0.1     0.046        83      22      32 ..      97     107 ..      70     108 .. 0.87
   2 ?    7.3   0.1    0.0026       4.7       3      12 ..     128     141 ..     127     150 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.046
                                       TB-TTT--.-B CS
                           ADK_lid  22 glCDkCGepLv 32 
                                         C  C+++L+
  gi|385805345|ref|YP_005841743.1|  97 SRCPLCNGKLM 107
                                       679******98 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0026
                                       E-TTT--EE....E CS
                           ADK_lid   3 vCpkCGrsY....h 12 
                                       vC +CG +Y    h
  gi|385805345|ref|YP_005841743.1| 128 VCQSCGNIYwigkH 141
                                       9********55544 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.051        92       6      14 ..      98     106 ..      94     111 .. 0.80
   2 ?    6.4   1.3    0.0041       7.4      21      30 ..     126     135 ..     126     136 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.051
                           zf-RRN7   6 pCgvCgcrs 14 
                                       +C+ C++++
  gi|385805345|ref|YP_005841743.1|  98 RCPLCNGKL 106
                                       8*****976 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0041
                           zf-RRN7  21 fyyCrrChtq 30 
                                       +++C++C+++
  gi|385805345|ref|YP_005841743.1| 126 YFVCQSCGNI 135
                                       59******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       976  (0.0544369); expected 358.6 (0.02)
Passed bias filter:                      677  (0.0377601); 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: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1052.80
//
Query:       gi|385805346|ref|YP_005841744.1|  [L=206]
Description: AMMECR1 family protein [Fervidicoccus fontis Kam940]
Scores for complete 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-47  159.7   0.0    5.5e-47  159.5   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 !  159.5   0.0   3.1e-51   5.5e-47       2     165 ..      19     191 ..      18     192 .. 0.93

  Alignments for each domain:
  == domain 1  score: 159.5 bits;  conditional E-value: 3.1e-51
                                       HHHHHHHHHHTTSS-S-HH---HHHHSEEEEEEEEE...EE..CCECCCECEEEEEEHHHHHHHHHHHHHHT-TTS- CS
                           AMMECR1   2 klareaieealkeekkleeeakeelkekaglFVtlk...ekkgeLRGCiGtleperpLaeevaenAlaaAfeDpRFs 75 
                                       k are++e+a+  e+++ ++ +e+l++++++FVt++   ++k+eLRGCiG+++p  pL ++v+e A +aAf+DpRF+
  gi|385805346|ref|YP_005841744.1|  19 KKARESVEKAFIYEEAKINDVPEKLRRPGAAFVTINiikNRKKELRGCIGYVKPVYPLIQTVIEVAREAAFNDPRFP 95 
                                       679****98888888877999***************9876667********************************** PP

                                       ---HHHHTTEEEEEEEE---EE-....-..GGG--TTT-EEEEEETTEEEEE-THHHHHTT--HHHHHHHHHHHHTS CS
                           AMMECR1  76 pvtaeElpeleveVsvLtepepi....v..ledlevgkhGliiekgsrsatlLPqvaveqgwdkeeflasllrKagl 146
                                       p++++E+p  ++eVsvL+ ++++    +  l+++ +gk Gl++ +g +s++lLPqv+ e+gwdke+fl+ ++ Kagl
  gi|385805346|ref|YP_005841744.1|  96 PLQRREYPFTHFEVSVLSGMRELprdpEerLKSIVMGKMGLMVVRGIFSGLLLPQVPIEEGWDKETFLEYTCYKAGL 172
                                       ***********************7654145777******************************************** PP

                                       -TTCCCSTTSEEEEE-EEE CS
                           AMMECR1 147 rpdewkdseikltryevek 165
                                       ++++wkd++++++ + +++
  gi|385805346|ref|YP_005841744.1| 173 EGSCWKDEKTEFYYFVARV 191
                                       *************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1358.64
//
Query:       gi|385805347|ref|YP_005841745.1|  [L=42]
Description: hypothetical protein FFONT_0303 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       217  (0.0121033); expected 358.6 (0.02)
Passed bias filter:                      201  (0.0112109); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 262.98
//
Query:       gi|385805348|ref|YP_005841746.1|  [L=599]
Description: ATP-dependent DNA ligase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-64  217.1   1.3    2.9e-64  216.5   1.3    1.3  1  DNA_ligase_A_M   ATP dependent DNA ligase domain
    5.6e-37  127.7   1.4    1.1e-36  126.7   1.4    1.5  1  DNA_ligase_A_N   DNA ligase N terminus
    2.4e-22   79.4   0.0    4.8e-22   78.4   0.0    1.5  1  DNA_ligase_A_C   ATP dependent DNA ligase C terminal region
    1.6e-06   28.5   0.4    2.5e-06   27.9   0.4    1.3  1  RNA_ligase       RNA ligase
  ------ inclusion threshold ------
      0.011   15.8   0.4       0.19   11.8   0.0    2.8  3  DNA_ligase_OB_2  DNA ligase OB-like domain
       0.13   12.0   1.5        3.8    7.2   0.0    2.4  2  BAR_3            BAR domain of APPL family


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 !  216.5   1.3   9.6e-68   2.9e-64       1     204 []     237     437 ..     237     437 .. 0.98

  Alignments for each domain:
  == domain 1  score: 216.5 bits;  conditional E-value: 9.6e-68
                                       -EEEEEESCHHHHHHHTTTSEEEEEEEESSEEEEEEEETTEEEEEETTS-B-GGGCHHHHHHHHHHBSTTESEEEEE CS
                    DNA_ligase_A_M   1 pmLAeslksiekalkkleekafivEiKyDGeRaqvhkegdkvklfSRrlkditaakpelvkalkeafkkdeksvilD 77 
                                       pmLAe+ ++ + +l+k+ +++++vE+KyDGeRaq+hk++d++++fSRrl++it+++p++v+  ++ +k++  ++i++
  gi|385805348|ref|YP_005841746.1| 237 PMLAERHNDPKVMLEKV-GGKAYVEYKYDGERAQIHKSNDEITIFSRRLENITHQYPDVVEYSRKYIKAN--EAIVE 310
                                       9***************9.89999*******************************************9997..8**** PP

                                       EEEEEEETTTTCBEHHHHHCHHHHCHCCTHHHHHHSEEEEEEEEEEEETTEEHTTSCHHHHHHHHHHHB--BTTTEE CS
                    DNA_ligase_A_M  78 GElvavdketgeilpfqklasrkkkkkkveeklkeaelclfvFDiLyldgesltdeplkeRrklLeeilkesedrve 154
                                       GE+va+d++t+e +pfq l++r k+k+++ +++ke+++++f+FD +y+dg++lt+ pl eRrk+Le+++  ++d+++
  gi|385805348|ref|YP_005841746.1| 311 GEIVAIDPDTRELRPFQILMTR-KRKHDITKMMKEVPVSVFLFDAIYVDGKDLTNFPLPERRKYLESVI-AQSDDMQ 385
                                       **********************.78899*****************************************.******* PP

                                       E--EEEESSHHHHHHHHHHHHHTTECEEEEEE..TT-CC-TTCEEEEEEEEE CS
                    DNA_ligase_A_M 155 laeslevkdveeleelleeaiseglEGlvvKn..pdskYepgkrsknwlKvK 204
                                       +a+ + ++++e+le+++ eais+g+EG+++K+   +s+Y++g+r++ w+K+K
  gi|385805348|ref|YP_005841746.1| 386 IAQYKYIDNAEDLEKMFYEAISNGAEGVMIKSisEKSIYQAGNRGWLWIKYK 437
                                       ********************************8889***************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 !  126.7   1.4   3.8e-40   1.1e-36       2     172 ..       3     185 ..       2     186 .. 0.95

  Alignments for each domain:
  == domain 1  score: 126.7 bits;  conditional E-value: 3.8e-40
                                       CHHHHHHHHHHCC.---HHHHHHHHHHHHHTS-..SHHHHHHHHHH....SS-CCCS-.-----HHHHHHHHHHHHT CS
                    DNA_ligase_A_N   2 FaelaelfekieestkkrlekrailanffrkvesagpedlypalrL....llPdydgr.eygigesllakalaealg 73 
                                       F+ +a++f+++e+  ++r++ +++l ++f+++    ++++ ++++L    l+Pd++g  e+g+ e+ll+ka + al+
  gi|385805348|ref|YP_005841746.1|   3 FEIIARTFDALEK-ISSRIALTNALVDLFKQTS---KDEVKIVVYLiqgrLWPDWKGMpEIGVAEKLLIKAASIALN 75 
                                       78899********.889************8854...568*****************999****************** PP

                                       --HHHHHHHHHHHS-HHHHHHHHHCCHHHH..........------BHHHHHHHHHHHHH-.STTHHHHHHHHHHHH CS
                    DNA_ligase_A_N  74 lskkkikdalakvgDlgevaeevlskrstl..........akkspltieevnelLdklaaa.gkgsedekkkilkkl 139
                                       +++++i++ +++vgDlg+++e++++++  +          +kk++l++++++e++ k+a+a g+gs+d k ++l++l
  gi|385805348|ref|YP_005841746.1|  76 VKEEQINKIYKEVGDLGKAIEQIKASKDATagtltsflgvQKKEKLSVKKIYESFVKIATAeGEGSRDIKLRVLAGL 152
                                       ***********************977777789***************************999*************** PP

                                       HHHS-HHHHHHHHHHHCT---SS--HHHHHHHH CS
                    DNA_ligase_A_N 140 lkraspeEakyliriilkdlriglsektvldal 172
                                       lk a+p Ea++++r+++++lri++++ tv+dal
  gi|385805348|ref|YP_005841746.1| 153 LKDAQPIEARFIVRFVEGRLRINIGDATVMDAL 185
                                       ********************************9 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 !   78.4   0.0   1.6e-25   4.8e-22       1      99 []     462     571 ..     462     571 .. 0.93

  Alignments for each domain:
  == domain 1  score: 78.4 bits;  conditional E-value: 1.6e-25
                                       GGGSEEEEEEEEEE..TTEEEEEEEE-SS--HHHHHHHHHHHG..GGEECTTCESS---HHHHTTEEE-TT-EEEEE CS
                    DNA_ligase_A_C   1 rgglvgslllgvyd..dgkleyvgkvgtGfsdaeleelrkklk..elerkkppfaekvpeeekrdvWvePelvveVk 73 
                                       r+g+++++l++ yd   + +++v+kvgtGf+d+el+++++++k   ++ k+p++ ++  ++    vW+ P++vveV 
  gi|385805348|ref|YP_005841746.1| 462 RAGKLSTILVAGYDpdADVFRTVCKVGTGFTDEELDKMTEEFKgyIIDHKDPRVISEITPD----VWLIPKKVVEVI 534
                                       57899*********98888************************877888888887777666....9*********** PP

                                       ESEEECTSSSTT...........EECT-EEEEE-TTS CS
                    DNA_ligase_A_C  74 faeitasgkyka...........slRfPrfkrlReDk 99 
                                       +ae+t s+ +++           s+RfPrf+++R+Dk
  gi|385805348|ref|YP_005841746.1| 535 GAELTLSPLHTCakgeiskeaglSIRFPRFINWRPDK 571
                                       ************************************8 PP

>> RNA_ligase  RNA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.4   8.4e-10   2.5e-06       4     161 .]     258     437 ..     255     437 .. 0.62

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 8.4e-10
                                       EEEEE-SSEEEEEEEETT.EEEEETTCEB..CTTTHHHHHHTHHHHHHHHHHHHH..ECCEEEEEEEES........ CS
                        RNA_ligase   4 vvtEKlDGtnfriylvke.vgvasRsqil..pfgeekfkefkrwaaalrkklkeklaneelilyGElig........ 69 
                                       +v+ K DG++++i+++++ ++++sR+ +   + +++++           ++ ++ ++ +e i+ GE++         
  gi|385805348|ref|YP_005841746.1| 258 YVEYKYDGERAQIHKSNDeITIFSRRLENitH-QYPDV---V-------EYSRKYIKANEAIVEGEIVAidpdtrel 323
                                       6899************777*******999421.22222...2.......233344454579********87766666 PP

                                       .............SS..TTSS...........EEEEEEEEEEE.CTTBECE--HH.HH.HHHHHCCTB..EEEEE.S CS
                        RNA_ligase  70 ............hsikygglpk..........efyvFdifdir.dkeeqrylspd.ev.ealakglgtvpvlyegkf 121
                                                   h        +            ++Fd + ++ ++ ++  l+ + ++ e + ++ +   ++ ++k+
  gi|385805348|ref|YP_005841746.1| 324 rpfqilmtrkrkH--------DitkmmkevpvSVFLFDAIYVDgKDLTNFPLPERrKYlESVIAQSDDMQIA-QYKY 391
                                       6555555444444........04444444555*********9965445554443302344444433355555.7778 PP

                                       S.HHHHHCCC...HHHHTC--EEEEEESSSSBE.TTE...BSEEEEE CS
                        RNA_ligase 122 l.aaeellel..llskgnkrEGlVikpeselyk.nkg...raifKvk 161
                                       + +ae+l+++  +   +n +EG+ ik+ se    + g     ++K+k
  gi|385805348|ref|YP_005841746.1| 392 IdNAEDLEKMfyE-AISNGAEGVMIKSISEKSIyQAGnrgWLWIKYK 437
                                       8677777777542.44679*******996654444444356667765 PP

>> DNA_ligase_OB_2  DNA ligase OB-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.82   2.5e+03      42      51 ..     257     266 ..     240     269 .. 0.69
   2 ?   11.8   0.0   6.4e-05      0.19       2      36 ..     458     498 ..     457     511 .. 0.74
   3 ?    0.2   0.0      0.27     8e+02      57      66 .]     559     568 ..     548     568 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.82
                                       -EEEEEEE-T CS
                   DNA_ligase_OB_2  42 kiitykyqel 51 
                                       ++++yky+++
  gi|385805348|ref|YP_005841746.1| 257 AYVEYKYDGE 266
                                       5799***987 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 6.4e-05
                                       ...EEEEEEEEEEEEE.T......TEEEEE-SS--HHHHHH CS
                   DNA_ligase_OB_2   2 GkGkykgmlGallvetkk......gkrfkiGsGlsdaqRen 36 
                                       GkGk +g+l  +lv   +      ++  k+G+G++d++  +
  gi|385805348|ref|YP_005841746.1| 458 GKGKRAGKLSTILVAGYDpdadvfRTVCKVGTGFTDEELDK 498
                                       9**************9864444444469********98555 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.27
                                       -EEEEEEEE- CS
                   DNA_ligase_OB_2  57 pRfPsflrvR 66 
                                        RfP+f  +R
  gi|385805348|ref|YP_005841746.1| 559 IRFPRFINWR 568
                                       7*****9998 PP

>> BAR_3  BAR domain of APPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.4      0.02        60      27      70 ..      77     120 ..      65     137 .. 0.78
   2 ?    7.2   0.0    0.0013       3.8      14      57 ..     267     310 ..     266     311 .. 0.95

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.02
                             BAR_3  27 lekklkkllKlckrlieagkaysaaqkqfaqsLrelkkeskgde 70 
                                        e++++k++K++ +l +a +++ a + + a +L ++   +k+++
  gi|385805348|ref|YP_005841746.1|  77 KEEQINKIYKEVGDLGKAIEQIKASKDATAGTLTSFLGVQKKEK 120
                                       5899**************************99999765555544 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0013
                             BAR_3  14 ResleevEaeleelekklkkllKlckrlieagkaysaaqkqfaq 57 
                                       R+++++  +e++  + +l+++++++ +++e  ++y +a++++++
  gi|385805348|ref|YP_005841746.1| 267 RAQIHKSNDEITIFSRRLENITHQYPDVVEYSRKYIKANEAIVE 310
                                       99*************************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (599 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); 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: 0.73u 0.34s 00:00:01.07 Elapsed: 00:00:00.52
# Mc/sec: 3465.55
//
Query:       gi|385805349|ref|YP_005841747.1|  [L=153]
Description: hypothetical protein FFONT_0305 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score 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   1.3      0.015   15.2   1.3    1.2  1  DUF3788     Protein of unknown function (DUF3788)
      0.022   14.4   8.6      0.037   13.7   8.6    1.5  1  CENP-F_N    Cenp-F N-terminal domain
      0.041   13.8   4.5      0.076   12.9   4.5    1.5  1  STAT_alpha  STAT protein, all-alpha domain
        1.3    9.6   4.1        1.2    9.7   2.0    1.9  2  Sec16       Vesicle coat trafficking protein Sec16 mid-region


Domain annotation for each model (and alignments):
>> DUF3788  Protein of unknown function (DUF3788)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   1.3   3.4e-06     0.015      13     104 ..      23     112 ..      13     132 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.4e-06
                           DUF3788  13 lgkeyelwdkllelleetyeepelewsyygkkkgWnvkykkkkktlctlypeegyFkvlivlgekkfealleslsee 89 
                                       l+ke+e+++ ll+ le+  ++++ +++  +k++  ++k+ k  k++  +++   y+k+   +  +k e++l++l++ 
  gi|385805349|ref|YP_005841747.1|  23 LKKEQEYYEFLLAILESGISSQKQNYQE-EKEESVEIKVNK--KSIAIISMSSSYIKLRPLFDVEKNEDMLKELKKD 96 
                                       77889************99999999999.999999999988..999999999************************* PP

                           DUF3788  90 vkklideaktyg.dgk 104
                                       ++ + ++akt+  + +
  gi|385805349|ref|YP_005841747.1|  97 IELIAEDAKTSViEDR 112
                                       ******9999876333 PP

>> CENP-F_N  Cenp-F N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   8.6   8.2e-06     0.037      23      72 ..      16      65 ..       8     128 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.2e-06
                          CENP-F_N 23 lesqldklkkerqqrqfqLesLeaalqkqkqkveseksevaaLkRenqsL 72
                                      le ++ +lkke++   f L  Le+ +  qkq  ++ek+e+ ++k + +s+
  gi|385805349|ref|YP_005841747.1| 16 LEEKIGQLKKEQEYYEFLLAILESGISSQKQNYQEEKEESVEIKVNKKSI 65
                                      8999***************************************9888775 PP

>> STAT_alpha  STAT protein, all-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   4.5   1.7e-05     0.076      17      67 ..      15      62 ..       7     124 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.7e-05
                        STAT_alpha 17 eteqdirkLedeqeeFdfqyqelqkleqeraesekkelkkqk.ellqqmlna 67
                                       +e++i +L++eqe+++f   +l++      +s+k++++++k e+++  +n+
  gi|385805349|ref|YP_005841747.1| 15 FLEEKIGQLKKEQEYYEFLLAILESG----ISSQKQNYQEEKeESVEIKVNK 62
                                      589**********************9....3333333444430444444333 PP

>> Sec16  Vesicle coat trafficking protein Sec16 mid-region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   2.0   0.00028       1.2      64     101 ..       6      52 ..       3      62 .. 0.73
   2 ?    0.4   0.9      0.21   9.5e+02      29      86 ..      49     105 ..      41     125 .. 0.52

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00028
                             Sec16  64 kskkkevlkwLserieeleaevay.............aegelesaaarrae 101
                                       + kk e+ k+L+e+i +l++e++y             +    +++++++++
  gi|385805349|ref|YP_005841747.1|   6 NDKKSELKKFLEEKIGQLKKEQEYyefllailesgisS----QKQNYQEEK 52 
                                       679999******************99999999755431....222222222 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.21
                             Sec16  29 sssksspgevkirslkelv.pssedaskfPGPlvkgkskkkevlkwLserieeleaeva 86 
                                       ++ k+ + e+k+++ +  + + s++      Pl  + +k++++lk L++ ie ++++ +
  gi|385805349|ref|YP_005841747.1|  49 QEEKEESVEIKVNKKSIAIiSMSSSYI-KLRPL-FDVEKNEDMLKELKKDIELIAEDAK 105
                                       444444444444442222211111111.22356.4555666666666666666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1973  (0.110045); 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:                         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: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 901.57
//
Query:       gi|385805350|ref|YP_005841748.1|  [L=601]
Description: serine protease-like protein [Fervidicoccus fontis Kam940]
Scores for complete 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   24.6   0.0    3.9e-05   23.3   0.0    1.5  1  Lon_C      Lon protease (S16) C-terminal proteolytic domain


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 !   23.3   0.0   2.2e-09   3.9e-05      34     178 ..      47     190 ..      42     210 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 2.2e-09
                                       EEETTEEEEEEEEEEEES.S-S-EEEEES-..-HHHHHHHHHHHHHHTSS-GGGSS-SS-TTT-EEEEEE-S-B-GG CS
                             Lon_C  34 awtevGGdlltieavllp.gkgklkltGkl..gdvmkesaqaalsyvrsraeelgidkevfekkdihihvPeGavPk 107
                                       a te GG +l +  +l+p g+g++ + G l  g+   +sa +a+  v   +   + ++ ++ +    i + +  +  
  gi|385805350|ref|YP_005841748.1|  47 AVTEKGGVILKLKISLIPnGSGNIYIKGALfaGNDTLNSAAVAFY-VGLLM--ANKNPMNY-NGI--IEFTSPLTQI 117
                                       678999999999988887689999999998544444455555543.32222..22233333.333..5555556777 PP

                                       GGGGGHHHHHHHHHHHHTS--B-..TTBEE--EE-TT-BEE--S-HHHHHHHHHHTT-SBEEEEGGGGGGTTT CS
                             Lon_C 108 dGPsaGvtlatalvslltgkkvr..kdvamtGeitLrGrvlpiGGlkekllaakragikkvilPkenekdled 178
                                       +GPsa +++a a++ l ++++    +   +tG i + G  + iGG+ +kl a+  +g +   lP +n + l++
  gi|385805350|ref|YP_005841748.1| 118 EGPSASLAIAEAFYMLAKDMNPTslSSSVITGAINIDGLSVIIGGVEDKLNASINSGASYFYLPYSNYNLLAE 190
                                       9************99999876541246679***********************************99887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (601 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1334  (0.0744046); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.70u 0.34s 00:00:01.04 Elapsed: 00:00:00.50
# Mc/sec: 3620.60
//
Query:       gi|385805351|ref|YP_005841749.1|  [L=195]
Description: Uracil-Dna Glycosylase [Fervidicoccus fontis Kam940]
Scores for 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-37  127.0   0.0    7.3e-37  126.7   0.0    1.0  1  UDG       Uracil DNA glycosylase superfamily


Domain annotation for each model (and alignments):
>> UDG  Uracil DNA glycosylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.7   0.0   4.1e-41   7.3e-37       2     153 ..      32     188 ..      31     190 .. 0.93

  Alignments for each domain:
  == domain 1  score: 126.7 bits;  conditional E-value: 4.1e-41
                                       HC-CTT-SEEEEESSTCHHHHHHSSSS.-STT--HHHHHHHCCCCCCCHHGCTEEEEESSS....SECGCTTCCCCT CS
                               UDG   2 gegppdakvvivGeaPgaeedatglpFsgragnllrkllneaglkrdleseqgvyitnvvkcrppgnrdtptsaeik 78 
                                       geg+ ++k v++GeaPg++ed  g+pF+grag+ l+++l+e++++r      +vyitnvvkcrpp+nr +p+  e+ 
  gi|385805351|ref|YP_005841749.1|  32 GEGNLNSKFVLIGEAPGKNEDIYGRPFVGRAGEVLNRALDEIKVDR-----INVYITNVVKCRPPKNR-KPKTNEVL 102
                                       89********************************************.....*****************.******** PP

                                       CCHHHHHHHHHHHHSSEEEEESHHHHHH.............HHHHSCESCCCSCT......SEEEEES-SSTTTTTT CS
                               UDG  79 acaplleeeiellkprlivllGktaakall...........geklgklrgklleak.....irvlplphPsplnrnf 139
                                        c  +l  ++ +++p  ivllG ta k+l+           ++k++++rgkl ++k      + ++++hP++++rn 
  gi|385805351|ref|YP_005841749.1| 103 SCLHYLIFQLMYINPLKIVLLGGTAVKYLYdesfpykkipkEKKISEIRGKLGNFKaydrsFQTYATYHPAMILRN- 178
                                       ****************************97889999***9666************888999***************. PP

                                       TTSHHHHHHHHH.HH CS
                               UDG 140 fksnpelkaeaw.ed 153
                                            +++ e++ ed
  gi|385805351|ref|YP_005841749.1| 179 -----PRLYEVFkED 188
                                       .....4444444355 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); 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: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1165.29
//
Query:       gi|385805352|ref|YP_005841750.1|  [L=377]
Description: family 2 glycosyltransferase [Fervidicoccus fontis Kam940]
Scores for complete 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  114.6   0.1      6e-33  114.0   0.1    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
    9.2e-27   93.6  11.9    1.5e-26   92.9  11.4    1.6  2  GtrA             GtrA-like protein
    2.2e-12   47.3   0.0      3e-12   46.9   0.0    1.1  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
      0.001   18.6   0.1     0.0017   17.9   0.1    1.3  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
     0.0067   15.9   0.0      0.012   15.1   0.0    1.3  1  LNS2             LNS2 (Lipin/Ned1/Smp2)
  ------ inclusion threshold ------
      0.019   14.4   0.0      0.032   13.7   0.0    1.3  1  Glyco_transf_21  Glycosyl transferase family 21
       0.56   10.7   4.9       0.59   10.6   0.8    2.5  3  PEN-2            Presenilin enhancer-2 subunit of gamma secre


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 !  114.0   0.1   2.3e-36     6e-33       1     166 [.       8     175 ..       8     178 .. 0.87

  Alignments for each domain:
  == domain 1  score: 114.0 bits;  conditional E-value: 2.3e-36
                                       EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCH...C-TTEEEEEESSS-HHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelak...edprvrvirreenvGkagalnag 74 
                                       s++ipt+Ne++++ +++e+++a    +d+e+i+vDD+S+D+t +++ + ak    +++vrvi r++ +G+++a+ +g
  gi|385805352|ref|YP_005841750.1|   8 SIIIPTFNEAENIGALFERIAASLANYDYEVIIVDDNSPDNTSKVAVQEAKrldIEKNVRVIVRNNERGLSTAVLRG 84 
                                       8****************************************************************999********* PP

                                       HHH--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCS CS
                   Glycos_transf_2  75 lraatgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnl 151
                                       + +a+g++++++DaD++++p+++++l++++  +++++v+++r+ ++g ++  + ++ +  +  +   +    +  n+
  gi|385805352|ref|YP_005841750.1|  85 MNEAKGKVLVVMDADLQHPPEKIPDLYRKIAIENYKIVIATRMGKNGYKNMPTYRRLI-SKIAGGLAKLLLPKLKNV 160
                                       *******************************************998877655555543.344444444445555577 PP

                                       TTCSTCCCEEEEHHH CS
                   Glycos_transf_2 152 sfeigsaallrreal 166
                                       s+  +++++l+re++
  gi|385805352|ref|YP_005841750.1| 161 SDPMSGFFALKREVY 175
                                       777777777777765 PP

>> GtrA  GtrA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.7   6.9e+03      50      69 ..     209     231 ..     208     235 .. 0.72
   2 !   92.9  11.4     6e-30   1.5e-26       1     117 []     243     359 ..     243     359 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.7
                              GtrA  50 wtFkdrekakl...lkqflkFvl 69 
                                       ++F++r  +k    lk++++++l
  gi|385805352|ref|YP_005841750.1| 209 YVFEKRYAGKSklgLKEYINYIL 231
                                       57777777766678888888886 PP

  == domain 2  score: 92.9 bits;  conditional E-value: 6e-30
                              GtrA   1 rFlivGvlgtlvdlallllllellglsyllAnaiafivailfnFilnrrwtFkdrekakllkqflkFvlvsllglll 77 
                                       +F++vG++gt+v+ a+l+++  +++l+++++ a++++++i++nFiln+++tFk++ek+ ++k+f+++++ s++g+ +
  gi|385805352|ref|YP_005841750.1| 243 KFMLVGLSGTAVNEAALWIFHYIFHLPLYISGAFSIELSIINNFILNSIYTFKSSEKSITFKKFFRYHISSAIGISI 319
                                       7*********************************************************99***************** PP

                              GtrA  78 nllilwllveklgleallaklvgiivalvlnyvlsklfvF 117
                                       n++il +l ++l++e+l+++lvgii+++v ny+ls+++v+
  gi|385805352|ref|YP_005841750.1| 320 NYVILLFLSTILKVEPLISNLVGIIFGFVANYLLSEHYVW 359
                                       ***************************************9 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 !   46.9   0.0   1.2e-15     3e-12       4     138 ..       7     140 ..       5     189 .. 0.77

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 1.2e-15
                   Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaq.eyprvevvvvvdesdaetlevaeelaaalp.dvrvrvvvnarnlgstgksra 78 
                                       +++++ptfne++ +g++ e ++a+ ++ ++ev++v+d+s + t +va + a++l+    vrv+v+ ++   +g s+a
  gi|385805352|ref|YP_005841750.1|   7 ISIIIPTFNEAENIGALFERIAASlANYDYEVIIVDDNSPDNTSKVAVQEAKRLDiEKNVRVIVRNNE---RGLSTA 80 
                                       89********************7746899*****************88889999995589***99774...578899 PP

                   Glyco_tranf_2_3  79 lnealravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfllnrstlvsalga 138
                                       + ++++ +k+++++++D+D    P+ ++ l + ++ +++++v + ++ +n+ + ++ + +
  gi|385805352|ref|YP_005841750.1|  81 VLRGMNEAKGKVLVVMDADLQHPPEKIPDLYRKIAIENYKIVIATRMGKNGYKNMPTYRR 140
                                       9*******************9999999887777767777777766666666655555555 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 !   17.9   0.1   6.5e-07    0.0017       1     114 [.       8     122 ..       8     130 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 6.5e-07
                   Glyco_tranf_2_2   1 svviplraseer.hyieervlqkakyydeeielivvddgSsekflee.vssi....idlnllvylkdeddkayslaa 71 
                                       s++ip  ++ e+   + er+      y  + e+i+vdd S++++ ++ v+      i++n +v ++++     +l+ 
  gi|385805352|ref|YP_005841750.1|   8 SIIIPTFNEAENiGALFERIAASLANY--DYEVIIVDDNSPDNTSKVaVQEAkrldIEKNVRVIVRNN---ERGLST 79 
                                       688987777666145678885555554..689***********7654233331112334444443443...567777 PP

                   Glyco_tranf_2_2  72 arNrGaskaesdlvlFlDaDcfissDkfekilklitikklren 114
                                       a  rG+++a++ +++ +DaD    ++k+  + + i i + + +
  gi|385805352|ref|YP_005841750.1|  80 AVLRGMNEAKGKVLVVMDADLQHPPEKIPDLYRKIAIENYKIV 122
                                       8889****************99888888777766666666555 PP

>> LNS2  LNS2 (Lipin/Ned1/Smp2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   4.6e-06     0.012      62     151 ..      87     183 ..      78     200 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.6e-06
                              LNS2  62 dvlGhilpllgkdwth..kgvaklyskikengYkilylsara...igqaeltreylksveq..dgvkLPkgPvllsp 131
                                       ++ G++l ++  d +h  +++ +ly+ki+ ++Yki+  +  +    +++ + r+++++++    ++ LPk   +  p
  gi|385805352|ref|YP_005841750.1|  87 EAKGKVLVVMDADLQHppEKIPDLYRKIAIENYKIVIATRMGkngYKNMPTYRRLISKIAGglAKLLLPKLKNVSDP 163
                                       678*************5558****************99876511155556667777777765456789********* PP

                              LNS2 132 drllsalkreviekkpeefk 151
                                        + + alkrev+ +++++++
  gi|385805352|ref|YP_005841750.1| 164 MSGFFALKREVYLETKDKLN 183
                                       ***********988777665 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.2e-05     0.032       8      72 ..      70     131 ..      64     173 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.2e-05
                   Glyco_transf_21   8 vsgdpvgvnpKvnnllqaleaakydllvisDsdvrvkpdyLeellaaledpkvglVtslpvgsda 72 
                                       v   ++g++  v   l+++++ak ++lv+ D+d   +p+++ +l ++++ ++ ++V ++ +g + 
  gi|385805352|ref|YP_005841750.1|  70 VRNNERGLSTAV---LRGMNEAKGKVLVVMDADLQHPPEKIPDLYRKIAIENYKIVIATRMGKNG 131
                                       555555555544...99***************************************999887765 PP

>> PEN-2  Presenilin enhancer-2 subunit of gamma secretase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       4.9   1.2e+04      71      86 ..     167     182 ..     165     183 .. 0.86
   2 ?    1.1   0.2       0.2   5.2e+02      45      90 ..     239     284 ..     226     287 .. 0.83
   3 ?   10.6   0.8   0.00023      0.59      25      70 ..     287     329 ..     284     336 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 4.9
                             PEN-2  71 vfqikraewgevgdkl 86 
                                       +f++kr+ + e+ dkl
  gi|385805352|ref|YP_005841750.1| 167 FFALKREVYLETKDKL 182
                                       7999999999999988 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.2
                             PEN-2  45 keirkyvilSaiGalvwlvvllaWalvfqikraewgevgdklsvvi 90 
                                        +i k++++ + G++v  ++l ++ ++f++     g++  +ls++ 
  gi|385805352|ref|YP_005841750.1| 239 YRILKFMLVGLSGTAVNEAALWIFHYIFHLPLYISGAFSIELSIIN 284
                                       5788999999999999999999999999998888888888888775 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00023
                             PEN-2  25 lvNvvyffkeaflkeafeeqkeirkyvilSaiGalvwlvvllaWal 70 
                                       ++N +y fk+  ++ +f   k++ +y i SaiG+ +  v+ll   +
  gi|385805352|ref|YP_005841750.1| 287 ILNSIYTFKSSEKSITF---KKFFRYHISSAIGISINYVILLFLST 329
                                       78********9999999...89*************99999876555 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:                      446  (0.0248759); 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: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 2332.59
//
Query:       gi|385805353|ref|YP_005841751.1|  [L=274]
Description: phosphoesterase [Fervidicoccus fontis Kam940]
Scores for 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-07   29.5   0.3      9e-06   26.3   0.0    1.9  2  Metallophos    Calcineurin-like phosphoesterase
     0.0046   17.2   0.0     0.0079   16.4   0.0    1.4  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0     1e-09     9e-06       5      84 ..      46     137 ..      44     168 .. 0.74
   2 ?    1.3   0.2     0.046   4.1e+02     178     203 ..     159     181 ..     144     182 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1e-09
                                       EEESBTB...........TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSS.....HHHHHHHHHHHHHHHH.. CS
                       Metallophos   5 vigDlHl...........algggqlddllkllddllreekpdlvllaGDlvdrg.....dlekellellaalvky.. 63 
                                       +i+DlHl            l   ql ++++l+ +l++  k+  ++++GD+ +       +  +e++++   ++k+  
  gi|385805353|ref|YP_005841751.1|  46 IIADLHLgfedeaaesgvFLPKMQLKKAIDLIIRLKELTKAKKLIINGDIKNSFnrltiQEREEIIRF---FGKSkd 119
                                       89**********99999978889999999999888888999********8888788766333336666...444444 PP

                                       .TSEEEEEC-TTSCHHHHHHHH CS
                       Metallophos  64 .pipvylllGNHegfeeellnk 84 
                                         + v+l++GNH+    ++ + 
  gi|385805353|ref|YP_005841751.1| 120 lYDEVILVRGNHD----NYVSI 137
                                       4799*********....44333 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.046
                                       SCCHHHHHHHHHHTTESEEEEESSSS CS
                       Metallophos 178 lfgdealedllkkygvdlvisGHtHv 203
                                       l+g + +e+++ +++   +i GH+H+
  gi|385805353|ref|YP_005841751.1| 159 LHGHKLTEEIFSYKN---IIIGHEHP 181
                                       667777777777777...999****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 !   16.4   0.0   8.8e-07    0.0079       4     114 ..      45     170 ..      43     204 .. 0.53

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 8.8e-07
                     Metallophos_2   4 aiiSDlH....................snldaleavlealkevgvdaiihaGDl.eeeep.....evleellela.. 52 
                                       +ii+DlH                    +++d++ + l++l ++   ++i  GD+ +  ++     +  ee+++ +  
  gi|385805353|ref|YP_005841751.1|  45 IIIADLHlgfedeaaesgvflpkmqlkKAIDLIIR-LKELTKA--KKLIINGDIkN--SFnrltiQEREEIIRFFgk 116
                                       799****8888777777777766544333444433.4444555..788999**731..2223333233333333355 PP

                     Metallophos_2  53 ......pvlaVrGNnD.......eevveedvlreaaelgtdlpeeaelelagekvlliHgdplgvkdalaellke 114
                                             +v+ VrGN+D       e            +++  + e+ +l+  ++   l+Hg+      +l+e +++
  gi|385805353|ref|YP_005841751.1| 117 skdlydEVILVRGNHDnyvsiiaE------------KMNVPIVESYKLS--NM-TILLHGH------KLTEEIFS 170
                                       56777***********33322221............2222221222222..21.2334444......33333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); 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:                         2  (0.000111551); expected 0.2 (1e-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: 1686.74
//
Query:       gi|385805354|ref|YP_005841752.1|  [L=145]
Description: hypothetical protein FFONT_0310 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1054.18
//
Query:       gi|385805355|ref|YP_005841753.1|  [L=346]
Description: Fe-S oxidoreductase [Fervidicoccus fontis Kam940]
Scores for 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-20   72.3   0.0    8.5e-20   71.8   0.0    1.2  1  Radical_SAM  Radical SAM superfamily
    0.00071   19.7   0.1     0.0025   17.9   0.0    1.9  2  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.8   0.0   9.5e-24   8.5e-20       3     166 ..      45     211 ..      43     212 .. 0.87

  Alignments for each domain:
  == domain 1  score: 71.8 bits;  conditional E-value: 9.5e-24
                                       EESEESS--TTTSCCTT..HHHHHHHHHHHHHHHHHHHHHHH.HHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCC CS
                                       xxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpet..vrregrgrslsveeileevkelk.aekgvkevilgggepllypdfvellerlaklavp 76 
                                       +t  C+l C+fC+++    + re+    +++e + e +k++  ++   + ++ g+g+p+ ++d+ e++++ ++ + +
  gi|385805355|ref|YP_005841753.1|  45 ITTLCSLSCIFCSVSAGpkSNREREFILRDPEWLYEWIKYACnFKSSFHLIFDGMGDPITHKDLPEFVKAVREMK-N 120
                                       7889***********99*77777777777777777777777655555***************************7.* PP

                                       TEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT..CTSHHHHHHHHHHHHHHTTSET.EEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                       Radical_SAM  77 giritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn..rghtfeevlealeklreagikr.vvdriv 150
                                         +itvet  +  + + le+l+++g+dr++++++++++e   kl+     +++++v+e++++++e  +   +    v
  gi|385805355|ref|YP_005841753.1| 121 VKSITVETRLFPANIKTLEKLKDAGIDRLNVSIDTLNEE-KGKLLSgnNFYSVKKVKELIKYAHEE-LGIaIHLAPV 195
                                       ************99*************************.5555532455888***********97.4444999999 PP

                                       EBTTTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxx RF
                       Radical_SAM 151 glpGendeeleellel 166
                                        +p +nde++ee++++
  gi|385805355|ref|YP_005841753.1| 196 WIPTVNDEDIEEIIQF 211
                                       9************998 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 !   17.9   0.0   2.8e-07    0.0025       6      96 ..      47     136 ..      43     160 .. 0.70
   2 ?   -1.5   0.0       0.3   2.7e+03      62      85 ..     170     192 ..     163     209 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.8e-07
                           Fer4_14   6 sgCnlsCkgCdnketwkselgkpq...teelleqilkdlkkseikiqglvltG.GePLhyenkkellklvkrlkeey 78 
                                         C+lsC +C  ++  ks+ + ++   + e l + +k + + +++ + l + G G+P+ +   k+l ++vk ++e +
  gi|385805355|ref|YP_005841753.1|  47 TLCSLSCIFCSVSAGPKSNREREFilrDPEWLYEWIKYACNFKSSFH-LIFDGmGDPITH---KDLPEFVKAVREMK 119
                                       56*********776666666655511156667778866666666566.9*********98...77777888888888 PP

                           Fer4_14  79 pekkiwletngtleiele 96 
                                       + k+i++et    + +++
  gi|385805355|ref|YP_005841753.1| 120 NVKSITVETRLFPA-NIK 136
                                       779*****976554.444 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.3
                           Fer4_14  62 enkkellklvkrlkeeypekkiwl 85 
                                       ++ k++ +l+k+ +ee   + i+l
  gi|385805355|ref|YP_005841753.1| 170 YSVKKVKELIKYAHEEL-GIAIHL 192
                                       56788999999999998.555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); 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: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2307.54
//
Query:       gi|385805356|ref|YP_005841754.1|  [L=185]
Description: Cyclopropane fatty acid synthase-like protein [Fervidicoccus fontis Kam940]
Scores for complete 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   29.8   0.0    1.4e-06   28.9   0.0    1.5  2  Methyltransf_25  Methyltransferase domain
    4.9e-06   26.2   0.3    0.00012   21.6   0.1    2.0  2  DOT1             Histone methylation protein DOT1
    3.4e-05   23.7   0.0      4e-05   23.5   0.0    1.1  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    7.3e-05   22.7   0.0     0.0001   22.1   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
     0.0002   22.0   0.0    0.00027   21.5   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    0.00028   20.4   0.0    0.00038   20.0   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
     0.0005   19.9   0.1    0.00069   19.4   0.1    1.2  1  Methyltransf_31  Methyltransferase domain
     0.0023   17.0   0.0     0.0028   16.8   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
     0.0078   15.8   0.0     0.0099   15.4   0.0    1.1  1  MTS              Methyltransferase small domain
  ------ inclusion threshold ------
      0.019   14.9   0.0      0.028   14.4   0.0    1.2  1  Methyltransf_18  Methyltransferase domain
       0.03   13.7   0.1      0.037   13.4   0.1    1.1  1  TehB             Tellurite resistance protein TehB
      0.038   14.0   0.0      0.054   13.5   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
      0.077   12.6   0.0      0.097   12.3   0.0    1.2  1  MetW             Methionine biosynthesis protein MetW
       0.11   12.1   0.0       0.11   12.0   0.0    1.2  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
       0.13   11.7   0.0       0.17   11.4   0.0    1.2  1  Methyltransf_4   Putative methyltransferase
       0.14   11.4   0.0       0.19   11.0   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
       0.18   11.1   0.0       0.25   10.6   0.0    1.2  1  Tmem26           Transmembrane protein 26


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 !   28.9   0.0   1.3e-09   1.4e-06       1      73 [.      41     111 ..      41     132 .. 0.88
   2 ?   -2.3   0.0         7   7.4e+03      13      30 ..     121     139 ..     114     155 .. 0.69

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 1.3e-09
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEEST CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssga 73 
                                       + d+GcG Gr+++ ++k +g ++ t+++  e++++ a ++a  +++  ++++++ da+++++ +  fD++++ ++
  gi|385805356|ref|YP_005841754.1|  41 ICDIGCGDGRVAIIASKYFG-CSSTCIEKREDLCALALSNAIYNSVndKFSVICEDARKIDYSE--FDFIYI-YM 111
                                       78*****************8.********************99999889999********9886..999988.44 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 7
                                       HHHHCTS.TSSEEEEEESS CS
                   Methyltransf_25  13 lalakrl.gkakvtgvDis 30 
                                       l+l k+l +  k++ +D+s
  gi|385805356|ref|YP_005841754.1| 121 LKLDKELkEGTKIVTLDFS 139
                                       5666666424888888888 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.1   1.2e-07   0.00012      38     111 ..      33     107 ..      23     115 .. 0.83
   2 ?    3.3   0.0     0.047        50     132     158 ..     111     137 ..     103     159 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.2e-07
                                       TT--TT-EEEEES-TTSHHHHHHHHHH--SEEEEEE--HHHHHHHHHHH..HHHHHHHHHTTB----EEEESS-ST CS
                              DOT1  38 vnlkkedvFvDLGSGvGnvvlqaalevgcklsvGvEimdnaselaekqk..eelkkrlklfGkklakiefirksFv 111
                                        +l+k++   D+G G G+v + a+ ++gc  s+ +E+ ++ ++la +++  + ++   ++   +  ki++++ +F+
  gi|385805356|ref|YP_005841754.1|  33 AKLNKDSKICDIGCGDGRVAIIASKYFGCS-STCIEKREDLCALALSNAiyNSVNDKFSVICEDARKIDYSEFDFI 107
                                       6899*************************9.9***********997765114455666667777888888888886 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.047
                                       T--HHHHHHHHHHHTT--TT-EEEESS CS
                              DOT1 132 aFdaelnkqlkellqdlkegtkiislk 158
                                       +F + l +   +l ++lkegtki++l 
  gi|385805356|ref|YP_005841754.1| 111 MFPSFLREISLKLDKELKEGTKIVTLD 137
                                       5555555555677789********985 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   3.8e-08     4e-05      64     170 ..      28     134 ..      13     152 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 3.8e-08
                                       HHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHH.HHHCTTCSEEEEES-GGGTTGG CS
                              PCMT  64 lalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrn.lkkldlenvivvvgDGrkGyee 139
                                       +  e  +l+k +++ ++G+G G  + + ++++g +     ie+ ++l++ a  n + ++  ++ +v++ D rk   +
  gi|385805356|ref|YP_005841754.1|  28 FSFEIAKLNKDSKICDIGCGDGRVAIIASKYFGCSS--TCIEKREDLCALALSNaIYNSVNDKFSVICEDARK--ID 100
                                       5568889**************************998..79*********9977637777888********998..57 PP

                                       G-SEEEEEESSBB...SS--HHHHHTEEEEEEEE CS
                              PCMT 140 kaPYdaihvgaaa...peiPealidQLkeGGrlv 170
                                       ++ +d i++   +    ei  +l + LkeG ++v
  gi|385805356|ref|YP_005841754.1| 101 YSEFDFIYIYMFPsflREISLKLDKELKEGTKIV 134
                                       7778888775443112688888888888888776 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   9.9e-08    0.0001      18      88 ..      33     109 ..      24     117 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 9.9e-08
                   Methyltransf_23  18 pklraggrvLdiGcGtGillevl.rengfsvtgvDlspeaveiae..kakkaqkdqfdeqeaaepqg...kfdlIvl 88 
                                       +kl+++++++diGcG+G+++ ++ +++g+s t ++ ++ + ++a    ++++++d+f  ++++  +     fd+I+ 
  gi|385805356|ref|YP_005841754.1|  33 AKLNKDSKICDIGCGDGRVAIIAsKYFGCSSTCIEKREDLCALALsnAIYNSVNDKFSVICEDARKIdysEFDFIYI 109
                                       5699*******************66669****999987766666577677777777766666664435557777775 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   2.6e-07   0.00027       2      73 ..      43     115 ..      42     139 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.6e-07
                                       EET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES-CCC CS
                   Methyltransf_11   2 dvGcGtGrlaealakrg.arvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvssevlhh 73 
                                       d+GcG Gr+a    k++ ++ ++++  + + +la ++a  + +  k++++++da+k+ + +  fD+++++++  +
  gi|385805356|ref|YP_005841754.1|  43 DIGCGDGRVAIIASKYFgCSSTCIEKREDLCALALSNAIYNSVndKFSVICEDARKIDYSE--FDFIYIYMFPSF 115
                                       9*************9999*************999777777777788999*******99888..****99876555 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   3.6e-07   0.00038     159     257 ..      35     134 ..      27     136 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 3.6e-07
                              PrmA 159 vkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevals.eellkeekadvivaNI 234
                                       +++++++ D+G+G G  ai a+k    + + +   e     a +Na +N+v++k++v+ + ++ ++ +++d i   +
  gi|385805356|ref|YP_005841754.1|  35 LNKDSKICDIGCGDGRVAIIASKYFGCSSTCIEKREDLCALALSNAIYNSVNDKFSVICEdARKIDYSEFDFIYIYM 111
                                       4677899********999988877667777788888888999*************99653144456899****9999 PP

                              PrmA 235 Laevlielaedikklvkegglli 257
                                         + l e+  ++ k +keg+ ++
  gi|385805356|ref|YP_005841754.1| 112 FPSFLREISLKLDKELKEGTKIV 134
                                       99999999999999999998887 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   6.5e-07   0.00069       2     119 ..      36     145 ..      35     165 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 6.5e-07
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDl 77 
                                       +k+ +++D+GCG G+ ++ + +  ++++  + i+  e+   lA +na  + ++  +++  +d+ +++  +++  fD+
  gi|385805356|ref|YP_005841754.1|  36 NKDSKICDIGCGDGRVAIIASK--YFGCSSTCIEKREDLCALALSNAIYNSVNdKFSVICEDARKID--YSE--FDF 106
                                       6899**************9994..5678899****************9999987889999*******..775..*** PP

                   Methyltransf_31  78 ilsnevlnaladpdkileeiervlkpggilliedprllaelp 119
                                       i      +  +++ +i  ++ + lk+g+ +++ d++++ + p
  gi|385805356|ref|YP_005841754.1| 107 IYIY---MFPSFLREISLKLDKELKEGTKIVTLDFSIEGWIP 145
                                       8773...33466666777777788888888888877665555 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   2.7e-06    0.0028      26      92 ..      33     103 ..      20     129 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.7e-06
                                       H-GGTTSEEEEES-TTTCCHHHHHCC-.SEEEEE-S-HHHHHHHHCHTT...TCCCEEEE-S-CCGHHHHH CS
                            RrnaAD  26 lnleekltvleigpGkGilTeeLakra.kqvvvlElderLakllqkkls...kdeklkvvhqDflkfetpe 92 
                                       ++l+++ ++ +ig G G    +  k++  + + +E++e+L++l   +      + k  v+ +D+ k +  e
  gi|385805356|ref|YP_005841754.1|  33 AKLNKDSKICDIGCGDGRVAIIASKYFgCSSTCIEKREDLCALALSNAIynsVNDKFSVICEDARKIDYSE 103
                                       566799**********************************9974433223689999999999999988766 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   9.4e-06    0.0099      28     101 ..      36     107 ..      29     126 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 9.4e-06
                                       HCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHH..HHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEE CS
                               MTS  28 pkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdar..Alesakenleanklevevvasdvleeveekkfdli 101
                                       +  ++ k+ D+GcG G +++ + k     + t++++     Al+++++ +++ + + +v+ +d+ +  +  +fd+i
  gi|385805356|ref|YP_005841754.1|  36 N--KDSKICDIGCGDGRVAIIASKYFGC-SSTCIEKREDlcALALSNAIYNSVNDKFSVICEDARKI-DYSEFDFI 107
                                       3..4678************998886665.67888865550055555555555555588888887653.33667766 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   2.6e-05     0.028      12      87 ..      35     108 ..      30     112 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.6e-05
                   Methyltransf_18  12 vekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklkeeevdtvv 87 
                                       ++k+s+++DiG+  g ++i + k   + + + ++ +e  ++ a +n+  ++++dk +v++ d   k++ +e+d + 
  gi|385805356|ref|YP_005841754.1|  35 LNKDSKICDIGCGDGRVAIIASKYFGC-SSTCIEKREDLCALALSNAIYNSVNDKFSVICEDA-RKIDYSEFDFIY 108
                                       46799****************998888.5567899999***9*9999999********99997.455555666665 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   3.6e-05     0.037      24     108 ..      31     116 ..      27     140 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.6e-05
                                       HHCCCS-S-EEEEES-TTSHHHHHHH.HTT-EEEEEES-HHHHHH.H.HHHHHHTT-TTEEEEE--GGG----S-EE CS
                              TehB  24 eavkivkpgkvldlgcgqgrnslyls.llgydvtawdknensiaf.l.eeikekenlknistalydineaklderyd 97 
                                       e +k+ k +k+ d+gcg+gr ++  s   g   t+++k e+  a  l + i +  n ++ s    d  +++ + ++d
  gi|385805356|ref|YP_005841754.1|  31 EIAKLNKDSKICDIGCGDGRVAIIASkYFGCSSTCIEKREDLCALaLsNAIYNSVN-DKFSVICEDARKIDYS-EFD 105
                                       56788899*************99877257999999999988655313033333333.3344444444444443.578 PP

                                       EEEEESSGGGS CS
                              TehB  98 filstvvlmfl 108
                                       fi   +   fl
  gi|385805356|ref|YP_005841754.1| 106 FIYIYMFPSFL 116
                                       87655555555 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   5.2e-05     0.054      21      68 ..      33      77 ..      20     103 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.2e-05
                   Methyltransf_32 21 akesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekae 68
                                      ak +++ +++D+G+G g  + + +     ++++ ++i+ +e+l++ a 
  gi|385805356|ref|YP_005841754.1| 33 AKLNKDSKICDIGCGDGRVAIIASK---YFGCSSTCIEKREDLCALAL 77
                                      5568899*************99999...89***********9987654 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   9.2e-05     0.097      11      58 ..      35      82 ..      29     138 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.2e-05
                              MetW 11 ikpgsrvldlGcGdGellellkeekqvdgrGleldeegvaecvakGls 58
                                      +++ s++ d+GcGdG +  +  +  + ++  +e+ e+  a +++  ++
  gi|385805356|ref|YP_005841754.1| 35 LNKDSKICDIGCGDGRVAIIASKYFGCSSTCIEKREDLCALALSNAIY 82
                                      4678************99999999999999999988877666665554 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00011      0.11       4      60 ..      41      98 ..      38     160 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                   Methyltransf_15  4 ilDlfsGaGGnviqfalv.fekviaieinleklacaqhNaevYgvsdkitlvlgdvfe 60
                                      i D+ +G G  +i   ++ +++  +ie+ ++ +a+a  Na    v+dk  +++ d  +
  gi|385805356|ref|YP_005841754.1| 41 ICDIGCGDGRVAIIASKYfGCSSTCIEKREDLCALALSNAIYNSVNDKFSVICEDARK 98
                                      779999998877777666358999****************99999****999999876 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00016      0.17       4      61 ..      40      97 ..      37     122 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00016
                                      EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTT.SSEEEEES-CC CS
                    Methyltransf_4  4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealel.kNlrilrgdal 61
                                       +++iGcG G++ + +A k   ++   iE+r+++ a +l+++  + +   + +++ da 
  gi|385805356|ref|YP_005841754.1| 40 KICDIGCGDGRVAI-IASKYFGCSSTCIEKREDLCALALSNAIYNSVnDKFSVICEDAR 97
                                      689********987.67777789999********9988877666555156999999993 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00018      0.19      55      99 ..      30      74 ..      23     118 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00018
                                      HTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHH CS
                              CMAS 55 leklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqak 99
                                      +e ++l++ +++ diGcG G +++ a + ++ +   +   ++  +
  gi|385805356|ref|YP_005841754.1| 30 FEIAKLNKDSKICDIGCGDGRVAIIASKYFGCSSTCIEKREDLCA 74
                                      677899999******************999998777655554444 PP

>> Tmem26  Transmembrane protein 26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00024      0.25      45      79 ..     139     174 ..     124     180 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00024
                            Tmem26  45 vlEtiltlilkkgkeykwfcpsvflYlvaiv.PsiW 79 
                                        +E+ + +++k+ ++ k ++ s+flY++ i  Ps W
  gi|385805356|ref|YP_005841754.1| 139 SIEGWIPILMKRIEDEKGIIRSIFLYFIGISnPSAW 174
                                       589*************************99549999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1171.68
//
Query:       gi|385805357|ref|YP_005841755.1|  [L=882]
Description: oligopeptide ABC transporter, oligopeptide binding protein [Fervidicoccus fontis Kam940]
Scores for complete 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   61.8   2.7    2.3e-09   36.7   0.0    3.5  3  SBP_bac_5  Bacterial extracellular solute-binding proteins, f
  ------ inclusion threshold ------
       0.15   11.9   0.5       0.31   10.9   0.5    1.5  1  RIFIN      Rifin
       0.22   12.0   2.7       0.51   10.8   2.7    1.6  1  MGC-24     Multi-glycosylated core protein 24 (MGC-24), sialo
          5    6.5   7.6       0.55    9.6   3.2    1.6  2  DUF5305    Family of unknown function (DUF5305)


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 !   21.1   0.2   2.8e-08   0.00012      27     181 ..     178     428 ..     171     461 .. 0.75
   2 !   36.7   0.0   5.1e-13   2.3e-09     199     365 ..     512     714 ..     489     721 .. 0.86
   3 ?    1.7   0.0     0.023     1e+02     250     282 ..     731     771 ..     719     792 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.8e-08
                                       T-B-TTSSB-SHHHHHH..HHHHHHTGGGHCTTHHHHHC............TCTEEEEEEEETTEEEEEESSETT.. CS
                         SBP_bac_5  27 gvkFsDGtpltAeDvvf..sferlldpdtasgyasllee............dqdikkveavddytvrftlkkpna.. 87 
                                        v ++DG  + ++Dv +  +f + +  dt++ ++++ ++                ++v+ ++d+ + ++++  +   
  gi|385805357|ref|YP_005841755.1| 178 QVPWHDGINFSVADVLAwlAFMWRWSTDTSYITNQTDQYydetfssqygptIGMFEGVQIINDTSLAIYTTYVDVdp 254
                                       588************99552333333333333333333346999999999966666666666666666655554333 PP

                                       .TTTTHCHHHHHHHGC............................................................. CS
                         SBP_bac_5  88 .lfltllaavpasiak............................................................. 102
                                        l  +++ ++p  +                                                               
  gi|385805357|ref|YP_005841755.1| 255 sLIAYTVDPYPGVP-Ydllaamelavmnstnlwwestttskgtvsgidmlinaqqikaaalaltpsnvyyfnglskf 330
                                       32233333333333.24777777777779999999999999999999999999999999999999999999999999 PP

                                       ...........CHTCTCTTTTTGTTTSE-BSSSEEEEEEETTT.EEEEEE.......-TTS.TTT.SCSSSSEEEEE CS
                         SBP_bac_5 103 ...........kaaekeddkdkdtnekpvgtGPYklkefkpgq.kivler.......npdY.wgg.gkpkldriefk 158
                                                  ++a  ++   ++   ++v++GP+ +++++ ++ ++vl+          +Y w++   p ld+i ++
  gi|385805357|ref|YP_005841755.1| 331 gynygsdlsqrVNALVNW--INTHGVAVVSNGPFYVDSYNAQSnTMVLKSrtflglpKIHYiWNNlTVPSLDEIFVE 405
                                       999999998754443333..4778888899***********7768888888888877667989666*********** PP

                                       E-.SHHHHHHHHHTTSSSEEEST CS
                         SBP_bac_5 159 vipdsdaraaalqsGeiddvaep 181
                                        ++++da ++a++sG +d++ + 
  gi|385805357|ref|YP_005841755.1| 406 SVTTEDAGIQAVKSGTADIFFYS 428
                                       *****************998544 PP

  == domain 2  score: 36.7 bits;  conditional E-value: 5.1e-13
                                       EEEEEEEEEEEEETTTSTGGGSHHHHHHHHHHS-HHHHHHHCTTTSSEEESSSSTTTSTTCCSCHCCCSHH...... CS
                         SBP_bac_5 199 yespgggvtylafNtkkppfddkrvRqAlsyAiDreeivkavlegyatpansllppsspgadeeykpayka...... 269
                                       ++s+ ++++y++fN      + + vR Al+  i+r+++v++v++g a+p  s++ p+sp+++  + + y+       
  gi|385805357|ref|YP_005841755.1| 512 INSTVMESNYFQFNPM----ALQGVRFALNVLINRNSLVQNVYQGSAVPCFSAIIPGSPAYKALNISTYEQqlglyg 584
                                       6667777788888876....5799*************************************99999987779***** PP

                                       ..........SH..HHHHHHHHHHTT-BCSSTSCEETC...............EEEEEEEEETTSHHHHHHHHHHHH CS
                         SBP_bac_5 270 ..........yd..pekAkklLkeaGykdgdggglrek...............klkltlllasgspaekaiaeliqq 319
                                                 y+  +++A++ L++ G   +    +++                k ++ +++ +++p +kai + i+q
  gi|385805357|ref|YP_005841755.1| 585 sgdpttavaiYNqsIQQANQSLNSYGMSLKY---ITDSsgtwlylilpdgtqkKVTIYFEVRGDDPFRKAIGDQITQ 658
                                       **********5556*************9994...4555678***********99999999999999999******** PP

                                       HHHH.TTEEEEEEEECHH...........HHHHHHHHCTTESEEEEEEECTTSTTHHH CS
                         SBP_bac_5 320 qlkk.iGikvevktvdwa...........atylervkdgdfdmillgwgadypdpdnf 365
                                         ++   i v+  ++  +           a +  ++ ++ + m+  gw a+y +p +f
  gi|385805357|ref|YP_005841755.1| 659 WIEQyFHIYVQEDYITRQvankaiygtdmASF--SMGNHPWTMYTEGWVANYDEPIYF 714
                                       ****9999999999977778898888776444..589999999999999999998776 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.023
                                       SSSTTTSTTCCSCHCCCSHH........SHHHHHHHHHHHT CS
                         SBP_bac_5 250 sllppsspgadeeykpayka........ydpekAkklLkea 282
                                       +++p++s+++++++++ y+         y p++A++lL++ 
  gi|385805357|ref|YP_005841755.1| 731 QPTPSNSQQWYPWNQTIYQLgqnlafgiYTPQQANQLLNDI 771
                                       456666666666666666558999**************976 PP

>> RIFIN  Rifin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.5   6.9e-05      0.31     254     306 ..     832     881 ..     806     882 .] 0.47

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6.9e-05
                             RIFIN 254 aaeataeaekaetaaveattaslqtaiiasivaivvIvLimvIIYLiLRY...rRK 306
                                       ++++t++ ++++t +++++ + +++a+   iv ++      +II +iL Y   rRK
  gi|385805357|ref|YP_005841755.1| 832 STTTTTTPTTTTTPTTTTALSGTSSALLWGIVIVI------IIIIVILAYyltRRK 881
                                       22333333333333344444444444444444333......333444444232455 PP

>> MGC-24  Multi-glycosylated core protein 24 (MGC-24), sialomucin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   2.7   0.00011      0.51      73     124 ..     824     873 ..     813     882 .] 0.69

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00011
                            MGC-24  73 psstttstsvatsgttnttvtptsqparkstFDaAsFiGGivLvLgvqAviF 124
                                        s ttts s++t++t++tt tpt+ +a + t  + + + Giv+v+ +  vi 
  gi|385805357|ref|YP_005841755.1| 824 VSGTTTSPSTTTTTTPTTTTTPTTTTALSGT--SSALLWGIVIVIIIIIVIL 873
                                       4556777778899999999999995544444..4557889999998877775 PP

>> DUF5305  Family of unknown function (DUF5305)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.1       1.4   6.5e+03      56      82 ..      86     112 ..      81     114 .. 0.82
   2 ?    9.6   3.2   0.00012      0.55      84     143 ..     819     881 ..     814     882 .] 0.72

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 1.4
                           DUF5305  56 vlevnvegeidgesieesktsrlpipl 82 
                                       +++ ++ g+++ +++++  t+ l+ip 
  gi|385805357|ref|YP_005841755.1|  86 TATYQYIGNYTVNQTTGVITPYLTIPS 112
                                       567788999999999999999999985 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00012
                           DUF5305  84 eqtyeikkdetdeengeitetvtvkespslae...gilliilgllaliglvvlirriiftssk 143
                                       + +y +++++t+  ++++t+ +t++ + +++        ++ g++++i+++++i+ ++ t++k
  gi|385805357|ref|YP_005841755.1| 819 NTAYVVSGTTTSPSTTTTTTPTTTTTPTTTTAlsgTSSALLWGIVIVIIIIIVILAYYLTRRK 881
                                       568999999999555555555555555555556887777888888888888888888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (882 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       850  (0.0474092); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.81u 0.32s 00:00:01.13 Elapsed: 00:00:00.47
# Mc/sec: 5607.15
//
Query:       gi|385805358|ref|YP_005841756.1|  [L=369]
Description: binding-protein-dependent transport system inner membrane protein [Fervidicoccus fontis Kam940]
Scores for 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-40  136.4  21.8      9e-40  136.4  21.8    2.7  3  BPD_transp_1    Binding-protein-dependent transport system in
  ------ inclusion threshold ------
        0.1   12.3   0.2       0.19   11.4   0.2    1.4  1  BNIP3           BNIP3
       0.17   12.5   0.0       0.31   11.6   0.0    1.4  1  Arg_decarbox_C  Arginine decarboxylase C-terminal helical ext


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   3.0      0.28   1.7e+03     155     172 ..      15      32 ..       2      43 .. 0.50
   2 ?   -2.2   0.4       0.5     3e+03     157     175 ..     113     131 ..      82     140 .. 0.47
   3 !  136.4  21.8   1.5e-43     9e-40       1     184 [.     141     361 ..     141     362 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.28
                      BPD_transp_1 155 nggvlalviavlllnlva 172
                                       n+++l++++av+  +lv+
  gi|385805358|ref|YP_005841756.1|  15 NIAALIIIVAVISALLVF 32 
                                       334444444444444444 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.5
                      BPD_transp_1 157 gvlalviavlllnlvadil 175
                                       +++ + ++++l n+v+ +l
  gi|385805358|ref|YP_005841756.1| 113 TSISGQVIFALKNTVILFL 131
                                       2222222333333322222 PP

  == domain 3  score: 136.4 bits;  conditional E-value: 1.5e-43
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf.................................. 43 
                                       g++lG++aa+++++++d l++++ i+ +slP+ ++++l++l+f                                  
  gi|385805358|ref|YP_005841756.1| 141 GLGLGMYAARRPHGIIDSLVSFFAILSSSLPMWWVGMLMLLAFafnlhwfptqslpvyfaiqqlhaqyasgaigfft 217
                                       799************************************************************************** PP

                      BPD_transp_1  44 ....vilsilghlilpviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglil 116
                                           +i+++l+++ lp+i+++l+s++++++++r+ ++  + +d+v +ara+G++++++++ +vl++a ppi+t+++l
  gi|385805358|ref|YP_005841756.1| 218 yvfdYIQTWLYYMTLPLITVVLVSIGGWAYIVRNVVIGKMAEDFVMTARAKGVPERRVLFGHVLRAASPPIVTTAVL 294
                                       ***************************************************************************** PP

                      BPD_transp_1 117 afggllggavlleflgswpGlgtllleailgydyseisnggvlalviavlllnlvadilqrlldprvr 184
                                       +++ +lgga+++e++++wpG+g+l++ ai+++   +i+ g v+++v+++++ +++++il+ +ldprv+
  gi|385805358|ref|YP_005841756.1| 295 NIIVSLGGAIITETVFGWPGMGLLFWIAIENSEPMLIA-GNVYITVLLFIIAVIILNILYVFLDPRVK 361
                                       **************************************.***************************97 PP

>> BNIP3  BNIP3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   3.2e-05      0.19     150     187 ..     114     151 ..      96     158 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.2e-05
                             BNIP3 150 kvmkkgglfS.aevLkvllpslllshllalGlgvyigkR 187
                                       ++  +  +f  ++    +l   l+s ll+lGlg+y  +R
  gi|385805358|ref|YP_005841756.1| 114 SISGQV-IFAlKNTVILFLTATLISTLLGLGLGMYAARR 151
                                       555554.665245556677889***************99 PP

>> Arg_decarbox_C  Arginine decarboxylase C-terminal helical extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.2e-05      0.31      14      45 ..      44      75 ..      42      76 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.2e-05
                    Arg_decarbox_C 14 eLlerlrrqveaagrLtpeerqalleeleagL 45
                                      e+++ + rq+++   ++p++rq+l++ ++++L
  gi|385805358|ref|YP_005841756.1| 44 EMVQDFARQLAKNPTIPPDQRQQLVNMYQQSL 75
                                      79999*****9999****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1157  (0.0645323); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 2395.48
//
Query:       gi|385805359|ref|YP_005841757.1|  [L=500]
Description: oligopeptide ABC transporter permease [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-27   96.6  15.1    1.5e-27   96.6  15.1    2.1  2  BPD_transp_1  Binding-protein-dependent transport system inne
    0.00067   19.6   0.3    0.00067   19.6   0.3    3.0  3  OppC_N        N-terminal TM domain of oligopeptide transport 
  ------ inclusion threshold ------
       0.27   10.7   1.9       0.76    9.2   1.9    1.8  1  Flp1_like     Putative Flagellin, Flp1-like, domain


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.41   2.4e+03     159     171 ..      40      50 ..      16      67 .. 0.60
   2 !   96.6  15.1   2.5e-31   1.5e-27       3     184 ..     316     499 ..     310     500 .] 0.94

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.41
                      BPD_transp_1 159 lalviavlllnlv 171
                                       l+  +++lll l+
  gi|385805359|ref|YP_005841757.1|  40 LF--LIFLLLALL 50 
                                       22..222222222 PP

  == domain 2  score: 96.6 bits;  conditional E-value: 2.5e-31
                      BPD_transp_1   3 llGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilp.viillllsaapyvrlirraalrs 78 
                                       l G++ + + ++k+d++l+++ ++++s+P++ ++ill        i+  +i+  + +l++++++ +++++r++al++
  gi|385805359|ref|YP_005841757.1| 316 LYGVIGG-YLGGKTDEILLRVAQIFYSIPILPILILLA------IIFRPSIWNvISMLIIFGWPSTAIVTRSMALQI 385
                                       5688888.9*****************************......99*******889999****************** PP

                      BPD_transp_1  79 lpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis. 154
                                        ++ +veaa+alGas  +i+ ++++P++lp+++++++l+++g++   + l+flg    lg++   +++g+ ++e+  
  gi|385805359|ref|YP_005841757.1| 386 KEETYVEAAKALGASSSRILLRYIFPQVLPYLFASMALSVPGAILTEASLSFLG----LGDPS-IVTWGRILNEAEi 457
                                       ******************************************************....99765.5788888888888 PP

                      BPD_transp_1 155 ............nggvlalviavlllnlvadilqrlldprvr 184
                                                   + + l+++++ l ++l+  +l ++l+p+++
  gi|385805359|ref|YP_005841757.1| 458 agatingywwwvIPPGLMITLIGLTFILIGQALDTILNPKLK 499
                                       89999***********************************97 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 !   19.6   0.3   1.1e-07   0.00067       4      41 ..      22      59 ..      21      78 .. 0.76
   2 ?   -0.8   2.2      0.25   1.5e+03      24      37 ..     347     360 ..     344     372 .. 0.77
   3 ?   -2.6   0.3      0.92   5.5e+03      18      25 ..     479     486 ..     474     498 .. 0.46

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.1e-07
                            OppC_N  4 qdawrrFkrNklAvvglvilllllliaifaPliaPydp 41
                                      ++++  +kr k+ ++g+ ++l++ll+a++ P+i + + 
  gi|385805359|ref|YP_005841757.1| 22 KRFFGELKRSKVGIAGFTLFLIFLLLALLFPYIGNMND 59
                                      6677789**************************64332 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.25
                            OppC_N  24 llllliaifaPlia 37 
                                       +l+ll+ if P i+
  gi|385805359|ref|YP_005841757.1| 347 ILILLAIIFRPSIW 360
                                       56777778899984 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.92
                            OppC_N  18 vglvilll 25 
                                       +gl ++l+
  gi|385805359|ref|YP_005841757.1| 479 IGLTFILI 486
                                       34444433 PP

>> Flp1_like  Putative Flagellin, Flp1-like, domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   1.9   0.00013      0.76      17      39 ..     344     366 ..     341     368 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00013
                         Flp1_like  17 IivVligLvliFKkqitslvnsi 39 
                                       I+ +li L++iF+  i ++++ +
  gi|385805359|ref|YP_005841757.1| 344 ILPILILLAIIFRPSIWNVISML 366
                                       889***********999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (500 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 3254.05
//
Query:       gi|385805360|ref|YP_005841758.1|  [L=320]
Description: putative ABC transport ATP binding protein [Fervidicoccus fontis Kam940]
Scores for complete 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-29  101.0   0.0    1.1e-28  100.4   0.0    1.2  1  ABC_tran     ABC transporter
    2.5e-20   72.7   0.0    4.6e-20   71.9   0.0    1.5  1  oligo_HPY    Oligopeptide/dipeptide transporter, C-terminal r
    7.6e-08   32.5   0.3      3e-07   30.6   0.0    1.9  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    1.9e-06   27.5   0.4    6.8e-05   22.4   0.1    2.0  2  SMC_N        RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
      0.015   15.2   0.0      0.033   14.1   0.0    1.5  1  RsgA_GTPase  RsgA GTPase
      0.021   14.6   0.1       0.04   13.7   0.1    1.4  1  AAA_29       P-loop containing region of AAA domain
      0.072   13.5   0.2        5.5    7.4   0.0    2.3  2  AAA          ATPase family associated with various cellular a
      0.088   13.1   0.6        7.3    6.9   0.1    2.2  2  AAA_22       AAA domain
       0.39    9.9   1.7       0.84    8.8   0.2    2.0  2  NB-ARC       NB-ARC domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.4   0.0   5.6e-32   1.1e-28       2     136 ..      25     181 ..      24     182 .. 0.96

  Alignments for each domain:
  == domain 1  score: 100.4 bits;  conditional E-value: 5.6e-32
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--....SEEEEEETTCEGGG.....B-HHHCCHCEEEE-SS.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxx.. RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkp....teGeilldgkdlke.....qeleslrkeigvlpqe.. 67 
                                       ++vs+kl++ e+++i Ge+G+GKStL   ++g+  p     +G++++dg d+ +     +++++l k+i++++q   
  gi|385805360|ref|YP_005841758.1|  25 HDVSFKLNKEEVLGIAGESGCGKSTLGWSIMGMPPPpgrvVKGSVKVDGIDVLKlsdaeRRRTVLWKKISMVFQGai 101
                                       79********************************9999999***********999999999999***********99 PP

                                       --S-TTSBHHHH...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEE CS
                                       xxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  68 pqlfpeltvren...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllD 133
                                       + ++p +t++++           +++e iek+ + l++++l+ +vvk+ p++LSgG+kqr ++a+al+ +p+++++D
  gi|385805360|ref|YP_005841758.1| 102 NAFNPVYTIGDQlaepliihenyTKKEAIEKVKEYLKMVGLNPDVVKRYPHELSGGMKQRAVIAMALILEPTVFIAD 178
                                       99999****************9888888************************************************* PP

                                       STT CS
                                       xxx RF
                          ABC_tran 134 Ept 136
                                       Ept
  gi|385805360|ref|YP_005841758.1| 179 EPT 181
                                       **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 !   71.9   0.0   2.3e-23   4.6e-20       1      65 []     233     297 ..     233     297 .. 0.99

  Alignments for each domain:
  == domain 1  score: 71.9 bits;  conditional E-value: 2.3e-23
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfaleeC 65 
                                       vE g+s+++f +p HPYT+aLlrs+prl+   +kle i+ge+p+l    +GCpF+pRC+ a+++C
  gi|385805360|ref|YP_005841758.1| 233 VELGTSEQIFLNPMHPYTQALLRSIPRLKGDIKKLEYIPGEPPNLIFPLKGCPFNPRCTKAVDIC 297
                                       8**************************************************************** PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.2      0.38   7.6e+02       3      15 ..      38      50 ..      36      51 .. 0.88
   2 !   30.6   0.0   1.5e-10     3e-07     220     302 ..     137     217 ..      76     218 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.38
                            AAA_21  3 vliGpNgsGKSnL 15
                                      ++ G  g+GKS+L
  gi|385805360|ref|YP_005841758.1| 38 GIAGESGCGKSTL 50
                                      689*********8 PP

  == domain 2  score: 30.6 bits;  conditional E-value: 1.5e-10
                            AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQvilt 295
                                         +   n+d  ++ ++elS G+k+  a++++ l + +  ++++ DEp + L+  +++ +l l+kel++ ++  +il 
  gi|385805360|ref|YP_005841758.1| 137 LKMVGLNPDVVKRYPHELSGGMKQR-AVIAMALILEP--TVFIADEPTTALDVVVQAQILNLMKELKKeKKLSFILI 210
                                       566677899999*************.99999999887..99999*******************8888889******* PP

                            AAA_21 296 THSplll 302
                                       TH+ +++
  gi|385805360|ref|YP_005841758.1| 211 THDMSVI 217
                                       ***9887 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.022        44      24      44 ..      34      54 ..      20      59 .. 0.80
   2 !   22.4   0.1   3.4e-08   6.8e-05     120     211 ..     130     226 ..      82     233 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.022
                                      SSEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 24 ksftaivGpNGSGKsnlldAi 44
                                      +++  i G+ G+GKs l  +i
  gi|385805360|ref|YP_005841758.1| 34 EEVLGIAGESGCGKSTLGWSI 54
                                      557789*********997776 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 3.4e-08
                                       HHHHHHHHHCTT-STT.......CS-HH..HHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHC CS
                                       xxxxxxxxxxxxxxxx.......xxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 120 kkevsellesagiske.......lLSgG..ektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeks 187
                                        ++v+e l+++g++++       +LSgG  +++++a+aL+      +p+ +++ De   aLD    +++ +l+ke +
  gi|385805360|ref|YP_005841758.1| 130 IEKVKEYLKMVGLNPDvvkryphELSGGmkQRAVIAMALI-----LEPT-VFIADEPTTALDVVVQAQILNLMKELK 200
                                       46789999999999999999999*****666678888888.....4565.6789********************765 PP

                                       TT..SEEEEE-SSHHHCCC-SCEEEE CS
                                       xx..xxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 188 kn..aQfivislreemlekadklvgv 211
                                       k+    fi i+++  ++++    v +
  gi|385805360|ref|YP_005841758.1| 201 KEkkLSFILITHDMSVIAELADKVAI 226
                                       543389******99988776444433 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.6e-05     0.033      80     116 ..      14      51 ..       4      64 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.6e-05
                                       EE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHH CS
                       RsgA_GTPase  80 llvsaktkegleelkellkd.ktsvlvGqSGvGKStLi 116
                                       +++s  t +++++++ +l++ ++  ++G+SG GKStL 
  gi|385805360|ref|YP_005841758.1|  14 YYTSRGTVKAVHDVSFKLNKeEVLGIAGESGCGKSTLG 51 
                                       4567788899999**9**9989999***********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 ?   13.7   0.1     2e-05      0.04      13      38 ..      22      50 ..      17      55 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2e-05
                            AAA_29 13 dg.htieidlkg..atlltGpsGsGKSTl 38
                                      +  h+++++l+   +  ++G+sG GKSTl
  gi|385805360|ref|YP_005841758.1| 22 KAvHDVSFKLNKeeVLGIAGESGCGKSTL 50
                                      55555555555544888***********8 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0      0.03        59       3      21 ..      39      57 ..      37     107 .. 0.72
   2 ?    7.4   0.0    0.0027       5.5      84     116 ..     187     218 ..     144     225 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.03
                                      EESSTTSSHHHHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavake 21
                                      + G  G+GK++l  +++  
  gi|385805360|ref|YP_005841758.1| 39 IAGESGCGKSTLGWSIMGM 57
                                      5799*******99888776 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0027
                                       HHHHHHHHHHHHTTTSSSTEEEEEEESSGGGST CS
                               AAA  84 rvvnqLlteldgvkkkeskvivigatnrpdkld 116
                                        v++q+l+ ++++kk+ +k+ +i++t++++ + 
  gi|385805360|ref|YP_005841758.1| 187 VVQAQILNLMKELKKE-KKLSFILITHDMSVIA 218
                                       5899***********6.66********998776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1    0.0037       7.3       7      21 ..      36      50 ..      31      58 .. 0.85
   2 ?    4.4   0.0     0.021        43      81     128 ..     158     210 ..     111     215 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0037
                            AAA_22  7 ilvvtGesGtGKTtl 21
                                      +l + GesG+GK+tl
  gi|385805360|ref|YP_005841758.1| 36 VLGIAGESGCGKSTL 50
                                      56689********98 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.021
                            AAA_22  81 aleqalrarav...ielliiDEaqh.lr...seealeeLrsllnlsrkgvqliLv 128
                                       + ++a+ a a    + ++i DE    l+   ++++l+  ++l +  +k++++iL+
  gi|385805360|ref|YP_005841758.1| 158 MKQRAVIAMALilePTVFIADEPTTaLDvvvQAQILNLMKELKK--EKKLSFILI 210
                                       33333333333778899*****999898887799**********..********8 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.2   0.00042      0.84      16      40 ..      32      54 ..      18      57 .. 0.73
   2 ?    0.2   0.1      0.18   3.5e+02     109     148 ..     184     221 ..      86     234 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00042
                                      TTSCSEEEEEEESTTSSHHHHHHHH CS
                            NB-ARC 16 delqslvvalvGmgGvGKttlakqi 40
                                      ++ +  v+++ G  G+GK+tl  +i
  gi|385805360|ref|YP_005841758.1| 32 NKEE--VLGIAGESGCGKSTLGWSI 54
                                      3444..99************97665 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.18
                                       EEEE-SHHHH.....HHHHCHTTSEEEEEESBCCCCCCS- CS
                            NB-ARC 109 lDDVweeedwdkigvvlparenrlrvllTTRdeevanavs 148
                                       lD V++ + + +++  l+ +e++l+ +l T d++v  + +
  gi|385805360|ref|YP_005841758.1| 184 LDVVVQAQIL-NLMKELK-KEKKLSFILITHDMSVIAELA 221
                                       5556666556.6666777.788888888888888866555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); expected 358.6 (0.02)
Passed bias filter:                      702  (0.0391544); 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: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.53
# Mc/sec: 1830.57
//
Query:       gi|385805361|ref|YP_005841759.1|  [L=383]
Description: oligopeptide ABC transporter, ATP binding protein [Fervidicoccus fontis Kam940]
Scores for complete 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-25   88.7   0.0    8.8e-25   87.8   0.0    1.5  1  ABC_tran     ABC transporter
    5.7e-17   62.0   0.0    1.5e-16   60.6   0.0    1.7  1  oligo_HPY    Oligopeptide/dipeptide transporter, C-terminal r
    0.00026   20.9   0.5      0.013   15.3   0.1    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    0.00029   21.1   0.5     0.0054   17.0   0.5    2.2  1  AAA_22       AAA domain
  ------ inclusion threshold ------
      0.044   13.8   0.1      0.087   12.8   0.1    1.5  1  AAA_5        AAA domain (dynein-related subfamily)
      0.066   12.7   0.1       0.12   11.9   0.1    1.3  1  AAA_7        P-loop containing dynein motor region
      0.073   12.8   0.0       0.15   11.8   0.0    1.4  1  IstB_IS21    IstB-like ATP binding protein
       0.18   11.7   0.0       0.31   10.9   0.0    1.3  1  RsgA_GTPase  RsgA GTPase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.8   0.0   3.9e-28   8.8e-25       1     136 [.      49     222 ..      49     223 .. 0.90

  Alignments for each domain:
  == domain 1  score: 87.8 bits;  conditional E-value: 3.9e-28
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG......................B-HH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......................xxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke......................qele 55 
                                       ++nvs+++k+ e+  +vGe+G+GK+t  k l++l+  t+G  l++  d++                       ++ +
  gi|385805361|ref|YP_005841759.1|  49 VDNVSFNIKKEETFCLVGESGCGKTTTGKSLLRLVPITSGVGLFRPSDITIerlkkegikvnngyvniyglppKKVK 125
                                       58***********************************99998666666666666667777788889999999999** PP

                                       HCCHCEEEE-SS..--S-TTSBHHHH...............HHHTC..HHHHHHHSTTGGTTCBGESTTSGGS-HHH CS
                                       xxxxxxxxxxxx..xxxxxxxxxxxx...............xxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  56 slrkeigvlpqe..pqlfpeltvren...............esdee..iekalsklglkelkdtvvksspssLSgGq 113
                                         rk i+++ q+   +l+p++++ +                e+  +  ++k l+k++lk  +++ ++++p++LSgGq
  gi|385805361|ref|YP_005841759.1| 126 PIRKDIQMIYQDpfGSLNPRYKIMDIlteplkihniglseeEE--RelVYKTLEKVKLKP-PEDFADRHPHQLSGGQ 199
                                       ************77789****999999**********986333..246***********9.99999*********** PP

                                       HHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 114 kqrvalarallkkpkllllDEpt 136
                                       +qr+a+a+a++  p+l+++DEp 
  gi|385805361|ref|YP_005841759.1| 200 RQRIAIAKAMIMGPRLIVADEPV 222
                                       **********************7 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.6   0.0   6.8e-20   1.5e-16       1      59 [.     274     335 ..     274     339 .. 0.92

  Alignments for each domain:
  == domain 1  score: 60.6 bits;  conditional E-value: 6.8e-20
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekd...klekikgeapslerldeGCpFapRCp 59 
                                       vE+g++++++++p HPYT+aL++++p++d+ ++   +   ikge++s+ ++++GC+F+pRC 
  gi|385805361|ref|YP_005841759.1| 274 VEMGKARNIIEQPMHPYTRALVAAIPEPDPSNRlkvRKLFIKGEVQSAANIPSGCRFHPRCM 335
                                       8********************************95544559********************5 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   0.1      0.02        44       3      23 ..      63      83 ..      62     154 .. 0.70
   2 !   15.3   0.1   5.8e-06     0.013     219     300 ..     173     256 ..     138     259 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.02
                            AAA_21  3 vliGpNgsGKSnLLdaldlla 23
                                      +l+G  g+GK++  + l  l 
  gi|385805361|ref|YP_005841759.1| 63 CLVGESGCGKTTTGKSLLRLV 83
                                      79**********999997773 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 5.8e-06
                            AAA_21 219 r....gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrnga 290
                                       +     v +  ++d  ++ +++lS G+++ +a++ a++  +   +l++ DEp + L+ ++ +++lell + +++n+ 
  gi|385805361|ref|YP_005841759.1| 173 YktleKVKLKPPEDFADRHPHQLSGGQRQRIAIAKAMIMGP---RLIVADEPVSMLDVSIRAEVLELLmNFKNENKL 246
                                       13444667778888889999******************988...************************64444478* PP

                            AAA_21 291 QviltTHSpl 300
                                         ++ TH+  
  gi|385805361|ref|YP_005841759.1| 247 SYLFITHDLA 256
                                       *******976 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.5   2.4e-06    0.0054       8     127 ..      62     250 ..      56     258 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.4e-06
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee.................erpevvfvtlpsstsskdllrellralgle 67 
                                        +++GesG+GKTt+ + ll+  ++ +                      + ++v ++   +++ k +++++  +++++
  gi|385805361|ref|YP_005841759.1|  62 FCLVGESGCGKTTTGKSLLRLVPITSGVGLfrpsditierlkkegikVNNGYVNIYGLPPKKVKPIRKDIQMIYQDP 138
                                       689*****************998765555587777777777665554444444444444446777777777777766 PP

                            AAA_22  68 lka..............................................erlsseell.ealeqalrarav...iel 94 
                                         +                                              +    ++l   + ++ + a+a+   ++l
  gi|385805361|ref|YP_005841759.1| 139 FGSlnprykimdilteplkihniglseeeerelvyktlekvklkppedfADRHPHQLSgGQRQRIAIAKAMimgPRL 215
                                       65577788888888888888888887777777777777777666666663333333333444444444444677888 PP

                            AAA_22  95 liiDEaqh.lr...seealeeLrsllnlsrkgvqliL 127
                                       ++ DE    l+   ++e+le L ++ n  + +++ ++
  gi|385805361|ref|YP_005841759.1| 216 IVADEPVSmLDvsiRAEVLELLMNFKN--ENKLSYLF 250
                                       888887775557444888888866666..77777655 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   3.9e-05     0.087       2      23 ..      62      83 ..      61     109 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.9e-05
                                      EEEE--SSSSHHHHHHHGGGGB CS
                             AAA_5  2 vlLvGppGtgKselaerlaaal 23
                                      ++LvG++G+gK++  ++l++++
  gi|385805361|ref|YP_005841759.1| 62 FCLVGESGCGKTTTGKSLLRLV 83
                                      79****************9987 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   5.3e-05      0.12      29      57 ..      55      83 ..      45      90 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.3e-05
                             AAA_7 29 llknkkpvllvGptGtGKtviikdllkkl 57
                                       +k++  ++lvG++G+GKt++ k+ll+ +
  gi|385805361|ref|YP_005841759.1| 55 NIKKEETFCLVGESGCGKTTTGKSLLRLV 83
                                      5889999***************9998765 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   6.7e-05      0.15      29      62 ..      40      74 ..      31      82 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.7e-05
                         IstB_IS21 29 sldkrkvkeLatlsf.iekkenivllGpsGvGKsh 62
                                         +r vk++ + sf i+k+e ++l+G sG GK+ 
  gi|385805361|ref|YP_005841759.1| 40 RKPQRYVKAVDNVSFnIKKEETFCLVGESGCGKTT 74
                                      55789999999999989999*************96 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00014      0.31      88     117 ..      47      77 ..      34      86 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00014
                                       TTHHHHHHHCTT.SEEEEECSTTSSHHHHHH CS
                       RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLin 117
                                       +++++++ ++k+ +t +lvG+SG GK+t  +
  gi|385805361|ref|YP_005841759.1|  47 KAVDNVSFNIKKeETFCLVGESGCGKTTTGK 77 
                                       56788889999889*************9655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); 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: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.51
# Mc/sec: 2269.11
//
Query:       gi|385805362|ref|YP_005841760.1|  [L=204]
Description: hypothetical protein FFONT_0318 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       973  (0.0542696); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); 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: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1205.18
//
Query:       gi|385805363|ref|YP_005841761.1|  [L=359]
Description: 3-hydroxy-3-methylglutaryl CoA synthase [Fervidicoccus fontis Kam940]
Scores for complete 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    6.2e-13   48.7   0.0    1.8  1  ACP_syn_III_C   3-Oxoacyl-[acyl-carrier-protein (ACP)] syntha
    3.7e-06   26.8   0.3    0.00064   19.4   0.0    2.3  2  HMG_CoA_synt_C  Hydroxymethylglutaryl-coenzyme A synthase C t
    8.9e-06   25.3   0.1    4.1e-05   23.1   0.4    1.8  2  Thiolase_N      Thiolase, N-terminal domain
    0.00087   19.1   0.7     0.0038   17.1   0.3    2.1  2  ACP_syn_III     3-Oxoacyl-[acyl-carrier-protein (ACP)] syntha
  ------ inclusion threshold ------
       0.16   12.0   0.0        5.9    7.0   0.0    2.5  2  HTH_35          Winged helix-turn-helix DNA-binding


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 !   48.7   0.0   1.7e-16   6.2e-13       1      81 [.     229     309 ..     229     317 .. 0.93

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 1.7e-16
                                       HHHTT--GGG-SEEEE-SSSHHHHHHHHHHHT--GGGB--TH..HHH-B-GGGHHHHHHHHHHHTTSS-TT-EEEEE CS
                     ACP_syn_III_C   1 Lekagltpedidalvphqanlriidavakklglpeekvvvnl..deyGntsaasiplaLdeaveegklkpgdlvllv 75 
                                       L+k+gl++ed+d+ ++hq n ++   va+klg+p+ekv+ ++  +++Gnt   s +l L++ ++   ++pg+++l++
  gi|385805363|ref|YP_005841761.1| 229 LNKTGLKVEDFDYAIFHQPNGKFPLRVAEKLGFPKEKVFPSIvvNKIGNTYNGSALLGLSKILD--SVDPGKRILVA 303
                                       6899********************************99877667********************..9********** PP

                                       EEETTT CS
                     ACP_syn_III_C  76 gfGaGl 81 
                                        fG G 
  gi|385805363|ref|YP_005841761.1| 304 PFGSGA 309
                                       ***996 PP

>> HMG_CoA_synt_C  Hydroxymethylglutaryl-coenzyme A synthase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.7   0.0    0.0027       9.8      62      82 ..     231     251 ..     184     261 .. 0.84
   2 !   19.4   0.0   1.8e-07   0.00064     141     220 ..     263     336 ..     253     357 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0027
                                       -----GGG-SEEEE--SSHHH CS
                    HMG_CoA_synt_C  62 dkeftlddfdyvifhsPfckl 82 
                                       ++   ++dfdy ifh P  k+
  gi|385805363|ref|YP_005841761.1| 231 KTGLKVEDFDYAIFHQPNGKF 251
                                       5667789**********9885 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 1.8e-07
                                       HHHTGGGGHHHHHH---GGGHHHHHHHHHHHHS-HHHHTT-EEEEEEEETTTEEEEEEEEE-S--STTSHHH.HHTT CS
                    HMG_CoA_synt_C 141 kkkvkpsllvptevGnmYtaslyaalasllskvsadelagkriglfsYGsGlaaslfslrvkqdvsedsild.iakv 216
                                       k+kv ps++v+ ++Gn Y  s+   l  +l  v      gkri++  +GsG  +  +s+  +++ ++   +d  +kv
  gi|385805363|ref|YP_005841761.1| 263 KEKVFPSIVVN-KIGNTYNGSALLGLSKILDSVD----PGKRILVAPFGSGAGSDAYSIVTTDKIKN--KRDlAKKV 332
                                       89999999886.69************99993332....58******************988877766..45523444 PP

                                       TTHH CS
                    HMG_CoA_synt_C 217 ldlk 220
                                       +d  
  gi|385805363|ref|YP_005841761.1| 333 SDYI 336
                                       4443 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.4   1.2e-08   4.1e-05      22     114 ..      59     151 ..      48     170 .. 0.92
   2 ?   -0.8   0.0      0.22     8e+02      30      74 ..     224     263 ..     222     346 .. 0.53

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.2e-08
                                       -HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS-TTSEEEEEEHGGGHHHHHHHHHHHH CS
                        Thiolase_N  22 saeeLlaealkallekagvdpeevdevivGnvlqagegqniarqaalkagipeevpavtvnkvcsSglkavalaaqs 98 
                                        a  ++ ea+k+++++a ++p++++ v++G   +  + +  a  +a ++gi  +++a+ ++ +c  g +++ + ++ 
  gi|385805363|ref|YP_005841761.1|  59 DAITMGYEAAKNAIKRALINPKQIEAVFFGSESKPYAVKPSATVIADALGITPTTMASDLEFACRAGSEGIRASIGL 135
                                       577899*********************************************************************** PP

                                       HHTTSHSEEEEEEEEE CS
                        Thiolase_N  99 iaageadvvvagGvEs 114
                                       + ++ ++ ++++G  +
  gi|385805363|ref|YP_005841761.1| 136 VSSQMVNYALVIGSDT 151
                                       ************9865 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.22
                                       HHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS-T CS
                        Thiolase_N  30 alkallekagvdpeevdevivGnvlqagegqniarqaalkagipe 74 
                                       a+k+ll+k+g++ e+ d+ i+ +     +g+ + r +a k+g+p+
  gi|385805363|ref|YP_005841761.1| 224 AVKGLLNKTGLKVEDFDYAIFHQP----NGKFPLR-VAEKLGFPK 263
                                       678888888888888888877543....3333333.233444444 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 !   17.1   0.3     1e-06    0.0038       2      67 ..     117     179 ..     116     189 .. 0.83
   2 ?   -0.7   0.0      0.37   1.3e+03      37      57 ..     287     310 ..     286     324 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1e-06
                                       EEE-GGGHHHHHHHHHHHHHHTTS-SEEEEEEEEEGGGCS-TTTHHHHTTB-EEEEEEEEEEESSS CS
                       ACP_syn_III   2 DlnaaCsgfvyalsvAdaliesgaakrvLvigaetlskilDwkdrstavlfGDGAgAvvleaseee 67 
                                       Dl+ aC +   ++    +l++s +++++Lvig++t     ++ d    ++ + GA+A+v+++s+e 
  gi|385805363|ref|YP_005841761.1| 117 DLEFACRAGSEGIRASIGLVSSQMVNYALVIGSDTAQA--NPGDV-LEYTASSGAAAFVIGPSNEA 179
                                       88999******************************655..88774.4457899********98543 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.37
                                       GGGCS-TTT...HHHHTTB-EEEE CS
                       ACP_syn_III  37 lskilDwkd...rstavlfGDGAg 57 
                                       lskilD  d   r  +  fG GAg
  gi|385805363|ref|YP_005841761.1| 287 LSKILDSVDpgkRILVAPFGSGAG 310
                                       577777766443666668999998 PP

>> HTH_35  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.048   1.7e+02      45      57 ..     101     113 ..      62     117 .. 0.90
   2 ?    7.0   0.0    0.0016       5.9      25      61 ..     232     269 ..     224     278 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.048
                            HTH_35  45 alIAeaLgvppee 57 
                                       ++IA+aLg++p +
  gi|385805363|ref|YP_005841761.1| 101 TVIADALGITPTT 113
                                       69*******9975 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0016
                            HTH_35  25 aglssstls.naltrpwpkgEalIAeaLgvppeeiwPs 61 
                                        gl+ + +  +++++p+ k   ++Ae Lg p e+++Ps
  gi|385805363|ref|YP_005841761.1| 232 TGLKVEDFDyAIFHQPNGKFPLRVAEKLGFPKEKVFPS 269
                                       566666665145789999999****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2296.27
//
Query:       gi|385805364|ref|YP_005841762.1|  [L=386]
Description: Acetyl-CoA acetyltransferase [Fervidicoccus fontis Kam940]
Scores for complete 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   49.0   0.0    1.5e-10   40.9   0.0    2.2  2  Thiolase_N   Thiolase, N-terminal domain
    7.7e-06   25.7   0.0     0.0015   18.4   0.0    2.6  2  ACP_syn_III  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase 
  ------ inclusion threshold ------
      0.023   14.3   0.6      0.077   12.7   0.1    2.0  2  Thiolase_C   Thiolase, C-terminal domain


Domain annotation for each model (and alignments):
>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   0.0   2.5e-14   1.5e-10      22     191 ..      20     181 ..       2     196 .. 0.87
   2 !    5.8   0.0    0.0013       7.5     245     260 .]     207     222 ..     204     222 .. 0.87

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 2.5e-14
                                       -HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCT.TSTSC.HHHHHHHHTTS-TTSEEEEEEHGGGHHHHHHHHHH CS
                        Thiolase_N  22 saeeLlaealkallekagvdpeevdevivGnvlqa.gegqn.iarqaalkagipeevpavtvnkvcsSglkavalaa 96 
                                       ++e++  +a+k++l++ g + + vd viv+n     ++ qn  +  ++ ++gi + + +  v+   +Sg ++++la 
  gi|385805364|ref|YP_005841762.1|  20 TIEDMVYNAVKKMLDQFG-NLSFVDTVIVANAFGYsMQRQNmFSSLISEELGI-KGARTFNVEAGQISGHSGLILAD 94 
                                       6899*************9.6789*********998899999677788899***.*********************** PP

                                       HHHHTTSHSEEEEEEEEESTTS-EEETCTTTTGGS.SSSEEEEEHHHHHHTEETTTTSEHHHHHHHHHHHHT--HHH CS
                        Thiolase_N  97 qsiaageadvvvagGvEsmsnaptaestdvrsglk.lgdekakdllipdgladafneehmGltaenlakkykisRee 172
                                         i++g ++ v+++G E+ms+ +  +  +++s+l+ ++ e + + ++ +           G+ a+ + +ky++  ee
  gi|385805364|ref|YP_005841762.1|  95 SLIKSGYSKHVLLIGFEKMSDYNSEVYNSLISQLTnIEYEGIYGSTLAS---------NFGIIARYYQEKYGLKEEE 162
                                       *********************9998887777665416667777777777.........89***************** PP

                                       HHHHHHHHHHHHHHHHHTT CS
                        Thiolase_N 173 qdefAvkshqkaaaaqkag 191
                                        +++ +  h++a++  +a+
  gi|385805364|ref|YP_005841762.1| 163 FASWPILMHENASETYHAQ 181
                                       *************998887 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0013
                                       --BEEEEEEEEEEEHH CS
                        Thiolase_N 245 sqisDGaaavllmses 260
                                        +isDGaaa+l+ +e+
  gi|385805364|ref|YP_005841762.1| 207 PPISDGAAALLISRED 222
                                       68**********9885 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 !   18.4   0.0   2.5e-07    0.0015      12      40 ..      88     116 ..      77     123 .. 0.88
   2 !    4.5   0.0    0.0051        30      53      66 ..     210     223 ..     205     236 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.5e-07
                                       HHHHHHHHHHHTTS-SEEEEEEEEEGGGC CS
                       ACP_syn_III  12 yalsvAdaliesgaakrvLvigaetlski 40 
                                        +l +Ad+li+sg  k+vL+ig e++s++
  gi|385805364|ref|YP_005841762.1|  88 SGLILADSLIKSGYSKHVLLIGFEKMSDY 116
                                       689***********************985 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0051
                                       -EEEEEEEEEEESS CS
                       ACP_syn_III  53 GDGAgAvvleasee 66 
                                       +DGA+A+++++++ 
  gi|385805364|ref|YP_005841762.1| 210 SDGAAALLISREDR 223
                                       8*********9853 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.22   1.3e+03      27      55 ..      28      55 ..      22      89 .. 0.51
   2 ?   12.7   0.1   1.3e-05     0.077      65     101 ..     319     355 ..     281     382 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.22
                                      HHHHHHHHHT--GGGESEEEE--SBHHHH CS
                        Thiolase_C 27 aikkvlkkagltvedidlfEinEAFaaqa 55
                                      a+kk+l++ g +++ +d + +  AF   +
  gi|385805364|ref|YP_005841762.1| 28 AVKKMLDQFG-NLSFVDTVIVANAFGYSM 55
                                      6777777777.566677777777775432 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 1.3e-05
                                       -GGGBSTT--HHHH-B-TTTHHHHHHHHHHHHHHHCT CS
                        Thiolase_C  65 dlekvNvnGGaialGHPlGasGaRivvtllselkkeg 101
                                       d++ +N+ GG+ a G P+Ga G+  ++ +   +  e+
  gi|385805364|ref|YP_005841762.1| 319 DKQMINITGGTKARGYPIGALGVYEAAEISAMMSGEK 355
                                       5689******************998888887776554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2753.02
//
Query:       gi|385805365|ref|YP_005841763.1|  [L=133]
Description: hypothetical protein FFONT_0321 [Fervidicoccus fontis Kam940]
Scores for complete 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   43.3   0.5    2.4e-11   43.3   0.5    1.5  2  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
    1.3e-07   31.5   0.0    1.9e-07   31.0   0.0    1.2  1  OB_aCoA_assoc   DUF35 OB-fold domain, acyl-CoA-associated
    0.00077   18.9   1.7      0.045   13.3   0.2    2.3  2  TF_Zn_Ribbon    TFIIB zinc-binding
     0.0073   16.0   0.4       0.01   15.5   0.4    1.2  1  TackOD1         Thaumarchaeal output domain 1
  ------ inclusion threshold ------
      0.037   14.0   1.4      0.045   13.8   0.5    1.5  2  HypA            Hydrogenase/urease nickel incorporation, meta
      0.044   13.8   0.9      0.069   13.2   0.9    1.3  1  DZR             Double zinc ribbon
      0.052   13.7   1.2         17    5.7   0.2    3.0  3  zinc_ribbon_13  Nucleic-acid-binding protein containing Zn-ri
      0.058   12.9   1.1      0.058   12.9   1.1    2.2  2  zf_C2H2_10      C2H2 type zinc-finger
      0.075   12.8   1.1         11    5.9   0.1    2.4  2  A2L_zn_ribbon   A2L zinc ribbon domain
      0.083   13.0   3.7       0.35   11.0   3.7    2.0  1  Zn-ribbon_8     Zinc ribbon domain
      0.099   13.0   0.1       0.14   12.4   0.1    1.4  1  DUF5603         Domain of unknown function (DUF5603)
       0.17   11.8   0.2       0.17   11.8   0.2    3.0  3  DUF1936         Domain of unknown function (DUF1936)
       0.42   10.6   6.0          2    8.4   0.8    2.4  2  Nudix_N_2       Nudix N-terminal
        0.7    9.7   3.9        2.4    8.0   3.9    1.8  1  Rubredoxin_2    Rubredoxin metal binding domain
        2.3    8.2   6.0          3    7.8   0.4    2.3  2  zinc_ribbon_4   zinc-ribbon domain
        3.6    7.6   7.4        0.5   10.4   0.4    2.2  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain


Domain annotation for each model (and alignments):
>> 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 !   43.3   0.5   2.2e-14   2.4e-11       7      37 .]      17      47 ..      16      47 .. 0.94
   2 ?   -3.1   0.2       7.1     8e+03      21      25 ..      49      53 ..      49      54 .. 0.82

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 2.2e-14
                           DUF35_N  7 grLvgqrCpdCGtvqfPPravCphCgsddle 37
                                      + Lvg rC++CG v++PP +vCp+C s+dle
  gi|385805365|ref|YP_005841763.1| 17 YNLVGKRCKKCGYVFYPPKHVCPKCNSSDLE 47
                                      579**********************999987 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 7.1
                           DUF35_N 21 qfPPr 25
                                      +fPP+
  gi|385805365|ref|YP_005841763.1| 49 YFPPE 53
                                      7**96 PP

>> 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 !   31.0   0.0   1.7e-10   1.9e-07       6      65 .]      53     112 ..      50     112 .. 0.93

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 1.7e-10
                                       GG-EEEEEEEEEE-TTS-EEEEEEEEEEEE-TT...-EE-EEEEEEES...TT-B-EEE-S CS
                     OB_aCoA_assoc   6 grGtvysftvvhrappgfaeeaPyvvgvVeLdegvrimarlvgvdpde.vriGmrVravfr 65 
                                        +Gt+ sft  ++ p +++ ++P  +g++++ e + +++++v+v  ++ ++ G  V+ vfr
  gi|385805365|ref|YP_005841763.1|  53 ETGTLISFTKLYETPNTYKSQKPIYLGIIKFGE-INVLTQIVDVQNEDeLKPGITVERVFR 112
                                       69*******************************.99********95555**********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 ?    4.9   0.1     0.017        19      21      28 ..      23      30 ..      22      32 .. 0.88
   2 !   13.3   0.2     4e-05     0.045       2      21 ..      37      58 ..      36      58 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.017
                                      EESSSSBE CS
                      TF_Zn_Ribbon 21 vCtdCGlV 28
                                      +C++CG+V
  gi|385805365|ref|YP_005841763.1| 23 RCKKCGYV 30
                                      5*****98 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 4e-05
                                      EETTTTCEEC..HEETSTTCEE CS
                      TF_Zn_Ribbon  2 kCPnCgstnl..veDpergelv 21
                                      +CP+C+s++l  +++pe+g+l+
  gi|385805365|ref|YP_005841763.1| 37 VCPKCNSSDLedYFPPETGTLI 58
                                      8******986568889999875 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   0.4   9.1e-06      0.01      75      99 ..      23      47 ..       3      49 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 9.1e-06
                           TackOD1 75 lCpsCksghlnvrevCpkCkSidie 99
                                       C++C       ++vCpkC+S+d+e
  gi|385805365|ref|YP_005841763.1| 23 RCKKCGYVFYPPKHVCPKCNSSDLE 47
                                      7**********************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 ?   13.8   0.5     4e-05     0.045      72      98 ..      23      47 ..      17      49 .. 0.85
   2 ?   -2.6   0.0       4.9   5.5e+03       3      18 ..      85     100 ..      84     114 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4e-05
                                      EETTTS-EEECHHHHHS-TTTSSS-EE CS
                              HypA 72 rCreCgkefeleekalrCpkCgsadve 98
                                      rC++Cg+ f   ++   CpkC+s+d+e
  gi|385805365|ref|YP_005841763.1| 23 RCKKCGYVFYPPKH--VCPKCNSSDLE 47
                                      8********97744..8******9875 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.9
                                       HHHHHHHHHHHHHHHH CS
                              HypA   3 Elsiaesivevveeea 18 
                                       E+ + ++iv+v +e  
  gi|385805365|ref|YP_005841763.1|  85 EINVLTQIVDVQNEDE 100
                                       5666777777655543 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.9   6.1e-05     0.069      28      48 ..      21      41 ..       7      44 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.1e-05
                               DZR 28 edrCpsCgekvdpearfCpeC 48
                                       +rC +Cg+   p + +Cp+C
  gi|385805365|ref|YP_005841763.1| 21 GKRCKKCGYVFYPPKHVCPKC 41
                                      578999999999999999999 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 ?    5.7   0.2     0.015        17      37      44 ..      23      30 ..       5      36 .. 0.68
   2 ?    5.1   0.0     0.022        25       1      23 [.      37      59 ..      37      70 .. 0.79
   3 ?   -0.4   0.0       1.1   1.3e+03      22      31 ..      89      98 ..      85      99 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.015
                    zinc_ribbon_13 37 sCknCgYt 44
                                       Ck+CgY+
  gi|385805365|ref|YP_005841763.1| 23 RCKKCGYV 30
                                      5*****97 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.022
                    zinc_ribbon_13  1 kCpKCgnteaevkevaatGsgls 23
                                      +CpKC++++ e      tG+ +s
  gi|385805365|ref|YP_005841763.1| 37 VCPKCNSSDLEDYFPPETGTLIS 59
                                      6******9999877777777654 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.1
                    zinc_ribbon_13 22 lskifdvqnk 31
                                      l++i+dvqn+
  gi|385805365|ref|YP_005841763.1| 89 LTQIVDVQNE 98
                                      7899****96 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 ?    1.5   0.4      0.19   2.2e+02       5      11 ..      24      30 ..      23      31 .. 0.88
   2 ?   12.9   1.1   5.2e-05     0.058       1       9 [.      34      42 ..      34      46 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.19
                        zf_C2H2_10  5 CPKCqek 11
                                      C KC+++
  gi|385805365|ref|YP_005841763.1| 24 CKKCGYV 30
                                      99***97 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 5.2e-05
                        zf_C2H2_10  1 PefsCPKCq 9 
                                      P++ CPKC+
  gi|385805365|ref|YP_005841763.1| 34 PKHVCPKCN 42
                                      9*******9 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1    0.0096        11      24      31 ..      24      31 ..      19      32 .. 0.92
   2 ?    5.2   0.1     0.016        18      23      30 ..      37      44 ..      36      45 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0096
                     A2L_zn_ribbon 24 CieCgasf 31
                                      C++Cg++f
  gi|385805365|ref|YP_005841763.1| 24 CKKCGYVF 31
                                      ******98 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.016
                     A2L_zn_ribbon 23 vCieCgas 30
                                      vC++C++s
  gi|385805365|ref|YP_005841763.1| 37 VCPKCNSS 44
                                      8*****97 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   3.7   0.00031      0.35       7      37 ..      23      47 ..      17      49 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00031
                       Zn-ribbon_8  7 rCeeCghefevlqsisdapltaCPeCgs.evr 37
                                      rC++Cg +f        +p+ +CP+C+s +++
  gi|385805365|ref|YP_005841763.1| 23 RCKKCGYVFY-------PPKHVCPKCNSsDLE 47
                                      7*****9999.......55667*****98875 PP

>> DUF5603  Domain of unknown function (DUF5603)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00013      0.14      65      87 ..     106     128 ..      62     131 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                                       HHHHHHHHHHHTTSSEEEEESSH CS
                           DUF5603  65 kvskvldklslegkielvyygek 87 
                                        v +v+ k++ +g++ l+yyg k
  gi|385805365|ref|YP_005841763.1| 106 TVERVFRKINEDGNYGLIYYGIK 128
                                       6899*****************98 PP

>> DUF1936  Domain of unknown function (DUF1936)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.7       1.8     2e+03       2      32 ..      24      29 ..      23      30 .. 0.53
   2 ?   11.8   0.2   0.00016      0.17       1      11 [.      37      47 ..      37      53 .. 0.90
   3 ?   -0.3   0.0      0.94   1.1e+03      21      32 ..     109     120 ..     108     121 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.8
                                      -TTTSSSBEEEEE-TTS-EEEEEES-TT--- CS
                           DUF1936  2 CPKCnvGkLEPVYNekGEIKvFRCdredCdY 32
                                      C KC                         +Y
  gi|385805365|ref|YP_005841763.1| 24 CKKC-------------------------GY 29
                                      5555.........................55 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00016
                                      B-TTTSSSBEE CS
                           DUF1936  1 lCPKCnvGkLE 11
                                      +CPKCn+  LE
  gi|385805365|ref|YP_005841763.1| 37 VCPKCNSSDLE 47
                                      6*******999 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.94
                                       EEEEES-TT--- CS
                           DUF1936  21 KvFRCdredCdY 32 
                                       +vFR  +ed +Y
  gi|385805365|ref|YP_005841763.1| 109 RVFRKINEDGNY 120
                                       599999999888 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.8    0.0018         2      24      33 ..      23      32 ..      22      33 .. 0.92
   2 ?    4.7   0.4     0.026        30      22      29 ..      35      42 ..      33      43 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0018
                                      EETTTTEEE- CS
                         Nudix_N_2 24 vCpaCgtihY 33
                                      +C++Cg+++Y
  gi|385805365|ref|YP_005841763.1| 23 RCKKCGYVFY 32
                                      6********9 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.026
                                      EEEETTTT CS
                         Nudix_N_2 22 RlvCpaCg 29
                                       +vCp+C+
  gi|385805365|ref|YP_005841763.1| 35 KHVCPKCN 42
                                      59*****7 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   3.9    0.0021       2.4       2      23 ..      23      44 ..      23      45 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0021
                      Rubredoxin_2  2 vCsqCGfesakwfGrCpsCgsW 23
                                      +C++CG+++      Cp C+s 
  gi|385805365|ref|YP_005841763.1| 23 RCKKCGYVFYPPKHVCPKCNSS 44
                                      8********999999****986 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.4    0.0027         3      27      35 ..      23      31 ..      22      32 .. 0.94
   2 ?    2.9   0.8     0.096   1.1e+02       4      10 ..      37      43 ..      35      44 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0027
                     zinc_ribbon_4 27 rCskCghvF 35
                                      rC+kCg vF
  gi|385805365|ref|YP_005841763.1| 23 RCKKCGYVF 31
                                      9******99 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.096
                     zinc_ribbon_4  4 tCpsCka 10
                                      +Cp+C++
  gi|385805365|ref|YP_005841763.1| 37 VCPKCNS 43
                                      5999986 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   1.2      0.41   4.5e+02      39      45 ..      23      29 ..      11      30 .. 0.80
   2 ?   10.4   0.4   0.00045       0.5      14      27 ..      31      44 ..      29      51 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.41
                     Zn_Tnp_IS1595 39 qCkeCrk 45
                                      +Ck+C++
  gi|385805365|ref|YP_005841763.1| 23 RCKKCGY 29
                                      5777775 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00045
                     Zn_Tnp_IS1595 14 rWpngfvCPhCgsr 27
                                      ++p ++vCP+C s+
  gi|385805365|ref|YP_005841763.1| 31 FYPPKHVCPKCNSS 44
                                      78999******998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 827.37
//
Query:       gi|385805366|ref|YP_005841764.1|  [L=113]
Description: hypothetical protein FFONT_0322 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); 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: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 723.64
//
Query:       gi|385805367|ref|YP_005841765.1|  [L=357]
Description: AIR synthase domain protein [Fervidicoccus fontis Kam940]
Scores for complete 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-18   65.3   0.1    9.2e-18   64.8   0.1    1.2  1  AIRS_C    AIR synthase related protein, C-terminal domain
    3.2e-07   30.9   0.0      6e-07   30.0   0.0    1.5  1  AIRS      AIR synthase related protein, N-terminal domain


Domain annotation for each model (and alignments):
>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.8   0.1     1e-21   9.2e-18       1     154 [.     162     329 ..     162     331 .. 0.88

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 1e-21
                                       STTEEEEEEET...SSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHH..HTTECEEEE--TTHH CS
                            AIRS_C   1 kpGdvliltgs...lGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaal..kglvkaahDvTgGGL 72 
                                       ++Gd++++t++     +g+++t+   +i+e+eg ++  ++    + ++ +++ +++l  l  +  ++++hD T+ G+
  gi|385805367|ref|YP_005841765.1| 162 EEGDLILMTKGpaiEAVGILSTMY-PEIVEKEGGNELRRKGESFFYKMSVVEDALSLSSLglRTAITSMHDATEYGV 237
                                       58*********7776666666333.56888888887788888889999***************************** PP

                                       HHHHHHHHHTTTEEEEEECG..........THHHHHHHH.HHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCC CS
                            AIRS_C  73 lgalaemapasgvgaeidld..........kvpifdele.splemllsensGrllvavppeeadavlaileeeglpe 138
                                       +gal+ + +as+  +ei+++           ++if+e    p++++ s ++G l+ +v++e ad+++++l++ g+ +
  gi|385805367|ref|YP_005841765.1| 238 WGALHDISRASNSLVEIQEEslfidddvekILRIFEEKTkIPIDPYASISEGTLIATVKKEYADQAIDVLSRKGI-K 313
                                       ********************888888888777777776699**********************************.7 PP

                                       EEEEEEEEESSSEEEE CS
                            AIRS_C 139 aavIGevtakeelsvi 154
                                       a +IG++ +k++  v+
  gi|385805367|ref|YP_005841765.1| 314 AGIIGRIREKGKRGVY 329
                                       *********9987776 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 !   30.0   0.0   6.7e-11     6e-07       5      89 ..      52     144 ..      30     150 .. 0.85

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 6.7e-11
                                       EEEEEEEEE.EECCTCCCC...HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......HHHHHHHHHHHHHHHTT-E CS
                              AIRS   5 vvvttdshnrpvlvepvhf...iGakavavnlsDlaamGArPlalllslalp......wleevvrglaeaaeelgvp 72 
                                       ++v+td    pv+v p  +    ++ av+  +sD+ + G    ++   l+lp      +++ + + +++ +++lg++
  gi|385805367|ref|YP_005841765.1|  52 IIVKTD----PVFVVPEYGwekSAWFAVHILASDVSTSGNPAQYMAIDLNLPkkitkeQFSVLWSKISDECKKLGIS 124
                                       478899....7777665556999***************98888********************************** PP

                                       EEEEEEEEESS...EEEEEE CS
                              AIRS  73 lvgGdtsfsne...ptisvt 89 
                                       +v G+t  +++   p+i  +
  gi|385805367|ref|YP_005841765.1| 125 IVAGHTGIYDGtdyPMIGGA 144
                                       *******9988777666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 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:                        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: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2368.38
//
Query:       gi|385805368|ref|YP_005841766.1|  [L=434]
Description: histidyl-tRNA synthetase [Fervidicoccus fontis Kam940]
Scores for complete 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-43  147.3   0.0    6.9e-43  147.1   0.0    1.1  1  tRNA-synt_His   Histidyl-tRNA synthetase
    1.3e-10   41.3   0.2    3.3e-10   40.0   0.2    1.7  1  HGTP_anticodon  Anticodon binding domain
    4.1e-10   39.9   0.0    7.1e-10   39.1   0.0    1.4  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
     0.0011   18.2   0.8       0.04   13.0   0.3    2.8  2  tRNA-synt_2     tRNA synthetases class II (D, K and N)
  ------ inclusion threshold ------
      0.022   14.9   0.2      0.047   13.8   0.2    1.6  1  DUF4327         Domain of unknown function (DUF4327)
       0.14   12.3   2.0       0.23   11.6   0.6    2.2  2  DUF3627         Protein of unknown function (DUF3627)


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 !  147.1   0.0   2.3e-46   6.9e-43       1     310 []      10     322 ..      10     322 .. 0.90

  Alignments for each domain:
  == domain 1  score: 147.1 bits;  conditional E-value: 2.3e-46
                                       T---EETCHHHHHHHHHHHHHHHHHHTT-EEEE--SEEEHHHHCTTSTCCHH..HS-EEE-T.TSSEEEE-SSSHHH CS
                     tRNA-synt_His   1 glrdllpeeaekieelrrrlldlfeswGYelVspPllEyldslltgagedld..qtfklvDq.sgrllglRaDiTpq 74 
                                       g+rd+ pe +e + ++ +++ ++fe +++ +  +P++Ey ++l  + g +++   +++++D  s++  +lR D+T+ 
  gi|385805368|ref|YP_005841766.1|  10 GFRDFPPEVMELRLKVINTVRNIFEINDFPPMDTPSIEYWETLAGKYGPEAEnkLIWRFKDPfSEKEYALRYDLTVP 86 
                                       89*******************************************9977765457******99************** PP

                                       HHHHHHHHHHTSS-EEEEEEEEEEESS-SSTT--CCEEEEEEEEESS-SHHHHHHHHHHHHHHHHHHCTSSSEEEEE CS
                     tRNA-synt_His  75 vaRiaahrlnrerplRlcYaGsvlrtrpdglgrsreplQvGaEliGaegleadlEvlslllealeaaagvkelrldl 151
                                        aR++a + + + p + + +  v+r ++ + gr re+lQ+ +  +G++ +e+d+E+++ +  +le  +g++++ +++
  gi|385805368|ref|YP_005841766.1|  87 LARYVASHPELQLPFKRHQISYVWRHEEPQRGRYREFLQADIDTVGSKFVESDAEIINTMSLVLE-ELGLDDFIVKI 162
                                       ****************************************************************7.*********** PP

                                       EETCHHHHHHH.HTT--HHHHHHHHHHHHCT-HHHHHHHHHCCT...THHHCCHCC....HCCHCCCHHHHCHCCHC CS
                     tRNA-synt_His 152 ghvglvralle.aaglsesleeallaalarkdlaelkelaaeag...lkealrellkal.elygdaevleealeala 223
                                       +h +++  ++e ++g   s    +l+a+++ d  +++ ++ e +   l+e+ ++++  l + + + + le+ +++l+
  gi|385805368|ref|YP_005841766.1| 163 NHRKILYIIFEkRLG---SNVTSVLRAIDKLDKIGIDGVILELQkigLDESSINWIINLiSNRDSIDNLENIKKNLV 236
                                       *********994555...66778888999999999998887643333889999999888888899999999999999 PP

                                       THHHHHHHHHHHHHHHHHHHHHHHH-TTEEE-TT--TTTTT--SEEEEEEE.TT-SS-SEEEEEECTTTGGG.T--- CS
                     tRNA-synt_His 224 aapalqaaldeleelaallealakpevrvtlDlaelrgyeYytGlvFaaya.egvgqaiarGGrYdelgaaf.grar 298
                                       + +   ++ d l+el +  e la ++ ++ +Dl+++rg++YytG++F++   +g++  ia+GGrYd+l+++f g+  
  gi|385805368|ref|YP_005841766.1| 237 EFDF--SLEDPLNELIEFREFLA-HRKHIVFDLSLVRGLDYYTGIIFEISLeKGSPGSIAGGGRYDNLIKMFkGSDL 310
                                       8864..56677777777777665.4679*********************98256779******************** PP

                                       EEEEEEEEHHHH CS
                     tRNA-synt_His 299 pAtGfsldleal 310
                                       pAtG sl +e++
  gi|385805368|ref|YP_005841766.1| 311 PATGGSLGIERI 322
                                       *********986 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.2   1.1e-13   3.3e-10       1      91 [.     340     427 ..     340     430 .. 0.97

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 1.1e-13
                                       SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTC CS
                    HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtr 77 
                                       +v++i+lne   +  +ya     eLr  gi++e+d   +++ k+ ++    +i f v +G+ke e + +t+ +rdt+
  gi|385805368|ref|YP_005841766.1| 340 KVFIITLNE---DSYKYAWNFSYELRTRGIKTEIDLMRRNVDKQKKKGASENILFHVYIGKKEKEGRYITIVERDTG 413
                                       79*******...899************************************************988*********** PP

                                       EEEEEETTHHHHHH CS
                    HGTP_anticodon  78 eqervsldelvekl 91 
                                       ++ ++++d++++++
  gi|385805368|ref|YP_005841766.1| 414 KRLELPYDKAIDYI 427
                                       ************98 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.0   2.4e-13   7.1e-10       8     108 ..      74     166 ..      66     347 .. 0.78

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 2.4e-13
                                       SEEEEE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b   8 dreyiLkPtneetfvelirdevlrskrLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeaslddslrdli 84 
                                       ++ey+L+   + ++++ +  +   + +LP+k +qi+ ++R+E++ +rG  R+reF q d   ++++    +s++++i
  gi|385805368|ref|YP_005841766.1|  74 EKEYALRYDLTVPLARYVASH--PELQLPFKRHQISYVWRHEEP-QRG--RYREFLQADIDTVGSKF--VESDAEII 143
                                       678888888888888888877..3345*****************.***..*********99988765..9******* PP

                                       HHHHHHHHHTT.SCEEEEEEGTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  85 kaisriferlglefraiielmsak 108
                                       +++s ++e+lgl  + i++++++k
  gi|385805368|ref|YP_005841766.1| 144 NTMSLVLEELGLDDF-IVKINHRK 166
                                       ************865.66666643 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 !   13.0   0.3   1.3e-05      0.04      20     139 ..      17     151 ..      12     158 .. 0.70
   2 ?    1.0   0.0     0.061   1.8e+02     270     298 ..     298     326 ..     294     334 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.3e-05
                                       HHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT...........TEEE-E-S-SHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  20 kvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrek..........ekeffaLtqspqlylell 86 
                                       +v++lr +v++ vr+++e n+f  ++tP +   +    a ++  + ++k          eke+  L+      l ++
  gi|385805368|ref|YP_005841766.1|  17 EVMELRLKVINTVRNIFEINDFPPMDTPSIEYWE--TLAGKYGPEAENKliwrfkdpfsEKEYA-LRYDLTVPLARY 90 
                                       6899************************887764..3333443333333334442445444555.555444444444 PP

                                       HHCTHS.....EEEEEEEEE--S--BTTB-S-CEEEEEEEE...ET-SCHH.HHHHHHHHHH CS
                                       xxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxx.xxxxxxxxxx RF
                       tRNA-synt_2  87 ivagid.....rvfqiaraFRaEdsrtdrhlaEFtqieaem...sfieeed.imqvleelik 139
                                       +++  +     +  qi+ ++R E+ +  r   EF q ++ +   +f+e +  i++++  +++
  gi|385805368|ref|YP_005841766.1|  91 VASHPElqlpfKRHQISYVWRHEEPQRGRYR-EFLQADIDTvgsKFVESDAeIINTMSLVLE 151
                                       444322222227789***********99999.******998777899998889998876665 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.061
                                       GHHHHHHHHCT--SEEEEEEEHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 270 fswylealeyGapphgGlglGldRlvmll 298
                                       +++++++++ +  p  G  lG++R+  +l
  gi|385805368|ref|YP_005841766.1| 298 YDNLIKMFKGSDLPATGGSLGIERIFDVL 326
                                       78999*****99************98766 PP

>> DUF4327  Domain of unknown function (DUF4327)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   1.6e-05     0.047      38      60 ..     229     251 ..     203     255 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.6e-05
                           DUF4327  38 aavekeLeendfllrDriadLlg 60 
                                       ++++k+L e+df+l D++ +L++
  gi|385805368|ref|YP_005841766.1| 229 ENIKKNLVEFDFSLEDPLNELIE 251
                                       689******************97 PP

>> DUF3627  Protein of unknown function (DUF3627)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       3.6   1.1e+04      76      90 ..      63      77 ..      55      80 .. 0.60
   2 ?   11.6   0.6   7.6e-05      0.23       4      39 ..     321     354 ..     319     392 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3.6
                           DUF3627 76 nlfnriKeklkskkk 90
                                      +l+ r+K+   +k++
  gi|385805368|ref|YP_005841766.1| 63 KLIWRFKDPFSEKEY 77
                                      355666666655554 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 7.6e-05
                           DUF3627   4 kleivvedrvpkpkekklkerlillkrndkeryeYy 39 
                                       ++ +v+e+r++ +k kk+++ +i+  ++d  +y+Y+
  gi|385805368|ref|YP_005841766.1| 321 RIFDVLEERNITSKFKKKNKVFIITLNED--SYKYA 354
                                       7789***********************99..77775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.28s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2794.29
//
Query:       gi|385805369|ref|YP_005841767.1|  [L=74]
Description: FeoA domain containing protein [Fervidicoccus fontis Kam940]
Scores for complete 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   1.5    6.3e-18   64.8   1.5    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 !   64.8   1.5   3.5e-22   6.3e-18       2      73 ..       3      71 ..       2      72 .. 0.94

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 3.5e-22
                                      EGGG--TT-EEEEEEE-TT.SSHHHHHHHHT--TT-EEEEEEE-TTS-SEEEEETTEEEEE-HHHHTTEEEE CS
                              FeoA  2 pLsdlkeGergeiarisdedpellrrLremGlvpGarievvarapfggplvvrvgdtrvaLgreeAqaIlVe 73
                                      +L d+ eGe+++i+ri d+++e  ++L+++G+ pG+++ev+ ++++ gpl+v+++d ++a+gr++ q+IlVe
  gi|385805369|ref|YP_005841767.1|  3 RLIDVREGEKVKIVRI-DAGEEAVKKLLRLGIIPGTEVEVI-KNNY-GPLLVKIRDLNIAIGRGISQKILVE 71
                                      6889************.667*********************.7887.9***********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); 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 0.29s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 487.03
//
Query:       gi|385805370|ref|YP_005841768.1|  [L=288]
Description: 2-oxoacid:ferredoxin oxidoreductase subunit beta [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-23   83.1   0.0    2.5e-23   82.6   0.0    1.2  1  TPP_enzyme_C    Thiamine pyrophosphate enzyme, C-terminal TPP
     0.0008   18.7   0.0      0.001   18.4   0.0    1.2  1  DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase


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 !   82.6   0.0   2.8e-27   2.5e-23      18     152 ..      49     195 ..      38     196 .. 0.87

  Alignments for each domain:
  == domain 1  score: 82.6 bits;  conditional E-value: 2.8e-27
                                       SSEEEC.ETTTS-TTTHHHHHHHHHHH.....STTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEEEEEEE-SBCCC CS
                      TPP_enzyme_C  18 prsylt.sgglgtmGyglpaAiGakla.....kpdrevvaivGDGgflmi.lqelatavrrnlpitvvvlnNegygm 87 
                                       p+s l+ + +++ +  + ++A+G+  a      +d +v++ +GDGg+++i +  l+ a++rn +i++++++Ne+y++
  gi|385805370|ref|YP_005841768.1|  49 PYSSLKmNIVHTPFASSASVASGLREAlkqrgLEDTQVIVWAGDGGTADIgMASLSGAAERNEDIIYIMYDNEAYMN 125
                                       5555664669**************985444334579***************************************** PP

                                       HHHH...HHHHTCCTTTTSBB..BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEEEEE CS
                      TPP_enzyme_C  88 tggq...qepfggkrksgpagk.dlkpvdfaklaealGak.garvekadveeleealkealekkgpalie 152
                                       tg q   ++p  ++++++p +   ++++d+a+++ a+ ++ +a+ + a++++l ++lk+a e +g+ +i+
  gi|385805370|ref|YP_005841768.1| 126 TGIQrssSTPIKAWTTTTPVYGkSEPKKDVARIMIAHNVPyVATASIAYPQDLYQKLKKAQEIRGFRFIQ 195
                                       ******9999999999998766469***************999999********************9996 PP

>> DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.1e-07     0.001     115     179 ..      64     128 ..      52     191 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.1e-07
                    DXP_synthase_N 115 tsisaalGlavardlkg.ekkkvvaviGDgaltgGmafealnnigelkkkllvilNdNemsisknv 179
                                       +s s+a Gl +a +++g e+++v+   GDg+ t+ + + +l  ++e +++++ i+ dNe  +++ +
  gi|385805370|ref|YP_005841768.1|  64 SSASVASGLREALKQRGlEDTQVIVWAGDGG-TADIGMASLSGAAERNEDIIYIMYDNEAYMNTGI 128
                                       5789************9899999999****9.77788889******************98876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        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 0.28s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1749.78
//
Query:       gi|385805371|ref|YP_005841769.1|  [L=404]
Description: 2-oxoacid:ferredoxin oxidoreductase subunit alpha [Fervidicoccus fontis Kam940]
Scores for complete 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-59  201.0   0.0    2.7e-59  200.7   0.0    1.1  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    1.1e-25   89.8   0.0    2.2e-25   88.9   0.0    1.5  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
     0.0035   17.2   0.0     0.0068   16.3   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 !  200.7   0.0   4.6e-63   2.7e-59       4     229 ..      22     242 ..      19     248 .. 0.88

  Alignments for each domain:
  == domain 1  score: 200.7 bits;  conditional E-value: 4.6e-63
                                       HHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCCHH CS
                             POR_N   4 iaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmienlg 80 
                                       +  +  vi+aYPITP++ i+e+l+e++++ge+ +++++++esE++a +a  GAa++Gara+TaTS++Gll+m+e l+
  gi|385805371|ref|YP_005841769.1|  22 KLSKASVISAYPITPQTAIIEKLSEFVERGEL-KARIIKVESEHSALAATFGAALGGARAFTATSSHGLLYMHEWLH 97 
                                       556678*************************9.8******************************************* PP

                                       HHHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHHS---EEEE-SSHHHHHHHHHHHHHHHHH..CTSEEEEEEEH CS
                             POR_N  81 laageelPvvivvvaRalpstglsirtdqsDlmaardtglivlasenvqeafdlalvAfnlAek..vrvPvivlfDg 155
                                       +++ +++Pvv+++v+R++  + ++i++d+sD m  rdtg+i+ +  ++qe+ dl+l+Af+l+e+  + +Pviv ++g
  gi|385805371|ref|YP_005841769.1|  98 WVSRSRIPVVMAIVTRTIGLP-WNIWPDHSDYMDQRDTGWIMTFGMDNQEVLDLTLQAFKLSEDpdIYLPVIVGLEG 173
                                       *********************.******************************************************* PP

                                       HHH.HEEEEEEC-SGG.GS-----SBXXXXXXXXSXXXBXXTXXTSSXXEEESBXBXTTSXBXXXXHHHHHHHH CS
                             POR_N 156 fllshevekvelpdeedelklikekleeyerkeyaldpekpiargtaanpdtglehrekgneaedaaekvveev 229
                                       f+l  ++ +v lpde      ++++  e+ ++ y +dp++pia+g  + p+   e+  +++++++++ k  +e+
  gi|385805371|ref|YP_005841769.1| 174 FVLGGTYMPVILPDER----EAEDFVGER-AQPYTIDPKNPIAIGNMTLPEGTEEMFMDMQKSMMNVYKKAKEI 242
                                       *************999....444444444.34559**********99988766666666655555555544443 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 !   88.9   0.0   3.6e-29   2.2e-25       1     102 []     266     370 ..     266     370 .. 0.93

  Alignments for each domain:
  == domain 1  score: 88.9 bits;  conditional E-value: 3.6e-29
                                       -SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHH CS
                           PFOR_II   1 AevvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaa 77 
                                       A++++v+mG+++g+a +av+ lR eg+ vGllr+r++rP P+e++k++l + k  +v+dr+is+gs+G ++++v ++
  gi|385805371|ref|YP_005841769.1| 266 AKYMMVTMGAWSGDAIEAVNVLRSEGYPVGLLRVRYFRPMPTEDYKKYLFNSKMTIVFDRSISYGSTGSIYQDVISS 342
                                       899***********************************************************************999 PP

                                       TGGG..TSEEE.EEE--GGG----HHHH CS
                           PFOR_II  78 lkks..kvkvv.nfvaglgGrditvedi 102
                                       l+    k++vv n++ag+gG d+t++d+
  gi|385805371|ref|YP_005841769.1| 343 LHLAssKINVVhNVIAGIGGVDMTLKDF 370
                                       98776655554289**********9985 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.1e-06    0.0068       6      85 ..     262     341 ..     258     362 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.1e-06
                                       EETTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHHHHHHH CS
                   Transketolase_C   6 lregkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGigsevaa 82 
                                       ++e  + ++v++G+    a+eA++ L++eg+ + ++ +r ++p+ +e+ ++ + + +  +v++     g+ gs   +
  gi|385805371|ref|YP_005841769.1| 262 KCEDAKYMMVTMGAWSGDAIEAVNVLRSEGYPVGLLRVRYFRPMPTEDYKKYLFNSKMTIVFDRSISYGSTGSIYQD 338
                                       677888899****************************************9999999888888888877777775555 PP

                                       HHH CS
                   Transketolase_C  83 ala 85 
                                       +++
  gi|385805371|ref|YP_005841769.1| 339 VIS 341
                                       555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); 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: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 2745.00
//
Query:       gi|385805372|ref|YP_005841770.1|  [L=98]
Description: 2-oxoacid:ferredoxin oxidoreductase subunit delta [Fervidicoccus fontis Kam940]
Scores for complete 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   59.6  15.7    5.9e-09   35.4   4.7    2.2  2  Fer4      4Fe-4S binding domain
    6.6e-15   55.4  35.6    7.4e-09   36.1  13.9    1.9  3  Fer4_7    4Fe-4S dicluster domain
    1.9e-11   43.5  14.6    3.5e-06   26.9   3.6    2.2  2  Fer4_6    4Fe-4S binding domain
    1.2e-10   41.3  13.0    2.2e-10   40.5  13.0    1.4  1  Fer4_21   4Fe-4S dicluster domain
    7.7e-10   38.7  23.5    1.7e-06   28.1  13.5    2.1  2  Fer4_10   4Fe-4S dicluster domain
    8.1e-10   39.5  10.0    4.8e-05   24.2   1.5    2.2  2  Fer4_16   4Fe-4S double cluster binding domain
    6.2e-09   36.2   5.5    0.00021   21.7   0.3    2.1  2  Fer4_8    4Fe-4S dicluster domain
    2.2e-08   33.7  12.7    0.00024   21.0   2.4    2.2  2  Fer4_2    4Fe-4S binding domain
    7.5e-08   32.4  12.1    1.4e-07   31.6  12.2    1.4  1  Fer4_9    4Fe-4S dicluster domain
      7e-07   29.3  12.7     0.0022   18.4   2.9    2.2  2  Fer4_4    4Fe-4S binding domain
    1.9e-06   28.3   7.1     0.0035   17.8   0.4    2.1  2  Fer4_17   4Fe-4S dicluster domain
    3.4e-05   24.5  18.7      0.025   15.5   6.6    2.3  2  Fer4_3    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.033   14.7  11.8       0.64   10.6   0.9    2.9  3  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
       0.39   11.6  12.8       0.23   12.3   2.6    2.1  3  Fer4_22   4Fe-4S dicluster domain
       0.82    9.9  10.7        1.8    8.8   2.2    2.1  2  Fer4_18   4Fe-4S dicluster domain
        4.8    8.0  15.8         16    6.3   3.4    3.5  3  Fer4_15   4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   3.3   2.2e-10   2.5e-07       1      24 []      34      57 ..      34      57 .. 0.93
   2 !   35.4   4.7   5.2e-12   5.9e-09       2      24 .]      65      87 ..      64      87 .. 0.95

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 2.2e-10
                                      EEEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  1 vvideekCigCGaCvevCPvgAIt 24
                                      +++d  kC++C++C+  CPv+AI+
  gi|385805372|ref|YP_005841770.1| 34 PIVDIKKCTRCMLCETYCPVNAIR 57
                                      579999*****************6 PP

  == domain 2  score: 35.4 bits;  conditional E-value: 5.2e-12
                                      EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  2 videekCigCGaCvevCPvgAIt 24
                                      +i++e C gCG+C++vCPv AIt
  gi|385805372|ref|YP_005841770.1| 65 TINYEYCKGCGICMNVCPVKAIT 87
                                      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 !   18.8   3.5   1.6e-06    0.0018      27      52 .]      30      55 ..      16      55 .. 0.81
   2 !   36.1  13.9   6.6e-12   7.4e-09       1      52 []      40      85 ..      40      85 .. 0.94
   3 !   23.8   2.6   4.5e-08   5.1e-05       2      24 ..      71      93 ..      70      96 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.6e-06
                            Fer4_7 27 gtekveidpekClgCgaCvavCPtga 52
                                      +te++ +d  kC+ C  C++ CP++a
  gi|385805372|ref|YP_005841770.1| 30 RTERPIVDIKKCTRCMLCETYCPVNA 55
                                      4477789999**************97 PP

  == domain 2  score: 36.1 bits;  conditional E-value: 6.6e-12
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      +C+ C  C+ +Cpv+ai+++++    g   ++i++e+C gCg C++vCP++a
  gi|385805372|ref|YP_005841770.1| 40 KCTRCMLCETYCPVNAIRVEKD---TG---ATINYEYCKGCGICMNVCPVKA 85
                                      7******************887...45...89*****************987 PP

  == domain 3  score: 23.8 bits;  conditional E-value: 4.5e-08
                            Fer4_7  2 CigCgaCvaaCpvkaieldeeen 24
                                      C gCg C+++Cpvkai++ +e++
  gi|385805372|ref|YP_005841770.1| 71 CKGCGICMNVCPVKAITMVPEQS 93
                                      ******************99864 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   3.3   6.9e-08   7.7e-05       3      24 .]      35      56 ..      33      56 .. 0.92
   2 !   26.9   3.6   3.1e-09   3.5e-06       2      24 .]      64      86 ..      64      86 .. 0.95

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 6.9e-08
                            Fer4_6  3 eidpdkCigCgdCvrvCPegai 24
                                       +d  kC+ C+ C++ CP +ai
  gi|385805372|ref|YP_005841770.1| 35 IVDIKKCTRCMLCETYCPVNAI 56
                                      68999***************98 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 3.1e-09
                            Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                      ++i+++ C gCg C++vCP +ai
  gi|385805372|ref|YP_005841770.1| 64 ATINYEYCKGCGICMNVCPVKAI 86
                                      689*****************998 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5  13.0     2e-13   2.2e-10       3      59 .]      36      88 ..      34      88 .. 0.96

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 2e-13
                           Fer4_21  3 idedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedciem 59
                                      +d +kC  C +C + C+   ++ai+++++t +++  + C GC +C++vCPv ++i+m
  gi|385805372|ref|YP_005841770.1| 36 VDIKKCTRCMLCETYCP---VNAIRVEKDTGATINYEYCKGCGICMNVCPV-KAITM 88
                                      7889*************...8*****************************9.99998 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1  13.5   1.5e-09   1.7e-06       3      56 .]      35      82 ..      33      82 .. 0.88
   2 !   22.2   2.4     1e-07   0.00012       3      23 ..      65      85 ..      63      97 .. 0.78

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 1.5e-09
                           Fer4_10  3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrk.kvekCtgcgaCveaCP 56
                                      ++d ++C+rC  C + CP+       ++++ e+++  + ++e C gcg C+ +CP
  gi|385805372|ref|YP_005841770.1| 35 IVDIKKCTRCMLCETYCPV-------NAIRVEKDTGATiNYEYCKGCGICMNVCP 82
                                      67899**************.......777777777777799*************9 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 1e-07
                           Fer4_10  3 vidddtCirCgkCvkaCPadl 23
                                       i+ + C +Cg C+++CP+++
  gi|385805372|ref|YP_005841770.1| 65 TINYEYCKGCGICMNVCPVKA 85
                                      6899***************55 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   1.7   7.4e-07   0.00083       1      23 [.      40      62 ..      40      69 .. 0.84
   2 !   24.2   1.5   4.3e-08   4.8e-05       2      24 ..      71      93 ..      70      98 .] 0.86

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 7.4e-07
                           Fer4_16  1 rCgtCgkCaevCPtnaikekkek 23
                                      +C++C  C   CP+nai+ +k++
  gi|385805372|ref|YP_005841770.1| 40 KCTRCMLCETYCPVNAIRVEKDT 62
                                      6*****************98554 PP

  == domain 2  score: 24.2 bits;  conditional E-value: 4.3e-08
                           Fer4_16  2 CgtCgkCaevCPtnaikekkeke 24
                                      C++Cg C++vCP++ai++  e++
  gi|385805372|ref|YP_005841770.1| 71 CKGCGICMNVCPVKAITMVPEQS 93
                                      *****************986655 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.3   1.9e-07   0.00021      27      64 ..      17      54 ..       8      55 .. 0.74
   2 !   17.3   0.7   4.5e-06     0.005       3      17 ..      69      83 ..      59      95 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.9e-07
                            Fer4_8 27 dargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                                      +++++aa++  e++ +     +++Ct c+ C++ Cpv+
  gi|385805372|ref|YP_005841770.1| 17 YPKEGAAGKTGEWRTERPIVDIKKCTRCMLCETYCPVN 54
                                      45555555566776666678899*************97 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 4.5e-06
                            Fer4_8  3 ekCieCgaCqsaCpv 17
                                      e+C +Cg C++ Cpv
  gi|385805372|ref|YP_005841770.1| 69 EYCKGCGICMNVCPV 83
                                      578888888888886 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   2.9   1.5e-06    0.0017       2      21 ..      33      52 ..      32      53 .. 0.91
   2 !   21.0   2.4   2.1e-07   0.00024       4      21 ..      65      82 ..      63      83 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.5e-06
                            Fer4_2  2 pvvvdtdrCigCgaCvsaCP 21
                                      ++ vd  +C++C  C + CP
  gi|385805372|ref|YP_005841770.1| 33 RPIVDIKKCTRCMLCETYCP 52
                                      7889999************* PP

  == domain 2  score: 21.0 bits;  conditional E-value: 2.1e-07
                            Fer4_2  4 vvdtdrCigCgaCvsaCP 21
                                       ++ + C gCg+C ++CP
  gi|385805372|ref|YP_005841770.1| 65 TINYEYCKGCGICMNVCP 82
                                      589999************ PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6  12.2   1.2e-10   1.4e-07       1      51 []      40      86 ..      40      86 .. 0.89

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 1.2e-10
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                      kCt+C  C++ Cp ++++ ++ ++   + ++    C gCg C+++Cp +ai
  gi|385805372|ref|YP_005841770.1| 40 KCTRCMLCETYCPVNAIRVEKDTGATINYEY----CKGCGICMNVCPVKAI 86
                                      7****************88888777777654....************9987 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   2.9   1.9e-06    0.0022       2      17 .]      39      54 ..      38      55 .. 0.92
   2 !   16.2   2.3   9.3e-06      0.01       2      16 ..      69      83 ..      68      87 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.9e-06
                            Fer4_4  2 erCigCgsCvaaCPqg 17
                                      ++C++C+ C+ +CP++
  gi|385805372|ref|YP_005841770.1| 39 KKCTRCMLCETYCPVN 54
                                      69************75 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 9.3e-06
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      e C gCg C+++CP+
  gi|385805372|ref|YP_005841770.1| 69 EYCKGCGICMNVCPV 83
                                      89************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 !   17.8   0.4   3.1e-06    0.0035      42      58 ..      37      53 ..       8      55 .. 0.78
   2 !   13.9   1.5   5.3e-05     0.059       2      18 ..      71      87 ..      70      96 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.1e-06
                           Fer4_17 42 kaslCieCgeCerkCPq 58
                                       +++C+ C +Ce++CP 
  gi|385805372|ref|YP_005841770.1| 37 DIKKCTRCMLCETYCPV 53
                                      789*************6 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 5.3e-05
                           Fer4_17  2 CiqCgyClpeCpsyeay 18
                                      C +Cg C+++Cp  +++
  gi|385805372|ref|YP_005841770.1| 71 CKGCGICMNVCPVKAIT 87
                                      ************87664 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   4.3   3.4e-05     0.038       1      15 []      41      55 ..      41      55 .. 0.98
   2 !   15.5   6.6   2.2e-05     0.025       1      15 []      71      85 ..      71      85 .. 0.97

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.4e-05
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      Ct C++C+  CPv+A
  gi|385805372|ref|YP_005841770.1| 41 CTRCMLCETYCPVNA 55
                                      **************9 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 2.2e-05
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C gCg C++vCPv+A
  gi|385805372|ref|YP_005841770.1| 71 CKGCGICMNVCPVKA 85
                                      9************98 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   3.5    0.0032       3.6       1      17 [.      36      52 ..      36      54 .. 0.94
   2 ?    4.1   0.1     0.061        68      51      58 .]      51      58 ..      49      58 .. 0.89
   3 ?   10.6   0.9   0.00057      0.64       1      17 [.      66      82 ..      66      93 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0032
                           Fer4_13  1 VDrdtCiacgaCvelaP 17
                                      VD ++C+ c++C   +P
  gi|385805372|ref|YP_005841770.1| 36 VDIKKCTRCMLCETYCP 52
                                      8999************9 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.061
                           Fer4_13 51 CPvesIgv 58
                                      CPv++I+v
  gi|385805372|ref|YP_005841770.1| 51 CPVNAIRV 58
                                      ******97 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00057
                           Fer4_13  1 VDrdtCiacgaCvelaP 17
                                      ++ + C +cg+C +++P
  gi|385805372|ref|YP_005841770.1| 66 INYEYCKGCGICMNVCP 82
                                      56788***********9 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   2.7     0.036        40      79      94 ..      38      53 ..      20      56 .. 0.70
   2 ?    3.5   3.2      0.11   1.3e+02       1      14 [.      40      53 ..      40      63 .. 0.81
   3 ?   12.3   2.6   0.00021      0.23      75      95 ..      64      84 ..      55      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.036
                           Fer4_22 79 esgCvGCgRCieacpv 94
                                       ++C+ C  C++ cpv
  gi|385805372|ref|YP_005841770.1| 38 IKKCTRCMLCETYCPV 53
                                      5666666666666665 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.11
                           Fer4_22  1 rClsCgaCtlvCpt 14
                                      +C +C  C + Cp 
  gi|385805372|ref|YP_005841770.1| 40 KCTRCMLCETYCPV 53
                                      69999999999986 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.00021
                           Fer4_22 75 ekfgesgCvGCgRCieacpvk 95
                                      ++++ + C GCg C+++cpvk
  gi|385805372|ref|YP_005841770.1| 64 ATINYEYCKGCGICMNVCPVK 84
                                      5678899***********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 ?    6.9   1.7    0.0061       6.8      56      74 ..      36      54 ..      16      67 .. 0.77
   2 ?    8.8   2.2    0.0016       1.8      53      74 ..      63      84 ..      54      89 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0061
                           Fer4_18 56 kgagdcidcescvkvcPtg 74
                                       +  +c+ c  c + cP++
  gi|385805372|ref|YP_005841770.1| 36 VDIKKCTRCMLCETYCPVN 54
                                      45678************86 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0016
                           Fer4_18 53 rkekgagdcidcescvkvcPtg 74
                                       ++ +   c  c+ c++vcP++
  gi|385805372|ref|YP_005841770.1| 63 GATINYEYCKGCGICMNVCPVK 84
                                      45556678************86 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   3.7     0.041        46       3      27 ..      36      61 ..      35      67 .. 0.71
   2 ?    6.3   3.4     0.014        16       2      19 ..      65      82 ..      64      83 .. 0.89
   3 ?    5.7   0.1     0.023        26      57      65 ..      79      87 ..      78      88 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.041
                           Fer4_15  3 vDrdaCigcglCvaeap.evfelded 27
                                      vD ++C+ c lC + +p + ++ ++d
  gi|385805372|ref|YP_005841770.1| 36 VDIKKCTRCMLCETYCPvNAIRVEKD 61
                                      78899999999999997244555555 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.014
                           Fer4_15  2 vvDrdaCigcglCvaeap 19
                                      +++ + C gcg C+ ++p
  gi|385805372|ref|YP_005841770.1| 65 TINYEYCKGCGICMNVCP 82
                                      578899*********998 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.023
                           Fer4_15 57 raCPvdAIr 65
                                       +CPv+AI+
  gi|385805372|ref|YP_005841770.1| 79 NVCPVKAIT 87
                                      68******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.59u 0.35s 00:00:00.94 Elapsed: 00:00:00.57
# Mc/sec: 519.47
//
Query:       gi|385805373|ref|YP_005841771.1|  [L=195]
Description: 2-oxoacid:ferredoxin oxidoreductase subunit gamma [Fervidicoccus fontis Kam940]
Scores for complete 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-35  120.8   0.7    7.6e-35  120.6   0.7    1.0  1  POR       Pyruvate ferredoxin/flavodoxin oxidoreductase
  ------ inclusion threshold ------
      0.037   13.8   0.0      0.065   13.0   0.0    1.4  1  P2_N      Viral coat protein P2 N-terminal domain


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 !  120.6   0.7   8.5e-39   7.6e-35       1     177 []      11     184 ..      11     184 .. 0.95

  Alignments for each domain:
  == domain 1  score: 120.6 bits;  conditional E-value: 8.5e-39
                                       CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGG.. CS
                               POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldg.. 75 
                                       GGqG+vt +++la+aa+++ +y qa+ +yg+e+rG+++++  risd++i+++    e+d lv+ld + l + l++  
  gi|385805373|ref|YP_005841771.1|  11 GGQGAVTSSELLAAAASYENFYSQAFAFYGAERRGAPVMAFSRISDSVIYKHGMFFEVDSLVVLDRAVL-PKLKDik 86 
                                       9****************************************************************9999.6666645 PP

                                       EEEEEEEEEECTCGTT-CCHHHCTS-HHHHHHHT-EEEEE-HHHHHHHCCC....CCHHHHHHHHHHHHHHT.S-HH CS
                               POR  76 lkpggiiiynseelkpdelkkakeeerelkerlgvrvygvdatkiakeiggn...eraaNtvmlGalaallg.lple 148
                                       ++++g +++n++ ++  +lkk++    ++      +vy+vda++iak+ g      +++Nt +lGa++++lg ++l+
  gi|385805373|ref|YP_005841771.1|  87 IRKNGNLLINASLINLNDLKKYLNFIENV------KVYTVDANAIAKNEGLVmagWPLVNTSILGAFIKILGiIKLD 157
                                       99*******************99887655......7***********888878889********************* PP

                                       HHHHHHHCCS-CH.HHHHHHHHHHHHHHH CS
                               POR 149 aleeaikkrfpkkkeviekNlkafragye 177
                                       +l+ ai ++f++  +++ekN+ka++ +ye
  gi|385805373|ref|YP_005841771.1| 158 SLLNAIDENFEG--QIAEKNKKAVKVAYE 184
                                       ***********9..6************97 PP

>> P2_N  Viral coat protein P2 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   7.3e-06     0.065      39      80 ..      80     121 ..      64     142 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.3e-06
                              P2_N  39 aqItrirvklNgkeiiqvsgadldklnaykglaadagflvid 80 
                                        ++++i+++ Ng+ +i++s  +l++l++y  + ++++ +++d
  gi|385805373|ref|YP_005841771.1|  80 PKLKDIKIRKNGNLLINASLINLNDLKKYLNFIENVKVYTVD 121
                                       5799**********************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       722  (0.04027); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 1082.86
//
Query:       gi|385805374|ref|YP_005841772.1|  [L=327]
Description: hypothetical protein FFONT_0330 [Fervidicoccus fontis Kam940]
Scores for complete 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  21.1    4.4e-13   49.4  21.1    1.3  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 !   49.4  21.1   2.5e-17   4.4e-13       4     269 ..      11     279 ..       7     308 .. 0.74

  Alignments for each domain:
  == domain 1  score: 49.4 bits;  conditional E-value: 2.5e-17
                   LPG_synthase_TM   4 glalsalllalllrgvdlaalaaalrsldpwwl........llalllallsvllralrWrlllrslgarislrrllr 72 
                                        +a+s ++++++     + ++   + +l++ +l        ll+ ll++++      r r+++++l++++sl +l+ 
  gi|385805374|ref|YP_005841772.1|  11 VVAVSSIFVVVA-----IYTILIKMFRLNFIYLiledptgfLLSTLLIFIAETMKIFRLRFIFNKLKVKVSLKTLFL 82 
                                       344443333333.....233333333334333333333222777776666645666788****************** PP

                   LPG_synthase_TM  73 ayliglfvnnvtPgalgGevvrayllkrkegvslskalasvvverlldllalvllgllallllggllaegaavllll 149
                                         ++g f + +t + +g e+ r++ +   eg++   a +s ++e+++d ++l ++ +++ + ++ ++     ++l+ 
  gi|385805374|ref|YP_005841772.1|  83 SRFMGDFMGLITVSNIGSEPTRIATIVSLEGIPIQIAISSGLLETFYDSIILTAIAFVGSIVFFPTSI----LVLIS 155
                                       ****************************************************************9976....55666 PP

                   LPG_synthase_TM 150 alallllavlalllllllrrrlarlarvlkrlarllarfarklasakr......klvlasprrlllafllslliwll 220
                                       +l+ + l ++++l++ l    l+++   l++ +  ++ f+  l++ k+      k + +   +   a+l++++i  +
  gi|385805374|ref|YP_005841772.1| 156 TLITISLWLFIFLGFVLKENILVKIVGKLFKKRLTPKIFGIFLEKYKDfrdlvkKGISSEINK--GAILYTIFI--I 228
                                       666666666666677777777777777777777777777766666666777887555554444..677777777..4 PP

                   LPG_synthase_TM 221 ealtlylllralgvdvslalll..lillaltlvgalpplPgGlGvrEaala 269
                                        + ++ +l+    +d+sl  ++  l    +++ + l p+PgG+G +E+al+
  gi|385805374|ref|YP_005841772.1| 229 IIYVFSFLVLDPSYDLSLINVIngLFAYSMSYSVQLYPTPGGSGFFEYALI 279
                                       4557777777888888888888888888899999999***********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1121  (0.0625244); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.26s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2210.13
//
Query:       gi|385805375|ref|YP_005841773.1|  [L=306]
Description: metalloaminopeptidase, family M24A [Fervidicoccus fontis Kam940]
Scores for complete 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-32  111.0   0.0    7.5e-32  110.7   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 !  110.7   0.0   4.2e-36   7.5e-32       5     207 ..      11     292 ..       7     294 .. 0.82

  Alignments for each domain:
  == domain 1  score: 110.7 bits;  conditional E-value: 4.2e-36
                                       HHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBC...SSSB--TTEEEE CS
                     Peptidase_M24   5 kaariasaaleavleaikpgvterelaaeieattlkrhgarglafppivasgenaavlhytp...ndrvlkegdlvl 78 
                                       +a++i+ +a +++ +  kpg+t  ela++ie +  +++ +++lafp + ++g  aa  hy+p   +++ + e+ +++
  gi|385805375|ref|YP_005841773.1|  11 NAGKISIEAKKYARSIAKPGMTFFELAEKIEGK--IQELGGKLAFPCNLSFGHVAA--HYSPlldSEDIIPENGILK 83 
                                       799**********999***************99..7778899****9999999999..****9966899******** PP

                                       EEEEEEETTEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTBCCGBSSCSEE CS
                     Peptidase_M24  79 idagaeydgyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesaglakffphglGH 155
                                       id+g++++g+++D+++ + +   + e ++l+ a +ea+e+ai+ ++pG+++sei++++++++ s++  k++++++GH
  gi|385805375|ref|YP_005841773.1|  84 IDLGVHVNGFIADTAFSIDF---SGENENLLMASKEALERAIDIIRPGIKISEISEIIEKTIISYEA-KPIRNLTGH 156
                                       ******************65...447789***********************************988.9******** PP

                                       EESS.SSSEEEEEESSSTT..CSSB--TTBEEEEEE......EEEEETTT........................... CS
                     Peptidase_M24 156 gvGl.evhdegpsvsresn..dgrkleeGmvftiEp......giyfapge........................... 196
                                        +   ++h +   +++++n   + +l+++  ++iEp      g++ ++++                           
  gi|385805375|ref|YP_005841773.1| 157 ELQNyKLHSG-LVIPNTKNllVSGRLKPNIAIAIEPfatngaGVV-IDSNftaiyslnlksphetkkleptlrdfyr 231
                                       ***77***87.77776555778999***********766666444.2222344444555555556666677777777 PP

                                       .................................................E.EEEEBEEEEE CS
                     Peptidase_M24 197 .................................................g.gvriedtvlv 207
                                                                                        g ++++e+ +l+
  gi|385805375|ref|YP_005841773.1| 232 yifdefkelpfneryfknyidkntfrkniatlvskklaigypmliesgnGeVAQFEESILI 292
                                       7777777777777777777777777777777777777777777777777557788777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 2023.93
//
Query:       gi|385805376|ref|YP_005841774.1|  [L=670]
Description: serine protease-like protein [Fervidicoccus fontis Kam940]
Scores for complete 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-13   48.3   0.4    1.6e-12   47.4   0.4    1.4  1  Lon_C          Lon protease (S16) C-terminal proteolytic doma
  ------ inclusion threshold ------
      0.021   15.1   4.2      0.021   15.1   4.2    3.1  3  DUF4064        Protein of unknown function (DUF4064)
      0.036   13.9   0.0       0.09   12.6   0.0    1.7  1  ChlI           Subunit ChlI of Mg-chelatase
      0.085   11.5   3.6       0.17   10.5   3.6    1.4  1  Fusion_F0      Fusion glycoprotein F0, Isavirus
        0.1   12.4   1.7       0.28   11.0   0.9    2.2  2  ECSCR          Endothelial cell-specific chemotaxis regulator
       0.14   12.0   1.3        5.1    7.0   0.6    2.8  2  Synaptobrevin  Synaptobrevin
       0.16   11.8   0.0       0.36   10.7   0.0    1.5  1  DUF746         Domain of Unknown Function (DUF746)
       0.45   10.9   4.1       0.17   12.2   1.1    1.8  2  DUF5383        Family of unknown function (DUF5383)


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 !   47.4   0.4   7.3e-16   1.6e-12      82     171 ..     102     188 ..      52     201 .. 0.82

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 7.3e-16
                                       GGGSS-SS-TTT-EEEEEE-S-B-GGGGGGGHHHHHHHHHHHHTS--B-TTBEE--EE-TT-BEE--S-HHHHHHHH CS
                             Lon_C  82 eelgidkevfekkdihihvPeGavPkdGPsaGvtlatalvslltgkkvrkdvamtGeitLrGrvlpiGGlkekllaa 158
                                       + lgid +   k+d  i + + +    GPsaG  ++  ++s+l + + +++vamtG i   G + p+GG+ ekl aa
  gi|385805376|ref|YP_005841774.1| 102 SILGIDYK---KYDYFISIKSPSYIVGGPSAGAIMTIGIISALLNLTPNTNVAMTGMINPDGTIGPVGGIPEKLQAA 175
                                       45566644...4455555555555568************************************************** PP

                                       HHTT-SBEEEEGG CS
                             Lon_C 159 kragikkvilPke 171
                                         ag k  ++P  
  gi|385805376|ref|YP_005841774.1| 176 AEAGYKIFLIPVG 188
                                       **********965 PP

>> DUF4064  Protein of unknown function (DUF4064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.4       1.2   2.7e+03      13      27 ..      16      30 ..       9     106 .. 0.52
   2 ?   -1.5   0.1       1.4   3.2e+03       5      17 ..     132     144 ..     119     160 .. 0.69
   3 ?   15.1   4.2   9.4e-06     0.021      15      87 ..     594     664 ..     581     668 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.2
                           DUF4064 13 gilgillglllllfl 27
                                      +++ ++++l   + +
  gi|385805376|ref|YP_005841774.1| 16 IVILLFISLNSSILI 30
                                      333333333333333 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.4
                           DUF4064   5 eiiLglIGgilgi 17 
                                        +++g+I++ l++
  gi|385805376|ref|YP_005841774.1| 132 IMTIGIISALLNL 144
                                       3445555555444 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 9.4e-06
                           DUF4064  15 lgillglllllflfllssgefsqelteeqalsgedasavleflstllivlgvialiaivlgivgalllkknkk 87 
                                          l++ l ++ ++++ ++ + q+l+  +  s++ +s+++  +    +++++i++++iv+ i+ga+ l+k+k+
  gi|385805376|ref|YP_005841774.1| 594 YASLFSMLSGINMSNITIQTQPQTLS--TTGSQTSSSTMSTTMIPNAYIILIIVIVIIVFVIAGAYALNKKKE 664
                                       33344444444444444444444443..6777778888888888888899999999*************9985 PP

>> ChlI  Subunit ChlI of Mg-chelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0     4e-05      0.09      64     119 ..     132     187 ..      74     189 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4e-05
                              ChlI  64 piAigilaaleqieaeeetlflGeLsldGslrpvkgvlpialaakkegikkvivpk 119
                                        + igi++al + + ++++ + G ++ dG++ pv g+ + + aa+++g+k +++p 
  gi|385805376|ref|YP_005841774.1| 132 IMTIGIISALLNLTPNTNVAMTGMINPDGTIGPVGGIPEKLQAAAEAGYKIFLIPV 187
                                       5789**************************************************96 PP

>> Fusion_F0  Fusion glycoprotein F0, Isavirus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   3.6   7.6e-05      0.17     305     429 ..     533     652 ..     518     659 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 7.6e-05
                         Fusion_F0 305 klngiidqinka.ntllegeieavrriaymnqasslqnqveigligeylnisswletttltkteeglmkngwcqsnt 380
                                        l+ ii +in+a n l +   +++  iay++q  +l  q +      yl  +  l   +   +    m  g   sn 
  gi|385805376|ref|YP_005841774.1| 533 MLEYIIAEINNAaNILNNSSYKSLISIAYLQQVQNLLSQYNQTKDSSYLTSAISLAVESSIYASLFSMLSGINMSNI 609
                                       6788999998761566678899***************************988778777777788888999******9 PP

                         Fusion_F0 381 hcwcppkptivptigyvdsikevtgtswwmvmihyiivglivivvvvfg 429
                                              p  + t g   s       s  m+   yii+ +iviv++vf 
  gi|385805376|ref|YP_005841774.1| 610 TIQTQ--PQTLSTTGSQTSSST---MSTTMIPNAYIIL-IIVIVIIVFV 652
                                       87665..556677777666554...4555777777765.5566666664 PP

>> ECSCR  Endothelial cell-specific chemotaxis regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.4   3.2e+03      54      94 ..     567     608 ..     555     614 .. 0.71
   2 ?   11.0   0.9   0.00013      0.28       4      58 ..     611     666 ..     608     669 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.4
                             ECSCR  54 nkesedpqkpeisglsescstaigekdsitlism.kninsnn 94 
                                       n  s+  q  ++s l+ ++s a+      +l sm   in+ n
  gi|385805376|ref|YP_005841774.1| 567 NLLSQYNQTKDSSYLTSAISLAVESSIYASLFSMlSGINMSN 608
                                       556777788888888888888887777778888734588776 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00013
                             ECSCR   4 ireektilpsptsetvltvaafgvi.sfivilvvvviilvsvvslrfkcrknkese 58 
                                       i+++   l +  s+t  +  +  +i    +il++v++i+v v++  +   k+ke e
  gi|385805376|ref|YP_005841774.1| 611 IQTQPQTLSTTGSQTSSSTMSTTMIpNAYIILIIVIVIIVFVIAGAYALNKKKEKE 666
                                       66666777777777776555555552567888888889999999999999999987 PP

>> Synaptobrevin  Synaptobrevin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.064   1.4e+02       6      53 ..     267     314 ..     263     329 .. 0.78
   2 ?    7.0   0.6    0.0023       5.1      68      84 ..     638     654 ..     602     659 .. 0.61

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.064
                                       HHHHHHHHCCCCHHCCHHHHCHCCCCCHHHHCCCCHHHHHHHHHHHHH CS
                     Synaptobrevin   6 akikaevdevkdimkeNidkvlergekldeLvdktenLqssaqqFkkq 53 
                                        + ka+++++ +i+++ + ++l++g   ++L +  ++  +++ +  ++
  gi|385805376|ref|YP_005841774.1| 267 YNWKAQLEQIYNITMKQVTDLLKSGVYSSNLISYVNQYINTSTSLYSN 314
                                       56799******************9988777766655555555555555 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0023
                                       XXXXXXXXXXXXXXXXX CS
                     Synaptobrevin  68 liiililvvlililiii 84 
                                        +iili+v++i++++i 
  gi|385805376|ref|YP_005841774.1| 638 AYIILIIVIVIIVFVIA 654
                                       35666666666666664 PP

>> DUF746  Domain of Unknown Function (DUF746)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00016      0.36       4      29 ..     206     231 ..     204     244 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00016
                            DUF746   4 elIrlLsqplslaeaadllgtdegii 29 
                                        +Ir+ +q++ ++e+++ lg+ +  +
  gi|385805376|ref|YP_005841774.1| 206 TIIRYVPQQINVTELGEKLGVKVIEV 231
                                       58******************986554 PP

>> DUF5383  Family of unknown function (DUF5383)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1       5.4   1.2e+04     101     119 ..      13      31 ..       8      34 .. 0.76
   2 ?   12.2   1.1   7.7e-05      0.17      69     116 ..     606     653 ..     588     654 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 5.4
                           DUF5383 101 llillivllivvllivliP 119
                                       +++++i+l i++   +liP
  gi|385805376|ref|YP_005841774.1|  13 AFGIVILLFISLNSSILIP 31 
                                       5788888888888888888 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 7.7e-05
                           DUF5383  69 akelgLfseekesvkqsateqeseeksnlLpillillivllivvlliv 116
                                       ++++ + ++ ++++++ ++ ++s  +++ +p ++i+li++++++++++
  gi|385805376|ref|YP_005841774.1| 606 MSNITIQTQPQTLSTTGSQTSSSTMSTTMIPNAYIILIIVIVIIVFVI 653
                                       667778888888888888888889999***************999954 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (670 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1776  (0.0990574); expected 358.6 (0.02)
Passed bias filter:                      604  (0.0336884); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.74u 0.33s 00:00:01.07 Elapsed: 00:00:00.49
# Mc/sec: 4077.08
//
Query:       gi|385805377|ref|YP_005841775.1|  [L=321]
Description: hypothetical protein FFONT_0333 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-05   24.3   0.3    0.00011   22.5   0.0    2.1  2  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 !   22.5   0.0     6e-09   0.00011      14      67 ..     125     174 ..     109     220 .. 0.76
   2 ?   -0.8   0.0      0.11   1.9e+03      63      86 ..     244     266 ..     221     295 .. 0.60

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 6e-09
                                       TSEEEEEHHHHCTTSCTT.SSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECT CS
                      NTP_transf_2  14 vakvvlfGSyarGtalkg.SDiDllvvlpeevsrekkeegleklaeiikfleell 67 
                                         ++ + GS a G ++++ SDiD++++ +++ +     ++++ ++ ++++ +el 
  gi|385805377|ref|YP_005841775.1| 125 LDSIGIGGSIALGIHNPNvSDIDVIIYDSKSLK-----VIEQSNIIEPYKNNELE 174
                                       568999*********************999966.....55555555555555544 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.11
                                       EEECTTEEEEEECEEECCCCTEEE CS
                      NTP_transf_2  63 leellglevdlvtrekledpllvk 86 
                                       l+++ ++ vdl +++ ++  ++++
  gi|385805377|ref|YP_005841775.1| 244 LSYFYPHVVDLTIKKVIK-GSKSI 266
                                       444444444444433333.33332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); 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: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2133.15
//
Query:       gi|385805378|ref|YP_005841776.1|  [L=139]
Description: cytidine deaminase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.3e-19   67.4   0.1    9.8e-19   67.1   0.1    1.1  1  dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-
      1e-10   41.9   0.1    2.4e-10   40.7   0.0    1.6  2  dCMP_cyt_deam_2  Cytidine and deoxycytidylate deaminase zinc-
    0.00098   18.8   0.4       0.25   10.9   0.0    2.1  2  LmjF365940-deam  A distinct subfamily of CDD/CDA-like deamina


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 !   67.1   0.1   1.6e-22   9.8e-19       4     100 ..      10     111 ..       7     112 .. 0.91

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 1.6e-22
                                       HHHHHHHHHHHHHHHH.TTTSCSEEEEEEETTEEEEEEESBHHCCTGTTB-HHHHHHHHHHHHTSSCETTEEEEE.. CS
                   dCMP_cyt_deam_1   4 dekllelalkaakeaq.kcsnfkVGavivkngeiistgyngepaggsktiHAEvnAilkaaknggsklegatlyv.. 77 
                                        ekll +a++  k+++ ++s+f+V+av+ +++  i+tg+n e+a++   i+AE++Ai ka+++g  ++e   +y+  
  gi|385805378|ref|YP_005841776.1|  10 LEKLLAIAKDIIKNSYsPYSHFPVAAVVKTKKGNIYTGVNIENASYGLSICAERVAIFKAVSEGDREIEILLVYTpt 86 
                                       6899**********************************************************975577556666699 PP

                                       ..EE--BHHHHHHHHHHT-SEEEEE CS
                   dCMP_cyt_deam_1  78 ..tlePCsmCakaiiqsgikkvvvg 100
                                          + PC+ C+++i +++++ +v++
  gi|385805378|ref|YP_005841776.1|  87 kqHIYPCGACRQVILEFNPNALVII 111
                                       9999**************9999985 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 !   40.7   0.0   4.1e-14   2.4e-10      44     110 ..      10      76 ..       1      85 [. 0.87
   2 ?   -1.8   0.0      0.54   3.2e+03       2      15 ..     124     137 ..     123     138 .. 0.82

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 4.1e-14
                                       S-HHHHHHHHHHTT-B-TTT---EEEEEEETTS-EEEEE-B--TTSTT-B-HHHHHHHHHHHTT--G CS
                   dCMP_cyt_deam_2  44 ddelkeaAlaaanasyapyskcpsGvaLvtkdgkvyaGsyiEsaAfNpsLpPlqaAlvalvlggkef 110
                                        ++l + A +  ++sy+pys+ p + +++tk+g++y+G  iE+a +  s+ + ++A+ ++v +g++ 
  gi|385805378|ref|YP_005841776.1|  10 LEKLLAIAKDIIKNSYSPYSHFPVAAVVKTKKGNIYTGVNIENASYGLSICAERVAIFKAVSEGDRE 76 
                                       45688889999**************************************************977654 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.54
                                       HHHSTT--SGGGGT CS
                   dCMP_cyt_deam_2   2 sslLPhsFgPkdLl 15 
                                       ++lLP sF  ++L 
  gi|385805378|ref|YP_005841776.1| 124 KDLLPMSFSKRSLR 137
                                       689*****988875 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 !   10.9   0.0   4.2e-05      0.25      55      87 ..      39      71 ..      28      78 .. 0.86
   2 !    6.4   0.1     0.001       6.1     154     177 ..      90     110 ..      72     126 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.2e-05
                   LmjF365940-deam 55 dgreelvrgvNlEvSmPtGSlCsErnaigkala 87
                                        + +++ gvN+E      S C+Er ai ka++
  gi|385805378|ref|YP_005841776.1| 39 TKKGNIYTGVNIENASYGLSICAERVAIFKAVS 71
                                      567789**********99**********99876 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.001
                   LmjF365940-deam 154 LkPCGaCeewLkkiaevnpdfkvl 177
                                       + PCGaC++    i e np+  v+
  gi|385805378|ref|YP_005841776.1|  90 IYPCGACRQV---ILEFNPNALVI 110
                                       79*****986...56777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 852.72
//
Query:       gi|385805379|ref|YP_005841777.1|  [L=130]
Description: S-adenosylmethionine decarboxylase [Fervidicoccus fontis Kam940]
Scores for 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-33  112.9   0.0    9.3e-33  112.7   0.0    1.1  1  AdoMet_dc  S-adenosylmethionine decarboxylase


Domain annotation for each model (and alignments):
>> AdoMet_dc  S-adenosylmethionine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.7   0.0   5.2e-37   9.3e-33       1     105 [.      23     127 ..      23     128 .. 0.99

  Alignments for each domain:
  == domain 1  score: 112.7 bits;  conditional E-value: 5.2e-37
                                       EEEEEEES--HHHCTSHHHHHHHHHHHHHHCT-EEEEEEEEE-SSS-EEEEEEETTEEEEEEEEGGGTEEEEEEEEE CS
                         AdoMet_dc   1 hllvdlygcdpelledaelleqilteaaeaigatvlsvafhkfepeGvsvvvliaeShlsiHtwpetgyaaiDvftc 77 
                                       h++ +l +c++++l+d+ +l++i+ +aa++ ++t+l+  ++k+  eGvsvv++i eSh+++Htwpe+++a++Dv++c
  gi|385805379|ref|YP_005841777.1|  23 HIYGNLKNCNRAKLSDEGELKNIVANAAKIGKMTMLDLRSWKIG-EGVSVVAVILESHITVHTWPEYNFATVDVYSC 98 
                                       999****************************************9.9******************************* PP

                                       ST.HHHHHHHHHHHHHHT-SEEEEEEEEE CS
                         AdoMet_dc  78 ge.ispekaleylieafkadrvtvdelkR 105
                                       g+ ++p++a+ey++++++a++v++ e++R
  gi|385805379|ref|YP_005841777.1|  99 GThTNPKAAFEYIARELEAEEVEYGEADR 127
                                       ************************99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); 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 0.28s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 814.85
//
Query:       gi|385805380|ref|YP_005841778.1|  [L=225]
Description: CDP-alcohol phosphatidyltransferase [Fervidicoccus fontis Kam940]
Scores for 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-11   42.3   0.2    9.9e-11   42.3   0.2    2.8  2  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
  ------ inclusion threshold ------
      0.078   13.4   2.1       0.43   11.0   0.0    2.6  3  DUF5455          Family of unknown function (DUF5455)


Domain annotation for each model (and alignments):
>> CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.2   1.1e-14   9.9e-11       2      66 .]       7      70 ..       7      70 .. 0.92
   2 ?   -3.5   6.7         2   1.8e+04      12      27 ..     146     194 ..      76     212 .. 0.59

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 1.1e-14
                                      -HHHHHHHHHHHHHHHHHGGGS-H..HHHHHHHHHHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
                   CDP-OH_P_transf  2 lPnaiTllrlllsvlailllltyyplvlailllliasltDalDGklARrlnqvstlGkllDslaD 66
                                      lPn++T+++ l + +a+l l++   + l i l++++  +D lDG lAR+ln  s+ G+llD++ D
  gi|385805380|ref|YP_005841778.1|  7 LPNLVTVINGLVGSFALL-LAIRGETELSIRLIFLSLSLDVLDGLLARKLNAMSESGELLDRVFD 70
                                      6***********999995.5566669**************************9*********988 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2
                                       HHHHHHHHGGGS-H...................................... CS
                   CDP-OH_P_transf  12 llsvlailllltyyp....................................l 27 
                                       +l++++++++    +                                    +
  gi|385805380|ref|YP_005841778.1| 146 VLVIASLFPIK---YfrrirtlspnetkgtfwqiriivplflsiipyskleI 194
                                       22223333332...02335555555555544444444444444444444441 PP

>> DUF5455  Family of unknown function (DUF5455)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   4.8e-05      0.43       1      75 [.       8      79 ..       8      88 .. 0.92
   2 ?   -2.4   0.0      0.75   6.7e+03      31      43 ..      90     102 ..      87     105 .. 0.81
   3 ?    1.0   0.2     0.065   5.8e+02      39      74 ..     122     154 ..     117     158 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.8e-05
                           DUF5455  1 plLlklikslfvslvtylatfltkklAvaivalgliialivgllvvllaalsglssiaetlpselsqgislvvPs 75
                                      p L+ +i+ l+ s++  la +  + l  ++++l+l +  + gll   l+a+s+ + +   l  ++  + +++ Ps
  gi|385805380|ref|YP_005841778.1|  8 PNLVTVINGLVGSFALLLAIRGETELSIRLIFLSLSLDVLDGLLARKLNAMSESGEL---LDRVFDRVYQVIAPS 79
                                      568999************************************************999...999999999999997 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.75
                           DUF5455  31 valgliialivgl 43 
                                       v + +++a+i++l
  gi|385805380|ref|YP_005841778.1|  90 VGSMFYSASIITL 102
                                       6678999999998 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.065
                           DUF5455  39 livgllvvllaalsglssiaetlpselsqgislvvP 74 
                                       l v  +v+l+ +lsg++    + + +l+ +i+   P
  gi|385805380|ref|YP_005841778.1| 122 LFVHTFVILSSYLSGIAL---PYYLMLVLVIASLFP 154
                                       567789999999999943...588888888776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.34s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1305.49
//
Query:       gi|385805381|ref|YP_005841779.1|  [L=414]
Description: amidohydrolase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       781  (0.0435607); 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: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2583.84
//
Query:       gi|385805382|ref|YP_005841780.1|  [L=189]
Description: metal dependent phosphohydrolase [Fervidicoccus fontis Kam940]
Scores for complete 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-21   74.5   0.0    1.5e-20   73.8   0.0    1.4  1  HD_3             HD domain
    1.1e-15   57.8   0.2    2.2e-15   56.9   0.2    1.4  1  HD_2             HD containing hydrolase-like enzyme
    0.00072   19.8   0.0     0.0018   18.5   0.0    1.7  1  HD               HD domain
  ------ inclusion threshold ------
       0.16   11.8   0.0       0.88    9.5   0.0    2.2  2  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
        8.5    6.3  11.1       0.29   10.9   3.8    2.3  2  Orthopox_B11R    Orthopoxvirus B11R protein


Domain annotation for each model (and alignments):
>> HD_3  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.8   0.0   4.2e-24   1.5e-20       1     140 [.      14     156 ..      14     181 .. 0.80

  Alignments for each domain:
  == domain 1  score: 73.8 bits;  conditional E-value: 4.2e-24
                              HD_3   1 vekLKfqkRqgwlqtgrvr..eesvaeHmwrvalmalllseelk...ekvdiarvikmfLiHDlvEiltgDiispde 72 
                                       ++ LK+  R+gw+q g+ +   e+va H++  a +a ++s+ l     +++++++i m+L+HD  E++ gDi+ ++ 
  gi|385805382|ref|YP_005841780.1|  14 IDALKKLARTGWMQRGIPPsiTETVASHSFESATIAGVISNILInhgYNINMEKTISMSLFHDFSECIIGDITLFA- 89 
                                       589*************855335************999998865423368**************************9. PP

                              HD_3  73 lakeekeeeekeaaerilkllpeelaeellalweEFeeretkeakfakdlDklepllqalekegdsla 140
                                        ++   +e++k+++ +i++ + ++  +++l++ eE+  ++t eak++k  D+l +++qa     + ++
  gi|385805382|ref|YP_005841780.1|  90 KENLLGDEKKKALELQIFSDIFKG-YNKILEIYEEYSIGKTLEAKIVKLSDRLSTCIQAQRFYDNGYE 156
                                       444555555566666666666666.7899*****************************9765555544 PP

>> HD_2  HD containing hydrolase-like enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.9   0.2   6.2e-19   2.2e-15       5     166 ..      13     172 ..      10     181 .. 0.86

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 6.2e-19
                              HD_2   5 llsrlkyieRwalmrn....treenvaeHslevaliahalalienkkfggkldaerlallalyHDasEiitGDlptp 77 
                                       ++  lk + R + m+     + +e+va Hs+e a+ia ++  i  ++ g ++++e+ ++++l+HD sE i+GD+   
  gi|385805382|ref|YP_005841780.1|  13 CIDALKKLARTGWMQRgippSITETVASHSFESATIAGVISNILINH-GYNINMEKTISMSLFHDFSECIIGDITLF 88 
                                       577889999999998744446789****************9999876.88***********************9655 PP

                              HD_2  78 vKyanpeireaykevEeeaeekllelLpeelreeyeelladeeaeeeekklvkaaDklsalikcleelkagnkeFee 154
                                          +n    e+ k++E +  + +++  ++ l e yee+   ++    e k+vk  D+ls+ i++ +  + g ++ ++
  gi|385805382|ref|YP_005841780.1|  89 A-KENLLGDEKKKALELQIFSDIFKGYNKIL-EIYEEYSIGKTL---EAKIVKLSDRLSTCIQAQRFYDNGYENVKD 160
                                       5.5667778899999*999999999987655.789999866666...89**********************999999 PP

                              HD_2 155 akkeieeklkel 166
                                       +  +++++++e+
  gi|385805382|ref|YP_005841780.1| 161 IIVNTKREVDEI 172
                                       999999998887 PP

>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   5.1e-07    0.0018       2     121 ..      39     143 ..      38     144 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 5.1e-07
                                       HHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHH CS
                                HD   2 leHsleVaklarrlaedlge...eedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlg 75 
                                       + Hs+e a +a+ + + l     + + e++  + L+HD  ++ +gd  + ++            g e+ +++e+   
  gi|385805382|ref|YP_005841780.1|  39 ASHSFESATIAGVISNILINhgyNINMEKTISMSLFHDFSECIIGDITLFAK--------ENLLGDEKKKALELQ-- 105
                                       68999999999998887766777**********************9444332........333333333333333.. PP

                                       HHHHHHHHHHHTTCCHHHHHHHHHHHHCCTSCHHHHHHHHHHHHHH CS
                                HD  76 ldledvaklirehheswegkkrprglaerqlslearivklaDrlaa 121
                                           +++++ +  ++  e++    +++   ++lea+ivkl Drl++
  gi|385805382|ref|YP_005841780.1| 106 ----IFSDIFKGYNKILEIY----EEYSIGKTLEAKIVKLSDRLST 143
                                       ....3333333333333333....36677779***********985 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 ?   -1.3   0.0      0.56     2e+03      34      49 ..      62      77 ..      54      78 .. 0.78
   2 ?    9.5   0.0   0.00024      0.88      13      30 ..     146     163 ..     145     174 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.56
                   DNA_pol_lambd_f 34 kLtreqqiGlkyyeDl 49
                                      + + e  i +  ++D+
  gi|385805382|ref|YP_005841780.1| 62 NINMEKTISMSLFHDF 77
                                      5677778999999999 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00024
                   DNA_pol_lambd_f  13 tAkkwyakGirtledlra 30 
                                       +A+++y++G+ +++d+  
  gi|385805382|ref|YP_005841780.1| 146 QAQRFYDNGYENVKDIIV 163
                                       7**************976 PP

>> Orthopox_B11R  Orthopoxvirus B11R protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.7      0.58   2.1e+03      54      68 ..      70      84 ..      49      87 .. 0.53
   2 ?   10.9   3.8   8.2e-05      0.29       5      33 ..     156     184 ..     152     187 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.58
                     Orthopox_B11R 54 sdsidkeviecichd 68
                                      s s+  +  eci  d
  gi|385805382|ref|YP_005841780.1| 70 SMSLFHDFSECIIGD 84
                                      444445555666555 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 8.2e-05
                     Orthopox_B11R   5 tnvediineidrekeeilknveiennkni 33 
                                        nv+dii +  re +eilk+ + e  k+i
  gi|385805382|ref|YP_005841780.1| 156 ENVKDIIVNTKREVDEILKEFDSEIRKDI 184
                                       79******************999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       802  (0.044732); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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 0.35s 00:00:00.95 Elapsed: 00:00:00.57
# Mc/sec: 1001.40
//
Query:       gi|385805383|ref|YP_005841781.1|  [L=414]
Description: hypothetical protein FFONT_0339 [Fervidicoccus fontis Kam940]
Scores for complete 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   63.0  54.6      1e-15   57.6  37.9    1.7  2  MFS_1           Major Facilitator Superfamily
  ------ inclusion threshold ------
       0.25   10.7   0.1       0.39   10.1   0.1    1.2  1  DAG1            Dystroglycan (Dystrophin-associated glycoprot
       0.32   10.3   0.6       0.52    9.6   0.6    1.2  1  Glycoprotein_G  Pneumovirus attachment glycoprotein G


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 !   57.6  37.9   1.7e-19     1e-15       3     351 ..      51     373 ..      49     375 .. 0.79
   2 !   19.3   8.7   7.3e-08   0.00044      40     172 ..     280     406 ..     279     413 .. 0.82

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 1.7e-19
                             MFS_1   3 laaflsalarsilgpalpl.alaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglll 78 
                                       ++ f+ +la++++++++   + +e+++ + s++ l++++     +++s+++G +sd++Gr+++++++ l+++++ l+
  gi|385805383|ref|YP_005841781.1|  51 VVMFIEGLAFGTYIVTIRTnIGMENYN-AYSFLTLIAAM-ETIPGIFSVFAGGISDKIGRKKIIFFSGLMSSIF-LI 124
                                       6889999*****999999988889988.66666665555.5569******************************.77 PP

                             MFS_1  79 llfa.sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravf 154
                                       ll +  +l  l ++ +l   ++ +++p++  +    +++   g  ++ +  ++s+G  lg +l gl++ +++   ++
  gi|385805383|ref|YP_005841781.1| 125 LL-SkVQLSQLPIFVFLFMSFYTMFYPIIFGISISKSKG--SGYSLSKFLFFNSFGWSLGGILPGLILNLWNLNILY 198
                                       77.3344554555555555556799****9999888887..9*********************************** PP

                             MFS_1 155 yilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllp 231
                                       +i+ai+ ++a v+ ++ + e++ + ++++ ++      + ++++      + p    +l+ l+l+++gf++l + + 
  gi|385805383|ref|YP_005841781.1| 199 IIAAILIIIASVITVISYNEKEYQDPTVTLTDF-----KNEIKK------AIP----FLFPLILGSAGFYMLNSIMS 260
                                       ***********9877777777777776644444.....222222......344....78888888888888777777 PP

                             MFS_1 232 l.ylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvl 307
                                       l ++ +v ++   l++ ++  +++l++ i++l+ag+ + ++ + + ++ ++++ l++al++  ++ t       l +
  gi|385805383|ref|YP_005841781.1| 261 LrLFISVNNIL--LYGIFYNTITGLLSSIARLIAGKAIEKIHPYKVTFSSFFSYLILALLMEKANST-------LTI 328
                                       73225555555..88888888999999999**********999666666666666666666666666.......555 PP

                             MFS_1 308 vliGf.glgfvfpsllalasdlappeeagtasglfntagslggal 351
                                       +l+ +  + f+ +s+ +++ +++ +  + tasglf+ta slgg++
  gi|385805383|ref|YP_005841781.1| 329 LLWLLpIYPFFETSSYYVLGRMIKTTFHSTASGLFTTAVSLGGII 373
                                       556666799**********************************97 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 7.3e-08
                             MFS_1  40 lyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fa.sslwlllvlrvlqGlgagalfpagaaliadwf 114
                                       + +l++++a l++G  ++++ + +v + +++++++  +ll+  a s+l++ll+l  +  +++    +++++++ ++ 
  gi|385805383|ref|YP_005841781.1| 280 ITGLLSSIARLIAGKAIEKIHPYKVTFSSFFSYLIL-ALLMeKAnSTLTILLWLLPIYPFFE----TSSYYVLGRMI 351
                                       6788999************99***************.7777544344446666666666666....88888888888 PP

                             MFS_1 115 pkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllll 172
                                       + + ++ a gl+++++slG i+   l+ +++ + +++ + +i  i++l+  +   l +
  gi|385805383|ref|YP_005841781.1| 352 KTTFHSTASGLFTTAVSLGGIINLSLSLVFY-HSSYQTLLIIDSILLLIPSIY--LIF 406
                                       888899*************************.889************998774..332 PP

>> DAG1  Dystroglycan (Dystrophin-associated glycoprotein 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   6.5e-05      0.39     153     195 ..     199     243 ..     191     248 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 6.5e-05
                                       XXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXX CS
                              DAG1 153 vvvaailliagiiamicyrkk..rkGkltledqatfikkGvPiif 195
                                       ++ a++++ia++i +i y+ k  +   +tl d +  ikk +P +f
  gi|385805383|ref|YP_005841781.1| 199 IIAAILIIIASVITVISYNEKeyQDPTVTLTDFKNEIKKAIPFLF 243
                                       444555567999999***955225678999************998 PP

>> Glycoprotein_G  Pneumovirus attachment glycoprotein G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.6   8.7e-05      0.52      34      80 ..     194     241 ..     189     244 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 8.7e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXX CS
                    Glycoprotein_G  34 LsvLamiistsLiiaaiifissanhkvkst.tttviqitnqiknhtst 80 
                                       L +L +i  + +iia +i ++s n+k  +  t+t+ + +n+ik+ ++ 
  gi|385805383|ref|YP_005841781.1| 194 LNILYIIAAILIIIASVITVISYNEKEYQDpTVTLTDFKNEIKKAIPF 241
                                       889999999999**************8765156667899***999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1101  (0.0614089); 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:                         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: 0.67u 0.34s 00:00:01.01 Elapsed: 00:00:00.57
# Mc/sec: 2199.41
//
Query:       gi|385805384|ref|YP_005841782.1|  [L=461]
Description: pyruvate kinase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.9e-90  303.3   0.5    2.4e-90  302.9   0.5    1.1  1  PK         Pyruvate kinase, barrel domain
    8.5e-14   51.8   0.0    2.3e-13   50.4   0.0    1.7  1  PK_C       Pyruvate kinase, alpha/beta domain
    2.7e-06   26.7   0.0    4.5e-06   26.0   0.0    1.3  1  HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family


Domain annotation for each model (and alignments):
>> PK  Pyruvate kinase, barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  302.9   0.5   4.1e-94   2.4e-90       2     341 ..       3     335 ..       2     340 .. 0.97

  Alignments for each domain:
  == domain 1  score: 302.9 bits;  conditional E-value: 4.1e-94
                                       --SEEEEEESCCCTSHHHHHHHHHHTEEEEEEETTSS-HHHHHHHHHHHHHHHHTTTTS-EEEEE---S-EBB--BT CS
                                PK   2 rrtkivctlGPasesvekleklieaGlnvvrlnfshGsheehqerienvreaekklgkkvaillDtkGpeirtgllk 78 
                                       ++tki+ t+GP+ e+ e l  l+++G+  +r+nfshG+  +  + i+n++++ek+l+  ++i+ D++Gp+ir+g+l 
  gi|385805384|ref|YP_005841782.1|   3 NKTKIIVTMGPSIEKYEVLLSLVKEGARGFRINFSHGDPSQWYNYINNLKSVEKELSIPLGIIGDLQGPNIRIGQLI 79 
                                       59**************************************************************************9 PP

                                       TCSSSEEE-TTSEEEEE-SCTCTTTBBTTEEEBS-TTHHHHS-TTEEEEETTTTEEEEEEEEETTEEEEEEESS-EE CS
                                PK  79 dgkkdielkegdklkvsldeklkeegdeelialdyknivkdvevGktilvdDGllslkvlevdeekeleveventgv 155
                                       +   +i+lk+ d +++       ++++++ i l y++ +k ve G++i ++DG+++l vle+++++ +  ++  +gv
  gi|385805384|ref|YP_005841782.1|  80 N---QINLKKDDIVQFFYG----NKSETNDIPLPYEEFFKTVERGDVIQLADGAIQLIVLETSPKS-FIAKTIAGGV 148
                                       9...69*****99987654....4456789********************************9999.999******* PP

                                       E-SS-BEE-TTS---S-SS-HHHHHHHHHHHHCT-SEEEETTE-SHHHHHHHHHHHTCCC.TTSEEEEEE-SCHHHH CS
                                PK 156 lgskkgvnlpgtkvdlpalsekDkadlrfgvkqgvdliaasfvrkasDvkevrevleeeg.keikiiakienqegve 231
                                       ++s+k++ + + ++++p ++ekD++d++f+ +++   ++asfv + +++ +++e+l+++  k+++i+akie ++gv 
  gi|385805384|ref|YP_005841782.1| 149 ITSRKSISIKDKDIEIPYVTEKDERDIEFACNNDFSHLMASFVESKDNIFQLKELLNKKCnKQLNILAKIETKRGVY 225
                                       *********************************************************9987**************** PP

                                       THHHHHHHSSEEEEEHHHHHHHSTCCCHHHHHHHHHHHHHHHT--EEEESSTTGGGGTSSS--HHHHHHHHHHHHHT CS
                                PK 232 nldeileasDgimvarGDlGieipaekvllvqkklikkcnlagkpvitatqmlesmiknPrptraevsDvanavlDG 308
                                       n++eil+++Dgi+varGDlG   p+e+++++qk li+k+  +gkp i+atq+l sm ++P ptr+e+ D+ nav + 
  gi|385805384|ref|YP_005841782.1| 226 NVEEILKVADGIVVARGDLGTHFPMETLPTIQKDLISKSIVQGKPSIVATQLLSSMLNSPIPTRSEIVDIYNAVQES 302
                                       ***************************************************************************** PP

                                       -SEEEESHHHHTSS-HHHHHHHHHHHHHHHHHT CS
                                PK 309 tDavmLsgetakGkyPveavkamaevaleaeka 341
                                       ++a+mL  et+ G+yP++av+ +++v +eaek+
  gi|385805384|ref|YP_005841782.1| 303 ANALMLTNETSIGNYPIDAVRWLKKVIIEAEKN 335
                                       ******************************986 PP

>> PK_C  Pyruvate kinase, alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   0.0   3.8e-17   2.3e-13      10     108 ..     360     453 ..     352     461 .] 0.88

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 3.8e-17
                                       HHHHHT-SEEEEE-SSSHHHHHHHHT-TSSEEEEEESHHHHHHHHHHCTTEEHHH.HHHHH...TTSHHHHHHHHHH CS
                              PK_C  10 aaeelgakaIvvltesGetArliskyrpkvpiiavtpneltarqlalyrGvypvlvekaktaestdellreavkvak 86 
                                        +++l+ak I v+t+sG tA+ is yrp   i+a  p+ +tar+l++ +Gv p  ++    a+s ++ l+++ kv++
  gi|385805384|ref|YP_005841782.1| 360 FSRQLNAK-ISVYTKSGLTAQNISLYRPYGIIYAGVPDMHTARKLSIIWGVEPYVLA----ADSYENGLEKIRKVLI 431
                                       56677777.*********************************************986....6789999********* PP

                                       HTTSS-STSEEEEEE-SSSS.. CS
                              PK_C  87 eaglvkkgdevvvtaGtpkges 108
                                       ++g ++kgd+++ t   ++ge 
  gi|385805384|ref|YP_005841782.1| 432 SEGKLSKGDTLIETYRFKEGEV 453
                                       ************9998887743 PP

>> HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   7.5e-10   4.5e-06      75     156 ..     172     246 ..     165     260 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 7.5e-10
                                       HHHGG.HHHTTSSEEEESS--SHHHHHHHHHHTSHTTTS---HCCC-EEEEEE-SHHHHHTHHHHHTSTTEEEEEE- CS
                         HpcH_HpaI  75 kqdle.vldlgaqvvlvPkvetaeealevvsalrepekgirganketrllaqiEsaegvknaeeIaavegldgvflG 150
                                       ++d+e + +  ++ ++  +ve+++++ +++++l++        nk++ +la iE+++gv n+eeI++v   dg++++
  gi|385805384|ref|YP_005841782.1| 172 ERDIEfACNNDFSHLMASFVESKDNIFQLKELLNKKC------NKQLNILAKIETKRGVYNVEEILKVA--DGIVVA 240
                                       568888999999**********************999......**********************9875..777777 PP

                                       HHHHHH CS
                         HpcH_HpaI 151 aeDlsa 156
                                         Dl +
  gi|385805384|ref|YP_005841782.1| 241 RGDLGT 246
                                       777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 2620.68
//
Query:       gi|385805385|ref|YP_005841783.1|  [L=286]
Description: methyltransferase [Fervidicoccus fontis Kam940]
Scores for complete 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-47  160.3   0.1    6.9e-47  159.8   0.1    1.2  1  Met_10           Met-10+ like-protein
    1.5e-07   31.1   0.0    2.4e-07   30.5   0.0    1.4  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    5.3e-05   22.8   0.1    8.2e-05   22.1   0.1    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    0.00053   19.3   0.0     0.0007   18.9   0.0    1.2  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
    0.00062   19.6   0.0     0.0013   18.5   0.0    1.6  1  Methyltransf_31  Methyltransferase domain
     0.0019   17.9   0.0     0.0029   17.3   0.0    1.2  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
     0.0027   17.3   0.0     0.0043   16.6   0.0    1.3  1  MTS              Methyltransferase small domain
     0.0097   15.9   0.0      0.019   14.9   0.0    1.5  1  Methyltransf_18  Methyltransferase domain
  ------ inclusion threshold ------
      0.014   14.8   0.1      0.086   12.2   0.0    1.9  2  DNA_methylase    C-5 cytosine-specific DNA methylase
       0.11   13.2   0.0       0.18   12.5   0.0    1.4  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 !  159.8   0.1   3.8e-50   6.9e-47       4     193 ..      24     221 ..      21     230 .. 0.91

  Alignments for each domain:
  == domain 1  score: 159.8 bits;  conditional E-value: 3.8e-50
                                       EEETTEEEEEB-TTSSHHHHHHHHHHHHH....S.S-SCEEEE-S-SBTTTTB--EEEEEES-.SEEEEEETTEEEE CS
                            Met_10   4 eiiGdvvilnlreelkeykkvigevildk....t.kvktvlrkvsevegefRtfelevlaGsdstetihkEngcrfk 75 
                                       + iGd+++++ +  +k+y+ +i + i++k       vk+++  ++ ++g  Rt+++ +l+G+ +t+ti kE+ c+f 
  gi|385805385|ref|YP_005841783.1|  24 DLIGDIAVIKSPVWIKNYELEIFKKIAEKlasrMpYVKSIWLTETPIYGIERTRKYIHLYGERKTVTIYKEHDCSFY 100
                                       679*******999999888665555544411115679**************************************** PP

                                       EETTTS---GGGHHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTC CS
                            Met_10  76 lDvskvyfsskleaErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekv 152
                                       +D+ k y s++l+ E+ r+aklv+++e+++++f GiG f+i+iakys++k++++id+nP sv++ k+n++lN++ ++
  gi|385805385|ref|YP_005841783.1| 101 VDIEKSYISPRLSYEHIRIAKLVKDNEIIINMFSGIGGFSIVIAKYSNPKIIYSIDINPFSVELQKKNVELNNLTEK 177
                                       ***************************************************************************** PP

                                       EEEEES-GGG---...TT-EEEEEE--TTTGGGGHHHHHHHEEE CS
                            Met_10 153 vkpileDgrevir...eqladrvvmnlpksaieFldkvlaalkd 193
                                       + ++l+D+re+++   +++adrv+++lp+   +F +++l+ l++
  gi|385805385|ref|YP_005841783.1| 178 IIVLLGDAREIMTrdlKNTADRVLLPLPNIDSSFYNAALTSLRN 221
                                       ***********98899999***************9998887765 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 !   30.5   0.0   1.3e-10   2.4e-07       2      81 ..     127     206 ..     126     251 .. 0.85

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 1.3e-10
                   Methyltransf_15   2 rvilDlfsGaGGnviqfalv..fekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvf 76 
                                       ++i+ +fsG GG +i +a++   + +++i+in+  +++ ++N e+ +  +ki + lgd  e++ +   +++  d v+
  gi|385805385|ref|YP_005841783.1| 127 EIIINMFSGIGGFSIVIAKYsnPKIIYSIDINPFSVELQKKNVELNNLTEKIIVLLGDAREIMTRDLKNTA--DRVL 201
                                       689****************96545699**********************************9887544444..7777 PP

                   Methyltransf_15  77 lSpPw 81 
                                       l  P 
  gi|385805385|ref|YP_005841783.1| 202 LPLPN 206
                                       77665 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.1   4.6e-08   8.2e-05     156     222 ..     120     186 ..     115     202 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 4.6e-08
                              PrmA 156 eklvkegeevlDvGtGSGiLaiaaakLga.kkvvavDiDevAvkvakeNaelNkveaklevalseell 222
                                        klvk +e ++ +  G G  +i+ ak    k ++ +Di++ +v+  k+N+elN++++k+ v l +++ 
  gi|385805385|ref|YP_005841783.1| 120 AKLVKDNEIIINMFSGIGGFSIVIAKYSNpKIIYSIDINPFSVELQKKNVELNNLTEKIIV-LLGDAR 186
                                       578999999**************99986516689***********************9966.544444 PP

>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   3.9e-07    0.0007      51     120 ..     127     196 ..      74     228 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 3.9e-07
                                       EEEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHHHHHTT--GGEEEE-S-HHHHHC.--SS- CS
                               TRM  51 ikvldaLsasGlRaiRfalEvpgvkevlaNDisekAvelikeNvklneveeivvineddAnvlla.ekkkr 120
                                         +++ +s+ G  +i  a+  ++ k ++  Di++  vel k+Nv+ln+  e + +  +dA+ +++   k++
  gi|385805385|ref|YP_005841783.1| 127 EIIINMFSGIGGFSIVIAKY-SNPKIIYSIDINPFSVELQKKNVELNNLTEKIIVLLGDAREIMTrDLKNT 196
                                       35778888888889988887.89999************************98888888******8544444 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   7.3e-07    0.0013       4      80 ..     126     202 ..     123     253 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 7.3e-07
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieelekl.ledekfDli 78 
                                       +  ++   +G G +++++a+  +p + +++iDi+++++el ++n + ++l+  + +  gd+ e+ +  l+ ++ D +
  gi|385805385|ref|YP_005841783.1| 126 NEIIINMFSGIGGFSIVIAKYSNP-KIIYSIDINPFSVELQKKNVELNNLTeKIIVLLGDAREIMTRdLK-NTADRV 200
                                       5667888999*********77666.449**********************99999999***996655576.666665 PP

                   Methyltransf_31  79 ls 80 
                                       l 
  gi|385805385|ref|YP_005841783.1| 201 LL 202
                                       54 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 !   17.3   0.0   1.6e-06    0.0029       7      88 ..     124     205 ..     119     210 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.6e-06
                                       -TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--.SEEEEES-CTCCHHHHCC..EEE CS
                   Methyltr_RsmB-F   7 qeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvt.ntivleaDarkidkvlggelfDr 82 
                                       +++e i+ + ++ Gg    ia+  +n + ++ +d+n   ++  ++n++  ++t ++ivl +Dar+i +   +++ Dr
  gi|385805385|ref|YP_005841783.1| 124 KDNEIIINMFSGIGGFSIVIAKY-SNPKIIYSIDINPFSVELQKKNVELNNLTeKIIVLLGDAREIMTRDLKNTADR 199
                                       799*******************9.9999*********9999999998877777569999*******999999***** PP

                                       EEEEE- CS
                   Methyltr_RsmB-F  83 iLlDaP 88 
                                       +Ll  P
  gi|385805385|ref|YP_005841783.1| 200 VLLPLP 205
                                       **9777 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   2.4e-06    0.0043      32      85 ..     126     181 ..     116     200 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.4e-06
                                       CSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEE CS
                               MTS  32 sgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevv 85 
                                       ++ ++ + +G+G  ++++ak s+   +  +d++  ++e+ k+n+e n+l   + v+
  gi|385805385|ref|YP_005841783.1| 126 NEIIINMFSGIGGFSIVIAKYSNPKIIYSIDINPFSVELQKKNVELNNLTekIIVL 181
                                       445889999***********999999**********************98554444 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0     1e-05     0.019       7      78 ..     118     189 ..     108     201 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1e-05
                   Methyltransf_18   7 aiaslvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGlekl 78 
                                       +ia+lv+++++++   +  g  +i ++k ++ k ++ +Din+ ++e  k+n+e ++l++ki v l+d  e +
  gi|385805385|ref|YP_005841783.1| 118 RIAKLVKDNEIIINMFSGIGGFSIVIAKYSNPKIIYSIDINPFSVELQKKNVELNNLTEKIIVLLGDAREIM 189
                                       5999**************************************************************987665 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 ?    0.2   0.1      0.21   3.8e+02     119     166 ..      42      90 ..      36     125 .. 0.73
   2 ?   12.2   0.0   4.8e-05     0.086       3      63 ..     129     198 ..     128     205 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.21
                                       CSHHHHHHHHHHHHHT.EEEEEEEEEGGGTT-SB--EEEEEEEEEGGG- CS
                     DNA_methylase 119 kgktlkvilekleelG.YevsykllnasdyGvpQnReRvfivgirkdle 166
                                       + + +k+i+ekl++   Y  s+ l +   yG+   R+ + + g rk  +
  gi|385805385|ref|YP_005841783.1|  42 ELEIFKKIAEKLASRMpYVKSIWLTETPIYGIERTRKYIHLYGERKTVT 90 
                                       5578999999998866699999999999999988888887777777654 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 4.8e-05
                                       EEEES-TT-HHHHHHHHTT.-EEEEEEE--TTTHHHHHHH-.........-SEEEES-TTTS-GS--.-S CS
                     DNA_methylase   3 fidLfaGiGGfrlgleaag.fecvaaseidkkaaktYeanfk........kvsigDitkidkkklpediD 63 
                                       +i +f+GiGGf++  ++ +  +++++++i++  +++ ++n +         v +gD ++i  ++l+++ D
  gi|385805385|ref|YP_005841783.1| 129 IINMFSGIGGFSIVIAKYSnPKIIYSIDINPFSVELQKKNVElnnltekiIVLLGDAREIMTRDLKNTAD 198
                                       689***********9999889************9999999987777765555667888888777777665 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0    0.0001      0.18       4      70 ..     132     202 ..     129     221 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0001
                                       ET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBS..SSTTTEEEEEE CS
                   Methyltransf_25   4 lGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlp..fedgsfDlvvs 70 
                                       +  G G +++ +ak  + + ++ +Di++  +e  ++++e ++l  ++ ++ gda+++     +++ D v++
  gi|385805385|ref|YP_005841783.1| 132 MFSGIGGFSIVIAKYSNPKIIYSIDINPFSVELQKKNVELNNLteKIIVLLGDAREIMtrDLKNTADRVLL 202
                                       56799********99878999*****************99999999********99752246678888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); 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: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1848.53
//
Query:       gi|385805386|ref|YP_005841784.1|  [L=54]
Description: hypothetical protein FFONT_0342 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.054   13.9   0.6      0.075   13.5   0.6    1.3  1  zf-H2C2_2  Zinc-finger double domain
       0.12   12.2   0.3       0.61    9.9   0.0    1.9  2  LBR_tudor  Lamin-B receptor of TUDOR domain
       0.31   10.9   1.8        1.2    9.0   0.3    2.3  2  zf-C2H2_9  C2H2 type zinc-finger (1 copy)


Domain annotation for each model (and alignments):
>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.6   1.3e-05     0.075      12      23 ..      18      29 ..       9      31 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.3e-05
                         zf-H2C2_2 12 ekpyeCplCdka 23
                                      +++y+Cp+C+++
  gi|385805386|ref|YP_005841784.1| 18 KSFYKCPVCNYK 29
                                      567*******97 PP

>> LBR_tudor  Lamin-B receptor of TUDOR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1      0.08   4.8e+02      40      46 ..       9      15 ..       2      19 .. 0.77
   2 ?    9.9   0.0    0.0001      0.61      22      47 ..      20      45 ..      17      51 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.08
                         LBR_tudor 40 kykDGTe 46
                                      k+ DGT 
  gi|385805386|ref|YP_005841784.1|  9 KFTDGTK 15
                                      7899985 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0001
                         LBR_tudor 22 yyevkvlsfdekkqlYtVkykDGTel 47
                                      +y+  v +++ ++q   V   DGTe 
  gi|385805386|ref|YP_005841784.1| 20 FYKCPVCNYKVNDQQISVSKVDGTEK 45
                                      8***********************96 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 ?    9.0   0.3    0.0002       1.2       4      14 ..      23      34 ..      20      43 .. 0.77
   2 ?    2.3   0.0     0.025   1.5e+02      40      58 ..      35      54 .]      33      54 .] 0.74

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0002
                                      -TTT--B-S.SH CS
                         zf-C2H2_9  4 CPvCevkfn.sw 14
                                      CPvC+ k+n + 
  gi|385805386|ref|YP_005841784.1| 23 CPVCNYKVNdQQ 34
                                      ********9533 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.025
                                      T-SS---.HHHHHHHHHHHH CS
                         zf-C2H2_9 40 iskkrls.kdELekklekff 58
                                      is  +++ ++ L  k+ekff
  gi|385805386|ref|YP_005841784.1| 35 ISVSKVDgTEKLIIKIEKFF 54
                                      66667651567999*****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 334.20
//
Query:       gi|385805387|ref|YP_005841785.1|  [L=923]
Description: pyruvate phosphate dikinase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-82  277.5   0.5    1.9e-82  276.7   0.5    1.4  1  PEP-utilizers_C  PEP-utilising enzyme, TIM barrel domain
    8.3e-59  199.5   0.0    1.6e-50  172.3   0.0    2.9  3  PPDK_N           Pyruvate phosphate dikinase, PEP/pyruvate bi
    1.8e-26   91.6   0.6    5.7e-26   90.0   0.6    1.9  1  PEP-utilizers    PEP-utilising enzyme, mobile domain
  ------ inclusion threshold ------
      0.077   12.7   0.4       0.24   11.2   0.4    1.8  1  Thymosin         Thymosin beta-4 family
        1.1    9.9   3.8        2.4    8.7   0.1    3.3  3  TipAS            TipAS antibiotic-recognition domain


Domain annotation for each model (and alignments):
>> PEP-utilizers_C  PEP-utilising enzyme, TIM barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  276.7   0.5   5.4e-86   1.9e-82       5     292 ..     555     915 ..     551     917 .. 0.95

  Alignments for each domain:
  == domain 1  score: 276.7 bits;  conditional E-value: 5.4e-86
                                       TSCCCCCCCHCCCXBCEEEEEESSCHHHHHHHHCTXSSEEEEEHHHHCTTSCCHHHHHH.................. CS
                   PEP-utilizers_C   5 gklktllavtkdgkkikvlaNidtpedaekalengaeGiGLlRtEflfmareelpteee.................. 63 
                                       g+l++ll+++++++ +kv aN+d peda+ a+e gaeGiGLlR+E++f   e+l ++++                  
  gi|385805387|ref|YP_005841785.1| 555 GELQELLTWADQVRVLKVKANADVPEDARIAREYGAEGIGLLRIERMFRRPERLEKLRKvilsetteertaameels 631
                                       678999*********************************************************************** PP

                                       ..HHHHHHHHHHHTTTSEEEEEXXXSSCCGGSGGC.............................HHHH.XSXGGGSS CS
                   PEP-utilizers_C  64 ..qaeaykkvleamngrpvvvRtlDiggdkelpel.............................keepeevNPmlGf 109
                                          ++++k++l+ m+g+pv++R++D++ +++lp+                              +e + e+NPm+G+
  gi|385805387|ref|YP_005841785.1| 632 emIKKDFKEMLSIMDGLPVTIRLIDPPLHEFLPKPeellrqiyeakmsgasedkikdleklykkVEALVEANPMMGH 708
                                       **9******************************98899*************************99999********* PP

                                       XTHHHHCCSHHHHHHHHHHHHHHCCCC.......EEEEEESSXXSHHHHHH.HHHHHHHHHHHHHHCTCTXXTTXEE CS
                   PEP-utilizers_C 110 RgirlglsepelfetqlrAllrasaag.......kleimlPmvasveelee.akkiieevkeelekegvkkkkkvkv 178
                                       Rg+r+g++ pe+++   rA+l+a+a+         ++im+P va ++e++  + k i +++ee++k+ +++k ++k+
  gi|385805387|ref|YP_005841785.1| 709 RGVRVGITFPEVYRGLTRAILEAQAELikegknpIVQIMIPQVAIADEIKFvKEKAILPTAEEIQKK-YEIKLNFKI 784
                                       *************************66678898899**************95556788888****99.********* PP

                                       EEEEXSHHHHHTHHHHCTTSSEEEEXHHHHHHHHHTXXCCCHC....HHHH......SXTTTCHHCCCHHHHHHHHH CS
                   PEP-utilizers_C 179 GiMiEvpsaalladklakevdFfSiGtNDLtQytlavdRdnee....vakl......ydplepavlrlikevikaae 245
                                       G+MiE+++ a++ad++ak+v+FfS+GtNDLtQ t++ +Rd+ e    +++l       +p+e+ + ++++e++k+a 
  gi|385805387|ref|YP_005841785.1| 785 GTMIETVRGAITADEIAKNVEFFSFGTNDLTQATFSFSRDDVEnkflPKYLeleilkNNPFEVIDEKGVGELVKIAV 861
                                       *****************************************9977776666999999******************** PP

                                       HCC......XEEEEESCCCCSCCCHHHHHHC.TXSEEEEXGGGHHHHHHHHHCT CS
                   PEP-utilizers_C 246 ekg......lkvgiCGelagdpsavellvgl.GldelSmsaasvpaaraalaqv 292
                                       +kg      +++g+CGe++gdp+++e+++++ G+d++S+s++++++ar a+a++
  gi|385805387|ref|YP_005841785.1| 862 QKGrsvnpnIEIGVCGEHGGDPTSIEFFHKIgGIDYVSASPFRILVARLAAAHA 915
                                       *******************************55*****************9987 PP

>> 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 !  172.3   0.0   4.4e-54   1.6e-50       2     221 ..      22     330 ..      21     342 .. 0.88
   2 !   23.7   0.1   7.3e-09   2.6e-05     272     326 ..     342     394 ..     338     396 .. 0.91
   3 ?   -2.0   0.0      0.46   1.6e+03      35      77 ..     661     705 ..     657     706 .. 0.77

  Alignments for each domain:
  == domain 1  score: 172.3 bits;  conditional E-value: 4.4e-54
                            PPDK_N   2 elvGGKganLaellneagipvPpgfaitadafrefleengleekideelkeldvddvdelrka.skeirelilsael 77 
                                       +l GGKga+La + ++ag+pvPpgf+it+da+r+f+++   +++ide++k+l+     ++r++  k++  +i + +l
  gi|385805387|ref|YP_005841785.1|  22 ALFGGKGAGLALM-TQAGLPVPPGFTITTDACRDFFQQR--KQEIDEIVKQLEKGVPPQVRDElIKKLWGIIDTLSL 95 
                                       578**********.66***********************..888888888888777777765424666666777777 PP

                            PPDK_N  78 Peeleeaikeayeel....gkkfgde..elpvaVRSSataEDlpkasfaGqqdtyLnvggeeevle........... 137
                                       P+ l ++++e +++l    g+kfgd+  +l+v+VRS+      +  s++G++dt+Ln+g ++e+++           
  gi|385805387|ref|YP_005841785.1|  96 PAGLMDEVREHMKKLemkrGRKFGDKnnPLLVSVRSG------APVSMPGMMDTVLNLGLNDETVKglaqqtnnerf 166
                                       77666666666666511115566666889********......99******************************** PP

                            PPDK_N 138 ............................................................................a 138
                                                                                                                   a
  gi|385805387|ref|YP_005841785.1| 167 aydsyrrflqlygkivlgiddkkfdetlnkikqkynakndidldtnalkelveeykkiireekgefiqdywyqlemA 243
                                       ***************************************************************************** PP

                            PPDK_N 139 ikavfaSlfnerAilYrkekgldheeva.lavvvqkmvnsdlg...asGVafsldpetG...fkdevlinasyGlGe 208
                                       ikavf+S++n+rAi+Yr +++++ e  + +av+vq+mv++++g    +GV+fs++ +tG     +e+l na   +Ge
  gi|385805387|ref|YP_005841785.1| 244 IKAVFRSWMNPRAIFYRIANKITPEIAGcTAVTVQSMVFGNMGmdsGTGVVFSRNVATGeneIYGEFLPNA---QGE 317
                                       **********************98866558***************99************666667888888...*** PP

                            PPDK_N 209 aVVaGrvtpdefv 221
                                       +VVaG++tp ++ 
  gi|385805387|ref|YP_005841785.1| 318 DVVAGIRTPMHIS 330
                                       *********8875 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 7.3e-09
                            PPDK_N 272 eLaeiakkiekhygtpmdiEfaideeegklyllQaRpetrtsekkekkaaetlee 326
                                        L + +k +ek  ++ +d+Ef+++  +gkl++lQ+R+ + t  + +k+a ++ +e
  gi|385805387|ref|YP_005841785.1| 342 DLYKNLKMLEKVNKDVQDVEFTVE--KGKLFFLQTRDAKMTPLARVKTAVDMAKE 394
                                       677888999***************..********************999999887 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.46
                            PPDK_N  35 efleeng..leekideelkeldvddvdelrkaskeirelilsael 77 
                                       efl + +  l++  +++++  + d++++l+k +k++++l+   ++
  gi|385805387|ref|YP_005841785.1| 661 EFLPKPEelLRQIYEAKMSGASEDKIKDLEKLYKKVEALVEANPM 705
                                       566555555788888888889999999999999999998877765 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 !   90.0   0.6   1.6e-29   5.7e-26       4      73 .]     458     539 ..     455     539 .. 0.97

  Alignments for each domain:
  == domain 1  score: 90.0 bits;  conditional E-value: 1.6e-29
                                       S-EEEEES---HHHHTTS-GEEEEEES--TTHHHHHHHHHHTT--EEE--SSHH.............HH--TEEEEE CS
                     PEP-utilizers   4 egvILvaeetspsdiagldkaaGivterGGmtSHaAivArelgiPaVvgvgeati............elkegdlitv 68 
                                       ++vILv+ et+p+d++g+ +a+Gi+t+rGGmtSHaA+vAr+ g+ aVvg++e++i            ++kegd+it+
  gi|385805387|ref|YP_005841785.1| 458 KEVILVRVETKPDDVHGFYAAKGILTSRGGMTSHAAVVARGIGKTAVVGAEEIQIdyekkefrvngvVIKEGDIITI 534
                                       45*************************************************************************** PP

                                       ETTTT CS
                     PEP-utilizers  69 DgstG 73 
                                       Dg+tG
  gi|385805387|ref|YP_005841785.1| 535 DGNTG 539
                                       ****9 PP

>> Thymosin  Thymosin beta-4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.4   6.7e-05      0.24      22      35 ..     761     774 ..     760     776 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.7e-05
                          Thymosin  22 qEKnvLPtkEdIeq 35 
                                       +EK +LPt+E+I++
  gi|385805387|ref|YP_005841785.1| 761 KEKAILPTAEEIQK 774
                                       7***********97 PP

>> TipAS  TipAS antibiotic-recognition domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.1   0.00068       2.4      31      85 ..     188     240 ..     184     245 .. 0.88
   2 ?   -1.3   0.0      0.84     3e+03      21      45 ..     614     639 ..     584     645 .. 0.57
   3 ?   -1.2   0.1      0.78   2.8e+03      18      43 ..     674     699 ..     670     705 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00068
                                       XXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TipAS  31 eelkaelkelfaklaaalaagkdpdseeaqelaeehralieefwgecskeilagl 85 
                                       +++++ l+++ +k +a   ++ d d ++ +el+ee++++i+e +ge+ +++++ l
  gi|385805387|ref|YP_005841785.1| 188 KKFDETLNKIKQKYNAK--NDIDLDTNALKELVEEYKKIIREEKGEFIQDYWYQL 240
                                       57788888999999888..79********************99999999999887 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.84
                                       XXXXXXXXXXXXXXXXX.XXXXXXXX CS
                             TipAS  21 kiaklskedweelkael.kelfakla 45 
                                        i + ++e+ +++++el + + ++++
  gi|385805387|ref|YP_005841785.1| 614 VILSETTEERTAAMEELsEMIKKDFK 639
                                       44344444444444444044444444 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.78
                                       XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TipAS  18 seekiaklskedweelkaelkelfak 43 
                                       +e+k+++ s++++++l++ +k++ a 
  gi|385805387|ref|YP_005841785.1| 674 YEAKMSGASEDKIKDLEKLYKKVEAL 699
                                       67788888888888888777776554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (923 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1035  (0.0577277); expected 358.6 (0.02)
Passed bias filter:                      688  (0.0383736); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); 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: 0.79u 0.30s 00:00:01.09 Elapsed: 00:00:00.47
# Mc/sec: 5945.38
//
Query:       gi|385805388|ref|YP_005841786.1|  [L=108]
Description: hypothetical protein FFONT_0344 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0001   22.1   0.4    0.00011   22.0   0.4    1.2  1  TFIIE_alpha    TFIIE alpha subunit
  ------ inclusion threshold ------
      0.021   14.7   0.0      0.027   14.4   0.0    1.3  1  TrmB           Sugar-specific transcriptional regulator TrmB
      0.068   13.1   0.0      0.071   13.0   0.0    1.1  1  PDDEXK_1       PD-(D/E)XK nuclease superfamily
      0.074   12.4   6.3       0.12   11.8   2.8    1.9  2  RNA_pol_Rpc34  RNA polymerase Rpc34 subunit


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 !   22.0   0.4   2.6e-08   0.00011      12      64 ..      15      68 ..       6      98 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.6e-08
                                      -HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHH.HCTSEEEEEEEE CS
                       TFIIE_alpha 12 geeavlvldvLlekgevteedlakelkidlnelrklLnrLy.earlvkykrrrd 64
                                      ++e +lvl++L + g++ e  l+ke+++d+ ++rk+L  L  +  l+  kr++ 
  gi|385805388|ref|YP_005841786.1| 15 NDEEILVLKILQKYGQIDEQILEKETSLDKSKIRKILDLLIiKNVLIPQKRSKS 68
                                      5799*********************************98852455677777765 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0     6e-06     0.027       6      58 ..      14      66 ..       9      86 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6e-06
                                      HHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB  6 LseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                      L++ E+ v + L k+g+ + + + +e+ +++sk+ ++L  L+ k +   +k++
  gi|385805388|ref|YP_005841786.1| 14 LNDEEILVLKILQKYGQIDEQILEKETSLDKSKIRKILDLLIIKNVLIPQKRS 66
                                      8999*************************************999988777765 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 ?   13.0   0.0   1.6e-05     0.071     223     254 ..      45      79 ..       4      80 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.6e-05
                          PDDEXK_1 223 qeleel..aeeilagefparpskk.CeyCpyksvC 254
                                       ++++++  +  i++  +p + sk  C+ Cp+k +C
  gi|385805388|ref|YP_005841786.1|  45 SKIRKIldLLIIKNVLIPQKRSKSfCDGCPFKNIC 79 
                                       333333222223333577777777*********** 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 ?   11.8   2.8   2.6e-05      0.12      76     130 ..       6      58 ..       2      68 .. 0.89
   2 ?    2.9   0.2     0.013        57     300     330 ..      62      92 ..      56      96 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.6e-05
                                       CCHHHHHTSXHHHHHHHHHHHHHXSSXEEHHHHHHTTGXXHHHHHHHHHHHHHTT CS
                     RNA_pol_Rpc34  76 eeAkkktslsedeslVysiIeesGneGIwsrtiksklnLhksvvkkcLksLeskk 130
                                       e  kk  +l+ +e lV++i ++ G+  I+++ +++ + L ks ++k+L +L  k+
  gi|385805388|ref|YP_005841786.1|   6 EKIKKTVTLNDEEILVLKILQKYGQ--IDEQILEKETSLDKSKIRKILDLLIIKN 58 
                                       67789999999999**********9..***********************98876 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.013
                                       SSSTTXXSSXSSSSSXXTSSSSSSSSSSTTS CS
                     RNA_pol_Rpc34 300 asglveapcgecpvfdlceeggavspkncvY 330
                                       +++  ++ c++cp  ++c  + + +++n +Y
  gi|385805388|ref|YP_005841786.1|  62 PQKRSKSFCDGCPFKNICYTSKNLNDENFIY 92 
                                       56667888*********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       837  (0.0466841); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); 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: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 671.42
//
Query:       gi|385805389|ref|YP_005841787.1|  [L=274]
Description: Wyosine base formation [Fervidicoccus fontis Kam940]
Scores for complete 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   73.2   0.0    3.2e-20   72.3   0.0    1.6  1  Wyosine_form  Wyosine base formation
    8.2e-18   65.3   0.3    3.3e-17   63.4   0.2    1.9  2  Radical_SAM   Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Wyosine_form  Wyosine base formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.3   0.0   3.5e-24   3.2e-20       3      63 .]     196     255 ..     194     255 .. 0.97

  Alignments for each domain:
  == domain 1  score: 72.3 bits;  conditional E-value: 3.5e-24
                                       T-SEEEEEE------------------HHHHHHHHHHHHTSSS.EEEEEEETTTTEEEEEE CS
                      Wyosine_form   3 epdFvEvKaytyvGssrsrLtmknvPwheevadfakrlegsaedYellaehrhSrvvllar 63 
                                       +p+++E K+y+yvG s  rL+++n+P+h+ev++fa++l++ ++ Y + +e+++Sr+vll++
  gi|385805389|ref|YP_005841787.1| 196 QPTYIEPKGYMYVGASMLRLSRDNMPTHDEVRKFAEELSKATG-YPIRSESKPSRIVLLSK 255
                                       8******************************************.**************985 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.4   0.2   3.6e-21   3.3e-17       6     159 ..       7     182 ..       3     186 .. 0.81
   2 ?   -3.5   0.0       1.3   1.2e+04     124     140 ..     220     236 ..     212     245 .. 0.61

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 3.6e-21
                                       EESS--TTTSCCTT.............................HHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEE CS
                                       xxxxxxxxxxxxxx.............................xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                       Radical_SAM   6 gCnlrCsfCarpet.............................vrregrgrslsveeileevkelkaekg.vkevil 52 
                                       +C ++C++C+r +                              +r+   g+   +   ++ ++e+   ++ +++ i+
  gi|385805389|ref|YP_005841787.1|   7 WCWNACVHCWRLRPsdtglkwnevkmpdynddvkrvvdrlieeQRKMLSGYKDHKNVDKKMFEEA---MDpKHVAIS 80 
                                       7**********99999**88888887777777777666666643333333333333333333444...333888888 PP

                                       ESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT...CTSH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxx RF
                       Radical_SAM  53 gggepllypdfvellerlaklavpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn...rght 126
                                       + gep+ly ++++l+ + +++   g++++++t g++  ++++  l+e  + +++++ ea+++e   +++n    ++ 
  gi|385805389|ref|YP_005841787.1|  81 LTGEPTLYNKLEDLIMEFHRR---GMTTFLVTRGVR--PDVILNLKEK-PSQLYISMEAYNKE-MYEWLNqplVPNA 150
                                       8*******************8...************..5899999995.5*************.77777778899** PP

                                       HHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 127 feevlealeklreagikrvvdrivglpGendee 159
                                       +e ++e+l+ l e+g + +v ri++++G n++e
  gi|385805389|ref|YP_005841787.1| 151 WELTMETLKGLPEYGRP-TVLRITLMKGINMDE 182
                                       **************999.*************97 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.3
                                       TSHHHHHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxx RF
                       Radical_SAM 124 ghtfeevlealeklrea 140
                                       ++t +ev +  e l +a
  gi|385805389|ref|YP_005841787.1| 220 MPTHDEVRKFAEELSKA 236
                                       45555555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1747.35
//
Query:       gi|385805390|ref|YP_005841788.1|  [L=152]
Description: DedA family protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.4e-20   72.4   0.4    4.4e-20   72.4   0.4    1.7  2  SNARE_assoc  SNARE associated Golgi protein


Domain annotation for each model (and alignments):
>> SNARE_assoc  SNARE associated Golgi protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.4   0.4   2.4e-24   4.4e-20      26     119 ..       2      98 ..       1      99 [. 0.93
   2 ?   -1.2   0.1      0.15   2.8e+03      39      57 ..     128     146 ..     116     151 .. 0.56

  Alignments for each domain:
  == domain 1  score: 72.4 bits;  conditional E-value: 2.4e-24
                       SNARE_assoc  26 gallGaslayllgrylgr....kalrrkllsekrvkalerlverygflallllrllpivPrdlvnyvaGltrvsfkr 98 
                                       g llG+++ yl+g ++g     ++++  l++   +++++rl+ ++g++++l++r+lp + r++++++aGl++++fk+
  gi|385805390|ref|YP_005841788.1|   2 GNLLGSIILYLVGEKIGLeflkYYGKYFLIDDSDLDRANRLFMNHGSKIILIGRMLPAI-RTVISLPAGLAKMNFKK 77 
                                       899**************77777777777788888888**********************.***************** PP

                       SNARE_assoc  99 FflatfiGsipwalvyaylGs 119
                                       F ++t+iGsipw+l ++y+G 
  gi|385805390|ref|YP_005841788.1|  78 FSIYTLIGSIPWNLMLIYIGI 98 
                                       *******************95 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.15
                       SNARE_assoc  39 rylgrkalrrkllsekrvk 57 
                                        y+ +k+ ++k ++++r++
  gi|385805390|ref|YP_005841788.1| 128 LYYYYKSTGKKGGKNERYR 146
                                       2222256666777777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       823  (0.0459033); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); 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: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 977.66
//
Query:       gi|385805391|ref|YP_005841789.1|  [L=172]
Description: hypothetical protein FFONT_0347 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      0.003   17.4   0.3     0.0098   15.7   0.1    2.0  2  HU-CCDC81_bac_2  CCDC81-like prokaryotic HU domain 2
  ------ inclusion threshold ------
      0.075   13.1   4.7       0.13   12.3   4.7    1.4  1  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP


Domain annotation for each model (and alignments):
>> HU-CCDC81_bac_2  CCDC81-like prokaryotic HU domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.39   3.5e+03      29      29 ..      36      36 ..       9      55 .. 0.58
   2 !   15.7   0.1   1.1e-06    0.0098      12      52 ..      67     107 ..      61     110 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.39
                   HU-CCDC81_bac_2 29 l 29
                                      l
  gi|385805391|ref|YP_005841789.1| 36 L 36
                                      2 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.1e-06
                   HU-CCDC81_bac_2  12 gisyeeAlqkiekeveelkqeLeeegrveleniGeLslnee 52 
                                       +++ + A+++i++  +elk+ + ++  + ++niGe++++++
  gi|385805391|ref|YP_005841789.1|  67 DTTIKAASEAIKTPLSELKSSITTQDYIIISNIGEITVSKN 107
                                       688999******************************99865 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 ?   12.3   4.7   1.4e-05      0.13      24      96 ..      17      90 ..       2     112 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.4e-05
                      Baculo_PEP_C 24 airlqnvqilaqlatlldaietqLnal.sedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsiltn 96
                                      +ir     +  ++++  ++++t++++l +e++ +lla++d  ++++++ ++++++a ++++++ L  l+s +t+
  gi|385805391|ref|YP_005841789.1| 17 TIRGIDKDLYEKISNKAKQLNTTVGSLvNEAIGNLLASIDIGIEKTSKIVDTTIKAASEAIKTPLSELKSSITT 90
                                      55666777778889999999999987625789**************************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       983  (0.0548274); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 1160.86
//
Query:       gi|385805392|ref|YP_005841790.1|  [L=47]
Description: hypothetical protein FFONT_0348 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 305.50
//
Query:       gi|385805393|ref|YP_005841791.1|  [L=450]
Description: MATE efflux family protein [Fervidicoccus fontis Kam940]
Scores for 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-49  166.0  24.8    1.2e-29  103.0   8.8    2.8  4  MatE             MatE
    7.2e-09   35.9  11.7    7.2e-09   35.9  11.7    4.7  4  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai


Domain annotation for each model (and alignments):
>> MatE  MatE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.0   8.8   1.4e-33   1.2e-29       1     160 [.      24     183 ..      24     184 .. 0.99
   2 ?   -3.8   0.3      0.97   8.7e+03      23      35 ..     206     218 ..     197     221 .. 0.50
   3 !   77.0   8.0   1.4e-25   1.3e-21       1     158 [.     249     407 ..     249     410 .. 0.96
   4 ?   -2.8   0.6       0.5   4.5e+03      75      97 ..     425     446 ..     416     448 .. 0.65

  Alignments for each domain:
  == domain 1  score: 103.0 bits;  conditional E-value: 1.4e-33
                              MatE   1 PialenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgli 77 
                                       P++++ l++++++++dt++++rlg++al+a  ++++ + +l++f+ gl ++  + ++q +G++++k a+e+  + ++
  gi|385805393|ref|YP_005841791.1|  24 PLIVSDLVQVIYNFVDTFWLSRLGTEALSAPVVSWPPVYFLISFGAGLLSSGIATISQDYGKGDYKSAREYSGVLFL 100
                                       99*************************************************************************** PP

                              MatE  78 lllllsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislll 154
                                       ++l++sli++++  +fs +il++++ +e+++++a+ ylr ++l +p+  + +++++i  + g++ +++ i+l+s+++
  gi|385805393|ref|YP_005841791.1| 101 FTLVFSLIVSVIPAIFSYYILKIMNIPEDLIPFANIYLRTILLATPFAYIGITFTTITSALGDVGLTMKINLLSVVI 177
                                       ***************************************************************************** PP

                              MatE 155 niplny 160
                                       n++l++
  gi|385805393|ref|YP_005841791.1| 178 NVILDP 183
                                       ***987 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 0.97
                              MatE  23 lgskalAavsial 35 
                                       ++++ +A +si++
  gi|385805393|ref|YP_005841791.1| 206 VSEVVVAIYSIFM 218
                                       2444455554444 PP

  == domain 3  score: 77.0 bits;  conditional E-value: 1.4e-25
                              MatE   1 PialenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgli 77 
                                       P+ ++    sl ++++++l++ +g++ +Aa++i+++i+ ++ ++ +g + a++++vg +lG k  +r ke++ ++l+
  gi|385805393|ref|YP_005841791.1| 249 PLGIHRSSNSLAQTFSISLLSFYGADVIAAYGITTRIIDFVQSITTGYARATAIMVGANLGRKFIDRSKEVVKKSLL 325
                                       6777888889999**************************************************************** PP

                              MatE  78 lllllsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislisl.l 153
                                        l l+ ++i ++++lf++q++ +ftqd+ v ++a +yl i  +++p+++ +++++g+ +g g+t +   +s++++ +
  gi|385805393|ref|YP_005841791.1| 326 DLSLILVFIGVILVLFRDQLIGIFTQDPSVFKYAVDYLFISSITLPFYGWFFISYGVANGSGNTYFFGLLSVLRMwV 402
                                       ******************************************************************99999999999 PP

                              MatE 154 lnipl 158
                                       ++i+ 
  gi|385805393|ref|YP_005841791.1| 403 FRILP 407
                                       99875 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 0.5
                              MatE  75 glilllllsliiallvllfseqi 97 
                                        + ++ ++s i+ l+ +++ + +
  gi|385805393|ref|YP_005841791.1| 425 VIAVSNIISGITGLM-WVNKKTW 446
                                       455666667777666.7777666 PP

>> Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   3.4      0.69   6.2e+03      83      83 ..      97      97 ..      14     126 .. 0.56
   2 !   35.9  11.7     8e-13   7.2e-09       2      84 ..     138     229 ..     137     286 .. 0.83
   3 ?   -0.4   1.0      0.12   1.1e+03      93     134 ..     295     339 ..     256     348 .. 0.54
   4 ?   -4.2  11.5       1.8   1.6e+04       1      82 [.     362     446 ..     362     449 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.69
                   Polysacc_synt_C 83 i 83
                                      +
  gi|385805393|ref|YP_005841791.1| 97 V 97
                                      2 PP

  == domain 2  score: 35.9 bits;  conditional E-value: 8e-13
                   Polysacc_synt_C   2 LailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllli......plfgivGaaiatvlallvvavl 72 
                                       L+ + l+++f+++ +++++i  +lg + +++k++++++++++il  ++i      p++g+ G a+at+++++vva++
  gi|385805393|ref|YP_005841791.1| 138 LRTILLATPFAYIGITFTTITSALGDVGLTMKINLLSVVINVILDPFMIfgiypfPKMGVFGSALATLVSEVVVAIY 214
                                       788899*******************************************9999999******************999 PP

                   Polysacc_synt_C  73 n...lyalrrllgik 84 
                                           l++ +++l+i 
  gi|385805393|ref|YP_005841791.1| 215 SifmLFYKYKKLNIG 229
                                       832233334444444 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.12
                   Polysacc_synt_C  93 kpllaalvmgivvylllllllglllla....al.alllavlvgalvY 134
                                        ++ a+++m+++   l + ++  +       +l   l+ v++g+++ 
  gi|385805393|ref|YP_005841791.1| 295 GYARATAIMVGA--NLGRKFIDRSKEVvkksLLdLSLILVFIGVILV 339
                                       445555555555..333333333333333322233344444444433 PP

  == domain 4  score: -4.2 bits;  conditional E-value: 1.8
                   Polysacc_synt_C   1 vLailalsiiflslstvlssiLqglgrqkialkalviga.lvklilnllli..plfgivGaaiatvlallvvavlnl 74 
                                       +L i++++++f++++ ++ ++ +g g + ++ + +v+ + ++ ++  +++i    f+++ + + ++++ +++ +  l
  gi|385805393|ref|YP_005841791.1| 362 YLFISSITLPFYGWFFISYGVANGSGNTYFFGLLSVLRMwVFRILPMFICIyiLTFNVIYIWLVIAVSNIISGITGL 438
                                       589999******************99999886666665515677777777744456777777777777777777777 PP

                   Polysacc_synt_C  75 yalrrllg 82 
                                       +++++++ 
  gi|385805393|ref|YP_005841791.1| 439 MWVNKKTW 446
                                       77777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       808  (0.0450667); 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):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2807.45
//
Query:       gi|385805394|ref|YP_005841792.1|  [L=58]
Description: hypothetical protein FFONT_0350 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       708  (0.0394891); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.47
# Mc/sec: 371.62
//
Query:       gi|385805395|ref|YP_005841793.1|  [L=132]
Description: HTH-type transcriptional regulator lrs14 [Fervidicoccus fontis Kam940]
Scores for 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-09   35.0   0.1    1.8e-08   34.1   0.1    1.5  1  HTH_5          Bacterial regulatory protein, arsR family
      5e-08   32.7   0.1    9.2e-08   31.9   0.1    1.5  1  TrmB           Sugar-specific transcriptional regulator TrmB
    1.4e-05   24.9   0.9    2.2e-05   24.3   0.9    1.3  1  TFIIE_alpha    TFIIE alpha subunit
    5.1e-05   23.1   0.0    7.1e-05   22.6   0.0    1.2  1  MarR_2         MarR family
     0.0002   21.1   0.2     0.0005   19.8   0.1    1.6  2  DUF4423        Domain of unknown function (DUF4423)
    0.00033   20.1   0.1    0.00065   19.2   0.1    1.6  1  HTH_24         Winged helix-turn-helix DNA-binding
    0.00043   20.0   0.0    0.00063   19.5   0.0    1.3  1  HTH_IclR       IclR helix-turn-helix domain
    0.00064   19.4   0.1     0.0013   18.4   0.1    1.5  1  HTH_DeoR       DeoR-like helix-turn-helix domain
    0.00067   19.5   0.2     0.0013   18.7   0.2    1.5  1  MarR           MarR family
     0.0011   19.5   0.0     0.0016   18.9   0.0    1.4  1  HTH_27         Winged helix DNA-binding domain
     0.0058   16.5   0.4      0.014   15.3   0.4    1.6  1  HTH_11         HTH domain
     0.0094   15.3   0.1     0.0097   15.2   0.1    1.2  1  FAM91_N        FAM91 N-terminus
     0.0098   15.8   0.1       0.02   14.9   0.1    1.6  1  HTH_36         Helix-turn-helix domain
  ------ inclusion threshold ------
      0.031   14.4   0.1      0.074   13.2   0.0    1.7  2  SpoIIID        Stage III sporulation protein D
      0.033   14.8   5.2      0.096   13.3   0.7    2.3  2  Mga            Mga helix-turn-helix domain
      0.042   13.8   0.0      0.062   13.3   0.0    1.3  1  HTH_Crp_2      Crp-like helix-turn-helix domain
      0.055   13.5   0.0      0.082   13.0   0.0    1.3  1  HTH_20         Helix-turn-helix domain
      0.079   13.1   0.1       0.17   12.0   0.1    1.5  1  Trp_repressor  Trp repressor protein
      0.091   12.5   0.0       0.14   11.8   0.0    1.3  1  HTH_41         Helix-turn-helix domain
       0.12   12.5   0.6       0.28   11.3   0.1    1.8  2  HTH_9          RNA polymerase III subunit RPC82 helix-turn-he


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 !   34.1   0.1     2e-11   1.8e-08       3      45 ..      34      76 ..      32      77 .. 0.95

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 2e-11
                                      HHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  3 tRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLV 45
                                      t l IL+   ++++++ el+++l+ls++t+S+ L  L ++G+V
  gi|385805395|ref|YP_005841793.1| 34 TDLMILFKIIDKKTTIEELSNDLKLSKATISRSLTNLLNLGFV 76
                                      6689*************************************99 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.1     1e-10   9.2e-08       2      59 ..      26      91 ..      25      99 .. 0.86

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 1e-10
                                      H.HCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST........T CS
                              TrmB  2 q.klGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr........p 59
                                      + ++++se++  + ++++  ++ t++e++++l+++++++ ++L +L++ G+V r+++         +
  gi|385805395|ref|YP_005841793.1| 26 KfCYDFSETDLMILFKII-DKKTTIEELSNDLKLSKATISRSLTNLLNLGFVVRNREIenygvgrpK 91
                                      5589*************9.7889******************************99976667777542 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.9   2.4e-08   2.2e-05      13      99 ..      33     119 ..      19     125 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 2.4e-08
                                       HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEE.TTTEEEEEEEEEECCCHCCCHHHH CS
                       TFIIE_alpha  13 eeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrd.eekswykyywrinyeklvdvvkrk 88 
                                       e    +l+ ++ + ++t e+l+++lk+ +  + + L +L + ++v   r+ +  + +  ky+++  +e +   +++ 
  gi|385805395|ref|YP_005841793.1|  33 ETDLMILFKII-DKKTTIEELSNDLKLSKATISRSLTNLLNLGFVVRNREIEnYGVGRPKYTYYSSKEIIESKLRKD 108
                                       44556777777.7889999*************************988888885678999****************** PP

                                       HHHHHHHHHHH CS
                       TFIIE_alpha  89 leevvkkLeek 99 
                                       +++ +k +++ 
  gi|385805395|ref|YP_005841793.1| 109 MDKCAKIIRDF 119
                                       *******9985 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   7.9e-08   7.1e-05       2      55 ..      30      80 ..      29      84 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 7.9e-08
                                      T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2  2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                      +++ +++++L+ + +      t+ el   l+lsk+++sr l  L   G+v+r +
  gi|385805395|ref|YP_005841793.1| 30 DFSETDLMILFKIIDKKT---TIEELSNDLKLSKATISRSLTNLLNLGFVVRNR 80
                                      67778999********95...*****************************9965 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.1   5.6e-07    0.0005      29      88 ..      39      99 ..      31     119 .. 0.80
   2 ?   -0.1   0.1      0.72   6.5e+02     128     146 ..     106     124 ..      98     128 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5.6e-07
                           DUF4423 29 llplkdfkadpeelakrlrpkisaeevekalefLlklgllkkded.gkyrqtekslt..tsse 88
                                      l ++ d+k ++eel++ l+  +s++ ++++l  Ll+lg++ ++++ ++y + + + t  +s+e
  gi|385805395|ref|YP_005841793.1| 39 LFKIIDKKTTIEELSNDLK--LSKATISRSLTNLLNLGFVVRNREiENYGVGRPKYTyySSKE 99
                                      67788999***********..***********************9999999998888333333 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.72
                           DUF4423 128 kedyekikkeirefrkkil 146
                                       ++d++k +k ir+f+ kil
  gi|385805395|ref|YP_005841793.1| 106 RKDMDKCAKIIRDFIGKIL 124
                                       5777778888888877776 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   7.3e-07   0.00065       2      47 ..      32      76 ..      31      77 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 7.3e-07
                            HTH_24  2 detdrkIL.elLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      +etd+ IL +++ k  ++++ eL+  l lS++t++r l +L + G++
  gi|385805395|ref|YP_005841793.1| 32 SETDLMILfKIIDK--KTTIEELSNDLKLSKATISRSLTNLLNLGFV 76
                                      58999999888888..9****************************98 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   7.1e-07   0.00063      19      51 ..      47      79 ..      35      80 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 7.1e-07
                                      -BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR 19 ltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                       t+ el++ + l+k+t +R L  L +lG+v ++
  gi|385805395|ref|YP_005841793.1| 47 TTIEELSNDLKLSKATISRSLTNLLNLGFVVRN 79
                                      5899**************************997 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   1.5e-06    0.0013      13      47 ..      45      79 ..      38      81 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.5e-06
                          HTH_DeoR 13 gklsveelvellgvSeaTiRRDLneLeeqglltRt 47
                                       k ++eel++ l+ S+aTi R L++L + g ++R+
  gi|385805395|ref|YP_005841793.1| 45 KKTTIEELSNDLKLSKATISRSLTNLLNLGFVVRN 79
                                      5789***************************9997 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.2   1.4e-06    0.0013       3      51 ..      33      80 ..      31      84 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.4e-06
                                      HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR  3 ltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsk 51
                                      +t ++iL+++ ++   ++ eL + l++sk+t++r l+ L   G++ R +
  gi|385805395|ref|YP_005841793.1| 33 ETDLMILFKIIDKK-TTIEELSNDLKLSKATISRSLTNLLNLGFVVRNR 80
                                      55666666666544.5888**************************9987 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.8e-06    0.0016       5      54 ..      35      82 ..      31      93 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.8e-06
                            HTH_27  5 qalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgde 54
                                      + ++L+ i   + + ++++l+  l++++++is sl  L + G+v+r++  
  gi|385805395|ref|YP_005841793.1| 35 DLMILFKII--DKKTTIEELSNDLKLSKATISRSLTNLLNLGFVVRNREI 82
                                      778999999..889999***************************998765 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.4   1.5e-05     0.014       7      46 ..      38      77 ..      33      81 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.5e-05
                            HTH_11  7 elLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpI 46
                                      +l++  +++ ++eeL+  L++S++t+ r +  L  lg+ +
  gi|385805395|ref|YP_005841793.1| 38 ILFKIIDKKTTIEELSNDLKLSKATISRSLTNLLNLGFVV 77
                                      5544455568***********************9999765 PP

>> FAM91_N  FAM91 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   1.1e-05    0.0097     245     296 ..      29      80 ..       7     111 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.1e-05
                           FAM91_N 245 gDylEtLLYkilvsidertsvkeLakvLqidlelvkqAvslycRLglakkkt 296
                                        D+ Et L  ++  id++t+++eL++ L++++ ++++    ++ Lg+  +++
  gi|385805395|ref|YP_005841793.1|  29 YDFSETDLMILFKIIDKKTTIEELSNDLKLSKATISRSLTNLLNLGFVVRNR 80 
                                       58889999999***********************************986644 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   2.2e-05      0.02      28      54 ..      49      75 ..      19      76 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.2e-05
                            HTH_36 28 qetlakrlglsknTvsraikeLeqlGy 54
                                       e l+++l+lsk T+sr + +L  lG+
  gi|385805395|ref|YP_005841793.1| 49 IEELSNDLKLSKATISRSLTNLLNLGF 75
                                      78899999**************99997 PP

>> SpoIIID  Stage III sporulation protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   8.2e-05     0.074      11      45 ..      38      72 ..      30      83 .. 0.89
   2 ?   -1.9   0.0         4   3.6e+03      36      53 ..     101     118 ..      91     128 .. 0.50

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.2e-05
                           SpoIIID 11 iakyiveskatvRkaakvfgvskstvhkDvterLk 45
                                      i   i+++k+t+ +  + + +sk+t+ + +t+ L+
  gi|385805395|ref|YP_005841793.1| 38 ILFKIIDKKTTIEELSNDLKLSKATISRSLTNLLN 72
                                      55679**************************9885 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4
                           SpoIIID  36 vhkDvterLkkinkklak 53 
                                       +   + + + k  k + +
  gi|385805395|ref|YP_005841793.1| 101 IESKLRKDMDKCAKIIRD 118
                                       444444444444444444 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.7   0.00011     0.096      19      54 ..      35      70 ..       9      73 .. 0.80
   2 ?    3.7   0.3       0.1        94      41      71 ..      99     130 ..      91     132 .] 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00011
                                      HHHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHH CS
                               Mga 19 yqllkflfeeeevsieelaqelyiSestlkrkikel 54
                                        ++ f + +++++ieel++ l +S++t+ r++ +l
  gi|385805395|ref|YP_005841793.1| 35 DLMILFKIIDKKTTIEELSNDLKLSKATISRSLTNL 70
                                      4455555569**********************9887 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.1
                                       T--HHHHHHHHHHHHHHCHCCT-EE.ETTCCE CS
                               Mga  41 yiSestlkrkikelnklLkefdlel.tkknlk 71 
                                        i es+l ++++++ k +++f  ++ ++k+lk
  gi|385805395|ref|YP_005841793.1|  99 EIIESKLRKDMDKCAKIIRDFIGKIlESKELK 130
                                       57799***************988887766666 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 ?   13.3   0.0   6.9e-05     0.062      20      57 ..      45      82 ..      20      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.9e-05
                                      EEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETEEE CS
                         HTH_Crp_2 20 lpltqeelAsmlGltretvsrilseLkreglisrgrri 57
                                       + t eel++ l l+  t+sr l+ L + g + r+r+i
  gi|385805395|ref|YP_005841793.1| 45 KKTTIEELSNDLKLSKATISRSLTNLLNLGFVVRNREI 82
                                      46799**************************9987545 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   9.1e-05     0.082      21      59 ..      43      81 ..      32      83 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.1e-05
                                      TCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                            HTH_20 21 raegltaselaerldlskntlsyHLrvLeeagLvevvre 59
                                       ++  t +el   l lsk+t+s+ L  L   g+v + re
  gi|385805395|ref|YP_005841793.1| 43 IDKKTTIEELSNDLKLSKATISRSLTNLLNLGFVVRNRE 81
                                      47889*****************************99997 PP

>> Trp_repressor  Trp repressor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00019      0.17      41      73 ..      38      70 ..      32      74 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00019
                     Trp_repressor 41 vvkeLLkeelsqreIaeelgvSiAtItRvsrsL 73
                                      ++ ++++++ + +e+++ l+ S AtI+R   +L
  gi|385805395|ref|YP_005841793.1| 38 ILFKIIDKKTTIEELSNDLKLSKATISRSLTNL 70
                                      5556999*********************86554 PP

>> HTH_41  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   0.00016      0.14       4      32 ..      44      72 ..      41      80 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00016
                            HTH_41  4 dRlktIeelakeleLSvGlvQkALklLed 32
                                      d+  tIeel+++l LS  ++   L  L +
  gi|385805395|ref|YP_005841793.1| 44 DKKTTIEELSNDLKLSKATISRSLTNLLN 72
                                      5668****************999887755 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00031      0.28      28      57 ..      47      76 ..      42      77 .. 0.94
   2 ?   -3.0   0.0       9.1   8.2e+03       3      14 ..     112     123 ..     112     125 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00031
                                      BEHHHHHHHHSSTHHHHHHHHHHHHHTTSE CS
                             HTH_9 28 ltlrelvkktkLsldqVkksLvvLiqhrlV 57
                                       t+ el++++kLs+  + +sL  L+++++V
  gi|385805395|ref|YP_005841793.1| 47 TTIEELSNDLKLSKATISRSLTNLLNLGFV 76
                                      699*************************99 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 9.1
                                       HHHHHHHCSTTH CS
                             HTH_9   3 cteiieehFGev 14 
                                       c  ii+++ G++
  gi|385805395|ref|YP_005841793.1| 112 CAKIIRDFIGKI 123
                                       677888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       932  (0.0519828); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 843.67
//
Query:       gi|385805396|ref|YP_005841794.1|  [L=170]
Description: heat shock protein Hsp20 [Fervidicoccus fontis Kam940]
Scores for complete 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   46.6   0.1    5.4e-12   45.1   0.1    1.7  2  ArsA_HSP20   HSP20-like domain found in ArsA
    5.7e-11   42.5   2.4    2.3e-09   37.3   2.4    2.3  1  HSP20        Hsp20/alpha crystallin family
     0.0092   16.4   0.1      0.015   15.7   0.1    1.3  1  PIH1_CS      PIH1 CS-like domain
  ------ inclusion threshold ------
       0.01   16.8   0.3      0.023   15.7   0.2    1.6  1  CS           CS domain
      0.037   14.1   0.0      0.063   13.4   0.0    1.4  1  GvpH         GvpH
        0.2   11.6   0.9       0.37   10.7   0.9    1.3  1  Stealth_CR3  Stealth protein CR3, conserved region 3


Domain annotation for each model (and alignments):
>> ArsA_HSP20  HSP20-like domain found in ArsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.11   3.2e+02      18      31 ..      83      96 ..      78      97 .. 0.86
   2 !   45.1   0.1   1.8e-15   5.4e-12       6      62 ..      94     153 ..      89     154 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.11
                        ArsA_HSP20 18 idlsrsgdeLtIki 31
                                      +d+++sg+ LtI +
  gi|385805396|ref|YP_005841794.1| 83 VDIFESGNLLTIVA 96
                                      799*********87 PP

  == domain 2  score: 45.1 bits;  conditional E-value: 1.8e-15
                        ArsA_HSP20   6 lkldLPfvdkeeidlsrsgdeLtIkignfrRq....itLPsvlarkevtsAkfedgvLeIr 62 
                                       ++++LP+v+k++id+  +++ L+I++ n  R+    i LP+ ++ +++ +A++++gvLe++
  gi|385805396|ref|YP_005841794.1|  94 IVAELPGVEKDKIDVKVVDSKLIIRASNGDRKyykeIELPKPVKPETA-KAQYKNGVLEVK 153
                                       6799***********************555555555**********66.**********97 PP

>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   2.4   7.6e-13   2.3e-09       2     101 ..      85     169 ..      84     170 .] 0.89

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 7.6e-13
                                       --SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--..---TT----SS---EEEEEE--STTB-TTT-EEEEET CS
                             HSP20   2 ikeeeeefevkldvpglkkeelkvkvednrvlvkgeheeeeedekglikerssrkFsrkftLPenvdadkvkaslkd 78 
                                       i e+ +  ++ +++pg++k+ ++vkv d ++++++ +                rk+ ++++LP+ v++++ ka++k+
  gi|385805396|ref|YP_005841794.1|  85 IFESGNLLTIVAELPGVEKDKIDVKVVDSKLIIRASNG----------D----RKYYKEIELPKPVKPETAKAQYKN 147
                                       66777788999***********************9998..........2....677889****************** PP

                                       TEEEEEEEBSS--..-------- CS
                             HSP20  79 GvLtvtvpkkepekkkkerkiqi 101
                                       GvL+v+++ ke+ek+ +  ki++
  gi|385805396|ref|YP_005841794.1| 148 GVLEVKIELKEREKE-EGHKIKV 169
                                       ************976.8888877 PP

>> PIH1_CS  PIH1 CS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   4.9e-06     0.015      33      89 ..      92     149 ..      85     157 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4.9e-06
                           PIH1_CS  33 laieielPllksikevklrvgerrleleskk..akyfLslkLpYpvdedkveAkFvkkt 89 
                                       l i  elP++ +  +++++v  ++l + + +   ky  +++Lp pv+ + ++A++++  
  gi|385805396|ref|YP_005841794.1|  92 LTIVAELPGV-EKDKIDVKVVDSKLIIRASNgdRKYYKEIELPKPVKPETAKAQYKNGV 149
                                       6778899**9.7799*********9998777789*********************7644 PP

>> CS  CS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   0.2   7.7e-06     0.023      10      74 ..      90     154 ..      84     157 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 7.7e-06
                                       TEEEEEEE-TTCTTTTTCEEEEEETTEEEEEE.TS.CEEEEECEBSS-BETTTEEEEEETTEEEEEE CS
                                CS  10 deVvvtiyvkkvnikkkdvkvefkerslkvki.gk.eklliegeLfgpIdpeesswtieskkveitL 74 
                                       + +++  ++++v  +k++++v+   ++l +   ++ +k ++e eL +p++pe ++   ++  +e+++
  gi|385805396|ref|YP_005841794.1|  90 NLLTIVAELPGV--EKDKIDVKVVDSKLIIRAsNGdRKYYKEIELPKPVKPETAKAQYKNGVLEVKI 154
                                       667899999999..666666666677766666556688999999**********9999988887765 PP

>> GvpH  GvpH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.1e-05     0.063      99     163 ..      88     154 ..      80     165 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.1e-05
                              GvpH  99 dsdelvvvadlpGvtdedvdvaletdeqaltlrv..ddd.vverlvlddpdvait.dltlrnqvlelrl 163
                                       +++ l +va+lpGv  +++dv +  d + l +r   +d    + + l +p    t +   +n vle+++
  gi|385805396|ref|YP_005841794.1|  88 SGNLLTIVAELPGVEKDKIDVKVV-DSK-LIIRAsnGDRkYYKEIELPKPVKPETaKAQYKNGVLEVKI 154
                                       677899***************998.443.3343311343144556666665544413445666666665 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 ?   10.7   0.9   0.00012      0.37      11      26 ..      17      32 ..      14      34 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00012
                       Stealth_CR3 11 vlkelerrfpeelart 26
                                       +ke+e++f+ee++r+
  gi|385805396|ref|YP_005841794.1| 17 FFKEIEDMFEEEFERM 32
                                      589***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1072.02
//
Query:       gi|385805397|ref|YP_005841795.1|  [L=126]
Description: hypothetical protein FFONT_0353 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.3e-09   35.1   0.0    0.00026   20.8   0.0    2.4  3  RHH_1     Ribbon-helix-helix protein, copG family
  ------ inclusion threshold ------
      0.017   15.3   0.8        1.4    9.1   0.1    2.4  3  RHH_8     Ribbon-Helix-Helix transcriptional regulator family
      0.097   12.6   0.0        1.5    8.8   0.0    2.2  2  RelB      RelB antitoxin


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 ?   -2.8   0.0       1.2   7.3e+03      18      29 ..       9      20 ..       8      20 .. 0.74
   2 !   11.8   0.0     3e-05      0.18       2      34 ..      27      60 ..      27      63 .. 0.94
   3 !   20.8   0.0   4.4e-08   0.00026       2      34 ..      85     118 ..      84     121 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.2
                                      HHHHTSSHHHHH CS
                             RHH_1 18 arrrgrSrSelI 29
                                      a++ ++Sr elI
  gi|385805397|ref|YP_005841795.1|  9 ADKKESSRFELI 20
                                      667789998887 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 3e-05
                                      EEEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHH CS
                             RHH_1  2 vsirldeellerLdelarrrg.rSrSelIReAlr 34
                                      vs+r+de+l++ ++   ++ g +SrS+ +R  ++
  gi|385805397|ref|YP_005841795.1| 27 VSFRVDENLKKWIESAWKENGfSSRSDYLRNIIE 60
                                      89*************************9998876 PP

  == domain 3  score: 20.8 bits;  conditional E-value: 4.4e-08
                                       EEEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHH CS
                             RHH_1   2 vsirldeellerLdelarrrg.rSrSelIReAlr 34 
                                       v++++d +lle+Ld+++++ g  +rS+++R+++ 
  gi|385805397|ref|YP_005841795.1|  85 VTFKIDNSLLEKLDKIVEKKGyYTRSDFLRDLFN 118
                                       89****************************9875 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 ?   -2.2   0.0      0.77   4.6e+03      28      53 ..      14      39 ..      12      45 .. 0.69
   2 ?    4.3   0.0    0.0072        43      24      43 ..      46      64 ..      39      73 .. 0.78
   3 ?    9.1   0.1   0.00024       1.4       6      36 ..      85     115 ..      81     124 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.77
                             RHH_8 28 snRtDlirtairaqLakhddalkqav 53
                                      s+R +li ++++    + d++lk+ +
  gi|385805397|ref|YP_005841795.1| 14 SSRFELIINSVKIVSFRVDENLKKWI 39
                                      56777777777776666677666655 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0072
                             RHH_8 24 eGfYsnRtDlirtairaqLa 43
                                      +G +s+R+D++r+ i + + 
  gi|385805397|ref|YP_005841795.1| 46 NG-FSSRSDYLRNIIEDVVI 64
                                      45.599*******9987665 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.00024
                             RHH_8   6 vtinlgvvDLgqiDlLveeGfYsnRtDlirt 36 
                                       vt  ++   L ++D +ve+  Y  R+D++r 
  gi|385805397|ref|YP_005841795.1|  85 VTFKIDNSLLEKLDKIVEKKGYYTRSDFLRD 115
                                       7888999999*******9766668*****96 PP

>> RelB  RelB antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00025       1.5       3      38 ..      26      62 ..      24      84 .. 0.76
   2 ?    1.7   0.0     0.042   2.5e+02       3      32 ..      84     114 ..      82     123 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00025
                                      EEEEEEEHHHHHHHHHHHHCCT--.HHHHHHHHHHHH CS
                              RelB  3 sislRidedlKaeatdvlekmGlt.iSqairlfLeki 38
                                      ++s+R+de+lK   + + ++ G +  S+ +r ++e +
  gi|385805397|ref|YP_005841795.1| 26 IVSFRVDENLKKWIESAWKENGFSsRSDYLRNIIEDV 62
                                      79**********9999999999862588887666554 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.042
                                       EEEEEEEHHHHHHHHHHHHCCT-.-HHHHHH CS
                              RelB   3 sislRidedlKaeatdvlekmGl.tiSqair 32 
                                       ++ + id++l  + ++++ek G  t S+ +r
  gi|385805397|ref|YP_005841795.1|  84 TVTFKIDNSLLEKLDKIVEKKGYyTRSDFLR 114
                                       68999**************999537777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       823  (0.0459033); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 798.43
//
Query:       gi|385805398|ref|YP_005841796.1|  [L=174]
Description: ZPR1-related zinc finger protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-24   86.9   0.9    1.5e-24   86.7   0.9    1.0  1  zf-ZPR1          ZPR1 zinc-finger domain
  ------ inclusion threshold ------
      0.023   15.1   0.0      0.045   14.1   0.0    1.5  1  Lar_restr_allev  Restriction alleviation protein Lar
      0.065   13.3   0.1       0.16   12.0   0.1    1.7  1  Elf1             Transcription elongation factor Elf1 like


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 !   86.7   0.9   2.5e-28   1.5e-24       2     158 ..      16     164 ..      15     165 .. 0.91

  Alignments for each domain:
  == domain 1  score: 86.7 bits;  conditional E-value: 2.5e-28
                           zf-ZPR1   2 lCpsCgkengetrlllt.kiPyfkeviimsfeCehCgyknnevksageieekGkritlkveseedlnrqvlkSetat 77 
                                       +Cp C+++n+     ++ ++P ++  +i+  +Ce+Cgy+ + + + +  ++  + i+lk+e+e+dln  ++  e + 
  gi|385805398|ref|YP_005841796.1|  16 DCPICKAKNSLVIREIIyDMPQYGMSLIVGAKCEKCGYRFSYIIPYEIGKK--RIIELKIENERDLNIIMFIGENTD 90 
                                       7****9888776666656***************************999999..9*********************** PP

                           zf-ZPR1  78 veipeleleippg.tlegrlttvEGlLeqikeelekeegdqaeredeekekieeflekleeliegeepftlildDpa 153
                                       +eipe++ ei ++   eg++ttvEGlL +i+e++++        +  +++++++ l ++++l++ +e+ft++l+D  
  gi|385805398|ref|YP_005841796.1|  91 IEIPEIKTEILSSeLDEGFVTTVEGLLVRIREQVKTI------CT--DEDNCKNYLMQIDRLLHLNEAFTIKLHDNY 159
                                       **********888799******************433......23..4789************************** PP

                           zf-ZPR1 154 gnSfi 158
                                       g + i
  gi|385805398|ref|YP_005841796.1| 160 GRTRI 164
                                       *9887 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   7.5e-06     0.045       3      56 ..      14      70 ..      12      71 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.5e-06
                   Lar_restr_allev  3 LkpCPfCggravlersqrvvaeigq.......cvyCadCgastpwfkiaedeaeaekeaie 56
                                      L +CP C+ ++ l+ ++  +    q          C++Cg+    f+++ +++  +k++ie
  gi|385805398|ref|YP_005841796.1| 14 LMDCPICKAKNSLVIREIIYDM-PQygmslivGAKCEKCGY---RFSYIIPYEIGKKRIIE 70
                                      679***********99888764.44699**9999*******...89999999988888886 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   0.1   2.7e-05      0.16      22      60 ..      15      60 ..       5      68 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.7e-05
                              Elf1 22 FdCpfCnheksvevkldkkek.......iaevsCkvCgesfetkvn 60
                                       dCp C++++s+ ++    +        i  ++C++Cg +f++ ++
  gi|385805398|ref|YP_005841796.1| 15 MDCPICKAKNSLVIREIIYDMpqygmslIVGAKCEKCGYRFSYIIP 60
                                      59*********88875444445678899999********9998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); 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: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 1070.87
//
Query:       gi|385805399|ref|YP_005841797.1|  [L=242]
Description: ABC transporter ATP-binding protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.4e-34  118.3   0.1      5e-34  117.7   0.1    1.2  1  ABC_tran      ABC transporter
    3.9e-06   26.5   0.6    0.00021   20.8   0.6    2.2  1  SMC_N         RecF/RecN/SMC N terminal domain
    3.7e-05   23.7   0.4      0.062   13.1   0.5    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    0.00026   20.7   0.1    0.00049   19.8   0.1    1.4  1  AAA_29        P-loop containing region of AAA domain
     0.0023   17.8   0.2     0.0051   16.7   0.2    1.6  1  RsgA_GTPase   RsgA GTPase
     0.0043   16.2   0.1     0.0077   15.3   0.0    1.6  2  T2SSE         Type II/IV secretion system protein
     0.0048   17.3   0.1     0.0096   16.3   0.1    1.6  1  AAA_16        AAA ATPase domain
     0.0055   17.0   0.0      0.024   14.9   0.0    1.9  2  AAA_22        AAA domain
     0.0065   17.0   0.4     0.0065   17.0   0.4    1.9  2  AAA_23        AAA domain
  ------ inclusion threshold ------
      0.013   14.3   0.0      0.019   13.7   0.0    1.2  1  RNA12         RNA12 protein
      0.014   15.3   0.0       0.12   12.3   0.0    2.0  2  Rad17         Rad17 P-loop domain
      0.019   14.9   0.1      0.032   14.2   0.1    1.7  1  ATPase_2      ATPase domain predominantly from Archaea
      0.021   15.4   0.0       0.25   11.9   0.0    2.2  2  AAA_18        AAA domain
      0.047   13.4   0.0       0.48   10.1   0.0    2.0  2  AAA_24        AAA domain
      0.055   12.6   0.2       0.11   11.7   0.2    1.7  1  NB-ARC        NB-ARC domain
      0.067   13.4   0.0        1.1    9.6   0.0    2.2  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
        0.1   12.3   0.0       0.16   11.7   0.0    1.4  1  PRK           Phosphoribulokinase / Uridine kinase family
       0.11   12.6   1.4       0.52   10.4   0.6    2.4  2  MMR_HSR1      50S ribosome-binding GTPase
       0.14   12.5   0.0       0.29   11.5   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 !  117.7   0.1   5.3e-37     5e-34       1     136 [.      27     176 ..      27     177 .. 0.88

  Alignments for each domain:
  == domain 1  score: 117.7 bits;  conditional E-value: 5.3e-37
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke....qeleslrkeigvlpqepqlfpe 73 
                                       lk ++l+++ ge + i+G++G+GKStL++++  l +p++G++ +dg d+ +    +  ++ +++ig+++q+ +l ++
  gi|385805399|ref|YP_005841797.1|  27 LKGINLTVRSGEFISIMGPSGSGKSTLMNIIGLLDRPNAGKVYIDGIDVAKlkdsEIAKIRNRKIGFVFQQFNLIQR 103
                                       789**********************************************9999988899999*************** PP

                                       SBHHHH...........HHHTC....HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEEST CS
                                       xxxxxx...........xxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  74 ltvren...........esdee....iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEp 135
                                       ltv+en           + +e+     e++l+  g+ ++ +++     ++LSgGq+qrva+aral+ kpkl+l+DEp
  gi|385805399|ref|YP_005841797.1| 104 LTVYENielpllirdisK-EEReklvREALLRAGGDLGWLKKKP----NQLSGGQQQRVAIARALVGKPKLILADEP 175
                                       **************9752.2222454455555555556666665....***************************** PP

                                       T CS
                                       x RF
                          ABC_tran 136 t 136
                                       t
  gi|385805399|ref|YP_005841797.1| 176 T 176
                                       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 !   20.8   0.6   2.2e-07   0.00021      24     212 ..      37     221 ..      24     226 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.2e-07
                                       SSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  24 ksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsis 100
                                        +f +i+Gp GSGKs l++ i  +L        r +  +  i    + a++k  e++ + +n +       +++++ 
  gi|385805399|ref|YP_005841797.1|  37 GEFISIMGPSGSGKSTLMNII-GLLD-------RPNAGKVYIDG-IDVAKLKDSEIAKI-RNRKIG--FVFQQFNLI 101
                                       46999*************999.3333.......45555555665.67777888887775.333333..344445555 PP

                                       EEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT...........CS-HHHHHHHHHHHHHHHHCCS--SEEEECT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 101 rrvkrkgeseykingkevtkkevsellesagiske...........lLSgGektLvalaLlfAiqkvkpaplyllDe 166
                                       +r+   ++ e  +  ++++k+e ++l+++a +              +LSgG+++ va+a       v +  l l De
  gi|385805399|ref|YP_005841797.1| 102 QRLTVYENIELPLLIRDISKEEREKLVREALLRAGgdlgwlkkkpnQLSGGQQQRVAIARA----LVGKPKLILADE 174
                                       5555555556666667788888888888888887788888888888********9998755....3556669999** PP

                                       TTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-SCEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 167 idaaLDeknvkkvaellkekskn.aQfivislreemlekadklvgvt 212
                                          +LD    ++v e lke +k    +i ++++ e+ + a+k++ ++
  gi|385805399|ref|YP_005841797.1| 175 PTGNLDRDSGRIVMETLKELNKAgETIILVTHDIEVGNCAQKIYYIK 221
                                       ********************999566778999999999999998876 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 !   13.1   0.5   6.6e-05     0.062       4      24 ..      42      62 ..      39     125 .. 0.77
   2 !    8.8   0.0    0.0013       1.2     235     299 ..     147     208 ..     105     210 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.6e-05
                            AAA_21  4 liGpNgsGKSnLLdaldllar 24
                                      + Gp gsGKS+L+ ++ ll r
  gi|385805399|ref|YP_005841797.1| 42 IMGPSGSGKSTLMNIIGLLDR 62
                                      78**************99844 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0013
                            AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSp 299
                                       ++lS G+++  a++ al     k++l+l DEp  +L+    r ++e lkel++ g  +il+TH+ 
  gi|385805399|ref|YP_005841797.1| 147 NQLSGGQQQRVAIARALVG---KPKLILADEPTGNLDRDSGRIVMETLKELNKAGETIILVTHDI 208
                                       5668888888566666665...449**************************************96 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.1   5.2e-07   0.00049      16      39 ..      31      54 ..      22      67 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5.2e-07
                            AAA_29 16 tieidlkgatlltGpsGsGKSTll 39
                                       ++++  +++ ++GpsGsGKSTl+
  gi|385805399|ref|YP_005841797.1| 31 NLTVRSGEFISIMGPSGSGKSTLM 54
                                      55666445999************9 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.2   5.4e-06    0.0051      90     119 ..      27      57 ..       2      68 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.4e-06
                                       HHHHHHHCTT.SEEEEECSTTSSHHHHHHHH CS
                       RsgA_GTPase  90 leelkellkd.ktsvlvGqSGvGKStLinal 119
                                       l+ ++  +++ +++ ++G+SG GKStL+n +
  gi|385805399|ref|YP_005841797.1|  27 LKGINLTVRSgEFISIMGPSGSGKSTLMNII 57 
                                       555555555558999**************86 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   8.2e-06    0.0077     104     149 ..      12      57 ..       3     106 .. 0.89
   2 ?   -3.2   0.0       3.6   3.4e+03     149     168 ..     190     209 ..     154     217 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 8.2e-06
                             T2SSE 104 tlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyal 149
                                       +++++ ++++ + +i + ++  vr+   i + G+ gsGK+tl++++
  gi|385805399|ref|YP_005841797.1|  12 NIHKIYKTGEIEYHILKGINLTVRSGEFISIMGPSGSGKSTLMNII 57 
                                       7888999999999******************************975 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.6
                             T2SSE 149 llkeinksderivtvEDpvE 168
                                        lke+nk  e i++v   +E
  gi|385805399|ref|YP_005841797.1| 190 TLKELNKAGETIILVTHDIE 209
                                       46667777666666655555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1     1e-05    0.0096      18      52 ..      33      90 ..      21     209 .. 0.60

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1e-05
                            AAA_16 18 rvrsgrpelvllsGesGvGKsslvrellralekd..........................g 52
                                      +vrsg  e + + G+sG+GKs+l++ +   l +                           +
  gi|385805399|ref|YP_005841797.1| 33 TVRSG--EFISIMGPSGSGKSTLMNIIG-LLDRPnagkvyidgidvaklkdseiakirnrK 90
                                      56666..78**************97665.44444444455555555555555555555543 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.5e-05     0.024       4      26 ..      36      58 ..      34      90 .. 0.83
   2 ?   -0.4   0.0       1.4   1.3e+03      79     105 ..     156     183 ..     103     209 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.5e-05
                            AAA_22  4 tagilvvtGesGtGKTtllrrll 26
                                      +  ++ ++G+sG+GK+tl++ + 
  gi|385805399|ref|YP_005841797.1| 36 SGEFISIMGPSGSGKSTLMNIIG 58
                                      67899*************98665 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.4
                            AAA_22  79 lealeqalraravielliiDEaqh.lr..s 105
                                       + a+++al  + +  l++ DE    l+  s
  gi|385805399|ref|YP_005841797.1| 156 RVAIARALVGKPK--LILADEPTGnLDrdS 183
                                       3344444444444..777777554455442 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.4   6.8e-06    0.0065       3      40 ..       9      58 ..       8      60 .. 0.77
   2 ?   -0.9   0.5       2.2     2e+03     160     160 ..     117     117 ..      66     202 .. 0.58

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.8e-06
                            AAA_23  3 kienfrsf.rdqeidF...........skgltlItGpNGaGKTTildAik 40
                                      ++en++++ +  ei+            s  +  I Gp G+GK+T+++ i 
  gi|385805399|ref|YP_005841797.1|  9 RLENIHKIyKTGEIEYhilkginltvrSGEFISIMGPSGSGKSTLMNIIG 58
                                      788888886556777767666666777777889*************9885 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.2
                            AAA_23 160 k 160
                                       +
  gi|385805399|ref|YP_005841797.1| 117 R 117
                                       2 PP

>> RNA12  RNA12 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0     2e-05     0.019      17      72 ..      37      93 ..      28     105 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2e-05
                             RNA12 17 ntFivvkGPrGSGkkeLvldrvlkdrkk..vlvidCdelvkarndaelisaaAsqlGY 72
                                        Fi + GP GSGk+ L+    l dr +  +++id  +++k + d+e+ +   +++G+
  gi|385805399|ref|YP_005841797.1| 37 GEFISIMGPSGSGKSTLMNIIGLLDRPNagKVYIDGIDVAKLK-DSEIAKIRNRKIGF 93
                                      57***************977788888888999**999999976.45555555556665 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00013      0.12      27     113 ..      18     111 ..       7     124 .. 0.68
   2 ?    0.9   0.0      0.39   3.7e+02     127     176 ..     161     209 ..     147     216 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                             Rad17  27 kieevk.ewlkadvLesrkkriLLisGPsGCgkstvvkvLsk....elgiklrewlnpvslkepdnqksdfkgltek 98 
                                       k  e++ + lk   L  r  + + i GPsG gkst ++++      + g  +++ ++  +lk+++  k   + +  +
  gi|385805399|ref|YP_005841797.1|  18 KTGEIEyHILKGINLTVRSGEFISIMGPSGSGKSTLMNIIGLldrpNAGKVYIDGIDVAKLKDSEIAKIRNRKIGFV 94 
                                       666676245777888888889999***********999875311124455667777777777777655555555555 PP

                             Rad17  99 esrf..lsqiesfkele 113
                                       +++f  + ++ +++++e
  gi|385805399|ref|YP_005841797.1|  95 FQQFnlIQRLTVYENIE 111
                                       55555455566666555 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.39
                             Rad17 127 ddlrtdkklilvedlPnkfyrds.dalrevirkylrssealplilviteie 176
                                         l ++ klil ++   +  rds + + e +++  + +e+  +ilv  +ie
  gi|385805399|ref|YP_005841797.1| 161 RALVGKPKLILADEPTGNLDRDSgRIVMETLKELNKAGET--IILVTHDIE 209
                                       556789999*999988999999966677777777777776..666666554 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 ?   14.2   0.1   3.4e-05     0.032      20      58 ..      37      74 ..      25     221 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.4e-05
                          ATPase_2 20 neiyfiYGpegsGKtaLlkeiienledkdkyviyyialr 58
                                       e++ i Gp gsGK++L++ ii  l+  +  ++y++ + 
  gi|385805399|ref|YP_005841797.1| 37 GEFISIMGPSGSGKSTLMN-IIGLLDRPNAGKVYIDGID 74
                                      67899************96.8888888899999987543 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00027      0.25       1      18 [.      40      57 ..      40     134 .. 0.72
   2 ?    1.4   0.0      0.47   4.4e+02      50      95 ..     177     219 ..     149     225 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00027
                            AAA_18  1 IlltGtpGvGKttlakeL 18
                                      I ++G++G+GK+tl + +
  gi|385805399|ref|YP_005841797.1| 40 ISIMGPSGSGKSTLMNII 57
                                      679***********9988 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.47
                            AAA_18  50 krldedkldklldaleenssaleegknlvidghlaeleseaakdik 95 
                                         ld+d    ++++l+e ++    g+++++  h  e    a+k+++
  gi|385805399|ref|YP_005841797.1| 177 GNLDRDSGRIVMETLKELNK---AGETIILVTHDIEVGNCAQKIYY 219
                                       56677777788899999876...89999999999999888888765 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00051      0.48       5      22 ..      40      57 ..      37     105 .. 0.83
   2 ?    1.1   0.0       0.3   2.8e+02     111     131 ..     187     207 ..     181     215 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00051
                            AAA_24  5 iliyGpsgiGKTtlakel 22
                                      i i+Gpsg+GK+tl++ +
  gi|385805399|ref|YP_005841797.1| 40 ISIMGPSGSGKSTLMNII 57
                                      679***********9876 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.3
                            AAA_24 111 frrllkklqelrknvifiahe 131
                                       ++++lk l+++++++i++ h 
  gi|385805399|ref|YP_005841797.1| 187 VMETLKELNKAGETIILVTHD 207
                                       5678888999999*****996 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   0.2   0.00011      0.11      21      40 ..      38      57 ..      25     227 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                                      EEEEEEESTTSSHHHHHHHH CS
                            NB-ARC 21 lvvalvGmgGvGKttlakqi 40
                                       +++++G  G+GK+tl++ i
  gi|385805399|ref|YP_005841797.1| 38 EFISIMGPSGSGKSTLMNII 57
                                      489*************9866 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 ?    9.6   0.0    0.0011       1.1      18      89 ..     134     192 ..     122     193 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0011
                           SbcCD_C  18 dedgkekelsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                       +++g  ++l+++ ++lSGG++q    +a+a   +al+++       ++l++ DE  ++lD +s + ++e+l+
  gi|385805399|ref|YP_005841797.1| 134 RAGGDLGWLKKKPNQLSGGQQQR---VAIA---RALVGK-------PKLILADEPTGNLDRDSGRIVMETLK 192
                                       47788888999999999999954...3444...233333.......78888888888888888888888876 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    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       1      39 [.      39      76 ..      39     101 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
                               PRK  1 vIgvagsSGaGkttvarklekifgrekvkaaeiegdsfl 39
                                      +I++ g+SG+Gk+t+++ +  ++ r +   ++i+g+ + 
  gi|385805399|ref|YP_005841797.1| 39 FISIMGPSGSGKSTLMNII-GLLDRPNAGKVYIDGIDVA 76
                                      69************99765.4566666666666666555 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.6   0.00055      0.52       2      19 ..      40      57 ..      39      69 .. 0.89
   2 ?   -0.8   0.0       1.6   1.5e+03      60      77 ..     181     199 ..     152     233 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00055
                                      EEEEESTTSSHHHHHHHH CS
                          MMR_HSR1  2 vaivGrpNvGKStLinal 19
                                      + i+G + +GKStL+n +
  gi|385805399|ref|YP_005841797.1| 40 ISIMGPSGSGKSTLMNII 57
                                      789*************75 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.6
                                       HHHHHHHHHHHHHHHCT.S CS
                          MMR_HSR1  60 aseekglgkaflaleea.d 77 
                                        ++++ + +++++l++a +
  gi|385805399|ref|YP_005841797.1| 181 RDSGRIVMETLKELNKAgE 199
                                       3333345555555555422 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00031      0.29       2      18 ..      41      57 ..      40      78 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00031
                      RNA_helicase  2 wlyGpsgeGKStlakeL 18
                                       + Gpsg GKStl++ +
  gi|385805399|ref|YP_005841797.1| 41 SIMGPSGSGKSTLMNII 57
                                      689***********983 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); 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: 0.65u 0.34s 00:00:00.99 Elapsed: 00:00:00.52
# Mc/sec: 1390.20
//
Query:       gi|385805400|ref|YP_005841798.1|  [L=84]
Description: methionyl-tRNA synthetase [Fervidicoccus fontis Kam940]
Scores for complete 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   0.0    2.9e-14   52.9   0.0    1.1  1  tRNA_bind  Putative tRNA binding domain


Domain annotation for each model (and alignments):
>> tRNA_bind  Putative tRNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   0.0   1.6e-18   2.9e-14       1      64 [.      19      83 ..      19      84 .] 0.97

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 1.6e-18
                                      EEEEEEEEEEEETTSSTEEEEEEEESSSS.EEEEEESCTTTSTHHHHTTEEEEEETTSESEEETT CS
                         tRNA_bind  1 lrvGkvleaeehpnadkLlvlkvdvGeee.prqivsgaknvyepeelvakkvvvvanlkpkklrG 64
                                      +r+G +  ae++p++ kLl+l++d+G  +  rqi+sg+++ y+peelv+kkv v+ nlkpk++ G
  gi|385805400|ref|YP_005841798.1| 19 IRIGLIKFAEKIPGSHKLLRLIIDLGPSIgERQIISGIAESYKPEELVGKKVPVLTNLKPKNFWG 83
                                      79*************************9999******************************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       180  (0.0100396); expected 358.6 (0.02)
Passed bias filter:                      178  (0.00992805); 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 0.28s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 592.51
//
Query:       gi|385805401|ref|YP_005841799.1|  [L=168]
Description: transcription elongation factor NusA-like protein [Fervidicoccus fontis Kam940]
Scores for complete 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-06   26.5   0.6    3.9e-05   23.7   0.6    2.2  1  KH_5           NusA-like KH domain
     0.0012   18.7   4.4      0.045   13.5   0.0    2.1  2  Ribosomal_S7e  Ribosomal protein S7e


Domain annotation for each model (and alignments):
>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.6   4.3e-09   3.9e-05      30      68 ..      84     121 ..      62     122 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 4.3e-09
                              KH_5  30 ikavsseLkgekidvvewseDlaefianalsPaevlsVk 68 
                                        ka+s++L + ++++ve + Dl++++ ++lsP+++  V+
  gi|385805401|ref|YP_005841799.1|  84 AKALSEKL-NVRVQIVEDTRDLKKLASELLSPVRIVGVN 121
                                       6899****.****************************98 PP

>> Ribosomal_S7e  Ribosomal protein S7e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.3   2.5    0.0016        14       8      80 ..      26      93 ..      21     102 .. 0.75
   2 !   13.5   0.0   5.1e-06     0.045     123     175 ..     108     160 ..     100     168 .] 0.91

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0016
                                      S---HHHHHHHHHHHHHHHHTSSCHHHHTT--ECEEEEEEETSSCEEEEEEEEHHHHHHTTTCHHHHHHHHHH CS
                     Ribosomal_S7e  8 eepteleeqvaqalldleanssdlkaelrelqissakevevkkkkkaivifvpvpllkafqkiqqrlvreLeK 80
                                       ++++ e  v +al++le++ +++k  l++l+    + +   ++  +iv+   +++  + +k+ ++l ++L+ 
  gi|385805401|ref|YP_005841799.1| 26 GKVDKKEIPVMKALIELEEE-KEFK-FLKDLNYI--RTIWS-EDLCVIVVKSDMQSQYQLKKVAKALSEKLNV 93
                                      5789999*************.9999.78888643..33332.4556677777777777788888888888765 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 5.1e-06
                                       HHHHCTTS-EEEEEEEE-SSS-EEEEEEEESCTCCCHHHHHHHHHHHHHHHHS CS
                     Ribosomal_S7e 123 LedlvyPseivGkrirvrldgskllkvfLdkkdqnnveekldtfsavykkLtg 175
                                         +l+ P+ ivG  +    dg+  + + + k d++ + +k++ +++v++kL +
  gi|385805401|ref|YP_005841799.1| 108 ASELLSPVRIVGVNTIWLPDGTTEYVIRISKYDARALPTKVEVLEDVFHKLFK 160
                                       5789**********************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1378  (0.0768587); expected 358.6 (0.02)
Passed bias filter:                      842  (0.046963); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1128.00
//
Query:       gi|385805402|ref|YP_005841800.1|  [L=447]
Description: amino acid transporter [Fervidicoccus fontis Kam940]
Scores for complete 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-37  127.3  55.3    8.1e-37  127.0  55.3    1.1  1  AA_permease_2  Amino acid permease
    6.4e-28   97.6  45.6    8.5e-28   97.2  45.6    1.0  1  AA_permease    Amino acid permease


Domain annotation for each model (and alignments):
>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.0  55.3     9e-41   8.1e-37       2     402 ..      12     408 ..      11     435 .. 0.77

  Alignments for each domain:
  == domain 1  score: 127.0 bits;  conditional E-value: 9e-41
                     AA_permease_2   2 sllsafalvigsvig...sgifvknlaasggpa.lilwvwiavligslavllvyaElssalprsgGiyvytkaafgk 74 
                                       +++  + lv+g++ +   +g++++  +  +gpa +++w++++++ g+la+ l+y  ++  + + g +y  +++a gk
  gi|385805402|ref|YP_005841800.1|  12 GWFVSASLVLGTLGSnglFGNYPV-TYRIAGPAaSFVWIVTMIFGGFLAMTLAYD-FTIWPDKAGSEYAPVRIALGK 86 
                                       677778888888755223445555.444488875788888888888899998884.454489*************** PP

                     AA_permease_2  75 kvaflsawfnwfayvpvlasilsvaasyllnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilk 151
                                       +++ l+aw + +++  ++++++ + + y+   ++     +t++t++ + + ++++++in++gik  + + +i+++l 
  gi|385805402|ref|YP_005841800.1|  87 YLGGLTAWGFYVSWGTAATIGTLITGWYIWP-TN-----TTYQTIFTG-VTVTVFFIINYFGIKLAGLAEVIMTLLR 156
                                       ************9998776666655555544.43.....555666655.55678999******************** PP

                     AA_permease_2 152 illpliiliilglitvdgggfssl.......stetdtffpngwpg..vllglli....vlwsfdGfesaanvseevk 215
                                       i +p i++ ++++ +v+ + f+         +       ++ +++  +++ +l+    ++ws+++ +  a+++ e+k
  gi|385805402|ref|YP_005841800.1| 157 I-VPTIFVGLVAIPYVNLSNFHPFwvasseiP------GASANSLygMFMLFLAaslySTWSTYATDIFASIVPEIK 226
                                       *.7*************7777663332222221......222222222455555555559****************66 PP

                     AA_permease_2 216 k..kdvpkaifigllivlvlyllvniaflgvvpddeianlsnlgsvaalffeavggkvvaiivvilialsllgaint 290
                                          k+vp+a+  + li l++  l++i+ +gv++ d  +  ++l      + + v g+v+ ++++ +++ + l ++n 
  gi|385805402|ref|YP_005841800.1| 227 DpeKNVPRAGLASTLIPLLFVSLITITGIGVLGSDLGTGEAPLF----EYSRIVLGGVGLALMWTALISGTLTNANV 299
                                       555******************************99988766644....56666678999****************** PP

                     AA_permease_2 291 avigssrvlealardgvlPrffakvnkfgspiraiiltaivslillllfllassaaynfllsvsslgliisylllii 367
                                       a+ig srvl+++a +g +P+ fak+nk+g pi ++i+t+i+++++ll + +     y +l++++++++++ ++ll++
  gi|385805402|ref|YP_005841800.1| 300 AMIGGSRVLYQMAVEGDIPKIFAKTNKYGVPIIGLIFTYIINIAMLLYTPI-----YAILVAMFQVPYMLTIFLLSV 371
                                       ******************************************877766666.....89******************* PP

                     AA_permease_2 368 galilrkkrp.hlkr.pgk..ilvaiigalfllfllval 402
                                       + l++r +++ h+k  +++  +l+  ++++++l l  + 
  gi|385805402|ref|YP_005841800.1| 372 ANLKIRATKEwHEKAaWKApwWLIIGFFIIGVLSL--MY 408
                                       ******99886776655553333333334444333..33 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.2  45.6   9.5e-32   8.5e-28       7     438 ..      21     417 ..      16     444 .. 0.79

  Alignments for each domain:
  == domain 1  score: 97.2 bits;  conditional E-value: 9.5e-32
                       AA_permease   7 lggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGlnyl 83 
                                       lg + + glf    v+ + aGp++ ++ ++ +++  fl+m   + + +   k+g+ y+ ++  lg+ lG+ +++ + 
  gi|385805402|ref|YP_005841800.1|  21 LGTLGSNGLFGNYPVTYRIAGPAASFVWIVTMIFGGFLAMTLAYDFTIWPDKAGSEYAPVRIALGKYLGGLTAWGFY 97 
                                       3444448999999999999*******************9999999977777************************99 PP

                       AA_permease  84 fswitvlaleltaasiliqfwelvtdlpkawvtgavflvvlliinlvgvkvygeaefilalikiiaiiafiivgiil 160
                                       +sw t++++++ + + +  +w ++t +  ++ tg v+++v++iin++g+k+ g ae+i++l+ i+  i + +v  i+
  gi|385805402|ref|YP_005841800.1|  98 VSWGTAATIGTLITGWY--IWPTNTTYQ-TIFTG-VTVTVFFIINYFGIKLAGLAEVIMTLLRIVPTIFVGLVA-IP 169
                                       99999999886666665..463344444.44555.*************************99988876544444.44 PP

                       AA_permease 161 laggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkdPeksiPkail 237
                                        ++  + +     f+ ++++     +p+  a++ +g f+ f+++   +  +   + + a i  E+kdPek++P+a l
  gi|385805402|ref|YP_005841800.1| 170 YVNLSNFHP----FWVASSE-----IPGASANSLYGMFMLFLAASLYSTWSTYATDIFASIVPEIKDPEKNVPRAGL 237
                                       444444444....4555555.....55554589999***************************************99 PP

                       AA_permease 238 qvviritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaalssansslysasRv 314
                                          ++  +++v ++ + g++v  +dlg  +     a++f++    +g  +la     ++++ +l  an +++ +sRv
  gi|385805402|ref|YP_005841800.1| 238 ASTLIP-LLFVSLITITGIGVLGSDLGTGE-----APLFEYSRIVLGGVGLALM-WTALISGTLTNANVAMIGGSRV 307
                                       877655.55666666677788888989999.....6899999999999999865.55556667777899999***** PP

                       AA_permease 315 lyslakdglaPkvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwlliilsylrfR 391
                                       ly +a +g +Pk+++k +k+gvP+ ++++++ii  ++l    l+++   ++++l+a+  +  +++  l +++ l++R
  gi|385805402|ref|YP_005841800.1| 308 LYQMAVEGDIPKIFAKTNKYGVPIIGLIFTYIINIAML----LYTP---IYAILVAMFQVPYMLTIFLLSVANLKIR 377
                                       **********************************9999....5566...5666777777766666556666666677 PP

                       AA_permease 392 kalkyqgrsieelgfkaallplgvilvlaaliiillilalyayltvk 438
                                        +++ +++        a+ +p+++i++++++  + l++ +++ + ++
  gi|385805402|ref|YP_005841800.1| 378 ATKEWHEK-------AAWKAPWWLIIGFFIIGVLSLMYCWAYGILFG 417
                                       77555555.......568899********999999999998766544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 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:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.35s 00:00:00.97 Elapsed: 00:00:00.50
# Mc/sec: 2670.84
//
Query:       gi|385805403|ref|YP_005841801.1|  [L=121]
Description: peptidyl-tRNA hydrolase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-41  139.7   0.0    5.5e-41  139.5   0.0    1.0  1  PTH2      Peptidyl-tRNA hydrolase PTH2


Domain annotation for each model (and alignments):
>> PTH2  Peptidyl-tRNA hydrolase PTH2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.5   0.0     3e-45   5.5e-41       1     117 []       3     121 .]       3     121 .] 0.96

  Alignments for each domain:
  == domain 1  score: 139.5 bits;  conditional E-value: 3e-45
                                       EEEEEEEESSSSS-HHHHHHHHHHHHHHHHHHHHHH.CH...HHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHHHT CS
                              PTH2   1 lkmvlvvrkDLkmskGkiaaqcahAavalvkkllkesne...kellkeWeeegqkkivlkveseeeLlelaakakal 74 
                                       +k+v+v rkDL +s Gk+aaq+ahA+v++v ++l+++ +   k++l+eW++egqkk+vlkv+s +eLl  +++ak+l
  gi|385805403|ref|YP_005841801.1|   3 CKQVIVARKDLRLSPGKLAAQVAHASVECVLQILNSN-RnewKKWLEEWIKEGQKKVVLKVSSLDELLVYYNNAKSL 78 
                                       79*******************************9985.335789********************************* PP

                                       T-SEEEEEETSSSSSSTTCEEEEEEEEEEHHHHHHHHTTSEB- CS
                              PTH2  75 glpaalirDagrtqiepgtkTvlaigPapksivdkvtgkLkll 117
                                       glpa+li+Dag tq++ gt T+++igPap+++vdk+tg L l+
  gi|385805403|ref|YP_005841801.1|  79 GLPASLIKDAGLTQVPEGTITAVGIGPAPEELVDKITGMLDLY 121
                                       ****************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      594  (0.0331307); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 816.37
//
Query:       gi|385805404|ref|YP_005841802.1|  [L=92]
Description: translation elongation factor 1B (aEF-1B) [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-15   55.8   0.0    4.5e-15   55.6   0.0    1.0  1  EF1_GNE   EF-1 guanine nucleotide exchange domain


Domain annotation for each model (and alignments):
>> EF1_GNE  EF-1 guanine nucleotide exchange domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.6   0.0   2.5e-19   4.5e-15       2      90 .]       6      89 ..       5      89 .. 0.94

  Alignments for each domain:
  == domain 1  score: 55.6 bits;  conditional E-value: 2.5e-19
                                      EEEEEEESSS---HHHHHHHHHH.HS-T.SEE--.--EEE-SSS-EEEEEEEEES.SS-GGGGHHHHHHTTS-S..... CS
                           EF1_GNE  2 vvlevkPeddetdleelekkvksikleg.lvwgeasklepiafGlkkLqiscvie.ddkvstdeleekieeiegeledl 78
                                      v l++ P+d+e   ee+++k+++ +l++ + + +   +epiafG ++L+++++ + +++++t++lee ++ ie+     
  gi|385805404|ref|YP_005841802.1|  6 VSLKIYPKDAEAKREEVADKIRK-ALPQdYIIIK-ASEEPIAFGYTALKLYLTFPeETEGGTEKLEEILRGIED----- 77
                                      789********************.9999899996.99*****************978899**************..... PP

                                      SEEEEEEEEEE- CS
                           EF1_GNE 79 Vqsveivsfnkl 90
                                      +   ei+s+++l
  gi|385805404|ref|YP_005841802.1| 78 IDDFEIESVSRL 89
                                      *********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); 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 0.28s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 594.24
//
Query:       gi|385805405|ref|YP_005841803.1|  [L=731]
Description: AAA family ATPase-domain containing protein [Fervidicoccus fontis Kam940]
Scores for complete 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-98  324.0   0.0    4.3e-48  163.1   0.0    2.4  2  AAA              ATPase family associated with various cellul
    4.9e-37  125.5   2.0    4.5e-19   68.0   0.6    2.7  2  AAA_lid_3        AAA+ lid domain
    3.5e-36  123.3   0.6    4.6e-35  119.7   1.4    2.5  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
    1.6e-14   53.9   0.0    7.2e-07   29.1   0.0    2.7  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      3e-14   52.6   1.1    9.5e-14   50.9   1.1    1.9  1  CDC48_2          Cell division protein 48 (CDC48), domain 2
    3.6e-14   53.5   0.3    1.2e-05   25.7   0.1    3.9  3  AAA_16           AAA ATPase domain
    3.5e-12   46.5   1.0    7.2e-05   22.8   0.1    3.7  2  AAA_5            AAA domain (dynein-related subfamily)
    1.1e-11   45.2   0.0    2.5e-05   24.5   0.0    2.6  2  AAA_2            AAA domain (Cdc48 subfamily)
    7.9e-11   42.4   1.2     0.0083   16.4   0.0    4.3  4  AAA_22           AAA domain
    1.8e-10   40.6   0.2    0.00017   20.9   0.0    2.7  2  TIP49            TIP49 P-loop domain
    3.5e-10   40.2   0.0    0.00042   20.5   0.0    2.7  2  AAA_33           AAA domain
    6.3e-09   36.0   0.0     0.0012   18.8   0.0    2.5  2  AAA_14           AAA domain
    4.3e-08   33.0   0.2      0.012   15.3   0.1    4.1  3  Sigma54_activat  Sigma-54 interaction domain
    1.8e-07   31.5   0.0      0.015   15.6   0.0    2.6  2  AAA_28           AAA domain
    4.1e-07   30.6   0.0      0.048   14.2   0.0    2.8  2  AAA_18           AAA domain
    4.3e-07   29.5   0.5     0.0078   15.6   0.1    2.6  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    4.4e-07   29.8   0.0      0.012   15.3   0.0    2.6  2  IstB_IS21        IstB-like ATP binding protein
    5.2e-07   29.1   0.0      0.035   13.3   0.0    2.6  2  DUF815           Protein of unknown function (DUF815)
    1.3e-06   28.3   0.1    0.00051   20.0   0.0    2.9  2  Vps4_C           Vps4 C terminal oligomerisation domain
    4.2e-06   26.5   3.4       0.23   11.0   0.2    4.3  3  AAA_25           AAA domain
    4.3e-06   26.6   0.2      0.078   12.7   0.1    2.8  2  AAA_24           AAA domain
    6.3e-06   26.5   0.0       0.17   12.3   0.0    2.7  2  RNA_helicase     RNA helicase
    6.4e-06   25.7   0.5       0.37   10.1   0.0    3.5  3  ATPase           KaiC
    7.3e-06   25.4   0.0       0.03   13.6   0.0    2.6  2  Zeta_toxin       Zeta toxin
    8.3e-06   25.9   0.2       0.84    9.5   0.1    3.9  3  ATPase_2         ATPase domain predominantly from Archaea
    1.1e-05   25.4   0.4        0.3   11.0   0.0    3.7  4  NACHT            NACHT domain
      2e-05   24.2   0.0       0.29   10.6   0.0    2.8  2  AAA_7            P-loop containing dynein motor region
      3e-05   23.9   0.0       0.19   11.6   0.0    2.7  2  AAA_3            ATPase family associated with various cellul
    4.5e-05   24.0   0.0       0.42   11.1   0.0    2.5  2  ABC_tran         ABC transporter
    6.8e-05   22.9   0.0       0.62   10.1   0.0    2.7  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    0.00014   21.0   0.7       0.38    9.8   0.0    2.6  3  Parvo_NS1        Parvovirus non-structural protein NS1
    0.00026   20.5   1.2       0.27   10.7   0.0    2.8  2  PhoH             PhoH-like protein
    0.00026   20.9   0.0       0.11   12.3   0.0    2.9  2  Bac_DnaA         Bacterial dnaA  protein
    0.00033   20.0   0.0      0.095   11.9   0.0    2.5  2  DUF2075          Uncharacterized conserved protein (DUF2075)
    0.00053   19.2   0.0       0.84    8.8   0.0    3.0  3  NB-ARC           NB-ARC domain
    0.00064   19.9   0.0        1.9    8.6   0.0    2.8  2  Sigma54_activ_2  Sigma-54 interaction domain
    0.00081   19.7   1.7        2.5    8.4   0.0    3.1  3  AAA_19           AAA domain
    0.00084   18.9   0.1      0.005   16.3   0.1    2.1  2  UFD1             Ubiquitin fusion degradation protein UFD1
      0.001   18.8   0.3          1    9.1   0.0    2.5  2  AAA_30           AAA domain
     0.0086   16.5   0.0          7    7.1   0.0    2.8  2  AAA_17           AAA domain
     0.0099   15.8   2.9        7.1    6.5   0.0    4.4  5  NTPase_1         NTPase
  ------ inclusion threshold ------
       0.01   15.6   0.1        7.8    6.1   0.0    3.8  4  Guanylate_kin    Guanylate kinase
      0.012   15.4   0.0        4.9    6.8   0.0    2.3  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.017   14.9   0.0        1.5    8.6   0.0    2.3  2  AAA_11           AAA domain
      0.017   14.0   0.0        1.7    7.5   0.0    2.4  2  AFG1_ATPase      AFG1-like ATPase
      0.022   14.2   0.0        3.6    7.0   0.0    3.0  3  TniB             Bacterial TniB protein
      0.023   14.5   0.0        6.4    6.5   0.0    2.6  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
      0.023   14.1   0.2        6.4    6.1   0.0    2.4  2  IPT              Isopentenyl transferase
      0.042   13.7   0.0        6.1    6.6   0.0    2.5  2  CPT              Chloramphenicol phosphotransferase-like prot
      0.059   13.0   0.0        7.5    6.1   0.0    2.5  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
      0.059   12.5   0.0        7.5    5.6   0.0    2.7  2  MCM              MCM P-loop domain
      0.089   12.6   0.0         11    5.9   0.0    2.3  2  AAA_29           P-loop containing region of AAA domain
      0.091   12.0   0.1       0.67    9.2   0.2    2.2  2  DUF2130          Uncharacterized protein conserved in bacteri
        0.1   12.2   0.0       0.61    9.7   0.0    2.2  2  Zot              Zonular occludens toxin (Zot)
       0.21   11.7   0.6         22    5.2   0.2    2.6  2  DUF1905          Domain of unknown function (DUF1905)


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 !  163.1   0.0   1.3e-50   4.3e-48       1     132 []     220     350 ..     220     350 .. 0.98
   2 !  158.7   0.0   3.1e-49     1e-46       1     131 [.     493     623 ..     493     624 .. 0.97

  Alignments for each domain:
  == domain 1  score: 163.1 bits;  conditional E-value: 1.3e-50
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTC CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgs 77 
                                       vllyG pGtGKTllakava+e++++f+ i+g+e++sk+ gese+++re+f+eak++  p i+fiDEida+a++r++ 
  gi|385805405|ref|YP_005841803.1| 220 VLLYGAPGTGKTLLAKAVANETQAYFVAINGPEIMSKFYGESEQRLREIFEEAKKHT-PAIIFIDEIDAIAPKRDEV 295
                                       79******************************************************8.****************99* PP

                                       CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETTS CS
                               AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieiel 132
                                         e+e+rvv+qLl+ +dg++++ ++vivi+atnrp+ +dpal+r gRfdr+iei+l
  gi|385805405|ref|YP_005841803.1| 296 IGEVERRVVAQLLALMDGLETR-GDVIVIAATNRPNAIDPALRRpGRFDREIEIPL 350
                                       *********************7.66****************************985 PP

  == domain 2  score: 158.7 bits;  conditional E-value: 3.1e-49
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.TT CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr.sg 76 
                                       vll+GppGtGKT+lakava+e++++f+ + g+e+lsk+vgesek ire+f++a++ + p+i+f+DEid+l++ r  +
  gi|385805405|ref|YP_005841803.1| 493 VLLFGPPGTGKTMLAKAVATESEANFIAVRGPEVLSKWVGESEKAIREIFRRARQYS-PVIIFFDEIDSLVPIRgMS 568
                                       79******************************************************9.****************988 PP

                                       CCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  77 seseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                       s+s ++ervv+qLlte+dg ++ e+ vivi+atnrpd +dpallr gR+++ i+i+
  gi|385805405|ref|YP_005841803.1| 569 SDSYVTERVVSQLLTEMDGIESLEN-VIVIAATNRPDIIDPALLRpGRLEKLIYIP 623
                                       8999******************865.***************************997 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.1   0.0     7e-18   2.3e-15       1      44 [.     372     432 ..     372     433 .. 0.78
   2 !   68.0   0.6   1.4e-21   4.5e-19       1      45 []     646     692 ..     646     692 .. 0.96

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 7e-18
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrr...............gik.e.itmedfe 44 
                                       dvdl+++A+ T+Gy+GADlaal reAa++Alrr               ++    +tm+df+
  gi|385805405|ref|YP_005841803.1| 372 DVDLEKIASITHGYTGADLAALSREAAMHALRRylpkidlnseripeeVLNsMvVTMQDFM 432
                                       9********************************6666666666655552332247777776 PP

  == domain 2  score: 68.0 bits;  conditional E-value: 1.4e-21
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgik..eitmedfee 45 
                                       dvdl+++Ae TeGy+GAD++al+reA+l+Alr+++   ei m++fe+
  gi|385805405|ref|YP_005841803.1| 646 DVDLERIAEITEGYTGADIEALVREAGLRALRENLSatEIRMRHFED 692
                                       9*********************************99755******96 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 !  119.7   1.4   1.4e-37   4.6e-35       2      84 ..      12      94 ..      11      95 .. 0.99

  Alignments for each domain:
  == domain 1  score: 119.7 bits;  conditional E-value: 1.4e-37
                                      EEEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEEE CS
                           CDC48_N  2 LrVaeapqedvgrgivridpedmeelglepgdvveiegkrkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkVtV 80
                                      LrVaea+q+dvgrg+vrid e ++e+g+epgdvveieg+rkT+ai+wp+++ed+g++iIrmdg++RknagvsiGdkV+V
  gi|385805405|ref|YP_005841803.1| 12 LRVAEAKQKDVGRGKVRIDLEMLKEIGVEPGDVVEIEGRRKTAAIAWPNYTEDQGQDIIRMDGLVRKNAGVSIGDKVIV 90
                                      8****************************************************************************** PP

                                      EEE- CS
                           CDC48_N 81 rkae 84
                                      rka+
  gi|385805405|ref|YP_005841803.1| 91 RKAQ 94
                                      **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 !   29.1   0.0   2.2e-09   7.2e-07      34     104 ..     218     296 ..     210     336 .. 0.86
   2 !   21.8   0.0   3.8e-07   0.00012      36      70 ..     493     527 ..     480     567 .. 0.73

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 2.2e-09
                            RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsravee 102
                                         vllyG+PG Gkt lak +a+e ++ + +  gP +      e ++ l  ++ + +++   ++fidei  ++++ +e
  gi|385805405|ref|YP_005841803.1| 218 KGVLLYGAPGTGKTLLAKAVANETQAYFVAINGPEImskfygESEQRLREIFEEAKKHtpAIIFIDEIDAIAPKRDE 294
                                       569*******************************994444334467799999988876336************9999 PP

                            RuvB_N 103 vl 104
                                       v+
  gi|385805405|ref|YP_005841803.1| 295 VI 296
                                       87 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 3.8e-07
                            RuvB_N  36 vllyGpPGlGkttlakiiakelgvklkitsgPvle 70 
                                       vll+GpPG Gkt lak +a+e ++++ +  gP + 
  gi|385805405|ref|YP_005841803.1| 493 VLLFGPPGTGKTMLAKAVATESEANFIAVRGPEVL 527
                                       9****************************999653 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 !   50.9   1.1   2.9e-16   9.5e-14       6      63 ..     116     173 ..     112     174 .. 0.95

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 2.9e-16
                                       CCHHHHCCCTTEEE-TTEEEEECCTCCCEEEEEEEECCCCSCEEECTSCCEEESTTCC CS
                           CDC48_2   6 emaylkrqFlgrpvtkGdlvvfefkgqeiklvVvstePkgpvgitetTeielgtkpve 63 
                                       ++ y+kr++ + pv++Gd+v ++++gq+i++ V  t+P+g+v+it++T   + +kpv+
  gi|385805405|ref|YP_005841803.1| 116 FVNYIKRRLIDTPVVEGDTVLIPVLGQPIPFSVIQTKPIGIVIITNETNLIVLDKPVD 173
                                       566*****************************************************96 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.1   3.7e-08   1.2e-05      23     139 ..     216     322 ..     207     324 .. 0.71
   2 !   18.4   0.0   6.6e-06    0.0022      24      58 ..     490     523 ..     462     533 .. 0.85
   3 ?    4.5   0.0      0.13        41     122     146 ..     537     560 ..     532     597 .. 0.70

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 3.7e-08
                            AAA_16  23 rpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqllde.aesaeleawr 98 
                                        p  vll+G++G+GK+ l++++++   ++ ++f++ +  +      +s +      e+ lr++ +e ++ + +  + 
  gi|385805405|ref|YP_005841803.1| 216 PPKGVLLYGAPGTGKTLLAKAVAN---ETQAYFVAINGPEI-----MSKFYGES--EQRLREIFEEaKKHTPAIIFI 282
                                       4689*******************7...34489999999999.....33333333..344455544424445556666 PP

                            AAA_16  99 ekleealaavpelagaeasrllellkrllallsrderplvl 139
                                       +++++ +   +e+ g+ ++r+ ++l +l++ l+++++ +++
  gi|385805405|ref|YP_005841803.1| 283 DEIDAIAPKRDEVIGEVERRVVAQLLALMDGLETRGD-VIV 322
                                       666666668888888888***********99999888.443 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 6.6e-06
                            AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrg 58 
                                       p+ vll G++G+GK+ l+++++++ e++ +i++rg
  gi|385805405|ref|YP_005841803.1| 490 PRGVLLFGPPGTGKTMLAKAVATESEAN-FIAVRG 523
                                       599*******************988887.555555 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.13
                            AAA_16 122 llkrllallsrderplvlvlDdlqw 146
                                       +++++++++++  +p+++++D+++ 
  gi|385805405|ref|YP_005841803.1| 537 AIREIFRRARQ-YSPVIIFFDEIDS 560
                                       67888999999.999********93 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 !   22.8   0.1   2.2e-07   7.2e-05       1     136 [.     219     338 ..     219     340 .. 0.76
   2 !   19.6   0.1   2.1e-06    0.0007       1     134 [.     492     610 ..     492     613 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 2.2e-07
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEve 75 
                                       +vlL G+pGtgK+ la+ +a  +++ ++ +++++ +++  + g+ e        +  ++ ++a+  +++i+++DE++
  gi|385805405|ref|YP_005841803.1| 219 GVLLYGAPGTGKTLLAKAVANETQAYFVAINGPEIMSK--FYGESE-------QRLREIFEEAKkhTPAIIFIDEID 286
                                       59********************************8875..555555.......34466666777789********** PP

                                       G--...HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHT CS
                             AAA_5  76 rae...sevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrs 136
                                        +    +ev++++ +    + l l++g e  +         + via++n+++     ++palr+
  gi|385805405|ref|YP_005841803.1| 287 AIApkrDEVIGEVERRVVAQLLALMDGLETRGD--------VIVIAATNRPN----AIDPALRR 338
                                       887333467777766666666666666555543........89999999988....88888876 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 2.1e-06
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEve 75 
                                       +vlL GppGtgK++la+ +a   ++++  v +++      ++ ++    g+ +    ++ r ar  ++ i+++DE++
  gi|385805405|ref|YP_005841803.1| 492 GVLLFGPPGTGKTMLAKAVATESEANFIAVRGPE------VLSKWV---GESEKAIREIFRRARqySPVIIFFDEID 559
                                       59******************99999999999987......666677...3444444555555555999999999999 PP

                                       G--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHH CS
                             AAA_5  76 raesevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspal 134
                                        + +   +s  s+  er ++  ++ ++++  +   le++ via++n++d     ++pal
  gi|385805405|ref|YP_005841803.1| 560 SLVPIRGMSSDSYVTERVVS--QLLTEMDGIE--SLENVIVIAATNRPD----IIDPAL 610
                                       88888888888888888877..4444444433..245589999999888....556665 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   7.6e-08   2.5e-05       6     105 ..     220     313 ..     216     327 .. 0.88
   2 !   18.0   0.0   7.5e-06    0.0024       6     104 ..     493     586 ..     488     599 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 7.6e-08
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       +ll g  g+Gkt+laka+a+  ++     ++ ++  e++     + + ++++  ++   +a+++   i+++DEid i
  gi|385805405|ref|YP_005841803.1| 220 VLLYGAPGTGKTLLAKAVANETQA----YFVAINGPEIMS----KFYGESEQRLREIFEEAKKHTpaIIFIDEIDAI 288
                                       5788999*************9995....************....99999999999999999999899********** PP

                                       ---.---------HHHHHHHHHHHH- CS
                             AAA_2  81 hpk.essgadvSregVqrdLLqileg 105
                                       +pk ++   +v r  V+  LL +++g
  gi|385805405|ref|YP_005841803.1| 289 APKrDEVIGEVERR-VVAQLLALMDG 313
                                       **977777777775.77778899987 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 7.5e-06
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       +ll gp g+Gkt+laka+a   ++    ++i +   e+l     + + ++++  ++   +a +    i+++DEid  
  gi|385805405|ref|YP_005841803.1| 493 VLLFGPPGTGKTMLAKAVATESEA----NFIAVRGPEVLS----KWVGESEKAIREIFRRARQYSpvIIFFDEIDSL 561
                                       6788***************99985....999999999999....66666667777777777777788********** PP

                                       ---.---------HHHHHHHHHHHH CS
                             AAA_2  81 hpk.essgadvSregVqrdLLqile 104
                                        p  + s+     e V+  LL  ++
  gi|385805405|ref|YP_005841803.1| 562 VPIrGMSSDSYVTERVVSQLLTEMD 586
                                       9986555555566777777776555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   7.3e-05     0.024       8      32 ..     220     244 ..     215     262 .. 0.81
   2 ?    5.7   0.0     0.052        17      72     112 ..     259     299 ..     249     327 .. 0.70
   3 !   16.4   0.0   2.5e-05    0.0083       8      30 ..     493     515 ..     488     535 .. 0.80
   4 ?   -0.2   0.0       3.4   1.1e+03      82     104 ..     538     562 ..     527     589 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 7.3e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldee 32 
                                       ++++G +GtGKT+l++ ++++ +++
  gi|385805405|ref|YP_005841803.1| 220 VLLYGAPGTGKTLLAKAVANETQAY 244
                                       689*****************98644 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.052
                            AAA_22  72 rlsseellealeqalraravielliiDEaqhlr..seealeeL 112
                                       + s+++l+e +e+a +++ +  ++ iDE++ +   ++e++ e+
  gi|385805405|ref|YP_005841803.1| 259 GESEQRLREIFEEAKKHTPA--IIFIDEIDAIApkRDEVIGEV 299
                                       56788888888888888877..*********976534444333 PP

  == domain 3  score: 16.4 bits;  conditional E-value: 2.5e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqld 30 
                                       ++++G++GtGKT+l++ ++ + +
  gi|385805405|ref|YP_005841803.1| 493 VLLFGPPGTGKTMLAKAVATESE 515
                                       689***************99863 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 3.4
                            AAA_22  82 leqalrarav..ielliiDEaqhlr 104
                                       +++ +r+++   ++++  DE++ l 
  gi|385805405|ref|YP_005841803.1| 538 IREIFRRARQysPVIIFFDEIDSLV 562
                                       44444444445559999*****995 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   9.9e-06    0.0032      51      96 ..     218     261 ..     211     286 .. 0.87
   2 !   20.9   0.0   5.3e-07   0.00017      51     106 ..     491     545 ..     481     548 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 9.9e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkt 96 
                                       ++vLl G +gtGkt la a+++e      fva++g e+ s     +
  gi|385805405|ref|YP_005841803.1| 218 KGVLLYGAPGTGKTLLAKAVANETQ--AYFVAINGPEIMSKFYGES 261
                                       89********************965..89*********99755555 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 5.3e-07
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte.vltqalrks 106
                                       r+vLl Gp+gtGkt la a++ e  ++  f+a+ g ev s  v  +e ++ + +r++
  gi|385805405|ref|YP_005841803.1| 491 RGVLLFGPPGTGKTMLAKAVATE--SEANFIAVRGPEVLSKWVGESEkAIREIFRRA 545
                                       89*******************98..5689**************99985688899997 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   1.3e-06   0.00042       2      47 ..     220     280 ..     220     343 .. 0.72
   2 !   17.0   0.0   1.6e-05    0.0051       2      46 ..     493     539 ..     493     601 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.3e-06
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt.............d 47 
                                       vll G+pG+GK+ la+ ++++++  +v ++ ++++++ +g+ +q+++              
  gi|385805405|ref|YP_005841803.1| 220 VLLYGAPGTGKTLLAKAVANETQayFVAINGPEIMSKFYGESEQRLReifeeakkhtpaiI 280
                                       7899***************999998889************888888744444444444440 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 1.6e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt 46 
                                       vll G+pG+GK+ la+ ++ +    ++ ++ ++++++ +g+ ++ ++
  gi|385805405|ref|YP_005841803.1| 493 VLLFGPPGTGKTMLAKAVATESEanFIAVRGPEVLSKWVGESEKAIR 539
                                       7899***************9999889999999988888886665554 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   3.8e-06    0.0012       5      77 ..     220     289 ..     217     329 .. 0.73
   2 !   14.4   0.0   8.8e-05     0.029       5      76 ..     493     561 ..     490     589 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3.8e-06
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevp 77 
                                       +++ Ga  +GKT l+k +++e       ++ in  +   k + ++e+ l++i+e++k++   ++f+DEi  + 
  gi|385805405|ref|YP_005841803.1| 220 VLLYGAPGTGKTLLAKAVANETQ---AYFVAINGPEIMSKFYGESEQRLREIFEEAKKHTPAIIFIDEIDAIA 289
                                       7899**************98888...8888888888777666666655666666656668999******9883 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 8.8e-05
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76 
                                       +++ G+  +GKT+l+k ++ e+     +++ +   +   k   ++ek +++i++++++    ++f+DEi  +
  gi|385805405|ref|YP_005841803.1| 493 VLLFGPPGTGKTMLAKAVATESE---ANFIAVRGPEVLSKWVGESEKAIREIFRRARQYSPVIIFFDEIDSL 561
                                       6899***************8888...8999999888888877777767766666644447899******865 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   3.8e-05     0.012      23     143 ..     218     328 ..     207     337 .. 0.68
   2 ?   -0.9   0.0       3.4   1.1e+03      21      70 ..     376     425 ..     363     430 .. 0.80
   3 !   11.0   0.0   0.00077      0.25      23      52 ..     491     517 ..     477     529 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.8e-05
                                       S-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BEHHHHHTTT...SE CS
                   Sigma54_activat  23 lsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFtGAekekkGlfekadg...Gt 96 
                                         vl+ G  GtGK+lla+a+ +++   ++ fva+n  +i     +s+++G ++       ++ +  fe+a++    +
  gi|385805405|ref|YP_005841803.1| 218 KGVLLYGAPGTGKTLLAKAVANET---QAYFVAINGPEI-----MSKFYGESE-------QRLREIFEEAKKhtpAI 279
                                       579****************98765...589**9998765.....566777544.......33345555555422256 PP

                                       EEEETGGGS-HHHHHHHHHHHHHSEEESBT...SSSEEE--EEEEEEESS CS
                   Sigma54_activat  97 lfLDeigelplelQekLlrvlqegevervG...sskeikvdvriiaatne 143
                                       +f+Dei  + ++  e  +  ++++ v ++    +  e++ dv +iaatn+
  gi|385805405|ref|YP_005841803.1| 280 IFIDEIDAIAPKRDEV-IGEVERRVVAQLLalmDGLETRGDVIVIAATNR 328
                                       8888888888876654.444566666555411134466777777777776 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 3.4
                                       SSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHH CS
                   Sigma54_activat  21 tdlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseL 70 
                                        ++  + +G +G+    l+r    +  r+  p + +n   ipee+l+s +
  gi|385805405|ref|YP_005841803.1| 376 EKIASITHGYTGADLAALSREAAMHALRRYLPKIDLNSERIPEEVLNSMV 425
                                       556667788888888888888888888999999************99965 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00077
                                       S-EEEECSTTSSHHHHHHHHHHHSTTTTS- CS
                   Sigma54_activat  23 lsvlitGesGtGKellaraiheaskrkekp 52 
                                         vl+ G  GtGK++la+a+ ++s+   ++
  gi|385805405|ref|YP_005841803.1| 491 RGVLLFGPPGTGKTMLAKAVATESE---AN 517
                                       569****************998876...44 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   4.5e-05     0.015       2      46 ..     220     269 ..     219     306 .. 0.75
   2 !   13.3   0.0   0.00022     0.071       2      35 ..     493     531 ..     492     549 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.5e-05
                            AAA_28   2 ivitGgestGKTtlleaLaar...gypvv..pEaareileeklakgedal 46 
                                       + + G+++tGKT l++a a++    ++ +  pE++ +++ e  ++ +++ 
  gi|385805405|ref|YP_005841803.1| 220 VLLYGAPGTGKTLLAKAVANEtqaYFVAIngPEIMSKFYGESEQRLREIF 269
                                       6799***************7654333333677777776666555555444 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00022
                            AAA_28   2 ivitGgestGKTtlleaLaar...gypvv..pEaareil 35 
                                       + ++G+++tGKT l++a a +   ++  v  pE+  + +
  gi|385805405|ref|YP_005841803.1| 493 VLLFGPPGTGKTMLAKAVATEseaNFIAVrgPEVLSKWV 531
                                       6799***************55434444444666665554 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   0.00015     0.048       1      40 [.     220     267 ..     220     329 .. 0.64
   2 !   13.5   0.0   0.00025      0.08       1      22 [.     493     514 ..     493     598 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 0.00015
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.................gvnlrdvakengllle 40 
                                       +ll G+pG+GKt lak++++++ ++                            + l e
  gi|385805405|ref|YP_005841803.1| 220 VLLYGAPGTGKTLLAKAVANETqAYfvaingpeimskfygesE----------QRLRE 267
                                       799****************998777888887744444444442..........33333 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00025
                            AAA_18   1 IlltGtpGvGKttlakeLskrl 22 
                                       +ll G+pG+GKt lak+++ + 
  gi|385805405|ref|YP_005841803.1| 493 VLLFGPPGTGKTMLAKAVATES 514
                                       799**************96553 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00049      0.16      25      42 ..     220     237 ..     217     242 .. 0.90
   2 !   15.6   0.1   2.4e-05    0.0078      25      43 ..     493     511 ..     484     516 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00049
                      Mg_chelatase  25 lllvGppGsGKtmlakrl 42 
                                       +ll+G+pG+GKt+lak++
  gi|385805405|ref|YP_005841803.1| 220 VLLYGAPGTGKTLLAKAV 237
                                       79*************987 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 2.4e-05
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll+GppG+GKtmlak+++
  gi|385805405|ref|YP_005841803.1| 493 VLLFGPPGTGKTMLAKAVA 511
                                       89*************9875 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00056      0.18      48      71 ..     218     241 ..     212     287 .. 0.87
   2 !   15.3   0.0   3.8e-05     0.012      48      71 ..     491     514 ..     486     525 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00056
                         IstB_IS21  48 enivllGpsGvGKshlaialgvea 71 
                                       ++++l G +G+GK+ la a++ e+
  gi|385805405|ref|YP_005841803.1| 218 KGVLLYGAPGTGKTLLAKAVANET 241
                                       6899*************9998764 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 3.8e-05
                         IstB_IS21  48 enivllGpsGvGKshlaialgvea 71 
                                        +++l+Gp+G+GK+ la a+++e 
  gi|385805405|ref|YP_005841803.1| 491 RGVLLFGPPGTGKTMLAKAVATES 514
                                       5799****************9886 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   0.00011     0.035      52     115 ..     216     284 ..     210     334 .. 0.66
   2 !   12.9   0.0   0.00014     0.045      24     116 ..     452     558 ..     442     610 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00011
                            DUF815  52 pannvLLwGarGtGKSslvkallneyaeegLrli..evek....edlkelpklvellrerperfilfvDD 115
                                       p + vLL+Ga GtGK  l ka+ ne+++  +++   e+      e+ + l +++e+ ++ ++  i+f+D 
  gi|385805405|ref|YP_005841803.1| 216 PPKGVLLYGAPGTGKTLLAKAVANETQAYFVAINgpEIMSkfygESEQRLREIFEEAKK-HTPAIIFIDE 284
                                       55789********************9998765522244440011333444444444332.3345777765 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00014
                            DUF815  24 evklddLvgidkqkealvente.......qfle..glpannvLLwGarGtGKSslvkallneyaeeg..Lrlievek 89 
                                       +vk++d+ g+++ k++l e +e        f +   +p + vLL+G  GtGK  l ka+ +e +++   +r  ev  
  gi|385805405|ref|YP_005841803.1| 452 NVKWSDIGGLEEAKQQLREAVEwplkypeSFKKigIRPPRGVLLFGPPGTGKTMLAKAVATESEANFiaVRGPEVLS 528
                                       56677777777777777776652221111222221357789*********************999985556678988 PP

                            DUF815  90 edlkelpklvellrerperf...ilfvDDL 116
                                       + + e +k ++++ +r++++   i+f D +
  gi|385805405|ref|YP_005841803.1| 529 KWVGESEKAIREIFRRARQYspvIIFFDEI 558
                                       888888877777765554432338888865 PP

>> Vps4_C  Vps4 C terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1     0.069        23      15      43 ..     412     440 ..     407     441 .. 0.77
   2 !   20.0   0.0   1.6e-06   0.00051      22      59 ..     678     715 ..     668     716 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.069
                            Vps4_C  15 twmdipsdkllePpvtlkDflkalkkarp 43 
                                       + + ip++ l    vt++Df++a k+  p
  gi|385805405|ref|YP_005841803.1| 412 NSERIPEEVLNSMVVTMQDFMEAYKEIIP 440
                                       5566887777777*********9987666 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 1.6e-06
                            Vps4_C  22 dkllePpvtlkDflkalkkarptVskeDLekheeFTke 59 
                                       + l + ++++++f++al+  +p+++k+ +e ++++ ++
  gi|385805405|ref|YP_005841803.1| 678 ENLSATEIRMRHFEDALQVIKPSITKQMIEYYIKWFEQ 715
                                       5677889****************************775 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.1    0.0042       1.4      36      53 ..     220     237 ..     216     242 .. 0.87
   2 ?    3.5   0.0      0.14        46     128     177 ..     263     312 ..     244     330 .. 0.76
   3 !   11.0   0.2   0.00071      0.23      36      55 ..     493     512 ..     486     596 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0042
                            AAA_25  36 allaGapgtGKttlaldl 53 
                                       +ll+GapgtGKt la  +
  gi|385805405|ref|YP_005841803.1| 220 VLLYGAPGTGKTLLAKAV 237
                                       69***********99665 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.14
                            AAA_25 128 advdaleaaieevegvrlvviDplsralggdensnsdv.galvealeriar 177
                                       + ++++ +++++ + ++ + iD ++++ +   +   +v +++v++l  + +
  gi|385805405|ref|YP_005841803.1| 263 QRLREIFEEAKK-HTPAIIFIDEIDAIAPKRDEVIGEVeRRVVAQLLALMD 312
                                       557889999999.88*************99555555555888888877765 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00071
                            AAA_25  36 allaGapgtGKttlaldlal 55 
                                       +ll+G+pgtGKt+la  +a 
  gi|385805405|ref|YP_005841803.1| 493 VLLFGPPGTGKTMLAKAVAT 512
                                       68***********9866554 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.1   0.00024     0.078       5      77 ..     220     288 ..     217     302 .. 0.62
   2 !   10.8   0.0   0.00094      0.31       5      22 ..     493     510 ..     490     529 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00024
                            AAA_24   5 iliyGpsgiGKTtlakel..gpkplfidtekGlksldadkfpdieswedfldevvelaaeladyktlviDtidel 77 
                                       +l+yG +g+GKT lak    + ++ f+ +++    +    ++   s + +++ ++e   ++++  +++iD id +
  gi|385805405|ref|YP_005841803.1| 220 VLLYGAPGTGKTLLAKAVanETQAYFVAING-PEIMSKFYGE---SEQRLREIFEEA--KKHTPAIIFIDEIDAI 288
                                       89**************997544444444443.3233333332...455555555544..5555577777777766 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00094
                            AAA_24   5 iliyGpsgiGKTtlakel 22 
                                       +l++Gp+g+GKT+lak  
  gi|385805405|ref|YP_005841803.1| 493 VLLFGPPGTGKTMLAKAV 510
                                       79*************987 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   0.00053      0.17       1      29 [.     220     248 ..     220     295 .. 0.80
   2 !   11.4   0.0   0.00098      0.32       1      25 [.     493     517 ..     493     561 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00053
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklk 29 
                                       ++lyG++g+GK++lak +a++ +  +  +
  gi|385805405|ref|YP_005841803.1| 220 VLLYGAPGTGKTLLAKAVANETQAYFVAI 248
                                       689**************999988766444 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00098
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkk 25 
                                       ++l+Gp+g+GK++lak +a++ + +
  gi|385805405|ref|YP_005841803.1| 493 VLLFGPPGTGKTMLAKAVATESEAN 517
                                       679**************88776544 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.1    0.0014      0.45      15      37 ..     213     235 ..     206     243 .. 0.84
   2 ?    1.1   0.1      0.62     2e+02     109     154 ..     263     314 ..     247     325 .. 0.69
   3 !   10.1   0.0    0.0011      0.37      14      42 ..     485     513 ..     460     544 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0014
                            ATPase  15 GipegrvvlitGepGtGKtifal 37 
                                       Gi   + vl++G pGtGKt++a+
  gi|385805405|ref|YP_005841803.1| 213 GIEPPKGVLLYGAPGTGKTLLAK 235
                                       67777889*************97 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.62
                            ATPase 109 eelaeaikeika...krvviDsitglayeeke...avaReilrqlvrvlkkl 154
                                       ++l+e+ +e k      + iD i+++a + +e   +v R+ + ql+  + +l
  gi|385805405|ref|YP_005841803.1| 263 QRLREIFEEAKKhtpAIIFIDEIDAIAPKRDEvigEVERRVVAQLLALMDGL 314
                                       45555555554433378999*****944444412245688888888888766 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.0011
                            ATPase  14 gGipegrvvlitGepGtGKtifalqFlik 42 
                                        Gi   r vl+ G pGtGKt++a+  + +
  gi|385805405|ref|YP_005841803.1| 485 IGIRPPRGVLLFGPPGTGKTMLAKAVATE 513
                                       58888999**************9876655 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   9.3e-05      0.03      14      51 ..     215     250 ..     207     272 .. 0.88
   2 !    9.0   0.0    0.0024      0.78      16      49 ..     490     521 ..     481     526 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.3e-05
                        Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrldp 51 
                                       e Pk +ll G+pG GK+ la+++++e+  q  +v +++
  gi|385805405|ref|YP_005841803.1| 215 EPPKGVLLYGAPGTGKTLLAKAVANET--QAYFVAING 250
                                       56999*********************9..788888876 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0024
                        Zeta_toxin  16 PklillgGqpGAGKselaellkdelerqgnvvrl 49 
                                       P  +ll G pG GK+ la+++++e   + n++ +
  gi|385805405|ref|YP_005841803.1| 490 PRGVLLFGPPGTGKTMLAKAVATES--EANFIAV 521
                                       77899*******************8..6777665 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.1    0.0026      0.84      17     122 ..     214     323 ..     206     337 .. 0.61
   2 ?    5.5   0.0     0.044        14      23      45 ..     493     515 ..     487     522 .. 0.85
   3 ?    5.5   0.0     0.044        14     107     167 ..     535     602 ..     517     662 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0026
                          ATPase_2  17 repneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekal..........g 83 
                                        ep + +++YG  g GKt L k ++++ +       y+ a+++ +i ++     e++ ++ +e+a+           
  gi|385805405|ref|YP_005841803.1| 214 IEPPKGVLLYGAPGTGKTLLAKAVANETQA------YFVAINGPEIMSKFYGESEQRLREIFEEAKkhtpaiifidE 284
                                       567777899**********99999999843......44455544444444441122222222222244444556664 PP

                          ATPase_2  84 iavpkaeleeilkeksklvfkaielllekikkkgkkiii 122
                                       i+    + +e++ e  + v +++ +l++ ++ +g  i+i
  gi|385805405|ref|YP_005841803.1| 285 IDAIAPKRDEVIGEVERRVVAQLLALMDGLETRGDVIVI 323
                                       444444455566666777777777777777777766665 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.044
                          ATPase_2  23 yfiYGpegsGKtaLlkeiienle 45 
                                       ++++Gp g GKt L k +++++e
  gi|385805405|ref|YP_005841803.1| 493 VLLFGPPGTGKTMLAKAVATESE 515
                                       689*************9998875 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.044
                          ATPase_2 107 elllekikkkgkk...iiiiiDelqklidlgln.....gaellvkeLlnliesltkekhlcvviclsSe 167
                                       e+++++i +++++   +ii++De+  l+ +          e +v++Ll+ ++   ++ + ++vi+++  
  gi|385805405|ref|YP_005841803.1| 535 EKAIREIFRRARQyspVIIFFDEIDSLVPIRGMssdsyVTERVVSQLLTEMDG-IESLENVIVIAATNR 602
                                       56778888888889989999****99996655522333344445556655555.455555556666655 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.1    0.0031         1       3      24 ..     220     241 ..     218     316 .. 0.88
   2 ?   -1.4   0.0         6     2e+03      80     115 ..     275     313 ..     251     341 .. 0.56
   3 !   11.0   0.0   0.00093       0.3       3      23 ..     493     513 ..     491     519 .. 0.88
   4 ?   -0.1   0.0       2.3   7.5e+02      60     113 ..     529     582 ..     522     608 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0031
                                       EEEEC-TTTCHHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklalaw 24 
                                       v+l G++G GKT L++ +a + 
  gi|385805405|ref|YP_005841803.1| 220 VLLYGAPGTGKTLLAKAVANET 241
                                       789*************999875 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 6
                                       CCCEEEEEE-STT-SS-TCH.............HHHHHCT CS
                             NACHT  80 perlLlilDglDelvtdlgq....kekqpvrtlLselirk 115
                                        + + + +D +D ++ + ++     e++ v +l   l+ +
  gi|385805405|ref|YP_005841803.1| 275 HTPAIIFIDEIDAIAPKRDEvigeVERRVVAQL-LALMDG 313
                                       344445567777777666666663333333333.355544 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00093
                                       EEEEC-TTTCHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                       v+l G++G GKT+L++ +a++
  gi|385805405|ref|YP_005841803.1| 493 VLLFGPPGTGKTMLAKAVATE 513
                                       7899************99986 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 2.3
                                       CCCTS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH..........HHHHH CS
                             NACHT  60 sqlpepaapvsevwavllelperlLlilDglDelvtdlgq.kekqpvrtlLseli 113
                                       +   e++++++e +  ++++   + + +D +D lv + g  ++   ++++ s+l+
  gi|385805405|ref|YP_005841803.1| 529 KWVGESEKAIRE-IFRRARQYSPVIIFFDEIDSLVPIRGMsSDSYVTERVVSQLL 582
                                       555677788888.666778888889999******998888634444444444444 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0     0.001      0.32      32      58 ..     216     242 ..     206     295 .. 0.80
   2 !   10.6   0.0   0.00088      0.29      34      58 ..     491     515 ..     481     522 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.001
                             AAA_7  32 nkkpvllvGptGtGKtviikdllkkld 58 
                                         k vll+G  GtGKt+++k + ++ +
  gi|385805405|ref|YP_005841803.1| 216 PPKGVLLYGAPGTGKTLLAKAVANETQ 242
                                       5688****************9998877 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00088
                             AAA_7  34 kpvllvGptGtGKtviikdllkkld 58 
                                       + vll Gp GtGKt+++k + ++ +
  gi|385805405|ref|YP_005841803.1| 491 RGVLLFGPPGTGKTMLAKAVATESE 515
                                       679**************99777665 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 !   11.6   0.0   0.00058      0.19       2      37 ..     220     254 ..     219     330 .. 0.74
   2 !    9.6   0.0    0.0024      0.78       2      30 ..     493     521 ..     492     603 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00058
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdll 37 
                                       vll g+PG++ktll+ka+a+  ++ f  i   p+++
  gi|385805405|ref|YP_005841803.1| 220 VLLYGAPGTGKTLLAKAVANETQAYFVAIN-GPEIM 254
                                       899******************999998775.45554 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0024
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                       vll g PG++kt+l+ka+a+  +++f  +
  gi|385805405|ref|YP_005841803.1| 493 VLLFGPPGTGKTMLAKAVATESEANFIAV 521
                                       7999****************999998766 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    0.0025      0.82       6      67 ..     212     271 ..     210     322 .. 0.74
   2 !   11.1   0.0    0.0013      0.42      11      67 ..     490     544 ..     484     598 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0025
                                       EEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   6 lklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe 67 
                                       l +++ + v + G  G+GK+ L+k++a++++     + ++g ++ ++   +++++++ +++e
  gi|385805405|ref|YP_005841803.1| 212 LGIEPPKGVLLYGAPGTGKTLLAKAVANETQAYF--VAINGPEIMSKFYGESEQRLREIFEE 271
                                       5677888899******************998643..44466666665555555555555555 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0013
                                       TSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  11 gekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe 67 
                                        + v ++G+ G+GK+ L+k++a +++  +  i ++g ++ ++   +++k i+ ++  
  gi|385805405|ref|YP_005841803.1| 490 PRGVLLFGPPGTGKTMLAKAVATESE--ANFIAVRGPEVLSKWVGESEKAIREIFRR 544
                                       566889****************9986..56666677777776666666666666555 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0    0.0022      0.72      19      46 ..     217     244 ..     194     263 .. 0.78
   2 !   10.1   0.0    0.0019      0.62      21      49 ..     487     522 ..     456     526 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0022
                                       TEEEEEEESTTSSHHHHHHHHHHHTT-- CS
                              TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve 46 
                                        + +lL+G  G+GKT l++++a++ +  
  gi|385805405|ref|YP_005841803.1| 217 PKGVLLYGAPGTGKTLLAKAVANETQAY 244
                                       3459******************998764 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0019
                                       E.....EEEEESTTSSHHHHHHHHHHHTT--..--- CS
                              TsaE  21 v.....ilLeGdLGaGKTtlvrglakalgve..evk 49 
                                       +     +lL G+ G+GKT+l++++a + + +  +v+
  gi|385805405|ref|YP_005841803.1| 487 IrpprgVLLFGPPGTGKTMLAKAVATESEANfiAVR 522
                                       0444449******************99877666665 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 !    9.8   0.0    0.0012      0.38     117     141 ..     220     244 ..     214     250 .. 0.89
   2 !    8.6   0.0    0.0026      0.85     117     136 ..     493     512 ..     487     517 .. 0.89
   3 ?   -2.3   0.0       5.7   1.9e+03     247     269 ..     700     722 ..     677     725 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0012
                         Parvo_NS1 117 vwfyGpantGktnlaeaIakavply 141
                                       v++yG++ tGkt la+a a+ ++ y
  gi|385805405|ref|YP_005841803.1| 220 VLLYGAPGTGKTLLAKAVANETQAY 244
                                       89*****************988766 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0026
                         Parvo_NS1 117 vwfyGpantGktnlaeaIak 136
                                       v+++Gp+ tGkt+la+a a+
  gi|385805405|ref|YP_005841803.1| 493 VLLFGPPGTGKTMLAKAVAT 512
                                       7899*************997 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 5.7
                         Parvo_NS1 247 kitredvkqflqWseqtsiditn 269
                                        it+++++  ++W eq    i++
  gi|385805405|ref|YP_005841803.1| 700 SITKQMIEYYIKWFEQARQAISK 722
                                       58999999999999996655555 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.1    0.0077       2.5      22      41 ..     220     239 ..     213     245 .. 0.86
   2 !   10.7   0.0   0.00083      0.27      22      42 ..     493     513 ..     486     522 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0077
                                       EEEE--TTSSTTHHHHHHHH CS
                              PhoH  22 vfaiGpaGtGKtylavalav 41 
                                       v   G  GtGKt+la a+a 
  gi|385805405|ref|YP_005841803.1| 220 VLLYGAPGTGKTLLAKAVAN 239
                                       67789**********99985 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00083
                                       EEEE--TTSSTTHHHHHHHHH CS
                              PhoH  22 vfaiGpaGtGKtylavalave 42 
                                       v  +Gp GtGKt+la a+a e
  gi|385805405|ref|YP_005841803.1| 493 VLLFGPPGTGKTMLAKAVATE 513
                                       6789************99976 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   0.00035      0.11      37     179 ..     220     364 ..     215     426 .. 0.75
   2 ?    5.3   0.0     0.048        16      37      64 ..     493     520 ..     487     554 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00035
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHTT-.SEEEEE-GGGGTT- CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklrkv.DvLliDDiqflagk 112
                                       +++yg  G Gkt L ka++ne+++ +     v +++ e ++++    +++  e f e  +++  ++ iD+i  +a k
  gi|385805405|ref|YP_005841803.1| 220 VLLYGAPGTGKTLLAKAVANETQAYF-----VAINGPEIMSKFYGESEQRLREIFEEAKKHTpAIIFIDEIDAIAPK 291
                                       79****************99887655.....6688899999999888888888888877754167789999999988 PP

                                       H.........HHHHHHHHHHHHHHTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHHHHH CS
                          Bac_DnaA 113 e.........ktqeelfhtfnalleegkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailkkki 179
                                                 ++  +l+ +++ l   g  +v+++   P++++    r   rf++   ++i  pd++ rl+il+ + 
  gi|385805405|ref|YP_005841803.1| 292 RdevigeverRVVAQLLALMDGLETRGDVIVIAATNRPNAIDPAL-RRPGRFDR--EIEIPLPDRQGRLEILQIHT 364
                                       522222111123445666667777788889999999999886543.33567776..45667788888888886443 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.048
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSSS CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenape 64 
                                       ++++g+ G Gkt L ka++ e ++n+ +
  gi|385805405|ref|YP_005841803.1| 493 VLLFGPPGTGKTMLAKAVATESEANFIA 520
                                       799****************999888765 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00029     0.095       4      55 ..     220     265 ..     217     297 .. 0.69
   2 ?    5.5   0.0     0.025       8.2       6      25 ..     495     514 ..     491     556 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00029
                           DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvl.vlrealakke 55 
                                       vl  G++GtGKt+++ ++++e        +a ++  N+p+++ + + + +++ 
  gi|385805405|ref|YP_005841803.1| 220 VLLYGAPGTGKTLLAKAVANET-------QAYFVAINGPEIMsKFYGESEQRL 265
                                       6789*************99998.......666666666664435555555555 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.025
                           DUF2075   6 VtGvaGtGKtvvllnllael 25 
                                         G +GtGKt+++ ++++e 
  gi|385805405|ref|YP_005841803.1| 495 LFGPPGTGKTMLAKAVATES 514
                                       5699*********9999987 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0    0.0026      0.84      23      45 ..     220     242 ..     206     246 .. 0.82
   2 ?   -0.4   0.0       1.6   5.2e+02     120     148 ..     345     374 ..     342     426 .. 0.80
   3 ?    6.1   0.0     0.017       5.4      23      44 ..     493     514 ..     489     542 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0026
                                       EEEEESTTSSHHHHHHHHCCSHC CS
                            NB-ARC  23 valvGmgGvGKttlakqilnksd 45 
                                       v l+G +G GKt lak + n+ +
  gi|385805405|ref|YP_005841803.1| 220 VLLYGAPGTGKTLLAKAVANETQ 242
                                       789***************99954 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.6
                                       ....HHHHCHTTSEEE.EEESBCCCCCCS- CS
                            NB-ARC 120 kigvvlparenrlrvl.lTTRdeevanavs 148
                                       +i ++lp+r+ rl++l + TR++ +a+ v 
  gi|385805405|ref|YP_005841803.1| 345 EIEIPLPDRQGRLEILqIHTRNMPLAEDVD 374
                                       7999*********99967899999988765 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.017
                                       EEEEESTTSSHHHHHHHHCCSH CS
                            NB-ARC  23 valvGmgGvGKttlakqilnks 44 
                                       v l G +G GKt lak +  +s
  gi|385805405|ref|YP_005841803.1| 493 VLLFGPPGTGKTMLAKAVATES 514
                                       6689************999874 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0089       2.9      24      81 ..     220     288 ..     215     299 .. 0.65
   2 !    8.6   0.0     0.006       1.9      24      81 ..     493     561 ..     484     565 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0089
                                       EEEEEETT--HHHHHHCC--TTS-E.E--SSTTHHHH-H..........HHHHHHT...TTSEEEEEE-TT- CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpw.leifvverlaklp..........ldlleqa...kggtLylkdiadl 81 
                                       v+l G++G+gk+l A++ +++ +   ++i   e                 +++e+a   +++++++ +i+ +
  gi|385805405|ref|YP_005841803.1| 220 VLLYGAPGTGKTLLAKAVANETQAYfVAINGPEIM---SkfygeseqrlREIFEEAkkhTPAIIFIDEIDAI 288
                                       9****************998766521222222222...1222333344477777765557788888888766 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.006
                                       EEEEEETT--HHHHHHCC--TTS-EE--SSTTHHHH-H.........HHHHHHT...TTSEEEEEE-TT- CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpwleifvverlaklp.........ldlleqa...kggtLylkdiadl 81 
                                       v+l G++G+gk++ A++ + +s+ +   +v    + +           +++ +a   +++++++ +i++l
  gi|385805405|ref|YP_005841803.1| 493 VLLFGPPGTGKTMLAKAVATESEANFI-AVRGPEVLSKwvgesekaiREIFRRArqySPVIIFFDEIDSL 561
                                       9*****************999887432.222222221122223333355555544447777777777766 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.2    0.0097       3.2      11      35 ..     218     242 ..     214     272 .. 0.78
   2 ?    0.0   0.0         3   9.8e+02      98     133 ..     272     308 ..     253     313 .. 0.69
   3 !    8.4   0.0    0.0078       2.5      12      31 ..     492     511 ..     485     541 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0097
                            AAA_19  11 kvllvtaGpGtGKTrvlkhivallv 35 
                                       k +l+ + pGtGKT + k++ ++ +
  gi|385805405|ref|YP_005841803.1| 218 KGVLLYGAPGTGKTLLAKAVANETQ 242
                                       56899*********98888776655 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 3
                            AAA_19  98 kklqeeellivDEfqdvdelqyrLlkallgek.kkll 133
                                        k +  +++++DE+  + +   +++ ++  +  ++ll
  gi|385805405|ref|YP_005841803.1| 272 AKKHTPAIIFIDEIDAIAPKRDEVIGEVERRVvAQLL 308
                                       23324559*******9999999988888765555555 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0078
                            AAA_19  12 vllvtaGpGtGKTrvlkhiv 31 
                                        +l+ ++pGtGKT + k++ 
  gi|385805405|ref|YP_005841803.1| 492 GVLLFGPPGTGKTMLAKAVA 511
                                       5899*********9877665 PP

>> UFD1  Ubiquitin fusion degradation protein UFD1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       2.6   8.6e+02      69      94 ..      25      50 ..      21      57 .. 0.85
   2 !   16.3   0.1   1.5e-05     0.005      71     168 ..      70     167 ..      52     171 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 2.6
                              UFD1 69 gtvylPewmmenlgleegdlveiesv 94
                                      g+v +   m++++g+e gd+veie  
  gi|385805405|ref|YP_005841803.1| 25 GKVRIDLEMLKEIGVEPGDVVEIEGR 50
                                      78888889***************865 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 1.5e-05
                              UFD1  71 vylPewmmenlgleegdlveiesvslpkgkfvklqpqsedfldisdpkavLekaLrnfatLtkgdvieikyndkvye 147
                                       + +   + +n g++ gd v +++++ + +++vkl p++ ++   +   + ++++L +  +  +gd++ i +  +   
  gi|385805405|ref|YP_005841803.1|  70 IRMDGLVRKNAGVSIGDKVIVRKAQTKPATYVKLAPNNYNIEVENSFVNYIKRRLIDTPV-VEGDTVLIPVLGQPIP 145
                                       566667889999*************************88865555578999*****9887.58************** PP

                              UFD1 148 lkvlevkpes.avsiietdlev 168
                                       ++v+++kp    + ++et+l v
  gi|385805405|ref|YP_005841803.1| 146 FSVIQTKPIGiVIITNETNLIV 167
                                       ********99677778888765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0     0.012       3.8      21      42 ..     220     241 ..     208     251 .. 0.84
   2 !    9.1   0.0    0.0031         1      21      44 ..     493     516 ..     483     524 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.012
                            AAA_30  21 avltGpAGtGKttalkalreaw 42 
                                       ++l G++GtGKt + ka+++  
  gi|385805405|ref|YP_005841803.1| 220 VLLYGAPGTGKTLLAKAVANET 241
                                       6789***********9998755 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0031
                            AAA_30  21 avltGpAGtGKttalkalreawea 44 
                                       ++l Gp+GtGKt++ ka++   ea
  gi|385805405|ref|YP_005841803.1| 493 VLLFGPPGTGKTMLAKAVATESEA 516
                                       5788************99876665 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0     0.021         7       1      31 [.     223     255 ..     223     304 .. 0.74
   2 ?    6.5   0.0     0.033        11       1      20 [.     496     515 ..     496     548 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.021
                                       EE-TTSSHHHHHHHHHHHH..TEEEEEHHHHHH CS
                            AAA_17   1 lGgPGsGKgtqceklveky..gfthlsaGdllr 31 
                                       +G PG GK+ +++ ++ +    f  ++  +++ 
  gi|385805405|ref|YP_005841803.1| 223 YGAPGTGKTLLAKAVANETqaYFVAINGPEIMS 255
                                       7***********999987633566666555554 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.033
                                       EE-TTSSHHHHHHHHHHHHT CS
                            AAA_17   1 lGgPGsGKgtqceklvekyg 20 
                                       +G+PG GK+ +++ ++ + +
  gi|385805405|ref|YP_005841803.1| 496 FGPPGTGKTMLAKAVATESE 515
                                       6***********99987653 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       6.9   2.2e+03      53      86 ..       4      39 ..       1      42 [. 0.63
   2 ?    5.1   0.0      0.06        19       2      32 ..     220     250 ..     219     266 .. 0.83
   3 ?    0.7   0.1       1.3   4.3e+02      81     114 ..     261     295 ..     252     311 .. 0.72
   4 ?   -1.9   0.0       8.6   2.8e+03     104     122 ..     458     476 ..     426     481 .. 0.87
   5 ?    6.5   0.0     0.022       7.1       2      32 ..     493     523 ..     492     558 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 6.9
                                      .T--EEEEEETT---SSEET..TEEE-HHHHHHHHH CS
                          NTPase_1 53 asgeegiLarveakreprvg..kyvvdvesfeelal 86
                                      ++++++ L rv + ++  vg  k  +d+e ++e+++
  gi|385805405|ref|YP_005841803.1|  4 TNEKKELLLRVAEAKQKDVGrgKVRIDLEMLKEIGV 39
                                      578888999999666666650055556666777766 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.06
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                       v++ G pG+GKt l k v+++ +   v ++G
  gi|385805405|ref|YP_005841803.1| 220 VLLYGAPGTGKTLLAKAVANETQAYFVAING 250
                                       6788***************999877777766 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHHHH.HHH-EEEE---STTGGG-HHH CS
                          NTPase_1  81 feelalealrkal.seadviviDEiGkmElkskkf 114
                                        e+   e++++a  +++ +i iDEi  +  k  ++
  gi|385805405|ref|YP_005841803.1| 261 SEQRLREIFEEAKkHTPAIIFIDEIDAIAPKRDEV 295
                                       577777888888844556******97665555555 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 8.6
                                       -STTGGG-HHHHHHHHHHH CS
                          NTPase_1 104 iGkmElkskkfkeaveevL 122
                                       iG +E   ++++eave  L
  gi|385805405|ref|YP_005841803.1| 458 IGGLEEAKQQLREAVEWPL 476
                                       99***********998666 PP

  == domain 5  score: 6.5 bits;  conditional E-value: 0.022
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                       v++ GppG+GKt l k v+ + + + + v+G
  gi|385805405|ref|YP_005841803.1| 493 VLLFGPPGTGKTMLAKAVATESEANFIAVRG 523
                                       6788************999988776666666 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.44   1.4e+02       4      31 ..     219     246 ..     217     254 .. 0.87
   2 ?    2.4   0.0      0.34   1.1e+02      75     100 ..     254     282 ..     247     292 .. 0.78
   3 ?    6.1   0.0     0.024       7.8       3      30 ..     491     518 ..     489     529 .. 0.88
   4 ?   -2.3   0.0       9.2     3e+03      78      95 ..     530     547 ..     524     561 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.44
                                       EEEEESTTTSSHHHHHHHHHHHSTTTEE CS
                     Guanylate_kin   4 pvvlvgpsgaGksslkkaLlselpekfg 31 
                                        v l g+ g+Gk  l ka+ +e + +f 
  gi|385805405|ref|YP_005841803.1| 219 GVLLYGAPGTGKTLLAKAVANETQAYFV 246
                                       6889***************999999885 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.34
                                       TTEEEEEEHHHHHHHHHTTSE...EEEE- CS
                     Guanylate_kin  75 sgnlygtsveaieevlekgki...viLDv 100
                                        ++ yg+s +  +e++e++k+   +i+ +
  gi|385805405|ref|YP_005841803.1| 254 MSKFYGESEQRLREIFEEAKKhtpAIIFI 282
                                       6789**************99866655444 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.024
                                       SEEEEESTTTSSHHHHHHHHHHHSTTTE CS
                     Guanylate_kin   3 rpvvlvgpsgaGksslkkaLlselpekf 30 
                                       r v l gp g+Gk +l ka+ +e + +f
  gi|385805405|ref|YP_005841803.1| 491 RGVLLFGPPGTGKTMLAKAVATESEANF 518
                                       6789****************99998887 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 9.2
                                       EEEEEHHHHHHHHHTTSE CS
                     Guanylate_kin  78 lygtsveaieevlekgki 95 
                                         g+s +ai+e++  +++
  gi|385805405|ref|YP_005841803.1| 530 WVGESEKAIREIFRRARQ 547
                                       678999999999988876 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     0.015       4.9       4      71 ..     223     285 ..     220     290 .. 0.61
   2 ?    6.4   0.0     0.021       6.8       4      71 ..     496     558 ..     493     563 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.015
                   Viral_helicase1   4 hGvpGcGKStlirkllrts.liltvnrptaelltegk...pklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                        G+pG GK+ l + ++++           +++++      ++ + ++ r  + f++a +k+ +  i+++DE+
  gi|385805405|ref|YP_005841803.1| 223 YGAPGTGKTLLAKAVANETqA-------YFVAINGPEimsKFYGESEQRLREIFEEA-KKH-TPAIIFIDEI 285
                                       59****************443.......34444443344333344444433333333.333.3679999997 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.021
                   Viral_helicase1   4 hGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                        G pG GK+ l + ++ +s  ++ ++r   e+l++++ ++++   + ++ + +  ++     i+++DE+
  gi|385805405|ref|YP_005841803.1| 496 FGPPGTGKTMLAKAVATESeANFIAVRG-PEVLSKWVGESEKAIREIFRRARQ-YSPV----IIFFDEI 558
                                       588*************999988888888.99*****96655555554444333.2332....6777776 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0      0.13        41      20      41 ..     220     241 ..     211     279 .. 0.75
   2 ?    8.6   0.0    0.0045       1.5      20      73 ..     493     544 ..     468     559 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.13
                            AAA_11  20 tliqGPPGtgKTktivellsql 41 
                                       +l+ G PGtgKT    ++ ++ 
  gi|385805405|ref|YP_005841803.1| 220 VLLYGAPGTGKTLLAKAVANET 241
                                       6899********7766666665 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0045
                            AAA_11  20 tliqGPPGtgKTktivellsqllsrrkseeeksakpriLv..CapSNaAvDeller 73 
                                       +l+ GPPGtgKT    ++  +     + +  + ++p++L    ++S++A+ e+  r
  gi|385805405|ref|YP_005841803.1| 493 VLLFGPPGTGKTMLAKAVATES----EANFIAVRGPEVLSkwVGESEKAIREIFRR 544
                                       6889********8888887777....334566777777643367777777777666 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.059        19      56      79 ..     211     234 ..     204     290 .. 0.90
   2 ?    7.5   0.0    0.0051       1.7      58      79 ..     486     507 ..     461     515 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.059
                       AFG1_ATPase  56 rksvepvrglYlwGgvGrGKtylm 79 
                                       r   ep++g+ l+G  G GKt l 
  gi|385805405|ref|YP_005841803.1| 211 RLGIEPPKGVLLYGAPGTGKTLLA 234
                                       44678****************985 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0051
                       AFG1_ATPase  58 svepvrglYlwGgvGrGKtylm 79 
                                         +p+rg+ l G+ G GKt+l 
  gi|385805405|ref|YP_005841803.1| 486 GIRPPRGVLLFGPPGTGKTMLA 507
                                       5679****************96 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0      0.14        45      35      60 ..     217     242 ..     202     253 .. 0.83
   2 ?   -2.6   0.0       9.6   3.1e+03     115     131 ..     272     288 ..     245     295 .. 0.69
   3 ?    7.0   0.0     0.011       3.6      35      59 ..     490     514 ..     460     524 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.14
                              TniB  35 mpnlllvGdsnnGKtmivekFarlhp 60 
                                       ++ +ll+G + +GKt +++  a++ +
  gi|385805405|ref|YP_005841803.1| 217 PKGVLLYGAPGTGKTLLAKAVANETQ 242
                                       6789*************998887765 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 9.6
                              TniB 115 lrelkvrvLiiDEihnl 131
                                        ++  + ++ iDEi+ +
  gi|385805405|ref|YP_005841803.1| 272 AKKHTPAIIFIDEIDAI 288
                                       34455779999999876 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.011
                              TniB  35 mpnlllvGdsnnGKtmivekFarlh 59 
                                       ++ +ll+G++ +GKtm+++  a + 
  gi|385805405|ref|YP_005841803.1| 490 PRGVLLFGPPGTGKTMLAKAVATES 514
                                       3689*************99877655 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0     0.019       6.4       2      28 ..     218     244 ..     217     247 .. 0.90
   2 ?    5.1   0.0     0.053        17       4      24 ..     493     513 ..     490     517 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.019
                         PduV-EutP   2 kkilliGkvgsGKttLtqalkgeelkY 28 
                                       k +ll G+ g+GKt L++a+ +e+  Y
  gi|385805405|ref|YP_005841803.1| 218 KGVLLYGAPGTGKTLLAKAVANETQAY 244
                                       5699*****************998777 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.053
                         PduV-EutP   4 illiGkvgsGKttLtqalkge 24 
                                       +ll+G+ g+GKt L++a+  e
  gi|385805405|ref|YP_005841803.1| 493 VLLFGPPGTGKTMLAKAVATE 513
                                       89**************98765 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0      0.02       6.4       5      31 ..     221     247 ..     218     251 .. 0.89
   2 ?    5.4   0.0     0.031        10       5      31 ..     494     520 ..     491     523 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.02
                               IPT   5 lifGatttGKtaeaiklaketgapviv 31 
                                       l++Ga +tGKt  a ++a+et a  ++
  gi|385805405|ref|YP_005841803.1| 221 LLYGAPGTGKTLLAKAVANETQAYFVA 247
                                       89******************9887776 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.031
                               IPT   5 lifGatttGKtaeaiklaketgapviv 31 
                                       l+fG+ +tGKt  a ++a e  a  i+
  gi|385805405|ref|YP_005841803.1| 494 LLFGPPGTGKTMLAKAVATESEANFIA 520
                                       89****************999888776 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.019       6.1       4      39 ..     220     255 ..     218     313 .. 0.84
   2 ?    4.3   0.0     0.099        32       4      32 ..     493     521 ..     491     534 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.019
                                       EEEEE-TTSSHHHHHHHHHHHSSS-EEEEEHHHHHH CS
                               CPT   4 ilLnGgsssGKsslaralqevldepwlhlgvDafve 39 
                                       +lL G++ +GK+ la+a+ + +++ +++++  + + 
  gi|385805405|ref|YP_005841803.1| 220 VLLYGAPGTGKTLLAKAVANETQAYFVAINGPEIMS 255
                                       89********************99999987665555 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.099
                                       EEEEE-TTSSHHHHHHHHHHHSSS-EEEE CS
                               CPT   4 ilLnGgsssGKsslaralqevldepwlhl 32 
                                       +lL G + +GK+ la+a+ + +++ ++++
  gi|385805405|ref|YP_005841803.1| 493 VLLFGPPGTGKTMLAKAVATESEANFIAV 521
                                       89*******************99999886 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 ?    4.0   0.0       0.1        33       4      31 ..     221     248 ..     219     271 .. 0.85
   2 ?    6.1   0.0     0.023       7.5       4      31 ..     494     521 ..     492     527 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.1
                                       EEEESTTCCHHHHHHHHHCT--SS-EEE CS
                              cobW   4 vltGflGsGKTtLlnhllenraglklav 31 
                                       +l G +G+GKT L +++ ++++ + +a+
  gi|385805405|ref|YP_005841803.1| 221 LLYGAPGTGKTLLAKAVANETQAYFVAI 248
                                       6889*******99999998888887776 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.023
                                       EEEESTTCCHHHHHHHHHCT--SS-EEE CS
                              cobW   4 vltGflGsGKTtLlnhllenraglklav 31 
                                       +l G++G+GKT+L +++ ++++ + +av
  gi|385805405|ref|YP_005841803.1| 494 LLFGPPGTGKTMLAKAVATESEANFIAV 521
                                       688************9999988888887 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.098        32      60      90 ..     220     249 ..     217     328 .. 0.78
   2 ?    5.6   0.0     0.023       7.5      52      87 ..     485     519 ..     464     526 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.098
                                       EEEEESSTSTHHHHHHHHHHHSSSEEEEESS CS
                               MCM  60 vllvgdpgtaKsqlLkyveklapravytsgk 90 
                                       vll g pgt+K+ l k+v+ +  +a ++ ++
  gi|385805405|ref|YP_005841803.1| 220 VLLYGAPGTGKTLLAKAVA-NETQAYFVAIN 249
                                       8999*******99999988.44555665555 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.023
                                       SBBCSS-EEEEEESSTSTHHHHHHHHHHHSSSEEEE CS
                               MCM  52 tklrgdinvllvgdpgtaKsqlLkyveklapravyt 87 
                                       + +r    vll g pgt+K+ l k+v++ + +a+++
  gi|385805405|ref|YP_005841803.1| 485 IGIRPPRGVLLFGPPGTGKTMLAKAVATES-EANFI 519
                                       556777789*************99999554.44444 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0      0.13        41      21      39 ..     217     234 ..     208     239 .. 0.77
   2 ?    5.9   0.0     0.033        11      21      42 ..     490     510 ..     479     512 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.13
                            AAA_29  21 lkgatlltGpsGsGKSTll 39 
                                       +kg +ll G+ G+GK+ l 
  gi|385805405|ref|YP_005841803.1| 217 PKG-VLLYGAPGTGKTLLA 234
                                       356.9**********8765 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.033
                            AAA_29  21 lkgatlltGpsGsGKSTllDAi 42 
                                       ++g +ll Gp G+GK+ l  A+
  gi|385805405|ref|YP_005841803.1| 490 PRG-VLLFGPPGTGKTMLAKAV 510
                                       356.9**********9887666 PP

>> DUF2130  Uncharacterized protein conserved in bacteria (DUF2130)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       2.1   6.8e+02      31      61 ..     528     560 ..     525     580 .. 0.78
   2 ?    9.2   0.2     0.002      0.67     163     221 ..     666     726 ..     664     729 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 2.1
                           DUF2130  31 tklqGEelEqhieeelnkkra.fpna..fdkine 61 
                                       +k +GE+ E +i e ++++r+  p    fd+i  
  gi|385805405|ref|YP_005841803.1| 528 SKWVGES-EKAIREIFRRARQySPVIifFDEIDS 560
                                       5788987.***********996564488998876 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.002
                           DUF2130 163 aliksleakkelenvkekneditefetkkeefkekfrkn.ieaavekfqkaieeidke.le 221
                                       al++++ ++   en+ + ++ + +fe+ ++ +k+  +k+ ie  ++ f++a ++i+k+ +e
  gi|385805405|ref|YP_005841803.1| 666 ALVREAGLRALRENLSATEIRMRHFEDALQVIKPSITKQmIEYYIKWFEQARQAISKKiIE 726
                                       67889999999***********************9987736889999**********9665 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0    0.0019      0.61       4      62 ..     221     285 ..     220     310 .. 0.82
   2 ?   -1.4   0.0       4.8   1.6e+03       6      17 ..     496     507 ..     493     561 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0019
                               Zot   4 lvtGapGsgKts..gavkkdllpalk..egRkiitnidGlrlerieqvlgekvs.tarlirid.n 62 
                                       l +GapG+gKt+  +av ++ +   +  +g +i+ +  G   +r++ +++e+++ t+ +i+id +
  gi|385805405|ref|YP_005841803.1| 221 LLYGAPGTGKTLlaKAVANETQAYFVaiNGPEIMSKFYGESEQRLREIFEEAKKhTPAIIFIDeI 285
                                       679********733679998888666346*********************99999******9942 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.8
                               Zot   6 tGapGsgKtsga 17 
                                        G+pG+gKt+ a
  gi|385805405|ref|YP_005841803.1| 496 FGPPGTGKTMLA 507
                                       699999999765 PP

>> DUF1905  Domain of unknown function (DUF1905)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.2     0.069        22      56      81 ..      23      48 ..      13      48 .. 0.82
   2 ?    4.0   0.0      0.16        52      55      80 ..      65      90 ..      57      91 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.069
                                      T-EEEEE-HHHHHHHT--TTSEEEEE CS
                           DUF1905 56 ggyiLpvkaavrkaigkeaGdtvtve 81
                                      g+  + ++ ++ k+ig+e+Gd+v++e
  gi|385805405|ref|YP_005841803.1| 23 GRGKVRIDLEMLKEIGVEPGDVVEIE 48
                                      5556778899*************985 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.16
                                      TT-EEEEE-HHHHHHHT--TTSEEEE CS
                           DUF1905 55 kggyiLpvkaavrkaigkeaGdtvtv 80
                                      +g+ i+ ++  vrk +g++ Gd+v v
  gi|385805405|ref|YP_005841803.1| 65 QGQDIIRMDGLVRKNAGVSIGDKVIV 90
                                      47889999999************977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (731 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      582  (0.0324614); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); expected 17.9 (0.001)
Passed Fwd filter:                        55  (0.00306766); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              55  [number of targets reported over threshold]
# CPU time: 0.85u 0.35s 00:00:01.20 Elapsed: 00:00:00.72
# Mc/sec: 3052.96
//
Query:       gi|385805406|ref|YP_005841804.1|  [L=81]
Description: hypothetical protein FFONT_0362 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); 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: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 539.63
//
Query:       gi|385805407|ref|YP_005841805.1|  [L=350]
Description: flap endonuclease-1 [Fervidicoccus fontis Kam940]
Scores for complete 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-24   85.1   0.0    7.6e-24   84.1   0.0    1.6  1  XPG_N       XPG N-terminal domain
    5.9e-24   84.2   0.0    1.5e-23   83.0   0.0    1.7  1  XPG_I       XPG I-region
    0.00045   20.8   0.3    0.00045   20.8   0.3    2.5  2  5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
  ------ inclusion threshold ------
      0.014   16.0   0.2      0.093   13.4   0.0    2.4  2  HHH_5       Helix-hairpin-helix domain
      0.023   15.1   1.3       0.52   10.8   0.1    2.5  2  eIF3_N      eIF3 subunit 6 N terminal domain
       0.11   12.1   0.8       0.85    9.2   0.3    2.0  2  INTS5_N     Integrator complex subunit 5 N-terminus
        2.4    8.2   5.9        0.8    9.8   0.5    2.1  2  QueH        Epoxyqueuosine reductase QueH


Domain annotation for each model (and alignments):
>> XPG_N  XPG N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.1   0.0     3e-27   7.6e-24       8     100 ..      10     106 ..       1     107 [. 0.91

  Alignments for each domain:
  == domain 1  score: 84.1 bits;  conditional E-value: 3e-27
                                       HHHHHH-GEEEEEGGGGTTEEEEEEHHHHHHHHHHHSE.ETTEE-BS.....-HHHHHHHHHHHHHHHTTEEEEEEE CS
                             XPG_N   8 kllkevaairsvsiealegkklaiDaslwlyrfliavreqlgnalen.....tshlmglfsrllrlldfgikPifVF 79 
                                       +l+ + a i+++++e+l+g+++aiDa+  ly+fl a+r+++g+ l       tshl g+f+r++ l++ gikPi+VF
  gi|385805407|ref|YP_005841805.1|  10 ELIPPEA-IKEIELESLKGRTIAIDAYNALYQFLAAIRQPDGTPLIDnkgrvTSHLSGIFYRTINLIEAGIKPIYVF 85 
                                       5566666.**********************************987666899************************** PP

                                       --S--GGGHHHHHHHHHHHHH CS
                             XPG_N  80 dgkapdlkkeelekrserrqe 100
                                       dg +p+lk++elekr++ ++e
  gi|385805407|ref|YP_005841805.1|  86 DGLPPSLKEKELEKRRKVKEE 106
                                       ****************99887 PP

>> XPG_I  XPG I-region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.0   0.0   5.7e-27   1.5e-23       2      94 .]     147     242 ..     146     242 .. 0.92

  Alignments for each domain:
  == domain 1  score: 83.0 bits;  conditional E-value: 5.7e-27
                                       HHT--EEE-SS-HHHHHHHHHHTTSSSEEE-SSSHHHHTT-SEEEESTT..ECECTT....EEECEEEEEEHHHHHH CS
                             XPG_I   2 lmgipyvvApgEAEAqcayLqkkglvdaviseDsDlllFGapkvlrnls.kkkskkk..kekekkkvevidlekvlk 75 
                                       +mg+p v+Ap E+EAq+ay++kkg+v+   s+D+D++lFG+p+v+rnl+ ++k+k    + + + k+evi+ + + +
  gi|385805407|ref|YP_005841805.1| 147 AMGLPTVQAPAEGEAQAAYMAKKGDVWSSGSQDYDSILFGSPRVVRNLTvSGKRKLPkkDVYIDIKPEVIESNVIYE 223
                                       79**********************************************975554444667888999*********** PP

                                       HHT--HHHHHHHHHHHCET CS
                             XPG_I  76 elgltreqlidlaillgcD 94 
                                       +lg++re+li + i+lg+D
  gi|385805407|ref|YP_005841805.1| 224 KLGINREKLIIIGIMLGTD 242
                                       *****************99 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 ?   -0.6   0.5      0.83   2.1e+03      55      73 ..     115     133 ..      92     149 .. 0.56
   2 !   20.8   0.3   1.8e-07   0.00045      21      51 ..     246     276 ..     240     342 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.83
                        5_3_exonuc  55 klkekLeenkeearlskkL 73 
                                        ++ek ee++++a++s +L
  gi|385805407|ref|YP_005841805.1| 115 IAEEKYEEARKYAQISTRL 133
                                       2445666666666666655 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 1.8e-07
                        5_3_exonuc  21 pGvpgiGektAakLlkeygsleeilenldel 51 
                                        G++g+G ktA k++k y++ eeil++l ++
  gi|385805407|ref|YP_005841805.1| 246 DGIKGVGIKTALKIVKSYEKTEEILKSLPQT 276
                                       69************************88653 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.2   5.6e+03      15      28 ..     141     155 ..     139     163 .. 0.80
   2 ?   13.4   0.0   3.6e-05     0.093       6      31 ..     247     271 ..     246     277 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.2
                                       HHHHHTT.T--SHHH CS
                             HHH_5  15 Alallsa.Giesved 28 
                                       A++ll+a G  +v++
  gi|385805407|ref|YP_005841805.1| 141 AIKLLDAmGLPTVQA 155
                                       899999999999987 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 3.6e-05
                                       TSTT--HHHHHHHHTTT--SHHHHHH CS
                             HHH_5   6 svsGiGpktAlallsaGiesvedlaa 31 
                                       +++G+G ktAl++++  +e  e++++
  gi|385805407|ref|YP_005841805.1| 247 GIKGVGIKTALKIVKS-YEKTEEILK 271
                                       69**************.999999865 PP

>> eIF3_N  eIF3 subunit 6 N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.2      0.05   1.3e+02      55     102 ..      95     143 ..      91     202 .. 0.77
   2 ?   10.8   0.1    0.0002      0.52      68     125 ..     263     325 ..     214     329 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.05
                            eIF3_N  55 kelegeeevpeelekkreevleeleeleee..aekvlelledeevvsnlr 102
                                       kele+ ++v ee +kk + +++  e++ee+   +++ + l+de v+++++
  gi|385805407|ref|YP_005841805.1|  95 KELEKRRKVKEEAAKKYQVAIA-EEKYEEArkYAQISTRLNDEMVKEAIK 143
                                       6777777777766666655555.444544434777888888887777765 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0002
                            eIF3_N  68 ekkreevleeleeleeeaekvlelledeevvsn....lrs.dkkqnlefLkeehgitpemida 125
                                        +k ee+l+ l + + +  ++++ + ++ev++n     ++   +++ e+L eeh+++++ ++ 
  gi|385805407|ref|YP_005841805.1| 263 YEKTEEILKSLPQTQVDYYEIFNYFMNPEVTDNytiqWKEpSVEKIKEILVEEHDFNEARVEN 325
                                       47999****************************655433356677777*********998876 PP

>> INTS5_N  Integrator complex subunit 5 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.11   2.7e+02      31      87 ..      83     144 ..      74     153 .. 0.58
   2 ?    9.2   0.3   0.00033      0.85      31      98 ..     268     344 ..     255     347 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.11
                           INTS5_N  31 nlLkklPaa.RsaVleylaqlfeeaveryl.....eevete..pilkesqina.eldeaieeiqtv 87 
                                        ++  lP + ++  le  +++ eea ++y      e    +  ++ k +qi++   de+++e  ++
  gi|385805407|ref|YP_005841805.1|  83 YVFDGLPPSlKEKELEKRRKVKEEAAKKYQvaiaeE----KyeEARKYAQISTrLNDEMVKEAIKL 144
                                       567777766567778888888888888887443322....12222333333330334444444444 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00033
                           INTS5_N  31 nlLkklPaaRsaVleylaqlfeeaveryl......eevete.......pilkesqinaeldeaieeiqtvleelvee 94 
                                       ++Lk+lP ++ + +e ++ +++  v+ +       +    +         +++  ++a +++aie +q+ ++e v++
  gi|385805407|ref|YP_005841805.1| 268 EILKSLPQTQVDYYEIFNYFMNPEVTDNYtiqwkeP----SvekikeiLVEEHDFNEARVENAIERLQKSFKENVKS 340
                                       68*****************99977766544744443....344346556777788899***************9998 PP

                           INTS5_N  95 npka 98 
                                       + k+
  gi|385805407|ref|YP_005841805.1| 341 QTKG 344
                                       8775 PP

>> QueH  Epoxyqueuosine reductase QueH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.5   0.00031       0.8      36      78 ..      93     136 ..      69     141 .. 0.78
   2 ?    0.8   0.7      0.18   4.7e+02      21      52 ..     279     310 ..     266     343 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00031
                              QueH  36 peeEyekRleelkrlieelkielieedydl.eefleavkgleke 78 
                                       +e+E ekR++  ++ ++++++ + ee+y++ +++ +  + l++e
  gi|385805407|ref|YP_005841805.1|  93 KEKELEKRRKVKEEAAKKYQVAIAEEKYEEaRKYAQISTRLNDE 136
                                       689************************98625666666666555 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.18
                              QueH  21 egfevtvffynpnihpeeEyekRleelkrlie 52 
                                       +++e+  +f+np+++++   + ++ +++++ e
  gi|385805407|ref|YP_005841805.1| 279 DYYEIFNYFMNPEVTDNYTIQWKEPSVEKIKE 310
                                       47899999999999987666655555555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1321  (0.0736795); expected 358.6 (0.02)
Passed bias filter:                      612  (0.0341346); 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: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2300.98
//
Query:       gi|385805408|ref|YP_005841806.1|  [L=290]
Description: succinyl-CoA synthetase subunit alpha [Fervidicoccus fontis Kam940]
Scores for complete 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-27   94.6   1.9    4.4e-27   94.6   1.9    1.9  2  CoA_binding    CoA binding domain
    2.5e-14   53.4   0.1    4.5e-14   52.5   0.1    1.4  1  Ligase_CoA     CoA-ligase
    4.4e-12   46.5   0.1    7.5e-12   45.8   0.1    1.4  1  CoA_binding_2  CoA binding domain
    5.9e-11   42.3   0.0    1.4e-10   41.1   0.0    1.6  2  Succ_CoA_lig   Succinyl-CoA ligase like flavodoxin domain
    8.1e-05   23.4   0.4    0.00021   22.1   0.2    1.8  2  GFO_IDH_MocA   Oxidoreductase family, NAD-binding Rossmann fo
    0.00044   19.9   0.9    0.00075   19.1   0.9    1.3  1  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind


Domain annotation for each model (and alignments):
>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.6   1.9   1.5e-30   4.4e-27       1      96 []       6     100 ..       6     100 .. 0.98
   2 ?   -1.8   0.0       1.7   5.1e+03       8      16 ..     176     184 ..     160     209 .. 0.66

  Alignments for each domain:
  == domain 1  score: 94.6 bits;  conditional E-value: 1.5e-30
                                       CTTEEEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHC.TTTEEEEES-HHHHH CS
                       CoA_binding   1 dkdtkviviGagglgiaglyhfkeklkygikavfgvnprkvgtevlglpvyksvdeleekt.evdvavitvPaesaq 76 
                                       +kdtkv+v+G++g+  +g +h+k +l+yg+k+v+gv+p+k g+ev g++vy+sv++++ +   +d+++i+vPa++ +
  gi|385805408|ref|YP_005841806.1|   6 NKDTKVLVQGITGK--EGSFHTKLMLEYGTKIVAGVSPGKEGQEVYGVKVYNSVENAMSENpHIDASIIFVPAAFTA 80 
                                       69************..********************************************955************** PP

                                       HHHHHHHHTT-SEEEEESST CS
                       CoA_binding  77 eavdelveagikgiviiteg 96 
                                       +av e+++++ik i++iteg
  gi|385805408|ref|YP_005841806.1|  81 DAVYEAIKNKIKNIIVITEG 100
                                       ******************97 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.7
                                       EETTTSHHH CS
                       CoA_binding   8 viGagglgi 16 
                                       viG+gg  i
  gi|385805408|ref|YP_005841806.1| 176 VIGVGGDPI 184
                                       556655522 PP

>> Ligase_CoA  CoA-ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.5   0.1   1.5e-17   4.5e-14       1     151 [.     152     272 ..     152     274 .. 0.92

  Alignments for each domain:
  == domain 1  score: 52.5 bits;  conditional E-value: 1.5e-17
                                       EESSHHHHHHHHHHHHHT..............T--BSEEEE-TSS--..........HHHHHHHHHHHHS-TT-SEE CS
                        Ligase_CoA   1 lvnGGtLayeamdlikealgdvasnkklknvlgseqheiidlGddaftkGrpHPmiDptkriealkklaadpevkvi 77 
                                       ++++GtL+ye  ++++ +              g +q+++i++G+d            + ++ie +k +  d+e+k++
  gi|385805408|ref|YP_005841806.1| 152 MSRSGTLTYEISYALSRE--------------GIGQSTVIGVGGDPII---------GLNFIEVMKLFNDDKETKAV 205
                                       689***************..............***************7.........9******************* PP

                                       EEEEEESSSEHHHHHHHHHHHHHHTT...--S-EEEEEECTTHH.....HHHHHHHTTTSSEEE-SSHHHHHHH CS
                        Ligase_CoA  78 lldivlGygahedpaaellkaikeakaegrelpvvarvaGteadpqelseqakaleeagveiasskaqalraak 151
                                       ++ +++G g  e+ +a   k+ +       ++p+va++aG +a+p++++++a+a+ + g  +++ k +al+ a+
  gi|385805408|ref|YP_005841806.1| 206 VMVGEIG-GDIEERVAMRFKKGE------FDKPIVAYIAGKTAPPGKRMGHAGAIITMGEGTYEGKIKALENAG 272
                                       *******.888887776555555......556**********************************99998775 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.1   2.5e-15   7.5e-12      10     114 ..      18     129 ..       9     131 .. 0.82

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 2.5e-15
                                       S-TTSHHHHHHHHHHHHT--.EEEESSS-..SEETTEES----T.......T--EEEE-S-HHHHGGGHHHHHHH-- CS
                     CoA_binding_2  10 dnpgkfgykvlryllehglp.vvpVnpke..eeilgekvyaslaed...pepvdlvdvftppeatpeivkealalga 80 
                                        ++g+f  k    +le g + v  V p +  +e+ g+kvy s++++     ++d+  +f+p++ t++ v ea++ ++
  gi|385805408|ref|YP_005841806.1|  18 GKEGSFHTK---LMLEYGTKiVAGVSPGKegQEVYGVKVYNSVENAmseNPHIDASIIFVPAAFTADAVYEAIKNKI 91 
                                       444444444...4444454404569999999*************63467899************************* PP

                                       SEEEE-TT....---HHHHHHHHHTT-EEE.ES-HHHH CS
                     CoA_binding_2  81 kavwlqpg....sedeeaaelaeeagirvvgdrCilve 114
                                       k +++  +     e  +++++a+e+gir++g++C++++
  gi|385805408|ref|YP_005841806.1|  92 KNIIVITEgipvHETMKFVNYANEKGIRIIGPNCPGII 129
                                       ***999999*999***********************97 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 ?   -2.7   0.0       1.6   4.7e+03      77      90 ..      86     100 ..      79     113 .. 0.65
   2 !   41.1   0.0   4.6e-14   1.4e-10       1     107 [.     146     254 ..     146     285 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.6
                      Succ_CoA_lig  77 raark.kpvvvlksG 90 
                                       ++++k k ++v+  G
  gi|385805408|ref|YP_005841806.1|  86 AIKNKiKNIIVITEG 100
                                       445556666666555 PP

  == domain 2  score: 41.1 bits;  conditional E-value: 4.6e-14
                      Succ_CoA_lig   1 pGkialisqSGalalalldwaasrglgfskvvslGn..eadvdvadlleylaedpetkvillylEsird.grkflsa 74 
                                       +G+++++s SG+l  ++  +++++g+g s+v+ +G    + +++ ++++ +++d+etk+++++ E  +d  ++ +  
  gi|385805408|ref|YP_005841806.1| 146 RGPVGIMSRSGTLTYEISYALSREGIGQSTVIGVGGdpIIGLNFIEVMKLFNDDKETKAVVMVGEIGGDiEERVAMR 222
                                       699********************************9445788999***********************977899999 PP

                      Succ_CoA_lig  75 arraarkkpvvvlksGrseagaraaashtgala 107
                                        ++   +kp+v++ +G+++   +  + h ga+ 
  gi|385805408|ref|YP_005841806.1| 223 FKKGEFDKPIVAYIAGKTAPPGKR-MGHAGAII 254
                                       9999999*********98654443.35555554 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.2     7e-08   0.00021       2      91 ..      10      96 ..       9     121 .. 0.79
   2 ?   -1.6   0.0       1.6   4.7e+03      20      38 ..     197     215 ..     176     238 .. 0.50

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 7e-08
                                      EEEEETT.SHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHH.HHHTCTTESEEEE-S-GGGHHHH CS
                      GFO_IDH_MocA  2 rvaiiGa.Gkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdle.elladpeidavivatpngtheel 78
                                      +v++ G+ Gk gs h  +l+ +  ++++va ++p++e +e     +gv++y+++e +++++p+ida i+ +p+   ++ 
  gi|385805408|ref|YP_005841806.1| 10 KVLVQGItGKEGSFHT-KLMLE-YGTKIVAGVSPGKEGQEV----YGVKVYNSVEnAMSENPHIDASIIFVPAAFTADA 82
                                      6788888788899998.55555.69999999****988884....8********96677777***************** PP

                                      HHHHHHTT-.EEEE CS
                      GFO_IDH_MocA 79 akaaleagk.hvll 91
                                      + +a+++++ ++++
  gi|385805408|ref|YP_005841806.1| 83 VYEAIKNKIkNIIV 96
                                      *******9986554 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.6
                                       HHTTTTEEEEEEECSSHHH CS
                      GFO_IDH_MocA  20 nesqrleevvalldpdaer 38 
                                       n+ +++  vv + +++   
  gi|385805408|ref|YP_005841806.1| 197 NDDKETKAVVMVGEIGGDI 215
                                       3333333444444433333 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 !   19.1   0.9   2.5e-07   0.00075       3     129 ..       7     135 ..       5     143 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2.5e-07
                                       HTS-EEEES-.SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEE.HHHHHH...T-SEEEE-S-HHHHH CS
                              IlvN   3 kgkkiaviGy.GsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevlt.vaeavk...kadvvmiliPDelqk 74 
                                       k+ k+ v G  G  G  +++ + + g ++v g+  g+   +  +  g++v++ v++a++   + d  +i +P  + +
  gi|385805408|ref|YP_005841806.1|   7 KDTKVLVQGItGKEGSFHTKLMLEYGTKIVAGVSPGK---EGQEVYGVKVYNsVENAMSenpHIDASIIFVPAAFTA 80 
                                       57788888854999**********************9...55566788877514445541115688899*****999 PP

                                       HHHHHHTGGG--TT-EEEESSSHHHHT..TSS---TTSEEEEEEESS-SHHHHHHHH CS
                              IlvN  75 evyeeeiepnlkegkalafahGfnihf..glikppkdvdvvlvAPkgpGhlvreeye 129
                                       + + e+i++++k  ++++ + G  +h   ++++  ++  + ++ P +pG +v +e +
  gi|385805408|ref|YP_005841806.1|  81 DAVYEAIKNKIK--NIIVITEGIPVHEtmKFVNYANEKGIRIIGPNCPGIIVPNETK 135
                                       8888*****997..578888999998622679999**************99987755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 2089.38
//
Query:       gi|385805409|ref|YP_005841807.1|  [L=384]
Description: succinyl-CoA synthetase subunit beta [Fervidicoccus fontis Kam940]
Scores for complete 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-55  186.6   0.1    6.9e-55  185.7   0.1    1.4  1  ATP-grasp_2    ATP-grasp domain
    7.4e-15   55.1   0.0    1.2e-14   54.4   0.0    1.3  1  Ligase_CoA     CoA-ligase
    0.00018   21.2   0.1    0.00034   20.3   0.1    1.5  1  RimK           RimK-like ATP-grasp domain
    0.00021   21.1   0.4    0.00038   20.3   0.4    1.3  1  GARS_A         Phosphoribosylglycinamide synthetase, ATP-gras
    0.00052   19.5   0.4     0.0028   17.1   0.3    2.2  2  ATP-grasp_5    ATP-grasp domain
     0.0096   15.4   0.0      0.017   14.6   0.0    1.3  1  Ins134_P3_kin  Inositol 1,3,4-trisphosphate 5/6-kinase ATP-gr


Domain annotation for each model (and alignments):
>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.7   0.1   2.3e-58   6.9e-55       1     201 [.       5     199 ..       5     200 .. 0.97

  Alignments for each domain:
  == domain 1  score: 185.7 bits;  conditional E-value: 2.3e-58
                                       BE-HHHHHHHHHCTT----SEEEESSHHHHHHHHHHHTSS.SEEEEE--SSSTCCCTTCEEEESSHHHHHHHHHCCT CS
                       ATP-grasp_2   1 nlhEyqakeilakygvkvpegevaesaeeaeeaakklgek.elvvKaQvlaGGRGKagGvklvkskeeakeaakell 76 
                                       +l+Ey+akei + +g+kvp+g v  + +++e+++++ + k  lvvK+Qvl+ GRGK+gGvk++k+ +ea ++ ++l+
  gi|385805409|ref|YP_005841807.1|   5 KLFEYEAKEIYKLHGIKVPKGVVIAKSDDIEKKIEESKLKfPLVVKSQVLVAGRGKSGGVKFAKDINEAVTVSNNLF 81 
                                       699****************************999987755258********************************** PP

                                       TSEEE-TTS-TT-EEE--EEEEE---ECEEEEEEEEEETTTTEEEEEEESSTTS-HHHHHHH-GGGEEEEEEBTTTB CS
                       ATP-grasp_2  77 gkelvtkqtgkeGkkvekvlveealdikkElYlsivlDraskkvvviaSseGGvdiEevaakkPekiikvaidpakg 153
                                       + e++       G k + +l+eea++ + E++ si++Dra++++v+++S++GG++iEev +k+Pe iik+++dp  g
  gi|385805409|ref|YP_005841807.1|  82 NLEIK-------GLKPNFLLIEEAVEHDNEYFASITIDRAERCPVILVSKSGGMEIEEVSKKSPESIIKYHVDPILG 151
                                       *****.......***************************************************************** PP

                                       --HHHHHHHHHHCT--CHHHHHHHHHHHHHHHHHHHTTEEEEEEEEEE CS
                       ATP-grasp_2 154 lkeeqareiakklglekelvkkaakiikklyklfveldatlvEiNPLv 201
                                       +++++ar+i  klgl+++++ ++++++k ly++f  +d  lvE NP++
  gi|385805409|ref|YP_005841807.1| 152 MRDFEARNIGYKLGLSGKELASFTSFLKSLYNIFEMYDGDLVESNPFT 199
                                       **********************************************86 PP

>> Ligase_CoA  CoA-ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.4   0.0     4e-18   1.2e-14       3     148 ..     261     374 ..     259     378 .. 0.94

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 4e-18
                                       SSHHHHHHHHHHHHHT..............T--BSEEEE-TSS--..........HHHHHHHHHHHHS-TT-SEEEE CS
                        Ligase_CoA   3 nGGtLayeamdlikealgdvasnkklknvlgseqheiidlGddaftkGrpHPmiDptkriealkklaadpevkvill 79 
                                       nG++L++++mdli e               g+ +++++d+G++a            +++ ea+  l++ p+ k i++
  gi|385805409|ref|YP_005841807.1| 261 NGAGLTMATMDLIYEF--------------GGSPANFLDIGGGAN----------SERVKEAVSLLLEYPKAKSIFI 313
                                       8***************..............***************..........8********************* PP

                                       EEEESSSEHHHHHHHHHHHHHHTT...--S-EEEEEECTTHH.....HHHHHHHTTTSSEEE-SSHHHH CS
                        Ligase_CoA  80 divlGygahedpaaellkaikeakaegrelpvvarvaGteadpqelseqakaleeagveiasskaqalr 148
                                       +i++G+ +++++a ++  a+k++    + +p+ +r+ Gt+++     e++++l+e g+  ++   +a+r
  gi|385805409|ref|YP_005841807.1| 314 NIFGGITRCDEVARGIEGALKSVG---KIKPIFVRLSGTNEE-----EGKRILKELGISSYNDPIEAAR 374
                                       ***********************7...9**************.....9999***999987776666655 PP

>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   1.1e-07   0.00034      13      71 ..      17      79 ..       8     128 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.1e-07
                                      HTT-----EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--....EEEEE-SHHHHHHHHHH CS
                              RimK 13 kakikvpntalardeedaekliekiklrfPvvvKsvegsqGi....kvvlakkeqklkqvlea 71
                                       ++ikvp+  ++ + +d+ek ie+ kl+fP+vvKs     G     +v +ak+ ++++ v + 
  gi|385805409|ref|YP_005841807.1| 17 LHGIKVPKGVVIAKSDDIEKKIEESKLKFPLVVKSQVLVAGRgksgGVKFAKDINEAVTVSNN 79
                                      589*******************************97654443112258888888888777444 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 !   20.3   0.4   1.3e-07   0.00038       6      92 ..      11     102 ..       7     120 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.3e-07
                                       HHHHHHHTT--B--EEEESSHHHHHHHHHHHSSSE.EEEEESC-GGGT....-EEEESSHHHHHHHHHHHCTS-TTC CS
                            GARS_A   6 akdllkkagiptaeyeaftdpeeakeyieeataka.lVvKadglaagK....gvivakseeealkavkeilekkkfG 77 
                                       ak++ k +gi+ ++  ++ + +++++ iee + k  lVvK++ l ag+    gv+ ak+ +ea+++ +++++ +  G
  gi|385805409|ref|YP_005841807.1|  11 AKEIYKLHGIKVPKGVVIAKSDDIEKKIEESKLKFpLVVKSQVLVAGRgksgGVKFAKDINEAVTVSNNLFNLEIKG 87 
                                       69999************************99988878*********984444599********************** PP

                                       CCCSSEEEEE---SE CS
                            GARS_A  78 eagekvviEelleGe 92 
                                          + ++iEe +e +
  gi|385805409|ref|YP_005841807.1|  88 LKPNFLLIEEAVEHD 102
                                       **********99854 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.3   9.4e-07    0.0028      10     148 ..       6     142 ..       3     214 .. 0.67
   2 ?   -3.7   0.0       2.3   6.8e+03      11      25 ..     350     364 ..     349     370 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 9.4e-07
                       ATP-grasp_5  10 Lteaeakelleaygipvvetrlassaeeaveaaeei..gypvvlKivspdilhKtdvgGvrlnlkdaeevraaaeei 84 
                                       L e+eake+ +  gi+v++  +++++++  + +ee   ++p v+K ++  +  + + gGv++    a+++++a+   
  gi|385805409|ref|YP_005841807.1|   6 LFEYEAKEIYKLHGIKVPKGVVIAKSDDIEKKIEESklKFPLVVKSQVL-VAGRGKSGGVKF----AKDINEAVTVS 77 
                                       789*******************999999999887652278888887754.889999*****9....77888888888 PP

                       ATP-grasp_5  85 lervkekspeariegvlVqemakrggrElivgvteDpv.FGpvilfGl.GGtavevlkdvavalpp 148
                                        + ++ + ++ + + +l++e ++ +  E + ++t D     pvil+   GG+++e +++ + +   
  gi|385805409|ref|YP_005841807.1|  78 NNLFNLEIKGLKPNFLLIEEAVE-HDNEYFASITIDRAeRCPVILVSKsGGMEIEEVSKKSPESII 142
                                       88888777888888999999999.899999999999642789988886578888877777655544 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 2.3
                       ATP-grasp_5  11 teaeakelleaygip 25 
                                       +e+e k++l+ +gi+
  gi|385805409|ref|YP_005841807.1| 350 NEEEGKRILKELGIS 364
                                       578999999999997 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 !   14.6   0.0   5.8e-06     0.017       6      48 ..      19      61 ..      15      76 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.8e-06
                                      TEE---EEEE-S-GTTHHHHHHHTT--SSEEEEESB.-SST.TT CS
                     Ins134_P3_kin  6 rvgvPkqlvvtkdasslseavakagLklPliakplv.adGtaks 48
                                       + vPk +v+  +++++ + +++++Lk+Pl+ k+ v + G  ks
  gi|385805409|ref|YP_005841807.1| 19 GIKVPKGVVIA-KSDDIEKKIEESKLKFPLVVKSQVlVAGRGKS 61
                                      5789*****99.89*******************98735677676 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); 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: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 2245.60
//
Query:       gi|385805410|ref|YP_005841808.1|  [L=263]
Description: radical SAM protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.3e-18   66.2   0.0    6.3e-18   65.7   0.0    1.2  1  Radical_SAM  Radical SAM superfamily
    6.7e-10   39.4   0.1      1e-09   38.8   0.1    1.4  1  Fer4_12      4Fe-4S single cluster domain
    9.3e-07   29.0   0.0    1.9e-06   28.0   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 !   65.7   0.0   1.1e-21   6.3e-18       6     143 ..      55     194 ..      53     207 .. 0.92

  Alignments for each domain:
  == domain 1  score: 65.7 bits;  conditional E-value: 1.1e-21
                                       EESS--TTTSCCTT.HHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEE CS
                                       xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   6 gCnlrCsfCarpet.vrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlaklavpgiri 80 
                                       gCnlrC+fC+ ++   ++e+ g + s+e+++ ++ +++ +    k++ ++ggep+l  +    +++  k+   ++++
  gi|385805410|ref|YP_005841808.1|  55 GCNLRCKFCWAWRQrDYPERFGNFYSPEQVASKLIRIA-NEKsYKNIRISGGEPTLGFEHLIQVLENLKN--YDMTF 128
                                       9************99999*******************6.4444*************98887777777777..7**** PP

                                       EEEECSSCHG..HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSE CS
                                       xxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  81 tvetngtlpd..eeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagik 143
                                        +etng+      e   +l + +  +v ++++  ++e+++ +++ +++ f+ +++al++l +++++
  gi|385805410|ref|YP_005841808.1| 129 ILETNGIYFGyyNELSPELSNFENVHVRVSIKGCTPEDFHSITGaKKEFFQVQINALKNLIDSNVR 194
                                       ********99999999*********************************************99887 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 !   38.8   0.1   1.7e-13     1e-09      14     105 ..      55     144 ..      46     192 .. 0.79

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 1.7e-13
                           Fer4_12  14 gCnlsCkgCfnketwsfk..sgkef.tkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekd 87 
                                       gCnl+Ck+C +   ++     g+ + +++++ ++i+ ++++s + + ++GGEP l    e l+++++++k+  ++  
  gi|385805410|ref|YP_005841808.1|  55 GCNLRCKFCWAWRQRDYPerFGNFYsPEQVASKLIRIANEKSYKNIRISGGEPTL--GFEHLIQVLENLKNYDMT-F 128
                                       9********954444322334444436****************************..****************95.8 PP

                           Fer4_12  88 iwlytgytleelskkeke 105
                                       i++++g  +   ++   +
  gi|385805410|ref|YP_005841808.1| 129 ILETNGIYFGYYNEL--S 144
                                       ******999888643..2 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 !   28.0   0.0   3.1e-10   1.9e-06       7      91 ..      55     136 ..      52     161 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 3.1e-10
                           Fer4_14   7 gCnlsCkgCd..nketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypek 81 
                                       gCnl Ck+C   ++ ++ ++ g+ ++ e++ + l    ++++ ++ + ++GGeP      ++l++++++lk+    +
  gi|385805410|ref|YP_005841808.1|  55 GCNLRCKFCWawRQRDYPERFGNFYSPEQVASKLIRIANEKSYKN-IRISGGEPT--LGFEHLIQVLENLKNYD--M 126
                                       8*********999999*******9999988888776666666455.9*******9..66899999999998765..8 PP

                           Fer4_14  82 kiwletngtl 91 
                                          letng +
  gi|385805410|ref|YP_005841808.1| 127 TFILETNGIY 136
                                       8889999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       798  (0.0445089); expected 358.6 (0.02)
Passed bias filter:                      650  (0.0362541); 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: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1653.40
//
Query:       gi|385805411|ref|YP_005841809.1|  [L=185]
Description: hypothetical protein FFONT_0367 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score 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   0.0      0.047   13.8   0.0    1.2  1  CNOT1_HEAT  CCR4-NOT transcription complex subunit 1 HEAT rep


Domain annotation for each model (and alignments):
>> CNOT1_HEAT  CCR4-NOT transcription complex subunit 1 HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.6e-06     0.047      52     120 ..      56     124 ..      40     137 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.6e-06
                                       HHHHHHTT-HHHHHHHS.-TTCHHHCHHHHHHHT---HHHHHHHH--TT....THHHHHHHHHHHHH--T. CS
                        CNOT1_HEAT  52 ldvaqelkilsellnkl.pfnfaldLaalasrreyldlekwledklkehgek.fvqalldfLeekakqele 120
                                       l+++ e +i+s +l  l   +f+++La l  + + l + +wl+  +  +  + +v +++  L+++++  l 
  gi|385805411|ref|YP_005841809.1|  56 LEMLNEVNIISTILLALiLPTFIVSLALLLDKGKRLSFLSWLTYGIYVS--QfVVISMMLTLKRRVELILP 124
                                       789999**9999999984446***********************99977..43666777789999887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       839  (0.0467957); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1308.39
//
Query:       gi|385805412|ref|YP_005841810.1|  [L=354]
Description: peptidase, family S26B [Fervidicoccus fontis Kam940]
Scores for complete 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   33.8   0.3    4.2e-08   33.0   0.3    1.4  1  Peptidase_S24   Peptidase S24-like
  ------ inclusion threshold ------
       0.47    9.8   3.5          1    8.7   3.5    1.5  1  Zn_peptidase_2  Putative neutral zinc metallopeptidase


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 !   33.0   0.3   4.7e-12   4.2e-08       2      65 ..      34      99 ..      33     104 .. 0.90

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 4.7e-12
                                      XXSSTTCCTXXTTXEEEEECTS---TTSEEEEEETTCE-EEEEEEEEETTEEEEE.SST..T.STEE CS
                     Peptidase_S24  2 vpGdSMeptlldGdlilVdkfsepkrGdivvfrlpgeeeayiKrviglpgdrvllasnn..e.yppl 65
                                      v G+SM+ptl+ Gd+++  ++ ++k+G++vv  + + +   i+r++g+ ++ v ++ +n  + +pp+
  gi|385805412|ref|YP_005841810.1| 34 VSGNSMYPTLKTGDIVVGITDKNYKNGEVVVWCVSKTQ-CVIHRIVGTYNEYVITKGDNnpYiDPPI 99
                                      89******************************999997.****************988755556665 PP

>> Zn_peptidase_2  Putative neutral zinc metallopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   3.5   0.00012         1     123     168 ..     118     169 ..     103     170 .. 0.57

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00012
                    Zn_peptidase_2 123 klslillliglllslss...lllligiilfalavlfq...lvtLPvEfdASk 168
                                        l ++l+ + ++++ +s   + + i +++f++ vl++   l+t+PvE++ S+
  gi|385805412|ref|YP_005841810.1| 118 ILIFLLVALYIFFNRKSflpSGFSISVLVFGIYVLISvilLITMPVEIETSS 169
                                       22333333334443333887456666666666665552227899****9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       826  (0.0460706); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.26s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2391.32
//
Query:       gi|385805413|ref|YP_005841811.1|  [L=185]
Description: hypothetical protein FFONT_0369 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1174.86
//
Query:       gi|385805414|ref|YP_005841812.1|  [L=369]
Description: hypothetical protein FFONT_0370 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-15   56.4  24.1    2.2e-15   56.4  24.1    2.0  2  MFS_1     Major Facilitator Superfamily


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.4  24.1   1.2e-19   2.2e-15      45     352 ..       2     329 ..       1     329 [. 0.74
   2 !   14.5  14.6   7.1e-07     0.013      72     172 ..     264     361 ..     251     366 .. 0.78

  Alignments for each domain:
  == domain 1  score: 56.4 bits;  conditional E-value: 1.2e-19
                             MFS_1  45 aavaslplGrlsdrfGrrrvlllglllfalglllllfasslw.lllvlrvlqGlgagalfpagaaliadwfpkeerg 120
                                       +a++s+ ++r+s ++    + +++l+l+a+++l+++f s++  +++++  + G+  +++ p++a +i  + +k   +
  gi|385805414|ref|YP_005841812.1|   2 YALGSYYYSRISGKLKQDQFAIFSLILMASSILFMAF-SPSAiFIILFNGVFGMSIAFISPLMAGMIINYLMK--DN 75 
                                       89999**********9999************777779.777778999999**********************9..55 PP

                             MFS_1 121 raigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeepperkrkspkeee......... 188
                                        +i   ++ +slG+i+g++++++  ++++   +++i+++++l ++ l + ++pe+ ++++  +   ++         
  gi|385805414|ref|YP_005841812.1|  76 IGITRTNVISSLGIIFGYIFAAFGGALFSSKDLMFINTAFTLAVLPL-VKYFPEKFKTKGERRALILSlmpqvagri 151
                                       66888999999999999999999998888777777777777777443.25665555555555555555999998885 PP

                             MFS_1 189 ........kgtgpaplvp.................awkallkdpvlwillialllfffgfsglltllplylqevlgl 240
                                               k                           +k+l+  p    +l+++ +  +++++++t +p+y  + +g+
  gi|385805414|ref|YP_005841812.1| 152 raipheivK--------YerelsfkalyndfkkmfYFKKLREMPT---VLLGATVLYTAIQIFFTPMPSY-LKIFGY 216
                                       555555553........0444444446677777777888888884...5555555556************.****** PP

                             MFS_1 241 sglllaglllallalvgailallagrlsdr...lgrrrrlllallllllaalglallavtssavllllvlvl...iG 311
                                       +    +++l+ +  + +    ll+  ++++   + + +  ll++++++   l+l++l ++ + ++ l+++++   iG
  gi|385805414|ref|YP_005841812.1| 217 T-DSDIYTLYLINNFTT----LLLYDFMRKrteTESGTWKLLIIAVMVRPILFLFPLLTYLKVPINLIFVIFyigIG 288
                                       *.466666677777776....45555564446645555555555555555555555555545555555333355799 PP

                             MFS_1 312 fglgfvfpsllalasdlappeeagtasglfntagslggalg 352
                                       + ++ ++++l +l++++a pe  g a++ +n + ++g+++g
  gi|385805414|ref|YP_005841812.1| 289 ISWSGISVALPVLIMKNADPESKGLALSKMNATTTIGTIVG 329
                                       999999*******************************9987 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 7.1e-07
                             MFS_1  72 falglllllfa...sslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggll 144
                                       f    l++l++    ++  +++++ +  G+  +++  a  +li + + +e +g+a++ ++a++ +G+i+g  +gg++
  gi|385805414|ref|YP_005841812.1| 264 F----LFPLLTylkVPINlIFVIFYIGIGISWSGISVALPVLIMKNADPESKGLALSKMNATTTIGTIVGSFVGGIV 336
                                       2....222222334566667888888888888999****************************************** PP

                             MFS_1 145 asslgWravfyilaivsllafvlfllll 172
                                       + ++  +++ +++ +++l+++    +++
  gi|385805414|ref|YP_005841812.1| 337 SKYYFITGTSILASLMALVSLA---IFF 361
                                       *999999999999999999855...333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       817  (0.0455686); 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:                         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: 0.63u 0.26s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2332.24
//
Query:       gi|385805415|ref|YP_005841813.1|  [L=40]
Description: hypothetical protein FFONT_0371 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      160  (0.00892409); 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: 0.29u 0.21s 00:00:00.50 Elapsed: 00:00:00.35
# Mc/sec: 339.75
//
Query:       gi|385805416|ref|YP_005841814.1|  [L=37]
Description: hypothetical protein FFONT_0372 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 274.26
//
Query:       gi|385805417|ref|YP_005841815.1|  [L=253]
Description: hypothetical protein FFONT_0373 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0046   17.3   6.8     0.0046   17.3   6.8    2.5  2  Peptidase_A24  Type IV leader peptidase family
     0.0078   16.7   1.1      0.044   14.3   1.1    2.2  1  Arc_PepC_II    Archaeal Peptidase A24 C-terminus Type II


Domain annotation for each model (and alignments):
>> Peptidase_A24  Type IV leader peptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   6.8   5.2e-07    0.0046       4      93 ..      33     130 ..      30     151 .. 0.66
   2 ?   -0.8   1.2      0.23   2.1e+03      58      89 ..     233     239 ..     216     253 .] 0.42

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.2e-07
                     Peptidase_A24   4 ltillvlsviDldtrtlpdeltlpllllgvlfa..qllllglpnlaqavlgalvgalvlllislvdeqamGgGDvkl 78 
                                       +++  ++ ++Dl++r+++d+  ++++ +++++   ++++  + ++   ++ga+++ + +++    + +++G +D+ +
  gi|385805417|ref|YP_005841815.1|  33 ALFFGYVGIVDLKYREIDDKAFYCFIPIILILSiySYFQNEIIEIVNIIIGAFLFIFAFFM---SRSGFIGSADAFI 106
                                       56778899**************999999999884444455555555555555555555554...7888******987 PP

                     Peptidase_A24  79 aavlgaflgwerl.........ll 93 
                                          + ++ +   l         ++
  gi|385805417|ref|YP_005841815.1| 107 TSYVFFLNPYVLLirhyvmpagIF 130
                                       666655555444455555555433 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.23
                     Peptidase_A24  58 lvlllislvdeqamGgGDvklaavlgaflgwe 89 
                                       +++l                          + 
  gi|385805417|ref|YP_005841815.1| 233 FIFLG-------------------------LL 239
                                       22222.........................11 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 !   14.3   1.1   4.9e-06     0.044      31      86 ..     185     241 ..     165     245 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.9e-06
                       Arc_PepC_II  31 kdgk.ikrkfisvekeldeelrkelkkykkkglieet.vWvtygvPflipitaGfiia 86 
                                       k++k      ++++k ++ +++ke  ++++kg i+ + +  +yg+P+  +i++G++++
  gi|385805417|ref|YP_005841815.1| 185 KKKKfYFVVATKSKKRIYANVEKEPFSFEEKG-IKTDwIIAMYGIPLGFFIFLGLLLT 241
                                       222222222345666777999999999*****.77777999*************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1190  (0.0663729); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         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: 1581.08
//
Query:       gi|385805418|ref|YP_005841816.1|  [L=45]
Description: hypothetical protein FFONT_0374 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score 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   15.3   0.0      0.013   15.0   0.0    1.2  1  HTH_OrfB_IS605  Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   7.1e-07     0.013       3      18 ..      26      41 ..      23      45 .] 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7.1e-07
                    HTH_OrfB_IS605  3 lkaykyrlyPTpeQee 18
                                      ++a+ky +yPT e   
  gi|385805418|ref|YP_005841816.1| 26 QLAFKYKIYPTREDVK 41
                                      78*********99655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       242  (0.0134977); expected 358.6 (0.02)
Passed bias filter:                      163  (0.00909142); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 292.71
//
Query:       gi|385805419|ref|YP_005841817.1|  [L=528]
Description: binding-protein-dependent transport system inner membrane protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.2e-16   59.2  66.6    2.1e-13   50.4  21.8    3.9  4  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4  21.8   1.2e-17   2.1e-13       5     178 ..      33     208 ..      11     214 .. 0.79
   2 ?    1.2   0.9     0.015   2.6e+02     131     170 ..     253     291 ..     240     297 .. 0.62
   3 ?   -5.6   9.1         1   1.8e+04     115     177 ..     282     345 ..     273     352 .. 0.33
   4 !   22.5  22.1   4.4e-09   7.8e-05      15     175 ..     352     506 ..     340     525 .. 0.67

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 1.2e-17
                      BPD_transp_1   5 Gilaa..lnrnkkldkllrpliivllslPsfvlaillvlvf.vilsilghlilpviillllsaapyvrlirraalrs 78 
                                       ++la+  + rn k+ k+l+p+i+vl+s+P++ +++l++l+f  +l ++    l+ i+l+++s+ +  ++ +++a+++
  gi|385805419|ref|YP_005841817.1|  33 AYLAGipMGRNEKVEKILYPIIDVLQSVPILGFFPLIILLFvNNLPGWLGPELASIFLIFTSQSWNLIIGVYSAVKV 109
                                       444446666*****************************9998777777779999*********************** PP

                      BPD_transp_1  79 lpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG......lgtllleailgyd 149
                                       +p++ +  a ++ +s+   ++k+ +P ++  ++  ++++++g l   ++ e ++ ++       +gt +  a  +++
  gi|385805419|ref|YP_005841817.1| 110 IPQEIIDMANIYKLSTVAKIFKIYIPYSKQALARNILISWAGGLFFLTASEVITLGSTnyeltgIGTYIQMAADSNN 186
                                       ******************************************98888888888844432333334444444444444 PP

                      BPD_transp_1 150 yseisnggvlalviavlllnlvadilqrl 178
                                       +s       l+++  ++l+++++ i + +
  gi|385805419|ref|YP_005841817.1| 187 FS-------LVFIGTFILMITSVLIYVLF 208
                                       44.......44444444444444444444 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.015
                      BPD_transp_1 131 lgswpGlgtllleailgydyseisnggvlalviavlllnl 170
                                       +++++ +++ +   +++++y +i+ +++la++ +++l+n+
  gi|385805419|ref|YP_005841817.1| 253 IINGK-INSKISLHTQSRNYKFIASFLLLAFLSVIILFNI 291
                                       44333.7777777888888887774444444445555544 PP

  == domain 3  score: -5.6 bits;  conditional E-value: 1
                      BPD_transp_1 115 ilafggllggavlleflgswpGlgtllleailgydyseis....nggvlalviavlllnlvadilqr 177
                                       +l++++l++ ++++e+  +     + + e+ +++ + +++    + ++ ++++++l l++++ i + 
  gi|385805419|ref|YP_005841817.1| 282 FLSVIILFNIYSIIEIPKAI---ENYIAETFQASLILNGIegllISTARVVLVMMLGLIFLILISYY 345
                                       33344444444444444422...22222222222222222333222222333333333333333332 PP

  == domain 4  score: 22.5 bits;  conditional E-value: 4.4e-09
                      BPD_transp_1  15 kldkllrpliivllslPsfvlaillvlvfvilsilghlilp.viillllsaapyvrl.irraalrslpkdlveaara 89 
                                       + + +++   +vl s+Ps++++++++l    l   g+  l   +++++ ++++y+++ ++  ++  ++k+l+e +r+
  gi|385805419|ref|YP_005841817.1| 352 IYRSIFTLAGEVLASMPSILWWPIFLL----LIERGFPPLLvSFFIIFQGSIWYIFFnVFLTGIGPIEKNLMEMSRI 424
                                       56677777789*************993....33334444443344444555555554267889999*********** PP

                      BPD_transp_1  90 lGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllle.ailgydyseisnggvlalviav 165
                                       +  + +  ++++ +P++ p++++gl   +gg++++ +++e+      +gt l++ + +gy +s+ +  +  +l++++
  gi|385805419|ref|YP_005841817.1| 425 YKIRGIYKLFYIYIPMISPYLVAGLSAGWGGAWNADIVAEYAS----IGTNLITfFGIGYLISLST-YSGNMLALST 496
                                       ****************************************988....4333333134555555555.3333333333 PP

                      BPD_transp_1 166 lllnlvadil 175
                                        +++lv++i+
  gi|385805419|ref|YP_005841817.1| 497 YVFLLVMFII 506
                                       3333333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (528 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1160  (0.0646996); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.33s 00:00:00.99 Elapsed: 00:00:00.50
# Mc/sec: 3166.78
//
Query:       gi|385805420|ref|YP_005841818.1|  [L=520]
Description: CTP synthetase [Fervidicoccus fontis Kam940]
Scores for complete 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-115  384.8   1.7   2.7e-115  384.2   1.7    1.3  1  CTP_synth_N    CTP synthase N-terminus
    6.3e-47  159.8   0.0    1.5e-46  158.6   0.0    1.6  2  GATase         Glutamine amidotransferase class-I
    6.3e-07   29.4   0.0    1.4e-06   28.3   0.0    1.6  1  Peptidase_C26  Peptidase C26
    0.00018   21.6   0.0    0.00038   20.5   0.0    1.5  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
     0.0062   16.0   0.7       0.13   11.7   0.2    2.5  3  ParA           NUBPL iron-transfer P-loop NTPase
  ------ inclusion threshold ------
      0.052   13.5   0.1       0.14   12.1   0.0    1.8  2  AAA_31         AAA domain
       0.14   12.3   3.2        5.8    7.1   1.4    3.0  3  SLBP_RNA_bind  Histone RNA hairpin-binding protein RNA-bindin


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 !  384.2   1.7    1e-118  2.7e-115      10     265 .]       1     256 [.       1     256 [. 0.99

  Alignments for each domain:
  == domain 1  score: 384.2 bits;  conditional E-value: 1e-118
                                       STTTTHHHHHHHHHHHHHCTT--EEEEEEE-SSSSSSTT--CCCC--EEE-TT--EEETHHHHHHHHHT----GGGE CS
                       CTP_synth_N  10 vSglGkGiiaaslgallksrglkvtlikiDPYlnvdagtlsplehGEvfvlddGaetDlDlGnYeRfldikltkenn 86 
                                       +Sg+GkGi++asl++llk++g++vt++kiDPYln dagt++p+ hGEvfv+ddG+etDlDlG+YeRfl+i+l+kenn
  gi|385805420|ref|YP_005841818.1|   1 MSGIGKGITTASLAMLLKKMGYTVTIVKIDPYLNKDAGTMNPYMHGEVFVTDDGGETDLDLGHYERFLGINLSKENN 77 
                                       69*************************************************************************** PP

                                       EEHHHHHHHHHHHHHTTTTTT----CCCHHHHHHHHHHHHHH.HCT-SEEEEEE-S-TTSGGGHHHHHHHHHHHHHH CS
                       CTP_synth_N  87 ittGkiyksviekerrGdylGktvqviphvtdeikeriekvakkveadvviveigGtvgdieslpfleairqlklel 163
                                       ittGkiy svieker+G +lG+tvq+iph+t+eik+++++++kk ++dv+ veigGtvgdieslpflea rq++ +l
  gi|385805420|ref|YP_005841818.1|  78 ITTGKIYGSVIEKERKGVFLGQTVQIIPHITNEIKDQLKDISKKYSSDVTFVEIGGTVGDIESLPFLEAARQMSIDL 154
                                       *******************************************99******************************** PP

                                       -TTTEEEEEEEE--B-TTTSSB-HHHHHHHHHHHHHHT---SEEEEEESS---HHHHHHHHHHCT--GGGEEEEE-- CS
                       CTP_synth_N 164 gkenvllihvtlvpvlkaagelktkptqhsvkelrslGiqpdiivcrsekeleeevkekialfcnvekeavisvkdv 240
                                       gkenv++ih++++p l ++gelktkp qhsv+elr++Giqpd+i+ rs+ +++ee+k+ki+lf+nv+++ vis++dv
  gi|385805420|ref|YP_005841818.1| 155 GKENVVYIHIAYIPLLPNTGELKTKPLQHSVNELRRIGIQPDMIFGRSTVPINEEIKSKISLFTNVPMNGVISTHDV 231
                                       ***************************************************************************** PP

                                       S-GGGHHHHHHHCTHHHHHHHHTT- CS
                       CTP_synth_N 241 esiyevpllleeqglaelileklkl 265
                                       + iyevp++l+++g +++i++kl l
  gi|385805420|ref|YP_005841818.1| 232 DIIYEVPIMLKKEGADKYIVQKLGL 256
                                       *********************9976 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.8   4.5e+03      11      31 ..      11      31 ..       9      42 .. 0.78
   2 !  158.6   0.0   5.9e-50   1.5e-46       2     189 ..     291     517 ..     290     518 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.8
                                      HHHHHHHHHTT-EEEEEETTS CS
                            GATase 11 enlvhalvelgvkvevvpida 31
                                       +l+  l ++g++v++v+id 
  gi|385805420|ref|YP_005841818.1| 11 ASLAMLLKKMGYTVTIVKIDP 31
                                      5677889999*******9994 PP

  == domain 2  score: 158.6 bits;  conditional E-value: 5.9e-50
                                       EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHH.....THHSTSEEEEEEESSCTTTTTHHHHHHHHCTSTS- CS
                            GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeile.....llknpdgilvsgGpgspgvegkieaikearenkiP 73 
                                       l D+y s++e+++ha++  ++k e+++i++++ e+++     +l++++g ++ +G+g++gvegki+aik +ren+iP
  gi|385805420|ref|YP_005841818.1| 291 LHDSYLSIKEAIIHASAFYRIKPELIWIESTDIEEDKinleeELNGINGGIILPGFGKRGVEGKIRAIKMLRENNIP 367
                                       78****************************98888566654459999999*************************** PP

                                       EEEETHHHHHHHHHTTTEEE.......................EEECEEEEEEEEEEEETTT........CGGTTTT CS
                            GATase  74 iLGICLGmQllaiefgrkvv.......................kekekehhggtmrlgddet........allyglk 119
                                       +LGIC+GmQl + ef+r+vv                       ++ + +++ggtmrlg++            +y++ 
  gi|385805420|ref|YP_005841818.1| 368 LLGICFGMQLSVVEFARNVVglegahsteinpqtpypvvslleEQMNVKYLGGTMRLGSYAIklvkntkvYDMYKQ- 443
                                       *****************99999999999999999999******6666************88799999666555555. PP

                                       SEEEEEEEEEEEEESG...CHHHTTEEEEEEEETTEEEEEEEEETT.T.EEEESSBTTSTTSTTHHHHHHHHHHH CS
                            GATase 120 nevierhrHryevnpk...elepaglevtakseddeelmeiiekkn.p.fvgvQFHPEststpegpellfnflik 189
                                       + v+erhrHrye+npk   +l ++gl++++ s +++ ++e+ie ++ + fvg+Q HPE++s+p  p+++  ++ik
  gi|385805420|ref|YP_005841818.1| 444 EIVYERHRHRYEINPKyidKLIENGLTISGYSLEGN-RVEFIEYNSnRfFVGTQSHPEYKSRPLTPSPVYLSFIK 517
                                       7899******************************96.555555555499*********************99987 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   5.4e-10   1.4e-06      98     216 .]     358     500 ..     352     500 .. 0.75

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 5.4e-10
                     Peptidase_C26  98 iraalergvPilgiCrGlqllnvalG.......Gtlyqdieeqsgltdhrehe............q......saash 149
                                       i+   e+++P+lgiC G+ql  v +        G   ++i+ q+                     +         s 
  gi|385805420|ref|YP_005841818.1| 358 IKMLRENNIPLLGICFGMQLSVVEFArnvvgleGAHSTEINPQTP-------YpvvslleeqmnvKylggtmRLGSY 427
                                       55567899***********98776541111111555555554322.......1334444444555145555688899 PP

                     Peptidase_C26 150 avkvekgsllaellgseeievnslHhqaike......laeelrveAvae.DgviEaieseeakafvlgvQwHPE 216
                                       a+k++k++ +++++++e +     H+  i+       ++++l ++  +   + +E+ie ++++ f++g Q HPE
  gi|385805420|ref|YP_005841818.1| 428 AIKLVKNTKVYDMYKQEIVYERHRHRYEINPkyidklIENGLTISGYSLeGNRVEFIEYNSNR-FFVGTQSHPE 500
                                       9**************999999999**9999889999999********986789******9966.*********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 !   20.5   0.0   1.5e-07   0.00038       8      48 ..       2      39 ..       1     286 [. 0.74

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.5e-07
                                      TTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  8 GGvGKTtlaanLaralarrglrVllvDaDpqannlailegl 48
                                      +G GK  ++a+La +l++ g+ V  v+ Dp  n +a   g+
  gi|385805420|ref|YP_005841818.1|  2 SGIGKGITTASLAMLLKKMGYTVTIVKIDPYLNKDA---GT 39
                                      89****************************988877...33 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 !   11.7   0.2     5e-05      0.13      14      41 ..       3      30 ..       2      40 .. 0.95
   2 ?   -2.7   0.0       1.2   3.1e+03     181     213 ..     209     241 ..     203     248 .. 0.77
   3 ?    1.6   0.0     0.062   1.6e+02     155     180 ..     356     381 ..     333     417 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5e-05
                              ParA 14 GVGKStvavnlAlaLakkglkvgllDaD 41
                                      G+GK  ++++lA+ L+k+g++v ++ +D
  gi|385805420|ref|YP_005841818.1|  3 GIGKGITTASLAMLLKKMGYTVTIVKID 30
                                      9************************998 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.2
                              ParA 181 kcgekteifgkgggeklaeelgvpllgeipldp 213
                                       + ++k+++f++  ++ + ++++v+++ e+p+  
  gi|385805420|ref|YP_005841818.1| 209 EIKSKISLFTNVPMNGVISTHDVDIIYEVPIML 241
                                       567788888888888888888888888888865 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.062
                              ParA 155 kaiemfkkvkvkvlGvveNmsgfvcp 180
                                       +ai+m+++ ++++lG+   m+  v++
  gi|385805420|ref|YP_005841818.1| 356 RAIKMLRENNIPLLGICFGMQLSVVE 381
                                       89**************9999887765 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   5.4e-05      0.14      12      46 ..       3      37 ..       2     122 .. 0.87
   2 ?   -3.0   0.0       2.3     6e+03      94     111 ..     428     445 ..     410     490 .. 0.49

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.4e-05
                            AAA_31 12 GvGKTTtsvnlaaalaklgkkvLlvDlDpQanatt 46
                                      G+GK  t+  la+ l k+g+ v +v +Dp  n   
  gi|385805420|ref|YP_005841818.1|  3 GIGKGITTASLAMLLKKMGYTVTIVKIDPYLNKDA 37
                                      99***************************999765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.3
                            AAA_31  94 eielvelekkeeilkell 111
                                        i+lv+ +k  +++k+ +
  gi|385805420|ref|YP_005841818.1| 428 AIKLVKNTKVYDMYKQEI 445
                                       444444444433333322 PP

>> SLBP_RNA_bind  Histone RNA hairpin-binding protein RNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.035        90       7      23 ..     146     162 ..     144     181 .. 0.82
   2 ?    7.1   1.4    0.0023       5.8      13      38 ..     429     453 ..     426     464 .. 0.77
   3 ?   -3.4   0.1       4.3   1.1e+04      29      44 ..     493     509 ..     484     511 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.035
                     SLBP_RNA_bind   7 aqRqkqIdlGKntegYe 23 
                                       a+Rq  IdlGK++  Y 
  gi|385805420|ref|YP_005841818.1| 146 AARQMSIDLGKENVVYI 162
                                       58***********9995 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0023
                     SLBP_RNA_bind  13 IdlGKntegYerYlkavpkekrkkke 38 
                                       I+l Knt+ Y+ Y +++  e++++ +
  gi|385805420|ref|YP_005841818.1| 429 IKLVKNTKVYDMYKQEIVYERHRH-R 453
                                       8999*************9888774.2 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 4.3
                     SLBP_RNA_bind  29 vpkekrkk.kehPktPd 44 
                                       v  + + + k+ P tP 
  gi|385805420|ref|YP_005841818.1| 493 VGTQSHPEyKSRPLTPS 509
                                       55556665677899997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (520 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      626  (0.0349155); 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: 0.72u 0.35s 00:00:01.06 Elapsed: 00:00:00.55
# Mc/sec: 2830.22
//
Query:       gi|385805421|ref|YP_005841819.1|  [L=160]
Description: peptidase S26B, signal peptidase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-08   33.6   0.4    4.2e-08   33.0   0.4    1.3  1  Peptidase_S24  Peptidase S24-like
  ------ inclusion threshold ------
      0.092   12.5   0.3       0.15   11.8   0.2    1.3  1  DUF2606        Protein of unknown function (DUF2606)


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 !   33.0   0.4   4.7e-12   4.2e-08       2      49 ..      47      95 ..      46     114 .. 0.87

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 4.7e-12
                                      XXSSTTCCTXXTTXEEEEECTS..---TTSEEEEEETTCE-EEEEEEEEE CS
                     Peptidase_S24  2 vpGdSMeptlldGdlilVdkfs..epkrGdivvfrlpgeeeayiKrvigl 49
                                      v+G SM p l++Gd+++  + s  ++k Gdivv    g+  ++i+rv+  
  gi|385805421|ref|YP_005841819.1| 47 VKGTSMLPLLKEGDIVFLIHKSpdQIKVGDIVVYERLGGG-YIIHRVVAI 95
                                      9***************97766569**********999997.******965 PP

>> DUF2606  Protein of unknown function (DUF2606)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   1.7e-05      0.15       8      71 ..       7      71 ..       2      84 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.7e-05
                           DUF2606  8 iGqlnkyskllillsvlvlivmssqivssek.kvvisvtlhvkdkkklPv.kdvevilvkdessde 71
                                       G l ky+  +i++ vl+++v+s +   se     ++v++ vk    lP+ k+ +++++  +s+d+
  gi|385805421|ref|YP_005841819.1|  7 KGFLSKYKSDMIFIIVLIILVISIRPALSEAtGLSNPVAV-VKGTSMLPLlKEGDIVFLIHKSPDQ 71
                                      6899*******************99887777467788875.8999999954888999999999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); 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: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 983.60
//
Query:       gi|385805422|ref|YP_005841820.1|  [L=171]
Description: hypothetical protein FFONT_0378 [Fervidicoccus fontis Kam940]
Scores for complete 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   84.4   0.1    1.1e-23   84.0   0.1    1.1  1  AAA_assoc_C  C-terminal AAA-associated domain
  ------ inclusion threshold ------
      0.014   15.2   0.0      0.025   14.5   0.0    1.4  1  DUF1507      Protein of unknown function (DUF1507)
       0.11   12.2   0.6       0.14   11.8   0.4    1.4  1  DUF1673      Protein of unknown function (DUF1673)
       0.14   11.7   0.4        0.5    9.9   0.2    1.8  2  Tsc35        Testis-specific protein 35


Domain annotation for each model (and alignments):
>> 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 !   84.0   0.1   2.5e-27   1.1e-23       3     119 .]      44     158 ..      42     158 .. 0.97

  Alignments for each domain:
  == domain 1  score: 84.0 bits;  conditional E-value: 2.5e-27
                       AAA_assoc_C   3 LaeelelevddLlpiveaaelLglveveegdielTelGrkfveadikerKeifreqllklvplaaairrvLderenk 79 
                                       +++ +++++d L +++++ e Lgl+++++gd+ lT+ G+k++ +++ e +++++e++++l p++++i++   +++n+
  gi|385805422|ref|YP_005841820.1|  44 INDVTDVDIDVLPHAIDISERLGLISYNNGDLLLTDFGKKIAMTHHLEVRDLLKEKISTLQPIKDIIKKS--RDSNN 118
                                       78899****************************************************************5..9999* PP

                       AAA_assoc_C  80 rlpeerfldeLeeklseeeaertletaieWgrYaelfeyd 119
                                        l+e+++ ++L++++ eee+ ++l+++  W  + e+  +d
  gi|385805422|ref|YP_005841820.1| 119 ILTEDEVYQILSRYYGEEEIGKALKCISMWLFFFEIAYWD 158
                                       ***********************************98876 PP

>> DUF1507  Protein of unknown function (DUF1507)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   5.5e-06     0.025      30      80 ..      38      88 ..      21      93 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.5e-06
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHT-XX CS
                           DUF1507 30 lsqCplyEevlDtqmyGlsrevdfavrlglieeeeGkqllseLekelnqly 80
                                      +++   +++v D  +  l + +d + rlgli+ ++G  ll++  k+++  +
  gi|385805422|ref|YP_005841820.1| 38 MADVSYINDVTDVDIDVLPHAIDISERLGLISYNNGDLLLTDFGKKIAMTH 88
                                      66667788999999999****************************998766 PP

>> DUF1673  Protein of unknown function (DUF1673)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.4   3.2e-05      0.14     193     219 ..     143     169 ..     122     171 .] 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.2e-05
                           DUF1673 193 lllllwliylqviywekkNkktivrkr 219
                                        ++++wl+++ + yw  +  + ivr++
  gi|385805422|ref|YP_005841820.1| 143 KCISMWLFFFEIAYWDYEEGVLIVRNK 169
                                       699**************9888888765 PP

>> Tsc35  Testis-specific protein 35
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.23     1e+03      67      90 ..      38      61 ..      35      65 .. 0.85
   2 ?    9.9   0.2   0.00011       0.5      58      82 ..      91     115 ..      72     123 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.23
                             Tsc35 67 meeikqikdimdkdfdklkefvei 90
                                      m ++  i d+ d d d l   ++i
  gi|385805422|ref|YP_005841820.1| 38 MADVSYINDVTDVDIDVLPHAIDI 61
                                      778899**********99887777 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00011
                             Tsc35  58 evreelkekmeeikqikdimdkdfd 82 
                                       evr+ lkek+  ++ ikdi+ k  d
  gi|385805422|ref|YP_005841820.1|  91 EVRDLLKEKISTLQPIKDIIKKSRD 115
                                       9*******************99766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); 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:                         4  (0.000223102); expected 0.2 (1e-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 0.30s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1057.88
//
Query:       gi|385805423|ref|YP_005841821.1|  [L=206]
Description: TATA-box-binding protein (TATA-box factor) [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.8e-60  200.8   0.5    3.8e-30  103.7   0.1    2.1  2  TBP         Transcription factor TFIID (or TATA-binding prote
    6.1e-07   29.5   0.0      0.024   14.8   0.0    2.5  2  DUF3378     Domain of unknown function (DUF3378)
     0.0057   16.9   0.1      0.017   15.4   0.1    1.8  1  TFIIE_beta  TFIIE beta subunit core domain


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 !   95.8   0.0   1.8e-31   1.1e-27       2      83 ..      18      97 ..      17      99 .. 0.96
   2 !  103.7   0.1   6.4e-34   3.8e-30       1      84 [.     108     189 ..     108     190 .. 0.98

  Alignments for each domain:
  == domain 1  score: 95.8 bits;  conditional E-value: 1.8e-31
                                      EEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHH CS
                               TBP  2 fkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkiap 80
                                      ++i+N+va+++l+++ldL+++++k+    +eY+p++fpglv+rl++pk+taliF+sGk+v+tG ks++el +a+k+i++
  gi|385805423|ref|YP_005841821.1| 18 VQIENIVATVTLDQQLDLHEIERKV--PRVEYNPDQFPGLVFRLDRPKITALIFKSGKMVVTGSKSTQELITAVKRIIK 94
                                      68*******************9888..**************************************************99 PP

                                      HHH CS
                               TBP 81 ilk 83
                                       + 
  gi|385805423|ref|YP_005841821.1| 95 TFY 97
                                      875 PP

  == domain 2  score: 103.7 bits;  conditional E-value: 6.4e-34
                                       EEEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHH CS
                               TBP   1 dfkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakk 77 
                                       +++iqN+vasanl+++++Le  a+k+  +n  Yepe+fpgl+ r+ +p v++liFssGk+vitGak eee+ +a+++
  gi|385805423|ref|YP_005841821.1| 108 KIQIQNIVASANLNVDVNLEDAAYKL--ENNMYEPEQFPGLIHRMTDPYVVLLIFSSGKMVITGAKREEEVSKAVEN 182
                                       589********************999..************************************************* PP

                                       HHHHHHH CS
                               TBP  78 iapilkk 84 
                                       i++ lk+
  gi|385805423|ref|YP_005841821.1| 183 IYKTLKE 189
                                       *****97 PP

>> DUF3378  Domain of unknown function (DUF3378)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0     4e-06     0.024      24      59 ..      49      84 ..      22      85 .. 0.86
   2 !   12.4   0.0   2.1e-05      0.13      23      62 ..     139     178 ..     128     189 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4e-06
                           DUF3378 24 skkppyavfaakkndttItaYtSgKVlFQGknaeae 59
                                        + p+ vf+ + +++t  +++SgK ++ G++  +e
  gi|385805423|ref|YP_005841821.1| 49 PDQFPGLVFRLDRPKITALIFKSGKMVVTGSKSTQE 84
                                      5689**************************987765 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 2.1e-05
                           DUF3378  23 rskkppyavfaakkndttItaYtSgKVlFQGknaeaeAsk 62 
                                       + ++ p+ + +  ++ ++  ++ SgK ++ G++ e+e sk
  gi|385805423|ref|YP_005841821.1| 139 EPEQFPGLIHRMTDPYVVLLIFSSGKMVITGAKREEEVSK 178
                                       56789999****************************9987 PP

>> TFIIE_beta  TFIIE beta subunit core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   2.9e-06     0.017       8      58 ..       3      50 ..       1      53 [. 0.76

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.9e-06
                        TFIIE_beta  8 iveylKkkdg....plsleeIlsylslqldlsdknwllleaLknnpkieyDpkkg 58
                                       v y+Kk++      +++e+I   + l     d++ +l e+ ++ p++ey+p  +
  gi|385805423|ref|YP_005841821.1|  3 MVCYMKKTNSiskpVVQIENIVATVTL-----DQQLDLHEIERKVPRVEYNP--D 50
                                      688****88886656666666666666.....55669*************88..3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1117  (0.0623013); expected 358.6 (0.02)
Passed bias filter:                      720  (0.0401584); 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: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 1426.79
//
Query:       gi|385805424|ref|YP_005841822.1|  [L=116]
Description: transcriptional regulator, HTH-type [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.9e-10   39.3   0.0    7.5e-10   38.7   0.0    1.2  1  HTH_20          Helix-turn-helix domain
    1.1e-09   37.9   0.0    1.9e-09   37.2   0.0    1.4  1  HTH_5           Bacterial regulatory protein, arsR family
      2e-07   30.8   0.0    3.2e-07   30.1   0.0    1.3  1  MarR_2          MarR family
    9.2e-06   25.5   0.0    1.6e-05   24.7   0.0    1.4  1  MarR            MarR family
    7.8e-05   22.1   0.2    0.00021   20.8   0.2    1.8  1  HTH_24          Winged helix-turn-helix DNA-binding
    0.00072   19.7   0.0     0.0011   19.1   0.0    1.4  1  HTH_34          Winged helix DNA-binding domain
     0.0023   18.4   0.0     0.0042   17.5   0.0    1.4  1  HTH_27          Winged helix DNA-binding domain
     0.0044   17.2   0.0     0.0096   16.1   0.0    1.6  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
     0.0082   16.2   0.1      0.012   15.7   0.1    1.3  1  DUF2250         Uncharacterized protein conserved in archaea 
     0.0093   15.7   0.0      0.015   15.1   0.0    1.3  1  HTH_IclR        IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.011   15.7   0.0       0.03   14.3   0.0    1.7  2  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.038   13.7   0.1      0.048   13.4   0.1    1.2  1  DUF4423         Domain of unknown function (DUF4423)
      0.046   13.6   0.1      0.067   13.1   0.1    1.3  1  TrmB            Sugar-specific transcriptional regulator TrmB
      0.061   13.3   0.1       0.13   12.3   0.1    1.6  1  HTH_36          Helix-turn-helix domain
       0.11   12.7   0.0       0.15   12.3   0.0    1.2  1  SgrR_N          Sugar transport-related sRNA regulator N-term


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   0.0   6.3e-13   7.5e-10       3      57 ..      39      92 ..      38      94 .. 0.96

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 6.3e-13
                                      HHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20  3 iaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                      +++ALa+ +R+ il+++  + +  ++e+a+++  sk+++s ++++LeeagL++++
  gi|385805424|ref|YP_005841822.1| 39 VTSALANSTRLFILKYI-KEHESDVGEIADLIKQSKANASAQIKKLEEAGLIRTT 92
                                      789**************.**********************************986 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   0.0   1.6e-12   1.9e-09       1      46 [.      45      90 ..      45      91 .. 0.97

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 1.6e-12
                                      SHHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  1 dptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      ++tRl ILk+  e e  v+e+a+ ++ s+++ S + kkL+eaGL++
  gi|385805424|ref|YP_005841822.1| 45 NSTRLFILKYIKEHESDVGEIADLIKQSKANASAQIKKLEEAGLIR 90
                                      58******************************************97 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0   2.7e-10   3.2e-07       7      55 ..      48      95 ..      41      99 .. 0.85

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 2.7e-10
                                      HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE..E CS
                            MarR_2  7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr..p 55
                                       + +L ++  ++     vge+a+  + sk+++s  +k+L++aGL++++  p
  gi|385805424|ref|YP_005841822.1| 48 RLFILKYIKEHES---DVGEIADLIKQSKANASAQIKKLEEAGLIRTTykP 95
                                      5667888999985...9****************************998544 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   1.4e-08   1.6e-05       4      52 ..      47      94 ..      45      98 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.4e-08
                                      HHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE CS
                              MarR  4 tqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsks 52
                                      t++ iL  ++e+++  v e+a+ ++ sk++++ ++++Le++Gli+ + +
  gi|385805424|ref|YP_005841822.1| 47 TRLFILKYIKEHES-DVGEIADLIKQSKANASAQIKKLEEAGLIRTTYK 94
                                      66677777777765.788**************************96655 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.2   1.7e-07   0.00021      21      48 .]      63      90 ..      45      90 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.7e-07
                            HTH_24 21 reLAerlglSpstvnrrlkrLeeeGlIk 48
                                       e+A+ +  S+++ ++++k+Lee+GlI+
  gi|385805424|ref|YP_005841822.1| 63 GEIADLIKQSKANASAQIKKLEEAGLIR 90
                                      69*************************7 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 !   19.1   0.0   9.2e-07    0.0011       2      47 ..      48      92 ..      47     108 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 9.2e-07
                            HTH_34  2 RlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievd 47
                                      Rl++l y  ++ e d  e+ + ++ +++n s+++kkLe+ag i  +
  gi|385805424|ref|YP_005841822.1| 48 RLFILKYI-KEHESDVGEIADLIKQSKANASAQIKKLEEAGLIRTT 92
                                      89999996.56788***************************99754 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 !   17.5   0.0   3.5e-06    0.0042      13      57 ..      56      97 ..      46     106 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.5e-06
                            HTH_27 13 rhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadr 57
                                      +  ++++   ++++  + +++++s  +kkL+e+GL+ +t ++  +
  gi|385805424|ref|YP_005841822.1| 56 K--EHESDVGEIADLIKQSKANASAQIKKLEEAGLIRTTYKP-GQ 97
                                      5..556666788999999******************888777.33 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0     8e-06    0.0096      25      55 ..      62      92 ..      53      97 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8e-06
                                      HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                    Fe_dep_repress 25 tkdlaerLnvspssVsemlkkLekdGyveye 55
                                      + ++a  +++s++ +s  +kkLe++G++ + 
  gi|385805424|ref|YP_005841822.1| 62 VGEIADLIKQSKANASAQIKKLEEAGLIRTT 92
                                      679************************9765 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 !   15.7   0.1   9.8e-06     0.012       7      54 ..      45      91 ..      39     110 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 9.8e-06
                           DUF2250  7 delalkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLler 54
                                      ++  l +lk++k+ ++d +  ia+ ++ ++ +++  +kkLee+GL+  
  gi|385805424|ref|YP_005841822.1| 45 NSTRLFILKYIKEHESDVG-EIADLIKQSKANASAQIKKLEEAGLIRT 91
                                      556899***********98.59***********************975 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.2e-05     0.015       8      50 ..      51      91 ..      49      92 .. 0.96

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.2e-05
                                      HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      iL+++ e+  +  + e+A+ +  +k++++  ++ L+e G++++
  gi|385805424|ref|YP_005841822.1| 51 ILKYIKEHESD--VGEIADLIKQSKANASAQIKKLEEAGLIRT 91
                                      9*********9..9**************************986 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 ?   -1.9   0.0       2.8   3.4e+03      45      61 ..      22      39 ..      16      45 .. 0.58
   2 ?   14.3   0.0   2.5e-05      0.03      26      61 ..      64     107 ..      60     111 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.8
                                      HHHTTSEE.ETEE.EEES- CS
                         HTH_Crp_2 45 Lkreglis.rgrr.irild 61
                                      +++ g++  +g +  +i+ 
  gi|385805424|ref|YP_005841822.1| 22 FEENGVLYvNG-DeYIIRV 39
                                      66777777334.2255544 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 2.5e-05
                                       HHHHHTTSSHHHHHHHHHHHHHTTSEE.E...T.EE...EEES- CS
                         HTH_Crp_2  26 elAsmlGltretvsrilseLkreglis.r...g.rr...irild 61 
                                       e+A+++  +    s  +++L+++gli+ +   g r+   i++ +
  gi|385805424|ref|YP_005841822.1|  64 EIADLIKQSKANASAQIKKLEEAGLIRtTykpGqRGvkkITVSN 107
                                       8**************************73334322233466655 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1     4e-05     0.048      32      73 ..      55      94 ..      39     114 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4e-05
                           DUF4423 32 lkdfkadpeelakrlrpkisaeevekalefLlklgllkkded 73
                                      +k+ ++d+ e+a+ ++   s++ +++ ++ L+++gl++ + +
  gi|385805424|ref|YP_005841822.1| 55 IKEHESDVGEIADLIK--QSKANASAQIKKLEEAGLIRTTYK 94
                                      677889**********..*******************98765 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   5.6e-05     0.067      19      56 ..      56      93 ..      50     108 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.6e-05
                                      HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB 19 klgpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                                      k+ ++++ eia  ++ +++++   +++Le++Gl+++  
  gi|385805424|ref|YP_005841822.1| 56 KEHESDVGEIADLIKQSKANASAQIKKLEEAGLIRTTY 93
                                      778999****************************9875 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1    0.0001      0.13      30      55 .]      64      89 ..      48      89 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0001
                            HTH_36 30 tlakrlglsknTvsraikeLeqlGyi 55
                                       +a + + sk  +s  ik+Le++G+i
  gi|385805424|ref|YP_005841822.1| 64 EIADLIKQSKANASAQIKKLEEAGLI 89
                                      7999********************98 PP

>> SgrR_N  Sugar transport-related sRNA regulator N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00012      0.15       8      56 ..      48      96 ..      43     112 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00012
                            SgrR_N  8 rLlqhfegkevevtLqelAdvlfCsrRhartlLkkmqeegwleWqpevG 56
                                      rL+     ke+e  + e+Ad++  s+ +a   +kk++e+g+++ + + G
  gi|385805424|ref|YP_005841822.1| 48 RLFILKYIKEHESDVGEIADLIKQSKANASAQIKKLEEAGLIRTTYKPG 96
                                      6666666789999****************************98766666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       839  (0.0467957); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 811.09
//
Query:       gi|385805425|ref|YP_005841823.1|  [L=452]
Description: glycine dehydrogenase subunit 1 [Fervidicoccus fontis Kam940]
Scores for 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-101  338.4   0.0   7.5e-101  338.0   0.0    1.0  1  GDC-P          Glycine cleavage system P-protein
  ------ inclusion threshold ------
      0.037   13.2   0.1        6.7    5.8   0.1    2.1  2  Aminotran_1_2  Aminotransferase class I and II


Domain annotation for each model (and alignments):
>> GDC-P  Glycine cleavage system P-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  338.0   0.0  8.4e-105  7.5e-101       4     386 ..       7     404 ..       4     444 .. 0.88

  Alignments for each domain:
  == domain 1  score: 338.0 bits;  conditional E-value: 8.4e-105
                                       -SS-HHHH.HHHHHHHT-SSHHHHHHHHS-GGGB--S------..---HHHHHHHHHHHHT.TB--..-EE--BTTB CS
                             GDC-P   4 igpsekdq.kemLetlGlkslddliekavPkeiklkkelklea..pksEeellaelekias.knkv..vksfiGaGy 74 
                                       i++++++  + mL+t+G+++ d+l+ +++P+eiklkk+lk+ a  p    el ++++++   +n v   + f G  +
  gi|385805425|ref|YP_005841823.1|   7 IPNDNEELlNIMLKTIGINNWDELF-TSIPEEIKLKKKLKIGAerPLNTIELEKHMKEVVRaQNIVdlERVFSGGPV 82 
                                       666655542679*************.9************98652269999999999998873555564577889889 PP

                                       ------HHHHHHTTT-HHHHS--S-SSGGG-HHHHHHHHHHHHHHHHHHT-SEE-S-BS-HHHHHHHHHHHHHHH-S CS
                             GDC-P  75 ydtilPaviqrnilenpewytaYtPYqaEisqGrLeallnfqtlvadltGldianasllDegtAaaEAvllaarask 151
                                         + +P+v +  +++++e++taYtPYqaEisqG L+al ++q+l+a l  ++i na ++D+gtA+aEA ll+ r++k
  gi|385805425|ref|YP_005841823.1|  83 APHFVPQVTTY-LINRGEFLTAYTPYQAEISQGLLKALYEYQSLMAILYDIEIVNAGMYDGGTALAEASLLSIRIKK 158
                                       99999*99988.***************************************************************99 PP

                                       SS--EEEEETTS-HHHHHHHHHHHGGGT-EEEEE-GGG--S-............S-EEEEEEEES-TTSB---.-HH CS
                             GDC-P 152 kkakkvvvdkkvhpqtlevlktrakglgieivevdlteekvtd.........kekevagvlvqypnteGried.lke 218
                                       +k  k+ +++++++++++v+kt+  g++  ++e d  +++  +         k+++ +gv++ yp+ +G i +  ke
  gi|385805425|ref|YP_005841823.1| 159 NK--KIAISSTLFEEYKSVIKTYLYGQNATLIEYDFDKDTG-EitgetiekiKNEKPSGVIIDYPSNFGPIRKsTKE 232
                                       99..****************************999654433.2356899999999****************87589* PP

                                       HHHHHHHTT-EEEEEE-TTGGGTB--HHHHT-SEEEEE-TTTT---GGG----EEEEE-GG..GGGG--S-EEEEEE CS
                             GDC-P 219 lvekakkkkslvvvaadllaLtllkpPgelgaDivvGsaqrfGvPlgyGGPhagffAvkek..lkRkiPGRlvGvsk 293
                                       l+e+++k+ sl + ++d+ +L +l+pPgelg+Di+vG++q +G+P++ GG   g + +k++  l R++PGRl+G + 
  gi|385805425|ref|YP_005841823.1| 233 LIEEVHKYGSLAITFSDPSSLPILTPPGELGSDIIVGEGQSLGLPMSGGGSLLGILGIKNDkeLLRNLPGRLIGETV 309
                                       *********************************************************9975569************* PP

                                       BTTS-EEEEEE-CCGSHHCCHHHCS-S--S--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT..T-E CS
                             GDC-P 294 DaegkralrlalqtREqHirRdkAtsniCtaqaLlAnlaalyavyhGkeglkeiarrihkkteilakelkkk.leee 369
                                       Da+gk+++ + lqtREqHirR+kAtsni ta +L+A++ a+ + ++G++glk+ a++i+++t++l+++l+k+ +e +
  gi|385805425|ref|YP_005841823.1| 310 DADGKKGYMMILQTREQHIRREKATSNITTATTLNAIAVAINVLLYGEKGLKTRAEKILENTKMLKQALEKNgIEAS 386
                                       ***********************************************************************999999 PP

                                       E--SSBSSEEEEE--T.T CS
                             GDC-P 370 lkkkkffdtllievee.k 386
                                        kk+ +f  +  ++++  
  gi|385805425|ref|YP_005841823.1| 387 YKKALHFKNISYKIDDpF 404
                                       999999999998888742 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 ?    5.3   0.0     0.001       9.2      73     159 ..     139     222 ..     108     242 .. 0.85
   2 ?    5.8   0.1   0.00074       6.7     234     298 ..     319     384 ..     313     393 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.001
                                       EESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHT....TSEEEEEEBEETTTTEE-HHHHHHHHTTHHCT CS
                     Aminotran_1_2  73 vgsGagaliealifllklnpgdeilvpdptyasyknilrls....ggevvryplyseedfhldlealeealkeapeg 145
                                       +  G +al+ea    +++ + ++i +++  +++yk +++ +     +++++y   ++++ +++ e +e+  +e    
  gi|385805425|ref|YP_005841823.1| 139 MYDGGTALAEASLLSIRIKKNKKIAISSTLFEEYKSVIKTYlygqNATLIEYD-FDKDTGEITGETIEKIKNE---- 210
                                       6678899999999999999*****************99975333368899999.5589999**9999998888.... PP

                                       TETEEEEEEESS-T CS
                     Aminotran_1_2 146 nkktkvilvesphN 159
                                         k+ ++++  p+N
  gi|385805425|ref|YP_005841823.1| 211 --KPSGVIIDYPSN 222
                                       ..899999999998 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.00074
                                       EEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHSTEE CS
                     Aminotran_1_2 234 lgnaavvsqlrklsrpflsssllqaavaaalsdallkqs.eleemrqrlqkrrkelrdeLaelglk 298
                                        + +   +++r+ +++ ++++++   + a++ ++ll+ +  l+++++++ +++k l+++L++ g++
  gi|385805425|ref|YP_005841823.1| 319 MILQTREQHIRREKATSNITTATTLNAIAVAINVLLYGEkGLKTRAEKILENTKMLKQALEKNGIE 384
                                       55555567888888888999999999999999999999989*******************998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 2975.98
//
Query:       gi|385805426|ref|YP_005841824.1|  [L=49]
Description: hypothetical protein FFONT_0382 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.014   15.7   0.3      0.018   15.3   0.1    1.4  1  C2        C2 domain


Domain annotation for each model (and alignments):
>> C2  C2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.1   9.9e-07     0.018      47      70 ..       6      29 ..       2      40 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 9.9e-07
                                      SEEEEEEEEEESCHTTSEEEEEEE CS
                                C2 47 PvWnekftfevaeleeakLeveVf 70
                                       +Wne + f+++++++++Le+eV 
  gi|385805426|ref|YP_005841824.1|  6 AKWNEPIAFDIEHQNRSSLEFEVD 29
                                      58********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.46
# Mc/sec: 323.15
//
Query:       gi|385805427|ref|YP_005841825.1|  [L=445]
Description: glycine dehydrogenase subunit 2 [Fervidicoccus fontis Kam940]
Scores for complete 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   34.2   0.0    2.2e-08   33.4   0.0    1.4  1  GDC-P            Glycine cleavage system P-protein
    6.7e-08   31.9   0.0    1.4e-07   30.8   0.0    1.5  2  Aminotran_5      Aminotransferase class-V
     0.0015   17.8   0.0     0.0027   17.0   0.0    1.4  1  Beta_elim_lyase  Beta-eliminating lyase


Domain annotation for each model (and alignments):
>> GDC-P  Glycine cleavage system P-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.0   3.6e-12   2.2e-08      90     298 ..      44     262 ..       2     268 .. 0.73

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 3.6e-12
                                       -HHHHS--S-..SSGGG-HHHHHHHHHHHHHHHHHHT-SEE-S-BS-HHHHHHH..HHHHHHHH-SSS--EEEEETT CS
                             GDC-P  90 npewytaYtP..YqaEisqGrLeallnfqtlvadltGldianasllDegtAaaE..Avllaaraskkkakkvvvdkk 162
                                       n+e++++  P   + E +q  L+ + + q  + ++tG+d     l   + A++E   vl++++  +++      d+ 
  gi|385805427|ref|YP_005841825.1|  44 NSEYLANIHPslLKFETAQNILKLMYQLQEWLKEITGMDAC--TLQPPAGASGEltGVLIIKKYFQER-GDTQRDEM 117
                                       56666666663336789999999999999999999999965..6777788888832345555544444.33334444 PP

                                       S-HHHHHHHHHHHG.GGT-EEEEE-GGG--S-..........S-EEEEEEEES-TTSB---.-HHHHHHHHHTT-EE CS
                             GDC-P 163 vhpqtlevlktrak.glgieivevdlteekvtd.......kekevagvlvqypnteGried.lkelvekakkkkslv 230
                                       + p++++  +  ++   g++ v  ++ e++  +       +++++ag+++  pnt G  e+ ++e+++ +++++++v
  gi|385805427|ref|YP_005841825.1| 118 LIPDSAHGSNPASSsMGGFKSVRIPSDEHGLVNlealrasVSNKTAGLMLTNPNTLGLFEKnITEVTKILHENEAIV 194
                                       44444444333332033444444444444444445555668999*************998659***********999 PP

                                       EE.EE-TTGGGTB--HHHHT-SEE.EEE-TTTT---GGG----EEEEE-GGGGGG--S-EEEEEEBTTS- CS
                             GDC-P 231 vv.aadllaLtllkpPgelgaDiv.vGsaqrfGvPlgyGGPhagffAvkeklkRkiPGRlvGvskDaegk 298
                                           a+l  +  ++ Pg++g Div +   + f  P g GGP ag + vk+ l+  +PG +v  skD +g+
  gi|385805427|ref|YP_005841825.1| 195 HYdGANLNGIIGIARPGDMGFDIVhLNLHKTFSAPHGGGGPGAGAVCVKKYLEDYLPGYIV--SKDDNGR 262
                                       8725677777779**********94566789*****************************7..8898886 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.0   2.4e-11   1.4e-07      87     217 ..     113     246 ..      94     270 .. 0.81
   2 ?   -3.2   0.0      0.53   3.2e+03     103     119 ..     339     355 ..     299     387 .. 0.68

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 2.4e-11
                                       TTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTE.B--HHHHH CS
                       Aminotran_5  87 pgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGt.iqpveeig 162
                                       ++de+++ ++ h +n  +   +    g+k + ip de+g+++l++l++ +++kt+ +++t   n++G   + + e++
  gi|385805427|ref|YP_005841825.1| 113 QRDEMLIPDSAHGSNP-ASSSM---GGFKSVRIPSDEHGLVNLEALRASVSNKTAGLMLTN-PNTLGLfEKNITEVT 184
                                       6788888888888888.44444...58888889************************9985.6788997899***** PP

                                       HHHHHTT-EEEEE-TTTTTTS---.HHHHTESEEEEETTT.TTSS.....TT-EEEEEEHHH CS
                       Aminotran_5 163 klakkkgalvlvDaaqavghipid.vkklgvDflafsghK.llgP.....tGiGvlyvrkel 217
                                       k++++++a+v+ D+a   g i i    ++g D++ +  hK + +P     +G G+++v+k l
  gi|385805427|ref|YP_005841825.1| 185 KILHENEAIVHYDGANLNGIIGIArPGDMGFDIVHLNLHKtFSAPhggggPGAGAVCVKKYL 246
                                       ****************999998862679************8778822222467788888744 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.53
                                       HHHHHHHHHHTEEEEEE CS
                       Aminotran_5 103 vpwqelakrtgakvkvi 119
                                       +  ++la++tg++v+ +
  gi|385805427|ref|YP_005841825.1| 339 LSFKKLAEETGVTVEDV 355
                                       34556666666666555 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   4.6e-07    0.0027      34     169 ..      68     199 ..      65     246 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.6e-07
                                       HHHHHHHHHHHTT-SEEEE.ES-HHHHHHHHH....HHH--TT....EEEEEETT-HHHHSSTTHHHHCC--EEEEE CS
                   Beta_elim_lyase  34 vnrLedavaelfgkeaalf.vpqGtaAnsill....killqrg....eevivtepahihfdetgaiaelagvklrdl 101
                                       +++L++ ++e++g++a     p G  ++   +    k++ +rg    +e+++ + ah+ +    a + ++g k + +
  gi|385805427|ref|YP_005841825.1|  68 MYQLQEWLKEITGMDACTLqPPAGASGELTGVliikKYFQERGdtqrDEMLIPDSAHGSN---PASSSMGGFKSVRI 141
                                       567777777777777554414456666665552233222222211113444444466554...466788999999** PP

                                       -EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEET CS
                   Beta_elim_lyase 102 knkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgA 169
                                       +++e G ++le+l+a + +      k++ ++lt+ n    G  +  +++ ev++i ++++  +h+DgA
  gi|385805427|ref|YP_005841825.1| 142 PSDEHGLVNLEALRASVSN------KTAGLMLTNPNTL--G--LFEKNITEVTKILHENEAIVHYDGA 199
                                       *****************99......588999***9998..4..789*********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); 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: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.52
# Mc/sec: 2555.93
//
Query:       gi|385805428|ref|YP_005841826.1|  [L=212]
Description: hypothetical protein FFONT_0384 [Fervidicoccus fontis Kam940]
Scores for complete 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-16   58.3   0.3    1.2e-15   57.7   0.3    1.2  1  MAF_flag10     Protein of unknown function DUF115
  ------ inclusion threshold ------
      0.031   14.3   0.0       0.05   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 !   57.7   0.3   1.3e-19   1.2e-15      26     164 ..      19     153 ..       4     157 .. 0.74

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 1.3e-19
                        MAF_flag10  26 kpaiivgaGPSLeknlell.kelrdkaviiaadtalkaLlkegIkPDivvs.lDpqeasyevfkeaekkgdiplvfa 100
                                       k++i++++    e+   ++  ++ ++a+i+ ad  +k L  ++IkP  +++ lD+  ++ +++ + ++k +  +++a
  gi|385805428|ref|YP_005841826.1|  19 KKVIVIAGSKCYED---YInCKNPNEAIIFVADKGIKCLSRNDIKPTAIITdLDG--INDNILFHPKYKNSYFFIHA 90 
                                       56666655544444...332346699*****************************..66665555555559****** PP

                        MAF_flag10 101 sgvnpellkkykgpkiflvtgstqalelleeekne..ilfgGgsvantaldlAvklgfkeIiliGq 164
                                       +g+n el+kky +  +   ++  + +  ++++  +   +fgG+++++++++ A+ +++keI ++G+
  gi|385805428|ref|YP_005841826.1|  91 HGDNQELIKKYLPSIM--KQKIKI-IGTTQTKPFYplFNFGGFTDGDRTVFTALFFKAKEIEIYGI 153
                                       ***********98733..233222.22222222234589***********************9995 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   5.5e-06      0.05       7      52 ..      40      80 ..      35     117 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.5e-06
                     TPK_catalytic  7 naslrvcaDgGanrlyeeekerlellpdvivGDlDSirpevkefye 52
                                      n +++ +aD+G++ l      r++++p +i+ DlD i+++++ + +
  gi|385805428|ref|YP_005841826.1| 40 NEAIIFVADKGIKCLS-----RNDIKPTAIITDLDGINDNILFHPK 80
                                      567899**********.....*****************99876544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1345.79
//
Query:       gi|385805429|ref|YP_005841827.1|  [L=149]
Description: 6-pyruvoyl-tetrahydropterin synthase [Fervidicoccus fontis Kam940]
Scores for complete 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-27   94.3   0.0    6.4e-27   94.0   0.0    1.0  1  PTPS      6-pyruvoyl tetrahydropterin synthase
  ------ inclusion threshold ------
       0.13   11.9   0.0       0.15   11.7   0.0    1.1  1  RE_MamI   MamI restriction endonuclease


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 !   94.0   0.0   7.2e-31   6.4e-27       5     122 ..      19     146 ..      15     147 .. 0.92

  Alignments for each domain:
  == domain 1  score: 94.0 bits;  conditional E-value: 7.2e-31
                                       EEEEEEEE--TTTTGGGGSTEEEEEEEEEEEEEC-STCTTBSS-HHHHHHHHHHHHHCTTTEEC.CCC-CCHHCCS. CS
                              PTPS   5 efeFdaaHrlrkhegkcrnlHGHnykvevtvegeeldetgmvvdfgelkealkeileelDhkfl.naddpeleell. 79 
                                       +++Fda+H+ ++++gkc+nlHGH++ + v+ eg+  +e+gmv+df elk+++k++++ +Dhk++  a+d+e   +  
  gi|385805429|ref|YP_005841827.1|  19 NISFDASHYTKSSDGKCENLHGHTFILSVEYEGNFNQESGMVFDFIELKKIIKDVIKDYDHKLIlPAKDKENTRIEg 95 
                                       589*************************************************************9988888887779 PP

                                       .............--HHHHHHHHHHHHHHHHGCCCGCEEEEEEEEETTEEEEEEE CS
                              PTPS  80 ............spTaEnlaklifeelkerlqekevklskvrvwEtpnswaeyre 122
                                                     T+E++a  if+ ++e+l +      k++++E  n+++ +++
  gi|385805429|ref|YP_005841827.1|  96 efslsvkyldypAATTEYIALSIFHDIAEKL-K---GRIKIKLYEGMNNYVVIEG 146
                                       9*********8877*****************.3...345699*******999876 PP

>> RE_MamI  MamI restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   1.6e-05      0.15      88     147 ..      40      98 ..       7     123 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.6e-05
                           RE_MamI  88 driyllllDysgefkdiRirifevrpkkerlfkeliknwyyklflpkqektkkinsvnFq 147
                                        + ++l+++y+g+f+++   +f   +  ++++k++ik++  kl lp ++k +      F 
  gi|385805429|ref|YP_005841827.1|  40 GHTFILSVEYEGNFNQESGMVFDF-IELKKIIKDVIKDYDHKLILPAKDKENTRIEGEFS 98 
                                       467899****************96.566789***************99887766555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 881.55
//
Query:       gi|385805430|ref|YP_005841828.1|  [L=275]
Description: regulatory protein [Fervidicoccus fontis Kam940]
Scores for complete 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-47  162.3   0.1    2.7e-47  161.5   0.1    1.4  1  GCHY-1    Type I GTP cyclohydrolase folE2
  ------ inclusion threshold ------
       0.11   12.4   0.0       0.25   11.3   0.0    1.6  1  GerD      Spore germination GerD central core 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 !  161.5   0.1     3e-51   2.7e-47       2     259 .]       6     265 ..       5     265 .. 0.84

  Alignments for each domain:
  == domain 1  score: 161.5 bits;  conditional E-value: 3e-51
                                       XXXXXXXXXX----SEEEEEEEEEEEEE--TTTS-EEEEEEEEEEEES-SS--GGGGGHHHHHHHHS-SSEEG.... CS
                            GCHY-1   2 pDvqsekderkipldrVGvkgvklpvkvkdkekkaqtlvaevdlfvdLpaekkGihmSRlvevleeaeeelee.... 74 
                                       pD++++++e+ki++++ G++g+k+ +k+k  ++   +  ++++l++dL++e +G+h+SRlv++l+   +el++    
  gi|385805430|ref|YP_005841828.1|   6 PDIHENPPEYKIAINKAGIEGLKKKIKIKIGNSC-SEKLCTINLYIDLDKELRGVHLSRLVNSLN---QELNSnecf 78 
                                       7*****************************7765.6999**************************...555543444 PP

                                       ...GGHHHHHHHHHHHTT.-SEEEEEEEEEEEEEEE-TTT--EEEEEEEEEEEEEE...TT.EEEEEEEEEEEEEEE CS
                            GCHY-1  75 ...ksleeileellekleyaeraevelkfeyfiekkapvsgkeglesyevtleaeler.ke.evkltvgvevpvttl 146
                                          + le++++++l+++ +++r+e++++fe +ie +  v +            a++ r k+ + + +v++e++++t 
  gi|385805430|ref|YP_005841828.1|  79 klnDLLEKTAKRVLNTHFSSSRSEIHVSFEDIIEDTRFVLH------------ASYVReKNgSQEGKVSIELNGITS 143
                                       55566677999999999999999999999888887777666............333331122367899********* PP

                                       -HHHHHHS.........SS---EEEEEEEEEEEE......--HHHHHHHH...HHHSSEE--S---HHHHHHHHHHH CS
                            GCHY-1 147 CPCskeisrell.....eagaHnQRsvvtvkvelaeeekeveiedlielv...essassevyellKReDEkavteka 215
                                       CPC+ke+ + ++     ++++H+QR++++++++++ + + +  e l++++   +ss+s  + e+l R++E ++++k+
  gi|385805430|ref|YP_005841828.1| 144 CPCAKEVFKFYEnteyeKTPTHMQRAELHITLNSKYNLDLLYNEYLLKAIsvgKSSFSDILKETLNRDEEYEFIKKT 220
                                       ********8877999999***************854555566666666655559*********************** PP

                                       HTS---HHHHHHHHHHHHHS-TTEEEE..EEEEEEE-TTTSSEEEE CS
                            GCHY-1 216 yenpkFvEDvvRevaaaleeeerveef..sveveneESiHnHnavA 259
                                       ++np+F EDv+R+++  l++e   +++  +++v ++ESiH++n++A
  gi|385805430|ref|YP_005841828.1| 221 INNPMFAEDVCRKAYFYLKKE-LPSDIglKIKVISYESIHPYNVIA 265
                                       ******************544.4455567***************98 PP

>> GerD  Spore germination GerD central core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.8e-05      0.25       8      39 ..     200     231 ..     193     240 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.8e-05
                              GerD   8 vkkaiektltsekgkkfwkklfkdpkfaeala 39 
                                        ++ +++tl  +++ +f+kk++++p fae++ 
  gi|385805430|ref|YP_005841828.1| 200 FSDILKETLNRDEEYEFIKKTINNPMFAEDVC 231
                                       56788999999999999999999999999875 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:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.34s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1618.38
//
Query:       gi|385805431|ref|YP_005841829.1|  [L=378]
Description: acetate kinase superfamily [Fervidicoccus fontis Kam940]
Scores for complete 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-73  247.0   0.2    3.1e-73  246.8   0.2    1.0  1  DUF1464   Protein of unknown function (DUF1464)


Domain annotation for each model (and alignments):
>> DUF1464  Protein of unknown function (DUF1464)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  246.8   0.2   1.7e-77   3.1e-73       1     326 [.       7     356 ..       7     357 .. 0.87

  Alignments for each domain:
  == domain 1  score: 246.8 bits;  conditional E-value: 1.7e-77
                           DUF1464   1 GiDPGtksydvvvvddlgkvvlekeiptdevekdpsvlvkaieea.radivalpSGyGlPlkriselae.....rei 71 
                                       GiDPGtks+d+vv+d+ +k++ ek+ipt+ ++ +p++l+  i +    d++++pSGyG P+++++++++     +ei
  gi|385805431|ref|YP_005841829.1|   7 GIDPGTKSFDIVVMDE-EKIIEEKSIPTEIIASNPDILIDEILKIkDFDVIIAPSGYGSPFVCNENIKDirlfaSEI 82 
                                       9***************.***********************99998789*********************99999888 PP

                           DUF1464  72 llltlaeeseegl.......vGLrellkelaskelnaftiPgVieLptvPewRKvnkiDmGtADKlasavlavadea 141
                                       lll+  +e  + +         L +  ++l ++++na++iP+V  L++v    K+n+iD GtADKlasa+  ++   
  gi|385805431|ref|YP_005841829.1|  83 LLLSKYKELLNLKdegsmvyKALYKTSVKLWKNKINACYIPSVKLLNSVELKFKINTIDCGTADKLASAFYVINYLR 159
                                       8888666654433433342234777777788888*************************************776666 PP

                           DUF1464 142 eee..eyrelsFilvEvGsgfnaviaVknGkivDGlGgti.lpGflsaGalDgEvAyllgkvakiekslifsgGvas 215
                                       ++e  +  +++F ++E+G+g+na+i V+ G+iv G+Ggt    G+l++G +D+E+        ++++++if gG + 
  gi|385805431|ref|YP_005841829.1| 160 DREsfDIDKINFTMLEIGYGYNALIKVRRGRIVGGIGGTKlGIGHLTIGPIDAEITAYKR---RWKRNDIFYGGLKD 233
                                       5557899*********************************778***********976555...9************* PP

                           DUF1464 216 iageaelekklsee......aferlke.vvksvaellsskykleeiivSGrlkrikelgkklesrleev........ 277
                                        + ++ l+++l+ +      a e++ + +   +  l  ++   + +iv Gr  + +el++kl+s+l +         
  gi|385805431|ref|YP_005841829.1| 234 YCKTSSLDDALKSTepicraAVEQMFDsIFEKILILNEDT--KDILIVTGRYSSSNELKEKLSSNLSKKferiifhp 308
                                       *********9998889888888888887666666666665..3447***************9998866667777653 PP

                           DUF1464 278 kllelaskaKeaaqGaAiianalaGgryrelvdhleiekssgtvldyvk 326
                                       k    +s  Ke+a G+A+i+ +++G +y+e  d l+i++s+gtvldy+ 
  gi|385805431|ref|YP_005841829.1| 309 K-YFENSFVKESALGQAMIGLGFMGSKYKETFDVLGIKESKGTVLDYIM 356
                                       2.2334568**************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.36s 00:00:01.02 Elapsed: 00:00:00.57
# Mc/sec: 1995.47
//
Query:       gi|385805432|ref|YP_005841830.1|  [L=376]
Description: cell division protein CdvC [Fervidicoccus fontis Kam940]
Scores for complete 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-38  131.5   0.0    6.1e-38  130.2   0.0    1.7  1  AAA              ATPase family associated with various cellul
      6e-11   42.2   0.7    1.9e-10   40.6   0.7    1.9  1  MIT              MIT (microtubule interacting and transport) 
    9.3e-08   32.2   0.0    2.7e-07   30.7   0.0    1.8  1  AAA_14           AAA domain
    1.1e-07   31.6   0.0    2.8e-07   30.2   0.0    1.7  1  AAA_lid_3        AAA+ lid domain
    4.2e-07   30.2   0.0    9.4e-07   29.1   0.0    1.5  1  AAA_2            AAA domain (Cdc48 subfamily)
    6.2e-07   29.5   0.0    4.9e-06   26.6   0.0    2.5  1  AAA_5            AAA domain (dynein-related subfamily)
    1.9e-06   28.2   0.1    0.00038   20.7   0.0    3.2  1  AAA_22           AAA domain
    1.1e-05   25.3   0.2      5e-05   23.2   0.0    2.1  2  Vps4_C           Vps4 C terminal oligomerisation domain
    9.2e-05   22.2   0.1    0.00055   19.7   0.0    2.2  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00019   21.9   0.0     0.0044   17.4   0.0    2.7  2  AAA_16           AAA ATPase domain
    0.00086   18.9   0.2     0.0025   17.4   0.2    1.8  1  TPR_11           TPR repeat
     0.0012   19.2   0.2      0.016   15.6   0.0    2.8  2  RNA_helicase     RNA helicase
     0.0018   17.6   0.1      0.011   15.0   0.0    2.0  2  TIP49            TIP49 P-loop domain
     0.0023   17.7   0.0     0.0053   16.5   0.0    1.6  1  IstB_IS21        IstB-like ATP binding protein
     0.0028   17.3   0.1      0.063   12.8   0.1    2.3  2  AAA_25           AAA domain
     0.0028   17.4   0.3     0.0076   16.0   0.3    1.8  1  TPR_1            Tetratricopeptide repeat
     0.0037   16.7   0.1      0.007   15.8   0.1    1.4  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0076   16.4   0.0      0.037   14.2   0.0    2.1  2  AAA_33           AAA domain
     0.0097   16.1   0.2     0.0097   16.1   0.2    2.8  2  TPR_8            Tetratricopeptide repeat
     0.0098   15.8   1.4       0.56   10.1   0.0    3.0  3  ATPase_2         ATPase domain predominantly from Archaea
  ------ inclusion threshold ------
       0.01   15.6   0.0      0.022   14.5   0.0    1.5  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.011   15.6   0.2       0.02   14.7   0.2    1.4  1  DUF5113          Domain of unknown function (DUF5113)
      0.012   15.4   0.1      0.075   12.7   0.1    2.2  1  AAA_24           AAA domain
      0.012   15.7   1.6       0.02   15.0   0.3    2.1  1  TPR_2            Tetratricopeptide repeat
      0.014   15.7   0.0      0.036   14.3   0.0    1.7  1  AAA_28           AAA domain
      0.015   15.8   0.0      0.045   14.3   0.0    1.9  1  AAA_18           AAA domain
      0.017   15.8   0.0      0.083   13.6   0.0    2.3  1  TPR_6            Tetratricopeptide repeat
      0.026   15.1   0.0       0.13   12.8   0.0    2.1  2  ABC_tran         ABC transporter
      0.031   14.2   0.0       0.06   13.3   0.0    1.4  1  NACHT            NACHT domain
      0.033   14.0   0.1        2.6    7.8   0.0    2.2  2  AAA_11           AAA domain
      0.035   14.1   0.0       0.12   12.5   0.0    1.9  1  TPR_7            Tetratricopeptide repeat
      0.037   13.9   0.0      0.075   12.9   0.0    1.5  1  Bac_DnaA         Bacterial dnaA  protein
      0.045   14.2   0.0       0.29   11.5   0.0    2.1  2  AAA_17           AAA domain
      0.054   12.8   0.0       0.15   11.3   0.0    1.7  1  Zeta_toxin       Zeta toxin
      0.062   13.6   0.1       0.14   12.4   0.1    1.6  1  TPR_12           Tetratricopeptide repeat
      0.085   11.9   0.0       0.13   11.3   0.0    1.3  1  Parvo_NS1        Parvovirus non-structural protein NS1
      0.094   12.0   0.9        4.6    6.5   0.0    2.8  3  ATPase           KaiC
        0.1   12.3   0.0        0.5   10.1   0.0    2.1  1  Sigma54_activat  Sigma-54 interaction domain
       0.11   12.8   1.4        1.3    9.3   0.1    2.6  2  FliS             Flagellar protein FliS
       0.12   11.6   0.0       0.52    9.5   0.0    1.9  2  NB-ARC           NB-ARC domain
        2.7    7.8   4.6          1    9.1   0.2    2.5  2  Vta1_C           Vta1 C-terminal 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 !  130.2   0.0   1.4e-40   6.1e-38       1     131 [.     140     273 ..     140     274 .. 0.95

  Alignments for each domain:
  == domain 1  score: 130.2 bits;  conditional E-value: 1.4e-40
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS...TSEEEEEETGGGHHHHH CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakeka...kpsilfiDEidalaksr 74 
                                       +ll+GppG+GKT+la ava+e++ +fl +++++++sk++ge+ek+++++fk a++k+   +p i+fiDEidal ++ 
  gi|385805432|ref|YP_005841830.1| 140 ILLFGPPGCGKTMLAAAVANEVNGYFLYVDAASIMSKWLGEAEKNVSKIFKYARQKSeegSPAIIFIDEIDALLGTF 216
                                       69*****************************************************999*999**************9 PP

                                       TTCCCHHHHHHHHHHHHHHHHTTTS..SSTEEEEEEESSGGGSTHHHHSTTSSEEEETT CS
                               AAA  75 sgseseeeervvnqLlteldgvkkk..eskvivigatnrpdkldpallrgRfdrkieie 131
                                        ++e + e rv nq+l+e+dg ++k  + +v vigatn+p++ld+a++ +Rf+++i i+
  gi|385805432|ref|YP_005841830.1| 217 -SGEVGGEVRVRNQFLKEMDGIQDKdkKIHVYVIGATNKPWQLDEAFV-RRFNKRILIP 273
                                       .8899999***************995544599****************.7******998 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 !   40.6   0.7   4.4e-13   1.9e-10       3      64 ..       9      71 ..       8      72 .. 0.95

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 4.4e-13
                               MIT  3 kAlelvkkAveeDnagnyeeAlelYkealelLlqalke.kneerrellrekieeYleRaeeLk 64
                                       A  ++++Av +D+ g+ye+A+++Y++a+e+L+++++   ++    ++ e i++Y +R+++L+
  gi|385805432|ref|YP_005841830.1|  9 MATRYARAAVAADKDGDYETAINNYRKAIEILTKIVRMyPDSPLISTYLEMIKSYEKRIQQLQ 71
                                      68999********************************55999*******************97 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.0   6.1e-10   2.7e-07       5     125 ..     140     274 ..     137     278 .. 0.84

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 6.1e-10
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe....kllelileklkeekktylflDEiqev. 76 
                                       +++ G+  +GKT+l+  +++e       +ly++  +   k l + e    k+ ++ ++k +e    ++f+DEi  + 
  gi|385805432|ref|YP_005841830.1| 140 ILLFGPPGCGKTMLAAAVANEVN---GYFLYVDAASIMSKWLGEAEknvsKIFKYARQKSEEGSPAIIFIDEIDALl 213
                                       6899**************98877...999***99999886544433223367777777754458899********** PP

                            AAA_14  77 ..............pewekalkslvdegknldvivtGSnskllskeiatslagrvaeielypl 125
                                                     +++ k + ++ d++k+++v+v G  +k    ++ + +++r ++  l pl
  gi|385805432|ref|YP_005841830.1| 214 gtfsgevggevrvrNQFLKEMDGIQDKDKKIHVYVIGATNKPW--QLDEAFVRRFNKRILIPL 274
                                       **************************************99988..678888888888777776 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   6.3e-10   2.8e-07       1      43 [.     296     347 ..     296     349 .. 0.89

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 6.3e-10
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrr........gik.eitmedf 43 
                                       dvdl++LA++TeGyS  D+  ++++   l +r+        g++ +itmedf
  gi|385805432|ref|YP_005841830.1| 296 DVDLDRLAQLTEGYSASDIRDIIQATHTLVIREffeqkngeGEPrSITMEDF 347
                                       9********************************7777776666656999999 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   2.2e-09   9.4e-07       6     105 ..     140     236 ..     138     248 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 2.2e-09
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG---..----THHHHHHHHHTTT-HHHHTTSEEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselle..eeevehlvsrligappgyvgaeegGivllDEidKi 80 
                                       ill gp g+Gkt+la a+a+  +      +  +da +++     e+e+ vs+    +    +     i+++DEid  
  gi|385805432|ref|YP_005841830.1| 140 ILLFGPPGCGKTMLAAAVANEVNG----YFLYVDAASIMSkwLGEAEKNVSKIFKYARQKSEEGSPAIIFIDEIDAL 212
                                       7899******************95....9**********9776899999**9999988888888888********88 PP

                                       ------------H.HHHHHHHHHHH- CS
                             AAA_2  81 hpkessgadvSre.gVqrdLLqileg 105
                                           + + +v +e  V + +L+ ++g
  gi|385805432|ref|YP_005841830.1| 213 LG--TFSGEVGGEvRVRNQFLKEMDG 236
                                       77..5555665554577777776665 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   1.1e-08   4.9e-06       2     138 .]     140     266 ..     139     266 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 1.1e-08
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------.....G-SEEEEES CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar.....egeilvlDE 73 
                                       +lL GppG+gK++la  +a  +n  ++yv   + +++   +g+ e kn  + ++        +     +++i+++DE
  gi|385805432|ref|YP_005841830.1| 140 ILLFGPPGCGKTMLAAAVANEVNGYFLYVDAASIMSK--WLGEAE-KNVSKIFKYAR-----QkseegSPAIIFIDE 208
                                       89***************************98886654..344444.24444444444.....355555********* PP

                                       GGG--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHTT- CS
                             AAA_5  74 veraesevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrsRf 138
                                       ++ +     +++      r   l e+++ ++++++     ++vi+++n++     +l++a+++Rf
  gi|385805432|ref|YP_005841830.1| 209 IDALLGTFSGEVGGEVRVRNQFLKEMDGIQDKDKK---IHVYVIGATNKPW----QLDEAFVRRF 266
                                       **887888888877777777777777777777663...349*********9....9999****99 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   8.7e-07   0.00038       8     130 ..     140     251 ..     137     254 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 8.7e-07
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseellealeq 84 
                                       ++++G++G+GKT+l++ ++++          +  +++v+++s +      ++ l + +    +   + + ++++ +q
  gi|385805432|ref|YP_005841830.1| 140 ILLFGPPGCGKTMLAAAVANEV---------NGYFLYVDAASIM------SKWLGEAE----K---NVSKIFKYARQ 194
                                       799*****************98.........7777788887766......33333333....3...77889999999 PP

                            AAA_22  85 alraravielliiDEaqhlr...s..........eealeeLrsllnlsrkgvqliLvGt 130
                                        +++ +  +++ iDE++ l    s          ++ l+e   +++ ++k++++ ++G 
  gi|385805432|ref|YP_005841830.1| 195 KSEEGSP-AIIFIDEIDALLgtfSgevggevrvrNQFLKEMDGIQD-KDKKIHVYVIGA 251
                                       9999999.99999999997656633444454444444444444444.677777777775 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 ?   -1.6   0.0       6.2   2.7e+03      38      53 ..      96     111 ..      92     115 .. 0.68
   2 !   23.2   0.0   1.1e-07     5e-05      26      60 ..     338     373 ..     332     373 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 6.2
                            Vps4_C  38 lkkarptVskeDLekh 53 
                                       + +++p V  +D++ +
  gi|385805432|ref|YP_005841830.1|  96 VLTQKPNVKFSDIADL 111
                                       5567777777777655 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 1.1e-07
                            Vps4_C  26 eP.pvtlkDflkalkkarptVskeDLekheeFTkef 60 
                                       eP ++t++Dfl++lk+ +p+V +  +++++ + ++f
  gi|385805432|ref|YP_005841830.1| 338 EPrSITMEDFLNILKERKPSVDPLFVKRYDAWFEKF 373
                                       4559****************************9987 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.3e-06   0.00055      36      69 ..     140     173 ..     137     218 .. 0.61
   2 ?   -1.2   0.0       3.3   1.4e+03       2      35 ..     227     260 ..     226     266 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.3e-06
                            RuvB_N  36 vllyGpPGlGkttlakiiakelgvklkitsgPvl 69 
                                       +ll+GpPG Gkt la+ +a+e++  +    +  +
  gi|385805432|ref|YP_005841830.1| 140 ILLFGPPGCGKTMLAAAVANEVNGYFLYVDAASI 173
                                       89*******************9976654433332 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.3
                            RuvB_N   2 rPksleeyigqekvkeklkifieaakkreealdh 35 
                                       r + l+e  g ++  +k+++++  a ++  +ld 
  gi|385805432|ref|YP_005841830.1| 227 RNQFLKEMDGIQDKDKKIHVYVIGATNKPWQLDE 260
                                       7788999999999999999999999888877776 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0     1e-05    0.0044      24      59 ..     137     169 ..     112     185 .. 0.82
   2 ?    0.8   0.0       1.3   5.7e+02     128     146 ..     194     211 ..     175     218 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1e-05
                            AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrgk 59 
                                       p+ +ll G++G+GK+ l+ +++++++   g+fl+ +
  gi|385805432|ref|YP_005841830.1| 137 PRGILLFGPPGCGKTMLAAAVANEVN---GYFLYVD 169
                                       599*******************8766...6676655 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1.3
                            AAA_16 128 allsrderplvlvlDdlqw 146
                                       +++++ ++p ++++D+++ 
  gi|385805432|ref|YP_005841830.1| 194 QKSEE-GSPAIIFIDEIDA 211
                                       33444.669*******995 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.2   5.8e-06    0.0025       8      23 ..      24      39 ..      22      40 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5.8e-06
                            TPR_11  8 GkyeeAieaYkkAlkl 23
                                      G+ye Ai++Y+kA+++
  gi|385805432|ref|YP_005841830.1| 24 GDYETAINNYRKAIEI 39
                                      9*************97 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1       3.9   1.7e+03      21      64 ..      69     114 ..      56     130 .. 0.65
   2 !   15.6   0.0   3.7e-05     0.016       1      34 [.     140     173 ..     140     205 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 3.9
                      RNA_helicase  21 allkklklkkkdsvysrnpeddfwdgYt..gqevvvidDfgqvkde 64 
                                       +l+++ + +++++    n +d+f +     +++ v + D++  k+ 
  gi|385805432|ref|YP_005841830.1|  69 QLQSNTEAIESNTASKSNEKDSFINDIVltQKPNVKFSDIADLKEA 114
                                       4444445555444444777777776665557778888888777755 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 3.7e-05
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsv 34 
                                       i+l+Gp+g+GK++la  +a+++ + + +  + s+
  gi|385805432|ref|YP_005841830.1| 140 ILLFGPPGCGKTMLAAAVANEVNGYFLYVDAASI 173
                                       689******************9988844444444 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.5e-05     0.011      51      91 ..     138     176 ..     113     190 .. 0.85
   2 ?    0.5   0.0      0.63   2.8e+02     264     289 ..     186     211 ..     165     214 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.5e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevysl 91 
                                       r++Ll Gp+g Gkt la a+++e++    f  + ++ + s 
  gi|385805432|ref|YP_005841830.1| 138 RGILLFGPPGCGKTMLAAAVANEVN--GYFLYVDAASIMSK 176
                                       89*********************98..45777777777665 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.63
                                       XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 264 kkvakyveegkaeivpGvlfiDevhm 289
                                        k+ ky  +   e  p ++fiDe+  
  gi|385805432|ref|YP_005841830.1| 186 SKIFKYARQKSEEGSPAIIFIDEIDA 211
                                       35678999999999*********975 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 !   16.5   0.0   1.2e-05    0.0053      49      83 ..     139     170 ..     134     214 .. 0.60

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.2e-05
                         IstB_IS21  49 nivllGpsGvGKshlaialgveavraglsvlfvrv 83 
                                       +i+l+Gp+G GK+ la+a++ e   +g+  l+v +
  gi|385805432|ref|YP_005841830.1| 139 GILLFGPPGCGKTMLAAAVANEV--NGY-FLYVDA 170
                                       699***************99875..333.334433 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.1   0.00014     0.063      36      55 ..     140     159 ..     123     163 .. 0.82
   2 ?    1.8   0.0      0.35   1.5e+02     134     191 ..     193     254 ..     164     256 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00014
                            AAA_25  36 allaGapgtGKttlaldlal 55 
                                       +ll+G+pg+GKt+la  +a 
  gi|385805432|ref|YP_005841830.1| 140 ILLFGPPGCGKTMLAAAVAN 159
                                       69*************98875 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.35
                            AAA_25 134 eaaieevegvrlvviDplsralgg.densnsdv...galvealeriar.rtgaavllvhHvgK 191
                                       +++ ee   ++ + iD ++++lg  + +   +v   +++++ ++ i++  ++++v ++  ++K
  gi|385805432|ref|YP_005841830.1| 193 RQKSEE-GSPAIIFIDEIDALLGTfSGEVGGEVrvrNQFLKEMDGIQDkDKKIHVYVIGATNK 254
                                       445556.5699*********99999666666644599******99987356688877766555 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.3   1.7e-05    0.0076       6      30 ..      15      39 ..      10      40 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.7e-05
                                      HHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1  6 nlGnayfklgkydeAleyyekALel 30
                                      + ++a  k g+y+ A+  y+kA+e+
  gi|385805432|ref|YP_005841830.1| 15 RAAVAADKDGDYETAINNYRKAIEI 39
                                      568899999**************98 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   1.6e-05     0.007      25      42 ..     140     157 ..     137     163 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.6e-05
                      Mg_chelatase  25 lllvGppGsGKtmlakrl 42 
                                       +ll+GppG+GKtmla+++
  gi|385805432|ref|YP_005841830.1| 140 ILLFGPPGCGKTMLAAAV 157
                                       89*************987 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       5.4   2.4e+03      96     124 ..      62      90 ..      54      99 .. 0.74
   2 !   14.2   0.0   8.4e-05     0.037       2      33 ..     140     171 ..     140     219 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 5.4
                            AAA_33  96 gvpvrivvvetdeetlkeRlakRaangdd 124
                                       +++ ri  +++  e +++++a +++++d+
  gi|385805432|ref|YP_005841830.1|  62 SYEKRIQQLQSNTEAIESNTASKSNEKDS 90 
                                       56677778888888888999888888765 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 8.4e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklgavllssdtl 33 
                                       +ll G+pG+GK+ la  ++++  +++l  d++
  gi|385805432|ref|YP_005841830.1| 140 ILLFGPPGCGKTMLAAAVANEVNGYFLYVDAA 171
                                       6899***************9999888777773 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.2   2.2e-05    0.0097       3      30 ..      12      39 ..      10      39 .. 0.92
   2 ?   -0.5   0.1       4.4   1.9e+03      15      28 ..     109     122 ..     105     122 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.2e-05
                                      HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8  3 ayynlgsiylklgdyeeAkeyyekalel 30
                                       y + + + +k gdye A+  y+ka+e+
  gi|385805432|ref|YP_005841830.1| 12 RYARAAVAADKDGDYETAINNYRKAIEI 39
                                      6899999*******************97 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 4.4
                                       T-HHHHHHHHHHHH CS
                             TPR_8  15 gdyeeAkeyyekal 28 
                                        d++eAk+++ +a+
  gi|385805432|ref|YP_005841830.1| 109 ADLKEAKQAIVEAI 122
                                       6899***9998886 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.2       2.7   1.2e+03      70     104 ..      78     116 ..      50     129 .. 0.51
   2 !   10.1   0.0    0.0013      0.56      23      55 ..     140     169 ..     136     176 .. 0.82
   3 ?    3.2   0.0      0.16        69      97     131 ..     176     213 ..     168     251 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 2.7
                          ATPase_2  70 e......eeeekkklekalgiavpkaeleeilkeksklvfk 104
                                       e       +e+++++++ ++++ p++++  i +   k++++
  gi|385805432|ref|YP_005841830.1|  78 EsntaskSNEKDSFINDIVLTQKPNVKFSDIAD--LKEAKQ 116
                                       222222245666667777777777777766644..222223 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0013
                          ATPase_2  23 yfiYGpegsGKtaLlkeiienledkdkyviyyi 55 
                                       ++++Gp g+GKt L   ++++ +    y +y++
  gi|385805432|ref|YP_005841830.1| 140 ILLFGPPGCGKTMLAAAVANEVNG---YFLYVD 169
                                       679************999998844...666665 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.16
                          ATPase_2  97 eksklvfkaielllekikkkgkk...iiiiiDelqkli 131
                                       +   +++k+++++++  ++k  +    ii+iDe+  l 
  gi|385805432|ref|YP_005841830.1| 176 KWLGEAEKNVSKIFKYARQKSEEgspAIIFIDEIDALL 213
                                       5556788899999999999988889788999**98776 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 ?   14.5   0.0     5e-05     0.022       3      71 ..     142     209 ..     140     216 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5e-05
                   Viral_helicase1   3 vhGvpGcGKStlirkllrts..liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                         G pGcGK+ l   ++++   +    ++ +a + ++++ +++++  + + ++  +++++ +  i+++DE+
  gi|385805432|ref|YP_005841830.1| 142 LFGPPGCGKTMLAAAVANEVngY--FLYVDAASIMSKWLGEAEKNVSK-IFKYARQKSEEGSPAIIFIDEI 209
                                       5688**************99643..4577889******9777776555.555666666666899******8 PP

>> DUF5113  Domain of unknown function (DUF5113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.2   4.5e-05      0.02       5      65 ..       7      66 ..       3      82 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.5e-05
                           DUF5113  5 lqiandYanlayylnvegeyeeALeyldsaleylNahyekYakkkadtldklkmllegege 65
                                       ++a +Ya +a ++  +g+ye+A++  ++a+e+l +  ++Y ++     + l+m+++ e++
  gi|385805432|ref|YP_005841830.1|  7 QEMATRYARAAVAADKDGDYETAINNYRKAIEILTKIVRMYPDSPL-ISTYLEMIKSYEKR 66
                                      57899************************************99884.44455565555555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00017     0.075       5      78 ..     140     213 ..     137     268 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00017
                            AAA_24   5 iliyGpsgiGKTtlakel..gpkplfidtekGlksldadkfpdieswedfldevvelaaeladyktlviDtidele 78 
                                       il++Gp+g GKT+la+    + +  f+ +++ +  +  + ++  +++ ++ +++ + ++e +   +++iD id l 
  gi|385805432|ref|YP_005841830.1| 140 ILLFGPPGCGKTMLAAAVanEVNGYFLYVDAAS-IMSKWLGEAEKNVSKIFKYARQKSEEGS-PAIIFIDEIDALL 213
                                       89**************99884444455444422.3444444433344444444444444433.4556666666554 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.3   4.6e-05      0.02       4      30 ..      13      39 ..      10      42 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.6e-05
                             TPR_2  4 lynlGlayyklgdyeeAleafekAlel 30
                                      + + + a+ k gdye A++ ++kA+e+
  gi|385805432|ref|YP_005841830.1| 13 YARAAVAADKDGDYETAINNYRKAIEI 39
                                      778999*******************97 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   8.3e-05     0.036       2      40 ..     140     180 ..     139     199 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.3e-05
                            AAA_28   2 ivitGgestGKTtlleaLaar..gypvvpEaareileekla 40 
                                       i ++G++++GKT l++a a++  gy  + +aa  + + +++
  gi|385805432|ref|YP_005841830.1| 140 ILLFGPPGCGKTMLAAAVANEvnGYFLYVDAASIMSKWLGE 180
                                       789****************9878888777777766665555 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    0.0001     0.045       1      25 [.     140     172 ..     140     247 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 0.0001
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.......g 25 
                                       Ill G+pG+GKt la +++++  g+       +
  gi|385805432|ref|YP_005841830.1| 140 ILLFGPPGCGKTMLAAAVANEVnGYflyvdaaS 172
                                       99****************999655556554442 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   0.00019     0.083      13      33 .]      24      50 ..       6      50 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00019
                                      H......HHHHHHHHHHHHHHHH-TT- CS
                             TPR_6 13 l......gdtdkAlealerlikeYPdS 33
                                      +      ++++kA+e+l ++++ YPdS
  gi|385805432|ref|YP_005841830.1| 24 GdyetaiNNYRKAIEILTKIVRMYPDS 50
                                      255555689*****************9 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1       5.6   2.5e+03      54      79 ..      60      86 ..      27     119 .. 0.57
   2 ?   12.8   0.0   0.00029      0.13      15      71 ..     141     195 ..     138     250 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 5.6
                                      HHHCCHCEEEE-SS--S-TTSB.HHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                          ABC_tran 54 leslrkeigvlpqepqlfpelt.vren 79
                                      ++s++k+i+ l+ +++  +  t  ++n
  gi|385805432|ref|YP_005841830.1| 60 IKSYEKRIQQLQSNTEAIESNTaSKSN 86
                                      344444444444442222222213333 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00029
                                       EEEESTTSSHHHHHHHHTTSS--SEEEEE.ETTCEGGGB-HHHCCHCEEEE-SS--S- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  15 aivGenGaGKStLlkllagllkpteGeil.ldgkdlkeqeleslrkeigvlpqepqlf 71 
                                        ++G+ G+GK+ L++++a++++   G  l +d +++ ++ l +++k+++ +++ ++ +
  gi|385805432|ref|YP_005841830.1| 141 LLFGPPGCGKTMLAAAVANEVN---GYFLyVDAASIMSKWLGEAEKNVSKIFKYARQK 195
                                       689****************997...444303567777777888888888877765544 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   0.00014      0.06       3      23 ..     140     160 ..     138     169 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00014
                                       EEEEC-TTTCHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                       ++l G++G+GKT+L++ +a +
  gi|385805432|ref|YP_005841830.1| 140 ILLFGPPGCGKTMLAAAVANE 160
                                       7899************99987 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.3      0.12        50      87     148 ..      40      96 ..      28     124 .. 0.63
   2 ?    7.8   0.0    0.0059       2.6      21      43 ..     141     172 ..     127     205 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.12
                            AAA_11  87 kpkivRvgneeeriseavksvsleekvekrlekeekaqlakeiskeleklakelrafeeeee 148
                                         kivR++++++ is+ ++ ++   + ekr+++   ++ ++ i+++++++++e ++f +++ 
  gi|385805432|ref|YP_005841830.1|  40 LTKIVRMYPDSPLISTYLEMIK---SYEKRIQQ--LQSNTEAIESNTASKSNEKDSFINDIV 96 
                                       5699999999987888877777...66666655..455555666666666666666655543 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0059
                            AAA_11  21 liqGPPGtgKTktivellsqll.........s 43 
                                       l+ GPPG+gKT   +++ ++++         s
  gi|385805432|ref|YP_005841830.1| 141 LLFGPPGCGKTMLAAAVANEVNgyflyvdaaS 172
                                       788********999999999975554444440 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00027      0.12       4      27 ..      15      38 ..      13      54 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00027
                             TPR_7  4 nLarlysrlGdyeeAielyeqsLa 27
                                      + a++  ++Gdye+Ai  y+++++
  gi|385805432|ref|YP_005841830.1| 15 RAAVAADKDGDYETAINNYRKAIE 38
                                      56889999*************664 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00017     0.075      37     214 ..     140     326 ..     137     331 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00017
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHT.....T-SEEEEE-GGG CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklr.....kvDvLliDDiqf 108
                                       ++++g+ G Gkt L  a++nev         +Y+ a + +++ +   +++  + fk   +     +  ++ iD+i  
  gi|385805432|ref|YP_005841830.1| 140 ILLFGPPGCGKTMLAAAVANEVNG-----YFLYVDAASIMSKWLGEAEKNVSKIFKYARQkseegSPAIIFIDEIDA 211
                                       689***************999865.....568999999999988888887777776544411111456999999998 PP

                                       GTT........-HHHHHHHHHHHHHHHTTT-EE...EEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHH CS
                          Bac_DnaA 109 lag........kektqeelfhtfnalleegkqv...vlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlai 174
                                       l g          ++++++++ ++ + +++k++   v+ +  +P++   l++ +  rf+  + + + + +   +l  
  gi|385805432|ref|YP_005841830.1| 212 LLGtfsgevggEVRVRNQFLKEMDGIQDKDKKIhvyVIGATNKPWQ---LDEAFVRRFNKRILIPLPDLESRRQLFA 285
                                       76411111111567999***************96566777788876...5778888999988877755555544444 PP

                                       HHHHHHHTT----TTHHHHHHHH--.S-HHHHHHHHHHHHH CS
                          Bac_DnaA 175 lkkkieaeklevpeevlefiaervt.dnvRelegalnrlka 214
                                       l  k  + + +v  + l  ++e ++ +++R++  a ++l++
  gi|385805432|ref|YP_005841830.1| 286 LYTKGLNLSSDVDLDRLAQLTEGYSaSDIRDIIQATHTLVI 326
                                       44444455556777777666665542568887777777665 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1       3.1   1.4e+03      45      89 ..      58     106 ..      46     128 .. 0.49
   2 ?   11.5   0.0   0.00067      0.29       1      34 [.     143     178 ..     143     210 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 3.1
                                       HHCTSHHHHHHHHH...HHHHHHHHHHH.HSSEEEEEE-SEEEETTEEE CS
                            AAA_17  45 emrklpleekkelq...keaaekiaeea.kkkgvlvdghprikeqagfl 89 
                                       em k ++++ ++lq   + ++ + a ++ +k+ ++ d   + k + +f 
  gi|385805432|ref|YP_005841830.1|  58 EMIKSYEKRIQQLQsntEAIESNTASKSnEKDSFINDIVLTQKPNVKFS 106
                                       4555444444444411123333444444233445555555544444443 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00067
                                       EE-TTSSHHHHHHHHHHHH..TEEEEEHHHHHHHHH CS
                            AAA_17   1 lGgPGsGKgtqceklveky..gfthlsaGdllreea 34 
                                       +G+PG+GK+ +++ ++ ++   f ++ a +++ +  
  gi|385805432|ref|YP_005841830.1| 143 FGPPGCGKTMLAAAVANEVngYFLYVDAASIMSKWL 178
                                       6****************9955577888888887655 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00034      0.15      16      50 ..     137     169 ..     132     175 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00034
                        Zeta_toxin  16 PklillgGqpGAGKselaellkdelerqgnvvrld 50 
                                       P  ill G pG+GK+ la+++++e+  +g ++ +d
  gi|385805432|ref|YP_005841830.1| 137 PRGILLFGPPGCGKTMLAAAVANEV--NGYFLYVD 169
                                       67799*******************9..67666665 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00033      0.14      49      76 ..      14      41 ..       5      58 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00033
                            TPR_12 49 rnLgrlyralgryeeAlelleealaiae 76
                                         + + ++ g+ye A++ +++a++i++
  gi|385805432|ref|YP_005841830.1| 14 ARAAVAADKDGDYETAINNYRKAIEILT 41
                                      3333334566666666666666666654 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   0.00031      0.13      49     140 ..      71     163 ..      52     168 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00031
                         Parvo_NS1  49 enaleqakirmfstkaaldilakkevtadfdieenriykllslngynpvevgqvllawlskqlgkrn...tvwfyGp 122
                                       ++  e+++ ++ s+ +  d  +   v    +  + ++ +++ l+ +  + v  +++++ + +l++ +    ++++Gp
  gi|385805432|ref|YP_005841830.1|  71 QSNTEAIESNTASKSNEKDSFINDIVL--TQKPNVKFSDIADLKEAKQAIVEAIVYPVKRPDLFPLGwprGILLFGP 145
                                       444444445555555554444444444..4555556666666666666666666666666666654311158999** PP

                         Parvo_NS1 123 antGktnlaeaIakavpl 140
                                       + +Gkt+la+a a+ v  
  gi|385805432|ref|YP_005841830.1| 146 PGCGKTMLAAAVANEVNG 163
                                       *************98865 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.3       2.9   1.3e+03      56     115 ..      63     122 ..      59     125 .. 0.79
   2 ?    6.5   0.0      0.01       4.6      21      37 ..     139     155 ..     130     159 .. 0.86
   3 ?    2.7   0.0      0.15        66      80     154 ..     162     234 ..     155     237 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.9
                            ATPase  56 veepaedlrenakslGwdlekleeegklaiidasesaeesaeekdkedleelieelaeai 115
                                        e + ++l+ n +++  ++    +e   +i d++ +++ + + +d +dl+e ++ + eai
  gi|385805432|ref|YP_005841830.1|  63 YEKRIQQLQSNTEAIESNTASKSNEKDSFINDIVLTQKPNVKFSDIADLKEAKQAIVEAI 122
                                       577778999999999999998888888899999888888777788888888888777766 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.01
                            ATPase  21 vvlitGepGtGKtifal 37 
                                        +l+ G pG+GKt++a+
  gi|385805432|ref|YP_005841830.1| 139 GILLFGPPGCGKTMLAA 155
                                       489***********996 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.15
                            ATPase  80 egklaiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitglayeekeavaReilrqlvrvlkkl 154
                                       +g + ++da++ +++    + +++++++ +  ++  +e     + iD i++l   + + ++  ++r   ++lk++
  gi|385805432|ref|YP_005841830.1| 162 NGYFLYVDAASIMSKWL-GEAEKNVSKIFKYARQKSEEGSPAIIFIDEIDAL-LGTFSGEVGGEVRVRNQFLKEM 234
                                       67889999999987744.389999****************************.8888888888888888888776 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0    0.0011       0.5      25     105 ..     140     212 ..     133     273 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0011
                                       EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCH.HHHHHEBSSSSSTTTSS-BEHHHHHTTTSEEEEE CS
                   Sigma54_activat  25 vlitGesGtGKellaraiheaskrkekpfvavncaaipeell.eseLFGhekGaFtGAekekkGlfekadgGtlfLD 100
                                       +l+ G  G+GK++la a+ ++ +   + f+ v+ a+i ++ l e+e    ++  F  A+++     e+ +  ++f+D
  gi|385805432|ref|YP_005841830.1| 140 ILLFGPPGCGKTMLAAAVANEVN---GYFLYVDAASIMSKWLgEAE--KNVSKIFKYARQK----SEEGSPAIIFID 207
                                       89**************9987655...88999999988655441333..2223344444443....355566666666 PP

                                       TGGGS CS
                   Sigma54_activat 101 eigel 105
                                       ei  l
  gi|385805432|ref|YP_005841830.1| 208 EIDAL 212
                                       66655 PP

>> FliS  Flagellar protein FliS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1     0.003       1.3      22      57 ..       7      42 ..       4      46 .. 0.85
   2 ?    1.6   0.1      0.72   3.1e+02      21      55 ..      62      96 ..      55     118 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.003
                                      HHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHH CS
                              FliS 22 ydgalkflkrakeaieekdiekkgeaiskaqdIise 57
                                       + a +  + a +a +++d+e++ ++  ka++I+++
  gi|385805432|ref|YP_005841830.1|  7 QEMATRYARAAVAADKDGDYETAINNYRKAIEILTK 42
                                      5667788888888889*****************986 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.72
                                      HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHH CS
                              FliS 21 LydgalkflkrakeaieekdiekkgeaiskaqdIi 55
                                       y++ +++l+   eaie++   k +e+ s   dI+
  gi|385805432|ref|YP_005841830.1| 62 SYEKRIQQLQSNTEAIESNTASKSNEKDSFINDIV 96
                                      69999***********9999999888877666666 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0         2   8.9e+02     212     242 ..      58      88 ..      33      96 .. 0.68
   2 ?    9.5   0.0    0.0012      0.52      23      43 ..     140     160 ..     137     178 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2
                                       CSCCHHHHHHHHHHCTGCCTS--SSSSSSSH CS
                            NB-ARC 212 ktveewkkvlekleskllevekstskslesv 242
                                       +++++++k +++l+s+   +e++t ++ ++ 
  gi|385805432|ref|YP_005841830.1|  58 EMIKSYEKRIQQLQSNTEAIESNTASKSNEK 88 
                                       5666777777777766666777766666554 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0012
                                       EEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC  23 valvGmgGvGKttlakqilnk 43 
                                       + l G +G+GKt la+ + n+
  gi|385805432|ref|YP_005841830.1| 140 ILLFGPPGCGKTMLAAAVANE 160
                                       5689**************998 PP

>> Vta1_C  Vta1 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.2    0.0024         1       7      38 .]      10      41 ..       7      41 .. 0.79
   2 ?   -0.6   0.1       2.6   1.1e+03       6      14 ..     184     192 ..     180     193 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0024
                            Vta1_C  7 AqKhaKfAiSALqYeDvetAiknLqeALklLt 38
                                      A+++a+ A+ A +  D+etAi n ++A+++Lt
  gi|385805432|ref|YP_005841830.1| 10 ATRYARAAVAADKDGDYETAINNYRKAIEILT 41
                                      666666666666667****************8 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.6
                            Vta1_C   6 eAqKhaKfA 14 
                                       ++ K++K+A
  gi|385805432|ref|YP_005841830.1| 184 NVSKIFKYA 192
                                       789*****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1224  (0.0682693); expected 358.6 (0.02)
Passed bias filter:                      869  (0.048469); expected 358.6 (0.02)
Passed Vit filter:                       137  (0.00764125); expected 17.9 (0.001)
Passed Fwd filter:                        41  (0.0022868); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              41  [number of targets reported over threshold]
# CPU time: 0.79u 0.39s 00:00:01.18 Elapsed: 00:00:00.55
# Mc/sec: 2041.02
//
Query:       gi|385805433|ref|YP_005841831.1|  [L=317]
Description: cell division protein CdvB [Fervidicoccus fontis Kam940]
Scores for complete 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   26.2   0.3    0.00023   21.0   0.0    2.6  2  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00067   19.3   0.0     0.0021   17.7   0.0    1.8  1  GntR            Bacterial regulatory proteins, gntR family
     0.0037   17.9   1.9     0.0037   17.9   1.9    1.9  2  RPA_C           Replication protein A C terminal
  ------ inclusion threshold ------
       0.02   14.9   1.0       0.02   14.9   1.0    3.0  4  z-alpha         Adenosine deaminase z-alpha domain
      0.044   13.6   0.0       0.11   12.3   0.0    1.6  1  LexA_DNA_bind   LexA DNA binding domain
       0.38   10.9   5.4       0.38   10.9   3.8    1.7  2  Membr_traf_MHD  Munc13 (mammalian uncoordinated) homology dom
       0.52   10.5   7.8       0.76   10.0   5.1    2.2  2  I_LWEQ          I/LWEQ 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 ?    2.4   0.0     0.057   1.5e+02       5      28 ..      77     100 ..      74     105 .. 0.87
   2 !   21.0   0.0   8.8e-08   0.00023      21      56 ..     279     314 ..     277     317 .] 0.91

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.057
                                       HHHHHCCCHCHHHHHHCCCHHCHH CS
                              TrmB   5 GLseyEakvYlaLlklgpatadei 28 
                                       +++e E ++Y  L k    +++e+
  gi|385805433|ref|YP_005841831.1|  77 NIKEDEKRTYHNLAKMYAEEVYEL 100
                                       699***********9998888887 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 8.8e-08
                                       CCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB  21 gpatadeiaeelgvprskvYevLrsLedkGlVerek 56 
                                       g+++++ei  + g+++ k+Ye+L +L++kG +e+++
  gi|385805433|ref|YP_005841831.1| 279 GKLNIQEITTNYGIDKEKIYEALYNLKKKGKIEIKD 314
                                       7899****************************9874 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   8.2e-07    0.0021       9      58 ..     266     314 ..     263     315 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 8.2e-07
                                       HHHHHHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                              GntR   9 LredIlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglverrq 58 
                                       +++ Il+   + G kL   +e+ + +g+++  + eAL +L+ +g +e+++
  gi|385805433|ref|YP_005841831.1| 266 VENIILNEIKKTGGKL-NIQEITTNYGIDKEKIYEALYNLKKKGKIEIKD 314
                                       455677777789****.******************************986 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 ?   -2.5   0.0       3.3   8.5e+03      27      40 ..     172     185 ..     157     199 .. 0.55
   2 !   17.9   1.9   1.5e-06    0.0037      18      97 ..     226     310 ..     212     310 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 3.3
                                       XXXXXXXXXXXXXX CS
                             RPA_C  27 samgtdgalsgnqa 40 
                                       s+++++g++++nq 
  gi|385805433|ref|YP_005841831.1| 172 STSNSMGGFNTNQT 185
                                       33444444444443 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 1.5e-06
                                       ...XXXXXXXXXXXX....XXXXXXXXXXXX.XSXHHHHHHHHHHHH.SXSTTT.EEHHHHHHHSTSXHHHHHHHHH CS
                             RPA_C  18 aavavsaggsamgtd....galsgnqaklankgltalaqqvlnlikqspeseeG.vhvdeiaqklrlsvndvkqavd 89 
                                       + + ++ + ++++++    ++ ++ q + ++++ + + ++v n+i ++++++ G ++++ei  + +++++++ +a+ 
  gi|385805433|ref|YP_005841831.1| 226 NLSTQQSTQREINQQksivNKTEKIQLEAQTSSSSYNIEIVENIILNEIKKTGGkLNIQEITTNYGIDKEKIYEALY 302
                                       3333344444444442223444444444444778999999999999999999999********************** PP

                                       HHHHTTSE CS
                             RPA_C  90 eLsneGii 97 
                                       +L ++G i
  gi|385805433|ref|YP_005841831.1| 303 NLKKKGKI 310
                                       ******88 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 ?   -2.5   0.0       2.1   5.4e+03       3      17 ..      60      74 ..      59      84 .. 0.81
   2 ?   -3.8   0.1       5.5   1.4e+04      37      45 ..     161     169 ..     159     170 .. 0.83
   3 ?    0.9   0.1      0.18   4.7e+02      25      51 ..     225     250 ..     207     256 .. 0.67
   4 ?   14.9   1.0   7.8e-06      0.02       6      54 ..     267     313 ..     264     316 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.1
                                      HHHHHHHHHHHHHC- CS
                           z-alpha  3 qeqaekilelLeelg 17
                                      qe  ++i+e L++ +
  gi|385805433|ref|YP_005841831.1| 60 QELTDRIVENLKKYD 74
                                      677889999999987 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 5.5
                                       HHHHHHHHH CS
                           z-alpha  37 eiNrvLydl 45 
                                       eiNr   d+
  gi|385805433|ref|YP_005841831.1| 161 EINRNITDM 169
                                       899998887 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.18
                                       HHHHHHHCC-HHHHHHHHHHHHHTTSE CS
                           z-alpha  25 lalergLstpkreiNrvLydlerkgkv 51 
                                        +l+ + st  reiN++    ++  k+
  gi|385805433|ref|YP_005841831.1| 225 TNLSTQQST-QREINQQKSIVNKTEKI 250
                                       456667776.89999875555555555 PP

  == domain 4  score: 14.9 bits;  conditional E-value: 7.8e-06
                                       HHHHHHHHHHC-TTCECCHHHHHHHHCC-HHHHHHHHHHHHHTTSEEEE CS
                           z-alpha   6 aekilelLeelgekkaatalalergLstpkreiNrvLydlerkgkvyre 54 
                                       +++il+ +++ g k   +++  + g+   k  i  +Ly+l++kgk+  +
  gi|385805433|ref|YP_005841831.1| 267 ENIILNEIKKTGGKLNIQEITTNYGID--KEKIYEALYNLKKKGKIEIK 313
                                       789************************..788*************9765 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 ?   12.3   0.0   4.4e-05      0.11      13      61 ..     268     315 ..     264     316 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.4e-05
                                       HHHHHHHHHHSS---HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE-GGG CS
                     LexA_DNA_bind  13 dlikasieetgypPsireiaralglkSpsaveehLkaLerKGyierdpg 61 
                                       ++i ++i++tg    i ei  + g+   + + e L  L++KG ie++++
  gi|385805433|ref|YP_005841831.1| 268 NIILNEIKKTGGKLNIQEITTNYGID-KEKIYEALYNLKKKGKIEIKDN 315
                                       568889999999999***********.99*****************986 PP

>> Membr_traf_MHD  Munc13 (mammalian uncoordinated) homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0         1   2.6e+03      92     111 ..     103     127 ..      54     171 .. 0.61
   2 ?   10.9   3.8   0.00015      0.38      24     105 ..     190     270 ..     179     277 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1
                    Membr_traf_MHD  92 sL.....tpkevevleaaLdtlkdf 111
                                        L     t+   e++ + L+t+ d+
  gi|385805433|ref|YP_005841831.1| 103 FLkailfTKISFERVIQRLQTVRDY 127
                                       2233334455555555555555444 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00015
                    Membr_traf_MHD  24 tvLkrvlkelWkvvlnalekllLPplsdakskkksss.lwenanaakkleslsklllsmvreevsgfeksLtpkeve 99 
                                       +  +++++e+Wk+  +++ek +LP+ ++  +++++ + l ++++++ ++++ +++++++ + +  ++++s +++++e
  gi|385805433|ref|YP_005841831.1| 190 EDVEKIIQEAWKLADSNVEK-MLPEPKKLIQQTTQITnLSTQQSTQREINQQKSIVNKTEKIQ-LEAQTSSSSYNIE 264
                                       556899**************.999988877666444414445555666666666666555555.6777777999999 PP

                    Membr_traf_MHD 100 vleaaL 105
                                       ++e ++
  gi|385805433|ref|YP_005841831.1| 265 IVENII 270
                                       998754 PP

>> I_LWEQ  I/LWEQ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.21   5.3e+02      63     102 ..      40      80 ..      33     126 .. 0.72
   2 ?   10.0   5.1    0.0003      0.76      80     138 ..     191     251 ..     181     259 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.21
                            I_LWEQ  63 KadknskslkrLe.aaskaVkkatkelvkavkeakekqeee 102
                                       + ++++++ ++Le ++ k +++ t+++v++ k+ ++ + +e
  gi|385805433|ref|YP_005841831.1|  40 RLKDEGEKFDELEyRTKKRIQELTDRIVENLKKYDSPNIKE 80 
                                       55666677777763466789999999999999887654443 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0003
                            I_LWEQ  80 aVkkatkelvkavkeakekqeeees..eeeeldisklslvqakrqemeaqvkilklekeLe 138
                                       +V+k ++e  k + +  ek  +e +   ++++ i++ls++q++++e+++q++i+++ ++++
  gi|385805433|ref|YP_005841831.1| 191 DVEKIIQEAWKLADSNVEKMLPEPKklIQQTTQITNLSTQQSTQREINQQKSIVNKTEKIQ 251
                                       455555555555555555555544256779999*********************9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2622  (0.146244); expected 358.6 (0.02)
Passed bias filter:                      591  (0.0329634); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.71u 0.37s 00:00:01.08 Elapsed: 00:00:00.56
# Mc/sec: 1697.22
//
Query:       gi|385805434|ref|YP_005841832.1|  [L=250]
Description: cell division protein CdvA [Fervidicoccus fontis Kam940]
Scores for complete 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  124.9  12.0    2.4e-36  124.3  12.0    1.3  1  CdvA           CdvA-like coiled-coil domain
    0.00016   21.7   5.5    0.00026   21.0   0.4    2.4  2  DUF1664        Protein of unknown function (DUF1664)
     0.0019   18.1   3.5     0.0019   18.1   3.5    2.2  2  Prefoldin      Prefoldin subunit
     0.0023   17.6   2.6     0.0038   16.9   0.6    2.4  2  SHOCT          Short C-terminal domain
     0.0025   17.3   2.6     0.0025   17.3   2.6    1.8  2  DUF4618        Domain of unknown function (DUF4618)
     0.0037   17.5   3.4     0.0037   17.5   3.4    3.0  4  DUF5082        Domain of unknown function (DUF5082)
     0.0051   16.8   2.9     0.0051   16.8   2.9    2.5  3  Prefoldin_2    Prefoldin subunit
     0.0068   16.1   5.2     0.0089   15.7   5.2    1.1  1  DUF4559        Domain of unknown function (DUF4559)
     0.0073   15.7   3.4     0.0088   15.4   3.4    1.2  1  CorA           CorA-like Mg2+ transporter protein
  ------ inclusion threshold ------
      0.013   15.2   1.0      0.083   12.7   0.2    2.6  2  B2             RNA binding protein B2
      0.042   14.2   0.5      0.057   13.7   0.5    1.3  1  Peptidase_M91  Effector protein
      0.063   13.3   0.9       0.12   12.4   0.9    1.5  1  DUF1451        Zinc-ribbon containing domain
      0.073   13.5   0.4      0.073   13.5   0.4    1.8  2  DUF4094        Domain of unknown function (DUF4094)
       0.13   12.3   2.4        5.4    7.1   0.1    2.5  2  GvpG           Gas vesicle protein G
       0.18   12.2   1.1       0.38   11.2   0.5    1.8  2  DUF2746        Protein of unknown function (DUF2746)
       0.29   11.7   4.1       0.35   11.4   0.6    2.2  2  MerR-DNA-bind  MerR, DNA binding
       0.31   11.2   6.4        0.4   10.9   1.3    2.4  2  Fib_alpha      Fibrinogen alpha/beta chain family
       0.58   10.2   5.5       0.17   11.9   1.7    1.9  2  FlxA           FlxA-like protein
       0.66    7.8   3.5       0.83    7.5   3.5    1.1  1  V_ATPase_I     V-type ATPase 116kDa subunit family
        1.1    9.9   4.6        5.7    7.5   4.6    2.3  1  YtxH           YtxH-like protein
        2.1    8.7  12.3       0.82   10.0   3.7    2.9  3  BLOC1_2        Biogenesis of lysosome-related organelles comp
        2.2    7.8   5.8       0.57    9.7   1.2    2.2  3  Fzo_mitofusin  fzo-like conserved region
        2.8    7.8   7.7        1.4    8.8   3.5    2.3  2  Mt_ATP-synt_D  ATP synthase D chain, mitochondrial (ATP5H)


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 !  124.3  12.0   3.1e-39   2.4e-36       1     119 [.      90     208 ..      90     212 .. 0.98

  Alignments for each domain:
  == domain 1  score: 124.3 bits;  conditional E-value: 3.1e-39
                              CdvA   1 krkkALeeLvsegdipkstyeeikekleealkklkekakelkeklkkrlkeledqikslekalanlkisyasGEidE 77 
                                       +r kAL+eL+++g+i ++ yee+k ++++ l++lk++a+e k+++kkr++eledqi ++eka+++lk+sy++GEi+E
  gi|385805434|ref|YP_005841832.1|  90 RRAKALDELYAKGEITRQSYEEFKANVSKDLDTLKKDANEAKDMIKKRINELEDQIVQIEKAITALKMSYIAGEISE 166
                                       8**************************************************************************** PP

                              CdvA  78 eaYksaieairellesaleekeeikklleklskleleeeeve 119
                                       + Yk a +++r +++++leek+++kk+++ + kle+++ +ve
  gi|385805434|ref|YP_005841832.1| 167 RGYKPAADILRLNKDRNLEEKNDAKKIMDLIVKLETSSLDVE 208
                                       ***********************************9988776 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.4   3.3e-07   0.00026      34      85 ..     104     155 ..      99     166 .. 0.91
   2 ?    2.5   0.7      0.19   1.4e+02      74     121 ..     183     225 ..     174     231 .. 0.49

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3.3e-07
                           DUF1664  34 vTkrslsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskei 85 
                                       +T++s +++ ++vsk+l++++++ +++k+ +++ri+++++++ + +++++++
  gi|385805434|ref|YP_005841832.1| 104 ITRQSYEEFKANVSKDLDTLKKDANEAKDMIKKRINELEDQIVQIEKAITAL 155
                                       6***************************************998887777665 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.19
                           DUF1664  74 kldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                       +l+e ++++k     ++++  +l++ + dvesv + v+++  ++ ++e
  gi|385805434|ref|YP_005841832.1| 183 NLEEKNDAKK-----IMDLIVKLETSSLDVESVVKEVQNVTPQVPQVE 225
                                       4454444444.....444444444444444444444444444444333 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   3.5   2.4e-06    0.0019      71     104 ..     123     156 ..      78     161 .. 0.87
   2 ?   -1.5   0.1       2.9   2.2e+03      14      31 ..     199     216 ..     182     235 .. 0.51

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.4e-06
                                       EEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  71 veksleeAiellkkkleelekqlekleeeleklk 104
                                       ++k+++eA++ +kk+++ele+q+ ++e++++ lk
  gi|385805434|ref|YP_005841832.1| 123 LKKDANEAKDMIKKRINELEDQIVQIEKAITALK 156
                                       689***************************9998 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.9
                                       HHHHHHHHHHHHHHHHHH CS
                         Prefoldin  14 qlkeaieelektletlkt 31 
                                       +l+++  ++e++ + +++
  gi|385805434|ref|YP_005841832.1| 199 KLETSSLDVESVVKEVQN 216
                                       333333333333333333 PP

>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.6   4.8e-06    0.0038       5      22 ..      94     111 ..      93     114 .. 0.91
   2 ?   -1.5   0.1         3   2.3e+03      12      17 ..     161     166 ..     159     166 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.8e-06
                             SHOCT   5 kLkeLyarGeIteEEFea 22 
                                        L+eLya+GeIt+  +e+
  gi|385805434|ref|YP_005841832.1|  94 ALDELYAKGEITRQSYEE 111
                                       69***********99996 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3
                             SHOCT  12 rGeIte 17 
                                       +GeI+e
  gi|385805434|ref|YP_005841832.1| 161 AGEISE 166
                                       7****8 PP

>> DUF4618  Domain of unknown function (DUF4618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   2.6   3.2e-06    0.0025      37     101 ..      92     156 ..      79     159 .. 0.89
   2 ?   -0.7   0.1      0.96   7.4e+02      60     105 ..     188     215 ..     164     234 .. 0.53

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.2e-06
                           DUF4618  37 akkvrklLqqyeklktvisileksskkqleqakaeLqeweekeekklekLeqqleqlnakvqklq 101
                                       ak   +l  + e+ ++  + ++ + +k+l+++k++ +e +++++k++++Le+q+ q+++ ++ l+
  gi|385805434|ref|YP_005841832.1|  92 AKALDELYAKGEITRQSYEEFKANVSKDLDTLKKDANEAKDMIKKRINELEDQIVQIEKAITALK 156
                                       66667788899999*********************************************998765 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.96
                           DUF4618  60 sskkqleqakaeLqeweekeekklekLeqqleqlnakvqklqeeln 105
                                       + +k++ ++  +L++    +e+ +                  +e++
  gi|385805434|ref|YP_005841832.1| 188 NDAKKIMDLIVKLETSSLDVESVV------------------KEVQ 215
                                       333444444444444433333222..................2222 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       2.4   1.9e+03      74      98 ..      18      42 ..       9      46 .. 0.68
   2 ?    0.6   0.1      0.81   6.3e+02      26      38 ..      82      94 ..      77     100 .. 0.82
   3 !   17.5   3.4   4.7e-06    0.0037      61     117 ..     101     158 ..      91     160 .. 0.93
   4 ?   -2.0   0.1       5.3   4.1e+03      73      81 ..     208     216 ..     179     232 .. 0.55

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2.4
                           DUF5082 74 nlessyqtyvdkldelidaieeEIe 98
                                      ++++ yq++v  l ++ ++++  ++
  gi|385805434|ref|YP_005841832.1| 18 KVKDPYQRVVGSLASIYSNVDGNVN 42
                                      6777788888777777777765554 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.81
                           DUF5082 26 IerLkeaktklsd 38
                                      IerL++a+++ ++
  gi|385805434|ref|YP_005841832.1| 82 IERLERARRRAKA 94
                                      9*******98766 PP

  == domain 3  score: 17.5 bits;  conditional E-value: 4.7e-06
                           DUF5082  61 kGk.eennydgirsnlessyqtyvdkldelidaieeEIerLenqiseaqgvldtlqsq 117
                                       kG+ ++++y+++ +n+ ++ +t +++  e++d i++ I++Le qi + ++ +  l+++
  gi|385805434|ref|YP_005841832.1| 101 KGEiTRQSYEEFKANVSKDLDTLKKDANEAKDMIKKRINELEDQIVQIEKAITALKMS 158
                                       6888999*********************************************999875 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 5.3
                           DUF5082  73 snlessyqt 81 
                                       +++ +++q+
  gi|385805434|ref|YP_005841832.1| 208 ESVVKEVQN 216
                                       233333333 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       1.9   1.5e+03      74     100 ..      91     117 ..      80     120 .. 0.67
   2 !   16.8   2.9   6.5e-06    0.0051      56      97 ..     116     157 ..     113     161 .. 0.94
   3 ?    0.0   0.9         1   8.2e+02      12      43 ..     188     219 ..     180     226 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.9
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  74 lekeiktlekqleklekeleelkeelq 100
                                         k +++l  + e  ++ +ee+k+++ 
  gi|385805434|ref|YP_005841832.1|  91 RAKALDELYAKGEITRQSYEEFKANVS 117
                                       456777788888888888888888765 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 6.5e-06
                                       EEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  56 vkqdkeevkeeLeerketlekeiktlekqleklekeleelke 97 
                                       v++d++++k++ +e k+ ++k+i++le+q+ ++ek ++ lk 
  gi|385805434|ref|YP_005841832.1| 116 VSKDLDTLKKDANEAKDMIKKRINELEDQIVQIEKAITALKM 157
                                       789**********************************99986 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 1
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-T CS
                       Prefoldin_2  12 qqlqqlaqqikqletqlkelelvleelellde 43 
                                       ++ ++++  i +let   ++e+v +e++++ +
  gi|385805434|ref|YP_005841832.1| 188 NDAKKIMDLIVKLETSSLDVESVVKEVQNVTP 219
                                       56677777888888888888888888877765 PP

>> DUF4559  Domain of unknown function (DUF4559)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   5.2   1.1e-05    0.0089     195     310 ..     103     216 ..      74     217 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.1e-05
                           DUF4559 195 ellkilkqefeislkeddevrvltdvllslqklkeleeellkedatkldelvlraeeqkiskeellkelqvlkefln 271
                                       e+++   +ef+ ++++  ++++l +  ++ +++ + + ++l+++++++++ + + + + i  e   +  +  +++l+
  gi|385805434|ref|YP_005841832.1| 103 EITRQSYEEFKANVSK--DLDTLKKDANEAKDMIKKRINELEDQIVQIEKAITALKMSYIAGEISERGYKPAADILR 177
                                       6667778888888888..666666667899999999************************99999999********* PP

                           DUF4559 272 knkdLkenlkedvkklqeieekldkldedvtelkkkvdq 310
                                        nkd +   k+d+kk+ ++  kl+    dv+++ k+v++
  gi|385805434|ref|YP_005841832.1| 178 LNKDRNLEEKNDAKKIMDLIVKLETSSLDVESVVKEVQN 216
                                       ****888899***********************999986 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   3.4   1.1e-05    0.0088      88     218 ..      82     217 ..      32     221 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.1e-05
                              CorA  88 lealdevikrlkdeggkpkspgellyrlldeivdrlfellekleeeldeledeledstkkeilrelaqlrrrlvkl. 163
                                       +e+l+ +++r+k + ++   +ge++ +  +e+  ++ + l++l+++ +e+ d++ +++ +e+ ++++q+++ ++ l 
  gi|385805434|ref|YP_005841832.1|  82 IERLERARRRAK-ALDELYAKGEITRQSYEEFKANVSKDLDTLKKDANEAKDMI-KKRINELEDQIVQIEKAITALk 156
                                       456688888888.7799999**********************************.89999999*******9999999 PP

                              CorA 164 .........rralapnrevlkrllakaddkllddedkeylrdlldelerllemlealrerlesl 218
                                                +r  +p  ++l rl +  d +l+++ d++ + dl+ +le ++ ++e++ + ++++
  gi|385805434|ref|YP_005841832.1| 157 msyiageisERGYKPAADIL-RLNK--DRNLEEKNDAKKIMDLIVKLETSSLDVESVVKEVQNV 217
                                       9999****************.7777..6666666666679999999999988888888777765 PP

>> B2  RNA binding protein B2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   0.00011     0.083      25      60 ..     107     142 ..      96     148 .. 0.88
   2 ?    1.2   0.1      0.41   3.2e+02       8      28 ..     138     160 ..     135     215 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                                B2  25 msyqeaPnnvrrdldnlqaclnkakltvsrmvtsll 60 
                                        sy e   nv +dld l+   n ak  +++ +  l 
  gi|385805434|ref|YP_005841832.1| 107 QSYEEFKANVSKDLDTLKKDANEAKDMIKKRINELE 142
                                       69***********************99998877665 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.41
                                B2   8 iqelPdriqkave..vvlamsyq 28 
                                       i+el d+i +  +  ++l msy 
  gi|385805434|ref|YP_005841832.1| 138 INELEDQIVQIEKaiTALKMSYI 160
                                       67777766433221135677774 PP

>> Peptidase_M91  Effector protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.5   7.3e-05     0.057       3      85 ..     102     185 ..     100     243 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.3e-05
                     Peptidase_M91   3 ssikvegsdeFkdrveadLdmlsss.ptGqqlLeelkssksegerkltikel.............vdedngtakyee 65 
                                       ++i+++  +eFk+ v +dLd+l++   ++++++++  ++ ++  + + i+++                         
  gi|385805434|ref|YP_005841832.1| 102 GEITRQSYEEFKANVSKDLDTLKKDaNEAKDMIKKRINELED--QIVQIEKAitalkmsyiageiS----------- 165
                                       67899999**************986167999*9887777776..4566766555333333333220........... PP

                     Peptidase_M91  66 kekgegtdaeinynpafsse 85 
                                       +++++    ++ +n++ ++e
  gi|385805434|ref|YP_005841832.1| 166 ERGYKPAADILRLNKDRNLE 185
                                       44444444444444444444 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.9   0.00015      0.12      20      76 ..      93     145 ..      77     168 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00015
                           DUF1451  20 kakeklseaeeltkeelelvaeylkrDleeaarsleeskeeleewlsldlelieesl 76 
                                       ka ++l +++e+t++  e++++ +++Dl  ++++ +e k+      +  ++ +e+++
  gi|385805434|ref|YP_005841832.1|  93 KALDELYAKGEITRQSYEEFKANVSKDLDTLKKDANEAKDM----IKKRINELEDQI 145
                                       56678999*****************************9994....444444444444 PP

>> DUF4094  Domain of unknown function (DUF4094)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.4   9.4e-05     0.073      29      80 ..     103     157 ..      87     161 .. 0.82
   2 ?   -2.5   0.1       9.3   7.2e+03      51      60 ..     187     197 ..     174     218 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.4e-05
                           DUF4094  29 diirqskeelkl.vsedcds.kdaesrskdilg.evskthkaiqtLdktissLem 80 
                                       +i+rqs ee k  vs+d d+ k+  ++ kd+++ ++++ ++ i +++k+i +L m
  gi|385805434|ref|YP_005841832.1| 103 EITRQSYEEFKAnVSKDLDTlKKDANEAKDMIKkRINELEDQIVQIEKAITALKM 157
                                       45555535555559******988889999****9*******************99 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 9.3
                           DUF4094  51 esrskdilg.e 60 
                                       +++ k+i++  
  gi|385805434|ref|YP_005841832.1| 187 KNDAKKIMDlI 197
                                       34455555522 PP

>> GvpG  Gas vesicle protein G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.3      0.03        23      36      74 ..      91     129 ..      82     133 .. 0.79
   2 ?    7.1   0.1     0.007       5.4      19      56 ..     134     171 ..     130     192 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.03
                              GvpG  36 eLaaLqqeLdaGeIdeeeFdrrEeelLdrLealerleae 74 
                                       +  aL+    +GeI+ + +++   ++   L++l++ ++e
  gi|385805434|ref|YP_005841832.1|  91 RAKALDELYAKGEITRQSYEEFKANVSKDLDTLKKDANE 129
                                       55667777889**********999999999999975544 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.007
                              GvpG  19 vqeraeeqlddqenlrkeLaaLqqeLdaGeIdeeeFdr 56 
                                       +++r +e  d+  +++k ++aL+ +  aGeI+e  +  
  gi|385805434|ref|YP_005841832.1| 134 IKKRINELEDQIVQIEKAITALKMSYIAGEISERGYKP 171
                                       67777776677789*******************99975 PP

>> DUF2746  Protein of unknown function (DUF2746)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.5   0.00049      0.38      40      84 ..     101     145 ..      86     156 .. 0.84
   2 ?   -1.9   0.0       5.7   4.4e+03      58      66 ..     179     187 ..     148     221 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00049
                           DUF2746  40 igeikeqvcnthdtnlrddldsvkadisdlkeivlqgfhqvnesi 84 
                                        gei  q  +   +n+  dld++k d  + k+++ + + ++++ i
  gi|385805434|ref|YP_005841832.1| 101 KGEITRQSYEEFKANVSKDLDTLKKDANEAKDMIKKRINELEDQI 145
                                       69*******************************999888877765 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.7
                           DUF2746  58 dldsvkadi 66 
                                       + d    + 
  gi|385805434|ref|YP_005841832.1| 179 NKDRNLEEK 187
                                       333322222 PP

>> MerR-DNA-bind  MerR, DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.2      0.78   6.1e+02      36      53 ..      83     100 ..      70     108 .. 0.74
   2 ?   11.4   0.6   0.00045      0.35      31      62 ..     124     155 ..     117     157 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.78
                                       HHHHHHHHHHHHHHHHHH CS
                     MerR-DNA-bind  36 dvrallarklaeleeria 53 
                                       ++++ ++r+++ l+e  a
  gi|385805434|ref|YP_005841832.1|  83 ERLERARRRAKALDELYA 100
                                       566788888888888655 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00045
                                       TTBHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     MerR-DNA-bind  31 appcqdvrallarklaeleeriaeLqalraeL 62 
                                       ++++ +++++++++++ele +i ++++  + L
  gi|385805434|ref|YP_005841832.1| 124 KKDANEAKDMIKKRINELEDQIVQIEKAITAL 155
                                       56788999******************998887 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.3   0.00051       0.4      61     110 ..     108     158 ..      75     165 .. 0.59
   2 ?    2.8   0.3      0.16   1.3e+02      34      69 ..     187     222 ..     174     242 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00051
                                       HHHHHHHHHHHHHHH.HHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHH CS
                         Fib_alpha  61 ikdslrekqkskkdn.dnvikksskeleeeilrlketidaqesnirvLqnv 110
                                        ++  +++ +++ d+ ++  ++ +++++++i++l+++i++ e+ i +L+  
  gi|385805434|ref|YP_005841832.1| 108 SYEEFKANVSKDLDTlKKDANEAKDMIKKRINELEDQIVQIEKAITALKMS 158
                                       222222222222222355667777777777777777777777777777755 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.16
                                       CHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  34 kkdlekleneleeisnstkeaeelvkeikdslrekq 69 
                                       k+d +k+ + + +++ s+ ++e++vke+++++ +  
  gi|385805434|ref|YP_005841832.1| 187 KNDAKKIMDLIVKLETSSLDVESVVKEVQNVTPQVP 222
                                       667788888888888888888888888888765544 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.7   0.00022      0.17      28      70 ..     115     150 ..     105     157 .. 0.59
   2 ?   -2.1   0.0       4.8   3.8e+03      18      36 ..     206     224 ..     199     235 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00022
                              FlxA  28 nlqkqLkelsesdeltkeekkkqqqliqaQIqqlqaQIaqlqq 70 
                                       n++k L+ l+++        ++ +++i++ I+ l+ QI q+++
  gi|385805434|ref|YP_005841832.1| 115 NVSKDLDTLKKD-------ANEAKDMIKKRINELEDQIVQIEK 150
                                       344444444444.......555566666666666666666553 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.8
                              FlxA  18 qiasLqkQiknlqkqLkel 36 
                                       +++s  k+++n++ q+ ++
  gi|385805434|ref|YP_005841832.1| 206 DVESVVKEVQNVTPQVPQV 224
                                       5666666666666666554 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   3.5    0.0011      0.83      27     120 ..      80     180 ..      73     230 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0011
                        V_ATPase_I  27 kevrrcdemerklrfleeeieklekavikeeea.......eesleapeekeldeleeelekleeelkelnenleklk 96 
                                       k + r++   r+ + l+e  +k e + +++ee         ++l+++ ++  d +++++++le+++ ++++  ++lk
  gi|385805434|ref|YP_005841832.1|  80 KVIERLERARRRAKALDELYAKGEITRQSYEEFkanvskdLDTLKKDANEAKDMIKKRINELEDQIVQIEKAITALK 156
                                       56888999999999999988885444444444477887777788888888888899999999999999999999999 PP

                        V_ATPase_I  97 kelnelvelkavlekakefleeee 120
                                        ++   +  +  ++ a+++l+ ++
  gi|385805434|ref|YP_005841832.1| 157 MSYIAGEISERGYKPAADILRLNK 180
                                       998877777777777777776543 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   4.6    0.0073       5.7      24      73 ..     110     144 ..      78     218 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0073
                              YtxH  24 ketRkdlkekaddlkekakelleeakekakekaedlkekvkekadelkek 73 
                                       +e+++ +++ +d+l               k+ a+++k+ +k++++el ++
  gi|385805434|ref|YP_005841832.1| 110 EEFKANVSKDLDTL---------------KKDANEAKDMIKKRINELEDQ 144
                                       33333444444444...............555555555555555555554 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       7.3   5.7e+03      80      89 ..       7      16 ..       6      17 .. 0.83
   2 ?   10.0   3.7     0.001      0.82      38      84 ..     108     155 ..      84     159 .. 0.85
   3 ?    3.6   0.3      0.11        85      29      72 ..     183     226 ..     172     240 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 7.3
                           BLOC1_2 80 avseLDeysk 89
                                      +v++LD+y+ 
  gi|385805434|ref|YP_005841832.1|  7 TVDMLDKYVG 16
                                      7999**9986 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.001
                           BLOC1_2  38 klkdvaaslekkleklnekyeelqpyl.qqidqiekqvteLeeavseL 84 
                                       ++++  a+++k+l+ l++  +e + ++ ++i+++e+q+ ++e+a+ +L
  gi|385805434|ref|YP_005841832.1| 108 SYEEFKANVSKDLDTLKKDANEAKDMIkKRINELEDQIVQIEKAITAL 155
                                       5667778999999***99999888876157*************99887 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.11
                           BLOC1_2  29 Neaasekykklkdvaaslekkleklnekyeelqpylqqidqiek 72 
                                       N +  +  kk+ d + +le+++ ++++  +e+q+   q+ q+e+
  gi|385805434|ref|YP_005841832.1| 183 NLEEKNDAKKIMDLIVKLETSSLDVESVVKEVQNVTPQVPQVEQ 226
                                       55555556666677777777777777777777777777777666 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       1.1   8.5e+02     126     143 ..      80      97 ..      75     116 .. 0.66
   2 ?    9.7   1.2   0.00073      0.57      98     139 ..     115     156 ..     102     162 .. 0.86
   3 ?   -2.7   0.1       4.8   3.7e+03      82     102 ..     196     217 ..     188     234 .. 0.53

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.1
                     Fzo_mitofusin 126 keiekleevqkkakllrn 143
                                       k ie+le++ ++ak+l +
  gi|385805434|ref|YP_005841832.1|  80 KVIERLERARRRAKALDE 97 
                                       568999999999998863 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00073
                     Fzo_mitofusin  98 elsstfarlcqqvdetekeleeeikelekeiekleevqkkak 139
                                       ++s+ ++ l+++ +e+++ ++++i+ele +i ++e++++ +k
  gi|385805434|ref|YP_005841832.1| 115 NVSKDLDTLKKDANEAKDMIKKRINELEDQIVQIEKAITALK 156
                                       566778899***************************998877 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 4.8
                     Fzo_mitofusin  82 livsltsancs.hqvqqelsst 102
                                       liv+l +++++ ++v +e++++
  gi|385805434|ref|YP_005841832.1| 196 LIVKLETSSLDvESVVKEVQNV 217
                                       5555544433313344444443 PP

>> Mt_ATP-synt_D  ATP synthase D chain, mitochondrial (ATP5H)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   3.5    0.0018       1.4      82     126 ..     110     154 ..      62     160 .. 0.67
   2 ?    0.1   0.1      0.81   6.3e+02      89     125 ..     183     219 ..     171     245 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0018
                                       -TTTTHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHT-XXXX CS
                     Mt_ATP-synt_D  82 dkyteevdaeekevkkeikefkeeskkrieelekeleklksllpf 126
                                       ++++++v +  ++ kk+++e k   kkri+ele+++ ++++++  
  gi|385805434|ref|YP_005841832.1| 110 EEFKANVSKDLDTLKKDANEAKDMIKKRINELEDQIVQIEKAITA 154
                                       344567777777777777777777777777777777777776655 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.81
                                       HHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHT-XXX CS
                     Mt_ATP-synt_D  89 daeekevkkeikefkeeskkrieelekeleklksllp 125
                                       + eek+++k+i   + + +    ++e+ +++++++ p
  gi|385805434|ref|YP_005841832.1| 183 NLEEKNDAKKIMDLIVKLETSSLDVESVVKEVQNVTP 219
                                       5578888888888888888888888888888887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2020  (0.112667); expected 358.6 (0.02)
Passed bias filter:                      907  (0.0505884); expected 358.6 (0.02)
Passed Vit filter:                       156  (0.00870099); 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):              23  [number of targets reported over threshold]
# CPU time: 0.75u 0.38s 00:00:01.12 Elapsed: 00:00:00.55
# Mc/sec: 1361.48
//
Query:       gi|385805435|ref|YP_005841833.1|  [L=371]
Description: glycine cleavage system aminomethyltransferase T [Fervidicoccus fontis Kam940]
Scores for 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-67  225.0   0.0    1.3e-66  224.6   0.0    1.1  1  GCV_T         Aminomethyltransferase folate-binding domain
    4.3e-12   45.8   0.0    8.6e-12   44.8   0.0    1.5  1  GCV_T_C       Glycine cleavage T-protein C-terminal barrel do
  ------ inclusion threshold ------
      0.062   13.6   0.0       0.16   12.2   0.0    1.6  1  PHA_gran_rgn  Putative polyhydroxyalkanoic acid system protei


Domain annotation for each model (and alignments):
>> GCV_T  Aminomethyltransferase folate-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  224.6   0.0   2.2e-70   1.3e-66       2     246 ..       7     247 ..       6     259 .. 0.93

  Alignments for each domain:
  == domain 1  score: 224.6 bits;  conditional E-value: 2.2e-70
                             GCV_T   2 ydrhkalgakfvefagwemPvqYasesikaehlavreaaglfDvShmgkievsGpdaaalLqrlltndisklkpgka 78 
                                        ++h+ lga+++efagwe+P+ Y  +s++ ehl+vr+++g+fDvShmg+++++G+d+++lL++++t++i+k+k + +
  gi|385805435|ref|YP_005841833.1|   7 KSLHESLGATIGEFAGWEVPMVY--NSTISEHLNVRNEVGIFDVSHMGRLRLKGKDSLELLEKVFTKKIAKTKINFM 81 
                                       679********************..************************************************9877 PP

                             GCV_T  79 t.ytlllnedGgvidDlivarldedefllvvnaankekdlawlekaaekkdldvevedvteelallalqGPkarevl 154
                                       +  +l+lne ++vidD + ++++++e+l v+naa++ ++l++lek  e+ ++d+e+ed+te++ +la+qGPk+ ev+
  gi|385805435|ref|YP_005841833.1|  82 SgPALALNEYARVIDDEMWYKVNDEEWLGVANAATRLRVLEHLEKVKEEFNFDAEIEDLTERYVMLAVQGPKSPEVA 158
                                       779******************************************9999**************************** PP

                             GCV_T 155 skllgadlselkffsfa.evelaggkk.vlvsRtgytGedGfeiyipaeeaeelweaLleagkeegvkpaGlgArdt 229
                                       +k       +lk  +f+ +++l  + + +l+sR+g+tGedGfei+++++ ae +++  leag+    kp+G+ Ardt
  gi|385805435|ref|YP_005841833.1| 159 EKAGINGALQLKPLEFKlDIKLG-EYPiFLISRSGWTGEDGFEIWVENSIAENVYKNFLEAGA----KPIGIVARDT 230
                                       ****5557777888888677776.888799****************************98887....********** PP

                             GCV_T 230 lRlEaglrlyghdldee 246
                                       lR+E+g+ l g++  e+
  gi|385805435|ref|YP_005841833.1| 231 LRMEMGYVLGGNEYGED 247
                                       *************8776 PP

>> GCV_T_C  Glycine cleavage T-protein C-terminal barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   0.0   1.4e-15   8.6e-12      12      78 ..     300     367 ..     290     369 .. 0.91

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 1.4e-15
                           GCV_T_C  12 apllrggepilrdgevvGhvTSgaysptlgksialAyvkaelaklgtevevevr.gkrvpaevvkkpf 78 
                                       + ++r g++i+ ++ +vG+vTSg+ysp l++ ia  y+++ +a +g++++++ + gk+ +a++++ p+
  gi|385805435|ref|YP_005841833.1| 300 RFVPRSGYKIYVEDIEVGWVTSGTYSPVLERGIAQLYIDSRYAIVGESIKIKDAkGKEAEAKLSDFPL 367
                                       4567*************************************************769*******99886 PP

>> PHA_gran_rgn  Putative polyhydroxyalkanoic acid system protein (PHA_gran_rgn)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.7e-05      0.16      12      65 ..     114     181 ..     104     183 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.7e-05
                      PHA_gran_rgn  12 eeAreraeelaekleeefglelewe...gdtlkfkrs...........gvdGqlevepdkvrleakLg 65 
                                       ++ r r+ e +ek++eef+++ e e   +  + + ++           g++G l+++p +++l++kLg
  gi|385805435|ref|YP_005841833.1| 114 AATRLRVLEHLEKVKEEFNFDAEIEdltERYVMLAVQgpkspevaekaGINGALQLKPLEFKLDIKLG 181
                                       445777889999******999999977644444444455888888999*******************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.63u 0.34s 00:00:00.97 Elapsed: 00:00:00.54
# Mc/sec: 2053.45
//
Query:       gi|385805436|ref|YP_005841834.1|  [L=259]
Description: putative thiazole biosynthetic enzyme [Fervidicoccus fontis Kam940]
Scores for complete 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-71  239.5   0.5    3.2e-71  239.3   0.5    1.0  1  Thi4            Thi4 family
    4.3e-12   45.8   3.2    2.5e-05   23.6   1.2    3.1  3  FAD_binding_2   FAD binding domain
    1.5e-09   37.9   0.4    1.6e-05   24.6   0.3    2.1  2  DAO             FAD dependent oxidoreductase
    1.2e-07   31.9   0.9    2.5e-07   30.8   0.9    1.5  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    1.6e-07   30.9   0.1    2.2e-07   30.4   0.1    1.4  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    4.2e-07   29.0   1.7    4.9e-06   25.5   1.2    2.1  2  HI0933_like     HI0933-like protein
    1.2e-06   28.1   0.0    1.8e-06   27.6   0.0    1.2  1  FAD_oxidored    FAD dependent oxidoreductase
    5.9e-05   22.5   0.0    0.00012   21.4   0.0    1.5  2  FAD_binding_3   FAD binding domain
     0.0002   20.7   0.0    0.00034   20.0   0.0    1.3  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
     0.0015   19.1   0.4     0.0051   17.3   0.4    2.0  1  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
     0.0016   18.5   0.0      0.004   17.2   0.0    1.6  1  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
      0.007   15.5   0.1       0.01   15.0   0.1    1.3  1  GIDA            Glucose inhibited division protein A
  ------ inclusion threshold ------
      0.014   15.1   0.0      0.089   12.5   0.0    2.1  2  MAF_flag10      Protein of unknown function DUF115
      0.014   14.4   0.1      0.022   13.8   0.1    1.3  1  Lycopene_cycl   Lycopene cyclase protein
      0.015   15.3   0.0      0.023   14.7   0.0    1.3  1  NAD_binding_9   FAD-NAD(P)-binding
      0.025   13.4   0.3      0.041   12.7   0.3    1.4  2  Trp_halogenase  Tryptophan halogenase
      0.039   13.3   0.0       0.06   12.6   0.0    1.3  1  Amino_oxidase   Flavin containing amine oxidoreductase
      0.074   12.2   0.0       0.11   11.6   0.0    1.2  1  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)


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 !  239.3   0.5   3.2e-74   3.2e-71       1     235 []      10     239 ..      10     239 .. 0.97

  Alignments for each domain:
  == domain 1  score: 239.3 bits;  conditional E-value: 3.2e-74
                                       HHHHHHHHHHHHHHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTBSEEEEETTTHHHH CS
                              Thi4   1 sraiveryfedllkyaesDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlfsaivvrkpakelL 77 
                                       ++ i+e++++dl+++a+sDv+ivGaG+sG+taa+yla k +lkv++ler++s+GGG+++GG l ++iv++ +a +++
  gi|385805436|ref|YP_005841834.1|  10 TKLILEHSMKDLIEFADSDVIIVGAGPSGMTAAKYLADK-KLKVLVLERKLSFGGGIGGGGNLMHKIVIKSDALKII 85 
                                       57899**********************************.************************************* PP

                                       HHTT---EEES.SEEEESEHHHHHHHHHHHHHTSTTEEEEESEEEEEEEEETB.TEEEEEEEEEHHHHTC..TTTSS CS
                              Thi4  78 delgikyedeg.dyvvvkdaalftstllskvlqlanvkllnavaveDlivreg.egvaGvvinwtlvela..hdtqs 150
                                       ++++i+y++++ + ++  da +++s+l++ +++ +++k+l + +veDlivre   +v+Gvv++w++++la  h    
  gi|385805436|ref|YP_005841834.1|  86 KDFEIEYKKTEfEDLYTLDASELISKLATGAIN-SGAKILFGYSVEDLIVREKpLRVSGVVVKWSAIDLAqlH---- 157
                                       *******87654779999***************.******************88**************99667.... PP

                                       .-B-EEEEEEEEEE--GSSSTTTTHHHHHHHHCTTTS-----ECB-HHHHHHHHHHHECEEETTEEE-THHHHHHHT CS
                              Thi4 151 cvDPlvirakvvvdatGhdgeivavvvkkikleakiekvkgeksldaekaedaivkktrevvpnlyvaGmevaevdg 227
                                        vDP +   k+++datGhd+e++++++kk+ + a   +vk+e s++ae +e+++v+ + +v ++ly+aGm va ++g
  gi|385805436|ref|YP_005841834.1| 158 -VDPIFFTGKAILDATGHDAELIKILAKKNPSFA--INVKNESSAHAELGEKQVVEFSGKVCDGLYAAGMSVATLHG 231
                                       .******************************999..79*************************************** PP

                                       -EB--SB- CS
                              Thi4 228 anRmGpif 235
                                       ++RmGpif
  gi|385805436|ref|YP_005841834.1| 232 LYRMGPIF 239
                                       *******9 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   1.2   2.5e-08   2.5e-05       1      36 [.      28      63 ..      28      69 .. 0.95
   2 !   10.6   0.0   0.00021      0.21     141     201 ..     106     174 ..      95     197 .. 0.76
   3 !   10.3   0.0   0.00026      0.26     384     413 ..     208     236 ..     204     240 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 2.5e-08
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36
                                      Dvi++G+G +G++AA  +a++ lkv+v+e + +fgg
  gi|385805436|ref|YP_005841834.1| 28 DVIIVGAGPSGMTAAKYLADKKLKVLVLERKLSFGG 63
                                      9****************************9998887 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00021
                                       HHHHHHHHHHHHTCTEEEEESEEEEEEEECTT..EEEEEEEEET......TTTCEE....EEEESEEEE---- CS
                     FAD_binding_2 141 hallarlvesarkagvdfqerteadeLivedg..rvtGavvenp......esgrev....rirakavvlatgG 201
                                        +l+  l+++a + g ++++ +++++Liv+++  rv+G+vv+ +           +     ++ ka+++atg 
  gi|385805436|ref|YP_005841834.1| 106 SELISKLATGAINSGAKILFGYSVEDLIVREKplRVSGVVVKWSaidlaqL----HvdpiFFTGKAILDATGH 174
                                       67889999*********************99999*******9776655432....123335566677777765 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00026
                                       ESTTEEESSBTEEE-STCEESSSSTTS--T CS
                     FAD_binding_2 384 vldadgqpipGLYAaGevaaggvhganrlg 413
                                       v + +g++++GLYAaG    + +hg +r+g
  gi|385805436|ref|YP_005841834.1| 208 VVEFSGKVCDGLYAAGMSV-ATLHGLYRMG 236
                                       5567899**********99.9*******98 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.3   1.7e-08   1.6e-05       1      46 [.      28      74 ..      28      91 .. 0.88
   2 !   11.3   0.0   0.00019      0.19     141     213 ..     101     182 ..      95     218 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.7e-08
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEES CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhs 46
                                      dv+i+G+G  G+++A +La ++  V++le++  +g g  g+ + l h 
  gi|385805436|ref|YP_005841834.1| 28 DVIIVGAGPSGMTAAKYLADKKlkVLVLERKLSFG-GGIGGGGNLMHK 74
                                      9*****************988789*******9999.888888877775 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00019
                                       EEEEHHHHHHHHHHHHHHTT-EEEESECEEEE..EEEETCEEEEE......EECTEEEE..........EEEEEEE- CS
                               DAO 141 gqvdpakltaalaraaealGveilegtevtgl..eeedgkvwgve......rttpgend..........aadavVna 199
                                        ++d+ +l+  la  a + G++il+g  v++l  +e+  +v+gv       +                 + +a+  a
  gi|385805436|ref|YP_005841834.1| 101 YTLDASELISKLATGAINSGAKILFGYSVEDLivREKPLRVSGVVvkwsaiD------LaqlhvdpiffTGKAILDA 171
                                       578999*************************744334488899965555542......1334444566655889999 PP

                                       -GGGHHHHHTTCTT CS
                               DAO 200 aGawsdllgllkel 213
                                       +G+ + l+   k+l
  gi|385805436|ref|YP_005841834.1| 172 TGHDAELI---KIL 182
                                       99999887...655 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 !   30.8   0.9   2.6e-10   2.5e-07       1      33 [.      31      63 ..      31      70 .. 0.96

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 2.6e-10
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSG CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGG 33
                                      IvGaG sG++aA +La+++++vl+le+  ++GG
  gi|385805436|ref|YP_005841834.1| 31 IVGAGPSGMTAAKYLADKKLKVLVLERKLSFGG 63
                                      9***************************99999 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.1   2.2e-10   2.2e-07       2      58 ..      28     112 ..      27     209 .. 0.71

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 2.2e-10
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEE....TTHCHHHCSHHHHCHHHHHHHHHHHHH................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxx................. RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlve....legtclnggcllskallgvaedaeias................. 57 
                                       dv+++G+Gp G++aa++la +++kv+++e     +g + +gg l++k++ ++ + + i++                 
  gi|385805436|ref|YP_005841834.1|  28 DVIIVGAGPSGMTAAKYLADKKLKVLVLErklsFGGGIGGGGNLMHKIVIKSDALK-IIKdfeieykktefedlytl 103
                                       8***************************9888855555555555555555444333.23334444477777777777 PP

                                       ........H CS
                                       ........x RF
                       Pyr_redox_2  58 ........e 58 
                                                
  gi|385805436|ref|YP_005841834.1| 104 daseliskL 112
                                       777444442 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   1.2   4.9e-09   4.9e-06       2      39 ..      28      65 ..      27      74 .. 0.88
   2 ?    1.8   0.0     0.077        77      81     140 ..      80     137 ..      77     186 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 4.9e-09
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHH CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrKi 39
                                      dvi++G+G++G+ aA  +a+++ +Vl+le++ ++g  i
  gi|385805436|ref|YP_005841834.1| 28 DVIIVGAGPSGMTAAKYLADKKLKVLVLERKLSFGGGI 65
                                      8******************************9999755 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.077
                                       HHHHHHHHTT--EEE-STTEEEETT.-CHHHHHHHHHHHHHHT-EEE-S--EEEEECETT CS
                       HI0933_like  81 dlialveelgvelkeedsgrlFpvsdkaedivdallkelkeagvklrletevksvekeed 140
                                       d ++++++ ++e+k+ +   l++ +  a+++++ l + + ++g k+    +v+++  +e+
  gi|385805436|ref|YP_005841834.1|  80 DALKIIKDFEIEYKKTEFEDLYTLD--ASELISKLATGAINSGAKILFGYSVEDLIVREK 137
                                       67788999999***********999..99*****************99999999876554 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   1.9e-09   1.8e-06       1     144 [.      28     173 ..      28     181 .. 0.71

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 1.9e-09
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaeeqvvtgiareflerlrqrggarlkk 77 
                                       Dv++vG+gp+G++AA   a +  kvl++e++   GG   +g+  +++++     v++  a ++++  +   ++++++
  gi|385805436|ref|YP_005841834.1|  28 DVIIVGAGPSGMTAAKYLADKKLKVLVLERKLSFGGGIGGGG--NLMHKI----VIKSDALKIIKDFEI--EYKKTE 96 
                                       9***********************************987666..777755....666666666666622..332222 PP

                      FAD_oxidored  78 rskwntfe.pevakavleemlaeagvtvllntrlvevekeg.........kriesvtveske.grktirAkvfiDAT 143
                                        ++  t +  e   +++   ++  g ++l++  +++ ++++          +  ++ +++     + +++k ++DAT
  gi|385805436|ref|YP_005841834.1|  97 FEDLYTLDaSELISKLATGAINS-GAKILFGYSVEDLIVREkplrvsgvvVKWSAIDLAQLHvDPIFFTGKAILDAT 172
                                       22222344045555666666655.99999999998888865566666555557777777777669999999999999 PP

                      FAD_oxidored 144 g 144
                                       g
  gi|385805436|ref|YP_005841834.1| 173 G 173
                                       8 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   1.2e-07   0.00012       2      33 ..      27      58 ..      26      61 .. 0.93
   2 ?   -3.1   0.0       3.6   3.6e+03      84     126 ..      86     127 ..      70     133 .. 0.64

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.2e-07
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekr 33
                                       dV+IVGaGp+G+++a+ L+ +  +v+++e+ 
  gi|385805436|ref|YP_005841834.1| 27 SDVIIVGAGPSGMTAAKYLADKKLKVLVLERK 58
                                      69********************999****995 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.6
                                       CEEEEEHHCHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSE CS
                     FAD_binding_3  84 pkaradlelesspervtvypqteleriLvehaeerglqvrfkt 126
                                       ++ +++++ +++ e+ +++  +el   L+  a + g+++ f+ 
  gi|385805436|ref|YP_005841834.1|  86 KDFEIEYK-KTEFEDLYTLDASELISKLATGAINSGAKILFGY 127
                                       55566666.6777777777777777777777777777777665 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 !   20.0   0.0   3.4e-07   0.00034       1      30 [.      30      58 ..       5      64 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 3.4e-07
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkg 30
                                      iI+GaGP G++aa  l +++l ++l+lE++
  gi|385805436|ref|YP_005841834.1| 30 IIVGAGPSGMTAAKYLADKKL-KVLVLERK 58
                                      788888888888888888888.68888875 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.4   5.1e-06    0.0051       2      34 ..      29      61 ..      28      78 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.1e-06
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkl 34
                                      v++vG+G +g+ +A++la+ + kV v+er+  +
  gi|385805436|ref|YP_005841834.1| 29 VIIVGAGPSGMTAAKYLADKKLKVLVLERKLSF 61
                                      89***************************8666 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   4.1e-06     0.004       9      46 ..      23      59 ..      15      62 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.1e-06
                                      ..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSH CS
                      Shikimate_DH  9 slkekkvlliGaGemaelvakhLlakgvkkvvvaNRtl 46
                                      +++++ v+++GaG  +  +ak+L++k++k v+v+ R l
  gi|385805436|ref|YP_005841834.1| 23 EFADSDVIIVGAGPSGMTAAKYLADKKLK-VLVLERKL 59
                                      68999***********************9.99*99975 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1     1e-05      0.01       1      31 [.      28      58 ..      28      93 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1e-05
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEEES- CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithk 31
                                      dvi++G+G +G+ AA  +a + +kvl +  k
  gi|385805436|ref|YP_005841834.1| 28 DVIIVGAGPSGMTAAKYLADKKLKVLVLERK 58
                                      8************************998655 PP

>> MAF_flag10  Protein of unknown function DUF115
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     9e-05     0.089      10      44 ..      13      45 ..       3      55 .. 0.72
   2 ?   -0.4   0.0       0.8   7.9e+02     138     163 ..     141     165 ..     100     166 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9e-05
                        MAF_flag10 10 nlkpslkellnkfkgnkpaiivgaGPSLeknlell 44
                                      +l++s+k+l++ f + +++iivgaGPS     ++l
  gi|385805436|ref|YP_005841834.1| 13 ILEHSMKDLIE-FAD-SDVIIVGAGPSGMTAAKYL 45
                                      44489999999.877.***********65555555 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.8
                        MAF_flag10 138 fgGgsvantaldlAvklgfkeIiliG 163
                                        +G  v   a+dlA +l++++I++ G
  gi|385805436|ref|YP_005841834.1| 141 VSGVVVKWSAIDLA-QLHVDPIFFTG 165
                                       56777888899999.99999999988 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   2.2e-05     0.022       1      31 [.      28      56 ..      28      63 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.2e-05
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlie 31
                                      Dv+++GaGp g+  A+ l  a ++lkv+++e
  gi|385805436|ref|YP_005841834.1| 28 DVIIVGAGPSGMTAAKYL--ADKKLKVLVLE 56
                                      9*****************..88999999987 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 ?   14.7   0.0   2.3e-05     0.023       1      41 [.      30      65 ..      30      99 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.3e-05
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsep.gagrv 41
                                      +ivGaGp+G+++++ L++++     l++ + +++ + g g++
  gi|385805436|ref|YP_005841834.1| 30 IIVGAGPSGMTAAKYLADKK-----LKVLVLERKLSfG-GGI 65
                                      59***************995.....9999999964426.655 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.3   4.1e-05     0.041       1      42 [.      28      66 ..      28      93 .. 0.82
   2 ?   -2.9   0.0       2.3   2.3e+03     149     177 ..     101     129 ..      86     185 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.1e-05
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS---SS- CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlveseeigtvgvG 42
                                      +++ivG+G++G +aA +la      l+v+++e +  +  g+G
  gi|385805436|ref|YP_005841834.1| 28 DVIIVGAGPSGMTAAKYLADKK---LKVLVLERKLSFGGGIG 66
                                      69****************9988...89999998766555555 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.3
                                       EEE-HHHHHHHHHHHHHHCT-EEEE--EE CS
                    Trp_halogenase 149 yhldaalyakfLrrvaearGvtrvegkvv 177
                                       y lda+++   L + a + G +++ g +v
  gi|385805436|ref|YP_005841834.1| 101 YTLDASELISKLATGAINSGAKILFGYSV 129
                                       55555555555555555555555444332 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   6.1e-05      0.06       2      28 ..      37      63 ..      36      66 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.1e-05
                                      HHHHHHHHHHHTTEEEEEEESSSSSBT CS
                     Amino_oxidase  2 aGLaaArqLlsaGfdVtvlEardrvGG 28
                                      +G++aA++L+++ ++V+vlE +  +GG
  gi|385805436|ref|YP_005841834.1| 37 SGMTAAKYLADKKLKVLVLERKLSFGG 63
                                      9********************999999 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 ?   11.6   0.0   0.00011      0.11       4      39 ..      28      61 ..      25      63 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                       K_oxygenase  4 DligiGiGpsnLsLailleevkkelkalflerqpef 39
                                      D+i++G+Gps ++ a  l+++k  lk+l+ler+ +f
  gi|385805436|ref|YP_005841834.1| 28 DVIIVGAGPSGMTAAKYLADKK--LKVLVLERKLSF 61
                                      9*******************99..********9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); 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 0.30s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 1663.43
//
Query:       gi|385805437|ref|YP_005841835.1|  [L=137]
Description: glycine cleavage system protein H [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-42  144.0   0.2    2.3e-42  143.7   0.2    1.1  1  GCV_H            Glycine cleavage H-protein
    3.6e-05   23.5   0.0    0.00034   20.4   0.1    2.1  2  Biotin_lipoyl    Biotin-requiring enzyme
    8.2e-05   22.5   0.0    0.00014   21.8   0.0    1.3  1  RnfC_N           RnfC Barrel sandwich hybrid domain
  ------ inclusion threshold ------
      0.012   15.4   0.1      0.057   13.2   0.1    2.1  2  Biotin_lipoyl_2  Biotin-lipoyl like


Domain annotation for each model (and alignments):
>> GCV_H  Glycine cleavage H-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.7   0.2   5.2e-46   2.3e-42       2     121 ..      17     135 ..      16     136 .. 0.98

  Alignments for each domain:
  == domain 1  score: 143.7 bits;  conditional E-value: 5.2e-46
                                       EE-TTSEEEEEETT.EEEEEE-HHHHHHH-SEEEEE---TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEEE-GGG CS
                             GCV_H   2 yytkehewvkveedgvatvGitdfaqeelgdvvfvelpevgtkvkkgeslaavEsvKaasevyapvsGevvevNekl 78 
                                       yyt+ +ew+k e+   a++Gitd+aq++l d++ ++lpe+g+k+kkge la+++s Ka+sevyap+sGe+++vNe l
  gi|385805437|ref|YP_005841835.1|  17 YYTETDEWIKLEGM-NARIGITDYAQKHLKDIIGIDLPEKGKKIKKGEVLATLDSIKATSEVYAPISGEILDVNETL 92 
                                       9**********997.9************************************************************* PP

                                       TT-TTHHHH-TTTTT--EEEEES-GGGGGGSEEHHHHHHHHHH CS
                             GCV_H  79 eeepeliNkdpyeegWliklklsnleeleeLlsaeeyekllke 121
                                        e+pel+N+dpye+gW++ +k++n++el++Ll+ e+y+kll++
  gi|385805437|ref|YP_005841835.1|  93 LESPELMNSDPYESGWIALIKIENNDELNSLLTFEQYVKLLES 135
                                       ***************************************9975 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1   7.6e-08   0.00034      22      56 ..      54      88 ..      52      91 .. 0.93
   2 ?    0.3   0.0      0.14   6.1e+02      49      64 ..     105     120 ..     101     122 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 7.6e-08
                                      STTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEE CS
                     Biotin_lipoyl 22 kvGdkVkagqvlaeveamKmemeieapkaGvvkei 56
                                      ++G k+k+g+vla++ + K++ e+ ap +G + ++
  gi|385805437|ref|YP_005841835.1| 54 EKGKKIKKGEVLATLDSIKATSEVYAPISGEILDV 88
                                      68****************************99776 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.14
                                       SSEEEEEESSTTTEEE CS
                     Biotin_lipoyl  49 kaGvvkeilvkeGdtv 64 
                                       ++G ++ i+++++d++
  gi|385805437|ref|YP_005841835.1| 105 ESGWIALIKIENNDEL 120
                                       6899*******99987 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 !   21.8   0.0   3.1e-08   0.00014      47      90 ..      54      98 ..      47     103 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 3.1e-08
                            RnfC_N 47 kvgdkVlkGqkiaeaeg.fvsapvhasvsGtVkaiekrlvahgsg 90
                                      ++g k++kG+++a+ ++   +++v+a++sG++ ++++ l  +++ 
  gi|385805437|ref|YP_005841835.1| 54 EKGKKIKKGEVLATLDSiKATSEVYAPISGEILDVNETLLESPEL 98
                                      79**************9667899*************998877765 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   1.3e-05     0.057      20      36 ..      55      71 ..      54      77 .. 0.89
   2 ?   -1.1   0.0      0.39   1.7e+03       4      17 ..      76      89 ..      73      89 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.3e-05
                   Biotin_lipoyl_2 20 dGqrVkaGdvLaelDsr 36
                                       G+ +k+G vLa+lDs 
  gi|385805437|ref|YP_005841835.1| 55 KGKKIKKGEVLATLDSI 71
                                      699************96 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.39
                   Biotin_lipoyl_2  4 sIaapvsGrVaqln 17
                                      ++ ap+sG +  +n
  gi|385805437|ref|YP_005841835.1| 76 EVYAPISGEILDVN 89
                                      57799***998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); 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:                         4  (0.000223102); expected 0.2 (1e-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 0.32s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 827.16
//
Query:       gi|385805438|ref|YP_005841836.1|  [L=262]
Description: 3-isopropylmalate dehydratase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-35  121.7   0.0    4.7e-35  121.5   0.0    1.0  1  PAC2      PAC2 family


Domain annotation for each model (and alignments):
>> PAC2  PAC2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.5   0.0   2.6e-39   4.7e-35       1     211 [.      32     237 ..      32     239 .. 0.91

  Alignments for each domain:
  == domain 1  score: 121.5 bits;  conditional E-value: 2.6e-39
                                       EEEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETTEEE-SEEEEEETTT.SEEEEEEEE-H CS
                              PAC2   1 LilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveegrelepprlyakdsgsrdllvlqgrep 77 
                                       Li+Gfp++G+Vg ++ ++Li++l+ ++++ id + l p     p++++++g+  +p+r++ kd    ++l+l++  p
  gi|385805438|ref|YP_005841836.1|  32 LIVGFPDAGLVGGISLNHLIRELNPKEIAGIDIPRLNP-----PIAIIRKGEYHPPIRIFKKD----NILFLVSEIP 99 
                                       89************************************.....********999*****9677....7******777 PP

                                       SCHHH..HHHHHHHHHHHHTTESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHHH..CT...-CEEEEHHH CS
                              PAC2  78 ilqye..efakalldwaeelgvkevvvLggldageradvphtrpekvtgaatdeelleele..es...eyggivgit 147
                                       i  ++   ++ a+l+++++ +v+ v+ L+g+++ er +  +++p +v+ a++ ++  + +   e    ++g+  g+ 
  gi|385805438|ref|YP_005841836.1| 100 IPANTvqPLSYAILEYCMRRRVDYVIGLTGIGSTERLN--KEKP-DVFIAYEGDQAKRMILinEGkvfDEGMLMGPF 173
                                       77777779*************************99964..5555.9999998888886664333378999******* PP

                                       HHHHHHHHHTT-EEEEEEEEEECCC--HHHHHHHHHHHHHHHT---HCHHHHHHHHHHHHHHHH CS
                              PAC2 148 glLlsaakergipavgllaevphylpdPkaaaalleflskllglevdtedLeedaeeleeqlee 211
                                       +++l++ak+ +++++ +lae+ + lpdP+aa++++e+lsk+l ++++ ++L e+ae ++ + +e
  gi|385805438|ref|YP_005841836.1| 174 AIFLKEAKRFNLQSLIILAESFPDLPDPEAASVAVEYLSKILSIKISIDKLLEEAEYIRLRTKE 237
                                       *********************************************************9987776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1544.67
//
Query:       gi|385805439|ref|YP_005841837.1|  [L=142]
Description: hypothetical protein FFONT_0395 [Fervidicoccus fontis Kam940]
Scores for complete 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   31.9   0.0    1.7e-07   31.3   0.0    1.3  1  HSP20          Hsp20/alpha crystallin family
    0.00052   19.5   0.0    0.00073   19.0   0.0    1.3  1  ArsA_HSP20     HSP20-like domain found in ArsA
  ------ inclusion threshold ------
      0.015   15.1   0.7          2    8.3   0.1    2.2  2  TFIIE_alpha    TFIIE alpha subunit
      0.039   12.6   0.0      0.041   12.5   0.0    1.1  1  LA-virus_coat  L-A virus, major coat protein
      0.057   13.6   0.1       0.09   13.0   0.1    1.3  1  UBX            UBX 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 !   31.3   0.0   4.6e-11   1.7e-07       2      90 ..      51     141 ..      50     142 .] 0.85

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 4.6e-11
                                       --SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--..---TT----SS..---EEEEEE--STTB-TTT-EEEE CS
                             HSP20   2 ikeeeeefevkldvpglkkeelkvkvednrvlvkgeheeeeedekgliker..ssrkFsrkftLPenvdadkvkasl 76 
                                       i e+e+++ v +d p ++++ l+++ +dn + ++ + +e+ + ++  ++ +  +  +++++++LP ++d ++ + s+
  gi|385805439|ref|YP_005841837.1|  51 IYESEDSYYVVIDAPYMDTSSLTIEAHDNILNIEVKLKEKINLGNIGYRLHscEIFNYRKTISLPPDADVSRLTYSI 127
                                       6799**************************9999999955555555554440155678899**************** PP

                                       ETTEEEEEEEBSS- CS
                             HSP20  77 kdGvLtvtvpkkep 90 
                                       k G   +++pkk++
  gi|385805439|ref|YP_005841837.1| 128 KSGRIIINIPKKHE 141
                                       ***********975 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 !   19.0   0.0     2e-07   0.00073       2      42 ..      56     116 ..      55     135 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2e-07
                        ArsA_HSP20   2 deyvlkldLPfvdkeeidlsrsgdeLtIkig....................nfrRqitLPs 42 
                                       d y +++d P +d++++ ++ +++ L I+++                    n+r++i+LP 
  gi|385805439|ref|YP_005841837.1|  56 DSYYVVIDAPYMDTSSLTIEAHDNILNIEVKlkekinlgnigyrlhsceifNYRKTISLPP 116
                                       88**********************************************************6 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1    0.0039        14      73      99 ..       2      28 ..       1      33 [. 0.92
   2 ?    8.3   0.1   0.00055         2      30      90 ..      78     141 ..      55     142 .] 0.84

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0039
                                      EEEEECCCHCCCHHHHHHHHHHHHHHH CS
                       TFIIE_alpha 73 ywrinyeklvdvvkrkleevvkkLeek 99
                                      yw+ + e++ + ++++++e+ ++ e++
  gi|385805439|ref|YP_005841837.1|  2 YWYDDFERIREYIRKRIKEMEREFEDA 28
                                      9*********************99986 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00055
                                       HHHHHHHHTS-HH.HHHHHHHHHHHCTSEEEEEEEE..TTTEEEEEEEEEECCCHCCCHHHHHH CS
                       TFIIE_alpha  30 eedlakelkidln.elrklLnrLyearlvkykrrrd..eekswykyywrinyeklvdvvkrkle 90 
                                       ++ l+ e+k++ + +l+++ +rL +  + +y++     ++  + + ++ i+  +++  + +k+e
  gi|385805439|ref|YP_005841837.1|  78 DNILNIEVKLKEKiNLGNIGYRLHSCEIFNYRKTISlpPDADVSRLTYSIKSGRIIINIPKKHE 141
                                       5556667777665369******************9999*************9999888877775 PP

>> LA-virus_coat  L-A virus, major coat protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.1e-05     0.041     185     252 ..      48     113 ..      28     140 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.1e-05
                                       ---EEEEE--SS-SSSS-EEE-TTS-HHHHHHHHHHCS-B---SSBG.GG--B--S-SEEEEE-SS--- CS
                     LA-virus_coat 185 sypdwaqlseslpvidvpyldlrpltveevkvvlmmtskwkrrtnlk.ldyeaprlaekiayryaltvs 252
                                        y  ++    ++ vid py+d   lt e  + +l +  k k++ nl  + y   +  e + yr   t+s
  gi|385805439|ref|YP_005841837.1|  48 LYTIYESEDSYYVVIDAPYMDTSSLTIEAHDNILNIEVKLKEKINLGnIGY-RLHSCEIFNYRK--TIS 113
                                       5666666677899*******************************9851444.344455555554..443 PP

>> UBX  UBX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   2.5e-05      0.09      27      69 ..       5      51 ..       4      63 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.5e-05
                                      SBHHHHHHHHHHHCCCCCTSEE...EEETTTTEEGGCCC.CSBCCCC CS
                               UBX 27 dtlesvyeyVdsklfekeepFq...LltsfPrreltksd.kktLsdl 69
                                      d+ e ++ey++    e+e++F+   L ts+P +e+t +d ++ L ++
  gi|385805439|ref|YP_005841837.1|  5 DDFERIREYIRKRIKEMEREFEdafLSTSLPIEEFTAEDiSSPLYTI 51
                                      56789*************9987777**************99999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); 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 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1043.46
//
Query:       gi|385805440|ref|YP_005841838.1|  [L=252]
Description: AAA ATPase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-21   75.7   0.1    4.1e-21   75.4   0.1    1.0  1  ATPase         KaiC
    1.3e-08   33.9   0.3    1.8e-08   33.5   0.3    1.1  1  GvpD           GvpD gas vesicle protein
    2.2e-06   27.7   0.1    0.00026   21.0   0.0    2.2  2  AAA_14         AAA domain
    6.1e-06   26.1   0.2      1e-05   25.3   0.2    1.3  1  AAA_24         AAA domain
    2.7e-05   24.2   0.4      4e-05   23.7   0.4    1.2  1  ATPase_2       ATPase domain predominantly from Archaea
    0.00069   19.9   0.0     0.0012   19.1   0.0    1.5  1  AAA_22         AAA domain
     0.0023   17.5   0.0       0.76    9.3   0.0    2.1  2  AAA_25         AAA domain
     0.0042   17.5   0.1       0.01   16.2   0.1    1.7  1  AAA            ATPase family associated with various cellular
     0.0043   16.4   0.1     0.0066   15.8   0.1    1.3  1  DnaB_C         DnaB-like helicase C terminal domain
     0.0043   17.5   0.0     0.0055   17.1   0.0    1.3  1  AAA_16         AAA ATPase domain
     0.0046   17.1   0.0     0.0062   16.7   0.0    1.3  1  AAA_33         AAA domain
     0.0083   15.1   0.0      0.012   14.6   0.0    1.2  1  AAA_10         AAA-like domain
     0.0087   15.8   0.4        1.2    8.8   0.0    2.4  2  DUF835         Protein of unknown function (DUF835)
  ------ inclusion threshold ------
      0.015   14.9   0.0      0.019   14.6   0.0    1.3  1  ATP-synt_ab    ATP synthase alpha/beta family, nucleotide-bin
      0.018   14.8   0.0      0.062   13.0   0.0    1.8  2  IstB_IS21      IstB-like ATP binding protein
      0.025   14.8   0.0      0.048   13.9   0.0    1.4  1  Roc            Ras of Complex, Roc, domain of DAPkinase
      0.026   14.4   0.2      0.038   13.8   0.2    1.2  1  Bac_DnaA       Bacterial dnaA  protein
      0.032   14.2   0.0        1.1    9.1   0.0    2.3  2  NTPase_1       NTPase
      0.038   14.4   0.0       0.12   12.7   0.0    1.7  1  RNA_helicase   RNA helicase
      0.045   14.3   0.0      0.099   13.2   0.0    1.4  1  ABC_tran       ABC transporter
      0.054   13.4   0.0       0.12   12.3   0.0    1.6  1  RsgA_GTPase    RsgA GTPase
      0.056   13.3   0.0       0.12   12.2   0.0    1.6  2  Helicase_RecD  Helicase
      0.082   13.2   0.2        3.2    8.2   0.1    2.4  2  Thioredoxin_8  Thioredoxin-like
       0.09   12.1   0.0       0.14   11.4   0.0    1.3  1  FtsK_SpoIIIE   FtsK/SpoIIIE family
       0.13   12.2   0.0        0.3   11.0   0.0    1.5  2  NACHT          NACHT 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 !   75.4   0.1   5.7e-24   4.1e-21      15     229 ..      17     235 ..       9     237 .. 0.87

  Alignments for each domain:
  == domain 1  score: 75.4 bits;  conditional E-value: 5.7e-24
                            ATPase  15 GipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeegklaiidases 91 
                                       G  ++ ++ i+G pG GK++f+++ + +++++     ++v+v+++ +d+ e  +++  ++ k++++  + ++da+++
  gi|385805440|ref|YP_005841838.1|  17 GNLSEGIYVIAGPPGIGKSVFVKRLIANSIAD--SYILYVSVDSSIKDMLEFLEKM--NISKYKDH--IQFLDAFST 87 
                                       555667999********************887..99*****************985..899***99..******999 PP

                            ATPase  92 aeesaee...kdkedleelieelaeaikeika....krvviDsitglayeekeavaReilrqlvrvlkklgvTailv 161
                                       + + +++    +k +le+ +++l ++ +++ +    k +viDsit +   +++++  + ++ l+++ + + +  +++
  gi|385805440|ref|YP_005841838.1|  88 TFTGIKQdiqYEKINLESASDSLFTIYSKLSQmdgnKILVIDSITEMLIGTDPDTSISFIKGLKQITESTHTLGVIT 164
                                       887777778778889999999999999888777777***********778888888899999999999999999999 PP

                            ATPase 162 sekssseeaaggygveefivdgvivLdlkeiee...elvRtleivkmRgtkhskkehpfeIte.egikvlee 229
                                             ++ +    + e+++dg i L+ + + e    l R ++i kmR + h+++ +p++I +  g + +++
  gi|385805440|ref|YP_005841838.1| 165 IHTG-PDSLKDILWILEYLSDGYIELAFEPNFEavgILLRRIRIKKMRNKFHDSNWYPYKIVKdYGLQFMSP 235
                                       8843.34566678899***********99888888899***********************99899888766 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.3   2.5e-11   1.8e-08      13     221 ..      24     241 ..      12     250 .. 0.71

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 2.5e-11
                              GvpD  13 llikGaPGtGktlftlrgldvlrresdvlyvstrvddetvseay.fsgeaeld....ktalldllkdpleldldvdv 84 
                                        +i G PG Gk +f  r +     +s +lyvs    d++++++  f ++ +++    + ++ld +   ++  +++d+
  gi|385805440|ref|YP_005841838.1|  24 YVIAGPPGIGKSVFVKRLIANSIADSYILYVSV---DSSIKDMLeFLEKMNISkykdHIQFLDAFSTTFT-GIKQDI 96 
                                       489***************9999999******96...5667777667777777744336678888888885.799*** PP

                              GvpD  85 Piekldle....sllefvdeiaaiatkliialdswelvyeylaerydsPediktvkndlvvlaresgvrlvlvleta 157
                                        +ek++le    sl+    +++++  + i+ +ds   + e+l    d   +i  +k  l  ++ es   l +++   
  gi|385805440|ref|YP_005841838.1|  97 QYEKINLEsasdSLFTIYSKLSQMDGNKILVIDS---ITEMLIG-TDPDTSISFIKG-LKQIT-ESTHTLGVITIHT 167
                                       ******962222688888999999999*******...7777654.344444666664.33233.3333333333322 PP

                              GvpD 158 ansr.......leyivdGvvtlnvked..drgrlrrdlrleklrGvrignrlqPftla.dGkfksitrvelvti 221
                                        +++       ley+ dG + l  + +    g l r +r++k+r    ++  +P+ +  d  ++ + + el  i
  gi|385805440|ref|YP_005841838.1| 168 GPDSlkdilwiLEYLSDGYIELAFEPNfeAVGILLRRIRIKKMRNKFHDSNWYPYKIVkDYGLQFMSPQELKAI 241
                                       222212233448**********6665422679************999999999987652555666777777654 PP

>> AAA_14  AAA 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   0.00026       3      69 ..      22      81 ..      20      95 .. 0.74
   2 ?    4.9   0.0     0.035        25      37      90 ..     102     157 ..      87     193 .. 0.67

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3.7e-07
                            AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylf 69
                                       i+vi G+  +GK++++k+li +++  ++ ily+++d+  +++l+ +  l+++  +k+   k+++ f
  gi|385805440|ref|YP_005841838.1| 22 GIYVIAGPPGIGKSVFVKRLIANSI-ADSYILYVSVDSSIKDMLE-F--LEKMNISKY---KDHIQF 81
                                      699******************9999.99*********96654444.3..223322222...234444 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.035
                            AAA_14  37 nldderdkkladpekllelilek.lkeekktylflDEiqev.........pewekalkslvdeg 90 
                                       nl++     ++  ++l +++ ++  + +++++l++D i e+          ++ k lk++ +++
  gi|385805440|ref|YP_005841838.1| 102 NLES-----AS--DSLFTIYSKLsQM-DGNKILVIDSITEMligtdpdtsISFIKGLKQITEST 157
                                       2222.....22..2466777776333.599********99988888866666666666666655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.2   1.4e-08     1e-05       5      78 ..      24     135 ..      21     143 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.4e-08
                            AAA_24   5 iliyGpsgiGKTtlakel......gpkplfidtekGlksl.dadkfpdieswedfldevvel............... 59 
                                       ++i Gp+giGK+ ++k+l         +l++ ++ + k++ ++ +  +i++++d +++++++               
  gi|385805440|ref|YP_005841838.1|  24 YVIAGPPGIGKSVFVKRLiansiaDSYILYVSVDSSIKDMlEFLEKMNISKYKDHIQFLDAFsttftgikqdiqyek 100
                                       589********************9999**********986378888999988888888888888899999999999* PP

                            AAA_24  60 ................aaeladyktlviDtidele 78 
                                                         + ++ k+lviD+i+e+ 
  gi|385805440|ref|YP_005841838.1| 101 inlesasdslftiyskLSQMDGNKILVIDSITEML 135
                                       **************998999999*********985 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.4   5.5e-08     4e-05      21     151 ..      22     156 ..      10     167 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 5.5e-08
                          ATPase_2  21 eiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie.....eeeekkklekalgiavpkaele 92 
                                        iy+i Gp g+GK+ ++k++i n+   d y++y++   ++si+ + ef+e     + ++  ++ +a+++++   + +
  gi|385805440|ref|YP_005841838.1|  22 GIYVIAGPPGIGKSVFVKRLIANSIA-DSYILYVSV--DSSIKDMLEFLEkmnisKYKDHIQFLDAFSTTFTGIKQD 95 
                                       69**********************66.557888764..566777777777665655555566666666666665555 PP

                          ATPase_2  93 eilk.eksklvfkaielllekikkkgkkiiiiiDelqklidlgln..gaellvkeLlnlies 151
                                         ++  + + +  ++  ++ k+++     i++iD + ++  +g +   + +++k L ++ es
  gi|385805440|ref|YP_005841838.1|  96 IQYEkINLESASDSLFTIYSKLSQMDGNKILVIDSITEML-IGTDpdTSISFIKGLKQITES 156
                                       44555688899999999999999999999******98776.666522555667777666665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.7e-06    0.0012       4     112 ..      20     147 ..      18     176 .. 0.59

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.7e-06
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka.......... 70 
                                       ++gi v+ G++G+GK++ ++rl  +           ++ +  ++++++s kd+l+ l ++++ ++ +          
  gi|385805440|ref|YP_005841838.1|  20 SEGIYVIAGPPGIGKSVFVKRLIANS---------IADSYILYVSVDSSIKDMLEFL-EKMNISKYKdhiqfldafs 86 
                                       579********************998.........4555555555555555554333.3333333333555555555 PP

                            AAA_22  71 ...............erlsseellealeqalraravielliiDEaqh.lr...seealeeL 112
                                                      +  s ++ l +++  l++ +  ++l+iD +   l+   +++ ++++
  gi|385805440|ref|YP_005841838.1|  87 ttftgikqdiqyekiNLESASDSLFTIYSKLSQMDGNKILVIDSITEmLIgtdPDTSISFI 147
                                       5555555566666665555555555555555555545777777766633354325555555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0    0.0011      0.76      19      52 ..       8      40 ..       3      49 .. 0.82
   2 !    6.3   0.0    0.0088       6.3     136     190 ..     116     168 ..      66     171 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0011
                            AAA_25 19 ppprrwlvkgllpagelallaGapgtGKttlald 52
                                      +p +++l++g l  +++ ++aG+pg GK++++  
  gi|385805440|ref|YP_005841838.1|  8 LPLVSDLMEGNL-SEGIYVIAGPPGIGKSVFVKR 40
                                      677889999998.5888999*********99855 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0088
                            AAA_25 136 aieevegvrlvviDplsralgg.densnsdvgalvealeriarrtgaavllvhHvg 190
                                       ++ ++ g + +viD+++++l g d++      ++++ l++i + t+   +++ H+g
  gi|385805440|ref|YP_005841838.1| 116 KLSQMDGNKILVIDSITEMLIGtDPD---TSISFIKGLKQITESTHTLGVITIHTG 168
                                       5667788999**********994444...337899******999999999999997 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   0.1   1.5e-05      0.01       2      74 ..      25     138 ..      24     182 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.5e-05
                                       EEESSTTSSHHHHHHHHHHHH..THEEEEEETTTCSSS....................................... CS
                               AAA   2 llyGppGtGKTllakavakel..gvefleisgsellsk....................................... 37 
                                       ++ GppG+GK+ ++k ++ ++  ++++l +s+ + +++                                       
  gi|385805440|ref|YP_005841838.1|  25 VIAGPPGIGKSVFVKRLIANSiaDSYILYVSVDSSIKDmleflekmniskykdhiqfldafsttftgikqdiqyeki 101
                                       578***********987777324566677777666633466666677777777788888888888878888777666 PP

                                       STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH CS
                               AAA  38 yvgesekkirelfkeakekakpsilfiDEidalaksr 74 
                                        ++ +++++  + ++++++ + +il+iD i ++    
  gi|385805440|ref|YP_005841838.1| 102 NLESASDSLFTIYSKLSQMDGNKILVIDSITEMLIGT 138
                                       4444555555555555555555888888887776555 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   0.1   9.3e-06    0.0066      11     142 ..      13     135 ..       4     165 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 9.3e-06
                                       HHCTSBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHHHHHHHHTXXHHHHHHT.TSXH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                            DnaB_C  11 kltsGlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqRllsseaeidskklrtg.klke 86 
                                       +l++G  +  +++iA+ p++Gk++++  +++n  +  +  ++++s++ s +++++       +++ +k++   ++ +
  gi|385805440|ref|YP_005841838.1|  13 DLMEGNLSEGIYVIAGPPGIGKSVFVKRLIANSIA--DSYILYVSVDSSIKDMLEF----LEKMNISKYKDHiQFLD 83 
                                       45666666779***************999887654..4569999999887776543....33333333332212223 PP

                                       HHHHHHHHHHHHHHHSEEEEEEXSSXCHHHHHHHHHHHHHHTTEEEEEEEEGGGTB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  87 edweklteaieelseaklfiddtpaltvseirskarrlkkekglgliviDyLqlme 142
                                       +  +++t   ++++  k+ ++  ++ ++ +i sk+ ++   +g +++viD +  m 
  gi|385805440|ref|YP_005841838.1|  84 AFSTTFTGIKQDIQYEKINLESASD-SLFTIYSKLSQM---DGNKILVIDSITEML 135
                                       3334444455566666777666554.566676665555...456777777776665 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   7.7e-06    0.0055      24      61 ..      19      57 ..       2     138 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 7.7e-06
                            AAA_16 24 p..elvllsGesGvGKsslv.rellralekdggiflrgkcd 61
                                         ++ ++ G++G+GKs  v r +++++ ++++  l+   d
  gi|385805440|ref|YP_005841838.1| 19 LseGIYVIAGPPGIGKSVFVkRLIANSIADSYI--LYVSVD 57
                                      3337999*************7777778888753..333333 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   8.6e-06    0.0062       3      58 ..      25      85 ..      23     128 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 8.6e-06
                            AAA_33  3 llvGlpGsGKstlaerllkklg...avl.lssdtlrrrlfg.tdqqsktdytrvldrlyqi 58
                                      ++ G+pG GKs +++rl+++     ++l +s d+ ++ + +  ++ ++++y++  + l ++
  gi|385805440|ref|YP_005841838.1| 25 VIAGPPGIGKSVFVKRLIANSIadsYILyVSVDSSIKDMLEfLEKMNISKYKDHIQFLDAF 85
                                      678**************97666899555599999888766656677777777655554444 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.6e-05     0.012      24     139 ..      24     139 ..       6     172 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.6e-05
                            AAA_10  24 sliiGdlGnGKSvlakllvlyisllggkaliiDpkke...rekfketl..peiakkinvvtLdseeenegvLdPlvl 95 
                                        +i G++G GKSv++k l+ +  +++  +l++        + +f e++   +++++i++++  s +   g    +  
  gi|385805440|ref|YP_005841838.1|  24 YVIAGPPGIGKSVFVKRLIANS-IADSYILYVSVDSSikdMLEFLEKMniSKYKDHIQFLDAFSTT-FTGIKQDIQY 98 
                                       5899**************9986.5677788875554400155565544335588899999876444.4466555544 PP

                            AAA_10  96 lkeekeaeslaedilelllgvkkkesekkaalseaveavlegkq 139
                                          + + es   ++++++ ++++++ +k  ++ +++ + l g +
  gi|385805440|ref|YP_005841838.1|  99 E--KINLESASDSLFTIYSKLSQMDGNKI-LVIDSITEMLIGTD 139
                                       3..33466667788888888888888887.56666666665444 PP

>> DUF835  Protein of unknown function (DUF835)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1     0.029        21      69     119 ..     115     165 ..      71     179 .. 0.78
   2 !    8.8   0.0    0.0017       1.2      22      68 ..     199     245 ..     192     251 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.029
                            DUF835  69 vkflkeaekgvvliDgleyLvlengFesvlkflltlkDavllkngtlilvi 119
                                       +k  + +++++ +iD++  +++ ++ ++ + f++ lk ++ +++++ +++i
  gi|385805440|ref|YP_005841838.1| 115 SKLSQMDGNKILVIDSITEMLIGTDPDTSISFIKGLKQITESTHTLGVITI 165
                                       4444556777***************************99887765555444 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0017
                            DUF835  22 vlaitRenpkkirekvkienvkviwltkveeentvsPtnleklteti 68 
                                       ++++ R + kk+r+k++ +n+  + + k  + + +sP++l+++ + +
  gi|385805440|ref|YP_005841838.1| 199 GILLRRIRIKKMRNKFHDSNWYPYKIVKDYGLQFMSPQELKAIADVV 245
                                       57888999**********************************99877 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 ?   14.6   0.0   2.7e-05     0.019      17      67 ..      24      74 ..      11     134 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.7e-05
                                      EEEEESTTSSHHHHHHHHHHHSSTSSEEEEEEESEEHHHHHHHHHHCHHSS CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab 17 tlipgafgvGktvisqslskqsnsddaiiyvgiGergnevaevleefpegt 67
                                       +i g  g+Gk+v ++ l+ +s +d++i yv +    +++ e+le+++ ++
  gi|385805440|ref|YP_005841838.1| 24 YVIAGPPGIGKSVFVKRLIANSIADSYILYVSVDSSIKDMLEFLEKMNISK 74
                                      6799***************9998888*******************998655 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 ?   13.0   0.0   8.7e-05     0.062      50     135 ..      24     115 ..      18     130 .. 0.66
   2 ?   -1.9   0.0       3.4   2.5e+03     113     134 ..     224     245 ..     203     249 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.7e-05
                         IstB_IS21  50 ivllGpsGvGKshlaialgveavraglsvlfvrv....edLveelkrarrdgklaralkrllkvdll...ilDdlgl 119
                                        v+ Gp+G+GKs +   l  + +++ + +l+v+v    +d++e l++  +  k++ +++ l +++     i  d+ +
  gi|385805440|ref|YP_005841838.1|  24 YVIAGPPGIGKSVFVKRLIANSIADSY-ILYVSVdssiKDMLEFLEKM-NISKYKDHIQFLDAFSTTftgIKQDIQY 98 
                                       4899**************999998765.78887511115777766654.3456666665555543221226677777 PP

                         IstB_IS21 120 lpldqaea.ellfevie 135
                                       ++++ ++a   lf + +
  gi|385805440|ref|YP_005841838.1|  99 EKINLESAsDSLFTIYS 115
                                       77775544145666655 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.4
                         IstB_IS21 113 ilDdlgllpldqaeaellfevi 134
                                       i+ d+gl+ ++ +e + + +v+
  gi|385805440|ref|YP_005841838.1| 224 IVKDYGLQFMSPQELKAIADVV 245
                                       8889999999999988887776 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 ?   13.9   0.0   6.7e-05     0.048       3      50 ..      25      73 ..      24      89 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.7e-05
                                      EEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGS.GGCTTB CS
                               Roc  3 vlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtki.kgvend 50
                                      v+ G  g+GK+ ++kr++ +++ +++   ++vd + k++ ++ ++++ +
  gi|385805440|ref|YP_005841838.1| 25 VIAGPPGIGKSVFVKRLIANSIADSYILYVSVDSSIKDMLEFlEKMNIS 73
                                      688*******************************999986541343333 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   5.3e-05     0.038      39     146 ..      26     137 ..      21     164 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.3e-05
                                       EE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHTT-SEE......EEE-GGGG CS
                          Bac_DnaA  39 iygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklrkvDvL......liDDiqfl 109
                                       i g+ G+Gk   +k     + ++  +  ++Y++ ++ ++++++ l++ +++++k++++ +D+       +  Diq+ 
  gi|385805440|ref|YP_005841838.1|  26 IAGPPGIGKSVFVK---RLIANSIADSYILYVSVDSSIKDMLEFLEKMNISKYKDHIQFLDAFsttftgIKQDIQYE 99 
                                       66788888887755...55677778899*********************************8755555567899986 PP

                                       T.T-HHHHHHHHHHHHHHHTTT-EEEEEESS-TTT-SS CS
                          Bac_DnaA 110 a.gkektqeelfhtfnalleegkqvvlssDrsPkelee 146
                                       + + e+  + lf+++ +l + + + +l  D   + l  
  gi|385805440|ref|YP_005841838.1| 100 KiNLESASDSLFTIYSKLSQMDGNKILVIDSITEMLIG 137
                                       5256889999********98887777777766666655 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0    0.0016       1.1       3      21 ..      25      43 ..      23      51 .. 0.86
   2 ?    2.6   0.0      0.15   1.1e+02      88     135 ..     113     168 ..      89     179 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0016
                                      EEE--TTSSHHHHHHHHHH CS
                          NTPase_1  3 fiTGppGvGKtTlvkkvle 21
                                      +i GppG+GK+ +vk+++ 
  gi|385805440|ref|YP_005841838.1| 25 VIAGPPGIGKSVFVKRLIA 43
                                      799************9875 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.15
                                       HHHHHHHHH-...EEEE---STTGG.....G-HHHHHHHHHHHT.TTSEEEEE--SS CS
                          NTPase_1  88 alrkalsead...viviDEiGkmEl.....kskkfkeaveevLk.sekpvlavihrr 135
                                       + +k ls+ d   ++viD i +m       +s +f++ ++++ + +++  +++ih  
  gi|385805440|ref|YP_005841838.1| 113 IYSK-LSQMDgnkILVIDSITEMLIgtdpdTSISFIKGLKQITEsTHTLGVITIHTG 168
                                       4433.3333334599999998885422222677899999999997788888888875 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00017      0.12       2      21 ..      25      44 ..      24      65 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00017
                      RNA_helicase  2 wlyGpsgeGKStlakeLaka 21
                                      ++ Gp+g+GKS+++k+L+++
  gi|385805440|ref|YP_005841838.1| 25 VIAGPPGIGKSVFVKRLIAN 44
                                      689*************8765 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00014     0.099      13      74 ..      23      92 ..      15     134 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00014
                                      EEEEEESTTSSHHHHHHHHTTSS--SEEEEEET.TCEGGG.......B-HHHCCHCEEEE-SS--S-TTS CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx.......xxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 13 kvaivGenGaGKStLlkllagllkpteGeilld.gkdlke.......qeleslrkeigvlpqepqlfpel 74
                                      +++i G+ G GKS ++k l+ ++  ++  + +  + ++k+        ++++++ +i++l   ++ f ++
  gi|385805440|ref|YP_005841838.1| 23 IYVIAGPPGIGKSVFVKRLIANSIADSYILYVSvDSSIKDmleflekMNISKYKDHIQFLDAFSTTFTGI 92
                                      789*******************998877776665556666666666666666666666666665555555 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00017      0.12      94     122 ..      16      44 ..       6      78 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00017
                                       HHHCTTSEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  94 kellkdktsvlvGqSGvGKStLinallpe 122
                                       + +l++ + v++G+ G+GKS ++++l+ +
  gi|385805440|ref|YP_005841838.1|  16 EGNLSEGIYVIAGPPGIGKSVFVKRLIAN 44 
                                       5679999******************9986 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   0.00017      0.12       1      82 [.      25     102 ..      25     130 .. 0.83
   2 ?   -3.0   0.0       7.8   5.6e+03      71      85 ..     225     239 ..     192     244 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00017
                     Helicase_RecD   1 vltAdRGRGKSaalGlalaaliaegksnilvtapskenvktlfeflakglealglkeeekkkkaekaelrvrkqrie 77 
                                       v+ + +G GKS  +  ++a+ ia+++  il ++   +++k ++efl ++++  ++k++ ++ +a +++++  kq i+
  gi|385805440|ref|YP_005841838.1|  25 VIAGPPGIGKSVFVKRLIANSIADSY--ILYVS-VDSSIKDMLEFL-EKMNISKYKDHIQFLDAFSTTFTGIKQDIQ 97 
                                       68899*******************88..55555.467899******.6678999***99999999999999999999 PP

                     Helicase_RecD  78 yiapd 82 
                                       y + +
  gi|385805440|ref|YP_005841838.1|  98 YEKIN 102
                                       98765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 7.8
                     Helicase_RecD  71 vrkqrieyiapdell 85 
                                       v++  +++++p+el+
  gi|385805440|ref|YP_005841838.1| 225 VKDYGLQFMSPQELK 239
                                       236677888888876 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1    0.0044       3.2      38      65 ..      51      80 ..      37     104 .. 0.80
   2 ?    2.9   0.0      0.19   1.4e+02      23      83 ..     182     241 ..     141     250 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0044
                                      EEEEE-SS-HHHHHHHGGGS..-TTSEE.E CS
                     Thioredoxin_8 38 ivyvsldkkeeefekylkkn..kkpwlsvp 65
                                      i+yvs+d++ +++ ++l+k+  +k   +++
  gi|385805440|ref|YP_005841838.1| 51 ILYVSVDSSIKDMLEFLEKMniSKYKDHIQ 80
                                      89******************4444444555 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.19
                                       HHHHHHHHHHTTSEEEEEEE-SS.-HHHHHHHGGGS-TTSEE.EE-TT-HHHHTT-S--TT- CS
                     Thioredoxin_8  23 lkelyeklkkkkkveivyvsldk.keeefekylkknkkpwlsvpfddkkrnklkkkynvkai 83 
                                       l++ y +l  ++++e v + l +   +++++ + +   +w+ +   ++   ++ +  ++kai
  gi|385805440|ref|YP_005841838.1| 182 LSDGYIELAFEPNFEAVGILLRRiRIKKMRNKFHDS--NWYPYKIVKDYGLQFMSPQELKAI 241
                                       444455554589999999999874679999999999..9*9999887777677666666665 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0002      0.14      30      63 ..       9      45 ..       2      50 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0002
                                      EEEEEGGGS-....SEEEE--TTSSHHHHHHHHHHHH CS
                      FtsK_SpoIIIE 30 plvldlkkma...shllvaGatgsGKStalntLilSl 63
                                      plv+dl +     +  ++aG +g GKS++++ Li++ 
  gi|385805440|ref|YP_005841838.1|  9 PLVSDLMEGNlseGIYVIAGPPGIGKSVFVKRLIANS 45
                                      77777777777667789*****************975 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   0.00042       0.3       4      22 ..      25      43 ..      23      52 .. 0.87
   2 ?   -3.2   0.0       9.7   6.9e+03      84      93 ..     125     134 ..     102     162 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00042
                                      EEEC-TTTCHHHHHHHHHH CS
                             NACHT  4 ilqGeaGsGKTtLlqklal 22
                                      ++ G++G+GK++++++l+ 
  gi|385805440|ref|YP_005841838.1| 25 VIAGPPGIGKSVFVKRLIA 43
                                      899*************975 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 9.7
                                       EEEEE-STT- CS
                             NACHT  84 LlilDglDel 93 
                                        l++D++ e+
  gi|385805440|ref|YP_005841838.1| 125 ILVIDSITEM 134
                                       4666766654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       763  (0.0425568); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); 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: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 1732.65
//
Query:       gi|385805441|ref|YP_005841839.1|  [L=344]
Description: hypothetical protein FFONT_0397 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-41  143.1   0.2    1.2e-41  142.9   0.2    1.0  1  DUF354    Protein of unknown function (DUF354)
  ------ inclusion threshold ------
       0.53   10.3   3.2       0.28   11.2   0.5    2.0  2  Spc42p    Spindle pole body component Spc42p


Domain annotation for each model (and alignments):
>> DUF354  Protein of unknown function (DUF354)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.9   0.2   1.4e-45   1.2e-41       1     314 [.       1     312 [.       1     341 [. 0.86

  Alignments for each domain:
  == domain 1  score: 142.9 bits;  conditional E-value: 1.4e-45
                            DUF354   1 ldvwidltnaphvryfrdlikkfeke.GievlltardsGdlaklvklynfvfksiGkhGvtlkekliesakrvinls 76 
                                       +++w+d      +  f    kk e+e  +e+llt r++ ++++l ++  f  k iG +G+ ++ekli  +kr+i+l 
  gi|385805441|ref|YP_005841839.1|   1 MKIWLDALTPKQLLLFSYTAKKVEEElNVEILLTSRNTEEIERLNRIIPFRAKLIGSYGKNFEEKLILDSKRIIDLY 77 
                                       589***999999999********999568************************************************ PP

                            DUF354  77 kliaevkpdvalakhsvelprvafGlnipvvyvldnehaeaankltlpladeiikpividendlkktG.adpnrirr 152
                                       +++    pd+ +a       rvafGl+  ++   d  ha  a +l++plad ++  + +d+n + ++   +  +i  
  gi|385805441|ref|YP_005841839.1|  78 EVVRRFEPDILVAYPNPTASRVAFGLKKKILIFSDTPHADHAHRLSVPLADWLVFSKFLDKNLFYRYIlPKFTKIVT 154
                                       **************************************************************988764156788999 PP

                            DUF354 153 yeGtsevinvqsyeideeilkdlnlkledektilmrpepslasyldadchkdvltkiveklkdrid.ilviprdeeq 228
                                       y+G  e++  ++y  ++e +k+++  l+  + +++rp    asy   d  +++  ki++ + +  + ++++pr+ee+
  gi|385805441|ref|YP_005841839.1| 155 YRGVEELAWTKDYFPNDEPIKKIG--LNPFEYVVFRPPERYASYYIWD-RNNLTKKIIQEIAELDKkVVLFPRYEED 228
                                       ************9999999*****..788899****999999999875.5677788888887765569********* PP

                            DUF354 229 keiyeevdnviviketvdalsllkrsdlviGaGGtmnreaallGipvvscypqkllsvdkyliekdlmirstdvdei 305
                                         +++  + vi+i  +v  l l + s l i  GGtm rea+llG+p  + +p+k+        e   ++r  +++e 
  gi|385805441|ref|YP_005841839.1| 229 SLLFKSEN-VIIIDVPVFGLDLEYFSALTISGGGTMAREASLLGVPSFTFFPGKIHINTALAKEGFPIYRFFELEET 304
                                       ****9877.********************************************975433333333446677777776 PP

                            DUF354 306 vntalrllv 314
                                       +   + ++ 
  gi|385805441|ref|YP_005841839.1| 305 LK-FIEMIL 312
                                       66.334443 PP

>> Spc42p  Spindle pole body component Spc42p
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.5   3.1e-05      0.28      17      36 ..      37      55 ..      21      68 .. 0.85
   2 ?   -2.8   0.1      0.74   6.6e+03      36      48 ..     316     328 ..     306     339 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.1e-05
                            Spc42p 17 kqeEierLnvlvgslRaKLi 36
                                        eEierLn ++  +RaKLi
  gi|385805441|ref|YP_005841839.1| 37 NTEEIERLNRII-PFRAKLI 55
                                      579********9.6*****8 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.74
                            Spc42p  36 iKYtelnkKLedq 48 
                                       +KY + +kKL ++
  gi|385805441|ref|YP_005841839.1| 316 EKYRVDTKKLIKD 328
                                       5777777887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2297.59
//
Query:       gi|385805442|ref|YP_005841840.1|  [L=280]
Description: xylose isomerase domain-containing protein [Fervidicoccus fontis Kam940]
Scores for complete 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-12   45.2   0.0      1e-11   44.7   0.0    1.2  1  AP_endonuc_2     Xylose isomerase-like TIM barrel
  ------ inclusion threshold ------
      0.042   13.9   0.4       0.16   12.1   0.0    2.0  2  Endonuclea_NS_2  DNA/RNA non-specific endonuclease
      0.046   14.1   0.1      0.084   13.3   0.1    1.5  1  FtsA             Cell division protein FtsA
       0.41   11.4   7.2       0.29   11.9   1.2    3.3  3  RecG_N           RecG N-terminal helical domain


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   0.0   2.2e-15     1e-11       2     193 ..      20     214 ..      19     234 .. 0.80

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 2.2e-15
                                       HHHHHCT-SEEEEECCTCSHHHHC..HHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCS..HHHHHHHHHH CS
                      AP_endonuc_2   2 aaaaeaGfdgvElfgrdlvpvsel..sdeelrelrkaldelglriaslslftrfgypdederear..reesvdalkr 74 
                                       +a+ + Gf + E+++ ++ p++    + e+++ +++   + g++++   + + + y        +  re + ++lk+
  gi|385805442|ref|YP_005841840.1|  20 EAIYSSGFSYAEISIEYPWPFWKSesFYEQIEFIKSSGLKIGVHLPWRDILIISPY--------DeiREGAANYLKK 88 
                                       67778899999999999999986544444444444444444444333333333333........134666699**** PP

                                       HHHHHHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTCHHHHHHHHHH CS
                      AP_endonuc_2  75 aielaaaLGapllvlhpGtagagpkgseeeawerlaeslneladyaekegvklalEtlagsgvelgdeelarlldav 151
                                        +++ ++++a++ v+h  t+    +  +e+ ++++  +ln+l+ + + +g++l++E+ +    +++   +  l++++
  gi|385805442|ref|YP_005841840.1|  89 LVQTLEKINAEYAVMHLTTR-EEINLKDETYLQNIETVLNQLISEYKMHGIELLFENPPAGILSNR-YNFTSLINRL 163
                                       ****************8844.777777789********************************9999.9999999999 PP

                                       TTTTEEEEEEHHHHHHH............TTTHHHHHHHHHGGEEEEEE.EESS CS
                      AP_endonuc_2 152 dspnvgvclDtgHllia............eedvddalraladrikhvHikDakg 193
                                       +    ++c+D gHl+ +             +  +d+l +l ++ik vHi+ a +
  gi|385805442|ref|YP_005841840.1| 164 N---ARICFDAGHLISRflkgnssnlqnvINFTNDWLFNLFEYIKVVHIHGATK 214
                                       9...9*****************999999999999999999999******99988 PP

>> Endonuclea_NS_2  DNA/RNA non-specific endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.5e-05      0.16      56      81 ..     169     195 ..     152     207 .. 0.80
   2 ?   -1.2   0.1      0.46   2.1e+03      96     118 ..     237     258 ..     212     270 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.5e-05
                   Endonuclea_NS_2  56 ynggHLigsqfgGsnek.kNlvtgtrq 81 
                                        ++gHLi + ++G++ + +N++  t+ 
  gi|385805442|ref|YP_005841840.1| 169 FDAGHLISRFLKGNSSNlQNVINFTND 195
                                       799*************99***988776 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.46
                   Endonuclea_NS_2  96 kylklsenkkvrvevtpvYkgns 118
                                       + + ++++k+v v  ++ Yk+ +
  gi|385805442|ref|YP_005841840.1| 237 E-KFNQNKKDVIVTLEIFYKNLE 258
                                       4.345556788899999998876 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   1.9e-05     0.084      29      87 ..      74     131 ..      60     197 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.9e-05
                                       -HHHHHHHHHHHHT--HHHHHHHHHHH--S--EEEEEHHHHH..GGGGSTTHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxx RF
                              FtsA  29 ggngitkdiakalrtaveeAerikikyGsalaekeigrkels..ggsalpnleelaerals 87 
                                       + + i++++a+ l++ v++ e+i  +y++   +   +r+e++  ++++l+n+e+++++ +s
  gi|385805442|ref|YP_005841840.1|  74 PYDEIREGAANYLKKLVQTLEKINAEYAVMHLT---TREEINlkDETYLQNIETVLNQLIS 131
                                       5589********************999887763...3333444499999999999999852 PP

>> RecG_N  RecG N-terminal helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.31   1.4e+03       3      20 ..     116     133 ..     114     144 .. 0.77
   2 ?   -1.3   0.0      0.82   3.7e+03      32      60 ..     177     205 ..     172     209 .. 0.61
   3 ?   11.9   1.2   6.4e-05      0.29       1      43 [.     224     266 ..     224     278 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.31
                                       HHHHHHHHHHHTS---TT CS
                            RecG_N   3 EeFLeelekllkkvlsgk 20 
                                       E +L+++e++l++  s+ 
  gi|385805442|ref|YP_005841840.1| 116 ETYLQNIETVLNQLISEY 133
                                       789999999999887764 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.82
                                       HHHHH---GGGG-HHHH.HHHHHHHHHHT CS
                            RecG_N  32 kkleliddplleneevlkeklskfldYik 60 
                                       ++l+ +  +l +  +  ++ l ++++Yik
  gi|385805442|ref|YP_005841840.1| 177 RFLKGNSSNLQNVINFTNDWLFNLFEYIK 205
                                       45555555555555666666777777776 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 6.4e-05
                                       SHHHHHHHHHHHHTS---TTT........HHHHHHH---GGGG CS
                            RecG_N   1 liEeFLeelekllkkvlsgkleteelieeikkkleliddplle 43 
                                       li ++ + ++++l+k+ ++k+++   +e ++k+le  + +l  
  gi|385805442|ref|YP_005841840.1| 224 LIDDYVDFFYNILEKFNQNKKDVIVTLEIFYKNLERKNADLTT 266
                                       799******************9999999999999887766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       910  (0.0507558); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); 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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2057.90
//
Query:       gi|385805443|ref|YP_005841841.1|  [L=200]
Description: Ribonuclease HII (rnhB) [Fervidicoccus fontis Kam940]
Scores for complete 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-43  147.1   0.5    6.2e-43  146.9   0.5    1.0  1  RNase_HII  Ribonuclease HII
  ------ inclusion threshold ------
      0.032   14.5   1.4      0.045   14.1   0.4    1.6  1  DUF3942    Protein of unknown function (DUF3942)


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 !  146.9   0.5     7e-47   6.2e-43       1     197 [.       8     197 ..       8     198 .. 0.84

  Alignments for each domain:
  == domain 1  score: 146.9 bits;  conditional E-value: 7e-47
                                       EEEEEE-TT-SBS-EEEEEEEECGHHHHHHHCTTGTTGTTS-HHHHHHHHHHHHSEEEEEEE-HHHHH.HHTTTS-H CS
                         RNase_HII   1 iGiDEaGrGpvlGplvvaavavekereeelkklgvkDSKkLskqkreeLaklikkkiekrklvaeeikyaseneinl 77 
                                       +GiDEaGrG+++G+++va+v++++++e+ +kk+gvkDSKkLsk+kre+L  +i      +++   e+++    ei+ 
  gi|385805443|ref|YP_005841841.1|   8 LGIDEAGRGCMIGSMFVAGVVIDDRAEKVFKKYGVKDSKKLSKNKREKLYDIIT-----SNALWFEVVEVTPLEIDN 79 
                                       6****************************************************9.....555556666666666666 PP

                                       HHHHHHHHHHHHH...HHHHTCEECCECCCE--SSHHHHHHHHHHHHCCEEEEETTGGGT-HHHHHHHHHHHHHHHH CS
                         RNase_HII  78 neikaaltlavik...lleklgvkvdeilvdgvttpeslkkkleqiikikvtvekkadekyllvaaASiiAkverde 151
                                       ++i+  ++ a++k      k+  +++ i  d v++ + +k    + i+    v kkade +++vaaASi+Akv+rd 
  gi|385805443|ref|YP_005841841.1|  80 QNINYLTIRAMRKianDATKEIKYLNRIIADIVGKGD-FKLVESDNIE--QLVLKKADENFIAVAAASIVAKVQRDR 153
                                       6666666666666211555666667788888777755.4444445555..47889********************** PP

                                       HHHHHHHHCSH.--TTSSTTSHHHHHHHHHHHHHS--TTB-TTSHH CS
                         RNase_HII 152 elellkrkpgtldkgsGyasdektrallkkgatsklpdivrlsfkt 197
                                        le+++++ g   +gsGy+ d+k+ ++lk    + +++  r+++kt
  gi|385805443|ref|YP_005841841.1| 154 ALEQIRNNFG--LIGSGYPGDKKSVEWLKLHYSKIPREYIRTKWKT 197
                                       ********87..9*******************************98 PP

>> DUF3942  Protein of unknown function (DUF3942)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.4     5e-06     0.045      20      93 ..      92     161 ..      82     167 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5e-06
                           DUF3942  20 klikdghrdvifneltaleteigvvkkmdfeffksGrvehlvleyvefkyvkigsdkleleldkkrnvivvtki 93 
                                       k+ +d+ +++   +l        +v k df++ +s + e lvl++++  ++ +++  +  +++++r + ++ + 
  gi|385805443|ref|YP_005841841.1|  92 KIANDATKEIK--YLNR--IIADIVGKGDFKLVESDNIEQLVLKKADENFIAVAAASIVAKVQRDRALEQIRNN 161
                                       55555444442..3333..223799***************************************9998888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       982  (0.0547716); expected 358.6 (0.02)
Passed bias filter:                      576  (0.0321267); 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: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1344.16
//
Query:       gi|385805444|ref|YP_005841842.1|  [L=390]
Description: small GTP-binding protein [Fervidicoccus fontis Kam940]
Scores for complete 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-20   71.2   0.0    1.1e-19   70.2   0.0    1.6  1  TGS            TGS domain
    1.3e-18   67.0   3.8    2.4e-18   66.1   3.8    1.5  1  MMR_HSR1_Xtn   C-terminal region of MMR_HSR1 domain
      5e-11   42.7   0.0    2.2e-10   40.6   0.0    2.1  2  MMR_HSR1       50S ribosome-binding GTPase
    1.4e-06   28.0   0.2    6.5e-06   25.8   0.0    2.0  2  FeoB_N         Ferrous iron transport protein B
    0.00013   21.4   0.1      0.007   15.8   0.0    2.4  2  SRPRB          Signal recognition particle receptor beta subu
    0.00028   20.7   2.4      0.035   13.9   0.0    2.5  2  PduV-EutP      Ethanolamine utilisation - propanediol utilisa
     0.0012   18.4   0.1          3    7.3   0.0    3.0  3  GTP_EFTU       Elongation factor Tu GTP binding domain
  ------ inclusion threshold ------
      0.012   15.1   0.2       0.14   11.6   0.0    2.5  2  Arf            ADP-ribosylation factor family
      0.019   15.3   0.0      0.056   13.8   0.0    1.8  1  Ub-RnfH        RnfH family Ubiquitin
      0.027   15.1   0.1        8.8    7.1   0.0    3.2  2  ThiS           ThiS family
      0.052   13.4   1.6        1.1    9.1   0.3    2.5  2  RsgA_GTPase    RsgA GTPase
      0.059   13.6   0.0       0.33   11.2   0.0    2.3  2  Roc            Ras of Complex, Roc, domain of DAPkinase
      0.065   13.4   1.3        1.4    9.2   0.0    2.8  2  YchF-GTPase_C  Protein of unknown function (DUF933)


Domain annotation for each model (and alignments):
>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.2   0.0   7.9e-23   1.1e-19       1      59 [.     316     387 ..     316     388 .. 0.98

  Alignments for each domain:
  == domain 1  score: 70.2 bits;  conditional E-value: 7.9e-23
                                       EEEEE..TTSSEEE....EETTB-HHHHHHHHSTTHHHHEEEEEECS.......EEEETTSBB-SSEEEEEE CS
                               TGS   1 irvyt..PdGkvpd....lprgatveDfAykIhrslakkfiyAlVnG.......qrvgldhvLedgdvveIv 59 
                                       ir+yt  P+G+v +    l++gatv+D+A +Ih+sl + f+yA+++G       +rvgldh+L+dgd+veI 
  gi|385805444|ref|YP_005841842.1| 316 IRIYTkqPNGDVAKkplvLKNGATVRDVASSIHSSLEEFFKYAKIWGksakypgERVGLDHELQDGDIVEIY 387
                                       89***9999***99********************************************************96 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 !   66.1   3.8   1.7e-21   2.4e-18       1     106 []     204     315 ..     204     315 .. 0.86

  Alignments for each domain:
  == domain 1  score: 66.1 bits;  conditional E-value: 1.7e-21
                      MMR_HSR1_Xtn   1 kgGikitstvkltkldeetvkkilkeykihnaevliredvtvDdlidviegnrvYipclyvlNKiDlis.leeldel 76 
                                       kgG++i+ + k  +   e++k+ilk+yki +a v+i+++++++d+   i g++vY p+++++NK Dli+ +ee+++ 
  gi|385805444|ref|YP_005841842.1| 204 KGGLNIILNGKIVDGRVEDIKSILKDYKIIHAVVKINGEISLEDIETSIIGSKVYRPTIITVNKSDLIDnIEEVEKE 280
                                       69999998888888888**************************************************7523444432 PP

                      MMR_HSR1_Xtn  77 are.....pnsvviSaekelnldeLkekiweeLnL 106
                                        +      + ++++S+ +++nl+++ e i+++L+L
  gi|385805444|ref|YP_005841842.1| 281 ISYiskevEGVIFTSTITNKNLEKIGELIFKSLRL 315
                                       2213344579999*******************987 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.0   1.6e-13   2.2e-10       2     102 ..      84     181 ..      83     212 .. 0.81
   2 ?   -1.7   0.0       2.2     3e+03      75     114 .]     228     267 ..     215     267 .. 0.62

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 1.6e-13
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHH.HHHHHHHHHHCTS CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseek.glgkaflaleead 77 
                                       ++ +G p +GK++L+++lt++k+++  ++  T+ ++ g +k+ +  ++l+Dtp +  + +e+  +l++++   ++ad
  gi|385805444|ref|YP_005841842.1|  84 IVMLGPPLSGKTSLLSKLTNAKVEILGYHYSTKIPQPGMLKYMDVYFQLIDTPSIPYKMDESVpWLNRTIGLARNAD 160
                                       8899*************************************9999*********643333333579999999999** PP

                                       EEEEEEETTTTCSHHHHHHHHHHHH CS
                          MMR_HSR1  78 lillvvdaseeklkpldeeleelle 102
                                       +i+lv+d s +++   +e++  +le
  gi|385805444|ref|YP_005841842.1| 161 AIILVLDGS-KNV---KEQILGYLE 181
                                       *******55.434...455555443 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.2
                                       C.TSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                          MMR_HSR1  75 e.adlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                       +  ++i  vv+++ ++++ +d e   + ++  +p+i+ +nk
  gi|385805444|ref|YP_005841842.1| 228 KdYKIIHAVVKIN-GEISLEDIETSIIGSKVYRPTIITVNK 267
                                       3356777788777.445555555555555577888888887 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 !   25.8   0.0   4.7e-09   6.5e-06       2     103 ..      83     184 ..      82     190 .. 0.84
   2 ?   -0.5   0.1      0.57   7.9e+02     106     152 ..     259     305 ..     250     309 .. 0.74

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 4.7e-09
                                       EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----.SSSSSSSHHHHHHHHHHHCT CS
                            FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGi.Yslsayseeekvardfllee 77 
                                       +++++G p +Gkt+l+ +lt+ak ++  +   t   + g lk+ +  ++++D P i Y++++      + r++ l +
  gi|385805444|ref|YP_005841842.1|  83 QIVMLGPPLSGKTSLLSKLTNAKVEILGYHYSTKIPQPGMLKYMDVYFQLIDTPSIpYKMDESVP--WLNRTIGLAR 157
                                       6899**************************************************99666655443..4578888899 PP

                                       SSSEEEEEEE.GGGHHHHHHHHHHHHH CS
                            FeoB_N  78 epdvvvnvvd.atnlernLyLtlqlle 103
                                       ++d+++ v+d ++n++ +++  l+lle
  gi|385805444|ref|YP_005841842.1| 158 NADAIILVLDgSKNVKEQILGYLELLE 184
                                       9********934567777766677766 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.57
                                       SSEEEEEETHHHHHH.TTEEE-HHHHHHHHTS-EEEEBTTTTBTHHHH CS
                            FeoB_N 106 vpvvlalnmideaek.kgieidlkkLsekLgvpvvktsakkkegieel 152
                                        p+++ +n++d +++ +++e +++ +s++++  v+ ts+ +++++e++
  gi|385805444|ref|YP_005841842.1| 259 RPTIITVNKSDLIDNiEEVEKEISYISKEVE-GVIFTSTITNKNLEKI 305
                                       6889999999988763567777788888876.4777777777777766 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   5.1e-06     0.007       5      91 ..      83     174 ..      79     203 .. 0.65
   2 ?    3.3   0.1     0.035        48      73     103 ..     285     313 ..     252     353 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.1e-06
                                       EEEEE-STTSSHHHHHHHHHHSS---..B---S..S-EEETTG...GGTT-SEEEETT-.GCCSHH...HHHHHHHH CS
                             SRPRB   5 avllvGlsdsGKTslftrLttdsvkk..tvtSq..essaalkvksekgskltliDfPGh.eklrqk...lleklkak 73 
                                       +++++G+  sGKTsl+ +Lt+ +v+      S    +   lk+    +  ++liD P    k+      l  ++   
  gi|385805444|ref|YP_005841842.1|  83 QIVMLGPPLSGKTSLLSKLTNAKVEIlgYHYSTkiPQPGMLKY---MDVYFQLIDTPSIpYKMDESvpwLNRTIGLA 156
                                       799*****************99665311233332122334555...8999999999974234443322255666667 PP

                                       GGEEEEEEEEETTS-HHH CS
                             SRPRB  74 sslkglvfvvDStidpke 91 
                                       +++ +++ v+D + + ke
  gi|385805444|ref|YP_005841842.1| 157 RNADAIILVLDGSKNVKE 174
                                       779999999998877664 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.035
                                       HGGEEEEEEEEETTS-HHHHHHHHHHHHHHH CS
                             SRPRB  73 ksslkglvfvvDStidpkevkevAEllyeil 103
                                       ++++ g++f   Sti +k+++++ El+++ l
  gi|385805444|ref|YP_005841842.1| 285 SKEVEGVIFT--STITNKNLEKIGELIFKSL 313
                                       5669999995..*************988755 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   2.5e-05     0.035       3      98 ..      83     191 ..      81     205 .. 0.75
   2 ?    5.4   1.2      0.01        14      83     140 ..     252     308 ..     220     311 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.5e-05
                         PduV-EutP   3 killiGkvgsGKttLtqalkg...eelkYkkt.........qaiefsdeviDtPG...eylenrklysalivtsaea 64 
                                       +i+++G+  sGKt+L  +l++   e l Y+           ++++++ ++iDtP    +  e+  + +  i ++ +a
  gi|385805444|ref|YP_005841842.1|  83 QIVMLGPPLSGKTSLLSKLTNakvEILGYHYStkipqpgmlKYMDVYFQLIDTPSipyKMDESVPWLNRTIGLARNA 159
                                       7999****************96664556764312332222257899999****98422334566789999999**** PP

                         PduV-EutP  65 dvialvqdateeesvfppgfasvfnkeviGiitk 98 
                                       d i lv+d +++ +    g+ ++++k   Gi+tk
  gi|385805444|ref|YP_005841842.1| 160 DAIILVLDGSKNVKEQILGYLELLEKA--GIMTK 191
                                       ********9999988888888888875..88887 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.01
                         PduV-EutP  83 gfasvfnkeviGiitkidlaedeenieaveelLksaGaekifevsavekegieellky 140
                                        + s + +++i  + k dl ++ e++e+  ++++   +e ++ +s+++++++e++ + 
  gi|385805444|ref|YP_005841842.1| 252 IIGSKVYRPTIITVNKSDLIDNIEEVEKEISYIS-KEVEGVIFTSTITNKNLEKIGEL 308
                                       5667789999999*******55555555444444.457888889*********99765 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.46   6.3e+02       6      27 ..      84     105 ..      82     117 .. 0.81
   2 !    7.3   0.0    0.0022         3      68     123 ..     126     188 ..      99     190 .. 0.79
   3 !    7.3   0.1    0.0022       3.1     119     188 ..     255     309 ..     226     352 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.46
                                       EEEEESTTSSHHHHHHHHHHHT CS
                          GTP_EFTU   6 igiighvDhGKtTLtdrLlykt 27 
                                       i+++g   +GKt+L+ +L+ ++
  gi|385805444|ref|YP_005841842.1|  84 IVMLGPPLSGKTSLLSKLTNAK 105
                                       566777779********99765 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0022
                                       SSEEEEEEEESS.......SGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTT CS
                          GTP_EFTU  68 kkylinliDtPG.......HvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegv 123
                                        +  ++liDtP         v + + +i  +r +D  +lv+d ++ v++q    l+l+ k g+
  gi|385805444|ref|YP_005841842.1| 126 MDVYFQLIDTPSipykmdeSVPWLNRTIGLARNADAIILVLDGSKNVKEQILGYLELLEKAGI 188
                                       566677777775444333357789999999********************9999998887766 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0022
                                       HHTTTEEEEEEESCGST..HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHH CS
                          GTP_EFTU 119 lkegvpiivfiNKmDrl..kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktlleal 188
                                       +k+  p+i+ +NK D +  ++e+++ ++ +++++            +      v+f+S +++++++++ e +
  gi|385805444|ref|YP_005841842.1| 255 SKVYRPTIITVNKSDLIdnIEEVEKEISYISKEV------------E-----GVIFTSTITNKNLEKIGELI 309
                                       5555679********9855444444444444444............2.....25555555555555554444 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0001      0.14      11      64 ..      78     134 ..      71     173 .. 0.87
   2 ?    0.5   0.0      0.27   3.7e+02     118     145 ..     261     288 ..     251     311 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0001
                                       .TTEEEEEEEESTTSSHHHHHHHHHHSSCEE...CSSSSSEEEEEEEETTEEEEEEE CS
                               Arf  11 kkkelrilllGLDnaGKtTilkklkleelvt...tvPTigfnveeleiknlkftvwD 64 
                                       k+ +++i++lG   +GKt +l kl++ +++    +  T  ++   l++ ++ f++ D
  gi|385805444|ref|YP_005841842.1|  78 KEGDAQIVMLGPPLSGKTSLLSKLTNAKVEIlgyHYSTKIPQPGMLKYMDVYFQLID 134
                                       566799******************999887655578888888888888888888877 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.27
                                       EEEEEE-TTSTTSS-HHHHHHHTTGGGS CS
                               Arf 118 llvlaNKqDlpealseeelrellgleel 145
                                        ++  NK Dl + ++e e + +   +e+
  gi|385805444|ref|YP_005841842.1| 261 TIITVNKSDLIDNIEEVEKEISYISKEV 288
                                       68999*****999988776555444444 PP

>> Ub-RnfH  RnfH family Ubiquitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0     4e-05     0.056      17      72 ..     330     388 ..     316     390 .] 0.68

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4e-05
                           Ub-RnfH  17 e.levpegttveeAie..aSgilekfpeidlekakvGifgkavkldavLqegDRvEiYR 72 
                                       + l +++g+tv++     +S + e f+  ++  ++    g++v ld++Lq+gD vEiY 
  gi|385805444|ref|YP_005841842.1| 330 KpLVLKNGATVRDVASsiHSSLEEFFKYAKIWGKSAKYPGERVGLDHELQDGDIVEIYS 388
                                       44889999999997542235566666555665555555566688**************5 PP

>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.044        61      26      55 ..     181     218 ..     163     233 .. 0.78
   2 ?    7.1   0.0    0.0064       8.8      16      70 ..     332     386 ..     316     388 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.044
                                       HHHHHHHHHTCHHG........TTTTEEEEETTEEEGC CS
                              ThiS  26 elleaLgerypela........lerrvavavNgeivpr 55 
                                       elle+ g + ++ +        ++ ++++ +Ng+iv+ 
  gi|385805444|ref|YP_005841842.1| 181 ELLEKAGIMTKKPKgsieikkaSKGGLNIILNGKIVDG 218
                                       677777766666667777889988************97 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0064
                                       EEESSTSBHHHHHHHHHHHTCHHG...TTTTEEEEETTEEEGCCTTTSB--TTCEEEE CS
                              ThiS  16 lelaegstvaelleaLgerypela...lerrvavavNgeivprlwldtelkdgDevai 70 
                                       l+l++g+tv+++  ++    +e +    + +  + + ge v     d+el+dgD v+i
  gi|385805444|ref|YP_005841842.1| 332 LVLKNGATVRDVASSIHSSLEEFFkyaKIWGKSAKYPGERVGL---DHELQDGDIVEI 386
                                       6677777777777777766666666665556667777777777...**********98 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.069        95      97     122 ..      79     104 ..      48     116 .. 0.77
   2 ?    9.1   0.3    0.0008       1.1      48      98 ..     260     310 ..     229     316 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.069
                                       CTTSEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  97 lkdktsvlvGqSGvGKStLinallpe 122
                                         d  +v++G+   GK++L+ +l++ 
  gi|385805444|ref|YP_005841842.1|  79 EGDAQIVMLGPPLSGKTSLLSKLTNA 104
                                       445778999*************9975 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0008
                                       EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCT CS
                       RsgA_GTPase  48 epvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkellk 98 
                                       + +i +nK Dl+++ ee+e+  + +++    v+++s+ t+++le++ el+ 
  gi|385805444|ref|YP_005841842.1| 260 PTIITVNKSDLIDNIEEVEKEISYISKEVEGVIFTSTITNKNLEKIGELIF 310
                                       56899***********99999988888888899***********9988765 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 ?   11.2   0.0   0.00024      0.33       2      25 ..      84     107 ..      83     137 .. 0.85
   2 ?   -1.7   0.0       2.4   3.3e+03      78      90 ..     157     170 ..     143     187 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00024
                                       EEEESSTTSSHHHHHHCHCT-CCC CS
                               Roc   2 vvlvGdsgvGKtsllkrfvedkfs 25 
                                       +v++G   +GKtsll+++++ k++
  gi|385805444|ref|YP_005841842.1|  84 IVMLGPPLSGKTSLLSKLTNAKVE 107
                                       89****************998774 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.4
                                       CTSCEEEEEEE.GH CS
                               Roc  78 reaalailvyd.sr 90 
                                       r+a+++ilv+d s+
  gi|385805444|ref|YP_005841842.1| 157 RNADAIILVLDgSK 170
                                       78888999998533 PP

>> YchF-GTPase_C  Protein of unknown function (DUF933)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0     0.001       1.4      16      43 ..     333     360 ..     319     367 .. 0.88
   2 ?    1.9   0.1      0.18   2.5e+02      66      81 ..     371     386 ..     365     388 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.001
                     YchF-GTPase_C  16 tikkgttapqaAgviHsDfekgFiraev 43 
                                        +k+g+t+ + A  iHs +e+ F  a++
  gi|385805444|ref|YP_005841842.1| 333 VLKNGATVRDVASSIHSSLEEFFKYAKI 360
                                       6799*******************99987 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.18
                     YchF-GTPase_C  66 legkdyvvqdgDiilf 81 
                                       + g d+ +qdgDi+++
  gi|385805444|ref|YP_005841842.1| 371 RVGLDHELQDGDIVEI 386
                                       568899*******976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       869  (0.048469); expected 358.6 (0.02)
Passed bias filter:                      591  (0.0329634); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 2550.43
//
Query:       gi|385805445|ref|YP_005841843.1|  [L=127]
Description: hypothetical protein FFONT_0401 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.5e-16   60.0   1.5    3.7e-16   59.5   1.5    1.3  1  Trm112p      Trm112p-like protein
  ------ inclusion threshold ------
       0.55   10.5   5.0       0.59   10.4   0.1    2.8  3  zf-RING_7    C4-type zinc ribbon domain
        1.3   10.0   6.0         13    6.9   0.0    3.4  3  zf-C2H2_4    C2H2-type zinc finger
        1.8    8.4   7.3        1.3    8.9   2.7    2.3  2  zf-RING_4    RING/Ubox like zinc-binding domain
          9    6.2   9.6         10    6.0   1.2    2.7  3  Prok-RING_4  Prokaryotic RING finger family 4


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 !   59.5   1.5     1e-19   3.7e-16       5      68 .]       1      82 [.       1      82 [. 0.91

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 1e-19
                                      CCC-B-TTTHH.C--HHHHHHHHHTT---S-SS----S.................CHHTTEECCCCEEEETTTTEEEEE CS
                           Trm112p  5 lniLaCpackg.pLdwealvevaalglnelpkekpedy.................ellleldieegeLvCpncgraYpI 65
                                      ++iLaCp+ck+ pL++ ++  v++++  + +++++e y                 e++++ +ie+g+L+Cp cgr+YpI
  gi|385805445|ref|YP_005841843.1|  1 MDILACPICKKfPLELIVIESVEKERKLSQKAPLCELYcayrgdfiknlttpppcEECFKREIETGVLYCPGCGRWYPI 79
                                      69**********9988888888876666688899999999***************99********************** PP

                                      ETT CS
                           Trm112p 66 kdG 68
                                       +G
  gi|385805445|ref|YP_005841843.1| 80 ING 82
                                      *98 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.45   1.6e+03      23      30 ..       3      10 ..       2      12 .. 0.77
   2 ?    0.9   0.2      0.15   5.5e+02      21      29 ..      50      58 ..      44      58 .. 0.73
   3 ?   10.4   0.1   0.00017      0.59      17      32 ..      63      76 ..      60      76 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.45
                                      -EE-TTT- CS
                         zf-RING_7 23 vvtCpeCG 30
                                      +  Cp C 
  gi|385805445|ref|YP_005841843.1|  3 ILACPICK 10
                                      567**995 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.15
                                      TB-EE-TTT CS
                         zf-RING_7 21 devvtCpeC 29
                                         + C+eC
  gi|385805445|ref|YP_005841843.1| 50 TTPPPCEEC 58
                                      55688**** PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00017
                                      HCCSTB-EE-TTT--E CS
                         zf-RING_7 17 lragdevvtCpeCGRI 32
                                      +  g  v +Cp CGR+
  gi|385805445|ref|YP_005841843.1| 63 IETG--VLYCPGCGRW 76
                                      5555..99*******6 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   0.2     0.041   1.5e+02       2       9 ..       5      11 ..       4      14 .. 0.76
   2 ?    0.4   0.5      0.47   1.7e+03       2       8 ..      54      60 ..      53      62 .. 0.76
   3 ?    6.9   0.0    0.0038        13       2      11 ..      69      78 ..      68      87 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.041
                         zf-C2H2_4  2 kCpiCgks 9 
                                       CpiC k 
  gi|385805445|ref|YP_005841843.1|  5 ACPIC-KK 11
                                      6****.44 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.47
                         zf-C2H2_4  2 kCpiCgk 8 
                                      +C+ C k
  gi|385805445|ref|YP_005841843.1| 54 PCEECFK 60
                                      6999976 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0038
                         zf-C2H2_4  2 kCpiCgksFs 11
                                      +Cp Cg++++
  gi|385805445|ref|YP_005841843.1| 69 YCPGCGRWYP 78
                                      7*******97 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 ?    1.3   0.2     0.084     3e+02      39      45 ..       5      11 ..       3      12 .. 0.84
   2 ?    8.9   2.7   0.00036       1.3      25      47 ..      55      77 ..      54      78 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.084
                         zf-RING_4 39 rCPaCre 45
                                       CP C++
  gi|385805445|ref|YP_005841843.1|  5 ACPICKK 11
                                      5999996 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00036
                         zf-RING_4 25 ClfCyhrileeeegrCPaCreeY 47
                                      C  C++r +e+    CP+C + Y
  gi|385805445|ref|YP_005841843.1| 55 CEECFKREIETGVLYCPGCGRWY 77
                                      99*****************8877 PP

>> Prok-RING_4  Prokaryotic RING finger family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.3    0.0051        18      32      38 ..       5      11 ..       1      13 [. 0.81
   2 ?   -1.7   0.1      0.79   2.8e+03      32      37 ..      31      36 ..      24      40 .. 0.71
   3 ?    6.0   1.2    0.0029        10      21      38 ..      55      75 ..      54      78 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0051
                       Prok-RING_4 32 sCPlCqr 38
                                      +CP+C++
  gi|385805445|ref|YP_005841843.1|  5 ACPICKK 11
                                      8****96 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.79
                       Prok-RING_4 32 sCPlCq 37
                                        PlC+
  gi|385805445|ref|YP_005841843.1| 31 KAPLCE 36
                                      679996 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.0029
                       Prok-RING_4 21 CkeCfdskdls...sCPlCqr 38
                                      C+eCf+ +  +    CP C r
  gi|385805445|ref|YP_005841843.1| 55 CEECFKREIETgvlYCPGCGR 75
                                      ******996655889**9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       881  (0.0491383); expected 358.6 (0.02)
Passed bias filter:                      616  (0.0343577); 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):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 853.93
//
Query:       gi|385805446|ref|YP_005841844.1|  [L=452]
Description: phosphoglucomutase/phosphomannomutase alpha/beta/alpha domain I [Fervidicoccus fontis Kam940]
Scores for complete 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  137.2   0.0    6.7e-40  136.0   0.0    1.6  1  PGM_PMM_I    Phosphoglucomutase/phosphomannomutase, alpha/bet
    2.2e-25   89.3   0.0    5.1e-25   88.1   0.0    1.6  2  PGM_PMM_II   Phosphoglucomutase/phosphomannomutase, alpha/bet
    1.2e-20   73.8   0.0    2.2e-20   73.0   0.0    1.5  1  PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/bet
    3.7e-12   46.2   0.0    1.2e-11   44.6   0.0    1.9  1  PGM_PMM_IV   Phosphoglucomutase/phosphomannomutase, C-termina


Domain annotation for each model (and alignments):
>> PGM_PMM_I  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.0   0.0   1.5e-43   6.7e-40       2     133 ..       3     131 ..       2     134 .. 0.96

  Alignments for each domain:
  == domain 1  score: 136.0 bits;  conditional E-value: 1.5e-43
                                       GGBBTTCEEEECCHCTBSCCHHHHHHHHHHHHCHHCSTS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEEEB- CS
                         PGM_PMM_I   2 qkfgtsGlRgkvgegeltpelveklgqaiaeylkaeakkkkvvvGrDtRvssrelaealaaglaanGvevillgllp 78 
                                       ++fgt+G+R kv+ +el++e++ k++qai+e + +   ++  ++GrD R+ ++ + +a+++g++ +G+ v+++gl++
  gi|385805446|ref|YP_005841844.1|   3 KIFGTDGIRLKVK-NELQAEFLVKISQAICEEFGE---RSVFLLGRDVRYGGELIRHAIISGFLTSGCRVYDAGLIT 75 
                                       68***********.66******************9...5************************************** PP

                                       HHHHHHHHHHCC.ECEEEEE--TTS-TTCCCEEEEETTTCE--CHHHHHHHHHHCC CS
                         PGM_PMM_I  79 tPavsfairklk.adagimitaSHnppeyngiKvylsnGgpispeveekIeaiiek 133
                                       tPa+++ i++ + +d+g+mitaSHnppeyngiKv++s+G++i++e+e++Ie+i+ +
  gi|385805446|ref|YP_005841844.1|  76 TPALQYVIKNEGfFDGGVMITASHNPPEYNGIKVIDSDGIEIPREKENEIEKIYLE 131
                                       **********7789**************************************9876 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 !   88.1   0.0   1.1e-28   5.1e-25       2     101 ..     155     253 ..     154     255 .. 0.97
   2 ?   -3.4   0.0       3.5   1.6e+04      33      48 ..     289     304 ..     287     306 .. 0.78

  Alignments for each domain:
  == domain 1  score: 88.1 bits;  conditional E-value: 1.1e-28
                                       HHHHHGGGTS-HHHHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-EEEES-----TT-TTSS----TT-TTTTHHHHG CS
                        PGM_PMM_II   2 aYiealkekvdseaikksglkvvidplhGaggeilkellkelgvdvvelnaepdpdfptkapnpeekealkllielv 78 
                                       +Y+e+++++vd e+ik++++kvv+d ++ +g+ ++++l k lg ++++ln++ dpdf+++ p+p++ e+l + +++v
  gi|385805446|ref|YP_005841844.1| 155 KYLEGILDNVDDEIIKRRNFKVVVDGANSVGSLVIPKLVKLLGGKPISLNSHLDPDFSGRLPEPTP-ETLFDTSNVV 230
                                       8*****************************************************************.9999999*** PP

                                       GGGG-SEEEEE-TTS-BEEEEET CS
                        PGM_PMM_II  79 kkegadlglafDgDaDRlgvvde 101
                                       k+ +adlg+a+DgDaDR ++ de
  gi|385805446|ref|YP_005841844.1| 231 KAVNADLGIAVDGDADRSIFLDE 253
                                       ********************998 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3.5
                                       HHHHHHHHHHTT-EEE CS
                        PGM_PMM_II  33 geilkellkelgvdvv 48 
                                       + +++ellk+ g+dv+
  gi|385805446|ref|YP_005841844.1| 289 SYFIEELLKKRGIDVI 304
                                       5688999999888875 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 !   73.0   0.0   4.8e-24   2.2e-20       2     111 ..     260     369 ..     259     372 .. 0.91

  Alignments for each domain:
  == domain 1  score: 73.0 bits;  conditional E-value: 4.8e-24
                                       HHHHHHHHHHHHHCH..CSTTTCEEEEETTS-THHHHHHHHTT-EEEEESSSCHHHHHHHHHTTECEEEETTCEEEE CS
                       PGM_PMM_III   2 gdqllallakyllee..klkpgagvvktvmtslalervakklgiklvetkvGdkyvleemkeegavlGgEeSghiif 76 
                                       gd+++++l+ yl e+  +l p+ +v + +++s  +e+ +kk+gi ++ +kvG+  +++++k+eg +lG+Ee+g+i++
  gi|385805446|ref|YP_005841844.1| 260 GDKTAVILSIYLSEKnpEL-PK-KVYTGISSSYFIEELLKKRGIDVIWMKVGSVDIARKLKKEGGLLGFEENGGIMY 334
                                       9***********8875333.34.5***************************************************** PP

                                       TTTBSS--HHHHHHHHHHHHHHHTS-HHHHHHHHH CS
                       PGM_PMM_III  77 ldeattkDGilaallvleilaetgkslselleell 111
                                       +++++ +D+ +a +l+le+++ + k++sel++  +
  gi|385805446|ref|YP_005841844.1| 335 PKHQYVRDAGMALALMLEVMSAERKKISELYSIYP 369
                                       *******************************4444 PP

>> PGM_PMM_IV  Phosphoglucomutase/phosphomannomutase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6   0.0   2.7e-15   1.2e-11      24      61 ..     402     438 ..     363     450 .. 0.78

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 2.7e-15
                                       HCCCCCCCCGCCEEEE.EEEETTCCEEEEEEEES.SHHH CS
                        PGM_PMM_IV  24 sikeglkilledGrrlavRpSGTepllrvyvEak.sdee 61 
                                         ++g+k+l ed ++l vRpSGTep+lrv+vE+k    +
  gi|385805446|ref|YP_005841844.1| 402 IDIDGVKVLQEDSWFL-VRPSGTEPVLRVMVESKiQN-K 438
                                       6789************.****************9444.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); 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: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 2999.91
//
Query:       gi|385805447|ref|YP_005841845.1|  [L=224]
Description: hexulose-6-phosphate synthase (D-arabino 3-hexulose-6-phosphate formaldehyde lyase) [Fervidicoccus fontis Kam940]
Scores for 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   86.4   1.8    2.3e-24   86.2   1.8    1.0  1  OMPdecase       Orotidine 5'-phosphate decarboxylase / HUMPS 
    0.00027   20.7   0.8    0.00065   19.5   0.4    1.7  2  QRPTase_C       Quinolinate phosphoribosyl transferase, C-ter
    0.00028   20.4   0.4    0.00052   19.5   0.4    1.5  1  PcrB            PcrB family
     0.0011   18.4   1.1     0.0025   17.2   0.4    1.8  2  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
     0.0014   17.9   0.6     0.0025   17.1   0.3    1.6  1  NanE            Putative N-acetylmannosamine-6-phosphate epim
     0.0037   17.0   0.1     0.0056   16.4   0.1    1.4  1  4HFCP_synth     4-HFC-P synthase
  ------ inclusion threshold ------
       0.01   15.2   0.3      0.019   14.3   0.3    1.4  1  TMP-TENI        Thiamine monophosphate synthase


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 !   86.2   1.8   9.1e-28   2.3e-24       2     224 ..      11     218 ..      10     219 .. 0.89

  Alignments for each domain:
  == domain 1  score: 86.2 bits;  conditional E-value: 9.1e-28
                                       EEEEEE-SSSHHHHHHHHHHHGG..GSSEEEEEHHHHHHHTHH.HHTHHHHHHHHHTSEEEEEEEE-S-HHHHHHHH CS
                         OMPdecase   2 nLclalDvatarelleladkvgp..sivvlKthydlvegwgfegtgaklaalarkhgflifeDrKfaDIGntvekqa 76 
                                        L++a+Dv++ +++l ++++v +    ++++++++l++++g   + +++++++  + ++i++D+K++D+G+ +++ a
  gi|385805447|ref|YP_005841845.1|  11 YLQVAIDVTDLKKALFIVRQVIDlsDKIIIEVGTPLIKSYG--MLPVEIISYLYPE-KIILADMKTMDVGYLEANLA 84 
                                       69*******************9987889*************..7788999999988.5******************* PP

                                       HSTCHHHHTTESEEEEEGTGHHHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHHHSHHHHHHHHHHHHHHHTTES CS
                         OMPdecase  77 tagsarikewadivtvhavaGkasvkalaeaaekwgnrgllilaqmsskgnlmlqekgytqacveaarehkaedfvm 153
                                             +k++a i tv ++a+ ++++++++a  +++  + ++++ ++ k+ +++++ ++++  v+ +  h+      
  gi|385805447|ref|YP_005841845.1|  85 ------FKSGATISTVLGAADNETIQGALKASLEYN--KFIQVDLINVKDLASRAR-EVAELGVHIVGLHA------ 146
                                       ......9****************************8..****************99.77777777777777...... PP

                                       EEECCCHTHHHHHHTTCSCEEEHHHTT.....EEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSSSHHHHHHH CS
                         OMPdecase 154 Gfvaqetlnateedaddfihltpgigl.....eqggdgkgqqyntpekligiagadiiivGRgIlkagdpveeaer 224
                                       G+  q +++ ++++  d+i l + i+         + ++g+++ + + +++ +gadii+vG +I+ ++dp+e a+ 
  gi|385805447|ref|YP_005841845.1| 147 GIDQQTNKK-LRAI--DMIELLKEIKNavektSLVSIAGGIKQGELKRFAE-NGADIIVVGGAITSSEDPREVAKN 218
                                       776666655.5555..7777777777667777789*******999999988.99******************9986 PP

>> QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.75   1.9e+03      64      88 ..      19      43 ..      14      57 .. 0.79
   2 !   19.5   0.4   2.5e-07   0.00065      75     161 ..     109     209 ..      90     212 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.75
                                      SSHHHHHHHHHHHHTTTSEEEEEES CS
                         QRPTase_C 64 gsiveavksvreavdkevkieveve 88
                                       ++++a+  vr+++d   ki +ev 
  gi|385805447|ref|YP_005841845.1| 19 TDLKKALFIVRQVIDLSDKIIIEVG 43
                                      5678888888888888878777765 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 2.5e-07
                                       HHHTTTSEEEEEESSHHH....HHHHHHHT-SEEEE....ES--HHHHH..HHHHHHHHHSTT....SEEEEESS-- CS
                         QRPTase_C  75 eavdkevkieveveslee....leevleaeadiimL....Dnfsveelk..kaveelkeknkr....vlievSGgvt 137
                                       + ++ ++ i+v+  ++++    ++ev+e ++ i+ L    D+ + ++l+  +++e+lke+++      l++ +Gg++
  gi|385805447|ref|YP_005841845.1| 109 ASLEYNKFIQVDLINVKDlasrAREVAELGVHIVGLhagiDQQTNKKLRaiDMIELLKEIKNAvektSLVSIAGGIK 185
                                       455555447777666554111267889999999987333355555555522234555544444444589******** PP

                                       TTTHHHHHCTT-SEEEECHHCHTB CS
                         QRPTase_C 138 lenveeyaksgvdvisvgalthsv 161
                                       + +++ +a+ g d+i vg +++s+
  gi|385805447|ref|YP_005841845.1| 186 QGELKRFAENGADIIVVGGAITSS 209
                                       *****************9888775 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.4     2e-07   0.00052     166     216 ..     160     211 ..     154     224 .] 0.77

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2e-07
                                       S-HHHHHHHHHHHSSSEEE.EESS--SHHHHHHHHCC.SSEEEE-CHHHHHHH CS
                              PcrB 166 edveevialkkklekarli.vGGGirsaEkAkevvea.ADvivvGnvveekde 216
                                       + +e+++++k+ +ek+ l+ + GGi+++E   + +e  AD+ivvG ++  +++
  gi|385805447|ref|YP_005841845.1| 160 DMIELLKEIKNAVEKTSLVsIAGGIKQGELK-RFAENgADIIVVGGAITSSED 211
                                       567999*******999987579******985.566666**********98773 PP

>> Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       0.2   5.1e+02      43     100 ..     102     158 ..      98     169 .. 0.62
   2 !   17.2   0.4   9.9e-07    0.0025     153     197 ..     162     206 ..     156     207 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.2
                                       -B-HHHHHHHGGGE-S-EEEEEE.SSSHHHCHHHHHHCT-SEEEEE-ST-TTHHHHHHH CS
                    Ribul_P_3_epim  43 tigplvvealrkltelpldvHLm.veevdrivpefaeagasiisvHaEalehlkrtiqe 100
                                       ti+ +   +l+  +  +++v L+ v+++   + e ae+g +i+ +Ha   +++++ ++ 
  gi|385805447|ref|YP_005841845.1| 102 TIQGALKASLEYNK--FIQVDLInVKDLASRAREVAELGVHIVGLHAGIDQQTNKKLRA 158
                                       55555555555444..3444443377888888888888888888888755554444444 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 9.9e-07
                                       HHHHHHHHHHHT---EEEEESS--TTTCHHHHHHT--EEEESHHH CS
                    Ribul_P_3_epim 153 ikkvrklidekeldlkievDGGvkldnieqiaeagadvlVagsav 197
                                       i+ ++++ ++ e++  + + GG+k+   ++ ae+gad++V+g a+
  gi|385805447|ref|YP_005841845.1| 162 IELLKEIKNAVEKTSLVSIAGGIKQGELKRFAENGADIIVVGGAI 206
                                       4445555555556999**************************997 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 !   17.1   0.3   9.6e-07    0.0025     106     180 ..     132     210 ..      97     223 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 9.6e-07
                                       HHHHHTT-SEEE-T..TTTSSTTS-.SS--HHHHHHHHHTT--...EEEES---SHHHHHHHHTT--SEEEE-HHHH CS
                              NanE 106 lvakklGvdivGtt..lsGytkeeekaepDfalvkalseaglk...viaeGrintPekakkaieiGvdavvvGsait 177
                                           +lGv ivG    +   t+++ +a + ++l+k++++a  k   v + G i+  e+ k+  e G+d +vvG+ait
  gi|385805447|ref|YP_005841845.1| 132 REVAELGVHIVGLHagIDQQTNKKLRAIDMIELLKEIKNAVEKtslVSIAGGIKQGEL-KRFAENGADIIVVGGAIT 207
                                       456789*****95411444455555566778899999887554445666788888765.8899************** PP

                                       -HH CS
                              NanE 178 rle 180
                                         e
  gi|385805447|ref|YP_005841845.1| 208 SSE 210
                                       765 PP

>> 4HFCP_synth  4-HFC-P synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   2.2e-06    0.0056     135     214 ..     131     211 ..      65     223 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.2e-06
                                       HHHHHHHT-SEEEEE-.SS-SS--HHHHS-HHHHHHHHHHHHHTT-EEEE-SS--GGGHHHHHHTT-SEEEESGGGB CS
                       4HFCP_synth 135 lelaaeagaagvmlDT.adKdgkslldflseeelaefveeareaglltaLAGslkledlpaLkklkpdilGvRgavC 210
                                        + +ae g+++v l   +d + ++ l+ +++ el + +++a e+  l+ +AG +k+ +l++ ++ ++di+ v ga++
  gi|385805447|ref|YP_005841845.1| 131 AREVAELGVHIVGLHAgIDQQTNKKLRAIDMIELLKEIKNAVEKTSLVSIAGGIKQGELKRFAENGADIIVVGGAIT 207
                                       45556667777755541455566788999999999999**************************************9 PP

                                       TTSS CS
                       4HFCP_synth 211 eegd 214
                                       +++d
  gi|385805447|ref|YP_005841845.1| 208 SSED 211
                                       7665 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.3   7.4e-06     0.019     108     181 .]     130     206 ..     122     206 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.4e-06
                          TMP-TENI 108 eaeeaealgadYigvGpifpTdtKkda.eplgleglkelaeale.iPvvai.GGitlenvaevleagadgvavvsai 181
                                        a+e+++lg+  +g+ +    +t k+  +   +e+lke+++a+e   +v i GGi++ ++++ +e gad + v  ai
  gi|385805447|ref|YP_005841845.1| 130 RAREVAELGVHIVGLHAGIDQQTNKKLrAIDMIELLKEIKNAVEkTSLVSIaGGIKQGELKRFAENGADIIVVGGAI 206
                                       38899999999999988888888777747777899*********756666559******************997776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1578.04
//
Query:       gi|385805448|ref|YP_005841846.1|  [L=453]
Description: RuvB-like 2 [Fervidicoccus fontis Kam940]
Scores for complete 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-141  470.1   1.4   6.3e-141  469.6   1.4    1.2  1  TIP49            TIP49 P-loop domain
    5.2e-20   71.3   0.4    6.8e-19   67.8   0.6    2.5  2  TIP49_C          TIP49 AAA-lid domain
    1.6e-10   41.6   2.1    4.8e-08   33.5   0.1    2.8  2  AAA              ATPase family associated with various cellul
    7.5e-08   32.3   0.4    2.4e-05   24.1   0.1    2.5  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    5.6e-07   29.9   0.2      0.016   15.5   0.0    2.4  2  AAA_22           AAA domain
    3.5e-05   24.2   0.3    0.00051   20.5   0.3    2.4  1  AAA_16           AAA ATPase domain
    3.7e-05   23.3   0.3    0.00038   20.0   0.0    2.1  2  AAA_7            P-loop containing dynein motor region
    0.00024   20.6   0.2    0.00068   19.0   0.1    1.8  2  DnaB_C           DnaB-like helicase C terminal domain
    0.00037   20.3   0.0    0.00081   19.2   0.0    1.5  1  IstB_IS21        IstB-like ATP binding protein
     0.0015   19.0   0.1     0.0031   18.0   0.1    1.5  1  ABC_tran         ABC transporter
     0.0016   17.6   2.0      0.086   11.9   0.1    2.6  2  T2SSE            Type II/IV secretion system protein
     0.0017   18.1   0.2      0.024   14.3   0.1    2.3  2  Sigma54_activat  Sigma-54 interaction domain
     0.0024   18.4   0.4     0.0024   18.4   0.4    1.7  2  AAA_23           AAA domain
     0.0043   16.5   0.7     0.0089   15.5   0.1    1.8  1  PhoH             PhoH-like protein
     0.0048   17.1   0.1      0.012   15.9   0.1    1.7  1  AAA_28           AAA domain
     0.0049   16.9   1.0      0.018   15.0   0.2    2.2  2  ResIII           Type III restriction enzyme, res subunit
      0.006   16.8   0.1      0.015   15.4   0.1    1.8  1  AAA_33           AAA domain
     0.0086   16.6   1.1       0.09   13.3   0.1    3.1  3  AAA_18           AAA domain
      0.009   16.0   0.4       0.07   13.1   0.1    2.5  3  AAA_5            AAA domain (dynein-related subfamily)
  ------ inclusion threshold ------
      0.013   15.1   0.0      0.029   13.9   0.0    1.6  1  AAA_25           AAA domain
      0.018   14.4   0.0       0.05   13.0   0.0    1.7  1  IPT              Isopentenyl transferase
       0.02   14.3   0.4      0.093   12.1   0.1    2.0  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.021   15.2   0.0      0.055   13.9   0.0    1.7  1  RNA_helicase     RNA helicase
      0.034   14.2   0.1       0.07   13.1   0.1    1.5  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.042   14.0   0.2       0.22   11.6   0.2    2.3  1  AAA_2            AAA domain (Cdc48 subfamily)
      0.044   13.7   0.0       0.14   12.1   0.0    1.8  2  NACHT            NACHT domain
        0.1   11.8   0.0       0.21   10.8   0.0    1.5  2  DUF2075          Uncharacterized conserved protein (DUF2075)
       0.15   11.2   0.1       0.33   10.0   0.1    1.5  1  Parvo_NS1        Parvovirus non-structural protein NS1
       0.46   10.8   1.9        7.9    6.8   1.9    2.3  1  AAA_19           AAA domain


Domain annotation for each model (and alignments):
>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  469.6   1.4    1e-143  6.3e-141       1     350 [.      15     365 ..      15     366 .. 0.96

  Alignments for each domain:
  == domain 1  score: 469.6 bits;  conditional E-value: 1e-143
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49   1 rislhshikgLGldedgeaekeeeglvGqkkareaagvivelikekklaGravLlaGpsgtGktalaiaiskelged 77 
                                       ri+ hshikgLGlde+g+a++ ++glvGq++areaag++v++ike+k+aGr++L++Gp+gtGktala+ai++elged
  gi|385805448|ref|YP_005841846.1|  15 RIGFHSHIKGLGLDENGKAKQIADGLVGQIEAREAAGIVVQMIKEGKMAGRGILFVGPTGTGKTALAVAIARELGED 91 
                                       799************************************************************************** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-S-EEEEEEEEEEE...-SSS-...TTS--EEEEEE-SS-E CS
                             TIP49  78 vpfvalsgsevyslevkktevltqalrksigvrikeekevleGevveleveeaenpls.kekkikevkitlktakee 153
                                       +pfv ++gse+ys+e+kkte+l+q+lrksigvrike+++v+eG v el++ + +np++ + +  +e+kitl+t++e+
  gi|385805448|ref|YP_005841846.1|  92 TPFVEFTGSEIYSTEMKKTEMLMQTLRKSIGVRIKEKRTVYEGAVKELKIRRLRNPYNpYMMIPREAKITLETKDEN 168
                                       **********************************************************999999************* PP

                                       EEEEE-HHHHHHHHHHT--TT-EEEEETTT--EEE-SSS-SS---..---S--------S---S----XXXXXXXXX CS
                             TIP49 154 kklklgskiaeellkekvkegDviviekesGkvkklGrsearake..fDiekdefvelPkGevekkkevvqevtLhd 228
                                        +l+++++i+++ll+  +k+gDvi i++++G++ k Gr +++a+e    i++++++e+P+G ++k ke+v+++tLhd
  gi|385805448|ref|YP_005841846.1| 169 ITLTVSEEITQQLLELGIKKGDVIWIDSQTGRIFKEGRLKEEAEEksPYISSERIMEMPQGPIKKDKEIVHTITLHD 245
                                       **************************************987765511568*************************** PP

                                       XXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 229 lDvanarpqdllslllqllkskkteiteklreeinkkvakyveegkaeivpGvlfiDevhmlDiecfsylnralese 305
                                       lD+  a ++  l +l     s  +ei +++r+e++++v+k++++g+ ei+pGvlfiD++hmlD+e+fs+l ra+ese
  gi|385805448|ref|YP_005841846.1| 246 LDIYFATRKAGLEIL--FGFSPLKEIGQDVRKEVDEQVKKWINDGMGEIIPGVLFIDDAHMLDLEAFSFLTRAMESE 320
                                       ***988887777777..45677889**************************************************** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 306 laPivilatnrgiakirGtdiisphGipvDlldrlliiktekytk 350
                                       laPi+ilatnrgi+kirGtdi+sphG+p+Dlldrllii+t++y++
  gi|385805448|ref|YP_005841846.1| 321 LAPIIILATNRGITKIRGTDIESPHGMPLDLLDRLLIITTRPYNR 365
                                       *******************************************97 PP

>> TIP49_C  TIP49 AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       1.4   8.5e+02      37      59 ..     321     343 ..     319     350 .. 0.88
   2 !   67.8   0.6   1.1e-21   6.8e-19       1      66 []     371     436 ..     371     436 .. 0.98

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.4
                           TIP49_C  37 ltpasilakkrkkkevevedvee 59 
                                       l+p  ila+ r+ +++   d+e+
  gi|385805448|ref|YP_005841846.1| 321 LAPIIILATNRGITKIRGTDIES 343
                                       678899**************996 PP

  == domain 2  score: 67.8 bits;  conditional E-value: 1.1e-21
                           TIP49_C   1 IlkiRakeEgvkldeeAldlLakigtetSLRYaiqLltpasilakkrkkkevevedveeveeLFlD 66 
                                       I+ iR +eE++ l+++A++ L++ig+++SLRYaiqL+ pa++la +++k++v++e+v e++  F+D
  gi|385805448|ref|YP_005841846.1| 371 IILIRSEEEDIPLSDDAIEELTNIGVNRSLRYAIQLMVPAKVLAIRKNKQKVTKEEVIEASAKFID 436
                                       899*********************************************************999998 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 !   33.5   0.1   7.7e-11   4.8e-08       1      50 [.      67     118 ..      67     131 .. 0.81
   2 ?    6.9   0.0     0.013         8      36     114 ..     271     335 ..     251     341 .. 0.78

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 7.7e-11
                                       EEEESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSSSTTHHHHHHHHHH CS
                               AAA   1 vllyGppGtGKTllakavakelg..vefleisgsellskyvgesekkirelf 50 
                                       +l++Gp GtGKT+la a+a+elg  ++f+e+ gse+ s  ++++e+ ++ l 
  gi|385805448|ref|YP_005841846.1|  67 ILFVGPTGTGKTALAVAIARELGedTPFVEFTGSEIYSTEMKKTEMLMQTLR 118
                                       69********************77799**********665555555554443 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.013
                                       SSSTTHHHHHHHHHHHH.HHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS CS
                               AAA  36 skyvgesekkirelfke.akekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnr 111
                                       +++ +e  +++++ +++ + e   p +lfiD+++ l  +             + L ++++ +       i+i+atnr
  gi|385805448|ref|YP_005841846.1| 271 QDVRKEVDEQVKKWINDgMGEI-IPGVLFIDDAHMLDLEA-----------FSFLTRAMESELA----PIIILATNR 331
                                       5566777888888888833444.48***********7777...........9999999999888....399999998 PP

                                       .GGG CS
                               AAA 112 .pdk 114
                                        + k
  gi|385805448|ref|YP_005841846.1| 332 gITK 335
                                       5555 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 !   24.1   0.1   3.9e-08   2.4e-05       7      60 ..      38      91 ..      33     119 .. 0.91
   2 ?    5.7   0.0     0.018        11      87     117 ..     296     326 ..     291     338 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 3.9e-08
                            RuvB_N  7 eeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvk 60
                                      +  +gq + +e   i+++  k+ + a   +l++Gp G Gkt+la  ia+elg +
  gi|385805448|ref|YP_005841846.1| 38 DGLVGQIEAREAAGIVVQMIKEGKMAGRGILFVGPTGTGKTALAVAIARELGED 91
                                      5689***********************************************975 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.018
                            RuvB_N  87 vlfideihrlsraveevlysamedfrldivi 117
                                       vlfid+ h l+ ++  +l  ame     i+i
  gi|385805448|ref|YP_005841846.1| 296 VLFIDDAHMLDLEAFSFLTRAMESELAPIII 326
                                       9**********************98877776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.6e-05     0.016       8      71 ..      67     132 ..      61     187 .. 0.72
   2 !   12.3   0.0   0.00025      0.15      77     135 ..     276     335 ..     233     336 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.6e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv.....fvtlpsstsskdllrellralglelka....e 71 
                                       ++ +G++GtGKT l+  ++++l e       + ++v     +++ ++ ++ + l++ l + +g++ k+    +
  gi|385805448|ref|YP_005841846.1|  67 ILFVGPTGTGKTALAVAIARELGE-------DTPFVeftgsEIYSTEMKKTEMLMQTLRKSIGVRIKEkrtvY 132
                                       7889******************54.......444443444444444444555567777777777666644443 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00025
                            AAA_22  77 ellealeqalrarav...ielliiDEaqhlrseealeeLrsllnlsrkgvqliLvGtp.elrk 135
                                       e+ e++ + +++ +    +++l iD+a+ l   ea+++L + ++  + + ++i+  t+ ++ k
  gi|385805448|ref|YP_005841846.1| 276 EVDEQVKKWINDGMGeiiPGVLFIDDAHML-DLEAFSFLTRAME--SELAPIIILATNrGITK 335
                                       3445555555555557778***********.9*******99999..99999999998877765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.3   8.2e-07   0.00051      24      85 ..      62     125 ..      48     327 .. 0.55

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 8.2e-07
                            AAA_16  24 p..elvllsGesGvGKsslvrellralekdggif.lrgkcdqlesaipysalaqalareellrql 85 
                                          + +l++G+ G+GK++l+ +++r+l +d  ++ ++g    +++     +l q+l r+++   +
  gi|385805448|ref|YP_005841846.1|  62 MagRGILFVGPTGTGKTALAVAIARELGEDTPFVeFTGSEIYSTEMKKTEMLMQTL-RKSIGVRI 125
                                       34489*************************54443333333332222224466666.43444433 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   6.1e-07   0.00038      32      89 ..      63     120 ..      35     128 .. 0.86
   2 ?    0.8   0.0      0.49     3e+02     103     117 ..     296     310 ..     274     313 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 6.1e-07
                             AAA_7  32 nkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiiesklekr 89 
                                       +++ +l+vGptGtGKt+++  + ++l +++  + +     + + ++  +++++ l k 
  gi|385805448|ref|YP_005841846.1|  63 AGRGILFVGPTGTGKTALAVAIARELGEDTPFVEFTGSEIYSTEMKKTEMLMQTLRKS 120
                                       56789**********************8888888888888888888899999999885 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.49
                             AAA_7 103 vvFvDDlnmpakeky 117
                                       v+F+DD +m   e +
  gi|385805448|ref|YP_005841846.1| 296 VLFIDDAHMLDLEAF 310
                                       79*******999876 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 !   19.0   0.1   1.1e-06   0.00068      19      96 ..      64     148 ..      54     198 .. 0.68
   2 ?   -2.2   0.0       3.4   2.1e+03      92     131 ..     285     322 ..     271     327 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.1e-06
                                       TXEEEEEEXTTSSHHHHHHHHHHHHHHCST....SEEEEEESSSXHHHHHHHHHHHHHTXXHHHH...HHTTSXHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxx RF
                            DnaB_C  19 gdliiiAarpsmGktalalniaenaavkek....lpvavfslemsaeqlvqRllsseaeidskkl...rtgklkeed 88 
                                       g  i+  +  ++Gktala+ ia++  +++     ++  ++s em++++++++ l +  +++ k+    ++g +ke +
  gi|385805448|ref|YP_005841846.1|  64 GRGILFVGPTGTGKTALAVAIARELGEDTPfvefTGSEIYSTEMKKTEMLMQTLRKSIGVRIKEKrtvYEGAVKELK 140
                                       55567778899************998744321114599*****************9998876554111668888888 PP

                                       HHHHHHHH CS
                                       xxxxxxxx RF
                            DnaB_C  89 weklteai 96 
                                       +++l +  
  gi|385805448|ref|YP_005841846.1| 141 IRRLRNPY 148
                                       88877643 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.4
                                       HHHHHHHHHHSEEEEEEXSSXCHHHHHHHHHHHHHHTTEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  92 lteaieelseaklfiddtpaltvseirskarrlkkekglg 131
                                       +++ ++e+    lfidd   l ++     +r +++  +l 
  gi|385805448|ref|YP_005841846.1| 285 INDGMGEIIPGVLFIDDAHMLDLEAFSFLTRAMES--ELA 322
                                       34457777778899999999999999988888855..444 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 !   19.2   0.0   1.3e-06   0.00081      48      83 ..      65     100 ..      52     121 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.3e-06
                         IstB_IS21  48 enivllGpsGvGKshlaialgveavraglsvlfvrv 83 
                                        +i+++Gp+G+GK+ la+a+++e  ++   v f+  
  gi|385805448|ref|YP_005841846.1|  65 RGILFVGPTGTGKTALAVAIARELGEDTPFVEFTGS 100
                                       5799******************99888888888755 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1     5e-06    0.0031      11      80 ..      64     172 ..      57     223 .. 0.66

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 5e-06
                                       TSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS..--S-TTSBHHHH...... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxx...... RF
                          ABC_tran  11 gekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe..pqlfpeltvren...... 79 
                                       g+ + +vG++G+GK+ L+ ++a++l  +   +++ g ++ ++e+++++  +++l +    +++++ tv+e       
  gi|385805448|ref|YP_005841846.1|  64 GRGILFVGPTGTGKTALAVAIARELGEDTPFVEFTGSEIYSTEMKKTEMLMQTLRKSigVRIKEKRTVYEGavkelk 140
                                       667889*********************99999999988888444444433333333333333333333333444446 PP

                                       ...............................H CS
                                       ...............................x RF
                          ABC_tran  80 ...............................e 80 
                                                                      +
  gi|385805448|ref|YP_005841846.1| 141 irrlrnpynpymmipreakitletkdenitlT 172
                                       66666666666666666666555444444443 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 !   11.9   0.1   0.00014     0.086     130     156 ..      65      91 ..      34     100 .. 0.83
   2 ?    4.8   0.1      0.02        12      38     104 ..     101     172 ..      90     189 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                             T2SSE 130 glilvsGgTgsGKttllyallkeinks 156
                                         il+ G+Tg+GKt l+ a+  e+ ++
  gi|385805448|ref|YP_005841846.1|  65 RGILFVGPTGTGKTALAVAIARELGED 91 
                                       459999*************99998776 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.02
                             T2SSE  38 eveelekaalerlisriaalakldiseerplqdarlp.ekgvrlrvvllPvvag...ealviR.kksakelt 104
                                       e+ + e +++e+l++++  + + +i+e+r + +++++  k  rlr    P +      ++++  k ++  lt
  gi|385805448|ref|YP_005841846.1| 101 EIYSTEMKKTEMLMQTLRKSIGVRIKEKRTVYEGAVKeLKIRRLRNPYNPYMMIpreAKITLEtKDENITLT 172
                                       6778889999**************************966777888888888776532334444445555555 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1   3.9e-05     0.024      11      61 ..      53     102 ..      43     116 .. 0.78
   2 ?    1.2   0.0      0.41   2.5e+02      95     119 ..     295     319 ..     288     324 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.9e-05
                                       HHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS CS
                   Sigma54_activat  11 lleqikkvaktdlsvlitGesGtGKellaraiheaskrkekpfvavncaai 61 
                                       ++++ik+       +l +G +GtGK+ la ai ++   +++pfv++  ++i
  gi|385805448|ref|YP_005841846.1|  53 VVQMIKEGKMAGRGILFVGPTGTGKTALAVAIARELG-EDTPFVEFTGSEI 102
                                       66777777777889******************98776.7899999987766 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.41
                                       SEEEEETGGGS-HHHHHHHHHHHHH CS
                   Sigma54_activat  95 GtlfLDeigelplelQekLlrvlqe 119
                                       G+lf+D+ + l+le+ + L r++++
  gi|385805448|ref|YP_005841846.1| 295 GVLFIDDAHMLDLEAFSFLTRAMES 319
                                       99*************9999999986 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.4     4e-06    0.0024      23     150 ..      68     214 ..      64     287 .. 0.64
   2 ?   -2.3   0.2       8.4   5.2e+03     143     143 ..     415     415 ..     353     450 .. 0.46

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 4e-06
                            AAA_23  23 lItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiese...gkvkayveltfenkdgry.......... 86 
                                       l++Gp+G+GKT++  Ai   L+++tp  + + g+ + + + + ++e    + ++++ ++++ k++ y          
  gi|385805448|ref|YP_005841846.1|  68 LFVGPTGTGKTALAVAIARELGEDTPFVEFT-GSEIYSTEMK-KTEmlmQTLRKSIGVRIKEKRTVYegavkelkir 142
                                       89*********************99866554.4344444443.1223442333444444444444444555555655 PP

                            AAA_23  87 ....trsiererelskkkgkttkkaklelleideleqfisellgskki....ilnlilflgqerfeefelkd 150
                                            ++   ++++  k + +tk+++  l+  +e +q++ el  +k +     ++   +++++r +e+++++
  gi|385805448|ref|YP_005841846.1| 143 rlrnPYNPYMMIPREAKITLETKDENITLTVSEEITQQLLELGIKKGDviwiDSQTGRIFKEGRLKEEAEEK 214
                                       667666777777777777766666666666666666666654444444566555666667777755555433 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 8.4
                            AAA_23 143 f 143
                                        
  gi|385805448|ref|YP_005841846.1| 415 I 415
                                       1 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   1.4e-05    0.0089      22      43 ..      67      88 ..      46      97 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.4e-05
                                      EEEE--TTSSTTHHHHHHHHHH CS
                              PhoH 22 vfaiGpaGtGKtylavalavea 43
                                      +  +Gp+GtGKt lava+a e+
  gi|385805448|ref|YP_005841846.1| 67 ILFVGPTGTGKTALAVAIAREL 88
                                      5679*************99776 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   1.9e-05     0.012       2      53 ..      67     121 ..      66     146 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.9e-05
                            AAA_28   2 ivitGgestGKTtlleaLaar...gypvvpEaareileeklakgedalpwv.edll 53 
                                       i ++G+ +tGKT l+ a+a++   ++p v+ ++ ei++ +++k+e  l ++ ++ +
  gi|385805448|ref|YP_005841846.1|  67 ILFVGPTGTGKTALAVAIARElgeDTPFVEFTGSEIYSTEMKKTEM-LMQTlRKSI 121
                                       789****************988888****************99884.666545444 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 !   15.0   0.2   2.9e-05     0.018      24      50 ..      64      90 ..      41     195 .. 0.83
   2 ?    0.0   0.0       1.2   7.4e+02     124     145 ..     277     306 ..     192     327 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.9e-05
                                      TSEEEEEESTTSTHHHHHHHHHHHH-S CS
                            ResIII 24 dkrglikmaTGtGKTlvaaklierllk 50
                                       + +l++ +TGtGKT +a++++++l +
  gi|385805448|ref|YP_005841846.1| 64 GRGILFVGPTGTGKTALAVAIARELGE 90
                                      34677*****************99876 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.2
                                       ...HHHTTT-S........EEEEETGGGTT CS
                            ResIII 124 eseellrdrfd........viiiDEaHrlg 145
                                        +e+ ++  +d        v++iD aH l 
  gi|385805448|ref|YP_005841846.1| 277 VDEQVKKWINDgmgeiipgVLFIDDAHMLD 306
                                       223322222225566777899999999765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   2.5e-05     0.015       2      42 ..      67     112 ..      67     195 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.5e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklg.....avllssdtlrrrlfgtdq 42 
                                       +l+vG+ G+GK+ la  ++++lg     +++  s ++++ +++t+ 
  gi|385805448|ref|YP_005841846.1|  67 ILFVGPTGTGKTALAVAIARELGedtpfVEFTGSEIYSTEMKKTEM 112
                                       69*********************99998888888888888888543 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.1   0.00015      0.09       1      24 [.      67      90 ..      67     210 .. 0.75
   2 ?   -0.9   0.0       3.6   2.2e+03      46      76 ..     263     292 ..     234     329 .. 0.70
   3 ?   -1.3   0.1       4.7   2.9e+03      89     118 ..     398     425 ..     358     433 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00015
                            AAA_18  1 IlltGtpGvGKttlakeLskrlgf 24
                                      Il  G+ G+GKt la +++++lg 
  gi|385805448|ref|YP_005841846.1| 67 ILFVGPTGTGKTALAVAIARELGE 90
                                      8999****************9833 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 3.6
                            AAA_18  46 ldeskrldedkldklldaleenssaleegkn 76 
                                       +++ k++ +d+++++ ++++++++  + g+ 
  gi|385805448|ref|YP_005841846.1| 263 FSPLKEIGQDVRKEVDEQVKKWIN-DGMGEI 292
                                       556677788888888888888876.333332 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 4.7
                            AAA_18  89 eaakdikkvvLtaspeelleRlekRgyeea 118
                                           ++  + L ++ ++l+ R +k++ ++ 
  gi|385805448|ref|YP_005841846.1| 398 R-SLRYA-IQLMVPAKVLAIRKNKQKVTKE 425
                                       2.22345.8888888888888888776654 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.1   0.00011      0.07       2      32 ..      67      99 ..      66     134 .. 0.79
   2 ?   -2.7   0.0       8.6   5.3e+03      39      67 ..     180     206 ..     165     207 .. 0.63
   3 ?   -0.8   0.0       2.3   1.4e+03      65      90 ..     293     318 ..     266     324 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00011
                                      EEEE--SSSSHHHHHHHGGGGB..S--EEEEE- CS
                             AAA_5  2 vlLvGppGtgKselaerlaaal..nreveyvql 32
                                      +l vGp+GtgK+ la  +a+ l   +++++  +
  gi|385805448|ref|YP_005841846.1| 67 ILFVGPTGTGKTALAVAIARELgeDTPFVEFTG 99
                                      799*****************9975555555544 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 8.6
                                       HHHH--B--.........--------G-S CS
                             AAA_5  39 edlkgrreikngttslvdsplvraarege 67 
                                       + l  ++  k+g+  + ds   r ++eg+
  gi|385805448|ref|YP_005841846.1| 180 QLLELGI--KKGDVIWIDSQTGRIFKEGR 206
                                       3232222..38888888888888888876 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 2.3
                                       G-SEEEEESGGG--HHHHHHHHHHHH CS
                             AAA_5  65 egeilvlDEveraesevlnsLlslle 90 
                                        + +l++D+ ++++ e+++ L + +e
  gi|385805448|ref|YP_005841846.1| 293 IPGVLFIDDAHMLDLEAFSFLTRAME 318
                                       56799*******99999998888776 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.7e-05     0.029      32      65 ..      63      96 ..      51     138 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.7e-05
                            AAA_25 32 agelallaGapgtGKttlaldlalavatGkpwlg 65
                                      ag  +l++G++gtGKt+la+ +a ++ ++ p+ +
  gi|385805448|ref|YP_005841846.1| 63 AGRGILFVGPTGTGKTALAVAIARELGEDTPFVE 96
                                      5777899*****************9999999876 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   8.2e-05      0.05       5      26 ..      68      89 ..      65      95 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.2e-05
                               IPT  5 lifGatttGKtaeaiklaketg 26
                                      l +G+t+tGKta a+++a+e g
  gi|385805448|ref|YP_005841846.1| 68 LFVGPTGTGKTALAVAIARELG 89
                                      789****************977 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00015     0.093      22      66 ..      64     108 ..      38     120 .. 0.71
   2 ?   -0.3   0.0      0.93   5.7e+02     108     133 ..     295     320 ..     290     331 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00015
                      Mg_chelatase  22 gHnlllvGppGsGKtmlakrlpsllpplseeealevakiasvagk 66 
                                       g  +l+vGp G+GKt la +++  l + +    +  ++i+s   k
  gi|385805448|ref|YP_005841846.1|  64 GRGILFVGPTGTGKTALAVAIARELGEDTPFVEFTGSEIYSTEMK 108
                                       4579***************99998888777777777777776664 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.93
                      Mg_chelatase 108 GvLfLDElpefkrkvlevLRePledg 133
                                       GvLf+D++  ++ +++  L + +e++
  gi|385805448|ref|YP_005841846.1| 295 GVLFIDDAHMLDLEAFSFLTRAMESE 320
                                       9*********9999999999999986 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   8.9e-05     0.055       1      43 [.      67     112 ..      67     139 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.9e-05
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl..klkkkdsvys.rnpeddf 43 
                                       i+++Gp+g+GK+ la  +a++l ++    + + +++ys   +++++
  gi|385805448|ref|YP_005841846.1|  67 ILFVGPTGTGKTALAVAIARELGEDTpfVEFTGSEIYStEMKKTEM 112
                                       6899*******************77766455558888866666665 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   0.00011      0.07      18      46 ..      61      91 ..      41     114 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00011
                                      H..TEEEEEEESTTSSHHHHHHHHHHHTT-- CS
                              TsaE 18 l..gdvilLeGdLGaGKTtlvrglakalgve 46
                                         g+ il+ G+ G+GKT+l+ ++a++lg +
  gi|385805448|ref|YP_005841846.1| 61 KmaGRGILFVGPTGTGKTALAVAIARELGED 91
                                      123455*********************9864 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   0.00036      0.22       6      56 ..      67     115 ..      65     196 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00036
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHH CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrl 56 
                                       il++gptg+Gkt la a+a+ l   ++ +++ +  se+   e  ++   + 
  gi|385805448|ref|YP_005841846.1|  67 ILFVGPTGTGKTALAVAIARELG--EDTPFVEFTGSEIYSTEMKKTEMLMQ 115
                                       89*******************96..67888888888887755555444444 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   0.00022      0.14       3      30 ..      67      94 ..      65     101 .. 0.89
   2 ?   -2.6   0.0       7.2   4.5e+03     123     137 ..     356     370 ..     353     381 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00022
                                      EEEEC-TTTCHHHHHHHHHHHHCTS-SC CS
                             NACHT  3 vilqGeaGsGKTtLlqklalawaegklp 30
                                      ++  G+ G GKT+L+  +a+++ e++++
  gi|385805448|ref|YP_005841846.1| 67 ILFVGPTGTGKTALAVAIARELGEDTPF 94
                                      7889******************999876 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 7.2
                                       EEEEEECCCHHHHCT CS
                             NACHT 123 llltvrpralrdlee 137
                                       l++t+rp ++ ++++
  gi|385805448|ref|YP_005841846.1| 356 LIITTRPYNRDEIKQ 370
                                       899****99998877 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   0.00034      0.21       7      55 ..      70     125 ..      65     181 .. 0.76
   2 ?   -3.0   0.0       5.3   3.3e+03     163     182 ..     268     287 ..     201     291 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00034
                           DUF2075   7 tGvaGtGKtvvllnllael.......eddeeertavylsvNhplvlvlrealakke 55 
                                        G +GtGKt ++++++ el       e + +e +++ + + + l+++lr+ +  + 
  gi|385805448|ref|YP_005841846.1|  70 VGPTGTGKTALAVAIARELgedtpfvEFTGSEIYSTEMKKTEMLMQTLRKSIGVRI 125
                                       4999***************8777777666688888888888999999998887666 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.3
                           DUF2075 163 hLksqfRvaaseaviewvda 182
                                       +  + +R + +e+v +w+++
  gi|385805448|ref|YP_005841846.1| 268 EIGQDVRKEVDEQVKKWIND 287
                                       66678888999999999986 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 ?   10.0   0.1   0.00054      0.33      97     137 ..      47      87 ..      43      92 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00054
                         Parvo_NS1  97 vevgqvllawlskqlgkrntvwfyGpantGktnlaeaIaka 137
                                       +e++ ++++++++ +     ++f+Gp  tGkt la aIa+ 
  gi|385805448|ref|YP_005841846.1|  47 REAAGIVVQMIKEGKMAGRGILFVGPTGTGKTALAVAIARE 87 
                                       57888888888888888889******************975 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   1.9     0.013       7.9       9      78 ..      63     271 ..      55     327 .. 0.50

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.013
                            AAA_19   9 kekvllvtaGpGtGKTrvlkhivallvelggvkp...........eeillvaftgrAakelrerlaalgaeatTiHr 74 
                                       + + +l +++ GtGKT + ++i ++l e +               +       t+  ++ lr+++ +  +e +T+ +
  gi|385805448|ref|YP_005841846.1|  63 AGRGILFVGPTGTGKTALAVAIARELGEDTPFVEftgseiystemK------KTEMLMQTLRKSIGVRIKEKRTVYE 133
                                       56667888999*****999999888876653222333221111110......1222222222233222222444444 PP

                            AAA_19  75 lal.......................................................................... 77 
                                        a+                                                                          
  gi|385805448|ref|YP_005841846.1| 134 GAVkelkirrlrnpynpymmipreakitletkdenitltvseeitqqllelgikkgdviwidsqtgrifkegrlkee 210
                                       44455555555555555555555555555555555555555555555555555555555555555555555555555 PP

                            AAA_19  78 ............................................................l 78 
                                                                                                    
  gi|385805448|ref|YP_005841846.1| 211 aeekspyisserimempqgpikkdkeivhtitlhdldiyfatrkagleilfgfsplkeigQ 271
                                       5555555555555555555555555555555555555566666666666666655555441 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); 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: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 2981.55
//
Query:       gi|385805449|ref|YP_005841847.1|  [L=258]
Description: short-chain dehydrogenase/reductase SDR [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-41  142.6   0.0    2.1e-41  142.0   0.0    1.2  1  adh_short_C2   Enoyl-(Acyl carrier protein) reductase
    6.3e-27   94.3   0.0    7.7e-27   94.0   0.0    1.1  1  adh_short      short chain dehydrogenase
    0.00067   19.6   0.0     0.0012   18.8   0.0    1.3  1  KR             KR domain
  ------ inclusion threshold ------
      0.013   13.9   0.8       0.36    9.1   0.2    2.0  2  DUF2194        Uncharacterised protein conserved in bacteria 
      0.041   13.2   0.1       0.78    9.0   0.0    2.2  2  THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase,
      0.049   13.7   0.1       0.26   11.4   0.0    2.0  3  Spore_III_AB   Stage III sporulation protein AB (spore_III_AB
        0.1   12.9   0.0       0.23   11.8   0.0    1.6  1  Mur_ligase     Mur ligase family, catalytic 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 !  142.0   0.0   8.3e-45   2.1e-41       4     233 ..      17     253 ..      13     254 .. 0.93

  Alignments for each domain:
  == domain 1  score: 142.0 bits;  conditional E-value: 8.3e-45
                                       TSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSEEEE--TTSHHHHHHHHHHHHHHHSSEEEEEE---- CS
                      adh_short_C2   4 sgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgaevlecDVtdeeqvealveevvekfgklDilvnnagi 79 
                                        g+G++i k l +eGa+vv++  ne++ k+++  l + ++ +   cD ++++++++++e+++e ++++D++v n g 
  gi|385805449|ref|YP_005841847.1|  17 TGMGFEITKNLVNEGAKVVFCSSNENNlKRAISLLGNPINLKGELCDLSSTNSIKNFFEKAKEYLENFDGMVYNTGG 93 
                                       79*************************777778788878888899******************************** PP

                                       -EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSCCEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHH CS
                      adh_short_C2  80 apklkgpfletsreefdraldvnlyslfllakaalplmkeggsivnlssvgaervvpnynaygaaKaalealtrylA 156
                                        ++  g++ ++s+e++  a +    s+f  +k++l+++++g+s+v ++s++ +  + n    ++ +  +++l+++l 
  gi|385805449|ref|YP_005841847.1|  94 PKT--GNINSLSEEDYYYAYKLLSESAFVSTKEFLKYANKGASVVYMTSTAVKEPIYNLLLSNTMRLTVIGLAKSLS 168
                                       999..*********************************************9988888888***************** PP

                                       HHHGGGTEEEEEEEE--BHCTGGGGSTT.........HHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--S CS
                      adh_short_C2 157 velgpkgiRvNavspgpikTlaasgikg.........fdelleelearaplgrlgtpeevaeaalfLasdeasyitG 224
                                       +e+ +   R N+v pg+i T+  +++ +         fd++ ++  +++p++rlg+p+eva+++lfL+sd++syi+G
  gi|385805449|ref|YP_005841847.1| 169 REYSD-FARFNVVMPGYILTEKLKQLLEeeakekattFDSIVSQYIKEIPMKRLGDPKEVANLVLFLLSDLSSYING 244
                                       ***99.**************9877665434444555588899999******************************** PP

                                       EEEEESTTG CS
                      adh_short_C2 225 qtlvvDgGl 233
                                         ++vDgG+
  gi|385805449|ref|YP_005841847.1| 245 VAIAVDGGM 253
                                       ********8 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.0   0.0     3e-30   7.7e-27       1     193 [.       8     196 ..       8     198 .. 0.97

  Alignments for each domain:
  == domain 1  score: 94.0 bits;  conditional E-value: 3e-30
                                       SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSS CS
                         adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgk 77 
                                       k +++  +s G+G +i k+l++eGakvv+++++e++l+++++ l++   ++    +D+++ +++++++eka++ l++
  gi|385805449|ref|YP_005841847.1|   8 KKIIILAGSTGMGFEITKNLVNEGAKVVFCSSNENNLKRAISLLGN-PINLKGELCDLSSTNSIKNFFEKAKEYLEN 83 
                                       6799***************************************998.5889************************** PP

                                       ESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHH CS
                         adh_short  78 ldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKa 154
                                        d +v N+G  ++g++++lsee++   +++   ++f  t+++l++  +++++++v ++S+a k+p  ++    +   
  gi|385805449|ref|YP_005841847.1|  84 FDGMVYNTGGPKTGNINSLSEEDYYYAYKLLSESAFVSTKEFLKY--ANKGASVVYMTSTAVKEPIYNLLLSNTMRL 158
                                       *********************************************..89**************************** PP

                                       HHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHHCTH CS
                         adh_short 155 avagltrslakelaptgirvnavaPGlvdTdmakelrek 193
                                        v+gl++sl++e+++   r n+v+PG++ T+  k+l e+
  gi|385805449|ref|YP_005841847.1| 159 TVIGLAKSLSREYSDF-ARFNVVMPGYILTEKLKQLLEE 196
                                       ***************9.9*************99888766 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   4.5e-07    0.0012       4     106 ..      11     108 ..       9     113 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 4.5e-07
                                       EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS CS
                                KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeep 80 
                                       +i  G  g+G e+++ l+++ga+ + + s +    ++ k+ i+ l  + ++ +   +D+s+ +++++ +e++k+  +
  gi|385805449|ref|YP_005841847.1|  11 IILAGSTGMGFEITKNLVNEGAKVVFCSSNE----NNLKRAIS-LLGNPINLKGELCDLSSTNSIKNFFEKAKEYLE 82 
                                       56667889*************9866665555....23333444.556688999999*****************999* PP

                                       ---EEEE---------TTT--HHHHH CS
                                KR  81 pikGvihaAgvlrdklleemtaedle 106
                                       +  G +   g  +++ ++++++ed+ 
  gi|385805449|ref|YP_005841847.1|  83 NFDGMVYNTGGPKTGNINSLSEEDYY 108
                                       *******************9999976 PP

>> DUF2194  Uncharacterised protein conserved in bacteria (DUF2194)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1    0.0058        15     245     301 ..       5      61 ..       2      88 .. 0.77
   2 ?    9.1   0.2   0.00014      0.36     245     288 ..     106     150 ..      61     179 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.0058
                           DUF2194 245 LlkyrliiitdakyletkeikkylesGGtvilitkeekikveklvlekelfpltnea 301
                                       L + ++ii  +++ +  + +k+ +++G  v++++++e+     ++l  + + l+ e 
  gi|385805449|ref|YP_005841847.1|   5 LRNKKIIILAGSTGMGFEITKNLVNEGAKVVFCSSNENNLKRAISLLGNPINLKGEL 61 
                                       566678889999***********************8888888887776666666555 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00014
                           DUF2194 245 LlkyrliiitdakyletkeikkylesGGtvilitk.eekikvekl 288
                                          y + + +++ ++ tke  ky + G +v+++t+   k  + +l
  gi|385805449|ref|YP_005841847.1| 106 DYYYAYKLLSESAFVSTKEFLKYANKGASVVYMTStAVKEPIYNL 150
                                       345777789************************995334444444 PP

>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0    0.0003      0.78      31      76 ..       2      47 ..       1      50 [. 0.92
   2 ?    2.0   0.0     0.045   1.1e+02      40      66 ..     135     161 ..     120     204 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0003
                                      T---TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTSCCHHHH CS
                     THF_DHG_CYH_C 31 gielegkkvvvvGrsnivgkplallLleknatVtvchsktkdlaei 76
                                      +++l++kk++++  s+ +g  ++  L +++a V  c s+ ++l++ 
  gi|385805449|ref|YP_005841847.1|  2 DMNLRNKKIIILAGSTGMGFEITKNLVNEGAKVVFCSSNENNLKRA 47
                                      57899***********************************999976 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.045
                                       EEE---TTTHHHHHHHHHCTT-EEEEE CS
                     THF_DHG_CYH_C  40 vvvGrsnivgkplallLleknatVtvc 66 
                                       vv   s+ v +p+  lLl++ +  tv+
  gi|385805449|ref|YP_005841847.1| 135 VVYMTSTAVKEPIYNLLLSNTMRLTVI 161
                                       44567999*******999986666554 PP

>> Spore_III_AB  Stage III sporulation protein AB (spore_III_AB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0001      0.26       6      82 ..      10      86 ..       9     106 .. 0.90
   2 ?   -1.6   0.0      0.96   2.5e+03     133     133 ..     187     187 ..     116     208 .. 0.61
   3 ?   -0.5   0.0      0.46   1.2e+03      66      94 ..     190     214 ..     159     229 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0001
                                      XXXXXXXXXXXXXXXXXXXHHHHHHHHHHHHHHHHHHHHHH-SS-HHHHHHHHHHCS-TTHHHHHHHHHHHHH.STS CS
                      Spore_III_AB  6 llillactgiGfalakrlkrrlkeleelkralellegeirygatpLpealeklaeksesplseffeevaerleekeg 82
                                      ++il+++tg+Gf + k+l ++  +     +  + l++ i+   +p++   e +  +s++++++ffe++ e le+ +g
  gi|385805449|ref|YP_005841847.1| 10 IIILAGSTGMGFEITKNLVNEGAKVVFCSSNENNLKRAISLLGNPINLKGELCDLSSTNSIKNFFEKAKEYLENFDG 86
                                      68*******************************************977666666778999***********998666 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.96
                                       H CS
                      Spore_III_AB 133 l 133
                                        
  gi|385805449|ref|YP_005841847.1| 187 T 187
                                       2 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.46
                                       HHHHHHHHHHHHH.STSS-HHHHHHHHHH CS
                      Spore_III_AB  66 lseffeevaerleekegesfeeaweeave 94 
                                       l++++ee a++    + ++f ++ ++ ++
  gi|385805449|ref|YP_005841847.1| 190 LKQLLEEEAKE----KATTFDSIVSQYIK 214
                                       22222222222....44455444444444 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 ?   11.8   0.0     9e-05      0.23      18      51 ..      10      43 ..       6      83 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9e-05
                                      HHHHTTSEEEEEESSHCHHHTT-EEEES-HGGGG CS
                        Mur_ligase 18 flalkGykvdGsdfieslialGaaavvghdaani 51
                                      ++ l G +  G ++ ++l+++Ga++v++++ +n 
  gi|385805449|ref|YP_005841847.1| 10 IIILAGSTGMGFEITKNLVNEGAKVVFCSSNENN 43
                                      778899999********************98843 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       913  (0.0509231); expected 358.6 (0.02)
Passed bias filter:                      704  (0.039266); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.59u 0.35s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 1487.13
//
Query:       gi|385805450|ref|YP_005841848.1|  [L=154]
Description: hypothetical protein FFONT_0406 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0089   16.1   0.5      0.021   14.9   0.5    1.6  1  DUF1192   Protein of unknown function (DUF1192)
  ------ inclusion threshold ------
       0.01   16.4   0.1      0.023   15.2   0.1    1.6  1  NLE       NLE (NUC135) domain


Domain annotation for each model (and alignments):
>> DUF1192  Protein of unknown function (DUF1192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.5   2.3e-06     0.021      23      49 ..     123     149 ..     121     152 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.3e-06
                           DUF1192  23 eELeerIalLeaEIaRleaaiakkkas 49 
                                       +EL++ +++L+ EIa++ea+++  +++
  gi|385805450|ref|YP_005841848.1| 123 NELKKAVEELRGEIAMVEAEVELQSKH 149
                                       7*******************9987777 PP

>> NLE  NLE (NUC135) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.1   2.6e-06     0.023      21      63 ..      39      82 ..      27      84 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.6e-06
                               NLE 21 lsvPasltrkqLselvnkLlkee..kpvpFdFlidgel.lrtsLee 63
                                      +++ +++t+k+L++l+ kL + +  +  +++F+  g+  + +sL+e
  gi|385805450|ref|YP_005841848.1| 39 IDIYGEITEKGLNTLIYKLKE-KgiQ-FDYTFFKVGNAiVSKSLKE 82
                                      789999*************99.4333.6688887777779999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1121  (0.0625244); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); 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: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1033.85
//
Query:       gi|385805451|ref|YP_005841849.1|  [L=140]
Description: putative stress protein [Fervidicoccus fontis Kam940]
Scores for complete 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-15   55.8   0.0    3.2e-13   50.4   0.0    2.1  1  Usp            Universal stress protein family
  ------ inclusion threshold ------
      0.015   15.0   0.0      0.016   14.8   0.0    1.2  1  SRP54          SRP54-type protein, GTPase domain
      0.026   15.0   0.2       0.23   11.9   0.2    2.0  1  NAD_binding_7  Putative NAD(P)-binding
      0.034   14.1   0.1      0.046   13.6   0.1    1.2  1  RsgA_GTPase    RsgA GTPase


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 !   50.4   0.0   7.1e-17   3.2e-13       3     139 ..      16     138 ..      14     140 .] 0.89

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 7.1e-17
                                       SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTT CS
                               Usp   3 krIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeagg 79 
                                       +rIlVa+Dgs +s++ l+ Alel ++ g+e++++++++  +  +    + e   +e   e                 
  gi|385805451|ref|YP_005841849.1|  16 RRILVAFDGSASSERGLKIALELSRMLGSEVHVIYACSNNSCNENIIKKAEILAKERGVEII--------------S 78 
                                       8*****************************99999999998888888888888888888877..............4 PP

                                       CEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEE CS
                               Usp  80 vkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlv 139
                                       +++++  ee +++ e++++ +++++dl+++G+rg++  +++  GS++  v  +++++ l 
  gi|385805451|ref|YP_005841849.1|  79 KVTKFNPEESSVSNELIKEINSKNYDLVIMGTRGKTISAEISKGSTAAGVFVNTDVSYLF 138
                                       5799******************************77777799******999988887665 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   3.6e-06     0.016      48      95 ..      65     114 ..      18     122 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.6e-06
                                       HHHHHHHTTEEEEE..SSTTSCHHHHHHHHHHHHHHTTSSEEEEEE--SS CS
                             SRP54  48 Lktlaeklgvpvik..kkeeadpaavakeavekakeekidvvlvDTaGrl 95 
                                        ++la++ gv++i+  +k + ++ +v +e +++ +++++d+v++ T G+ 
  gi|385805451|ref|YP_005841849.1|  65 AEILAKERGVEIISkvTKFNPEESSVSNELIKEINSKNYDLVIMGTRGKT 114
                                       578999*******94444445778999*********************86 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   5.1e-05      0.23      27      91 ..      68     132 ..      16     134 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.1e-05
                     NAD_binding_7  27 leagakvtvvapevkeeleelvklaeeel.ekdlegadlviaatddrelneriaeaakarrilvnv 91 
                                       l+++  v ++++  +++ +e  ++++e + e + +++dlvi+ t  + ++++i +   a++++vn 
  gi|385805451|ref|YP_005841849.1|  68 LAKERGVEIISKV-TKFNPEESSVSNELIkEINSKNYDLVIMGTRGKTISAEISKGSTAAGVFVNT 132
                                       2233555566655.4444454455555553344778****************************95 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1     1e-05     0.046      19      90 ..      46     116 ..      43     130 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1e-05
                                       EEEEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTH CS
                       RsgA_GTPase  19 llivvslkepelslnlldrfLvlaeekgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegl 90 
                                       + ++ +++++++++n+++++ +la+e+g+e++  ++K +  e++   +el +e+++ +y+++++ ++ k+  
  gi|385805451|ref|YP_005841849.1|  46 VHVIYACSNNSCNENIIKKAEILAKERGVEIISKVTKFNPEESSV-SNELIKEINSKNYDLVIMGTRGKTIS 116
                                       77999********************************99988888.99*************99977755444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 942.84
//
Query:       gi|385805452|ref|YP_005841850.1|  [L=415]
Description: 3-phosphoglycerate kinase [Fervidicoccus fontis Kam940]
Scores for complete 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  327.2   0.1    1.4e-97  327.0   0.1    1.0  1  PGK       Phosphoglycerate kinase
  ------ inclusion threshold ------
      0.022   14.4   0.0       0.05   13.3   0.0    1.5  1  DUF4874   Domain of unknown function (DUF4874)


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 !  327.0   0.1  1.6e-101   1.4e-97       2     377 ..       9     391 ..       8     392 .. 0.93

  Alignments for each domain:
  == domain 1  score: 327.0 bits;  conditional E-value: 1.6e-101
                                       GGS--TT-EEEEEE-----EECTTEES--HHHHHHHHHHHHHHHTT-EEEEEE--S--TTS-GGG-SHHHHHHHHHH CS
                               PGK   2 kdldlkgkrvlvRvDfNvplkkegkitddtriraalpTikyllekgakvvllsHlgrpkgekeklslkpvaerLsel 78 
                                       + +dl+gk+vl+RvDfN+pl++++ki d +ri+ +++Ti +l++k+a+vv+l+H+grp g ++  +l+++   L++ 
  gi|385805452|ref|YP_005841850.1|   9 DSVDLNGKKVLLRVDFNSPLNENKKIIDFSRIKIHVKTIGELIDKNASVVILTHQGRP-GMEDFSDLSEHSLLLEKE 84 
                                       6789******************************************************.7889999*********** PP

                                       HTT-EEEESSTTSHHHHHHHHT-TTT-EEEES-GGGSTTTTTT-H.....H..HHHHHHHT-SEEEE--GGGTTS-- CS
                               PGK  79 lgkeVkfvedvvgeeveeaiaelkegevllLeNvrfykeEeknde.....e..lakklasladvyVnDAFgtahrah 148
                                       lg +V+f++d++g+++++ i  lk+gevl+L+Nvrf +eE+ + +     +  +++kla l+++++nDAF+tahr+h
  gi|385805452|ref|YP_005841850.1|  85 LGYKVNFIDDIIGPHARNSIFMLKDGEVLMLDNVRFLSEENIEASgdfhsKsyMVRKLAPLFNYFINDAFATAHRKH 161
                                       ****************************************7543344444145************************ PP

                                       TTTTHHHHCSEEEE-HHHHHHHHHHHHHHHS--SSEEEEEEES-HHHCHHHHHHHTTT-...SEEEEETCHHHHHHH CS
                               PGK 149 aStvgiakvlsaaaGllmekElealskvlenperplvailGGakvsdkikvienLlekv...dkliigGgmantFlk 222
                                       aS+vg++ vl+++aG++me+E+ al+++ + +  p +++lGG+k++d i++i+n+l++     +++++G++   Fl 
  gi|385805452|ref|YP_005841850.1| 162 ASIVGFPYVLPSLAGRVMESEVIALKEIRDPKISPKIFVLGGTKINDSIRIINNILKNSnssTRVLLTGLVSELFLF 238
                                       **********99*****************9999************************9977689************* PP

                                       HTT-B-TTSS--G.......GGHHHHHHHHHHHHHHT-EEE--SEEEEESSSSTTS.EEEECCG--TT-.EEEEE-H CS
                               PGK 223 aqgleigkslvee.......dklelakellekakkkgvkillpvDvvvakeeaekeakvveveaipede.malDigp 291
                                       a+g++igks  e+       + l+ ak++l ++k   ++illp D+v++       + vv+++++p++e  + Dig+
  gi|385805452|ref|YP_005841850.1| 239 ASGIDIGKSNKEKleklggiSLLSNAKSILLNYK---DRILLPEDFVIEG------GGVVDIKELPKKEgLIKDIGE 306
                                       ***********996545444459********998...89*********96......6899*****99998******* PP

                                       HHHHHHHHHHCC-SEEEEES-SS-TTSGCCCHHHHHHHHHHHHHCHTSEEEEESHHHHHHHHHTT-GG.GSSEEESS CS
                               PGK 292 ktielfaeaikeaktvvwnGpmGvfeiekfakGTkaiakalaeatkgalsivGGgdsaaaveklglad.kvshvStG 367
                                       ktie+++++++eak++v+ Gp+Gv+e +++ kG+ +++k +a+++  a +i GGg+  a+++ +  +     h S+G
  gi|385805452|ref|YP_005841850.1| 307 KTIEEYSNIMREAKVIVLRGPAGVIEEKEYMKGSIELVKNAASTN--AKVILGGGHLTAVLDFIPENLrTRIHNSSG 381
                                       ******************************************974..69********999998886653567***** PP

                                       SHHHHHHHCT CS
                               PGK 368 GgAsLelLeg 377
                                       GgA+L +L+g
  gi|385805452|ref|YP_005841850.1| 382 GGALLLYLSG 391
                                       ********99 PP

>> DUF4874  Domain of unknown function (DUF4874)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   5.5e-06      0.05      58     115 ..       8      64 ..       5      68 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.5e-06
                           DUF4874  58 letlrkagkkvilRfaYdtegkateeedasleqilrHieqlkpileenkdvIavvqag 115
                                       l+ +  +gkkv+lR+ +++   +++++  ++++i+ H++ +++++ +n+ v+++++ g
  gi|385805452|ref|YP_005841850.1|   8 LDSVDLNGKKVLLRVDFNSP-LNENKKIIDFSRIKIHVKTIGELIDKNASVVILTHQG 64 
                                       6677789************9.88888999********************998877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); 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: 0.63u 0.26s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 2632.75
//
Query:       gi|385805453|ref|YP_005841851.1|  [L=131]
Description: hypothetical protein FFONT_0409 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score 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   13.1   3.6        1.3    9.0   3.6    2.0  1  ResIII         Type III restriction enzyme, res subunit
       0.08   14.0   5.9      0.096   13.7   4.4    1.9  2  CS             CS domain
       0.17   12.5   1.5       0.24   12.0   1.0    1.6  1  T_Ag_DNA_bind  Origin of replication binding protein
        2.4    8.5  10.4        1.4    9.2   2.8    3.1  3  MecA_N         NTF2-like N-terminal transpeptidase domain


Domain annotation for each model (and alignments):
>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   3.6   0.00029       1.3      63     135 ..       9     112 ..       7     117 .. 0.54

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00029
                                       SHHHHHHHHHHGGGGTGG.................GEEEESSS-B--.............................. CS
                            ResIII  63 rkslleqtleefkkflseayke.............igkkvsgdkkka........................kekdst 102
                                        k+lle+ ++ f +++ ++++              i          +                          +d++
  gi|385805453|ref|YP_005841851.1|   9 DKNLLERIINSFLNIFFNYNNIeaysiaqsltdieIF---------EkidanevkiyimlpeslseeqvkvVPIDKN 76 
                                       6789999999998888887766644433333332222.........1222222222444444444444444666777 PP

                                       .-SEEEEEHHHHHHTH...........HHHTTT-SE CS
                            ResIII 103 nkkilvttiqsldadseee...eeeseellrdrfdv 135
                                       ++ki+v+++++++++++ +   + +s +++r+++d+
  gi|385805453|ref|YP_005841851.1|  77 HIKIFVEKYEEIYRKIKLHykiDIKSVQAERKKKDL 112
                                       777777777777777766666644444555555555 PP

>> CS  CS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   4.4   2.1e-05     0.096      10      66 ..      51     108 ..      49     119 .. 0.83
   2 ?    0.1   0.4      0.38   1.7e+03      21      39 ..     105     125 ..      97     130 .. 0.45

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.1e-05
                                       TEEEEEEE-TTCTTTTTCEEEE.EETTEEEEEETS.CEEEEECEBSS-BETTTEEEEEE CS
                                CS  10 deVvvtiyvkkvnikkkdvkve.fkerslkvkigk.eklliegeLfgpIdpeesswtie 66 
                                       +eV+++i +++ + ++++vkv  + ++++k+ ++k e+++ + +L  +Id ++     +
  gi|385805453|ref|YP_005841851.1|  51 NEVKIYIMLPE-SLSEEQVKVVpIDKNHIKIFVEKyEEIYRKIKLHYKIDIKSVQAERK 108
                                       89*********.8********99**********88899998889999999988777666 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.38
                                       CTTTTTCEEEEEETTE..EEE CS
                                CS  21 vnikkkdvkvefkers..lkv 39 
                                       +++kkkd+ v   +++  lk+
  gi|385805453|ref|YP_005841851.1| 105 AERKKKDLIVLTAKKKkfLKI 125
                                       344455544443333335555 PP

>> T_Ag_DNA_bind  Origin of replication binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.0   5.4e-05      0.24      30      69 ..      82     121 ..      57     126 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.4e-05
                     T_Ag_DNA_bind  30 keKlkeLykkllekfkvkfkllakyeekavlllitakkhR 69 
                                        eK +e+y+k++ ++k++ k+++  ++k+ l+++takk++
  gi|385805453|ref|YP_005841851.1|  82 VEKYEEIYRKIKLHYKIDIKSVQAERKKKDLIVLTAKKKK 121
                                       69********************999999999999999865 PP

>> MecA_N  NTF2-like N-terminal transpeptidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.05   2.2e+02      29      62 ..       3      36 ..       1      43 [. 0.80
   2 ?    1.2   0.2     0.094   4.2e+02      44      57 ..      43      64 ..      41      80 .. 0.68
   3 ?    9.2   2.8    0.0003       1.4      31      69 ..      74     113 ..      56     123 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.05
                                      SSBSS-HHHHHHHHHHHCCCTT-EEEEEEEEEEE CS
                            MecA_N 29 skkeisekeavekyqaiydglqvkklkieakkvk 62
                                      +k ++  k++ e++ + + ++  +  +iea +++
  gi|385805453|ref|YP_005841851.1|  3 KKDDLNDKNLLERIINSFLNIFFNYNNIEAYSIA 36
                                      467999***********99998888888766655 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.094
                                      HHCCCTT-EEEEE........E CS
                            MecA_N 44 aiydglqvkklki........e 57
                                      +i++ ++++++ki        +
  gi|385805453|ref|YP_005841851.1| 43 EIFEKIDANEVKIyimlpeslS 64
                                      69999*******9666664442 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0003
                                       BSS-HHHHHHHHHHHCCCTT-E.EEEEEEEEEEEEETTEE CS
                            MecA_N  31 keisekeavekyqaiydglqvk.klkieakkvkkdkenta 69 
                                        ++  k +veky++iy  +++  k++i+  + +++k++  
  gi|385805453|ref|YP_005841851.1|  74 DKNHIKIFVEKYEEIYRKIKLHyKIDIKSVQAERKKKDLI 113
                                       4556688*************96589998888888887755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1488  (0.082994); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); 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: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 840.05
//
Query:       gi|385805454|ref|YP_005841852.1|  [L=541]
Description: hypothetical protein FFONT_0410 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.09   13.1  11.0       0.43   10.9   0.3    3.8  3  Vps39_1       Vacuolar sorting protein 39 domain 1
       0.24   11.3   5.1       0.53   10.2   0.4    3.0  3  YfdX          YfdX protein
        3.5    8.5   6.1       0.53   11.1   0.2    2.7  3  DUF3349       Protein of unknown function (DUF3349)


Domain annotation for each model (and alignments):
>> Vps39_1  Vacuolar sorting protein 39 domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.3   7.1e-05      0.43      40      87 ..      73     120 ..      55     138 .. 0.67
   2 ?    6.3   0.2    0.0019        11      25     108 .]     237     322 ..     219     322 .. 0.73
   3 ?    0.9   0.4     0.089   5.3e+02      61     100 ..     397     431 ..     361     439 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 7.1e-05
                           Vps39_1  40 kkykeLidlYygkklheeALeLlkeladedeedeedsslkgeketiiq 87 
                                       + ++++id+Y++k+l  + LeLl ++  ++ ++ee+ +  + +  i++
  gi|385805454|ref|YP_005841852.1|  73 NSINNIIDYYKSKGLNTSQLELLLTQFISALQSEEQGKATQIYIEIVK 120
                                       67899****************976555443333333333333333344 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0019
                           Vps39_1  25 NaCdlkdveeiLkkekkykeLidlYygkklheeALeLlkelade.deed.eedsslkgeketiiqylq..klseedl 97 
                                       N  ++ +v++i +k+  ++ L ++  +++++e+  ++++++ ++ ++++ +   s+++ ++tiiqy q   ls+++ 
  gi|385805454|ref|YP_005841852.1| 237 NSTEILNVKNIREKAMAVRGLGIM--QREMEENIQQIMNQIQNQiENSNlSSVISKDEINKTIIQYMQgePLSKKFG 311
                                       777778888888888888888875..778888888889998888644440344456667888****97446999999 PP

                           Vps39_1  98 dlileyskwvl 108
                                         i++ s+++l
  gi|385805454|ref|YP_005841852.1| 312 FNIFTSSEVLL 322
                                       99999999986 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.089
                           Vps39_1  61 Llkeladedeedeedsslkgeketiiqylqklseedldli 100
                                       L+ el    ++ + d++l+  k +i++ l++l+++ + li
  gi|385805454|ref|YP_005841852.1| 397 LISEL----SNITVDKQLNSVKVLILNALKNLDNS-ISLI 431
                                       22333....33566777777777788888888544.4444 PP

>> YfdX  YfdX protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.19   1.1e+03      29      94 ..       6     115 ..       1     128 [. 0.55
   2 ?   10.2   0.4   8.9e-05      0.53     113     143 ..     170     200 ..     164     226 .. 0.83
   3 ?    1.5   0.1     0.044   2.6e+02       6      52 ..     369     415 ..     363     437 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.19
                                       HHHTS-HHHHHCCB-.................................S--SSSS............-EEEEEEEEE CS
                              YfdX  29 gkleaaladdpklvk.................................kapasad............alvPvdaevi 60 
                                       + +e+++++ +kl++                                 +     +            + v v++  +
  gi|385805454|ref|YP_005841852.1|   6 QLMEKMRKKSKKLFAgtvsgllfilltfsfgnvftissaestntssvmT-----TtaqgsqvtnqtaEQVIVNSINN 77 
                                       5566666666666555555555555555555555444433333323331.....03333344444556677777777 PP

                                       EE--....----HHHHHHHHHHHHHHHTT-HHHHHHHH CS
                              YfdX  61 vidd....ladtpekkaaikkanellkkgdtqaArelL 94 
                                       +id+      +t++ +  +++  ++l+++++ +A ++ 
  gi|385805454|ref|YP_005841852.1|  78 IIDYykskGLNTSQLELLLTQFISALQSEEQGKATQIY 115
                                       77773323235777777778888888888888887765 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 8.9e-05
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHT- CS
                              YfdX 113 ypaavkkAaelleegkyyeAkeaLkealntl 143
                                         +++++A++l+++g+y+ A+ +Lk++ + l
  gi|385805454|ref|YP_005841852.1| 170 LTQQLNQALNLINQGNYTGASIILKNVVKEL 200
                                       5678899999999999999999999887666 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.044
                                       HHHHHHHCTT-HHHHHHHHHHHHHHHTS-HHHHHCCB-S--SSSS-E CS
                              YfdX   6 qkArlaldqgdtkeAkkllekAqgkleaaladdpklvkkapasadal 52 
                                       + A l+l + + + A + l++ ++++e + ++ ++ ++ +++++ + 
  gi|385805454|ref|YP_005841852.1| 369 NAAVLDLSATNAQNAFSSLQQISNQTEQLISELSNITVDKQLNSVKV 415
                                       6799999999***********99999999999999887776666644 PP

>> DUF3349  Protein of unknown function (DUF3349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1         3   1.8e+04      54      68 ..      59      73 ..      47      81 .. 0.47
   2 ?   -2.2   0.2       1.3   7.6e+03      44      68 ..     194     218 ..     189     228 .. 0.64
   3 ?   11.1   0.2   8.8e-05      0.53      27      75 ..     257     306 ..     250     310 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 3
                                      SS.BSHHHCHHHHHH CS
                           DUF3349 54 deavdeedieelitk 68
                                       ++v+++  e++i +
  gi|385805454|ref|YP_005841852.1| 59 GSQVTNQTAEQVIVN 73
                                      333444444444333 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.3
                                       HHHHHH--.SSS.BSHHHCHHHHHH CS
                           DUF3349  44 eelvaeaaeadeavdeedieelitk 68 
                                       +++v+e ++ +++++e++i++ +++
  gi|385805454|ref|YP_005841852.1| 194 KNVVKELNDMENSIKEAKIQAELSD 218
                                       4445555556677888877766554 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 8.8e-05
                                       HHHHCTT--HHHHHHHHHHHHHH--...SSS.BSHHHCHHHHHHHCTS--- CS
                           DUF3349  27 lalLrrrLsdeevkevaeelvaeaa..eadeavdeedieelitkvteeeps 75 
                                       l +++r++ +e+++++++++ ++ +  + ++ +++++i+++i + ++ ep 
  gi|385805454|ref|YP_005841852.1| 257 LGIMQREM-EENIQQIMNQIQNQIEnsNLSSVISKDEINKTIIQYMQGEPL 306
                                       66777776.689********99984458899**************999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (541 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2037  (0.113615); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 3814.18
//
Query:       gi|385805455|ref|YP_005841853.1|  [L=291]
Description: HTH_ARSR multi-domain protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-12   46.4   0.4    4.6e-12   45.3   0.4    1.6  1  HTH_24         Winged helix-turn-helix DNA-binding
     0.0001   22.2   0.0    0.00019   21.3   0.0    1.5  1  HTH_11         HTH domain
    0.00016   21.5   0.0    0.00028   20.7   0.0    1.4  1  TrmB           Sugar-specific transcriptional regulator TrmB
    0.00032   20.5   0.0    0.00071   19.5   0.0    1.5  1  MarR           MarR family
    0.00037   20.3   0.0    0.00066   19.5   0.0    1.3  1  MarR_2         MarR family
    0.00068   19.4   0.1      0.001   18.8   0.1    1.3  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain
     0.0011   18.8   0.0      0.024   14.5   0.0    2.2  2  HTH_5          Bacterial regulatory protein, arsR family
     0.0019   18.3   0.0     0.0044   17.1   0.0    1.6  1  AbiEi_4        Transcriptional regulator, AbiEi antitoxin
     0.0031   17.6   0.0     0.0049   16.9   0.0    1.2  1  HTH_20         Helix-turn-helix domain
     0.0098   15.6   0.0      0.024   14.4   0.0    1.5  1  HTH_39         Helix-turn-helix domain
  ------ inclusion threshold ------
      0.094   12.2   0.1      0.094   12.2   0.1    2.3  2  SieB           Super-infection exclusion protein B
       0.14   12.0   0.0       0.25   11.2   0.0    1.3  1  HTH_IclR       IclR helix-turn-helix domain
        3.2    8.1   5.4        1.7    9.0   0.8    2.4  2  Wzz            Chain length determinant protein
        3.8    7.9  10.2         14    6.0   0.0    3.6  3  Sigma_reg_N    Sigma factor regulator N-terminal


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.4   3.6e-15   4.6e-12       1      48 []     228     275 ..     228     275 .. 0.98

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 3.6e-15
                            HTH_24   1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                       ld+ drkI e++++++ i+  +L  +l++++s+  rr++rL+++G+I+
  gi|385805455|ref|YP_005841853.1| 228 LDDRDRKIVEIIREKGPITPGDLLNQLNIPRSAFYRRINRLKKDGIIE 275
                                       79*********************************************7 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   1.5e-07   0.00019       1      44 [.     231     273 ..     231     285 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.5e-07
                            HTH_11   1 RllqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44 
                                       R ++i+e++ +++gpi+  +L  +Ln+ r++ +r+I +L++ g+
  gi|385805455|ref|YP_005841853.1| 231 RDRKIVEII-REKGPITPGDLLNQLNIPRSAFYRRINRLKKDGI 273
                                       6689*****.88889***************************93 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   2.2e-07   0.00028      19      63 ..     241     285 ..     228     289 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.2e-07
                                       HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEE CS
                              TrmB  19 klgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYr 63 
                                       ++gp t  ++ ++l++prs  Y+ +++L++ G++e  +   k+Y 
  gi|385805455|ref|YP_005841853.1| 241 EKGPITPGDLLNQLNIPRSAFYRRINRLKKDGIIEQFEVGGKVYY 285
                                       7899********************************997755543 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   5.5e-07   0.00071       7      48 ..     234     275 ..     231     278 .. 0.95

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 5.5e-07
                                       HHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR   7 viLrilyeqgplsvseLakklgvskstvtrvldrLekkGlie 48 
                                       +i++i++e+gp++  +L ++l++ +s+  r + rL k+G ie
  gi|385805455|ref|YP_005841853.1| 234 KIVEIIREKGPITPGDLLNQLNIPRSAFYRRINRLKKDGIIE 275
                                       5889************************************98 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   5.2e-07   0.00066      13      53 ..     237     276 ..     230     279 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 5.2e-07
                                       HHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2  13 aLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53 
                                       ++ r+ g+ +t+g+l   l++++sa  r+++rL + G +e+
  gi|385805455|ref|YP_005841853.1| 237 EIIREKGP-ITPGDLLNQLNIPRSAFYRRINRLKKDGIIEQ 276
                                       56667776.9****************************985 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   0.1     8e-07     0.001       1      42 []     228     269 ..     228     269 .. 0.98

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 8e-07
                     HTH_AsnC-type   1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42 
                                       LD+ DrkI+e+++e + i+  +L  ++++ +s+  rR++rL+
  gi|385805455|ref|YP_005841853.1| 228 LDDRDRKIVEIIREKGPITPGDLLNQLNIPRSAFYRRINRLK 269
                                       8***************************************95 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.15   1.9e+02      17      37 ..      58      78 ..      56      79 .. 0.89
   2 !   14.5   0.0   1.8e-05     0.024       5      46 ..     233     275 ..     229     276 .. 0.95

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.15
                                      EHHHHHHHHTS-HHHHHHHHH CS
                             HTH_5 17 cvcelaeelglsqstvShHLk 37
                                      c++ +   l+++ s+v+++L 
  gi|385805455|ref|YP_005841853.1| 58 CIGNCLYVLNINTSNVDYYLE 78
                                      88888899**********995 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 1.8e-05
                                       HHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5   5 lkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVe 46 
                                       +kI+ + +e g+ + ++l ++l++++s+  +  ++L++ G++e
  gi|385805455|ref|YP_005841853.1| 233 RKIVEIIREkGPITPGDLLNQLNIPRSAFYRRINRLKKDGIIE 275
                                       699**************************************97 PP

>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   3.4e-06    0.0044       1      40 [.     233     276 ..     233     280 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.4e-06
                           AbiEi_4   1 erlpelasrqvGlfttrelea.aGispsa....lrrLvrkGwLvr 40 
                                       ++++e++ r++G +t  +l   ++i++sa    ++rL + G +++
  gi|385805455|ref|YP_005841853.1| 233 RKIVEII-REKGPITPGDLLNqLNIPRSAfyrrINRLKKDGIIEQ 276
                                       6899999.889*******9999**********************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 !   16.9   0.0   3.8e-06    0.0049      13      56 ..     233     276 ..     228     280 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.8e-06
                                       HHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20  13 rrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56 
                                       r+i   ++++++ t+++l  +l ++++  +++++ L + g++e+
  gi|385805455|ref|YP_005841853.1| 233 RKIVEIIREKGPITPGDLLNQLNIPRSAFYRRINRLKKDGIIEQ 276
                                       78999999**********************************96 PP

>> HTH_39  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   1.9e-05     0.024       4      42 ..     233     273 ..     231     274 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.9e-05
                            HTH_39   4 arilaaLrqhgsittleamrelditrla..aRIkeLrekGy 42 
                                       ++i++++r++g+it   ++++l+i+r a  +RI +L+++G+
  gi|385805455|ref|YP_005841853.1| 233 RKIVEIIREKGPITPGDLLNQLNIPRSAfyRRINRLKKDGI 273
                                       89************************87669*******996 PP

>> SieB  Super-infection exclusion protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   1.8       5.1   6.5e+03      34      48 ..       5      19 ..       2      24 .. 0.62
   2 ?   12.2   0.1   7.3e-05     0.094      18      85 ..     178     235 ..     174     243 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 5.1
                              SieB 34 wiglvflisiaylla 48
                                      +i+l+f+i++ y+++
  gi|385805455|ref|YP_005841853.1|  5 IIVLAFIIIFIYSIT 19
                                      566666666666654 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 7.3e-05
                              SieB  18 lleklnlgkfleeyglwiglvflisiayllaqvvskllaeikekikkkreqkkvekklknLteeekav 85 
                                        + + +l++ +++y+l+i  ++li+i++l+ ++ +++ ++           k  e+k+k L+++ +++
  gi|385805455|ref|YP_005841853.1| 178 TPSTAGLHQGISNYALYIIGIILIAIGLLIGYLYFRGPKK----------GKSLEEKIKYLDDRDRKI 235
                                       566789999************************9999954..........445555555555555544 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 ?   11.2   0.0   0.00019      0.25      14      50 ..     240     276 ..     234     277 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00019
                                       TTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  14 eapqeltlselArrtglpkStvhRlLqtLvelGyveq 50 
                                       ++ ++ t  +l +++ +p+S+ +R ++ L + G++eq
  gi|385805455|ref|YP_005841853.1| 240 REKGPITPGDLLNQLNIPRSAFYRRINRLKKDGIIEQ 276
                                       45566899**************************998 PP

>> Wzz  Chain length determinant protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.8    0.0013       1.7      14      45 ..       2      33 ..       1      54 [. 0.87
   2 ?    0.6   0.3      0.55   7.1e+02      18      36 ..     194     212 ..     186     216 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0013
                                      XXXXXXXXXXXXXXXXXXXXXXXXXX-EEEEE CS
                               Wzz 14 krkklIilvtllfallaviyaflatpkYtata 45
                                      ++k+++++++++f+    ++++++ p Yt   
  gi|385805455|ref|YP_005841853.1|  2 RKKIIVLAFIIIFIYSITFISIAQEPSYTNAV 33
                                      7899999*********************9753 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.55
                                       XXXXXXXXXXXXXXXXXXX CS
                               Wzz  18 lIilvtllfallaviyafl 36 
                                        Ii ++l+++ l ++y+++
  gi|385805455|ref|YP_005841853.1| 194 YIIGIILIAIGLLIGYLYF 212
                                       5888888888888888866 PP

>> Sigma_reg_N  Sigma factor regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   1.8      0.15   1.9e+02      15      33 ..       5      23 ..       2      35 .. 0.56
   2 ?    2.7   0.4      0.12   1.5e+02      27      61 ..      55      89 ..      53     100 .. 0.87
   3 ?    6.0   0.0     0.011        14      13      50 ..     188     226 ..     185     230 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.15
                       Sigma_reg_N 15 ivlislivlllifvilvvt 33
                                      i+++++i+++++++ ++++
  gi|385805455|ref|YP_005841853.1|  5 IIVLAFIIIFIYSITFISI 23
                                      4444444444444444433 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.12
                       Sigma_reg_N 27 fvilvvtllylaekegnklrevlelaveitsPNvy 61
                                      +v ++ ++ly+++ ++++ +++le+   +  PN +
  gi|385805455|ref|YP_005841853.1| 55 VVNCIGNCLYVLNINTSNVDYYLENNTIVLVPNNF 89
                                      566799*****************999999999866 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.011
                       Sigma_reg_N  13 lrivlislivlllifvilvvtllyl.aekegnklrevle 50 
                                       +++  + +i ++li + l++++ly+  +k+g+ l+e+++
  gi|385805455|ref|YP_005841853.1| 188 ISNYALYIIGIILIAIGLLIGYLYFrGPKKGKSLEEKIK 226
                                       567777888888888999*******99999998888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       965  (0.0538234); expected 358.6 (0.02)
Passed bias filter:                      596  (0.0332422); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1764.73
//
Query:       gi|385805456|ref|YP_005841854.1|  [L=799]
Description: family B-type DNA polymerase [Fervidicoccus fontis Kam940]
Scores for complete 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-73  246.1   0.5    1.1e-72  245.2   0.5    1.5  1  DNA_pol_B       DNA polymerase family B
    7.8e-45  153.5   3.9    1.8e-42  145.7   3.9    2.3  1  DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
      1e-09   38.6   0.1    2.7e-09   37.3   0.1    1.8  1  RNase_H_2       RNase_H superfamily
    9.1e-08   32.0   0.0    1.6e-07   31.2   0.0    1.3  1  DNA_pol_B_exo2  Predicted 3'-5' exonuclease related to the ex
    6.8e-06   25.2   0.9    5.9e-05   22.1   0.9    2.3  1  DNA_pol_B_2     DNA polymerase type B, organellar and viral
  ------ inclusion threshold ------
      0.013   15.3   0.0      0.027   14.3   0.0    1.5  1  UPF0167         Uncharacterised protein family (UPF0167)
      0.022   14.8   0.0      0.084   12.9   0.0    2.0  1  DUF5415         Family of unknown function (DUF5415)


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 !  245.2   0.5   4.5e-76   1.1e-72       4     457 ..     379     769 ..     376     771 .. 0.88

  Alignments for each domain:
  == domain 1  score: 245.2 bits;  conditional E-value: 4.5e-76
                                       HHHHHS-HHHHHHHHHHHHHHHTTBE-B-----.--SS.-S----BE----EEESS-EEEEEETTHHHHHHHHTT-S CS
                         DNA_pol_B   4 srvledgqqirveslLlrlakeegfilpdrtekkgkeeegYqGatVlePkkglydkpvlvlDFaSLYPsiiqahNlc 80 
                                        ++++ +   r e+ L+r+a + + i+p+r+e  ++e+  Y+Ga Vl+Pk+g+++ +++vlDFaS+YP+i++++N+ 
  gi|385805456|ref|YP_005841854.1| 379 DQLMATSVGYRLEYYLIRKAYRFNEIVPNREER-ERES--YKGAIVLKPKSGVHE-NIAVLDFASMYPNIMIKYNVG 451
                                       5566666678999***************55555.5555..*************97.69******************* PP

                                       TTTCE-HCCHCC.T--BTT...TEEE-TCC-EEE-TTS---HHHHHHHHHHHHHHHHHHHHHCS--HH.HHHHHHHH CS
                         DNA_pol_B  81 yttlvaseeeak.eleaedeyleveveprlvefvkksvregllpklLkdllakRkaikkelkeekdef.ekalldkq 155
                                       + tlv++ ++++  + ++           +++f   ++  g + ++L dlla+R++i+++lk+ k    e  +ld++
  gi|385805456|ref|YP_005841854.1| 452 PDTLVKECKNDEcYVAPD----------VGHKF--RKEPPGFFKSVLSDLLAARQKIRQQLKKLKPGDpEYNVLDER 516
                                       *****9999876333332..........34445..67789**********************666543399****** PP

                                       HHHHHHHHHHHHHHHTSTTSTT--HHHHHHHHHHHHHHHHHHHHHHHHT...SSGGGT-SS.....T-EEEEEBSSE CS
                         DNA_pol_B 156 QlalKvtaNsvYGftGvansrlpclalAasvTtiGRemLektkelvekkaellskllalpeeaeeeklkviYGDTDS 232
                                       Q+a+Kv+aN+ YG++G +  r +c++ A+ +T+ GR++++ + e  +k                  +l+viYGDTDS
  gi|385805456|ref|YP_005841854.1| 517 QKAIKVLANASYGYMGWQGARWYCKECAEAITAWGRQNITFAIEKAKKL-----------------GLDVIYGDTDS 576
                                       ***************************************9887777755.................9********** PP

                                       EEEE-S-SSHHHHHHHHHHHHHHHHT.TSTTT--EEEEEEEEEEEEE.ETTEEEEEEEEESSTTSEEEEESSGGGST CS
                         DNA_pol_B 233 vfielkvkdveellkigkelaeevseklfkkplklefekvykkllLi.sKKkYaglkvektskanklliKGvdlvRr 308
                                       +f++++ k+++ell+i       ++++l    l+++++k+ykkl ++ +KK+Y+g++++     n ++i G + +R 
  gi|385805456|ref|YP_005841854.1| 577 LFVQFDEKKINELLNI-------INSELG---LEIKIDKIYKKLFFTeAKKRYVGITID-----NIIDIVGFEAIRG 638
                                       *********9988875.......788444...66999*********846**********.....889********** PP

                                       TS-HHHHHHHHHHHHHHSSS....S-HHHHHHHHHHHHHHHHHHHHTT-S-GGGG-EEEEESS.CCCSSGCCSHHHH CS
                         DNA_pol_B 309 dncklvkevikkvlelllkdeteersleeglealksilkdvleeleenkvplekfvlskelskepenyksknlphle 385
                                       d+++++k++ +++ +l+l++      +e+++e+ k+i+    ++l+e+k+p++k+v+ k+++k+ e+y+  + ph++
  gi|385805456|ref|YP_005841854.1| 639 DWSEISKDIQTEIARLILEK----GTTEKAIEYTKEII----RNLKEKKIPIDKLVIWKTITKPIEEYEVDA-PHVT 706
                                       ********************....99999999999999....**************************9888.***9 PP

                                       HHHHHHHHCSS---TTCEEEEEEBETSS.....SS-GGGTEEEHHHHHHCCSEB-HHHHHH.TTHHHHHHHHT CS
                         DNA_pol_B 386 vakrlkkrneeapevgdrisYvivekkkevkkknllaseraedpeyvleknlpidieyYls.qllkevarlle 457
                                       +ak + ++ + ++++gd++ Yv+v+ +        ++se+++   y  +   +id++yY++ q++++++r+le
  gi|385805456|ref|YP_005841854.1| 707 AAKLY-QEYGLKISPGDKVGYVVVSGEG-------KISEKVK--PYFAATLDEIDVDYYVDhQIIPAAMRILE 769
                                       88655.55699**************964.......6666653..577777889******************97 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 !  145.7   3.9   7.2e-46   1.8e-42      13     335 ..      43     309 ..      31     311 .. 0.90

  Alignments for each domain:
  == domain 1  score: 145.7 bits;  conditional E-value: 7.2e-46
                                       EE---EEEEEESSCGGHHHHHHHHHHHCCTTCCCEEEEEEEECCCCEECCTSSCCHHCEEEEEESSTCHHHHHHHHH CS
                    DNA_pol_B_exo1  13 fgfkpyfYceapdgkeleevkeelkelyeelskkvtkivkvelvlkkslygyekkpvpylkvsvsnpnelkkirkel 89 
                                         fkpyfY+  +++++ e+vk+e+  l++++  k +    ve  + k+lyg   k    lk+ +  p++++++r+++
  gi|385805456|ref|YP_005841854.1|  43 WRFKPYFYAILEEESNIEKVKNEVLTLVRRKEPKAS----VE-LVEKKLYGKPVK---ALKIIMMIPEQVREVRDRV 111
                                       579******************************999....66.444789999988...9****************** PP

                                       HHCCCCCCCCSSS--HHHHHHHHCTS-TTCEEEEETEEEEGCC--C-.SEEEEEETTTSCEETTTCC.S-EEEEEEE CS
                    DNA_pol_B_exo1  90 spleeivdvyeydvdylerflidnkivgfgwysvkkylvraegkisncdveidcdvddliakpkese.pplrvlsFD 165
                                       ++   + dv e+d+ + +r++id++i++f+wy+v++++v++++  s + +e+  d  +l+a   e++ p l+ + FD
  gi|385805456|ref|YP_005841854.1| 112 KNVPMVKDVLEADIRFSMRYMIDKDIKPFRWYKVPVREVSKKKYRSAKIYEVLEDPIELEA---EASfPSLKTMVFD 185
                                       ***************************************************9998888888...7789********* PP

                                       EEETEETTSEETTTT..--EEEEEEEECCTC.SS.SEEEEEEECCCTSS----EE--SSTCSTTEEEEEESSHHHHH CS
                    DNA_pol_B_exo1 166 IeckskkgkfpdaensedpiiqIscvldglgekepearklftlrecaseeeedfeltpkpeypgvkvlefdsEkelL 242
                                       Ie++s++g  p +e+  dpii I ++  gl+             ++             +        e +++ke +
  gi|385805456|ref|YP_005841854.1| 186 IEVYSTTG-SPRPEK--DPIIIIGLMDGGLK-------------QFY------------S--------ENKDDKETI 226
                                       ********.******..*******9977655.............666............3........467899*** PP

                                       HHHHHHHHHH--SEEEESSTTTTHHHHHHHHHHHCCTCCHCG.SCCS.CTCEECCCCESEEEEEECEEEETTSEEEE CS
                    DNA_pol_B_exo1 243 qaflefikqydPdvitgYNidnFDlpYilnRakelykvklsklgrln.kggrskvseigfskqarekvkisgrihlD 318
                                       ++f+e ++++dPd+i gYNi+ FD+ Y+l+Rak         ++ ln + +r  +++++ s  ++++++++gr+++D
  gi|385805456|ref|YP_005841854.1| 227 KKFIEEVQKIDPDIISGYNINVFDWNYLLQRAK---------YNGLNlDVTREIGKSPATS--TAGHISVAGRLNVD 292
                                       *********************************.........6666667777777777777..************** PP

                                       HHHHHHHHSSSSG-SHH CS
                    DNA_pol_B_exo1 319 lyrvvkrklklpsYkLn 335
                                       +++++++ +  +  +L+
  gi|385805456|ref|YP_005841854.1| 293 IFDFAQEISEVKRKTLE 309
                                       ******98888776665 PP

>> RNase_H_2  RNase_H superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.1     1e-12   2.7e-09       2     164 ..     183     362 ..     182     364 .. 0.67

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 1e-12
                         RNase_H_2   2 ffDiEttGl....spkknliyliGvldvdekeiekltqllaeepeeekailelfle.llekkkalvtfngksFDvpf 73 
                                        fDiE +       p+k+ i+ iG++d  +  ++   q+  e++++++ i++++ e +  + + +  +n + FD+ +
  gi|385805456|ref|YP_005841854.1| 183 VFDIEVYSTtgspRPEKDPIIIIGLMD--GG-LK---QFYSENKDDKETIKKFIEEvQKIDPDIISGYNINVFDWNY 253
                                       5999955443335678899*******5..43.33...333455555555555443303556677888********** PP

                         RNase_H_2  74 lkrlf..kkyklde.......................eefrhiDLlkelrkkklesysLksvekelgierreedlsG 125
                                       l +++  +  +                           +++ +D  +e+++ k +   L+++ +++g+  +    + 
  gi|385805456|ref|YP_005841854.1| 254 LLQRAkyNGLN--LdvtreigkspatstaghisvagrLNVDIFDFAQEISEVKRK--TLEDISEYMGVMKK----DE 322
                                       *****553333..244878999999988888777444444444555555544444..69*********999....56 PP

                         RNase_H_2 126 sqavklyq...eylrtgdeellekilaYNedDvralatlyek 164
                                       + + ++y+    +  tg +e  ek+l+YN+dDv+++++l+ek
  gi|385805456|ref|YP_005841854.1| 323 RVLLEWYDipkLW-DTG-KEGREKVLRYNRDDVISTYRLMEK 362
                                       7788888644235.444.55679*****************97 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 !   31.2   0.0   6.4e-11   1.6e-07      28     174 ..     213     364 ..     206     375 .. 0.79

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 6.4e-11
                    DNA_pol_B_exo2  28 kslgeeessekelikkffegvekkkpqlVs.fngrgfDlpvleyralkhgvsapkyfdegdedrekkwnnylsryst 103
                                       k++ +e++++ke ikkf+e v+k  p ++s +n + fD   l +ra ++g++     + g++   +     +s   +
  gi|385805456|ref|YP_005841854.1| 213 KQFYSENKDDKETIKKFIEEVQKIDPDIISgYNINVFDWNYLLQRAKYNGLNLDVTREIGKSP-ATSTAGHISVAGR 288
                                       567788999*******************977***********************999999954.3444445555555 PP

                    DNA_pol_B_exo2 104 rhlDLmdllseygaranakLdelakllglPGK...lgvdGskVaelyqegk..lkeireYcetDvlnTYlvylrle 174
                                         +D+ d   e    +++ L+++++ +g+  K   + ++  ++ +l+++gk   +++ +Y++ Dv++TY +  ++ 
  gi|385805456|ref|YP_005841854.1| 289 LNVDIFDFAQEISEVKRKTLEDISEYMGVMKKderVLLEWYDIPKLWDTGKegREKVLRYNRDDVISTYRLMEKFL 364
                                       56666666666666667777777777777665211568999*******99844589*************9877776 PP

>> DNA_pol_B_2  DNA polymerase type B, organellar and viral
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.9   2.3e-08   5.9e-05     104     246 ..     310     448 ..     294     460 .. 0.69

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2.3e-08
                       DNA_pol_B_2 104 sdgfpvekywkekeeivenkelwkekeekkydivketleYckqDvlvlaklllklkesideff.easinifkrpTis 179
                                       + + +    +k++ +++e++++ k   +  ++ +++ l Y + Dv+++++l++k+     +    + i + + + +s
  gi|385805456|ref|YP_005841854.1| 310 DISEYMGVMKKDERVLLEWYDIPKL-WDTGKEGREKVLRYNRDDVISTYRLMEKFLPFGIQLSgLTGIPLDQLMATS 385
                                       4555556667888888888887544.3345667888999***************98854433354455555555555 PP

                       DNA_pol_B_2 180 slalaifkqilyrkkkkellapskeldkyiRkayrGGrc.ypsvlgiyeeniyvyDvnSlYPsamthy 246
                                             +  i  ++++ +  +p++e+ +  R++y G ++ +p+  g + eni v D+ S+YP++m +y
  gi|385805456|ref|YP_005841854.1| 386 VGYRLEYYLIR-KAYRFNEIVPNREERE--RESYKGAIVlKPK-SG-VHENIAVLDFASMYPNIMIKY 448
                                       44333333333.3333333677777766..*********8777.55.56****************996 PP

>> UPF0167  Uncharacterised protein family (UPF0167)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.1e-05     0.027      71     138 ..     511     575 ..     489     597 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.1e-05
                           UPF0167  71 lveeeldeelleellkrtpgyiswqqeqWlahCddacaflgevgaeelealkiklekeelaaikddle 138
                                       +v  +  +++++ l++   gy++wq  +W+  C + ++ +  +g ++++ + +k +k  l+ i  d++
  gi|385805456|ref|YP_005841854.1| 511 NVL-DERQKAIKVLANASYGYMGWQGARWY--CKECAEAITAWGRQNITFAIEKAKKLGLDVIYGDTD 575
                                       355.34567788999999***********6..9999999******99987777777777777766665 PP

>> DUF5415  Family of unknown function (DUF5415)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.3e-05     0.084      11      44 ..     763     798 ..     760     799 .] 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.3e-05
                           DUF5415  11 aaskilerrGvseaqwkkevlekvq..fdllrGkdk 44 
                                       aa +ile  Gvse+  k+  +ek +  fd l  k k
  gi|385805456|ref|YP_005841854.1| 763 AAMRILEYFGVSESVLKQGAIEKQKslFDYLSSKQK 798
                                       899******************9864449**999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (799 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1012  (0.0564449); expected 358.6 (0.02)
Passed bias filter:                      682  (0.0380389); 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: 0.83u 0.34s 00:00:01.17 Elapsed: 00:00:00.52
# Mc/sec: 4648.26
//
Query:       gi|385805457|ref|YP_005841855.1|  [L=239]
Description: purine or other phosphorylase, family 1 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.3e-40  137.8   0.0    3.8e-40  137.6   0.0    1.0  1  PNP_UDP_1  Phosphorylase superfamily


Domain annotation for each model (and alignments):
>> PNP_UDP_1  Phosphorylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.6   0.0   2.1e-44   3.8e-40       2     229 ..      15     234 ..      14     238 .. 0.87

  Alignments for each domain:
  == domain 1  score: 137.6 bits;  conditional E-value: 2.1e-44
                                       EEEEESSHHHHHHHHHHEEEEEEEEEE.TTEEEEEEEETTEEEEEEE--SSHHHHHHHHHHHHHHHC--SEEEEEEE CS
                         PNP_UDP_1   2 iaiivgspgevellaespleetpfgregrgfkfvtGtlkgkpvvivstGiGkpnaavvaeirllkefgvkaiiriGt 78 
                                        +++vg+p+++ lla+s l+  + ++e+rg   +tGt+kg++++iv++GiG+p+a  +   +l+  +g+kaiir+Gt
  gi|385805457|ref|YP_005841855.1|  15 KVVTVGDPNRASLLANSLLDYPKLINENRGLLSYTGTYKGERISIVTHGIGMPSAL-IVFEELVS-LGAKAIIRFGT 89 
                                       589**************6666666666*****************************.77777777.46********* PP

                                       EEESSTTT-TT-EEEEEEEEESSSCCGCCTHHCCTCCCCTTSSEE--HHHHHHHHHCHHTTTTTEEEEEEEEESESS CS
                         PNP_UDP_1  79 aGglnpdlkvGDvvipddainfdgrsplygpkeegqyfpdsydapadpelrallkeaaealgikvhrGvvatadgfy 155
                                       +G+l++++k+GD+vi+++  ++ + s+ ++           ++  ++ +l+++l+ + ++++ ++h+G+++++d fy
  gi|385805457|ref|YP_005841855.1|  90 SGSLKEQVKIGDIVIAES-AGHFNSSAIRQ-----YFDDIIPPNGFSFDLINTLVDNFKRSDFNFHVGPIISSDAFY 160
                                       ******************.57777777554.....34445566689******************************* PP

                                       -CHHHHHHHHHHTC-CEEESSHHHHHHHHHHTT--EEEEEEEEETTTBETTCTCH.HCCCHHHHHHHHHHHHHH CS
                         PNP_UDP_1 156 aeteaelrllrrlgadaveMEtaavaqlArelgipfaairvvsdlaaggadaeatheeveefaqeaaknaaall 229
                                       +e+++ +  l+rlg  a+eME+a +a++  ++g++ +++  v++++ + +++  + + + + +   a+n+  +l
  gi|385805457|ref|YP_005841855.1| 161 SESKDLALKLSRLGFFAIEMECAGLAMIGWLRGLKTGCVLYVTNHLLRNGEEMLDSAQINKKMVSVATNIFDAL 234
                                       ***99999*************************************99988777777777777777777766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1512.10
//
Query:       gi|385805458|ref|YP_005841856.1|  [L=397]
Description: Pua [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-16   59.0   0.0      6e-16   58.4   0.0    1.2  1  Methyltrans_SAM  S-adenosylmethionine-dependent methyltransfe
    6.4e-13   48.7   0.0      1e-12   48.1   0.0    1.2  1  Cons_hypoth95    Conserved hypothetical protein 95
    1.9e-09   37.5   0.0    3.2e-09   36.8   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    1.1e-06   28.3   0.1    4.4e-06   26.4   0.2    2.0  2  PUA_3            PUA-like domain
    2.9e-05   23.7   0.0    4.4e-05   23.1   0.0    1.2  1  MTS              Methyltransferase small domain
    0.00011   21.4   1.0    0.00028   20.1   1.0    1.6  1  Methyltransf_3   O-methyltransferase
    0.00023   20.6   0.0    0.00036   20.0   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    0.00032   20.5   0.0    0.00048   19.9   0.0    1.2  1  Met_10           Met-10+ like-protein
     0.0064   16.1   0.0      0.013   15.1   0.0    1.4  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
  ------ inclusion threshold ------
      0.021   15.8   0.0      0.042   14.9   0.0    1.5  1  Methyltransf_24  Methyltransferase domain
      0.076   12.7   0.0       0.12   12.0   0.0    1.3  1  UPF0020          Putative RNA methylase family UPF0020
        0.2   11.0   0.0       0.33   10.3   0.0    1.2  1  Methyltransf_10  RNA methyltransferase


Domain annotation for each model (and alignments):
>> Methyltrans_SAM  S-adenosylmethionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.4   0.0     4e-19     6e-16      76     253 ..     173     354 ..     162     366 .. 0.86

  Alignments for each domain:
  == domain 1  score: 58.4 bits;  conditional E-value: 4e-19
                   Methyltrans_SAM  76 evlvgeldespvvvesglkyqldigrnqnfglfldmrlgrdwvqena.kdknvlnlfaytcgfsvaaiaggaskvvn 151
                                       ++l ge+     ++e+ l +++d+   q++g++ld r  r+ +   +  + ++l+lf+yt  fs  a+  gas  + 
  gi|385805458|ref|YP_005841856.1| 173 KFLHGEPPPYTYIKEDDLIFKIDFLNGQKTGFYLDQREARKKISSLSlDGAKILDLFSYTGSFSAHALKAGASFSLL 249
                                       5799999999********************************9986626789************************* PP

                   Methyltrans_SAM 152 vdmargslnkgrdnhrlnghdlrrvsflgydifkswgk.ikksgpydlviidppsfqkgsfal...tkdykkilrrl 224
                                       vd    +ln  ++n   ng + ++ +++   + k     + k+ ++d+vi+dpp+f           k ykk++   
  gi|385805458|ref|YP_005841856.1| 250 VDEDDRALNIAKENLIKNGFE-DKFEIIRGRVEKVIDSlLIKKMQFDIVIVDPPAFIPSKNLYekgIKAYKKLFGNT 325
                                       ******************998.4566666666666554156888************7554433112689******** PP

                   Methyltrans_SAM 225 pellveggevlacvnspavspdflieema 253
                                         l+  gg + a   s  +s+d l++ ++
  gi|385805458|ref|YP_005841856.1| 326 LRLVKLGGYIYASSCSFHLSSDELLKILQ 354
                                       *************9999999999987665 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   0.0   6.9e-16     1e-12      39     122 ..     219     302 ..     206     326 .. 0.91

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 6.9e-16
                                       CHCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEE CS
                     Cons_hypoth95  39 eiegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefd 115
                                        ++ga++LDlf+ +G+ +  Al  ga+ ++lv++d++a++i kenl + ++e+++++++   ++ +++l  kk +fd
  gi|385805458|ref|YP_005841856.1| 219 SLDGAKILDLFSYTGSFSAHALKAGASFSLLVDEDDRALNIAKENLIKNGFEDKFEIIRGRVEKVIDSLLIKKMQFD 295
                                       5899************************************************************************* PP

                                       EEEE--S CS
                     Cons_hypoth95 116 ivflDPP 122
                                       iv +DPP
  gi|385805458|ref|YP_005841856.1| 296 IVIVDPP 302
                                       ******* PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   0.0   2.1e-12   3.2e-09       4     130 ..     222     365 ..     219     382 .. 0.88

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 2.1e-12
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdiee.lekl.ledekfDl 77 
                                       g ++lDl + tG ++  +  ++g  +   ++D + +a++ A+en+ k+g++  +e  +g +e+ +++l +++ +fD+
  gi|385805458|ref|YP_005841856.1| 222 GAKILDLFSYTGSFSAHAL-KAGA-SFSLLVDEDDRALNIAKENLIKNGFEdKFEIIRGRVEKvIDSLlIKKMQFDI 296
                                       6789********9999999.6664.5579**********************9************************* PP

                   Methyltransf_31  78 ilsnevl.........naladpdkileeiervlkpggilliedpr...llaelpakveeeskay....e 130
                                       ++ + +            +++ +k +++  r++k gg++ +++++     +el+++++e+ ++y    +
  gi|385805458|ref|YP_005841856.1| 297 VIVDPPAfipsknlyeKGIKAYKKLFGNTLRLVKLGGYIYASSCSfhlSSDELLKILQEWINYYgyksR 365
                                       ***955566777667888999999999******************998899999*99999998866554 PP

>> PUA_3  PUA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.2     3e-09   4.4e-06       1      63 [.       7      67 ..       7      68 .. 0.96
   2 ?   -2.1   0.0       2.4   3.5e+03      34      50 ..     224     240 ..     211     241 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 3e-09
                             PUA_3  1 viLkkkaekrlrqGhPwvfsneiasvegeledGdvVdvfsekgkflGtGyynpqskiavRils 63
                                      v +kk+a + +++++  ++s+ ++s +  l +Gd+V+    +g+ +G+G+y +   i +Ri+s
  gi|385805458|ref|YP_005841856.1|  7 VEIKKGAKSLIEKHFYSIYSKWVKSDS-SLSNGDFVKFLF-NGEVIGYGFYEKIGSIGGRIIS 67
                                      679************************.69*******998.9*******************98 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.4
                             PUA_3  34 dvVdvfsekgkflGtGy 50 
                                        + d+fs  g f ++++
  gi|385805458|ref|YP_005841856.1| 224 KILDLFSYTGSFSAHAL 240
                                       68899******999885 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0     3e-08   4.4e-05      32     107 ..     222     303 ..     213     348 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 3e-08
                                       CSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.....EEEEE-STTTT..STTS-EEEE CS
                               MTS  32 sgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.....vevvasdvlee..veekkfdli 101
                                         k+lDl + +G  +a+++k+  + +  lvd+d rAl++akenl +n++e     ++ + + v++   +++++fd++
  gi|385805458|ref|YP_005841856.1| 222 GAKILDLFSYTGSFSAHALKAGASFS-LLVDEDDRALNIAKENLIKNGFEdkfeiIRGRVEKVIDSllIKKMQFDIV 297
                                       568*****************999975.589*******************999666555556666652245899**** PP

                                       EE---S CS
                               MTS 102 vsNPPf 107
                                       +  PP 
  gi|385805458|ref|YP_005841856.1| 298 IVDPPA 303
                                       *****5 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   1.0   1.9e-07   0.00028      77     153 ..     249     335 ..     217     343 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.9e-07
                                       EEES-HHHHHHHHHHHHHTT-GGGEEEEES-HHHHHHHHHTSSS---EEEEEE-S.....-G.......GGHHHHHH CS
                    Methyltransf_3  77 aididreayeialkfiqkagvaekieliegdalkvLeelvkdkklpefDfifvDa.....Dk.......ssyvnyye 141
                                        +d d  a +ia++ + k g+++k e+i+g   kv++ l+ +k   +fD++ vD       k       ++y++ + 
  gi|385805458|ref|YP_005841856.1| 249 LVDEDDRALNIAKENLIKNGFEDKFEIIRGRVEKVIDSLLIKKM--QFDIVIVDPpafipSKnlyekgiKAYKKLFG 323
                                       5899999********************************99995..9*****9952222223111112245666666 PP

                                       HHHHTEEEEEEE CS
                    Methyltransf_3 142 klleLvkvGgli 153
                                       ++l+Lvk Gg i
  gi|385805458|ref|YP_005841856.1| 324 NTLRLVKLGGYI 335
                                       777777777765 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   2.4e-07   0.00036     158     231 ..     218     298 ..     211     302 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.4e-07
                              PrmA 158 lvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveakleva..lseell.....keeka 227
                                       l   g+++lD+   +G  +  a+k ga+  + vD D+ A+++akeN+ +N+ e+k+e++    e+++     k+ ++
  gi|385805458|ref|YP_005841856.1| 218 LSLDGAKILDLFSYTGSFSAHALKAGASFSLLVDEDDRALNIAKENLIKNGFEDKFEIIrgRVEKVIdslliKKMQF 294
                                       566788999999999999**************************************994221222222333458899 PP

                              PrmA 228 dviv 231
                                       d+++
  gi|385805458|ref|YP_005841856.1| 295 DIVI 298
                                       9987 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   3.2e-07   0.00048      54     168 ..     172     288 ..     139     318 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 3.2e-07
                                       EEEEEES-.SEEEEEETTEEEEEET...TTS---GGGHHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEE CS
                            Met_10  54 levlaGsdstetihkEngcrfklDv...skvyfsskleaErerlaklveegevVvdvfAGiGpfaipiakyskakrv 127
                                        + l G+    t  kE    fk+D+   +k  f     + r+++ +l  +g  ++d+f   G f+  + k + a++ 
  gi|385805458|ref|YP_005841856.1| 172 KKFLHGEPPPYTYIKEDDLIFKIDFlngQKTGFYLDQREARKKISSLSLDGAKILDLFSYTGSFSAHALK-AGASFS 247
                                       578899888999************9666689999999*****************************9999.888999 PP

                                       EEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---TT- CS
                            Met_10 128 laidlnPesvkylkeniklNkvekvvkpileDgrevireql 168
                                       l +d + ++ +  ken+  N  e++ + i + +++vi + l
  gi|385805458|ref|YP_005841856.1| 248 LLVDEDDRALNIAKENLIKNGFEDKFEIIRGRVEKVIDSLL 288
                                       99*******************************99997433 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   8.4e-06     0.013       3      81 ..     224     303 ..     222     309 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 8.4e-06
                   Methyltransf_15   3 vilDlfsGaGGnviqfalv.fekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvflS 78 
                                        ilDlfs +G  + +  +   +    ++ + + l++a++N    g +dk  ++ g v++++ +l  +k+++d+v++ 
  gi|385805458|ref|YP_005841856.1| 224 KILDLFSYTGSFSAHALKAgASFSLLVDEDDRALNIAKENLIKNGFEDKFEIIRGRVEKVIDSLLIKKMQFDIVIVD 300
                                       589999998876655444423335679************************************************** PP

                   Methyltransf_15  79 pPw 81 
                                       pP 
  gi|385805458|ref|YP_005841856.1| 301 PPA 303
                                       *96 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   2.8e-05     0.042      13      78 ..     235     302 ..     230     338 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.8e-05
                   Methyltransf_24  13 wllralrrngagrlvavdhdpgaeeaaalare....aglddrvrlikadseealasla..agsiDllfiDgg 78 
                                       + + al++ +    + vd d    +a ++a+e    +g++d +++i+++ e+++ sl   + ++D++++D +
  gi|385805458|ref|YP_005841856.1| 235 FSAHALKAGAS-FSLLVDEDD---RALNIAKEnlikNGFEDKFEIIRGRVEKVIDSLLikKMQFDIVIVDPP 302
                                       55667777776.445678888...6666777666669*********************99899*******55 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   8.3e-05      0.12      82     130 ..     250     302 ..     237     330 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.3e-05
                                       EES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--....STTS---EEEE--- CS
                           UPF0020  82 sDldrrvvqgareNaekagvgdliefsqadaakLr....lkegevdvivtnpP 130
                                       +D d r+++ a+eN+ k g +d+ e+    + k+      k+ ++d+++ +pP
  gi|385805458|ref|YP_005841856.1| 250 VDEDDRALNIAKENLIKNGFEDKFEIIRGRVEKVIdsllIKKMQFDIVIVDPP 302
                                       799**************************999987787667779********9 PP

>> Methyltransf_10  RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00022      0.33     132     189 ..     250     305 ..     240     327 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00022
                                       EES-HHHHHHHHHHHHHT.T-TTTEEEEE--TT-SCCHHSSTTSS-EEEEEE-S---S CS
                   Methyltransf_10 132 sevddvslasakaivesnsklsdaiklrkqkekkaifdglieenerydvtlCnPPfha 189
                                        + dd +l+ ak ++ +n  ++d+ ++ + +  ++++d+l  ++ ++d+++ +PP + 
  gi|385805458|ref|YP_005841856.1| 250 VDEDDRALNIAKENLIKN-GFEDKFEIIRGRV-EKVIDSLLIKKMQFDIVIVDPPAFI 305
                                       57799*************.9********9876.567899999999**********774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.66u 0.33s 00:00:00.99 Elapsed: 00:00:00.52
# Mc/sec: 2316.14
//
Query:       gi|385805459|ref|YP_005841857.1|  [L=295]
Description: alpha-L-glutamate ligase [Fervidicoccus fontis Kam940]
Scores for complete 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-39  133.7   0.0    7.3e-39  133.3   0.0    1.1  1  RimK             RimK-like ATP-grasp domain
    3.3e-19   68.9   0.0    4.9e-19   68.4   0.0    1.2  1  GSH-S_ATP        Prokaryotic glutathione synthetase, ATP-gras
    1.3e-10   41.0   0.1    2.4e-05   23.7   0.0    3.1  2  ATPgrasp_YheCD   YheC/D like ATP-grasp
    2.4e-09   36.9   0.0    2.6e-05   23.6   0.0    2.3  2  ATPgrasp_ST      Sugar-transfer associated ATP-grasp
    2.8e-07   30.7   0.0    1.2e-06   28.7   0.0    2.0  2  ATP-grasp_3      ATP-grasp domain
     0.0007   19.9   0.1     0.0016   18.8   0.1    1.7  1  Rimk_N           RimK PreATP-grasp domain
     0.0014   18.4   0.0       0.13   12.0   0.0    2.2  2  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr
  ------ inclusion threshold ------
      0.025   14.2   0.0      0.041   13.5   0.0    1.4  1  ATP-grasp        ATP-grasp domain
      0.062   13.3   0.0       0.13   12.3   0.0    1.4  1  R2K_3            ATP-grasp domain, R2K clade family 3
       0.11   12.0   0.0        1.8    8.0   0.0    2.5  2  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus


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 !  133.3   0.0   4.1e-42   7.3e-39       1     186 [.     102     287 ..     102     289 .. 0.95

  Alignments for each domain:
  == domain 1  score: 133.3 bits;  conditional E-value: 4.1e-42
                                       HH-HHHHHHHHHHTT-----EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHH...GGG CS
                              RimK   1 ardKlkslklLakakikvpntalardeedaekliekiklrfPvvvKsvegsqGikvvlakkeqklkqvlea...lke 74 
                                       ardK +   +L k++++ p+t +++d ++a ++i++++    vvvK + gs G +v+l  + + +  vl+     ++
  gi|385805459|ref|YP_005841857.1| 102 ARDKSLLPLILSKNGLPYPKTIITEDLQKALDVINEYG---KVVVKPIIGSLGRGVMLLDNVDVAYTVLKQllsWNQ 175
                                       789999999****************************6...8***********************999998777899 PP

                                       --EEEEE--SS-SEEEEEEEETTEEEEEEEEE--SSS----TTTT-EEEE----HHHHHHHHHHHHHCT-SEEEEEE CS
                              RimK  75 ailvqeyieeaenediRvlvvddevvaalrrvskeGdFRsnlhrGgvaeklqlseeekelAikaakamelvvaGvDl 151
                                        il+qe+i++++n+diR+lv+++e+ aa+ r+++ G F++n+ +G+  e++ l+ee+kel ik +++++l++aG+D+
  gi|385805459|ref|YP_005841857.1| 176 PILLQEFINKKDNRDIRILVINGEIYAAYYRKARPGLFKTNIAQGATPEPAVLDEELKELSIKTTELLGLFYAGIDI 252
                                       9**************************************************************************** PP

                                       EEETTE.EEEEEEESS--SHHHHHHHT--HHHHHHH CS
                              RimK 152 lrakrg.llvlEvnsspglekiektlgidiakklie 186
                                        ++++g  ++lE n+sp+ ++    +g++ a kl+e
  gi|385805459|ref|YP_005841857.1| 253 AESEKGeRYILEANASPNWKGP-LSMGLNPARKLVE 287
                                       *99987369**********998.8999999999986 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 !   68.4   0.0   2.7e-22   4.9e-19      12     154 ..     119     255 ..     111     269 .. 0.92

  Alignments for each domain:
  == domain 1  score: 68.4 bits;  conditional E-value: 2.7e-22
                                       S--EEEES-HHHHHHHHHHHSSEEEEESS--TTTT-EEE-TT-TTHHHHHHHHTTTTTS-EEEEE--GGGGG-EEEE CS
                         GSH-S_ATP  12 ipktlvskdkeeirafleeqgdvilKPldgkgGegvfrvkksdpnlksilellteegkepviaqrylpeikeGDkRi 88 
                                        pkt++++d ++  ++++e+g+v++KP+ g+ G+gv+ +++ d   +++ +ll+ +  +p+++q+++++  + D Ri
  gi|385805459|ref|YP_005841857.1| 119 YPKTIITEDLQKALDVINEYGKVVVKPIIGSLGRGVMLLDNVDVAYTVLKQLLSWN--QPILLQEFINKKDNRDIRI 193
                                       59***************************************999999998888765..57***************** PP

                                       EEETTEE-SEEEEEE--SS-S---GGGTSCEEEEE--HHHHHHHHHHHHHHHHTT--EEEEEEETT CS
                         GSH-S_ATP  89 llvdGepigyalaRvpaegevRsnlaaggraeatelterdreiaeelapkLkekGllfvGlDvigd 154
                                       l+++Ge    a  R ++ g +++n+a g++ e   l+e+ +e++ + ++ L   Gl+++G+D+ ++
  gi|385805459|ref|YP_005841857.1| 194 LVINGEIYA-AYYRKARPGLFKTNIAQGATPEPAVLDEELKELSIKTTELL---GLFYAGIDIAES 255
                                       ******999.*********************************99888776...********9865 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 !   23.7   0.0   1.3e-08   2.4e-05      30      74 ..     120     164 ..     111     172 .. 0.89
   2 !   11.2   0.0   8.8e-05      0.16     108     238 ..     177     279 ..     157     294 .. 0.65

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.3e-08
                    ATPgrasp_YheCD  30 PetellesledleemlekyksvylKpanGskGkgilriekeekel 74 
                                       P+t+  e+l++  +++++y++v++Kp+ Gs+G+g++ +++ + ++
  gi|385805459|ref|YP_005841857.1| 120 PKTIITEDLQKALDVINEYGKVVVKPIIGSLGRGVMLLDNVDVAY 164
                                       99**********************************999855444 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 8.8e-05
                    ATPgrasp_YheCD 108 ylvQqgidlatidgrpfDfRvlvqKngkgkWevtgiaaRiagkgsittnlsrGGtalpleellkkafgeekaekile 184
                                       +l+Q+ i+ ++      D+R+lv        e+ +++ R a++g + tn+++G+t  p              + + e
  gi|385805459|ref|YP_005841857.1| 177 ILLQEFINKKD----NRDIRILVING-----EIYAAYYRKARPGLFKTNIAQGATPEP--------------AVLDE 230
                                       55555555333....44666666622.....356666777777777777777665443..............34556 PP

                    ATPgrasp_YheCD 185 eleelalelaealeesfgrlgElGlDlgidkegkvWllEvNskpgrsifkeagd 238
                                       el+el++++ e l      l+  G+D++  ++g+ ++lE+N+ p+ +    +g 
  gi|385805459|ref|YP_005841857.1| 231 ELKELSIKTTELLG-----LFYAGIDIAESEKGERYILEANASPNWKGPLSMGL 279
                                       78888888888777.....55569*****************9998776665555 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 !   23.6   0.0   1.5e-08   2.6e-05      10      81 ..      93     159 ..      88     175 .. 0.89
   2 !   10.9   0.0   0.00011       0.2     227     268 ..     231     271 ..     229     286 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.5e-08
                       ATPgrasp_ST  10 yNpraefplvddKlkfkelalraglkvpkllgvikeqaeiseleafvkeleegvviKpakgsgGkGilvite 81 
                                       +N+++ + +  dK++   +++++gl+ pk++++    ++++++ ++++e+ + vv+Kp+ gs+G+G++ + +
  gi|385805459|ref|YP_005841857.1|  93 INSYSSIMTARDKSLLPLILSKNGLPYPKTIIT----EDLQKALDVINEYGK-VVVKPIIGSLGRGVMLLDN 159
                                       799999***********************8776....789999999999*55.***************9865 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00011
                       ATPgrasp_ST 227 evlelaakaaeklpglgylGwDivldeekgplllElNarpgl 268
                                       e+ el  k  e l+gl y G+Di+  e+++ ++lE+Na p  
  gi|385805459|ref|YP_005841857.1| 231 ELKELSIKTTE-LLGLFYAGIDIAESEKGERYILEANASPNW 271
                                       67899999999.**************************9875 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       2.6   4.6e+03      76     105 ..      29      68 ..      18      84 .. 0.59
   2 !   28.7   0.0   6.5e-10   1.2e-06       2     156 ..     103     267 ..     102     270 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.6
                                       EEEEEE.SSSEEEEEEEEEEEET...............TEE CS
                       ATP-grasp_3  76 Svsllsdgekvlvlavnrqliekaeke...........fvy 105
                                       S++ +  + +  v+ vn+ +i  ++k+           ++y
  gi|385805459|ref|YP_005841857.1|  29 SANYIRPQ-ELNVIYVNNSRIIIRGKReikpeiafirgMSY 68 
                                       56666644.44455555555544444446666644444444 PP

  == domain 2  score: 28.7 bits;  conditional E-value: 6.5e-10
                                       TSHHHHHHHHTTT.S---....-EESS--......SSSEEEEESS-------B--SS--TTE.............EE CS
                       ATP-grasp_3   2 sdKlktykkLkeagvkvPtkleaeeleee......ekklvvKprdGaggesvrvveekeeaeaaieeve......lv 66 
                                        dK  +   L+++g++ P+++  e l+++        k+vvKp+ G+ g +v++ ++ + a + ++++       l+
  gi|385805459|ref|YP_005841857.1| 103 RDKSLLPLILSKNGLPYPKTIITEDLQKAldvineYGKVVVKPIIGSLGRGVMLLDNVDVAYTVLKQLLswnqpiLL 179
                                       699999999*********55555555555566665789********************999888877667889999* PP

                                       EE---SEEEEEEEEE.SSSEEEEEEEEEEEET...........TEEEEEEES----HHHHHHHHHHHHHTTSTT--E CS
                       ATP-grasp_3  67 qefieGkplSvsllsdgekvlvlavnrqliekaeke.......fvyaGnvtpietelkeevvelaeevvekleglaG 136
                                       qefi+ k        d+ ++++l++n ++     ++          a + tp +  l+ee+ el  +++e l gl+ 
  gi|385805459|ref|YP_005841857.1| 180 QEFINKK--------DNRDIRILVINGEIYAAYYRKarpglfkTNIAQGATPEPAVLDEELKELSIKTTELL-GLF- 246
                                       ****987........577888888888887776666778777755666678999999*************99.887. PP

                                       EEEEEEEESS..SEEEEEEES CS
                       ATP-grasp_3 137 yvGvDlvlkd.eepyviEvNP 156
                                       y+G+D+  ++ +e y++E N+
  gi|385805459|ref|YP_005841857.1| 247 YAGIDIAESEkGERYILEANA 267
                                       9******888799*****996 PP

>> Rimk_N  RimK PreATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   8.8e-07    0.0016      13      94 .]      14      99 ..       1      99 [. 0.77

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 8.8e-07
                            Rimk_N 13 ystrrLveaaekrghevevldplrcylkieaekpevyykgekleefdavipR.i...gasi.tfygtavlrqFemmgvf 86
                                      +s r+++++a++rgh+++ + p+++++   + + +++++g++  + ++   R +   g+ +     t++++ +e++g+f
  gi|385805459|ref|YP_005841857.1| 14 FSARQIIREAKARGHSANYIRPQELNVIYVN-NSRIIIRGKREIKPEIAFIRgMsypGSIEhFIWMTNIVKILEETGTF 91
                                      899**********************996666.677777776666666666665778777663556899*********** PP

                            Rimk_N 87 vlneseAi 94
                                      ++n+ ++i
  gi|385805459|ref|YP_005841857.1| 92 TINSYSSI 99
                                      ***97776 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 !   12.0   0.0   7.2e-05      0.13       8      72 ..     110     172 ..     103     186 .. 0.87
   2 ?    4.2   0.0     0.018        32     149     187 ..     226     267 ..     215     269 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.2e-05
                                       HHHHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHHCT CS
                            GARS_A   8 dllkkagiptaeyeaftdpeeakeyieeatakalVvKadglaagKgvivakseeealkavkeile 72 
                                        +l+k g+p ++   ++d ++a ++i+e ++  +VvK+   + g+gv++ ++++ a +++k++l+
  gi|385805459|ref|YP_005841857.1| 110 LILSKNGLPYPKTIITEDLQKALDVINEYGK--VVVKPIIGSLGRGVMLLDNVDVAYTVLKQLLS 172
                                       5789999********************9986..37****99********************9996 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.018
                                       HTHHHHHHHHHCTT---EEEEEEEEEEETTE...EEEEEEES CS
                            GARS_A 149 eileptveglkkegipfkGvLyaglmlvedg...pkvlefnv 187
                                       ++l++ +++l+ ++++  G+ yag+ + e+     ++le n+
  gi|385805459|ref|YP_005841857.1| 226 AVLDEELKELSIKTTELLGLFYAGIDIAESEkgeRYILEANA 267
                                       6889999*******************9955445888999886 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.3e-05     0.041       2      75 ..     113     186 ..     112     250 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.3e-05
                                       HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC..GTTCEEEEE----S CS
                         ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal..keekvivEefvpfe 75 
                                       +k+glp p+ ++ e+ +++ ++++e g +vvvK ++ g+ G+G +++ + + + ++l++l   ++++++ ef++ +
  gi|385805459|ref|YP_005841857.1| 113 SKNGLPYPKTIITEDLQKALDVINEYG-KVVVK-PIIGSLGRGVMLLDNVDVAYTVLKQLlsWNQPILLQEFINKK 186
                                       678999999999999999999999988.57899.************************9998899*******9854 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 ?   12.3   0.0   7.1e-05      0.13      71     183 ..     138     267 ..     111     269 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.1e-05
                             R2K_3  71 eepvFvkprgdklfggvVlrefeelr..alaakle.dtevlvsevvrf..saEwRvFvvdGevvaasrYrkanddpd 142
                                        ++v vkp+   l +gv l +  ++    l+++l+ + ++l+ e ++       R+ v++Ge+ aa  Yr  +++p+
  gi|385805459|ref|YP_005841857.1| 138 YGKVVVKPIIGSLGRGVMLLDNVDVAytVLKQLLSwNQPILLQEFINKkdNRDIRILVINGEIYAA-YYR--KARPG 211
                                       466677777666556666554444443333344445778888887744337889*******99876.555..45555 PP

                             R2K_3 143 l.........epdlaafaeavralv......gappfyvlDvavtadGrwkVVEvnd 183
                                       l          p++a+++e++++l         +    +D+a +++G+ ++ E+n+
  gi|385805459|ref|YP_005841857.1| 212 LfktniaqgaTPEPAVLDEELKELSikttelLGLFYAGIDIAESEKGERYILEANA 267
                                       555588888899************99998875577789****************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 ?   -1.7   0.0         1   1.8e+03     161     199 ..      85     123 ..      83     126 .. 0.80
   2 ?    8.0   0.0     0.001       1.8     134     176 ..     228     269 ..     111     277 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1
                                       EETTTEEEEEEEESS---STTSHHHHHHHCTT--HHHHH CS
                   Dala_Dala_lig_C 161 lteegeivlnEvNtlPGfTeiSlfpklakasGlefkkLv 199
                                       l+e+g++ +n    +    + Sl+p + +++Gl ++k +
  gi|385805459|ref|YP_005841857.1|  85 LEETGTFTINSYSSIMTARDKSLLPLILSKNGLPYPKTI 123
                                       577888888888888777789999999999999998754 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.001
                                       HHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEESS- CS
                   Dala_Dala_lig_C 134 veekiqelalkaykaldlrGlaRvDfflteegeivlnEvNtlP 176
                                         e+++el++k+ ++l+l   a +D+  +e+ge ++ E N  P
  gi|385805459|ref|YP_005841857.1| 228 LDEELKELSIKTTELLGLF-YAGIDIAESEKGERYILEANASP 269
                                       4578999999999999986.788*****************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); 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):              10  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1801.03
//
Query:       gi|385805460|ref|YP_005841858.1|  [L=338]
Description: glycosyltransferase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.9e-24   84.3  13.9    8.9e-24   84.3  13.9    2.5  3  Glycos_transf_4  Glycosyl transferase family 4


Domain annotation for each model (and alignments):
>> Glycos_transf_4  Glycosyl transferase family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.2      0.11     2e+03      59      81 ..      49      70 ..       4      73 .. 0.49
   2 !   84.3  13.9     5e-28   8.9e-24       2     159 ..      79     241 ..      78     242 .. 0.83
   3 ?   -1.8   0.1      0.15   2.6e+03      46      74 ..     302     330 ..     285     337 .. 0.59

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.11
                   Glycos_transf_4 59 ielglilavlltllvivgvtNav 81
                                        lg ++ + +++l+ +++ Na 
  gi|385805460|ref|YP_005841858.1| 49 GGLGFLFGWSFSILIYMFM-NAG 70
                                      3444444444444444444.555 PP

  == domain 2  score: 84.3 bits;  conditional E-value: 5e-28
                   Glycos_transf_4   2 llllltillilllGflDDvlglkarlKlilqilaalililtldlslttlgllltqvlielglilavlltllvivgvt 78 
                                       + +ll i++++++G++DD++ l  ++K++l++l  + + ++     + + +++  ++ +l +++ +ll +++ v ++
  gi|385805460|ref|YP_005841858.1|  79 ITILLIIWFVGIVGLYDDMKRLGGITKVLLTALPGIAIYFASL-YRPFVFIPFL-GNARLSIVYPILLPIIYAV-AS 152
                                       6789999************************999888766544.6666777777.8899995555555555555.55 PP

                   Glycos_transf_4  79 NavNliDGldGlaagvsiiialalvvla.......avdgrsellllalallg.allGfllfNrypAkvFmGDsgslf 147
                                       Na+N++D + G+a gv++i +++ ++ +        +d  +++++++++l + +l+G+l++N+yp k F GD+gsl+
  gi|385805460|ref|YP_005841858.1| 153 NAINMTDTFTGVAPGVVLILTIFTFLSFlffpllpKSDPLYQIAIILAVLTIsSLIGYLPHNFYPGKSFNGDCGSLS 229
                                       ******************9988888888778876655678888888888888799********************** PP

                   Glycos_transf_4 148 lGlvlavlailg 159
                                        G++la++ail+
  gi|385805460|ref|YP_005841858.1| 230 WGAILATIAILS 241
                                       **********86 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.15
                   Glycos_transf_4  46 slttlgllltqvlielglilavlltllvi 74 
                                       +l tl+++l+++ + + l+l+v ++ ++ 
  gi|385805460|ref|YP_005841858.1| 302 HLLTLKNPLSEKELVISLYLLVSISSIFT 330
                                       45566666665555555555444432222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       901  (0.0502538); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.64u 0.34s 00:00:00.98 Elapsed: 00:00:00.56
# Mc/sec: 1829.59
//
Query:       gi|385805461|ref|YP_005841859.1|  [L=462]
Description: Dimethylamine permease [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-41  142.2  58.7    3.3e-41  141.5  58.7    1.3  1  AA_permease_2  Amino acid permease
    6.7e-28   97.5  51.1    8.3e-28   97.2  51.1    1.0  1  AA_permease    Amino acid permease


Domain annotation for each model (and alignments):
>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.5  58.7   3.7e-45   3.3e-41       6     420 ..      31     442 ..      26     455 .. 0.81

  Alignments for each domain:
  == domain 1  score: 141.5 bits;  conditional E-value: 3.7e-45
                     AA_permease_2   6 afalvigsvigsgifvkn..laas.ggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkvafl 79 
                                        +alvig++  +g f  n  +++s +gpa++l+++++ l g +a + +   ++  + + g +y  +++a gk ++ +
  gi|385805461|ref|YP_005841859.1|  31 SAALVIGTLGATGLFG-NlpVTYSmAGPAAALVWIVTLLFGAFAAVVLAYNFTIWPDKAGAEYAPVRIALGKIPGAI 106
                                       6789999886666554.34646667*******999999999766666666667669999****************** PP

                     AA_permease_2  80 sawfnwfayvpvlasilsvaasyllnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilkillpl 156
                                       ++w + + +  + a+ + +++ y+ + ++p+++    +  l+a+a++++++++n++gik+ +  q+il+ilk+ +pl
  gi|385805461|ref|YP_005841859.1| 107 AGWGFYINWGTAGAIASLILGRYIFG-TDPSTFL---HRQLFAFALVTIFFVFNYFGIKIAGITQTILTILKV-VPL 178
                                       ***********999999999999999.6786544...4579999*****************************.7** PP

                     AA_permease_2 157 iiliilglitvdgggfsslstetdtffpngwpgv............llgllivlwsfdGfesaanvsee..vkkkdv 219
                                       i++ ++++ +v+ + f       + f+ +g pgv            l++ li++ws++  +  a+++ e  +++k +
  gi|385805461|ref|YP_005841859.1| 179 ILVGLVAIPFVNLSNF-------HPFWVSGVPGVqantmegmlmlfLSAALIATWSTYSTDIFASIVPEieDPEKGI 248
                                       **********955555.......46666666665445555555554777788*****************6666799* PP

                     AA_permease_2 220 pkaifigllivlvlyllvniaflgvvpddeianlsnlgsvaalffeavggkvvaiivvilialsllgaintavigss 296
                                       p+a+ ++++++l +  l++i+++gv++    + +++l +++++++ ++g    +i+++i+++ ++l   n a++++s
  gi|385805461|ref|YP_005841859.1| 249 PRAAWFSVVVSLAFVGLITITAIGVLGSQMGTLSKPLFQYGQIVLGNAG----EILLWIALVCGALTVPNVALMSAS 321
                                       ***************************9999999999988888888877....999999999999************ PP

                     AA_permease_2 297 rvlealardgvlPrffakvnkfgspiraiiltaivslillllfllassaaynfllsvsslgliisyllliigalilr 373
                                       rv +++a +g +P+ fak+nk+g p  ++il++++++i++  f++   aay +l+++ +++ i++++ll ++ l++r
  gi|385805461|ref|YP_005841859.1| 322 RVTYQMAVEGDMPKIFAKTNKYGVPHWGLILIYLINVIMI--FYT---AAYAVLVAIVQVPWIVCWFLLGVANLKIR 393
                                       ************************************8875..443...58*************************** PP

                     AA_permease_2 374 kkrp.hlkr.pgkilvaiigalfllfllvalffppkgpatqssliytii 420
                                        +++ h+k  +++++++ iga+++ ++ +  ++   ++  ++ +i+ i+
  gi|385805461|ref|YP_005841859.1| 394 ATKEwHEKAiFKAPWWVVIGAFIVGLIGFGYCYAYGVLWGWHDIILGIV 442
                                       9988677667333333333444444443334444445555555555543 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.2  51.1   9.2e-32   8.3e-28       7     471 ..      36     459 ..      31     462 .] 0.83

  Alignments for each domain:
  == domain 1  score: 97.2 bits;  conditional E-value: 9.2e-32
                       AA_permease   7 lggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngp.ksggfytyasrflgpelGfviGlny 82 
                                       +g +  tglf  l v+ s aGp++a l+++++ ++ +++++ l++  t+ p k+g+ y+ ++  lg+  G   G+ +
  gi|385805461|ref|YP_005841859.1|  36 IGTLGATGLFGNLPVTYSMAGPAAA-LVWIVTLLFGAFAAVVLAYNFTIWPdKAGAEYAPVRIALGKIPGAIAGWGF 111
                                       3333359***************777.55555555555566666666677777************************* PP

                       AA_permease  83 lfswitvlaleltaasiliqfwelvtdlpkawvtgavflvvlliinlvgvkvygeaefilalikiiaiiafiivgii 159
                                        ++w t+ a++  +++ +i      t l+    ++  ++++++++n++g+k  g +++il+++k++ +i + +v  i
  gi|385805461|ref|YP_005841859.1| 112 YINWGTAGAIASLILGRYIFGTDPSTFLH-RQLFAFALVTIFFVFNYFGIKIAGITQTILTILKVVPLILVGLVA-I 186
                                       *******************9999999999.9999999******************************99888887.3 PP

                       AA_permease 160 llaggkpnkgagfrflgdngsifknnlppgfa.keeegafknfisvfvivvfaftGielvaiiagEvkdPeksiPka 235
                                       + ++  +      + ++ +g        pg + +  eg ++ f+s++ i+  +  ++ + a i  E++dPek iP+a
  gi|385805461|ref|YP_005841859.1| 187 PFVNLSNF-----HPFWVSGV-------PGVQaNTMEGMLMLFLSAALIATWSTYSTDIFASIVPEIEDPEKGIPRA 251
                                       44444333.....34555555.......44444666779************************************** PP

                       AA_permease 236 ilqvviritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaalssansslysas 312
                                         + v+  + f  l++++++ +++ ++ g l+     + p+  +++    ++   l+ +++   al + n +l+sas
  gi|385805461|ref|YP_005841859.1| 252 AWFSVVVSLAFVGLITITAIGVLGSQM-GTLS-----K-PLFQYGQIVLGNAGEILLWIALVCGALTVPNVALMSAS 321
                                       *99988776555555555555555555.5555.....2.66667777777788999999999999************ PP

                       AA_permease 313 RvlyslakdglaPkvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwlliilsylr 389
                                       Rv y +a +g +Pk+++k +k+gvP+ +++l ++i ++++    +++a   ++++l+ai+ +  +++w l  ++ l+
  gi|385805461|ref|YP_005841859.1| 322 RVTYQMAVEGDMPKIFAKTNKYGVPHWGLILIYLINVIMI----FYTA---AYAVLVAIVQVPWIVCWFLLGVANLK 391
                                       **************************************99....9999...9************************8 PP

                       AA_permease 390 fRkalkyqgrsieelgfkaallplgvilvlaaliiillilalyayltvkkgpkdwgaasfaaaylivllfliilvgv 466
                                       +R +    + ++e++ fka   p++v+++ +++ +i   + +++ +        wg+ + ++ ++ vll+l+i+ + 
  gi|385805461|ref|YP_005841859.1| 392 IRAT----KEWHEKAIFKA---PWWVVIGAFIVGLIGFGYCYAYGVL-------WGWHDIILGIVFVLLILVIMAVD 454
                                       8877....77777787886...7899999888888888888776666.......*************9999998766 PP

                       AA_permease 467 klhvk 471
                                        l  +
  gi|385805461|ref|YP_005841859.1| 455 SLVSR 459
                                       55555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (462 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       985  (0.0549389); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); 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):               2  [number of targets reported over threshold]
# CPU time: 0.68u 0.36s 00:00:01.04 Elapsed: 00:00:00.52
# Mc/sec: 2669.39
//
Query:       gi|385805462|ref|YP_005841860.1|  [L=320]
Description: ornithine carbamoyltransferase [Fervidicoccus fontis Kam940]
Scores for complete 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-53  179.9   0.0      5e-53  179.4   0.0    1.3  1  OTCace           Aspartate/ornithine carbamoyltransferase, As
    1.5e-48  164.5   0.0    2.2e-48  164.0   0.0    1.2  1  OTCace_N         Aspartate/ornithine carbamoyltransferase, ca
  ------ inclusion threshold ------
      0.019   15.4   0.0      0.053   13.9   0.0    1.8  1  UDPG_MGDP_dh_C   UDP-glucose/GDP-mannose dehydrogenase family
        0.1   11.5   0.0       0.16   10.9   0.0    1.2  1  OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin famil


Domain annotation for each model (and alignments):
>> OTCace  Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.4   0.0   1.1e-56     5e-53       1     156 [.     162     317 ..     162     318 .. 0.98

  Alignments for each domain:
  == domain 1  score: 179.4 bits;  conditional E-value: 1.1e-56
                                       CC.EEEEESSTTSHHHHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEEE CS
                            OTCace   1 kglkiafvGdkknnvanslikllarlgmdvvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvyt 77 
                                       +gl++++ Gd   nva+sli  + r gmd+ ++ Pkg+ep++e+++ a+++a k g +++i +dl+eavkgaDvv+ 
  gi|385805462|ref|YP_005841860.1| 162 DGLRVVYTGDI-WNVAHSLIVEAPRHGMDFIIAVPKGYEPNEEIWKFAEQEARKRGTRLEIVHDLNEAVKGADVVIA 237
                                       5899******9.8**************************************************************** PP

                                       --SSETTC.CGGHHHHHHHHCCCSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHHHHHHH CS
                            OTCace  78 dvwvsmge.ekereerlkklkdyqvteellklakkdaivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlhtikAl 153
                                       ++w smg+ e+e+++r +++k+++vt   ++lak+d+i++HcLPa rg+E+t+eV++++ svvf++aeNrlht+kA+
  gi|385805462|ref|YP_005841860.1| 238 NTWWSMGKpEQEKDKRKEDFKPFTVTPSHMELAKPDVIFMHCLPAYRGNEMTEEVIEGKWSVVFDEAENRLHTEKAV 314
                                       ********99999**************************************************************** PP

                                       HHH CS
                            OTCace 154 lvl 156
                                       l +
  gi|385805462|ref|YP_005841860.1| 315 LTA 317
                                       986 PP

>> OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.0   0.0   4.9e-52   2.2e-48       1     148 []      16     156 ..      16     156 .. 0.98

  Alignments for each domain:
  == domain 1  score: 164.0 bits;  conditional E-value: 4.9e-52
                                       S-BSSGGGS-HHHHHHHHHHHHHHHHHHHTTT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTTTS CS
                          OTCace_N   1 rhllsledlskeeieelldlaaelkekvkkekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseaedi 77 
                                       r++++++ +s+eei++l+dla elk+ ++ e +   l+gkt+++lF +pStRTr+Sfev++++lGg + ++  ++++
  gi|385805462|ref|YP_005841860.1|  16 RDFITTRAFSREEIDYLIDLAVELKQLRELEIEFLPLRGKTIGMLFRKPSTRTRSSFEVGIAELGGIPFYFR-PDEM 91 
                                       89************************9998999999************************************.8899 PP

                                       CTTTGGSTTSSCHHHHHHHHHHHTSEEEEEESSHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHHHHHH CS
                          OTCace_N  78 qlssvskgrkEsleDtarvlsryvdaiviRhpgaeeleelakyasvpviNagdgdgeHPtQaLaDlltire 148
                                       ql+     r+E+++Dtarvl+ry  ++viR++g++e+ee+aky +vpviNa+ +d eHP+Q+LaDl+tire
  gi|385805462|ref|YP_005841860.1|  92 QLT-----RGEPVKDTARVLDRYLKGFVIRTFGQDEVEEFAKYMKVPVINAL-TDLEHPCQVLADLMTIRE 156
                                       999.....77******************************************.****************98 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 ?   13.9   0.0   1.2e-05     0.053      42      78 ..     210     243 ..     192     263 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.2e-05
                                       HCCCCHHGGBTCCEEES-CHHHHTT-SEEEE-S--GG CS
                    UDPG_MGDP_dh_C  42 eeaveaeleekgvevvdsleealkgadaiviltehde 78 
                                       +ea+++    +++e+v++l+ea+kgad+++  t ++ 
  gi|385805462|ref|YP_005841860.1| 210 QEARKR---GTRLEIVHDLNEAVKGADVVIANTWWSM 243
                                       222222...5799********************9975 PP

>> OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   3.6e-05      0.16     165     201 ..     202     239 ..     196     243 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.6e-05
                                       HHHHHHHHHCCS..CTT-EEECSCHHHHTTSSEEEE-- CS
                   OCD_Mu_crystall 165 eaaekfaenlqe.fefevsackseeeavegadivvtvT 201
                                       e++ kfae+  +  +   + +++ +eav+gad+v++ T
  gi|385805462|ref|YP_005841860.1| 202 EEIWKFAEQEARkRGTRLEIVHDLNEAVKGADVVIANT 239
                                       556788887666479********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); 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: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2022.98
//
Query:       gi|385805463|ref|YP_005841861.1|  [L=472]
Description: Amidinotransf domain containing protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.8e-17   61.8   0.0    3.9e-16   59.1   0.0    2.1  1  Amidinotransf  Amidinotransferase


Domain annotation for each model (and alignments):
>> Amidinotransf  Amidinotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.1   0.0   2.2e-20   3.9e-16      83     339 ..     192     468 ..     113     469 .. 0.75

  Alignments for each domain:
  == domain 1  score: 59.1 bits;  conditional E-value: 2.2e-20
                                       GGGS-S-HHHHHHHHHHHHH----EEE---GGGG-TTTTEEEEBSEEEE---SSGGGHHHHHHHHHHHHHSH..TSB CS
                     Amidinotransf  83 gvklseeikiekleladkatsnnsflipplpnlvFtrdwfstigggvvlnpmaapnRrrErllaeliykkhp..gvk 157
                                        v   +ei  e+++l  +++  +  + +++    +trd+++t  ++ ++++m  + Rr E+++   iy + +    +
  gi|385805463|ref|YP_005841861.1| 192 FVAIDSEIYDEAKNLFVRSKIFKVNVPENMAKIFYTRDQSVTWLKYPIIGNMSLKLRRGEEEVLNEIYYNLNiyPMA 268
                                       5555555666666667777777777779999******************************9999999998989888 PP

                                       -EEEEE-TTS--TT----GGGEEEEETTE...EEEEESSS.S-HHHHHHHHHHHHHTTS-SEEEEEE--G..GSSTS CS
                     Amidinotransf 158 vakvldisgkeeesktlEGGdfvvlskgv...vaigvssR.tdeegieelakklfyktvafkviaieipk..graim 228
                                        a+++ ++  +  ++ +EGG f++++ ++   ++ g++ R ++++ ++ l + l +++++ +v  + + k  +  ++
  gi|385805463|ref|YP_005841861.1| 269 RARWVKFD-NMLVRAVMEGGNFFIIKTEKgvaLLTGIGVRgSNYATFKFLGEILPEDVRIIGVPLAGYIKywEFGAV 344
                                       899*****.5***************99865447789***72566666666666666677777755444441133469 PP

                                       -GGGTEEEEETTEEEE-HHHH.TT-E............SS-HHHHHHHHTT-SS-EEEE-C.S-SS-B---S-EEEE CS
                     Amidinotransf 229 Hldtvftvvdddavvclpsildaegv............kakereavaqaLkekgleiIeig.eeeqwnfggNvLelk 292
                                       Hldt f+ + d     +  i+ +++v               + +++ + +ke +++i e++ e +     +N+L+l+
  gi|385805463|ref|YP_005841861.1| 345 HLDTAFAYLGDVGGERVGIID-PSRVgfysaleydrksGMFRVTEFLKLMKELEVKIDEMPrESQSPITMTNALNLG 420
                                       ******987765554444333.5555667777788774444557899999999999999995555556789****** PP

                                       TTEEEEETTGHHHHHHHHHT.T-EEEEE-HTTTGGGS--TTTT-EEEE CS
                     Amidinotransf 293 pgvvvaydrntvtnekleea.gievievpiselerGgGgarCmsaplf 339
                                       +g+  + + n ++ne +e+  g+e++ ++i+++e GgGg+rC + +l+
  gi|385805463|ref|YP_005841861.1| 421 NGKLAVDSYNEKANEYIEKTyGLELLRIKIPQIEAGGGGVRCSTRELW 468
                                       ***9666667777777766579***********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 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:                        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: 00:00:00.49
# Mc/sec: 2925.26
//
Query:       gi|385805464|ref|YP_005841862.1|  [L=323]
Description: putative Fe-S oxidoreductase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-09   35.8   0.0    7.2e-07   29.3   0.0    2.4  2  CCG       Cysteine-rich 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 !    4.2   0.0    0.0027        48      23      79 ..     119     176 ..     107     182 .. 0.80
   2 !   29.3   0.0     4e-11   7.2e-07       2      84 ..     219     301 ..     218     302 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0027
                               CCG  23 kllealgveleel.ekesCCGagggrsgkeelaealakrnvetaeetgadaivtacpg 79 
                                       +l++ +g+++ +l +k++  G   +  g ++ +++ a+   ++++e g++a++t++p+
  gi|385805464|ref|YP_005841862.1| 119 ELIKSTGTDFGYLyDKDMYTGVLLFDYGLKDAFKEHAESVHKNLKESGVKAVITIDPH 176
                                       556677777777777777777777778888899999999***************9997 PP

  == domain 2  score: 29.3 bits;  conditional E-value: 4e-11
                               CCG   2 ayfdgChllraa..ypevrkalkkllealgveleel.ekesCCGagggrsgkeelaealakrnvetaeetgadaivt 75 
                                       +++d+C+++r+     ++r++l +  +++  e  +  e   CCG++    +   l++++ak ++e++  t  d i+t
  gi|385805464|ref|YP_005841862.1| 219 TIHDPCYYARNLniITQPRELLLNG-GVKINEPFRTkELTFCCGSPVETLSPS-LSKEIAKTRLEELVLT-SDRIIT 292
                                       79****9999999999999999998.5555555555599*******9966666.9*************97.999*** PP

                               CCG  76 acpgCllql 84 
                                        cp C l+l
  gi|385805464|ref|YP_005841862.1| 293 MCPMCNLSL 301
                                       *****9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       839  (0.0467957); expected 358.6 (0.02)
Passed bias filter:                      626  (0.0349155); 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: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 1961.66
//
Query:       gi|385805465|ref|YP_005841863.1|  [L=109]
Description: 4Fe-4S ferredoxin [Fervidicoccus fontis Kam940]
Scores for complete 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   45.9   2.7    7.7e-12   45.5   2.7    1.2  1  Fer4_8    4Fe-4S dicluster domain
    1.1e-09   38.2   4.0    7.8e-05   22.7   0.5    2.2  2  Fer4_10   4Fe-4S dicluster domain
    2.9e-09   37.4   4.3    0.00072   20.1   0.3    2.1  2  Fer4_7    4Fe-4S dicluster domain
    4.9e-09   36.6   3.5    1.1e-08   35.5   3.6    1.5  1  Fer4_17   4Fe-4S dicluster domain
    5.3e-08   32.9  31.3    0.00016   21.8  12.6    2.1  3  Fer4_9    4Fe-4S dicluster domain
    1.1e-07   31.4  12.8    0.00064   19.4   1.6    2.5  2  Fer4      4Fe-4S binding domain
    3.7e-06   26.8  11.2     0.0023   17.9   3.1    2.4  2  Fer4_6    4Fe-4S binding domain
    8.4e-06   25.6  13.3     0.0038   17.2   3.7    2.3  2  Fer4_2    4Fe-4S binding domain
    2.9e-05   24.9  10.5    0.00064   20.6  11.5    2.1  3  Fer4_16   4Fe-4S double cluster binding domain
    8.3e-05   22.8   9.3     0.0028   18.1   1.8    2.2  2  Fer4_4    4Fe-4S binding domain
    0.00011   22.0   3.6     0.0029   17.3   0.2    2.1  2  Fer4_20   Dihydroprymidine dehydrogenase domain II, 4Fe-4S cl
    0.00039   20.6   5.6      0.023   14.9   0.5    2.1  2  Fer4_18   4Fe-4S dicluster domain
    0.00054   20.0   7.2       0.12   12.6   1.1    2.2  2  Fer4_21   4Fe-4S dicluster domain
    0.00092   20.0   6.5       0.21   12.4   0.3    2.2  2  Fer4_22   4Fe-4S dicluster domain
     0.0026   18.6  16.4       0.12   13.4   5.6    2.2  2  Fer4_3    4Fe-4S binding domain
     0.0069   16.9   8.3       0.11   13.0   0.7    2.3  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
  ------ inclusion threshold ------
      0.016   15.9   5.3      0.056   14.2   0.4    2.3  2  Fer4_15   4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   2.7   7.3e-15   7.7e-12       2      65 .]      23      90 ..      22      90 .. 0.84

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 7.3e-15
                            Fer4_8  2 lekCieCgaCqsaCpvlrrtkkhlldargeaae......dvqeeqvlee..eealwsCttcgaCtevCpvgi 65
                                      + +C  Cg C+  Cp+l+ +k++++ +rg+ ++      +     vl++   +a+++C++cgaC+++Cp +i
  gi|385805465|ref|YP_005841863.1| 23 ALSCAFCGNCEWVCPTLKIKKNRIYGPRGRITAilnfvrE----NVLTDgaVDAIFTCLQCGACVTQCPANI 90
                                      678***************************9998864432....222224589****************997 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.2     4e-06    0.0042       4      21 ..      21      38 ..       4      58 .. 0.72
   2 !   22.7   0.5   7.4e-08   7.8e-05       7      24 ..      74      94 ..      69     108 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4e-06
                           Fer4_10  4 idddtCirCgkCvkaCPa 21
                                       d+ +C  Cg+C  +CP+
  gi|385805465|ref|YP_005841863.1| 21 DDALSCAFCGNCEWVCPT 38
                                      344457777777777777 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 7.4e-08
                           Fer4_10  7 dtCirCgkCvkaCPadl...t 24
                                       tC++Cg+Cv+ CPa++   +
  gi|385805465|ref|YP_005841863.1| 74 FTCLQCGACVTQCPANIridE 94
                                      58*************775542 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.5   1.4e-06    0.0014      21      50 ..       9      38 ..       1      39 [. 0.64
   2 !   20.1   0.3   6.8e-07   0.00072      37      52 .]      75      90 ..      47      91 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.4e-06
                            Fer4_7 21 eeenekgtekveidpekClgCgaCvavCPt 50
                                      ee ++++++ v  d+ +C +Cg+C+ vCPt
  gi|385805465|ref|YP_005841863.1|  9 EEIVNEKIKVVLDDALSCAFCGNCEWVCPT 38
                                      33333333333335679************8 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 6.8e-07
                            Fer4_7 37 kClgCgaCvavCPtga 52
                                      +Cl+CgaCv+ CP+++
  gi|385805465|ref|YP_005841863.1| 75 TCLQCGACVTQCPANI 90
                                      7999999999999875 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   3.6     1e-11   1.1e-08       2      60 ..      26      90 ..      25      91 .. 0.84

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 1e-11
                           Fer4_17  2 CiqCgyClpeCpsyeaydnepkkllraakl...glleeaeke...ekaslCieCgeCerkCPqgl 60
                                      C+ Cg C+ +Cp++++ +n+   ++ ++++      e++ ++   +++ +C++Cg C+++CP+++
  gi|385805465|ref|YP_005841863.1| 26 CAFCGNCEWVCPTLKIKKNRIYGPRGRITAilnFVRENVLTDgavDAIFTCLQCGACVTQCPANI 90
                                      9******************999999999887752444544445568****************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 !   15.0   1.3     2e-05     0.021      23      48 ..      13      38 ..       3      41 .. 0.69
   2 !   21.8  12.6   1.5e-07   0.00016       2      49 ..      26      89 ..      25      91 .. 0.73
   3 !   19.0   2.4   1.1e-06    0.0012       2      25 ..      76      99 ..      75     106 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2e-05
                            Fer4_9 23 erkarlraaseeaCigCgaCveaCpk 48
                                      ++k+++  +++ +C +Cg C+ +Cp+
  gi|385805465|ref|YP_005841863.1| 13 NEKIKVVLDDALSCAFCGNCEWVCPT 38
                                      4444555555578***********97 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 1.5e-07
                            Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraase.................eaCigCgaCveaCpkg 49
                                      C+ Cg+C+ +Cp+  +++ +  +  r r++                     C++CgaCv  Cp +
  gi|385805465|ref|YP_005841863.1| 26 CAFCGNCEWVCPTLKIKKNRIYGP-RGRITAIlnfvrenvltdgavdaiFTCLQCGACVTQCPAN 89
                                      ***********7665544433322.22222223456669**********99************87 PP

  == domain 3  score: 19.0 bits;  conditional E-value: 1.1e-06
                            Fer4_9  2 CtgCgaCveaCpagvvvedaaerk 25
                                      C +CgaCv++Cpa++ +++++++ 
  gi|385805465|ref|YP_005841863.1| 76 CLQCGACVTQCPANIRIDEDVRTV 99
                                      999999999999999988887765 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   1.6   6.1e-07   0.00064       4      20 ..      22      38 ..      19      39 .. 0.88
   2 !   17.0   4.0   3.6e-06    0.0038       8      22 ..      76      90 ..      75      92 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 6.1e-07
                                      ETTTSSS-THHHHHSTT CS
                              Fer4  4 deekCigCGaCvevCPv 20
                                      d   C +CG+C+ vCP+
  gi|385805465|ref|YP_005841863.1| 22 DALSCAFCGNCEWVCPT 38
                                      5567************8 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 3.6e-06
                                      SSS-THHHHHSTTTE CS
                              Fer4  8 CigCGaCvevCPvgA 22
                                      C  CGaCv  CP + 
  gi|385805465|ref|YP_005841863.1| 76 CLQCGACVTQCPANI 90
                                      99**********986 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   1.2   4.9e-05     0.052       9      21 ..      26      38 ..      22      45 .. 0.86
   2 !   17.9   3.1   2.2e-06    0.0023       9      22 ..      76      89 ..      75      94 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.9e-05
                            Fer4_6  9 CigCgdCvrvCPe 21
                                      C  Cg+C+ vCP+
  gi|385805465|ref|YP_005841863.1| 26 CAFCGNCEWVCPT 38
                                      666*********7 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 2.2e-06
                            Fer4_6  9 CigCgdCvrvCPeg 22
                                      C++Cg+Cv+ CP++
  gi|385805465|ref|YP_005841863.1| 76 CLQCGACVTQCPAN 89
                                      ************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 !   13.7   2.1   4.8e-05     0.051       4      22 .]      20      38 ..      17      38 .. 0.82
   2 !   17.2   3.7   3.6e-06    0.0038       9      22 .]      75      88 ..      69      88 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.8e-05
                            Fer4_2  4 vvdtdrCigCgaCvsaCPa 22
                                        d+ +C  Cg C ++CP+
  gi|385805465|ref|YP_005841863.1| 20 LDDALSCAFCGNCEWVCPT 38
                                      456788988*********7 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 3.6e-06
                            Fer4_2  9 rCigCgaCvsaCPa 22
                                      +C++CgaCv+ CPa
  gi|385805465|ref|YP_005841863.1| 75 TCLQCGACVTQCPA 88
                                      6************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 !   11.9   2.0   0.00032      0.34      51      65 ..      23      37 ..       3      39 .. 0.66
   2 !   20.6  11.5   6.1e-07   0.00064       2      67 .]      26      89 ..      25      89 .. 0.81
   3 !   14.9   2.8   3.7e-05     0.039       1      20 [.      75      95 ..      75     107 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00032
                           Fer4_16 51 qeaitgCdiCqdvCP 65
                                      +  +++C++C+ vCP
  gi|385805465|ref|YP_005841863.1| 23 ALSCAFCGNCEWVCP 37
                                      356799999999999 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 6.1e-07
                           Fer4_16  2 CgtCgkCaevCPtnaikekkekeiearecisy.ntaekkdlaedeekckkqeaitgCdiCqdvCPan 67
                                      C  Cg+C  vCPt  ik++  + + +r  i +  +  ++++ +d + +     +  C++C++ CPan
  gi|385805465|ref|YP_005841863.1| 26 CAFCGNCEWVCPTLKIKKN--RIYGPRGRITAiLNFVRENVLTDGAVDA-IFTCLQCGACVTQCPAN 89
                                      999****************..5555555555547777777777777777.788************98 PP

  == domain 3  score: 14.9 bits;  conditional E-value: 3.7e-05
                           Fer4_16  1 rCgtCgkCaevCPtna.ikek 20
                                      +C +Cg+C+  CP+n  i+e+
  gi|385805465|ref|YP_005841863.1| 75 TCLQCGACVTQCPANIrIDED 95
                                      59***********99755555 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   1.0    0.0019         2       4      16 ..      26      38 ..      23      48 .. 0.88
   2 !   18.1   1.8   2.6e-06    0.0028       3      16 ..      75      88 ..      73      95 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0019
                            Fer4_4  4 CigCgsCvaaCPq 16
                                      C  Cg C+ +CP+
  gi|385805465|ref|YP_005841863.1| 26 CAFCGNCEWVCPT 38
                                      666*********5 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 2.6e-06
                            Fer4_4  3 rCigCgsCvaaCPq 16
                                      +C++Cg+Cv  CP 
  gi|385805465|ref|YP_005841863.1| 75 TCLQCGACVTQCPA 88
                                      6************6 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 !    6.1   0.3    0.0086       9.1      15      38 ..      17      38 ..       4      46 .. 0.77
   2 !   17.3   0.2   2.8e-06    0.0029      12      52 ..      64     102 ..      52     108 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0086
                                      HHHHHHHTT----TT-HHHHCSTT CS
                           Fer4_20 15 eealeeAsRClqCkkapcvkgCPv 38
                                      + +l++A  C  C   +c++ CP+
  gi|385805465|ref|YP_005841863.1| 17 KVVLDDALSCAFC--GNCEWVCPT 38
                                      456889999****..78******7 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 2.8e-06
                                       --HHHHHHHHTT----TT-HHHHCSTT---HHHHHHHHHTT CS
                           Fer4_20  12 lteeealeeAsRClqCkkapcvkgCPveidipefikkiaeg 52 
                                       + ++ a++    ClqC    cv++CP++i+i+e ++++++ 
  gi|385805465|ref|YP_005841863.1|  64 VLTDGAVDAIFTCLQC--GACVTQCPANIRIDEDVRTVKSY 102
                                       555567777778****..78*************99999876 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   0.5    0.0019       2.1      44      73 ..       9      38 ..       2      47 .. 0.71
   2 !   14.9   0.5   2.2e-05     0.023      57      79 ..      72      94 ..      50     100 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0019
                           Fer4_18 44 kkalkekeerkekgagdcidcescvkvcPt 73
                                      ++ ++ek +   ++a  c  c+ c  vcPt
  gi|385805465|ref|YP_005841863.1|  9 EEIVNEKIKVVLDDALSCAFCGNCEWVCPT 38
                                      44445555555677789************8 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 2.2e-05
                           Fer4_18 57 gagdcidcescvkvcPtgidirk 79
                                      +   c++c++cv+ cP +i i +
  gi|385805465|ref|YP_005841863.1| 72 AIFTCLQCGACVTQCPANIRIDE 94
                                      5567**************99866 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.6   0.00032      0.34      33      53 ..      16      38 ..       3      43 .. 0.69
   2 !   12.6   1.1   0.00011      0.12       7      25 ..      75      89 ..      69     104 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00032
                           Fer4_21 33 vlkvved..eCvGCnlCssvCPv 53
                                      +  v++d  +C  C  C  vCP+
  gi|385805465|ref|YP_005841863.1| 16 IKVVLDDalSCAFCGNCEWVCPT 38
                                      333444434799999999****7 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00011
                           Fer4_21  7 kCigCgkCliaCedtshqa 25
                                      +C++Cg C++ C+      
  gi|385805465|ref|YP_005841863.1| 75 TCLQCGACVTQCPA----N 89
                                      69999999999994....3 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   1.3   0.00075      0.79       2      15 ..      26      39 ..      25      47 .. 0.88
   2 !   12.4   0.3    0.0002      0.21       2      14 ..      76      88 ..      57     102 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00075
                           Fer4_22  2 ClsCgaCtlvCptC 15
                                      C  Cg+C  vCpt 
  gi|385805465|ref|YP_005841863.1| 26 CAFCGNCEWVCPTL 39
                                      999*********95 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.0002
                           Fer4_22  2 ClsCgaCtlvCpt 14
                                      Cl+CgaC + Cp+
  gi|385805465|ref|YP_005841863.1| 76 CLQCGACVTQCPA 88
                                      6666666666665 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   2.9   0.00064      0.68       1      13 [.      26      38 ..      26      41 .. 0.89
   2 !   13.4   5.6   0.00011      0.12       1      14 [.      76      89 ..      76      90 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00064
                            Fer4_3  1 CtgCgaCvevCPv 13
                                      C  Cg C+ vCP+
  gi|385805465|ref|YP_005841863.1| 26 CAFCGNCEWVCPT 38
                                      778*********6 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00011
                            Fer4_3  1 CtgCgaCvevCPvg 14
                                      C++CgaCv  CP +
  gi|385805465|ref|YP_005841863.1| 76 CLQCGACVTQCPAN 89
                                      ************65 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 !    7.8   1.6    0.0044       4.7       5      18 ..      25      38 ..      19      39 .. 0.88
   2 !   13.0   0.7   0.00011      0.11       5      25 ..      75      95 ..      70     106 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0044
                           Fer4_13  5 tCiacgaCvelaPd 18
                                      +C  cg+C +++P 
  gi|385805465|ref|YP_005841863.1| 25 SCAFCGNCEWVCPT 38
                                      7************6 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00011
                           Fer4_13  5 tCiacgaCvelaPdvFeedde 25
                                      tC  cgaCv  +P   ++d++
  gi|385805465|ref|YP_005841863.1| 75 TCLQCGACVTQCPANIRIDED 95
                                      8************99888887 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   0.6     0.078        83       5      20 ..      23      38 ..      18      47 .. 0.78
   2 ?   14.2   0.4   5.3e-05     0.056       7      28 ..      75      96 ..      70     107 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.078
                           Fer4_15  5 rdaCigcglCvaeape 20
                                         C  cg+C  ++p+
  gi|385805465|ref|YP_005841863.1| 23 ALSCAFCGNCEWVCPT 38
                                      568*******999986 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 5.3e-05
                           Fer4_15  7 aCigcglCvaeapevfeldedg 28
                                      +C  cg+Cv+ +p  +++ded 
  gi|385805465|ref|YP_005841863.1| 75 TCLQCGACVTQCPANIRIDEDV 96
                                      799****************874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); 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:                        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 0.33s 00:00:00.83 Elapsed: 00:00:00.52
# Mc/sec: 633.82
//
Query:       gi|385805466|ref|YP_005841864.1|  [L=478]
Description: D-lactate dehydrogenase [Fervidicoccus fontis Kam940]
Scores for complete 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  178.6   0.0    2.2e-52  178.2   0.0    1.2  1  FAD-oxidase_C  FAD linked oxidases, C-terminal domain
    3.6e-37  127.2   0.0    8.8e-37  125.9   0.0    1.7  1  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 !  178.2   0.0   2.5e-56   2.2e-52       2     250 .]     220     475 ..     219     475 .. 0.89

  Alignments for each domain:
  == domain 1  score: 178.2 bits;  conditional E-value: 2.5e-56
                                       -SEEEEEEEEESSHHHHHHHHHHHHHHT---SEEEEE-HHHHHHHHHTS-SSTTS-TTT-EEEEEEEEE-HHHHHHH CS
                     FAD-oxidase_C   2 pearavalvafpsfeaavkavreiaqagiipaalelmdkkaldlveatkgakkglpdeeealllvefegddeeeaee 78 
                                       pe++ +++++f+++e  v+a+ ei++++++++ +e++d+k+++l++++++     +   +   +v    +++e  e+
  gi|385805466|ref|YP_005841864.1| 220 PENVITLAAFFDDIEGLVNALLEIKKNKLDILIMEFVDDKSVELTLKVLKI----NIAGNGHYFVTSIITSPESSER 292
                                       89999**********************************************....5555555555555555578999 PP

                                       HHHHHHHHTTT-EEEEE............ETGGGGGGGGHH.......HHHHHHHCTTEEEEEEEEEEEHHHHHHHH CS
                     FAD-oxidase_C  79 elealveaileatgaadv..lvaqdeaeaealwkaRkaalp.......ylrdallkagvavlseDtsvPvsrladlv 146
                                        l+ lve+il+ +ga++v  + + deae e + ++R++           +r+   +++ + + eD+svP+s+l+++v
  gi|385805466|ref|YP_005841864.1| 293 VLS-LVENILKRNGAKNVykAKTLDEAESEGIFDIRRNYDIglrdlvvKMRKN-PASKIIDYNEDISVPPSKLPEAV 367
                                       999.**************5555556666669***9997766355533223332.4578999**************** PP

                                       HHHHHHHHHHHEEEEEEEEEETTEEEEEEEEEEE..--TT--THHHHHHHHHHHHTT---------------....- CS
                     FAD-oxidase_C 147 rdikalldkyglevvlfgHagdgnlhlyilfdladeaeeeraeklvdevvdlavelgGsisgEHGvGldkka....y 219
                                       r+i+++ ++ygl  +l gH+gdgnlh+ i +++++ ++ e++ek+  e+ ++++elgG++s EHG+Gldkk+    +
  gi|385805466|ref|YP_005841864.1| 368 RRIREIEKRYGLPLTLAGHVGDGNLHPVIKIEEKNIEQIETYEKMKSEILKAVIELGGTVSSEHGIGLDKKKdlimE 444
                                       ***************************************************************************** PP

                                       -------THHHHHHHHHHHH-TT--BSTT-- CS
                     FAD-oxidase_C 220 lerekgeeglalmrriKaalDPkgiLNPgkv 250
                                       l+ +++ +++++m++iK+++DPk+iLNPgk+
  gi|385805466|ref|YP_005841864.1| 445 LKSKNSVKAIDIMKSIKQTFDPKNILNPGKI 475
                                       *****************************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 !  125.9   0.0   9.8e-41   8.8e-37       3     132 ..      44     174 ..      42     183 .. 0.95

  Alignments for each domain:
  == domain 1  score: 125.9 bits;  conditional E-value: 9.8e-41
                                       EEEEESSHHHHHHHHHHHHHCTSCEEEESSSTTEESTTC.SCCEEEEEETTS--EEEEETTTTEEEEETTSBHHHHH CS
                     FAD_binding_4   3 avvrpeseeevaaalrlaneaglpvlvrGgGssllgqav.atggvvldlsrlnrileideeegtatveaGvtlgdlv 78 
                                       avv+p ++eev+++++++ ++++++ ++++ s l+g+++ +++gv+++++r+n+i +i+  + +++ve+Gv+l dl+
  gi|385805466|ref|YP_005841864.1|  44 AVVFPNNTEEVSEIVKYCYKNNIKIYPQASASELTGSSLpREDGVIVSFERMNKIKNINILDSYVVVEPGVRLYDLN 120
                                       8**************************************************************************** PP

                                       HHHHHHTTECSSGGGTTCGSBHHHTTTTT-EETTEEGG--HHGTEEEEEEEETT CS
                     FAD_binding_4  79 ealaakglllglepgsgipgtvGGaiatnagGygsekyGlirdnvlglevvlad 132
                                        +l+ +g++++++p+s++ +tvGGai t+agG++  kyG+++d+v +le+v ++
  gi|385805466|ref|YP_005841864.1| 121 LELSIYGFMFPIDPASIKIATVGGAINTGAGGMRGVKYGTMKDWVNELEIVIPN 174
                                       ***************************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (478 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       749  (0.0417759); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); 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: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 2801.05
//
Query:       gi|385805467|ref|YP_005841865.1|  [L=476]
Description: Acyl-CoA synthetase (NDP forming), alpha subunit [Fervidicoccus fontis Kam940]
Scores for complete 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-44  148.8   1.0    4.3e-42  143.2   0.0    2.7  3  Succ_CoA_lig   Succinyl-CoA ligase like flavodoxin domain
    1.5e-20   73.8   0.4      6e-20   71.9   0.1    2.1  2  CoA_binding_2  CoA binding domain
    2.6e-12   47.3   2.4    1.1e-11   45.3   0.1    2.6  2  CoA_binding    CoA binding domain
  ------ inclusion threshold ------
      0.051   12.9   0.5      0.091   12.0   0.1    1.6  2  SUa-2TM        SMODS- and Ubiquitin system-associated 2TM eff


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 ?   -2.1   0.2      0.66     3e+03      72     100 ..      81     111 ..      77     122 .. 0.68
   2 !  143.2   0.0   9.6e-46   4.3e-42       1     138 []     153     292 ..     153     292 .. 0.98
   3 ?    3.3   0.0     0.015        67       3      26 ..     306     329 ..     305     333 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.66
                      Succ_CoA_lig  72 lsaarraark..kpvvvlksGrseagaraaa 100
                                       lsa+++a +k  k  +++ sG  e+g++  +
  gi|385805467|ref|YP_005841865.1|  81 LSAIEEACKKkvKASIIITSGFAETGEQGRK 111
                                       5566666554478889999998888876555 PP

  == domain 2  score: 143.2 bits;  conditional E-value: 9.6e-46
                      Succ_CoA_lig   1 pGkialisqSGalalalldwaasrglgfskvvslGneadvdvadlleylaedpetkvillylEsird..grkflsaa 75 
                                       +G+ a+isqSGa+a   +dw +++g+gfs +v+lGn+ dv++a+++ +l+ed+ t++i++ylE++ +  gr+fl+a+
  gi|385805467|ref|YP_005841865.1| 153 KGSTAFISQSGAIADGTFDWFQDEGIGFSILVNLGNRGDVNEAEIIGFLKEDETTNTIGIYLEGLPNglGREFLKAV 229
                                       5999***************************************************************778******* PP

                      Succ_CoA_lig  76 rraarkkpvvvlksGrseagaraaashtgalagsdavvdaafrqaGvlrvdsleelfdaaell 138
                                       +++  +kp+vvlksGrs++gar a+shtg+lags++++++a++q+ + +v+s+++l+d++++l
  gi|385805467|ref|YP_005841865.1| 230 EETISEKPIVVLKSGRSSSGARGAMSHTGSLAGSYNIYKTAIQQHHAFVVESMQDLIDYIRAL 292
                                       **********************************************************99875 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.015
                      Succ_CoA_lig   3 kialisqSGalalalldwaasrgl 26 
                                       +i+++s SG+l++  +d a++ g+
  gi|385805467|ref|YP_005841865.1| 306 GIGILSNSGGLGILAADEAEKVGF 329
                                       69**********999999987544 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.9   0.1   1.3e-23     6e-20       2     114 ..      13     136 ..      12     138 .. 0.96
   2 ?   -1.1   0.0      0.59   2.7e+03      86     101 ..     425     440 ..     377     464 .. 0.60

  Alignments for each domain:
  == domain 1  score: 71.9 bits;  conditional E-value: 1.3e-23
                                       -EEEET--S-TTSHHHHHHHHHHH..HT--EEEESSS-SEETTEES----T....T--EEEE-S-HHHHGGGHHHHH CS
                     CoA_binding_2   2 tiaVvGasdnpgkfgykvlrylle..hglpvvpVnpkeeeilgekvyaslaedpepvdlvdvftppeatpeivkeal 76 
                                       ++a++Gas++p k g  v+r++ +  +g +v+p+npk+  + g kvy+s+ + p +vdl+ v++p++ +++ ++ea+
  gi|385805467|ref|YP_005841865.1|  13 SVAIIGASEDPLKIGGLVFRNVISgyKG-KVFPINPKHNMLNGYKVYRSILDVPDEVDLAIVVIPAAGVLSAIEEAC 88 
                                       79***********************999.**********************758*********************** PP

                                       HH--SEEEE-TT..........---HHHHHHHHHTT-EEE.ES-HHHH CS
                     CoA_binding_2  77 algakavwlqpg..........sedeeaaelaeeagirvvgdrCilve 114
                                       ++++ka ++  +            +e+++++a++ g+rv+g+++ +++
  gi|385805467|ref|YP_005841865.1|  89 KKKVKASIIITSgfaetgeqgrKLQEQVIARAKSCGMRVIGPNSFGIV 136
                                       ***9998888888*******************************9986 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.59
                                       -TT---HHHHHHHHHT CS
                     CoA_binding_2  86 qpgsedeeaaelaeea 101
                                        + s  e++a++ e++
  gi|385805467|ref|YP_005841865.1| 425 AAKSIIEDLAKKIENE 440
                                       3333333333333333 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.1   2.4e-15   1.1e-11       3      96 .]      11     101 ..       9     101 .. 0.96
   2 ?    1.0   0.3      0.15   6.8e+02      35      94 ..     357     415 ..     354     417 .. 0.82

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 2.4e-15
                                       TEEEEEETTTSHHHHHH.HHHHHHHHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHH CS
                       CoA_binding   3 dtkviviGagglgiagl.yhfkeklkygikavfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqea 78 
                                       +++v++iGa+    +++ ++f++ ++    +vf++np+   +  +g +vy s+ +++++  vd a++++Pa+ + +a
  gi|385805467|ref|YP_005841865.1|  11 PSSVAIIGASEDPLKIGgLVFRNVISGYKGKVFPINPK--HNMLNGYKVYRSILDVPDE--VDLAIVVIPAAGVLSA 83 
                                       679***********************8888********..99999**************..**************** PP

                                       HHHHHHTT-SEEEEESST CS
                       CoA_binding  79 vdelveagikgiviiteg 96 
                                       ++e+ ++++k  +iit+g
  gi|385805467|ref|YP_005841865.1|  84 IEEACKKKVKASIIITSG 101
                                       ***************986 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.15
                                       EC-TTTTTCEETTEEEESCHHHHHHHCT.TTEEEEES-HHHHHHHHHHHHHTT-SEEEEES CS
                       CoA_binding  35 gvnprkvgtevlglpvyksvdeleekte.vdvavitvPaesaqeavdelveagikgiviit 94 
                                       +v+ +  gt  +  + y +  ++ e+++ vd  v+ +   + +e+v++  +a i+ iv it
  gi|385805467|ref|YP_005841865.1| 357 DVTAQ--GTPKQQYEFYSKTFKVLEEHNvVDGYVVIIEGSFPRETVEAITDAIINEIVPIT 415
                                       56666..888888888888888889996799999999999999999999999999999887 PP

>> SUa-2TM  SMODS- and Ubiquitin system-associated 2TM effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1      0.95   4.2e+03      74      92 ..     283     301 ..     263     303 .. 0.65
   2 ?   12.0   0.1     2e-05     0.091     210     263 ..     336     389 ..     326     401 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.95
                           SUa-2TM  74 valilFiRKvnmekekiln 92 
                                         li +iR  +m+k++  n
  gi|385805467|ref|YP_005841865.1| 283 QDLIDYIRALSMQKNRTTN 301
                                       5688889999999988776 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 2e-05
                           SUa-2TM 210 eefikeikklvrklpedistiNifattnPkntveiikkvfvlaerenikkvyvy 263
                                       ++ i+ei+k++  +   ++ i + a   Pk+++e   k+f + e++n+ + yv 
  gi|385805467|ref|YP_005841865.1| 336 QNVIDEIRKIIPPYGAPYNPIDVTAQGTPKQQYEFYSKTFKVLEEHNVVDGYVV 389
                                       789*********************************************999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (476 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); 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: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 2897.58
//
Query:       gi|385805468|ref|YP_005841866.1|  [L=204]
Description: Indolepyruvate:ferredoxin oxidoreductase subunit beta [Fervidicoccus fontis Kam940]
Scores for complete 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  120.0   0.1    1.3e-34  119.8   0.1    1.0  1  POR       Pyruvate ferredoxin/flavodoxin oxidoreductase


Domain annotation for each model (and alignments):
>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.8   0.1   7.4e-39   1.3e-34       1     175 [.      14     193 ..      14     195 .. 0.93

  Alignments for each domain:
  == domain 1  score: 119.8 bits;  conditional E-value: 7.4e-39
                                       CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEE CS
                               POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglk 77 
                                       GGqG v++++il +aa ++G++    + ygs++rGg++ shv+++++  +p i   ead ++ l+ ++  + l+ lk
  gi|385805468|ref|YP_005841866.1|  14 GGQGNVLMARILVAAAIDSGLEGRVGELYGSAQRGGPVASHVKFGKKAFSPIILEHEADAIISLELSESLRRLNMLK 90 
                                       9**********************************************999****************8888******* PP

                                       EEEEEEEECTCGTT-CCHHHCTS-HHHHHHH.......T-EEEEE-HHHHHHHCCC.CCHHHHHHHHHH..HHHHTS CS
                               POR  78 pggiiiynseelkpdelkkakeeerelkerl.......gvrvygvdatkiakeiggneraaNtvmlGal..aallgl 145
                                       p+g i++n  ++ p+ +    + +++ +e           +++ ++at++ak++g+ +r+aN++mlGa+  +  +g+
  gi|385805468|ref|YP_005841866.1|  91 PNGAILINDYRIIPSSVMLGESKYPTKEE-VieaikkvTDKICIIPATDMAKQLGN-ARIANVLMLGAFrvFFDTGI 165
                                       ***************99999888875554.35899999899**********99888.***********955555569 PP

                                       -HHHHHHHHHCCS-CH.HHHHHHHHHHHHH CS
                               POR 146 plealeeaikkrfpkkkeviekNlkafrag 175
                                       ++e++++aik++++ k   +e+N+kaf++g
  gi|385805468|ref|YP_005841866.1| 166 DREYFIQAIKENVRPK--YVELNIKAFEKG 193
                                       **************95..9*********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1265.25
//
Query:       gi|385805469|ref|YP_005841867.1|  [L=645]
Description: Indolepyruvate:ferredoxin oxidoreductase subunit alpha [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.3e-20   72.0   0.3    9.1e-20   71.0   0.1    1.7  2  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    1.8e-15   57.3   0.0    3.3e-15   56.5   0.0    1.4  1  POR_N         Pyruvate flavodoxin/ferredoxin oxidoreductase, 
    3.6e-11   42.4  13.0    2.8e-07   30.0   4.9    2.5  2  Fer4          4Fe-4S binding domain
    3.3e-08   33.5   8.4    9.4e-08   32.1   8.4    1.8  1  Fer4_21       4Fe-4S dicluster domain
    3.8e-08   33.1   0.3    5.7e-07   29.3   0.4    2.2  2  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
    3.9e-07   29.9  13.7    8.5e-05   22.5   3.9    2.6  2  Fer4_6        4Fe-4S binding domain
    1.6e-06   28.6  10.1    0.00012   22.6  10.8    2.5  2  Fer4_7        4Fe-4S dicluster domain
    1.1e-05   25.2  18.1    0.00099   19.1   2.3    2.7  2  Fer4_2        4Fe-4S binding domain
    4.1e-05   23.7   9.8    4.1e-05   23.7   9.8    1.7  1  Fer4_9        4Fe-4S dicluster domain
     0.0005   20.1  11.5     0.0045   17.1  12.0    2.2  2  Fer4_10       4Fe-4S dicluster domain
     0.0019   19.1   2.0     0.0019   19.1   2.0    2.7  2  Fer4_16       4Fe-4S double cluster binding domain
  ------ inclusion threshold ------
      0.037   14.6   6.3        0.7   10.5   0.9    2.6  2  Fer4_13       4Fe-4S single cluster domain of Ferredoxin I
       0.12   12.5   0.0       0.58   10.3   0.1    2.1  2  IF-2          Translation-initiation factor 2
       0.24   12.2   9.7          3    8.7   0.6    2.9  2  Fer4_15       4Fe-4S single cluster domain
        1.1    9.9  12.1         79    3.9  12.2    2.6  1  Fer4_17       4Fe-4S dicluster domain
        1.6    9.4  21.4      0.058   13.9   3.3    2.8  2  Fer4_4        4Fe-4S binding domain
        6.1    8.0  18.2       0.21   12.6   8.0    2.6  2  Fer4_3        4Fe-4S binding 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 ?   -3.4   0.0       7.2   7.6e+03     120     143 ..     359     379 ..     347     383 .. 0.70
   2 !   71.0   0.1   8.6e-23   9.1e-20       1     144 [.     421     560 ..     421     569 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 7.2
                                       TTSEEEEESSH.HHHHHHHHHHHH CS
                      TPP_enzyme_C 120 lGakgarvekadveeleealkeal 143
                                       lGakg+  e +   +++ea+k+a 
  gi|385805469|ref|YP_005841867.1| 359 LGAKGLP-EIP--TQVKEAVKKAQ 379
                                       5666653.244..88999999996 PP

  == domain 2  score: 71.0 bits;  conditional E-value: 8.6e-23
                                       ESSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHH.STTSEEEEEEEHHHHHHT.GGGHHHHHHTT-.S CS
                      TPP_enzyme_C   1 diGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGakla.kpdrevvaivGDGgflmi.lqelatavrrnl.p 74 
                                       diGc+ l         +p ++ +  +   mG g+++  G+ +a k + +v+ ivGD++f++  +++l++a  ++   
  gi|385805469|ref|YP_005841867.1| 421 DIGCYGL------APFSPMRIGD--VSLNMGSGFGFPQGLRVAlKTKDPVIGIVGDSTFFHAsMPALINAKWNGQkG 489
                                       7888888......3333444444..88899999999999999635678*************************9999 PP

                                       EEEEEEE-SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHH....C CS
                      TPP_enzyme_C  75 itvvvlnNegygmtggqqepfggkrksgpagkdlkpvdfaklaealGakgarvekadveeleealkeal....e 144
                                       ++++v +N++++mtggq++p  g r  + +    ++++ + +++a+G ++ +++++dv+   ea+++a+    e
  gi|385805469|ref|YP_005841867.1| 490 MLFIVADNRITAMTGGQPNPSSGMRGDHSQ---NPSINAEDVIKAMGYEVEVIDPYDVKGSIEAFRKAIkkirE 560
                                       *******************99998877765...9***************************9999999955543 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 !   56.5   0.0   3.1e-18   3.3e-15       2     169 ..      28     190 ..      27     221 .. 0.87

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 3.1e-18
                                       HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCC CS
                             POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmien 78 
                                       +a++a+vdv+a+YP TPsse++e+l+e+ ++ ++   +     +E+ a++++ GAaaaG +a+++    G+  +++ 
  gi|385805469|ref|YP_005841867.1|  28 GALEADVDVVAGYPGTPSSEVLEMLNEMRKQLGI---YAEISVNEMVAAEVAGGAAAAGLKALVTMKHVGVNVASDF 101
                                       899***************************9997...6666779********************************9 PP

                                       HHHHHHTT--EEEEEEEEE-STTB.EEEEE--TTCHHHHS---EEEE-SSHHHHHHHHHHHHHHHHHCTSEEEEEEE CS
                             POR_N  79 lglaageelPvvivvvaRalpstg.lsirtdqsDlmaardtglivlasenvqeafdlalvAfnlAekvrvPvivlfD 154
                                       + ++ ++ +   +v++   ++++g +  +++q   +++  + +  l + ++q a dl ++Af l+ k+++Pviv + 
  gi|385805469|ref|YP_005841867.1| 102 FNVINMTGIDGALVIYV--GDDPGaWVSQNEQDTRIYCEMFHFPCLEPYDQQTAKDLMIKAFELSKKYSLPVIVRST 176
                                       88888888876666664..445540445666666788999**********************************999 PP

                                       HHHH.HEEEEEEC-S CS
                             POR_N 155 gfllshevekvelpd 169
                                         ++ h+  +v++ +
  gi|385805469|ref|YP_005841867.1| 177 HRIA-HASGSVTIGK 190
                                       8888.9999988755 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   1.0   3.8e-06    0.0041       1      14 [.     584     597 ..     584     599 .. 0.93
   2 !   30.0   4.9   2.7e-10   2.8e-07       5      23 ..     619     637 ..     615     638 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.8e-06
                                       EEEETTTSSS-THH CS
                              Fer4   1 vvideekCigCGaC 14 
                                       ++id++kC+gC  C
  gi|385805469|ref|YP_005841867.1| 584 YYIDPDKCTGCRVC 597
                                       69************ PP

  == domain 2  score: 30.0 bits;  conditional E-value: 2.7e-10
                                       TTTSSS-THHHHHSTTTEE CS
                              Fer4   5 eekCigCGaCvevCPvgAI 23 
                                        e+C+gCG C++vCP++AI
  gi|385805469|ref|YP_005841867.1| 619 DELCVGCGVCAQVCPYNAI 637
                                       69****************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 !   32.1   8.4   8.9e-11   9.4e-08       3      56 ..     586     637 ..     584     639 .. 0.81

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 8.9e-11
                           Fer4_21   3 idedkCigCgkCliaCedtshqaieidakt.vlkvvedeCvGCnlCssvCPvedc 56 
                                       id+dkC gC  Cl++      qa++ d+ + ++++ ++ CvGC +C++vCP +  
  gi|385805469|ref|YP_005841867.1| 586 IDPDKCTGCRVCLLTLG---CQALQWDSVKkKAHIADELCVGCGVCAQVCPYNAI 637
                                       9************9866...789998865515566799*************7444 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 !   29.3   0.4   5.4e-10   5.7e-07       3     156 ..      21     172 ..      19     188 .. 0.79
   2 ?    1.2   0.0      0.23   2.5e+02      80     156 ..     476     567 ..     455     571 .. 0.66

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 5.4e-10
                                       HHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT....TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHH CS
                      TPP_enzyme_N   3 vaealvraLkalgvehvfgvpGsrilplldalseeq...girvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGa 76 
                                       + +a+vr   +++v++v g+pG+ + ++l++l+e +   gi    +++E +aa  A g a a  k  v + ++g+++
  gi|385805469|ref|YP_005841867.1|  21 GNQAIVRGALEADVDVVAGYPGTPSSEVLEMLNEMRkqlGIYAEISVNEMVAAEVAGGAAAAGLKALVTMKHVGVNV 97 
                                       789999999999*********************999988999999******************************** PP

                                       HHCHHHHHHHHHHT--EEEEEEE--CCCHHS..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS-- CS
                      TPP_enzyme_N  77 tnaltalaeAkvdriPllvlsgdrptslrgqgvlqqeldqlalfrpvtkyaervtspeelpealrrAirtalsgrpg 153
                                       ++ + ++++       l++ +gd p + ++q+ +  +    ++f      + ++++ ++++ ++ +A++ + ++ + 
  gi|385805469|ref|YP_005841867.1|  98 ASDFFNVINMTGIDGALVIYVGDDPGAWVSQNEQD-TRIYCEMFH---FPCLEPYDQQTAKDLMIKAFELS-KKYSL 169
                                       *************************9999944333.222333322...12445555555555555555555.55555 PP

                                       EEE CS
                      TPP_enzyme_N 154 Pvy 156
                                       Pv 
  gi|385805469|ref|YP_005841867.1| 170 PVI 172
                                       554 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.23
                                       HHHHHHHHHH.T--EEEEEEE--CCCHH............S..TC--T-CCHHHCCCSSEEEE-SSG...GGHHHHH CS
                      TPP_enzyme_N  80 ltalaeAkvd.riPllvlsgdrptslrg............qgvlqqeldqlalfrpvtkyaervtsp...eelpeal 140
                                       ++al++Ak + +  +l++++d+  +               ++ +++ ++++++++ +  y ++v +p   +   ea+
  gi|385805469|ref|YP_005841867.1| 476 MPALINAKWNgQKGMLFIVADNRITAMTggqpnpssgmrgDHSQNPSINAEDVIKAMG-YEVEVIDPydvKGSIEAF 551
                                       6777777776234577777777766666577777777876777777778888877555.555555550005555777 PP

                                       HHHHHHHHSSS--EEE CS
                      TPP_enzyme_N 141 rrAirtalsgrpgPvy 156
                                       r+Ai++  ++   +v+
  gi|385805469|ref|YP_005841867.1| 552 RKAIKKIRETGENVVV 567
                                       7888888555444544 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   2.3   0.00013      0.13       4      16 ..     586     598 ..     585     603 .. 0.89
   2 !   22.5   3.9   8.1e-08   8.5e-05       2      24 .]     615     637 ..     614     637 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                            Fer4_6   4 idpdkCigCgdCv 16 
                                       idpdkC+gC+ C 
  gi|385805469|ref|YP_005841867.1| 586 IDPDKCTGCRVCL 598
                                       9***********6 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 8.1e-08
                            Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                       ++i +++C+gCg C+ vCP++ai
  gi|385805469|ref|YP_005841867.1| 615 AHIADELCVGCGVCAQVCPYNAI 637
                                       78889*****************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 !   11.4   0.7   0.00035      0.36      28      45 ..     581     598 ..     558     600 .. 0.81
   2 !   22.6  10.8   1.1e-07   0.00012       1      52 []     590     636 ..     590     636 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00035
                            Fer4_7  28 tekveidpekClgCgaCv 45 
                                       +  ++idp+kC+gC++C 
  gi|385805469|ref|YP_005841867.1| 581 KTPYYIDPDKCTGCRVCL 598
                                       445799***********5 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 1.1e-07
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       +C+gC+ C  +   +a+++d +     ++k++i  e C+gCg+C++vCP++a
  gi|385805469|ref|YP_005841867.1| 590 KCTGCRVCLLTLGCQALQWDSV-----KKKAHIADELCVGCGVCAQVCPYNA 636
                                       7********999999****998.....56799*****************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 !   17.6   1.7   2.9e-06     0.003       2      17 ..     583     598 ..     582     605 .. 0.83
   2 !   19.1   2.3   9.4e-07   0.00099       4      22 .]     616     634 ..     613     634 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.9e-06
                            Fer4_2   2 pvvvdtdrCigCgaCv 17 
                                       p+++d+d+C+gC+ C+
  gi|385805469|ref|YP_005841867.1| 583 PYYIDPDKCTGCRVCL 598
                                       789************6 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 9.4e-07
                            Fer4_2   4 vvdtdrCigCgaCvsaCPa 22 
                                       ++  + C+gCg C ++CP+
  gi|385805469|ref|YP_005841867.1| 616 HIADELCVGCGVCAQVCPY 634
                                       555678************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 !   23.7   9.8   3.9e-08   4.1e-05       1      51 []     590     637 ..     590     637 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 3.9e-08
                            Fer4_9   1 kCtgCgaC..veaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                       kCtgC+ C  +  C+a  +  d++++ka +     e C+gCg C+++Cp +ai
  gi|385805469|ref|YP_005841867.1| 590 KCTGCRVCllTLGCQALQW--DSVKKKAHIAD---ELCVGCGVCAQVCPYNAI 637
                                       7*******66666877665..55555555433...37*************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 !   17.1  12.0   4.3e-06    0.0045       3      56 .]     585     633 ..     583     633 .. 0.94
   2 !   16.5   2.3   6.6e-06    0.0069       2      22 ..     615     635 ..     614     644 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.3e-06
                           Fer4_10   3 vidddtCirCgkCvka..CPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       +id+d+C++C+ C     C       +a + +s +++ +++ e C gcg C+++CP
  gi|385805469|ref|YP_005841867.1| 585 YIDPDKCTGCRVCLLTlgC-------QALQWDSVKKKAHIADELCVGCGVCAQVCP 633
                                       79***********98556*.......69***************************9 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 6.6e-06
                           Fer4_10   2 vvidddtCirCgkCvkaCPad 22 
                                       ++i d+ C++Cg C ++CP++
  gi|385805469|ref|YP_005841867.1| 615 AHIADELCVGCGVCAQVCPYN 635
                                       678899*************94 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   0.4      0.58   6.1e+02      53      60 ..     590     597 ..     554     604 .. 0.80
   2 !   19.1   2.0   1.8e-06    0.0019       2      20 ..     622     640 ..     621     644 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.58
                           Fer4_16  53 aitgCdiC 60 
                                       ++tgC++C
  gi|385805469|ref|YP_005841867.1| 590 KCTGCRVC 597
                                       56677766 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 1.8e-06
                           Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                       C++Cg Ca+vCP nai ++
  gi|385805469|ref|YP_005841867.1| 622 CVGCGVCAQVCPYNAIIKP 640
                                       ****************887 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 ?    6.3   0.4     0.013        14       1      13 [.     586     598 ..     586     601 .. 0.90
   2 ?   10.5   0.9   0.00066       0.7       2      18 ..     619     634 ..     617     644 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.013
                           Fer4_13   1 VDrdtCiacgaCv 13 
                                       +D d+C++c +C 
  gi|385805469|ref|YP_005841867.1| 586 IDPDKCTGCRVCL 598
                                       899*********6 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00066
                           Fer4_13   2 DrdtCiacgaCvelaPd 18 
                                       D + C++cg+C++++P 
  gi|385805469|ref|YP_005841867.1| 619 D-ELCVGCGVCAQVCPY 634
                                       4.88************6 PP

>> IF-2  Translation-initiation factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       5.9   6.3e+03      15      37 ..     387     409 ..     373     420 .. 0.65
   2 ?   10.3   0.1   0.00055      0.58      13      46 ..     534     567 ..     523     573 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 5.9
                                       CEEEEEESSHHHHHHHHHHHHCT CS
                              IF-2  15 lnviikaDvqGsleAlkeaLekl 37 
                                       l ++  +  qG+  Alk aL + 
  gi|385805469|ref|YP_005841867.1| 387 LTFCAGCPHQGTFYALKMALLRE 409
                                       55555566788888888888764 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00055
                                       SCCEEEEEESSHHHHHHHHHHHHCTT.SSTEEEE CS
                              IF-2  13 kelnviikaDvqGsleAlkeaLekleseevkvkv 46 
                                        e++vi   Dv+Gs+eA ++a++k++++  +v v
  gi|385805469|ref|YP_005841867.1| 534 YEVEVIDPYDVKGSIEAFRKAIKKIRETGENVVV 567
                                       566777777****************873333333 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   1.2    0.0039       4.1       2      16 ..     585     599 ..     585     611 .. 0.91
   2 ?    8.7   0.6    0.0028         3       6      19 ..     620     633 ..     616     644 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0039
                           Fer4_15   2 vvDrdaCigcglCva 16 
                                       ++D d+C+gc +C+ 
  gi|385805469|ref|YP_005841867.1| 585 YIDPDKCTGCRVCLL 599
                                       69***********86 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0028
                           Fer4_15   6 daCigcglCvaeap 19 
                                       ++C gcg+C++++p
  gi|385805469|ref|YP_005841867.1| 620 ELCVGCGVCAQVCP 633
                                       79***********8 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  12.2     0.075        79      41      59 ..     617     635 ..     590     637 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.075
                           Fer4_17  41 ekaslCieCgeCerkCPqg 59 
                                        + +lC++Cg C+++CP++
  gi|385805469|ref|YP_005841867.1| 617 IADELCVGCGVCAQVCPYN 635
                                       34489************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 ?    7.7   2.7    0.0052       5.5       1      10 [.     588     597 ..     588     603 .. 0.90
   2 ?   13.9   3.3   5.5e-05     0.058       2      17 .]     620     635 ..     619     635 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0052
                            Fer4_4   1 qerCigCgsC 10 
                                       +++C+gC++C
  gi|385805469|ref|YP_005841867.1| 588 PDKCTGCRVC 597
                                       69******** PP

  == domain 2  score: 13.9 bits;  conditional E-value: 5.5e-05
                            Fer4_4   2 erCigCgsCvaaCPqg 17 
                                       e C+gCg+C  +CP++
  gi|385805469|ref|YP_005841867.1| 620 ELCVGCGVCAQVCPYN 635
                                       67************86 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   2.5       1.7   1.8e+03       1       8 [.     591     598 ..     591     600 .. 0.88
   2 ?   12.6   8.0    0.0002      0.21       1      15 []     622     636 ..     622     636 .. 0.98

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.7
                            Fer4_3   1 CtgCgaCv 8  
                                       CtgC+ C+
  gi|385805469|ref|YP_005841867.1| 591 CTGCRVCL 598
                                       ****9997 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.0002
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C+gCg C +vCP++A
  gi|385805469|ref|YP_005841867.1| 622 CVGCGVCAQVCPYNA 636
                                       *************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (645 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       755  (0.0421105); expected 358.6 (0.02)
Passed bias filter:                      653  (0.0364214); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); 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: 0.77u 0.36s 00:00:01.12 Elapsed: 00:00:00.56
# Mc/sec: 3489.11
//
Query:       gi|385805470|ref|YP_005841868.1|  [L=443]
Description: C69 family peptidase [Fervidicoccus fontis Kam940]
Scores for complete 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  107.2   0.4    1.9e-30  106.7   0.4    1.2  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 !  106.7   0.4   1.1e-34   1.9e-30       5     279 .]      27     304 ..      23     304 .. 0.75

  Alignments for each domain:
  == domain 1  score: 106.7 bits;  conditional E-value: 1.1e-34
                                       EEEEEEEEEEEEETTEEEEEEEEEEEEEEEEEEETTEEEEEE...ESSHHHHHHHHHHHHHHCCS---TT-.....G CS
                         PmbA_TldD   5 rleesestsvrfengevetnsssedsglgvrvikggrlgfastldtsdealeeaveraveiaklapedpea.....e 76 
                                        ++  e+t  +++n++++ +++++++ l + + k++r+ + st  +s+e++ + ++ + +   + ++ + +     +
  gi|385805470|ref|YP_005841868.1|  27 KITYLEETMTKAANNTITITQNWSNKRLDLYLAKDKRISVMSTHFSSFEDIGKILDSSSNVISKIQPSELYaelpkP 103
                                       56666889999*****************************665545558999****988877666666666687442 PP

                                       GS-HHHHHHH.....HHHHHHH.CHCST.....TEEEEEEEEEE......EEE.EEEEEEETTSE.EEEEEEEEEEE CS
                         PmbA_TldD  77 evsaeekiel.....leelekalrsadp.....kienskgarisgvsaslsaskeeklianSeGl.dveqtrtrvsl 142
                                         +ae   ++     +e++++      p     +ie+s + ++ +v + ls  keek++   +G  +  + +t v  
  gi|385805470|ref|YP_005841868.1| 104 --NAEHSSKIldikvIEKMSEV-----PvymqkMIEKSLESGAEKVAGVLSFIKEEKVLS-INGEeNFNEVSTAVKT 172
                                       ..33333322221224444432.....134444666666556666667788886776666.5666566666666655 PP

                                       EEEEEE..STCSETEEEEEEEE...SSHHHS..SSHHHHHHHHHHCTTT-B---SEEEEEEE-HHHHHHHHHGHHHH CS
                         PmbA_TldD 143 slsvia.ddggsgdgmgggsgy...edleeedleeiaeeaaekalasleakplppgkypVvlspeavgsllheavgh 215
                                       ++     +   +     +g+++   + l+e++l +  e+a + al + + +++ +gky+++lsp  +g+ll +++  
  gi|385805470|ref|YP_005841868.1| 173 YIRSFKgE---K-----SGMWSfgsRYLDEKELLNTSEKATQFALLQNKKEKIDSGKYDIILSPLIAGNLLNYIMF- 240
                                       55554422...1.....223333555578888999*************************************9885. PP

                                       HTBHHHHHTT--TTTT-TTS.B-S-TT--EEEETT-......-SB-TTSBB---EEEEETTEE--- CS
                         PmbA_TldD 216 aleadavlegrSflkdklGe.kvaselltivddpts.gglgsypfDdEGvptqrtvlIenGvLkny 279
                                       +++a ++l+g Sf+  k +e    se l+++d p   + +gs+ fDdEG++t  +++Ie+G +k++
  gi|385805470|ref|YP_005841868.1| 241 SASAFNALAGLSFF--KNNEnNMYSEQLSLYDSPEEtDLPGSTKFDDEGLATYTKPIIEKGMFKTF 304
                                       **************..86776999***********99***************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); 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: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 3110.93
//
Query:       gi|385805471|ref|YP_005841869.1|  [L=479]
Description: C69 family peptidase [Fervidicoccus fontis Kam940]
Scores for complete 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-44  152.7   0.2    2.3e-44  152.4   0.2    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 !  152.4   0.2   1.3e-48   2.3e-44       1     277 [.      20     328 ..      20     329 .. 0.86

  Alignments for each domain:
  == domain 1  score: 152.4 bits;  conditional E-value: 1.3e-48
                                       EEEEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEEEEETTEEEEEE...ESSHHHHHHHHHHHHHHCCS---TT-.. CS
                         PmbA_TldD   1 eaevrleesestsvrfengevetnsssedsglgvrvikggrlgfastldtsdealeeaveraveiaklapedpea.. 75 
                                       +ae+r++++e++ v ++ng++ +++ s+++g+++rv+++g l+f+st+d+s+e++   +++a+++ak  + ++++  
  gi|385805471|ref|YP_005841869.1|  20 YAEIRFHKNEENYVILRNGNLISAGKSSRKGIAIRVLYNGNLAFSSTNDISKESIFTGIDKAIANAKALNINKKEnf 96 
                                       89****************************************************************99988888899 PP

                                       .....................GGS-HHHHHHHHHHHHHH.CHCSTTEEEEEEEEEE......EEE.EEEEEEETTSE CS
                         PmbA_TldD  76 .....................eevsaeekielleelekalrsadpkienskgarisgvsaslsaskeeklianSeGl 131
                                                            ++++++eki++l++l   +      ++++k+a+++    s+s++ eek+i+nS+G 
  gi|385805471|ref|YP_005841869.1|  97 slseerslgkskyevyvkesfDQLPIDEKISYLKNLYMVA------LDSMKNAKLNAMFESYSDEIEEKVIVNSDGG 167
                                       99**********9999999999999999999999999543......2334466777777799*************** PP

                                       EEEEEEEEEEEEEEEEE...STCS..ET.EEEEEEEESSHHHS..SS.HHHHHHHHHHCTTT-B---SEEEEEEE-H CS
                         PmbA_TldD 132 dveqtrtrvslslsvia.d.dggs..gd.gmgggsgyedleeedlee.iaeeaaekalasleakplppgkypVvlsp 202
                                       +ve++ +r +++ ++i  d + gs  +  ++g  +g e l++++le+ i  +++   + +le k++p    +Vv ++
  gi|385805471|ref|YP_005841869.1| 168 YVESKIPRLYFFGNIIIyDpQKGSmqKMiEKGASGGLELLKGWRLEDeIKNDLKSLEKVLLEGKSPPKDAVDVVVGS 244
                                       *****************99875555544444444444333333333303333333333344567878889******* PP

                                       HHHHHHHHGHHHHHTBHHHHH......TT--TTTT.-TTS.B-S-TT--EEEETT-......-SB-TTSBB---EEE CS
                         PmbA_TldD 203 eavgsllheavghaleadavl......egrSflkd.klGe.kvaselltivddpts.gglgsypfDdEGvptqrtvl 270
                                       e vg+++he+ gh++ead++       +g Sf k+ ++G+  +++++ t++ddpt+ ++ g+y +DdE vp++++++
  gi|385805471|ref|YP_005841869.1| 245 EIVGLIVHESAGHPMEADRIWgresaqAGESFVKPeMIGKvYIGNSNATVIDDPTIpESNGFYLYDDETVPARKRYI 321
                                       **********************999999*****9977***999************99******************** PP

                                       EETTEE- CS
                         PmbA_TldD 271 IenGvLk 277
                                         +G L+
  gi|385805471|ref|YP_005841869.1| 322 YYKGLLN 328
                                       ****996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (479 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.48
# Mc/sec: 3003.34
//
Query:       gi|385805472|ref|YP_005841870.1|  [L=422]
Description: metalloexopeptidase, family M20 [Fervidicoccus fontis Kam940]
Scores for complete 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    1.7e-38  132.4   0.0    1.1  1  Peptidase_M20  Peptidase family M20/M25/M40
    5.4e-23   81.0   0.1    1.1e-21   76.8   0.0    2.4  2  M20_dimer      Peptidase dimerisation domain
    1.8e-08   34.3   0.0    3.3e-08   33.4   0.0    1.4  1  Peptidase_M28  Peptidase family M28
  ------ inclusion threshold ------
      0.013   14.5   0.0        8.9    5.2   0.0    3.0  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 !  132.4   0.0   3.8e-42   1.7e-38       3     205 ..      97     421 ..      95     422 .] 0.89

  Alignments for each domain:
  == domain 1  score: 132.4 bits;  conditional E-value: 3.8e-42
                                       EEES-BSSTTCGGGSSS..TTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTT.T CS
                                       xxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                     Peptidase_M20   3 gsHlDvVpeeetdgwtt..pfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggr.g 76 
                                         H+DvVp++e ++wt+  pf++ +++Gk+yGrG++d+  +++a l+a++al d gi+p +t+ l+f+ dEE+g+  
  gi|385805472|ref|YP_005841870.1|  97 LTHMDVVPPGELSKWTEckPFEPVVKNGKVYGRGSVDNGQSLVASLYAVKALMDLGIRPSRTVALAFVSDEETGSeY 173
                                       57******99999***********************************************************9889* PP

                                       HHHHHHH...HHHTTTCESEEEEEEEESSSBTCHSTETEEEE................................... CS
                                       xxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................... RF
                     Peptidase_M20  77 Gakalle...gleerekvdavfelhieepgileagklaigvv................................... 115
                                       Ga++ll+    l+   + d++   ++ ++g++e g   i +                                    
  gi|385805472|ref|YP_005841870.1| 174 GAQYLLKarpDLF--GENDWI---VVPDGGNSE-GS-FIEIAekgilwlrvkvtgkqvhgsmpdkglnahrvaadfv 243
                                       *******655333..355663...377777777.44.3333356777777778899********************* PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Peptidase_M20 116 ............................................................................. 115
                                                                                                                    
  gi|385805472|ref|YP_005841870.1| 244 itldkklhekfnkrndlfdpprstfeptmvrgsagsvniipsdheitfdcrilpeytidevlnvvnqtkneiiakhk 320
                                       ***************************************************************************** PP

                                       .........EEEEEEE..EEESHEEEC.CHHHHHHHHHHHHHHHTSCEEEEEESSSBHTHHHH..TTTEEEEEEESS CS
                                       .........xxxxxxx..xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxx RF
                     Peptidase_M20 116 .........kvevell..eggapvtln.dsplvkalaeaaeelfgekvelivsgpggtdarff..agiptvmifgpg 178
                                                k+e+e +  +++   +++ +s++vk+l e++++l g ++++   g ggt a+ff  +gip+v+++  +
  gi|385805472|ref|YP_005841870.1| 321 kviegeslpKIEIEIVnrSDSTK-PTDpNSEIVKKLTESIQKLRGITPKTGGIG-GGTVAAFFrqKGIPAVVWCTID 395
                                       ********978888775233333.33369*************999777666666.********99999***999988 PP

                                       GGCTTSTTTEEEHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 179 sglaHspnEyvdledlekgikvlarll 205
                                        +  H+pnEy +++++++ +kv+ +l+
  gi|385805472|ref|YP_005841870.1| 396 -EVEHQPNEYASIKNMVEDAKVFLSLM 421
                                       .99*******************99876 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.8   0.0   2.4e-25   1.1e-21       1     101 [.     207     312 ..     207     320 .. 0.94
   2 ?    1.3   0.0     0.068     3e+02      36      73 ..     351     387 ..     344     405 .. 0.74

  Alignments for each domain:
  == domain 1  score: 76.8 bits;  conditional E-value: 2.4e-25
                                       SEB-EEEEEEEEEE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC.........TCCTCCCCCEECCE-C.CCCEE CS
                         M20_dimer   1 ighkGlaggkitvkgkagHsgapgagaNAieklarllaeledeegdia....eerslprttlnvtgiegGs.aknvi 72 
                                       i++kG+++ +++v+gk++H+++p++g NA + +a+++  l ++ +++     + +++pr+t+++t+++g   + n+i
  gi|385805472|ref|YP_005841870.1| 207 IAEKGILWLRVKVTGKQVHGSMPDKGLNAHRVAADFVITLDKKLHEKFnkrnDLFDPPRSTFEPTMVRGSAgSVNII 283
                                       689***************************************988877*********************99****** PP

                                       SSEEEEEEEEEHHHHHHHHHHHHHHHHHH CS
                         M20_dimer  73 pdeaeakidiRllpgedpeevleeieeil 101
                                       p+  e ++d+R+lp+ + +evl+ +++  
  gi|385805472|ref|YP_005841870.1| 284 PSDHEITFDCRILPEYTIDEVLNVVNQTK 312
                                       **********************9998765 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.068
                                       HHHCSCTTEEC.....TCCTCCCCCEECCE-C.....CCCEES CS
                         M20_dimer  36 llaeledeegdiaeerslprttlnvtgiegGs.....aknvip 73 
                                       ++ +l +        + l++ t+  +gi gG+         ip
  gi|385805472|ref|YP_005841870.1| 351 IVKKLTES------IQKLRGITPKTGGIGGGTvaaffRQKGIP 387
                                       55555555......3457899**********976655555555 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.0   7.4e-12   3.3e-08       1      86 [.      80     183 ..      80     209 .. 0.90

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 7.4e-12
                                       EEEEEESTTCESEEEEEEEE--B-TTT................TCC.T---TTTTHHHHHHHHHHHHHCHHGGCCSS CS
                     Peptidase_M28   1 NviatlegkatdevlllgAHyDsvgvg................rgp.ifvGAdDnAsgvaalLelarvlaasgsrpk 60 
                                       N++a ++gk+++  + +  H+D v+ g                +g+    G  Dn+ + +a L+ +++l + g rp 
  gi|385805472|ref|YP_005841870.1|  80 NIVAIYKGKNEKDKIWFLTHMDVVPPGelskwteckpfepvvkNGKvYGRGSVDNGQSLVASLYAVKALMDLGIRPS 156
                                       9*********988************99********999999885556668*********************9*9*** PP

                                       EEEEEEEESSCSG.SSHHHHHHHHHHC CS
                     Peptidase_M28  61 rgvrflffdaEEa.gllGSkafakakp 86 
                                       r+v ++f++ EE  + +G++++ ka+p
  gi|385805472|ref|YP_005841870.1| 157 RTVALAFVSDEETgSEYGAQYLLKARP 183
                                       *************667******97554 PP

>> Peptidase_M42  M42 glutamyl aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.002       8.9       2      25 ..      80     103 ..      79     104 .. 0.94
   2 ?    5.0   0.0    0.0023        10     123     193 ..     121     194 ..     114     228 .. 0.79
   3 ?    0.2   0.0     0.067     3e+02     248     288 ..     372     412 ..     335     416 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.002
                                       -EEEEEESSTTSSEEEEEEE--B- CS
                     Peptidase_M42   2 nliakkkgkekepkvmiaAHmDei 25 
                                       n++a  kgk+++ k+ + +HmD +
  gi|385805472|ref|YP_005841870.1|  80 NIVAIYKGKNEKDKIWFLTHMDVV 103
                                       89********************66 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0023
                                       ETTECEEET.THHHHHHHHHHHHHHHHHCTSS-S..SEEEEEEESTCTTTSH.HHHHHHHHH--SEEEEEEEEEE CS
                     Peptidase_M42 123 langkivsk.alDdragvavllellkelkeeele..atvylvatvqEEvGlr.GaktsaekikpdiaiavDvtaa 193
                                       ++ngk+ ++  +D+  ++++ l+++k+l +  +    tv l++   EE G   Ga+++ +  +pd++   D  ++
  gi|385805472|ref|YP_005841870.1| 121 VKNGKVYGRgSVDNGQSLVASLYAVKALMDLGIRpsRTVALAFVSDEETGSEyGAQYLLKA-RPDLFGENDWIVV 194
                                       677788887469*******************999989999999*******86477766665.8887755555555 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.067
                                       SSSTHHHHHTSTTTSEEEEEEEEEBSTTSTTEEEEHHHHHH CS
                     Peptidase_M42 248 ggtDAgaihltgegvptalisiptryiHspvevahlddlea 288
                                        g  + a+ + ++g+p+++ ++  +  H p+e a+++ + +
  gi|385805472|ref|YP_005841870.1| 372 IGGGTVAAFFRQKGIPAVVWCTIDEVEHQPNEYASIKNMVE 412
                                       3444456677788********************99998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 2626.57
//
Query:       gi|385805473|ref|YP_005841871.1|  [L=141]
Description: AbrB family transcriptional regulator [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.8e-06   25.8   0.0    1.4e-05   24.8   0.0    1.6  1  ACT             ACT domain
     0.0021   18.6   0.0     0.0046   17.5   0.0    1.7  2  ACT_4           ACT domain
  ------ inclusion threshold ------
      0.017   15.0   0.1      0.037   14.0   0.1    1.5  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an


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 !   24.8   0.0   2.3e-09   1.4e-05       1      54 [.      60     113 ..      60     128 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 2.3e-09
                                       EEEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHH CS
                               ACT   1 tvlrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeed 54 
                                       + +rv+++D+PG+La+++ a+ d+ + i     ++ +++  g+ +++++++ ++
  gi|385805473|ref|YP_005841871.1|  60 YEIRVELQDKPGALADLTKAFLDMKLDILISKCSTIKRGEIGECTMIVEPGNKE 113
                                       679*********************************998666666666665554 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.7   9.9e+03      47      61 ..      30      44 ..      25      52 .. 0.69
   2 !   17.5   0.0   7.7e-07    0.0046       8      55 ..      61     108 ..      56     133 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.7
                             ACT_4 47 laeikitveVkdveh 61
                                      + e++  v + dv++
  gi|385805473|ref|YP_005841871.1| 30 ISEGRYMVLIADVDK 44
                                      667777788888775 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 7.7e-07
                             ACT_4   8 rleveaedrkglLaditqviseekanivsvnaktrkkdglaeikitve 55 
                                       +++ve +d++g+Lad+t+++ ++k +i   + +t k+ ++ e+++ ve
  gi|385805473|ref|YP_005841871.1|  61 EIRVELQDKPGALADLTKAFLDMKLDILISKCSTIKRGEIGECTMIVE 108
                                       79*************************999999998888888877776 PP

>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   6.1e-06     0.037       1      42 [.      10      53 ..      10      56 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.1e-06
                                      EEETTEEEEEE-CCCHHHCCEECTCEEEEEECTT..CCCCCCCH CS
                    MazE_antitoxin  1 fkvGnsgavriPkevrfelgireGdevelevdgd..kiilrplk 42
                                      +k++ +g+v+iP  +r++++i+eG   +l+ d d   +il+p+ 
  gi|385805473|ref|YP_005841871.1| 10 VKIDPKGRVTIPLFIRESMDISEGRYMVLIADVDkkEMILTPIT 53
                                      58899*****************************9999999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); 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: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 943.18
//
Query:       gi|385805474|ref|YP_005841872.1|  [L=240]
Description: hypothetical protein FFONT_0430 [Fervidicoccus fontis Kam940]
Scores for complete 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   84.2   0.0    1.6e-23   84.0   0.0    1.0  1  DUF72         Protein of unknown function DUF72
  ------ inclusion threshold ------
      0.018   14.5   0.0      0.024   14.1   0.0    1.3  1  AP_endonuc_2  Xylose isomerase-like TIM barrel


Domain annotation for each model (and alignments):
>> DUF72  Protein of unknown function DUF72
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.0   0.0   1.8e-27   1.6e-23      16     203 ..       6     222 ..       1     234 [. 0.83

  Alignments for each domain:
  == domain 1  score: 84.0 bits;  conditional E-value: 1.8e-27
                                       CT-SEEEE-HHCCSSS-HHHHHHHHCTS-TT-EEEEE--CCCCC.....S.............G...-.SCHHHHHH CS
                             DUF72  16 rhfntVEinstFYalpspetvakwaaqtpedFrFavKapraith.....e.........r...n...e.daeealer 71 
                                       + +++VEi+ +FY l+s++ +++  ++  ++ + ++K+++ ith               +   n      ++e +e+
  gi|385805474|ref|YP_005841872.1|   6 SLVDVVEIQKSFYDLLSDKEISNILKNKRNENKITLKCWQVITHpstspTwkkmknkinGeinNygyLkPTKENFEA 82 
                                       55799***************************************655550545555454145423332368899999 PP

                                       HHHH.CHHH.CT-EEEEEEE--TT--S.HHHHHHHHHHTTTS-......S.EEEE--BGGGH.H.HHHHHHHTT-EE CS
                             DUF72  72 flesalepL.geklgpllfQlppsfkfdeenlerLeaflaalp......l.lavEvRhrswf.e.llellrehgvav 138
                                       f +  +++  + ++ ++++Q pps+ +de   +r+ +f++++         +a+E R +    + +le +++++v +
  gi|385805474|ref|YP_005841872.1|  83 FSKV-VDQArKLNAEVIVLQSPPSMPYDEYTKDRISSFFKEITsiveknIkIAWEPRGKYAEdDsFLEKIENEKVEI 158
                                       9995.88885689999*********99988********9999889999956*******8555856************ PP

                                       EEE--SSC--------SSTEEEEEE--S...H.HTTB----HHHHHHHHHHHHHHHTCSSEEEEEE-SB CS
                             DUF72 139 vldepkkpklpledvttadfvyvRlhgr...e.eryayrYseeelaewaerikawaaegrevyvffnnd 203
                                       v+d     +l+  ++  ++f y+Rlhg    +  +y+y+Y++e+l  + + i ++  +++++yv+fnn 
  gi|385805474|ref|YP_005841872.1| 159 VTD-----ALRRGKIFYEHFLYIRLHGLggkReTNYKYKYTDEDLISLSKLIGKAIVHNKNIYVLFNNI 222
                                       **9.....56667777789*********9995599********************************94 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 ?   14.1   0.0   2.7e-06     0.024      65     156 ..      76     156 ..       9     163 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.7e-06
                                       HHHHHHHHHHHHHHHHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTC CS
                      AP_endonuc_2  65 reesvdalkraielaaaLGapllvlhpGtagagpkgseeeawerlaeslneladyaekegvklalEtlagsgvelgd 141
                                        +e ++a+ + ++ a++L+a+++vl++     ++   +e + +r+ + ++e+  +  ++++k+a E+  +       
  gi|385805474|ref|YP_005841872.1|  76 TKENFEAFSKVVDQARKLNAEVIVLQSP----PSMPYDEYTKDRISSFFKEITSIV-EKNIKIAWEPRGKYA----- 142
                                       35569*********************44....555555589999999999999997.69*******987765..... PP

                                       HHHHHHHHHHTTTTE CS
                      AP_endonuc_2 142 eelarlldavdspnv 156
                                        e + +l+++++++v
  gi|385805474|ref|YP_005841872.1| 143 -EDDSFLEKIENEKV 156
                                       .33345555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       989  (0.055162); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); 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: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1583.44
//
Query:       gi|385805475|ref|YP_005841873.1|  [L=81]
Description: hypothetical protein FFONT_0431 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score 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   13.2   0.9      0.015   13.2   0.9    1.0  1  PolC_DP2     DNA polymerase II large subunit DP2
      0.026   14.7   0.0      0.027   14.6   0.0    1.1  1  DUF4825      Domain of unknown function (DUF4825)
       0.26   11.2   3.1       0.53   10.2   3.1    1.6  1  zf-C4_ClpX   ClpX C4-type zinc finger
        0.5   10.5   3.8       0.64   10.2   3.0    1.7  1  Zn-ribbon_8  Zinc ribbon domain


Domain annotation for each model (and alignments):
>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.9   3.2e-06     0.015     613     681 ..       3      69 ..       1      81 [] 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.2e-06
                          PolC_DP2 613 eveiarrkCkkCgketlearCeeCgekteeklvCkkceeeve.eekcekcekeakavkkkkidlkellek 681
                                       +++i  ++C+ Cgk++ +a+C+    k ++ +vC +c  + + ++kc+  + + + ++  + + +e+lek
  gi|385805475|ref|YP_005841873.1|   3 TLSIYWYRCDLCGKNSPTANCT---IKNRKLNVCYRCFITFKlWNKCSDYGWKIEVKRLSNANTEEKLEK 69 
                                       6788999************999...44555568****999999999999999999999999888888776 PP

>> DUF4825  Domain of unknown function (DUF4825)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0     6e-06     0.027       4      62 ..       9      69 ..       6      79 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6e-06
                           DUF4825  4 yktpYvGdnsavgk.ilkaLplpeglsyd.gieLqtekePYgltvnyeeketekeeeelke 62
                                      y+    G ns   + ++k+ +l+  +++  +++L ++ + Yg+++ +++ +++++ee+l++
  gi|385805475|ref|YP_005841873.1|  9 YRCDLCGKNSPTANcTIKNRKLNVCYRCFiTFKLWNKCSDYGWKIEVKRLSNANTEEKLEK 69
                                      666667777766552578889999999989***********************99999877 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 ?   10.2   3.1   0.00012      0.53       2      29 ..      10      36 ..       9      41 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00012
                        zf-C4_ClpX  2 rCSFCgksesevkklIagpngvyICdeC 29
                                      rC  Cgk+  +++  I   + +++C +C
  gi|385805475|ref|YP_005841873.1| 10 RCDLCGKNSPTANCTIKNRK-LNVCYRC 36
                                      8***************9997.8***999 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   3.0   0.00014      0.64       3      32 ..       6      36 ..       5      41 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00014
                       Zn-ribbon_8  3 iYeYrCeeCghefe.vlqsisdapltaCPeC 32
                                      iY YrC+ Cg+    + ++i+ ++l +C +C
  gi|385805475|ref|YP_005841873.1|  6 IYWYRCDLCGKNSPtANCTIKNRKLNVCYRC 36
                                      8*********876655555556667778777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1087  (0.060628); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 535.48
//
Query:       gi|385805476|ref|YP_005841874.1|  [L=249]
Description: Proliferating cell nuclear antigen, PCNA [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-14   52.8   4.2    3.7e-14   52.5   2.7    1.8  2  PCNA_N          Proliferating cell nuclear antigen, N-termina
    1.6e-09   37.6   0.2    2.3e-09   37.1   0.2    1.2  1  Rad9            Rad9
    3.3e-06   26.4   0.1    3.7e-06   26.3   0.1    1.2  1  Hus1            Hus1-like protein
  ------ inclusion threshold ------
      0.015   15.8   0.1      0.039   14.4   0.1    1.8  1  Ribosomal_L25p  Ribosomal L25p family
      0.097   12.6   3.3        3.1    7.8   0.1    3.2  3  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an


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 !   52.5   2.7     1e-17   3.7e-14       6     120 ..       5     119 ..       1     124 [. 0.95
   2 ?   -1.2   0.0      0.43   1.5e+03      12      39 ..     143     170 ..     138     182 .. 0.76

  Alignments for each domain:
  == domain 1  score: 52.5 bits;  conditional E-value: 1e-17
                                       ESSHHHHHHHHHHHTTTCSEEEEEEETTEEEEEEE-TTSSEEEEEEEEGGGSSEEEESS-EEEEEEHHHHHHHHTTS CS
                            PCNA_N   6 leqasllkklleaikdlvneanfdcddsGislqalDsshvaLvslelrsegfekyrCDrnlalgvnlnslskilkca 82 
                                       l++as lk +++ +  + +e+ + ++++Gis ++l + + ++  le+ se f+++  + n+++ v++  ++kilk a
  gi|385805476|ref|YP_005841874.1|   5 LNDASDLKDIIDVLAKVAEEVPLTISEKGISSKTLSEDKTTMSILEIPSEIFNEFELEENISFRVKIRDFNKILKRA 81 
                                       899************************************************************************** PP

                                       TTTSEEEEEEETTSSEEEEEEEECTSSEEEEEEEEEEE CS
                            PCNA_N  83 nnedsvtlkaedeadtlalvfesekkdkiaeydlklkl 120
                                        ++d++ l+ e ++  l++vf+++k+  i ++dl++  
  gi|385805476|ref|YP_005841874.1|  82 TKNDVLELSLEKDKGILKIVFKNSKNGAIRSFDLQVSI 119
                                       ******************************99998764 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.43
                                       HHHHHHHHTTTCSEEEEEEETTEEEEEE CS
                            PCNA_N  12 lkklleaikdlvneanfdcddsGislqa 39 
                                       lk +l+ +  + +e+ f+ ++s i +++
  gi|385805476|ref|YP_005841874.1| 143 LKDILDDVSKVGEEVEFEYKNSSIVIKS 170
                                       7888888888888888888888877665 PP

>> Rad9  Rad9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.2   6.4e-13   2.3e-09       4     165 ..      14     170 ..      11     183 .. 0.90

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 6.4e-13
                              Rad9   4 alqclsrigdelyleisedglelrtvnssrSayalvtlkksfFdkyekevseqirckilvKsvlsvfrslsakektv 80 
                                       ++  l+++ +e+ l ise+g++ +t+   +++ +++++ +++F+++  e +e+i ++++++ + ++++ +     + 
  gi|385805476|ref|YP_005841874.1|  14 IIDVLAKVAEEVPLTISEKGISSKTLSEDKTTMSILEIPSEIFNEF--ELEENISFRVKIRDFNKILKRAT----KN 84 
                                       6789******************************************..899****************7444....44 PP

                              Rad9  81 ekvkisidekksrlivqll.CkhgvkkthkisledseslkavfdkettpsklriksrvLsdllehfsssleeitiel 156
                                       + +++s++++k+ l++ +   k+g ++ + +++  ++   +   k   p +++i +  L+d+l+  s+  ee+ +e 
  gi|385805476|ref|YP_005841874.1|  85 DVLELSLEKDKGILKIVFKnSKNGAIRSFDLQVSIENVEDIGEPKVDLPIEFEILAGDLKDILDDVSKVGEEVEFEY 161
                                       5577888888888877775379*********9999999999999999****************************** PP

                              Rad9 157 akervllks 165
                                       ++ ++++ks
  gi|385805476|ref|YP_005841874.1| 162 KNSSIVIKS 170
                                       ********9 PP

>> Hus1  Hus1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.1     1e-09   3.7e-06       4     180 ..       2     161 ..       1     222 [. 0.85

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1e-09
                              Hus1   4 kaqltdaetlkkvlqslsklgkecilrltpeklrfiiiteaddgvqvwaqlqvdaiFeeyeieSndeneInlevdla 80 
                                       k  l+da+ lk+++ +l+k++ e+ l ++++ +   + +  d+++  + +++++ iF+e+e+e    ++I++ v++ 
  gi|385805476|ref|YP_005841874.1|   2 KIILNDASDLKDIIDVLAKVAEEVPLTISEKGISSKTLS-EDKTTMSILEIPSE-IFNEFELE----ENISFRVKIR 72 
                                       77899***************************9988885.888889999***98.******96....679******* PP

                              Hus1  81 aLlraLksaeaaksvqlrLtkkgrvplLaleisglssreretvvthdiPvkvlseseveelkePelrdpdvsilLP. 156
                                       ++ ++Lk a+++  ++l L k     +L++  ++++      + ++d+ v++   ++ve++ eP++   d++i +  
  gi|385805476|ref|YP_005841874.1|  73 DFNKILKRATKNDVLELSLEKD--KGILKIVFKNSKN---GAIRSFDLQVSI---ENVEDIGEPKV---DLPIEFEi 138
                                       ********************99..7888888888877...555566888877...55666888877...77777775 PP

                              Hus1 157 dllqLkklvdkfkklssdlltlsa 180
                                           Lk ++d + k+ ++ ++++ 
  gi|385805476|ref|YP_005841874.1| 139 LAGDLKDILDDVSKV-GEEVEFEY 161
                                       555788888888888.77776665 PP

>> Ribosomal_L25p  Ribosomal L25p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   1.1e-05     0.039      31      70 ..      62     104 ..      22     115 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.1e-05
                                       SCEEEEEEEHHHHHHHCH....CSEEEEEETTCEEEEEEEEEE CS
                    Ribosomal_L25p  31 kepisisvdakelrkllkt...stlieLevdgekvllkdvqrh 70 
                                       +e+is+ v+ ++++k+lk+   + ++eL++++ k +lk v ++
  gi|385805476|ref|YP_005841874.1|  62 EENISFRVKIRDFNKILKRatkNDVLELSLEKDKGILKIVFKN 104
                                       35***************9899*********9756777655544 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 ?    3.8   0.3     0.016        58      23      40 ..      83     102 ..      72     107 .. 0.73
   2 ?    0.6   0.0      0.15   5.5e+02       1      10 [.     102     111 ..     102     111 .. 0.96
   3 ?    7.8   0.1   0.00087       3.1      20      41 ..     149     171 ..     132     176 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.016
                                       CTCEEEEEECTT..CCCCCC CS
                    MazE_antitoxin  23 eGdevelevdgd..kiilrp 40 
                                       ++d +el+ ++d  ++ +++
  gi|385805476|ref|YP_005841874.1|  83 KNDVLELSLEKDkgILKIVF 102
                                       48**********84444444 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.15
                                       EEETTEEEEE CS
                    MazE_antitoxin   1 fkvGnsgavr 10 
                                       fk++++ga+r
  gi|385805476|ref|YP_005841874.1| 102 FKNSKNGAIR 111
                                       8********9 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.00087
                                       CEEC.TCEEEEEECTTCCCCCCC CS
                    MazE_antitoxin  20 gire.Gdevelevdgdkiilrpl 41 
                                       ++++ G eve+e ++ +i+++  
  gi|385805476|ref|YP_005841874.1| 149 DVSKvGEEVEFEYKNSSIVIKSE 171
                                       66677*********988888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); 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: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1696.01
//
Query:       gi|385805477|ref|YP_005841875.1|  [L=214]
Description: 30S ribosomal protein S3Ae [Fervidicoccus fontis Kam940]
Scores for complete 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-68  229.8   4.0    2.7e-68  229.6   4.0    1.0  1  Ribosomal_S3Ae  Ribosomal S3Ae family
  ------ inclusion threshold ------
       0.12   12.0   0.0       0.23   11.1   0.0    1.4  1  Abhydro_lipase  Partial alpha/beta-hydrolase lipase region


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 !  229.6   4.0     3e-72   2.7e-68       2     200 ..       7     194 ..       6     196 .. 0.97

  Alignments for each domain:
  == domain 1  score: 229.6 bits;  conditional E-value: 3e-72
                                       S----S-TCCSEEEEEEEB-TTSSSSEEEEEEEE--BSSSESHHSHTT-EEEEESHHHHTCSHTSSSEEEEEEEEEE CS
                    Ribosomal_S3Ae   2 kkkkvvDkfkkKeWydvkaPslfgkreiGktlvnrtqgtkiaseklkgrvvevslaDLtndekeqafrklklkieev 78 
                                       k+++ ++++k K+Wy+v aPs+fg+++iG++++        ++e+l+gr+ve++l+D+t+d+  q+++kl ++i +v
  gi|385805477|ref|YP_005841875.1|   7 KRRELKETWKMKKWYEVIAPSVFGEVSIGSIPA-------LTPEQLIGRTVEATLYDITGDY-TQVHIKLNFQIIKV 75 
                                       678899***************************.......*********************9.668*********** PP

                                       ESSEEEEEEEEEEE-HHHHHHH--SSB-EEEEEEEEEESSSEEEEEEEEEEE-STTB---HHHHHHHHHHHHHHHHH CS
                    Ribosomal_S3Ae  79 qgknaltnFkgmeltrDklrslvrkwsslIeaivdvktkDgyllrvfvvafTkkrnsYakssqkkaIrkkmveilte 155
                                       +g+na t+Fkg+el+rD+++ l+r++ss+++ i++v+tkDgy+lr+ +++fT+++   a++sqk+aIrk+m++i+te
  gi|385805477|ref|YP_005841875.1|  76 EGHNAHTRFKGHELARDYIKVLTRRKSSKVQGIFNVETKDGYKLRIIAITFTSYK---ANTSQKRAIRKIMEKIITE 149
                                       *******************************************************...******************* PP

                                       HHHHS-HHHHHHHHTTTHHHHHHHHHHTTTS-EEEEEEEEEEEEE CS
                    Ribosomal_S3Ae 156 easeldlkelvkklipeslgkeiekeakkIyplrnveirKvkvlk 200
                                       +++e++++e+++ l+ ++l++ei+ eakkIyp+r+vei+K+k+l 
  gi|385805477|ref|YP_005841875.1| 150 RIKEKSFDEVIQLLVGNDLSTEIFSEAKKIYPIRKVEIYKSKLLF 194
                                       ****************77************************985 PP

>> Abhydro_lipase  Partial alpha/beta-hydrolase lipase region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   2.5e-05      0.23      15      35 ..     109     129 ..     106     143 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.5e-05
                    Abhydro_lipase  15 heVqTeDGYiLtlhRipaknk 35 
                                       ++V+T+DGY L +  i     
  gi|385805477|ref|YP_005841875.1| 109 FNVETKDGYKLRIIAITFTSY 129
                                       68**********998876663 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       699  (0.0389871); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1535.96
//
Query:       gi|385805478|ref|YP_005841876.1|  [L=93]
Description: hypothetical protein FFONT_0434 [Fervidicoccus fontis Kam940]
Scores for complete 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   23.1   0.1      7e-05   22.9   0.1    1.1  1  Pcc1      Transcription factor Pcc1


Domain annotation for each model (and alignments):
>> Pcc1  Transcription factor Pcc1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.1   3.9e-09     7e-05       2      72 ..      13      85 ..      12      87 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 3.9e-09
                                      EEEEEE-SSHHHHHHHHHHHHHHCHC-TTE.CEEEEEEETTEE.EEEEEESSHHHHHHHHHHHHHHHHHHHHH CS
                              Pcc1  2 ltisvpfpterlAsialrtLqvDkelspla.vkrslslegnvL.qveykAttnrmLRvavngfleslglvlet 72
                                      ++i++++ +e l ++++++L +D   s+++   +++ l++++L q+ yk       R ++  +++s+++v+  
  gi|385805478|ref|YP_005841876.1| 13 ADIQISLTNENLCKSIINSLVPDDLTSSPElQVKTYNLKTSILiQIVYKGINILTVRNTIEDYINSIETVINS 85
                                      5799*******************7777766566688999986626*************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.30s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 636.99
//
Query:       gi|385805479|ref|YP_005841877.1|  [L=398]
Description: hypothetical protein FFONT_0435 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); 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: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2493.44
//
Query:       gi|385805480|ref|YP_005841878.1|  [L=64]
Description: hypothetical protein FFONT_0436 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.023   15.2   0.8      0.026   15.0   0.8    1.1  1  DUF3802   Protein of unknown function (DUF3802)


Domain annotation for each model (and alignments):
>> DUF3802  Protein of unknown function (DUF3802)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.8   1.4e-06     0.026       3      53 ..      10      62 ..       8      64 .] 0.75

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.4e-06
                           DUF3802  3 vekdgYialieylt.enLalFekssekataeetvee.lveeqlaenlivvceq 53
                                      ++k++Y ++i+y+t enL  +e++ +k    +t+++ +v   + ++++++++ 
  gi|385805480|ref|YP_005841878.1| 10 INKKAYSQVIDYFTtENLLTYEQKLKKIINFYTIHSnVVLVIINKRILIIFQN 62
                                      6899********96378999999999988888997615556666666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1161  (0.0647554); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 453.63
//
Query:       gi|385805481|ref|YP_005841879.1|  [L=87]
Description: hypothetical protein FFONT_0437 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.039   14.1   1.0      0.059   13.5   0.5    1.5  1  DUF2387   Probable metal-binding protein (DUF2387)
      0.066   13.3   0.4       0.12   12.4   0.4    1.4  1  Nop10p    Nucleolar RNA-binding protein, Nop10p family


Domain annotation for each model (and alignments):
>> DUF2387  Probable metal-binding protein (DUF2387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.5   6.6e-06     0.059      24      65 ..       5      43 ..       2      53 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.6e-06
                           DUF2387 24 eedeveyrECvsCgftdelsekgqsvakelktrvnkdeekea 65
                                      ++d++ +  C++Cg+  + ++k   ++  +k++v ++++ ++
  gi|385805481|ref|YP_005841879.1|  5 KKDGETVLRCTKCGYEMKAKKK---ESYVIKEKVKEKDKPKT 43
                                      68999**********8887777...77777888877766333 PP

>> Nop10p  Nucleolar RNA-binding protein, Nop10p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.4   1.3e-05      0.12       3      47 ..      19      65 ..      11      66 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.3e-05
                                      ---EE-TTT--EESSSB-TTT-S...B-B-SS--S--TT-TTCHHHHH CS
                            Nop10p  3 sylrkcgkcrvYTLkkvcpecgg...ptksahPaRFSPdDkyskyRra 47
                                      + ++ ++k + Y +k+++ e+ +      ++ P +F + D  +++R++
  gi|385805481|ref|YP_005841879.1| 19 YEMKAKKK-ESYVIKEKVKEKDKpktTSLVSEPSKFGVSDEEQQQRVE 65
                                      55666666.7*****9999988865456789***************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1297  (0.0723409); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 560.55
//
Query:       gi|385805482|ref|YP_005841880.1|  [L=427]
Description: nucleotidyltransferase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-30  107.0   0.0    1.5e-30  106.6   0.0    1.1  1  NTP_transferase  Nucleotidyl transferase
    6.9e-10   39.5   0.0    9.6e-10   39.0   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
    6.3e-07   28.9  11.7     0.0078   15.9   3.3    3.6  3  Hexapep          Bacterial transferase hexapeptide (six repea
     0.0003   20.6   0.0    0.00055   19.7   0.0    1.4  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
  ------ inclusion threshold ------
      0.028   12.6   1.1      0.073   11.2   0.1    1.9  2  DUF4954          Domain of unknown function (DUF4954)
       0.15   11.6   0.0       0.34   10.5   0.0    1.5  1  DUF1264          Protein of unknown function (DUF1264)


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 !  106.6   0.0     5e-34   1.5e-30       2     242 ..       7     242 ..       6     247 .. 0.92

  Alignments for each domain:
  == domain 1  score: 106.6 bits;  conditional E-value: 5e-34
                                       EEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGT.SEEEE CS
                   NTP_transferase   2 avILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfg.vevli 77 
                                       avILa G+G+R+wPLt +++k+l+p+l k +l+++ l++l +++  +  +vlt+++++ + e+l+  ++++  +++ 
  gi|385805482|ref|YP_005841880.1|   7 AVILAAGKGERMWPLTYDTPKPLLPILCK-PLLNIHLNALEEADLLNSAIVLTYKNKEKIFEYLNGYNNLTgKKIKL 82 
                                       8****************************.**************9999****************98777665899** PP

                                       EEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEEST.THHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEE CS
                   NTP_transferase  78 alepegkgtAdAvalaaelledeksdelvlvLggDhlikd.ayeeavkkaiekaakgtvtfgivpveeateyGviea 153
                                       + ++ + gt +A++ ++e +ed  +   +lv+ gD+++   ++++++k+  e +     ++++++v++ ++yG++++
  gi|385805482|ref|YP_005841880.1|  83 MEQSLPLGTGHAIKEILEGAEDLGD--EILVVYGDIFVPSkEMSRILKNILEFDG---NIIAVKEVNNLSKYGLVKV 154
                                       *********************9995..788888999888879********99999...68999************** PP

                                       CTTSBEEEEECS-SSHSH..CSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE- CS
                   NTP_transferase 154 deegrverfvEKPkeaka..selassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaey 228
                                       de+g+  +++EK k  +   + ++++Gi     + l++ +++ e ++rge e+t++l+ + ++ +v+ + +++    
  gi|385805482|ref|YP_005841880.1| 155 DEHGNLLEIQEKRKDIPPdvNGYVNAGIMKLRIGDLKKYIDKTEISPRGEIELTSVLNLIAKNNSVKIYPIESS--- 228
                                       ************9985544599*****************99*******************99999998866666... PP

                                       EEEXSSHHHHHHHH CS
                   NTP_transferase 229 WsDvGtldsllean 242
                                       W+DvGt+ +ll+an
  gi|385805482|ref|YP_005841880.1| 229 WMDVGTPWDLLKAN 242
                                       ***********998 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 !   39.0   0.0   3.2e-13   9.6e-10       1     122 [.       7     141 ..       7     169 .. 0.76

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 3.2e-13
                                       EEEEEESS-TTT.....TTTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH...CHHHHHHTTC......TS-EE CS
                      NTP_transf_3   1 aviLAGGrSsRm.....ggdKallplggkpllervldalraagvdevvvvggd...eevlaalarl......gvrvv 63 
                                       aviLA+G++ Rm      ++K+llp+  kpll  +l+al++a + +  +v  +   e++ ++l+++      +++++
  gi|385805482|ref|YP_005841880.1|   7 AVILAAGKGERMwpltyDTPKPLLPILCKPLLNIHLNALEEADLLNSAIVLTYknkEKIFEYLNGYnnltgkKIKLM 83 
                                       79**********7777667***********************86444444433123666666655544443378888 PP

                                       E-TTSS-SHHHHHHHHHHHH..SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEE CS
                      NTP_transf_3  64 ededpgkgplaslaaalraaa.dadavlvlacDmPlltpelverllaaaaasgadvvvpt 122
                                       e++    g++++++  l+ a+   d +lv+ +D+ +++++ + r+l+++ + ++++++++
  gi|385805482|ref|YP_005841880.1|  84 EQSL-PLGTGHAIKEILEGAEdLGDEILVVYGDI-FVPSKEMSRILKNILEFDGNIIAVK 141
                                       8876.58***********988669**********.6777777777777766666666655 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.023        68       4      34 ..     282     312 ..     279     314 .. 0.82
   2 !   13.7   0.3   1.3e-05     0.039       1      34 [.     314     346 ..     314     348 .. 0.87
   3 !   15.9   3.3   2.6e-06    0.0078       1      35 [.     373     407 ..     373     408 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.023
                                       EETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
                           Hexapep   4 IGsnvlIgpfaviggnVkIGdnvkIgagvvi 34 
                                       I  ++ Igp +++++++++    kIg  v i
  gi|385805482|ref|YP_005841880.1| 282 ISGKAEIGPCSHLREHTILCGENKIGFSVQI 312
                                       5567889999999999999999999987776 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1.3e-05
                                       TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
                           Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvi 34 
                                       s++I  +++I +  ++ g+ +IG++v +gag+v 
  gi|385805482|ref|YP_005841880.1| 314 SSIIMRGAKIPHLNYV-GDSVIGEYVNLGAGTVT 346
                                       578999**********.5556**********996 PP

  == domain 3  score: 15.9 bits;  conditional E-value: 2.6e-06
                                       TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                       ++++G+ ++ g ++ i++++kIG n+ I ag+ i 
  gi|385805482|ref|YP_005841880.1| 373 GAIVGNYTKTGINTSILPGIKIGANTWINAGCIID 407
                                       5799**************************99985 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 !   19.7   0.0   1.8e-07   0.00055       1      65 [.       5      72 ..       5     115 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.8e-07
                                      EEEEEECTTSSCTT...-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGG CS
                              IspD  1 vvvvipAAGsGkRm...kaglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllld 65
                                      +++vi AAG+G+Rm     ++pK +l +  ++ll+  ++al +   ++  +v+  +++ + fe l + 
  gi|385805482|ref|YP_005841880.1|  5 ITAVILAAGKGERMwplTYDTPKPLLPILCKPLLNIHLNALEEADLLNSAIVLTYKNKEKIFEYLNGY 72
                                      579**********955568****************************999998888887888888765 PP

>> DUF4954  Domain of unknown function (DUF4954)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1     0.084   2.5e+02     465     537 ..      71     145 ..      45     149 .. 0.77
   2 ?   11.2   0.1   2.4e-05     0.073     191     257 ..     280     343 ..     249     361 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.084
                           DUF4954 465 aiekflgnslikrleklelkseeeiaaaLkpdseegkgeWvdlaGlivpkeeieklikdies..gkiksleeiee 537
                                       + ++  g+++  + ++l l + + i++ L+  ++ g++  v  + ++vp +e+++++k+i +  g+i  ++e+++
  gi|385805482|ref|YP_005841880.1|  71 GYNNLTGKKIKLMEQSLPLGTGHAIKEILEGAEDLGDEILVVYGDIFVPSKEMSRILKNILEfdGNIIAVKEVNN 145
                                       55555666665555556778888999999999999999999999999***********99643378888888876 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 2.4e-05
                           DUF4954 191 vkigdyatiegasklengtinSskeapveiGegViledfiissGskikdgavisrcfvGqavklkkq 257
                                       ++i   a+i  +s+l++ ti   ++   +iG +V+++ +ii+ G+ki +   + ++++G+ v+l+ +
  gi|385805482|ref|YP_005841880.1| 280 IYISGKAEIGPCSHLREHTILCGEN---KIGFSVQIKSSIIMRGAKIPHLNYVGDSVIGEYVNLGAG 343
                                       5677889999999999999998876...6*********************************99876 PP

>> DUF1264  Protein of unknown function (DUF1264)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00011      0.34      23      48 ..     242     267 ..     237     270 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00011
                           DUF1264  23 rqveahhycshlnedlrQcliydsde 48 
                                       +++e  hycs+l ++   cliyd ++
  gi|385805482|ref|YP_005841880.1| 242 NIIELDHYCSELGKNPEDCLIYDKST 267
                                       68999******************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); 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: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2697.66
//
Query:       gi|385805483|ref|YP_005841881.1|  [L=463]
Description: Fe-S oxidoreductase [Fervidicoccus fontis Kam940]
Scores for 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   55.3   0.0    4.1e-14   53.3   0.0    2.1  3  Radical_SAM  Radical SAM superfamily
    0.00025   21.0   0.0    0.00049   20.1   0.0    1.4  1  B12-binding  B12 binding domain
  ------ inclusion threshold ------
        0.2   11.6   0.2         16    5.4   0.1    2.2  2  Lipase_GDSL  GDSL-like Lipase/Acylhydrolase


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.61   3.6e+03      47      74 ..      64      91 ..      38     126 .. 0.59
   2 !   53.3   0.0   6.9e-18   4.1e-14       1     165 [.     212     370 ..     212     372 .. 0.90
   3 ?   -3.1   0.0       1.5   9.1e+03      78      97 ..     383     408 ..     375     428 .. 0.56

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.61
                                      SEEEEEESSTGGGSTTHHHHHHHHHHTC CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 47 vkevilgggepllypdfvellerlakla 74
                                      ++++ +  g+pl   d++++ +++  + 
  gi|385805483|ref|YP_005841881.1| 64 GDYISIETGTPLSKFDIIFASAHYELEY 91
                                      4555555555555555544444443333 PP

  == domain 2  score: 53.3 bits;  conditional E-value: 6.9e-18
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlaklavp 76 
                                       v+++rgCn++C fC  +         r++s  +i+e+++++  e +  + vi+++   ++ + + e++++++     
  gi|385805483|ref|YP_005841881.1| 212 VETSRGCNRGCFFCMESA---ISLFRRERSENKIIELIEQGL-EVNnLNRVIFFSLSFFD-SALGEKILKYVV---- 279
                                       5789*************8...6999****************6.4444*********7777.557777777777.... PP

                                       TEEEEEEECSSCHG...HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEE CS
                                       xxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  77 giritvetngtlpd...eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdriv 150
                                       ++ i  +++ +++d   + k+e+++++g  ++++  e++ +e  +k ++++   e +l+  ekl+++++    + ++
  gi|385805483|ref|YP_005841881.1| 280 DRGIEASIPSVRIDsldDNKIELIKKAGQKTLTVAPETGIYE-LRKSIGKPIKDEMILQIAEKLKALDMGIKLYYMI 355
                                       57888899999999999*************************.******99***************999988***** PP

                                       EBTTTSHHHHHHHHH CS
                                       xxxxxxxxxxxxxxx RF
                       Radical_SAM 151 glpGendeeleelle 165
                                       glpGe  ++l++++ 
  gi|385805483|ref|YP_005841881.1| 356 GLPGERQSDLDAIIA 370
                                       *********999875 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 1.5
                                       EEEEEEECSSCHG......HHHHHHH CS
                                       xxxxxxxxxxxxx......xxxxxxx RF
                       Radical_SAM  78 iritvetngtlpd......eeklerl 97 
                                        +i v++n++ p        ek+e+ 
  gi|385805483|ref|YP_005841881.1| 383 KKIKVSVNPFIPKpltkmeNEKMEEA 408
                                       55666666666655555553333333 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   8.1e-08   0.00049      51     116 ..      77     144 ..      74     149 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 8.1e-08
                       B12-binding  51 kpdvvglSalltsqleavkelvel.....lkrirprvkvvvGGahpsldpeetleaklgiddvvvgegeda 116
                                       k+d++  Sa++  +++++ +++ +     lk++r+r ++++GG+ p++ p   + +  + d++ +ge e++
  gi|385805483|ref|YP_005841881.1|  77 KFDIIFASAHYELEYPEIIRTLLRsrispLKEERNRPILIIGGPSPTANPFP-MGK-VA-DFIFRGEFEST 144
                                       789**************977666669**************************.554.77.*******9987 PP

>> Lipase_GDSL  GDSL-like Lipase/Acylhydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0    0.0073        43      93     138 ..      88     147 ..      79     185 .. 0.69
   2 ?    5.4   0.1    0.0027        16      92     166 ..     361     431 ..     354     445 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0073
                                       CEEHHHHHHH.HHHHHHHHHHHHHTTEEEEEEE-SSTCH.............CTCCCCHC CS
                                       xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx.............xxxxxxxx RF
                       Lipase_GDSL  93 kkeaeeyikn.lreaikelkeegapkaivvlvsppglgp.............qeekdakk 138
                                       ++e +e+i+  lr+ i+ lkee ++ ++++  + p  +p             ++e++ kk
  gi|385805483|ref|YP_005841881.1|  88 ELEYPEIIRTlLRSRISPLKEERNRPILIIGGPSPTANPfpmgkvadfifrgEFESTGKK 147
                                       555555555515666*****9998888888888888887666666666666644444444 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0027
                                       TCEEHHHHHHHHHHHHHHHHHHHHTTEEEEEEE-SSTCHCTCCCCHCCHHHHHHHHHHHHHHHHHHHHHCTEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Lipase_GDSL  92 akkeaeeyiknlreaikelkeegapkaivvlvsppglgpqeekdakklgekgnefvgeynqrlndlaekdgfavv 166
                                        + + +++i++++ + k l++++  k  v+ + p +l++  e++++++ +++ + +++ n +l+++ e   f++ 
  gi|385805483|ref|YP_005841881.1| 361 RQSDLDAIIAQVEYFWKTLRNKKKIKVSVNPFIPKPLTK-MENEKMEEANELQRKIDYLNAKLSKISE---FEYY 431
                                       56788999************9999999999999999999.9999999999999999999999999998...6554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); 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: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 2916.70
//
Query:       gi|385805484|ref|YP_005841882.1|  [L=407]
Description: translation-associated GTPase [Fervidicoccus fontis Kam940]
Scores for complete 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-35  121.4   0.3    4.1e-35  120.7   0.3    1.4  1  MMR_HSR1_C  GTPase of unknown function C-terminal
    2.5e-20   72.7   0.0    1.1e-19   70.6   0.0    2.1  2  MMR_HSR1    50S ribosome-binding GTPase
    0.00011   21.7   0.2      0.003   17.1   0.2    2.4  2  FeoB_N      Ferrous iron transport protein B
  ------ inclusion threshold ------
      0.041   13.4   0.7         14    5.1   0.0    3.3  3  GTP_EFTU    Elongation factor Tu GTP binding domain
      0.068   13.2   0.0       0.16   12.0   0.0    1.6  1  TGS         TGS 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 !  120.7   0.3   1.1e-38   4.1e-35       1     112 []     230     338 ..     230     338 .. 0.97

  Alignments for each domain:
  == domain 1  score: 120.7 bits;  conditional E-value: 1.1e-38
                        MMR_HSR1_C   1 alNKaDlpaadenieklkekypkdkkvvpvsAaaElaLrkaakqglikYepgdedfeikedklkeldekqkkaLeki 77 
                                       a+NKaDlp+a enie+lk+++p+   vvpvs+++ElaLrkaak +li+Y+pgd+ f ike+   +l+ +q+ aL++i
  gi|385805484|ref|YP_005841882.1| 230 AANKADLPTAYENIERLKKEFPEVP-VVPVSSESELALRKAAKMNLIDYIPGDSIFFIKEN--VKLTPQQEVALKYI 303
                                       89********************766.**********************************9..56************ PP

                        MMR_HSR1_C  78 rdlvlkrygsTGVqealnaavfelldlivVYPVed 112
                                       ++ vlkrygsTGVq+++n++++++l+ +vV+PVed
  gi|385805484|ref|YP_005841882.1| 304 EEKVLKRYGSTGVQKVINSIIYDVLKKVVVFPVED 338
                                       *********************************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 !   70.6   0.0     3e-23   1.1e-19       2     102 ..       9     145 ..       8     168 .. 0.76
   2 ?   -1.7   0.0      0.81   2.9e+03      89     114 .]     207     233 ..     180     233 .. 0.54

  Alignments for each domain:
  == domain 1  score: 70.6 bits;  conditional E-value: 3e-23
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEE..........................EEEEE CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgke..........................ielvD 52 
                                       ++++G++NvGKSt+++a t +++++s++p+tT+++n+g   +k                             iel+D
  gi|385805484|ref|YP_005841882.1|   9 IGVIGKTNVGKSTFFSAATMTTVEISNRPFTTIKPNHGIGYVKI-TcphldfgleacnprtgycqngnrfvpIELLD 84 
                                       89************************************866431.123344444455555555666666666***** PP

                                       CGGCSSHHHHHHHHHHHHHHHHC.TSEEEEEEETT...........TTCSHHHHHHHHHHHH CS
                          MMR_HSR1  53 tpGliegaseekglgkaflalee.adlillvvdas...........eeklkpldeeleelle 102
                                       ++Gli ga+ ++glg++f +  + ad+++lv+das            ++++p+ ee++++++
  gi|385805484|ref|YP_005841882.1|  85 VAGLIPGAHMGRGLGNKFMDDLRkADAFILVIDASgstneegnpvpPGTYDPI-EEVKQIIN 145
                                       *******************96666*********99888776666662245555.55555443 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.81
                                       CSHHHHHHH.HHHHHHTTSEEEEEEES CS
                          MMR_HSR1  89 klkpldeel.eelleeakkplilvlnk 114
                                       ++k++d  + ++ l+++ kp i+++nk
  gi|385805484|ref|YP_005841882.1| 207 NWKEEDFYIfAKELRKTAKPHIIAANK 233
                                       354554333123334478899999987 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 !   17.1   0.2   8.5e-07     0.003       3      40 ..       9      46 ..       8      54 .. 0.90
   2 ?    1.8   0.0     0.044   1.6e+02      98     148 ..     217     265 ..     207     273 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 8.5e-07
                                      EEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEE CS
                            FeoB_N  3 valvGnpnvGkttlfnaltgakqkvgNwpGvtvekkeg 40
                                      + ++G+ nvGk+t+f a t ++ +++N p +t++ ++g
  gi|385805484|ref|YP_005841882.1|  9 IGVIGKTNVGKSTFFSAATMTTVEISNRPFTTIKPNHG 46
                                      5689****************************987766 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.044
                                       HHHHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHH.TS-EEEEBTTTTBT CS
                            FeoB_N  98 tlqllelgvpvvlalnmideaekkgieidlkkLsekL.gvpvvktsakkkeg 148
                                         +l  + +p ++a n+ d  ++ +   ++++L++++ +vpvv++s++++  
  gi|385805484|ref|YP_005841882.1| 217 AKELRKTAKPHIIAANKADLPTAYE---NIERLKKEFpEVPVVPVSSESELA 265
                                       4578889999999999999876654...678888887579999999987765 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 ?    5.1   0.0    0.0039        14       6      33 ..       9      36 ..       7      45 .. 0.88
   2 ?    4.1   0.2    0.0084        30     117     144 ..     219     248 ..      99     309 .. 0.70
   3 ?   -2.1   0.0      0.66   2.4e+03      68      97 ..     268     299 ..     253     345 .. 0.63

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0039
                                      EEEEESTTSSHHHHHHHHHHHTTSSCHH CS
                          GTP_EFTU  6 igiighvDhGKtTLtdrLlyktgaiskk 33
                                      ig+ig ++ GK+T+  + +++t +is++
  gi|385805484|ref|YP_005841882.1|  9 IGVIGKTNVGKSTFFSAATMTTVEISNR 36
                                      89************99999999888875 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0084
                                       HHHHTTTEEEEEEESCGST..HHHHHHHHH CS
                          GTP_EFTU 117 lalkegvpiivfiNKmDrl..kaelkeive 144
                                        ++k   p i++ NK+D +   ++++++++
  gi|385805484|ref|YP_005841882.1| 219 ELRKTAKPHIIAANKADLPtaYENIERLKK 248
                                       344455556666666666644333333333 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.66
                                       SSEEEEEEE.ESSSGG.GHHHHHHHHHT-SEE CS
                          GTP_EFTU  68 kkylinliD.tPGHvd.FskevirglrvlDga 97 
                                       k  ++nliD  PG+   F+ke  + + + ++a
  gi|385805484|ref|YP_005841882.1| 268 KAAKMNLIDyIPGDSIfFIKENVKLTPQQEVA 299
                                       56677788844777653555555555555544 PP

>> TGS  TGS domain
   #    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       5      45 ..     350     390 ..     342     404 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.5e-05
                                       ETTSSEEEEETTB-HHHHHHHHSTTHHHHEEEEEECS..EEEE CS
                               TGS   5 tPdGkvpdlprgatveDfAykIhrslakkfiyAlVnG..qrvg 45 
                                       +Pd+ +  +++ a+++ +A  Ih++l k f yA+     q+ g
  gi|385805484|ref|YP_005841882.1| 350 LPDALI--VDHEASPKVVAGLIHTELEKGFQYAIDARtkQKMG 390
                                       455555..9999**********************988776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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: 00:00:00.49
# Mc/sec: 2489.49
//
Query:       gi|385805485|ref|YP_005841883.1|  [L=174]
Description: hypothetical protein FFONT_0441 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-28   99.0   0.4    1.8e-28   98.7   0.4    1.1  1  DUF359    Protein of unknown function (DUF359)
  ------ inclusion threshold ------
      0.022   15.4   0.2       0.38   11.4   0.0    2.6  3  PglD_N    PglD N-terminal domain


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 !   98.7   0.4     2e-32   1.8e-28       2     125 ..      43     168 ..      42     169 .. 0.88

  Alignments for each domain:
  == domain 1  score: 98.7 bits;  conditional E-value: 2e-32
                            DUF359   2 tknllk.agikPdlaivDgktkReeveeeekeeekekekekevievkNpaGtiteelieaikeal....eseekvli 73 
                                       t+++++ a+ +P l++vD++tkRe    +++++ k+k+  +++ie+ N++Gti++e+i++  + +     ++ + l+
  gi|385805485|ref|YP_005841883.1|  43 TEKYIEiAEKSPVLSFVDMQTKRE----RYDIS-KIKSYYTDIIEIYNKQGTISKETINEELSEVlinyIQGISSLV 114
                                       55555425678*************....33444.478899*****************9987666669999******* PP

                            DUF359  74 lVdGEEDLavlpaillapegsv..vvYGqpdeGvvlvkvteeakeeaeellekf 125
                                       +V+GEEDL++l++ ll+p++s+  v+YGqp++G+v+++v+e++k+e++++l++f
  gi|385805485|ref|YP_005841883.1| 115 IVRGEEDLLSLYVPLLIPMNSSgrVIYGQPGMGAVVFDVNEKTKREISNILQDF 168
                                       ********************9999***************************998 PP

>> PglD_N  PglD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.27   2.4e+03      48      69 ..      20      42 ..       3      48 .. 0.63
   2 ?    0.4   0.1      0.12     1e+03      17      45 ..      49      74 ..      41      96 .. 0.60
   3 ?   11.4   0.0   4.2e-05      0.38       3      32 ..     139     167 ..     138     172 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.27
                            PglD_N 48 iellkslseeeyev.viAIGnnk 69
                                      +++++ ++  ++++  i IG+  
  gi|385805485|ref|YP_005841883.1| 20 SSFENLIKTTHNKFrYITIGDYV 42
                                      34555555555555478899865 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.12
                            PglD_N 17 iieangeyeiigflDdnkktevegypvlg 45
                                      i+e+     ++ f+D + k e  ++  ++
  gi|385805485|ref|YP_005841883.1| 49 IAEK---SPVLSFVDMQTKRERYDISKIK 74
                                      3333...4488899998865544433333 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 4.2e-05
                            PglD_N   3 vIiGaGGhgkvvadiieangeyeiigflDd 32 
                                       vI+G+ G+g vv d++e+++  ei  +l d
  gi|385805485|ref|YP_005841883.1| 139 VIYGQPGMGAVVFDVNEKTK-REISNILQD 167
                                       7*****************99.566666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1294.31
//
Query:       gi|385805486|ref|YP_005841884.1|  [L=69]
Description: DNA-directed RNA polymerase subunit E [Fervidicoccus fontis Kam940]
Scores for complete 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-15   55.2   0.2    6.8e-15   54.9   0.2    1.1  1  Spt4            Spt4/RpoE2 zinc finger
      0.001   18.7   0.1     0.0014   18.3   0.1    1.3  1  zf-RRN7         Zinc-finger of RNA-polymerase I-specific TFII
     0.0011   18.9   0.9     0.0015   18.5   0.9    1.2  1  DZR             Double zinc ribbon
     0.0028   18.3   0.7     0.0037   18.0   0.7    1.2  1  zinc_ribbon_15  zinc-ribbon family
     0.0034   16.7   2.8     0.0046   16.3   2.8    1.2  1  zf-ribbon_3     zinc-ribbon domain
     0.0077   15.9   1.2      0.012   15.4   1.2    1.3  1  zinc_ribbon_2   zinc-ribbon domain
  ------ inclusion threshold ------
      0.018   14.5   1.1      0.031   13.8   0.1    1.9  2  TF_Zn_Ribbon    TFIIB zinc-binding
      0.018   15.4   1.2      0.024   15.0   1.2    1.1  1  zf-C4H2         Zinc finger-containing protein
      0.032   14.1   0.2      0.047   13.6   0.2    1.2  1  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
       0.17   12.1   1.2       0.84    9.9   0.6    1.9  2  DUF2072         Zn-ribbon containing protein


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 !   54.9   0.2   3.8e-18   6.8e-15       2      77 .]      10      69 .]       9      69 .] 0.97

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 3.8e-18
                              Spt4  2 rACllCklvktedqFeeegCpnCeilelkgdkekvsectseefeGlvaildpekSwvAkwqrldkkvpglYAlkve 77
                                      +AC++Ck++++ +    e Cp+C           +s+++++++eGlv++ld ++S++A+   l+ ++pg+YA+k++
  gi|385805486|ref|YP_005841884.1| 10 KACIKCKALVEPNV---EVCPVC-----------GSKEFTNDWEGLVIVLDVNNSKIAQI--LGITKPGKYAIKIR 69
                                      9************9...******...........**************************..************95 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 !   18.3   0.1   7.9e-07    0.0014       4      17 ..      23      36 ..      20      43 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 7.9e-07
                           zf-RRN7  4 gppCgvCgcrsftl 17
                                      +++C+vCg+++ft 
  gi|385805486|ref|YP_005841884.1| 23 VEVCPVCGSKEFTN 36
                                      69**********98 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.9   8.3e-07    0.0015      28      49 .]       9      30 ..       2      30 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 8.3e-07
                               DZR 28 edrCpsCgekvdpearfCpeCG 49
                                       ++C +C++ v+p+ ++Cp CG
  gi|385805486|ref|YP_005841884.1|  9 YKACIKCKALVEPNVEVCPVCG 30
                                      579******************9 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.7     2e-06    0.0037      61      86 .]       5      30 ..       1      30 [. 0.86

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2e-06
                    zinc_ribbon_15 61 essekkeCknCgkeveeefkyCpkCg 86
                                       +s +k C +C++ ve++++ Cp Cg
  gi|385805486|ref|YP_005841884.1|  5 LKSPYKACIKCKALVEPNVEVCPVCG 30
                                      455689*******************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 !   16.3   2.8   2.6e-06    0.0046       3      25 ..      10      32 ..       8      32 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.6e-06
                       zf-ribbon_3  3 vrCPnCGaplssddnvCpyCGtk 25
                                      + C +C+a++++ + vCp CG+k
  gi|385805486|ref|YP_005841884.1| 10 KACIKCKALVEPNVEVCPVCGSK 32
                                      6799****99***********86 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   1.2   6.5e-06     0.012       2      22 ..      12      32 ..      11      32 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6.5e-06
                     zinc_ribbon_2  2 CpnCGaelqdnakFCpyCGtp 22
                                      C +C a +++n+  Cp CG++
  gi|385805486|ref|YP_005841884.1| 12 CIKCKALVEPNVEVCPVCGSK 32
                                      99*****************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 ?   -0.8   0.1      0.63   1.1e+03      22      28 ..      12      19 ..      11      23 .. 0.62
   2 ?   13.8   0.1   1.7e-05     0.031       2      14 ..      25      37 ..      24      49 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.63
                                      ESSS.SBE CS
                      TF_Zn_Ribbon 22 CtdC.GlV 28
                                      C +C  lV
  gi|385805486|ref|YP_005841884.1| 12 CIKCkALV 19
                                      88884444 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.7e-05
                                      EETTTTCEECHEE CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveD 14
                                      +CP+Cgs+++++D
  gi|385805486|ref|YP_005841884.1| 25 VCPVCGSKEFTND 37
                                      8********9888 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   1.2   1.3e-05     0.024     176     201 ..       7      32 ..       3      35 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.3e-05
                           zf-C4H2 176 PPMKsClsChqqIHRNAPiCPlCKaK 201
                                        P K+C  C++ +  N  +CP+C +K
  gi|385805486|ref|YP_005841884.1|   7 SPYKACIKCKALVEPNVEVCPVCGSK 32 
                                       599********************988 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   2.6e-05     0.047      14      36 ..      12      34 ..       9      35 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.6e-05
                           DUF35_N 14 CpdCGtvqfPPr.avCphCgsddl 36
                                      C +C ++ + P   vCp Cgs+++
  gi|385805486|ref|YP_005841884.1| 12 CIKCKAL-VEPNvEVCPVCGSKEF 34
                                      8899999.68888********998 PP

>> DUF2072  Zn-ribbon containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.6   0.00047      0.84       3      31 ..      11      35 ..       8      39 .. 0.86
   2 ?    1.1   0.0      0.25   4.4e+02     114     126 ..      55      67 ..      44      69 .] 0.59

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00047
                           DUF2072  3 kCtkCekvfedgskeilkGCpsCGgkkFl 31
                                       C kC+ + e   +     Cp+CG k F+
  gi|385805486|ref|YP_005841884.1| 11 ACIKCKALVEPNVE----VCPVCGSKEFT 35
                                      59999999998776....7*******996 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.25
                           DUF2072 114 vmalkeegkYvvd 126
                                       ++ + + gkY+++
  gi|385805486|ref|YP_005841884.1|  55 ILGITKPGKYAIK 67 
                                       4455555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); 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 0.26s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 460.23
//
Query:       gi|385805487|ref|YP_005841885.1|  [L=158]
Description: DNA-directed RNA polymerase subunit E' [Fervidicoccus fontis Kam940]
Scores for complete 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-13   49.5   0.7    1.1e-12   48.1   0.7    1.9  1  S1             S1 RNA binding domain
    2.3e-07   31.1   0.2    5.9e-07   29.8   0.1    1.8  2  SHS2_Rpb7-N    SHS2 domain found in N terminus of Rpb7p/Rpc25
    0.00065   19.9   0.0    0.00088   19.5   0.0    1.2  1  RNA_pol_Rbc25  RNA polymerase III subunit Rpc25
  ------ inclusion threshold ------
      0.096   12.3   0.0       0.19   11.4   0.0    1.5  1  EABR           TSG101 and ALIX binding domain of CEP55


Domain annotation for each model (and alignments):
>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   0.7   2.4e-16   1.1e-12       5      63 ..      65     132 ..      61     148 .. 0.86

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 2.4e-16
                                       TCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSS..........CEESCHHHCEETTEEEEEEEEEE CS
                                S1   5 gevveGeVtsvtkgGafVelgngvegfvpaselsrd..........arvedpdevlkvGdevkvkvlkv 63 
                                       +evveG Vt+v ++G+f+++g +++gfv++s++s++             +++++ +  Gd v+++++ +
  gi|385805487|ref|YP_005841885.1|  65 HEVVEGFVTDVKDYGLFIRIG-PIDGFVHKSQISDEyveydssreaFILKNSNRIIERGDIVRARIIAL 132
                                       79*******************.**************999999999844478999999999999999865 PP

>> SHS2_Rpb7-N  SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.1   1.3e-10   5.9e-07      12      66 ..       2      56 ..       1      59 [. 0.93
   2 ?   -2.2   0.0       1.2   5.6e+03      32      41 ..      75      84 ..      64     102 .. 0.67

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 1.3e-10
                                      TSTHHHHHHHHHHHHHTTBEETTTEEEEEEEEEEEECCEEE-TTTSSEEEEEEEE CS
                       SHS2_Rpb7-N 12 gstledallerllekyegkvvpslGvivavldiaeysegkvlggsGsvyvrVtfr 66
                                      +++l++ + e+l++ y g ++++lG+i+ v++ + +  gk+++g+G++y++V++ 
  gi|385805487|ref|YP_005841885.1|  2 NEDLDKVASEILNQYYSGYYDDELGIIIGVEKAKVDPFGKIVHGDGASYHNVEAS 56
                                      469999999*******************************************986 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.2
                                      ETTTEEEEEE CS
                       SHS2_Rpb7-N 32 vpslGvivav 41
                                      v+++G+ + +
  gi|385805487|ref|YP_005841885.1| 75 VKDYGLFIRI 84
                                      4445555444 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 !   19.5   0.0     2e-07   0.00088       1      81 [.      62     139 ..      62     154 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2e-07
                                       -STTSEEEEEEEEEETTCEEEEBTTBSEEEEECCCCS.TTEEEECCCTCEEEEESSSEEEEE-TTSEEEEEEEEEEE CS
                     RNA_pol_Rbc25   1 PfvgevltgkiksstregikvslgffddifvpkelLf.epsefdeeeqawvweveeeeelyldvgeeirfrveeeif 76 
                                       P++ ev++g +++ +  g+++++g +d  fv k+++  e+ e+d++++a++++    ++  ++ g+ +r r+   +f
  gi|385805487|ref|YP_005841885.1|  62 PLMHEVVEGFVTDVKDYGLFIRIGPIDG-FVHKSQISdEYVEYDSSREAFILKN---SNRIIERGDIVRARIIALSF 134
                                       8899*********************998.566666652789***********98...7789***************9 PP

                                       ----- CS
                     RNA_pol_Rbc25  77 vdvkp 81 
                                       + +k+
  gi|385805487|ref|YP_005841885.1| 135 STEKK 139
                                       54443 PP

>> EABR  TSG101 and ALIX binding domain of CEP55
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   4.3e-05      0.19      16      25 ..     102     111 ..      99     119 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.3e-05
                              EABR  16 kYDqsREeYV 25 
                                       +YD+sRE+++
  gi|385805487|ref|YP_005841885.1| 102 EYDSSREAFI 111
                                       7********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1026.83
//
Query:       gi|385805488|ref|YP_005841886.1|  [L=142]
Description: Nucleotide binding protein, PINc [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-21   75.7   0.3      4e-21   75.5   0.3    1.0  1  PIN_9     PIN like domain
    1.2e-07   32.1   0.1    1.4e-07   31.8   0.1    1.1  1  Fcf1      Fcf1
    1.3e-07   31.9   4.0    1.4e-05   25.4   4.0    2.1  1  PIN_4     PIN domain
     0.0089   16.5   1.0      0.016   15.7   1.0    1.4  1  PIN       PIN domain
  ------ inclusion threshold ------
      0.021   15.0   0.0      0.035   14.3   0.0    1.4  1  PilI      Plasmid conjugative transfer protein PilI


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 !   75.5   0.3   1.1e-24     4e-21       1     115 [.      12     129 ..      12     130 .. 0.85

  Alignments for each domain:
  == domain 1  score: 75.5 bits;  conditional E-value: 1.1e-24
                             PIN_9   1 vilDtnaLmipvqfgvdifeelerll.gsvelvvpkavleELerlakagkgkertaakvalsLaerceiveaeeeka 76 
                                       v+lDtn+L++    + d+fee++ l+  + e++ +++vl+ELe+l++++++++++  k    ++e+ce+ +++  +a
  gi|385805488|ref|YP_005841886.1|  12 VVLDTNFLFMHL-RKFDVFEEISSLInYKPEFICLESVLNELEKLERKNRKNDNEIKKRIGLIKEKCELQKSNYFSA 87 
                                       8********976.589**********7789***************877777665544444446889*******999* PP

                             PIN_9  77 Ddailelakeld...aavlvTnDreLkkrllekgipvilLRq 115
                                       D  ile+a +l    + +++TnDreL+++l++ gi+ i+ R+
  gi|385805488|ref|YP_005841886.1|  88 DKDILEIALNLTekgIVIVATNDRELRRKLRQIGIKSIYYRE 129
                                       *******9865422388999*******************996 PP

>> Fcf1  Fcf1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.1   3.9e-11   1.4e-07       6      96 ..      39     133 ..      34     136 .. 0.72

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 3.9e-11
                                       -EEEEEEHHHHHHHHHCT..-HHH.HHHHTT..SEEE----..SS---HHHHHHHHH-BTB-TT-EEEE-S-HHHHH CS
                              Fcf1   6 kvkpliTqCviaeleklgkklkea.lkiakt..ferlkCnh..kkptsaddClvsvvkkkknkkryivAtqDkdlrr 77 
                                       k +++  + v++elekl++k+++   +i k+  + + kC+   ++  sad+ ++++  + ++k   ivAt+D++lrr
  gi|385805488|ref|YP_005841886.1|  39 KPEFICLESVLNELEKLERKNRKNdNEIKKRigLIKEKCELqkSNYFSADKDILEIALNLTEKGIVIVATNDRELRR 115
                                       5566677899********885544044555435666778775344569*******9997789*************** PP

                                       HHHTSTT--EEEEE--EEE CS
                              Fcf1  78 rlrkipgvPilyikrsvmv 96 
                                       +lr+i     +y+++s  +
  gi|385805488|ref|YP_005841886.1| 116 KLRQIGIKS-IYYRESENS 133
                                       ****96554.455555555 PP

>> PIN_4  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   4.0   3.9e-09   1.4e-05       1     130 [.      12     127 ..      12     128 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 3.9e-09
                             PIN_4   1 fVlDTnvlLhdpealksf.......keehdvviPitVleELdklKkgsserelarlarqanrlldellekesgrlkv 70 
                                       +VlDTn+l  +++ ++ f       + + + +    Vl+EL+kl ++++  + ++++++ + l++e  e       +
  gi|385805488|ref|YP_005841886.1|  12 VVLDTNFLFMHLRKFDVFeeissliNYKPEFICLESVLNELEKLERKNR--KNDNEIKKRIGLIKEKCE-------L 79 
                                       69********999888889999999999999999********9999998..555555555555543333.......3 PP

                             PIN_4  71 qtsaeelpeeeseseknDnrIlavalelkeekpdrkvvLvskDinlrikAkalgieaedy 130
                                       q+s+  +        ++D+ Il++al+l e+     v+  ++D++lr k ++ gi++  y
  gi|385805488|ref|YP_005841886.1|  80 QKSN--Y-----F--SADKDILEIALNLTEKG---IVIVATNDRELRRKLRQIGIKSIYY 127
                                       3332..1.....2..689************97...89999**************998766 PP

>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   1.0   4.5e-06     0.016       1     109 [.      12     125 ..      12     131 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4.5e-06
                                       EEE-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHS...SCHCHHHHHHHHHHHHHHHTSEEEEBC CS
                               PIN   1 ivlDTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlar...rkskrekaaelvelllllsalkilpid 74 
                                       +vlDT++l+ +lr+ +  e++  l++   e +  + vl El    ++   +  +++k++ l +++++l   ++++ d
  gi|385805488|ref|YP_005841886.1|  12 VVLDTNFLFMHLRKFDVFEEISSLINYKPEFICLESVLNELEKLERKnrkNDNEIKKRIGLIKEKCELQKSNYFSAD 88 
                                       69**********99999999*****98899999999****999999999999999999999999999********** PP

                                       HHHHHHHHHHHHHHH..SBHHHHHHHHHHHHHT-EEE CS
                               PIN  75 aeiaeeaaeialkyg..llpnDaliaAtAkehgikli 109
                                       ++i+e+a+ + +k    + +nD  +    ++ gik i
  gi|385805488|ref|YP_005841886.1|  89 KDILEIALNLTEKGIviVATNDRELRRKLRQIGIKSI 125
                                       ********99998668888888766666666666655 PP

>> PilI  Plasmid conjugative transfer protein PilI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   9.7e-06     0.035      13      64 ..      72     122 ..      61     141 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 9.7e-06
                              PilI  13 vvdatCk.kklssikatedidelirrfqtadngLvvvlrdsrilfrkeriPGs 64 
                                       +++++C+ +k  +  a  d d+l   +  ++ g+v+v  ++r l+rk r  G 
  gi|385805488|ref|YP_005841886.1|  72 LIKEKCElQKSNYFSA--DKDILEIALNLTEKGIVIVATNDRELRRKLRQIGI 122
                                       5667777334455555..55556666677899***************998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1118  (0.0623571); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); 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: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 845.26
//
Query:       gi|385805489|ref|YP_005841887.1|  [L=416]
Description: translation initiation factor IF-2 [Fervidicoccus fontis Kam940]
Scores for complete 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-29  101.2   0.0    3.5e-28   98.5   0.0    2.1  1  GTP_EFTU      Elongation factor Tu GTP binding domain
    1.6e-25   89.2   0.3    4.4e-25   87.8   0.3    1.8  2  eIF2_C        Initiation factor eIF2 gamma, C terminal
    2.1e-07   31.2   2.2    7.3e-07   29.5   1.1    2.2  2  GTP_EFTU_D2   Elongation factor Tu domain 2
     0.0041   17.0   0.2      0.036   14.0   0.0    2.0  2  RsgA_GTPase   RsgA GTPase
     0.0054   15.7   0.0      0.011   14.7   0.0    1.4  1  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
     0.0098   16.0   0.0       0.02   15.0   0.0    1.5  1  MMR_HSR1      50S ribosome-binding GTPase
  ------ inclusion threshold ------
      0.018   15.1   0.0      0.034   14.2   0.0    1.4  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
        0.2   11.2   0.5         13    5.3   0.1    2.4  2  FeoB_N        Ferrous iron transport protein B


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.5   0.0   1.5e-31   3.5e-28       4     193 ..      11     204 ..       8     205 .. 0.90

  Alignments for each domain:
  == domain 1  score: 98.5 bits;  conditional E-value: 1.5e-31
                                       EEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE................ CS
                          GTP_EFTU   4 rnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle................ 64 
                                       +nig++ghvDhGKtTL+ +L+   g+ +             +++eE +rg+Tik   +                   
  gi|385805489|ref|YP_005841887.1|  11 VNIGTAGHVDHGKTTLVYSLT---GIWT------------SKHSEELKRGMTIKLGYADGGiyrcsncpfpeeyqpl 72 
                                       7******************99...5533............4567899999999999998888899999999****** PP

                                       ..........TTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTB.STHHHHHHHHHHHHTTTE.EEEEE CS
                          GTP_EFTU  65 ..........ketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveG.vepqteevlrlalkegvp.iivfi 129
                                                 + +  ++i+ +D+PGH+  + ++  g++++Dga+lv++a+e  ++pqt e+++ +   g++ +i++ 
  gi|385805489|ref|YP_005841887.1|  73 peckecpsgsEPELLRRISYVDAPGHEILMTTMLSGAAIMDGALLVIAANEKcPQPQTFEHFKALEIIGIKnLIIVQ 149
                                       ****9998865777899*********************************8879*********************** PP

                                       ESCGST.HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHHSH CS
                          GTP_EFTU 130 NKmDrl.kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealvellp 193
                                       NK+D + +++ +e+ +e+k +l      +e  ++++    p++++Salkg +++ l+ a+ +++p
  gi|385805489|ref|YP_005841887.1| 150 NKVDVVsRERARESYNEIK-RL------IEGTWAEN---APIIPISALKGANIDVLMAAIQKYIP 204
                                       ******8899999999999.66......67777665...6***********************98 PP

>> eIF2_C  Initiation factor eIF2 gamma, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       5.9   1.3e+04      26      38 ..       4      16 ..       3      19 .. 0.80
   2 !   87.8   0.3     2e-28   4.4e-25       2      85 ..     330     413 ..     329     414 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 5.9
                                      -TTEEEEEEETTE CS
                            eIF2_C 26 kkkEvLmlniGsa 38
                                      +kkE+  +niG+a
  gi|385805489|ref|YP_005841887.1|  4 EKKEQPEVNIGTA 16
                                      57888899***97 PP

  == domain 2  score: 87.8 bits;  conditional E-value: 2e-28
                                       EEEEEEEE-SBESSSSSCCC-----TTEEEEEEETTEEEEEEEEEEESSEEEEEEEEEEE-STTEEEEEEEEETTSE CS
                            eIF2_C   2 eleieyellerlvgvkeekkveklkkkEvLmlniGsastggvvtsvkkdeakvkLkkPvcaekgekialsRrvekrW 78 
                                       ++e+ey+ller+vg+ke  + ++++ kE Lm++iG+a t gvv +v++++++++L+kP++   g++ ++sR ++++W
  gi|385805489|ref|YP_005841887.1| 330 HIEMEYHLLERVVGAKEFITARPIQAKERLMITIGTALTKGVVERVSSNVIEISLSKPIVGISGSRAVFSREINGKW 406
                                       69*************************************************************************** PP

                                       EEEEEEE CS
                            eIF2_C  79 rLiGwGe 85 
                                       rL GwG+
  gi|385805489|ref|YP_005841887.1| 407 RLAGWGI 413
                                       ******7 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 ?   -0.2   0.0      0.59   1.3e+03      13      21 ..      42      50 ..      41      56 .. 0.81
   2 !   29.5   1.1   3.3e-10   7.3e-07       1      62 [.     236     305 ..     236     319 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.59
                                      EETTEEEEE CS
                       GTP_EFTU_D2 13 lkkGdevri 21
                                      lk+G+++++
  gi|385805489|ref|YP_005841887.1| 42 LKRGMTIKL 50
                                      9******98 PP

  == domain 2  score: 29.5 bits;  conditional E-value: 3.3e-10
                                       EEEEEEEEEESEEETTEEEEEEC.TCTTSEE.......EEEEEEEEEEETEEESEEETTSEEEEEEEESS CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskke.......ivtrissletfhededeavaganaGvivaikg 62 
                                       G+v++g++ +G+lk Gde++il+ ++++k++       i t+++sl   + +++ a +g+   v++++++
  gi|385805489|ref|YP_005841887.1| 236 GGVVGGTLSQGELKIGDEIVILPgMKVKKSGgreeyqaIYTEVTSLRFGEIEVEKALPGGLLAVGTKLDP 305
                                       89*************************9999******************999999999999999988876 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.21   4.8e+02     105     137 ..      16      45 ..       6      47 .. 0.79
   2 !   14.0   0.0   1.6e-05     0.036      13      99 ..     109     201 ..      85     204 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.21
                                       ECSTTSSHHHHHHHHCTT-----S--------- CS
                       RsgA_GTPase 105 vGqSGvGKStLinallpelelktgevseklgrG 137
                                       +G+   GK+tL+ +l++     t++ se+l+rG
  gi|385805489|ref|YP_005841887.1|  16 AGHVDHGKTTLVYSLTGI---WTSKHSEELKRG 45 
                                       455567********9986...788888888888 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 1.6e-05
                                       EES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-.EEEEEEE-GGG--HHH......HHHHHHHHHHHTTSEEEE- CS
                       RsgA_GTPase  13 vaNvdqllivvslkepelslnlldrfLvlaeekgi.epvivlnKiDlleeee......eleelkeelealgyevllv 82 
                                       +a +d +l+v++++e+  ++++ + f  ++e  gi +++iv nK+D++++e+      e+++l e + a + +++ +
  gi|385805489|ref|YP_005841887.1| 109 AAIMDGALLVIAANEKCPQPQTFEHFK-ALEIIGIkNLIIVQNKVDVVSRERaresynEIKRLIEGTWAENAPIIPI 184
                                       7889**********9999999998875.56777774788999********998886666666666777778999999 PP

                                       -TTTHTTHHHHHHHCTT CS
                       RsgA_GTPase  83 saktkegleelkellkd 99 
                                       sa ++++++ l +++++
  gi|385805489|ref|YP_005841887.1| 185 SALKGANIDVLMAAIQK 201
                                       99999999999888765 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   5.1e-06     0.011     166     229 ..     140     203 ..     124     209 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.1e-06
                                       HHH-SE.EEEE---HHHHHHHHHHHHHHHHHCSTTBTTB--EEEEEBCCCTBSHHHHHHHHHHHH CS
                              MeaB 166 leiaDi.ivvnkaDkkeaekaarelraaleleeekekeWrpkvlktsavegeGidelvdaieehr 229
                                       + i ++ iv nk D    e+a++ ++ + +l e + +e +++++ +sa++g  id l++ai+++ 
  gi|385805489|ref|YP_005841887.1| 140 IGIKNLiIVQNKVDVVSRERARESYNEIKRLIEGTWAE-NAPIIPISALKGANIDVLMAAIQKYI 203
                                       5566651566***************9998888765444.789********************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 !   15.0   0.0   8.8e-06      0.02       2     113 ..      13     150 ..      12     151 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8.8e-06
                                       EEEEESTTSSHHHHHHHHHTS.TEEESSST..TSSSSEEEEEEE...ETTEE......................... CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltge.kaivsdkp..gtTrdinegrvk...lkgke......................... 47 
                                       ++ +G+   GK+tL+ +ltg  +++ s++   g T++  ++          +                         
  gi|385805489|ref|YP_005841887.1|  13 IGTAGHVDHGKTTLVYSLTGIwTSKHSEELkrGMTIKLGYADGGiyrC---Sncpfpeeyqplpeckecpsgsepel 86 
                                       7889****************7766666655226666666655443231...13445555556777777777777777 PP

                                       ...EEEEECGGCSSHHHHHHHHHHHHHHHHC.TSEEEEEEETTTTCSHHHHHHHHHHHHH.TTSEEEEEEE CS
                          MMR_HSR1  48 ...ielvDtpGliegaseekglgkaflalee.adlillvvdaseeklkpldeeleellee.akkplilvln 113
                                          i  vD pG  e       l  ++l+    +d +llv+ a+e+  +p+  e  + le    k+li+v n
  gi|385805489|ref|YP_005841887.1|  87 lrrISYVDAPG-HE------ILMTTMLSGAAiMDGALLVIAANEKCPQPQTFEHFKALEIiGIKNLIIVQN 150
                                       777********.44......7888888877768*******9884433333333222222223345566655 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 ?   14.2   0.0   1.5e-05     0.034      58     103 ..     145     202 ..     141     204 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.5e-05
                      MMR_HSR1_Xtn  58 clyvlNKiDlisleeldelare............pnsvviSaekelnldeLkekiwee 103
                                        ++v NK+D +s e  +e ++e              +++iSa k+ n+d L+ +i ++
  gi|385805489|ref|YP_005841887.1| 145 LIIVQNKVDVVSRERARESYNEikrliegtwaenAPIIPISALKGANIDVLMAAIQKY 202
                                       68999*****99988877776556678899997668999*************999776 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.017        39       2      23 ..      12      33 ..      11      37 .. 0.88
   2 ?    5.3   0.1    0.0057        13     106     156 .]     143     199 ..     134     199 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.017
                                      EEEEEESTTSSHHHHHHHHHTT CS
                            FeoB_N  2 tvalvGnpnvGkttlfnaltga 23
                                      ++ ++G  + Gkttl+ +ltg 
  gi|385805489|ref|YP_005841887.1| 12 NIGTAGHVDHGKTTLVYSLTGI 33
                                      577899**************96 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0057
                                       SSEEEEEETHHHHHHTTEEE-HHHHHHHHT......S-EEEEBTTTTBTHHHHHHHH CS
                            FeoB_N 106 vpvvlalnmideaekkgieidlkkLsekLg......vpvvktsakkkegieellkai 156
                                       ++++++ n++d++++++ +   +++++ ++       p++++sa k+ +i+ l++ai
  gi|385805489|ref|YP_005841887.1| 143 KNLIIVQNKVDVVSRERARESYNEIKRLIEgtwaenAPIIPISALKGANIDVLMAAI 199
                                       5789999********9999999999988854444448**************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); 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: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.52
# Mc/sec: 2407.55
//
Query:       gi|385805490|ref|YP_005841888.1|  [L=223]
Description: 30S ribosomal protein S6e [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.8e-29  101.2   0.4    2.4e-28   98.6   0.1    2.2  2  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 ?    0.2   0.0      0.04   7.2e+02       1      15 [.      16      30 ..      16      64 .. 0.67
   2 !   98.6   0.1   1.3e-32   2.4e-28      11     114 ..     124     223 .]     117     223 .] 0.93

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.04
                                      -EEEEEETTTTEEEE CS
                     Ribosomal_S6e  1 mklnisdpatgkqkl 15
                                      +kl++s p++++q+ 
  gi|385805490|ref|YP_005841888.1| 16 FKLVVSVPKHNNQSI 30
                                      689999999877653 PP

  == domain 2  score: 98.6 bits;  conditional E-value: 1.3e-32
                                       TEEEEEE-CHHHCTTCTT-BSSEEEECCTTTSSSTS-EEEEEEEEETTC-BB-TTS-SSSEEEEEEETTSSSS-SSS CS
                     Ribosomal_S6e  11 gkqklievdekklrtligkrigeevdgdalGeelkgyvlkitggsdkqGfpmkqgvltpgrvrlLlskggvgyrprr 87 
                                       +k+ ++ +d++  r+++g +ig+e+d+ +++  lkg +  ++ggsd++Gfpm+++++++ +++lLls+  +gy+p+r
  gi|385805490|ref|YP_005841888.1| 124 SKAFQLTLDDSTSRRFVGMKIGDEIDAVIID--LKGKL-VVKGGSDNSGFPMRKDLPGAVKKKLLLSG-PPGYHPER 196
                                       46667777***********************..***65.59**************************9.******** PP

                                       SS-EEEEEEE-SB--SSEEEEEEEEEE CS
                     Ribosomal_S6e  88 kGerkrksvrGcivsadisqlnlvivk 114
                                       +Ge++rk+vrG++++++++q+n+++v+
  gi|385805490|ref|YP_005841888.1| 197 NGEKRRKMVRGNTIDESFVQINTILVQ 223
                                       ************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1587.03
//
Query:       gi|385805491|ref|YP_005841889.1|  [L=606]
Description: translation initiation factor aIF-2 [Fervidicoccus fontis Kam940]
Scores for complete 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-36  122.9   1.2    1.6e-35  120.9   1.2    2.1  1  GTP_EFTU_D4  Elongation factor Tu domain 4
      3e-29  102.0   0.0    8.7e-29  100.5   0.0    1.7  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    7.7e-22   77.4   2.3    7.7e-22   77.4   2.3    2.1  2  IF-2         Translation-initiation factor 2
    8.5e-12   45.3   3.2    9.9e-11   41.9   0.1    2.9  2  GTP_EFTU_D2  Elongation factor Tu domain 2
    1.9e-05   24.7   0.4    0.00013   22.1   0.0    2.4  2  MMR_HSR1     50S ribosome-binding GTPase
     0.0073   15.8   0.1         17    4.8   0.0    3.9  3  Arf          ADP-ribosylation factor family
      0.008   16.2   0.1       0.07   13.2   0.0    2.4  2  Dynamin_N    Dynamin family
  ------ inclusion threshold ------
      0.017   14.9   0.1       0.76    9.5   0.0    3.0  4  PduV-EutP    Ethanolamine utilisation - propanediol utilisati
      0.036   14.3   0.0      0.075   13.2   0.0    1.6  1  Roc          Ras of Complex, Roc, domain of DAPkinase
      0.056   13.4   0.8       0.66    9.9   0.1    3.1  4  RsgA_GTPase  RsgA GTPase
      0.064   13.8   1.4         18    5.8   0.0    2.6  2  AAA_23       AAA domain


Domain annotation for each model (and alignments):
>> 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 !  120.9   1.2   9.5e-39   1.6e-35       2      86 .]     477     562 ..     476     562 .. 0.99

  Alignments for each domain:
  == domain 1  score: 120.9 bits;  conditional E-value: 9.5e-39
                                       -CEEEEEEEEEEETCCCEEEEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEEEEESS-.TTT CS
                       GTP_EFTU_D4   2 PgkikilpgvvfrrsdpaivGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevaisiegki.vGr 77 
                                       P+k++i+pg+vfrrsdp+ivG+evlgG++kpg +l++e Gr++G ++qiqdkg++l+eak G++vais++g+i vGr
  gi|385805491|ref|YP_005841889.1| 477 PAKFRIIPGFVFRRSDPVIVGIEVLGGILKPGSPLMDEAGRKLGILQQIQDKGQSLKEAKPGMQVAISVKGNImVGR 553
                                       9**************************************************************************** PP

                                       S--TT-EEE CS
                       GTP_EFTU_D4  78 qikegdily 86 
                                       qi+egdi+y
  gi|385805491|ref|YP_005841889.1| 554 QINEGDIIY 562
                                       *******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 !  100.5   0.0   5.3e-32   8.7e-29       5     190 ..      19     226 ..      16     230 .. 0.83

  Alignments for each domain:
  == domain 1  score: 100.5 bits;  conditional E-value: 5.3e-32
                                       EEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHH..HHHSTHCHSHHHHHHTSCSSCEEEEEETTCSSEEEEEEEESS CS
                          GTP_EFTU   5 nigiighvDhGKtTLtdrLlyktgaiskkgeka..eeervlDtlkeErergiTiksaaisleketkkylinliDtPG 79 
                                        ++++ghvDhGKtTL+d++  ++ a ++ ge +   +++v+ ++  E+      k+  ++l+       + +iDtPG
  gi|385805491|ref|YP_005841889.1|  19 IVVVMGHVDHGKTTLLDKIRGTSVAKREPGEITqhVGASVVPSRVIEQLAEPLKKIIPVKLK----IPGLLFIDTPG 91 
                                       689*****************999999998887743235666666666666666666666655....9999******* PP

                                       SGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGST...........HHHHHHHHHH CS
                          GTP_EFTU  80 HvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrl...........kaelkeivee 145
                                       H+ F++    g ++ D+ +lvvd+ eG ++qt e l+l+++++vp+ v+ NK+D++           ++++ ++ + 
  gi|385805491|ref|YP_005841889.1|  92 HELFMNMRRIGGAISDFSILVVDIIEGFKEQTVESLQLLRARKVPFLVAANKIDKIpgwkpypneafINSYAKQSQR 168
                                       ***********************************************************999988885555555555 PP

                                       HHHHHHHH....HHHHHHHHHTTT.........TTEEEEEEBTTTTBTHHHHHHHHHH CS
                          GTP_EFTU 146 vkqklsrk....eeklekygekge.........kevpvvfgSalkgegvktllealve 190
                                        k+ l+++    +++l  yg++++         ++v++v++Sa++geg+ +ll +l  
  gi|385805491|ref|YP_005841889.1| 169 TKELLDERiyhlMGELGRYGFNSDrfdrikdftRTVSIVPVSAKTGEGIPELLAMLAG 226
                                       5544433355568888888888779999999999********************9875 PP

>> IF-2  Translation-initiation factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.4   2.3   4.7e-25   7.7e-22       4     104 ..     354     455 ..     351     456 .. 0.94
   2 ?   -1.0   0.1       1.2   1.9e+03      50      81 ..     550     586 ..     520     599 .. 0.57

  Alignments for each domain:
  == domain 1  score: 77.4 bits;  conditional E-value: 4.7e-25
                                       HHHCCCSCSSCCEEEEEESSHHHHHHHHHHHHCTT.SSTEEEECEEEESSB-HHHHHHHHHST......EEEEEESS CS
                              IF-2   4 lfeeikeegkelnviikaDvqGsleAlkeaLekleseevkvkvihsgvGaitesDvelasasn......aiiigFnv 74 
                                       ++++ik ++++ +v+ kaD+ G+l+Al eaL++      +++v  +++G+it++Dv  as s+      ++i+gFnv
  gi|385805491|ref|YP_005841889.1| 354 ELSKIKIKTDKSGVVAKADTLGTLDALVEALKRN-----NIPVRIADIGNITKRDVVEASISKqddetlGVILGFNV 425
                                       568899999999*********************7.....599999***************977788999******** PP

                                       SCTHHHHHCCCCCTSEEEEESSHHHHHHHH CS
                              IF-2  75 kvskkakklaekegvkirlynvIYkliddv 104
                                       kv ++ak++aek +vki+l+n+IYkl++d+
  gi|385805491|ref|YP_005841889.1| 426 KVMPDAKEEAEKLNVKIMLNNIIYKLLEDY 455
                                       ****************************96 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.2
                                       EES.SB-HHHHHHHHHST....EEEEEESSSCTHHHH CS
                              IF-2  50 gvG.aitesDvelasasn....aiiigFnvkvskkak 81 
                                        vG +i+e D+ + ++ +     ++  F+ ++s ++k
  gi|385805491|ref|YP_005841889.1| 550 MVGrQINEGDIIYTDVPDlharTFLTKFKGDISDDVK 586
                                       4552477888877777552222444455544444444 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 !   41.9   0.1     6e-14   9.9e-11       1      73 [.     257     335 ..     257     336 .. 0.87
   2 ?    2.8   0.5     0.097   1.6e+02       3      60 ..     495     547 ..     494     562 .. 0.80

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 6e-14
                                       EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEE...........ETTSEEEEEEEESSCCSG CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededea...........vaganaGvivaikgleda 66 
                                       G ++++++y+G+l+kGd++++++    + +ivt+++ l+++ ++++e            ++ a++Gv++ +++l++a
  gi|385805491|ref|YP_005841889.1| 257 GNTIDVIIYDGILRKGDTIVLGS---AEGPIVTKVRNLLMP-KPLQEIrspedkflsvdEVVAAVGVKIVAPDLDNA 329
                                       6799*****************44...3558***********.6677777********99999999999999999998 PP

                                       SSTTCEE CS
                       GTP_EFTU_D2  67 iivGdtl 73 
                                        ++G  l
  gi|385805491|ref|YP_005841889.1| 330 -VAGTQL 335
                                       .888765 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.097
                                       EEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEE CS
                       GTP_EFTU_D2   3 valgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivai 60 
                                       ++++ v  G+lk+G  ++      ++k  ++  ++++   + ++ea +g ++ + v++
  gi|385805491|ref|YP_005841889.1| 495 IVGIEVLGGILKPGSPLMD--E-AGRK--LGILQQIQDKGQSLKEAKPGMQVAISVKG 547
                                       6777788899999999987..4.5666..89999999999999***999999998887 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   7.8e-08   0.00013       2     114 .]      20     143 ..      19     143 .. 0.71
   2 ?   -0.3   0.1       0.7   1.1e+03      33      64 ..     376     402 ..     328     472 .. 0.62

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 7.8e-08
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEE...ETTEE..................EEEEECGGCS CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvk...lkgke..................ielvDtpGli 57 
                                       v+++G+   GK+tL+ ++ g+ +   +    T+++    v    +   e                  + ++DtpG  
  gi|385805491|ref|YP_005841889.1|  20 VVVMGHVDHGKTTLLDKIRGTSVAKREPGEITQHVGASVVPsrvI---EqlaeplkkiipvklkipgLLFIDTPG-H 92 
                                       899***************996444444444555555554442221...1344455666666677777********.4 PP

                                       SHHHHHHHHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                          MMR_HSR1  58 egaseekglgkaflaleeadlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                       e      +  +++   + +d  +lvvd+  e++k++  e  +ll+ +k p+++++nk
  gi|385805491|ref|YP_005841889.1|  93 E----LFMNMRRIGGAI-SDFSILVVDII-EGFKEQTVESLQLLRARKVPFLVAANK 143
                                       4....334555555444.5********98.77*99999*9***9999*****99998 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.7
                                       SSSEEEEEEEETTEEEEEEECGGCSSHHHHHH CS
                          MMR_HSR1  33 TrdinegrvklkgkeielvDtpGliegaseek 64 
                                       T+d   + +k ++ +++++D+  + +     +
  gi|385805491|ref|YP_005841889.1| 376 TLDALVEALKRNNIPVRIADIGNITK-----R 402
                                       56666666666667777777777332.....2 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.011        17      14      44 ..      17      47 ..       6      59 .. 0.81
   2 ?    4.8   0.0      0.01        17     107     128 ..     126     147 ..     107     227 .. 0.70
   3 ?   -0.7   0.0      0.53   8.6e+02      42      67 ..     373     398 ..     347     451 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.011
                                      EEEEEEEESTTSSHHHHHHHHHHSSCEECSS CS
                               Arf 14 elrilllGLDnaGKtTilkklkleelvttvP 44
                                      +  ++++G    GKtT+l k++  ++++  P
  gi|385805491|ref|YP_005841889.1| 17 QPIVVVMGHVDHGKTTLLDKIRGTSVAKREP 47
                                      445788999999*********9999998887 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.01
                                       HCTSGCCTTSEEEEEEE-TTST CS
                               Arf 107 lleeeelkevallvlaNKqDlp 128
                                        l+  + ++v++lv aNK+D  
  gi|385805491|ref|YP_005841889.1| 126 SLQLLRARKVPFLVAANKIDKI 147
                                       4455567899999999999964 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.53
                                       CSSSSSEEEEEEEETTEEEEEEEE-S CS
                               Arf  42 tvPTigfnveeleiknlkftvwDvGG 67 
                                       t  T+   ve l+ +n+ +++ D+G 
  gi|385805491|ref|YP_005841889.1| 373 TLGTLDALVEALKRNNIPVRIADIGN 398
                                       56688888999999999999999985 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   4.3e-05      0.07       1      34 [.      20      53 ..      20      56 .. 0.94
   2 ?   -0.6   0.0      0.72   1.2e+03      97     111 ..      78      92 ..      65      98 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.3e-05
                                      EEEEEBTTTTHHHHHHHHHTS--S---SSS---S CS
                         Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrr 34
                                      ++v+G++ +GK+++l+++ g  +  r+p+ +T+ 
  gi|385805491|ref|YP_005841889.1| 20 VVVMGHVDHGKTTLLDKIRGTSVAKREPGEITQH 53
                                      79***************************99975 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.72
                                       ETTS-SEEEEE---B CS
                         Dynamin_N  97 sllvkgltlvDlPGl 111
                                       +l+ +gl ++D+PG 
  gi|385805491|ref|YP_005841889.1|  78 KLKIPGLLFIDTPGH 92 
                                       56778999******5 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00046      0.76       4      26 ..      20      42 ..      17      57 .. 0.86
   2 ?    1.3   0.0      0.16   2.5e+02      40      67 ..      86     116 ..      83     130 .. 0.78
   3 ?   -2.3   0.0         2   3.3e+03     123     141 ..     206     224 ..     203     225 .. 0.87
   4 ?   -3.8   0.0       5.9   9.6e+03      93     108 ..     396     409 ..     394     425 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00046
                         PduV-EutP  4 illiGkvgsGKttLtqalkgeel 26
                                      ++++G+v+ GKttL  +++g ++
  gi|385805491|ref|YP_005841889.1| 20 VVVMGHVDHGKTTLLDKIRGTSV 42
                                      899***************99876 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.16
                         PduV-EutP  40 viDtPGe..ylenrklysalivtsa.eadvi 67 
                                       +iDtPG   +++ r++  a+  +s+  +d+i
  gi|385805491|ref|YP_005841889.1|  86 FIDTPGHelFMNMRRIGGAISDFSIlVVDII 116
                                       69****7779999**9999998886134555 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2
                         PduV-EutP 123 ifevsavekegieellkyl 141
                                       i  vsa + egi ell++l
  gi|385805491|ref|YP_005841889.1| 206 IVPVSAKTGEGIPELLAML 224
                                       7889***********9887 PP

  == domain 4  score: -3.8 bits;  conditional E-value: 5.9
                         PduV-EutP  93 iGiitkidlaedeeni 108
                                       iG itk d++  e++i
  gi|385805491|ref|YP_005841889.1| 396 IGNITKRDVV--EASI 409
                                       8999999998..4444 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 ?   13.2   0.0   4.6e-05     0.075       2     120 .]      20     146 ..      19     146 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.6e-05
                                       EEEESSTTSSHHHHHHCHCT-CCC-EE....ETTTTEEEEEEECGGSGGCT.TBTTTTCEEEEE.....EEE-SGGC CS
                               Roc   2 vvlvGdsgvGKtsllkrfvedkfseke....kstigvdfltkevtkikgve.ndkkvkkvklni.....WDtaGqer 68 
                                       vv++G    GKt+ll+++   ++ ++e    ++ +g++++ ++v +  ++    kk+  vkl+i      Dt G+e 
  gi|385805491|ref|YP_005841889.1|  20 VVVMGHVDHGKTTLLDKIRGTSVAKREpgeiTQHVGASVVPSRVIE--QLAePLKKIIPVKLKIpgllfIDTPGHEL 94 
                                       7899**************9988876542223688999999988853..3330334444455543222228******* PP

                                       TTTT-HHHHCTSCEEEEEEEGHHHHCHHHHHHHHHHH.CSSS-EEEEEE-TTT CS
                               Roc  69 frslhplylreaalailvydsrssenlkeWlkelkkv.agkspvilvgnkiDl 120
                                       f +++++    ++  ilv+d  +  + ++ +++l+   a+k p+++ +nkiD+
  gi|385805491|ref|YP_005841889.1|  95 FMNMRRIGGAISDFSILVVDIIEGFK-EQTVESLQLLrARKVPFLVAANKIDK 146
                                       ********************544332.234666665515577999999**995 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1    0.0004      0.66      95     133 ..      13      53 ..       3      95 .. 0.81
   2 ?   -1.1   0.0      0.97   1.6e+03      30      61 ..     119     149 ..     105     184 .. 0.72
   3 ?   -2.3   0.0       2.2   3.5e+03      77      99 ..     204     226 ..     193     231 .. 0.81
   4 ?   -2.5   0.1       2.5   4.1e+03      42      66 ..     384     412 ..     364     450 .. 0.53

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0004
                                       HHCTTSEEEEECSTTSSHHHHHHHHCTT-..----S----- CS
                       RsgA_GTPase  95 ellkdktsvlvGqSGvGKStLinallpel..elktgevsek 133
                                       ++l++ ++v++G+   GK+tL+++++++   + + ge+ ++
  gi|385805491|ref|YP_005841889.1|  13 QKLRQPIVVVMGHVDHGKTTLLDKIRGTSvaKREPGEITQH 53 
                                       679999********************975224555666655 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.97
                                       --HHHHHHHHHHHHHTT-EEEEEEE-GGG--H CS
                       RsgA_GTPase  30 lslnlldrfLvlaeekgiepvivlnKiDllee 61 
                                       +++++++  L l+ +++++ +++ nKiD +  
  gi|385805491|ref|YP_005841889.1| 119 FKEQTVE-SLQLLRARKVPFLVAANKIDKIPG 149
                                       5555554.577888899999999999998764 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.2
                                       SEEEE--TTTHTTHHHHHHHCTT CS
                       RsgA_GTPase  77 yevllvsaktkegleelkellkd 99 
                                       ++++ vsakt+eg+ el ++l++
  gi|385805491|ref|YP_005841889.1| 204 VSIVPVSAKTGEGIPELLAMLAG 226
                                       6788999999****999999876 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 2.5
                                       HHHTT-EEEEE....EE-GGG--HHHHHH CS
                       RsgA_GTPase  42 aeekgiepviv....lnKiDlleeeeele 66 
                                       +++++i++ i+    ++K D++e + + +
  gi|385805491|ref|YP_005841889.1| 384 LKRNNIPVRIAdignITKRDVVEASISKQ 412
                                       44555555553333367777776665222 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.011        18      17      40 ..      15      38 ..       8      46 .. 0.90
   2 ?    2.3   4.1      0.12     2e+02     124     190 ..     396     470 ..     324     475 .. 0.62

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.011
                            AAA_23 17 FskgltlItGpNGaGKTTildAik 40
                                      + ++++++ G+   GKTT+ld i+
  gi|385805491|ref|YP_005841889.1| 15 LRQPIVVVMGHVDHGKTTLLDKIR 38
                                      57899****************886 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.12
                            AAA_23 124 llgskkiilnlilflgqer........feefelkdkkerleelekeleeledekkllekleqekekekeleelee 190
                                       + +++k+     ++ +q++        f+ +   d ke+ e+l+ ++  ++ + klle+  + ke+ k+le+++e
  gi|385805491|ref|YP_005841889.1| 396 IGNITKRDVVEASISKQDDetlgvilgFNVKVMPDAKEEAEKLNVKIMLNNIIYKLLEDYFNWKEEVKRLEKIKE 470
                                       33344443333333333334666666655556688899**********************999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (606 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       721  (0.0402142); expected 358.6 (0.02)
Passed bias filter:                      572  (0.0319036); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.45
# Mc/sec: 4065.29
//
Query:       gi|385805492|ref|YP_005841890.1|  [L=141]
Description: nucleoside diphosphate kinase [Fervidicoccus fontis Kam940]
Scores for complete 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-56  187.9   0.1    8.1e-56  187.8   0.1    1.0  1  NDK           Nucleoside diphosphate kinase
  ------ inclusion threshold ------
       0.08   13.0   0.1       0.12   12.4   0.1    1.3  1  RNA_pol_RpbG  DNA-directed RNA polymerase, subunit G


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 !  187.8   0.1   9.1e-60   8.1e-56       1     134 [.       4     137 ..       4     138 .. 0.99

  Alignments for each domain:
  == domain 1  score: 187.8 bits;  conditional E-value: 9.1e-60
                                       EEEEEEE-HHHHHTT-HHHHHHHHHHHT-EEEEEEEECE-HHHHHHHTGGGTTSTTHHHHHHHHTSSEEEEEEEEST CS
                               NDK   1 ertlvliKPdavkrgligeiisrleekglkivalkmlrlteeqaeehYaehkgkpffeelvefmtsgpvvalvlege 77 
                                       ert+v+iKPdav+r+ligeiisr+e+k+lkiva+k++++t+eqa+e+Y  hk+kpf+++lv+f t gpvv++vleg+
  gi|385805492|ref|YP_005841890.1|   4 ERTFVMIKPDAVERKLIGEIISRFERKNLKIVAMKLIKMTKEQAKELYIPHKDKPFYNDLVNFATRGPVVVMVLEGD 80 
                                       89*************************************************************************** PP

                                       THHHHHHHHH--SSTTTSSTTSHHHHH-SSSTT-SEEE-SSHHHHHHHHHHHSTGGG CS
                               NDK  78 daiekvreliGatnpaeaapgtiRadfgvslgeNlvHgSdseesaereiklfFkeee 134
                                       +a+e+vr+liG+t+ ++a pgtiR+df+++++eN++H+Sds+es ere k+fF e+e
  gi|385805492|ref|YP_005841890.1|  81 SAVEVVRTLIGSTDGRKALPGTIRGDFALDIQENVIHASDSKESYEREHKIFFLESE 137
                                       *****************************************************9887 PP

>> RNA_pol_RpbG  DNA-directed RNA polymerase, subunit G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   1.4e-05      0.12      10      84 ..       9      85 ..       1      92 [. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.4e-05
                      RNA_pol_RpbG 10 sieksklkdlkivkikcqne..eielDiiselnifkeedkveviisrekPeyldgkdFcghGylvtekeeenkiitl 84
                                       i++++++   i +i +  e  ++++  ++ +++ ke+ k   i  ++kP y d ++F ++G +v    e+++ +++
  gi|385805492|ref|YP_005841890.1|  9 MIKPDAVERKLIGEIISRFErkNLKIVAMKLIKMTKEQAKELYIPHKDKPFYNDLVNFATRGPVVVMVLEGDSAVEV 85
                                      5666666666666666655523566666777888888888888899*******************998888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1045.53
//
Query:       gi|385805493|ref|YP_005841891.1|  [L=59]
Description: 50S ribosomal protein L24E [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-19   69.2   0.6    2.7e-19   69.1   0.6    1.0  1  Ribosomal_L24e  Ribosomal protein L24e
    2.5e-05   24.1   0.3    3.2e-05   23.8   0.3    1.2  1  zf-FCS          MYM-type Zinc finger with FCS sequence motif
     0.0036   17.6   0.3     0.0039   17.5   0.3    1.1  1  Ta0938          Ta0938
  ------ inclusion threshold ------
      0.021   15.1   0.2      0.025   14.9   0.2    1.1  1  DUF2175         Uncharacterized protein conserved in archaea 


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 !   69.1   0.6   6.1e-23   2.7e-19       3      57 ..       4      59 .]       2      59 .] 0.95

  Alignments for each domain:
  == domain 1  score: 69.1 bits;  conditional E-value: 6.1e-23
                                      X-B-TTT-SB--SS--EEEE-TTS-EEEESSHHH.HHHHHTT--GGGSTTSTTT-X CS
                    Ribosomal_L24e  3 tekCsFsgykiyPGhGkrfvrnDgkvfrFlssKc.eklfkqkrnPrklkWTkayRr 57
                                      + kC+F+g++i PG+G ++++ Dg+v+ F+s+Kc +++    r++ klkWTk+++r
  gi|385805493|ref|YP_005841891.1|  4 LVKCAFCGNEILPGTGLMYIKVDGSVMWFCSRKCyKNMLVLNRKATKLKWTKVAKR 59
                                      679*******************************999999************9986 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 !   23.8   0.3   7.1e-09   3.2e-05       4      37 ..       5      37 ..       2      40 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 7.1e-09
                            zf-FCS  4 krCwfCkkyikgkpeftyvlendgvvgqFCStsC 37
                                       +C fC+++i  ++    ++  dg+v  FCS+ C
  gi|385805493|ref|YP_005841891.1|  5 VKCAFCGNEILPGT-GLMYIKVDGSVMWFCSRKC 37
                                      69************.6899*************** PP

>> Ta0938  Ta0938
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.3   8.6e-07    0.0039      16      64 ..       6      57 ..       2      59 .] 0.79

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 8.6e-07
                                      S-SS---S....---SS-B-TT--BSSS--SSSS-TTS-THHHHHHHHHHHS- CS
                            Ta0938 16 gcalcgat....wgdyyeevdgeklffccdicakefvnllnevkkrtglskid 64
                                       ca+cg       g  y +vdg  ++fc   c k+++ +ln+   + +++k+ 
  gi|385805493|ref|YP_005841891.1|  6 KCAFCGNEilpgTGLMYIKVDGSVMWFCSRKCYKNML-VLNRKATKLKWTKVA 57
                                      59***98522225899****************99876.567777778898885 PP

>> DUF2175  Uncharacterized protein conserved in archaea (DUF2175)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.2   5.5e-06     0.025       4      45 ..       6      48 ..       4      57 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.5e-06
                           DUF2175  4 kCyiCgkeivegekFTft.kkgvvHyeClvekarkklkeseda 45
                                      kC++Cg+ei  g    ++  +g+v + C ++  ++ l  + +a
  gi|385805493|ref|YP_005841891.1|  6 KCAFCGNEILPGTGLMYIkVDGSVMWFCSRKCYKNMLVLNRKA 48
                                      8*****************889*******988777666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 433.29
//
Query:       gi|385805494|ref|YP_005841892.1|  [L=79]
Description: 30S ribosomal protein S28e [Fervidicoccus fontis Kam940]
Scores for complete 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-31  107.3   3.3    3.3e-31  107.1   3.3    1.1  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 !  107.1   3.3   1.8e-35   3.3e-31       4      64 .]      16      76 ..      13      76 .. 0.98

  Alignments for each domain:
  == domain 1  score: 107.1 bits;  conditional E-value: 1.8e-35
                                      EEEEEEEEEE---SSSSEEEEEEEE-S-SS-S-EEEEEEES---TT-EEEES--S--TT-- CS
                    Ribosomal_S28e  4 klAeVikvlgrtGsrGevtqVrvellegkdkgriiiRnVkGPvreGDiLtLlEterEArrL 64
                                      ++AeVi+++grtG++Ge++qVrv++leg+dkgr+++RnVkGPvr GDiL+L+EterEArrL
  gi|385805494|ref|YP_005841892.1| 16 YPAEVIQIIGRTGVTGEIIQVRVRVLEGRDKGRVLTRNVKGPVRIGDILILRETEREARRL 76
                                      79**********************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.49
# Mc/sec: 484.73
//
Query:       gi|385805495|ref|YP_005841893.1|  [L=126]
Description: 50S ribosomal protein L7Ae [Fervidicoccus fontis Kam940]
Scores for complete 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-31  106.4   0.5      6e-31  106.0   0.5    1.1  1  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil
    3.8e-06   26.7   0.1    5.6e-06   26.1   0.1    1.3  1  PELOTA_1        PELOTA RNA binding domain
     0.0096   16.0   0.0      0.011   15.8   0.0    1.1  1  RNase_P_pop3    RNase P subunit Pop3


Domain annotation for each model (and alignments):
>> Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.0   0.5     1e-34     6e-31       2      93 ..      18     109 ..      17     110 .. 0.97

  Alignments for each domain:
  == domain 1  score: 106.0 bits;  conditional E-value: 1e-34
                                       HHHHHHHHHHHHTEEEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHHHTTEEEEEESCHHHHHHHTTSSS CS
                    Ribosomal_L7Ae   2 aieevlkkakkagklvlGlkevtkalergeaklvilAedvepeekkkllealckekevpyvkvkskkeLGelvgkkr 78 
                                       + +++l+k+k++gk+++G++e+tka+erg aklv++Aedv+p+e +++l+ lc ek++py +v+skk+LGe vg  +
  gi|385805495|ref|YP_005841893.1|  18 ETYKLLEKVKQSGKIKKGTNETTKAVERGVAKLVVIAEDVDPPEVVAHLPLLCDEKKIPYTYVPSKKKLGESVGIDV 94 
                                       6799************************************************************************* PP

                                       ECSEEEEEESTTTHH CS
                    Ribosomal_L7Ae  79 pvsalaikdegdskd 93 
                                       +++a+ai+d+gd+k+
  gi|385805495|ref|YP_005841893.1|  95 QAAAVAIIDPGDAKE 109
                                       ************985 PP

>> PELOTA_1  PELOTA RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.1   9.4e-10   5.6e-06      15      71 ..      25      83 ..      14      92 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 9.4e-10
                          PELOTA_1 15 giedinliKPgigEaTRvlLRRvPekvlvrdeee..pdlahlllLakekgvpveevpdl 71
                                      ++++   iK g  E+T+++ R v + v+++++ +  + +ahl lL++ek++p++ vp++
  gi|385805495|ref|YP_005841893.1| 25 KVKQSGKIKKGTNETTKAVERGVAKLVVIAEDVDppEVVAHLPLLCDEKKIPYTYVPSK 83
                                      6788899**********************9988865679**************999876 PP

>> RNase_P_pop3  RNase P subunit Pop3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.9e-06     0.011      43     146 ..      20     117 ..      11     124 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.9e-06
                      RNase_P_pop3  43 vrlleskeneeseltvglneivelLecsesddvvllvcnkDtPsvLlsqlpllvavanltvklvqlpksaqakldek 119
                                        +lle k ++  ++  g ne  +  e  + ++ v+++ + D P   + +lpll+  +++  + v+     ++kl e 
  gi|385805495|ref|YP_005841893.1|  20 YKLLE-KVKQSGKIKKGTNETTKAVE-RGVAKLVVIAEDVD-PPEVVAHLPLLCDEKKIPYTYVPS----KKKLGES 89 
                                       55566.6677889999*******999.88888888888888.88889**********977777774....4456666 PP

                      RNase_P_pop3 120 lGls.kagmllvrkdasldkklaklvsk 146
                                       +G   +a ++++ +    ++ l +l+sk
  gi|385805495|ref|YP_005841893.1|  90 VGIDvQAAAVAIIDPGDAKEGLNSLISK 117
                                       6543134555555555555566666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); 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: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 950.94
//
Query:       gi|385805496|ref|YP_005841894.1|  [L=580]
Description: glutamyl-tRNA synthetase [Fervidicoccus fontis Kam940]
Scores for complete 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-72  242.6   0.0    4.4e-72  242.6   0.0    1.4  2  tRNA-synt_1c    tRNA synthetases class I (E and Q), catalytic
      2e-18   66.9   0.0      6e-18   65.3   0.0    1.9  1  tRNA-synt_1c_C  tRNA synthetases class I (E and Q), anti-codo
  ------ inclusion threshold ------
       0.15   12.1   1.2       0.43   10.6   1.2    1.8  1  NEMO            NF-kappa-B essential modulator NEMO
        1.4    9.2   4.3        0.9    9.8   0.8    2.2  2  Cas_Csa5        CRISPR-associated protein (Cas_Csa5)


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 ?   -3.8   0.4       1.1   4.7e+03      59     142 ..      47      66 ..      35      84 .. 0.45
   2 !  242.6   0.0   9.9e-76   4.4e-72       1     312 [.     101     411 ..     101     413 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 1.1
                                       HHHHTT---SSEEEEGGGGHHHHHHHHHHHHHTTSEEEE-STHHHHHHHHCCSSHSS-TTTTS-HHHHHHHHHHHHH CS
                      tRNA-synt_1c  59 dlkwlgikwdekptyqsdrfdelkkyaeeLikkGkAYvcectkeeleeereeqeklgskerdrydeenlklfeeemk 135
                                       +++ ++ k                                                                 ee++
  gi|385805496|ref|YP_005841894.1|  47 IIESVKKKV----------------------------------------------------------------EEIN 59 
                                       222222222................................................................2333 PP

                                       TTHSTTT CS
                      tRNA-synt_1c 136 kgkaege 142
                                       +++ +++
  gi|385805496|ref|YP_005841894.1|  60 SKSIDEQ 66 
                                       3333333 PP

  == domain 2  score: 242.6 bits;  conditional E-value: 9.9e-76
                                       S-EEEE---SSSS-BHHHHHHHHHHHHHHHHTT-EEEEEE--SSCCC--H..HHHHHHHHHHHHTT---SSEEEEGG CS
                      tRNA-synt_1c   1 kVrtRfaPePtGyLHiGhakaallnylfAknnnGkfilRieDTdpereke..eaeesiledlkwlgikwdekptyqs 75 
                                       k+ tRfaP+P    H+G+a+ a+l++ +A+ ++Gk+ilR+eDTdp  +++  ea   i edlkwlgi w ++ + qs
  gi|385805496|ref|YP_005841894.1| 101 KIITRFAPNPDFVIHLGNARPAILSHEYARMYKGKMILRFEDTDPRTKTPmiEAYSLIREDLKWLGIRW-DEEYIQS 176
                                       688******************************************9998733667789***********.55899** PP

                                       GGHHHHHHHHHHHHHTTSEEEE-STHHHHHHHHCCSSHSS-TTTTS-HHHHHHHHHHHHHTTHSTTTS-EEEESSBT CS
                      tRNA-synt_1c  76 drfdelkkyaeeLikkGkAYvcectkeeleeereeqeklgskerdrydeenlklfeeemkkgkaegekavvRlkide 152
                                        r  +++++a+eLi kG AYv++ tk e ee   +   +  ++r+++ e+nl+lf e+m +g +++++av+R+k d 
  gi|385805496|ref|YP_005841894.1| 177 LRIPIYYQIAKELILKGGAYVDDSTKQEYEEIVSA--GQVHPNRNKSPEDNLELF-EKMLSGYYKEGEAVLRVKTDL 250
                                       ********************************988..55559*************.9******************** PP

                                       TSS.GGGSSTEEEEEEESGGGSBTTTBTSTSEEE-HHHHHHHHHHHTT-SEEEEEGGGGCCHHHHHHHHHHTT-S.- CS
                      tRNA-synt_1c 153 ess.vefrDlvrgriklepqeihdlvivksdiyPtYdfavvidDaleeithvlrteefldntpkyiwllealglevp 228
                                       +++   + D v+ ri  +++  h+ v++k+ + PtY+fa  +dD+l+++thv+r++e+++nt k+  l++++g+++p
  gi|385805496|ref|YP_005841894.1| 251 KYTdKSLIDWVAFRIIDTEKTPHPIVGSKYIVWPTYNFAAGVDDHLMGVTHVIRGKEHKQNTIKQSHLYQYMGWKQP 327
                                       ***9************999999*****************************************************77 PP

                                       EEEEEE--EEETTSB-SHHHHHHHHHTT..SSSSTT-TTSCBHHHHHHCTB-HHHHHHHHHHHCCCSSS.EEEEHHH CS
                      tRNA-synt_1c 229 pfiheylrlnlekkklSKRklsllvdek..qvkewddlreallnflrrlGwtpekerelftreeliksfdlnresks 303
                                       + ih+  rl le+  +SK +++ + +e+   + + dd+r+ ++ +lr +G+ pe++r+l+ + +   s+  ++++ +
  gi|385805496|ref|YP_005841894.1| 328 ETIHL-GRLKLEDFIMSKSQIKRILKESrgLYSGPDDPRFGTIMGLRERGILPEAIRNLILTVGAKSSD-ASISYVN 402
                                       77775.899*********9999887664238*********************************99888.8888888 PP

                                       HHHHHHHHH CS
                      tRNA-synt_1c 304 leafdrkkL 312
                                       l++ +rk +
  gi|385805496|ref|YP_005841894.1| 403 LASENRKII 411
                                       777777655 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 !   65.3   0.0   1.3e-21     6e-18       1     173 [.     415     566 ..     415     567 .. 0.85

  Alignments for each domain:
  == domain 1  score: 65.3 bits;  conditional E-value: 1.3e-21
                    tRNA-synt_1c_C   1 ApRymaVldpvkvtienlpegkeeelevplhpknpelgtrkvpfsk..eiyiereDakrlkpg..eevrLkelynik 73 
                                       A R+m+V++pv ++i+nl+e      ++++hp+n++lg+r++++ +   i i+r+D++++ +   + +rL+el n++
  gi|385805496|ref|YP_005841894.1| 415 AYRIMFVIEPVYLKIDNLKE-GCLRTTISYHPDNKSLGSREYEVCNgdIISISRDDYESINNSgtKSLRLMELANFE 490
                                       78****************96.56899*****************9965599********999855699********** PP

                    tRNA-synt_1c_C  74 veevekdesgevtelkleydgesleearkkkg.iihWvsaeeaveaevrlYdrLfkeeededfl..lnpdslkvlee 147
                                       ++             +l ++++s++ ark+k  ii+Wv++++++ a                +l    +++lkv + 
  gi|385805496|ref|YP_005841894.1| 491 ISGE-----------RLVFKSKSVDIARKEKLsIIQWVKKKNSTIA----------------SLliPSKEELKV-KY 539
                                       *775...........477888889889*************999999................662233344443.78 PP

                    tRNA-synt_1c_C 148 glaep.alanlkkgdivQfeRiGyfrv 173
                                       g +e+ ++ ++ +g+ +Q+ R G++rv
  gi|385805496|ref|YP_005841894.1| 540 GDIEKvEILESLSGKTIQLIRVGFARV 566
                                       8888757889999************98 PP

>> NEMO  NF-kappa-B essential modulator NEMO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.2   9.6e-05      0.43       7      59 ..      29      84 ..      23      89 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 9.6e-05
                              NEMO  7 qlkellteNneLkealkqsNqalkeRlEeLsaw...qekqkeerefleeklreare 59
                                       + +++ e  eLk  +k   ++ k  +Ee+      ++k+ +e+ef e  l e+++
  gi|385805496|ref|YP_005841894.1| 29 VVSKIVAEKPELKSSIKEIIESVKKKVEEINSKsidEQKKILEKEFPEVSLTEEKK 84
                                      6789999***********************754221456669**********9998 PP

>> Cas_Csa5  CRISPR-associated protein (Cas_Csa5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.8    0.0002       0.9      24      77 ..      46      97 ..      37     106 .. 0.77
   2 ?   -0.7   0.1      0.38   1.7e+03      42      87 ..     498     543 ..     487     546 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0002
                          Cas_Csa5 24 kvlydaqRivqmglergeiksdtvkikekeyPaivikkkegkkyevvGylpsde 77
                                      +++  +++ v+  +++ +i  +++ i eke+P + ++++++k+ +v+  lp  e
  gi|385805496|ref|YP_005841894.1| 46 EIIESVKKKVE-EINSKSIDEQKK-ILEKEFPEVSLTEEKKKEEKVLPPLPNAE 97
                                      44555555554.578899998776.********************999999776 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.38
                          Cas_Csa5  42 iksdtvkikekeyPaivikkkegkkyevvGyl.psdedvedFlelve 87 
                                        ks++v i  ke  +i i+  ++k+ ++   l ps+e+++    ++e
  gi|385805496|ref|YP_005841894.1| 498 FKSKSVDIARKEKLSI-IQWVKKKNSTIASLLiPSKEELKVKYGDIE 543
                                       5778888999999999.666666666666654389998886665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (580 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1179  (0.0657594); expected 358.6 (0.02)
Passed bias filter:                      607  (0.0338558); 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: 0.66u 0.28s 00:00:00.94 Elapsed: 00:00:00.47
# Mc/sec: 3677.77
//
Query:       gi|385805497|ref|YP_005841895.1|  [L=145]
Description: hypothetical protein FFONT_0453 [Fervidicoccus fontis Kam940]
Scores for complete 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   35.1   0.0    1.4e-08   34.8   0.0    1.1  1  DUF2118   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2118  Uncharacterized protein conserved in archaea (DUF2118)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.0     8e-13   1.4e-08       9     149 ..       9     144 ..       6     145 .] 0.89

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 8e-13
                           DUF2118   9 EgkeseeevevileeeeevekfadkveekklkgkvvYeelldeivdvleekvtrdviivlpderklillkkGdklkl 85 
                                       E +++ + v+ +l+++e++e  +d + +++  +  ++++   ++ ++     + ++ii+ p++    l+++ ++lk 
  gi|385805497|ref|YP_005841895.1|   9 EDDKKIPSVKNYLKSNENIESKLDISLDRIACEEIIFNN--ISFGERNICVSKGNFIIKTPKN--SFLIERNEELKY 81 
                                       6777778999****************9999999999999..46666666667789*****975..6899******** PP

                           DUF2118  86 ipvegvkvtlivdvGdrveegdtlaavttrkgevrylrapvegvVvfikeepagkrpnyiyyil 149
                                       + +e  ++    + Gd v++ d +a  +++kg  r+++ p eg +++++++p   +p+ i++il
  gi|385805497|ref|YP_005841895.1|  82 FIIEASQINTRKKPGDSVKKWDEIAVSKSKKGILRRIKIPFEGQIILVEQDPT-YKPERIVFIL 144
                                       *****************************************************.5566666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); 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 0.28s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 944.01
//
Query:       gi|385805498|ref|YP_005841896.1|  [L=333]
Description: geranylgeranyl pyrophosphate synthase [Fervidicoccus fontis Kam940]
Scores for complete 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  230.9   0.0    1.5e-68  230.6   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 !  230.6   0.0   8.3e-73   1.5e-68       4     246 ..      30     272 ..      27     285 .. 0.93

  Alignments for each domain:
  == domain 1  score: 230.6 bits;  conditional E-value: 8.3e-73
                                       HHHHHHHHHHSSS--HHHHHHHHHHHHHSCGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEETTEE-HHHCTCH CS
                   polyprenyl_synt   4 leealeylveagGKrlRpllvllaaealkeeeeelekaavlawivellhaasLvhDDimDdsetRRGqpcahrlvGn 80 
                                       ++e++ y+++agGKrlRp+lv+++  a++ +e   + ++  a+ vellh+++L+hDDimD+++ RRG p++h+l+G 
  gi|385805498|ref|YP_005841896.1|  30 FYESSLYILKAGGKRLRPALVFASGYAFGGSE---KYLLPFAAGVELLHNFTLIHDDIMDNDDYRRGVPTVHKLWGI 103
                                       678889***********************666...6789************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHH......STTHHHHHHHHHHHHHHHHHHHHHHHHTTTTTCCC.SHHHHHHHHHHHT CS
                   polyprenyl_synt  81 klAindgdfllarafellaklf......ekslellelfsevllqtveGqlldleeekdddlskfsleeyleivkyKT 151
                                       ++Ai++gd+l++ +++l  + +      ++++++ + ++ ++l+++eGq+ld++ ek++++s   +eey++++++KT
  gi|385805498|ref|YP_005841896.1| 104 PTAILAGDLLFSYSLYLPLHSCddfeikDRCIKASKKLAWASLTVAEGQALDMSFEKKESVS---EEEYMNMIEKKT 177
                                       **************99988776788985555***********************99999999...************ PP

                                       HHHCHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHSS-TSHHHHTT---HHHHHHHHCT- CS
                   polyprenyl_synt 152 aylfalpvalaallagasdeelealkdiglelGlaFQiqDDylDlfgdpevlgKpagtDiqegkctlpilkalelas 228
                                       a+l++ ++ ++a ++ga++++l +++++g+++G+aFQi+DD+l +fg++e++gKp+ +Di+egk tl+i+ al l++
  gi|385805498|ref|YP_005841896.1| 178 AALIESSAYIGATIGGADEKDLMHISEFGRKIGIAFQIVDDILGIFGKEEETGKPVYSDIREGKKTLLIIRALALSN 254
                                       *****************99********************************************************** PP

                                       HHHHHHHHHHTTSSHHHH CS
                   polyprenyl_synt 229 peqrkvlkeilgkkaeke 246
                                       +e+r++l +ilgkk   +
  gi|385805498|ref|YP_005841896.1| 255 KEERNKLISILGKKGLGK 272
                                       ************765333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); 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: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2048.06
//
Query:       gi|385805499|ref|YP_005841897.1|  [L=367]
Description: isopentenyl pyrophosphate isomerase [Fervidicoccus fontis Kam940]
Scores for complete 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-24   85.2   1.3    3.7e-18   65.7   1.1    2.2  2  FMN_dh        FMN-dependent dehydrogenase
    1.5e-06   27.7   1.5    3.2e-06   26.5   1.5    1.5  1  Glu_synthase  Conserved region in glutamate synthase
    0.00025   20.1   8.6    0.00035   19.7   0.7    3.5  4  IMPDH         IMP dehydrogenase / GMP reductase domain
  ------ inclusion threshold ------
      0.047   13.2   2.5       0.13   11.7   0.1    2.6  3  His_biosynth  Histidine biosynthesis protein
       0.35   10.0   3.3       0.36   10.0   1.2    1.9  2  DHO_dh        Dihydroorotate dehydrogenase


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 !   17.7   0.0   3.9e-07    0.0014      28      96 ..      24      94 ..      16     129 .. 0.83
   2 !   65.7   1.1     1e-21   3.7e-18     205     343 ..     171     334 ..     111     338 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.9e-07
                                      HGGGGEEE---SSSS-S..S-B--EEETTEEESSSEEE--BSTGGGTSTTHHHHHHHHHHHHTS-EEEETT CS
                            FMN_dh 28 aaferirlrprvlrdvs..kvdlsttllGqklslPvliaPvglaklahpdgelalaraaakagipfvlstv 96
                                      + +++i+l +++l + s  ++++++++lG+kls+P+++  +    +++ d ++ la+ a++ +i + ++++
  gi|385805499|ref|YP_005841897.1| 24 TLLKNIQLIHQALPELSfdSINTTVEFLGKKLSAPLMFTGITGGHVYAGDINRVLAKVAEENKIAIEVGSQ 94
                                      55789999999999876326799999*************************************99877766 PP

  == domain 2  score: 65.7 bits;  conditional E-value: 1e-21
                                       HHHHHHHHHHHSSEEEEEEE...-SHHHHHHHHHTTESEEEE--GGG..........TSSTT---HHHCHHHH.... CS
                            FMN_dh 205 wddikwlreqtklplvvKGv...ltaedakraveaGvdgivvSNHGG..........RqldgapatidvLpei.... 264
                                        ++i+ lr+++++p++vK++   +++e a  +v+aGv+ i v+  GG          R+l+g    +  + e     
  gi|385805499|ref|YP_005841897.1| 171 LKNIEILRNELSVPIIVKEIgygISKEVASALVKAGVKYIDVAGAGGtswikveilrRKLRGEKVDLPGIYEFynwg 247
                                       56899****************************************************77777666655554444444 PP

                                       .........HHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            FMN_dh 265 .........veavggrievlvDgGirrGsDvlkAlalGAdavllGRpflyglaagGeeGvervleilraelertmal 332
                                                 + v ++i+++++gGir+G+ v+k +a+GAd+ +++ p+l   aa  +e ++r+++ +  el+ +m l
  gi|385805499|ref|YP_005841897.1| 248 iptalsiieTRSVSSEIKIIASGGIRNGVEVAKSIAIGADIAGFALPALKE-AARSKECLDRYVRNIIMELKIAMLL 323
                                       444455566677788*********************************877.889********************** PP

                                       HT-SBHHHHHC CS
                            FMN_dh 333 lGvksvaeldr 343
                                       + +k+v+el++
  gi|385805499|ref|YP_005841897.1| 324 TSAKDVEELKN 334
                                       ********975 PP

>> Glu_synthase  Conserved region in glutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   1.5   8.9e-10   3.2e-06     190     307 ..     170     296 ..     164     305 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 8.9e-10
                                       HHHHHHHHHHH-TTSEEEEEEE-STTHHHHHHHHHHTT-SEEEEE-TT---SSEEHHHH......HHB---.....H CS
                      Glu_synthase 190 laqliedLkevnkeakvsvKlvaeagvetiaagvakanadiilidGleGGTGAspkssi......khaGlP.....l 255
                                       + + ie L++   ++++ vK       + +a+ ++ka++  i + G  GGT   + ++       +++ lP      
  gi|385805499|ref|YP_005841897.1| 170 ILKNIEILRNEL-SVPIIVKEIGYGISKEVASALVKAGVKYIDVAGA-GGTSWIKVEILrrklrgEKVDLPgiyefY 244
                                       556677777654.78999998877778889999*************6.77877666553222223456677332333 PP

                                       HHHHHHHHHHHHHTT-GGG-EEEEESS--SHHHHHHHHHHT-SEEE-SHHHH CS
                      Glu_synthase 256 elalaevdqtlkeeglrdrvsliadGglktgadvvkalalGAdavgigtaal 307
                                         +++ +   + +  + +++++ia+Gg++ g++v+k++a+GAd  g++  al
  gi|385805499|ref|YP_005841897.1| 245 NWGIPTALSIIETRSVSSEIKIIASGGIRNGVEVAKSIAIGADIAGFALPAL 296
                                       479*****************************************99997776 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.44   1.6e+03     286     308 ..      61      83 ..      48      95 .. 0.73
   2 ?    2.0   0.2     0.023        81     130     175 ..     168     216 ..     106     228 .. 0.75
   3 !   19.7   0.7   9.7e-08   0.00035     189     245 ..     247     299 ..     242     307 .. 0.78
   4 ?    1.9   0.0     0.025        89     296     327 ..     303     334 ..     296     345 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.44
                                       -SBEEEEEE--B-HHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 286 peGvegrvpykgsvkevveqlvg 308
                                         G+ g   y+g++++v+ ++++
  gi|385805499|ref|YP_005841897.1|  61 FTGITGGHVYAGDINRVLAKVAE 83 
                                       56788888888888887777665 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.023
                                       HHHHHHHHHHHHHTTTSEEEEEEE...-SHHHHHHHHHTT-SEEEE.-SS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxx.xxx RF
                             IMPDH 130 ekvleavkeikkkveeveviaGnv...ataegakaLieagadavkv.GiG 175
                                       +++l+ ++ +++++ +v +i+ ++    ++e a+aL++ag++ + v G G
  gi|385805499|ref|YP_005841897.1| 168 RNILKNIEILRNEL-SVPIIVKEIgygISKEVASALVKAGVKYIDVaGAG 216
                                       46777888888888.57787655522257888999999999998883444 PP

  == domain 3  score: 19.7 bits;  conditional E-value: 9.7e-08
                                       ---HHHHHHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCCCTTBTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 189 GvpqltAvaevaeaakkagvpviaDGGikysgdivkAlaaGadavmlGsllagteEs 245
                                       G+p + +++e+ ++  + ++++ia GGi++  +++k++a+Gad+   G  l + +E+
  gi|385805499|ref|YP_005841897.1| 247 GIPTALSIIETRSV--SSEIKIIASGGIRNGVEVAKSIAIGADI--AGFALPALKEA 299
                                       66766666666655..56899*********************96..46666666666 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.025
                                       -B-HHHHHHHHHHHHHHHHHHHT-SSHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 296 kgsvkevveqlvgglrsgmgylGaktieelke 327
                                       k  ++++v++++ +l+ +m  + ak++eelk+
  gi|385805499|ref|YP_005841897.1| 303 KECLDRYVRNIIMELKIAMLLTSAKDVEELKN 334
                                       6678899***********************86 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.35   1.2e+03      46      80 ..      59      93 ..      47      93 .. 0.84
   2 ?   -0.2   0.2      0.16   5.6e+02      63     101 ..     172     212 ..     125     229 .. 0.75
   3 ?   11.7   0.1   3.5e-05      0.13      59     152 ..     249     357 ..     235     365 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.35
                                      EEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEEEES CS
                      His_biosynth 46 lhvvDldaakegreanldlveeiaeevfipvqvGG 80
                                      l++  +++ +   +    +++++aee +i ++vG+
  gi|385805499|ref|YP_005841897.1| 59 LMFTGITGGHVYAGDINRVLAKVAEENKIAIEVGS 93
                                      6677788888888888899999****999999995 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.16
                                       HHHHHHHHH-SSEE...EEESSSSSHHHHHHHHHCT-SEEEE CS
                      His_biosynth  63 dlveeiaeevfipv...qvGGGIrsledveelleagadkvii 101
                                       + +e +++e+++p+   ++G GI++   + +l++ag++++ +
  gi|385805499|ref|YP_005841897.1| 172 KNIEILRNELSVPIivkEIGYGISKEV-ASALVKAGVKYIDV 212
                                       445666777777773335699998866.99999999987655 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 3.5e-05
                                       HHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEE... CS
                      His_biosynth  59 eanldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarr... 132
                                       ++ l+++e+   + +i++   GGIr+  +v++ + +gad    +  a+k+    ke+++++ + +i++ + +     
  gi|385805499|ref|YP_005841897.1| 249 PTALSIIETRSVSSEIKIIASGGIRNGVEVAKSIAIGADIAGFALPALKEAARSKECLDRYVR-NIIMELKIAMllt 324
                                       567788888888889********************************************9999.8887776555554 PP

                                       .....C........EEEEETTTTEEEEEEHHHH CS
                      His_biosynth 133 .....g........ykvaikgwreetgldavel 152
                                            +        ++  i +w  + g+d++++
  gi|385805499|ref|YP_005841897.1| 325 sakdvEelknvpivFDEKITNWLSQRGIDPIKF 357
                                       443330344455555556666666666666555 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.17   5.9e+02      66     107 ..     119     158 ..      43     219 .. 0.63
   2 ?   10.0   1.2    0.0001      0.36     239     268 ..     258     287 ..     248     293 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.17
                                       EEE---S-BS-HHHHHHHHHHHHHHHHCC.CEEEEEEE-TTS CS
                            DHO_dh  66 vlNslGlnneGldavlekllkrrkeqeekkelginlskakkt 107
                                       v+  lG +  G + v    ++ +   ++  +++i l++a++ 
  gi|385805499|ref|YP_005841897.1| 119 VIANLGAQQLGDKPVEIAEKAIKM--IDADAIAIHLNVAQEL 158
                                       344444444443332222222111..1112344444444443 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0001
                                       HHTTT.S-EEEESS--SHHHHHHHHHHTEC CS
                            DHO_dh 239 krlkkeipiIgvGGiesgeDalekieaGAs 268
                                       + +++ei+iI++GGi  g  +   i  GA 
  gi|385805499|ref|YP_005841897.1| 258 RSVSSEIKIIASGGIRNGVEVAKSIAIGAD 287
                                       456779*******************99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); 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: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2418.06
//
Query:       gi|385805500|ref|YP_005841898.1|  [L=264]
Description: acetylglutamate kinase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.3e-31  108.7   0.1    4.1e-31  108.4   0.1    1.1  1  AA_kinase  Amino acid kinase family
  ------ inclusion threshold ------
      0.062   13.4   0.1       0.11   12.7   0.1    1.3  1  Ocnus      Janus/Ocnus family (Ocnus)


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 !  108.4   0.1   4.6e-35   4.1e-31       1     230 [.       1     228 [.       1     239 [. 0.90

  Alignments for each domain:
  == domain 1  score: 108.4 bits;  conditional E-value: 4.6e-35
                                       TEEEEEE-TTCCCCTCC......HHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHH....TCCCCCHHHC.... CS
                         AA_kinase   1 krvVvKlGGssltdkee......aslrrlaeqiaalkesgnklvvVhGggsftdgllal....ksglssgelaaglr 67 
                                       ++vV+KlGGs++tdk++      +++ r+a++i+++  ++++lvv+hGggsf++  +++    +  +s + + +   
  gi|385805500|ref|YP_005841898.1|   1 MKVVIKLGGSLITDKSKpysfrkEVVIRIAKEIKRAIDEKIDLVVIHGGGSFGHVEAKRaidiYGRISNETISP--- 74 
                                       789**********99999*****************************************555433333333331... PP

                                       E..HHHHHHHHHHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEE CS
                         AA_kinase  68 stleeagevatrdalaslgerlvaallaaglpavglsaaaldateagrdegsdgnvesvdaeaieelleagvvpvlt 144
                                                    ++  l+  +++ l+++ ++av+ ++++l++   ++     g++ s d + +++ +e+g vp+l 
  gi|385805500|ref|YP_005841898.1|  75 ----------IAFSMQELNYMMTSILVSNRIKAVSFPPHSLCVNLCNI-----GERFSCDLKIVKTAIEKGSVPILF 136
                                       ..........22688899999**********************99999.....************************ PP

                                       SEEEEETTTE.EEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHH........CSS CS
                         AA_kinase 145 gfigldeege.lgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaee........sas 212
                                       g+i++ ++    +++s+D +a +++ +++A+++i++tdVdGV+   ++ +   ++l+ei+ +e+++        ++ 
  gi|385805500|ref|YP_005841898.1| 137 GDIVYGDNFCdPAIISGDDLALMIGSYINAERIIFFTDVDGVFLELGHPE---TILKEIRLNEIDSvikkasiyNNV 210
                                       ***7776655989*************************************...*******************99999 PP

                                       S.TTTHHHHCHHHHHHHH CS
                         AA_kinase 213 elatgGmkvkhpaalaaa 230
                                        ++t G   k++++ + +
  gi|385805500|ref|YP_005841898.1| 211 VDVTSGLLGKLKKTYQYL 228
                                       9*********99998876 PP

>> Ocnus  Janus/Ocnus family (Ocnus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   1.2e-05      0.11      44      83 ..      23      66 ..      10      70 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.2e-05
                             Ocnus 44 adifekveeelek.....lglevkclGGGriehdeekkkikvYGy 83
                                      ++++ ++++e+++     ++l v + GGG   h e+k+ i +YG 
  gi|385805500|ref|YP_005841898.1| 23 KEVVIRIAKEIKRaidekIDL-VVIHGGGSFGHVEAKRAIDIYGR 66
                                      555555555555433322344.6789******************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1900.70
//
Query:       gi|385805501|ref|YP_005841899.1|  [L=256]
Description: hypothetical protein FFONT_0457 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score 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   13.3   0.3       0.16   12.0   0.3    1.7  1  HTH_45    Winged helix-turn-helix


Domain annotation for each model (and alignments):
>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.3   8.8e-06      0.16      33      65 ..     190     222 ..     154     229 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.8e-06
                            HTH_45  33 ykllnkYLdmLvekglikkskekYvlTekGlel 65 
                                       y+ ln+YL +L  +g+++k+kek++   +Gl+ 
  gi|385805501|ref|YP_005841899.1| 190 YSKLNSYLLILNVNGIVEKNKEKFEQSIRGLNS 222
                                       999*********************988888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); 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: 00:00:00.42
# Mc/sec: 1815.48
//
Query:       gi|385805502|ref|YP_005841900.1|  [L=287]
Description: putative dioxygenase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-76  255.6   0.0      5e-76  255.4   0.0    1.0  1  Memo      Memo-like protein


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 !  255.4   0.0   2.8e-80     5e-76       2     270 ..       9     283 ..       8     284 .. 0.96

  Alignments for each domain:
  == domain 1  score: 255.4 bits;  conditional E-value: 2.8e-80
                              Memo   2 aavAGsfYpedeeelkkqleeflekntgkkei....arviis..........PHagyvysgevaakayaeles.skv 63 
                                       + vAG fY+ ++e+l +q+++ +++ +g++++    +    s          PHagy+ysg+vaa+ y++++  +k+
  gi|385805502|ref|YP_005841900.1|   9 PVVAGEFYELRKEKLLEQIRWAFLHPIGPGKEaifsN----SitknnfgyiaPHAGYIYSGPVAAHTYYNISLeKKP 81 
                                       789***************************8766542....13346778888*********************99** PP

                              Memo  64 ervvilGpsHtilgskvsvlaaseleTPlGdlkvDeelveeLvkkeeiadldetaalaEHSlEvqlpfLkellkekk 140
                                       ++++i+Gp+Ht+lg +vs+ + ++++TPlG ++vD el   L+ k+++  +d  a+l+EHS+EvqlpfL++++++  
  gi|385805502|ref|YP_005841900.1|  82 DTFIIIGPNHTGLGAQVSLAPWKQWRTPLGLINVDIELRDYLITKSKVLVPDYNAHLYEHSIEVQLPFLQYIFQK-D 157
                                       ***************************************************************************.6 PP

                              Memo 141 fkivPilvsaqseetakevgealakvikdes..nlviiSsDlsHygrrFgspqeiaesieDrevikaleelneeelk 215
                                       f+i+Pi++++q++++ ++++e l  + +       +i+SsD+sHy+     p ++a+++ D ++ + +++ + + ++
  gi|385805502|ref|YP_005841900.1| 158 FQILPIVLMRQTPKVVEKIAEELLDATEHLGrdFTIIASSDMSHYE-----PYDVAKRK-DLKAFEMIKKRDINLFY 228
                                       *****************************998899***********.....********.***************** PP

                              Memo 216 eylektnnticGekpiavilkalkklgakkakllkYaqssdvtsdtdsvVsyasl 270
                                       +yle+ n ++cG + +++++ ++k  + ++ ++lkYa+s+d t+d+d+vV+y+s+
  gi|385805502|ref|YP_005841900.1| 229 NYLETENVSMCGPGGVMILMTISKMKNGREPEILKYATSGDLTGDKDAVVGYLSA 283
                                       ***************************9************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1908.26
//
Query:       gi|385805503|ref|YP_005841901.1|  [L=220]
Description: 30S ribosomal protein S2 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-27   96.2   0.9    2.7e-15   56.2   0.7    2.1  2  Ribosomal_S2  Ribosomal protein S2
  ------ inclusion threshold ------
       0.12   12.5   0.0       0.32   11.1   0.0    1.7  2  BRCT_3        BRCA1 C Terminus (BRCT) 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 !   38.6   0.0   7.4e-14   6.6e-10       2      95 ..      30     120 ..      29     127 .. 0.94
   2 !   56.2   0.7   3.1e-19   2.7e-15     148     213 ..     128     193 ..     123     195 .. 0.96

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 7.4e-14
                      Ribosomal_S2   2 LeagvhfGhqtrrwnpkmkpyIyger.ngihiidlektlaalrraykvvkevaakggkilfvgtkkqakeavkeaak 77 
                                       L+agvh+G  t   n++mk+++y  r +g +++d++k+ + lr a k++ +   + +kil v+ ++  ++ vk+ ++
  gi|385805503|ref|YP_005841901.1|  30 LAAGVHIG--TYVCNKNMKEFVYRIRpDGLYVLDVRKIDERLRIASKMLAR--YEPQKILVVSVRQYGHNPVKKFSQ 102
                                       89******..7788*********999779*******************986..57899******************* PP

                      Ribosomal_S2  78 rangyyvnerWlgGtLTN 95 
                                        +++ y+  r ++G+LTN
  gi|385805503|ref|YP_005841901.1| 103 YVGSKYIAGRVIPGILTN 120
                                       ****************** PP

  == domain 2  score: 56.2 bits;  conditional E-value: 3.1e-19
                      Ribosomal_S2 148 lPdlvvvldpkkekiavkEakklgipviaivDtnvdpdlvdypIpaNddsirsiklilgvladaie 213
                                        Pd+vvv+dp+ ++ +++Ea+k gip+i+++Dt+   d++d +IpaN++  +s+ l++ +l+++i 
  gi|385805503|ref|YP_005841901.1| 128 EPDIVVVTDPRADQQIINEASKIGIPIISFTDTDNRIDNIDLIIPANNKGRKSLALLYWILTRQIL 193
                                       69***********************************************************99886 PP

>> BRCT_3  BRCA1 C Terminus (BRCT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       0.7   6.3e+03      58      75 ..      72      89 ..      61      90 .. 0.78
   2 ?   11.1   0.0   3.6e-05      0.32      50      75 ..     132     157 ..     109     158 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.7
                            BRCT_3 58 peevlkkaeqlkipvvSt 75
                                       +++l + e +ki vvS+
  gi|385805503|ref|YP_005841901.1| 72 ASKMLARYEPQKILVVSV 89
                                      567788888889999985 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 3.6e-05
                            BRCT_3  50 vvvtdsscpeevlkkaeqlkipvvSt 75 
                                       vvvtd++  +++ ++a++ +ip++S 
  gi|385805503|ref|YP_005841901.1| 132 VVVTDPRADQQIINEASKIGIPIISF 157
                                       78**********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); 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: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 1275.25
//
Query:       gi|385805504|ref|YP_005841902.1|  [L=66]
Description: RNA polymerase, N/8 Kd subunits [Fervidicoccus fontis Kam940]
Scores for complete 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  104.5   0.1    2.9e-30  104.4   0.1    1.0  1  RNA_pol_N       RNA polymerases N / 8 kDa subunit
  ------ inclusion threshold ------
      0.058   13.7   0.0      0.096   13.0   0.0    1.4  1  Chordopox_RPO7  Chordopoxvirus DNA-directed RNA polymerase 7 


Domain annotation for each model (and alignments):
>> RNA_pol_N  RNA polymerases N / 8 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.4   0.1   3.2e-34   2.9e-30       1      58 [.       1      58 [.       1      59 [. 0.98

  Alignments for each domain:
  == domain 1  score: 104.4 bits;  conditional E-value: 3.2e-34
                                      ----SS-TTT--B-STHHHHHHHHHHTT--HHHHHHHHT--SHHHHHHHHTB--THHH CS
                         RNA_pol_N  1 MiiPVrCFtCGkvigekweeylellekgeepkdaLdaLglkryCCrrmllthvdliek 58
                                      MiiPVrC+tCGk++g+ we ++e+++kge+p+++Ld+Lg++ryCCrr+l++hvdlie+
  gi|385805504|ref|YP_005841902.1|  1 MIIPVRCYTCGKPLGQYWEPFKERVSKGEDPEKVLDDLGIDRYCCRRTLISHVDLIEQ 58
                                      9*******************************************************98 PP

>> Chordopox_RPO7  Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide (RPO7)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.1e-05     0.096       1      46 [.       1      51 [.       1      62 [. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.1e-05
                    Chordopox_RPO7  1 mvfplvCstCGrDlse..eryrLlvkk.kkLkdvlat..vkrkCCrlkLst 46
                                      m+ p+ C tCG+ l +  e ++  v k ++ ++vl+   + r CCr  L  
  gi|385805504|ref|YP_005841902.1|  1 MIIPVRCYTCGKPLGQywEPFKERVSKgEDPEKVLDDlgIDRYCCRRTLIS 51
                                      8999**********98446788877662668999997235899**987755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.48
# Mc/sec: 411.75
//
Query:       gi|385805505|ref|YP_005841903.1|  [L=131]
Description: 30S ribosomal protein S9 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-30  106.6   0.1    1.2e-30  106.5   0.1    1.0  1  Ribosomal_S9   Ribosomal protein S9/S16
  ------ inclusion threshold ------
      0.046   13.5   0.0      0.084   12.7   0.0    1.4  1  TrkA_C         TrkA-C domain
       0.16   11.5   0.0        0.3   10.7   0.0    1.3  1  Mso1_Sec1_bdg  Sec1-binding region of Mso1


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 !  106.5   0.1     2e-34   1.2e-30       1     121 []       6     131 .]       6     131 .] 0.93

  Alignments for each domain:
  == domain 1  score: 106.5 bits;  conditional E-value: 2e-34
                                       EECTTEEEEEEEEESSSEEEETTEECCHHSTTSCHHHHHCHHHHHTTTSS..SEEEEEEEESS-HHHHHHHHHHHHH CS
                      Ribosomal_S9   1 GrrKesvArvwikegkgkilvngksleeYfkeeaarekvleplkltgllg..kfdvfvkvkgGGlsgqaeAirlgia 75 
                                       G+rK+++A+v ik+gkg++lvn+ ++e   + e  r+k++e lkl+g+ +  ++d++++v+gGG+++qa+A r++ia
  gi|385805505|ref|YP_005841903.1|   6 GKRKSAIAKVVIKPGKGRVLVNEMPIEL-HPVELFRNKIVEVLKLLGKDHreQVDIIASVNGGGFMAQADATRTAIA 81 
                                       8**************************9.899**************9987657************************ PP

                                       HHHHHHHHHHHHHHC......TCCCTS-B--------TTSSCTTB----S-- CS
                      Ribosomal_S9  76 raLvalekeekkeLk......kaglltrDpRvvErkKtgkkkARkkyqwskR 121
                                       r+Lv++ ++  + Lk      ++ ll  DpR++E+ K+ +  AR+++q+s+R
  gi|385805505|ref|YP_005841903.1|  82 RGLVKYFES--ERLKtifqeyDRVLLAGDPRRTEPEKYMRYSARRRWQKSYR 131
                                       ******883..44554445889****************************99 PP

>> TrkA_C  TrkA-C 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     0.084      30      61 ..      78     111 ..      68     113 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.4e-05
                                       EEEE-T..-EEES--TT-B--TT-EEEEEEEHHH CS
                            TrkA_C  30 vairRg..geliipsgdtvLeeGDvllvvgspsd 61 
                                        ai Rg  + +++ +  t+++e D++l++g+p  
  gi|385805505|ref|YP_005841903.1|  78 TAIARGlvKYFESERLKTIFQEYDRVLLAGDPRR 111
                                       5899999999999999***************976 PP

>> Mso1_Sec1_bdg  Sec1-binding region of Mso1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   5.1e-05       0.3      17      33 ..      76      92 ..      74      96 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 5.1e-05
                     Mso1_Sec1_bdg 17 ddTlvhraLvkYYdekg 33
                                      + T + r LvkY+++++
  gi|385805505|ref|YP_005841903.1| 76 TRTAIARGLVKYFESER 92
                                      679**********9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); 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: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 830.16
//
Query:       gi|385805506|ref|YP_005841904.1|  [L=149]
Description: 50S ribosomal protein L13 [Fervidicoccus fontis Kam940]
Scores for complete 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   48.0   0.8    1.5e-10   41.4   0.8    2.3  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 !   41.4   0.8   8.1e-15   1.5e-10       3     114 ..       7     107 ..       5     117 .. 0.85

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 8.1e-15
                                       EEEEETTSBHHHHHHHHHHHHHTTTSTT--TTS--S-EEEEEEGGCBB-SSTHHTT-EEEEE-SSTTSEEEEEHHH. CS
                     Ribosomal_L13   3 yviDAegqvlgrlaskiakvLrGkhkptytphvdcGdyvvvinaekvaltgkkleqkvyyrhtgypgglkevtake. 78 
                                       ++++Ae+ +lgr+askiak+L             +G  vvv+naek  ++g++      y++   ++ l++   +  
  gi|385805506|ref|YP_005841904.1|   7 VIVNAENLILGRMASKIAKMLL------------TGKRVVVVNAEKAMISGERNMVIEGYKKLWSVRTLRNPDKQGp 71 
                                       6899**************9985............7889*************98887777777777777777655552 PP

                                       HHCCSHHHHHHHHHHCCS-SSHHHHHHGCTEEEESS CS
                     Ribosomal_L13  79 llekkpeeilekaVkgmLpknklgrrrlkrLkvyag 114
                                        + ++p++i+++aV+gmLp++  g++ l++Lkvy g
  gi|385805506|ref|YP_005841904.1|  72 RRPQSPRNIVKRAVRGMLPRKPKGKEALSNLKVYIG 107
                                       457799****************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 948.63
//
Query:       gi|385805507|ref|YP_005841905.1|  [L=125]
Description: 50S ribosomal protein L18e [Fervidicoccus fontis Kam940]
Scores for complete 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   24.4   2.3    5.7e-05   23.8   2.3    1.4  1  Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27
    0.00021   20.7   0.0    0.00026   20.5   0.0    1.0  1  Ribosomal_L18   Ribosomal protein 60S L18 and 50S L18e


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 !   23.8   2.3   6.3e-09   5.7e-05      76     126 ..      48     100 ..       4     102 .. 0.68

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 6.3e-09
                                       EGGGTTTTSSS...........SEEEE--S---.--EEEESEE-HHHHHHHHHTT-EE CS
                    Ribosomal_L27A  76 dleelaeaglikk.......kdgvKvlgkgeltkklkvkaskfSkkAkekIeaaGGkv 126
                                       +++++  ++   +           Kvlg+g+ltkk+ + a++ S kA ek ++ G ++
  gi|385805507|ref|YP_005841905.1|  48 NISKI--NR---NanegevvVVPGKVLGSGKLTKKIVIIAESYSMKAYEKLKKSGAEI 100
                                       33333..22...122345433344*******************************987 PP

>> Ribosomal_L18  Ribosomal protein 60S L18 and 50S L18e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   2.9e-08   0.00026      24     126 ..      11     107 ..       3     114 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.9e-08
                     Ribosomal_L18  24 lklLvklyrfLarRtdskFnkvvlkrLfmsrinrpplslsrlvkkvkkkeeekkiavvvgtvtdDvrllevPklsva 100
                                        + L+k  + L++  +++  + +   L   r++     +s++ ++ +    e++++vv g+v+   +l++  k+ + 
  gi|385805507|ref|YP_005841905.1|  11 KRKLIKGLKKLSKDEQANIWERISEELSAPRRKMVEANISKINRNAN----EGEVVVVPGKVLGSGKLTK--KIVII 81 
                                       56678888889999999999999************99***9999887....579**************87..9**** PP

                     Ribosomal_L18 101 ALrftetararilkaGGeiltlDqLa 126
                                       A   + +a +++ k+G ei  lD+L 
  gi|385805507|ref|YP_005841905.1|  82 AESYSMKAYEKLKKSGAEIYLLDDLL 107
                                       ***********************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       947  (0.0528195); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 930.93
//
Query:       gi|385805508|ref|YP_005841906.1|  [L=281]
Description: RNA polymerase, insert [Fervidicoccus fontis Kam940]
Scores for complete 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  102.1   2.6    4.4e-29  101.1   0.0    2.3  2  RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain
    2.5e-12   46.0   0.0    3.8e-12   45.5   0.0    1.3  1  RNA_pol_L      RNA polymerase Rpb3/Rpb11 dimerisation domain


Domain annotation for each model (and alignments):
>> RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.1   0.0   4.9e-33   4.4e-29       1     112 []      44     157 ..      44     157 .. 0.97
   2 ?    0.7   0.3     0.075   6.7e+02      31      63 ..     209     243 ..     189     271 .. 0.58

  Alignments for each domain:
  == domain 1  score: 101.1 bits;  conditional E-value: 4.9e-33
                                       EEEEECTSSS.HHHHHCHHHCSTCBSSCHHHHHHHHCTT-ETSSSSTTCSEEEEEEEEESSEC....EEGGGCBESS CS
                     RNA_pol_A_bac   1 VeieentsvlqDEvvaHrlgliplvsedvleillnlkelveeeeegeeeksvelkLnvkgpge....vtagdlkled 73 
                                       V i en+svl+DEv+aHrlg+ipl s+ +le++   +e+   e +++e++  +l+L+v++++e    v++g+lk+ed
  gi|385805508|ref|YP_005841906.1|  44 VLILENNSVLHDEVLAHRLGMIPLYSDRALEKYRAPEEC--AECTNCENCFDILHLEVENKDEdkkvVYTGELKSED 118
                                       66899**************************99999999..5679******************************** PP

                                       SSCEESSTTSEEEEEETT-EEEEEEEEEEESSEECTTT- CS
                     RNA_pol_A_bac  74 adveivnpdilIakLrkgqeleleakvkkGiGkehakfs 112
                                       +d+ +v +di+I+ L kgq++ lea+++ G+Gkeh k+s
  gi|385805508|ref|YP_005841906.1| 119 PDIYPVFKDIPIVVLGKGQKIVLEAEARLGRGKEHIKWS 157
                                       **************************************8 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.075
                                       HHHHHHCTT-..E.TSSSSTTCSEEEEEEEEESSEC CS
                     RNA_pol_A_bac  31 eillnlkelv..e.eeeegeeeksvelkLnvkgpge 63 
                                       e l+n+k+    +  e++ + ++  + +L+ k+  +
  gi|385805508|ref|YP_005841906.1| 209 E-LENFKNTSllRfCEDKVCRKCMKINYLENKKILR 243
                                       3.5666666543146777888885555555544433 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 !   45.5   0.0   4.2e-16   3.8e-12      11      68 ..      24     266 ..      14     267 .. 0.80

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 4.2e-16
                                       xxxxxxxxxxxxxxxxxxxx......................................................... RF
                         RNA_pol_L  11 lgNaLRrillsevpgvaiea......................................................... 30 
                                       + ++LRri++ evp++a+++                                                         
  gi|385805508|ref|YP_005841906.1|  24 VLTSLRRIIIEEVPTMAVDNvlilennsvlhdevlahrlgmiplysdralekyrapeecaectncencfdilhleve 100
                                       6789***************************************************9999999999999999999999 PP

                                       .........................................................xx.................. RF
                         RNA_pol_L  31 .........................................................pv.................. 32 
                                                                                                pv                  
  gi|385805508|ref|YP_005841906.1| 101 nkdedkkvvytgelksedpdiypvfkdipivvlgkgqkivleaearlgrgkehikwsPVsisalisvpeiifsfeqc 177
                                       99999999999999999999998888777777777777666666666666666666622555556666666666666 PP

                                       .....................................................xxxxxxxxxxxxxxxxxxxxxxxx RF
                         RNA_pol_L  33 .....................................................vkvntdkdklilevetdgslkPee 56 
                                                                                             k+n  ++k il+ve++gsl+ + 
  gi|385805508|ref|YP_005841906.1| 178 eeqesneclkcigefseelaekmmemkkgkielenfkntsllrfcedkvcrkcMKINYLENKKILRVESTGSLSTKL 254
                                       666666666666666666666666666777777777777777777777777778999******************** PP

                                       xxxxxxxxxxxx RF
                         RNA_pol_L  57 alkeAlkiLkek 68 
                                       ++++Al+iL++k
  gi|385805508|ref|YP_005841906.1| 255 IIEKALEILNKK 266
                                       *********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       983  (0.0548274); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 1639.67
//
Query:       gi|385805509|ref|YP_005841907.1|  [L=105]
Description: 30S ribosomal protein S11 [Fervidicoccus fontis Kam940]
Scores for complete 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-36  124.3   4.2    3.4e-36  124.0   4.2    1.1  1  Ribosomal_S11  Ribosomal protein S11


Domain annotation for each model (and alignments):
>> Ribosomal_S11  Ribosomal protein S11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.0   4.2   1.9e-40   3.4e-36      20     110 .]       2     101 ..       1     101 [. 0.98

  Alignments for each domain:
  == domain 1  score: 124.0 bits;  conditional E-value: 1.9e-40
                     Ribosomal_S11  20 kGaevlvksaGglgvkasr.kssPyaaqlaaekaaekvldkGikavevkvkg........pGpGreaalralaraGl 87 
                                       +Gae++++ +Gg++vka+r k+sPyaa+  a +aa++++++Gi+a+++kv++        pGpG++aa+ralar+G+
  gi|385805509|ref|YP_005841907.1|   2 SGAETASRVSGGMVVKADReKPSPYAAMISAARAAQQAMERGITAIHIKVRApgghgpktPGPGAQAAIRALARSGF 78 
                                       79*************************************************************************** PP

                     Ribosomal_S11  88 kigriedvtPiPhdgirrpkkrr 110
                                       +igriedvtPiPhd++rrp++rr
  gi|385805509|ref|YP_005841907.1|  79 IIGRIEDVTPIPHDTTRRPGGRR 101
                                       *********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 643.55
//
Query:       gi|385805510|ref|YP_005841908.1|  [L=168]
Description: 30S ribosomal protein S4 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-17   62.8   0.2    3.8e-17   61.7   0.2    1.6  1  S4            S4 domain
    1.7e-05   25.6   0.9    8.1e-05   23.5   0.3    2.1  2  Ribosomal_S4  Ribosomal protein S4/S9 N-terminal domain
  ------ inclusion threshold ------
      0.028   14.2   0.1      0.037   13.8   0.1    1.1  1  PCMT          Protein-L-isoaspartate(D-aspartate) O-methyltra


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 !   61.7   0.2   6.4e-21   3.8e-17       1      47 [.     103     149 ..     103     152 .. 0.94

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 6.4e-21
                                       EEHHHHHHHTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TTCE CS
                                S4   1 rRLdkvlarlglassrreArqlIehGrVlVNGkvvkdpsyrVkpgDv 47 
                                       rRL+++++++gla+++ +Arq+I hG++ +NG++v++p+y Vk +++
  gi|385805510|ref|YP_005841908.1| 103 RRLQTIVYQKGLAKTIYQARQMIVHGHIGINGRRVTSPGYLVKRSEE 149
                                       8******************************************6654 PP

>> Ribosomal_S4  Ribosomal protein S4/S9 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.3   1.4e-08   8.1e-05      38      81 ..      17      61 ..       4      75 .. 0.92
   2 ?    0.4   0.0      0.22   1.3e+03       9      26 ..     101     140 ..      95     168 .] 0.65

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.4e-08
                                      CHCH.HHHHHHHHHHHHT-S.HHHHHHHHHHHHHCCSHHHHHHHHH CS
                      Ribosomal_S4 38 eYgk.qlrekqklkrrYgll.ekqfrryfkearrirGktgenLlql 81
                                      ++ k +l+++ +l +++gl+ +k+++ ++++ar+ir + +++Ll+l
  gi|385805510|ref|YP_005841908.1| 17 PWDKtRLENELRLLGKFGLRnKKELWIAQTMARKIR-HRARELLAL 61
                                      89999*******************************.******986 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.22
                                       HHCHCTS-STSSS......................S-S-S CS
                      Ribosomal_S4   9 llRrvgfklflkg......................reypp 26 
                                       l Rr+++ +++kg                      r + p
  gi|385805510|ref|YP_005841908.1| 101 LNRRLQTIVYQKGlaktiyqarqmivhghigingrRVTSP 140
                                       6788998888888887777775555444444444444444 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 ?   13.8   0.1   6.2e-06     0.037       2      49 ..      69     116 ..      67     130 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.2e-06
                                       HHHHHHHHHHHTTS---HHHHHHHHHS-GGGGSSCGGGGGTTSSS-EE CS
                              PCMT   2 kkealieelkkkgviksdkvaealeevdReefvpesfkekaYedapls 49 
                                       ++e+l+++l ++g+++s++v++ l++++ e+ +++ +++ +Y++   +
  gi|385805510|ref|YP_005841908.1|  69 EEENLLKRLYSQGIVQSNAVLDDLLSINAEHILNRRLQTIVYQKGLAK 116
                                       5789**************************************976554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       769  (0.0428914); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1085.61
//
Query:       gi|385805511|ref|YP_005841909.1|  [L=164]
Description: 30S ribosomal protein S13 [Fervidicoccus fontis Kam940]
Scores for complete 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  145.0   0.3    1.8e-42  144.8   0.3    1.1  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 !  144.8   0.3   9.8e-47   1.8e-42       1     127 [.      13     141 ..      13     142 .. 0.96

  Alignments for each domain:
  == domain 1  score: 144.8 bits;  conditional E-value: 9.8e-47
                     Ribosomal_S13   1 RilgtdidgkkkveialtaikGiGrrkakiilkkadvdedkrigelteeeiekieeivenkaq.ykipnwi.nrqkd 75 
                                       R++gtd+dg+kk+++ l+ ikGiG+++a  +l+ +++d +kr+g l++eei++ie+ +++    +  p+w+ nr+kd
  gi|385805511|ref|YP_005841909.1|  13 RVAGTDLDGRKKLAYGLAGIKGIGYTTAVCLLRMLNIDPEKRTGFLSDEEISRIEKAISEISAsNLLPKWMlNRRKD 89 
                                       99********************************************************99655155799999***** PP

                     Ribosomal_S13  76 ikdGkdshvvendlrrklredieRlkkirsyrGlRHkrGlkvRGQrTkttgR 127
                                       +++G+d h++ ++l +k+++dieR+kki+s+rG+RH+ GlkvRGQrT+ttgR
  gi|385805511|ref|YP_005841909.1|  90 YETGDDIHLIGSELIFKVKQDIEREKKIKSWRGIRHSLGLKVRGQRTHTTGR 141
                                       ***************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); 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: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1032.09
//
Query:       gi|385805512|ref|YP_005841910.1|  [L=458]
Description: MATE efflux family protein [Fervidicoccus fontis Kam940]
Scores for complete 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-51  172.4  32.4    1.7e-28   99.3  11.9    2.8  4  MatE             MatE
    0.00048   20.2  42.0      0.017   15.2  18.6    4.1  3  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai


Domain annotation for each model (and alignments):
>> MatE  MatE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.3  11.9   1.9e-32   1.7e-28       1     160 [.      28     187 ..      28     188 .. 0.99
   2 ?   -3.0   0.2      0.57   5.1e+03      28      60 ..     201     214 ..     191     221 .. 0.52
   3 !   87.1  12.5   1.1e-28   9.9e-25       1     161 []     253     414 ..     253     414 .. 0.99
   4 ?   -3.4   0.4      0.72   6.5e+03      75      93 ..     430     447 ..     427     451 .. 0.66

  Alignments for each domain:
  == domain 1  score: 99.3 bits;  conditional E-value: 1.9e-32
                              MatE   1 PialenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgli 77 
                                       P+al+ ++++ + l+  +++gr+g++a+Aa s++++++  +++ + gl ++ ttlv+q+ Ga+n +++++++ q+++
  gi|385805512|ref|YP_005841910.1|  28 PLALSEMVQVAYDLANLYWLGRVGKDAVAAPSASWPFTYTFIAAMNGLLASGTTLVSQYRGANNINMMNKSVAQTFV 104
                                       99*************************************************************************** PP

                              MatE  78 lllllsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislll 154
                                       l+++ slii++ ++l +++il+  + + +v +l+  y ri+++ +++++l + +++++ + g+t +p+  +++++ l
  gi|385805512|ref|YP_005841910.1| 105 LAIISSLIISVSGILTIPYILYAAGIPSDVYPLSVVYSRIMFVALIFISLWESFRAVVSASGNTITPMKYNFFGVGL 181
                                       ***************************************************************************** PP

                              MatE 155 niplny 160
                                       n+++++
  gi|385805512|ref|YP_005841910.1| 182 NMIFDP 187
                                       ***987 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.57
                              MatE  28 lAavsialsilsllfvfllglstalttlvgqal 60 
                                       +A+                   ++++tl+++a+
  gi|385805512|ref|YP_005841910.1| 201 VAG-------------------AGISTLISRAI 214
                                       333...................34444444443 PP

  == domain 3  score: 87.1 bits;  conditional E-value: 1.1e-28
                              MatE   1 PialenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgli 77 
                                       P+ ++ ++e l + i+t ++++ gs+alAa +i+ + l+ll +  +g+ +a+ ++vgq+lGa n+kra+e++ ++l+
  gi|385805512|ref|YP_005841910.1| 253 PLSVAWVMEALGFSILTAIISMEGSTALAAWGIGDRPLNLLNFATIGFINATGIMVGQSLGASNRKRAEESAEKSLM 329
                                       8899999********************************************************************** PP

                              MatE  78 lllllsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislisl.l 153
                                       +  l+++i  l+  +f ++i+s+f qd++v+e++  y  +++ +i+++ + ++  +i +g g t++++++s++++ +
  gi|385805512|ref|YP_005841910.1| 330 IISLIGVIGGLIFGAFGRHIASFFIQDPDVIEATIYYYIYMGSTIVFFYYIQLMGAIAQGSGHTRFVMVVSILRIwI 406
                                       ***************************************************************************** PP

                              MatE 154 lniplnyl 161
                                       ++ +l+y+
  gi|385805512|ref|YP_005841910.1| 407 IRNVLAYI 414
                                       ******97 PP

  == domain 4  score: -3.4 bits;  conditional E-value: 0.72
                              MatE  75 glilllllsliiallvllf 93 
                                       g+ l+ ++s ++al+ ++f
  gi|385805512|ref|YP_005841910.1| 430 GMSLSNIISGLVALI-WIF 447
                                       455677778888877.555 PP

>> Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   1.1     0.076   6.8e+02      68     104 ..      80     116 ..      53     135 .. 0.49
   2 !   15.2  18.6   1.9e-06     0.017       3      85 ..     143     232 ..     141     347 .. 0.80
   3 !   13.4   7.2   6.6e-06      0.06       8      77 ..     373     446 ..     366     454 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.076
                   Polysacc_synt_C  68 vvavlnlyalrrllgiklellrrllkpllaalvmgiv 104
                                       +++v +++ ++++  ++ ++ ++++  ++++l++++ 
  gi|385805512|ref|YP_005841910.1|  80 TTLVSQYRGANNINMMNKSVAQTFVLAIISSLIISVS 116
                                       3333333333333333333344444444444444444 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.9e-06
                   Polysacc_synt_C   3 ailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllli......plfgivGaaiatvlallvvavln 73 
                                       +i+ +++if+sl   + ++  + g + +++k++++g+ +++i+  +li      p++g+ Ga i+t+++ ++va++ 
  gi|385805512|ref|YP_005841910.1| 143 RIMFVALIFISLWESFRAVVSASGNTITPMKYNFFGVGLNMIFDPFLIlgigpfPMLGVAGAGISTLISRAIVAFIS 219
                                       68999*******************************************999999999******************99 PP

                   Polysacc_synt_C  74 lyalrr.llgikl 85 
                                       l  + + +  ++l
  gi|385805512|ref|YP_005841910.1| 220 LNNIIQgKSDVRL 232
                                       6544332555555 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 6.6e-06
                   Polysacc_synt_C   8 siiflslstvlssiLqglgrqkialkalviga.lvklilnlllip...lfgivGaaiatvlallvvavlnlyal 77 
                                       +i+f+++++++++i qg g+++++++++++ + ++  +l +++ p    +gi G+ i++ l+ +++ ++ l+++
  gi|385805512|ref|YP_005841910.1| 373 TIVFFYYIQLMGAIAQGSGHTRFVMVVSILRIwIIRNVLAYIFGPgplNMGIPGIWIGMSLSNIISGLVALIWI 446
                                       57788888*****************9998865279*********655699**8888888888888877777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (458 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 3231.63
//
Query:       gi|385805513|ref|YP_005841911.1|  [L=367]
Description: metalloexopeptidase, family M42 [Fervidicoccus fontis Kam940]
Scores for complete 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-102  342.7   0.3   1.6e-102  342.5   0.3    1.0  1  Peptidase_M42  M42 glutamyl aminopeptidase
    3.2e-07   30.3   0.1    5.2e-07   29.6   0.1    1.3  1  Peptidase_M20  Peptidase family M20/M25/M40
    6.6e-06   25.2   0.0    1.1e-05   24.5   0.0    1.4  1  Peptidase_M18  Aminopeptidase I zinc metalloprotease (M18)
    0.00089   19.0   0.0      0.024   14.3   0.0    2.2  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 !  342.5   0.3  3.6e-106  1.6e-102       1     292 []      50     345 ..      50     345 .. 0.98

  Alignments for each domain:
  == domain 1  score: 342.5 bits;  conditional E-value: 3.6e-106
                                       S-EEEEEESSTTSSEEEEEEE--B-EEEEEEEETTSEEEEEEESS--GGGTTTEEEEEEETTE.EEEEEEEE--CGG CS
                     Peptidase_M42   1 GnliakkkgkekepkvmiaAHmDeiGfmVkeIkedGflrfekvGGvdpkvlegqrvkiltkkg.kisGvigskppHl 76 
                                       Gn+i  kkg  +++k+miaAHmDei ++Vk I+++Gflrf++vGG+++++l+++rvk++t+kg  i+Gvig+kppHl
  gi|385805513|ref|YP_005841911.1|  50 GNVISLKKG-VSGKKLMIAAHMDEISLIVKYIDDNGFLRFSPVGGWSERILPATRVKVRTNKGdWIPGVIGVKPPHL 125
                                       9********.99***************************************************************** PP

                                       CHHHHHHCT--GCGEEEEGSGSSHHHHHHTTS-TT-EEEES---EEETTECEEETTHHHHHHHHHHHHHHHHHCTSS CS
                     Peptidase_M42  77 lkeeerkkaleikelfiDigakskeeaeelGisvGdivvfdkefvelangkivskalDdragvavllellkelkeee 153
                                        ++ee+kk +e+++lfiD+ga+s++ea ++Gi+ G +v +d +f+ l ++++++ka+Ddrag++v+l+++ e++ ++
  gi|385805513|ref|YP_005841911.1| 126 ITPEEEKKVIEMNKLFIDVGASSRQEALSMGIEHGSRVLLDYDFADLIGNRVTGKAFDDRAGLVVALKTFMEVEPND 202
                                       *************************************************************************9998 PP

                                       -SSEEEEEEESTCTTTSHHHHHHHHHH--SEEEEEEEEEE-CSTTSTTTTSS..TTS-CEEEEEETT....CCSHHH CS
                     Peptidase_M42 154 leatvylvatvqEEvGlrGaktsaekikpdiaiavDvtaagdtpgskekeak..lgkGpvirvkDas....giyhpk 224
                                         +++y+vatvqEEvGl+Ga+tsa++i+pd+aia+Dvt+a+d p+++e+++   lgkGp+i++ D +    +i++  
  gi|385805513|ref|YP_005841911.1| 203 --IDLYFVATVQEEVGLKGARTSAYQISPDVAIALDVTTANDVPDVDEQDQVakLGKGPAIKIIDGRsgsgLITNTA 277
                                       ..***********************************************98899***********9989999***** PP

                                       HHHHHHHHHHHTT--EEEEEESSSSSTHHHHHTSTTTSEEEEEEEEEBSTTSTTEEEEHHHHHHHHHH CS
                     Peptidase_M42 225 lrkkllelAkknnipyqlevlsgggtDAgaihltgegvptalisiptryiHspvevahlddleatvkL 292
                                       + +k++ +Ak+ +ipyq evl+gg+tD++ai+lt+egvp+++isip+ryiHspvev++l d+   v+L
  gi|385805513|ref|YP_005841911.1| 278 VLEKMISVAKERGIPYQAEVLTGGTTDSSAIQLTKEGVPAGTISIPARYIHSPVEVIDLVDIHYSVEL 345
                                       **************************************************************988776 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 !   29.6   0.1   1.2e-10   5.2e-07      35     205 ..     181     350 ..     169     352 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 1.2e-10
                                       TTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTHHHHHHHHHHTTTCESEEEEEE....EESSSBTCH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxx RF
                     Peptidase_M20  35 addmkggvlaalealralkdegikpkgtivllfqpdEEggrgGakallegleerekvdavfelh....ieepgilea 107
                                       a d+ +g++ al+ + +++ +      ++ +++++ EE+g +Ga+  +     +  +d +++l        p++ e+
  gi|385805513|ref|YP_005841911.1| 181 AFDDRAGLVVALKTFMEVEPND----IDLYFVATVQEEVGLKGARTSAY----QISPDVAIALDvttaNDVPDVDEQ 249
                                       7899999999999999988885....599*********98899999999....555666555541121333444442 PP

                                       STETEEEE......EEEEEEEEEESHEEECCHHHHHHHHHHHHHHHTSCEEEE.EESSSBHTHHHH....TTTEEEE CS
                                       xxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx....xxxxxxx RF
                     Peptidase_M20 108 gklaigvv......kvevelleggapvtlndsplvkalaeaaeelfgekveli.vsgpggtdarff....agiptvm 173
                                       +    +v       ++++ + ++g    +n  ++ +++ ++a+e  g  ++ +  +g g+td++ +    +g+p+  
  gi|385805513|ref|YP_005841911.1| 250 D----QVAklgkgpAIKIIDGRSGSGLITN-TAVLEKMISVAKER-GIPYQAEvLTG-GTTDSSAIqltkEGVPAGT 319
                                       2....2335668866999988899999998.*************8.99955555999.********99999999998 PP

                                       EEESSGGCTTSTTTEEEHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 174 ifgpgsglaHspnEyvdledlekgikvlarll 205
                                       i  p    +Hsp E +dl d++  +++l+++ 
  gi|385805513|ref|YP_005841911.1| 320 ISIPA-RYIHSPVEVIDLVDIHYSVELLKAFY 350
                                       88899.9****************999998875 PP

>> Peptidase_M18  Aminopeptidase I zinc metalloprotease (M18)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   2.4e-09   1.1e-05     312     432 .]     226     350 ..     193     350 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 2.4e-09
                                       EEEE--EE---....TTSGGGS-TTTS--TTSEEEEEE...ETTSSSTT-HHHHHHHHHHHHHHC-EEEEEEE-TTS CS
                     Peptidase_M18 312 liSaDvahaih....PnysskheenhapllnkGvvikv...nanqryatnsagaallkevaqkanvklQelvvrnds 381
                                        iS Dva a++       +++ e+++ ++l+kG+ ik+    ++ +  tn+a ++++ +va++ +++ Q  v+    
  gi|385805513|ref|YP_005841911.1| 226 QISPDVAIALDvttaNDVPDVDEQDQVAKLGKGPAIKIidgRSGSGLITNTAVLEKMISVAKERGIPYQAEVLT--- 299
                                       4555555554311113578899999************9332345569**********************87764... PP

                                       ----H.CHHHHHHHHT-EEEEEE-EEBSTTSSSEEEECCHHHHHHHHHHHCC CS
                     Peptidase_M18 382 pcGst.igpilaaktGirtiDlGaaqlsmHSireltgskdveeavklfkaFf 432
                                        +G+t   +i  +k G+    + ++   +HS+ e+++  d+ + v l+kaF+
  gi|385805513|ref|YP_005841911.1| 300 -GGTTdSSAIQLTKEGVPAGTISIPARYIHSPVEVIDLVDIHYSVELLKAFY 350
                                       .56552467899***************************************9 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.026   1.2e+02       2      38 ..      52      83 ..      51      85 .. 0.66
   2 !   14.3   0.0   5.4e-06     0.024      42     177 ..     188     332 ..     174     349 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.026
                                      EEEEESTTCESEEEEEEEE--B-TTTTCCT---TTTT CS
                     Peptidase_M28  2 viatlegkatdevlllgAHyDsvgvgrgpifvGAdDn 38
                                      vi   +g +  + l+++AH+D ++     i+  +dDn
  gi|385805513|ref|YP_005841911.1| 52 VISLKKGVS-GKKLMIAAHMDEISL----IVKYIDDN 83
                                      555555555.789********9886....33345665 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 5.4e-06
                                       HHHHHHHHHHCHHGGCCSSEEEEEEEESSCSGSSHHHHHHHH..HHC.........CCTTEEEEEEECS-SSSS--E CS
                     Peptidase_M28  42 vaalLelarvlaasgsrpkrgvrflffdaEEagllGSkafak..akp.........elkkiaavlnlDmvgsggkel 107
                                        ++ L++   ++     ++ ++ f+++  EE gl G++  a   + p         +++++  v + D v++ gk +
  gi|385805513|ref|YP_005841911.1| 188 LVVALKTFMEVE----PNDIDLYFVATVQEEVGLKGARTSAYqiS-PdvaialdvtTANDVPDVDEQDQVAKLGKGP 259
                                       444443333333....359**********************7421.2566666666666667777888888888888 PP

                                       EE.HHHHHHCHHHHHHHHHHHHHTT-TTSC.CEEEEES.STT-STTHHHH..TTT--EEEECTSSS-TTT.TSTTS CS
                     Peptidase_M28 108 lf.esgdkssselekelkalakpvgraaae.dpfders.grgrsDhspfl..kagvpvldlaetgfpevy.HtprD 177
                                        +  + ++s s+l   +  l k++++a++   p + ++ + g++D s+++  k+gvp+ ++     p +y H+p  
  gi|385805513|ref|YP_005841911.1| 260 AIkIIDGRSGSGLITNTAVLEKMISVAKERgIPYQAEVlTGGTTDSSAIQltKEGVPAGTI---SIPARYiHSPVE 332
                                       8875666666677777777777777777776777777767777888777666999***999...566666677755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); 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: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2653.30
//
Query:       gi|385805514|ref|YP_005841912.1|  [L=391]
Description: amidohydrolase [Fervidicoccus fontis Kam940]
Scores for complete 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   0.2    1.7e-35  122.6   0.2    1.2  1  Peptidase_M20  Peptidase family M20/M25/M40
    3.5e-16   59.1   0.2    1.6e-15   56.9   0.0    2.0  2  M20_dimer      Peptidase dimerisation domain
  ------ inclusion threshold ------
        1.8    8.5   6.6       0.48   10.3   2.6    2.1  2  PKcGMP_CC      Coiled-coil N-terminus of cGMP-dependent prote


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 !  122.6   0.2   2.9e-39   1.7e-35       1     201 [.      73     381 ..      73     386 .. 0.91

  Alignments for each domain:
  == domain 1  score: 122.6 bits;  conditional E-value: 2.9e-39
                                       EEEEES-BSS.TTCGGGSSSTTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTT. CS
                                       xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                     Peptidase_M20   1 llgsHlDvVp.eeetdgwttpfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggr. 75 
                                       ++++++D++p +ee+d    p+++ +e G+++++G+d ++ +v +a+ +l +l+d+    +g ++ll qp+EE g  
  gi|385805514|ref|YP_005841912.1|  73 AIRADMDALPiKEENDV---PYKSLNE-GFMHACGHDAHMSMVYGAALILNELRDKL---NGRVRLLYQPAEEEGTl 142
                                       589*******8888866...*****88.****************************8...*************8778 PP

                                       THHHHHHH.HHHTTTCESEEEEEEEESSSBTCHSTETEEEE.................................... CS
                                       xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................... RF
                     Peptidase_M20  76 gGakalle.gleerekvdavfelhieepgileagklaigvv.................................... 115
                                       gGak ++e g++  ++vd+++++h++ p ++e g ++++ +                                    
  gi|385805514|ref|YP_005841912.1| 143 GGAKPMIEeGAL--DGVDYILGMHVW-PELPE-GVIGYRKGpffaaadtikitvkgkgghgakpnlavdpimisakv 215
                                       ********6665..69**********.*****.88777777************************************ PP

                                       ........................................................................EEEEE CS
                                       ........................................................................xxxxx RF
                     Peptidase_M20 116 ........................................................................kveve 120
                                                                                                               ++++e
  gi|385805514|ref|YP_005841912.1| 216 vdalhtissrevdplepfvitigsihggtahniipdkvemlgtvrtlskelrdsmeerlrriirgvtsafngDFSLE 292
                                       **********************************************************************9889999 PP

                                       EEEEESHEEECCHHHHHHHHHHHHHHHTSCEEEEEES.SSBHTHHHH.TTTE.EEEEEE.SSG..GCTTS.TTTEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx.xxxx.xxxxxx.xxx..xxxxx.xxxxxx RF
                     Peptidase_M20 121 lleggapvtlndsplvkalaeaaeelfgekvelivsg.pggtdarff.agip.tvmifg.pgs..glaHs.pnEyvd 190
                                        +  g+pv +n++++++++++++e l+g++  ++ ++ +gg+d++++ +++p t+m++g  ++  g +++ +  +++
  gi|385805514|ref|YP_005841912.1| 293 -YLYGYPVLINHQEVTEIMKNVVEGLLGKEKVVESKPtMGGEDFAYYlEKVPgTFMFLGtYNEkmGYIYGvHTSKFN 368
                                       .99***********************998877777889*********99999899****555358555555555555 PP

                                       ..HHHHHHHHHHH CS
                                       ..xxxxxxxxxxx RF
                     Peptidase_M20 191 ..ledlekgikvl 201
                                         ++ l+ g  v+
  gi|385805514|ref|YP_005841912.1| 369 lnEKILPIGSSVF 381
                                       3377777776666 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.29   1.7e+03      14      44 ..     102     125 ..      92     139 .. 0.68
   2 !   56.9   0.0   2.7e-19   1.6e-15       8     102 ..     187     279 ..     184     285 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.29
                                       E-B-EEGG-TTTTB-HHHHHHHHHHCSCTTE CS
                         M20_dimer  14 kgkagHsgapgagaNAieklarllaeledee 44 
                                        g+++H +        ++ +a +l+el+d+ 
  gi|385805514|ref|YP_005841912.1| 102 CGHDAHMS-------MVYGAALILNELRDKL 125
                                       58888888.......3445555555555553 PP

  == domain 2  score: 56.9 bits;  conditional E-value: 2.7e-19
                                       EEEEEEE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC.....TCCTCCCCCEECCE-CCCCEESSEEEEEEEEEH CS
                         M20_dimer   8 ggkitvkgkagHsgapgagaNAieklarllaeledeegdiaeerslprttlnvtgiegGsaknvipdeaeakidiRl 84 
                                       + kitvkgk+gH++ p+ ++++i++ a+++++l+   +++    +l +  +++++i+gG+a n+ipd++e+  ++R+
  gi|385805514|ref|YP_005841912.1| 187 TIKITVKGKGGHGAKPNLAVDPIMISAKVVDALHTISSREV--DPLEPFVITIGSIHGGTAHNIIPDKVEMLGTVRT 261
                                       689*********************************99977..********************************** PP

                                       HHHHHHHHHHHHHHHHHT CS
                         M20_dimer  85 lpgedpeevleeieeile 102
                                       l +e +++ +e+++ i++
  gi|385805514|ref|YP_005841912.1| 262 LSKELRDSMEERLRRIIR 279
                                       *************99987 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 ?   10.3   2.6     8e-05      0.48      18      32 ..       9      23 ..       5      25 .. 0.91
   2 ?   -2.0   0.1      0.56   3.4e+03      25      31 ..     119     125 ..     118     126 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 8e-05
                         PKcGMP_CC 18 aekdeEIqELrskLD 32
                                      +ek++EI ELr+ L+
  gi|385805514|ref|YP_005841912.1|  9 REKEKEIVELRRLLH 23
                                      69**********999 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.56
                         PKcGMP_CC  25 qELrskL 31 
                                       +ELr kL
  gi|385805514|ref|YP_005841912.1| 119 NELRDKL 125
                                       7999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2585.91
//
Query:       gi|385805515|ref|YP_005841913.1|  [L=496]
Description: Na+ symporter [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-18   65.4  33.3    9.1e-18   64.3  33.3    1.6  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 !   64.3  33.3   5.1e-22   9.1e-18       3     398 ..      41     420 ..      39     428 .. 0.80

  Alignments for each domain:
  == domain 1  score: 64.3 bits;  conditional E-value: 5.1e-22
                               SSF   3 lagrsltgfvlglslaasnisaasfvGlaGavaasGlavvllelgalllvlllllllaerlr....nagalTlpdyl 75 
                                       ++gr+ + + +   ++++   a  ++ ++G ++  G  ++  ++   +++ +l++ +a+rl     ++g +T  dy+
  gi|385805515|ref|YP_005841913.1|  41 IGGRKFGTLIVWFLMGGDIYTAYALISVPGGAYGQGGFILYSAVYGAMAYPFLYY-VAPRLYliakKKGMITGGDYV 116
                                       689999999999999999999************9998887777777777777666.5666555999*********** PP

                               SSF  76 skRfkgkrilvylsalslllvitlklsvdlvggaklielalGlnyetavlllaaltalYtviGGllAvvytdtiqav 152
                                       ++Rfk+   l +l +l+ ++++  +++ ++vg  k++ +a+ + +  + ++  +++a +tv+ Gl+   +  +i+ +
  gi|385805515|ref|YP_005841913.1| 117 RERFKSDT-LSLLISLTGIIAMLPYIALQIVGI-KYVLQAMNFPIVESYIIAFLIVAAFTVVAGLRGPALGAIIKDI 191
                                       ********.555555666778899******976.66667899**********************************9 PP

                               SSF 153 lmlvgalilliivllevGgleslveklkeaapkvvdlltpdslkllrdpltalslwlglvlGvagl..philvRfla 227
                                       l+ +  ++++++  + + g++ +++ l + +    + + p +l      +  + l  +++ G+a l  p  l  +l 
  gi|385805515|ref|YP_005841913.1| 192 LLWAVIITITVVLAIRFDGFSLVFKSLDA-QG--LNYMIPPNL-----MIGYMTL--AFGNGIAWLlfPNLLTGILG 258
                                       99888888888888888899999876543.33..466667775.....3444444..44444444466********* PP

                               SSF 228 akdakailkgvlkltivlilvligmisiilfaiklagavpkavgtevgvsniaypeLvvkllpnllaGlllavmlAa 304
                                        kdak+i k  +  ++v  + ++   + +l a +            ++vs +a+p      + + +  +  a+++  
  gi|385805515|ref|YP_005841913.1| 259 SKDAKTIKKNSVL-LPVYQVWMLILAIFGLVALSENL-------VPNKVSSLAFPSVLTTYFSPTFVSIAFAAIIIG 327
                                       *******998764.45555555543333444333222.......2468899**************999999999988 PP

                               SSF 305 imstltslllsassaftkDlYkkirrkasakekelvgvsriivlvvislaillavqeeqkgvlklvelafaglasav 381
                                        m   + + lsa+ ++t+ +Y + + k+ a+e+++v v+ri v ++i+ +++ +++++ +g++++  +++       
  gi|385805515|ref|YP_005841913.1| 328 AMIPASLQALSAANLITRNIYLQYINKQ-ASERKQVLVGRISVFIMIVASLIFVLTPAASGLIFYLLTMSYAWLLQT 403
                                       888889999**************99999.999999999999999999999999999999998887777777777788 PP

                               SSF 382 lavillalfwkrvneqG 398
                                       l+ i+l+++w+ + ++ 
  gi|385805515|ref|YP_005841913.1| 404 LPAIILSMYWHSLDKYS 420
                                       999*******9887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (496 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1018  (0.0567795); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); 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: 0.71u 0.32s 00:00:01.03 Elapsed: 00:00:00.52
# Mc/sec: 2846.35
//
Query:       gi|385805516|ref|YP_005841914.1|  [L=73]
Description: hypothetical protein FFONT_0472 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-12   46.8   5.5    2.9e-12   46.3   5.5    1.1  1  DUF3311   Protein of unknown function (DUF3311)


Domain annotation for each model (and alignments):
>> DUF3311  Protein of unknown function (DUF3311)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.3   5.5   1.6e-16   2.9e-12       2      55 ..      18      71 ..      17      72 .. 0.91

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 1.6e-16
                           DUF3311  2 lllvpvlvalllvpfynrvdpvllGlPffywwqllwvllasvvtwlayrlakre 55
                                      l+l+p    +   p+ynr +p+l G+Pf+yw+++ w+++  v+t++++++ +re
  gi|385805516|ref|YP_005841914.1| 18 LMLIPWTALVFTAPIYNRKEPYLGGWPFLYWYLFSWIFIQPVLTFIVFKFIDRE 71
                                      7899966666678************************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      195  (0.0108762); 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 0.29s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 489.56
//
Query:       gi|385805517|ref|YP_005841915.1|  [L=1257]
Description: subtilisin [Fervidicoccus fontis Kam940]
Scores for 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  120.3   0.7    1.6e-34  119.5   0.7    1.3  1  Peptidase_S8  Subtilase family
  ------ inclusion threshold ------
       0.41   10.6   1.8       0.51   10.3   0.2    2.0  2  DUF2141       Uncharacterized protein conserved in bacteria (


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 !  119.5   0.7   1.8e-38   1.6e-34       1     298 []     182     643 ..     182     648 .. 0.84

  Alignments for each domain:
  == domain 1  score: 119.5 bits;  conditional E-value: 1.8e-38
                                       -TT-EEEEECS-B-TT-TTTGGGEEE..EEEE---TTSG...................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..................................... RF
                      Peptidase_S8   1 gkgvlvavlDtGvdpshpdlsvttdgerklvdvideegag..................................... 40 
                                       g+gv++a++DtGvd+ hpdl++++  ++ +  +   + ++                                     
  gi|385805517|ref|YP_005841915.1| 182 GSGVKIAIVDTGVDYAHPDLQSKLIYYVGSYRTVYGTTSNirepmvldadesqviltnsfqanssgyinvgqnyfvv 258
                                       79*******************9999999997777777777999**99999999999999999999999999999999 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                      Peptidase_S8  41 ............................................................................. 40 
                                                                                                                    
  gi|385805517|ref|YP_005841915.1| 259 ldpyyetvppsyssyyvgnipsssgiykfgmtleytvaglvsvgvlmsdpdtpgnytllvidanndgvfgdngdivv 335
                                       99999999999999999999999999999999999999999999999998888888888888888888888888888 PP

                                       ............................GGEETT-SS-TT-SC-SSS.........HHHHHHHHHH-B..SSSSSB- CS
                                       ............................xxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8  41 ............................fngadsettstnwarddngnsie.....HGthvAGiaaanapeegekng 84 
                                                                   +  +++ ++ + w+ +++  s+      HGt +A+ aa+n    g +ng
  gi|385805517|ref|YP_005841915.1| 336 tydgnrilyspeedlslgvaggffydvgLWFNSYGAYYPGWDLNGDYISLFydfegHGTSCASAAAGN----GIVNG 408
                                       88888888888888888888888888776666777777777777776555488999************....***** PP

                                       SSTTSEEEEEE-SSTTSB-HH..HHHHHH.........HHHHHHCT-SEEEE-EE...SCETTCHHCHHHHHH.... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxx.... RF
                      Peptidase_S8  85 vapgakilsvkvldtsggsmetgtelira.........ieeaaedkvdvinmslg...estslpktgrsieal.... 145
                                       +a +a +++vk+l   + +m     l++          i++  e+++dvi+ s+g     ++ + +g +ie +    
  gi|385805517|ref|YP_005841915.1| 409 IAKDANVIGVKALWYGDVEMGL---LWASgfdvnnngtIYYTGEKRADVISDSWGisnFIYDISGFGYDIESMlina 482
                                       ********88888777777632...2222345555566999999***********7665566777777788776676 PP

                                       .....HHHHHH.CCT-EEEEE--SS-T-HHEEE-TTCEECTTTSTTCEEEEEES..............TTSSB-TT- CS
                                       .....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..............xxxxxxxxx RF
                      Peptidase_S8 146 .....ainravnkkgvlvviSaGNngktgsslqagspvgtpstsknvitvgayt..............tegkiapfS 203
                                            +++      g+lvv +aGN g      +   +v +p+ + +++tv+a t              t+++i  +S
  gi|385805517|ref|YP_005841915.1| 483 lttpgFLDPSF--PGILVVQAAGNGG------PGFGTVTSPGAAVGALTVSASTlwkvyqvgygyggyTQDNIIMWS 551
                                       65443333333..4************......999****************************************** PP

                                       -B-TT.......-EEEE-S-CCCCCCCCCHHHTTTHHEEEE-SHHHCHHHHHHHHHHHHHHHTT........--HHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxx RF
                      Peptidase_S8 204 srGpssdgklkpdivapGgnivstwsrqsnnsaglssyqsmsGTSmAsPnaagaaAlllsalpk........ltpet 272
                                        rGp+  g lkpdiv  G+     ++  + +   +  y+ + GTS A+P+ aga+All++al++          p +
  gi|385805517|ref|YP_005841915.1| 552 ARGPVPMGYLKPDIVDVGAW---GITAAPIPI--Y--YNIFGGTSYATPLTAGAVALLIQALEEkvgssansVPPSM 621
                                       *******************8...444444333..3..99*********************99999*99988888899 PP

                                       HHHHHHCCS-EE......SSSSSSTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 273 vraallntAqdlgkadniesfaqGaG 298
                                       ++++l+ntA+ l     + ++ qGaG
  gi|385805517|ref|YP_005841915.1| 622 LKEILMNTADSL----GYMPYDQGAG 643
                                       *********877....3444555555 PP

>> DUF2141  Uncharacterized protein conserved in bacteria (DUF2141)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1      0.84   7.6e+03      53      71 ..     311     328 ..     308     331 .. 0.79
   2 ?   10.3   0.2   5.7e-05      0.51      53      95 ..     817     859 ..     812     865 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.84
                           DUF2141  53 pGtYAvavfhDengngkld 71 
                                       pG+Y + v+ D n++g + 
  gi|385805517|ref|YP_005841915.1| 311 PGNYTLLVI-DANNDGVFG 328
                                       899999876.899999776 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 5.7e-05
                           DUF2141  53 pGtYAvavfhDengngkldknllgiPkEgyGfSnnakillgpP 95 
                                          YA + + D+ngng  d+n l + + gy++Sn  +i ++ P
  gi|385805517|ref|YP_005841915.1| 817 IDVYAYVWINDTNGNGVPDRNELAFINVGYATSNYNSIEISNP 859
                                       568*******************************999988877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.78u 0.33s 00:00:01.11 Elapsed: 00:00:00.52
# Mc/sec: 7227.46
//
Query:       gi|385805518|ref|YP_005841916.1|  [L=893]
Description: hypothetical protein FFONT_0474 [Fervidicoccus fontis Kam940]
Scores for complete 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-07   29.1  41.2    3.8e-06   27.0  26.6    2.6  2  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
    6.6e-05   22.9   3.3    6.6e-05   22.9   3.3    2.7  2  DUF1664          Protein of unknown function (DUF1664)
    0.00026   18.7   7.2    0.00035   18.3   7.2    1.0  1  DUF3584          Protein of unknown function (DUF3584)
    0.00052   20.1   9.1      0.013   15.6   1.2    2.7  3  MbeD_MobD        MbeD/MobD like
    0.00062   19.9   8.9     0.0016   18.5   3.0    2.8  3  COG2             COG (conserved oligomeric Golgi) complex com
    0.00075   18.5   6.3     0.0011   17.9   6.3    1.1  1  Spc7             Spc7 kinetochore protein
    0.00091   18.6   6.5     0.0017   17.7   6.5    1.3  1  SF-assemblin     SF-assemblin/beta giardin
    0.00099   19.4  37.5      0.052   13.9  11.3    4.5  4  LPP              Lipoprotein leucine-zipper
     0.0015   18.4   9.2     0.0024   17.8   9.2    1.2  1  Apolipoprotein   Apolipoprotein A1/A4/E domain
     0.0017   18.6   4.8     0.0017   18.6   4.8    4.1  3  DUF948           Bacterial protein of unknown function (DUF94
     0.0025   18.1  43.7      0.031   14.6  11.7    2.9  2  Alanine_zipper   Alanine-zipper, major outer membrane lipopro
     0.0043   16.1   7.8     0.0069   15.4   7.4    1.5  1  IFT57            Intra-flagellar transport protein 57
     0.0048   14.9  12.6     0.0073   14.3  12.6    1.2  1  Prominin         Prominin
     0.0055   16.5  16.9     0.0057   16.4  15.6    1.6  1  Laminin_I        Laminin Domain I
  ------ inclusion threshold ------
      0.011   14.0   3.8      0.016   13.4   3.8    1.2  1  EzrA             Septation ring formation regulator, EzrA
       0.02   15.3   7.0      0.054   13.9   0.4    3.4  3  FlaC_arch        Flagella accessory protein C (FlaC)
      0.076   13.5   3.9       0.11   12.9   3.9    1.1  1  Fez1             Fez1
       0.15   11.3   4.0       0.31   10.3   4.0    1.5  1  CorA             CorA-like Mg2+ transporter protein
       0.21   11.3   4.0       0.37   10.4   4.0    1.3  1  MAGE             MAGE family
       0.23   11.5   2.7        3.9    7.5   0.4    2.2  2  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
       0.24   11.5   3.3       0.42   10.7   0.6    2.2  2  DHR10            Designed helical repeat protein 10 domain
       0.27   11.5  12.3       0.86    9.9   5.1    2.7  2  BLOC1_2          Biogenesis of lysosome-related organelles co
       0.29   11.6  17.6        9.4    6.8   8.6    3.9  4  NPV_P10          Nucleopolyhedrovirus P10 protein
       0.29   11.5  15.6       0.31   11.4   6.0    2.5  2  Syntaxin_2       Syntaxin-like protein
        0.3    8.8   0.8       0.44    8.3   0.8    1.1  1  Myosin_tail_1    Myosin tail
       0.31   10.1   7.7       0.49    9.4   7.7    1.3  1  AIP3             Actin interacting protein 3
       0.31   11.0   5.3       0.28   11.2   1.5    2.1  2  YscO             Type III secretion protein YscO
       0.42   10.5  12.5       0.36   10.7  10.4    1.8  2  Vip3A_N          Vegetative insecticide protein 3A N terminal
       0.46    9.3  11.5       0.83    8.5   3.3    2.5  2  DUF677           Protein of unknown function (DUF677)
        0.5   11.5   1.5       0.58   11.3   0.4    1.6  1  SOGA             Protein SOGA
        0.5   10.7   7.1       0.51   10.7   3.6    2.2  2  YlqD             YlqD protein
       0.57    9.4   8.9       0.87    8.8   8.9    1.2  1  FmiP_Thoc5       Fms-interacting protein/Thoc5
       0.59    9.4  18.8        2.6    7.3  18.0    2.1  1  DUF4407          Domain of unknown function (DUF4407)
       0.62   10.2  19.3       0.13   12.5   3.5    3.2  3  COG5             Golgi transport complex subunit 5
       0.62   10.2   6.8       0.13   12.3   0.5    2.7  3  TolA_bind_tri    TolA binding protein trimerisation
       0.62   10.0   5.4        9.5    6.2   0.0    2.9  2  Prefoldin        Prefoldin subunit
       0.79    9.5   5.1       0.95    9.3   2.9    2.1  2  Phage_GP20       Phage minor structural protein GP20
       0.83    8.5   9.8        1.2    8.0   9.8    1.1  1  DUF812           Protein of unknown function (DUF812)
       0.94    9.1   6.6        1.5    8.5   6.6    1.2  1  BAR_3            BAR domain of APPL family
       0.95    9.1  30.6        0.2   11.4  13.5    2.2  2  DUF745           Protein of unknown function (DUF745)
          1    8.7   3.7        2.1    7.7   1.0    2.0  2  DUF4618          Domain of unknown function (DUF4618)
        1.2    9.6  28.3       0.19   12.2  22.6    2.1  2  T3SSipB          Type III cell invasion protein SipB
        1.3    8.9  10.2         28    4.6  10.5    2.1  1  DASH_Spc19       Spc19
        1.7    8.8   9.4        1.8    8.7   5.1    2.7  3  Vps51            Vps51/Vps67
        1.7    8.1   8.1         12    5.3   8.1    1.9  1  Filament         Intermediate filament protein
        2.1    8.1   5.6        8.4    6.1   0.1    2.3  2  DUF842           Eukaryotic protein of unknown function (DUF8
        2.1    8.2   7.0        4.8    7.1   3.6    3.1  2  ECR1_N           Exosome complex exonuclease RRP4 N-terminal 
        2.3    8.0   6.9       0.91    9.3   1.9    2.6  3  ATP-synt_D       ATP synthase subunit D
        2.3    8.4   9.5        2.6    8.3   0.4    2.4  2  FliJ             Flagellar FliJ protein
        2.9    7.6   4.3         18    4.9   0.4    2.3  2  DotU             Type VI secretion system protein DotU
        2.9    8.0   6.6          7    6.8   1.5    2.2  3  Tropomyosin_1    Tropomyosin like
        3.6    7.9   7.6        3.7    7.8   3.6    2.3  2  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
        3.8    7.6  21.6        3.1    7.9  15.3    2.3  2  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
        3.8    7.7  14.1       0.67   10.1   6.6    2.3  2  Fib_alpha        Fibrinogen alpha/beta chain family
          4    6.9  32.2         11    5.5  31.5    1.9  1  MscS_porin       Mechanosensitive ion channel porin domain
        4.2    6.4   9.7        6.7    5.7   9.7    1.3  1  CCDC144C         CCDC144C protein coiled-coil region
        4.2    7.6  14.3        3.6    7.9   1.4    3.7  3  Spc24            Spc24 subunit of Ndc80
        4.4    7.8  10.4        3.8    8.0   3.7    2.4  2  Snapin_Pallidin  Snapin/Pallidin
        4.7    7.8   6.2         21    5.7   2.2    2.5  2  HisKA_3          Histidine kinase
        4.9    7.7  32.4       0.99    9.9   1.5    3.4  3  T7SS_ESX_EspC    Excreted virulence factor EspC, type VII ESX
          5    6.6   8.5        7.8    6.0   8.5    1.2  1  CCDC84           Coiled coil protein 84
        6.8    6.5  10.2        1.5    8.6   3.9    2.7  2  DASH_Duo1        DASH complex subunit Duo1
        7.9    5.0  15.2         11    4.6  15.2    1.1  1  WEMBL            Weak chloroplast movement under blue light
          8    6.2  13.1         41    3.9  13.1    1.9  1  SKA1             Spindle and kinetochore-associated protein 1
        8.9    6.5   7.8         21    5.2   0.4    2.5  2  RasGAP_C         RasGAP C-terminus


Domain annotation for each model (and alignments):
>> 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 !   27.0  26.6   1.4e-08   3.8e-06      28     132 ..     691     794 ..     683     798 .. 0.89
   2 !    9.1  18.7    0.0045       1.2      34     109 ..     765     842 ..     763     859 .. 0.71

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 1.4e-08
                      Baculo_PEP_C  28 qnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsiltnLlssvtNi 104
                                        +v + ++l++++ +i +++n+ +++l+s l++++t+l+++lt+L++ lna   t++n+L+++ns l+++ s++  +
  gi|385805518|ref|YP_005841916.1| 691 TEVATYSDLQNAVSTITSSINSAQSALSSQLTSVSTQLSNSLTTLQNNLNAAVGTINNALNGINSSLNTMSSQLSTL 767
                                       45677799********************************************************************* PP

                      Baculo_PEP_C 105 nstLnnllqalnnldlgalsqeledald 132
                                        + +n+l +++n l + ++sq+ ++a +
  gi|385805518|ref|YP_005841916.1| 768 SNNVNSLSTSVNQL-SSQVSQAVTAAQN 794
                                       *************9.4566666665554 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0045
                      Baculo_PEP_C  34 aqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq..dtlrneLtnlnsiltnLlssvtNinstL 108
                                       + l++ ++++ t++n+ls+++++++++ +++ ++++++ t+a na +   +  n++++l s+++nL s+v N  s+ 
  gi|385805518|ref|YP_005841916.1| 765 STLSNNVNSLSTSVNQLSSQVSQAVTAAQNAATSASSAATQAQNAATaaSNAANQINALSSQVSNLSSQVSNAVSAA 841
                                       45677777777777777777777777777777777777777777766667777888888888888888888776654 PP

                      Baculo_PEP_C 109 n 109
                                       n
  gi|385805518|ref|YP_005841916.1| 842 N 842
                                       4 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   3.3   2.4e-07   6.6e-05       7     122 ..     672     783 ..     668     789 .. 0.73
   2 ?    1.8   0.4      0.84   2.3e+02      56     117 ..     788     834 ..     779     849 .. 0.43

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 2.4e-07
                           DUF1664   7 ivpaavvgavgYgyvwwkGwklsdlmfvTkrslsdavesvskqleqvseslaatkrhLssridrvdkkld.eqkeis 82 
                                        +p++ +  ++Y+yv     +l++   +T   l++av+++++++++ +++l+++    s ++ +  ++l+ + +++ 
  gi|385805518|ref|YP_005841916.1| 672 STPVIQATDASYAYVI---NNLTE--VATYSDLQNAVSTITSSINSAQSALSSQLTSVSTQLSNSLTTLQnNLNAAV 743
                                       5677777777777776...45555..489999*************99988888777777777654444440445666 PP

                           DUF1664  83 keikeevtevredlseigedvesvkeavegleskleriee 122
                                         i++ ++ +++ l++++++++++++ v++l ++++++++
  gi|385805518|ref|YP_005841916.1| 744 GTINNALNGINSSLNTMSSQLSTLSNNVNSLSTSVNQLSS 783
                                       7788888888888888888888888888888888888764 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.84
                           DUF1664  56 slaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskl 117
                                       +++a+++  +s               +++ + + +++    s+  ++++++++ v++l s++
  gi|385805518|ref|YP_005841916.1| 788 AVTAAQNAATS---------------ASSAATQAQNAATAASNAANQINALSSQVSNLSSQV 834
                                       33333333333...............333333333333333333334444444444443333 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   7.2   1.3e-06   0.00035     366     531 ..     695     857 ..     685     870 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.3e-06
                           DUF3584 366 eldaltekhqdvqekydrrkqkikeeleeeleklkerleaireekdrlkaaieealealesqlrkqleaqkeelnee 442
                                        +  l +++  +++  +  +++++++l  ++ +l ++l  ++++ ++   +i++al+ ++s+l+  +  q + l+++
  gi|385805518|ref|YP_005841916.1| 695 TYSDLQNAVSTITSSINSAQSALSSQLTSVSTQLSNSLTTLQNNLNAAVGTINNALNGINSSLN-TMSSQLSTLSNN 770
                                       56778899999**************************9999999999999**************.888999999999 PP

                           DUF3584 443 ekelesrlselklrldsatateEeleqieeadealekaqeelekaeaevealqaeeeqlrkkrdeadealqkaerrl 519
                                          l  ++++l  ++ +a        + + a +a  +aq+++++a+++ ++ +a   q+ + + + ++a + a++++
  gi|385805518|ref|YP_005841916.1| 771 VNSLSTSVNQLSSQVSQAVTAAQ--NAATSASSAATQAQNAATAASNAANQINALSSQVSNLSSQVSNAVSAANAAT 845
                                       99999999999999988766554..4556677889999999999999999999999999999999999999999999 PP

                           DUF3584 520 eqlrqaleelee 531
                                        q  +a++++  
  gi|385805518|ref|YP_005841916.1| 846 TQASDAASKAAY 857
                                       999999887665 PP

>> MbeD_MobD  MbeD/MobD like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.2      0.84   2.3e+02      30      59 ..     696     729 ..     694     741 .. 0.62
   2 !   15.6   1.2   4.6e-05     0.013       2      66 ..     722     786 ..     721     789 .. 0.95
   3 !    8.6   0.6     0.007       1.9      45      66 ..     809     835 ..     795     839 .. 0.55

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.84
                         MbeD_MobD  30 faelqrmfe.ltqrena...aLseqvtgLsqQVe 59 
                                       + +lq+ ++ +t+  n+   aLs q t  s Q  
  gi|385805518|ref|YP_005841916.1| 696 YSDLQNAVStITSSINSaqsALSSQLTSVSTQLS 729
                                       6666654331333333334499999999999964 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 4.6e-05
                         MbeD_MobD   2 telekqLLsAlEqLQqdYeqrlqeWesafaelqrmfeltqrenaaLseqvtgLsqQVesLseqvr 66 
                                       t   +qL + l  LQ++ +      ++a + +    + ++ +++ Ls+ v+ Ls  V++Ls qv+
  gi|385805518|ref|YP_005841916.1| 722 TSVSTQLSNSLTTLQNNLNAAVGTINNALNGINSSLNTMSSQLSTLSNNVNSLSTSVNQLSSQVS 786
                                       778899*********************************************************97 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.007
                         MbeD_MobD  45 a.....aLseqvtgLsqQVesLseqvr 66 
                                       a        +q++ Ls QV +Ls qv+
  gi|385805518|ref|YP_005841916.1| 809 AataasNAANQINALSSQVSNLSSQVS 835
                                       434433233455555555555555553 PP

>> COG2  COG (conserved oligomeric Golgi) complex component, COG2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1      0.28        79      72     105 ..     697     730 ..     686     743 .. 0.76
   2 !   18.5   3.0   5.9e-06    0.0016      31     113 ..     717     799 ..     714     813 .. 0.88
   3 ?    3.1   0.3      0.33        92      77     113 ..     812     848 ..     801     868 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.28
                              COG2  72 eevesplaaarkkvesvreklsereeevesklee 105
                                       + ++  ++++++ ++s++++ls + + v+ +l++
  gi|385805518|ref|YP_005841916.1| 697 SDLQNAVSTITSSINSAQSALSSQLTSVSTQLSN 730
                                       5677788888888888888888888888888875 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 5.9e-06
                              COG2  31 lrrdLeaylkllekellelvnedyadFvslSghLvglqeeleevesplaaarkkvesvreklsereeeveskleeak 107
                                       l+++L + +++l+++l  l n+  a    + ++L g++++l++++s+l+++ ++v+s+  ++++ +++v++ + +a+
  gi|385805518|ref|YP_005841916.1| 717 LSSQLTSVSTQLSNSLTTLQNNLNAAVGTINNALNGINSSLNTMSSQLSTLSNNVNSLSTSVNQLSSQVSQAVTAAQ 793
                                       789999999999999998877666668899********************************************999 PP

                              COG2 108 eleekr 113
                                       +++   
  gi|385805518|ref|YP_005841916.1| 794 NAATSA 799
                                       887665 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.33
                              COG2  77 plaaarkkvesvreklsereeeveskleeakeleekr 113
                                         ++a ++++++ +++s+ +++v++ +++a++++ + 
  gi|385805518|ref|YP_005841916.1| 812 AASNAANQINALSSQVSNLSSQVSNAVSAANAATTQA 848
                                       5677788888888888888888888888887776655 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   6.3     4e-06    0.0011     149     293 ..     697     845 ..     689     863 .. 0.56

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 4e-06
                              Spc7 149 egleedkelLekqeeeldell.peleeekaeleeeleklqeaaeelesid.......keeLeelreelaelkaeiee 217
                                       ++l++  ++++++ + ++++l  +l++  ++l++ l++lq+  +             + +L+++ ++l++l++++++
  gi|385805518|ref|YP_005841916.1| 697 SDLQNAVSTITSSINSAQSALsSQLTSVSTQLSNSLTTLQNNLNAAVGTInnalngiNSSLNTMSSQLSTLSNNVNS 773
                                       55555555555555555443314555555566666666665333333333000001134666666666666666666 PP

                              Spc7 218 kkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkaleeltgwkivslsgst 293
                                       +++ +++l +q+ +  ++ ++++++ s++ ++ ++a        +  ++++++l ++v++l ++   ++  +++ t
  gi|385805518|ref|YP_005841916.1| 774 LSTSVNQLSSQVSQAVTAAQNAATSASSAATQAQNAAT----AASNAANQINALSSQVSNLSSQVSNAVSAANAAT 845
                                       66666666666655555555554444444444443333....3446778899999999999988887777776554 PP

>> SF-assemblin  SF-assemblin/beta giardin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   6.5   6.2e-06    0.0017      58     198 ..     707     848 ..     696     858 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 6.2e-06
                      SF-assemblin  58 aesdkdiqeefkkeikklqekikeevddlalelkkaveelnekinnveanvenekakrrdaieklakelvkelnele 134
                                         s +  q+ ++++   +  +  + +++l+ +l+ av  +n+ +n +++ + n   ++ + + +  ++l  ++n+l 
  gi|385805518|ref|YP_005841916.1| 707 TSSINSAQSALSSQLTSVSTQLSNSLTTLQNNLNAAVGTINNALNGINSSL-NTMSSQLSTLSNNVNSLSTSVNQLS 782
                                       566778899*****************************************9.6789999****************** PP

                      SF-assemblin 135 aaideEkaerkkk..edqlnkkveEdlkklsakidtEkniRdsevsaltaeveeiklekklaneql 198
                                       +++ +  +  ++      +    + + +    +  +  n+  s+vs+l ++v ++    ++a  q 
  gi|385805518|ref|YP_005841916.1| 783 SQVSQAVTAAQNAatSASSAATQAQNAATAASNAANQINALSSQVSNLSSQVSNAVSAANAATTQA 848
                                       ***997655544400444555555566666666777889999************999988887765 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.5      0.88   2.4e+02      10      31 ..     697     718 ..     694     721 .. 0.89
   2 ?    1.2   0.3       1.8   4.9e+02      10      22 ..     737     749 ..     717     763 .. 0.46
   3 !   13.9  11.3   0.00019     0.052       1      40 [.     763     802 ..     763     819 .. 0.88
   4 !   13.5   7.8   0.00026     0.071       1      37 [.     819     855 ..     814     858 .. 0.64

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.88
                               LPP  10 sqLkskvdqlssdvnsakaaaq 31 
                                       s+L++ v+ ++s +nsa++a+ 
  gi|385805518|ref|YP_005841916.1| 697 SDLQNAVSTITSSINSAQSALS 718
                                       78999************99975 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 1.8
                               LPP  10 sqLkskvdqlssd 22 
                                       ++L++ v  +++ 
  gi|385805518|ref|YP_005841916.1| 737 NNLNAAVGTINNA 749
                                       1223333333333 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 0.00019
                               LPP   1 kldeLssqVsqLkskvdqlssdvnsakaaaqaakeEAaRA 40 
                                       +l+ Ls++V++L++ v+qlss+v++a +aaq+a   A+ A
  gi|385805518|ref|YP_005841916.1| 763 QLSTLSNNVNSLSTSVNQLSSQVSQAVTAAQNAATSASSA 802
                                       5789*****************************9999876 PP

  == domain 4  score: 13.5 bits;  conditional E-value: 0.00026
                               LPP   1 kldeLssqVsqLkskvdqlssdvnsakaaaqaakeEA 37 
                                       +++ LssqVs+L+s+v++  s +n+a ++a +a   A
  gi|385805518|ref|YP_005841916.1| 819 QINALSSQVSNLSSQVSNAVSAANAATTQASDAASKA 855
                                       4666777777777777666666666666666665555 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   9.2   8.7e-06    0.0024      23     178 ..     696     849 ..     678     859 .. 0.59

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 8.7e-06
                                       HHH..HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHCCCHHHHHHHHHCCHHHHHHHH...HHHHCHHCCH CS
                    Apolipoprotein  23 laq..elrdrlskeleelrarlraeleevrarlepyrdevqeqlgqnleelrqrlapyteelre...rlaadaeelq 94 
                                       +++  +++ +++   ++++ +l+++l++v  +l++ +  +q++l++ +  +++ l+ + + l+    +l+  + +  
  gi|385805518|ref|YP_005841916.1| 696 YSDlqNAVSTITSSINSAQSALSSQLTSVSTQLSNSLTTLQNNLNAAVGTINNALNGINSSLNTmssQLS-TLSNNV 771
                                       4334357777777778888888888888888888888888888888888888887777777766443222.444445 PP

                                       HCHCCHCHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH-----..-----SSSHHHHHHHTS-TTSHHHH CS
                    Apolipoprotein  95 eqlavyaeelrerlerhvealkarlapyveelrqklaerleelkeslaphaeeveerlssrveelrekleeqaeelr 171
                                       ++l++  ++l ++++++v a +   +  +  + q  a+++    +++a++  ++     s+v++l+ +++ ++++ +
  gi|385805518|ref|YP_005841916.1| 772 NSLSTSVNQLSSQVSQAVTAAQNAATSASSAATQ--AQNAATAASNAANQINALS----SQVSNLSSQVSNAVSAAN 842
                                       5556666667777777777777766666666666..5555555555555555555....444444444444333333 PP

                                       HS--XXX CS
                    Apolipoprotein 172 erleanl 178
                                       +   +++
  gi|385805518|ref|YP_005841916.1| 843 AATTQAS 849
                                       3333322 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.4       2.1   5.7e+02      22      67 ..     697     743 ..     682     749 .. 0.48
   2 !   18.6   4.8   6.1e-06    0.0017      22      86 ..     737     801 ..     731     804 .. 0.93
   3 ?    7.5   1.0     0.018       4.9      24      64 ..     809     849 ..     803     856 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 2.1
                            DUF948  22 lklkktldeaaatieelekqvdpilkev.edllakvnelledvnekl 67 
                                         l++ ++ ++++i++ ++ + + l+ v ++l +   +l++++n  +
  gi|385805518|ref|YP_005841916.1| 697 SDLQNAVSTITSSINSAQSALSSQLTSVsTQLSNSLTTLQNNLNAAV 743
                                       44555566666666666544444333331223333333444455444 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 6.1e-06
                            DUF948  22 lklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvse 86 
                                       ++l+  +  ++++++++++ ++ ++ ++ +l ++vn l   vn+ + +v + ++a++++++s s+
  gi|385805518|ref|YP_005841916.1| 737 NNLNAAVGTINNALNGINSSLNTMSSQLSTLSNNVNSLSTSVNQLSSQVSQAVTAAQNAATSASS 801
                                       5788899999***************************************************9886 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.018
                            DUF948  24 lkktldeaaatieelekqvdpilkevedllakvnelledvn 64 
                                       ++  +++aa++i+ l +qv +++ +v ++++ +n+ + + +
  gi|385805518|ref|YP_005841916.1| 809 AATAASNAANQINALSSQVSNLSSQVSNAVSAANAATTQAS 849
                                       5667789999***********************99776654 PP

>> Alanine_zipper  Alanine-zipper, major outer membrane lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4  20.6   0.00027     0.075       2      60 ..     763     821 ..     762     823 .. 0.67
   2 !   14.6  11.7   0.00011     0.031       2      41 ..     819     858 ..     818     862 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00027
                    Alanine_zipper   2 qveelqakadqaeqdaaaaksaadeAkskAdeAaarAenAeaaAeeAqkaAeeanerad 60 
                                       q++ l + ++++++ +++++s+ ++A ++A+ Aa+ A  A+ +A+ A+ aA+ a+ +++
  gi|385805518|ref|YP_005841916.1| 763 QLSTLSNNVNSLSTSVNQLSSQVSQAVTAAQNAATSASSAATQAQNAATAASNAANQIN 821
                                       56667777777777777777777777777777777777777777777777777766665 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 0.00011
                    Alanine_zipper   2 qveelqakadqaeqdaaaaksaadeAkskAdeAaarAenA 41 
                                       q+ +l +++ ++++++++a saa++A ++A +Aa++A+ A
  gi|385805518|ref|YP_005841916.1| 819 QINALSSQVSNLSSQVSNAVSAANAATTQASDAASKAAYA 858
                                       7888999999999999999999999999999999999876 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   7.4   2.5e-05    0.0069     232     332 ..     717     817 ..     694     837 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.5e-05
                             IFT57 232 hkksieeslpetksqlkklhedisktlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegvseltrela 308
                                       +++++++  ++++++l+ l+++++ ++  i++  + +ns+l+++ ++++++++++++++ +++qls++vs+  +  +
  gi|385805518|ref|YP_005841916.1| 717 LSSQLTSVSTQLSNSLTTLQNNLNAAVGTINNALNGINSSLNTMSSQLSTLSNNVNSLSTSVNQLSSQVSQAVTAAQ 793
                                       33344555555555666677777777777777777777777777777777777777777777777777777777776 PP

                             IFT57 309 eiseelekvkqemeergssmtDgs 332
                                       +  +  +++ ++ ++  + +++++
  gi|385805518|ref|YP_005841916.1| 794 NAATSASSAATQAQNAATAASNAA 817
                                       666666666666666666666654 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3  12.6   2.6e-05    0.0073     255     429 ..     700     875 ..     677     884 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.6e-05
                          Prominin 255 LeqvnklekeLrksgsqLrdglrgvkrdlnqalsnlCq..seeCskilssleiekldtskcl..dqlpnvdevleal 327
                                        ++v+  ++++ + +s L++ l++v ++l+++l+ l +  ++   +i++ l+   +++s +   +ql+ +++ +++l
  gi|385805518|ref|YP_005841916.1| 700 QNAVSTITSSINSAQSALSSQLTSVSTQLSNSLTTLQNnlNAAVGTINNALNG--INSSLNTmsSQLSTLSNNVNSL 774
                                       33444455555555555555555555555555555222122444445555544..4444444457777777777777 PP

                          Prominin 328 eevletnlssivkeglarlneipekvknqtaevvpdlkkalakgreqikklakkiprealdavisdlenterssktf 404
                                        +   ++lss+v ++++  ++  + +    ++  +    a +++ +qi+ l++++ ++  ++v+++++  +  + ++
  gi|385805518|ref|YP_005841916.1| 775 STS-VNQLSSQVSQAVTAAQNAATSASSAATQAQN-AATAASNAANQINALSSQV-SNLSSQVSNAVSAANAATTQA 848
                                       776.4567777777777777777777666665544.4455566677888888888.788888888888777777777 PP

                          Prominin 405 ddvvek..yekyrwliglivcslllli 429
                                       +d   k  y  y +l+ li+ ++ l i
  gi|385805518|ref|YP_005841916.1| 849 SDAASKaaYALYISLVTLILVLVALAI 875
                                       777666113333334444444333333 PP

>> Laminin_I  Laminin Domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4  15.6   2.1e-05    0.0057      15     116 ..     737     841 ..     723     854 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.1e-05
                         Laminin_I  15 ykinanledltkeLqeklskesakkskieilekelesLaqeteeLqkkatqvlakaqkvnaesertlnnakeLaeki 91 
                                       +++na +   ++ L+   s  +  +s+++ l ++++sL   +++L  ++ q+   aq+    ++ +  +a+++a+++
  gi|385805518|ref|YP_005841916.1| 737 NNLNAAVGTINNALNGINSSLNTMSSQLSTLSNNVNSLSTSVNQLSSQVSQAVTAAQNAATSASSAATQAQNAATAA 813
                                       67899999999****************************************************************** PP

                         Laminin_I  92 kkladnikeilekvatlne...neealp 116
                                        + a++i+++ ++v++l+    n+  ++
  gi|385805518|ref|YP_005841916.1| 814 SNAANQINALSSQVSNLSSqvsNAVSAA 841
                                       *****************99544333333 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   3.8   5.9e-05     0.016     300     455 ..     695     847 ..     681     856 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.9e-05
                                       HHHHHTTTSSSSSHHHHT--HHHHTTGGG-TTTS-GGGSSTTTSTTHHHHHHHHHHHHHHHHHHHHHHS-SS---ST CS
                              EzrA 300 AkkeveknlkelkeklehlekqnkelkeeldrlkqsYeLseeeleklrelekelkelekdyeeleekleekkvaYSe 376
                                        + + ++ ++++++    +++  + l+++l+ ++   +Ls++ ++ +++l++ + ++++ ++ ++  l++ +   S+
  gi|385805518|ref|YP_005841916.1| 695 TYSDLQNAVSTITS---SINSAQSALSSQLTSVST--QLSNSLTTLQNNLNAAVGTINNALNGINSSLNTMSSQLST 766
                                       44444444444444...455555677788888877..699999999******************************* PP

                                       TGGGTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSS..S-SS-S-TTTHHHHSTTTST CS
                              EzrA 377 lqeeleeleekleeieekqeeileslkslrkdEkrAreqldeikkelkeikrkie..ksnLPgiPesyleelkeasd 451
                                       l++++++l+ +++++++++ +  ++ ++   + + A  q+++  +  +++ ++i+  +s+   +++++ +++++a+ 
  gi|385805518|ref|YP_005841916.1| 767 LSNNVNSLSTSVNQLSSQVSQAVTAAQNAATSASSAATQAQNAATAASNAANQINalSSQVSNLSSQVSNAVSAANA 843
                                       ******************************************99999999999983345677777777776666666 PP

                                       TTHH CS
                              EzrA 452 eiee 455
                                       +  +
  gi|385805518|ref|YP_005841916.1| 844 ATTQ 847
                                       6555 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.3       1.3   3.6e+02       4      27 ..     698     721 ..     697     740 .. 0.71
   2 ?   13.9   0.4    0.0002     0.054       2      40 ..     743     781 ..     742     788 .. 0.87
   3 ?    1.1   0.0       1.9   5.2e+02      18      38 ..     815     835 ..     806     841 .. 0.58

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 1.3
                         FlaC_arch   4 elEnklsklsteletvkkeneels 27 
                                       +l+n +s + ++++++++ +++  
  gi|385805518|ref|YP_005841916.1| 698 DLQNAVSTITSSINSAQSALSSQL 721
                                       578888888888888888776533 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 0.0002
                         FlaC_arch   2 idelEnklsklsteletvkkeneelsksveelkenVkdl 40 
                                       ++++ n l+ + ++l+t+ ++++ ls++v+ l  +V++l
  gi|385805518|ref|YP_005841916.1| 743 VGTINNALNGINSSLNTMSSQLSTLSNNVNSLSTSVNQL 781
                                       678899999999999999999999999999999999776 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 1.9
                         FlaC_arch  18 tvkkeneelsksveelkenVk 38 
                                       ++ ++++ ls++v +l  +V 
  gi|385805518|ref|YP_005841916.1| 815 NAANQINALSSQVSNLSSQVS 835
                                       455555555555555555543 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   3.9    0.0004      0.11      35     146 ..     716     836 ..     697     849 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.0004
                              Fez1  35 alkaqlrelrakleekeeei.keleesleektlelevcenelqrkkseaellrekvekleeelkelreelselslee 110
                                       al +ql  ++++l+++ +++ ++l++++ + ++ l+ +++ l+ ++s+ ++l+++v++l++ +++l +++s++ + +
  gi|385805518|ref|YP_005841916.1| 716 ALSSQLTSVSTQLSNSLTTLqNNLNAAVGTINNALNGINSSLNTMSSQLSTLSNNVNSLSTSVNQLSSQVSQAVTAA 792
                                       46667777777776665544146777788888888888888888888889999999999999999988888887777 PP

                              Fez1 111 eeaalesdeakaqrqe........aeeleelkreverlraeLke 146
                                       ++aa+++++a +q q+        a+++++l+++v +l +++++
  gi|385805518|ref|YP_005841916.1| 793 QNAATSASSAATQAQNaataasnaANQINALSSQVSNLSSQVSN 836
                                       77776666666665554444444466666777777776666554 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   4.0    0.0011      0.31      99     228 ..     714     840 ..     689     848 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0011
                              CorA  99 k.deggkpkspgellyrlldeivdrlfellekleeeldeledeledstkkeilrelaqlrrrlvklrralapnrevl 174
                                       + + +++ +s+++ l   l ++ ++l++++ +++  l+ + + l     + + ++l++l  ++  l ++++++   +
  gi|385805518|ref|YP_005841916.1| 714 QsALSSQLTSVSTQLSNSLTTLQNNLNAAVGTINNALNGINSSL-----NTMSSQLSTLSNNVNSLSTSVNQLSSQV 785
                                       23445777888888888888888899999999999999999988.....5555555555556666666666665555 PP

                              CorA 175 krlla.kaddkllddedkeylrdlldelerllemlealrerleslqdtyssllse 228
                                       ++ ++   ++ +  + ++ + ++    +++++++++al++++++l+++ s+ +s 
  gi|385805518|ref|YP_005841916.1| 786 SQAVTaAQNAATSASSAATQAQNAATAASNAANQINALSSQVSNLSSQVSNAVSA 840
                                       5555533444444444455677999999999999999999999999999998886 PP

>> MAGE  MAGE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   4.0    0.0014      0.37      67     149 ..     801     888 ..     776     891 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0014
                              MAGE  67 sqekraaekak...skkstrsksy.iL...vstlpeeyreaaaii..apskiesealeekeaa.......ykGiltv 127
                                       s    aa++a+   +++s+++++  +L   vs+l++++ +a++++  a+++++++       a       y+ ++t+
  gi|385805518|ref|YP_005841916.1| 801 S----AATQAQnaaTAASNAANQInALssqVSNLSSQVSNAVSAAnaATTQASDA-------AskaayalYISLVTL 866
                                       1....12222212222222222220220013444444443332220022222333.......13445667******* PP

                              MAGE 128 vlslillsggsiseqeLekyLk 149
                                       +l l++l   ++  + L+k+L 
  gi|385805518|ref|YP_005841916.1| 867 ILVLVALAISTMVYNTLKKSLA 888
                                       *****************99996 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.4     0.014       3.9      41     103 ..     722     785 ..     696     795 .. 0.58
   2 ?    3.5   0.1      0.24        67      35      78 ..     794     837 ..     789     848 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.014
                    CENP-F_leu_zip  41 ekvileaEtskaevet.lkeeieelaeelreleldLvalrsekeeLekelqkkqervseLesln 103
                                       ++v ++  +s  ++++ l++ + ++++ l+ +++ L++++s+  +L ++++     v++L s  
  gi|385805518|ref|YP_005841916.1| 722 TSVSTQLSNSLTTLQNnLNAAVGTINNALNGINSSLNTMSSQLSTLSNNVNSLSTSVNQLSSQV 785
                                       4455555555555543455555555555555555555555555555555555555555554443 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.24
                    CENP-F_leu_zip  35 mseenqekvileaEtskaevetlkeeieelaeelreleldLval 78 
                                       ++  + +++ ++a ++  ++++  ++i+ l+++ ++l++++++ 
  gi|385805518|ref|YP_005841916.1| 794 NAATSASSAATQAQNAATAASNAANQINALSSQVSNLSSQVSNA 837
                                       55667788999***************************999886 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.6    0.0015      0.42      50     115 ..     748     813 ..     721     815 .. 0.87
   2 ?    9.1   2.4    0.0048       1.3      56     115 ..     754     813 ..     747     859 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0015
                             DHR10  50 akleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqaeekreaakarleel 115
                                       ++l+  ++ l+  + +l++++++++ l++   +l  q+++a    + +  +a+  + +a+++ +++
  gi|385805518|ref|YP_005841916.1| 748 NALNGINSSLNTMSSQLSTLSNNVNSLSTSVNQLSSQVSQAVTAAQNAATSASSAATQAQNAATAA 813
                                       567777889999*******************************************99999987765 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0048
                             DHR10  56 kkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqaeekreaakarleel 115
                                       ++ l+  + +l++++++++ l++   +l  q+++a    + +  +a+  + +a+++ +++
  gi|385805518|ref|YP_005841916.1| 754 NSSLNTMSSQLSTLSNNVNSLSTSVNQLSSQVSQAVTAAQNAATSASSAATQAQNAATAA 813
                                       444555555555555555555555555555555555555555555555555555544433 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   5.1    0.0031      0.86       5      82 ..     711     786 ..     700     788 .. 0.71
   2 ?    5.8   1.0     0.062        17      33      82 ..     786     835 ..     783     837 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0031
                           BLOC1_2   5 ekvskyleaelea.tvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeea 80 
                                       +++++ l+++l++ +++  + L++l ++ ++ +  +++++++++++l+ +++   +l+ + ++++ + ++v++L + 
  gi|385805518|ref|YP_005841916.1| 711 NSAQSALSSQLTSvSTQLSNSLTTLQNNLNAAVGTINNALNGINSSLNTMSS---QLSTLSNNVNSLSTSVNQLSSQ 784
                                       5566666677655144445678888888888888888888888888777777...7777777777777888877777 PP

                           BLOC1_2  81 vs 82 
                                       vs
  gi|385805518|ref|YP_005841916.1| 785 VS 786
                                       76 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.062
                           BLOC1_2  33 sekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavs 82 
                                       s+ +++ +++a s+++ + + ++   + ++  +qi+++  qv+ L + vs
  gi|385805518|ref|YP_005841916.1| 786 SQAVTAAQNAATSASSAATQAQNAATAASNAANQINALSSQVSNLSSQVS 835
                                       566777888999999999999999999*****************999886 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       5.7   1.6e+03      50      66 ..     695     711 ..     688     715 .. 0.81
   2 ?    6.8   8.6     0.034       9.4       9      61 ..     710     767 ..     697     785 .. 0.58
   3 ?    2.5   5.9      0.75   2.1e+02      15      60 ..     773     836 ..     760     845 .. 0.62
   4 ?    4.5   0.5      0.17        48      12      33 ..     819     840 ..     807     855 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 5.7
                           NPV_P10  50 qLaeletkvenIqdiLn 66 
                                       +  +l+++v++I++  n
  gi|385805518|ref|YP_005841916.1| 695 TYSDLQNAVSTITSSIN 711
                                       56789999999999877 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.034
                           NPV_P10   9 IradikavddkVdalqqqv....ddvqenlpd.vtelnekLdaqsaqLaeletkvenI 61 
                                       I ++ +a++++++++++q+    + +q+nl+  v  +n+ L++++ +L+++++++++ 
  gi|385805518|ref|YP_005841916.1| 710 INSAQSALSSQLTSVSTQLsnslTTLQNNLNAaVGTINNALNGINSSLNTMSSQLSTL 767
                                       5555556666666666665444455555554324455555555555555555544444 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.75
                           NPV_P10  15 avddkVdalqqqv..................ddvqenlpdvtelnekLdaqsaqLaeletkven 60 
                                        +++ V+ l++qv                  ++ q+     ++  ++++a+s q+ +l+++v+n
  gi|385805518|ref|YP_005841916.1| 773 SLSTSVNQLSSQVsqavtaaqnaatsassaaTQAQNAATAASNAANQINALSSQVSNLSSQVSN 836
                                       5555555555555444444444445555555777777777777778888888888888888876 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.17
                           NPV_P10  12 dikavddkVdalqqqvddvqen 33 
                                        i+a++++V+ l++qv +  + 
  gi|385805518|ref|YP_005841916.1| 819 QINALSSQVSNLSSQVSNAVSA 840
                                       5777777777777777665544 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   4.7      0.27        74      12      63 ..     707     760 ..     695     766 .. 0.56
   2 ?   11.4   6.0    0.0011      0.31       8      63 ..     760     848 ..     753     858 .. 0.40

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.27
                        Syntaxin_2  12 vstleklvkqLgtk..kdteelreklhelieeinelikktnellkklsqldnss 63 
                                       +s++++ ++ L+++    +++l ++l +l++++n  + ++n+ l+ +++  n+ 
  gi|385805518|ref|YP_005841916.1| 707 TSSINSAQSALSSQltSVSTQLSNSLTTLQNNLNAAVGTINNALNGINSSLNTM 760
                                       233333333333333223777777777777777777777777777777665554 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.0011
                        Syntaxin_2   8 insnvstleklvkqLgtkkdteelr...................................eklhelieeinelikkt 49 
                                       ++s++stl + v++L+t+    +l                                    ++++ l +++++l++++
  gi|385805518|ref|YP_005841916.1| 760 MSSQLSTLSNNVNSLSTS--VNQLSsqvsqavtaaqnaatsassaatqaqnaataasnaaNQINALSSQVSNLSSQV 834
                                       555555555555555555..333330000111112122222333343333444444444444444444444444444 PP

                        Syntaxin_2  50 nellkklsqldnss 63 
                                       ++ ++  ++ + + 
  gi|385805518|ref|YP_005841916.1| 835 SNAVSAANAATTQA 848
                                       44444444444444 PP

>> Myosin_tail_1  Myosin tail
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.8    0.0016      0.44     384     497 ..     719     833 ..     691     861 .. 0.40

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0016
                     Myosin_tail_1 384 senkelqaelk.slqqakqdseqkrkkleaqlqelqvklseserqreelaekvsklqaelesvsslleeaegksikl 459
                                       s+ + ++++l  sl++ +++ +     +++ l+ +++ l+    q + l++ v+ l++ ++++ss++++a + +  +
  gi|385805518|ref|YP_005841916.1| 719 SQLTSVSTQLSnSLTTLQNNLNAAVGTINNALNGINSSLNTMSSQLSTLSNNVNSLSTSVNQLSSQVSQAVTAAQNA 795
                                       33333333332123333333333333333333333333333333333333333333333333333333333333333 PP

                     Myosin_tail_1 460 skdvsslesqlqDtqellqeetrqkLalssrlrqleee 497
                                       +  +ss   q q++    ++   q  alss++ +l  +
  gi|385805518|ref|YP_005841916.1| 796 ATSASSAATQAQNAATAASNAANQINALSSQVSNLSSQ 833
                                       33333333333333333333333333333333333222 PP

>> AIP3  Actin interacting protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   7.7    0.0018      0.49      35     207 ..     669     834 ..     658     853 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0018
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXX CS
                              AIP3  35 ggedfPeiyiqDpksgvrYeLedlsdvkdrsvLsLniepldevkkhideslaslskelkelkssiesqkaslqevse 111
                                       ++ + P i   D   +  Y  ++l++v + s L+   ++++++ + i++ ++ ls++l++++++++++ ++lq+  +
  gi|385805518|ref|YP_005841916.1| 669 SSTSTPVIQATD--ASYAYVINNLTEVATYSDLQ---NAVSTITSSINSAQSALSSQLTSVSTQLSNSLTTLQNNLN 740
                                       555555555555..44568888888888887765...4678889999999999999999999999999999988777 PP

                                       XXXXXXXXXXXXXXX.........XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXHHHH CS
                              AIP3 112 rqeeaakekaseslakkelkaqlkevqslrrdLavlrqlysefkseikeslselrekakkvkeaslastkkssnray 188
                                           +++++ + ++  ++l++  +++++l +++++l    ++ +s++++ +++ ++ a++  +a+++ ++  ++ + 
  gi|385805518|ref|YP_005841916.1| 741 AAVGTINNALNGIN--SSLNTMSSQLSTLSNNVNSLSTSVNQLSSQVSQAVTAAQNAATSASSAATQAQNAATAASN 815
                                       77777777777444..5888888899999999999988888888888888888888888887444433333333333 PP

                                       HHHHHHHHHHHHHHHHHHH CS
                              AIP3 189 iekgkkkLseesdklvtkv 207
                                         +  + Ls+++++l ++v
  gi|385805518|ref|YP_005841916.1| 816 AANQINALSSQVSNLSSQV 834
                                       3333344444444443333 PP

>> YscO  Type III secretion protein YscO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.5     0.001      0.28      67     127 ..     763     827 ..     711     829 .. 0.73
   2 ?    3.1   0.4      0.31        84      73     110 ..     818     855 ..     813     859 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.001
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YscO  67 elekvkqqvalLrekeaelekqveeakqqlea....erealrqarkelqearraveKfaelarlv 127
                                       +l ++ ++v +L   +++l +qv +a   +++    +  a++qa+++ ++a+ a + +++l ++v
  gi|385805518|ref|YP_005841916.1| 763 QLSTLSNNVNSLSTSVNQLSSQVSQAVTAAQNaatsASSAATQAQNAATAASNAANQINALSSQV 827
                                       45666778888999999998888876555554000045556666666666666666666666655 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.31
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YscO  73 qqvalLrekeaelekqveeakqqleaerealrqarkel 110
                                       +q+ +L  ++ +l +qv  a   ++a+ +++ +a  + 
  gi|385805518|ref|YP_005841916.1| 818 NQINALSSQVSNLSSQVSNAVSAANAATTQASDAASKA 855
                                       69999999*********999999999988877766554 PP

>> Vip3A_N  Vegetative insecticide protein 3A N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7  10.4    0.0013      0.36      37     136 ..     690     786 ..     675     794 .. 0.84
   2 ?   -1.6   0.1       7.9   2.2e+03     113     136 ..     812     835 ..     778     844 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0013
                           Vip3A_N  37 ldeilknqqllndisgkldgvngslndliaq.gnlntelskeilkianeqnqvlndvnnkldaintmlrvylpkits 112
                                       l e+    +l n +s     +n + + l +q   + t+ls+ +  + n+ n  +  +nn l+ in+ l++   ++  
  gi|385805518|ref|YP_005841916.1| 690 LTEVATYSDLQNAVSTITSSINSAQSALSSQlTSVSTQLSNSLTTLQNNLNAAVGTINNALNGINSSLNTMSSQL-- 764
                                       678888999*******************99956799******************************999866555.. PP

                           Vip3A_N 113 mlsdvmkqnyalslqieylskqlq 136
                                         s + ++  +ls  ++ ls q+ 
  gi|385805518|ref|YP_005841916.1| 765 --STLSNNVNSLSTSVNQLSSQVS 786
                                       ..4444455678888888888875 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 7.9
                           Vip3A_N 113 mlsdvmkqnyalslqieylskqlq 136
                                         s+  +q  als q+  ls q+ 
  gi|385805518|ref|YP_005841916.1| 812 AASNAANQINALSSQVSNLSSQVS 835
                                       456667777788888888888765 PP

>> DUF677  Protein of unknown function (DUF677)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   3.3     0.003      0.83     202     286 ..     713     798 ..     686     808 .. 0.56
   2 ?    5.0   0.6     0.034       9.3     255     289 ..     816     850 ..     803     860 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.003
                            DUF677 202 aalaapavva.vagalavPleavgkwvasawkkyeealkrqkeivssmekgievakkdvenisilverleseiksil 277
                                       a  a  + ++ v++ l+  l ++ + ++ a    ++al + +   ++m + + +  ++v+++s+ v++l+s+++  +
  gi|385805518|ref|YP_005841916.1| 713 AQSALSSQLTsVSTQLSNSLTTLQNNLNAAVGTINNALNGINSSLNTMSSQLSTLSNNVNSLSTSVNQLSSQVSQAV 789
                                       33333333333555555555555555555555666666666666666666666666666666666666666666666 PP

                            DUF677 278 ktvefAvek 286
                                        ++++A ++
  gi|385805518|ref|YP_005841916.1| 790 TAAQNAATS 798
                                       666666554 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.034
                            DUF677 255 akkdvenisilverleseiksilktvefAvekeen 289
                                       a ++++ +s++v++l+s++++ + +++ A+++ ++
  gi|385805518|ref|YP_005841916.1| 816 AANQINALSSQVSNLSSQVSNAVSAANAATTQASD 850
                                       55678888899999999999999999988888663 PP

>> SOGA  Protein SOGA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.4    0.0021      0.58      19      89 ..     760     831 ..     753     838 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0021
                              SOGA  19 lrrslseleeenkqlteeLnkyksklgeeessleeee.eassdsskeaelkeeLklarlqineLsgkvvkLq 89 
                                       +  +ls l ++ ++l + +n++ s+ ++  +++++++ +ass+++++++       a  qin Ls +v +L 
  gi|385805518|ref|YP_005841916.1| 760 MSSQLSTLSNNVNSLSTSVNQLSSQVSQAVTAAQNAAtSASSAATQAQNAATAASNAANQINALSSQVSNLS 831
                                       6678999999999***********9999888877766366666777777888889999**********9984 PP

>> YlqD  YlqD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1      0.32        88      21      89 ..     706     774 ..     696     776 .. 0.73
   2 ?   10.7   3.6    0.0019      0.51      23      90 ..     765     831 ..     760     840 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.32
                              YlqD  21 lqqqlqaqieqldkelqqLefqakrlikeikkqsaqqieeiqeqvekekserlekkkqllqqleqvqkL 89 
                                       + ++++++ ++l ++l  +++q+   ++ ++++ ++++ +i++ ++   s ++   +ql    ++v++L
  gi|385805518|ref|YP_005841916.1| 706 ITSSINSAQSALSSQLTSVSTQLSNSLTTLQNNLNAAVGTINNALNGINSSLNTMSSQLSTLSNNVNSL 774
                                       566777788888888888888888888888887777777777777777777777777766666666665 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0019
                              YlqD  23 qqlqaqieqldkelqqLefqakrlikeikkqsaqqieeiqeqvekekserlekkkqllqqleqvqkLe 90 
                                       ++l+++++ l + ++qL+ q  ++++ +++  a++++++ +q+++      ++ +q+++  +qv++L 
  gi|385805518|ref|YP_005841916.1| 765 STLSNNVNSLSTSVNQLSSQVSQAVTAAQN-AATSASSAATQAQNAATAASNAANQINALSSQVSNLS 831
                                       678999******************999977.5568888888888888888899999999888888886 PP

>> FmiP_Thoc5  Fms-interacting protein/Thoc5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   8.9    0.0032      0.87     110     233 ..     695     827 ..     691     872 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0032
                        FmiP_Thoc5 110 qlkeleekkkkleqeieekkkfLssLppkLk.slkkatkplqealgl...plt.kerkqhelaslLPkPLYvlYvql 181
                                       ++++l++ ++++ + i++ ++ Lss  + ++ +l+++++ lq++l+    +++   +  +++ +  ++ L +l  ++
  gi|385805518|ref|YP_005841916.1| 695 TYSDLQNAVSTITSSINSAQSALSSQLTSVStQLSNSLTTLQNNLNAavgTINnALNGINSSLNTMSSQLSTLSNNV 771
                                       67899******************8776666649************885554443566777888888*********** PP

                        FmiP_Thoc5 182 eaykeavdkkleveIeGdveeakafnkssnsaeekkaeaessdsdsesq.....eek 233
                                       ++++++v ++l+ ++   v+ a++ ++s +sa+ + ++a ++ s++ +q     ++ 
  gi|385805518|ref|YP_005841916.1| 772 NSLSTSV-NQLSSQVSQAVTAAQNAATSASSAATQAQNAATAASNAANQinalsSQV 827
                                       ******9.88**************999999988887777788888877765555222 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3  18.0    0.0095       2.6     130     221 ..     731     849 ..     691     865 .. 0.57

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0095
                           DUF4407 130 a............................ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgv 178
                                       +                            ++++l++l +++++l++ +++++++++++ ++aq+ ++ ++++  t+ 
  gi|385805518|ref|YP_005841916.1| 731 SlttlqnnlnaavgtinnalnginsslntMSSQLSTLSNNVNSLSTSVNQLSSQVSQAVTAAQNAATSASSAA-TQA 806
                                       0333333333336666666777555555566666666666666666666666666666666666666554444.345 PP

                           DUF4407 179 aGkgpaakekkaqldaaqaelaelkakld......atarlaalraelae 221
                                       +   +aa ++ +q++a++ ++ +l+++++      +      + +++a+
  gi|385805518|ref|YP_005841916.1| 807 QNAATAASNAANQINALSSQVSNLSSQVSnavsaaN------AATTQAS 849
                                       666677777777777777777777777553332221......2222222 PP

>> COG5  Golgi transport complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8  10.1    0.0064       1.8      24     113 ..     692     782 ..     677     786 .. 0.88
   2 ?   12.5   3.5   0.00046      0.13      64     110 ..     753     800 ..     747     815 .. 0.82
   3 ?    2.9   0.9      0.43   1.2e+02      66     111 ..     805     850 ..     800     869 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0064
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXX-TTHHHH CS
                              COG5  24 nddteldlstplkrlnydiqeldkrlrqlitsnhleLlehlskskslss.vlselksslesLsasyerlkskvlepy 99 
                                       +  t +dl+ +++++++ i+  ++ l +++ts  ++L + l++ ++  +  + +++  l+ +++s++ ++s++++  
  gi|385805518|ref|YP_005841916.1| 692 EVATYSDLQNAVSTITSSINSAQSALSSQLTSVSTQLSNSLTTLQNNLNaAVGTINNALNGINSSLNTMSSQLSTLS 768
                                       556778999*******************************9998776665*************************** PP

                                       HHHHHHHHHHHHHH CS
                              COG5 100 eeaeklqsalkrlh 113
                                       +++++l+++ ++l 
  gi|385805518|ref|YP_005841916.1| 769 NNVNSLSTSVNQLS 782
                                       ******99998886 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00046
                                       XXXXXXXXX.XXXXXXXXXXXXXXXXXXXX-TTHHHHHHHHHHHHHHH CS
                              COG5  64 lskskslss.vlselksslesLsasyerlkskvlepyeeaeklqsalk 110
                                       +++s+++ s  ls+l  +++sLs s+++l+s+v++  + a++  ++++
  gi|385805518|ref|YP_005841916.1| 753 INSSLNTMSsQLSTLSNNVNSLSTSVNQLSSQVSQAVTAAQNAATSAS 800
                                       5666666666****************************9998876655 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.43
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXX-TTHHHHHHHHHHHHHHHH CS
                              COG5  66 kskslssvlselksslesLsasyerlkskvlepyeeaeklqsalkr 111
                                       + +++    s+   ++++Ls+ ++ l+s+v++    a+  +++++ 
  gi|385805518|ref|YP_005841916.1| 805 QAQNAATAASNAANQINALSSQVSNLSSQVSNAVSAANAATTQASD 850
                                       4455555777888899999999999999999998888887777664 PP

>> TolA_bind_tri  TolA binding protein trimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1       4.4   1.2e+03      18      33 ..     723     738 ..     699     742 .. 0.56
   2 ?   12.3   0.5   0.00048      0.13       3      53 ..     740     790 ..     738     814 .. 0.84
   3 ?    0.3   0.2       2.7   7.3e+02      17      41 ..     810     834 ..     799     847 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 4.4
                     TolA_bind_tri  18 qlllelqqqlealqqe 33 
                                       ++ ++l + l +lq+ 
  gi|385805518|ref|YP_005841916.1| 723 SVSTQLSNSLTTLQNN 738
                                       3445555555555544 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00048
                     TolA_bind_tri   3 edrvarLErilearsqlllelqqqlealqqelreLRGqiEelqyqleqlee 53 
                                       ++ v +++++l++ +++l  + +ql++l++ +++L  ++ +l+ q++q+ +
  gi|385805518|ref|YP_005841916.1| 740 NAAVGTINNALNGINSSLNTMSSQLSTLSNNVNSLSTSVNQLSSQVSQAVT 790
                                       6678889999*************************************9865 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 2.7
                     TolA_bind_tri  17 sqlllelqqqlealqqelreLRGqi 41 
                                         +  +  +q++al+++++ L  q+
  gi|385805518|ref|YP_005841916.1| 810 ATAASNAANQINALSSQVSNLSSQV 834
                                       4566677788888888888886665 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.2     0.042        12      68     117 ..     692     742 ..     690     745 .. 0.87
   2 ?    6.2   0.0     0.034       9.5      74     118 ..     745     789 ..     741     791 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.042
                                       TEEEEEEHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  68 gyyveksleeAiellkkkleelekql.ekleeeleklkdqittleanlaql 117
                                       +++   +l++A+ ++   +++++++l  +l+   ++l++ +ttl++nl++ 
  gi|385805518|ref|YP_005841916.1| 692 EVATYSDLQNAVSTITSSINSAQSALsSQLTSVSTQLSNSLTTLQNNLNAA 742
                                       56666799***************9983589*****************9875 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.034
                                       EHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  74 sleeAiellkkkleelekqlekleeeleklkdqittleanlaqly 118
                                       ++++A   ++  l+++++ql +l ++++ l++ +++l  +++q +
  gi|385805518|ref|YP_005841916.1| 745 TINNALNGINSSLNTMSSQLSTLSNNVNSLSTSVNQLSSQVSQAV 789
                                       7889999999****************************9999875 PP

>> Phage_GP20  Phage minor structural protein GP20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   2.9    0.0034      0.95      17      95 ..     740     813 ..     719     822 .. 0.72
   2 ?   -0.1   0.9       2.7   7.5e+02      23      62 ..     802     838 ..     794     860 .. 0.47

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0034
                        Phage_GP20  17 kakldeveeerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakaeyeakiadlkldnaielaLkeak 93 
                                       +a++ +++++ + ++++l++  +qL++L +   ++++L + +++l  ++ +a + ++   a++  ++a ++a ++a 
  gi|385805518|ref|YP_005841916.1| 740 NAAVGTINNALNGINSSLNTMSSQLSTLSN---NVNSLSTSVNQLSSQVSQAVTAAQ--NAATSASSAATQAQNAAT 811
                                       788999**********************55...599999999999999998665544..445555555555555444 PP

                        Phage_GP20  94 ak 95 
                                       a 
  gi|385805518|ref|YP_005841916.1| 812 AA 813
                                       44 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 2.7
                        Phage_GP20  23 veeerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelq 62 
                                       + ++ ++  +   ++ +q++ L  +   + +L  q+ +  
  gi|385805518|ref|YP_005841916.1| 802 AATQAQNAATAASNAANQINALSSQ---VSNLSSQVSNAV 838
                                       4555555555555555555555544...333333333222 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   9.8    0.0042       1.2     272     414 ..     700     836 ..     677     846 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0042
                            DUF812 272 sksksdlaellsefseksetdslktkgsrfthaeklqftkeelakkaeteeelkkkreeeleelqeqieeleskiee 348
                                       +++ s++ ++++++  +s+ +s++t  s+  ++  ++++++ l++++ t +++ +  + +l+++++q+++l++++++
  gi|385805518|ref|YP_005841916.1| 700 QNAVSTITSSINSA--QSALSSQLTSVSTQLSNSLTTLQNN-LNAAVGTINNALNGINSSLNTMSSQLSTLSNNVNS 773
                                       22333334444444..2222222333333333333355555.66788999999999999999999999999999999 PP

                            DUF812 349 leeeikklessikqveeeleeekeeneelekevklkkktlellpdaeeniekLqalveasaqrlve 414
                                       l+  +++l+s+++q+  ++++  ++ +  + + +++   +  + +a ++i++L + v + ++++ +
  gi|385805518|ref|YP_005841916.1| 774 LSTSVNQLSSQVSQAVTAAQNAATSASSAATQAQNA---ATAASNAANQINALSSQVSNLSSQVSN 836
                                       999999999999999988888877777777666655...4556799***********999988876 PP

>> BAR_3  BAR domain of APPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   6.6    0.0053       1.5      44     161 ..     706     832 ..     692     851 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0053
                             BAR_3  44 agkaysaaqkqfaqsLrelkkeskgdeetd............esLkkfsellqelenehtilldqaqrsikkpLekF 108
                                        + ++++aq++++++L +++ + ++   t             ++L+ ++++l++++++ ++l++++++  +++++++
  gi|385805518|ref|YP_005841916.1| 706 ITSSINSAQSALSSQLTSVSTQLSNSLTTLqnnlnaavgtinNALNGINSSLNTMSSQLSTLSNNVNSL-STSVNQL 781
                                       344555666666666666555552222222334444555667***********************9876.7777777 PP

                             BAR_3 109 rkedlkevkekkkkFdkesekleaaleknaqlskkkkeseleeadnelkatrk 161
                                         +  ++v+ ++++   +s+  ++a++   ++s+   +++++  ++++++  +
  gi|385805518|ref|YP_005841916.1| 782 SSQVSQAVTAAQNAATSASSAATQAQNAATAASN--AANQINALSSQVSNLSS 832
                                       7766666666666666666665555444444444..46667777776665544 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4  13.5   0.00071       0.2      72     182 ..     697     805 ..     685     806 .. 0.83
   2 ?    7.2  20.7     0.014       3.8      64     136 ..     778     850 ..     775     858 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00071
                            DUF745  72 reaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqlleaAkkRv 148
                                       ++ +++v+ +++s++s+++++++     +  +q  ++l++l ++ ++++ +++++ +g +++l+  ++ l +  + v
  gi|385805518|ref|YP_005841916.1| 697 SDLQNAVSTITSSINSAQSALSSQ--LTSVSTQLSNSLTTLQNNLNAAVGTINNALNGINSSLNTMSSQLSTLSNNV 771
                                       677888899999999998887654..44455666777777778888888889999999999999999999999**** PP

                            DUF745 149 eeLkkqlkearkdlektkkaAykAacAAqeAkqk 182
                                       ++L++ +++  +   +   aA++Aa++A+ A  +
  gi|385805518|ref|YP_005841916.1| 772 NSLSTSVNQLSSQVSQAVTAAQNAATSASSAATQ 805
                                       ****************************999866 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.014
                            DUF745  64 veqleqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelae 136
                                       v+ql ++++ a ++ q+  +s +s+ ++a+ aa+aa++a +q++al++ + + +++++na ++a+ a +++++
  gi|385805518|ref|YP_005841916.1| 778 VNQLSSQVSQAVTAAQNAATSASSAATQAQNAATAASNAANQINALSSQVSNLSSQVSNAVSAANAATTQASD 850
                                       89*************************************************************9999887765 PP

>> DUF4618  Domain of unknown function (DUF4618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   1.0    0.0078       2.1      47     109 ..     714     776 ..     675     785 .. 0.68
   2 ?    2.5   0.5       0.3        84     152     217 ..     772     835 ..     763     845 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0078
                           DUF4618  47 yeklktvisileksskkqleqakaeLqeweekeekklekLeqqleqlnakvqklqeelnvLst 109
                                       ++ l +  + ++++ ++ l +++++L+    ++++ l+ ++  l+ + +++  l++++n Lst
  gi|385805518|ref|YP_005841916.1| 714 QSALSSQLTSVSTQLSNSLTTLQNNLNAAVGTINNALNGINSSLNTMSSQLSTLSNNVNSLST 776
                                       445555556666666777777777777777777777777777777777777777777777776 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.3
                           DUF4618 152 eklskkiqkkkekllkslaektlkatqeaLlqktlenqvlkkeiekfrefieeleeeipeLkaeve 217
                                       ++ls+++ + + ++ ++++  + +a  ++    + + q+ ++   +  ++i+ l  ++++L ++v 
  gi|385805518|ref|YP_005841916.1| 772 NSLSTSVNQLSSQVSQAVTAAQNAA--TSASSAATQAQNAATAASNAANQINALSSQVSNLSSQVS 835
                                       5566666666666655554433333..334444555555556666666677777777777777765 PP

>> T3SSipB  Type III cell invasion protein SipB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.3       3.2   8.8e+02      80      92 ..     707     719 ..     676     753 .. 0.44
   2 ?   12.2  22.6   0.00069      0.19      17     119 ..     754     854 ..     739     860 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 3.2
                                       HHHHHHHHHHHTT CS
                           T3SSipB  80 tkkvdeaqkrlke 92 
                                       t  ++ aq  l++
  gi|385805518|ref|YP_005841916.1| 707 TSSINSAQSALSS 719
                                       1111111111111 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00069
                                       HHCHHHHHHHHHHHHHHHHHTTTTT----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT- CS
                           T3SSipB  17 nkSLsqLenrlaawkamskaqqeaasklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeL 93 
                                       n+SL+ ++++l +     ++  +   +lS ++ +a+ +a++a+  +  a+ +a++a  aa +a +++++   ++++L
  gi|385805518|ref|YP_005841916.1| 754 NSSLNTMSSQLSTLSNNVNSLSTSVNQLSSQVSQAVTAAQNAATSASSAATQAQNAATAASNAANQINALSSQVSNL 830
                                       89******************************************************999*99*************** PP

                                       ---.-----CHHHHHHHHH..HHHHHH CS
                           T3SSipB  94 aPd.ePekakleaaeqQagaaadalqa 119
                                       + + +    +++aa+ Qa +a   +++
  gi|385805518|ref|YP_005841916.1| 831 SSQvSNAVSAANAATTQASDA---ASK 854
                                       665234456677777888755...333 PP

>> DASH_Spc19  Spc19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6  10.5       0.1        28      64     155 ..     745     835 ..     699     836 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.1
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHT-XXXXXXXXXXXX....XXXXXXXXXXXXX CS
                        DASH_Spc19  64 qieellekaekeleklerreetLkaklelqegrlsnaesskkeeeeseeskeeeeeeenkeeekskkkltkeelerl 140
                                        i++ l+ ++++l+ ++++ +tL ++++ ++  +++ +s+ +++ ++++++ ++ +++  ++++++++++++ ++++
  gi|385805518|ref|YP_005841916.1| 745 TINNALNGINSSLNTMSSQLSTLSNNVNSLSTSVNQLSSQVSQAVTAAQNAATSASSA-ATQAQNAATAASNAANQI 820
                                       4777777788888888888888888888888877776555555554444444333333.333444444777788999 PP

                                       XXXXXXXXXXXXXXX CS
                        DASH_Spc19 141 kkLkqkKerLkytle 155
                                       ++L ++   L+ +++
  gi|385805518|ref|YP_005841916.1| 821 NALSSQVSNLSSQVS 835
                                       999998888888876 PP

>> Vps51  Vps51/Vps67
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       3.7     1e+03      13      41 ..     688     716 ..     678     719 .. 0.72
   2 ?    8.7   5.1    0.0066       1.8      21      86 ..     717     783 ..     697     784 .. 0.87
   3 ?    0.7   0.1         2   5.4e+02      56      79 ..     816     839 ..     809     846 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 3.7
                             Vps51  13 rellakstlkellkveasllseiraldse 41 
                                       ++l + +t ++l++  ++++s+i   +s 
  gi|385805518|ref|YP_005841916.1| 688 NNLTEVATYSDLQNAVSTITSSINSAQSA 716
                                       55666677788888888888888877775 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0066
                             Vps51  21 l.kellkveasllseiraldselkalVydnYskLisasdtIrkmksemdkldqklselkqaiskiae 86 
                                       l ++l  v  +l  + ++l+++l a V++  + L  +++ +++m+s++++l++++++l+ +++++++
  gi|385805518|ref|YP_005841916.1| 717 LsSQLTSVSTQLSNSLTTLQNNLNAAVGTINNALNGINSSLNTMSSQLSTLSNNVNSLSTSVNQLSS 783
                                       2589999******************************************************999876 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 2
                             Vps51  56 asdtIrkmksemdkldqklselkq 79 
                                       a+++I+ ++s++++l++++s+  +
  gi|385805518|ref|YP_005841916.1| 816 AANQINALSSQVSNLSSQVSNAVS 839
                                       677788888888888887777555 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   8.1     0.045        12     121     264 ..     698     845 ..     692     860 .. 0.57

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.045
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXX..XXX CS
                          Filament 121 dLekkvesLkeelaflkkvheeEvkelqkqvs.eqvlvevdaarkld.Lteilkeiraqyeelaeknreeae..ewy 193
                                       dL++ v +++  ++  ++  +  ++ + +q+s + ++++ + +  +  ++++l+ i +  +++ ++  + ++  +  
  gi|385805518|ref|YP_005841916.1| 698 DLQNAVSTITSSINSAQSALSSQLTSVSTQLSnSLTTLQNNLNAAVGtINNALNGINSSLNTMSSQLSTLSNnvNSL 774
                                       66666666666666666666666666666665322222222222222466666666666666665544333301344 PP

                                       XXXXXXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 194 kskleelqeaaeknsealrsakeeitelrrqiqsleieleslkkqkasleaqlaeleerleaeleklqekl 264
                                       ++ +++l++++++   a+++a +  + +  q q+  +  ++  +q ++l +q+++l  +++++++ ++++ 
  gi|385805518|ref|YP_005841916.1| 775 STSVNQLSSQVSQAVTAAQNAATSASSAATQAQNAATAASNAANQINALSSQVSNLSSQVSNAVSAANAAT 845
                                       55666666666666666666666666666666666666666666666666666666666666666665555 PP

>> DUF842  Eukaryotic protein of unknown function (DUF842)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1     0.031       8.4      44      93 ..     697     747 ..     691     771 .. 0.75
   2 ?    2.1   3.1      0.53   1.5e+02      62     103 ..     772     812 ..     758     855 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.031
                            DUF842  44 esveqCvekCseplqkaqkvvqqEleqfqerLqrcvmvCqdkakdklgp.n 93 
                                        ++++ v    +++++aq+++++ l+++  +L++++ + q++++ ++g+ n
  gi|385805518|ref|YP_005841916.1| 697 SDLQNAVSTITSSINSAQSALSSQLTSVSTQLSNSLTTLQNNLNAAVGTiN 747
                                       677888888889999999999999999999999999999999999886542 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.53
                            DUF842  62 kvvqqEleqfqerLqrcvmvCqdkakdklgpnssekqtakae 103
                                       + +++ ++q+ ++++++v  +q+ a ++ +++ +++q a+  
  gi|385805518|ref|YP_005841916.1| 772 NSLSTSVNQLSSQVSQAVTAAQNAATSASSAA-TQAQNAATA 812
                                       55666677777777777777777777776332.222222222 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 ?    0.1   0.0       2.6   7.2e+02       4      18 ..      48      63 ..      46      70 .. 0.67
   2 ?    7.1   3.6     0.017       4.8       1      21 [.     353     372 ..     353     382 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 2.6
                                      TT-EEEETTT.SEE-T CS
                            ECR1_N  4 PGevlttdee.fmrGh 18
                                      PGe++t + +  ++G 
  gi|385805518|ref|YP_005841916.1| 48 PGEPITVSLQiNLPGT 63
                                      9999986555355554 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.017
                                       EE-TT-EEEETTTSEE-TTEE CS
                            ECR1_N   1 iVtPGevlttdeefmrGhGTY 21 
                                       iVtPG+++ t   +  G+GTY
  gi|385805518|ref|YP_005841916.1| 353 IVTPGQTI-TVVAYGYGPGTY 372
                                       9*******.666799999999 PP

>> ATP-synt_D  ATP synthase subunit D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       9.9   2.7e+03      77     115 ..     266     302 ..     263     308 .. 0.71
   2 ?   -0.0   0.1       2.4   6.5e+02      82     140 ..     638     696 ..     608     740 .. 0.66
   3 ?    9.3   1.9    0.0033      0.91       6     100 ..     747     840 ..     742     891 .. 0.60

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 9.9
                                       ..TSS-SEEEEEEBTTSEEEEEEE-..S.SSTSSSSSSS CS
                        ATP-synt_D  77 lakvvkvelktenvaGVkvpvfeleeeksdstelygllr 115
                                        ++v++v+l+ +n  +V +   ++++ ++ +t++yg+++
  gi|385805518|ref|YP_005841916.1| 266 NVQVMNVTLHNKNFTNVSYTF-NVSS-GNITTNSYGFFN 302
                                       468999**********98876.3422.444556677665 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 2.4
                                       -SEEEEEEBTTSEEEEEEE-..S.SSTSSSSS.SSSTCHHHHHHHHCHHHHHHHHHHHHH CS
                        ATP-synt_D  82 kvelktenvaGVkvpvfeleeeksdstelygl.lrtgaqldeavealrellellvelasl 140
                                        ++++  nv G+ +p +e      +   +y   +++++ ++ + ++++ ++++l e+a +
  gi|385805518|ref|YP_005841916.1| 638 LLTSQFTNVLGLWIPFVEPGAYMVN-LTYYVPsSTSTPVIQATDASYAYVINNLTEVATY 696
                                       4677788999999999976443223.3333331344446666666777777777777753 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0033
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSTST.TSTSHHHHHHHSSS.SS-..TSS CS
                        ATP-synt_D   6 kkrlklaqrghslLkkKrdaLilefreilkelkelreeleeelkeayfslaea.faaggeediesavlesvklakvv 81 
                                       ++ l++++  ++++ +  + L   + ++   +++l  ++ +++ +a+++ + a  aa + ++   a+ + ++  +  
  gi|385805518|ref|YP_005841916.1| 747 NNALNGINSSLNTMSSQLSTLSNNVNSLSTSVNQLSSQVSQAVTAAQNAATSAsSAATQAQNAATAASNAAN--QIN 821
                                       567889999999999999999999999999999999999999999999999996666644444444443333..333 PP

                                       -SEEEEEEBTTSEEEEEEE CS
                        ATP-synt_D  82 kvelktenvaGVkvpvfel 100
                                        +++++ n+      +++ 
  gi|385805518|ref|YP_005841916.1| 822 ALSSQVSNLSSQVSNAVSA 840
                                       4444444444333333333 PP

>> FliJ  Flagellar FliJ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.4    0.0096       2.6      15      84 ..     726     794 ..     711     799 .. 0.81
   2 ?    3.6   3.1      0.26        72       3      51 ..     802     847 ..     800     857 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0096
                              FliJ  15 qqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvekareewqe 84 
                                       +q  + l+ l+++++     ++++ +g++ + l + ++++s+l + ++++  +++q+  qv++a  + q 
  gi|385805518|ref|YP_005841916.1| 726 TQLSNSLTTLQNNLNAAVGTINNALNGIN-SSLNTMSSQLSTLSNNVNSLSTSVNQLSSQVSQAVTAAQN 794
                                       56677888899999999999999988887.5689999999999999999999999999999998776665 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.26
                              FliJ   3 aareLaeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyq 51 
                                       aa++ ++a ++  +a +++++l ++ +++++q s++    saa+  ++q
  gi|385805518|ref|YP_005841916.1| 802 AATQAQNAATAASNAANQINALSSQVSNLSSQVSNAV---SAANAATTQ 847
                                       89999999999******************99999998...555555544 PP

>> DotU  Type VI secretion system protein DotU
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.5      0.14        40      20      59 ..     771     812 ..     755     817 .. 0.80
   2 ?    4.9   0.4     0.067        18     144     198 ..     819     876 ..     810     883 .. 0.48

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.14
                              DotU  20 as..epdvealrerlveelrafeqrlkaagysaediedarya 59 
                                           + +v++l  ++ ++++a+++++ +a+ +a +++ a  a
  gi|385805518|ref|YP_005841916.1| 771 VNslSTSVNQLSSQVSQAVTAAQNAATSASSAATQAQNAATA 812
                                       33456899**********************999999988755 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.067
                              DotU 144 lrqrlyeeirrlrgeaeealsphwqagdeaarrllrrelplw...vilalallvllll 198
                                        +++l+ ++++l  ++++a+s +++a ++a++++++  + l    v+l+l+l++l++ 
  gi|385805518|ref|YP_005841916.1| 819 QINALSSQVSNLSSQVSNAVSAANAATTQASDAASKAAYALYislVTLILVLVALAIS 876
                                       3455666666666666666666666666666666544333330003333333333333 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.2      0.34        93      38     123 ..     697     784 ..     688     789 .. 0.77
   2 ?    5.6   0.7     0.058        16      26      72 ..     760     806 ..     730     811 .. 0.56
   3 ?    6.8   1.5     0.025         7       9      72 ..     792     855 ..     789     859 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.34
                     Tropomyosin_1  38 ksLtkknqqleeevekleeklkeakekaee..sekkktnnealtrkiqlLEeeleesdkkLkettekLretdvkaee 112
                                       ++L++ ++++ + ++ ++++l+ + ++++   s+++ t +++l+  +  + + l+  +++L++   +L+  + + + 
  gi|385805518|ref|YP_005841916.1| 697 SDLQNAVSTITSSINSAQSALSSQLTSVSTqlSNSLTTLQNNLNAAVGTINNALNGINSSLNTMSSQLSTLSNNVNS 773
                                       57888888888889999998888766554411566777788999999999999999999999999999988888888 PP

                     Tropomyosin_1 113 lERkvkaLeqe 123
                                       l   v++L ++
  gi|385805518|ref|YP_005841916.1| 774 LSTSVNQLSSQ 784
                                       88888877665 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.058
                     Tropomyosin_1  26 leqenlekeqeiksLtkknqqleeevekleeklkeakekaeesekkk 72 
                                       + ++     ++++sL++ ++ql ++v ++ ++ ++a ++a+++++++
  gi|385805518|ref|YP_005841916.1| 760 MSSQLSTLSNNVNSLSTSVNQLSSQVSQAVTAAQNAATSASSAATQA 806
                                       33344444455555555555555555555555555555554444444 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.025
                     Tropomyosin_1   9 aeeaqekaeeleekvKeleqenlekeqeiksLtkknqqleeevekleeklkeakekaeesekkk 72 
                                       a++a + a+ +  +++++   + +  ++i+ L+ ++++l ++v ++ ++ + a+++a+++++k+
  gi|385805518|ref|YP_005841916.1| 792 AQNAATSASSAATQAQNAATAASNAANQINALSSQVSNLSSQVSNAVSAANAATTQASDAASKA 855
                                       5788888999999999999999999*********************999999999999998876 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 ?    1.3   0.1       1.4   3.9e+02      67     100 ..     716     749 ..     688     765 .. 0.51
   2 ?    7.8   3.6     0.014       3.7      34     106 ..     760     836 ..     754     838 .. 0.66

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 1.4
                                       S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  67 edaeeliaevkelkeelkaleaelkeleaelekl 100
                                       +  ++l   + +l++ l +l+++l+++   ++++
  gi|385805518|ref|YP_005841916.1| 716 ALSSQLTSVSTQLSNSLTTLQNNLNAAVGTINNA 749
                                       2334444444444444444444444444444444 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.014
                                       HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT....S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCTS-- CS
                      Seryl_tRNA_N  34 ldekrrelqveleelqaerNelskeIgkakkkk....edaeeliaevkelkeelkaleaelkeleaeleklllaiPN 106
                                       + ++  +l + +++l +  N+ls ++++a  +       a++   ++++  +  +++ ++ ++l++++ +l +++ N
  gi|385805518|ref|YP_005841916.1| 760 MSSQLSTLSNNVNSLSTSVNQLSSQVSQAVTAAqnaaTSASSAATQAQNAATAASNAANQINALSSQVSNLSSQVSN 836
                                       55677788899999999999999999999987644444445555555555555555555666666666666666555 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 ?    3.1   0.4      0.35        96      65      98 ..     695     728 ..     684     754 .. 0.73
   2 ?    7.9  15.3     0.011       3.1       2      92 ..     763     853 ..     762     857 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.35
                        TPR_MLP1_2  65 elnelkaeiaelkaeaesakaeleeseesweeqk 98 
                                        +++l++ +++++++ +sa+++l+ +  s ++q 
  gi|385805518|ref|YP_005841916.1| 695 TYSDLQNAVSTITSSINSAQSALSSQLTSVSTQL 728
                                       5778888888888888888888888777776664 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.011
                        TPR_MLP1_2   2 elksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelka 78 
                                       +l++l ++++sl+++ +++ ++++++ +  ++ a +a+ a  + ++  +  ++++++++al +++++l ++++++ +
  gi|385805518|ref|YP_005841916.1| 763 QLSTLSNNVNSLSTSVNQLSSQVSQAVTAAQNAATSASSAATQAQNAATAASNAANQINALSSQVSNLSSQVSNAVS 839
                                       7899999999999999999999999999999999999999999999******************************* PP

                        TPR_MLP1_2  79 eaesakaeleesee 92 
                                       +a++a+++ + + +
  gi|385805518|ref|YP_005841916.1| 840 AANAATTQASDAAS 853
                                       *****999877655 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 ?    2.7   1.0      0.48   1.3e+02      51     104 ..     696     746 ..     676     756 .. 0.54
   2 ?   10.1   6.6    0.0024      0.67      25     120 ..     745     836 ..     742     850 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.48
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHH CS
                         Fib_alpha  51 tkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesni 104
                                       +++ ++ v++i++s++++q+  +   + ++++s++l +  ++l+++++a + +i
  gi|385805518|ref|YP_005841916.1| 696 YSDLQNAVSTITSSINSAQSALS---SQLTSVSTQLSNSLTTLQNNLNAAVGTI 746
                                       44455555555555555555544...3344444444444444544444444433 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0024
                                       CCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCH CS
                         Fib_alpha  25 lllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqe 101
                                       ++++  + ++ +l+++ ++l+++sn+ ++ ++ v+++++++ ++ + ++  + +++ ss   +   ++     ++  
  gi|385805518|ref|YP_005841916.1| 745 TINNALNGINSSLNTMSSQLSTLSNNVNSLSTSVNQLSSQVSQAVTAAQ--NAATSASSAATQ--AQNAATAASNAA 817
                                       67888889999******************99999999999999888888..345555444444..444445555666 PP

                                       HHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 102 snirvLqnvlesneqkiqk 120
                                       ++i++L + ++++++++++
  gi|385805518|ref|YP_005841916.1| 818 NQINALSSQVSNLSSQVSN 836
                                       8888888888888777654 PP

>> MscS_porin  Mechanosensitive ion channel porin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5  31.5     0.038        11      41     177 ..     698     827 ..     691     847 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.038
                        MscS_porin  41 elqkaiddaPkelrelqqelealqkkkeeaskeilaklsleeLeqrllqtssqlqelqeqlaqlnsqlvelqtrper 117
                                       +lq a+ + +  + ++q  l++      +++ ++l+    + L   +++ ++++ + +++l+ +ns+l+++++++++
  gi|385805518|ref|YP_005841916.1| 698 DLQNAVSTITSSINSAQSALSSQ----LTSVSTQLS----NSLTTLQNNLNAAVGTINNALNGINSSLNTMSSQLST 766
                                       45555555555555566555555....444444444....455555666678899999******************* PP

                        MscS_porin 118 aqqqltearqrlqeirnrL.nstaaagealsqaqrtalqaelaaleaqieeleqellsnnn 177
                                       + +   + ++  ++++++  ++  aa++a + a  +a+qa+ aa  a ++ ++  +ls+++
  gi|385805518|ref|YP_005841916.1| 767 LSNNVNSLSTSVNQLSSQVsQAVTAAQNAATSASSAATQAQNAATAASNAANQINALSSQV 827
                                       *******************655556666***************************999875 PP

>> CCDC144C  CCDC144C protein coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   9.7     0.024       6.7      42     163 ..     727     844 ..     695     857 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.024
                          CCDC144C  42 dlqkslKlneetltktvfqyngqLnvlkaentmlnskLekekqnkerleaevesyrsrLaaAiqdheqsqtskrdle 118
                                       +l +sl   ++ l  +v   n+ Ln +++  ++++s+L    +n + l + v+ + s+++ A+  +++  ts + + 
  gi|385805518|ref|YP_005841916.1| 727 QLSNSLTTLQNNLNAAVGTINNALNGINSSLNTMSSQLSTLSNNVNSLSTSVNQLSSQVSQAVTAAQNAATSASSAA 803
                                       45555555666677777777777777777777777777777777777777777777777777777777777776665 PP

                          CCDC144C 119 lalqrerdewlrlqdklnfdvsnlkdknevLsqqLskaeskansL 163
                                        + q +         +   ++  l  +++ Ls q+s+a s an  
  gi|385805518|ref|YP_005841916.1| 804 TQAQNAAT----AASNAANQINALSSQVSNLSSQVSNAVSAANAA 844
                                       55555555....444444466677777777777777777777654 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.4       2.6   7.2e+02      14      38 ..     711     736 ..     696     743 .. 0.40
   2 ?    7.9   1.4     0.013       3.6       8      47 ..     745     784 ..     738     801 .. 0.70
   3 ?    5.7   1.0     0.064        18       4      51 ..     804     851 ..     798     870 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 2.6
                             Spc24  14 sdlesele.sleselaelkeeleele 38 
                                       ++++s+l+ +l+s  ++l + l++l+
  gi|385805518|ref|YP_005841916.1| 711 NSAQSALSsQLTSVSTQLSNSLTTLQ 736
                                       33322222123333333333333333 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.013
                             Spc24   8 riakelsdleselesleselaelkeeleeleeeseekese 47 
                                       +i ++l+ ++s+l+ ++s+l+ l ++++ l+++ ++ +s+
  gi|385805518|ref|YP_005841916.1| 745 TINNALNGINSSLNTMSSQLSTLSNNVNSLSTSVNQLSSQ 784
                                       5777888888888888888888888888888877772222 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.064
                             Spc24   4 nekfriakelsdleselesleselaelkeeleeleeeseekeserved 51 
                                       ++ +++a ++s++ +++++l+s+ ++l +++ +  +  ++ ++++++ 
  gi|385805518|ref|YP_005841916.1| 804 TQAQNAATAASNAANQINALSSQVSNLSSQVSNAVSAANAATTQASDA 851
                                       566777888888888888888888888888777766666633333333 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.5      0.44   1.2e+02      24      51 ..     709     736 ..     697     755 .. 0.73
   2 ?    8.0   3.7     0.014       3.8       8      86 ..     757     834 ..     753     836 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.44
                   Snapin_Pallidin  24 elrqsQeeLleqldrlnekLkeleeaqe 51 
                                       ++   Q++L++ql++ +++L +   + +
  gi|385805518|ref|YP_005841916.1| 709 SINSAQSALSSQLTSVSTQLSNSLTTLQ 736
                                       4567899999999999999987666555 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.014
                   Snapin_Pallidin   8 lellepkldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqklkk 84 
                                       l++++++l +l +++++l +s ++L++q+++  ++ ++++  ++ ++ +++++ a   +n+ +++++l++++++l  
  gi|385805518|ref|YP_005841916.1| 757 LNTMSSQLSTLSNNVNSLSTSVNQLSSQVSQAVTAAQNAATSAS-SAATQAQNAATAASNAANQINALSSQVSNLSS 832
                                       6788899999**********************999997777666.9999999*******************999987 PP

                   Snapin_Pallidin  85 Ra 86 
                                        +
  gi|385805518|ref|YP_005841916.1| 833 QV 834
                                       65 PP

>> HisKA_3  Histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1      0.45   1.2e+02      14      58 ..     718     762 ..     715     771 .. 0.78
   2 ?    5.7   2.2     0.078        21      16      62 ..     780     826 ..     777     832 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.45
                                       HHHHHHHHHHHHHHHHHTTT-HHHHHHHHHHHHHHHHHHHHHHHH CS
                           HisKA_3  14 gqsLsaiklqlelakrllekdpekaaeqlreieelarealqevRr 58 
                                       + +L++++ ql+   ++l+++ ++a  ++ ++ + ++++l+ +  
  gi|385805518|ref|YP_005841916.1| 718 SSQLTSVSTQLSNSLTTLQNNLNAAVGTINNALNGINSSLNTMSS 762
                                       568999999999999999888888888888888888888887755 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.078
                                       HHHHHHHHHHHHHHHTTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           HisKA_3  16 sLsaiklqlelakrllekdpekaaeqlreieelarealqevRrllhn 62 
                                       +Ls+   q+ +a++++++++  aa+q+++++++a++a +++ +l+++
  gi|385805518|ref|YP_005841916.1| 780 QLSSQVSQAVTAAQNAATSASSAATQAQNAATAASNAANQINALSSQ 826
                                       68999999******************************999888765 PP

>> T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX diderm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.5    0.0036      0.99      18      81 ..     698     758 ..     686     759 .. 0.88
   2 ?    3.1  11.6      0.47   1.3e+02       1      57 [.     760     816 ..     760     818 .. 0.77
   3 ?    1.1  13.2       2.1   5.7e+02      18      74 ..     801     857 ..     798     864 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0036
                     T7SS_ESX_EspC  18 khdevaaeiasavaaaagasaavldshGpicaatndavaaaeaarraagealaaasteLadkLr 81 
                                       ++++++++i+s+ ++a   ++a++++ ++++ ++ ++++ ++ + +aa+  ++ a++++   L+
  gi|385805518|ref|YP_005841916.1| 698 DLQNAVSTITSSINSA---QSALSSQLTSVSTQLSNSLTTLQNNLNAAVGTINNALNGINSSLN 758
                                       5678889999999998...9999**********************************9999887 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.47
                     T7SS_ESX_EspC   1 mtdnLsVdpdhlrelaakhdevaaeiasavaaaagasaavldshGpicaatndavaa 57 
                                       m+ +Ls     +++l++ +++ ++++++av+aa++a+++ ++  +    a ++a +a
  gi|385805518|ref|YP_005841916.1| 760 MSSQLSTLSNNVNSLSTSVNQLSSQVSQAVTAAQNAATSASSAATQAQNAATAASNA 816
                                       8889999999***********************777777776655544444444443 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 2.1
                     T7SS_ESX_EspC  18 khdevaaeiasavaaaagasaavldshGpicaatndavaaaeaarraagealaaast 74 
                                          + a+++a+a++ aa++ +a++++   +++++ +av+aa aa ++a +a  +a+ 
  gi|385805518|ref|YP_005841916.1| 801 SAATQAQNAATAASNAANQINALSSQVSNLSSQVSNAVSAANAATTQASDAASKAAY 857
                                       455667888888888889999999999999************999999988887765 PP

>> CCDC84  Coiled coil protein 84
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   8.5     0.028       7.8     126     255 ..     704     840 ..     620     853 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.028
                            CCDC84 126 kdlesteekedefekeeaasiketesnrvevlqslleeeaqises..lgslaelletrkqqsalleslkesaskkst 200
                                       +++ s  +  +++  ++  s++++ sn+ + lq++l+ +  + ++   g + +l ++++q s+l++++++ +++ ++
  gi|385805518|ref|YP_005841916.1| 704 STITSSINSAQSALSSQLTSVSTQLSNSLTTLQNNLNAAVGTINNalNGINSSLNTMSSQLSTLSNNVNSLSTSVNQ 780
                                       56677888888888999999*****************9988777755333344445556666666666655444444 PP

                            CCDC84 201 leestsvlqnpkgshqqagssvaksaeevtqlssge.....eltfissqdaaskgNvhtg 255
                                       l++++s   +  + + +++ss+a++a++   ++s++      l++  s+ ++++ N  ++
  gi|385805518|ref|YP_005841916.1| 781 LSSQVSQAVTAAQNAATSASSAATQAQNAATAASNAanqinALSSQVSNLSSQVSNAVSA 840
                                       433333332222222222222222222222222222233332222223445555555555 PP

>> DASH_Duo1  DASH complex subunit Duo1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.8       2.4   6.5e+02       9      41 ..     699     732 ..     694     740 .. 0.72
   2 ?    8.6   3.9    0.0056       1.5       8      54 ..     742     788 ..     734     793 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 2.4
                         DASH_Duo1   9 LrkinevienviesLkkak.sniervketvestn 41 
                                       L++  ++i ++i+s ++a  s++ +v+++++++ 
  gi|385805518|ref|YP_005841916.1| 699 LQNAVSTITSSINSAQSALsSQLTSVSTQLSNSL 732
                                       6667777777777777777777888888777765 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0056
                         DASH_Duo1   8 qLrkinevienviesLkkaksniervketvestntLLdkWirIlsqt 54 
                                        + +in++++++++sL++++s++++++++v+s +t +++ ++  sq+
  gi|385805518|ref|YP_005841916.1| 742 AVGTINNALNGINSSLNTMSSQLSTLSNNVNSLSTSVNQLSSQVSQA 788
                                       5778***************************9998877777666665 PP

>> WEMBL  Weak chloroplast movement under blue light
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6  15.2      0.04        11     332     449 ..     727     852 ..     684     862 .. 0.62

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.04
                             WEMBL 332 kekaeLaslrqregmasiavss....LeaelsrtkselelvqakekearekmvelpkeLqeAaqeaeeAkslAqaar 404
                                       +  ++L++l+++ ++a  ++++    ++  l+ + s+l+++ ++ +     + +l  ++++A   a++A ++A +a 
  gi|385805518|ref|YP_005841916.1| 727 QLSNSLTTLQNNLNAAVGTINNalngINSSLNTMSSQLSTLSNNVNSLSTSVNQLSSQVSQAVTAAQNAATSASSAA 803
                                       22345677777666666555432222778888888888888888888888888888888888888888777777777 PP

                             WEMBL 405 eelrkakeeaeqakaavstvesrLea....vlkEieAakaseklAlaai 449
                                        + ++a   a +a  +++++ s+++     v+  + Aa+a+   A +a+
  gi|385805518|ref|YP_005841916.1| 804 TQAQNAATAASNAANQINALSSQVSNlssqVSNAVSAANAATTQASDAA 852
                                       7777777777777777777777665411114455555555555555443 PP

>> SKA1  Spindle and kinetochore-associated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9  13.1      0.15        41      37     124 ..     730     819 ..     676     865 .. 0.50

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.15
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXX......XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..X CS
                              SKA1  37 ellnklkkelqeeeeaikklkkeieaslkqqek.lqhlkenlpshlpkktaassaeeskssspeeeeeteskke..k 110
                                       ++l  l+  l+    +i+++ + i+ sl+   + l+ l++n++s   + ++ ss+++++    + + +t+++++  +
  gi|385805518|ref|YP_005841916.1| 730 NSLTTLQNNLNAAVGTINNALNGINSSLNTMSSqLSTLSNNVNSLSTSVNQLSSQVSQAVTAAQ-NAATSASSAatQ 805
                                       3444444444444444444444444444444444555555555543333333333222222222.211111111122 PP

                                       XXXXXXXXXXXX-S CS
                              SKA1 111 eeeaekakkpkkre 124
                                       +++a++a  +++++
  gi|385805518|ref|YP_005841916.1| 806 AQNAATAASNAANQ 819
                                       22222222222222 PP

>> RasGAP_C  RasGAP C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.4     0.077        21      57      90 ..     705     738 ..     692     749 .. 0.84
   2 ?    4.4   3.9      0.14        38      25      94 ..     730     803 ..     729     857 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.077
                          RasGAP_C  57 etlktLseknnylesqlesYkayienvleqlkkk 90 
                                       +  +++++ ++ l+sql s ++ ++n+l +l+++
  gi|385805518|ref|YP_005841916.1| 705 TITSSINSAQSALSSQLTSVSTQLSNSLTTLQNN 738
                                       44578999***********************987 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.14
                          RasGAP_C  25 nnyqellneIakdirnkgrlrekrkeElesleetlktLseknnylesqlesYkayienvleqlkkkkgk....l 94 
                                       n++ +l n +++ + + +++ + +++ l+++ + l+tLs++ n l++ ++++++ +++++   +++ ++     
  gi|385805518|ref|YP_005841916.1| 730 NSLTTLQNNLNAAVGTINNALNGINSSLNTMSSQLSTLSNNVNSLSTSVNQLSSQVSQAVTAAQNAATSassaA 803
                                       66777777777777777777788888888888888888888888888888888888888888877753332220 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (893 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2549  (0.142172); expected 358.6 (0.02)
Passed bias filter:                      898  (0.0500865); expected 358.6 (0.02)
Passed Vit filter:                       239  (0.0133304); expected 17.9 (0.001)
Passed Fwd filter:                       100  (0.00557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              65  [number of targets reported over threshold]
# CPU time: 1.62u 0.38s 00:00:02.00 Elapsed: 00:00:00.61
# Mc/sec: 4393.41
//
Query:       gi|385805519|ref|YP_005841917.1|  [L=194]
Description: hypothetical protein FFONT_0475 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00031   20.6   0.1     0.0011   18.9   0.1    2.0  2  RHH_3     Ribbon-helix-helix domain


Domain annotation for each model (and alignments):
>> RHH_3  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   5.9e-08    0.0011       8      41 ..      11      44 ..       6      49 .. 0.90
   2 ?   -2.9   0.0      0.39   7.1e+03       2      11 ..     109     118 ..     108     118 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 5.9e-08
                             RHH_3  8 sidpelaekLkaLSekTrIprSklldeAiellLe 41
                                      +i +++ ++ +++Sek +Ip + l++ A++++++
  gi|385805519|ref|YP_005841917.1| 11 AISEDIITEAMNISEKVGIPFTTLIERALSDVFK 44
                                      7889999999**********************97 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.39
                             RHH_3   2 ktrttvsidp 11 
                                       k+++++s+d+
  gi|385805519|ref|YP_005841917.1| 109 KVKRGISVDE 118
                                       8999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); 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 0.29s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1218.77
//
Query:       gi|385805520|ref|YP_005841918.1|  [L=173]
Description: hypothetical protein FFONT_0476 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0096   16.1   0.1      0.059   13.6   0.0    2.1  2  MatP_C          MatP C-terminal ribbon-helix-helix domain
  ------ inclusion threshold ------
      0.066   13.8   0.0       0.19   12.3   0.0    1.8  1  CopG_antitoxin  CopG antitoxin of type II toxin-antitoxin sys
       0.18   11.8   0.1       0.18   11.8   0.1    2.3  3  RHH_3           Ribbon-helix-helix domain


Domain annotation for each model (and alignments):
>> 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 !   13.6   0.0     1e-05     0.059       4      39 ..       5      40 ..       2      57 .. 0.88
   2 ?    0.0   0.0      0.17     1e+03      27      53 ..      91     115 ..      84     120 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1e-05
                            MatP_C  4 KKSiDLdyavWqrLsklsqrrgsTLSetivqLieea 39
                                      +KSi  dy   +rL + s++rg+  S  +++++e+ 
  gi|385805520|ref|YP_005841918.1|  5 RKSIAADYDLAERLKEFSKNRGMNFSKYLNEILEQC 40
                                      69***************************9999975 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.17
                            MatP_C  27 TLSetivqLieeaerkekyeeqvsslk 53 
                                        +  ti++L +e  + e +e  v+++k
  gi|385805520|ref|YP_005841918.1|  91 SIGKTISELSDE--SFEIVEMLVNNMK 115
                                       344555555554..3455555555555 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 ?   12.3   0.0   3.1e-05      0.19      40      78 ..       3      39 ..       1      40 [. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.1e-05
                    CopG_antitoxin 40 kktksislrlpedlLealkekAnkrdvpyqslikellee 78
                                      k+ ksi  + + dl e+lke  ++r+++++++++e+le+
  gi|385805520|ref|YP_005841918.1|  3 KNRKSI--AADYDLAERLKEFSKNRGMNFSKYLNEILEQ 39
                                      566666..8999************************986 PP

>> RHH_3  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   3.1e-05      0.18       2      36 ..       3      37 ..       2      39 .. 0.88
   2 ?   -2.7   0.1         1     6e+03      29      35 ..      73      79 ..      73      79 .. 0.91
   3 ?   -3.9   0.1       2.4   1.5e+04      32      37 ..     164     169 ..     164     169 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.1e-05
                             RHH_3  2 ktrttvsidpelaekLkaLSekTrIprSklldeAi 36
                                      k r +++ d +lae+Lk+ S+  + + Sk+l e +
  gi|385805520|ref|YP_005841918.1|  3 KNRKSIAADYDLAERLKEFSKNRGMNFSKYLNEIL 37
                                      6777899999*********************9855 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1
                             RHH_3 29 SklldeA 35
                                      S+++++A
  gi|385805520|ref|YP_005841918.1| 73 SDIIEKA 79
                                      899**98 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 2.4
                             RHH_3  32 ldeAie 37 
                                       +deA++
  gi|385805520|ref|YP_005841918.1| 164 IDEAMK 169
                                       899985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.32s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 1021.22
//
Query:       gi|385805521|ref|YP_005841919.1|  [L=185]
Description: isochorismatase hydrolase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.8e-46  156.9   0.0    6.4e-46  156.7   0.0    1.0  1  Isochorismatase  Isochorismatase family
  ------ inclusion threshold ------
      0.052   13.7   0.0      0.096   12.8   0.0    1.4  1  Ku_PK_bind       Ku C terminal domain like


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 !  156.7   0.0   7.1e-50   6.4e-46       3     172 ..       5     171 ..       3     174 .. 0.96

  Alignments for each domain:
  == domain 1  score: 156.7 bits;  conditional E-value: 7.1e-50
                   Isochorismatase   3 lvviDmqndfveegvkeseeisavveninkllkaarkagipviftrdvheleevkgdlderkaaphfkpgttgaelv 79 
                                       l++iDm  dfv +g   +e+++++++ i++l + a+k++ipvi+  d+h     + d + + + +h ++g++g++++
  gi|385805521|ref|YP_005841919.1|   5 LIIIDMIHDFV-DGKFGNENVKKIIPCIRELKEFAKKNSIPVIYAVDSHI---KGVDREIEVWGEHAIEGEWGSKII 77 
                                       9**********.**************************************...99999******************* PP

                   Isochorismatase  80 pelaplegdvvvdKtrfsafagtdldeiLkelgiktivlaGiatdvCVeatardaldlGyevvvvsDAvaalspelh 156
                                       +el+p+ g++++ K+r+saf++t+ld +L+el ++t++l+G +t++CV++ta da+ +Gy++++++++vaa+s+ +h
  gi|385805521|ref|YP_005841919.1|  78 EELEPQNGEFIIKKRRYSAFFSTGLDLLLRELDVDTLILTGTSTHICVLHTAADAFFRGYKIIIPKECVAAFSESDH 154
                                       ***************************************************************************** PP

                   Isochorismatase 157 daalkrlkq.afatvit 172
                                        +al  ++q ++a+v++
  gi|385805521|ref|YP_005841919.1| 155 GYALVYMSQvYGAKVLS 171
                                       *******9614577766 PP

>> Ku_PK_bind  Ku C terminal domain like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.1e-05     0.096      28      66 ..       9      47 ..       5      62 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.1e-05
                        Ku_PK_bind 28 svIeqlvedslgdssydkaveclkalReeaieeeepely 66
                                      ++I+++v+ ++g+++++k++ c++ l+e a +++ p  y
  gi|385805521|ref|YP_005841919.1|  9 DMIHDFVDGKFGNENVKKIIPCIRELKEFAKKNSIPVIY 47
                                      68****************************999988877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); 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: 1144.92
//
Query:       gi|385805522|ref|YP_005841920.1|  [L=200]
Description: HD superfamily metal-dependent phosphohydrolase [Fervidicoccus fontis Kam940]
Scores for complete 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   47.0   2.0    2.7e-12   47.0   2.0    1.8  2  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 !   47.0   2.0   1.5e-16   2.7e-12       2     121 ..      33     133 ..      32     134 .. 0.92
   2 ?   -2.0   0.1      0.22     4e+03      60      67 ..     173     180 ..     148     197 .. 0.50

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 1.5e-16
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHHH CS
                                HD   2 leHsleVaklarrlaedlgeeedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgldl 78 
                                       +eH  +V +l+  ++e+++ee d  +ll+ a+lHDi  +             +++   +++++ ilr++++r+++ +
  gi|385805522|ref|YP_005841920.1|  33 IEHVERVVRLCLYIGEKVEEEVDTFVLLASAYLHDISRVSDD---------ENHEALASEISEDILRKFGIREEK-I 99 
                                       79*************************************933.........35667899**************44.* PP

                                       HHHHHHHHTTCCHHHHHHHHHHHHCCTSCHHHHHHHHHHHHHH CS
                                HD  79 edvaklirehheswegkkrprglaerqlslearivklaDrlaa 121
                                       + ++++ir+h++s+ ++         + s+ea+i+++aD+++a
  gi|385805522|ref|YP_005841920.1| 100 KKISHAIRAHSFSSGIE---------PGSIEAKILSDADKIDA 133
                                       **************866.........**************998 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.22
                                       HHHHHHHH CS
                                HD  60 ekvgaeil 67 
                                       +k g ei+
  gi|385805522|ref|YP_005841920.1| 173 TKPGKEIA 180
                                       22333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       892  (0.0497518); expected 358.6 (0.02)
Passed bias filter:                      641  (0.0357521); 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: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1340.69
//
Query:       gi|385805523|ref|YP_005841921.1|  [L=137]
Description: hypothetical protein FFONT_0479 [Fervidicoccus fontis Kam940]
Scores for 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  115.0   0.0    2.3e-33  114.8   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 !  114.8   0.0   1.3e-37   2.3e-33       1     113 [.      20     132 ..      20     134 .. 0.94

  Alignments for each domain:
  == domain 1  score: 114.8 bits;  conditional E-value: 1.3e-37
                                       E-HHHHHHHHHHHT.SEEEEEEEESSSSEEEEEEESSSHHHHHHHHHHHHHHSTTT.T-GGG.TTS..THHHHHHHH CS
                           UPF0047   1 diteeveeavkesgvkeGlvlvfsrhttasltinEnadpdvqeDleealeklvpee.eYrhn.aegpdnadaHlkss 75 
                                       +it+ ve+avkesg+++G+vl+f+ h+ta +++nE+ ++++++D+ +++++++ +e +Y hn ++  +nad+H+ +s
  gi|385805523|ref|YP_005841921.1|  20 NITSFVEQAVKESGINNGIVLIFVLHATATIVVNED-EQGLKKDIINWIDEFLDKErKYYHNlID--NNADSHIAAS 93 
                                       69**********************************.*****************999*****454..5********* PP

                                       HH-SEEEEEEETTEE---TTEEEEEEESS-SSE.EEEEE CS
                           UPF0047  76 llgssltipvedgklalGtwqsiylveldgpre.Rkvvv 113
                                       ++g+s ++p+++gkl  Gtwq+i+l+eldgpr+ R+v++
  gi|385805523|ref|YP_005841921.1|  94 FFGPSKVFPLVNGKLIKGTWQEIMLFELDGPRNrRQVLI 132
                                       *******************************99566665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); 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: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 802.65
//
Query:       gi|385805524|ref|YP_005841922.1|  [L=222]
Description: hydroxyacylglutathione hydrolase [Fervidicoccus fontis Kam940]
Scores for complete 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   88.0   0.0    9.5e-25   87.8   0.0    1.1  1  Lactamase_B    Metallo-beta-lactamase superfamily
    0.00037   20.1   0.0     0.0005   19.6   0.0    1.3  1  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
       0.17   11.1   0.0       0.58    9.4   0.0    1.7  2  Peptidase_U57  YabG peptidase U57


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 !   87.8   0.0   1.6e-28   9.5e-25       2     197 .]      20     203 ..      19     203 .. 0.87

  Alignments for each domain:
  == domain 1  score: 87.8 bits;  conditional E-value: 1.6e-28
                                       CCCSSEEEEEE..ETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCE CS
                       Lactamase_B   2 gpdpvnsylie..gdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgava 76 
                                       g++ +n+y+i   +++++++iD+G s+     +     l+  +++  +vi TH+H+DH+ g++++++a++++ ++ +
  gi|385805524|ref|YP_005841922.1|  20 GVLRTNTYIIFskDPKKALMIDPGESSNVIVDF-----LKNRDLNSIWVIGTHGHFDHVCGVDEIKSAYNAKFFMSS 91 
                                       77889*******999*****************9.....566777777****************************** PP

                                       HHHHCCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTS CS
                       Lactamase_B  77 eeapalfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDall 153
                                       e+++  +++ +   +       + + + +pd+d+ +l+ +++++++ +v  +pgh++g++ +++++ +++f+GD+++
  gi|385805524|ref|YP_005841922.1|  92 EDLFLKEHNKKVLKRFNLN---EKDCPLDPDIDLKDLEKIEFDDQEIEVLKTPGHTPGSILLYLREVDLAFSGDTIF 165
                                       ***********88888875...799999************************************************* PP

                                       SHHCCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEE.SS CS
                       Lactamase_B 154 agetgridltlrgaevrdpsdaekyldsllklaglkaevlvp.gH 197
                                       ag++gr+d+     + +   + +k+++ +l  ++ +a+ lv+ gH
  gi|385805524|ref|YP_005841922.1| 166 AGSIGRTDF-----FGGNEEEMKKSIKLIL--ERVNADALVLpGH 203
                                       *********.....4445555555554333..3444555554466 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 !   19.6   0.0   8.4e-08    0.0005      26     115 ..      56     145 ..      37     205 .. 0.60

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 8.4e-08
                                       --..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEE.EEHHHHHHCCTTCGHHHCHTT.....TTEEEEEE-TTSEE CS
                     Lactamase_B_2  26 delppidaVllthaHyDHlaglltlrelrpkklply.apkgvlavleanfvylaleee.....pavnvheldwgesf 96 
                                       ++l++i  V+ th+H+DH++g++ ++  ++ k+ +   ++ + ++ ++ +++++l+e+     p     +l+  e++
  gi|385805524|ref|YP_005841922.1|  56 RDLNSIW-VIGTHGHFDHVCGVDEIKSAYNAKFFMSsEDLFLKEHNKKVLKRFNLNEKdcpldP---DIDLKDLEKI 128
                                       3677787.9******************6665532221234444555555555555555542333...3344444566 PP

                                       EECSTTEEEEEEEE-EE-- CS
                     Lactamase_B_2  97 elgdggleitatparhksg 115
                                       e++d   ei++   ++ ++
  gi|385805524|ref|YP_005841922.1| 129 EFDDQ--EIEVLKTPGHTP 145
                                       66643..355555555444 PP

>> Peptidase_U57  YabG peptidase U57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.15   8.9e+02     139     186 ..      44      91 ..      35     133 .. 0.73
   2 ?    9.4   0.0   9.8e-05      0.58     136     162 ..     178     204 ..     173     217 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.15
                     Peptidase_U57 139 eqpekvkellekvkpdilvlTGHDgllkkkkdlkdlknYrnskyFvea 186
                                       e +++++++l++   + + + G  g   +   ++++k+  n+k+F+++
  gi|385805524|ref|YP_005841922.1|  44 ESSNVIVDFLKNRDLNSIWVIGTHGHFDHVCGVDEIKSAYNAKFFMSS 91 
                                       566777777777766555555555666677777888887788888765 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 9.8e-05
                     Peptidase_U57 136 kEkeqpekvkellekvkpdilvlTGHD 162
                                       +E+e+++++k +le+v++d lvl GH 
  gi|385805524|ref|YP_005841922.1| 178 NEEEMKKSIKLILERVNADALVLPGHG 204
                                       69************************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.48
# Mc/sec: 1390.05
//
Query:       gi|385805525|ref|YP_005841923.1|  [L=227]
Description: dolichol kinase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        9.4    5.9  13.0       0.67    9.6   8.0    1.6  2  DUF2101   Predicted membrane protein (DUF2101)


Domain annotation for each model (and alignments):
>> DUF2101  Predicted membrane protein (DUF2101)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   8.0   3.8e-05      0.67      49     155 ..       6     110 ..       3     116 .. 0.85
   2 ?   -2.6   0.2       0.2   3.7e+03      50      62 ..     208     220 ..     178     225 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 3.8e-05
                           DUF2101  49 vlvflksllvlllaalleflllryilirnielli..dfeayrafylavsviailaylgyvllrklslelyyylvyll 123
                                       + vf+++l v +++a+  fll+ y+  +  + +i  + +  +a y+   +i i  ++g v+   +++ ++  ++ +l
  gi|385805525|ref|YP_005841923.1|   6 IDVFIRDLAVAIPLAIYVFLLICYVTRKTYDAMIkrGVKERKAVYYNRKIIHI--FVGGVVSAFIPFIFKEPFTPFL 80 
                                       679*******************************8888999999**9998876..6777888888888888888766 PP

                           DUF2101 124 vivivvlvfryyfksrygrDytyGvveevked 155
                                       ++  v l  ++ +k++  + y +  v e k +
  gi|385805525|ref|YP_005841923.1|  81 FA--VLLGSFLLYKHKSRKKYYWFQVDENKYE 110
                                       55..5678889999999999999999887765 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.2
                           DUF2101  50 lvflksllvllla 62 
                                       l+ l s  +l++a
  gi|385805525|ref|YP_005841923.1| 208 LIVLSSSIILIIA 220
                                       2333333334433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       708  (0.0394891); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1454.31
//
Query:       gi|385805526|ref|YP_005841924.1|  [L=203]
Description: hypothetical protein FFONT_0482 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score 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   14.0   0.0       0.09   13.1   0.0    1.5  1  FCH       Fes/CIP4, and EFC/F-BAR homology domain


Domain annotation for each model (and alignments):
>> FCH  Fes/CIP4, and EFC/F-BAR homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     5e-06      0.09      24      47 ..      31      54 ..      29      98 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5e-06
                                      HHHHHHHHHHHHHHHHHCT----T CS
                               FCH 24 keRaeiEkeYakkLqkLakkylkr 47
                                      ++ ++ ++e a kL+kLa+ky+ +
  gi|385805526|ref|YP_005841924.1| 31 RKIMAADQELAEKLSKLAEKYNTS 54
                                      678999***************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       866  (0.0483016); expected 358.6 (0.02)
Passed bias filter:                      628  (0.0350271); 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: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1266.80
//
Query:       gi|385805527|ref|YP_005841925.1|  [L=157]
Description: ADP-ribose pyrophosphatase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.1e-19   69.3   0.0    3.7e-19   69.1   0.0    1.1  1  NUDIX      NUDIX domain
  ------ inclusion threshold ------
       0.13   11.8   0.0       0.14   11.7   0.0    1.1  1  WASH_WAHD  WAHD domain of WASH complex


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 !   69.1   0.0   4.2e-23   3.7e-19       4     116 ..       7     120 ..       4     134 .. 0.74

  Alignments for each domain:
  == domain 1  score: 69.1 bits;  conditional E-value: 4.2e-23
                                       EEEEEEEEETTSEEEEEEESSSSTTT..EESSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEEE CS
                             NUDIX   4 ravgvvllnekgevLlvrrskkpfpg..WelPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapydgpy 78 
                                       ++vg+v++nekge+Llv+r  +p+++  W++PgG++e  Et+ + A REl EEtGl+ +  +++  +++l   ++ +
  gi|385805527|ref|YP_005841925.1|   7 VGVGAVVFNEKGEILLVKRI-YPPQEgkWAIPGGHLELEETIFDGAKRELYEETGLIGDA-KCIVNVDELIVLKEDK 81 
                                       78******************.777778*************999************74433.3333344444443333 PP

                                       EE.EEEEE.EEEEEEECSGCSSTSTTTEEEEEEEEHHHH.H CS
                             NUDIX  79 gd.eheil.yvfleevegelepndenevsevrwvpleel.l 116
                                          +h+il  v++e+v gel+ +   +  +++++++ e+ +
  gi|385805527|ref|YP_005841925.1|  82 SVwRHYILiDVLFENVRGELKAG--SDAGDAKFFSPSEAiN 120
                                       33334544345558999999999..55569999*****942 PP

>> WASH_WAHD  WAHD domain of WASH complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   1.5e-05      0.14     140     211 ..      51     122 ..      30     149 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.5e-05
                         WASH_WAHD 140 letekeveeGlgtlpkkiksvssLLlfntneneYkkYvtldplrgavkktkkaveaekeeklldaplsisks 211
                                        ++e   e Gl    k i  v++L+++ + +  ++ Y+ +d l  +v+ + ka     ++k ++ + +i  +
  gi|385805527|ref|YP_005841925.1|  51 AKRELYEETGLIGDAKCIVNVDELIVLKEDKSVWRHYILIDVLFENVRGELKAGSDAGDAKFFSPSEAINSK 122
                                       456666777999999999************************999988888877777777777777666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); 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: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 941.25
//
Query:       gi|385805528|ref|YP_005841926.1|  [L=242]
Description: NADPH-dependent FMN reductase [Fervidicoccus fontis Kam940]
Scores for 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  111.5   0.0    4.6e-32  110.9   0.0    1.2  1  FMN_red       NADPH-dependent FMN reductase
    1.2e-13   51.2   0.0    1.8e-13   50.7   0.0    1.2  1  Flavodoxin_2  Flavodoxin-like fold
  ------ inclusion threshold ------
       0.25   10.8   0.0       0.33   10.4   0.0    1.2  1  T6SS_VasJ     Type VI secretion, EvfE, EvfF, ImpA, BimE, VC_A


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 !  110.9   0.0   7.6e-36   4.6e-32       2     144 ..       7     160 ..       6     169 .. 0.90

  Alignments for each domain:
  == domain 1  score: 110.9 bits;  conditional E-value: 7.6e-36
                                       EEEEEES--STT-HHHHHHHHHHCCT-T.T-CEEEEETTTS..--........---HCHGHTCGGSHHHHHHHHHHH CS
                           FMN_red   2 kilvisGSlrkgsntrklaewaaealkeagaevelidladl.ilpc......alcdkdlesegqtsddvaellekia 71 
                                       kil i +S+rkg+n+ kl+ +a+  ++++g+e+e+i l+d+ i+pc      ++  +++++   ++dd+++l +k+ 
  gi|385805528|ref|YP_005841926.1|   7 KILFIDASARKGGNSTKLMYVAELGARKRGCETEIIYLKDHkIKPCagcvsdDIMACKFPC-VIDDDDFNSLARKLI 82 
                                       9*************************999*****************986666555556655.899************ PP

                                       H-SCEEEEEEECTTCE-HHHHHHHHCHT-.......SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHHHHHHHTT-EE CS
                           FMN_red  72 aadaliivtPeYngsysgllKnalDrlsr......trgkkelrgKpvalvavgggrrgglraeeqlrqvlaelgaiv 142
                                       ++d+++i+tP+Y++++sg++Kn++Drl        + gk  + gK++a++a+g ++ g++ + + l++v++ +g ++
  gi|385805528|ref|YP_005841926.1|  83 ESDGVVIATPVYWYMVSGIMKNFIDRLTSlenmlfHTGKSLVDGKVAAFIATG-SDTGTSMTIAYLMDVFNSFGYHI 158
                                       ***************************99*****999999999*******999.67**************9777666 PP

                                       EE CS
                           FMN_red 143 vp 144
                                       +p
  gi|385805528|ref|YP_005841926.1| 159 PP 160
                                       65 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.7   0.0     3e-17   1.8e-13       2     179 ..       7     168 ..       6     183 .. 0.75

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 3e-17
                                       EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTTTEEEEEEHHCC...T-----CCCCHC.CHHHHTT..C.HHHHHHH CS
                      Flavodoxin_2   2 kiLiinahprpeksfssalaqafvealekagphevtvrdLyad...flpvlttrdlaa.klayeek..p.adveseq 71 
                                       kiL+i+a+ r+ + +s +l   +  +++k g  e +++ L +    +++ +  +d+ a k     +     d + + 
  gi|385805528|ref|YP_005841926.1|   7 KILFIDASARK-GGNSTKLMYVAELGARKRG-CETEIIYLKDHkikPCAGCVSDDIMAcK-----FpcViDDDDFNS 76 
                                       9*********9.6999***************.7777777777620333344444444332.....123223444445 PP

                                       .HHHHHCSSEEEEEEE-BTTB--HHHHHHHHHHS-TTT.SCEETTCSSCCCCTTTTSEEEEEEEESS-GGGSSTTSS CS
                      Flavodoxin_2  72 .iekllaadaivlqfPlwwfgvPailKgwiDrvltagf.afyteeggegrgggLkgkkalvivttGgpeesyqergl 146
                                          kl ++d +v+++P++w++v+ i+K++iDr  +     f        +g+ L + k+   ++tG+++        
  gi|385805528|ref|YP_005841926.1|  77 lARKLIESDGVVIATPVYWYMVSGIMKNFIDRLTSLENmLF-------HTGKSLVDGKVAAFIATGSDT-------- 138
                                       55*******************************99887355.......345889988888888999992........ PP

                                       S-S-HHHHHHHHHHHHHHTT-EEEEEEEEESCT CS
                      Flavodoxin_2 147 egaamdellpplrgilgfiGikdvepvlvegva 179
                                          +  +++ +l ++++ +G +  ++ l++ ++
  gi|385805528|ref|YP_005841926.1| 139 ---GTSMTIAYLMDVFNSFGYHIPPWSLAYHHS 168
                                       ...45677888***********99999999853 PP

>> T6SS_VasJ  Type VI secretion, EvfE, EvfF, ImpA, BimE, VC_A0119, VasJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   5.5e-05      0.33     119     153 ..     102     136 ..      95     180 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 5.5e-05
                         T6SS_VasJ 119 laalLarlPgLeeLsFsDgtPFadeetraWlaeea 153
                                       ++++++rl +Le++ F+ g  ++d +++a +a+ +
  gi|385805528|ref|YP_005841926.1| 102 MKNFIDRLTSLENMLFHTGKSLVDGKVAAFIATGS 136
                                       689************************99998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 1566.50
//
Query:       gi|385805529|ref|YP_005841927.1|  [L=494]
Description: hypothetical protein FFONT_0485 [Fervidicoccus fontis Kam940]
Scores for complete 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  57.5      1e-15   57.9  31.5    2.2  2  Polysacc_synt    Polysaccharide biosynthesis protein
      8e-12   45.4  43.7      4e-07   30.2  18.9    4.0  3  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
    0.00022   20.0  39.7    0.00034   19.4  39.0    1.9  1  MurJ             Lipid II flippase MurJ


Domain annotation for each model (and alignments):
>> Polysacc_synt  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.9  31.5   1.7e-19     1e-15       4     271 ..      13     282 ..       6     285 .. 0.94
   2 !    8.5  17.9   0.00019       1.2      74     235 ..     293     451 ..     286     454 .. 0.90

  Alignments for each domain:
  == domain 1  score: 57.9 bits;  conditional E-value: 1.7e-19
                     Polysacc_synt   4 gvivlllsqlitkllafvtlvylarilgpegfGlvalalaivtllviltdlGlnaalvre......iakyrekkelv 74 
                                         ++l ls++i++l +f +  +++ri g   +G v++++ + +l++ l++lG+++ l+r+      i k++e    +
  gi|385805529|ref|YP_005841927.1|  13 SGFWLYLSTIISNLQGFFYWLIISRIAGGSVVGTVSAIVGLSSLISGLISLGITTGLSRYtglcigIKKSNE--CAS 87 
                                       579********************************************************9777766788888..8** PP

                     Polysacc_synt  75 slillnvllvllvlvllfllllliaaflglpelavlylilalmllllvgvasfrrglfqglermkyaavsqvveqls 151
                                        +++ +v+++ll+ ++  +l +  + f+g+    +   + +++ll++vg+a  +++++q l   ky+++s+v+  ++
  gi|385805529|ref|YP_005841927.1|  88 EYLWTSVYFSLLIYIIGGILVFIYSKFFGGAGSYSTEELTIAALLVFVGFAGSFTSFLQSLLLTKYIFISVVAAAIF 164
                                       **************99999888888988887777777777777777******************************* PP

                     Polysacc_synt 152 rvilvliavflfldivaavlgavlaalvggivslavlrkkfrprfvilslklvrellsfsapltisslaillytyid 228
                                        ++l +++v+ ++  v+a+lg++++++v+ ++  + + k+ +++ +++ +   +ell+ ++p  +  +++++ +++ 
  gi|385805529|ref|YP_005841927.1| 165 KFTLGVLLVYFGYGWVGAALGYFVSTVVQFVINSYHSLKITGFKIYFS-KDKLKELLRAGIPSWLPGVISTIGQWFG 240
                                       **************************************9999******.**************************** PP

                     Polysacc_synt 229 sillglllgaeavGiYnaayqllvaisgllapivtaalfPvfs 271
                                       +ill   +g+ + G Y  a ql++++ ++ +  ++  l Pv+s
  gi|385805529|ref|YP_005841927.1| 241 VILLYGTIGSLETGSYFIASQLANVVLNISNILNG-LLLPVLS 282
                                       **999999***********************9999.99**998 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00019
                     Polysacc_synt  74 vslillnvllvllvlvllfllllliaaflglpelavlylilalmll.llvgvasfrrglfqglermkyaavsqvveq 149
                                       ++++ +++ l+l v++ +++   l+ +++g++  +  +++ +l +  + v+++ f+++l+ +  +   ++ s ++++
  gi|385805529|ref|YP_005841927.1| 293 SRVFRISLALMLPVSFYIMVYPTLLLDIFGKELSSGSIPLVILLFGsIPVAFSGFVSSLVYAYGDYLTILKSGLITN 369
                                       67788899999999999999999999********************999**************************** PP

                     Polysacc_synt 150 lsrvilvliavflfldivaavlgavlaalvggivslavlrkkfrprfvilslklvrellsfsapltisslaillyty 226
                                       + rvil +i+v  ++   +a+++ + ++ +g++++l++ +    + +v +++k +  l+s+ + + +  +++ l++y
  gi|385805529|ref|YP_005841927.1| 370 VPRVILYFILVPKMS-GIGAAISFTTGSYLGALYLLYIAY----KLQVQFKKKEIAILISVPLIFSVLLFFVRLSWY 441
                                       ***************.677888888888899999999999....888888899******999999999999****** PP

                     Polysacc_synt 227 idsi.llgll 235
                                       + ++ +++++
  gi|385805529|ref|YP_005841927.1| 442 LGMLiMASSY 451
                                       *999666655 PP

>> Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   8.2       2.2   1.3e+04      60     133 ..      19     108 ..      14     117 .. 0.50
   2 !   30.2  18.9   6.8e-11     4e-07       6     110 ..     129     237 ..     126     321 .. 0.84
   3 !   29.3  16.8   1.2e-10   7.4e-07       2     117 ..     332     446 ..     331     456 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 2.2
                   Polysacc_synt_C  60 iatvlallvvavlnlyalrrllgiklellrrllkpllaalvmgivvylllllllglllla................. 119
                                       ++t+++ l ++++ l++ r   g  +   +    + l++l+ g++    l ++ gl+++                  
  gi|385805529|ref|YP_005841927.1|  19 LSTIISNLQGFFYWLIISRIAGGSVV--GTVSAIVGLSSLISGLI---SLGITTGLSRYTglcigikksnecaseyl 90 
                                       57777777777776555555555554..33333444444444444...33333333333333444456667765555 PP

                   Polysacc_synt_C 120 ....alalllavlvgalv 133
                                            ++ll+ ++ g+lv
  gi|385805529|ref|YP_005841927.1|  91 wtsvYFSLLIYIIGGILV 108
                                       553222555555333333 PP

  == domain 2  score: 30.2 bits;  conditional E-value: 6.8e-11
                   Polysacc_synt_C   6 alsiiflslstvlssiLqglgrqkialkalvigalvklilnllli.plfgivGaaiatvlallvvavlnlyalrrll 81 
                                       a  ++f +++  ++s Lq+l  +k++++++v++a++k+ l +ll+   +g vGaa++  ++ +v +v+n y+  +++
  gi|385805529|ref|YP_005841927.1| 129 AALLVFVGFAGSFTSFLQSLLLTKYIFISVVAAAIFKFTLGVLLVyFGYGWVGAALGYFVSTVVQFVINSYHSLKIT 205
                                       6678999**************************************667888************************** PP

                   Polysacc_synt_C  82 gikl....ellrrllkpllaalvmgivvyllll 110
                                       g+k+    + l+ ll+  + + + g++ + + +
  gi|385805529|ref|YP_005841927.1| 206 GFKIyfskDKLKELLRAGIPSWLPGVIST-IGQ 237
                                       ****7666445555555555555555533.222 PP

  == domain 3  score: 29.3 bits;  conditional E-value: 1.2e-10
                   Polysacc_synt_C   2 LailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgivGaaiatvlallvvavlnlyalr 78 
                                       L+il ++ i+ ++s ++ss+  + g   ++lk+ +i+ +  +il ++l+p+++ +Gaai+ + +  ++a+++ly+++
  gi|385805529|ref|YP_005841927.1| 332 LVILLFGSIPVAFSGFVSSLVYAYGDYLTILKSGLITNVPRVILYFILVPKMSGIGAAISFTTGSYLGALYLLYIAY 408
                                       89**********************************************************************99999 PP

                   Polysacc_synt_C  79 r.llgikl.ellrrll.kpllaalvmgivvylllllllglll 117
                                       + ++++k  e +  l+ +pl+++++++ v    l++ lg+l 
  gi|385805529|ref|YP_005841927.1| 409 KlQVQFKKkE-IAILIsVPLIFSVLLFFV---RLSWYLGMLI 446
                                       9566666655.444445999999999999...3333333333 PP

>> MurJ  Lipid II flippase MurJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4  39.0   5.6e-08   0.00034      55     439 ..      85     449 ..      69     459 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 5.6e-08
                              MurJ  55 fvrkvltllilvlllvtligilaapllirllatgfdeetlelavsllrillpylllvslsavfgavLnarkkFfapa 131
                                        +++ l + +++ ll+ +ig ++  +  +++       t+el+  ++++l+   +  s++++++++L ++  F ++ 
  gi|385805529|ref|YP_005841927.1|  85 CASEYLWTSVYFSLLIYIIGGILVFIYSKFFGGAGSYSTEELT--IAALLVFVGFAGSFTSFLQSLLLTKYIFISVV 159
                                       5555566667778888888777777777777777799999**9..88999999999*****************9999 PP

                              MurJ 132 fsPvllNvsvIltllllanklgeeailaLaiGvliGgvlqllvqlpalkkaglllkprfafrdeglkkflklllptl 208
                                        ++++      +tl++l +++g    ++ a+G ++  v+q++++ ++  k+   +   ++f + +lk++l+  +p+ 
  gi|385805529|ref|YP_005841927.1| 160 AAAIFK-----FTLGVLLVYFG-YGWVGAALGYFVSTVVQFVINSYHSLKITGFK---IYFSKDKLKELLRAGIPSW 227
                                       999886.....67777777777.44556799999999999999999988876663...4466777999999999999 PP

                              MurJ 209 lgvsvsqlnllvdtalAsf....laegsvsi.layadrilqlPlglfgvsistvlLPrlSrsakekdedevrdllsq 280
                                       l   +s +++   ++l       l++gs  i  + a+++l++     ++ +   lLP lS      d+   ++  s 
  gi|385805529|ref|YP_005841927.1| 228 LPGVISTIGQWFGVILLYGtigsLETGSYFIaSQLANVVLNI-----SNILNGLLLPVLSGLS---DGR--KRVGSR 294
                                       999999998877776644222336666644313455555543.....3334455666666333...333..345788 PP

                              MurJ 281 airltllllipvsfgllvlskpivsllferGnFseedveataevLaayalgLipyalvklllrvfYAredtktPvki 357
                                         r++l+l++pvsf ++v    ++ + f       +++   +  L + ++g ip+a   +++++ YA++d+ t +k 
  gi|385805529|ref|YP_005841927.1| 295 VFRISLALMLPVSFYIMVYPTLLLDI-F------GKELSSGSIPLVILLFGSIPVAFSGFVSSLVYAYGDYLTILKS 364
                                       9****************997665554.4......367888999999999**************************** PP

                              MurJ 358 slislvlnillsllllpplgvvglalatslsaliglvllyvllrkrlklteargiktflak...lvvllalaavvil 431
                                       +li+ v  ++l+++l+p+++ +g a++ + ++ +g+++l+++++k  + +++++i++ +      +vll+++   ++
  gi|385805529|ref|YP_005841927.1| 365 GLITNVPRVILYFILVPKMSGIGAAISFTTGSYLGALYLLYIAYKLQVQFKKKEIAILISVpliFSVLLFFVRLSWY 441
                                       ***************************99999999999999999998888888888777777666777777777777 PP

                              MurJ 432 llssltqa 439
                                       l   +++ 
  gi|385805529|ref|YP_005841927.1| 442 LGMLIMAS 449
                                       76666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (494 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       989  (0.055162); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.75u 0.32s 00:00:01.07 Elapsed: 00:00:00.51
# Mc/sec: 2921.45
//
Query:       gi|385805530|ref|YP_005841928.1|  [L=211]
Description: PAP2 superfamily phosphatase [Fervidicoccus fontis Kam940]
Scores for complete 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   68.9   2.1    3.5e-19   68.9   2.1    1.7  2  PAP2      PAP2 superfamily
    2.8e-09   36.9   3.0    2.3e-08   33.9   3.0    2.0  1  PAP2_3    PAP2 superfamily
     0.0091   16.5   1.4     0.0091   16.5   1.4    2.1  2  PAP2_C    PAP2 superfamily C-terminal


Domain annotation for each model (and alignments):
>> PAP2  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1      0.48   2.9e+03      90      90 ..      45      45 ..       4      65 .. 0.50
   2 !   68.9   2.1   5.8e-23   3.5e-19       2     123 ..      73     177 ..      72     188 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.48
                              PAP2 90 i 90
                                       
  gi|385805530|ref|YP_005841928.1| 45 T 45
                                      1 PP

  == domain 2  score: 68.9 bits;  conditional E-value: 5.8e-23
                              PAP2   2 llalllalalaalltsvlKdlvgrpRPfflaeetkldtqvstletseskeakesfPSgHsafafalalllalllrrk 78 
                                       ll ++ a +++ +l+ +lKd+ + pRP+++ +      +  + +        +sfPSgHs++a ++ ++l+   + +
  gi|385805530|ref|YP_005841928.1|  73 LLDFASAFIISSVLVLILKDVTKVPRPNATVPPPAGFLSLLSDY--------YSFPSGHSTRASVASYYLSKKGKIA 141
                                       5788999999*******************999999988877776........6**********99998888755555 PP

                              PAP2  79 rkkiglvllalillllavlvalsRlylgvHflsDvlaGlliGial 123
                                        +           +++++l+a+sR+ lgvH++sDv++G+++Gi  
  gi|385805530|ref|YP_005841928.1| 142 SIL---------SWIYTILIAISRIMLGVHWFSDVVFGIFLGIES 177
                                       555.........9*****************************955 PP

>> PAP2_3  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   3.0   3.9e-12   2.3e-08     121     185 ..     113     175 ..      21     180 .. 0.72

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 3.9e-12
                            PAP2_3 121 englaafPSlHvawallvalalwrlrrkrllrvlalllnvlmivatvatgnHYlvDviaGvalal 185
                                        + +++fPS H + a +  ++    ++ ++  +l +++ +l++++ + +g H + Dv++G++l++
  gi|385805530|ref|YP_005841928.1| 113 LSDYYSFPSGHSTRASVASYY--LSKKGKIASILSWIYTILIAISRIMLGVHWFSDVVFGIFLGI 175
                                       3679***********999999..45566699*****************************99976 PP

>> PAP2_C  PAP2 superfamily C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.2      0.44   2.7e+03      52      52 ..      67      67 ..      35      91 .. 0.49
   2 !   16.5   1.4   1.5e-06    0.0091       8      65 ..     121     174 ..     118     181 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.44
                            PAP2_C 52 k 52
                                      k
  gi|385805530|ref|YP_005841928.1| 67 K 67
                                      2 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1.5e-06
                            PAP2_C   8 SGHtvvltlavlfileyspkklailkvillllallglfliiasrkHYtvDVllglyit 65 
                                       SGH++  +    ++ +y +kk +i +++++++++l+ ++ i+   H+  DV++g+++ 
  gi|385805530|ref|YP_005841928.1| 121 SGHSTRAS----VASYYLSKKGKIASILSWIYTILIAISRIMLGVHWFSDVVFGIFLG 174
                                       56655544....4567888888899******************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       869  (0.048469); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); 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: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 1242.78
//
Query:       gi|385805531|ref|YP_005841929.1|  [L=317]
Description: hypothetical protein FFONT_0487 [Fervidicoccus fontis Kam940]
Scores for complete 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   24.3   0.0    6.8e-05   22.2   0.0    1.9  2  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 ?   -1.3   0.0     0.051   9.2e+02      76     105 ..      75     101 ..      42     111 .. 0.71
   2 !   22.2   0.0   3.8e-09   6.8e-05     150     324 ..     117     304 ..      98     316 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.051
                                       HHHHHHHHHHHHHHHTTT-EEEEEESS-TH CS
                     Aminotran_1_2  76 Gagaliealifllklnpgdeilvpdptyas 105
                                        +g+ +  li+ +   +g++i+ ++p+y +
  gi|385805531|ref|YP_005841929.1|  75 TTGEEDLSLIATF---TGKRIIFSNPYYFN 101
                                       4445555555555...79999999999966 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 3.8e-09
                                       EEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHH........HGGSTTSTTEEEEEE CS
                     Aminotran_1_2 150 kvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavat........ranveeepnllivgs 218
                                       ++ +  +p+ P G  +++e+++++   akk n l++vD +Y  +  ++l  +++        +++  +e ++l+   
  gi|385805531|ref|YP_005841929.1| 117 CMSYASNPNIPLGFFMNEEKIVEI---AKKLNGLVVVDSTYDFLFDNDL--NQIiineklarLLDQFREAEVLVIKK 188
                                       5667789*****************...**************88888866..444556787643333344459***** PP

                                       SSSTTSSGGG-EEEEEEEH....HHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Aminotran_1_2 219 lsKafGlaGeRvGyilgna....avvsqlrklsrpflsssllqaavaaalsdallkqseleemrqrlqkrrkelrde 291
                                       l K fGl+   +  ++ n+    + +s +++   +++++     +   +lsd +l + +++  +++l+++ kel + 
  gi|385805531|ref|YP_005841929.1| 189 LHKIFGLYENPLILLYTNShrvfETLSLITNNEERLCID--CLSLYGRILSDNELLN-RINIIKEKLEEKKKELINV 262
                                       *********999999997786666666667777776663..3456689999999875.9****************** PP

                                       HHHSTEEEECCSCSSEEEEEETHHCHHHHHHH.........H CS
                     Aminotran_1_2 292 Laelglkvlasqsgmflltdlsaetakelskk.........L 324
                                       +++ g +v++s + +f+ + l+++  kelskk         L
  gi|385805531|ref|YP_005841929.1| 263 IRSNGGIVFESLAPYFVASSLNEKVLKELSKKaelekageyL 304
                                       ************************999999986644444441 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       921  (0.0513693); expected 358.6 (0.02)
Passed bias filter:                      626  (0.0349155); 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):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 1913.04
//
Query:       gi|385805532|ref|YP_005841930.1|  [L=163]
Description: hypothetical protein FFONT_0488 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-05   24.7   0.0    1.2e-05   24.5   0.0    1.0  1  LMBR1            LMBR1-like membrane protein
     0.0075   16.3   0.0      0.012   15.7   0.0    1.3  1  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
  ------ inclusion threshold ------
      0.026   13.3   0.1      0.057   12.2   0.1    1.6  2  DUF2254          Predicted membrane protein (DUF2254)
      0.099   12.0   3.1       0.13   11.6   3.1    1.1  1  Neuregulin       Neuregulin intracellular region
       0.16   13.2   7.4       0.27   12.4   7.4    1.3  1  DUF4168          Domain of unknown function (DUF4168)
        0.7    8.6   6.7        1.1    7.9   6.7    1.3  1  O-antigen_lig    O-antigen ligase like membrane protein


Domain annotation for each model (and alignments):
>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0     4e-09   1.2e-05     131     288 ..      10     161 ..       3     163 .] 0.56

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 4e-09
                             LMBR1 131 llllvivlglliyvliilqklsllsiksllpilislantwGlvllilllGyGlvel.Prslwreiksdldeelkkly 206
                                       ll++v  +++++y +i+     l+s + +l  l + + ++G++ ++  +Gy l+ + P + + ei++++deelkkl+
  gi|385805532|ref|YP_005841930.1|  10 LLIAVSAIVIVLYGYIL----FLTSYSGILIELTAFIAILGIFGIVGWIGYTLATTpPPKPIEEIEKEIDEELKKLE 82 
                                       22222222222222222....2222226667778999999****************86677788************7 PP

                             LMBR1 207 feaaklntekeeaereledllkevkklrksisesdplrkyleeilkkvPeeiaeklks..nenkteeslaklekqli 281
                                        e    +++++e + + e +++++  +++  + ++  +k ++ +lk      +++ +s  +++++  +++k ek  i
  gi|385805532|ref|YP_005841930.1|  83 QEQNVEQKTRSEGNAQGE-KKENIVGNYSDQTAKAVEQKEVSSLLKD----EEKDSNSgkGNEDAVGEVVKKEKGHI 154
                                       776655555555433333.3333333333333333344566666662....22222223244446666666666666 PP

                             LMBR1 282 kalqkre 288
                                       ++++k++
  gi|385805532|ref|YP_005841930.1| 155 RKSRKSK 161
                                       6666555 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 !   15.7   0.0   3.9e-06     0.012      34     108 ..       7      73 ..       2      80 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.9e-06
                   Phage_holin_3_6  34 gsgagllgaagvlallalllllvalalalaalwlaalivaavllvlagvlalvglkklkkakplpertieelked 108
                                       +  +++++ a v++l++ +l+l     +l       l  +++ l + g+++++g+  +     +p + iee+++ 
  gi|385805532|ref|YP_005841930.1|   7 IGILLIAVSAIVIVLYGYILFLTSYSGIL-----IELTAFIAILGIFGIVGWIGYTLATT---PPPKPIEEIEKE 73 
                                       45556666677777777777777775333.....35556677777779999999985555...355667777665 PP

>> DUF2254  Predicted membrane protein (DUF2254)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   1.9e-05     0.057     119     192 ..      31     103 ..       6     130 .. 0.66
   2 ?    0.0   0.0     0.097   2.9e+02     152     204 ..     103     155 ..      97     156 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.9e-05
                           DUF2254 119 vpqlsvlvalllaivsvllLiyFihhlarsiqvsnviarveeelrkai...learedeeeeeeeeakdeeeseeeea 192
                                         ++++ ++ ++ai+ ++ ++ +i  +  +    + i+++e+e+++++   +    +e++ e++++++ +++ e+++
  gi|385805532|ref|YP_005841930.1|  31 YSGILIELTAFIAILGIFGIVGWIGYTLATTPPPKPIEEIEKEIDEELkklE----QEQNVEQKTRSEGNAQGEKKE 103
                                       55699999****************************************3321....222222222223323333333 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.097
                           DUF2254 152 snviarveeelrkailearedeeeeeeeeakdeeeseeeeatpiraersGylq 204
                                       +n++ + ++++ ka+++++ ++  ++ee++++  + +e++   ++++++G+++
  gi|385805532|ref|YP_005841930.1| 103 ENIVGNYSDQTAKAVEQKEVSSLLKDEEKDSNSGKGNEDAVGEVVKKEKGHIR 155
                                       68899999999999965666666666666666667777777778888888775 PP

>> Neuregulin  Neuregulin intracellular region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   3.1   4.5e-05      0.13     248     321 ..      60     135 ..      55     143 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.5e-05
                        Neuregulin 248 gslpssPlrived...eeYettqeyessleqpkrsstnsrrarrsklnghvaqreeaardsssesslseseteeerv 321
                                       + +p++P++  e+   ee +   e+e+  eq++rs  n +  ++  + g+ ++++ +a +++ +ssl ++e+++ + 
  gi|385805532|ref|YP_005841930.1|  60 TTPPPKPIEEIEKeidEELK-KLEQEQNVEQKTRSEGNAQGEKKENIVGNYSDQTAKAVEQKEVSSLLKDEEKDSNS 135
                                       67899**9887743424444.447778999999*********************97777777788888777777655 PP

>> DUF4168  Domain of unknown function (DUF4168)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   7.4     9e-05      0.27      15      67 ..      67     121 ..      65     124 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9e-05
                           DUF4168  15 ieplrqeaqqeikqaiedesvpeisceeqks..eeaqaiqkeaceesekivekeg 67 
                                       ie++++e+++e+k+  ++++v++++ +e +   e++++i  ++ ++ +k+ve++ 
  gi|385805532|ref|YP_005841930.1|  67 IEEIEKEIDEELKKLEQEQNVEQKTRSEGNAqgEKKENIVGNYSDQTAKAVEQKE 121
                                       9***********88888878888888887779*******************9875 PP

>> O-antigen_lig  O-antigen ligase like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   6.7   0.00038       1.1     217     325 ..       6     121 ..       3     149 .. 0.50

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00038
                     O-antigen_lig 217 lfGliiiliialillliklilkkkklkkkkl..llaiillvligill.aiypyspiyrrkelkekeieiksekkeee 290
                                       ++G+++i++ a++++l  +il  ++ +   +  + +i +l ++gi+  + y + ++   k ++e e ei++e  ++ 
  gi|385805532|ref|YP_005841930.1|   6 YIGILLIAVSAIVIVLYGYILFLTSYSGILIelTAFIAILGIFGIVGwIGYTLATTPPPKPIEEIEKEIDEEL-KKL 81 
                                       7899998888888888778887777776666766666666666666653333333333333333333332222.222 PP

                     O-antigen_lig 291 eikneikenykseglk.....eavleqyeyandkqfsqel 325
                                       e +++++++  seg       e+++ +y+ ++ k   q+ 
  gi|385805532|ref|YP_005841930.1|  82 EQEQNVEQKTRSEGNAqgekkENIVGNYSDQTAKAVEQKE 121
                                       2222222222222222222244444444444444333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2984  (0.166434); expected 358.6 (0.02)
Passed bias filter:                     1096  (0.06113); expected 358.6 (0.02)
Passed Vit filter:                       131  (0.0073066); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 1007.93
//
Query:       gi|385805533|ref|YP_005841931.1|  [L=331]
Description: bifunctional phosphoglucose/phosphomannose isomerase [Fervidicoccus fontis Kam940]
Scores for 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-30  104.5   0.0    2.7e-28   98.9   0.0    2.2  2  bact-PGI_C  Bacterial phospho-glucose isomerase C-terminal SI
    1.2e-07   31.6   0.8    4.9e-06   26.4   0.2    2.9  3  SIS         SIS domain


Domain annotation for each model (and alignments):
>> bact-PGI_C  Bacterial phospho-glucose isomerase C-terminal SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.5   0.0    0.0075        68      17      47 ..      81     111 ..      77     115 .. 0.79
   2 !   98.9   0.0   3.1e-32   2.7e-28       2     152 .]     177     322 ..     176     322 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.0075
                                       EEEE-..TT-THHHHHHHHHHHHTT----B- CS
                        bact-PGI_C  17 pviygssellevaArRfknqlnenAKipafa 47 
                                        ++++ s+ +       k+ l+enAK+++++
  gi|385805533|ref|YP_005841931.1|  81 FIVISYSGNTIETLSAYKQLLEENAKTLVIT 111
                                       55666677777778899***********987 PP

  == domain 2  score: 98.9 bits;  conditional E-value: 3.1e-32
                                       G-HHHHHHHHHTTSEEEEE-..TT-THHHHHHHHHHHHTT----B---.SSHHHHHHHTT...SS-GGGGTTEEEEE CS
                        bact-PGI_C   2 knpakqlAlelagklpviygssellevaArRfknqlnenAKipafagvlpeanhneivgl...eaeeelkkrlrlvl 75 
                                       +n+ak++A+e ++k++++++ s+++ ++A+Rfkn+++en+K+++f++++pe+ hn+i g+         k+r++++ 
  gi|385805533|ref|YP_005841931.1| 177 ENYAKNIANEAKDKIVIFIS-SKPYLSVAIRFKNDFAENSKSISFVEEIPEFLHNSIEGInrlL--MFYKDRIKILS 250
                                       69******************.***************************************6431..46788999999 PP

                                       ES.SHH........HHHHHHHHTTTS.SEEEEE---SSSHHHHHHHHHHHHHHHHHHHHHHCT---S-TTTTHHHHH CS
                        bact-PGI_C  76 lr.deeehprvkkraeivkelaeerg.vrvtevkaegesplerlaslillgDfvSvylAllrgvDPtpvpaIdelKe 150
                                       ++ +           +i  e ++e+   ++tev++  +++l++++ ++ l ++vS++lA ++++DP ++++Id +Ke
  gi|385805533|ref|YP_005841931.1| 251 IGgKML-------FNNIFYESFKEALnLKITEVDLGSDGVLNEIVRGFKLSGLVSLKLASIYDIDPDETSSIDVYKE 320
                                       994444.......6666666666665599***********************************************9 PP

                                       .. CS
                        bact-PGI_C 151 el 152
                                       +l
  gi|385805533|ref|YP_005841931.1| 321 KL 322
                                       86 PP

>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.2   5.5e-10   4.9e-06       6      88 ..      33     112 ..      30     120 .. 0.76
   2 ?    0.5   0.0     0.057   5.1e+02      48      67 ..     183     202 ..     171     221 .. 0.81
   3 ?    1.7   0.0     0.023   2.1e+02      14      48 ..     197     232 ..     183     238 .. 0.64

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 5.5e-10
                                       SEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG.-STTCEEEEEESSSHHHHHHHHHHHHHHTTS CS
                               SIS   6 kriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlal.ideddlvilisfsgetkdlvaaaelakerga 81 
                                       + i+++G+G s+ +++ l      i+ +     + ++ k++v++   de+ l+i+is+sg+t +++ a +++ e +a
  gi|385805533|ref|YP_005841931.1|  33 REIVIVGMGGSGIVGNTLE----DISHFYGMNAKVTTVKSNVIPFkPDERSLFIVISYSGNTIETLSAYKQLLEENA 105
                                       6799999999999997654....444444444444444445444413699*************************** PP

                                       EEEEEES CS
                               SIS  82 kiiaITd 88 
                                       k+++IT+
  gi|385805533|ref|YP_005841931.1| 106 KTLVITS 112
                                       ******6 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.057
                                       GGG-STTCEEEEEESSSHHH CS
                               SIS  48 lalideddlvilisfsgetk 67 
                                       +a+  +d +vi+is  ++ +
  gi|385805533|ref|YP_005841931.1| 183 IANEAKDKIVIFISSKPYLS 202
                                       5666789999***9999875 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.023
                                       HHHHH.HHHHHHHHHHHHHTSEEEEEEHHHHHHTGG CS
                               SIS  14 Gtsya.iakelalkleeiggivvevedaselkhgvl 48 
                                        + y  +a  ++  ++e ++ +++ve+ +e+ h+ +
  gi|385805533|ref|YP_005841931.1| 197 SKPYLsVAIRFKNDFAENSKSISFVEEIPEFLHNSI 232
                                       333333777777778888888888888888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       986  (0.0549947); expected 358.6 (0.02)
Passed bias filter:                      723  (0.0403257); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.35s 00:00:00.97 Elapsed: 00:00:00.53
# Mc/sec: 1892.24
//
Query:       gi|385805534|ref|YP_005841932.1|  [L=197]
Description: putative Methyltransferase [Fervidicoccus fontis Kam940]
Scores for complete 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-38  130.5   0.0    5.1e-38  130.3   0.0    1.0  1  MTS              Methyltransferase small domain
      6e-10   39.0   0.1    6.4e-10   38.9   0.1    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    2.8e-09   36.9   0.1    4.9e-09   36.1   0.1    1.3  1  Methyltransf_16  Lysine methyltransferase
    2.3e-08   34.1   0.6    4.1e-08   33.3   0.6    1.4  1  Methyltransf_18  Methyltransferase domain
    2.1e-07   30.8   0.0      3e-07   30.3   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    2.4e-07   30.7   0.1      3e-07   30.4   0.1    1.4  1  Met_10           Met-10+ like-protein
    2.5e-07   31.3   0.0    3.6e-07   30.8   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    5.6e-05   23.8   0.0    9.1e-05   23.1   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
    7.9e-05   22.6   0.0    9.8e-05   22.2   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    0.00086   19.9   0.0     0.0012   19.4   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
     0.0023   17.2   0.0     0.0029   16.8   0.0    1.2  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
     0.0049   16.5   0.0      0.006   16.2   0.0    1.1  1  Cons_hypoth95    Conserved hypothetical protein 95
  ------ inclusion threshold ------
      0.011   15.1   0.0      0.019   14.3   0.0    1.5  1  GidB             rRNA small subunit methyltransferase G
      0.012   15.6   1.0       0.46   10.5   1.0    2.1  1  rRNA_methylase   Putative rRNA methylase
      0.019   14.6   0.1      0.027   14.0   0.1    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
      0.026   14.1   0.6      0.036   13.6   0.6    1.3  1  TrmK             tRNA (adenine(22)-N(1))-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 !  130.3   0.0   4.6e-41   5.1e-38       2     168 ..      28     193 ..      27     194 .. 0.95

  Alignments for each domain:
  == domain 1  score: 130.3 bits;  conditional E-value: 4.6e-41
                                       EEEEEETTSTTTTS--HHHHHHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHT CS
                               MTS   2 ltlktlpgvFskdklDkGsklLletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenlean 78 
                                       l+l++ p vFs d++D G++lLl++l   ++g+vlDlG+G+G++g+ lak++p+++v + dv+  A++++k+n+++n
  gi|385805534|ref|YP_005841932.1|  28 LKLYSSPSVFSSDEIDPGTDLLLKNLIIPEKGNVLDLGTGIGIIGIYLAKANPKLHVYMSDVNPIAIKLSKKNIKEN 104
                                       7899************************************************************************* PP

                                       TGC..EEEEE-STTTTSTTS-EEEEEE---STTTCHCHHHHHHHHHHHHHHHEEEEEEEEEEEET.TSCHHHHHHHH CS
                               MTS  79 kle..vevvasdvleeveekkfdlivsNPPfhagkatelavaeeliaeAkeaLkegGeLliVanr.klgyeslleel 152
                                       ++e  + vv+++++e+++e+ f +i +NPP+ ag +    ++e++i++  ++L+e+G L++V +  + ++ ++ +++
  gi|385805534|ref|YP_005841932.1| 105 NVEknTVVVECNLYEKFKENFFVAIYTNPPISAGWE----TIEKIITDGIKYLQEKGVLQMVLSVgHERALEVGKKI 177
                                       ***99999****************************....99********************985255566667999 PP

                                       HS--EEEEEESSEEEE CS
                               MTS 153 fgnvevvaktkkfkvl 168
                                       +++ve+++k+k++ ++
  gi|385805534|ref|YP_005841932.1| 178 YKSVEIIEKKKGYAII 193
                                       *************996 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.1   5.8e-13   6.4e-10     160     232 ..      56     128 ..      45     197 .] 0.71

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 5.8e-13
                              PrmA 160 kegeevlDvGtGSGiLaiaaakLgak.kvvavDiDevAvkvakeNaelNkveaklevalseellkeekadviva 232
                                        e+ +vlD+GtG Gi+ i  ak + k +v+  D++++A+k +k+N++ N+ve++  v ++ +l ++ k +  va
  gi|385805534|ref|YP_005841932.1|  56 PEKGNVLDLGTGIGIIGIYLAKANPKlHVYMSDVNPIAIKLSKKNIKENNVEKNTVV-VECNLYEKFKENFFVA 128
                                       34559*****************99875899***********************8855.5555555444444444 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.1   4.4e-12   4.9e-09      47     103 ..      58     114 ..      50     129 .. 0.86

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 4.4e-12
                   Methyltransf_16  47 klsvlELGsGtGlvGlavaellpeakviltDlee.llellkknielnknalkskvkve 103
                                       k +vl+LG G G++G+ +a++ p+++v+++D++  +++l kkni+ n+   k++v+ve
  gi|385805534|ref|YP_005841932.1|  58 KGNVLDLGTGIGIIGIYLAKANPKLHVYMSDVNPiAIKLSKKNIKENN-VEKNTVVVE 114
                                       569*****************************99899*********77.666666655 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.6   3.7e-11   4.1e-08      11     148 ..      54     190 ..      49     193 .. 0.75

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 3.7e-11
                   Methyltransf_18  11 lvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklkeee.vdtv 86 
                                       +++++ +v+D Gt  g++ iyl+k +   +v++sD+n+ +++ +k+ni+++++e++  v+ ++  ek+ke+  v + 
  gi|385805534|ref|YP_005841932.1|  54 IIPEKGNVLDLGTGIGIIGIYLAKANPKLHVYMSDVNPIAIKLSKKNIKENNVEKNTVVVECNLYEKFKENFfVAIY 130
                                       478888******************************************************99999999977433322 PP

                   Methyltransf_18  87 v..iaGmGgelileILeeakeklkkikklilqpnseaeelRkylvengfkiedEelvkeegkiY 148
                                       +      G e+i +I++++ ++l++  k +lq   ++ + R    e g ki +   + e++k Y
  gi|385805534|ref|YP_005841932.1| 131 TnpPISAGWETIEKIITDGIKYLQE--KGVLQMVLSVGHERA--LEVGKKIYKSVEIIEKKKGY 190
                                       2112346889999999999777774..456665555554443..34444455555555555555 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0   2.7e-10     3e-07       5     113 ..      59     165 ..      55     194 .. 0.73

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 2.7e-10
                   Methyltransf_31   5 lrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdiee.leklledekfDlil 79 
                                        +vlDlG+G G +++ la +++pk +v+  D ++ ai+l+++n ++++++ n  + +++  e +++    + f  i 
  gi|385805534|ref|YP_005841932.1|  59 GNVLDLGTGIGIIGIYLA-KANPKLHVYMSDVNPIAIKLSKKNIKENNVEkNTVVVECNLYEkFKE----NFFVAIY 130
                                       68****************.******************************98777777887774553....4455566 PP

                   Methyltransf_31  80 snevl.naladpdkileeiervlkpggilliedpr 113
                                       +n ++ +     +ki+   +++l+++g+l +    
  gi|385805534|ref|YP_005841932.1| 131 TNPPIsAGWETIEKIITDGIKYLQEKGVLQMVLSV 165
                                       66555666666666666666666666666555444 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.1   2.7e-10     3e-07     100     158 ..      57     115 ..      17     173 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 2.7e-10
                                       TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES CS
                            Met_10 100 egevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpile 158
                                       e   V+d+  GiG   i +ak   +  v+  d+nP ++k+ k+nik N+vek   +++ 
  gi|385805534|ref|YP_005841932.1|  57 EKGNVLDLGTGIGIIGIYLAKANPKLHVYMSDVNPIAIKLSKKNIKENNVEKNTVVVEC 115
                                       55679****************888889************************97666554 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.0   3.2e-10   3.6e-07       1      95 [.      61     155 ..      61     157 .. 0.77

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 3.2e-10
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBS.SSTTTEEEEEEEST.GG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlp.fedgsfDlvvssga.lh 75 
                                       vLdlG+G G + ++lak+ +k +v++ D+++ +++  +++++e++++ + v+ +++ ++ f+++ f +++  +  ++
  gi|385805534|ref|YP_005841932.1|  61 VLDLGTGIGIIGIYLAKANPKLHVYMSDVNPIAIKLSKKNIKENNVEKNTVVVECNLYEkFKENFFVAIYT-NPpIS 136
                                       9*****************879***********************996666666665543278888888888.45466 PP

                                       GSSHHHHHHHHHHHHHHEEE CS
                   Methyltransf_25  76 hlsdedlekalkeiarvLkp 95 
                                         + e +ek++    + L++
  gi|385805534|ref|YP_005841932.1| 137 AGW-ETIEKIITDGIKYLQE 155
                                       543.5667776666666655 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   8.1e-08   9.1e-05       1      53 [.      62     113 ..      62     155 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 8.1e-08
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvel 53 
                                       L++G+G G +  +l++++p ++++ +D++p ai+  k+ +++++    n v +
  gi|385805534|ref|YP_005841932.1|  62 LDLGTGIGIIGIYLAKANPKLHVYMSDVNPIAIKLSKKNIKENN-VEKNTVVV 113
                                       8********************************44444444444.33333333 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   8.7e-08   9.8e-05      16      62 ..      49     105 ..      38     160 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 8.7e-08
                   Methyltransf_23  16 llpk..lraggrvLdiGcGtGillevl.rengf.svtgvDlspeaveiae......k 62 
                                       ll++   +++g+vLd+G+G Gi   +l ++n++ +v++ D +p+a+++ +      +
  gi|385805534|ref|YP_005841932.1|  49 LLKNliIPEKGNVLDLGTGIGIIGIYLaKANPKlHVYMSDVNPIAIKLSKknikenN 105
                                       4444336899*************99994455558*************9764333330 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   1.1e-06    0.0012       1      67 [.      62     131 ..      62     159 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.1e-06
                                       EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEE CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvs 67 
                                       Ld+G+G G++  +lak+    +v+  D+++ ++kl+k++++e+++  +  +v++++ + +f++n f +++ 
  gi|385805534|ref|YP_005841932.1|  62 LDLGTGIGIIGIYLAKANpkLHVYMSDVNPIAIKLSKKNIKENNVekNTVVVECNLYE-KFKENFFVAIYT 131
                                       8**************88889***********************999866667777776.799999988775 PP

>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   2.6e-06    0.0029      51     105 ..      59     113 ..      19     133 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.6e-06
                                       EEEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHHHHHTT--.GGEEE CS
                               TRM  51 ikvldaLsasGlRaiRfalEvpgvkevlaNDisekAvelikeNvklneve.eivvi 105
                                        +vld  ++ G+ +i  a+  + + +v++ D+++ A++l k+N+k n+ve ++vv+
  gi|385805534|ref|YP_005841932.1|  59 GNVLDLGTGIGIIGIYLAKA-NPKLHVYMSDVNPIAIKLSKKNIKENNVEkNTVVV 113
                                       57888888899999988887.9999*************************545554 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   5.3e-06     0.006      42     174 ..      58     189 ..      49     197 .] 0.72

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.3e-06
                                       C-EEEETT-TTSHHHHH.HHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEE CS
                     Cons_hypoth95  42 garvLDlfaGsGalglE.AlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdiv 117
                                       + +vLDl  G G +g+  A      ++++ + ++ a+k+ k+n++e ++e++t ++  + +e+++++      f  +
  gi|385805534|ref|YP_005841932.1|  58 KGNVLDLGTGIGIIGIYlAKANPKLHVYMSDVNPIAIKLSKKNIKENNVEKNTVVVECNLYEKFKEN-----FFVAI 129
                                       5678999999999998635555567999********************9987888777777777666.....799** PP

                                       EE--SSSTTCH......HHHHHHHHHTT-EEEEEEEEEEEECCSSS--.-TTEEEEEEEEET CS
                     Cons_hypoth95 118 flDPPyakell.....ieevlelleekkllkenalvvvetekekelpespenlelvkekkyg 174
                                       + +PP  ++       i + +++l+ek++l+    v   +e++ e+ +++ +   + ekk g
  gi|385805534|ref|YP_005841932.1| 130 YTNPPISAGWEtiekiITDGIKYLQEKGVLQMVLSVG--HERALEVGKKIYKSVEIIEKKKG 189
                                       *****99874353333555667888888887555444..44455555555555555555555 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.7e-05     0.019      45      79 ..      55      88 ..      46     124 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.7e-05
                                      S-CCC-.EEEETSTTTTTHHHHHHH-TTSEEEEEE CS
                              GidB 45 lkekrdkviDvGsGaGlPGipLaiarpelkltLle 79
                                      + ek  +v+D+G+G G+ Gi La a+p+l++++ +
  gi|385805534|ref|YP_005841932.1| 55 IPEKG-NVLDLGTGIGIIGIYLAKANPKLHVYMSD 88
                                      44444.7***********************99866 PP

>> rRNA_methylase  Putative rRNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.0   0.00041      0.46       1     115 [.      84     188 ..      84     196 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00041
                                       EEEEES-HHHHHHHHHHHHHTT-GGSEEEEES-GGGGGGT--S-EEEEEEEESB-CTS-TTSB--HHHHHHHHHHHH CS
                    rRNA_methylase   1 vyafDiQeeAleatkerleeekleervelildsHekleeyvkekvkavifNLGYLPggdksivTkaettlkAlekal 77 
                                       vy  D+   A++ +k++++e+++e+++ +++ +  +l e  ke++ ++i+       ++  i    et  k ++ ++
  gi|385805534|ref|YP_005841932.1|  84 VYMSDVNPIAIKLSKKNIKENNVEKNTVVVE-C--NLYEKFKENFFVAIY-------TNPPISAGWETIEKIITDGI 150
                                       5666777777777777777777775433332.2..455555555566655.......4566777778888889999* PP

                                       HHEEEEEEEEEEE--STCHHHHHHHHHHHHHHTS-TTT CS
                    rRNA_methylase  78 elLkkgGlitivvYpGheeGkeEkeavleflssLdqkk 115
                                       + L+++G++ +v+ +Ghe+  e  +++ + ++ +++kk
  gi|385805534|ref|YP_005841932.1| 151 KYLQEKGVLQMVLSVGHERALEVGKKIYKSVEIIEKKK 188
                                       *******************9999999999999888876 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 ?   14.0   0.1   2.4e-05     0.027       4      64 ..      61     123 ..      58     164 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.4e-05
                   Methyltransf_15   4 ilDlfsGaGGnviqfalv..fekviaieinleklacaqhNaevYgvsdkitlvlgdvfellak 64 
                                       +lDl +G G   i +a+     +v+ +++n+  ++++++N +  +v+++  +v +++ e +++
  gi|385805534|ref|YP_005841932.1|  61 VLDLGTGIGIIGIYLAKAnpKLHVYMSDVNPIAIKLSKKNIKENNVEKNTVVVECNLYEKFKE 123
                                       7899999998888888774445799*******************************9997765 PP

>> TrmK  tRNA (adenine(22)-N(1))-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.6   3.2e-05     0.036       2     137 ..      62     195 ..      61     197 .] 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.2e-05
                              TrmK   2 aDiGsDHAyLpiylvknnkvsvaiagevnegplesAkknvkkskleekievrlgdGlavlekedeidvivia..GmG 76 
                                       +D+G+  + + iyl k n   ++  ++vn  + + +kkn+k+++ e+++ v   + ++ ++++  ++  +      G
  gi|385805534|ref|YP_005841932.1|  62 LDLGTGIGIIGIYLAKANPKLHVYMSDVNPIAIKLSKKNIKENNVEKNTVVVECNLYEKFKENFFVAIYTNPpiSAG 138
                                       799999999****************************************************9887777775411458 PP

                              TrmK  77 galIaeILeegkekLkkvkrliLQpnnqeeelRewlsknsyeikaEkileekkkiYeilvv 137
                                        ++I +I+ +g + L+  ++ +LQ   +  + R+    ++  i +   + ekkk Y i++ 
  gi|385805534|ref|YP_005841932.1| 139 WETIEKIITDGIKYLQ--EKGVLQMVLSVGHERALEVGKK--IYKSVEIIEKKKGYAIIIF 195
                                       899********99995..5589998887777777655554..3333334466677777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       800  (0.0446204); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 1132.45
//
Query:       gi|385805535|ref|YP_005841933.1|  [L=236]
Description: H/ACA RNA-protein complex component Cbf5p [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-24   85.2   0.2    7.1e-24   83.7   0.0    1.8  2  TruB_C_2  tRNA pseudouridylate synthase B C-terminal domain
    2.8e-09   37.5   0.0    2.2e-07   31.4   0.0    2.7  2  TruB_N    TruB family pseudouridylate synthase (N terminal do
    5.9e-05   23.2   0.3     0.0012   19.1   0.0    2.4  2  UPF0113   UPF0113 PUA domain
    0.00015   21.7   0.0    0.00038   20.4   0.0    1.7  2  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 ?   -2.0   0.0      0.94   4.2e+03      36      56 ..      14      30 ..       6      31 .. 0.68
   2 !   83.7   0.0   1.6e-27   7.1e-24       1      60 [.      82     144 ..      82     147 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.94
                                      HHHHHHHHHHHHT--HHHHHE CS
                          TruB_C_2 36 ledLedavllykedeeLdrll 56
                                      + +L+d+v     +eeL+r++
  gi|385805535|ref|YP_005841933.1| 14 VMELHDEVN----NEELKRVI 30
                                      456666666....78888887 PP

  == domain 2  score: 83.7 bits;  conditional E-value: 1.6e-27
                                       HHHHHHHHHHTTS-EEEEEEEEEEETTEGG-..B-HHHHHHHHHHHHT..--H.HHHHEEEGG CS
                          TruB_C_2   1 RtLcdDiGeaLgcgAhveeLRRtrvgpfdeedmvtledLedavllyke..dee.LdrlllPle 60 
                                       R+Lc+DiG++Lg+gAh++eLRRt +gpf+e+++v++++L +a++l+k+  +++ L++++lP+e
  gi|385805535|ref|YP_005841933.1|  82 RKLCHDIGLLLGVGAHMRELRRTVSGPFTEDHAVRMQELSEAIYLWKNygNDSaLRKMILPVE 144
                                       9***********************************************996657********9 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 ?    1.9   0.0     0.059   2.6e+02      35      55 ..       2      22 ..       1      24 [. 0.85
   2 !   31.4   0.0   4.9e-11   2.2e-07      69     149 .]      18      81 ..       9      81 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.059
                                      HHCTTS-EEEEEEEEETEEET CS
                            TruB_N 35 eylleadKeYeatirlgaetd 55
                                       y+ ++ KeY+++++l+ e +
  gi|385805535|ref|YP_005841933.1|  2 PYVVHSVKEYVCVMELHDEVN 22
                                      5788999*********98876 PP

  == domain 2  score: 31.4 bits;  conditional E-value: 4.9e-11
                                       -TT--HHHHHHHHHHC-EEE---------------------------------EEEEEEEEEEEEEEEEEEEEEEST CS
                            TruB_N  69 veklteekleevlkkftGeieqvppmySAvkvnGkrlyelaregeeverkkrkvtiyelelleveepevelevecsk 145
                                        +++++e+l++v+++f+G+i+q+pp+ S+vk                 r+ r  +i+++elle + ++v ++++c +
  gi|385805535|ref|YP_005841933.1|  18 HDEVNNEELKRVIEMFKGRIYQRPPVRSNVK-----------------RRIRIRKIHDIELLERKGNHVLMRIKCDA 77 
                                       57899**************************.................88999************************ PP

                                       TTTH CS
                            TruB_N 146 GtYi 149
                                       GtY+
  gi|385805535|ref|YP_005841933.1|  78 GTYM 81 
                                       ***6 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.067     3e+02      58      76 .]      65      83 ..      52      83 .. 0.78
   2 !   19.1   0.0   2.6e-07    0.0012       1      63 [.     152     215 ..     152     220 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.067
                           UPF0113 58 spgkivvknlaDiGeYlRr 76
                                      + + ++++  +D G+Y+R+
  gi|385805535|ref|YP_005841933.1| 65 KGNHVLMRIKCDAGTYMRK 83
                                      56677788889******96 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 2.6e-07
                           UPF0113   1 kvvvkekaeklFLYGrdvlkesilkitesvkenqvvvVlnengeplGiGkirkdtk.aspgkiv 63 
                                       k+ vk +a +++LYG  + k ++  ++e++++n+ ++V+  + e++Gi  i  + k  ++gk+v
  gi|385805535|ref|YP_005841933.1| 152 KILVKDSAISSLLYGAPLAKGGVAAYSEDLQTNKIAAVFTSKIELIGIYEILNNPKkNKNGKVV 215
                                       789*********************************************9997766634444444 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   8.4e-08   0.00038       1      49 [.     151     199 ..     151     205 .. 0.96
   2 ?   -3.3   0.0         2     9e+03      41      52 ..     209     220 ..     206     223 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 8.4e-08
                                       CEEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEE CS
                               PUA   1 grvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvav 49 
                                       +++ v+d+A+  ll+ga L   Gv  + +d++ + + a+++ + el+++
  gi|385805535|ref|YP_005841933.1| 151 PKILVKDSAISSLLYGAPLAKGGVAAYSEDLQTNKIAAVFTSKIELIGI 199
                                       699***************************************9999986 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2
                                       ETTSCEEEEEEE CS
                               PUA  41 dedgelvavGla 52 
                                       +++g++v++ la
  gi|385805535|ref|YP_005841933.1| 209 NKNGKVVGRPLA 220
                                       678999998665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1557.84
//
Query:       gi|385805536|ref|YP_005841934.1|  [L=108]
Description: H/ACA RNA-protein complex component Cbf5p [Fervidicoccus fontis Kam940]
Scores for complete 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   44.3   0.1      2e-11   43.8   0.1    1.3  1  DKCLD     DKCLD (NUC011) domain
  ------ inclusion threshold ------
      0.056   13.8   0.5      0.089   13.2   0.5    1.3  1  TruB_N    TruB family pseudouridylate synthase (N terminal do


Domain annotation for each model (and alignments):
>> DKCLD  DKCLD (NUC011) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.1   2.3e-15     2e-11      28      58 .]      39      69 ..      28      69 .. 0.95

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 2.3e-15
                                      --GGG--HHHHHHTEEEEEEE-SSS-HHHHH CS
                             DKCLD 28 ssPlkRpieeyikyGvinLDKPsnPsSHEVV 58
                                      s+P +R+i+++i+ G+i +DKP +P+SHEVV
  gi|385805536|ref|YP_005841934.1| 39 SNPFERDINSLIERGIIVIDKPPGPTSHEVV 69
                                      79****************************9 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 ?   13.2   0.5   9.9e-06     0.089       1      17 [.      73      89 ..      73      93 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.9e-06
                                      HHHTT-S-EEESS---T CS
                            TruB_N  1 krllkakkvGhtGtLDp 17
                                      kr+l++kkvGh+GtL  
  gi|385805536|ref|YP_005841934.1| 73 KRMLGVKKVGHGGTLEG 89
                                      89*************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 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:                        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 0.28s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 691.29
//
Query:       gi|385805537|ref|YP_005841935.1|  [L=98]
Description: 50S ribosomal protein L14e [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      0.003   18.0   0.1      0.004   17.6   0.1    1.2  1  Ribosomal_L14e  Ribosomal protein L14
  ------ inclusion threshold ------
      0.054   13.5   0.5      0.097   12.7   0.5    1.4  1  KOW             KOW motif
      0.064   13.6   0.0      0.077   13.4   0.0    1.1  1  XisI            XisI protein


Domain annotation for each model (and alignments):
>> Ribosomal_L14e  Ribosomal protein L14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   6.8e-07     0.004       2      38 ..      46      82 ..      45      93 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 6.8e-07
                    Ribosomal_L14e  2 RqaiplkrlkLtkivlklprgartgavkkawekadve 38
                                      R ++++++++  + ++ +++ga+ + v+ka+++a+++
  gi|385805537|ref|YP_005841935.1| 46 RRKVNINHIEVLDAKVPINKGASDEEVEKAINAAGLT 82
                                      899******************************9987 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.5   1.6e-05     0.097       2      31 ..       7      35 ..       6      37 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.6e-05
                                      TSEEEESSSTTTTCEEEEEEEETTTTEEEE CS
                               KOW  2 GdhVkVvsGphkGktGkVvkvdqhkvrVfv 31
                                      G+++  + G+ +G+++++ ++ +++ +V+v
  gi|385805537|ref|YP_005841935.1|  7 GRVCVKTYGREAGRKCVIIDIVDEN-FVLV 35
                                      899999******************9.4444 PP

>> XisI  XisI protein
   #    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      28      89 ..      19      82 ..       8      89 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.3e-05
                                      EEEEEEEETTTTEEEEEEEEEE..TTEEEEEEEEEEEEETTEEEEEEE-SS--HHHHHHTTT-- CS
                              XisI 28 veeelifDeerdhYlllevgwe..kkkrvygillhldikdgkiwiqedgteegiaeeLveaGvp 89
                                       ++++i+D   ++++l++   +  + +r +  + h+++ d k+ i++   +e++ + + +aG  
  gi|385805537|ref|YP_005841935.1| 19 GRKCVIIDIVDENFVLVTGPKNisGVRRRKVNINHIEVLDAKVPINKGASDEEVEKAINAAGLT 82
                                      567899999999**99986655436788999999**********************99999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.50
# Mc/sec: 584.65
//
Query:       gi|385805538|ref|YP_005841936.1|  [L=189]
Description: cytidylate kinase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-15   58.1   0.8    9.4e-14   51.9   0.8    2.1  1  Cytidylate_kin2  Cytidylate kinase-like family
    1.3e-15   58.1   0.0    1.8e-15   57.6   0.0    1.3  1  AAA_18           AAA domain
      2e-15   57.4   0.0    6.2e-15   55.8   0.0    1.8  1  AAA_17           AAA domain
    8.6e-15   55.0   3.5      3e-07   30.4   0.6    2.1  2  Cytidylate_kin   Cytidylate kinase
    6.7e-07   29.6   0.1    1.7e-05   25.0   0.1    2.1  1  AAA_33           AAA domain
    5.2e-05   23.4   0.2    0.00084   19.5   0.0    2.2  2  ADK              Adenylate kinase
     0.0001   22.2   1.5      0.096   12.5   0.1    2.2  2  dNK              Deoxynucleoside kinase
     0.0056   16.0   0.8       0.14   11.4   0.1    2.6  3  Zeta_toxin       Zeta toxin
     0.0061   16.6   0.0      0.015   15.3   0.0    1.7  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
     0.0088   16.0   0.0       0.02   14.8   0.0    1.6  1  Rad17            Rad17 P-loop domain
     0.0099   15.8   1.4      0.026   14.4   1.4    1.8  1  ATPase_2         ATPase domain predominantly from Archaea
  ------ inclusion threshold ------
      0.014   15.5   0.4      0.024   14.8   0.4    1.6  1  SKI              Shikimate kinase
      0.024   14.9   0.1      0.041   14.1   0.1    1.5  1  AAA_28           AAA domain
      0.027   14.9   0.0      0.054   13.9   0.0    1.5  1  AAA              ATPase family associated with various cellul
      0.035   13.7   0.0       0.42   10.2   0.0    2.1  2  SRP54            SRP54-type protein, GTPase domain
      0.039   13.9   0.0      0.066   13.1   0.0    1.5  1  NACHT            NACHT domain
      0.043   13.5   0.7       0.37   10.5   0.2    2.2  2  PRK              Phosphoribulokinase / Uridine kinase family
      0.049   13.3   0.3       0.51   10.0   0.0    2.1  2  CoaE             Dephospho-CoA kinase
      0.052   13.0   0.2      0.088   12.3   0.1    1.4  1  PhoH             PhoH-like protein
      0.054   13.9   0.0       0.12   12.8   0.0    1.6  1  RNA_helicase     RNA helicase
      0.085   12.6   0.1       0.26   11.0   0.1    1.7  2  AAA_30           AAA domain
      0.092   12.5   0.0       0.17   11.6   0.0    1.5  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
       0.13   11.3   0.4        0.3   10.1   0.2    1.7  2  T2SSE            Type II/IV secretion system protein
       0.14   12.5   0.1       0.33   11.3   0.1    1.6  1  AAA_19           AAA domain
       0.19   11.1   3.3       0.48    9.8   0.2    2.2  2  IPT              Isopentenyl transferase
       0.44   11.0   0.2       0.44   11.0   0.2    2.0  2  AAA_23           AAA 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 !   51.9   0.8   1.4e-16   9.4e-14       1     179 []       7     161 ..       7     161 .. 0.93

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 1.4e-16
                   Cytidylate_kin2   1 iITIsreyGsgGetigeaLAekLglpfydr.eiieevakelglseeeveevdersrlssflskllaarvagdtldek 76 
                                       +I I++  Gsg++t    +A+kLg+ +++  +i++ +ake gls +e+ e+ e+                    d++
  gi|385805538|ref|YP_005841936.1|   7 VIVIGGPAGSGKTTYSTYIAKKLGFSYVSSgMIFRSIAKERGLSISELNELAEK--------------------DSS 63 
                                       799***************************9*****************888882....................344 PP

                   Cytidylate_kin2  77 lddelfeaqervirelaaeesvVivGRgadliLkdrpnvlrvfltapledrvkrvaereglseeearekiketDkrr 153
                                       +d +   +++r+++e++++ +vV+ G  a  i+ ++   l++++ a+l+ rv r+aere+ + +++  +  +++  +
  gi|385805538|ref|YP_005841936.1|  64 IDYY---IDRRTLEEAMKG-NVVLEGHLAPWIVSNIA-DLKIYFNASLKTRVMRIAEREKRNWKDVLIETAKREYSQ 135
                                       4444...7899******99.***************99.9********************99999999999999**** PP

                   Cytidylate_kin2 154 akyykkytgqdwgdaenYdlvlntsk 179
                                       a ++kk++g d+ d + +d+++ t+k
  gi|385805538|ref|YP_005841936.1| 136 AMRFKKMYGIDVLDLSIFDFIVSTEK 161
                                       *********************99975 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.6   0.0   2.6e-18   1.8e-15       1     119 [.       8     122 ..       8     138 .. 0.89

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 2.6e-18
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpealdeskrldedkldklldaleenssale 72 
                                       I++ G++G+GKtt + +++k+lgf     g + r++ake+gl++++ +e  ++   +d   + + l++ ++      
  gi|385805538|ref|YP_005841936.1|   8 IVIGGPAGSGKTTYSTYIAKKLGFsyvssGMIFRSIAKERGLSISELNELAEKDSSIDYYIDRRTLEEAMK------ 78 
                                       89***********************************************7777788888887777777777...... PP

                            AAA_18  73 egknlvidghlaeleseaakdikkvvLtaspeelleRlekRgyeeak 119
                                         +n+v++ghla ++  +  d+k ++  as +++  R+++R++++ k
  gi|385805538|ref|YP_005841936.1|  79 --GNVVLEGHLAPWIVSNIADLK-IYFNASLKTRVMRIAEREKRNWK 122
                                       ..889******************.*****************988755 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.8   0.0     9e-18   6.2e-15       2     134 ..      12     128 ..      11     130 .. 0.88

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 9e-18
                                       E-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEEEE CS
                            AAA_17   2 GgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemrklpleekkelqkeaaekiaeeakkkgvlvdg 78 
                                       G+ GsGK+t++  +++k+gf+++s G ++r+ ak++gl  + +e+++l  e++  ++  + ++  eea k++v+++g
  gi|385805538|ref|YP_005841936.1|  12 GPAGSGKTTYSTYIAKKLGFSYVSSGMIFRSIAKERGL--SISELNELA-EKDSSIDYYIDRRTLEEAMKGNVVLEG 85 
                                       899***********************************..677887776.777889999999999************ PP

                                       -SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHTTST-TS-SHHH CS
                            AAA_17  79 hprikeqagfldglpkevleelkpdaiilleadpeeilerrlkdrtrgrdddnees 134
                                       h               +++ ++  d+ i+++a+ ++ + r +++++r+ +d  +e+
  gi|385805538|ref|YP_005841936.1|  86 HLAP------------WIVSNI-ADLKIYFNASLKTRVMRIAEREKRNWKDVLIET 128
                                       *952............455555.5889********************999988887 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.6   4.3e-10     3e-07       1      37 [.       8      44 ..       8      73 .. 0.87
   2 !   26.2   0.2   8.4e-09   5.8e-06     103     208 ..      69     177 ..      46     180 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 4.3e-10
                                      EEEE-STTSSHHHHHHHHHHHHT-EEEEHHHHHHHHH CS
                    Cytidylate_kin  1 iaiDGPagsGKssvaralaeklglkyldtgalYRala 37
                                      i i GPagsGK + +  +a+klg++y+++g+++R +a
  gi|385805538|ref|YP_005841936.1|  8 IVIGGPAGSGKTTYSTYIAKKLGFSYVSSGMIFRSIA 44
                                      7799******************************998 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 8.4e-09
                                       HHHHHTT-BSSBEEEEESSIIIIISTT-SEEEEEE--HHHHHHHHHHHHHHTT----HHHHHHHHHHHHHHHHCTSS CS
                    Cytidylate_kin 103 vkklrelvkkarvvveGRDigtvvfpdaelKifldAsveeRakRRlkqlkakgtsvsleellaeikeRDklDkerev 179
                                        ++  e + k++vv+eG      v   a+lKi+ +As ++R+ R ++  k++ ++v +e+  +e  +  +  k   +
  gi|385805538|ref|YP_005841936.1|  69 DRRTLEEAMKGNVVLEGHLAPWIVSNIADLKIYFNASLKTRVMRIAEREKRNWKDVLIETAKREYSQAMRFKKMYGI 145
                                       55556667799*******999999999****************9999877777777777777777777777777788 PP

                                       S-S---TT-EEEETTTS-HHHH...HHHHHHH CS
                    Cytidylate_kin 180 gpLklaedaliidtskltieev...vekilel 208
                                       + L l+   +i+ t+kltie+v   v++i+e+
  gi|385805538|ref|YP_005841936.1| 146 DVLDLSIFDFIVSTEKLTIEQVkfiVDQIIEY 177
                                       899999999***********975547888776 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.1   2.5e-08   1.7e-05       1      74 [.       7      82 ..       7     141 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 2.5e-08
                            AAA_33  1 lvllvGlpGsGKstlaerllkklgavllssdtlrrrlfgtdqqsktdytrvldr...lyqil.nelarkalsagrnvi 74
                                      ++++ G++GsGK+t+++ ++kklg+  +ss  ++r ++++   s++++++++++   + + + ++++    + ++nv+
  gi|385805538|ref|YP_005841936.1|  7 VIVIGGPAGSGKTTYSTYIAKKLGFSYVSSGMIFRSIAKERGLSISELNELAEKdssIDYYIdRRTL--EEAMKGNVV 82
                                      78999**********************************9999999888866554554444403333..344455555 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.2e-06   0.00084       3      69 ..      12      78 ..       9      89 .. 0.77
   2 ?    1.9   0.1      0.31   2.1e+02      71     114 ..     118     160 ..     100     184 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.2e-06
                                      ESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHHCT-HHHHHHHHHHHTTSS--HHHHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK  3 GaPgaGKGtqaeklvkkyglahlstGdllRaevksgtelGkeakevmdkgelvpdevvvklvkeele 69
                                      G+ g+GK t ++ ++kk+g+  +s+G ++R+  k+      e++e+ +k + +   +  + ++e+++
  gi|385805538|ref|YP_005841936.1| 12 GPAGSGKTTYSTYIAKKLGFSYVSSGMIFRSIAKERGLSISELNELAEKDSSIDYYIDRRTLEEAMK 78
                                      5669**************************9998877777777777777666666665555555555 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.31
                                       HGTTTEEEEESB-SSHHHHHHHHHHHHHHTSEESEEEEEE--HH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK  71 edkkkgfllDGfPRtveqaealeelleeekvkldlvleldvpee 114
                                       +++ k+ l++   R+++qa++++++   +  +l  ++++ v+ e
  gi|385805538|ref|YP_005841936.1| 118 KRNWKDVLIETAKREYSQAMRFKKMYGIDVLDLS-IFDFIVSTE 160
                                       4556778888889999999999996655544443.344444444 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.1   0.00014     0.096       1      27 [.       8      34 ..       8      46 .. 0.93
   2 !    9.1   0.2    0.0016       1.1     115     188 ..      90     158 ..      72     175 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                                      EEEEESTTSSHHHHHHHHHCCSTCEEE CS
                               dNK  1 ivveGnIgaGKstlvklLskklgvkvf 27
                                      iv+ G+ g+GK+t  + ++kklg+  +
  gi|385805538|ref|YP_005841936.1|  8 IVIGGPAGSGKTTYSTYIAKKLGFSYV 34
                                      89*********************9876 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0016
                                       HHHHHCCH-SEEEEEE--HHHHHHHHHHCTTCCCTTS-HHHHHHHHHHHHHHHTSGGCS-EEEEETSS.-TTTH CS
                               dNK 115 nlleelakpdlliYLkasletclerikkRgreeekkieldYlekLhekyeewlkklnevpvlvidveeldlvae 188
                                       ++++++a  dl iY +asl+t + ri +R++ + k +    +e+ +++y+++++  +   + v+d +  d++ +
  gi|385805538|ref|YP_005841936.1|  90 WIVSNIA--DLKIYFNASLKTRVMRIAEREKRNWKDVL---IETAKREYSQAMRFKKMYGIDVLDLSIFDFIVS 158
                                       5555565..9*******************998877655...456677777777776666777777777555544 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.1   0.00021      0.14      18      41 ..       7      30 ..       3      39 .. 0.87
   2 ?   -2.7   0.0       4.3   2.9e+03      94     103 ..     120     129 ..      95     141 .. 0.54
   3 ?    2.1   0.0      0.14        97      74      95 ..     161     182 ..     157     183 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00021
                        Zeta_toxin 18 lillgGqpGAGKselaellkdele 41
                                      +i++gG  G+GK++ +++++++l+
  gi|385805538|ref|YP_005841936.1|  7 VIVIGGPAGSGKTTYSTYIAKKLG 30
                                      799*****************9984 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.3
                        Zeta_toxin  94 ngyniivegt 103
                                       n  ++++e++
  gi|385805538|ref|YP_005841936.1| 120 NWKDVLIETA 129
                                       2234444444 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.14
                        Zeta_toxin  74 eltqkdaselvekllqeaieng 95 
                                       +lt ++++ +v++++++aien+
  gi|385805538|ref|YP_005841936.1| 161 KLTIEQVKFIVDQIIEYAIENK 182
                                       68889999************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 !   15.3   0.0   2.2e-05     0.015      19      50 ..       5      36 ..       1      41 [. 0.90

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.2e-05
                                      TEEEEEEESTTSSHHHHHHHHHHHTT------ CS
                              TsaE 19 gdvilLeGdLGaGKTtlvrglakalgveevkS 50
                                      ++vi++ G+ G+GKTt +  +ak+lg++ v+S
  gi|385805538|ref|YP_005841936.1|  5 NNVIVIGGPAGSGKTTYSTYIAKKLGFSYVSS 36
                                      57899**********************99988 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   2.9e-05      0.02      45      85 ..       5      43 ..       1      70 [. 0.76

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.9e-05
                             Rad17 45 kriLLisGPsGCgkstvvkvLskelgiklrewlnpvslkep 85
                                      +++++i GP+G gk+t    ++k+lg+++   + ++ +++ 
  gi|385805538|ref|YP_005841936.1|  5 NNVIVIGGPAGSGKTTYSTYIAKKLGFSYV--SSGMIFRSI 43
                                      4599***********************996..456666665 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   1.4   3.8e-05     0.026      19      82 ..       4      68 ..       2     186 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.8e-05
                          ATPase_2 19 pneiyfiYGpegsGKtaLlkeiienl..edkdkyviyyialree..siskldefieeeeekkklekal 82
                                      pn++++i Gp gsGKt+    i+++l  +  +   i+ +  +e+  sis+l+e     e++++++ ++
  gi|385805538|ref|YP_005841936.1|  4 PNNVIVIGGPAGSGKTTYSTYIAKKLgfSYVSSGMIFRSIAKERglSISELNEL---AEKDSSIDYYI 68
                                      799*****************9999994333344777755443331155566665...33333344333 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.4   3.4e-05     0.024       2     108 ..      15     119 ..      14     177 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.4e-05
                                       TSSHHHHHHHHHHHHTSEEEEHHHHH...HHHHTS-HHHH..HHHHHHHHHHHHHHHHHHHHCCCSSEEEEE-TTGG CS
                               SKI   2 GaGKstvGkllAkklglefiDlDeli...ekrtgksiaei..feeegeegFrelEsevlkelleeeglViatGGGav 73 
                                       G+GK+t    +Akklg++++ +  ++    k+ g si+e+  ++e++ + +   ++++l+e ++    V+  G  a+
  gi|385805538|ref|YP_005841936.1|  15 GSGKTTYSTYIAKKLGFSYVSSGMIFrsiAKERGLSISELneLAEKDSSIDYYIDRRTLEEAMKG--NVVLEGHLAP 89 
                                       9********************99865333778889999983344666777888899999998887..4666667777 PP

                                       GSHHHHHHHHHHSEEEEEE--HHHHHHHHHHTTSS CS
                               SKI  74 lseenrellkekgiviyLdvsleellerlkadkeR 108
                                           n + lk     iy ++sl++ + r++++++R
  gi|385805538|ref|YP_005841936.1|  90 WIVSNIADLK-----IYFNASLKTRVMRIAEREKR 119
                                       7777777777.....88888888888888888775 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   5.9e-05     0.041       2      67 ..       8      80 ..       7     157 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.9e-05
                            AAA_28  2 ivitGgestGKTtlleaLaar.gypvv..pEaareileekl..akgedalpwv..edllafaervleeqleee 67
                                      ivi G+ ++GKTt +  +a++ g+++v    ++r i +e++   ++ ++l++        + +r lee+++  
  gi|385805538|ref|YP_005841936.1|  8 IVIGGPAGSGKTTYSTYIAKKlGFSYVssGMIFRSIAKERGlsISELNELAEKdsSIDYYIDRRTLEEAMKGN 80
                                      8999999************988999887677888888887755444444444311112234455555555554 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   7.8e-05     0.054       3      54 ..      10      59 ..       8      72 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.8e-05
                                      EESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeak 54
                                      + Gp G GKT+    +ak+lg+++++     ++ ++ +e+  +i+el + a+
  gi|385805538|ref|YP_005841936.1| 10 IGGPAGSGKTTYSTYIAKKLGFSYVS--SGMIFRSIAKERGLSISELNELAE 59
                                      679****************9987654..344444566666666666555555 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00061      0.42       2      25 ..       6      29 ..       5      71 .. 0.86
   2 ?    1.7   0.1      0.26   1.8e+02      76     108 ..     113     145 ..      96     182 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00061
                                      EEEEEEESTTSSHHHHHHHHHHHH CS
                             SRP54  2 nvillvGlqGaGKTttlaKLaall 25
                                      nvi++ G+ G+GKTt  + +a++l
  gi|385805538|ref|YP_005841936.1|  6 NVIVIGGPAGSGKTTYSTYIAKKL 29
                                      799************999999876 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.26
                                       HHHHHHTTSSEEEEEE--SSTTHHHHHHHHHHH CS
                             SRP54  76 vekakeekidvvlvDTaGrlqndkelmeelkki 108
                                       + + ++++   vl+ Ta r  +++  ++ +  i
  gi|385805538|ref|YP_005841936.1| 113 IAEREKRNWKDVLIETAKREYSQAMRFKKMYGI 145
                                       455556666667788888877777777776555 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   9.5e-05     0.066       2      30 ..       7      35 ..       6      77 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.5e-05
                                      CEEEEC-TTTCHHHHHHHHHHHHCTS-SC CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalawaegklp 30
                                      ++++ G+aGsGKTt    +a ++  ++  
  gi|385805538|ref|YP_005841936.1|  7 VIVIGGPAGSGKTTYSTYIAKKLGFSYVS 35
                                      799************99999998766655 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2   0.00054      0.37       1      32 [.       7      38 ..       7      67 .. 0.80
   2 ?    1.4   0.0      0.34   2.3e+02     126     147 ..      92     113 ..      69     137 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00054
                               PRK  1 vIgvagsSGaGkttvarklekifgrekvkaae 32
                                      vI ++g+ G+Gktt +  + k +g   v +  
  gi|385805538|ref|YP_005841936.1|  7 VIVIGGPAGSGKTTYSTYIAKKLGFSYVSSGM 38
                                      799******************99977777544 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.34
                               PRK 126 vaelldlkiyvdisidlelark 147
                                       v + +dlkiy  +s   +++r 
  gi|385805538|ref|YP_005841936.1|  92 VSNIADLKIYFNASLKTRVMRI 113
                                       778899****999887766654 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00075      0.51       2      68 ..       7      73 ..       6      97 .. 0.76
   2 ?    1.7   0.1      0.26   1.8e+02     126     161 ..     100     139 ..      87     150 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00075
                                      EEEEEESTTSSHHHHHHHHHH.TT-EEEEHHHHHHHTTCCTHHHHHHHHHHHGGGCB.TTSSE-HHHH CS
                              CoaE  2 ivgltGgiasGKstvanlfad.lgvpivDaDlvArqvvepgsealkkiveeFgeeildedGeLdReaL 68
                                      ++ + G  +sGK+t + ++a+ lg+  v   ++ r++ ++     +++ e   ++    d  +dR++L
  gi|385805538|ref|YP_005841936.1|  7 VIVIGGPAGSGKTTYSTYIAKkLGFSYVSSGMIFRSIAKERGLSISELNELAEKDS-SIDYYIDRRTL 73
                                      6778999************999*************999998888877755444333.44455555555 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.26
                                       EEEE--HHHHHHHHHHCCTSTHHHH....HHHHHHS--HH CS
                              CoaE 126 lvvdvelelqveRlvardgvseeev....kaiiaaQlsee 161
                                       +  +++l+++v R+ +r++ + ++v    +++  +Q+ + 
  gi|385805538|ref|YP_005841936.1| 100 IYFNASLKTRVMRIAEREKRNWKDVlietAKREYSQAMRF 139
                                       5667899999999999999888877222234555555555 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00013     0.088      19      49 ..       5      39 ..       1      82 [. 0.73

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                                      -SEEEEE--TTSSTT....HHHHHHHHHHHHTTS- CS
                              PhoH 19 ndivfaiGpaGtGKt....ylavalavealkkkkv 49
                                      n+++++ GpaG+GKt    y+a  l++++++++ +
  gi|385805538|ref|YP_005841936.1|  5 NNVIVIGGPAGSGKTtystYIAKKLGFSYVSSGMI 39
                                      789999********733335555566655555544 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00017      0.12       1      23 [.       8      30 ..       8      62 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00017
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakall 23
                                      i++ Gp+g GK+t+++++ak+l 
  gi|385805538|ref|YP_005841936.1|  8 IVIGGPAGSGKTTYSTYIAKKLG 30
                                      67899*************99987 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00037      0.26      18      38 ..       5      25 ..       1      30 [. 0.81
   2 ?   -1.9   0.0       3.3   2.3e+03     131     154 ..      34      57 ..      31      75 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00037
                            AAA_30 18 drvavltGpAGtGKttalkal 38
                                      + v v+ GpAG+GKtt  + +
  gi|385805538|ref|YP_005841936.1|  5 NNVIVIGGPAGSGKTTYSTYI 25
                                      56899***********86655 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.3
                            AAA_30 131 VeaGgvlrdlveaagigtaeLtev 154
                                       V+ G ++r++++++g    eL+e+
  gi|385805538|ref|YP_005841936.1|  34 VSSGMIFRSIAKERGLSISELNEL 57 
                                       788999999988888888888876 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 ?   11.6   0.0   0.00025      0.17      36      66 ..       8      37 ..       2      76 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00025
                            RuvB_N 36 vllyGpPGlGkttlakiiakelgvklkitsg 66
                                      +++ Gp G Gktt ++ iak+lg +   +sg
  gi|385805538|ref|YP_005841936.1|  8 IVIGGPAGSGKTTYSTYIAKKLGFSYV-SSG 37
                                      6788999***************98753.344 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 ?   10.1   0.2   0.00044       0.3     130     148 ..       6      24 ..       1      32 [. 0.79
   2 ?   -1.8   0.0       1.8   1.3e+03      76     122 ..      79     125 ..      47     135 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00044
                             T2SSE 130 glilvsGgTgsGKttllya 148
                                        +i++ G+ gsGKtt    
  gi|385805538|ref|YP_005841936.1|   6 NVIVIGGPAGSGKTTYSTY 24 
                                       6799***********7644 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.8
                             T2SSE  76 kgvrlrvvllPvvagealviRkksakeltlddlgaeealkekiaevl 122
                                       ++v l++ l+P +  + + +    +++l+ + ++++e+ k + ++vl
  gi|385805538|ref|YP_005841936.1|  79 GNVVLEGHLAPWIVSNIADLKIYFNASLKTRVMRIAEREKRNWKDVL 125
                                       44555555555555555555555555555555555555555555555 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00048      0.33       8      32 ..       3      27 ..       1      39 [. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00048
                            AAA_19  8 lkekvllvtaGpGtGKTrvlkhiva 32
                                      l+++v+++ +++G+GKT+  + i +
  gi|385805538|ref|YP_005841936.1|  3 LPNNVIVIGGPAGSGKTTYSTYIAK 27
                                      567888888889*****98777665 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.2   0.00069      0.48       2      31 ..       6      35 ..       5      76 .. 0.89
   2 ?    2.2   0.3      0.14        97     111     182 ..     101     178 ..      59     188 .. 0.43

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00069
                               IPT  2 evylifGatttGKtaeaiklaketgapviv 31
                                      +v +i G+ ++GKt  +  +ak+ g++ ++
  gi|385805538|ref|YP_005841936.1|  6 NVIVIGGPAGSGKTTYSTYIAKKLGFSYVS 35
                                      678999********************9887 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.14
                               IPT 111 ywnadfewevkrlrlpd......edvflakakkRvrqmlrpee.egaslldElaelwkepkarailedidG.yryil 179
                                       y+na+   + +++r+++      +dv ++ ak+   q +r ++  g  +ld     +   +++ ++e+++   ++i+
  gi|385805538|ref|YP_005841936.1| 101 YFNAS--LKTRVMRIAErekrnwKDVLIETAKREYSQAMRFKKmYGIDVLDLSIFDFIVSTEKLTIEQVKFiVDQII 175
                                       22222..2222333332111111344555555554444443321233444433333334444444555543134555 PP

                               IPT 180 dya 182
                                       +ya
  gi|385805538|ref|YP_005841936.1| 176 EYA 178
                                       554 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2   0.00063      0.44      19      34 ..       5      20 ..       2      26 .. 0.91
   2 ?   -0.4   0.2         2   1.4e+03      64      97 ..      99     132 ..      77     185 .. 0.47

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00063
                            AAA_23 19 kgltlItGpNGaGKTT 34
                                      +++ +I Gp G+GKTT
  gi|385805538|ref|YP_005841936.1|  5 NNVIVIGGPAGSGKTT 20
                                      799************9 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2
                            AAA_23  64 eiesegkvkayveltfenkdgry....trsiererels 97 
                                       +i ++++ k+ v +  e++++ +         ++ ++ 
  gi|385805538|ref|YP_005841936.1|  99 KIYFNASLKTRVMRIAEREKRNWkdvlI----ETAKRE 132
                                       4445544555533333332222221111....111111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       891  (0.049696); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.51
# Mc/sec: 1116.40
//
Query:       gi|385805539|ref|YP_005841937.1|  [L=56]
Description: hypothetical protein FFONT_0495 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.8e-11   42.0   0.1    9.5e-11   41.9   0.1    1.0  1  Ribosomal_L34e  Ribosomal protein L34e
  ------ inclusion threshold ------
      0.036   14.0   0.0       0.05   13.6   0.0    1.3  1  Gin             Inhibitor of sigma-G Gin
       0.04   13.8   0.1      0.048   13.6   0.1    1.3  1  DUF4428         Domain of unknown function (DUF4428)


Domain annotation for each model (and alignments):
>> Ribosomal_L34e  Ribosomal protein L34e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   0.1   1.6e-14   9.5e-11      47      92 ..       3      48 ..       1      50 [. 0.95

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 1.6e-14
                    Ribosomal_L34e 47 ckkkLqGipalrpkelsrlsktkktvsRaYGgslcakcvkerivra 92
                                      c++ L G p+    e++rlsktkk+++R +Gg++c++c+ + i+++
  gi|385805539|ref|YP_005841937.1|  3 CGRPLGGTPNGSYVEIKRLSKTKKRPNRIFGGVVCPECLAKIIKNE 48
                                      9****************************************99875 PP

>> Gin  Inhibitor of sigma-G Gin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   8.3e-06      0.05      13      31 ..      30      48 ..      22      52 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.3e-06
                                      -SSS--EEHHHHHHHHHHS CS
                               Gin 13 iilgkfICeeCekkivnte 31
                                      +i+g  +C eC +ki++ e
  gi|385805539|ref|YP_005841937.1| 30 RIFGGVVCPECLAKIIKNE 48
                                      79*************9876 PP

>> DUF4428  Domain of unknown function (DUF4428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1     8e-06     0.048      17      31 ..      31      45 ..      17      55 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8e-06
                           DUF4428 17 leDgyvCkdClkKls 31
                                      +  g+vC++Cl K++
  gi|385805539|ref|YP_005841937.1| 31 IFGGVVCPECLAKII 45
                                      5679*********94 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); 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: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.90
# Mc/sec: 187.96
//
Query:       gi|385805540|ref|YP_005841938.1|  [L=206]
Description: adenylate kinase [Fervidicoccus fontis Kam940]
Scores for complete 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-36  123.4   0.1    1.2e-35  122.9   0.1    1.2  1  AAA_17           AAA domain
    8.4e-12   45.8   0.0    1.2e-11   45.3   0.0    1.2  1  AAA_18           AAA domain
    1.3e-06   28.9   0.0    4.8e-06   27.1   0.0    1.8  1  AAA_16           AAA ATPase domain
    1.4e-05   25.4   0.0    2.5e-05   24.6   0.0    1.6  1  AAA_28           AAA domain
    2.3e-05   24.7   0.0    5.8e-05   23.4   0.0    1.6  1  AAA_22           AAA domain
    0.00014   21.8   0.0    0.00017   21.5   0.0    1.2  1  NACHT            NACHT domain
    0.00026   20.5   0.3    0.00045   19.7   0.3    1.4  1  KTI12            Chromatin associated protein KTI12
    0.00026   21.4   0.1    0.00049   20.5   0.0    1.6  1  AAA              ATPase family associated with various cellul
    0.00075   19.1   0.1     0.0013   18.4   0.1    1.6  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
    0.00076   18.8   0.1     0.0011   18.3   0.1    1.2  1  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.001   18.7   0.2      0.002   17.8   0.2    1.6  1  SRP54            SRP54-type protein, GTPase domain
     0.0012   18.8   0.1     0.0023   18.0   0.1    1.5  1  AAA_14           AAA domain
     0.0017   18.1   0.3     0.0055   16.5   0.3    1.8  1  AAA_30           AAA domain
     0.0021   18.2   0.1      0.011   15.9   0.1    2.0  1  AAA_33           AAA domain
     0.0053   16.5   0.1       0.01   15.6   0.1    1.6  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
  ------ inclusion threshold ------
       0.01   15.8   2.7      0.015   15.3   0.5    2.0  2  NTPase_1         NTPase
      0.013   14.5   0.1      0.027   13.5   0.1    1.5  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
      0.013   15.2   0.5       0.03   14.0   0.4    1.8  2  AAA_24           AAA domain
      0.014   15.3   0.2      0.019   14.9   0.2    1.2  1  ATPase_2         ATPase domain predominantly from Archaea
      0.016   15.3   0.8       0.15   12.2   0.1    2.2  2  MMR_HSR1         50S ribosome-binding GTPase
      0.029   14.3   0.1      0.079   12.9   0.1    1.7  1  RsgA_GTPase      RsgA GTPase
       0.03   14.5   0.6      0.042   14.1   0.6    1.3  1  DNA_pol_B_3      DNA polymerase family B viral insert
       0.03   13.8   0.0      0.059   12.9   0.0    1.5  1  AAA_7            P-loop containing dynein motor region
      0.034   14.5   0.8      0.065   13.6   0.1    1.8  2  AAA_19           AAA domain
      0.043   13.1   0.4      0.095   12.0   0.1    1.6  2  6PF2K            6-phosphofructo-2-kinase
      0.052   12.6   0.8       0.11   11.6   0.4    1.7  1  T2SSE            Type II/IV secretion system protein
       0.06   12.5   0.2       0.09   11.9   0.2    1.3  1  DAP3             Mitochondrial ribosomal death-associated pro
       0.08   12.2   0.3       0.18   11.1   0.0    1.6  2  Zeta_toxin       Zeta toxin


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 !  122.9   0.1   1.9e-38   1.2e-35       1     135 [.      13     157 ..      13     158 .. 0.93

  Alignments for each domain:
  == domain 1  score: 122.9 bits;  conditional E-value: 1.9e-38
                                       EE-TTSSHHHHHHHHH.....HHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHH... CS
                            AAA_17   1 lGgPGsGKgtqceklv.....ekygfthlsaGdllreeakrgglakardemrklpleekkelqkeaaekiaeea... 69 
                                       +G+PG+GK+t++++l+     + + +++l++Gd+++ ea++++l+++rde+rklp++++ +lq+ aa+ki +ea   
  gi|385805540|ref|YP_005841938.1|  13 TGVPGVGKTTVLNELKleaskKSIYIKVLNFGDYMFFEAQKSKLVNNRDELRKLPHRVQLQLQEVAARKIIDEAnvs 89 
                                       7**************755554677***********************************************999899 PP

                                       ..HSSEEEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHTTST-TS-SHHHH CS
                            AAA_17  70 ..kkkgvlvdghprikeqagfldglpkevleelkpdaiilleadpeeilerrlkdrtrgrdddneesi 135
                                         +++ +++d+h+++k++ gf++glp++v+++l pd i+l+ea+p ei++r +kd+tr+r+d + + i
  gi|385805540|ref|YP_005841938.1|  90 lkANDVLIIDTHAVVKTKTGFWPGLPQHVITQLYPDSIVLIEAEPREIIDRQAKDTTRERKDISGKGI 157
                                       8666778******************************************************9887655 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.0   1.8e-14   1.2e-11       1     119 [.      10     150 ..      10     161 .. 0.85

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 1.8e-14
                            AAA_18   1 IlltGtpGvGKttlakeL....skrlgf........gvnlrdvakenglllevdpealdeskrldedkldklldale 65 
                                       I++tG+pGvGKtt+ +eL    sk+  +        g+   + a+++ l+  +d+   +  +r++ + ++++ +++ 
  gi|385805540|ref|YP_005841938.1|  10 IIVTGVPGVGKTTVLNELkleaSKK--SiyikvlnfGDYMFFEAQKSKLVNNRDEL-RKLPHRVQLQLQEVAARKII 83 
                                       9*****************6654333..146777777********************.66667777777777666666 PP

                            AAA_18  66 enss.aleegknlvidghlaeleseaakdikk............vvLtaspeelleRlekRgyeeak 119
                                         ++ +l  +++l+id h +   ++ ++ +              v ++a+p e ++R +k+ ++e+k
  gi|385805540|ref|YP_005841938.1|  84 DEANvSLKANDVLIIDTHAVVKTKTGFWPGLPqhvitqlypdsiVLIEAEPREIIDRQAKDTTRERK 150
                                       6666689999******************9888***********9999**************999988 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   7.4e-09   4.8e-06      21     123 ..       4     164 ..       1     206 [] 0.54

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 7.4e-09
                            AAA_16  21 sgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleaw 97 
                                       ++    ++++G +GvGK+++++el+ +++k+ ++    ++ ++       ++ +a  +++l++  ++    +++ + 
  gi|385805540|ref|YP_005841938.1|   4 RNAFKTIIVTGVPGVGKTTVLNELKLEASKKSIYIKVLNFGDY-------MFFEAQ-KSKLVNNRDEL--RKLPHRV 70 
                                       5556889******************999999555544444444.......455555.33444444333..2233333 PP

                            AAA_16  98 rekleeala.................................................................... 106
                                       + +l+e++a                                                                    
  gi|385805540|ref|YP_005841938.1|  71 QLQLQEVAArkiideanvslkandvliidthavvktktgfwpglpqhvitqlypdsivlieaepreiidrqakdttr 147
                                       33333333333333333555555555555555666666666666666666666666666666666665554444444 PP

                            AAA_16 107 avpelagaeasrllell 123
                                       + ++++g++ ++l el+
  gi|385805540|ref|YP_005841938.1| 148 ERKDISGKGIQDLVELM 164
                                       44444444445555554 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0     4e-08   2.5e-05       2      83 ..      10     103 ..       9     163 .. 0.73

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 4e-08
                            AAA_28   2 ivitGgestGKTtlleaLa...ar..gypvvpEaareileekl....akgedalpwvedllafaer.vleeqleeea 68 
                                       i++tG ++ GKTt+l++L+   ++   y  v  ++  +++e +     +++d+l++   +++++ + v + ++ +ea
  gi|385805540|ref|YP_005841938.1|  10 IIVTGVPGVGKTTVLNELKleaSKksIYIKVLNFGDYMFFEAQksklVNNRDELRKLPHRVQLQLQeVAARKIIDEA 86 
                                       89*****************8642244344457777777777773333555566665544455554303333334444 PP

                            AAA_28  69 aa..aankvlfcDrgll 83 
                                       +   +an+vl++D+ ++
  gi|385805540|ref|YP_005841938.1|  87 NVslKANDVLIIDTHAV 103
                                       44889*********876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   9.1e-08   5.8e-05       8     100 ..      10      86 ..       6     101 .. 0.63

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 9.1e-08
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseellealeq 84 
                                       ++vtG +G+GKTt+l++l+ ++         +++ +++++ + +    ++++  ++l +    +r++++ l ++++ 
  gi|385805540|ref|YP_005841938.1|  10 IIVTGVPGVGKTTVLNELKLEA---------SKKSIYIKVLNFG-DYMFFEAQKSKLVN----NRDELRKLPHRVQL 72 
                                       89*******************9.........6677777777766.22333444444443....23445555555555 PP

                            AAA_22  85 alraravielliiDEa 100
                                       +l++ a+    iiDEa
  gi|385805540|ref|YP_005841938.1|  73 QLQEVAA--RKIIDEA 86 
                                       5555555..4455555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   2.7e-07   0.00017       2     140 ..       9     143 ..       8     173 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.7e-07
                                       CEEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC..-SEEEEEETTTTTTS-...-HCHHHCCCCTS--SSS-CCHHHH CS
                             NACHT   2 lvilqGeaGsGKTtLlqklalawaegklpqga..fklvFflslrelsrsgnarsladllfsqlpepaapvsevwavl 76 
                                       ++i++G +G+GKTt l +l l++ ++  + +   f    f++ ++ +  +n   l++l +++++++++   +    +
  gi|385805540|ref|YP_005841938.1|   9 TIIVTGVPGVGKTTVLNELKLEASKKSIYIKVlnFGDYMFFEAQKSKLVNNRDELRKLPHRVQLQLQEVAAR---KI 82 
                                       89**********************999988766655566677777777788889999999999999988777...34 PP

                                       CCSCCCEE.....EEEE-STT-SS-TCH.........HHHHHCTTTTT--EEEEEEECCCHHHHCTTSS CS
                             NACHT  77 lelperlL.....lilDglDelvtdlgqkekqpvrtlLselirkkllpeasllltvrpralrdleeqle 140
                                       +  ++  L     li+D    ++t+ g+        l ++ i++ l p + +l+ + pr    + +q +
  gi|385805540|ref|YP_005841938.1|  83 IDEANVSLkandvLIIDTHAVVKTKTGF-----WPGLPQHVITQ-LYPDSIVLIEAEPREI--IDRQAK 143
                                       4444444455555999998888888888.....44444444454.6666666666666666..555555 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.3   7.1e-07   0.00045       4      83 ..      10     105 ..       8     108 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 7.1e-07
                                       EEEE--TTSSHHHHHHHHHHHHHH.................TT--EEEE-THHHH.TTSSS--GGGHHHHHHHHHHH CS
                             KTI12   4 vvltGlPssGKstrakeLakalee.................ekrsvvviddeslgiekdsykdsakekalRsslrsa 63 
                                       +++tG+P +GK+t+ +eL+ + ++                  ++s  v + + l+   + ++ + +e a+R+ ++ +
  gi|385805540|ref|YP_005841938.1|  10 IIVTGVPGVGKTTVLNELKLEASKksiyikvlnfgdymffeAQKSKLVNNRDELRKLPHRVQLQLQEVAARK-IIDE 85 
                                       89******************9999778888888877777754444444444444434444566666666664.6667 PP

                                       HHHHHTT.SEEEE-S---SH CS
                             KTI12  64 vkrdLskekvVIvDslnyik 83 
                                       ++ +L+ ++v I+D  + +k
  gi|385805540|ref|YP_005841938.1|  86 ANVSLKANDVLIIDTHAVVK 105
                                       78888888888888766655 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   7.6e-07   0.00049       1      74 [.      10     107 ..      10     132 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 7.6e-07
                                       EEEESSTTSSHHHHHHHHHHHHTHE.............EEEEETTTCSSS...........STTHHHHHHHHHHHHH CS
                               AAA   1 vllyGppGtGKTllakavakelgve.............fleisgsellsk...........yvgesekkirelfkea 53 
                                       ++++G pG+GKT++ + +  e++ +             f+e + s+l+++            ++ +e   r++++ea
  gi|385805540|ref|YP_005841938.1|  10 IIVTGVPGVGKTTVLNELKLEASKKsiyikvlnfgdymFFEAQKSKLVNNrdelrklphrvQLQLQEVAARKIIDEA 86 
                                       5899**************99985333334445555555999999999977899999999987788888888899888 PP

                                       HHTS.TSEEEEEETGGGHHHHH CS
                               AAA  54 keka.kpsilfiDEidalaksr 74 
                                         +  +  +l+iD  +a++k++
  gi|385805540|ref|YP_005841938.1|  87 NVSLkANDVLIID-THAVVKTK 107
                                       7777445999998.45555555 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1     2e-06    0.0013       2      96 ..       9     106 ..       8     161 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2e-06
                                       EEEEEESTTCCHHHHHHHHHCT--SS-EEEEESS-SSCHCCCCCCHCCCT.EEEETT..TTECCHCTT-HHHHHHHH CS
                              cobW   2 vtvltGflGsGKTtLlnhllenraglklavivNefgevsiDaellretgveivelen..GciCctlredllkeleal 76 
                                       ++++tG +G GKTt+ln+l  +++++++ + v +fg    D  + +++++++v+  +   ++++ ++ +l++++++ 
  gi|385805540|ref|YP_005841938.1|   9 TIIVTGVPGVGKTTVLNELKLEASKKSIYIKVLNFG----DYMFFEAQKSKLVNNRDelRKLPHRVQLQLQEVAARK 81 
                                       589****************97777887777776777....5555555544433322211356777666666554433 PP

                                       HHHH.....TT-SEEEEEECTTTTH CS
                              cobW  77 eere.....erldviliEttGlaeP 96 
                                         +e     +  dv++i t  +++ 
  gi|385805540|ref|YP_005841938.1|  82 IIDEanvslKANDVLIIDTHAVVKT 106
                                       3222356666667777766655555 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   1.8e-06    0.0011       3      55 ..       9      74 ..       8     102 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.8e-06
                           DUF2075  3 vvlVtGvaGtGKtvvllnllaeledde.............eertavylsvNhplvlvlrealakke 55
                                       ++VtGv+G GKt vl++l  e+++++              e ++  l+ N++++++l ++++ + 
  gi|385805540|ref|YP_005841938.1|  9 TIIVTGVPGVGKTTVLNELKLEASKKSiyikvlnfgdymfFEAQKSKLVNNRDELRKLPHRVQLQL 74
                                      699*******************94444566666666666655666666777777777777666555 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.2   3.1e-06     0.002       3     120 ..       9     130 ..       7     157 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.1e-06
                                       EEEEEESTTSSHHHHHHHHHHHHHHT.TS-EEEEEESTSSTTHH.HHHHHHHHHTTEEEEE.....SSTTSCHHHHH CS
                             SRP54   3 villvGlqGaGKTttlaKLaallkke.gkkvllvaaDtfRaaAv.eQLktlaeklgvpvik.....kkeeadpaava 72 
                                        i++ G+ G+GKTt l  L    +k+  +  +l   D +   A+   L  + ++l+   +      + +e  + +++
  gi|385805540|ref|YP_005841938.1|   9 TIIVTGVPGVGKTTVLNELKLEASKKsIYIKVLNFGDYMFFEAQkSKLVNNRDELR--KLPhrvqlQLQEVAARKII 83 
                                       6899***************9888888555556666776555554145666655554..3331222233334455555 PP

                                       HHHHHHHHHTTSSEEEEEE--SSTTHHHHHHHH.HHHHHHHSSSEEEEE CS
                             SRP54  73 keavekakeekidvvlvDTaGrlqndkelmeel.kkikkvvkpdevllv 120
                                        ea  + k+   dv+++DT    ++++     l +++ + + pd+++l+
  gi|385805540|ref|YP_005841938.1|  84 DEANVSLKA--NDVLIIDTHAVVKTKTGFWPGLpQHVITQLYPDSIVLI 130
                                       555555444..89******999999998888883345666677777665 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   3.6e-06    0.0023       3      74 ..       8      87 ..       6     104 .. 0.55

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.6e-06
                            AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyi...nldderdkkladpe.........kllelileklkeekktylf 69
                                      k +++tG+  vGKTt+l++l  e     ++ +yi   n+ d  + ++++++         kl++ ++ +l+e      +
  gi|385805540|ref|YP_005841938.1|  8 KTIIVTGVPGVGKTTVLNELKLEAS---KKSIYIkvlNFGDYMFFEAQKSKlvnnrdelrKLPHRVQLQLQE-VAARKI 82
                                      789*****************65555...55555511155555554444332221111222222222222222.233346 PP

                            AAA_14 70 lDEiq 74
                                      +DE+ 
  gi|385805540|ref|YP_005841938.1| 83 IDEAN 87
                                      66655 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.3   8.5e-06    0.0055      19     102 ..       8     106 ..       2     109 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 8.5e-06
                            AAA_30  19 rvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgi.eastiakllkrlk............. 81 
                                       ++ ++tG++G GKtt+l++l+  + ++   + +l     +  + +++  + + + + kl +r +             
  gi|385805540|ref|YP_005841938.1|   8 KTIIVTGVPGVGKTTVLNELKLEASKKSIYIKVLNFGDYMFFEAQKSKLVnNRDELRKLPHRVQlqlqevaarkiid 84 
                                       5679****************766666655555555444444444433222245555555555555555555666666 PP

                            AAA_30  82 .grarlepgtllivDEagmvdt 102
                                        + ++l+++++li+D  ++v t
  gi|385805540|ref|YP_005841938.1|  85 eANVSLKANDVLIIDTHAVVKT 106
                                       6556677777777777776666 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   1.7e-05     0.011       2     117 ..      10     143 ..      10     160 .. 0.51

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.7e-05
                            AAA_33   2 vllvGlpGsGKstlaerl.lkklg.avllssdtlrrrlfgtdqqsktdytrvldrlyqilnelarkalsagrnvild 76 
                                       +++ G+pG+GK+t++ +l l++ +  + +   ++ + +f + q+sk    + +d+l++  +++  + ++ ++  i+d
  gi|385805540|ref|YP_005841938.1|  10 IIVTGVPGVGKTTVLNELkLEASKkSIYIKVLNFGDYMFFEAQKSKL--VNNRDELRKLPHRVQLQLQEVAARKIID 84 
                                       6899*************975555577777777766666666666554..2333333333222222222222334444 PP

                            AAA_33  77 atnls...............rrer...arflklarrlgvp.........vrivvvetdeetlkeRlak 117
                                         n+s               + +      +         p         ++iv +e+ ++++ +R ak
  gi|385805540|ref|YP_005841938.1|  85 EANVSlkandvliidthavvKTKTgfwPGL---------PqhvitqlypDSIVLIEAEPREIIDRQAK 143
                                       444442222222221100002222122111.........12222233338888888888888888876 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   1.6e-05      0.01       1      21 [.      10      30 ..      10      99 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.6e-05
                   Viral_helicase1  1 ivvhGvpGcGKStlirkllrt 21
                                      i+v GvpG GK+t++ +l  +
  gi|385805540|ref|YP_005841938.1| 10 IIVTGVPGVGKTTVLNELKLE 30
                                      79************9998766 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.5   2.3e-05     0.015       2      22 ..      10      30 ..       9      40 .. 0.81
   2 ?    0.0   0.1       1.1   7.1e+02      76     102 ..      70      99 ..      50     100 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.3e-05
                                      EEEE--TTSSHHHHHHHHHHH CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlel 22
                                      +++TG pGvGKtT+++ +  +
  gi|385805540|ref|YP_005841938.1| 10 IIVTGVPGVGKTTVLNELKLE 30
                                      89************9987655 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.1
                                       E-HHHHHHHHHHHHHHHH...HHH-EEEE- CS
                          NTPase_1  76 vdvesfeelalealrkal...seadviviD 102
                                       v+++  e  a +++++a+   + +dv++iD
  gi|385805540|ref|YP_005841938.1|  70 VQLQLQEVAARKIIDEANvslKANDVLIID 99 
                                       454444445555566665666899999999 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 ?   13.5   0.1   4.2e-05     0.027      31      59 ..       9      37 ..       3      44 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.2e-05
                                      EEEEEE-TTSSHHHHHHHHHHHHHCTT-- CS
                              MeaB 31 vvGltGvPGaGkstlvealglelrrrGkr 59
                                       + +tGvPG+Gk t++++l le  ++   
  gi|385805540|ref|YP_005841938.1|  9 TIIVTGVPGVGKTTVLNELKLEASKKSIY 37
                                      5779**************99887776655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.4   4.7e-05      0.03       3      29 ..       8      38 ..       6     106 .. 0.67
   2 ?   -3.2   0.0       9.2   5.9e+03      86     107 ..     139     160 ..     127     167 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.7e-05
                            AAA_24  3 lkiliyGpsgiGKTtlakel....gpkplfi 29
                                      + i+++G +g+GKTt+++el     +k ++i
  gi|385805540|ref|YP_005841938.1|  8 KTIIVTGVPGVGKTTVLNELkleaSKKSIYI 38
                                      5799***************976664444444 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 9.2
                            AAA_24  86 irqnekaeskedkgdgkGygel 107
                                       +rq+++ + + ++ +gkG ++l
  gi|385805540|ref|YP_005841938.1| 139 DRQAKDTTRERKDISGKGIQDL 160
                                       4444444444445555665554 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 ?   14.9   0.2     3e-05     0.019      17      99 ..       4      87 ..       1     106 [. 0.75

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3e-05
                          ATPase_2 17 repneiyfiYGpegsGKtaLlkeiienledkdkyviyyialree..siskldefieeeeekkklekalgiavpkaelee 93
                                      r+  + + ++G  g+GKt++l+e+  + ++k    i + ++ ++  +++++++ +++ +e +kl   ++ +++++++ +
  gi|385805540|ref|YP_005841938.1|  4 RNAFKTIIVTGVPGVGKTTVLNELKLEASKK-SIYIKVLNFGDYmfFEAQKSKLVNNRDELRKLPHRVQLQLQEVAARK 81
                                      66778899**************986666443.35666777777633566666666799999999999999999999999 PP

                          ATPase_2 94 ilkeks 99
                                      i++e +
  gi|385805540|ref|YP_005841938.1| 82 IIDEAN 87
                                      977433 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   0.1   0.00023      0.15       2      22 ..      10      30 ..       9      48 .. 0.83
   2 ?    1.5   0.1      0.48   3.1e+02      37      82 ..      84     130 ..      53     164 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00023
                                      EEEEESTTSSHHHHHHHHHTS CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltge 22
                                      +++ G p vGK+t++n l  e
  gi|385805540|ref|YP_005841938.1| 10 IIVTGVPGVGKTTVLNELKLE 30
                                      899**************9654 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.48
                                       EEEEEEETTEEEEEEECGGCSSHHHHHH.HHHHHHHHHHCTSEEEEE CS
                          MMR_HSR1  37 negrvklkgkeielvDtpGliegaseek.glgkaflaleeadlillv 82 
                                        e++v+lk +++ ++Dt  +++++   + gl +++      d i+l+
  gi|385805540|ref|YP_005841938.1|  84 DEANVSLKANDVLIIDTHAVVKTKTGFWpGLPQHVITQLYPDSIVLI 130
                                       45566677788999999987664444557777776665555555443 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   0.00012     0.079     100     124 ..       8      32 ..       2      45 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00012
                                       SEEEEECSTTSSHHHHHHHHCTT-- CS
                       RsgA_GTPase 100 ktsvlvGqSGvGKStLinallpele 124
                                       kt+++ G  GvGK+t++n+l+ e++
  gi|385805540|ref|YP_005841938.1|   8 KTIIVTGVPGVGKTTVLNELKLEAS 32 
                                       7999****************87755 PP

>> DNA_pol_B_3  DNA polymerase family B viral insert
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.6   6.5e-05     0.042      26      95 ..      27     100 ..       3     108 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.5e-05
                       DNA_pol_B_3  26 tkdakdkisiFsevlstgnYvtiddnvlkilekkin....ekkFtvkvkaeneiaigdtytlsfgkDDvdlsdl 95 
                                        k    k si+ +vl+ g+Y++ + +  k+++ + +     ++ ++++++ ++ +i d+ ++s+  +Dv + d 
  gi|385805540|ref|YP_005841938.1|  27 LKLEASKKSIYIKVLNFGDYMFFEAQKSKLVNNRDElrklPHRVQLQLQEVAARKIIDEANVSLKANDVLIIDT 100
                                       344456789********************9988775443466777788888999999***********988775 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   9.1e-05     0.059      34      71 ..       8      45 ..       2      63 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.1e-05
                             AAA_7 34 kpvllvGptGtGKtviikdllkkldkekylsltinfsa 71
                                      k ++++G  G+GKt+++++l  + +k+++ ++++nf  
  gi|385805540|ref|YP_005841938.1|  8 KTIIVTGVPGVGKTTVLNELKLEASKKSIYIKVLNFGD 45
                                      67899**************8888888999999999965 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1    0.0001     0.065      11      29 ..       8      26 ..       2      41 .. 0.86
   2 ?   -2.3   0.0       7.8     5e+03      96     109 ..      86      99 ..      57     107 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.0001
                            AAA_19 11 kvllvtaGpGtGKTrvlkh 29
                                      k+++vt+ pG GKT+vl++
  gi|385805540|ref|YP_005841938.1|  8 KTIIVTGVPGVGKTTVLNE 26
                                      789*************987 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 7.8
                            AAA_19  96 eekklqeeellivD 109
                                        +  l+++++li+D
  gi|385805540|ref|YP_005841938.1|  86 ANVSLKANDVLIID 99 
                                       33345445566666 PP

>> 6PF2K  6-phosphofructo-2-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00015     0.095      15      85 ..       9      83 ..       2     106 .. 0.70
   2 ?   -1.7   0.0       2.3   1.5e+03      65      93 ..     137     165 ..     129     170 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00015
                                      EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHHHHHHSS....---GGGGSTT-HHHHHHHHHHHHHHH CS
                             6PF2K 15 vivlvGLpargKtyiskkltrylkwlgvrtkvFnvgkyrreaska....lsdaeffrpdneealklreklalaal 85
                                       i++ G p  gKt++ ++l    +  +++ kv n+g+y    +++    ++  e  ++  + +l+l+e +a++ +
  gi|385805540|ref|YP_005841938.1|  9 TIIVTGVPGVGKTTVLNELKLEASKKSIYIKVLNFGDYMFFEAQKsklvNNRDELRKLPHRVQLQLQEVAARKII 83
                                      57889********************************97443333233333333344444444555555555555 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.3
                                       GGSTT-HHHHHHHHHHHHHHHHHHHHHHH CS
                             6PF2K  65 ffrpdneealklreklalaalkdllayln 93 
                                       +++ + ++ ++ r+ +  + ++dl++ +n
  gi|385805540|ref|YP_005841938.1| 137 IIDRQAKDTTRERKDISGKGIQDLVELMN 165
                                       55667778888888888888888888776 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 ?   11.6   0.4   0.00017      0.11     130     156 ..       8      34 ..       2      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00017
                             T2SSE 130 glilvsGgTgsGKttllyallkeinks 156
                                       ++i+v+G  g GKtt+l+ l  e  k+
  gi|385805540|ref|YP_005841938.1|   8 KTIIVTGVPGVGKTTVLNELKLEASKK 34 
                                       78****************987776665 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 ?   11.9   0.2   0.00014      0.09      24      55 ..       8      38 ..       3     106 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                                      -EEEEE-SSSSSTTTTHHHHHHHGGGS--EEE CS
                              DAP3 24 krlvltGekgsGKSvlLlqalayAlekgwvvl 55
                                      k +++tG +g+GK+++L+ +   A +k  + +
  gi|385805540|ref|YP_005841938.1|  8 KTIIVTGVPGVGKTTVLNELKLEASKKS-IYI 38
                                      5689**************9998887763.333 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00028      0.18      17      45 ..       8      36 ..       2      42 .. 0.83
   2 ?   -2.8   0.1       5.1   3.2e+03     169     182 ..      73      86 ..      52     101 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00028
                        Zeta_toxin 17 klillgGqpGAGKselaellkdelerqgn 45
                                      k i++ G pG GK++++++lk e  +++ 
  gi|385805540|ref|YP_005841938.1|  8 KTIIVTGVPGVGKTTVLNELKLEASKKSI 36
                                      679******************99865544 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 5.1
                        Zeta_toxin 169 svealeeekqldrv 182
                                       ++++++ +k +d+ 
  gi|385805540|ref|YP_005841938.1|  73 QLQEVAARKIIDEA 86 
                                       33333334444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       826  (0.0460706); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); expected 358.6 (0.02)
Passed Vit filter:                       111  (0.00619109); 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: 0.69u 0.38s 00:00:01.06 Elapsed: 00:00:00.58
# Mc/sec: 1060.93
//
Query:       gi|385805541|ref|YP_005841939.1|  [L=465]
Description: preprotein translocase subunit SecY [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-60  204.8  16.3    2.3e-60  204.4  16.3    1.1  1  SecY             SecY translocase
    1.4e-08   34.5   0.9    1.4e-08   34.5   0.9    2.4  2  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 !  204.4  16.3   2.6e-64   2.3e-60       1     306 []      76     444 ..      76     444 .. 0.85

  Alignments for each domain:
  == domain 1  score: 204.4 bits;  conditional E-value: 2.6e-64
                                       BTTSSTCHHHHHHHHHHHHH.HHHSSSSSSTS-SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC........... CS
                              SecY   1 sifaLGImPyitasIilqLl.tvvipkleelkkegeegrkkinqitryltvvlalvqalgialslg........... 65 
                                       ++++LGI+P++t ++ilq+l ++   kl  l+  + ++r+k++++++ l++++ +++al+++l+ +           
  gi|385805541|ref|YP_005841939.1|  76 TLMELGIGPIVTGGLILQILvGA---KLIDLDLSDVDDRRKFTEAQKTLSFLFGIFEALAYVLASRywpyvgnpitg 149
                                       89******************999...77777756999***********************8876559********** PP

                                       .....HH.HHHHHHHHHHHHHHHHHHHHHHH.HSSTTHHHHHHHHHHHHHHC.CHSS-HHHH............... CS
                              SecY  66 .....lalllivlqltagtvllmwLgEqite.kGiGnGisllifagivarlp.kalsgliel............... 120
                                            ++ + ++lqlt++t+l+m ++E++++ +GiG+ isl+i+ag++++++ + +  ++++               
  gi|385805541|ref|YP_005841939.1| 150 sqaswAIRIGVLLQLTFATYLVMVFDEMLQKgWGIGSAISLFILAGVAKTMFwDLFGYTPQYaqqiglipyivqate 226
                                       ****977899******************************************5555525555444555555554444 PP

                                       SS..........THHHHHHHHHHHHHHHHHCHHHHBEEEECBBBSTT....S.S-EEEEETTCCCSCHHHHHHHHHH CS
                              SecY 121 ale........gilallllllvtllvillvvyveeaerripvqyakrgrkggqssylPlklnyagviPiIfasslla 189
                                       a +        + l+ ++ ll+t++ i+++vy++ ++++ipv+++k    gg +s++Pl+++y  +iPi+++  +++
  gi|385805541|ref|YP_005841939.1| 227 A-NnltsivvrQGLPDVVGLLATIIAIIGLVYLQGMRVEIPVTSQKY---GGIRSKIPLQFLYVTNIPILLVGIIVS 299
                                       1.044455566669******************************999...99************************* PP

                                       HHHCCCCS...............................TCCCS...THHHHHHHHHHHHHHHHHHHHTCT.THHHH CS
                              SecY 190 lpstiaqfl..............................lalls...psvlyvvlyvlliifFayfyteit.fnpke 232
                                         + +a+ +                              +   +   + ++ ++  v+l ++F y+++ei+ + pke
  gi|385805541|ref|YP_005841939.1| 300 DFQLFANAFasisgtqnlgyrilyelsyylspprglysaT---AdltKLFIFIISWVVLSVLFGYMWVEIAgLGPKE 373
                                       7777766666666777777777766666666655554321...1342445577777888888*************** PP

                                       HHHCCHHTBSSSCTTT.TCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS.TT.TTHHHHHHHHHHHHHHH CS
                              SecY 233 vaenlkksggfipgir.pgketakyLekvlsritliGalflaliavlpdllgasligafggtslLivVgvaletv 306
                                        a+ l k +  ipg+r + k  +k+L+k++  +t++++l++a+ia+++d++ga  +g  +gt++L++Vg++ +++
  gi|385805541|ref|YP_005841939.1| 374 QADRLIKGELDIPGVRrNPKFFEKMLAKYIYPLTVLSSLIVAFIAIVADIFGA--YG--SGTGILLAVGIINQYY 444
                                       ****************999**********************************..66..************9986 PP

>> Plug_translocon  Plug domain of Sec61p
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.9   1.5e-12   1.4e-08       1      35 []      42      75 ..      42      75 .. 0.95
   2 ?   -3.5   0.1       1.1   9.8e+03       7      11 ..     287     291 ..     284     302 .. 0.69

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 1.5e-12
                                      HHHHHHCCSB-TT--SSS-TCCHTTTCCCCTSSTT CS
                   Plug_translocon  1 llYlvlsqiPLyGissssssDpfywlRaifAsnrG 35
                                      +lYl+++ +PLyG+++ +s+ ++ +++++fA+n G
  gi|385805541|ref|YP_005841939.1| 42 VLYLIMADTPLYGVPY-TSQSQISLFQILFAANTG 75
                                      79*************5.59**************98 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.1
                                       CCSB- CS
                   Plug_translocon   7 sqiPL 11 
                                       ++iP+
  gi|385805541|ref|YP_005841939.1| 287 TNIPI 291
                                       78885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (465 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.65u 0.34s 00:00:00.99 Elapsed: 00:00:00.54
# Mc/sec: 2575.10
//
Query:       gi|385805542|ref|YP_005841940.1|  [L=148]
Description: 50S ribosomal protein L15 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.7e-21   75.8   0.8    6.3e-21   75.4   0.8    1.2  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 !   75.4   0.8   3.5e-25   6.3e-21       2     127 ..      31     145 ..      30     146 .. 0.89

  Alignments for each domain:
  == domain 1  score: 75.4 bits;  conditional E-value: 3.5e-25
                                       GGGTSSTTTTTTTTT-..S--........S--.........---.GGG..---EEEEHHHHHHTTTTGTTS.--... CS
                    Ribosomal_L27A   2 GktgGrGhkGqkkrsg..vkk.kpg.feGGqmplyrrlpkrGfk.nskfkkeykvvnlkdLdelideerle.la... 69 
                                       G++gGrG +G+ k+++  + k +pg +  G++         Gf+    +k++  ++nl +Ldel++e+  + +    
  gi|385805542|ref|YP_005841940.1|  31 GSKGGRGAAGMLKHKEswMRKyAPGwI--GKH---------GFTsPYEKKEKVYEINLLQLDELVEELASKgVLked 96 
                                       99************9988777788866..999.........***64444566699************9998644786 PP

                                       ----EEEGGGTTTTSSS....SE.EEE--S---.--EEEESEE-HHHHHHHHHTT-EEE CS
                    Ribosomal_L27A  70 deaeeidleelaeaglikkkdgv.KvlgkgeltkklkvkaskfSkkAkekIeaaGGkve 127
                                       ++++ i+l++l          g+ K+lg+g++++++kv ++++S+kA+ek++++GG+v+
  gi|385805542|ref|YP_005841940.1|  97 SGKPIIELDKL----------GFtKLLGTGRISRPIKVVVKEASEKAIEKVKSVGGEVI 145
                                       789********..........************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 953.38
//
Query:       gi|385805543|ref|YP_005841941.1|  [L=149]
Description: 50S ribosomal protein L30 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00016   21.5   0.0    0.00037   20.3   0.0    1.7  1  Ribosomal_L30    Ribosomal protein L30p/L7e
  ------ inclusion threshold ------
      0.069   13.4   0.0       0.13   12.5   0.0    1.4  1  Lipoprotein_Ltp  Host cell surface-exposed lipoprotein


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 !   20.3   0.0   4.2e-08   0.00037       7      50 ..       2      46 ..       1      47 [. 0.93

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 4.2e-08
                                      S-STTS-HHHHHHHHHTT-SSTT.EEEE--SSHHHHHHHHHCCCG CS
                     Ribosomal_L30  7 rsiigvppkvrktLqlLgLrkin.gtvvklntpsirGmLkkVkhl 50
                                      ++  ++ ++   tL+l++L +   ++ ++ n p + GmL+k+k +
  gi|385805543|ref|YP_005841941.1|  2 KGRTNIRHDAEYTLRLFRLYRKYhASIYPSNFPGLSGMLNKIKNY 46
                                      67788999999********99888*******************88 PP

>> Lipoprotein_Ltp  Host cell surface-exposed lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.5e-05      0.13       7      38 ..      40      75 ..      39      76 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.5e-05
                   Lipoprotein_Ltp  7 lkkAksYadtmnmSkqglydqLtse....yGekFte 38
                                      l+k k+Ya  + +S++ l++ L++      GekFt+
  gi|385805543|ref|YP_005841941.1| 40 LNKIKNYATWGEISREMLIELLKKRgrivGGEKFTQ 75
                                      67779***********************99*****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1019.02
//
Query:       gi|385805544|ref|YP_005841942.1|  [L=212]
Description: 30S ribosomal protein S5 [Fervidicoccus fontis Kam940]
Scores for complete 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   88.4   0.0    2.5e-25   87.7   0.0    1.3  1  Ribosomal_S5_C  Ribosomal protein S5, C-terminal domain
    6.8e-24   83.6   3.3    1.2e-22   79.7   0.6    2.6  3  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 !   87.7   0.0   2.8e-29   2.5e-25       2      66 ..     140     205 ..     139     210 .. 0.95

  Alignments for each domain:
  == domain 1  score: 87.7 bits;  conditional E-value: 2.8e-29
                                       EEETTEEEEEEE--TT--EES-HHHHHHHHHHT--SEE---BS.-SSHHHHHHHHHHHHHHTTTT- CS
                    Ribosomal_S5_C   2 gkfgavkvllkpaprGtGiiaggavravlelaGikDvlakslg.srnpinvvkAtfeALkklrspe 66 
                                       gk g+v++ l+pap+GtG++ag+ ++ vl+laGikDv++ks g +r ++n++kAt++ALk+++s+ 
  gi|385805544|ref|YP_005841942.1| 140 GKSGSVEIVLYPAPKGTGLVAGDIAKIVLRLAGIKDVWSKSFGeTRSTYNFAKATYNALKNTYSFV 205
                                       9**************************************************************986 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 !    3.8   0.0    0.0064        57      10      24 ..      18      32 ..      11      35 .. 0.82
   2 !   79.7   0.6   1.3e-26   1.2e-22       1      65 []      54     118 ..      54     118 .. 0.98
   3 ?   -2.3   0.0      0.49   4.4e+03      51      61 ..     191     201 ..     190     203 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.0064
                                      EEEEEETTEEEEEEE CS
                      Ribosomal_S5 10 rvqkvtkgGrrtsfs 24
                                      +v k++k G++ts+ 
  gi|385805544|ref|YP_005841942.1| 18 KVGKMVKEGKITSIN 32
                                      789*********975 PP

  == domain 2  score: 79.7 bits;  conditional E-value: 1.3e-26
                                       XEEEEEEEEEEEEEETTEEEEEEEEEEEEEETTTEEEEEEEEESSHHHHHHHHHHHHHHTEEE-- CS
                      Ribosomal_S5   1 lkekvlkikrvqkvtkgGrrtsfsalvvvGdgnGlvGlGvgkakevatAirkAiekAkknlvpvp 65 
                                       l+++v+++  vqk+t++G   +f+ +vv+G+gnG +G+G+gkak+ + +i+kAi +Ak+n+vp++
  gi|385805544|ref|YP_005841942.1|  54 LQHEVIDVGIVQKQTDAGELSRFKTVVVIGNGNGFIGIGTGKAKQLRYSIEKAITNAKLNIVPIR 118
                                       689************************************************************96 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.49
                                       HHHHHHHHHTE CS
                      Ribosomal_S5  51 rkAiekAkknl 61 
                                        kA+ +A kn 
  gi|385805544|ref|YP_005841942.1| 191 AKATYNALKNT 201
                                       59999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); 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 0.26s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1398.17
//
Query:       gi|385805545|ref|YP_005841943.1|  [L=199]
Description: 50S ribosomal protein L18 [Fervidicoccus fontis Kam940]
Scores for complete 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   88.0   5.3    8.2e-17   61.7   3.1    2.4  2  Ribosomal_L5e    Ribosomal large subunit proteins 60S L5, and
    1.1e-09   39.0   0.1    2.5e-09   37.9   0.1    1.5  1  Ribosomal_L18_c  Ribosomal L18 C-terminal region
    1.1e-08   35.4   0.5    1.5e-08   35.0   0.5    1.2  1  Ribosomal_L18p   Ribosomal L18 of archaea, bacteria, mitoch. 


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 !   61.7   3.1   1.4e-20   8.2e-17       2      99 ..       7      98 ..       6     103 .. 0.94
   2 !   26.8   0.0   7.1e-10   4.2e-06     130     162 ..     102     134 ..      97     135 .. 0.92

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 1.4e-20
                     Ribosomal_L5e  2 rfqvkfrrrregktdYyarkrliiqdknkyntpkyRlvVrvtnkdiicqiayakiegdkvlaaayskelp.kygvkvgl 79
                                      r++v  rrrregkt+Y++r   +          + RlvVr tnk i ++i+    +gd v ++a+s el  kyg k + 
  gi|385805545|ref|YP_005841943.1|  7 RYKVARRRRREGKTNYRKRYTYVFS-------GRIRLVVRKTNKYIEAKIVDCDPKGDLVKVSAHSIELIkKYGWKGSG 78
                                      9*******************99985.......579*********************************8549******* PP

                     Ribosomal_L5e 80 tnyaaaYatglllarrllkk 99
                                      ++  aaY+ g+l+++r+++k
  gi|385805545|ref|YP_005841943.1| 79 KSTPAAYLLGYLIGKRAIEK 98
                                      ****************9987 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 7.1e-10
                     Ribosomal_L5e 130 kaiLdvGLartttgakvfgalkgavdgglsiph 162
                                        a+Ld+GL r  + +k+f+++kga+d+gl++p 
  gi|385805545|ref|YP_005841943.1| 102 DAVLDIGLYRVVKQSKLFAVVKGAIDAGLKVPV 134
                                       689****************************96 PP

>> Ribosomal_L18_c  Ribosomal L18 C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.1   4.2e-13   2.5e-09       7      59 ..     144     196 ..     141     199 .] 0.94

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 4.2e-13
                   Ribosomal_L18_c   7 rIfgkhvaeYmeeLkeedeekykkqFskyikkgieaddleelykkahaaIred 59 
                                       rI g+h+a+Y ++Lke ++e+y++qFsk i++g+ +++    ++++ +aI+++
  gi|385805545|ref|YP_005841943.1| 144 RIRGEHIANYAKMLKESNPERYNRQFSKIINSGLLPEEYVAHFESVLNAIKNE 196
                                       89************************************************976 PP

>> Ribosomal_L18p  Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.5   2.6e-12   1.5e-08       5      99 ..      11     113 ..       7     132 .. 0.72

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 2.6e-12
                                       HHHCHH..HHHHTTT--.TTSSS-EEEEEE-SS-EEEEEE-TTT--EEEEECS-SCCCT.....S-SSSCHHHHHHH CS
                    Ribosomal_L18p   5 earkrR..hkRirkkls.gtaerprlvvfrsnrhiyaQviddvkgktlasastlekelk.....lkstknkeaakkv 73 
                                       ++r+rR  ++  rk+ +   + r rlvv ++n++i a+++d   +  l+++s+   el      + s+k++ aa  +
  gi|385805545|ref|YP_005841943.1|  11 ARRRRRegKTNYRKRYTyVFSGRIRLVVRKTNKYIEAKIVDCDPKGDLVKVSAHSIELIkkygwKGSGKSTPAAYLL 87 
                                       4555552234456666657788******************97777667666665555433477778899999***** PP

                                       HHHHHHHHCHHCHTC-EE--TTSSS- CS
                    Ribosomal_L18p  74 geliAerakekgiekvvfDrggykYh 99 
                                       g li +ra ekg++++v D g y+  
  gi|385805545|ref|YP_005841943.1|  88 GYLIGKRAIEKGLKDAVLDIGLYRVV 113
                                       *******************9987754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1375.83
//
Query:       gi|385805546|ref|YP_005841944.1|  [L=153]
Description: 50S ribosomal protein L19e [Fervidicoccus fontis Kam940]
Scores for complete 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-49  166.4  10.4    4.6e-49  166.2  10.4    1.0  1  Ribosomal_L19e  Ribosomal protein L19e
  ------ inclusion threshold ------
      0.027   14.6   0.0      0.048   13.8   0.0    1.4  1  HSR             HSR domain


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 !  166.2  10.4   5.2e-53   4.6e-49       2     143 ..       4     148 ..       3     149 .. 0.97

  Alignments for each domain:
  == domain 1  score: 166.2 bits;  conditional E-value: 5.2e-53
                                       THHHHHHHHHHTTS-GGGEEE...-GGGHHHHHH--SHHHHHHHHHTTSEEE-------THHHHHHHHHHHTT-S-S CS
                    Ribosomal_L19e   2 lklqkrlaasvlkvGknrvwl...dpeeleeiaeAitredirklikdglIikkpkkgnsrararerkekkrkgrrrg 75 
                                       ++lqkrla+++l++G++rv++     ++ e++++Ait edi+klik+g+I+++p+k nsr+r+re+kek++kg+rrg
  gi|385805546|ref|YP_005841944.1|   4 YTLQKRLASKILGIGESRVRIyikSDDDREDLENAITAEDIKKLIKRGVITEEPEKSNSRGRWRELKEKRSKGQRRG 80 
                                       689***************999776668899*********************************************** PP

                                       GGG--S-HHHHS-HHHHHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHTT--SSHHHHHHHHT-X CS
                    Ribosomal_L19e  76 sGkrkGtkeaRlpekelWikriRalRrlLkelrekkkidkktYrelYrkakGgefknkavLkeyiekk 143
                                       +GkrkG ++aR++ k++Wi+ iR++Rr+Lk lr+kk i++++Yr++Y+ akGg+f++ +vL+ +iek+
  gi|385805546|ref|YP_005841944.1|  81 PGKRKGVASARIDPKRRWISSIRKMRRYLKYLRDKKIITTQQYRRYYKLAKGGAFSSLSVLRMHIEKE 148
                                       *****************************************************************985 PP

>> HSR  HSR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   5.4e-06     0.048      17      47 ..     100     129 ..      92     140 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.4e-06
                               HSR  17 asaikkpfpflegLrDkslitekmykeslea 47 
                                       +  i+k   +l+ LrDk++it + y+++ + 
  gi|385805546|ref|YP_005841944.1| 100 S-SIRKMRRYLKYLRDKKIITTQQYRRYYKL 129
                                       5.7999999****************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       931  (0.051927); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 954.67
//
Query:       gi|385805547|ref|YP_005841945.1|  [L=129]
Description: 50S ribosomal protein L32e [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-29  102.1   0.1    2.5e-29  101.9   0.1    1.1  1  Ribosomal_L32e  Ribosomal protein L32
  ------ inclusion threshold ------
       0.14   11.9   0.0       0.16   11.7   0.0    1.1  1  HERV-K_env_2    Retro-transcribing viruses envelope glycoprot


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 !  101.9   0.1   2.8e-33   2.5e-29       1     108 []      16     123 ..      16     123 .. 0.98

  Alignments for each domain:
  == domain 1  score: 101.9 bits;  conditional E-value: 2.8e-33
                                       ------TTTTT-TTS-S..S------TT-TTTTT-TTS-----GGG---TTTTT--TTS-EEEEESSGGGGTT--TT CS
                    Ribosomal_L32e   1 tkkFirhqsdryvklke..swrkprGidnrvrrrfkgqilmpkiGYgspkktrgllpsGfkkvlVhnvkeLevllme 75 
                                       +++F+rh  + + k+++  swrkp+Gidn++r ++kg+ + ++iGY++p+ +rg++psG++ v++++ ++Le+l+++
  gi|385805547|ref|YP_005841945.1|  16 KPEFKRHLFHMFIKFRNqdSWRKPKGIDNKMRLKYKGYAKPVEIGYKNPEIVRGVHPSGLRPVVIESRSQLENLDPK 92 
                                       689************9778********************************************************** PP

                                       TE..EEEE-TTS-HHHHHHHHHHHHHTT-EBSS CS
                    Ribosomal_L32e  76 nksyaaeiahsVsskkrkeiverAaelgikVtN 108
                                        +  +++++++ + kk++e+++ A+e g++++N
  gi|385805547|ref|YP_005841945.1|  93 IH--IVYLSSKLGLKKKIELMKLAREKGLRIAN 123
                                       99..***************************98 PP

>> HERV-K_env_2  Retro-transcribing viruses envelope glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   1.8e-05      0.16      15      95 ..      34     111 ..      24     127 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.8e-05
                      HERV-K_env_2  15 dsvwvpgpiddrcpakpeeegmminisigyryppiclgrapgclmpavqnwlvevptvspisrftyhmvsgmslrpr 91 
                                       ds   p  id++   k   +g    + igy+ p i+ g  p  l p v +   ++  + p  ++ y + s + l+ +
  gi|385805547|ref|YP_005841945.1|  34 DSWRKPKGIDNKMRLK--YKGYAKPVEIGYKNPEIVRGVHPSGLRPVVIESRSQLENLDPKIHIVY-LSSKLGLKKK 107
                                       4544566777776655..468888999**********************99999999999998887.5677888877 PP

                      HERV-K_env_2  92 vnyl 95 
                                       ++ +
  gi|385805547|ref|YP_005841945.1| 108 IELM 111
                                       7654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 844.98
//
Query:       gi|385805548|ref|YP_005841946.1|  [L=185]
Description: 50S ribosomal protein L6 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.6e-27   94.8   7.1    1.1e-15   58.0   2.0    2.1  2  Ribosomal_L6  Ribosomal protein L6


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 !   58.0   2.0   6.3e-20   1.1e-15       1      76 []      16      89 ..      16      89 .. 0.98
   2 !   40.0   0.2   2.7e-14   4.8e-10      13      76 .]     113     175 ..     101     175 .. 0.91

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 6.3e-20
                                      CSTTEEEEEETTTEEEEEESSEEEEEE-CTTSEEEEEECSTEEEEEECSESCHHHHHHHHHHHHHHHHHHHHHHTC CS
                      Ribosomal_L6  1 iPvgvrvsikggqlvlvlGpkgeltreipegvtvevkvegnkvtvivvsgidkekvAligtvrslinnmikGVteg 76
                                      iP+gv++si+g   v v Gpkg ++ ++++  +v+++  ++kv+v++ +  +++k+ l+gt+ ++i+nmi+GV++g
  gi|385805548|ref|YP_005841946.1| 16 IPEGVKISIEG-MKVVVEGPKGKIEKDFSHTRNVAISLSDGKVVVESYFARREQKA-LVGTIAAHIRNMITGVQKG 89
                                      8*********8.********************************************.*****************98 PP

  == domain 2  score: 40.0 bits;  conditional E-value: 2.7e-14
                                       TEEEEEESSEEEEEE-CTTSEEEEEECSTEEEEEECSESCHHHH....HHHHHHHHHHHHHHHHHHTC CS
                      Ribosomal_L6  13 qlvlvlGpkgeltreipegvtvevkvegnkvtvivvsgidkekv....AligtvrslinnmikGVteg 76 
                                        + ++lG+k +++++i +gv+v+++     +++++v+g d+e v    A++++++++++++ +++++g
  gi|385805548|ref|YP_005841946.1| 113 LVKNFLGEKSPRKARIMPGVKVKIE-----KEDVIVEGLDIEAVgqtaANLEQATKVKEYDRRVFMDG 175
                                       5679*******************99.....9999********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1259.11
//
Query:       gi|385805549|ref|YP_005841947.1|  [L=131]
Description: 30S ribosomal protein S8 [Fervidicoccus fontis Kam940]
Scores for 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   85.9   0.2    2.5e-24   85.7   0.2    1.1  1  Ribosomal_S8  Ribosomal protein S8


Domain annotation for each model (and alignments):
>> Ribosomal_S8  Ribosomal protein S8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.7   0.2   1.4e-28   2.5e-24       1     127 []       3     131 .]       3     131 .] 0.81

  Alignments for each domain:
  == domain 1  score: 85.7 bits;  conditional E-value: 1.4e-28
                                       -HHHHHHHHHHHHHHTT-SEEEE.E--HHHHHHHHHHHHCTSEEEEEEE.CCCCCC..EEEEE-BSSS-SBSSSEEE CS
                      Ribosomal_S8   1 DpiadmltrirNaekakkeevev.pasklkeeilkvLkeeGyikdfeve.eekkkk..ikielkynkkkksvikklk 73 
                                       D+++++l+++ Na ++ k+ev + pas+l+ + +++L++eGyi ++e+  + ++ k  i++ +++nk    +ik   
  gi|385805549|ref|YP_005841947.1|   3 DTLSNALNELTNADRRAKKEVIIsPASRLIIQTMRLLQSEGYIGEIEYIdDGRQGKlkIQLLGRINK--AAAIKPRY 77 
                                       89**********************************************9665666633555567766..89999444 PP

                                       E-SBTTC--EE-CCC---CGGGTSEEEEEETTEEEEHHHHHHCT--EEEEEEEE CS
                      Ribosomal_S8  74 rvskpgrrvYakvkelpkvlnglGiaivsTskGvmtdkeArkkkvGGevlayvw 127
                                        ++ + +    +  + +   + +Gi+i+sTskG+m+++++ k+++GG +l yv+
  gi|385805549|ref|YP_005841947.1|  78 SLKVSELSALPEWLKKKLPSREIGILIISTSKGIMSHHQTIKENIGGILLGYVY 131
                                       4444444433343334444688*******************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 816.92
//
Query:       gi|385805550|ref|YP_005841948.1|  [L=54]
Description: 30S ribosomal protein S14 [Fervidicoccus fontis Kam940]
Scores for complete 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   50.4   4.4    1.5e-13   50.2   4.4    1.1  1  Ribosomal_S14  Ribosomal protein S14p/S29e
     0.0027   17.7   0.8     0.0028   17.7   0.8    1.1  1  Zn_Tnp_IS91    Transposase zinc-binding domain
  ------ inclusion threshold ------
      0.036   13.7   0.6      0.048   13.3   0.6    1.3  1  zf-P11         P-11 zinc finger
      0.094   12.5   5.7       0.11   12.3   0.1    2.4  2  zf-HYPF        HypF 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 !   50.2   4.4   3.4e-17   1.5e-13       6      54 .]       7      54 .]       4      54 .] 0.93

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 3.4e-17
                                      --SS..CTTT---SSS--SSSEE-GGG-..EHHHHHHHTTT...TT-EE-- CS
                     Ribosomal_S14  6 prnssptrirnrCrvtGrprGvirkfgL..sRicfRelAlkgelpGvkKaS 54
                                      pr  + ++   +C+ +G ++Gvir+++L  +R+cfRelA++   +G+kK+S
  gi|385805550|ref|YP_005841948.1|  7 PRERKYGKAVIKCQRCGSRKGVIRRYNLylCRQCFRELAYE---MGFKKYS 54
                                      66666699999******************************...******8 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.8   6.2e-07    0.0028      25      65 ..       2      42 ..       1      52 [. 0.90

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 6.2e-07
                       Zn_Tnp_IS91 25 ekilrCrtaalGfaryeCeeCghekivyfsCksrhCpsCqk 65
                                      +k+ + r++++G a+++C+ Cg++k v  + +   C +C +
  gi|385805550|ref|YP_005841948.1|  2 TKYVQPRERKYGKAVIKCQRCGSRKGVIRRYNLYLCRQCFR 42
                                      67888899*******************************65 PP

>> zf-P11  P-11 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.6   1.1e-05     0.048       4      29 ..      18      42 ..      13      46 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.1e-05
                                      SBTTTSS--SSEEE-SSSEEEHHHHH CS
                            zf-P11  4 sCksCWfkdksLveCsdHYLClrClq 29
                                      +C+ C    k++++  + YLC++C++
  gi|385805550|ref|YP_005841948.1| 18 KCQRCG-SRKGVIRRYNLYLCRQCFR 42
                                      577775.5799*************85 PP

>> zf-HYPF  HypF finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   2.5e-05      0.11       8      30 ..       3      25 ..       1      29 [. 0.90
   2 ?    3.3   0.4     0.016        72       1       9 [.      36      44 ..      36      48 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.5e-05
                                      HHC-TTSTTTT-TT---TTTS-- CS
                           zf-HYPF  8 EykdpldRRfhaqfisCtnCGPr 30
                                      +y  p  R +    i C +CG r
  gi|385805550|ref|YP_005841948.1|  3 KYVQPRERKYGKAVIKCQRCGSR 25
                                      68899****************88 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.016
                                      --HHHHHHH CS
                           zf-HYPF  1 lCedClrEy 9 
                                      lC +C rE+
  gi|385805550|ref|YP_005841948.1| 36 LCRQCFREL 44
                                      7*****997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 359.72
//
Query:       gi|385805551|ref|YP_005841949.1|  [L=188]
Description: 50S ribosomal protein L5 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-25   89.0   0.0    3.4e-25   88.0   0.0    1.5  1  Ribosomal_L5_C  ribosomal L5P family C-terminus
    3.8e-17   62.4   0.3    8.9e-17   61.2   0.3    1.6  1  Ribosomal_L5    Ribosomal protein L5
  ------ inclusion threshold ------
       0.12   12.1   0.0       0.12   12.1   0.0    1.5  2  Casc1_N         Cancer susceptibility candidate 1 N-terminus
       0.21   10.0   0.0       0.26    9.8   0.0    1.1  1  DUF4962         Domain of unknown function (DUF4962)


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 !   88.0   0.0   7.6e-29   3.4e-25       2      92 ..      79     164 ..      78     181 .. 0.85

  Alignments for each domain:
  == domain 1  score: 88.0 bits;  conditional E-value: 7.6e-29
                    Ribosomal_L5_C   2 iGvkvtLrgekmyefldkllevvlprlrdFkGiskssfdgrGnvsfGikeqiifpeieydkdkgifGmditivttak 78 
                                       i+v vtLrgek+ +fl+k+le+v ++++      k sfd++GnvsfGike+i +p+++yd+++g+fGmd++i+++++
  gi|385805551|ref|YP_005841949.1|  79 IAVAVTLRGEKATKFLKKALEAVGNKIN------KDSFDDNGNVSFGIKEHISIPGVKYDPEIGVFGMDVCITIERP 149
                                       99**************************......******************************************* PP

                    Ribosomal_L5_C  79 ...tdeearallkelgi 92 
                                          +  + r++ k+ +i
  gi|385805551|ref|YP_005841949.1| 150 gyrI--KRRRVKKAKRI 164
                                       7542..33334444333 PP

>> Ribosomal_L5  Ribosomal protein L5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.2   0.3     2e-20   8.9e-17       1      57 []      21      74 ..      21      74 .. 0.99

  Alignments for each domain:
  == domain 1  score: 61.2 bits;  conditional E-value: 2e-20
                                      SCTTS-EEEEEEEEEE-SSSSSCHHHHHCCHHHHCCCHSS--EECC--TTCTTTCSC CS
                      Ribosomal_L5  1 NvMqvPrleKivinmgvGeagedkkllekaakeLaeItGQkPvvtkakksianFkiR 57
                                      N+M +Pr++K+++n+ +G+ ge+   l k a++L+eIt Q+P ++kak++i++F+iR
  gi|385805551|ref|YP_005841949.1| 21 NPMLKPRITKVTVNVSLGQGGER---LAKIAEVLKEITNQEPKLRKAKRTIRDFGIR 74
                                      9**********************...******************************9 PP

>> Casc1_N  Cancer susceptibility candidate 1 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.6e-05      0.12      85     139 ..       6      68 ..       4     122 .. 0.66
   2 ?   -3.8   0.7         2   8.7e+03      17      28 ..     160     171 ..     152     180 .. 0.39

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.6e-05
                           Casc1_N  85 tdekeiNtflslwseeee..edieevmetc......tlvlklieeLeelledtaeeelsekev 139
                                       t+++e+N f+  w+e+++    i++v+  +      +++ k++e L+e+ +++++  +++ ++
  gi|385805551|ref|YP_005841949.1|   6 TVTEEVNKFIEAWNENPMlkPRITKVTVNVslgqggERLAKIAEVLKEITNQEPKLRKAKRTI 68 
                                       5789**************995666665555455555555555666655554545444444444 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 2
                           Casc1_N  17 ererleeerrek 28 
                                       +++r+ ++ r k
  gi|385805551|ref|YP_005841949.1| 160 KAKRIPRRHRVK 171
                                       222222222222 PP

>> DUF4962  Domain of unknown function (DUF4962)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   5.7e-05      0.26     125     188 ..      46     111 ..      19     122 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 5.7e-05
                           DUF4962 125 slkevlaklkkeHPrvlllkkewedfikknkdnpeakayl..ekaekllkkplkklereidttgvk 188
                                        ++evl+++ ++ P++   k++  df  +  +n      l  eka+k lkk l+++ ++i+ +   
  gi|385805551|ref|YP_005841949.1|  46 KIAEVLKEITNQEPKLRKAKRTIRDFGIRKGENIAVAVTLrgEKATKFLKKALEAVGNKINKDSFD 111
                                       5789*****************************99998885569****************988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       813  (0.0453455); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1167.07
//
Query:       gi|385805552|ref|YP_005841950.1|  [L=248]
Description: 30S ribosomal protein S4e [Fervidicoccus fontis Kam940]
Scores for complete 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   61.3   1.4    1.3e-16   60.4   1.4    1.5  1  RS4NT          RS4NT (NUC023) domain
    7.4e-17   61.0   0.0    1.4e-16   60.1   0.0    1.4  1  Ribosomal_S4e  Ribosomal family S4e
    1.9e-10   40.3   1.1      1e-09   38.0   0.2    2.3  2  S4             S4 domain


Domain annotation for each model (and alignments):
>> RS4NT  RS4NT (NUC023) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.4   1.4   2.2e-20   1.3e-16       1      36 [.       4      39 ..       4      40 .. 0.98

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 2.2e-20
                                      -S----EETTTS-TTS---SSSSSEE----SSSS-T CS
                             RS4NT  1 rGpkkHLKrlaAPkhWpldkkegvfavkPspGPHkl 36
                                      +G++kHL++++AP++Wp++ ke+ +a+kPspGPH+l
  gi|385805552|ref|YP_005841950.1|  4 MGGSKHLRSYSAPDFWPISTKERFWAIKPSPGPHSL 39
                                      8*********************************98 PP

>> Ribosomal_S4e  Ribosomal family S4e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.1   0.0   2.4e-20   1.4e-16       5      75 .]     100     178 ..      97     178 .. 0.96

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 2.4e-20
                                       EEEEE-TTSSEEEEEE-TTCCCEEEEEECEEEEECCCEEEEEETTS-EEEES.........STT-STTEEEEEETTT CS
                     Ribosomal_S4e   5 yrllydtkgrfalhkItseeakyKLcKikkkttvkkgipqlvthdGrtiryp.........dpdikvnDtvkidlee 72 
                                       +r +++ ++ + +++I +eea++K ++i++kttv+ g++ql++ dG++i+++          p +++  tv ++++e
  gi|385805552|ref|YP_005841950.1| 100 FRAVPNMDKFISFVEIPKEEASIKPLRIENKTTVNHGHIQLNLFDGSNILIKvsdpknpteVP-YRTLSTVIVKIPE 175
                                       9************************************************99999999999677.************* PP

                                       TEE CS
                     Ribosomal_S4e  73 nkI 75 
                                       ++I
  gi|385805552|ref|YP_005841950.1| 176 REI 178
                                       998 PP

>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.2   1.7e-13     1e-09      10      48 .]      53      91 ..      44      91 .. 0.93
   2 ?    0.4   0.1     0.094   5.6e+02      23      31 ..     133     141 ..     130     141 .. 0.86

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 1.7e-13
                                      TTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TTCEE CS
                                S4 10 lglassrreArqlIehGrVlVNGkvvkdpsyrVkpgDvi 48
                                      l++a ++re+ ++ + G V+V+Gkv+kd++y+V+++Dvi
  gi|385805552|ref|YP_005841950.1| 53 LKYARTKREVIRALSMGLVKVDGKVRKDYKYPVGAMDVI 91
                                      89***********************************98 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.094
                                       HHTTTEEET CS
                                S4  23 IehGrVlVN 31 
                                       ++hG++++N
  gi|385805552|ref|YP_005841950.1| 133 VNHGHIQLN 141
                                       89****998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.52
# Mc/sec: 1445.34
//
Query:       gi|385805553|ref|YP_005841951.1|  [L=158]
Description: 50S ribosomal protein L24 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-35  120.7   2.0    4.4e-35  120.0   2.0    1.3  1  Ribosomal_L26  Ribosomal proteins L26 eukaryotic, L24P archae
    6.3e-10   38.7   2.0    1.6e-09   37.4   2.0    1.8  1  KOW            KOW motif
  ------ inclusion threshold ------
        6.7    6.2   9.5         28    4.2   0.0    2.1  2  Drf_GBD        Diaphanous GTPase-binding Domain


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 !  120.0   2.0   7.4e-39   4.4e-35       1      82 []       6     120 ..       6     120 .. 0.99

  Alignments for each domain:
  == domain 1  score: 120.0 bits;  conditional E-value: 7.4e-39
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................xx RF
                     Ribosomal_L26   1 sssrrkqrKahfnapshirrklmsapLskeLrekygvrslpir................................gv 45 
                                       s +++kqrK +fnap+hir+kl+++pLskeLr+kyg+++lp+r                                +v
  gi|385805553|ref|YP_005841951.1|   6 SIKPKKQRKILFNAPLHIREKLVTSPLSKELRNKYGIKRLPVRsgdtvkimrgnnaglegkvvkvnrktgrvhieKV 82 
                                       6689************************************************************************* PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                     Ribosomal_L26  46 trekangttvpvgihpSkvvItklkl.DkdrkkiLerk 82 
                                       tr++a+gt+v ++ih+Skv+Itkl+l Dk+rk+i+erk
  gi|385805553|ref|YP_005841951.1|  83 TRDRADGTPVFIPIHASKVMITKLDLsDKERKQIIERK 120
                                       *************************************9 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   2.0   2.7e-13   1.6e-09       2      32 .]      50      80 ..      49      80 .. 0.98

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 2.7e-13
                                      TSEEEESSSTTTTCEEEEEEEETTTTEEEEE CS
                               KOW  2 GdhVkVvsGphkGktGkVvkvdqhkvrVfvd 32
                                      Gd+Vk+++G ++G +GkVvkv++++ rV+++
  gi|385805553|ref|YP_005841951.1| 50 GDTVKIMRGNNAGLEGKVVKVNRKTGRVHIE 80
                                      9****************************97 PP

>> Drf_GBD  Diaphanous GTPase-binding Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0    0.0047        28      23      56 ..       9      42 ..       2      80 .. 0.83
   2 ?    3.1   6.7      0.01        62      16      70 ..     102     154 ..      98     156 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0047
                           Drf_GBD 23 peekreallalpiekKwqlvvqdkkkkakkeekl 56
                                      p+++r+ l++ p + + +lv++  +k+  +++++
  gi|385805553|ref|YP_005841951.1|  9 PKKQRKILFNAPLHIREKLVTSPLSKELRNKYGI 42
                                      78999*****************999998888444 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.01
                           Drf_GBD  16 lleelnlpeekreallalpiekKwqlvvqdkkkkakkeeklsksksksneeespe 70 
                                       ++++l+l++++r+++++ ++ +K   ++ +++ k+++e++++k+++++++ e++e
  gi|385805553|ref|YP_005841951.1| 102 MITKLDLSDKERKQIIERKTGRK--VIEEKEEEKKETETAEAKEEKEESKVEKSE 154
                                       899*************9999876..688888888888866777666666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2444  (0.136315); expected 358.6 (0.02)
Passed bias filter:                      854  (0.0476323); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.33s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 950.59
//
Query:       gi|385805554|ref|YP_005841952.1|  [L=138]
Description: 50S ribosomal protein L14 [Fervidicoccus fontis Kam940]
Scores for complete 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-34  116.6   0.2    7.5e-34  116.4   0.2    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 !  116.4   0.2   4.2e-38   7.5e-34       2     121 ..      18     137 ..      17     138 .] 0.94

  Alignments for each domain:
  == domain 1  score: 116.4 bits;  conditional E-value: 4.2e-38
                                       .CSS-EEE--SSSSBSEEEEEEETT-.....---EE-SSSEEEEEESSS-T...TTSSCEEEEEEEE-SS-EE-TTS CS
                     Ribosomal_L14   2 iqlktrlkvaDNsgakevecikvlggk....krkaasvGdiivvsvkkakpkgkvkkgdvvkavvvrtkkevrrkdG 74 
                                       +q++tr+ v DNsga+e+++i v g++    + ++a +Gd+++vsvkk++p   + +++v+ avv+r+++++rr+dG
  gi|385805554|ref|YP_005841952.1|  18 VQVGTRVVVSDNSGAREAMIIGVPGYRgrlrRIPKAGIGDKVIVSVKKGIP---EIRKQVLPAVVIRQRRPYRRSDG 91 
                                       6899********************998655344******************...899******************** PP

                                       -EEEESS-EEEEB-TTS-BSS-.B-SBEEHHHHHH.-HHHHHTBSBE CS
                     Ribosomal_L14  75 svirfddnaaVllnkkgeplGtrifgpvarelrekkflkivslApev 121
                                       +++ f+dna+V+++ +g+++G++i gpva+e++e+ ++ ++++A+ +
  gi|385805554|ref|YP_005841952.1|  92 TWVAFEDNAVVIITPEGTLKGSEIRGPVAKEAAER-WPSLANMASII 137
                                       **********************************9.*****999876 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:                      234  (0.0130515); 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 0.28s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 914.57
//
Query:       gi|385805555|ref|YP_005841953.1|  [L=116]
Description: 30S ribosomal protein S17 [Fervidicoccus fontis Kam940]
Scores for complete 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   95.4   3.5    2.2e-27   94.9   3.5    1.2  1  Ribosomal_S17  Ribosomal protein S17
  ------ inclusion threshold ------
       0.36   10.6   2.7       0.64    9.8   2.7    1.3  1  zf-C3H1        Putative zinc-finger domain


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 !   94.9   3.5   2.5e-31   2.2e-27       1      67 [.      42     109 ..      42     110 .. 0.99

  Alignments for each domain:
  == domain 1  score: 94.9 bits;  conditional E-value: 2.5e-31
                                       EEEEE--STTEEEEEEEEEEEETTTTEEEEEEEEEEEE-TTTS.--TT-EEEEEEECECSSSEEEEEE CS
                     Ribosomal_S17   1 GvVvsdkmdkTvvVrverlvkhpkykkyvkrrkkylahdenns.vkvGDiVrieecrPlSktkrfvvv 67 
                                       G+Vvsdkmd TvvV +++l++++kyk+y+kr++k++ah +++  vk+GD+V i+e+rP+Skt++fvv+
  gi|385805555|ref|YP_005841953.1|  42 GKVVSDKMDGTVVVVHDYLYYDKKYKRYEKRKSKIHAHVSPCLdVKIGDTVIIGETRPISKTVSFVVL 109
                                       99****************************************************************97 PP

>> zf-C3H1  Putative zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   2.7   7.2e-05      0.64      10      18 ..      21      29 ..      20      29 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 7.2e-05
                           zf-C3H1 10 vCnDpsCef 18
                                      +CnDp+C+f
  gi|385805555|ref|YP_005841953.1| 21 KCNDPNCPF 29
                                      8******99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.30s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 770.11
//
Query:       gi|385805556|ref|YP_005841954.1|  [L=94]
Description: ribonuclease P, Rpp29 [Fervidicoccus fontis Kam940]
Scores for complete 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   53.0   0.1    2.7e-14   52.9   0.1    1.1  1  UPF0086   Domain of unknown function UPF0086


Domain annotation for each model (and alignments):
>> UPF0086  Domain of unknown function UPF0086
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   0.1   1.5e-18   2.7e-14       2      83 ..       5      84 ..       4      85 .. 0.95

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 1.5e-18
                                      HHCCSXXSS-EEEEEECSSTTTTTEEEEEEEEETTEEEEEECTTEEEEEESTTCEEEEEE.TTEEEEEECCCCSSXHHH CS
                           UPF0086  2 kLlkadlhGaeveVvrsknpslvgikGiVvkEtkntlkivtkksrvktvpKegsvFefevkdvlevevdGsqlryrpad 80
                                      +++  dl G eveV+   +++++g+ GiV +Et++t++i   ++++ t+ K+  vF+++  ++ e  ++G+++  rp+d
  gi|385805556|ref|YP_005841954.1|  5 NITFGDLFGSEVEVLMYPDRNVIGLIGIVENETQKTISIYR-NEKTITLFKDYIVFKIRS-KNSETVIYGNEIVGRPED 81
                                      67788***********************************8.899***************.699*************** PP

                                      HHC CS
                           UPF0086 81 Rae 83
                                      R++
  gi|385805556|ref|YP_005841954.1| 82 RTK 84
                                      *97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 636.77
//
Query:       gi|385805557|ref|YP_005841955.1|  [L=67]
Description: Ribosomal_L29 domain containing protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-19   69.0   3.0    3.2e-19   68.6   3.0    1.1  1  Ribosomal_L29  Ribosomal L29 protein


Domain annotation for each model (and alignments):
>> Ribosomal_L29  Ribosomal L29 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.6   3.0   1.8e-23   3.2e-19       2      56 ..       7      61 ..       6      61 .. 0.98

  Alignments for each domain:
  == domain 1  score: 68.6 bits;  conditional E-value: 1.8e-23
                                      HHHHS-HHHHHHHHHHHHHHHHHHHHHHHHTSSS-CHHHHHHHHHHHHHHHHHHH CS
                     Ribosomal_L29  2 elrelsdeeLkeklkelkkeLfnLrfqkatgqlenpsrirkvRkdIARikTvlre 56
                                      e+r+l+ e+ kekl+el+ eL +L +q+ +g+++np++i+ +Rk+IARi+T+ +e
  gi|385805557|ref|YP_005841955.1|  7 EIRKLTPEQRKEKLNELRLELSKLQMQAHVGTVDNPGKIKVLRKTIARILTIENE 61
                                      9****************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       743  (0.0414412); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 433.87
//
Query:       gi|385805558|ref|YP_005841956.1|  [L=251]
Description: 30S ribosomal protein S3 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-23   82.6   2.5    8.6e-23   80.7   1.2    2.1  2  Ribosomal_S3_C  Ribosomal protein S3, C-terminal domain
    2.6e-13   49.6   0.0    9.6e-13   47.8   0.0    2.0  2  KH_2            KH domain
  ------ inclusion threshold ------
       0.03   14.2   0.1       0.14   12.0   0.0    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 ?    0.7   0.0      0.13   7.7e+02       5      32 ..       9      36 ..       6      38 .. 0.73
   2 !   80.7   1.2   1.4e-26   8.6e-23       2      83 .]     101     183 ..     100     183 .. 0.98

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.13
                                      HHTT--HHHHHHHHHHHHHHCC-SEEEE CS
                    Ribosomal_S3_C  5 lekrvsfRramkkairramkagakGiki 32
                                      +ek++s+ ++ ++  ++  +ag  G+ +
  gi|385805558|ref|YP_005841956.1|  9 IEKNMSVVKVDEYLAKQFYRAGYAGVDV 36
                                      7777777777778888888888888766 PP

  == domain 2  score: 80.7 bits;  conditional E-value: 1.4e-26
                                       HHHHHTT--HHHHHHHHHHHHHHCC-SEEEEEEEC-SS.TTT--EEEEEEC----..TCHHHH-EEEEEEEEETTEE CS
                    Ribosomal_S3_C   2 aeqlekrvsfRramkkairramkagakGikiqvsGrLggaeiarsekykeGrvpl..htlradidyavaeaktkyGi 76 
                                       a +le++++fR+ +  a+rr+m aga G++i++sG+++ +e+ar ek+++G++++  +++   +d+ava+a +k Gi
  gi|385805558|ref|YP_005841956.1| 101 AVSLERGFHFRKLAFAALRRIMAAGAAGAEIIISGKIT-SERARYEKFRAGKIYKtgEQATYIVDKAVAHALLKPGI 176
                                       779***********************************.****************999******************* PP

                                       EEEEEEE CS
                    Ribosomal_S3_C  77 iGvkVwI 83 
                                       +GvkV I
  gi|385805558|ref|YP_005841956.1| 177 YGVKVII 183
                                       *****98 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   0.0   1.6e-16   9.6e-13       1      73 [.      17      86 ..      17      91 .. 0.91
   2 ?   -2.5   0.1      0.79   4.7e+03      19      29 ..     185     195 ..     172     203 .. 0.51

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 1.6e-16
                                      HHHHHHHHHTECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEEEEEEE CS
                              KH_2  1 eipeslaveikkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkkVklnivkV 73
                                      +++e+la++++ ag+++v++ rt+ ++++vir+++p+ +IG++G++ik++   +++ ++ le+ ++   +  V
  gi|385805558|ref|YP_005841956.1| 17 KVDEYLAKQFYRAGYAGVDVYRTPLGTRVVIRAERPAFIIGRRGQTIKTLSNVFENYFG-LENPQIT--VMPV 86
                                      6899******************************************************8.9999998..4455 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.79
                                       EEECCSCEEEE CS
                              KH_2  19 eIertanrvii 29 
                                       + ert++ +ii
  gi|385805558|ref|YP_005841956.1| 185 KPERTKDSIII 195
                                       23333333333 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.4e-05      0.14      35      54 ..      47      66 ..      20      79 .. 0.82
   2 ?   -1.3   0.1      0.35   2.1e+03      11      26 ..     194     209 ..     178     218 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.4e-05
                              KH_4 35 vegedlGrvIGkrGrtldAl 54
                                      +  e  + +IG+rG+t++ l
  gi|385805558|ref|YP_005841956.1| 47 IRAERPAFIIGRRGQTIKTL 66
                                      55677899*********987 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.35
                              KH_4  11 lvddpeevevteeeee 26 
                                       ++++pee+ ++ e ++
  gi|385805558|ref|YP_005841956.1| 194 IIKSPEEIGINKESTA 209
                                       5667777777777443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1538  (0.0857828); expected 358.6 (0.02)
Passed bias filter:                      686  (0.038262); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 1600.48
//
Query:       gi|385805559|ref|YP_005841957.1|  [L=156]
Description: 50S ribosomal protein L22 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.6e-30  103.9   0.5    5.5e-30  103.6   0.5    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 !  103.6   0.5   3.1e-34   5.5e-30       2     103 .]      20     154 ..      19     154 .. 0.97

  Alignments for each domain:
  == domain 1  score: 103.6 bits;  conditional E-value: 3.1e-34
                                       EEEEESS-HHHHHHHHHHHTTSBHHHHHHHHHT..-SST...............................THHHHHH CS
                     Ribosomal_L22   2 kgsnlrvsfkklrevarlIrgmkveeAlkyLkf..skkk...............................aakfvlk 45 
                                         ++l++s+kk++++ar+++gm +++A+kyL+   +k++                               aakf+lk
  gi|385805559|ref|YP_005841957.1|  20 VMRDLPISPKKVHNLARAVNGMMLQDAKKYLERviAKEEavphfihrkkiphhkglserwgipvgkypvkAAKFLLK 96 
                                       6789*****************************9655559************************************* PP

                                       HHHHHHHHHH..HT-GGGEEEEEEEEEEEEEEEEEEEESTTEEEEEEEEEEEEEEEEE CS
                     Ribosomal_L22  46 lLknaeanaelkgldvdslvIeeiqvnkgpklkrrtyrArGrinpirkspchievvlk 103
                                        L+n+eanae+k+ld+++l I +  v++g +lkr+++rA Gr +p  k++++iev++k
  gi|385805559|ref|YP_005841957.1|  97 ALNNVEANAESKELDAEKLKIIHLSVQQGYTLKRYMPRAFGRSTPKFKRYSNIEVIVK 154
                                       ********************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); 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 0.28s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1118.87
//
Query:       gi|385805560|ref|YP_005841958.1|  [L=138]
Description: 30S ribosomal protein S19 [Fervidicoccus fontis Kam940]
Scores for complete 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  108.0   0.5    2.1e-31  107.6   0.5    1.1  1  Ribosomal_S19  Ribosomal protein S19
  ------ inclusion threshold ------
       0.17   12.4   0.1       0.26   11.8   0.1    1.3  1  bZIP_Maf       bZIP Maf transcription factor


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 !  107.6   0.5   2.4e-35   2.1e-31       1      81 []      41     121 ..      41     121 .. 0.96

  Alignments for each domain:
  == domain 1  score: 107.6 bits;  conditional E-value: 2.4e-35
                                       .HHHSS.TTCCCHHHHHHHHHHTS-----EEES-TT-B--GGGTT-EEEEE-SSSEEEEE--CCCTTSBCGGGT-SS CS
                     Ribosomal_S19   1 rslkkg.pfvqesllkkvrkakaekkkevikthsRdstIlPemvgltvgVynGktfvpveikeemvGhkLgEFspTr 76 
                                       rs+++g + +q ++l+k+r+ k+ + k+vikth+R++++lPem+glt++VynGk+f+pv+i++em G +LgEF+pT 
  gi|385805560|ref|YP_005841958.1|  41 RSITRGfTPEQIRFLQKIRRGKK-EGKKVIKTHLRNMIVLPEMIGLTIAVYNGKEFIPVRITPEMLGKRLGEFAPTT 116
                                       78999999999**********95.6799************************************************* PP

                                       ----S CS
                     Ribosomal_S19  77 kpvkh 81 
                                       k vkh
  gi|385805560|ref|YP_005841958.1| 117 KSVKH 121
                                       ****9 PP

>> bZIP_Maf  bZIP Maf transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   2.9e-05      0.26       2      37 ..      27      63 ..      21      68 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.9e-05
                          bZIP_Maf  2 sdeellsl.svrEfnrflrglteeeverLKqrRRrlK 37
                                      s +el+sl + rE +  +rg+t e++  L ++RR +K
  gi|385805560|ref|YP_005841958.1| 27 SMDELVSLfPARERRSITRGFTPEQIRFLQKIRRGKK 63
                                      457777764677777777****************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); 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 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 955.09
//
Query:       gi|385805561|ref|YP_005841959.1|  [L=435]
Description: hypothetical protein FFONT_0517 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.8e-10   39.5   0.0    6.2e-10   38.8   0.0    1.2  1  VWA_CoxE    VWA domain containing CoxE-like protein
     0.0049   17.5   0.5      0.054   14.2   0.5    2.5  1  VWA_2       von Willebrand factor type A domain
  ------ inclusion threshold ------
      0.041   14.5   0.4       0.13   12.9   0.4    1.9  1  DUF5344     Family of unknown function (DUF5344)
      0.067   13.2   1.8         26    4.9   0.1    3.6  3  Phage_XkdX  Phage uncharacterised protein (Phage_XkdX)
       0.07   12.8   0.0        1.6    8.5   0.0    2.6  2  TPR_11      TPR repeat


Domain annotation for each model (and alignments):
>> 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 !   38.8   0.0   1.7e-13   6.2e-10      26     190 ..     266     416 ..     249     429 .. 0.84

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 1.7e-13
                          VWA_CoxE  26 rriDlrrtlranlrhggelvelvrrkprerkprelvllvDvSgSmaaysaiflallhAllqqlp.rtevfaFdtr.. 99 
                                       +r+D+r+tl +  r    ++elv+++ ++r++   +l++D S Sm + s+ +++++       p   ++++Fdt+  
  gi|385805561|ref|YP_005841959.1| 266 GRVDIRKTLFELSR--NHPEELVFKQ-KKREN-GAILVIDKSDSMRKRSTSVIKIASQYY---PfLKSLILFDTEvk 335
                                       78999999988665..4699******.66666.89************7777666654444...44666777777622 PP

                          VWA_CoxE 100 lvdlTralrerDpaeaLarvsaavedlgGgTrigaalaeflelvtrpaLsrravvvlvsDglergdreellaelarl 176
                                       + +++r  +    ++ L +++      +G T+i++al++++e  + +      +v+++sD++++ + e   + +++l
  gi|385805561|ref|YP_005841959.1| 336 VKKISRSSSRWNIVKDLLSMN-----FSGYTNISKALRQVIEISKPK-----DTVIIISDMEQTVEDEFYISLIDKL 402
                                       679999999999999999999.....***************998843.....5899********************* PP

                          VWA_CoxE 177 vrrarrlvwlnpls 190
                                        r+ +rl++ ++++
  gi|385805561|ref|YP_005841959.1| 403 IRKKVRLIIFTSEE 416
                                       *********99984 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 !   14.2   0.5   1.5e-05     0.054       2     105 ..     297     385 ..     296     387 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.5e-05
                             VWA_2   2 vfvlDtSgSmrngdygptrleaakdaveallkslpgdrvglvtfsdgpevl.ipltkdkakilnalrnleakgggtn 77 
                                       ++v+D S Smr +    t   ++++    +lks       l+ f+++++v+ i+ ++++  i + l +++  +g tn
  gi|385805561|ref|YP_005841959.1| 297 ILVIDKSDSMRKR---STSVIKIASQYYPFLKS-------LILFDTEVKVKkISRSSSRWNIVKDLLSMNF-SGYTN 362
                                       79**********9...34444444444445555.......99****9965438999999999999999998.5**** PP

                             VWA_2  78 laaaLqlarkalkkrrkgekrvivlitD 105
                                       + +aL+++ ++ k      k ++++i+D
  gi|385805561|ref|YP_005841959.1| 363 ISKALRQVIEISKP-----KDTVIIISD 385
                                       ***********993.....569999999 PP

>> DUF5344  Family of unknown function (DUF5344)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.4   3.6e-05      0.13      34      86 ..     136     188 ..     121     189 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.6e-05
                           DUF5344  34 sgknsldvvekineleeeleellkaYktlllknvedtesaVdslkeaDealas 86 
                                       + k +l+  +kin l++ +e+    Y +ll++ ++++++   s++ +D   as
  gi|385805561|ref|YP_005841959.1| 136 ENKRKLEIARKINTLQKYYETGNRGYIDLLESELKASQKKKGSYESKDSYSAS 188
                                       56789*******************************************87776 PP

>> Phage_XkdX  Phage uncharacterised protein (Phage_XkdX)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.018        63      12      31 ..      28      46 ..      26      47 .. 0.89
   2 ?    1.5   0.0     0.088   3.1e+02       4      15 ..      64      75 ..      63      76 .. 0.88
   3 ?    4.9   0.1    0.0073        26      20      37 ..     405     422 ..     400     425 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.018
                        Phage_XkdX 12 lwtkeqvrdaVgkgkITkee 31
                                      l++ +++ +aV++ +IT+ +
  gi|385805561|ref|YP_005841959.1| 28 LVSTSEIENAVKL-YITATQ 46
                                      678899*******.***976 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.088
                        Phage_XkdX  4 iKeyYdwglwtk 15
                                      +K+ Yd+ ++++
  gi|385805561|ref|YP_005841959.1| 64 VKRKYDEEIFND 75
                                      9******99986 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.0073
                        Phage_XkdX  20 daVgkgkITkeeYeeITG 37 
                                       + V++  +T+eeY +I+ 
  gi|385805561|ref|YP_005841959.1| 405 KKVRLIIFTSEEYAKIFK 422
                                       55777679********85 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0   0.00044       1.6       2      25 ..      26      49 ..      26      50 .. 0.93
   2 ?    1.3   0.0     0.076   2.7e+02      24      34 ..     204     214 ..     192     217 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00044
                            TPR_11  2 dayyeqGkyeeAieaYkkAlkldP 25
                                      +++++  ++e+A++ Y +A +l+P
  gi|385805561|ref|YP_005841959.1| 26 NVLVSTSEIENAVKLYITATQLSP 49
                                      6889999***************99 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.076
                            TPR_11  24 dPdnaeayynL 34 
                                       +Pdna+a+++L
  gi|385805561|ref|YP_005841959.1| 204 NPDNANALLAL 214
                                       8******9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       816  (0.0455129); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.54
# Mc/sec: 2435.83
//
Query:       gi|385805562|ref|YP_005841960.1|  [L=313]
Description: putative ATPase [Fervidicoccus fontis Kam940]
Scores for complete 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   65.6   0.0    9.8e-18   64.5   0.0    1.6  2  AAA_5            AAA domain (dynein-related subfamily)
    0.00048   20.6   0.1     0.0021   18.5   0.1    2.0  1  AAA              ATPase family associated with various cellul
    0.00083   19.2   0.0     0.0049   16.7   0.0    2.2  2  AAA_3            ATPase family associated with various cellul
      0.002   17.9   0.0       0.87    9.3   0.1    2.2  2  Sigma54_activat  Sigma-54 interaction domain
     0.0024   18.4   0.1      0.013   16.1   0.0    2.2  3  AAA_18           AAA domain
  ------ inclusion threshold ------
      0.042   13.2   0.1       0.68    9.3   0.0    2.3  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.045   14.1   0.0      0.077   13.4   0.0    1.4  1  AAA_16           AAA ATPase domain
      0.065   12.9   0.0       0.11   12.2   0.0    1.5  1  AAA_30           AAA domain
       0.12   12.4   0.0       0.29   11.2   0.0    1.6  1  AAA_2            AAA domain (Cdc48 subfamily)
       0.15   11.5   0.0       0.64    9.5   0.0    1.9  2  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 !   64.5   0.0   5.5e-21   9.8e-18       1     137 [.      65     204 ..      65     205 .. 0.97
   2 ?   -2.4   0.0       2.5   4.5e+03      26      42 ..     271     287 ..     227     302 .. 0.65

  Alignments for each domain:
  == domain 1  score: 64.5 bits;  conditional E-value: 5.5e-21
                                       EEEEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT--HHHHH--B--...............--------G-SEEE CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaal.nreveyvqltrdtteedlkgrreik......ngttslvdsplvraaregeilv 70 
                                       +vl  GppGtgK+e+ e l+++  +r+  +  +++++ e  ++g  +++        ++s+ + pl  a    + ++
  gi|385805562|ref|YP_005841960.1|  65 PVLFEGPPGTGKTEIGEALLSLWaGRKAIILPCSENYDEYRVLGDFHPMkaykegFNEESFIPRPLLAALILDSGIL 141
                                       5899********************************************99999887899********99999999** PP

                                       EESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHTT CS
                             AAA_5  71 lDEveraesevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrsR 137
                                       +DE+ r + e +n Ll ++++rr+ ++e++++ kak  +    f++i+t+np d  +nels a+ +R
  gi|385805562|ref|YP_005841960.1| 142 IDEIRRSSEEFQNLLLDVIDKRRIIIPELKKVYKAKGIG----FQLIFTSNPEDLAQNELSDAFMRR 204
                                       ***********************************9987....***********************9 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.5
                                       -EEEEE--TT--HHHHH CS
                             AAA_5  26 eveyvqltrdtteedlk 42 
                                       ++ +  ++++ +eedl+
  gi|385805562|ref|YP_005841960.1| 271 RIAMLRGHERVSEEDLL 287
                                       33444455555555554 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   1.1e-06    0.0021       1     120 [.      66     198 ..      66     211 .. 0.62

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.1e-06
                                       EEEESSTTSSHHHHHHHHHHHH.THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS............TSEEEEE CS
                               AAA   1 vllyGppGtGKTllakavakel.gvefleisgsellskyvgesekkirelfkeakeka............kpsilfi 64 
                                       vl+ GppGtGKT + +a+ + + g++ + + +se  ++y   +  +  +  ke  +++              s ++i
  gi|385805562|ref|YP_005841960.1|  66 VLFEGPPGTGKTEIGEALLSLWaGRKAIILPCSENYDEYRVLGDFHPMKAYKEGFNEEsfiprpllaaliLDSGILI 142
                                       799*****************964899999999999988555444444444444322222555444333332244566 PP

                                       ETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS...........SSTEEEEEEESSGGGSTHHHH CS
                               AAA  65 DEidalaksrsgseseeeervvnqLlteldgvkkk...........eskvivigatnrpdkldpall 120
                                       DEi +             e+ +n Ll ++d+ +                + +i ++n +d  +++l 
  gi|385805562|ref|YP_005841960.1| 143 DEIRRSS-----------EEFQNLLLDVIDKRRIIipelkkvykakGIGFQLIFTSNPEDLAQNELS 198
                                       6665553...........3457777777777766666666666665333666777776655555555 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 ?   -3.4   0.0       4.5   8.1e+03      37      68 ..      10      41 ..       5      44 .. 0.64
   2 !   16.7   0.0   2.7e-06    0.0049       2     115 ..      66     192 ..      65     206 .. 0.70

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 4.5
                             AAA_3 37 lPsdilGtevfeekekefefkkGpvfanllla 68
                                       P ++   +++e++  +++  + p+ a+ +l 
  gi|385805562|ref|YP_005841960.1| 10 DPIEVKVRDIYEQAYPRIREVRNPIEAKKILR 41
                                      56666666777777777777777777666665 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 2.7e-06
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpd.....llPsdilGtevfeekekefefkkGpvfanll.....la 68 
                                       vl+eg PG++kt + +al +    +   i   ++      + +d   ++ ++e  +e +f + p++a l+     l 
  gi|385805562|ref|YP_005841960.1|  66 VLFEGPPGTGKTEIGEALLSLWAGRKAIILPCSEnydeyRVLGDFHPMKAYKEGFNEESFIPRPLLAALIldsgiLI 142
                                       78999999999999999888777666666443331111135567777788888889999999999998862222268 PP

                             AAA_3  69 deinrappktqsalleameerqvtvegethklpep...flvlatqnPieq 115
                                       dei r++   q  ll++++ r++ + + ++  + +   f ++ t nP + 
  gi|385805562|ref|YP_005841960.1| 143 DEIRRSSEEFQNLLLDVIDKRRIIIPELKKVYKAKgigFQLIFTSNPEDL 192
                                       ***********************987654443332223999999999654 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.0    0.0035       6.3      21      44 ..      62      85 ..      48     104 .. 0.77
   2 !    9.3   0.1   0.00049      0.87      97     122 ..     140     165 ..     132     210 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0035
                                      SSS-EEEECSTTSSHHHHHHHHHH CS
                   Sigma54_activat 21 tdlsvlitGesGtGKellaraihe 44
                                        l+vl +G  GtGK+ + +a+ +
  gi|385805562|ref|YP_005841960.1| 62 DGLPVLFEGPPGTGKTEIGEALLS 85
                                      5689************99998865 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00049
                                       EEEETGGGS-HHHHHHHHHHHHHSEE CS
                   Sigma54_activat  97 lfLDeigelplelQekLlrvlqegev 122
                                       +++Dei + + e+Q+ Ll v++++++
  gi|385805562|ref|YP_005841960.1| 140 ILIDEIRRSSEEFQNLLLDVIDKRRI 165
                                       679********************986 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       6.9   1.2e+04      56      69 ..      26      39 ..       5      61 .. 0.46
   2 !   16.1   0.0   7.1e-06     0.013       1      45 [.      66     141 ..      66     217 .. 0.56
   3 ?   -0.9   0.0       1.3   2.3e+03      13      68 ..     228     282 ..     227     307 .. 0.61

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 6.9
                            AAA_18 56 kldklldaleenss 69
                                      +  ++ + +e+   
  gi|385805562|ref|YP_005841960.1| 26 RIREVRNPIEAKKI 39
                                      33333333333222 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 7.1e-06
                            AAA_18   1 IlltGtpGvGKttlakeL.....skrlgf.................gvnlrdvakenglllevdpe........... 44 
                                       +l  G+pG+GKt+++++L                            g+ +   a+++g  +e + +           
  gi|385805562|ref|YP_005841960.1|  66 VLFEGPPGTGKTEIGEALlslwaG----RkaiilpcsenydeyrvlGDFHPMKAYKEGFNEESFIPrpllaalilds 138
                                       6789**************555541....2333445555557734443333333333333333333354444444444 PP

                            AAA_18  45 ..a 45 
                                          
  gi|385805562|ref|YP_005841960.1| 139 giL 141
                                       553 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.3
                            AAA_18  13 tlakeLskrlgf.gvnlrdvakenglllevdpealdeskrldedkldklldaleens 68 
                                       t++  +s+ + + g++ + v+++++l +    +  d+ + + +  + + l+++e+ s
  gi|385805562|ref|YP_005841960.1| 228 TVSSLISEDMMMkGIEAINVLRKSDLMYKPGIA--DSVRWMGISARIAMLRGHERVS 282
                                       677777777644777777777777777766655..5555555555555555555544 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00038      0.68      24      46 ..      65      87 ..      53      94 .. 0.85
   2 ?    1.2   0.0      0.11     2e+02     109     160 ..     140     191 ..     128     211 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00038
                      Mg_chelatase 24 nlllvGppGsGKtmlakrlpsll 46
                                       +l+ GppG+GKt + ++l sl 
  gi|385805562|ref|YP_005841960.1| 65 PVLFEGPPGTGKTEIGEALLSLW 87
                                      589************99998875 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.11
                      Mg_chelatase 109 vLfLDElpefkrkvlevLRePledgevtisrakakvefp.arfqlvaamNpcp 160
                                       + ++DE+   +++  + L + ++++++ i   k+  +     fql+ + Np  
  gi|385805562|ref|YP_005841960.1| 140 I-LIDEIRRSSEEFQNLLLDVIDKRRIIIPELKKVYKAKgIGFQLIFTSNPED 191
                                       4.579***999****************99987776554314699999999965 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.3e-05     0.077      25      76 ..      64     120 ..      53     208 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.3e-05
                            AAA_16  25 elvllsGesGvGKsslvrellralekdggif..lrgkcdql...esaipysalaqal 76 
                                         vl+ G++G+GK+ + ++ll  + ++++i    ++++d++   +   p+ a+ + +
  gi|385805562|ref|YP_005841960.1|  64 LPVLFEGPPGTGKTEIGEALLSLWAGRKAIIlpCSENYDEYrvlGDFHPMKAYKEGF 120
                                       5699*****************999999877645555555553333334444444444 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     6e-05      0.11      21      49 ..      66      94 ..      56     166 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6e-05
                            AAA_30 21 avltGpAGtGKttalkalreaweaaggrv 49
                                      ++ +Gp+GtGKt + +al  +w+ ++  +
  gi|385805562|ref|YP_005841960.1| 66 VLFEGPPGTGKTEIGEALLSLWAGRKAII 94
                                      5789******************9776444 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00016      0.29       6     108 ..      66     165 ..      64     200 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00016
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHH.HHHHHTTT-HHHHTTS........... CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvs.rligappgyvgaeegG........... 70 
                                       +l+ gp g+Gkte+ +al +l      +k i++ +se       e  v   +   + +  g++e+            
  gi|385805562|ref|YP_005841960.1|  66 VLFEGPPGTGKTEIGEALLSLWA---GRKAIILPCSENYD----EYRVLgDFHPMKAYKEGFNEESfiprpllaali 135
                                       6899*****************98...57777777777666....55555055555555567888889*******998 PP

                                       ...EEEEETGGG-------------HHHHHHHHHHHH--EE CS
                             AAA_2  71 ...ivllDEidKihpkessgadvSregVqrdLLqileggtl 108
                                           +l+DEi + ++           + q++LL ++++ ++
  gi|385805562|ref|YP_005841960.1| 136 ldsGILIDEIRRSSE-----------EFQNLLLDVIDKRRI 165
                                       888889999876655...........***********9776 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00036      0.64      33      55 ..      63      85 ..      52     100 .. 0.82
   2 ?   -1.0   0.0      0.61   1.1e+03      73      90 ..     147     164 ..     144     210 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00036
                             AAA_7 33 kkpvllvGptGtGKtviikdllk 55
                                      + pvl+ Gp GtGKt i + ll+
  gi|385805562|ref|YP_005841960.1| 63 GLPVLFEGPPGTGKTEIGEALLS 85
                                      679************99888776 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.61
                             AAA_7  73 tsanqlqdiiesklekrr 90 
                                        s++++q+++ + ++krr
  gi|385805562|ref|YP_005841960.1| 147 RSSEEFQNLLLDVIDKRR 164
                                       578888888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); 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: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 1887.28
//
Query:       gi|385805563|ref|YP_005841961.1|  [L=80]
Description: hypothetical protein FFONT_0519 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       790  (0.0440627); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 513.57
//
Query:       gi|385805564|ref|YP_005841962.1|  [L=246]
Description: 50S ribosomal protein L2 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.2e-43  145.4   1.4    1.4e-42  144.9   1.4    1.2  1  Ribosomal_L2_C  Ribosomal Proteins L2, C-terminal domain
    4.9e-14   52.1   0.1    1.6e-13   50.4   0.0    2.0  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 !  144.9   1.4   1.6e-46   1.4e-42       2     123 ..      94     220 ..      93     227 .. 0.93

  Alignments for each domain:
  == domain 1  score: 144.9 bits;  conditional E-value: 1.6e-46
                                       SSS-EBSSSS-TTB-BBSE-SSTTS--SSS-SSSB-EEBB-B.SSEEEEEETTS-EEEEETTSBEBES-BS-TTCTT CS
                    Ribosomal_L2_C   2 vGnvlplknipeGtivhnielkpgkggklarsaGtyaqvvakegkkvtvklpSgevrkvssecrAtiGvvsngehke 78 
                                       +Gn+lpl++ipeGt+v+nie+kp +ggkl+r+ G yaq+++k  ++vtv lpSg+ ++++ ++rAtiGv ++g++ e
  gi|385805564|ref|YP_005841962.1|  94 NGNILPLQSIPEGTQVFNIEIKPMDGGKLVRTGGGYAQIISKGVNTVTVVLPSGKSKEIDGRSRATIGVAAGGGRIE 170
                                       6*****************************************99********************************* PP

                                       ----STTHHHHT.....TBS----SSSS-TTTSSS--SSSS--SSSSTEE CS
                    Ribosomal_L2_C  79 kklgkAgrkrwl.....grrpkvrGvamnpvdHphGGGeGktksrkapvs 123
                                       k+l+kAg+++w+     +++pkvrGvamn v Hp+GGG+ +++s+ + vs
  gi|385805564|ref|YP_005841962.1| 171 KPLLKAGNSYWKwkpkaRKYPKVRGVAMNVVSHPFGGGHHQSESKPTTVS 220
                                       ****************99*********************66655544444 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 !   50.4   0.0   1.8e-17   1.6e-13       1      76 [.      14      85 ..      14      86 .. 0.97
   2 ?   -2.6   0.1      0.64   5.7e+03       8      19 ..     200     211 ..     194     213 .. 0.78

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 1.8e-17
                                      TB-TT.--BSSTT--------EE-B--S---SS--EEEEEEE--TT-SS-EEEEEETTTEEEEEE--SS--SS-EE- CS
                      Ribosomal_L2  1 Grnns.gritvrhrggGhkkkyrlidfkrnkekvkgkVveieyDpgRsApiAlvkyedgekryiiapeglkvGdtvv 76
                                      Gr+++ +r++ + ++    + y++i+     e++kg +vei++DpgR  p+A vk+e+g ++y ia eg  +G++++
  gi|385805564|ref|YP_005841962.1| 14 GRGSPtFRSRKHLHEA--PAAYPAIKE---DETFKGHIVEIIHDPGRWVPLAKVKLENGVEFYTIASEGSYIGQEIE 85
                                      9***************..********9...679******************************************98 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.64
                                       BSSTT------- CS
                      Ribosomal_L2   8 itvrhrggGhkk 19 
                                       + ++  ggGh +
  gi|385805564|ref|YP_005841962.1| 200 VVSHPFGGGHHQ 211
                                       568999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); 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: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 1482.46
//
Query:       gi|385805565|ref|YP_005841963.1|  [L=86]
Description: 50S ribosomal protein L25 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-15   56.3   3.2    4.6e-15   55.7   3.2    1.3  1  Ribosomal_L23  Ribosomal protein L23
  ------ inclusion threshold ------
      0.018   15.0   0.1      0.021   14.8   0.1    1.1  1  ResIII         Type III restriction enzyme, res subunit
      0.053   13.6   0.1      0.053   13.6   0.1    1.1  1  ALG11_N        ALG11 mannosyltransferase N-terminus
      0.062   13.1   0.2      0.087   12.6   0.2    1.2  1  ubiquitin      Ubiquitin family


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 !   55.7   3.2     1e-18   4.6e-15       2      72 ..       6      75 ..       5      80 .. 0.93

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 1e-18
                                      SEEEE--SHHHHHHHTT.E.EEEEE-SS-THHHHHHHHHHHHT--EEEEEEEEE--EBESSSSSEEBE--EE CS
                     Ribosomal_L23  2 vilkPvitEkstklaek.nkyvFeVakdanKleikkaveklFgVkVekVntlnvkgkkkrvgrkvgrrksyK 72
                                      vi++P+ tE + +  ek n++vF V+++a+Kl ik+ vek FgVkVekV+t + ++ +kr   +v+ +++yK
  gi|385805565|ref|YP_005841963.1|  6 VIISPLHTELALNYIEKyNTIVFVVDRKATKLRIKEEVEKRFGVKVEKVRTEITPKGEKRA--FVKLTPEYK 75
                                      79***************99*************************************99994..677777777 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 ?   14.8   0.1   4.7e-06     0.021      43      96 ..      14      65 ..      10      82 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.7e-06
                                      HHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B-- CS
                            ResIII 43 klierllkkgkeekflflvprkslleqtleefkkflseaykeigkkvsgdkkka 96
                                      +l+ ++ +k++   ++f+v+rk+   + +ee++k +  +++++ ++++ +++k+
  gi|385805565|ref|YP_005841963.1| 14 ELALNYIEKYN--TIVFVVDRKATKLRIKEEVEKRFGVKVEKVRTEITPKGEKR 65
                                      67788888866..9*************************999888888887776 PP

>> ALG11_N  ALG11 mannosyltransferase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   1.2e-05     0.053      30      70 ..      18      58 ..       5      80 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.2e-05
                           ALG11_N 30 kekkkvkivvYtgdlevskeeilekvkerfnieldkkrikf 70
                                      +  +k +++v+  d +++k +i e+v++rf+++++k r ++
  gi|385805565|ref|YP_005841963.1| 18 NYIEKYNTIVFVVDRKATKLRIKEEVEKRFGVKVEKVRTEI 58
                                      45578899**************************9966555 PP

>> ubiquitin  Ubiquitin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   1.9e-05     0.087       7      40 ..      22      55 ..      17      56 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.9e-05
                                      TSEEEEEEEETTSBHHHHHHHHHHHHTSSGGGEE CS
                         ubiquitin  7 dgkkitleveesdtveelKekiaekegipaeqqr 40
                                      + ++i + v+++ t + +Ke +++++g+ +e+ r
  gi|385805565|ref|YP_005841963.1| 22 KYNTIVFVVDRKATKLRIKEEVEKRFGVKVEKVR 55
                                      5689999***********************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); 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: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 567.77
//
Query:       gi|385805566|ref|YP_005841964.1|  [L=272]
Description: 50S ribosomal protein L4P [Fervidicoccus fontis Kam940]
Scores for complete 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    1.2e-38  132.7   0.0    1.1  1  Ribosomal_L4   Ribosomal protein L4/L1 family
  ------ inclusion threshold ------
      0.075   13.2   0.3       0.13   12.4   0.3    1.3  1  Kinesin_assoc  Kinesin-associated


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 !  132.7   0.0   1.4e-42   1.2e-38       2     192 .]      27     263 ..      26     263 .. 0.93

  Alignments for each domain:
  == domain 1  score: 132.7 bits;  conditional E-value: 1.4e-42
                                       EE-HHHHSS---HHHHHHHHHHHHHSS-EE-----.-TTTSS---S-SS-SSSSSS---S-TT.......STTSTT- CS
                      Ribosomal_L4   2 eLspkvFaapirrdlihravvaylanrrqgtastk.arsevsgsgrklwkQKGtGrARvgsir.......spiargG 70 
                                       eL p vF +pir+dli+ra+ a+ ++  q++++++ a++++ +  ++l+   G+G ARv+++        +p+++gG
  gi|385805566|ref|YP_005841964.1|  27 EL-PLVFYIPIRKDLIRRAFHAEFTAGLQPKGRDPmAGKRTPA--ESLGV--GRGLARVPRVPgtsegafAPMTVGG 98 
                                       67.88**************************************..6****..************************* PP

                                       --SS---S.EEHHHHHHHHHHHHHHHHHHHHHHHTT-EEEES.--.-..-S..........S--HHHHHHHHHHTT- CS
                      Ribosomal_L4  71 gvahgpkperdystklnkKvrrlAlrsaLsakakqglllvvd.nl.e.ple..........esktkelvellkklgl 134
                                       +vah++k+e+++ +++nkK+r lA +sa++a+ + + ++ ++ ++ +  l+          + k +e++ellkklg+
  gi|385805566|ref|YP_005841964.1|  99 RVAHPIKTEEKIVEEINKKERLLATASAVAATSSIEFVKKRGhKFtStALPivldssiekeITKLSEAKELLKKLGV 175
                                       ******************************************855222333778888777788999********999 PP

                                       ..........................TTSSEEEEESSSSCHHHHHHTT-TTEEEEESTT--CHHHHHSSE....EEE CS
                      Ribosomal_L4 135 ..........................ksksvLivvsekdenlvlaarnlpgvevieveslnvydllkadk....vvi 181
                                                                 ++ks+L+v+s+ ++ +++a+rnlpgv+v+++++l++++l+++      +++
  gi|385805566|ref|YP_005841964.1| 176 wedversysririrsgkgkmrgrryiEPKSLLFVLSSINTPFAKAVRNLPGVDVVSADNLSILHLAPGGVpgrlTIY 252
                                       99999999999999999999999999*************************************************** PP

                                       EHHHHHHHHHH CS
                      Ribosomal_L4 182 tksavekleek 192
                                       tk+ + kl+e+
  gi|385805566|ref|YP_005841964.1| 253 TKDSLLKLQER 263
                                       *******9985 PP

>> Kinesin_assoc  Kinesin-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3   1.4e-05      0.13      40     130 ..     102     189 ..      88     195 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.4e-05
                     Kinesin_assoc  40 eplkeglvllaseraknlsavtaavaglspssslsalssraesvssleerivfspaseeaierlketekiiaelnet 116
                                       +p+k+ ++++++ ++k+     a+ +++++ ss    ++r+++++s +  iv  ++ e+ i +l e+  ++  l   
  gi|385805566|ref|YP_005841964.1| 102 HPIKTEEKIVEEINKKERL--LATASAVAATSSIEFVKKRGHKFTSTALPIVLDSSIEKEITKLSEAKELLKKLG-V 175
                                       5566665555555444433..3444455566778888899********************************996.8 PP

                     Kinesin_assoc 117 Weeklrkteairle 130
                                       We+  r    ir+ 
  gi|385805566|ref|YP_005841964.1| 176 WEDVERSYSRIRIR 189
                                       *9999988888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 1737.55
//
Query:       gi|385805567|ref|YP_005841965.1|  [L=347]
Description: 50S ribosomal protein L3P [Fervidicoccus fontis Kam940]
Scores for complete 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-69  234.8   0.0    1.8e-69  234.5   0.0    1.0  1  Ribosomal_L3  Ribosomal protein L3


Domain annotation for each model (and alignments):
>> Ribosomal_L3  Ribosomal protein L3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  234.5   0.0     1e-73   1.8e-69       1     347 [.       1     327 [.       1     338 [. 0.90

  Alignments for each domain:
  == domain 1  score: 234.5 bits;  conditional E-value: 1e-73
                                       XX.S.SXXXXSSXCCCTTXSBXSXSSXXXSX.XXSBTTTTTXBSEEEEEEEEEEEEEEECHHTTSCCCCCEEEEEEE CS
                      Ribosomal_L3   1 mshrkfeaprhgslGflprkRaerergkvksfPkddtskpvkltaflGyKaGmthiVrevdkpgskldkkevveavt 77 
                                       m hrk +apr+g lG++pr+R e  +++v+++P  +++ +++  +f+GyK Gmth   ++d+ +s + +k++  +vt
  gi|385805567|ref|YP_005841965.1|   1 MGHRKKSAPRRGTLGVRPRQRFEGIVPRVRTWPVLEEK-KIFPLGFIGYKVGMTHALVVDDRKTSITFGKQIFTPVT 76 
                                       89*******************************98776.78888********************************* PP

                                       EEEC--EEEEEEEEE.EEETTEEEEEEEEESSS.SHHHHCCCSTSTTTSSSSSSHCCCCHCSSCCCCCCHHHHHHHH CS
                      Ribosomal_L3  78 vvetppmvivgvvgy.vetprGlrslktvwaehlseevkrrlyknwykskkkaftkyskkyeskdvkklieadleei 153
                                       ++etppm ++g++gy  +++ G+++l++ wa    + +k +      k    +f+    +  ++++ + +e++l+e+
  gi|385805567|ref|YP_005841965.1|  77 LLETPPMILAGIRGYsFDINEGKQPLTEAWAT--GDTLKNTNIERLIK----SFS----PNSTQQKLEELEKSLSEM 143
                                       ***************559*************9..77776665444443....344....444566888899999999 PP

                                       HHSCSCEEEEEEEECCCSS-SCCSSHHEEEEECHCSCHHHHHHHHHHCCTCEEECCCCS-TTSEEEEEEEE---EEE CS
                      Ribosomal_L3 154 kkeasvvrviahtvirktkslaqKkahllEiqvngGtiaekldfarealektvavaavFrqgeliDvigvtkGkGfe 230
                                       ++     r + +++     ++ +Kk++l+E+ + g  +  ++ +a e+l kt++++++F++g+++D+i+vtkGkGf+
  gi|385805567|ref|YP_005841965.1| 144 AE----LRALLLSQPTLAGGISKKKPELIEVGLSGKDLKAQFSYAVEKLGKTIKISEIFNPGKFVDIIAVTKGKGFQ 216
                                       98....9********************************************************************** PP

                                       -HHHHCT----STTTSSS..SSS-S-SS-SSSSS--TTS--SEEESCCEEEEEEEEEEEEETTTSSTTTSSTTT.SS CS
                      Ribosomal_L3 231 GvvkRWgvkklprkthrg..lRkvaaigawdparVsstvaraGqkGyhhRtelnkkiyrigkgedaknastefdlte 305
                                       G+vkR+g+k lpr +++    Rk++a g++  a   st ++aGq+G+h+R+++nk+i  i + +++k+         
  gi|385805567|ref|YP_005841965.1| 217 GPVKRFGIKVLPRWHKHRkaARKIGARGPGMGA--LSTAPQAGQMGFHQRVDYNKRILYIAD-TEGKDK-----ELL 285
                                       ************965332259999999998766..6899**********************9.444433.....234 PP

                                       ..SS.TTTCTTCB..TSCEEEEES--SSSTTEEEEEEE-SSG CS
                      Ribosomal_L3 306 keitPmGGfvhyGevkndfilvkGsvpGpkkrlvklrksllt 347
                                        +i+P  G+ +yG ++ df+++ Gs+pG +kr v lr+ +++
  gi|385805567|ref|YP_005841965.1| 286 AKINPSSGWHKYGLIRTDFVILAGSIPGSRKRPVILRQPVRP 327
                                       68***********************************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 2131.18
//
Query:       gi|385805568|ref|YP_005841966.1|  [L=278]
Description: hypothetical protein FFONT_0524 [Fervidicoccus fontis Kam940]
Scores for complete 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-59  200.3   0.0    4.9e-59  200.2   0.0    1.0  1  Methyltrn_RNA_3  Putative RNA methyltransferase
  ------ inclusion threshold ------
      0.045   13.6   0.0       0.24   11.3   0.0    2.2  2  TrkA_C           TrkA-C domain
      0.049   13.0   0.0      0.083   12.2   0.0    1.4  1  SPOUT_MTase_2    AF2226-like SPOUT RNA Methylase fused to THU


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 !  200.2   0.0   8.2e-63   4.9e-59       2     286 .]       4     273 ..       3     273 .. 0.93

  Alignments for each domain:
  == domain 1  score: 200.2 bits;  conditional E-value: 8.2e-63
                   Methyltrn_RNA_3   2 vsiaiPssiisnaqsleqktylagqIARaaaiFnVdeivvfddseseeekkekpseflarlLqYletPpYLrkelFp 78 
                                       + i++P   ++n  ++  +t +a+ IARaa+iF+V++i ++++++++++ k +++e+l  lL+Y++tPpYL+k++F+
  gi|385805568|ref|YP_005841966.1|   4 IEILLPYCSLENEPDQIRITLKANIIARAASIFKVERITLYRSRSDKKSCK-DQKEILGLLLRYFVTPPYLKKKIFG 79 
                                       6799*****************************************999887.799********************** PP

                   Methyltrn_RNA_3  79 lhkelkyaglLppldaphhl.rsse.egeyreGvvvekskekkskkklVniGlkkevklel.kqevpegtRVtVkls 152
                                       ++kelky+g+  pl++p h  ++++ eg++r G+v +++++      + +iG+ k+vk+++ + e+++g  + Vk++
  gi|385805568|ref|YP_005841966.1|  80 KRKELKYVGMAYPLQIPTHSlSKKAkEGDIRVGLVERVKES-AI---FADIGVGKQVKISNsNYELKRGDLIFVKVK 152
                                       *******************9855556*********999875.44...9****************************6 PP

                   Methyltrn_RNA_3 153 seesveakvVspsepreeaglywGYsVrlakslsavftespfeggydlsigtsergekveeklaelekkk.efkhll 228
                                       + +  e +++++       ++y+GYsVr +++  ++++e+   ++  l+igts+ g+++ e+l+e+e+k  + ++++
  gi|385805568|ref|YP_005841966.1| 153 KGDLSELEIIKN------PDIYVGYSVRECENPLDYLKEK---KKDGLVIGTSKFGDPIWENLKEVEEKLkSSDKVV 220
                                       655555555555......5669*****************8...5889*********************9988***** PP

                   Methyltrn_RNA_3 229 ivfGg.vrgleaaleadeelklegekaeelFdlwlntvpnqgsrtirtEEavliaLalL 286
                                       +vfG+ +rg+ +++++       g ++++lF+++ n+v +qg++tir+EEa++iaL+lL
  gi|385805568|ref|YP_005841966.1| 221 VVFGEpYRGIFEIFKQL------GGNTDDLFHGIYNLVRDQGTKTIRMEEALFIALSLL 273
                                       **************666......99*******************************987 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   3.9e-05      0.24      28      65 ..     122     159 ..     107     164 .. 0.80
   2 ?   -0.8   0.0      0.24   1.4e+03      44      56 ..     210     222 ..     161     224 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.9e-05
                                       EEEEEE-T-EEES--TT-B--TT-EEEEEEEHHHHHHH CS
                            TrkA_C  28 lvvairRggeliipsgdtvLeeGDvllvvgspsdlael 65 
                                       + + i  g+++ i +++++L+ GD+++v +++ dl+el
  gi|385805568|ref|YP_005841966.1| 122 IFADIGVGKQVKISNSNYELKRGDLIFVKVKKGDLSEL 159
                                       5555544567888999******************9987 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.24
                                       T-B--TT-EEEEE CS
                            TrkA_C  44 dtvLeeGDvllvv 56 
                                       + +L++ D+++vv
  gi|385805568|ref|YP_005841966.1| 210 EEKLKSSDKVVVV 222
                                       5667777777775 PP

>> SPOUT_MTase_2  AF2226-like SPOUT RNA Methylase fused to THUMP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.4e-05     0.083      87     130 ..     182     225 ..     148     235 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.4e-05
                     SPOUT_MTase_2  87 lvrkrrkkellivtdPeGeeisevkeelaealrkakevvvlvGs 130
                                       ++++++k  l+i t   G++i e  +e++e+l+++++vvv++G 
  gi|385805568|ref|YP_005841966.1| 182 YLKEKKKDGLVIGTSKFGDPIWENLKEVEEKLKSSDKVVVVFGE 225
                                       55677777899******************************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.48
# Mc/sec: 1735.15
//
Query:       gi|385805569|ref|YP_005841967.1|  [L=43]
Description: hypothetical protein FFONT_0525 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       854  (0.0476323); expected 358.6 (0.02)
Passed bias filter:                      181  (0.0100954); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.30u 0.23s 00:00:00.53 Elapsed: 00:00:00.38
# Mc/sec: 337.26
//
Query:       gi|385805570|ref|YP_005841968.1|  [L=229]
Description: putative Acetyltransferase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.5e-26   89.9  32.8      2e-07   30.5   6.3    5.5  6  Hexapep    Bacterial transferase hexapeptide (six repeats)
    1.7e-22   78.9  23.3      2e-08   33.8   6.1    6.2  6  Hexapep_2  Hexapeptide repeat of succinyl-transferase
  ------ inclusion threshold ------
      0.024   14.8   2.2      0.064   13.4   2.2    1.7  1  DUF2613    Protein of unknown function (DUF2613)
      0.089   12.9   1.6       0.76    9.9   0.5    2.7  2  SH3_12     Xrn1 SH3-like domain


Domain annotation for each model (and alignments):
>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.3   1.4e-05     0.063       2      35 ..       6      39 ..       5      40 .. 0.94
   2 !   26.8   0.8   6.3e-10   2.8e-06       1      29 [.      61      89 ..      61      91 .. 0.92
   3 !   27.2   0.7   4.7e-10   2.1e-06       1      34 [.      97     130 ..      97     132 .. 0.95
   4 !    9.7   0.1   0.00015      0.68       2      18 ..     134     150 ..     133     151 .. 0.77
   5 !   30.5   6.3   4.4e-11     2e-07       2      36 .]     162     196 ..     161     196 .. 0.95
   6 ?   -2.5   0.0       1.1     5e+03      29      35 ..     199     205 ..     198     206 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.4e-05
                                      EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep  2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35
                                      +vI ++++++ +a i+g  +IG+++ I  g+v+g
  gi|385805570|ref|YP_005841968.1|  6 SVISKDAIVREGALILGSSIIGSRAFIDTGTVVG 39
                                      68999*************************9997 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 6.3e-10
                                      TEEEETTEEE-TTEEEETTEEE-TTEEEE CS
                           Hexapep  1 stvIGsnvlIgpfaviggnVkIGdnvkIg 29
                                      +++IG+n++I+++++i++ VkIG+nv  g
  gi|385805570|ref|YP_005841968.1| 61 GATIGDNSVIRSNSIIYERVKIGKNVETG 89
                                      589***********************876 PP

  == domain 3  score: 27.2 bits;  conditional E-value: 4.7e-10
                                       TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
                           Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvi 34 
                                       +t IG+n++Ig  +vi g VkIG+ ++I+ gv+i
  gi|385805570|ref|YP_005841968.1|  97 DTEIGDNSIIGTDTVIDGRVKIGEFARIETGVYI 130
                                       589*****************************99 PP

  == domain 4  score: 9.7 bits;  conditional E-value: 0.00015
                                       EEEETTEEE-TTEEEET CS
                           Hexapep   2 tvIGsnvlIgpfavigg 18 
                                       t+IG+nv++gp +v+ +
  gi|385805570|ref|YP_005841968.1| 134 TIIGKNVFLGPRVVFTN 150
                                       68888888888888766 PP

  == domain 5  score: 30.5 bits;  conditional E-value: 4.4e-11
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36 
                                       +++++nv Ig++a+i ++V IG++++I++g+v+++
  gi|385805570|ref|YP_005841968.1| 162 AIVEDNVAIGANATIIAGVRIGKGAVIASGAVVTK 196
                                       789******************************86 PP

  == domain 6  score: -2.5 bits;  conditional E-value: 1.1
                                       ETTEEEE CS
                           Hexapep  29 gagvvig 35 
                                       ++++v++
  gi|385805570|ref|YP_005841968.1| 199 EPNTVVA 205
                                       6666665 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1     0.017        76       9      21 ..      25      39 ..      23      40 .. 0.79
   2 !   13.0   0.1   1.4e-05     0.065      17      33 ..      61      77 ..      52      78 .. 0.84
   3 ?    1.0   0.0     0.079   3.6e+02       2       8 ..      80      86 ..      79      89 .. 0.82
   4 !   23.6   0.1   7.1e-09   3.2e-05       3      32 ..      99     130 ..      97     132 .. 0.95
   5 !   12.4   0.0   2.2e-05     0.098       2      15 ..     134     147 ..     133     150 .. 0.89
   6 !   33.8   6.1   4.4e-12     2e-08       3      34 .]     163     196 ..     161     196 .. 0.94

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.017
                                      EE-TT-EE..SEEE- CS
                         Hexapep_2  9 liGanagi..GvslG 21
                                      +iG++a i  G+ +G
  gi|385805570|ref|YP_005841968.1| 25 IIGSRAFIdtGTVVG 39
                                      789999987788887 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 1.4e-05
                                      SEEE-TT-EE-TT-EE- CS
                         Hexapep_2 17 GvslGdncvvgaGvvit 33
                                      G ++Gdn+v+ ++++i+
  gi|385805570|ref|YP_005841968.1| 61 GATIGDNSVIRSNSIIY 77
                                      999*************8 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.079
                                      EEE-TT- CS
                         Hexapep_2  2 viIGdnC 8 
                                      v+IG+n+
  gi|385805570|ref|YP_005841968.1| 80 VKIGKNV 86
                                      8899986 PP

  == domain 4  score: 23.6 bits;  conditional E-value: 7.1e-09
                                       EE-TT-EE-TT-EE.S.EEE-TT-EE-TT-EE CS
                         Hexapep_2   3 iIGdnCliGanagi.G.vslGdncvvgaGvvi 32 
                                        IGdn++iG + +i G v++G+ + ++ Gv+i
  gi|385805570|ref|YP_005841968.1|  99 EIGDNSIIGTDTVIdGrVKIGEFARIETGVYI 130
                                       6*************88***************9 PP

  == domain 5  score: 12.4 bits;  conditional E-value: 2.2e-05
                                       EEE-TT-EE-TT-E CS
                         Hexapep_2   2 viIGdnCliGanag 15 
                                       +iIG+n+++G++ +
  gi|385805570|ref|YP_005841968.1| 134 TIIGKNVFLGPRVV 147
                                       89*********975 PP

  == domain 6  score: 33.8 bits;  conditional E-value: 4.4e-12
                                       EE-TT-EE-TT-EE..SEEE-TT-EE-TT-EE-S CS
                         Hexapep_2   3 iIGdnCliGanagi..GvslGdncvvgaGvvita 34 
                                       i++dn+ iGana+i  Gv +G+++v+++G v+t+
  gi|385805570|ref|YP_005841968.1| 163 IVEDNVAIGANATIiaGVRIGKGAVIASGAVVTK 196
                                       89***********77******************7 PP

>> DUF2613  Protein of unknown function (DUF2613)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   2.2   1.4e-05     0.064       4      43 ..     170     209 ..     168     218 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.4e-05
                           DUF2613   4 gPaaaSaVaGivlGvvavfgvtavvqqdsrPstdravnad 43 
                                       ++a a ++aG+ +G +av+  +avv++d  P+t  a+ ++
  gi|385805570|ref|YP_005841968.1| 170 IGANATIIAGVRIGKGAVIASGAVVTKDVEPNTVVAGVPA 209
                                       677799**************************98554444 PP

>> SH3_12  Xrn1 SH3-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.12   5.2e+02      24      30 ..      34      49 ..      31      77 .. 0.76
   2 ?    9.9   0.5   0.00017      0.76       2      30 ..     139     169 ..     138     204 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.12
                            SH3_12 24 rGtVVg.........r 30
                                      +GtVVg          
  gi|385805570|ref|YP_005841968.1| 34 TGTVVGypirsrikmL 49
                                      79***98886544440 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00017
                            SH3_12   2 qfrLgdrVvyvrdngksVPlGlrGtVVg...r 30 
                                       +++Lg rVv+ +d+   V+  l G +V    +
  gi|385805570|ref|YP_005841968.1| 139 NVFLGPRVVFTNDKY-PVSKRLLGAIVEdnvA 169
                                       789**********55.6*9999****994440 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.25s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1416.61
//
Query:       gi|385805571|ref|YP_005841969.1|  [L=951]
Description: DEAD/DEAH box helicase [Fervidicoccus fontis Kam940]
Scores for complete 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-35  120.4   0.0    2.8e-34  118.4   0.0    2.1  2  DEAD             DEAD/DEAH box helicase
    5.3e-20   72.0   0.0    6.4e-19   68.5   0.0    2.6  2  DEAD_assoc       DEAD/H associated
    2.1e-18   66.7   0.5    3.5e-17   62.7   0.1    3.1  3  Helicase_C       Helicase conserved C-terminal domain
      9e-09   35.6   0.1    2.8e-07   30.7   0.0    3.1  4  ResIII           Type III restriction enzyme, res subunit
     0.0097   16.2   1.7       0.35   11.1   1.7    2.8  1  AAA_22           AAA domain
  ------ inclusion threshold ------
      0.037   14.4   0.0       0.16   12.3   0.0    2.1  2  AAA_19           AAA domain
      0.065   13.4   0.3      0.065   13.4   0.3    1.9  2  Zn-ribbon_8      Zinc ribbon domain
      0.077   12.7   0.9       0.19   11.4   0.9    1.7  1  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
      0.085   12.9   0.1       0.38   10.8   0.0    2.2  2  HypA             Hydrogenase/urease nickel incorporation, met
       0.11   12.5   0.9        1.7    8.7   0.2    2.4  2  Elf1             Transcription elongation factor Elf1 like
       0.15   12.4   3.1        1.1    9.7   0.2    2.6  2  Lar_restr_allev  Restriction alleviation protein Lar
       0.17   11.7   1.8       0.18   11.6   0.4    1.8  2  DUF4923          Lipocalin-like domain (DUF4923)


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 !  118.4   0.0   1.9e-37   2.8e-34       1     171 [.      44     214 ..      44     219 .. 0.92
   2 ?   -3.1   0.0       3.9   5.9e+03      37      82 ..     261     306 ..     257     329 .. 0.60

  Alignments for each domain:
  == domain 1  score: 118.4 bits;  conditional E-value: 1.9e-37
                                       -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHS.TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyet.kgktgpkalivePtreLaeqtlnnlkkfkkyidl 76 
                                       t+iQ +aip il+g+d+++ a+TGsGKT+a+++p+++ ++++   + +p +++v+P+r+L ++++ +l+ + ++i+l
  gi|385805571|ref|YP_005841969.1|  44 TSIQNKAIPKILQGRDLIITAPTGSGKTEAAVFPIFSLMLKDeSWNGKPLMVYVTPLRALNRDIFVRLEDISNKIGL 120
                                       78***********************************9999866788999*************************** PP

                                       EEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHH...HCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  77 rvlliiggvaardqlskldngvdivvgtpgrlddll...stgklnlsqvrflVlDEadrlldqgfsdfinrilnqlp 150
                                       +  +  g++++r+  + l+++++ +++tp+ l  l+    t+   l +++f+V+DE+++l d++++++++ +l++l+
  gi|385805571|ref|YP_005841969.1| 121 KSIVRHGDSSKRERGDFLRSSYHWFITTPESLSMLIthsATRD-MLTDIKFVVIDEVHELIDSERGNTLEVVLKRLK 196
                                       ***9999***********999************9996632333.4*******************************9 PP

                                       HHCTTSTTTSEEEEEESSBS.H CS
                                       xxxxxxxxxxxxxxxxxxxx.x RF
                              DEAD 151 qitcdgklqrqvivlSATlp.k 171
                                       +i ++     q+i +SAT+p  
  gi|385805571|ref|YP_005841969.1| 197 RIVKKY----QFIGISATIPdA 214
                                       987764....4********943 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.9
                                       HHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTT.STSEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                              DEAD  37 qivyetkgktgpkalivePtreLaeqtlnnlkkfkky.idlrvllii 82 
                                       +i+ e + ++++  +i + tr +ae    +l++++   i++   ++ 
  gi|385805571|ref|YP_005841969.1| 261 KIINE-EIERAKSSIIFTNTRDMAEFLTYKLRELGRDdIEIHHGSLA 306
                                       45544.66667778888999999998888888888854544333333 PP

>> DEAD_assoc  DEAD/H associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.55   8.3e+02      33      64 ..     150     181 ..     147     206 .. 0.78
   2 !   68.5   0.0   4.3e-22   6.4e-19      21     190 ..     627     786 ..     612     787 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.55
                        DEAD_assoc  33 ealalllaarlsrrfgidvqvaanDdgivlll 64 
                                       e l++l+++  +r + +d+++++ D+  +l+ 
  gi|385805571|ref|YP_005841969.1| 150 ESLSMLITHSATRDMLTDIKFVVIDEVHELID 181
                                       6799*******************999999833 PP

  == domain 2  score: 68.5 bits;  conditional E-value: 4.3e-22
                        DEAD_assoc  21 lvvhspfGrrvnealalllaarlsrrfgidvqvaanDdgivlll....pleerlpllldellellspdeleedleaa 93 
                                       lv+  p+G++ ne+l+ll++  + +++g +v+++ ++++i +++    +l++ +++l    l+l ++de+ee+++++
  gi|385805571|ref|YP_005841969.1| 627 LVLTYPLGSNGNETLSLLISNYIFSKTGRSVSTSSDPYRIYMEStfplTLNDLIEAL--YSLSLKEKDEIEEMIKSQ 701
                                       78889*************************************775544333333322..35788899********** PP

                        DEAD_assoc  94 lnaselfkrrFrevAaralllprrypgkrkplwqqrlraaqLldvareypdfpllleavrevledqlDlerlaellr 170
                                       l++s++f  ++  vA+++++++++               ++  +v++ y+d+++ +ea+rev+ ++lD+ ++ e+l+
  gi|385805571|ref|YP_005841969.1| 702 LKKSNIFMYKLSTVAKKMGAISKNATL------------SEVKKVLKYYKDTLIGEEAFREVFYEKLDIRSVIEMLK 766
                                       ***********************9876............67778888888*************************** PP

                        DEAD_assoc 171 riaageirvvevetprpSpf 190
                                       +i++g++r+v+   +  Sp+
  gi|385805571|ref|YP_005841969.1| 767 DIKSGKVRIVAQPIEGLSPL 786
                                       ***********889999997 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.91   1.4e+03      33      60 ..     112     139 ..      79     152 .. 0.74
   2 !   62.7   0.1   2.3e-20   3.5e-17       5     108 ..     258     363 ..     254     365 .. 0.87
   3 ?   -2.5   0.0       4.2   6.3e+03      12      28 ..     444     460 ..     419     491 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.91
                                       HHHHHHTTSTEEEESTTSTHHHHHHHHH CS
                        Helicase_C  33 klllekkgikvavlhgelpqnereeile 60 
                                       + + +k g+k++v hg+ +++er + l+
  gi|385805571|ref|YP_005841969.1| 112 EDISNKIGLKSIVRHGDSSKRERGDFLR 139
                                       34445669**************987665 PP

  == domain 2  score: 62.7 bits;  conditional E-value: 2.3e-20
                                       HHHHHH.HHTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSS CS
                        Helicase_C   5 allell.kleeeggkilifvntidrlek.vklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerG 79 
                                        +l+++ ++ e+ + ++if+nt+d++e  +  l+e     + ++hg+l ++ r+ + ++ + ge++ +iat+ +e G
  gi|385805571|ref|YP_005841969.1| 258 EILKIInEEIERAKSSIIFTNTRDMAEFlTYKLRELGRDDIEIHHGSLATEVRKSVEKKLKGGEIKGIIATSSLELG 334
                                       5666666677999999**********66444444444789999********************************** PP

                                       STSTTESEEEESSSSSSHHHHHHHHTTSS CS
                        Helicase_C  80 idipkvnlVinfdlprnvtsyiqriGRtg 108
                                       idi +v+lVi+++ pr+  ++ qr+GR g
  gi|385805571|ref|YP_005841969.1| 335 IDIGSVDLVIQYGSPRQAIRMLQRVGRSG 363
                                       ***************************87 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 4.2
                                       HTTTTSEEEEEESSHHH CS
                        Helicase_C  12 leeeggkilifvntidr 28 
                                       +eee +k++ f++ i+ 
  gi|385805571|ref|YP_005841969.1| 444 TEEELKKAIEFCEGIKL 460
                                       45666777777777773 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.0   1.9e-10   2.8e-07       6     170 ..      45     212 ..      40     213 .. 0.74
   2 ?   -3.9   0.0       8.3   1.2e+04      96     116 ..     258     284 ..     231     298 .. 0.65
   3 ?    0.3   0.0      0.41   6.1e+02      65      96 ..     577     608 ..     570     632 .. 0.74
   4 ?   -1.8   0.0       1.9   2.8e+03      12      42 ..     865     907 ..     857     916 .. 0.44

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 1.9e-10
                                       HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S..........-EEEEESSHHHHHHHHHHGGGG CS
                            ResIII   6 eyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkee.....kflflvprkslleqtleefkkf 77 
                                       + Q +ai ++l+       + ++i ++TG+GKT  a+  i +l+ k + +      ++ + p ++l      +++++
  gi|385805571|ref|YP_005841969.1|  45 SIQNKAIPKILQ------GRDLIITAPTGSGKTEAAVFPIFSLMLKDE-SwngkpLMVYVTPLRALNRDIFVRLEDI 114
                                       667777777774......4569**************888888887644.3467667888999999999999888888 PP

                                       TGG........GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T.. CS
                            ResIII  78 lseayke....igkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk.. 148
                                       +++   +    +g + + ++ ++    +++ + ++tt +sl+  +   +   ++   + +++++iDE+H l +++  
  gi|385805571|ref|YP_005841969.1| 115 SNKIGLKsivrHGDSSKRERGDF---LRSSYHWFITTPESLSMLI---THSATRDMLTDIKFVVIDEVHELIDSErg 185
                                       87765544444333333333333...4679999************...8899999999999************8455 PP

                                       .....TTHHHHHT---SEEEEEESS-S CS
                            ResIII 149 .....swreilekfkeavllglTATpe 170
                                              +++++ +k++  +g++AT++
  gi|385805571|ref|YP_005841969.1| 186 ntlevVLKRLKRIVKKYQFIGISATIP 212
                                       5455544555566677889******86 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 8.3
                                       -.............-SEEEEEHHHHHH CS
                            ResIII  96 a......kekdstnkkilvttiqslda 116
                                       +      +e+++ +++i++t++  + +
  gi|385805571|ref|YP_005841969.1| 258 EilkiinEEIERAKSSIIFTNTRDMAE 284
                                       033333455566688888888776655 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.41
                                       HHHHHHHHHGGGGTGG....GEEEESSS-B-- CS
                            ResIII  65 slleqtleefkkflseaykeigkkvsgdkkka 96 
                                       +++e+ ++++++++ eay++++k+ ++ +k+ 
  gi|385805571|ref|YP_005841969.1| 577 EVYEKIKSQYQSITIEAYDFVKKVCEDTRKQG 608
                                       79***************997655555544443 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 1.9
                                       HHHHT....................TTSEEEEEESTTSTHHHHHH CS
                            ResIII  12 ienlleklks..............krdkrglikmaTGtGKTlvaa 42 
                                       ++++++ +k+              +  kr+ ++++   GKT v+a
  gi|385805571|ref|YP_005841969.1| 865 VNAIRKYFKEgkkslkgkekeyfeDAVKRAKLVIT--HGKTAVMA 907
                                       44444444333334433333332222222222222..35565555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   1.7   0.00024      0.35       8     120 ..      60     201 ..      56     210 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00024
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee...erpevvfvtlpsstsskdl..lrellralglelka......... 70 
                                       l++t+++G+GKT  +     +l       e    +p  v+vt+    +++ +  l+++ +++gl   +         
  gi|385805571|ref|YP_005841969.1|  60 LIITAPTGSGKTEAAVFPIFSLMLKD---EswnGKPLMVYVTPLRALNRDIFvrLEDISNKIGL---Ksivrhgdss 130
                                       67888888888887765333332111...12222333334443333333333223333333332...1233555555 PP

                            AAA_22  71 .................erlsseellealeqalrarav...ielliiDEaqhlr.s......eealeeLrsllnlsr 120
                                                         + s    l++l  ++ +r++   i++++iDE++ l+ s      e +l+ L+++++  +
  gi|385805571|ref|YP_005841969.1| 131 krergdflrssyhwfitTPES----LSMLITHSATRDMltdIKFVVIDEVHELIdSergntlEVVLKRLKRIVK--K 201
                                       555555677777654333333....333334444444447778*********9883456778888888888887..4 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00011      0.16       1     115 [.      47     180 ..      47     200 .. 0.63
   2 ?   -2.8   0.0       4.7     7e+03      42      75 ..     270     303 ..     257     435 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                            AAA_19   1 qreave.alkekvllvtaGpGtGKTrvlk.hivallvelggvkpeeill.vaftgrAakelrerlaalgae...... 68 
                                       q++a+   l+ + l++ta+ G+GKT+  +  i +l+++ ++++ +++++ v++ +   + +  rl+ +  +      
  gi|385805571|ref|YP_005841969.1|  47 QNKAIPkILQGRDLIITAPTGSGKTEAAVfPIFSLMLKDESWNGKPLMVyVTPLRALNRDIFVRLEDISNKiglksi 123
                                       789995599****************9766156777888888887766551444444444566666665555665566 PP

                            AAA_19  69 ...............atTiHrlalldfddlltealelleeaeeekklqeeellivDEfqdvd 115
                                                       + +H +  +++ + l     l+ ++++++ l++ + +++DE+ ++ 
  gi|385805571|ref|YP_005841969.1| 124 vrhgdsskrergdflRSSYHWF--ITTPESL---SMLITHSATRDMLTDIKFVVIDEVHELI 180
                                       6666666666666665555544..4333333...2223355666677666799999988764 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.7
                            AAA_19  42 peeillvaftgrAakelrerlaalgaeatTiHrl 75 
                                       +++ ++ + t+  a+ l+ +l++lg++   iH+ 
  gi|385805571|ref|YP_005841969.1| 270 AKSSIIFTNTRDMAEFLTYKLRELGRDDIEIHHG 303
                                       4666777777777777777777777664444432 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       7.1   1.1e+04       6      12 ..     221     227 ..     221     234 .. 0.66
   2 ?   13.4   0.3   4.3e-05     0.065       7      35 ..     825     853 ..     824     855 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 7.1
                       Zn-ribbon_8   6 YrCeeCg 12 
                                       Y C  C 
  gi|385805571|ref|YP_005841969.1| 221 YSCPFCE 227
                                       5566664 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 4.3e-05
                       Zn-ribbon_8   7 rCeeCghefevlqsisdaplta.CPeCgs.e 35 
                                       +C +Cg   e+ +++s+ p++  C +Cg+ +
  gi|385805571|ref|YP_005841969.1| 825 KCMNCG--WEKSVKVSELPDIIsCEKCGArA 853
                                       8*****..9999999****9999*****944 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.9   0.00013      0.19       2      27 ..     825     853 ..     824     854 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00013
                                       B-SSS--B----SS...S----SSS---- CS
                    DNA_RNApol_7kD   2 iCgeCgaevslkkg...dpiRCkeCGhRi 27 
                                       +C++Cg e s+k +   d+i C +CG R 
  gi|385805571|ref|YP_005841969.1| 825 KCMNCGWEKSVKVSelpDIISCEKCGARA 853
                                       6*****9999887633479********96 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       6.5   9.7e+03      87     106 ..     221     240 ..     213     242 .. 0.69
   2 ?   10.8   0.0   0.00025      0.38      46      97 ..     799     854 ..     785     865 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 6.5
                                       HS-TTTSSS-EEEEESSSEE CS
                              HypA  87 lrCpkCgsadveivsGeell 106
                                       ++Cp C+  + ++++  e++
  gi|385805571|ref|YP_005841969.1| 221 YSCPFCEVIEDDVKKDIEIK 240
                                       58999998777777666665 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00025
                                       HHHHHHHCC.TTTT-EEEEEEE--EEEETTTS-EEECHHHHH....S-TTTSSS-E CS
                              HypA  46 fafellaegtvlegaeLeieevpvkvrCreCgkefeleekal....rCpkCgsadv 97 
                                       +a+e+l ++ +++  e +i e+ v ++C +Cg e +++ ++l    +C+kCg++ v
  gi|385805571|ref|YP_005841969.1| 799 YALETLPQELLIKVLEKRILEKTVLLKCMNCGWEKSVKVSELpdiiSCEKCGARAV 854
                                       5666666666666666678899999*******87776653224455******9877 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.21   3.2e+02      18      29 ..     217     228 ..     209     242 .. 0.78
   2 ?    8.7   0.2    0.0012       1.7      22      61 ..     824     859 ..     811     871 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.21
                              Elf1  18 lptkFdCpfCnh 29 
                                       +++ ++CpfC+ 
  gi|385805571|ref|YP_005841969.1| 217 IKKFYSCPFCEV 228
                                       67889*****85 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0012
                              Elf1  22 FdCpfCnheksvevkldkkekiaevsCkvCgesfetkvna 61 
                                        +C++C+ eksv+v+        ++sC++Cg+++    ++
  gi|385805571|ref|YP_005841969.1| 824 LKCMNCGWEKSVKVSE----LPDIISCEKCGARAVAPLPP 859
                                       69********999864....4559*******988776655 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.2      0.14   2.1e+02       2      10 ..     219     227 ..     218     232 .. 0.85
   2 ?    9.7   0.2   0.00071       1.1       2      37 ..     822     856 ..     821     877 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.14
                   Lar_restr_allev   2 eLkpCPfCg 10 
                                       + + CPfC 
  gi|385805571|ref|YP_005841969.1| 219 KFYSCPFCE 227
                                       6799****5 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00071
                   Lar_restr_allev   2 eLkpCPfCggravlersqrvvaeigqcvyCadCga....s 37 
                                        L+ C  Cg ++ ++ s++++      ++C++Cga     
  gi|385805571|ref|YP_005841969.1| 822 VLLKCMNCGWEKSVKVSELPD-----IISCEKCGAravaP 856
                                       5889999*************9.....9********65540 PP

>> DUF4923  Lipocalin-like domain (DUF4923)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.4   0.0       9.8   1.5e+04      59      73 ..     578     592 ..     575     600 .. 0.73
   2 ?   11.6   0.4   0.00012      0.18     137     171 ..     710     744 ..     681     748 .. 0.88

  Alignments for each domain:
  == domain 1  score: -4.4 bits;  conditional E-value: 9.8
                           DUF4923  59 veekLkeyykkvgik 73 
                                       v ek+k++y+ + i+
  gi|385805571|ref|YP_005841969.1| 578 VYEKIKSQYQSITIE 592
                                       667888888888887 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00012
                           DUF4923 137 dkLlelltalsskssnstlktvssllknYdgillG 171
                                        kL ++ ++++++s+n+tl+ v+++lk Y++ l+G
  gi|385805571|ref|YP_005841969.1| 710 YKLSTVAKKMGAISKNATLSEVKKVLKYYKDTLIG 744
                                       5999***************************9999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (951 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       903  (0.0503653); expected 358.6 (0.02)
Passed bias filter:                      641  (0.0357521); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.84u 0.26s 00:00:01.10 Elapsed: 00:00:00.47
# Mc/sec: 6080.72
//
Query:       gi|385805572|ref|YP_005841970.1|  [L=438]
Description: hypothetical protein FFONT_0528 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-10   38.9  54.4    7.1e-05   21.9  10.0    2.0  2  MFS_1     Major Facilitator Superfamily


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8  46.8   4.2e-09   7.5e-05       8     329 ..      31     362 ..      25     366 .. 0.60
   2 !   21.9  10.0     4e-09   7.1e-05      79     187 ..     321     437 ..     310     438 .] 0.79

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 4.2e-09
                             MFS_1   8 salarsilgpalplalaedlg.ispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fa 82 
                                       + l+r++ ++++   l++++  is+  +g++ + y+++ a++ ++ G + + +G+   ++++  l++++ ++++ fa
  gi|385805572|ref|YP_005841970.1|  31 VVLMRAANASFII-SLTTAFPdISAWMQGIIQASYSFTEALFGIFSGIIYEYLGSSISIIFSSSLLFISYAIMTvFA 106
                                       3333333333333.44444433788889*****************************77777777777734444587 PP

                             MFS_1  83 ...sslw.lllvlrvlqGlgagalfpagaaliadwfpk.eergrai..gllsagfslGailgpllgg....lla.ss 147
                                          +s   ++ +  +l+Gl a++l+++++a+i++ + k + +gr +  g l +++ +G+++g  ++g    +l  + 
  gi|385805572|ref|YP_005841970.1| 107 dmsIS-AeAFTIPSALAGLSASFLLTSSLAVISEETIKaSTKGRLFgvGGLEVSNIIGYAVGFTFAGtlqlILPsAI 182
                                       76444.459***********************998777566666662256666999999999999994432222233 PP

                             MFS_1 148 lgWravfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfs 224
                                        g++ +f++  +++l +++l     +++ +e k+k+ +      ++ +++   k l+  p    +++++ +++ + +
  gi|385805572|ref|YP_005841970.1| 183 KGFSPSFLFSFLAFLSSIILSKSMGRRNISEFKNKKIT------FHLKAKIEGKVLKLVP----MWFGFSIVMGVAF 249
                                       33666666666666665554333333333322222222......3333333234444444....4445444444444 PP

                             MFS_1 225 g.....lltllplylqevlglsglllaglllallalvgailallagrls.drlgrrrrlllallllllaalglalla 295
                                       +        ++p+  ++  gl+ l+++   + l+al+++ l++++g ++   lg+ + ll + l+l  ++++l +l 
  gi|385805572|ref|YP_005841970.1| 250 IspkflSELFSPIE-VSNPGLK-LFSSF--MLLFALIILSLGVMGGSYIaSILGKVNSLLAGSLSLPSTLVMLSILV 322
                                       44554444555553.5555555.55555..99999999999889998886778886666666555555555555555 PP

                             MFS_1 296 vtssavllll......vlvliGfglgfvfpsllalasdla 329
                                        + s++ ++       +l+++++ +  + p+ll+l++d++
  gi|385805572|ref|YP_005841970.1| 323 SYGSNIKGISmffftlILLIFSVLALSIPPTLLSLLADFT 362
                                       5545555554112222555577755556888888888775 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 4e-09
                             MFS_1  79 ll.fa.....sslw.lllvlrvlqGlgagalfpagaaliadwfpk.eergraigllsagfslGailgpllggllass 147
                                       l+ ++     +s++ + l+l ++ ++ a ++ p+ ++l+ad +   + rg   g++ +++++G++lg  lgg +++ 
  gi|385805572|ref|YP_005841970.1| 321 LVsYGsnikgISMFfFTLILLIF-SVLALSIPPTLLSLLADFTDLsRIRGPSSGVYVTSMGIGIALGESLGGKIYDV 396
                                       22232233445555245555555.5555699**************999***************************** PP

                             MFS_1 148 lgWravfyilaivsllafv.lfllllpeepperkrkspkee 187
                                       +g + + +ilaiv+l +++  +++l++e+ +++  ++p+++
  gi|385805572|ref|YP_005841970.1| 397 FGLETLLLILAIVFLPLGLsTWIMLYFERSRKNISSKPIPQ 437
                                       *******************9899999999999998888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.64u 0.38s 00:00:01.02 Elapsed: 00:00:00.53
# Mc/sec: 2503.81
//
Query:       gi|385805573|ref|YP_005841971.1|  [L=272]
Description: aldo/keto reductase [Fervidicoccus fontis Kam940]
Scores for complete 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-62  209.9   0.5    5.8e-60  203.0   0.5    2.0  1  Aldo_ket_red  Aldo/keto reductase family


Domain annotation for each model (and alignments):
>> Aldo_ket_red  Aldo/keto reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.0   0.5   3.2e-64   5.8e-60       2     293 ..      15     271 ..      14     272 .] 0.95

  Alignments for each domain:
  == domain 1  score: 203.0 bits;  conditional E-value: 3.2e-64
                                       EEEE-SSS-ST.....TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE--SS CS
                      Aldo_ket_red   2 lglGtwqlgsk....eeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKvdlrd 74 
                                       lg+Gtw +g++    ++ ++ e  ++l++a+ +Gi+++DtAe+Yg g+see++G+a+k   ++r+e++i+tKv    
  gi|385805573|ref|YP_005841971.1|  15 LGIGTWGIGGGfwtpDYSQDLENEKILKYAIRNGITLIDTAEMYGGGHSEEIVGNAIKG--ERRDELFIVTKV---- 85 
                                       9*********9777667777777777*********************************..************.... PP

                                       STTSSSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEES--HHHHHHH.H CS
                      Aldo_ket_red  75 aeiksglskeniresleeslkrLgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvSnfsveqleka.k 150
                                         ++++ s +++ +s e s krLgt y+Dl+llH+p  ++  i+e+++a+eelv+ G ir++GvSnfsve+le a +
  gi|385805573|ref|YP_005841971.1|  86 --WNANASYDRVLKSAEMSSKRLGT-YIDLYLLHWPSDTVN-ICETIRAFEELVERGIIRYYGVSNFSVERLEGAmN 158
                                       ..**********************6.***************.*********************************9* PP

                                       HTTT--EEEEE-B-BTT-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC-------TS-HHHHH CS
                      Aldo_ket_red 151 kkkkvkivavqveynllreleeegllelckkkgvpliaysplggGlltgkyqseedkedkeprkdlkrdertsknld 227
                                        +kk +ivav+++ +l ++++  +++e++k kg+   ay+p+ +G +                              
  gi|385805573|ref|YP_005841971.1| 159 CQKKFEIVAVENQLSLKNKEDLYNVVEYAKRKGMLYLAYTPIDKGTIA----------------------------- 206
                                       **********************************************99............................. PP

                                       HHHHHHHHHHHTT--HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHGGGG----HHHHHHHHHHH CS
                      Aldo_ket_red 228 aaeelselakehgvslaqlalryalsqpavgivipgasnieqlednldalelklseeevaeldell 293
                                          +l+e++++++ s+ q+al++++s  + +++ip+asn+++l++nl+a+ +++see+++ l++++
  gi|385805573|ref|YP_005841971.1| 207 NSGILKEIGQKYNRSPVQVALNWLIS-IQPVVPIPKASNLKHLKENLGAVGWRISEEDWKLLEKAY 271
                                       4689*********************5.77789****************************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.35s 00:00:00.93 Elapsed: 00:00:00.56
# Mc/sec: 1452.18
//
Query:       gi|385805574|ref|YP_005841972.1|  [L=313]
Description: family 2 glycosyltransferase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-24   86.8   0.1    1.9e-24   86.4   0.1    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
    3.5e-09   36.9   0.1    5.2e-09   36.3   0.1    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
     0.0041   16.6   0.1     0.0063   16.0   0.1    1.3  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
  ------ inclusion threshold ------
      0.041   12.6   0.0      0.041   12.6   0.0    1.1  1  ResB             ResB-like family
      0.054   14.0   0.0       0.11   13.0   0.0    1.5  1  Glyco_tranf_2_4  Glycosyl transferase family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.4   0.1   5.2e-28   1.9e-24       1     121 [.      18     131 ..      18     175 .. 0.91

  Alignments for each domain:
  == domain 1  score: 86.4 bits;  conditional E-value: 5.2e-28
                                       EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglra 77 
                                       +vvip+ Nee+ + ++le +++q + p+++i++vD  StD+tvei++++     +v+vi +e   Gk+ a+ ++l +
  gi|385805574|ref|YP_005841972.1|  18 TVVIPVLNEEEAIGKVLEEVINQAKVPKDKILIVDGKSTDKTVEIAKSY-----GVKVIEQEGI-GKSMAIKTALNY 88 
                                       69***********************************************.....9*******55.************ PP

                                       --SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEEC CS
                   Glycos_transf_2  78 atgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifg 121
                                       + ++yil++D D +++ +++ +l+++++k ++d+v+g+r + ++
  gi|385805574|ref|YP_005841972.1|  89 VGTEYILIMDGDYTYPAKYIVDLYREIKK-EKDIVIGSRKKLEK 131
                                       *****************************.********987655 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 !   36.3   0.1   1.5e-12   5.2e-09       4      98 ..      17     101 ..      15     122 .. 0.89

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 1.5e-12
                   Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqey.prvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksral 79 
                                       l+v++p++nee+ +g+vle++++q+  p +++ +v+ +s+++t+e a+     +   +v+v+ +    g+ gks a+
  gi|385805574|ref|YP_005841972.1|  17 LTVVIPVLNEEEAIGKVLEEVINQAKvPKDKILIVDGKSTDKTVEIAKS----Y---GVKVIEQ---EGI-GKSMAI 82 
                                       89**********************96599****************9976....4...7899833...476.9***** PP

                   Glyco_tranf_2_3  80 nealravksdlvllvDdDt 98 
                                       + al+ v ++++l++D+D 
  gi|385805574|ref|YP_005841972.1|  83 KTALNYVGTEYILIMDGDY 101
                                       *****************96 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   1.8e-06    0.0063       1      91 [.      18     100 ..      18     119 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.8e-06
                   Glyco_tranf_2_2   1 svviplraseer.hyieervlqkakyydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrG 76 
                                       +vvip+ ++ee    + e v ++ak   ++ ++++vd+ S++k++e  +s      +v     +++  +++ a    
  gi|385805574|ref|YP_005841972.1|  18 TVVIPVLNEEEAiGKVLEEVINQAKV--PKDKILIVDGKSTDKTVEIAKSYG---VKVI----EQEGIGKSMAIKTA 85 
                                       79****99998724689999******..***************887666542...3333....34577888888888 PP

                   Glyco_tranf_2_2  77 askaesdlvlFlDaD 91 
                                        ++  ++++l +D+D
  gi|385805574|ref|YP_005841972.1|  86 LNYVGTEYILIMDGD 100
                                       888888888888888 PP

>> ResB  ResB-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.1e-05     0.041     409     460 ..     206     259 ..       6     270 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.1e-05
                              ResB 409 l.srygsplllqlddfe.qrqasgLqvsrdpgknlvllgalllvlGlvlslyvr 460
                                         +r g++ l +l +f   +++++L ++++p+  + +lg+lll+ Gl l lyv 
  gi|385805574|ref|YP_005841972.1| 206 YrKRIGKKKLGVLHGFHiFVDMIKLMLNYNPTFFIFILGSLLLIPGLALGLYVA 259
                                       256778888999******9*********************************96 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 ?   13.0   0.0   3.1e-05      0.11       2      80 ..      25      99 ..      24     105 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.1e-05
                   Glyco_tranf_2_4  2 neadiLpeflahh.lalgf..drilvydndstDgtrailkelpevkllhvdksyederrqvellkallaryaeadwvlv 77
                                      ne+++++++l+    ++ +  d+il++d +stD+t +i k+ + vk+++ ++  +     +++ +al  +y  ++++l 
  gi|385805574|ref|YP_005841972.1| 25 NEEEAIGKVLEEViNQAKVpkDKILIVDGKSTDKTVEIAKS-YGVKVIEQEGIGK----SMAIKTAL--NYVGTEYILI 96
                                      78888999998551445556599***************999.5788887766544....23333332..3555666666 PP

                   Glyco_tranf_2_4 78 vDa 80
                                      +D 
  gi|385805574|ref|YP_005841972.1| 97 MDG 99
                                      665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       864  (0.0481901); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); 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: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2144.20
//
Query:       gi|385805575|ref|YP_005841973.1|  [L=185]
Description: hypothetical protein FFONT_0531 [Fervidicoccus fontis Kam940]
Scores for 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-32  110.6  14.0    1.3e-31  110.1  14.0    1.2  1  DUF1616   Protein of unknown function (DUF1616)


Domain annotation for each model (and alignments):
>> DUF1616  Protein of unknown function (DUF1616)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.1  14.0   7.5e-36   1.3e-31       4     108 ..      70     174 ..      65     177 .. 0.89

  Alignments for each domain:
  == domain 1  score: 110.1 bits;  conditional E-value: 7.5e-36
                           DUF1616   4 lalllllailvpvlnetplRivlglplvLflPGYaliaaLFPekrdidgieRlaLSfglSiaivpliglvlnvtpwg 80 
                                       l+ l+l+ ++ +     plR ++g ++vLflPGY l+ aL+P+++d++ +eRlaLS+glS+a+vpligl+ln+tp g
  gi|385805575|ref|YP_005841973.1|  70 LVSLTLIYVTNFLSILMPLRYIFGSIFVLFLPGYSLVEALYPGEGDLSPLERLALSIGLSLAVVPLIGLLLNYTPFG 146
                                       34444455555556678************************************************************ PP

                           DUF1616  81 irlepilvslslftlllalvAivrRsrl 108
                                       irl pi++sls+f+++l++ A++r+ ++
  gi|385805575|ref|YP_005841973.1| 147 IRLLPIAASLSMFIIILSVYALYRKFSI 174
                                       ************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       919  (0.0512577); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1107.15
//
Query:       gi|385805576|ref|YP_005841974.1|  [L=172]
Description: hypothetical protein FFONT_0532 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-09   37.9   0.1    1.5e-09   37.7   0.1    1.0  1  DUF1616   Protein of unknown function (DUF1616)


Domain annotation for each model (and alignments):
>> DUF1616  Protein of unknown function (DUF1616)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.1   8.3e-14   1.5e-09     144     270 ..      17     144 ..       6     166 .. 0.73

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 8.3e-14
                           DUF1616 144 lLvvsivlavaalgyavva.PkegekfTelyllgedgdelvaenypteltagesqevivgieNhEheevnYtvvvll 219
                                       +++++i++ +  lg+a++  P+++e fT+l ll ++      + yp+++  g++ ++ + + Nh + +  Y+vv  +
  gi|385805576|ref|YP_005841974.1|  17 AVILAIIVVGSVLGVAMIIrPSSEEPFTALGLLDQNC---QIGSYPSTVVNGTNVNLCLFVYNHMGHPIYYEVVYKI 90 
                                       456666666666666554449***************9...************************************* PP

                           DUF1616 220 qev....tdeeevevlerteldrrevtladnetweqelevepeatgenlrleflL 270
                                        ++    t+++  +     +  r  ++ +dnet + ++ v  +++++++ l f L
  gi|385805576|ref|YP_005841974.1|  91 GNNltipTNTTPSSS-LAIKNWRGVLNNDDNETFHVSVPVYANNNETSVALIFEL 144
                                       998866533322222.233333444555667777777766666666666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1080.84
//
Query:       gi|385805577|ref|YP_005841975.1|  [L=144]
Description: hypothetical protein FFONT_0533 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score 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   14.8   7.1      0.041   14.0   0.4    2.4  2  Insulin_TMD  Insulin receptor trans-membrane segment
      0.088   12.6   0.1       0.14   11.9   0.1    1.3  1  DUF3836      Family of unknown function (DUF3836)


Domain annotation for each model (and alignments):
>> Insulin_TMD  Insulin receptor trans-membrane segment
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   1.3    0.0077        69      24      39 ..       8      23 ..       5      28 .. 0.80
   2 ?   14.0   0.4   4.5e-06     0.041      11      39 ..      96     124 ..      92     126 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0077
                       Insulin_TMD 24 ciillllvigavfvvv 39
                                       +i+ll+vi + f++v
  gi|385805577|ref|YP_005841975.1|  8 SVIILLIVIISPFIIV 23
                                      5788888888889887 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 4.5e-06
                       Insulin_TMD  11 psnivkIvigPviciillllvigavfvvv 39 
                                        sn  kI+   +i iilll + + ++v++
  gi|385805577|ref|YP_005841975.1|  96 ESNYYKIIALKIIEIILLLSIPVLTYVFL 124
                                       57999**********************97 PP

>> DUF3836  Family of unknown function (DUF3836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   1.5e-05      0.14       1      76 [.       1      78 [.       1      83 [. 0.73

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.5e-05
                                      XXXXXXXXXXXXXXXXXXXXXXXXXTTTTEECEEEEEEETTEEEEEEEEEEE....TTEEEEEEEEEEEEETTTTEEEE CS
                           DUF3836  1 Mkttvllkalvvsavllvtsltasaaaneknfiyneeeenglvvsktvyked....gklLtnklkYeYkyddqgrviek 75
                                      Mk+  ++  +++++v++   + +s+++  ++ +  ++ + +++ ++ vy  d     + L nkl Y  k +++g+++++
  gi|385805577|ref|YP_005841975.1|  1 MKAYKVYSVIILLIVIISPFIIVSSQS--SEDVIGTNSTITQLLGEIVYLYDhgvnVSQLVNKLNYAVKLEQEGNITAS 77
                                      777777766666666655555555554..5557788888899999****9884444568****************9987 PP

                                      E CS
                           DUF3836 76 e 76
                                      +
  gi|385805577|ref|YP_005841975.1| 78 S 78
                                      5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       917  (0.0511462); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); 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: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 944.68
//
Query:       gi|385805578|ref|YP_005841976.1|  [L=386]
Description: hypothetical protein FFONT_0534 [Fervidicoccus fontis Kam940]
Scores for complete 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    2.8e-07   30.7   0.0    1.4  1  DUF58     Protein of unknown function DUF58
  ------ inclusion threshold ------
      0.043   13.8   0.5       0.09   12.8   0.5    1.6  1  DUF999    Protein of unknown function (DUF999)
      0.064   12.6   0.1       0.16   11.4   0.1    1.6  2  DUF2045   Uncharacterized conserved protein (DUF2045)


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 !   30.7   0.0   4.7e-11   2.8e-07       3      52 ..     158     207 ..     156     232 .. 0.84

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 4.7e-11
                             DUF58   3 dfaglReYvpgDplrrIdWkatARtgelyvrefeaerartvllvldlspe 52 
                                       ++   R ++pgD ++rIdWk++ +  +l++re+ ++  ++v+l++d +  
  gi|385805578|ref|YP_005841976.1| 158 EYIRNRFFEPGDVPKRIDWKSSMKNLRLIIREYGENPHGSVMLLVDYTCA 207
                                       66777999**************************************9866 PP

>> DUF999  Protein of unknown function (DUF999)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.5   1.5e-05      0.09      46      86 ..      36      76 ..      27     113 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.5e-05
                            DUF999 46 dklniktnkikeflndlftefskfhnsyypdgristrsklr 86
                                       k+nik +k k+f + +f+ f k  +      ++s   kl 
  gi|385805578|ref|YP_005841976.1| 36 PKINIKIDKCKNFKEAIFSSFVKVEEIKKARDKVSISAKLL 76
                                      69**********************99998888888877765 PP

>> DUF2045  Uncharacterized conserved protein (DUF2045)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   2.6e-05      0.16     163     198 ..      43      78 ..       6      95 .. 0.86
   2 ?   -2.7   0.0      0.53   3.1e+03      65      81 ..     171     188 ..     162     190 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.6e-05
                           DUF2045 163 dkadklkavlFsgsvryealkkaydakassakslaq 198
                                       dk +++k  +Fs++v+ e++kka+d+ + sak l++
  gi|385805578|ref|YP_005841976.1|  43 DKCKNFKEAIFSSFVKVEEIKKARDKVSISAKLLFN 78 
                                       788999*******************99666665555 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.53
                           DUF2045  65 saevdWeetvy.Lnlilq 81 
                                        +++dW+ ++  L li++
  gi|385805578|ref|YP_005841976.1| 171 PKRIDWKSSMKnLRLIIR 188
                                       5789***99854788776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2455.28
//
Query:       gi|385805579|ref|YP_005841977.1|  [L=317]
Description: methanol dehydrogenase regulatory - like protein [Fervidicoccus fontis Kam940]
Scores for complete 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-43  146.7   0.0    4.6e-43  146.2   0.0    1.2  1  AAA_3            ATPase family associated with various cellul
    3.3e-16   58.9   0.0    5.8e-16   58.1   0.0    1.4  1  AAA_lid_2        AAA lid domain
    5.7e-15   55.5   0.0    9.2e-15   54.9   0.0    1.4  1  AAA_5            AAA domain (dynein-related subfamily)
    8.4e-08   32.7   0.0    2.8e-07   31.0   0.0    1.9  1  AAA              ATPase family associated with various cellul
    5.6e-06   26.2   0.0      0.035   13.8   0.0    2.2  2  Sigma54_activat  Sigma-54 interaction domain
    6.2e-06   26.1   0.6    7.5e-05   22.5   0.0    2.6  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    3.6e-05   23.3   0.0     0.0025   17.2   0.0    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    4.4e-05   23.9   0.0       0.02   15.3   0.0    2.6  3  AAA_16           AAA ATPase domain
     0.0016   18.7   0.0     0.0041   17.4   0.0    1.7  1  AAA_22           AAA domain
     0.0087   15.2   0.0      0.029   13.5   0.0    2.1  1  MCM              MCM P-loop domain
  ------ inclusion threshold ------
      0.016   15.5   0.1        1.6    9.0   0.1    2.6  2  AAA_19           AAA domain
      0.017   14.9   0.0       0.02   14.7   0.0    1.5  1  DEAD             DEAD/DEAH box helicase
      0.022   14.7   0.0      0.054   13.5   0.0    1.7  1  DUF771           Domain of unknown function (DUF771)
      0.037   14.2   0.0       0.13   12.4   0.0    1.9  1  AAA_2            AAA domain (Cdc48 subfamily)
      0.047   13.8   0.0       0.19   11.9   0.0    2.0  1  Sigma54_activ_2  Sigma-54 interaction domain
       0.05   13.3   0.1       0.84    9.3   0.1    2.3  2  AAA_30           AAA domain
      0.055   14.0   0.0       0.12   12.9   0.0    1.7  1  AAA_18           AAA domain
       0.08   12.7   0.1       0.14   11.9   0.1    1.3  1  AAA_11           AAA domain
      0.082   13.4   0.9       0.28   11.6   0.9    1.8  1  AAA_23           AAA domain
       0.15   11.4   0.0       0.26   10.6   0.0    1.4  1  FtsK_SpoIIIE     FtsK/SpoIIIE family


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 !  146.2   0.0   5.2e-46   4.6e-43       1     130 [.      39     168 ..      39     169 .. 0.99

  Alignments for each domain:
  == domain 1  score: 146.2 bits;  conditional E-value: 5.2e-46
                             AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanllladeinrappk 77 
                                       hvl+eg PG +ktl+++ la +++ +fkriq+tpd+lPsdilG  +++  + e+ f++Gp+fan+++ de+nra+p+
  gi|385805579|ref|YP_005841977.1|  39 HVLIEGPPGSGKTLTARLLALSIGGTFKRIQMTPDMLPSDILGGFFYDIGKGEWIFREGPIFANVIFIDELNRASPR 115
                                       9**************************************************************************** PP

                             AAA_3  78 tqsalleameerqvtvegethklpepflvlatqnPieqeGtyplpeaqldrfl 130
                                       tqsalleam+e + ++eg t++lp+p l +atq    + G ypl  + ldrf 
  gi|385805579|ref|YP_005841977.1| 116 TQSALLEAMQEGRASIEGVTKELPRPNLFIATQMTKSEVGIYPLTPTLLDRFA 168
                                       ****************************************************7 PP

>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.1   0.0   6.5e-19   5.8e-16      15      70 ..     248     305 ..     235     308 .. 0.86

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 6.5e-19
                         AAA_lid_2  15 grRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlr..repeaegetteeiv 70 
                                       + Ra++ l + +rAlA+leg dyV+p++vk++a++VL+HRl   +e+e +++t+e i+
  gi|385805579|ref|YP_005841977.1| 248 STRASVWLFKGSRALAFLEGNDYVSPDHVKKIARYVLRHRLFfnPEAELKNVTSENII 305
                                       566***************************************7777777778777776 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 !   54.9   0.0     1e-17   9.2e-15       1     138 []      39     167 ..      39     188 .. 0.84

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 1e-17
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--...........--------G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik..ngttslvdsplvraaregeilvlDEve 75 
                                       +vl+ GppG+gK+  a+ la  ++ ++  +q+t d+ ++d++g+  ++  +g+  ++++p+      + ++++DE++
  gi|385805579|ref|YP_005841977.1|  39 HVLIEGPPGSGKTLTARLLALSIGGTFKRIQMTPDMLPSDILGGFFYDigKGEWIFREGPIF-----ANVIFIDELN 110
                                       79******************************************988877999999******.....9********* PP

                                       G--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--..-TT-TTHHHHTT- CS
                             AAA_5  76 raesevlnsLlslleerrllleeggelvkaknddllerfrviatanpld.rslnelspalrsRf 138
                                       ra++ ++++Ll  + e r ++e  +++   +n        +iat  + +  +  +l+p l++Rf
  gi|385805579|ref|YP_005841977.1| 111 RASPRTQSALLEAMQEGRASIEGVTKELPRPN-------LFIATQMTKSeVGIYPLTPTLLDRF 167
                                       ********************777777776665.......4555555555566666666666665 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 !   31.0   0.0   3.2e-10   2.8e-07       1     101 [.      40     142 ..      40     175 .. 0.68

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 3.2e-10
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEET.TTCS.SSSTTHHHHHHHH...HHHHHHHTS.TSEEEEEETGGGHH CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisg.sell.skyvgesekkire...lfkeakeka.kpsilfiDEidala 71 
                                       vl+ GppG GKTl+a+ +a ++g +f +i++ +++l s+++g    +i +   +f+e         ++fiDE+ +  
  gi|385805579|ref|YP_005841977.1|  40 VLIEGPPGSGKTLTARLLALSIGGTFKRIQMtPDMLpSDILGGFFYDIGKgewIFREG---PiFANVIFIDELNRAS 113
                                       6899**********************99997356665665555555554411134333...24339**********9 PP

                                       HHHTTCCCHHHHHHHHHHHHHHHHTTTS..........SS CS
                               AAA  72 ksrsgseseeeervvnqLlteldgvkkk..........es 101
                                       ++            +++Ll+++++ + +           +
  gi|385805579|ref|YP_005841977.1| 114 PRT-----------QSALLEAMQEGRASiegvtkelprPN 142
                                       988...........99999999988877666666665433 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00053      0.48      12      42 ..      27      57 ..      21      80 .. 0.84
   2 !   13.8   0.0   3.9e-05     0.035      96     138 ..     103     145 ..      98     157 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00053
                                      HHHHHHHCTSSS-EEEECSTTSSHHHHHHHH CS
                   Sigma54_activat 12 leqikkvaktdlsvlitGesGtGKellarai 42
                                      +e ++    +  +vli+G  G+GK+l ar++
  gi|385805579|ref|YP_005841977.1| 27 FELLSISLLSGGHVLIEGPPGSGKTLTARLL 57
                                      5555666667789***************987 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 3.9e-05
                                       EEEEETGGGS-HHHHHHHHHHHHHSEEESBTSSSEEE--EEEE CS
                   Sigma54_activat  96 tlfLDeigelplelQekLlrvlqegevervGsskeikvdvrii 138
                                       ++f+De+++ ++++Q+ Ll+++qeg+ +  G +ke +    +i
  gi|385805579|ref|YP_005841977.1| 103 VIFIDELNRASPRTQSALLEAMQEGRASIEGVTKELPRPNLFI 145
                                       79***********************998888888776655555 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 !   22.5   0.0   8.4e-08   7.5e-05      34     112 ..      38     128 ..      33     169 .. 0.84
   2 ?   -2.6   0.1       4.4     4e+03      82     102 ..     198     218 ..     183     242 .. 0.55

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 8.4e-08
                            RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklk.itsgPvlekagdlaalltnleekd...........vlfideihrlsr 98 
                                        hvl+ GpPG Gkt  a+++a  +g ++k i  +P +  +  l +++ ++ +++           v+fide+ r s+
  gi|385805579|ref|YP_005841977.1|  38 GHVLIEGPPGSGKTLTARLLALSIGGTFKrIQMTPDMLPSDILGGFFYDIGKGEwifregpifanVIFIDELNRASP 114
                                       5************************998626778999888888999999987533222333333399********** PP

                            RuvB_N  99 aveevlysamedfr 112
                                        ++  l  am++ r
  gi|385805579|ref|YP_005841977.1| 115 RTQSALLEAMQEGR 128
                                       **********8765 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.4
                            RuvB_N  82 leekdvlfideihrlsravee 102
                                        + + +l i +i  l+++++ 
  gi|385805579|ref|YP_005841977.1| 198 TSVSPILSIKDILMLQEEIKK 218
                                       334444444444444444433 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.8e-06    0.0025       5      42 ..      20      57 ..      17      66 .. 0.86
   2 ?    3.5   0.0     0.045        40     109     145 ..     103     139 ..      87     161 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.8e-06
                      Mg_chelatase  5 vkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrl 42
                                      ++G ee  + l i+   g ++l+ GppGsGKt+ a+ l
  gi|385805579|ref|YP_005841977.1| 20 IIGYEELFELLSISLLSGGHVLIEGPPGSGKTLTARLL 57
                                      6788888899999998888899***********99876 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.045
                      Mg_chelatase 109 vLfLDElpefkrkvlevLRePledgevtisrakakve 145
                                       v+f+DEl   + ++  +L e +++g+ +i+  ++++ 
  gi|385805579|ref|YP_005841977.1| 103 VIFIDELNRASPRTQSALLEAMQEGRASIEGVTKELP 139
                                       99***********************999988777665 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   2.3e-05      0.02      12      49 ..      26      62 ..      23      85 .. 0.78
   2 ?    5.7   0.0      0.02        18     138     161 ..     103     127 ..      96     145 .. 0.82
   3 ?   -1.3   0.0       2.7   2.4e+03      67     106 ..     157     196 ..     128     245 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.3e-05
                            AAA_16 12 Llsale.rvrsgrpelvllsGesGvGKsslvrellrale 49
                                      L ++l+ ++ sg  + vl+ G++G+GK+  +r l+ ++ 
  gi|385805579|ref|YP_005841977.1| 26 LFELLSiSLLSG--GHVLIEGPPGSGKTLTARLLALSIG 62
                                      566666555555..79****************9987665 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.02
                            AAA_16 138 vlvlDdlqwadeaslql.laaLlrl 161
                                       v+++D+l +a + ++++ l+a+ + 
  gi|385805579|ref|YP_005841977.1| 103 VIFIDELNRASPRTQSAlLEAMQEG 127
                                       8****************66665544 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 2.7
                            AAA_16  67 ipysa.laqalareellrqlldeaesaeleawrekleeala 106
                                        p+ + l++ +a+ ++++  l+ ++++e+ +  ++++e+++
  gi|385805579|ref|YP_005841977.1| 157 YPLTPtLLDRFAF-SYITNYLETDKEKEVLDKVDAIDEVIK 196
                                       4556667777766.444444444455577777777777777 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   4.6e-06    0.0041       5      65 ..      37      88 ..      34     131 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.6e-06
                            AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralg 65
                                       g++++ G++G+GKT+++r l+ +          + ++ +++++ ++ ++d+l  ++ ++g
  gi|385805579|ref|YP_005841977.1| 37 GGHVLIEGPPGSGKTLTARLLALSI---------GGTFKRIQMTPDMLPSDILGGFFYDIG 88
                                      6899*****************9987.........555556666666666666666555555 PP

>> MCM  MCM P-loop domain
   #    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     124     157 ..     103     134 ..      31     189 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.2e-05
                                       EEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSC CS
                               MCM 124 vcciDefdkmkeedrsalhEamEqqtisiaKaGi 157
                                       v+ iDe+++ + +++sal+Eam +   si   G+
  gi|385805579|ref|YP_005841977.1| 103 VIFIDELNRASPRTQSALLEAMQEGRASIE--GV 134
                                       89*********************9999986..55 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1    0.0018       1.6       8      27 ..      35      54 ..      30      68 .. 0.85
   2 ?    3.4   0.0     0.099        89     104     127 ..     102     126 ..      91     133 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0018
                            AAA_19  8 lkekvllvtaGpGtGKTrvl 27
                                      l+ +++l+ ++pG+GKT + 
  gi|385805579|ref|YP_005841977.1| 35 LSGGHVLIEGPPGSGKTLTA 54
                                      567899***********886 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.099
                            AAA_19 104 ellivDEfqdvd.elqyrLlkallg 127
                                       +++++DE    +  +q +Ll+a+ +
  gi|385805579|ref|YP_005841977.1| 102 NVIFIDELNRASpRTQSALLEAMQE 126
                                       589*********99*******9984 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   2.2e-05      0.02      11      38 ..      34      61 ..      28     306 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.2e-05
                                      HHTTCEEEEEESTTSSHHHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 11 ilgggdvlvaaeTGsGKTlaflipvlqi 38
                                      +l+gg+vl++++ GsGKTl + + +l+i
  gi|385805579|ref|YP_005841977.1| 34 LLSGGHVLIEGPPGSGKTLTARLLALSI 61
                                      56899***************99988855 PP

>> DUF771  Domain of unknown function (DUF771)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     6e-05     0.054      14      86 ..     195     268 ..     181     271 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6e-05
                            DUF771  14 LkkkdlsGvywtlkdlekkls.kssewikeni.LenprfrkeldiekggfvlypkgkgkkwlfkakkmakFlden 86 
                                       +k++++s+ ++++kd+    +  ++  + ++i L+   +  el+ +++ fv+ p +  + wlfk +++  Fl+ n
  gi|385805579|ref|YP_005841977.1| 195 IKSTSVSP-ILSIKDILMLQEeIKKVYVDDKIkLYIASIVGELRKKEDMFVIAPSTRASVWLFKGSRALAFLEGN 268
                                       34445555.68899988887767777888888899999**********************************987 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00014      0.13       5     108 ..      39     129 ..      36     153 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
                                       -EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG CS
                             AAA_2   5 silllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidK 79 
                                        +l+ gp g+Gkt++a+ la  +      ++ r+ ++  +   ++      +ig+ + + +       ++++DE+ +
  gi|385805579|ref|YP_005841977.1|  39 HVLIEGPPGSGKTLTARLLALSIG----GTFKRIQMTPDMLPSDILGGFFYDIGKGEWIFREGPIFanVIFIDELNR 111
                                       67899***********99999998....59********999888888888888888888765554499********* PP

                                       -------------HHHHHHHHHHHH--EE CS
                             AAA_2  80 ihpkessgadvSregVqrdLLqileggtl 108
                                       ++p+            q +LL  + +g++
  gi|385805579|ref|YP_005841977.1| 112 ASPR-----------TQSALLEAMQEGRA 129
                                       ***4...........45555555555544 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 ?   11.9   0.0   0.00021      0.19      23      95 ..      39     126 ..      25     135 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00021
                                       -EEEEEETT--HHHHHHCC--TTS-EE--SSTTHHHH-HHHHHHH................TTTSEEEEEE-TT--H CS
                   Sigma54_activ_2  23 pvfltGekGsgkelvArlLhknsgpwleifvverlaklpldlleq................akggtLylkdiadlsk 83 
                                        v++ G++Gsgk+l ArlL+ + g+  +  ++ ++  lp+d+l                  +   ++++ +++  s+
  gi|385805579|ref|YP_005841977.1|  39 HVLIEGPPGSGKTLTARLLALSIGGTFKRIQM-TPDMLPSDILGGffydigkgewifregpIFANVIFIDELNRASP 114
                                       59*****************9888886666666.55567766665544444444443333443555667777777777 PP

                                       HHHHHHHHHHHH CS
                   Sigma54_activ_2  84 aeqkeLlellak 95 
                                         q+ Lle++++
  gi|385805579|ref|YP_005841977.1| 115 RTQSALLEAMQE 126
                                       777777777766 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1   0.00094      0.84      15      38 ..      36      57 ..      30      69 .. 0.82
   2 ?    1.2   0.0      0.29   2.6e+02      90     118 ..     102     130 ..      92     135 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00094
                            AAA_30 15 tsgdrvavltGpAGtGKttalkal 38
                                      ++g   ++++Gp+G+GKt + + l
  gi|385805579|ref|YP_005841977.1| 36 SGG--HVLIEGPPGSGKTLTARLL 57
                                      444..589**********998766 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.29
                            AAA_30  90 tllivDEagmvdtkqlaallkaaekagak 118
                                       +++ +DE   ++ ++  all+a+++  a+
  gi|385805579|ref|YP_005841977.1| 102 NVIFIDELNRASPRTQSALLEAMQEGRAS 130
                                       57889999999999999999998886565 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00013      0.12       1      21 [.      40      60 ..      40     127 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00013
                            AAA_18  1 IlltGtpGvGKttlakeLskr 21
                                      +l+ G+pG+GKt  a+ L+ +
  gi|385805579|ref|YP_005841977.1| 40 VLIEGPPGSGKTLTARLLALS 60
                                      79***************9755 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00016      0.14      14      36 ..      35      56 ..      28      76 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00016
                            AAA_11 14 lseseitliqGPPGtgKTktive 36
                                      ls  + +li+GPPG+gKT t   
  gi|385805579|ref|YP_005841977.1| 35 LSGGH-VLIEGPPGSGKTLTARL 56
                                      56666.8***********87654 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.9   0.00032      0.28      16      55 ..      28      84 ..      12     245 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00032
                            AAA_23 16 dF......skgltlItGpNGaGKTTildAiklaLygetprlsrks...........g 55
                                      ++      s g +lI Gp G+GKT   + + l  +g ++r   +             
  gi|385805579|ref|YP_005841977.1| 28 ELlsisllSGGHVLIEGPPGSGKTLTARLLALSIGGTFKRIQMTPdmlpsdilggfF 84
                                      3344444899**************************998877665556555555551 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00029      0.26      17      63 ..      10      61 ..       1      64 [. 0.77

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00029
                                      TTEEEEEEET.TS-EEEEEGGGS-.....SEEEE--TTSSHHHHHHHHHHHH CS
                      FtsK_SpoIIIE 17 qlpvalgkei.sgnplvldlkkma....shllvaGatgsGKStalntLilSl 63
                                      ++ + + k   +g  + ++l +      +h+l+ G +gsGK+ + + L lS+
  gi|385805579|ref|YP_005841977.1| 10 RNVIEFLKSYiIGYEELFELLSISllsgGHVLIEGPPGSGKTLTARLLALSI 61
                                      55555555555777777777777788889*************9999888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); 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: 00:00:00.51
# Mc/sec: 1853.99
//
Query:       gi|385805580|ref|YP_005841978.1|  [L=324]
Description: hypothetical protein FFONT_0536 [Fervidicoccus fontis Kam940]
Scores for complete 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-05   22.1   0.0    0.00014   21.4   0.0    1.3  1  ABC_transp_aux  ABC-type uncharacterized transport system
  ------ inclusion threshold ------
      0.042   14.3   0.0      0.071   13.5   0.0    1.4  1  DUF4350         Domain of unknown function (DUF4350)


Domain annotation for each model (and alignments):
>> 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 !   21.4   0.0   1.6e-08   0.00014     174     232 ..      43     100 ..      20     118 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.6e-08
                    ABC_transp_aux 174 eenYnveevdldsedilpedidvlviakptkdlseeelykldqflmnGgkllvfldpva 232
                                         ++nv+ ++++s ++l ++  v+ +++p+k+++e+e   +  +++nGg l+++ d  +
  gi|385805580|ref|YP_005841978.1|  43 VHEFNVTLIPINSLNNL-KQGTVVFLIGPSKNFTEQEGMEILSYVENGGELVIMDDFGT 100
                                       5689************9.7888888888*************************998665 PP

>> DUF4350  Domain of unknown function (DUF4350)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   7.9e-06     0.071      34      69 .]      61      96 ..      33      96 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.9e-06
                           DUF4350 34 edgtllvvapdlrlteeelaallewvarGntlvlaa 69
                                       ++++++++p  ++te+e  ++l +v++G+ lv+++
  gi|385805580|ref|YP_005841978.1| 61 QGTVVFLIGPSKNFTEQEGMEILSYVENGGELVIMD 96
                                      57889***********9999*************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       934  (0.0520944); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); 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: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 1975.03
//
Query:       gi|385805581|ref|YP_005841979.1|  [L=589]
Description: hypothetical protein FFONT_0537 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0032   17.7   0.0      0.014   15.7   0.0    2.1  2  CarboxypepD_reg  Carboxypeptidase regulatory-like domain


Domain annotation for each model (and alignments):
>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0      0.85   1.5e+04      14      24 ..     102     112 ..      98     117 .. 0.80
   2 !   15.7   0.0   7.6e-07     0.014       1      43 [.     204     244 ..     204     255 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 0.85
                   CarboxypepD_reg  14 iagatVtvtna 24 
                                       i++atV ++n+
  gi|385805581|ref|YP_005841979.1| 102 ISNATVLIQNN 112
                                       8999*999974 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 7.6e-07
                   CarboxypepD_reg   1 tisGrVtdasgapiagatVtvtnadtgtvastttdadGafrlr 43 
                                       +i+G+ t +sg+p++  +V +    + + ++  t+++G+++l+
  gi|385805581|ref|YP_005841979.1| 204 SIQGSLTEESGNPLSDREVLIH--IGAKIYTIYTNSSGQYNLD 244
                                       69*******************9..67889************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (589 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); 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: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 3786.38
//
Query:       gi|385805582|ref|YP_005841980.1|  [L=44]
Description: hypothetical protein FFONT_0538 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.04   13.9   0.6      0.048   13.7   0.6    1.2  1  SNARE     SNARE domain
      0.093   12.7   0.3      0.093   12.7   0.3    1.1  1  LRR19-TM  Leucine-rich repeat family 19 TM domain


Domain annotation for each model (and alignments):
>> SNARE  SNARE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.6   5.4e-06     0.048      25      50 ..      10      35 ..       7      37 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.4e-06
                                      HHHHHHHCTXXXXXXXXXXXXXXXXX CS
                             SNARE 25 kkavkyqksnRklkciillilviill 50
                                      k +v+  ++ R +++iil+ ++ i++
  gi|385805582|ref|YP_005841980.1| 10 KAVVRPRRKGRDWLFIILIAVFAIFV 35
                                      56778889**************9997 PP

>> LRR19-TM  Leucine-rich repeat family 19 TM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.3     1e-05     0.093       9      34 ..      16      41 ..       8      44 .] 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1e-05
                          LRR19-TM  9 eksgksWaylvgvvvlalvtsllill 34
                                      ++ g+ W +++ ++v a+++s+ i  
  gi|385805582|ref|YP_005841980.1| 16 RRKGRDWLFIILIAVFAIFVSIRIYE 41
                                      578*******************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       796  (0.0443973); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 279.91
//
Query:       gi|385805583|ref|YP_005841981.1|  [L=224]
Description: hypothetical protein FFONT_0539 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1456.60
//
Query:       gi|385805584|ref|YP_005841982.1|  [L=102]
Description: hypothetical protein FFONT_0540 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00043   19.3   0.0    0.00049   19.1   0.0    1.0  1  LMBR1            LMBR1-like membrane protein
      0.006   16.6   0.0     0.0078   16.2   0.0    1.2  1  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
  ------ inclusion threshold ------
      0.059   12.2   0.0      0.066   12.0   0.0    1.1  1  DUF2254          Predicted membrane protein (DUF2254)


Domain annotation for each model (and alignments):
>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   8.3e-08   0.00049     128     216 ..       9      92 ..       3     101 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 8.3e-08
                             LMBR1 128 iiyllllvivlglliyvliilqklsllsiksllpilislantwGlvllilllGyGlvel.Prslwreiksdldeelk 203
                                       i+++++ +iv++l  y+l++ +  s +    +l  l + + ++G++ ++  +Gy l+ + P + + ei++++deelk
  gi|385805584|ref|YP_005841982.1|   9 ILLISVSAIVIVLYGYILFL-T--SYS---GILIELTAFIAILGIFGIVGWIGYTLATTpPPKPIEEIEKEIDEELK 79 
                                       33344444444444444444.2..222...667777899999*****************86677788********** PP

                             LMBR1 204 klyfeaaklntek 216
                                       kl+ e    ++++
  gi|385805584|ref|YP_005841982.1|  80 KLEQEQNVEQKTR 92 
                                       **76655544444 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 !   16.2   0.0   1.3e-06    0.0078      34     108 ..       7      73 ..       2      84 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.3e-06
                   Phage_holin_3_6  34 gsgagllgaagvlallalllllvalalalaalwlaalivaavllvlagvlalvglkklkkakplpertieelked 108
                                       +  +++ + a v++l++ +l+l     +l       l  +++ l + g+++++g+  +     +p + iee+++ 
  gi|385805584|ref|YP_005841982.1|   7 IGILLISVSAIVIVLYGYILFLTSYSGIL-----IELTAFIAILGIFGIVGWIGYTLATT---PPPKPIEEIEKE 73 
                                       45556666777777777777777775333.....35556677777779999999995555...355667777665 PP

>> DUF2254  Predicted membrane protein (DUF2254)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.1e-05     0.066     118     183 ..      24      92 ..       6     102 .] 0.68

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.1e-05
                           DUF2254 118 e......vpqlsvlvalllaivsvllLiyFihhlarsiqvsnviarveeelrkai....learedeeeeeeeeakd 183
                                       +        ++++ ++ ++ai+ ++ ++ +i  +  +    + i+++e+e+++++    +       e++ e++++
  gi|385805584|ref|YP_005841982.1|  24 YilfltsYSGILIELTAFIAILGIFGIVGWIGYTLATTPPPKPIEEIEKEIDEELkkleQ-------EQNVEQKTR 92 
                                       233433355699999****************************************33221.......222211111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2364  (0.131853); expected 358.6 (0.02)
Passed bias filter:                     1227  (0.0684366); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 645.86
//
Query:       gi|385805585|ref|YP_005841983.1|  [L=477]
Description: anion transporter [Fervidicoccus fontis Kam940]
Scores for complete 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-148  495.8  39.5   1.8e-148  495.5  39.5    1.0  1  Na_sulph_symp  Sodium:sulfate symporter transmembrane region
    1.5e-17   63.8  64.3    1.4e-13   50.7  32.8    2.5  2  CitMHS         Citrate transporter


Domain annotation for each model (and alignments):
>> Na_sulph_symp  Sodium:sulfate symporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  495.5  39.5    2e-152  1.8e-148       3     466 ..       9     472 ..       7     476 .. 0.98

  Alignments for each domain:
  == domain 1  score: 495.5 bits;  conditional E-value: 2e-152
                     Na_sulph_symp   3 klaklllllvvlliilllPapdgleskawrllaifiaaivglileplplavialialsllavligvla..akalsev 77 
                                       kl+k ++++++ +ii+++P+p+ l+s+aw+++a f+++i   ilep+p a+i+li++ + +v   v +  + ++s+ 
  gi|385805585|ref|YP_005841983.1|   9 KLLKAIIPIIIGIIIAIIPHPSALTSNAWYYFALFATVIAATILEPMPIAAISLIGVVVAVVARLVYSspSSSISWG 85 
                                       78899***************************************************9988776666656799***** PP

                     Na_sulph_symp  78 lsgfssdttlLvfaalliaaavektgLgkRiAlvlvkivGkrtliLgyalvladlllapatpsntAraggivfpvik 154
                                       l gfs+++++L+faa+l+a ++ ktgLg+RiAl+++k +Gk++l+Lgya+ l+dl+lap++psntAr+gg++fp+++
  gi|385805585|ref|YP_005841983.1|  86 LTGFSNSIVWLIFAAYLFALGYSKTGLGRRIALIFIKYLGKKPLGLGYAIALSDLVLAPFMPSNTARSGGTIFPIVS 162
                                       ***************************************************************************** PP

                     Na_sulph_symp 155 slssafgsepekqserkigaylmltvvqsasitsiaflTamApNllllglinsilgveitwasWflaaiptgvilll 231
                                       ++++ +gs+p +++e+kig+ylm+t++ +++its++flT+ ApN+l+++l++  +g++ +w+ Wf+ + p+g+ l++
  gi|385805585|ref|YP_005841983.1| 163 NIPPMYGSSPREGTEKKIGSYLMWTAFAATCITSSMFLTGLAPNVLVQSLAA-KQGIQFSWITWFIGFAPVGIFLFI 238
                                       **************************************************99.68********************** PP

                     Na_sulph_symp 232 lvplllyvlyppeikkkeeakavaktelkelGpltarekallilfvlllllWifgeslnidattvaivvlvillllr 308
                                       ++p+l++++yppeik+++ea ++a++el+++G ++ re a li ++l+l+lWi g+++ idat+va++v+++ ll++
  gi|385805585|ref|YP_005841983.1| 239 ITPYLIFKIYPPEIKESPEAPKWAQEELNKMGKIKGREIAFLIEVILALVLWIVGSNY-IDATAVALLVVALSLLSN 314
                                       **********************************************************.****************** PP

                     Na_sulph_symp 309 vldWkDivkqktaWntllllgglialakllersgliewlgnklttslsglspavaiiiilslfvlvhylfaSatAtt 385
                                       v +WkD++ +++aWntl+++++l +la +l+r+g+++++g+ ++ts   +sp++a+i+i+slf+ +hy+faS tA+ 
  gi|385805585|ref|YP_005841983.1| 315 VYSWKDVLTYESAWNTLVWFATLFTLADGLSRVGFVSYVGKEIATSIGWMSPTIALIVIVSLFYWLHYMFASLTAHA 391
                                       ***************************************************************************** PP

                     Na_sulph_symp 386 aallpillavaqaipgappllvalllalatslagfllpyatgpnpivfgagylkvkdywrlGfilsiigllillllg 462
                                       +al pi+la a +i+g++p+++a +l  + +++g++ pyatgp+p+++g+gy+k +d+w+lG+i++ii+++i++ +g
  gi|385805585|ref|YP_005841983.1| 392 TALFPIFLATAMGISGMNPVVAAYALSYTLGIMGIISPYATGPAPVYYGSGYIKGNDFWKLGLIFGIIYYVIFIAIG 468
                                       ***************************************************************************** PP

                     Na_sulph_symp 463 alww 466
                                       + w 
  gi|385805585|ref|YP_005841983.1| 469 MPWL 472
                                       9974 PP

>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.7  32.8   1.6e-17   1.4e-13       2     281 ..      48     401 ..      47     403 .. 0.72
   2 !   27.1  23.5   2.4e-10   2.2e-06       2     168 ..     288     474 ..     285     477 .] 0.81

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 1.6e-17
                                       xxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS   2 vllileklrldvvallvlvll..........vltieealsgiaspiillllgamiigaaleetGlfdrlaakllrla 68 
                                       ++ ile +++++++l+++v++            +i   l+g++++i++l+++a +++ + ++tGl +r+a  +++  
  gi|385805585|ref|YP_005841983.1|  48 AATILEPMPIAAISLIGVVVAvvarlvysspSSSISWGLTGFSNSIVWLIFAAYLFALGYSKTGLGRRIALIFIKYL 124
                                       6779999999999999999999999975555555555**************************************** PP

                                       xxxxx.xxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxx RF
                            CitMHS  69 ggkrd.llvllvlltallsafvsndgv..vlimipivlslakrlkklppl.........lliplalaaniggaltpi 133
                                       g+k+  l  +++l   +l++f+  +++     + piv ++     +++p+         +l+  a+aa      +++
  gi|385805585|ref|YP_005841983.1| 125 GKKPLgLGYAIALSDLVLAPFMPSNTArsGGTIFPIVSNIPPM-YGSSPRegtekkigsYLMWTAFAATCIT-SSMF 199
                                       **********************998888*77777777777774.4444444777789**99*9***999875.6666 PP

                                       xxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................. RF
                            CitMHS 134 Gtpttraa...........arpglslpnllllalllvgllplvllfmfgvalalpvnap.................. 181
                                        t +++ +           +  + +++ + +++ ++ ++++ +l+f        p+++                   
  gi|385805585|ref|YP_005841983.1| 200 LTGLAPNVlvqslaakqgiQFSWITWFIGFAPVGIFLFIITPYLIF-----KIYPPEIKespeapkwaqeelnkmgk 271
                                       6665555566787777665555555666666888999999999999.....44444444777777877775443333 PP

                                       .xxxxxxxxxxxxxxxxxxxxxxxxxx................................xxxxxxxxxxxxxxxxxx RF
                            CitMHS 182 .kvkkqkaiieaiarsllpvatillla................................ykkveWsvlllfaGvfll 225
                                        k         +   +l++v+++l+l+                                  +  W++l++fa +f+l
  gi|385805585|ref|YP_005841983.1| 272 iK--------GREIAFLIEVILALVLWivgsnyidatavallvvalsllsnvyswkdvlTYESAWNTLVWFATLFTL 340
                                       32........22223333344444444445555555555555667888899999999999999************** PP

                                       xxxxxxxx....xxxxxxxxxxx...x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 226 vgaleqtG....ilealadllga...g.gplvalalvlgliallsafisnvavaalmapialgm 281
                                       +++l+++G    +++ +a+++g    +  ++v+++l+++l  ++ +++  +   + ++pi l++
  gi|385805585|ref|YP_005841983.1| 341 ADGLSRVGfvsyVGKEIATSIGWmspTiALIVIVSLFYWLHYMFASLTAHA---TALFPIFLAT 401
                                       ********8888777777777554322344444466677766644444444...3347777665 PP

  == domain 2  score: 27.1 bits;  conditional E-value: 2.4e-10
                                       xxxxxxx..xxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                            CitMHS   2 vllilek..lrldvvallvlvll..........vltieealsgiaspiillllgamiigaaleetGlfdrlaakll. 65 
                                       vl+i++   ++ ++vallv++l           vlt e      a+++++ ++ +++++ +l+++G++ ++++ ++ 
  gi|385805585|ref|YP_005841983.1| 288 VLWIVGSnyIDATAVALLVVALSllsnvyswkdVLTYE-----SAWNTLVWFATLFTLADGLSRVGFVSYVGKEIAt 359
                                       55555557999999999888888999955555555555.....5***************************999997 PP

                                       ...xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS  66 ...rlaggkrd.llvllvlltallsafvsndgvvlimipivlslakrlkklppl.lliplalaaniggaltpiGtpt 137
                                          +++ +    l+v+++l+  l  +f+s+++ +  + pi+l+ a  +++++p+ ++ +l++  +i+g+++p  t +
  gi|385805585|ref|YP_005841983.1| 360 sigWMSPT--IaLIVIVSLFYWLHYMFASLTAHATALFPIFLATAMGISGMNPVvAAYALSYTLGIMGIISPYATGP 434
                                       65333333..46889999999999999999999777777777666665555555599*******************8 PP

                                       xxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 138 traa.........arpglslpnllllalllvgllplvllf 168
                                       +++          +  +l l+++++  ++++++ + +llf
  gi|385805585|ref|YP_005841983.1| 435 APVYygsgyikgnDFWKLGLIFGIIYYVIFIAIGMPWLLF 474
                                       8888*****9998888888999999999999999999888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       988  (0.0551063); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); 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):               2  [number of targets reported over threshold]
# CPU time: 0.72u 0.35s 00:00:01.06 Elapsed: 00:00:00.56
# Mc/sec: 2563.29
//
Query:       gi|385805586|ref|YP_005841984.1|  [L=208]
Description: L(+)-tartrate dehydratase subunit beta [Fervidicoccus fontis Kam940]
Scores for complete 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  150.2   0.0    5.7e-44  149.9   0.0    1.0  1  Fumerase_C  Fumarase C-terminus


Domain annotation for each model (and alignments):
>> Fumerase_C  Fumarase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.9   0.0   3.2e-48   5.7e-44      32     202 ..       9     179 ..       2     183 .. 0.92

  Alignments for each domain:
  == domain 1  score: 149.9 bits;  conditional E-value: 3.2e-48
                        Fumerase_C  32 Lnq.keteeelskykvgtrlllsGkllvaRDaaHkrlkerlekgeelpeyvklkdrviYyaGPv..ktpedeavgsa 105
                                       +++  + +++l+++++g+++ lsG l++aRDa+Hkr+      ge+lp  ++lkd +i +aGPv  k  e++++ s+
  gi|385805586|ref|YP_005841984.1|   9 IKTpVIDSSQLEELRIGDMFYLSGILVTARDAVHKRFL---IDGESLP--IDLKDLAILHAGPVmkKVGEKWQCISI 80 
                                       5553344679**************************97...78*****..9999**********866678899**** PP

                        Fumerase_C 106 GPTTatRmdkyvekllkktgllimlaKgnrskkvleaikkhggvYLgaiGGaAilakkaikkvevvefeelGm.EAi 181
                                       GPTT+ Rm+ y +++++ktg+ i+++Kg+++kk+ +a+ kh+++Y +  GG  +l ++ +++v  v++e+lGm EA+
  gi|385805586|ref|YP_005841984.1|  81 GPTTSRRMEYYEDEFIEKTGVKIIIGKGGMGKKTADACSKHKAIYAIFPGGCGVLGASEVEEVIDVKWEDLGMpEAL 157
                                       ***************************************************************************** PP

                        Fumerase_C 182 yeievedf.pafvvvddkGndl 202
                                       + ++v++f p +v +d++Gn+l
  gi|385805586|ref|YP_005841984.1| 158 WILKVKEFgPLIVSIDTRGNNL 179
                                       ********788999******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 1164.31
//
Query:       gi|385805587|ref|YP_005841985.1|  [L=302]
Description: tartrate dehydratase subunit alpha [Fervidicoccus fontis Kam940]
Scores for complete 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-77  259.3   0.0    4.3e-77  259.2   0.0    1.0  1  Fumerase  Fumarate hydratase (Fumerase)
  ------ inclusion threshold ------
      0.073   13.0   0.0       0.17   11.9   0.0    1.6  1  RHH_1     Ribbon-helix-helix protein, copG family


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 !  259.2   0.0   4.8e-81   4.3e-77       7     267 ..      17     280 ..      11     283 .. 0.96

  Alignments for each domain:
  == domain 1  score: 259.2 bits;  conditional E-value: 4.8e-81
                          Fumerase   7 alkeastelpedvlealkkalekEesenakevleqlleNaeiAaeeklplCqDTGiavvfvkigeevevetgdleea 83 
                                       +++ ++++l++dv e+l++++ekE+s+++k v+e++ +N ++A e+k plCqDTG+  +fvk+ge++   ++ l +a
  gi|385805587|ref|YP_005841985.1|  17 FINVVAIKLSDDVNEKLNELIEKEQSDVGKLVYEAVKKNLSLALERKAPLCQDTGVLEFFVKFGENFP-YKSMLLKA 92 
                                       6777899************************************************************5.88888888 PP

                          Fumerase  84 ineGvreaykegplRksvvadplerkntgd....nlPavihielvpg.deleitvlakGgGsenksklkmlnpsdgl 155
                                       i+eG+   +k+g lR++vv dp ++kn+gd    ++P +i+ie+ ++ d+ ++++++ GgG++   ++++l p++g+
  gi|385805587|ref|YP_005841985.1|  93 IREGTVISTKNGFLRPNVV-DPSTEKNSGDntgpKIP-WIEIEIEENsDYADVQLYLAGGGASRPGSARTLDPAEGW 167
                                       *******************.**********8888899.*******97799*************************** PP

                          Fumerase 156 egvkkfvletvkeagtnaCpPlv.lgvgiGgtseeaallakkallrelgeenpdeelaeleeellekinklgiGpqG 231
                                       +g+ k+v++ v+++g+ aCpPl+ +gvgiG tse aa+l+kkallr++ge+n ++++a++ee l e++n+lg+GpqG
  gi|385805587|ref|YP_005841985.1| 168 SGIAKYVIDVVSSYGPPACPPLMvVGVGIGATSEIAAMLSKKALLRKMGERNINPKIAKFEEFLEEELNNLGFGPQG 244
                                       *********************7538**************************************************** PP

                          Fumerase 232 lGGkttvldvkierlprhiAslpvavnvsCsadRra 267
                                       lGGkt + +v++e++ rh+A+l v+v++sC+a R+ 
  gi|385805587|ref|YP_005841985.1| 245 LGGKTSIGEVHVEYAGRHPATLAVGVSTSCWALRKG 280
                                       **********************************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 ?   11.9   0.0   1.9e-05      0.17       2      34 ..      21      53 ..      20      56 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.9e-05
                                      EEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHH CS
                             RHH_1  2 vsirldeellerLdelarrrgrSrSelIReAlr 34
                                      v i+l++++ e+L+el++++++ ++ l+ eA++
  gi|385805587|ref|YP_005841985.1| 21 VAIKLSDDVNEKLNELIEKEQSDVGKLVYEAVK 53
                                      569********************9999988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2149.60
//
Query:       gi|385805588|ref|YP_005841986.1|  [L=441]
Description: Malate dehydrogenase (oxaloacetate-decarboxylating) [Fervidicoccus fontis Kam940]
Scores for complete 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-28   99.1   0.1    2.3e-25   89.5   0.1    2.8  1  malic     Malic enzyme, N-terminal domain
    5.1e-20   71.8   0.2    1.1e-18   67.5   0.2    2.2  1  Malic_M   Malic enzyme, NAD binding 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 !   89.5   0.1   2.5e-29   2.3e-25       2     182 .]      22     154 ..      21     154 .. 0.97

  Alignments for each domain:
  == domain 1  score: 89.5 bits;  conditional E-value: 2.5e-29
                                       TTECCCCCCHHCCCHHHHHHHHSTTCHHHHHHHHHHHGGCHHSCCCEGGGETCHHHHHTTSS.SS..EEEEE-SSSB CS
                             malic   2 eknetlfykllkekleellpivYtPtvgeacqeyseeyrkarglylsikdkekikeilknlpeedvkvivvtdgeri 78 
                                       +k+e+l++ ++++   ++++i+YtP+v+e+c++++++ +  + +y+ + +                 ++v++dg+r+
  gi|385805588|ref|YP_005841986.1|  22 GKIEVLPKVPITSL--DDFSIWYTPGVAEPCKRINKDEDLSY-EYTLRWNY----------------AAVISDGTRV 79 
                                       68999999999999..9*************************.*******9................9********* PP

                                       TTTBS-G.HHHHHHHHHHHHHHHHHHS-EGGGEEEEEECS-BS.HHHHC.TT..S.SSB...SHHHHHHHHHHHHHH CS
                             malic  79 LGlGdlG.vagvgimvGKlaLytalagidPekvlpvvldvgtnneelledplYlGlrkkRvkgeeydefvdefveav 154
                                       LGlG++G  ag+++m+GK  L++ l+g+d   ++p+vl  +                           + ++f+++v
  gi|385805588|ref|YP_005841986.1|  80 LGLGNIGpSAGLPVMEGKSLLFKYLGGVD---AIPLVLGER---------------------------DPEKFIAVV 126
                                       *****************************...******999...........................89******* PP

                                       HHHHGCTSEEEE-S--CCHHHHHHHHHC CS
                             malic 155 kelfppkaliqfEDfkaknafeileryr 182
                                       k+l+p+++ i++ED++++++f+iler++
  gi|385805588|ref|YP_005841986.1| 127 KALEPTFGAINLEDIESPKCFYILERLQ 154
                                       *************************985 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 !   67.5   0.2   1.2e-22   1.1e-18       2     253 ..     167     393 ..     166     398 .. 0.82

  Alignments for each domain:
  == domain 1  score: 67.5 bits;  conditional E-value: 1.2e-22
                                       HHHHHHHHHHHHHHHHHH-S-GGG--EEEEC-SHHHHHHHHHHHHHHHTTTS-HHHHHTTEEEEETTEE-BTT-S-- CS
                           Malic_M   2 qgTaavalagllaalkitgkklseqkivvlGaGsagiGiaeqivealvkeGlseeeakkkiylvDrkGLltedrekl 78 
                                       qgTa v l++l++alk+tg++++++kiv++G G+a +       + l+ +G+      k+i  vD++G+++ +r+++
  gi|385805588|ref|YP_005841986.1| 167 QGTALVILSALINALKLTGRRIKDTKIVLVGIGAANMAT----YRYLKVAGA----NPKNIIAVDKNGIVHPERDDI 235
                                       9******************************99998754....445555664....4589***************** PP

                                       ..-TTTGGGSBS--SS--S....SHHHHHHHH--SEEEE-SSS.SS-S-HHHHHHHHHHSSS-EEEE--SSGGGSSS CS
                           Malic_M  79 ..eeekkpfakkkeelkeakdkltLeevvkkvkptvliGlsgv.agafteeivremaksterPiilplSNPtskaEa 152
                                         e+ ++p+  k +e ++ + +  + e+++   ++v+i +s+  +g++++e v +m k     i+++  NP    E 
  gi|385805588|ref|YP_005841986.1| 236 krEKDRNPWLFKVAEETSPEIRGGIPEAMNG--ADVVIAASAPgPGTIKKEWVSKMNK---DAIVFAEANPIP--EI 305
                                       4334456777776666656566778888775..6899999985379*******99976...56********86..66 PP

                                       -HHHHHHHTTT-SEEEESS----EEETSEEE--EE--GGGTHHHHHHHHHHTT-SS--HHHHHHHHHHHHTT--HHH CS
                           Malic_M 153 taedvlkwtdgkalvasGsPfkpvelngktyeigQaNNayifPglglgvivarakritdemllaaaealaelvseee 229
                                        + ++ +   g+ +va+G          +   ++Q NN++ fP++  gv+ ++ak+++d+m+laaa a+a++++++ 
  gi|385805588|ref|YP_005841986.1| 306 WPWEAKE--TGAKIVATG----------RSDFPNQVNNSLGFPAVFRGVLSVGAKKMNDDMFLAAAYAIADYTEKTG 370
                                       7777765..578899997..........556799******************************************* PP

                                       HHTT-SS--GGGHHHHHHHHHHHH CS
                           Malic_M 230 lkegsllPelseirevslkvavav 253
                                       l+++++  +++e++   ++ a+av
  gi|385805588|ref|YP_005841986.1| 371 LSKDRIIASMDEMEL-YVQEALAV 393
                                       ******999998753.33444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2857.22
//
Query:       gi|385805589|ref|YP_005841987.1|  [L=51]
Description: hypothetical protein FFONT_0545 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); 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:                         0  (0); expected 0.2 (1e-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 0.31s 00:00:00.83 Elapsed: 00:00:00.54
# Mc/sec: 284.27
//
Query:       gi|385805590|ref|YP_005841988.1|  [L=111]
Description: hypothetical protein FFONT_0546 [Fervidicoccus fontis Kam940]
Scores for complete 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   56.4   0.1    3.5e-15   56.3   0.1    1.1  1  DUF134        Protein of unknown function  DUF134
     0.0053   16.9   0.0     0.0072   16.5   0.0    1.4  1  DUF1492       Protein of unknown function (DUF1492)
  ------ inclusion threshold ------
      0.033   13.9   0.0      0.086   12.5   0.0    1.7  1  Sigma70_r4_2  Sigma-70, region 4
      0.044   13.6   0.0       0.19   11.6   0.0    1.8  2  HTH_23        Homeodomain-like domain


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 !   56.3   0.1   7.9e-19   3.5e-15       6      90 ..      12     102 ..       1     110 [. 0.74

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 7.9e-19
                            DUF134   6 rprklrdileePkv..rifkPea....veetgkvaisldeleairlvdyedlkqeeaaklmGiskatlwrllteark 76 
                                       r+r + di  + k+   +f P       +e + v+i   elea++l+  ++l+ +ea+ +mGiskat+wr+l+++r 
  gi|385805590|ref|YP_005841988.1|  12 RGRPPIDIRSSMKIeeITFLPIKevkgLSEENAVEIYDYELEALKLIHIDNLTTDEASLKMGISKATFWRVLEDCRF 88 
                                       4555556665544411355564321113334459***9*************************************** PP

                            DUF134  77 kiakalveGraiil 90 
                                       kia al+e ++i +
  gi|385805590|ref|YP_005841988.1|  89 KIAMALLEQKPIKI 102
                                       **********7644 PP

>> DUF1492  Protein of unknown function (DUF1492)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.6e-06    0.0072      62      94 ..      53      85 ..      18      91 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.6e-06
                           DUF1492 62 svLrmvyidkltvwqvidklnisrstyyrllrv 94
                                        L++++id+lt+++   k++is++t++r+l+ 
  gi|385805590|ref|YP_005841988.1| 53 EALKLIHIDNLTTDEASLKMGISKATFWRVLED 85
                                      4599*************************9865 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.9e-05     0.086      17      42 ..      53      78 ..      51      82 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.9e-05
                                      HHHHHHHTS---HHHHHHHHT--HHH CS
                      Sigma70_r4_2 17 eifllryleglsykEIAellgisegt 42
                                      e++ l+++++l+++E++ ++gis +t
  gi|385805590|ref|YP_005841988.1| 53 EALKLIHIDNLTTDEASLKMGISKAT 78
                                      7999*******************998 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   4.3e-05      0.19       8      40 ..      52      85 ..      51      87 .. 0.88
   2 ?   -0.0   0.0      0.18   8.2e+02       6      25 ..      86     105 ..      83     107 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.3e-05
                            HTH_23  8 lrillllae.GlsvreIAreLgvsrrTvyrwlkr 40
                                      l++l+l     l++ e++ ++g+s+ T +r+l+ 
  gi|385805590|ref|YP_005841988.1| 52 LEALKLIHIdNLTTDEASLKMGISKATFWRVLED 85
                                      57888888669*******************9976 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.18
                            HTH_23   6 eRlrillllaeGlsvreIAr 25 
                                        R++i+ +l+e ++++ +++
  gi|385805590|ref|YP_005841988.1|  86 CRFKIAMALLEQKPIKIVSK 105
                                       69999999999999987776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.33s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 638.61
//
Query:       gi|385805591|ref|YP_005841989.1|  [L=83]
Description: hypothetical protein FFONT_0547 [Fervidicoccus fontis Kam940]
Scores for complete 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-09   37.5   0.0    4.5e-09   37.3   0.0    1.2  1  DUF5320   Family of unknown function (DUF5320)


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 !   37.3   0.0   2.5e-13   4.5e-09      41      98 ..      24      79 ..       1      80 [. 0.71

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 2.5e-13
                           DUF5320 41 rggrglgrgfgrrrraggarlaaaetaeaskeeekelLeeqaeaLeeeleaikkrlke 98
                                      r g+ +grg+++++++ +a +  +  ++ skeee+++Leeq+++Le++l++i++rlk 
  gi|385805591|ref|YP_005841989.1| 24 RPGWKYGRGWCWQGYGRVAWP--YSESPLSKEEEIRYLEEQKKYLEDSLKEIDERLKV 79
                                      236677888888555544444..489999***************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       902  (0.0503096); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); 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: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 517.13
//
Query:       gi|385805592|ref|YP_005841990.1|  [L=216]
Description: Class II aldolase/adducin, N-terminal [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-48  164.6   0.2    2.6e-48  164.4   0.2    1.0  1  Aldolase_II   Class II Aldolase and Adducin N-terminal domain
  ------ inclusion threshold ------
       0.11   10.8   0.0       0.35    9.1   0.0    1.7  2  Silic_transp  Silicon transporter


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 !  164.4   0.2   2.9e-52   2.6e-48       2     185 ..       8     183 ..       7     184 .. 0.95

  Alignments for each domain:
  == domain 1  score: 164.4 bits;  conditional E-value: 2.9e-52
                                       HHHHHHHHHHHTTSSCTTBCEEEEEETSTTEEEEEBTSS-GGGHTGGGEEEEETTSCEEEECECSSSTB-TTHHHHH CS
                       Aldolase_II   2 elaeasrllarrglvegtgGniSvrvpeedsflitpsgvdfeeltaedlvvvdldsgevvegkekggkpssetplHl 78 
                                       +++e+++ + ++ l+ g +Gn+S+r ++++++litp+gv ++ l ++d++vvdl  g+ +eg   ++kps+e+plHl
  gi|385805592|ref|YP_005841990.1|   8 KVVEVMKFMEQHELNYGRSGNVSIRIQDTGHILITPTGVKKSALAEDDIAVVDLS-GKTIEG---KRKPSVEMPLHL 80 
                                       7899*********************87799************************8.****66...579********* PP

                                       HHHHH-TT-SEEEEE--HHHHHHHTCCSTSCHCCSSHHHHC.HSSSEEEEES-SSTTCHHHHHHHHHHHHHS-SEEE CS
                       Aldolase_II  79 aiykarpdaravvHtHspaavalsalagkeglppltqeaaklllgdevpvipyaapgteelgealaealkedakavl 155
                                       aiyk+   ++av+H+H  + +al+ +a +e+lppl +e+  l+ g++v v++ya+ gt+el+e++++al+ ++kavl
  gi|385805592|ref|YP_005841990.1|  81 AIYKNYDYINAVIHAHGIYSTALA-VA-REPLPPLVEEMVSLT-GGDVKVAEYAPSGTDELAENAVKALH-ERKAVL 153
                                       ************************.65.799**********66.666**********************6.99**** PP

                                       ETTTEEEEEESSHHHHHHHHHHHHHHHHHH CS
                       Aldolase_II 156 lrnHGlltvGetleeAvalaetleeaaeiq 185
                                       l+nHG++++Get++eA++ ++ +e+  +++
  gi|385805592|ref|YP_005841990.1| 154 LANHGIVACGETIDEALEILVLVERISKVY 183
                                       *************************99988 PP

>> Silic_transp  Silicon transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0     0.052   4.7e+02     183     219 ..      40      77 ..      37     110 .. 0.63
   2 ?    9.1   0.0   3.9e-05      0.35     106     159 ..     151     204 ..     139     209 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.052
                      Silic_transp 183 vieasGvmhasyliqni.lalvaGkpvktneeprsalq 219
                                       +i  +Gv++++    +i +  ++Gk ++ + +p  ++ 
  gi|385805592|ref|YP_005841990.1|  40 LITPTGVKKSALAEDDIaVVDLSGKTIEGKRKPSVEMP 77 
                                       56678888877776666245688999888888876653 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 3.9e-05
                      Silic_transp 106 mvllivfvinlcgapledavevlglpeiikeifldsGiamillvviigqltaqv 159
                                        vll +  i  cg  +++a+e+l l e i ++++ s +a +  v     l  qv
  gi|385805592|ref|YP_005841990.1| 151 AVLLANHGIVACGETIDEALEILVLVERISKVYILSKVAGVPKVLPFESLEKQV 204
                                       5999**********************************9999988888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1313.11
//
Query:       gi|385805593|ref|YP_005841991.1|  [L=472]
Description: peptidase, family S54 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-38  132.0  18.4    1.7e-38  132.0  18.4    2.0  3  Rhomboid  Rhomboid family
    0.00066   20.2   0.3    0.00066   20.2   0.3    3.4  4  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 ?   -3.9   0.0       1.4   1.3e+04     107     121 ..      43      57 ..      26      62 .. 0.51
   2 !  132.0  18.4   1.9e-42   1.7e-38       7     147 ..      89     242 ..      84     245 .. 0.96
   3 ?   -2.5   0.1      0.51   4.6e+03      43      60 ..     274     291 ..     258     305 .. 0.54

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 1.4
                                       CCCCCCCCCCHHHCT CS
                          Rhomboid 107 lllfillnlvlgllp 121
                                        + +il+n+++ +++
  gi|385805593|ref|YP_005841991.1|  43 TYSLILINIIVYVYT 57 
                                       333444444444444 PP

  == domain 2  score: 132.0 bits;  conditional E-value: 1.9e-42
                                       TTHHHHGGG--SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-S........-EESSHHH CS
                          Rhomboid   7 lwrlltsmflHagwlHllfNmlallvfGsplerrlGslrflllyllsglagsllsllfsaeses.....plvGaSGa 78 
                                       + r++tsmf Ha+++H++fNm++l++fG ++e+ +G++rfl+lyllsg+a+s+++++f + +++     p++GaSGa
  gi|385805593|ref|YP_005841991.1|  89 VLRIFTSMFTHANIFHIFFNMYFLWIFGRSVENAIGHKRFLILYLLSGIAASIFYFAFIPIGGYdslviPAIGASGA 165
                                       789**********************************************************9999************ PP

                                       HHHHHHHHHHHHHCCCCGS----HC............CCCCCCCCCCHHHCTSSSTTTHHHHHHHHHHHHHHHHHHC CS
                          Rhomboid  79 ifgllgallvlvprnrkllrkliia.........llllllfillnlvlgllpraggvsnlAHlgGllaGlllgllll 146
                                       i+g+lga+l+l+p+++ ++  ++i+         +++l+++++ ++++g+l+  ggv+++AH+gG+++G++l+++++
  gi|385805593|ref|YP_005841991.1| 166 ISGILGAYLLLFPNTKLMFCLFFIFipicipvssIIFLIIWFSEQVIYGFLEL-GGVAYFAHVGGFITGIFLSYVFF 241
                                       ****************99888888899******99*****************9.5********************99 PP

                                       C CS
                          Rhomboid 147 r 147
                                       +
  gi|385805593|ref|YP_005841991.1| 242 K 242
                                       7 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.51
                                       HHHHHHHHHHHHHHHHHH CS
                          Rhomboid  43 slrflllyllsglagsll 60 
                                       ++   +l++l  l+  ++
  gi|385805593|ref|YP_005841991.1| 274 KWTKYFLTFLFILILLAF 291
                                       333333333333332222 PP

>> DUF1751  Eukaryotic integral membrane protein (DUF1751)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.3         1   9.3e+03      57      69 ..      48      60 ..      40      74 .. 0.49
   2 !   20.2   0.3   7.4e-08   0.00066       9      94 ..      90     170 ..      83     174 .. 0.77
   3 ?   -1.7   1.8      0.48   4.3e+03      49      86 ..     183     221 ..     180     235 .. 0.56
   4 ?   -2.6   0.4      0.97   8.7e+03      50      76 ..     278     304 ..     275     320 .. 0.51

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1
                           DUF1751 57 itnllvvlltlll 69
                                      + n++v+++t   
  gi|385805593|ref|YP_005841991.1| 48 LINIIVYVYTSYN 60
                                      3334444333333 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 7.4e-08
                           DUF1751   9 wtlltasfveqnvwkvlvslltlllggkylErlWgskEllkFilvvnvitnllvvlltlllylvtkseelllvpisG 85 
                                         ++t++f  +n++++ +++  l+++g+ +E++ g+k +l+  l+     ++ + ++++++  +   ++ l++p  G
  gi|385805593|ref|YP_005841991.1|  90 LRIFTSMFTHANIFHIFFNMYFLWIFGRSVENAIGHKRFLILYLLS----GIAASIFYFAFIPIGGYDS-LVIPAIG 161
                                       679********************************99877666555....5555566666666666666.6666666 PP

                           DUF1751  86 lagilagfl 94 
                                       + g  +g+l
  gi|385805593|ref|YP_005841991.1| 162 ASGAISGIL 170
                                       666666665 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.48
                           DUF1751  49 kFilvvnvitnllvvlltlllylvtkseelll..vpisGl 86 
                                        F+l+  +i+  + v   ++l + +++++ ++  +++ G 
  gi|385805593|ref|YP_005841991.1| 183 MFCLFFIFIPICIPVSSIIFLIIWFSEQV-IYgfLELGGV 221
                                       57777777775555555554444444444.3324666664 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 0.97
                           DUF1751  50 Filvvnvitnllvvlltlllylvtkse 76 
                                       ++l   +i  ll++   ++ +++t+ +
  gi|385805593|ref|YP_005841991.1| 278 YFLTFLFILILLAFSSGTAEVYATNTN 304
                                       555555555555555555544444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       771  (0.043003); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); 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: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.49
# Mc/sec: 2897.99
//
Query:       gi|385805594|ref|YP_005841992.1|  [L=248]
Description: Threonyl/alanyl tRNA synthetase, SAD [Fervidicoccus fontis Kam940]
Scores for complete 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-12   46.1   0.2    6.2e-12   45.4   0.2    1.4  1  tRNA_SAD      Threonyl and Alanyl tRNA synthetase second addi
    3.5e-10   39.0   0.0    5.2e-10   38.5   0.0    1.3  1  tRNA-synt_2c  tRNA synthetases class II (A)


Domain annotation for each model (and alignments):
>> tRNA_SAD  Threonyl and Alanyl tRNA synthetase second additional domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   0.2   6.9e-16   6.2e-12       1      44 []     201     244 ..     201     244 .. 0.93

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 6.9e-16
                                       EEEEEETT.EEEEESS---SBGGGC-SEEEECCECCCTCEEEEE CS
                          tRNA_SAD   1 vrvvsiGdisvelCgGtHvpnTgeIgafkilseesiakglrRIy 44 
                                       +r+v+i  +++++ gG+Hv+nTgeIg+++i++ e+++k+  R y
  gi|385805594|ref|YP_005841992.1| 201 LRIVEIPGVDIQADGGPHVKNTGEIGEIVITKIENKGKNRKRMY 244
                                       69****558*****************************999976 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 !   38.5   0.0   5.8e-14   5.2e-10     461     552 .]      11     104 ..       1     104 [. 0.83

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 5.8e-14
                                       XXXXTSXXXXXXSEEEEE.EEEEETTEEEESEEXXXXSSSSCSXXXEEEEESSEEEEESEEEEET..TEEEEEXSS. CS
                      tRNA-synt_2c 461 eaeakvlallkdkefvee.veegeevgvvLdrTpfYaesGGqigDeGliekegaefrvkdvqkak..gvvlhkgkle 534
                                       +++ ++++l +  ++ ++ + +++++ ++Ld+T f +  GG ++D+G++e +g + +v +v ++k  + vlh+ ++ 
  gi|385805594|ref|YP_005841992.1|  11 NMTEHIYQLDSYLKEYDSiIVSIKDNSIILDKTIFHPRAGGLESDTGFLEVNGRRYKVLNVLQEKdsEDVLHQLDTV 87 
                                       66777888877655555516689999**********************************98877678899*99997 PP

                                       XSXXXTTSEEEEEEXHHH CS
                      tRNA-synt_2c 535 egklkvgdkvkaevdeer 552
                                        + l+ gd+v++++d+er
  gi|385805594|ref|YP_005841992.1|  88 -DGLNPGDRVHLALDWER 104
                                       .89************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1584.61
//
Query:       gi|385805595|ref|YP_005841993.1|  [L=311]
Description: 2-oxoacid:ferredoxin oxidoreductase subunit beta [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-29  102.7   0.1    2.4e-29  102.1   0.1    1.3  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    3.9e-21   74.9   0.2    7.8e-21   74.0   0.2    1.5  1  PFO_beta_C    Pyruvate ferredoxin oxidoreductase beta subunit


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.1   0.1   2.7e-33   2.4e-29       3     153 .]      50     196 ..      48     196 .. 0.94

  Alignments for each domain:
  == domain 1  score: 102.1 bits;  conditional E-value: 2.7e-33
                                       SHHHHHHHHHHTTSSSSEEEC.ETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEEE CS
                      TPP_enzyme_C   3 Gcltlwaarllkvkrprsylt.sgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpitv 77 
                                       Gc+              +y++ +g+++ +G+++p+AiG+kl +pd +v++  GDG++l i   +++   rrnl++t+
  gi|385805595|ref|YP_005841993.1|  50 GCSAK----------IIHYINaNGVHSLHGRAIPFAIGIKLVRPDLTVIVNGGDGDLLGIgAGHFVALGRRNLQMTI 116
                                       55555..........568999899************************************99*************** PP

                                       EEEE-SBCCCHHHH...HHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEEE CS
                      TPP_enzyme_C  78 vvlnNegygmtggq...qepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkgpal 150
                                       ++++N++yg+t+gq   + p g k+k+   +++ +++++ +la + G + +ar    d e+l+e++k+a++++g++l
  gi|385805595|ref|YP_005841993.1| 117 ILHDNRVYGLTKGQaapTLPLGVKTKALAIPNIYTDINPIALAISSGYTfVARAYAFDSEHLKEIIKKAIMHRGVSL 193
                                       **************9988899999999988889****************9999999999****************** PP

                                       EEE CS
                      TPP_enzyme_C 151 iev 153
                                       ++v
  gi|385805595|ref|YP_005841993.1| 194 VDV 196
                                       *98 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 !   74.0   0.2   8.6e-25   7.8e-21       1      63 [.     200     271 ..     200     274 .. 0.96

  Alignments for each domain:
  == domain 1  score: 74.0 bits;  conditional E-value: 8.6e-25
                                       XTTTXSSSXSXXXXX-EEEGGGST---EE.........HHHHHHHHT-----EEEEEEEE.TTS--HHHHHHT CS
                        PFO_beta_C   1 CvtFNkvnTfdwYkervykleedgyDpsd.........lekAlekalewgdkiplGifYk.eekptyeerlee 63 
                                       CvtFN+++T d++k+++ykle++g+Dp +           +A++k++e ++kip+GifY+    ptyeerl++
  gi|385805595|ref|YP_005841993.1| 200 CVTFNDIHTADYFKKKIYKLEDEGWDPVVrdpkdieekALNAIRKSFE-EEKIPVGIFYEnSLLPTYEERLKN 271
                                       ***********************************999999*******.***********999*******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.23s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2111.57
//
Query:       gi|385805596|ref|YP_005841994.1|  [L=633]
Description: 2-oxoacid:ferredoxin oxidoreductase alpha subunit [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-56  191.2   0.0    3.1e-56  190.7   0.0    1.2  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    3.8e-27   95.5   0.0      9e-27   94.3   0.0    1.5  1  POR              Pyruvate ferredoxin/flavodoxin oxidoreductas
    1.1e-09   38.5   0.0    2.8e-09   37.2   0.0    1.7  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
     0.0041   17.0   0.0      0.017   15.0   0.0    1.9  2  Transketolase_C  Transketolase, C-terminal domain
  ------ inclusion threshold ------
      0.024   14.6   0.1       0.11   12.5   0.0    2.2  3  Lac_bphage_repr  Lactococcus bacteriophage repressor
      0.032   13.9   0.0      0.064   12.9   0.0    1.4  1  TPP_enzyme_N     Thiamine pyrophosphate enzyme, N-terminal TP


Domain annotation for each model (and alignments):
>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.7   0.0     1e-59   3.1e-56       3     231 .]     253     492 ..     251     492 .. 0.88

  Alignments for each domain:
  == domain 1  score: 190.7 bits;  conditional E-value: 1e-59
                                       HHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTT....EE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHC CS
                             POR_N   3 aiaagvdviaaYPITPsseiaeelaellakgev....gdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLm 75 
                                       +i +g ++ ++YPITP+ +    l++l+ +       g+  v+q+e+Ei+a+  +iGAa+aG+r+ T TSg+G+ Lm
  gi|385805596|ref|YP_005841994.1| 253 KIVGGERFESYYPITPAVDECLLLERLAYSKFQdnnlGNLLVLQTEDEIAAATSAIGAALAGVRSSTSTSGPGFDLM 329
                                       566777999*********955444444332222355689************************************** PP

                                       CCCHHHHHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHH.....S---EEEE-SSHHHHHHHHHHHHHHHHHCTS CS
                             POR_N  76 ienlglaageelPvvivvvaRalpstglsirtdqsDlmaar.....dtglivlasenvqeafdlalvAfnlAekvrv 147
                                        e++ +a+++e+P+vi+ ++Ra+pstg+++r+ q+Dl+ a+     ++  +vl+s+++ eaf +a++Afn+Aek+++
  gi|385805596|ref|YP_005841994.1| 330 AESISFAGMNEVPLVITFYQRAGPSTGMATRGGQGDLFTAIfsghgEFARVVLSSGDHTEAFYDAIEAFNIAEKYQL 406
                                       ***************************************************************************** PP

                                       EEEEEEEHHHH.HEEEEEEC-SGG....GS-----SBXXXXXXXX..SXXXBXXTXXTSSXXEEESBXBXTTSXBXX CS
                             POR_N 148 PvivlfDgfllshevekvelpdee...delklikekleeyerkey..aldpekpiargtaanpdtglehrekgneae 219
                                       Pvi+l+D+fl+ ++ + +++p+ e    e+ +i ++ ++y+r++    ++p+ +i      +++tg+eh+e g+++e
  gi|385805596|ref|YP_005841994.1| 407 PVIHLLDKFLA-NTLSVIPIPELEkvsIERGIIVNDTKNYKRFDLssLISPRAFI-GSNSVMWYTGDEHDEIGHISE 481
                                       ***********.*********9995222455777888888887767688888887.677889*************** PP

                                       XXHHHHHHHHHH CS
                             POR_N 220 daaekvveevek 231
                                       d  e++ +++ek
  gi|385805596|ref|YP_005841994.1| 482 D-PENRKKMYEK 492
                                       *.******9985 PP

>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.3   0.0     3e-30     9e-27       2     173 ..      14     215 ..      11     218 .. 0.95

  Alignments for each domain:
  == domain 1  score: 94.3 bits;  conditional E-value: 3e-30
                                       TSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEEE CS
                               POR   2 GqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglkp 78 
                                       G G+ t   ++ + + r+Gy v a rey s+i G+hsy+h+ri +++i  si+ ++++ll  ldaet++ h++++ +
  gi|385805596|ref|YP_005841994.1|  14 GGGIDTSMSVIVRGLGRSGYGVIAEREYFSNIAGRHSYAHIRIKSSEIPLSIR-YPVQLLASLDAETIFVHYKDVEE 89 
                                       99*******************************************97888888.*********************** PP

                                       EEEEEEECTCGTT-CCHHHCTS-HHHHHHH.......................T-EEEEE-HHHHHHHCCC...... CS
                               POR  79 ggiiiynseelkpdelkkakeeerelkerl.......................gvrvygvdatkiakeiggn..... 127
                                       ggi+iyn+++ +++  +   +ee  +++ +                       +++++ +++++i+++i+       
  gi|385805596|ref|YP_005841994.1|  90 GGILIYNKSDEEKKLSEIVSLEESIREKISkeleekgisdkvssllsflenerKIKLVSFNYNEILRRIAEMhklpl 166
                                       *********9999999999998877777779************************************9998899999 PP

                                       ...CCHHHHHHHHHHHHHHTS-HHHHHHHHHCCS-CH.HHHHHHHHHHH CS
                               POR 128 ...eraaNtvmlGalaallglplealeeaikkrfpkkkeviekNlkafr 173
                                          +r+++ +++Ga++ +l l l++l    + +f+++++ +++N++ ++
  gi|385805596|ref|YP_005841994.1| 167 symSRYLSSILVGAVWSVLELNLDDLMYSYSIQFKGRSDRVQHNIELVK 215
                                       9*************************************99****99876 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 !   37.2   0.0   9.3e-13   2.8e-09       2     102 .]     519     612 ..     519     612 .. 0.84

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 9.3e-13
                                       SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHHT CS
                           PFOR_II   2 evvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaal 78 
                                       ++++++ Gsv g   +a++el+ eg++  ++ +++l+PFP+ee+k++lk  + ++ +d  ++    + + + vk++ 
  gi|385805596|ref|YP_005841994.1| 519 DFLLLGWGSVKGASVEAIKELKSEGMNGAYINVKMLWPFPSEEVKKYLKISEDIIAIDYTYD----SLISKLVKMSS 591
                                       678999*****************************************************993....44555555543 PP

                                       GGGTSEEEEEE--GGG----HHHH CS
                           PFOR_II  79 kkskvkvvnfvaglgGrditvedi 102
                                           +++ + + + +Gr it++++
  gi|385805596|ref|YP_005841994.1| 592 ---GINIEKSIVKYNGRPITIDEV 612
                                       ...245777788888888888775 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.3     4e+03      27      44 ..     118     135 ..     115     138 .. 0.80
   2 !   15.0   0.0   5.5e-06     0.017       8      59 ..     516     567 ..     512     579 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.3
                                       HHHHHHTTTTCEEEEE-S CS
                   Transketolase_C  27 AaeeLekegisaeVvdlr 44 
                                       + +eLe++gis +V +l 
  gi|385805596|ref|YP_005841994.1| 118 ISKELEEKGISDKVSSLL 135
                                       6789******99887775 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 5.5e-06
                                       TTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHH CS
                   Transketolase_C   8 egkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvk 59 
                                       e+ d +l+++Gs    ++eA++eL++eg++   +++  ++p+  e +++ +k
  gi|385805596|ref|YP_005841994.1| 516 ENFDFLLLGWGSVKGASVEAIKELKSEGMNGAYINVKMLWPFPSEEVKKYLK 567
                                       67899**************************************999997766 PP

>> Lac_bphage_repr  Lactococcus bacteriophage repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.8   8.3e+03       3      13 ..     444     454 ..     443     467 .. 0.75
   2 ?   -3.8   0.0       4.4   1.3e+04      32      40 ..     559     567 ..     559     568 .. 0.84
   3 ?   12.5   0.0   3.7e-05      0.11      24      46 ..     600     623 ..     596     625 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.8
                   Lac_bphage_repr   3 tqepvDLaklv 13 
                                       + +++DL  l+
  gi|385805596|ref|YP_005841994.1| 444 NYKRFDLSSLI 454
                                       56899**9998 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 4.4
                   Lac_bphage_repr  32 tDeVKkilk 40 
                                       ++eVKk lk
  gi|385805596|ref|YP_005841994.1| 559 SEEVKKYLK 567
                                       689***998 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 3.7e-05
                   Lac_bphage_repr  24 VSFDGkPlt.DeVKkilkailGkk 46 
                                       V + G+P+t DeVKk +k+il k+
  gi|385805596|ref|YP_005841994.1| 600 VKYNGRPITiDEVKKSIKLILEKR 623
                                       7899****99**********9876 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 ?   12.9   0.0   2.1e-05     0.064      34     147 ..     284     398 ..     277     410 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.1e-05
                                       HHCT...TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHHHHHHHHHHT--EEEEEEE--CCCHH.. CS
                      TPP_enzyme_N  34 lseeq..girvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnaltalaeAkvdriPllvlsgdrptslrg.. 106
                                       +++++  ++ v+++ +E +aa  A g a a   +     tsgpG+  +  ++  A  + +Pl++   +r+  ++g  
  gi|385805596|ref|YP_005841994.1| 284 FQDNNlgNLLVLQTEDEIAAATSAIGAALAG--VRSSTSTSGPGFDLMAESISFAGMNEVPLVITFYQRAGPSTGma 358
                                       5556566777899999***********9996..77788999********************************9965 PP

                                       S..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHH CS
                      TPP_enzyme_N 107 qgvlqqeldqlalfrpvtkyaervtspeelpealrrAirta 147
                                       + + q     +a+f  + ++a+ v s+ +  ea+ +Ai++ 
  gi|385805596|ref|YP_005841994.1| 359 TRGGQ-GDLFTAIFSGHGEFARVVLSSGDHTEAFYDAIEAF 398
                                       44444.33478899999999999999999999999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (633 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.73u 0.32s 00:00:01.05 Elapsed: 00:00:00.53
# Mc/sec: 3619.31
//
Query:       gi|385805597|ref|YP_005841995.1|  [L=522]
Description: bifunctional GMP synthase/glutamine amidotransferase protein [Fervidicoccus fontis Kam940]
Scores for complete 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  108.8   0.1    2.1e-31  107.8   0.1    1.5  1  GMP_synt_C     GMP synthase C terminal domain
    1.3e-28  100.0   0.0    2.1e-28   99.4   0.0    1.3  1  GATase         Glutamine amidotransferase class-I
      3e-11   43.5   0.0    1.6e-10   41.1   0.0    2.2  1  Peptidase_C26  Peptidase C26
      1e-09   37.9   0.5    0.00017   20.8   0.0    2.8  3  NAD_synthase   NAD synthase
    0.00015   21.3   0.0      0.013   15.0   0.0    2.3  2  QueC           Queuosine biosynthesis protein QueC
    0.00022   21.0   0.0    0.00042   20.1   0.0    1.5  1  ATP_bind_3     PP-loop family
    0.00063   19.4   0.0     0.0014   18.3   0.0    1.5  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
  ------ inclusion threshold ------
      0.095   12.3   0.2       0.25   10.9   0.2    1.9  1  ThiI           Thiamine biosynthesis protein (ThiI)
        0.1   12.6   0.0        0.2   11.7   0.0    1.5  1  PAPS_reduct    Phosphoadenosine phosphosulfate reductase fami


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 !  107.8   0.1     1e-34   2.1e-31       2      91 ..     431     520 ..     430     521 .. 0.98

  Alignments for each domain:
  == domain 1  score: 107.8 bits;  conditional E-value: 1e-34
                                       CCCTTT-GGGSSEEEEEEEEEEE----------EEEEEEEEE---------B----HHHHHHHHHHHHHHSTT---E CS
                        GMP_synt_C   2 elkkaglykkiwQafavllpvksvGvmgdkRtyeyvvalRaveseDamtadvaelpyevLekissrivnevkgvnrv 78 
                                        lkk gly+k+wQafa + + k vGv+gd+R+y+y+v++R+ves+D+mta+++++pye+L++i ++i+ ++k+v+ v
  gi|385805597|ref|YP_005841995.1| 431 VLKKYGLYEKVWQAFATVGEDKWVGVKGDSRSYGYIVTIRIVESTDGMTANYVRMPYEILDEIVKKITGSIKSVTMV 507
                                       5899************************************************************************* PP

                                       EEE---TTTS-S- CS
                        GMP_synt_C  79 vyditskPpatiE 91 
                                       +y itskPp+tiE
  gi|385805597|ref|YP_005841995.1| 508 TYAITSKPPSTIE 520
                                       ************9 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.4   0.0     1e-31   2.1e-28       2     188 ..      15     196 ..      14     198 .. 0.86

  Alignments for each domain:
  == domain 1  score: 99.4 bits;  conditional E-value: 1e-31
                                       EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT...TTTHHHHHHHHCTSTS-EE CS
                            GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg...vegkieaikearenkiPiL 75 
                                       +iD++ ++t+ + ++++elg+ + +vp++  ++++    ++++  ++sg   s +    e   +ai  +r+ +  +L
  gi|385805597|ref|YP_005841995.1|  15 IIDFGGQYTHLISRRIRELGAFTIIVPYNRLNDIE---INSFKSMILSGSHMSIEnfsKESLEKAIDAIRSFNGTVL 88 
                                       89***************************855555...469*********9999999855666666666666669** PP

                                       EETHHHHHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTE CS
                            GATase  76 GICLGmQllaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtaksedde 152
                                       GIC+G+Q+l + fg+kv +    e+   + ++ + +  l++g +ne +++++H+++v +    p++ ev+ +se++ 
  gi|385805597|ref|YP_005841995.1|  89 GICFGLQILSYYFGGKVNHDC-GEYGETKVKILK-NDPLFKGWNNEEKVWMSHGDCVSK---PPQNSEVISVSENG- 159
                                       ******************988.666666666666.779*********************...9**********999. PP

                                       EEEEEEEETT.T.EEEESSBTTSTTSTTHHHHHHHHHH CS
                            GATase 153 elmeiiekkn.p.fvgvQFHPEststpegpellfnfli 188
                                        ++++  + n + ++gvQFHPE+++tp+g  l++nf +
  gi|385805597|ref|YP_005841995.1| 160 YIAALKLDLNgKvIYGVQFHPEVVHTPKGVILFENF-L 196
                                       6888887777899***************77666666.4 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.0   7.9e-14   1.6e-10     108     216 .]      87     181 ..       8     181 .. 0.94

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 7.9e-14
                     Peptidase_C26 108 ilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgsllaellgseeievnslHhqaikelaee 184
                                       +lgiC Glq+l   +GG+++ d  e               + +vk+ k+  l + ++ +e +v   H  ++++  ++
  gi|385805597|ref|YP_005841995.1|  87 VLGICFGLQILSYYFGGKVNHDCGE-------------YGETKVKILKNDPLFKGWN-NEEKVWMSHGDCVSKPPQN 149
                                       8******************999995.............3467899999999999999.999**************** PP

                     Peptidase_C26 185 lrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                        +v++v+e g i a+++  + ++++gvQ+HPE
  gi|385805597|ref|YP_005841995.1| 150 SEVISVSENGYIAALKLDLNGKVIYGVQFHPE 181
                                       *******************99**********9 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   8.4e-08   0.00017       2      81 ..     211     287 ..     210     309 .. 0.77
   2 !   13.9   0.1   1.1e-05     0.021     148     177 ..     370     399 ..     365     407 .. 0.95
   3 ?   -1.9   0.0      0.71   1.4e+03     192     204 ..     484     496 ..     479     509 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 8.4e-08
                                       HHHHHHHHHHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE CS
                      NAD_synthase   2 ieelvdflkeyvkkagakgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievkt 78 
                                       ++++ + l+++v++ g  ++++ +SGG+DS++ a +a+k++g+   ++  + +    e ++e+ +++ + l+++  +
  gi|385805597|ref|YP_005841995.1| 211 VNSIIEGLRKEVSDDG--KALVAVSGGIDSTVSAIIAKKIFGDR-LITAFVDHGLLREGEKEEVIEMLNFLELKPLV 284
                                       6778889999998887..678899*****************765.55555557777777777777777777776666 PP

                                       --- CS
                      NAD_synthase  79 idi 81 
                                       id 
  gi|385805597|ref|YP_005841995.1| 285 IDA 287
                                       665 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 1.1e-05
                                       BETTTTS-HHHHHHHHHHTT--HHHHCS-- CS
                      NAD_synthase 148 lapiaellKtevkeLakelnvPervlkkpP 177
                                       ++p++ l+K ev+++   l+vPe ++k++P
  gi|385805597|ref|YP_005841995.1| 370 IEPLKFLYKDEVRKIGTILGVPETLIKRHP 399
                                       78**************************99 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.71
                                       SS-HHHHHHHHTH CS
                      NAD_synthase 192 gikYdelDeiLkl 204
                                        ++Y++lDei+k 
  gi|385805597|ref|YP_005841995.1| 484 RMPYEILDEIVKK 496
                                       589*******983 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   6.7e-06     0.013       1      61 [.     227     287 ..     227     316 .. 0.78
   2 ?    4.0   0.0     0.015        30     128     176 ..     333     391 ..     311     396 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 6.7e-06
                                       EEEEE--SSHHHHHHHHHHHHH-.SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE- CS
                              QueC   1 kavvllSGGlDSttvlalakkeg.kevealtfdYgqrhkkeleaakkiakelgveehkildl 61 
                                       ka+v +SGG+DSt+ +++akk + +++++  +d g  ++ e e + ++ + l++ +  ++d 
  gi|385805597|ref|YP_005841995.1| 227 KALVAVSGGIDSTVSAIIAKKIFgDRLITAFVDHGLLREGEKEEVIEMLNFLEL-KPLVIDA 287
                                       79******************9875888888899999888888888888888888.6666665 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.015
                                       --GGGSHHHHHHHHHHHHHH..........HTS--EEE-TTTT--HHHHHHHHHHTTHH CS
                              QueC 128 gYPDcrdefvkalnkalnlg..........edkkieieaPlidlsKaeivklgkelgvp 176
                                       +YPD  +   ++  +a+  +           ++k++i  Pl  l K e+ k+g+ lgvp
  gi|385805597|ref|YP_005841995.1| 333 TYPDVVESGKTQGSAAVIKShhnvgglpdwFKEKVKIIEPLKFLYKDEVRKIGTILGVP 391
                                       566655443333333222223344477777679*********************99987 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   2.1e-07   0.00042       2     153 ..     228     382 ..     227     387 .. 0.63

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.1e-07
                                       EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H...HHCTTST CS
                        ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikleiekvdv...akkkgkn 75 
                                       +lvAvSgG+DS++   +++k    +g +l+ + vdhgl  e ++e e+++ l+     +l+i+  +      +  + 
  gi|385805597|ref|YP_005841995.1| 228 ALVAVSGGIDSTVSAIIAKKI---FGDRLITAFVDHGLLREGEKE-EVIEMLNFLELKPLVIDAEERflnRLEGISD 300
                                       79***********99999998...556999*******98776554.4555555544455555554444533344566 PP

                                       CCCHHHHHH...HHHHHHCHHCCT.CEEE---BHHHHHHHHHHHHCCT--C..CHHH-S-SEEEETTCCEE-CCCT- CS
                        ATP_bind_3  76 leeaARelR...YevlkealkkegievlllAhhadDqaEtfllrlargsgl..aglagikeaseiasirlvRPlLkv 147
                                        ee+ R +     ++++e+++kegi++++ + +  D +E    + +    +  +++ g++     ++++++ Pl  +
  gi|385805597|ref|YP_005841995.1| 301 CEERRRIIGeefAKIFEEIIEKEGIRYFVQGTTYPDVVESGKTQGSAAVIKshHNVGGLPDW-FKEKVKIIEPLKFL 376
                                       77777766422135788899999999999888888888876655444322211333444332.23446666666666 PP

                                       -HHHHH CS
                        ATP_bind_3 148 skeele 153
                                       +k+e++
  gi|385805597|ref|YP_005841995.1| 377 YKDEVR 382
                                       666665 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 !   18.3   0.0     7e-07    0.0014      26      92 ..      39     101 ..      31     120 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 7e-07
                          GATase_3  26 rvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGeei 92 
                                        v + +l+d ++++    +il G+   i++   +   +l++ai +  + +g+vlgiC Glq+L+ ++
  gi|385805597|ref|YP_005841995.1|  39 IVPYNRLNDIEINS-FKSMILSGSHMSIENFSKE---SLEKAIDAIRSFNGTVLGICFGLQILSYYF 101
                                       57788899999966.99*******9888765444...6677777777789*************9876 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2   0.00013      0.25       3      52 ..     225     275 ..     223     399 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00013
                              ThiI   3 qgkvlaLlSgGiDSpVaaylllkR.Gcrvvlvhlknepgtseeaiekvekl 52 
                                        gk+l+ +SgGiDS V+a ++ k  G r  + +++  +  + e++e++e+l
  gi|385805597|ref|YP_005841995.1| 225 DGKALVAVSGGIDSTVSAIIAKKIfGDRLITAFVDHGLLREGEKEEVIEML 275
                                       599***************987663366666666665555555555555554 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0    0.0001       0.2       3      47 ..     229     274 ..     227     319 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0001
                                       EEE--SSCTCHHHHHHHHHHCTTH.EEEEEE-STB-HHHHHHHHHH CS
                       PAPS_reduct   3 vvsvsgGkdslVllhLalkafkpv.pvvfvdtghefpetiefvdel 47 
                                        v+vsgG+ds+V  ++a k+f ++  + fvd g   +   e v e+
  gi|385805597|ref|YP_005841995.1| 229 LVAVSGGIDSTVSAIIAKKIFGDRlITAFVDHGLLREGEKEEVIEM 274
                                       689********************74599999987655444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (522 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       671  (0.0374254); expected 358.6 (0.02)
Passed bias filter:                      610  (0.0340231); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.30s 00:00:00.99 Elapsed: 00:00:00.48
# Mc/sec: 3263.22
//
Query:       gi|385805598|ref|YP_005841996.1|  [L=335]
Description: Adenylosuccinate synthase [Fervidicoccus fontis Kam940]
Scores for 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  251.0   1.3    9.7e-38  130.2   0.1    3.0  3  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 !   98.7   0.1     2e-32   3.5e-28       1     142 [.       3     136 ..       3     143 .. 0.93
   2 !  130.2   0.1   5.4e-42   9.7e-38     189     332 ..     141     282 ..     134     286 .. 0.95
   3 !   21.2   0.0   6.5e-09   0.00012     377     418 ..     285     326 ..     281     327 .. 0.90

  Alignments for each domain:
  == domain 1  score: 98.7 bits;  conditional E-value: 2e-32
                                       .EEEE-SSS-S-HHHHHHHH..HTT-SEEEE-SB-TTSSEEEEETTEEEEESSS-GGGGSTT-EEEE-TTBEE-HHH CS
                   Adenylsucc_synt   1 vvvvGaqwGDEGKGkivDll..aeeadvvvRfqGGanAGHtvvvdgkkyklhllpSGilnpgvvnviGngvvvdpea 75 
                                       +v+vG  +GDEGKGki  +l  a+++++ vR  G  nAGHtv+ +gk ykl+ +pSG +n+++  +i++g ++ +++
  gi|385805598|ref|YP_005841996.1|   3 TVIVGGFFGDEGKGKIAAYLaiADNCRYAVRT-GSINAGHTVYFEGKAYKLRSIPSGFVNKSTELLIAPGALIRLDV 78 
                                       69*****************977789*****95.99****************************************** PP

                                       HHHHHTTSS-TT......TEEEETTSEE--HHHHHHHHHHHHH----------TTHHHHHHHHHTT- CS
                   Adenylsucc_synt  76 lleEieeleakgvelskerllisdrahlvlpyhkalDkleeaakgkkkiGtTkkGiGpayadkvarr 142
                                       l +E++el+       ker +i+ +a ++ + h++l+k  +  +   +iG+T +G+G a++d+v r+
  gi|385805598|ref|YP_005841996.1|  79 LWNELKELNV------KERTKIDYNAGIIEEKHIELEKRDSVLT---SIGSTFQGVGAAMSDRVLRK 136
                                       ********64......46999****************9999855...8****************997 PP

  == domain 2  score: 130.2 bits;  conditional E-value: 5.4e-42
                                       HHHHHHGGGEE-HHHHHHHHHHTT--EEEE--S-GGG-TTTSSTTSS-SS--SHHHHHHHTT--GGGEEEEEEEEES CS
                   Adenylsucc_synt 189 kyaerlkpyvvdtvallnealkegkkvLfEGaqgtllDidhGtYPfvTsSnttaggaltglglapkkidevlgvvKA 265
                                       k +e+l+ +++d+++ +n a+++g++v++EG qgt+l++ hGtYP+vTs  tta+g+++  g++pkk+++v+ v+K+
  gi|385805598|ref|YP_005841996.1| 141 KDTEELRGMLIDVSEKVNYAVDSGENVIIEGTQGTFLSLYHGTYPYVTSRDTTASGIISEVGIGPKKVGDVILVFKS 217
                                       5679999********************************************************************** PP

                                       SEEESSSS--TTB--SHHHHHHHHHTT.-B-TTT--B-EEE-EEHHHHHHHHHHHT-SEEEEE-GGGG CS
                   Adenylsucc_synt 266 yttrvGeGpfptelkdevgeklrekGk.EfgtttgrpRrcGwlDlvllryavrvngvtelaltklDvl 332
                                       ++trvGeGp+  e+++e++ekl   G  E gt+tgr Rr+  + + l+++a+++n++t++a+tk+D l
  gi|385805598|ref|YP_005841996.1| 218 FVTRVGEGPLENEMSKEEAEKL---GLvEKGTVTGRMRRVAPFNVNLAKRAIMLNSATQIAITKIDWL 282
                                       **************99999999...4349*************************************98 PP

  == domain 3  score: 21.2 bits;  conditional E-value: 6.5e-09
                                       --TT---GGGS-HHHHHHHHHHHHHHTS-EEEEE-SSSTT-E CS
                   Adenylsucc_synt 377 disgvrsfedlpenakkyvefieellgvpvkiisvGpereqt 418
                                       +  gv+++++lp +a+k++e +e +l+vp++++++G++  q+
  gi|385805598|ref|YP_005841996.1| 285 EAYGVKEWSKLPPEARKWIEGLEAELKVPITLVGTGEDTMQV 326
                                       45689********************************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); 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: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2097.97
//
Query:       gi|385805599|ref|YP_005841997.1|  [L=474]
Description: FAD dependent oxidoreductase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-11   43.5   1.1     0.0006   19.1   0.1    3.1  3  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.8e-10   40.1   0.3    3.6e-05   22.6   0.2    2.2  2  HI0933_like     HI0933-like protein
    3.4e-09   36.4   0.8     0.0012   18.2   0.0    2.8  3  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    2.1e-08   34.2   0.3    0.00056   19.6   0.2    2.4  2  DAO             FAD dependent oxidoreductase
    4.5e-07   29.3   2.4      0.003   16.7   0.0    3.0  3  GIDA            Glucose inhibited division protein A
      7e-05   22.9   0.0     0.0051   16.8   0.0    2.2  2  NAD_binding_9   FAD-NAD(P)-binding
    7.4e-05   22.0   0.8    0.00056   19.1   0.4    2.2  2  FAD_binding_2   FAD binding domain
    0.00038   19.8   0.1     0.0006   19.2   0.1    1.3  1  FAD_binding_3   FAD binding domain
     0.0014   17.9   0.7     0.0069   15.7   0.1    2.1  2  Thi4            Thi4 family
     0.0024   18.1   0.6     0.0065   16.7   0.2    2.0  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
     0.0099   15.0   0.1      0.015   14.4   0.1    1.2  1  Lycopene_cycl   Lycopene cyclase protein
  ------ inclusion threshold ------
      0.014   14.3   0.2       0.02   13.7   0.2    1.2  1  Trp_halogenase  Tryptophan halogenase
      0.061   12.7   0.9       0.38   10.0   0.5    2.0  2  FAD_oxidored    FAD dependent oxidoreductase
       0.18   11.1   0.1        0.6    9.4   0.1    1.7  2  ThiF            ThiF family
       0.42   11.2   3.2         26    5.4   0.1    2.7  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.1     5e-07    0.0006       1      31 [.       4      42 ..       4      91 .. 0.85
   2 !   10.6   0.0    0.0002      0.23     188     241 ..     171     223 ..     137     241 .. 0.70
   3 !   11.1   0.0   0.00014      0.16     259     284 ..     431     456 ..     410     463 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 5e-07
                                      CSEEEE--SHHHHHHHHHHHH...HTS-EEEEE.....T CS
                                      xxxxxxxxxxxxxxxxxxxxx...xxxxxxxxx.....x RF
                       Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaq...agakvtlve.....l 31
                                      +dv+++G+GpAGl aa++l +    +++++l++     +
  gi|385805599|ref|YP_005841997.1|  4 FDVAIVGAGPAGLFAAIELVKtgsGKLNIALIDkgfkvE 42
                                      69*******************8866999***96444433 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0002
                                       HHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 188 aleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvrpst 241
                                        ++  lek+ v+++ gt vk++++++ ++++++++g ei a+ v++a G+   +
  gi|385805599|ref|YP_005841997.1| 171 NITGFLEKNEVKIMEGTDVKDLKKENGQIKLITDKG-EIFAKKVLLAPGRGGAR 223
                                       446678999999999999999999888777555555.57888888888876654 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00014
                                       E--TTSBESSTTEEE-GGGCTECCSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 259 vvdeflrtnvpgiyaiGDvaggkggp 284
                                       +v ++l+tn+++iy++GD ag  +g+
  gi|385805599|ref|YP_005841997.1| 431 KVTPSLETNIDNIYVAGDGAGLSRGI 456
                                       79999*************99444433 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.2     3e-08   3.6e-05       1      39 [.       4      45 ..       4      47 .. 0.84
   2 !   15.4   0.0   4.7e-06    0.0056     110     189 ..     167     238 ..     140     257 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 3e-08
                                      -SEEEE--SHHHHHHHHHH...HHTT--EEEE-SSSSS-HHH CS
                       HI0933_like  1 kdviviGgGaAGlmaAisa...akrgkrVlllekakklgrKi 39
                                      +dv+++G+G+AGl+aAi++   ++ + +++l++k+ k+ ++i
  gi|385805599|ref|YP_005841997.1|  4 FDVAIVGAGPAGLFAAIELvktGSGKLNIALIDKGFKVEKRI 45
                                      59****************95445556799*****99998876 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 4.7e-06
                                       HHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----SS-GGGT--SHHHHHHHHTT-- CS
                       HI0933_like 110 divdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGlSiPklGstgkgyklaeqfght 186
                                       ++++ ++  l++++vk++  t+vk+++ke+++ +++ t +++e+ a+k++lA      P  G     ++la++ g++
  gi|385805599|ref|YP_005841997.1| 167 KVISNITGFLEKNEVKIMEGTDVKDLKKENGQ-IKLIT-DKGEIFAKKVLLA------PGRGGARWFHDLAQKIGID 235
                                       57777777899***************776666.88888.89***********......999999999*******999 PP

                                       EEE CS
                       HI0933_like 187 ivp 189
                                       i p
  gi|385805599|ref|YP_005841997.1| 236 IEP 238
                                       865 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   0.1   7.1e-06    0.0085       2      30 ..       8      38 ..       7      60 .. 0.84
   2 !   18.2   0.0     1e-06    0.0012      90     134 ..     175     219 ..     166     224 .. 0.93
   3 ?   -1.2   0.0      0.81   9.6e+02     294     305 .]     436     447 ..     427     447 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7.1e-06
                       Pyr_redox_3  2 IiGaGPaGlaaaielkkagl..edylilEkg 30
                                      I+GaGPaGl aaiel k g    ++  ++kg
  gi|385805599|ref|YP_005841997.1|  8 IVGAGPAGLFAAIELVKTGSgkLNIALIDKG 38
                                      9****************98743466778887 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 1e-06
                       Pyr_redox_3  90 vaksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGe 134
                                         +++e++i++ ++V+++kke+++ ++ t+k+++ Akkv++A G+
  gi|385805599|ref|YP_005841997.1| 175 FLEKNEVKIMEGTDVKDLKKENGQIKLITDKGEIFAKKVLLAPGR 219
                                       57899*************************************995 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.81
                       Pyr_redox_3 294 eetnvpglflaG 305
                                        etn++++++aG
  gi|385805599|ref|YP_005841997.1| 436 LETNIDNIYVAG 447
                                       59*********9 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.2   4.7e-07   0.00056       1      29 [.       5      38 ..       5      43 .. 0.92
   2 !   12.2   0.0   8.1e-05     0.097     152     270 ..     172     285 ..     164     316 .. 0.55

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 4.7e-07
                                      EEEEECTSHHHHHHHHHHHHTT.....EEEEESS CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg.....Vtllekg 29
                                      dv+i+G+G +Gl++A eL + g     ++l++kg
  gi|385805599|ref|YP_005841997.1|  5 DVAIVGAGPAGLFAAIELVKTGsgklnIALIDKG 38
                                      8*****************9997779********9 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 8.1e-05
                                       HHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEEEEEEEEEE--GGGHHHH..HTTCTTTSEEEE......E CS
                               DAO 152 laraaealGveilegtevtgleeedgkvwgverttpgendaadavVnaaGawsdll..gllkeldlpisp......v 220
                                       +   +e++ v+i egt v++l++e+g+++ +  t +ge++a ++v +a G +   +  +l++++ + i+p      v
  gi|385805599|ref|YP_005841997.1| 172 ITGFLEKNEVKIMEGTDVKDLKKENGQIKLI--TDKGEIFA-KKVLLAPGRGGARWfhDLAQKIGIDIEPgpldigV 245
                                       5566899**************9999998888..66677655.99*****9775534333333332333332221112 PP

                                       EEEE..EEEEECCTHSTGSGCSEEEEEEEETTTTEEEEEETTSEEE.EEESSE CS
                               DAO 221 rgqv..lvlkplseklvspaailpvpetdddgrgvyvtprkdgrvl.vGgtad 270
                                       r ++  + +++++              ++d++ ++y   + d++v+ ++++++
  gi|385805599|ref|YP_005841997.1| 246 RVEIpyYITEHITSI------------NHDPKIVMYTKFY-DDKVRtFCTNPH 285
                                       222211222233221............3333333333333.344442355544 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.1   0.00024      0.29       1      23 [.       5      27 ..       5      91 .. 0.89
   2 ?    0.6   0.0      0.19   2.3e+02     101     150 ..     172     219 ..     163     234 .. 0.74
   3 !   16.7   0.0   2.5e-06     0.003     322     384 ..     409     470 ..     378     473 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00024
                                      CEEEE-SSHHHHHHHHHHHHTT- CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGa 23
                                      dv ++G+G AG+ AA+++ + G 
  gi|385805599|ref|YP_005841997.1|  5 DVAIVGAGPAGLFAAIELVKTGS 27
                                      799***************99985 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.19
                                       HHHHHHTSTTEEEEES-.EEEEEECTTEEEEEEETTS-EEEECEEEE--TT CS
                              GIDA 101 vteklenepnleiieee.veeliveekkvkgvvtedgetikakavviatGt 150
                                       +t  le+ ++++i+e++ v++l+ e++++k ++ +   +i ak+v +a G 
  gi|385805599|ref|YP_005841997.1| 172 ITGFLEK-NEVKIMEGTdVKDLKKENGQIKLITDK--GEIFAKKVLLAPGR 219
                                       5555666.899999985499**9999999977543..45567788888775 PP

  == domain 3  score: 16.7 bits;  conditional E-value: 2.5e-06
                                       TT-TT--EEE--EEEEEEEE-GGGB-TTSBBSSSBTEEE-CGGGTB.-SHHHHHHHHHHHHHHH CS
                              GIDA 322 pGLenaeivrpGyaieydyvdprqllntLetkkvkgLflAGqinGt.eGYeEaaaqGllAGina 384
                                       pG    + + ++  i+y  v+++ ++++Let+ ++++++AG+  G   G   aa++G++A++ +
  gi|385805599|ref|YP_005841997.1| 409 PGVSSPQTLLYAPEIKYYGVKAK-VTPSLETN-IDNIYVAGDGAGLsRGINVAASTGVIAARAI 470
                                       4555556677799999*999998.999****9.*************89************9875 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   4.3e-06    0.0051       1      33 [.       7      37 ..       7      59 .. 0.89
   2 ?    3.9   0.0     0.041        50     115     155 ..     179     219 ..     152     220 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.3e-06
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdp 33
                                      aivGaGp+Gl ++ +L++    + +l+i l+d+
  gi|385805599|ref|YP_005841997.1|  7 AIVGAGPAGLFAAIELVKTG--SGKLNIALIDK 37
                                      8******************7..9*********8 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.041
                     NAD_binding_9 115 vtvevhra.evvdleeradgqavlladgaslaadaVvLAlGh 155
                                        +v+++++ +v dl++++++ ++  +d+ ++ a++V LA G 
  gi|385805599|ref|YP_005841997.1| 179 NEVKIMEGtDVKDLKKENGQIKL-ITDKGEIFAKKVLLAPGR 219
                                       4677775449999*999998877.5666677899*****995 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.4   4.7e-07   0.00056       1      33 [.       5      40 ..       5      44 .. 0.88
   2 ?    0.4   0.0      0.23   2.7e+02     152     208 ..     177     226 ..     140     234 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 4.7e-07
                                      SEEEE--SHHHHHHHHHHHH..TTT.-EEEEESSSG CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaae..aGl.kvavvekeqe 33
                                      Dv ++G+G AGL AA+e+ +   G+ ++a+++k+++
  gi|385805599|ref|YP_005841997.1|  5 DVAIVGAGPAGLFAAIELVKtgSGKlNIALIDKGFK 40
                                      9*****************995566689*****9987 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.23
                                       HTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG.... CS
                     FAD_binding_2 152 rkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgrallk 208
                                       +k++v+++e t++++L  e+g++  +  +  ++g+++   ak+v+la g  g+ +++
  gi|385805599|ref|YP_005841997.1| 177 EKNEVKIMEGTDVKDLKKENGQIKLI--T--DKGEIF---AKKVLLAPGRGGARWFH 226
                                       45569999999999999999988764..3..445554...79999999887775554 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1     5e-07    0.0006       2      25 ..       4      27 ..       3      40 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 5e-07
                                      EEEEEE--SHHHHHHHHHHHHTTH CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGv 25
                                       dV+IVGaGpaGl +a +L + G 
  gi|385805599|ref|YP_005841997.1|  4 FDVAIVGAGPAGLFAAIELVKTGS 27
                                      69******************9995 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   5.7e-06    0.0069      18      49 ..       4      37 ..       1      41 [. 0.87
   2 ?   -0.1   0.0      0.38   4.5e+02      97     126 ..     166     194 ..     140     204 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.7e-06
                                      EEEEEE--SHHHHHHHHHHHHC..TTS-EEEEES CS
                              Thi4 18 sDvvivGaGssGLtaayylakk..pdlkvailer 49
                                       Dv+ivGaG++GL aa  l k    +l++a++++
  gi|385805599|ref|YP_005841997.1|  4 FDVAIVGAGPAGLFAAIELVKTgsGKLNIALIDK 37
                                      69*****************999766799999876 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.38
                                       HHHHHHHHHHHHTSTTEEEEESEEEEEEEE CS
                              Thi4  97 alftstllskvlqlanvkllnavaveDliv 126
                                       ++++s+++   l++ +vk+++++ v Dl  
  gi|385805599|ref|YP_005841997.1| 166 VKVISNIT-GFLEKNEVKIMEGTDVKDLKK 194
                                       34445444.3567799*********99854 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.2   5.4e-06    0.0065       1      28 [.       8      38 ..       8      41 .. 0.90
   2 ?   -2.8   0.0       6.6   7.9e+03      48      55 ..     221     228 ..     219     231 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.4e-06
                                      EE--SHHHHHHHHHHHCC...TEEEEEE-SS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLaka...gfdvlllekr 28
                                      IvGaG +Gl aA +L k    ++++ l++k+
  gi|385805599|ref|YP_005841997.1|  8 IVGAGPAGLFAAIELVKTgsgKLNIALIDKG 38
                                      9****************8675669*****97 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 6.6
                                       S---EEET CS
                     NAD_binding_8  48 gahifhgs 55 
                                       ga++fh+ 
  gi|385805599|ref|YP_005841997.1| 221 GARWFHDL 228
                                       9*****95 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   0.1   1.2e-05     0.015       1      33 [.       5      38 ..       5      44 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.2e-05
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakp.glkvvlieas 33
                                      Dv+++GaGpAgl  A +l++    +l++ li+ +
  gi|385805599|ref|YP_005841997.1|  5 DVAIVGAGPAGLFAAIELVKTGSgKLNIALIDKG 38
                                      9*****************8765516999999987 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   1.7e-05      0.02       1      33 [.       5      37 ..       5      42 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.7e-05
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE- CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlves 33
                                      ++ ivG+G+aG  aA+ l k+++gkl++ l+++
  gi|385805599|ref|YP_005841997.1|  5 DVAIVGAGPAGLFAAIELVKTGSGKLNIALIDK 37
                                      699***************************986 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.5   0.00032      0.38       1      22 [.       5      26 ..       5      37 .. 0.90
   2 ?    0.7   0.0      0.22   2.7e+02      83     124 ..     159     203 ..     117     216 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00032
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraG 22
                                      Dv +vG+gpaG+ AAi   + G
  gi|385805599|ref|YP_005841997.1|  5 DVAIVGAGPAGLFAAIELVKTG 26
                                      9***************988877 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.22
                      FAD_oxidored  83 tfepevakavleeml...aeagvtvllntrlvevekegkriesvt 124
                                       +   +v+ +v+ ++    ++++v+++ +t++++ +ke+++i+ +t
  gi|385805599|ref|YP_005841997.1| 159 VLGTDVMVKVISNITgflEKNEVKIMEGTDVKDLKKENGQIKLIT 203
                                       456667777777766776999***************998998776 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.1    0.0005       0.6      18      50 ..       3      37 ..       1      43 [. 0.86
   2 ?   -0.9   0.0      0.72   8.6e+02     126     181 ..     141     276 ..     135     471 .. 0.53

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0005
                                      TSEEEEE--SHHHHHHHHHHHHHTTT..EEEEEES CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxx RF
                              ThiF 18 dskvllvGaGglGsellknLalsGvg..kltlvDn 50
                                      d  v++vGaG  G +++ +L+++G g  ++ l+D 
  gi|385805599|ref|YP_005841997.1|  3 DFDVAIVGAGPAGLFAAIELVKTGSGklNIALIDK 37
                                      6689**********************666677775 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.72
                                       HHHHHHHHT-EEEEE..EEETTEEEEEEEEECCS-ECTSS-T.......GGS.EECCCCEEHHH............. CS
                                       xxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxx............. RF
                              ThiF 126 vnracvkkgipliea..gtlgfegqvvviipgktgcyeCldp.......sstedptekkvplct............. 180
                                       + r+++k g ++i +   +lg++  v vi ++ tg +e +++        ++ ++++ ++ l+t             
  gi|385805599|ref|YP_005841997.1| 141 IERLAAKAGAKYIPTpqRVLGTDVMVKVI-SNITGFLEKNEVkimegtdVKDLKKENGQIKLITdkgeifakkvlla 216
                                       55666666666665311444444444444.34455554444333333333444444444444444444444444444 PP

                                       ...........................................................H CS
                                       ...........................................................x RF
                              ThiF 181 ...........................................................s 181
                                                                                                  +
  gi|385805599|ref|YP_005841997.1| 217 pgrggarwfhdlaqkigidiepgpldigvrveipyyitehitsinhdpkivmytkfyddK 276
                                       444444444444444444444444444444444444444444444444444444444440 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1     0.022        26       2      23 ..       6      27 ..       5      51 .. 0.85
   2 ?    5.3   0.4     0.024        29      45      72 ..     171     198 ..     162     205 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.022
                                      EEEECSSHHHHHHHHHHHHTTS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgk 23
                                      v++vG+G  gl +A +l + g+
  gi|385805599|ref|YP_005841997.1|  6 VAIVGAGPAGLFAAIELVKTGS 27
                                      89***************99885 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.024
                                       HHHHHHHHTTEEEECSEEEEEEEEETTS CS
                         Pyr_redox  45 ilqeklekngievllntkveeiegsedg 72 
                                       +++  lekn ++++ +t v+ +++++ +
  gi|385805599|ref|YP_005841997.1| 171 NITGFLEKNEVKIMEGTDVKDLKKENGQ 198
                                       677789*****************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.53
# Mc/sec: 2715.90
//
Query:       gi|385805600|ref|YP_005841998.1|  [L=245]
Description: phosphoribosylaminoimidazolesuccinocarboxamide synthase [Fervidicoccus fontis Kam940]
Scores for complete 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  170.9   0.0    4.5e-50  170.6   0.0    1.1  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 !  170.6   0.0   2.5e-54   4.5e-50       2     237 ..       8     220 ..       7     232 .. 0.93

  Alignments for each domain:
  == domain 1  score: 170.6 bits;  conditional E-value: 2.5e-54
                                       EEE-SSEEEEE-.SSTTEEEEEEESEEEECCCTEEEEETTHHHHHHHHHHHHHHHHH.H.--BSEEEE.....-SSS CS
                       SAICAR_synt   2 lyeGKvrdvYel.edddklllvakDrisAfdvvlkeeipgKGkvltqlsafwfekle.k.ipnhliksldpeqlegr 75 
                                       +y GK +++Y+   d++ l++++kD+++A d++ ++  p+KG ++ ++s+f+f++le k +++h+++        ++
  gi|385805600|ref|YP_005841998.1|   8 IYVGKSKNIYKHpYDEKLLIMEFKDDVTAGDGAIRTIAPHKGIINARTSHFFFKLLEgKgLKTHMVEF-----NGNN 79 
                                       799*********66668999*************************************758******44.....4689 PP

                                       EEEEE-EEEESEEEEEEEE--HHH.......HH....HH..T--TT-EEEEEEEEEEE--CCCT.S-EE-HHHHH.H CS
                       SAICAR_synt  76 smlvkklkmlpvEvvvRgyltGslwkeykksgkvcgirlpeglkegeklpepiftpstKaeegehDeniseeevvea 152
                                       +m+vk+lkm+p+E+++R+y+ Gsl        k    rl + +k  + l++p++++ +K++++ hD+ i++++++ +
  gi|385805600|ref|YP_005841998.1|  80 KMIVKRLKMIPIEFIARNYAYGSL-------LK----RL-PLFKLMQPLDPPLIEFHYKDDSL-HDPLITHDDII-L 142
                                       ************************.......66....66.45999*****************9.7*********9.7 PP

                                       TT..-HHHHHHHHHHHHHHHHHHHHHHHHTTEEEEEEEEEEEEETTTTEEEEES--.STTTEEEEETTT.....GGG CS
                       SAICAR_synt 153 lg..teeeaeeieelalavyekaaelaaergiilvDtKlEFGldeedgelvLaDevltpDssRfwdaetyeegkeqe 227
                                        g  t+ ++ +i +++ +++ +++ +++e+g+ lvD+KlE+G+de +ge++LaDe+ t D  R  d+         +
  gi|385805600|ref|YP_005841998.1| 143 SGllTKGQLGKIVSITADINMILRTFLEEKGLKLVDIKLEYGFDE-NGEIILADEI-TGDGFRVVDERG-------N 210
                                       7899****************************************5.9*********.********9877.......9 PP

                                       B-STHHHHTT CS
                       SAICAR_synt 228 slDKqfvRdw 237
                                       +lDK+++R+ 
  gi|385805600|ref|YP_005841998.1| 211 HLDKEIFRKT 220
                                       9*******75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1547.36
//
Query:       gi|385805601|ref|YP_005841999.1|  [L=423]
Description: amidophosphoribosyltransferase [Fervidicoccus fontis Kam940]
Scores for complete 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    0.00082   18.9   0.1    1.7  1  Pribosyltran  Phosphoribosyl transferase domain
  ------ inclusion threshold ------
        0.1   12.1   0.0       0.25   10.8   0.0    1.6  1  PRTase_2      Phosphoribosyl transferase


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   9.2e-08   0.00082      21     120 ..     243     350 ..     235     356 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 9.2e-08
                                       EEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE...............EE----TTSEE CS
                      Pribosyltran  21 eileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes.......rlledpagkkV 90 
                                       e+  ++ +  d+vvg++  ++p a   ++++  p+    +      +s   a g++  +          +  +gk++
  gi|385805601|ref|YP_005841999.1| 243 ELALNFSHDVDIVVGVPETAYPYAIGFSQAIRKPFELSFIPTAGRMRSMLKASGIERLIavhlkmnPVKSAMEGKRI 319
                                       555566677889999999999999999999955544333332222222222222222224456777789999***** PP

                                       EEE-SEESSSHHHHHHHHHHHC.C-BSEEEE CS
                      Pribosyltran  91 liVDDildtGgTllaalelLke.kgpeevri 120
                                        ++DD + tG+T++ + ++L++ +g+ee+++
  gi|385805601|ref|YP_005841999.1| 320 ALIDDSMVTGSTIKTVSQILRNrVGVEEIHL 350
                                       ******************9987368888875 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   2.8e-05      0.25     117     154 ..     312     349 ..     231     354 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 2.8e-05
                          PRTase_2 117 llaaakelvLvDDEistGktalnliralqeklprkryv 154
                                          + k++ L+DD + tG+t+  + + l++++  ++++
  gi|385805601|ref|YP_005841999.1| 312 SAMEGKRIALIDDSMVTGSTIKTVSQILRNRVGVEEIH 349
                                       3345678***************9999999987766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       851  (0.047465); expected 358.6 (0.02)
Passed bias filter:                      740  (0.0412739); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2666.87
//
Query:       gi|385805602|ref|YP_005842000.1|  [L=501]
Description: phosphoribosylamine--glycine ligase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-40  139.2   0.0    2.1e-40  138.6   0.0    1.3  1  GARS_A          Phosphoribosylglycinamide synthetase, ATP-gra
    2.7e-21   76.1   0.0    4.8e-21   75.3   0.0    1.4  1  GARS_N          Phosphoribosylglycinamide synthetase, N domai
    8.1e-07   29.2   0.0    1.9e-06   28.1   0.0    1.6  1  GARS_C          Phosphoribosylglycinamide synthetase, C domai
    4.8e-05   22.8   0.0    8.9e-05   21.9   0.0    1.4  1  ATPgrasp_ST     Sugar-transfer associated ATP-grasp
     0.0004   20.5   0.0     0.0017   18.4   0.0    2.0  2  ATP-grasp_3     ATP-grasp domain
     0.0073   16.1   0.1      0.021   14.6   0.0    1.7  2  ATPgrasp_TupA   TupA-like ATPgrasp
  ------ inclusion threshold ------
      0.018   14.7   0.0      0.041   13.5   0.0    1.6  1  ATP-grasp_4     ATP-grasp domain
      0.025   14.0   0.0      0.054   12.9   0.0    1.5  1  GSH-S_ATP       Prokaryotic glutathione synthetase, ATP-grasp
      0.033   13.4   0.0      0.056   12.7   0.0    1.3  1  ATPgrasp_YheCD  YheC/D like ATP-grasp
      0.034   13.6   0.0      0.072   12.6   0.0    1.5  1  CPSase_L_D2     Carbamoyl-phosphate synthase L chain, ATP bin
      0.053   12.3   0.0       0.09   11.5   0.0    1.3  1  Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase


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 !  138.6   0.0   1.3e-43   2.1e-40       2     193 ..     109     314 ..     108     315 .. 0.90

  Alignments for each domain:
  == domain 1  score: 138.6 bits;  conditional E-value: 1.3e-43
                                       BHHHHHHHHHHTT--B-.-EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEE.........SSHHHHHHHHH CS
                            GARS_A   2 sKsfakdllkkagipta.eyeaftdpeeakeyieeatakalVvKadglaagKgviva.........kseeealkavk 68 
                                       sK fa++++ + +ip+   ++af+d +ea+e+++ a++ + VvK+++ a+gKgv v          ++++  +k+++
  gi|385805602|ref|YP_005842000.1| 109 SKVFARSFMWRNEIPGRlFFQAFKDLSEAEEFMKYAGD-V-VVKPARQAGGKGVRVIrdtkaylseEKSSVKMKVAE 183
                                       8***************98899************98876.4.7**************988888775444445567888 PP

                                       HHCTS-TTC..CCCSSEEEEE---SEEEEEEEEECTTEEEE---BEEEEEEECCCEEEEECECEEEE....S-TTS- CS
                            GARS_A  69 eilekkkfG..eagekvviEelleGeEvsllalvdgktvkplplaqdhkrvlegDkgpnTGGmGays....papvvt 139
                                       ++ ++ + G  +   k+++E++ eG E +l++++dg   +plp+ qdh +++e D gp TGGmG++s      p++t
  gi|385805602|ref|YP_005842000.1| 184 DVYKQLS-GydDIDYKILLEQRAEGVEYTLHVISDGFYSIPLPIIQDHAHAFEYDIGPETGGMGCISgpgmYPPFLT 259
                                       8887654.3237899****************************************************9887779*** PP

                                       HHHHHHHHHHTHHHHHHHHHCTT.---EEEEEEEEEEE.TTEEEEEEEESS--TTC CS
                            GARS_A 140 eellekikeeileptveglkkeg.ipfkGvLyaglmlv.edgpkvlefnvRfgDpe 193
                                       +e+ +k ke i+e+++e+lkke+  p++GvL +++ml+   gp v+ef  RfgDpe
  gi|385805602|ref|YP_005842000.1| 260 KEEFNKTKE-IVEKVLENLKKETkEPYVGVLAGQMMLTwVWGPTVIEFYSRFGDPE 314
                                       *****9999.**********996268************9999*************9 PP

>> GARS_N  Phosphoribosylglycinamide synthetase, N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.3   0.0     3e-24   4.8e-21       1      90 []       1     107 [.       1     107 [. 0.94

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 3e-24
                                       EEEEEEESSHHHHHHHHHHTTSTTESEEEEEE..--CGG................TTHHHHHHHHHHCTESEEEE-S CS
                            GARS_N   1 mkvLvvGsGGRehalawklaqspkvekvyvap..gNagt................edlealvefakeekidlvvvGp 59 
                                       m+vL+vGsG+Rehala+ + +s+ ++++yv+    N+g                 +++e++ e ake + dl+v+G 
  gi|385805602|ref|YP_005842000.1|   1 MRVLIVGSGAREHALAKLFMDSTMLSRIYVFAdyLNPGLkretektggsivimntNNAETVREKAKEVNPDLIVIGG 77 
                                       9*****************************99889****999999999999988766778***************** PP

                                       HHHHHTTHHHHHHHHHT-EEES--CCCCHHH CS
                            GARS_N  60 eapLvaGvadaleeekgikvfGpskeaAqlE 90 
                                       e+pL+ Gv+dal+ee g+ vfG+s++ A++E
  gi|385805602|ref|YP_005842000.1|  78 EEPLFMGVSDALREE-GFFVFGASRKNAMIE 107
                                       ************877.**************9 PP

>> GARS_C  Phosphoribosylglycinamide synthetase, C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   1.2e-09   1.9e-06       2      79 ..     352     446 ..     351     447 .. 0.81

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 1.2e-09
                                       EEEEEEETTTT..SS--ST-EEBS.......TTEEEEESSEE.....EEE-SSEEEEEEEEESSHHHHHHHHHHHHT CS
                            GARS_C   2 vgvvlaskGYP..gsyekgkeitg.......egvkvfhagtk.....lvtsGGRvlavvavgetleeArakayeavk 64 
                                       v   +a+ GYP   + +++++it         g++ ++ +++     ++t+G+R + +v ++++ e A +k+++a +
  gi|385805602|ref|YP_005842000.1| 352 VVKAIAPLGYPlyRNEASNHPITIdekkirnLGCEALYGSVEqkdgkMLTKGSRAIEIVCYDSKYEVAYEKSEKASN 428
                                       5678999****6656668999988666555544445555544888889***************************** PP

                                       TCB-TT...EE--STTTH CS
                            GARS_C  65 kikfeg...lfyRkDIGa 79 
                                        i+ e+   lfyR+DIG+
  gi|385805602|ref|YP_005842000.1| 429 LIEAEDgwpLFYRSDIGS 446
                                       **998766689*****95 PP

>> ATPgrasp_ST  Sugar-transfer associated ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   5.5e-08   8.9e-05      42      99 ..     127     181 ..      99     195 .. 0.67

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 5.5e-08
                       ATPgrasp_ST  42 vikeqaeiseleafvkeleegvviKpakgsgGkGilviteredqdylkssgksallde 99 
                                        ++  +++se+e+f+k    +vv+Kpa++ gGkG++vi ++  + yl++++ s++++ 
  gi|385805602|ref|YP_005842000.1| 127 FFQAFKDLSEAEEFMKYA-GDVVVKPARQAGGKGVRVIRDT--KAYLSEEKSSVKMKV 181
                                       444558999******999.66*****************664..444444444333332 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.1   3.4e+03     105     129 ..      46      70 ..      33      77 .. 0.76
   2 !   18.4   0.0   1.1e-06    0.0017      23     140 ..     136     288 ..     116     312 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.1
                                       EEEEEES----HHHHHHHHHHHHHT CS
                       ATP-grasp_3 105 yaGnvtpietelkeevvelaeevve 129
                                         G+++ ++t+++e v+e a+ev  
  gi|385805602|ref|YP_005842000.1|  46 TGGSIVIMNTNNAETVREKAKEVNP 70 
                                       5577788888889999999998865 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 1.1e-06
                                       .-EESS--SSSEEEEESS-------B--SS--TTE.............................EEEE---SEEEEE CS
                       ATP-grasp_3  23 eaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve......................lvqefieGkplSv 77 
                                       eaee+ + +  +vvKp++ agg++vrv+++ ++  +  ++                        l+ +  eG ++++
  gi|385805602|ref|YP_005842000.1| 136 EAEEFMKYAGDVVVKPARQAGGKGVRVIRDTKAYLSEEKSSVkmkvaedvykqlsgyddidykiLLEQRAEGVEYTL 212
                                       67788888999*******************987665544444678899****************9************ PP

                                       EEEE.SSSEEEEEEEEEEEET..............TEEEEEEES----H.HHHHHHHHHHHHTTST..T--EEEEE CS
                       ATP-grasp_3  78 sllsdgekvlvlavnrqliekaeke..........fvyaGnvtpietel.keevvelaeevvekle..glaGyvGv 140
                                        ++sdg    +l + + + +  e +          ++  G   p+ t++  +++ e++e+v+e+l+      yvGv
  gi|385805602|ref|YP_005842000.1| 213 HVISDGFYSIPLPIIQDHAHAFEYDigpetggmgcISGPGMYPPFLTKEeFNKTKEIVEKVLENLKkeTKEPYVGV 288
                                       ******8888887777777655555999999997766667777888777578899999999999976433455555 PP

>> ATPgrasp_TupA  TupA-like ATPgrasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       2.3   3.7e+03      68     106 ..      47      66 ..      42     114 .. 0.62
   2 !   14.6   0.0   1.3e-05     0.021      54     119 ..     142     206 ..     124     215 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.3
                     ATPgrasp_TupA  68 Gsrgvlevkneldilkvkskllkylerndlkekrekkyk 106
                                       G+ +v+++ n+ + ++ k                    k
  gi|385805602|ref|YP_005842000.1|  47 GGSIVIMNTNNAETVREKA-------------------K 66 
                                       5555555555555444442...................3 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 1.3e-05
                     ATPgrasp_TupA  54 vikesiViKpthdsGsrgvlevkneldilkvkskllkylerndlkekrekkykdvkpriilEkklk 119
                                       +    +V+Kp  ++G++gv + +++   l+  +++ k ++    ++k+   y d+  +i+lE+  +
  gi|385805602|ref|YP_005842000.1| 142 KYAGDVVVKPARQAGGKGVRVIRDTKAYLSEEKSSVK-MKVAEDVYKQLSGYDDIDYKILLEQRAE 206
                                       556689**************99999999999999999.99988889999*************9765 PP

>> ATP-grasp_4  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.5e-05     0.041       5      70 ..     147     214 ..     143     233 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.5e-05
                       ATP-grasp_4   5 vviKPsvgffSlGVykinneeew.kaavaaieeeleqakeeykeev.ve..eesflvEeyieGeEfavda 70 
                                       vv+KP+ +++  GV++i++ + + ++  ++++  +++a++ yk+    +  + ++l+E+  eG E+ + +
  gi|385805602|ref|YP_005842000.1| 147 VVVKPARQAGGKGVRVIRDTKAYlSEEKSSVK--MKVAEDVYKQLSgYDdiDYKILLEQRAEGVEYTLHV 214
                                       9****************998877244444444..44555555542211123789************9865 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 ?   12.9   0.0   3.3e-05     0.054      21      58 ..     134     171 ..     122     201 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.3e-05
                                       HHHHHHHHHHHSSEEEEESS--TTTT-EEE-TT-TTHH CS
                         GSH-S_ATP  21 keeirafleeqgdvilKPldgkgGegvfrvkksdpnlk 58 
                                        +e ++f++  gdv++KP  + gG+gv  ++++++ l+
  gi|385805602|ref|YP_005842000.1| 134 LSEAEEFMKYAGDVVVKPARQAGGKGVRVIRDTKAYLS 171
                                       567899*********************99988776665 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 ?   12.7   0.0   3.4e-05     0.056      35      79 ..     131     174 ..     127     197 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.4e-05
                    ATPgrasp_YheCD  35 lesledleemlekyksvylKpanGskGkgilriekeekellllsr 79 
                                       +++l++ ee+++  ++v++Kpa+  +Gkg+  i+  +k++l  ++
  gi|385805602|ref|YP_005842000.1| 131 FKDLSEAEEFMKYAGDVVVKPARQAGGKGVRVIRD-TKAYLSEEK 174
                                       6778999***********************99999.443333332 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.4e-05     0.072      26     102 ..     133     202 ..     115     211 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.4e-05
                                       SHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHSTS-EEEEE--SSSEEEEEEEEEE CS
                       CPSase_L_D2  26 tleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafgnkqvlvekslkgpkeiEvevlrD 102
                                       +l ea ++ k  g  v++k+a   GGkG rv+r+++      k+++++       + v+  k l+g+ +i++++l  
  gi|385805602|ref|YP_005842000.1| 133 DLSEAEEFMKYAG-DVVVKPARQAGGKGVRVIRDTKAYLSEEKSSVKMKV----AEDVY--KQLSGYDDIDYKILLE 202
                                       5555555555554.59******************9998888888887773....45555..7788888888887765 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 ?   11.5   0.0   5.5e-05      0.09     274     349 ..       2      76 ..       1      82 [. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.5e-05
                                       EEEEECSSHHHHHHHHHHHHHT-EEEEEEESSS-HHHHHHHHHHS.TT.SEEEES.CHHHHHHHHHHHT-SEEEE- CS
                    Oxidored_nitro 274 rvaiygdpdrvvalarllkelGmevvaagtetahrddeerlkaeleegepeviddadleeleelikelkpdlllgg 349
                                       rv+i+g + r +ala+l+ +  m     ++ +  ++  +r  ++ +++  +++++++ e+++e +ke +pdl++ g
  gi|385805602|ref|YP_005842000.1|   2 RVLIVGSGAREHALAKLFMDSTMLSRIYVFADYLNPGLKRETEKTGGS-IVIMNTNNAETVREKAKEVNPDLIVIG 76 
                                       89*****************99998777777766666555666655555.577777999**************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (501 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       735  (0.040995); 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:                        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: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.48
# Mc/sec: 3165.64
//
Query:       gi|385805603|ref|YP_005842001.1|  [L=404]
Description: ATPase [Fervidicoccus fontis Kam940]
Scores for complete 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-43  147.7   0.1    3.7e-43  147.0   0.1    1.3  1  ATP-grasp        ATP-grasp domain
    7.1e-13   48.6   0.0    1.2e-12   47.8   0.0    1.3  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    2.7e-08   33.6   0.1    5.8e-08   32.5   0.0    1.6  2  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    9.3e-05   22.5   0.0    0.00023   21.3   0.0    1.6  1  ATP-grasp_3      ATP-grasp domain
     0.0035   16.6   0.0        1.8    7.7   0.0    2.2  2  ATPgrasp_YheCD   YheC/D like ATP-grasp
  ------ inclusion threshold ------
       0.13   11.7   0.0       0.28   10.6   0.0    1.6  1  ATP-grasp_5      ATP-grasp domain
       0.16   11.0   0.0       0.23   10.5   0.0    1.3  1  RmlD_sub_bind    RmlD substrate binding domain


Domain annotation for each model (and alignments):
>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.0   0.1   1.5e-46   3.7e-43       3     170 ..     125     304 ..     123     305 .. 0.92

  Alignments for each domain:
  == domain 1  score: 147.0 bits;  conditional E-value: 1.5e-46
                                       TTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEEC..TCCGHHCHHHHC......GTTCEEEEE- CS
                         ATP-grasp   3 klglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvr..seedleqaleal......keekvivEef 71 
                                       +l+lp++r+ ++e++ee+ e +e++g+p+++K + ++++G+G++ ++  s+e++++  +++      k+++vivEef
  gi|385805603|ref|YP_005842001.1| 125 QLNLPTTRYFVAENEEEAIEGCEKVGYPCIIK-PEMSSSGHGHFKIKegSKEEIRKGYTYAighargKSKRVIVEEF 200
                                       789*****************************.*************9444788888888889****99********* PP

                                       ---SEEEEEEEEE..ETTC-..EEE--EEEEEEE.TTEEEEEEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEE CS
                         ATP-grasp  72 vpfekElsvlvvr..saeGe..tafypvvetvqe.dgilrlsvapaevsekaqkkaeeiakkiveeLggvGvfavEl 143
                                       v++e+El+vlv r  s++G   t+++++ve+ +  +  + +s++p+  +++++++a++ia k++++Lgg G+f+vEl
  gi|385805603|ref|YP_005842001.1| 201 VELETELTVLVYRyeSESGGisTETCEPVEHWRYgKYHYIESWQPSVKDKNILASAKSIAIKVANRLGGKGIFGVEL 277
                                       *************887777545899******9862557899************************************ PP

                                       EEETTCTEEEEEEESS--GGGGGHHHH CS
                         ATP-grasp 144 FvledgellvnElapRpHnsGhvtlda 170
                                       F+++dg++l++E+apRpH++G+vt+ +
  gi|385805603|ref|YP_005842001.1| 278 FLTKDGRVLFSEVAPRPHDTGMVTMVT 304
                                       ************************976 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 !   47.8   0.0   4.7e-16   1.2e-12      17     179 ..     138     297 ..     121     312 .. 0.83

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 4.7e-16
                                       TTHHCH-H-HHHHHHHHHC-SSEEEEESSSSTTTTEEEES..SGGGHHH....HHHHHHTT-SCEEEEE--.ESEEE CS
                   Dala_Dala_lig_C  17 keeakeekkellekveeelgypvfVKpareGSSvGvskve..seeelke....aieeafkydekvlvEeai.egrei 86 
                                       +       +e   + +e++gyp+++Kp  + S  G  k++  s+ee+++    ai +a  + ++v+vEe++    e+
  gi|385805603|ref|YP_005842001.1| 138 N-------EEEAIEGCEKVGYPCIIKPEMSSSGHGHFKIKegSKEEIRKgytyAIGHARGKSKRVIVEEFVeLETEL 207
                                       2.......2334455899******************9998445666544333399999999**********5568** PP

                                       EEEEEETSSCEEEEEEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEET CS
                   Dala_Dala_lig_C  87 evavlgneklevsevgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflte 163
                                       +v v   e+       e     + ++y  ky  + ++   p   +k++ ++ + +a+k+ + l+++G+  v +flt+
  gi|385805603|ref|YP_005842001.1| 208 TVLVYRYESESGGISTETCEPVEHWRYG-KY--HYIESWQPSVKDKNILASAKSIAIKVANRLGGKGIFGVELFLTK 281
                                       ******9999999999999999****96.67..46888999999********************************* PP

                                       TTEEEEEEEESS---S CS
                   Dala_Dala_lig_C 164 egeivlnEvNtlPGfT 179
                                       +g+++++Ev + P  T
  gi|385805603|ref|YP_005842001.1| 282 DGRVLFSEVAPRPHDT 297
                                       *********9999544 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 ?   -3.6   0.0       2.5   6.5e+03     127     148 ..      47      70 ..      44      72 .. 0.78
   2 !   32.5   0.0   2.3e-11   5.8e-08      12     191 ..     124     305 ..     113     325 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.5
                                       EES-SS--HHHH..HHHHHHHHHH CS
                       CPSase_L_D2 127 vAPsqtLtdeer..qalreaavkv 148
                                        AP+  ++++++  ++++++a+k+
  gi|385805603|ref|YP_005842001.1|  47 FAPAMHVSSKRYivDMMNKEAIKA 70 
                                       689999998887557888888886 PP

  == domain 2  score: 32.5 bits;  conditional E-value: 2.3e-11
                                       TT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEES..SHHHHHHHHHHHHHHHHHHHSTS-EEEE CS
                       CPSase_L_D2  12 invpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvar..neeelaelvkkalaeakaafgnkqvlve 86 
                                       ++ ++      ++e++eea++  +++gyP+iik+ ++  G+G   ++  ++ee+++ ++ a+ +a+    +k+v ve
  gi|385805603|ref|YP_005842001.1| 124 VQLNLPTTRYFVAENEEEAIEGCEKVGYPCIIKPEMSSSGHGHFKIKegSKEEIRKGYTYAIGHAR--GKSKRVIVE 198
                                       4444444444556*****************************85555135899************7..56789**** PP

                                       E--SSSEEEEEEEEEETTS.-EEEEEEEEECCECTCCCC.EEEES-SS--HHH.HHHHHHHHHHHHHHHT-EEEEEE CS
                       CPSase_L_D2  87 kslkgpkeiEvevlrDakg.nvitvcerenslqlrtqkv.ievAPsqtLtdee.rqalreaavkvvrevgvvgagtv 160
                                       ++++   e+ v v r +++   i   + e +   r +k    +   + ++d++     ++ a+kv++ +g +g   v
  gi|385805603|ref|YP_005842001.1| 199 EFVELETELTVLVYRYESEsGGISTETCEPVEHWRYGKYhYIESWQPSVKDKNiLASAKSIAIKVANRLGGKGIFGV 275
                                       ****9999998888865541578888888888889998533444555555555156778889999999999999999 PP

                                       EEEEETTTTEEEEEEEESS--CCHHHHHHHH CS
                       CPSase_L_D2 161 eflldpkskeyyviEvNtRlsvesalaekaT 191
                                       e  l + +++  + Ev +R      ++  + 
  gi|385805603|ref|YP_005842001.1| 276 ELFLTK-DGRVLFSEVAPRPHDTGMVTMVTQ 305
                                       999996.999999999999776666665555 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   8.9e-08   0.00023      16     158 ..     126     294 ..     116     297 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 8.9e-08
                                       S---.............-EESS--SSSEEEEESS-------B--SS--TTE...................EEEE--- CS
                       ATP-grasp_3  16 vkvP.........tkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve............lvqefie 71 
                                       +++P         ++   e +e++ +++++Kp  ++ g++ ++++e+ ++e    ++             +v ef+e
  gi|385805603|ref|YP_005842001.1| 126 LNLPttryfvaenEEEAIEGCEKVGYPCIIKPEMSSSGHGHFKIKEGSKEEIRKGYTYaighargkskrvIVEEFVE 202
                                       566664444443333445566777***********************999977777668899999999999999999 PP

                                       SE.EEEEEEEE.SSSEEEEEE..EEEEEET....TEEEEEEES----H..HHHHHHHHHHHHTTSTT--EEEEEEEE CS
                       ATP-grasp_3  72 Gk.plSvsllsdgekvlvlav..nrqliekaekefvyaGnvtpietel..keevvelaeevvekleglaGyvGvDlv 143
                                        + +l+v +   +++   +++  ++ + +++  ++ y  +  p+ +++    ++ ++a +v ++l g +G++Gv+l 
  gi|385805603|ref|YP_005842001.1| 203 LEtELTVLVYRYESESGGISTetCEPVEHWRYGKYHYIESWQPSVKDKniLASAKSIAIKVANRL-GGKGIFGVELF 278
                                       642788888776666655554115555555555699999****99888555788999********.*********99 PP

                                       ESS..SEEEEEEESS- CS
                       ATP-grasp_3 144 lkd.eepyviEvNPRl 158
                                       l++ +   + Ev PR+
  gi|385805603|ref|YP_005842001.1| 279 LTKdGRVLFSEVAPRP 294
                                       8774777788*****8 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 !    6.5   0.0    0.0017       4.3      23      96 ..     122     204 ..     117     213 .. 0.61
   2 !    7.7   0.0    0.0007       1.8     180     231 ..     250     297 ..     231     312 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0017
                    ATPgrasp_YheCD  23 pelrpyLPetelle..sledleemlekyks.vylKpanGskGkgilriek......eekellllsrekkkkkkkrla 90 
                                        +++  LP t+ +   + e+  e +ek +  +++Kp+ +s G+g ++i++      +++ +++ ++ ++k+k+  ++
  gi|385805603|ref|YP_005842001.1| 122 ASVQLNLPTTRYFVaeNEEEAIEGCEKVGYpCIIKPEMSSSGHGHFKIKEgskeeiRKGYTYAIGHARGKSKRVIVE 198
                                       55666678887763224555555566666568******************655543333333334444445555555 PP

                    ATPgrasp_YheCD  91 slsele 96 
                                       ++ ele
  gi|385805603|ref|YP_005842001.1| 199 EFVELE 204
                                       555555 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0007
                    ATPgrasp_YheCD 180 ekileeleelalelaealeesfgrlgElGlDlgidkegkvWllEvNskpgrs 231
                                       ++il +++++a+++a    +++g+ g +G+ l ++k+g+v + Ev  +p+ +
  gi|385805603|ref|YP_005842001.1| 250 KNILASAKSIAIKVA----NRLGGKGIFGVELFLTKDGRVLFSEVAPRPHDT 297
                                       555555555555555....55567899******************9999876 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00011      0.28      22      88 ..     126     188 ..     108     216 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00011
                       ATP-grasp_5  22 ygipvvetrlassaeeaveaaeeigypvvlKivspdilhKtdvgGvrlnlkdaeevraaaeeilerv 88 
                                       +++p+++  +a+++eea+e +e++gyp+ +K    +  h    g  +++  ++ee+r+ +   + ++
  gi|385805603|ref|YP_005842001.1| 126 LNLPTTRYFVAENEEEAIEGCEKVGYPCIIKPEMSSSGH----GHFKIKEGSKEEIRKGYTYAIGHA 188
                                       4567777777*********************77654433....334444445666666666655555 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   9.1e-05      0.23       3      57 ..      16      82 ..      14     136 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 9.1e-05
                                      EEEESTTSHHHHHHHHHCTTTSEEEEEE-TT.............T--TTSHHHHHHHHHHH--SEEEE CS
                     RmlD_sub_bind  3 ilvtGanGqlGseLakqlaeeglevlaltre.............eldltdaeavaellkeakpdvvvn 57
                                      ++++G +G lG+e+  ++++ g+e++a++r               +d+ ++ea+++l    +pdv++ 
  gi|385805603|ref|YP_005842001.1| 16 VMLLG-SGELGKEISIEAQRLGAETIAVDRYdfapamhvsskryIVDMMNKEAIKALAYRERPDVIIP 82
                                      56666.69**********************99***********99********************973 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.29s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 2623.61
//
Query:       gi|385805604|ref|YP_005842002.1|  [L=134]
Description: phosphoribosylaminoimidazole carboxylase [Fervidicoccus fontis Kam940]
Scores for 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-49  165.4   0.1    7.4e-49  165.1   0.1    1.0  1  AIRC      AIR carboxylase
     0.0095   15.7   0.0      0.012   15.4   0.0    1.1  1  Fe-ADH_2  Iron-containing alcohol dehydrogenase


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 !  165.1   0.1   8.2e-53   7.4e-49       1     129 [.       6     130 ..       6     132 .. 0.97

  Alignments for each domain:
  == domain 1  score: 165.1 bits;  conditional E-value: 8.2e-53
                                       EEEEEESSGGGHHHHHHHHHHHHHTT-EEEEEE--TTTSHHHHHHHHHHCHTTTEEEEEEEEESS--HHHHHHHHSS CS
                              AIRC   1 kVgiimGSdsDlevmkkaaeilkelgveyevrvvSahrtpeelleyaeeaeerglkviIagAGgaahLpgvvasltt 77 
                                       kV ii+GS+ Dl++ ++a +ilke ++e+e++v+Sahr+p++l++y+++    +++v+Ia+AG +ahLpg++as t+
  gi|385805604|ref|YP_005842002.1|   6 KVSIIVGSERDLPFSERASKILKENSIEFEIKVLSAHRNPKDLENYISNS---DVDVFIAMAGLSAHLPGFIASRTN 79 
                                       69********************************************9965...599********************* PP

                                       S-EEEEEE--STTCCHHHHHHHHT--TTS--EE-SSTHHHHHHHHHHHHHTT CS
                              AIRC  78 lPVigvPvkskalkgldsllSivqmPsgvpvatvaigkaknAallAaqilal 129
                                        PVigvP++  +l gldsllSivqmP+gvpvatv+i++++nAa lA++i++l
  gi|385805604|ref|YP_005842002.1|  80 KPVIGVPLNV-SLGGLDSLLSIVQMPKGVPVATVGIDNPENAAHLAVRIISL 130
                                       **********.9*************************************986 PP

>> Fe-ADH_2  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.3e-06     0.012      21     119 ..       6      99 ..       2     113 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.3e-06
                          Fe-ADH_2  21 kvllvadentkkaagekveeslkeagikvevveeveeeadleeveklvealreketdlvvavGgGtiiDiakyvsak 97 
                                       kv ++++++      e+ ++ lke+ i+ e+    +++++ ++ e+    ++++++d+++a+ +G    +  +++++
  gi|385805604|ref|YP_005842002.1|   6 KVSIIVGSERDLPFSERASKILKENSIEFEIK-VLSAHRNPKDLENY---ISNSDVDVFIAM-AGLSAHLPGFIASR 77 
                                       6788888888888999999********99944.46666677766655...56679*******.788888******** PP

                          Fe-ADH_2  98 lnvpyvsvpTaaSvDGfaspga 119
                                       +n+p++ vp   S  G  s  +
  gi|385805604|ref|YP_005842002.1|  78 TNKPVIGVPLNVSLGGLDSLLS 99 
                                       **************99988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 891.48
//
Query:       gi|385805605|ref|YP_005842003.1|  [L=78]
Description: hypothetical protein FFONT_0561 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-18   66.5   0.3    1.9e-18   66.4   0.3    1.0  1  PurS          Phosphoribosylformylglycinamidine (FGAM) syntha
  ------ inclusion threshold ------
      0.035   14.6   0.1       0.04   14.4   0.1    1.2  1  DUF1878       Protein of unknown function (DUF1878)
       0.12   12.4   0.0       0.12   12.4   0.0    1.1  1  Terminase_6C  Terminase RNaseH-like domain


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 !   66.4   0.3   3.1e-22   1.9e-18       5      75 ..       2      74 ..       1      76 [. 0.96

  Alignments for each domain:
  == domain 1  score: 66.4 bits;  conditional E-value: 3.1e-22
                                      EEEE-TTS--HHHHHHHHHHHHT.THTTEEEEEEEEEEEEEEE-SSHHHHHHHHHHHHHHT.TS-TTTEEEEE CS
                              PurS  5 eVtlKkgvlDpqGkavkkalksl.gyeevedvrvgkyieleleaedeeeaeeeveemcekl.LaNpviedyei 75
                                      ++t++k+++Dp+ + ++k+l    gy +v++v +gky+++ +e++++e+a ++v+e+cekl ++Np+ +++e+
  gi|385805605|ref|YP_005842003.1|  2 IITYRKELRDPESEIIHKDLILKkGYANVKKVTTGKYFSMLVESDTKENAISTVRELCEKLrIYNPIAQEIEV 74
                                      69******************9888*********************************************9997 PP

>> DUF1878  Protein of unknown function (DUF1878)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   6.6e-06      0.04      24      54 ..      33      63 ..      13      76 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6.6e-06
                                      TTT-HHHHHHHHTT--HHHHHHHHHHHHHHH CS
                           DUF1878 24 eeklpfyklviekklskeeveeilklCekLs 54
                                       ++ +++++++e + +++ + ++ +lCekL 
  gi|385805605|ref|YP_005842003.1| 33 VTTGKYFSMLVESDTKENAISTVRELCEKLR 63
                                      45668************************95 PP

>> Terminase_6C  Terminase RNaseH-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0     2e-05      0.12      67     119 ..      24      74 ..       5      78 .] 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2e-05
                                       HHHHHHHHCCT--S-SCEESSH..HHHHHHHHHHHHHHHTTSEEEETHHCECC CS
                      Terminase_6C  67 esvaellkrdlesealavkpepaskdkatrvskvkdliesgrlkvdkgaecak 119
                                       ++ ++++k+   ++++ +++e+   +k++ +s+v++l+e+ r++ + ++e++ 
  gi|385805605|ref|YP_005842003.1|  24 KKGYANVKKVTTGKYFSMLVES--DTKENAISTVRELCEKLRIYNPIAQEIEV 74 
                                       566788888888899******9..****************9998776656655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); 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: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 503.53
//
Query:       gi|385805606|ref|YP_005842004.1|  [L=224]
Description: phosphoribosylformylglycinamidine synthase I [Fervidicoccus fontis Kam940]
Scores for complete 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-41  139.8   0.0    1.5e-40  138.9   0.0    1.4  1  GATase_5       CobB/CobQ-like glutamine amidotransferase doma
    4.3e-10   39.7   0.0    5.5e-10   39.3   0.0    1.2  1  GATase         Glutamine amidotransferase class-I
    1.9e-08   34.1   0.0    3.2e-08   33.4   0.0    1.3  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
    5.1e-07   29.6   0.0    7.1e-07   29.2   0.0    1.2  1  DJ-1_PfpI      DJ-1/PfpI family
    0.00096   19.0   0.0     0.0018   18.2   0.0    1.4  1  SNO            SNO glutamine amidotransferase family
  ------ inclusion threshold ------
       0.02   14.7   0.0      0.029   14.1   0.0    1.2  1  Peptidase_C26  Peptidase C26


Domain annotation for each model (and alignments):
>> GATase_5  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.9   0.0   5.1e-44   1.5e-40       7     235 ..       2     201 ..       1     214 [. 0.86

  Alignments for each domain:
  == domain 1  score: 138.9 bits;  conditional E-value: 5.1e-44
                          GATase_5   7 lreeGvngeyemaaafek.aGfeavdvhmsdllegrvslddfqilalpGGfsygDelgsgkgwakslllneklreal 82 
                                       + ++G+n++ ++ +a+++    +a+ v  +d      + +++  +++pGGfsygD l +g+++a+s  ++e ++ea+
  gi|385805606|ref|YP_005842004.1|   2 ISFPGTNCDLDTVSAIKElTSLDAEIVWHKDF-----KGKKYDAIIIPGGFSYGDWLRAGAIAARSKAMEEVVEEAI 73 
                                       679*************8724566666776666.....5569***********************8887766666666 PP

                          GATase_5  83 ekflnredtlaLGiCnGfqlLvklglvpggeieeaeksptltrNksgrfesrlvsv.vvsekspsvfl.kgmeglsl 157
                                             +++ +LGiCnGfq+Lv+  l+pg           l  N+ grf++r+++v + + k p++ l ++ e++++
  gi|385805606|ref|YP_005842004.1|  74 ------NGKPVLGICNGFQILVESSLLPG----------VLLPNELGRFICRWTRVsIENPKGPWLKLaNKKEKIDM 134
                                       ......3799*******************..........8****************8888999*****56667**** PP

                          GATase_5 158 pvahGeGrfvfkseevlkeleangqvalrYvdeegkpteeyplNPNgSpegiagitspdGRvlalmpHpervveavq 234
                                       p+ah+eGrf + ++e +k++ ++   ++ Y+++         +NPNgS ++iagi +++G vl+lmpHper+++++ 
  gi|385805606|ref|YP_005842004.1| 135 PIAHAEGRFYI-DSEKFKAISNS--SPIIYYEN--------GWNPNGSFYDIAGIGNEEGNVLGLMPHPERAYTEIL 200
                                       ***********.66777776554..45556666........6*****************************998776 PP

                          GATase_5 235 k 235
                                        
  gi|385805606|ref|YP_005842004.1| 201 S 201
                                       5 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   0.0   1.9e-13   5.5e-10      24     128 ..      25     156 ..       9     198 .. 0.65

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 1.9e-13
                                       EEEEETTSHHHHHHH...THHSTSEEEEEEESSCTT..TTTHHHHHHHHCT.......STS-EEEETHHHHHHHHHT CS
                            GATase  24 vevvpidasaeeile...llknpdgilvsgGpgspg..vegkieaikeare.......nkiPiLGICLGmQllaief 88 
                                        e+v         ++   + k++d+i+++gG+ +    + g+i+a ++a+e       n++P+LGIC G+Q+l++++
  gi|385805606|ref|YP_005842004.1|  25 AEIV---------WHkdfKGKKYDAIIIPGGFSYGDwlRAGAIAARSKAMEevveeaiNGKPVLGICNGFQILVESS 92 
                                       2333.........333345789************9999889999988888888889999***************998 PP

                                       TT..................EEE.........EEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEE CS
                            GATase  89 gr..................kvv.........kekekehhggtmrlgddetallyglknevierhrH 128
                                                                       k   +++ +  m++ +  ++++y +++++++  + 
  gi|385805606|ref|YP_005842004.1|  93 LLpgvllpnelgrficrwtrV-SienpkgpwlKLA-NKKEKIDMPIAH-AEGRFYIDSEKFKAISNS 156
                                       775555555555544444440.1444444444555.555666666666.345666666666655555 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 !   33.4   0.0   1.1e-11   3.2e-08      29      91 ..      27      91 ..       9      96 .. 0.70

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 1.1e-11
                          GATase_3 29 fvplkdeslgedadlvilpGgkdt...iqdlallresgldeaikeaaeaggpvlgiCGGlqmLGee 91
                                      +v  +++  g+++d++i+pGg+++   +++ a++++s+  e++ e a +g+pvlgiC G+q+L e+
  gi|385805606|ref|YP_005842004.1| 27 IVW-HKDFKGKKYDAIIIPGGFSYgdwLRAGAIAARSKAMEEVVEEAINGKPVLGICNGFQILVES 91
                                      444.33444478**********982223344555555666666666668**************875 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 !   29.2   0.0   2.4e-10   7.1e-07      55     115 ..      31      96 ..       6      99 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 2.4e-10
                                       GGCTCCG-SEEEE--BHHHHHHHHTSH.....HHHHHHHHHHHTT-EEEEETTTHHHHHHTTTTTT CS
                         DJ-1_PfpI  55 ddvkaaeyDalvlpGGragperlrene.....kvvelvkefaekgklvaaICagpqlLaaagvlkg 115
                                       +d k ++yDa+++pGG +  + lr+ +     k++e v e a +gk+v  IC g q+L++ ++l+g
  gi|385805606|ref|YP_005842004.1|  31 KDFKGKKYDAIIIPGGFSYGDWLRAGAiaarsKAMEEVVEEAINGKPVLGICNGFQILVESSLLPG 96 
                                       388899************98888765433333888888888889*****************99987 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   5.9e-07    0.0018      32      82 ..      36      89 ..      11      96 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 5.9e-07
                                      CC-SEEEE-SS-HHH....HHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHHHC CS
                               SNO 32 aevdaliiPGGesta....mskliertglyedllefvknsekvvlGtCaGlills 82
                                      ++ da+iiPGG s       + ++ r + +e++ e + n+ k+vlG C G+ +l 
  gi|385805606|ref|YP_005842004.1| 36 KKYDAIIIPGGFSYGdwlrAGAIAARSKAMEEVVEEAING-KPVLGICNGFQILV 89
                                      578*******999643322689******************.*********97775 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   9.7e-06     0.029      95     118 ..      66      88 ..      38      97 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9.7e-06
                     Peptidase_C26  95 laLiraalergvPilgiCrGlqll 118
                                         ++++a+ +g+P+lgiC G+q+l
  gi|385805606|ref|YP_005842004.1|  66 EEVVEEAI-NGKPVLGICNGFQIL 88 
                                       45555555.589**********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.32s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1372.13
//
Query:       gi|385805607|ref|YP_005842005.1|  [L=730]
Description: phosphoribosylformylglycinamidine synthase II [Fervidicoccus fontis Kam940]
Scores for complete 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-45  151.3   0.0    4.2e-23   81.8   0.0    2.3  2  AIRS            AIR synthase related protein, N-terminal doma
    1.1e-41  142.6   0.2    2.1e-24   86.4   0.1    2.2  2  AIRS_C          AIR synthase related protein, C-terminal doma
    5.6e-11   42.8   0.2    1.3e-10   41.7   0.2    1.7  1  FGAR-AT_linker  Formylglycinamide ribonucleotide amidotransfe
  ------ inclusion threshold ------
       0.19   11.8   0.0       0.34   11.0   0.0    1.3  1  DUF3801         Protein of unknown function (DUF3801)


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 !   81.8   0.0   9.5e-27   4.2e-23       2      94 .]      72     176 ..      62     176 .. 0.95
   2 !   67.2   0.0   3.3e-22   1.5e-18       2      93 ..     424     540 ..     423     543 .. 0.91

  Alignments for each domain:
  == domain 1  score: 81.8 bits;  conditional E-value: 9.5e-27
                                       SSEEEEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.........HHHHHHHHHHHHHHHT CS
                              AIRS   2 DaavvvttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalp.........wleevvrglaeaaeel 69 
                                       D  vv++++shn+p++v+p+++ +a++++++++D+++ GA+P+all+ l l+          ++++v+g++++++++
  gi|385805607|ref|YP_005842005.1|  72 DTLVVFKIESHNHPSAVDPYNG-AATGIGGVVRDVLTLGAKPVALLDLLYLGepknphanwLIKGIVKGISDYGNRI 147
                                       44489*****************.*************************************999************** PP

                                       T-EEEEEEEEEESS....EEEEEEEEEEE CS
                              AIRS  70 gvplvgGdtsfsne....ptisvtavGlv 94 
                                       gvp+v+Gdt f+++    p+++v++vG+v
  gi|385805607|ref|YP_005842005.1| 148 GVPTVSGDTWFDPSfntqPLVNVGCVGIV 176
                                       ************99999**********97 PP

  == domain 2  score: 67.2 bits;  conditional E-value: 3.3e-22
                                       SSEE...........EEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.........HHHHH CS
                              AIRS   2 Daav...........vvttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalp.........wleev 58 
                                       Daav           +v+ d+++r+++++p+++  a  va+n+++l a+GA+Pla+++ l+ +          +e++
  gi|385805607|ref|YP_005842005.1| 424 DAAVlrlgpgdkrgfAVKGDGNPRYTFLDPFKG-SANIVAENYRNLTAVGAEPLAIVDELNAGnpekpdhywYFEKM 499
                                       8886666667777779*****************.*************************************99**** PP

                                       HHHHHHHHHHTT-EEEEEEEEEESS......EEEEEEEEEE CS
                              AIRS  59 vrglaeaaeelgvplvgGdtsfsne......ptisvtavGl 93 
                                       ++g++ + e+l+ p+vgG++sf+ne      + +++t++G+
  gi|385805607|ref|YP_005842005.1| 500 IKGVSWMSEQLNLPVVGGKVSFYNEdskgkmIKPTTTIIGI 540
                                       ***********************999*****6666666664 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 !   86.4   0.1   4.8e-28   2.1e-24       2     152 ..     188     338 ..     187     341 .. 0.92
   2 !   54.1   0.0     4e-18   1.8e-14       2     151 ..     557     700 ..     556     703 .. 0.90

  Alignments for each domain:
  == domain 1  score: 86.4 bits;  conditional E-value: 4.8e-28
                                       TTEEEEEEET....SSCTCCHHHHHHHCHHHCTSHTT.TSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHH CS
                            AIRS_C   2 pGdvliltgs....lGlggagtslkrkileeegldds.avqlgdvlleptliyvkralaalkglvkaahDvTgGGLl 73 
                                        G++++++g+    +G+ g+++++k   +e+e+  ++ avq+gd+l e+ li + ++++++ +lv+ ++D++gGGL+
  gi|385805607|ref|YP_005842005.1| 188 SGNLIVVIGNptgrDGILGSSFASKSLSGEPEK--EIgAVQIGDALTEKLLISAILEMIER-KLVNYVKDLGGGGLT 261
                                       699******************777775555555..345**********************8.*************** PP

                                       HHHHHHHHTTTEEEEEECGTHHHHHHHHHHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEESSS CS
                            AIRS_C  74 galaemapasgvgaeidldkvpifdelesplemllsensGrllvavppeeadavlaileeeglpeaavIGevtakee 150
                                        al+e + +  +gae+ ldk+ ++ +l +pleml+se+++r+l++++ ++ + v++ile++++  ++vIG++ +++ 
  gi|385805607|ref|YP_005842005.1| 262 TALSETLSEFSLGAEVKLDKLHLRTNL-TPLEMLVSESQERMLLIIDGKNFEDVKKILEKYEI-AYSVIGTLNNSGI 336
                                       *********99***************9.***********************************.7******999876 PP

                                       EE CS
                            AIRS_C 151 ls 152
                                       ls
  gi|385805607|ref|YP_005842005.1| 337 LS 338
                                       65 PP

  == domain 2  score: 54.1 bits;  conditional E-value: 4e-18
                                       TTEEEEEEET..SSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHH CS
                            AIRS_C   2 pGdvliltgs..lGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaalkglvkaahDvTgGGLlgal 76 
                                       +G  +  +g+    +gg+ ++ + ++ e+ + +        +l+e +    +r+l+ + +   a+hD++ GG+++a+
  gi|385805607|ref|YP_005842005.1| 557 AGSIIAIVGEtlPEIGGSEYLYAIHGKEFGEIP-----YPRPLAEVKAGSFVRELIKR-NIPLAVHDIGSGGISVAI 627
                                       678888888888999999988888888888877.....8999***************8.****************** PP

                                       HHHHHTTTEEEEEECG.THHHHHHHHHHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEESSSE CS
                            AIRS_C  77 aemapasgvgaeidld.kvpifdelesplemllsensGrllvavppeeadavlaileeeglpeaavIGevtakeel 151
                                       +em   +++ga++dl+  +   ++  + +e+l+se+  r+++ +p+e +d+v++i++   + + + IG v + ++ 
  gi|385805607|ref|YP_005842005.1| 628 MEMSISGKIGATVDLSlVPNRGCK--TLTEVLFSESGARYILEIPREMKDTVIQIARTFKV-DLSFIGMVSDNNRI 700
                                       ****************55555555..69********************************9.8*******998876 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 !   41.7   0.2   2.8e-14   1.3e-10      10      50 .]       3      40 ..       1      40 [. 0.96

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 2.8e-14
                    FGAR-AT_linker 10 laLsdeEidylqeafeklgrnPtdvElemfaqvwSEHCrHK 50
                                      + L++eE++ +++    lgr+Pt  El mf + wSEHC++K
  gi|385805607|ref|YP_005842005.1|  3 MPLTKEEVQEIKSL---LGREPTGEELAMFEAQWSEHCSYK 40
                                      679***********...9**********************9 PP

>> DUF3801  Protein of unknown function (DUF3801)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   7.5e-05      0.34      24      73 ..     291     340 ..     261     349 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7.5e-05
                           DUF3801  24 lkkLlkkggdlkvlqlddsdlkefkkeAkkyGilYavkkdkndkgqteii 73 
                                       l+ L+ + ++   l +d ++  ++kk + ky i Y+v+ + n++g   i+
  gi|385805607|ref|YP_005842005.1| 291 LEMLVSESQERMLLIIDGKNFEDVKKILEKYEIAYSVIGTLNNSGILSIY 340
                                       556677778888899**********************9998877766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (730 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); 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: 0.68u 0.32s 00:00:01.00 Elapsed: 00:00:00.48
# Mc/sec: 4527.64
//
Query:       gi|385805608|ref|YP_005842006.1|  [L=476]
Description: amidophosphoribosyltransferase [Fervidicoccus fontis Kam940]
Scores for complete 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   0.0      8e-12   45.2   0.0    2.1  2  GATase_7      Glutamine amidotransferase domain
    4.7e-11   43.0   0.0    8.1e-11   42.2   0.0    1.5  1  GATase_6      Glutamine amidotransferase domain
    2.6e-06   27.1   0.2    4.8e-06   26.2   0.2    1.4  1  Pribosyltran  Phosphoribosyl transferase domain


Domain annotation for each model (and alignments):
>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   0.0   1.3e-15     8e-12      10     121 ..      90     214 ..      80     216 .. 0.82
   2 ?   -1.1   0.0      0.29   1.7e+03      41      66 ..     447     471 ..     441     475 .. 0.76

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 1.3e-15
                          GATase_7  10 eagaQPmvs.sedgrlvivfnGeiyNykelreeLeakg..hrf...rtksDtevllallea..........ewgeea 70 
                                       +a +QP++  s+d ++ ++fnG+i Nykel ++L++++  +r+    ++ D+ +l+++l +          e ++ +
  gi|385805608|ref|YP_005842006.1|  90 SAPSQPVLLeSNDIKFSLAFNGTIANYKELDSKLARRKgeYRIspkIKNNDSITLANVLYSlyidnekdivEALRYL 166
                                       56689*9988999**********************9863443322246778888777766678889*9999999999 PP

                          GATase_7  71 lerlnGmfAfaiwdeeekrlllaRDrlGikPLyygedkgdallfaSelkal 121
                                        + + G +++++ + +e r+++a+D++G++PL y +++  +++ aSe  al
  gi|385805608|ref|YP_005842006.1| 167 PNYVIGGYSIVVET-NEPRIVIAKDPYGFRPLSYSYES--GFYAASENPAL 214
                                       9********98755.555*******************5..7******9998 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.29
                          GATase_7  41 eLeakghrfrtksDtevllalleaew 66 
                                        + + ++ f++ks +e +  l+++ +
  gi|385805608|ref|YP_005842006.1| 447 ACFSCKYPFSEKSSCEYIKMLIDR-G 471
                                       55667899*********9888775.4 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.0   1.4e-14   8.1e-11      13     134 .]      73     210 ..      32     210 .. 0.77

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 1.4e-14
                          GATase_6  13 e..valaHvRlaivglaeeegaqPf..psedgrlllvhNGeiynykelreelpalkgla....frsrsDtevlla.l 80 
                                       +   +++HvR +++g   ++  qP+   s+d +++l++NG+i nykel  +l++ kg        +++D+  l++ l
  gi|385805608|ref|YP_005842006.1|  73 KviGGIGHVRYSTTGSY-SAPSQPVllESNDIKFSLAFNGTIANYKELDSKLARRKGEYrispKIKNNDSITLANvL 148
                                       35579***********8.6666***99999999*************999999997776656534569********55 PP

                          GATase_6  81 l.....eelG.eevle....rlrGmfafaiwdk.rentlilardrlgvkplyyavdesglafase 134
                                       +     +e +  e+l+     + G +++  + +  e ++++a+d  g +pl+y++ esg++ ase
  gi|385805608|ref|YP_005842006.1| 149 YslyidNEKDiVEALRylpnYVIGGYSI--VVEtNEPRIVIAKDPYGFRPLSYSY-ESGFYAASE 210
                                       5755443333433332112244444444..44549999****************8.9******98 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.2     8e-10   4.8e-06      30     120 ..     290     386 ..     267     388 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 8e-10
                                       GEEEEEEETTTHHHHHHHHHHSTT-EE.-EEEEEE-TTT..--EE...........EE----TTSEEEEE-SEESSS CS
                      Pribosyltran  30 pdvvvgiargGvpfakiladeLevpla.yvrkvkyrpdg..seeaargssdes...rlledpagkkVliVDDildtG 100
                                        dvv++++  G ++a  ++++ ++p+   + + ky + g  ++ ++r ++  +     +e ++gk V+++DD +  G
  gi|385805608|ref|YP_005842006.1| 290 GDVVIPVPDSGRVIALGYSKASGIPIEeGIVVNKYLGRGfiTPPFQRPLVTKIkynIVEEAVRGKEVVLIDDSIVRG 366
                                       58***********************998999999998883345677777766699889******************* PP

                                       HHHHHHHHHHHCC-BSEEEE CS
                      Pribosyltran 101 gTllaalelLkekgpeevri 120
                                       +T+   +  Lk kg+++v+i
  gi|385805608|ref|YP_005842006.1| 367 TTMSDLVPKLKLKGAKKVHI 386
                                       *****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (476 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 2967.07
//
Query:       gi|385805609|ref|YP_005842007.1|  [L=336]
Description: phosphoribosylformylglycinamidine cyclo-ligase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-18   67.1   0.0    3.2e-18   66.3   0.0    1.3  1  AIRS_C    AIR synthase related protein, C-terminal domain
    6.7e-11   42.7   0.1    1.5e-10   41.6   0.1    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 !   66.3   0.0   3.6e-22   3.2e-18       1     149 [.     163     320 ..     163     323 .. 0.91

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 3.6e-22
                                       STTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTT....TSEHHHHHHHHHHHHHHHHHHHH.HTTECEEEE--TTHH CS
                            AIRS_C   1 kpGdvliltgslGlggagtslkrkileeegldds....avqlgdvlleptliyvkralaal.kglvkaahDvTgGGL 72 
                                       k+Gdv+++++s Gl+++g+sl+rk++ee+   ++    +  l  +l +pt +y ++++  + k+l+++a++vTgGG 
  gi|385805609|ref|YP_005842007.1| 163 KEGDVVVGVESNGLHSNGYSLVRKVVEEKIGGYDreieGLDLKVELTKPTFLYYNLIIESIkKDLINSAAHVTGGG- 238
                                       79**************************98888889*6556*********************************87. PP

                                       HHHHHHHHHTTTEEEEEECG.THHHHHHHH.....HHHHHHHCSTTTEEEEEEEHGGH.HHHHHHHHHTTCCCEEEE CS
                            AIRS_C  73 lgalaemapasgvgaeidld.kvpifdele.....splemllsensGrllvavppeea.davlaileeeglpeaavI 142
                                       +  l++++ +  + ++++ +  ++if+ l        +e++ ++n+G++lv+  ++e+ +++++++e++      ++
  gi|385805609|ref|YP_005842007.1| 239 WKKLKRVLGEV-LDMNLSPPpPPQIFEVLLkygeiPIEEAYSVFNMGVGLVFTTEKESlEELIELIERHSF-RPVIL 313
                                       799****9997.8888888866666666669999999999999**************************99.699** PP

                                       EEEEESS CS
                            AIRS_C 143 Gevtake 149
                                       Gev ++ 
  gi|385805609|ref|YP_005842007.1| 314 GEVSKGS 320
                                       ***9886 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 !   41.6   0.1   1.7e-14   1.5e-10       7      91 ..      54     151 ..       5     153 .. 0.84

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 1.7e-14
                                       EEEEEEE.EECC....TCCCC...HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.....HHHHHHHHHHHHHHHTT- CS
                              AIRS   7 vttdshnrpvlv....epvhf...iGakavavnlsDlaamGArPlalllslalp.....wleevvrglaeaaeelgv 71 
                                       +++d+++++v +    +       +G+ ++a+n++D+a+ G r la+++++a+       +ee+++g+ +a++++++
  gi|385805609|ref|YP_005842007.1|  54 LHVDGVGTKVQIlskfK---KldvAGWDCIAMNANDMACEGFRTLAFSDYIAMDsadeeGFEEIIKGMIDALRKVKA 127
                                       55666666666632223...25669**************************************************** PP

                                       EEEEEEEEEESS....EEEEEEEE CS
                              AIRS  72 plvgGdtsfsne....ptisvtav 91 
                                       pl++G+t+ +++      ++++a+
  gi|385805609|ref|YP_005842007.1| 128 PLLSGETAIMPGivsgKDVVCFAL 151
                                       ********9987655555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 2086.87
//
Query:       gi|385805610|ref|YP_005842008.1|  [L=369]
Description: IMP biosynthesis enzyme PurP-like protein [Fervidicoccus fontis Kam940]
Scores for 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-77  256.7   0.1    1.4e-76  256.3   0.1    1.2  1  DUF1297   Domain of unknown function (DUF1297)
    2.9e-51  172.6   0.6    1.8e-50  170.0   0.1    2.0  2  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 !  256.3   0.1   1.5e-80   1.4e-76       1     188 []     179     369 .]     179     369 .] 0.99

  Alignments for each domain:
  == domain 1  score: 256.3 bits;  conditional E-value: 1.5e-80
                                       HHHHHHHHHHCTTSSSHHHHCCEEEEE---SEEEEEEEEEETTTTEEEEEEEEEEEEEECCCHCCS-HHHHHCCT-. CS
                           DUF1297   1 efeekleellekglieeedlkkasieeyvvGanfnlnyfysplkeevellgidrRyesnldglvrlpakeqlelev. 76 
                                       +f++k+++l+++g++++ed+++asiee+v+G +fn+nyf s+  ++ e+++idrR++++ldg++rlpa+ ql+l++ 
  gi|385805610|ref|YP_005842008.1| 179 DFYRKFNRLVNDGIVNKEDINHASIEELVIGSHFNVNYFNSIAFNRNEIISIDRRIQTDLDGFLRLPADIQLDLKEf 255
                                       89*************************************************************************98 PP

                                       .---EEEEEEEEEEE-GGGHHHHHHHHHHHHHHHHHHSTT---EEEEEEEEE-TTS-EEEEEEESSB-GGGGGGTT. CS
                           DUF1297  77 .epeyvvvGnipvvlREsllekvfelgekfveaakklvppGiiGpFcLqsvvtkdlelvvfdvsaRivggtnvyme. 151
                                        ++e++++G++pv++REs+lek+fe+g+kfvea++++ +pGiiGp++Lq +vtk+le +vfdv++Ri+ggtn+ym+ 
  gi|385805610|ref|YP_005842008.1| 256 iDVEMIEIGHEPVTIRESMLEKLFEIGDKFVEASREIESPGIIGPYTLQLIVTKNLEPIVFDVATRIGGGTNAYMGi 332
                                       89*************************************************************************** PP

                                       --CCHHHTTSS---HHHHHHHHHHHHHHCT-GGGCEE CS
                           DUF1297 152 gspyskllfgeplsmGrrialEikeaiekdrleeivt 188
                                       gs+yskl+fg+p+s+Grri++E+ke+++k++leei+t
  gi|385805610|ref|YP_005842008.1| 333 GSQYSKLYFGKPISLGRRISIELKECLTKGCLEEILT 369
                                       ***********************************98 PP

>> DUF1246  Protein of unknown function (DUF1246)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.0   0.1     2e-54   1.8e-50       1     122 []      21     146 ..      21     146 .. 0.98
   2 ?    0.5   0.0     0.061   5.5e+02      29      48 ..     175     196 ..     163     214 .. 0.67

  Alignments for each domain:
  == domain 1  score: 170.0 bits;  conditional E-value: 2e-54
                                       EEEESSTTHHHHHHHHHHTT--EEEEC-CCCHHHHHTT.TT-SEEEE.S.S..TTSS--HHHHHHTTCEE--BTTHH CS
                           DUF1246   1 iatlaSHsalqilkgAkkegfrtlavcekgreklYekf.kvidevivldkfkdilkeevqeklreenailvPhgsfv 76 
                                       ++++aSHsal++++gA++egf+t+a+c+kgrek+Ye+f +vi evi+l+kf+di+k+e+q+kl+e+n+i+vP++sf 
  gi|385805610|ref|YP_005842008.1|  21 VSAVASHSALDVFDGAHDEGFKTIAICQKGREKTYERFiSVISEVIILEKFSDIVKKEHQKKLQEKNSIFVPNRSFS 97 
                                       679***********************************999************************************ PP

                                       HHC-HHHHH.C-SS-EES-TTHHHHHCSHHHHHHH..HHHTT-BB--BE CS
                           DUF1246  77 eYvgiekie.elkvpifGnrkllrwEerrekkrky..LekAgiriPkki 122
                                       +Yvg++kie e+++pifGnr +lr+Eer+ +k++y  L+kAgir+Pk++
  gi|385805610|ref|YP_005842008.1|  98 VYVGYDKIEeEFEIPIFGNRFMLRYEERTGEKNYYklLDKAGIRRPKTF 146
                                       **********************************************986 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.061
                                       CCCHHHHHTT.TT-.SEEEE.S CS
                           DUF1246  29 kgreklYekf.kvi.devivld 48 
                                        +re +Y+kf +++ d ++  +
  gi|385805610|ref|YP_005842008.1| 175 IDREDFYRKFnRLVnDGIVNKE 196
                                       57999*****755524443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2439.28
//
Query:       gi|385805611|ref|YP_005842009.1|  [L=451]
Description: adenylosuccinate lyase [Fervidicoccus fontis Kam940]
Scores for complete 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  158.9   0.0    3.6e-46  158.0   0.0    1.4  1  Lyase_1      Lyase
    5.8e-13   49.2   0.8    1.9e-12   47.5   0.3    2.2  2  ADSL_C       Adenylosuccinate lyase C-terminus
    5.2e-05   23.3   1.3    0.00015   21.8   1.3    1.8  1  ASL_C        Adenylosuccinate lyase C-terminal
  ------ inclusion threshold ------
      0.029   15.1   1.1       0.15   12.8   0.0    2.8  3  RecG_N       RecG N-terminal helical domain
      0.029   14.8   0.1      0.094   13.2   0.1    2.0  1  FumaraseC_C  Fumarase C C-terminus


Domain annotation for each model (and alignments):
>> Lyase_1  Lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.0   0.0     1e-49   3.6e-46      77     307 ..      76     294 ..      15     298 .. 0.83

  Alignments for each domain:
  == domain 1  score: 158.0 bits;  conditional E-value: 1e-49
                                       SSHHHHHHHHHHHHHHHHTTHSSGIIIIITTT--HHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHTTT-E CS
                           Lyase_1  77 egsgtavnmnlnevigellgekvepndkvhtgqSsnDqvpTalrlalkkalsekLlpaleqLidalkekakefkdvv 153
                                       +  g+++   l++++ge+ g   e  ++vh g++s D+v+T  +l++k+a  ++L+++l+++i+ l e ak++++ v
  gi|385805611|ref|YP_005842009.1|  76 KVLGHDIAS-LTYILGEVCG---ECGKYVHLGATSYDIVDTTWSLLIKQAD-DVLISKLKKIIEKLIELAKNYANYV 147
                                       444555555.7888888888...9*************************99.99*********************** PP

                                       EEEEETTEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHTCEETTTTTTTSSTTTSCC.THHHHHHHHHHHHHCST CS
                           Lyase_1 154 kiGrThlqdAtPvtlgqelsayaealerdrerlkellkrllvellgggtavgtglnadp.efaelvakelakvtglp 229
                                        +GrTh+q+A P+t+g +++ y  +l+r++er+k++ kr+++ +++g++++ ++ n +  e +e v k+l+ ++   
  gi|385805611|ref|YP_005842009.1| 148 EPGRTHGQHADPITFGFKFANYIYELTRSLERIKDAEKRTVKIKMSGAVGTMAAWNGKGlEIEESVSKQLN-IEP-- 221
                                       *******************************************************99988999********.444.. PP

                                       EESSSHHHHHHC-HHHHHHHHHHHHHHHHHHHHHHHHHHHTSTTTSSEEEEGCCTSSC-TTSTTTEBTHHHHHHHHH CS
                           Lyase_1 230 vkapnsfeavsdrDavvellgalkllatsLskfaeDlrllssgeaglvelslaesepGSSiMPgKvNPvqlElltgv 306
                                            + ++v++rD ++e+++ l++la +L +fa ++r ls   + ++e+   ++ +GSS+MP+K+NPv++E + g 
  gi|385805611|ref|YP_005842009.1| 222 ---HLISTQVAPRDGLAEVISSLAILASQLDRFALEVRELSR--TEINEMYEYAERIGSSTMPHKRNPVTAERISGL 293
                                       ...56678**********************************..5566777777888***************99887 PP

                                       H CS
                           Lyase_1 307 a 307
                                       a
  gi|385805611|ref|YP_005842009.1| 294 A 294
                                       6 PP

>> ADSL_C  Adenylosuccinate lyase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.5   8.8e+03      46      65 ..     255     275 ..     231     277 .. 0.70
   2 !   47.5   0.3   5.3e-16   1.9e-12       1      72 [.     363     439 ..     363     440 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.5
                                       HHC.HHCHHHHHT-GGGCCTT CS
                            ADSL_C  46 vkk.seeeldalfdpayylgs 65 
                                       v++ s+ e++++ ++a  +gs
  gi|385805611|ref|YP_005842009.1| 255 VRElSRTEINEMYEYAERIGS 275
                                       443466678887777776665 PP

  == domain 2  score: 47.5 bits;  conditional E-value: 5.3e-16
                                       TGGGHHHHHHHHH.HTH-HHHHHHHHHHHHHHHHHC..HHHHHHT-HHHHC..HHCHHHHHT-GGGCCTTHHHHHHH CS
                            ADSL_C   1 GlifservllaLv.kglgReeAyelVqeaamkawee..llelLaadpevkk..seeeldalfdpayylgsadeivdr 72 
                                       G  +se+++l Lv +g  R+eA++ V + +++  e   l+++ + d++++k  ++eel++ ++p++ylg+ +e+++r
  gi|385805611|ref|YP_005842009.1| 363 GATLSEKLMLLLVeRGFARHEAHKKVMQISRALKEGesLIDAALRDEDISKlfTREELERELKPEKYLGNYRELIER 439
                                       7889*********66***************999988**************55*999******************998 PP

>> ASL_C  Adenylosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   1.3   4.2e-08   0.00015       4     114 ..     313     429 ..     311     430 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 4.2e-08
                                       T--TCHHHHHTTCHHHHHHHHH..HHHHHHHHHCCEEE-HHHHHHHHHT-.GGGGHHHHHHHHHHTT-..TTHHHHH CS
                             ASL_C   4 QRDLtdStvlRnlgvalahsli..alksllkglsklevneealaedLden.wevlaEaiqtvlrregi..ekpYekl 75 
                                        RDLt+S+  R +  + a+ ++   ++ ++k l+ l +n+ea++++L+ +  + l+E +  +l + g+  +++++k+
  gi|385805611|ref|YP_005842009.1| 313 ERDLTNSSSERVIL-PHAYLTMdqMMDDMIKLLNTLYINTEAAKKNLEITkGATLSEKLMLLLVERGFarHEAHKKV 388
                                       6**********763.34444431246778999****************763799******99977665226899999 PP

                                       HHHHTTS---HHHHHHHHHCS-S-HH.HHHHH.HC--CCC- CS
                             ASL_C  76 keltrgkkitkeslkefieslevsee.akeeL.kaltpatY 114
                                        ++ r  k  ++ +++ +++ ++s+  ++eeL ++l+p++Y
  gi|385805611|ref|YP_005842009.1| 389 MQISRALKEGESLIDAALRDEDISKLfTREELeRELKPEKY 429
                                       99999999999***********9986245677357999999 PP

>> RecG_N  RecG N-terminal helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1         3   1.1e+04      52      57 ..     129     134 ..     118     148 .. 0.46
   2 ?   -2.8   0.0       3.2   1.1e+04      27      44 ..     170     187 ..     165     192 .. 0.60
   3 ?   12.8   0.0   4.2e-05      0.15      20      80 ..     231     293 ..     217     300 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3
                                       HHHHHH CS
                            RecG_N  52 lskfld 57 
                                       l+k+++
  gi|385805611|ref|YP_005842009.1| 129 LKKIIE 134
                                       222222 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.2
                                       ...HHHHHHH---GGGG- CS
                            RecG_N  27 ieeikkkleliddpllen 44 
                                       i e+ + le i+d ++  
  gi|385805611|ref|YP_005842009.1| 170 IYELTRSLERIKDAEKRT 187
                                       556666677776666554 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 4.2e-05
                                       TT........HHHHHHH---GGGG-HHHH.HHHHHHHHHHTTS..SSS-HHHHHHHHHHHHHH CS
                            RecG_N  20 kleteelieeikkkleliddplleneevlkeklskfldYikpi..asLpeeRkikRlknglem 80 
                                       +    e+i  +   ++++d+  le  e+++  ++++++Y+++i    +p+ R+ + + +++++
  gi|385805611|ref|YP_005842009.1| 231 RDGLAEVISSLAILASQLDRFALEVRELSRTEINEMYEYAERIgsSTMPHKRNPVTAERISGL 293
                                       55678999999999****************************933469999988777776666 PP

>> FumaraseC_C  Fumarase C C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   2.6e-05     0.094      20      51 ..     393     428 ..     385     431 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.6e-05
                                       HHHHHT--HHHHHHH....TT-.-HHHHHHHT-HHH CS
                       FumaraseC_C  20 eAlkegktlreavle....lgllteeeldelldpek 51 
                                       +Alkeg +l +a+l+     +l+t+eel++ l+pek
  gi|385805611|ref|YP_005842009.1| 393 RALKEGESLIDAALRdediSKLFTREELERELKPEK 428
                                       79************97888888************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); 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:                         5  (0.000278878); expected 0.2 (1e-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 0.27s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 2776.69
//
Query:       gi|385805612|ref|YP_005842010.1|  [L=355]
Description: 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase [Fervidicoccus fontis Kam940]
Scores for complete 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-77  257.3   0.0      9e-77  256.9   0.0    1.2  1  DUF1297      Domain of unknown function (DUF1297)
    1.2e-46  157.6   0.1    1.8e-46  157.0   0.1    1.3  1  DUF1246      Protein of unknown function (DUF1246)
     0.0099   15.9   0.1       0.02   15.0   0.1    1.5  1  ATP-grasp_3  ATP-grasp domain
  ------ inclusion threshold ------
      0.039   13.4   0.0      0.067   12.7   0.0    1.3  1  CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP bindin
      0.071   12.9   0.0       0.28   10.9   0.0    1.9  2  GARS_A       Phosphoribosylglycinamide synthetase, ATP-grasp 
       0.13   11.8   0.1       0.36   10.4   0.1    1.7  1  RimK         RimK-like ATP-grasp domain
       0.17   11.5   0.4       0.94    9.0   0.1    2.2  3  ATP-grasp    ATP-grasp domain
        2.6    8.4   5.2        6.5    7.1   0.3    3.6  4  DUF1947      Domain of unknown function (DUF1947)


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 !  256.9   0.0     4e-80     9e-77       1     188 []     170     355 .]     170     355 .] 0.99

  Alignments for each domain:
  == domain 1  score: 256.9 bits;  conditional E-value: 4e-80
                                       HHHHHHHHHHCTTSSSHHHHCCEEEEE---SEEEEEEEEEETTTTEEEEEEEEEEEEEECCCHCCS-HHHHHCCT-- CS
                           DUF1297   1 efeekleellekglieeedlkkasieeyvvGanfnlnyfysplkeevellgidrRyesnldglvrlpakeqleleve 77 
                                       +++ekl++l+++g+i  +d k+++i+eyv+G++++++yfysp+k+++e+lg d+Ryesn+dgl rlp++  ++  +e
  gi|385805612|ref|YP_005842010.1| 170 DIKEKLSDLKKSGII--DDEKNVIIQEYVIGTPAYFHYFYSPIKNRIEILGADIRYESNIDGLKRLPSEFGITNFIE 244
                                       689************..78899******************************************************* PP

                                       --EEEEEEEEEEE-GGGHHHHHHHHHHHHHHHHHHSTT---EEEEEEEEE-TTS-EEEEEEESSB-GGGGGGTT--C CS
                           DUF1297  78 peyvvvGnipvvlREsllekvfelgekfveaakklvppGiiGpFcLqsvvtkdlelvvfdvsaRivggtnvymegsp 154
                                       p++vvvGn p+vlREsll+kv+++ge+fv+a+k++++pGiiGpF++++++++dle++ f++s Riv+gtn+y++gsp
  gi|385805612|ref|YP_005842010.1| 245 PSFVVVGNLPMVLRESLLPKVLDYGERFVKASKTEAQPGIIGPFSIETIIRDDLEIIAFEFSGRIVAGTNLYISGSP 321
                                       ***************************************************************************** PP

                                       CHHHTTSS---HHHHHHHHHHHHHHCT-GGGCEE CS
                           DUF1297 155 yskllfgeplsmGrrialEikeaiekdrleeivt 188
                                       ys+l+f+e++smGrria+Eik+a e+++le ++t
  gi|385805612|ref|YP_005842010.1| 322 YSWLYFNEEMSMGRRIAREIKMAKENNSLELVLT 355
                                       ******************************9987 PP

>> DUF1246  Protein of unknown function (DUF1246)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.0   0.1   8.2e-50   1.8e-46       1     122 []      17     139 ..      17     139 .. 0.99

  Alignments for each domain:
  == domain 1  score: 157.0 bits;  conditional E-value: 8.2e-50
                                       EEEESSTTHHHHHHHHHHTT--EEEEC-CCCHHHHHTT.TT-SEEEE.S.S..TTSS--HHHHHHTTCEE--BTTHH CS
                           DUF1246   1 iatlaSHsalqilkgAkkegfrtlavcekgreklYekf.kvidevivldkfkdilkeevqeklreenailvPhgsfv 76 
                                       iatlaSHs+lqi++gAkkegf+t++++ ++re++Y++f ++id++iv++++++i++e+v++kl + n+i+vPhgs+v
  gi|385805612|ref|YP_005842010.1|  17 IATLASHSSLQIVHGAKKEGFKTALITLHDREHFYRNFeNLIDHLIVVNSWNEICTEKVEKKLESLNSIFVPHGSLV 93 
                                       89************************************999************************************ PP

                                       HHC-HHHHHC-SS-EES-TTHHHHHCSHHHHHHHHHHTT-BB--BE CS
                           DUF1246  77 eYvgiekieelkvpifGnrkllrwEerrekkrkyLekAgiriPkki 122
                                       eYvgi+ +e++k+p+fG+rk++r+E+++ kk+++L +Agi+iPk++
  gi|385805612|ref|YP_005842010.1|  94 EYVGIKCAESFKIPYFGTRKMFRIEADQYKKMSLLYQAGIPIPKEY 139
                                       *******************************************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 !   15.0   0.1   8.7e-06      0.02       2      75 ..     119     201 ..     118     213 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8.7e-06
                                       TSHHHHHHHHTTT.S---....-EESS--SSSEEEEESS-------B--SS--TTE..................EEE CS
                       ATP-grasp_3   2 sdKlktykkLkeagvkvPtkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve...........lvq 67 
                                       +d +k +  L +ag+++P++++ e  +  ek+++vK   + gg++ +++  k++ ++++  ++           ++q
  gi|385805612|ref|YP_005842010.1| 119 ADQYKKMSLLYQAGIPIPKEYSLE--DDIEKPVIVKLPGAKGGKGYFIATSKKDIKEKLSDLKksgiiddeknvIIQ 193
                                       689999999*********555444..577***********************99999999988999*********** PP

                                       E---SEEE CS
                       ATP-grasp_3  68 efieGkpl 75 
                                       e++ G+p+
  gi|385805612|ref|YP_005842010.1| 194 EYVIGTPA 201
                                       ***99985 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0     3e-05     0.067      33      89 ..     141     196 ..     131     200 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3e-05
                                       HHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHSTS-EEEEE-- CS
                       CPSase_L_D2  33 iakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafgnkqvlveksl 89 
                                       + ++i  Pvi+k   + GGkG  +a+++++++e ++    ++     +k+v +++++
  gi|385805612|ref|YP_005842010.1| 141 LEDDIEKPVIVKLPGAKGGKGYFIATSKKDIKEKLSDLK-KSGIIDDEKNVIIQEYV 196
                                       5678999************************99887644.44455566666666665 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 ?   10.9   0.0   0.00012      0.28      36      94 ..     145     201 ..     116     213 .. 0.83
   2 ?   -1.6   0.0      0.86   1.9e+03     174     190 ..     255     273 ..     248     275 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00012
                                       HSSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TTCCCCSSEEEEE---SEEE CS
                            GARS_A  36 atakalVvKadglaagKgvivakseeealkavkeilekkkfGeagekvviEelleGeEv 94 
                                        +++ ++vK  g  +gKg  +a+s+++  + ++++ ++    + +++v+i e++ G+  
  gi|385805612|ref|YP_005842010.1| 145 IEKP-VIVKLPGAKGGKGYFIATSKKDIKEKLSDLKKSGII-DDEKNVIIQEYVIGTPA 201
                                       3344.59***************************8775555.6899*******999765 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.86
                                       EEETTE..EEEEEEESS-- CS
                            GARS_A 174 mlvedg..pkvlefnvRfg 190
                                       m+ +++  pkvl++  Rf 
  gi|385805612|ref|YP_005842010.1| 255 MVLRESllPKVLDYGERFV 273
                                       44455558*******9995 PP

>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00016      0.36      39      82 ..     145     196 ..     118     199 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00016
                                       .-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHHGGG--........EEEEE- CS
                              RimK  39 lrfPvvvKsvegsqGikvvlakkeqklkqvlealkeai........lvqeyi 82 
                                       ++ Pv+vK   ++ G + ++a  ++++k+ l+ lk++         ++qey+
  gi|385805612|ref|YP_005842010.1| 145 IEKPVIVKLPGAKGGKGYFIATSKKDIKEKLSDLKKSGiiddeknvIIQEYV 196
                                       367**************************99996554324444555888886 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.3   5.1e+03     120     144 ..      80     104 ..      47     106 .. 0.48
   2 ?    9.0   0.1   0.00042      0.94      25      71 ..     143     195 ..     135     197 .. 0.82
   3 ?   -0.7   0.0      0.42   9.4e+02     134     159 ..     283     308 ..     272     310 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.3
                                       HHHHHHHHHHHHHHTSSEEEEEEEE CS
                         ATP-grasp 120 kkaeeiakkiveeLggvGvfavElF 144
                                       ++ ++i     + +++vG+   E F
  gi|385805612|ref|YP_005842010.1|  80 ESLNSIFVPHGSLVEYVGIKCAESF 104
                                       3333333333445677777777766 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00042
                                       HHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC.......GTTCEEEEE- CS
                         ATP-grasp  25 eelglpvvvKarrlgydGkGqsvvrseedleqaleal.......keekvivEef 71 
                                       ++++ pv+vK   ++  GkG ++  s++d+++ l+ l       +e++vi+ e+
  gi|385805612|ref|YP_005842010.1| 143 DDIEKPVIVK-LPGAKGGKGYFIATSKKDIKEKLSDLkksgiidDEKNVIIQEY 195
                                       68999*****.999******************9999966666666666666665 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.42
                                       TSSEEEEEEEEEETTCTEEEEEEESS CS
                         ATP-grasp 134 ggvGvfavElFvledgellvnElapR 159
                                       g++G f++E  + +d e+++ E++ R
  gi|385805612|ref|YP_005842010.1| 283 GIIGPFSIETIIRDDLEIIAFEFSGR 308
                                       789**********9999999999988 PP

>> DUF1947  Domain of unknown function (DUF1947)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       0.6   1.3e+03      31      49 ..     117     135 ..     111     140 .. 0.89
   2 ?    7.1   0.3    0.0029       6.5       6      36 ..     167     195 ..     162     204 .. 0.84
   3 ?   -2.1   0.0       2.3   5.1e+03      13      31 ..     210     227 ..     209     229 .. 0.83
   4 ?   -0.1   0.0      0.53   1.2e+03      40      60 ..     246     265 ..     241     266 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.6
                                       -EEEE-SS-EEEEETTEEE CS
                           DUF1947  31 iEieeekkeklYlingvpi 49 
                                       iE +++kk +l++  g+pi
  gi|385805612|ref|YP_005842010.1| 117 IEADQYKKMSLLYQAGIPI 135
                                       8999*********999997 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0029
                                       -HHHHHHHHHHHHTTT---TT--..-EEEE- CS
                           DUF1947   6 SkKeakeileklkekyisislesdkiEieee 36 
                                       SkK++ke l+ lk+ +  i+ e++ + i+e+
  gi|385805612|ref|YP_005842010.1| 167 SKKDIKEKLSDLKKSG-IIDDEKN-VIIQEY 195
                                       9***************.9999998.777665 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 2.3
                                       HHHHHHTTT---TT--..- CS
                           DUF1947  13 ileklkekyisislesdki 31 
                                       i+++++  + +i  es+ i
  gi|385805612|ref|YP_005842010.1| 210 IKNRIEILGADIRYESN-I 227
                                       78899999999999997.6 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 0.53
                                       EEEEETTEEEEEESSSEEE-H CS
                           DUF1947  40 klYlingvpilfeeekliPtL 60 
                                       ++ ++++ p+++  e+l+P +
  gi|385805612|ref|YP_005842010.1| 246 SFVVVGNLPMVL-RESLLPKV 265
                                       57799*******.99999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 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:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2244.08
//
Query:       gi|385805613|ref|YP_005842011.1|  [L=68]
Description: hypothetical protein FFONT_0569 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.30s 00:00:00.69 Elapsed: 00:00:00.46
# Mc/sec: 443.68
//
Query:       gi|385805614|ref|YP_005842012.1|  [L=45]
Description: hypothetical protein FFONT_0570 [Fervidicoccus fontis Kam940]
Scores for complete 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   35.2   0.1    1.3e-08   35.0   0.1    1.1  1  Nitroreductase  Nitroreductase family
    0.00039   20.1   0.3    0.00075   19.1   0.3    1.5  1  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 !   35.0   0.1   1.5e-12   1.3e-08       1      32 [.      13      44 ..      13      45 .] 0.97

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 1.5e-12
                                      HHH--B---B-S----HHHHHHHHHHHHTS-- CS
                    Nitroreductase  1 irkRrSiRkFddepvpkeelekileaarraPs 32
                                      i++RrSiRk+ d++vp+ +++ki+ea+rraP+
  gi|385805614|ref|YP_005842012.1| 13 ILSRRSIRKYIDKKVPENDVKKIMEAGRRAPT 44
                                      789****************************7 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.3   8.3e-08   0.00075       2      32 ..       9      39 ..       8      44 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 8.3e-08
                                      HHHHHHH--B---B--S---HHHHHHHHH-- CS
                    TM1586_NiRdase  2 lyeaiekRhsvRkYkdealeeelleelkeai 32
                                      +++ai  R+s+RkY d++++e+ ++++ ea 
  gi|385805614|ref|YP_005842012.1|  9 VFNAILSRRSIRKYIDKKVPENDVKKIMEAG 39
                                      789**********************998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); 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 0.29s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 285.30
//
Query:       gi|385805615|ref|YP_005842013.1|  [L=368]
Description: major facilitator superfamily protein [Fervidicoccus fontis Kam940]
Scores for complete 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-37  127.3  57.6    4.9e-29  101.4  31.3    2.0  2  MFS_1     Major Facilitator Superfamily
     0.0011   18.9   0.0     0.0044   17.1   0.0    2.2  1  DUF962    Protein of unknown function (DUF962)


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 !  101.4  31.3   5.5e-33   4.9e-29      33     351 ..      19     328 ..       7     329 .. 0.83
   2 !   39.6  18.3   3.2e-14   2.9e-10      24     178 ..     212     366 ..     210     368 .] 0.87

  Alignments for each domain:
  == domain 1  score: 101.4 bits;  conditional E-value: 5.5e-33
                             MFS_1  33 eigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fasslwlllvlrvlqGlgagalfpagaa 108
                                        ++++ ++y+ ++a ++l++G+l d +G +r+  ++l++++lg ++l+ +  + + l+v+r l G++a+++f + + 
  gi|385805615|ref|YP_005842013.1|  19 LLSTMSSAYFYAYATSQLITGPLLDSYGVKRIGATMLAVLSLG-TILMlL-KNEFGLIVGRTLIGFAAAVAFLSYMR 93 
                                       4899***************************************.555524.88888********************* PP

                             MFS_1 109 liadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeepperkrkspk 185
                                         + +f+k+ +++ ++++ +  ++++i+      ++++ +g++ + +ila +s l+     l++  ++++   + +k
  gi|385805615|ref|YP_005842013.1|  94 SSSLYFSKSMQAKLTSFAIMIGNFSTIVSTYPLRIFLQRFGYTTTLLILASISSLLSY---LVF--KKSSDVGSIEK 165
                                       *****************************777789999*****************944...444..33333333333 PP

                             MFS_1 186 eeekgtgpaplvpawkallkdpvlw.illialllfffgfsglltllplylqevlglsglllaglllallalvgaila 261
                                       +    + +  +++  k++ + +++w + ++al++ ++ +++  t+    l e +g+s    a+++l+++a+ + i++
  gi|385805615|ref|YP_005842013.1| 166 TS---KLRERFAE-MKKIASEKHIWgVGIAALAGYGTSIAYQATWGQRNLTEMFGFS-IGKASIMLMIIAITATIFS 237
                                       33...25788888.9**********9666666666556666666666667*******.6788888************ PP

                             MFS_1 262 llagrlsdr.lgrrrrlllallllllaalglallavtssavllll.vlvliGfglgfvfpsllalasdlappeeagt 336
                                       +++g++sd  ++rr+++l++ +l +l+  +l++++++ ++++ll+ +++ +G+  ++ ++ + ++a + +  +++gt
  gi|385805615|ref|YP_005842013.1| 238 PIVGFISDNvIKRRKPILISTPLSSLIGWFLIYISFYLHNSILLYaSMISLGLSIAL-QIVAPVMAREEVQSKYSGT 313
                                       *******776***************************66666555144446665554.99999999999999***** PP

                             MFS_1 337 asglfntagslggal 351
                                       a++ fn+   +g+a+
  gi|385805615|ref|YP_005842013.1| 314 ATAMFNVQVFFGIAI 328
                                       ******999988876 PP

  == domain 2  score: 39.6 bits;  conditional E-value: 3.2e-14
                             MFS_1  24 aedlgispseigllltlyalgaavaslplGrlsdr.fGrrrvlllglllfalglllllfa....sslwlllvlrvlq 95 
                                       +e +g+s   ++++l + a++a ++s+++G++sd+ + rr+ +l++  l++l +++l+++    +++ ll+++ +  
  gi|385805615|ref|YP_005842013.1| 212 TEMFGFSIGKASIMLMIIAITATIFSPIVGFISDNvIKRRKPILISTPLSSLIGWFLIYIsfylHNSILLYASMISL 288
                                       6679*******************************8899998888888888777888853366799889******** PP

                             MFS_1  96 GlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllll 172
                                       Gl   al  ++ +++++ +  +  g a++++++ + +G+++   ++g+l+     +++ ++  +vsl++++  +l+ 
  gi|385805615|ref|YP_005842013.1| 289 GLSI-ALQIVAPVMAREEVQSKYSGTATAMFNVQVFFGIAILQTISGFLS----ISSMIIVSIGVSLFGILASILFT 360
                                       **96.88888889999999999***************************9....99*************99777777 PP

                             MFS_1 173 peeppe 178
                                       +e++++
  gi|385805615|ref|YP_005842013.1| 361 RETYKP 366
                                       776655 PP

>> DUF962  Protein of unknown function (DUF962)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0     5e-07    0.0044      43      92 ..     156     275 ..      50     278 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5e-07
                            DUF962  43 k......................................................................lkllla 49 
                                       k                                                                      + ++++
  gi|385805615|ref|YP_005842013.1| 156 KssdvgsiektsklrerfaemkkiasekhiwgvgiaalagygtsiayqatwgqrnltemfgfsigkasimlMIIAIT 232
                                       05555555555555555555555555555555555555555556666677888888888888888888877788999 PP

                            DUF962  50 lfvvgyifafvGHfvfEkrkPAlfknplqsllidplmvllell 92 
                                       + ++  i+ f+++ v+ +rkP l++ pl+sl++ +l+++++ l
  gi|385805615|ref|YP_005842013.1| 233 ATIFSPIVGFISDNVIKRRKPILISTPLSSLIGWFLIYISFYL 275
                                       999999*************************999988887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       888  (0.0495287); 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:                         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: 0.65u 0.35s 00:00:01.00 Elapsed: 00:00:00.53
# Mc/sec: 2102.77
//
Query:       gi|385805616|ref|YP_005842014.1|  [L=39]
Description: hypothetical protein FFONT_0572 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       581  (0.0324056); 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:                         0  (0); expected 0.2 (1e-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 0.26s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 281.13
//
Query:       gi|385805617|ref|YP_005842015.1|  [L=475]
Description: Phosphate transporter related protein [Fervidicoccus fontis Kam940]
Scores for complete 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-54  183.8  22.8    6.7e-54  183.4  22.8    1.0  1  Sugar_tr  Sugar (and other) transporter
    2.2e-37  128.8  34.4    2.9e-35  121.8  29.0    2.1  2  MFS_1     Major Facilitator Superfamily


Domain annotation for each model (and alignments):
>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.4  22.8   7.5e-58   6.7e-54       3     450 ..      25     458 ..      23     459 .. 0.87

  Alignments for each domain:
  == domain 1  score: 183.4 bits;  conditional E-value: 7.5e-58
                                       HHHHHHHHHHHHHHHCGGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHH CS
                          Sugar_tr   3 lvaalggllfgYdtgvigafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkksl 79 
                                       +v  lg +   Yd++vig +l+ll+  ++  +  s   +e     +g++ ++ l+ a+iG+l++g+++d++GRkk++
  gi|385805617|ref|YP_005842015.1|  25 IVSGLGFFTDAYDLFVIGIVLMLLSGPYQTSFHLSG--HE-----IGAVGASSLAFAMIGQLLFGKIADKYGRKKIY 94 
                                       45555668999**************54444444444..44.....69999999999********************* PP

                                       HHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHH CS
                          Sugar_tr  80 liaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaai 156
                                        i   +++iga+l+a++    ++e l+++R+++Gig+G+ + ++ + +sE+A +k Rg+lv+l   +  fG + a +
  gi|385805617|ref|YP_005842015.1|  95 GIELSILIIGALLSAISW---NFESLLISRIFLGIGIGGDYPVSATIMSEYANAKDRGKLVGLVFAMQGFGAITAVV 168
                                       *****************9...******************************************************** PP

                                       HHHHH.HTSS-TTHHHHHHHCCHHHHHHHHHHGGGS---HHHHHHTT-HH.HHHHHHHHHHHCHHHHHHHHHHHHHH CS
                          Sugar_tr 157 fglgl.nktsnadgwrillglqlvpallllilllflPESPrylvekgkee.eakevlaklrgeedadrelaeekdsl 231
                                         ++l ++  ++ +wr ll++ ++p+l +++l+  +PE+Pry + + + + eak+  + + g+e +    ++ ++ l
  gi|385805617|ref|YP_005842015.1| 169 ASVILvSYLPAEITWRALLAIGAIPPLSVVYLRRKVPETPRYALLVSNNQeEAKKASKIIIGKEIRFNVGNNGINHL 245
                                       *****777778*******************************97766655499988888777776666666666666 PP

                                       HHHHH.......HTTHHHHSH...HHHHHHHHHHHHHHTTHHHHHHHTTTHHHHSS-THHHHHHHHHHHHHHHHHHH CS
                          Sugar_tr 232 eaeqeee..kaswkellssktvrqrlligvvlqifqqltGinaimyysptifenlglsksllvtiivgvvnfvatfv 306
                                             e  +++wk+l+         + +++++i+   tGi + ++ + +i  +    k  l+++i ++v ++  f+
  gi|385805617|ref|YP_005842015.1| 246 TFR---EflEKYWKSLFIA------SFAWFLMDIAFYGTGIYSSFIVPQMISVDSIHMKI-LISGIPYFVGAFGYFF 312
                                       666...2224566666666......7******************9999999765444444.8*************** PP

                                       HHHHHHHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS........CHHHHHHHHHHHHHHHTTTTHHHHHHHHHH CS
                          Sugar_tr 307 aiflvdrfGRRtllllGaagmaicfvilgivalllvaks.....kaasivaivfialfialfalgwgpvpwvlvsEl 378
                                       a+fl+d +GR+++ + G++ ma+  +i++    l+++++      + +++a   + l +++ ++g++ + +v  +El
  gi|385805617|ref|YP_005842015.1| 313 AAFLMDSLGRKRIQIQGFIAMAAIYLIVA--LSLVSNGKdvlgfYVPKYLAFLIYSLSFFFINFGPNETTFVFPTEL 387
                                       ****************************9..555555555669999999**************************** PP

                                       SHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHT-HHHHHHHHHHHHHHHHHHHHS--STT--CCCCGG CS
                          Sugar_tr 379 fpqsvRskalaiavavnwlanflisllfpiiteaigggyvflvfaglavlfiifvfffvpetkgrtleeiee 450
                                       fp++ Rs+   ia+a+      l ++lfp ++e+ig  +v ++  g+ +l++i+  + + e +g++leei+e
  gi|385805617|ref|YP_005842015.1| 388 FPTKYRSTSHGIAAATGKAGAALSTYLFPLALESIGIRGVLFILSGVSMLGAIIS-IWLKEPAGKSLEEITE 458
                                       ************************************8888888888888777654.5578999******987 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.8  29.0   3.2e-39   2.9e-35      12     352 ..      41     411 ..      24     412 .. 0.77
   2 !   19.0   1.0   5.9e-08   0.00053     111     187 ..     385     458 ..     379     469 .. 0.83

  Alignments for each domain:
  == domain 1  score: 121.8 bits;  conditional E-value: 3.2e-39
                             MFS_1  12 rsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslwll 88 
                                       ++i++++l+  +++++++s++eig + +   ++a++++l++G ++d++Gr++++ + l ++++g+ll +++ ++  l
  gi|385805617|ref|YP_005842015.1|  41 IGIVLMLLSGPYQTSFHLSGHEIGAVGASSLAFAMIGQLLFGKIADKYGRKKIYGIELSILIIGALLSAISWNFESL 117
                                       233333333367999*************************************************555555466668* PP

                             MFS_1  89 lvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg....Wravfyilaivs 161
                                       l++r++ G+g g+ +p++a++++++++ ++rg+ +gl+ a+ ++Gai + +++ +l+s+l     Wra+  i ai  
  gi|385805617|ref|YP_005842015.1| 118 LISRIFLGIGIGGDYPVSATIMSEYANAKDRGKLVGLVFAMQGFGAITAVVASVILVSYLPaeitWRALLAIGAIPP 194
                                       *********************************************************99999*******99999999 PP

                             MFS_1 162 llafvlfllllpeepperkrkspkeee...................kgtgpaplvp....awkallkdpvlwillia 215
                                       l + v     +pe+p+    +s  +ee                   +g  +  +++     wk+l+   + w     
  gi|385805617|ref|YP_005842015.1| 195 LSV-VYLRRKVPETPRYALLVSNNQEEakkaskiiigkeirfnvgnNGINHLTFREflekYWKSLFIASFAW----- 265
                                       998.43455557777777777777776777777777777776666644444444443334555555555555..... PP

                             MFS_1 216 lllfffgfsglltllplylqevlgls.glllaglllallalvgailallagrlsdrlgrrrrlllallllllaalgl 291
                                        +l+ ++f+g+ +++ +++ +    +    +  l+++++++vga++ ++a++l+d lgr+r+ + +++++++++l++
  gi|385805617|ref|YP_005842015.1| 266 -FLMDIAFYGTGIYSSFIVPQMISVDsI-HMKILISGIPYFVGAFGYFFAAFLMDSLGRKRIQIQGFIAMAAIYLIV 340
                                       .444444444444444443333333321.22233589**************************************** PP

                             MFS_1 292 allavt......ssavllll......vlvliGfglgfv....fpsllalasdlappeeagtasglfntagslggalg 352
                                       al  v+             +      +++++++ ++f+    + + +++ ++l+p++++ t  g++  +g +g+al+
  gi|385805617|ref|YP_005842015.1| 341 ALSLVSngkdvlG------FyvpkylAFLIYSLSFFFInfgpNETTFVFPTELFPTKYRSTSHGIAAATGKAGAALS 411
                                       ******7633332......23466667777777555555667889999************************99986 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 5.9e-08
                             MFS_1 111 adwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeepperkrkspkee 187
                                       +++fp + r+   g+++a+  +Ga+l   l +l ++s+g r+v +il +vs+l+++   + ++ ++p+ k  ++++e
  gi|385805617|ref|YP_005842015.1| 385 TELFPTKYRSTSHGIAAATGKAGAALSTYLFPLALESIGIRGVLFILSGVSMLGAI---ISIWLKEPAGKSLEEITE 458
                                       689****************************************9999999999999...555555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); 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:                         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: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 2983.50
//
Query:       gi|385805618|ref|YP_005842016.1|  [L=130]
Description: hypothetical protein FFONT_0574 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.021   14.8   0.1      0.046   13.7   0.1    1.5  1  NPM1-C    Nucleophosmin C-terminal domain
       0.12   12.2   0.0       0.18   11.5   0.0    1.3  1  DUF4194   Domain of unknown function (DUF4194)


Domain annotation for each model (and alignments):
>> NPM1-C  Nucleophosmin C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   5.1e-06     0.046       9      34 ..       8      33 ..       6      41 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.1e-06
                            NPM1-C  9 asieKGvsLPkveaKFinyvkncFkm 34
                                      +++ K vsL+++  KF ny+kn  + 
  gi|385805618|ref|YP_005842016.1|  8 KEYNKNVSLSEILDKFSNYLKNNGWQ 33
                                      5789*****************96544 PP

>> DUF4194  Domain of unknown function (DUF4194)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0     2e-05      0.18      99     141 ..      13      55 ..       6      65 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2e-05
                           DUF4194  99 vvsveeiveklesflpldrdeakfkkrldaalrklkelgllrr 141
                                        vs+ ei +k++++l++++ ++++k+ +d+a+ + ++ g+lr 
  gi|385805618|ref|YP_005842016.1|  13 NVSLSEILDKFSNYLKNNGWQVQQKTGVDKAILQARKGGILRD 55 
                                       599*************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       911  (0.0508115); expected 358.6 (0.02)
Passed bias filter:                      681  (0.0379832); 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: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 830.06
//
Query:       gi|385805619|ref|YP_005842017.1|  [L=98]
Description: hypothetical protein FFONT_0575 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.054   13.5   0.2      0.098   12.6   0.2    1.5  1  Y_Y_Y     Y_Y_Y 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 ?   12.6   0.2   5.5e-06     0.098      30      63 ..      11      44 ..       2      47 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.5e-06
                                      EEEEES--SEEEEEEEEEEETTS-B-SS-EEEEE CS
                             Y_Y_Y 30 easytnlppGdYtlkVkakdndgqwnyditslsf 63
                                      +++ ++++pG Y++++++k+  + + +      f
  gi|385805619|ref|YP_005842017.1| 11 SIKLSENKPGIYKITIFIKNVGEVKADINSAYVF 44
                                      688899**************99988876555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 718.26
//
Query:       gi|385805620|ref|YP_005842018.1|  [L=572]
Description: Na_H_Exchanger domain containing protein [Fervidicoccus fontis Kam940]
Scores for complete 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  54.0    1.8e-24   86.3  54.0    2.6  2  Na_H_Exchanger  Sodium/hydrogen exchanger family
      0.006   16.4   8.2      0.006   16.4   8.2    5.0  5  Asp-Al_Ex       Predicted Permease Membrane Region


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 !   86.3  54.0     2e-28   1.8e-24       3     374 ..      16     379 ..      13     383 .. 0.89
   2 ?   -9.0  15.5         2   1.8e+04     138     224 ..     424     507 ..     411     555 .. 0.68

  Alignments for each domain:
  == domain 1  score: 86.3 bits;  conditional E-value: 2e-28
                                       HHHHHHHHHHHH.HHHTTSXHHHHHHHHHHHHTTTTTS......HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTHH CS
                    Na_H_Exchanger   3 llillallvgll.arrlklpeivgliiaGlllGpsglgl.iepseedlevlselglilllFlaGleldlrelrknlk 77 
                                       l++l+++ +++  ++r++ + i+g+i+ G++++++ l + i+ + + ++ l e+gl+l+ F+aG +++++ lr+ + 
  gi|385805620|ref|YP_005842018.1|  16 LILLTVSGFIAStFQRFGFGRILGYIFGGIIIAYIALHFhISVDFSYTDALREIGLVLFFFEAGSSISISGLRASFS 92 
                                       4444444444455*************************656655899****************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHHHHHHHH CS
                    Na_H_Exchanger  78 silllallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailkeegrvperlgtlllgesvlnDav 154
                                        ++++ l+++++ + l + ++++   lg++ +e l+  ++l   + v+ + i +++gr+ +++ +++     ++D+v
  gi|385805620|ref|YP_005842018.1|  93 RVVAIELVSITFIWTL-SSIVSF--TLGFSQIERLFTFLLLVNCSMVTFYLISSDRGRLGTKIKQIATLQFSMEDIV 166
                                       ****************.999**7..689************************************************* PP

                                       CCCCCHHHHHHTXXXXXTSSSTSXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS.CTHHHHHHHHHHHHHHHHHHHH CS
                    Na_H_Exchanger 155 avvllavllalakeeaggetslllllliflvvavgglllglvigwllrlitrft.dddrelevllvlllallaalla 230
                                        + l+++l ++     + ++++++++  fl +a+++l++ +   ++lr+++ ++  +++   ++l+l++al+ + ++
  gi|385805620|ref|YP_005842018.1| 167 QFSLFSILFSFS----SSNVGIISGFQLFLKIAALSLIMFASAYLILRILSSSAlVQEKTNKFILSLAIALGYVSIS 239
                                       ***********8....55555556666666666666666666666666666665559******************** PP

                                       HTSXXXHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHSXHHHHHXXHHHHHHHHHHHHHHHTHH CS
                    Na_H_Exchanger 231 ellgvsgilgaflaGlvlseyefsnklseklesfreglfnplfFvlvGlsldlkvlnnhlsvlilvllilvaillgr 307
                                       + +g+  ++gaf+ Gl++s +  + +++  l  +   +   ++F+++G+ +    l+n+++v+ + +++  + + +r
  gi|385805620|ref|YP_005842018.1| 240 QYFGLPPLFGAFISGLAFSSTLGAGEIADMLVGMK-EIGMLFYFSSLGADIG---LFNSIKVIKYGIILGMLAVPIR 312
                                       *******************8888888999988888.8999************...44579999999999999999** PP

                                       HHHHHHHTTTXSSXHHHHHHCCCCSS.BHHHHHHHHHHHHHHXHHHHTTSSTTTCSTSXHHHHHHHH CS
                    Na_H_Exchanger 308 ilavflllrllglslrealiigfgglqrgavalalaalgpalgllarelyallivvvlftvlvqGls 374
                                        ++ f+   l g++  +a +i++ ++++ +  +++a  + ++g la++++ + +++v+ t++v G +
  gi|385805620|ref|YP_005842018.1| 313 MIGLFIGGILGGVTPENASLISLTLFPIAESGIIFADTLASSGMLASQMVGISTIAVMSTLIVSGAI 379
                                       *********99***************************************************99975 PP

  == domain 2  score: -9.0 bits;  conditional E-value: 2
                                       CCCCCCHHHHHHHHHHHCCCCCHHHHHHTXXXXXTSSSTSXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTHHHH CS
                    Na_H_Exchanger 138 erlgtlllgesvlnDavavvllavllalakeeaggetslllllliflvvavgglllglvigwllrlitrftdddrel 214
                                       +r+  ++l +s l D +++++  + l++          ++ +l++ lv++++++++   + +++++++  + ++++ 
  gi|385805620|ref|YP_005842018.1| 424 TRFVAIVLLVSYLSDMFSLIFQHINLSFS--IEIIIRVIIGVLGSSLVLLAFIVTTNSMLRFISKRFNMLS-NSSSG 497
                                       56677777777777777777777777776..3333444445555666666666666666666666666664.55544 PP

                                       HHHHHHHHHH CS
                    Na_H_Exchanger 215 evllvlllal 224
                                       ++  v++ ++
  gi|385805620|ref|YP_005842018.1| 498 NIGRVFVYLF 507
                                       4444444444 PP

>> Asp-Al_Ex  Predicted Permease Membrane Region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   8.2   6.7e-07     0.006      17     100 ..      29     113 ..      13     128 .. 0.86
   2 ?    0.5   4.0     0.051   4.6e+02      54     115 ..     169     231 ..     145     236 .. 0.64
   3 ?   -1.7  11.9      0.25   2.2e+03       5     106 ..     226     324 ..     222     338 .. 0.85
   4 ?   -4.4   8.0       1.7   1.5e+04       2     102 ..     279     377 ..     278     389 .. 0.62
   5 ?    1.5   0.8     0.026   2.3e+02      90     165 ..     430     519 ..     417     521 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.7e-07
                         Asp-Al_Ex  17 ikvglsLGvaggvLivglllGqlgktgpivldisalsllrelgLllFlaavGlsaG.pgffsslkkd.Glklvllal 91 
                                       +   + +G   g ++ g++++ +  + +i +d+s +++lre+gL+lF +  G s+  +g+ +s+++   ++lv +++
  gi|385805620|ref|YP_005842018.1|  29 F-QRFGFGRILGYIFGGIIIAYIALHFHISVDFSYTDALREIGLVLFFFEAGSSISiSGLRASFSRVvAIELVSITF 104
                                       4.67999****************9999999**********************9987467889999888999999999 PP

                         Asp-Al_Ex  92 lvtvvplll 100
                                       + t+ +++ 
  gi|385805620|ref|YP_005842018.1| 105 IWTLSSIVS 113
                                       988888775 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.051
                         Asp-Al_Ex  54 llrelgLllFlaavGlsaGpgffsslkkdGlklvllallvtvvplllalvlakl.vlkldlal 115
                                        l ++ +++    vG+ +G ++f ++++ +l +++ a l++ +    alv  k+  + l+la+
  gi|385805620|ref|YP_005842018.1| 169 SLFSILFSFSSSNVGIISGFQLFLKIAALSLIMFASAYLILRILSSSALVQEKTnKFILSLAI 231
                                       3333444444457*************9999999999999988887777777664344445555 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.25
                         Asp-Al_Ex   5 vlalGlllGsikikvglsLGvaggvLivglllGqlgktgpivldisalsllrelgLllFlaavGlsaGpgffsslkk 81 
                                       +l l ++lG ++i+  + L    g++i gl ++     g+i     +l  ++e+g+l++   +G ++G     ++ k
  gi|385805620|ref|YP_005842018.1| 226 ILSLAIALGYVSISQYFGLPPLFGAFISGLAFSSTLGAGEI---ADMLVGMKEIGMLFYFSSLGADIGLFNSIKVIK 299
                                       66778899*****999****999********9988444444...5677889****************9766667778 PP

                         Asp-Al_Ex  82 dGlklvllallvtvvplllalvlak 106
                                       +G+ l +la+ + +++l++  +l+ 
  gi|385805620|ref|YP_005842018.1| 300 YGIILGMLAVPIRMIGLFIGGILGG 324
                                       8**************9999998876 PP

  == domain 4  score: -4.4 bits;  conditional E-value: 1.7
                         Asp-Al_Ex   2 lalvlalGlllGsikik....vglsLGvaggvL.ivglllGqlgktgpivldisalsllrelgLllFlaavGlsaGp 73 
                                       l+ +  lG  +G ++      +g+ LG+ + ++ ++gl++G +       l   +++ ++ + L+lF  a   ++G 
  gi|385805620|ref|YP_005842018.1| 279 LFYFSSLGADIGLFNSIkvikYGIILGMLAVPIrMIGLFIGGI-------LGGVTPENASLISLTLFPIA---ESGI 345
                                       5667778888887765423345555555555444567777777.......78888888999999999664...7888 PP

                         Asp-Al_Ex  74 gffsslkkdGl...klvllallvtvvplllal 102
                                        f ++l+++G+   ++v+++ ++++ +l++  
  gi|385805620|ref|YP_005842018.1| 346 IFADTLASSGMlasQMVGISTIAVMSTLIVSG 377
                                       88888888887222344555555555544444 PP

  == domain 5  score: 1.5 bits;  conditional E-value: 0.026
                         Asp-Al_Ex  90 allvtvvplllalvlaklvlkldlallaGllaGalTstpalgaandalaeldlpa...............vgyavtY 151
                                        llv+ ++ ++ l++ ++ l +++ +++ +++G l s+ +l a + + +++ l                 +g   +Y
  gi|385805620|ref|YP_005842018.1| 430 VLLVSYLSDMFSLIFQHINLSFSIEIIIRVIIGVLGSSLVLLAFIVT-TNSMLRFiskrfnmlsnsssgnIGRVFVY 505
                                       55555555566666666666666666666666666666555544444.23322223345555555567889999999 PP

                         Asp-Al_Ex 152 plgvvllilvaqvl 165
                                        +g + l++ +q+l
  gi|385805620|ref|YP_005842018.1| 506 LFGGITLVIELQLL 519
                                       99999999888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (572 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       892  (0.0497518); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.29s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 3643.50
//
Query:       gi|385805621|ref|YP_005842019.1|  [L=91]
Description: ATP-cone domain-containing protein [Fervidicoccus fontis Kam940]
Scores for complete 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-09   36.7   0.1    5.9e-09   36.4   0.1    1.1  1  ATP-cone  ATP cone domain


Domain annotation for each model (and alignments):
>> ATP-cone  ATP cone domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.1   3.3e-13   5.9e-09       1      70 [.       3      71 ..       3      79 .. 0.93

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 3.3e-13
                                      -EEE-TTS-EEE--HHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHIIT-BHHHHHHHHHHHHHHSS- CS
                          ATP-cone  1 ikViKRdGtvepfdvekIkraiekAcegseeeideiaeeveaevrkrlrdgisteeIqdlvektliehpd 70
                                      i V KR+G++e+f +ekI+ ++ k     +e +++ia+ +e ++ +r++++i t+++ + v + l+++++
  gi|385805621|ref|YP_005842019.1|  3 ISVLKRNGEKEEFMPEKIIVSLVKTGAT-PEVARKIAKIIEGRLLERGVSEIATKDLMKEVLELLKKENE 71
                                      579**********************777.******************************99999997654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       854  (0.0476323); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.51
# Mc/sec: 539.71
//
Query:       gi|385805622|ref|YP_005842020.1|  [L=300]
Description: Fis family transcriptional regulator [Fervidicoccus fontis Kam940]
Scores for complete 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-44  149.1   0.0    1.1e-43  148.7   0.0    1.1  1  ThiP_synth  Thiamine-phosphate synthase
     0.0018   18.3   0.0     0.0046   17.0   0.0    1.6  1  Cro         Cro


Domain annotation for each model (and alignments):
>> ThiP_synth  Thiamine-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.7   0.0   1.2e-47   1.1e-43       1     164 [.     137     297 ..     137     298 .. 0.97

  Alignments for each domain:
  == domain 1  score: 148.7 bits;  conditional E-value: 1.2e-47
                                       HHHHHHHHHHCC--.GCC--TT-B-EEEE-ST--SGGGEEEETT-EEE-TSSEEE-S-EEETS-CHHHHHHHHHHCC CS
                        ThiP_synth   1 eleralelleeeeefakliPevgsNiayalpdAksieDvaavpGRIvrvkgrvkvvgepefgasshvarvllaamkf 77 
                                       e+++a+el++++++ + liPevgsNi++  +  +s+ + ++++G+Iv++++rv++vgep+ g+s+h+a+vl ++++ 
  gi|385805622|ref|YP_005842020.1| 137 EVRTAFELFNSNPNSYLLIPEVGSNIVAFPESGRSYIEAVGFSGKIVNIGSRVIAVGEPMRGGSRHTATVLSKVKNR 213
                                       699************************************************************************** PP

                                       -TT--EEEEEE--HHHHHHHCCTTSEEEE--CCCS-CCCT-HHHHHHHHHHHCC.S-ECEEEE--BCTB--EEEEEE CS
                        ThiP_synth  78 dpevraainirydekilealeelglkvvefdreeepeevgstmewgvaeaieel.evpdviydeGgvGkEpmiyvlg 153
                                       ++ev  +i iryd+ki+e++++lg+k+++++++++ ee         +e + el ++pdvi+deGg G+Ep++y++g
  gi|385805622|ref|YP_005842020.1| 214 FNEVCGVIVIRYDRKIIEKMDRLGYKISKVKPHSSMEE----FYLYLDELLGELkDPPDVIVDEGGEGIEPVCYIFG 286
                                       **************************************....67789999999988********************* PP

                                       SSHHHHHHHHH CS
                        ThiP_synth 154 kdaeevvekvl 164
                                       k+a ++v+k+l
  gi|385805622|ref|YP_005842020.1| 287 KNAIDAVKKAL 297
                                       ********987 PP

>> Cro  Cro
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   5.2e-07    0.0046      13      54 ..      28      69 ..      19      71 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.2e-07
                                      HHHHHHHHHHTS-HHHHHHHHHCT-EEEEEEETTSEEEEEEE CS
                               Cro 13 vGQaktAkdlgvkqsaIsKAlkakRnIylivdedGsveaeEv 54
                                       GQ k+ k lg+ q  ++K l ++  Iy+ + ++  ++ eEv
  gi|385805622|ref|YP_005842020.1| 28 YGQFKVGKLLGISQPMVNKYLSVNESIYIEKLKKVGINEEEV 69
                                      6*****************************999998988888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); 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: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1745.33
//
Query:       gi|385805623|ref|YP_005842021.1|  [L=184]
Description: ABC transporter permease [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-33  115.8  12.7    1.2e-33  115.8  12.7    2.0  2  ABC_cobalt     ABC-type cobalt transport system, permease com
  ------ inclusion threshold ------
      0.022   14.6   6.9      0.037   13.8   0.7    2.7  2  LapA_dom       Lipopolysaccharide assembly protein A domain
        0.9   10.0   6.1        7.5    7.0   0.3    3.1  3  MtrB           Tetrahydromethanopterin S-methyltransferase su
        0.9    9.3   9.0        5.9    6.7   3.8    2.1  2  FA_desaturase  Fatty acid desaturase


Domain annotation for each model (and alignments):
>> ABC_cobalt  ABC-type cobalt transport system, permease component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.8  12.7   2.7e-37   1.2e-33       2     119 ..      18     135 ..      17     137 .. 0.98
   2 ?    2.8   1.3     0.028   1.3e+02      61      94 ..     143     173 ..     136     182 .. 0.71

  Alignments for each domain:
  == domain 1  score: 115.8 bits;  conditional E-value: 2.7e-37
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-GGG.GGGGGGGGGHHHHHHHHHH-STTHHHHHHHHHHHHHHHTT-T CS
                        ABC_cobalt   2 diilvavigvvfGviflawglvynalsaaltPlgaealllGlWllagvlaaliirkpgaallaellaAlvemllgsq 78 
                                       d+ ++a++gvv+G+if + + +y+a++a+ +P+ga+ + +GlW++ ++laa +irkp +al++e+++A+ve+l++ +
  gi|385805623|ref|YP_005842021.1|  18 DLAILALVGVVTGIIFAGSWSIYYAVEAVGGPVGARLASYGLWFIGAPLAATLIRKPLSALFGEVIGAFVETLIAPA 94 
                                       99*************************************************************************** PP

                                       TTTHHHHHHHHHHHHHHHHHHHTTT---SHHHHHHHHHHHH CS
                        ABC_cobalt  79 wGastllsglvqGlgaElafaltrYrrftllvlllsgalaa 119
                                        G++++++gl+qGl++E++++l+rY+r+++++ +ls+++a+
  gi|385805623|ref|YP_005842021.1|  95 GGITNIIYGLLQGLASEFVYFLFRYKRWDIISGVLSAIAAG 135
                                       *************************************9986 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.028
                                       HHHHHHHHHHHHHHTT-TTTTHHHHHHHHHHHHH CS
                        ABC_cobalt  61 allaellaAlvemllgsqwGastllsglvqGlga 94 
                                       all  ++++ +em l   w ++ ++sg+v G++a
  gi|385805623|ref|YP_005842021.1| 143 ALLFGTIGSSIEMSL---WVIASMVSGAVYGFIA 173
                                       556666666666655...8888888888888776 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 ?    3.3   0.8     0.016        70      23      40 ..      19      37 ..      13      44 .. 0.71
   2 ?   13.8   0.7   8.2e-06     0.037      12      40 ..     146     176 ..     127     184 .] 0.79

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.016
                          LapA_dom 23 llvafgiGallgwllsl.w 40
                                      l++ +++G++ g++++  w
  gi|385805623|ref|YP_005842021.1| 19 LAILALVGVVTGIIFAGsW 37
                                      5677777888777777633 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 8.2e-06
                          LapA_dom  12 faq..velpLsllllvafgiGallgwllslw 40 
                                       f++  +++  sl+++++++ Ga+ g+++++ 
  gi|385805623|ref|YP_005842021.1| 146 FGTigSSIEMSLWVIASMVSGAVYGFIATYA 176
                                       555434999******************9985 PP

>> MtrB  Tetrahydromethanopterin S-methyltransferase subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.9   8.5e+03      79      88 ..      24      33 ..       5      36 .. 0.59
   2 ?    7.0   0.3    0.0017       7.5      69      90 ..      91     112 ..      87     116 .. 0.80
   3 ?    4.7   0.2    0.0087        39      70      86 ..     159     175 ..     154     180 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.9
                              MtrB 79 fyGfivglvi 88
                                      + G++ g+++
  gi|385805623|ref|YP_005842021.1| 24 LVGVVTGIIF 33
                                      3455555444 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0017
                              MtrB  69 lviaGlltnlfyGfivglviaa 90 
                                       ++ aG +tn++yG++ gl+  +
  gi|385805623|ref|YP_005842021.1|  91 IAPAGGITNIIYGLLQGLASEF 112
                                       5679***********9997655 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.0087
                              MtrB  70 viaGlltnlfyGfivgl 86 
                                       via+++++++yGfi + 
  gi|385805623|ref|YP_005842021.1| 159 VIASMVSGAVYGFIATY 175
                                       79***********9865 PP

>> FA_desaturase  Fatty acid desaturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.2    0.0025        11     133     179 ..      10      54 ..       2      61 .. 0.79
   2 ?    6.7   3.8    0.0013       5.9     127     183 ..     114     176 ..      64     179 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0025
                     FA_desaturase 133 rkwrllawlllllawlglwlalllllglalllwlvplllllfllalv 179
                                       +k  ++++ l++la++g++ +++++++++  +++++ ++++++ a++
  gi|385805623|ref|YP_005842021.1|  10 KKTSYTGIDLAILALVGVVTGIIFAGSWS--IYYAVEAVGGPVGARL 54 
                                       446677888888889************99..9999988888876655 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0013
                     FA_desaturase 127 psksrrrkwrllawlllllaw..lglwlalllllglall....lwlvplllllfllalvlnyv 183
                                        +  r ++w ++  +l ++a+  ++++l +ll++ ++ +    lw+++ ++ ++++ ++++y+
  gi|385805623|ref|YP_005842021.1| 114 YFLFRYKRWDIISGVLSAIAAgpVAVALDALLFGTIGSSiemsLWVIASMVSGAVYGFIATYA 176
                                       3333333477777777777766688888888877777779999**************998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1167.89
//
Query:       gi|385805624|ref|YP_005842022.1|  [L=240]
Description: cobalt transport protein [Fervidicoccus fontis Kam940]
Scores for complete 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   47.6   7.1    1.5e-12   47.6   7.1    1.3  1  CbiQ      Cobalt transport protein


Domain annotation for each model (and alignments):
>> CbiQ  Cobalt transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   7.1   8.2e-17   1.5e-12      10     211 ..       8     206 ..       1     213 [. 0.82

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 8.2e-17
                                       HHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHTTS---.HHHHHHHCCCHCHHHHHHHHHHE.......EECTT CS
                              CbiQ  10 prvkliwlfllllalvlapnlvtlliiiallllllllvilp.rvlaqalilpllflllgllillfqlittegefvfa 85 
                                       p    i  +++++++++ + + +l +i +ll ++l++   +  ++++ + + l+ +  g+li  +  +  +g ++f+
  gi|385805624|ref|YP_005842022.1|   8 PSMLFIYAIAVSIMAFVFNLPSSL-LIPSLLNFILGICYGRkTLPMKLIFVILMINAWGALINGI-YFHNTGPMLFK 82 
                                       444444445555555555555555.6666666666666555366677777777777777777777.8889******* PP

                                       EEE...E-TTHHHHHHHHHHHHHHHHHHHHH.HHHHS-HHHHHHHCCC.SS--HHHHHHHHHHHHHHHHHHHHHHHH CS
                              CbiQ  86 gggqisitseGllrglllalRiltllsllll.lalTTppeeltssler.lgvPlelalillLayRfiflLleevqri 160
                                       +gg +s+ +  l+  ll+ lR++ ++  +l+ l ++    el+ sler lg+P+ +a+ ++ a+R+++l+   ++++
  gi|385805624|ref|YP_005842022.1|  83 IGG-LSVRYNALTSFLLVNLRFFLIIGSTLFmLGMSGGSRELIRSLERdLGMPPWIAFSISHAFRLFPLISRDYREL 158
                                       ***.*********99*******999988777799************866**************************** PP

                                       HHHHHHTTTTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS-SS CS
                              CbiQ 161 kqAqklRlgdsklgirrslrslgkliaalflralkraervalAmeaRGYtg 211
                                       + A+k R   +  +i +    l++++++ +  +++ra+   ++ e RG + 
  gi|385805624|ref|YP_005842022.1| 159 QIARKERKAGT--NILN-PLILKEVLISILNVSYERAQWSGISAELRGVKL 206
                                       ***********..****.9****************************9665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); 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 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1572.25
//
Query:       gi|385805625|ref|YP_005842023.1|  [L=482]
Description: ABC transporter [Fervidicoccus fontis Kam940]
Scores for complete 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-46  158.1   0.0    3.1e-23   82.8   0.0    2.3  2  ABC_tran      ABC transporter
    3.3e-23   83.0  10.7    2.6e-10   40.6   0.0    4.3  4  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    2.4e-13   50.0   0.7    2.3e-05   23.9   0.2    4.0  3  SMC_N         RecF/RecN/SMC N terminal domain
    2.4e-11   44.5   8.0      4e-05   24.2   4.0    3.3  2  AAA_23        AAA domain
      5e-10   39.0   1.5    0.00037   20.2   0.5    2.5  2  AAA_29        P-loop containing region of AAA domain
    2.7e-08   34.4   0.0     0.0091   16.4   0.0    2.5  2  AAA_16        AAA ATPase domain
    9.9e-08   32.1   3.9    4.5e-05   23.3   0.0    3.9  3  AAA_15        AAA ATPase domain
    3.7e-07   30.1   0.5     0.0012   18.6   0.0    2.2  2  AAA_30        AAA domain
    7.6e-07   28.2   4.9      0.076   11.6   0.1    3.9  4  AAA_13        AAA domain
    9.2e-07   29.2   0.1     0.0054   17.0   0.0    2.7  2  AAA_22        AAA domain
    1.3e-06   28.4   0.3     0.0091   15.9   0.0    2.4  2  RsgA_GTPase   RsgA GTPase
    2.1e-06   27.0   0.2      0.028   13.5   0.3    2.3  2  T2SSE         Type II/IV secretion system protein
    3.1e-06   26.9   0.3      0.035   13.7   0.0    2.4  2  AAA_25        AAA domain
    4.7e-06   26.8   0.4      0.019   15.1   0.0    2.5  2  AAA_33        AAA domain
    8.7e-06   25.1   0.1      0.039   13.2   0.0    2.3  2  Zeta_toxin    Zeta toxin
    1.5e-05   25.0   3.7      0.012   15.6   0.1    2.5  2  NACHT         NACHT domain
    3.2e-05   23.2   0.1      0.034   13.3   0.0    2.3  2  NB-ARC        NB-ARC domain
    6.6e-05   22.9   1.1      0.048   13.6   0.1    3.0  3  ATPase_2      ATPase domain predominantly from Archaea
    9.6e-05   22.4   0.6        0.1   12.6   0.0    3.2  3  AAA_14        AAA domain
    0.00011   22.1   0.0       0.17   11.8   0.0    2.4  2  Rad17         Rad17 P-loop domain
    0.00017   22.2   0.0       0.98   10.0   0.0    3.0  2  AAA_18        AAA domain
    0.00022   20.5   0.2      0.042   13.0   0.1    2.4  2  PIF1          PIF1-like helicase
    0.00024   20.9   4.8       0.19   11.4   0.1    3.7  3  AAA_24        AAA domain
    0.00029   20.6   0.3       0.56    9.9   0.0    2.7  2  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
    0.00029   20.8   0.2       0.16   12.0   0.0    2.4  2  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
    0.00029   21.2   0.5       0.62   10.4   0.0    2.4  2  AAA_19        AAA domain
    0.00045   20.6   0.2      0.092   13.2   0.0    3.3  3  AAA           ATPase family associated with various cellular 
     0.0005   19.3   0.3      0.061   12.5   0.0    2.3  2  G-alpha       G-protein alpha subunit
    0.00057   19.5   6.3      0.036   13.7   0.1    2.4  2  cobW          CobW/HypB/UreG, nucleotide-binding domain
     0.0011   16.7   0.7     0.0024   15.5   0.0    1.7  2  DUF3584       Protein of unknown function (DUF3584)
     0.0017   18.2   2.5        1.2    9.0   0.3    2.4  2  MobB          Molybdopterin guanine dinucleotide synthesis pr
     0.0024   16.9   0.0        1.5    7.7   0.0    2.2  2  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
     0.0025   16.7   0.6        1.3    7.7   0.1    2.1  2  DLIC          Dynein light intermediate chain (DLIC)
     0.0028   17.7   0.6        1.3    9.2   0.0    2.8  2  MMR_HSR1      50S ribosome-binding GTPase
     0.0028   18.0   0.1        1.2    9.6   0.0    2.7  2  RNA_helicase  RNA helicase
     0.0033   16.9   0.4        1.9    7.9   0.0    2.4  2  Pox_A32       Poxvirus A32 protein
     0.0046   16.6   0.2        3.3    7.2   0.0    2.3  2  AAA_27        AAA domain
     0.0065   15.7   0.0       0.23   10.6   0.1    2.2  2  TIP49         TIP49 P-loop domain
     0.0079   15.8   3.9      0.036   13.7   0.1    2.3  2  SRP54         SRP54-type protein, GTPase domain
     0.0081   16.1   3.4        1.9    8.3   0.2    2.6  2  NTPase_1      NTPase
  ------ inclusion threshold ------
       0.01   15.3   0.1          4    6.8   0.0    2.4  2  PhoH          PhoH-like protein
      0.011   15.3   0.1       0.94    9.0   0.0    2.5  2  AAA_7         P-loop containing dynein motor region
      0.013   15.2   0.1          4    7.1   0.0    2.5  2  IstB_IS21     IstB-like ATP binding protein
      0.013   15.7   1.3       0.79   10.0   0.0    2.6  2  Roc           Ras of Complex, Roc, domain of DAPkinase
      0.014   14.8   0.1        5.7    6.3   0.0    2.3  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.016   14.6   1.1        3.3    7.0   0.3    2.4  2  ATPase        KaiC
      0.017   14.9   0.2        1.7    8.3   0.0    2.4  2  PRK           Phosphoribulokinase / Uridine kinase family
      0.017   14.6   0.2        1.2    8.7   0.0    2.6  2  FeoB_N        Ferrous iron transport protein B
      0.022   14.1   0.2        7.2    5.9   0.1    2.3  2  FtsK_SpoIIIE  FtsK/SpoIIIE family
      0.031   14.5   4.3       0.33   11.2   0.1    2.6  2  AAA_28        AAA domain
      0.057   13.4   1.7       0.64   10.0   0.0    2.5  2  AAA_5         AAA domain (dynein-related subfamily)
      0.058   13.1   0.1         13    5.5   0.0    2.4  2  RuvB_N        Holliday junction DNA helicase RuvB P-loop doma
      0.081   12.4   0.1       0.65    9.4   0.0    2.0  2  RecA          recA bacterial DNA recombination protein
       0.11   12.2   0.0         14    5.3   0.0    2.3  2  AAA_11        AAA domain
       0.14   11.4   1.1        6.8    5.9   0.0    2.8  3  Septin        Septin
       0.14   12.1   0.0        2.9    7.9   0.0    2.3  2  RepB-RCR_reg  Replication regulatory protein RepB
       0.14   11.4   0.0        2.1    7.6   0.0    2.2  2  DnaB_C        DnaB-like helicase C terminal domain
       0.22   11.7   0.2       0.22   11.7   0.2    2.4  2  DMAP1_like    Putative DMAP1-like
       0.27   11.0   3.2        3.9    7.2   0.2    2.4  2  ATP_bind_1    Conserved hypothetical ATP binding protein
       0.32   10.9   1.8        6.6    6.6   0.4    2.4  2  APS_kinase    Adenylylsulphate kinase
       0.38    9.9   1.2        4.8    6.3   0.4    2.2  2  DUF2075       Uncharacterized conserved protein (DUF2075)
       0.63    9.4   3.7        6.7    6.1   0.0    2.6  2  SRPRB         Signal recognition particle receptor beta subun
        7.2    5.3   8.5        1.4    7.6   0.1    2.5  2  ABC_ATPase    Predicted ATPase of the ABC class


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.8   0.0   1.1e-25   3.1e-23       1     137 []      18     171 ..      18     171 .. 0.90
   2 !   73.3   0.0   9.2e-23   2.6e-20       1     136 [.     279     410 ..     279     411 .. 0.79

  Alignments for each domain:
  == domain 1  score: 82.8 bits;  conditional E-value: 1.1e-25
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--.....SEEEEEETTCEGGG..B-HHHCCHCEEEE-SS..- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx..x RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp.....teGeilldgkdlke..qeleslrkeigvlpqe..p 68 
                                       l+n+s++ + g+++ i G++G+GK+tLl +++g l+      + G++ ++++d+ +  ++l+++ k +g++ q+   
  gi|385805625|ref|YP_005842023.1|  18 LNNISFDAESGKLILIGGHSGSGKTTLLFAITGVLTSllkgwADGKVIYRSTDILKldEPLSFSGKIFGFVLQDpdR 94 
                                       79*******************************999888888*************9999***************863 PP

                                       -S-TTSBHHHH............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEE CS
                                       xxxxxxxxxxx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  69 qlfpeltvren............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllD 133
                                       ql   +   e             e++++ e++l+++glk++  ++v    ++LSgG+k+r++la a++ +p+++++D
  gi|385805625|ref|YP_005842023.1|  95 QLLMPTPFDEVmftlenfgfeesEAKKKTENLLETFGLKKKMFEHV----ENLSGGEKRRLSLASAIAHDPPIIIFD 167
                                       44433334444777788***99888899*********999888888....*************************** PP

                                       STTT CS
                                       xxxx RF
                          ABC_tran 134 Epta 137
                                       Epta
  gi|385805625|ref|YP_005842023.1| 168 EPTA 171
                                       **97 PP

  == domain 2  score: 73.3 bits;  conditional E-value: 9.2e-23
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l+n++l+l++ge+va+vG+nG+GK+tLlk++ag +k+ +Gei++  +  +  +   + +   +l+ +++l++el+  
  gi|385805625|ref|YP_005842023.1| 279 LRNIDLDLRRGEVVALVGPNGSGKTTLLKTIAGFHKKYSGEIKIYAERKNV-KPFYVPQVPDYLFIKNTLKEELEFL 354
                                       789***************************************776332222.2233444456666666666666666 PP

                                       HHHHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 enesdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       +++  ++ +++++ l+  e ++   +ssp++LS Gq++ ++ + a   +p+++l+DEpt
  gi|385805625|ref|YP_005842023.1| 355 SKKTGKRKDELIALLDFYESRK---NSSPYTLSLGQRRWLSAVIAWSYEPSIVLFDEPT 410
                                       6677888888888888777333...4579*****************************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 ?    5.5   0.7     0.046        13       3      26 ..      32      56 ..      30      88 .. 0.70
   2 !   17.6   0.1   9.2e-06    0.0026     206     273 ..     141     176 ..      67     198 .. 0.75
   3 !   24.4   0.2     8e-08   2.3e-05       2      24 ..     292     314 ..     291     335 .. 0.77
   4 !   40.6   0.0   9.3e-13   2.6e-10     220     302 ..     366     445 ..     313     446 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.046
                            AAA_21  3 vliGpNgsGKSnLLdaldllarl.d 26
                                      ++ G  gsGK++LL a+ ++    +
  gi|385805625|ref|YP_005842023.1| 32 LIGGHSGSGKTTLLFAITGVLTSlL 56
                                      567889***********98865553 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 9.2e-06
                            AAA_21 206 eeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPk 273
                                       e                             +lS G kr l l++a++ ++   +++++DEp ++L+P+
  gi|385805625|ref|YP_005842023.1| 141 E-----------------------------NLSGGEKRRLSLASAIAHDP---PIIIFDEPTASLDPW 176
                                       3.............................56***************999...**************6 PP

  == domain 3  score: 24.4 bits;  conditional E-value: 8e-08
                            AAA_21   2 nvliGpNgsGKSnLLdaldllar 24 
                                        +l+GpNgsGK++LL+++ +++ 
  gi|385805625|ref|YP_005842023.1| 292 VALVGPNGSGKTTLLKTIAGFHK 314
                                       68****************98853 PP

  == domain 4  score: 40.6 bits;  conditional E-value: 9.3e-13
                            AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrll.ellkelsrngaQvilt 295
                                          +  ++++++ +++ lS G++r+l  + a  + +   s++l+DEp  gL+  +l  ++  ++k++++ g+ ++++
  gi|385805625|ref|YP_005842023.1| 366 IALLDFYESRKNSSPYTLSLGQRRWLSAVIAWSYEP---SIVLFDEPTVGLDKFMLFDFFsNVIKLKEK-GTSFLIS 438
                                       34445578889999************9999999999...*****************99999******99.******* PP

                            AAA_21 296 THSplll 302
                                       TH+p +l
  gi|385805625|ref|YP_005842023.1| 439 THDPRVL 445
                                       ****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 !   23.9   0.2   8.2e-08   2.3e-05      26     208 ..      30     212 ..      17     222 .. 0.71
   2 !   13.4   0.0   0.00014      0.04      25      44 ..     290     309 ..     277     317 .. 0.84
   3 ?    6.6   0.0     0.016       4.6     155     212 ..     398     456 ..     313     462 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 8.2e-08
                                       EEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--.....BTTCSSTTEEEEEEEE.EETTEESSSSSSC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxx.xxxxxxxxxxxxx RF
                             SMC_N  26 ftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk.....skekasvkkaeveitf.dnedkklkiekee 96 
                                       +  i G+ GSGK+ ll Ai  vL   s   l+     ++i++     + +++ + ++++  ++ +++d++l + ++ 
  gi|385805625|ref|YP_005842023.1|  30 LILIGGHSGSGKTTLLFAITGVLT--S--LLKGWADGKVIYRstdilKLDEPLSFSGKIFGFVlQDPDRQLLMPTPF 102
                                       567889999999999999998888..3..589999999999866665555666666777554358888887777766 PP

                                       EEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  97 vsisrrvkrkgeseykingkevtkkevsellesagiske......lLSgGektLvalaLlfAiqkvkpaplyllDei 167
                                        +++ ++++ g  e + ++      + ++lle+ g++k+      +LSgGek  ++la       ++  p+ ++De 
  gi|385805625|ref|YP_005842023.1| 103 DEVMFTLENFGFEESEAKK------KTENLLETFGLKKKmfehveNLSGGEKRRLSLASA----IAHDPPIIIFDEP 169
                                       6676666666654444444......44555555555555444445*******97666544....44678******** PP

                                       TTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-.SCE CS
                                       xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx.xxx RF
                             SMC_N 168 daaLDeknvkkvaellkekskn.aQfivislreemleka.dkl 208
                                        a LD   ++ v +++ ++      +iv+ ++ + + ++ ++l
  gi|385805625|ref|YP_005842023.1| 170 TASLDPWGINDVRNFIASEIRMgKSIIVVEHKVKYFIDMaSEL 212
                                       ****************966555388999999988777662444 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00014
                                       SEEEEEESTTSSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAi 44 
                                       ++ a+vGpNGSGK+ ll  i
  gi|385805625|ref|YP_005842023.1| 290 EVVALVGPNGSGKTTLLKTI 309
                                       5789************9988 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.016
                                       CCS--SEEEECTTTTTS-HHHH.HHHHHHHHHHCTTSEEEEE-SSHHHCCC-.SCEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                             SMC_N 155 kvkpaplyllDeidaaLDeknv.kkvaellkeksknaQfivislreemleka.dklvgvt 212
                                       +++p +++l+De    LD+      +++++k k+k + f++ +++ ++l++  d+ + ++
  gi|385805625|ref|YP_005842023.1| 398 SYEP-SIVLFDEPTVGLDKFMLfDFFSNVIKLKEKGTSFLISTHDPRVLSEIaDRAYATY 456
                                       3444.5899*********97651678999****************999987547777666 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   4.0   1.4e-07     4e-05      14      55 ..      20      68 ..      10     266 .. 0.65
   2 !   20.2   0.0   2.3e-06   0.00066      11      39 ..     280     309 ..     263     311 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.4e-07
                            AAA_23 14 eidF...skgltlItGpNGaGKTTildAiklaLygetprlsrks....g 55
                                      +i F   s +l lI G+ G+GKTT+l Ai+ +L+   ++  +++    +
  gi|385805625|ref|YP_005842023.1| 20 NISFdaeSGKLILIGGHSGSGKTTLLFAITGVLTSLLKGWADGKviyrS 68
                                      4777777889************************988888776544332 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 2.3e-06
                            AAA_23  11 rdqeidF.skgltlItGpNGaGKTTildAi 39 
                                       r+ ++d+    +++++GpNG+GKTT+l  i
  gi|385805625|ref|YP_005842023.1| 280 RNIDLDLrRGEVVALVGPNGSGKTTLLKTI 309
                                       5556666544799*************9876 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   0.5   1.3e-06   0.00037      20      48 ..      26      54 ..      15      57 .. 0.81
   2 !   16.9   0.0   1.4e-05    0.0039      17      39 ..     284     306 ..     277     311 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.3e-06
                            AAA_29 20 dlkg.atlltGpsGsGKSTllDAiqalLvp 48
                                      + +g  +l+ G+sGsGK+Tll Ai+ +L++
  gi|385805625|ref|YP_005842023.1| 26 E-SGkLILIGGHSGSGKTTLLFAITGVLTS 54
                                      3.3468999*****************9985 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 1.4e-05
                            AAA_29  17 ieidlkgatlltGpsGsGKSTll 39 
                                       +++++ +++ l+Gp+GsGK+Tll
  gi|385805625|ref|YP_005842023.1| 284 LDLRRGEVVALVGPNGSGKTTLL 306
                                       45554459**************9 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   3.2e-05    0.0091      10      44 ..      15      48 ..      12     168 .. 0.75
   2 !   15.5   0.0   5.9e-05     0.017      23      45 ..     288     310 ..     275     353 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.2e-05
                            AAA_16 10 eqLlsale.rvrsgrpelvllsGesGvGKsslvrel 44
                                      e++l+ ++ ++ sg   l+l+ G+sG+GK++l+ ++
  gi|385805625|ref|YP_005842023.1| 15 EKILNNISfDAESG--KLILIGGHSGSGKTTLLFAI 48
                                      56666666333333..89**************9443 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 5.9e-05
                            AAA_16  23 rpelvllsGesGvGKsslvrell 45 
                                       r+e+v l+G+ G+GK++l+++++
  gi|385805625|ref|YP_005842023.1| 288 RGEVVALVGPNGSGKTTLLKTIA 310
                                       4489***************9998 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   2.5      0.16        47      19      55 ..      21     102 ..      16     270 .. 0.70
   2 !   23.3   0.0   1.6e-07   4.5e-05      14     104 ..     279     362 ..     278     388 .. 0.60
   3 ?    1.4   0.0      0.75   2.1e+02     324     368 ..     401     444 ..     383     445 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.16
                            AAA_15  19 idlsee...ltvliGkNnsGKSsilealdlFlnnkekkn...................................... 54 
                                       i+++ e   l ++ G+ +sGK+++l a+   l+     +                                      
  gi|385805625|ref|YP_005842023.1|  21 ISFDAEsgkLILIGGHSGSGKTTLLFAITGVLTSLL--Kgwadgkviyrstdilkldeplsfsgkifgfvlqdpdrq 95 
                                       55555556577777899********99987777442..133555555555555555555555555555555555555 PP

                            AAA_15  55 ......k 55 
                                             +
  gi|385805625|ref|YP_005842023.1|  96 llmptpF 102
                                       5555553 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 1.6e-07
                            AAA_15  14 lkdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekkn.kkvikiekedleifeniseskdikIdvefaekek 88 
                                       l+++++dl    +  l+G+N+sGK+++l+ +  F ++    + + +i+ e ++++ f   +    + I+ +      
  gi|385805625|ref|YP_005842023.1| 279 LRNIDLDLRRGeVVALVGPNGSGKTTLLKTIAGFHKKY---SgEIKIYAERKNVKPFYVPQVPDYLFIKNTL----- 347
                                       5677778877789******************9999933...4433444444444444444444444444444..... PP

                            AAA_15  89 akeyektlkskekkka 104
                                        ke++++l +k  k +
  gi|385805625|ref|YP_005842023.1| 348 -KEELEFLSKKTGKRK 362
                                       .333333333333333 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.75
                            AAA_15 324 nvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSphi 368
                                       + i+l++EP + L   +   ++ + ++l +++    +i+TH p +
  gi|385805625|ref|YP_005842023.1| 401 PSIVLFDEPTVGLDKFMLFDFFSNVIKLKEKGT-SFLISTHDPRV 444
                                       679999999999999999999999999999996.9******9965 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.1    0.0027      0.76      16      44 ..      27      54 ..      22      68 .. 0.82
   2 !   18.6   0.0   4.2e-06    0.0012      19      56 ..     290     327 ..     284     330 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0027
                            AAA_30 16 sgdrvavltGpAGtGKttalkalreawea 44
                                      sg ++ ++ G  G+GKtt+l a++ ++++
  gi|385805625|ref|YP_005842023.1| 27 SG-KLILIGGHSGSGKTTLLFAITGVLTS 54
                                      44.59999************999988776 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 4.2e-06
                            AAA_30  19 rvavltGpAGtGKttalkalreaweaaggrviglAptg 56 
                                        v++l+Gp G+GKtt+lk+++  +++  g++ ++A  +
  gi|385805625|ref|YP_005842023.1| 290 EVVALVGPNGSGKTTLLKTIAGFHKKYSGEIKIYAERK 327
                                       5999***********************99999999765 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1       1.1   3.2e+02      20      39 ..      32      51 ..      27      75 .. 0.72
   2 !   11.6   0.1   0.00027     0.076     467     579 ..     109     210 ..      99     255 .. 0.74
   3 !    9.0   0.0    0.0016      0.47      23      52 ..     296     319 ..     288     355 .. 0.78
   4 !    6.5   0.1    0.0097       2.8     526     580 ..     400     451 ..     395     468 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.1
                            AAA_13 20 liYGwNGaGKTtLSrllrsl 39
                                      li G  G+GKTtL  ++  +
  gi|385805625|ref|YP_005842023.1| 32 LIGGHSGSGKTTLLFAITGV 51
                                      566999******97777665 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00027
                            AAA_13 467 LkafGlgeleLkfeee..kkgYrivrkggsqaaetLSeGEktaIaflYFlkslkeddseigkdkivviDDPvSSLDs 541
                                       L++fG++e e k+  e   +++ + +k   ++ e+LS GEk    +          ++      i+++D P  SLD 
  gi|385805625|ref|YP_005842023.1| 109 LENFGFEESEAKKKTEnlLETFGLKKK-MFEHVENLSGGEKRRLSL-------A--SAIAHDPPIIIFDEPTASLDP 175
                                       666666666666665533344444443.335666777777654332.......2..22224789************* PP

                            AAA_13 542 nslfivfsliksrllkkkkakQlfiLTHnleffkevkk 579
                                         ++ v ++i s++      k +++  H +++f  +  
  gi|385805625|ref|YP_005842023.1| 176 WGINDVRNFIASEI---RMGKSIIVVEHKVKYFIDMAS 210
                                       **************...89999********99976655 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0016
                            AAA_13  23 GwNGaGKTtLSrllrslelgetepkfangs 52 
                                       G NG+GKTtL + ++ +      +k+ +g+
  gi|385805625|ref|YP_005842023.1| 296 GPNGSGKTTLLKTIAGFH-----KKY-SGE 319
                                       99**************94.....444.333 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.0097
                            AAA_13 526 kdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkevkkn 580
                                       +  iv +D P   LD+ +lf  fs + +     +k   ++i+TH    + e+ ++
  gi|385805625|ref|YP_005842023.1| 400 EPSIVLFDEPTVGLDKFMLFDFFSNVIKLK---EKGTSFLISTHDPRVLSEIADR 451
                                       578*********************999997...99999******99888888765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.1    0.0043       1.2       4      22 ..      27      45 ..      24      77 .. 0.92
   2 !   17.0   0.0   1.9e-05    0.0054       5      47 ..     289     334 ..     285     438 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0043
                            AAA_22  4 tagilvvtGesGtGKTtll 22
                                      + +++++ G+sG+GKTtll
  gi|385805625|ref|YP_005842023.1| 27 SGKLILIGGHSGSGKTTLL 45
                                      67899************97 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 1.9e-05
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee...erpevvfvtl 47 
                                         +++++G+ G+GKTtll++++  +++++   +   er+ v  +++
  gi|385805625|ref|YP_005842023.1| 289 GEVVALVGPNGSGKTTLLKTIAGFHKKYSGEIKiyaERKNVKPFYV 334
                                       56789*****************999766555557864444433333 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.1     0.002      0.57      90     121 ..      18      50 ..       5      60 .. 0.79
   2 !   15.9   0.0   3.2e-05    0.0091      65     131 ..     256     321 ..     234     327 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.002
                                       HHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  90 leelkellkd.ktsvlvGqSGvGKStLinallp 121
                                       l++++   ++ k++++ G+SG GK+tL+ a+++
  gi|385805625|ref|YP_005842023.1|  18 LNNISFDAESgKLILIGGHSGSGKTTLLFAITG 50 
                                       56666666665899999**********988876 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 3.2e-05
                                       HHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S--- CS
                       RsgA_GTPase  65 leelkeelealgyevllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpelelktgevs 131
                                        ++ ++ le  g+e+ + +++    l+++   l+  ++++lvG+ G GK+tL++++++ ++   ge++
  gi|385805625|ref|YP_005842023.1| 256 ENRREKILEMRGVECWYDESD--YILRNIDLDLRRgEVVALVGPNGSGKTTLLKTIAGFHKKYSGEIK 321
                                       455566666666666666444..6788888888877********************997777777775 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 !   13.5   0.3   9.9e-05     0.028     117     153 ..      16      52 ..       3      57 .. 0.78
   2 !   11.2   0.0   0.00049      0.14     117     158 ..     277     318 ..     229     325 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.9e-05
                             T2SSE 117 kiaevlrkavrerglilvsGgTgsGKttllyallkei 153
                                       ki + ++   ++ +lil+ G  gsGKttll a+   +
  gi|385805625|ref|YP_005842023.1|  16 KILNNISFDAESGKLILIGGHSGSGKTTLLFAITGVL 52 
                                       455555555577899****************998766 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00049
                             T2SSE 117 kiaevlrkavrerglilvsGgTgsGKttllyallkeinksde 158
                                        i + +   +r+  ++ + G+ gsGKttll ++  + +k++ 
  gi|385805625|ref|YP_005842023.1| 277 YILRNIDLDLRRGEVVALVGPNGSGKTTLLKTIAGFHKKYSG 318
                                       5555666666777788899*************9988887755 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.2   0.00095      0.27      32      76 ..      27      66 ..      21      72 .. 0.73
   2 !   13.7   0.0   0.00012     0.035      30      50 ..     286     306 ..     274     312 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00095
                            AAA_25 32 agelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVly 76
                                       g+l+l+ G++g+GKttl+  +   ++ + k w        gkV+y
  gi|385805625|ref|YP_005842023.1| 27 SGKLILIGGHSGSGKTTLLFAITGVLTsLLKGW------ADGKVIY 66
                                      5899**************998876666422323......3355555 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.00012
                            AAA_25  30 lpagelallaGapgtGKttla 50 
                                       l++ge+++l+G+ g+GKttl+
  gi|385805625|ref|YP_005842023.1| 286 LRRGEVVALVGPNGSGKTTLL 306
                                       689****************98 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.6    0.0051       1.5       1      16 [.      30      45 ..      30      55 .. 0.89
   2 !   15.1   0.0   6.6e-05     0.019       1      39 [.     291     331 ..     291     410 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0051
                            AAA_33  1 lvllvGlpGsGKstla 16
                                      l+l+ G++GsGK+tl+
  gi|385805625|ref|YP_005842023.1| 30 LILIGGHSGSGKTTLL 45
                                      78999*********96 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 6.6e-05
                            AAA_33   1 lvllvGlpGsGKstlaerllkklg.avl.lssdtlrrrlfg 39 
                                       +v lvG++GsGK+tl++ ++  ++ +   +   ++r+++++
  gi|385805625|ref|YP_005842023.1| 291 VVALVGPNGSGKTTLLKTIAGFHKkYSGeIKIYAERKNVKP 331
                                       799*************9987655553323555555555555 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   0.00014     0.039      12      38 ..      24      50 ..      14      65 .. 0.82
   2 !    9.6   0.0    0.0017       0.5      16      51 ..     289     324 ..     276     337 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00014
                        Zeta_toxin 12 sqerPklillgGqpGAGKselaellkd 38
                                      + e+ klil+gG +G+GK++l+ +++ 
  gi|385805625|ref|YP_005842023.1| 24 DAESGKLILIGGHSGSGKTTLLFAITG 50
                                      557889***************988765 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0017
                        Zeta_toxin  16 PklillgGqpGAGKselaellkdelerqgnvvrldp 51 
                                         ++ l+G  G+GK++l++ ++  ++++++ +++++
  gi|385805625|ref|YP_005842023.1| 289 GEVVALVGPNGSGKTTLLKTIAGFHKKYSGEIKIYA 324
                                       568999****************99999999888876 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   1.0    0.0029      0.82       2      20 ..      30      48 ..      29      65 .. 0.85
   2 !   15.6   0.1   4.1e-05     0.012       2      21 ..     291     310 ..     290     317 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0029
                                      CEEEEC-TTTCHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqkl 20
                                      l+++ G +GsGKTtLl  +
  gi|385805625|ref|YP_005842023.1| 30 LILIGGHSGSGKTTLLFAI 48
                                      6899***********9766 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 4.1e-05
                                       CEEEEC-TTTCHHHHHHHHH CS
                             NACHT   2 lvilqGeaGsGKTtLlqkla 21 
                                       +v+l G++GsGKTtLl+ +a
  gi|385805625|ref|YP_005842023.1| 291 VVALVGPNGSGKTTLLKTIA 310
                                       799**************998 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.1    0.0075       2.1       6      40 ..      15      48 ..      12      57 .. 0.81
   2 !   13.3   0.0   0.00012     0.034      21      48 ..     290     317 ..     278     369 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0075
                                      HHHHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHH CS
                            NB-ARC  6 ekviekLlekdelqslvvalvGmgGvGKttlakqi 40
                                      ek+ ++ +   e++  ++ + G  G+GKttl+  i
  gi|385805625|ref|YP_005842023.1| 15 EKILNNISFDAESG-KLILIGGHSGSGKTTLLFAI 48
                                      67788888777777.68889***********8666 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00012
                                       EEEEEEESTTSSHHHHHHHHCCSHCCCC CS
                            NB-ARC  21 lvvalvGmgGvGKttlakqilnksdeve 48 
                                        vvalvG  G+GKttl+k i   +++  
  gi|385805625|ref|YP_005842023.1| 290 EVVALVGPNGSGKTTLLKTIAGFHKKYS 317
                                       499***************9976665555 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.032         9      17      44 ..      25      52 ..      14      73 .. 0.78
   2 ?   -0.1   0.0       2.6   7.4e+02      85     127 ..     126     169 ..      99     211 .. 0.54
   3 !   13.6   0.1   0.00017     0.048      20      53 ..     289     323 ..     278     377 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.032
                          ATPase_2 17 repneiyfiYGpegsGKtaLlkeiienl 44
                                       e+ + ++i G  gsGKt+Ll  i   l
  gi|385805625|ref|YP_005842023.1| 25 AESGKLILIGGHSGSGKTTLLFAITGVL 52
                                      5668899*************98776555 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 2.6
                          ATPase_2  85 avpkaeleeilkeksklvfkaielllekikkkgkk........iiiiiDel 127
                                        ++++ l+       k++f+ +e+l    k++           +iii+De 
  gi|385805625|ref|YP_005842023.1| 126 LLETFGLK-------KKMFEHVENLSGGEKRRLSLasaiahdpPIIIFDEP 169
                                       33333332.......222222222222222222212222223488888884 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 0.00017
                          ATPase_2  20 neiyfiYGpegsGKtaLlkeiienledkdk.yviy 53 
                                        e++ + Gp gsGKt+Llk i+  +++++   +iy
  gi|385805625|ref|YP_005842023.1| 289 GEVVALVGPNGSGKTTLLKTIAGFHKKYSGeIKIY 323
                                       6788899**************99886655414444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0     0.025       7.1       2      26 ..      28      52 ..      27     107 .. 0.74
   2 ?   -1.7   0.0       9.5   2.7e+03      66      76 ..     162     172 ..     114     225 .. 0.62
   3 !   12.6   0.0   0.00036       0.1       3      27 ..     290     314 ..     288     374 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.025
                            AAA_14  2 rkilvitGaRrvGKTtllkqlikel 26
                                      +k+++i G   +GKTtll+ +   l
  gi|385805625|ref|YP_005842023.1| 28 GKLILIGGHSGSGKTTLLFAITGVL 52
                                      68899*************9986444 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 9.5
                            AAA_14  66 tylflDEiqev 76 
                                        ++++DE   +
  gi|385805625|ref|YP_005842023.1| 162 PIIIFDEPTAS 172
                                       45555554443 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 0.00036
                            AAA_14   3 kilvitGaRrvGKTtllkqlikell 27 
                                       ++++++G+  +GKTtllk+++  + 
  gi|385805625|ref|YP_005842023.1| 290 EVVALVGPNGSGKTTLLKTIAGFHK 314
                                       799****************975444 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00059      0.17      32      89 ..      15      74 ..       5      90 .. 0.83
   2 ?    7.7   0.0     0.011         3      40      69 ..     284     313 ..     273     333 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00059
                             Rad17 32 kewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklrewlnp.vslkepdn.qk 89
                                      ++ l+  + + +  +++Li G sG gk+t +  ++  l+  l+ w ++ v ++++d  + 
  gi|385805625|ref|YP_005842023.1| 15 EKILNNISFDAESGKLILIGGHSGSGKTTLLFAITGVLTSLLKGWADGkVIYRSTDIlKL 74
                                      667777888888899******************************998356788876444 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.011
                             Rad17  40 LesrkkriLLisGPsGCgkstvvkvLskel 69 
                                       L+ r+ +++ + GP G gk+t +k ++  +
  gi|385805625|ref|YP_005842023.1| 284 LDLRRGEVVALVGPNGSGKTTLLKTIAGFH 313
                                       56666679999*************998654 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0067       1.9       1      18 [.      31      48 ..      31     105 .. 0.87
   2 !   10.0   0.0    0.0034      0.98       1      19 [.     292     310 ..     292     380 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0067
                            AAA_18  1 IlltGtpGvGKttlakeL 18
                                      Il+ G +G+GKttl  ++
  gi|385805625|ref|YP_005842023.1| 31 ILIGGHSGSGKTTLLFAI 48
                                      99***********98776 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0034
                            AAA_18   1 IlltGtpGvGKttlakeLs 19 
                                       ++l G+ G+GKttl k ++
  gi|385805625|ref|YP_005842023.1| 292 VALVGPNGSGKTTLLKTIA 310
                                       6899**********99884 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.1   0.00015     0.042       5      48 ..      13      54 ..      11      60 .. 0.90
   2 ?    5.0   0.0     0.041        12      18      47 ..     285     314 ..     272     324 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00015
                                      HHHHHHHHH......HCTS-EEEEESTTSSCHHHHHHHHHHCHC CS
                              PIF1  5 eQkkvfdaiieavlnekgklfFvtGsgGtgKtflwkallkklrs 48
                                      e +k++++i  +  +e+gkl+ + G++G+gKt l+ a++ +l s
  gi|385805625|ref|YP_005842023.1| 13 ESEKILNNI--SFDAESGKLILIGGHSGSGKTTLLFAITGVLTS 54
                                      678899999..9999***********************998876 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.041
                                       ..HCTS-EEEEESTTSSCHHHHHHHHHHCH CS
                              PIF1  18 lnekgklfFvtGsgGtgKtflwkallkklr 47 
                                         ++g+++ + G  G+gKt l+k++  + +
  gi|385805625|ref|YP_005842023.1| 285 DLRRGEVVALVGPNGSGKTTLLKTIAGFHK 314
                                       457899999***************987655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.4     0.027       7.8       4      21 ..      30      47 ..      27      56 .. 0.83
   2 ?    2.6   0.0      0.34        97     113     142 ..     232     261 ..     197     269 .. 0.89
   3 !   11.4   0.1   0.00067      0.19       4      22 ..     291     309 ..     288     329 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.027
                            AAA_24  4 kiliyGpsgiGKTtlake 21
                                       ili G sg+GKTtl+  
  gi|385805625|ref|YP_005842023.1| 30 LILIGGHSGSGKTTLLFA 47
                                      58999*********9876 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.34
                            AAA_24 113 rllkklqelrknvifiahektrkdedpege 142
                                       ++l+kl++l+ + + ++++k++kde+++++
  gi|385805625|ref|YP_005842023.1| 232 EFLEKLDSLGVDSYPVSETKKKKDENRREK 261
                                       6899**********************9887 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00067
                            AAA_24   4 kiliyGpsgiGKTtlakel 22 
                                        ++++Gp+g+GKTtl+k++
  gi|385805625|ref|YP_005842023.1| 291 VVALVGPNGSGKTTLLKTI 309
                                       689**************98 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.1    0.0082       2.3       3      23 ..      29      50 ..      27      77 .. 0.71
   2 !    9.9   0.0     0.002      0.56       4      29 ..     292     317 ..     290     327 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0082
                         PduV-EutP  3 killi.GkvgsGKttLtqalkg 23
                                      k++li G++gsGKttL  a++g
  gi|385805625|ref|YP_005842023.1| 29 KLILIgGHSGSGKTTLLFAITG 50
                                      556662689*******998887 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.002
                         PduV-EutP   4 illiGkvgsGKttLtqalkgeelkYk 29 
                                       + l+G+ gsGKttL +++ g + kY+
  gi|385805625|ref|YP_005842023.1| 292 VALVGPNGSGKTTLLKTIAGFHKKYS 317
                                       679***************99887775 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1      0.03       8.6      18      39 ..      25      48 ..      10      55 .. 0.72
   2 !   12.0   0.0   0.00056      0.16      18      40 ..     286     310 ..     273     321 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.03
                                      H..TEEEEEEESTTSSHHHHHHHH CS
                              TsaE 18 l..gdvilLeGdLGaGKTtlvrgl 39
                                      +  g++il+ G  G+GKTtl  ++
  gi|385805625|ref|YP_005842023.1| 25 AesGKLILIGGHSGSGKTTLLFAI 48
                                      244789*************98666 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00056
                                       H..TEEEEEEESTTSSHHHHHHHHH CS
                              TsaE  18 l..gdvilLeGdLGaGKTtlvrgla 40 
                                       l  g+v++L G+ G+GKTtl + +a
  gi|385805625|ref|YP_005842023.1| 286 LrrGEVVALVGPNGSGKTTLLKTIA 310
                                       234889****************997 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    0.0077       2.2       9      36 ..      27      54 ..      19      65 .. 0.75
   2 !   10.4   0.0    0.0022      0.62      10      37 ..     289     316 ..     282     325 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0077
                            AAA_19  9 kekvllvtaGpGtGKTrvlkhivallve 36
                                      + k++l+ +  G+GKT++l +i  +l +
  gi|385805625|ref|YP_005842023.1| 27 SGKLILIGGHSGSGKTTLLFAITGVLTS 54
                                      45566666669********999887765 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0022
                            AAA_19  10 ekvllvtaGpGtGKTrvlkhivallvel 37 
                                        +v++++++ G+GKT++lk+i    ++ 
  gi|385805625|ref|YP_005842023.1| 289 GEVVALVGPNGSGKTTLLKTIAGFHKKY 316
                                       67999**************998766665 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1      0.33        95       1      20 [.      31      50 ..      31      83 .. 0.86
   2 ?   -1.3   0.0       9.8   2.8e+03      53      66 ..     154     168 ..     117     172 .. 0.72
   3 !   13.2   0.0   0.00032     0.092       2      23 ..     293     314 ..     292     382 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.33
                                      EEEESSTTSSHHHHHHHHHH CS
                               AAA  1 vllyGppGtGKTllakavak 20
                                      +l+ G  G GKT+l  a+  
  gi|385805625|ref|YP_005842023.1| 31 ILIGGHSGSGKTTLLFAITG 50
                                      578899********988765 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 9.8
                                       HHHTS.TSEEEEEET CS
                               AAA  53 akeka.kpsilfiDE 66 
                                       a++ a +p i+++DE
  gi|385805625|ref|YP_005842023.1| 154 ASAIAhDPPIIIFDE 168
                                       333334589999999 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 0.00032
                                       EEESSTTSSHHHHHHHHHHHHT CS
                               AAA   2 llyGppGtGKTllakavakelg 23 
                                        l+Gp G GKT+l k +a   +
  gi|385805625|ref|YP_005842023.1| 293 ALVGPNGSGKTTLLKTIAGFHK 314
                                       69***************98655 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.049        14      25      41 ..      30      46 ..       7      55 .. 0.71
   2 !   12.5   0.0   0.00021     0.061      26      54 ..     292     319 ..     244     400 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.049
                                      EEEEEESTTSSHHHHHH CS
                           G-alpha 25 kllllGqseSGKsTilk 41
                                       +l+ G+s+SGK+T+l 
  gi|385805625|ref|YP_005842023.1| 30 LILIGGHSGSGKTTLLF 46
                                      3777899*******985 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00021
                                       EEEEESTTSSHHHHHHHHHHHCS----HH CS
                           G-alpha  26 llllGqseSGKsTilkqlkllykkgfsee 54 
                                       + l+G ++SGK+T+lk +  ++kk  s e
  gi|385805625|ref|YP_005842023.1| 292 VALVGPNGSGKTTLLKTIAGFHKKY-SGE 319
                                       789****************999764.444 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   2.3     0.011         3       3      20 ..      31      48 ..      29      58 .. 0.87
   2 !   13.7   0.1   0.00013     0.036       2      22 ..     291     313 ..     290     323 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.011
                                      EEEEESTTCCHHHHHHHH CS
                              cobW  3 tvltGflGsGKTtLlnhl 20
                                      ++++G  GsGKTtLl ++
  gi|385805625|ref|YP_005842023.1| 31 ILIGGHSGSGKTTLLFAI 48
                                      789***********9776 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.00013
                                       EEEEEESTTCCHHHHHHHHH..C CS
                              cobW   2 vtvltGflGsGKTtLlnhll..e 22 
                                       v+ l+G+ GsGKTtLl+++   +
  gi|385805625|ref|YP_005842023.1| 291 VVALVGPNGSGKTTLLKTIAgfH 313
                                       6889*************997543 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1         1   2.9e+02      22      34 ..      33      45 ..      30      48 .. 0.88
   2 !   15.5   0.0   8.3e-06    0.0024      18      64 ..     290     336 ..     281     343 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1
                           DUF3584 22 ieGtNaaGKTtLl 34
                                      i G  ++GKTtLl
  gi|385805625|ref|YP_005842023.1| 33 IGGHSGSGKTTLL 45
                                      8999********8 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 8.3e-06
                           DUF3584  18 ghtnieGtNaaGKTtLlrLiPlFYGeePsrivsktgrksfedyyLPr 64 
                                       + + ++G N++GKTtLl++i  F  ++  +i     rk+ + +y P+
  gi|385805625|ref|YP_005842023.1| 290 EVVALVGPNGSGKTTLLKTIAGFHKKYSGEIKIYAERKNVKPFYVPQ 336
                                       56889*************************977777**********8 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 !    9.0   0.3    0.0043       1.2       2      24 ..      31      53 ..      30      60 .. 0.86
   2 !    8.9   0.1    0.0047       1.3       1      19 [.     291     309 ..     291     322 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0043
                              MobB  2 lgivgksgsGKTtLleklipelk 24
                                      + i g+sgsGKTtLl  +  +l+
  gi|385805625|ref|YP_005842023.1| 31 ILIGGHSGSGKTTLLFAITGVLT 53
                                      56789**********99988886 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0047
                              MobB   1 vlgivgksgsGKTtLlekl 19 
                                       v+++vg +gsGKTtLl+ +
  gi|385805625|ref|YP_005842023.1| 291 VVALVGPNGSGKTTLLKTI 309
                                       6899************976 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 !    6.9   0.1    0.0094       2.7      11      52 ..      10      51 ..       3      57 .. 0.87
   2 !    7.7   0.0    0.0054       1.5       8      50 ..     268     310 ..     263     322 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0094
                                      -SHHHHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHH CS
                              MeaB 11 erpeakellerllakaGraqvvGltGvPGaGkstlvealgle 52
                                       + e++++l++++ +a   + + + G  G+Gk tl+ a++  
  gi|385805625|ref|YP_005842023.1| 10 GYNESEKILNNISFDAESGKLILIGGHSGSGKTTLLFAITGV 51
                                      56799******************************9888765 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0054
                                       HH--SHHHHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHH CS
                              MeaB   8 veserpeakellerllakaGraqvvGltGvPGaGkstlvealg 50 
                                       ve  + e+  +l+++  +  r +vv l G  G+Gk tl++ ++
  gi|385805625|ref|YP_005842023.1| 268 VECWYDESDYILRNIDLDLRRGEVVALVGPNGSGKTTLLKTIA 310
                                       78888999******************************98764 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.1    0.0046       1.3      23      48 ..      26      51 ..      14      60 .. 0.85
   2 !    7.2   0.0    0.0069         2      24      54 ..     288     318 ..     282     329 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0046
                              DLIC 23 PsgksvlvlGedgsGkttliaklqGv 48
                                       sgk +l+ G++gsGkttl+  + Gv
  gi|385805625|ref|YP_005842023.1| 26 ESGKLILIGGHSGSGKTTLLFAITGV 51
                                      589*****************999998 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0069
                              DLIC  24 sgksvlvlGedgsGkttliaklqGveeekkG 54 
                                        g  v ++G +gsGkttl+  + G  ++  G
  gi|385805625|ref|YP_005842023.1| 288 RGEVVALVGPNGSGKTTLLKTIAGFHKKYSG 318
                                       5677899*****************9876665 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1     0.043        12       2      21 ..      31      50 ..      30      67 .. 0.86
   2 !    9.2   0.0    0.0044       1.3       2      22 ..     292     312 ..     291     335 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.043
                                      EEEEESTTSSHHHHHHHHHT CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltg 21
                                      ++i G++ +GK+tL+ a+tg
  gi|385805625|ref|YP_005842023.1| 31 ILIGGHSGSGKTTLLFAITG 50
                                      6788**************98 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0044
                                       EEEEESTTSSHHHHHHHHHTS CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltge 22 
                                       va+vG   +GK+tL++++ g 
  gi|385805625|ref|YP_005842023.1| 292 VALVGPNGSGKTTLLKTIAGF 312
                                       89***************9984 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1     0.074        21       1      25 [.      31      54 ..      31      71 .. 0.69
   2 !    9.6   0.0    0.0042       1.2       2      36 ..     293     324 ..     292     342 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.074
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallkk 25
                                      i++ G+sg GK+tl   ++  l+ +
  gi|385805625|ref|YP_005842023.1| 31 ILIGGHSGSGKTTLLFAITGVLT-S 54
                                      578899********999554444.3 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0042
                      RNA_helicase   2 wlyGpsgeGKStlakeLakallkklklkkkdsvys 36 
                                        l+Gp+g GK+tl k++ + + kk+    + ++y+
  gi|385805625|ref|YP_005842023.1| 293 ALVGPNGSGKTTLLKTI-AGFHKKY--SGEIKIYA 324
                                       689*************4.4444444..33345555 PP

>> Pox_A32  Poxvirus A32 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1     0.012       3.4      12      33 ..      26      48 ..      15      73 .. 0.75
   2 !    7.9   0.0    0.0066       1.9      16      41 ..     292     316 ..     285     377 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.012
                           Pox_A32 12 kpFrlalvGg.sGsGktvyLlsL 33
                                      +  +l+l+Gg sGsGkt+ L ++
  gi|385805625|ref|YP_005842023.1| 26 ESGKLILIGGhSGSGKTTLLFAI 48
                                      556788997659******99765 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0066
                           Pox_A32  16 lalvGgsGsGktvyLlsLlrtlvkky 41 
                                       +alvG  GsGkt+ L+ +   + kky
  gi|385805625|ref|YP_005842023.1| 292 VALVGPNGSGKTTLLKTI-AGFHKKY 316
                                       69***********88864.6677777 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1     0.015       4.4      18      50 ..      20      52 ..      18      59 .. 0.91
   2 ?    7.2   0.0     0.012       3.3      19      47 ..     282     310 ..     279     314 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.015
                            AAA_27 18 sldfsaeeadlhliyGpNEAGKstalrAisdll 50
                                      +++f+ae+ +l li G   +GK+t+l Ai+ +l
  gi|385805625|ref|YP_005842023.1| 20 NISFDAESGKLILIGGHSGSGKTTLLFAITGVL 52
                                      689999***********************9776 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.012
                            AAA_27  19 ldfsaeeadlhliyGpNEAGKstalrAis 47 
                                       +d++  + ++  ++GpN +GK+t+l+ i 
  gi|385805625|ref|YP_005842023.1| 282 IDLDLRRGEVVALVGPNGSGKTTLLKTIA 310
                                       45555577788899***********9886 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.1   0.00081      0.23      46      74 ..      24      52 ..      13      66 .. 0.84
   2 ?    2.7   0.0       0.2        58      49      70 ..     288     309 ..     238     317 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00081
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 46 kklaGravLlaGpsgtGktalaiaiskel 74
                                      +  +G+ +L+ G+sg+Gkt l  ai+  l
  gi|385805625|ref|YP_005842023.1| 24 DAESGKLILIGGHSGSGKTTLLFAITGVL 52
                                      5568******************9998655 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.2
                                       XXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  49 aGravLlaGpsgtGktalaiai 70 
                                        G +v l+Gp+g+Gkt l  +i
  gi|385805625|ref|YP_005842023.1| 288 RGEVVALVGPNGSGKTTLLKTI 309
                                       588999**********997665 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.6      0.24        67       3      18 ..      30      45 ..      28      64 .. 0.86
   2 !   13.7   0.1   0.00013     0.036       3      31 ..     291     319 ..     289     325 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.24
                                      EEEEEESTTSSHHHHH CS
                             SRP54  3 villvGlqGaGKTttl 18
                                      +il+ G  G+GKTt l
  gi|385805625|ref|YP_005842023.1| 30 LILIGGHSGSGKTTLL 45
                                      68999*********86 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.00013
                                       EEEEEESTTSSHHHHHHHHHHHHHHTTS- CS
                             SRP54   3 villvGlqGaGKTttlaKLaallkkegkk 31 
                                       v++lvG++G+GKTt l  +a   kk   +
  gi|385805625|ref|YP_005842023.1| 291 VVALVGPNGSGKTTLLKTIAGFHKKYSGE 319
                                       899*************9999988876555 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.3      0.01       2.9       2      24 ..      31      53 ..      30      59 .. 0.89
   2 !    8.3   0.2    0.0068       1.9       2      21 ..     292     311 ..     291     321 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.01
                                      EEEE--TTSSHHHHHHHHHHHH. CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellk 24
                                      ++i G++G+GKtTl+  ++ +l 
  gi|385805625|ref|YP_005842023.1| 31 ILIGGHSGSGKTTLLFAITGVLT 53
                                      7899***********99999886 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0068
                                       EEEE--TTSSHHHHHHHHHH CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvle 21 
                                       v++ Gp G+GKtTl+k ++ 
  gi|385805625|ref|YP_005842023.1| 292 VALVGPNGSGKTTLLKTIAG 311
                                       7899***********99986 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.028       7.9      14      55 ..      19      66 ..       9      83 .. 0.65
   2 ?    6.8   0.0     0.014         4      16      37 ..     286     307 ..     278     326 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.028
                                      HHHH....H-SEEEEE--TTSSTTHH..HHHHHHHHHHTTS-SEEEEE CS
                              PhoH 14 ealk....kndivfaiGpaGtGKtyl..avalavealkkkkvkriilt 55
                                      ++++    + +++ + G++G+GKt l  a++  ++ l k+  +  ++ 
  gi|385805625|ref|YP_005842023.1| 19 NNISfdaeSGKLILIGGHSGSGKTTLlfAITGVLTSLLKGWADGKVIY 66
                                      555544435579999*********772355555666666666544444 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.014
                                       HHH-SEEEEE--TTSSTTHHHH CS
                              PhoH  16 lkkndivfaiGpaGtGKtylav 37 
                                       l++ ++v  +Gp G+GKt l  
  gi|385805625|ref|YP_005842023.1| 286 LRRGEVVALVGPNGSGKTTLLK 307
                                       557789***********97643 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 ?    3.8   0.0      0.12        36      31      51 ..      26      46 ..      14      70 .. 0.86
   2 ?    9.0   0.0    0.0033      0.94      29      53 ..     285     309 ..     272     322 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.12
                             AAA_7 31 knkkpvllvGptGtGKtviik 51
                                      +++k +l+ G++G+GKt+++ 
  gi|385805625|ref|YP_005842023.1| 26 ESGKLILIGGHSGSGKTTLLF 46
                                      5678899**********9865 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0033
                             AAA_7  29 llknkkpvllvGptGtGKtviikdl 53 
                                        l+++  v lvGp G+GKt+++k++
  gi|385805625|ref|YP_005842023.1| 285 DLRRGEVVALVGPNGSGKTTLLKTI 309
                                       56788899************99875 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.043        12      48      68 ..      29      49 ..      10      73 .. 0.73
   2 ?    7.1   0.0     0.014         4      45      67 ..     287     309 ..     279     323 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.043
                         IstB_IS21 48 enivllGpsGvGKshlaialg 68
                                      + i++ G+sG GK+ l  a+ 
  gi|385805625|ref|YP_005842023.1| 29 KLILIGGHSGSGKTTLLFAIT 49
                                      34556689********99985 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.014
                         IstB_IS21  45 ekkenivllGpsGvGKshlaial 67 
                                       ++ e ++l+Gp G GK+ l  ++
  gi|385805625|ref|YP_005842023.1| 287 RRGEVVALVGPNGSGKTTLLKTI 309
                                       68899************997665 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 ?    3.8   0.4      0.22        64       1      17 [.      29      46 ..      29      51 .. 0.76
   2 ?   10.0   0.0    0.0028      0.79       2      40 ..     292     328 ..     291     337 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.22
                                      EEEEE.SSTTSSHHHHHH CS
                               Roc  1 Kvvlv.GdsgvGKtsllk 17
                                      K++l+ G sg+GKt+ll 
  gi|385805625|ref|YP_005842023.1| 29 KLILIgGHSGSGKTTLLF 46
                                      6677725899******85 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0028
                                       EEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEE CS
                               Roc   2 vvlvGdsgvGKtsllkrfvedkfsekekstigvdfltke 40 
                                       v lvG +g+GKt+llk +    f++k++  i +   +k+
  gi|385805625|ref|YP_005842023.1| 292 VALVGPNGSGKTTLLKTIA--GFHKKYSGEIKIYAERKN 328
                                       679*************998..677777777777666655 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0      0.02       5.7      23      49 ..      29      55 ..      12      82 .. 0.86
   2 ?    6.3   0.0      0.02       5.7      25      44 ..     292     311 ..     286     326 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.02
                      Mg_chelatase 23 HnlllvGppGsGKtmlakrlpsllppl 49
                                        +l+ G +GsGKt l  +++++l++l
  gi|385805625|ref|YP_005842023.1| 29 KLILIGGHSGSGKTTLLFAITGVLTSL 55
                                      45677789**************99877 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.02
                      Mg_chelatase  25 lllvGppGsGKtmlakrlps 44 
                                       + lvGp GsGKt l k +++
  gi|385805625|ref|YP_005842023.1| 292 VALVGPNGSGKTTLLKTIAG 311
                                       679***********999876 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.3     0.011       3.3      18      44 ..      27      51 ..      22      58 .. 0.83
   2 ?    5.6   0.0     0.031       8.9      16      36 ..     286     306 ..     279     320 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.011
                            ATPase 18 egrvvlitGepGtGKtifalqFlikga 44
                                      +g+ +li G++G+GKt++   F+i+g+
  gi|385805625|ref|YP_005842023.1| 27 SGKLILIGGHSGSGKTTL--LFAITGV 51
                                      5899************97..4666665 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.031
                            ATPase  16 ipegrvvlitGepGtGKtifa 36 
                                       + +g+vv ++G  G+GKt++ 
  gi|385805625|ref|YP_005842023.1| 286 LRRGEVVALVGPNGSGKTTLL 306
                                       6799**************985 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0     0.006       1.7       2      25 ..      31      54 ..      30      76 .. 0.81
   2 ?    4.1   0.0      0.12        33       1      20 [.     291     310 ..     291     330 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.006
                               PRK  2 IgvagsSGaGkttvarklekifgr 25
                                      I ++g SG+Gktt+  +++ ++  
  gi|385805625|ref|YP_005842023.1| 31 ILIGGHSGSGKTTLLFAITGVLTS 54
                                      789***********9999988874 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.12
                               PRK   1 vIgvagsSGaGkttvarkle 20 
                                       v+++ g+ G+Gktt+ +++ 
  gi|385805625|ref|YP_005842023.1| 291 VVALVGPNGSGKTTLLKTIA 310
                                       78999**********99986 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1      0.21        60       4      23 ..      32      51 ..      29      65 .. 0.85
   2 ?    8.7   0.0    0.0041       1.2       2      26 ..     291     315 ..     290     327 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.21
                                      EEEESTTSSHHHHHHHHHTT CS
                            FeoB_N  4 alvGnpnvGkttlfnaltga 23
                                       + G   +Gkttl+ a+tg+
  gi|385805625|ref|YP_005842023.1| 32 LIGGHSGSGKTTLLFAITGV 51
                                      5568899***********97 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0041
                                       EEEEEESTTSSHHHHHHHHHTTSEE CS
                            FeoB_N   2 tvalvGnpnvGkttlfnaltgakqk 26 
                                        valvG   +Gkttl+ +++g ++k
  gi|385805625|ref|YP_005842023.1| 291 VVALVGPNGSGKTTLLKTIAGFHKK 315
                                       589******************9876 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1     0.025       7.2      31      58 ..      21      47 ..      14      56 .. 0.80
   2 ?    5.8   0.0     0.028       7.9      33      59 ..     284     309 ..     274     310 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.025
                                      EEEEGGGS-.SEEEE--TTSSHHHHHHH CS
                      FtsK_SpoIIIE 31 lvldlkkmashllvaGatgsGKStalnt 58
                                      + +d+ +    +l+ G +gsGK+t l +
  gi|385805625|ref|YP_005842023.1| 21 ISFDAESGK-LILIGGHSGSGKTTLLFA 47
                                      566777777.799***********9865 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.028
                                       EEGGGS-.SEEEE--TTSSHHHHHHHH CS
                      FtsK_SpoIIIE  33 ldlkkmashllvaGatgsGKStalntL 59 
                                       ldl+  +  + ++G  gsGK+t l+t+
  gi|385805625|ref|YP_005842023.1| 284 LDLRRGE-VVALVGPNGSGKTTLLKTI 309
                                       6777777.7899************996 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   1.1      0.24        69       3      18 ..      31      47 ..      29      57 .. 0.75
   2 ?   11.2   0.1    0.0011      0.33       2      20 ..     292     310 ..     291     326 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.24
                            AAA_28  3 vitGge.stGKTtllea 18
                                      +++Gg+ ++GKTtll a
  gi|385805625|ref|YP_005842023.1| 31 ILIGGHsGSGKTTLLFA 47
                                      566665168*****865 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0011
                            AAA_28   2 ivitGgestGKTtlleaLa 20 
                                       ++++G+ ++GKTtll+ +a
  gi|385805625|ref|YP_005842023.1| 292 VALVGPNGSGKTTLLKTIA 310
                                       89**************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 ?    2.1   0.4      0.64   1.8e+02       3      18 ..      32      47 ..      29      57 .. 0.76
   2 ?   10.0   0.0    0.0022      0.64       2      22 ..     292     312 ..     291     327 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.64
                                      EEE--SSSSHHHHHHH CS
                             AAA_5  3 lLvGppGtgKselaer 18
                                      l+ G +G+gK++l   
  gi|385805625|ref|YP_005842023.1| 32 LIGGHSGSGKTTLLFA 47
                                      55589*******9755 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0022
                                       EEEE--SSSSHHHHHHHGGGG CS
                             AAA_5   2 vlLvGppGtgKselaerlaaa 22 
                                       v LvGp G+gK++l + +a +
  gi|385805625|ref|YP_005842023.1| 292 VALVGPNGSGKTTLLKTIAGF 312
                                       579*************99876 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 ?    5.0   0.0     0.064        18      35      78 ..      30      74 ..      17      85 .. 0.83
   2 ?    5.5   0.0     0.045        13      36      54 ..     292     310 ..     281     322 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.064
                            RuvB_N 35 hvllyGpPGlGkttlakiiakelgvklk.itsgPvlekagdlaal 78
                                       +l+ G  G Gkttl   i+  l + lk  + g v+ +++d+  l
  gi|385805625|ref|YP_005842023.1| 30 LILIGGHSGSGKTTLLFAITGVLTSLLKgWADGKVIYRSTDILKL 74
                                      589999*************99999999834678999999998765 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.045
                            RuvB_N  36 vllyGpPGlGkttlakiia 54 
                                       v l+Gp G Gkttl k ia
  gi|385805625|ref|YP_005842023.1| 292 VALVGPNGSGKTTLLKTIA 310
                                       789***********99988 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1       1.4     4e+02      52      72 ..      27      47 ..      22      54 .. 0.85
   2 ?    9.4   0.0    0.0023      0.65      51      90 ..     287     325 ..     283     337 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.4
                                      TTSEEEEEESTTSSHHHHHHH CS
                              RecA 52 kGriieiyGpessGkttlalh 72
                                       G++i i G   sGkttl + 
  gi|385805625|ref|YP_005842023.1| 27 SGKLILIGGHSGSGKTTLLFA 47
                                      599999***********9654 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0023
                                       ETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEESS CS
                              RecA  51 pkGriieiyGpessGkttlalhaiaeaqkkggvaafidae 90 
                                        +G ++ + Gp+ sGkttl l++ia   kk      i ae
  gi|385805625|ref|YP_005842023.1| 287 RRGEVVALVGPNGSGKTTL-LKTIAGFHKKYSGEIKIYAE 325
                                       699***************9.88999888775544445444 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0      0.05        14       8      42 ..      19      53 ..      11     135 .. 0.80
   2 ?    4.7   0.0     0.081        23      10      40 ..     282     315 ..     274     363 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.05
                            AAA_11  8 eaiksalseseitliqGPPGtgKTktivellsqll 42
                                      ++i++  ++ ++ li G  G+gKT+ + ++  +l+
  gi|385805625|ref|YP_005842023.1| 19 NNISFDAESGKLILIGGHSGSGKTTLLFAITGVLT 53
                                      5666777788899***********77666665553 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.081
                            AAA_11  10 iksalseseitliqGPPGtgKT...ktivellsq 40 
                                       i   l++ e++ + GP G+gKT   kti+++ ++
  gi|385805625|ref|YP_005842023.1| 282 IDLDLRRGEVVALVGPNGSGKTtllKTIAGFHKK 315
                                       5556778889999*********555555555444 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.4       0.3        86       7      22 ..      31      46 ..      27      57 .. 0.85
   2 ?   -1.0   0.0       2.9   8.3e+02     226     251 ..     175     200 ..     170     212 .. 0.84
   3 ?    5.9   0.0     0.024       6.8       8      29 ..     293     314 ..     290     333 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.3
                                      EEEEEBTTSSCCCCCC CS
                            Septin  7 lmvvGesglGkttlin 22
                                      +++ G+sg Gkttl+ 
  gi|385805625|ref|YP_005842023.1| 31 ILIGGHSGSGKTTLLF 46
                                      68899********985 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.9
                                       TTEEEETT-TTT-SCCHHHHHHHHHC CS
                            Septin 226 pWGvvevenekhsdFlkLrklllkth 251
                                       pWG+ +v n   s+  + +++++ +h
  gi|385805625|ref|YP_005842023.1| 175 PWGINDVRNFIASEIRMGKSIIVVEH 200
                                       9********99999999998887666 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.024
                                       EEEEBTTSSCCCCCCTTSSSS- CS
                            Septin   8 mvvGesglGkttlintlfetdl 29 
                                        +vG +g Gkttl++t+   + 
  gi|385805625|ref|YP_005842023.1| 293 ALVGPNGSGKTTLLKTIAGFHK 314
                                       589*************965544 PP

>> RepB-RCR_reg  Replication regulatory protein RepB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0         1   2.9e+02      12      33 ..     133     154 ..     121     165 .. 0.81
   2 ?    7.9   0.0      0.01       2.9      44      72 ..     341     369 ..     339     377 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 1
                      RepB-RCR_reg  12 lkriyrkGkPltdaekqrlsvs 33 
                                       +k+++ + + l++ ek+rls++
  gi|385805625|ref|YP_005842023.1| 133 KKKMFEHVENLSGGEKRRLSLA 154
                                       3889999999*********987 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.01
                      RepB-RCR_reg  44 vfiknelkdslvqlCeeeGitqaqliekl 72 
                                       +fikn+lk++l  l +++G  + +li +l
  gi|385805625|ref|YP_005842023.1| 341 LFIKNTLKEELEFLSKKTGKRKDELIALL 369
                                       6*******************999999765 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 ?    7.6   0.0    0.0073       2.1      11      42 ..      20      51 ..      10      71 .. 0.81
   2 ?    1.2   0.0      0.65   1.8e+02      15      42 ..     285     312 ..     267     326 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0073
                                      HHCTSBXTTXEEEEEEXTTSSHHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C 11 kltsGlqkgdliiiAarpsmGktalalniaen 42
                                      ++    ++g+li+i++ ++ Gkt+l + i   
  gi|385805625|ref|YP_005842023.1| 20 NISFDAESGKLILIGGHSGSGKTTLLFAITGV 51
                                      555566899***************99888754 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.65
                                       SBXTTXEEEEEEXTTSSHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  15 GlqkgdliiiAarpsmGktalalniaen 42 
                                        l++g+++ + +  + Gkt+l  +ia  
  gi|385805625|ref|YP_005842023.1| 285 DLRRGEVVALVGPNGSGKTTLLKTIAGF 312
                                       58899*****************999964 PP

>> DMAP1_like  Putative DMAP1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   0.00078      0.22      60      93 ..     110     142 ..     102     152 .. 0.82
   2 ?   -1.1   0.4       7.3   2.1e+03      78      78 ..     330     330 ..     249     376 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00078
                        DMAP1_like  60 SslgfskstwnkkvekiLkkfgldkklkyptlrn 93 
                                        + gf  s  +kk e++L+ fgl+kk+ +  ++n
  gi|385805625|ref|YP_005842023.1| 110 ENFGFEESEAKKKTENLLETFGLKKKM-FEHVEN 142
                                       578********************9996.455555 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 7.3
                        DMAP1_like  78 k 78 
                                       k
  gi|385805625|ref|YP_005842023.1| 330 K 330
                                       2 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 ?    3.9   0.4      0.14        38       3      20 ..      35      52 ..      33      57 .. 0.81
   2 ?    7.2   0.2     0.014       3.9       2      19 ..     295     312 ..     294     321 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.14
                        ATP_bind_1  3 GpaGsGKttfvgalseil 20
                                      G+ GsGKtt+  a++ +l
  gi|385805625|ref|YP_005842023.1| 35 GHSGSGKTTLLFAITGVL 52
                                      999*******99887665 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.014
                        ATP_bind_1   2 vGpaGsGKttfvgalsei 19 
                                       vGp GsGKtt+ ++++ +
  gi|385805625|ref|YP_005842023.1| 295 VGPNGSGKTTLLKTIAGF 312
                                       8**********9998765 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.4     0.023       6.6       2      27 ..      28      53 ..      27      65 .. 0.86
   2 ?    3.1   0.0      0.28        80       1      22 [.     288     309 ..     288     322 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.023
                                      -EEEEEESSTTSSHHHHHHHHHHHHH CS
                        APS_kinase  2 gvvvwltGlsgsGKstianalekkLv 27
                                      g  +++ G sgsGK+t+ +a+   L+
  gi|385805625|ref|YP_005842023.1| 28 GKLILIGGHSGSGKTTLLFAITGVLT 53
                                      67899************999887765 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.28
                                       S-EEEEEESSTTSSHHHHHHHH CS
                        APS_kinase   1 rgvvvwltGlsgsGKstianal 22 
                                       rg vv l G  gsGK+t+ +++
  gi|385805625|ref|YP_005842023.1| 288 RGEVVALVGPNGSGKTTLLKTI 309
                                       578999***********97665 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.4     0.017       4.8       2      23 ..      29      50 ..      28      68 .. 0.88
   2 ?    1.9   0.0      0.36     1e+02       7      68 ..     295     363 ..     290     382 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.017
                           DUF2075  2 avvlVtGvaGtGKtvvllnlla 23
                                      +++l+ G +G+GKt +l+++  
  gi|385805625|ref|YP_005842023.1| 29 KLILIGGHSGSGKTTLLFAITG 50
                                      689*************999865 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.36
                           DUF2075   7 tGvaGtGKtvvllnllael........eddeeertavylsvNhplvlvlrealakkeekkkkkeafekls 68 
                                        G  G+GKt +l +++  +           e+++ + + +   p  l ++++l+++  +   k++ ++ +
  gi|385805625|ref|YP_005842023.1| 295 VGPNGSGKTTLLKTIAGFHkkysgeikIYAERKNVKPFYVPQVPDYLFIKNTLKEEL-EFLSKKTGKRKD 363
                                       5889********999998866666655555577788888888888888888888777.333333334444 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.4      0.13        36       4      23 ..      29      48 ..      26      57 .. 0.82
   2 ?    6.1   0.0     0.023       6.7       5      23 ..     291     309 ..     287     325 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.13
                                      -EEEEE-STTSSHHHHHHHH CS
                             SRPRB  4 pavllvGlsdsGKTslftrL 23
                                      + +l+ G s sGKT+l+  +
  gi|385805625|ref|YP_005842023.1| 29 KLILIGGHSGSGKTTLLFAI 48
                                      5689999********98665 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.023
                                       EEEEE-STTSSHHHHHHHH CS
                             SRPRB   5 avllvGlsdsGKTslftrL 23 
                                        v lvG+  sGKT+l++ +
  gi|385805625|ref|YP_005842023.1| 291 VVALVGPNGSGKTTLLKTI 309
                                       6889***********9876 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 ?    1.6   1.7      0.33        94     246     265 ..      30      49 ..      25      58 .. 0.87
   2 ?    7.6   0.1     0.005       1.4     242     265 ..     286     310 ..     283     319 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.33
                                       EEEEEE-TTSSHHHHHHHHH CS
                        ABC_ATPase 246 vtlIvGggfhGKsTLLeAle 265
                                       ++lI G    GK+TLL A+ 
  gi|385805625|ref|YP_005842023.1|  30 LILIGGHSGSGKTTLLFAIT 49 
                                       8899999***********96 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.005
                                       E-SS.EEEEEE-TTSSHHHHHHHHH CS
                        ABC_ATPase 242 ipkG.vtlIvGggfhGKsTLLeAle 265
                                       +++G v+++vG++  GK+TLL+ ++
  gi|385805625|ref|YP_005842023.1| 286 LRRGeVVALVGPNGSGKTTLLKTIA 310
                                       688999****************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (482 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); expected 358.6 (0.02)
Passed Vit filter:                       119  (0.00663729); expected 17.9 (0.001)
Passed Fwd filter:                        63  (0.00351386); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              63  [number of targets reported over threshold]
# CPU time: 0.80u 0.36s 00:00:01.16 Elapsed: 00:00:00.55
# Mc/sec: 2651.93
//
Query:       gi|385805626|ref|YP_005842024.1|  [L=249]
Description: MS_channel domain containing protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.2e-15   56.7   4.3    2.2e-15   56.7   4.3    1.6  2  MS_channel  Mechanosensitive ion channel
  ------ inclusion threshold ------
        6.3    6.7   6.8        2.6    8.0   0.1    2.7  2  YajC        Preprotein translocase subunit


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 ?   -3.7   2.0      0.81   7.2e+03       4      19 ..      12      27 ..       9      35 .. 0.53
   2 !   56.7   4.3   2.5e-19   2.2e-15       2     177 ..      52     231 ..      51     249 .] 0.86

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 0.81
                                      HHHHHHHHHHHHHHHT CS
                        MS_channel  4 lkiliivvgilivlsl 19
                                      ++++i v++i+ + ++
  gi|385805626|ref|YP_005842024.1| 12 IRVIISVIFIIFIYFF 27
                                      4455555554444433 PP

  == domain 2  score: 56.7 bits;  conditional E-value: 2.5e-19
                                       .HHHHHHHHHHHHHHHHTTT--SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEEEE CS
                        MS_channel   2 kilkiliivvgilivlsllgvnvsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveigdieGtVed 78 
                                        ++++ i+v+g li++s +  ++s+l ++  +lgla+ + + d+++n    ++l  +k+fkiGD++e+ +i G+V++
  gi|385805626|ref|YP_005842024.1|  52 SVFSYAIYVLGALIAISIISPQTSILDVIILLLGLAIVISFADVLRNWGIQFLLRGTKSFKIGDWIEVDGIFGRVIS 128
                                       5789*******************************************98888888899******************* PP

                                       E-SSEEEEEETTSEEEEEEHHHHHTS-EEESSS....SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-T CS
                        MS_channel  79 iglrttkirtfdgrivtiPnsslvtsnieNlsr...esgtrrikvsigvtyssdvkklekvleelkealkekpevlk 152
                                       i+   + ++t  ++ ++i n  l++s i+N +     + ++ri +  +v+  +  ++++++++++k +l+++p+vl 
  gi|385805626|ref|YP_005842024.1| 129 IEDNGIFLETARRERIFISNIRLSNSIIINRTTpigYMYRVRIYIPQTVKPLEALERVKEIVSKIKGELSSEPTVLL 205
                                       ********************************99888999999999999999999********************98 PP

                                       TS-EEEEEEEE-SSSEEE.EEEEEEE CS
                        MS_channel 153 dkellvvldefgdsslnf.evrvfvk 177
                                         e +  + +++ + ln+ ++ vf +
  gi|385805626|ref|YP_005842024.1| 206 GLEKNMTVVDLTMEFLNVyKLEVFSE 231
                                       55555555555555554314555555 PP

>> YajC  Preprotein translocase subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   3.6      0.22     2e+03       6      17 ..      15      28 ..      10      33 .. 0.59
   2 ?    8.0   0.1   0.00029       2.6      37      66 ..     113     141 ..     108     156 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.22
                              YajC  6 lv.lifvif.yfll 17
                                      ++ +if+if yf++
  gi|385805626|ref|YP_005842024.1| 15 IIsVIFIIFiYFFV 28
                                      23355655537764 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00029
                              YajC  37 kGdeVvtigGivGkvvkvdddevtveiges 66 
                                        Gd +    Gi+G+v++++d+ + +e++  
  gi|385805626|ref|YP_005842024.1| 113 IGDWIEV-DGIFGRVISIEDNGIFLETARR 141
                                       5555554.49*********99999999654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1116  (0.0622455); 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:                         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 0.30s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1544.52
//
Query:       gi|385805627|ref|YP_005842025.1|  [L=216]
Description: putative phosphoserine phosphatase [Fervidicoccus fontis Kam940]
Scores for complete 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   24.4   0.0    7.4e-05   23.2   0.0    1.6  1  HAD              haloacid dehalogenase-like hydrolase
     0.0038   17.5   0.0     0.0048   17.2   0.0    1.3  1  Hydrolase        haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.013   14.9   0.5      0.025   14.0   0.5    1.4  1  Put_Phosphatase  Putative Phosphatase
      0.015   15.0   0.2      0.053   13.3   0.0    1.8  2  Hydrolase_3      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 !   23.2   0.0   1.6e-08   7.4e-05       1     187 [.       3     173 ..       3     174 .. 0.67

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.6e-08
                               HAD   1 alfDfDgTLldgdslelllrfllrrgaprlwralreklllalfrellrldraglaelleallaglseelaaelerfv 77 
                                       a+ D+D T++ + +++++ r             l+ek++++l   l+r d+  +   +++ll+g +    + ++++v
  gi|385805627|ref|YP_005842025.1|   3 AFIDLDLTITSERTAFVISR----------SFGLEEKTRQIL---LSREDEYIKSIKISNLLSGID---LRGINKAV 63 
                                       789*****************..........445555555555...455544445566667777776...47777777 PP

                               HAD  78 aevirpklldpgalellaahraaGdrvvvvSgglrplveplla.elg..adevlatelevdd...rltge....lgl 144
                                          +     ++++l ll+   ++G+++ +vS ++++ +++l + +l+    ++ a el v++   ++ g     +++
  gi|385805627|ref|YP_005842025.1|  64 LNTKIFD-CTEKLLNLLK---EKGFEINIVSLAYKQPIQALFKyKLNisNVNIFAPELVVERensKVIGVkisiGKI 136
                                       3222222.3347777777...*********************76899555555888888887778444443333334 PP

                               HAD 145 egkpvrgegkvaalrewlaaegegidleevvayGDspsDlpll 187
                                       e + +     + + ++++ ++ +++++  + a+GDs+ Dl+++
  gi|385805627|ref|YP_005842025.1| 137 ETPWCLN---CPVCKRYIVRR-NKDEF--TLAIGDSIVDLCMF 173
                                       4444444...44445544444.45555..9***********96 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.1e-06    0.0048     117     210 .]      66     177 ..      15     177 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.1e-06
                                       HHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHH.TT....GGGE.SEEEEHHCESSTTT............. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx....xxxx.xxxxxxxxxxxxxx............. RF
                         Hydrolase 117 lkvkpeaaeavasLkaagievvlltgdnpetaeraanq.lG....ddyf.daviasdietvakp............. 174
                                        k+++ ++++++ Lk++g+e+ +++   +++ +++ +  l+    + +  + v+++++++v ++             
  gi|385805627|ref|YP_005842025.1|  66 TKIFDCTEKLLNLLKEKGFEINIVSLAYKQPIQALFKYkLNisnvNIFApELVVERENSKVIGVkisigkietpwcl 142
                                       457888899*****************************999999655556777777777766667777777999*** PP

                                       .SHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 175 .spegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                         p +k++++r+ + +   ++++GD++ D+ ++ +A+
  gi|385805627|ref|YP_005842025.1| 143 nCPVCKRYIVRRNKDEF--TLAIGDSIVDLCMFLEAD 177
                                       ************98888..***********9998887 PP

>> Put_Phosphatase  Putative Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.5   5.5e-06     0.025       5     187 ..       5     175 ..       2     182 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.5e-06
                   Put_Phosphatase   5 fDFDktiidedsdnwvvdelpatelfeelretlrkglwnelmdrvlkelheqgvseadikkvlrsiplspglvelik 81 
                                       +D D ti +e +  ++++  + +e+++++  + +     e+++ +      +g   + i+k++ +  +     +l++
  gi|385805627|ref|YP_005842025.1|   5 IDLDLTITSERTAFVISRSFGLEEKTRQILLSRE----DEYIKSIKISNLLSGIDLRGINKAVLNTKIFDCTEKLLN 77 
                                       8****************************99988....666666655545568888889898888889888999999 PP

                   Put_Phosphatase  82 slakkkleldliiiSDaNsffieeileaagledlFseiftNPaavdasG......eltvlpyhehsCklcpsNlCKg 152
                                        l  k++++++ i+S a +  i+ +++ ++l+    +if+    v+ +       ++ +   ++  C +cp  +CK+
  gi|385805627|ref|YP_005842025.1|  78 LL--KEKGFEINIVSLAYKQPIQALFK-YKLNISNVNIFAPELVVERENskvigvKISIGKIETPWCLNCP--VCKR 149
                                       99..5779**************87665.55666666777654444443311111245555555577****9..7**9 PP

                   Put_Phosphatase 153 kvleelvaeqaregveyerliYvGDganDlCpvlk 187
                                        ++ + ++e           + +GD++ DlC  l+
  gi|385805627|ref|YP_005842025.1| 150 YIVRRNKDE---------FTLAIGDSIVDLCMFLE 175
                                       999876665.........24678999999997665 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.21   9.3e+02      20      20 ..      72      72 ..       5     129 .. 0.63
   2 ?   13.3   0.0   1.2e-05     0.053     204     234 ..     158     188 ..     147     203 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.21
                                      H CS
                       Hydrolase_3 20 t 20
                                      t
  gi|385805627|ref|YP_005842025.1| 72 T 72
                                      2 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 1.2e-05
                                       GGEEEEESSGGGHHHHHHSSEEEEETTS-HH CS
                       Hydrolase_3 204 eeviafGDgeNDieMLeaaglgvAmgnasee 234
                                       e ++a+GD+  D+ M+  a+ ++ ++n++  
  gi|385805627|ref|YP_005842025.1| 158 EFTLAIGDSIVDLCMFLEADKSILIDNGNVP 188
                                       5699***********************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1271.05
//
Query:       gi|385805628|ref|YP_005842026.1|  [L=233]
Description: TrkA-N domain-containing protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-16   59.7   0.1    5.9e-16   58.8   0.1    1.5  1  TrkA_N    TrkA-N domain


Domain annotation for each model (and alignments):
>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   0.1   3.3e-20   5.9e-16       2     116 .]       4     121 ..       3     121 .. 0.93

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 3.3e-20
                                       EEES-SHHHHHHHHHHHHTT...EEEEEEESSHHHHHHHHHTT.SEEEES-TTSHHHHHHTTGGGESEEEE-SSSHH CS
                            TrkA_N   2 iiiGlGrvGrslaeeLsegg...kdvvvidkdeerveelreeg.levvvgdatdeevLeeagiekadaviaatgdde 74 
                                       +i+G   +++  ++ ++e+    + ++vi+++ e++  ++++   ++v gd  d++vLe+a+i+ ad++  +t++d+
  gi|385805628|ref|YP_005842026.1|   4 VIVGSTHFTTFALKGIREADpsgI-IIVIERSIEVATIMAKQVnGKAVAGDLRDKKVLESAEINLADTFFSLTDSDA 79 
                                       7999999999999***99666877.9******99998888777788******************************* PP

                                       HHHHHHHHHHHHTSSSEEEEEESSGGGHHHHHHHTTSEEEEH CS
                            TrkA_N  75 anilavllakelnpkkkiiaraqdpehaellkklgadvvisp 116
                                        ni ++  ak+ ++ + ++  +++p + e+++++gad +i p
  gi|385805628|ref|YP_005842026.1|  80 LNIKLCSFAKKDFSVPIVVGLINNPMNYENMREAGADFIIDP 121
                                       ***********9**9************************966 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1454.08
//
Query:       gi|385805629|ref|YP_005842027.1|  [L=249]
Description: glycosyltransferase [Fervidicoccus fontis Kam940]
Scores for complete 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-19   68.4   0.0    8.8e-19   67.9   0.0    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
      0.004   17.1   0.0     0.0058   16.5   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
     0.0074   15.8   0.0      0.012   15.2   0.0    1.2  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
      0.009   16.5   0.0      0.017   15.6   0.0    1.4  1  Glyco_tranf_2_4  Glycosyl transferase family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.9   0.0     2e-22   8.8e-19       1     125 [.       5     125 ..       5     160 .. 0.90

  Alignments for each domain:
  == domain 1  score: 67.9 bits;  conditional E-value: 2e-22
                                       EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-..HHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenv..Gkagalnagl 75 
                                       sv+ p+  eek ++ +++ +++   +   eii+vD gS D+t++i+++l     + +vi ++  +  Gk+ a++ g 
  gi|385805629|ref|YP_005842027.1|   5 SVIFPAKDEEKFIAHSVKTAKKA--KNVREIILVDGGSVDNTPAIAKKL-----GAKVIFQSILKypGKGVAMRDGY 74 
                                       8*****************99999..************************.....8999999987779********** PP

                                       HH--SSEEEEEESSEE.E-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCC CS
                   Glycos_transf_2  76 raatgdyilflDaDde.pdpdwleklvealekdgadvvlgqrprifgetde 125
                                        ++t d+i+flDaD    +pd++ kl+e++ k+++d v g++ r++g  +e
  gi|385805629|ref|YP_005842027.1|  75 YYSTKDIIVFLDADIKnLTPDFINKLIEPILKGETDFVKGTFGRKSGRVTE 125
                                       **************8537999*******************99988877665 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 !   16.5   0.0   1.3e-06    0.0058       4     114 ..       4     106 ..       2     117 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.3e-06
                   Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksraln 80 
                                       ++v++p+ +ee+ +   +  + + +    e+++v+ +s + t + a+     l   + +v++++  l   gk  a+ 
  gi|385805629|ref|YP_005842027.1|   4 VSVIFPAKDEEKFIAHSVKTAKK-AKNVREIILVDGGSVDNTPAIAKK----L---GAKVIFQSI-LKYPGKGVAMR 71 
                                       89999999999999999988876.467799999999999999998876....4...457887754.65558999999 PP

                   Glyco_tranf_2_3  81 ealravksdlvllvDdDtvv.ePdtlkrllqfflt 114
                                       +++   + d+++++D+D     Pd++ +l   +l 
  gi|385805629|ref|YP_005842027.1|  72 DGYYYSTKDIIVFLDADIKNlTPDFINKLIEPILK 106
                                       *****************9977*****998877744 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 !   15.2   0.0   2.6e-06     0.012       6     103 ..       8     101 ..       4     107 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.6e-06
                   Glyco_tranf_2_2   6 lraseerhyieervlqkakyydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGaskaes 82 
                                       + a++e+++i   v+  +k   +  e+i+vd+gS +++    +++ ++    ++ +      +++ a   G  ++  
  gi|385805629|ref|YP_005842027.1|   8 FPAKDEEKFIAHSVKTAKKA-KNVREIILVDGGSVDNTPAIAKKLGAKVIFQSILK----YPGKGVAMRDGYYYSTK 79 
                                       445566668*****888887.77889***********8888888777665554333....34999999********* PP

                   Glyco_tranf_2_2  83 dlvlFlDaDc.fissDkfekil 103
                                       d+++FlDaD    ++D ++k++
  gi|385805629|ref|YP_005842027.1|  80 DIIVFLDADIkNLTPDFINKLI 101
                                       *********6257888888776 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 !   15.6   0.0   3.8e-06     0.017       1      81 [.      11      88 ..      11      95 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.8e-06
                   Glyco_tranf_2_4  1 rneadiLpeflahhlalg.fdrilvydndstDgtrailkelpevkllhvdksyederrqvellkallaryaeadwvlvv 78
                                      ++e++++ + ++ ++++  +++i+++d +s D+t ai k+l +  ++++  +y     +v++++     y+ +d ++++
  gi|385805629|ref|YP_005842027.1| 11 KDEEKFIAHSVKTAKKAKnVREIILVDGGSVDNTPAIAKKLGAKVIFQSILKYP--GKGVAMRDGYY--YSTKDIIVFL 85
                                      689999999999987766589********************8888888888886..46778888776..6678999999 PP

                   Glyco_tranf_2_4 79 DaD 81
                                      DaD
  gi|385805629|ref|YP_005842027.1| 86 DAD 88
                                      998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1497.84
//
Query:       gi|385805630|ref|YP_005842028.1|  [L=105]
Description: hypothetical protein FFONT_0586 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00081   19.7   2.5    0.00081   19.7   2.5    1.6  1  UPF0223          Uncharacterised protein family (UPF0223)
  ------ inclusion threshold ------
      0.056   13.3   0.0      0.082   12.8   0.0    1.3  1  YdaS_antitoxin   Putative antitoxin of bacterial toxin-antito
          9    6.0  18.7         13    5.6  18.7    1.3  1  RR_TM4-6         Ryanodine Receptor TM 4-6


Domain annotation for each model (and alignments):
>> UPF0223  Uncharacterised protein family (UPF0223)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   2.5   1.4e-07   0.00081       8      64 ..      33      86 ..      26      96 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.4e-07
                                      ----HHHHHHHHHHHHHHHHHHTT-EEHHHHHHHHHHHHHH---HHHHHHHHHHHHC CS
                           UPF0223  8 ldwsteeiidVveffeavekayekgvereellkaYrrFkevvpskseekqldreFek 64
                                       d s +ei + +e+ e++e+a e ++++e+l kaY +    +  k++ek+ +++ e+
  gi|385805630|ref|YP_005842028.1| 33 FDISPDEINTMIEIVEKIEQASEGKISKEDLDKAYGE---LISHKAKEKEKKEKSER 86
                                      68999****************************9975...56666666665555444 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.4e-05     0.082      37      56 ..      44      63 ..      34      71 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.4e-05
                    YdaS_antitoxin 37 aervpeIekatnGeVtreeL 56
                                      +e v +Ie+a++G+++ e+L
  gi|385805630|ref|YP_005842028.1| 44 IEIVEKIEQASEGKISKEDL 63
                                      68999**************9 PP

>> RR_TM4-6  Ryanodine Receptor TM 4-6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6  18.7    0.0021        13       8     107 ..       5     101 ..       1     105 [] 0.43

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0021
                                       XXXXXXXXXXXXXXXXXXXXX.XXXXX....XXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXX CS
                          RR_TM4-6   8 devegdveedekeeeeeesle.edlae.aageeeeedllsdvfgldlkkeggqykvvakkseagLgDlseteaeesp 82 
                                       +eve+   e+e+e+ee +++e e+ +     + +e +++ +++   ++  +g  k+ +++ ++  g+l +++a+e+ 
  gi|385805630|ref|YP_005842028.1|   5 EEVEEVEIEEEEEKEEASEMEeEESSIgFDISPDEINTMIEIVEKIEQASEG--KISKEDLDKAYGELISHKAKEKE 79 
                                       5565544333333222223331222223444555555555554433333333..57788888888888888888874 PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXX CS
                          RR_TM4-6  83 tpelkkklaeeeeaeeekeeeeepe 107
                                       +   k+k ++++e++++ ++ ++p+
  gi|385805630|ref|YP_005842028.1|  80 K---KEKSERKKEKSNKSKKGRKPK 101
                                       3...333322222222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2854  (0.159183); expected 358.6 (0.02)
Passed bias filter:                      633  (0.0353059); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 697.06
//
Query:       gi|385805631|ref|YP_005842029.1|  [L=385]
Description: hypothetical protein FFONT_0587 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-06   26.1  48.7    5.7e-05   22.2  39.4    2.1  2  MFS_1     Major Facilitator Superfamily


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2  39.4   3.2e-09   5.7e-05       2     329 ..       3     333 ..       2     344 .. 0.74
   2 !    6.1  16.2   0.00024       4.4      43     166 ..     260     381 ..     259     385 .] 0.80

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 3.2e-09
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglll 78 
                                       ++++ +s    s++++al+ ++a ++++s +++g+++++ ++++++++ +l++lsd    + +  ++++++a + ++
  gi|385805631|ref|YP_005842029.1|   3 FFIGTISLSFLSFINSALSTYIAYNFHVSSQVYGFITAMWSVTFILSNKILSPLSDSEDNKLLSAISVITMATS-FV 78 
                                       55666666677777888888*************************************98999************.66 PP

                             MFS_1  79 llfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGa.ilgpllggllasslgWravf 154
                                       ll+++s+  + ++ +l ++  ++++ +  + i ++   ++ ++   l ++ + +   +l  l+gg+++  l+    f
  gi|385805631|ref|YP_005842029.1|  79 LLYVHSFLSVTIAFLLNAISNSSSTLSLTTTIFEMNDSSQWSKKSILQNMISYITRgVLLILIGGVFL-GLSLDI-F 153
                                       665688889**********************************************9666688888888.444543.4 PP

                             MFS_1 155 yilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvp...................awkallkdpvlwil 212
                                       +++a+++ ++f    l lp  p   +rk ++      + +++++                    ++ ++k++   ++
  gi|385805631|ref|YP_005842029.1| 154 MLIAVILSILFF---LSLPSIPFGFERKFHAFS----QSFNWINfylggftssdlisnsyylkKFEGIRKSKSSISI 223
                                       444444444433...444444444444444444....3444444444444444444466666678888888865589 PP

                             MFS_1 213 lialllfffgfsglltllplylqevlgls.glllaglllallalvgailallagrls.drlgrrrrlllalllllla 287
                                       lia+l+++++ +++ t lp+ l++   +   +l++g+++ l++lv       +  ls ++   +   l ++++l+ +
  gi|385805631|ref|YP_005842029.1| 224 LIAILGTTLVGNYMITALPIVLRSSVPMHiMWLSNGVAYVLMGLV-------LLMLSsTK--VKSLSLASFSILIRG 291
                                       9999999999999*******7766655553355555444444444.......44444244..444778888888888 PP

                             MFS_1 288 alglallavtssavllllvlvliGf.glgfvfpsllalasdla 329
                                       a ++++l ++  ++ +l +++ +++  +++++++l ++ ++l+
  gi|385805631|ref|YP_005842029.1| 292 AWFIFFLDAA-RNPQFLPIYIAFSLiMYSIINSTLYNYFVELT 333
                                       8888888888.77777777777888899999999999988876 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.00024
                             MFS_1  43 lgaavaslpl.GrlsdrfGrrrvlllglllfalglllllf..asslw.lllvlrvlqGlgagalfpagaaliadwfp 115
                                       ++++++ l+l +  s+++ + ++  +++l+ +++  +++f  a+  + +l +  +++ +++++++++ + +++++++
  gi|385805631|ref|YP_005842029.1| 260 VAYVLMGLVLlMLSSTKVKSLSLASFSILIRGAW--FIFFldAARNPqFLPIYIAFSLIMYSIINSTLYNYFVELTS 334
                                       5777777777355566675666666666666666..444424488888999999999999999*****999999999 PP

                             MFS_1 116 keergraigllsagfslGailgpllggllasslgWravfyilaivsllafv 166
                                       +     ++  ++++  +G ++g +l+gl+++ +  +  f i ai+++++f 
  gi|385805631|ref|YP_005842029.1| 335 G----YGNHSYYMAREVGNLIGSVLSGLMLTFGESPIFFSIPAIITAISFA 381
                                       8....888889999****************9999**************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1081  (0.0602934); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 2299.29
//
Query:       gi|385805632|ref|YP_005842030.1|  [L=764]
Description: V-type H(+)-translocating pyrophosphatase [Fervidicoccus fontis Kam940]
Scores for complete 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-238  793.7  32.2   1.8e-238  793.5  32.2    1.0  1  H_PPase   Inorganic H+ pyrophosphatase
  ------ inclusion threshold ------
        5.3    7.7   5.9         44    4.7   0.2    4.1  4  TMEM141   TMEM141 protein family


Domain annotation for each model (and alignments):
>> H_PPase  Inorganic H+ pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  793.5  32.2    2e-242  1.8e-238       1     650 []      14     750 ..      14     750 .. 0.97

  Alignments for each domain:
  == domain 1  score: 793.5 bits;  conditional E-value: 2e-242
                                       HHHHHHHHHHHHHHHTS--SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT............... CS
                           H_PPase   1 vlallfalvllkkvlkedegtekmkeiaeaikegaeaflkrqykviailvvvlavlllllal............... 62 
                                       +l+++ al++++++ ++++gtekm ei + i+ega+a++krq k+i++++ ++av+  + ++               
  gi|385805632|ref|YP_005842030.1|  14 LLGIISALYIYNWIGRQPTGTEKMVEIWKSIREGASAYMKRQLKTIIVFSFIMAVIAGISVYigydvkllpqhpemr 90 
                                       5799***************************************************9999777899999999999999 PP

                                       ........HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           H_PPase  63 .....lsvltaiaflvGallSalagyigmkvavranvrtakaarkslkkalkvafrsGavmgllvvglallgvslll 134
                                             s+l+a+++++G++ S++a++++m  +++anvrt++aar+++ +al++a+ +G+v g+lv +++++++sll+
  gi|385805632|ref|YP_005842030.1|  91 sevisESILIAVSVVLGSASSVTAAFLSMDASTKANVRTTEAARRGTWEALRTAVLGGSVLGFLVPSMSVFMLSLLY 167
                                       99888778********************************************************************* PP

                                       HHTTT.....TS-EE-HHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHTCHHHHTS---TT-TT-TTHHHHHHH CS
                           H_PPase 135 lllka.....aalelekllellvgfglGaslvalfarvgGGiytKaADvGaDLvGKveagipEDdprnpaviADnvG 206
                                       l+++      + l+++ +l+ l+gf++Gasl alfa+vgGGiytKaAD+GaDLvGKveagipEDdprnpaviAD+vG
  gi|385805632|ref|YP_005842030.1| 168 LVYSFfvggsNPLSIRIVLDSLAGFAFGASLSALFAQVGGGIYTKAADMGADLVGKVEAGIPEDDPRNPAVIADQVG 244
                                       ****9999999999*************************************************************** PP

                                       HHHHHTHHHHHHHHHHHHHHHHHHHHH................SHHHHHHHHHHHHHHHHHHHHHHHHHH....... CS
                           H_PPase 207 DnvGDvaGmgADlfesyvasivaamvlg...............aavklvllpllvaavgilasiigillvktkedas 268
                                       DnvGD+aG+gAD+fes++a+++++m++g               +a+k++llpll+ av+i+ +i g++++     as
  gi|385805632|ref|YP_005842030.1| 245 DNVGDCAGRGADIFESITAELLGSMIVGwavyfilinagtsqdTAIKFMLLPLLIGAVKIISTIPGVVTA-----AS 316
                                       ********************************9999888765549***********************99.....45 PP

                                       HHSS--HHHHHHHHHHHHHHHHHHHHHHHHH-S-TTTTSHHHHHHHHHHHHHHHHHHHHHHHH-TTSHHHHHHHHHG CS
                           H_PPase 269 skkkeellkaLkkgllvsavlsvvlvallslllkeaaalklflavlvGlvagllivllteyytsteykpvkeiaeas 345
                                       +kk +++ + +++g++v+av++++++a++ +l+ ++ + +l+   l+G++++++ivl+t+yyt +e+k v eia+ s
  gi|385805632|ref|YP_005842030.1| 317 QKKFNDPIEPMRNGVIVTAVVALIGFAIVYILFFRQYWGYLLSESLIGIISAVIIVLATNYYTGRESKAVVEIAQVS 393
                                       566789********************999998888899999************************************ PP

                                       GG-HHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHH........................HHHHHHHHHHHHTTTH CS
                           H_PPase 346 etGaatniisGlavgmestvlpvlviavaillsylla........................glygialaavgmLstl 398
                                       ++++a++i++Gl++gm++t++p++vi+ a+l++++++                        g++g+ala++gmLs+ 
  gi|385805632|ref|YP_005842030.1| 394 QSSSALTILKGLTIGMRATFVPIIVISSALLIAFMIGmhmplpstsnslaiagipiekflyGIFGTALATLGMLSLS 470
                                       ************************************99999**********99999999999*************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHT--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT........ CS
                           H_PPase 399 gitlavdayGPiaDNAggiaemseleeevreitdklDavGNttkAitKgfaigsAalaalaLfaaylee........ 467
                                       gi++++d  GPi+DNAggiaem++leeevr+++d lD +GN+tkA+tKgfa+gsA+laal+Lf+a++++        
  gi|385805632|ref|YP_005842030.1| 471 GIIMTLDGAGPISDNAGGIAEMAGLEEEVRNRLDPLDVLGNVTKALTKGFAMGSASLAALLLFQAFVQDyvardpsv 547
                                       ***************************************************************************** PP

                                       ....................HHCS--BTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTTTT CS
                           H_PPase 468 ....................aklekvdllnpevlvglliGamlvflfsaltmkaVgkaAeevveevrrqfkeipgil 524
                                                           + ++++ l++p++++++liGam+++lfs+++++aV++aA  +veevrrqfke+pgil
  gi|385805632|ref|YP_005842030.1| 548 iqlvsgiaqinmqnflvimqQFINRLVLIRPDIMLSFLIGAMIPYLFSSFALDAVTRAAWMMVEEVRRQFKERPGIL 624
                                       ******************9977899**************************************************** PP

                                       TTSS---HHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           H_PPase 525 egkekpdykkcveistkaalkemilpgllavlapivvglllgaealagllagalvsgvllAifmanaGgawDNAKky 601
                                       e+kekpdy ++v+ist++a+++mi p+l+++l p+v+g+l+g +a+++l++ga++s+v+lAi+m  +G+awDNAKky
  gi|385805632|ref|YP_005842030.1| 625 EWKEKPDYYRAVDISTQYAIRNMISPALTVILPPLVIGILFGGAAVGALVVGATASAVTLAILMMWGGAAWDNAKKY 701
                                       ***************************************************************************** PP

                                       HHTTSTT.SSSHHHHHHHHHHHHHHHHHCTHHHHHHHHHHHHHHHHHHH CS
                           H_PPase 602 iEegelggkgseahkaaVvGDtVGDPfKDtagpslniliklmsivslvi 650
                                       iE+g++ggk+s+ah+aaVvGDtVGDP+KDtagpsl+i+ikl++++slv+
  gi|385805632|ref|YP_005842030.1| 702 IEAGHFGGKKSPAHAAAVVGDTVGDPLKDTAGPSLHIVIKLLNTISLVF 750
                                       ***********************************************97 PP

>> TMEM141  TMEM141 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1      0.26   2.3e+03      44      73 ..      49      80 ..      46      83 .. 0.76
   2 ?   -3.4   0.1       1.7   1.6e+04      22      52 ..     394     424 ..     392     433 .. 0.68
   3 ?    4.7   0.2    0.0049        44      22      65 ..     512     555 ..     495     567 .. 0.89
   4 ?    2.9   0.0     0.018   1.7e+02      54      90 ..     575     612 ..     557     613 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.26
                           TMEM141 44 qklvkkklpyplkwnllvsvvags..vasykv 73
                                      + ++k++l+  + ++++++v+ag    ++y v
  gi|385805632|ref|YP_005842030.1| 49 SAYMKRQLKTIIVFSFIMAVIAGIsvYIGYDV 80
                                      56789999999999999999987533567765 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.7
                           TMEM141  22 qsrallkGlatfvlgtaaafflqklvkkklp 52 
                                       qs + l+ l + ++g+ a+f+   ++++ l 
  gi|385805632|ref|YP_005842030.1| 394 QSSSALTILKGLTIGMRATFVPIIVISSALL 424
                                       5666667777778888888877666666554 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.0049
                           TMEM141  22 qsrallkGlatfvlgtaaafflqklvkkklpyplkwnllvsvva 65 
                                        ++al kG+a   ++ aa + +q +v+  ++   ++  lvs +a
  gi|385805632|ref|YP_005842030.1| 512 VTKALTKGFAMGSASLAALLLFQAFVQDYVARDPSVIQLVSGIA 555
                                       589*************************9999999999998776 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.018
                           TMEM141  54 plkwnllvsvvagsvasykvtsvetkkC.qalWlalEt 90 
                                        ++  +++s ++g+++ y  +s +  +   a+W+++E+
  gi|385805632|ref|YP_005842030.1| 575 LIRPDIMLSFLIGAMIPYLFSSFALDAVtRAAWMMVEE 612
                                       467899****************9988752689***996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (764 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       982  (0.0547716); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); 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):               2  [number of targets reported over threshold]
# CPU time: 0.81u 0.33s 00:00:01.14 Elapsed: 00:00:00.51
# Mc/sec: 4545.49
//
Query:       gi|385805633|ref|YP_005842031.1|  [L=177]
Description: methyltransferase [Fervidicoccus fontis Kam940]
Scores for complete 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   35.0   0.0    1.3e-08   34.8   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
    5.9e-06   26.2   0.0    8.2e-06   25.7   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
      4e-05   24.3   0.0    6.3e-05   23.7   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    4.3e-05   24.1   0.0    5.8e-05   23.7   0.0    1.2  1  Methyltransf_11  Methyltransferase domain
    5.5e-05   23.8   0.0    7.9e-05   23.3   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    0.00022   20.4   0.0    0.00028   20.0   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
     0.0003   20.6   0.0    0.00039   20.2   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
     0.0016   17.8   0.0     0.0021   17.4   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
      0.004   17.1   0.0     0.0061   16.6   0.0    1.3  1  Methyltransf_32  Methyltransferase domain
     0.0044   16.6   0.0     0.0059   16.2   0.0    1.2  1  MTS              Methyltransferase small domain
  ------ inclusion threshold ------
      0.018   14.8   0.0      0.024   14.4   0.0    1.2  1  Met_10           Met-10+ like-protein
      0.032   13.3   0.0      0.036   13.2   0.0    1.2  1  DREV             DREV methyltransferase
      0.045   13.5   0.0      0.078   12.7   0.0    1.4  1  DUF938           Protein of unknown function (DUF938)
      0.049   14.0   0.0        9.5    6.6   0.0    2.2  2  AdoMet_MTase     Predicted AdoMet-dependent methyltransferase
        0.1   11.5   0.0       0.13   11.1   0.0    1.2  1  Methyltransf_9   Protein of unknown function (DUF1698)


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 !   34.8   0.0   1.1e-11   1.3e-08       3     114 ..      21     133 ..      19     175 .. 0.79

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 1.1e-11
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiD...iseeaielArenaqklgldnveFeqgdiee.leklledekf 75 
                                       ++ ++lD+G+G G+++f + +     ++v+ iD   ++e   ++  ++ +++g++n+eF + d+ e le  ++   f
  gi|385805633|ref|YP_005842031.1|  21 NEDVILDIGSGDGYYSFIFSKH---AKKVYAIDkayMDESLMNSLIQEGKEKGISNLEFLAKDVCEgLE--IK--YF 90 
                                       56789***************54...567*****6655777777778899*****************999..55..6* PP

                   Methyltransf_31  76 Dlilsnevlnaladpdkileeiervlkpggilliedpr....l 114
                                       +l +  + +++++ +++ l  + ++  ++g+lli +++    +
  gi|385805633|ref|YP_005842031.1|  91 NLAFFSNSFHDINCKKELLSYLYKNSAENGRLLIIEFKpsdsW 133
                                       ***********************************99964441 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   6.9e-09   8.2e-06       7     126 ..       6     133 ..       2     166 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 6.9e-09
                   Methyltransf_23   7 eelsdklerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae........kakkaqkdqfdeqe 75 
                                       ++l ++l+  l+ l     +LdiG G+G+ + +++++ ++v+++D   ++ ++          k             
  gi|385805633|ref|YP_005842031.1|   6 KRLEENLLLELAQLSNEDVILDIGSGDGYYSFIFSKHAKKVYAIDKAYMDESLMNsliqegkeK------------- 69 
                                       556666644445599999****************************988777764333333220............. PP

                   Methyltransf_23  76 aaepqg..................kfdlIvlrevlehvpdppellrqiatllkpgGylllseplaslke 126
                                            g                  +f+l+  +++++ +    ell+ ++++ +++G+ll+ e+  s+++
  gi|385805633|ref|YP_005842031.1|  70 -----GisnleflakdvcegleikYFNLAFFSNSFHDINCKKELLSYLYKNSAENGRLLIIEFKPSDSW 133
                                       .....2333333444666667777**************************************9877644 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   5.3e-08   6.3e-05       1      99 []      26     122 ..      26     122 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 5.3e-08
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       L+iG+G+G +++ + ++   ++++++D            +++ +++  +n+e+ a+d+ +  + ++f l + sn +h
  gi|385805633|ref|YP_005842031.1|  26 LDIGSGDGYYSFIFSKH--AKKVYAIDKAYMDESLMNSLIQEGKEKGISNLEFLAKDVCEGLEIKYFNLAFFSNSFH 100
                                       8****************..********876666556777777788889***********99999************* PP

                   Methyltransf_12  78 hlkdirevldnirklLkpgGrl 99 
                                        ++ ++e+l+ ++k  + +Grl
  gi|385805633|ref|YP_005842031.1| 101 DINCKKELLSYLYKNSAENGRL 122
                                       ********************97 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   4.9e-08   5.8e-05       1      95 [.      26     123 ..      26     124 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 4.9e-08
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHH.HHHHHHCCHHT-....EEEETTEECCCTSS-TT-EEEEEEES-CC CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskeml.klakekaseegl....kvefvvadaeklpfednsfDlvvssevlh 72 
                                       Ld+G+G G+++  + k++++v+++D  ++m   l ++ ++e ++    ++ef+  d+ +  +e ++f l + s+++h
  gi|385805633|ref|YP_005842031.1|  26 LDIGSGDGYYSFIFSKHAKKVYAID-KAYMDeSLMNSLIQEGKEkgisNLEFLAKDVCE-GLEIKYFNLAFFSNSFH 100
                                       8************************.5555514455555555557789**********9.9**************** PP

                                       C-CCHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  73 hvedpekalkeiaRvLkpgGllv 95 
                                        ++  +++l+ +++    +G+l+
  gi|385805633|ref|YP_005842031.1| 101 DINCKKELLSYLYKNSAENGRLL 123
                                       **999999998888888888776 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   6.6e-08   7.9e-05       1      84 [.      25     107 ..      25     120 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 6.6e-08
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEES...SHHHHHHHHHHHHHTTT.TEEEEESBCCG.BSSSTTTEEEEEEES CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDi...seemleaareraeeegl.nvefvqgdaed.lpfedgsfDlvvssg 72 
                                       +Ld+G G G +++ ++k+   +kv+++D    +e++++   ++ +e+g+ n+ef+ +d+ + l+ +   f+l + s+
  gi|385805633|ref|YP_005842031.1|  25 ILDIGSGDGYYSFIFSKHA--KKVYAIDKaymDESLMNSLIQEGKEKGIsNLEFLAKDVCEgLEIK--YFNLAFFSN 97 
                                       8*****************6..9******733368888888888888999**********5537655..599999988 PP

                                       TGGGSSHHHHHH CS
                   Methyltransf_25  73 alhhlsdedlek 84 
                                       ++h ++ ++  +
  gi|385805633|ref|YP_005842031.1|  98 SFHDINCKK--E 107
                                       888776543..4 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   2.4e-07   0.00028      23      85 ..      14      81 ..       4     102 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.4e-07
                                      HHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-...S-HHHHHHHHCHTT..TCCCEEEE-S-C CS
                            RrnaAD 23 ldklnleekltvleigpGkGilTeeLakrakqvvvlE...lderLakllqkkls..kdeklkvvhqDf 85
                                      l+ ++l++++ +l+ig+G G  + ++ k ak+v ++    +de+L+++l ++ +    ++l+ + +D+
  gi|385805633|ref|YP_005842031.1| 14 LELAQLSNEDVILDIGSGDGYYSFIFSKHAKKVYAIDkayMDESLMNSLIQEGKekGISNLEFLAKDV 81
                                      567899******************************84445999999887644444455666666665 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   3.3e-07   0.00039      64     138 ..      12      86 ..       7     124 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 3.3e-07
                                       HHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTG CS
                              PCMT  64 lalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGye 138
                                       l+lel +l++ + +L++GsG Gy + ++++  +++  +      ++l+++  ++ k+++++n+ +   D  +G e
  gi|385805633|ref|YP_005842031.1|  12 LLLELAQLSNEDVILDIGSGDGYYSFIFSKHAKKVYAIDKAYMDESLMNSLIQEGKEKGISNLEFLAKDVCEGLE 86 
                                       5789999***********************999988444444456788888899999999999999888877765 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.8e-06    0.0021      47     154 ..      21     127 ..       3     136 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.8e-06
                                       -TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--T.TT-TTS-T-EEEEEE CS
                   Ubie_methyltran  47 rgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqana.eeLpfeddsfDvvtv 122
                                       +   +lD+ +G g ++f +s+++++ + ++ + ++e++++   +  ke+g +n+efl  +  e L+ +   f++   
  gi|385805633|ref|YP_005842031.1|  21 NEDVILDIGSGDGYYSFIFSKHAKKVYAIDKAYMDESLMNSLIQEGKEKGISNLEFLAKDVcEGLEIK--YFNLAFF 95 
                                       45679****************************************************88751445544..5666666 PP

                                       ES-GGG-S-HHHHHHHHHHHEEEEEEEEEEEE CS
                   Ubie_methyltran 123 sfGlrnvtDklkaLkeayrvlkpGGrlvvlef 154
                                       s  + ++  k++ L  +y+     Grl+++ef
  gi|385805633|ref|YP_005842031.1|  96 SNSFHDINCKKELLSYLYKNSAENGRLLIIEF 127
                                       77777788888888888888888888888888 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   5.1e-06    0.0061      19      60 ..      15      52 ..       7      87 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.1e-06
                   Methyltransf_32 19 elakesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidak 60
                                      ela+ s++  ++D+G+G gY sf+ +     +  kv++id  
  gi|385805633|ref|YP_005842031.1| 15 ELAQLSNEDVILDIGSGDGYYSFIFSK----HAKKVYAIDKA 52
                                      4456688999****************9....68899999965 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0     5e-06    0.0059      22     108 ..      12     100 ..       8     128 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5e-06
                                       HHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.E.EEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTSTTS CS
                               MTS  22 lLletlpkelsgkvlDlGcGaGvlgaalakespeae.vtlvdvdarAlesakenleankle.vevvasdvleeveek 96 
                                       lLle  + + ++ +lD+G+G G+ +  + k+ +++  ++    d   ++s  +  ++++++ +e++a+dv e +e k
  gi|385805633|ref|YP_005842031.1|  12 LLLELAQLSNEDVILDIGSGDGYYSFIFSKHAKKVYaIDKAYMDESLMNSLIQEGKEKGISnLEFLAKDVCEGLEIK 88 
                                       6666666667888****************9998854455554555556666666666777689*********99988 PP

                                       -EEEEEE---ST CS
                               MTS  97 kfdlivsNPPfh 108
                                        f+l      fh
  gi|385805633|ref|YP_005842031.1|  89 YFNLAFFSNSFH 100
                                       888765555555 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0     2e-05     0.024      83     141 ..       2      60 ..       1      83 [. 0.76

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2e-05
                                       --GGGHHHHHHHHTT..--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHH CS
                            Met_10  83 fsskleaErerlakl..veegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylk 141
                                       +s+k   E + l +l   ++ +v++d+  G G+++   +k  +ak+v+aid+      +++
  gi|385805633|ref|YP_005842031.1|   2 HSNKKRLEENLLLELaqLSNEDVILDIGSGDGYYSFIFSK--HAKKVYAIDKAYMDESLMN 60 
                                       5666666666666653367889******************..67789****8765555555 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0     3e-05     0.036      94     144 ..      21      75 ..       6     131 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3e-05
                              DREV  94 edkklldlGaGdGeitkrvaptfeevyatels....etmrdrlkkkkynvlsale 144
                                       ++  +ld+G+GdG  + + +++ ++vya + +    + m   ++  k + +s+le
  gi|385805633|ref|YP_005842031.1|  21 NEDVILDIGSGDGYYSFIFSKHAKKVYAIDKAymdeSLMNSLIQEGKEKGISNLE 75 
                                       46679***********************986511112233444444555555555 PP

>> DUF938  Protein of unknown function (DUF938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   6.5e-05     0.078      10      79 ..       4      76 ..       1      87 [. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.5e-05
                            DUF938 10 nrepilevLksylaktte..rvLEiasGtGqHAvffApalpnlkwq.psdqdeelresiaawadelalsnlkp 79
                                      n++ + e L+  la+ ++   +L+i+sG G +   f ++ +++  +  +  de+l++s+ +  +e ++snl++
  gi|385805633|ref|YP_005842031.1|  4 NKKRLEENLLLELAQLSNedVILDIGSGDGYYSFIFSKHAKKVYAIdKAYMDESLMNSLIQEGKEKGISNLEF 76
                                      566666666555554443346****************999887655156679999***************986 PP

>> AdoMet_MTase  Predicted AdoMet-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0079       9.5      59      88 ..      22      51 ..      11      64 .. 0.86
   2 ?    5.4   0.0     0.018        22      60      84 ..      97     121 ..      85     147 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0079
                      AdoMet_MTase 59 etsfvdvgcgngllvyvlaaegykgygidl 88
                                      e  + d+g g+g   ++++    k y id 
  gi|385805633|ref|YP_005842031.1| 22 EDVILDIGSGDGYYSFIFSKHAKKVYAIDK 51
                                      56789*********************9995 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.018
                      AdoMet_MTase  60 tsfvdvgcgngllvyvlaaegykgy 84 
                                       +sf d+ c   ll y+ +    +g 
  gi|385805633|ref|YP_005842031.1|  97 NSFHDINCKKELLSYLYKNSAENGR 121
                                       79**************998877774 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 ?   11.1   0.0   0.00011      0.13     110     147 ..      15      52 ..       4      78 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00011
                                       GS.--TT-.EEEEET-TTSHHHHHHHHCT-SEEEEE--- CS
                    Methyltransf_9 110 hlsdlkgr.tildvGcgnGyhlwrmvgegaklvvGidPs 147
                                        l++l +  +ild+G g+Gy+ + + +++ak v  id +
  gi|385805633|ref|YP_005842031.1|  15 ELAQLSNEdVILDIGSGDGYYSF-IFSKHAKKVYAIDKA 52 
                                       56777664279***********9.578899999999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 1194.81
//
Query:       gi|385805634|ref|YP_005842032.1|  [L=235]
Description: nucleotidyltransferase [Fervidicoccus fontis Kam940]
Scores for complete 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    1.4e-36  126.4   0.0    1.1  1  NTP_transferase  Nucleotidyl transferase
    3.1e-09   37.4   0.0    3.9e-09   37.1   0.0    1.1  1  NTP_transf_3     MobA-like NTP transferase domain


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 !  126.4   0.0   1.5e-40   1.4e-36       2     246 ..       6     228 ..       5     230 .. 0.95

  Alignments for each domain:
  == domain 1  score: 126.4 bits;  conditional E-value: 1.5e-40
                                       EEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEE CS
                   NTP_transferase   2 avILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlia 78 
                                       a ILaGG+G+RL+PLt +++k+++ v+g  ++++ ++  l + gi++  v l  +  +++++++++g+k++ve++++
  gi|385805634|ref|YP_005842032.1|   6 AAILAGGYGKRLRPLTDSIPKPMIEVGGR-PILEWQMLWLRSLGIKK-FVLLVGYLGEIIKSYFGNGEKLKVEIKYS 80 
                                       67***************************.*****************.999999*********************** PP

                                       EESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECT CS
                   NTP_transferase  79 lepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvieade 155
                                       +e+e+ gt +A++ a ++++dek   +++v++gD++++ +  e+v + +++        +i     +++yGv+ +d 
  gi|385805634|ref|YP_005842032.1|  81 FENEPLGTGGAIKNAYNVMKDEK---YFFVVNGDIITNLNPYEMVSDLEDEIG------VIALAPLQSQYGVVDVDT 148
                                       ***********************...7******************99988777......555667889********* PP

                                       TSBEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEEX CS
                   NTP_transferase 156 egrverfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsDv 232
                                       +g ++ f EKPk +    ++++G+Y+ +se++++l       +++ d  ++++pk+ e+ k + +  f+   yW+ +
  gi|385805634|ref|YP_005842032.1| 149 NGHIRGFREKPKIEG--IWINAGVYLLKSEIFEML-------PKKGDIEKETFPKVAEQNKLKGKKYFDI--YWKSI 214
                                       *************98..79****************.......67889999***************99999..9**** PP

                                       SSHHHHHHHHHHHH CS
                   NTP_transferase 233 Gtldslleanekla 246
                                        ++++l e+ ++++
  gi|385805634|ref|YP_005842032.1| 215 DSHKDLEEVDKAIR 228
                                       *******9998876 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.0   4.3e-13   3.9e-09       1      97 [.       6     113 ..       6     142 .. 0.83

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 4.3e-13
                                       EEEEEESS-TTTT....T.THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH.CHHHHHH....TTCTS-EEE-.T CS
                      NTP_transf_3   1 aviLAGGrSsRmg....g.dKallplggkpllervldalraagvdevvvvggd.eevlaal....arlgvrvved.e 66 
                                       a+iLAGG ++R+     + +K+++++gg+p+le+++  lr++g+++ v+ +g+  e+ + +    ++l+v++ +  e
  gi|385805634|ref|YP_005842032.1|   6 AAILAGGYGKRLRpltdSiPKPMIEVGGRPILEWQMLWLRSLGIKKFVLLVGYlGEIIKSYfgngEKLKVEIKYSfE 82 
                                       68**********7443349*************************999999999856655442433566677655523 PP

                                       TSS-SHHHHHHHHHHHH.SSSCEEEEETT-T CS
                      NTP_transf_3  67 dpgkgplaslaaalraaadadavlvlacDmP 97 
                                       ++  g++++++ a +  +d+++++v+ +D++
  gi|385805634|ref|YP_005842032.1|  83 NEPLGTGGAIKNAYNVMKDEKYFFVVNGDII 113
                                       3469************99***********75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1460.44
//
Query:       gi|385805635|ref|YP_005842033.1|  [L=117]
Description: hypothetical protein FFONT_0591 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                      313  (0.0174578); 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 0.28s 00:00:00.71 Elapsed: 00:00:00.47
# Mc/sec: 748.30
//
Query:       gi|385805636|ref|YP_005842034.1|  [L=108]
Description: 30S ribosomal protein S10P [Fervidicoccus fontis Kam940]
Scores for complete 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-28   97.5   0.0    4.4e-28   97.4   0.0    1.0  1  Ribosomal_S10  Ribosomal protein S10p/S20e
  ------ inclusion threshold ------
       0.06   14.2   0.0       0.11   13.3   0.0    1.4  1  PriA_C         Primosomal protein N C-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_S10  Ribosomal protein S10p/S20e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.4   0.0   4.9e-32   4.4e-28       1      97 [.      12     105 ..      12     106 .. 0.98

  Alignments for each domain:
  == domain 1  score: 97.4 bits;  conditional E-value: 4.9e-32
                                       EEEEEESSHHHHHHHHHHHHHHTTSSS-EE---EEEEEEEEEEEEE--SS--.S--EEEEEEEEEEEEEEEE.E-HH CS
                     Ribosomal_S10   1 rirlkSydsklLekavkkivraakelgikvkgpvplPtkrkrvtvlksphvd.kksreqfeirthkRlidisdatke 76 
                                       rirl S + ++L+k++++i+ +a++ g+k++gpvplPtkr+ v+vl+ ph++ +k++e++e+r+hkRlidi  ++++
  gi|385805636|ref|YP_005842034.1|  12 RIRLWSANVESLDKVTSQIKAIAEKGGVKMRGPVPLPTKRLVVPVLRLPHGEgSKHWEHWEMRIHKRLIDI-ASDER 87 
                                       8**********************************************************************.5999* PP

                                       HHHHHS-...S---SS-EEEE CS
                     Ribosomal_S10  77 tidtllkllqlnlpegVsvev 97 
                                        ++++++   +++pe V +e+
  gi|385805636|ref|YP_005842034.1|  88 IMRQIMR---VRVPEDVYIEI 105
                                       *******...*********98 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 ?   13.3   0.0   1.2e-05      0.11       4      51 ..       9      52 ..       8      53 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.2e-05
                            PriA_C  4 rlalirvsgkdeekveeaaeelaellkealkleeveilgpapapiaki 51
                                       +a+ir+ + + e + ++ ++++++ ++     +v++ gp+p p +++
  gi|385805636|ref|YP_005842034.1|  9 TMARIRLWSANVESLDKVTSQIKAIAEK----GGVKMRGPVPLPTKRL 52
                                      599********************99998....7899********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 658.46
//
Query:       gi|385805637|ref|YP_005842035.1|  [L=441]
Description: elongation factor 1-alpha [Fervidicoccus fontis Kam940]
Scores for complete 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-54  183.7   0.0    4.5e-54  183.0   0.0    1.3  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    3.2e-36  124.0   0.1    3.1e-35  120.9   0.1    2.3  2  GTP_EFTU_D3  Elongation factor Tu C-terminal domain
    2.8e-16   59.7   3.1      3e-16   59.6   1.4    2.0  2  GTP_EFTU_D2  Elongation factor Tu domain 2
    9.3e-05   22.3   1.5    0.00035   20.4   1.5    1.9  1  GTP_EFTU_D4  Elongation factor Tu domain 4
     0.0002   21.4   0.0     0.0019   18.3   0.0    2.3  1  MMR_HSR1     50S ribosome-binding GTPase
  ------ inclusion threshold ------
      0.046   14.0   0.1       0.74   10.1   0.0    2.5  2  SepF         Cell division protein SepF
       0.12   13.0   0.4       0.24   12.0   0.1    1.6  2  Amelogenin   Amelogenin
       0.13   12.4   0.0       0.23   11.6   0.0    1.4  1  TetR_C_2     MAATS-type transcriptional repressor, C-terminal
       0.19   11.8   0.3         27    4.8   0.0    2.7  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 !  183.0   0.0   2.2e-57   4.5e-54       1     190 [.       9     226 ..       9     230 .. 0.90

  Alignments for each domain:
  == domain 1  score: 183.0 bits;  conditional E-value: 2.2e-57
                                       TCEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHH..HHHST............HCHSHHHHHHTSCSSCEEEEE CS
                          GTP_EFTU   1 krirnigiighvDhGKtTLtdrLlyktgaiskkgeka..eeerv............lDtlkeErergiTiksaaisl 63 
                                       k+++n+++ighvDhGK+T+++++ly++g ++ k+  +  e e+             lD+lkeErerg+Ti+ + +++
  gi|385805637|ref|YP_005842035.1|   9 KPHLNLVVIGHVDHGKSTTVGHILYRLGYVDPKKLAEleE-EAKkkgkesfkyawlLDNLKEERERGVTIDLSFMKF 84 
                                       579*****************************88888742.3335789999************************** PP

                                       ETTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTB.......STHHHHHHHHHHHHTTTE.EEEEEESC CS
                          GTP_EFTU  64 eketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveG.......vepqteevlrlalkegvp.iivfiNKm 132
                                       e  tkky +++iD+PGH+dF+k++i+g++++D a+lvv+a++G       +e qt+e+l la+++g++ iiv++NKm
  gi|385805637|ref|YP_005842035.1|  85 E--TKKYYFTIIDAPGHRDFVKNMITGASQADAAILVVSARKGefeagmsPEGQTREHLILAKTMGIEqIIVAVNKM 159
                                       *..************************************************************************** PP

                                       GST.....HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHH............HHHHHHHH CS
                          GTP_EFTU 133 Drl.....kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvk............tllealve 190
                                       D +     ++++k+++++++ k+      ++  g++ + ++p++++S+++g+++             tl+eal++
  gi|385805637|ref|YP_005842035.1| 160 DATeppysQERYKQVIDTLQ-KF------MKGLGFDIS-KIPFIPISGWNGDNLIerspampwyngpTLVEALDN 226
                                       ***99997788888888777.88......8999***95.*************87656666666666677777765 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 ?    0.2   0.0      0.45   8.9e+02       3      45 ..     108     149 ..     106     169 .. 0.74
   2 !  120.9   0.1   1.6e-38   3.1e-35       3     111 ..     326     432 ..     324     433 .. 0.98

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.45
                                       EEECCEEEEEEESSS..SS-BSTT-EEEEESSS-EEEEEEEEE CS
                       GTP_EFTU_D3   3 kphtkfeAqvyilekerhtpitagYrpvlyirtadvtgkvveL 45 
                                       + +++ +A +++++  r++++ ag +p    r   + +k++ +
  gi|385805637|ref|YP_005842035.1| 108 TGASQADAAILVVSA-RKGEFEAGMSPEGQTREHLILAKTMGI 149
                                       566777899999999.******999997666666555555555 PP

  == domain 2  score: 120.9 bits;  conditional E-value: 1.6e-38
                                       EEECCEEEEEEESSS..SS-BSTT-EEEEESSS-EEEEEEEEEEECCSSTTSB-BSS-SSCCSTT-CEEEEEEECCE CS
                       GTP_EFTU_D3   3 kphtkfeAqvyilekerhtpitagYrpvlyirtadvtgkvveLlskldkktekvsekkpefvkpGdnvivevelikp 79 
                                       + +++f+A++ i+ +  ++++t gY+pv++++ta++++k++eL+skld++t+k++ek+p+f+k+Gd++iv+ ++ik+
  gi|385805637|ref|YP_005842035.1| 326 TIAKEFTARLFIIWH--PSAVTVGYTPVIHAHTASIAAKITELVSKLDPRTGKEAEKNPQFLKQGDTAIVKFQPIKQ 400
                                       5689***********..************************************************************ PP

                                       EEE--TTTHCCCCEEEEECTTCEEEEEEEEEE CS
                       GTP_EFTU_D3  80 ialekgseypqlGrFaiReggrTvaaGvvtei 111
                                       +++ek+se+p lGrFa+R++g+T+++Gv+t++
  gi|385805637|ref|YP_005842035.1| 401 MVVEKFSEFPALGRFAMRDMGKTIGIGVITDV 432
                                       ******************************98 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       3.9   7.8e+03      20      39 ..      15      32 ..      13      34 .. 0.74
   2 !   59.6   1.4   1.5e-19     3e-16       1      72 [.     252     317 ..     252     319 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.9
                                      EEEC.TCTTSEEEEEEEEEEE CS
                       GTP_EFTU_D2 20 rilg.ndtskkeivtrissle 39
                                      +++g +d +k+   t+++ ++
  gi|385805637|ref|YP_005842035.1| 15 VVIGhVDHGKS---TTVGHIL 32
                                      45566888899...9998875 PP

  == domain 2  score: 59.6 bits;  conditional E-value: 1.5e-19
                                       EEEEEEEEEESEEETTEEEEEECTCTTSEE.EEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCE CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskke.ivtrissletfhededeavaganaGvivaikgledaiivGdt 72 
                                       Gtv  grv+sG+lkkGd++++++      + iv++++s+e++h + + a++g+n+G++v+++   d i++Gd+
  gi|385805637|ref|YP_005842035.1| 252 GTVPVGRVESGVLKKGDRIVFMP------PaIVGEVRSIEMHHTQIEKAEPGDNIGFNVRGVTKTD-IKRGDV 317
                                       99*******************77......3488*********************************.*****9 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 !   20.4   1.5   1.7e-07   0.00035      21      84 ..     256     317 ..     242     318 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.7e-07
                                       EEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEEEEESS-TTTS--TT-E CS
                       GTP_EFTU_D4  21 vGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevaisiegkivGrqikegdi 84 
                                       vG +v +Gv+k g +++      vGe+++i+ ++ ++e+a+ G++++  ++g +   +ik gd+
  gi|385805637|ref|YP_005842035.1| 256 VG-RVESGVLKKGDRIVFMPPAIVGEVRSIEMHHTQIEKAEPGDNIGFNVRGVT-KTDIKRGDV 317
                                       88.9************************************************88.778999986 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   9.3e-07    0.0019       3      93 ..      15     134 ..      13     183 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 9.3e-07
                                       EEEESTTSSHHHHHHHHH..................T.............STEEESSSTTSSSSEEEEEEEETTEEE CS
                          MMR_HSR1   3 aivGrpNvGKStLinalt..................g.............ekaivsdkpgtTrdinegrvklkgkei 48 
                                       +++G+   GKSt +  ++                  +             ++ + +++ g+T+d  + ++++k+  +
  gi|385805637|ref|YP_005842035.1|  15 VVIGHVDHGKSTTVGHILyrlgyvdpkklaeleeeaKkkgkesfkyawllDNLKEERERGVTIDLSFMKFETKKYYF 91 
                                       78888888888888888866665555555555544404555555555554688999999************99999* PP

                                       EEEECGGCSSHHHHHHHHHHHHHHHHCTSEEEEEEETT....TTCSHHH CS
                          MMR_HSR1  49 elvDtpGliegaseekglgkaflaleeadlillvvdas....eeklkpl 93 
                                       +++D pG  +    +  +++ +    +ad+++lvv+a+    e++++p+
  gi|385805637|ref|YP_005842035.1|  92 TIIDAPG--H----RDFVKNMITGASQADAAILVVSARkgefEAGMSPE 134
                                       *******..3....23466666667779*******98855552223332 PP

>> SepF  Cell division protein SepF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.33   6.5e+02      34      58 ..     161     192 ..     150     193 .. 0.71
   2 ?   10.1   0.0   0.00037      0.74       4      72 .]     370     439 ..     367     439 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.33
                                       C.......HHHHHHHHHHHHHHHHCT-EEEEE CS
                              SepF  34 k.......eeakrivdflsgvvyaldGdiqkv 58 
                                               e +k+++d l++ +++l+ di k+
  gi|385805637|ref|YP_005842035.1| 161 AteppysqERYKQVIDTLQKFMKGLGFDISKI 192
                                       3335666699999***9999999999888776 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00037
                                       EE-SSGGGHHHHHHHHHTT-EEEEE-CCCTCHHHHHHHHHHHHHHHHCT..-EEEEECTTEEEEE-TT-EE CS
                              SepF   4 veprsfedaqeiadalkegkiVilnledldkeeakrivdflsgvvyald..GdiqkvgkkvflitPknvdi 72 
                                       + pr+ ++a++  + lk+g++ i++++ +++ + +++ +f +   +a++  G+   +g  +  ++P++v+i
  gi|385805637|ref|YP_005842035.1| 370 LDPRTGKEAEKNPQFLKQGDTAIVKFQPIKQMVVEKFSEFPALGRFAMRdmGKTIGIG-VITDVVPEQVQI 439
                                       5799999*********************************999999998334444444.477788888876 PP

>> Amelogenin  Amelogenin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00012      0.24      26      93 ..     185     253 ..     162     263 .. 0.81
   2 ?   -2.9   0.0       4.6   9.2e+03     107     127 ..     367     388 ..     334     404 .. 0.48

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                        Amelogenin  26 ikhqypsyGyepmgGwlhhavvpvlsqltfqqhpsvhsll.hhvvpklpalqpflvpqqplvpvpgqhs 93 
                                       ++ +  +  + p++Gw  ++++   + ++  + p+    l + ++p+ p  +p  +p q + ++ g  +
  gi|385805637|ref|YP_005842035.1| 185 LGFDISKIPFIPISGWNGDNLIERSPAMPWYNGPTLVEALdNIQIPPKPIDKPLRIPIQAVYAISGIGT 253
                                       55566677899***********************97665538899***************999988655 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.6
                        Amelogenin 107 qqplqpqave.hplkptqlsnp 127
                                          l+p++++  + +p+ l++ 
  gi|385805637|ref|YP_005842035.1| 367 VSKLDPRTGKeAEKNPQFLKQG 388
                                       2345555555344455555444 PP

>> TetR_C_2  MAATS-type transcriptional repressor, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00012      0.23      23      67 ..     114     158 ..     103     180 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00012
                          TetR_C_2  23 qralleilfhKCEFvgemsavleirkelllaeysrleevlqecie 67 
                                         a+l +   K EF  +ms++ + r++l la+   +e+++ +  +
  gi|385805637|ref|YP_005842035.1| 114 DAAILVVSARKGEFEAGMSPEGQTREHLILAKTMGIEQIIVAVNK 158
                                       5678899999***************************99977655 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.018        36       1      19 [.      14      32 ..      14      35 .. 0.86
   2 ?    4.8   0.0     0.013        27      54     137 ..      49     122 ..      37     158 .. 0.71
   3 ?   -3.1   0.0       3.6   7.1e+03      36      87 ..     364     385 ..     350     408 .. 0.42

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.018
                                      EEEEEBTTTTHHHHHHHHH CS
                         Dynamin_N  1 iavvGsqSsGKSSvlnaLl 19
                                      ++v+G++ +GKS+ + ++l
  gi|385805637|ref|YP_005842035.1| 14 LVVIGHVDHGKSTTVGHIL 32
                                      69***********887765 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.013
                                       SEEEET-EB--CHHHHHHHHHHHHHHHTSSSS--SS-EEEEEEETTS-SEEEEE---B-SSSGTTSHHHHHHHSTTE CS
                         Dynamin_N  54 elkekekkledfsevreeieketekiagankgiskkvillkilsllvkgltlvDlPGldsvnkrdqelvkeyikkad 130
                                       e k+k k+  ++  + +++++e+e+         ++ +++ +++ ++   t++D PG  +  k   ++++ + +  +
  gi|385805637|ref|YP_005842035.1|  49 EAKKKGKESFKYAWLLDNLKEERERGV-------TIDLSFMKFETKKYYFTIIDAPGHRDFVK---NMITGASQADA 115
                                       444445555555555666665555555.......2356667778888999*******988433...46777766666 PP

                                       EEEEEEE CS
                         Dynamin_N 131 iilavts 137
                                       +il+v++
  gi|385805637|ref|YP_005842035.1| 116 AILVVSA 122
                                       6666655 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 3.6
                                       EEEEECCT---CCS...SSEEEET-EB--CHHHHHHHHHHHHHHHTSSSS-- CS
                         Dynamin_N  36 lelqlgeeeeaseravkeelkekekkledfsevreeieketekiagankgis 87 
                                       +el  + +++                              t k a++n ++ 
  gi|385805637|ref|YP_005842035.1| 364 TELVSKLDPR------------------------------TGKEAEKNPQFL 385
                                       3333322222..............................222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 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:                        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: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 3198.94
//
Query:       gi|385805638|ref|YP_005842036.1|  [L=200]
Description: 30S ribosomal protein S7 [Fervidicoccus fontis Kam940]
Scores for complete 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-43  146.0   0.2    7.8e-43  145.7   0.2    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 !  145.7   0.2   4.3e-47   7.8e-43      18     149 .]      60     200 .]      50     200 .] 0.95

  Alignments for each domain:
  == domain 1  score: 145.7 bits;  conditional E-value: 4.3e-47
                                       TTSBHHHHHHHHHSB....TTBHHHHHHHHHHHHHHHHHHHSS-HHHHHHHHHHHCS-SEEEEEEBSSSSBEEEEEE CS
                      Ribosomal_S7  18 ynselveklinklmk....dGkkslAekivygaldiieektkkdplevleeAlenvkPrvevksrrvGGatyqvpve 90 
                                        + ++ve+lin+lmk     Gkk+lA++iv++a++ii  +tk++pl+vl++A+en++Pr+e++++++GG+ y+v+v+
  gi|385805638|ref|YP_005842036.1|  60 SRIPIVERLINNLMKhgrnMGKKHLAYNIVKNAFEIIYLQTKQNPLQVLVRAIENAAPREETTRIMYGGIIYHVAVD 136
                                       6779***********999889******************************************************** PP

                                       E-HHHHHHHHHHHHHHHH...STSSSS-HHHHHHHHHHHHHTT-..SHHHHHHHHHHHHHHHTG CS
                      Ribosomal_S7  91 vrpkRrqalAlrwiieaa...rkrkeksmaekLaeElidAaege..gaavkkreethrmAeanr 149
                                       v+p+Rr++lAlr+i+++a   +++  k+++e+La+E+i++a+++  ++++ k+ee++r+A ++r
  gi|385805638|ref|YP_005842036.1| 137 VAPQRRVDLALRNITDGArncAFNGPKPIEECLADEIIAVANNDpkSYSIAKKEEVERIALSSR 200
                                       ******************88778999*****************999**************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1250.28
//
Query:       gi|385805639|ref|YP_005842037.1|  [L=456]
Description: pyruvate carboxylase subunit B [Fervidicoccus fontis Kam940]
Scores for complete 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-41  141.6   0.0    4.3e-41  141.2   0.0    1.1  1  HMGL-like     HMGL-like
    3.1e-39  134.8   0.0    6.3e-39  133.8   0.0    1.6  1  PYC_OADA      Conserved carboxylase domain
  ------ inclusion threshold ------
      0.022   14.2   0.0      0.047   13.1   0.0    1.6  1  PEP_mutase    Phosphoenolpyruvate phosphomutase
      0.062   12.8   0.0       0.11   11.9   0.0    1.3  1  His_biosynth  Histidine biosynthesis protein


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 !  141.2   0.0   9.6e-45   4.3e-41       2     263 ..       2     266 ..       1     267 [. 0.94

  Alignments for each domain:
  == domain 1  score: 141.2 bits;  conditional E-value: 9.6e-45
                                       -EEEE-TTTHHHHTS.SS---HHHHHHHHHHHHHHT-SEE--........TSGGGT.THHHHHHHS---TT-B.... CS
                         HMGL-like   2 vkivdttLRDGeqal.kaalsveeklaiakaLdeagvdeiEv........gfpaaseddfevvraiakavkkar... 66 
                                       vki+dttLRD++q+l +++ls ++ + ia+  d+ag+ ++Ev         ++ + ed++ ++++i ++vkk++   
  gi|385805639|ref|YP_005842037.1|   2 VKIIDTTLRDAHQSLiATRLSQDDARDIAEIIDRAGFYSLEVwggatfdvDVRYLKEDPWSRLKKIREVVKKTKlqm 78 
                                       89************9999****************************9999999********************6666 PP

                                       .......--EE-SSHHHHHHHHH....TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-E..TTT CS
                         HMGL-like  67 ......ilalvrarekdikaavealkgagakrvhvfiatselhlkaklkkdreevakkaeeavkaarslgkd..vel 135
                                             +++++++ +++ ka++e++ ++g +++++f+a ++              +++++e++k a++ g+    +l
  gi|385805639|ref|YP_005842037.1|  79 llrgrnLVGYRKYPIDVSKAFIEKAYENGIDIFRIFDALND--------------IDNIAEVIKIAKRTGAIvqGAL 141
                                       666778***********************************..............***************9855789 PP

                                       -BTTTBS--HHHHHHHHHHHHHHT-SEEEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHH CS
                         HMGL-like 136 sledasrtdleflaevveaaeeaGatriniaDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaA 212
                                       s++ ++ +++++ ++++e   eaGa+ i i+D+ G+l+P+ a+ lis++k+++k  v++++H+H+  Gl va  la 
  gi|385805639|ref|YP_005842037.1| 142 SYTISPIHTVDYYVKLAESYLEAGADLITIKDMAGLLDPSTARSLISRIKKELK--VKVNIHTHDSCGLSVATYLAS 216
                                       ******************************************************..********************* PP

                                       HHTT--EEEEBTTS--SSBBB-BHHHHHHHHHHTT-B----HHHHHHHHHH CS
                         HMGL-like 213 veaGadrvdgtvnGlGeraGnaaleelvaalealgvdtgldlqklrsiaal 263
                                       +eaGad +d+++  l  ++  +a+ ++ +++  ++  ++l++++++++++ 
  gi|385805639|ref|YP_005842037.1| 217 IEAGADFIDTSIYPLAFGTAQPAIQTV-YNILLKKDRKKLKMSEIEKASRH 266
                                       ***************999999999875.66666677788999999998875 PP

>> PYC_OADA  Conserved carboxylase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.8   0.0   1.4e-42   6.3e-39       3     168 ..     292     442 ..     290     456 .] 0.86

  Alignments for each domain:
  == domain 1  score: 133.8 bits;  conditional E-value: 1.4e-42
                                       CCT--CCHHHHHHHHHHHTT-GGGHHHHHHHHHHHHHHTT----STTHHHHHHHHHHHHHHH........TS.TTSS CS
                          PYC_OADA   3 kheiPGGqltnlkeqakeqglldkfeevlkeyaevnkllGdivkVTPsSkvvgdlAvfnvlnklteedvleegrykd 79 
                                        h+iPGG+l+n+  q++e+ +ld++eevl e+++++k+lG +++VTP S++vg +Av+nv +        +e ry  
  gi|385805639|ref|YP_005842037.1| 292 IHQIPGGMLSNMIAQLNELQALDRLEEVLMEIPKIRKELGWPPLVTPMSQIVGAQAVLNVIS--------GE-RYSI 359
                                       7*************************************************************........86.**** PP

                                       --HHHHHHHTTSS---SS---HHHHHHHHT.-----S-GGGG---.-HHHHHHHTTTTSSSHHHHHHHHHSHHHHHH CS
                          PYC_OADA  80 ipdsvvdllkGelGkppggfpeelvkkvlkgeepitsrpadslepedleklrkeleekakteedvlsyalypkvaek 156
                                       + +++vd++kG +Gkpp+++++++ +++l g+    + p++sl+  + ++  k+l +  + eedv++ +l+pk ae+
  gi|385805639|ref|YP_005842037.1| 360 VVKELVDYVKGLYGKPPAPIDKNVAEIILAGDG---GLPEKSLSLIECREYMKKLLN-DPREEDVITFCLFPKEAEA 432
                                       *****************************8855...579999999995555555444.3699*************** PP

                                       HHHHHHHHHHHH CS
                          PYC_OADA 157 flkfreeygdvs 168
                                       f+k  e++ +vs
  gi|385805639|ref|YP_005842037.1| 433 FFK--EKFVSVS 442
                                       **9..4444443 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.1e-05     0.047     121     207 ..     122     211 ..      63     243 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.1e-05
                        PEP_mutase 121 efaekiaaaraaaeeagfvinARtdalllsagagleeaieRaraYaeAGAdgvfvpgl.......qkdaeiaelvaa 190
                                       +    ia++ + a+ +g ++       + s+  +++  ++ a+ Y+eAGAd +++  +       + ++ i ++ ++
  gi|385805639|ref|YP_005842037.1| 122 N----IAEVIKIAKRTGAIVQGALSYTI-SPIHTVDYYVKLAESYLEAGADLITIKDMaglldpsTARSLISRIKKE 193
                                       3....33333333555555555554445.588889999999*************98776775542222235555555 PP

                        PEP_mutase 191 vdvplnvvplkgt.lsva 207
                                       ++v +n+  ++++ lsva
  gi|385805639|ref|YP_005842037.1| 194 LKVKVNIHTHDSCgLSVA 211
                                       557777777533246665 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.5e-05      0.11      29      78 ..     152     200 ..     125     202 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.5e-05
                                       TSHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEEE CS
                      His_biosynth  29 gdpvelakryeeegadelhvvDldaakegreanldlveeiaeevfipvqv 78 
                                       +  v+la++y e+gad +++ D+ +     ++  +l+++i +e++++v +
  gi|385805639|ref|YP_005842037.1| 152 DYYVKLAESYLEAGADLITIKDMAGLL-DPSTARSLISRIKKELKVKVNI 200
                                       56799******************9997.677889*********9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); 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: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.51
# Mc/sec: 2701.86
//
Query:       gi|385805640|ref|YP_005842038.1|  [L=150]
Description: hypothetical protein FFONT_0596 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.2e-05   22.9   0.1    6.1e-05   22.7   0.1    1.3  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 !   22.7   0.1   3.4e-09   6.1e-05      59     122 ..      81     146 ..      29     150 .] 0.87

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 3.4e-09
                                       HHHHHTTEEEEEEEEEEEETTE..EEEEEEEEET---EEEEE-HHHHHHHHHHHT--EEEEHHHHH CS
                       DNase-RNase  59 sllealgakvervvItdledgt..fyAelvlrkeeeeleidaRpSDaiaLAlrtgapIyveeevle 122
                                       ++l+ ++ ++e+vvI++++  t  + A++++rk+++ l     pS ai LA+ +g ++yv+e++l+
  gi|385805640|ref|YP_005842038.1|  81 DILNLIKDDLEKVVIDEYDPTTmlYTAKVYFRKGKTMLVRRFIPSHAIFLAMIAGKDVYVSERILN 146
                                       678888999********9975444********96433666778*********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); 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: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1064.72
//
Query:       gi|385805641|ref|YP_005842039.1|  [L=147]
Description: 30S ribosomal protein S12 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-48  162.8   0.9    2.3e-48  162.5   0.9    1.1  1  Ribosom_S12_S23  Ribosomal protein S12/S23


Domain annotation for each model (and alignments):
>> Ribosom_S12_S23  Ribosomal protein S12/S23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.5   0.9   1.3e-52   2.3e-48       1     113 [.      32     145 ..      32     146 .. 0.98

  Alignments for each domain:
  == domain 1  score: 162.5 bits;  conditional E-value: 1.3e-52
                                       --------S-TSSTTSSEEEEEEEEEEEE---TT--S-EEEEEEEET.TSEEEEEEE-SSS..----TT-EEEEEE- CS
                   Ribosom_S12_S23   1 rkelrkktksdalegapqkrGvvlekvtveakkPnsAlRkvvrvrLikngkevtafipgegalnfldEhdevlvrGi 77 
                                       r+ l++k+k+d+legap ++G+vlekv+ve+++PnsA+Rk+vrv+L kngk vtaf+p++g lnf+dEhdev+++Gi
  gi|385805641|ref|YP_005842039.1|  32 RRMLNLKKKADPLEGAPRASGIVLEKVGVESRQPNSAVRKCVRVQLVKNGKVVTAFVPSDGGLNFIDEHDEVVIEGI 108
                                       678899*********************************************************************** PP

                                       -......BTTSTTEEEEBETS---TSSSTTTTT---- CS
                   Ribosom_S12_S23  78 rrk.gkavkDlpGvrykvvkvagvslkalskykkekp 113
                                       +++ g++++D+pGvrykvv v+gvsl al k+kk+kp
  gi|385805641|ref|YP_005842039.1| 109 GGPkGRSMGDIPGVRYKVVMVNGVSLDALLKGKKQKP 145
                                       *999*******************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 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:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 974.43
//
Query:       gi|385805642|ref|YP_005842040.1|  [L=143]
Description: transcription elongation factor NusA-like protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-22   78.0   6.8    9.8e-16   57.4   3.4    2.1  2  KH_2      KH domain
    4.1e-13   49.2   4.9    2.6e-12   46.7   1.9    2.2  2  KH_5      NusA-like KH domain
    7.6e-09   35.3   1.0    4.8e-05   23.1   0.0    2.1  2  KH_4      KH domain
    9.8e-06   25.3   3.4    0.00055   19.7   1.1    2.6  2  KH_1      KH domain


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 !   57.4   3.4   2.2e-19   9.8e-16       4      74 ..      14      96 ..      11      98 .. 0.90
   2 !   23.8   0.3   6.6e-09   2.9e-05      11      56 ..      86     133 ..      77     142 .. 0.76

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 2.2e-19
                                      HHHHHHTECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTC............EEEEE CS
                              KH_2  4 eslaveikkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkk............Vklni 70
                                      ++l++ +++ +v++++I++++n +i+v+++++ g +IG+gGsnikk++k l+k+ie++e++             ++++ 
  gi|385805642|ref|YP_005842040.1| 14 IALFQDVTGTTVKDCIIDNENNMIIFVVKKGEAGAAIGRGGSNIKKLRKVLGKEIEIVEDGTtleelaknavapARVKA 92
                                      7899********************************************************9988888888888877777 PP

                                      EEET CS
                              KH_2 71 vkVk 74
                                      vkV 
  gi|385805642|ref|YP_005842040.1| 93 VKVV 96
                                      7775 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 6.6e-09
                                       ECETEEEEEEECCS..CEEEEEEEESCHHHHHTGGGHHHHHHHHHHHH CS
                              KH_2  11 kkagvskveIerta..nrviiviresqpgivIGkgGsnikkigkelrk 56 
                                       + a v+ v++ +t+  + v i++  s +g++IGk+G+n+ + +  l++
  gi|385805642|ref|YP_005842040.1|  86 APARVKAVKVVETPskKTVYITVEPSDKGVAIGKNGKNVTRAKLLLKR 133
                                       4555677777664444788899******************99988876 PP

>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   1.9   5.7e-16   2.6e-12       2      69 .]      34      95 ..      33      95 .. 0.96
   2 ?    3.4   0.1     0.019        83       7      31 ..     106     125 ..     101     132 .. 0.82

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 5.7e-16
                              KH_5  2 GertkvaVkshnpnvdpvGaivgkkGsrikavsseLkgekidvvewseDlaefianalsPaevlsVki 69
                                      +++++++Vk+++     +Ga++g++Gs+ik++ + L g+ i++ve    l+e+++na +Pa+v+ Vk+
  gi|385805642|ref|YP_005842040.1| 34 NNMIIFVVKKGE-----AGAAIGRGGSNIKKLRKVL-GKEIEIVEDGTTLEELAKNAVAPARVKAVKV 95
                                      58999*******.....*******************.*****************************86 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.019
                              KH_5   7 vaVkshnpnvdpvGaivgkkGsrik 31 
                                       + V+ ++      G ++gk+G+++ 
  gi|385805642|ref|YP_005842040.1| 106 ITVEPSD-----KGVAIGKNGKNVT 125
                                       7788888.....9*********986 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.3   7.2e-05      0.32      22      58 ..      28      64 ..      14      66 .. 0.75
   2 !   23.1   0.0   1.1e-08   4.8e-05       4      52 ..      77     125 ..      75     138 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 7.2e-05
                              KH_4 22 eeeeeeeveielnvegedlGrvIGkrGrtldAlqylv 58
                                      + +++e++ i   v++ + G  IG+ G +++ l+ ++
  gi|385805642|ref|YP_005842040.1| 28 CIIDNENNMIIFVVKKGEAGAAIGRGGSNIKKLRKVL 64
                                      335556666666779999*************999775 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 1.1e-08
                              KH_4   4 vedilkalvddpeevevtee.eeeeeveielnvegedlGrvIGkrGrtld 52 
                                       +e+++k+ v +p+ v+     e+ +++++ ++ve++d+G+ IGk+G++++
  gi|385805642|ref|YP_005842040.1|  77 LEELAKNAV-APARVKAVKVvETPSKKTVYITVEPSDKGVAIGKNGKNVT 125
                                       789999999.677776544448899**********************986 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   1.1   1.2e-07   0.00055       4      38 ..      39      72 ..      35      84 .. 0.84
   2 !    5.3   0.0    0.0038        17       3      23 ..     105     125 ..     103     127 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.2e-07
                                      EEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEESS CS
                              KH_1  4 ilvPsslvgriIGkgGsnIkeIreetgakIkvpks 38
                                      + v++  +g+ IG+gGsnIk++r+  g  I ++ +
  gi|385805642|ref|YP_005842040.1| 39 FVVKKGEAGAAIGRGGSNIKKLRKVLGKEIEIV-E 72
                                      5788899*****************779999987.3 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0038
                                       EEEEGGGHHHHHHTGGGHHHH CS
                              KH_1   3 rilvPsslvgriIGkgGsnIk 23 
                                        i+v  s  g  IGk+G+n+ 
  gi|385805642|ref|YP_005842040.1| 105 YITVEPSDKGVAIGKNGKNVT 125
                                       577888889999******985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 858.49
//
Query:       gi|385805643|ref|YP_005842041.1|  [L=91]
Description: ribosomal protein L7Ae/L30e/S12e/Gadd45 [Fervidicoccus fontis Kam940]
Scores for complete 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   75.9   0.0    1.6e-21   75.8   0.0    1.0  1  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil


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 !   75.8   0.0     9e-26   1.6e-21      12      94 ..       4      86 ..       1      87 [. 0.97

  Alignments for each domain:
  == domain 1  score: 75.8 bits;  conditional E-value: 9e-26
                                      HHTEEEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHH..HTTEEEEEESCHHHHHHHTTSSSECSEEEEEES CS
                    Ribosomal_L7Ae 12 kagklvlGlkevtkalergeaklvilAedvepeekkkllealck..ekevpyvkvkskkeLGelvgkkrpvsalaikde 88
                                      ++gkl +G + ++k+l++g+ k+v++A++++p  kk+ +e+++k  ++++++++++s  eLG+l+gk++p +al+i+d+
  gi|385805643|ref|YP_005842041.1|  4 RTGKLEIGSQSTIKTLKHGKSKMVVIASNADPSVKKD-IEYYAKlsQTPIYVFQGTS-VELGTLLGKPFPIQALSIIDV 80
                                      799**********************************.*******************.********************* PP

                                      TTTHHH CS
                    Ribosomal_L7Ae 89 gdskdl 94
                                      gdsk+l
  gi|385805643|ref|YP_005842041.1| 81 GDSKIL 86
                                      ****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); 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: 00:00:00.46
# Mc/sec: 594.50
//
Query:       gi|385805644|ref|YP_005842042.1|  [L=409]
Description: DNA-directed RNA polymerase subunit A'' [Fervidicoccus fontis Kam940]
Scores for complete 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-57  194.2   3.2    5.2e-57  193.3   3.2    1.4  1  RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
     0.0014   16.4   0.1      0.002   15.9   0.1    1.2  1  ACR_tran        AcrB/AcrD/AcrF family
  ------ inclusion threshold ------
      0.021   14.8   0.8      0.078   13.0   0.1    2.3  2  RNA_pol_Rpb1_7  RNA polymerase Rpb1, domain 7


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 !  193.3   3.2   8.7e-61   5.2e-57      65     265 ..      55     337 ..      12     339 .. 0.91

  Alignments for each domain:
  == domain 1  score: 193.3 bits;  conditional E-value: 8.7e-61
                                       TSB--TT-BHHHHHHHHHHHHHHCCCSSTTSSTCSSTSSSSSSHHHHHHHHTT-SS-SS-EEEEEB-SSSSSCHHHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_5  65 dglvepGeavGiiaaQSiGePgTQltlnTFHfaGvasknvtlGvprlkeilnvskniksksltvllvdeeakeleka 141
                                       ++lvepGe +G++ aQSiGePgTQ+tl+TFH+aGv + nvtlG+prl ei+++ k+ ++++++v+l +e++ ++eka
  gi|385805644|ref|YP_005842042.1|  55 NSLVEPGEPIGTVTAQSIGEPGTQMTLRTFHYAGVRELNVTLGLPRLIEIVDARKVPSTPMMEVYLDEEHKYDREKA 131
                                       349************************************************************************** PP

                                       HHHHHHHSE.................................................................... CS
                                       xxxxxxxxx.................................................................... RF
                    RNA_pol_Rpb1_5 142 kkvkkaiek.................................................................... 150
                                       k+v+++ie                                                                     
  gi|385805644|ref|YP_005842042.1| 132 KEVARRIEFtkienvanvveadlfsnsirveldpamledkgltveevyevikksnvgkaeitgentiaiylkessdl 208
                                       ***99999899999*************************************************************** PP

                                       ................CBTTEEEEEEEEEEEEEEETEEEEEEECS--HHHHTTSTTTBETTTEEESSHHHHHHHHCH CS
                                       ................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_5 151 ................gikkikrilvkeaekgkeeekelvletegvnlsevlkveevvdageilsndiaeileilgi 211
                                                       gi +ikr+++++ + ++   +e+v+ t+g nl++vlkv++ vd +++ +n++ e++ +lgi
  gi|385805644|ref|YP_005842042.1| 209 syiskkrekvlnlkikGIAGIKRAIIQSRRGEDGR-EEYVIVTDGSNLEQVLKVKG-VDPTRTRTNSVYETMMVLGI 283
                                       *************************9977766666.89******************.******************** PP

                                       HHHHHHHHHHHHHHHHHTTS---HHHHHHHHHHHTTTSS---SSTTCHCCSSSH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_5 212 eaarkallkeiqevykvqgvsvndrHlelivdqmtkkgeivavnrsGinkaels 265
                                       eaark++++ei +v+++qg++v+ rH+ l++d+mt++g + +++r+G+  +++s
  gi|385805644|ref|YP_005842042.1| 284 EAARKVIINEIMNVLREQGLDVDVRHVYLVADIMTQTGVVRQIGRHGVSGEKES 337
                                       ***********************************************9988776 PP

>> ACR_tran  AcrB/AcrD/AcrF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   3.3e-07     0.002     129     214 ..     108     189 ..      93     218 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.3e-07
                                       EEEECCECEEEEEEESSSSS-HHHHHHHHHHHTHHHHHTSTTEEEEEESS.-SEEEEEEE-HHHHHCTT--HHHHHH CS
                          ACR_tran 129 iktssseilvlavtskdgsltktelrdlaetnikdqLsrveGVgdvqliGgsekavriwldpqklaklgltltdvvs 205
                                        k +s++++++ ++ + ++++ ++ +++a +       ++e V++v     +++++r+ ldp+ l+  glt+++v +
  gi|385805644|ref|YP_005842042.1| 108 RKVPSTPMMEVYLDEE-HKYDREKAKEVARRIE---FTKIENVANVVEADLFSNSIRVELDPAMLEDKGLTVEEVYE 180
                                       5667778888888887.7788877777776654...45555666666666667************************ PP

                                       HHHHHSSB- CS
                          ACR_tran 206 alkeqnvnv 214
                                        +k+ nv  
  gi|385805644|ref|YP_005842042.1| 181 VIKKSNVGK 189
                                       ****99865 PP

>> RNA_pol_Rpb1_7  RNA polymerase Rpb1, domain 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   1.3e-05     0.078      46      77 ..     154     185 ..     115     209 .. 0.84
   2 ?   -1.0   0.1      0.28   1.7e+03      81     102 ..     244     265 ..     210     295 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.3e-05
                                       --SBEEEEEE-SHHHHHTT--HHHHHHHHHHH CS
                    RNA_pol_Rpb1_7  46 lspWlLRieLdrkkmtdkkltmeevaekikee 77 
                                       l +  +R+eLd +++ dk lt+eev e ik++
  gi|385805644|ref|YP_005842042.1| 154 LFSNSIRVELDPAMLEDKGLTVEEVYEVIKKS 185
                                       555679***********************865 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.28
                                       TEEEEE--TTSSSEEEEEEE-- CS
                    RNA_pol_Rpb1_7  81 dlkvifsddnaeklvlririvk 102
                                       +  vi++d ++ ++vl+++ v+
  gi|385805644|ref|YP_005842042.1| 244 EEYVIVTDGSNLEQVLKVKGVD 265
                                       3468899998889999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       952  (0.0530983); expected 358.6 (0.02)
Passed bias filter:                      609  (0.0339673); 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: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 2633.01
//
Query:       gi|385805645|ref|YP_005842043.1|  [L=882]
Description: DNA-directed RNA polymerase subunit alpha [Fervidicoccus fontis Kam940]
Scores for complete 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-101  338.5   0.0   6.5e-101  337.8   0.0    1.3  1  RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
    2.5e-73  245.8   0.0    4.4e-73  245.0   0.0    1.4  1  RNA_pol_Rpb1_2  RNA polymerase Rpb1, domain 2
    8.5e-36  123.3   0.0    1.4e-35  122.5   0.0    1.4  1  RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3
    8.2e-32  109.4   0.2    6.5e-31  106.5   0.0    2.2  2  RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4
    2.5e-22   79.6   0.0      5e-22   78.6   0.0    1.5  1  RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
     0.0017   18.2   1.7       0.51   10.2   0.1    2.7  2  zf-FPG_IleRS    Zinc finger found in FPG and IleRS
     0.0082   16.2   0.9       0.48   10.6   0.1    2.7  2  Zn-ribbon_8     Zinc ribbon domain
  ------ inclusion threshold ------
      0.028   13.8   0.3      0.048   13.0   0.3    1.3  1  PhoU_div        Protein of unknown function DUF47
      0.054   13.5   1.4          2    8.5   0.2    2.3  2  DZR             Double zinc ribbon
       0.28   11.5   1.1         16    5.9   0.0    2.5  2  zf-Di19         Drought induced 19 protein (Di19), zinc-bindi
        0.6    9.6   9.7        2.2    7.8   0.1    3.4  3  zf-ribbon_3     zinc-ribbon domain
       0.85    9.6   2.4         11    6.1   0.1    2.6  2  Ogr_Delta       Ogr/Delta-like zinc finger
        1.5    8.8   8.5        1.5    8.9   0.1    3.2  3  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
        1.9    9.2   4.4         10    6.9   0.1    2.7  2  zf-ISL3         zinc-finger of transposase IS204/IS1001/IS109
        2.5    8.0   9.8        9.8    6.0   0.2    3.3  3  zinc_ribbon_2   zinc-ribbon domain
          4    7.9   5.9         30    5.1   0.1    3.7  3  zf-IS66         zinc-finger binding domain of transposase IS6


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 !  337.8   0.0  5.8e-104  6.5e-101       1     312 []       5     315 ..       5     315 .. 0.93

  Alignments for each domain:
  == domain 1  score: 337.8 bits;  conditional E-value: 5.8e-104
                                       BE---EEEEEE--HHHHHHH-SBB--STTSTCSTSSSSBBSSSSSSSSS-SSSSSTSTTTSSTTTT-----EEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1   1 ekkikeiqfgiaspeeirkwSvvevtkaetieekslkPeegGllDerlgtidkdleCetCgkkkkeCeghfGhieLa 77 
                                       +kkik i+++++sp+eir++S+v++ +aet++++   P +gG++D+rlg+i+   +C +Cg+++++C+ghfGhieLa
  gi|385805645|ref|YP_005842043.1|   5 QKKIKGIKLSVLSPDEIRRMSKVQIITAETYDDDG-LPIQGGVMDPRLGVIEPGQKCPVCGNTMQSCPGHFGHIELA 80 
                                       599******************************95.9**************************************** PP

                                       CEEE-HHHHHHHHHHCTTCETTTTEBSS-TTSH....HHHHHHCSSSCC.....CCHHHHHHHHCCS-BE-SSSSB- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1  78 kPvfhigffklilkilecvckecskllldeekkkllsklkkrekleelk.....krlkaieelckkinlcekCgavq 149
                                       kPv+hig++k+i+ +l+ +c +c+++ll ee+ k++ +l   +++e++      + +++i+++ +k ++c +Cga+q
  gi|385805645|ref|YP_005842043.1|  81 KPVIHIGYVKEIYDLLRGTCWKCGRILLPEEEIKQYLDLM--RRVEKYMpfllpRLYEHIKQKASKTTVCPHCGAAQ 155
                                       ******************************9885555443..33344445678899******************999 PP

                                       EEEEEETTEEEEEESSSSTSCEEEE-HHHHHHHHHCSTHHHHHHTTSBTTTB-GGGCCECCEEE--GGGS-BEESSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1 150 pkleeegeklkaalkkskeeekeklsaekvkkllkriededvevlgfkssgsrPewliltvlPVpPpeiRPsvqldg 226
                                        k+  + e+ ++ l+++k  +++kl ++++++ l++ +d+dv++ g++++ srPew+iltvlPVpP+++RPs++l++
  gi|385805645|ref|YP_005842043.1| 156 RKI--KLERPTTFLEEEKG-SSRKLAPDEIRNRLSNTPDDDVRLFGINPEDSRPEWFILTVLPVPPVQVRPSIMLET 229
                                       887..45555566666655.88******************************************************* PP

                                       SSEEBECCCCHHHHHHHHHHHHHHHHHSSSSSTCHHHHHHHHHHHHHHCC-TTSSSSSEEBSTTSSS--THHHHHTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1 227 grrsedDlteklrdiikrNnrLkkaeeegapeliieeekelLQehvatlfdneisglkpatqkskrplkslsqrLkG 303
                                       g r+edDlt+kl+di+++N+rLk+ +e+ ap ++i++ +elLQ+hv+t+fdne++g++pa+++ +r lk+l qrLkG
  gi|385805645|ref|YP_005842043.1| 230 GIRAEDDLTHKLVDIVRTNQRLKESMEAAAPPIVIDDIWELLQYHVTTYFDNEVPGIPPAKHRTGRALKTLAQRLKG 306
                                       ***************************************************************************** PP

                                       SSSCCCCCT CS
                                       xxxxxxxxx RF
                    RNA_pol_Rpb1_1 304 KeGrfRgnL 312
                                       KeGrfRg L
  gi|385805645|ref|YP_005842043.1| 307 KEGRFRGYL 315
                                       ******965 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 !  245.0   0.0   3.9e-76   4.4e-73       1     166 []     317     484 ..     317     484 .. 0.98

  Alignments for each domain:
  == domain 1  score: 245.0 bits;  conditional E-value: 3.9e-76
                                       SEEESSEEEEEEEEESSS-TTEEEEEHHHHTTSEEEEE-STTTHHHHHHHHHHTTTSSSSEEEEESTTSSEEETTTT CS
                    RNA_pol_Rpb1_2   1 GkrvdysaRsvispdpnlkldevgvPisvakkltvpeivtelnikklrklvengpevyPgasyvkredgsekklkak 77 
                                       Gkrvd+s+R+vispdpn+ ++evgvP   ak+ltvp +vt++n +++r++v ngp ++Pga+y++r dg++ +l++ 
  gi|385805645|ref|YP_005842043.1| 317 GKRVDFSSRTVISPDPNIGINEVGVPEDAAKILTVPVKVTQWNLEEMRSYVLNGPYKWPGANYIIRPDGKRVDLRYF 393
                                       9**************************************************************************98 PP

                                       -SC..HHCCTTTTSEEEEE--TTSEEEEE-SSTTSGGGEEEEEEEEESSSSEEEEGGGHCCCT--SSS-EEEEE--S CS
                    RNA_pol_Rpb1_2  78 krk..lakelekgdiverhvkdgdvvllNRqPsLhklsimahrvkvlekktlrlnlsvttayNaDFDGDemnlhlpq 152
                                       k++  la++l+ g+i+erh++dgd+vl+NRqPsLh++simah+vkvl+++t+rlnl+v+ +yNaDFDGDemnlh+pq
  gi|385805645|ref|YP_005842043.1| 394 KDRkaLASSLTPGYIIERHLIDGDIVLFNRQPSLHRMSIMAHQVKVLPGRTFRLNLLVCPPYNADFDGDEMNLHVPQ 470
                                       8743599********************************************************************** PP

                                       SHHHHHHHHHCSBT CS
                    RNA_pol_Rpb1_2 153 seearaEaeelllv 166
                                       +eearaEa+el+lv
  gi|385805645|ref|YP_005842043.1| 471 TEEARAEAKELMLV 484
                                       ************86 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 !  122.5   0.0   1.3e-38   1.4e-35       1     157 []     487     653 ..     487     653 .. 0.94

  Alignments for each domain:
  == domain 1  score: 122.5 bits;  conditional E-value: 1.3e-38
                                       CSEETTTTEESSS--THHHHHHHHHSSTTEEEEHHHHHHHHHHSSSCCSSSSSSSSSBESSSEBEEHHHHHHCCCHC CS
                    RNA_pol_Rpb1_3   1 nilspqsgkPvigivQDsllGvyllTkedvfidreeaqqllykgvgsdsktvtlrpailkpkelwtgkqtfsrilpn 77 
                                       +ilsp+ g P+ig  QD ++G yllT + +++++e+++++l+    +   +++++pai+ pke wtgkq++s++lp+
  gi|385805645|ref|YP_005842043.1| 487 HILSPRYGGPIIGGLQDYISGGYLLTSKATLLEKEDVIEVLSVTGYK---EELPEPAIYSPKEFWTGKQLVSLFLPK 560
                                       7*******************************************776...899************************ PP

                                       CCCEEEE...SSSS............STSEEECSSEEEES--SHHHHSSSSTTSHHHHHHHHCHHHHHHHHHHHHHH CS
                    RNA_pol_Rpb1_3  78 einyerk...neek............dgkvlikngelikGvidkkvvgkksqgslihvlakeygiketvrfldslqr 139
                                       ++ ++ k   n               d++++ik+g   +Gvidkk +g+++ +s  h ++keyg++ ++ + d + +
  gi|385805645|ref|YP_005842043.1| 561 DFTLKTKasiN--AgklkcededclnDSYIVIKKGKMHTGVIDKKSIGAQQPESFYHWITKEYGSDYARYISDVMFK 635
                                       99999986552..2446677799****************************************************** PP

                                       HHHHHHHHHCEB-TGGGG CS
                    RNA_pol_Rpb1_3 140 lgfkyllqsgftigigDt 157
                                       ++++y+ ++gft++++D+
  gi|385805645|ref|YP_005842043.1| 636 MFIRYIEKHGFTMSLDDV 653
                                       *****************6 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 ?    1.7   0.1      0.21   2.4e+02      28      58 ..     654     684 ..     647     685 .. 0.75
   2 !  106.5   0.0   5.8e-34   6.5e-31       6     108 .]     683     784 ..     678     784 .. 0.96

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.21
                                       HHHHHHHHHHHHHHHHCSTTTSHHHHHHHCT CS
                    RNA_pol_Rpb1_4  28 kilnkardkagkiaskslaasNsiliMvksG 58 
                                       +i+++ar++++ki +k  ++ N ++ M++ G
  gi|385805645|ref|YP_005842043.1| 654 EISEEAREEIRKILKKAEDDVNELIRMMEEG 684
                                       4677888888888888777568888888755 PP

  == domain 2  score: 106.5 bits;  conditional E-value: 5.8e-34
                                       THTCCHHHTTHCHHHHHHHHHHHHHHHHHHHHHHHHHHCST.TTSHHHHHHHCTSSS-HHHHHHHHTB-EEEEBTTB CS
                    RNA_pol_Rpb1_4   6 rygkledlpgksleelfeakinkilnkardkagkiasksla.asNsiliMvksGaKGsiinisqiagclGqqnvegk 81 
                                       + g+le+lpg++ ee++e+ki++ l+kard+ag+ a ++l+ + N+ +iM+++Ga+G+i+n++q++++lGqq+++g+
  gi|385805645|ref|YP_005842043.1| 683 E-GRLEPLPGRTIEETLETKIMERLSKARDDAGEYAANNLDiF-NNAFIMARTGARGNILNLTQMSATLGQQSIRGE 757
                                       4.89*************************************55.********************************* PP

                                       SS--SSTSCSSTTSSSSESSTTTSSEE CS
                    RNA_pol_Rpb1_4  82 ripkgfsgrtlphfkkidespesrGFv 108
                                       ri++g+++r lphfk++d+sp srGFv
  gi|385805645|ref|YP_005842043.1| 758 RINRGYRNRPLPHFKENDKSPASRGFV 784
                                       **************************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 !   78.6   0.0   4.5e-25     5e-22       1      66 [.     791     856 ..     791     875 .. 0.93

  Alignments for each domain:
  == domain 1  score: 78.6 bits;  conditional E-value: 4.5e-25
                                       B--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTEEEETTSEEEETTS-EEESSGGGTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_5   1 GLkvkefffhtmggReGLiDtAvkTaesGYlqRrlvkaledvvvkyddtvrnsggeivqflygedg 66 
                                       GL++ e f+h+ ggReGL+DtAv+T++sGY+qRrl++al dv ++yd++ r  +g++vqf+yg d+
  gi|385805645|ref|YP_005842043.1| 791 GLNPVELFYHAAGGREGLVDTAVRTSQSGYMQRRLINALLDVRIEYDGSARLPDGTVVQFKYGYDQ 856
                                       9**************************************************************997 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 !   10.2   0.1   0.00046      0.51       1      11 [.      57      67 ..      57      69 .. 0.88
   2 !    6.7   0.1    0.0061       6.8      12      27 ..     136     151 ..     133     152 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00046
                                      TSB-TTT--BB CS
                      zf-FPG_IleRS  1 GepCpRCwryi 11
                                      G++Cp+C+++ 
  gi|385805645|ref|YP_005842043.1| 57 GQKCPVCGNTM 67
                                      9********86 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0061
                                       EEEECTTEEEEE-TTT CS
                      zf-FPG_IleRS  12 ervgqagrstyfCprC 27 
                                       e+++q    t++Cp+C
  gi|385805645|ref|YP_005842043.1| 136 EHIKQKASKTTVCPHC 151
                                       78999999******** PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1     0.078        88      25      36 ..      56      67 ..      45      69 .. 0.78
   2 !   10.6   0.1   0.00042      0.48      23      38 ..     141     157 ..     134     158 .. 0.65

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.078
                       Zn-ribbon_8 25 pltaCPeCgsev 36
                                      p ++CP Cg ++
  gi|385805645|ref|YP_005842043.1| 56 PGQKCPVCGNTM 67
                                      5677****9865 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00042
                       Zn-ribbon_8  23 daplta.CPeCgsevrr 38 
                                       +a++t+ CP+Cg++ r+
  gi|385805645|ref|YP_005842043.1| 141 KASKTTvCPHCGAAQRK 157
                                       3446777****995554 PP

>> PhoU_div  Protein of unknown function DUF47
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.3   4.3e-05     0.048      93     136 ..     640     683 ..     635     713 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.3e-05
                          PhoU_div  93 vlediamlvtlrkvefpeelkdeflallkktveaiealaeviee 136
                                       ++e+ +++++l +ve+ ee ++e++++lkk  + +++l +++ee
  gi|385805645|ref|YP_005842043.1| 640 YIEKHGFTMSLDDVEISEEAREEIRKILKKAEDDVNELIRMMEE 683
                                       7999*******************************999999985 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.2    0.0018         2      14      41 ..      59     110 ..      54     113 .. 0.90
   2 ?    3.6   0.1     0.059        66      28      36 ..     145     153 ..     135     161 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0018
                               DZR  14 fCseCgtklkavaa........................edrCpsCgekvdpe 41 
                                        C+ Cg+++++ +                           +C++Cg+ + pe
  gi|385805645|ref|YP_005842043.1|  59 KCPVCGNTMQSCPGhfghielakpvihigyvkeiydllRGTCWKCGRILLPE 110
                                       6********988889*******************************986665 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.059
                               DZR  28 edrCpsCge 36 
                                        ++Cp+Cg+
  gi|385805645|ref|YP_005842043.1| 145 TTVCPHCGA 153
                                       344444444 PP

>> zf-Di19  Drought induced 19 protein (Di19), zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.3      0.07        78      33      49 ..      59      77 ..      56      81 .. 0.67
   2 ?    5.9   0.0     0.014        16      16      39 ..     133     153 ..     126     163 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.07
                           zf-Di19 33 vCPvCaekvtk..dlvaHl 49
                                       CPvC ++++     ++H+
  gi|385805645|ref|YP_005842043.1| 59 KCPVCGNTMQScpGHFGHI 77
                                      6999998877434555555 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.014
                           zf-Di19  16 eLveHvedeHrveskevvCPvCae 39 
                                       +L+eH+++   ++sk +vCP C +
  gi|385805645|ref|YP_005842043.1| 133 RLYEHIKQ---KASKTTVCPHCGA 153
                                       68888887...7889999999964 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   2.6      0.17   1.9e+02       3      10 ..      58      65 ..      56      71 .. 0.81
   2 ?    2.9   0.0     0.069        77       4      13 ..      99     109 ..      99     114 .. 0.72
   3 ?    7.8   0.1     0.002       2.2      17      24 ..     146     153 ..     142     156 .. 0.66

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.17
                       zf-ribbon_3  3 vrCPnCGa 10
                                      ++CP CG+
  gi|385805645|ref|YP_005842043.1| 58 QKCPVCGN 65
                                      68999998 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.069
                       zf-ribbon_3   4 rCPnCGa.pls 13 
                                       +C++CG  +l 
  gi|385805645|ref|YP_005842043.1|  99 TCWKCGRiLLP 109
                                       5*****85555 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.002
                       zf-ribbon_3  17 nvCpyCGt 24 
                                       +vCp+CG+
  gi|385805645|ref|YP_005842043.1| 146 TVCPHCGA 153
                                       46666664 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 ?    2.8   0.3       0.1   1.2e+02       1       9 [.      59      67 ..      59      69 .. 0.88
   2 ?    6.1   0.1      0.01        11       2      11 ..     148     157 ..     147     169 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.1
                         Ogr_Delta  1 rCPhCgapa 9 
                                      +CP Cg+ +
  gi|385805645|ref|YP_005842043.1| 59 KCPVCGNTM 67
                                      6******99 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.01
                         Ogr_Delta   2 CPhCgapaaa 11 
                                       CPhCga+ + 
  gi|385805645|ref|YP_005842043.1| 148 CPHCGAAQRK 157
                                       ******9776 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   1.8      0.18     2e+02      18      28 ..      57      68 ..      55      71 .. 0.79
   2 ?   -1.0   0.0       1.6   1.8e+03       5      18 ..      91     104 ..      90     106 .. 0.75
   3 ?    8.9   0.1    0.0013       1.5      19      36 ..     146     164 ..     139     167 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.18
                     Zn_Tnp_IS1595 18 gfvCPhCgsr.k 28
                                      g+ CP Cg++ +
  gi|385805645|ref|YP_005842043.1| 57 GQKCPVCGNTmQ 68
                                      789*****9855 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.6
                     Zn_Tnp_IS1595   5 earalLealrWpng 18 
                                       e+++lL   +W+ g
  gi|385805645|ref|YP_005842043.1|  91 EIYDLLRGTCWKCG 104
                                       67888999999866 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0013
                     Zn_Tnp_IS1595  19 fvCPhCgsr.kayriktrg 36 
                                        vCPhCg + + ++++++ 
  gi|385805645|ref|YP_005842043.1| 146 TVCPHCGAAqRKIKLERPT 164
                                       68*****998888888765 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.8      0.17     2e+02       3      13 ..      58      68 ..      56      79 .. 0.84
   2 ?    6.9   0.1     0.009        10       2      20 ..     145     163 ..     144     167 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.17
                           zf-ISL3  3 hrCPnCgsktv 13
                                      ++CP Cg++++
  gi|385805645|ref|YP_005842043.1| 58 QKCPVCGNTMQ 68
                                      58******975 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.009
                           zf-ISL3   2 phrCPnCgsktvvkhgkke 20 
                                       +++CP+Cg+  ++++  ++
  gi|385805645|ref|YP_005842043.1| 145 TTVCPHCGAAQRKIKLERP 163
                                       579*****99887776655 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   1.7     0.084        94       1      10 [.      59      68 ..      59      70 .. 0.84
   2 ?    2.7   0.1     0.099   1.1e+02       2      10 ..     100     108 ..      99     112 .. 0.78
   3 ?    6.0   0.2    0.0088       9.8       2      21 ..     148     153 ..     142     154 .. 0.63

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.084
                     zinc_ribbon_2  1 fCpnCGaelq 10
                                      +Cp CG++ q
  gi|385805645|ref|YP_005842043.1| 59 KCPVCGNTMQ 68
                                      7*****9876 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.099
                     zinc_ribbon_2   2 CpnCGaelq 10 
                                       C++CG+ l 
  gi|385805645|ref|YP_005842043.1| 100 CWKCGRILL 108
                                       *****9775 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.0088
                     zinc_ribbon_2   2 CpnCGaelqdnakFCpyCGt 21 
                                       Cp+CG              +
  gi|385805645|ref|YP_005842043.1| 148 CPHCG--------------A 153
                                       55555..............4 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.3      0.15   1.7e+02       3      16 ..      59      72 ..      58      84 .. 0.85
   2 ?   -0.0   0.1       1.1   1.2e+03       3      25 ..      99     119 ..      98     122 .. 0.76
   3 ?    5.1   0.1     0.027        30       2      14 ..     146     158 ..     145     165 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.15
                           zf-IS66  3 tCpcCGgllkpige 16
                                      +Cp CG +++ +++
  gi|385805645|ref|YP_005842043.1| 59 KCPVCGNTMQSCPG 72
                                      7*****99987765 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.1
                           zf-IS66   3 tCpcCGg.llkpigedrvreeldi 25 
                                       tC +CG  l   ++e+++ + ld+
  gi|385805645|ref|YP_005842043.1|  99 TCWKCGRiL---LPEEEIKQYLDL 119
                                       799***977...466668888886 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.027
                           zf-IS66   2 rtCpcCGg.llkpi 14 
                                       ++Cp+CG+ + ++i
  gi|385805645|ref|YP_005842043.1| 146 TVCPHCGAaQ-RKI 158
                                       68*****955.566 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (882 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      616  (0.0343577); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); 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: 0.80u 0.34s 00:00:01.14 Elapsed: 00:00:00.52
# Mc/sec: 5109.21
//
Query:       gi|385805646|ref|YP_005842044.1|  [L=1141]
Description: RNA Polymerase [Fervidicoccus fontis Kam940]
Scores for complete 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-131  439.0   0.0   2.4e-131  438.4   0.0    1.3  1  RNA_pol_Rpb2_6   RNA polymerase Rpb2, domain 6
    2.7e-56  190.3   0.1    4.6e-56  189.6   0.1    1.4  1  RNA_pol_Rpb2_1   RNA polymerase beta subunit
    1.3e-31  109.7   0.0    2.2e-31  109.0   0.0    1.4  1  RNA_pol_Rpb2_2   RNA polymerase Rpb2, domain 2
    5.4e-29  100.4   0.0      1e-28   99.6   0.0    1.5  1  RNA_pol_Rpb2_7   RNA polymerase Rpb2, domain 7
      1e-26   92.9   0.0    2.5e-26   91.6   0.0    1.7  1  RNA_pol_Rpb2_3   RNA polymerase Rpb2, domain 3
      5e-22   78.0   0.6    1.2e-21   76.7   0.6    1.7  1  RNA_pol_Rpb2_4   RNA polymerase Rpb2, domain 4
    4.9e-11   43.0   0.0    1.2e-10   41.8   0.0    1.7  1  RNA_pol_Rpb2_5   RNA polymerase Rpb2, domain 5
  ------ inclusion threshold ------
      0.014   15.5   0.3        1.9    8.7   0.0    3.2  3  AbiEi_4          Transcriptional regulator, AbiEi antitoxin
      0.061   13.6   0.0       0.13   12.5   0.0    1.5  1  PFU              PFU (PLAA family ubiquitin binding)
       0.16   12.2   1.0       0.71   10.2   0.8    2.3  1  RNA_pol_Rpb2_45  RNA polymerase beta subunit external 1 domai


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 !  438.4   0.0  1.3e-134  2.4e-131       2     390 .]     671    1042 ..     670    1042 .. 0.96

  Alignments for each domain:
  == domain 1  score: 438.4 bits;  conditional E-value: 1.3e-134
                                        HHT-SS-TTB-HHHHHHHHHHGGGB-S---TTTTT---SSEEEESS----SSB-S.TTTTTS........GGGS- CS
                    RNA_pol_Rpb2_6    2 aklapvvehvqspriiiqaamekqalgiyslnkfkrsnqktyllcinqkPlvktgdkveagqvldgpatekgela 76  
                                        a+ +p++eh+qspr+++q+am kqalg+y++n   r++++ ++l+ ++kPlv+t+  +e ++        ++e +
  gi|385805646|ref|YP_005842044.1|  671 ASTIPYIEHNQSPRNTYQSAMVKQALGLYAANFNVRTDSRGHILHHPEKPLVQTK-PLEVIR--------YNEKP 736 
                                        899****************************************************.999999........***** PP

                                        SEEEEEBBBS--TTTTTTT-EEEBCHHHHTTTT-EEEEEE..EEE--SSSS---.-S--..-.....-SS-GGGS CS
                    RNA_pol_Rpb2_6   77 lGqnavVAvmsyeGYniEDaiilnerlvdrdvftsihikeyeveardtklgeeeitrdipnv.....seealkkL 146 
                                        +GqnavVA+msy+GYniEDa+i+n+++v+r++++s++++ y++e +++++g+e+ ++ ++       + e +kkL
  gi|385805646|ref|YP_005842044.1|  737 AGQNAVVAIMSYTGYNIEDALIFNKSSVERGFMRSTFFRLYSTEEKKYPGGQEDKIEVPEAGvkiyrGFEVYKKL 811 
                                        ****************************************************77666665557999999****** PP

                                        -TTSB--SS-EEETT-EEE---..B-----...-----------..-B---EE--TT-EEEEEEEEE.......E CS
                    RNA_pol_Rpb2_6  147 dedGivrvgaevkegdilvgkvtkgeteltpeekllraifgekarevkdtslrvksgeegvVdkvkvfsrekgde 221 
                                        d dGi+++++ev +g+ l+gk+  ++ ++ +e k++   fg++    kdts++++ ge+gvVd+v +       +
  gi|385805646|ref|YP_005842044.1|  812 DPDGIISPETEVADGEALIGKT--SPPRFLEEFKEY--GFGASV--RKDTSVTIRYGEKGVVDSVFI-------S 873 
                                        *********************8..899998666654..666666..59*******************.......8 PP

                                        E-TT--EEEEEEEEEEE---TT-BEEETTS---BBEEEB-TTTSEEETTS---SEEE-GGGCHHH-BTTHHHHHH CS
                    RNA_pol_Rpb2_6  222 lkagvnklvkvyvaqkRklqvGDKfasrhGqKGvvslilpqeDmPfledGivvDivlNPlgvPSRmtigqllEtl 296 
                                        +++++ klvkv+v++ R +++GDKfasrhGqKGv+++++pq DmP++e+Giv+Di++NP+++PSRmt+gqllE+l
  gi|385805646|ref|YP_005842044.1|  874 ETQEGDKLVKVRVRDYRIPEIGDKFASRHGQKGVIGMLIPQYDMPYTEEGIVPDIIINPHAFPSRMTLGQLLEML 948 
                                        89999********************************************************************** PP

                                        HHHCCCSSSS--B--TT-...-HHHHHHHHHTTS-TT-EE-EEETTTS-B-SS-EEB-EEEEEEBS--CCCS--- CS
                    RNA_pol_Rpb2_6  297 lgkaaalegkkvdatvFdgakeeeikelLeeagleasGkevlydGrtGekleaeifvGviYylkLkhlvedKiha 371 
                                        +gk+aal gk vdat+F+++  eei+ +L ++g++ +G+ev+ydGrtGe +  +i++G++Yy++L+h+v+dK+ha
  gi|385805646|ref|YP_005842044.1|  949 AGKTAALLGKTVDATPFSKEPVEEIRMKLMKKGYSPDGREVMYDGRTGEIIGVPIMIGIVYYQRLHHMVADKFHA 1023
                                        ******************8888***************************************************** PP

                                        -SS--B-TTT--B-SCGGG CS
                    RNA_pol_Rpb2_6  372 RstGpyslltqQPlgGkaq 390 
                                        Rs+Gp++llt+QP++G+a+
  gi|385805646|ref|YP_005842044.1| 1024 RSRGPVQLLTRQPTEGRAR 1042
                                        *****************96 PP

>> RNA_pol_Rpb2_1  RNA polymerase beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.6   0.1   2.6e-59   4.6e-56       1     202 [.      39     408 ..      39     409 .. 0.99

  Alignments for each domain:
  == domain 1  score: 189.6 bits;  conditional E-value: 2.6e-59
                                       CTTHHHHHHHHHHHHTHHHHHCTTSSECCHCSSSHCSSSCEEEEEEEEEEESCSSECTTSCEEES.HHHHHHCTSBX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb2_1   1 gLvsqqldSFnkfveqdlekiikeeaaieseeeiqssgeelelkfvsirlgkPvvdesdasereiyPkearlrnltY 77 
                                       gL +q+ldS+n fve+ l++ii+e++ ie+++++      ++ k+++i + kPv++e+d+se ei+P ear+rn+tY
  gi|385805646|ref|YP_005842044.1|  39 GLSRQHLDSYNRFVETMLQEIIDEQEIIETAFPE------VKFKLGKIEVLKPVSREADGSEVEITPFEARVRNITY 109
                                       5899*****************************6......8************************************ PP

                                       EEEEEEEEEEEECCCCTCCEEEEEEEEEEEEEXBTTSTTSSSTTS.HHHHHHTTS.TTS..SSEEETTCEEEEXEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb2_1  78 saplyvklklvvyekdnkeeikeeevyiGelPlMlrskacvlseaseeelvelkEcpldqGGyFiinGtekvivaqe 154
                                        +p+y++++lv     n+ e+ +++vyiG+lP+M++sk + ls++s+eel++++E+p+d+GGyFiinGtekvi+aqe
  gi|385805646|ref|YP_005842044.1| 110 ASPMYLEITLVE----NGVESIKDKVYIGDLPIMIKSKLDPLSKMSPEELIKINEDPDDPGGYFIINGTEKVIIAQE 182
                                       ************....8999999****************************************************** PP

                                       E............................................................................ CS
                                       x............................................................................ RF
                    RNA_pol_Rpb2_1 155 k............................................................................ 155
                                       +                                                                            
  gi|385805646|ref|YP_005842044.1| 183 Dmvtnrvlvdegkagsnvlytakaisstgsyrisvmmelhkdgtitisfggvpgklpfailmralgfekdqdivyav 259
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                    RNA_pol_Rpb2_1 156 ............................................................................. 155
                                                                                                                    
  gi|385805646|ref|YP_005842044.1| 260 slnpevqslllpsleasrsiatvddaldyigtrvaigqvrenrierakqvidkyffphlgsspkdrrkkgfflaqma 336
                                       ***************************************************************************** PP

                                       .........................XHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSSSSSHHHHSCSHHHH CS
                                       .........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb2_1 156 .........................laGeLlaslfrvllkklerdvkerlqksleklddlmlqllvnakpit 202
                                                                laG+Lla lfr  +k++++d+  + +k+l++ ++++ + +v+++ +t
  gi|385805646|ref|YP_005842044.1| 337 nmilelslgwrepddrdhyankrlkLAGDLLATLFRASFKNFVKDFNYQAEKVLTRSKRFKISSIVRSDVMT 408
                                       *******************************************************************98776 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 !  109.0   0.0   1.2e-34   2.2e-31       2     190 .]     186     361 ..     185     361 .. 0.93

  Alignments for each domain:
  == domain 1  score: 109.0 bits;  conditional E-value: 1.2e-34
                                       TSCEEEEE-SSSSSE..SSSCCEECCCEEEEECCCCSTSCEEEEECTTSSSEEEHHHHHHHTT--STTHHHHHHTSS CS
                    RNA_pol_Rpb2_2   2 sngiyvekekdknki..satvtsslisqrgsvlklekdgktliwtriskkrkipivivlkAlglvsdreIlericyd 76 
                                       +n+++v   k+ +++   a+  ss+ s+r sv+ +  +++t+ ++   +  k p++i+++Alg+ +d++I+++++  
  gi|385805646|ref|YP_005842044.1| 186 TNRVLVDEGKAGSNVlyTAKAISSTGSYRISVMMELHKDGTITISFGGVPGKLPFAILMRALGFEKDQDIVYAVS-- 260
                                       6899999999999997767777788888888899999999999********************************.. PP

                                       STTHHHHHHHHHHHHHHCTSSSCHHHHHHHHHCSSTTSSSCCCCCHHHHHHHCHHHHHHHTTTTSSTTTTTSSSTCH CS
                    RNA_pol_Rpb2_2  77 sedsqlleelleeleekeeiqtqeealdyigkvvalrrgeearlqsareilqkrydlgeigreklnkhlglseslen 153
                                         +++++ +ll++le   +i+t ++aldyig +va+++ +e+r+++a++++         +++ ++ hlg+s +  +
  gi|385805646|ref|YP_005842044.1| 261 -LNPEVQSLLLPSLEASRSIATVDDALDYIGTRVAIGQVRENRIERAKQVI---------DKYFFP-HLGSSPKDRR 326
                                       .79*********************************************996.........8*****.*******665 PP

                                       H..HHHHHHHHHHHHHHHHTTSSSS--TTSGGGEEEE CS
                    RNA_pol_Rpb2_2 154 krlkaqdilymidrLlslklgrrevDDiDhlgnkRvr 190
                                       k  k ++++ m++ +l+l+lg re+DD+Dh++nkR++
  gi|385805646|ref|YP_005842044.1| 327 K--KGFFLAQMANMILELSLGWREPDDRDHYANKRLK 361
                                       5..********************************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 !   99.6   0.0   5.7e-32     1e-28       1      85 [.    1044    1134 ..    1044    1136 .. 0.98

  Alignments for each domain:
  == domain 1  score: 99.6 bits;  conditional E-value: 5.7e-32
                                        BBEEEEHHHHHHHHHHTBHHHHHHHHTTTTTEEEEEEESSSSSCCCEE......EBTTTTCSSSEEEEEEEHHHH CS
                    RNA_pol_Rpb2_7    1 GGlrfGEMErdaliayGaaalLkerltikSDavevdvcgrckllaaan......eCkivkseekiekveipeafk 69  
                                        GGlrfGEMErd+l+++Ga++lL+erl+++SD++ ++vc +c+++ + +       C+i+ ++ +i +ve+ ++fk
  gi|385805646|ref|YP_005842044.1| 1044 GGLRFGEMERDVLVGHGASMLLRERLLESSDKTVIYVCAKCGHIGWFDrnknayVCPIHGDKGEIYPVEVAYGFK 1118
                                        9*********************************************9999***9********************* PP

                                        HHHHHHHHTTBEEEEE CS
                    RNA_pol_Rpb2_7   70 lLlqeLqslgialkll 85  
                                        lL+qeL+s+gi ++l+
  gi|385805646|ref|YP_005842044.1| 1119 LLIQELMSMGIMPRLK 1134
                                        ************9986 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 !   91.6   0.0   1.4e-29   2.5e-26       1      68 []     429     493 ..     429     493 .. 0.98

  Alignments for each domain:
  == domain 1  score: 91.6 bits;  conditional E-value: 1.4e-29
                    RNA_pol_Rpb2_3   1 qvldrlnplselshlrrvsslrgglskerkttevRdlhpshwGriCpveTPEGencGlvksLallarv 68 
                                       q+ldr+n++s lshlrrv s+   ls+++  +++Rdlh ++wGr+Cp+eTPEG+ncGlvk+L+ll+++
  gi|385805646|ref|YP_005842044.1| 429 QLLDRTNWMSMLSHLRRVVSP---LSRSQPLFKARDLHGTQWGRMCPFETPEGPNCGLVKNLSLLTYI 493
                                       89*******************...***************************************99876 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 !   76.7   0.6     7e-25   1.2e-21       1      61 [.     535     597 ..     535     598 .. 0.98

  Alignments for each domain:
  == domain 1  score: 76.7 bits;  conditional E-value: 7e-25
                                       EECTT-BEEE-S-HCCHHHHHHHHCCTTSS-TT-EEEE-TT..T--EEEE-SSEEB-EEEEE- CS
                    RNA_pol_Rpb2_4   1 VfvNGrllGvtrdpkklvetlRelRRkgkiseevsivlnek..qkevkiatDgGRvcRPliiV 61 
                                       V++NGr +G++ d++kl++t+Re+RRkg++++e+++v++e+   ke++++tD+GR++RPliiV
  gi|385805646|ref|YP_005842044.1| 535 VYLNGRHIGYYPDGEKLASTIREMRRKGDLHHEINVVYYERpqIKELYVNTDAGRIRRPLIIV 597
                                       9**************************************99999******************9 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 !   41.8   0.0   6.7e-14   1.2e-10       1      55 [.     619     660 ..     619     661 .. 0.88

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 6.7e-14
                                       HHHHHHTTSEEEEEHHHHTT--EESSTTTCSST-SSTTTSS--TTSSSST-SEEE CS
                    RNA_pol_Rpb2_5   1 wddLlregvvEylDaeEEetamIamtpedleksreekealeekenskshtyTHcE 55 
                                       ++dL++eg +EylDaeEEe+a+Ia++p+dl                + ++yTH+E
  gi|385805646|ref|YP_005842044.1| 619 FSDLVKEGKIEYLDAEEEENAYIALDPSDLLGP-------------NGKEYTHLE 660
                                       89****************************665.............234899998 PP

>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       6.4   1.1e+04       7      19 ..     450     462 ..     445     464 .. 0.86
   2 ?    3.2   0.0     0.054        98      27      39 ..     553     565 ..     550     566 .. 0.89
   3 ?    8.7   0.0     0.001       1.9       6      39 ..     596     629 ..     591     631 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 6.4
                           AbiEi_4   7 asrqvGlfttrel 19 
                                       +sr+++lf  r+l
  gi|385805646|ref|YP_005842044.1| 450 LSRSQPLFKARDL 462
                                       689999***9998 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.054
                           AbiEi_4  27 salrrLvrkGwLv 39 
                                       s++r+++rkG+L+
  gi|385805646|ref|YP_005842044.1| 553 STIREMRRKGDLH 565
                                       78********996 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.001
                           AbiEi_4   6 lasrqvGlfttreleaaGispsalrrLvrkGwLv 39 
                                       +++ +++ +t r++ea+ + +++ + Lv++G+++
  gi|385805646|ref|YP_005842044.1| 596 IVRNGKPAVTKRDIEALRKGEKTFSDLVKEGKIE 629
                                       56677899************************97 PP

>> PFU  PFU (PLAA family ubiquitin binding)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   7.5e-05      0.13      66     109 ..      13      56 ..       7      59 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.5e-05
                               PFU  66 gkpplkLpynksdnpyeaAekFleknelsqsyleqivnFiiknt 109
                                        k++  L y  ++  + +A+kF+e++ ls+++l++  +F+++  
  gi|385805646|ref|YP_005842044.1|  13 SKKKEDLSYLDGEARWLLAKKFIEEQGLSRQHLDSYNRFVETML 56 
                                       5667799********************************98765 PP

>> RNA_pol_Rpb2_45  RNA polymerase beta subunit external 1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.8    0.0004      0.71       9      26 ..     625     642 ..     607     648 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0004
                                       EEEEEEEEHHHHTTSEEE CS
                   RNA_pol_Rpb2_45   9 tdevvYLtAdeEekyviA 26 
                                       + +++YL A+eEe+ +iA
  gi|385805646|ref|YP_005842044.1| 625 EGKIEYLDAEEEENAYIA 642
                                       568**************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); 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):              10  [number of targets reported over threshold]
# CPU time: 0.84u 0.36s 00:00:01.20 Elapsed: 00:00:00.52
# Mc/sec: 6578.09
//
Query:       gi|385805647|ref|YP_005842045.1|  [L=81]
Description: DNA-directed RNA polymerase subunit H [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.1e-26   90.1   0.2    6.8e-26   89.9   0.2    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 !   89.9   0.2   3.8e-30   6.8e-26       1      73 []       6      78 ..       6      78 .. 0.98

  Alignments for each domain:
  == domain 1  score: 89.9 bits;  conditional E-value: 3.8e-30
                                      ..-TSSSS--EEEEE-HHHHHHHHHHTT--TTCSS-EETTSHHHHCCT--TTSEEEEEEEETTTEEEEEEEEE CS
                    RNA_pol_Rpb5_C  1 vnitkHelvPkhevlseeekkellkklkikeeqLPkisksDpvarylglkkGdvvkItrksetageavtYRlV 73
                                      +++++H+lvPkhe +   e+ ++lk+l+++ +qLP i++sDpvar++g+k+G++vkItr+ e +ge+v+YRlV
  gi|385805647|ref|YP_005842045.1|  6 FSVQDHVLVPKHERIPITEVPKVLKELNVSINQLPLIRSSDPVAREIGAKPGELVKITRRDEITGESVVYRLV 78
                                      5799********************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 542.16
//
Query:       gi|385805648|ref|YP_005842046.1|  [L=623]
Description: Aldehyde:ferredoxin oxidoreductase [Fervidicoccus fontis Kam940]
Scores for 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-123  411.6   0.0   3.8e-123  411.3   0.0    1.1  1  AFOR_C    Aldehyde ferredoxin oxidoreductase, domains 2 & 3
    1.9e-75  253.1   0.1    3.4e-75  252.3   0.1    1.4  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 !  411.3   0.0  4.2e-127  3.8e-123       3     382 .]     225     613 ..     223     613 .. 0.97

  Alignments for each domain:
  == domain 1  score: 411.3 bits;  conditional E-value: 4.2e-127
                                       HHHHHHHHHHSH.HHHHHHHH-GGGHHHHHHHTT---BTTTTBS--TTGGGGSHHHHHHHTEEEE.E-TT-SS--EE CS
                            AFOR_C   3 gkkiqkeiksspqvtaelrkyGTaelvnianetgalptknfqegtfekaekisgealeekylvknegCfsCpiaCgr 79 
                                       +k+  + +++sp+   ++r++GTa++v++  + g  p  nf +  f++ ++ +++++ + y +k++gC++C i+C +
  gi|385805648|ref|YP_005842046.1| 225 VKEEIQTYQKSPALE-GFRALGTAGVVDLFYSLGHNPSFNFMQREFNGIDNYKADVFPR-YIIKRGGCYGCMISCWQ 299
                                       667778899999666.***************************99*************9.*****99********** PP

                                       EEE......ET..EE---HHHHHHHTGGGT---HHHHHHHHHHHHHHTB-HHHHHHHHHHHHHHHHTTSS-HHHHTS CS
                            AFOR_C  80 evkveegkkvk..vegpeyetlaalGsnlgiddleailklnelcdelGlDtisaGntiafamelyekGllkkedtdg 154
                                        +k+++g+++    + peye l+++Gsnlg+ +lea++++n lcd++GlD+is+G++i++a elyekG+l++++tdg
  gi|385805648|ref|YP_005842046.1| 300 FLKTTDGPYAGffWDKPEYEALWSFGSNLGNANLEAVMQANMLCDKYGLDVISVGSAIGMAYELYEKGILTRKETDG 376
                                       *****9999556*99************************************************************** PP

                                       ----TT-THHHHHHHHHHHTT-TTHHHHTT-HHHHHHCTT..-GGG--EETTEE--SS-GGG-HHHHHHHHH-TTSS CS
                            AFOR_C 155 lelefgdaeallellekiAkregigdllAeGvkrlaeklg..aeelamhvkGlelpaydprgakgmalaYatsnrGa 229
                                       +el++gd+e +le+++kiA regig++l+eG+kr+ae +g  ae++a+++kGlelpaydpr+ak+++l+  tsn Ga
  gi|385805648|ref|YP_005842046.1| 377 MELRWGDPEPALEIIRKIALREGIGRILGEGTKRAAEIIGrgAEKYAIQIKGLELPAYDPRAAKAHGLSLVTSNIGA 453
                                       ***************************************************************************** PP

                                       -SGGG-THHHH.......S---TT--HHHHHHHHHHHHHHHHHHHHT--GGGG-HHH......HHHHHHHHHT--.. CS
                            AFOR_C 230 cHlrayliale.......ekvdpletegkaelvkwfqdltalvdslglCkftseaeerldlelyakllsavtGid.. 297
                                       +H  ++ ++         ++vdpl+ egk+el+k+ qd ta+++ +g C f++   ++++ e++akll+ +tGi+  
  gi|385805648|ref|YP_005842046.1| 454 SHNMGWNYFEItgvpkdgKQVDPLSIEGKGELTKYVQDETAMYEVAGKCTFPA-DFVMFTRENLAKLLYYATGIEef 529
                                       ****99988778******99*********************************.788999**************877 PP

                                       --HHHHHHHHHHHHHHHHHHHHHHT--HHHS---HHHHHS---SSTTTT---..-HHHHHHHHHHHHT--T.TS--- CS
                            AFOR_C 298 vteeellkaGeRiynleRlfnlreGltrkddtlperlleeplkegpakgkvledeleemldeyYelrGWde.tGvPt 373
                                        +++ l+ +GeR+ynleR+fn+reG++r++dt+per+++ep + +pakg+v   el+++ld+yY++rGWd  tG+Pt
  gi|385805648|ref|YP_005842046.1| 530 KNPDYLMLVGERVYNLERAFNVREGFGREHDTIPERFVKEPFPRTPAKGQVF--ELDKLLDDYYKARGWDLkTGKPT 604
                                       899************************************************9..9***************99***** PP

                                       HHHHHHCT- CS
                            AFOR_C 374 ketlkrLgL 382
                                       k++l+ LgL
  gi|385805648|ref|YP_005842046.1| 605 KAKLESLGL 613
                                       ********8 PP

>> AFOR_N  Aldehyde ferredoxin oxidoreductase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  252.3   0.1   3.8e-79   3.4e-75       1     197 [.      11     209 ..      11     210 .. 0.98

  Alignments for each domain:
  == domain 1  score: 252.3 bits;  conditional E-value: 3.8e-79
                                       SEEEEEETTTTEEEEEE--HHHHHHH-SCHHHHHHHHHHHS-TTS-TTSTTS-EEEEE-TTTTSSSTTB-EEEEEEE CS
                            AFOR_N   1 gkilrvdLstgkieveelpeelaekylGgrglaakllldevppgvdplspenplvfatGpltgtpapgsgrlvvvak 77 
                                       gkil++dL+++++++ el++e+a++y+G rg+++k+l+d++++g+dplspe  lv+++Gpl+gt+  +++r+ vv+k
  gi|385805648|ref|YP_005842046.1|  11 GKILWLDLTKREAKKLELSREMARDYIGARGFGIKILWDNMKKGTDPLSPESLLVVSVGPLAGTSSQSASRWFVVFK 87 
                                       79*************************************************************************** PP

                                       -TTTSSEEEEEEETCHHHHHHHCT-SEEEEES--SS-EEEEEETTEEEEEE-TTTTTS-HHHHHHHHHHHHTSEEE. CS
                            AFOR_N  78 sPltgtlgesnaGgrfgaelkraGydaivieGkaekpvylvieddkveiedaedlwgldtyettealkeelgdkva. 153
                                       sPltgt+ +s  Gg+fgae+k+aGydaiv+ G+aekp+y++i+dd+ve++da+  wgl+t  tte lkee++++++ 
  gi|385805648|ref|YP_005842046.1|  88 SPLTGTYFRSVGGGYFGAEMKFAGYDAIVVSGRAEKPTYVWIKDDNVEFRDATRAWGLTTNMTTELLKEETDKSARl 164
                                       *********************************************************************99885555 PP

                                       .EE-HHHHTT-TTB-E.EETTEEE-SSSHHHHHHHTTEEEEEEE- CS
                            AFOR_N 154 .viGpaGenlvrfAsisvddgraagrgGlGavmgsKnlkaivvrg 197
                                        +iGpaGe+lv+++si+ dd+r+agrgG Gav+g+Knlkaivv+g
  gi|385805648|ref|YP_005842046.1| 165 iTIGPAGERLVKISSIQSDDQRSAGRGGGGAVLGAKNLKAIVVKG 209
                                       6***************999************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (623 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        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 0.32s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 3954.98
//
Query:       gi|385805649|ref|YP_005842047.1|  [L=91]
Description: hypothetical protein FFONT_0605 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score 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   15.9   0.0      0.016   15.8   0.0    1.1  1  ThiS      ThiS family


Domain annotation for each model (and alignments):
>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.8   0.0   9.1e-07     0.016       1      70 [.       9      84 ..       9      91 .] 0.89

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 9.1e-07
                                      EEETTCCHHHHT..CEEEEESSTSBHHHHHHHHHHHTCHHG......TTTTEEEEETTEEEGCCTTTSB--TTCEEEE CS
                              ThiS  1 vllfaelrelag..eeelelaegstvaelleaLgerypela......lerrvavavNgeivprlwldtelkdgDevai 70
                                      v + + ++e++g     + l++gs+++  + ++ ++ +e++      +++ + v +Ng+ +++  l++ l+dgD++ +
  gi|385805649|ref|YP_005842047.1|  9 VEFVGPAKEKVGrgFMWVKLPSGSNLRNFFYSIFQNRNEAEdflsriEREELFVFLNGRRARD--LSAMLNDGDKIYV 84
                                      678888888888877778899************999988889*****9***************..**********965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 608.42
//
Query:       gi|385805650|ref|YP_005842048.1|  [L=386]
Description: acetyl-CoA C-acyltransferase 7 [Fervidicoccus fontis Kam940]
Scores for complete 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-29  102.9   0.0      4e-29  101.8   0.0    1.6  1  Thiolase_N       Thiolase, N-terminal domain
    3.2e-09   36.5   0.1    7.2e-09   35.3   0.1    1.6  1  Thiolase_C       Thiolase, C-terminal domain
     0.0011   18.8   0.0       0.14   12.1   0.0    2.4  2  ACP_syn_III      3-Oxoacyl-[acyl-carrier-protein (ACP)] synth
      0.002   18.2   0.1       0.03   14.3   0.1    2.4  1  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
  ------ inclusion threshold ------
      0.033   14.3   0.0      0.074   13.2   0.0    1.5  1  SspH             Small acid-soluble spore protein H family


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 !  101.8   0.0   1.1e-32     4e-29       1     259 [.       5     221 ..       5     222 .. 0.96

  Alignments for each domain:
  == domain 1  score: 101.8 bits;  conditional E-value: 1.1e-32
                                       EEEEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCT.TSTSC.HHHHHHHHTTS-TT CS
                        Thiolase_N   1 vvivsaartpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqa.gegqn.iarqaalkagipee 75 
                                       v+i+s+ ++++gk     +     +L  ea++++++++++  e +d +i + +  +  e+ + +a+ +a  +gi ee
  gi|385805650|ref|YP_005842048.1|   5 VAIISSGMSKFGK----REGKGLIDLYLEAIEEVIQSTKL--ERIDALIAASMSPGrYENIMgPANILAGLLGI-EE 74 
                                       79***********....788899**************987..68**********997888889***********.99 PP

                                       SEEEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTTTGGSSSSEEEEEHHHHHHTEETTTT CS
                        Thiolase_N  76 vpavtvnkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvrsglklgdekakdllipdgladafne 152
                                        ++++v+++++Sg +a+  + q + +g++d ++++G+E+m++ +t e+t++++gl ++ e + ++++p+        
  gi|385805650|ref|YP_005842048.1|  75 GTVMRVENTSGSGGAAIFVGYQLVSSGRSDFALVIGGEKMTHLSTEENTSIIAGLVHEYERKLGITLPS-------- 143
                                       999******************************************************************........ PP

                                       SEHHHHHHHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHHTS CS
                        Thiolase_N 153 ehmGltaenlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLakl 229
                                         ++l a+ + ++++++ e+++++Avk+h +++ ++ka+ F++ i              + +++ +s+v+ ++L+ +
  gi|385805650|ref|YP_005842048.1| 144 -YAALLARAYMNEFNAPQEALASVAVKNHLHGSMNPKAH-FQKRI--------------TIEDYFNSKVVSDPLRVM 204
                                       .9*************************************.***99..............7899************** PP

                                       -BSSSTTSS-BTTSB--BEEEEEEEEEEEH CS
                        Thiolase_N 230 kpaFkkeGtvtAgnasqisDGaaavllmse 259
                                                    ++ +isDGaaa+ll+++
  gi|385805650|ref|YP_005842048.1| 205 -------------DYTPISDGAAAILLTPK 221
                                       .............*************9876 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.1     2e-12   7.2e-09      26     102 ..     260     354 ..     235     372 .. 0.87

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 2e-12
                                       HHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--G..................GGBSTT--HHHH-B-TTT CS
                        Thiolase_C  26 yaikkvlkkagltvedidlfEinEAFaaqaLavakaldldl..................ekvNvnGGaialGHPlGa 84 
                                         +kk+lk+ gl++++idl+E+++  +   ++ ++++++ +                    vN  GG  a GHP+Ga
  gi|385805650|ref|YP_005842048.1| 260 ISSKKALKESGLDLKNIDLIELHDMATILEIVELESMGFYKrgeawkaemngenrydgdLPVNTSGGLKAKGHPIGA 336
                                       46799********************99999*********999**************99889**************** PP

                                       HHHHHHHHHHHHHHHCTT CS
                        Thiolase_C  85 sGaRivvtllselkkegg 102
                                       +G+ ++  +  ++ k+ g
  gi|385805650|ref|YP_005842048.1| 337 TGVAQAYEISMQMWKRAG 354
                                       ******999999987765 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 !   12.1   0.0   3.8e-05      0.14      11      41 ..      88     118 ..      79     128 .. 0.79
   2 ?    4.1   0.0     0.011        41      51      64 ..     208     221 ..     183     231 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.8e-05
                                       HHHHHHHHHHHHTTS-SEEEEEEEEEGGGCS CS
                       ACP_syn_III  11 vyalsvAdaliesgaakrvLvigaetlskil 41 
                                        +a+ v  +l++sg+   +Lvig+e+++++ 
  gi|385805650|ref|YP_005842048.1|  88 GAAIFVGYQLVSSGRSDFALVIGGEKMTHLS 118
                                       5789999*******************99854 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.011
                                       TB-EEEEEEEEEEE CS
                       ACP_syn_III  51 lfGDGAgAvvleas 64 
                                         +DGA+A++l+++
  gi|385805650|ref|YP_005842048.1| 208 PISDGAAAILLTPK 221
                                       579********986 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 !   14.3   0.1   8.4e-06      0.03      16     106 ..     248     349 ..     233     357 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.4e-06
                                       SSSTSTTHHHHHHHHHHHHHHHT--GGGEEEEE-SS-SSHHHHHHHHHHHH.....HHHGGGGG.....SCTSEEE- CS
                   Ketoacyl-synt_C  16 nsltapngeaqaraiekalaeagvdpedvdyveahgtgtplgDpiElealk.....kvfgekar.....kqplavgS 82 
                                       +     n +a +   +kal+e+g+d +++d++e h+ +t l   +Ele++      ++++++ +     +  l+v++
  gi|385805650|ref|YP_005842048.1| 248 ERDDFLNLKAVEISSKKALKESGLDLKNIDLIELHDMATILE-IVELESMGfykrgEAWKAEMNgenryDGDLPVNT 323
                                       5555567788888899***********************875.6777766411111333333336666644455544 PP

                                       T..HHHH-B-GGGHHHHHHHHHHHHH CS
                   Ketoacyl-synt_C  83 v..KsniGHleaAaGvaelikvvlal 106
                                              GH  +A Gva++  + +++
  gi|385805650|ref|YP_005842048.1| 324 SggLKAKGHPIGATGVAQAYEISMQM 349
                                       31134567777777777777777776 PP

>> SspH  Small acid-soluble spore protein H family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.1e-05     0.074       6      54 ..     213     261 ..     212     263 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.1e-05
                              SspH   6 akeIlnskemieVtYngkpVwIehvdeenetAtVhfldnpeeeqeVpvn 54 
                                       a  Il  ++ i  +Y +kp++I++v  +++t  Vh +d+  + + V+++
  gi|385805650|ref|YP_005842048.1| 213 AAAILLTPKDIALSYTSKPIIIKGVAGATDTLVVHERDDFLNLKAVEIS 261
                                       5679999*****************************9887777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 2610.89
//
Query:       gi|385805651|ref|YP_005842049.1|  [L=106]
Description: hypothetical protein FFONT_0607 [Fervidicoccus fontis Kam940]
Scores for complete 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-08   32.1   0.0    1.1e-07   31.7   0.0    1.2  1  OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
     0.0024   17.7   1.6     0.0038   17.1   1.6    1.3  1  DUF35_N        Rubredoxin-like zinc ribbon domain (DUF35_N)
  ------ inclusion threshold ------
      0.058   13.0   0.7       0.11   12.1   0.7    1.5  1  zf_C2H2_13     Zinc finger domain
       0.11   11.3   0.9       0.14   11.0   0.9    1.1  1  DUF674         Protein of unknown function (DUF674)
       0.14   10.5   0.6       0.17   10.2   0.6    1.1  1  DUF530         Protein of unknown function (DUF530)


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 !   31.7   0.0   3.2e-11   1.1e-07       7      64 ..      40      93 ..      37      94 .. 0.91

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 3.2e-11
                                      G-EEEEEEEEEE-TTS-EEEEEEEEEEEE-TT...-EE-EEEEEEES..TT-B-EEE- CS
                     OB_aCoA_assoc  7 rGtvysftvvhrappgfaeeaPyvvgvVeLdegvrimarlvgvdpdevriGmrVravf 64
                                      +G++y++t+++ +p  ++ ++P +v++ e  +  r ++   g++ + ++iG +Vr+++
  gi|385805651|ref|YP_005842049.1| 40 EGKIYTYTIIYVPP--KGFTPPIAVAIAEYNG-MRFLGKYNGDP-GKIKIGEKVRLDT 93
                                      8*************..889***********99.99****99865.6799******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 !   17.1   1.6   1.1e-06    0.0038      12      36 ..       8      31 ..       5      32 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.1e-06
                           DUF35_N 12 qrCpdCGtvqfPPravCphCgsddl 36
                                        C +CG+ ++P+   C +Cgs+++
  gi|385805651|ref|YP_005842049.1|  8 YVCEKCGKGYYPKKVRC-RCGSTSF 31
                                      68***************.6***975 PP

>> zf_C2H2_13  Zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.7   3.1e-05      0.11      14      25 ..       4      15 ..       1      17 [. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.1e-05
                        zf_C2H2_13 14 nlnYRvCnkCGk 25
                                       ++Y vC+kCGk
  gi|385805651|ref|YP_005842049.1|  4 MFKYYVCEKCGK 15
                                      589********9 PP

>> DUF674  Protein of unknown function (DUF674)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.9   3.9e-05      0.14     108     143 ..       5      37 ..       2      49 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.9e-05
                            DUF674 108 tkyfvCssfsCskllSnfntsrCsCgklmakeeies 143
                                        ky+vC++  C  +  + +++rC+Cg++  ke+i++
  gi|385805651|ref|YP_005842049.1|   5 FKYYVCEK--C-GKGYYPKKVRCRCGSTSFKEVIDE 37 
                                       69******..9.44556799******9976777776 PP

>> DUF530  Protein of unknown function (DUF530)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.6   4.8e-05      0.17     124     173 ..       6      52 ..       2      56 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 4.8e-05
                            DUF530 124 aelkCksCekkyklseleleskkCecgseefklkvnkeg..iyRleiipyLp 173
                                        +  C++C+k y  ++++     C cgs+ fk  +++++     +  i y+p
  gi|385805651|ref|YP_005842049.1|   6 KYYVCEKCGKGYYPKKVR-----CRCGSTSFKEVIDENAegKIYTYTIIYVP 52 
                                       5667********999865.....********977666541144444455665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 674.63
//
Query:       gi|385805652|ref|YP_005842050.1|  [L=52]
Description: hypothetical protein FFONT_0608 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score 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   14.0   0.1      0.034   13.6   0.1    1.2  1  HTH_OrfB_IS605  Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_OrfB_IS605  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   1.9e-06     0.034       3      15 ..      35      47 ..      32      51 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.9e-06
                    HTH_OrfB_IS605  3 lkaykyrlyPTpe 15
                                      ++a+ky +yPT e
  gi|385805652|ref|YP_005842050.1| 35 QLAFKYKIYPTRE 47
                                      78*********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       190  (0.0105974); expected 358.6 (0.02)
Passed bias filter:                      140  (0.00780858); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 359.92
//
Query:       gi|385805653|ref|YP_005842051.1|  [L=130]
Description: hypothetical protein FFONT_0609 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-11   44.5   1.9    3.5e-10   39.6   0.1    3.2  3  DUF1641   Protein of unknown function (DUF1641)
  ------ inclusion threshold ------
      0.012   15.7   0.2      0.033   14.3   0.1    1.8  2  FANC_SAP  Fanconi anemia-associated nuclease SAP domain
      0.043   13.3   0.5      0.056   13.0   0.5    1.2  1  DUF2192   Uncharacterized protein conserved in archaea (DUF21
        0.1   12.5   3.6        3.9    7.4   1.0    2.1  2  GerD      Spore germination GerD central core domain
          4    8.0   6.4        3.7    8.1   0.6    3.0  3  COMP      Cartilage oligomeric matrix protein


Domain annotation for each model (and alignments):
>> DUF1641  Protein of unknown function (DUF1641)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.13   4.6e+02      13      22 ..      13      22 ..      13      23 .. 0.90
   2 ?    1.5   0.0     0.075   2.7e+02       8      22 ..      39      53 ..      36      62 .. 0.81
   3 !   39.6   0.1   9.7e-14   3.5e-10       4      39 .]      91     126 ..      90     126 .. 0.96

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.13
                           DUF1641 13 gLlraLrDPD 22
                                      +Ll++L +P+
  gi|385805653|ref|YP_005842051.1| 13 ELLKLLQNPE 22
                                      59*******8 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.075
                           DUF1641  8 pvGlfgLlraLrDPD 22
                                      ++Gl+++l a  ++D
  gi|385805653|ref|YP_005842051.1| 39 KTGLLDMLNAIVNED 53
                                      789999999977766 PP

  == domain 3  score: 39.6 bits;  conditional E-value: 9.7e-14
                           DUF1641   4 eepkpvGlfgLlraLrDPDVqrGLGfllalLKalGk 39 
                                       +e+k++Gl+gL+ra +DPDVq + + l+++LK +G+
  gi|385805653|ref|YP_005842051.1|  91 KEEKKTGLTGLMRAFSDPDVQLAATKLVKILKVIGS 126
                                       89********************************96 PP

>> FANC_SAP  Fanconi anemia-associated nuclease SAP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   9.2e-06     0.033       6      39 ..      13      47 ..      12      59 .. 0.93
   2 ?   -1.7   0.0      0.94   3.4e+03      26      34 ..      90      98 ..      75     115 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 9.2e-06
                          FANC_SAP  6 eLFaLltkpELlqaFaavla.aksarKaelleaLr 39
                                      eL  Ll+ pEL++ + ++l+   +++K++ll+ L 
  gi|385805653|ref|YP_005842051.1| 13 ELLKLLQNPELVESLNKTLSlLINLNKTGLLDMLN 47
                                      89******************************997 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.94
                          FANC_SAP 26 aksarKael 34
                                       k  +K++l
  gi|385805653|ref|YP_005842051.1| 90 EKEEKKTGL 98
                                      455555554 PP

>> DUF2192  Uncharacterized protein conserved in archaea (DUF2192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.5   1.6e-05     0.056      78     159 ..      13      94 ..       5     106 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.6e-05
                           DUF2192  78 elfdkifsvE..ekleealeiilskkkeeavekvkevlgkidenkvarvlrlvltkvvlgfade.eelikllrklee 151
                                       el++ + + E  e+l++ l+++++ +k+   +++++    ++e+ +a +++l++t   l+ +d  ++l+ +l+++++
  gi|385805653|ref|YP_005842051.1|  13 ELLKLLQNPElvESLNKTLSLLINLNKTGLLDMLNA---IVNEDFIASLMKLIMTPEFLRLMDSiNDLMAVLQQVTD 86 
                                       555555555522457778888888888888888886...89*********************97579********99 PP

                           DUF2192 152 afpelekt 159
                                       ++ e e++
  gi|385805653|ref|YP_005842051.1|  87 VMIEKEEK 94 
                                       98887766 PP

>> GerD  Spore germination GerD central core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   3.8    0.0015       5.4      17      95 ..       6      90 ..       1      94 [. 0.76
   2 ?    7.4   1.0    0.0011       3.9      50     111 ..      58     119 ..      44     122 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0015
                              GerD 17 tsekgkkfwkklfkdpkfaealaksmk...kenekllkdLmk...DpeYqkmlleilkdpemekqllellkskeyrkql 89
                                      +sek+++ + kl+++p+ +e+l k+++   + n++ l d+++   + ++ ++l++++  pe+ + + ++    ++ +q+
  gi|385805653|ref|YP_005842051.1|  6 LSEKEEQELLKLLQNPELVESLNKTLSlliNLNKTGLLDMLNaivNEDFIASLMKLIMTPEFLRLMDSINDLMAVLQQV 84
                                      57888888888*************9753334455555555432337899999999999999999999998888888898 PP

                              GerD 90 ekviqe 95
                                       +v+ e
  gi|385805653|ref|YP_005842051.1| 85 TDVMIE 90
                                      888877 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0011
                              GerD  50 lkdLmkDpeYqkmlleilkdpemekqllellkskeyrkqlekviqetlesPlfkaklqellk 111
                                       l +L+  pe+ + + +i     + +q+++++  ke +k+  + ++ +++ P ++   ++l+k
  gi|385805653|ref|YP_005842051.1|  58 LMKLIMTPEFLRLMDSINDLMAVLQQVTDVMIEKEEKKTGLTGLMRAFSDPDVQLAATKLVK 119
                                       34566689**9999999999999**************9999999999**9999988887765 PP

>> COMP  Cartilage oligomeric matrix protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.2     0.097   3.5e+02       2      20 ..      19      37 ..      18      40 .. 0.84
   2 ?   -2.6   0.0       2.2     8e+03      10      19 ..      43      52 ..      40      52 .. 0.67
   3 ?    8.1   0.6     0.001       3.7       6      26 ..      70      90 ..      67      93 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.097
                              COMP  2 vtkqLlrqLseltqllkeL 20
                                      ++++L+ +L+ +++ll  L
  gi|385805653|ref|YP_005842051.1| 19 QNPELVESLNKTLSLLINL 37
                                      5789*******99999665 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.2
                              COMP 10 Lseltqllke 19
                                      L  l+++++e
  gi|385805653|ref|YP_005842051.1| 43 LDMLNAIVNE 52
                                      6667888876 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.001
                              COMP  6 LlrqLseltqllkeLreelrq 26
                                      L+ ++++l+++l+ + +++++
  gi|385805653|ref|YP_005842051.1| 70 LMDSINDLMAVLQQVTDVMIE 90
                                      78899**************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1133  (0.0631937); expected 358.6 (0.02)
Passed bias filter:                      590  (0.0329076); 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: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 855.04
//
Query:       gi|385805654|ref|YP_005842052.1|  [L=395]
Description: FAD-dependent pyridine nucleotide-disulfide oxidoreductase [Fervidicoccus fontis Kam940]
Scores for complete 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-21   74.6   0.1    3.6e-20   72.4   0.1    1.9  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    7.5e-06   25.8   2.5      0.069   12.7   2.3    2.2  2  DAO             FAD dependent oxidoreductase
    8.4e-06   25.1   2.3     0.0095   15.1   0.0    2.5  3  GIDA            Glucose inhibited division protein A
    1.9e-05   25.2   2.5     0.0057   17.2   1.0    2.5  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    4.3e-05   22.9   0.7    8.6e-05   21.9   0.3    1.6  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
      6e-05   22.4   0.2     0.0036   16.6   0.5    2.1  2  FAD_binding_3   FAD binding domain
     0.0011   18.1   0.2       0.42    9.6   0.0    2.1  2  Lycopene_cycl   Lycopene cyclase protein
     0.0013   17.5   4.9     0.0059   15.3   0.6    2.3  3  HI0933_like     HI0933-like protein
     0.0019   18.4   0.2     0.0043   17.3   0.2    1.6  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
     0.0026   17.8   0.4       0.39   10.7   0.0    2.6  3  NAD_binding_9   FAD-NAD(P)-binding
     0.0069   15.5   0.6      0.012   14.7   0.6    1.3  1  FAD_binding_2   FAD binding domain
     0.0087   15.0   1.3     0.0098   14.8   0.4    1.5  2  Trp_halogenase  Tryptophan halogenase
  ------ inclusion threshold ------
      0.012   14.9   0.6       0.02   14.3   0.6    1.3  1  FAD_oxidored    FAD dependent oxidoreductase
      0.024   15.1   0.0      0.076   13.5   0.0    1.9  2  NAD_binding_7   Putative NAD(P)-binding
      0.031   13.9   0.2      0.077   12.6   0.2    1.6  1  ApbA            Ketopantoate reductase PanE/ApbA


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 !   72.4   0.1     3e-23   3.6e-20       3     283 ..       7     292 ..       5     305 .. 0.77

  Alignments for each domain:
  == domain 1  score: 72.4 bits;  conditional E-value: 3e-23
                                       EEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHH.HCHHHHHHHHHHHHH...HHHHCHHHHCCCCHCCTC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2   3 vvviGgGpAGlaaaltlaqagakvtlvelegtclnggcll.skallgvaedaeias...evvkklnqgielllgeev 75 
                                       +v+iGgG++G+ +a  la++g +vtl+ ++ +++ +++ +   a+ g +  +  ++   e    l   ++++ + +v
  gi|385805654|ref|YP_005842052.1|   7 IVIIGGGAGGIITANILAEKGKDVTLI-SDSNIHPFQPGYlFIAFKGHEPSKY-IRtveE---LLDPRVKFIQD-KV 77 
                                       8**************************.6666666666660333333333333.333542...35667999999.9* PP

                                       EEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T.....SEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxx RF
                       Pyr_redox_2  76 vkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllp.....krivv 147
                                       +++d +++ +k      +++++i y+k+v+AtG+s +   ipG  en+ k+ +++ + ea  + +++     k  +v
  gi|385805654|ref|YP_005842052.1|  78 TEVDLKERSIKT-----EKGKSISYEKVVVATGASLNYDLIPGHRENYEKMGDYYSTPEAAVKVWNNikdmkKGKLV 149
                                       *******99999.....56779***********9988888**************************9966665559* PP

                                       ES-SHHHHHHHHH.....HHHHT-........EEEEEESSSSSSTTS-HHHHHHHHHHHHHT.TEEEEESCEEEEEE CS
                                       xxxxxxxxxxxxx.....xxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                       Pyr_redox_2 148 vGgGyiGvElAaa.....laklgk........evtlveardrllraldkelsaaleealeke.Gvevklgtsvkeid 210
                                       +G     + +  a     + ++g+        +v l++ +++++   +ke+s+a+ee++++  +++ ++   +  id
  gi|385805654|ref|YP_005842052.1| 150 IGVPDLVIKCPPAphkgtFLSAGYfkekradvRVELLYPAPHVY--GEKEVSKAIEEKMKEFgNIDYRTSFLIDSID 224
                                       **9999999877765666555555555666559***********..68**************99*********9999 PP

                                       ETTEEEEEEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EE.EETTEEE--TTS.BES.STTEEE-GGGCTECCS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx.xxx.xxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 211 gngeklevvledgeeidadlvvvavGvrpstelleeklglel.derggivvdefl.rtn.vpgiyaiGDvaggkgg 283
                                       ++++   v   +gee+  d +++   +   t++  +    e+ d++++++v +++ + +  ++ +a+GD++   + 
  gi|385805654|ref|YP_005842052.1| 225 NEKK--VVRSATGEEVSFDALIMIP-MHKGTNI--KFNPPEVlDDDRYVKVHKNYlNIEgYDDAFAVGDCT---NL 292
                                       8887..4677788888888888654.3333333..3333333389999977665548877**********9...33 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   2.3   5.8e-05     0.069       2      29 ..       7      36 ..       6      44 .. 0.92
   2 !   11.2   0.0   0.00017       0.2     144     227 ..      54     129 ..      41     184 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.8e-05
                                      EEEECTSHHHHHHHHHHHHTT..EEEEESS CS
                               DAO  2 vviiGGGiiGlstAyeLarrg..Vtllekg 29
                                      +viiGGG  G+ tA  La++g  Vtl+  +
  gi|385805654|ref|YP_005842052.1|  7 IVIIGGGAGGIITANILAEKGkdVTLISDS 36
                                      8*******************99****9765 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00017
                                       EHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHH..HHHTTCTTTSEE CS
                               DAO 144 dpakltaalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsd..llgllkeldlpi 217
                                       +p k+++ + + +  + v++++  +vt+++ +      +  +t+ g   ++++vV+a+Ga  +  l+   +  +   
  gi|385805654|ref|YP_005842052.1|  54 EPSKYIRTVEELLDPR-VKFIQD-KVTEVDLK---ERSI--KTEkGKSISYEKVVVATGASLNydLI---PGHR-EN 119
                                       5777777766666555.99***9.****9665...4566..444476556799*******9877444...2222.22 PP

                                       EEEEEEEEEE CS
                               DAO 218 spvrgqvlvl 227
                                       +   g ++ +
  gi|385805654|ref|YP_005842052.1| 120 YEKMGDYYST 129
                                       5566666666 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.2   0.00037      0.44       2      29 ..       7      34 ..       6      44 .. 0.90
   2 !   15.1   0.0     8e-06    0.0095     100     162 ..      61     118 ..      49     155 .. 0.79
   3 ?   -3.1   0.1       2.6   3.2e+03      95     142 ..     196     241 ..     192     245 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00037
                                      EEEE-SSHHHHHHHHHHHHTT--EEEEE CS
                              GIDA  2 viViGgGhAGceAAlaaarlGakvlLit 29
                                      +++iGgG  G+  A  +a++G +v+Li 
  gi|385805654|ref|YP_005842052.1|  7 IVIIGGGAGGIITANILAEKGKDVTLIS 34
                                      79************************94 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 8e-06
                                       HHHHHHHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT-BT-EEEETTEE CS
                              GIDA 100 evteklenepnleiieeeveeliveekkvkgvvtedgetikakavviatGtflkgkihigeke 162
                                       +v+e l   p ++ i+++v+e+++   k + ++te+g+ i+ ++vv+atG+ l+   + g++e
  gi|385805654|ref|YP_005842052.1|  61 TVEELL--DPRVKFIQDKVTEVDL---KERSIKTEKGKSISYEKVVVATGASLNYDLIPGHRE 118
                                       444444..479***********99...778899******************888777666654 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 2.6
                                       HHHHHHHHHHHHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEEC CS
                              GIDA  95 elyskevteklenepnleiieeeveeliveekkvkgvvtedgetikak 142
                                       +++sk+++ek+++  n++ ++    + i+  ++ k+v+ ++ge+++ +
  gi|385805654|ref|YP_005842052.1| 196 KEVSKAIEEKMKEFGNIDYRTSFLIDSID--NEKKVVRSATGEEVSFD 241
                                       67778888888888888877776655544..45555666666666555 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   1.0   4.8e-06    0.0057       2      31 ..       7      36 ..       6      39 .. 0.94
   2 !    6.7   0.0    0.0087        10      15      73 ..     171     230 ..     170     237 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.8e-06
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvvers 31
                                      +v++GgG  g+  A++lae gk+Vt++  s
  gi|385805654|ref|YP_005842052.1|  7 IVIIGGGAGGIITANILAEKGKDVTLISDS 36
                                      8**************************876 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0087
                                       HHHHHHTT..SEEEEEESSSSSSTTSSHHHHHHHHHHHHHT.TEEEECSEEEEEEEEETTS.E CS
                         Pyr_redox  15 Agalaelg..kkVtvversdkllrllDeeaskilqeklekn.gievllntkveeiegsedg.v 73 
                                       Ag+++e +   +V ++  ++++    ++e+sk+++ek+++  +i+ +++  + +i+ ++ + v
  gi|385805654|ref|YP_005842052.1| 171 AGYFKEKRadVRVELLYPAPHVY--GEKEVSKAIEEKMKEFgNIDYRTSFLIDSIDNEK-KvV 230
                                       67776655235778888888888..899***********9999*************555.434 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.3   7.2e-08   8.6e-05     165     277 ..       5     116 ..       2     133 .. 0.73
   2 ?   -3.7   0.0       4.6   5.5e+03     212     250 ..     200     233 ..     179     247 .. 0.56

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 7.2e-08
                       Pyr_redox_3 165 qkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdp.syslkpdienrleelvke...ekikvlfnaevke 237
                                       + +v+iGg+  ++ +A  l++kg++Vt++ +++ i+  +  +  +  k +  ++  + v+e    ++k++++ +v+e
  gi|385805654|ref|YP_005842052.1|   5 RGIVIIGGGAGGIITANILAEKGKDVTLISDSN-IHPFQPGYlFIAFKGHEPSKYIRTVEElldPRVKFIQD-KVTE 79 
                                       5689*************************9987.66665333033455444443333334456566998888.9999 PP

                       Pyr_redox_3 238 ikekeeeykvktedgkkvevkddvvlatGykpdlsflkks 277
                                       ++ ke++  +kte+gk++ ++++vv+atG + +++++  +
  gi|385805654|ref|YP_005842052.1|  80 VDLKERS--IKTEKGKSI-SYEKVVVATGASLNYDLIPGH 116
                                       9988665..889999875.6899*********99998754 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 4.6
                       Pyr_redox_3 212 pdienrleelvkeekikvlfnaevkeikekeeeykvkte 250
                                         ie++++e    ++i+  +   +++i+++++ ++  ++
  gi|385805654|ref|YP_005842052.1| 200 KAIEEKMKEF---GNIDYRTSFLIDSIDNEKKVVR--SA 233
                                       3444444443...4466666666666666554433..33 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.5     3e-06    0.0036       4      31 ..       7      34 ..       4      39 .. 0.92
   2 ?    3.6   0.0     0.028        33      83     138 ..     172     230 ..     124     242 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3e-06
                                      EEEE--SHHHHHHHHHHHHTTHHEEEEE CS
                     FAD_binding_3  4 VlIVGaGpaGlmlallLseaGvrvvlve 31
                                      ++I+G+G  G+++a++L+e+G +v+l+ 
  gi|385805654|ref|YP_005842052.1|  7 IVIIGGGAGGIITANILAEKGKDVTLIS 34
                                      68************************96 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.028
                                       C..CEEEEEHHCHHCST-CEE--HHHHHHHHHHHHHHHT.EEETCSEEEECCEECCCCC CS
                     FAD_binding_3  83 t..pkaradlelesspervtvypqteleriLvehaeerg.lqvrfktevesleqdeegv 138
                                          ++ rad+ +e  +++++vy+ +e+ ++++e+ +e g ++ r +  + s+ ++++ v
  gi|385805654|ref|YP_005842052.1| 172 GyfKEKRADVRVELLYPAPHVYGEKEVSKAIEEKMKEFGnIDYRTSFLIDSIDNEKKVV 230
                                       1347899999999**********************999988888776666665555544 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0   0.00035      0.42       2      47 ..       7      51 ..       6      66 .. 0.79
   2 !    7.1   0.0     0.002       2.4      96     145 ..      64     109 ..      58     123 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00035
                     Lycopene_cycl  2 vvviGaGpAglslAarlteakpglkvvlieaspsllfpnny.vWsde 47
                                      +v+iG+G+ g+  A+ l  a++g  v+li  s+  +f + y    + 
  gi|385805654|ref|YP_005842052.1|  7 IVIIGGGAGGIITANIL--AEKGKDVTLISDSNIHPFQPGYlFIAFK 51
                                      89***************..999*******888888887777444455 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.002
                     Lycopene_cycl  96 rlvengvklleakvesveeeeageslvvleggrkirarlvvdarglaslk 145
                                       +l + +vk+ + kv++v  +e    ++ +e g+ i    vv+a+g asl+
  gi|385805654|ref|YP_005842052.1|  64 ELLDPRVKFIQDKVTEVDLKER---SIKTEKGKSISYEKVVVATG-ASLN 109
                                       5677889999999998887776...9*******************.5554 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.6     5e-06    0.0059       3      31 ..       7      35 ..       5      39 .. 0.92
   2 ?    3.9   0.0     0.015        18     129     164 ..      74     106 ..      60     109 .. 0.77
   3 ?   -3.7   0.0       3.1   3.6e+03     111     159 ..     198     244 ..     195     245 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5e-06
                                      EEEE--SHHHHHHHHHHHHTT--EEEE-S CS
                       HI0933_like  3 viviGgGaAGlmaAisaakrgkrVlllek 31
                                      +++iGgGa G+ +A  +a++gk+V+l+  
  gi|385805654|ref|YP_005842052.1|  7 IVIIGGGAGGIITANILAEKGKDVTLISD 35
                                      89************************975 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.015
                                       S--EEEEECETTE.EEEEE.TTEEEEESEEEE---- CS
                       HI0933_like 129 etevksvekeedgkfrvktkseeeleadklvlAtGG 164
                                       + +v++v+ +e    ++kt+++++++ +k+v+AtG 
  gi|385805654|ref|YP_005842052.1|  74 QDKVTEVDLKE---RSIKTEKGKSISYEKVVVATGA 106
                                       56777775544...4599999************996 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 3.1
                                       HHHHHHHHHHH.HT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEE CS
                       HI0933_like 111 ivdallkelke.agvklrletevksvekeedgkfrvktkseeeleadklv 159
                                       + +a+++++ke  ++++r++  + s+++ e++   v+  ++ee++ d+l+
  gi|385805654|ref|YP_005842052.1| 198 VSKAIEEKMKEfGNIDYRTSFLIDSIDN-EKK--VVRSATGEEVSFDALI 244
                                       5566666776645677777777788733.222..3444458888888877 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.2   3.6e-06    0.0043       1      25 [.       9      33 ..       9      38 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.6e-06
                                      EE--SHHHHHHHHHHHCCTEEEEEE CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlll 25
                                      I+G+G++G  +A  La++g+dv+l+
  gi|385805654|ref|YP_005842052.1|  9 IIGGGAGGIITANILAEKGKDVTLI 33
                                      9**********************98 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 ?    4.5   0.1     0.026        31       1      20 [.       8      27 ..       8      45 .. 0.81
   2 !   10.7   0.0   0.00033      0.39     115     155 ..      68     106 ..      56     107 .. 0.83
   3 ?   -2.6   0.0       4.2     5e+03     131     151 ..     225     245 ..     200     245 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.026
                     NAD_binding_9  1 aivGaGprGlavlerLlara 20
                                      +i+G+G+ G+ +++ L+++ 
  gi|385805654|ref|YP_005842052.1|  8 VIIGGGAGGIITANILAEKG 27
                                      7***********99998885 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00033
                     NAD_binding_9 115 vtvevhraevvdleeradgqavlladgaslaadaVvLAlGh 155
                                        +v++++++v++++ ++++  + +++g+s+ +++Vv+A+G 
  gi|385805654|ref|YP_005842052.1|  68 PRVKFIQDKVTEVDLKERS--IKTEKGKSISYEKVVVATGA 106
                                       389***********99876..799***************95 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 4.2
                     NAD_binding_9 131 adgqavlladgaslaadaVvL 151
                                       +++  v+ a+g+++ +da+++
  gi|385805654|ref|YP_005842052.1| 225 NEKKVVRSATGEEVSFDALIM 245
                                       344578889999999999886 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   0.6   9.9e-06     0.012       2      30 ..       7      35 ..       6      40 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 9.9e-06
                                      EEEE--SHHHHHHHHHHHHTTT-EEEEES CS
                     FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvek 30
                                      +++iG+G++G   A  +ae+G++v++++ 
  gi|385805654|ref|YP_005842052.1|  7 IVIIGGGAGGIITANILAEKGKDVTLISD 35
                                      79************************986 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.4   8.2e-06    0.0098       2      42 ..       7      44 ..       6      49 .. 0.92
   2 ?   -3.3   0.0       2.4   2.9e+03     169     208 ..      70     105 ..      66     108 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 8.2e-06
                                      EEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS---SS- CS
                    Trp_halogenase  2 ivivGGGtaGwlaAaalakalkgklevtlveseeigtvgvG 42
                                      ivi+GGG  G ++A++la+ +    +vtl+  ++i + + G
  gi|385805654|ref|YP_005842052.1|  7 IVIIGGGAGGIITANILAEKG---KDVTLISDSNIHPFQPG 44
                                      9*******************9...57********9998887 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.4
                                       -EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SG CS
                    Trp_halogenase 169 vtrvegkvvevqldedgrveslrledgreveadlfiDcsG 208
                                       v+ +++kv+ev+l+e+    s+++e+g++++++ ++ ++G
  gi|385805654|ref|YP_005842052.1|  70 VKFIQDKVTEVDLKER----SIKTEKGKSISYEKVVVATG 105
                                       6777777777777774....67777788888877777776 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.6   1.7e-05      0.02       2      32 ..       7      37 ..       6      39 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.7e-05
                      FAD_oxidored  2 vvVvGGgpaGvaAAiaAaraGakvlLveerg 32
                                      +v++GGg++G++ A   a++G+ v L+++++
  gi|385805654|ref|YP_005842052.1|  7 IVIIGGGAGGIITANILAEKGKDVTLISDSN 37
                                      8**************************9875 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 ?   13.5   0.0   6.4e-05     0.076       7      46 ..       4      78 ..       2     151 .. 0.72
   2 ?   -2.5   0.0       5.9     7e+03      72      84 ..     196     208 ..     174     239 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.4e-05
                     NAD_binding_7  7 gkkvlvvGgGevAarkvrklleagakvtvvapev.keele.....................................e 46
                                      ++ ++++GgG  +   ++ l+e+g++vt+++    +   +                                      
  gi|385805654|ref|YP_005842052.1|  4 KRGIVIIGGGAGGIITANILAEKGKDVTLISDSNiH---PfqpgylfiafkghepskyirtveelldprvkfiqdkvT 78
                                      6779***************************99532...133566666666666666666666555543333333332 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.9
                     NAD_binding_7  72 relneriaeaaka 84 
                                       +e++++i e++k+
  gi|385805654|ref|YP_005842052.1| 196 KEVSKAIEEKMKE 208
                                       3444444444333 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   6.5e-05     0.077       1      31 [.       7      37 ..       7      64 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.5e-05
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr 31
                                      i+i+G Ga G + a  La++g dvtli  s+
  gi|385805654|ref|YP_005842052.1|  7 IVIIGGGAGGIITANILAEKGKDVTLISDSN 37
                                      89*************************9888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 2476.04
//
Query:       gi|385805655|ref|YP_005842053.1|  [L=78]
Description: SirA family protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-20   72.1   0.0    2.7e-20   71.9   0.0    1.0  1  TusA      Sulfurtransferase TusA


Domain annotation for each model (and alignments):
>> TusA  Sulfurtransferase TusA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.9   0.0   1.5e-24   2.7e-20       1      69 [.       5      73 ..       5      74 .. 0.96

  Alignments for each domain:
  == domain 1  score: 71.9 bits;  conditional E-value: 1.5e-24
                                      EEEEBTT-STTCCHHHHHHHHCCCGCT-EEEEEESSCHHHHHHHHHHHHHTEEEEEEE-GCC-EEEEEE CS
                              TusA  1 ielDlrGlvCPePllklkkalekleegevlevladdpaatediprfakklghelveveeedgeyrivir 69
                                      +++D+rG++CP+P+ kl +a ++++ g+++e la+d++++ed++++++++g++l+e + e++++r +i+
  gi|385805655|ref|YP_005842053.1|  5 KVVDARGMACPGPISKLTRAYREAKNGDIIEALATDKGFIEDVKAWCQSTGNKLLELKVEGDVIRATIE 73
                                      579******************************************************999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); 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 0.34s 00:00:00.84 Elapsed: 00:00:00.54
# Mc/sec: 431.92
//
Query:       gi|385805656|ref|YP_005842054.1|  [L=137]
Description: hypothetical protein FFONT_0612 [Fervidicoccus fontis Kam940]
Scores for complete 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-11   41.9   0.2    1.1e-07   31.9   0.0    2.0  2  DrsE_2    DsrE/DsrF/DrsH-like family
    6.5e-07   29.7   0.0    9.8e-07   29.1   0.0    1.4  1  DrsE      DsrE/DsrF-like family


Domain annotation for each model (and alignments):
>> DrsE_2  DsrE/DsrF/DrsH-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.1   0.00011      0.99       5      39 ..       7      41 ..       3      69 .. 0.81
   2 !   31.9   0.0   1.2e-11   1.1e-07      77     145 ..      60     129 ..      43     135 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00011
                                      EEEEE----H.HHHHHHHHHHHHHHTT-EEEEEE- CS
                            DrsE_2  5 laiifskgtldkalaalilAsgAaalglevtiFft 39
                                      l+ii+  g+ +  +   +l  +Aa+lg+ v++F t
  gi|385805656|ref|YP_005842054.1|  7 LSIIIARGQAENFISLGVLTYTAANLGVPVKVFVT 41
                                      67888899998888888*****************9 PP

  == domain 2  score: 31.9 bits;  conditional E-value: 1.2e-11
                                       -GGGHHHHHHHHHHHHCT---HHHHHHHHHHT.T-EEEEEHHHHHHHT--GGGB-TT-.EEE-HHHHHHHH CS
                            DrsE_2  77 nmagigtkmmkkvmkekgvasleeLleaakea.gvklvaCqmtmdlmglkkeelidgv.eiagaatylkea 145
                                       ++++ ++km +  m++ + +s  ++l++ake  +vk+++C mt + +g+k+e+  + v ei+ga+ +l + 
  gi|385805656|ref|YP_005842054.1|  60 EFEDYAKKMFE-GMEKLKSPSWYDMLKEAKEVgEVKIYGCSMTAEALGVKREDWDPLVdEIVGATFFLTQT 129
                                       56777777776.57888899**********9736************************9999999998764 PP

>> DrsE  DsrE/DsrF-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   1.1e-10   9.8e-07      24     115 ..      26     135 ..       9     137 .] 0.83

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 1.1e-10
                                       HHHHHTTT-EEEEEE-GGGGGGGBS..................---TGGGTS---GGGGGGCGGGT.-EEEEEHHHH CS
                              DrsE  24 alaaaalghevsvffygdGvllllk..................gqtanpadeknlaellkalkeyg.vklyvCgqaa 81 
                                        + aa+lg  v+vf++g +v +++k                   +  ++ ++++ +++lk++ke g vk+y C ++a
  gi|385805656|ref|YP_005842054.1|  26 TYTAANLGVPVKVFVTGLAVPYFTKnkpelrpskefedyakkmFEGMEKLKSPSWYDMLKEAKEVGeVKIYGCSMTA 102
                                       56789999************************99999999999666677778999*********888********** PP

                                       HHTT--GGGE-T--EEEE-HHHHHHHHHH-SEEE CS
                              DrsE  82 kargldededlgvgvevsglgelaelqnegdrvi 115
                                       +a g++ +++  +  e++g+ ++   q +gd vi
  gi|385805656|ref|YP_005842054.1| 103 EALGVKREDWDPLVDEIVGA-TFFLTQTKGDTVI 135
                                       ******87755234556655.5555566666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 827.46
//
Query:       gi|385805657|ref|YP_005842055.1|  [L=594]
Description: phosphoenolpyruvate carboxykinase-like protein [Fervidicoccus fontis Kam940]
Scores for complete 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   53.9   0.0      3e-13   49.3   0.0    2.2  2  PEPCK_ATP  Phosphoenolpyruvate carboxykinase


Domain annotation for each model (and alignments):
>> PEPCK_ATP  Phosphoenolpyruvate carboxykinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.3   0.0   1.7e-17     3e-13      68     294 ..      83     336 ..      64     363 .. 0.84
   2 !    2.3   0.0     0.003        55     420     464 ..     502     545 ..     493     546 .. 0.86

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 1.7e-17
                                       HHHHHHHHHHHHHHHHTS.-EEEEEEEE-S.STTT-EEEEEEES-HHHHHHHH..HHSBGGS-S-TTT---SEEEEE CS
                         PEPCK_ATP  68 eekfealkekvleylkek.elyvvdafaga.dpkyrlkvrviterawqalfvk..nllirpteeeleefepdftiln 140
                                       + +++ l+ +vle++  +  ++ vd+ +g+ ++k+r+++rv++++++  l  +  +l++  ++e+    + d t++ 
  gi|385805657|ref|YP_005842055.1|  83 K-EHKLLMLRVLEHILAQgPMIRVDGAYGSpNSKVRMHIRVYVDTQFPDLAYRwkQLVFDVDKES----KVDATLFV 154
                                       3.44555666666665555999***9998747899************999877558888877766....78999999 PP

                                       ETT----HHHH--SSS-EEEEETTTTEEEEES---THHHHHHHHHHHHHHHHHTT-EEEEEEEEE......-T.TS- CS
                         PEPCK_ATP 141 apefkadpekdglnsetvvalnlekklvlilgteYaGEikKsifsvmnyllpkkgvlsmhcsanv......gekkgd 211
                                       +p++  +p+  g  +  +v+    ++ ++i+ ++Y GEikK+ +    +   k+g+ + h++         +e+ + 
  gi|385805657|ref|YP_005842055.1| 155 VPHYLGNPNIPGSDKLLAVIRFPFQNFTIITLSSYQGEIKKGALCHWIFHAYKQGCTGEHAALREfsvrtvEESWKR 231
                                       ************99999999888999***********************************9886666666444445 PP

                                       EE.EEEE-TTSSHHHHH......................-BTTB-EEESSEEEE-SS-EEES-SEEEEE-TT--TTT CS
                         PEPCK_ATP 212 va.lfFGLSGtGKTtLs......................adperkligdDehgwsdegvfniegGcYaKtidLskek 265
                                       v    +GL+G+GK t                          +++++  dD +++ ++ v++ e G + Kt+dL+ + 
  gi|385805657|ref|YP_005842055.1| 232 VVlAIWGLTGSGKSTHGfymwteknaplyvknfgtnpldYVKDQEVKNDDIVAICEDRVYGSELGAWTKTEDLTPDM 308
                                       542689*********9999***************88876445666677888889999*******************9 PP

                                       SHHHHHHHSTT-EEES-EE-TTT--EETT CS
                         PEPCK_ATP 266 epeiynairfgavlENvvldeetrevdfd 294
                                       e     a +  a+ EN+ +de ++++ f+
  gi|385805657|ref|YP_005842055.1| 309 EAMWNGAFSSRALHENTEFDE-NGNPSFE 336
                                       998888999**********86.5667776 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.003
                                       SEE--HHHHHHHHHHHHTTCCCTS-EEE-TTT-..-EEES-BTTC-G CS
                         PEPCK_ATP 420 gkrislkatraiikaildgeleavefekdpvfg..levptevpgvps 464
                                       g+r ++++t   + ++++g +   e++ +pv+g  + vp++vpg+++
  gi|385805657|ref|YP_005842055.1| 502 GERPTIEETEFFLLQATRGAV---EYKPHPVWGekVLVPKHVPGIKD 545
                                       89999**************99...89******844668******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (594 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); 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: 0.69u 0.34s 00:00:01.03 Elapsed: 00:00:00.55
# Mc/sec: 3262.04
//
Query:       gi|385805658|ref|YP_005842056.1|  [L=254]
Description: hypothetical protein FFONT_0614 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-47  160.3  12.9    7.1e-47  159.6  12.9    1.3  1  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 !  159.6  12.9     4e-51   7.1e-47       2     169 ..      66     248 ..      65     249 .. 0.87

  Alignments for each domain:
  == domain 1  score: 159.6 bits;  conditional E-value: 4e-51
                           DUF1614   2 lgslinipvaelkske.el.ve...vkvlgisykvpvleeeekktvvavNvGGaviPlllslylllrlavs....ll 69 
                                       + s++ni++ +++ +   + +e   v+++gi+++v +   +++++v+a+N+GGaviP+++s+ ll+rl+++    ++
  gi|385805658|ref|YP_005842056.1|  66 VFSFMNIVIRRIRLEGfFYtIEsryVYFMGIPFPVYYPVYQRREIVIAINIGGAVIPITFSALLLARLYCMsslyFI 142
                                       689***********8754334479999****9999555555577************************98889999* PP

                           DUF1614  70 aallavlivaavvyllarpvpgvGivvpllipplvaalaalllaeeea.aavaYisgvlGtLiGadllnl.....kk 140
                                        al++++i++++++l++r+vp+vGi++p lipplv+ ++al++  +++ ++vaY++gvlG+LiGad+l+l     k 
  gi|385805658|ref|YP_005842056.1| 143 DALIVIAITSIITFLISRTVPNVGIATPSLIPPLVSGISALAICGTNYiFPVAYVGGVLGSLIGADVLRLskdfsKF 219
                                       ****************************************655555555*********************9555444 PP

                           DUF1614 141 ieklgapvvsIGGaGtFdGifltgilavl 169
                                       +++lg  ++sIGGaGtFdG+fl+gi+a++
  gi|385805658|ref|YP_005842056.1| 220 THQLGPVFLSIGGAGTFDGVFLSGIIAAI 248
                                       4556777********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       789  (0.0440069); 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:                         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 0.35s 00:00:00.92 Elapsed: 00:00:00.55
# Mc/sec: 1402.72
//
Query:       gi|385805659|ref|YP_005842057.1|  [L=151]
Description: ribosomal protein-alanine acetyltransferase RimI-like protein [Fervidicoccus fontis Kam940]
Scores for complete 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   76.5   0.2    2.3e-21   76.2   0.2    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    1.3e-17   64.0   0.1    1.6e-17   63.6   0.1    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    2.1e-15   56.9   0.2    2.7e-15   56.5   0.2    1.1  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    5.8e-10   39.0   0.1    7.9e-10   38.6   0.1    1.1  1  FR47             FR47-like protein
    1.1e-07   32.1   0.1    1.5e-07   31.7   0.1    1.2  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    1.2e-07   31.5   0.0    1.4e-07   31.2   0.0    1.1  1  PanZ             Acetyltransferase (GNAT) domain, PanZ
    4.5e-05   23.0   0.2    5.1e-05   22.8   0.2    1.2  1  Acetyltransf_15  Putative acetyl-transferase
    4.5e-05   23.5   0.0    0.00013   22.0   0.0    1.9  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
    7.9e-05   23.3   0.0    8.9e-05   23.2   0.0    1.1  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
    0.00021   21.0   0.0    0.00029   20.5   0.0    1.3  1  Acetyltransf_8   Acetyltransferase (GNAT) domain
      0.002   18.2   0.1     0.0034   17.5   0.1    1.5  1  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 !   76.2   0.2   1.4e-24   2.3e-21       3     117 .]      19     128 ..      14     128 .. 0.82

  Alignments for each domain:
  == domain 1  score: 76.2 bits;  conditional E-value: 1.4e-24
                                       HHHHHHHHHTHHHHHHHHHHH.HHHH.HHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSH CS
                    Acetyltransf_1   3 dlvellvesffppnedaseee.fees.fsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGl 77 
                                       +++e++  sf    ++ ++ + +  s + l +e +l+a+++++++G+i +++  +   ++++i s+aV+ eyrg+G+
  gi|385805659|ref|YP_005842057.1|  19 EVYEIELSSF----PRYPYSIsVLVSfLTLFPELFLIARHEERIVGYIAGFMEKE---DRGHIASIAVRQEYRGRGI 88 
                                       4555555554....44444444333303336666777****************99...9****************** PP

                                       HHHHHHHHHHHHHHTTESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  78 GsaLlealeerareegikkivlaveedndaairlYeklGF 117
                                       G++Lle+ e ++r+  +k++vl+v+e+n+ airlY+ +G+
  gi|385805659|ref|YP_005842057.1|  89 GRKLLEEEENKMRNLDVKEVVLEVSENNEVAIRLYTSMGY 128
                                       ***********************************99*98 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.6   0.1     1e-20   1.6e-17      32     126 ..      48     150 ..      44     151 .] 0.86

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 1e-20
                   Acetyltransf_10  32 lllvaeeggkivGvi....elrdgshisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yavpfYe 102
                                       l+l+a  +++ivG+i    e +d++hi+ ++V++eyrg+Gig++Lle+ e+++++ + k+  l+v +++  a+++Y 
  gi|385805659|ref|YP_005842057.1|  48 LFLIARHEERIVGYIagfmEKEDRGHIASIAVRQEYRGRGIGRKLLEEEENKMRNLDVKEvVLEVSENNeVAIRLYT 124
                                       58999999****9996533335555********************************************9******* PP

                   Acetyltransf_10 103 klGFkav..geeqeenGirfvpMeke 126
                                       ++G+k++   ++ + +G     M+k+
  gi|385805659|ref|YP_005842057.1| 125 SMGYKKIkrVKNYYPDGSAAFIMKKT 150
                                       *******6666677788888888776 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.5   0.2   1.7e-18   2.7e-15       4      76 .]      48     130 ..      45     130 .. 0.76

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 1.7e-18
                                       EEEEEEETTEEEEEEEEEEES...TCTEEEEE-GGGTTSSHHHHHHHHTT...SEEE.EE.EEEE..THHHHHHHHH CS
                    Acetyltransf_7   4 evfVaeddgkivGfialslld...aeitrlaVdpeyrgkGiGraLleaae...kgii.le.qlel..naekaikfYe 70 
                                        +++a+++++ivG+ia   ++   ++i  +aV++eyrg+GiGr+Lle +e   +++   e +le+  n+e ai++Y 
  gi|385805659|ref|YP_005842057.1|  48 LFLIARHEERIVGYIAGFMEKedrGHIASIAVRQEYRGRGIGRKLLEEEEnkmRNLDvKEvVLEVseNNEVAIRLYT 124
                                       6899************9999988777777*****************9733344332231223333434459****** PP

                                       HTTEEE CS
                    Acetyltransf_7  71 klGFee 76 
                                       ++G+++
  gi|385805659|ref|YP_005842057.1| 125 SMGYKK 130
                                       ****85 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   0.1   4.8e-13   7.9e-10      10      81 ..      60     132 ..      53     138 .. 0.88

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 4.8e-13
                                       --EEEEEEE-TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHH.S-S-EEEEEETT-HHHHHHHHHHT-EEEE CS
                              FR47  10 gelaawilrkdggelgalqvlpehrrrGlgsrlvkalakeiae.rgktvllvvvasNtpsirlyeklGfekie 81 
                                       g +a+ + ++d g + ++ v++e r+rG g++l ++  +++++   k+v+l v ++N+ +irly+++G++ki+
  gi|385805659|ref|YP_005842057.1|  60 GYIAGFMEKEDRGHIASIAVRQEYRGRGIGRKLLEEEENKMRNlDVKEVVLEVSENNEVAIRLYTSMGYKKIK 132
                                       556677788888*******************************88899999********************93 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.1   8.9e-11   1.5e-07      51     145 ..      48     139 ..      31     147 .. 0.92

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 8.9e-11
                    Acetyltransf_4  51 vflvae.sdrivGyaylgqfkkrakdwkaelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensi 126
                                       +fl+a  ++rivGy ++  ++k  +d   + s+ + ++  + +g+gr+l++  e+ +++  +++ + e+  +ne +i
  gi|385805659|ref|YP_005842057.1|  48 LFLIARhEERIVGYIAGF-MEK--EDRGHIASIAV-RQEYRGRGIGRKLLEEEENKMRNLDVKEVVLEVSENNEVAI 120
                                       6999999*******9988.888..99999******.589************************************** PP

                    Acetyltransf_4 127 qfhkalGFelvgifkkcik 145
                                        ++ ++G+++ +++k+++ 
  gi|385805659|ref|YP_005842057.1| 121 RLYTSMGYKKIKRVKNYYP 139
                                       ***************9986 PP

>> PanZ  Acetyltransferase (GNAT) domain, PanZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   8.9e-11   1.4e-07      12     120 ..      11     128 ..       3     138 .. 0.69

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 8.9e-11
                              PanZ  12 aqdkiDLakIy..........paqsaealeaalte.egalfaarFNdRlLgAvkvele.dkeaelsdlcVRevTRrR 76 
                                       +   +DL+ +y          p++  + l + lt   + +++ar  +R  g ++  +e ++ +++ ++ VR++ R R
  gi|385805659|ref|YP_005842057.1|  11 SASMRDLKEVYeielssfpryPYSI-SVLVSFLTLfPELFLIARHEERIVGYIAGFMEkEDRGHIASIAVRQEYRGR 86 
                                       5667788888888888886645444.4444444441555679*********98865550569*************** PP

                              PanZ  77 GVgsyLleearrqa..Pevkswvlaeedvkeldlavlqaflealgf 120
                                       G+g++Llee  +++   +vk+ vl  ++    +++v+ ++ +++g+
  gi|385805659|ref|YP_005842057.1|  87 GIGRKLLEEEENKMrnLDVKEVVLEVSE----NNEVAIRLYTSMGY 128
                                       *******888877722455555555444....33455555566666 PP

>> Acetyltransf_15  Putative acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.2   3.1e-08   5.1e-05      64     144 ..      54     136 ..       9     148 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 3.1e-08
                   Acetyltransf_15  64 s.........silieknvleiYtlyvsekyrgkGlakklLeeslkelkknYkvdnelllaLHlnpkDksMnisfalY 131
                                       +          ++++++   i ++ v ++yrg+G+ +klLee  +++    ++d  + ++L ++++    +++ +lY
  gi|385805659|ref|YP_005842057.1|  54 HeerivgyiaGFMEKEDRGHIASIAVRQEYRGRGIGRKLLEEEENKM---RNLD-VKEVVLEVSENN---EVAIRLY 123
                                       4555555665788888888999********************94433...3344.66799****987...69***** PP

                   Acetyltransf_15 132 yslgFrkglfvks 144
                                        s+g++k+  vk+
  gi|385805659|ref|YP_005842057.1| 124 TSMGYKKIKRVKN 136
                                       *******987775 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   8.1e-08   0.00013      74     127 ..      72     130 ..      11     131 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 8.1e-08
                                       EEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--.....SSHHHHHTTT-EE CS
                    Acetyltransf_9  74 agvtgVavapehrgrgvlskLlaraleemreegqplsllfP.....ssipiYrrfGyei 127
                                       + ++++av  e+rgrg+ +kLl++  ++mr  +++ ++l        +i++Y ++Gy++
  gi|385805659|ref|YP_005842057.1|  72 GHIASIAVRQEYRGRGIGRKLLEEEENKMRNLDVKEVVLEVsenneVAIRLYTSMGYKK 130
                                       6899***************************99999999986766656799*****986 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   5.5e-08   8.9e-05      56     138 .]      49     129 ..      14     129 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 5.5e-08
                    Acetyltransf_3  56 waivlkdtgv.iGsv.glrdleeedeeaelg.ymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSi 129
                                       ++i  ++++  +G++ g+ + e++   +++  + ++++++g+G+++  ++   + + ++l+++++v +++++Ne  i
  gi|385805659|ref|YP_005842057.1|  49 FLIA-RHEERiVGYIaGFMEKEDR---GHIAsIAVRQEYRGRGIGRKLLEEEENKM-RNLDVKEVVLEVSENNEVAI 120
                                       6674.555444****777766665...66664778899**************9999.9999**************** PP

                    Acetyltransf_3 130 rvleklGfe 138
                                       r+++++G++
  gi|385805659|ref|YP_005842057.1| 121 RLYTSMGYK 129
                                       *******86 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   1.8e-07   0.00029      75     143 ..      66     134 ..      46     136 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.8e-07
                                       --TT-EEEEEEES.SHHHCTTTCHHHHHHHHHHHHHCCTT--EEEE--BTT-HHHHHHHHHTT-EEEEEE CS
                    Acetyltransf_8  75 aepgdrGiHllig.eaeargkglttallralvhylfadprtrrvvvEPdvrNerairllekaGfekekev 143
                                       +e+ drG    i+  +e+rg+g++++ll++  + +  + +++ vv+E + +Ne airl+ ++G++k k+v
  gi|385805659|ref|YP_005842057.1|  66 MEKEDRGHIASIAvRQEYRGRGIGRKLLEEEENKMR-NLDVKEVVLEVSENNEVAIRLYTSMGYKKIKRV 134
                                       478899999999978899***********9877765.447**************************9987 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   2.1e-06    0.0034      16      54 ..      64     101 ..      49     111 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.1e-06
                   Acetyltransf_CG  16 eYevrkegvldfthTeVpeelrGkGiAkkLvkaalddar 54 
                                        +  +ke++ ++  + V +e+rG+Gi++kL ++  +++r
  gi|385805659|ref|YP_005842057.1|  64 GFM-EKEDRGHIASIAVRQEYRGRGIGRKLLEEEENKMR 101
                                       554.78889999******************998666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 898.75
//
Query:       gi|385805660|ref|YP_005842058.1|  [L=146]
Description: hypothetical protein FFONT_0616 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-07   31.9   0.0    2.2e-07   31.1   0.0    1.4  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 !   31.1   0.0   1.2e-11   2.2e-07       2      88 ..      50     137 ..      49     144 .. 0.84

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 1.2e-11
                                       TSCB-STCCC-SEEEEEEESSSCEE...EEEEEE.GCCCTSSCSSTHHHHHHHHTT-SEEEESSSCHHHHHHHCTTT CS
                     Nitro_FeMo-Co   2 gsrvdqhFGrapyFaiyeveegevk...ivenrveeaadaegggggklaqllaeegvdvvivgkiGpralakleaag 75 
                                       +s+ d+   ++ ++a+ + + +evk   +v n+    ++ +gg g+ +a+++ ++ +d++++g+iG + ++++++ +
  gi|385805660|ref|YP_005842058.1|  50 ESTYDPFLNHSNFLAVLDFSGDEVKsvrFVRNE---ISNLRGGVGIGIAKWIVDNRADAIVAGRIGYHVQEAMDKMK 123
                                       6778888999*********97766543366777...999************************************** PP

                                       SEEEES.-SSBHHH CS
                     Nitro_FeMo-Co  76 ievykg.aggtvee 88 
                                       i++++     ++++
  gi|385805660|ref|YP_005842058.1| 124 IKIIECyNPLQLKD 137
                                       ****9766555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 978.26
//
Query:       gi|385805661|ref|YP_005842059.1|  [L=159]
Description: phenylacetic acid degradation protein paaI [Fervidicoccus fontis Kam940]
Scores for complete 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-16   58.5   0.0    8.1e-16   58.1   0.0    1.2  1  4HBT      Thioesterase superfamily
     0.0073   16.6   0.0     0.0087   16.3   0.0    1.1  1  4HBT_3    Thioesterase-like superfamily


Domain annotation for each model (and alignments):
>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.1   0.0   9.1e-20   8.1e-16       2      79 .]      71     148 ..      70     148 .. 0.97

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 9.1e-20
                                       SSB-HHHHHHHHHHHHHHHHHHTTSTTEEEEEEEEEEEESS-.BBTTCEEEEEEEEEEEESSEEEEEEEEEETTSCE CS
                              4HBT   2 GvvhgGvylallDeaagaalrslggrgilvvvvelsidflrp.vrlgdeltvearvlrlgrtsavvevevrdedgrl 77 
                                       G +hgG +++l+D+++++a++s + +    v+ el+i++l p    g+++tve++v+++g++s+v+ v+++++++++
  gi|385805661|ref|YP_005842059.1|  71 GSIHGGIIATLIDQVGAIAAWSTHMS-EQQVTMELKINYLLPmLESGSPFTVEGSVVHAGKRSIVTLVTIKSSKDET 146
                                       89************************.***************9999****************************998 PP

                                       EE CS
                              4HBT  78 va 79 
                                       va
  gi|385805661|ref|YP_005842059.1| 147 VA 148
                                       75 PP

>> 4HBT_3  Thioesterase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   9.7e-07    0.0087       6      85 ..      68     156 ..      63     159 .] 0.77

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9.7e-07
                                       ECTTC.-HHHHHHH.....HHHHHHHT.-S.SS.EEEEEEE-S---SE..EEEEEEEEEE--SS-EEEEEEE.EETT CS
                            4HBT_3   6 tpggagyGGyvlAl.....alraaqrtvpdprl.hslhvyFlrpgdag..pviyhvervrdGrsfstrtvel.sqgg 73 
                                       +p+g ++GG ++ l     a++a  +++++ ++   l +++l+p  ++  p++++  +v  G++  +  v++ s ++
  gi|385805661|ref|YP_005842059.1|  68 NPDGSIHGGIIATLidqvgAIAAWSTHMSEQQVtMELKINYLLPMLESgsPFTVEGSVVHAGKRSIVTLVTIkSSKD 144
                                       577779****9999333333444447775544578*********876449**********************55569 PP

                                       EEEEEEEEEEE- CS
                            4HBT_3  74 rpiftatasfgr 85 
                                       +++++at ++ +
  gi|385805661|ref|YP_005842059.1| 145 ETVAIATGTWYK 156
                                       999**9999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       843  (0.0470188); expected 358.6 (0.02)
Passed bias filter:                      699  (0.0389871); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1157.64
//
Query:       gi|385805662|ref|YP_005842060.1|  [L=400]
Description: exopeptidase, family M19 [Fervidicoccus fontis Kam940]
Scores for complete 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-70  238.1   0.0    1.6e-70  237.8   0.0    1.0  1  Peptidase_M19  Membrane dipeptidase (Peptidase family M19)


Domain annotation for each model (and alignments):
>> Peptidase_M19  Membrane dipeptidase (Peptidase family M19)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  237.8   0.0   8.9e-75   1.6e-70      44     318 ..      93     396 ..      67     397 .. 0.91

  Alignments for each domain:
  == domain 1  score: 237.8 bits;  conditional E-value: 8.9e-75
                                       HHTEEEEEEEEE--C...CCCCCCHHHHHHHHHHHHHHHHHHGTTTEEE-SSHHHHHHHHHTT-EEEEEEEESCGGG CS
                     Peptidase_M19  44 aggvsavlfaifvpe...dasyeeavkatleqidlirrlvrknpeqlklvrtaddierakkegkiavllgiegaeal 117
                                       a+g++av+ + +  e      ++ +++ ++ qi  i++ v  +++ + + r+++diera++egkia++l++e a ++
  gi|385805662|ref|YP_005842060.1|  93 ASGLDAVFENMMDGEtytYSPDSWSWENQVFQIGMIQSDVD-HQDMVFIGRRVEDIERAHNEGKIAMILSLESAPSI 168
                                       55555555555533334444667789999999******999.5566******************************* PP

                                       TT-HHHHHHHHHTTEEEEES-SSS-BSSB-BCCGTT.SSSSB-HHHHHHHHHHHHHT-EEE-TTB-HHHHHHHHHH- CS
                     Peptidase_M19 118 gddlallrafyalGvrvlgltynrnnkfAdgaleekdedgGLsefGkelVrelNrlgiliDlShlsektfldvlelS 194
                                       gdd+a+++a+y lGvrv+g +y +nn+f++g +++  +d+GL+++G  l++++N+lgiliD+Sh++++t ++++e S
  gi|385805662|ref|YP_005842060.1| 169 GDDIAKIDALYGLGVRVMGVVYGNNNEFGSGLTSK--KDNGLTDLGYGLIERCNKLGILIDVSHAGDRTGMEAVEAS 243
                                       **********************************9..**************************************** PP

                                       SSE.EECCEEBTTTS--TTSB-HHHHHHHHHTT-EEEE-SSHHH..CTTTS--BHHHHHHHHHHHHHHT-GGGEEE- CS
                     Peptidase_M19 195 kaPvvaSHSnaralcdhpRNltDeqlkaiaesgGvvgvtfvpaf..lkekaeatledvvdhidyivelaGidhVGlG 269
                                       k Pvv++H+ aral + +R  +De + aiae+gG++g+ ++p+    k+++  ++e+v++h +y+ +l+GidhV++G
  gi|385805662|ref|YP_005842060.1| 244 KYPVVVTHAGARALWPTRRMKPDELIHAIAEKGGFFGIEAAPHStlTKNHPVHSIESVMEHFQYVEKLVGIDHVAFG 320
                                       *****************************************99863455599************************* PP

                                       --TTTTSS-...........................BBTBSSGGGHHHHHHHHHHTTS-HHHHHHHHTHHHHHHHH CS
                     Peptidase_M19 270 sDfdgggel...........................pegledvsklpnltaeLlrrgyseadiekilggNflrvle 318
                                        D   g+ +                           ++gle++s+++n++ +++++gys+++i+k +ggN++rvl+
  gi|385805662|ref|YP_005842060.1| 321 PDTLFGDHVayhkifggasalkalydlapnfksveyVDGLENPSEFSNIIRWMIKNGYSDEEISKAVGGNVIRVLK 396
                                       **84444345789*************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 2383.47
//
Query:       gi|385805663|ref|YP_005842061.1|  [L=501]
Description: family 2 glycosyltransferase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-26   93.8   0.0    1.9e-26   93.4   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    3.3e-25   89.2   0.9    3.3e-25   89.2   0.9    2.8  3  Glyco_trans_2_3  Glycosyl transferase family group 2
    1.2e-17   64.2   0.0    1.9e-17   63.6   0.0    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
    3.5e-16   59.2   0.0    5.3e-16   58.6   0.0    1.2  1  Glyco_transf_21  Glycosyl transferase family 21
      2e-06   27.5   0.1    4.1e-06   26.5   0.1    1.5  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
    3.3e-05   22.6  14.1    0.00023   19.8  10.9    2.7  2  Cellulose_synt   Cellulose synthase
  ------ inclusion threshold ------
       0.25   11.4   0.2       0.52   10.4   0.2    1.5  1  SapB_1           Saposin-like type B, region 1


Domain annotation for each model (and alignments):
>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.4   0.0   7.4e-30   1.9e-26       4     230 .]      73     296 ..      70     296 .. 0.87

  Alignments for each domain:
  == domain 1  score: 93.4 bits;  conditional E-value: 7.4e-30
                   Glyco_tranf_2_3   4 lavlVptfneed.vlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksral 79 
                                       +a +V+++ne++  ++e+l s+ +  ++r ev++ +d  ++e +e+++     ++++++++v+++++ g   k+ a+
  gi|385805663|ref|YP_005842061.1|  73 IAAFVTSYNEDPkIVEETLLSVKSALRGRGEVFLLDDSTKKEIAEELKN---FCEKNGITYVHRENRKG--FKAGAI 144
                                       899********96677788888775579**************7776666...69999*******99777..599*** PP

                   Glyco_tranf_2_3  80 nealravk..sdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfll.nrstlvsalgalefaerhlrflaarr 153
                                       n+al+ +   +dlv ++D+D +   d+++ + ++f +pkvg+v+ p++    rs+     ga +f+++ + +  +  
  gi|385805663|ref|YP_005842061.1| 145 NNALKLYGdkYDLVSIFDADQRPRSDYFDHIIPYFSDPKVGFVQIPQRYTeTRSKIAH--GA-KFQQEPFLRVIMKG 218
                                       ******876699********************************99966515665554..44.88899998999998 PP

                   Glyco_tranf_2_3 154 algv.ltlnGsgslirrevlkelegldplflltdDyelglrlrragfrtayvpgaavrevfp.sslkayikqrnRwv 228
                                       +  v +++ Gsg+ +r + +++ + +d+ + +t+D+e+++r+  +g+++ y+ + +++  +p  + + yi+q nRw+
  gi|385805663|ref|YP_005842061.1| 219 RNIVsAFSLGSGTTFRIDAVRDVGYFDE-SAITEDAEISVRMHGRGWKSIYHDEQLIWYGEPpLDAASYIQQQNRWA 294
                                       888846666*******************.***************************997755399***********9 PP

                   Glyco_tranf_2_3 229 yg 230
                                       +g
  gi|385805663|ref|YP_005842061.1| 295 FG 296
                                       86 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 ?   -5.2   8.5         7   1.8e+04     163     194 ..       9      43 ..       2      48 .. 0.37
   2 !   89.2   0.9   1.3e-28   3.3e-25       3     194 ..     159     368 ..     157     409 .. 0.71
   3 ?   -1.7   0.6      0.88   2.3e+03     181     182 ..     456     466 ..     413     486 .. 0.49

  Alignments for each domain:
  == domain 1  score: -5.2 bits;  conditional E-value: 7
                   Glyco_trans_2_3 163 lwsalplhla...llllfsllalalvlllllllaa 194
                                       ++s+++++l+   +++++ +la+++++++l+++++
  gi|385805663|ref|YP_005842061.1|   9 FLSPFLIALIftiFTMTSIYLAWLTYFIWLAMVVG 43 
                                       22333333320002222223334444455444444 PP

  == domain 2  score: 89.2 bits;  conditional E-value: 1.3e-28
                   Glyco_trans_2_3   3 lllDaDtvlppdclreiaaelaspevaivqgpvlvmnvanwleelaalffaedhgkdilvrealgrvvpsvGsgafl 79 
                                        + DaD ++  d++  i+  +++p+v++vq+p  +++ ++ +++ a+  f +      ++  ++   ++s Gsg+ +
  gi|385805663|ref|YP_005842061.1| 159 SIFDADQRPRSDYFDHIIPYFSDPKVGFVQIPQRYTETRSKIAHGAK--FQQEPFLRVIMKGRNIVSAFSLGSGTTF 233
                                       589*********************************88877755555..6556666678888888999********* PP

                   Glyco_trans_2_3  80 rrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslv.kekspltlraalrQrkRwayGc.......elek 148
                                       r++a+++vg++d  es+++ED ++++r+  +G++ ++++e l+ + + pl+   +++Q  Rwa+G+       +   
  gi|385805663|ref|YP_005842061.1| 234 RIDAVRDVGYFD--ESAITEDAEISVRMHGRGWKSIYHDEQLIwYGEPPLDAASYIQQQNRWAFGNfkitgkiL--- 305
                                       ************..***************************775777888***************985444320... PP

                   Glyco_trans_2_3 149 lil......................lvrllgylgsllwsalplhl..allllfsllalalvlllllllaa 194
                                         +                             l+ l++  ++l++   +  + +++++++++ ++++  +
  gi|385805663|ref|YP_005842061.1| 306 --RsdlsfiaffdyisgffywlkegI----LTLFELIAPVVFLLFkqGFIAMNPYAYILAYI-PYMIITF 368
                                       ..244444445554444443322220....22223232222222210122222222222222.2222211 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.88
                   Glyco_trans_2_3 181 a.........l 182
                                       +         l
  gi|385805663|ref|YP_005842061.1| 456 PtergaiavnL 466
                                       12333333331 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 !   63.6   0.0   7.2e-21   1.9e-17       3     169 ..      76     241 ..      74     242 .. 0.89

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 7.2e-21
                                       EEEESS-.TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-.HHHHHHHHHHHH CS
                   Glycos_transf_2   3 viptyNe.ektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenv.Gkagalnaglra 77 
                                       ++++yNe +k ++etl s+++   + + e++++DD+ + e +e l+++++ + ++++++re+++  kaga+n++l+ 
  gi|385805663|ref|YP_005842061.1|  76 FVTSYNEdPKIVEETLLSVKSA-LRGRGEVFLLDDSTKKEIAEELKNFCE-KNGITYVHRENRKgFKAGAINNALKL 150
                                       89********************.*************************96.9************99*********** PP

                                       --SS..EEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCST CS
                   Glycos_transf_2  78 atgd..yilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnls 152
                                          +  ++ ++DaD  p  d++  ++ ++ + ++ ++++ + r+   + +i +  +  +++ ++ +  ++ +++ ++
  gi|385805663|ref|YP_005842061.1| 151 YGDKydLVSIFDADQRPRSDYFDHIIPYFSD-PKVGFVQIPQRYTETRSKIAHGAK--FQQEPFLRVIMKGRNIVSA 224
                                       988899*************************.666666666666666666666654..7888888888899999999 PP

                                       TCSTCCCEEEEHHHHHC CS
                   Glycos_transf_2 153 feigsaallrrealeel 169
                                       f  gs + +r +a++++
  gi|385805663|ref|YP_005842061.1| 225 FSLGSGTTFRIDAVRDV 241
                                       99999999998888776 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 !   58.6   0.0   2.1e-19   5.3e-16      17     172 ..     139     294 ..     126     295 .. 0.86

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 2.1e-19
                   Glyco_transf_21  17 pKvnnllqalea..akydllvisDsdvrvkpdyLeellaaledpkvglVtslpvgsdakglaaaleaaflntlagvl 91 
                                        K  ++++al+    kydl+ i D+d r ++dy++++  +++dpkvg+V+ + +++++++  a+ ++ + +++ +v+
  gi|385805663|ref|YP_005842061.1| 139 FKAGAINNALKLygDKYDLVSIFDADQRPRSDYFDHIIPYFSDPKVGFVQIPQRYTETRSKIAHGAKFQQEPFLRVI 215
                                       466677777776679**********************************************************9999 PP

                   Glyco_transf_21  92 qa..klsglgfavGksmalrreaLeaiGGfealadeLAeDyalgkllraaGlkvvlspapiaqtsvprrsslralla 166
                                       +   +     f +G+  ++r +a++++G f +    + eD++++ +++ +G+k +  ++ + +   p     +++ +
  gi|385805663|ref|YP_005842061.1| 216 MKgrNI-VSAFSLGSGTTFRIDAVRDVGYFDE--SAITEDAEISVRMHGRGWKSIYHDEQLIWYGEP-PLDAASYIQ 288
                                       996433.448**********************..9*******************9998886654333.224566889 PP

                   Glyco_transf_21 167 RqlrWa 172
                                       +q rWa
  gi|385805663|ref|YP_005842061.1| 289 QQNRWA 294
                                       999997 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.1   1.6e-09   4.1e-06      10     104 ..      82     177 ..      75     263 .. 0.80

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1.6e-09
                   Glyco_tranf_2_2  10 eerhyieervlqkakyydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGaska.esdlv 85 
                                       e+ + +ee++l  ++      e+ ++dd   ++++ee+++++++n+  y++ e+ k +  +a  N    +  + dlv
  gi|385805663|ref|YP_005842061.1|  82 EDPKIVEETLLSVKSALRGRGEVFLLDDSTKKEIAEELKNFCEKNGITYVHRENRKGFKAGAINNALKLYGdKYDLV 158
                                       5556899******9999********************************9999999********98877762579** PP

                   Glyco_tranf_2_2  86 lFlDaDcfissDkfekilk 104
                                       +  DaD    sD f+ i+ 
  gi|385805663|ref|YP_005842061.1| 159 SIFDADQRPRSDYFDHIIP 177
                                       **************99875 PP

>> Cellulose_synt  Cellulose synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1     0.012        31     168     287 ..     128     237 ..     100     244 .. 0.68
   2 !   19.8  10.9   8.9e-08   0.00023     414     671 ..     240     476 ..     235     490 .. 0.69

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.012
                    Cellulose_synt 168 lvyvsrekrpGydhnkkaGamnalvrvsavlsnapfilnldcdhyinnskalreamcflldrelGkkvcyvqfpqrf 244
                                       + yv re r G+    kaGa+n  ++  +       +  +d d     s  + + + ++ d++    v++vq+pqr+
  gi|385805663|ref|YP_005842061.1| 128 ITYVHRENRKGF----KAGAINNALKLYGDKY--DLVSIFDADQR-PRSDYFDHIIPYFSDPK----VGFVQIPQRY 193
                                       678888888888....7888887777654333..33334555554.45777777788888877....8899999999 PP

                    Cellulose_synt 245 dGidksdryan..rnvvffdinlraldGiqGpvyvGtGcvfrrqa 287
                                            +  +    ++  f+ + +++ + i     +G+G+ fr  a
  gi|385805663|ref|YP_005842061.1| 194 TETRSKIAHGAkfQQEPFLRVIMKGRN-IVSAFSLGSGTTFRIDA 237
                                       766555444331145568888888865.55667788888887666 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 8.9e-08
                    Cellulose_synt 414 eiGwiyGs.vtedvltGfkmharGwrsvycvtkrdafkGsapinlsdrlhqvlrwalGsveiffsrnnalfagykkk 489
                                       ++G+   s +ted     +mh rGw+s+y   ++  + G  p++ +  ++q  rwa G  +i       ++ +    
  gi|385805663|ref|YP_005842061.1| 240 DVGYFDESaITEDAEISVRMHGRGWKSIYH-DEQLIWYGEPPLDAASYIQQQNRWAFGNFKI----TGKILRS---D 308
                                       5676654339*******************7.5667899********************9888....4678877...9 PP

                    Cellulose_synt 490 lkllerlaylnviiypftsifllvy.cilpals.llsgkfivkelsnlasiyl..lllflslivlavlelkwsGvsl 562
                                       l ++  + y+    y +    l ++  i p +  l+ + fi  +  ++++ y+  +++++ +++ ++    ++  ++
  gi|385805663|ref|YP_005842061.1| 309 LSFIAFFDYISGFFYWLKEGILTLFeLIAPVVFlLFKQGFIAMNPYAYILAYIpyMIITFLIFAFSIRGTSYGVRGF 385
                                       ***************99876665551556666525667799888777777776115555555555555554443344 PP

                    Cellulose_synt 563 eewwrneqfwvigGvsahlfavlqGllkvlaGvdisftvtskasddeddefadlyivkwttllippltllivnlvav 639
                                         +  ne +          f +   ++  l G +i f vt k+ +        +  +     +ip + ++i+ + +v
  gi|385805663|ref|YP_005842061.1| 386 LVHQANEYLAF--------FGITMAFISFLLGRKIPFKVTPKGKG--------MRSF---KAIIPHIIIFILLIASV 443
                                       33344444333........33444456667788888888888877........2222...34566666666666666 PP

                    Cellulose_synt 640 vvgvsrainsaye.swgkllGklffafwvlvhl 671
                                       v g    ++s+ + + g +  +lf+a+w ++ l
  gi|385805663|ref|YP_005842061.1| 444 VNGSYWLLTSSLPtERGAIAVNLFWALWHIIFL 476
                                       666666666666524677777888888877765 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 ?   10.4   0.2    0.0002      0.52      16      36 ..     105     125 ..     102     125 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0002
                                       HH-SS--HHHHHHHHHHHHHH CS
                            SapB_1  16 lLkdNkTeeeIieaLekvCsk 36 
                                       +L d +T++eI e L++ C+k
  gi|385805663|ref|YP_005842061.1| 105 FLLDDSTKKEIAEELKNFCEK 125
                                       78899**************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (501 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1112  (0.0620224); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); 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):               7  [number of targets reported over threshold]
# CPU time: 0.73u 0.29s 00:00:01.02 Elapsed: 00:00:00.46
# Mc/sec: 3238.38
//
Query:       gi|385805664|ref|YP_005842062.1|  [L=452]
Description: hypothetical protein FFONT_0620 [Fervidicoccus fontis Kam940]
Scores for complete 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-08   32.7   0.0    1.6e-07   31.4   0.0    1.6  1  AAA_31       AAA domain
    1.7e-07   31.4   0.0    3.9e-07   30.2   0.0    1.6  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
     0.0012   18.4   0.0     0.0022   17.5   0.0    1.6  1  ParA         NUBPL iron-transfer P-loop NTPase
     0.0021   17.3   1.5      0.067   12.4   0.1    2.8  3  ArsA_ATPase  Anion-transporting ATPase
  ------ inclusion threshold ------
      0.067   12.7   0.1       0.15   11.5   0.1    1.5  1  CBP_BcsQ     Cellulose biosynthesis protein BcsQ


Domain annotation for each model (and alignments):
>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.0   4.4e-11   1.6e-07       4     126 ..       3     125 ..       2     135 .. 0.70

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 4.4e-11
                            AAA_31   4 IaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekneiektlyevlieeknikeaiiktkven 80 
                                       I i   KGGvG +  s+ l++ +a  gk+vLlvD D+ + a+++lg++       l++++ + + +++a+ k ++ +
  gi|385805664|ref|YP_005842062.1|   3 IDILRAKGGVGGSSISLSLSKYFAMIGKRVLLVDRDAISTASSYLGLS----GLGLIQLIKKGEGYEKALAKVQFGR 75 
                                       567889***************************************984....4456666656666666666555544 PP

                            AAA_31  81 l.....dlipssidLaeaeielvelekkeeilkellekvkde..YDyiiiDcp 126
                                             +l    i +    ++l    k++e+++e+  k+ ++  +D++i+D++
  gi|385805664|ref|YP_005842062.1|  76 GsitalKLFSDGIPIEYERDDL---IKNKERISEAYGKILENgsFDIVIVDTM 125
                                       4111114444444444444444...4555555666666655445999999986 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   1.1e-10   3.9e-07       4     101 ..       6     206 ..       3     232 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 1.1e-10
                                       EESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH...........HTTEB-HHHH............... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxx............... RF
                              CbiA   4 astkGGvGKTtlaanLaralarrglrVllvDaDpqannlai...........leglendiep............... 54 
                                          kGGvG ++++++L +++a  g+rVllvD D  ++++++           ++       +               
  gi|385805664|ref|YP_005842062.1|   6 LRAKGGVGGSSISLSLSKYFAMIGKRVLLVDRDAISTASSYlglsglgliqlIK-------Kgegyekalakvqfgr 75 
                                       567*************************************97776555555433.......255555559******* PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|385805664|ref|YP_005842062.1|  76 gsitalklfsdgipieyerddliknkeriseaygkilengsfdivivdtmaattplevvtgweyatfhqhsseksty 152
                                       ***************************************************************************** PP

                                       .........CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHH CS
                                       .........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 .........dlkrllellealgkkkalllkiagvvlnrvdgeneetllkealeelk 101
                                                +++  ++ +++l+++     +i   vln+vd +    +++e+l +l+
  gi|385805664|ref|YP_005842062.1| 153 imisdpskaSIEGSIRYFKVLKENGHISERIDAAVLNKVDFS--RISQSEFLSTLL 206
                                       ******99977777788888887766669999*******988..777788888776 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 !   17.5   0.0   6.2e-07    0.0022       6      44 ..       3      41 ..       1     179 [. 0.66

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 6.2e-07
                              ParA  6 iavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyG 44
                                      i +l +KGGVG S+++ +l+  +a  g++v l+D D + 
  gi|385805664|ref|YP_005842062.1|  3 IDILRAKGGVGGSSISLSLSKYFAMIGKRVLLVDRDAIS 41
                                      668899******************************764 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.1   1.9e-05     0.067       5      38 ..       5      38 ..       1      48 [. 0.88
   2 ?   -0.0   0.0      0.11     4e+02     118     133 ..     110     125 ..     100     141 .. 0.82
   3 ?    1.6   0.0     0.035   1.2e+02     204     245 ..     147     191 ..     139     216 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.9e-05
                                      EEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                       ArsA_ATPase  5 lvgGKGGVGKttvsaatavklsekgkkvllistD 38
                                      ++  KGGVG +++s +++ + +  gk+vll+  D
  gi|385805664|ref|YP_005842062.1|  5 ILRAKGGVGGSSISLSLSKYFAMIGKRVLLVDRD 38
                                      6678***************************888 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.11
                                       HHHHCSSSSEEEEESB CS
                       ArsA_ATPase 118 kyvkeeeydvvvlDta 133
                                       k +++  +d+v++Dt 
  gi|385805664|ref|YP_005842062.1| 110 KILENGSFDIVIVDTM 125
                                       6677899*******95 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.035
                                       TTTEEEEEEEESSHHHHHHHHHHHHHHHHTT-...EEEEEEEEEE CS
                       ArsA_ATPase 204 pertsfrlVvipEklslkEteRaikeLkkygi...kvdavivNkl 245
                                        e+++ ++++ p k s++ + R +k Lk+ g    ++da + Nk+
  gi|385805664|ref|YP_005842062.1| 147 SEKSTYIMISDPSKASIEGSIRYFKVLKENGHiseRIDAAVLNKV 191
                                       578899*********************987632225677778875 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   4.2e-05      0.15      10      38 ..       9      37 ..       2      69 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.2e-05
                          CBP_BcsQ 10 RGGvGttsllaaLawalhelgesvlviDl 38
                                      +GGvG +s++ +L++ + + g++vl++D 
  gi|385805664|ref|YP_005842062.1|  9 KGGVGGSSISLSLSKYFAMIGKRVLLVDR 37
                                      7**************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 2636.67
//
Query:       gi|385805665|ref|YP_005842063.1|  [L=39]
Description: hypothetical protein FFONT_0621 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.30s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 254.10
//
Query:       gi|385805666|ref|YP_005842064.1|  [L=242]
Description: hypothetical protein FFONT_0622 [Fervidicoccus fontis Kam940]
Scores for complete 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   21.5   6.9    0.00024   21.5   6.9    2.2  2  FtsX             FtsX-like permease family
      0.008   16.2   7.4      0.011   15.7   7.4    1.2  1  ABC2_membrane_4  ABC-2 family transporter protein
  ------ inclusion threshold ------
      0.051   12.7  16.3      0.078   12.1  16.2    1.4  1  ABC2_membrane_3  ABC-2 family transporter protein
       0.23   11.6   2.0       0.41   10.8   2.0    1.4  1  DUF4079          Protein of unknown function (DUF4079)


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   0.4     0.051   2.3e+02      72      86 ..     105     119 ..      64     131 .. 0.50
   2 !   21.5   6.9   5.3e-08   0.00024       3      86 ..     138     221 ..     136     232 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.051
                              FtsX  72 iivlllllallagll 86 
                                       ++++++l ++++++l
  gi|385805666|ref|YP_005842064.1| 105 AFGISILWISFSLIL 119
                                       222222222222222 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 5.3e-08
                              FtsX   3 eigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivlllll 79 
                                       ei  l ++G ++++ ll  ++ +l+++l++++++l +g++  +l+    +s ++ s l+++i l + l ++ ++ l 
  gi|385805666|ref|YP_005842064.1| 138 EIKALISMGIRRRHFLLSSILYSLILSLLSSFMALSIGIFSMKLVAYASSSLFNLSILQPYITLDHALSLLSVSALS 214
                                       8999****************************************999999999988888888777766666666555 PP

                              FtsX  80 allagll 86 
                                       + + ++ 
  gi|385805666|ref|YP_005842064.1| 215 VFVPSFS 221
                                       5544333 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 !   15.7   7.4   2.4e-06     0.011      51     162 ..     105     220 ..      74     229 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.4e-06
                   ABC2_membrane_4  51 vfgft.lllllplilgiia...sylifrEeqndtlknLltiPvsrtklllaKlivllllsvllmlvtflitvlfall 123
                                       +fg++ l++ + lil  ++    +l +rE+ ++ +k L  + + r+++ll+ +++ l+ls+l +++++ +  +f++ 
  gi|385805666|ref|YP_005842064.1| 105 AFGISiLWISFSLILSSLTtalLMLKNRERAEGEIKALISMGIRRRHFLLSSILYSLILSLLSSFMAL-SIGIFSMK 180
                                       555553334444444443311157889**********************************9998855.55566666 PP

                   ABC2_membrane_4 124 sgfvgfsvklvlellkkcl.elgllvffavlpiialvllk 162
                                       +   + s+   l++l+ ++ +  +l+++ v+++ ++v  +
  gi|385805666|ref|YP_005842064.1| 181 LVAYASSSLFNLSILQPYItLDHALSLLSVSALSVFVPSF 220
                                       6555555555666666555366666666666666655554 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 ?   12.1  16.2   1.7e-05     0.078     163     261 ..     106     219 ..      60     223 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.7e-05
                   ABC2_membrane_3 163 lvgliliilifitasfiavsi....veEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll.afgl... 231
                                       + + il+i++++++s++++++     +E+  + ++ ++++g+++  ++ls+il +++++ll+++ +l + +f+    
  gi|385805666|ref|YP_005842064.1| 106 FGISILWISFSLILSSLTTALlmlkNRERAEGEIKALISMGIRRRHFLLSSILYSLILSLLSSFMALSIgIFSMklv 182
                                       3334555555555555555553445699999*******************************987776665665666 PP

                   ABC2_membrane_3 232 ...gipfgnl....glllllfllfglayialgyllss 261
                                          + + +nl     ++ l + l +l+++al+ ++ s
  gi|385805666|ref|YP_005842064.1| 183 ayaSSSLFNLsilqPYITLDHALSLLSVSALSVFVPS 219
                                       6665555555444456668888888888888888755 PP

>> DUF4079  Protein of unknown function (DUF4079)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   2.0     9e-05      0.41      10      69 ..     112     170 ..     107     217 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9e-05
                           DUF4079  10 vllvfpllgavaylGwqtrqrrlqskaerkekipkkvrdeHvklgslllllvvlgaiggl 69 
                                       ++++ ++l+  + +++ + + r   + e k +i+  +r++H+ l s+l +l++ ++   +
  gi|385805666|ref|YP_005842064.1| 112 WISFSLILSS-LTTALLMLKNRERAEGEIKALISMGIRRRHFLLSSILYSLILSLLSSFM 170
                                       4555555555.88898888888888889********************666655443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1601.08
//
Query:       gi|385805667|ref|YP_005842065.1|  [L=380]
Description: hypothetical protein FFONT_0623 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0061   17.0   1.0     0.0061   17.0   1.0    3.7  3  FtsX      FtsX-like permease family


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 ?   -0.4   4.3      0.09   1.6e+03      16      37 ..      17      38 ..       4     101 .. 0.67
   2 ?   -2.4   4.4      0.39     7e+03      58      86 ..     255     283 ..     155     292 .. 0.57
   3 !   17.0   1.0   3.4e-07    0.0061       4      84 ..     291     369 ..     288     375 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.09
                              FtsX 16 qvlllllteillitlvalviGl 37
                                      +vl l+++ i+ ++l+++ +++
  gi|385805667|ref|YP_005842065.1| 17 EVLSLFFILIFSYSLISITSSV 38
                                      3444444444444444444443 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.39
                              FtsX  58 selkisidlitvliiivlllllallagll 86 
                                        +  +++  +  + +++ ++l ++l+g+ 
  gi|385805667|ref|YP_005842065.1| 255 EAERVTLIASLSVSVALSSILAFSLSGAS 283
                                       34444444444444444444444444433 PP

  == domain 3  score: 17.0 bits;  conditional E-value: 3.4e-07
                              FtsX   4 igilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivllllla 80 
                                       i  lr +Gm+k++vl+ + +e  + +  +l+++++  ll+ ++    + ++v   ++++s+++i+  i  + ++ ++
  gi|385805667|ref|YP_005842065.1| 291 IKALRDMGMRKRDVLKSVAVEKSIAFSSSLILSIASYLLMEKM--GIIYAYVLEHRIPPSLSWIDAMIYTIAVFSIY 365
                                       788******************9988888888884443333333..22222233378888888888888888877777 PP

                              FtsX  81 llag 84 
                                       ++++
  gi|385805667|ref|YP_005842065.1| 366 IAIS 369
                                       7773 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.49
# Mc/sec: 2352.18
//
Query:       gi|385805668|ref|YP_005842066.1|  [L=507]
Description: hypothetical protein FFONT_0624 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (507 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 3331.15
//
Query:       gi|385805669|ref|YP_005842067.1|  [L=216]
Description: ABC transporter [Fervidicoccus fontis Kam940]
Scores for complete 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  118.8   0.1    3.1e-34  118.4   0.1    1.1  1  ABC_tran     ABC transporter
    3.1e-05   24.0   0.9     0.0071   16.2   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    0.00014   22.3   0.1    0.00019   21.8   0.1    1.2  1  AAA_16       AAA ATPase domain
     0.0013   18.5   0.0     0.0022   17.7   0.0    1.3  1  AAA_29       P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.011   15.2   0.1       0.33   10.4   0.1    2.1  1  SMC_N        RecF/RecN/SMC N terminal domain
      0.015   15.2   0.0       0.15   12.0   0.0    2.0  2  Rad17        Rad17 P-loop domain
      0.035   14.0   0.0      0.065   13.1   0.0    1.4  1  NACHT        NACHT domain
      0.035   14.4   0.2        0.3   11.4   0.2    2.1  1  AAA_22       AAA domain
       0.13   11.9   0.0       0.24   11.1   0.0    1.4  1  AAA_30       AAA domain
       0.16   11.9   0.1       0.26   11.2   0.1    1.3  1  RsgA_GTPase  RsgA GTPase
        0.2   10.8   0.0        0.2   10.8   0.0    1.2  1  G-alpha      G-protein alpha subunit


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.4   0.1   1.9e-37   3.1e-34       1     137 []      17     163 ..      17     163 .. 0.96

  Alignments for each domain:
  == domain 1  score: 118.4 bits;  conditional E-value: 1.9e-37
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG...B-HHHCCHCEEEE-SS--S-TTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke...qeleslrkeigvlpqepqlfpel 74 
                                       l+ vsl+  ege++ i G++G+GKStLl++++ l kp+ Ge+++ gk+  +    e+e+lr +i+++pq  +l ++l
  gi|385805669|ref|YP_005842067.1|  17 LNGVSLSADEGELMRIRGRSGSGKSTLLRIMSLLQKPNVGEVEVLGKSAWSiseGEREELRGKISYIPQFLELIENL 93 
                                       789*****************************************98876555669********************** PP

                                       BHHHH...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  75 tvren...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       tv en           + ++++ +al+ lg+ +++++      ++LSgGq+qrva+aral++ pk+l++DEpt+
  gi|385805669|ref|YP_005842067.1|  94 TVLENvqlalevrgieNGEDRAREALEVLGIRGFEERLP----RELSGGQRQRVAIARALVSSPKILIADEPTS 163
                                       **************9999999****************99....*****************************96 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   4.4e-06    0.0071       6      39 ..      34      61 ..      32      94 .. 0.65
   2 !    6.7   0.2    0.0034       5.5     230     287 ..     128     182 ..      81     193 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.4e-06
                            AAA_21  6 GpNgsGKSnLLdaldllarldrdvegltdelsgg 39
                                      G+ gsGKS+LL++++ll+       +   e    
  gi|385805669|ref|YP_005842067.1| 34 GRSGSGKSTLLRIMSLLQK------PNVGEVEVL 61
                                      899**************84......333333333 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0034
                            AAA_21 230 qelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr 287
                                        e+ +relS G+++  a++ al + +   ++l+ DEp ++L+  + +++++ll+els+
  gi|385805669|ref|YP_005842067.1| 128 EERLPRELSGGQRQRVAIARALVSSP---KILIADEPTSFLDDIASSSFYRLLEELSS 182
                                       5677899*******999999999988...9************9999999999988876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.1   1.2e-07   0.00019      20     107 ..      23     145 ..      16     186 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.2e-07
                            AAA_16  20 rsgrpelvllsGesGvGKsslvrellralekd...........ggiflrgkcdqlesaipysa.laqalareellrq 84 
                                       +++++el+ ++G sG+GKs+l+r     l+k             +   +g+ ++l+ +i+y++ +++++++ ++l+ 
  gi|385805669|ref|YP_005842067.1|  23 SADEGELMRIRGRSGSGKSTLLRIMS-LLQKPnvgevevlgksAWSISEGEREELRGKISYIPqFLELIENLTVLEN 98 
                                       567779999*************5555.5556578778888753344477788888888***999************9 PP

                            AAA_16  85 lldeaesaeleawrekleeala........................a 107
                                       +  ++e +  e   ++ +eal+                        +
  gi|385805669|ref|YP_005842067.1|  99 VQLALEVRGIENGEDRAREALEvlgirgfeerlprelsggqrqrvaI 145
                                       99999999999999999999988888888877444444443333330 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   1.4e-06    0.0022      15      39 ..      20      44 ..      14      57 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.4e-06
                            AAA_29 15 htieidlkgatlltGpsGsGKSTll 39
                                       +++ d+ + + + G+sGsGKSTll
  gi|385805669|ref|YP_005842067.1| 20 VSLSADEGELMRIRGRSGSGKSTLL 44
                                      566667555899************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 ?   10.4   0.1    0.0002      0.33     135     197 ..     111     192 ..      21     203 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0002
                                       T......................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT CS
                                       x......................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 135 e......................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn 189
                                                              +LSgG+++ va+a  +    v+   + + De  + LD+   + + +ll+e s++
  gi|385805669|ref|YP_005842067.1| 111 GedrarealevlgirgfeerlprELSGGQRQRVAIARAL----VSSPKILIADEPTSFLDDIASSSFYRLLEELSSS 183
                                       155555555555555555556668******999987553....444557889********************99988 PP

                                       SEE.EEE-S CS
                                       xxx.xxxxx RF
                             SMC_N 190 aQf.ivisl 197
                                       + + i++s 
  gi|385805669|ref|YP_005842067.1| 184 FKMgIIVST 192
                                       554233333 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   9.1e-05      0.15      35     110 ..      17      94 ..       3     119 .. 0.74
   2 ?    0.9   0.0      0.23   3.7e+02     136     178 ..     155     198 ..     146     202 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.1e-05
                             Rad17  35 lkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklrew..lnpvslkepdnqksdfkgltekesrflsqiesf 109
                                       l+  +L   + +++ i G sG gkst ++++s    +++ e   l       ++ ++++++g++    +fl +ie  
  gi|385805669|ref|YP_005842067.1|  17 LNGVSLSADEGELMRIRGRSGSGKSTLLRIMSLLQKPNVGEVevLGKSAWSISEGEREELRGKISYIPQFLELIENL 93 
                                       55667777778899******************999888876421333333444448888888888888888888765 PP

                             Rad17 110 k 110
                                       +
  gi|385805669|ref|YP_005842067.1|  94 T 94 
                                       5 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.23
                             Rad17 136 ilvedlPnkfyrds..dalrevirkylrssealplilviteiesl 178
                                       il+ d P  f  d    ++  ++ + l ss  + +i+  te++ +
  gi|385805669|ref|YP_005842067.1| 155 ILIADEPTSFLDDIasSSFYRLLEE-LSSSFKMGIIVSTTELNLP 198
                                       8899999999888654677776654.6666666999999988765 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     4e-05     0.065       2      28 ..      29      54 ..      28      62 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4e-05
                                      CEEEEC-TTTCHHHHHHHHHHHHCTS- CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalawaegk 28
                                      l+ ++G++GsGK+tLl+ +++++++++
  gi|385805669|ref|YP_005842067.1| 29 LMRIRGRSGSGKSTLLR-IMSLLQKPN 54
                                      5779***********96.777777766 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   0.00018       0.3      10      38 ..      32      75 ..      24     200 .. 0.47

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00018
                            AAA_22 10 vtGesGtGKTtllrrlleql.deeakaee..............e 38
                                      + G sG+GK+tllr +     +++ + e               e
  gi|385805669|ref|YP_005842067.1| 32 IRGRSGSGKSTLLRIMSLLQkPNVGEVEVlgksawsisegereE 75
                                      779**********9776543033333333666666666655552 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00015      0.24      16      54 ..      25      63 ..      20     103 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00015
                            AAA_30 16 sgdrvavltGpAGtGKttalkalreaweaaggrviglAp 54
                                      ++  ++ + G+ G+GK+t+l+ +  + + + g+v +l  
  gi|385805669|ref|YP_005842067.1| 25 DEGELMRIRGRSGSGKSTLLRIMSLLQKPNVGEVEVLGK 63
                                      45568999*************988777777566666655 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00016      0.26     100     130 ..      28      58 ..      20      64 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00016
                                       SEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                       RsgA_GTPase 100 ktsvlvGqSGvGKStLinallpelelktgev 130
                                       +++ + G SG GKStL+  +   ++ ++gev
  gi|385805669|ref|YP_005842067.1|  28 ELMRIRGRSGSGKSTLLRIMSLLQKPNVGEV 58 
                                       667789***********99888778888877 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00012       0.2      30      55 ..      34      59 ..      27     181 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00012
                                      ESTTSSHHHHHHHHHHHCS----HHH CS
                           G-alpha 30 GqseSGKsTilkqlkllykkgfseee 55
                                      G s+SGKsT+l+ + ll k+++ e e
  gi|385805669|ref|YP_005842067.1| 34 GRSGSGKSTLLRIMSLLQKPNVGEVE 59
                                      99****************99965544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); 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: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1284.80
//
Query:       gi|385805670|ref|YP_005842068.1|  [L=135]
Description: hypothetical protein FFONT_0626 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score 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   12.0   0.0        0.1   11.8   0.0    1.1  1  GRDB      Glycine/sarcosine/betaine reductase selenoprotein B
      0.097   13.1   0.3       0.74   10.3   0.1    2.4  2  RuvA_C    RuvA, C-terminal domain


Domain annotation for each model (and alignments):
>> GRDB  Glycine/sarcosine/betaine reductase selenoprotein B (GRDB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.1e-05       0.1     143     196 ..       7      59 ..       1      79 [. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.1e-05
                              GRDB 143 rkavkamaklakkllkgeeigsaeeegyiergirknvfaekrgaeRavdmLlkk 196
                                        ka+++  +l + +l  e+i+ a+ e+yi++ ir nv++     +R + ++l++
  gi|385805670|ref|YP_005842068.1|   7 GKAIEKAKSLLSEILLSERITGADVEKYIRKAIRYNVWRLLPDERR-IFLILAR 59 
                                       6899999*******************************87665555.4444444 PP

>> RuvA_C  RuvA, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   8.2e-05      0.74      27      44 ..      17      40 ..       7      41 .. 0.71
   2 ?   -0.2   0.0      0.16   1.4e+03      35      43 ..      69      77 ..      59      80 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 8.2e-05
                                      HHC......-TTS-HHHHHHHHHC CS
                            RuvA_C 27 vla......npgasveelIraALk 44
                                      +++       +ga+ve +Ir+A++
  gi|385805670|ref|YP_005842068.1| 17 LSEillserITGADVEKYIRKAIR 40
                                      44444467889***********98 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.16
                                      HHHHHHHHH CS
                            RuvA_C 35 veelIraAL 43
                                      ++e+Ir +L
  gi|385805670|ref|YP_005842068.1| 69 ISEVIRSSL 77
                                      789999888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 835.06
//
Query:       gi|385805671|ref|YP_005842069.1|  [L=346]
Description: AIR synthase related protein domain protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-21   76.1   1.1    5.8e-21   75.2   1.1    1.4  1  AIRS_C         AIR synthase related protein, C-terminal domai
    2.6e-14   53.6   0.0    4.6e-14   52.8   0.0    1.4  1  AIRS           AIR synthase related protein, N-terminal domai
  ------ inclusion threshold ------
      0.035   14.0   0.1       0.19   11.7   0.0    2.0  2  Peptidase_S49  Peptidase family S49


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 !   75.2   1.1   9.8e-25   5.8e-21       1     147 [.     151     303 ..     151     311 .. 0.81

  Alignments for each domain:
  == domain 1  score: 75.2 bits;  conditional E-value: 9.8e-25
                                       STTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTT....TSE.HHHHHHH.HHHHHHHHHHHHH..HTTECEEEE--T CS
                            AIRS_C   1 kpGdvliltgslGlggagtslkrkileeegldds....avq.lgdvlle.ptliyvkralaal..kglvkaahDvTg 69 
                                       ++Gd +++t++ G+ g +++  +  +   +   +    +v  +g ++l+   ++++++a   l  +gl++++hD T+
  gi|385805671|ref|YP_005842069.1| 151 REGDEIVMTKTAGIEGTAILVTDFKDVLLK---KgikeEVLeRGREFLKmVSVVKEALA---LsrRGLANSMHDATN 221
                                       69****************776653333322...23455443344444440244444444...3367*********** PP

                                       THHHHHHHHHHHTTTEEEEEECGTHHHHHHHH.....HHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEE CS
                            AIRS_C  70 GGLlgalaemapasgvgaeidldkvpifdele.....splemllsensGrllvavppeeadavlaileeeglpeaav 141
                                       GG+l+ +aema as+ ++e+ +d++p+ +e++     +++++l+  +sG+l+ +vp+ +  +++++l++ g+ + +v
  gi|385805671|ref|YP_005842069.1| 222 GGVLEGVAEMAYASRKTIELFEDRIPVAEETAsmskaLGIDPLKLISSGVLIASVPSGRGREAVELLRSIGI-KGSV 297
                                       ************************************************************************.7*** PP

                                       EEEEEE CS
                            AIRS_C 142 IGevta 147
                                       +G+v +
  gi|385805671|ref|YP_005842069.1| 298 VGRVKE 303
                                       ****87 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 !   52.8   0.0   7.7e-18   4.6e-14      16      93 ..      48     138 ..      33     139 .. 0.88

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 7.7e-18
                                       ECCTCCCC....HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......HHHHHHHHHHHHHHHTT-EEEEEEEEEES CS
                              AIRS  16 vlvepvhf....iGakavavnlsDlaamGArPlalllslalp......wleevvrglaeaaeelgvplvgGdtsfsn 82 
                                       + v+p+ +    iG+++v  + +D+a+ G +P++ll  + lp       l+++ +++ eaa+e+gv +vgG+t f +
  gi|385805671|ref|YP_005842069.1|  48 SHVDPIVGaiesIGWLSVNIVSNDIAVRGVEPRWLLSDILLPesssidLLDRITSQIDEAAKEVGVMIVGGHTVFAP 124
                                       334444448888****************************************************************9 PP

                                       S...EEEEEEEEEE CS
                              AIRS  83 e...ptisvtavGl 93 
                                       +   p++s+ta+G+
  gi|385805671|ref|YP_005842069.1| 125 KltrPIVSMTAIGI 138
                                       9999*********7 PP

>> Peptidase_S49  Peptidase family S49
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   3.1e-05      0.19      27     107 ..     152     232 ..     148     251 .. 0.81
   2 ?   -0.5   0.0      0.18   1.1e+03      89     105 ..     327     343 ..     324     345 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.1e-05
                                       TSSEEEE-TT-EEE---EEEEEEE-HHHHHHTT-EEEEEESS.TTCCCC.CTTSS--HHHHHHHHHHHHHHHHHHHH CS
                     Peptidase_S49  27 aadkivanpstivgsiGvitqllnlenlldklgvevqvvkaG.eyksav.slrrelteeereilqrlldetyqqFvq 101
                                         d+iv+++++  g+ G +   ++++++l k g++ +v+++G e+ ++v  ++++l    r   +++ d+t   +++
  gi|385805671|ref|YP_005842069.1| 152 EGDEIVMTKTA--GIEGTAILVTDFKDVLLKKGIKEEVLERGrEFLKMVsVVKEALALSRRGLANSMHDATNGGVLE 226
                                       5799***9998..6679999**********************55666663666677777777788888999999999 PP

                                       HHHHHH CS
                     Peptidase_S49 102 tVaknR 107
                                        Va++ 
  gi|385805671|ref|YP_005842069.1| 227 GVAEMA 232
                                       999875 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.18
                                       HHHHHHHHHHHHHHHHH CS
                     Peptidase_S49  89 qrlldetyqqFvqtVak 105
                                       + +ld++++ + + V+k
  gi|385805671|ref|YP_005842069.1| 327 EDELDNLWESYRKEVSK 343
                                       6799***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.30s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 2126.43
//
Query:       gi|385805672|ref|YP_005842070.1|  [L=323]
Description: NAD-dependent epimerase/dehydratase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.2e-57  192.8   0.0    7.6e-57  192.5   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    1.9e-53  182.0   0.0    2.2e-53  181.8   0.0    1.0  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    2.8e-23   82.3   0.0    3.8e-23   81.9   0.0    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    7.7e-20   71.2   0.0    9.4e-20   70.9   0.0    1.1  1  RmlD_sub_bind    RmlD substrate binding domain
    2.6e-18   66.2   0.0    2.9e-17   62.8   0.0    2.0  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    2.9e-14   52.8   0.3    1.9e-12   46.9   0.3    2.2  1  NAD_binding_4    Male sterility protein
      7e-09   35.8   0.0    1.1e-08   35.2   0.0    1.3  1  NAD_binding_10   NAD(P)H-binding
    1.7e-05   24.8   0.1    8.8e-05   22.5   0.0    2.2  2  KR               KR domain
    7.6e-05   22.2   0.0    0.00037   20.0   0.0    2.1  3  adh_short        short chain dehydrogenase
  ------ inclusion threshold ------
      0.015   14.9   0.0      0.089   12.3   0.0    2.0  2  NmrA             NmrA-like family
      0.074   13.3   0.0       0.26   11.6   0.0    1.9  1  TrkA_N           TrkA-N domain


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.5   0.0   4.6e-60   7.6e-57       1     241 []       5     243 ..       5     243 .. 0.94

  Alignments for each domain:
  == domain 1  score: 192.5 bits;  conditional E-value: 4.6e-60
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC......EEEE--TT-HHHHHHHHHHHT-SEEEE- CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl......elveldltdrsalerlfkeeqpdavihl 71 
                                       ilVtG++GfiGs+lv++l e+g ev+++d lss++  ++le+       +++++dl ++ ++ + +k  +++av+h+
  gi|385805672|ref|YP_005842070.1|   5 ILVTGGAGFIGSHLVDRLIERGEEVLVIDDLSSGKT-ENLERWfgekkfKFIKADLSEPGKWIDELK--GIEAVFHF 78 
                                       8******************************65555.555555699*********************..9******* PP

                                       -S---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHH CS
                         Epimerase  72 AavggvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKla 148
                                       Aa   v++s ++p+  +++n+q t n+lea+r++g++ ++++sSs+vYG+   +p+ e+   +p +p s Y+a+Kl+
  gi|385805672|ref|YP_005842070.1|  79 AANPEVRVSTTNPEVHYRANVQATFNVLEASRANGAEIFIYASSSTVYGEARVIPTPEDY--EPKEPISIYGASKLM 153
                                       ***************************************************999966666..588************ PP

                                       HHHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHH CS
                         Epimerase 149 geklveayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillv 225
                                       ge lv  y + yg++   lr  n++G+r    ++++vi+ +i+k+++  + + +lgdg+++  ++y++D++ea l v
  gi|385805672|ref|YP_005842070.1| 154 GEVLVSTYSRIYGVKSAMLRFANVVGKR----SNHGVIFDFIAKLKRDPERLEILGDGKQRKSYIYIDDAIEATLKV 226
                                       ****************************....**************9999*************************** PP

                                       HHHHTT-ST.TEEEEES CS
                         Epimerase 226 lehvdagdk.geiyniG 241
                                       +eh ++ ++  e++n+G
  gi|385805672|ref|YP_005842070.1| 227 MEHMESSQEmSEAFNVG 243
                                       ***99987756799998 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 !  181.8   0.0   1.3e-56   2.2e-53       1     331 [.       6     312 ..       6     313 .. 0.89

  Alignments for each domain:
  == domain 1  score: 181.8 bits;  conditional E-value: 1.3e-56
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       L+TG+aGfiGs+l+++L+e+g ev +i+++ss  +t+++e++        e+++k++k+Dl++  + ++ l+ +  +
  gi|385805672|ref|YP_005842070.1|   6 LVTGGAGFIGSHLVDRLIERGEEVLVIDDLSS-GKTENLERWFG------EKKFKFIKADLSEPGKWIDELKGI--E 73 
                                       9***********************99887765.699*****996......4689**********9888888877..8 PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TT.S-----SHH CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEt.tpfyPrsPY 153
                                       +v+++AA   V+vs ++Pe  +++nv +t+++Lea ra g e    f+ aS+s+vYG+++ +p  E+  p +P s Y
  gi|385805672|ref|YP_005842070.1|  74 AVFHFAANPEVRVSTTNPEVHYRANVQATFNVLEASRANGAE---IFIYASSSTVYGEARVIPTPEDyEPKEPISIY 147
                                       **************************************9976...8*****************98876899****** PP

                                       HHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHH CS
                     GDP_Man_Dehyd 154 aaaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyv 230
                                       +a+Kl+ + +v  y + yg+     ++ n  + r  ++     i +++a+ +++ +   +lG++++++++ +++D +
  gi|385805672|ref|YP_005842070.1| 148 GASKLMGEVLVSTYSRIYGVKSAMLRFANVVGKRS-NH---GVIFDFIAKLKRDPERLEILGDGKQRKSYIYIDDAI 220
                                       *********************************95.44...56************999999**************** PP

                                       HHHHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB-- CS
                     GDP_Man_Dehyd 231 eamwlmlqqdkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlll 307
                                       ea  +++++ +++    +  e ++v+++  + + ++   ie e       g++++  k   + d +    g+v+ + 
  gi|385805672|ref|YP_005842070.1| 221 EATLKVMEHMESS---QEMSEAFNVGSLDAIGVDDIAYIIEEE----MGLGKVEHVFK-SATHDGR-GWIGDVKVMQ 288
                                       ********99865...577999********9999999866554....23444444433.3444433.3469****** PP

                                       B-THHHHHHH----SS-HHHHHHH CS
                     GDP_Man_Dehyd 308 gdaskakeeLgWkpkvsfeelvre 331
                                        d sk+  + +Wkpk++ +e vr+
  gi|385805672|ref|YP_005842070.1| 289 LDVSKIMGKTNWKPKMNSREAVRK 312
                                       *******************99986 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 !   81.9   0.0   2.3e-26   3.8e-23       1     239 [.       6     237 ..       6     245 .. 0.85

  Alignments for each domain:
  == domain 1  score: 81.9 bits;  conditional E-value: 2.3e-26
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkk..viegDvtdkdkleealegvdvvihlas 75 
                                       +vtGgaGF+G++lv +L++++e  ev v+D   s ++ +  + ++ kk  +i++D+ +  k  + l+g+++v+h a+
  gi|385805672|ref|YP_005842070.1|   6 LVTGGAGFIGSHLVDRLIERGE--EVLVIDDLSSGKTENLERWFGEKKfkFIKADLSEPGKWIDELKGIEAVFHFAA 80 
                                       69*******************6..******77777776666666666666*************************** PP

                         3Beta_HSD  76 lvdvag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKa 151
                                         +v+  +++ +  +++nv+ T nvlea + +g ++++Y Ss  v g+      ++   E+ + ++ + ++y  sK 
  gi|385805672|ref|YP_005842070.1|  81 NPEVRVsTTNPEVHYRANVQATFNVLEASRANGAEIFIYASSSTVYGE----ARVIPTPED-YEPKEPISIYGASKL 152
                                       **999747778889*********************************9....556645554.5567799******** PP

                         3Beta_HSD 152 laEklvlkaNgrtlknggrlyTcaLRpagiyGegdk..llvpllkqlaklglalfkigdeevlsdrvYvgNvawahi 226
                                       + E lv       + +   +    LR a + G +++  +++ ++ +l++  + l  +gd ++ ++++Y +    a +
  gi|385805672|ref|YP_005842070.1| 153 MGEVLVSTYSR--IYG---VKSAMLRFANVVGKRSNhgVIFDFIAKLKRDPERLEILGDGKQRKSYIYIDDAIEATL 224
                                       ***98866554..443...57889*********9873358899**************************99888877 PP

                         3Beta_HSD 227 lAaralqdpkkks 239
                                         + ++++ +++s
  gi|385805672|ref|YP_005842070.1| 225 KVMEHMESSQEMS 237
                                       7777777765555 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.9   0.0   5.8e-23   9.4e-20       2     235 ..       4     265 ..       3     317 .. 0.87

  Alignments for each domain:
  == domain 1  score: 70.9 bits;  conditional E-value: 5.8e-23
                                       EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT....................T--TTSHHHHHHHHHHH--SEEEE- CS
                     RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre....................eldltdaeavaellkeakpdvvvna 58 
                                       +ilvtG+ G +Gs+L+++l e+g evl ++                      ++dl+++ +  + lk    ++v + 
  gi|385805672|ref|YP_005842070.1|   4 RILVTGGAGFIGSHLVDRLIERGEEVLVIDDLssgktenlerwfgekkfkfiKADLSEPGKWIDELKG--IEAVFHF 78 
                                       89***************************665689999999999999998888888888888887777..567**** PP

                                       -----HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-E.EEEEEEGGGS-S-TTS-B-TT.S----SSHHHHHHHHHH CS
                     RmlD_sub_bind  59 AAytavDkaEseeeaayavnaeavealAeaaaavgal.LihvStDyVFdGekkrpYeed.detsPlnvYGrtKlaGE 133
                                       AA  +v    +++e  y++n++a+ ++ ea +a ga  +i+ S+  V+  ++  p  ed ++++P+++YG++Kl GE
  gi|385805672|ref|YP_005842070.1|  79 AANPEVRVSTTNPEVHYRANVQATFNVLEASRANGAEiFIYASSSTVYGEARVIPTPEDyEPKEPISIYGASKLMGE 155
                                       ***********************************9736*********9998777555426789************* PP

                                       HHHHH....H-SSEEEEEE-SEESSSSS-..HHHHHHHHHHH-SEEEEESS..-EE--EEHHHHHHHHHHHHHHCHH CS
                     RmlD_sub_bind 134 qavla....agkkalivRtswvygekgkn..fvktmlrlakereelkvvaD..qlgsPTsardlAevllqllekaae 202
                                         v      +g k +++R++ v g++ +       + +l ++ e+l++  D  q  s  + +d  e++l+++e++ +
  gi|385805672|ref|YP_005842070.1| 156 VLVSTysriYGVKSAMLRFANVVGKRSNHgvIFDFIAKLKRDPERLEILGDgkQRKSYIYIDDAIEATLKVMEHMES 232
                                       ***99766678899*********99555411335678888999******997678888899**************** PP

                                       .GGG-EEEE---BS-EEHHHHHHHHHHHHCHTT CS
                     RmlD_sub_bind 203 ekelagvyHlanegetswlefArailkeagads 235
                                       ++e+++ + +++ +++   ++A  i +e+g  +
  gi|385805672|ref|YP_005842070.1| 233 SQEMSEAFNVGSLDAIGVDDIAYIIEEEMGLGK 265
                                       9*99***99999999999999998888887644 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.8   0.0   1.8e-20   2.9e-17       1     224 [.       5     234 ..       5     267 .. 0.84

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 1.8e-20
                                       EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelk 77 
                                       +lvtG++G iGs+lv++++++  + +++ + +  k  ++e+ +     +kk+k+      +d+ +  +  + l+  +
  gi|385805672|ref|YP_005842070.1|   5 ILVTGGAGFIGSHLVDRLIERGEEVLVIDDLSSGKTENLERWF----GEKKFKFI----KADLSEPGKWIDELK--G 71 
                                       89**************************9*9*99999999987....34455444....79********99999..* PP

                                       -SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEGGGS...............S--SHHH CS
                   Polysacc_synt_2  78 vdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStDKAv...............nPtnvmG 139
                                       +++vfh AA  +V +  +np    + Nv +t nv+ea+ ++g + +++ S+                   +P++++G
  gi|385805672|ref|YP_005842070.1|  72 IEAVFHFAANPEVRVSTTNPEVHYRANVQATFNVLEASRANGAEIFIYASSSTVYgearviptpedyepkEPISIYG 148
                                       ************************************************998643222222333333333479***** PP

                                       HHHHHHHHHHHHGGG--SSS--EEEEEEE-EETT..GTTSSHHHHHHHHHTT.SSEEE.S-TT-EEEEE-HHHHHHH CS
                   Polysacc_synt_2 140 atKrlaekllqalakeseekktkfvvvRfGNVlg..SrGSviplFkkqikeg.gpvtv.TdpemtRyfmtieeavqL 212
                                       a+K++ e l+ ++++       k ++ Rf NV+g  S+  vi  F +++k++ + + +  d +  + ++ i++a++ 
  gi|385805672|ref|YP_005842070.1| 149 ASKLMGEVLVSTYSRIY---GVKSAMLRFANVVGkrSNHGVIFDFIAKLKRDpERLEIlGDGKQRKSYIYIDDAIEA 222
                                       *************9999...8999*********95567789999999999998888872567777789999999999 PP

                                       HHHHHHH--SS- CS
                   Polysacc_synt_2 213 vlqalalakgge 224
                                        l+ ++++++++
  gi|385805672|ref|YP_005842070.1| 223 TLKVMEHMESSQ 234
                                       999999888765 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.9   0.3   1.1e-15   1.9e-12       1     215 [.       7     187 ..       7     194 .. 0.80

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 1.1e-15
                                       EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHHHHHHHHHHT-SS-HHHHHHHHHTTTEEEEE--TTSGGGG-- CS
                     NAD_binding_4   1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksgesaeeRleeelekkelfsallkelaerikvveGDlseprlGLs 77 
                                       +TG+ GF+G++L+ +L+++ +e  + +    + ++  +e l         ++ +    +++ k++++Dlsep     
  gi|385805672|ref|YP_005842070.1|   7 VTGGAGFIGSHLVDRLIERGEE--VLVI--DDLSSGKTENL---------ERWF---GEKKFKFIKADLSEPG---- 63 
                                       7*******************96..3333..33222222333.........2223...467899********98.... PP

                                       HHHHHHHHHH--EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS CS
                     NAD_binding_4  78 eedlqelaeevdviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekv 151
                                         ++ +  + +++++h aA+ ++  ++ +    +r+Nv++t +vle +++  +   +++ S+++v+ge +  v    
  gi|385805672|ref|YP_005842070.1|  64 --KWIDELKGIEAVFHFAANPEVRVSTTNpevHYRANVQATFNVLEASRANGAE-IFIYASSSTVYGEAR--V---- 131
                                       ..555555***********866555443322499************99977666.**************9..3.... PP

                                       -H......HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE-.-SSST-- CS
                     NAD_binding_4 152 yeegekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg.esktGwi 215
                                                  + e  + k+    Y  sK ++E lv +++r  g++ + +R  +++g +s  G+i
  gi|385805672|ref|YP_005842070.1| 132 ---------IPTPEDYEPKEPISIYGASKLMGEVLVSTYSRIYGVKSAMLRFANVVGkRSNHGVI 187
                                       .........67889999999999*********************************966666765 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 !   35.2   0.0   6.7e-12   1.1e-08       1     105 [.       9     129 ..       9     171 .. 0.76

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 6.7e-12
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETT..HHHCHHHH...CTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TC CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRn..peklaele...aeeglevvegdvtdvedlaealkgadaVvsalgggg 72 
                                       G+ G +G++lv++l++rg  e ++++ +  + k+++le    e++ + +++d++++ +  + lkg++aV+  +++ +
  gi|385805672|ref|YP_005842070.1|   9 GGAGFIGSHLVDRLIERG-EE-VLVIDDlsSGKTENLErwfGEKKFKFIKADLSEPGKWIDELKGIEAVFHFAANPE 83 
                                       99***************6.56.5888885433455555444889*************************98886665 PP

                                       C.....HHHH..........HHHHHHHHHHCT--EEEEEEETTTTSGC CS
                    NAD_binding_10  73 k.....deeg..........aknivdaakeagvkRfvlvsaigvgdev 105
                                             +             + n+++a +++g + f++ s+  v+ e+
  gi|385805672|ref|YP_005842070.1|  84 VrvsttN--PevhyranvqaTFNVLEASRANGAEIFIYASSSTVYGEA 129
                                       5555441..04455556667************************9764 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   5.4e-08   8.8e-05       3     138 ..       5     124 ..       3     132 .. 0.79
   2 ?   -2.0   0.0       1.7   2.8e+03      54      64 ..     283     293 ..     228     317 .. 0.65

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 5.4e-08
                                       EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHT..T-EEEE----TT-HHHHHHHHHHHHH CS
                                KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaeleal..gaevevvaaDvsdkdavealleeika 77 
                                        l+tGG+G +G +l++ l+e+g++ lv+   s+        ++++le+   + + ++++aD+s++    ++++e+k 
  gi|385805672|ref|YP_005842070.1|   5 ILVTGGAGFIGSHLVDRLIERGEEVLVIDDLSSG-------KTENLERWfgEKKFKFIKADLSEPG---KWIDELK- 70 
                                       69*************************9777733.......33444443325699*******9997...5677776. PP

                                       HSS---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTTS--SEEEEEEEHH CS
                                KR  78 eeppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelledesldffvlfSSia 138
                                           i+ v+h A   +     ++++ + e  +++ v+++ n+ e+++ +  ++f++ SS  
  gi|385805672|ref|YP_005842070.1|  71 ---GIEAVFHFAANPE----VRVSTTNPEVHYRANVQATFNVLEASRANGAEIFIYASSST 124
                                       ...899****997544....45566666777999********************9988853 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.7
                                       EEEE----TT- CS
                                KR  54 evevvaaDvsd 64 
                                       +v+v+++Dvs+
  gi|385805672|ref|YP_005842070.1| 283 DVKVMQLDVSK 293
                                       34444444444 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   2.3e-07   0.00037       3      65 ..       5      66 ..       3      78 .. 0.79
   2 ?   -1.9   0.0       1.2   1.9e+03     146     162 ..     144     160 ..     139     168 .. 0.75
   3 ?   -2.8   0.0       2.2   3.6e+03     132     136 ..     240     244 ..     214     310 .. 0.59

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.3e-07
                                      EEEESTTSHHHHHHHHHHHHTT-EEEEEES.CHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHH CS
                         adh_short  3 vlvtGassGIGraiakelakeGakvvvvdr.seekleevakelkeegakalaiqvDvtdreeve 65
                                      +lvtG+++ IG  ++++l+++G +v+v+d  s+ k e++   ++e  +k+ +i++D+++  ++ 
  gi|385805672|ref|YP_005842070.1|  5 ILVTGGAGFIGSHLVDRLIERGEEVLVIDDlSSGKTENLERWFGE--KKFKFIKADLSEPGKWI 66
                                      89*************************765155566555556665..68*******99876665 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.2
                                       BHHHHHHHHHHHHHHHH CS
                         adh_short 146 vaaYsAsKaavagltrs 162
                                        + Y+AsK   + l+++
  gi|385805672|ref|YP_005842070.1| 144 ISIYGASKLMGEVLVST 160
                                       689*****877776665 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 2.2
                                       EEEEE CS
                         adh_short 132 vnvsS 136
                                        nv+S
  gi|385805672|ref|YP_005842070.1| 240 FNVGS 244
                                       33333 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   5.5e-05     0.089       1     101 [.       5     121 ..       5     164 .. 0.74
   2 ?    0.1   0.0       0.3   4.9e+02     160     225 ..     194     261 ..     183     268 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.5e-05
                                       EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S....-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE--- CS
                              NmrA   1 IlviGaTGrqGksvvrallkaghkvralvRdt....kselakslkeaGvelvkgdlddkeslvealkgvdvvfsvtg 73 
                                       Ilv+G++G +G+++v+ l+++g +v + + d+    +++l + + e+  +++k+dl +       lkg ++vf   +
  gi|385805672|ref|YP_005842070.1|   5 ILVTGGAGFIGSHLVDRLIERGEEVLV-IDDLssgkTENLERWFGEKKFKFIKADLSEPGKWIDELKGIEAVFHFAA 80 
                                       9**********************9965.4555566344444557788889999999999888888999999987766 PP

                                       GG.............S-HHHHHHHHHHHHHHHS-SEEEEEE CS
                              NmrA  74 fy.............skeiedgkklvdAakeaGvkhfiySs 101
                                                      +++++   ++ +A  + G + fiy+s
  gi|385805672|ref|YP_005842070.1|  81 NPevrvsttnpevhyRANVQATFNVLEASRANGAEIFIYAS 121
                                       33455666666666666666666666666666666666665 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.3
                                       E-TTS.-EEEEESS-TTS-EE-HHHHHHHHHHHHHHHHHHH...TTEEEEE-SEEE-HHHHHHHHHHHH CS
                              NmrA 160 tappedkvtllgpgnpkavlldaeeDiGafvikilkdprkl...kgkriklagntlsgneivelfekki 225
                                       ++ + + +++lg+g+    ++   +D  ++++k++++ +     +      + + + +++i+ ++e+++
  gi|385805672|ref|YP_005842070.1| 194 LKRDPERLEILGDGKQRKSYI-YIDDAIEATLKVMEHMESSqemSEAFNVGSLDAIGVDDIAYIIEEEM 261
                                       444555799999999888888.99999999999999865542112333334556666666666666665 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00016      0.26       5      51 ..      10      61 ..       5      73 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00016
                                      S-SHHHHHHHHHHHHTTEEEEEEESSH....HHHHHH.HHTTSEEEES-TTS CS
                            TrkA_N  5 GlGrvGrslaeeLseggkdvvvidkde....erveel.reeglevvvgdatd 51
                                      G+G +G++l+++L e+g++v+vid+      e++e+   e++++++++d ++
  gi|385805672|ref|YP_005842070.1| 10 GAGFIGSHLVDRLIERGEEVLVIDDLSsgktENLERWfGEKKFKFIKADLSE 61
                                      89*************7768*****8653222223332234447777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 2152.34
//
Query:       gi|385805673|ref|YP_005842071.1|  [L=367]
Description: family 2 glycosyltransferase [Fervidicoccus fontis Kam940]
Scores for complete 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   98.9   0.0    4.1e-28   98.3   0.0    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
      1e-21   77.9   0.0    2.1e-21   76.9   0.0    1.4  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    7.2e-12   45.6   0.0      1e-11   45.2   0.0    1.2  1  Glyco_trans_2_3  Glycosyl transferase family group 2
    4.6e-08   32.7   0.0    2.1e-07   30.6   0.0    2.0  3  Glyco_transf_21  Glycosyl transferase family 21
    2.6e-06   27.1   0.0    4.1e-06   26.5   0.0    1.2  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
    0.00039   20.9   0.1    0.00067   20.1   0.1    1.4  1  Glyco_tranf_2_4  Glycosyl transferase family 2
  ------ inclusion threshold ------
      0.069   13.1   0.0       0.16   11.9   0.0    1.5  1  YAcAr            YspA, cpYpsA-related SLOG family
       0.68   10.0   2.5         69    3.6   0.0    2.4  2  Col_cuticle_N    Nematode cuticle collagen N-terminal domain


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.3   0.0   1.8e-31   4.1e-28       1     170 []      46     215 ..      46     215 .. 0.93

  Alignments for each domain:
  == domain 1  score: 98.3 bits;  conditional E-value: 1.8e-31
                                       EEEEEESS-TTTHHHHHHHHHHH.GGCCEEEEEEEEES-SSCHHHHHGGGCH..C-TTEEEEEESSS-HHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaq.dpypdfeiivvDDgStDetveileelak..edprvrvirreenvGkagalnag 74 
                                       +v++ptyNe+k++++ l+ + aq +p++++e+i++D +S+D+t ei+e++ +  ++ ++++i  + ++Gka +ln++
  gi|385805673|ref|YP_005842071.1|  46 TVIVPTYNEAKLIEKKLDDIYAQeYPRDRLEVILIDSASSDGTLEIAEKWKEehGEINLKIIGEDSRRGKAHSLNEA 122
                                       69************************************************99************************* PP

                                       HHH--SSEEEEEESSEEE-TT.HHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCC CS
                   Glycos_transf_2  75 lraatgdyilflDaDdepdpd.wleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgn 150
                                       l+++tg+++++ DaD+ +     l + +e++ ++ +++v +  +  ++e   ie  +    +  ++  +   s+ ++
  gi|385805673|ref|YP_005842071.1| 123 LKHSTGEIVVITDADSFWGTRdSLGRAAEWFSDPSVGAVSCLKDPEGSEAPSIELGY----RGYYNVLRVAESKAYS 195
                                       ****************996655***********888777777777777777777775....6999999999****** PP

                                       STTCSTCCCEEEEHHHHHCH CS
                   Glycos_transf_2 151 lsfeigsaallrrealeell 170
                                       +++++g  a +r+++lee++
  gi|385805673|ref|YP_005842071.1| 196 TPIFHGELASFRKDLLEEVG 215
                                       *****************985 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 !   76.9   0.0   9.2e-25   2.1e-21       1     215 [.      43     253 ..      42     267 .. 0.85

  Alignments for each domain:
  == domain 1  score: 76.9 bits;  conditional E-value: 9.2e-25
                   Glyco_tranf_2_3   1 prdlavlVptfneedvlgevlesllaqeypr..vevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgk 75 
                                       p  ++v+Vpt+ne++ +++ l+++ aqeypr  +ev++++  s+++tle ae   ++++ + ++++  ++  +++gk
  gi|385805673|ref|YP_005842071.1|  43 PK-ITVIVPTYNEAKLIEKKLDDIYAQEYPRdrLEVILIDSASSDGTLEIAEKWKEEHGEINLKII-GED--SRRGK 115
                                       45.9*************************7777*******************************88.444..789** PP

                   Glyco_tranf_2_3  76 sralnealravksdlvllvDdDtvv.ePdtlkrllqffltpkvgavgtpvfllnrstlvsalgalefaerhl.rfla 150
                                       +++lneal++ ++++v++ D+D+ +   d+l r++ +f +p+vgav + +  +  ++        e++ r   ++l+
  gi|385805673|ref|YP_005842071.1| 116 AHSLNEALKHSTGEIVVITDADSFWgTRDSLGRAAEWFSDPSVGAVSCLKDPEGSEAPSI-----ELGYRGYyNVLR 187
                                       *************************88999****************99887765444444.....444444413334 PP

                   Glyco_tranf_2_3 151 ar..ralgvltlnGsgslirrevlkelegldplflltdDyelglrlrragfrtayvpgaavrevfps 215
                                       ++  +a ++++++G++  +r ++l+e + +    +  dD +++  + + g+r  + +++++ e+ p+
  gi|385805673|ref|YP_005842071.1| 188 VAesKAYSTPIFHGELASFRKDLLEEVGEFPV-DIGSDDSHTATKIAAMGYRAIIPEDVLCKELVPK 253
                                       442255578999***************99999.9999****************99999999998664 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 !   45.2   0.0   4.5e-15     1e-11       1     192 [.     130     332 ..     130     352 .. 0.72

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 4.5e-15
                   Glyco_trans_2_3   1 iilllDaDtv.lppdclreiaaelaspevaivqgpvlvm.nvanwleelaalffaedhgkdilvrealgrvvpsvGs 75 
                                       i+++ DaD+   ++d+l ++a+++++p v++v++   ++   a+ +e  +   ++     +++  ++  ++  ++G 
  gi|385805673|ref|YP_005842071.1| 130 IVVITDADSFwGTRDSLGRAAEWFSDPSVGAVSCLKDPEgSEAPSIELGYRGYYN----VLRVAESKAYSTPIFHGE 202
                                       68999****9679*************************96679999999999885....3444444555566799** PP

                   Glyco_trans_2_3  76 gaflrrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkekspl.tlraalrQrkRwayGc.....el 146
                                        a++r ++l+evg ++   +  s+D + + ++++ Gyr +  +++l+ke +p   +  ++ +r+ ++        +l
  gi|385805673|ref|YP_005842071.1| 203 LASFRKDLLEEVGEFP--VDIGSDDSHTATKIAAMGYRAIIPEDVLCKELVPKrGYNSWRIRRAQHLVQHfmkamKL 277
                                       ****************..99*********************************78999*******999966655411 PP

                   Glyco_trans_2_3 147 .......eklillvrllgylgsl.lwsa.lplhlallllfsllalalvlllllll 192
                                              + +il+v  +  l+++ ++ +  +l+ a +++ sl++l++++l ++ll
  gi|385805673|ref|YP_005842071.1| 278 kvkapknFDRILKVEEYLHLMNPwILLGgAVLLSASAIMGSLISLIFLALGIALL 332
                                       4455555555555544433333212222122222333444444444433333332 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 ?   -2.8   0.0       1.7   3.8e+03      12      30 ..      38      56 ..      36      56 .. 0.87
   2 !   30.6   0.0   9.4e-11   2.1e-07      16     162 ..     113     260 ..     105     269 .. 0.87
   3 ?   -2.2   0.2       1.1   2.5e+03     160     173 .]     351     364 ..     338     364 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.7
                   Glyco_transf_21 12 pvgvnpKvnnllqaleaak 30
                                      ++g +pK+  +++++++ak
  gi|385805673|ref|YP_005842071.1| 38 EEGFKPKITVIVPTYNEAK 56
                                      68999*********99986 PP

  == domain 2  score: 30.6 bits;  conditional E-value: 9.4e-11
                   Glyco_transf_21  16 npKvnnllqaleaakydllvisDsdvrv.kpdyLeellaaledpkvglVtslpvgsdakglaaaleaaflntlagvl 91 
                                       + K + l+ al+    +++vi D+d +  ++d L + ++ ++dp vg V++l    + +    +l     + + +v+
  gi|385805673|ref|YP_005842071.1| 113 RGKAHSLNEALKHSTGEIVVITDADSFWgTRDSLGRAAEWFSDPSVGAVSCLKDPEGSEAPSIELGYRGYYNVLRVA 189
                                       5699999******************998468*******************997555555555555555558999999 PP

                   Glyco_transf_21  92 qaklsglgfavGksmalrreaLeaiGGfealadeLAeDyalgkllraaGlkvvlspapiaqtsvpr..rsslr 162
                                        +k+  + +  G    +r++ Le++G f    d   +D  +++ ++a G++ ++ +++++++ vp+  ++s+r
  gi|385805673|ref|YP_005842071.1| 190 ESKAYSTPIFHGELASFRKDLLEEVGEFPV--DIGSDDSHTATKIAAMGYRAIIPEDVLCKELVPKrgYNSWR 260
                                       9999999*********************99..7778****************************987777776 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.1
                   Glyco_transf_21 160 slrallaRqlrWar 173
                                        +++l++R++ W +
  gi|385805673|ref|YP_005842071.1| 351 AIKNLWSREIVWEK 364
                                       57899******975 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   1.8e-09   4.1e-06       1      99 [.      46     146 ..      46     153 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1.8e-09
                   Glyco_tranf_2_2   1 svviplraseerhyieervlqk.akyy.deeielivvddgSsekfleevssiidlnllvylkdeddk.ayslaaarN 74 
                                       +v++p +++ +   ie ++  + a+ y  + +e+i++d  Ss+ +le  ++ ++ ++++ lk   +    ++a + N
  gi|385805673|ref|YP_005842071.1|  46 TVIVPTYNEAKL--IEKKLDDIyAQEYpRDRLEVILIDSASSDGTLEIAEKWKEEHGEINLKIIGEDsRRGKAHSLN 120
                                       799999998887..****9554133355899****************************99987665599******* PP

                   Glyco_tranf_2_2  75 rGaskaesdlvlFlDaDcfi.ssDkf 99 
                                          +++ +++v+  DaD f+ + D +
  gi|385805673|ref|YP_005842071.1| 121 EALKHSTGEIVVITDADSFWgTRDSL 146
                                       *******************9455666 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 !   20.1   0.1     3e-07   0.00067       1      89 [.      52     145 ..      52     152 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3e-07
                   Glyco_tranf_2_4   1 rneadiLpefla..hhlalgfdr..ilvydndstDgtrailkelpe.vkllhvdksyederrq.vellkallaryae 71 
                                       +nea+++++ l+  ++ ++ +dr  ++++d  s+Dgt +i ++++e    ++ +   ed+rr+  + l+++l++ + 
  gi|385805673|ref|YP_005842071.1|  52 YNEAKLIEKKLDdiYAQEYPRDRleVILIDSASSDGTLEIAEKWKEeHGEINLKIIGEDSRRGkAHSLNEALKH-ST 127
                                       5999999999994444444456555999****************663445556655578888834588988866.79 PP

                   Glyco_tranf_2_4  72 adwvlvvDaDEflvvpds 89 
                                       ++ v+  DaD f  ++ds
  gi|385805673|ref|YP_005842071.1| 128 GEIVVITDADSFWGTRDS 145
                                       **********99888774 PP

>> YAcAr  YspA, cpYpsA-related SLOG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   7.1e-05      0.16      10      54 ..      51     100 ..      48     104 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.1e-05
                             YAcAr  10 dfadleliwatLdklhaeapi....dmvlvhGga.kGaDrlAarWAaerg 54 
                                       ++++ +li+++Ld ++a+       +++l+  ++  G   +A++W +e+g
  gi|385805673|ref|YP_005842071.1|  51 TYNEAKLIEKKLDDIYAQEYPrdrlEVILIDSASsDGTLEIAEKWKEEHG 100
                                       699*************9877779999********9**********99987 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 ?    3.6   0.0     0.031        69      17      39 ..     195     217 ..     193     220 .. 0.92
   2 ?    2.2   4.1     0.088     2e+02       2      20 ..     306     324 ..     306     327 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.031
                     Col_cuticle_N  17 tlpsiyndiqsfqsevldemdef 39 
                                       + p+ + ++ sf+ ++l+e+ ef
  gi|385805673|ref|YP_005842071.1| 195 STPIFHGELASFRKDLLEEVGEF 217
                                       78999****************99 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.088
                     Col_cuticle_N   2 vavalStvailsslitlps 20 
                                       +av lS+ ai +sli+l +
  gi|385805673|ref|YP_005842071.1| 306 GAVLLSASAIMGSLISLIF 324
                                       699************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.54
# Mc/sec: 2034.22
//
Query:       gi|385805674|ref|YP_005842072.1|  [L=332]
Description: glycosyltransferase, family 4 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-30  106.4   1.4    3.8e-30  105.1   1.2    1.7  2  Glyco_transf_4   Glycosyltransferase Family 4
    1.5e-19   70.2   0.1    2.7e-19   69.3   0.1    1.4  1  Glycos_transf_1  Glycosyl transferases group 1
    4.4e-17   63.0   0.0    6.7e-17   62.4   0.0    1.3  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    9.7e-14   51.9   0.0    6.6e-13   49.2   0.0    2.0  2  Glyco_trans_1_4  Glycosyl transferases group 1
    2.1e-05   24.6   0.9    5.4e-05   23.2   0.3    1.8  2  Glyco_trans_4_2  Glycosyl transferase 4-like
  ------ inclusion threshold ------
      0.021   14.5   1.1       0.69    9.6   0.0    2.2  2  Glyco_transf_5   Starch synthase catalytic domain
      0.023   14.1   0.4       0.56    9.6   0.0    2.7  2  AP_endonuc_2     Xylose isomerase-like TIM barrel


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 !  105.1   1.2   1.5e-33   3.8e-30       1     169 [.       9     181 ..       9     182 .. 0.92
   2 ?   -1.5   0.0      0.84   2.1e+03     118     144 ..     247     273 ..     211     289 .. 0.62

  Alignments for each domain:
  == domain 1  score: 105.1 bits;  conditional E-value: 1.5e-33
                    Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvvtpgddgpleeev.elvvrvprvplpllkrllrslaflrrlrrllkre..kpD 74 
                                       +GGve +v  +a++Lar+Gh+V +++ ++d + ++e+ ++ v+v+r+p +++ ++++++ ++++l ++l+      D
  gi|385805674|ref|YP_005842072.1|   9 IGGVEYVVKSIAERLARMGHDVIILAGKPDSEKPYEEvVNEVNVIRWPVWSPSGAYHIPKMHSKLDKQLRDVlnYLD 85 
                                       7***************************99999999999999*****************************9*999* PP

                    Glyco_transf_4  75 vvHahspaalgaallalrr...rlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSeatadel 148
                                       vvH+hs+++++ ++  l+    + +i+lV+t H +   + + + ++ l+ l+r+ + +l+  +  v avS+ +a ++
  gi|385805674|ref|YP_005842072.1|  86 VVHVHSAHSIFSVYTGLAVkklKPDIRLVFTPHYHG--GGHSFTRNALWFLWRRRMSKLVEISSMVHAVSKPEASRI 160
                                       *******999765544444449**********9999..778888888888888888999****************** PP

                    Glyco_transf_4 149 rerygvppekitVipnGvDle 169
                                       + +y+ ++ek++VipnG+  +
  gi|385805674|ref|YP_005842072.1| 161 LNHYPKANEKLVVIPNGIEED 181
                                       ******************876 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.84
                    Glyco_transf_4 118 plsrllralerrllrradrviavSeat 144
                                       +++ l ra +  ll++a+ vi +Se +
  gi|385805674|ref|YP_005842072.1| 247 FKNFLPRAQYLDLLSKARYVINPSERE 273
                                       333333333444477777777777765 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 !   69.3   0.1   1.1e-22   2.7e-19      13     157 ..     190     330 ..     184     332 .] 0.93

  Alignments for each domain:
  == domain 1  score: 69.3 bits;  conditional E-value: 1.1e-22
                                       TT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHH CS
                   Glycos_transf_1  13 ekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleel 89 
                                       ++  ++++ gr+ek+K+++ +i+++++l       +kl+++Gng+++k+l+++ae +   + v f  +++r +   l
  gi|385805674|ref|YP_005842072.1| 190 KDSDYMIYAGRIEKYKNLEKAIEVARQL------GLKLLLIGNGPYKKRLEAKAE-RTYPNAVAFKNFLPRAQYLDL 259
                                       678899********************77......89*****************65.5666***************** PP

                                       HHCESEEEEEESSBSS-HHHHHHHHTT--EEEET.TTTHCHHCHTTT.SEEEE-TT.-HHHHHHHHHHHHH CS
                   Glycos_transf_1  90 lknadifvlpsisEgfGivllEAmaaglpviasn.aggpaevvkdge.tGllvkpn.naealaeairklle 157
                                       l++a  ++ ps++E+f i + EA+a g+p+i+s  +  +++v  ++   Gl+v ++  +e++++ +rk+l+
  gi|385805674|ref|YP_005842072.1| 260 LSKARYVINPSEREAFSIFIAEALAMGVPAIISRnIAENLDVNGSEMvEGLVVVEKgLVETWNNVLRKYLS 330
                                       *********************************999*******999889**99999999999999999886 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 !   62.4   0.0   2.6e-20   6.7e-17       1     160 []      10     177 ..      10     177 .. 0.74

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 2.6e-20
                   Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapg.apeleedgvrvhrlpvprrps...pladlaal.ralrrllrqrre 72 
                                       gG++ +v  +a++La+ Gh+V +l+ +p+ + ++e++ + v v+r pv   ++    +++++ l  +lr++l     
  gi|385805674|ref|YP_005842072.1|  10 GGVEYVVKSIAERLARMGHDVIILAGKPDSEkPYEEVVNEVNVIRWPVWSPSGayhIPKMHSKLdKQLRDVL----N 82 
                                       8************************8877772557999*******997644432235556655534667776....9 PP

                   Glyco_trans_4_4  73 rpdvvhahspt...aglaarlar.rrrgiplvvtlh....glllrrgsgavrrlyralerrllrradavlvvseaea 141
                                         dvvh+hs +   + + +++ + ++ +i+lv+t+h    g+ ++r + +   l+r+  + l+     v++vs  ea
  gi|385805674|ref|YP_005842072.1|  83 YLDVVHVHSAHsifSVYTGLAVKkLKPDIRLVFTPHyhggGHSFTRNALW--FLWRRRMSKLVEISSMVHAVSKPEA 157
                                       99****999664544444445553456*********44433444444333..3446667899999************ PP

                   Glyco_trans_4_4 142 eelra.lgvpadrvvvvpng 160
                                        ++   +  + +++vv+png
  gi|385805674|ref|YP_005842072.1| 158 SRILNhYPKANEKLVVIPNG 177
                                       *****6667899*******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 ?    0.3   0.0      0.34   8.7e+02      12      51 ..       7      48 ..       3      96 .. 0.71
   2 !   49.2   0.0   2.6e-16   6.6e-13       4     118 ..     195     315 ..     192     330 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.34
                                      GG.GTHHHHHHHH.HHHH.H.HEEEEEES---...HHHHHHHT CS
                   Glyco_trans_1_4 12 envkgvdllleav.pllrkk.dvrlvivGdgp.rpeeleelaa 51
                                      +++ gv+++++ + ++l++  +  ++++G +p  ++ +ee ++
  gi|385805674|ref|YP_005842072.1|  7 PHIGGVEYVVKSIaERLARMgHDVIILAG-KPdSEKPYEEVVN 48
                                      56678999999997777744323577777.4443345554444 PP

  == domain 2  score: 49.2 bits;  conditional E-value: 2.6e-16
                                       EEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---...HHHHHHHT.T-T.TEEEE---..THHHHHHHH-SEE CS
                   Glyco_trans_1_4   4 ilfvGrleenvkgvdllleavpllrkkdvrlvivGdgp.rpeeleelaa.gleerveftGfv..edlaellaaadvf 76 
                                       +++ Gr+ e++k+++  +e + +l    ++l+++G+gp + ++le++a+  + + v f  f+  ++  +ll++a+ +
  gi|385805674|ref|YP_005842072.1| 195 MIYAGRI-EKYKNLEKAIEVARQLG---LKLLLIGNGPyK-KRLEAKAErTYPNAVAFKNFLprAQYLDLLSKARYV 266
                                       7899999.67799999999998888...79********65.6***9997566566*******76679999******* PP

                                       EE--..---SHHHHHHHHTT-EEEE-TGGGTTT--...T...TSSEE-.-T CS
                   Glyco_trans_1_4  77 vaPs..egfglkllEamaaglpvVatdvggiaevv...g...engllv.pp 118
                                       ++Ps  e f++ + Ea+a+g+p + ++   iae +   g   ++gl+v ++
  gi|385805674|ref|YP_005842072.1| 267 INPSerEAFSIFIAEALAMGVPAIISRN--IAENLdvnGsemVEGLVVvEK 315
                                       ****888*******************86..445443443444566555243 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 !   23.2   0.3   2.1e-08   5.4e-05      11     107 ..      14     118 ..       9     143 .. 0.77
   2 ?   -1.1   0.0      0.69   1.8e+03      47     103 ..     149     211 ..     136     231 .. 0.70

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 2.1e-08
                   Glyco_trans_4_2  11 vhtlrlakeLakrgyeVhvitpkkga.kdele.aegihvhrlkvdrkgpleyl.kaf.kl.kklikkikP.Dvvhah 81 
                                       ++++ +a+ La  g++V ++  k+++ k ++e  + ++v+r++v + + +  + k+  kl k+l + +++ Dvvh+h
  gi|385805674|ref|YP_005842072.1|  14 YVVKSIAERLARMGHDVIILAGKPDSeKPYEEvVNEVNVIRWPVWSPSGAYHIpKMHsKLdKQLRDVLNYlDVVHVH 90 
                                       567788999************988887776664999******98777766666566557766666666655****** PP

                   Glyco_trans_4_2  82 yakpy..gllgslaarlsgvipvvlsvw 107
                                        a ++  ++ g ++++l+  i++v++ +
  gi|385805674|ref|YP_005842072.1|  91 SAHSIfsVYTGLAVKKLKPDIRLVFTPH 118
                                       **99985566666667888888888765 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.69
                   Glyco_trans_4_2  47 vhrlkvd..rkgpleylkaf.klkklikkikPDvvhahya...kpygllgslaarlsgvipvv 103
                                       vh + ++  +++   y ka+ kl+ + + i+ Dv+   ++   ++y+++++ + + ++  + +
  gi|385805674|ref|YP_005842072.1| 149 VHAVSKPeaSRILNHYPKANeKLVVIPNGIEEDVLEYKWIgkdSDYMIYAGRIEKYKNLEKAI 211
                                       444544433666777777776788888888888888877777778888887777777766665 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 ?    9.6   0.0   0.00027      0.69      14      45 ..       8      39 ..       1      74 [. 0.76
   2 ?    3.4   0.3     0.021        54     133     222 ..      84     153 ..      73     171 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00027
                    Glyco_transf_5 14 ktGGLadvvgaLpkaLaklghdvrvilPryga 45
                                        GG+  vv+++++ La++ghdv ++  + ++
  gi|385805674|ref|YP_005842072.1|  8 HIGGVEYVVKSIAERLARMGHDVIILAGKPDS 39
                                      68*********************999866633 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.021
                    Glyco_transf_5 133 pdvihahDWhtalvpallkelykerglfkkiktvftiHNlayqgrfpkdelaalglpaedfekldglefygkvnflk 209
                                        dv+h+h  h+ +  ++   +   ++l  +i++vft H   y+g  ++ + +al++ ++++              + 
  gi|385805674|ref|YP_005842072.1|  84 LDVVHVHSAHSIFS-VYTGLAV--KKLKPDIRLVFTPH---YHGGGHSFTRNALWFLWRRR--------------MS 140
                                       69999999998877.4444443..245567********...44444433334566664432..............44 PP

                    Glyco_transf_5 210 agivyadavttVS 222
                                         + ++ +v++VS
  gi|385805674|ref|YP_005842072.1| 141 KLVEISSMVHAVS 153
                                       4444555555555 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 ?    0.7   0.2      0.12     3e+02     163     192 ..      64      93 ..      62     123 .. 0.85
   2 ?    9.6   0.0   0.00022      0.56      61     108 ..     200     240 ..     179     247 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.12
                                       HHHHHHTTTHHHHHHHHHGGEEEEEE.EES CS
                      AP_endonuc_2 163 gHlliaeedvddalraladrikhvHikDak 192
                                       +H+  ++  +d++lr + +++  vH++ a 
  gi|385805674|ref|YP_005842072.1|  64 YHIPKMHSKLDKQLRDVLNYLDVVHVHSAH 93 
                                       57777788999*********9999998665 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00022
                                       TTCSHHHHHHHHHHHHHHHHHHTBSEEEEEBCCGBCTTTSGHHHHHHH CS
                      AP_endonuc_2  61 rearreesvdalkraielaaaLGapllvlhpGtagagpkgseeeawer 108
                                       r ++     ++l++aie a++LG +ll ++ G    + k+ e+ a ++
  gi|385805674|ref|YP_005842072.1| 200 RIEK----YKNLEKAIEVARQLGLKLLLIGNG---PYKKRLEAKAERT 240
                                       4455....899*******************88...7777777766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2018.82
//
Query:       gi|385805675|ref|YP_005842073.1|  [L=169]
Description: glycosyltransferase [Fervidicoccus fontis Kam940]
Scores for complete 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   83.3   0.0    1.7e-23   83.0   0.0    1.0  1  Glycos_transf_1  Glycosyl transferases group 1
      7e-18   65.4   0.0    8.9e-18   65.0   0.0    1.1  1  Glyco_trans_1_4  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.0   0.0   1.9e-27   1.7e-23      40     170 ..      11     143 ..       7     145 .. 0.94

  Alignments for each domain:
  == domain 1  score: 83.0 bits;  conditional E-value: 1.9e-27
                                       CCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHHCESEEEEEESS...BSS-HHHHHHH CS
                   Glycos_transf_1  40 lkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleellknadifvlpsis...EgfGivllEAm 113
                                       l  +++ n++ vi+G   ++  +++la++l++s++v f+g+v+++ ++  + ++ ++ lps s   E+  ++++EA 
  gi|385805675|ref|YP_005842073.1|  11 LATREELNLRAVIVG-PGDQRLYRELADKLGISNKVLFTGFVDEDTKIGAIDASIALTLPSLSnyvEAYSLAITEAW 86 
                                       55567899*******.77778899*******************999******************************* PP

                                       HTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHHHHHHHH CS
                   Glycos_transf_1 114 aaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelrerlgenar 170
                                       a  +pvias++g ++  vk+  +Gl+v+p +++alaeai+ l++d+ l e+lge ++
  gi|385805675|ref|YP_005842073.1|  87 AREKPVIASATGEIPYRVKHMINGLVVPPRDPKALAEAIKILIQDRGLGEKLGEIGK 143
                                       **********************************************99999999887 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 !   65.0   0.0   9.9e-22   8.9e-18      29     134 .]      15     131 ..       5     131 .. 0.84

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 9.9e-22
                                       .H.HEEEEEES---..HHHHHHHT..T-T.TEEEE---.TH.HHHHHHH-SEEEE--.....---SHHHHHHHHTT- CS
                   Glyco_trans_1_4  29 kk.dvrlvivGdgprpeeleelaa..gleerveftGfv.ed.laellaaadvfvaPs.....egfglkllEamaagl 95 
                                       ++ ++r vivG g+++  ++ela+  g++++v ftGfv ed +  +++a+  + +Ps     e  +l++ Ea a ++
  gi|385805675|ref|YP_005842073.1|  15 EElNLRAVIVGPGDQR-LYRELADklGISNKVLFTGFVdEDtKIGAIDASIALTLPSlsnyvEAYSLAITEAWAREK 90 
                                       333599*****88643.4444443569999********7556888888888889999*99999************** PP

                                       EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH- CS
                   Glyco_trans_1_4  96 pvVatdvggiaevv..gengllvppgdpealaeailrLled 134
                                       pv+a+++g i+  v    ngl+vpp+dp+alaeai  L++d
  gi|385805675|ref|YP_005842073.1|  91 PVIASATGEIPYRVkhMINGLVVPPRDPKALAEAIKILIQD 131
                                       *******99999887669********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 1074.32
//
Query:       gi|385805676|ref|YP_005842074.1|  [L=127]
Description: Methylase involved in ubiquinone/menaquinone biosynthesis-like protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-19   69.8   0.0    2.7e-19   69.6   0.0    1.1  1  Methyltransf_11  Methyltransferase domain
      1e-16   61.1   0.0    1.3e-16   60.8   0.0    1.0  1  MetW             Methionine biosynthesis protein MetW
    5.4e-15   55.9   0.0    6.5e-15   55.6   0.0    1.1  1  Methyltransf_25  Methyltransferase domain
    6.5e-15   55.3   0.0    7.8e-15   55.1   0.0    1.0  1  Methyltransf_23  Methyltransferase domain
    2.5e-13   50.6   0.0    3.5e-13   50.1   0.0    1.2  1  Methyltransf_12  Methyltransferase domain
    1.3e-12   47.8   0.0    1.9e-12   47.3   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
      2e-07   30.6   0.0    2.6e-07   30.2   0.0    1.0  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    2.4e-06   26.4   0.0    2.6e-06   26.3   0.0    1.0  1  Methyltransf_29  Putative S-adenosyl-L-methionine-dependent m
     0.0052   16.2   0.1       0.15   11.4   0.1    2.0  1  Spermine_synth   Spermine/spermidine synthase domain
  ------ inclusion threshold ------
      0.021   14.4   0.0      0.025   14.2   0.0    1.1  1  NodS             Nodulation protein S (NodS)
      0.042   13.4   0.0      0.081   12.5   0.0    1.6  1  MTS              Methyltransferase small domain
      0.054   12.9   0.0      0.068   12.5   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
       0.19   11.2   0.0       0.67    9.4   0.0    1.8  2  Methyltransf_4   Putative methyltransferase


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.6   0.0     2e-22   2.7e-19       2      96 .]      11     103 ..      10     103 .. 0.89

  Alignments for each domain:
  == domain 1  score: 69.6 bits;  conditional E-value: 2e-22
                                       EET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECC..CTSS-TT-EEEEEEES-CCC- CS
                   Methyltransf_11   2 dvGcGtGrlaealakrg..arvvgvDlskemlklakekaseeglkvefvvadae..klpfednsfDlvvssevlhhv 74 
                                       ++G G G+++ ++ak++  + ++g+D++ e+l+ a+ek+         v+ad+   kl f+dn+fD+v++ ev++h+
  gi|385805676|ref|YP_005842074.1|  11 ELGFGDGSILSEVAKHVrvRALYGCDINYEALNKASEKGIIT------VKADLNtdKLSFPDNYFDAVIMEEVIEHL 81 
                                       79************99999*************7776555443......777777336******************** PP

                                       CCHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  75 edpekalkeiaRvLkpgGllvi 96 
                                        +p+ al+e++R+Lkp+G++++
  gi|385805676|ref|YP_005842074.1|  82 VNPDNALEEAYRILKPDGIFIL 103
                                       *******************985 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.8   0.0   9.3e-20   1.3e-16      17     123 ..       9     119 ..       5     124 .. 0.92

  Alignments for each domain:
  == domain 1  score: 60.8 bits;  conditional E-value: 9.3e-20
                              MetW  17 vldlGcGdGellellkeekqvdg.rGleldeegvaecvakGlsviqgdldkdlenfedksfdyvvlsqtlqatrnpk 92 
                                       +++lG GdG++l+ ++++  v++ +G +++ e+++++ +kG+  ++ dl++d   f+d+ fd v++   +  + np+
  gi|385805676|ref|YP_005842074.1|   9 IIELGFGDGSILSEVAKHVRVRAlYGCDINYEALNKASEKGIITVKADLNTDKLSFPDNYFDAVIMEEVIEHLVNPD 85 
                                       789**********999999999879**************************************************** PP

                              MetW  93 evldellrigrr...aivsfPnfGhWrvrlslls 123
                                       + l+e  ri +     i++ Pn+ +W  r+ ll 
  gi|385805676|ref|YP_005842074.1|  86 NALEEAYRILKPdgiFILTTPNLAWWVNRFILLL 119
                                       *********874333799***********99985 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.6   0.0   4.7e-18   6.5e-15       1      97 []       9      99 ..       9      99 .. 0.92

  Alignments for each domain:
  == domain 1  score: 55.6 bits;  conditional E-value: 4.7e-18
                                      EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBC..CGBSSSTTTEEEEEEESTGGGS CS
                   Methyltransf_25  1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgda..edlpfedgsfDlvvssgalhhl 77
                                      +++lG G G ++ ++ak++    ++g+Di+ e+l++a e+       +  v++d+  ++l+f+d+ fD+v++  +++hl
  gi|385805676|ref|YP_005842074.1|  9 IIELGFGDGSILSEVAKHVRVRALYGCDINYEALNKASEKG------IITVKADLntDKLSFPDNYFDAVIMEEVIEHL 81
                                      789***************9889*****************99......899999995556*************777***8 PP

                                      SHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25 78 sdedlekalkeiarvLkpgG 97
                                       ++d  +al+e++r+Lkp+G
  gi|385805676|ref|YP_005842074.1| 82 VNPD--NALEEAYRILKPDG 99
                                      8777..89***********9 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.1   0.0   5.7e-18   7.8e-15      25     123 ..       8     109 ..       4     121 .. 0.83

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 5.7e-18
                   Methyltransf_23  25 rvLdiGcGtG.illevlrengf.svtgvDlspeaveiae.......kakkaqkdqfdeqeaaepqgkfdlIvlrevl 92 
                                       +++++G G+G il+ev++  ++  ++g D++ ea ++a+       k      d    ++ ++p+++fd +++ ev+
  gi|385805676|ref|YP_005842074.1|   8 SIIELGFGDGsILSEVAKHVRVrALYGCDINYEALNKASekgiitvK-----ADLN-TDKLSFPDNYFDAVIMEEVI 78 
                                       689*******55666666666689**************997444433.....3333.566669************** PP

                   Methyltransf_23  93 ehvpdppellrqiatllkpgGylllseplas 123
                                       eh+ +p  +l  ++++lkp+G ++l++p+  
  gi|385805676|ref|YP_005842074.1|  79 EHLVNPDNALEEAYRILKPDGIFILTTPNLA 109
                                       ****************************754 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1   0.0   2.5e-16   3.5e-13       2      99 .]      11     101 ..      10     101 .. 0.80

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 2.5e-16
                   Methyltransf_12   2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhh 78 
                                       e+G G+Gs+l++++++ +   ++g+Di+ +a+++a+ek   ++    + ++ ++l+    ++ ++fD+v++ +v++h
  gi|385805676|ref|YP_005842074.1|  11 ELGFGDGSILSEVAKHVRVRALYGCDINYEALNKASEK--GIIT-VKADLNTDKLS----FPDNYFDAVIMEEVIEH 80 
                                       99**************9999999*********444444..4442.22333333333....3345************* PP

                   Methyltransf_12  79 lkdirevldnirklLkpgGrl 99 
                                       l +++ +l+++++ Lkp+G++
  gi|385805676|ref|YP_005842074.1|  81 LVNPDNALEEAYRILKPDGIF 101
                                       *******************85 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   0.0   1.3e-15   1.9e-12       6     114 ..       8     108 ..       6     120 .. 0.85

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 1.3e-15
                   Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsne 82 
                                       ++++lG G G ++ e a+ ++    ++G Di+ ea+++A e    +g+  v+    +  +l+  + d+ fD ++  e
  gi|385805676|ref|YP_005842074.1|   8 SIIELGFGDGSILSEVAKHVRV-RALYGCDINYEALNKASE----KGIITVKADL-NTDKLS--FPDNYFDAVIMEE 76 
                                       5899*************84443.348**************9....6888777655.233344..779********** PP

                   Methyltransf_31  83 vlnaladpdkileeiervlkpggilliedprl 114
                                       v+ +l +pd++lee+ r lkp+gi+++++p+l
  gi|385805676|ref|YP_005842074.1|  77 VIEHLVNPDNALEEAYRILKPDGIFILTTPNL 108
                                       ******************************93 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   1.9e-10   2.6e-07      50     150 ..       8     102 ..       2     109 .. 0.89

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 1.9e-10
                                       EEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES-G CS
                   Ubie_methyltran  50 kvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtvsfGl 126
                                       +++++  G g +  +++++v+ +  + ++Din + L+    k+ e+g i ++    n+ +L f d+ fD v +   +
  gi|385805676|ref|YP_005842074.1|   8 SIIELGFGDGSILSEVAKHVRVR-ALYGCDINYEALN----KASEKGIITVKA-DLNTDKLSFPDNYFDAVIMEEVI 78 
                                       789999999***********988.589*****99886....667778888875.6699******************* PP

                                       GG-S-HHHHHHHHHHHEEEEEEEE CS
                   Ubie_methyltran 127 rnvtDklkaLkeayrvlkpGGrlv 150
                                         + + ++aL+eayr+lkp G+++
  gi|385805676|ref|YP_005842074.1|  79 EHLVNPDNALEEAYRILKPDGIFI 102
                                       *********************986 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 !   26.3   0.0   1.9e-09   2.6e-06     115     222 ..       3     108 ..       1     114 [. 0.88

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.9e-09
                   Methyltransf_29 115 ggkvrtvlDvGCgvasfgayllsrdvltlslapkDeheaqvqfaLeRgvpailavlgtkrlpyPsrsfdlihCsrCr 191
                                       gg++  ++++G g  s  + +  ++v   +l   D   + +  a e+g+ ++ a l t +l++P + fd +      
  gi|385805676|ref|YP_005842074.1|   3 GGRIDSIIELGFGDGSILSEV-AKHVRVRALYGCDINYEALNKASEKGIITVKADLNTDKLSFPDNYFDAVIMEE-V 77 
                                       678888999999999988876.467888888899999999999**************************998766.6 PP

                   Methyltransf_29 192 idwteedgilllevdRvlRpgGyfvlsappv 222
                                       i++  +    l e  R+l+p+G f+l++p++
  gi|385805676|ref|YP_005842074.1|  78 IEHLVNPDNALEEAYRILKPDGIFILTTPNL 108
                                       8888888899****************99875 PP

>> Spermine_synth  Spermine/spermidine synthase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.1   0.00011      0.15      25     132 ..      12     104 ..       5     117 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                                       ESSTTSHHHHHHTTSTT-SEEEEEES-HHHHH.HHHHHSHHHHTTCGGCTTEEEEESTCHHHHCTCSS-EEEEEEEC CS
                    Spermine_synth  25 iGGgDGgvlrevvkhntvekitlvdiDqkvid.fskkflpslaisafndarvklvlgdgfkflkayekkfdvvivds 100
                                       +G gDG +l ev kh  v     +di  ++++  s k + +++++            ++   l    + fd+vi+ +
  gi|385805676|ref|YP_005842074.1|  12 LGFGDGSILSEVAKHVRVRALYGCDINYEALNkASEKGIITVKAD------------LNTDKLSFPDNYFDAVIMEE 76 
                                       677999999999999999999999999887742455556555555............33333444444577777777 PP

                                       CSTTCSSCGCSSHHHHHHHHHTEEEEEEEEEE CS
                    Spermine_synth 101 ldpvgpaenlFskeffdllkkvlkedGviilq 132
                                       + + +   +    + ++  +++lk+dG++il 
  gi|385805676|ref|YP_005842074.1|  77 VIEHLVNPD----NALEEAYRILKPDGIFILT 104
                                       777776666....6677777777777777765 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.8e-05     0.025      41     147 ..       3     106 ..       1     115 [. 0.79

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.8e-05
                              NodS  41 qgsiadalevGcaaGalterlapyc..krltvvdvveeaiararervkesshiswivsdvq..qfs.tdekfdlivv 112
                                       +g+i +++e+G   G++  ++a +   + l   d+  ea+++a e+      i+ +++d++  ++s  d+ fd +++
  gi|385805676|ref|YP_005842074.1|   3 GGRIDSIIELGFGDGSILSEVAKHVrvRALYGCDINYEALNKASEK-----GIITVKADLNtdKLSfPDNYFDAVIM 74 
                                       6889999*********999999886225688899999999999875.....466666665422555357899***** PP

                              NodS 113 aevlyyiedvaelraavrnlvsllapdgqlvfGsa 147
                                        ev+   e++++   a+++  ++l+pdg +++ ++
  gi|385805676|ref|YP_005842074.1|  75 EEVI---EHLVNPDNALEEAYRILKPDGIFILTTP 106
                                       **95...66777889***************98766 PP

>> MTS  Methyltransferase small 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     0.081      34      74 ..       8      48 ..       4     109 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.9e-05
                                      EEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHH CS
                               MTS 34 kvlDlGcGaGvlgaalakespeaevtlvdvdarAlesaken 74
                                      +++ lG G G +  ++ak+    ++  +d++++Al+ a e 
  gi|385805676|ref|YP_005842074.1|  8 SIIELGFGDGSILSEVAKHVRVRALYGCDINYEALNKASEK 48
                                      6999*******************************987653 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     5e-05     0.068     163     258 ..       7     103 ..       2     105 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5e-05
                              PrmA 163 eevlDvGtGSG.iLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellkeekadvivaNILaev 238
                                       ++++ +G G G iL+ +a+ +  +  ++ Di+  A++ a e      v+a l++  + + ++ + +d ++   + e 
  gi|385805676|ref|YP_005842074.1|   7 DSIIELGFGDGsILSEVAKHVRVRALYGCDINYEALNKASEKGI-ITVKADLNT-DKLSFPD-NYFDAVIMEEVIEH 80 
                                       578999999877************************99988644.456666643.3445555.78887765544444 PP

                              PrmA 239 li...elaedikklvkeggllil 258
                                       l+   + +e++++++k++g++il
  gi|385805676|ref|YP_005842074.1|  81 LVnpdNALEEAYRILKPDGIFIL 103
                                       43122356899**********97 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00049      0.67       5      44 ..       9      48 ..       6      74 .. 0.89
   2 ?   -0.4   0.0      0.51     7e+02      98     117 ..      86     105 ..      55     112 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00049
                                      EEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHH CS
                    Methyltransf_4  5 vleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkk 44
                                      ++e+G+G G++l++ Ak+     + G +i+ + ++k+ +k
  gi|385805676|ref|YP_005842074.1|  9 IIELGFGDGSILSEVAKHVRVRALYGCDINYEALNKASEK 48
                                      79***************99988888999988888887765 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.51
                                       HHHHHHHHHEEEEEEEEEEE CS
                    Methyltransf_4  98 ellkelarvLkkgGvlelaT 117
                                       + l+e+ r+Lk+ G++ l T
  gi|385805676|ref|YP_005842074.1|  86 NALEEAYRILKPDGIFILTT 105
                                       56778888888888877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); 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):              13  [number of targets reported over threshold]
# CPU time: 0.55u 0.37s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 707.68
//
Query:       gi|385805677|ref|YP_005842075.1|  [L=40]
Description: hypothetical protein FFONT_0633 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       124  (0.00691617); expected 358.6 (0.02)
Passed bias filter:                      110  (0.00613531); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.32s 00:00:00.74 Elapsed: 00:00:00.51
# Mc/sec: 234.84
//
Query:       gi|385805678|ref|YP_005842076.1|  [L=355]
Description: glycosyltransferase, family 4 [Fervidicoccus fontis Kam940]
Scores for complete 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   77.1   0.1    4.1e-21   75.3   0.0    1.9  2  Glycos_transf_1  Glycosyl transferases group 1
    1.8e-19   70.5   0.1    5.7e-18   65.6   0.0    2.4  3  Glyco_trans_1_4  Glycosyl transferases group 1
    1.2e-10   41.7   0.0    4.1e-10   39.9   0.0    1.9  2  Glyco_transf_4   Glycosyltransferase Family 4
    1.4e-09   38.2   0.0    4.9e-09   36.5   0.0    1.9  2  Glyco_trans_1_2  Glycosyl transferases group 1
  ------ inclusion threshold ------
      0.079   13.4   0.0       0.73   10.3   0.0    2.5  3  Glyco_trans_4_4  Glycosyl transferase 4-like domain
       0.13   12.5   0.0         17    5.7   0.0    2.4  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma


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 ?   -1.5   0.0      0.52   1.6e+03      86     112 ..     133     162 ..     118     163 .. 0.71
   2 !   75.3   0.0   1.4e-24   4.1e-21      25     170 ..     191     329 ..     177     331 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.52
                                       HHHHHHCESEEEEEESS...BSS-HHHHHH CS
                   Glycos_transf_1  86 leellknadifvlpsis...EgfGivllEA 112
                                       +++l+   d++++ s +   E   iv  EA
  gi|385805678|ref|YP_005842076.1| 133 IKALYATYDMVICVSSKsrqEYASIVNCEA 162
                                       677777766665555555889999999998 PP

  == domain 2  score: 75.3 bits;  conditional E-value: 1.4e-24
                                       TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHHCESEEEEEES CS
                   Glycos_transf_1  25 ekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleellknadifvlpsi 101
                                       + +K+++  ik ++ l+++   +v+l ++G  ++ k++++la+     + ++++++ ++ +++ +l  a++++lps 
  gi|385805678|ref|YP_005842076.1| 191 RSVKNPEISIKTIDILRRK-GYDVNLAVIG--PYSKQVEELAKGD---NSIELHFNAEEREKMRILCGAKALILPSS 261
                                       567*************998.**********..9999999986543...4466666666889**************** PP

                                       SBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHHHHHHHH CS
                   Glycos_transf_1 102 sEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelrerlgenar 170
                                       +E f  +++EAma+g+pv++s+a  p evv dg +G+ v + n++++a+ +++ll d+el  rl+ n+ 
  gi|385805678|ref|YP_005842076.1| 262 NETFSFTAMEAMACGTPVVVSDA-VPEEVVIDGYNGVRVRSLNPKDYAAVLERLLVDKELWIRLSTNGI 329
                                       *********************96.799********************************9999999986 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       3.4     1e+04      18      51 ..      22      55 ..      14      72 .. 0.55
   2 ?    2.4   0.0     0.067     2e+02      17      88 ..      84     160 ..      76     164 .. 0.62
   3 !   65.6   0.0   1.9e-21   5.7e-18       2     133 ..     183     316 ..     182     317 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.4
                                      HHHHHHHHHHH.HHEEEEEES---...HHHHHHHT CS
                   Glyco_trans_1_4 18 dllleavpllrkkdvrlvivGdgp.rpeeleelaa 51
                                       +l ea+ +l  +dv ++  G  + +++el + ++
  gi|385805678|ref|YP_005842076.1| 22 AWLGEAFRKLG-HDVVVISWGFYNvDRDELSKWIK 55
                                      56666666665.33556666654444445554443 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.067
                                       HHHHHHHHHHHH.HHEEEEEES---.......HHHHHHHTT-T.T...EEEE---THHHHHHHH-SEEEE--..... CS
                   Glyco_trans_1_4  17 vdllleavpllrkkdvrlvivGdgp.....rpeeleelaagleer...veftGfvedlaellaaadvfvaPs..... 80 
                                       +d+l++ ++ll+k++v + iv  g      r +++      ++++   ++   ++  +++l+a  d++++ s     
  gi|385805678|ref|YP_005842076.1|  84 FDWLIKGAKLLKKEEVDIAIVN-GViplssR-PKIA-----IAHGpisISKIQHM-VIKALYATYDMVICVSsksrq 152
                                       7999999999998889999998.43222111.2442.....23332013333333.599999999999888766544 PP

                                       ---SHHHH CS
                   Glyco_trans_1_4  81 egfglkll 88 
                                       e  +++  
  gi|385805678|ref|YP_005842076.1| 153 EYASIVNC 160
                                       44555555 PP

  == domain 3  score: 65.6 bits;  conditional E-value: 1.9e-21
                                       EEEEEES---GG.GTHHHHHHHHHHHH.H..HEEEEEES---..HHHHHHHTT-T.TEEEE---..THHHHHHHH-S CS
                   Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkk..dvrlvivGdgprpeeleelaagleerveftGfv..edlaellaaad 74 
                                       ++i+++G     vk+ ++ ++ +  lr+k  dv+l ++G  p ++++eela+g ++++e++      ++ ++l  a+
  gi|385805678|ref|YP_005842076.1| 183 NTIVHIGTR--SVKNPEISIKTIDILRRKgyDVNLAVIG--PYSKQVEELAKG-DNSIELHFNAeeREKMRILCGAK 254
                                       578999966..67**************88755*******..644599988876.46788888885455999****** PP

                                       EEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH CS
                   Glyco_trans_1_4  75 vfvaPs..egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLle 133
                                        +++Ps  e+f+ +++Eama+g+pvV++d+  ++evv  g ng+ v + +p+++a+ ++rLl 
  gi|385805678|ref|YP_005842076.1| 255 ALILPSsnETFSFTAMEAMACGTPVVVSDA-VPEEVVidGYNGVRVRSLNPKDYAAVLERLLV 316
                                       *******99********************9.6688889*********99***********996 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.0   1.4e-13   4.1e-10       2     150 ..      15     156 ..      14     167 .. 0.83
   2 ?   -2.7   0.0       1.7     5e+03      15      36 ..     206     227 ..     203     246 .. 0.74

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 1.4e-13
                    Glyco_transf_4   2 GGverhvleLaraLarrGheVtvvtpgddgpleeev...........elvvrvprvplpllkrllrslaflrrl..r 65 
                                        Gv+r++  L +a++++Gh+V+v++ g     ++e            e +  ++    p +++++ +++f + +  +
  gi|385805678|ref|YP_005842076.1|  15 DGVNRFIAWLGEAFRKLGHDVVVISWGFYNVDRDELskwikdihaldEEIEVMTLMDKPTHGDPWSRITFDWLIkgA 91 
                                       7***********************88888888888788899998888555555555566666666666665544228 PP

                    Glyco_transf_4  66 rllkrekpDvvHahspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSe 142
                                       +llk+e++D+  +++ ++l          +  p ++ +Hg+             s++ +++ + l+   d vi+vS 
  gi|385805678|ref|YP_005842076.1|  92 KLLKKEEVDIAIVNGVIPL----------SSRPKIAIAHGPI----------SISKIQHMVIKALYATYDMVICVSS 148
                                       9**************8887..........688**********..........7999********************* PP

                    Glyco_transf_4 143 atadelre 150
                                       + ++e+++
  gi|385805678|ref|YP_005842076.1| 149 KSRQEYAS 156
                                       ****9987 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.7
                    Glyco_transf_4  15 LarrGheVtvvtpgddgpleee 36 
                                       L+r+G++V + + g+  ++ ee
  gi|385805678|ref|YP_005842076.1| 206 LRRKGYDVNLAVIGPYSKQVEE 227
                                       7888888888877777666666 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0         4   1.2e+04      46      67 ..      43      65 ..      41      67 .. 0.77
   2 !   36.5   0.0   1.6e-12   4.9e-09       4      90 ..     258     344 ..     255     346 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 4
                   Glyco_trans_1_2 46 fe.dleelaekiryllanpeerr 67
                                      +  d +el + i+  +a +ee++
  gi|385805678|ref|YP_005842076.1| 43 YNvDRDELSKWIKDIHALDEEIE 65
                                      55688999999999888888875 PP

  == domain 2  score: 36.5 bits;  conditional E-value: 1.6e-12
                   Glyco_trans_1_2   4 npsrsespnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarervl 78 
                                        ps +e++++   Ea+acG++++++da  +ee + +g  ++ ++  ++++ a+ +++ll + e++ +++++++e+v+
  gi|385805678|ref|YP_005842076.1| 258 LPSSNETFSFTAMEAMACGTPVVVSDA-VPEEVVIDGYNGVRVRslNPKDYAAVLERLLVDKELWIRLSTNGIEFVK 333
                                       5899999******************86.9**********************************************75 PP

                   Glyco_trans_1_2  79 aehtydhraeql 90 
                                        +++y + a+++
  gi|385805678|ref|YP_005842076.1| 334 -QFDYINIAKRY 344
                                       .67887777665 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 ?   10.3   0.0   0.00024      0.73       2      34 ..      16      48 ..      15     122 .. 0.61
   2 ?   -0.9   0.0      0.68     2e+03     123     145 ..     133     155 ..     126     161 .. 0.83
   3 ?   -2.0   0.0       1.5   4.3e+03      49      49 ..     241     241 ..     205     282 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00024
                   Glyco_trans_4_4  2 GigryvaelaraLaarGheVtvltpapapgape 34
                                      G++r +a l +a++++Gh+V+v+  + ++++++
  gi|385805678|ref|YP_005842076.1| 16 GVNRFIAWLGEAFRKLGHDVVVISWGFYNVDRD 48
                                      99*********************9555555333 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.68
                   Glyco_trans_4_4 123 errllrradavlvvseaeaeelr 145
                                        ++l++  d v++vs   ++e++
  gi|385805678|ref|YP_005842076.1| 133 IKALYATYDMVICVSSKSRQEYA 155
                                       567889999*******9999986 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.5
                   Glyco_trans_4_4  49 r 49 
                                       +
  gi|385805678|ref|YP_005842076.1| 241 A 241
                                       2 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 ?    5.7   0.0    0.0056        17      17      88 ..     205     272 ..     200     280 .. 0.88
   2 ?    4.1   0.0     0.017        51      46      79 ..     294     327 ..     276     330 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0056
                                       HHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-SSGGGHHHHHHH CS
                   Sacchrp_dh_NADP  17 larhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnlsppissldvlka 88 
                                       ++r++ +d +++v++++ +++e+la   +g + +   ++ae++e+ +  l+  + l++  s  ++s + ++a
  gi|385805678|ref|YP_005842076.1| 205 ILRRKGYDVNLAVIGPYSKQVEELA---KGDNSIELHFNAEEREK-MRILCGAKALILPSSNETFSFTAMEA 272
                                       667777877***********99998...8****************.99999999999999999988888886 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.017
                                       TTCEEEEE--TTTHHHHHHHHHTTSSEEEE-SSG CS
                   Sacchrp_dh_NADP  46 gvrfeaialdaenyeavLaallkegdlvvnlspp 79 
                                          +  ++l++++y+avL++ll +++l + ls++
  gi|385805678|ref|YP_005842076.1| 294 YNGVRVRSLNPKDYAAVLERLLVDKELWIRLSTN 327
                                       45677899****************9999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); 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:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2321.36
//
Query:       gi|385805679|ref|YP_005842077.1|  [L=395]
Description: glycosyltransferase, family 4 [Fervidicoccus fontis Kam940]
Scores for complete 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   41.6   0.0    2.8e-10   40.5   0.0    1.5  1  Glyco_transf_4   Glycosyltransferase Family 4
    1.1e-07   31.5   0.0    2.4e-07   30.4   0.0    1.6  1  Glycos_transf_1  Glycosyl transferases group 1
    4.1e-06   27.3   0.0    9.3e-06   26.1   0.0    1.6  1  Glyco_trans_1_4  Glycosyl transferases group 1
     0.0017   18.8   0.0     0.0023   18.4   0.0    1.2  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain


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 !   40.5   0.0   6.2e-14   2.8e-10       2     165 ..      16     204 ..      15     205 .. 0.75

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 6.2e-14
                    Glyco_transf_4   2 GGverhvleLaraLarrGheVtvvtpgddgpleeevelvvrvprvpl..pllkrllrslaflrrlrrllkre..kpD 74 
                                       GG+e  ++ ++  L r+ ++Vtv+t +  +++ +     vr+   pl   ++k  l++ + l++   ++k+   + D
  gi|385805679|ref|YP_005842077.1|  16 GGAELATYLITDMLSRH-FKVTVITGSKLHKSLNG----VRMFNTPLliSHSKHELWIKTTLLANESWFKKLikNTD 87 
                                       78888888888888888.*******9999999888....33333333014455556666666666667777777*** PP

                    Glyco_transf_4  75 vvHahspaalgaallalrrrlgiplVltvHglye............................krllkarlkpl.srl 122
                                       +v + ++ +    ++ l++r g+++++++Hg  +                            ++l++  l  l s++
  gi|385805679|ref|YP_005842077.1|  88 IVYIPGFSFP---VISLAKRMGKKVIVHLHGYIPvsytslipapyeenknsiwkfniwlehrRGLVNLLLAGLsSYI 161
                                       **88885444...45555668****************************9999988888877555555554440444 PP

                    Glyco_transf_4 123 lralerrllrradrviavSeatadelrerygvppekitVipnG 165
                                         ++ r +l +ad+v++vS+  a+ + e+ +  ++ki+Vi+n+
  gi|385805679|ref|YP_005842077.1| 162 MPRIARTWLEQADKVLCVSNRHAKIISELAPKLKNKIAVIYNP 204
                                       44555555********************8886669*******5 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 !   30.4   0.0   5.4e-11   2.4e-07      70     159 ..     267     357 ..     215     366 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 5.4e-11
                                       CTTCGGGEEECCHSSSHHHHHHCESEEEEEESS.BSS-HHHHHHHHTT--EEEETTTTHCHHCHTTT.SEEEE-TT- CS
                   Glycos_transf_1  70 elsdnviflgevsredleellknadifvlpsis.EgfGivllEAmaaglpviasnaggpaevvkdge.tGllvkpnn 144
                                       e  + +++  ++s+e++++++ ++ +++  si  E fG ++l A  a  + ia ++gg++e+++  +   + vkp++
  gi|385805679|ref|YP_005842077.1| 267 EK-NILHYPRRLSHEEVIKIYMRSWAALSLSIVeETFGYAVLDAGLATAIPIAFKVGGISEIIEGTHaESFSVKPYD 342
                                       33.4467778888**************************************************9888788******* PP

                                       HHHHHHHHHHHHHSH CS
                   Glycos_transf_1 145 aealaeairkllede 159
                                       + +l ++i+ + + +
  gi|385805679|ref|YP_005842077.1| 343 ISSLLDKIEYISSMS 357
                                       *********998776 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 !   26.1   0.0   2.1e-09   9.3e-06      14     130 ..     233     352 ..     224     355 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 2.1e-09
                                       .GTHHHHHHHHHHHH.HHEEEEEES---..HHHHHHHTT-T.T.EEEE---..THHHHHHHH-SEEEE--...---S CS
                   Glyco_trans_1_4  14 vkgvdllleavpllrkkdvrlvivGdgprpeeleelaagleer.veftGfv..edlaellaaadvfvaPs...egfg 84 
                                       +kg +++l+ + +   ++ r++  G+   p++++++     ++  ++  ++  e++ +++ +++ ++  s   e+fg
  gi|385805679|ref|YP_005842077.1| 233 IKGYHIFLKVLLRSS-DNTRFITFGST-IPANIKNKE----KNiLHYPRRLshEEVIKIYMRSWAALSLSiveETFG 303
                                       689999999985555.358******55.556887544....45256666669889***********99999*88*** PP

                                       HHHHHHHHTT-EEEE-TGGGTTT--.TTSS..EE--TT-HHHHHHHHHH CS
                   Glyco_trans_1_4  85 lkllEamaaglpvVatdvggiaevv.geng..llvppgdpealaeailr 130
                                       +++l+a  a    +a++vggi+e++ g+++  + v+p d ++l ++i+ 
  gi|385805679|ref|YP_005842077.1| 304 YAVLDAGLATAIPIAFKVGGISEIIeGTHAesFSVKPYDISSLLDKIEY 352
                                       *************************9866556***********999986 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   5.1e-07    0.0023       2     159 ..      17     203 ..      15     204 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 5.1e-07
                   Glyco_trans_4_4   2 GigryvaelaraLaarGheVtvltpapapgapeleedgvrvhrlpvprrps......pladlaalralrrllrqrre 72 
                                       G++  ++ +   L ++   Vtv+t ++  ++     +gvr  + p+  ++s       ++ la   +++ l+     
  gi|385805679|ref|YP_005842077.1|  17 GAELATYLITDMLSRH-FKVTVITGSKLHKSL----NGVRMFNTPLLISHSkhelwiKTTLLANESWFKKLI----K 84 
                                       4444444444444444.888888887777777....788888888665543222223333344446666666....9 PP

                   Glyco_trans_4_4  73 rpdvvhahsptaglaarlarrrrgiplvvtlh.........................g..lllrrg......sgavr 116
                                       + d+v++ ++ + +++ la+ r g +++v+lh                         +  l++rrg      +g + 
  gi|385805679|ref|YP_005842077.1|  85 NTDIVYIPGF-SFPVISLAK-RMGKKVIVHLHgyipvsytslipapyeenknsiwkfNiwLEHRRGlvnlllAGLSS 159
                                       99*****998.677799999.99*********999999999999999999887777733233444566666555565 PP

                   Glyco_trans_4_4 117 rlyralerrllrradavlvvseaeaeelralg.vpadrvvvvpn 159
                                        ++ ++ r+ l +ad vl+vs+ +a+ + +l     ++++v+ n
  gi|385805679|ref|YP_005842077.1| 160 YIMPRIARTWLEQADKVLCVSNRHAKIISELApKLKNKIAVIYN 203
                                       566999**********************9977334578888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); 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 0.27s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2522.57
//
Query:       gi|385805680|ref|YP_005842078.1|  [L=351]
Description: family 2 glycosyltransferase [Fervidicoccus fontis Kam940]
Scores for complete 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   83.5   0.2    2.3e-23   82.8   0.2    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
    2.9e-12   47.0   0.0    4.5e-10   39.8   0.0    2.1  2  Glyco_tranf_2_3  Glycosyltransferase like family 2
    1.9e-11   44.0   0.5    4.8e-11   42.7   0.2    1.9  2  Glyco_tranf_2_2  Glycosyltransferase like family 2
    4.4e-05   23.0   0.0     0.0005   19.6   0.0    2.1  2  Glyco_transf_21  Glycosyl transferase family 21
    5.8e-05   23.1   3.1    0.00092   19.2   3.1    2.5  1  Glyco_trans_2_3  Glycosyl transferase family group 2
     0.0022   18.5   0.0     0.0044   17.5   0.0    1.5  1  Glyco_tranf_2_4  Glycosyl transferase family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.8   0.2   7.8e-27   2.3e-23       1     109 [.      14     127 ..      14     152 .. 0.95

  Alignments for each domain:
  == domain 1  score: 82.8 bits;  conditional E-value: 7.8e-27
                                       EEEEEESS-TTTHHHHHHHHHHH.GGCCEEEEEEEEES-SSCHHHHHGGGCH....C-TTEEEEEESSS-HHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaq.dpypdfeiivvDDgStDetveileelak....edprvrvirreenvGkagaln 72 
                                       s+v +tyN e+t+ ++l+s+     +  ++e+i+vD gStD+t +i+ ++ +    +++r  +i +++n G ++a+n
  gi|385805680|ref|YP_005842078.1|  14 SIVLTTYNDEDTISAVLNSIYTLgLDLNHIELIIVDGGSTDKTLSIINDFLSnnaiYFKRNLLIVHDKNYGISRARN 90 
                                       89*********************99**************************************************** PP

                                       HHHHH--SSEEEEEESSEEE-TTHHHHHHHHHHH.TT CS
                   Glycos_transf_2  73 aglraatgdyilflDaDdepdpdwleklvealekdga 109
                                        g+r+a+  y+l+lD+D + + + le ++++l  +++
  gi|385805680|ref|YP_005842078.1|  91 DGIREARCPYVLILDSDIVLPSNALETMLQYLISERK 127
                                       *******************************988654 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 !   39.8   0.0   1.5e-13   4.5e-10       4     122 ..      13     134 ..      11     142 .. 0.81
   2 !    5.1   0.0    0.0061        18     178     205 ..     180     207 ..     156     245 .. 0.78

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 1.5e-13
                   Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqey..prvevvvvvdesdaetl....evaeelaaalpdvrvrvvvnarnlgstg 74 
                                       ++++ +t+n ed++ +vl+s+ +       +e+++v+ +s+++tl    +++    a++ +  + +v++++    +g
  gi|385805680|ref|YP_005842078.1|  13 VSIVLTTYNDEDTISAVLNSIYTLGLdlNHIELIIVDGGSTDKTLsiinDFLSN-NAIYFKRNLLIVHDKN----YG 84 
                                       799********************9864477************999444334544.6666665788887755....55 PP

                   Glyco_tranf_2_3  75 ksralnealravksdlvllvDdDtvvePdtlkrllqff..ltpkvgavgt 122
                                        sra n+++r +++ +vl++D+D v+  ++l+ +lq++  +++  ++vg+
  gi|385805680|ref|YP_005842078.1|  85 ISRARNDGIREARCPYVLILDSDIVLPSNALETMLQYLisERKTKKVVGV 134
                                       67888*********************************874444455554 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0061
                   Glyco_tranf_2_3 178 ldplflltdDyelglrlrragfrtayvp 205
                                        +p+ +  +D+elg rl ++g  ++++ 
  gi|385805680|ref|YP_005842078.1| 180 MGPPHSSDEDIELGARLLKQGLEIHMLG 207
                                       44477889****************9975 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   0.2   1.6e-14   4.8e-11       3     107 ..      16     123 ..      14     206 .. 0.75
   2 ?   -2.5   0.0      0.91   2.7e+03     248     275 ..     210     237 ..     197     238 .. 0.84

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 1.6e-14
                   Glyco_tranf_2_2   3 viplraseerhyieervlqkakyy..d.eeielivvddgSsekfleevssiidlnllvylkde....ddkayslaaa 72 
                                       v+  ++ e++  i   +  + +    d ++ieli+vd+gS++k+l+ ++ +   n  +y+k +     dk y+ ++a
  gi|385805680|ref|YP_005842078.1|  16 VLTTYNDEDT--ISAVLNSIYT-LglDlNHIELIIVDGGSTDKTLSIINDFLSNNA-IYFKRNllivHDKNYGISRA 88 
                                       5555555555..4433322222.23442679********************98776.555543233389******** PP

                   Glyco_tranf_2_2  73 rNrGaskaesdlvlFlDaDcfissDkfekilklit 107
                                       rN G+ +a   +vl lD+D    s+ +e +l+ + 
  gi|385805680|ref|YP_005842078.1|  89 RNDGIREARCPYVLILDSDIVLPSNALETMLQYLI 123
                                       ******************************98332 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.91
                   Glyco_tranf_2_2 248 hlYheepksedylkkkdwkrellykafK 275
                                        + h+++++  y+     k+++l k +K
  gi|385805680|ref|YP_005842078.1| 210 TAHHIKSPQSLYVTTTRSKKKYLIKILK 237
                                       5789999999999999999999988887 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 !   19.6   0.0   1.7e-07    0.0005      24      57 ..      91     124 ..      74     149 .. 0.87
   2 ?    1.0   0.0     0.088   2.6e+02     128     147 ..     188     207 ..     187     224 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.7e-07
                   Glyco_transf_21  24 qaleaakydllvisDsdvrvkpdyLeellaaled 57 
                                        ++++a+ ++++i+Dsd+++++++Le++l++l +
  gi|385805680|ref|YP_005842078.1|  91 DGIREARCPYVLILDSDIVLPSNALETMLQYLIS 124
                                       57899*************************9865 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.088
                   Glyco_transf_21 128 eDyalgkllraaGlkvvlsp 147
                                       eD +lg++l ++Gl +++  
  gi|385805680|ref|YP_005842078.1| 188 EDIELGARLLKQGLEIHMLG 207
                                       9**************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 !   19.2   3.1   3.1e-07   0.00092       1     191 [.     100     282 ..     100     339 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 3.1e-07
                   Glyco_trans_2_3   1 iilllDaDtvlppdclreiaa.elas.pevaivqgpvlvmnvanwleelaalffaedhgkdilvrealgrvvpsvGs 75 
                                       ++l+lD+D vlp + l+  ++ ++++   +++v  + l++  a+++ +++a       g   + r++lg +  +  s
  gi|385805680|ref|YP_005842078.1| 100 YVLILDSDIVLPSNALETMLQyLISErKTKKVVGVKPLID-TAPFIFKVIA------QG--KIHRKNLGACEAFLAS 167
                                       5777777777777777777663344313333333333333.3455555554......23..3566777777777777 PP

                   Glyco_trans_2_3  76 gaflrrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpes.lvkekspltlraalrQrkRwayGceleklil 151
                                         +l   + +e  g +    s  ED ++g rl+++G+ +++     + + ksp +l+    + k+ ++  ++ k+i+
  gi|385805680|ref|YP_005842078.1| 168 TEILMKNMYDETMGPP---HSSDEDIELGARLLKQGLEIHMLGFItAHHIKSPQSLYVTTTRSKKKYLI-KILKIIR 240
                                       7777777777777777...8999*************99976655545599*****99999999998888.3333333 PP

                   Glyco_trans_2_3 152 ..lvrllgylgsllwsalplhlallllfsllalalvllllll 191
                                         ++  ++y ++  +++lp+++ ++++  ++ +++++++++l
  gi|385805680|ref|YP_005842078.1| 241 syYTPYVKYGFKRYFKSLPILIKFSYILDMITYMTMIMIIAL 282
                                       5577888999999******99998888888887777766655 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 !   17.5   0.0   1.5e-06    0.0044       1      81 [.      20     107 ..      20     121 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.5e-06
                   Glyco_tranf_2_4   1 rneadiLpeflahhlalgfd..r..ilvydndstDgtrailke...lpevkllhvdksyederrqve.llkallary 69 
                                       +n++d++ ++l  +++lg d  +  ++++d +stD+t  i+     + ++ + ++   ++d++++++ +++  +++ 
  gi|385805680|ref|YP_005842078.1|  20 YNDEDTISAVLNSIYTLGLDlnHieLIIVDGGSTDKTLSIINDflsNNAIYFKRNLLIVHDKNYGISrARNDGIRE- 95 
                                       69**********99999975324669***************88422223334444456688899965377777766. PP

                   Glyco_tranf_2_4  70 aeadwvlvvDaD 81 
                                       a+  +vl +D+D
  gi|385805680|ref|YP_005842078.1|  96 ARCPYVLILDSD 107
                                       588899999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       766  (0.0427241); 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:                         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: 00:00:00.46
# Mc/sec: 2314.30
//
Query:       gi|385805681|ref|YP_005842079.1|  [L=587]
Description: hypothetical protein FFONT_0637 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (587 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       993  (0.0553851); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); 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):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 4109.03
//
Query:       gi|385805682|ref|YP_005842080.1|  [L=381]
Description: glycosyltransferase, family 4 [Fervidicoccus fontis Kam940]
Scores for complete 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   89.3   0.3    3.3e-25   88.6   0.3    1.2  1  Glycos_transf_1  Glycosyl transferases group 1
    4.1e-12   46.7   0.0    6.9e-12   45.9   0.0    1.3  1  Glyco_trans_1_4  Glycosyl transferases group 1
    7.9e-05   22.7   0.1    0.00016   21.7   0.1    1.5  1  Glyco_transf_4   Glycosyltransferase Family 4
  ------ inclusion threshold ------
      0.024   14.4   0.0      0.041   13.6   0.0    1.3  1  FMN_red          NADPH-dependent FMN reductase
       0.17   12.3   0.0       0.35   11.3   0.0    1.5  1  Glyco_trans_1_2  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.6   0.3   9.3e-29   3.3e-25      11     150 ..     205     341 ..     196     359 .. 0.90

  Alignments for each domain:
  == domain 1  score: 88.6 bits;  conditional E-value: 9.3e-29
                                       TTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES....STTHHHHHHHHHHHCTTCGGGEEECCHSS CS
                   Glycos_transf_1  11 knekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaG...ngeeekelkklaeelelsdnviflgevsre 84 
                                        ++++++++s+gr+e+ Kg++++  +++     + + +k+ i+G   + ++++e+ +l+++l+++d+v++l +++++
  gi|385805682|ref|YP_005842080.1| 205 NKQRDNLVVSIGRIERAKGLHVIPYVAK-----ETSGIKYAIVGlvsDHKYLAEINELIKKLNVEDKVKILNNLNED 276
                                       45899****************9999999.....489***************************************** PP

                                       SHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEET.TTTHCHHCHTTTSEEEE-TT-HHHHHH CS
                   Glycos_transf_1  85 dleellknadifvlpsisEgfGivllEAmaaglpviasn.aggpaevvkdgetGllvkpnnaealae 150
                                       ++ ++l++a+++++p+ +E+fGi+++EAmaagl  ++   +g  ++++k g+ Gl ++    ++ a+
  gi|385805682|ref|YP_005842080.1| 277 KKLKILSRAKVYFHPMKYEHFGISIIEAMAAGLVPVVNRmSGSWSDIIKFGKYGLGCDGQ--DDCAN 341
                                       ***************************************9************99988887..44444 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 !   45.9   0.0   1.9e-15   6.9e-12       3     126 ..     211     341 ..     209     350 .. 0.77

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 1.9e-15
                                       EEEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES...---...HHHHHHHT..T-T.TEEEE---.TH.HHHHHH CS
                   Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkkdvrlvivG...dgp.rpeeleelaa..gleerveftGfv.ed.laella 71 
                                        ++ +Gr+ e+ kg++++   +++     ++  ivG   d++   +e++el++  ++e++v+++  + ed + ++l+
  gi|385805682|ref|YP_005842080.1| 211 LVVSIGRI-ERAKGLHVIPYVAKETS--GIKYAIVGlvsDHKyL-AEINELIKklNVEDKVKILNNLnEDkKLKILS 283
                                       57888999.66688876555555544..4899999954333333.5777777668899*********955699**** PP

                                       H-SEEEE--..---SHHHHHHHHTT-EEEE-TGGG.TTT--..TTSSEE--TT-HHHHHH CS
                   Glyco_trans_1_4  72 aadvfvaPs..egfglkllEamaaglpvVatdvgg.iaevv..gengllvppgdpealae 126
                                       +a+v+  P+  e fg++++Eamaagl  V+ +++g +++++  g+ gl ++ +  ++ a+
  gi|385805682|ref|YP_005842080.1| 284 RAKVYFHPMkyEHFGISIIEAMAAGLVPVVNRMSGsWSDIIkfGKYGLGCDGQ--DDCAN 341
                                       **********99*******************9986379999999999988643..44444 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1   4.4e-08   0.00016       2     169 ..      14     197 ..      13     198 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 4.4e-08
                    Glyco_transf_4   2 GGverhvleLaraLarrGheVtvvtpgddgpleeev.......elvvrvprvplpllkrllrslaflrrlrrllkre 71 
                                       GG+er ++++a+ L + G++V++vt +    l+ +         +++  + +p+++l+  l++  +++ +r ++   
  gi|385805682|ref|YP_005842080.1|  14 GGAERLAVYMAKTLSESGYDVYLVTMEKTNWLRLRGimgddveSYFKGEVIIPYLKLPLSLYDRFNAWLIRDIVAFS 90 
                                       9***********************77666555555556666675666666666666666666666666666665544 PP

                    Glyco_transf_4  72 .....kpDvvHahspaalgaallalrrrlgipl...VltvHglye...............krllkarlkplsrllra 125
                                            ++D+  +                +gip+   ++++H+++                +++l+ +++p++ +l+a
  gi|385805682|ref|YP_005842080.1|  91 lkvrsRYDLTIVTKQ-------------YGIPIladIAYIHFPDFypgveslyyperyvkNTFLRIYSMPYRLILKA 154
                                       445667777744442.............4444433368899999999999999999888877777777788777777 PP

                    Glyco_transf_4 126 lerrl..lrradrviavSeatadelrerygvppekitVipnGvDle 169
                                       l++    ++    ++++S + ++ ++++++ p     V++++v++e
  gi|385805682|ref|YP_005842080.1| 155 LLELYkvIDYRPLILTNSSFSKAVIERWLRTP---AIVLYPPVNVE 197
                                       766557799999***************77766...58999999987 PP

>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.2e-05     0.041       1      41 [.       1      41 [.       1      58 [. 0.92

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.2e-05
                                      -EEEEEES--STT-HHHHHHHHHHCCT-T.T-CEEEEETTT CS
                           FMN_red  1 mkilvisGSlrkgsntrklaewaaealkeagaevelidlad 41
                                      mki+vi+ Sl+ g+  ++la ++a++l e+g +v l+++ +
  gi|385805682|ref|YP_005842080.1|  1 MKIAVIHDSLNNGGGAERLAVYMAKTLSESGYDVYLVTMEK 41
                                      9**********************************999876 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   9.7e-05      0.35       4      71 ..     290     358 ..     269     373 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9.7e-05
                   Glyco_trans_1_2   4 npsrsespnlrlfEaaacGafaltdda.egleelftpgkevilfedleelaekiryllanpeerraiae 71 
                                       +p  +e +   + Ea+a+G + ++++   +  ++++ gk ++  +  +++a  i y+++  ++ ++ia+
  gi|385805682|ref|YP_005842080.1| 290 HPMKYEHFGISIIEAMAAGLVPVVNRMsGSWSDIIKFGKYGLGCDGQDDCANMITYAVNKYDQLSKIAT 358
                                       4555678888899*******99999888889****************************9999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2822.72
//
Query:       gi|385805683|ref|YP_005842081.1|  [L=52]
Description: hypothetical protein FFONT_0639 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       201  (0.0112109); expected 358.6 (0.02)
Passed bias filter:                      160  (0.00892409); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 337.38
//
Query:       gi|385805684|ref|YP_005842082.1|  [L=327]
Description: hypothetical protein FFONT_0640 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        1.7    9.0  10.9       0.46   10.9   6.4    2.5  2  TM2       TM2 domain


Domain annotation for each model (and alignments):
>> TM2  TM2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   6.4   2.6e-05      0.46       6      39 ..      80     111 ..      77     123 .. 0.75
   2 ?   -3.1   0.1       0.6   1.1e+04      32      44 ..     177     189 ..     172     191 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 2.6e-05
                               TM2   6 lvaylLwffLGglGvHRFYlGktgsGvlqlltfv 39 
                                       l++yl  f    lG+H FY+G+ + Gv+   ++v
  gi|385805684|ref|YP_005842082.1|  80 LTMYLAVF--TLLGLHAFYVGRATLGVALVMLYV 111
                                       55555555..79*************998777775 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.6
                               TM2  32 vlqlltfvGglgi 44 
                                       vl+ l+++G++ i
  gi|385805684|ref|YP_005842082.1| 177 VLKTLAIIGLILI 189
                                       5555666555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1198  (0.0668191); 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:                         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: 0.60u 0.35s 00:00:00.95 Elapsed: 00:00:00.53
# Mc/sec: 1865.33
//
Query:       gi|385805685|ref|YP_005842083.1|  [L=159]
Description: hypothetical protein FFONT_0641 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.023   14.7   0.1       0.37   10.9   0.0    2.2  2  Longin    Regulated-SNARE-like domain
      0.084   12.5   1.6        0.1   12.2   1.6    1.1  1  CbiQ      Cobalt transport protein
       0.16   11.2   0.0       0.19   10.9   0.0    1.1  1  CNF1      Rho-activating domain of cytotoxic necrotizing fact


Domain annotation for each model (and alignments):
>> Longin  Regulated-SNARE-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.041   2.4e+02      30      43 ..      84      97 ..      56     104 .. 0.68
   2 ?   10.9   0.0   6.2e-05      0.37      21      44 ..     122     144 ..     110     146 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.041
                            Longin 30 edgltylviadesy 43
                                      ++ lty +++++s+
  gi|385805685|ref|YP_005842083.1| 84 AAFLTYFCVTSNSM 97
                                      45679****99987 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 6.2e-05
                            Longin  21 dsytfhylaedgltylviadesyp 44 
                                       d +++h l e+g+tylv  d+ yp
  gi|385805685|ref|YP_005842083.1| 122 D-FIIHNLKEGGITYLVYVDDGYP 144
                                       4.99*****************998 PP

>> CbiQ  Cobalt transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.6   1.7e-05       0.1      41     136 ..       4     120 ..       1     128 [. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.7e-05
                                       HHHHTTS---.HHHHHHHCCCHCHHHHHHHHHHE..........................EECTTEEE....E-TTH CS
                              CbiQ  41 llllllvilp.rvlaqalilpllflllgllillf...................qlittegefvfaggg.qisitseG 96 
                                       lll++++++  + +++ ++++l+++++ +++ll+                    +i++  +f+ +  g +i+i    
  gi|385805685|ref|YP_005842083.1|   4 LLLIVVKGFQnKGKSRHIVVRLFSIIIMVVVLLNffaniysstkyshprifgiENIRPLTKFICSNSGsHIQIAASD 80 
                                       55556666667888899999999999999999999999****9*******99999*********99888******** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHCCCSS-- CS
                              CbiQ  97 llrglllalRiltllslllllalTTppeeltsslerlgvP 136
                                         ++++l+ + +t+ s+ + ++l  + + l  +l+ + + 
  gi|385805685|ref|YP_005842083.1|  81 AYYAAFLTYFCVTSNSMFITVPLGKNAISLKLALHNVSML 120
                                       ************9999998888888888887777777665 PP

>> CNF1  Rho-activating domain of cytotoxic necrotizing factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   3.2e-05      0.19      66     150 ..      61     143 ..      43     149 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.2e-05
                              CNF1  66 vlhgyikswaGdeieaaqiggtrlgkfyngapLddnvrvvrlenGdeGviGlrirlselpsekkliltaGeLsGCtt 142
                                       +l  +i s  G+ i+ a  +      f +   +++n   + ++ G++ +i l++ l ++   + +i+ + +  G t 
  gi|385805685|ref|YP_005842083.1|  61 PLTKFICSNSGSHIQIAA-SDAYYAAFLTYFCVTSNSMFITVPLGKN-AISLKLALHNVSMLTDFIIHNLKEGGITY 135
                                       56789**********999.7788899999999*************76.899************************** PP

                              CNF1 143 ivavkega 150
                                       +v v++g+
  gi|385805685|ref|YP_005842083.1| 136 LVYVDDGY 143
                                       ******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       899  (0.0501422); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); 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: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 983.29
//
Query:       gi|385805686|ref|YP_005842084.1|  [L=419]
Description: glycosyltransferase, family 4 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.3e-24   84.4   0.0      1e-23   83.7   0.0    1.3  1  Glycos_transf_1  Glycosyl transferases group 1
    2.2e-17   63.7   0.0    4.1e-17   62.9   0.0    1.4  1  Glyco_trans_1_4  Glycosyl transferases group 1
    5.8e-06   26.4   0.0    0.00012   22.2   0.0    2.3  1  Glyco_transf_4   Glycosyltransferase Family 4
     0.0013   19.2   0.0     0.0033   17.9   0.0    1.6  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
  ------ inclusion threshold ------
      0.017   15.5   0.0      0.035   14.5   0.0    1.5  1  Glyco_trans_1_2  Glycosyl transferases group 1
      0.045   13.6   0.1       0.22   11.3   0.0    2.1  2  SPAM             Salmonella surface presentation of antigen g


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.7   0.0   3.5e-27     1e-23      16     166 ..     241     388 ..     231     393 .. 0.92

  Alignments for each domain:
  == domain 1  score: 83.7 bits;  conditional E-value: 3.5e-27
                                       EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHHC CS
                   Glycos_transf_1  16 kiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleellkn 92 
                                       ++i++ +  ++ Kg+++l+ka+  + k+  +++kl ++    +   ++++a++l l +n++f+ +v++++  el+ +
  gi|385805686|ref|YP_005842084.1| 241 NYIVYASGENPLKGPHVLLKAWVAVSKE-LKDLKLYMIR--CKDTCVERQAKKLAL-KNITFTDYVPPKEHYELMYR 313
                                       566777777889************9886.*********9..788899*******99.9******************* PP

                                       ESEEEEEESS.BSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHHHH CS
                   Glycos_transf_1  93 adifvlpsis.EgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelrerlg 166
                                       a ++v+ps + E+fG  ++EA  +g+p+i+s++gg++e++ +  tG+++k +++ +l+ +i k+ + + +r+r++
  gi|385805686|ref|YP_005842084.1| 314 ARAVVMPSLWpEPFGRIPIEANRLGVPAIVSDTGGLPEIIINDTTGFIFKRGDPGDLITKILKVFDLNFERQRII 388
                                       *****************************************************************9998888876 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 !   62.9   0.0   1.4e-20   4.1e-17       7     132 ..     246     378 ..     240     379 .. 0.85

  Alignments for each domain:
  == domain 1  score: 62.9 bits;  conditional E-value: 1.4e-20
                                       ES---GG.GTHHHHHHHHHHHH.H..HEEEEEES---..HHHHHHHT..T-T.TEEEE---..THHHHHHHH-SEEE CS
                   Glyco_trans_1_4   7 vGrleenvkgvdllleavpllrkk..dvrlvivGdgprpeeleelaa..gleerveftGfv..edlaellaaadvfv 77 
                                        +    + kg ++ll+a+ ++ k+  d++l+++  +  +  +e++a+   l ++++ft +v  ++  el+ +a+ +v
  gi|385805686|ref|YP_005842084.1| 246 ASGE-NPLKGPHVLLKAWVAVSKElkDLKLYMIRCK--DTCVERQAKklAL-KNITFTDYVppKEHYELMYRARAVV 318
                                       4444.478**********999988745******944..3356666653345.79*******87779999******** PP

                                       E--...---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHH CS
                   Glyco_trans_1_4  78 aPs...egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLl 132
                                       +Ps   e fg   +Ea  +g+p +++d+gg++e++   ++g++++ gdp +l+ +il+++
  gi|385805686|ref|YP_005842084.1| 319 MPSlwpEPFGRIPIEANRLGVPAIVSDTGGLPEIIinDTTGFIFKRGDPGDLITKILKVF 378
                                       *********************************99*7799****************9875 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   3.9e-08   0.00012       2     165 ..      13     167 ..      12     222 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 3.9e-08
                    Glyco_transf_4   2 GGverhvleLaraLarrGheVtvvtpgddgpleeev..elvvrvprvplpllkrllrslaflrrlrrllkrekpDvv 76 
                                       GG++ ++le+ + L +r +eV v+t +    +  +    l+ +v +v  +l+k ++ ++ + +++ +l+k    D++
  gi|385805686|ref|YP_005842084.1|  13 GGAQLSTLEFLELLKDR-VEVKVLTCDNAVNSFTQGlrNLGLEVYKVT-CLRKLNYPIMLYNPSVEKLVK--WADII 85 
                                       9**************99.******877776666665645555555555.666666666666678999999..99*** PP

                    Glyco_transf_4  77 .HahspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSeatadelrery 152
                                         +  ++++ +    ++  ++ip+V+++H+ +    + + ++ ++ +++ + rr   + +r+i +   + +el +  
  gi|385805686|ref|YP_005842084.1|  86 wITDIEFTIAYQIKEIK--KNIPIVAHLHSYAL---VCPWWGAYYSFRETCTRRC--SIRRIIQCKLGINNELSK-V 154
                                       99999999999988888..6************5...4444555666666666666..777888888888888888.8 PP

                    Glyco_transf_4 153 gvppekitVipnG 165
                                       g+ +++ + i+nG
  gi|385805686|ref|YP_005842084.1| 155 GYLNKRKACIYNG 167
                                       8777888888887 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.1e-06    0.0033       1     126 [.      13     135 ..      13     141 .. 0.87
   2 ?   -2.9   0.0       2.7   8.2e+03     113     139 ..     174     200 ..     166     203 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.1e-06
                   Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgape..leedgvrvhrlpvprrpspladlaalralrrllrqrrerpd 75 
                                       gG++  + e+++ L +r +eV vlt + a +++   l+  g++v+ +   r+    + + + + ++ l+       d
  gi|385805686|ref|YP_005842084.1|  13 GGAQLSTLEFLELLKDR-VEVKVLTCDNAVNSFTqgLRNLGLEVYKVTCLRKL-NYPIMLYNPSVEKLV----KWAD 83 
                                       89999************.*******999999775559999********99998.4667778899****9....889* PP

                   Glyco_trans_4_4  76 vvhahsptaglaarlarrrrgiplvvtlhglllrrg.sgavrrlyralerrl 126
                                       ++++ ++   +a  +   +++ip+v +lh+ +l+ +  ga ++++ ++ rr+
  gi|385805686|ref|YP_005842084.1|  84 IIWITDIEFTIAYQIKEIKKNIPIVAHLHSYALVCPwWGAYYSFRETCTRRC 135
                                       *******9999999999999*********97777666777778888887776 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.7
                   Glyco_trans_4_4 113 gavrrlyralerrllrradavlvvsea 139
                                       + ++  +r l   ++ + d++++vs++
  gi|385805686|ref|YP_005842084.1| 174 PLDYTRWRQLVGDVVDNIDGFIAVSNS 200
                                       556677888999999999999999975 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 ?   14.5   0.0   1.2e-05     0.035      17      70 ..     333     388 ..     325     408 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.2e-05
                   Glyco_trans_1_2  17 EaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraia 70 
                                       Ea   G++a+++d+ gl+e++ +++++++f+  d+ +l+ ki ++ +   er++i 
  gi|385805686|ref|YP_005842084.1| 333 EANRLGVPAIVSDTGGLPEIIINDTTGFIFKrgDPGDLITKILKVFDLNFERQRII 388
                                       66678*************************************99988888888775 PP

>> SPAM  Salmonella surface presentation of antigen gene type M protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.79   2.4e+03       4      33 ..      25      54 ..      23      65 .. 0.78
   2 ?   11.3   0.0   7.4e-05      0.22      43      87 ..     254     298 ..     249     309 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.79
                              SPAM  4 vLlarCevaqsrCeaallqlkdeereldke 33
                                       L+ r ev    C+ a+  + ++ r+l  e
  gi|385805686|ref|YP_005842084.1| 25 LLKDRVEVKVLTCDNAVNSFTQGLRNLGLE 54
                                      688899999999999999988887777655 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 7.4e-05
                              SPAM  43 gLkeLLdlqrpegksldreelyallrkqaivrrqlkeLeLqlvai 87 
                                       g + LL++  + +k+l+  +ly +  k + v rq k+L L+ ++ 
  gi|385805686|ref|YP_005842084.1| 254 GPHVLLKAWVAVSKELKDLKLYMIRCKDTCVERQAKKLALKNITF 298
                                       5568999999*******************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 2631.89
//
Query:       gi|385805687|ref|YP_005842085.1|  [L=396]
Description: hypothetical protein FFONT_0643 [Fervidicoccus fontis Kam940]
Scores for complete 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   94.4   1.6    2.1e-26   93.5   1.6    1.4  1  PS_pyruv_trans  Polysaccharide pyruvyl transferase
  ------ inclusion threshold ------
       0.16   11.3   1.3       0.19   11.0   0.4    1.6  2  Heliorhodopsin  Heliorhodopsin
       0.22   10.3   0.0       0.61    8.9   0.0    1.6  2  Epimerase_2     UDP-N-acetylglucosamine 2-epimerase


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 !   93.5   1.6   3.4e-30   2.1e-26       2     281 ..      15     329 ..      14     331 .. 0.83

  Alignments for each domain:
  == domain 1  score: 93.5 bits;  conditional E-value: 3.4e-30
                                       HHHHHHHHHHHHHHHHTT-EEEEEESSTTT--HHHHHHHHHTS-GGGEE............................ CS
                    PS_pyruv_trans   2 yGDelilealvklLrelgpdaeiivltpdpsetkkllkvktpilkklskvllkrlrkkdi................. 61 
                                       +G++l++++++ +L +lg d+e+i++ p+ ++  k++++  +i++k s ++        +                 
  gi|385805687|ref|YP_005842085.1|  15 VGAVLQAYCMQSILSDLGFDVEFINYIPKLESLVKTYSDVLKIPRKYSVIRG-------Llnlsmfsafrtivgela 84 
                                       69********************************999999777755443322.......24556678********** PP

                                       ............................................EEE--E......EEEETT-HHH.HHHHHHHHHH CS
                    PS_pyruv_trans  62 .......................................ddaddviivGgd..gtlgndgdlsrlp.dalrllflak 96 
                                                                               +++d+++vG+d  +     ++++  + d+  +l +++
  gi|385805687|ref|YP_005842085.1|  85 nslyaykmerlkneefeifrkshlkltkpltsltelkqaAEKYDYVVVGSDqvW-----NPIFLMYsDYAYILPFKT 156
                                       **************************************************7443.....666677778899999999 PP

                                       S-SSEEEE-SEEE.....-S-HHHHHHHHHHHHHTTEEEESSHHHHH.HHHHHHTT-EEE---GGGGG---HHHHHH CS
                    PS_pyruv_trans  97 kagkpviilgqgi..Gp.flnealrkllkkilakadlisvRdelSaelleslglkrnveltpDpaflleqlapseil 170
                                        ++k   +l+++i   p ++++  +++++ +l+ +d+isvR+++ + +l +l  + ++++ pDp++l+ + + s ++
  gi|385805687|ref|YP_005842085.1| 157 SSKK--MALAASIgvDPsNIPNHILNYFRLALRDFDFISVREKRHVSILSKLIGR-DIYHIPDPVLLVRSEILSNLE 230
                                       9999..*******88666888888889********************55555544.**********99976555544 PP

                                       S-------------SS--EE---SSS---HH...............................HH-TTS-HHHHHHHH CS
                    PS_pyruv_trans 171 etdkrkylrvakssekdledleellakvydlllekgarllllpivkkdglelddlyllllraaakkekvtildrfas 247
                                       +            +++d++    +l   +  l++k  + l lp+v++    +  l   l     ++    +  ++ +
  gi|385805687|ref|YP_005842085.1| 231 Q---------RVEFPFDEFVMVYNLDPTILPLIDKISEDLGLPVVIYSKPYVFPLSQYL---QYRRWGKYVSIYNVG 295
                                       4.........4444455666666666666666667777777888888888777777777...6677788899999** PP

                                       HHHHHHHHHTSSEEEE--HHHHHHHHHHT--EEE CS
                    PS_pyruv_trans 248 peellsliaradfvitsRlHglifalsfgvPvig 281
                                       p  +++li++a++vit+++Hg+i+++ f++ + +
  gi|385805687|ref|YP_005842085.1| 296 PKGFIYLIKKASYVITNSYHGVILSIRFKKSFAI 329
                                       *****************************98865 PP

>> Heliorhodopsin  Heliorhodopsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       0.5     3e+03      35      91 ..      38      97 ..      14      99 .. 0.54
   2 ?   11.0   0.4   3.3e-05      0.19     197     225 ..     273     302 ..     263     312 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.5
                    Heliorhodopsin 35 legdpetaalapeteelfevelgvlv.alFllls..alahlliatvlfkrYeenLkkgin 91
                                      +++ p+ ++l+++ + +++++  + v    l ls  +++ +++    ++ Y  ++++  n
  gi|385805687|ref|YP_005842085.1| 38 INYIPKLESLVKTYSDVLKIPRKYSViRGLLNLSmfSAFRTIVGELANSLYAYKMERLKN 97
                                      444455555555555566665443331334444411344556666688888888777666 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 3.3e-05
                    Heliorhodopsin 197 lFalnmllqykkvgkw.kdylyGErvYivL 225
                                       +F+l ++lqy+++gk+ + y +G + +i L
  gi|385805687|ref|YP_005842085.1| 273 VFPLSQYLQYRRWGKYvSIYNVGPKGFIYL 302
                                       8***************55699****99987 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 ?   -2.2   0.0      0.24   1.4e+03      35      73 ..     104     132 ..      88     137 .. 0.47
   2 ?    8.9   0.0    0.0001      0.61     236     271 ..     282     318 ..     247     327 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.24
                                       ---SEEE---S--HHHHHHHHHHHHHHHHHHH--SEEEE CS
                       Epimerase_2  35 ekpdydlnsdsqslakstgrvligleevleeekpDlvlv 73 
                                       +k +++l+++          +++  e   ++ek+D+v+v
  gi|385805687|ref|YP_005842085.1| 104 RKSHLKLTKP----------LTSLTELKQAAEKYDYVVV 132
                                       4444444433..........3333333334455555555 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0001
                                       HHH-TTEEEE----HHHHHHHHHC-SEEEES-H.HHH CS
                       Epimerase_2 236 leelenvtlieplgyldflsllknaklvltdSg.Giq 271
                                       ++++ +   i ++g + f+ l+k+a +v+t+S  G++
  gi|385805687|ref|YP_005842085.1| 282 YRRWGKYVSIYNVGPKGFIYLIKKASYVITNSYhGVI 318
                                       455557888999********************88886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); 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: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 2340.86
//
Query:       gi|385805688|ref|YP_005842086.1|  [L=437]
Description: coenzyme F420-reducing hydrogenase subunit beta [Fervidicoccus fontis Kam940]
Scores for complete 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-30  103.9   0.0    1.2e-29  103.2   0.0    1.4  1  FrhB_FdhB_C  Coenzyme F420 hydrogenase/dehydrogenase, beta su
    1.2e-17   63.8   0.0    2.5e-17   62.8   0.0    1.6  1  FrhB_FdhB_N  Coenzyme F420 hydrogenase/dehydrogenase, beta su
    1.6e-11   43.5  10.9      4e-06   26.4   2.9    2.3  2  Fer4         4Fe-4S binding domain
    7.5e-10   39.3   4.4    1.8e-09   38.1   4.4    1.7  1  Fer4_7       4Fe-4S dicluster domain
    1.1e-08   34.8  11.6    0.00037   20.5   1.6    2.4  2  Fer4_6       4Fe-4S binding domain
    8.5e-07   28.7  11.5     0.0017   18.3   1.5    2.6  2  Fer4_2       4Fe-4S binding domain
    1.6e-06   28.2   5.3    2.3e-06   27.6   4.0    2.0  2  Fer4_9       4Fe-4S dicluster domain
    4.3e-06   26.8   8.6    1.5e-05   25.1   8.6    1.9  1  Fer4_21      4Fe-4S dicluster domain
    5.7e-06   26.3   9.9    0.00027   21.0  11.6    2.3  2  Fer4_10      4Fe-4S dicluster domain
    0.00011   22.7   5.6      0.033   14.7   0.2    2.6  2  Fer4_17      4Fe-4S dicluster domain
     0.0016   18.9   9.7     0.0094   16.4   0.1    2.6  2  Fer4_8       4Fe-4S dicluster domain
     0.0035   17.7  15.9      0.041   14.4   1.2    2.6  2  Fer4_4       4Fe-4S binding domain
     0.0041   17.6   5.6       0.41   11.2   0.1    2.3  2  Fer4_13      4Fe-4S single cluster domain of Ferredoxin I
  ------ inclusion threshold ------
      0.035   15.1   1.0      0.035   15.1   1.0    2.6  2  Fer4_16      4Fe-4S double cluster binding domain
      0.046   14.5   3.3        4.9    8.0   0.4    2.4  2  Fer4_15      4Fe-4S single cluster domain
      0.048   14.6   3.3      0.048   14.6   3.3    2.9  3  Fer4_3       4Fe-4S binding domain
       0.48   11.3   5.6        6.3    7.7   0.9    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 !  103.2   0.0   1.1e-32   1.2e-29       3     152 ..     173     333 ..     171     335 .. 0.92

  Alignments for each domain:
  == domain 1  score: 103.2 bits;  conditional E-value: 1.1e-32
                       FrhB_FdhB_C   3 kvavvGtPCqiaalrklqk..kklkekilltiglfCggnfspealrklleelgvdpedvkklefr..gk.gkfrvel 74 
                                       k+a+v +PC i++lr++++  ++l++ i+++ g++C  ++s +a++ +++    + ++v +++fr  g+ g++++ +
  gi|385805688|ref|YP_005842086.1| 173 KIAIVALPCLIRGLRNAMRfnPRLRNSIRYVFGVYCYNTPSASATEYVMNTFLNNVSNVNHVRFRgfGWpGYLIIRT 249
                                       89*******************99************************99999989********************99 PP

                       FrhB_FdhB_C  75 kd..ekeislkelee......firpsCkvCkdktaelADisvGdvwgpekk.gdddegvstvlvrtekgeellekav 142
                                        +  + +i+++e  +      f   sC +C+d+taelADis++d w  +   g    g ++v++rt++g +++++av
  gi|385805688|ref|YP_005842086.1| 250 VNgrSFRIKYQEYSDsgfgqyFYDYSCFMCNDQTAELADISFADPWTYQVDiG---LGKTLVVIRTAEGWRVFSEAV 323
                                       995544555555555888888999***********************998866...********************* PP

                       FrhB_FdhB_C 143 eageleleel 152
                                       e+g++e++el
  gi|385805688|ref|YP_005842086.1| 324 EEGYIEYREL 333
                                       ******9987 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 !   62.8   0.0   2.4e-20   2.5e-17       2      78 .]      86     165 ..      85     165 .. 0.95

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 2.4e-20
                       FrhB_FdhB_N   2 vaArstdkeirkkaqsGGivtallkylLeegiidgvivvaps..kdpwrpkpviattkeellaaaGskYt.lspnlk 75 
                                       v A+st+k +r  ++sGG++t+ll+ylL++  +d+v+v + +  + ++  ++ ++t++++l++ +Gs+Y+ +  + k
  gi|385805688|ref|YP_005842086.1|  86 VLAWSTNKYVRFMGSSGGVITSLLIYLLRKRHVDAVVVPKLHviNGRVFGVYEVVTDPAKLIEYSGSIYApIFGVHK 162
                                       88**************************************999988999*********************9999998 PP

                       FrhB_FdhB_N  76 lLk 78 
                                       +Lk
  gi|385805688|ref|YP_005842086.1| 163 ALK 165
                                       886 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   2.9   3.8e-09     4e-06       2      24 .]       6      28 ..       5      28 .. 0.92
   2 !   21.8   1.1   1.1e-07   0.00011       3      20 ..      41      58 ..      39      59 .. 0.91

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 3.8e-09
                                      EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  2 videekCigCGaCvevCPvgAIt 24
                                       i +++C gCG C  +CP +AI+
  gi|385805688|ref|YP_005842086.1|  6 RIPPDLCSGCGVCSLICPKNAIR 28
                                      5779******************6 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 1.1e-07
                                      EETTTSSS-THHHHHSTT CS
                              Fer4  3 ideekCigCGaCvevCPv 20
                                       d + Ci+C +C++vCP+
  gi|385805688|ref|YP_005842086.1| 41 LDSSNCINCYLCEKVCPF 58
                                      5899*************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 !   38.1   4.4   1.7e-12   1.8e-09       2      50 ..      12      58 ..      11      59 .. 0.93

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 1.7e-12
                            Fer4_7  2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPt 50
                                      C gCg C   Cp +ai+++ ++  +g  ++ +d+++C++C+ C++vCP+
  gi|385805688|ref|YP_005842086.1| 12 CSGCGVCSLICPKNAIRFRVFT--NGYIRPLLDSSNCINCYLCEKVCPF 58
                                      ******************9984..588999******************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 !   19.1   2.9   9.4e-07     0.001       6      24 .]       9      27 ..       4      27 .. 0.91
   2 !   20.5   1.6   3.5e-07   0.00037       5      21 ..      42      58 ..      41      61 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 9.4e-07
                            Fer4_6  6 pdkCigCgdCvrvCPegai 24
                                      pd+C gCg C  +CP +ai
  gi|385805688|ref|YP_005842086.1|  9 PDLCSGCGVCSLICPKNAI 27
                                      9****************98 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 3.5e-07
                            Fer4_6  5 dpdkCigCgdCvrvCPe 21
                                      d ++Ci C+ C++vCP+
  gi|385805688|ref|YP_005842086.1| 42 DSSNCINCYLCEKVCPF 58
                                      789*************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 !   14.9   2.9   1.9e-05      0.02       3      21 ..       5      23 ..       3      24 .. 0.90
   2 !   18.3   1.5   1.6e-06    0.0017       3      21 ..      39      57 ..      37      58 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.9e-05
                            Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                      + + +d C gCg C   CP
  gi|385805688|ref|YP_005842086.1|  5 PRIPPDLCSGCGVCSLICP 23
                                      56889*************9 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 1.6e-06
                            Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                      +  d+ +Ci+C  C ++CP
  gi|385805688|ref|YP_005842086.1| 39 PLLDSSNCINCYLCEKVCP 57
                                      78899************** PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   4.0   2.2e-09   2.3e-06       2      47 ..      12      57 ..      10      60 .. 0.92
   2 ?   -1.9   0.0       3.6   3.8e+03      34      40 ..     274     280 ..     246     281 .. 0.64

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 2.2e-09
                            Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCp 47
                                      C gCg C   Cp+++++ + +++       + ++Ci C  C+++Cp
  gi|385805688|ref|YP_005842086.1| 12 CSGCGVCSLICPKNAIRFRVFTNGYIRPLLDSSNCINCYLCEKVCP 57
                                      ****************999999988888888899***********9 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.6
                            Fer4_9  34 eaCigCg 40 
                                        +C++C+
  gi|385805688|ref|YP_005842086.1| 274 YSCFMCN 280
                                       5788886 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   8.6   1.4e-08   1.5e-05       2      53 ..       6      58 ..       5      61 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.4e-08
                           Fer4_21  2 ridedkCigCgkCliaCedtshqaieidaktvlkvv.edeCvGCnlCssvCPv 53
                                      ri +d C gCg C + C+++++    +++  + +++ +++C+ C lC +vCP 
  gi|385805688|ref|YP_005842086.1|  6 RIPPDLCSGCGVCSLICPKNAIRFRVFTNGYIRPLLdSSNCINCYLCEKVCPF 58
                                      68899*************765555556555566665479*************6 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0  11.6   2.5e-07   0.00027       3      56 .]       6      57 ..       4      57 .. 0.94
   2 !   16.5   1.5   6.4e-06    0.0068       4      21 ..      41      58 ..      38      82 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.5e-07
                           Fer4_10  3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      +i++d C +Cg C   CP   ++ + + ++++  +   ++++C++c  C ++CP
  gi|385805688|ref|YP_005842086.1|  6 RIPPDLCSGCGVCSLICPK--NAIRFRVFTNGYIRPLLDSSNCINCYLCEKVCP 57
                                      799****************..88889999999999999***************9 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 6.4e-06
                           Fer4_10  4 idddtCirCgkCvkaCPa 21
                                      +d++ Ci+C  C k+CP+
  gi|385805688|ref|YP_005842086.1| 41 LDSSNCINCYLCEKVCPF 58
                                      78999************9 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   1.3    0.0017       1.8      44      59 ..      10      25 ..       3      27 .. 0.86
   2 !   14.7   0.2   3.2e-05     0.033       1      21 [.      45      74 ..      45      95 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0017
                           Fer4_17 44 slCieCgeCerkCPqg 59
                                      +lC++Cg C+  CP++
  gi|385805688|ref|YP_005842086.1| 10 DLCSGCGVCSLICPKN 25
                                      6899999999999986 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 3.2e-05
                           Fer4_17  1 rCiqCgyClpeCpsyea.........ydne 21
                                      +Ci+C  C+++Cp++e+         y+n+
  gi|385805688|ref|YP_005842086.1| 45 NCINCYLCEKVCPFLEEpnslmsrglYGNK 74
                                      6************99885444444444444 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   1.1    0.0035       3.6      49      64 ..      10      25 ..       6      27 .. 0.82
   2 !   16.4   0.1   8.9e-06    0.0094       2      22 ..      43      63 ..      42      97 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0035
                            Fer4_8 49 wsCttcgaCtevCpvg 64
                                      + C++cg C+  Cp++
  gi|385805688|ref|YP_005842086.1| 10 DLCSGCGVCSLICPKN 25
                                      5799999999999986 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 8.9e-06
                            Fer4_8  2 lekCieCgaCqsaCpvlrrtk 22
                                       ++Ci+C +C++ Cp+l++ +
  gi|385805688|ref|YP_005842086.1| 43 SSNCINCYLCEKVCPFLEEPN 63
                                      589************998755 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   1.6   6.7e-05      0.07       1      16 [.       9      24 ..       9      30 .. 0.91
   2 !   14.4   1.2   3.9e-05     0.041       2      16 ..      44      58 ..      43      68 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.7e-05
                            Fer4_4  1 qerCigCgsCvaaCPq 16
                                      ++ C gCg+C  +CP 
  gi|385805688|ref|YP_005842086.1|  9 PDLCSGCGVCSLICPK 24
                                      588************6 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 3.9e-05
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      ++Ci+C  C+ +CP+
  gi|385805688|ref|YP_005842086.1| 44 SNCINCYLCEKVCPF 58
                                      69************5 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   2.0     0.005       5.3       4      18 ..      10      24 ..       7      25 .. 0.90
   2 !   11.2   0.1   0.00039      0.41       2      17 ..      42      57 ..      41      80 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.005
                           Fer4_13  4 dtCiacgaCvelaPd 18
                                      d C++cg+C  ++P+
  gi|385805688|ref|YP_005842086.1| 10 DLCSGCGVCSLICPK 24
                                      67************7 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00039
                           Fer4_13  2 DrdtCiacgaCvelaP 17
                                      D ++Ci+c +C +++P
  gi|385805688|ref|YP_005842086.1| 42 DSSNCINCYLCEKVCP 57
                                      889************* PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   1.0   3.3e-05     0.035       2      20 ..      12      30 ..      11      40 .. 0.88
   2 ?    7.0   3.2     0.011        12      53      66 ..      45      58 ..      36      59 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.3e-05
                           Fer4_16  2 CgtCgkCaevCPtnaikek 20
                                      C +Cg C  +CP nai+ +
  gi|385805688|ref|YP_005842086.1| 12 CSGCGVCSLICPKNAIRFR 30
                                      9***************976 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.011
                           Fer4_16 53 aitgCdiCqdvCPa 66
                                      +++ C  C++vCP+
  gi|385805688|ref|YP_005842086.1| 45 NCINCYLCEKVCPF 58
                                      45666666666665 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.4    0.0046       4.9       6      20 ..      10      24 ..       6      30 .. 0.88
   2 ?    6.8   0.1     0.011        12       3      20 ..      41      58 ..      40      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0046
                           Fer4_15  6 daCigcglCvaeape 20
                                      d+C gcg+C   +p+
  gi|385805688|ref|YP_005842086.1| 10 DLCSGCGVCSLICPK 24
                                      89***********97 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.011
                           Fer4_15  3 vDrdaCigcglCvaeape 20
                                      +D ++Ci c lC +++p 
  gi|385805688|ref|YP_005842086.1| 41 LDSSNCINCYLCEKVCPF 58
                                      799*************93 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   4.8   0.00069      0.73       1      15 []      12      26 ..      12      26 .. 0.98
   2 ?   14.6   3.3   4.5e-05     0.048       1      12 [.      46      57 ..      46      59 .. 0.96
   3 ?   -1.9   0.6       8.8   9.3e+03       1       5 [.     276     280 ..     276     283 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00069
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C gCg C   CP++A
  gi|385805688|ref|YP_005842086.1| 12 CSGCGVCSLICPKNA 26
                                      99***********99 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 4.5e-05
                            Fer4_3  1 CtgCgaCvevCP 12
                                      C++C++C++vCP
  gi|385805688|ref|YP_005842086.1| 46 CINCYLCEKVCP 57
                                      ************ PP

  == domain 3  score: -1.9 bits;  conditional E-value: 8.8
                            Fer4_3   1 CtgCg 5  
                                       C +C+
  gi|385805688|ref|YP_005842086.1| 276 CFMCN 280
                                       99996 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.9     0.006       6.3      81      95 ..      11      25 ..       3      26 .. 0.80
   2 ?    5.3   0.3     0.033        35       1      13 [.      45      57 ..      28      60 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.006
                           Fer4_22 81 gCvGCgRCieacpvk 95
                                       C GCg C+  cp++
  gi|385805688|ref|YP_005842086.1| 11 LCSGCGVCSLICPKN 25
                                      699999999999875 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.033
                           Fer4_22  1 rClsCgaCtlvCp 13
                                      +C++C  C  vCp
  gi|385805688|ref|YP_005842086.1| 45 NCINCYLCEKVCP 57
                                      4777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2677.16
//
Query:       gi|385805689|ref|YP_005842087.1|  [L=44]
Description: hypothetical protein FFONT_0645 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.13   12.5   0.0       0.17   12.1   0.0    1.2  1  TUG-UBL1  TUG ubiquitin-like domain


Domain annotation for each model (and alignments):
>> TUG-UBL1  TUG ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   9.4e-06      0.17      12      31 ..      16      35 ..      15      42 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.4e-06
                          TUG-UBL1 12 vtpnttlndvLeeackkfkl 31
                                      v+++ ++ dv++e+c+k++l
  gi|385805689|ref|YP_005842087.1| 16 VNAGRSVDDVVQEVCEKLGL 35
                                      789999************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.51
# Mc/sec: 261.64
//
Query:       gi|385805690|ref|YP_005842088.1|  [L=79]
Description: hypothetical protein FFONT_0646 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       210  (0.0117129); expected 358.6 (0.02)
Passed bias filter:                      195  (0.0108762); 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: 0.46u 0.33s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 471.12
//
Query:       gi|385805691|ref|YP_005842089.1|  [L=198]
Description: hypothetical protein FFONT_0647 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score 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   15.2   0.0      0.018   15.1   0.0    1.1  1  DUF72     Protein of unknown function DUF72


Domain annotation for each model (and alignments):
>> DUF72  Protein of unknown function DUF72
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0     1e-06     0.018     108     178 ..      42     143 ..      11     195 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1e-06
                                       HTTTS-SEEEE--BGGGH..............HHHHHHHHTT-E.EEEE--...SSC--------SSTEEEEEE--S CS
                             DUF72 108 flaalpllavEvRhrswf..............ellellrehgva.vvldep...kkpklpledvttadfvyvRlhgr 166
                                       +l+ l+   vE+ h++wf               l+e l++ gv+ vv+d p   k+p   +  v t++ v ++++gr
  gi|385805691|ref|YP_005842089.1|  42 VLRTLK-NNVELEHPQWFstqsidtrdefsagSLFETLENFGVNeVVVD-PdlsKEPGEAQIYVLTDKGVAIKYLGR 116
                                       344443.89********8899999999999855***********99997.335566666667788899999999999 PP

                                       ...............HHTTB----HHH CS
                             DUF72 167 ...............eeryayrYseee 178
                                                       +  + +Y+ + 
  gi|385805691|ref|YP_005842089.1| 117 edpqrdiyiplkpvsIRLPRGKYQIKH 143
                                       777666666666664134444555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1238.66
//
Query:       gi|385805692|ref|YP_005842090.1|  [L=60]
Description: hypothetical protein FFONT_0648 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       199  (0.0110993); expected 358.6 (0.02)
Passed bias filter:                      182  (0.0101512); expected 358.6 (0.02)
Passed Vit filter:                         4  (0.000223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.50
# Mc/sec: 358.81
//
Query:       gi|385805693|ref|YP_005842091.1|  [L=220]
Description: UDP-glucose 4-epimerase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-49  167.5   0.0      4e-49  167.3   0.0    1.0  1  Epimerase        NAD dependent epimerase/dehydratase family
    1.2e-47  163.0   0.0    1.4e-47  162.7   0.0    1.0  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    5.7e-28   97.7   0.0    7.3e-28   97.4   0.0    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    5.4e-22   78.2   0.0    6.5e-22   78.0   0.0    1.0  1  RmlD_sub_bind    RmlD substrate binding domain
    2.6e-13   49.8   0.7    2.6e-10   39.9   0.7    2.5  1  NAD_binding_4    Male sterility protein
    1.4e-12   47.3   0.0    4.8e-12   45.6   0.0    1.7  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    2.6e-09   37.2   0.0    3.3e-09   36.9   0.0    1.1  1  NAD_binding_10   NAD(P)H-binding
    5.6e-07   29.2   0.1    2.8e-05   23.7   0.1    2.2  2  adh_short        short chain dehydrogenase
    3.1e-05   23.7   0.4    3.9e-05   23.3   0.4    1.2  1  NmrA             NmrA-like family
     0.0005   20.0   0.9     0.0016   18.4   0.9    1.7  1  KR               KR domain


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.3   0.0   2.2e-52     4e-49       1     204 [.       9     206 ..       9     212 .. 0.94

  Alignments for each domain:
  == domain 1  score: 167.3 bits;  conditional E-value: 2.2e-52
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC....EEEE--TT-HHHHHHHHHHHT-SEEEE--S CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl....elveldltdrsalerlfkeeqpdavihlAa 73 
                                       +lVtG++GfiGs+lv+ l   g +v +ld+ls++s  + +  +    e+ve+d++d   + ++++  ++dav+hlAa
  gi|385805693|ref|YP_005842091.1|   9 VLVTGGAGFIGSHLVRSLVFSGFQVRVLDNLSRGSLDNIRG-VldsiEFVEGDVRDYGTVGDAVR--GVDAVVHLAA 82 
                                       79*****************************6665555444.45999******************..9********* PP

                                       ---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHH CS
                         Epimerase  74 vggvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlage 150
                                         +va+s  +p  +++ n++gt+n+++a+r   v  ++f+sSs+vYG++ + p  e+    pl+p spYaa+K+age
  gi|385805693|ref|YP_005842091.1|  83 LTDVAESTVEPDLYFDVNVRGTYNVAKASRSVSV--FVFASSSAVYGEPVKLPIPEDH---PLQPKSPYAATKVAGE 154
                                       ******************************8877..************9999999999...**************** PP

                                       HHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEET CS
                         Epimerase 151 klveayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllg 204
                                        lv ++ + yg + ++lrlfn+yGpr + ++ ++vi+ +i+++ +g+ + +++g
  gi|385805693|ref|YP_005842091.1| 155 ALVLSFSELYGYRPVVLRLFNVYGPR-QSKSYTGVITEFIKRVSRGE-PPVIYG 206
                                       *************************9.8888****************.777776 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 !  162.7   0.0   7.9e-51   1.4e-47       1     214 [.      10     205 ..      10     209 .. 0.93

  Alignments for each domain:
  == domain 1  score: 162.7 bits;  conditional E-value: 7.9e-51
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       L+TG+aGfiGs+l++ L+  g++v +++++s   ++++i+ +         +++++++gD++D   + ++++ v  d
  gi|385805693|ref|YP_005842091.1|  10 LVTGGAGFIGSHLVRSLVFSGFQVRVLDNLSR-GSLDNIRGVL--------DSIEFVEGDVRDYGTVGDAVRGV--D 75 
                                       9***********************99887654.4555555554........4689******************9..9 PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHH CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYa 154
                                       +v++LAA   V++s  +P+ +++vnv Gt+++ +a r++ +     f++aS+s vYG++ + p+ E++p++P+sPYa
  gi|385805693|ref|YP_005842091.1|  76 AVVHLAALTDVAESTVEPDLYFDVNVRGTYNVAKASRSVSV-----FVFASSSAVYGEPVKLPIPEDHPLQPKSPYA 147
                                       **************************************975.....9****************************** PP

                                       HHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EEC CS
                     GDP_Man_Dehyd 155 aaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlyl 214
                                       a+K++ + +v ++ e yg   v+ +lfn ++pr++++  t  it+++ r+ +g+ +v+ +
  gi|385805693|ref|YP_005842091.1| 148 ATKVAGEALVLSFSELYGYRPVVLRLFNVYGPRQSKS-YTGVITEFIKRVSRGEPPVI-Y 205
                                       *********************************9887.88*************97766.4 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 !   97.4   0.0   4.1e-31   7.3e-28       1     191 [.      10     186 ..      10     198 .. 0.88

  Alignments for each domain:
  == domain 1  score: 97.4 bits;  conditional E-value: 4.1e-31
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslv 77 
                                       +vtGgaGF+G++lv++Lv  +   +vrvlD   + +l +    ++ ++++egDv+d  ++ +a++gvd+v+hla+l+
  gi|385805693|ref|YP_005842091.1|  10 LVTGGAGFIGSHLVRSLVFSG--FQVRVLDNLSRGSLDNIRGVLDSIEFVEGDVRDYGTVGDAVRGVDAVVHLAALT 84 
                                       69*****************99..6*********999988888899999***************************** PP

                         3Beta_HSD  78 dvag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKala 153
                                       dva  +++ d + +vnv+GT nv +a +  +v v+v+ Ss  v g+   + +i      + ++ +++++y+ +K   
  gi|385805693|ref|YP_005842091.1|  85 DVAEsTVEPDLYFDVNVRGTYNVAKASR--SVSVFVFASSSAVYGE-PVKLPIP-----EDHPLQPKSPYAATKVAG 153
                                       **9868899**************99875..7889******999998.6777777.....56778899********** PP

                         3Beta_HSD 154 EklvlkaNgrtlknggrlyTcaLRpagiyGegdkllvp 191
                                       E+lvl+  +  l +      + LR   +yG+++++  +
  gi|385805693|ref|YP_005842091.1| 154 EALVLSFSE--LYG---YRPVVLRLFNVYGPRQSKSYT 186
                                       *****9988..333...46799*********9877655 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 !   78.0   0.0   3.6e-25   6.5e-22       1     163 [.       7     189 ..       7     200 .. 0.92

  Alignments for each domain:
  == domain 1  score: 78.0 bits;  conditional E-value: 3.6e-25
                                       EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT..................T--TTSHHHHHHHHHHH--SEEEE-- CS
                     RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeeglevlaltre..................eldltdaeavaellkeakpdvvvnaA 59 
                                       m++lvtG+ G +Gs+L+++l  +g++v  l++                   e d++d  +v ++++    d+vv++A
  gi|385805693|ref|YP_005842091.1|   7 MRVLVTGGAGFIGSHLVRSLVFSGFQVRVLDNLsrgsldnirgvldsiefvEGDVRDYGTVGDAVRG--VDAVVHLA 81 
                                       89**************************99766789******************************9..789***** PP

                                       ----HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHH CS
                     RmlD_sub_bind  60 AytavDkaEseeeaayavnaeavealAeaaaavgalLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqav 136
                                       A t+v +   e+++ + vn++++ ++A+a ++v + +++ S+  V+    k p  ed++ +P++ Y++tK+aGE  v
  gi|385805693|ref|YP_005842091.1|  82 ALTDVAESTVEPDLYFDVNVRGTYNVAKASRSVSV-FVFASSSAVYGEPVKLPIPEDHPLQPKSPYAATKVAGEALV 157
                                       ******9999******************9999976.7999******999**************************** PP

                                       HH....H-SSEEEEEE-SEESS.SSS-HHHHH CS
                     RmlD_sub_bind 137 la....agkkalivRtswvyge.kgknfvktm 163
                                       l+    +g + +++R   vyg  + k++  ++
  gi|385805693|ref|YP_005842091.1| 158 LSfselYGYRPVVLRLFNVYGPrQSKSYTGVI 189
                                       *9877778899*********973555555555 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.7   1.5e-13   2.6e-10       1     217 [.      11     191 ..      11     199 .. 0.83

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 1.5e-13
                                       EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHHHHHHHHHHT-SS-HHHHHHHHHTTTEEEEE--TTSGGGG-- CS
                     NAD_binding_4   1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksgesaeeRleeelekkelfsallkelaerikvveGDlseprlGLs 77 
                                       +TG+ GF+G++L++ L+ +                  + R+ ++l + +l +     +++ i++veGD+ +      
  gi|385805693|ref|YP_005842091.1|  11 VTGGAGFIGSHLVRSLVFSGF----------------QVRVLDNLSRGSLDNIR--GVLDSIEFVEGDVRDYG---- 65 
                                       799999999999999998765................33444555555665444..478999******99765.... PP

                                       HHHHHHHHHH--EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS CS
                     NAD_binding_4  78 eedlqelaeevdviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekv 151
                                         ++ + ++ vd+++h aA +++ e++ e    ++vNv+Gt +v + ++++    v+++ S+++v+ge  +      
  gi|385805693|ref|YP_005842091.1|  66 --TVGDAVRGVDAVVHLAALTDVAESTVEpdlYFDVNVRGTYNVAKASRSV---SVFVFASSSAVYGEPVK------ 131
                                       ..88889999***************887766699********997776654...69******999999984...... PP

                                       -H......HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE-....-SSST---T CS
                     NAD_binding_4 152 yeegekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg....esktGwing 217
                                                     +++  + +  Y  +K+++E lv + ++  g++ v++R+ +++g    +s tG+i +
  gi|385805693|ref|YP_005842091.1| 132 ----------LPIPEDHPLQPKSPYAATKVAGEALVLSFSELYGYRPVVLRLFNVYGprqsKSYTGVITE 191
                                       ..........3566788888899**********************************9999999998765 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.0   2.7e-15   4.8e-12       1     191 [.       9     201 ..       9     205 .. 0.82

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 2.7e-15
                                       EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelk 77 
                                       vlvtG++G iGs+lvr ++ +  +  +l + +  +l++i+  l      +++++    v gdvrd  ++ +a++  +
  gi|385805693|ref|YP_005842091.1|   9 VLVTGGAGFIGSHLVRSLVFSGFQVRVLDNLSRGSLDNIRGVL------DSIEF----VEGDVRDYGTVGDAVR--G 73 
                                       8***************999887776666667888999999988......24544....47**************..* PP

                                       -SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEE............GGGSS--SHHHHHH CS
                   Polysacc_synt_2  78 vdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliSt............DKAvnPtnvmGatK 142
                                       vd+v+h AAl  V     +p   ++ Nv gt nv++a+ +  v  +   S+            D   +P + + atK
  gi|385805693|ref|YP_005842091.1|  74 VDAVVHLAALTDVAESTVEPDLYFDVNVRGTYNVAKASRSVSVFVFASSSAvygepvklpipeDHPLQPKSPYAATK 150
                                       **************************************998886654433233333334444499999999999999 PP

                                       HHHHHHHHHGGG--SSS--EEEEEEE-EETTGTTS.....SHHHHHHHHHTTSS CS
                   Polysacc_synt_2 143 rlaekllqalakeseekktkfvvvRfGNVlgSrGS.....viplFkkqikeggp 191
                                        + e l+ ++++       + vv R  NV g r S     vi+ F k++++g+p
  gi|385805693|ref|YP_005842091.1| 151 VAGEALVLSFSELY---GYRPVVLRLFNVYGPRQSksytgVITEFIKRVSRGEP 201
                                       99999999999998...7889999999999877655555599999999999976 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 !   36.9   0.0   1.8e-12   3.3e-09       1     129 [.      13     155 ..      13     164 .. 0.67

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 1.8e-12
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETT..HHHCHHHHCT.TTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC. CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRn..peklaeleae.eglevvegdvtdvedlaealkgadaVvsalggggk. 73 
                                       G+ G +G++lv+ l+ + g++v++l  n    +l++++   + +e vegdv d  ++ +a++g+daVv  ++ ++  
  gi|385805693|ref|YP_005842091.1|  13 GGAGFIGSHLVRSLVFS-GFQVRVL-DNlsRGSLDNIRGVlDSIEFVEGDVRDYGTVGDAVRGVDAVVHLAALTDVa 87 
                                       99***************.5***987.55124456677655589***********************98888555553 PP

                                       HHHH.............HHHHHHHHHHCT--EEEEEEETTTTSG.CGCHHHHHHHHCC.HHHHHHHHHHHH CS
                    NAD_binding_10  74 deeg.............aknivdaakeagvkRfvlvsaigvgde.vpgefgewnkell.kaylaakraaee 129
                                       +  +             + n+++a +   v+ fv+ s+  v+ e v+ + +e       ++y+a k a e+
  gi|385805693|ref|YP_005842091.1|  88 E-STvepdlyfdvnvrgTYNVAKASRS--VSVFVFASSSAVYGEpVKLPIPEDHPLQPkSPYAATKVAGEA 155
                                       2.2234555666663446666666655..666*****9999864133333333333331344444545444 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.1   1.5e-08   2.8e-05       3     118 ..       9     110 ..       7     125 .. 0.82
   2 ?    3.4   0.0     0.026        47     145     169 ..     142     166 ..     136     176 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.5e-08
                                       EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSES CS
                         adh_short   3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkld 79 
                                       vlvtG+++ IG  +++ l+ +G++v v+d+ ++     +++++   +++ ++++Dv+d+  v ++v+ +       d
  gi|385805693|ref|YP_005842091.1|   9 VLVTGGAGFIGSHLVRSLVFSGFQVRVLDNLSRGS---LDNIRGVLDSIEFVEGDVRDYGTVGDAVRGV-------D 75 
                                       9**************************99987776...7777777778**********99888888765.......8 PP

                                       EEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHH CS
                         adh_short  80 vLvnNAGitgsgpfselseeewervievNltgvflltra 118
                                       ++v+ A++t +      s  e + +++vN+ g++++++a
  gi|385805693|ref|YP_005842091.1|  76 AVVHLAALTDV----AESTVEPDLYFDVNVRGTYNVAKA 110
                                       99999999322....223344677899999999998876 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.026
                                       TBHHHHHHHHHHHHHHHHHHHHHGG CS
                         adh_short 145 gvaaYsAsKaavagltrslakelap 169
                                         ++Y+A+K a ++l+ s+++ + +
  gi|385805693|ref|YP_005842091.1| 142 PKSPYAATKVAGEALVLSFSELYGY 166
                                       5689***********9998877665 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.4   2.2e-08   3.9e-05       1      73 [.       9      82 ..       9     121 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 2.2e-08
                                      EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHH..STTEEEES-TT-HHHHHHHHTT-SEEEE--- CS
                              NmrA  1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslke..aGvelvkgdlddkeslvealkgvdvvfsvtg 73
                                      +lv+G++G +G+++vr l+ +g++vr+l  ++++  ++++       e+v+gd+ d+  +  a++gvd+v    +
  gi|385805693|ref|YP_005842091.1|  9 VLVTGGAGFIGSHLVRSLVFSGFQVRVLD-NLSRGSLDNIRGvlDSIEFVEGDVRDYGTVGDAVRGVDAVVHLAA 82
                                      79************************985.55444445444322469**********************987655 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.9   9.1e-07    0.0016       3     141 ..       9     126 ..       8     132 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 9.1e-07
                                       EEEETTTSHHHHHHHHHHHHHH..S-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHH CS
                                KR   3 ylitGGlGgLGlelarwlaekg..arhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeika 77 
                                       +l+tGG+G +G +l+r l+ +g   r l  lsR           +++++    ++e+v+ Dv d   v  +++ ++ 
  gi|385805693|ref|YP_005842091.1|   9 VLVTGGAGFIGSHLVRSLVFSGfqVRVLDNLSRG---------SLDNIRGVLDSIEFVEGDVRDYGTVGDAVRGVD- 75 
                                       69********************655555667777.........57778888889************9999998876. PP

                                       HSS---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTTS--SEEEEEEEHHHHH CS
                                KR  78 eeppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelledesldffvlfSSiagll 141
                                              v+h A +++    +e t  + +  +   v+G+ n+ ++++  s+ +fv+ SS a ++
  gi|385805693|ref|YP_005842091.1|  76 ------AVVHLAALTDV---AESTV-EPDLYFDVNVRGTYNVAKASR--SVSVFVFASSSA-VY 126
                                       ......8*****87653...33333.345678999*********998..799999888865.44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.49
# Mc/sec: 1349.04
//
Query:       gi|385805694|ref|YP_005842092.1|  [L=90]
Description: NAD-dependent epimerase/dehydratase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.12   11.8   0.0       0.16   11.3   0.0    1.4  1  GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase


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 ?   11.3   0.0     9e-06      0.16     294     330 ..      42      78 ..       2      80 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9e-06
                                       ECGG--SS--SB--B-THHHHHHH----SS-HHHHHH CS
                     GDP_Man_Dehyd 294 dpkyfrpgevdlllgdaskakeeLgWkpkvsfeelvr 330
                                        +k+ rpg+v+  ++++s+a +eL ++p++ + e++r
  gi|385805694|ref|YP_005842092.1|  42 IYKPPRPGDVRHSVANISRAFTELRFNPRIYLLEGLR 78 
                                       46788*************************9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 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:                        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 0.28s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 628.54
//
Query:       gi|385805695|ref|YP_005842093.1|  [L=287]
Description: hypothetical protein FFONT_0651 [Fervidicoccus fontis Kam940]
Scores for complete 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-09   36.8   0.0    6.2e-09   35.8   0.0    1.4  1  NTP_transf_5  Uncharacterised nucleotidyltransferase
  ------ inclusion threshold ------
      0.072   13.4   0.1       0.54   10.5   0.0    2.2  3  AdoMet_dc     S-adenosylmethionine decarboxylase


Domain annotation for each model (and alignments):
>> NTP_transf_5  Uncharacterised nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.0     7e-13   6.2e-09      93     197 ..      88     188 ..      57     207 .. 0.88

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 7e-13
                      NTP_transf_5  93 emgDiDllvkredldraeelLeelGyelesdgsekhevyyrekkgveielhwrllppesprlepdfddlleerarpv 169
                                        + DiD+l++r+dl +a++ L++ G++ e   ++++ +++r    + ++l ++        ++ d ++lle+  +  
  gi|385805695|ref|YP_005842093.1|  88 VSVDIDVLIDRKDLTKAARRLSDRGFRVEVS-EKYTVTMTR--GSTIVDLYTNPAFA--WVIYLDGSKLLECCIEDF 159
                                       677****************************.****99999..99**********66..68999************* PP

                      NTP_transf_5 170 eiggksilvlspedlllylalHl.akhfw 197
                                       e++g +++ ls e ++++ a H+ +k+  
  gi|385805695|ref|YP_005842093.1| 160 EFEGYTLKGLSREAEVVVSASHAvYKEHI 188
                                       **********************8567765 PP

>> AdoMet_dc  S-adenosylmethionine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.27   2.4e+03      19      44 ..      56      84 ..      47      92 .. 0.64
   2 ?   -1.1   0.0      0.26   2.3e+03      66      89 ..      86     109 ..      74     128 .. 0.64
   3 ?   10.5   0.0   6.1e-05      0.54      32      92 ..     148     212 ..     139     224 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.27
                                      HHHHHHHHHHHHCT-.EEEEEEEEE-..S CS
                         AdoMet_dc 19 lleqilteaaeaiga.tvlsvafhkf..e 44
                                      + +++   ++e ++a + l+ a+hkf   
  gi|385805695|ref|YP_005842093.1| 56 RYRRFAGSVIEVAEAlKDLNYALHKFrkP 84
                                      55666666777777634788888888532 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.26
                                       GGTEEEEEEEEESTHHHHHHHHHH CS
                         AdoMet_dc  66 etgyaaiDvftcgeispekaleyl 89 
                                       e+  ++iDv    +  +++a+++ 
  gi|385805695|ref|YP_005842093.1|  86 EHVSVDIDVLIDRKDLTKAARRLS 109
                                       444566666665554444444444 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 6.1e-05
                                       T-EEEEEEEEE-SSS-EEEEEEETTEEEEE...E.EEGGGTEEEEEEEEESTHHHHHHHHHHHHH CS
                         AdoMet_dc  32 gatvlsvafhkfepeGvsvvvliaeShlsi...H.twpetgyaaiDvftcgeispekaleyliea 92 
                                       g ++l+ ++ +fe eG+++  l  e+ + +   H  + e+ y+ iD ft ++   ekal++ +e 
  gi|385805695|ref|YP_005842093.1| 148 GSKLLECCIEDFEFEGYTLKGLSREAEVVVsasHaVYKEHIYLLIDYFTVKKWLDEKALKLSVEF 212
                                       567899999***************9777662222269***************9999999986654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); 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 0.25s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2126.82
//
Query:       gi|385805696|ref|YP_005842094.1|  [L=400]
Description: ABC-type phosphate transport, periplasmic protein [Fervidicoccus fontis Kam940]
Scores for complete 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-51  174.7   5.6    4.6e-51  174.2   5.6    1.2  1  PBP_like_2  PBP superfamily domain
    2.6e-14   53.9   5.3    1.3e-12   48.4   5.3    2.1  1  SBP_bac_1   Bacterial extracellular solute-binding protein
    8.3e-06   25.1   0.0    1.7e-05   24.1   0.0    1.6  1  PBP_like    PBP superfamily domain


Domain annotation for each model (and alignments):
>> PBP_like_2  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.2   5.6   7.7e-55   4.6e-51      11     279 ..      66     368 ..      40     370 .. 0.86

  Alignments for each domain:
  == domain 1  score: 174.2 bits;  conditional E-value: 7.7e-55
                        PBP_like_2  11 e........ifgaGsttpapalrkladafekaapgakvnyastGSgagikalrngdvdfagsdrplteseiaagwaa 79 
                                       +        +++ G+t+p p + +++  f+k++p++k+ y+++GSgag+  + +g  dfagsd pl++s+       
  gi|385805696|ref|YP_005842094.1|  66 TttsqlsvtLKAGGATFPLPQYIAWINEFMKNYPNIKISYEGVGSGAGQSNFFAGVFDFAGSDPPLSKSQW----SN 138
                                       033344444************************************************************55....33 PP

                        PBP_like_2  80 ngaggliqvpvaigaialvvnkd...nplnlsreaLakIfsgkItnWnd........vlglpadgpIkvvhrsdgsg 145
                                          g+ +q+p++ gai++v+n++   + l+ + e La I+ g+I  W+d         l+lp  + I vv+rsd sg
  gi|385805696|ref|YP_005842094.1| 139 YT-GRVMQIPIVAGAIVIVYNVPnlnGQLKVTPEILAMIYNGTIEYWDDpairqvnpNLNLP-HQKIFVVFRSDASG 213
                                       33.677***************888999999**************************988877.************** PP

                        PBP_like_2 146 ttflfstalaeq....gpwt...............asgigasgsegvasav.snngaigyvsvaywlavkgysladv 202
                                       t++ f+t+l+ +    +  +                ++ g +g++gva ++ ++++ ig+v+++y+ ++ ++++a +
  gi|385805696|ref|YP_005842094.1| 214 TQEIFTTYLNVAapqyW--PtslvgkapdypvkatGRAAGGQGNPGVAAILnQTPYSIGFVEWNYAIQQ-NMTMALL 287
                                       **********9966552..044666666666665544444556*******9999*************99.******* PP

                        PBP_like_2 203 tngagkfvlptaataasalkvakias.......nplawslqpveeniadgayPlsrftyiivyqpyayhgnn.aala 271
                                        n++g++vlpt++++ +al+ a   +        + +++++   + +++++yP+ ++t+++v  +y+++  + a+++
  gi|385805696|ref|YP_005842094.1| 288 RNANGNYVLPTTQGIIEALNSAG--GsipldpfADFSQDIKAFLNLPGNDSYPIIAATHLLVWGKYQNK--DiAKGI 360
                                       ***************99999833..25688889667788999**999*****************77543..469*** PP

                        PBP_like_2 272 kaFldyll 279
                                        +Fl+++l
  gi|385805696|ref|YP_005842094.1| 361 ATFLEWIL 368
                                       ******97 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 !   48.4   5.3   2.1e-16   1.3e-12      11     307 ..      88     366 ..      83     373 .. 0.77

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 2.1e-16
                                       HHHHHHHHHHHHTTEEEEEEEECHHHHHH...HHHHHHHTTSSSCSEEEECGGHHHHHHHT..TSBECCHHHHHHTT CS
                         SBP_bac_1  11 qalvakafekehpgikVeiesvgsgslaq...kltlaiaaGdgpaDviavdndwiarlaka..glllpldpyvkayl 82 
                                        a + ++f+k +p+ik+ +e vgsg+++    ++  ++a++d+p  + ++   +++ +     + ++  +++v+ y+
  gi|385805696|ref|YP_005842094.1|  88 IAWI-NEFMKNYPNIKISYEGVGSGAGQSnffAGVFDFAGSDPP--LSKS---QWSNYTGRvmQIPIVAGAIVIVYN 158
                                       5667.99***********************************88..4445...222222222477777777777776 PP

                                       ECTTCCTEEEEHHHHTHHHHCEEEESEEEEE.EEEEEEETTTHHCTTGGGSHBHHHHHHHHHHHHHHCTCT.HCCHC CS
                         SBP_bac_1  83 apgvkdaadklsssvlpkildskvlyvPlya.argliYNkdlfekagldppwtWdelveaakklkekgkkp.iggar 157
                                       +p  + + +k    v+p il+         + ++g                + Wd++++  +++  + +   i +++
  gi|385805696|ref|YP_005842094.1| 159 VPNLN-GQLK----VTPEILA---------MiYNGT--------------IEYWDDPAIRQVNPNLNLPHQkIFVVF 207
                                       66654.3333....4455444.........112344..............45************************* PP

                                       CEEHHHHHHHHHHHHHHHHTGGGEECCCT....................HHCSHHHHS..HHHHHHHHHHHHHHHHH CS
                         SBP_bac_1 158 ggsasgtayyfalalakslggkvfdkdgg....................gldnpegvt..aatylvklyavanltke 212
                                       +++asgt  +f+++l   +++++ ++ +g                    g+++   +t  +++++++ ya++    +
  gi|385805696|ref|YP_005842094.1| 208 RSDASGTQEIFTTYLNVAAPQYWPTSLVGkapdypvkatgraaggqgnpGVAAILNQTpySIGFVEWNYAIQQ---N 281
                                       ***********************999999****************************************9998...* PP

                                       HHTTEEECSSHHHHHHHHHTTSCSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEE.EEEEE CS
                         SBP_bac_1 213 lkgkgaenkdgaaalalfeaGeaamaivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgi.lgayg 288
                                       ++++   n++g+ +l+   +G + ++ + +++             ++ ++ +++  ++ ++   +g+     + a +
  gi|385805696|ref|YP_005842094.1| 282 MTMALLRNANGNYVLPTT-QGIIEALNSAGGS-------------IPLDPFADFSQDIKAFLNLPGNDSYPiIAATH 344
                                       ****************99.5777776555555.............44444444455555555555555445366666 PP

                                       EEEBTTCSTHHH...HHHHHHH CS
                         SBP_bac_1 289 laipkgsknpea...AkkFldf 307
                                       l ++ + +n++    +  Fl++
  gi|385805696|ref|YP_005842094.1| 345 LLVWGKYQNKDIakgIATFLEW 366
                                       7777777777773345555555 PP

>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   2.8e-09   1.7e-05       2     115 ..      92     224 ..      91     271 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 2.8e-09
                                       HHHHHH-TTCEEEEEES-HHHHHHHHHTTS-SEEEESS---CCCH....................HCCCCCEEEEEE CS
                          PBP_like   2 eelaeknpgvrvavanvGsggGlkalrageadiagshlldketee....................ynapalrkaldg 58 
                                       +e+++  p++++++ +vGsg+G +++ ag  d ags+ + ++++                     yn+p l   l+ 
  gi|385805696|ref|YP_005842094.1|  92 NEFMKNYPNIKISYEGVGSGAGQSNFFAGVFDFAGSDPPLSKSQWsnytgrvmqipivagaivivYNVPNLNGQLKV 168
                                       6899**********************************987665455444444444444444444555555555555 PP

                                       EEEEEE-CC-HCHCCCCHCCHHHS--BGGGC-S-B-EEEEE-TTSHHHHHHHHHHC- CS
                          PBP_like  59 ievvlvnlarreqglvvakgnpkkitnwkdladaplrlvnRetGSGtrdlfdellkk 115
                                       ++ +l+  ++  +++   +   ++++    l+ +++ +v R   SGt+  f++ l+ 
  gi|385805696|ref|YP_005842094.1| 169 TPEILAMIYNGTIEYWDDPA-IRQVNPNLNLPHQKIFVVFRSDASGTQEIFTTYLNV 224
                                       55555555555555554444.224666667899********************9964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       911  (0.0508115); expected 358.6 (0.02)
Passed bias filter:                      653  (0.0364214); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.53
# Mc/sec: 2290.68
//
Query:       gi|385805697|ref|YP_005842095.1|  [L=307]
Description: ABC-type phosphate transport, permease [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-11   44.2  17.2    1.7e-11   44.2  17.2    2.3  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   8.2      0.14   2.6e+03      26      67 ..      12      89 ..       9      95 .. 0.59
   2 !   44.2  17.2   9.7e-16   1.7e-11       9     184 ..      90     302 ..      81     303 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.14
                      BPD_transp_1 26 vllslPsfvlaillvlvf....................................vilsilghlilpviillllsaapy 67
                                      +l+ lP+  ++i +++++                                    ++l+ l +++++++i + ls+a++
  gi|385805697|ref|YP_005842095.1| 12 FLSLLPFASILIAIFMFLfyflyeksipilssegmkfligsvwnpemneyqifpMLLGTLETAAIALLISIPLSLAAV 89
                                      556666666444444333455588888888888888888888888888888443333455555555555555555444 PP

  == domain 2  score: 44.2 bits;  conditional E-value: 9.7e-16
                      BPD_transp_1   9 a....lnrnkkldkllrpliivllslPsfvlaillvlvf......................vilsilghlilpviil 59 
                                       a    + +++++ k+++ +++++ ++Ps++++i     +                      + +   g++ + + il
  gi|385805697|ref|YP_005842095.1|  90 AflneYVPSGRVAKWITLIFELFAGMPSIIFGIWGAQYLagalkdslmvplhnyfgfiplfSCSPMSGFTLFTASIL 166
                                       13446899**********************6666333334455555555566666888887777788999999**** PP

                      BPD_transp_1  60 lllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG 136
                                       l l+++py++ + ++  +s+p+  +eaa+  G+++ q +++++l  ++p + ++l+l fg + g++v++++++++  
  gi|385805697|ref|YP_005842095.1| 167 LSLMITPYMFSMLNSSYNSIPSHIREAAYSIGLRKYQ-VFRILLSYMKPGTYASLLLGFGKAAGETVAVSLVIGNIN 242
                                       *************************************.666********************************7777 PP

                      BPD_transp_1 137 .......lgtllleailgydyseis.....nggvlalviavlllnlvadilqrlldprvr 184
                                                 ++++++++++++e +       +++a+++++l++  v++ l  +  +++r
  gi|385805697|ref|YP_005842095.1| 243 vasyclfSPGMTISSLIASQFPESYlypnmLSALYAGGLILLIIGMVFNYLGFVQTKKFR 302
                                       999997733455666666666666677777699999999999999999999988888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 2025.27
//
Query:       gi|385805698|ref|YP_005842096.1|  [L=280]
Description: phosphate ABC transporter permease [Fervidicoccus fontis Kam940]
Scores for complete 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   60.8  15.1    1.3e-16   60.8  15.1    2.2  2  BPD_transp_1   Binding-protein-dependent transport system inn
  ------ inclusion threshold ------
       0.62   10.2   6.2        2.8    8.0   0.2    2.6  3  DHHC           DHHC palmitoyltransferase


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 ?   -2.9   8.6      0.53   4.7e+03      22      65 ..      10      80 ..       2      91 .. 0.75
   2 !   60.8  15.1   1.5e-20   1.3e-16      10     184 ..      95     279 ..      82     280 .] 0.85

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.53
                      BPD_transp_1 22 pliivllslPsfvlaillvlvf...........................vilsilghlilpviillllsaa 65
                                       ++ ++ls+  +++++++vl+f                             ++++g ++l+ +i++ ls++
  gi|385805698|ref|YP_005842096.1| 10 AFFLAVLSMTAIAIFPFFVLLFhviengieailqvgilrfltslppspgNGMGGVGPAVLGTVIVVGLSTL 80
                                      46666778888888888888888888888888888888888888888888888888888886666555554 PP

  == domain 2  score: 60.8 bits;  conditional E-value: 1.5e-20
                      BPD_transp_1  10 lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrslpkdlvea 86 
                                        ++n++++k++++l++ ll lPs+++++l+++++v+  +  ++i + i+l+++s+++yv+++r+a l s+p +++ea
  gi|385805698|ref|YP_005842096.1|  95 EFPNSRISKISSVLTDSLLELPSIIVGMLIYVLVVVPMKTPSMIAGSIALTVVSLPIYVTYMRNA-LLSVPPQYREA 170
                                       489****************************999***************************9975.5689999**** PP

                      BPD_transp_1  87 aralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG..........lgtllleailgydysei 153
                                        +  G+++ q++ kv++P a + +  +++l +++++g+++ l+f+ ++             +tl++ +++  +++++
  gi|385805698|ref|YP_005842096.1| 171 GYSIGLKKLQVLLKVMMPIARRGLSLSVVLGIARAMGETASLLFTVGNVLyyypkdvaepGTTLTILIYNFVQTPYG 247
                                       **********************************************6653666666555544444455555555554 PP

                      BPD_transp_1 154 s.nggvlalviavlllnlvadilqrlldprvr 184
                                       + +++++ ++++++l+ l+++++ +ll + vr
  gi|385805698|ref|YP_005842096.1| 248 NyIAMAWGAALMIVLFYLLLFAISKLLVKEVR 279
                                       49899999999999999999999999988877 PP

>> DHHC  DHHC palmitoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.2   0.00031       2.8      50     115 ..      11      90 ..       8     110 .. 0.80
   2 ?    0.0   0.4     0.094   8.5e+02      68     110 ..      87     128 ..      69     161 .. 0.48
   3 ?    4.8   0.5    0.0031        28      86     119 ..     238     271 ..     204     278 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00031
                              DHHC  50 yFllfllylllllilalvlllialvklveeekkseflavtllkk................llsilllvlsllfllll 110
                                       +Fl++l +++++++ ++vll+  + + +e   +  +l++ +  +                l++++++ ls+lf + +
  gi|385805698|ref|YP_005842096.1|  11 FFLAVLSMTAIAIFPFFVLLFHVIENGIEAILQVGILRFLT--SlppspgngmggvgpavLGTVIVVGLSTLFSIPI 85 
                                       78999999999999999999999999999988877776654..2459999999999999988888888888888877 PP

                              DHHC 111 gllll 115
                                       ++ l 
  gi|385805698|ref|YP_005842096.1|  86 SFALS 90 
                                       76655 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.094
                              DHHC  68 lllialvklveeekkseflavtllkkllsilllvlsllfllll 110
                                       ++l  l +++++++ s++  v + + ll++ ++++ +l+++l+
  gi|385805698|ref|YP_005842096.1|  87 FALSVLFVEFPNSRISKISSVLTDS-LLELPSIIVGMLIYVLV 128
                                       2333333333333333333332222.33333333333333333 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.0031
                              DHHC  86 lavtllkk..llsilllvlsllfllllgllllfhly 119
                                        + +   +  +++++ +++ + ++++l++lllf + 
  gi|385805698|ref|YP_005842096.1| 238 IYNFV--QtpYGNYIAMAWGAALMIVLFYLLLFAIS 271
                                       22222..14589999999999999999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1736.28
//
Query:       gi|385805699|ref|YP_005842097.1|  [L=256]
Description: phosphate import ATP-binding protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      4e-34  118.1   0.0    5.2e-34  117.7   0.0    1.1  1  ABC_tran     ABC transporter
      2e-09   37.7   0.0     0.0015   18.4   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    1.8e-06   27.6   0.1      0.011   15.2   0.0    2.2  2  SMC_N        RecF/RecN/SMC N terminal domain
      5e-05   23.0   0.5    9.8e-05   22.0   0.3    1.6  2  AAA_29       P-loop containing region of AAA domain
    0.00056   19.7   0.4      0.023   14.4   0.0    2.1  2  AAA_15       AAA ATPase domain
    0.00071   19.9   0.0      0.002   18.4   0.0    1.8  1  AAA_22       AAA domain
     0.0011   19.0   0.0     0.0025   17.7   0.0    1.6  1  RsgA_GTPase  RsgA GTPase
     0.0016   19.0   0.0     0.0059   17.1   0.0    1.8  2  AAA_23       AAA domain
     0.0072   16.4   0.3      0.095   12.8   0.1    2.1  2  DUF87        Helicase HerA, central domain
  ------ inclusion threshold ------
      0.014   14.6   0.0      0.021   14.0   0.0    1.3  1  NB-ARC       NB-ARC domain
      0.021   15.2   0.1      0.049   14.0   0.1    1.5  1  AAA_16       AAA ATPase domain
      0.026   13.9   0.1          3    7.2   0.0    2.2  2  TniB         Bacterial TniB protein
      0.077   12.1   0.0       0.12   11.5   0.0    1.2  1  G-alpha      G-protein alpha subunit
       0.11   12.0   0.0        3.8    7.0   0.0    2.4  2  AAA_25       AAA domain
       0.13   11.9   0.0       0.29   10.8   0.0    1.5  1  AAA_30       AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.7   0.0   4.4e-37   5.2e-34       1     137 []      20     176 ..      20     176 .. 0.96

  Alignments for each domain:
  == domain 1  score: 117.7 bits;  conditional E-value: 4.4e-37
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--.....SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-T CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp.....teGeilldgkdlkeqeleslrkeigvlpqepqlfp 72 
                                       l++v+l++ e++++ai+G++G+GKStLlk++ ++++       +G++++ gkd++e +  +lr+++g+l+q p+ fp
  gi|385805699|ref|YP_005842097.1|  20 LHDVELSIMENSITAILGHSGSGKSTLLKVFNRMTDLipgarMSGKVEVFGKDVREWDPYELRRRMGMLFQIPNPFP 96 
                                       789*******************************9988899999********************************* PP

                                       TSBHHHH...............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEES CS
                                       xxxxxxx...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  73 eltvren...............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDE 134
                                       +l++++n               e ++ +e al+   l ++ ++++++ p++LSgGq+qr++laral+ kp++lllDE
  gi|385805699|ref|YP_005842097.1|  97 HLSIYDNvaiaaqvsrnikdkkEIQATVEWALRAAALWDDVEDRLDDFPYKLSGGQQQRLCLARALAMKPEILLLDE 173
                                       **************9999776666666************************************************** PP

                                       TTT CS
                                       xxx RF
                          ABC_tran 135 pta 137
                                       pta
  gi|385805699|ref|YP_005842097.1| 174 PTA 176
                                       *97 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   2.4e-06    0.0028       1      51 [.      32      82 ..      32      96 .. 0.79
   2 !   18.4   0.0   1.3e-06    0.0015     234     299 ..     145     208 ..     115     209 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.4e-06
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldl 51
                                      ++++ G  gsGKS+LL+ +  + +l++ +++++ ++  g++ r+++ +  +
  gi|385805699|ref|YP_005842097.1| 32 ITAILGHSGSGKSTLLKVFNRMTDLIPGARMSGKVEVFGKDVREWDPYELR 82
                                      799**********************99999999999666666666555544 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 1.3e-06
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSp 299
                                       +++lS G+++ l+l+ al+  +    +ll+DEp ++++ + +  +   lk+ ++  g+ ++++TH p
  gi|385805699|ref|YP_005842097.1| 145 PYKLSGGQQQRLCLARALAMKP---EILLLDEPTANIDFENTIIIENALKDIAKsSGITIVIVTHLP 208
                                       5789******99******9988...9***********************6666669*********66 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 !   10.5   0.0   0.00024      0.29      22      41 ..      28      47 ..      16      52 .. 0.85
   2 !   15.2   0.0   8.9e-06     0.011     135     201 ..     136     210 ..      61     226 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00024
                                      TTSSEEEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 22 fsksftaivGpNGSGKsnll 41
                                      +++s+tai+G+ GSGKs ll
  gi|385805699|ref|YP_005842097.1| 28 MENSITAILGHSGSGKSTLL 47
                                      57899************987 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 8.9e-06
                                       T..........CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSH CS
                                       x..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxx RF
                             SMC_N 135 e..........lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislre 199
                                       +           LSgG+++ + la  +A+   kp+ + llDe  a++D++n+ ++ + lk   k+    ++++++  
  gi|385805699|ref|YP_005842097.1| 136 DvedrlddfpyKLSGGQQQRLCLARALAM---KPE-ILLLDEPTANIDFENTIIIENALKDIAKSsgITIVIVTHLP 208
                                       255555555558******99888888776...454.789*********************76665224444555544 PP

                                       HH CS
                                       xx RF
                             SMC_N 200 em 201
                                       ++
  gi|385805699|ref|YP_005842097.1| 209 DQ 210
                                       33 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.3   8.2e-08   9.8e-05      15      39 ..      21      47 ..       9      62 .. 0.77
   2 ?   -2.9   0.0         5     6e+03      25      35 ..      55      65 ..      48      66 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 8.2e-08
                            AAA_29 15 htieidlkg..atlltGpsGsGKSTll 39
                                      h++e++  +  +t + G+sGsGKSTll
  gi|385805699|ref|YP_005842097.1| 21 HDVELSIMEnsITAILGHSGSGKSTLL 47
                                      44554444445***************8 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5
                            AAA_29 25 tlltGpsGsGK 35
                                       l+ G+  sGK
  gi|385805699|ref|YP_005842097.1| 55 DLIPGARMSGK 65
                                      58999999999 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   1.9e-05     0.023      14      48 ..      20      55 ..      18     126 .. 0.84
   2 ?    4.1   0.2     0.026        32     323     364 ..     165     206 ..      99     209 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.9e-05
                            AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsilealdlFln 48
                                      l dve+++ e+ +t + G+ +sGKS++l++++ + +
  gi|385805699|ref|YP_005842097.1| 20 LHDVELSIMENsITAILGHSGSGKSTLLKVFNRMTD 55
                                      678999998889*******************98876 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.026
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                       k+ ill++EP a++  ++  ++ ++lk++a+++   ++i TH
  gi|385805699|ref|YP_005842097.1| 165 KPEILLLDEPTANIDFENTIIIENALKDIAKSSGITIVIVTH 206
                                       4589*****************************99******* PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.7e-06     0.002       5      90 ..      30     132 ..      26     206 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.7e-06
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee...................erpevvfvtlpsstsskdllrellr 62 
                                        +i+++ G+sG+GK+tll+ + +  d  + a++                   +r+  +++++p++    +++ +++ 
  gi|385805699|ref|YP_005842097.1|  30 NSITAILGHSGSGKSTLLKVFNRMTDLIPGARMsgkvevfgkdvrewdpyelRRRMGMLFQIPNPFPHLSIYDNVAI 106
                                       6899*******************998777777799999999999999988876677779999999999999999999 PP

                            AAA_22  63 alglelkaerlsseellealeqalrara 90 
                                       a +++++   ++++e+ +++e alra+a
  gi|385805699|ref|YP_005842097.1| 107 AAQVSRNI--KDKKEIQATVEWALRAAA 132
                                       99988888..888888888888888776 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   2.1e-06    0.0025      95     121 ..      26      52 ..       8      65 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.1e-06
                                       HHCTTSEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  95 ellkdktsvlvGqSGvGKStLinallp 121
                                       + +++++++++G+SG GKStL+++++ 
  gi|385805699|ref|YP_005842097.1|  26 SIMENSITAILGHSGSGKSTLLKVFNR 52 
                                       346679****************98765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0     5e-06    0.0059      15      37 ..      25      48 ..      11      54 .. 0.81
   2 ?   -0.6   0.0       1.4   1.6e+03      89     125 ..     105     141 ..      62     195 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5e-06
                            AAA_23 15 idF.skgltlItGpNGaGKTTild 37
                                      +   ++ +t+I G+ G+GK+T+l 
  gi|385805699|ref|YP_005842097.1| 25 LSImENSITAILGHSGSGKSTLLK 48
                                      3337889***************97 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.4
                            AAA_23  89 siererelskkkgkttkkaklelleideleqfisell 125
                                        i  + +++ k++k+++ + +  l+ ++l++ +++ l
  gi|385805699|ref|YP_005842097.1| 105 AIAAQVSRNIKDKKEIQATVEWALRAAALWDDVEDRL 141
                                       4555666666666666666666666655555555533 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.1     8e-05     0.095      26      43 ..      33      50 ..      19      54 .. 0.88
   2 ?    1.6   0.0      0.21   2.5e+02     156     218 ..     150     214 ..      95     222 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8e-05
                             DUF87 26 lAilgsTGsGKSntvavL 43
                                      +Ailg +GsGKS++ +v 
  gi|385805699|ref|YP_005842097.1| 33 TAILGHSGSGKSTLLKVF 50
                                      69************9985 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.21
                             DUF87 156 elrklknqaiarlldkledllrkggsf..snsstdliallleklekegkitiidlsgvdelaqql 218
                                       + ++++  ++++l +k e ll+++ +   + ++t +i++ l+++ k++ iti+ +  ++++a+++
  gi|385805699|ref|YP_005842097.1| 150 GGQQQRLCLARALAMKPEILLLDEPTAniDFENTIIIENALKDIAKSSGITIVIVTHLPDQAVRV 214
                                       55566666677777777777777766664556677788899999999999999888888888776 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.8e-05     0.021      20     121 ..      30     183 ..      17     207 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.8e-05
                                       SEEEEEEESTTSSHHHHHHHHCCSHCCCCC.CBTEEEEE...................................... CS
                            NB-ARC  20 slvvalvGmgGvGKttlakqilnksdeveg.rFdsvawv...................................... 57 
                                         + a+ G  G+GK+tl+k  ++  d + g r  + + v                                      
  gi|385805699|ref|YP_005842097.1|  30 NSITAILGHSGSGKSTLLKVFNRMTDLIPGaRMSGKVEVfgkdvrewdpyelrrrmgmlfqipnpfphlsiydnvai 106
                                       45789*************99999988888888889999999999999999999999999999999999999999999 PP

                                       ..EEESXXH.HHHHHHXXHHHHHCCCTTSSSS-STTS...........HHHHHHHHCCCTTEEEEEEEE-SHHHH.. CS
                            NB-ARC  58 ..vvsktdk.seeiletilkeLslseddleekeeves...........lkrklvrlLltkrfllvlDDVweeedwdk 120
                                         +vs++ k ++ei+ t+   L ++ + ++  e++ +               l r+L  k  +l+lD    + d+++
  gi|385805699|ref|YP_005842097.1| 107 aaQVSRNIKdKKEIQATVEWAL-RAAALWDDVEDRLDdfpyklsggqqQRLCLARALAMKPEILLLDEPTANIDFEN 182
                                       9999988651667888888888.555888888888888888888985444456689999999999998777766666 PP

                                       . CS
                            NB-ARC 121 i 121
                                       +
  gi|385805699|ref|YP_005842097.1| 183 T 183
                                       5 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   4.1e-05     0.049      25      45 ..      31      51 ..      17      74 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.1e-05
                            AAA_16 25 elvllsGesGvGKsslvrell 45
                                      +++ + G+sG+GKs+l++ + 
  gi|385805699|ref|YP_005842097.1| 31 SITAILGHSGSGKSTLLKVFN 51
                                      7899*************8776 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    0.0025         3      38      60 ..      33      55 ..      20      73 .. 0.84
   2 ?    4.6   0.0     0.016        19     109     160 ..     155     204 ..     142     215 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0025
                              TniB 38 lllvGdsnnGKtmivekFarlhp 60
                                        ++G+s  GK+++++ F r+  
  gi|385805699|ref|YP_005842097.1| 33 TAILGHSGSGKSTLLKVFNRMTD 55
                                      579***************99875 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.016
                              TniB 109 qqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlv 160
                                       + +l+   ++k+++L++DE    +    ++   + nalk +     i+iv+v
  gi|385805699|ref|YP_005842097.1| 155 RLCLARALAMKPEILLLDEPTANI--DFENTIIIENALKDIAKSSGITIVIV 204
                                       4555555679999******87766..677788899***************87 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0    0.0001      0.12      28      47 ..      35      54 ..      26      75 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0001
                                      EEESTTSSHHHHHHHHHHHC CS
                           G-alpha 28 llGqseSGKsTilkqlklly 47
                                      +lG+s+SGKsT+lk + ++ 
  gi|385805699|ref|YP_005842097.1| 35 ILGHSGSGKSTLLKVFNRMT 54
                                      79**************9875 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0032       3.8      30      50 ..      27      47 ..      18      50 .. 0.89
   2 ?    2.2   0.0     0.097   1.2e+02     170     189 ..     188     207 ..     173     211 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0032
                            AAA_25 30 lpagelallaGapgtGKttla 50
                                      + +++++++ G++g+GK+tl+
  gi|385805699|ref|YP_005842097.1| 27 IMENSITAILGHSGSGKSTLL 47
                                      568899*************97 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.097
                            AAA_25 170 ealeriarrtgaavllvhHv 189
                                       +al++ia+  g+++++v H+
  gi|385805699|ref|YP_005842097.1| 188 NALKDIAKSSGITIVIVTHL 207
                                       789****************7 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00024      0.29      18      42 ..      30      54 ..      23      70 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00024
                            AAA_30 18 drvavltGpAGtGKttalkalreaw 42
                                      + ++++ G  G+GK+t+lk+ +++ 
  gi|385805699|ref|YP_005842097.1| 30 NSITAILGHSGSGKSTLLKVFNRMT 54
                                      45999**************998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      608  (0.0339115); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.65u 0.36s 00:00:01.01 Elapsed: 00:00:00.54
# Mc/sec: 1416.88
//
Query:       gi|385805700|ref|YP_005842098.1|  [L=130]
Description: hypothetical protein FFONT_0656 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-07   32.4   2.5    1.8e-07   31.7   2.5    1.4  1  PIN       PIN domain
  ------ inclusion threshold ------
      0.049   13.7   0.1       0.59   10.2   0.0    2.0  2  MoaC      MoaC family


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 !   31.7   2.5     2e-11   1.8e-07       1     120 [.       2     117 ..       2     119 .. 0.75

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 2e-11
                                       EEE-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHS.....SCHCHHHHHHHHHHHHH.HHTSEEE CS
                               PIN   1 ivlDTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlar.....rkskrekaaelvellll.lsalkil 71 
                                       ++lD+s++i+l+++++     ++++   e+  t++l+l+E+l+ + +     +++k+e a +l  +     s+++  
  gi|385805700|ref|YP_005842098.1|   2 YLLDASAIINLIKNKK-----LEAF---ENASTTDLALYECLNAVWKeafllKRLKEETALKLAGSIAKiFSSIEAY 70 
                                       689*********8888.....4455...6799***************665443333333333333333334444444 PP

                                       EBCHHHHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHHH CS
                               PIN  72 pidaeiaeeaaeialkygllpnDaliaAtAkehgikliatfDedfrrva 120
                                       +  ++   ea+ +alk g++++Da+ +  A+++g++l+ t De+++++a
  gi|385805700|ref|YP_005842098.1|  71 S-ITGFEGEALNLALKEGITVYDAVYLYIAIRNGFTLV-TDDEKLKDIA 117
                                       4.5666778999999999********************.*******998 PP

>> MoaC  MoaC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.031   2.8e+02      99     123 ..      18      42 ..      14      52 .. 0.87
   2 ?   10.2   0.0   6.6e-05      0.59      81     116 ..      59      94 ..      43      99 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.031
                                       HHHHHHHHHHHHHHHHHHTTTHTT- CS
                              MoaC  99 mEALtavsvaaltvyDmvKavdkem 123
                                       +EA++ +s++ l++y  + av ke+
  gi|385805700|ref|YP_005842098.1|  18 LEAFENASTTDLALYECLNAVWKEA 42 
                                       79****************9998875 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 6.6e-05
                                       TEEEEEEEEEEEESS--HHHHHHHHHHHHHHHHHHH CS
                              MoaC  81 esveieatvktegktGvemEALtavsvaaltvyDmv 116
                                       +  +i +++++ + tG e EAL  +    +tvyD v
  gi|385805700|ref|YP_005842098.1|  59 SIAKIFSSIEAYSITGFEGEALNLALKEGITVYDAV 94 
                                       4558999999************************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.50
# Mc/sec: 784.98
//
Query:       gi|385805701|ref|YP_005842099.1|  [L=75]
Description: hypothetical protein FFONT_0657 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0031   17.6   0.5     0.0033   17.5   0.5    1.1  1  YpjP             YpjP-like protein
     0.0076   16.3   0.2     0.0094   16.0   0.2    1.2  1  GerPC            Spore germination protein GerPC
  ------ inclusion threshold ------
      0.026   14.1   0.0      0.062   12.9   0.0    1.6  1  LEM              LEM domain
      0.048   13.4   0.5      0.053   13.2   0.5    1.0  1  Pox_VLTF3        Poxvirus Late Transcription Factor VLTF3 lik
      0.056   13.0   0.1      0.062   12.9   0.1    1.1  1  Imm70            Immunity protein 70
      0.066   13.2   0.2      0.082   12.9   0.2    1.2  1  tRNA_NucTran2_2  tRNA nucleotidyltransferase domain 2 putativ
       0.07   13.6   0.3        1.8    9.1   0.0    2.0  2  DUF4733          Domain of unknown function (DUF4733)
       0.59   10.6   5.0        1.5    9.2   2.3    2.5  2  FlaC_arch        Flagella accessory protein C (FlaC)


Domain annotation for each model (and alignments):
>> YpjP  YpjP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.5   1.5e-06    0.0033      11      58 ..      14      64 ..       4      74 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.5e-06
                              YpjP 11 leeaeeqsllKlGkkiaekiedefeeeilpkieevieellekv...eeekl 58
                                      l+e  ++  +K G+ i++ ie+e+++ +l ++e++++e+ +++   +++++
  gi|385805701|ref|YP_005842099.1| 14 LKELMDKYGIKPGPVIRKAIEEEVKKYVLKEVEKELSEISQELsaiQDDEI 64
                                      67788888899************************9998887633345544 PP

>> GerPC  Spore germination protein GerPC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.2   4.2e-06    0.0094      74     121 ..      24      71 ..       4      73 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.2e-06
                             GerPC  74 eaeselfqeiqeeveayLeeeapelleelekqyeveldeeyrefileD 121
                                       ++ + + ++i+eev++y  +e++++l+e+ ++++   d+e +++i eD
  gi|385805701|ref|YP_005842099.1|  24 KPGPVIRKAIEEEVKKYVLKEVEKELSEISQELSAIQDDEIARLIRED 71 
                                       566778899***********************************9998 PP

>> LEM  LEM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.8e-05     0.062       9      25 ..      13      29 ..      12      31 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.8e-05
                               LEM  9 eLreeLkkyGvspGPIt 25
                                       L+e + kyG++pGP+ 
  gi|385805701|ref|YP_005842099.1| 13 RLKELMDKYGIKPGPVI 29
                                      69999**********96 PP

>> Pox_VLTF3  Poxvirus Late Transcription Factor VLTF3 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.5   2.4e-05     0.053      27      91 ..       4      68 ..       1      72 [. 0.93

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.4e-05
                         Pox_VLTF3 27 tkiseevldelkkklkkknisikevtkakvlkiLKelglkklyedvklIleiltgkrpdklssle 91
                                      +++s+++ + lk+ ++k+ i++  v ++ + +  K+  lk+  ++ + I + l+ ++ d++ +l+
  gi|385805701|ref|YP_005842099.1|  4 ETVSAKIPKRLKELMDKYGIKPGPVIRKAIEEEVKKYVLKEVEKELSEISQELSAIQDDEIARLI 68
                                      589*******************************************************9998875 PP

>> Imm70  Immunity protein 70
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   2.8e-05     0.062      30      75 ..      19      64 ..       4      72 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.8e-05
                             Imm70 30 eawGskfPtllnelydgelsvddlekaeaeLkeirkelkklppekv 75
                                      +++G+k   ++ +  ++e+++  l+++e+eL+ei +el++ +  ++
  gi|385805701|ref|YP_005842099.1| 19 DKYGIKPGPVIRKAIEEEVKKYVLKEVEKELSEISQELSAIQDDEI 64
                                      6788888788899999**********************99877665 PP

>> tRNA_NucTran2_2  tRNA nucleotidyltransferase domain 2 putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   3.7e-05     0.082     108     145 ..      15      52 ..      10      60 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.7e-05
                   tRNA_NucTran2_2 108 kdLlealgvkpGpwlgeiLkeleqavvegeleNekeal 145
                                       k+L+ ++g+kpGp + ++++e  ++ v +e+e e   +
  gi|385805701|ref|YP_005842099.1|  15 KELMDKYGIKPGPVIRKAIEEEVKKYVLKEVEKELSEI 52 
                                       69*******************99999999999876666 PP

>> DUF4733  Domain of unknown function (DUF4733)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0   0.00079       1.8      49      63 ..      12      26 ..       3      34 .. 0.79
   2 ?    3.2   0.1     0.054   1.2e+02      36      57 ..      41      62 ..      27      66 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00079
                           DUF4733 49 qplsgllddyGilPk 63
                                      + l++l+d yGi+P 
  gi|385805701|ref|YP_005842099.1| 12 KRLKELMDKYGIKPG 26
                                      56899********95 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.054
                           DUF4733 36 avleelsaplelsqplsglldd 57
                                       + e ++++ e+sq ls + dd
  gi|385805701|ref|YP_005842099.1| 41 VLKEVEKELSEISQELSAIQDD 62
                                      34455667789******99998 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.21   4.8e+02      44      51 ..       3      10 ..       1      12 [. 0.88
   2 ?    9.2   2.3   0.00069       1.5      16      35 ..      42      61 ..      30      69 .. 0.62

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.21
                         FlaC_arch 44 YEvVsnqv 51
                                      YE+Vs ++
  gi|385805701|ref|YP_005842099.1|  3 YETVSAKI 10
                                      *****987 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00069
                         FlaC_arch 16 letvkkeneelsksveelke 35
                                      l+ v+ke++e+s+++  +++
  gi|385805701|ref|YP_005842099.1| 42 LKEVEKELSEISQELSAIQD 61
                                      56667777777777666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1775  (0.0990016); expected 358.6 (0.02)
Passed bias filter:                     1017  (0.0567237); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); 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: 499.60
//
Query:       gi|385805702|ref|YP_005842100.1|  [L=42]
Description: hypothetical protein FFONT_0658 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 270.40
//
Query:       gi|385805703|ref|YP_005842101.1|  [L=110]
Description: ATPase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 756.34
//
Query:       gi|385805704|ref|YP_005842102.1|  [L=312]
Description: family 2 glycosyltransferase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-13   49.4   0.0    6.9e-13   48.8   0.0    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
    2.7e-08   34.0   0.0    4.7e-08   33.2   0.0    1.3  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
  ------ inclusion threshold ------
      0.036   14.2   0.0      0.078   13.1   0.0    1.5  1  COX6C            Cytochrome c oxidase subunit VIc


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 !   48.8   0.0   1.2e-16   6.9e-13       1     132 [.       8     138 ..       8     169 .. 0.87

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 1.2e-16
                                       EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglra 77 
                                       +vv+ ty ++  l+ ++ sl++q   +  ++i+v   S De++e++e+ a+ + +  ++ ++ +  +  a+  g++a
  gi|385805704|ref|YP_005842102.1|   8 CVVTATYKRAWALPYFIGSLKRQ-SLLPSKVIFVLKPSGDESEEVIEKEAQ-GLNYEIVLQKSG-NFVEAVELGIKA 81 
                                       79*********************.*************************96.888888888877.9*********** PP

                                       --SS.EEEEEESSEEE-TTHHHHHHHHHH.H.TTCEEEEEEEEEECCCCCCCHC-SS CS
                   Glycos_transf_2  78 atgd.yilflDaDdepdpdwleklveale.kdgadvvlgqrprifgetdeiernkrv 132
                                       + g  +ilf+D+D + +++w+ek v++++ + +a+++ g++++   + d i+++  +
  gi|385805704|ref|YP_005842102.1|  82 CGGHsLILFIDDDAIASENWIEKYVQFFNlRKDAGGAGGAVYKAIFDGDDISPTGDH 138
                                       ***************************974558899999999998888888887665 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 !   33.2   0.0   7.9e-12   4.7e-08       4     143 ..       7     142 ..       4     152 .. 0.83

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 7.9e-12
                   Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksraln 80 
                                       + v+ +t++++  l   + sl +q+  +++v++v  +s +e  ev+e  a+ l   +++    ++   s+ +++a++
  gi|385805704|ref|YP_005842102.1|   7 TCVVTATYKRAWALPYFIGSLKRQSLLPSKVIFVLKPSGDESEEVIEKEAQGLNY-EIV---LQK---SGNFVEAVE 76 
                                       56777899999999********************************997777755.444...345...45799999* PP

                   Glyco_tranf_2_3  81 ealravk.sdlvllvDdDtvvePdtlkrllqff.ltpkvgavgtpvfll.nrstlvsalgalefae 143
                                        +++a+  + l+l++DdD++ + + +++++qff l++++g +g+ v+    +   +s++g++++++
  gi|385805704|ref|YP_005842102.1|  77 LGIKACGgHSLILFIDDDAIASENWIEKYVQFFnLRKDAGGAGGAVYKAiFDGDDISPTGDHFYGR 142
                                       *****99778*********************************98854326666677777766655 PP

>> COX6C  Cytochrome c oxidase subunit VIc
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.3e-05     0.078      30      65 ..     244     279 ..     239     280 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.3e-05
                             COX6C  30 aaaykfavaepRKkayadFYknYDaekefeemrkaG 65 
                                       + ++ +   ++RK  ++dF  +YD   +f ++r+ G
  gi|385805704|ref|YP_005842102.1| 244 YHIVEIESLKRRKGFMNDFWIHYDIARDFWRLRELG 279
                                       55566667789***********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1956.48
//
Query:       gi|385805705|ref|YP_005842103.1|  [L=193]
Description: hypothetical protein FFONT_0662 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); 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: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1317.85
//
Query:       gi|385805706|ref|YP_005842104.1|  [L=257]
Description: radical SAM protein [Fervidicoccus fontis Kam940]
Scores for 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-19   70.6   0.0    2.8e-19   70.1   0.0    1.2  1  Radical_SAM  Radical SAM superfamily
    1.8e-08   34.8   0.0    3.4e-08   33.8   0.0    1.4  1  Fer4_12      4Fe-4S single cluster domain
    2.5e-06   27.6   0.0    3.9e-06   27.0   0.0    1.3  1  Fer4_14      4Fe-4S single cluster domain
  ------ inclusion threshold ------
       0.15   12.1   0.2       0.35   11.0   0.2    1.5  1  Mst1_SARAH   C terminal SARAH domain of Mst1


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 !   70.1   0.0   6.2e-23   2.8e-19       5     156 ..      48     199 ..      46     210 .. 0.91

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 6.2e-23
                                       SEESS--TTTSCCTT.HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEE CS
                                       xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   5 rgCnlrCsfCarpet.vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiri 80 
                                        gCnl+C+fC+ ++   +++ +g++ s+e ++e +  +++ekg  +v ++ggep+l  +    ++r  +   ++ ++
  gi|385805706|ref|YP_005842104.1|  48 VGCNLKCKFCWSWRQrDSPRSYGEFYSPEAVAERLSLIAEEKGYSYVRISGGEPTLGFEHLLGVLRTFRD--RDKTF 122
                                       69************9*9*********************99999*************99999999999999..8**** PP

                                       EEEECSSCHG..HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBTT CS
                                       xxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  81 tvetngtlpd..eeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivglpG 154
                                        +etng+ +   +e +++l +    +v ++++  ++e++ ++++ r++ fe +++ale+l +ag++   +  v++  
  gi|385805706|ref|YP_005842104.1| 123 ILETNGIYLGysRELAQELSPFVNLHVRVSIKGCNSEEFFEITGaRQEFFELQIRALENLLDAGVE--AHPAVMMSF 197
                                       ********99******************************************************99..455555544 PP

                                       TS CS
                                       xx RF
                       Radical_SAM 155 en 156
                                         
  gi|385805706|ref|YP_005842104.1| 198 SG 199
                                       44 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 !   33.8   0.0   7.7e-12   3.4e-08      13     118 ..      48     156 ..      39     165 .. 0.76

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 7.7e-12
                           Fer4_12  13 sgCnlsCkgCfnketwsfk..sgkeftkelleeiiedlkkesi.egltllGGEPllpenaeallelvkevkeekpek 86 
                                        gCnl+Ck+C     ++    +g+ ++ e+ +e +  +++e+  + + ++GGEP l    e ll +++ ++ +    
  gi|385805706|ref|YP_005842104.1|  48 VGCNLKCKFCWSWRQRDSPrsYGEFYSPEAVAERLSLIAEEKGySYVRISGGEPTL--GFEHLLGVLRTFRDRDK-T 121
                                       59********9654443223488888866666666666665545************..***************98.5 PP

                           Fer4_12  87 diwlytgytleelskk..ekeellkeid.vlvdGk 118
                                        i++++g  l   ++   e +++++ +  v ++G+
  gi|385805706|ref|YP_005842104.1| 122 FILETNGIYLGYSRELaqELSPFVNLHVrVSIKGC 156
                                       89*****9998776445477887776544666665 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   8.8e-10   3.9e-06       7      91 ..      49     130 ..      46     160 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 8.8e-10
                           Fer4_14   7 gCnlsCkgCd..nketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypek 81 
                                       gCnl+Ck+C   ++ +   ++g+ ++ e + ++l+ l ++e   + + ++GGeP      ++ll +++  +++   k
  gi|385805706|ref|YP_005842104.1|  49 GCNLKCKFCWswRQRDSPRSYGEFYSPEAVAERLS-LIAEEKGYSYVRISGGEPT--LGFEHLLGVLRTFRDRD--K 120
                                       9*********887888888***************5.44444445889*******9..67899*******99999..9 PP

                           Fer4_14  82 kiwletngtl 91 
                                          letng +
  gi|385805706|ref|YP_005842104.1| 121 TFILETNGIY 130
                                       9999999976 PP

>> Mst1_SARAH  C terminal SARAH domain of Mst1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2   7.9e-05      0.35       8      29 ..     202     223 ..     197     224 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7.9e-05
                        Mst1_SARAH   8 svdeLqqrlasLDpeMEqEiee 29 
                                       s  eL++rl s+Dp +E+  ee
  gi|385805706|ref|YP_005842104.1| 202 SCRELKERLGSIDPSLEESFEE 223
                                       789**************98886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.33s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 1441.60
//
Query:       gi|385805707|ref|YP_005842105.1|  [L=42]
Description: hypothetical protein FFONT_0664 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       109  (0.00607954); expected 358.6 (0.02)
Passed bias filter:                       97  (0.00541023); expected 358.6 (0.02)
Passed Vit filter:                         4  (0.000223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.32s 00:00:00.73 Elapsed: 00:00:00.49
# Mc/sec: 258.98
//
Query:       gi|385805708|ref|YP_005842106.1|  [L=2036]
Description: hypothetical protein FFONT_0665 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
        5.4    6.3   8.5        6.5    6.0   0.6    2.2  2  7TM_GPCR_Srz  Serpentine type 7TM GPCR chemoreceptor Srz


Domain annotation for each model (and alignments):
>> 7TM_GPCR_Srz  Serpentine type 7TM GPCR chemoreceptor Srz
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.6   0.00036       6.5     194     233 ..    1115    1154 ..    1113    1171 .. 0.85
   2 ?    3.7   2.0    0.0018        32     132     189 ..    1236    1293 ..    1226    1299 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.00036
                      7TM_GPCR_Srz  194 KlshLaSaqqnkpqkYIfwQtilvlifKliaipliillll 233 
                                        K+++L   q + ++ YI+  +i+ l++K+ia+ + + ++ 
  gi|385805708|ref|YP_005842106.1| 1115 KFAKLIVLQAMMLKTYIYAESITLLASKIIALAVTLETFK 1154
                                        888888999***********************99998874 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0018
                      7TM_GPCR_Srz  132 kilylvfvlkdiilflllvlkeekellevetikvvylilfiilnillflsallYipIm 189 
                                          + l++++k i +++++++ + +   e+    +++++ f++ ++l+f+++l+   I+
  gi|385805708|ref|YP_005842106.1| 1236 ASIILALIFKVIRFVMVFLVGWGEFAGEMGFEIMFQIVNFVVAHVLMFFTSLMNQLIV 1293
                                        55677888888888888888888887776556666677777778*****999876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (2036 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); 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: 0.88u 0.25s 00:00:01.12 Elapsed: 00:00:00.48
# Mc/sec: 12665.60
//
Query:       gi|385805709|ref|YP_005842107.1|  [L=43]
Description: hypothetical protein FFONT_0666 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      0.003   17.6   0.1     0.0036   17.3   0.1    1.2  1  Cullin_Nedd8  Cullin protein neddylation domain


Domain annotation for each model (and alignments):
>> Cullin_Nedd8  Cullin protein neddylation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1     2e-07    0.0036      46      60 ..      15      29 ..       5      31 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2e-07
                      Cullin_Nedd8 46 krIesLiekeYleRd 60
                                      + IesLiek+Y+eR 
  gi|385805709|ref|YP_005842107.1| 15 RIIESLIEKGYIERG 29
                                      67************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.30s 00:00:00.69 Elapsed: 00:00:00.46
# Mc/sec: 281.90
//
Query:       gi|385805710|ref|YP_005842108.1|  [L=40]
Description: hypothetical protein FFONT_0667 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       239  (0.0133304); expected 358.6 (0.02)
Passed bias filter:                      180  (0.0100396); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.45
# Mc/sec: 267.00
//
Query:       gi|385805711|ref|YP_005842109.1|  [L=60]
Description: hypothetical protein FFONT_0668 [Fervidicoccus fontis Kam940]
Scores for complete 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   18.6   0.0     0.0016   18.6   0.0    1.1  1  RHH_8     Ribbon-Helix-Helix transcriptional regulator family
     0.0024   17.8   0.0      0.003   17.4   0.0    1.2  1  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 !   18.6   0.0   1.8e-07    0.0016      16      46 ..      19      49 ..       5      60 .] 0.79

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.8e-07
                             RHH_8 16 gqiDlLveeGfYsnRtDlirtairaqLakhd 46
                                       +iD Lv+ G++ +R+D ir ai   L++++
  gi|385805711|ref|YP_005842109.1| 19 QEIDDLVNRGHFESRSDAIRYAIGLLLSSKQ 49
                                      46*********************98887654 PP

>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   3.4e-07     0.003       5      33 ..      12      41 ..       8      45 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.4e-07
                                      EEEHHHHHHHHHHHHHHT.SSHHHHHHHHH CS
                             RHH_1  5 rldeellerLdelarrrg.rSrSelIReAl 33
                                      +++ e++ ++d l+ r++  SrS++IR A+
  gi|385805711|ref|YP_005842109.1| 12 KIPIEMAQEIDDLVNRGHfESRSDAIRYAI 41
                                      67789**********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); 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:                         2  (0.000111551); expected 0.2 (1e-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: 405.30
//
Query:       gi|385805712|ref|YP_005842110.1|  [L=191]
Description: hypothetical protein FFONT_0669 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-38  132.1   0.0    2.7e-38  131.5   0.0    1.3  1  TYW3      Methyltransferase TYW3
  ------ inclusion threshold ------
      0.055   13.3   0.0        0.3   11.0   0.0    2.1  3  DUF2691   Protein of unknown function (DUF2691)


Domain annotation for each model (and alignments):
>> TYW3  Methyltransferase TYW3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.5   0.0     3e-42   2.7e-38       2     212 ..       8     190 ..       7     191 .] 0.95

  Alignments for each domain:
  == domain 1  score: 131.5 bits;  conditional E-value: 3e-42
                                       HHHHHHHHH....HHHHHCCHC-GGGHHHHHHHHC-SSEEEEEEES-EEEEE............EESSTT-STT-EE CS
                              TYW3   2 rKakiLeeLsvpdtdkspkGsvDekirelideinsledlvTtSSCsGRvsvflegrksaeaeeeaaksggkkgggkw 78 
                                       rK+++Le++    +++ + G++D++i e +d+ins+e+ +TtSSCsGR+s +            +++  +k+++ + 
  gi|385805712|ref|YP_005842110.1|   8 RKSAFLERI----KRDREIGYLDPGIEETLDLINSREKSYTTSSCSGRISAV------------DSEFPWKRDDEHP 68 
                                       899999999....8899***********************************............789999999999* PP

                                       EEEESS---HHHHHHHHCS--..............SSEEEEEEE--EEEEEESSHHHHHHHHHHHHHCT-TT-EEEE CS
                              TYW3  79 lfvsHdpvkeeellaelfgleeeegsaksseseeeerlilfkfePmILHvlcrslesAqkllsaAleaGfreSGivs 155
                                       +f++H p++eeel + l+ +               ++ i++ +  +ILH+ cr++e+A+++l++A++aGf++SGi+s
  gi|385805712|ref|YP_005842110.1|  69 IFKKHAPITEEELEDFLKVEP--------------KDIIWLIVSGPILHICCRDIEEAREMLRVARQAGFKHSGIMS 131
                                       ********9988877777765..............689*************************************** PP

                                       ECTTEEEEEEE---EEEEEEE..STS---HHHHHHHHHHHHHHHHHHHHHHHHHHHHC- CS
                              TYW3 156 lkkkkvivairsglklevpig..kellvseeylkllvklanerfeenkkrierfeealk 212
                                       ++++ ++v++ sg++l +p+   ++l+++   ++ ++ l+ne + e ++r++r++eal+
  gi|385805712|ref|YP_005842110.1| 132 ISEDCFMVELISGTQLFLPLKsrTKLFIEAGSMNDILFLVNESLSEGRNRLKRLNEALR 190
                                       *********************9644********************************97 PP

>> DUF2691  Protein of unknown function (DUF2691)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.51   4.6e+03      94     112 ..      41      59 ..      36      60 .. 0.83
   2 ?   11.0   0.0   3.3e-05       0.3      84     137 ..      72     126 ..      65     136 .. 0.85
   3 ?   -1.2   0.0      0.18   1.6e+03      38      66 ..     157     185 ..     145     188 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.51
                           DUF2691  94 eeflkskcelvllivDssy 112
                                       +++  s+c   + +vDs++
  gi|385805712|ref|YP_005842110.1|  41 KSYTTSSCSGRISAVDSEF 59 
                                       5799999999999999876 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 3.3e-05
                           DUF2691  84 kklakdiktyeeflkskc.elvllivDssyvtiyckdqeiieklyknakeqgfed 137
                                       k+++   + +e+flk +  +++ liv    + i c+d e   ++ + a++ gf++
  gi|385805712|ref|YP_005842110.1|  72 KHAPITEEELEDFLKVEPkDIIWLIVSGPILHICCRDIEEAREMLRVARQAGFKH 126
                                       4566677899*****99725888******************************85 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.18
                           DUF2691  38 yliedgeLdealFpeeeevlegeelkktl 66 
                                        +ie g +++ lF  +e++ eg +  k+l
  gi|385805712|ref|YP_005842110.1| 157 LFIEAGSMNDILFLVNESLSEGRNRLKRL 185
                                       68999999999999999999887655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); 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 0.28s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 1141.66
//
Query:       gi|385805713|ref|YP_005842111.1|  [L=201]
Description: protoheme IX farnesyltransferase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-24   85.9   0.6    3.6e-24   85.4   0.6    1.1  1  UbiA            UbiA prenyltransferase family
  ------ inclusion threshold ------
      0.084   13.2   4.7       0.17   12.2   4.7    1.5  1  Transgly_assoc  Transglycosylase associated protein


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 !   85.4   0.6     4e-28   3.6e-24       2     116 ..      20     133 ..      19     137 .. 0.96

  Alignments for each domain:
  == domain 1  score: 85.4 bits;  conditional E-value: 4e-28
                              UbiA   2 lipalvglalaaggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivlli 78 
                                       +++ l+++++++ gspd+++ll l++ +++ ++++ +lN+y+Dr+iD+ mert++R+l+s++++   a+ +++++l 
  gi|385805713|ref|YP_005842111.1|  20 VLSGLISYTVSSDGSPDWRVLLMLTFSLYFTISGTTGLNMYLDRDIDSMMERTKKRALPSRKLNEGDAVYASALFLS 96 
                                       6778999********************************************************************** PP

                              UbiA  79 lgllllalllnpltallgllallly.vvYtglrlKrrtl 116
                                       +glll  + +n+ +++ gll+ ++   +Yt  +lKrrt+
  gi|385805713|ref|YP_005842111.1|  97 IGLLLF-ASINWGVFIAGLLGAIVDlAIYT-RMLKRRTP 133
                                       ******.*************999999****.7*****98 PP

>> Transgly_assoc  Transglycosylase associated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   4.7   1.9e-05      0.17       9      46 ..      88     126 ..      87     129 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.9e-05
                    Transgly_assoc   9 fvGgfllgllgi.gvgggelaslivaiiGAiILLfivrl 46 
                                       + + +l+ ++g+   ++++++ +i++++GAi+ L+i+  
  gi|385805713|ref|YP_005842111.1|  88 VYASALFLSIGLlLFASINWGVFIAGLLGAIVDLAIYTR 126
                                       557788888888878999******************975 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:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1234.73
//
Query:       gi|385805714|ref|YP_005842112.1|  [L=90]
Description: hypothetical protein FFONT_0672 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0094   14.4   7.4       0.01   14.3   7.4    1.0  1  DcuC            C4-dicarboxylate anaerobic carrier
  ------ inclusion threshold ------
      0.021   14.1   9.0     0.0097   15.2   7.1    1.4  1  UbiA            UbiA prenyltransferase family
       0.44    8.9   5.0       0.44    8.9   5.0    1.1  1  SID-1_RNA_chan  dsRNA-gated channel SID-1


Domain annotation for each model (and alignments):
>> DcuC  C4-dicarboxylate anaerobic carrier
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   7.4   1.7e-06      0.01     259     333 ..      17      88 ..       6      90 .] 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.7e-06
                              DcuC 259 lfvlplilvllglafvivngewylpeiavlflamgilvefiaklnglkekeiveafveGaaellgvalvvglarg 333
                                       ++vl +i+++++    +v + + + ++++lf  m+ ++ +  k+ +++e +i++  ++G   +lg+a+v +l+ +
  gi|385805714|ref|YP_005842112.1|  17 TVVLAMIIIVTS--MWMVGI-LKFWTLIILFAYMTYMLFLQFKYMRSGERAIAKRIFRGYTAFLGIAMVLMLLSA 88 
                                       568888999998..455665.9999*********99988888889***************************977 PP

>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   7.1   1.6e-06    0.0097     178     247 ..       1      75 [.       1      80 [. 0.71

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.6e-06
                              UbiA 178 tlpvvlGrkaaril...lalllavlllallllllalllllylllalllaalallraarlvrrrdakkaakff....l 247
                                       +lpvv+Gr+a+ +    +  +la+++++  +++++ l  ++l+++++ ++++l+ +++ +r+ +++ a++ f    +
  gi|385805714|ref|YP_005842112.1|   1 MLPVVAGRNATGNAsgtV--VLAMIIIVTSMWMVGILKFWTLIILFAYMTYMLFLQFKYMRSGERAIAKRIFrgytA 75 
                                       8************87532..233333334578888888888888888999999998888888777766666655554 PP

>> SID-1_RNA_chan  dsRNA-gated channel SID-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   5.0   7.4e-05      0.44     374     441 ..       9      73 ..       1      88 [. 0.75

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 7.4e-05
                    SID-1_RNA_chan 374 hpdinasaysafallavvillgvigvlegknkfw.ilfsiihllatlllslqiyymgrwkldvgilrri 441
                                           nas    +a++++v  + ++g+l+    fw +++ + +++ +l+l +++   g   +++ i+r  
  gi|385805714|ref|YP_005842112.1|   9 NATGNASGTVVLAMIIIVTSMWMVGILK----FWtLIILFAYMTYMLFLQFKYMRSGERAIAKRIFRGY 73 
                                       5555677777777777777777888887....8878888999**********88888877777777754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1062  (0.0592336); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 542.31
//
Query:       gi|385805715|ref|YP_005842113.1|  [L=157]
Description: carbon monoxide dehydrogenase [Fervidicoccus fontis Kam940]
Scores for complete 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   98.5   1.5    1.9e-28   98.3   0.1    1.7  2  Fer2_2    [2Fe-2S] binding domain
    1.3e-08   34.6   2.9    1.8e-08   34.2   0.4    2.1  2  Fer2      2Fe-2S iron-sulfur cluster binding domain
    8.3e-05   22.6   0.1    0.00014   21.8   0.1    1.4  1  Fer2_3    2Fe-2S iron-sulfur cluster binding domain
     0.0068   16.4   0.9      0.086   12.9   0.9    2.3  1  Fer2_4    2Fe-2S iron-sulfur cluster binding domain


Domain annotation for each model (and alignments):
>> Fer2_2  [2Fe-2S] binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1      0.63   2.8e+03      26      31 ..      45      50 ..      34      52 .. 0.84
   2 !   98.3   0.1   4.2e-32   1.9e-28       1      75 [.      75     147 ..      75     148 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.63
                            Fer2_2 26 qCGyCt 31
                                       CG Ct
  gi|385805715|ref|YP_005842113.1| 45 ECGLCT 50
                                      699998 PP

  == domain 2  score: 98.3 bits;  conditional E-value: 4.2e-32
                            Fer2_2   1 TveglgeeleelhpvqeafveegasqCGyCtpGfvmsaaalleenepkpteeeirealsgnlCRCtgYrpivdAv 75 
                                       T++g++++  el pvq+af+e+ga+qCG+Ctp fv++++ +l++n p+pt+ee++e lsg lCRCtgY++i+dAv
  gi|385805715|ref|YP_005842113.1|  75 TAAGISRD-GELAPVQKAFIEHGAFQCGFCTPAFVVATHYFLQKN-PNPTREEVKEFLSGILCRCTGYKQIIDAV 147
                                       78899877.689*********************************.99999***********************9 PP

>> Fer2  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.4     4e-12   1.8e-08       2      49 ..       8      55 ..       7      76 .. 0.84
   2 ?    0.5   0.1      0.13   5.9e+02      38      55 ..      96     118 ..      94     138 .. 0.55

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 4e-12
                                      ETTTEEEEEEEETTTHBHHHHHHH.TTTTTSTTSSSSSSSSTTEEEEEE CS
                              Fer2  2 tidgkevevevadgettlldaaee.nggidipysCggggCgtClvevle 49
                                      +++g+ ++vev+d+et ll+++++  g + ++++C  g Cg C+v  + 
  gi|385805715|ref|YP_005842113.1|  8 KLNGRMRTVEVEDNET-LLEVLRDrLGEMSVKAACWKGECGLCTVLFNG 55
                                      6799************.******98********************8773 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.13
                                       SS..SSTTE.EEEEESCE..CTT CS
                              Fer2  38 gg..CgtCl.vevlegev..qsd 55 
                                       g+  Cg C+ + v++ ++  q++
  gi|385805715|ref|YP_005842113.1|  96 GAfqCGFCTpAFVVATHYflQKN 118
                                       55559999833445555554444 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 !   21.8   0.1   3.1e-08   0.00014      29      75 ..      22      64 ..      10      93 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 3.1e-08
                            Fer2_3 29 dtvldaLlkikeevdptlafrasCregiCGscavainGkptlaCtat 75
                                      +t+l++     ++   +++ +a C +g CG c+v  nG+p   C   
  gi|385805715|ref|YP_005842113.1| 22 ETLLEV----LRDRLGEMSVKAACWKGECGLCTVLFNGRPVKSCMVL 64
                                      444444....4556688999************************865 PP

>> Fer2_4  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.9   1.9e-05     0.086       2      69 ..       3      63 ..       2      78 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.9e-05
                            Fer2_4  2 rpvtltfDGk..evtvpeGdtvasAllan.gvdvp.rsckygrprgelcaggeCrnClVevegepnvracst 69
                                      r++tl+++G+  +v+v+ ++t++++l +  g   + +           c  geC  C V  +g+p v++c++
  gi|385805715|ref|YP_005842113.1|  3 RTITLKLNGRmrTVEVEDNETLLEVLRDRlGEMSVkA----------ACWKGECGLCTVLFNGRP-VKSCMV 63
                                      6899999996337888999999999986413322223..........5666**************.****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); 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: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1039.72
//
Query:       gi|385805716|ref|YP_005842114.1|  [L=294]
Description: aerobic-type carbon monoxide dehydrogenase, middle subunit CoxM/CutM - like protein [Fervidicoccus fontis Kam940]
Scores for complete 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-35  121.1   0.0    6.5e-35  120.4   0.0    1.3  1  FAD_binding_5  FAD binding domain in molybdopterin dehydrogen
    4.3e-12   46.1   0.1      9e-12   45.1   0.1    1.6  2  CO_deh_flav_C  CO dehydrogenase flavoprotein C-terminal domai
  ------ inclusion threshold ------
      0.031   14.6   0.3       0.06   13.7   0.3    1.4  1  CLU_N          Mitochondrial function, CLU-N-term


Domain annotation for each model (and alignments):
>> FAD_binding_5  FAD binding domain in molybdopterin dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.4   0.0   1.1e-38   6.5e-35       2     166 ..      10     180 ..       9     182 .. 0.96

  Alignments for each domain:
  == domain 1  score: 120.4 bits;  conditional E-value: 1.1e-38
                                       EEEEEE-SSHHHHHHHHHH.CTTSEEESS-TTHHHHHHHTT---SEEEEGTTSGGGS-EEEE.SSEEEEETTSBHHH CS
                     FAD_binding_5   2 kfeylrpasleealallaa.epdaklvaGgtdlgvlmkekvarpehliditgipelkeieet.eggleiGAavtlse 76 
                                       +f+y+rp+sleeal+ll++ ++ ak++ Gg +l+  mke++++ + ++di+gi elk+ie   ++gl iGA+vt +e
  gi|385805716|ref|YP_005842114.1|  10 EFKYVRPKSLEEALKLLKEnGDAAKVMNGGVGLIGFMKERLVEAQYIVDIKGIGELKKIEYVpGKGLLIGATVTGNE 86 
                                       799**************9978999************************************999***********999 PP

                                       HH....HHHHHHHHHHHSHHHHHTSS-HHHHHH-BHHHHHHHT-TT-SSHHHHHHTTEEEEEEESSEEEEEECHHHE CS
                     FAD_binding_5  77 la....aealvrerypalsealekiAspqiRnvaTiGGNlataspisDlapaLlaldAevelrsaegerevpleefl 149
                                       l     +++ vre++ al ea++++A+  +Rn++Ti GN+  + p  D+  + + +dAev+  s eger++p++ ++
  gi|385805716|ref|YP_005842114.1|  87 LLeffeKNPEVREKFRALYEAASHMADAILRNRGTIVGNILEGLPYVDMSGPAVLFDAEVHAVSLEGERWLPVDGLV 163
                                       963333699******************************************************************** PP

                                       EETTEESS-TT-EEEEE CS
                     FAD_binding_5 150 kgpgktalepgelitav 166
                                        gp  t+l pge++t++
  gi|385805716|ref|YP_005842114.1| 164 LGPAMTQLFPGEIVTEI 180
                                       ***************99 PP

>> CO_deh_flav_C  CO dehydrogenase flavoprotein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       1.8   1.1e+04      62      74 ..      17      29 ..      14      38 .. 0.70
   2 !   45.1   0.1   1.5e-15     9e-12       2     102 ..     192     291 ..     191     292 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.8
                                      HHHHHHHHHHHTT CS
                     CO_deh_flav_C 62 elleeaakaleee 74
                                      + leea+k+l+e+
  gi|385805716|ref|YP_005842114.1| 17 KSLEEALKLLKEN 29
                                      5678888888775 PP

  == domain 2  score: 45.1 bits;  conditional E-value: 1.5e-15
                                       EE.EEESSSSSS-ESEEEEEEEEEETTCEECEEEEEEESSSSS-EE-HHHHHHHTTSBSSHHHHHHHHHHHHTTCHH CS
                     CO_deh_flav_C   2 ay.klsrrrendiaivnaAfrveleedgkiedariafggvaptpvraekaeaaLiGkplseelleeaakaleeelsp 77 
                                       +y kl+ r e  + ivn  ++++  ++   +d+r++++++ + p ra++ e+ L+  +  +++le+ a+ l++ l++
  gi|385805716|ref|YP_005842114.1| 192 TYiKLQSRTE--YGIVNLSALLSNAGSPGKRDVRLVVTAATQLPYRAREFEENLKKAERIDDVLEQEAEKLANSLDV 266
                                       7889999999..99*********9988899*********************************************** PP

                                       HTCTTC-HHHHHHHHHHHHHHHHHH CS
                     CO_deh_flav_C  78 asdprasaeYRrslavsllfrflle 102
                                       ++dp asae+R++l+++l+ r++++
  gi|385805716|ref|YP_005842114.1| 267 IEDPYASAEFRKHLIKVLTIRAFKT 291
                                       **********************986 PP

>> CLU_N  Mitochondrial function, CLU-N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.3     1e-05      0.06      33      75 ..     240     283 ..     230     286 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1e-05
                             CLU_N  33 gerlnefvtlseiieeedv.delkLelkekpYterealeHvlrf 75 
                                       +e+l+  + + +++e+e +    +L++ e+pY  +e ++H++++
  gi|385805716|ref|YP_005842114.1| 240 EENLKKAERIDDVLEQEAEkLANSLDVIEDPYASAEFRKHLIKV 283
                                       688999999999999998844558*****************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); 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: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 1908.93
//
Query:       gi|385805717|ref|YP_005842115.1|  [L=132]
Description: aldehyde oxidase and xanthine dehydrogenase, molybdopterin binding protein [Fervidicoccus fontis Kam940]
Scores for complete 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   45.6   0.0    5.6e-12   44.9   0.0    1.3  1  Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehyd


Domain annotation for each model (and alignments):
>> Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.9   0.0   3.1e-16   5.6e-12     499     550 .]       1      52 [.       1      52 [. 0.99

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 3.1e-16
                                       -S-HHHHHHHHHHHHHHHHHHHHT---EEETTTEESS-STTTS----GGGS- CS
                     Ald_Xan_dh_C2 499 siNpaivegQieGGfvqGiGlalmEelvydedGqlltasladYkiPtaadiP 550
                                       +iNp ++ gQ  GG+v+G+  al+Ee+++d++G + + +++ Y i +a+d+P
  gi|385805717|ref|YP_005842115.1|   1 MINPLTATGQAIGGLVMGMSRALFEEIIFDDTGGVANPNFSFYYIARAKDVP 52 
                                       69*************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); 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: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 834.01
//
Query:       gi|385805718|ref|YP_005842116.1|  [L=62]
Description: hypothetical protein FFONT_0676 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); 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: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 406.74
//
Query:       gi|385805719|ref|YP_005842117.1|  [L=45]
Description: hypothetical protein FFONT_0677 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       175  (0.00976072); expected 358.6 (0.02)
Passed bias filter:                      122  (0.00680462); 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: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 310.81
//
Query:       gi|385805720|ref|YP_005842118.1|  [L=62]
Description: Glu/Leu/Phe/Val dehydrogenase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-14   52.3   0.0      5e-14   52.3   0.0    1.1  1  ELFV_dehydrog_N  Glu/Leu/Phe/Val dehydrogenase, dimerisation 


Domain annotation for each model (and alignments):
>> 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 !   52.3   0.0   2.8e-18     5e-14      13      50 ..       1      39 [.       1      57 [. 0.87

  Alignments for each domain:
  == domain 1  score: 52.3 bits;  conditional E-value: 2.8e-18
                                      -TTSBEEEEEEEEEEEE-TTSSEEEEEEEETT--HH.HH CS
                   ELFV_dehydrog_N 13 rdnGelevikgyraqhssalgPakGGiRfhpsvnld.ev 50
                                      +dnG+lev++gyr+q+++algP+kGGiRfhp+v+l+ ++
  gi|385805720|ref|YP_005842118.1|  1 MDNGKLEVFEGYRVQYNNALGPYKGGIRFHPEVTLEtDI 39
                                      79********************************98544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 404.93
//
Query:       gi|385805721|ref|YP_005842119.1|  [L=398]
Description: class I and II aminotransferase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-41  142.4   0.0    2.3e-41  142.2   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
  ------ inclusion threshold ------
       0.11   11.1   0.0       0.16   10.5   0.0    1.1  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
       0.13   11.5   0.0       0.18   11.1   0.0    1.5  1  Beta_elim_lyase  Beta-eliminating lyase


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.2   0.0   3.9e-45   2.3e-41      19     361 ..      42     381 ..      29     383 .. 0.87

  Alignments for each domain:
  == domain 1  score: 142.2 bits;  conditional E-value: 3.9e-45
                                       HHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-E CS
                     Aminotran_1_2  19 tlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgde 95 
                                        ++ v+ a ++   a +++  y++ +   e+ e++  ++ r++k ++kre  +v+++G   +i+++i+ +  npgd+
  gi|385805721|ref|YP_005842119.1|  42 SPKPVIDAIIK--RAEHGIFGYTDLT--EEYYETVVNWFERRYKWSIKRE-WIVYTPGVIPAISTAIATF-TNPGDK 112
                                       44555666665..5555666666655..**********************.*******************.7***** PP

                                       EEEEESS-THHHHHHHHTTSEEEEEEB.EETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHH CS
                     Aminotran_1_2  96 ilvpdptyasyknilrlsggevvrypl.yseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleele 171
                                       i+v  p+y ++ + ++ +g  +   pl  + + +++++ +lee+ k+      + ++i++++phNP G v+ +eele
  gi|385805721|ref|YP_005842119.1| 113 IIVQPPVYYPFFRSVESNGRRILANPLvLHDKRYEMNFRDLEEKAKDP-----RARMIILCNPHNPVGRVWRKEELE 184
                                       *********************77666515669***********99984.....789********************* PP

                                       HHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTT..EEEEEESSSTTSSGGG-EEEEEE.EHHHHHHHHH CS
                     Aminotran_1_2 172 klldlakkynlllfvDeaYagfvfgsldavatranveeepn..llivgslsKafGlaGeRvGyilg.naavvsqlrk 245
                                        l ++a ++nl++++De++++  +   ++ +  a ++ee +   ++++s sK f+laG+    i++ n ++++  r+
  gi|385805721|ref|YP_005842119.1| 185 RLGEIAIENNLIVVSDEIHSDIRYPGISFKN-FASISEELAdiSITCTSPSKTFNLAGIKASNIIVpNRKMREMFRS 260
                                       ************************9888877.777777777777**********************99********9 PP

                                       HHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS..TEEEECCSCSSEEEEEETHH..C CS
                     Aminotran_1_2 246 lsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLael..glkvlasqsgmflltdlsae..t 316
                                          ++ +  +++ ++ +++a+  + +   +l++m   l+ + ++l+   +e   +++v+++++++++++d+++   +
  gi|385805721|ref|YP_005842119.1| 261 SLEAMGIskPNVFAEEAVKAAYREGEG--WLNDMLNYLKGNLDFLKRFVEENmpEVEVIEPEGTYLVWMDFRKVesD 335
                                       888887768666666555555555544..*****************999988**********************876 PP

                                       HHHHHHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHH CS
                     Aminotran_1_2 317 akelskkLleevgvyvtpgtsftv..pgrlRitvAglteeeleelve 361
                                        k+l + +++  +v++  g +f+   +g+ Ri++ ++++++le+++ 
  gi|385805721|ref|YP_005842119.1| 336 PKKLERLMRDIAKVALDEGYIFGSggEGFERINI-ACPRSMLERALV 381
                                       67777779999***********************.999999999986 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   2.6e-05      0.16      78     173 ..      97     200 ..      85     205 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 2.6e-05
                                       HHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHH.....TTCEEEEESTTSHHHHHHHCCTTEEEEEEESS-TT CS
                   Cys_Met_Meta_PP  78 aAiaaailallkaGdeivvsddlYggtqrllkkvlkk.....lgievkfvdtsdleelekaikentklvylEtptnp 149
                                        Ai++ai ++ + Gd+i+v+  +Y + +r +++  ++     l ++ k ++++  +  eka +++ +++ l  p np
  gi|385805721|ref|YP_005842119.1|  97 PAISTAIATFTNPGDKIIVQPPVYYPFFRSVESNGRRilanpLVLHDKRYEMNFRDLEEKAKDPRARMIILCNPHNP 173
                                       5999************************999987766211113344444555445555667777************* PP

                                       TT---...-HHHHHHHHHHTT-EEEEE CS
                   Cys_Met_Meta_PP 150 llkvv...DiekiaklakkagvlvvvD 173
                                       + +v     +e++ ++a +++++vv D
  gi|385805721|ref|YP_005842119.1| 174 VGRVWrkeELERLGEIAIENNLIVVSD 200
                                       988853337888888888888888877 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0     3e-05      0.18     108     167 ..     147     200 ..      98     352 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3e-05
                                       BE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEE CS
                   Beta_elim_lyase 108 kmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlD 167
                                       +m++ +le++ k+     ++ ++i+l + +n   G+v+  eel+++ +ia ++++ ++ D
  gi|385805721|ref|YP_005842119.1| 147 EMNFRDLEEKAKD-----PRARMIILCNPHNP-VGRVWRKEELERLGEIAIENNLIVVSD 200
                                       6777777777766.....899**********6.9*********************99988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 2584.25
//
Query:       gi|385805722|ref|YP_005842120.1|  [L=48]
Description: hypothetical protein FFONT_0680 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); 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: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 320.49
//
Query:       gi|385805723|ref|YP_005842121.1|  [L=99]
Description: hypothetical protein FFONT_0681 [Fervidicoccus fontis Kam940]
Scores for complete 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   27.9   1.6    3.7e-05   24.7   1.6    1.9  1  DUF5320   Family of unknown function (DUF5320)


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 !   24.7   1.6   2.1e-09   3.7e-05      10      99 .]       8      94 ..       1      94 [. 0.67

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 2.1e-09
                           DUF5320 10 mGlGpmtGrglGyCagadapgyans...agfGrgrggrglgrgfgrrrraggarlaaaetaeaskeeekelLeeqaeaL 85
                                      +G+G   Grg     g+   +y  +    g+ +   grg++ ++ +  + ++++++  ++  a+k++e ++Le+  ++L
  gi|385805723|ref|YP_005842121.1|  8 WGRG--WGRGWSPYPGNGPFSYLPPwerPGWKY---GRGWCWWYYGYPYSSSYPYP-VAPFWADKSAELRYLEDMRKYL 80
                                      4444..345555555555555554453334444...66666666665555555555.7888899*************** PP

                           DUF5320 86 eeeleaikkrlkel 99
                                      e+  ++i++r++el
  gi|385805723|ref|YP_005842121.1| 81 EDVKKDIEARIEEL 94
                                      ************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1159  (0.0646439); expected 358.6 (0.02)
Passed bias filter:                      823  (0.0459033); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 705.71
//
Query:       gi|385805724|ref|YP_005842122.1|  [L=646]
Description: hypothetical protein FFONT_0682 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (646 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.50
# Mc/sec: 3906.28
//
Query:       gi|385805725|ref|YP_005842123.1|  [L=309]
Description: family 2 glycosyltransferase [Fervidicoccus fontis Kam940]
Scores for 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   55.7   0.0    7.4e-15   55.2   0.0    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
    1.1e-11   45.1   0.0    2.5e-11   43.9   0.0    1.5  2  Glyco_tranf_2_3  Glycosyltransferase like family 2
  ------ inclusion threshold ------
      0.015   15.0   0.1      0.026   14.2   0.1    1.3  1  Glyco_tranf_2_5  Glycosyltransferase like family
       0.11   12.9   0.0       0.25   11.8   0.0    1.6  1  DUF5313          Family of unknown function (DUF5313)


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 !   55.2   0.0   1.7e-18   7.4e-15       1     111 [.       4     112 ..       4     159 .. 0.83

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 1.7e-18
                                       EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglra 77 
                                       +vvi+ty ++  l+ +++sl++q   p  ++++v   S De+++++ee a+ + +  ++ ++e+   a a+  g++a
  gi|385805725|ref|YP_005842123.1|   4 CVVITTYKRAWALPYSIASLKDQ-SIPPSKVVFVLKPSGDESEKVIEECAE-GLNYEIVIQNEG-NVAMAVELGIKA 77 
                                       79*********************.*************************97.666666666655.79********** PP

                                       --SS.EEEEEESSEEE-TTHHHHHHHHHHH.TTCE CS
                   Glycos_transf_2  78 atgd.yilflDaDdepdpdwleklvealekdgadv 111
                                       ++   +ilflD+D   +++w+ek  e++e++  ++
  gi|385805725|ref|YP_005842123.1|  78 CKEHdLILFLDDDALASKNWIEKYTEFFERNKSAG 112
                                       *9777*************************75532 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.0   5.5e-15   2.5e-11       5     123 ..       4     117 ..       2     149 .. 0.87
   2 ?   -2.3   0.0      0.75   3.4e+03     159     201 ..     182     228 ..     178     243 .. 0.71

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 5.5e-15
                   Glyco_tranf_2_3   5 avlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralne 81 
                                        v+++t++++  l   ++sl  q+ p+++vv+v  +s +e  +v+ee a+ l   +++ ++n    g ++++  ++ 
  gi|385805725|ref|YP_005842123.1|   4 CVVITTYKRAWALPYSIASLKDQSIPPSKVVFVLKPSGDESEKVIEECAEGLNY-EIV-IQN---EG-NVAMA-VEL 73 
                                       69**************************************************87.455.333...35.46655.899 PP

                   Glyco_tranf_2_3  82 alravk.sdlvllvDdDtvvePdtlkrllqff.ltpkvgavgtp 123
                                       +++a+k +dl+l++DdD++ +++ +++++ ff + +++g + + 
  gi|385805725|ref|YP_005842123.1|  74 GIKACKeHDLILFLDDDALASKNWIEKYTEFFeRNKSAGGASGI 117
                                       ******9*************************888777776655 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.75
                   Glyco_tranf_2_3 159 tlnGsgslirrevlkelegldp....lflltdDyelglrlrragfrt 201
                                       +l G  +++ +  ++ + ++      +++l   + l++ +++ gf t
  gi|385805725|ref|YP_005842123.1| 182 ILIGVNMAFKTNAVEKCPLSALyknsRKCLHYEVMLSYCAKKKGFET 228
                                       57788999999998888733332235667777777777777777766 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 ?   14.2   0.1   5.7e-06     0.026      24      86 ..      51     112 ..      43     143 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.7e-06
                   Glyco_tranf_2_5  24 vpegyeveiiairnaksiaeaynkalsasdakykvYlhqDvliinkdfikdlleiFkkdkkiG 86 
                                         eg+++ei  i+n+ ++a a++ +++a + + ++   +D  + +k++i++  e F+ +k+ G
  gi|385805725|ref|YP_005842123.1|  51 CAEGLNYEI-VIQNEGNVAMAVELGIKACKEHDLILFLDDDALASKNWIEKYTEFFERNKSAG 112
                                       568899997.5*****************9987766555555689************9999886 PP

>> DUF5313  Family of unknown function (DUF5313)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   5.6e-05      0.25      20      72 ..     256     308 ..     251     309 .] 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.6e-05
                           DUF5313  20 smrdWvleDlagkgaaaRhviraavplvlilavllLlpgslyvrlemtllill 72 
                                       s++ W+++D +++ +++R +  ++  l+ ++a+ ++  g+l++++ +tl +++
  gi|385805725|ref|YP_005842123.1| 256 SHQFWIQYDFSKDYWRLRKLGARVNFLHYLIAMGIIARGNLFIKIPATLYAIV 308
                                       6788***************98777778888888899************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); 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):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1888.04
//
Query:       gi|385805726|ref|YP_005842124.1|  [L=162]
Description: hypothetical protein FFONT_0684 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       920  (0.0513135); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); 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: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.48
# Mc/sec: 1013.44
//
Query:       gi|385805727|ref|YP_005842125.1|  [L=378]
Description: glycosyl transferase family protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-22   79.3   0.5    5.4e-22   78.1   0.1    1.7  2  Glycos_transf_1  Glycosyl transferases group 1
    9.6e-11   42.2   0.0    2.1e-10   41.2   0.0    1.5  1  Glyco_trans_1_4  Glycosyl transferases group 1
     0.0014   18.7   0.0      0.018   15.0   0.0    2.7  2  Glyco_transf_4   Glycosyltransferase Family 4
  ------ inclusion threshold ------
       0.15   12.5   0.0       0.32   11.4   0.0    1.5  1  Glyco_trans_1_2  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.65   2.9e+03      77     101 ..     140     165 ..     137     182 .. 0.75
   2 !   78.1   0.1   1.2e-25   5.4e-22      10     163 ..     196     348 ..     188     356 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.65
                                       EEECCH.SSSHHHHHHCESEEEEEES CS
                   Glycos_transf_1  77 flgevs.redleellknadifvlpsi 101
                                       f+ +++ +e++   +kn+ i++ +s 
  gi|385805727|ref|YP_005842125.1| 140 FIPYQKiQEAIAGHFKNSGIILTNSK 165
                                       78888888999999999999988886 PP

  == domain 2  score: 78.1 bits;  conditional E-value: 1.2e-25
                                       TTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.......STTHHHHHHHHHHHCTTCGGGEEEC CS
                   Glycos_transf_1  10 gknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaG......ngeeekelkklaeelelsdnviflge 80 
                                       +  e++  +++ gr ++eK+++ +++++ ll     p++k+ i+G      + ++  +l k+ ee +l +nv +l+ 
  gi|385805727|ref|YP_005842125.1| 196 KNEEREDKVITCGRYSPEKNYEFVLRVASLL-----PEIKFEIIGsakekvSYQYYSKLVKMKEEMNL-KNVSLLKD 266
                                       44588999*********************87.....89**********99988899999999999999.9******* PP

                                       CHSSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTH.CHHCHTTTSEEEE-TT-HHHHHHHHHHHH CS
                   Glycos_transf_1  81 vsredleellknadifvlpsisEgfGivllEAmaaglpviasnaggp.aevvkdgetGllvkpnnaealaeairkll 156
                                       ++r++  e +++a+++++ ++ E+fGi+++E maagl+ +++++ggp  ++v  g+ G+ +++   e++++ai+k++
  gi|385805727|ref|YP_005842125.1| 267 LPRKEQVERYSRAKVYFHAMRGEHFGIAPVEGMAAGLIPVVHKIGGPwTDIVDYGKYGFGYESL--EDAKRAIEKAI 341
                                       *******************************************777725555555566666555..*********** PP

                                       HSHHHHH CS
                   Glycos_transf_1 157 edeelre 163
                                       ++ e+ +
  gi|385805727|ref|YP_005842125.1| 342 NNYEKMK 348
                                       **97655 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 !   41.2   0.0   4.6e-14   2.1e-10       3     133 ..     203     342 ..     201     343 .. 0.79

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 4.6e-14
                                       EEEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---........HHHHHHHT..T-T.TEEEE---..THHHHH CS
                   Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkkdvrlvivGdgprp......eeleelaa..gleerveftGfv..edlael 69 
                                       +++++Gr++ ++k+ +++l+ + ll   ++++ i+G+ +++      ++l ++ +  +l ++v+++  +  ++  e 
  gi|385805727|ref|YP_005842125.1| 203 KVITCGRYS-PEKNYEFVLRVASLLP--EIKFEIIGSAKEKvsyqyySKLVKMKEemNL-KNVSLLKDLprKEQVER 275
                                       78999***5.56*************9..68******77533566555444433334677.69*******66567777 PP

                                       HHH-SEEEE--..---SHHHHHHHHTT-EEEE-TGGG.TTT--..TTSSEE--TT-HHHHHHHHHHHHH CS
                   Glyco_trans_1_4  70 laaadvfvaPs..egfglkllEamaaglpvVatdvgg.iaevv..gengllvppgdpealaeailrLle 133
                                       +++a+v+   +  e fg++ +E maagl  V+ ++gg + ++v  g+ g+  +  + e+  +ai++ ++
  gi|385805727|ref|YP_005842125.1| 276 YSRAKVYFHAMrgEHFGIAPVEGMAAGLIPVVHKIGGpWTDIVdyGKYGFGYE--SLEDAKRAIEKAIN 342
                                       ***********8889********************984599999999998876..66666666666555 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0     4e-06     0.018       2     169 ..      17     189 ..      16     190 .. 0.59
   2 ?   -1.4   0.0      0.46   2.1e+03      44      76 ..     202     234 ..     193     240 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4e-06
                    Glyco_transf_4   2 GGverhvleLaraLarrGheVtvvtpgddgpleeev..elvvrvprvplpllkrllrslaflrrlrrllkre...kp 73 
                                       GG +++++++++   +rG  Vt++t ++   ++ ++   ++   p + l  l+ + +++  ++r+ + l+     + 
  gi|385805727|ref|YP_005842125.1|  17 GGGNVVLERMIEISKKRGDFVTLITNEPTNWEGLNRyyANGFPKPDRDLHALPVNVNIFGIYLRILQPLHPSmqkDC 93 
                                       88888888888888889999999987776666666544344444444444444444444444444444444455566 PP

                    Glyco_transf_4  74 Dvv.HahspaalgaallalrrrlgiplVltvHglye..............krllkarlkplsrllralerrllrrad 135
                                       D+   ah+ +  + +            V+++H +                + ++ka+  p++++ +a+  + ++++ 
  gi|385805727|ref|YP_005842125.1|  94 DLYiNAHGDFMPFPVD-----------VIYLHYPTFsmtseqfmdvkynkSLFWKAYFIPYQKIQEAIAGH-FKNSG 158
                                       6665555433333221...........22223222233333333334433334555555555555554444.6**** PP

                    Glyco_transf_4 136 rviavSeatadelrerygvppekitVipnGvDle 169
                                        ++++S++ +d +++++g   +   Vi+++vD++
  gi|385805727|ref|YP_005842125.1| 159 IILTNSKFSQDAIKRHLG---KESFVIHPPVDVS 189
                                       ******************...779********86 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.46
                    Glyco_transf_4  44 prvplpllkrllrslaflrrlrrllkrekpDvv 76 
                                        +v +++++ + +++ f++r++ ll + k+ ++
  gi|385805727|ref|YP_005842125.1| 202 DKVITCGRYSPEKNYEFVLRVASLLPEIKFEII 234
                                       566778889999999999999999999999998 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   7.2e-05      0.32      11      66 ..     291     347 ..     278     359 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.2e-05
                   Glyco_trans_1_2  11 pnlrlfEaaacGafaltdda.egleelftpgkevilfedleelaekiryllanpeer 66 
                                       +    +E +a+G + ++ ++     ++++ gk ++ +e+le++ ++i+++++n e+ 
  gi|385805727|ref|YP_005842125.1| 291 FGIAPVEGMAAGLIPVVHKIgGPWTDIVDYGKYGFGYESLEDAKRAIEKAINNYEKM 347
                                       5556689******999998966668999***********************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       741  (0.0413297); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); 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: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 2452.38
//
Query:       gi|385805728|ref|YP_005842126.1|  [L=120]
Description: iron-molybdenum cofactor-binding protein [Fervidicoccus fontis Kam940]
Scores for complete 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   1.0    4.9e-14   52.4   1.0    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 !   52.4   1.0   2.7e-18   4.9e-14       2      91 ..      21     112 ..      20     115 .. 0.94

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 2.7e-18
                                       TSCB-STCCC-SEEEEEEESSSCEEEEEEE..E.GCCCTSSCSSTHHHHHHHHTT-SEEEESSSCHHHHHHHCTTTS CS
                     Nitro_FeMo-Co   2 gsrvdqhFGrapyFaiyeveegevkivenr..veeaadaegggggklaqllaeegvdvvivgkiGpralakleaagi 76 
                                       ++ v + F+rap ++++e+e++  +i++++   ++ a+ae+g+  k+ q++ +eg+++v++ + Gp+a+a l++ ++
  gi|385805728|ref|YP_005842126.1|  21 EDIVASKFARAPKIVFVELEDE-GRILDVKaiDNPGANAESGAAVKIIQTVIDEGAEAVVAPAFGPNAQAILDEVKV 96 
                                       678999**************75.689999999999****************************************** PP

                                       EEEES.-SSBHHHHHH CS
                     Nitro_FeMo-Co  77 evykg.aggtveealk 91 
                                       + +++ ag++v+ea++
  gi|385805728|ref|YP_005842126.1|  97 KGITVpAGTKVREAVE 112
                                       **************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 800.98
//
Query:       gi|385805729|ref|YP_005842127.1|  [L=323]
Description: Cobyrinic acid a,c-diamide synthase [Fervidicoccus fontis Kam940]
Scores for complete 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   84.4   0.0    8.9e-24   84.0   0.0    1.1  1  CbiA            CobQ/CobB/MinD/ParA nucleotide binding domain
    1.4e-15   57.4   0.3    2.4e-10   40.3   0.0    2.9  2  ParA            NUBPL iron-transfer P-loop NTPase
    4.1e-10   39.1  11.5    8.2e-05   22.2   2.2    2.4  2  Fer4            4Fe-4S binding domain
    3.1e-09   36.7   0.0     0.0015   18.0   0.0    2.1  2  CBP_BcsQ        Cellulose biosynthesis protein BcsQ
    1.5e-08   34.5   0.1     0.0014   18.2   0.1    2.2  2  Fer4_NifH       4Fe-4S iron sulfur cluster binding proteins, 
    2.6e-07   30.8   0.0    4.7e-06   26.6   0.0    2.2  2  AAA_31          AAA domain
    5.1e-07   29.7   1.9     0.0036   17.4   0.1    2.3  2  Fer4_10         4Fe-4S dicluster domain
    8.7e-07   29.4   9.5    1.9e-06   28.3   9.5    1.6  1  Fer4_7          4Fe-4S dicluster domain
    1.1e-06   29.5   2.1      0.015   16.2   0.2    2.5  2  Fer4_16         4Fe-4S double cluster binding domain
    1.3e-06   28.1  10.3     0.0031   17.5   1.5    2.4  2  Fer4_2          4Fe-4S binding domain
    2.1e-06   27.2   0.0    6.8e-06   25.5   0.0    1.7  2  ArsA_ATPase     Anion-transporting ATPase
    1.2e-05   25.4   9.3    0.00013   22.0  10.3    2.0  3  Fer4_9          4Fe-4S dicluster domain
    1.9e-05   24.7   9.1    2.9e-05   24.1   7.5    2.1  2  Fer4_21         4Fe-4S dicluster domain
    0.00014   21.8  13.0      0.025   14.6   2.8    2.4  2  Fer4_6          4Fe-4S binding domain
    0.00089   19.2   0.3        1.1    9.1   0.1    2.2  2  RsgA_GTPase     RsgA GTPase
     0.0017   17.7   0.0     0.0047   16.3   0.0    1.7  2  MipZ            ATPase MipZ
      0.005   16.4   0.3      0.073   12.6   0.1    2.2  2  GTP_EFTU        Elongation factor Tu GTP binding domain
     0.0061   16.4   0.0       0.83    9.4   0.0    2.1  2  ATP_bind_1      Conserved hypothetical ATP binding protein
     0.0066   16.3   0.0      0.013   15.3   0.0    1.5  1  CLP1_P          mRNA cleavage and polyadenylation factor CLP1
  ------ inclusion threshold ------
      0.023   13.7   0.0      0.043   12.8   0.0    1.4  1  MeaB            Methylmalonyl Co-A mutase-associated GTPase M
      0.079   12.8   1.1        5.9    6.7   0.1    2.4  2  AAA_26          AAA domain
      0.099   12.3   0.2        7.6    6.1   0.0    2.8  3  SRP54           SRP54-type protein, GTPase domain
       0.12   12.4   0.0        0.8    9.8   0.0    2.1  2  B12-binding     B12 binding domain
       0.15   12.9   5.3        1.3    9.9   0.4    2.5  2  Fer4_22         4Fe-4S dicluster domain
       0.16   11.9   0.0       0.36   10.7   0.0    1.5  1  MobB            Molybdopterin guanine dinucleotide synthesis 
       0.18   11.2   0.0       0.25   10.7   0.0    1.1  1  SAM_MT          Putative SAM-dependent methyltransferase
       0.18   11.7   0.0       0.82    9.6   0.0    2.0  2  NTPase_1        NTPase
       0.19   11.1   0.1       0.38   10.1   0.1    1.4  1  Glyco_hydro_20  Glycosyl hydrolase family 20, catalytic domai
       0.95   10.1  11.4        2.4    8.7   2.2    2.4  4  Fer4_17         4Fe-4S dicluster domain
        1.1   10.4  17.7          2    9.6   4.0    2.4  2  Fer4_3          4Fe-4S binding domain
        1.1    9.7  12.5        2.1    8.9   3.2    2.4  2  Fer4_8          4Fe-4S dicluster domain
        1.8    9.3  12.1       0.44   11.2   3.2    2.3  2  Fer4_4          4Fe-4S binding 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 !   84.0   0.0   1.6e-26   8.9e-24       1     127 [.       4     268 ..       4     269 .. 0.95

  Alignments for each domain:
  == domain 1  score: 84.0 bits;  conditional E-value: 1.6e-26
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep....................... 54 
                                       ia+as+kGGvGK+tl+ +L+ +l++rg+++++vDaD +a+nl++++ +e   ++                       
  gi|385805729|ref|YP_005842127.1|   4 IAVASGKGGVGKSTLSSTLILYLKERGYDIIAVDADADAPNLHLIFEVERWDKEepysdswvseidyfrcvncgich 80 
                                       89*****************************************95555554444589999***************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|385805729|ref|YP_005842127.1|  81 nvctygavslvegryyinpmicegcltcslacpekairrkrvnrgvirlsytkygfplwaselspgrpnsgrlvtei 157
                                       ***************************************************************************** PP

                                       ................................................CCHCCCHHHHHHCHCHHHH..EEEEEEEE CS
                                       ................................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ................................................dlkrllellealgkkkalllkiagvvlnr 83 
                                                                                       dlkr+  ++++++ +         +v+n+
  gi|385805729|ref|YP_005842127.1| 158 knrakamakentisvvdsaagigcqvisslsganvallvaeptpaslsDLKRIHTIAKQFSLP-------SALVINK 227
                                       *********************************************999999999999999976.......99***** PP

                                       ESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHTS- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  84 vdgeneetllkealeelkqrygvpvlgviprdeavaeapargep 127
                                       +d + e+ +++  +++++   ++ v+g++p+d++v++a a+ +p
  gi|385805729|ref|YP_005842127.1| 228 YDMNSEFVEEIIKYAREE---NIDVIGMVPYDDHVPKAMAEMRP 268
                                       ****99999999999988...*****************999876 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 !   40.3   0.0   4.4e-13   2.4e-10       6      57 ..       4      55 ..       2      68 .. 0.89
   2 !   13.6   0.1   5.8e-05     0.033     136     244 ..     190     288 ..     170     290 .. 0.77

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 4.4e-13
                              ParA  6 iavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeek 57
                                      iav+SgKGGVGKSt++++l l L+++g+++  +DaD   p++  +++ve+ +
  gi|385805729|ref|YP_005842127.1|  4 IAVASGKGGVGKSTLSSTLILYLKERGYDIIAVDADADAPNLHLIFEVERWD 55
                                      89********************************************999843 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 5.8e-05
                              ParA 136 lagaviVttpqevaladvkkaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipld 212
                                        + a++V+ p  ++l+d k+  +++k+ +++   v++   +        ++  f  ++  k+a+e +++++g +p d
  gi|385805729|ref|YP_005842127.1| 190 ANVALLVAEPTPASLSDLKRIHTIAKQFSLPSALVINKYDM--------NS-EFV-EEIIKYAREENIDVIGMVPYD 256
                                       34578899999999999999999999999987666654322........11.233.3456899999*********** PP

                              ParA 213 peireasdegkplvlkepeseaakaleeiaek 244
                                        ++ +a+ e +pl+++ +e++a+kal eia+ 
  gi|385805729|ref|YP_005842127.1| 257 DHVPKAMAEMRPLIKQYNEAPASKALVEIARI 288
                                       ***************************99975 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   2.1   1.8e-07    0.0001       2      23 ..      67      88 ..      66      89 .. 0.92
   2 !   22.2   2.2   1.5e-07   8.2e-05       1      24 []      95     118 ..      95     118 .. 0.95

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.8e-07
                                      EEETTTSSS-THHHHHSTTTEE CS
                              Fer4  2 videekCigCGaCvevCPvgAI 23
                                      +id+ +C++CG+C +vC +gA 
  gi|385805729|ref|YP_005842127.1| 67 EIDYFRCVNCGICHNVCTYGAV 88
                                      5999***************996 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 1.5e-07
                                       EEEETTTSSS-THHHHHSTTTEEE CS
                              Fer4   1 vvideekCigCGaCvevCPvgAIt 24 
                                       ++i++  C gC +C  +CP  AI+
  gi|385805729|ref|YP_005842127.1|  95 YYINPMICEGCLTCSLACPEKAIR 118
                                       69********************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 !   16.7   0.0   6.9e-06    0.0039       3      52 ..       3      53 ..       1      78 [. 0.84
   2 !   18.0   0.0   2.7e-06    0.0015     104     230 ..     156     286 ..     148     289 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.9e-06
                          CBP_BcsQ  3 vlalqGvRGGvGttsllaaLawalhelgesvlviDlspdn.lLrlhFnvdi 52
                                       +a+   +GGvG+++l+++L   l+e g+ ++++D+ +d   L+l F+v+ 
  gi|385805729|ref|YP_005842127.1|  3 EIAVASGKGGVGKSTLSSTLILYLKERGYDIIAVDADADApNLHLIFEVER 53
                                      57777779****************************998537999999874 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 2.7e-06
                          CBP_BcsQ 104 allaalkelkeqyrwillDlpagasaltrellaladlvllvvepdanchvrLhq.....qalpaaellLiNqfeaas 175
                                       +++++ k+++++ +  ++D  ag   ++ + l+ a++ llv+ep  ++   L++     +++   + l iN+++++s
  gi|385805729|ref|YP_005842127.1| 156 EIKNRAKAMAKENTISVVDSAAGIGCQVISSLSGANVALLVAEPTPASLSDLKRihtiaKQFSLPSALVINKYDMNS 232
                                       57788899999999999***********9******************998887621122445666789********* PP

                          CBP_BcsQ 176 qlqqDllqlWlqslrrllPlvihrDealaEalaakqPlgeyrpdslaaeevktLa 230
                                       +  ++++++ +++  +++ +v   D+ ++ a+a   Pl +  +++ a++++  +a
  gi|385805729|ref|YP_005842127.1| 233 EFVEEIIKYAREENIDVIGMV-PYDDHVPKAMAEMRPLIKQYNEAPASKALVEIA 286
                                       ************999999875.678889**********98888888888777666 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 !   14.1   0.0   4.1e-05     0.023       6      47 ..       8      49 ..       3      55 .. 0.85
   2 !   18.2   0.1   2.5e-06    0.0014     177     246 ..     221     291 ..     175     295 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.1e-05
                         Fer4_NifH  6 yGkGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrlll 47
                                       GkGG+Gkst s+ l   l+e+g  ++ v  D  a   +l++
  gi|385805729|ref|YP_005842127.1|  8 SGKGGVGKSTLSSTLILYLKERGYDIIAVDADADAPNLHLIF 49
                                      5**************************999998877776666 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 2.5e-06
                         Fer4_NifH 177 gGliinsrkvdde.reliekfaeelgtkvlevvPrdeivrkaelrkktvieyapeseqakeyrelarkile 246
                                       + l+in+ ++++e  e i k+a+e +++v+ +vP d++v ka ++ + +i+  +e++ +k   e+ar + e
  gi|385805729|ref|YP_005842127.1| 221 SALVINKYDMNSEfVEEIIKYAREENIDVIGMVPYDDHVPKAMAEMRPLIKQYNEAPASKALVEIARIVEE 291
                                       5689997777766458899****************************99999999999********98876 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   8.4e-09   4.7e-06       4      42 ..       4      42 ..       1      82 [. 0.88
   2 ?    2.1   0.0      0.29   1.6e+02     108     166 ..     158     216 ..     138     250 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 8.4e-09
                            AAA_31  4 IaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQa 42
                                      Ia+a  KGGvGK+T s  l   l ++g+ ++ vD+D+ a
  gi|385805729|ref|YP_005842127.1|  4 IAVASGKGGVGKSTLSSTLILYLKERGYDIIAVDADADA 42
                                      9***********************************865 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.29
                            AAA_31 108 kellekvkdeYDyiiiDcpPsLglltenaLvasdsviipvqaeayaleGleqllktiee 166
                                       k+  +++ +e  + ++D    +g+ ++++L  ++  + + ++++ +l+ l+++ +  ++
  gi|385805729|ref|YP_005842127.1| 158 KNRAKAMAKENTISVVDSAAGIGCQVISSLSGANVALLVAEPTPASLSDLKRIHTIAKQ 216
                                       5666667777777889999999999999**************99999999988766665 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.3   0.00041      0.23       3      19 ..      67      83 ..      59      92 .. 0.86
   2 !   17.4   0.1   6.5e-06    0.0036       3      24 ..      96     120 ..      94     173 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00041
                           Fer4_10  3 vidddtCirCgkCvkaC 19
                                      +id  +C++Cg C ++C
  gi|385805729|ref|YP_005842127.1| 67 EIDYFRCVNCGICHNVC 83
                                      57889999999999999 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 6.5e-06
                           Fer4_10   3 vidddtCirCgkCvkaCPadl...t 24 
                                       +i++  C +C +C  aCP ++   +
  gi|385805729|ref|YP_005842127.1|  96 YINPMICEGCLTCSLACPEKAirrK 120
                                       79999**************554431 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   9.5   3.4e-09   1.9e-06       1      52 []      72     116 ..      72     124 .. 0.95

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 3.4e-09
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       rC++Cg C ++C ++a++l e        +++i+p+ C gC  C  +CP +a
  gi|385805729|ref|YP_005842127.1|  72 RCVNCGICHNVCTYGAVSLVEG-------RYYINPMICEGCLTCSLACPEKA 116
                                       8******************874.......79******************876 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 !   12.7   0.1   0.00035      0.19       1      18 [.      72      89 ..      52      98 .. 0.78
   2 !   16.2   0.2   2.7e-05     0.015       2      22 ..     102     122 ..     101     182 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00035
                           Fer4_16  1 rCgtCgkCaevCPtnaik 18
                                      rC++Cg C +vC  +a++
  gi|385805729|ref|YP_005842127.1| 72 RCVNCGICHNVCTYGAVS 89
                                      477777777777777765 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 2.7e-05
                           Fer4_16   2 CgtCgkCaevCPtnaikekke 22 
                                       C +C  C  +CP++ai+ k+ 
  gi|385805729|ref|YP_005842127.1| 102 CEGCLTCSLACPEKAIRRKRV 122
                                       *****************9943 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   1.9   2.9e-05     0.016       5      21 ..      68      84 ..      64      85 .. 0.85
   2 !   17.5   1.5   5.5e-06    0.0031       2      22 .]      94     114 ..      93     114 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.9e-05
                            Fer4_2  5 vdtdrCigCgaCvsaCP 21
                                      +d  rC++Cg+C ++C 
  gi|385805729|ref|YP_005842127.1| 68 IDYFRCVNCGICHNVCT 84
                                      67779***********6 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 5.5e-06
                            Fer4_2   2 pvvvdtdrCigCgaCvsaCPa 22 
                                       ++++++ +C gC +C  aCP+
  gi|385805729|ref|YP_005842127.1|  94 RYYINPMICEGCLTCSLACPE 114
                                       689*****************5 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   1.2e-08   6.8e-06       3      52 ..       4      54 ..       2      74 .. 0.84
   2 ?   -1.2   0.0       1.6   9.2e+02     211     244 ..     195     227 ..     175     271 .. 0.61

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1.2e-08
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-ST.TTHHHHHHTS--B CS
                       ArsA_ATPase  3 vilvgGKGGVGKttvsaatavklsekgkkvllistDP.AhslsDsfdqklg 52
                                      + + +GKGGVGK+t+s+++ ++l e g++++ +  D  A++l  +f+ +  
  gi|385805729|ref|YP_005842127.1|  4 IAVASGKGGVGKSTLSSTLILYLKERGYDIIAVDADAdAPNLHLIFEVERW 54
                                      55779******************************9559****99998754 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.6
                                       EEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEEE CS
                       ArsA_ATPase 211 lVvipEklslkEteRaikeLkkygikvdavivNk 244
                                       lV  p   sl + +R ++  k++++ + + ++Nk
  gi|385805729|ref|YP_005842127.1| 195 LVAEPTPASLSDLKRIHTIAKQFSLPSAL-VINK 227
                                       44555555555555555555555555433.3344 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   2.4   0.00028      0.16      33      50 ..      67      87 ..      48      88 .. 0.68
   2 !   22.0  10.3   2.3e-07   0.00013       1      51 []      72     117 ..      72     117 .. 0.94
   3 !   14.5   1.7   5.2e-05     0.029       2      25 ..     102     125 ..     101     132 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00028
                            Fer4_9 33 e...eaCigCgaCveaCpkga 50
                                      e    +C+ Cg C ++C  ga
  gi|385805729|ref|YP_005842127.1| 67 EidyFRCVNCGICHNVCTYGA 87
                                      144467999999999998876 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 2.3e-07
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                       +C++Cg C+++C +g+v+  +++++++  +     C gC +C  aCp++ai
  gi|385805729|ref|YP_005842127.1|  72 RCVNCGICHNVCTYGAVSLVEGRYYINPMI-----CEGCLTCSLACPEKAI 117
                                       6***********************999754.....*************987 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 5.2e-05
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerk 25 
                                       C gC +C  aCp +++++++++r 
  gi|385805729|ref|YP_005842127.1| 102 CEGCLTCSLACPEKAIRRKRVNRG 125
                                       *****************9999876 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   7.5   5.2e-08   2.9e-05       2      57 ..      67     117 ..      66     119 .. 0.80
   2 ?   -1.2   0.0       4.1   2.3e+03      31      46 ..     167     183 ..     157     187 .. 0.62

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 5.2e-08
                           Fer4_21   2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedci 57 
                                        id  +C++Cg C+ +C      a+++ + ++  +    C GC  Cs  CP e++i
  gi|385805729|ref|YP_005842127.1|  67 EIDYFRCVNCGICHNVCTY---GAVSLVEGRY-YINPMICEGCLTCSLACP-EKAI 117
                                       588889************5...5555554455.567889************.6887 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 4.1
                           Fer4_21  31 ktvlkvv.edeCvGCnl 46 
                                       ++++ vv +   +GC++
  gi|385805729|ref|YP_005842127.1| 167 ENTISVVdSAAGIGCQV 183
                                       44444442667788876 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   2.8   4.5e-05     0.025       2      23 ..      66      87 ..      65      88 .. 0.89
   2 !   12.5   2.7   0.00022      0.12       4      24 .]      97     117 ..      96     117 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.5e-05
                            Fer4_6  2 veidpdkCigCgdCvrvCPega 23
                                      +eid+ +C+ Cg C +vC +ga
  gi|385805729|ref|YP_005842127.1| 66 SEIDYFRCVNCGICHNVCTYGA 87
                                      6888889***********9998 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00022
                            Fer4_6   4 idpdkCigCgdCvrvCPegai 24 
                                       i+p  C gC  C  +CPe+ai
  gi|385805729|ref|YP_005842127.1|  97 INPMICEGCLTCSLACPEKAI 117
                                       56668**************98 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.1     0.002       1.1     101     120 ..       4      23 ..       2      37 .. 0.84
   2 !    8.2   0.0    0.0037       2.1      28      82 ..     200     252 ..     159     274 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.002
                                       EEEEECSTTSSHHHHHHHHC CS
                       RsgA_GTPase 101 tsvlvGqSGvGKStLinall 120
                                       ++v  G+ GvGKStL  +l+
  gi|385805729|ref|YP_005842127.1|   4 IAVASGKGGVGKSTLSSTLI 23 
                                       67889**********99886 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0037
                                       TT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE- CS
                       RsgA_GTPase  28 pelslnlldrfLvlaeekgiepvivlnKiDlleeeeeleelkeelealgyevllv 82 
                                          sl+ l+r+ ++a++  ++  +v+nK D+ +e    ee+ +  ++ +++v+ +
  gi|385805729|ref|YP_005842127.1| 200 TPASLSDLKRIHTIAKQFSLPSALVINKYDMNSEFV--EEIIKYAREENIDVIGM 252
                                       35688999**********************988866..77887777777777644 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   8.4e-06    0.0047       3      46 ..       4      47 ..       2      58 .. 0.87
   2 ?   -1.4   0.0         2   1.1e+03     188     214 ..     272     298 ..     156     300 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 8.4e-06
                                      EEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHH CS
                              MipZ  3 ivlgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlar 46
                                      i ++  kGG Gkst +  ++  L ++G  + a+d d+    l+ 
  gi|385805729|ref|YP_005842127.1|  4 IAVASGKGGVGKSTLSSTLILYLKERGYDIIAVDADADAPNLHL 47
                                      789999******************************97666665 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2
                                       HHHHHHHHHHHHHHHHHHT-EEE---B CS
                              MipZ 188 arnkkkveealeeLskrvGfrvasGls 214
                                         n+    +al e+++ v  r++ G s
  gi|385805729|ref|YP_005842127.1| 272 QYNEAPASKALVEIARIVEERIIRGWS 298
                                       445666667777777777777777766 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 ?    1.7   0.0      0.28   1.6e+02      14      30 ..      13      29 ..       4      42 .. 0.83
   2 !   12.6   0.1   0.00013     0.073      86     149 ..     182     245 ..     152     291 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.28
                                      SSHHHHHHHHHHHTTSS CS
                          GTP_EFTU 14 hGKtTLtdrLlyktgai 30
                                       GK+TL+ +L+ ++++ 
  gi|385805729|ref|YP_005842127.1| 13 VGKSTLSSTLILYLKER 29
                                      6*********9998765 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00013
                                       HHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHH CS
                          GTP_EFTU  86 evirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrlkaelkeiveevkqk 149
                                       +vi +l+ +++a+lv + +    +  +++  +a++  +p  ++iNK D+  + ++ei++ ++++
  gi|385805729|ref|YP_005842127.1| 182 QVISSLSGANVALLVAEPTPASLSDLKRIHTIAKQFSLPSALVINKYDMNSEFVEEIIKYAREE 245
                                       79999*********************************************99999888877755 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0    0.0015      0.83       3      37 ..       9      43 ..       7      54 .. 0.85
   2 ?    5.0   0.0     0.033        18     151     213 ..     213     275 ..     180     287 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0015
                        ATP_bind_1  3 GpaGsGKttfvgalseilelrgrsvavvNLDPAae 37
                                      G  G+GK+t+ ++l+ +l++rg+++  v  D  a 
  gi|385805729|ref|YP_005842127.1|  9 GKGGVGKSTLSSTLILYLKERGYDIIAVDADADAP 43
                                      889******************99999998876555 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.033
                        ATP_bind_1 151 amlrlelPhvvvlnkfDllkeklekeleffedve.alslllekeeekykklaeaiaelleefal 213
                                       +  + +lP   v+nk D+ +e  e+ +++  + + ++  +   + + + k +++++ l++++++
  gi|385805729|ref|YP_005842127.1| 213 IAKQFSLPSALVINKYDMNSEFVEEIIKYAREENiDVIGMVPYD-DHVPKAMAEMRPLIKQYNE 275
                                       667899************77445555555543221333333333.4455666677777776665 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 !   15.3   0.0   2.3e-05     0.013       1      34 [.       9      42 ..       9      47 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.3e-05
                            CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGq 34
                                      G+  +GKSTl+ +L+ y+ ++g+ ++ vD+D   
  gi|385805729|ref|YP_005842127.1|  9 GKGGVGKSTLSSTLILYLKERGYDIIAVDADADA 42
                                      66789**************************865 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 ?   12.8   0.0   7.8e-05     0.043      35      67 ..       8      38 ..       3      44 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.8e-05
                                      EE-TTSSHHHHHHHHHHHHHCTT--EEEEEE-- CS
                              MeaB 35 tGvPGaGkstlvealglelrrrGkrvavlavDP 67
                                       G  G+Gkstl + l+l l++rG+   ++avD 
  gi|385805729|ref|YP_005842127.1|  8 SGKGGVGKSTLSSTLILYLKERGYD--IIAVDA 38
                                      5889*******************96..678875 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.052        29       3      30 ..       4      31 ..       3      34 .. 0.88
   2 ?    6.7   0.1     0.011       5.9      93     194 ..     162     259 ..     137     262 .. 0.66

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.052
                            AAA_26  3 ifvtgtdtgvGKTvvslgLvralkrkgv 30
                                      i v++   gvGK+++s  L+ +lk++g+
  gi|385805729|ref|YP_005842127.1|  4 IAVASGKGGVGKSTLSSTLILYLKERGY 31
                                      66888899***************99987 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.011
                            AAA_26  93 kelekdadivvVEGagglgvpiteellnadiaknlgapvilVargglgtinqllltiealrqknvrvlGvilNkvrn 169
                                       k+++k++ i vV+ a g+g ++++ l+ a +a       +lVa ++  ++ +l     +++q      ++++Nk   
  gi|385805729|ref|YP_005842127.1| 162 KAMAKENTISVVDSAAGIGCQVISSLSGANVA-------LLVAEPTPASLSDLKRIHTIAKQFS-LPSALVINKYDM 230
                                       55666666666666666666666666666665.......7888888888888776666666643.357899999633 PP

                            AAA_26 170 p....envetlekksgipvlGvvPylpdl 194
                                            e++ ++    +i+v+G vPy++++
  gi|385805729|ref|YP_005842127.1| 231 NsefvEEIIKYAREENIDVIGMVPYDDHV 259
                                       34233344444444569*******99865 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.014       7.6       6      38 ..       7      39 ..       2      41 .. 0.87
   2 ?    1.8   0.0      0.29   1.6e+02     100     126 ..     152     178 ..     146     193 .. 0.87
   3 ?    0.5   0.0      0.72   4.1e+02      50      87 ..     212     250 ..     204     290 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.014
                                      EEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                             SRP54  6 lvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                        G  G+GK t  + L  +lk++g++++ v aD
  gi|385805729|ref|YP_005842127.1|  7 ASGKGGVGKSTLSSTLILYLKERGYDIIAVDAD 39
                                      56889********************99988877 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.29
                                       HHHHHHHHHHHHHSSSEEEEEEETTBH CS
                             SRP54 100 elmeelkkikkvvkpdevllvldattg 126
                                       +l++e+k+ +k++++++++ v+d+++g
  gi|385805729|ref|YP_005842127.1| 152 RLVTEIKNRAKAMAKENTISVVDSAAG 178
                                       7899*******************9987 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.72
                                       HHHHHTTEEEEE.SSTTSCHHHHHHHHHHHHHHTTSSEE CS
                             SRP54  50 tlaeklgvpvik.kkeeadpaavakeavekakeekidvv 87 
                                       t+a++   p     ++ +   ++++e ++ a+ee+idv+
  gi|385805729|ref|YP_005842127.1| 212 TIAKQFSLPSALvINKYDMNSEFVEEIIKYAREENIDVI 250
                                       555665555444445556678899999999999999987 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.8     1e+03      23      40 ..      25      42 ..      20      55 .. 0.79
   2 ?    9.8   0.0    0.0014       0.8      36      79 ..     230     274 ..     211     279 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.8
                       B12-binding 23 alrdagfeVqllganven 40
                                      +l+++g++++ ++a++++
  gi|385805729|ref|YP_005842127.1| 25 YLKERGYDIIAVDADADA 42
                                      799999999999888876 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0014
                       B12-binding  36 anven.edivaairaekpdvvglSalltsqleav.kelvellkrir 79 
                                       +n e  e+i++ +r+e+ dv+g+   +  +++++ +e+  l+k+++
  gi|385805729|ref|YP_005842127.1| 230 MNSEFvEEIIKYAREENIDVIGMVP-YDDHVPKAmAEMRPLIKQYN 274
                                       4444469****************77.55555544277777788775 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.4    0.0023       1.3      73      93 ..      64      84 ..      55      87 .. 0.78
   2 ?    4.6   0.5       0.1        58      79      94 ..      99     114 ..      89     116 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0023
                           Fer4_22 73 fkekfgesgCvGCgRCieacp 93
                                      ++++++   Cv Cg C+++c+
  gi|385805729|ref|YP_005842127.1| 64 WVSEIDYFRCVNCGICHNVCT 84
                                      677778888888888888886 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.1
                           Fer4_22  79 esgCvGCgRCieacpv 94 
                                        + C GC  C+ acp+
  gi|385805729|ref|YP_005842127.1|  99 PMICEGCLTCSLACPE 114
                                       5678888888888887 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00063      0.36       5      36 ..       8      39 ..       3      47 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00063
                              MobB  5 vgksgsGKTtLleklipelkarglrvgtiKha 36
                                       gk g GK tL + li  lk+rg+ + ++  +
  gi|385805729|ref|YP_005842127.1|  8 SGKGGVGKSTLSSTLILYLKERGYDIIAVDAD 39
                                      48899********************9887655 PP

>> SAM_MT  Putative SAM-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00044      0.25      59     199 ..     156     293 ..     140     310 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00044
                            SAM_MT  59 eaiakavglkkgvlptvlDaTaGlGrDafvlasl.GckvtliErhpvvaaLLedglkRakqdaeige....llaerl 130
                                       e   +a  ++k+ + +v+D+ aG+G    v++sl G++v l+  +p  a+L    lkR ++ a+  +    l+ ++ 
  gi|385805729|ref|YP_005842127.1| 156 EIKNRAKAMAKENTISVVDSAAGIGC--QVISSLsGANVALLVAEPTPASLS--DLKRIHTIAKQFSlpsaLVINKY 228
                                       455677788888999**********6..58888779********99988874..37887765554330000233333 PP

                            SAM_MT 131 kLlaasslealakleeekpdvvYlDPmyPhkkksalvKKemrvfqqlvGadedadeLleaalalakkRv 199
                                       ++ ++   e+++ ++ee+ dv+    m P ++    +  emr + +   +   +++L+e+a+   ++R+
  gi|385805729|ref|YP_005842127.1| 229 DMNSEFVEEIIKYAREENIDVI---GMVPYDDHVPKAMAEMRPLIKQYNEAPASKALVEIARI-VEERI 293
                                       3333444444555555577777...56666666665666777776666777777788887763.45555 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0    0.0015      0.82       5      30 ..       8      33 ..       4      39 .. 0.91
   2 ?   -1.8   0.0       4.5   2.5e+03      13      34 ..     232     253 ..     229     258 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0015
                                      E--TTSSHHHHHHHHHHHH...GGGE CS
                          NTPase_1  5 TGppGvGKtTlvkkvlellkssgvkv 30
                                      +G+ GvGK+Tl + ++  lk++g+ +
  gi|385805729|ref|YP_005842127.1|  8 SGKGGVGKSTLSSTLILYLKERGYDI 33
                                      7999*******************987 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.5
                                       HHHHHHHHHHH...GGGEEEEE CS
                          NTPase_1  13 tTlvkkvlellkssgvkvgGfy 34 
                                       + +v+ +++  +++++ v G++
  gi|385805729|ref|YP_005842127.1| 232 SEFVEEIIKYAREENIDVIGMV 253
                                       6789999999999999999986 PP

>> Glyco_hydro_20  Glycosyl hydrolase family 20, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00067      0.38      78     119 ..     233     274 ..     223     303 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00067
                    Glyco_hydro_20  78 edireiveYAaergieVipEidmPgHaraalkaypelvtkek 119
                                       e ++ei++YA+e +i+Vi  +    H+ +a++++  l+++ +
  gi|385805729|ref|YP_005842127.1| 233 EFVEEIIKYAREENIDVIGMVPYDDHVPKAMAEMRPLIKQYN 274
                                       6789*****************************999998833 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   2.2    0.0043       2.4      43      59 ..      70      86 ..      51      88 .. 0.76
   2 ?    7.6   2.7    0.0098       5.5       1      16 [.      72      87 ..      72     101 .. 0.72
   3 ?    3.8   2.6      0.15        84      46      58 ..     102     114 ..      92     116 .. 0.75
   4 ?    5.1   2.2      0.06        34       2      17 ..     102     117 ..     101     135 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0043
                           Fer4_17 43 aslCieCgeCerkCPqg 59
                                        +C++Cg C  +C +g
  gi|385805729|ref|YP_005842127.1| 70 YFRCVNCGICHNVCTYG 86
                                      56788888888888765 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0098
                           Fer4_17  1 rCiqCgyClpeCpsye 16
                                      rC +Cg C ++C +++
  gi|385805729|ref|YP_005842127.1| 72 RCVNCGICHNVCTYGA 87
                                      5778888888887765 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.15
                           Fer4_17  46 CieCgeCerkCPq 58 
                                       C +C  C+ +CP+
  gi|385805729|ref|YP_005842127.1| 102 CEGCLTCSLACPE 114
                                       7777777777776 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.06
                           Fer4_17   2 CiqCgyClpeCpsyea 17 
                                       C +C  C  +Cp  ++
  gi|385805729|ref|YP_005842127.1| 102 CEGCLTCSLACPEKAI 117
                                       7788888888887655 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   5.9     0.032        18       1      15 []      73      87 ..      73      87 .. 0.98
   2 ?    9.6   4.0    0.0035         2       1      15 []     102     116 ..     102     116 .. 0.95

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.032
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C++Cg C +vC +gA
  gi|385805729|ref|YP_005842127.1| 73 CVNCGICHNVCTYGA 87
                                      *************98 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0035
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C gC +C  +CP++A
  gi|385805729|ref|YP_005842127.1| 102 CEGCLTCSLACPEKA 116
                                       99**99******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 ?    8.9   3.2    0.0037       2.1       3      15 ..      71      83 ..      37      87 .. 0.71
   2 ?    0.1  13.0       2.1   1.2e+03       3      18 ..      71      86 ..      69     116 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0037
                            Fer4_8  3 ekCieCgaCqsaC 15
                                      ++C++Cg C + C
  gi|385805729|ref|YP_005842127.1| 71 FRCVNCGICHNVC 83
                                      4566666666666 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 2.1
                            Fer4_8  3 ekCieCgaCqsaCpvl 18
                                      ++C++Cg C + C   
  gi|385805729|ref|YP_005842127.1| 71 FRCVNCGICHNVCTYG 86
                                      7999999999999533 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   3.2   0.00078      0.44       3      16 ..      72      85 ..      70      86 .. 0.90
   2 ?    2.8   1.6      0.37   2.1e+02       4      16 ..     102     114 ..      99     123 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00078
                            Fer4_4  3 rCigCgsCvaaCPq 16
                                      rC++Cg C+++C +
  gi|385805729|ref|YP_005842127.1| 72 RCVNCGICHNVCTY 85
                                      8***********76 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.37
                            Fer4_4   4 CigCgsCvaaCPq 16 
                                       C gC  C  aCP 
  gi|385805729|ref|YP_005842127.1| 102 CEGCLTCSLACPE 114
                                       889********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       896  (0.0499749); expected 358.6 (0.02)
Passed bias filter:                      723  (0.0403257); expected 358.6 (0.02)
Passed Vit filter:                       126  (0.00702772); expected 17.9 (0.001)
Passed Fwd filter:                        33  (0.00184059); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              32  [number of targets reported over threshold]
# CPU time: 0.71u 0.31s 00:00:01.02 Elapsed: 00:00:00.50
# Mc/sec: 1943.80
//
Query:       gi|385805730|ref|YP_005842128.1|  [L=295]
Description: ATPase, ParA/MinD family, containing ferredoxin domains [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-19   69.8   0.0    2.8e-19   69.4   0.0    1.1  1  CbiA            CobQ/CobB/MinD/ParA nucleotide binding domain
    8.4e-14   51.6   0.2    4.6e-07   29.5   0.1    2.4  2  ParA            NUBPL iron-transfer P-loop NTPase
    3.2e-10   39.4  14.4    2.5e-05   23.9   4.6    2.3  2  Fer4            4Fe-4S binding domain
    8.6e-10   38.3  11.5    0.00013   21.9   2.6    2.3  2  Fer4_6          4Fe-4S binding domain
    7.9e-08   31.9  10.5    0.00092   19.2   1.9    2.4  2  Fer4_2          4Fe-4S binding domain
    9.8e-08   32.5   5.4     0.0032   18.0   0.2    2.2  2  Fer4_7          4Fe-4S dicluster domain
    7.7e-07   29.1   7.3    1.3e-06   28.4   7.3    1.4  1  Fer4_21         4Fe-4S dicluster domain
      1e-06   28.5   0.0       0.02   14.4   0.0    2.2  2  Fer4_NifH       4Fe-4S iron sulfur cluster binding proteins, 
    1.5e-06   28.3  31.5    2.5e-05   24.3  11.5    2.0  3  Fer4_9          4Fe-4S dicluster domain
    3.7e-06   27.8   9.4     0.0015   19.4   1.4    2.4  2  Fer4_16         4Fe-4S double cluster binding domain
    3.4e-05   23.8   0.0    0.00047   20.1   0.0    2.2  1  AAA_31          AAA domain
    5.4e-05   23.2  12.6     0.0026   17.8  13.0    2.2  2  Fer4_10         4Fe-4S dicluster domain
    0.00073   18.9   0.0     0.0044   16.3   0.0    1.9  2  MipZ            ATPase MipZ
     0.0011   19.2  13.5      0.086   13.4   4.1    2.3  2  Fer4_4          4Fe-4S binding domain
     0.0078   16.7  11.3        4.4    7.9  11.3    2.4  1  Fer4_17         4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.015   14.9   0.1      0.033   13.7   0.0    1.6  2  AAA_25          AAA domain
      0.036   14.8   7.3       0.15   12.8   1.2    2.6  2  Fer4_15         4Fe-4S single cluster domain
      0.046   13.2   0.0        4.7    6.6   0.0    2.1  2  CBP_BcsQ        Cellulose biosynthesis protein BcsQ
      0.057   13.9  11.1       0.78   10.2   1.9    2.3  2  Fer4_8          4Fe-4S dicluster domain
      0.082   13.8   5.7       0.53   11.2   0.5    2.3  2  Fer4_22         4Fe-4S dicluster domain
      0.084   12.7   0.0       0.15   11.9   0.0    1.3  1  Tir_receptor_N  Translocated intimin receptor (Tir) N-terminu
       0.13   11.5   0.2       0.28   10.3   0.2    1.5  1  ArsA_ATPase     Anion-transporting ATPase
       0.39   11.7  17.1        1.2   10.2   4.5    2.3  2  Fer4_3          4Fe-4S binding domain
        1.9    9.1  13.2        4.2    8.0   3.5    2.3  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 !   69.4   0.0   3.8e-22   2.8e-19       2     128 .]       6     271 ..       5     271 .. 0.93

  Alignments for each domain:
  == domain 1  score: 69.4 bits;  conditional E-value: 3.8e-22
                                       EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH.HTTEB-HHHH....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx....................... RF
                              CbiA   2 aiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai.leglendiep....................... 54 
                                        ++++kGG+GK+++a+n+a +lar +++ +l D+D++a+n+++ l  + +++ep                       
  gi|385805730|ref|YP_005842128.1|   6 GVTGGKGGTGKSMVAVNIASLLAR-ERELVLADLDVEAPNDHLlLNAKLENEEPveimlpfidykkctgcgvcakic 81 
                                       589*********************.*****************96555555555589********************* PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|385805730|ref|YP_005842128.1|  82 dtggiimtrekmpmvlprlcsgcracyfacpekaivegkrvegyiyytrvrlkdceftlvtgmlregeehtppvvlp 158
                                       ***************************************************************************** PP

                                       ...............................................CCHCCCHHHHHHCHCHHHH..EEEEEEEEE CS
                                       ...............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ...............................................dlkrllellealgkkkalllkiagvvlnrv 84 
                                                                                      dl+ +l++l++l++        a v++nr+
  gi|385805730|ref|YP_005842128.1| 159 akkkaislsrdllvidtsagtanhvstalegskialavteptplglhDLELILKVLNELRID-------AWVLVNRW 228
                                       *************************************************************9.......******** PP

                                       SS...-TTCHHHHHHHHHHCTS-EEE.EEE--CCHCCCCHHTS-H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                              CbiA  85 dgeneetllkealeelkqrygvpvlg.viprdeavaeapargepv 128
                                       +   +++++++  e++ ++ ++ v++ +ip++ +++ea+ rg p+
  gi|385805730|ref|YP_005842128.1| 229 GIG-SSEKMYSIAEKI-AKKHNAVIKaKIPYSRDLVEAYVRGIPI 271
                                       **9.344455555555.4557777777***************986 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 !   29.5   0.1   6.2e-10   4.6e-07       4      67 ..       3      64 ..       1      92 [. 0.84
   2 !   19.9   0.0   5.3e-07    0.0004     113     245 ..     169     291 ..     162     292 .. 0.88

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 6.2e-10
                              ParA  4 kviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqsekkliP 67
                                        i v+ gKGG GKS vavn+A  La+ + +  l D+D+  p+   ll+++ e+ e  e  ++P
  gi|385805730|ref|YP_005842128.1|  3 GSIGVTGGKGGTGKSMVAVNIASLLAR-ERELVLADLDVEAPNDHLLLNAKLENEEPVE-IMLP 64
                                      5689******************98875.67888**********9999998876554444.4556 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 5.3e-07
                              ParA 113 DyLiiDlPPGtgDeqltvaqklplagaviVttpqevaladvkkaiemfkkvkvkvlGvveNmsgfvcpkcgekteif 189
                                       D+L+iD+  Gt+    t ++  +   a+ Vt p  + l+d +  ++++++++++   +v+   +   +      +++
  gi|385805730|ref|YP_005842128.1| 169 DLLVIDTSAGTANHVSTALEGSK--IALAVTEPTPLGLHDLELILKVLNELRIDAWVLVNRWGIGSSE------KMY 237
                                       99**********98888877775..5789***************************999766544333......333 PP

                              ParA 190 gkgggeklaeelgvpllgeipldpeireasdegkplvlkepeseaakaleeiaekv 245
                                         + +ek+a+++++ + ++ip + +++ea  +g p+v+  p++e++k++++ia+++
  gi|385805730|ref|YP_005842128.1| 238 --SIAEKIAKKHNAVIKAKIPYSRDLVEAYVRGIPIVEFYPDHEISKIFRSIAKEI 291
                                       ..35899**********************************************998 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   4.6   3.4e-08   2.5e-05       2      23 ..      65      86 ..      64      87 .. 0.90
   2 !   21.1   2.2   2.6e-07   0.00019       5      23 ..      98     116 ..      94     117 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 3.4e-08
                                      EEETTTSSS-THHHHHSTTTEE CS
                              Fer4  2 videekCigCGaCvevCPvgAI 23
                                       id+ kC+gCG C+++C +g I
  gi|385805730|ref|YP_005842128.1| 65 FIDYKKCTGCGVCAKICDTGGI 86
                                      79***************99866 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 2.6e-07
                                       TTTSSS-THHHHHSTTTEE CS
                              Fer4   5 eekCigCGaCvevCPvgAI 23 
                                       + +C gC aC+ +CP  AI
  gi|385805730|ref|YP_005842128.1|  98 PRLCSGCRACYFACPEKAI 116
                                       779***************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 !   21.4   1.7   2.4e-07   0.00018       2      22 ..      64      84 ..      63      87 .. 0.89
   2 !   21.9   2.6   1.7e-07   0.00013       7      24 .]      99     116 ..      96     116 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.4e-07
                            Fer4_6  2 veidpdkCigCgdCvrvCPeg 22
                                      + id+ kC+gCg C+++C +g
  gi|385805730|ref|YP_005842128.1| 64 PFIDYKKCTGCGVCAKICDTG 84
                                      789***************885 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 1.7e-07
                            Fer4_6   7 dkCigCgdCvrvCPegai 24 
                                        +C gC++C+ +CPe+ai
  gi|385805730|ref|YP_005842128.1|  99 RLCSGCRACYFACPEKAI 116
                                       68**************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 !   17.5   1.6   4.2e-06    0.0031       3      20 ..      64      81 ..      62      82 .. 0.94
   2 !   19.2   1.9   1.2e-06   0.00092       3      22 .]      94     113 ..      91     113 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.2e-06
                            Fer4_2  3 vvvdtdrCigCgaCvsaC 20
                                      +++d  +C+gCg C + C
  gi|385805730|ref|YP_005842128.1| 64 PFIDYKKCTGCGVCAKIC 81
                                      799************999 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 1.2e-06
                            Fer4_2   3 vvvdtdrCigCgaCvsaCPa 22 
                                       + v ++ C gC+aC+ aCP+
  gi|385805730|ref|YP_005842128.1|  94 PMVLPRLCSGCRACYFACPE 113
                                       5677899************5 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.2   4.3e-06    0.0032      31      51 ..      64      84 ..      41      95 .. 0.75
   2 !   16.2   1.2   1.6e-05     0.012       2      22 ..     101     121 ..      98     141 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4.3e-06
                            Fer4_7 31 veidpekClgCgaCvavCPtg 51
                                      + id+ kC+gCg+C++ C tg
  gi|385805730|ref|YP_005842128.1| 64 PFIDYKKCTGCGVCAKICDTG 84
                                      467888899999999998776 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.6e-05
                            Fer4_7   2 CigCgaCvaaCpvkaieldee 22 
                                       C gC+aC  aCp kai   ++
  gi|385805730|ref|YP_005842128.1| 101 CSGCRACYFACPEKAIVEGKR 121
                                       9************99976665 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   7.3   1.7e-09   1.3e-06       2      57 ..      65     116 ..      64     118 .. 0.90

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 1.7e-09
                           Fer4_21   2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedci 57 
                                       +id +kC gCg C++ C++     i ++ +++  v+   C GC  C+  CP e++i
  gi|385805730|ref|YP_005842128.1|  65 FIDYKKCTGCGVCAKICDT---GGIIMTREKMPMVLPRLCSGCRACYFACP-EKAI 116
                                       699***************5...77899999999999***************.5665 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   0.00014       0.1       7      51 ..      10      53 ..       5      61 .. 0.80
   2 !   14.4   0.0   2.7e-05      0.02     189     246 ..     236     293 ..     216     295 .] 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                         Fer4_NifH  7 GkGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrlllggka 51
                                      GkGG Gks+ + n+++ la+  + vl    D  a   +lll++k+
  gi|385805730|ref|YP_005842128.1| 10 GKGGTGKSMVAVNIASLLARERELVL-ADLDVEAPNDHLLLNAKL 53
                                      9**************99998766554.567777777777777765 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 2.7e-05
                         Fer4_NifH 189 ereliekfaeelgtkvlevvPrdeivrkaelrkktvieyapeseqakeyrelarkile 246
                                          ++ek+a++ +  + +++P + ++ +a +r   ++e+ p++e++k +r +a++il+
  gi|385805730|ref|YP_005842128.1| 236 MYSIAEKIAKKHNAVIKAKIPYSRDLVEAYVRGIPIVEFYPDHEISKIFRSIAKEILD 293
                                       5678899999*9*999***************************************987 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   2.0   2.3e-05     0.017      33      49 ..      68      84 ..      44      87 .. 0.71
   2 !   24.3  11.5   3.4e-08   2.5e-05       1      51 []      70     116 ..      70     116 .. 0.92
   3 !   14.7   2.7   3.4e-05     0.026       2      31 ..     101     131 ..     100     138 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.3e-05
                            Fer4_9 33 eeaCigCgaCveaCpkg 49
                                      +++C+gCg C+++C +g
  gi|385805730|ref|YP_005842128.1| 68 YKKCTGCGVCAKICDTG 84
                                      278***********985 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 3.4e-08
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                       kCtgCg C + C +g +++ + +  + l +     C gC+aC+ aCp++ai
  gi|385805730|ref|YP_005842128.1|  70 KCTGCGVCAKICDTGGIIMTREKMPMVLPR----LCSGCRACYFACPEKAI 116
                                       7***********999999999999999866....5*************987 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 3.4e-05
                            Fer4_9   2 CtgCgaCveaCpagvv.vedaaerkarlraa 31 
                                       C gC+aC  aCp +++ +++++e+++ +++ 
  gi|385805730|ref|YP_005842128.1| 101 CSGCRACYFACPEKAIvEGKRVEGYIYYTRV 131
                                       99*********99999344555555555555 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 !   12.5   1.4    0.0003      0.22       1      21 [.      70      90 ..      68      96 .. 0.82
   2 !   19.4   1.4     2e-06    0.0015       2      21 ..     101     120 ..     100     137 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0003
                           Fer4_16  1 rCgtCgkCaevCPtnaikekk 21
                                      +C++Cg Ca++C t+ i +++
  gi|385805730|ref|YP_005842128.1| 70 KCTGCGVCAKICDTGGIIMTR 90
                                      599999999999999887774 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 2e-06
                           Fer4_16   2 CgtCgkCaevCPtnaikekk 21 
                                       C +C++C  +CP++ai e k
  gi|385805730|ref|YP_005842128.1| 101 CSGCRACYFACPEKAIVEGK 120
                                       ****************9983 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   6.3e-07   0.00047       4     167 ..       5     217 ..       3     223 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 6.3e-07
                            AAA_31   4 IaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanatt...glgiekne..iek.................t 58 
                                       I ++  KGG GK+  +vn+a+ la++ + vL  DlD  a       ++++e++e                      +
  gi|385805730|ref|YP_005842128.1|   5 IGVTGGKGGTGKSMVAVNIASLLARERELVL-ADLDVEAPNDHlllNAKLENEEpvE-ImlpfidykkctgcgvcaK 79 
                                       667788******************9888776.6999887555523333332222330.1333333333333333333 PP

                            AAA_31  59 lyev......................lieeknikeaiiktkvenldlipssidLaeaeielvelekkeei....... 106
                                       ++++                       +  +  ++ai++ k  + ++  + + L ++e  lv+ + +e         
  gi|385805730|ref|YP_005842128.1|  80 ICDTggiimtrekmpmvlprlcsgcrACYFACPEKAIVEGKRVEGYIYYTRVRLKDCEFTLVTGMLREGEehtppvv 156
                                       33336666666666666666555443234556788888888888899999999999999999887773333345555 PP

                            AAA_31 107 lkellekvkdeYDyiiiDcpPsLglltenaLvasdsviipvqaeayaleGleqllktieev 167
                                       l  + ++++ + D+ +iD++      + +aL  s   + +++++++ l+ le +lk ++e+
  gi|385805730|ref|YP_005842128.1| 157 LPAKKKAISLSRDLLVIDTSAGTANHVSTALEGSKIALAVTEPTPLGLHDLELILKVLNEL 217
                                       7888888999999999999999999999999999999999999999999999999999886 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8  13.0   3.5e-06    0.0026       3      56 .]      65     112 ..      63     112 .. 0.84
   2 !   16.1   1.5   1.2e-05    0.0092       6      34 ..      98     128 ..      93     139 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.5e-06
                           Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                        id ++C++Cg C k C      + +  + ++e++  + +  C gc aC+ aCP
  gi|385805730|ref|YP_005842128.1|  65 FIDYKKCTGCGVCAKIC------DTGGIIMTREKMPMVLPRLCSGCRACYFACP 112
                                       699**************......44555666666777799*************9 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.2e-05
                           Fer4_10   6 ddtCirCgkCvkaCPadl..tsvgakgease 34 
                                       +  C +C++C  aCP ++  ++++++g++ +
  gi|385805730|ref|YP_005842128.1|  98 PRLCSGCRACYFACPEKAivEGKRVEGYIYY 128
                                       578*************766544444444444 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   5.9e-06    0.0044       5      67 ..       7      68 ..       4      87 .. 0.84
   2 ?    0.0   0.0      0.56   4.2e+02      91     139 ..     159     210 ..     134     219 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.9e-06
                                      E--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHHHHHHHHHHHHT------EE CS
                              MipZ  5 lgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlarylenraataerkglsLplpea 67
                                      ++  kGG+Gks +av +a  L+++       dld+     +  l+ +++ +e  ++ Lp  ++
  gi|385805730|ref|YP_005842128.1|  7 VTGGKGGTGKSMVAVNIASLLAREREL-VLADLDVEAPNDHLLLNAKLENEEPVEIMLPFIDY 68
                                      6678************99877766555.56699999999999999999999999999998766 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.56
                                       HHHHHHHHH-SEEEEE--SS--HHHHHH...HHT-SEEEEEEESSHHHHCCC CS
                              MipZ  91 elvadleaeldfividtPGsdsalsrla...hsladtlvtPlndsfvdfdll 139
                                       +  ++++ + d++vidt     + + +a    + a ++  P    + d++l+
  gi|385805730|ref|YP_005842128.1| 159 AKKKAISLSRDLLVIDTSAGTANHVSTAlegSKIALAVTEPTPLGLHDLELI 210
                                       5566778889999999975544443333010334444444555555566555 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   4.1   0.00011     0.086       2      14 ..      69      81 ..      68      84 .. 0.90
   2 !   11.0   1.9   0.00065      0.49       4      16 ..     101     113 ..      98     124 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00011
                            Fer4_4  2 erCigCgsCvaaC 14
                                      ++C+gCg+C  +C
  gi|385805730|ref|YP_005842128.1| 69 KKCTGCGVCAKIC 81
                                      89*********** PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00065
                            Fer4_4   4 CigCgsCvaaCPq 16 
                                       C gC++C+ aCP 
  gi|385805730|ref|YP_005842128.1| 101 CSGCRACYFACPE 113
                                       ************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 !    7.9  11.3    0.0059       4.4       1      58 [.      70     113 ..      70     116 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0059
                           Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPq 58 
                                       +C++Cg C++ C ++ ++ +++k+++                  lC++C+ C  +CP+
  gi|385805730|ref|YP_005842128.1|  70 KCTGCGVCAKICDTGGIIMTREKMPMVL--------------PRLCSGCRACYFACPE 113
                                       6**************9999888887776..............468************8 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.5e-05     0.033      32      62 ..       2      32 ..       1      49 [. 0.86
   2 ?   -3.7   0.0       9.8   7.3e+03     144     153 ..     169     178 ..     148     185 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.5e-05
                            AAA_25 32 agelallaGapgtGKttlaldlalavatGkp 62
                                      +g++++  G +gtGK+++a+++a  +a+ ++
  gi|385805730|ref|YP_005842128.1|  2 KGSIGVTGGKGGTGKSMVAVNIASLLARERE 32
                                      68999******************99887665 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 9.8
                            AAA_25 144 rlvviDplsr 153
                                       +l+viD+ + 
  gi|385805730|ref|YP_005842128.1| 169 DLLVIDTSAG 178
                                       7889998665 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   1.2    0.0002      0.15       3      19 ..      66      82 ..      65      88 .. 0.91
   2 ?    4.7   0.6     0.067        50       7      20 ..     100     113 ..      98     138 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.0002
                           Fer4_15  3 vDrdaCigcglCvaeap 19
                                      +D ++C+gcg+C++ ++
  gi|385805730|ref|YP_005842128.1| 66 IDYKKCTGCGVCAKICD 82
                                      9*************997 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.067
                           Fer4_15   7 aCigcglCvaeape 20 
                                       +C gc +C+ ++pe
  gi|385805730|ref|YP_005842128.1| 100 LCSGCRACYFACPE 113
                                       69999999999975 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0062       4.7       4      45 ..       5      48 ..       1      62 [. 0.79
   2 ?    4.7   0.0     0.025        18     109     231 ..     161     289 ..     146     292 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0062
                          CBP_BcsQ  4 lalqGvRGGvGttsllaaLawalhelgesvlv.iDl.spdnlLr 45
                                      + ++G +GG+G++ +++ +a  l + +e vl+ +D+ +p++ L 
  gi|385805730|ref|YP_005842128.1|  5 IGVTGGKGGTGKSMVAVNIASLLARERELVLAdLDVeAPNDHLL 48
                                      889999*******************9999997566523455554 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.025
                          CBP_BcsQ 109 lkelkeqyrwillDlpagasaltrellaladlvllvvepdanc.h...vrLh.qqalpaaellLiNqfeaasqlqq. 179
                                        k+++ + +++++D  ag+++ ++++l+ + + l+v+ep     h   + L+  ++l   +++L+N++ + s  +  
  gi|385805730|ref|YP_005842128.1| 161 KKAISLSRDLLVIDTSAGTANHVSTALEGSKIALAVTEPTPLGlHdleLILKvLNELRIDAWVLVNRWGIGSSEKMy 237
                                       566667779999**************************986441322133331356778899999999988764431 PP

                          CBP_BcsQ 180 DllqlWlqslrrllPlvihrDealaEalaakqPlgeyrpdslaaeevktLan 231
                                        +     ++ + ++  +i     l+Ea +   P+ e+ pd   ++  +++a+
  gi|385805730|ref|YP_005842128.1| 238 SIAEKIAKKHNAVIKAKIPYSRDLVEAYVRGIPIVEFYPDHEISKIFRSIAK 289
                                       4444455666666777777777788888888888888888877777777665 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.9     0.001      0.78       3      16 ..      69      82 ..      67      99 .. 0.71
   2 ?    7.1   2.6    0.0096       7.2      50      64 ..     100     114 ..      97     115 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.001
                            Fer4_8  3 ekCieCgaCqsaCp 16
                                      +kC++Cg C + C 
  gi|385805730|ref|YP_005842128.1| 69 KKCTGCGVCAKICD 82
                                      78999999999995 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0096
                            Fer4_8  50 sCttcgaCtevCpvg 64 
                                        C++c+aC  +Cp++
  gi|385805730|ref|YP_005842128.1| 100 LCSGCRACYFACPEK 114
                                       588888888888875 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.5   0.00071      0.53      77      94 ..      66      83 ..      52      85 .. 0.84
   2 ?    4.9   0.6     0.062        46      81      94 ..     100     113 ..      89     138 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00071
                           Fer4_22 77 fgesgCvGCgRCieacpv 94
                                      ++ ++C+GCg C + c +
  gi|385805730|ref|YP_005842128.1| 66 IDYKKCTGCGVCAKICDT 83
                                      47889*********9975 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.062
                           Fer4_22  81 gCvGCgRCieacpv 94 
                                        C GC  C  acp+
  gi|385805730|ref|YP_005842128.1| 100 LCSGCRACYFACPE 113
                                       57777777777765 PP

>> Tir_receptor_N  Translocated intimin receptor (Tir) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0    0.0002      0.15     155     188 ..       7      42 ..       2      61 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0002
                    Tir_receptor_N 155 ftggrggaghamvtv..asdiaearqrildklepkd 188
                                        tgg+gg+g++mv+v  as +a  r+ +l+ l+ + 
  gi|385805730|ref|YP_005842128.1|   7 VTGGKGGTGKSMVAVniASLLARERELVLADLDVEA 42 
                                       79**********976448889999999999998654 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.2   0.00037      0.28       6      33 ..       8      35 ..       4      39 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00037
                                      EEESTTSSHHHHHHHHHHHHHHTTS-EE CS
                       ArsA_ATPase  6 vgGKGGVGKttvsaatavklsekgkkvl 33
                                       gGKGG GK+ v+  +a  l+++++ vl
  gi|385805730|ref|YP_005842128.1|  8 TGGKGGTGKSMVAVNIASLLARERELVL 35
                                      69*******************9998776 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   4.7     0.014        10       1      14 [.      71      84 ..      71      85 .. 0.91
   2 ?   10.2   4.5    0.0017       1.2       1      15 []     101     115 ..     101     115 .. 0.97

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.014
                            Fer4_3  1 CtgCgaCvevCPvg 14
                                      CtgCg C + C +g
  gi|385805730|ref|YP_005842128.1| 71 CTGCGVCAKICDTG 84
                                      ***********776 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0017
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C gC+aC  +CP++A
  gi|385805730|ref|YP_005842128.1| 101 CSGCRACYFACPEKA 115
                                       99**********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 ?    8.0   3.5    0.0056       4.2       1      16 [.      66      81 ..      66      83 .. 0.92
   2 ?    6.3   2.2     0.019        14       6      18 ..     101     113 ..      98     114 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0056
                           Fer4_13  1 VDrdtCiacgaCvela 16
                                      +D ++C++cg+C++++
  gi|385805730|ref|YP_005842128.1| 66 IDYKKCTGCGVCAKIC 81
                                      7899**********99 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.019
                           Fer4_13   6 CiacgaCvelaPd 18 
                                       C++c aC+ ++P+
  gi|385805730|ref|YP_005842128.1| 101 CSGCRACYFACPE 113
                                       ************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); 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: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 1908.99
//
Query:       gi|385805731|ref|YP_005842129.1|  [L=143]
Description: hypothetical protein FFONT_0689 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score 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   0.9      0.023   14.6   0.9    1.5  1  Tnp_22_trimer  L1 transposable element trimerization domain
      0.096   13.6   0.0       0.12   13.3   0.0    1.2  1  DUF4065        Protein of unknown function (DUF4065)


Domain annotation for each model (and alignments):
>> Tnp_22_trimer  L1 transposable element trimerization domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.9   2.6e-06     0.023      15      35 ..      63      84 ..      60      85 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.6e-06
                                      HHHHHHHHHHH.HHHHHHHHHH CS
                     Tnp_22_trimer 15 eieeidrevKe.reKrkkileQ 35
                                      eieei+r  K   e+++ki+eQ
  gi|385805731|ref|YP_005842129.1| 63 EIEEIKRRIKDgSERCIKINEQ 84
                                      8*********8579******** PP

>> DUF4065  Protein of unknown function (DUF4065)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.3e-05      0.12       6     109 ..      33     127 ..      28     131 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.3e-05
                           DUF4065   6 YfadflhlkrtgkpitglkyiawkyGPVvpevydeikelgskpieekeeeisdeklekkekkeveeleddkeaelse 82 
                                        +a++++lk++g+  +  k    + G  vpe+ +         i++++++ s++ ++ +e+k+  e+ ++++ el  
  gi|385805731|ref|YP_005842129.1|  33 VLANWKMLKEKGTIALRFKVDGFQAGFAVPEIEE---------IKRRIKDGSERCIKINEQKKCFEYVCEEKVELPR 100
                                       5666666677777666666666777766674444.........4444555555555555555555555666666*** PP

                           DUF4065  83 eekevidkvikkykdlsaseLselthk 109
                                       e  +vi+kv+++ ++l+   L +++ +
  gi|385805731|ref|YP_005842129.1| 101 EVSDVIQKVFDEIRSLDDISLNRIVVR 127
                                       ****************99999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); 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: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 934.01
//
Query:       gi|385805732|ref|YP_005842130.1|  [L=281]
Description: hypothetical protein FFONT_0690 [Fervidicoccus fontis Kam940]
Scores for complete 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-116  386.3   0.5   7.2e-116  386.2   0.5    1.0  1  SDH_sah        Serine dehydrogenase proteinase
    0.00047   20.1   0.4     0.0046   16.9   0.0    2.4  3  CLP_protease   Clp protease
     0.0015   18.5   0.0     0.0021   18.0   0.0    1.3  1  Peptidase_S49  Peptidase family S49
  ------ inclusion threshold ------
      0.022   14.8   0.6      0.056   13.5   0.1    2.0  2  Dimerisation   Dimerisation domain
      0.045   13.5   0.1        1.2    9.0   0.1    2.5  2  MaAIMP_sms     Putative methionine and alanine importer, smal
      0.051   13.2   0.0      0.086   12.5   0.0    1.4  1  CDKN3          Cyclin-dependent kinase inhibitor 3 (CDKN3)


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 !  386.2   0.5  2.4e-119  7.2e-116       7     277 ..       3     277 ..       1     281 [] 0.97

  Alignments for each domain:
  == domain 1  score: 386.2 bits;  conditional E-value: 2.4e-119
                           SDH_sah   7 lsslssllwfllflylllapqlkrkqlllarlkvlrkleekrksrvitmihrqesigflGipiykfitiedseevlr 83 
                                       l+ + s+l++++f++l+++p+  + ++ +ar ++l  le+k k r it+ihrqe +g++Gip+y++i+i+dseevlr
  gi|385805732|ref|YP_005842130.1|   3 LADIASILFWFVFFLLIFSPTTSQARIRAARARILASLESKMKMRFITLIHRQERVGIFGIPVYRYIDIDDSEEVLR 79 
                                       678999*********************************************************************** PP

                           SDH_sah  84 airltpkdkpidliihtpGGlvlaatqiakalkehkaktrvivphyamsGGtlialaadeiildenavlGpvdpql. 159
                                       air tpkd+ i +i+htpGGlvlaa qia alk h+ k  vi+phyamsGGtli+laadei +d+navlGp+dpq+ 
  gi|385805732|ref|YP_005842130.1|  80 AIRETPKDMGIAIILHTPGGLVLAASQIALALKRHPGKKVVIIPHYAMSGGTLISLAADEIWMDRNAVLGPIDPQIq 156
                                       **************************************************************************985 PP

                           SDH_sah 160 ....gqypaasilkvvekkeakdiddktliladiakkaikqveefvyellkdkydeekakeiakklteGrwthdypl 232
                                           g +pa+si+k  + k+ + ++d tli+adia+ka k v+e+v+ell+dk++ee+a+e+a+ lt G wthd+p+
  gi|385805732|ref|YP_005842130.1| 157 fqqyGSLPAPSIIKLAKMKG-ERAEDITLIMADIAEKATKGVQEIVVELLRDKMGEERARELADLLTRGDWTHDHPI 232
                                       5444567*********9999.99****************************************************** PP

                           SDH_sah 233 tveelkelGlevntnvpeevyellelyeqplgqrpsveyipvpvk 277
                                       t ee+k+lGl+v+ ++pee+y+l+ ly+ pl+qr+ veyip+ ++
  gi|385805732|ref|YP_005842130.1| 233 TFEEAKKLGLPVKDEIPEEIYDLMALYKAPLMQRSGVEYIPYTPQ 277
                                       *****************************************9765 PP

>> CLP_protease  Clp protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.5e-06    0.0046      40      98 ..      81     139 ..      61     148 .. 0.89
   2 ?    0.6   0.0      0.15   4.5e+02     133     174 ..     195     242 ..     168     251 .. 0.61
   3 ?   -2.5   0.0       1.3     4e+03      65      77 ..     251     263 ..     247     265 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.5e-06
                                       HHHH-SSS-EEEEEEE--B-HHHHHHHHHHHHHSSS-EEEEEEEEEETHHHHHHHTS-T CS
                      CLP_protease  40 LeaedpdkdillyinspGGsvtaglaIydtmqyikpdvsticlGlaaSmgslllaagek 98 
                                       + ++ +d  i +++++pGG v a+  I+ +++ +  + ++i    a+S g+l+ +a+++
  gi|385805732|ref|YP_005842130.1|  81 IRETPKDMGIAIILHTPGGLVLAASQIALALKRHPGKKVVIIPHYAMSGGTLISLAADE 139
                                       556678889**********************************************9985 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.15
                                       HHHHHHHHHHHHHHHTS-HH.HHHH.....HHCSTEEEEHHHHHHHTS CS
                      CLP_protease 133 lkikerlneilakhtgqsle.kiek.....dldrdtflsaeeAveyGL 174
                                       + ++e ++e+l ++ g+++  +++      d + d+ ++ eeA++ GL
  gi|385805732|ref|YP_005842130.1| 195 KGVQEIVVELLRDKMGEERArELADlltrgDWTHDHPITFEEAKKLGL 242
                                       344555555555555544331344444455667777788899999998 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1.3
                                       HHHHHHHHSSS-E CS
                      CLP_protease  65 aIydtmqyikpdv 77 
                                       +Iyd+m++ k++ 
  gi|385805732|ref|YP_005842130.1| 251 EIYDLMALYKAPL 263
                                       69*****999875 PP

>> Peptidase_S49  Peptidase family S49
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   7.1e-07    0.0021       6      42 ..     116     151 ..     111     205 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 7.1e-07
                                       T--EEEEEEEEEETHHHHHHTTSSEEEE-TT-EEE-- CS
                     Peptidase_S49   6 kkPvvasaenvaaSggYylasaadkivanpstivgsi 42 
                                       +k+vv ++  +a Sgg +++ aad+i+++ +++ g i
  gi|385805732|ref|YP_005842130.1| 116 GKKVV-IIPHYAMSGGTLISLAADEIWMDRNAVLGPI 151
                                       56665.5789999********************9976 PP

>> Dimerisation  Dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       1.8   5.5e+03      23      32 ..       1      10 [.       1      10 [. 0.89
   2 ?   13.5   0.1   1.9e-05     0.056       8      42 ..      87     120 ..      77     122 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.8
                      Dimerisation 23 lspsEiaskL 32
                                      +++ +ias+L
  gi|385805732|ref|YP_005842130.1|  1 MTLADIASIL 10
                                      899****987 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 1.9e-05
                      Dimerisation   8 ELglldiiakaggkplspsEiaskLptknpeapvl 42 
                                       ++g++ i+++ gg  l++s+ia +L+ ++p + v+
  gi|385805732|ref|YP_005842130.1|  87 DMGIAIILHTPGGLVLAASQIALALK-RHPGKKVV 120
                                       699***********************.99987665 PP

>> MaAIMP_sms  Putative methionine and alanine importer, small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.082   2.5e+02      25      41 ..      49      64 ..      44      77 .. 0.80
   2 ?    9.0   0.1   0.00039       1.2      16      38 ..      96     122 ..      88     133 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.082
                        MaAIMP_sms 25 iaLrrePDeksGilGts 41
                                      i+L+ +  e++Gi+G  
  gi|385805732|ref|YP_005842130.1| 49 ITLI-HRQERVGIFGIP 64
                                      6776.4589******75 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00039
                        MaAIMP_sms  16 iWGGLvlal....iaLrrePDeksGil 38 
                                         GGLvla+    +aL+r+P +k+ i+
  gi|385805732|ref|YP_005842130.1|  96 TPGGLVLAAsqiaLALKRHPGKKVVII 122
                                       459***9954444899******99775 PP

>> CDKN3  Cyclin-dependent kinase inhibitor 3 (CDKN3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.9e-05     0.086      44     116 ..     170     240 ..     146     268 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.9e-05
                                       EEES-TT-EETTEEB-HHHHHHHHHHTT--EEEE-S-HHHHHHTT-TTHHHHHHHTT-EEEE----TTS---H CS
                             CDKN3  44 glcalpgckfkdvrrnvqkdteelksygiqdvfvfctrgelskyrvpnlldlyqqygivthhhpiadggtpdi 116
                                        l+ + g + +d+   +  d  e  + g+q+++v   r ++ + r  +l dl  + g  th hpi+   +  +
  gi|385805732|ref|YP_005842130.1| 170 KLAKMKGERAEDIT-LIMADIAEKATKGVQEIVVELLRDKMGEERARELADLLTR-GDWTHDHPITFEEAKKL 240
                                       55566666666665.4778999999***************************975.889******86665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); 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: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 1757.90
//
Query:       gi|385805733|ref|YP_005842131.1|  [L=220]
Description: beta-lactamase [Fervidicoccus fontis Kam940]
Scores for complete 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   28.8   0.0    1.8e-06   28.1   0.0    1.3  1  Lactamase_B    Metallo-beta-lactamase superfamily
     0.0013   18.3   0.0     0.0019   17.8   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 !   28.1   0.0     2e-10   1.8e-06       7     150 ..      19     141 ..      16     171 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 2e-10
                                       EEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCH CS
                       Lactamase_B   7 nsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalf 83 
                                       +s +ie +g+ iL+D+ t +e      + ++l +++  +d  +l+H+H DH+Gg +++  +  ++v++  ++    +
  gi|385805733|ref|YP_005842131.1|  19 WSLFIEFNGREILFDADTRGEIIAY--NSQKLNIDLSSIDFSFLSHYHGDHYGGYEYFEGKKSFKVYVPDKDRILRK 93 
                                       7889999999999999777776666..56************************************987766655544 PP

                                       CHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECT CS
                       Lactamase_B  84 meeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGD 150
                                          +                    ++ e  ++++ g+ ++++    g   +++v+ +++ ++l++G+
  gi|385805733|ref|YP_005842131.1|  94 LGLL-------------------PIVVEKFEEIEEGVFSTGPLSSLGLKEHSMVLKIDDLNILIVGC 141
                                       4444...................47888888888888888888888888888888888888888886 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 !   17.8   0.0   2.1e-07    0.0019       3      65 ..      30      87 ..      28     114 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.1e-07
                                      EEES--TTHHHH.HTCGGS--S.SS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHH CS
                     Lactamase_B_2  3 iLiDagpdlrqq.alralqPve.lrdelppidaVllthaHyDHlaglltlrelrpkklplyapkg 65
                                      iL+Da +  r+     a  + + l  +l++id+ +l+h H DH+ g+  +     k++++y+p++
  gi|385805733|ref|YP_005842131.1| 30 ILFDADT--RGEiI--AY-NSQkLNIDLSSIDFSFLSHYHGDHYGGYEYFEGK--KSFKVYVPDK 87
                                      6666633..44421..11.1222678899*****************9999994..4599**9954 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); 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: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 1450.24
//
Query:       gi|385805734|ref|YP_005842132.1|  [L=113]
Description: hypothetical protein FFONT_0692 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); 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: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 697.39
//
Query:       gi|385805735|ref|YP_005842133.1|  [L=198]
Description: hypothetical protein FFONT_0693 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); 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: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1305.88
//
Query:       gi|385805736|ref|YP_005842134.1|  [L=630]
Description: hypothetical protein FFONT_0694 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (630 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); 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: 0.72u 0.32s 00:00:01.04 Elapsed: 00:00:00.54
# Mc/sec: 3521.60
//
Query:       gi|385805737|ref|YP_005842135.1|  [L=157]
Description: putative, serine protease [Fervidicoccus fontis Kam940]
Scores for complete sequence (score 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   3.8       0.21   11.9   3.8    2.1  1  CARDB     CARDB
       0.47   11.4   9.7       0.37   11.7   6.9    2.2  2  Pilin_N   Archaeal Type IV pilin, N-terminal


Domain annotation for each model (and alignments):
>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   3.8   2.3e-05      0.21      14      70 ..      62     143 ..      49     156 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.3e-05
                                       EEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEE...........................SEE-CTEEE CS
                             CARDB  14 eafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtv...........................psLaagest 63 
                                       + +++++ ti ++vkN+G+a+++ +   + l+g +  ++++                           +s  +g+s+
  gi|385805737|ref|YP_005842135.1|  62 SSTNNTNATIWLHVKNSGSADAQIIA--VKLNGVNLPSSDIqtsapitvkagsdfnfiinvtssdvglTSFTPGTSY 136
                                       66899*************99988665..5568888866666667555667777776666666666666666666666 PP

                                       EEEEEEE CS
                             CARDB  64 tvsftwt 70 
                                       +v++   
  gi|385805737|ref|YP_005842135.1| 137 QVTIITS 143
                                       6666555 PP

>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   6.9   4.2e-05      0.37       1      42 [.      11      52 ..      11      94 .. 0.68
   2 ?   -0.1   0.1       0.2   1.8e+03      60      60 ..     121     121 ..      83     155 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.2e-05
                           Pilin_N  1 eAVSpViGviLmvaitvIlaAviaafvlglasneekapqasi 42
                                      +++Sp+i  +++v+it+ la  +a  + g+ + + +  q  i
  gi|385805737|ref|YP_005842135.1| 11 RGISPIIATVILVVITIALAVGVALWMSGIIGGAGRGEQLGI 52
                                      69******************9999999998444444444444 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.2
                           Pilin_N  60 e 60 
                                       +
  gi|385805737|ref|YP_005842135.1| 121 T 121
                                       1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       947  (0.0528195); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.57
# Mc/sec: 836.69
//
Query:       gi|385805738|ref|YP_005842136.1|  [L=48]
Description: hypothetical protein FFONT_0696 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.45
# Mc/sec: 319.06
//
Query:       gi|385805739|ref|YP_005842137.1|  [L=610]
Description: type II secretion system protein [Fervidicoccus fontis Kam940]
Scores for complete 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-23   81.6   9.2    2.7e-12   46.7   0.0    3.3  3  T2SSF     Type II secretion system (T2SS), protein F
  ------ inclusion threshold ------
       0.02   13.7   0.3       0.02   13.7   0.3    3.9  4  DUF2207   Predicted membrane protein (DUF2207)
          3    7.4   8.7       0.73    9.4   4.6    2.1  2  DUF3483   Domain of unknown function (DUF3483)


Domain annotation for each model (and alignments):
>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.0   4.5e-16   2.7e-12       1     121 [.     133     258 ..     133     262 .. 0.91
   2 ?   -4.7   2.8         3   1.8e+04     108     124 ..     290     306 ..     285     307 .. 0.52
   3 !   40.1   0.1   5.1e-14   3.1e-10       1     123 [.     390     515 ..     390     519 .. 0.93

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 4.5e-16
                                       HHHHHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTS..SHHHHHC....T-TT.TS-HHHHHHHHHH CS
                             T2SSF   1 flrqlatllsaGvplveaLellaeeaengplaeelkriarrlraGg..slseale....rtpssefpelvvqlirag 71 
                                       f+ +l +++ +G+++++++e++ae++ + ++++e + i+r++r  g  sls a+e    ++ps+ef+e+++ +++++
  gi|385805739|ref|YP_005842137.1| 133 FASYLTSMVVSGIGPQRVIEAIAESDLFDAIKKEAQLIKRNMRIFGldSLS-AIEsvakNHPSKEFREFMIGYVSTI 208
                                       7889******************************************65333.2224447****************** PP

                                       HHHT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXX CS
                             T2SSF  72 eeggnLaevLerlaeyleeerelrrkllaallepllllvvallvllilla 121
                                       + gg++ ++L+   e + +e e+  ++l +  +++l+ +++++v++ l +
  gi|385805739|ref|YP_005842137.1| 209 RGGGDVVHYLQLKTESYFKEKERDMDKLVEGVGTVLSTYMIIFVVVGLTI 258
                                       **********************************************9976 PP

  == domain 2  score: -4.7 bits;  conditional E-value: 3
                                       XXXXXXXXXXXXXXXXX CS
                             T2SSF 108 llvvallvllillaill 124
                                       l++++ ++++i+++ +l
  gi|385805739|ref|YP_005842137.1| 290 LMPIVTIFSIIIVGGIL 306
                                       44455555555554444 PP

  == domain 3  score: 40.1 bits;  conditional E-value: 5.1e-14
                                       HHHHHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTSSHHHHHC....T-TT.TS.-HHHHHHHHHHH CS
                             T2SSF   1 flrqlatllsaGvplveaLellaeeaengplaeelkriarrlraGgslseale....rtpssef.pelvvqlirage 72 
                                       fl+ l+   +aG+++++++ +l++ + +g ++++l+++   l+ G ++++a++     +++ +f +  +++l+ ++e
  gi|385805739|ref|YP_005842137.1| 390 FLTDLSEIRKAGLNPEKSIIYLSSKD-YGSFTPILRKLSSSLQVGVNMRRAVRiaivGYKN-WFmRAIMRMLVDIIE 464
                                       8999999*******************.***************************9984443.888************ PP

                                       HHT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXX CS
                             T2SSF  73 eggnLaevLerlaeyleeerelrrkllaallepllllvvallvllillail 123
                                       +gg  ++ L+ +a+y ++  + +++l+++l + ++l ++++++ ++  +++
  gi|385805739|ref|YP_005842137.1| 465 YGGGTPQLLDTIASYGRKLSDFENQLKTSLRSDVFLPYIGSILNIVSTVMI 515
                                       ****************************************99766666665 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   3.0    0.0069        41     381     436 ..      58     117 ..       9     140 .. 0.65
   2 ?   13.7   0.3   3.3e-06      0.02     319     441 ..     156     313 ..     148     320 .. 0.68
   3 ?    3.4   0.4    0.0045        27     381     464 ..     321     400 ..     312     410 .. 0.63
   4 ?   -1.0   1.8     0.094   5.6e+02     373     409 ..     487     582 ..     448     609 .. 0.59

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.0069
                           DUF2207 381 kklsalglgliilglilillallllvll....lvfllilllillliaiivlllfsrllgr 436
                                        kl +  +++++ +li+++++++++ +l      f ++l +++l++ i+++ll  ++l  
  gi|385805739|ref|YP_005842137.1|  58 SKLLMNTFLIAVPSLIISVYLFIQFKALvlnlKAFGVVLPILILFAPILYFLLRIAFLNS 117
                                       344444444444444444444444444444448888888888888888888887777655 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 3.3e-06
                           DUF2207 319 EkalldlLfdkseegks..........lkeikkyakkskkkakkfkkalkkwksavkk..........kergyfdkk 375
                                       E +l+d+++++++   +          l++i++ ak+     k+f++++  + s ++           k++ yf++k
  gi|385805739|ref|YP_005842137.1| 156 ESDLFDAIKKEAQLI-KrnmrifgldsLSAIESVAKNH--PSKEFREFMIGYVSTIRGggdvvhylqlKTESYFKEK 229
                                       556666666333322.1346666755555555555553..6788888888888888889999999***99******* PP

                           DUF2207 376 gkkklkklsalglgliilglilillallllvll.....................lvfllilllillliaiivlllfs 431
                                       ++   k +  +g++l   ++i+++++l +++++                     +v ++++l+ ++ i++i+++   
  gi|385805739|ref|YP_005842137.1| 230 ERDMDKLVEGVGTVLSTYMIIFVVVGL-TINIIiavqggglsqyigssmsatpmIVTFNFILMPIVTIFSIIIVG-- 303
                                       988888888888887777777665554.3444458889999*******988877666666666666665555555.. PP

                           DUF2207 432 rllgrrteeG 441
                                       ++l++++  +
  gi|385805739|ref|YP_005842137.1| 304 GILPKYNVVY 313
                                       4677766554 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.0045
                           DUF2207 381 kklsalglgliilglilillallllvll......lvfllilllillliaiivlllfsrllgrrteeGaellakwkgF 451
                                        +++ l+l+++ ++++l+                  + + l++  + ia+i++ ++ +l +rr e+  +  ++   +
  gi|385805739|ref|YP_005842137.1| 321 GISIPLSLFAFSILMALGG--------YrvftspDRMSVNLAISAIGIAFILASIPPMLAYRRIEKMERNISR--YL 387
                                       3333333333333333333........1334556666677777777777778888888899999999888888..55 PP

                           DUF2207 452 kkyLeDfsefker 464
                                         +L+D se++++
  gi|385805739|ref|YP_005842137.1| 388 GSFLTDLSEIRKA 400
                                       5899999999887 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 0.094
                           DUF2207 373 dkkgkkklkklsalglgliilglilillallllvll......................................... 408
                                       +++ k+ l +  +l  ++ il ++ ++++++l+v+                                          
  gi|385805739|ref|YP_005842137.1| 487 ENQLKTSLRSDVFLPYIGSILNIVSTVMIIYLMVTSlhvmnptgasavgayssvnparlssltfqlllgllmnswla 563
                                       44444444444444444444444444444444444444455558888888888888887666666666666666666 PP

                           DUF2207 409 ..................l 409
                                                          
  gi|385805739|ref|YP_005842137.1| 564 gllvgksisltvaggfkhA 582
                                       6666666666655554443 PP

>> DUF3483  Domain of unknown function (DUF3483)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1      0.99   5.9e+03     129     158 ..     324     354 ..     316     370 .. 0.57
   2 ?    9.4   4.6   0.00012      0.73      81     169 ..     503     594 ..     496     610 .] 0.64

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 0.99
                           DUF3483 129 LpksLlafalglllvallaal.edvlsella 158
                                       +p+sL af++ ++l    + +  d +s  la
  gi|385805739|ref|YP_005842137.1| 324 IPLSLFAFSILMALGGYRVFTsPDRMSVNLA 354
                                       5667777776655554444433344444333 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00012
                           DUF3483  81 layglalasasldwlllaaal..vmlvGallvakRRrakparLSkGrwqrLpksLlafalglllvallaaledvlse 155
                                       +  +l++ s+++   l++++l  +  +Ga  v +  + +parLS   +q L  +L+   l+ llv   + l+ +++ 
  gi|385805739|ref|YP_005842137.1| 503 IGSILNIVSTVMIIYLMVTSLhvMNPTGASAVGAYSSVNPARLSSLTFQLLLGLLMNSWLAGLLVGKSISLTVAGGF 579
                                       666788888877777777766525569**********************9988888766666666555555333444 PP

                           DUF3483 156 llalvllal.vaaga 169
                                         a++l+++ +a+++
  gi|385805739|ref|YP_005842137.1| 580 KHAVILVTVsLAVSL 594
                                       444433332022333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (610 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       902  (0.0503096); 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:                         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: 0.69u 0.33s 00:00:01.02 Elapsed: 00:00:00.52
# Mc/sec: 3527.13
//
Query:       gi|385805740|ref|YP_005842138.1|  [L=554]
Description: putative Type II/IV secretion system protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-47  162.2   0.0      2e-47  161.6   0.0    1.2  1  T2SSE            Type II/IV secretion system protein
     0.0025   18.3   0.0     0.0053   17.3   0.0    1.5  1  ABC_tran         ABC transporter
     0.0033   17.1   0.1     0.0068   16.1   0.1    1.5  1  AAA_29           P-loop containing region of AAA domain
     0.0038   17.6   0.0     0.0069   16.8   0.0    1.4  1  AAA_16           AAA ATPase domain
  ------ inclusion threshold ------
      0.015   14.6   0.4      0.051   12.9   0.0    1.9  2  FtsK_SpoIIIE     FtsK/SpoIIIE family
      0.026   14.3   0.0      0.045   13.5   0.0    1.4  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.063   12.8   0.0       0.11   12.0   0.0    1.3  1  FBP_C            FBP C-terminal treble-clef zinc-finger
      0.085   12.5   0.1       0.15   11.7   0.1    1.3  1  SRP54            SRP54-type protein, GTPase domain
       0.14   11.8   0.0       0.23   11.1   0.0    1.2  1  AAA_30           AAA domain
       0.18   12.1   0.0        0.4   11.0   0.0    1.6  1  AAA_22           AAA domain
       0.18   11.5   0.9         13    5.4   0.0    2.5  2  Thymidylate_kin  Thymidylate kinase


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 !  161.6   0.0   1.2e-50     2e-47       5     245 ..     165     414 ..     162     430 .. 0.94

  Alignments for each domain:
  == domain 1  score: 161.6 bits;  conditional E-value: 1.2e-50
                             T2SSE   5 leallddekvsdihvekper.vkvrervdgielreveelekaalerlisriaalakldiseerplqdarlpekgvrl 80 
                                       ++ l++d+++ di     ++ + v  r+ +    +++  +++al  ++ ++ ++a+++is   p++da lp +g+rl
  gi|385805740|ref|YP_005842138.1| 165 IDSLMRDPNIEDISCDGVGKpIYVWHRKYESLPTNIKIDDEEALDSFLVKLSHMAGAHISVAFPIVDAILP-GGHRL 240
                                       567899******************99999978888888899999***************************.***** PP

                             T2SSE  81 rvvllPvvag..ealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeink 155
                                        + +   v +   ++++Rk s+  +tl d++  ++l+e++++ l   ++++++ lv G TgsGKtt+l+a+ + i  
  gi|385805740|ref|YP_005842138.1| 241 AGTFKKEVTTkgSSFTVRKFSEDPITLVDMIGWNNLSEEMSAYLWLMLEHKMTGLVLGVTGSGKTTSLNAIASLIRP 317
                                       *9998766554699*************************************************************** PP

                             T2SSE 156 sderivtvEDpvEiqleganqvqlnak.........kakvtfadllraaLRlrPDrimvGEiRdketleilkAvnTG 223
                                       s  ++vt+ED+ E++l  +n vql+++          +++++ dl++ +LR rPD i+vGE+R++e++++++Av TG
  gi|385805740|ref|YP_005842138.1| 318 S-MKVVTIEDTPELRLPLENWVQLVTRqsygigsekIGEINLFDLIKVSLRYRPDYIIVGEVRGEEAYSLMQAVATG 393
                                       *.*******************************998899************************************** PP

                             T2SSE 224 HlgslsTlHansaagalerLeq 245
                                       H g l+TlHa+s+++a++rL  
  gi|385805740|ref|YP_005842138.1| 394 HGG-LTTLHAESVVQAINRLTS 414
                                       *99.****************75 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   3.2e-06    0.0053      12      51 ..     292     331 ..     284     385 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.2e-06
                                       SEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  12 ekvaivGenGaGKStLlkllagllkpteGeilldgkdlke 51 
                                        +  ++G +G+GK+t l+++a l +p +  +++++++  +
  gi|385805740|ref|YP_005842138.1| 292 MTGLVLGVTGSGKTTSLNAIASLIRPSMKVVTIEDTPELR 331
                                       455679**********************999999876555 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   4.2e-06    0.0068      23      51 ..     292     320 ..     267     323 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.2e-06
                            AAA_29  23 gatlltGpsGsGKSTllDAiqalLvpakk 51 
                                        + l+ G +GsGK+T l Ai+ l+ p+ k
  gi|385805740|ref|YP_005842138.1| 292 MTGLVLGVTGSGKTTSLNAIASLIRPSMK 320
                                       356*********************99875 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   4.2e-06    0.0069      28      85 ..     295     349 ..     288     418 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.2e-06
                            AAA_16  28 llsGesGvGKsslvrellralekdg.giflrgkcdqlesaipysalaqalareellrql 85 
                                       l+ G  G+GK++ +++++  ++ +  +++++ + +     +p+  ++q+ +r + +   
  gi|385805740|ref|YP_005842138.1| 295 LVLGVTGSGKTTSLNAIASLIRPSMkVVTIEDTPELR---LPLENWVQLVTR-QSYGIG 349
                                       89****************9999885488899999999...9*999***9966.555444 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.1e-05     0.051      36      61 ..     290     312 ..     261     318 .. 0.82
   2 ?   -1.3   0.1       0.7   1.1e+03     109     136 ..     497     524 ..     481     539 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.1e-05
                                       GGS-.SEEEE--TTSSHHHHHHHHHH CS
                      FtsK_SpoIIIE  36 kkmashllvaGatgsGKStalntLil 61 
                                        km+  +lv+G tgsGK+t ln++ +
  gi|385805740|ref|YP_005842138.1| 290 HKMT--GLVLGVTGSGKTTSLNAI-A 312
                                       5666..9***************94.4 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.7
                                       HHHHHHHHHHHHHHHHHTT-SSHHHHHH CS
                      FtsK_SpoIIIE 109 leeLvkemeeryalfreagvrsiaaydg 136
                                       +e+++ke+e+r+ ++r  + ++ ++y +
  gi|385805740|ref|YP_005842138.1| 497 MEWIEKEIENRKLVLRYLRLEKKRFYLD 524
                                       89**********9999988888777665 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 ?   13.5   0.0   2.8e-05     0.045       2      39 ..     295     326 ..     294     360 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.8e-05
                   Viral_helicase1   2 vvhGvpGcGKStlirkllrtsliltvnrptaelltegk 39 
                                       +v Gv G+GK+t++  +++       +rp+ +++t   
  gi|385805740|ref|YP_005842138.1| 295 LVLGVTGSGKTTSLNAIASL------IRPSMKVVTIED 326
                                       799************99988......555555554433 PP

>> FBP_C  FBP C-terminal treble-clef zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     7e-05      0.11      21      66 ..     258     303 ..     248     320 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7e-05
                             FBP_C  21 rdldelpwddldflgWrDpkaperaylvvelddelvGvaLraaeaa 66 
                                       r+++e p   +d +gW++ + +  ayl + l+++++G++L  + + 
  gi|385805740|ref|YP_005842138.1| 258 RKFSEDPITLVDMIGWNNLSEEMSAYLWLMLEHKMTGLVLGVTGSG 303
                                       57888999999*****************************988633 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   9.1e-05      0.15       5      32 ..     295     322 ..     291     331 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.1e-05
                                       EEEESTTSSHHHHHHHHHHHHHHTTS-E CS
                             SRP54   5 llvGlqGaGKTttlaKLaallkkegkkv 32 
                                       l++G++G+GKTt+l  +a l++ + k v
  gi|385805740|ref|YP_005842138.1| 295 LVLGVTGSGKTTSLNAIASLIRPSMKVV 322
                                       799***************9987766555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00014      0.23      18      45 ..     291     318 ..     276     327 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00014
                            AAA_30  18 drvavltGpAGtGKttalkalreaweaa 45 
                                       +++ ++ G+ G+GKtt+l+a++ +++ +
  gi|385805740|ref|YP_005842138.1| 291 KMTGLVLGVTGSGKTTSLNAIASLIRPS 318
                                       4577899**************9998755 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00024       0.4       4      28 ..     290     314 ..     287     347 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00024
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleq 28 
                                       ++  ++v G +G+GKTt+l+ +++ 
  gi|385805740|ref|YP_005842138.1| 290 HKMTGLVLGVTGSGKTTSLNAIASL 314
                                       677899*************998876 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.008        13       3      25 ..     298     320 ..     296     329 .. 0.81
   2 ?    3.6   0.5     0.028        46     122     169 ..     476     521 ..     471     530 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.008
                                       ESTTSSHHHHHHHHHHHHHHTTE CS
                   Thymidylate_kin   3 GlDGaGKttqaellkerlkeegi 25 
                                       G+ G+GKtt ++++++ ++ + +
  gi|385805740|ref|YP_005842138.1| 298 GVTGSGKTTSLNAIASLIRPSMK 320
                                       899************99888774 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.028
                                       EEEESSHHHHHTSCCTTSSTTTSHHHHHHHHHHHHHHHHHHHHTTSTE CS
                   Thymidylate_kin 122 flldvdpevalkRlakrdeldeeeeeqldflrkvrerylelakederi 169
                                       f++d++++++lk++a+ + +d e  e++   rk+  ryl+l   ++r+
  gi|385805740|ref|YP_005842138.1| 476 FYFDISKSENLKKIAEMRGKDMEWIEKEIENRKLVLRYLRLE--KKRF 521
                                       899*************99999999999999999999999987..4554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (554 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 3906.94
//
Query:       gi|385805741|ref|YP_005842139.1|  [L=978]
Description: hypothetical protein FFONT_0699 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-06   27.5  20.9    8.6e-06   25.9   0.1    5.6  6  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
     0.0083   16.1   0.0          3    7.9   0.0    3.2  3  bMG3             Bacterial alpha-2-macroglobulin MG3 domain
  ------ inclusion threshold ------
      0.018   14.9   1.2       0.96    9.4   0.3    3.1  2  PEGA             PEGA domain
      0.027   13.0   0.0      0.045   12.3   0.0    1.2  1  Cytochrom_D1     Cytochrome D1 heme domain
       0.03   14.3   8.7       0.16   12.0   0.8    3.5  3  Big_1            Bacterial Ig-like domain (group 1)
       0.26   11.5   1.2        4.8    7.4   0.0    3.1  4  MG4              Macroglobulin domain MG4


Domain annotation for each model (and alignments):
>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1     0.086   2.6e+02       8      48 ..     215     254 ..     208     262 .. 0.85
   2 ?   -1.7   0.0       1.2   3.7e+03      32      58 ..     383     408 ..     378     421 .. 0.74
   3 ?   -0.1   0.1      0.38   1.1e+03      42      79 ..     554     590 ..     517     593 .. 0.70
   4 ?   -0.4   0.4      0.48   1.4e+03       5      62 ..     689     747 ..     687     760 .. 0.71
   5 !    9.9   0.9   0.00029      0.85       1      70 [.     775     837 ..     775     847 .. 0.83
   6 !   25.9   0.1   2.9e-09   8.6e-06       6      79 ..     857     928 ..     852     931 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.086
                   CarboxypepD_reg   8 dasgapiagatVtvtnadtgtvastttdadGafrlrglppg 48 
                                       +++ + ++g +V v  ++ +  +   td++G+  ++ +p g
  gi|385805741|ref|YP_005842139.1| 215 SSNSTSVSGIEVLVNFTGVNLISKGITDSNGSLEVS-VPSG 254
                                       5678899********999999**********98875.7765 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.2
                   CarboxypepD_reg  32 tttdadGafrlrglppgtysvtvsapG 58 
                                         + +dG++ + g p gt  + +s++G
  gi|385805741|ref|YP_005842139.1| 383 FDSTKDGSYLILGYPDGT-LIAFSYNG 408
                                       56889******9999987.45555555 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.38
                   CarboxypepD_reg  42 lrglppgtysvtv..sapGyatatreevtltagqtttldi 79 
                                       ++++ +g y++tv    + y++    +v++++ +++++ i
  gi|385805741|ref|YP_005842139.1| 554 FKDVVQGAYTLTVtpYQSIYDPE---AVSIDVTGSSRIPI 590
                                       56788899999992222233333...34444445555555 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 0.48
                   CarboxypepD_reg   5 rVtda.sgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyata 62 
                                       +V d+ +g p +g  ++  n+  g ++s +t  +    ++    g+ sv++s +G  +a
  gi|385805741|ref|YP_005842139.1| 689 QVIDQlTGSPAKGTFLITLNDTLGNSYSSVTQYNTIAYFTLNDVGNMSVEISPSGGSSA 747
                                       68888789999998888887777777777776555555554466888888887776665 PP

  == domain 5  score: 9.9 bits;  conditional E-value: 0.00029
                   CarboxypepD_reg   1 tisGrVtda.sgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtlt 70 
                                       t++ +V+d  sga   ga+V++     g ++++ ++  G+ ++  lp +ty+v v    y+++ + +v l 
  gi|385805741|ref|YP_005842139.1| 775 TLTISVRDLdSGAYARGANVSIG----GLEYTVPSN--GTISII-LPSDTYTVNVGGGIYQSYLQ-AVNLY 837
                                       57889***659************....999988875..99**95.**********9999999997.57776 PP

  == domain 6  score: 25.9 bits;  conditional E-value: 2.9e-09
                   CarboxypepD_reg   6 VtdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtltagqtttldi 79 
                                       V   sg pi+ga V ++  d++ +++  td++G+ r + +p g y + v+ap   ++t+  + ++    +t+ +
  gi|385805741|ref|YP_005842139.1| 857 VSLGSGSPISGAVVNIEGLDNKNSYTFITDSTGEVRAS-IPYGLYAINVTAPYCSSFTQ-IINVNSSSIQTIYV 928
                                       55569*******************************75.******************97.68888777776655 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 ?    2.9   0.0     0.038   1.1e+02      26      60 ..     219     253 ..     204     275 .. 0.82
   2 ?    0.7   0.0      0.17   5.2e+02       8      35 ..     769     796 ..     766     798 .. 0.86
   3 !    7.9   0.0   0.00099         3      19      56 ..     856     893 ..     840     906 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.038
                              bMG3  26 kPvagaeVrlldkkgevlaegtTDaqGvarfaall 60 
                                        +v+g+eV +     +++ +g TD++G ++++ ++
  gi|385805741|ref|YP_005842139.1| 219 TSVSGIEVLVNFTGVNLISKGITDSNGSLEVSVPS 253
                                       578999998888888999*********99998874 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.17
                              bMG3   8 aklgrdkllvwvtsLdsgkPvagaeVrl 35 
                                         + +  l++ v+ Ldsg  + ga+V++
  gi|385805741|ref|YP_005842139.1| 769 IERNNYTLTISVRDLDSGAYARGANVSI 796
                                       567788899***************9985 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.00099
                              bMG3  19 vtsLdsgkPvagaeVrlldkkgevlaegtTDaqGvarf 56 
                                       + sL sg P++ga V++   +++   +  TD++G +r 
  gi|385805741|ref|YP_005842139.1| 856 IVSLGSGSPISGAVVNIEGLDNKNSYTFITDSTGEVRA 893
                                       458*******************************9985 PP

>> PEGA  PEGA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.3   0.00032      0.96      11      62 ..     790     844 ..     787     848 .. 0.82
   2 ?    2.5   0.0     0.046   1.4e+02      27      65 ..     891     929 ..     888     933 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00032
                              PEGA  11 eGatVyidGkylG...kTPvtlsleaGnyslrvekeGYedlektvtvtagetvkl 62 
                                        Ga+V+i+G ++    +  +++ l++ +y++ v    Y+ + + v+++ ++ +++
  gi|385805741|ref|YP_005842139.1| 790 RGANVSIGGLEYTvpsNGTISIILPSDTYTVNVGGGIYQSYLQAVNLYGNTSISI 844
                                       599******999884444555559***********************97776665 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.046
                              PEGA  27 vtlsleaGnyslrvekeGYedlektvtvtagetvklnlt 65 
                                       v+ s++ G y + v +++ + +++ ++v++   ++++++
  gi|385805741|ref|YP_005842139.1| 891 VRASIPYGLYAINVTAPYCSSFTQIINVNSSSIQTIYVK 929
                                       56789***********************98776666655 PP

>> Cytochrom_D1  Cytochrome D1 heme domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.5e-05     0.045       8      70 ..     104     165 ..     101     183 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.5e-05
                                       EEEEGGGTEEEEEETTT-SEEEEEE-STTEEEEEE-TT.SSEEEEEETTSEEEEEESSSSSEE CS
                      Cytochrom_D1   8 vvverdagkvalldgdskeilavletgyalHisrvfasdgRyvyvigRDgkvtliDLwakeiv 70 
                                        vv   +g+v ++d +s+ ++ ++e+g+   +s+++  d Ryv+ +  Dg +  +D+++   +
  gi|385805741|ref|YP_005842139.1| 104 IVVGTSTGEVLIIDESSNYSVRRFEAGFS-QVSQLYVLDSRYVLSLFSDGSMLQYDILNDSWI 165
                                       588899*********************98.69*************************998744 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 ?   12.0   0.8   5.5e-05      0.16      16      62 ..     216     261 ..     209     263 .. 0.86
   2 ?   -0.9   0.2      0.57   1.7e+03      19      42 ..     730     756 ..     729     757 .. 0.84
   3 ?    5.2   0.1    0.0069        21      16      51 ..     860     894 ..     852     895 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.5e-05
                             Big_1  16 angnpvagatVtfsvsggalsassgtTdanGkatvtltstkagtvtv 62 
                                       +n + v+g++V ++ +g +l  s+g+Td+nG  +v++ s  + +++v
  gi|385805741|ref|YP_005842139.1| 216 SNSTSVSGIEVLVNFTGVNL-ISKGITDSNGSLEVSVPSGASLSSSV 261
                                       68899************777.68************998877766665 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.57
                             Big_1  19 npvagatVtfsvsggals...assgtT 42 
                                       n v + +V +s sgg+ +   ++++tT
  gi|385805741|ref|YP_005842139.1| 730 NDVGNMSVEISPSGGSSAqmyQPTSTT 756
                                       668899********8777788888887 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.0069
                             Big_1  16 angnpvagatVtfsvsggalsassgtTdanGkatvt 51 
                                        +g p++ga V+++  ++++ + + +Td+ G+++++
  gi|385805741|ref|YP_005842139.1| 860 GSGSPISGAVVNIEGLDNKN-SYTFITDSTGEVRAS 894
                                       689**********9666555.899********9987 PP

>> MG4  Macroglobulin domain MG4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       3.1   9.3e+03      30      63 ..     221     252 ..     213     272 .. 0.65
   2 ?    1.0   0.1      0.16   4.9e+02      16      63 ..     684     730 ..     682     741 .. 0.76
   3 ?   -3.1   0.0       2.9   8.7e+03      16      61 ..     774     812 ..     773     819 .. 0.69
   4 ?    7.4   0.0    0.0016       4.8      18      62 ..     853     895 ..     852     906 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.1
                               MG4  30 aknvpVkiealkseteekeslttdedGtakfsin 63 
                                       ++++ V +++  ++ +  ++  td++G  ++s+ 
  gi|385805741|ref|YP_005842139.1| 221 VSGIEVLVNF--TGVNLISKGITDSNGSLEVSVP 252
                                       5666666666..2455566778999998888874 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.16
                               MG4  16 fsikVlvkdp.dgspaknvpVkiealkseteekeslttdedGtakfsin 63 
                                       + + ++v d+  gspak+  + +   +    +  s  t+ + +a+f++n
  gi|385805741|ref|YP_005842139.1| 684 YVFGIQVIDQlTGSPAKGTFLITLN-D-TLGNSYSSVTQYNTIAYFTLN 730
                                       5666777766259999998887777.5.56677788899********99 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 2.9
                               MG4  16 fsikVlvkdpd.gspaknvpVkiealkseteekeslttdedGtakfs 61 
                                       ++++++v d d g  a++  V+i  l        ++t  ++Gt++++
  gi|385805741|ref|YP_005842139.1| 774 YTLTISVRDLDsGAYARGANVSIGGL--------EYTVPSNGTISII 812
                                       78888888865477888888888773........3555566666665 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.0016
                               MG4  18 ikVlvkdpdgspaknvpVkiealkseteekeslttdedGtakfsi 62 
                                       + + v+   gsp+++  V ie l+   ++  +  td+ G ++ si
  gi|385805741|ref|YP_005842139.1| 853 LDIIVSLGSGSPISGAVVNIEGLD--NKNSYTFITDSTGEVRASI 895
                                       56889999**************76..4666777899***999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (978 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); 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:                         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: 0.78u 0.33s 00:00:01.11 Elapsed: 00:00:00.49
# Mc/sec: 6007.43
//
Query:       gi|385805742|ref|YP_005842140.1|  [L=133]
Description: hypothetical protein FFONT_0700 [Fervidicoccus fontis Kam940]
Scores for complete 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   17.5   0.1     0.0056   16.8   0.1    1.3  1  UPF0242         Uncharacterised protein family (UPF0242) N-te
     0.0059   16.4   0.1      0.014   15.3   0.1    1.6  1  Matrilin_ccoil  Trimeric coiled-coil oligomerisation domain o
  ------ inclusion threshold ------
      0.095   13.1   0.0       0.11   12.8   0.0    1.3  1  BDV_M           ssRNA-binding matrix protein of Bornaviridae
        0.1   12.5   1.0        4.8    7.0   0.1    2.3  2  CdvA            CdvA-like coiled-coil domain


Domain annotation for each model (and alignments):
>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   1.2e-06    0.0056     131     185 ..       4      58 ..       1      62 [. 0.95

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.2e-06
                           UPF0242 131 edfeelkleleeqLaekqellqeyqetieeqrsvlekrqdqieqLeskVrDlnyE 185
                                       e++e+lk+++e+++ae    l e  + i  ++  +e++    e L  k +D+ yE
  gi|385805742|ref|YP_005842140.1|   4 ENIEKLKQFVEKRIAELSAELGEVLRRIDALHGIVENKRRVFEALGLKLQDRGYE 58 
                                       5799**************************************************9 PP

>> Matrilin_ccoil  Trimeric coiled-coil oligomerisation domain of matrilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1     3e-06     0.014      11      41 ..       4      34 ..       3      41 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3e-06
                                      THHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Matrilin_ccoil 11 EalvkFQtkVeseiqaLtqkLeavtkRleal 41
                                      E++ k+++ Ve++i  L++ L +v +R+ al
  gi|385805742|ref|YP_005842140.1|  4 ENIEKLKQFVEKRIAELSAELGEVLRRIDAL 34
                                      889999**********************998 PP

>> BDV_M  ssRNA-binding matrix protein of Bornaviridae
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.5e-05      0.11      34      81 ..      58     105 ..      26     126 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.5e-05
                             BDV_M  34 rekkltdyftidvepaghslvniyfqiddfllltlnslsvykdpirky 81 
                                          kl   +ti ++p   +lvniy  i + l   ln+    k+ + k 
  gi|385805742|ref|YP_005842140.1|  58 EGIKLGGDITIMIDPPPDALVNIYEGISENLNKELNAYRNLKNALSKL 105
                                       556888999***************************999999988775 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1    0.0085        38      38      61 ..       6      29 ..       3      48 .. 0.67
   2 ?    7.0   0.1    0.0011       4.8      86     116 ..      80     110 ..      75     116 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0085
                              CdvA 38 akelkeklkkrlkeledqikslek 61
                                       ++lk+ ++kr++el  ++ ++ +
  gi|385805742|ref|YP_005842140.1|  6 IEKLKQFVEKRIAELSAELGEVLR 29
                                      456666666677666666655543 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0011
                              CdvA  86 airellesaleekeeikklleklskleleee 116
                                       ++++  e++++e+++ ++l++ lskl +++e
  gi|385805742|ref|YP_005842140.1|  80 IYEGISENLNKELNAYRNLKNALSKLLSSPE 110
                                       5677789999999999999999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 846.84
//
Query:       gi|385805743|ref|YP_005842141.1|  [L=167]
Description: PadR family transcriptional regulator [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-15   56.6   0.5    3.4e-15   55.7   0.2    1.6  2  PadR             Transcriptional regulator PadR-like family
    0.00011   20.7   1.5    0.00016   20.2   1.5    1.2  1  DUF505           Protein of unknown function (DUF505)
     0.0016   18.3   0.9      0.006   16.5   0.9    2.1  1  HTH_45           Winged helix-turn-helix
     0.0037   17.0   1.8     0.0037   17.0   1.8    1.9  2  DUF4364          Domain of unknown function (DUF4364)
     0.0073   16.9   3.5      0.029   15.0   1.5    2.2  2  RTP              Replication terminator protein
  ------ inclusion threshold ------
      0.029   14.7   0.1       0.25   11.7   0.1    2.4  1  Penicillinase_R  Penicillinase repressor
      0.069   13.3   0.5       0.49   10.5   0.0    2.4  3  FUR              Ferric uptake regulator family
      0.071   13.0   0.3      0.071   13.0   0.3    2.2  3  DUF3116          Protein of unknown function (DUF3116)
      0.076   13.4   0.0       0.12   12.7   0.0    1.4  1  Nitro_FeMo-Co    Dinitrogenase iron-molybdenum cofactor
       0.11   13.1   0.1       0.27   11.9   0.0    1.8  2  YbjQ_1           Putative heavy-metal-binding
       0.15   12.1   0.0       0.19   11.8   0.0    1.2  1  Replic_Relax     Replication-relaxation
       0.71   10.1   4.8        2.2    8.5   1.1    2.2  2  DUF5618          Domain of unknown function (DUF5618)


Domain annotation for each model (and alignments):
>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   0.2   2.3e-18   3.4e-15       2      75 .]      29      97 ..      27      97 .. 0.94
   2 ?   -2.8   0.0       4.2   6.3e+03      29      41 ..     115     127 ..     103     144 .. 0.64

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 2.3e-18
                                      HHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHHH CS
                              PadR  2 LalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrelae 75
                                      ++ lee+ + Gyei+k +e +++g++ +s+G +Yp+L+ Le+ ++v+s+       +++k+Y lT++G+++l+e
  gi|385805743|ref|YP_005842141.1| 29 MYFLEEKSMSGYEIMKTIESYFNGEYSPSPGIVYPTLQMLEEVEFVKSQAI-----GNKKIYMLTEKGKKYLEE 97
                                      57799******************************************9966.....59*************986 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.2
                                       TTHHHHHHHHHHH CS
                              PadR  29 lseGslYpaLkrL 41 
                                       l++ +++  Lk+L
  gi|385805743|ref|YP_005842141.1| 115 LKDNTIFNSLKKL 127
                                       4555555555555 PP

>> DUF505  Protein of unknown function (DUF505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   1.5   1.1e-07   0.00016     324     411 ..      14     105 ..       4     114 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.1e-07
                            DUF505 324 eYkellekYGRkleempkkkeeiakkfeeakdlekWyednfd.....lreaLysLesfeLieseveekgkevyvlTe 395
                                       + k++++k G k+  m+  +e+  + +e +k++e +++ +++     +   L  Le +e+++s+    +k++y+lTe
  gi|385805743|ref|YP_005842141.1|  14 DSKRIMQKGGFKMILMYFLEEKSMSGYEIMKTIESYFNGEYSpspgiVYPTLQMLEEVEFVKSQA-IGNKKIYMLTE 89 
                                       568899999999999999999999999999999999998887555545889*************5.688******** PP

                            DUF505 396 yGekvledqekklrev 411
                                       +G+k le+++++++ +
  gi|385805743|ref|YP_005842141.1|  90 KGKKYLEENREEVEAI 105
                                       *******998776665 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.9     4e-06     0.006      40      71 ..      65     100 ..      60     116 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4e-06
                            HTH_45  40 LdmLvekgli....kkskekYvlTekGlelleklke 71 
                                       L+mL e +++      +k+ Y+lTekG+++le+ +e
  gi|385805743|ref|YP_005842141.1|  65 LQMLEEVEFVksqaIGNKKIYMLTEKGKKYLEENRE 100
                                       89********6533338999***********98765 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       3.4   5.1e+03       2      11 ..      25      34 ..      24      51 .. 0.67
   2 !   17.0   1.8   2.5e-06    0.0037      39      83 ..      64     108 ..      60     160 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.4
                           DUF4364  2 KllilYllkk 11
                                      K++++Y+l++
  gi|385805743|ref|YP_005842141.1| 25 KMILMYFLEE 34
                                      6777777765 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 2.5e-06
                           DUF4364  39 alseLvesglieeeekenktlykiTekGketlelfenripksire 83 
                                       +l+ L+e ++++++   nk++y +TekGk+ le+  +++   +r+
  gi|385805743|ref|YP_005842141.1|  64 TLQMLEEVEFVKSQAIGNKKIYMLTEKGKKYLEENREEVEAILRK 108
                                       6889******************************99998876665 PP

>> RTP  Replication terminator protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   1.5   1.9e-05     0.029       5      99 ..      19     105 ..      16     117 .. 0.77
   2 ?    4.0   0.8      0.05        75      11      71 ..      83     143 ..      73     160 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.9e-05
                                       -HHHHHHHHHHHHHHTT-EBCTCHHHHHHHHHTTTT----HHHHHHHHHHHHHTTSEEEEEEEBTSSSSSEEEEEEE CS
                               RTP   5 kqrAFlklylitlvekkklyglklldelkkeFkelgykPnhseiyralhelvedgilkrrkelkekaklqevviYsl 81 
                                        q+   k+ l+ ++e+k + g++++ ++ + F+   y+P++  +y +l+ l e  ++k +   +     +   iY l
  gi|385805743|ref|YP_005842141.1|  19 MQKGGFKMILMYFLEEKSMSGYEIMKTIESYFN-GEYSPSPGIVYPTLQMLEEVEFVKSQAIGN-----K--KIYML 87 
                                       5777789*********************99996.57************9999888876543322.....2..25777 PP

                                       SS..HHHHHHHHHHHHHH CS
                               RTP  82 tdeGkekaklykkqvkid 99 
                                       t++Gk  ++  + +v + 
  gi|385805743|ref|YP_005842141.1|  88 TEKGKKYLEENREEVEAI 105
                                       777777777666666555 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.05
                                       HHHHHHHHHTT-EBCTCHHHHHHHHHTTTT..----HHHHHHHHHHHHHTTSEEEEEEEBTSS CS
                               RTP  11 klylitlvekkklyglklldelkkeFkelg..ykPnhseiyralhelvedgilkrrkelkeka 71 
                                       k+y++t  ek k+y  +  +e+ +  +++    + ++ +i+++l+ l+    l+  +  +eka
  gi|385805743|ref|YP_005842141.1|  83 KIYMLT--EKGKKYLEENREEVEAILRKIRevSSLKDNTIFNSLKKLIGTLHLYSSEINEEKA 143
                                       788875..7788888888888887777776545667889999999999777776655444333 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00017      0.25      20      78 ..      43     101 ..      25     152 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
                                       HHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE----XXXXXXXXXXX CS
                   Penicillinase_R  20 vkevveeleeekelaysTVktllrrLvkKgllsrekegrafiYsplvseeeavasavkq 78 
                                       +k + + ++ e+++++  V  +l+ L++ ++++++  g++ iY  + + ++++++  ++
  gi|385805743|ref|YP_005842141.1|  43 MKTIESYFNGEYSPSPGIVYPTLQMLEEVEFVKSQAIGNKKIYMLTEKGKKYLEENREE 101
                                       5678888999999999****************************999999998765444 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00033      0.49      42      74 ..      58      89 ..      25      98 .. 0.79
   2 ?    0.8   0.4      0.36   5.3e+02      27      53 ..     100     128 ..      82     160 .. 0.55
   3 ?   -2.2   0.0         3   4.5e+03       9      19 ..     153     163 ..     150     166 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00033
                                      HHHHHHHHHHHHHTTSEEEEEETTSEEEEEESS CS
                               FUR 42 laTVYrtLklleeaglvkelefedgesryelak 74
                                         VY tL++lee+++vk+  +  +++ y l++
  gi|385805743|ref|YP_005842141.1| 58 PGIVYPTLQMLEEVEFVKSQAIG-NKKIYMLTE 89
                                      556****************9998.888888876 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.36
                                       HHHHHHHHHTTTT--H..HHHHHHHHHHH CS
                               FUR  27 eevykelkeedpeisl..aTVYrtLklle 53 
                                       eev   l++ ++  sl   T+++ Lk l 
  gi|385805743|ref|YP_005842141.1| 100 EEVEAILRKIREVSSLkdNTIFNSLKKLI 128
                                       34444443322222222246666666554 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 3
                                       HHHHHHHHHHH CS
                               FUR   9 qRekilevlek 19 
                                        R+ki++++e 
  gi|385805743|ref|YP_005842141.1| 153 ARKKIIKIFEG 163
                                       69999999975 PP

>> DUF3116  Protein of unknown function (DUF3116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       2.7   4.1e+03      48      54 ..      29      35 ..      10      47 .. 0.74
   2 ?   13.0   0.3   4.8e-05     0.071      51      82 ..      68      97 ..      61     106 .. 0.84
   3 ?   -2.7   0.0       3.8   5.6e+03       2      23 ..     139     160 ..     138     162 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.7
                           DUF3116 48 vYWLElk 54
                                      +Y LE+k
  gi|385805743|ref|YP_005842141.1| 29 MYFLEEK 35
                                      5666655 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 4.8e-05
                           DUF3116 51 LElkgyilRkeekannkkrYelTekGellyke 82
                                      LE+ ++++ +   + nkk Y lTekG++ ++e
  gi|385805743|ref|YP_005842141.1| 68 LEEVEFVKSQA--IGNKKIYMLTEKGKKYLEE 97
                                      88889987655..58************98865 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 3.8
                           DUF3116   2 kePseelilevLelvkdpnfti 23 
                                       +e++++++ e+L  ++++ ++i
  gi|385805743|ref|YP_005842141.1| 139 NEEKAKAVTEILDDARKKIIKI 160
                                       5677777788887777776665 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 ?   12.7   0.0   8.3e-05      0.12      37      94 ..      52     110 ..      32     111 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.3e-05
                                       CTSSCSSTHHHHHHHH.TT-SEEEESSSCHHHHHHHCTTTSEEEES-SSBHHHHHHHHH CS
                     Nitro_FeMo-Co  37 daegggggklaqllae.egvdvvivgkiGpralakleaagievykgaggtveealkevl 94 
                                       ++ +  +g +  +l++ e v+ v  ++iG + +  l ++g + ++  +++ve++l++++
  gi|385805743|ref|YP_005842141.1|  52 GEYSPSPGIVYPTLQMlEEVEFVKSQAIGNKKIYMLTEKGKKYLEENREEVEAILRKIR 110
                                       455566677778899999************************************99875 PP

>> YbjQ_1  Putative heavy-metal-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0         7   1.1e+04       8      40 ..      36      47 ..      29      55 .. 0.55
   2 ?   11.9   0.0   0.00018      0.27      33      71 ..     118     155 ..      86     157 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 7
                            YbjQ_1  8 siegkeivevlgivtgetvrsrnvlkdilaglr 40
                                      s++g+ei +++                     +
  gi|385805743|ref|YP_005842141.1| 36 SMSGYEIMKTI---------------------E 47
                                      45555555444.....................3 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00018
                            YbjQ_1  33 kdilaglrslvGGelkayeeeleeareeAlerlkeeAee 71 
                                       ++i+++l++l+G  l+ y++e++e + +A+ ++ ++A++
  gi|385805743|ref|YP_005842141.1| 118 NTIFNSLKKLIG-TLHLYSSEINEEKAKAVTEILDDARK 155
                                       4699*******9.9*********************9987 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00013      0.19      30      82 ..      64     108 ..      32     121 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00013
                      Replic_Relax  30 rLarLrelgllsrlrkrvggarggsepyvYaLtpkGarllaaqraepeprskr 82 
                                        L+ L+e +++++  +    +    ++ +Y Lt+kG+++l+++r+e e+  ++
  gi|385805743|ref|YP_005842141.1|  64 TLQMLEEVEFVKS--QA---I---GNKKIYMLTEKGKKYLEENREEVEAILRK 108
                                       5555555555555..22...3...3488************7777655543322 PP

>> DUF5618  Domain of unknown function (DUF5618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1     0.074   1.1e+02      19      70 ..       3      49 ..       1      55 [. 0.70
   2 ?    8.5   1.1    0.0015       2.2      53     121 ..      87     160 ..      81     162 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.074
                                      HHS-EETTEE--HHHHHHHHHHHHHHHHHHHHHHH---S...SS-.--HHHH CS
                           DUF5618 19 ekakkedklYkdkkyvkeAggtAYsgvLlaldellgkkglekkkrpksvetY 70
                                      ++ kked +++d+k + + gg  ++   ++l  +l++k ++  +  k +e Y
  gi|385805743|ref|YP_005842141.1|  3 KRRKKEDYIFEDSKRIMQKGG--FK---MILMYFLEEKSMSGYEIMKTIESY 49
                                      567899999999999877654..34...444456777777667777777777 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0015
                                       H---S....SS-.--HHHHHHHHHC....C-HHHHHHHHHHHHHHIIIICCT---BHHHHHHHHHHHHHHHHHH CS
                           DUF5618  53 lgkkglek.kkrpksvetYkealkk....ldkkllkefnsaydvLhlagyydGiksakvvkeglkaaeklikki 121
                                       l++kg +  ++ +++ve    ++++    +d+++ ++++++  +Lhl  +    ++ak v e l+ a k i ki
  gi|385805743|ref|YP_005842141.1|  87 LTEKGKKYlEENREEVEAILRKIREvsslKDNTIFNSLKKLIGTLHLYSSEINEEKAKAVTEILDDARKKIIKI 160
                                       666775555777799999999998888899*******************99999***********998877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1640  (0.0914719); expected 358.6 (0.02)
Passed bias filter:                      809  (0.0451224); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 1069.40
//
Query:       gi|385805744|ref|YP_005842142.1|  [L=337]
Description: ABC transporter ATP-binding protein [Fervidicoccus fontis Kam940]
Scores for complete 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-29  101.4   0.0    1.3e-28  100.2   0.0    1.6  2  ABC_tran  ABC transporter
    2.3e-14   53.9   0.4    4.8e-14   52.8   0.4    1.6  1  DUF4162   Domain of unknown function (DUF4162)
    6.5e-12   45.9   0.9      2e-07   31.1   0.0    2.4  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
     0.0007   19.4   1.7       0.24   11.1   0.0    2.9  3  AAA_15    AAA ATPase domain
     0.0052   16.5   0.2     0.0098   15.6   0.2    1.4  1  AAA_29    P-loop containing region of AAA domain
     0.0073   16.8   2.1      0.024   15.1   0.3    2.3  2  AAA_23    AAA domain
  ------ inclusion threshold ------
       0.01   16.2   1.0       0.24   11.8   1.0    2.6  1  AAA       ATPase family associated with various cellular acti
      0.011   15.7   0.1       0.45   10.6   0.0    2.4  2  PepSY_2   Peptidase propeptide and YPEB domain
      0.012   15.1   0.3        2.2    7.7   0.0    2.3  2  SMC_N     RecF/RecN/SMC N terminal domain
      0.046   13.4   0.4      0.082   12.5   0.4    1.4  1  SRP54     SRP54-type protein, GTPase domain
      0.046   13.4   0.2       0.97    9.1   0.0    2.2  2  AAA_24    AAA domain
      0.064   13.0   0.0       0.11   12.2   0.0    1.4  1  AAA_30    AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.2   0.0   8.6e-32   1.3e-28       2     136 ..      21     163 ..      20     164 .. 0.95
   2 ?   -2.3   0.0       3.9   5.9e+03       8      93 ..     241     254 ..     193     285 .. 0.70

  Alignments for each domain:
  == domain 1  score: 100.2 bits;  conditional E-value: 8.6e-32
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       k +s+k+++ge+  ++G+nGaGK+t +++l+ l +pt+G  ++ g d+ + + +++r+ ig +pq+   +++l+  +
  gi|385805744|ref|YP_005842142.1|  21 KGISFKVEHGEVFSLLGPNGAGKTTTISILTTLINPTKGVAKVGGYDVVT-QANKVRSIIGLVPQDVVTDDDLSGWD 96 
                                       789*********************************************99.8999********************** PP

                                       H.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       n              + +++e++l+ ++lke+++++     +++SgG+++r++la+all +pk+l+lDEpt
  gi|385805744|ref|YP_005842142.1|  97 NlmiqaslyhlprsVAVKRAEELLEFMELKEFANKKT----ETYSGGMRRRLELAAALLHRPKILFLDEPT 163
                                       ********99987766777999999999999999888....*****************************9 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.9
                                       EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHHHHHTC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvrenesdee 84 
                                       +k+ e                                                                        
  gi|385805744|ref|YP_005842142.1| 241 IKREE------------------------------------------------------------------------ 245
                                       33333........................................................................ PP

                                       HHHHHHHST CS
                                       xxxxxxxxx RF
                          ABC_tran  85 iekalsklg 93 
                                       ++k+ls+ g
  gi|385805744|ref|YP_005842142.1| 246 VQKILSSNG 254
                                       333333333 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.8   0.4   3.2e-17   4.8e-14       1      81 []     218     312 ..     218     312 .. 0.86

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 3.2e-17
                                       E-HHHHHTTS-SSEEEEE......-------.......--.-EEEE-TT.S-EEEEE--.-----------.----E CS
                           DUF4162   1 GtleeiKrsygknrieve......adaeellee.....pg.veeveeeg.gelelkled.eeaanellkal.tsgve 62 
                                       Gt++e+K+s+g+++ie++      +  ee++++     +g v+ev+  + g l++k  + ee+ +e++++l ++g++
  gi|385805744|ref|YP_005842142.1| 218 GTPKELKDSLGGDIIEIQlisdqiK-REEVQKIlssngNGsVKEVSIGDsGLLRIKTANgEEVLPEIITKLyEKGYK 293
                                       9*****************9954330.33333337778888899999988788******99***********99**** PP

                                       EEEEEEE---HHHHHHHHH CS
                           DUF4162  63 irsFeeeePsLndIFiekv 81 
                                       i+s+ +++PsL+++F++++
  gi|385805744|ref|YP_005842142.1| 294 IKSVDLKKPSLDEVFLQYT 312
                                       ****************986 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   0.3   4.6e-05     0.069       3      22 ..      34      53 ..      32      74 .. 0.81
   2 !   31.1   0.0   1.3e-10     2e-07     238     297 ..     137     194 ..      89     198 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.6e-05
                            AAA_21  3 vliGpNgsGKSnLLdaldll 22
                                       l GpNg+GK++ + +l  l
  gi|385805744|ref|YP_005842142.1| 34 SLLGPNGAGKTTTISILTTL 53
                                      589**************666 PP

  == domain 2  score: 31.1 bits;  conditional E-value: 1.3e-10
                            AAA_21 238 SdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTH 297
                                       S G++r l l++all ++   ++l++DEp +gL+ ++ + ++  +++l++ ++  ++ltTH
  gi|385805744|ref|YP_005842142.1| 137 SGGMRRRLELAAALLHRP---KILFLDEPTLGLDVQVRTAVWNYINRLRKeEDMTIFLTTH 194
                                       99****************...9***********************99998999******** PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00016      0.24      19      50 ..      27      57 ..      21     119 .. 0.79
   2 !    5.9   0.0    0.0061       9.1     323     364 ..     153     194 ..     134     195 .. 0.93
   3 ?   -0.4   0.9       0.5   7.5e+02     185     257 ..     222     295 ..     197     327 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00016
                            AAA_15 19 idlseeltvliGkNnsGKSsilealdlFlnnk 50
                                      ++  e +  l G+N++GK++ + +l  ++n +
  gi|385805744|ref|YP_005842142.1| 27 VEHGE-VFSLLGPNGAGKTTTISILTTLINPT 57
                                      55455.77899*****************9977 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0061
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                       +++il+++EP + L  q  + +++++ +l +++++ +++tTH
  gi|385805744|ref|YP_005842142.1| 153 RPKILFLDEPTLGLDVQVRTAVWNYINRLRKEEDMTIFLTTH 194
                                       5789************************************** PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.5
                            AAA_15 185 elknvlksaiiklllisakRnvsdedsekkssllgklkekileealqekl.eeelteklkeiqeklkeidkkla 257
                                       elk +l   ii+++lis++ + ++ ++  +s+  g++ke  + +++  +  + + +e l+ei +kl e+  k++
  gi|385805744|ref|YP_005842142.1| 222 ELKDSLGGDIIEIQLISDQIKREEVQKILSSNGNGSVKEVSIGDSGLLRIkTANGEEVLPEIITKLYEKGYKIK 295
                                       55566666666777777777777777777777777777777776654444655566666666666666665553 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   0.2   6.6e-06    0.0098      16      50 ..      24      58 ..      16      62 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 6.6e-06
                            AAA_29 16 tieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      +++++  +++ l Gp+G+GK+T +  +++l+ p+k
  gi|385805744|ref|YP_005842142.1| 24 SFKVEHGEVFSLLGPNGAGKTTTISILTTLINPTK 58
                                      56666555999*************88888888876 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.3   1.6e-05     0.024      15      40 ..      23      51 ..      11      72 .. 0.82
   2 ?    0.7   0.0      0.41   6.2e+02     153     180 ..     203     245 ..     106     277 .. 0.57

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.6e-05
                            AAA_23 15 idF...skgltlItGpNGaGKTTildAik 40
                                      i F   +  ++ + GpNGaGKTT +  ++
  gi|385805744|ref|YP_005842142.1| 23 ISFkveHGEVFSLLGPNGAGKTTTISILT 51
                                      444444446999***********997776 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.41
                            AAA_23 153 e...............rleelekeleeledekkllekleqeke 180
                                       +                 +el+++l     e++l+ ++++++e
  gi|385805744|ref|YP_005842142.1| 203 SdrvaiidygeikiigTPKELKDSLGGDIIEIQLISDQIKREE 245
                                       1333333333333333344455555555555555555554444 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   1.0   0.00016      0.24       3     117 ..      35     201 ..      33     210 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00016
                                       EESSTTSSHHHHHHHHHHHHTHE...................................................... CS
                               AAA   3 lyGppGtGKTllakavakelgve...................................................... 25 
                                       l Gp G GKT++++ + + ++ +                                                      
  gi|385805744|ref|YP_005842142.1|  35 LLGPNGAGKTTTISILTTLINPTkgvakvggydvvtqankvrsiiglvpqdvvtdddlsgwdnlmiqaslyhlprsv 111
                                       78**************9998633343344455555555566666666666666666666666666666666666666 PP

                                       ........EEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHH CS
                               AAA  26 ........fleisgsellskyvgesekkirelfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLltel 93 
                                               +  ++++e+ +k  +  +  +r  ++ a +   +p+ilf+DE       +          v  +  + +
  gi|385805744|ref|YP_005842142.1| 112 avkraeelLEFMELKEFANKKTETYSGGMRRRLELAAALLhRPKILFLDEPTLGLDVQ----------VRTAVWNYI 178
                                       6666666433444445555555555555555555554444568999999966555444..........666677777 PP

                                       HHTTTSSSTEEEEEEESSGGGSTH CS
                               AAA  94 dgvkkkeskvivigatnrpdkldp 117
                                       ++++k+ +++++ ++t+++d+ d+
  gi|385805744|ref|YP_005842142.1| 179 NRLRKE-EDMTIFLTTHYMDEADK 201
                                       777774.44777777777777665 PP

>> PepSY_2  Peptidase propeptide and YPEB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0    0.0003      0.45      27      63 ..     238     275 ..     235     283 .. 0.88
   2 ?    2.7   0.0     0.086   1.3e+02      35      52 ..     283     300 ..     280     316 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0003
                           PepSY_2  27 adwlpreklvakleaqGy.kvkkievddggcyEvegld 63 
                                       +d+++re+++++l  +G  +vk++ + d g   +++++
  gi|385805744|ref|YP_005842142.1| 238 SDQIKREEVQKILSSNGNgSVKEVSIGDSGLLRIKTAN 275
                                       6899*************************999999544 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.086
                           PepSY_2  35 lvakleaqGykvkkievd 52 
                                       + +kl ++Gyk+k+++++
  gi|385805744|ref|YP_005842142.1| 283 IITKLYEKGYKIKSVDLK 300
                                       67899*********9985 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1    0.0084        12      26      41 ..      32      47 ..      19      63 .. 0.83
   2 ?    7.7   0.0    0.0015       2.2     151     208 ..     146     202 ..      99     211 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0084
                                      EEEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxxx RF
                             SMC_N 26 ftaivGpNGSGKsnll 41
                                      + +++GpNG+GK+  +
  gi|385805744|ref|YP_005842142.1| 32 VFSLLGPNGAGKTTTI 47
                                      56799*******9765 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0015
                                       HHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 151 fAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadkl 208
                                       +A    ++  + +lDe    LD + +++v +++++ +k+  +  i l+++ + +adkl
  gi|385805744|ref|YP_005842142.1| 146 LAAALLHRPKILFLDEPTLGLDVQVRTAVWNYINRLRKEEDM-TIFLTTHYMDEADKL 202
                                       34444444556789********************98877554.344555556666655 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.4   5.5e-05     0.082       3      27 ..      32      56 ..      30      72 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.5e-05
                                      EEEEEESTTSSHHHHHHHHHHHHHH CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkk 27
                                      v+ l+G++GaGKTtt++ L  l++ 
  gi|385805744|ref|YP_005842142.1| 32 VFSLLGPNGAGKTTTISILTTLINP 56
                                      67799***********999887765 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0   0.00065      0.97       6      42 ..      34      67 ..      30     136 .. 0.78
   2 ?    2.2   0.0     0.088   1.3e+02     106     149 ..     169     213 ..     168     226 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00065
                            AAA_24  6 liyGpsgiGKTtlakelgpkplfidtekGlksldadk 42
                                       + Gp+g+GKTt+++ l   + +i+  kG++++ + +
  gi|385805744|ref|YP_005842142.1| 34 SLLGPNGAGKTTTISIL---TTLINPTKGVAKVGGYD 67
                                      589***********999...55555556666665555 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.088
                            AAA_24 106 elaeefrrllkklqelrk.nvifiahektrkdedpegeakytrle 149
                                       ++++ +++++++l++  + ++ ++ h   + d+  ++ a +++ e
  gi|385805744|ref|YP_005842142.1| 169 QVRTAVWNYINRLRKEEDmTIFLTTHYMDEADKLSDRVAIIDYGE 213
                                       6889999******999999*********99999987775555544 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   7.3e-05      0.11      19      51 ..      31      70 ..      23     135 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.3e-05
                            AAA_30 19 rvavltGpAGtGKttalkalreaweaa.g......grvig 51
                                       v  l Gp G+GKtt+++ l+ +++   g      ++v+ 
  gi|385805744|ref|YP_005842142.1| 31 EVFSLLGPNGAGKTTTISILTTLINPTkGvakvggYDVVT 70
                                      477899**************99999885576666644443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       774  (0.0431703); expected 358.6 (0.02)
Passed bias filter:                      610  (0.0340231); 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: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 2091.21
//
Query:       gi|385805745|ref|YP_005842143.1|  [L=294]
Description: ABC transporter [Fervidicoccus fontis Kam940]
Scores for complete 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-31  108.6  22.3    2.1e-30  105.7  22.3    2.0  1  ABC2_membrane    ABC-2 type transporter
    1.5e-16   60.5  26.8    1.5e-16   60.5  26.8    1.5  2  ABC2_membrane_3  ABC-2 family transporter protein
    1.1e-09   38.0  22.1    1.6e-09   37.5  22.1    1.1  1  ABC2_membrane_2  ABC-2 family transporter protein
  ------ inclusion threshold ------
        3.1    7.7  17.8        1.8    8.5  14.1    2.5  2  ABC2_membrane_4  ABC-2 family transporter protein
        4.7    6.7  19.3        2.5    7.6  16.9    1.9  1  ABC2_membrane_5  ABC-2 family transporter protein
        7.4    6.5   7.7         13    5.7   0.1    3.3  3  Deltameth_res    Deltamethrin resistance


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 !  105.7  22.3     7e-34   2.1e-30       2     209 ..      11     254 ..      10     255 .. 0.84

  Alignments for each domain:
  == domain 1  score: 105.7 bits;  conditional E-value: 7e-34
                     ABC2_membrane   2 qikallkreflqrwrdpslgllwrliqplllalvfgtvfgnlg..nsedglnr........................ 52 
                                       +i al+ re+++++  p    +++liqp+l++ +fg +f  +g  +      +                        
  gi|385805745|ref|YP_005842143.1|  11 EINALTYRELKKWINKPHVV-IMMLIQPVLWMGLFGKAFNLTGifK------Ipenilnslppyatqavqqifnsil 80 
                                       5889*************888.******************9644432......23333445677777788888999** PP

                     ABC2_membrane  53 ................pgllffsvlflafsaltsvapvferergvlerelvsplyslsayvlakvlvelpvsllqal 113
                                                       +g+ +  +lf +  + t+++++++r+ g l+++l+sp+ s+ +++++kvl+  + +l+q+l
  gi|385805745|ref|YP_005842143.1|  81 tnlfgqanidyfsymaIGMTAVVALFAG--LQTGMSLSWDRRLGYLNKLLASPI-SRGSIIVGKVLGGTVKALVQVL 154
                                       *************966666666666666..9999********************.********************** PP

                     ABC2_membrane 114 ifllivyflvgldls..rfflflllllltalaasslgllisal...apsfedasqlaslvllpllllsGffipidsm 185
                                       +++li++++ gl+l+  +   +++++l ++l+a+++g+l++++   ++s e+ +++++l+ lpl++ s ++ p+ +m
  gi|385805745|ref|YP_005842143.1| 155 VIILIAIPF-GLKLQiaSASAVVAAALGITLFAMGIGMLMISItlrVKSWETQMTVMNLLNLPLMFASNVLTPLAMM 230
                                       ********9.****987445555555555555555555555541116899999************************ PP

                     ABC2_membrane 186 pkwlqwiaylnPltyavealrsnl 209
                                       p+wlq +a++nPltya +++r++l
  gi|385805745|ref|YP_005842143.1| 231 PSWLQTVAKFNPLTYAADIMRQAL 254
                                       *********************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 ?   -0.7   0.5       0.2   5.9e+02     214     231 ..      30      50 ..      28      76 .. 0.59
   2 !   60.5  26.8     5e-20   1.5e-16     138     344 ..      69     284 ..      49     285 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.2
                   ABC2_membrane_3 214 flvyllqlllilll...afgl 231
                                       ++++l+q +l+++l   af+l
  gi|385805745|ref|YP_005842143.1|  30 VIMMLIQPVLWMGLfgkAFNL 50 
                                       456666666666643444442 PP

  == domain 2  score: 60.5 bits;  conditional E-value: 5e-20
                   ABC2_membrane_3 138 atstsaninvestqleeel.snvasflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgd 213
                                       ++   + +n+ +t+l+ ++  ++ s++++ + ++++++ ++++ +s+  +++ + +  +l s++s+ +++++k+lg 
  gi|385805745|ref|YP_005842143.1|  69 TQAVQQIFNSILTNLFGQAnIDYFSYMAIGMTAVVALFAGLQTGMSLSWDRRLGYLNKLLASPISRGSIIVGKVLGG 145
                                       333333444444555544446677777776666666666666999******************************** PP

                   ABC2_membrane_3 214 flvyllqlllilll..afgl..gipfg.nlglllllfllfglayialgyllsslfknsetaqilifivilllsgffg 285
                                        +++l+q+l+i+l+   fgl  +i     ++++ l + lf++ + +l+  ++  +k+ et ++++ +++l+l++++ 
  gi|385805745|ref|YP_005842143.1| 146 TVKALVQVLVIILIaiPFGLklQIASAsAVVAAALGITLFAMGIGMLMISITLRVKSWETQMTVMNLLNLPLMFASN 222
                                       ***********99743355434333333444555******************************************* PP

                   ABC2_membrane_3 286 glfpledlpsalkwifsiiPffapglgllrli...tgdplweillsliilalfavvylllal 344
                                       +l pl  +ps+l++++ ++P+++ ++ + + +   ++++++ei+++l+ila+ a++++ +++
  gi|385805745|ref|YP_005842143.1| 223 VLTPLAMMPSWLQTVAKFNPLTYAADIMRQALimgSYASYAEIMRDLVILAGVAIALITIGV 284
                                       *******************************66665559999***************99876 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 !   37.5  22.1   5.3e-13   1.6e-09       6     282 ..      18     286 ..      14     291 .. 0.71

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 5.3e-13
                   ABC2_membrane_2   6 kEfrdlvrsrrfllltvllpli...............dvalaylkdlgsslqseakaikeatlaleyveaasasdea 67 
                                       +E+++ + ++ +++++++ p++               +    +l++l  + ++ +++i+++ l+  +++a +     
  gi|385805745|ref|YP_005842143.1|  18 RELKKWINKPHVVIMMLIQPVLwmglfgkafnltgifKIPENILNSLPPYATQAVQQIFNSILTNLFGQANI----- 89 
                                       688888888899999999999999999999999888888888888888888888888888888887777733..... PP

                   ABC2_membrane_2  68 edtdqdlkvvstimavlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaigla.iavallatvl 143
                                       + +++++      m+ +++++a l +  +++ ++  g l  lL++P+sR++i++gK++gg + +l+ ++v++l++  
  gi|385805745|ref|YP_005842143.1|  90 DYFSYMA----IGMTAVVALFAGLQTGMSLSWDRRLGYLNKLLASPISRGSIIVGKVLGGTVKALVqVLVIILIA-- 160
                                       3444443....67788888889999999***********************************555555555555.. PP

                   ABC2_membrane_2 144 lalaiilalgivlaledllllvvasvlllllvvflalgl.llSsvarssreaaalalglfvvlailv...pivlygv 216
                                           i  +l+ ++a ++ ++ +++ ++l++    +++g+ ++S+++r ++   +    ++ +l++     ++vl ++
  gi|385805745|ref|YP_005842143.1| 161 ----IPFGLKLQIASASAVVAAALGITLFA----MGIGMlMISITLRVKS--WETQMTVMNLLNLPLmfaSNVLTPL 227
                                       ....55555555655565555555555555....5666415677777444..3333344444433330003444444 PP

                   ABC2_membrane_2 217 aellagpavpqeindflsllspts.ayntllneilagsdlnalgstatnllilllllavllvlgyvl 282
                                       a++++       + +++  ++p   a +++++++++gs   +++  +  l+il +++++l+ +g v+
  gi|385805745|ref|YP_005842143.1| 228 AMMPS-------WLQTVAKFNPLTyAADIMRQALIMGS-YASYAEIMRDLVILAGVAIALITIGVVA 286
                                       44444.......66667777775516799999999999.5669999999999999999999998875 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 ?    8.5  14.1   0.00059       1.8      33     154 ..      81     197 ..      15     221 .. 0.73
   2 ?    0.3   4.2      0.19   5.7e+02     109     157 ..     182     234 ..     166     258 .. 0.50

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00059
                   ABC2_membrane_4  33 fnllgktgldpaefyslsvfgftlllllplilgiiasylifrEeqndtlknLltiPvsrtklllaKlivllllsvll 109
                                        nl+g+ ++d   ++s++++g  ++ ++ l  g+ ++++++  +  + l++Ll  P+sr +++++K++   + +++ 
  gi|385805745|ref|YP_005842143.1|  81 TNLFGQANID---YFSYMAIG--MTAVVALFAGLQTGMSLSWDRRLGYLNKLLASPISRGSIIVGKVLGGTVKALVQ 152
                                       3445555544...55555555..566788899999**********************************99999999 PP

                   ABC2_membrane_4 110 mlvtflitvlfallsgfvgfsvklvlellkkcl.elgllvffavlp 154
                                       +lv  li++ f+l +  ++ s + v+ +l ++l  +g++++++++ 
  gi|385805745|ref|YP_005842143.1| 153 VLVIILIAIPFGLKLQIASAS-AVVAAALGITLfAMGIGMLMISIT 197
                                       999999999898888877655.344444444442455544443332 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.19
                   ABC2_membrane_4 109 lmlvtf.....litvlfallsgfvgfsvklvlellkkclelgllvffavlpiia 157
                                       ++l+++     +i++ + + s  ++++v+ +l+ l  ++  ++l+ +a++p ++
  gi|385805745|ref|YP_005842143.1| 182 ITLFAMgigmlMISITLRVKSWETQMTVMNLLN-LPLMFASNVLTPLAMMPSWL 234
                                       222222000002222222222233333333322.33555666677777777655 PP

>> ABC2_membrane_5  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6  16.9   0.00084       2.5      36     166 ..      95     225 ..      67     285 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00084
                   ABC2_membrane_5  36 vllifsilslvisiililttlsyDekskwnkylltLPvtrkeiVksKYlfvlililiailitlllliiavlikgnvt 112
                                       +++ +++++++++ +   ++ls D++ +    ll  P++r  i+  K l++++  l+ +l+++l++i  +l  +   
  gi|385805745|ref|YP_005842143.1|  95 MAIGMTAVVALFAGLQTGMSLSWDRRLGYLNKLLASPISRGSIIVGKVLGGTVKALVQVLVIILIAIPFGLKLQIAS 171
                                       233344444444444455999********99*******************************999976555555566 PP

                   ABC2_membrane_5 113 isevllsiliglvialiflaivlPlyfkfgvekgrivliiiifgiifllvaifs 166
                                        s v+ ++l + ++a+ ++ +++ ++++ + +++++ ++ +  +  ++ ++++ 
  gi|385805745|ref|YP_005842143.1| 172 ASAVVAAALGITLFAMGIGMLMISITLRVKSWETQMTVMNLLNLPLMFASNVLT 225
                                       67777777777788899999**************99555555554455554444 PP

>> Deltameth_res  Deltamethrin resistance
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.2       1.5   4.5e+03      21      35 ..      91     104 ..      84     113 .. 0.58
   2 ?    4.1   0.4     0.015        44      24      42 ..     184     202 ..     176     207 .. 0.88
   3 ?    5.7   0.1    0.0044        13      24      43 ..     270     289 ..     268     294 .] 0.84

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.5
                     Deltameth_res  21 YNavLaaGiviligT 35 
                                       Y  ++a+G ++++ +
  gi|385805745|ref|YP_005842143.1|  91 YFSYMAIGMTAVV-A 104
                                       5566777765543.3 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.015
                     Deltameth_res  24 vLaaGiviligTialakes 42 
                                        +a+Gi +l+++i+l ++s
  gi|385805745|ref|YP_005842143.1| 184 LFAMGIGMLMISITLRVKS 202
                                       5799**********97765 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.0044
                     Deltameth_res  24 vLaaGiviligTialakesg 43 
                                       v +aG++i  +Ti+++ ++ 
  gi|385805745|ref|YP_005842143.1| 270 VILAGVAIALITIGVVAANR 289
                                       679************98775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       994  (0.0554409); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); 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: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 1865.64
//
Query:       gi|385805746|ref|YP_005842144.1|  [L=209]
Description: maf protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-48  164.8   0.1    1.7e-48  164.6   0.1    1.0  1  Maf       Maf-like protein


Domain annotation for each model (and alignments):
>> Maf  Maf-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.6   0.1   9.7e-53   1.7e-48       1     165 [.       6     189 ..       6     190 .. 0.94

  Alignments for each domain:
  == domain 1  score: 164.6 bits;  conditional E-value: 9.7e-53
                                       EEEEE---HHHHHHHHCT-..EEEE------......HHHHHHHHHHHHHHHHH......TCEEEEEEEEEE....C CS
                               Maf   1 kliLASaSprRkelLeqlg..fevvpsdvde......aeelvlrlAeaKaeava......alvigaDtvvvl....i 59 
                                       +l+LAS+S+rR e+L+++g  f v++++  e      + ++vl+ A++K  +v+      +l+++aDtvvv     i
  gi|385805746|ref|YP_005842144.1|   6 QLVLASTSKRRIEILREIGvdFLVIEPKYREiiiekePLRTVLNNAKNKGMSVLdaspsnSLILSADTVVVAeegeI 82 
                                       69*****************9999******999999997778*******************99*********876666 PP

                                       E---SSHHHHHHHHHHHTTSEEEEEEEEEEEE..EEE..EEEEEEEEEE----HHHHHHHHHCTSGCCSTTS--TTC CS
                               Maf  60 lgKPkdeeealemLkklsgrthevvTgvavlk..ekevksfvettevtfkelsdeeieaYvatgepldkAGaygiqg 134
                                       lgKP++ +  ++mLkkl+gr h v+Tg++v++  +++ +  +ett+v+f+++sde+i +Y +t e +dkAG+y+ qg
  gi|385805746|ref|YP_005842144.1|  83 LGKPDSLSTSISMLKKLNGRYHYVLTGICVIDkdSGSLECSHETTKVKFRKVSDEMIIQYASTLEGMDKAGSYAAQG 159
                                       ********************************9966788889*********************************** PP

                                       GGGGGCEEEECS-HHHHHT--HHHHHHHHCC CS
                               Maf 135 llglalverieGsysnVvGLPlaellelLke 165
                                       l g+ l+e+ieG+++nV+GLP+  +++lL++
  gi|385805746|ref|YP_005842144.1| 160 L-GALLIESIEGDFYNVIGLPIGLVYALLAK 189
                                       9.777***********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); 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: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1280.55
//
Query:       gi|385805747|ref|YP_005842145.1|  [L=58]
Description: hypothetical protein FFONT_0705 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.29s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 401.97
//
Query:       gi|385805748|ref|YP_005842146.1|  [L=530]
Description: hypothetical protein FFONT_0706 [Fervidicoccus fontis Kam940]
Scores for complete 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-98  330.8  26.9    5.1e-97  325.5   0.3    2.0  2  DUF2070   Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5  21.3   1.5e-05      0.27       1     145 [.       5     148 ..       5     151 .. 0.78
   2 !  325.5   0.3  2.9e-101   5.1e-97     181     563 ..     150     527 ..     148     528 .. 0.96

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 1.5e-05
                           DUF2070   1 leklskyifr..lPswk.vsllliillalligllaflssklfgillfglpalvaflltlpvlrilggrltykrslfl 74 
                                       +e+ +k++f   + +++  sl++++++++l g l++  +   ++   +l ++ + +l l+ + +++++     ++f 
  gi|385805748|ref|YP_005842146.1|   5 FESSYKLLFGfsAKKLSiASLVITVVISYLRGSLVYFGEL--AFATGTLYFFRTPFLSLKKIIYISSITVGFVAAFE 79 
                                       6889999999778999988999999999999999877764..3333333355566666666666655544456799* PP

                           DUF2070  75 alltelivviisllaillsallqalvllalvlslalvfalrllvlvavsdesllkavlpaliqpllailll 145
                                        +l   ++ +++ +++++s++l   +++    s+++ f+l+ l+++ +s e +++++l+a+ +p+l ++++
  gi|385805748|ref|YP_005842146.1|  80 TVLLRPPFTFFLAIPVVTSLIL--ATIDPKSKSWIIPFILSSLIYYKISMEAMITSLLLAIGIPILRFAFS 148
                                       ******************9988..4455555678899****************************999886 PP

  == domain 2  score: 325.5 bits;  conditional E-value: 2.9e-101
                           DUF2070 181 rnlgvsaldllsaFlahilegskelEeffeeigeeadvpvkvlsfrredgekallvvPniHPGPlgeiGGsnLpkil 257
                                        ++g+++++l+saFl +++ + +++Ee +++igee++v++++++++ e +  a+ vv+n+HPGP++++ G++L++ +
  gi|385805748|ref|YP_005842146.1| 150 ISYGIDPFNLFSAFLFSVFGEGEQFEEELKKIGEEKEVDIHLFKLHGE-KSRAVAVVSNVHPGPFKGVSGAKLIDFI 225
                                       589******************************************555.7899999********************* PP

                           DUF2070 258 aerldel...vlvlHgtatHdfNlvserevekiveavkealeele....ysskaskpvrvesgdvkllgqrfgd.sl 326
                                       +++++++   +l++Hg+++H+++++s+++v+ki+e + ++le+       ++ ++ p +   +dv +++++++   +
  gi|385805748|ref|YP_005842146.1| 226 NSEVGKKgykLLFMHGVGSHENDPASSEDVKKIAEIIGSKLEDGGslwrSANPCI-PGQGIKKDVMVTSLPLDPgPN 301
                                       *******************************************999995555555.77777788**********99* PP

                           DUF2070 327 llvitrapegiDDiplsvglsimaeakaegfedvllVDaHNsfseeagevlpgsedaeeliraaekalekleaaees 403
                                       + ++++ ++++DDip+s+   i+        e+ +lVDa+N f+++++++   +ed ++li++++++    ++++++
  gi|385805748|ref|YP_005842146.1| 302 IHIVSKVKSSMDDIPSSFARMIK--------ENDILVDAQNRFDGDVQWS---EEDLKDLISLIDNI----KKEKCE 363
                                       ******************55555........367***************9...*************9....89**** PP

                           DUF2070 404 elkvgvarsetpkltpe.eglGdlgiqvlvlevdgqktayvliDgNNmepglreeirealke.vdlevevmTTDtHv 478
                                       ++++g+ ++++ +++++ +++G+lgi+ lv+++ ++kta++++D+NN++ g+re+++e+lke ++++ve+++TD+H 
  gi|385805748|ref|YP_005842146.1| 364 DYYIGIGNVSMGDADKTrSEFGQLGISSLVISCSNKKTALLIFDSNNIKVGIRERLVEKLKEkGYDTVEIISTDNHR 440
                                       *****************999******************************************9999*********** PP

                           DUF2070 479 vngvsl..gynpvGekvskdelielvlelvekAiadlepvevgyatervevkvfgedrfeelvstvnsvvsvakila 553
                                       ++gv +  gy   Ge+v+ + + +++l++++ A +d+e+ +v+y + rv+ k++ge+ f+ l s++ +   +a +++
  gi|385805748|ref|YP_005842146.1| 441 ETGVGRgfGYRVAGERVPFEVIEKKALQAISMAESDMEKKRVEYLKLRVKAKFLGEKGFKLLTSIAMKRSYFASAIF 517
                                       ***************************************************************************** PP

                           DUF2070 554 aallllaill 563
                                       a+++++++l+
  gi|385805748|ref|YP_005842146.1| 518 AYIIIAMFLT 527
                                       ********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (530 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       926  (0.0516482); expected 358.6 (0.02)
Passed bias filter:                      614  (0.0342462); 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: 0.64u 0.34s 00:00:00.98 Elapsed: 00:00:00.51
# Mc/sec: 3138.55
//
Query:       gi|385805749|ref|YP_005842147.1|  [L=258]
Description: short chain dehydrogenase [Fervidicoccus fontis Kam940]
Scores for 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-72  244.5   0.1    1.3e-72  244.2   0.1    1.0  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
      1e-56  191.5   0.3    1.3e-56  191.2   0.3    1.1  1  adh_short     short chain dehydrogenase
    3.1e-11   43.5   0.0    5.3e-11   42.8   0.0    1.3  1  KR            KR domain
     0.0018   17.3   0.1     0.0026   16.8   0.1    1.2  1  3Beta_HSD     3-beta hydroxysteroid dehydrogenase/isomerase f
     0.0026   17.3   0.0     0.0036   16.8   0.0    1.4  1  Epimerase     NAD dependent epimerase/dehydratase family
  ------ inclusion threshold ------
      0.055   13.7   0.1       0.12   12.7   0.1    1.5  1  TrkA_N        TrkA-N 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 !  244.2   0.1   4.3e-76   1.3e-72       4     234 .]      18     256 ..      14     256 .. 0.95

  Alignments for each domain:
  == domain 1  score: 244.2 bits;  conditional E-value: 4.3e-76
                                       TSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSE.EEE--TTSHHHHHHHHHHHHHHHSSEEEEEE--- CS
                      adh_short_C2   4 sgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgae.vlecDVtdeeqvealveevvekfgklDilvnnag 78 
                                       sgIGraiA++l + G +v++ d++ee+  ++v+e+ +++g++ ++++DV++ee+v++ +e++vek+g++D+lvnnag
  gi|385805749|ref|YP_005842147.1|  18 SGIGRAIAEKLSSLGSTVIIFDVSEEGgLSTVREINSKGGSSyFFKVDVSNEESVKRGIENAVEKTGGIDVLVNNAG 94 
                                       8***************************************9956********************************* PP

                                       --EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSC.CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHH CS
                      adh_short_C2  79 iapklkgpfletsreefdraldvnlyslfllakaalp.lmkeg.gsivnlssvgaervvpnynaygaaKaalealtr 153
                                       i p+ ++++le+s ee+dr+l++nl++++l++k+a p ++k+g gs++n++sv++ + +++   y+++Ka+++ lt+
  gi|385805749|ref|YP_005842147.1|  95 IEPP-SKSLLELSVEEYDRVLNINLKGVWLMTKYATPyIAKRGgGSVINIASVAGIMPLAGAMPYSVSKAGVIMLTK 170
                                       ****.********************************6555558********************************* PP

                                       HHHHHHGGGTEEEEEEEE--BHCTGGGGSTT.....HHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SE CS
                      adh_short_C2 154 ylAvelgpkgiRvNavspgpikTlaasgikg.....fdelleelearaplgrlgtpeevaeaalfLasdeasyitGq 225
                                         Avelg+ +iRvNa++pg+++T++ +++++      +e+++   +r+ lgr+++pee+a+a++fLasde+syitG+
  gi|385805749|ref|YP_005842147.1| 171 VSAVELGKLKIRVNAIAPGWVDTPMIERAARnlkltPEEFKKINSQRIILGRFASPEEIANAVAFLASDESSYITGS 247
                                       *************************66665545666677999999******************************** PP

                                       EEEESTTGG CS
                      adh_short_C2 226 tlvvDgGlt 234
                                        +vvDgG++
  gi|385805749|ref|YP_005842147.1| 248 LVVVDGGIS 256
                                       *******85 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.2   0.3   4.2e-60   1.3e-56       1     191 [.       9     200 ..       9     204 .. 0.97

  Alignments for each domain:
  == domain 1  score: 191.2 bits;  conditional E-value: 4.2e-60
                                       SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSS CS
                         adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgk 77 
                                       k+ +vtG++sGIGraia++l + G +v+++d see    ++ e++++g + ++++vDv+++e+v++ +e+av+k+g+
  gi|385805749|ref|YP_005842147.1|   9 KISIVTGGGSGIGRAIAEKLSSLGSTVIIFDVSEEGGLSTVREINSKGGSSYFFKVDVSNEESVKRGIENAVEKTGG 85 
                                       5679************************************************************************* PP

                                       ESEEEE---S.S--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHH CS
                         adh_short  78 ldvLvnNAGi.tgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsK 153
                                       +dvLvnNAGi   s++  els ee++rv+++Nl+gv l+t+ ++p++ k+ +G+++n++Svag +p+ag  +Ys sK
  gi|385805749|ref|YP_005842147.1|  86 IDVLVNNAGIePPSKSLLELSVEEYDRVLNINLKGVWLMTKYATPYIAKRGGGSVINIASVAGIMPLAGAMPYSVSK 162
                                       **********7778999************************************************************ PP

                                       HHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHHC CS
                         adh_short 154 aavagltrslakelaptgirvnavaPGlvdTdmakelr 191
                                       a+v++lt+  a el + +irvna+aPG vdT+m +++ 
  gi|385805749|ref|YP_005842147.1| 163 AGVIMLTKVSAVELGKLKIRVNAIAPGWVDTPMIERAA 200
                                       *********************************87765 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.8   0.0   1.8e-14   5.3e-11       4     151 ..      12     160 ..      10     167 .. 0.91

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 1.8e-14
                                       EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS CS
                                KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeep 80 
                                       ++tGG  g+G+++a+ l + g + +++   +    e   ++++e++++g +  ++++Dvs++++v++ +e++ ++++
  gi|385805749|ref|YP_005842147.1|  12 IVTGGGSGIGRAIAEKLSSLGSTVIIFDVSE----EGGLSTVREINSKGGSSYFFKVDVSNEESVKRGIENAVEKTG 84 
                                       89*******************9988885555....4556689*********************************** PP

                                       ---EEEE------.---TTT--HHHHHHHHTTTTHHHHHHHHHTTT....S--SEEEEEEEHHHHH--TT-HHHHH CS
                                KR  81 pikGvihaAgvlr.dklleemtaedleqvlapKvkGawnLhelled....esldffvlfSSiagllgsagqanYaa 151
                                        i   ++ Ag+    k l e++ e++++vl+  +kG+w + ++ ++    +    ++ ++S+ag++  ag + Y+ 
  gi|385805749|ref|YP_005842147.1|  85 GIDVLVNNAGIEPpSKSLLELSVEEYDRVLNINLKGVWLMTKYATPyiakRGGGSVINIASVAGIMPLAGAMPYSV 160
                                       ***********875899************************987766665888999**********9999999986 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 !   16.8   0.1   8.6e-07    0.0026       1      67 [.      12      79 ..      12     125 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 8.6e-07
                         3Beta_HSD  1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkk....viegDvtdkdkleealegv 67
                                      +vtGg+  +Gra+ ++L +l++  +v ++D+ e+  l ++++++n k     + ++Dv +++++++ +e++
  gi|385805749|ref|YP_005842147.1| 12 IVTGGGSGIGRAIAEKLSSLGS--TVIIFDVSEEGGL-STVREINSKGgssyFFKVDVSNEESVKRGIENA 79
                                      69*******************6..9******998665.445555444444559********9998877643 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.2e-06    0.0036       2      74 ..      12      95 ..      11     170 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.2e-06
                                      EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC......EEEE--TT-HHHHHH....HHHHH.T-SEEE CS
                         Epimerase  2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl......elveldltdrsaler....lfkee.qpdavi 69
                                      +VtG+   iG+a++++l + g +vi +d  ++++ +  +e         + ++d+ ++++++r    +++++ ++d+ +
  gi|385805749|ref|YP_005842147.1| 12 IVTGGGSGIGRAIAEKLSSLGSTVIIFDVSEEGGLSTVREINskggssYFFKVDVSNEESVKRgienAVEKTgGIDVLV 90
                                      79****************************77666555544499***************87661111445555677777 PP

                                      E--S- CS
                         Epimerase 70 hlAav 74
                                      + A++
  gi|385805749|ref|YP_005842147.1| 91 NNAGI 95
                                      77764 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   3.9e-05      0.12       5      57 ..      16      74 ..      12      80 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.9e-05
                                      S-SHHHHHHHHHHHH.TTEEEEEEESSH....HHHHHHHHTT..SEEEES-TTSHHHHHH CS
                            TrkA_N  5 GlGrvGrslaeeLse.ggkdvvvidkde....erveelreeg..levvvgdatdeevLee 57
                                      G + +Gr++ae+Ls+ g+  v++ d +e    ++v+e+  +g    +++ d+++ee +++
  gi|385805749|ref|YP_005842147.1| 16 GGSGIGRAIAEKLSSlGS-TVIIFDVSEegglSTVREINSKGgsSYFFKVDVSNEESVKR 74
                                      6778***********777.6********55555599999998655599999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
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 0.32s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1492.18
//
Query:       gi|385805750|ref|YP_005842148.1|  [L=410]
Description: major facilitator superfamily protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-27   95.6  16.8    5.1e-27   94.8  16.8    1.3  1  Sugar_tr  Sugar (and other) transporter
    7.1e-21   74.5  34.2    4.2e-13   48.9  12.1    2.0  2  MFS_1     Major Facilitator Superfamily
  ------ inclusion threshold ------
        1.8    8.4  14.8       0.99    9.2   4.1    2.5  2  VIT1      VIT family


Domain annotation for each model (and alignments):
>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.8  16.8   8.5e-31   5.1e-27      50     449 ..      29     408 ..      24     410 .] 0.83

  Alignments for each domain:
  == domain 1  score: 94.8 bits;  conditional E-value: 8.5e-31
                                       HHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGG..HHHHHHHHHHHHHHHH CS
                          Sugar_tr  50 livsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivg..RvlvGigvGlasvlvP 124
                                       li+ + ++  ++Gsl++g ++dr+GR+ +l+++  ++ i+++  +a   ++++ ++ ++    ++  g+G++++ + 
  gi|385805750|ref|YP_005842148.1|  29 LILMLNSASFMLGSLTFGVVSDRIGRRRGLITSLSIYTISTIAFIAFSYAEKIGLIEAAilTSIINYGIGAETGPSY 105
                                       556666677799****************************9999888867666666555336666677777777777 PP

                                       HHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-..TTHHHHHHHCCHHHHHHHHHHGGGS---HHHHH CS
                          Sugar_tr 125 myisEiApkklRgalvslyqlaitfGilvaaifglglnktsn..adgwrillglqlvpallllilllflPESPrylv 199
                                         +sE+ p+++Rg++ +l   ++ +G  v a + l+++k +   ++   ++l+++l++++++l+++l +PESPr+lv
  gi|385805750|ref|YP_005842148.1| 106 AALSEFMPDDHRGKMLMLALNFWNVGAAVIALLSLFYSKLTTdlNTILLYTLFSALFLSIVVLFARLHIPESPRWLV 182
                                       7789*********************************55555599999999************************** PP

                                       HTT-HHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH.....HTTHHHHSH...HHHHHHHHHHHHHHTTHHHHHHH CS
                          Sugar_tr 200 ekgkeeeakevlaklrgeedadrelaeekdsleaeqeeekaswkellssktvrqrlligvvlqifqqltGinaimyy 276
                                        k++++ea+++ +k             +++s e +     + ++  +++  +  r++i +v+ ++q  ++ n+  yy
  gi|385805750|ref|YP_005842148.1| 183 LKDRKDEAEKIAEK--------FPNISIITSEEGG-----VGIGDAIRK--YSLRFFILAVIVAAQAINY-NFPSYY 243
                                       **************........3334455555555.....345666666..6789*********999998.9999** PP

                                       TTTHHHHSS-THHHHHHHHHHHHHHHHHHHHHHHHHHS-S.HHHHHHHHHHHHHHHHHHH..HHHHTTSS...CHHH CS
                          Sugar_tr 277 sptifenlglsksllvtiivgvvnfvatfvaiflvdrfGR.RtllllGaagmaicfvilgivalllvakskaasiva 352
                                        p+  +n  + +  ++ +i+ + n+ a++ ai+++  + R R+l l+ +++   ++++l i + +++++    s+ +
  gi|385805750|ref|YP_005842148.1| 244 VPY-SKNFPFGEN-TAPLIIAISNIGASVGAIPFIWLIDRsRKLSLFASFIFGSATALL-IYFSAISQEF---SYFL 314
                                       998.899999999.9****************8555555444556666666665555555.4699999996...**** PP

                                       HHHHHHHHHHHHTTTTHHHHHHHHHHSHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHT-HHHHHHHHHHHHH CS
                          Sugar_tr 353 ivfialfialfalgwgpvpwvlvsElfpqsvRskalaiavavnwlanflisllfpiiteaigggyvflvfaglavlf 429
                                       iv+++ +i++ ++  g+    l  Elfp+++R++a+   +a  wl n +   ++ +++++     + +   +l +++
  gi|385805750|ref|YP_005842148.1| 315 IVLFLNMIFC-EWVYGSEA-TLEGELFPTGMRASAAGAITAFAWLLNTIDVGIMGYLDSSTM-LEINFAVWILGLFA 388
                                       **99999876.99999999.888*************************99999999998888.88888888888888 PP

                                       HHHHHHHS--STT--CCCCG CS
                          Sugar_tr 430 iifvfffvpetkgrtleeie 449
                                         + ++   et+ ++l+e  
  gi|385805750|ref|YP_005842148.1| 389 SSVWLIRGKETAKKPLDETA 408
                                       88899999999999998865 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9  12.1   7.1e-17   4.2e-13      33     233 ..      26     242 ..       1     246 [. 0.64
   2 !   32.5  17.4   7.2e-12   4.3e-08       3     182 ..     226     404 ..     219     410 .] 0.83

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 7.1e-17
                             MFS_1  33 eigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalg.lllllfa....sslwlllvlrvlqGlgagalfp 104
                                        ++l+l l ++ ++++sl +G++sdr+Grrr l+++l ++ ++ +++++f+    ++l   ++l  +   g ga + 
  gi|385805750|ref|YP_005842148.1|  26 YASLILMLNSASFMLGSLTFGVVSDRIGRRRGLITSLSIYTIStIAFIAFSyaekIGLIEAAILTSIINYGIGAETG 102
                                       4899***************************************5555556455665555344555555555568*** PP

                             MFS_1 105 agaaliadwfpkeergraigllsagfslGailgpllggllasslg...Wravfyilaivsllafvlfllllpeeppe 178
                                        ++a++++  p+++rg+++ l+  ++++Ga++ +ll+ + + +       +++ ++ +++l  +v+ ++ l  ++++
  gi|385805750|ref|YP_005842148.1| 103 PSYAALSEFMPDDHRGKMLMLALNFWNVGAAVIALLSLFYSKLTTdlnTILLYTLFSALFLS-IVVLFARLHIPESP 178
                                       *********************************99999887555565333333333333333.44334444666666 PP

                             MFS_1 179 rkrkspkeee........kgtgpaplvp.............awkallkdpvlwillialllfffgfsglltllply 233
                                       r+ + + ++                  p             +  a++k   l  ++i ++++  + +++ + +p+y
  gi|385805750|ref|YP_005842148.1| 179 RWLVLKDRKDeaekiaekF--------PnisiitseeggvgIGDAIRKYS-LR-FFILAVIV--AAQAINYNFPSY 242
                                       6666665554445444330........13334445555563222344444.32.33333333..555566666665 PP

  == domain 2  score: 32.5 bits;  conditional E-value: 7.2e-12
                             MFS_1   3 laaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalgllll 79 
                                       la++++a a++  +p++   +++++ + + ++ l++++  +ga+v+++p+ +l+dr  r+  l++++++ ++++ll+
  gi|385805750|ref|YP_005842148.1| 226 LAVIVAAQAINYNFPSYYVPYSKNFPFGENTAPLIIAISNIGASVGAIPFIWLIDRS-RKLSLFASFIFGSATALLI 301
                                       4444444444445555554779999999****************************5.7778888888888886777 PP

                             MFS_1  80 lfa..sslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWrav 153
                                        f+  s+ + ++l++ +l  +++ +++ + a+l  ++fp   r++a g ++a++ l   +  ++ g+l ss   +  
  gi|385805750|ref|YP_005842148.1| 302 YFSaiSQEFsYFLIVLFLNMIFCEWVYGSEATLEGELFPTGMRASAAGAITAFAWLLNTIDVGIMGYLDSSTMLEIN 378
                                       7855766666***********************************************************99998888 PP

                             MFS_1 154 fyilaivsllafvlfllllpeepperkrk 182
                                       f +  + ++ + v   +l++ +++++k+ 
  gi|385805750|ref|YP_005842148.1| 379 FAVWILGLFASSV---WLIRGKETAKKPL 404
                                       8888888888877...8887777776665 PP

>> VIT1  VIT family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   4.1   0.00017      0.99     142     209 ..       4      74 ..       1      78 [. 0.87
   2 ?    4.2   3.0    0.0057        34     139     209 ..     285     355 ..     281     359 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00017
                              VIT1 142 alsfliGgliPllpylfve...svglalvvsiavtllalllfGavkalltgssklvsalrmlliGalAaaa 209
                                       +l  ++++liP   yl+ +    ++l l++  a ++l  l fG+v++++++++ l+  l+   i  +A +a
  gi|385805750|ref|YP_005842148.1|   4 FLDGVLFSLIPTTLYLIPSilpYASLILMLNSASFMLGSLTFGVVSDRIGRRRGLITSLSIYTISTIAFIA 74 
                                       55557889999999999887766999999999*********************************999876 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0057
                              VIT1 139 lssalsfliGgliPllpylfve..svglalvvsiavtllalllfGavkalltgssklvsalrmlliGalAaaa 209
                                       ls ++sf++G++  ll y+ +   + +  l+v ++ ++++  +  + +   ++ + +  ++r  + Ga++a a
  gi|385805750|ref|YP_005842148.1| 285 LSLFASFIFGSATALLIYFSAIsqEFSYFLIVLFLNMIFCEWV--YGSEATLEGELFPTGMRASAAGAITAFA 355
                                       6899***************876222333333333333333333..3333344556677777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       790  (0.0440627); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 2533.53
//
Query:       gi|385805751|ref|YP_005842149.1|  [L=288]
Description: P-loop ATPase/GTPase-like protein [Fervidicoccus fontis Kam940]
Scores for complete 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   0.0     0.0075   16.1   0.0    2.0  2  AAA_26           AAA domain
  ------ inclusion threshold ------
      0.043   13.7   0.0       0.73    9.7   0.0    2.2  2  Glutaredoxin2_C  Glutaredoxin 2, C terminal domain
      0.087   12.6   0.0       0.14   11.9   0.0    1.3  1  DUF5449          Family of unknown function (DUF5449)


Domain annotation for each model (and alignments):
>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.3e-06    0.0075       2      60 ..       3      78 ..       2      98 .. 0.74
   2 ?   -0.3   0.0      0.13     8e+02     105     138 ..     190     223 ..     126     227 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.3e-06
                            AAA_26  2 tifvtgtd.tgvGKTvvslgLvralkrkgvkvgyfKPiqtgie................ededselikellgldqt 60
                                      +i+++g    ++GKT+ s  L+  l++ g+k++ fKP+++ +                 +++d+  +k++++ d +
  gi|385805751|ref|YP_005842149.1|  3 KILIAGLLpYDSGKTTFSISLILHLRDMGIKAHPFKPVSSHNIftqsssfsesinmkllAGGDALQYKHAFDFDID 78
                                      57777764158***************************99887666666666666666556666666666666665 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.13
                            AAA_26 105 EGagglgvpiteellnadiaknlgapvilVargg 138
                                        G+ ++ v ++++ l  ++    ++ +i+V+++g
  gi|385805751|ref|YP_005842149.1| 190 KGFNTIIVESFSDSLFPYFSSLKDSSMIIVVSPG 223
                                       3555566666666666666666677777776665 PP

>> Glutaredoxin2_C  Glutaredoxin 2, C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00012      0.73      24      78 ..     121     176 ..     116     188 .. 0.86
   2 ?    1.4   0.0     0.043   2.6e+02      33      74 ..     224     268 ..     221     282 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00012
                   Glutaredoxin2_C  24 aplpEFatqsAreyftkkkeksig.dfeellaktpeliaelnalLeelepliksse 78 
                                       + + E +t sA++yf++  +  +  +f +++++ +++ ++l   L+e  ++++s+e
  gi|385805751|ref|YP_005842149.1| 121 MRITECKTMSAKHYFIRDNTDLFPpSFRKNIEHLSSITEALPISLDEALKILRSRE 176
                                       5678999************999999***************9999999888887655 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.043
                   Glutaredoxin2_C  33 sAreyftkkkeksigdfeellaktp...eliaelnalLeelepli 74 
                                       +A +yf ++k k+i++++ + + +p    li++++++L+e   l 
  gi|385805751|ref|YP_005842149.1| 224 RAFAYFDEEKVKKIKELKGIPKGSPrtmYLISRYEPDLDEALDLK 268
                                       5889********999999888887733346788888888765554 PP

>> DUF5449  Family of unknown function (DUF5449)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.4e-05      0.14       6      87 ..     162     247 ..     157     262 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.4e-05
                           DUF5449   6 kvslerikkvvpeklltkvlkaaieklderisqiivndkdnskeilltsihk...fykya.neeltefkkesvkkve 78 
                                        +sl+   k++ ++ l++ +   +e++++ +  iiv+  ++s   +++s++    + +++    ++ f+ e+vkk++
  gi|385805751|ref|YP_005842149.1| 162 PISLDEALKILRSRELEDNFDICLERIGKGFNTIIVESFSDSLFPYFSSLKDssmIIVVSpGRAFAYFDEEKVKKIK 238
                                       56777777888888999********************************986222333331467999********** PP

                           DUF5449  79 fvkGtpdGk 87 
                                         kG p+G 
  gi|385805751|ref|YP_005842149.1| 239 ELKGIPKGS 247
                                       *******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1788.21
//
Query:       gi|385805752|ref|YP_005842150.1|  [L=304]
Description: radical SAM protein [Fervidicoccus fontis Kam940]
Scores for complete 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-12   47.0   0.0    5.8e-12   46.3   0.0    1.4  1  Radical_SAM  Radical SAM superfamily
    3.7e-09   36.7   2.4    0.00075   19.3   0.0    2.2  2  DUF1848      Domain of unknown function (DUF1848)


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.3   0.0   6.4e-16   5.8e-12       2     166 ..      28     191 ..      27     195 .. 0.84

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 6.4e-16
                                       EEESEESS--TTTSCCTT.HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC..C CS
                                       xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..x RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpet.vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla..v 75 
                                       +++ gC+++C +C+ +   ++re +++   v  +++ +++l  +    + i ++ +p  + +  ++l r++     +
  gi|385805752|ref|YP_005842150.1|  28 NPYTGCSFGCLYCYAKGYiGKRESTPKKDYVKLLERSARKL-NRA-LPVNIGTSSDPYPDIEQKFKLTRASLSIliN 102
                                       6789************9776677777777777777777777.455.888888888888888888888888887799* PP

                                       CTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHH..HHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  76 pgiritvetngtlpdeeklerllelgvdrvslgleaadde..kvlklmnrghtfeevlealeklreagikrvvdriv 150
                                        ++++ ++t g+ +  + ++++++     v+ ++ +++++  k l++m   ++++e+++++e +++++i+    + +
  gi|385805752|ref|YP_005842150.1| 103 MNFKVLITTKGGELLLRDADLMKKGK-VAVTPTVTTLNEDlaKKLEPM--APSPKERIRVMEEMNKNDIPLGARVDP 176
                                       ************************55.*************55555555..69******************8778889 PP

                                       EBTTTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxx RF
                       Radical_SAM 151 glpGendeeleellel 166
                                       ++pG nd+e +el el
  gi|385805752|ref|YP_005842150.1| 177 IIPGLNDDE-KELKEL 191
                                       9******98.776665 PP

>> DUF1848  Domain of unknown function (DUF1848)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   3.2   2.3e-06      0.02     238     265 .]      15      42 ..       8      42 .. 0.92
   2 !   19.3   0.0   8.3e-08   0.00075      52     216 ..     108     287 ..      84     303 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.3e-06
                           DUF1848 238 qrkeCgCveskDiGayntClhgCvYCYA 265
                                       q + C+C +   +  y  C+ gC+YCYA
  gi|385805752|ref|YP_005842150.1|  15 QSSLCTCPKKYSLNPYTGCSFGCLYCYA 42 
                                       6778***********************9 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 8.3e-08
                           DUF1848  52 vFwtknpkpllkkleelkergiklyfqf.Tltd.yekelepnvpsleerietfkelseklgkerviwRyDPilltek 126
                                       +  tk  + ll+ ++ +k+ ++ ++  + Tl++   k+lep  ps +eri+ ++e++++     +  R DPi+   +
  gi|385805752|ref|YP_005842150.1| 108 LITTKGGELLLRDADLMKKGKVAVTPTVtTLNEdLAKKLEPMAPSPKERIRVMEEMNKND--IPLGARVDPIIPGLN 182
                                       456777788888888888777776655415664145669***************999864..45789*****98766 PP

                           DUF1848 127 ltvelhlekfeklaeelk.....gytekvviSfvdl...ykkvkrnlkk.......k.lelrelseeekeelaeela 187
                                        +++++ e +++lae+ +      + +   + f d+   +  ++++ k+       +   +  ls++ +e+l++ + 
  gi|385805752|ref|YP_005842150.1| 183 DDEKELKELVNALAEAGArliitSTYKARFVDFKDMinvFPDMREKWKRlyfeegeRiGGYMYLSKSLRERLLKLVV 259
                                       6666655555555554332213223333344454445556666666654455445335678899999999******* PP

                           DUF1848 188 eiakklglelatCaekedlselgieknkC 216
                                       + akklgle atC e  +  e  +++++C
  gi|385805752|ref|YP_005842150.1| 260 DEAKKLGLEYATCREGLTSPE-YFKARSC 287
                                       **************9986444.4566666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1988.69
//
Query:       gi|385805753|ref|YP_005842151.1|  [L=85]
Description: hypothetical protein FFONT_0711 [Fervidicoccus fontis Kam940]
Scores for 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-05   21.8   5.5    0.00046   19.5   1.1    2.0  2  Peptidase_M50  Peptidase family M50


Domain annotation for each model (and alignments):
>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.7   0.5   0.00089        16      87     107 ..       7      27 ..       3      32 .. 0.86
   2 !   19.5   1.1   2.6e-08   0.00046     189     221 ..      34      66 ..      26      72 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.00089
                                       XXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50  87 rllivlAGplanfilailvfv 107
                                        l i ++G+ +n+ilai+ ++
  gi|385805753|ref|YP_005842151.1|   7 NLNISASGITVNLILAIAGLA 27 
                                       67899************8776 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 2.6e-08
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50 189 ssflqllalisvnLgilNLlPipvLDGghllfa 221
                                        +f+  + +i+  L+++NL+P+ ++DG ++++a
  gi|385805753|ref|YP_005842151.1|  34 PAFFINFSIINTWLALFNLIPFGPFDGAKIFKA 66 
                                       577888899*********************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); 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 0.27s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 533.09
//
Query:       gi|385805754|ref|YP_005842152.1|  [L=239]
Description: proteasome subunit Alpha [Fervidicoccus fontis Kam940]
Scores for complete 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-62  208.4   0.0    9.2e-62  207.9   0.0    1.2  1  Proteasome      Proteasome subunit
    8.3e-14   51.0   1.4    3.3e-13   49.0   0.5    2.4  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 !  207.9   0.0     1e-65   9.2e-62       1     190 []      33     217 ..      33     217 .. 0.98

  Alignments for each domain:
  == domain 1  score: 207.9 bits;  conditional E-value: 1e-65
                                       HHHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSS CS
                        Proteasome   1 vkkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygr 77 
                                       vk+G+++vGik+ +gvvlaa+k +t   +l++  ++eK++ id higv+faG  +D+r+l+++ar+ a ++rl+yg+
  gi|385805754|ref|YP_005842152.1|  33 VKQGWSTVGIKTPGGVVLAAEKAVT--KSLMDVVSIEKVSMIDTHIGVTFAGFGGDGRVLIEYARQIAVSHRLTYGE 107
                                       799**********************..9999********************************************** PP

                                       GTCHHHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHH CS
                        Proteasome  78 pipverlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekey 154
                                       pip+e+l+++v++++qaytq++g+rpfgvslli+g+d  g p+L+++dp+G+y+++  a+++G g+  + + lek+y
  gi|385805754|ref|YP_005842152.1| 108 PIPIEYLTKQVSDLKQAYTQHGGVRPFGVSLLIGGIDSSG-PQLFKTDPAGQYFGY-FATSMGRGEAQIEEKLEKNY 182
                                       *************************************888.***************.7******************* PP

                                       STTBSHHHHHHHHHHHHHHHHHHBTTSCSSEEEEEE CS
                        Proteasome 155 kedltleeavelavkalkealerdklsgknievavi 190
                                       ++d++lee++ la+k+lke++++d l+ +n++v++i
  gi|385805754|ref|YP_005842152.1| 183 RKDMSLEEGILLALKVLKESSDQD-LKAQNFDVGII 217
                                       **********************77.********997 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 !   49.0   0.5   3.7e-17   3.3e-13       1      23 []      10      32 ..      10      32 .. 0.99
   2 ?   -0.3   0.0       0.1   9.1e+02      17      20 ..      91      94 ..      83      96 .. 0.70

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 3.7e-17
                    Proteasome_A_N  1 YDrslttFSPdGRLfQVEYAmkA 23
                                      YDr+lt+FSPdGRL+QV YA++A
  gi|385805754|ref|YP_005842152.1| 10 YDRALTVFSPDGRLYQVQYAFEA 32
                                      **********************9 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.1
                    Proteasome_A_N 17 VEYA 20
                                      +EYA
  gi|385805754|ref|YP_005842152.1| 91 IEYA 94
                                      8999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        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 0.27s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1542.06
//
Query:       gi|385805755|ref|YP_005842153.1|  [L=124]
Description: superoxide reductase [Fervidicoccus fontis Kam940]
Scores for complete 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   96.1   0.1    1.7e-27   95.9   0.1    1.1  1  Desulfoferrodox  Desulfoferrodoxin
    2.2e-09   37.5   0.0    2.6e-09   37.3   0.0    1.1  1  SoxY             Sulfur oxidation protein SoxY


Domain annotation for each model (and alignments):
>> Desulfoferrodox  Desulfoferrodoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.9   0.1   1.9e-31   1.7e-27       3      95 ..      19     117 ..      17     118 .. 0.95

  Alignments for each domain:
  == domain 1  score: 95.9 bits;  conditional E-value: 1.9e-31
                                       HTTTHTTSEEEEEESEEEETTEEEEEEEESSSS--BSSSS-EEEEEEEEEETTSS.......EEEE-TBS.ESEEEE CS
                   Desulfoferrodox   3 dekeekHvPvieadevvkagelfevkvkvgkipHpneeeHyIewielyleeegek.......rvelsaed.epevtf 71 
                                        +k e+H+P iea+e+vka+e+f+vk++vg  pHpn+ +H+I+ +++y+ eeg++       +ve+++e+ ep +t+
  gi|385805755|ref|YP_005842153.1|  19 ISKVETHTPKIEAPESVKANEAFTVKISVG--PHPNQVSHFIRSLTVYFVEEGRAfnpvhlaTVEFEPEYsEPIITL 93 
                                       57899*************************..**********************9****9999*****9956***** PP

                                       EEEESSSEEEEEEEEETTTEEEEE CS
                   Desulfoferrodox  72 tvklkkekklvalsyCnlHGlWes 95 
                                       t+klkk+++++al yCnlHG+We 
  gi|385805755|ref|YP_005842153.1|  94 TLKLKKSGTIYALGYCNLHGVWEG 117
                                       **********************97 PP

>> SoxY  Sulfur oxidation protein SoxY
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.0   2.9e-13   2.6e-09      16     107 ..      26     123 ..      12     124 .] 0.78

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 2.9e-13
                              SoxY  16 kvkldaPeiAengavVpvtvsvd.lpgteadkvksial.lvdk..Npapl.aatfelgp.ageaevstrirlaetsn 86 
                                       + k++aPe ++  +++ v++sv  +p++ ++ ++s+++ +v++    +p+ +at+e++p   e+ +++ ++l+++ +
  gi|385805755|ref|YP_005842153.1|  26 TPKIEAPESVKANEAFTVKISVGpHPNQVSHFIRSLTVyFVEEgrAFNPVhLATVEFEPeYSEPIITLTLKLKKSGT 102
                                       349*******999999999999524455555666677724444223456668999999978**************** PP

                              SoxY  87 vravaetsdgklyvaskeVkv 107
                                       ++a+ +++ + +++++keVkv
  gi|385805755|ref|YP_005842153.1| 103 IYALGYCNLHGVWEGKKEVKV 123
                                       ********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 849.07
//
Query:       gi|385805756|ref|YP_005842154.1|  [L=183]
Description: NUDIX hydrolase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-20   72.6   0.1    4.3e-20   72.1   0.1    1.3  1  NUDIX     NUDIX domain
  ------ inclusion threshold ------
       0.47   11.0   3.1       0.67   10.5   1.7    1.9  2  Kri1      KRI1-like family


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 !   72.1   0.1   4.8e-24   4.3e-20       3     122 ..      44     158 ..      42     170 .. 0.77

  Alignments for each domain:
  == domain 1  score: 72.1 bits;  conditional E-value: 4.8e-24
                                       EEEEEEEEEETTSEEEEEEESSSSTTTE..ESSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEE CS
                             NUDIX   3 rravgvvllnekgevLlvrrskkpfpgW..elPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapydgp 77 
                                       +++++v+ +n++ +++l++++++p + W  e+P+G+ve+gE+p++AA+REl+EEtG++a+++e ++   +++ ++g+
  gi|385805756|ref|YP_005842154.1|  44 GKSAAVLPINDD-RIVLIEQFRYPINKWiiEIPAGRVEKGEDPRNAALRELKEETGYTARNIEEVA---SFFVSPGY 116
                                       578999988888.5*******788888*766****************************8887777...44444444 PP

                                       EEEEEEEEEEEEEEECSGCSSTSTTTEEEEEEEEHHHHHHHHTHC CS
                             NUDIX  78 ygdeheilyvfleevegelepndenevsevrwvpleellkeklaa 122
                                        + e ++ly+ ++ +++e+ ++ ++e+  ++ ++++e+ ke+l++
  gi|385805756|ref|YP_005842154.1| 117 SD-ELMYLYIAEDLKKSEQSLE-KGELIRLKELSIKEV-KEMLKK 158
                                       44.5666666667777776666.*******99999999.444333 PP

>> Kri1  KRI1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.43   3.8e+03      28      45 ..      89     106 ..      80     111 .. 0.67
   2 ?   10.5   1.7   7.5e-05      0.67       3      37 ..     130     164 ..     128     172 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.43
                              Kri1  28 klekikkaageeeaalke 45 
                                        l+++k+++g ++++++e
  gi|385805756|ref|YP_005842154.1|  89 ALRELKEETGYTARNIEE 106
                                       467777777755555554 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 7.5e-05
                              Kri1   3 keeekeekkeelkrlkklkreeieeklekikkaag 37 
                                       k++e+   k el rlk+l ++e++e+l+k + + g
  gi|385805756|ref|YP_005842154.1| 130 KKSEQSLEKGELIRLKELSIKEVKEMLKKREITDG 164
                                       7889999999******************9777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       723  (0.0403257); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1145.60
//
Query:       gi|385805757|ref|YP_005842155.1|  [L=147]
Description: carbon monoxide dehydrogenase subunit G [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-23   83.4   0.1    1.4e-23   83.2   0.1    1.0  1  COXG             Carbon monoxide dehydrogenase subunit G (Cox
    2.4e-05   24.6   0.0    2.8e-05   24.4   0.0    1.0  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra
  ------ inclusion threshold ------
      0.065   13.0   0.1       0.15   11.8   0.1    1.6  1  RFX5_N           RFX5 N-terminal domain
       0.13   12.4   0.0       0.25   11.4   0.0    1.5  1  DUF2505          Protein of unknown function (DUF2505)


Domain annotation for each model (and alignments):
>> COXG  Carbon monoxide dehydrogenase subunit G (CoxG)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.2   0.1   3.1e-27   1.4e-23       5     140 .]      12     146 ..       9     146 .. 0.96

  Alignments for each domain:
  == domain 1  score: 83.2 bits;  conditional E-value: 3.1e-27
                                       ESS-HHHHHHHHT-HHHHGGGSTTEEEEEEETTEEEEEEEEESSSSEEEEEEEEEEEEEETTTEEE..EEEEEE-SS CS
                              COXG   5 vaapkeavwefLndpeklarciPGvksvekegdeykvkvklkvGplkgsfkarvelselekensttieikGkGrgag 81 
                                       ++a++ +v  +L+d  +++ ciP+v s  +eg +++ kv+ k+G+++g+f ++ e+ e e+e+ +   ik   +g  
  gi|385805757|ref|YP_005842155.1|  12 INANRGKVASILKDVRNFSDCIPNVISSRTEGSKFSGKVRFKIGSVSGTFDVDGEILEKEPERAYDFYIKSGTSGNI 88 
                                       789999*********************************************************99999999999999 PP

                                       EEEEEEEEEEEEEETTEEEEEEEEEEEEEHHHHS-HHHHHHHHHHHHHHHHHHHHHHHT CS
                              COXG  82 vaidfalvvlveegggtrlswsakvnvggllaslGsrlidsaarklinelfecissklg 140
                                       ++ ++++++++ ++g+t l++ a++++gg++a lG + i+s+ + li+++f+ci++k++
  gi|385805757|ref|YP_005842155.1|  89 IETKGTITLSDADNGKTLLEYHAEAKLGGMIAALG-KIIESTSNDLIKQMFSCIEQKIS 146
                                       99*********99999******************9.69******************986 PP

>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   6.3e-09   2.8e-05       7     129 ..       9     124 ..       4     137 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 6.3e-09
                                       EEEESS-HHHHHHHHTTTTGGGGT-TTEEEEECSESTSSSTTTEEEEE.CCCS..SE..EEEEEEEEETTTTEEEEE CS
                   Polyketide_cyc2   7 svviaappekVwalvsdfenwprWhpevarveleggggpargvegtvr.vggr..gt..vreelvevdpegrllsyr 78 
                                       s  i+a   kV +++ d +n++  +p+v +++ e  g++  ++ g+vr + g   gt  v  e++e +p +r++ + 
  gi|385805757|ref|YP_005842155.1|   9 SLIINANRGKVASILKDVRNFSDCIPNVISSRTE--GSK--FS-GKVRfKIGSvsGTfdVDGEILEKEP-ERAYDFY 79 
                                       55699999*********************99655..444..44.445533333442233**********.******* PP

                                       EE...SSS-TSEEEEEEEEECCET.EEEEEEEEEEEE--TT--HHHHHHHHHHH CS
                   Polyketide_cyc2  79 iv..kpvpvanyvatwtvtpdggg.trvtwtgefdagplggpfekpaaakavkg 129
                                       i   +   +   ++t+t+ +++ g t +++++e++    gg+       +a+++
  gi|385805757|ref|YP_005842155.1|  80 IKsgTSGNIIETKGTITLSDADNGkTLLEYHAEAKL---GGM------IAALGK 124
                                       *65778888889**********88699*****8884...233......334444 PP

>> RFX5_N  RFX5 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   3.4e-05      0.15       7      31 ..       6      31 ..       3      33 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.4e-05
                            RFX5_N  7 ikns.icKavqsKvdgiLqdveKFtD 31
                                      ikns i  a   Kv +iL+dv  F+D
  gi|385805757|ref|YP_005842155.1|  6 IKNSlIINANRGKVASILKDVRNFSD 31
                                      788756789999*************9 PP

>> DUF2505  Protein of unknown function (DUF2505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   5.7e-05      0.25      92     146 ..      80     137 ..      57     144 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.7e-05
                           DUF2505  92 vsasvkgapvelsGtltLepege.gtrlevegevkv..kiPlvGgklEklvaenleel 146
                                       ++   +g+  e++Gt+tL+++++ +t le+ +e+k    i  +G+ +E++  + ++++
  gi|385805757|ref|YP_005842155.1|  80 IKSGTSGNIIETKGTITLSDADNgKTLLEYHAEAKLggMIAALGKIIESTSNDLIKQM 137
                                       55566788899*********77757********9983358888888888766666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); 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: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 997.04
//
Query:       gi|385805758|ref|YP_005842156.1|  [L=355]
Description: hypothetical protein FFONT_0716 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-26   93.0   0.0      3e-22   79.1   0.0    2.4  2  DUF711    Uncharacterised ACR (DUF711)


Domain annotation for each model (and alignments):
>> DUF711  Uncharacterised ACR (DUF711)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   5.1e-06     0.092       6      70 ..       3      57 ..       1      87 [. 0.82
   2 !   79.1   0.0   1.7e-26     3e-22     143     394 ..     101     333 ..      68     343 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.1e-06
                            DUF711  6 kldiRtvTlgislldcasedleklaekiyekiikkaaklvktveeieeeyGievvtkRisvtpis 70
                                      +l+iR+ Tl ++l+ + +e+++           +  ++l ++ e+ie+e G+ev + R+s+ pi+
  gi|385805758|ref|YP_005842156.1|  3 DLRIRALTLHLNLSRERKEEEA---------LKNAVSDLYSAKEKIEKEIGLEVWSLRVSI-PIN 57
                                      589***********88877755.........6788999*********************98.454 PP

  == domain 2  score: 79.1 bits;  conditional E-value: 1.7e-26
                            DUF711 143 aginmdavraaaevikeiaeltkdkdglgnaklvvfan.vpednPFfpgAfhgvgeaeavinvGvsgpgvvkkalee 218
                                       agi +++ r +++++  i +l+ + d   +++++v ++     +P+fp ++h+++ +e  +++++  p+ v      
  gi|385805758|ref|YP_005842156.1| 101 AGIFLRSERDLSKILDLIYNLSLK-DPAFSTRFAVEMSgLGITTPYFPLSIHDSSVKEDYFSIALLYPKDV------ 170
                                       566666666666666666666665.5556688888655257789********************9999644...... PP

                            DUF711 219 akkeasleelaeaikktafkitrlgel.varevakrlgvefggiDlSlaPtpavgdSvaeileelglesfGapGtla 294
                                        + +++l+ ++ ai+k+   + ++  + ++++       + +giD Sl+P   +++Sv+++le++g+ ++     ++
  gi|385805758|ref|YP_005842156.1| 171 -EGGEDLRAVELAIEKAYRSLSKFIREgIGKK-------KLRGIDYSLSPW--MEESVGRALEKIGRCKLSDLKCMK 237
                                       .4557899999999999999988765415555.......899*********..78********************** PP

                            DUF711 295 alalltdavkkGGvmasskvgGlsGlflpvsEDaglaeaaeegaltiekLlamsaVCsvGLDmvpipgdtsaetiaa 371
                                       ++  ++  + +   +++ +  G++ ++lp+ ED+ l+  a +g+lti++Ll +s VC  G+Dm+p+ g+  +e+ + 
  gi|385805758|ref|YP_005842156.1| 238 TVYEVNSILSD--FASKHEGLGFNEIMLPLGEDSYLMSLALNGELTIKDLLLLSYVCVAGMDMIPVRGK--KEQFED 310
                                       ***********..55556678*********************************************996..679*** PP

                            DUF711 372 liaDeaalavrlnKtlavRliPv 394
                                       l++D  a+a + +++ +vRli +
  gi|385805758|ref|YP_005842156.1| 311 LLRDIYAVARVKRRPYGVRLIYI 333
                                       ********************966 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); 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: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2378.29
//
Query:       gi|385805759|ref|YP_005842157.1|  [L=229]
Description: putative phosphoserine phosphatase, SerB [Fervidicoccus fontis Kam940]
Scores for 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   47.9   0.0    7.2e-11   42.8   0.0    2.1  1  Hydrolase        haloacid dehalogenase-like hydrolase
    1.8e-06   28.5   0.0    2.2e-06   28.2   0.0    1.3  1  HAD              haloacid dehalogenase-like hydrolase
     0.0006   19.6   0.0      0.018   14.8   0.0    2.7  3  Hydrolase_3      haloacid dehalogenase-like hydrolase
    0.00076   19.0   0.0      0.002   17.6   0.0    1.6  2  Put_Phosphatase  Putative Phosphatase
  ------ inclusion threshold ------
      0.018   15.2   0.1       0.19   11.8   0.0    2.3  2  HAD_2            Haloacid dehalogenase-like hydrolase
      0.056   13.5   0.4       0.29   11.2   0.5    2.1  2  HTH_19           Helix-turn-helix domain
      0.072   12.6   0.0       0.19   11.3   0.0    1.6  2  S6PP             Sucrose-6F-phosphate phosphohydrolase
      0.081   13.0   0.0         11    6.2   0.0    2.8  3  Hydrolase_6      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 !   42.8   0.0   3.2e-14   7.2e-11       1     207 [.       4     182 ..       4     185 .. 0.75

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 3.2e-14
                                       SSEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTEHHHHTHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase   1 iktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrgayaigkpewl 77 
                                       +k+v+fD+dG+ ++ ++s  +v   +                         + + ++++++       +  gk  + 
  gi|385805759|ref|YP_005842157.1|   4 VKLVAFDVDGVFLENRNSWDTVSSFL-------------------------GTEKNIQNYQL------FISGKISYY 49 
                                       58899999999998887777777666.........................44555555555......666777777 PP

                                       HHHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  78 taldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanq 154
                                       +++     + ++ +   +  +  + +      +  + +++kvk e++++ ++L++ g ++vll+g+   +++++a  
  gi|385805759|ref|YP_005842157.1|  50 EWM-----YLDTLSWIRGSKKGYVSK----EDLERAFQSIKVKVEVVDLAKRLRQSGKKIVLLSGGIDVFVRKVALM 117
                                       777.....222222222223333333....33334445567************************************ PP

                                       TT..GGGESEEEEHHCES..........STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHH CS
                                       xx..xxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 155 lG..ddyfdaviasdiet..........vakpspegkvaaireLqgkpeevamVGDgvnDaaala 207
                                       +G     f++++  d ++           a+ + e+++++ ++L++ ++e+a++GD+++D +++ 
  gi|385805759|ref|YP_005842157.1| 118 IGedVTWFANILIFDSNGrlvpggiplvPAGKKGEILRRIREKLNIIKKETAFIGDSAWDKEGFT 182
                                       **966666999999999989888888877888****************************88765 PP

>> HAD  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   9.7e-10   2.2e-06      69     183 ..      69     177 ..       7     181 .. 0.74

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 9.7e-10
                               HAD  69 laaelerfvaevirpklldpgalellaahraaGdrvvvvSgglrplvepllaelgadev..latelevdd...rltg 140
                                        +++ler++++++ +     ++++l ++ r+ G ++v++Sgg++ +v+ ++   g ++v   a+ l +d        
  gi|385805759|ref|YP_005842157.1|  69 SKEDLERAFQSIKVKV----EVVDLAKRLRQSGKKIVLLSGGIDVFVRKVALMIG-EDVtwFANILIFDSngrL--- 137
                                       4688899997777655....8888888888*********************8889.444346664444434444... PP

                               HAD 141 elglegkpvrgegkv.aalrewlaaegegidleevvayGDspsD 183
                                          + g p   +gk    lr+   +e+ +i  +e+ ++GDs +D
  gi|385805759|ref|YP_005842157.1| 138 --VPGGIPLVPAGKKgEILRR--IREKLNIIKKETAFIGDSAWD 177
                                       ..4444555555555144445..77799999999*********9 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.48   1.1e+03       1      15 [.       7      21 ..       2      45 .. 0.73
   2 ?    1.3   0.0      0.11   2.4e+02      16      66 ..      82     138 ..      77     141 .. 0.79
   3 !   14.8   0.0     8e-06     0.018     187     229 ..     149     191 ..     139     211 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.48
                                      EEEEIIIIIS-TTS- CS
                       Hydrolase_3  1 ialDlDGTLlnsdkk 15
                                      +a+D+DG +l + ++
  gi|385805759|ref|YP_005842157.1|  7 VAFDVDGVFLENRNS 21
                                      578888887776654 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.11
                                       --HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCC......SEEEEGGGTEE CS
                       Hydrolase_3  16 isektkeaikklkekgikvviATGRslravlpvleelgld......lpvialNGali 66 
                                       ++ + ++  k+l++ g k+v+ +G   ++v++v+  +g d        +  +NG l+
  gi|385805759|ref|YP_005842157.1|  82 VKVEVVDLAKRLRQSGKKIVLLSGGIDVFVRKVALMIGEDvtwfanILIFDSNGRLV 138
                                       5667788899**************999999999998886655666555556888766 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 8e-06
                                       SHHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEET CS
                       Hydrolase_3 187 sKgtalkklakelnisleeviafGDgeNDieMLeaaglgvAmg 229
                                       +Kg+ l+++ ++lni ++e++ +GD+  D e ++ +gl++  +
  gi|385805759|ref|YP_005842157.1| 149 KKGEILRRIREKLNIIKKETAFIGDSAWDKEGFTESGLSILYN 191
                                       79************************************99655 PP

>> Put_Phosphatase  Putative Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   8.7e-07     0.002       2     109 ..       6     117 ..       5     141 .. 0.72
   2 ?   -1.8   0.0      0.74   1.7e+03     151     181 ..     150     177 ..     144     178 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 8.7e-07
                   Put_Phosphatase   2 lvvfDFDktiid.edsdnwvvdelpatelfeelretlr.kglwnelmd.rvlkelheqg...vseadikkvlrsipl 72 
                                       lv+fD D   ++  +s ++v++ l++++  ++ +  +  k  + e+m    l  ++ ++   vs++d++++++si +
  gi|385805759|ref|YP_005842157.1|   6 LVAFDVDGVFLEnRNSWDTVSSFLGTEKNIQNYQLFISgKISYYEWMYlDTLSWIRGSKkgyVSKEDLERAFQSIKV 82 
                                       89******9986269************999887766652445666553244555543322479************** PP

                   Put_Phosphatase  73 spglvelikslakkkleldliiiSDaNsffieeilea 109
                                       + ++v+l k l  ++++  ++++S    +f+ ++   
  gi|385805759|ref|YP_005842157.1|  83 KVEVVDLAKRL--RQSGKKIVLLSGGIDVFVRKVALM 117
                                       ***********..4578999****9999999876433 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.74
                   Put_Phosphatase 151 KgkvleelvaeqaregveyerliYvGDganD 181
                                       Kg++l +++++    ++  +   ++GD+a D
  gi|385805759|ref|YP_005842157.1| 150 KGEILRRIREKL---NIIKKETAFIGDSAWD 177
                                       889999999884...5567888999999866 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   0.2      0.19   4.2e+02       2      17 ..       8      23 ..       7     119 .. 0.62
   2 ?   11.8   0.0   8.4e-05      0.19     138     174 ..     151     187 ..     145     191 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.19
                             HAD_2  2 iFDlDgTlldteelii 17
                                       FD+Dg+ l  ++ + 
  gi|385805759|ref|YP_005842157.1|  8 AFDVDGVFLENRNSWD 23
                                      5888888877666553 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 8.4e-05
                             HAD_2 138 peviekaleklklkkeeviyvGDsptDieaakkagik 174
                                        e+++++ ekl++ k+e+ ++GDs  D e+  + g+ 
  gi|385805759|ref|YP_005842157.1| 151 GEILRRIREKLNIIKKETAFIGDSAWDKEGFTESGLS 187
                                       6789999********************9998888765 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.88     2e+03      45      60 ..     111     126 ..      88     127 .. 0.67
   2 ?   11.2   0.5   0.00013      0.29       1      54 [.     151     211 ..     151     221 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.88
                            HTH_19  45 llkiaealgidleyll 60 
                                       ++k+a   g d++++ 
  gi|385805759|ref|YP_005842157.1| 111 VRKVALMIGEDVTWFA 126
                                       4778888888888875 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00013
                            HTH_19   1 GerLkeaReelgltqeelae.......rlgisrskisaiEngkkdvpsaelllkiaealgi 54 
                                       Ge L+++Re+l++ ++e a        + g++ s +s + ng k+++s +++ ++ae ++ 
  gi|385805759|ref|YP_005842157.1| 151 GEILRRIREKLNIIKKETAFigdsawdKEGFTESGLSILYNGIKEELSEMKVCAVAENVEE 211
                                       89******************99999999999999999999997779999999999998876 PP

>> S6PP  Sucrose-6F-phosphate phosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.1   2.4e+03       4      42 ..       6      43 ..       4      47 .. 0.72
   2 ?   11.3   0.0   8.3e-05      0.19     163     227 ..     147     215 ..     142     223 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.1
                                      EEEE-TBTTTB.S-HHHHHHHHHHHH.GGGGGEEEEEE- CS
                              S6PP  4 llvsdLDntlvdgdnealarlnelleaeerkdvllvfaT 42
                                      l++ d+D+ ++ +++++ +   ++l +e++ + +  f++
  gi|385805759|ref|YP_005842157.1|  6 LVAFDVDGVFL-ENRNSWDTVSSFLGTEKNIQNYQLFIS 43
                                      77889999999.888888888888886666555555555 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 8.3e-05
                                       T-SHHHHHHHHHHHHT--GGGEEEEE-SGGGHHHHTSSSEEEE-TT--HH....HHHHHHHH--TTE.. CS
                              S6PP 163 raskgeAlryLakkleleleqilvcGdsgnDeellignvlgVvVgnaqee....llqwllenakeneri 227
                                       +++kge lr + +kl++  +++ + Gds  D+e ++++ l++     +ee    ++   +en +e e+i
  gi|385805759|ref|YP_005842157.1| 147 AGKKGEILRRIREKLNIIKKETAFIGDSAWDKEGFTESGLSILYNGIKEElsemKVCAVAENVEEVEKI 215
                                       5789*************************************9988877774444455556666666555 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0    0.0048        11       1      25 [.       7      31 ..       7      58 .. 0.85
   2 ?    3.6   0.0     0.032        71      18      37 ..      85     104 ..      77     117 .. 0.88
   3 ?   -1.5   0.0       1.2   2.8e+03       2      21 ..     130     149 ..     129     172 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0048
                                      EEEESTTTSEETTEE-TTHHHHHHH CS
                       Hydrolase_6  1 flfDidGvLwrgdkaipgaaealna 25
                                      ++fD+dGv++++++  + +  +l +
  gi|385805759|ref|YP_005842157.1|  7 VAFDVDGVFLENRNSWDTVSSFLGT 31
                                      68*********99999998888865 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.032
                                       THHHHHHHHHHTT-EEEEEE CS
                       Hydrolase_6  18 gaaealnalraagkpvvllT 37 
                                       +++++ ++lr++gk++vll+
  gi|385805759|ref|YP_005842157.1|  85 EVVDLAKRLRQSGKKIVLLS 104
                                       5788999***********98 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.2
                                       EEESTTTSEETTEE-TTHHH CS
                       Hydrolase_6   2 lfDidGvLwrgdkaipgaae 21 
                                       +fD  G L+ g+ ++  a +
  gi|385805759|ref|YP_005842157.1| 130 IFDSNGRLVPGGIPLVPAGK 149
                                       78999999977777655543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); 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: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 1593.21
//
Query:       gi|385805760|ref|YP_005842158.1|  [L=441]
Description: hypothetical protein FFONT_0718 [Fervidicoccus fontis Kam940]
Scores for complete 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-30  104.2  20.5    7.5e-30  104.2  20.5    2.3  2  DUF4010   Domain of unknown function (DUF4010)
    9.4e-18   64.7   4.6    9.4e-18   64.7   4.6    3.5  3  MgtC      MgtC family
  ------ inclusion threshold ------
        2.4    8.0   4.7        2.5    8.0   0.2    2.9  3  Lig_chan  Ligand-gated ion channel


Domain annotation for each model (and alignments):
>> DUF4010  Domain of unknown function (DUF4010)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   4.0      0.77   4.6e+03      59      82 ..      79     101 ..      54     175 .. 0.52
   2 !  104.2  20.5   1.3e-33   7.5e-30       2     208 ..     200     409 ..     199     411 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.77
                           DUF4010  59 gillAnavmllrvllivavvnpal 82 
                                        +l  + + ++ +l++ ++  + l
  gi|385805760|ref|YP_005842158.1|  79 EVLTVSGAIFVTILMVSYIYFR-L 101
                                       4444444444444444444222.1 PP

  == domain 2  score: 104.2 bits;  conditional E-value: 1.3e-33
                           DUF4010   2 lisaisfagYvalrllgarrGllltgllGGlvSStAvtlslarrskeepelarllaagillAnavmllrvllivavv 78 
                                       li+ais+++Y+a +l g+ ++ll+++llGGl++S+A+ +++ +   +     ++la    + n+ m++r++l v++ 
  gi|385805760|ref|YP_005842158.1| 200 LILAISYISYMAYKLKGE-KSLLAVSLLGGLINSEATLMNILKIGVK----GKKLAKLSSINNSGMVIRTALTVLIG 271
                                       89***************9.*************************999....5667777799***************8 PP

                           DUF4010  79 npallv....ala...lpllalallallvaalllrrrekeeeee...elelenPlelksAlkfallfalilllakaa 145
                                       + + l+    +++   +   +l+ +++l+ +++l  rek++ee+    l l +Ple+k A +  +l++li +l+k+ 
  gi|385805760|ref|YP_005842158.1| 272 AYPFLIsdgyEIFaryIISGVLLSIMILYLTYTLSGREKKAEENgekVLYLASPLEVKIATRGVILYILIFVLVKVS 348
                                       8755553332222332334455556666666666666666666678999**************************** PP

                           DUF4010 146 qeyfGdaglyalaalsGladvdAitlslarlaaegtlsaataalaillavlsntlvKavlalv 208
                                       + y+G+ +l+++++++G+a++ A++lsl++l   +t+s +++  a ll++ + +l+K+++a +
  gi|385805760|ref|YP_005842158.1| 349 NYYLGSYALFITSFIGGFASSIATVLSLLSLG--STVSIKIISSASLLSMGAAMLNKIIYAKI 409
                                       *******************************9..7*************************976 PP

>> MgtC  MgtC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.7   4.6   1.6e-21   9.4e-18       1     119 [.      17     151 ..      17     153 .. 0.79
   2 ?   -1.8   4.0      0.65   3.9e+03      24      71 ..     262     310 ..     198     388 .. 0.75
   3 ?    0.2   1.1      0.15   9.1e+02      35      66 ..     369     400 ..     355     440 .. 0.55

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 1.6e-21
                              MgtC   1 LllAlllGlliGleRel.....rek......aaGlRTfaLvalgaalfvllslelae.srvaaq..vvsgigflg.. 61 
                                       L++++l G+l+GleR +     +          G+RT+ L+++++++++ll++   + s  a++  +vsg +f++  
  gi|385805760|ref|YP_005842158.1|  17 LIISFLEGGLLGLERYKvgmekQ-DkieseeLPGVRTYGLMSILGTILALLNSDKISvSPFANEvlTVSGAIFVTil 92 
                                       789************99776542.1455556********************77666666666665556666666653 PP

                              MgtC  62 ..agvilkekega..kvkglTTaaslwvtaaiGllvglglyllavvatvlvllllallrele 119
                                           + ++       k+ glT+  ++++t++iG+l+g+g+y+l++ +t+l++ +la++r ++
  gi|385805760|ref|YP_005842158.1|  93 mvSYIYFRL---YrlKIAGLTSYFVFFLTFIIGFLTGYGYYILSMSLTFLIAGILAFKRAIT 151
                                       213333322...246*******************************************9886 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.65
                              MgtC  24 lRTfaLvalgaalfvllslelae.srvaaqvvsgigflgagvilkekeg 71 
                                       +RT   v +ga+ f + + +      ++++v++ i++l     l+ +e+
  gi|385805760|ref|YP_005842158.1| 262 IRTALTVLIGAYPFLISDGYEIFaRYIISGVLLSIMILYLTYTLSGREK 310
                                       6777777777777777744332225566667777766665555544443 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.15
                              MgtC  35 alfvllslelaesrvaaqvvsgigflgagvil 66 
                                       +++++lsl    s v  +++s   +l +g+ +
  gi|385805760|ref|YP_005842158.1| 369 SIATVLSLLSLGSTVSIKIISSASLLSMGAAM 400
                                       44555544444455555555555555544443 PP

>> Lig_chan  Ligand-gated ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.25   1.5e+03      50      90 ..      59      97 ..      31      98 .. 0.71
   2 ?    8.0   0.2   0.00041       2.5      74     105 ..     191     222 ..     168     318 .. 0.83
   3 ?   -0.3   0.4      0.15   8.9e+02      68      97 ..     329     359 ..     323     376 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.25
                                      HHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Lig_chan 50 lwfslgalvqqGcdesprsvsgRivvavWwffvlillssYt 90
                                      l  +l+ l     ++s+  ++  +++++ ++fv il+ sY+
  gi|385805760|ref|YP_005842158.1| 59 LGTILALLNS--DKISVSPFANEVLTVSGAIFVTILMVSYI 97
                                      4444444444..47777778888889999999999999995 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00041
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Lig_chan  74 vvavWwffvlillssYtAnLaafltvermqtp 105
                                       + +v++ff+lil  sY+  +a  l  e+    
  gi|385805760|ref|YP_005842158.1| 191 LQGVYIFFTLILAISYISYMAYKLKGEKSLLA 222
                                       6789*************999988877776555 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.15
                                       XXXXXXXXXXXXXXXXXXXXXX.XXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                          Lig_chan  68 svsgRivvavWwffvlillssY.tAnLaafl 97 
                                       ++++R v++  ++fvl+ +s Y  ++ a f+
  gi|385805760|ref|YP_005842158.1| 329 KIATRGVILYILIFVLVKVSNYyLGSYALFI 359
                                       5678888888899999988876145555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       867  (0.0483574); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 2865.44
//
Query:       gi|385805761|ref|YP_005842159.1|  [L=91]
Description: hypothetical protein FFONT_0719 [Fervidicoccus fontis Kam940]
Scores for complete 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-10   38.3   1.6    1.2e-09   37.9   1.6    1.1  1  Alba      Alba


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 !   37.9   1.6   6.5e-14   1.2e-09       3      61 ..       9      69 ..       7      73 .. 0.82

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 6.5e-14
                                      EEE-STS-HHHHHHHHHHHHTHTT.ESEEEEEEETTHHHHHHHHHHHHHHHTCT..T.EEEE CS
                              Alba  3 iyVsskspimsyvkralklLsnkk.eeeVvlkatGraIskAvsvaeilkrrfgk..glyqvn 61
                                      i Vs+ ++++ y++r++  L+n + +e+Vv+k++G  I+kA++v++ +k r+g+  +l+ vn
  gi|385805761|ref|YP_005842159.1|  9 IIVSN-KDVSEYALRVIVALRNITeNEVVVIKGRGDFIEKAIDVYNEVKARMGDsiKLVSVN 69
                                      66666.**************5544488999**********************9855555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 624.60
//
Query:       gi|385805762|ref|YP_005842160.1|  [L=1260]
Description: reverse gyrase [Fervidicoccus fontis Kam940]
Scores for complete 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-81  272.6   0.1      1e-80  271.8   0.1    1.4  1  Topoisom_bac   DNA topoisomerase
    5.1e-22   78.1   0.0    2.1e-21   76.0   0.0    2.2  1  Toprim         Toprim domain
    2.1e-15   57.0   0.5    1.1e-14   54.5   0.2    2.4  2  DEAD           DEAD/DEAH box helicase
    4.6e-15   54.8   0.8    4.6e-15   54.8   0.8    2.1  2  zf_Rg          Reverse gyrase zinc finger
    3.5e-10   40.1   0.4      2e-09   37.7   0.2    2.1  2  ResIII         Type III restriction enzyme, res subunit
      3e-08   34.0   0.4    4.4e-05   23.8   0.2    3.8  3  Helicase_C     Helicase conserved C-terminal domain
    3.3e-05   23.4   0.4      0.001   18.5   0.1    2.7  2  ATPase         KaiC
    4.1e-05   23.9   0.2     0.0002   21.7   0.2    2.2  1  AAA_22         AAA domain
    0.00039   20.1   0.0    0.00083   19.0   0.0    1.5  1  AAA_25         AAA domain
    0.00052   18.8   0.0    0.00095   18.0   0.0    1.3  1  SNF2_N         SNF2 family N-terminal domain
  ------ inclusion threshold ------
      0.014   15.1   0.0      0.033   13.9   0.0    1.6  1  AAA_30         AAA domain
      0.017   15.0   0.0       0.04   13.8   0.0    1.6  1  Helicase_RecD  Helicase
      0.021   15.2   0.0      0.048   14.0   0.0    1.6  1  AAA_19         AAA domain
      0.063   13.7   0.0       0.44   11.0   0.0    2.5  1  Toprim_4       Toprim domain
      0.076   12.6   0.4       0.34   10.5   0.2    2.2  1  cobW           CobW/HypB/UreG, nucleotide-binding domain
      0.093   12.4   0.1       0.32   10.6   0.1    1.9  1  SRP54          SRP54-type protein, GTPase domain
      0.097   12.6   5.1        1.8    8.5   0.7    2.9  2  zf-C2HC_2      zinc-finger of a C2HC-type
        0.1   12.0   0.3        3.4    7.1   0.1    2.8  2  PhoH           PhoH-like protein
       0.12   12.1   0.2       0.47   10.2   0.1    2.0  2  AAA_24         AAA domain
       0.16   11.2   0.5       0.31   10.3   0.4    1.5  1  SecA_DEAD      SecA DEAD-like domain
        0.2   12.2   3.2        1.3    9.6   0.3    2.6  2  zf-C2H2        Zinc finger, C2H2 type
       0.29   12.1   6.5       0.37   11.7   0.1    3.0  2  zf-C2H2_4      C2H2-type zinc finger
       0.65   10.1   4.3       0.48   10.5   0.3    2.2  2  DZR            Double zinc ribbon
       0.78    9.7   2.9        2.1    8.3   0.8    2.2  2  zf-C3HC4_3     Zinc finger, C3HC4 type (RING finger)
        3.5    7.2   5.4        1.3    8.5   0.8    2.4  2  zf-ribbon_3    zinc-ribbon domain
        8.2    6.4   7.6       0.38   10.7   1.5    1.9  2  DUF35_N        Rubredoxin-like zinc ribbon domain (DUF35_N)


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 !  271.8   0.1   1.5e-83     1e-80       1     411 [.     823    1227 ..     823    1229 .. 0.85

  Alignments for each domain:
  == domain 1  score: 271.8 bits;  conditional E-value: 1.5e-83
                      Topoisom_bac    1 einenlvdaaeaRrelDwliGinlsrlltkklkgkkvlsaGRVqtptLaliveRereienFvpeeyweveatlkk 75  
                                        +i+e++v ++  Rr+ D++iG+ ls  l+ + + k +l aGRVqtptL++i+ R++e +n   + yw     ++ 
  gi|385805762|ref|YP_005842160.1|  823 KIDESQVSSQILRRVTDRWIGFPLSSRLWSEFQ-KPWLGAGRVQTPTLGWIISRHEEWKNA--RGYWVRIPLINL 894 
                                        58999************************9666.7*************************8..889965433332 PP

                      Topoisom_bac   76 ekkekekkkkkkkerikdkeeaeaileklkkk.eakvesvekkekkk.ppplpfdtttLqkeasrklglsakktl 148 
                                         +          k   kdk+eae++ +++ k+ ++k++s+e  e++  ppp p++t++L+ +a+  +g++a+ t+
  gi|385805762|ref|YP_005842160.1|  895 FA---------VKLFKKDKKEAEDLKNAIIKSgSLKIDSYEIYEQQLlPPP-PYTTDELLHDANMVYGYGAQFTM 959 
                                        22.........22223578999999999988669*************6666.*********************** PP

                      Topoisom_bac  149 siaqkLYekaglitYpRTdstrlseeaelkailealakkygkeylefaekllkktkkksvvknkkveaHeAIrPt 223 
                                        ++ q+L+e  glitY+RTdst++s++  ++ + e+l+k  gk      ++ +  ++++    +++ + HeAIrPt
  gi|385805762|ref|YP_005842160.1|  960 KLSQDLFEA-GLITYHRTDSTHVSNKG-IQIASEYLSKGIGK------PEIFY-PRSW----GSE-GTHEAIRPT 1020
                                        ********5.****************9.99*******98554......44554.6666....666.9******** PP

                      Topoisom_bac  224 eelpklkels...............ddekklYelIvrrflaslmkdakyeettvklev....eeeefkas.gkti 278 
                                        + l+  ++l+               + + klY+lI+rrf+as++++ ++e+ +++l++    e+e f+ +   + 
  gi|385805762|ref|YP_005842160.1| 1021 KALSA-SDLKksivdgtlktyinvtEAHIKLYDLIFRRFIASQSRPSVVEKLKLNLSIsynrEKEVFEKElILRE 1094
                                        **993.344445799*********988889**************************8877766677766624678 PP

                      Topoisom_bac  279 lekGfkkvykeekkeeeeeelpelkegeevkvkeveleekkTkppkryteasLikamekagiGtpaTraeiiekl 353 
                                        +e Gf+ + ++ +++++   + ++ ++ +++v+  ++e  + +  + yt+++++k+m++++iG+p+T+a+i++ l
  gi|385805762|ref|YP_005842160.1| 1095 KETGFYGLLYNINEQTQ---IADYIKEGRIPVDVSKVEIYRGSLIPLYTQGEIVKLMKEKKIGRPSTYAKILDSL 1166
                                        89******997766654...5555555555677777999999999****************************** PP

                      Topoisom_bac  354 vergYverkk..kslvptelGkalvell.ekfkdlvspelTaeleekLdeIaegkadakev 411 
                                         ++gYv+ +k  + ++pt++G+++++ l +++++lvs+e+T++lee++d+I+egk+++ ++
  gi|385805762|ref|YP_005842160.1| 1167 RRHGYVVISKkrNFVIPTNTGIKVYQYLsSNYSSLVSEETTRKLEEDMDAIEEGKESYLAL 1227
                                        ******9885345599************7777***********************998766 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.0   0.0   3.1e-24   2.1e-21       2     103 .]     645     809 ..     644     809 .. 0.96

  Alignments for each domain:
  == domain 1  score: 76.0 bits;  conditional E-value: 3.1e-24
                                       EEEESSHHHHHHHHHTHT........................STEEEEEEESSSSEEEHS..............TTE CS
                            Toprim   2 lvivEgpsdaktiakalg........................sgfqavtaslGhildlet..............efk 40 
                                       +++vE+p +aktia ++g                            +++a++Gh++dl++              ef 
  gi|385805762|ref|YP_005842160.1| 645 MFVVESPHKAKTIAGFFGrpakrrfgsvvvyeipivdqetleTYLAMIVATKGHLFDLVSdnnigtygvikvneEFI 721
                                       59***************************************999999***************************999 PP

                                       EEEE..........................ECTTTHHHHHHHHHHHHHHSEEEEECSSSHHHHHHHHHHHHHHTHHH CS
                            Toprim  41 pvye..........................eiedkkkvlkalkelakradeiilatDpDreGeaiawellevlkell 91 
                                       pvy                           +i++  +++ +l+++a + +ei++atDpD+eGe+iaw++  ++k+++
  gi|385805762|ref|YP_005842160.1| 722 PVYApiskclscgrtfvslhnkcpycgesfKIKSSMETVHVLRKIAMESEEIYIATDPDVEGEKIAWDVEMAIKPYN 798
                                       99999999999999999999999999999999999999999************************************ PP

                                       TTTEEEEEESSS CS
                            Toprim  92 enkigrvefsei 103
                                       ++ i r+ef+e+
  gi|385805762|ref|YP_005842160.1| 799 SK-IIRAEFHEV 809
                                       **.*******96 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.5   0.2   1.7e-17   1.1e-14       4     148 ..     101     242 ..      98     307 .. 0.80
   2 ?   -1.1   0.0         2   1.4e+03      92     116 ..     683     707 ..     677     714 .. 0.80

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 1.7e-17
                                       HHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEE. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                              DEAD   4 QaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvl. 79 
                                       Q+   + +l g+++ + a+TG GKT+  l  +  ++     k+g k+ i++Pt++L +qt ++lk+++ ++++ ++ 
  gi|385805762|ref|YP_005842160.1| 101 QKTWAHRLLLGESFAITAPTGVGKTTLLLHYAAYQL-----KKGEKVYILVPTESLLNQTEEKLKEICYKMGIDAEi 172
                                       7777788888*****************999999777.....8999************************97755553 PP

                                       EEET....TSSHHHHHHHHHTT.CSEEEEEHHHHHHHHHCTSSHCTTEEE..EEEETHHHHHHTTTHHHHHHHHHH CS
                                       xxxx....xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  80 liig....gvaardqlskldng.vdivvgtpgrlddllstgklnlsqvrf..lVlDEadrlldqgfsdfinrilnq 148
                                       ++++    ++++++ l+k+++g   ++++t++ l +  +     l++++f  +V+D ad ll++  s  i+++l  
  gi|385805762|ref|YP_005842160.1| 173 VVYQsrasKKKREEVLKKIEEGkFGVLITTTSFLSRRYD--I--LKKLKFdlIVVDDADSLLKN--SVNIEKVLVL 242
                                       44442222556666666666667999**99988887332..3..56665555**********98..6666666655 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2
                                       HHHHTTCSEEEEEHHHHHHHHHCTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  92 skldngvdivvgtpgrlddllstgk 116
                                       ++l+  + ++v+t g l+dl+s+++
  gi|385805762|ref|YP_005842160.1| 683 ETLETYLAMIVATKGHLFDLVSDNN 707
                                       556555899************8776 PP

>> zf_Rg  Reverse gyrase zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.8   0.8   6.6e-18   4.6e-15       1      43 [.       6      49 ..       6      55 .. 0.93
   2 ?   -1.8   0.3       3.1   2.1e+03       7      14 ..     741     748 ..     739     751 .. 0.86

  Alignments for each domain:
  == domain 1  score: 54.8 bits;  conditional E-value: 6.6e-18
                             zf_Rg  1 MikavfeklCPNCgGdisdeRlekGLpCkrClPke.gdvckaLk 43
                                      Mikavf++lCP C G+is++Rl  G pC++ClP +  d  +++ 
  gi|385805762|ref|YP_005842160.1|  6 MIKAVFQSLCPSCAGPISSYRLSLGVPCNSCLPSSkLDNMEDIS 49
                                      9**********************************999988876 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.1
                             zf_Rg   7 eklCPNCg 14 
                                       ++ CP Cg
  gi|385805762|ref|YP_005842160.1| 741 HNKCPYCG 748
                                       899****8 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.2   2.9e-12     2e-09      26     141 ..     113     226 ..      81     246 .. 0.79
   2 ?   -0.7   0.0       1.8   1.3e+03      42     141 ..    1160    1258 ..    1154    1258 .. 0.70

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 2.9e-12
                                       EEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG.............GEEEESSS- CS
                            ResIII  26 rglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseayke.........igkkvsgdk 93 
                                        + i ++TG+GKT ++++ +++ lkkg+  k+ +lvp++sll+qt+e++k++  +   +         +     +  
  gi|385805762|ref|YP_005842160.1| 113 SFAITAPTGVGKTTLLLHYAAYQLKKGE--KVYILVPTESLLNQTEEKLKEICYKMGIDaeivvyqsrA-----S-- 180
                                       56799***************99999977..*******************99988876655454322111.....1.. PP

                                       B--..............-SEEEEEHHHHHHTH........HHHTTT-SEEEEETG CS
                            ResIII  94 kka.......kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEa 141
                                         +       k++++ +  +l+tt++ l+++        + l++ +fd+i++D a
  gi|385805762|ref|YP_005842160.1| 181 --KkkreevlKKIEEGKFGVLITTTSFLSRRY-------DILKKLKFDLIVVDDA 226
                                       ..123346767788888888888888888877.......788899999***9987 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.8
                                        HHHHHHH-S........-EEEEESSH...HHHHHHHHHGGGGTGG....GEEEESSS-B--.......-SEEEEE CS
                            ResIII   42 aklierllkkgkee...kflflvprk...slleqtleefkkflseaykeigkkvsgdkkkakekdstnkkilvtt 110 
                                        ak+ ++l+++g+     k  f++p++   ++++ + ++++++ se+   ++ k+++d + +    ++ k+ +++ 
  gi|385805762|ref|YP_005842160.1| 1160 AKILDSLRRHGYVViskKRNFVIPTNtgiKVYQYLSSNYSSLVSEE---TTRKLEEDMDAI----EEGKESYLAL 1227
                                        5555555555554455555566666544477888888999888888...678888888888....7788888888 PP

                                        HHHHHHTH........HHHTTT-SEEEEETG CS
                            ResIII  111 iqsldadseeeeeeseellrdrfdviiiDEa 141 
                                          +l+ ++++    se  l  + +v i+DEa
  gi|385805762|ref|YP_005842160.1| 1228 LAKLYDALTRLGLISEVELAAETPVKIMDEA 1258
                                        8888888855577788888888888888887 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 !   23.8   0.2   6.3e-08   4.4e-05      11      92 ..     134     246 ..     124     256 .. 0.77
   2 ?    3.1   0.0      0.17   1.1e+02      56      96 ..     398     443 ..     349     460 .. 0.76
   3 ?    2.2   0.0      0.33   2.3e+02      96     110 ..     560     574 ..     553     575 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 6.3e-08
                                       HHTTTTSEEEEEESSHHHHHH.HHHHHHHT.......TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGG.... CS
                        Helicase_C  11 kleeeggkilifvntidrlek.vklllekk.......gikvavlhgelpqnereeileqfnkgesdvLiatdv.... 75 
                                        + ++g+k++i v+t + l++  + l  k+       + +++v++++ ++++ree+l++  +g++ vLi+t+     
  gi|385805762|ref|YP_005842160.1| 134 YQLKKGEKVYILVPTESLLNQtEEKL--KEicykmgiDAEIVVYQSRASKKKREEVLKKIEEGKFGVLITTTSflsr 208
                                       35689************776664444..22234556789999************************99988876666 PP

                                       .....................GTSSSTSTTESEEEESS CS
                        Helicase_C  76 .....................aerGidipkvnlVinfd 92 
                                                            + ++++i+kv ++i fd
  gi|385805762|ref|YP_005842160.1| 209 rydilkklkfdlivvddadslLKNSVNIEKVLVLIGFD 246
                                       66666666666666666666666699999999999887 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.17
                                       HHHHHHHHTTSSSEEEESGG....GTSSSTSTTE.SEEEESSSSSS CS
                        Helicase_C  56 eeileqfnkgesdvLiatdv....aerGidipkv.nlVinfdlprn 96 
                                       + ++++  +ge++vL+  +     + rGid+p+v ++ i++++p+n
  gi|385805762|ref|YP_005842160.1| 398 KSVIKKLARGEVQVLVGVSSyygvIVRGIDLPEViKYAIFVGVPKN 443
                                       678999999******99886666699******87366666666655 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.33
                                       SHHHHHHHHTTSSST CS
                        Helicase_C  96 nvtsyiqriGRtgRa 110
                                       ++ +yiq++GRt R+
  gi|385805762|ref|YP_005842160.1| 560 DPLTYIQASGRTSRF 574
                                       6779********995 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   1.5e-06     0.001       5     131 ..      97     229 ..      92     242 .. 0.70
   2 ?    1.8   0.0      0.18   1.3e+02      58     131 ..     273     343 ..     262     365 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.5e-06
                            ATPase   5 IeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepg.vfvtveepa....edlrenakslGwdlek 76 
                                       I+ l +     +  g++  it  +G GKt++ l+++  +++k ge++ ++v +e+      e+l+e + ++G+d e 
  gi|385805762|ref|YP_005842160.1|  97 IWSLQKTWAHRLLLGESFAITAPTGVGKTTLLLHYAAYQLKK-GEKVyILVPTESLLnqteEKLKEICYKMGIDAEI 172
                                       66667777778889999**********************999.88874677777643555599***********998 PP

                            ATPase  77 leeegklaiidasesaeesaee....kdkedleelieelaeaikeikakrvviDsitgl 131
                                       +  + +       e  +  + e         + +++++  +++k++k   +v+D  ++l
  gi|385805762|ref|YP_005842160.1| 173 VVYQSRASKKKREEVLK--KIEegkfGVLITTTSFLSRRYDILKKLKFDLIVVDDADSL 229
                                       77663333222222222..2221333444555666667777777777777777777776 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.18
                            ATPase  58 epaedlrenakslGwdlekleeegklaiidasesaeesaeekdkedleelieelaeaikeika.krvviDsitgl 131
                                       e+ e+l++ +++l + le+ +++ k+  + +++ + ++a     ++++ ++e l   i  i+   r +iDs   +
  gi|385805762|ref|YP_005842160.1| 273 EKTENLKKGCEELEVSLEEAKAKKKIGQLAVASATGRQA----GSKPKLFKELLGFEIGGIHDyMRNIIDSFYLY 343
                                       677999999999999999999999988887777665533....45555566666666666655566677766555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.2   2.9e-07    0.0002       8     111 ..     114     238 ..     111     257 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.9e-07
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee........................erpevv...fvtlpsstsskdll 57 
                                        ++t+++G+GKTtll  ++    +  k e+                        +        ++ + +s  sk+ +
  gi|385805762|ref|YP_005842160.1| 114 FAITAPTGVGKTTLLLHYAAYQLK--KGEKvyilvptesllnqteeklkeicykM----GidaEIVVYQSRASKKKR 184
                                       689************999886543..22225578888888888887765555442....033444444444455666 PP

                            AAA_22  58 rellralglelkaerlsseellealeqalraravielliiDEaqhlr.seealee 111
                                       +e+l+++++++ +   ++  +l++ ++ l++ +   l+++D+a+ l  +  ++e+
  gi|385805762|ref|YP_005842160.1| 185 EEVLKKIEEGKFGVLITTTSFLSRRYDILKKLKF-DLIVVDDADSLLkNSVNIEK 238
                                       7777777776666778899999************.**********7443444444 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.2e-06   0.00083      26     160 ..     104     235 ..      80     238 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.2e-06
                            AAA_25  26 vkgllpagelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgealrdda 101
                                       +   l +ge  ++++++g+GKttl+l+ a+  + +G+++           ++v +E   ++++++l++++ ++  da
  gi|385805762|ref|YP_005842160.1| 104 WAHRLLLGESFAITAPTGVGKTTLLLHYAAYQLkKGEKV----------YILVPTESLLNQTEEKLKEICYKMGIDA 170
                                       444456899********************9999677743..........4677788889999999999999996666 PP

                            AAA_25 102 rllvld.lagv.eslpLfakdrggtl.....ltadvdaleaaieevegvrlvviDplsralggden 160
                                       +  v++ +a++ ++  +++k+ +g+      +t+++ +  + +++  + +l+v+D  +++l ++ n
  gi|385805762|ref|YP_005842160.1| 171 EIVVYQsRASKkKREEVLKKIEEGKFgvlitTTSFLSRRYDILKKL-KFDLIVVDDADSLLKNSVN 235
                                       6655553223333333334433333332255588888888888885.5999999999999988776 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 !   18.0   0.0   1.4e-06   0.00095      99     198 ..     142     238 ..      62     244 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.4e-06
                                       EEEE--H.HHHHHHHHHHHH..H-TTS-EEE--SSHHHH-----------------EEEE-HHHHHHHT......TT CS
                                       xxxxxxx.xxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N  99 tLivvPa.slldqWeneier..hvsssalrvlvyggqkkmkkkntkvapklladydvvittYdvlsreaelqkkrsv 172
                                       + i+vP+ sll+q e+++++  +  +   +++vy+++ ++kk+++++++    +++v+itt + lsr+       + 
  gi|385805762|ref|YP_005842160.1| 142 VYILVPTeSLLNQTEEKLKEicYKMGIDAEIVVYQSRASKKKREEVLKKIEEGKFGVLITTTSFLSRRY------DI 212
                                       56889998999999999998334445567899****9878888777777778899***********777......9* PP

                                       S-S-S-SEEEES-GGGT--TTSHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 173 lkqvewkrvvlDEghtlknstskaae 198
                                       lk+++ + +v+D +  l ++  ++++
  gi|385805762|ref|YP_005842160.1| 213 LKKLKFDLIVVDDADSLLKNSVNIEK 238
                                       **************998777665555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.7e-05     0.033       6      64 ..     101     157 ..      99     229 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.7e-05
                            AAA_30   6 QaaavealltsgdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLae 64 
                                       Q++ + +ll ++    ++t+p G GKtt+l ++++   ++g++v +l pt+   ++ +e
  gi|385805762|ref|YP_005842160.1| 101 QKTWAHRLLLGE--SFAITAPTGVGKTTLLLHYAAYQLKKGEKVYILVPTESLLNQTEE 157
                                       555566666666..3799********************************987766665 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   5.9e-05      0.04       2     101 ..     116     228 ..     115     236 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.9e-05
                     Helicase_RecD   2 ltAdRGRGKSaalGlalaaliaegksnilvtapskenvktlfeflakglealglke.........eekkkkaekael 69 
                                       +tA  G GK+++l   +a  +++g+ ++++  p+++ +++  e l++ + ++g++          +    k+++ e+
  gi|385805762|ref|YP_005842160.1| 116 ITAPTGVGKTTLLLHYAAYQLKKGE-KVYILVPTESLLNQTEEKLKEICYKMGIDAeivvyqsraS----KKKREEV 187
                                       9************999999999988.9**********************99999999999976442....2222233 PP

                     Helicase_RecD  70 rvr.........kqrieyiapdellklkeqadllvvDEAAa 101
                                        ++          ++  +++ +  + +k + dl+vvD A +
  gi|385805762|ref|YP_005842160.1| 188 LKKieegkfgvlITTTSFLSRRYDILKKLKFDLIVVDDADS 228
                                       3333355788888888898887777777789******9965 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   6.9e-05     0.048      10      68 ..     111     165 ..     101     255 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.9e-05
                            AAA_19  10 ekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae 68 
                                        + +++ta+ G GKT++l h  a+ ++ g    e+++++ +t+   ++ +e+l+++  +
  gi|385805762|ref|YP_005842160.1| 111 GESFAITAPTGVGKTTLLLHYAAYQLKKG----EKVYILVPTESLLNQTEEKLKEICYK 165
                                       56789******************999999....78999999987777777776554443 PP

>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00065      0.44      53      71 ..     769     787 ..     751     803 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00065
                          Toprim_4  53 kvkevilaldgDaeGeata 71 
                                       + +e+++a+d+D+eGe+ a
  gi|385805762|ref|YP_005842160.1| 769 ESEEIYIATDPDVEGEKIA 787
                                       349*************987 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    0.0005      0.34       4      33 ..     115     146 ..     113     226 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0005
                                       EEEESTTCCHHHHHHHHH..CT--SS-EEEEE CS
                              cobW   4 vltGflGsGKTtLlnhll..enraglklaviv 33 
                                        +t + G GKTtLl h+   + ++g+k+ ++v
  gi|385805762|ref|YP_005842160.1| 115 AITAPTGVGKTTLLLHYAayQLKKGEKVYILV 146
                                       5899*************999999999998876 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00046      0.32       7      91 ..     117     203 ..     112     239 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00046
                                       EESTTSSHHHHHHHHHHHHHHTTS-E.EEEEESTSSTTHHHHHHHHHHHTTEEEEE.SSTTSCHHHHHHHHHHHHHH CS
                             SRP54   7 vGlqGaGKTttlaKLaallkkegkkv.llvaaDtfRaaAveQLktlaeklgvpvik.kkeeadpaavakeavekake 81 
                                         ++G+GKTt l   aa+  k+g+kv +lv +        e Lk++  k+g++     ++ + + +  +e ++k +e
  gi|385805762|ref|YP_005842160.1| 117 TAPTGVGKTTLLLHYAAYQLKKGEKVyILVPTESLLNQTEEKLKEICYKMGIDAEIvVYQSRASKKKREEVLKKIEE 193
                                       5679***************9997777257889999999999999999999887544233333344444555555555 PP

                                       TTSSEEEEEE CS
                             SRP54  82 ekidvvlvDT 91 
                                        k+ v++  T
  gi|385805762|ref|YP_005842160.1| 194 GKFGVLITTT 203
                                       5566655544 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 ?    4.9   0.3     0.036        24       4      12 ..     729     737 ..     728     739 .. 0.89
   2 ?    8.5   0.7    0.0026       1.8       4      14 ..     743     753 ..     742     755 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.036
                         zf-C2HC_2   4 pCpkCgRsF 12 
                                       +C  CgR+F
  gi|385805762|ref|YP_005842160.1| 729 KCLSCGRTF 737
                                       799****** PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0026
                         zf-C2HC_2   4 pCpkCgRsFnp 14 
                                       +Cp+Cg sF+ 
  gi|385805762|ref|YP_005842160.1| 743 KCPYCGESFKI 753
                                       7********75 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1    0.0049       3.4      20      52 ..     112     144 ..      99     161 .. 0.72
   2 ?    1.2   0.0      0.31   2.1e+02      29     106 ..    1035    1122 ..    1019    1135 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0049
                                       SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEE CS
                              PhoH  20 divfaiGpaGtGKtylavalavealkkkkvkri 52 
                                       +   +++p+G GKt l + +a+ +lkk++   i
  gi|385805762|ref|YP_005842160.1| 112 ESFAITAPTGVGKTTLLLHYAAYQLKKGEKVYI 144
                                       5567899******************99654333 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.31
                                        TSSTTHHHHHHHHHHHHTTS-SEEEEE..E-S--T..T----SS---------..TTTHH....HHHHHTTTS-T CS
                              PhoH   29 GtGKtylavalavealkkkkvkriilt..rpavea..geelGflpgdleekvd..pylrp....lydaLkdllga 93  
                                        Gt Kty+ v+ a   l +  ++r+i +  rp+v    + +l +    ++e ++   +lr     +y  L+++ ++
  gi|385805762|ref|YP_005842160.1| 1035 GTLKTYINVTEAHIKLYDLIFRRFIASqsRPSVVEklKLNLSISYNREKEVFEkeLILREketgFYGLLYNINEQ 1109
                                        899*********999999999999985337877442333333333333333331122222122266677777777 PP

                                        TCHHHHHHTTSEE CS
                              PhoH   94 ekvekllekgkie 106 
                                         ++++++++g+i 
  gi|385805762|ref|YP_005842160.1| 1110 TQIADYIKEGRIP 1122
                                        7777777777764 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00067      0.47       4      79 ..     113     231 ..     110     235 .. 0.60
   2 ?   -2.1   0.0       3.8   2.6e+03     147     176 ..     492     521 ..     478     540 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00067
                            AAA_24   4 kiliyGpsgiGKTtlakel.......gpkplfi.....................................dtekGlk 36 
                                       +++i++p g+GKTtl++++       g+k+ ++                                       e+ lk
  gi|385805762|ref|YP_005842160.1| 113 SFAITAPTGVGKTTLLLHYaayqlkkGEKVYILvptesllnqteeklkeicykmgidaeivvyqsraskkKREEVLK 189
                                       6799***************9999996444444477777777444444444444444444444444444444444444 PP

                            AAA_24  37 sldadkfpdieswedfldevvelaaeladyktlviDtidelee 79 
                                       +++  kf  + + + fl+    + ++  +++ +v+D +d l +
  gi|385805762|ref|YP_005842160.1| 190 KIEEGKFGVLITTTSFLSRRYDILKK-LKFDLIVVDDADSLLK 231
                                       44444444444444444444444444.4599999999998765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.8
                            AAA_24 147 rlepklgkktanelkeevDlvlranlkred 176
                                        l++ l+k+t ++l +++ +v+++ lk+ +
  gi|385805762|ref|YP_005842160.1| 492 ALRIALQKGTTKQLSGWLGEVADVILKTIS 521
                                       5788999**************999998654 PP

>> SecA_DEAD  SecA DEAD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.4   0.00045      0.31      95     211 ..     116     231 ..      40     382 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00045
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                         SecA_DEAD  95 aemkTGEGKtlvatlpaylnaltgkgvhvvtvndYLakrdaewmgpvyeflGlsvgvieselesee.rreaYeadit 170
                                           TG GKt      a+++  +g++v ++   + L ++  e+++++   +G++ +++  + ++++ +re   + i 
  gi|385805762|ref|YP_005842160.1| 116 ITAPTGVGKTTLLLHYAAYQLKKGEKVYILVPTESLLNQTEEKLKEICYKMGIDAEIVVYQSRASKkKREEVLKKI- 191
                                       4557*********999999999*********************************998877655440444444444. PP

                                       xxxxxxxxxxxxxxx..xxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                         SecA_DEAD 171 YgtnnelgfdyLrDn..lalskeelvq.rglnfaivDEvDsvLi 211
                                           +e  f  L     +  ++ ++++  ++++ +vD++Ds+L 
  gi|385805762|ref|YP_005842160.1| 192 ----EEGKFGVLITTtsFLSRRYDILKkLKFDLIVVDDADSLLK 231
                                       ....5555555554422444444444435777788888888875 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   0.2      0.35   2.4e+02       2      14 ..     729     741 ..     728     742 .. 0.85
   2 ?    9.6   0.3    0.0019       1.3       2      16 ..     743     757 ..     743     759 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.35
                                       EETTTTEEESSHH CS
                           zf-C2H2   2 kCpdCgksFkrks 14 
                                       kC  Cg++F + +
  gi|385805762|ref|YP_005842160.1| 729 KCLSCGRTFVSLH 741
                                       7999*****9876 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0019
                                       EETTTTEEESSHHHH CS
                           zf-C2H2   2 kCpdCgksFkrksnL 16 
                                       kCp+Cg+sFk ks++
  gi|385805762|ref|YP_005842160.1| 743 KCPYCGESFKIKSSM 757
                                       7*********88876 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 ?    3.4   0.2      0.26   1.8e+02       2      14 ..     729     741 ..     728     743 .. 0.88
   2 ?   11.7   0.1   0.00054      0.37       2      22 ..     743     764 ..     742     765 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.26
                         zf-C2H2_4   2 kCpiCgksFsskk 14 
                                       kC  Cg++F s +
  gi|385805762|ref|YP_005842160.1| 729 KCLSCGRTFVSLH 741
                                       7********9975 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00054
                         zf-C2H2_4   2 kCpiCgksFsskkaLlr.Hlkt 22 
                                       kCp+Cg+sF+ k+++ + H+++
  gi|385805762|ref|YP_005842160.1| 743 KCPYCGESFKIKSSMETvHVLR 764
                                       8***********9997669875 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.4         1   7.1e+02      14      34 ..      14      36 ..       8      44 .. 0.61
   2 ?   10.5   0.3    0.0007      0.48      29      49 .]     728     748 ..     712     750 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1
                               DZR 14 fCseCgtklkavaa..edrCpsC 34
                                       C+ C  +++++       C sC
  gi|385805762|ref|YP_005842160.1| 14 LCPSCAGPISSYRLslGVPCNSC 36
                                      46666666654443555555555 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0007
                               DZR  29 drCpsCgekvdpearfCpeCG 49 
                                        +C sCg+   + ++ Cp+CG
  gi|385805762|ref|YP_005842160.1| 728 SKCLSCGRTFVSLHNKCPYCG 748
                                       68*******99999******9 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0       0.8   5.5e+02      37      49 ..      12      24 ..       6      25 .. 0.78
   2 ?    8.3   0.8     0.003       2.1      26      46 ..     730     750 ..     727     753 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.8
                                      T-B-TTT--B--E CS
                        zf-C3HC4_3 37 kkkCpiCrrpiek 49
                                      +  Cp C  pi++
  gi|385805762|ref|YP_005842160.1| 12 QSLCPSCAGPISS 24
                                      5679999999986 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.003
                                       -HHHHHHHHHTT-B-TTT--B CS
                        zf-C3HC4_3  26 CeeCaekllkrkkkCpiCrrp 46 
                                       C +C +++ + ++kCp+C ++
  gi|385805762|ref|YP_005842160.1| 730 CLSCGRTFVSLHNKCPYCGES 750
                                       9*****************986 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.3         1   7.2e+02      19      22 ..      15      18 ..      12      24 .. 0.61
   2 ?    8.5   0.8     0.002       1.3       8      24 ..     733     749 ..     729     758 .. 0.66

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1
                       zf-ribbon_3 19 CpyC 22
                                      Cp+C
  gi|385805762|ref|YP_005842160.1| 15 CPSC 18
                                      5555 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.002
                       zf-ribbon_3   8 CGa.plssddnvCpyCGt 24 
                                       CG     s  n+CpyCG+
  gi|385805762|ref|YP_005842160.1| 733 CGRtF-VSLHNKCPYCGE 749
                                       55555.556677777774 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 ?   -2.4   0.5       6.9   4.7e+03      27      33 ..      14      20 ..      12      21 .. 0.72
   2 ?   10.7   1.5   0.00055      0.38      11      33 ..     727     749 ..     726     751 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 6.9
                           DUF35_N 27 vCphCgs 33
                                       Cp C +
  gi|385805762|ref|YP_005842160.1| 14 LCPSCAG 20
                                      7999964 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00055
                           DUF35_N  11 gqrCpdCGtvqfPPravCphCgs 33 
                                       +++C +CG+ ++   + Cp+Cg 
  gi|385805762|ref|YP_005842160.1| 727 ISKCLSCGRTFVSLHNKCPYCGE 749
                                       579********9999******85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1134  (0.0632495); expected 358.6 (0.02)
Passed bias filter:                      844  (0.0470746); expected 358.6 (0.02)
Passed Vit filter:                       120  (0.00669307); 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):              26  [number of targets reported over threshold]
# CPU time: 1.05u 0.33s 00:00:01.38 Elapsed: 00:00:00.53
# Mc/sec: 7144.88
//
Query:       gi|385805763|ref|YP_005842161.1|  [L=793]
Description: plasma-membrane proton-efflux P-type ATPase [Fervidicoccus fontis Kam940]
Scores for complete 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-48  163.2   6.8    4.5e-48  163.2   6.8    3.6  5  E1-E2_ATPase     E1-E2 ATPase
    1.1e-26   94.4   0.6      2e-26   93.6   0.6    1.5  1  Hydrolase        haloacid dehalogenase-like hydrolase
    7.4e-17   60.8   0.0    2.1e-16   59.4   0.0    1.8  1  Cation_ATPase_N  Cation transporter/ATPase, N-terminus
    1.5e-06   28.2   0.9    4.7e-06   26.5   0.6    2.0  1  Hydrolase_3      haloacid dehalogenase-like hydrolase
    7.1e-06   26.0   0.0    1.9e-05   24.7   0.0    1.8  1  Cation_ATPase    Cation transport ATPase (P-type)
  ------ inclusion threshold ------
        7.3    6.7  16.0       0.68   10.0   0.4    4.2  4  ETRAMP           Malarial early transcribed membrane protein 


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 ?   -3.0   0.0       1.5   4.5e+03     128     151 ..      59      78 ..      35      93 .. 0.45
   2 !  163.2   6.8   1.5e-51   4.5e-48       4     180 ..     106     283 ..     103     284 .. 0.85
   3 ?    3.2   0.0     0.019        56      48      80 ..     467     502 ..     459     514 .. 0.72
   4 ?   -2.6   0.7       1.1   3.4e+03     106     152 ..     598     644 ..     566     653 .. 0.54
   5 ?   -3.6   0.2       2.2   6.6e+03     120     144 ..     743     767 ..     721     779 .. 0.53

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.5
                                       HHHHHHHHS-STTTSSTTHHHHHH CS
                      E1-E2_ATPase 128 liallvflialllgkslaeallra 151
                                       ++++l +li  +l+     a++ a
  gi|385805763|ref|YP_005842161.1|  59 IAIVLSILIEHYLEA----AIIAA 78 
                                       333333333322222....22222 PP

  == domain 2  score: 163.2 bits;  conditional E-value: 1.5e-51
                                       --EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEEE-E CS
                      E1-E2_ATPase   4 pptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvvsge 80 
                                       + ++kv+rdg+++eida+e+vpGDi+++  gd+vpaD++++eg+ +vd+saLTGEslpve+++g  +fs++ +++g+
  gi|385805763|ref|YP_005842161.1| 106 KIKSKVLRDGSWKEIDASEIVPGDIIVVGLGDVVPADCKVIEGELSVDQSALTGESLPVEVSAGGIIFSSSLIKRGK 182
                                       67899************************************************************************ PP

                                       EEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHH...HHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHH CS
                      E1-E2_ATPase  81 akavVtatgedtelgkiarlveeakskktplqkkldklgkv...lvpvvlliallvflialllgkslaeallralal 154
                                       a++vV++tg++t++gk ++lv+ a + k++ q+ l +++k    + +++++ia + ++ia +++++++ +l++ +++
  gi|385805763|ref|YP_005842161.1| 183 AVCVVVNTGKNTYFGKTVELVKIA-HPKSHQQEVLLSVTKAmmiFGVIAMAIATAYAIIA-HVKNDIISILTFDVGV 257
                                       ***********************9.56666666666666652004444444444444443.556666688999**** PP

                                       HHHHS-TTHHHHHHHHHHHHHHHHHH CS
                      E1-E2_ATPase 155 lvaaiPcaLplavplalalgarrlak 180
                                       l+a +P aLp++++++ a+ga+rla 
  gi|385805763|ref|YP_005842161.1| 258 LMACVPVALPAVMTIIQAVGAMRLAS 283
                                       ************************96 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.019
                                       S..EEE-TTTS---S-EE-G-TTEE-TT-EEEE.-E CS
                      E1-E2_ATPase  48 a..evdesaLTGEslpvekekgdmvfsGtvvvs.ge 80 
                                       +  ++   ++TG+s+ + k+  ++v  G  ++s ge
  gi|385805763|ref|YP_005842161.1| 467 KslQIRPKMITGDSVLIAKQIAKEVGIGDKIFSmGE 502
                                       33799999***********87666666655555455 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 1.1
                                       ----HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHH CS
                      E1-E2_ATPase 106 skktplqkkldklgkvlvpvvlliallvflialllgkslaeallral 152
                                       s +  l+  ++k +kvl  v+l+ + ++++   +++ + +  +l+a 
  gi|385805763|ref|YP_005842161.1| 598 SYQRALTWVINKTIKVLQYVMLMTVGFILFKYDIITLFGVALILFAN 644
                                       44444444555555555544444444444444444444435555555 PP

  == domain 5  score: -3.6 bits;  conditional E-value: 2.2
                                       HHHHHHHHHHHHHHHHS-STTTSST CS
                      E1-E2_ATPase 120 kvlvpvvlliallvflialllgksl 144
                                       +vlv++ ++ al +++  + l+ sl
  gi|385805763|ref|YP_005842161.1| 743 SVLVIFTIIGALGIIIEPVGLKASL 767
                                       3333444444443333333333333 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.6   0.6   6.8e-30     2e-26       1     209 [.     300     559 ..     300     560 .. 0.75

  Alignments for each domain:
  == domain 1  score: 93.6 bits;  conditional E-value: 6.8e-30
                                       SSEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHH.......HHCHHHHHHHHHHHHHHHHHHHHHH.....ETT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxx.....xxx RF
                         Hydrolase   1 iktvvfDkdGTLttgepsvedvivsaalalaaaletg.......sehpigkalvaaakarsgaltgfat.....fig 65 
                                       ++++++Dk+GT+t  + sv+dv++    +++++le +           i + ++ +a++ +++  ++++     f  
  gi|385805763|ref|YP_005842161.1| 300 VDVIALDKTGTITMNKLSVVDVVPFKGHSEKEVLEAAliasseeGGDAIDQTVIDYAQKKGISRNNYTVvkfipF-- 374
                                       689***********************9999999998877765555556666666666666555555555332220.. PP

                                       TE.................HHHHTHHHHHHHH....HCHHHHHHHHHHHHHHCHHHHHH.................. CS
                                       xx.................xxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxx.................. RF
                         Hydrolase  66 rg.................ayaigkpewltal....dippdlgaaigsaqsqgrtvall.................. 103
                                                          ++ +g p+ + +l    + +++ +++i +                             
  gi|385805763|ref|YP_005842161.1| 375 -DpalkraeaiakidgrevRFTKGAPQVILQLcgyeNGSKEIEEKIREM---------Sekgyrtllvarkdessdg 441
                                       .133333333333333337666666665555544444444444444444.........2445555555898888877 PP

                                       TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT..GGGE.SEEEEHHCES....... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxx.xxxxxxxxxx....... RF
                         Hydrolase 104 qaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG..ddyf.daviasdiet....... 170
                                       + + l++ ++adp  ++p+  +++++Lk+  i+  ++tgd+   a+ +a+++G  d++f  ++i + +e        
  gi|385805763|ref|YP_005842161.1| 442 KYEPLGIMALADP--PRPDSMKLIEELKSLQIRPKMITGDSVLIAKQIAKEVGigDKIFsMGEIKGKNEDemkkiie 516
                                       77***********..****************************************7777777777777777888888 PP

                                       ....STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHT CS
                                       ....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 171 ....vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaA 209
                                           +a++ pe+k  +++ Lq++++ v m GDgvnDa+al++A
  gi|385805763|ref|YP_005842161.1| 517 eadgFAEVYPEDKYTIVKTLQENGHIVGMTGDGVNDAPALKQA 559
                                       8999*******************999***************99 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 !   59.4   0.0   6.9e-20   2.1e-16       5      69 .]       2      64 ..       1      64 [. 0.97

  Alignments for each domain:
  == domain 1  score: 59.4 bits;  conditional E-value: 6.9e-20
                   Cation_ATPase_N  5 sleevlekLetdlenGLtqaeaaerlkkyGpNelkekkkkslwvkllkqftnplvilLlvaalvs 69
                                      ++e vle+L+ ++ nGL+++ea++rlk yG+N + e+k+++ +v +lk+f  p+++lL++a ++s
  gi|385805763|ref|YP_005842161.1|  2 DIEKVLEELK-TSRNGLSEEEAKNRLKIYGRNSI-EEKRENPIVEFLKKFYGPMPWLLEIAIVLS 64
                                      789******9.8**********************.***************************998 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.6   1.6e-09   4.7e-06     197     255 .]     534     592 ..     495     592 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1.6e-09
                                       HHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GGGTHHHHHH CS
                       Hydrolase_3 197 kelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnnedGVakal 255
                                       k+l+ +   v   GDg ND + L++a++g+A+ nas+ +k+aA+ v       G+++a+
  gi|385805763|ref|YP_005842161.1| 534 KTLQENGHIVGMTGDGVNDAPALKQAEVGIAVSNASDAAKAAASLVLLEPGLKGIVEAI 592
                                       4444555556678********************************99888777777776 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 !   24.7   0.0   6.4e-09   1.9e-05      21      90 ..     345     408 ..     311     409 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 6.4e-09
                     Cation_ATPase  21 GnktEsALlvlaeklgldteelreetkkvqeipFnssrKrmsvvlklepekkvrlyvKGApeiilkrCth 90 
                                       G++ ++  + +a+k+       r++++ v+ ipF+   Kr+  + k++  ++ + ++KGAp++il+ C++
  gi|385805763|ref|YP_005842161.1| 345 GDAIDQTVIDYAQKK----GISRNNYTVVKFIPFDPALKRAEAIAKID--GREVRFTKGAPQVILQLCGY 408
                                       666666666666666....567999*********************96..99999*************97 PP

>> ETRAMP  Malarial early transcribed membrane protein (ETRAMP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1      0.76   2.3e+03      60      77 ..      73      90 ..      70      95 .. 0.64
   2 ?   -0.2   0.2      0.35     1e+03      61      80 ..     225     244 ..     204     246 .. 0.69
   3 ?   10.0   0.4   0.00023      0.68      37      77 ..     651     691 ..     566     694 .. 0.92
   4 ?    4.8   0.9    0.0098        29      54      77 ..     735     758 ..     732     760 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.76
                            ETRAMP 60 tiatalallvasalGlgi 77
                                      ++++a++l+v++++G+ +
  gi|385805763|ref|YP_005842161.1| 73 AAIIAALLVVNAVIGYRH 90
                                      455666666677777765 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.35
                            ETRAMP  61 iatalallvasalGlgiykk 80 
                                       i  ++a+++a+a+++  + k
  gi|385805763|ref|YP_005842161.1| 225 IFGVIAMAIATAYAIIAHVK 244
                                       45566777777777665555 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00023
                            ETRAMP  37 kaikkiddkiekkkkkkKliiistiatalallvasalGlgi 77 
                                        a++++  +i+ +k + K+i +s+ +++++l + ++lG+ i
  gi|385805763|ref|YP_005842161.1| 651 IATDNVISTINPNKWNVKNITLSSSVIGILLFIEGMLGIFI 691
                                       57899999******************************876 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.0098
                            ETRAMP  54 KliiistiatalallvasalGlgi 77 
                                       K+++ist ++ ++  + +alG+ i
  gi|385805763|ref|YP_005842161.1| 735 KALLISTSSVLVIFTIIGALGIII 758
                                       899******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (793 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1078  (0.0601261); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); 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: 0.78u 0.32s 00:00:01.10 Elapsed: 00:00:00.50
# Mc/sec: 4757.87
//
Query:       gi|385805764|ref|YP_005842162.1|  [L=258]
Description: type 11 methyltransferase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-17   62.5   0.1    4.6e-17   62.1   0.1    1.0  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    7.6e-13   49.0   0.0    1.3e-12   48.2   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    4.5e-12   46.5   0.0    8.5e-12   45.6   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
    6.6e-10   39.0   0.0    1.4e-09   37.9   0.0    1.5  1  Methyltransf_31  Methyltransferase domain
    3.9e-06   26.8   0.0    5.2e-06   26.4   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    0.00045   20.9   0.0    0.00088   20.0   0.0    1.5  1  Methyltransf_12  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.1   0.1   1.5e-20   4.6e-17      14     227 ..      24     242 ..      13     247 .. 0.83

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 1.5e-20
                                       X-HHHHHHHHHHHHHTTTHHHHHH....HHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHH CS
                   Ubie_methyltran  14 esvaskyDlmndvlslgihrlWkk....fveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLk 86 
                                       +++   y++ n+++sl   +  ++    fv +   + ++ ++lD  +G g   + ++++ g++   ++lD  ++m++
  gi|385805764|ref|YP_005842162.1|  24 SEIVGVYEKANNIMSLFTLKYVREkffqFVFENIEDGKALRILDAGTGPGTSLVYILKKSGKEHYCIGLDPLPEMIN 100
                                       567788*********98888777732113444445555569************************************ PP

                                       HHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEEE----SHHHH CS
                   Ubie_methyltran  87 vgekklkeegkinieflqanaeeLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvlefskvelplls 163
                                       +++k   +    n++f+ +  e+Lpf +d+fD+   sf  r+  ++l +  e+ r lk  G+l++l++ k+  + + 
  gi|385805764|ref|YP_005842162.1| 101 TSRKNFID--LDNVDFVRGVFEHLPFREDTFDLEVSSFAYRDAINYLSVALELSRTLKRSGQLFILDLNKPYEKRII 175
                                       99998765..679*********************************************************9877665 PP

                                       HHH.HHHHH.HHH.HHHHHHH..S-HHHHHHHHHHHHHS--HHHHHHHHHHTTEEEEEEEEEGGGTEE CS
                   Ubie_methyltran 164 qay.elyskevlP.vlGklla..kdldsyryLvesirafPdqetlkeliedaGfksveyesltgGvva 227
                                         + e   ++++P ++G +l   + ++ yr L+++  + P   ++  ++++  fk+ +y+ +  G+v 
  gi|385805764|ref|YP_005842162.1| 176 ANFmEKIYMSIFPiFAGTILMgkNGFELYRILKKTYIRLPSSAEIYLIFKKV-FKHCKYYVMLHGAVM 242
                                       555245555688834687764336799******************9888775.999999987776553 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.2   0.0   4.4e-16   1.3e-12       1      97 []      65     159 ..      65     159 .. 0.91

  Alignments for each domain:
  == domain 1  score: 48.2 bits;  conditional E-value: 4.4e-16
                                       EEEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEESTGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssgalh 75 
                                       +Ld+G+G+G+ + +++k+ g ++  +g+D+ +em+++ r+++ +  l nv+fv+g +e+lpf +++fDl vss  + 
  gi|385805764|ref|YP_005842162.1|  65 ILDAGTGPGTSLVYILKKSGkEHYCIGLDPLPEMINTSRKNFID--LdNVDFVRGVFEHLPFREDTFDLEVSS--FA 137
                                       8*************99998659999*****************65..35************************8..55 PP

                                       GSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  76 hlsdedlekalkeiarvLkpgG 97 
                                       + +  ++  +  e++r Lk  G
  gi|385805764|ref|YP_005842162.1| 138 YRDAINYLSVALELSRTLKRSG 159
                                       7777789999999999999887 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.0   2.8e-15   8.5e-12       1      96 []      66     163 ..      66     163 .. 0.94

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 2.8e-15
                                       EEET-TTSHHHHHHH.HTT..SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC- CS
                   Methyltransf_11   1 LdvGcGtGrlaeala.krg..arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhv 74 
                                       Ld+G+G G  + ++  k g  + ++g+D+ +em+++++++  + ++ v+fv++ +e+lpf++++fDl vss++    
  gi|385805764|ref|YP_005842162.1|  66 LDAGTGPGTSLVYILkKSGkeHYCIGLDPLPEMINTSRKNFIDLDN-VDFVRGVFEHLPFREDTFDLEVSSFAYRDA 141
                                       89********9999955559999*****************999995.****************************** PP

                                       CCHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  75 edpekalkeiaRvLkpgGllvi 96 
                                        +  ++  e+ R Lk  G l+i
  gi|385805764|ref|YP_005842162.1| 142 INYLSVALELSRTLKRSGQLFI 163
                                       9999**************9986 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.0   4.7e-13   1.4e-09       2     119 ..      60     171 ..      59     211 .. 0.77

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 4.7e-13
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDli 78 
                                        k+lr+lD+G+G G+ +  + ++ g++   +G+D  +e+i+ +r+n     ldnv F +g +e+l+  + +++fDl 
  gi|385805764|ref|YP_005842162.1|  60 GKALRILDAGTGPGTSLVYILKKSGKEHYCIGLDPLPEMINTSRKNFI--DLDNVDFVRGVFEHLP--FREDTFDLE 132
                                       5899***********99999989999999****************976..899*************..99******9 PP

                   Methyltransf_31  79 lsnevlnaladpdkileeiervlkpggilliedpr..llaelp 119
                                       +s  +  +  +  ++  e++r lk  g l i d +        
  gi|385805764|ref|YP_005842162.1| 133 VSSFAYRDAINYLSVALELSRTLKRSGQLFILDLNkpY----E 171
                                       9987777777777777788************9999332....2 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   1.8e-09   5.2e-06      12     124 ..      49     170 ..      35     205 .. 0.77

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 1.8e-09
                   Methyltransf_23  12 klerllpklragg..rvLdiGcGtGillevl.rengf..svtgvDlspeaveiae.......kakkaqkdqfdeqea 76 
                                       + ++++++ + g+  r+Ld G+G G+ l ++ ++ g+   ++g D+ pe+++  +       +     ++    +  
  gi|385805764|ref|YP_005842162.1|  49 FFQFVFENIEDGKalRILDAGTGPGTSLVYIlKKSGKehYCIGLDPLPEMINTSRknfidldN---VDFVRGVFEHL 122
                                       445555553333345**********87777768889873566**********98887774432...33333333577 PP

                   Methyltransf_23  77 aepqgkfdlIvlrevlehvpdppellrqiatllkpgGylllseplasl 124
                                       ++ +++fdl v+++      ++ ++   + + lk  G l++++ +++ 
  gi|385805764|ref|YP_005842162.1| 123 PFREDTFDLEVSSFAYRDAINYLSVALELSRTLKRSGQLFILDLNKPY 170
                                       88999***********9999************************9873 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0     3e-07   0.00088       1      93 [.      66     155 ..      66     161 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 3e-07
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieyt.gvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvl 76 
                                       L+ G+G G+ l ++l+k    +y+ g+D+ p++i+  ++ + + +n ++ +  +e+l    ++  ++fDl v+s++ 
  gi|385805764|ref|YP_005842162.1|  66 LDAGTGPGTSLVYILKKSGKEHYCiGLDPLPEMINTSRKNFIDLDNVDFVRGVFEHLP--FRE--DTFDLEVSSFAY 138
                                       89****************9999999*********777777777666555555555555..443..389987766554 PP

                   Methyltransf_12  77 hhlkdirevldnirklL 93 
                                           +  +v  ++ + L
  gi|385805764|ref|YP_005842162.1| 139 RDAINYLSVALELSRTL 155
                                       44434444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 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:                        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: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1577.43
//
Query:       gi|385805765|ref|YP_005842163.1|  [L=475]
Description: cysteinyl-tRNA synthetase [Fervidicoccus fontis Kam940]
Scores for complete 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-129  430.3   0.5   3.9e-129  430.3   0.5    1.5  2  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
      1e-16   60.7   2.5    2.6e-09   36.3   1.1    2.2  2  tRNA-synt_1g  tRNA synthetases class I (M)
    1.1e-09   37.2   0.2    1.4e-07   30.2   0.0    2.9  2  tRNA-synt_1   tRNA synthetases class I (I, L, M and V)
    7.7e-08   31.6   0.1    3.5e-06   26.2   0.0    2.3  2  tRNA-synt_1f  tRNA synthetases class I (K)
     0.0021   17.1   2.8      0.044   12.7   0.1    3.2  3  tRNA-synt_1d  tRNA synthetases class I (R)
  ------ inclusion threshold ------
      0.052   13.9   0.1       0.11   12.8   0.1    1.6  1  CBM46         Carbohydrate binding domain
      0.069   13.6   0.0       0.19   12.2   0.0    1.8  1  DALR_2        DALR domain


Domain annotation for each model (and alignments):
>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  430.3   0.5  1.5e-132  3.9e-129       3     300 ..      18     313 ..      16     314 .. 0.96
   2 ?   -2.6   0.1         1   2.6e+03     221     256 ..     354     389 ..     348     404 .. 0.72

  Alignments for each domain:
  == domain 1  score: 430.3 bits;  conditional E-value: 1.5e-132
                                       --SBTTEEEEEEEEEBTTS--BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTTS-HHHHHHHH CS
                      tRNA-synt_1e   3 kpleekkvtlYvCGptvydashlGhaRslvafDilrrilqalgYdvqfvqnvtDidDkiikrareeeksvkelaekf 79 
                                       +++ee+ v++YvCGptvyd+sh+GhaR++++fD +++++q +gY+v +vqnvtDidDkiikra++e+ks+ke+a+ +
  gi|385805765|ref|YP_005842163.1|  18 VSSEEGIVKMYVCGPTVYDYSHIGHARTYISFDAIKKYFQLRGYKVIHVQNVTDIDDKIIKRANQEGKSWKEIADFY 94 
                                       5678899********************************************************************** PP

                                       HHHHHHHHHHTT----SB--BGGGGHHHHHHHHHHHHHTTSEEE-TTS-EEE-GGG-TTTTTTTT--HHHHHHT--- CS
                      tRNA-synt_1e  80 ieefkkdleaLnvlkptleprvsekvdeiielvekliekgyaYavsdgdvyfdvskkeeYgklskqnleelelgaeg 156
                                        e++ +++e+L + + ++ prv++++++ii+ v++liekgyaY+++ g vyfdvsk++ Yg+lsk++ +e    +e+
  gi|385805765|ref|YP_005842163.1|  95 TEDYINAIEKLRIEP-DILPRVTHHIEDIIDAVKRLIEKGYAYESN-GSVYFDVSKYDAYGELSKKTGGENW-RQEE 168
                                       *************87.999*************************99.*****************99988654.5555 PP

                                       -S--S-SSTT-EEEEEE--TTS--B--TTSSEEE-SSHHHHHHHHHHH-SSEEEEEEEGGGTTTHHHHHHHHHHHHS CS
                      tRNA-synt_1e 157 evseekkdkkDfaLWkaskegepswdsPwgkGRPGWhieCsvmaskllgseidihsGGiDLafPhhenelaqseaaf 233
                                       ev +ekk++ DfaLWk+ kegep w+sPwg GRPGWhieCsvm+sk+lg  idih+GG DL+fPhhene aqsea+f
  gi|385805765|ref|YP_005842163.1| 169 EVIKEKKNPFDFALWKKMKEGEPYWESPWGYGRPGWHIECSVMSSKYLGVPIDIHGGGGDLIFPHHENERAQSEALF 245
                                       6779************************************************************************* PP

                                       S.S--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS-TTS-EEE-HHHHHHHH CS
                      tRNA-synt_1e 234 d.kqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRllllsahyrsqldfkeelleeak 300
                                       + k++v+y+lh+g+l+i gekmsksL+n++++kd+l k++p+++Rl +lsahyr+q++f+eell++a+
  gi|385805765|ref|YP_005842163.1| 246 GiKPWVRYWLHTGMLTIRGEKMSKSLGNIVFLKDLLSKYKPEVIRLWVLSAHYRNQIEFNEELLRQAE 313
                                       ****************************************************************9985 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1
                                       HHHHHHHHHHHHSSS--EEEEEEE--EEETTBE--T CS
                      tRNA-synt_1e 221 hhenelaqseaafdkqlvkyflhnghlkiegekmsk 256
                                       h e   a+se    +   ky++ +  +  ++   s 
  gi|385805765|ref|YP_005842163.1| 354 HREFHRAMSEDFNTTLAFKYWMEATSIYYKKVSNSE 389
                                       777888888888888888999998877665544444 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 !   36.3   1.1     1e-12   2.6e-09      12     127 ..      36     149 ..      27     158 .. 0.91
   2 !   23.4   0.0   8.6e-09   2.2e-05     317     367 ..     256     305 ..     245     321 .. 0.83

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 1e-12
                                       S---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHTT---SEE CS
                      tRNA-synt_1g  12 gklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvheeikelfkklnisfdky 88 
                                       +  H+Gh++++is D++ +y +lrg++v++v        +i  +A++eg + +e+++ ++e + +  +kl i+ d  
  gi|385805765|ref|YP_005842163.1|  36 DYSHIGHARTYISFDAIKKYFQLRGYKVIHVQNVTDIDDKIIKRANQEGKSWKEIADFYTEDYINAIEKLRIEPDIL 112
                                       568*****************************999999**************************************9 PP

                                       EETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTT CS
                      tRNA-synt_1g  89 grttseehkelvqeifkklkekgliyekeieqlycpkde 127
                                        r t+  h e   + +k+l ekg+ ye++ ++++++++ 
  gi|385805765|ref|YP_005842163.1| 113 PRVTH--HIEDIIDAVKRLIEKGYAYESNGSVYFDVSKY 149
                                       99875..667777899******************99875 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 8.6e-09
                                       EE--EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE- CS
                      tRNA-synt_1g 317 aheyltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfs 367
                                        +++lt++g+K+SkS g++v+ k++l +++++++R ++++++   + ++f+
  gi|385805765|ref|YP_005842163.1| 256 HTGMLTIRGEKMSKSLGNIVFLKDLLSKYKPEVIRLWVLSAHY-RNQIEFN 305
                                       5799*******************************98877543.3345555 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 !    3.2   0.1    0.0083        21      32      67 ..      32      67 ..      20     160 .. 0.76
   2 !   30.2   0.0   5.5e-11   1.4e-07     515     601 ..     218     304 ..     199     305 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.0083
                       tRNA-synt_1 32 PyvtGslHiGhalaktlkdivirykrmkGkevlyvp 67
                                      P v    HiGha + +  d + +y +++G++v +v 
  gi|385805765|ref|YP_005842163.1| 32 PTVYDYSHIGHARTYISFDAIKKYFQLRGYKVIHVQ 67
                                      666667799999999999999999999999886654 PP

  == domain 2  score: 30.2 bits;  conditional E-value: 5.5e-11
                       tRNA-synt_1 515 fpadmlleGlDiirgWvarlillslaltgsePfkevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltli 591
                                       +p d+   G D i+   ++   +s al+g +P+ +  +h  ++   G KmSKslgN++  +d+++ky  +++Rl+++
  gi|385805765|ref|YP_005842163.1| 218 VPIDIHGGGGDLIFPHHENERAQSEALFGIKPWVRYWLHTGMLTIRGEKMSKSLGNIVFLKDLLSKYKPEVIRLWVL 294
                                       689999999999999999999******************99************************************ PP

                       tRNA-synt_1 592 lsdvgrdinl 601
                                       ++++ ++i++
  gi|385805765|ref|YP_005842163.1| 295 SAHYRNQIEF 304
                                       ***9999886 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 ?    3.0   0.0     0.015        38      36      73 ..      37      74 ..      10      90 .. 0.87
   2 !   26.2   0.0   1.4e-09   3.5e-06     274     356 ..     260     339 ..     214     343 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.015
                      tRNA-synt_1f 36 liHiGnlrevltadlvaralrkrgeevrlilisDdmDg 73
                                        HiG +r  ++ d++ + ++ rg +v ++  + d+D 
  gi|385805765|ref|YP_005842163.1| 37 YSHIGHARTYISFDAIKKYFQLRGYKVIHVQNVTDIDD 74
                                      67************************999999999884 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 1.4e-09
                      tRNA-synt_1f 274 illkggekmssSkGnvltledwlevaepevlrflilrrkPkkakkldldleilrlvdeYdklerkyfaeqeeeeeke 350
                                       ++++ gekms+S Gn++ l+d+l+ ++pev+r+ +l+++ +++++++ +  + ++  +Y+++  +y+ e e++ ++ 
  gi|385805765|ref|YP_005842163.1| 260 LTIR-GEKMSKSLGNIVFLKDLLSKYKPEVIRLWVLSAHYRNQIEFNEE-LLRQAEANYKRITTAYI-EIENQMKSA 333
                                       4444.45******************************999999999999.8889999*********9.555555555 PP

                      tRNA-synt_1f 351 krvyel 356
                                       k+ ++l
  gi|385805765|ref|YP_005842163.1| 334 KPRFSL 339
                                       555555 PP

>> tRNA-synt_1d  tRNA synthetases class I (R)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.1   1.7e-05     0.044      25      68 ..      28      71 ..       5      77 .. 0.82
   2 ?    0.9   0.0      0.07   1.8e+02     134     198 ..      85     150 ..      75     167 .. 0.72
   3 ?    1.4   0.0     0.047   1.2e+02     272     298 ..     259     284 ..     251     316 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.7e-05
                                      E----BTTS--BHHHHHHHHHHHHHHHHHHHCT-EEEEEE--B- CS
                      tRNA-synt_1d 25 dfssPniakemhvGhLrstiiGdavsrlleflGydvirlnhvGD 68
                                          P +    h+Gh r+ i  da+ + +++ Gy+vi +  v D
  gi|385805765|ref|YP_005842163.1| 28 YVCGPTVYDYSHIGHARTYISFDAIKKYFQLRGYKVIHVQNVTD 71
                                      44679999999***************************999988 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.07
                                       HHHHHHHHHHHHHHHHHHHHCT---EC--CC.CCCCCHHHHHHHHHCTT-EEECTTCEEEEECCCT CS
                      tRNA-synt_1d 134 klwkllvditrtelqklydrldvtlierGes.lykeslneivkelkkkglvkesdGalvvfldefg 198
                                       k wk + d+  +++ +  ++l +          + e + ++vk l +kg++ es+G    +++++ 
  gi|385805765|ref|YP_005842163.1|  85 KSWKEIADFYTEDYINAIEKLRIEPDILPRVtHHIEDIIDAVKRLIEKGYAYESNGSVYFDVSKYD 150
                                       56777777777777777777777653333222445677899999*************999998883 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.047
                                       -EE-TTSSBSBCSSSTC-BHHHHHHHH CS
                      tRNA-synt_1d 272 mvlgkdkkkfktrkGetvkLadlLdea 298
                                       m l   ++k++   G++v+L+dlL   
  gi|385805765|ref|YP_005842163.1| 259 M-LTIRGEKMSKSLGNIVFLKDLLSKY 284
                                       4.467789999************9865 PP

>> CBM46  Carbohydrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   4.4e-05      0.11      57      94 ..     345     382 ..     295     391 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.4e-05
                             CBM46  57 dyaageivltpeflaevkdgekvtltfhfwsgakvtyk 94 
                                       ++ ++ i l+ ef ++++++ ++tl f++w  a+  y 
  gi|385805765|ref|YP_005842163.1| 345 ETMNEIINLHREFHRAMSEDFNTTLAFKYWMEATSIYY 382
                                       34567899**********************98876554 PP

>> DALR_2  DALR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   7.5e-05      0.19       2      21 ..     357     376 ..     356     418 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.5e-05
                                       HHHHHTBT--HHHHHHHHHH CS
                            DALR_2   2 FeeaMdDDFNTaeAiavlFe 21 
                                       F  aM +DFNT  A+    e
  gi|385805765|ref|YP_005842163.1| 357 FHRAMSEDFNTTLAFKYWME 376
                                       999*********99876555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       999  (0.0557198); expected 358.6 (0.02)
Passed bias filter:                      572  (0.0319036); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.70u 0.27s 00:00:00.97 Elapsed: 00:00:00.51
# Mc/sec: 2793.99
//
Query:       gi|385805766|ref|YP_005842164.1|  [L=39]
Description: hypothetical protein FFONT_0724 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      194  (0.0108205); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 263.29
//
Query:       gi|385805767|ref|YP_005842165.1|  [L=79]
Description: chromatin protein [Fervidicoccus fontis Kam940]
Scores for complete 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   60.7   1.3    1.2e-16   60.3   1.3    1.2  1  Alba      Alba
  ------ inclusion threshold ------
      0.013   15.5   1.3      0.018   15.0   0.9    1.5  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 !   60.3   1.3   1.3e-20   1.2e-16      12      66 ..       1      54 [.       1      55 [. 0.97

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 1.3e-20
                                      HHHHHHHHHHHTHTTESEEEEEEETTHHHHHHHHHHHHHHHTCTT.EEEEEEEEE CS
                              Alba 12 msyvkralklLsnkkeeeVvlkatGraIskAvsvaeilkrrfgkglyqvnvltss 66
                                      m+yv ++l lL n++ +eV++ka+GraIskAv+ +ei+++++++++++v++++++
  gi|385805767|ref|YP_005842165.1|  1 MNYVMAVLALL-NQGVDEVIVKARGRAISKAVDAVEIIRNKLLAEKVEVKDIKIG 54
                                      9**********.**************************************99986 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 ?   15.0   0.9     2e-06     0.018      60      94 ..      14      47 ..      10      64 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2e-06
                             Rpp20 60 kkeeVfvkatGrAiekalsvgrwfqekeeykvrve 94
                                        +eV+vka GrAi ka+   +  ++k  ++ +ve
  gi|385805767|ref|YP_005842165.1| 14 GVDEVIVKARGRAISKAVDAVEIIRNK-LLAEKVE 47
                                      579**************9877666555.3333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 507.56
//
Query:       gi|385805768|ref|YP_005842166.1|  [L=342]
Description: sodium/calcium exchanger membrane region [Fervidicoccus fontis Kam940]
Scores for complete 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-11   42.5  29.7    5.7e-08   32.8   8.6    2.2  2  Na_Ca_ex  Sodium/calcium exchanger protein


Domain annotation for each model (and alignments):
>> Na_Ca_ex  Sodium/calcium exchanger protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   8.6   3.2e-12   5.7e-08      10     146 ..      40     182 ..      30     186 .. 0.81
   2 !   15.8  13.1   5.9e-07     0.011       3     144 ..     204     338 ..     202     342 .] 0.85

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 3.2e-12
                                       HHHHHHHHHHHHHHHHHHHH.HTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHTHHHH CS
                          Na_Ca_ex  10 lllisvladflvssaeeiak.slgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnlllviGl 85 
                                        +l+s+ a +lv+ +  + +  ++ s   ++++l ++++s+pEl++ +ia+ +g+ ++  g++++  ++  ++v ++
  gi|385805768|ref|YP_005842166.1|  40 GVLVSIYAGMLVEQLVDWISwRFKKSSIGISMILAPIFTSAPELAILLIALFEGKYRIFWGSIVSQPFMASTIVYPV 116
                                       578889999999766666632667777777788******************************************** PP

                                       HHHHHH.....BTTSSCE..CCHHHHHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex  86 ialigs.....lkvdses..lkldlgllllvallllllvlllllplfvpgrltvleglvllllYalyl 146
                                       i++ +       k+ s+   +++++ ++ l+++ l ll +++l p++  g l +  g++lll+Y++y+
  gi|385805768|ref|YP_005842166.1| 117 IVIAAFlgyylGKRSSRIlhVDRSV-AIPLLIFTLPLLPIIFLHPEK-YGLLGRIYGVALLLIYFVYA 182
                                       **99777765424444443355555.778888888888888888875.9*****************96 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 5.9e-07
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex   3 fvlfilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnl 79 
                                       ++ +++s++l++v+ +++v+ + ++++  g+ +s l++++ +l++ +pE+i+ +i++++g  + +i+ ++G  ++  
  gi|385805768|ref|YP_005842166.1| 204 ILQVFVSIVLLYVGGELIVNGIFSLGQEYGLDQSALSVIITPLAGIIPEFIVGLIFVIKGRDSEGISVIIGEKALFG 280
                                       567899*********************************************************************99 PP

                                       HTHHHHHHHHHHBTTSSCECCHHHHHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHHH CS
                          Na_Ca_ex  80 llviGlialigslkvdseslkldlgllllvallllllvlllllplfvpgrltvleglvllllYal 144
                                       ++  ++++++    ++++s+  ++++l ++++++ + +++++   f+   +t   gl+  ++Y++
  gi|385805768|ref|YP_005842166.1| 281 TFYPAIALIL---NIYELSY-SSVSALAIALIISPIEAIAIY---FGYFGVTAPIGLAGYIWYVI 338
                                       9999999999...6777663.344788888888888888888...44567777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); 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 0.24s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2353.00
//
Query:       gi|385805769|ref|YP_005842167.1|  [L=426]
Description: glutamate dehydrogenase [Fervidicoccus fontis Kam940]
Scores for 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  215.7   0.0      1e-63  215.3   0.0    1.1  1  ELFV_dehydrog    Glutamate/Leucine/Phenylalanine/Valine dehyd
    8.7e-52  174.4   0.0    1.3e-51  173.9   0.0    1.3  1  ELFV_dehydrog_N  Glu/Leu/Phe/Val dehydrogenase, dimerisation 
    0.00054   19.4   0.0    0.00093   18.6   0.0    1.3  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
  ------ inclusion threshold ------
      0.041   14.3   0.0      0.074   13.5   0.0    1.4  1  NAD_binding_7    Putative NAD(P)-binding
       0.23   11.5   1.4       0.37   10.8   0.3    1.8  2  AdoHcyase_NAD    S-adenosyl-L-homocysteine hydrolase, NAD bin


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 !  215.3   0.0   2.9e-67     1e-63       4     243 .]     185     424 ..     183     424 .. 0.92

  Alignments for each domain:
  == domain 1  score: 215.3 bits;  conditional E-value: 2.9e-67
                                       TTTTTHHHHHHHHHHHHHHHHTTTS-STTEEEEEE--SHHHHHHHHHHHHCT-EEEEEEESSEEEEETTEE-HHHHH CS
                     ELFV_dehydrog   4 ldrpeaTglGvvyyveemlkklkldslegkrvaisGsGnvgsyaallltelgakvvavsDssGviydpeGldieell 80 
                                        +r  +Tg+Gv+++++e+++   +  l++k+va+ G+Gnvgsyaa  +++ gakv+a+s+  G +ydpeG+d+e  l
  gi|385805769|ref|YP_005842167.1| 185 PVRIYSTGYGVAVMAKEAADLWMGG-LKDKKVAVHGFGNVGSYAAYWISKFGAKVIAISNAYGSVYDPEGIDVELAL 260
                                       578899**************97777.*************************************************** PP

                                       HHHHCSSSSTTHSHHSTSTSEEESHHSHHHHSS-SEEEE-SSTTSB-HHHHTHTHHTT-SEEE-SSSS-B-HHHHHH CS
                     ELFV_dehydrog  81 elkeerksvkeykkssekkaeyieneeellelkvdilvPcAtqneideenakalikngvklvvEgANlpttqeAkei 157
                                       +  e  k v++y++      ++ ++ + +l ++vdil+Pc ++n+i++e+ak +ik  +kl+vEgAN+ptt++A++i
  gi|385805769|ref|YP_005842167.1| 261 KSPEILKDVRNYPR--G---QKSNDPDTILYTDVDILLPCSLENVITAEKAK-NIK--AKLIVEGANGPTTPDAEKI 329
                                       *************3..2...333444489999********************.***..******************* PP

                                       HHHTT..-EEE-HHHHTTHHHHHHHHHHHHHHCT----HHHHHHHHHHHHHHHHHHHHHHHHHCT-T.......HHH CS
                     ELFV_dehydrog 158 leeag..vlvvpdkaaNaGGVtvSslEmlqnlarlswteeevdeklkkimkeifkavveeaeeykqe.......lvk 225
                                       l +++  v v+pd++aNaGGV++S+lE++ nl+ ++w+eee+++kl +im++ f++   + ++ ++        +++
  gi|385805769|ref|YP_005842167.1| 330 LYSRKdfVAVIPDILANAGGVIMSYLEWVENLQWYFWDEEETRQKLSSIMSNNFNRTNIYWNKLRERhperlvtMRD 406
                                       ***9999**********************************************998655555544444569999*** PP

                                       HHHHHHHHHHHHHHHHCT CS
                     ELFV_dehydrog 226 ganiagfekvaeamkaqG 243
                                       +a ++++e+v  amk +G
  gi|385805769|ref|YP_005842167.1| 407 AAFALAVERVYTAMKLRG 424
                                       ***************998 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 !  173.9   0.0   3.6e-55   1.3e-51       1     130 []      36     164 ..      36     164 .. 0.99

  Alignments for each domain:
  == domain 1  score: 173.9 bits;  conditional E-value: 3.6e-55
                                       -SEEEEEEEEEE-TTSBEEEEEEEEEEEE-TTSSEEEEEEEETT--HHHHHHHHHHHHHHHHHTTSS-EEEEEEEES CS
                   ELFV_dehydrog_N   1 pervlqvtvpvkrdnGelevikgyraqhssalgPakGGiRfhpsvnldevkaLaalmtyKnalvdlpfGGakggvki 77 
                                       p+r++qv++p++ dnG+l v++gyr+qh++algP+kGGiR+hp+v+l++ +aLa  mt+Kn+l+++p+GG+kg+vk+
  gi|385805769|ref|YP_005842167.1|  36 PDRIIQVKIPLRLDNGKLVVFEGYRVQHNNALGPYKGGIRYHPEVTLETDMALALGMTLKNSLAGIPYGGGKGAVKV 112
                                       789************************************************************************** PP

                                       -GGGS-HHHHHHHHHHHHHHHG.GG-BTTTEEEEBBTTB-HHHHHHHHHHHHH CS
                   ELFV_dehydrog_N  78 dpkklseeeleritrrfvrelakkfiGpgiDvpApDvgtgaremawladeykk 130
                                       dp+kls +ele + r +vr ++ k+iGp+ D+pApDv+t+++ maw++dey+k
  gi|385805769|ref|YP_005842167.1| 113 DPSKLSMRELEALSRTYVRGIY-KLIGPEEDIPAPDVNTNPQIMAWMVDEYSK 164
                                       **********************.****************************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 !   18.6   0.0   2.6e-07   0.00093      33      68 ..     209     244 ..     194     267 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.6e-07
                                       -GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSS CS
                      2-Hacid_dh_C  33 elsgktvGiiGlGrIGqavakrlkafgmkviaydrs 68 
                                        l++k+v++ G+G++G+ +a  +++fg+kvia++  
  gi|385805769|ref|YP_005842167.1| 209 GLKDKKVAVHGFGNVGSYAAYWISKFGAKVIAISNA 244
                                       699****************************99865 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 ?   13.5   0.0   2.1e-05     0.074       5      40 ..     210     245 ..     207     324 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.1e-05
                     NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleagakvtvvapev 40 
                                       lk+kkv v G G+v+   ++ + ++gakv+ ++++ 
  gi|385805769|ref|YP_005842167.1| 210 LKDKKVAVHGFGNVGSYAAYWISKFGAKVIAISNAY 245
                                       799******************************986 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 ?   10.8   0.3    0.0001      0.37      14      50 ..     200     239 ..     188     244 .. 0.86
   2 ?   -1.8   0.0      0.81   2.9e+03      79     106 ..     289     315 ..     284     319 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0001
                                       HHHH-S--TT...SEEEEE--SHHHHHHHHHHHHCT-EEE CS
                     AdoHcyase_NAD  14 kratdvllaG...kvavvaGyGdvGkGcaaslkglGarvi 50 
                                       k a+d+ ++G   k++ v G+G+vG  +a  + ++Ga+vi
  gi|385805769|ref|YP_005842167.1| 200 KEAADLWMGGlkdKKVAVHGFGNVGSYAAYWISKFGAKVI 239
                                       678888888776689***********************98 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.81
                                       -SEEEE-SSSSSSB-HHHHCCS-TTEEE CS
                     AdoHcyase_NAD  79 adivvtttGnkdiitlehlkkmkddaiv 106
                                       +di++ ++  +++it+e+ k++k + iv
  gi|385805769|ref|YP_005842167.1| 289 VDILLPCS-LENVITAEKAKNIKAKLIV 315
                                       56666554.6799999999999999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 3407.03
//
Query:       gi|385805770|ref|YP_005842168.1|  [L=428]
Description: cytochrome c biogenesis protein, transmembrane region [Fervidicoccus fontis Kam940]
Scores for complete 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   24.9   7.2    1.2e-05   24.9   7.2    2.3  3  SfLAP     Sap, sulfolipid-1-addressing protein
    0.00025   21.0  18.4    0.00026   20.9  16.9    1.8  2  DsbD      Cytochrome C biogenesis protein transmembrane regio
     0.0032   17.3   0.1     0.0049   16.7   0.1    1.2  1  dCache_1  Cache domain


Domain annotation for each model (and alignments):
>> SfLAP  Sap, sulfolipid-1-addressing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.2      0.58   3.5e+03      41      60 ..      14      32 ..      11      42 .. 0.45
   2 !   24.9   7.2   1.9e-09   1.2e-05      22     174 ..     240     396 ..     212     403 .. 0.79
   3 !    3.2   7.4    0.0088        53      14      85 ..     354     426 ..     337     428 .] 0.81

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.58
                             SfLAP 41 vlvalglivlfvlrsllsga 60
                                      +++ l li+l++++s++ +a
  gi|385805770|ref|YP_005842168.1| 14 AIALLSLIFLTATASIM-HA 32
                                      33333344444444443.33 PP

  == domain 2  score: 24.9 bits;  conditional E-value: 1.9e-09
                             SfLAP  22 lsrprpvlnllaFlvgwlvvlvalglivlfvlrsllsgasaapssaikalqivlGvlllllaaveavrr........ 90 
                                        sr+r+  ++l F +g++++++algl +l v +sl+  +   ps++++ +  + G++l++++a+ +++         
  gi|385805770|ref|YP_005842168.1| 240 KSRKRAAISGLGFALGIFTGYLALGLGLLKVISSLG-TL---PSTIARYILAFYGIILIIYSAYSYLTQkrnciick 312
                                       3679********************************.66...9***********************99999***964 PP

                             SfLAP  91 pkassrselprl..lsrleslleggalwvAlvlgllsakplllylaalaaigasgasvgtqvvalvvFvvvalavve 165
                                          ++++  ++   +++ ++ +++   +++l+l +  ++ +    ++ +++++    + t+++ l+++ ++++a+++
  gi|385805770|ref|YP_005842168.1| 313 E--NEGKNNKSFlnIKSWMNKSPALHYILGLILSISLIPCSAGPYIVFILLLSTVSGMLTKILYLLIYDIIFVAPLL 387
                                       2..3333333320145555888888999999999988888888888888888899999******************* PP

                             SfLAP 166 ipllaylva 174
                                       i+l   +++
  gi|385805770|ref|YP_005842168.1| 388 ILLEIIVLT 396
                                       *99666655 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.0088
                             SfLAP  14 rlgvavlllsrprpvlnllaFlvgwlvvlvalglivlfvlrsllsgasaa.pssaikalqivlGvlllllaav 85 
                                       + +v++llls+   +l+ +++l+   +  va  li+l +   +l+++++     + + + i+ G+ll++la++
  gi|385805770|ref|YP_005842168.1| 354 PYIVFILLLSTVSGMLTKILYLLIYDIIFVAPLLILLEIIVLTLKKVNERkVAIVRELVFIIAGLLLIVLAIR 426
                                       457899*******************99999999999999999998665553777777889999*******987 PP

>> DsbD  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       0.6   3.6e+03      48      64 ..     163     179 ..     143     195 .. 0.76
   2 !   20.9  16.9   4.4e-08   0.00026      23     207 ..     231     423 ..     208     426 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.6
                              DsbD  48 lFvlGlslvfvslglsa 64 
                                        F+lG  ++f++ +  +
  gi|385805770|ref|YP_005842168.1| 163 RFILGQNVTFTTTSTLT 179
                                       48889888888766544 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 4.4e-08
                              DsbD  23 syisgvsvedvktekkkvkvllkallFvlGlslvfvslglsaaflgqllkdvkevirrvaglivillGlhflgvfk. 98 
                                         i +++v     +k++ ++ ++ l F+lG+ + +++lgl+  ++++ l+ + +   ++a  i  + G+ ++ +++ 
  gi|385805770|ref|YP_005842168.1| 231 LLIVTIAV-----NKSRKRAAISGLGFALGIFTGYLALGLGLLKVISSLGTLPS---TIARYILAFYGIILI-IYSa 298
                                       23333333.....3444568899******************9999999955554...556667778888888.4543 PP

                              DsbD  99 ievleklkll..............lkikkkaelsvlgalllGltFalgwsPCi.gPvlasvlalaaskeslakgall 160
                                        + l++++ +              l+ik+  + s +  ++lGl+ ++   PC+ gP +  +l+l++ ++ +++ +l+
  gi|385805770|ref|YP_005842168.1| 299 YSYLTQKRNCiickenegknnksfLNIKSWMNKSPALHYILGLILSISLIPCSaGPYIVFILLLSTVSG-MLTKILY 374
                                       566666666678888889999998667777777777899*************649****9**9999999.888999* PP

                              DsbD 161 llvyvlGlaipfl.lvglllellkk.klkslkkyskaveiaggvllvll 207
                                       ll+y + +++p+l l+ +++  lkk + +++    + v i++g+ll++l
  gi|385805770|ref|YP_005842168.1| 375 LLIYDIIFVAPLLiLLEIIVLTLKKvNERKVAIVRELVFIIAGLLLIVL 423
                                       ***********87244454444443134666667777777777777776 PP

>> dCache_1  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   8.2e-07    0.0049     143     208 ..     101     183 ..      79     220 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 8.2e-07
                          dCache_1 143 iyddsgkfiGvlaadldldnlqdllsniklgetgy.vfivdsdGniiah.....pdkdl.........lgknlrdel 204
                                       iy+ + + + ++++d+  +++++l+ + ++++tg+ v++ +++G+++a+     ++  +         lg+n+  + 
  gi|385805770|ref|YP_005842168.1| 101 IYN-NTNLLAIVIGDVENTTFWNLFLSSPPNQTGFpVYVATDTGEVLAGyvnanTQ--QqeyiiyrfiLGQNVTFTT 174
                                       555.56899*************************55************86654422..2346999999999988888 PP

                          dCache_1 205 kaq.....e 208
                                       +++     +
  gi|385805770|ref|YP_005842168.1| 175 TSTltnttT 183
                                       776654330 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1499  (0.0836076); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.68u 0.32s 00:00:01.00 Elapsed: 00:00:00.51
# Mc/sec: 2546.70
//
Query:       gi|385805771|ref|YP_005842169.1|  [L=195]
Description: hypothetical protein FFONT_0729 [Fervidicoccus fontis Kam940]
Scores for 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   23.0   0.0    0.00017   22.2   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
     0.0014   19.3   0.2       0.01   16.5   0.1    2.2  2  Methyltransf_25  Methyltransferase domain
  ------ inclusion threshold ------
      0.013   15.5   0.0       0.02   14.9   0.0    1.3  1  Methyltransf_32  Methyltransferase domain
      0.022   14.6   0.0      0.026   14.3   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
      0.025   14.4   0.2      0.076   12.8   0.2    1.7  2  Methyltransf_31  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 !   22.2   0.0   4.7e-08   0.00017       1      89 [.      52     131 ..      52     136 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 4.7e-08
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT.-EEEEEEES-CCC-CC CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfedn.sfDlvvssevlhhved 76 
                                       Ld+GcG+G + + l  +++ ++gvD+ + +     +  ++e     ++++++ +lpf+++  fD+ +  +++++ + 
  gi|385805771|ref|YP_005842169.1|  52 LDIGCGKGNFGKILD-NFEMYIGVDVLNIFD----KDDKRE-----YIRSSMDSLPFREGfFFDCSFFINSIFYSNS 118
                                       8*************9.7789*****766666....444444.....59***********8789************** PP

                                       HHHHHHHHHHHEE CS
                   Methyltransf_11  77 pekalkeiaRvLk 89 
                                       ++  l e+++  k
  gi|385805771|ref|YP_005842169.1| 119 WKNSLTEAKKYSK 131
                                       *******998655 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   2.8e-06      0.01       1      91 [.      51     128 ..      51     132 .. 0.76
   2 ?   -1.1   0.0       0.9   3.2e+03      16      32 ..     126     141 ..     119     145 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.8e-06
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTT.TEEEEEEESTGGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedg.sfDlvvssgalhh 76 
                                       +Ld+GcG+G++ + l  ++  + ++gvD+     ++  +       + e+++ ++++lpf +g  fD+ + ++++ +
  gi|385805771|ref|YP_005842169.1|  51 ILDIGCGKGNFGKILD-NF--EMYIGVDVL----NIFDKDD-----KREYIRSSMDSLPFREGfFFDCSFFINSIFY 115
                                       8********9998887.55..9******85....4555554.....3468999999999988878999999888666 PP

                                       SSHHHHHHHHHHHHH CS
                   Methyltransf_25  77 lsdedlekalkeiar 91 
                                          + +++ l e+++
  gi|385805771|ref|YP_005842169.1| 116 S--NSWKNSLTEAKK 128
                                       3..357777777765 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.9
                                       HCTSTSSEEEEEESSHH CS
                   Methyltransf_25  16 akrlgkakvtgvDisee 32 
                                       ak++ ++k++ +Di+++
  gi|385805771|ref|YP_005842169.1| 126 AKKY-SKKIVLIDIDKT 141
                                       4555.5999****9876 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   5.7e-06      0.02      18      57 ..      40      79 ..      33     101 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.7e-06
                   Methyltransf_32 18 kelakesgaltvvDvGaGkgYLsfvlalkekeyklkvvgi 57
                                      k+ a+ +++ +++D+G+Gkg  + +l   e+  ++ v+ i
  gi|385805771|ref|YP_005842169.1| 40 KNEAELNNCRKILDIGCGKGNFGKILDNFEMYIGVDVLNI 79
                                      44466799******************98444455555555 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   7.4e-06     0.026      18      37 ..      43      86 ..      21     163 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.4e-06
                   Methyltransf_23 18 pklraggrvLdiGcGtGil........................l 37
                                      ++l+   ++LdiGcG+G++                         
  gi|385805771|ref|YP_005842169.1| 43 AELNNCRKILDIGCGKGNFgkildnfemyigvdvlnifdkddkR 86
                                      33566669***********4444444444444444444444440 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   2.1e-05     0.076       6      35 ..      50      75 ..      46      79 .. 0.83
   2 ?   -2.0   0.0      0.77   2.7e+03      28      38 ..     130     140 ..     116     142 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.1e-05
                   Methyltransf_31  6 rvlDlGCGtGeltfelae.elgpkaevvGiD 35
                                      ++lD+GCG+G++++ l   e+     ++G+D
  gi|385805771|ref|YP_005842169.1| 50 KILDIGCGKGNFGKILDNfEM-----YIGVD 75
                                      79*************995444.....78887 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.77
                   Methyltransf_31  28 kaevvGiDise 38 
                                        +++v+iDi++
  gi|385805771|ref|YP_005842169.1| 130 SKKIVLIDIDK 140
                                       46799999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); 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: 00:00:00.50
# Mc/sec: 1161.80
//
Query:       gi|385805772|ref|YP_005842170.1|  [L=99]
Description: hypothetical protein FFONT_0730 [Fervidicoccus fontis Kam940]
Scores for complete 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-06   26.0   0.2    1.5e-05   25.1   0.1    1.5  2  Glutaredoxin  Glutaredoxin
     0.0039   17.6   0.0     0.0053   17.1   0.0    1.2  1  GST_N_3       Glutathione S-transferase, N-terminal domain


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 !   25.1   0.1   1.7e-09   1.5e-05       2      33 ..       8      39 ..       7      49 .. 0.91
   2 ?   -2.8   0.0      0.89   7.9e+03      20      27 ..      82      89 ..      73      97 .. 0.54

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.7e-09
                                      EEEESTSSHHHHHHHHHHHHTTGGEEEEEGCC CS
                      Glutaredoxin  2 vlftkptCpyCkkakrlLkelgvkfeeidvdk 33
                                      v+++ ++C  C +a  +Lk+ g++fe++++++
  gi|385805772|ref|YP_005842170.1|  8 VVYGLKGCSPCERAFLFLKKAGIEFEYVEISN 39
                                      89****************************97 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.89
                                      HHTTGGEE CS
                      Glutaredoxin 20 kelgvkfe 27
                                      +el+ +++
  gi|385805772|ref|YP_005842170.1| 82 EELRKSIK 89
                                      34443333 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 !   17.1   0.0     6e-07    0.0053       2      52 ..      10      63 ..       9      72 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6e-07
                                      ES-TTSHHHHHHHHHHHHHT--EEEE---..TTTTHHHHHHH-.TT--SSEEET CS
                           GST_N_3  2 ygfpaSpyarrvrlaLnekglpvevvevt..pgehdeellakn.plgkvPvLed 52
                                      yg +++  + r+ l+L+  g+++e+ve++   + + ee+l +  +   +P + d
  gi|385805772|ref|YP_005842170.1| 10 YGLKGCSPCERAFLFLKKAGIEFEYVEISncDDANIEEVLFYEdGEALLPLILD 63
                                      8999************************94333357777776667777777755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 605.70
//
Query:       gi|385805773|ref|YP_005842171.1|  [L=60]
Description: hypothetical protein FFONT_0731 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.084   13.4   1.6       0.11   13.0   1.6    1.4  1  YtxH      YtxH-like protein


Domain annotation for each model (and alignments):
>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.6   6.3e-06      0.11      28      66 ..      17      59 ..       2      60 .] 0.72

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.3e-06
                              YtxH 28 kdlkekaddlkekakelleeakeka....kekaedlkekvkek 66
                                      k l ek+++++e +++l +++ +      k+k+++++ek+ke+
  gi|385805773|ref|YP_005842171.1| 17 KILDEKYKNASEEIDDLFQSTLNEFehllKSKGKEYSEKLKER 59
                                      4456666677777766666665555777799999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1629  (0.0908584); expected 358.6 (0.02)
Passed bias filter:                      627  (0.0349713); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 368.82
//
Query:       gi|385805774|ref|YP_005842172.1|  [L=271]
Description: NH(3)-dependent NAD(+) synthetase [Fervidicoccus fontis Kam940]
Scores for complete 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-78  261.1   0.0      9e-78  260.7   0.0    1.0  1  NAD_synthase   NAD synthase
    1.8e-07   30.3   0.0    9.4e-05   21.4   0.0    2.3  2  tRNA_Me_trans  tRNA methyl transferase
     0.0013   18.3   0.0     0.0072   15.8   0.0    2.0  2  QueC           Queuosine biosynthesis protein QueC
  ------ inclusion threshold ------
      0.014   15.2   0.1      0.031   14.0   0.1    1.7  1  ATP_bind_3     PP-loop family
      0.062   13.6   0.5        1.4    9.2   0.5    2.3  2  A_thal_3526    Plant protein 1589 of unknown function (A_thal
      0.098   12.2   0.0       0.16   11.6   0.0    1.4  1  ThiI           Thiamine biosynthesis protein (ThiI)


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 !  260.7   0.0     3e-81     9e-78       5     239 ..      20     258 ..      17     260 .. 0.97

  Alignments for each domain:
  == domain 1  score: 260.7 bits;  conditional E-value: 3e-81
                                       HHHHHHHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE--- CS
                      NAD_synthase   5 lvdflkeyvkkagakgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktidi 81 
                                       +   +k+y+++++a+g v+GlSGG+DS+++ ++ v+ +g+e+v++l++P+  s+ ed++da+ +ae+lgi++ ++di
  gi|385805774|ref|YP_005842172.1|  20 ISSCIKNYLERSNASGYVIGLSGGLDSTVTLYMLVRSVGREKVFGLIMPEIESNLEDINDAIYIAEKLGIKYSVLDI 96 
                                       56789************************************************************************ PP

                                       HHHHHHHHHHHHHHH...-HHHHHHHHHHHHHHHHHHHHHHHTEEEB---BHHHHTTT-S-TTTTT--SBETTTTS- CS
                      NAD_synthase  82 kpivrafeqelkeak...edlakgNlkaRiRmailyaianklnllvlgTgnksElvvGyfTkyGDgaadlapiaell 155
                                       +++vr+  + + e+    ++ akgNlkaR+Rm+ily++ank n+lv++T++ksE+++GyfTk+GDga+d+ pia+l+
  gi|385805774|ref|YP_005842172.1|  97 TNVVRSALDLFGESYetaDKKAKGNLKARARMMILYYFANKNNYLVAATSDKSEYLLGYFTKWGDGAGDIYPIANLY 173
                                       ******999766655555899******************************************************** PP

                                       HHHHHHHHHHTT--HHHHCS--B--SSTT-BHHHHHSS-HHHHHHHHT.HSSSS...HHHHHTTT--HHHHHHHHHH CS
                      NAD_synthase 156 KtevkeLakelnvPervlkkpPsAdLkpgqtDeeeLgikYdelDeiLk.lvekkkspeeiikekelpaevvekiekl 231
                                       Kt+v++La +l+vPe++  kp s +L+pgq  ++eL + Y++lD+i+  lvek+++ e++ k ++++++ ve+i + 
  gi|385805774|ref|YP_005842172.1| 174 KTQVRQLALYLGVPEKISYKPSSPGLWPGQKATDELKYDYSILDKIIFlLVEKQETVENVSKMLNIEKSDVENIWNT 250
                                       **********************************************9989*************************** PP

                                       HHHTGGGG CS
                      NAD_synthase 232 vkksehKr 239
                                       + k+ hKr
  gi|385805774|ref|YP_005842172.1| 251 ILKNSHKR 258
                                       *******9 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   3.1e-08   9.4e-05       4      73 ..      37      99 ..      35     114 .. 0.82
   2 !    6.6   0.0   0.00095       2.8     165     194 ..     166     197 ..     146     201 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 3.1e-08
                     tRNA_Me_trans  4 vvalSgGVDSsvaaallkeqg..yevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfeke 73
                                      v++lSgG DS+v++++l +     +v g+++  +e+           ed++da  +aeklgi+++v+d+++ 
  gi|385805774|ref|YP_005842172.1| 37 VIGLSGGLDSTVTLYMLVRSVgrEKVFGLIMPEIES---------NLEDINDAIYIAEKLGIKYSVLDITNV 99
                                      689*************99875346677887776665.........348*******************99865 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.00095
                     tRNA_Me_trans 165 lfPlgeltKeevrkiAkeagla..vaekkdSq 194
                                       ++P+++l K++vr++A   g++  +  k+ S 
  gi|385805774|ref|YP_005842172.1| 166 IYPIANLYKTQVRQLALYLGVPekISYKPSSP 197
                                       79***************999876566666665 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   2.4e-06    0.0072       3      70 ..      37     102 ..      35     145 .. 0.79
   2 ?   -0.3   0.0      0.21   6.2e+02     157     180 ..     168     191 ..     166     195 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.4e-06
                                       EEE--SSHHHHHHHHHHHHH-..SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-GGGGGGSCG CS
                              QueC   3 vvllSGGlDSttvlalakkeg..kevealtfdYgqrhkkeleaakkiakelgveehkildldllkelggs 70 
                                       v+ lSGGlDSt+ l++  +++  ++v  l +   + + ++++ a  ia++lg+ +  +ld++   ++ +s
  gi|385805774|ref|YP_005842172.1|  37 VIGLSGGLDSTVTLYMLVRSVgrEKVFGLIMPEIESNLEDINDAIYIAEKLGI-KYSVLDIT---NVVRS 102
                                       7889************9998755778888888888899999************.99999998...33333 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.21
                                       TTTT--HHHHHHHHHHTTHHHHH- CS
                              QueC 157 PlidlsKaeivklgkelgvpleet 180
                                       P+ +l K+++ +l+  lgvp + +
  gi|385805774|ref|YP_005842172.1| 168 PIANLYKTQVRQLALYLGVPEKIS 191
                                       999***************997765 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   1.1e-05     0.031       2      81 ..      36     127 ..      35     150 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.1e-05
                                       EEEE--SCHHHHHHHHHHHHHCTTTTT.EEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H......... CS
                        ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgi.klvaihvdhglreeskeeaelvkelckklnikleiekvdv......... 68 
                                       +++++SgGlDS++ l++l+++  ++++  l++  ++ +l +  ++       +++kl+ik+ + +++          
  gi|385805774|ref|YP_005842172.1|  36 YVIGLSGGLDSTVTLYMLVRSVGREKVfGLIMPEIESNLEDINDA-----IYIAEKLGIKYSVLDITNvvrsaldlf 107
                                       689**********99999988766555455555555444332221.....123334444444443333333344445 PP

                                       .......HHCTTSTCCCHHH CS
                        ATP_bind_3  69 .......akkkgknleeaAR 81 
                                              +kk + nl+++AR
  gi|385805774|ref|YP_005842172.1| 108 gesyetaDKKAKGNLKARAR 127
                                       55555444445555555555 PP

>> A_thal_3526  Plant protein 1589 of unknown function (A_thal_3526)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0       0.1     3e+02       4      16 ..      19      31 ..      16      37 .. 0.83
   2 ?    9.2   0.5   0.00047       1.4      13      42 ..     224     253 ..     215     257 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.1
                       A_thal_3526  4 lIErCLqlymske 16
                                       I  C+++y+ + 
  gi|385805774|ref|YP_005842172.1| 19 AISSCIKNYLERS 31
                                      6899*****9875 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00047
                       A_thal_3526  13 mskeevvraLeeqanIepeftslVWkkLek 42 
                                         k+e+v+ +++  nIe++  + +W+ + k
  gi|385805774|ref|YP_005842172.1| 224 VEKQETVENVSKMLNIEKSDVENIWNTILK 253
                                       5799*********************98765 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.2e-05      0.16       9      95 ..      39     126 ..      32     148 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.2e-05
                              ThiI   9 LlSgGiDSpVaaylllkR.Gcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlkeilekvk 84 
                                        lSgG+DS V+ y+l++  G + v+  +  e   + e i+    +ae+l    + l+++ vv +  ++  e  e ++
  gi|385805774|ref|YP_005842172.1|  39 GLSGGLDSTVTLYMLVRSvGREKVFGLIMPEIESNLEDINDAIYIAEKLGIKYSVLDITNVVRSALDLFGESYETAD 115
                                       48************998636666665666677777788888888888887555567888777777777777777777 PP

                              ThiI  85 ekltivllkrk 95 
                                       +k +  l  r 
  gi|385805774|ref|YP_005842172.1| 116 KKAKGNLKARA 126
                                       76666554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1674.54
//
Query:       gi|385805775|ref|YP_005842173.1|  [L=290]
Description: TatD-related deoxyribonuclease [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.4e-19   68.8   0.0    5.4e-19   68.6   0.0    1.1  1  TatD_DNase  TatD related DNase


Domain annotation for each model (and alignments):
>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.6   0.0     3e-23   5.4e-19       2     254 ..      10     286 ..       9     287 .. 0.83

  Alignments for each domain:
  == domain 1  score: 68.6 bits;  conditional E-value: 3e-23
                                       EEEE-TTS.CCCTTTHHHHHHHHHHTTEEEEEEE-SSG..................GGHHHHHHHHTT.TTTEEEEE CS
                        TatD_DNase   2 DaHcHlds.kefeedreeileraeeagvaavvvvgtss..................kdskavlelakkypnkvyavl 59 
                                       D+H+H +  k +   +++i e+++e+++  ++  +                     + + +  ++a +   kv + +
  gi|385805775|ref|YP_005842173.1|  10 DSHAHNNPiKGI--GAKKIAEKFRENNGWFIAFLNNPAwdysdsyifdvdeylklvNLHMRDCKSATETGLKVKCFA 84 
                                       99******7776..4555559999999999995555445556666666666665533334788888889999***** PP

                                       ---GGGGGC..........C.CCHHHHHHHH.HHCCCTSEEEEEEEEEET-CCCCCGHHHHHHHHHHHHHHHHHTTE CS
                        TatD_DNase  60 GiHPnevde..........asedlleelkel.anvkhskvvaiGeiGLDyysreestkeaqeevFeeqlrlAkelkl 125
                                       GiHP+e+d+          +++  l++++++   +k+    +iGeiG+ +y+ + +     +e++e  +  Ak++++
  gi|385805775|ref|YP_005842173.1|  85 GIHPAEIDKlaeyglptlkVRDFALKTIEKIfDMCKEGLLDGIGEIGRQHYKIRMDVAVITQEILESSFTFAKDYGC 161
                                       ***************9997677777999999999******************************************* PP

                                       EEEEEEES....-HHHHHHHHHHCGGCCS...EEEETT--S-HHHHHHHHHTTEEEEE-GGGGTTTTHHHHHHH.HH CS
                        TatD_DNase 126 plviHlrk....aeedlleilkeaaeaka...kvvlHsfsgsaeeakkflklgyyislsglltfknakelrelv.ka 194
                                        +++Hl++    + e++ +++ +++   +   ++ +H+ ++s+ e +k    +++ +++g++       l++l    
  gi|385805775|ref|YP_005842173.1| 162 KIQLHLENikgfTVENIASLAYKTG---LksdQFLIHHATSSIVEEAKNR--RVWTTYPGIIEG-----LKSLFtTI 228
                                       ********66655555555555555...33359*****999987777765..9*******9877.....88998445 PP

                                       S-GGGEEE---TTSSEECCCTTSE--GGGHHHHHHHHHHHHTS-HHHHHHHHHHHHHHHH CS
                        TatD_DNase 195 vpldrlLiETDaPyltpkpyrgkrnepanvayvveklaelkaltleelaeitaeNakrlf 254
                                          + +LiE+D  y + k+  g+  +p+n++ +   l e  +++   l++i  +N++ +f
  gi|385805775|ref|YP_005842173.1| 229 RNPEYVLIESD--YVDSKKEGGRITYPWNLPDIQLSLLEKGDVSKYFLEKINIDNVESFF 286
                                       567899*****..999977766***********************************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.48
# Mc/sec: 1820.16
//
Query:       gi|385805776|ref|YP_005842174.1|  [L=471]
Description: Acyl-CoA synthetase (NDP forming), alpha subunit [Fervidicoccus fontis Kam940]
Scores for complete 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-51  172.3   0.2    1.1e-50  171.1   0.2    1.7  1  Succ_CoA_lig   Succinyl-CoA ligase like flavodoxin domain
    1.6e-24   86.7   0.5    1.9e-23   83.1   0.3    2.3  2  CoA_binding_2  CoA binding domain
    1.1e-13   51.6   1.6    7.9e-13   48.9   0.7    2.5  2  CoA_binding    CoA binding 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 !  171.1   0.2   1.8e-54   1.1e-50       1     137 [.     158     296 ..     158     297 .. 0.98

  Alignments for each domain:
  == domain 1  score: 171.1 bits;  conditional E-value: 1.8e-54
                      Succ_CoA_lig   1 pGkialisqSGalalalldwaasrglgfskvvslGneadvdvadlleylaedpetkvillylEsird..grkflsaa 75 
                                       +Gkia+++qSGal++al++w++ +++g+s++vs+Gn++d+d+ dl +++++d++tkvi+lylE+++   g +f+++ 
  gi|385805776|ref|YP_005842174.1| 158 KGKIAFLTQSGALGIALMHWTSMEKIGLSSIVSMGNMTDIDAIDLAKFFEKDENTKVIGLYLEGLGTgkGHEFIEVF 234
                                       69**************************************************************9985579****** PP

                      Succ_CoA_lig  76 rraarkkpvvvlksGrseagaraaashtgalagsdavvdaafrqaGvlrvdsleelfdaael 137
                                        ++++kkpv++lk+Grse+g+ra+ashtg+lagsdav+d+a++qaGvlr++++e+lf+ a++
  gi|385805776|ref|YP_005842174.1| 235 SEITKKKPVIALKAGRSERGTRAVASHTGSLAGSDAVYDSALKQAGVLRASDVEQLFNWAKM 296
                                       ***********************************************************997 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.1   0.3   3.2e-27   1.9e-23       1     115 [.      18     142 ..      18     143 .. 0.96
   2 ?    1.0   0.0     0.097   5.8e+02      71     106 ..     408     444 ..     393     459 .. 0.71

  Alignments for each domain:
  == domain 1  score: 83.1 bits;  conditional E-value: 3.2e-27
                                       --EEEET--S-TTSHHHHHHHHHHH...HT--EEEESSS-SEETTEES----T....T--EEEE-S-HHHHGGGHHH CS
                     CoA_binding_2   1 rtiaVvGasdnpgkfgykvlrylle...hglpvvpVnpkeeeilgekvyaslaedpepvdlvdvftppeatpeivke 74 
                                       ++iaVvGas n +k g  +l++l++   +g ++++Vnp ++eilg+++y+sl + p +v+ ++v++p+e++pei++e
  gi|385805776|ref|YP_005842174.1|  18 KSIAVVGASRNLEKIGGVILSNLVKnkfNG-KIYAVNPSAKEILGVPSYPSLLDIPDEVEHIVVAIPAEKVPEIIEE 93 
                                       79***********************99889.**********************868********************* PP

                                       HHHH--SEEEE-TT........---HHHHHHHHHTT-EEE.ES-HHHHH CS
                     CoA_binding_2  75 alalgakavwlqpg........sedeeaaelaeeagirvvgdrCilveg 115
                                       a+++g+k++ + ++          +e+++++a+++gir++g++  +v++
  gi|385805776|ref|YP_005842174.1|  94 AGKKGVKVATIIASgfkevgraDLEEKVVNIAKKYGIRILGPNVFGVVY 142
                                       **********99999***************************9988875 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.097
                                       GHHHH.HHH--SEEEE-TT---HHHHHHHHHTT-EEE CS
                     CoA_binding_2  71 ivkea.lalgakavwlqpgsedeeaaelaeeagirvv 106
                                       ++ke  +++++  v++  g+  +   e++ee+g++v 
  gi|385805776|ref|YP_005842174.1| 408 TLKEYnKSRKPVNVVMLGGEKTKMGTEILEENGVPVY 444
                                       5555545556777777777777777777777776654 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   0.7   1.3e-16   7.9e-13       2      96 .]      16     108 ..      15     108 .. 0.98
   2 ?    0.5   0.0      0.17     1e+03      35      53 ..     425     446 ..     404     458 .. 0.74

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 1.3e-16
                                       TTEEEEEETTTSHHHHHH.HHHHHHHHECEE.EEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHH CS
                       CoA_binding   2 kdtkviviGagglgiagl.yhfkeklkygik.avfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaq 76 
                                       k+++++v+Ga+++  +++ +  ++  k +++ +++ vnp   ++e+lg+p y+s+ +++++  v+  v+++Pae++ 
  gi|385805776|ref|YP_005842174.1|  16 KPKSIAVVGASRNLEKIGgVILSNLVKNKFNgKIYAVNPS--AKEILGVPSYPSLLDIPDE--VEHIVVAIPAEKVP 88 
                                       7899************************************..*******************..************** PP

                                       HHHHHHHHTT-SEEEEESST CS
                       CoA_binding  77 eavdelveagikgiviiteg 96 
                                       e+++e+ ++g+k++ ii++g
  gi|385805776|ref|YP_005842174.1|  89 EIIEEAGKKGVKVATIIASG 108
                                       *****************986 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.17
                                       EC-TTTTTCEET...TEEEESC CS
                       CoA_binding  35 gvnprkvgtevl...glpvyks 53 
                                       g   +k+gte+l   g+pvy+ 
  gi|385805776|ref|YP_005842174.1| 425 GGEKTKMGTEILeenGVPVYPI 446
                                       445668999999999****964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.29s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 2952.18
//
Query:       gi|385805777|ref|YP_005842175.1|  [L=376]
Description: exopeptidase, family M24B [Fervidicoccus fontis Kam940]
Scores for complete 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  173.7   0.0    5.4e-51  173.3   0.0    1.2  1  Peptidase_M24  Metallopeptidase family M24
    1.7e-08   35.1   0.0    4.1e-08   33.9   0.0    1.6  2  Creatinase_N   Creatinase/Prolidase N-terminal domain
  ------ inclusion threshold ------
      0.065   12.3   0.6        1.3    8.1   0.4    2.2  2  Effector_1     Effector from type III secretion system


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 !  173.3   0.0     9e-55   5.4e-51       2     208 ..     161     360 ..     160     361 .. 0.95

  Alignments for each domain:
  == domain 1  score: 173.3 bits;  conditional E-value: 9e-55
                                       HHHHHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBCSSSB--TTEEEE CS
                     Peptidase_M24   2 lirkaariasaaleavleaikpgvterelaaeieattlkrhgarglafppivasgenaavlhytpndrvlkegdlvl 78 
                                       li+ka +i+++al +++e+++ g++e+e+  e     l + ga++laf+piva+ ena+ +h++ ++r+lk++d++l
  gi|385805777|ref|YP_005842175.1| 161 LIKKAVEITEKALSQTIENLRNGMREKEIYSEHICQ-LYKSGAEYLAFDPIVAITENASNPHAISGNRELKADDILL 236
                                       79******************************9966.7889************************************ PP

                                       EEEEEEETTEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTBCCGBSSCSEE CS
                     Peptidase_M24  79 idagaeydgyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesaglakffphglGH 155
                                       id ga++ gyasD+trT++    + e ++ +e+++ea    ++a+k G+ ++eid +ar++l+++gl+k+f h+lGH
  gi|385805777|ref|YP_005842175.1| 237 IDTGAKFGGYASDMTRTIIPE--KGEFKKYIELLEEAYFSSLDALKTGAGAKEIDGIARNILKKYGLEKYFIHSLGH 311
                                       *******************96..668999************************************************ PP

                                       EESSSSSEEEEEESSSTTCSSB--TTBEEEEEEEEEEETTTEEEEEBEEEEEE CS
                     Peptidase_M24 156 gvGlevhdegpsvsresndgrkleeGmvftiEpgiyfapgeggvriedtvlvt 208
                                       gvG++vh+  p++   + ++++  e++v++iEpgiyf+ ++ g r+e+tv+v 
  gi|385805777|ref|YP_005842175.1| 312 GVGIDVHEA-PNIG--PTSNEVFMENEVVAIEPGIYFP-EKIGFRLENTVIVG 360
                                       *******98.**98..6789****************75.666********995 PP

>> Creatinase_N  Creatinase/Prolidase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0   6.9e-12   4.1e-08       2     124 ..      18     145 ..      17     152 .. 0.84
   2 ?   -3.7   0.0       2.9   1.7e+04       2      14 ..     177     189 ..     177     190 .. 0.87

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 6.9e-12
                                       HHHHHHHHHHTT-SEEEEECCHHHHHHHSS...-SSSEEEEEEESSCEEEEEECTTHHHHHHHH.TTSEEEEEST.. CS
                      Creatinase_N   2 lerlralmeekgldallvtspenlrYltGfatetgsrglalvvtadgalllvdalryteaaeesatveevveydd.. 76 
                                       l+++ ++ +ekg++ +++++++n+rYltG    + s  ++l + +++++++++ ++ +  ++    +++v+++++  
  gi|385805777|ref|YP_005842175.1|  18 LKKIEEIAQEKGISKIVLMNDTNIRYLTGL---ELSGAAILDFVNKEHTIIIPFMENWKIKKLFGGYFRVIGVTRyd 91 
                                       79999*************************...5555555544555669***************9*****9999999 PP

                                       .........HSSHHHHHHHHHHHHT-EEEE-TTSSBHHHHHHHHHHCTTSEEEETHH CS
                      Creatinase_N  77 .........pvealadllkellesekrvgveldaltvafyealkealpdaelvdase 124
                                                +  ++ +++++ l ++ ++g++ld l  ++ +++k++++  ++v +  
  gi|385805777|ref|YP_005842175.1|  92 fgleegvekFIGSINEAVAKFLIESDKIGIDLD-LNKSSDSNIKSKVK--SVVQIND 145
                                       *****99999999999999999999********.57776688888875..6666655 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 2.9
                                       HHHHHHHHHHTT- CS
                      Creatinase_N   2 lerlralmeekgl 14 
                                       +e+lr+ m+ek++
  gi|385805777|ref|YP_005842175.1| 177 IENLRNGMREKEI 189
                                       6899*****9986 PP

>> Effector_1  Effector from type III secretion system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.4   0.00021       1.3     175     251 ..      96     173 ..      78     180 .. 0.85
   2 ?    6.3   0.3   0.00075       4.5     188     242 ..     152     206 ..     142     219 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00021
                        Effector_1 175 mgeneFagsieeakdklakEkeqvrkdlksaekAkekvkellkrv.eadkkltteqkaklkdelngYadeleaiveq 250
                                       +g ++F gsi+ea +k+  E +++  dl   +     +k  +k+v + ++++   +++kl +e+    + +e+  + 
  gi|385805777|ref|YP_005842175.1|  96 EGVEKFIGSINEAVAKFLIESDKIGIDLDLNKSSDSNIKSKVKSVvQINDEMIRVRRTKLPEEIDLIKKAVEITEKA 172
                                       68899**********************************99998627788999999999999988777776666555 PP

                        Effector_1 251 L 251
                                       L
  gi|385805777|ref|YP_005842175.1| 173 L 173
                                       5 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.00075
                        Effector_1 188 kdklakEkeqvrkdlksaekAkekvkellkrveadkkltteqkaklkdelngYad 242
                                        +kl +E++ ++k ++++ekA  +  e l++   +k++ +e+  +l +  ++Y+ 
  gi|385805777|ref|YP_005842175.1| 152 RTKLPEEIDLIKKAVEITEKALSQTIENLRNGMREKEIYSEHICQLYKSGAEYLA 206
                                       6899******************9999999999999***********999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       805  (0.0448993); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); 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: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 2406.57
//
Query:       gi|385805778|ref|YP_005842176.1|  [L=123]
Description: hypothetical protein FFONT_0736 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     0.0063   16.4   0.0      0.091   12.7   0.0    2.2  2  TBPIP       TBPIP/Hop2 winged helix domain
  ------ inclusion threshold ------
      0.027   14.7   0.0      0.035   14.3   0.0    1.2  1  DUF3333     Domain of unknown function (DUF3333)
      0.098   13.0   0.1       0.44   10.9   0.0    2.0  2  TFIIE_beta  TFIIE beta subunit core domain


Domain annotation for each model (and alignments):
>> TBPIP  TBPIP/Hop2 winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   1.5e-05     0.091       4      49 ..      28      73 ..      25      76 .. 0.95
   2 ?    1.5   0.0     0.048   2.9e+02      37      51 ..      89     103 ..      85     115 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.5e-05
                             TBPIP  4 elvleylqeqnrPfsvqdvvanlqkklgKtavqkaLdeLvdegkii 49
                                      el+ ++ +++ rP+  q   + +   +g     +aL +Lv+e++++
  gi|385805778|ref|YP_005842176.1| 28 ELIMDLFKKKQRPLTWQQLREHFSAIIGEDRLRRALRQLVSEERLV 73
                                      7899***************************************997 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.048
                             TBPIP  37 kaLdeLvdegkiieK 51 
                                       ++++eL+++ +i ++
  gi|385805778|ref|YP_005842176.1|  89 EIIEELENKRRISST 103
                                       6899*****999875 PP

>> DUF3333  Domain of unknown function (DUF3333)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   5.9e-06     0.035      65     124 ..      25      86 ..       7     103 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.9e-06
                           DUF3333  65 k.aeeskklatanyeklirdalkaklpeve.errekrelaelissgaayqlrdrvladpsli 124
                                       + +e   +l + + + l  ++l+++++++  e+r +r+l++l+s++  +ql +   adp+ +
  gi|385805778|ref|YP_005842176.1|  25 EiPELIMDLFKKKQRPLTWQQLREHFSAIIgEDRLRRALRQLVSEERLVQLNRTTYADPETL 86 
                                       444555677777778888999******88889***************************987 PP

>> TFIIE_beta  TFIIE beta subunit core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   7.4e-05      0.44       8      45 ..      30      66 ..      29      87 .. 0.73
   2 ?   -0.4   0.0      0.24   1.4e+03      38      54 ..      87     103 ..      75     113 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 7.4e-05
                        TFIIE_beta  8 iveylKkkdgplsleeIlsylslqldls.dknwllleaL 45
                                      i++  Kkk++pl+ +++ ++ s    ++ d+ +  l+ L
  gi|385805778|ref|YP_005842176.1| 30 IMDLFKKKQRPLTWQQLREHFSA--IIGeDRLRRALRQL 66
                                      78899*****************7..44436444444444 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.24
                        TFIIE_beta  38 nwllleaLknnpkieyD 54 
                                        ++++e L n  +i+  
  gi|385805778|ref|YP_005842176.1|  87 TPEIIEELENKRRISST 103
                                       45778888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       899  (0.0501422); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); 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: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 836.79
//
Query:       gi|385805779|ref|YP_005842177.1|  [L=96]
Description: hypothetical protein FFONT_0737 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-14   52.9   0.3    3.7e-14   52.7   0.3    1.0  1  Ribosomal_S25    S25 ribosomal protein
  ------ inclusion threshold ------
       0.02   15.1   1.0      0.025   14.8   0.3    1.5  2  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
       0.03   14.7   0.2      0.042   14.2   0.1    1.3  1  Penicillinase_R  Penicillinase repressor


Domain annotation for each model (and alignments):
>> Ribosomal_S25  S25 ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.7   0.3   6.2e-18   3.7e-14      12      99 ..       7      91 ..       2      93 .. 0.85

  Alignments for each domain:
  == domain 1  score: 52.7 bits;  conditional E-value: 6.2e-18
                     Ribosomal_S25 12 aakaggkakkKKwskgkvkdklnnavlfdketydkllkevpkyklitpsvvserlkingslArraLreleekgliklvs 90
                                      ++++gg++k  K    ++ ++++ +v + +e++++   e +++++itp ++s++l +++s ++++L+ l+ekg++k ++
  gi|385805779|ref|YP_005842177.1|  7 KKREGGEEK-PK--ARTMTEQAEMNVSVPDELLKRAERELKQVEYITPFMLSQKLSVSISTSKKILKMLAEKGTLKTIV 82
                                      444455443.33..45566777777****************************************************** PP

                     Ribosomal_S25 91 khraqviYt 99
                                      ++r+  iY+
  gi|385805779|ref|YP_005842177.1| 83 QNRRAPIYV 91
                                      ********7 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 ?   -2.7   0.0       1.2   7.1e+03      25      35 ..      20      30 ..      13      32 .. 0.54
   2 ?   14.8   0.3   4.1e-06     0.025      19      53 ..      45      79 ..      34      84 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.2
                                      HHHHHHHHTS- CS
                    Fe_dep_repress 25 tkdlaerLnvs 35
                                      t+    ++nvs
  gi|385805779|ref|YP_005842177.1| 20 TMTEQAEMNVS 30
                                      44444567766 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 4.1e-06
                                      HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                    Fe_dep_repress 19 ekkvvktkdlaerLnvspssVsemlkkLekdGyve 53
                                      + +++++ +l++ L vs s+  + lk L+++G ++
  gi|385805779|ref|YP_005842177.1| 45 QVEYITPFMLSQKLSVSISTSKKILKMLAEKGTLK 79
                                      67899**************************9765 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1     7e-06     0.042      27      64 ..      54      92 ..      33      95 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7e-06
                                      --GGG---HHHHHHHHHHHHHTTS-EEEEE.TTEEEEE- CS
                   Penicillinase_R 27 leeekelaysTVktllrrLvkKgllsreke.grafiYsp 64
                                      l+++ +++ sT k +l+ L +Kg l++  +  ra iY p
  gi|385805779|ref|YP_005842177.1| 54 LSQKLSVSISTSKKILKMLAEKGTLKTIVQnRRAPIYVP 92
                                      889999*********************988466778887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       855  (0.0476881); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); 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: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 649.20
//
Query:       gi|385805780|ref|YP_005842178.1|  [L=207]
Description: phosphoesterase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-16   59.4   2.9    2.8e-13   49.8   0.9    3.1  2  Metallophos_3  Metallophosphoesterase, calcineurin superfamil
    1.3e-15   58.0   0.6    2.6e-15   57.0   0.6    1.5  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    4.8e-11   43.6   0.5    7.5e-11   42.9   0.5    1.3  1  Metallophos    Calcineurin-like phosphoesterase


Domain annotation for each model (and alignments):
>> 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    0.0021        13       4      42 ..       4      42 ..       1      47 [. 0.90
   2 !   49.8   0.9   4.6e-17   2.8e-13     161     256 ..     106     205 ..      39     206 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0021
                                      ---EEEEEE--TT-GGGHHHHHHHHHHH--SEEEEES-- CS
                     Metallophos_3  4 lvrkvlaisdlkgevellerlveviedkdpDllvlvGdl 42
                                         k+l i d++ +   l+rl+e+ ++ + ++ ++ Gdl
  gi|385805780|ref|YP_005842178.1|  4 KWMKLLQIGDIHCSLKNLKRLLELRDELEYEIAIVHGDL 42
                                      56799*********************************9 PP

  == domain 2  score: 49.8 bits;  conditional E-value: 4.6e-17
                                       HHHHGGGGGGS---EEEEEE.SS--S-SST.BTTBS---S-HHHHHHHHHH--SEEEE-SS--EE..EEETTEEEEE CS
                     Metallophos_3 161 veyrLkvlkelkdrrkvlll.atpPigelv.adkglkekgsevvaelvktlnPevvvvghavkeh..eelgktlvvn 233
                                         y+Lk l+e+k++r ++++ + pPi +   +  g  + g  ++ e+  +++P   + gh++ +   + +g+tlvvn
  gi|385805780|ref|YP_005842178.1| 106 YTYALKKLEEMKEKRNLVIVsHHPPITQNTdVSFGGIHIGLPELTEIDEKYSPLAHLHGHVHESPgiDYIGDTLVVN 182
                                       469*********9997655428899987654888989************************998889********** PP

                                       --BGGGTEEEEEETTTTEEEEEE CS
                     Metallophos_3 234 PGaleeGdfavvdleekkveleq 256
                                        G+l +G+fa+vd++++k e+++
  gi|385805780|ref|YP_005842178.1| 183 AGSLMHGNFAIVDIKNRKAEIKK 205
                                       ******************99876 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 !   57.0   0.6   4.3e-19   2.6e-15       1     164 [.       6     198 ..       6     199 .. 0.78

  Alignments for each domain:
  == domain 1  score: 57.0 bits;  conditional E-value: 4.3e-19
                     Metallophos_2   1 MklaiiSDlHsnldaleavlealkevgvdaiihaGDleeeepevleellela.pvlaVrGNnDeev.veedvlreaa 75 
                                       Mkl+ i D+H +l+ l+++le  +e +++  i+ GDl e + e+++ l++l  ++l V+GN+D +v +++ + +++ 
  gi|385805780|ref|YP_005842178.1|   6 MKLLQIGDIHCSLKNLKRLLELRDELEYEIAIVHGDL-ECDGEIVDLLEKLSdKILFVPGNMD-DVgLIKIFTEKSY 80 
                                       9***********************************8.677778888888878**********.3346666666666 PP

                     Metallophos_2  76 elgtdl........................peeaelelagek..vlliHgdpl.........gvkdalaellkeaee 117
                                        ++ +l                        ++ +e++ ++ +  v + H+ p          g + +l el++  e+
  gi|385805780|ref|YP_005842178.1|  81 NIDSKLvklgeyyflgiggqnfyssytyalKKLEEMK-EK-RnlVIVSHHPPItqntdvsfgGIHIGLPELTEIDEK 155
                                       6666666766666777777666665544333333333.33.255777777766*********999999999999666 PP

                     Metallophos_2 118 gsd.vvvcGHtHvp.evekeggvlvvnPGsvgeprdgdpetyaildtde 164
                                        s    ++GH H+  +++ +g++lvvn+Gs+  +       +ai+d+++
  gi|385805780|ref|YP_005842178.1| 156 YSPlAHLHGHVHESpGIDYIGDTLVVNAGSLMHG------NFAIVDIKN 198
                                       6667999*****977*****************99......788888775 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.5   1.3e-14   7.5e-11       1     203 [.       6     168 ..       6     169 .. 0.73

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 1.3e-14
                                       EEEEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTS.. CS
                       Metallophos   1 lrilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvkypipvylllGNHe.. 75 
                                       +++l+igD+H      +l +l++ll +l++e +  + ++ GDl  +g    e+++ll++l +   ++ +++GN +  
  gi|385805780|ref|YP_005842178.1|   6 MKLLQIGDIH-----CSLKNLKRLL-ELRDELEYEIAIVHGDLECDG----EIVDLLEKLSD---KILFVPGNMDdv 69 
                                       799*******.....**********.88999888888888**99999....69999999999...999*******33 PP

                                       CHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESECEEETHHHHHHHHHHHSCHHHHCCHHHHH CS
                       Metallophos  76 gfeeellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGgspellvsldklgslnleleapepgdewlk 152
                                       g    l      +++ s ++ s+  +++ ++  ++g++  +++  +                             lk
  gi|385805780|ref|YP_005842178.1|  70 G----LIKI---FTEKSYNIDSKLVKLGEYYFLGIGGQ--NFYSSYTY--------------------------ALK 111
                                       2....2222...22224444555555566666666666..44444444..........................222 PP

                                       HHHHHTTCSEEEEEESSESS......CSSSCSCCHHHHHHHHHHTTESEEEEESSSS CS
                       Metallophos 153 dlekrekadwvivlgHsply......rgsgylfgdealedllkkygvdlvisGHtHv 203
                                       +le+ ++++ +++++H+p+       + +g + g ++l ++ +ky + + ++GH+H+
  gi|385805780|ref|YP_005842178.1| 112 KLEEMKEKRNLVIVSHHPPItqntdvSFGGIHIGLPELTEIDEKYSPLAHLHGHVHE 168
                                       334455556666666666666***********************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); 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: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1168.05
//
Query:       gi|385805781|ref|YP_005842179.1|  [L=208]
Description: hypothetical protein FFONT_0739 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); 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: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1327.85
//
Query:       gi|385805782|ref|YP_005842180.1|  [L=105]
Description: hypothetical protein FFONT_0740 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00091   19.4   0.5     0.0015   18.8   0.5    1.3  1  Ost5      Oligosaccharyltransferase subunit 5
     0.0091   14.9   0.1       0.01   14.7   0.1    1.1  1  STELLO    STELLO glycosyltransferases
  ------ inclusion threshold ------
      0.046   13.9   0.2      0.055   13.7   0.2    1.1  1  DUF4330   Domain of unknown function (DUF4330)


Domain annotation for each model (and alignments):
>> Ost5  Oligosaccharyltransferase subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.5   2.5e-07    0.0015       4      49 ..      11      56 ..       8      61 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.5e-07
                              Ost5  4 sppvppslqptlafvllligllltalfflyevtstkkkrs.lvkell 49
                                      +++++p++q +l++vll+++l+l+ +++++ ++ +k++ +  vk ++
  gi|385805782|ref|YP_005842180.1| 11 TSIFSPEVQGILTLVLLAATLALFYYAMIQ-MSPKKTQEEvEVKTVI 56
                                      799************************877.5555555444555554 PP

>> STELLO  STELLO glycosyltransferases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   1.7e-06      0.01     146     192 ..      57     103 ..      42     105 .] 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.7e-06
                            STELLO 146 prekeeenikkaeqklnyfGdlvewcnetgysnlskkfpsaeqlakk 192
                                       + +++ +++++a qk +y+G+++  c+++g+s +++ f   ++++k 
  gi|385805782|ref|YP_005842180.1|  57 TCTSTGQTTERAFQKGDYVGKILGECENSGQSVITSIFEVKKEINKS 103
                                       555667899******************************99999876 PP

>> DUF4330  Domain of unknown function (DUF4330)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   9.2e-06     0.055      20      94 ..      21      93 ..      18     104 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.2e-06
                           DUF4330 20 lailvilavivgiflkpgtsgsvaqaeaaatkpvevdvvvrglevpeelak.vkegekt.niiirnqPagdveikdv 94
                                      ++ lv+la+  ++f++   +       ++++++vev+ v+ + ++ +++ +  ++g+ + +i  + + +g+  i+++
  gi|385805782|ref|YP_005842180.1| 21 ILTLVLLAATLALFYYAMIQ----MSPKKTQEEVEVKTVITCTSTGQTTERaFQKGDYVgKILGECENSGQSVITSI 93
                                      45678888888888888777....3334467899***********88888856899887344455555666655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       831  (0.0463495); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 669.61
//
Query:       gi|385805783|ref|YP_005842181.1|  [L=368]
Description: hypothetical protein FFONT_0741 [Fervidicoccus fontis Kam940]
Scores for complete 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-139  462.8   8.5   7.8e-139  462.6   8.5    1.0  1  DUF1512   Protein of unknown function (DUF1512)


Domain annotation for each model (and alignments):
>> DUF1512  Protein of unknown function (DUF1512)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  462.6   8.5  4.3e-143  7.8e-139       2     355 ..      12     367 ..      11     368 .] 0.98

  Alignments for each domain:
  == domain 1  score: 462.6 bits;  conditional E-value: 4.3e-143
                           DUF1512   2 isliifllllillllglnqklqlavllrdiekklakleklaeeakkkvvellkklgkedpkklverlleffviePvd 78 
                                       is++ fl++++ll+lg+nq++q+++ +r+i+ kl++lek+a ++++k++++lk lg e+p+ +ver +++fvi+Pv+
  gi|385805783|ref|YP_005842181.1|  12 ISQLAFLIVFLLLFLGFNQRFQIYISSRNIKLKLNILEKMALDSQNKTINFLKGLGLEKPEPVVERGINYFVIDPVN 88 
                                       899************************************************************************** PP

                           DUF1512  79 lePtgivkrlehllrtsedklkklvekllpeadeversnvetaleiasalnliykvvrHylllakktknlvlllqlq 155
                                       +ePt+i+kr++ l++t+ed+++ l+e+++p+a++ve+s + taleiasal+l++k+vrHyl++++kt+n++l++ql+
  gi|385805783|ref|YP_005842181.1|  89 VEPTDIIKRMDILFKTREDRIEGLLEQVVPKASKVEKSIAVTALEIASALTLVFKYVRHYLITGQKTNNWILIMQLE 165
                                       ***************************************************************************** PP

                           DUF1512 156 mllplllklaeayekalkaflkgkPvGDgaGplvaakllekkekksleaakdtviaevelegrkvivvkaeGpgstv 232
                                       m+lp+l+k+aeay+kal++fl+gkPvGDgaGpl+++kl+  ++++ +e++kdtv+ e+ +e+rk +++ka+Gp+s+v
  gi|385805783|ref|YP_005842181.1| 166 MILPMLIKQAEAYSKALDVFLEGKPVGDGAGPLTVFKLAGPNAQP-VEIVKDTVYFETIIENRKAYLIKASGPESNV 241
                                       ***************************************999999.9****************************** PP

                           DUF1512 233 Grlgeavekivekl....kekvdliitvDAalkLEGEetgsvaeGvGvaiGdpGvekikiErvatkygipldaviik 305
                                       G++g ave++++kl    ++kv +iitvDAalkLEGE tg+v+eG+G+aiGd+G+eki+iEr+a++ygipl+a+i+k
  gi|385805783|ref|YP_005842181.1| 242 GHPGFAVESLLNKLvneeGKKVGMIITVDAALKLEGEPTGEVTEGAGAAIGDVGPEKIRIERAAANYGIPLHAIIVK 318
                                       *******9877665555599********************************************************* PP

                           DUF1512 306 msleeAitaMtkeiaeavdkavervkeiikektkegetvivvGvGNtvGv 355
                                       ms+eeAi +M+kei++a+dk++er+ke++k+  +++  +i++G+GN++G+
  gi|385805783|ref|YP_005842181.1| 319 MSMEEAILTMKKEIVDAIDKVTERIKELVKNIPEDS-IIIIAGIGNSCGI 367
                                       *****************************9998875.************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       869  (0.048469); expected 358.6 (0.02)
Passed bias filter:                      645  (0.0359752); 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: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.47
# Mc/sec: 2349.19
//
Query:       gi|385805784|ref|YP_005842182.1|  [L=154]
Description: hypothetical protein FFONT_0742 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score 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   13.8   0.3        3.2    8.0   0.1    2.4  2  Drf_DAD   DRF Autoregulatory Domain


Domain annotation for each model (and alignments):
>> Drf_DAD  DRF Autoregulatory Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.005        90       7      12 ..      13      18 ..      11      19 .. 0.91
   2 ?    8.0   0.1   0.00018       3.2       2      10 ..     130     138 ..     130     140 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.005
                           Drf_DAD  7 LEALqs 12
                                      LEAL++
  gi|385805784|ref|YP_005842182.1| 13 LEALST 18
                                      9***98 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00018
                           Drf_DAD   2 VMDsLLEAL 10 
                                       +MDs  EAL
  gi|385805784|ref|YP_005842182.1| 130 IMDSVMEAL 138
                                       6*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       985  (0.0549389); expected 358.6 (0.02)
Passed bias filter:                      614  (0.0342462); 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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1249.82
//
Query:       gi|385805785|ref|YP_005842183.1|  [L=358]
Description: ABC-type iron(III) transport system, ATPase component [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-36  124.7   0.0    6.7e-36  123.8   0.0    1.5  1  ABC_tran      ABC transporter
    7.1e-08   32.6   0.1     0.0004   20.3   0.0    2.4  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    1.3e-05   25.3   0.0    0.00073   19.6   0.0    3.2  4  TOBE_2        TOBE domain
    8.2e-05   22.1   0.2      0.002   17.6   0.1    2.4  3  SMC_N         RecF/RecN/SMC N terminal domain
     0.0081   16.6   0.3       0.12   12.8   0.0    2.3  2  AAA           ATPase family associated with various cellular 
  ------ inclusion threshold ------
      0.012   15.5   0.0      0.018   14.9   0.0    1.3  1  Rad17         Rad17 P-loop domain
      0.016   15.5   2.2       0.14   12.4   2.2    2.1  1  AAA_22        AAA domain
      0.025   15.0   0.0       0.04   14.3   0.0    1.4  1  AAA_16        AAA ATPase domain
      0.042   14.7   0.1        0.5   11.2   0.0    2.7  2  OB_MalK       MalK OB fold domain
      0.042   13.3   1.1       0.28   10.6   0.7    2.1  2  TniB          Bacterial TniB protein
       0.05   13.2   0.0       0.22   11.1   0.0    1.9  2  AAA_25        AAA domain
      0.087   13.2   0.0        0.2   12.1   0.0    1.6  1  RNA_helicase  RNA helicase
       0.18   12.1   0.1        1.5    9.1   0.1    2.1  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
        3.2    8.2   5.6         15    6.0   5.5    2.2  1  AAA_23        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.8   0.0   5.3e-39   6.7e-36       1     136 [.      21     163 ..      21     164 .. 0.97

  Alignments for each domain:
  == domain 1  score: 123.8 bits;  conditional E-value: 5.3e-39
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       ++n++l+++ege   ++G++G+GK+t l+l+ag + p+eG+i + ++d+++  ++ +++  ++++q+  l+p++tv 
  gi|385805785|ref|YP_005842183.1|  21 VDNLNLTINEGEFFTLLGPSGCGKTTTLRLIAGFEIPDEGKIFFGDEDVTY--KKPYERGTAMVFQNYALWPHMTVF 95 
                                       589************************************************..99********************** PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       en             e +++++++l+ ++lk+++++      ++LSgGq+qrvalaral+ kp+llllDEp 
  gi|385805785|ref|YP_005842183.1|  96 ENvayglkvrkvskeEINKRVTEVLELVKLKGMEKRYP----NQLSGGQQQRVALARALVIKPRLLLLDEPL 163
                                       ***********999999999************999998....*****************************7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0   0.00047       0.6       2      22 ..      34      54 ..      33      77 .. 0.78
   2 !   20.3   0.0   3.1e-07    0.0004     220     299 ..     119     196 ..      82     200 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00047
                            AAA_21  2 nvliGpNgsGKSnLLdaldll 22
                                        l Gp g+GK++ L+++ ++
  gi|385805785|ref|YP_005842183.1| 34 FTLLGPSGCGKTTTLRLIAGF 54
                                      6799**************776 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 3.1e-07
                            AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQvilt 295
                                        + +++ ++  ++ +++lS G+++  al+ al   +   +lll+DEp ++L+ kl  +  e +k+ +r  ++  i +
  gi|385805785|ref|YP_005842183.1| 119 VLELVKLKGMEKRYPNQLSGGQQQRVALARALVIKP---RLLLLDEPLSNLDAKLRVEMREEIKRIQReLKITTIYV 192
                                       5555666666788999********999999999988...************************888887999***** PP

                            AAA_21 296 THSp 299
                                       TH+ 
  gi|385805785|ref|YP_005842183.1| 193 THDQ 196
                                       **85 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.41   5.2e+02      22      51 ..     119     148 ..     102     154 .. 0.80
   2 ?   -1.8   0.0       2.9   3.7e+03      54      75 ..     209     232 ..     188     232 .. 0.58
   3 ?    5.3   0.0     0.017        22      38      74 ..     253     287 ..     241     288 .. 0.81
   4 !   19.6   0.0   5.7e-07   0.00073       2      76 .]     280     355 ..     279     355 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.41
                            TOBE_2  22 tVedveylGsstryvvelaggqlvvvrqpn 51 
                                       + e v   G + ry  +l ggq+++v+ + 
  gi|385805785|ref|YP_005842183.1| 119 VLELVKLKGMEKRYPNQLSGGQQQRVALAR 148
                                       567788899999***********9998765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.9
                            TOBE_2  54 r.d.salapGdtVelswdpddavv 75 
                                         + + l++G+  e+ ++p  ++v
  gi|385805785|ref|YP_005842183.1| 209 MnAgKVLQVGTPEEVYFSPKNIFV 232
                                       223347888888888888887765 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.017
                            TOBE_2  38 elaggqlvvvrqpnadrdsalapGdtVelswdpddav 74 
                                       +l+ g++++++++ +    ++a G+++++ ++p++++
  gi|385805785|ref|YP_005842183.1| 253 SLDKGTKIKISKAEEG--VTFAKGERIRILIRPEHII 287
                                       6899999999999998..5999999999999999985 PP

  == domain 4  score: 19.6 bits;  conditional E-value: 5.7e-07
                            TOBE_2   2 aiRPEklrla.aagga.....nglsGtVedveylGsstryvvelaggqlvvvrqpnadrdsalapGdtVelswdpdd 72 
                                        iRPE++     +  +     n ++G+V+   + G+  ++ ve++++ ++ +  p+      l++GdtV+l+++ ++
  gi|385805785|ref|YP_005842183.1| 280 LIRPEHIIPYeRK--EkisefNIVKGKVVFKMFTGTMQELKVEIGENVFLYTLIPSDY---KLEVGDTVGLQIPVER 351
                                       7********6422..245567899********************99977666666665...9***********9999 PP

                            TOBE_2  73 avvl 76 
                                       ++++
  gi|385805785|ref|YP_005842183.1| 352 TLAF 355
                                       8876 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 ?    1.8   0.0      0.11   1.3e+02      25      40 ..      32      47 ..       5      52 .. 0.80
   2 !   17.6   0.1   1.6e-06     0.002     106     204 ..     105     201 ..      82     214 .. 0.78
   3 ?   -3.7   0.0       5.3   6.8e+03      36      44 ..     237     245 ..     237     246 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.11
                                      SEEEEEESTTSSHHHH CS
                                      xxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnl 40
                                      +f  ++Gp G+GK+  
  gi|385805785|ref|YP_005842183.1| 32 EFFTLLGPSGCGKTTT 47
                                      588899*******975 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 1.6e-06
                                       TSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 106 kgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvael 182
                                        + s+ +in++  +  e+ +l  +++ ++++LSgG+++ vala  + i+   p  l llDe  ++LD+k + ++ e 
  gi|385805785|ref|YP_005842183.1| 105 RKVSKEEINKRVTEVLELVKLKGMEKRYPNQLSGGQQQRVALARALVIK---P-RLLLLDEPLSNLDAKLRVEMREE 177
                                       4557778999999999999999999999************999887664...4.4899*****************99 PP

                                       HHHHCTT..SEEEEE-SSHHHCCC CS
                                       xxxxxxx..xxxxxxxxxxxxxxx RF
                             SMC_N 183 lkekskn..aQfivislreemlek 204
                                       +k+ + +     i +++++e    
  gi|385805785|ref|YP_005842183.1| 178 IKRIQRElkITTIYVTHDQEEAMS 201
                                       997776612445666665554333 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 5.3
                                       SHHHHHHHH CS
                                       xxxxxxxxx RF
                             SMC_N  36 GKsnlldAi 44 
                                       GK n+++Ai
  gi|385805785|ref|YP_005842183.1| 237 GKPNIIEAI 245
                                       9*******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 !   12.8   0.0   9.3e-05      0.12       3      20 ..      36      53 ..      34      86 .. 0.94
   2 ?    1.5   0.1      0.29   3.7e+02      24      74 ..     120     169 ..      92     207 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.3e-05
                                      EESSTTSSHHHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavak 20
                                      l Gp G+GKT++ + +a 
  gi|385805785|ref|YP_005842183.1| 36 LLGPSGCGKTTTLRLIAG 53
                                      89************9985 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.29
                                       HEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHH CS
                               AAA  24 vefleisgsellskyvgesekkirelfkeakeka.kpsilfiDEidalaksr 74 
                                        e+++++g+e +  y  + +   ++ ++ a++   kp  l++DE  +   ++
  gi|385805785|ref|YP_005842183.1| 120 LELVKLKGMEKR--YPNQLSGGQQQRVALARALViKPRLLLLDEPLSNLDAK 169
                                       457777777777..77777777777777777777789999999955444444 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.4e-05     0.018      46      68 ..      32      54 ..       8     132 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.4e-05
                             Rad17 46 riLLisGPsGCgkstvvkvLske 68
                                      +   + GPsGCgk+t+++ ++  
  gi|385805785|ref|YP_005842183.1| 32 EFFTLLGPSGCGKTTTLRLIAGF 54
                                      467788***********998865 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   2.2   0.00011      0.14       6     117 ..      32     183 ..      28     199 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee.................................erpevvfvtlps 49 
                                        + ++ G+sG+GKTt+lr ++        ++e                                    e v + l++
  gi|385805785|ref|YP_005842183.1|  32 EFFTLLGPSGCGKTTTLRLIAGFEI----PDEgkiffgdedvtykkpyergtamvfqnyalwphmTVFENVAYGLKV 104
                                       678899************9987752....222445677777777777666666666666666444222333333333 PP

                            AAA_22  50 st.sskdllrellralglelka...erlsseellealeqalrarav...ielliiDEaqh.lr...seealeeLrsl 115
                                        + s +++ +++ + l+l + +   +r  ++    + ++ + ara    ++ll++DE    l+   + e+ ee++++
  gi|385805785|ref|YP_005842183.1| 105 RKvSKEEINKRVTEVLELVKLKgmeKRYPNQLSGGQQQRVALARALvikPRLLLLDEPLSnLDaklRVEMREEIKRI 181
                                       33334444333333333333334433333333333333333333334556677777743335554346666666666 PP

                            AAA_22 116 ln 117
                                       + 
  gi|385805785|ref|YP_005842183.1| 182 QR 183
                                       55 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.1e-05      0.04      23      51 ..      30      59 ..      20     161 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.1e-05
                            AAA_16 23 rpelvllsGesGvGKsslvrellr.alekd 51
                                      ++e   l G+sG+GK++ +r ++  ++ ++
  gi|385805785|ref|YP_005842183.1| 30 EGEFFTLLGPSGCGKTTTLRLIAGfEIPDE 59
                                      4578899*************9985344444 PP

>> OB_MalK  MalK OB fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00039       0.5       6      53 .]     240     286 ..     240     286 .. 0.92
   2 ?   -0.3   0.0       1.5     2e+03       6      32 ..     299     325 ..     298     345 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00039
                           OB_MalK   6 NflpatveedgvlvegggvtlplpeeqklalklyagkevilGiRPEhi 53 
                                       N+++a +e+d+++ +++g+++++++++      ++g+++ + iRPEhi
  gi|385805785|ref|YP_005842183.1| 240 NIIEAIYEGDDIASLDKGTKIKISKAE-EGVTFAKGERIRILIRPEHI 286
                                       9**********99999*******9998.67777899***********9 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.5
                           OB_MalK   6 Nflpatveedgvlvegggvtlplpeeq 32 
                                       N+++++v+ + ++ + +++++++ e+ 
  gi|385805785|ref|YP_005842183.1| 299 NIVKGKVVFKMFTGTMQELKVEIGENV 325
                                       889999997766666777777776655 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0       0.3   3.8e+02      39      53 ..      35      49 ..      29      57 .. 0.87
   2 ?   10.6   0.7   0.00022      0.28      95     161 ..     129     193 ..     102     206 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.3
                              TniB 39 llvGdsnnGKtmive 53
                                       l+G+s +GKt+ ++
  gi|385805785|ref|YP_005842183.1| 35 TLLGPSGCGKTTTLR 49
                                      689********9875 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00022
                              TniB  95 gaplkararvskleqqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlvG 161
                                       ++++ ++ +  ++++ +l+    +k+r+L++DE  + l   a+ + e+ + +k++++elki+ ++v 
  gi|385805785|ref|YP_005842183.1| 129 EKRYPNQLSGGQQQRVALARALVIKPRLLLLDEPLSNL--DAKLRVEMREEIKRIQRELKITTIYVT 193
                                       4455444455555555555566689********87777..788899****************99985 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   0.00017      0.22      30      66 ..      28      71 ..      20      85 .. 0.74
   2 ?   -0.7   0.0      0.67   8.6e+02     168     188 ..     174     194 ..     141     200 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00017
                            AAA_25 30 lpagelallaGapgtGKttlaldlalava..tGkpwlg.....p 66
                                      + +ge+  l G++g+GKtt +  +a      +Gk ++g      
  gi|385805785|ref|YP_005842183.1| 28 INEGEFFTLLGPSGCGKTTTLRLIAGFEIpdEGKIFFGdedvtY 71
                                      789****************9887777777788888888765551 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.67
                            AAA_25 168 lvealeriarrtgaavllvhH 188
                                       + e ++ri+r+++++++ v H
  gi|385805785|ref|YP_005842183.1| 174 MREEIKRIQRELKITTIYVTH 194
                                       557899999999999999999 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00015       0.2       3      59 ..      36      87 ..      34     116 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00015
                      RNA_helicase  3 lyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevvvidDfg 59
                                      l Gpsg+GK+t+ +         ++ + +++++++  + ++ + Y++ +++v++  +
  gi|385805785|ref|YP_005842183.1| 36 LLGPSGCGKTTTLRL-----IAGFEIPDEGKIFFGDEDVTYKKPYERGTAMVFQNYA 87
                                      78***********99.....3355689999**99*******9999999999988765 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1    0.0012       1.5      62      83 ..     152     173 ..     118     179 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0012
                           SbcCD_C  62 palrlvfLDEAFsklDeesiat 83 
                                        ++rl++LDE  s+lD++ + +
  gi|385805785|ref|YP_005842183.1| 152 IKPRLLLLDEPLSNLDAKLRVE 173
                                       469*************997765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   5.5     0.011        15      20      40 ..      32      52 ..      11     211 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.011
                            AAA_23 20 gltlItGpNGaGKTTildAik 40
                                       ++ + Gp G+GKTT l+ i 
  gi|385805785|ref|YP_005842183.1| 32 EFFTLLGPSGCGKTTTLRLIA 52
                                      578999*********998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       731  (0.0407719); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); 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 0.29s 00:00:00.92 Elapsed: 00:00:00.47
# Mc/sec: 2303.81
//
Query:       gi|385805786|ref|YP_005842184.1|  [L=604]
Description: iron(III) ABC transporter permease [Fervidicoccus fontis Kam940]
Scores for complete 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   91.5  41.3    2.2e-15   56.9  15.4    4.2  4  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
        2.6    8.2   5.8        6.4    6.9   1.6    2.7  2  YebO          YebO-like protein


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -7.9  10.2         2   1.8e+04      22      61 ..      28      97 ..      17     106 .. 0.44
   2 !   49.0  17.9   6.4e-17   5.7e-13       2     176 ..     104     298 ..     103     303 .. 0.79
   3 ?   -1.4   5.8      0.18   1.6e+03     108     174 ..     344     409 ..     330     418 .. 0.57
   4 !   56.9  15.4   2.5e-19   2.2e-15      16     178 ..     417     594 ..     403     600 .. 0.84

  Alignments for each domain:
  == domain 1  score: -7.9 bits;  conditional E-value: 2
                      BPD_transp_1 22 pliivllslPsfvlaillvlvf..............................vilsilghlilp.viilll 61
                                       + i+++ lP++ ++  +   f                              + +s++ ++i+   ii+++
  gi|385805786|ref|YP_005842184.1| 28 SYLILFMILPIVSIFASVRN-FnfslflqpqyinlhpigtaisvnkfgsttfIKISGVSYGIILnSIIIAI 97
                                      45555555555553333221.13433344455555555555555555444442222222333322333333 PP

  == domain 2  score: 49.0 bits;  conditional E-value: 6.4e-17
                      BPD_transp_1   2 illGilaa...lnrnkkldkllrpliivllslPsfv............laillvlvf............vilsilgh 51 
                                       i++G+l+a    +++++l+ llr+l iv+l + +f+            +                      +  l +
  gi|385805786|ref|YP_005842184.1| 104 IFIGLLVAfvlARYSFPLKTLLRILAIVPLLMTPFIntyvmkkfigpsF-------GvntlswilshilNQDVRLSF 173
                                       677888888877****************997777775776666655552.......033344446776656666667 PP

                      BPD_transp_1  52 lilp.viillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavl 127
                                       + ++ +ii+ ++++ p+v+l++++ + +++ +l+e a+ lGa+ +++fr v++P+++p +++g++l+f++++ +  +
  gi|385805786|ref|YP_005842184.1| 174 SDIAgIIIAQAITFYPIVYLNVYSSMMNIDPSLEEQAENLGAKGFKLFRSVTFPLSFPGLAAGAVLVFIFSIEDVGA 250
                                       77777************************************************************************ PP

                      BPD_transp_1 128 leflgswpGlgtllleailgydyseis.....nggvlalviavlllnlvadilq 176
                                       ++++g       + + ++++y y +++     n ++ al++ +ll++lv++i  
  gi|385805786|ref|YP_005842184.1| 251 PLIFG------FRDVLSYQIYSYFQGMsvgigNPVAGALALTMLLISLVLFISI 298
                                       *9999......4455555555555555688886777777777777777777655 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.18
                      BPD_transp_1 108 ppiitglilafggllggavlleflgswpGlgtllleailgydyseis...nggvlalviavlllnlvadi 174
                                       +p i  ++laf   + ++ l+  ++    l++++  +++   y  i+   + +++a++i++ll + ++++
  gi|385805786|ref|YP_005842184.1| 344 SPQIGVAMLAFSKQWSQSPLPQGFT----LNYFFQLFSIPGVYRGIInslVYSTAAVAIIILLGLSISYV 409
                                       3444445555555577777777777....77777777777777777777534444444444443333333 PP

  == domain 4  score: 56.9 bits;  conditional E-value: 2.5e-19
                      BPD_transp_1  16 ldkllrpliivllslPsfvlaillvlvf......vilsilghlilpviillllsaapyvrlirraalrslpkdlvea 86 
                                       +  ll+ l+ + l++P +v+a+  +++f       +l+ +++ ++p+i+++ +  +p++ + ++a+l++   +l+ea
  gi|385805786|ref|YP_005842184.1| 417 GISLLDYLSTIALAIPGLVVAFGYFFFFhdvfpnTLLDPIYNPAIPLILAYSVRRLPFTSRSIYAGLQQTHLSLEEA 493
                                       55689999***********999999888************************************************* PP

                      BPD_transp_1  87 aralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis......... 154
                                       +  lGasr +++  +v+P+++  i +g++++f++ +g++++  ++g   Glg  + +++   ++++ +         
  gi|385805786|ref|YP_005842184.1| 494 SINLGASRARTLASIVIPLIILNITSGAMITFVYCMGETSVSITIG---GLGGDVSSPNHKGPITMVMldlivsgri 567
                                       **********************************************...7888888888888888777888888888 PP

                      BPD_transp_1 155 ...nggvlalviavlllnlvadilqrl 178
                                          n +++ +v+++ll ++v+ i++ +
  gi|385805786|ref|YP_005842184.1| 568 dgtNLAAALGVLLMLLQIIVIIIITLV 594
                                       885455555555555555555554444 PP

>> YebO  YebO-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   1.6   0.00071       6.4       1      31 [.      98     128 ..      98     132 .. 0.86
   2 ?    2.4   0.2     0.019   1.7e+02       3      20 ..     396     413 ..     394     428 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00071
                              YebO   1 vvlvivvlvgllvwFFvnRasvrAneqieLl 31 
                                       +v vi++ +gllv F + R+s    +++++l
  gi|385805786|ref|YP_005842184.1|  98 FVTVISIFIGLLVAFVLARYSFPLKTLLRIL 128
                                       689******************8777776666 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.019
                              YebO   3 lvivvlvgllvwFFvnRa 20 
                                       ++i++l+gl +++ v R+
  gi|385805786|ref|YP_005842184.1| 396 VAIIILLGLSISYVVARV 413
                                       6899************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (604 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1014  (0.0565564); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); 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):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.40
# Mc/sec: 4477.43
//
Query:       gi|385805787|ref|YP_005842185.1|  [L=491]
Description: ABC-type iron(III) transport system, substrate-binding component [Fervidicoccus fontis Kam940]
Scores for complete 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-17   62.2   0.7    7.4e-17   61.6   0.7    1.2  1  SBP_bac_6   Bacterial extracellular solute-binding protein
    5.9e-15   55.8   4.6    5.9e-15   55.8   4.6    1.7  2  SBP_bac_8   Bacterial extracellular solute-binding protein
    5.1e-14   53.0   3.8      9e-14   52.1   3.8    1.4  1  SBP_bac_1   Bacterial extracellular solute-binding protein
     0.0018   18.1   0.8     0.0052   16.6   0.2    2.0  2  SBP_bac_11  Bacterial extracellular solute-binding protein
  ------ inclusion threshold ------
      0.012   15.3   0.1      0.029   14.1   0.1    1.5  1  NCE101      Non-classical export protein 1
      0.024   14.9   0.2      0.044   14.0   0.2    1.4  1  DUF4330     Domain of unknown function (DUF4330)
       0.15   11.9   1.3       0.38   10.6   1.3    1.6  1  DUF4307     Domain of unknown function (DUF4307)


Domain annotation for each model (and alignments):
>> SBP_bac_6  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.6   0.7   2.9e-20   7.4e-17       3     226 ..     106     348 ..     104     360 .. 0.88

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 2.9e-20
                         SBP_bac_6   3 lpdlilsfdkdflekfieeglfqpld...........panlpnvnkdfaeeglkdpdgkyy..pygvgplvlavnkd 66 
                                        +d++++ ++ +++ + + +l++pl+           p++++ v+      +  d++g++y  + +++ +++ vn++
  gi|385805787|ref|YP_005842185.1| 106 NVDVGWGGGPTLFDSMYSYNLLAPLNttialnaasqiPNSIAGVP-----MKRVDSNGNIYwvAAAISSFGFTVNTQ 177
                                       5799**********************9999999988888888888.....888888888777799************ PP

                         SBP_bac_6  67 rlkgrpv..PksWaDLldPeykgkvalpgnng........sdlfealllalykdfgedgvkkllrnlkanlhpaq.. 131
                                         k+  +  P+sW+DL + +++  +a  gn+         s++++ +  ++ +++g+d+++kll  ++an   +   
  gi|385805787|ref|YP_005842185.1| 178 LAKQYGLpiPQSWQDLASLNFARVYAETGNAPlamadptvSTSNARIYEIILTKYGWDQGWKLLTLMAANAYISSsg 254
                                       9987655449*************999999888899999999999999***************************999 PP

                         SBP_bac_6 132 ..mvkaagslesgepavsvvpyffadilpekkkgknlkvvwPedGalvspifmlvkkg.kkkelakafidfllspev 205
                                         + +  +s++ ge +v ++++f++ i+++++   +   + P + ++++ + +++ +  k++ +a+afi + l +  
  gi|385805787|ref|YP_005842185.1| 255 saSSDVRDSVIRGERVVGITIDFYGYIAQYQN--PSCVYIAPANETIINGDPIALFATsKHPTEAQAFIAWVLTDGQ 329
                                       999999*************************8..46666778889************99**************9955 PP

                         SBP_bac_6 206 qailakaggvfPvvtnpavln 226
                                       q  l+ + + +P+  npav n
  gi|385805787|ref|YP_005842185.1| 330 QIWLNPNVNRLPA--NPAVFN 348
                                       5555555558886..555554 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 !   55.8   4.6   2.3e-18   5.9e-15      35     270 ..     102     348 ..      84     359 .. 0.80
   2 ?   -2.1   0.1       1.1   2.8e+03      23      55 ..     449     479 ..     438     488 .. 0.58

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 2.3e-18
                                       T---SEE.EEE-HHH.HHHHHHTTSB--GG...GSTTHHH-HHHHHTT.....--TS.----EEEEEEE-EEEEEHH CS
                         SBP_bac_8  35 gtapdidvvwaneda.latlaeeglladls...dldnlddltdalaav.....gydgklygvPyasetpyvliynkd 102
                                        ta  +dv w+ +   ++ +   +lla+l+    l  + ++++ +a+v     + +g++y+v  a+++  ++ +n+ 
  gi|385805787|ref|YP_005842185.1| 102 ATAKNVDVGWGGGPTlFDSMYSYNLLAPLNttiALNAASQIPNSIAGVpmkrvDSNGNIYWVAAAISS-FGFTVNTQ 177
                                       34456788888866568999999*******6444455555888888889999899************8.9******* PP

                                       HHHHS...---BHHHHHHH.HHHH...HHH-..SEGG--..-GGGGGGTHHETTEE---H..HHH.HHHHHHHHHHH CS
                         SBP_bac_8 103 lleka..edpktwdellaa.akkl...kgkf..glpdpa..sgwlqaallakdgksldddggkdglkealellkklk 169
                                       l+++     p++w++l ++ ++ +   +g++  +++dp+  +++++++ ++ +    +    k g+++ ++ll+ + 
  gi|385805787|ref|YP_005842185.1| 178 LAKQYglPIPQSWQDLASLnFARVyaeTGNAplAMADPTvsTSNARIYEII-L----T----KYGWDQGWKLLTLMA 245
                                       **985788********87553333344466666666665324677888888.5....4....559************ PP

                                       HTT-EE...-S..--SSTTTTTSBSEEEE-TTHHHHHH-TTTSEEEE--S--EEEEEEEEEEBTTS-HHHHHHHHHH CS
                         SBP_bac_8 170 dngkty...dtgadavsefanGevaftingswdiaaaqkagkklgaivpkqgsfaggkglavpknaknedlaAldFl 243
                                       +n ++    ++++d+ + +  Ge + +i+ +     aq +++   +i+p++ ++++g+++a ++ +k++++ A++F+
  gi|385805787|ref|YP_005842185.1| 246 ANAYISssgSASSDVRDSVIRGERVVGITIDFYGYIAQYQNPSCVYIAPANETIINGDPIALFATSKHPTE-AQAFI 321
                                       99987756556689*********9999996655444444559****************************7.***** PP

                                       HHHTTSHHHHHHHH.HH---BS-S-TTT CS
                         SBP_bac_8 244 kwltspenqaalae.ktgyipvnksaal 270
                                        w++++ +q+ + + + + +p+n+++ +
  gi|385805787|ref|YP_005842185.1| 322 AWVLTD-GQQIWLNpNVNRLPANPAVFN 348
                                       ****86.677799999******999865 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.1
                                       SHHHHHHHHHHTT---SEE.EEE-HHHHHHHHH CS
                         SBP_bac_8  23 dleqklkaalaagtapdidvvwanedalatlae 55 
                                       +++q l++a+++g++ di+ ++    +lat + 
  gi|385805787|ref|YP_005842185.1| 449 EAIQ-LNSAVQSGKV-DINSLMNTWTNLATQKY 479
                                       5444.8999999987.65433333333444443 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 !   52.1   3.8   3.5e-17     9e-14      20     314 ..      81     330 ..      67     331 .. 0.83

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 3.5e-17
                                       HHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEE.CGGHHHHHHHTTSBECCHHHHHHTTECTTCCTEEEEHH CS
                         SBP_bac_1  20 kehpgikVeiesvgsgslaqkltlaiaaGdgpaDviav.dndwiarlakaglllpldpyvkaylapgvkdaadklss 95 
                                       k+++ ++ ++ sv+ + +a        a+++  Dv ++ +++ ++ + + +ll+pl++ ++ ++a + +   +   +
  gi|385805787|ref|YP_005842185.1|  81 KQYNIVDLQFLSVPENLWAS------TATAKNVDVGWGgGPTLFDSMYSYNLLAPLNTTIALNAASQIPNSIAGVPM 151
                                       44677888888888888888......3333334*****999999999999**************9999866666555 PP

                                       HHTHHHHCEEE..ES.EEEE.EEEEEEEETTTHHCTTGGGSHBHHHHHHH..HHHHHHHCTCTHCCHCCEEHHHHHH CS
                         SBP_bac_1  96 svlpkildskv..ly.vPly.aargliYNkdlfekagldppwtWdelvea..akklkekgkkpiggarggsasgtay 166
                                       + +++     +  +y v    ++ g+ +N++l +++gl+ p +W++l+ +  a+   e g++p   ++  + s+ ++
  gi|385805787|ref|YP_005842185.1| 152 KRVDS-----NgnIYwVAAAiSSFGFTVNTQLAKQYGLPIPQSWQDLASLnfARVYAETGNAP-LAMADPTVSTSNA 222
                                       55543.....247999999966*************************9764478888888888.6666666666666 PP

                                       HHHHHHHHHHTGGGEECCCTHHCSHHHHSHHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHHHHHTTSCSEEEEEHH CS
                         SBP_bac_1 167 yfalalakslggkvfdkdgggldnpegvtaatylvklyavanltkelkgkgaenkdgaaalalfeaGeaamaivglw 243
                                         ++ ++  +g                  +++ ++ l ++a     ++  +++++ ++++++ + +Ge  ++i   +
  gi|385805787|ref|YP_005842185.1| 223 RIYEIILTKYG------------------WDQGWKLLTLMA----ANAYISSSGSASSDVRDSVIRGERVVGITIDF 277
                                       67777777777..................788888888666....7999**********************99999* PP

                                       HHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEEEEEEEEEEBTTCSTHHHHHHHHHHHTSHHHH CS
                         SBP_bac_1 244 aalaamkvapkvafaadkekpkeelgvaplPagkggkpgilgayglaipkgsknpeaAkkFldfllspeaq 314
                                       + ++a +++p   ++a++ +  +                  +++++a++++sk+p +A++F++++l++++q
  gi|385805787|ref|YP_005842185.1| 278 YGYIAQYQNPSCVYIAPANETII------------------NGDPIALFATSKHPTEAQAFIAWVLTDGQQ 330
                                       *9999999999999999999977..................*****************************9 PP

>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.2     2e-06    0.0052      77     223 ..     166     331 ..     157     334 .. 0.70
   2 ?   -2.0   0.0      0.95   2.4e+03     132     160 ..     434     463 ..     379     483 .. 0.49

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2e-06
                                       EEEEEEEEESTT-TT-.....--SHHHHHHS..........S--EEEE--T-TTTTHH.H.HHHGGG--...HHHHH CS
                        SBP_bac_11  77 assplviavpkgnpkk.....ikgwadLlkp..........glklavadPttspsGlaal.alleaaga...qellk 134
                                       a+s   + v++  +k+     +++w+dL+            +  la+adPt s+s  +++  +l+++g     +ll+
  gi|385805787|ref|YP_005842185.1| 166 AISSFGFTVNTQLAKQyglpiPQSWQDLASLnfarvyaetgNAPLAMADPTVSTSNARIYeIILTKYGWdqgWKLLT 242
                                       566666666666655444444789***99975666666554447********9998877746777887443333444 PP

                                       HHHHT..EEEEESSHHHHHHHHHTTT-SEEEEEHHHHH..H.STTSSEEEE--TTT--...EEEEEEEE-TT--HHH CS
                        SBP_bac_11 135 alekk..vvklgessrqlltaveageadagivyeseakaae.ngdkleavylpeglnldpldypaavlkkaakreaA 208
                                        ++ +  +  +g +s+++ + v +ge  +gi+     + a+ + +  +++++  ++ +     p+a+ ++++++++A
  gi|385805787|ref|YP_005842185.1| 243 LMAANayISSSGSASSDVRDSVIRGERVVGITIDFYGYIAQyQNPSCVYIAPANETII-N-GDPIALFATSKHPTEA 317
                                       444441144445555888999*****99999988877555437788888888888876.3.34999999******** PP

                                       HHHHHHTTSHHHHHH CS
                        SBP_bac_11 209 raFlafLrspeaqai 223
                                       +aF+a+++++ +q+i
  gi|385805787|ref|YP_005842185.1| 318 QAFIAWVLTD-GQQI 331
                                       *******965.5555 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.95
                                       HHHHHHHTEEEEESSH.HHHHHHHHTTT-S CS
                        SBP_bac_11 132 llkalekkvvklgess.rqlltaveagead 160
                                       + + + ++ ++++ ++  ql +av++g++d
  gi|385805787|ref|YP_005842185.1| 434 FTDPITGNQTTFTMNEaIQLNSAVQSGKVD 463
                                       222233332222222234444556666555 PP

>> NCE101  Non-classical export protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   1.1e-05     0.029      13      31 ..      19      37 ..      16      47 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.1e-05
                            NCE101 13 ifiGvaaYylyEkrterpe 31
                                      i+iGvaaYy yE+  ++  
  gi|385805787|ref|YP_005842185.1| 19 IVIGVAAYYAYESSKGTST 37
                                      89**********9776554 PP

>> DUF4330  Domain of unknown function (DUF4330)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   1.7e-05     0.044      12     115 ..       7     109 ..       2     136 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.7e-05
                           DUF4330  12 gkvnilDllailvilavivgiflkpgtsgsvaqaeaaatkpve..vdvvvrglevpeelak.vkegektniiirnqP 85 
                                         + ++ +++il+++ v++  ++  ++++s+ ++++a t++ +    v++ +l+ +++++  +  +  +n +i    
  gi|385805787|ref|YP_005842185.1|   7 STLAVVGIIIILIVIGVAAYYAYESSKGTSTTTTTTAITQTNTsaSGVTLTILTRHPSVITdLARSTFLNSSI---- 79 
                                       5566777777777777777777777666666444443333333336777788888888888577788888888.... PP

                           DUF4330  86 agdveikdvkvlprkvvvpqpdGkvkaled 115
                                       a++ +i+d + l+     ++++ + k++++
  gi|385805787|ref|YP_005842185.1|  80 AKQYNIVDLQFLSVPENLWASTATAKNVDV 109
                                       6899***99999988888888887777665 PP

>> DUF4307  Domain of unknown function (DUF4307)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.3   0.00015      0.38       4      54 ..       8      59 ..       6      67 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00015
                           DUF4307  4 llvillvvlvvvalalvawigysq.gsadvsaevvgfevvddstvevtfeVt 54
                                      +l+++++++++++++++a+++y++ + ++ ++++++++ ++ s+  vt+++ 
  gi|385805787|ref|YP_005842185.1|  8 TLAVVGIIIILIVIGVAAYYAYESsKGTSTTTTTTAITQTNTSASGVTLTIL 59
                                      58999999***************98666666666666666666666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (491 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1054  (0.0587874); expected 358.6 (0.02)
Passed bias filter:                      596  (0.0332422); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.69u 0.29s 00:00:00.98 Elapsed: 00:00:00.48
# Mc/sec: 3061.88
//
Query:       gi|385805788|ref|YP_005842186.1|  [L=196]
Description: Flavoprotein, 3-polyprenyl-4-hydroxybenzoate decarboxylase, UbiX [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.7e-26   91.8   1.0    7.1e-26   90.8   1.0    1.4  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 !   90.8   1.0     4e-30   7.1e-26       1     125 [.       2     171 ..       2     185 .. 0.85

  Alignments for each domain:
  == domain 1  score: 90.8 bits;  conditional E-value: 4e-30
                                       EEEEEEE-SSCGGGCHHHHHHHHHHTTEEEEEEESCHHHHCCHHG.GS...............TCSSHHHHHHCT.. CS
                      Flavoprotein   1 kkillgiTGsvaaikalellekLkkegievqvvltkaAkkfiske.klklaa...........redpilhielrr.. 63 
                                       k+i++++TG++++i++++l+e L +++++++++ t+ A+ + + e  ++l++           +      i++ +  
  gi|385805788|ref|YP_005842186.1|   2 KRIVVALTGASGIIYGKKLIEVLVEKSYNMEIIYTEHANLVSKLEeGVSLEEflvgiskkhsdK------IKIYKek 72 
                                       79***************************************99886566655887874444440......4442245 PP

                                       ...........TESEEEEEEEEHHHHHHHHTT--SSHH..............................HHHHHTHCC CS
                      Flavoprotein  64 ...........wadllviaPasantlakianGiadnll..............................tlilratak 99 
                                                    d++vi+P+s +tl++i +Gi+dnl+                              +      ak
  gi|385805788|ref|YP_005842186.1|  73 dfmsplasssnIGDAMVIVPCSVKTLSQISYGISDNLVvraalaflrmkkklvvvpretplglielnaMVE---LAK 146
                                       5666666666699*************************************************998655444...599 PP

                                       TTEEEEE.--HHCCTCSTCHHHHHHH CS
                      Flavoprotein 100 kpiliaPamnpamyenpqtlknlekl 125
                                       ++++i+P ++pa+y++p+ +++++++
  gi|385805788|ref|YP_005842186.1| 147 AGAIILP-AMPAFYHKPKGIDDIVNF 171
                                       *******.****************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1328.14
//
Query:       gi|385805789|ref|YP_005842187.1|  [L=131]
Description: hypothetical protein FFONT_0747 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       975  (0.0543812); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 820.50
//
Query:       gi|385805790|ref|YP_005842188.1|  [L=140]
Description: hypothetical protein FFONT_0748 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 876.03
//
Query:       gi|385805791|ref|YP_005842189.1|  [L=559]
Description: type III restriction enzyme, res subunit [Fervidicoccus fontis Kam940]
Scores for complete 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   89.5   0.0    3.4e-25   88.7   0.0    1.3  1  ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
    2.7e-21   76.3   0.7    8.6e-21   74.7   0.1    2.1  2  ResIII         Type III restriction enzyme, res subunit
    4.3e-17   62.5   0.0    1.7e-16   60.6   0.0    2.1  2  Helicase_C     Helicase conserved C-terminal domain
    3.2e-07   30.3   0.2    1.3e-06   28.3   0.0    2.1  2  DEAD           DEAD/DEAH box helicase
    0.00071   19.9   0.0     0.0098   16.2   0.0    2.7  3  AAA_22         AAA domain
  ------ inclusion threshold ------
      0.037   14.2   0.2       0.92    9.7   0.1    2.8  3  DNA_pol3_chi   DNA polymerase III chi subunit, HolC
      0.095   12.5   0.1       0.19   11.6   0.1    1.4  1  DAPDH_C        Diaminopimelic acid dehydrogenase C-terminal d
       0.15   11.9   0.9        9.6    6.1   0.0    3.3  3  SinI           Anti-repressor SinI


Domain annotation for each model (and alignments):
>> ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.7   0.0   1.5e-28   3.4e-25      38     187 ..     403     545 ..     390     548 .. 0.90

  Alignments for each domain:
  == domain 1  score: 88.7 bits;  conditional E-value: 1.5e-28
                     ERCC3_RAD25_C  38 lyvmnpnkfracefLikyhekrgDkiivfsDnvfaLkeyakklkkpyiyGetseaerlkilqkfkknpkvntiflsk 114
                                       +y     k +a++ +++   k g ki+vf+  v   ++++++l  p ++G+t+++ r+kil++fkk  +  +++l  
  gi|385805791|ref|YP_005842189.1| 403 IYQKAKAKEEAVKKIVEQELKNGSKILVFTQYVEQAEKLGNMLGAPVLTGSTETKLRKKILEDFKKA-QSGVLVLTT 478
                                       55566678889999999999*********************************************98.567899*** PP

                     ERCC3_RAD25_C 115 vgDtsiDlPeanvliqisshfgsrrqeaqrlGriLrakkksneeefnaffYsLvskDtkemaystkrqqflvd 187
                                       vgD+ +D+P+ nv i + + +gsrrq  qrlGr+Lr+k +     + a  Y +v k t e   ++kr++  +d
  gi|385805791|ref|YP_005842189.1| 479 VGDEGLDIPDVNVGIIV-AGTGSRRQFVQRLGRLLRPKPE-----KTAKLYEIVTKGTAEESLARKRKKLEID 545
                                       *************9966.568*****************99.....5799******************998776 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 !   74.7   0.1   3.8e-24   8.6e-21       3     169 ..     169     308 ..     167     310 .. 0.95
   2 ?   -1.1   0.1      0.75   1.7e+03     121     131 ..     414     424 ..     357     476 .. 0.58

  Alignments for each domain:
  == domain 1  score: 74.7 bits;  conditional E-value: 3.8e-24
                                       EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTG CS
                            ResIII   3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkfls 79 
                                       elr+yQ+ea+e+++     ++  rg+i+++TG+GKT++ a++i++l +      +l++  +k+ l q++e +k+f++
  gi|385805791|ref|YP_005842189.1| 169 ELRNYQKEALESWK-----NNSSRGIIALPTGSGKTVIGAAAIAELGE-----MTLIITYTKEQLLQWMEMLKNFTD 235
                                       79***********8.....7889************************9.....7*********************** PP

                                       G....GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHHHHHT CS
                            ResIII  80 eaykeigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswreilek 156
                                        +++ i  ++s++k++a         i+++t+q++ +++        + l  rf ++++DE+H+l a ++++ i+  
  gi|385805791|ref|YP_005842189.1| 236 IPQSMIAAFYSEEKRIA--------PITISTYQTAFRHI--------KTLAYRFSLLVVDEVHHLPA-DKFKTIALG 295
                                       **999************........**************........9999****************.9****9777 PP

                                       ---SEEEEEESS- CS
                            ResIII 157 fkeavllglTATp 169
                                       + +  +lgl+AT 
  gi|385805791|ref|YP_005842189.1| 296 MYSPHRLGLSATV 308
                                       777*********7 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.75
                                       ......HHHTT CS
                            ResIII 121 eeeeseellrd 131
                                        ++  e+ l++
  gi|385805791|ref|YP_005842189.1| 414 VKKIVEQELKN 424
                                       12222222222 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0         5   1.1e+04      16      39 ..     210     233 ..     204     254 .. 0.59
   2 !   60.6   0.0   7.4e-20   1.7e-16       5     109 ..     413     513 ..     409     515 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 5
                                       TSEEEEEESSHHHHHH.HHHHHHHT CS
                        Helicase_C  16 ggkilifvntidrlek.vklllekk 39 
                                       g+ +li++ t+++l + +++l +++
  gi|385805791|ref|YP_005842189.1| 210 GEMTLIITYTKEQLLQwMEML-KNF 233
                                       566788888888664445555.233 PP

  == domain 2  score: 60.6 bits;  conditional E-value: 7.4e-20
                                       HHHHHH.HHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSS CS
                        Helicase_C   5 allell.kleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGi 80 
                                       a+++++ ++ ++g+kil+f+++++++e    l   + + + vl+g+++++ r++ile+f+k +s vL+ t+v+ +G+
  gi|385805791|ref|YP_005842189.1| 413 AVKKIVeQELKNGSKILVFTQYVEQAE---KL--GNMLGAPVLTGSTETKLRKKILEDFKKAQSGVLVLTTVGDEGL 484
                                       555555566799**************5...55..45578888******************99999************ PP

                                       TSTTESEEEESSSSSSHHHHHHHHTTSSS CS
                        Helicase_C  81 dipkvnlVinfdlprnvtsyiqriGRtgR 109
                                       dip+vn+ i++    + ++++qr GR  R
  gi|385805791|ref|YP_005842189.1| 485 DIPDVNVGIIVAGTGSRRQFVQRLGRLLR 513
                                       **************************999 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   5.7e-10   1.3e-06       2     170 ..     172     309 ..     171     316 .. 0.78
   2 ?   -1.4   0.1      0.78   1.7e+03      92     104 ..     420     432 ..     384     478 .. 0.61

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 5.7e-10
                                       HHHHHHHHHHHTTC.EEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSE CS
                                       xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   2 diQaeaiplilggg.dvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlr 77 
                                       ++Q+ea++   ++    ++a +TGsGKT + + ++         + g ++li++ t+e   q ++ lk+f++  +  
  gi|385805791|ref|YP_005842189.1| 172 NYQKEALESWKNNSsRGIIALPTGSGKTVIGAAAIA--------ELGEMTLIITYTKEQLLQWMEMLKNFTDIPQ-- 238
                                       579999999995543899**********99777777........457799**********************433.. PP

                                       EEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  78 vlliiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitc 154
                                        ++i    a  ++ +++   + i+++t +  +++++t      ++++lV+DE++ l  ++f+     + +       
  gi|385805791|ref|YP_005842189.1| 239 -SMI---AAFYSEEKRI---APITISTYQTAFRHIKTLA---YRFSLLVVDEVHHLPADKFKTIALGMYSPH----- 300
                                       .222...2344455556...99*************8555...8899**********9999988777666555..... PP

                                       TSTTTSEEEEEESSBS CS
                                       xxxxxxxxxxxxxxxx RF
                              DEAD 155 dgklqrqvivlSATlp 170
                                               + lSAT+ 
  gi|385805791|ref|YP_005842189.1| 301 -------RLGLSATVI 309
                                       .......566666665 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.78
                                       HHHHTTCSEEEEE CS
                                       xxxxxxxxxxxxx RF
                              DEAD  92 skldngvdivvgt 104
                                       ++l+ng +i+v t
  gi|385805791|ref|YP_005842189.1| 420 QELKNGSKILVFT 432
                                       2334444444444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   4.4e-06    0.0098      13     112 ..     193     292 ..     183     305 .. 0.80
   2 ?   -0.7   0.0      0.68   1.5e+03      59      96 ..     440     475 ..     394     503 .. 0.71
   3 ?   -1.6   0.0       1.4   3.1e+03      45      74 ..     493     521 ..     482     545 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.4e-06
                            AAA_22  13 esGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst..sskdllrellralglelka......erlsseell.e 80 
                                       ++G+GKT+  +    +l         +  ++ +t +++    + ++l+++  + ++          e+++   +  +
  gi|385805791|ref|YP_005842189.1| 193 PTGSGKTVIGAAAIAEL---------GEMTLIITYTKEQllQWMEMLKNFTDIPQS---MiaafysEEKRIAPITiS 257
                                       89***************.........888888888888844555555555555554...455599988899999889 PP

                            AAA_22  81 aleqalrarav....ielliiDEaqhlrseealeeL 112
                                       + + a+r+ ++     +ll++DE++hl +++ ++++
  gi|385805791|ref|YP_005842189.1| 258 TYQTAFRHIKTlayrFSLLVVDEVHHL-PADKFKTI 292
                                       9999999999999999***********.98888776 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.68
                            AAA_22  59 ellralglelkaerlsseellealeqalraravielli 96 
                                       +l + lg +  + + ++  l++++ + +++++  ++l+
  gi|385805791|ref|YP_005842189.1| 440 KLGNMLGAPVLT-GSTETKLRKKILEDFKKAQS-GVLV 475
                                       444444444444.66666666777777776666.6665 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.4
                            AAA_22  45 vtlpsstsskdllrellralglelkaerls 74 
                                       + +++ +s++++ ++l r l  + ++ +++
  gi|385805791|ref|YP_005842189.1| 493 IIVAGTGSRRQFVQRLGRLLRPKPEK-TAK 521
                                       55666778889999998888876666.333 PP

>> DNA_pol3_chi  DNA polymerase III chi subunit, HolC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.5   3.4e+03      27      79 ..     208     259 ..     203     289 .. 0.63
   2 ?    9.7   0.1   0.00041      0.92       7      49 ..     404     445 ..     399     446 .. 0.92
   3 ?    0.6   0.0      0.25   5.6e+02      87     124 ..     502     539 ..     484     542 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.5
                      DNA_pol3_chi  27 ragkrvlvlcedeeqlealdelLWtfep..dsFlPHglagegdaaaaqpvlltad 79 
                                       + g+  l+++ ++eql ++ e+L +f +  +s ++    +e+++   +p+ +++ 
  gi|385805791|ref|YP_005842189.1| 208 ELGEMTLIITYTKEQLLQWMEMLKNFTDipQSMIAAFY-SEEKR--IAPITISTY 259
                                       56777788888888888888888666541144444422.11111..126666655 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00041
                      DNA_pol3_chi   7 yllnaedreelacrllekalragkrvlvlcedeeqlealdelL 49 
                                       y+ +a+++ee++ +++e+ l++g ++lv+++  eq+e+l ++L
  gi|385805791|ref|YP_005842189.1| 404 YQ-KAKAKEEAVKKIVEQELKNGSKILVFTQYVEQAEKLGNML 445
                                       66.8999********************************9887 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.25
                      DNA_pol3_chi  87 advlinladevpefferfervieivdgdeeakqaaRer 124
                                       ++++ +l   + ++ e++++++eiv++  ++   aR+r
  gi|385805791|ref|YP_005842189.1| 502 RQFVQRLGRLLRPKPEKTAKLYEIVTKGTAEESLARKR 539
                                       555556666667889999******************98 PP

>> 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 ?   11.6   0.1   8.3e-05      0.19      30      98 ..     351     419 ..     340     441 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.3e-05
                                       EE-HHHHHHHCTSTTECEEEEEEEE-HHHHHHHHTT--TT--HHHHEEEEEEEEE.SCCGHHHHHHHHH CS
                           DAPDH_C  30 GvsqghsdairriegvkdavqytiPveealekvrsgekpelttrekhtrecyvvaeegadkekiekeik 98 
                                       G+s+   +   +++ + +a    iP  e+l++++sg++   ++ + h+  + +  + +a++e+++k ++
  gi|385805791|ref|YP_005842189.1| 351 GLSKEEEEKYEKLKNIYKALTLGIPFAEVLKRAKSGDSRMAKALKIHNEMVQIYQKAKAKEEAVKKIVE 419
                                       889999999999************************************999999988888888876554 PP

>> SinI  Anti-repressor SinI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.14   3.1e+02      13      24 ..      52      63 ..      52      67 .. 0.82
   2 ?    6.1   0.0    0.0043       9.6       7      20 ..     136     149 ..     135     150 .. 0.90
   3 ?    0.6   0.1      0.23   5.2e+02      14      21 ..     349     356 ..     349     360 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.14
                                      HHHT--SHHHHH CS
                              SinI 13 kesGlskeEfRe 24
                                      +e G++ eE+ +
  gi|385805791|ref|YP_005842189.1| 52 RENGITLEEVLN 63
                                      577******986 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0043
                                       HHHHHHHHHT--SH CS
                              SinI   7 eLikEAkesGlske 20 
                                       +L+k+Ak++Gl +e
  gi|385805791|ref|YP_005842189.1| 136 DLLKKAKDIGLEIE 149
                                       79*********887 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.23
                                       HHT--SHH CS
                              SinI  14 esGlskeE 21 
                                       ++GlskeE
  gi|385805791|ref|YP_005842189.1| 349 KVGLSKEE 356
                                       57*****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (559 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1096  (0.06113); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.70u 0.32s 00:00:01.02 Elapsed: 00:00:00.50
# Mc/sec: 3376.09
//
Query:       gi|385805792|ref|YP_005842190.1|  [L=279]
Description: nucleotide binding protein 2 [Fervidicoccus fontis Kam940]
Scores for complete 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-72  243.5   0.0    2.5e-72  243.3   0.0    1.0  1  ParA         NUBPL iron-transfer P-loop NTPase
    1.8e-07   31.3   0.0    2.6e-07   30.7   0.0    1.4  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    2.5e-06   26.9   4.8     0.0019   17.5   1.6    2.5  2  ArsA_ATPase  Anion-transporting ATPase
     0.0012   18.4   1.2       0.17   11.3   0.2    2.2  2  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
     0.0038   17.2   1.7      0.057   13.3   1.7    2.2  1  AAA_31       AAA domain
     0.0048   16.2   0.0     0.0097   15.2   0.0    1.5  1  MipZ         ATPase MipZ
  ------ inclusion threshold ------
       0.03   13.3   0.4        4.3    6.2   0.1    2.1  2  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
      0.045   13.6   1.1       0.18   11.6   0.1    2.0  2  AAA_26       AAA domain
      0.086   12.4   0.1       0.15   11.6   0.1    1.3  1  AAA_25       AAA domain


Domain annotation for each model (and alignments):
>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  243.3   0.0   1.2e-75   2.5e-72       2     245 ..      25     272 ..      24     273 .. 0.92

  Alignments for each domain:
  == domain 1  score: 243.3 bits;  conditional E-value: 1.2e-75
                              ParA   2 vkkviavlSgKGGVGKStvavnlAlaLakkgl..kvgllDaDiyGpsiprllgveeekpeqsekkliPvea.kgikv 75 
                                       ++ +++vlSgKGGVGKS v++nl la++k g+  k+g+lDaDi+Gpsipr lg e++++ ++ +kl+Pve+ +gik+
  gi|385805792|ref|YP_005842190.1|  25 IRYKFIVLSGKGGVGKSIVTANLGLAFSKLGFkgKIGILDADIHGPSIPRYLGYENAEVLTDGEKLYPVETkYGIKL 101
                                       677899************************98446*************************9999******999**** PP

                              ParA  76 mSigfllesedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqkl.plagaviVttpqevala 151
                                       mS  f+l++++ +++wrGp+k k+i+++++++ewg+lD+L+iD+PPGtgDe   +++ + +++gav+Vt p +v+l+
  gi|385805792|ref|YP_005842190.1| 102 MSASFFLKDKELPIIWRGPLKIKLIRDMITSTEWGNLDLLLIDTPPGTGDEIQGIVEYIsKITGAVVVTIPSDVSLH 178
                                       ***********************************************************99**************** PP

                              ParA 152 dvkkaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdegkplvlk 228
                                       +vk+a++++k+v+v++ G++eNms + c++ g+ ++ fg+gg +k+ +elg +++++ip++p +++ +d+ ++ ++ 
  gi|385805792|ref|YP_005842190.1| 179 VVKRAVSFLKTVNVPLKGIIENMSFVRCND-GSVKRPFGEGG-AKVEKELGEKIIARIPMNPLLSNPIDDTNNPYEY 253
                                       ****************************97.88889**9876.5799*******************99988864443 PP

                              ParA 229 e..peseaakaleeiaekv 245
                                       +  +++e+a +++e a+k+
  gi|385805792|ref|YP_005842190.1| 254 DnlNNNEVAISFMEAAKKL 272
                                       3114566777777777765 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.0   1.3e-10   2.6e-07       2      67 ..      30     164 ..      29     244 .. 0.76

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 1.3e-10
                                       EEEESSTTSSHHHHHHHHHHHHHHTT-..-EEEEEEEESSCCCCHHTTEB-HHHH...................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxx...................... RF
                              CbiA   2 aiastkGGvGKTtlaanLaralarrgl..rVllvDaDpqannlaileglendiep...................... 54 
                                       ++ s+kGGvGK+ ++anL+ a+++ g+  ++  +DaD  +++   + g en +                        
  gi|385805792|ref|YP_005842190.1|  30 IVLSGKGGVGKSIVTANLGLAFSKLGFkgKIGILDADIHGPSIPRYLGYENAEVLtdgeklypvetkygiklmsasf 106
                                       799*********************766336999********999788888877778888899999999888888888 PP

                                       .............................................CCHCCCHHHHHHC CS
                                       .............................................xxxxxxxxxxxxx RF
                              CbiA  55 .............................................dlkrllellealg 67 
                                                                                     ++ ++e ++++ 
  gi|385805792|ref|YP_005842190.1| 107 flkdkelpiiwrgplkiklirdmitstewgnldlllidtppgtgdEIQGIVEYISKIT 164
                                       8888888888888887777777777777777777777777777664444444444443 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   1.6   9.4e-07    0.0019       2      29 ..      28      55 ..      27      63 .. 0.92
   2 !   10.0   0.1   0.00018      0.36     205     246 ..     162     203 ..     123     230 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 9.4e-07
                                      EEEEEEESTTSSHHHHHHHHHHHHHHTT CS
                       ArsA_ATPase  2 kvilvgGKGGVGKttvsaatavklsekg 29
                                      k+i+++GKGGVGK+ v a +++  s+ g
  gi|385805792|ref|YP_005842190.1| 28 KFIVLSGKGGVGKSIVTANLGLAFSKLG 55
                                      89*********************99987 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00018
                                       TTEEEEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEEEE- CS
                       ArsA_ATPase 205 ertsfrlVvipEklslkEteRaikeLkkygikvdavivNkll 246
                                       ++t  ++V+ip  +sl+  +Ra++ Lk +++  + +i N  +
  gi|385805792|ref|YP_005842190.1| 162 KITGAVVVTIPSDVSLHVVKRAVSFLKTVNVPLKGIIENMSF 203
                                       578899*******************************99754 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 !   11.3   0.2   8.7e-05      0.17       3      28 ..      30      55 ..      28      71 .. 0.85
   2 !    6.2   0.1    0.0031       6.2     163     249 ..     181     277 ..     153     279 .] 0.75

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.7e-05
                         Fer4_NifH  3 iaiyGkGGiGksttsqnlsaalaemg 28
                                      i + GkGG+Gks+ ++nl  a+++ g
  gi|385805792|ref|YP_005842190.1| 30 IVLSGKGGVGKSIVTANLGLAFSKLG 55
                                      6788**************99999887 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0031
                         Fer4_NifH 163 kgiekyaksggvrlgGliinsrkvdderelie........kfaeelgtkvlevvPrdeivrkaelrkktvieyap.. 229
                                       k  + + k+ +v l G+i n   v  +++ ++        k  +elg k+++ +P++  + +     +   ey++  
  gi|385805792|ref|YP_005842190.1| 181 KRAVSFLKTVNVPLKGIIENMSFVRCNDGSVKrpfgeggaKVEKELGEKIIARIPMNPLLSNPIDDTNNPYEYDNln 257
                                       455567788888888988887666655555542222222267789***************99888888888888622 PP

                         Fer4_NifH 230 eseqakeyrelarkilenkk 249
                                       ++e+a  + e a+k++e + 
  gi|385805792|ref|YP_005842190.1| 258 NNEVAISFMEAAKKLIESQS 277
                                       5569999*******999875 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   1.7   2.9e-05     0.057       7     129 ..      32     149 ..      27     200 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.9e-05
                            AAA_31   7 anqKGGvGKTTtsvnlaaalaklgk..kvLlvDlDpQanatt.glgiekneiektlyevlieeknikeaiiktkven 80 
                                          KGGvGK+  + nl+ a++klg   k+ + D+D  + +   +lg+e+        evl++ +++  + +      
  gi|385805792|ref|YP_005842190.1|  32 LSGKGGVGKSIVTANLGLAFSKLGFkgKIGILDADIHGPSIPrYLGYENA-------EVLTDGEKLYPVET---KYG 98 
                                       567******************99972358888999876543314443222.......33333333333322...234 PP

                            AAA_31  81 ldlipssidLaeaeielvelekkeeil.kellekvk.deYDyiiiDcpPsL 129
                                       ++l+ +s  L + e  ++     +  l ++++++ +  + D+ +iD+pP  
  gi|385805792|ref|YP_005842190.1|  99 IKLMSASFFLKDKELPIIWRGPLKIKLiRDMITSTEwGNLDLLLIDTPPGT 149
                                       566666666666666666665555554444444443245666666666654 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   4.9e-06    0.0097       3      71 ..      30     100 ..      28     171 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.9e-06
                                       EEE--SSTTSSHHHHHHHHHHHHHTTT-..-EEEEE--TTT-HHHHHHHHHHHHHHHHT---.---EEE-SS CS
                              MipZ   3 ivlgnekGGsGksttavhvavaLlkkGa..rvaaidldlrqrtlarylenraataerkglsL.plpealals 71 
                                       ivl   kGG Gks ++  +  a++k G+  +++ +d d+   ++ ryl+   a +   g +L p+ + + ++
  gi|385805792|ref|YP_005842190.1|  30 IVL-SGKGGVGKSIVTANLGLAFSKLGFkgKIGILDADIHGPSIPRYLGYENAEVLTDGEKLyPVETKYGIK 100
                                       555.46*********************84459***************9766554433333321233333333 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 ?    6.2   0.1    0.0022       4.3      29      64 ..      27      64 ..      10      77 .. 0.80
   2 ?    5.3   0.0    0.0042       8.4     145     176 ..     140     171 ..     136     195 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0022
                                      SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--..EEEEE CS
                              MeaB 29 aqvvGltGvPGaGkstlvealglelrrrGkr..vavla 64
                                       + + l G  G+Gks ++ +lgl + + G +  +++l 
  gi|385805792|ref|YP_005842190.1| 27 YKFIVLSGKGGVGKSIVTANLGLAFSKLGFKgkIGILD 64
                                      5678899*******************999752255554 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0042
                                       EEEEEEESSTTTTTTT--CCCHHH-SEEEEE- CS
                              MeaB 145 tfvvlllpeaGDelqgikkGileiaDiivvnk 176
                                       + ++ + p++GDe+qgi + i  i+  +vv  
  gi|385805792|ref|YP_005842190.1| 140 LLLIDTPPGTGDEIQGIVEYISKITGAVVVTI 171
                                       55666779*************99998888764 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.22   4.4e+02       5      26 ..      31      52 ..      27      59 .. 0.74
   2 ?   11.6   0.1     9e-05      0.18     132     197 ..     167     243 ..     122     244 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.22
                            AAA_26  5 vtgtdtgvGKTvvslgLvralk 26
                                      v +   gvGK++v++ L  a++
  gi|385805792|ref|YP_005842190.1| 31 VLSGKGGVGKSIVTANLGLAFS 52
                                      5556679*******99877774 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 9e-05
                            AAA_26 132 ilVargglgtinqllltiealrqknvrvlGvilNk..vrnp...........envetlekksgipvlGvvPylpdle 195
                                       ++V+ + + ++  +  ++++l++ nv+++G+i N   v              e  +++ek  g ++++++P++p l+
  gi|385805792|ref|YP_005842190.1| 167 VVVTIPSDVSLHVVKRAVSFLKTVNVPLKGIIENMsfV--RcndgsvkrpfgEGGAKVEKELGEKIIARIPMNPLLS 241
                                       444445556778888899999*************9541..233356655566699*********************9 PP

                            AAA_26 196 ap 197
                                       +p
  gi|385805792|ref|YP_005842190.1| 242 NP 243
                                       97 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   7.6e-05      0.15      31      58 ..      25      52 ..       7      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.6e-05
                            AAA_25 31 pagelallaGapgtGKttlaldlalava 58
                                      ++ ++++l G +g+GK+ ++ +l+la +
  gi|385805792|ref|YP_005842190.1| 25 IRYKFIVLSGKGGVGKSIVTANLGLAFS 52
                                      567899*****************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 1880.79
//
Query:       gi|385805793|ref|YP_005842191.1|  [L=453]
Description: DNA topoisomerase VI subunit A [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-21   74.6   0.1    7.9e-21   73.8   0.1    1.4  1  TP6A_N           Type IIB DNA topoisomerase
  ------ inclusion threshold ------
      0.015   15.5   2.6      0.063   13.5   0.2    2.4  2  DUF313           Domain of unknown function (DUF313)
       0.04   13.7   0.2       0.14   12.0   0.2    1.9  1  PhdYeFM_antitox  Antitoxin Phd_YefM, type II toxin-antitoxin 
      0.045   13.7   0.0       0.11   12.4   0.0    1.6  1  DUF2399          Protein of unknown function C-terminus (DUF2
       0.13   12.9   2.9        2.5    8.8   1.8    2.9  2  MRP-63           Mitochondrial ribosome protein 63


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 !   73.8   0.1   2.2e-24   7.9e-21       1      62 []      76     150 ..      76     150 .. 0.97

  Alignments for each domain:
  == domain 1  score: 73.8 bits;  conditional E-value: 2.2e-24
                                       HHHHHHHHHHHHHHHHHHTT--EEHHHHHHH.............GGGS-SSHHHHHHHHHHHHHHHTS-GGGGTE CS
                            TP6A_N   1 rkfaqllkvlelihelleegkvvTkRdiYYr.............dvelFksQaesdrliddievllgvsReeLnv 62 
                                       r+f+q+++++++i+e+l++++++T+RdiYYr              ++++++Q+esd++++d+evl+g +Ree+ +
  gi|385805793|ref|YP_005842191.1|  76 RRFMQTVLMARIIYEALVNNEYPTIRDIYYRgkhtlphvspkdkFKNTWEEQQESDAVLRDVEVLTGKLREEMLI 150
                                       79***************************************97659**************************986 PP

>> DUF313  Domain of unknown function (DUF313)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   1.8e-05     0.063       9      61 ..      26      78 ..      19      99 .. 0.80
   2 ?    1.2   0.2      0.11     4e+02      45      62 ..     341     362 ..     335     386 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.8e-05
                            DUF313  9 kvmrkmngaedpkliiektlfktdvkkkqsrlsipfkklirndFLteeElrai 61
                                      k++++ +  e+pklii+k+  ++ + ++q +l++  ++ ++  F  e+E r  
  gi|385805793|ref|YP_005842191.1| 26 KLIEQVRKGEEPKLIIKKRTLANTIYDRQRKLLLLGEQKLTRKFFDENEARRF 78
                                      55666777899********9999999999999888777778888888887754 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.11
                            DUF313  45 kklirndFLteeElrai....k 62 
                                       +kl ++ F+teeE++      k
  gi|385805793|ref|YP_005842191.1| 341 EKLTKKPFMTEEERKNFiiraK 362
                                       589999*******986534332 PP

>> PhdYeFM_antitox  Antitoxin Phd_YefM, type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   3.8e-05      0.14       3      32 ..      14      43 ..      13      45 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.8e-05
                                      EEEHHHHHHTHHHHHHHHHHHT-EEEEEET CS
                   PhdYeFM_antitox  3 ivsiseakanlselldeveegeepviItrr 32
                                      + si   k+ + +l+++v++geep +I ++
  gi|385805793|ref|YP_005842191.1| 14 ELSIKAVKKAFEKLIEQVRKGEEPKLIIKK 43
                                      67999*******************998765 PP

>> DUF2399  Protein of unknown function C-terminus (DUF2399)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0     3e-05      0.11      18      83 ..     196     264 ..     182     269 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3e-05
                           DUF2399  18 egravyVvENpavlaaaadr..lgakaaplvctsGqpsaaalelldklaaa.garlrYhGDfDwpGlai 83 
                                       ++++v VvE  av++ + +     a++a lv  +Gqp +a+ +++++l ++    ++  +D D+ G  i
  gi|385805793|ref|YP_005842191.1| 196 NAEYVLVVEKDAVFQQLHRFgyWKANKAILVTSAGQPDRATRRFVRRLNEElKLPVYILADSDPYGFYI 264
                                       5667***********98876555569999999****************654266777778888877655 PP

>> MRP-63  Mitochondrial ribosome protein 63
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.11   3.9e+02       5      38 ..     105     135 ..     103     137 .. 0.78
   2 ?    8.8   1.8   0.00069       2.5      13      64 ..     320     381 ..     315     398 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.11
                            MRP-63   5 wiGKhRrvrkvtlsekeklvkrleieeeneyyLs 38 
                                       ++GKh +++    s k+k+++  e ++e +++L+
  gi|385805793|ref|YP_005842191.1| 105 YRGKHTLPH---VSPKDKFKNTWEEQQESDAVLR 135
                                       79***9999...5556778888888888888876 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00069
                            MRP-63  13 rkvtlsekeklvkrleieeeneyyLsrPYLtkeqesghakerrkkekk..........lkki 64 
                                       +k+  ++ke++ k+l+    +e++ ++P++t+e+ +++    +++  +          +k++
  gi|385805793|ref|YP_005842191.1| 320 KKLREEKKERFLKALKTFGYKEKLTKKPFMTEEERKNFIIRAKEQDLEravelvgdkvYKEF 381
                                       7888999***************************9998777777664455444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       810  (0.0451782); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.69u 0.33s 00:00:01.02 Elapsed: 00:00:00.56
# Mc/sec: 2444.32
//
Query:       gi|385805794|ref|YP_005842192.1|  [L=561]
Description: DNA topoisomerase VI subunit B [Fervidicoccus fontis Kam940]
Scores for 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-61  206.5   0.1      2e-61  206.5   0.1    1.6  2  Topo-VIb_trans  Topoisomerase VI B subunit, transducer
    1.1e-10   42.0   0.0    3.7e-10   40.3   0.0    1.8  2  HATPase_c       Histidine kinase-, DNA gyrase B-, and HSP90-l
    6.3e-10   39.0   0.0    1.4e-09   37.9   0.0    1.6  1  HATPase_c_3     Histidine kinase-, DNA gyrase B-, and HSP90-l
    4.8e-08   32.2   4.9    8.1e-08   31.4   0.0    2.2  2  FbpA            Fibronectin-binding protein A N-terminus (Fbp
    0.00076   19.4   0.2     0.0033   17.4   0.0    2.1  2  H2TH            Formamidopyrimidine-DNA glycosylase H2TH doma
     0.0032   17.8   0.1      0.027   14.8   0.0    2.6  3  Ribosomal_S13   Ribosomal protein S13/S18
  ------ inclusion threshold ------
      0.084   13.4   0.1       0.24   11.9   0.1    1.8  1  DcpS_C          Scavenger mRNA decapping enzyme C-term bindin
        1.5    8.4   8.2         14    5.2   4.6    2.5  2  CENP-K          Centromere-associated protein K


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 !  206.5   0.1     9e-65     2e-61       1     159 []     332     506 ..     332     506 .. 0.94
   2 ?   -4.0   0.3       5.2   1.2e+04     126     142 ..     534     550 ..     530     559 .. 0.64

  Alignments for each domain:
  == domain 1  score: 206.5 bits;  conditional E-value: 9e-65
                    Topo-VIb_trans   1 PstdclspigeeliekglkkelkpefvaavtrkpkvyeghpfivEvgiayGGele............keeka..eil 63 
                                       Ps d lspigeeli+ glk++l+pefv+a+trkpk+y ghpfivE+giayGG+l+             ++ +  ++l
  gi|385805794|ref|YP_005842192.1| 332 PSPDPLSPIGEELIKIGLKQVLNPEFVDAITRKPKSYGGHPFIVEAGIAYGGKLSenldeiardsikGQSGPfiALL 408
                                       899************************************************999889999988877533333689** PP

                    Topo-VIb_trans  64 RfaNrvPLlydegadvitkavk..sinwkr.YkleqpedpvvvlvhvastkvPfksegKeaiadveeiekeiklalq 137
                                       R+aN++PLlyde+ad i+++v+  ++nwk+ Ykl+ p+d vvvlvh+astkvP+k++gKe+ia+veei+ke+++a+q
  gi|385805794|ref|YP_005842192.1| 409 RYANKIPLLYDEKADLIWSVVNpdDFNWKNtYKLD-PSDIVVVLVHIASTKVPYKGVGKESIAQVEEIRKEVEAAVQ 484
                                       *********************656****998***9.999************************************** PP

                    Topo-VIb_trans 138 evarkLkkylskkekekeekek 159
                                       e+ar+L+ky+ kk+k++e++ek
  gi|385805794|ref|YP_005842192.1| 485 ELARRLRKYIVKKRKREEAEEK 506
                                       *****************99986 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 5.2
                    Topo-VIb_trans 126 eeiekeiklalqevark 142
                                       ++i++e++++l+ +a k
  gi|385805794|ref|YP_005842192.1| 534 KKIAQELESTLKAIAEK 550
                                       56777777777777655 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 !   40.3   0.0   1.6e-13   3.7e-10       3      81 ..      40     127 ..      38     160 .. 0.70
   2 ?   -2.3   0.0       2.7   6.1e+03      28      63 ..     185     225 ..     166     243 .. 0.70

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 1.6e-13
                                       HHHHHHHHHHHHHHHHHHHSTTT...EEEEEEEEEE....TEEEEEEEESSSSSTTHHHTGTCS..TTCHHCSTCHT CS
                         HATPase_c   3 ekrLrqiisnlvdNavkfatkag...eieveikase....ddlvisveDnGiGipkedlkklfe..kfsqddstkrg 70 
                                       ++ L+q ++++v+N+++++   g   ++ ++i++++    +++++sveDnGiGip ++++  f+   +s++ + +++
  gi|385805794|ref|YP_005842192.1|  40 SRALYQTVREFVENSLDATEVHGilpNVVISISREDssnpNYFTVSVEDNGIGIPSNIIPDAFGriLYSSKYKFRQT 116
                                       678**************933333333556677752256789*******************99986333333333334 PP

                                       STSSSHHHHHH CS
                         HATPase_c  71 gggtGlGlsiv 81 
                                        g  GlG++++
  gi|385805794|ref|YP_005842192.1| 117 RGMYGLGAKMA 127
                                       47888888776 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.7
                                       EEEEEE..EE...TEEEEEEEESSSSSTTHHHTGTCSTTCH CS
                         HATPase_c  28 eveika..se...ddlvisveDnGiGipkedlkklfekfsq 63 
                                       +v+i+   ++   d++++ v+ + i  p +d+ +++ kf  
  gi|385805794|ref|YP_005842192.1| 185 KVTIEGdwNKrtrDYISVYVKRTAIIAPYADITLIMPKFNG 225
                                       56666433125568999999999998888888866668888 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 !   37.9   0.0   6.3e-13   1.4e-09       5     106 ..      45     159 ..      41     182 .. 0.77

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 6.3e-13
                       HATPase_c_3   5 kAlaelvdNsldAdaen.....vkievnknrgkt...geivieDdGkGmseeelknal.rlatsskeakrkstslGk 72 
                                       + + e+v+NsldA   +     v i+++++++++    ++++eD+G G++ + + +a+ r+  ssk+  + ++++G 
  gi|385805794|ref|YP_005842192.1|  45 QTVREFVENSLDATEVHgilpnVVISISREDSSNpnyFTVSVEDNGIGIPSNIIPDAFgRILYSSKY--KFRQTRGM 119
                                       5689*********999999999666666655433456999***************98869*******..589***** PP

                       HATPase_c_3  73 kGiGlklAsl....slgkkltvitkkegess..tltldvd 106
                                       +G+G k+A+l      gk ++++++++ +     ++l+vd
  gi|385805794|ref|YP_005842192.1| 120 YGLGAKMAILygqiTTGKPFEIYSSTSRSNKifYYKLSVD 159
                                       ********97333357888999887765555345666665 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 !   31.4   0.0   3.6e-11   8.1e-08     160     237 ..     249     326 ..     245     334 .. 0.92
   2 ?    0.8   2.4      0.07   1.6e+02     233     320 ..     477     556 ..     456     561 .] 0.49

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 3.6e-11
                                       XSXXXSXBXTTSXXH.HHHHHHHHH.S.XXXHHHHHHHBTTXXHHHHHHHHTTXSSSH...............HHHH CS
                              FbpA 160 lPpsqdklnPleaeeleefkellsk.kekdlvkaLvkafqGlspllaeelleragldketsakelseedlerlyeal 235
                                        Pp+ +k+ Pl ++  e +k ++s+ k+k+++++L+k+fq +++  aee+l+ ag+d + + k+l+++++e+ly+++
  gi|385805794|ref|YP_005842192.1| 249 VPPKETKPHPLGIDL-EMLKMSISEsKNKTIKDFLMKNFQRIGEKKAEEILKIAGIDFDRNPKNLNDKEIEALYKSI 324
                                       69*********7777.767777777799***********************************************99 PP

                                       HH CS
                              FbpA 236 qe 237
                                       ++
  gi|385805794|ref|YP_005842192.1| 325 KS 326
                                       86 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.07
                                       HHHHHHHTXXX....XXEE.....XSSSEESSXXTTXX.SSXXXXSXHHHHHHHHTTTXXX--SHHHHHHHHHHHHH CS
                              FbpA 233 ealqelleeleeekfepqlvlkeekpeefsvvplkslselekesfdslsealdeyYakkaerdrveqkrsdlekrve 309
                                       ++++  ++el   +++  +v+k +++e+   +++        ++ +++ + l  +Y+    ++r +  +++le +++
  gi|385805794|ref|YP_005842192.1| 477 KEVEAAVQELA-RRLRKYIVKKRKREEAEEKFRIFL------KYIPEVAQNLAVFYDGVSPEERKKI-AQELESTLK 545
                                       33333333333.233344444443222222222222......4566666666666666655554433.555555555 PP

                                       HHHHHHHHHHH CS
                              FbpA 310 neleklekklk 320
                                       ++ ek  k ++
  gi|385805794|ref|YP_005842192.1| 546 AIAEKKVKIIE 556
                                       55555555544 PP

>> H2TH  Formamidopyrimidine-DNA glycosylase H2TH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.5e-06    0.0033      19      77 ..     271     327 ..     256     328 .. 0.86
   2 ?   -2.1   0.0       1.7   3.8e+03      62      83 ..     528     549 ..     522     557 .. 0.60

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.5e-06
                                       HHT--SBHHHHHHCTTTSCS--HHHHHHHHHHTT--TTSBGGGS-HHHHHHHHHHHHHH CS
                              H2TH  19 lkkkkrkiktlLLDqklvaGlGNiyadEvLfrakihPerlakslskeelellhqeikev 77 
                                        ++k+++ik +L+ +     +G   a+E+L  a+i+ +r  k+l+++e+e+l+++ik+v
  gi|385805794|ref|YP_005842192.1| 271 SESKNKTIKDFLMKN--FQRIGEKKAEEILKIAGIDFDRNPKNLNDKEIEALYKSIKSV 327
                                       3456899******75..6789***********************************987 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.7
                                       S-HHHHHHHHHHHHHHHHHHHH CS
                              H2TH  62 lskeelellhqeikevlkeaie 83 
                                       +s ee + ++qe+ ++lk+  e
  gi|385805794|ref|YP_005842192.1| 528 VSPEERKKIAQELESTLKAIAE 549
                                       4556667777777777754333 PP

>> Ribosomal_S13  Ribosomal protein S13/S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       4.4   9.8e+03      51      76 ..       8      33 ..       5      40 .. 0.84
   2 !   14.8   0.0   1.2e-05     0.027      17      60 ..     283     326 ..     268     334 .. 0.87
   3 ?   -1.9   0.0       1.8     4e+03      50      62 ..     471     483 ..     451     513 .. 0.54

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4.4
                     Ribosomal_S13 51 iekieeivenkaqykipnwinrqkdi 76
                                      +++++e ve ++q  + +++ r+k+i
  gi|385805794|ref|YP_005842192.1|  8 VDTMTENVESFRQLSPSEFFYRNKEI 33
                                      78889999999999999999998887 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.2e-05
                     Ribosomal_S13  17 ltaikGiGrrkakiilkkadvdedkrigelteeeiekieeiven 60 
                                       +++ + iG++ka++ilk a++d d   ++l+++eie + + ++ 
  gi|385805794|ref|YP_005842192.1| 283 MKNFQRIGEKKAEEILKIAGIDFDRNPKNLNDKEIEALYKSIKS 326
                                       667889********************************999986 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.8
                     Ribosomal_S13  50 eiekieeivenka 62 
                                       ++e+i+++ve  +
  gi|385805794|ref|YP_005842192.1| 471 QVEEIRKEVEAAV 483
                                       3333333333322 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 ?   11.9   0.1   0.00011      0.24      40      93 ..     464     518 ..     440     525 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                                       EESS---SGGG--TTTTTHHHHHHHHHHHHHHHTT-T.-EEEEE--SCCCT--S- CS
                            DcpS_C  40 ipkrdikslrdLtkehlpllkemrekakkvieekyne.vdaeelrvgvhyqPsvy 93 
                                       + k++i+++++++ke    ++e+ + ++k i +k ++   +e++r++++y P v+
  gi|385805794|ref|YP_005842192.1| 464 VGKESIAQVEEIRKEVEAAVQELARRLRKYIVKKRKReEAEEKFRIFLKYIPEVA 518
                                       56789************************99888877677889*********886 PP

>> CENP-K  Centromere-associated protein K
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1     0.015        33      92     124 ..     260     293 ..     231     303 .. 0.82
   2 ?    5.2   4.6    0.0062        14      58     116 ..     503     561 .]     465     561 .] 0.75

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.015
                            CENP-K  92 ksqLelv.lsiiqsknkklkedLkrEqewleeqq 124
                                         +Le++ +si +sknk +k+ L +  + + e++
  gi|385805794|ref|YP_005842192.1| 260 GIDLEMLkMSISESKNKTIKDFLMKNFQRIGEKK 293
                                       5699998468999**********99988887765 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0062
                            CENP-K  58 LtaeleqwekktpeiislneevllalgkeelqklksqLelvlsiiqsknkklkedLkrE 116
                                         ++++ + k  pe+  +   + + ++ ee +k++++Le +l++i  k+ k+ e+ k+E
  gi|385805794|ref|YP_005842192.1| 503 AEEKFRIFLKYIPEVAQNLAVFYDGVSPEERKKIAQELESTLKAIAEKKVKIIEEVKEE 561
                                       4555666777888886666666778999**************************99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (561 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1254  (0.0699426); expected 358.6 (0.02)
Passed bias filter:                      758  (0.0422779); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); 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: 0.76u 0.38s 00:00:01.14 Elapsed: 00:00:00.55
# Mc/sec: 3065.31
//
Query:       gi|385805795|ref|YP_005842193.1|  [L=314]
Description: putative deoxyhypusine synthase [Fervidicoccus fontis Kam940]
Scores for complete 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-93  311.0   0.0    7.8e-93  310.9   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 !  310.9   0.0   4.4e-97   7.8e-93       2     287 ..      29     312 ..      28     313 .. 0.96

  Alignments for each domain:
  == domain 1  score: 310.9 bits;  conditional E-value: 4.4e-97
                                DS   2 llesyeki.gfqatslgeaidilnkmrkdekctiflgltsnlissGlreiiadlvkeklvdvivtTaggieeDlika 77 
                                       l++ y++i gf+a +l++a++il++ r +e+   fl++t+nl+s+Glr+++a+l+++++++v+vtTag++++D++ka
  gi|385805795|ref|YP_005842193.1|  29 LISYYSQIhGFMAGHLSKAAEILSEGR-KESELRFLSFTGNLVSTGLRGLFAKLIRDGHFNVVVTTAGTLDHDIAKA 104
                                       8999**********************5.56669******************************************** PP

                                DS  78 lgkktylgdfelddeeLrekginRignllvpneny.ckfedwvreildkleeeqkvwspselikelGkeindeeSil 153
                                       lg+ +++g fe+dd++L+e +i+R+gn++vp e+y + +e+ v+e++++ +   k++++ e ++ +G++i+d++Sil
  gi|385805795|ref|YP_005842193.1| 105 LGPGYFKGGFEYDDSMLYEYNIHRLGNVFVPFESYgEVVEKAVKEFMEEKKG--KTLAVYEALWSIGEKIEDKNSIL 179
                                       ***********************************999*********99887..478******************** PP

                                DS 154 ywAykndipvfcpaltDgslGdqlllfhsvkekkklkldivkDirelndialka..kktgaiilGGGvpKhhilnan 228
                                       ++Ay++++p+ +p++ Dgs+G+++l++    +  ++kld+  D + l+d+++++  kk+ a+i+GGG++Khh++++n
  gi|385805795|ref|YP_005842193.1| 180 RAAYERKVPIIVPGMYDGSFGTNALIYG---RIYNVKLDLSLDEKLLEDMTFESqdKKSLALIIGGGISKHHVIWWN 253
                                       **********************999999...456699***************87558999***************** PP

                                DS 229 lmrngadyavyittaqefdGslsgatldEavSwgkikaeaksvkvyaDaTivlPLlvaa 287
                                       +++ng+dya+y+tta e+dGslsga+++Ea+Swgk+k+++k++ vy+DaTi+lP+l++a
  gi|385805795|ref|YP_005842193.1| 254 QFKNGLDYAIYLTTAVEYDGSLSGAQTREAISWGKLKSKSKHIVVYGDATITLPILASA 312
                                       ********************************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); 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: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1891.76
//
Query:       gi|385805796|ref|YP_005842194.1|  [L=949]
Description: hypothetical protein FFONT_0754 [Fervidicoccus fontis Kam940]
Scores for complete 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-160  534.3   0.0   2.7e-160  534.1   0.0    1.0  1  RtcB             tRNA-splicing ligase RtcB
    1.7e-18   66.8   0.0    9.6e-18   64.4   0.0    2.5  1  Intein_splicing  Intein splicing domain
    1.9e-06   28.1   2.7       0.06   13.7   0.6    3.1  2  LAGLIDADG_3      LAGLIDADG-like domain
    0.00049   20.3   0.4      0.012   15.8   0.0    2.7  2  PT-HINT          Pretoxin HINT domain
     0.0068   15.9   0.0      0.032   13.7   0.0    1.9  2  Hint             Hint module
  ------ inclusion threshold ------
      0.037   14.0   0.0      0.084   12.8   0.0    1.6  1  Hom_end_hint     Hom_end-associated Hint
      0.087   12.6   0.6       0.21   11.3   0.3    1.7  2  DUF5449          Family of unknown function (DUF5449)


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 !  534.1   0.0  1.1e-163  2.7e-160       1     412 []      47     949 .]      47     949 .] 0.99

  Alignments for each domain:
  == domain 1  score: 534.1 bits;  conditional E-value: 1.1e-163
                                       HHHHHTTSTTB-S-EEEEEEEE--SSS-EEEEEEE-....-EE-HHHC-SST......................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxx......................... RF
                              RtcB   1 qlknvaslpgivkhvaamPDvHlGkgapiGsViatk....gviiPaaVGvDI......................... 48 
                                       q++nva+l+giv ++++mPD H+G+g+piG+V+ ++    gvi+P++VG+DI                         
  gi|385805796|ref|YP_005842194.1|  47 QAANVACLNGIVDASYVMPDGHQGYGFPIGGVAGMDieenGVISPGGVGYDIncltpdmkvldsygawryikelkig 123
                                       89*************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              RtcB  49 ............................................................................. 48 
                                                                                                                    
  gi|385805796|ref|YP_005842194.1| 124 dkvlvnngrsrdaevvfwfyrkeekiyiiktktgriikashdhpiltdrgmilakdlqkgmriatypfsgvryeapa 200
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              RtcB  49 ............................................................................. 48 
                                                                                                                    
  gi|385805796|ref|YP_005842194.1| 201 kkllldrkdleeniakelekrgllplytdnpklpliikllgyftgdgtfdgkktwfygseegleeirkdiellgykp 277
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              RtcB  49 ............................................................................. 48 
                                                                                                                    
  gi|385805796|ref|YP_005842194.1| 278 sniktrrraseyngrtikgkensvyvsaksfrklleklgapigkkthvpftvpswikelplwmkrlylaayfgaemn 354
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              RtcB  49 ............................................................................. 48 
                                                                                                                    
  gi|385805796|ref|YP_005842194.1| 355 kpqtingykfehpfvsvnklkeleknaeeflkdiasmleefgiktlgmsredlgdkvrikllvstkpkflirlwtrv 431
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              RtcB  49 ............................................................................. 48 
                                                                                                                    
  gi|385805796|ref|YP_005842194.1| 432 gyiynprrqrlaiaaaswlrlkinvlkekasvaekaasmhvkgqsagalfimlsqeskwinkkyveraiydgitvpr 508
                                       ***************************************************************************** PP

                                       ..........................................................-EEEEEEEEEEHHHHGGGH CS
                                       ..........................................................xxxxxxxxxxxxxxxxxxx RF
                              RtcB  49 ..........................................................CGvrllktnltaeeleekl 67 
                                                                                                 CGvrll+t+l+++++++k+
  gi|385805796|ref|YP_005842194.1| 509 vsynfprfedwikdnlqgdivydmiedikiktydgyvyditvnddahnfvangiivsnCGVRLLRTELDEKDVRSKI 585
                                       ***************************************************************************** PP

                                       HHHHHHHHHHS-------------HHHHHHHHHHTHHHHHHTTSS-GGGGGGBGGGG--TT--GGGS-HHHHHHHGG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB  68 kelvkelekavpvglgskkkvklskkeleevleegakwaveeglgeeedlekieeegalkeadlekvskkakerark 144
                                       kelv+++ ++vp+glgs++k+k++ + l+evl++g++wave+g+g++ed e+iee+g+++ ad++kvs++ak+r+++
  gi|385805796|ref|YP_005842194.1| 586 KELVDTIARNVPSGLGSEGKIKVTPTILDEVLNRGVEWAVEHGFGRSEDPEHIEERGSWSIADSSKVSSRAKSRGAP 662
                                       ***************************************************************************** PP

                                       GTT---STT-EEEEEEEEEES-HHHHHHHT-.-TTEEEEEEEE--HHHHHHHHHHHHHHHHCCHHHCT---SSGGG- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB 145 qlGtlGsGNHFiEvqlveeildeeaakalgl.eegqvvvmlHsGSRglGhqiaedylkiakkalkkkgiklpdrdLa 220
                                       +lG+lGsGNHF+Evq+ve+i+d+++a+ lg+ +egqv+vm+H+GSRglGhq+a+dyl+i++k ++k+g+  pdr+La
  gi|385805796|ref|YP_005842194.1| 663 ELGSLGSGNHFLEVQVVEKIFDRKIAEFLGItHEGQVTVMIHTGSRGLGHQVASDYLQIMEKVMRKYGTVPPDRELA 739
                                       *******************************889******************************************* PP

                                       -EETTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT.T--HHHH--EEEEEEESEEEEEEEE..T...EEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x...xxxx RF
                              RtcB 221 ylpagseegqaYlkamqaaanyAkaNRqvitervreilekvlkkekedlelelvvdvaHNiakkEehe.d...ekvl 293
                                        +p++s+e+q+Y+kam+aaanyA++NRq+it++vre++++v+k++ ++l+le+++dvaHNiak Eehe +   ++++
  gi|385805796|ref|YP_005842194.1| 740 SIPFNSPEAQDYVKAMAAAANYAWTNRQLITHWVRESFKEVFKTDDDKLGLEIIYDVAHNIAKIEEHEvNgkrKRLV 816
                                       ********************************************999*********************945889*** PP

                                       EEEES-EE-.............TT--EEEE--STTS-EEEEE--HHHH.SSSEE---S-----------------TT CS
                                       xxxxxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB 294 VhRKGAtrA.............kvgqpviipGsmgtkSyivkGkgnae.sfgStsHGAGRlmsRakakkkfkleevk 356
                                       VhRKGAtrA             ++gq+v+ipGsmgt+Sy+++G+++ + ++ ++ HGAGR msR++a k+++++++ 
  gi|385805796|ref|YP_005842194.1| 817 VHRKGATRAfppghpdipkdhkNIGQVVLIPGSMGTASYVLVGTNEGKrTWFTAPHGAGRWMSRSRALKNYTADQLI 893
                                       *********************************************9999**************************** PP

                                       TTTCCCT-EEEE------------------HHHHHHHHCTS-EEEEEEEEEEEEE- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB 357 kdleeqgigvearkkegvleEapeaYKdideVveaqaeaglvevvarlkpvlvvkg 412
                                       ++l+++gi+v+a++k +++eEap+aYKd+d+V+ ++++ g+ + v +l+p++v kg
  gi|385805796|ref|YP_005842194.1| 894 SELSKKGIYVKASSKGVLIEEAPSAYKDVDRVALVADKVGIGKLVLKLRPIGVTKG 949
                                       ******************************************************97 PP

>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.4   0.0   3.8e-21   9.6e-18      12     134 .]     117     566 ..     107     566 .. 0.96

  Alignments for each domain:
  == domain 1  score: 64.4 bits;  conditional E-value: 3.8e-21
                                       HHHHCCECTTEEEEEETTTTEEEEEEEEEEEEEEEE.EEEEEEETTS-EEEEETT-EEEECCTTEEEEEECCC--TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Intein_splicing  12 ieelvekegeevlslnledlklevksvkkliklklk.elyeiklesgrkikaTpeHkllvvrdegivEkradeLkeg 87 
                                       i+el  k g++vl   +++ +   ++v  ++ ++++ ++y ik++ gr ika+ +H++l+    g+    a++L++g
  gi|385805796|ref|YP_005842194.1| 117 IKEL--KIGDKVL---VNNGRSRDAEVV-FWFYRKEeKIYIIKTKTGRIIKASHDHPILTD--RGM--ILAKDLQKG 183
                                       5555..5666666...446666666754.66666666**********************99..788..79******* PP

                                       -EEEEE....................................................................... CS
                                       xxxxxx....................................................................... RF
                   Intein_splicing  88 dliavp....................................................................... 93 
                                         ia+                                                                        
  gi|385805796|ref|YP_005842194.1| 184 MRIATYpfsgvryeapakkllldrkdleeniakelekrgllplytdnpklpliikllgyftgdgtfdgkktwfygse 260
                                       ****999********************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                   Intein_splicing  94 ............................................................................. 93 
                                                                                                                    
  gi|385805796|ref|YP_005842194.1| 261 egleeirkdiellgykpsniktrrraseyngrtikgkensvyvsaksfrklleklgapigkkthvpftvpswikelp 337
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                   Intein_splicing  94 ............................................................................. 93 
                                                                                                                    
  gi|385805796|ref|YP_005842194.1| 338 lwmkrlylaayfgaemnkpqtingykfehpfvsvnklkeleknaeeflkdiasmleefgiktlgmsredlgdkvrik 414
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                   Intein_splicing  94 ............................................................................. 93 
                                                                                                                    
  gi|385805796|ref|YP_005842194.1| 415 llvstkpkflirlwtrvgyiynprrqrlaiaaaswlrlkinvlkekasvaekaasmhvkgqsagalfimlsqeskwi 491
                                       ***************************************************************************** PP

                                       .................................HSCEEEEEEEEEEEEECEEEEEEEEETT.T-EEEECTTEEE- CS
                                       .................................xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx RF
                   Intein_splicing  94 .................................dadvvwdkvksievedeeeyVYdltved.nhNFvangiivHN 134
                                                                        ++d+v+d +++i+ + +++yVYd+tv+d  hNFvangiiv N
  gi|385805796|ref|YP_005842194.1| 492 nkkyveraiydgitvprvsynfprfedwikdnlQGDIVYDMIEDIKIKTYDGYVYDITVNDdAHNFVANGIIVSN 566
                                       ***********************************************************8537*********876 PP

>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.6   2.3e-05      0.06       7      83 .]     239     316 ..     236     316 .. 0.67
   2 !   12.8   0.1   4.2e-05      0.11       2      51 ..     340     399 ..     339     424 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.3e-05
                                       HHHHHHHCCECCECSTTTTSEEEEES-HHHHHHHHHHHHHCT.H.SCEEEE.EEE-SCCCC.....ECCCHCHCTTC CS
                       LAGLIDADG_3   7 LrGlfdaDGsvskskkkgvsisltssskelledvqrlLlrlGIe.stiyek.kkakgrgvy.....rlliisgenlk 76 
                                       L G+f++DG+++++k+      ++  s+e le++++  + lG + s+i+++ + ++ +g         +++s ++++
  gi|385805796|ref|YP_005842194.1| 239 LLGYFTGDGTFDGKKT-----WFYG-SEEGLEEIRKDIELLGYKpSNIKTRrRASEYNGRTikgkeNSVYVSAKSFR 309
                                       88*************4.....4444.44455555555555555424444444333333333458889********** PP

                                       GGGTTTX CS
                       LAGLIDADG_3  77 rFlekig 83 
                                       ++lek+g
  gi|385805796|ref|YP_005842194.1| 310 KLLEKLG 316
                                       ****987 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 4.2e-05
                                       HHHHHHHHHHHHCCECCECSTTTTS....EEEEES-........HHHHHHHHHHHHHCT.HS CS
                       LAGLIDADG_3   2 vkaafLrGlfdaDGsvskskkkgvs....isltsss........kelledvqrlLlrlGIes 51 
                                        k+ +L+++f a+     + ++ +     +s+   +        +e+l+d++ +L+++GI++
  gi|385805796|ref|YP_005842194.1| 340 MKRLYLAAYFGAEMNKPQTINGYKFehpfVSVN--KlkeleknaEEFLKDIASMLEEFGIKT 399
                                       577777888888765544443322244332222..133555555****************97 PP

>> PT-HINT  Pretoxin HINT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   4.9e-06     0.012       9      87 ..     115     186 ..     105     195 .. 0.78
   2 ?    1.6   0.1      0.12   3.1e+02      96     134 ..     532     564 ..     523     571 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.9e-06
                           PT-HINT   9 kaiarikaGdrvlakdeasgkvaekpvlarygneyqelvylkisdgignsevlisnkihPfyskgkfieakelkvGd 85 
                                       + i+++k Gd+vl ++  s ++    v   y +  +e +y+  +      +++++++ hP  ++ ++i ak+l++G 
  gi|385805796|ref|YP_005842194.1| 115 RYIKELKIGDKVLVNNGRSRDA--EVVFWFYRK--EEKIYIIKTK---TGRIIKASHDHPILTDRGMILAKDLQKGM 184
                                       569999********99887654..344544544..4667764444...469*************************8 PP

                           PT-HINT  86 kl 87 
                                       ++
  gi|385805796|ref|YP_005842194.1| 185 RI 186
                                       76 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.12
                           PT-HINT  96 vveeiklkdePlkaynlkvadfhtyfvkgnraeteGvlv 134
                                       ++e+ik+k     +y+++v+d    fv       +G++v
  gi|385805796|ref|YP_005842194.1| 532 MIEDIKIKTYDGYVYDITVNDDAHNFVA------NGIIV 564
                                       6899999*9999*******765555554......33333 PP

>> Hint  Hint module
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   1.2e-05     0.032      11      88 ..      99     171 ..      95     187 .. 0.88
   2 ?   -1.2   0.0      0.48   1.2e+03     154     176 ..     757     779 ..     754     805 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.2e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              Hint  11 gCFpgestvtvedgeqkslseLepGdkVlavdesgevvfsevllfldrdseqraefveietengekltlTpaHLvfv 87 
                                        C + +++v  + g+ + ++eL++GdkVl  +  g+    ev+ +  r++e   + ++i+t+ g+ ++  + H + +
  gi|385805796|ref|YP_005842194.1|  99 NCLTPDMKVLDSYGAWRYIKELKIGDKVLVNN--GRSRDAEVVFWFYRKEE---KIYIIKTKTGRIIKASHDHPILT 170
                                       699**************************876..88889999999999876...5799******9999999997766 PP

                                       X CS
                              Hint  88 s 88 
                                       +
  gi|385805796|ref|YP_005842194.1| 171 D 171
                                       5 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.48
                                       XXXXXXXXXXXXXXXXXXXXXXX CS
                              Hint 154 laScYavieshslahtafapvrl 176
                                       +a +Ya ++++ + h++   ++ 
  gi|385805796|ref|YP_005842194.1| 757 AAANYAWTNRQLITHWVRESFKE 779
                                       6899************9887764 PP

>> Hom_end_hint  Hom_end-associated Hint
   #    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       1      55 [.     100     157 ..     100     170 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.3e-05
                                       CEETT-EEEBTTS-EEEGGG--TT-EEEBTTSSEEE...EEE--EEEEEEEEEEE-SS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxx RF
                      Hom_end_hint   1 cFakgTevlmadGsdksiedievgekvmGkdGkpre...VvalprgvetmYevkektk 55 
                                       c++ + +vl + G+ + i+++++g+kv+ ++G++r+   V  + r  e++Y +k+kt 
  gi|385805796|ref|YP_005842194.1| 100 CLTPDMKVLDSYGAWRYIKELKIGDKVLVNNGRSRDaevVFWFYRKEEKIYIIKTKTG 157
                                       7777889999***********************99544477899*******9999984 PP

>> DUF5449  Family of unknown function (DUF5449)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.3   8.3e-05      0.21      32     130 ..     457     551 ..     444     558 .. 0.85
   2 ?   -3.5   0.0         3   7.8e+03      42      73 ..     784     815 ..     773     829 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.3e-05
                           DUF5449  32 lderisqiivndkdnskeilltsihkfykyaneeltefkkesvkkvefvkGtpdGkviiklkdgkelklddiiyGra 108
                                       l+e+ s   v +k  s ++   s   ++ + ++e + ++k+ v+++   +G    +v  ++  ++++  d++     
  gi|385805796|ref|YP_005842194.1| 457 LKEKAS---VAEKAASMHVKGQSAGALFIMLSQESKWINKKYVERAI-YDGITVPRVSYNFPRFEDWIKDNLQGDIV 529
                                       555544...67788888888888999999999999999999999875.6899999******************99** PP

                           DUF5449 109 fdfiqdvkpkeinsagydntir 130
                                       +d+i+d+k k+ +   yd t+ 
  gi|385805796|ref|YP_005842194.1| 530 YDMIEDIKIKTYDGYVYDITVN 551
                                       ******************9986 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3
                           DUF5449  42 ndkdnskeilltsihkfykyaneeltefkkes 73 
                                       +d++ + ei+    h++ k+ ++e++  +k  
  gi|385805796|ref|YP_005842194.1| 784 DDDKLGLEIIYDVAHNIAKIEEHEVNGKRKRL 815
                                       55666778888888888888888888766654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (949 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      618  (0.0344693); 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: 0.85u 0.31s 00:00:01.15 Elapsed: 00:00:00.49
# Mc/sec: 5769.70
//
Query:       gi|385805797|ref|YP_005842195.1|  [L=515]
Description: DNA repair and recombination protein RadA [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-85  284.9   2.0      3e-70  236.4   0.0    2.1  2  Rad51            Rad51
    2.7e-17   63.0   4.4    2.9e-17   62.9   0.8    2.7  3  Intein_splicing  Intein splicing domain
    2.6e-13   50.4   0.5    8.3e-13   48.7   0.5    1.9  1  HHH_5            Helix-hairpin-helix domain
    6.7e-11   42.2   0.4    3.5e-07   30.0   0.1    2.2  2  RecA             recA bacterial DNA recombination protein
    1.4e-07   31.1   1.3    0.00097   18.5   0.0    2.4  2  ATPase           KaiC
    2.1e-05   24.6   0.0     0.0001   22.4   0.0    2.1  2  Cdd1             Pathogenicity locus
    0.00027   20.6   0.3    0.00073   19.2   0.1    1.7  2  AAA_25           AAA domain
    0.00091   19.0   0.0     0.0047   16.7   0.0    2.2  2  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
     0.0018   18.0   0.2     0.0081   16.0   0.1    2.2  2  HHH              Helix-hairpin-helix motif
     0.0045   17.6   0.6      0.017   15.7   0.1    2.2  2  5_3_exonuc       5'-3' exonuclease, C-terminal SAM fold
     0.0057   17.0   0.1       0.26   11.7   0.0    2.7  2  DUF296           Plants and Prokaryotes Conserved (PCC) domai
  ------ inclusion threshold ------
      0.023   14.8   0.1      0.088   12.9   0.1    2.0  1  HHH_2            Helix-hairpin-helix motif
      0.027   14.8   0.0      0.095   13.1   0.0    1.9  1  IMS_HHH          IMS family HHH motif
      0.036   13.9   0.1       0.16   11.8   0.0    2.2  2  HTH_23           Homeodomain-like domain
      0.047   14.1   0.1       0.14   12.5   0.1    1.8  1  HHH_8            Helix-hairpin-helix domain
      0.064   13.5   0.6         13    6.2   0.0    3.2  3  HHH_3            Helix-hairpin-helix motif


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 !   47.8   0.6   9.5e-16   1.1e-12       3      51 ..      94     142 ..      92     150 .. 0.95
   2 !  236.4   0.0   2.7e-73     3e-70      51     254 ..     313     512 ..     309     513 .. 0.99

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 9.5e-16
                                       -EBHHHHHHHHHSS-EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHH CS
                             Rad51   3 fvsavellekrsellqlttGskklDelLgGGietgsiteifGefrsGkt 51 
                                       f +a el ++r+++ ++ttGsk+lD+lLgGG+et ++te fGef++Gk 
  gi|385805797|ref|YP_005842195.1|  94 FKTALELKKERQSVGKITTGSKSLDDLLGGGVETRTMTEFFGEFGTGKC 142
                                       889********************************************96 PP

  == domain 2  score: 236.4 bits;  conditional E-value: 2.7e-73
                                       HHHHHHHHHHTTS-TTTS--SSEEEEEESSS---GGGGHHHHHHTT--HHHHGGGEEEEE--STTHHHHHHHHTHHH CS
                             Rad51  51 tqlchtlcvtvqlplelgGgegkavyidtegtfrperlveiaerykldkeevlenvayaRaytiehqeellqqaaal 127
                                       tq++h+l+v vqlp ++gG  g+avyid+egtfr er+ ++a   +l+++ev+en+ y Ra +++hq+ ++++++++
  gi|385805797|ref|YP_005842195.1| 313 TQISHQLSVNVQLPPDKGGLSGRAVYIDSEGTFRWERIEAMARALGLNPDEVMENIFYIRAVNSDHQMAVVEEVTKM 389
                                       9**************************************************************************** PP

                                       HHHS-EEEEEEETTTGGGCH-------THHHHHHHHHHHHHHHHHHHHH--EEEEEEE-------.----------- CS
                             Rad51 128 laedkfallivDsvtalyRtdfsgrgelakRqqklgkllrtLrkladefevavvitnqvvaqvdgqaalfsadpkkP 204
                                       ++e+ ++l++vDs+t ++R+++ gr++la+Rqqkl+++l++L ++a+ +++avvitnqv+a++d     f +dp++ 
  gi|385805797|ref|YP_005842195.1| 390 IQEKGIKLVVVDSITGHFRAEYPGRENLASRQQKLNRHLHQLMRIAEIYNIAVVITNQVMARPDV----FYGDPTQA 462
                                       ****************************************************************9....******** PP

                                       -HHHHHHHH-SEEEEEEE-STTEEEEEEES-SSS-S-EEEEEEETTEEE- CS
                             Rad51 205 igGlvlahasttRlalrkgkgeeRivkvvdsPnlpeleavfaigeeGied 254
                                       +gG+vl ha  +R++lrk +g++Ri+kvvd+P+lpe e+vf+i+e Gi d
  gi|385805797|ref|YP_005842195.1| 463 VGGHVLYHAPGVRVQLRKSRGNKRIAKVVDAPHLPEGEVVFSITEYGIRD 512
                                       ************************************************98 PP

>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       3.9   4.4e+03      40      61 ..      48      69 ..       9     116 .. 0.55
   2 !   62.9   0.8   2.6e-20   2.9e-17      23     134 .]     190     312 ..     149     312 .. 0.90
   3 ?   -0.1   0.0      0.73   8.2e+02      63      91 ..     375     404 ..     363     506 .. 0.65

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3.9
                                      EEEEEEEEEEEEEEETTS-EEE CS
                                      xxxxxxxxxxxxxxxxxxxxxx RF
                   Intein_splicing 40 kliklklkelyeiklesgrkik 61
                                      kli+ ++ +l  i ++  ++i 
  gi|385805797|ref|YP_005842195.1| 48 KLIEAGYGTLEAIAVATPQEIS 69
                                      4444444444444444333333 PP

  == domain 2  score: 62.9 bits;  conditional E-value: 2.6e-20
                                       EEEEETTTTEEEEEEEEEEEEEEEEEEEEEEETTS-EEEEETT-EEEECCTTEEEEEECCC--TT-EEEEE...... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...... RF
                   Intein_splicing  23 vlslnledlklevksvkkliklklkelyeiklesgrkikaTpeHkllvvrdegivEkradeLkegdliavp...... 93 
                                       + ++ ++ +++e ++ + + k k+++l+eikl++g+ki +T  H++lv +++++v k+  +Lkegd + v       
  gi|385805797|ref|YP_005842195.1| 190 NKVITFSGNRMELSEAEYIYKQKVEKLVEIKLSNGEKIEVTLSHPFLVSSKGKLVWKKSYTLKEGDEVPVFetsgvl 266
                                       444778888889999999*******************************99*****************9999***** PP

                                       ....HSCEEEEEEEEEEEEECEEEEEEEEETTT-EEEE.CTTEEE- CS
                                       ....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                   Intein_splicing  94 ....dadvvwdkvksievedeeeyVYdltvednhNFva.ngiivHN 134
                                           +++   +k+++ +  + ++ VYdl v+++hNF++  g+i+HN
  gi|385805797|ref|YP_005842195.1| 267 sqksNERFNIEKIVEKKLVNRKGFVYDLVVPGTHNFLSaSGLILHN 312
                                       **988889999***************************9******9 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.73
                                       ETT-EEEECCT.TEEEEEECCC--TT-EEE CS
                                       xxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                   Intein_splicing  63 TpeHkllvvrd.egivEkradeLkegdlia 91 
                                        ++H++ vv++ ++++  ++ +L + d i+
  gi|385805797|ref|YP_005842195.1| 375 NSDHQMAVVEEvTKMIQEKGIKLVVVDSIT 404
                                       567888888778777777777777777776 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.7   0.5   7.4e-16   8.3e-13       2      57 .]      33      88 ..      32      88 .. 0.97

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 7.4e-16
                                      HHHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHHHH CS
                             HHH_5  2 eeLlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilelkd 57
                                      + L++++GiGp+tA +l++aG++++e++a a+++e++++ Gi   tA+r i +++d
  gi|385805797|ref|YP_005842195.1| 33 KTLTDLPGIGPATATKLIEAGYGTLEAIAVATPQEISAAVGIPINTAQRAIKAARD 88
                                      68****************************************************98 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0    0.0003      0.34      20      67 ..      98     142 ..      81     162 .. 0.82
   2 !   30.0   0.1   3.1e-10   3.5e-07      82     227 ..     334     486 ..     315     494 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0003
                                       --TTS--.-----EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHH CS
                              RecA  20 mklgdekeklkvetissGslaldialGiGGlpkGriieiyGpessGkt 67 
                                       ++l  +ke+++v  i++Gs +ld  lG GG+    ++e +G   +Gk 
  gi|385805797|ref|YP_005842195.1|  98 LEL--KKERQSVGKITTGSKSLDDLLG-GGVETRTMTEFFGEFGTGKC 142
                                       455..555799****************.9************9999985 PP

  == domain 2  score: 30.0 bits;  conditional E-value: 3.1e-10
                                       --EEEEESS----....HHHHHHTT--GGG-E.....E..E--SSHHHHHHHHHHHHTTT--SEEEEE-TTT---ST CS
                              RecA  82 gvaafidaehald....pkyakklGvdidell.....v..sqpdtGeqaleiadalvrsgaidlivvdsvaalvpka 147
                                       g a++id+e ++      + a++lG++ de++     +   + d+    +e + ++++  +i l+vvds++    +a
  gi|385805797|ref|YP_005842195.1| 334 GRAVYIDSEGTFRweriEAMARALGLNPDEVMenifyIraVNSDHQMAVVEEVTKMIQEKGIKLVVVDSITGH-FRA 409
                                       677888888776522224578999998766542222221134555556677788899*************986.589 PP

                                       T-----------HHHHHHHHHHHHHHHHHTTT--EEEEEEE-----------------HHHHHHH-SEEEEEEEES- CS
                              RecA 148 eieGemgdskvglqarlmsqalrkltgaisksntvvifinqirekiGvmfgnpetttGGralkfyasvrldvrriee 224
                                       e  G   ++  + q + + + l +l    +  n++v+  nq+  +  v +g+p  + GG+ l     vr+++r++  
  gi|385805797|ref|YP_005842195.1| 410 EYPGR--ENLASRQQK-LNRHLHQLMRIAEIYNIAVVITNQVMARPDVFYGDPTQAVGGHVLYHAPGVRVQLRKSRG 483
                                       99985..455555655.567899999999999*****************************************9976 PP

                                       --- CS
                              RecA 225 ike 227
                                        k+
  gi|385805797|ref|YP_005842195.1| 484 NKR 486
                                       665 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.4   0.00018       0.2       2      33 ..     111     142 ..     110     147 .. 0.93
   2 !   18.5   0.0   8.6e-07   0.00097      61     167 ..     348     459 ..     332     511 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00018
                            ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKt 33 
                                        tg + lD++l gG+  ++++   Ge GtGK 
  gi|385805797|ref|YP_005842195.1| 111 TTGSKSLDDLLGGGVETRTMTEFFGEFGTGKC 142
                                       7999***************************6 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 8.6e-07
                            ATPase  61 edlrenakslGwdlekleeegklaiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitgl.aye.. 134
                                       e +   a++lG + +++ e+  +++i a++s++           ++++ee++++i+e+++k vv+Dsitg+   e  
  gi|385805797|ref|YP_005842195.1| 348 ERIEAMARALGLNPDEVMEN--IFYIRAVNSDH----------QMAVVEEVTKMIQEKGIKLVVVDSITGHfRAEyp 412
                                       55666667777777777777..77777776654..........48899*********************99532222 PP

                            ATPase 135 ......ekeavaReilrqlvrvlkklgvTailvsekss........s 167
                                             ++++++ + l+ql+r+ + +++  ++++++           
  gi|385805797|ref|YP_005842195.1| 413 grenlaSRQQKLNRHLHQLMRIAEIYNIAVVITNQVMArpdvfygdP 459
                                       22222245666777899999999999999999999866555555433 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   9.3e-08    0.0001       3      43 ..      30      70 ..      28      80 .. 0.91
   2 ?   -1.5   0.0       2.6     3e+03      22      42 ..     157     177 ..     155     179 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 9.3e-08
                              Cdd1  3 kalkelqdiPniGkalaedlvelGirsveelkgedpeelye 43
                                      +a+k+l+d+P+iG+a+a +l+e G+ ++e ++  +p+e+ +
  gi|385805797|ref|YP_005842195.1| 30 NAIKTLTDLPGIGPATATKLIEAGYGTLEAIAVATPQEISA 70
                                      6899********************************99865 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.6
                              Cdd1  22 lvelGirsveelkgedpeely 42 
                                       + +++i+s+ e+k ++++el+
  gi|385805797|ref|YP_005842195.1| 157 VKKIDIESFYEMKASEGKELM 177
                                       5689***********999975 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.8   2.1e+03       8      48 ..     103     143 ..      96     144 .. 0.82
   2 !   19.2   0.1   6.5e-07   0.00073      71     188 ..     333     447 ..     319     450 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.8
                            AAA_25   8 savsvadlaapppprrwlvkgllpagelallaGapgtGKtt 48 
                                       + +sv+++ +  +++++l++g +   + + ++G  gtGK +
  gi|385805797|ref|YP_005842195.1| 103 ERQSVGKITTGSKSLDDLLGGGVETRTMTEFFGEFGTGKCF 143
                                       4477888888999999999999999**************76 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 6.5e-07
                            AAA_25  71 qgkVlyvsaEdsedelrrRlravgeal...rddarllvldlagveslpLfakdrggtlltadvdaleaaieevegvr 144
                                        g+ +y++ E++  ++ +R++a+ +al   +d   + +        ++ + +d++     a+v+++ + i+e +g++
  gi|385805797|ref|YP_005842195.1| 333 SGRAVYIDSEGTF-RW-ERIEAMARALglnPDEVMENIF------YIRAVNSDHQ----MAVVEEVTKMIQE-KGIK 396
                                       5889999999998.44.6899999888443222222222......2333333333....37889999*****.9*** PP

                            AAA_25 145 lvviDplsralgg....densnsd...vgalvealeriarrtgaavllvhH 188
                                       lvv+D+++  +++     en +s     ++ + +l ria+ +++av+++ +
  gi|385805797|ref|YP_005842195.1| 397 LVVVDSITGHFRAeypgRENLASRqqkLNRHLHQLMRIAEIYNIAVVITNQ 447
                                       ******99877776776666555445459*****************99865 PP

>> DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   4.2e-06    0.0047       2      29 ..      34      61 ..      33      74 .. 0.85
   2 ?   -1.7   0.0       2.4   2.7e+03      21      30 ..     113     122 ..     110     129 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.2e-06
                   DNA_pol_lambd_f  2 lFtkvyGVGpktAkkwyakGirtledlr 29
                                      ++t   G+Gp+tA k++++G+ tle + 
  gi|385805797|ref|YP_005842195.1| 34 TLTDLPGIGPATATKLIEAGYGTLEAIA 61
                                      577788*******************886 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.4
                   DNA_pol_lambd_f  21 Girtledlra 30 
                                       G ++l+dl+ 
  gi|385805797|ref|YP_005842195.1| 113 GSKSLDDLLG 122
                                       889****975 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   7.2e-06    0.0081      10      29 ..      32      51 ..      30      52 .. 0.86
   2 ?   -1.3   0.0       2.1   2.4e+03       1      15 [.      56      70 ..      56      74 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 7.2e-06
                                      HHHHHTSTT-SHHHHHHHHH CS
                               HHH 10 reeLlalPGVGpktAeaIls 29
                                      ++ L++lPG+Gp+tA + ++
  gi|385805797|ref|YP_005842195.1| 32 IKTLTDLPGIGPATATKLIE 51
                                      689************88765 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.1
                                      SHHHHHTSSHHHHHT CS
                               HHH  1 sleglipasreeLla 15
                                      +le++  a++ e+ a
  gi|385805797|ref|YP_005842195.1| 56 TLEAIAVATPQEISA 70
                                      589999****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 !   15.7   0.1   1.5e-05     0.017      23      86 ..      38     102 ..      31     112 .. 0.70
   2 ?   -1.7   0.0       4.1   4.6e+03      55      75 ..     419     439 ..     384     451 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.5e-05
                        5_3_exonuc  23 vpgiGektAakLlk.eygsleeilenld.elkekklkekLeenkeearlskkLatiktdvplelel 86 
                                        pgiG+ tA+kL++  yg+le+i  ++  e+++ ++   +++++  ++ +++  +i+ ++ lel+ 
  gi|385805797|ref|YP_005842195.1|  38 LPGIGPATATKLIEaGYGTLEAIAVATPqEISA-AVGIPINTAQRAIKAARDALEIRFKTALELKK 102
                                       79***********626*******9988646654.66666666666666666666666665555554 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4.1
                        5_3_exonuc  55 klkekLeenkeearlskkLat 75 
                                       ++++kL+++  +++   ++ +
  gi|385805797|ref|YP_005842195.1| 419 SRQQKLNRHLHQLMRIAEIYN 439
                                       344555555555544444444 PP

>> DUF296  Plants and Prokaryotes Conserved (PCC) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.22   2.4e+02      31      73 ..     259     321 ..     247     336 .. 0.67
   2 !   11.7   0.0   0.00023      0.26      10      88 ..     379     468 ..     373     478 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.22
                                       EEEEEEEEEEEE.EEECTTT...EE-..............S-EEEEEEEEEEEETT...EEEEE CS
                            DUF296  31 vlsaiGavsnvt.rladgee...kll..............grfeilslsGtilpdg...lHlhv 73 
                                       v+  +G +s+ + + ++ e+   k +              g ++ ls+sG il++    + l+v
  gi|385805797|ref|YP_005842195.1| 259 VFETSGVLSQKSnERFNIEKiveK-KlvnrkgfvydlvvpGTHNFLSASGLILHNTqisHQLSV 321
                                       556677777777655666665541.134556666677778*************95444334554 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00023
                                       TSBHHHHHHHHHHHHT-SSEEEEEEEEEEEEEE....EEECTTT.......EE-S-EEEEEEEEEEEETT..EEEEE CS
                            DUF296  10 GediveaieefarkrgiraacvlsaiGavsnvt....rladgee.......kllgrfeilslsGtilpdg..lHlhv 73 
                                          +ve+++++++++gi+ ++v s +G ++       +la++++       +l    ei ++   i++ +  ++  v
  gi|385805797|ref|YP_005842195.1| 379 QMAVVEEVTKMIQEKGIKLVVVDSITGHFRAEYpgreNLASRQQklnrhlhQLMRIAEIYNIAVVITN-QvmARPDV 454
                                       5679*************************965566655555555666655433356677777434444.44667899 PP

                                       EEEETTSEEEEEEEE CS
                            DUF296  74 slagedgqvvgGhla 88 
                                         +++  q+vgGh++
  gi|385805797|ref|YP_005842195.1| 455 FYGDP-TQAVGGHVL 468
                                       99997.*******97 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   7.9e-05     0.088       9      50 ..      39      81 ..      35      89 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.9e-05
                             HHH_2  9 rhVGektAklLakr.FksldaLkkasleeLlevddiGeeiAqs 50
                                      + +G +tA +L ++ +++l+a++ a+ +e+++  +i   +Aq 
  gi|385805797|ref|YP_005842195.1| 39 PGIGPATATKLIEAgYGTLEAIAVATPQEISAAVGIPINTAQR 81
                                      789*****9999866*****************99998888876 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   8.4e-05     0.095      13      31 ..      35      53 ..      31      54 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.4e-05
                           IMS_HHH 13 itkipGiGgklgekLeklG 31
                                      +t++pGiG+ ++ kL   G
  gi|385805797|ref|YP_005842195.1| 35 LTDLPGIGPATATKLIEAG 53
                                      89************87666 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   0.00015      0.16      17      44 ..      62      88 ..      56     106 .. 0.87
   2 ?   -1.8   0.0       2.7     3e+03      25      42 ..     422     439 ..     421     441 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                            HTH_23 17 GlsvreIAreLgvsrrTvyrwlkryree 44
                                       ++++eI+++ g++ +T +r +k+  ++
  gi|385805797|ref|YP_005842195.1| 62 VATPQEISAAVGIPINTAQRAIKAA-RD 88
                                      6899*******************95.34 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.7
                            HTH_23  25 reLgvsrrTvyrwlkryr 42 
                                       ++L+++ +++ r+ + y+
  gi|385805797|ref|YP_005842195.1| 422 QKLNRHLHQLMRIAEIYN 439
                                       578888888888776664 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00013      0.14      40      65 ..      27      51 ..      22      52 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                                      S-HHHHTTHCTTSTT--HHHHHHHHH CS
                             HHH_8 40 eeitsleeeltklpgiGkkiaakiee 65
                                       ei+ ++  lt+lpgiG+++a k+ e
  gi|385805797|ref|YP_005842195.1| 27 SEINAIKT-LTDLPGIGPATATKLIE 51
                                      48888887.**************987 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.011        13      14      32 ..      33      51 ..      30      53 .. 0.88
   2 ?    3.8   0.2     0.063        71      11      48 ..      63     102 ..      59     105 .. 0.80
   3 ?   -2.5   0.0       5.6   6.3e+03      43      60 ..     151     168 ..     151     170 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.011
                             HHH_3 14 eeLqklpGlgpklAknIva 32
                                      + L+ lpG+gp++A ++++
  gi|385805797|ref|YP_005842195.1| 33 KTLTDLPGIGPATATKLIE 51
                                      57999**********9997 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.063
                             HHH_3  11 AsaeeLqklpGlgpklAknIv.ayReknG.pfksreeLlk 48 
                                       A+ +e++   G+  ++A++ + a+R++   +fk+  eL+k
  gi|385805797|ref|YP_005842195.1|  63 ATPQEISAAVGIPINTAQRAIkAARDALEiRFKTALELKK 102
                                       8999999999999999998662679998559999888886 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 5.6
                             HHH_3  43 reeLlkvkglgpktfeql 60 
                                       +e++ +vk+++ + f ++
  gi|385805797|ref|YP_005842195.1| 151 IEDFGSVKKIDIESFYEM 168
                                       589999***999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (515 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1303  (0.0726756); expected 358.6 (0.02)
Passed bias filter:                      880  (0.0490825); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.77u 0.35s 00:00:01.12 Elapsed: 00:00:00.54
# Mc/sec: 2867.01
//
Query:       gi|385805798|ref|YP_005842196.1|  [L=223]
Description: TenA family transcriptional regulator [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.6e-34  119.5   1.5    1.8e-34  119.4   1.5    1.0  1  TENA_THI-4  TENA/THI-4/PQQC family
  ------ inclusion threshold ------
      0.041   14.1   0.7      0.041   14.1   0.7    1.8  2  RhoGEF      RhoGEF domain


Domain annotation for each model (and alignments):
>> TENA_THI-4  TENA/THI-4/PQQC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.4   1.5     2e-38   1.8e-34       3     209 ..      10     215 ..       8     216 .. 0.96

  Alignments for each domain:
  == domain 1  score: 119.4 bits;  conditional E-value: 2e-38
                                       HCHHHHHHHHCSHHHHHHHTT-S-HHHHHHHHHHHHHHHHHHHHHHHHHHHC-SSHHHHHHHHHHHHHHHHCHHHHH CS
                        TENA_THI-4   3 qlrpiwkeyinHpFvkalakGtlpreqfqayviqdylylknfvrvlaiilskssdlevrrelesrivdhdgeeielh 79 
                                       +++ i k + nHpF k l++G+l+ e+f+ y+iqdy yl+n+ ++l++  sk++ +e  + +++ ++  ++ e +  
  gi|385805798|ref|YP_005842196.1|  10 SIEDIFKAILNHPFLKELSEGSLNEEVFREYIIQDYIYLTNYSKALSLLSSKMPKEEWQKTFIEDAIGVYEVEKAMQ 86 
                                       67889999********************************************************************* PP

                                       HHHHHHTT-HHHHHCTTT--HHHHHHHHHHHHHHCHS-HHHHHHHHHHHHHHHHHHHHHHCCHHHS-TSCHHHHHHH CS
                        TENA_THI-4  80 lrlaealGlsreelsktkpspatkayvrylldlarrgslaeavaallpclfvyqeiaerlkeklralegpeyyewvk 156
                                       +++ + + ++r++l++++p + t ay+++l+++    ++   + ++lpc++ y e+ ++l+e+ +   +p y++w++
  gi|385805798|ref|YP_005842196.1|  87 ESFFSFWNIDRKKLEEVRPNQVTLAYSNHLISTIVLEDYPIGISSVLPCYWIYLEVGKKLAEESS--PNPLYKKWIE 161
                                       *********************************9999999*********************9966..********** PP

                                       HHC.SHHHHHHHHHHHHHHHHHHHTSHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                        TENA_THI-4 157 eya.seefraaveeakrllerllakvsdeqleelqeiflkalefetsfltmald 209
                                       +y+ +  ++  v++  +++e+   ++ +++l++ ++ f  ++ +e++f +++++
  gi|385805798|ref|YP_005842196.1| 162 TYSiNIKYENIVNRILKIAEETFSELDEKALKKVKRTFRLSTIYEYMFFDAVYK 215
                                       **84569******************************************99885 PP

>> RhoGEF  RhoGEF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.7   4.6e-06     0.041      38     121 ..       4      75 ..       2      91 .. 0.81
   2 ?   -1.0   0.1       0.2   1.8e+03     147     161 ..     170     184 ..     139     211 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.6e-06
                                       HHHHCTTHHHHHHHH.HHHHHHHHHHHH.HHHTTSS-S-SHHHHHHHHSTHHHHHHHHHCHHHHHHHHHHHHHHHHH CS
                            RhoGEF  38 ikiiFsnieeilelh.rsflleeLeerlkeseeqkeaqsigdvflkfadkfkkYseYcsnypnalkllkelskknkk 113
                                       ++++F  ie+i++   ++ +l+eL+e               +vf++++  ++  + Y++ny++al+ll++++ k++ 
  gi|385805798|ref|YP_005842196.1|   4 LNMLFDSIEDIFKAIlNHPFLKELSEGS---L-------NEEVFREYI--IQ-DYIYLTNYSKALSLLSSKMPKEEW 67 
                                       6789********8765688899887765...2.......3579****9..44.457**************9999999 PP

                                       HHHHHHHH CS
                            RhoGEF 114 fkafleea 121
                                        k+f+e+a
  gi|385805798|ref|YP_005842196.1|  68 QKTFIEDA 75 
                                       99999875 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.2
                                       HHHHHHHHHTS-TTS CS
                            RhoGEF 147 pLLLkellkntpesh 161
                                       + +++++lk  +e+ 
  gi|385805798|ref|YP_005842196.1| 170 ENIVNRILKIAEETF 184
                                       333333333333321 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); 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: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1466.52
//
Query:       gi|385805799|ref|YP_005842197.1|  [L=58]
Description: hypothetical protein FFONT_0757 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.042   13.9   0.5      0.042   13.9   0.5    1.2  1  LRR19-TM  Leucine-rich repeat family 19 TM domain


Domain annotation for each model (and alignments):
>> LRR19-TM  Leucine-rich repeat family 19 TM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.5   2.3e-06     0.042      12      43 ..      24      56 ..       4      58 .] 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.3e-06
                          LRR19-TM 12 gksWaylvg.vvvlalvtsllillaikckllyk 43
                                       +s+ + +g ++  a  +s++i+l+ik+k++y 
  gi|385805799|ref|YP_005842197.1| 24 RQSFIFSIGsIINKAFAISIFIILIIKAKIYYV 56
                                      5788898883456799**************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      163  (0.00909142); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 352.77
//
Query:       gi|385805800|ref|YP_005842198.1|  [L=291]
Description: putative permease (drug/metabolite transporter superfamily) [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.1e-22   79.7  39.2    6.8e-19   68.4  14.8    2.2  2  EamA       EamA-like transporter family
  ------ inclusion threshold ------
          1    9.3   0.0          1    9.3   0.0    3.7  4  RseC_MucC  Positive regulator of sigma(E), RseC/MucC


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4  16.3   4.3e-07    0.0039       6     133 ..      10     125 ..       5     129 .. 0.73
   2 !   68.4  14.8   7.6e-23   6.8e-19       2     136 ..     138     272 ..     137     273 .. 0.97

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.3e-07
                              EamA   6 lallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafllf 82 
                                       ++l+ ++ +    ++ k ll+++s  + +f+rf+i   +ll+++l++++ +     k+++ l ++    ++l   l+
  gi|385805800|ref|YP_005842198.1|  10 FFLIYVIGSVPLNFFVKDLLEYFSIGFSLFIRFII---MLLFTILFSKKII---LNKNIAVLSFF----VFLSTTLW 76 
                                       55555555555667888889999999999999974...4444444444444...44454444444....4566689* PP

                              EamA  83 fyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvl 133
                                       +y+l ++s++   ++++ +P+++ +++  +l+ek  + ++ g+++++lG +
  gi|385805800|ref|YP_005842198.1|  77 LYSLIYLSPADSLVLSYSMPLIASLIGRRILNEK--SGEIYGVLVAFLGYI 125
                                       *********************************8..567888888888865 PP

  == domain 2  score: 68.4 bits;  conditional E-value: 7.6e-23
                              EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegkl.aklslkdwllllllgllgtvl 77 
                                        g +l ++ a+ wa+y vl ++ lr+++ + l+   fli++++ l++++l +  + a  + + ++ ++ ++++g+++
  gi|385805800|ref|YP_005842198.1| 138 YGTVLSFINAFAWAYYSVLYRK-LRTFDVFVLNSSVFLICSLFSLAVLPLYQPIIkAGADDNVFADVIWFATIGGAI 213
                                       578899****************.7**************************9999999999999************** PP

                              EamA  78 afllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                        fl ++  l+ +sas+a+++++++P++t i+  +  +e+++l+q++gi+li +Gv+l++
  gi|385805800|ref|YP_005842198.1| 214 QFLSWNRVLSIWSASKATVLSYIVPILTFIIQCFSNKESPSLLQVIGIALITIGVILTF 272
                                       ********************************************************986 PP

>> RseC_MucC  Positive regulator of sigma(E), RseC/MucC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   2.6     0.088   7.9e+02      75     112 ..      43      79 ..      33      84 .. 0.75
   2 ?    6.8   0.3   0.00067         6      66     108 ..      88     128 ..      83     136 .. 0.87
   3 ?   -1.9   0.1      0.34     3e+03      70      90 ..     137     163 ..     128     199 .. 0.54
   4 ?    9.3   0.0   0.00011         1      63     110 ..     227     271 ..     222     286 .. 0.63

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.088
                         RseC_MucC  75 llllilgallgsallgssellaalgallglvlgflivr 112
                                       +++l++++l+ + + + ++ +a+l  +++l  ++++  
  gi|385805800|ref|YP_005842198.1|  43 IIMLLFTILFSKKI-ILNKNIAVLSFFVFLSTTLWLYS 79 
                                       45666666666666.79999999999999998888765 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.00067
                         RseC_MucC  66 aallvYllPllllilgallgsallgssellaalgallglvlgf 108
                                       + +l Y +Pl++ ++g  + +    s+e++ +l+a+lg +++ 
  gi|385805800|ref|YP_005842198.1|  88 SLVLSYSMPLIASLIGRRILNEK--SGEIYGVLVAFLGYIAYS 128
                                       67899**********99999998..79**********998875 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.34
                         RseC_MucC  70 vYllPllllilgallgsall......g 90 
                                       +Y++ l ++ ++a++ +++l      +
  gi|385805800|ref|YP_005842198.1| 137 LYGTVLSFINAFAWAYYSVLyrklrtF 163
                                       444444444445544444444443330 PP

  == domain 4  score: 9.3 bits;  conditional E-value: 0.00011
                         RseC_MucC  63 llkaallvYllPllllilgallgsallgssellaalgallglvlgfli 110
                                         ka++l Y++P+l++i+  +  +      +ll+++g  l+++  +l 
  gi|385805800|ref|YP_005842198.1| 227 ASKATVLSYIVPILTFIIQCFSNKESP---SLLQVIGIALITIGVILT 271
                                       56999**********999988777763...333333333333322222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       916  (0.0510904); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1840.81
//
Query:       gi|385805801|ref|YP_005842199.1|  [L=182]
Description: nicotinamide-nucleotide adenylyltransferase [Fervidicoccus fontis Kam940]
Scores for complete 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   0.0    2.2e-15   57.1   0.0    1.2  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 !   57.1   0.0   1.2e-19   2.2e-15       1     142 [.      13     143 ..      13     144 .. 0.93

  Alignments for each domain:
  == domain 1  score: 57.1 bits;  conditional E-value: 1.2e-19
                                       EEEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHHHHH CS
                   CTP_transf_like   1 lagGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkkkplasaeeRlemlelakevdevisvdpweltrevl 77 
                                       l++G+F+p+H+GH+++++++++ ++e +i+++ s+++++    ++++a eR+ m+++a ++ e +  +++++++   
  gi|385805801|ref|YP_005842199.1|  13 LFPGRFQPLHYGHIEVIKWMLNFGDE-IIIAIGSAQKSHMV-DNPFTAGERMVMIREALKE-EGFDLSKFYIVPVPD 86 
                                       799***********************.************99.****************555.55*********9666 PP

                                       HHTTTTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHHHH CS
                   CTP_transf_like  78 kklkpdklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstkire 142
                                        ++++   +++   ++l        ++ + ++++lv++  +e ++ vl+++   ++++S+ kir+
  gi|385805801|ref|YP_005842199.1|  87 IEYNS---IWISYLESLLP-----PFDAVCSRNPLVIRLAKEERYDVLVPPFFLRSEYSGKKIRK 143
                                       66655...9**99999999.....6**************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1227.41
//
Query:       gi|385805802|ref|YP_005842200.1|  [L=270]
Description: hypothetical protein FFONT_0760 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.3e-69  231.6   0.0    9.3e-69  231.4   0.0    1.0  1  SAM_adeno_trans  S-adenosyl-l-methionine hydroxide adenosyltr
  ------ inclusion threshold ------
       0.09   13.1   0.3       0.27   11.6   0.3    1.8  1  DUF1947          Domain of unknown function (DUF1947)


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 !  231.4   0.0     1e-72   9.3e-69       1     234 [.      10     266 ..      10     267 .. 0.91

  Alignments for each domain:
  == domain 1  score: 231.4 bits;  conditional E-value: 1e-72
                                       EEEEESSTSSSSHHHHHHHHHHHH-TTSEEEEEES-S-TT-HHHHHHHHHHHHGGS-TTEEEEEE--TTTTSS--EE CS
                   SAM_adeno_trans   1 itLlTDFGlkdpyvgamkgvilsiapdarivDitHdippfdvreaaflLaaalpyfpkgtvhlavVDpgvgterral 77 
                                       i++lTDFG  d yv++mk+vi++++++++ +Di+ ++ pf++ ++++lL+++++yfp+gtv+lav+Dpgvg++r+al
  gi|385805802|ref|YP_005842200.1|  10 IAILTDFGDIDNYVAVMKAVIMKENRRVKTLDISNNVLPFSIISGSYLLYTSYKYFPSGTVFLAVIDPGVGSDRKAL 86 
                                       889************************************************************************** PP

                                       EEEETTSEEEEESSSTTHHHH....SEEEEEEGSSCC.....--TS-HHHHTHHHHHHHHHCT--GGGCSEEESGGG CS
                   SAM_adeno_trans  78 vveakggyfvgPDNGlltlal....lleeaveieeee.....ssatFhgrDvFapvaarlaagvsleelgeeldpee 145
                                       +v+a++ +fvgPDNG++ +++    + +ea++i+ e+      s+tFhgrDvFap+aarla++ ++  +g++l+ e+
  gi|385805802|ref|YP_005842200.1|  87 IVKAGDWFFVGPDNGIFWPIIeenfSQAEAYSISIEKsdlrnISSTFHGRDVFAPIAARLAKNGDPGFFGDPLNLES 163
                                       ******************99987663388998885555799988********************************* PP

                                       S-SSS.....E.CSCEEEEEEEE-TTS-EEEEEE...EHHHHHTTCEE........EEEEESSGGGSTTTSEEEEE- CS
                   SAM_adeno_trans 146 lvrle.....e.derlegevlyvDrFGNvitniskelleelekerkva........klkkvetyaevaegellalvn 208
                                       l +l+     +  + +  e+++ D FGNv+++ ++++l+ ++k+ +v          +k+v t++ ++e+el ++ n
  gi|385805802|ref|YP_005842200.1| 164 LSKLSlikmqKdGAYICFEIIHKDVFGNVVLSSKGKILSIMGKDVEVLkksdnkkyIFKNVPTFSLLEENELAIYEN 240
                                       98888886532344567*********************98888766225567777755678**************** PP

                                       TTSEEEEEETTC-HHHHHT--TT-EE CS
                   SAM_adeno_trans 209 ssglleiavnkgsaaellglkvgdev 234
                                       s g+le+a nkg+  + +g k+g++v
  gi|385805802|ref|YP_005842200.1| 241 SFGFLELAKNKGNLFADYGFKIGEKV 266
                                       ***********************987 PP

>> DUF1947  Domain of unknown function (DUF1947)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3     3e-05      0.27      17      54 ..     194     232 ..     191     236 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3e-05
                                       HHTTT---TT--..-EEEE-SS-EEEEETTEEEEEE.SS CS
                           DUF1947  17 lkekyisislesdkiEieeekkeklYlingvpilfe.ee 54 
                                       l +k+  +s+ ++++E+ ++ + k Y + +vp +   ee
  gi|385805802|ref|YP_005842200.1| 194 LSSKGKILSIMGKDVEVLKKSDNKKYIFKNVPTFSLlEE 232
                                       56788888999988******************9987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 1722.98
//
Query:       gi|385805803|ref|YP_005842201.1|  [L=133]
Description: hypothetical protein FFONT_0761 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       509  (0.0283898); 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: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 857.45
//
Query:       gi|385805804|ref|YP_005842202.1|  [L=403]
Description: Threonyl-tRNA synthetase-like protein (thrS-like) [Fervidicoccus fontis Kam940]
Scores for 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-49  165.9   0.6    9.5e-49  165.0   0.6    1.5  1  tRNA-Thr_ED     Archaea-specific editing domain of threonyl-t
    1.8e-14   53.6   0.3    5.3e-14   52.1   0.3    1.8  1  HGTP_anticodon  Anticodon binding domain
  ------ inclusion threshold ------
      0.071   13.3   0.0       0.24   11.7   0.0    1.9  1  Glutaredoxin    Glutaredoxin
      0.094   12.0   0.6       0.16   11.2   0.6    1.4  1  NosD            Periplasmic copper-binding protein (NosD)


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 !  165.0   0.6   2.1e-52   9.5e-49       1     136 [.       5     137 ..       5     138 .. 0.99

  Alignments for each domain:
  == domain 1  score: 165.0 bits;  conditional E-value: 2.1e-52
                                       -EEEEEEEEEEEEEEEEESSSS-.SS---EEEESSEEEEEEE-BTT--H...HHHHHHHHHHHHHHHHHT-SEEEEE CS
                       tRNA-Thr_ED   1 mrlLlihadeleyeakkkalkeaeeeeekegrleealvvFiavEkeDeeekekvvekavkeikkvakkvkakkvvly 77 
                                       mr+L+iha++++++++++al++++e++ +e + e++lv+Fi+vE++D+e   kv+e+a+++i+++akkv+a+++++y
  gi|385805804|ref|YP_005842202.1|   5 MRILQIHAKKFSFRTVSEALQKKDETPIHELSKENVLVAFISVERGDDE---KVIENATESIAEHAKKVNANSIIIY 78 
                                       9************************************************...9************************ PP

                                       E-STS-SSB--HHHHHHHHHHHHHHHHTT.-EEEE--SSEEEEEEEEE--STTSEEEEE CS
                       tRNA-Thr_ED  78 pyaHLssslaspevakeilkkleeklkekglevkraPFGwykefeisckGhpLaelsre 136
                                       pyaHLss+l++p+++++il++l+e+lk+k+lev+raPFGwykefe+s+ GhpLaelsre
  gi|385805804|ref|YP_005842202.1|  79 PYAHLSSNLEKPDQSIKILDELSERLKDKKLEVARAPFGWYKEFELSSFGHPLAELSRE 137
                                       *********************************************************97 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1   0.3   1.2e-17   5.3e-14       2      93 ..     309     398 ..     308     399 .. 0.91

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 1.2e-17
                                       EEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEES.SSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTC CS
                    HGTP_anticodon   2 vvviplnekaeeleeyakklaeeLraagirveldd.snesigkkireadllgipfavvvGekelekgtvtvrdrdtr 77 
                                        v++ +++     ee   ++++ L+  g+++++ d sne+ig k+r++ ++++p++++ Ge+e e++t+ +r+r+t 
  gi|385805804|ref|YP_005842202.1| 309 SVILKVGN---VNEEKIIEVKRLLESIGLKRVYLDlSNEKIGSKLRKWGMKWVPLVFIYGEREEETNTIILRERKTN 382
                                       57777887...67899999*********87776666***************************************** PP

                                       EEEEEETTHHHHHHHH CS
                    HGTP_anticodon  78 eqervsldelveklke 93 
                                        q+++sl+el++++k+
  gi|385805804|ref|YP_005842202.1| 383 VQYTISLSELEGAVKK 398
                                       ************9986 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   5.3e-05      0.24      15      58 ..     325     366 ..     323     367 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.3e-05
                                       HHHHHHHTTGGEEEEEGCCSHHHHHHHHHHHTSSSSSEEEETTE CS
                      Glutaredoxin  15 akrlLkelgvkfeeidvdkdeeireelkelsgvrtvPqvfidgk 58 
                                       +krlL++ g+k  + d++++ +i  +l++  g + vP vfi g+
  gi|385805804|ref|YP_005842202.1| 325 VKRLLESIGLKRVYLDLSNE-KIGSKLRKW-GMKWVPLVFIYGE 366
                                       8******************7.*********.**********886 PP

>> NosD  Periplasmic copper-binding protein (NosD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.6   3.5e-05      0.16      75     148 ..     192     269 ..     150     279 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.5e-05
                              NosD  75 dntlssnesGialmsssnntle......nNtisnnenyGillsdssnntisnNtisnnnkGiflens.ssntitgNr 144
                                       +n+++++ +G++l++ s+++++      nN+i +++   i  s ++nn i+n +  +n++Gi +++s + + i   +
  gi|385805804|ref|YP_005842202.1| 192 ENEFYETLNGVTLKEGSRSFFKakilpgNNEIFDCTM-DIDFSIIRNN-IKNLKL-ENEEGIAFYRSeNVDSIPVAT 265
                                       799**************99999666666666777766.7777776654.666655.99********96666777777 PP

                              NosD 145 iesn 148
                                       i +n
  gi|385805804|ref|YP_005842202.1| 266 IINN 269
                                       7777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 2825.17
//
Query:       gi|385805805|ref|YP_005842203.1|  [L=282]
Description: prenyltransferase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-34  119.4  15.2    1.9e-34  119.1  15.2    1.2  1  UbiA           UbiA prenyltransferase family


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.1  15.2   1.1e-38   1.9e-34       4     245 ..       5     259 ..       2     279 .. 0.84

  Alignments for each domain:
  == domain 1  score: 119.1 bits;  conditional E-value: 1.1e-38
                              UbiA   4 palvg..lalaaggspdl.llllllllgtllaaaaanalNdyfDreiDadme.....rtpnRPlvsGrispkealif 72 
                                       ++ +g  +al  g spd+ l  l+++lg++l++a+an++Ndy+D++ + d +       ++ P+ s+ is +  +i+
  gi|385805805|ref|YP_005842203.1|   5 AISFGvfYALLKGFSPDIlLKSLIVILGGILFHASANLWNDYYDYKRGVDIKeaptnIYRKHPILSNSISSQGIFIY 81 
                                       455562255555555555777889999999********************999999544899*************** PP

                              UbiA  73 aivllilgllll....alllnpltallgllalllyvvYt.g.lrlKrrtllgtvvggiafglppllgwaa.vtgsls 142
                                       a +++i+g+ll+    +++ n + +++g+++ +l ++Yt   + lK+ +l g++  +ia+g+++ +g +a +tg+l+
  gi|385805805|ref|YP_005842203.1|  82 ASLSAIVGVLLGiliyIFWGNIWGIIFGIIGPFLSFMYTgSkFALKYLSL-GELEAFIAYGFLFSIGSYAiITGDLT 157
                                       ***************999*********************978********.************************** PP

                              UbiA 143 llalllalavflltwaialandlrdregDrkagiktlpvvlGrkaarillalllavlllallllllalllllyllla 219
                                       + +++++++ ++l++a+++an+ rd++ D+ +g ktl+v++G+k ++ill + l++++++ +l+l+++   + +++ 
  gi|385805805|ref|YP_005842203.1| 158 FRPAIFSIPYGFLVAAVLTANNTRDIDFDLSRGAKTLSVRIGKKLSLILLECELTLPYIL-TLILVFMKIFPVWVII 233
                                       ************************************************944444455554.3455666666666666 PP

                              UbiA 220 lllaalallraarlvrrrdakkaakf 245
                                       +l+ ++  l+ +++++ + ++ a  +
  gi|385805805|ref|YP_005842203.1| 234 SLASLYRALKTIKNFKEKVPSNADPL 259
                                       66666666666777777766666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       723  (0.0403257); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.34s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 1746.32
//
Query:       gi|385805806|ref|YP_005842204.1|  [L=378]
Description: SufBD protein [Fervidicoccus fontis Kam940]
Scores for 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-27   94.1   0.3    1.3e-26   93.6   0.3    1.3  1  UPF0051   Uncharacterized protein family (UPF0051)


Domain annotation for each model (and alignments):
>> UPF0051  Uncharacterized protein family (UPF0051)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.6   0.3   7.4e-31   1.3e-26       5     217 ..     131     349 ..     113     350 .. 0.82

  Alignments for each domain:
  == domain 1  score: 93.6 bits;  conditional E-value: 7.4e-31
                           UPF0051   5 rtlivveegaevtiieey.......agcgvveifvgenAklkyvkvqnwsedavnlstkra.eegrdaklelttvsl 73 
                                       ++ i +e  a++++   y       ++   +ei  + + k+k++ + +  +++  + ++r+   g+d    ++   +
  gi|385805806|ref|YP_005842204.1| 131 HLSIKLERSASLNLEVIYapisessLSSFTLEIDGEGENKIKILNLVKAPNNSPFFYETRIlGRGKD--DISVRTAT 205
                                       4446666666666654455554433222445555555556666655555555555555555333332..35667778 PP

                           UPF0051  74 ggkltrkepsvelkgegaeaelnglylakgkqhldtrtkvdhngpntssrilskgvlkdearavfrgkikvrkgaqk 150
                                       +g+++ ++ ++++ g+ ++a+++ l l+++++++d++t++  +  ++ ++il++g+ + ++++v rg++k + ++ +
  gi|385805806|ref|YP_005842204.1| 206 SGGIIHNRADIVILGSMSKANIKALSLVTNNNRADLTTNILNDSSQGIAEILVRGINA-GGEIVHRGTLKAETNSIE 281
                                       888999****************************************************.699*************** PP

                           UPF0051 151 tdahqenrnLllsdkaradtiPeleidaddvk.asHgAtvGkideeqlfYLmsRGlseeeArrlivrg 217
                                       ++++ ++  +  s+++ ++++P+lei+++ +k a+H   ++ i e+ lfYL sRGl++eeA  l++++
  gi|385805806|ref|YP_005842204.1| 282 SENKLRSYLIKTSKNSINHSVPILEITTNLIKtAEHSTDISDIPEDILFYLSSRGLKREEAVFLLTQS 349
                                       ****************************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 2661.11
//
Query:       gi|385805807|ref|YP_005842205.1|  [L=476]
Description: FeS assembly protein SufB [Fervidicoccus fontis Kam940]
Scores for 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  218.2   1.4    1.4e-64  217.8   1.4    1.1  1  UPF0051   Uncharacterized protein family (UPF0051)


Domain annotation for each model (and alignments):
>> UPF0051  Uncharacterized protein family (UPF0051)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  217.8   1.4   7.6e-69   1.4e-64       2     218 .]     220     445 ..     219     445 .. 0.96

  Alignments for each domain:
  == domain 1  score: 217.8 bits;  conditional E-value: 7.6e-69
                           UPF0051   2 qfertlivveegaevtiieeyagc............gvveifvgenAklkyvkvqnwsedavnlstkraeegrdakl 66 
                                       q+e+tliv++e++ +++i   +gc            g vei++++n+++k++++qnwse+++n+++kra  ++ a++
  gi|385805807|ref|YP_005842205.1| 220 QYEHTLIVLDENSYIEFI---EGCsapmyktysfhdGAVEIYAHKNSHIKFTTLQNWSENVINFNNKRAIAEEGAEV 293
                                       889***************...666666666666667*********************************9999999* PP

                           UPF0051  67 elttvslggkltrkepsvelkgegaeaelnglylakgkqhldtrtkvdhngpntssrilskgvlkdearavfrgkik 143
                                       ++ ++s+g+k+t+ +ps+ lkg+++++++++++l+kg++  d + kv++ng+nt ++i++k++++d++ +++rg i+
  gi|385805807|ref|YP_005842205.1| 294 DWLEGSVGSKVTYVYPSTILKGDNSKTTIYTITLSKGNKIKDAGAKVIMNGKNTAAKIVNKSISADGGINIYRGLIR 370
                                       ***************************************************************************** PP

                           UPF0051 144 vrkgaqktdahqenrnLllsdkaradtiPeleidaddvkasHgAtvGkideeqlfYLmsRGlseeeArrlivrgf 218
                                       ++kga +++a  ++++L+l++k++a+t P+ ++ +d + ++H+A +Gki+e+qlfYL+sRGl e+eA+++iv g+
  gi|385805807|ref|YP_005842205.1| 371 INKGAINSRATSSCESLILDEKSKAYTYPHNQVLEDTAFVNHEAKTGKINEDQLFYLESRGLRENEAKSIIVLGY 445
                                       ************************************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (476 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); 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: 0.72u 0.35s 00:00:01.06 Elapsed: 00:00:00.56
# Mc/sec: 2554.35
//
Query:       gi|385805808|ref|YP_005842206.1|  [L=262]
Description: putative ABC transporter [Fervidicoccus fontis Kam940]
Scores for complete 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-22   78.1   0.0    1.3e-21   77.6   0.0    1.2  1  ABC_tran     ABC transporter
      6e-08   32.4   0.3    6.1e-06   25.8   0.3    2.2  1  SMC_N        RecF/RecN/SMC N terminal domain
    6.3e-08   32.8   1.6    0.00017   21.5   0.0    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    1.7e-05   23.8   0.0      0.059   12.0   0.0    2.1  2  AAA_13       AAA domain
     0.0016   18.3   0.1     0.0033   17.4   0.1    1.5  1  RsgA_GTPase  RsgA GTPase
     0.0021   18.5   0.3      0.035   14.5   0.3    2.2  1  AAA          ATPase family associated with various cellular a
     0.0097   16.3   0.0      0.015   15.6   0.0    1.5  1  AAA_16       AAA ATPase domain
  ------ inclusion threshold ------
      0.011   16.3   0.3      0.026   15.0   0.3    1.6  1  AAA_23       AAA domain
      0.017   15.4   0.1       0.48   10.7   0.0    2.2  2  AAA_22       AAA domain
      0.023   14.9   0.0      0.058   13.6   0.0    1.7  2  AAA_33       AAA domain
      0.035   13.9   0.0      0.067   13.0   0.0    1.4  1  AAA_29       P-loop containing region of AAA domain
       0.05   12.8   0.0       0.09   11.9   0.0    1.3  1  NB-ARC       NB-ARC domain
       0.07   13.0   0.7      0.073   13.0   0.0    1.5  2  ATPase_2     ATPase domain predominantly from Archaea
       0.14   11.9   0.1       0.32   10.7   0.0    1.6  2  AAA_24       AAA domain
       0.15   12.0   0.0       0.36   10.7   0.0    1.6  1  NACHT        NACHT domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.6   0.0   1.1e-24   1.3e-21       1     136 [.      21     178 ..      21     179 .. 0.85

  Alignments for each domain:
  == domain 1  score: 77.6 bits;  conditional E-value: 1.1e-24
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--..SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp..teGeilldgkdlke.qeleslrkeigvlpqepqlfpel 74 
                                       +knvslk+++ge++ai+G+nG+GK++L+++++g+ +    +G+i ++g+d+++   +e++ + +  l+q p   p++
  gi|385805808|ref|YP_005842206.1|  21 IKNVSLKCNNGEVLAIMGPNGSGKTSLANVIMGHPRYevISGKIYINGEDVTNlSAHERSLRGLMLLFQSPPEIPGV 97 
                                       58*******************************9776669*************9999999***************** PP

                                       BHHHH.....................HHHTCHHHHHHHSTTGGTTCBGESTTS.GGS-HHHHHHHHHHHHHHHTSSE CS
                                       xxxxx.....................xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  75 tvren.....................esdeeiekalsklglkelkdtvvkssp.ssLSgGqkqrvalarallkkpkl 129
                                       ++ +                      e  +e+++a s++gl+    + ++++    +SgG+++r +l +al+ kp  
  gi|385805808|ref|YP_005842206.1|  98 RLSNIilssynkkigkevellkvhrpEVIKEMNEATSEVGLST---DFLYRELnVGFSGGERKRAELLQALVLKPIN 171
                                       6655599999999988888877755544555666666666665...444443349********************** PP

                                       EEEESTT CS
                                       xxxxxxx RF
                          ABC_tran 130 lllDEpt 136
                                       +++DEp 
  gi|385805808|ref|YP_005842206.1| 172 IIMDEPD 178
                                       *****95 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.3   5.1e-09   6.1e-06      25     205 ..      32     216 ..      18     230 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 5.1e-09
                                       SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCC...CCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrsekl...sdlihkskekasvkkaeveitfdnedkklkiekeevs 98 
                                       ++ ai+GpNGSGK++l + i   +G+  ++ +  + +   +d+ +  ++++++ ++ + ++f+ + +   ++ +++ 
  gi|385805808|ref|YP_005842206.1|  32 EVLAIMGPNGSGKTSLANVI---MGHPRYEVISGKIYingEDVTNL-SAHERSLRG-LMLLFQSPPEIPGVRLSNII 103
                                       5779***************9...9*887766655533222555554.555555555.55668999998788888888 PP

                                       EEEEEETTSEEEEEETTEEE-H.HHHHHHHHCTT-STT........CS-HHHHHHHHHHHHHHHHCCS--SEEEECT CS
                                       xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  99 isrrvkrkgeseykingkevtk.kevsellesagiske........lLSgGektLvalaLlfAiqkvkpaplyllDe 166
                                       +s   k+ g+    ++ ++ +  ke++e  +++g+s +         +SgGe++ + l  l A    kp    ++De
  gi|385805808|ref|YP_005842206.1| 104 LSSYNKKIGKEVELLKVHRPEViKEMNEATSEVGLSTDflyrelnvGFSGGERKRAEL--LQA-LVLKPIN-IIMDE 176
                                       888877777755555555555459999999999999999999998889*****98775..323.2345555.489** PP

                                       TTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC- CS
                                       xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                             SMC_N 167 idaaLDeknvkkvaellkekskn.aQfivislreemleka 205
                                        d+ LD    k+v++++k+ +++   +i i++ +++++ +
  gi|385805808|ref|YP_005842206.1| 177 PDSGLDVDGLKIVSNIIKRMKEEdRAVILITHYTRLFKYV 216
                                       ******************76665489999***99998866 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   0.4   0.00032      0.38       3      16 ..      35      48 ..      33      54 .. 0.84
   2 !   21.5   0.0   1.5e-07   0.00017     132     301 ..      59     212 ..      53     214 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00032
                            AAA_21  3 vliGpNgsGKSnLL 16
                                      ++ GpNgsGK++L 
  gi|385805808|ref|YP_005842206.1| 35 AIMGPNGSGKTSLA 48
                                      789*********95 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 1.5e-07
                            AAA_21 132 vsepndlqfgkaltditsrawsllllldglrke.rigllnifadyfgfakekrllqrlvrslklveielsdlgegee 207
                                       v++  ++++g++ t+++++ +sl+ l+  +    +i+  ++++  +  +++k   +  + +++++e   +++++ +e
  gi|385805808|ref|YP_005842206.1|  59 VISGKIYINGEDVTNLSAHERSLRGLMLLFQSPpEIPGVRLSNIILSSYNKKIGKEVELLKVHRPEVIKEMNEATSE 135
                                       55566778888888888888888888866655588888888888888888888888888888888888888888888 PP

                            AAA_21 208 liasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHP...kllrrllel 281
                                          s+d++ re                  +S G ++ + ll al   +     ++ DEp++gL+    k+++ +++ 
  gi|385805808|ref|YP_005842206.1| 136 VGLSTDFLYRE--------------LNVGFSGGERKRAELLQALVLKPIN---IIMDEPDSGLDVdglKIVSNIIKR 195
                                       88877777666..............77777***************99977...************888888888888 PP

                            AAA_21 282 lkelsrngaQviltTHSpll 301
                                       +ke+ r    vil TH + l
  gi|385805808|ref|YP_005842206.1| 196 MKEEDR---AVILITHYTRL 212
                                       888866...*******7655 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0    0.0002      0.24      21      39 ..      36      54 ..      26     134 .. 0.85
   2 !   12.0   0.0     5e-05     0.059     528     578 ..     170     217 ..     160     229 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0002
                            AAA_13 21 iYGwNGaGKTtLSrllrsl 39
                                      i G NG+GKT+L++++   
  gi|385805808|ref|YP_005842206.1| 36 IMGPNGSGKTSLANVIMGH 54
                                      88*************9875 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 5e-05
                            AAA_13 528 kivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkevk 578
                                         +++D P S LD + l iv++ ik      ++ + +++ TH + +fk+v+
  gi|385805808|ref|YP_005842206.1| 170 INIIMDEPDSGLDVDGLKIVSNIIKRMK---EEDRAVILITHYTRLFKYVE 217
                                       55999*******************9986...99999*************97 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   2.7e-06    0.0033      80     126 ..      11      58 ..       1      76 [. 0.82

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.7e-06
                                       EE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT---- CS
                       RsgA_GTPase  80 llvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpelelk 126
                                       l+ s+++k  +++++ ++++ ++ +++G+ G GK++L n+++++ + +
  gi|385805808|ref|YP_005842206.1|  11 LTASVRDKIIIKNVSLKCNNgEVLAIMGPNGSGKTSLANVIMGHPRYE 58 
                                       566778888899999999998********************9985544 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.3   2.9e-05     0.035       3      43 ..      36      78 ..      34     219 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.9e-05
                                      EESSTTSSHHHHHHHHHHHHTHE....EEEEETTTCSSSSTTHHH CS
                               AAA  3 lyGppGtGKTllakavakelgve....fleisgsellskyvgese 43
                                      ++Gp G GKT+la+ ++ +   e     + i+g +++   +++ e
  gi|385805808|ref|YP_005842206.1| 36 IMGPNGSGKTSLANVIMGHPRYEvisgKIYINGEDVT--NLSAHE 78
                                      78****************9654411223455555555..233333 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   1.3e-05     0.015      24      66 ..      31      70 ..      20     207 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.3e-05
                            AAA_16 24 pelvllsGesGvGKsslvrellralekdggiflrgkcdqlesa 66
                                      +e++ + G+ G+GK+sl++ ++ + + +   +++gk   ++++
  gi|385805808|ref|YP_005842206.1| 31 GEVLAIMGPNGSGKTSLANVIMGHPRYE---VISGKIYINGED 70
                                      48899****************9988888...566666666444 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.3   2.2e-05     0.026      21      39 ..      33      51 ..      18      53 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.2e-05
                            AAA_23 21 ltlItGpNGaGKTTildAi 39
                                      + +I GpNG+GKT++ + i
  gi|385805808|ref|YP_005842206.1| 33 VLAIMGPNGSGKTSLANVI 51
                                      678************9876 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    0.0004      0.48       5      25 ..      31      51 ..      28      90 .. 0.81
   2 ?    2.7   0.0      0.12   1.5e+02      38     131 ..     121     209 ..      99     216 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0004
                            AAA_22  5 agilvvtGesGtGKTtllrrl 25
                                        +l+++G+ G+GKT l++ +
  gi|385805808|ref|YP_005842206.1| 31 GEVLAIMGPNGSGKTSLANVI 51
                                      56899**********998754 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.12
                            AAA_22  38 erpevv.fvtlpsst..sskdl.lrellralglelkaerlsseellealeqalraravielliiDEaqh.lr..see 107
                                       +rpev+ +++ + s+   s+d+ +rel   +  +  +        ++ l qal  +     +i DE +  l+    +
  gi|385805808|ref|YP_005842206.1| 121 HRPEVIkEMNEATSEvgLSTDFlYRELNVGFSGGERK--------RAELLQALVLKPI--NIIMDEPDSgLDvdGLK 187
                                       5555555444444444433333355555555532222........4344444444444..69999999999775589 PP

                            AAA_22 108 aleeLrsllnlsrkgvqliLvGtp 131
                                       +++++ ++++  + + ++iL+ ++
  gi|385805808|ref|YP_005842206.1| 188 IVSNIIKRMK--EEDRAVILITHY 209
                                       9999988888..888888888766 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   4.8e-05     0.058       2      34 ..      34      66 ..      33     101 .. 0.87
   2 ?   -2.4   0.0         4   4.8e+03      80      80 ..     181     181 ..     125     208 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.8e-05
                            AAA_33  2 vllvGlpGsGKstlaerllkklgavllssdtlr 34
                                      + + G++GsGK+ la  ++ +  ++++s  +++
  gi|385805808|ref|YP_005842206.1| 34 LAIMGPNGSGKTSLANVIMGHPRYEVISGKIYI 66
                                      6789***************9999****987766 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4
                            AAA_33  80 l 80 
                                       l
  gi|385805808|ref|YP_005842206.1| 181 L 181
                                       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 ?   13.0   0.0   5.6e-05     0.067      16      38 ..      25      47 ..      19      57 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.6e-05
                            AAA_29 16 tieidlkgatlltGpsGsGKSTl 38
                                      +++ +  ++  ++Gp+GsGK++l
  gi|385805808|ref|YP_005842206.1| 25 SLKCNNGEVLAIMGPNGSGKTSL 47
                                      55666444999**********98 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   7.5e-05      0.09       9      43 ..      21      54 ..      15      61 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.5e-05
                                      HHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC  9 iekLlekdelqslvvalvGmgGvGKttlakqilnk 43
                                      i++ + k++ +  v+a++G  G+GKt la+ i+ +
  gi|385805808|ref|YP_005842206.1| 21 IKNVSLKCNNG-EVLAIMGPNGSGKTSLANVIMGH 54
                                      55555578887.8****************998765 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 ?   13.0   0.0   6.1e-05     0.073      18      64 ..      29      76 ..      20     171 .. 0.71
   2 ?   -4.0   0.2       9.4   1.1e+04     106     123 ..     189     206 ..     186     208 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.1e-05
                          ATPase_2 18 epneiyfiYGpegsGKtaLlkeiienl.edkdkyviyyialreesisk 64
                                      ++ e++ i Gp gsGKt+L + i+     +    +iy++     ++s 
  gi|385805808|ref|YP_005842206.1| 29 NNGEVLAIMGPNGSGKTSLANVIMGHPrYEVISGKIYINGEDVTNLSA 76
                                      5689999**************998766233344666666555555555 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 9.4
                          ATPase_2 106 ielllekikkkgkkiiii 123
                                       ++++++ +k++ + +i+i
  gi|385805808|ref|YP_005842206.1| 189 VSNIIKRMKEEDRAVILI 206
                                       455566666666666665 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   0.00027      0.32       4      22 ..      33      51 ..      30      70 .. 0.85
   2 ?   -2.4   0.0       2.8   3.3e+03     113     135 ..     191     213 ..     187     250 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00027
                            AAA_24  4 kiliyGpsgiGKTtlakel 22
                                       ++i+Gp+g+GKT+la+ +
  gi|385805808|ref|YP_005842206.1| 33 VLAIMGPNGSGKTSLANVI 51
                                      689************9866 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.8
                            AAA_24 113 rllkklqelrknvifiahektrk 135
                                       +++k+++e +  vi+i h +   
  gi|385805808|ref|YP_005842206.1| 191 NIIKRMKEEDRAVILITHYTRLF 213
                                       56666666666777777765433 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0    0.0003      0.36       2      21 ..      33      52 ..      32      57 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0003
                                      CEEEEC-TTTCHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqkla 21
                                      ++++ G++GsGKT L+  ++
  gi|385805808|ref|YP_005842206.1| 33 VLAIMGPNGSGKTSLANVIM 52
                                      7899************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      619  (0.0345251); expected 358.6 (0.02)
Passed Vit filter:                       123  (0.00686039); 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: 0.65u 0.37s 00:00:01.02 Elapsed: 00:00:00.55
# Mc/sec: 1439.59
//
Query:       gi|385805809|ref|YP_005842207.1|  [L=138]
Description: hypothetical protein FFONT_0767 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00019   21.2  25.6       0.13   12.1   8.9    3.2  3  Prok-RING_4  Prokaryotic RING finger family 4
    0.00042   20.4  33.3      0.007   16.5   8.7    3.5  3  zf-B_box     B-box zinc finger
    0.00096   19.2  36.2     0.0059   16.7  10.6    3.7  2  FYVE         FYVE zinc finger
     0.0057   16.6  21.2     0.0077   16.2  21.2    1.2  1  DUF753       Protein of unknown function (DUF753)
  ------ inclusion threshold ------
        2.7    8.2  25.9        1.1    9.5   9.5    2.9  2  Prok-RING_2  Prokaryotic RING finger family 2
        5.9    7.0  15.9        1.5    9.0   7.5    2.3  2  Fer2_4       2Fe-2S iron-sulfur cluster binding domain


Domain annotation for each model (and alignments):
>> Prok-RING_4  Prokaryotic RING finger family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   8.9   4.5e-05      0.13       1      41 [.      28      67 ..      28      68 .. 0.93
   2 !    9.0  10.1   0.00042       1.2       1      31 [.      67      97 ..      59      99 .. 0.94
   3 ?    4.5   0.2      0.01        31      19      27 ..      99     107 ..      97     112 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.5e-05
                       Prok-RING_4  1 CvlCgeqekkailepCgHlvCkeCfdskdlssCPlCqrris 41
                                      C +Cg++e+k     Cg  vC++C+++++   C +C + ++
  gi|385805809|ref|YP_005842207.1| 28 CEICGKKERKNKCRICGREVCNDCYNKEKGM-CIVCSETLC 67
                                      99************************99987.999998876 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00042
                       Prok-RING_4  1 CvlCgeqekkailepCgHlvCkeCfdskdls 31
                                      C +C++++ + + + Cg lvC +C    d s
  gi|385805809|ref|YP_005842207.1| 67 CEICKRRNAVERCQICGKLVCPDCMVRIDKS 97
                                      99**********************9988766 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.01
                       Prok-RING_4  19 lvCkeCfds 27 
                                       +vC++C+++
  gi|385805809|ref|YP_005842207.1|  99 VVCRDCYEK 107
                                       79*****87 PP

>> zf-B_box  B-box zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5  13.3   0.00037       1.1       3      31 ..      25      53 ..      23      65 .. 0.91
   2 !   16.5   8.7   2.3e-06     0.007       3      31 ..      64      92 ..      62      97 .. 0.92
   3 ?    1.4   0.3      0.12   3.7e+02      24      29 ..      99     104 ..      95     109 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00037
                          zf-B_box  3 etkCpeHknkpatlfCedCqqplCeeCst 31
                                      e+kC+++++k+ +  C+ C+  +C++C +
  gi|385805809|ref|YP_005842207.1| 25 EKKCEICGKKERKNKCRICGREVCNDCYN 53
                                      789************************43 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 2.3e-06
                          zf-B_box  3 etkCpeHknkpatlfCedCqqplCeeCst 31
                                      et C+++k+++a   C+ C++++C++C++
  gi|385805809|ref|YP_005842207.1| 64 ETLCEICKRRNAVERCQICGKLVCPDCMV 92
                                      789************************65 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.12
                          zf-B_box  24 plCeeC 29 
                                        +C +C
  gi|385805809|ref|YP_005842207.1|  99 VVCRDC 104
                                       567777 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7  10.6     2e-06    0.0059       9      42 ..      25      54 ..      19      58 .. 0.88
   2 ?    4.8  17.6     0.011        32      11      65 ..      58     107 ..      54     110 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2e-06
                                      -SB-TTT--B--SSS--EE-TTT--EE-STTS-E CS
                              FYVE  9 vkkCeiCakkFsllrrrhhCrlCGkvvCekCssk 42
                                       kkCeiC kk    +r+  Cr+CG+ vC++C +k
  gi|385805809|ref|YP_005842207.1| 25 EKKCEICGKK----ERKNKCRICGREVCNDCYNK 54
                                      589****997....7****************987 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.011
                                       B-TTT--B-.-SSS--E...E-TTT--EE-STTS-EEE.EEGGGTEEEEEEE-HHHHHH CS
                              FYVE  11 kCeiCakkF.sllrrrh...hCrlCGkvvCekCssklvallekeaeeksvrvCkeClae 65 
                                        C  C+++  ++ +rr     C++CGk+vC +C+             ks  vC++C+++
  gi|385805809|ref|YP_005842207.1|  58 MCIVCSETLcEICKRRNaveRCQICGKLVCPDCMVRID---------KSRVVCRDCYEK 107
                                       577788877667777643337************85544.........445678888876 PP

>> DUF753  Protein of unknown function (DUF753)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2  21.2   2.6e-06    0.0077      49     132 ..      26     109 ..      16     126 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.6e-06
                            DUF753  49 edrekCaagek.eeceaCsgakCNkevfpeerlsClqCesskdseCeeeeslkakvCeayk..eedqCytkldesek 122
                                       ++ e C ++e+ ++c+ C  + CN+  + +e+  C+ C+++  + C++   ++++ C++        C++++d+s+ 
  gi|385805809|ref|YP_005842207.1|  26 KKCEICGKKERkNKCRICGREVCNDC-YNKEKGMCIVCSETLCEICKRR--NAVERCQICGklVCPDCMVRIDKSRV 99 
                                       4455676655549***********99.99**********8889999888..5677777666445789********** PP

                            DUF753 123 vergCasele 132
                                       v r+C  +l 
  gi|385805809|ref|YP_005842207.1| 100 VCRDCYEKLG 109
                                       *****98876 PP

>> Prok-RING_2  Prokaryotic RING finger family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   9.5   0.00036       1.1      21      48 ..      36      63 ..      24      66 .. 0.82
   2 ?    1.8  10.9     0.094   2.8e+02       8      47 ..      65     104 ..      62     111 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00036
                       Prok-RING_2 21 glrqcvlcGrWacdacWkdeyytcksca 48
                                         +c +cGr  c+ c++ e  +c  c+
  gi|385805809|ref|YP_005842207.1| 36 RKNKCRICGREVCNDCYNKEKGMCIVCS 63
                                      4568********************9997 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.094
                       Prok-RING_2   8 yvcdlcatahplaglrqcvlcGrWacdacW...kdeyytcksc 47 
                                        +c++c+  +++    +c +cG+  c  c         +c+ c
  gi|385805809|ref|YP_005842207.1|  65 TLCEICKRRNAV---ERCQICGKLVCPDCMvriDKSRVVCRDC 104
                                       578888877766...68***********963212345667777 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 ?    0.4   4.3      0.24     7e+02      21      55 ..      15      52 ..       3      70 .. 0.75
   2 ?    9.0   7.5   0.00049       1.5      32      67 ..      66     104 ..      59     109 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.24
                            Fer2_4 21 vasAllangvdvp.rsckygrp..rgelcaggeCrnCl 55
                                      +++ +lan+++   + c ++++  +  +c + +C++C 
  gi|385805809|ref|YP_005842207.1| 15 IIDDILANNIEKKcEICGKKERknKCRICGREVCNDCY 52
                                      66667777776443777765555688999999999996 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00049
                            Fer2_4  32 vprsckygrp..rgelcaggeCrnClVevegepnv.rac 67 
                                       +++ ck  ++  r  +c   +C++C+V++++ + v r c
  gi|385805809|ref|YP_005842207.1|  66 LCEICKRRNAveRCQICGKLVCPDCMVRIDKSRVVcRDC 104
                                       567788655577******************999887777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1135  (0.0633053); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); 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):               6  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 796.22
//
Query:       gi|385805810|ref|YP_005842208.1|  [L=239]
Description: deoxyribose-phosphate aldolase [Fervidicoccus fontis Kam940]
Scores for complete 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   0.0    1.5e-06   28.1   0.0    1.3  1  DeoC      DeoC/LacD family aldolase
  ------ inclusion threshold ------
      0.036   13.1   0.3      0.061   12.3   0.3    1.3  1  FMN_dh    FMN-dependent dehydrogenase
      0.096   12.7   0.1       0.19   11.8   0.1    1.5  1  CbiA      CobQ/CobB/MinD/ParA nucleotide binding domain


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 !   28.1   0.0   2.4e-10   1.5e-06      57     205 ..      64     197 ..      22     236 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 2.4e-10
                                       CTTSEEEEETECSSCCTTSTTEEEETTCHHHHHHHTT-SEEEEEEEEHTTTTCHHHHHHHHHHHHHHHHHHHT..EE CS
                              DeoC  57 akdiallvkldkgtyllkskqrdvdevasveeakalGAdavkvvvyyradgseeeqqklaeikrvkeacheeg..lp 131
                                       +  i+ ++ ++ g++ l++k        ++e a+ +GA++v+vv+++ +  s+++  + +eik+ +   he+g   +
  gi|385805810|ref|YP_005842208.1|  64 KVPISAVISFPFGQDPLEIK------QKQIELAFSNGAKEVDVVINVMSYISGDKSYVENEIKKLSDLTHELGgkVK 134
                                       44566666666666666666......8899****************************************8865599 PP

                                       EEEE.EEE-CTTBSSTTCHHHHHHHHHHHHTCCT-SEEEE--SSCC.B.HHHHHHHHHHHHHCHSSTEEEEETTS CS
                              DeoC 132 lile.lylrdeaikdekvdpdlvaeAarvsaelGaDiiKvevpkevvnateedaevfkdvikaapvpgvvlsGGv 205
                                       +i+e +yl ++           +ae +++  + + D iK++++        +d+ v++ +++  +  +++ sGG+
  gi|385805810|ref|YP_005842208.1| 135 FIIEtGYLDNAG----------IAELSKMIEKSNGDYIKTSTGFGPRGVNIDDILVIRSAVS--REQKIKASGGI 197
                                       ****99998877..........9********************5555566677777887777..45678888887 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.3     1e-05     0.061     258     298 ..     175     215 ..     173     222 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1e-05
                                       HHCHHHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEE CS
                            FMN_dh 258 idvLpeiveavggrievlvDgGirrGsDvlkAlalGAdavl 298
                                       id +  i+ av ++ ++ ++gGir+G  +l  la GA++ +
  gi|385805810|ref|YP_005842208.1| 175 IDDILVIRSAVSREQKIKASGGIRSGIQALLLLAFGANILG 215
                                       56667899*****************************9866 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   3.2e-05      0.19      35     104 ..      98     161 ..      95     190 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.2e-05
                                       EEESSCCCCHHTTEB-HHHHCCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  35 aDpqannlaileglendiepdlkrllellealgkkkalllkiagvvlnrvdgeneetllkealeelkqry 104
                                       +D+  n  +++ g++ ++e+ +k+l+ l ++lg+k      +++++ + +  ++ +++l++++e+ + +y
  gi|385805810|ref|YP_005842208.1|  98 VDVVINVMSYISGDKSYVENEIKKLSDLTHELGGK------VKFIIETGYLDNAGIAELSKMIEKSNGDY 161
                                       79999999*************************98......89**********************99766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 1502.60
//
Query:       gi|385805811|ref|YP_005842209.1|  [L=66]
Description: hypothetical protein FFONT_0769 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00086   19.6   0.1     0.0014   19.0   0.1    1.4  1  zf-C2H2   Zinc finger, C2H2 type


Domain annotation for each model (and alignments):
>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   7.9e-08    0.0014       1      23 []      26      53 ..      26      53 .. 0.97

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 7.9e-08
                                      EEETTTT.....EEESSHHHHHHHHHCC CS
                           zf-C2H2  1 ykCpdCg.....ksFkrksnLkrHirtH 23
                                      ++Cp+Cg       F + s+L rHi+ H
  gi|385805811|ref|YP_005842209.1| 26 FYCPICGagenaPIFFTESDLIRHICNH 53
                                      89************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 450.34
//
Query:       gi|385805812|ref|YP_005842210.1|  [L=111]
Description: hypothetical protein FFONT_0770 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 729.11
//
Query:       gi|385805813|ref|YP_005842211.1|  [L=575]
Description: glycyl-tRNA synthetase [Fervidicoccus fontis Kam940]
Scores for complete 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-24   83.5   0.1    2.5e-23   82.0   0.0    1.8  2  HGTP_anticodon  Anticodon binding domain
    3.7e-08   33.5   0.1    1.6e-07   31.5   0.1    2.0  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
     0.0031   17.6   0.4        2.2    8.5   0.1    2.5  2  zf-RING_7       C4-type zinc ribbon domain
  ------ inclusion threshold ------
       0.18   11.3   0.0       0.49    9.9   0.0    1.7  1  TF_Zn_Ribbon    TFIIB zinc-binding


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 ?   -2.7   0.0       1.5   6.8e+03      19      30 ..     393     404 ..     371     419 .. 0.76
   2 !   82.0   0.0   5.6e-27   2.5e-23       1      93 [.     473     563 ..     473     564 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.5
                                       HHHHHHHHTTTS CS
                    HGTP_anticodon  19 kklaeeLraagi 30 
                                       k+l+e L+++g+
  gi|385805813|ref|YP_005842211.1| 393 KELKETLEKNGF 404
                                       577778888775 PP

  == domain 2  score: 82.0 bits;  conditional E-value: 5.6e-27
                                       SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTC CS
                    HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtr 77 
                                       +v+v pl + +e++e +ak+++e L+  g+ + + d+++sig+++++ad++g+pfav+v++++le+ t+t+r rdt 
  gi|385805813|ref|YP_005842211.1| 473 KVAVFPLVN-DEKIEALAKSIYESLKMSGFMALY-DDSGSIGRRYARADEIGVPFAVTVDYQSLEDSTITIRFRDTW 547
                                       79******9.999****************96666.589*************************************** PP

                                       EEEEEETTHHHHHHHH CS
                    HGTP_anticodon  78 eqervsldelveklke 93 
                                       eq r+++del e+lk+
  gi|385805813|ref|YP_005842211.1| 548 EQKRLKIDELTEALKN 563
                                       ************9997 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 !   31.5   0.1   3.6e-11   1.6e-07      14     177 ..     162     451 ..     156     453 .. 0.71

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 3.6e-11
                                       -SSSHHHHHHHHHHHEEEB.GGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESG......GGHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxx RF
                      tRNA-synt_2b  14 kPtneetfvelirdevlrs.krLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhae......aslddslrdl 83 
                                       +P+  +++   ++       +rLPl ++qi+++ R+E s  +G+lR+reF+  + + f  +      + l+ ++ + 
  gi|385805813|ref|YP_005842211.1| 162 RPELAQGMFLSFKRVFTTMrERLPLGIAQIGRVGRNEISPRQGMLRLREFTIMEIEFFFDPedpgaeDALKKVYDKK 238
                                       5555566555555444433489****************9566****************9861222112223333333 PP

                                       HHHHHHHHHHTT.SCEEEEEEGTTSC................................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx................................................... RF
                      tRNA-synt_2b  84 ikaisriferlglefraiielmsaks................................................... 109
                                       ++   +  +r+g  + +i  + +a +                                                   
  gi|385805813|ref|YP_005842211.1| 239 LRILTEDAKRMGEREPKIFTIKEALEtgliktpwlaywmyvsqeflyslgipyenqyfeeklpeerahyskqtfdql 315
                                       33333333344444444444433333777889999999999999999999999999999999999988888888888 PP

                                       ....................................................................BTTSEEEEE CS
                                       ....................................................................xxxxxxxxx RF
                      tRNA-synt_2b 110 ....................................................................adykdkkef 118
                                                                                                           +++ ++++ 
  gi|385805813|ref|YP_005842211.1| 316 vkterwgwievsghayrgdydlsrhsiyskedlsifkqyqtphiekslkiminkaavgkafksesedvISALNSLDP 392
                                       88888888888888888888888888888888888888888888888888888888877666666666666666666 PP

                                       EEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTTS...SEEEEEEEEEEEEHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b 119 eavsesltkgieigtiqklgtrlserlgatvldenn...reksvimicaaigveRllsaile 177
                                       + + e l+k +    i  +g++  +++   v +e++   ++  ++++  ++gveRll +++e
  gi|385805813|ref|YP_005842211.1| 393 KELKETLEKNG---FITIKGKKITKEMVNMVEEEEKitgKRFIPHVVEPSFGVERLLYVVME 451
                                       66666677777...4444455777777776665554433777899************99988 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 !    6.7   0.0    0.0019       8.3      21      32 ..      85      96 ..      70      96 .. 0.80
   2 !    8.5   0.1   0.00049       2.2      10      30 ..     115     134 ..     115     136 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0019
                                      TB-EE-TTT--E CS
                         zf-RING_7 21 devvtCpeCGRI 32
                                      d +v C +C+RI
  gi|385805813|ref|YP_005842211.1| 85 DPIVSCTSCHRI 96
                                      78*********9 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00049
                                       -CCHHHHHCCSTB-EE-TTT- CS
                         zf-RING_7  10 ppqvlselragdevvtCpeCG 30 
                                       +p +l e+ ++++  +Cp+CG
  gi|385805813|ref|YP_005842211.1| 115 SPKELTEIIRNND-LRCPYCG 134
                                       6889999988877.******9 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00011      0.49      16      33 ..     124     141 ..     114     145 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00011
                                       STTCEEESSSSBEEEECC CS
                      TF_Zn_Ribbon  16 ergelvCtdCGlVledns 33 
                                        +++l+C+ CG Vl + s
  gi|385805813|ref|YP_005842211.1| 124 RNNDLRCPYCGGVLGEVS 141
                                       5899*********99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (575 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      595  (0.0331865); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.69u 0.33s 00:00:01.02 Elapsed: 00:00:00.50
# Mc/sec: 3471.13
//
Query:       gi|385805814|ref|YP_005842212.1|  [L=120]
Description: hypothetical protein FFONT_0772 [Fervidicoccus fontis Kam940]
Scores for 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   24.5   0.0    2.9e-05   24.0   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 !   24.0   0.0   1.6e-09   2.9e-05      23      93 ..      47     114 ..      35     119 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.6e-09
                                       HHHCSSS-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-TTEEEEESSHCC.....S-GHCT CS
                   Molydop_binding  23 rlakpepevveinpedAaalGikdGdlVevesrrGsvevrakvtervrpGvvfmpfgwweagekggnaNal 93 
                                       r+++++pe + inp+ A++lGikd   ++++ +  ++ +++ ++e+v++  v+++  + +  e+g++ N++
  gi|385805814|ref|YP_005842212.1|  47 RYSSTKPEHITINPKLASELGIKDKAYIVIAGK-KRFLFNVILDENVPENEVYANNEFMK--ENGVSDNSI 114
                                       455566699*******************88765.59********************9988..777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 819.68
//
Query:       gi|385805815|ref|YP_005842213.1|  [L=131]
Description: hypothetical protein FFONT_0773 [Fervidicoccus fontis Kam940]
Scores for complete 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   16.3   0.1      0.006   15.9   0.1    1.3  1  DUF685          Protein of unknown function (DUF685)
  ------ inclusion threshold ------
      0.017   14.7   2.3      0.018   14.5   2.3    1.1  1  UvrD-helicase   UvrD/REP helicase N-terminal domain
       0.54    9.1   5.8       0.83    8.5   2.5    1.9  2  Phage_min_cap2  Phage minor capsid protein 2
        8.6    6.2   9.9         18    5.1   0.3    2.3  2  Vpu             Vpu protein


Domain annotation for each model (and alignments):
>> DUF685  Protein of unknown function (DUF685)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   1.3e-06     0.006      22      85 ..      39     101 ..      20     115 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.3e-06
                            DUF685  22 ndtdllllddgaassnaitfknfldavkdkifkgeeldyfkeiikstiaeelaadkdfvkkiyd 85 
                                       n+ ++l l +    s a  +knfl++ +++i   ee++y++ ii       +  + d+ ++i +
  gi|385805815|ref|YP_005842213.1|  39 NEEEILKLLEMNKNSRA-DLKNFLKTYHENINSEEEMEYYRTIIDFVRLVYMQIEEDLFERILE 101
                                       55566666665555555.79************************99988889999998888876 PP

>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   2.3   4.1e-06     0.018     180     255 ..      22     101 ..       2     122 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.1e-06
                                       CHHHHHHHHHHHTTCCTTHHCHSS..TSCSHHHHHHHHHHHHHHHHHHHHTCEEHHHHHHHHHHHHHH..CHHHHHH CS
                     UvrD-helicase 180 eelrelvskakekqlspkelkkaf..ekasdlqkkiaeflkeyqeqkkeenalDfsdllhallellee..neelaea 252
                                       + l+ + +k+ke+q  ++e++     e +++ + ++++flk+y+e+ + e+ +++   ++ +++l     +e+l+e+
  gi|385805815|ref|YP_005842213.1|  22 KILSTIEEKLKEEQSVENEEEILKllEMNKNSRADLKNFLKTYHENINSEEEMEYYRTIIDFVRLVYMqiEEDLFER 98 
                                       23334444555555444444333366**************************8888888888875444345666655 PP

                                       HHH CS
                     UvrD-helicase 253 lre 255
                                       + e
  gi|385805815|ref|YP_005842213.1|  99 ILE 101
                                       554 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 ?    8.5   2.5   0.00019      0.83      74     148 ..       5      82 ..       1      85 [. 0.84
   2 ?    4.1   0.2    0.0039        18       4      52 ..      75     124 ..      72     130 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00019
                    Phage_min_cap2  74 lrkllkeagdkaiksddkelaiykeaglepkplekseelqqlveaylkqtegelkNltnttal....tslekaYeri 146
                                       +  ++k+  ++ +++  k l++ +e+ +e++++e++ee+ +l+e   k+   +lkN+++t       ++ +++Y+ i
  gi|385805815|ref|YP_005842213.1|   5 VLVIIKKSFQEIMEERGKILSTIEEKLKEEQSVENEEEILKLLEM-NKNSRADLKNFLKTYHEninsEEEMEYYRTI 80 
                                       55689999999999999999*******999************985.67788999****9998666766777888888 PP

                    Phage_min_cap2 147 ld 148
                                       +d
  gi|385805815|ref|YP_005842213.1|  81 ID 82 
                                       77 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0039
                    Phage_min_cap2   4 eqleelsdkivdlysaleqeiiediarrikktge.ltntaewqieklael 52 
                                       e++  ++d +  +y+++e++++e i +r ++    l+   +w ++++a++
  gi|385805815|ref|YP_005842213.1|  75 EYYRTIIDFVRLVYMQIEEDLFERILERAERSIGpLKANKDWILKEAADI 124
                                       5777888889999*************998775444777788887777776 PP

>> Vpu  Vpu protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   3.6    0.0046        20      36      73 ..      14      51 ..       6      58 .. 0.80
   2 ?    5.1   0.3    0.0041        18      40      53 ..      93     106 ..      74     108 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0046
                               Vpu 36 qkeierlikrireraedSgnESdGeeeeelakLvhshg 73
                                      q+ +e++ k ++ ++e+ ++E   e+eee+ kL++ + 
  gi|385805815|ref|YP_005842213.1| 14 QEIMEERGKILSTIEEKLKEEQSVENEEEILKLLEMNK 51
                                      3445788999999********999**********9554 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0041
                               Vpu  40 erlikrireraedS 53 
                                       e+l++ri erae S
  gi|385805815|ref|YP_005842213.1|  93 EDLFERILERAERS 106
                                       579*********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2516  (0.140331); expected 358.6 (0.02)
Passed bias filter:                      874  (0.0487478); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.32s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 843.24
//
Query:       gi|385805816|ref|YP_005842214.1|  [L=227]
Description: putative phosphate transport regulator [Fervidicoccus fontis Kam940]
Scores for complete 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   28.0   7.6    1.6e-06   27.6   7.6    1.2  1  PhoU_div  Protein of unknown function DUF47
  ------ inclusion threshold ------
        0.3   11.6  12.7       0.43   11.1   2.4    3.3  3  PhoU      PhoU domain


Domain annotation for each model (and alignments):
>> PhoU_div  Protein of unknown function DUF47
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   7.6   1.8e-10   1.6e-06      26     212 ..      38     223 ..       9     225 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 1.8e-10
                          PhoU_div  26 kliellkallegdyekveellkeiselEreADeikreirlklekglflP.vdRedllel.veslDeildvlediaml 100
                                        ++el++ +++g +e v +  + i ++   A  +k+     + +  + P  + ++l ++ ++ lD i   + +i  +
  gi|385805816|ref|YP_005842214.1|  38 MAQELISGFIQGKMELVKKGYEPIKKIKDDAQRMKESTMEYVVR--VSPtLMTKELYMFsLSHLDRISQIIDSIIYR 112
                                       57899******************************998888888..44513566776643899****9999999998 PP

                          PhoU_div 101 vtlrk...vefpeelkdeflallkktveaiealaevieeleklletalskkdiveeieslEdeiDqlqrklikklfs 174
                                       +++     + +++++ + f ++ +++ +++e+l    + l+    ++ +  +i  ei+++Ed +Dql+r+l  +   
  gi|385805816|ref|YP_005842214.1| 113 LSILAhsgFTLDQSIAELFSQFSSTSFNMVELLYTESKYLS---SNSKKVGEIHDEINRKEDLVDQLYRRLELEIIR 186
                                       88764233789**********************99999999...46666569******************9888887 PP

                          PhoU_div 175 redasnplevlllveiieklenvsdraedvadrisiil 212
                                       + +       lll+e ++ +e++sd++ d++  ++ i+
  gi|385805816|ref|YP_005842214.1| 187 KYS-NDLFHLLLLKEVVDLIEELSDKIRDASHDFRYIS 223
                                       544.78999***********************999886 PP

>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.7      0.03   2.6e+02      29      65 ..       4      42 ..       3      48 .. 0.60
   2 ?    5.6   0.0    0.0025        22      10      86 ..      37     110 ..      36     113 .. 0.84
   3 ?   11.1   2.4   4.8e-05      0.43      20      83 ..     156     213 ..     133     219 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.03
                                      HHHHHHHHHHHH...HHHHHHHHHHHHHH.HGG-SHHHHHH CS
                              PhoU 29 evierddeidrl...ekeiersllealak.rqplaedlrel 65
                                      e+i rddei ++   e+++ +++ ++l + +q+  +  +el
  gi|385805816|ref|YP_005842214.1|  4 EII-RDDEILNMnlaEMNLAEQITNILLTiNQEGKM-AQEL 42
                                      555.55555555577888899999999553554444.4444 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0025
                                       HHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              PhoU  10 emlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERigDhavnia 86 
                                       +m +++++ + ++  el+++ +e  ++i +  +++++s +e + + +p  +  +el  ++   ++l Ri+  + +i 
  gi|385805816|ref|YP_005842214.1|  37 KMAQELISGFIQGKMELVKKGYEPIKKIKDDAQRMKESTMEYVVRVSPTLM-TKEL--YMFSLSHLDRISQIIDSII 110
                                       688899999999999999999999899999999999999999988777777.6676..***********99888775 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 4.8e-05
                                       HCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHHHHH CS
                              PhoU  20 eekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERigDhav 83 
                                       ++k  e+ +e+ +++d +d+l++++e ++++++++      dl  ll l +++  +E  +D ++
  gi|385805816|ref|YP_005842214.1| 156 SKKVGEIHDEINRKEDLVDQLYRRLELEIIRKYSN------DLFHLLLLKEVVDLIEELSDKIR 213
                                       445557779****************9999999955......34444444556666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       861  (0.0480228); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); 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: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 1470.88
//
Query:       gi|385805817|ref|YP_005842215.1|  [L=156]
Description: tRNA-splicing endonuclease subunit alpha [Fervidicoccus fontis Kam940]
Scores for complete 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-28   96.2   0.1    1.5e-27   95.5   0.1    1.3  1  tRNA_int_endo    tRNA intron endonuclease, catalytic C-termin
    1.1e-13   50.7   2.2    1.1e-13   50.6   0.8    1.7  2  tRNA_int_endo_N  tRNA intron endonuclease, N-terminal domain
     0.0026   17.9   0.1     0.0051   17.0   0.1    1.5  1  tRNA_int_end_N2  tRNA-splicing endonuclease subunit sen54 N-t
  ------ inclusion threshold ------
      0.055   13.6   0.1       0.13   12.3   0.0    1.6  2  cNMP_binding     Cyclic nucleotide-binding domain


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 !   95.5   0.1   3.2e-31   1.5e-27       1      79 [.      65     142 ..      65     148 .. 0.95

  Alignments for each domain:
  == domain 1  score: 95.5 bits;  conditional E-value: 3.2e-31
                                       HHHHHHHHHHHHHTT-EEEECGGGTSSEEEETSCTTTSSCSEEEEEEETTSEEEHHHHHHHHHHHHHTTSEEEEEEE CS
                     tRNA_int_endo   1 falkyavyrdLrekGyvvrsGlkFGadFrvYqrrpslehseylVvvvsedeeldwpdlsaavrlahsvkKklilaiv 77 
                                       f   y++yrdLrekGyvvrsGlkFG+d+ +Y+++p+ eh+ yl++v++ de +d+ +l++ +rl+hsvkKk++l iv
  gi|385805817|ref|YP_005842215.1|  65 FKSLYIIYRDLREKGYVVRSGLKFGSDYSLYRHGPGIEHAPYLIHVYEGDEIIDPIELVRMGRLSHSVKKKFMLGIV 141
                                       56679***********************************************************************9 PP

                                       TT CS
                     tRNA_int_endo  78 da 79 
                                        +
  gi|385805817|ref|YP_005842215.1| 142 -R 142
                                       .4 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 !   50.6   0.8   2.4e-17   1.1e-13      25      67 .]       3      55 ..       1      55 [. 0.97
   2 ?   -2.0   0.0      0.65   2.9e+03      52      66 ..     108     122 ..     107     123 .. 0.79

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 2.4e-17
                                      TT-SEE.........CCTSSEEEEHHHHHHHHHTTSEEEE.TTSEEE-HHHHH CS
                   tRNA_int_endo_N 25 gfYGkp.........lidepLqLslvEAlYLlekGklevv.kggeplsfeell 67
                                      gfYGkp         + +e L+LslvEAlYL+ekGkl+v   +g+++sf+ell
  gi|385805817|ref|YP_005842215.1|  3 GFYGKPfgikkperrEYNEVLELSLVEALYLVEKGKLSVLnSEGKEMSFDELL 55
                                      8**************************************************96 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.65
                                       EEEETTSEEE-HHHH CS
                   tRNA_int_endo_N  52 levvkggeplsfeel 66 
                                       + v++g+e +++ el
  gi|385805817|ref|YP_005842215.1| 108 IHVYEGDEIIDPIEL 122
                                       789999999988776 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 !   17.0   0.1   1.1e-06    0.0051      48      70 ..      19      41 ..       3      43 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.1e-06
                   tRNA_int_end_N2 48 rrgrlwLlpeEaLYLvErGsldi 70
                                       +  l+L   EaLYLvE G+l +
  gi|385805817|ref|YP_005842215.1| 19 YNEVLELSLVEALYLVEKGKLSV 41
                                      677899**************987 PP

>> cNMP_binding  Cyclic nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0     3e-05      0.13      18      48 ..      29      57 ..      25      60 .. 0.88
   2 ?   -3.6   0.0       2.7   1.2e+04      19      26 ..      78      85 ..      69      86 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3e-05
                                      SEEEEEEES-EEEEEEETTS.EEEEEEE-TT CS
                      cNMP_binding 18 dslyivlsGevrvyrlsedgkevvlavlgpG 48
                                      + ly+v++G+++v  l+++gke+ +++l + 
  gi|385805817|ref|YP_005842215.1| 29 EALYLVEKGKLSV--LNSEGKEMSFDELLNE 57
                                      789**********..9******999988665 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.7
                                      EEEEEEES CS
                      cNMP_binding 19 slyivlsG 26
                                      + y+v+sG
  gi|385805817|ref|YP_005842215.1| 78 KGYVVRSG 85
                                      45888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); 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: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 954.72
//
Query:       gi|385805818|ref|YP_005842216.1|  [L=162]
Description: hypothetical protein FFONT_0776 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 1220.67
//
Query:       gi|385805819|ref|YP_005842217.1|  [L=235]
Description: UBA/THIF-type NAD/FAD binding protein [Fervidicoccus fontis Kam940]
Scores for 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-64  215.0   0.0    1.2e-63  214.7   0.0    1.0  1  ThiF             ThiF family
    5.2e-05   23.6   1.2     0.0067   16.8   1.0    3.0  2  NAD_binding_7    Putative NAD(P)-binding
     0.0085   15.5   0.2      0.057   12.8   0.1    2.0  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
  ------ inclusion threshold ------
      0.014   15.4   0.5       0.12   12.4   0.1    2.2  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
      0.051   13.8   0.4       0.14   12.4   0.4    1.7  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
       0.17   11.1   0.0        0.2   10.8   0.0    1.2  1  FAD_binding_3    FAD binding domain


Domain annotation for each model (and alignments):
>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.7   0.0   4.1e-67   1.2e-63       1     241 [.       4     231 ..       4     234 .. 0.93

  Alignments for each domain:
  == domain 1  score: 214.7 bits;  conditional E-value: 4.1e-67
                                       THHHHHHHHHHHHHHHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEEEESSB--GGGGGTBTTS-GGGTTSBHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF   1 ysrqlallgedgqekLrdskvllvGaGglGsellknLalsGvgkltlvDnDkielsNlnRqflfreediGkpKaeva 77 
                                       y+rql +l+++gq+kL++s+vl+vG+GglGs   ++La sG+gkl +vD Dkie+sNlnRq+l++eed+Gk+Ka  a
  gi|385805819|ref|YP_005842217.1|   4 YTRQLKILSDEGQRKLKNSTVLIVGVGGLGSASSVYLAYSGIGKLLVVDKDKIEKSNLNRQILYKEEDVGKYKAIIA 80 
                                       789************************************************************************** PP

                                       HHHHHHT-TTSEEEEEES-CCGCCS-HHHHTT-SEEEEESSSHHHHHHHHHHHHHHT-EEEEEEEETTEEEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  78 aealqeinpdveveavteritdetvleellesvDlVvdalDniearrlvnracvkkgiplieagtlgfegqvvviip 154
                                       ae+l+ein +++ve+++ +++de++ ee+++++D+Vvd+lDn++ar+ vn+++v++ +p+++a++++++gq++++ip
  gi|385805819|ref|YP_005842217.1|  81 AERLREINKEIHVEPFVIDVNDENF-EEIIKRADVVVDGLDNWKARLRVNKLAVRYLKPFVHAAVEEWYGQLFTVIP 156
                                       ***********************95.7************************************************** PP

                                       CCS-ECTSS-TGGS.EECCCCEEHHHHHHCTE-B-HHHHHHHHHHHHHHHHHHHTTBCGGGCCEEEECCTTTTEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF 155 gktgcyeCldpsstedptekkvplctsiagnipaiatttavvaglaalellkllsgkeklenslltqvdllesrfen 231
                                       +k +c+ C +   ++ +t+k+++          ++ +++++++ ++a e++k++ g  k +  +  ++d ++ + ++
  gi|385805819|ref|YP_005842217.1| 157 KKGPCLNCIFG--ETEETKKEIQ----------VVPPLPGILGTMQAIEVIKIITGIGKVASDRIIYIDSKNLSIHE 221
                                       *********96..3333333333..........479******************888888888888*********** PP

                                       ECCEEEEEEC CS
                                       xxxxxxxxxx RF
                              ThiF 232 velerakksk 241
                                       +++ +++++k
  gi|385805819|ref|YP_005842217.1| 222 IQVTKDPNCK 231
                                       **98888664 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   1.0   2.2e-06    0.0067       4      79 ..      18      92 ..      17     152 .. 0.81
   2 ?    0.9   0.0       0.2   6.1e+02      12      26 ..     198     212 ..     193     231 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.2e-06
                     NAD_binding_7  4 dlkgkkvlvvGgGevAarkvrklleag.akvtvvapevkeeleelvklaeeel..ekdlegadlviaatddrelneria 79
                                      +lk+ +vl+vG G ++      l+ +g  k+ vv+++   ++e+  +l+++ l  e+d+ +++ +iaa   re+n++i+
  gi|385805819|ref|YP_005842217.1| 18 KLKNSTVLIVGVGGLGSASSVYLAYSGiGKLLVVDKD---KIEK-SNLNRQILykEEDVGKYKAIIAAERLREINKEIH 92
                                      6899************99999999999789*******...4443.3444444345788888888888888888888875 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.2
                     NAD_binding_7  12 vvGgGevAarkvrkl 26 
                                       + G G+vA  ++  +
  gi|385805819|ref|YP_005842217.1| 198 ITGIGKVASDRIIYI 212
                                       889*******99765 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 !   12.8   0.1   1.9e-05     0.057      27      73 ..      12      59 ..       1      76 [. 0.79
   2 ?    0.6   0.0       0.1   3.1e+02      80      96 ..     100     116 ..      71     120 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.9e-05
                                      CCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-.EEEEESSSHHHHH CS
                      2-Hacid_dh_C 27 kallgkelsgktvGiiGlGrIGqavakrlkafgm.kviaydrskkkee 73
                                      ++  +++l+++tv i+G+G +G+a   +l+  g+ k++++d+ k +++
  gi|385805819|ref|YP_005842217.1| 12 SDEGQRKLKNSTVLIVGVGGLGSASSVYLAYSGIgKLLVVDKDKIEKS 59
                                      4566789**********************9999989999988866554 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.1
                                       CEECSHHHHHHH-SEEE CS
                      2-Hacid_dh_C  80 velvsleellaesDivs 96 
                                       v+ +++ee+++++D+v+
  gi|385805819|ref|YP_005842217.1| 100 VNDENFEEIIKRADVVV 116
                                       44568999999999997 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1     4e-05      0.12       8      56 ..      17      65 ..      10      92 .. 0.82
   2 ?    1.2   0.1      0.11   3.4e+02      47      81 ..      82     117 ..      74     132 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4e-05
                                      S..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHH CS
                      Shikimate_DH  8 eslkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeel 56
                                       +lk+++vl++G G +++    +L+ +g+ k++v+  +    ++l +++
  gi|385805819|ref|YP_005842217.1| 17 RKLKNSTVLIVGVGGLGSASSVYLAYSGIGKLLVVDKDKIEKSNLNRQI 65
                                      4799*******************************99888877887776 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.11
                                       HHHHHHHHHHT.ET-E.EEEGCGHHHHHHT-SEEEE CS
                      Shikimate_DH  47 erakelaeelkgeeie.alkleelkellaeadvvis 81 
                                       er +e+ +e++ e +   ++ e+ +e++++advv+ 
  gi|385805819|ref|YP_005842217.1|  82 ERLREINKEIHVEPFViDVNDENFEEIIKRADVVVD 117
                                       555666666644433203444678899999999985 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.4   4.8e-05      0.14       1      91 [.      24     134 ..      24     161 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.8e-05
                                       EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH.......................TTTCEEEEE- CS
                   Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka.......................lgvrfeaial 54 
                                       vli+G G+ G+a   +la ++    ++ v+d++k +  +l  ++                       +++ +e+  +
  gi|385805819|ref|YP_005842217.1|  24 VLIVGVGGLGSASSVYLAYSGIG--KLLVVDKDKIEKSNLNRQIlykeedvgkykaiiaaerlreinKEIHVEPFVI 98 
                                       79999999999999999999854..999999999998998888899999999999999999**99999999999999 PP

                                       -TTTHHHHHHHHHTTSSEEEE-SSGG.GHHHHHHHHHH CS
                   Sacchrp_dh_NADP  55 daenyeavLaallkegdlvvnlsppi.ssldvlkaCie 91 
                                       d++++    ++++k +d+vv+ + ++   l v k++++
  gi|385805819|ref|YP_005842217.1|  99 DVNDENF--EEIIKRADVVVDGLDNWkARLRVNKLAVR 134
                                       9999885..************99999666677777766 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   6.8e-05       0.2       3      34 ..      23      55 ..      21     108 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6.8e-05
                                      EEEEE--SHHHHHHHHHHHHTTHH.EEEEESSS CS
                     FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvr.vvlvekrs 34
                                      +VlIVG G  G  ++  L+  G+   ++v+k +
  gi|385805819|ref|YP_005842217.1| 23 TVLIVGVGGLGSASSVYLAYSGIGkLLVVDKDK 55
                                      7**********************8456677765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); 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: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1609.56
//
Query:       gi|385805820|ref|YP_005842218.1|  [L=64]
Description: hypothetical protein FFONT_0778 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.33s 00:00:00.80 Elapsed: 00:00:00.52
# Mc/sec: 367.52
//
Query:       gi|385805821|ref|YP_005842219.1|  [L=124]
Description: thioesterase superfamily protein [Fervidicoccus fontis Kam940]
Scores for complete 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   22.4   0.0    0.00015   22.1   0.0    1.2  1  4HBT      Thioesterase superfamily


Domain annotation for each model (and alignments):
>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   8.3e-09   0.00015       9      76 ..      37     104 ..      30     107 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 8.3e-09
                                       HHHHHHHHHHHHHHHTTSTTEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEETTSC CS
                              4HBT   9 ylallDeaagaalrslggrgilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrdedgr 76 
                                       + ++++e+a  ++  + +++   v+v+  + +++p+++g++l v a++l+  ++++ + ve   +d++
  gi|385805821|ref|YP_005842219.1|  37 MINFMEETALQCVQPHLKDNETTVGVRVDVYHIAPAKVGETLKVVAKLLESDGKRLIFWVEAICGDRV 104
                                       6689******************************************************9999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 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:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.37s 00:00:00.89 Elapsed: 00:00:00.55
# Mc/sec: 675.69
//
Query:       gi|385805822|ref|YP_005842220.1|  [L=601]
Description: exopeptidase, family M28 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-09   37.6   0.0      3e-09   36.9   0.0    1.4  1  Peptidase_M28  Peptidase family M28
    1.9e-08   33.5   0.3    2.3e-07   29.9   0.0    2.4  3  DUF4910        Domain of unknown function (DUF4910)
     0.0053   16.8   0.0      0.011   15.7   0.0    1.6  1  PA             PA domain


Domain annotation for each model (and alignments):
>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.0     5e-13     3e-09      47     190 ..     262     415 ..     222     423 .. 0.81

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 5e-13
                                       HHHHHCHHGGCCSSEEEEEEEESSCSGSSHHHHHHHHHHC..CCTTEEEEEEECS-SSSS--EEE..........HH CS
                     Peptidase_M28  47 elarvlaasgsrpkrgvrflffdaEEagllGSkafakakp..elkkiaavlnlDmvgsggkellf..........es 111
                                         +++l +  s++k ++r+ f+   E+   GS  +  +k   e  ki   +nlDm+g  ++   +           +
  gi|385805822|ref|YP_005842220.1| 262 IAMKYLDR--SDLKDNIRINFVWVPEY--SGSVSYL-RKAlsEGRKIIGTVNLDMIGEVQDITGSslnfvrspisLI 333
                                       34566665..46788888888888885..69*****.54456****************99999999999******** PP

                                       HHHHCHHHHHHHHHHHHHTT-TTSCCEEEEES....STT-STTHHHHTTT--EEEECTSSS-TTTTSTTSSGGGB-H CS
                     Peptidase_M28 112 gdkssselekelkalakpvgraaaedpfders....grgrsDhspflkagvpvldlaetgfpevyHtprDtldnidk 184
                                       ++ ++s+++  l+al k +g ++ +++ ++++    + + sDh +++ +g+p + l + + +++yH+++Dt+d+ d 
  gi|385805822|ref|YP_005842220.1| 334 SPLEASTFKYMLDALPKSYGFSSITTFPTKKVwlinYEVGSDHDVYVSYGIPSVML-NMWPDKYYHSSEDTIDKFDI 409
                                       *********************9998777777767666677****************.99999999*********999 PP

                                       HHHHHH CS
                     Peptidase_M28 185 dtlari 190
                                       +++a +
  gi|385805822|ref|YP_005842220.1| 410 KQVASL 415
                                       887765 PP

>> DUF4910  Domain of unknown function (DUF4910)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0   3.9e-11   2.3e-07      64     149 ..     228     318 ..     222     328 .. 0.85
   2 ?    0.4   0.1     0.039   2.3e+02     183     240 ..     371     424 ..     361     430 .. 0.68
   3 ?   -2.1   0.0      0.24   1.4e+03     132     155 ..     435     458 ..     424     465 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 3.9e-11
                                       -SSS-EEEEEEE----S-.TTTTHHHH..HHHHHHHHHHTTS--.SSEEE..EEEE-TTHHHHHHHHH-GGGGGGEE CS
                                       xxxxxxxxxxxxxxxxxx.xxxxxxxx..xxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DUF4910  64 geteeevllsahvChPsl.andnlsGi..avatalakalaerkerrysyr..llfvPetiGsitylsrneeklkkik 135
                                       g+ e+e  + +h+ChP    ndn+sG    +a+ +a +   r++ + + r  +++vPe  Gs+ yl +  ++ +ki 
  gi|385805822|ref|YP_005842220.1| 228 GNGENEYHIISHLCHPGYtVNDNISGSigNIAASIAMKYLDRSDLKDNIRinFVWVPEYSGSVSYLRKALSEGRKII 304
                                       6778899999******9636******734599999999988887776666337899********************* PP

                                       EEEE--S--SSS-E CS
                                       xxxxxxxxxxxxxx RF
                           DUF4910 136 aGlvltcvGdegal 149
                                         + l ++G+ +++
  gi|385805822|ref|YP_005842220.1| 305 GTVNLDMIGEVQDI 318
                                       *9*******97765 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.039
                                       S-SSTHHHHTSTTT---EEEEESS-TT.-TTTTBTTSSGGG--HHHHHH.HHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                           DUF4910 183 pygyDerqycsPgvdlpvgslaRskygeypeYhtsaDnldfvkpealee.sfelllevl 240
                                       ++g+D   y s g+  p ++l  ++ +    Yh+s+D +d    +++++ +++ ll++l
  gi|385805822|ref|YP_005842220.1| 371 EVGSDHDVYVSYGI--PSVMLNMWPDK---YYHSSEDTIDKFDIKQVASlGIASLLSIL 424
                                       57888888888775..66777777643...499**999997766665432455555555 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.24
                                       GGEEEEEE--S--SSS-EEEE--T CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                           DUF4910 132 kkikaGlvltcvGdegalsykksr 155
                                        ++  G+ l ++Gd++  +y+++ 
  gi|385805822|ref|YP_005842220.1| 435 MNMVYGYDLMAIGDKELKKYRETL 458
                                       57889999********99999875 PP

>> PA  PA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.9e-06     0.011       2      88 ..     111     193 ..     110     194 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.9e-06
                                PA   2 tgplVyscfagygisadfegvdvkGkivLvqrtf.aeKarnAqaaGAagviivndge...lgaatgasgnegepdgi 74 
                                        g+lV   + ++g+ +    +++++kivL ++ + a+ +    ++GA+gvi ++ ++    ++     + ++e ++ 
  gi|385805822|ref|YP_005842220.1| 111 AGELV---YLPSGKCD----KNCENKIVLTDD-WsATNYFSFVDNGAIGVIAFRREGsetAYPYFSIFPSFEEISKA 179
                                       69999...54444333....4899******54.3699999999**********444435544555556666677779 PP

                                PA  75 tiPavgvsredgea 88 
                                         Pa++v+red+  
  gi|385805822|ref|YP_005842220.1| 180 KAPAFTVTREDAMH 193
                                       99*******99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (601 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); 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: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.49
# Mc/sec: 3661.01
//
Query:       gi|385805823|ref|YP_005842221.1|  [L=417]
Description: threonine dehydratase [Fervidicoccus fontis Kam940]
Scores for complete 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-80  270.1   0.2    2.9e-80  269.8   0.2    1.1  1  PALP      Pyridoxal-phosphate dependent enzyme
    3.8e-06   26.6   0.9    8.6e-06   25.4   0.0    2.0  2  ACT       ACT domain
    0.00047   20.7   0.0      0.002   18.7   0.0    2.1  1  ACT_4     ACT domain
     0.0032   17.4   0.0     0.0082   16.1   0.0    1.8  1  ACT_6     ACT domain


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  269.8   0.2   6.5e-84   2.9e-80       2     294 .]      27     315 ..      26     315 .. 0.96

  Alignments for each domain:
  == domain 1  score: 269.8 bits;  conditional E-value: 6.5e-84
                                       GGCSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT CS
                              PALP   2 tlgigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallG 78 
                                       +++i +TP+  +  +sk +g +l++KlE++++tgSfK+Rga+y + ++k + ++k+v++assGNh++++A+a++ lG
  gi|385805823|ref|YP_005842221.1|  27 SGVIHKTPVDYSATFSKMTGNKLYFKLENMQKTGSFKVRGAYYKIFKHKDEIKGKGVIAASSGNHAQGVAFASNSLG 103
                                       67899******************************************99999************************* PP

                                       -EEEEEEETTS-HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHHTT CS
                              PALP  79 lkvtivvpadaspekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileqlg 155
                                       +k+tiv+p+ +++ kv ++r +Gaevv++g+ ydea ++  e+ ++ +g +++++f++  ++ g+gtiglEi++ql 
  gi|385805823|ref|YP_005842221.1| 104 IKSTIVMPEITPAFKVNATRNYGAEVVLYGKVYDEAYKKSIEISQQ-TGSVFIHPFNDIEIMGGQGTIGLEIASQL- 178
                                       **********************************************.*****************************. PP

                                       TTEEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCSCGTTCCHHH CS
                              PALP 156 gkpdavvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvsdtiadglavgspselafel 232
                                        ++d v+vpvGgGgli+Gi++++k+ +p+++vi+vep+++++++ s+++g+ +t+++ +++adg+ ++ +++l+fe+
  gi|385805823|ref|YP_005842221.1| 179 SDIDMVLVPVGGGGLISGIGTAIKKLKPSTKVIAVEPKNAPKYYVSRKNGKIETIEPLPSLADGVVTKGVGDLTFEV 255
                                       5**************************************************************************** PP

                                       HSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHCCTTC.EEEEEEE-B CS
                              PALP 233 ldrlvdeivtvsdeealeamrllarregivvepssaaalaalklreagelkeg.drvvviltg 294
                                       + + vd++v v+++ ++ a+ l+ +r +i+ve ++a  laa+     g +++  +++ ++++g
  gi|385805823|ref|YP_005842221.1| 256 MSEVVDDVVVVDENSIATAIYLMLERSKIMVEGAGALPLAAM---LEGYYNNMnKKIALVVSG 315
                                       ******************************************...555555544667777776 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.2      0.79   3.5e+03      43      58 ..     259     274 ..     256     275 .. 0.82
   2 !   25.4   0.0   1.9e-09   8.6e-06       2      62 ..     339     403 ..     338     406 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.79
                                       EEEEEEEEEHHHHHHH CS
                               ACT  43 ivfvvivvdeedleev 58 
                                        v+ v+vvde++++++
  gi|385805823|ref|YP_005842221.1| 259 VVDDVVVVDENSIATA 274
                                       5788999**9999887 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 1.9e-09
                                       EEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTT....ECEEEEEEEEEEHHHHHHHHHHH CS
                               ACT   2 vlrvgvpDrPGlLarvfgaladrgiNidsieqrssedk....vagivfvvivvdeedleevleal 62 
                                       vl v+ +D+PG La+++++l ++  Ni+ + + +   +    +a+  ++++v+d +++e +++ l
  gi|385805823|ref|YP_005842221.1| 339 VLKVLTKDQPGELAKILNVLYKYKCNIVEVKHDRFSLRspvgFASVEVIFEVPDIAVVERLKKDL 403
                                       788999********************************999999999999999999999999887 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   4.4e-07     0.002       7      69 ..     338     403 ..     335     406 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 4.4e-07
                             ACT_4   7 vrleveaedrkglLaditqviseekanivsvnaktrkk...dglaeikitveVkdvehLsrviakL 69 
                                       v l+v ++d++g La+i++v+ + k niv+v+ +  +     g+a++++ +eV d++ ++r+ + L
  gi|385805823|ref|YP_005842221.1| 338 VVLKVLTKDQPGELAKILNVLYKYKCNIVEVKHDRFSLrspVGFASVEVIFEVPDIAVVERLKKDL 403
                                       6799***************************987644344599*************9999987765 PP

>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.8e-06    0.0082       2      35 ..     337     370 ..     336     411 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.8e-06
                             ACT_6   2 illitvtGpdrpGltasLtsvlaefgvnilDieq 35 
                                       i+++ v+ +d+pG +a+++ vl ++++ni++++ 
  gi|385805823|ref|YP_005842221.1| 337 IVVLKVLTKDQPGELAKILNVLYKYKCNIVEVKH 370
                                       7999**************************9974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); 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: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2797.71
//
Query:       gi|385805824|ref|YP_005842222.1|  [L=416]
Description: S-adenosyl-L-homocysteine hydrolase [Fervidicoccus fontis Kam940]
Scores for complete 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-73  246.0   0.0    2.8e-42  144.9   0.1    2.0  2  AdoHcyase      S-adenosyl-L-homocysteine hydrolase
    9.8e-58  194.8   0.8    9.8e-58  194.8   0.8    1.8  3  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi
    8.7e-11   41.5   0.3    2.2e-10   40.2   0.2    1.8  2  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    7.1e-10   38.7   0.4    1.4e-09   37.7   0.4    1.5  1  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
     0.0026   17.5   0.1     0.0084   15.9   0.0    1.9  2  NifT           NifT/FixU protein
  ------ inclusion threshold ------
      0.012   15.0   4.0       0.04   13.2   3.6    2.1  1  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
      0.026   14.8   0.3      0.088   13.1   0.3    2.0  1  TrkA_N         TrkA-N domain
      0.054   12.9   0.2        4.3    6.7   0.1    2.3  2  PALP           Pyridoxal-phosphate dependent enzyme
       0.08   12.8   0.8       0.18   11.7   0.8    1.7  1  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d


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 !  144.9   0.1   1.4e-45   2.8e-42       1     138 [.       3     135 ..       3     137 .. 0.98
   2 !  100.5   0.0   4.7e-32   9.3e-29     171     286 ..     135     411 ..     134     414 .. 0.99

  Alignments for each domain:
  == domain 1  score: 144.9 bits;  conditional E-value: 1.4e-45
                                       --B-S-GGGHHHHHHHHHHHHCC-HHHHHHHHHCTTT-TTTT-EEEEES--SHHHHHHHHHHHHTT-EEEEE-SSTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase   1 dykvkdislaefGrkeielaekempglmalreeyaeekplkgariaGslhmtiqtavLietLvalGaevrWasCnif 77 
                                       +y v di++ae G  ++e ae++mp lm+lr++y++ekpl+ga+ia +lh+t +t vL+ tL+a Gaev  a+ n  
  gi|385805824|ref|YP_005842222.1|   3 EYWVSDINKAEEGVAQLEWAERNMPVLMSLRKKYSDEKPLRGAKIAACLHVTKETGVLVRTLKAWGAEVYLAASNPL 79 
                                       699************************************************************************** PP

                                       T--HHHHHHHCCTTEEEE--TT--HHHHHHHHHHCHS-SSTS-S-SEEEESSSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase  78 stqdeaaaaiaeagvpvfawkgetleeywwcieqalkwaedekepnlilDdGGDltllvhk 138
                                       stqd++aaa+a++gv vfa kge+++ey w ie++ +      +p++++DdG Dl  l+h+
  gi|385805824|ref|YP_005842222.1|  80 STQDDIAAALATEGVCVFAKKGESEKEYFWAIEKVASI-----HPDIVIDDGADLHSLLHE 135
                                       **********************************9966.....7**************998 PP

  == domain 2  score: 100.5 bits;  conditional E-value: 4.7e-32
                                       THHCCCHCC--EEEE-SHHHHHHHHHHHHTT---SEEEESTTSHHHCTTH........................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................... RF
                         AdoHcyase 171 kkytellkkikGvseetttGvhrLyelakkgkLlvpainvndsvtkskfD........................... 220
                                       +k++e+l+kikG +eetttGv rL  l+k++kL  p + vnd++tk+ fD                           
  gi|385805824|ref|YP_005842222.1| 135 EKHPEMLNKIKGGAEETTTGVVRLRALEKEKKLGYPVFAVNDAMTKQMFDnrygtgqstidgllratnilisgktiv 211
                                       6899************************************************************************* PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                         AdoHcyase 221 ............................................................................. 220
                                                                                                                    
  gi|385805824|ref|YP_005842222.1| 212 vagygwvgrgiaarargmgaeviitevdpvkaleavmdgyrvmkmeeaakigdvfitatgdkdvitwkhmekmkdga 288
                                       ***************************************************************************** PP

                                       ..........................................................S-HHHHHHHHHHHHHHHHH CS
                                       ..........................................................xxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase 221 ..........................................................hpsfvmsasftnqvlaqie 239
                                                                                                 hps vm++sf+nq+l   +
  gi|385805824|ref|YP_005842222.1| 289 ilansghfnvevsvkdleensissrelrrymkeykmkngkvlyllaegrllnlvaaegHPSEVMDMSFANQALIAKK 365
                                       ***************************************************************************** PP

                                       HHHTTSSS-SSEEE--CHHHHHHHHHCCCCCT-------HHHHHCCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase 240 lfkkekkyekkvyvlpkklDekvarlhleklgaklteltkeqaeyig 286
                                       ++++ +  e kvy +p  +D ++a+l+l+++g++++elt eq ey++
  gi|385805824|ref|YP_005842222.1| 366 VWTEPR-LEPKVYKVPLDIDQNIAMLKLKSMGIEIDELTPEQKEYLD 411
                                       ***765.99************************************97 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 ?   -3.9   0.0       6.2   1.2e+04      41      58 ..      63      80 ..      59      85 .. 0.82
   2 !  194.8   0.8   4.9e-61   9.8e-58       1     161 [.     185     345 ..     185     346 .. 0.99
   3 ?   -3.3   0.0       4.3   8.5e+03     113     137 ..     384     408 ..     382     410 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 6.2
                                      HHHHCT-EEEEE-S-HHH CS
                     AdoHcyase_NAD 41 slkglGarvivtevdPic 58
                                      +lk+ Ga v+++  +P++
  gi|385805824|ref|YP_005842222.1| 63 TLKAWGAEVYLAASNPLS 80
                                      799999999999888875 PP

  == domain 2  score: 194.8 bits;  conditional E-value: 4.9e-61
                                       HHHHHCCCCCHHHHHHH-S--TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HHHCTT CS
                     AdoHcyase_NAD   1 nlygcreslvdgikratdvllaGkvavvaGyGdvGkGcaaslkglGarvivtevdPicalqaameGfevvtleevvk 77 
                                       n yg+ +s +dg+ rat++l++Gk++vvaGyG vG+G aa  +g+Ga vi+tevdP+ al a+m+G++v+++ee++k
  gi|385805824|ref|YP_005842222.1| 185 NRYGTGQSTIDGLLRATNILISGKTIVVAGYGWVGRGIAARARGMGAEVIITEVDPVKALEAVMDGYRVMKMEEAAK 261
                                       78*************************************************************************** PP

                                       T-SEEEE-SSSSSSB-HHHHCCS-TTEEEEE-SSTTTTBTHHHHHTTT-EEEEEETTEEEEE-TTS-EEEEEGGGSB CS
                     AdoHcyase_NAD  78 kadivvtttGnkdiitlehlkkmkddaivcniGhfdseidvaaleanalkkeevkpqvdrvtlkdgkkiillaeGrl 154
                                        +d+++t+tG kd+it +h++kmkd ai++n Ghf+ e+ v+ le+n+++  e++  ++++++k+gk + llaeGrl
  gi|385805824|ref|YP_005842222.1| 262 IGDVFITATGDKDVITWKHMEKMKDGAILANSGHFNVEVSVKDLEENSISSRELRRYMKEYKMKNGKVLYLLAEGRL 338
                                       ***************************************************************************** PP

                                       CHHHTS- CS
                     AdoHcyase_NAD 155 lnlgcat 161
                                       lnl +a 
  gi|385805824|ref|YP_005842222.1| 339 LNLVAAE 345
                                       ***9886 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 4.3
                                       TTTBTHHHHHTTT-EEEEEETTEEE CS
                     AdoHcyase_NAD 113 dseidvaaleanalkkeevkpqvdr 137
                                       d++i + +l++++++++e+ p+ ++
  gi|385805824|ref|YP_005842222.1| 384 DQNIAMLKLKSMGIEIDELTPEQKE 408
                                       7889999999999999999887665 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 ?   -3.0   0.0         2   4.1e+03      52      73 ..      61      82 ..      59      91 .. 0.74
   2 !   40.2   0.2   1.1e-13   2.2e-10      32     128 ..     203     295 ..     161     312 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2
                                      HHHHHHTT-EEEEESSSHHHHH CS
                      2-Hacid_dh_C 52 akrlkafgmkviaydrskkkee 73
                                       ++lka+g++v+    ++ +++
  gi|385805824|ref|YP_005842222.1| 61 VRTLKAWGAEVYLAASNPLSTQ 82
                                      5789999999998887776555 PP

  == domain 2  score: 40.2 bits;  conditional E-value: 1.1e-13
                                       S-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S--STTTTTS CS
                      2-Hacid_dh_C  32 kelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvsleellaesDivslhlpltpetrhl 108
                                         +sgkt+ + G+G +G+ +a r++++g++vi++++ + k  e+   g++++++ee+ +  D+ + ++      +++
  gi|385805824|ref|YP_005842222.1| 203 ILISGKTIVVAGYGWVGRGIAARARGMGAEVIITEVDPVKALEAVMDGYRVMKMEEAAKIGDVFITATG----DKDV 275
                                       4689*********************************998889999999*************9887665....688* PP

                                       BSHHHHHCSTTTEEEEESS- CS
                      2-Hacid_dh_C 109 inaeelakmkkgailiNtaR 128
                                       i+ ++++kmk+gail N + 
  gi|385805824|ref|YP_005842222.1| 276 ITWKHMEKMKDGAILANSGH 295
                                       *****************875 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 !   37.7   0.4     7e-13   1.4e-09       2     102 ..     205     301 ..     204     310 .. 0.91

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 7e-13
                                       HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHHHHHH CS
                              IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelqkevye 78 
                                       ++gk+i+v GyG  G+  a   r  g +v+++  +   ++ +A  +g++v++++ea+k  dv ++ + D+   +v++
  gi|385805824|ref|YP_005842222.1| 205 ISGKTIVVAGYGWVGRGIAARARGMGAEVIITEVDPV-KALEAVMDGYRVMKMEEAAKIGDVFITATGDK---DVIT 277
                                       789****************************999888.677899*******************9999995...7888 PP

                                       HHTGGG--TT-EEEESSSHHHHTT CS
                              IlvN  79 eeiepnlkegkalafahGfnihfg 102
                                        + ++++k+g++la +  fn+  +
  gi|385805824|ref|YP_005842222.1| 278 WKHMEKMKDGAILANSGHFNVEVS 301
                                       99999***************9865 PP

>> NifT  NifT/FixU protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       5.6   1.1e+04      33      42 ..      65      74 ..      61      76 .. 0.80
   2 !   15.9   0.0   4.2e-06    0.0084       9      49 ..     292     332 ..     288     337 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 5.6
                                      SS-SSEEEET CS
                              NifT 33 ekwGgevtLa 42
                                      ++wG ev La
  gi|385805824|ref|YP_005842222.1| 65 KAWGAEVYLA 74
                                      4799999886 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 4.2e-06
                                       SS-E.EEEETTTTEEEEEEEESSSSS-SSEEEETTS-EEE- CS
                              NifT   9 eeGklsvYvpKkDLEekvveeekeekwGgevtLanGwelel 49 
                                       ++G++ v v  kDLEe+ +++ + +++ +e++++nG+ l+l
  gi|385805824|ref|YP_005842222.1| 292 NSGHFNVEVSVKDLEENSISSRELRRYMKEYKMKNGKVLYL 332
                                       67999999******************************998 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 ?   13.2   3.6     2e-05      0.04      28     124 ..     207     290 ..     184     292 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2e-05
                                       --EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TTTCECEEHCHHHHHHHHHHHH-SEEEE---BTT CS
                       AlaDh_PNT_C  28 pakvlviGgGvaGlqAiatakglgakVtvlDvrparleqles.lgakfvevlksqeellaeavkeadvvigtvlipG 103
                                         +++v G G +G   +a a+g+ga+V +++v+p ++  le+ + +   +       +++ea+k  dv i++   +G
  gi|385805824|ref|YP_005842222.1| 207 GKTIVVAGYGWVGRGIAARARGMGAEVIITEVDPVKA--LEAvMDGY--R-----VMKMEEAAKIGDVFITA---TG 271
                                       4568999*************************99654..44423333..2.....23566777778888888...66 PP

                                       SS---SC-HHHHHTS-TTEEE CS
                       AlaDh_PNT_C 104 kkaPkLvteemvksMkpgsVi 124
                                        k   ++t +++++Mk+g+++
  gi|385805824|ref|YP_005842222.1| 272 DK--DVITWKHMEKMKDGAIL 290
                                       66..58888888999888875 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.3   4.4e-05     0.088       1      46 [.     210     255 ..     210     263 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.4e-05
                                       EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEEEE CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeglevvv 46 
                                       i+++G+G vGr +a + +  g  +v++ + d+ ++ e+  +g++v++
  gi|385805824|ref|YP_005842222.1| 210 IVVAGYGWVGRGIAARARGmGA-EVIITEVDPVKALEAVMDGYRVMK 255
                                       89*****************666.6**********9999999999876 PP

>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.012        25      92     136 ..      59     103 ..      42     131 .. 0.70
   2 ?    6.7   0.1    0.0021       4.3      54      98 ..     206     257 ..     148     301 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.012
                                       HHHHHHHHTT-EEEEECCHHHHHHHH.HHHHHHHSTTCEE--TTTS CS
                              PALP  92 ekvallrllGaevvevggdydeavaa.aaelaaegegaylvsqfdn 136
                                         v+ l+++Gaev +  +++ ++++  aa+la e + ++++  +++
  gi|385805824|ref|YP_005842222.1|  59 VLVRTLKAWGAEVYLAASNPLSTQDDiAAALATE-GVCVFAKKGES 103
                                       678899**********777444444437788888.88888877773 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0021
                                       TTSEEEEEBSSHHHHHHHHHHHHHT-EEEEE.......EETTS-HHHHHHHH CS
                              PALP  54 gaktvveassGNhgralAaaaallGlkvtiv.......vpadaspekvallr 98 
                                       ++kt+v+a+ G  gr++Aa a+ +G +v+i        ++a +  ++v +++
  gi|385805824|ref|YP_005842222.1| 206 SGKTIVVAGYGWVGRGIAARARGMGAEVIITevdpvkaLEAVMDGYRVMKME 257
                                       6899999999999999999999999888887554444433333345555555 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.8     9e-05      0.18       2      43 ..     210     252 ..     209     290 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9e-05
                                       EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHH.HHHHHHHHH CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseea.lekalekie 43 
                                       + v G G +G+giaa +   g eV ++++++ + le++++  +
  gi|385805824|ref|YP_005842222.1| 210 IVVAGYGWVGRGIAARARGMGAEVIITEVDPVKaLEAVMDGYR 252
                                       7899*************************88550454444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 3076.89
//
Query:       gi|385805825|ref|YP_005842223.1|  [L=324]
Description: ornithine cyclodeaminase/mu-crystallin [Fervidicoccus fontis Kam940]
Scores for complete 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-69  233.6   0.1    3.2e-69  233.3   0.1    1.0  1  OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin famil
    0.00036   20.6   0.0     0.0043   17.1   0.0    2.1  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
  ------ inclusion threshold ------
      0.021   14.1   0.2      0.037   13.4   0.2    1.3  1  THF_DHG_CYH_C    Tetrahydrofolate dehydrogenase/cyclohydrolas
      0.068   13.5   0.1       0.24   11.7   0.0    1.9  2  CRF1             Transcription factor CRF1
      0.072   13.7   0.0       0.22   12.1   0.0    1.9  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent


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 !  233.3   0.1   8.9e-73   3.2e-69       9     317 ..      11     316 ..       3     317 .. 0.92

  Alignments for each domain:
  == domain 1  score: 233.3 bits;  conditional E-value: 8.9e-73
                                       HHHHCCH-HCCCHHHHHHHHHHHHCC-CE----EEEEECCGTEEEEEEEEEETTTTEEEEEEEEEETTTCCCTSSSE CS
                   OCD_Mu_crystall   9 veveeelllddlakaveeafrrlasgkvkkpprvalevkdsrgelevmpaylagrellgvKlvnshpenkksglptv 85 
                                       +e+e+++ l+ + ka+e+a+ ++++ +   p r+++ +k       vm +y++  e +gvK+v   pen  +glpt 
  gi|385805825|ref|YP_005842223.1|  11 NEIENLMDLNLVSKAIEDALIKFSKRETLTPERTVMRIKG--NWWAVMQSYIPS-EGIGVKVVSQIPENFSRGLPTI 84 
                                       5788888888999************666666666666666..7789*******9.99******************** PP

                                       EEEEEEE-TTT--EEEEEE-HHHHHHHHHHHHHHHHHHHS-TT--EEEEE--SHHHHHHHHHHCCCS--SEEEEE-S CS
                   OCD_Mu_crystall  86 talvvLndpetGvplalmdatlltalRTaAvsavaakyLarkdasvlaiiGaGvqaetqlealkavldikevriydr 162
                                       +a+ +L++ ++G  + + d+++ltalRT+A+sa++ kyLa+k+   ++iiG G qa+ ql+  +   + +e+ i+d+
  gi|385805825|ref|YP_005842223.1|  85 QAVTLLFNESNGELIGIFDGNILTALRTGAASAISIKYLAPKNTGPIGIIGTGYQAKYQLKFSSLFYKTRELMIFDI 161
                                       ***************************************************************************** PP

                                       SHHHHHHHHHHCCS.CTT-EEECSCHHHHTTSSEEEE----SS-SB-GGGS-TT-EEEE-S--STT--SB-HHHHHC CS
                   OCD_Mu_crystall 163 deeaaekfaenlqefefevsackseeeavegadivvtvTaakapilkaewvkpGahinavgadapgkteLdddilkr 239
                                       +++  + f ++++  +  vs ++s ee v+   +v+ +T++k pi+  ew++   hi  +ga   +++ Ldd+++k+
  gi|385805825|ref|YP_005842223.1| 162 NKNRENEFKTWAESLGYVVSSANSIEELVKSSKVVIEATTTKTPIILGEWLDDDKHIISIGAHSLEERALDDEAIKK 238
                                       *************************************************************************9998 PP

                                       C.EEEE.SHHHHHHHCCCCHCHHHTTSSTCGGEEEEHHHHHCTSS-..-STTSEEEEE----HHHHHHHHHHHHHHH CS
                   OCD_Mu_crystall 240 a.difv.dseaqareeGeiqvaiekgvlaedakvaelgeviaGkkpGRtsdeeitlfdsvGlaveDvaaaklvyera 314
                                         +i+v + +a ++e G+i+ +++kg+l+ ++ ++e+ge+ aGkk+GR+  +eitlf+svGlaveDva+a l+y+ a
  gi|385805825|ref|YP_005842223.1| 239 IgKIVVdSRNATLNEAGDIAEPVKKGILDFED-ITEIGEIAAGKKKGREG-NEITLFKSVGLAVEDVAVALLAYNIA 313
                                       638888556677899*********99987765.79*************86.68*********************999 PP

                                       CCC CS
                   OCD_Mu_crystall 315 eek 317
                                       ++k
  gi|385805825|ref|YP_005842223.1| 314 KSK 316
                                       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 !   17.1   0.0   1.2e-06    0.0043      15      95 ..     131     212 ..     123     217 .. 0.80
   2 ?    1.3   0.0      0.09   3.2e+02      12      71 ..     215     273 ..     212     279 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.2e-06
                                       EEEES-SHHHH..HHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS-S CS
                      Shikimate_DH  15 vlliGaGemae..lvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisataseepi 89 
                                       + +iG+G  a+  l ++ L  k+ ++++++  + +r +e+ +  ++  + + + ++++el++++ vvi at +++pi
  gi|385805825|ref|YP_005842223.1| 131 IGIIGTGYQAKyqLKFSSLFYKT-RELMIFDINKNRENEFKTWAESLGYVVSSANSIEELVKSSKVVIEATTTKTPI 206
                                       67999999887224556777665.55999888888877777777777778*************************** PP

                                       B-HHHH CS
                      Shikimate_DH  90 lekeev 95 
                                       +  e++
  gi|385805825|ref|YP_005842223.1| 207 ILGEWL 212
                                       988776 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.09
                                       T-EEEEES-SHHHHHHHHHHHCCT-CEEEEEES..SHHHHHHHHHHHT.ET-EEEEGCGHHH CS
                      Shikimate_DH  12 ekkvlliGaGemaelvakhLlakgvkkvvvaNR..tlerakelaeelkgeeiealkleelke 71 
                                       +k+++ iGa  + e+++   + k++ k+vv  R  tl+ a ++ae +k+    +l++e+++e
  gi|385805825|ref|YP_005842223.1| 215 DKHIISIGAHSLEERALDDEAIKKIGKIVVDSRnaTLNEAGDIAEPVKKG---ILDFEDITE 273
                                       67788899999999999999999999999987733578999999999777...555555544 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 ?   13.4   0.2     1e-05     0.037      68     139 ..     181     264 ..     173     268 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1e-05
                                       TTSCCHHHHHCCSSEEEE-SS.-TT-B-GGGS-TT-EEEE---EEC...........-TTEEE-SB-HHHHCTTSSE CS
                     THF_DHG_CYH_C  68 sktkdlaeitreadivvvavG.kpelikaemvkegavviDvGinrv...........ekgklvGDvdfeevkevasa 132
                                       s++++++e+++++ +v+ a+  k  +i +e++ ++  +i +G +++           + gk+v D + ++++e   +
  gi|385805825|ref|YP_005842223.1| 181 SSANSIEELVKSSKVVIEATTtKTPIILGEWLDDDKHIISIGAHSLeeralddeaikKIGKIVVDSRNATLNEAGDI 257
                                       667899***********9976266799*******************7777777666555666667666666666666 PP

                                       E--TTTS CS
                     THF_DHG_CYH_C 133 itPvpgG 139
                                         Pv++G
  gi|385805825|ref|YP_005842223.1| 258 AEPVKKG 264
                                       6777766 PP

>> CRF1  Transcription factor CRF1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.74   2.7e+03      48      64 ..      95     111 ..      91     136 .. 0.72
   2 ?   11.7   0.0   6.7e-05      0.24      24     104 ..     191     265 ..     162     277 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.74
                              CRF1  48 dnkpfgiiDGlstkSLq 64 
                                       +  ++gi DG    +L 
  gi|385805825|ref|YP_005842223.1|  95 NGELIGIFDGNILTALR 111
                                       56789999998777764 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 6.7e-05
                              CRF1  24 katelvssanislkPPvlGtWakednkpfgiiDGlstkSLqekdkedactkgentanngagaqtlnetsesdkdels 100
                                       k  ++v  a+ +  P +lG W + d++ ++i     ++SL e++  d + k+  +    +++ tlne+ +    e+ 
  gi|385805825|ref|YP_005842223.1| 191 KSSKVVIEATTTKTPIILGEWLDDDKHIISI----GAHSLEERALDDEAIKKIGKIVVDSRNATLNEAGD--IAEPV 261
                                       33445555555588999*************9....46788777666666666666666666777777665..44444 PP

                              CRF1 101 Lddl 104
                                        + +
  gi|385805825|ref|YP_005842223.1| 262 KKGI 265
                                       4444 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 ?   12.1   0.0     6e-05      0.22       2      96 ..     131     223 ..     130     224 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6e-05
                                       EEEETTSHHHHHHHHHHHHTTS-GGCEEE..EEESSCCCHHHHHHHHC.-EEECECHHHHHHH-SEEEE-S-HHHHH CS
                     F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivv..ansrnpekaeelaeelg.vkvtavdneeaaeeadvvvlavkpedve 75 
                                       igiiG+G +++  ++ +++  ++ +e+++  +n++ +++ + +ae+lg v  +a + ee++++++vv+ a  +++++
  gi|385805825|ref|YP_005842223.1| 131 IGIIGTGYQAKYQLK-FSSLFYKTRELMIfdINKNRENEFKTWAESLGyVVSSANSIEELVKSSKVVIEAT-TTKTP 205
                                       9*********98877.5555336677776446788888899999999964444457889999777777765.66788 PP

                                       HHHHHCGHHHHTTSEEEEESS CS
                     F420_oxidored  76 evlselakdalkgklvisvla 96 
                                        +l e+   ++ +k +is+ a
  gi|385805825|ref|YP_005842223.1| 206 IILGEW---LDDDKHIISIGA 223
                                       999999...888999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); 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: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1884.53
//
Query:       gi|385805826|ref|YP_005842224.1|  [L=208]
Description: translin family, DNA-binding protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-12   46.5   0.1    1.2e-10   41.7   0.1    2.1  1  Translin  Translin family
     0.0079   16.4   3.9       0.57   10.4   0.2    3.7  4  PPR_2     PPR repeat family
  ------ inclusion threshold ------
      0.051   12.6   0.0      0.087   11.8   0.0    1.4  1  Paf67     RNA polymerase I-associated factor PAF67
      0.056   13.0   0.1      0.075   12.6   0.1    1.2  1  YycI      YycH protein
        1.5    9.3   4.4         21    5.7   0.2    3.8  4  PPR       PPR repeat


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 !   41.7   0.1   3.3e-14   1.2e-10       2     188 ..      22     179 ..      21     187 .. 0.88

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 3.3e-14
                                       HHHHHHHHHHHHHHHHHHHHHHHHTTGSSTTTHHHHHHH.HHHHHHHHHHHTTSS..........GHHHHGGGTH.H CS
                          Translin   2 rreriikasrditaaskkiifllhrvrsekteaqdkkakikkeakeklkeiakllasvaeelqgsnayrYqrqisgg 78 
                                       +re++i +srd+ ++s ++i+l+++ +         k   ++e+ +k+ke+ +++    +el++ +   Y+    + 
  gi|385805826|ref|YP_005842224.1|  22 EREKLIVISRDVIRLSGNAIVLIEKGD--------FKG--AEENINKMKELVEVF---LSELKNFPELYYSGIAYNM 85 
                                       69*********************9966........222..368889999999999...9999999999********* PP

                                       HHHHHHHHHHHHHHHHSS---HHHHHHHTT.---SSSSSS---HHHHHHHHHHHHHHHHHHHHHHHCTT--S.HHHH CS
                          Translin  79 lqeliealsfahYletqtLitleevqkilealkeneedafhltpedYllGlfdLtgELmRfainsvalgdkeekplq 155
                                       l e+ ea+++ h ++++++i+++e++               ++p  YllGl d++gE+ R+ i  + ++d+e ++ +
  gi|385805826|ref|YP_005842224.1|  86 LTEYAEAILLFHIMNENNIISYKEMN---------------ISPVPYLLGLGDVIGEIRRVIIDMIRKEDFE-NAWK 146
                                       **********************9865...............45667************************99.9*** PP

                                       HHHHHHHHHHHHHTS----HH....HHHHHTTHH CS
                          Translin 156 ilkflrelragfellnlknds.akdlrkKldvlk 188
                                         + ++e++ +++ ++ + d+    lr+K+d+ +
  gi|385805826|ref|YP_005842224.1| 147 LFEIMEEVFFQLSNMDYP-DAlVPGLRHKVDTAR 179
                                       ********9999988888.443558999999876 PP

>> PPR_2  PPR repeat family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       2.5     9e+03      10      20 ..      12      22 ..      12      23 .. 0.85
   2 ?    2.8   0.0     0.038   1.3e+02      13      31 ..      43      61 ..      40      63 .. 0.91
   3 ?    1.8   0.0     0.077   2.8e+02      19      34 ..      89     104 ..      82     111 .. 0.88
   4 !   10.4   0.2   0.00016      0.57      14      31 ..     136     153 ..     131     157 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.5
                             PPR_2 10 Isglckkgkve 20
                                      I g++ ++++e
  gi|385805826|ref|YP_005842224.1| 12 IRGYLDERDME 22
                                      78999999987 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.038
                             PPR_2 13 lckkgkveeAfklfneMkk 31
                                      l +kg+++ A +  n+Mk+
  gi|385805826|ref|YP_005842224.1| 43 LIEKGDFKGAEENINKMKE 61
                                      5789*************97 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.077
                             PPR_2  19 veeAfklfneMkkrgl 34 
                                       + eA+ lf+ M ++++
  gi|385805826|ref|YP_005842224.1|  89 YAEAILLFHIMNENNI 104
                                       6799********9987 PP

  == domain 4  score: 10.4 bits;  conditional E-value: 0.00016
                             PPR_2  14 ckkgkveeAfklfneMkk 31 
                                        +k+++e A+klf+ M++
  gi|385805826|ref|YP_005842224.1| 136 IRKEDFENAWKLFEIMEE 153
                                       689*************85 PP

>> Paf67  RNA polymerase I-associated factor PAF67
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.4e-05     0.087     165     188 ..      74      97 ..      40     109 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.4e-05
                             Paf67 165 sllYyvGfaylmlrrYkDAirtls 188
                                         lYy G+ay ml +Y++Ai +++
  gi|385805826|ref|YP_005842224.1|  74 PELYYSGIAYNMLTEYAEAILLFH 97 
                                       458*****************9885 PP

>> YycI  YycH protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   2.1e-05     0.075     106     180 ..      68     142 ..      43     151 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.1e-05
                                       EEETTTTEEEEEEEETTEEBE-G-SSEEEEEEETTTEEEEEEEE-EEEEEEE.EEEEB--HH.HHHHHHHHTT-S- CS
                              YycI 106 kelsskkkivykQkykgkpiyeneqaqlvlelnndneivsYkqtylekikelrekkelisar.eAvetLyennelk 180
                                       +el++  +++y+    +  +    +a l +++ n+n i+sYk++ ++ +  l    ++i ++ ++++ + ++++++
  gi|385805826|ref|YP_005842224.1|  68 SELKNFPELYYSGIAYNMLTE-YAEAILLFHIMNENNIISYKEMNISPVPYLLGLGDVIGEIrRVIIDMIRKEDFE 142
                                       455566677777776666666.899**********************99999888888877415666666666655 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0         3   1.1e+04       7      17 ..      12      22 ..      12      23 .. 0.78
   2 ?    0.3   0.1       0.3   1.1e+03      12      28 ..      45      61 ..      42      62 .. 0.84
   3 ?    2.0   0.0     0.086   3.1e+02      16      31 .]      89     104 ..      82     104 .. 0.85
   4 ?    5.7   0.2    0.0058        21      12      28 ..     137     153 ..     131     154 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3
                               PPR  7 IsgycknGkle 17
                                      I+gy  ++++e
  gi|385805826|ref|YP_005842224.1| 12 IRGYLDERDME 22
                                      78998888877 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.3
                               PPR 12 knGkleeAlelfkeMke 28
                                       +G+++ A+e +++Mke
  gi|385805826|ref|YP_005842224.1| 45 EKGDFKGAEENINKMKE 61
                                      57999999999999997 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.086
                               PPR  16 leeAlelfkeMkekGi 31 
                                       + eA+ lf+ M e++i
  gi|385805826|ref|YP_005842224.1|  89 YAEAILLFHIMNENNI 104
                                       569********99986 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.0058
                               PPR  12 knGkleeAlelfkeMke 28 
                                       ++ ++e A +lf+ M+e
  gi|385805826|ref|YP_005842224.1| 137 RKEDFENAWKLFEIMEE 153
                                       7889***********87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       804  (0.0448435); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1279.48
//
Query:       gi|385805827|ref|YP_005842225.1|  [L=148]
Description: metal-binding protein [Fervidicoccus fontis Kam940]
Scores for 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-31  106.1   0.4    1.2e-30  105.8   0.4    1.1  1  CGGC      CGGC domain


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 !  105.8   0.4   6.7e-35   1.2e-30       1     106 []       6     109 ..       6     109 .. 0.98

  Alignments for each domain:
  == domain 1  score: 105.8 bits;  conditional E-value: 6.7e-35
                              CGGC   1 kiaiirCekvedvCpgvkClkalkerkgaFeeye.eevelvgfvtCggCpgkkvveklkelkkegvdvihlssCikt 76 
                                       ki+ii C+++++ C+g kC++al+er g F+ y+ +eve+vg++tCggCpg +++   +e+kk+g++vih+++ +  
  gi|385805827|ref|YP_005842225.1|   6 KIGIIICDRYKN-CAGGKCFRALRERVGGFSIYKdKEVEVVGYTTCGGCPGGNIEYAPEEMKKNGATVIHFATGMV- 80 
                                       8*********99.*************************************************************83. PP

                              CGGC  77 kkakkeCpeieeikeaieeklgievvegth 106
                                          +++Cp+i+++k+ ieek++++vv gth
  gi|385805827|ref|YP_005842225.1|  81 -VGYPPCPYIQYFKKYIEEKYNMKVVIGTH 109
                                       .5799************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 918.67
//
Query:       gi|385805828|ref|YP_005842226.1|  [L=43]
Description: hypothetical protein FFONT_0786 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 291.40
//
Query:       gi|385805829|ref|YP_005842227.1|  [L=345]
Description: transcriptional regulator of molybdate metabolism, LysR family [Fervidicoccus fontis Kam940]
Scores for complete 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-31  107.4   0.0    6.6e-31  106.9   0.0    1.1  1  PBP_like  PBP superfamily domain
    2.1e-05   24.4   0.0    3.9e-05   23.5   0.0    1.4  1  HTH_1     Bacterial regulatory helix-turn-helix protein, lysR


Domain annotation for each model (and alignments):
>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.9   0.0   7.4e-35   6.6e-31      10     192 ..     141     328 ..     136     329 .. 0.90

  Alignments for each domain:
  == domain 1  score: 106.9 bits;  conditional E-value: 7.4e-35
                                       TCEEEEEES-HHHHHHHHHTTS-SEEEESS---CCCHHCCCCCEEEEEEEEEEEE-CC-HCHCCCCHCCHHHS--BG CS
                          PBP_like  10 gvrvavanvGsggGlkalrageadiagshlldketeeynapalrkaldgievvlvnlarreqglvvakgnpkkitnw 86 
                                       g+++    +Gsg  l++l+ ++adia +hl+d+ t++yn +++++   + +v  +  ++re  + ++++ p+    +
  gi|385805829|ref|YP_005842227.1| 141 GCKIDDLIIGSGLSLAMLALEKADIACMHLYDPITDDYNKSFIERFWLKDRVEKIISFKRELVFAYRRDLPH--MEL 215
                                       666777789*************************************99999999999999999999999886..455 PP

                                       GGC....-S-B-EEEEE-TTSHHHHHHHHHHC-C..EECT....E-SSTTSEEESSHHHHHCCHCCETTCCECCCGG CS
                          PBP_like  87 kdl....adaplrlvnRetGSGtrdlfdellkke..gisk....ssikgyaqearshlavaaaVaagradvgvgiea 153
                                       kd+     + +l l+nR++GSGtrdl+d llk+e  +       +++ gy++e+++ +++ +++++g++d+g++++ 
  gi|385805829|ref|YP_005842227.1| 216 KDIihklLNGELKLINRNRGSGTRDLLDLLLKEEakH--LnkevEKVVGYESEYQTDDEIIKMISSGKGDIGLTLRY 290
                                       555444499**********************887443..15588********************************* PP

                                       -HCCCCCCECTTCE-EEEEEEEECTCCCSHHHHHHHHHH CS
                          PBP_like 154 vaeelkgldfvplaeerydlvvrkealddpevqaflefl 192
                                        ae+ ++l+++ +++e y+    k+ ++++ev ++ +++
  gi|385805829|ref|YP_005842227.1| 291 LAEK-HNLKYTHVKWETYECFSLKNIANKEEVSKLKDIY 328
                                       **98.8****************************98876 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 !   23.5   0.0   4.3e-09   3.9e-05       6      59 ..      29      87 ..      26      88 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 4.3e-09
                                      HHHHHHHHSSHHHHHHHHTS-HHHHHHHHHHHHHHHTS-SEEESSSE.....EEE-HHH CS
                             HTH_1  6 lfvavaeegsftrAAeeLglsqpavsrqikrLEeelgvpLfeRtgrg.....lrLTeaG 59
                                      +++a+ +e+s+    ++Lg+ ++ v+  i r E+  g + ++ +++g     ++LT+ G
  gi|385805829|ref|YP_005842227.1| 29 ILKAIEREESMISVSKKLGIPYSRVWELIVRIERVTGKKVVITQKGGkrggkTKLTDFG 87
                                      699***************************************6554334567*****99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 2116.05
//
Query:       gi|385805830|ref|YP_005842228.1|  [L=379]
Description: pyridoxal-5'-phosphate-dependent protein subunit beta [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-11   44.8   0.0    3.9e-05   23.2   0.0    2.7  2  PALP      Pyridoxal-phosphate dependent enzyme
  ------ inclusion threshold ------
      0.042   13.8   0.2        0.1   12.6   0.2    1.7  1  PadR      Transcriptional regulator PadR-like family
      0.045   13.7   0.4        4.5    7.3   0.1    2.7  2  HTH_11    HTH 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 !   23.2   0.0   6.6e-09   3.9e-05       2     101 ..      66     160 ..      65     165 .. 0.80
   2 !   19.3   0.0     1e-07   0.00062     128     202 ..     168     247 ..     140     360 .. 0.70

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 6.6e-09
                                       GGCSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHH. CS
                              PALP   2 tlgigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaall. 77 
                                       t g+g TPl+r           ++lKlE++nptg + dRg + l +  k  ++++  +   s + ++++A +     
  gi|385805830|ref|YP_005842228.1|  66 TRGEGFTPLRRWSEKD------IYLKLEGFNPTGTYMDRGSSVLASFFKTYKPNDSAIIRYSKDFAISAATYLTPSh 136
                                       789999***8888865......*************************888889999999999999999999988763 PP

                                       T-EEEEEEETTS-HHHHHHHHHTT CS
                              PALP  78 GlkvtivvpadaspekvallrllG 101
                                         kv+i  p +a pe +  l  l+
  gi|385805830|ref|YP_005842228.1| 137 RTKVVIEDPLKADPEELTSLVYLN 160
                                       456666666666666665555555 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 1e-07
                                       CEE--TTTSHHHHHHHHTHHHHHHHHTTTTEEEEEEE-SSSHHHHHHHHHHHH...HSTT....-EEEEEEEC.TTC CS
                              PALP 128 aylvsqfdnptviegygtiglEileqlggkpdavvvpvGgGgliaGiaaglke...rrpd....vrvigvepe.gsd 196
                                       +  + ++dnp+ ieg +ti +Ei+e  g     ++vp  +G l+  i++g+k+   +  +     ++i++  e + +
  gi|385805830|ref|YP_005842228.1| 168 YREAISYDNPLTIEGLKTIIFEIVE-RGITEGKILVPSESGVLALSIWKGIKDlekA--NfetnFKIIAAVLEdNYP 241
                                       55566899***************64.4434446********************7552..144346666442222344 PP

                                       GGTTCC CS
                              PALP 197 alarsl 202
                                       ++ + +
  gi|385805830|ref|YP_005842228.1| 242 SYLKNI 247
                                       444444 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   1.7e-05       0.1       8      62 ..     326     374 ..     318     376 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.7e-05
                                       S-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEE CS
                              PadR   8 qpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprky 62 
                                       + +  yei +el+e ++    l    +Y+aL++Le+eg+v s  e  ++++ rky
  gi|385805830|ref|YP_005842228.1| 326 KGMTAYEIWRELKEKYT----L--RGIYKALESLEAEGIVISFFEMRKNKKVRKY 374
                                       66778889999988854....2..259****************999999999997 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.011        64      32      47 ..     213     232 ..     212     234 .. 0.81
   2 ?    7.3   0.1   0.00076       4.5       4      46 ..     317     360 ..     314     361 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.011
                            HTH_11  32 vrrdIkaLeelg....vpIe 47 
                                       +++ Ik+Le++     ++I+
  gi|385805830|ref|YP_005842228.1| 213 IWKGIKDLEKANfetnFKII 232
                                       9********99967776666 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00076
                            HTH_11   4 qilelLleargpisgeeLAeeLnv..SrrtvrrdIkaLeelgvpI 46 
                                       +i + L e ++ +++ e+ +eL+   + r +++ +++Le+ g+ I
  gi|385805830|ref|YP_005842228.1| 317 DIAKAL-EGKKGMTAYEIWRELKEkyTLRGIYKALESLEAEGIVI 360
                                       677778.77777999999999986669***************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.30s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 2244.57
//
Query:       gi|385805831|ref|YP_005842229.1|  [L=371]
Description: peptidase M29, aminopeptidase II [Fervidicoccus fontis Kam940]
Scores for complete 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-89  301.0   0.0    1.4e-89  300.7   0.0    1.0  1  Peptidase_M29   Thermophilic metalloprotease (M29)
  ------ inclusion threshold ------
      0.044   13.1   0.0      0.068   12.5   0.0    1.2  1  Glyco_hydro_62  Glycosyl hydrolase family 62


Domain annotation for each model (and alignments):
>> Peptidase_M29  Thermophilic metalloprotease (M29)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  300.7   0.0   1.6e-93   1.4e-89       6     406 .]       9     366 ..       5     366 .. 0.98

  Alignments for each domain:
  == domain 1  score: 300.7 bits;  conditional E-value: 1.6e-93
                                       HHHHHHHHHTTT---TT-EEEEEEETT-HHHHHHHHHHHHHTT-SEEEEEEE-HHHHHHHHHHS-TT-TT---HHHH CS
                     Peptidase_M29   6 ekyAellvkvglnlqkgqevvinaevealelarlvaeeaykagakkvvvewsdeeltkerlknaseeqleevpewea 82 
                                       ek+A llv++++ +++  e+ ++ +++a++l+++++++++++g  + +v +++eel++ ++++as+e le+v++++ 
  gi|385805831|ref|YP_005842229.1|   9 EKFALLLVDYCIGVKRLSEIQVSGTINAMPLINELFKKIVDRGGYPRIV-ITNEELSEYFYRYASKELLEYVSPID- 83 
                                       79********************************************999.**************************. PP

                                       HHHHHHHHTT-EEEEEE--.-GGGSTTS-HHHHHHHHHHHHHHHHHHHHHHHTTSS-B-BEE---TTTHHHH---S- CS
                     Peptidase_M29  83 ekleelveegaarlsilae.dpkllkgvdpekiaaaqkarskalkeyreriasgklrWcvvavPteawAkkvfpdle 158
                                          ++++e+ + +++ila+ + k+l gvdpe+i+ a+ a + +++++ +r a g+l+W+++ +Pt+a+A+      e
  gi|385805831|ref|YP_005842229.1|  84 ---KYVMENINGLIRILAPsHSKHLIGVDPERIKIATLAGKVISDIMLKRDAMGTLKWTITVYPTNAMAQ------E 151
                                       ...*******************************************************************......* PP

                                       HHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHTT-SEEEEE.ETTEEEEEEE-TTB--EESS---S CS
                     Peptidase_M29 159 aeealeklwdaifkavrldeedpvaaWeehnaelekrakyLnelkfkeLhyksspgtdLtvglaeghiWiggaektk 235
                                       a+ +  ++ +++++a+ l ++dp+++W+++   +ek++k Ln+  ++eL + s+ +t+L +++ +g++Wi+ ++k+ 
  gi|385805831|ref|YP_005842229.1| 152 AGFSPIEWKNFVYSALKLYSSDPIEEWKKQALMQEKITKLLNK--VDELLVLSD-DTELFMKF-AGRTWISDDGKN- 223
                                       *******************************************..*******66.********.9**********9. PP

                                       SS----SBSS---EEE-EEEEEEEEEEE-SS-EEETTEEEBS-EEEEETTEEEEEE-SB-HHHHHHHTTSSSGGGSE CS
                     Peptidase_M29 236 kgiefvaNiPteevftaPdkrgvnGvvratkPlsysGnliegirltFedGkvveakAekGeevLkklletDegarrL 312
                                              N+P +evf+aP +++++G++++t+P++++G ++e+++l+F+ G+++ea+A+kGe++Lkk+++tDeg++r+
  gi|385805831|ref|YP_005842229.1| 224 -------NMPGGEVFSAPIEDSIEGYITFTYPAIWKGVEVENVKLKFKSGTIIEANASKGEDFLKKMISTDEGSKRV 293
                                       .......********************************************************************** PP

                                       EEEE---TTSHHHHHT-----HHHHHT..TS-EEEEE---GGGB--..-----SHHHHT----S-EEEEE---TT-E CS
                     Peptidase_M29 313 GEvALvpndspisqsgilfyntLfDen..ascHlAlGaaypecleggeelteeelkaaglNdSlihvDfmigsedld 387
                                       GE+A++ n+  i++   +++++LfDe+  +++H+AlGaay ++              +g N+S ih+D +++++++ 
  gi|385805831|ref|YP_005842229.1| 294 GEFAFGLNY-DITR---FTKEILFDEKigGTIHMALGAAYLQT--------------GGKNTSSIHWD-IVKDMRK- 350
                                       *********.****...**************************..............9**********.9****99. PP

                                       EEEE-TTS-EEEEEETTEE CS
                     Peptidase_M29 388 idgitedgkevpifrnGef 406
                                         gi + +k ++i++nG+f
  gi|385805831|ref|YP_005842229.1| 351 --GIIKADK-EKIYENGRF 366
                                       ..7776655.89*****98 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 ?   12.5   0.0   7.6e-06     0.068     106     220 ..     171     285 ..     156     295 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.6e-06
                    Glyco_hydro_62 106 ssdptnangwsaeqalfsgkisdsstgaidqtvigddknmylffagdn..gkiyrssmpidn.fpgsfgsqsevils 179
                                       ssdp +   w  +qal+  ki++    + +  v++dd+++++ fag        +  mp ++ f + +  + e  ++
  gi|385805831|ref|YP_005842229.1| 171 SSDPIE--EWK-KQALMQEKITKLLNKVDELLVLSDDTELFMKFAGRTwiSDDGKNNMPGGEvFSAPIEDSIEGYIT 244
                                       677765..574.79********999888888999***********95411223346677654366777788888899 PP

                    Glyco_hydro_62 180 dttenlfeavqvytvdgqnkylmivealgangkryfrsfta 220
                                        t   +++ v+v +v+ + k   i+ea  ++g+ +++ + +
  gi|385805831|ref|YP_005842229.1| 245 FTYPAIWKGVEVENVKLKFKSGTIIEANASKGEDFLKKMIS 285
                                       9999****************************999987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); 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: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2356.78
//
Query:       gi|385805832|ref|YP_005842230.1|  [L=54]
Description: hypothetical protein FFONT_0790 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       419  (0.02337); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.48
# Mc/sec: 335.35
//
Query:       gi|385805833|ref|YP_005842231.1|  [L=292]
Description: cation efflux family protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      6e-41  140.4  14.5      7e-41  140.2  14.5    1.1  1  Cation_efflux  Cation efflux family
    9.1e-22   77.0   1.8    1.6e-21   76.2   1.8    1.4  1  ZT_dimer       Dimerisation domain of Zinc Transporter
  ------ inclusion threshold ------
        2.5    8.4  14.2       0.42   10.9   5.6    2.8  2  DUF996         Protein of unknown function (DUF996)


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 !  140.2  14.5   1.2e-44     7e-41       2     192 ..      16     204 ..      15     211 .. 0.95

  Alignments for each domain:
  == domain 1  score: 140.2 bits;  conditional E-value: 1.2e-44
                     Cation_efflux   2 ilsllanlilalvelivglltnSlalladafhslsdlvsllllllalklsrkppderfpfGygrlevlgalvsglll 78 
                                       ++s+++n++l+++ li+g+l nS al+ da h lsd++++l +l+  k+++kppd+++pfG+gr+  lg++  g++l
  gi|385805833|ref|YP_005842231.1|  16 VVSIIINVALWVIRLIAGILLNSIALITDAWHGLSDALTSLGVLIFSKIASKPPDKEHPFGHGRAADLGSFLIGIML 92 
                                       689************************************************************************** PP

                     Cation_efflux  79 lglavfllleaiqkli.kegereihaglalvvalvslvvnlalllilrragrklrsaalkaaalhvlgDaltslgvl 154
                                       ++++++ l+++iq l+ + +    + gl l+v+++ ++++++ +l+  + g+ ++s + k++alh+  Dal +++v+
  gi|385805833|ref|YP_005842231.1|  93 FIIGFYFLYDGIQGLMtEREIVYSYLGLSLIVTVITIFIKIFNYLYAQKLGKDYNSNLCKTDALHHKLDALVTAVVV 169
                                       ****************6666667788999************************************************ PP

                     Cation_efflux 155 vsalvillfnlksgplaDpvaslligliilysalkllk 192
                                       v+++  ++fn +     D++++++++ +i+y + +++ 
  gi|385805833|ref|YP_005842231.1| 170 VGLSMYYFFNIPK---MDSILTIFVSSLIIYEGGETVY 204
                                       ************9...****************998765 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 !   76.2   1.8   2.7e-25   1.6e-21       3      78 ..     216     291 ..     215     292 .] 0.97

  Alignments for each domain:
  == domain 1  score: 76.2 bits;  conditional E-value: 2.7e-25
                                       ..HHHHHHHHHTT-SS-EEEEEEEEE-S----EEEEEEEE-TTS-HHHHHHHHHHHHHHHHHH-TT--EEEEEEEE CS
                          ZT_dimer   3 eeeeeeireiiksvpgvkgvhdlrtrksGskifvdlhievdgdlsvkeaHeiadevekrikeefpgvadvliHveP 78 
                                       e++ eei++i+k+ ++++++ d+r+r +Gs+++v+l i +++d+++++aHei+d+ve+++k+++p++ +v iH eP
  gi|385805833|ref|YP_005842231.1| 216 EDISEEIKSILKEFKDIEKISDIRVRSIGSYYYVELNISLKKDMKLSRAHEISDKVEDELKKRIPQILEVHIHEEP 291
                                       56789**********************************************************************9 PP

>> DUF996  Protein of unknown function (DUF996)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.4     0.029   1.7e+02      71      95 ..      16      40 ..       2      66 .. 0.64
   2 ?   10.9   5.6     7e-05      0.42      44     129 ..      88     174 ..      80     180 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.029
                            DUF996 71 lllllvliiayvlliisavflkksy 95
                                      ++++++ ++++v+ +i++++l +++
  gi|385805833|ref|YP_005842231.1| 16 VVSIIINVALWVIRLIAGILLNSIA 40
                                      3445555667777777666665554 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 7e-05
                            DUF996  44 ilalllvlgalatalelpgleeaaslilllllvliiayvlliisavflkksyellgkrtgvklFetagllyfiGaiL 120
                                       i ++l+++g+++ + +++gl +  +++   l + +i++v++i+  +f +  +++lgk ++++l +t +l  ++ a+ 
  gi|385805833|ref|YP_005842231.1|  88 IGIMLFIIGFYFLYDGIQGLMTEREIVYSYLGLSLIVTVITIFIKIFNYLYAQKLGKDYNSNLCKTDALHHKLDALV 164
                                       44566677777777777777777778888888889999**********************************98876 PP

                            DUF996 121 t.ivlvGlii 129
                                       t +v+vGl +
  gi|385805833|ref|YP_005842231.1| 165 TaVVVVGLSM 174
                                       6156699865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1273  (0.0710023); expected 358.6 (0.02)
Passed bias filter:                      593  (0.0330749); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 1728.87
//
Query:       gi|385805834|ref|YP_005842232.1|  [L=238]
Description: hypothetical protein FFONT_0792 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1405.32
//
Query:       gi|385805835|ref|YP_005842233.1|  [L=60]
Description: chromatin protein Cren7 [Fervidicoccus fontis Kam940]
Scores for complete 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-31  106.7   2.6    4.2e-31  106.6   2.6    1.0  1  Cren7     Chromatin protein Cren7
  ------ inclusion threshold ------
      0.091   12.7   0.0        0.1   12.5   0.0    1.0  1  PH_15     PH domain


Domain annotation for each model (and alignments):
>> Cren7  Chromatin protein Cren7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.6   2.6   4.7e-35   4.2e-31       4      58 .]       3      58 ..       1      58 [. 0.98

  Alignments for each domain:
  == domain 1  score: 106.6 bits;  conditional E-value: 4.7e-35
                                      -S-EEEE-T.TS-EEEE--SEEEEESSTTS--EEEEEEE-TTT--EEEEEE-TTS- CS
                             Cren7  4 kkpvkVktp.eGkeleLvPvKvWqLaPkgkkGvkvgLFkdPetgkyfRakvpddyP 58
                                      k+pvkVk++ +Gke+eLvP+KvW+L+P++k+G+k+gLF++Pet++yfRa+vpddyP
  gi|385805835|ref|YP_005842233.1|  3 KRPVKVKDRiTGKEYELVPIKVWKLSPNKKRGIKMGLFQNPETKIYFRARVPDDYP 58
                                      89*****************************************************9 PP

>> PH_15  PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.1e-05       0.1      53      96 ..       9      52 ..       3      57 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.1e-05
                             PH_15 53 gkpliGqtlslnklkklkvvkeekgviivkivtedekkitlrvk 96
                                      + ++ G++++l ++k  k++ ++k  i++ + ++ e+ki +r  
  gi|385805835|ref|YP_005842233.1|  9 KDRITGKEYELVPIKVWKLSPNKKRGIKMGLFQNPETKIYFRAR 52
                                      56899************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 405.84
//
Query:       gi|385805836|ref|YP_005842234.1|  [L=419]
Description: metallophosphoesterase Mre11-like protein [Fervidicoccus fontis Kam940]
Scores for complete 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   51.2   0.3      4e-13   50.3   0.3    1.4  1  Metallophos      Calcineurin-like phosphoesterase
      1e-05   25.8   0.0    6.4e-05   23.2   0.0    2.0  1  Metallophos_2    Calcineurin-like phosphoesterase superfamily
  ------ inclusion threshold ------
      0.021   14.9   0.1       0.04   14.0   0.1    1.4  1  ssDNA_DBD        Non-canonical single-stranded DNA-binding do
      0.081   12.6   0.2        1.2    8.9   0.0    2.6  2  N_formyltrans_C  N-formyltransferase dimerization C-terminal 


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 !   50.3   0.3     9e-17     4e-13       3     202 ..       4     198 ..       2     200 .. 0.70

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 9e-17
                                       EEEEESBTB...TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHH....TSEEEEEC- CS
                       Metallophos   3 ilvigDlHl...algggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvky....pipvylllG 72 
                                       i++ +DlH+    +++   ++l++++d l++e    ++++aGD++dr  +e+ +l+ + +  k     + +v++++G
  gi|385805836|ref|YP_005842234.1|   4 IAHAADLHFghtRRAEDIESSLREMIDILKKE-HLKFLIIAGDVFDRDRPENIILKRFHEIMKDfydsGGRVFAVRG 79 
                                       89******999988888889999999888777.99*************999977777876666678889******** PP

                                       TTSCHHHHHHHHHHHHHHH.HHHHEHHHCEEETSEEEEEETTEEEEEEEESECEEETHHHHHHHHHHHSCHHHHCC. CS
                       Metallophos  73 NHegfeeellnkygylgif.sepwrsdaevfnnlplaslgsgslkvlllhGgspellvsldklgslnleleapepg. 147
                                        H+      + +  ++g+    +  + ++ f nl ++  g+   +++   G+         k+  +++++ ++  + 
  gi|385805836|ref|YP_005842234.1|  80 DHD----TPKAS--KKGNPlDTISTYIGGSFLNLEINLNGNP-AYIIEESGE---------KIFLYSFPFVPKAVRr 140
                                       ***....22222..2222212222333556666666654444.555555555.........6666666666666666 PP

                                       ....HHHHHH..HHHHTTCSEEEEEESSESSCSSSCSCCHHHHHHH.HHHTTESEEEEESSS CS
                       Metallophos 148 ....dewlkd..lekrekadwvivlgHsplyrgsgylfgdealedl.lkkygvdlvisGHtH 202
                                            +++k+  + ++e++   i++gH p++     lf+ e+   l +    + ++  GH H
  gi|385805836|ref|YP_005842234.1| 141 redyLNIFKKieKNAKENGGKSILIGHFPIS----ELFPFEEGYSLsELPDYINYYALGHLH 198
                                       66667888889********************....444444444442223337888888888 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 !   23.2   0.0   1.4e-08   6.4e-05       3     148 ..       4     218 ..       2     242 .. 0.65

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.4e-08
                     Metallophos_2   3 laiiSDlH........snldaleavlealkevgvdaiihaGDl.eeeepe..vleellela........pvlaVrGN 60 
                                       +a+ +DlH        +  + l++++++lk++ +  +i aGD+     pe  +l+++ e+         +v aVrG+
  gi|385805836|ref|YP_005842234.1|   4 IAHAADLHfghtrraeDIESSLREMIDILKKEHLKFLIIAGDVfDRDRPEniILKRFHEIMkdfydsggRVFAVRGD 80 
                                       899*****99988776666778888*****************98666664557777777767777778********* PP

                     Metallophos_2  61 nD...............................................eev..veedvlreaaelgtdl.p.eeae 86 
                                       +D                                               +    v ++v r++  l+  + + e+  
  gi|385805836|ref|YP_005842234.1|  81 HDtpkaskkgnpldtistyiggsflnleinlngnpayiieesgekiflyS-FpfVPKAVRRREDYLNI-FkKiEKNA 155
                                       **777777777777777777777777777777776666655554333321.12122222222222222.12223333 PP

                     Metallophos_2  87 lelagekvlliHgdpl..gvkdalaellkeaeegsd..vvvcGHtHvpevekeggvlvvnPGsvge 148
                                        e +g+++l+ H        + +  + l+e   +++  ++++GH H + +ek +  ++ +P s++ 
  gi|385805836|ref|YP_005842234.1| 156 KENGGKSILIGHFP-IseLFPFEEGYSLSE--LPDYinYYALGHLHFRIIEKVKRGILAYPSSIEI 218
                                       33366667777765.346344444444444..4444459999999999999988888888888875 PP

>> ssDNA_DBD  Non-canonical single-stranded DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   8.8e-06      0.04      17      65 ..     335     384 ..     323     409 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8.8e-06
                                       HHHHT-GGGGGSTHHH.HHHHHHHHHHH-HHHHHHHGGGCHHHHH----- CS
                         ssDNA_DBD  17 aselqlpelsqtkLae.NLlLLllKynESpkLseqfqleYqelleerkqe 65 
                                        +e++  ++  ++L + NL+LLll  +E ++ s+ f+ e +e+l++  q+
  gi|385805836|ref|YP_005842234.1| 335 RKESESVDIITSRLGDkNLALLLLELKECAIESKDFEKECNEILNSLFQN 384
                                       55555566788888655*************************99887665 PP

>> N_formyltrans_C  N-formyltransferase dimerization C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.12   5.4e+02      15      23 ..      24      32 ..      20      34 .. 0.85
   2 ?    8.9   0.0   0.00026       1.2      32      46 ..     114     128 ..     112     129 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.12
                                      EHHHHHHHH CS
                   N_formyltrans_C 15 tlrElidlL 23
                                      +lrE+id+L
  gi|385805836|ref|YP_005842234.1| 24 SLREMIDIL 32
                                      79******9 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00026
                                       --EEEE-TTS-EEEE CS
                   N_formyltrans_C  32 knAyfiddtGekvFv 46 
                                       ++Ay+i++ Gek+F 
  gi|385805836|ref|YP_005842234.1| 114 NPAYIIEESGEKIFL 128
                                       79************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       863  (0.0481343); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 2758.81
//
Query:       gi|385805837|ref|YP_005842235.1|  [L=930]
Description: Rad50 zinc hook domain protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.1e-19   69.3  26.8    6.1e-19   69.3  26.8    6.6  1  AAA_23          AAA domain
    5.3e-15   56.0  62.1    5.9e-13   49.3  29.5    4.1  3  AAA_15          AAA ATPase domain
    1.9e-11   43.6   1.9    1.9e-11   43.6   1.9    8.8  9  Rad50_zn_hook   Rad50 zinc hook motif
    7.4e-10   38.6  51.5    1.2e-08   34.7  51.5    2.9  1  SMC_N           RecF/RecN/SMC N terminal domain
    9.9e-10   38.7  30.9    1.5e-06   28.3   4.6    4.3  4  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
    3.5e-07   30.4   0.0    9.9e-07   28.9   0.0    1.8  1  SbcCD_C         Putative exonuclease SbcCD, C subunit
    1.6e-06   27.7   0.0    3.3e-06   26.8   0.0    1.4  1  AAA_29          P-loop containing region of AAA domain
    1.7e-06   27.2  92.6     0.0065   15.4  18.3    4.5  4  Spc7            Spc7 kinetochore protein
    1.4e-05   25.1  15.1    1.4e-05   25.1  15.1    5.7  3  CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein C
    0.00026   18.7  64.8      0.019   12.5  26.4    3.5  3  DUF3584         Protein of unknown function (DUF3584)
    0.00099   18.7   0.2    0.00099   18.7   0.2    3.9  4  AAA_27          AAA domain
      0.001   19.6   0.0      0.001   19.6   0.0    6.0  3  ABC_tran        ABC transporter
     0.0021   18.5   1.3     0.0084   16.5   0.0    2.8  2  AAA_16          AAA ATPase domain
  ------ inclusion threshold ------
      0.012   15.6   8.3      0.012   15.6   8.3    8.6  9  DHR10           Designed helical repeat protein 10 domain
      0.025   13.3  92.4     0.0078   14.9  22.3    5.0  4  AAA_13          AAA domain
      0.057   13.6   0.1       0.26   11.4   0.0    2.2  1  AAA_33          AAA domain
       0.13   12.1   0.0       0.13   12.1   0.0    4.0  3  MukB            MukB N-terminal
       0.13   12.2   0.1       0.13   12.2   0.1    4.5  6  RsgA_GTPase     RsgA GTPase
       0.17   11.9   3.3       0.45   10.5   0.0    3.0  3  AAA_5           AAA domain (dynein-related subfamily)
       0.36   10.5   2.7        1.1    8.8   2.7    1.9  1  CRPV_capsid     CRPV capsid protein like
       0.53   10.7  31.7       0.11   12.9  10.1    5.7  5  HrpB7           Bacterial type III secretion protein (HrpB7)
       0.77   10.3 119.6      0.024   15.2  18.7    7.6  8  APG6_N          Apg6 coiled-coil region
       0.86    9.7  80.3       0.11   12.6  12.7    6.3  6  ADIP            Afadin- and alpha -actinin-Binding
          3    8.1  74.3      0.037   14.3  14.9    6.7  4  DUF5082         Domain of unknown function (DUF5082)
        3.8    7.5  28.4       0.99    9.4   1.1    5.6  5  Baculo_PEP_C    Baculovirus polyhedron envelope protein, PEP,
        7.3    7.1  33.1         12    6.4   1.3    7.6  8  NPV_P10         Nucleopolyhedrovirus P10 protein


Domain annotation for each model (and alignments):
>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.3  26.8   8.9e-22   6.1e-19       1     200 []      12     290 ..      12     291 .. 0.64

  Alignments for each domain:
  == domain 1  score: 69.3 bits;  conditional E-value: 8.9e-22
                            AAA_23   1 kLkienfrsf.rdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkay.. 74 
                                       ++++enfr + ++++++F+kg+t+++G+NGaGK++i++Ai +aL+ge  r   +          + +++  +k+y  
  gi|385805837|ref|YP_005842235.1|  12 SVTLENFRNYsERTTLNFGKGITVLVGENGAGKSSIVEAILFALTGELLRGTIE--------QARTKDS--KKKYfe 78 
                                       689*******77788*******************************86443322........2222222..223313 PP

                            AAA_23  75 veltfenkdgrytrsiererelskkkgktt..........kkaklellei..deleqfisellgskki........i 131
                                       vel++++ d++    i+  r  +k+ g+             ++ ++l+    +  +++i+ell s+++        +
  gi|385805837|ref|YP_005842235.1|  79 VELELKDRDNTV---IKILRR-RKETGEAEdelricyccdEEKRFKLIARgaNGVNEKIRELLLSDENskekdffkS 151
                                       555555555532...222222.2222222212244444422222223322566677777777777766555555554 PP

                            AAA_23 132 lnlilflgqer........................feefelkdkke............................... 153
                                       + +++++gq++                                  +                               
  gi|385805837|ref|YP_005842235.1| 152 IIRLSIIGQGElinranalqsnsaskldfidiplgL---------Ssfekankklgefsirlenisdlissftykvn 219
                                       455566666666666554444444444444444442.........04444444557788888899999999999999 PP

                            AAA_23 154 ................rleelekeleeledekkllekl........eqekekekeleeleeeleeilkele 200
                                                       +l el++++e++++e + lek+        +  +ekekel++  e+l +  kele
  gi|385805837|ref|YP_005842235.1| 220 dnslsnlcgskkllgkKLSELKNDYEKKKAELESLEKEraiverelKMMEEKEKELNATMENLLSKSKELE 290
                                       9999**************************************99985556666666666666666666654 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.3  29.5   8.5e-16   5.9e-13       3     270 ..      10     336 ..       9     348 .. 0.67
   2 ?   -1.4  16.3       2.1   1.4e+03     172     264 ..     496     582 ..     485     599 .. 0.69
   3 !   21.7  24.6     2e-07   0.00014     103     366 ..     618     903 ..     581     905 .. 0.57

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 8.5e-16
                            AAA_15   3 IkkikikNFRslkd.veidlseeltvliGkNnsGKSsilealdlFlnnk.ekkn....................... 54 
                                       +++++++NFR +++ +++++ + +tvl+G+N++GKSsi+ea+ + l+ +                            
  gi|385805837|ref|YP_005842235.1|  10 LSSVTLENFRNYSErTTLNFGKGITVLVGENGAGKSSIVEAILFALTGElL--Rgtieqartkdskkkyfevelelk 84 
                                       89****************************************555555431..244444555555666666666664 PP

                            AAA_15  55 ............kkvikiekedleifeniseskdikIdvef...........................aek.ekake 91 
                                                                                                           a +  ++k+
  gi|385805837|ref|YP_005842235.1|  85 drdntvikilrrR---------------------------KetgeaedelricyccdeekrfkliargA-NgVNEKI 133
                                       4443333333333...........................03333333333333556666655554423.3577777 PP

                            AAA_15  92 yektlkskekkkadlllkkkesdlk.ktikdkklklkknelsdekisvekkkskkelpkekeeklekekeelkidke 167
                                       +e +l ++++k++d    +++s +  ++i + +l + +n l++++ s + +     l  ++ ek++k+  e++i  e
  gi|385805837|ref|YP_005842235.1| 134 RELLLSDENSKEKD----FFKSIIRlSIIGQGELINRANALQSNSAS-KLDFIDIPLGLSSFEKANKKLGEFSIRLE 205
                                       77777777777776....44444440455555555555555555544.5555677899999**************** PP

                            AAA_15 168 dlkklikkleeslkkee................elknvlksaiiklllisakRnvsd...edsekkssllgklkeki 225
                                       ++ +li+ ++++++ ++                elkn ++++  +l+  +++R + +   +  e+k++ l++++e++
  gi|385805837|ref|YP_005842235.1| 206 NISDLISSFTYKVNDNSlsnlcgskkllgkklsELKNDYEKKKAELESLEKERAIVErelKMMEEKEKELNATMENL 282
                                       *****************************************************999977766677777788888888 PP

                            AAA_15 226 leealqekl....eeelteklkeiqeklkeidkklaeelk.....kilkkkidk 270
                                       l+++++ ++    ++e++  +k +++kl+e +  l+e ++     +++++k++ 
  gi|385805837|ref|YP_005842235.1| 283 LSKSKELEQarskRDEKEARFKLLKNKLEENEARLKELEEktskkDDIINKVQA 336
                                       776544444677744444444444444444444443222233222444444443 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.1
                            AAA_15 172 likkleeslkkeeelknvlksaiiklllisakRnvsdedsekkssllgklkekileealqekleeelteklkeiqek 248
                                       li k+ee       ++n+++++ ++    ++ ++  ++ +e+k+s l+k ++ + +ea     +  ++e++++i+++
  gi|385805837|ref|YP_005842235.1| 496 LIHKFEE------AINNNINEKKRLENELKDLKSTYEKAYESKNSPLMKYLSFLQHEA-----DVLKEEDIEKINSE 561
                                       3443333......346667777777777777777777888888888888888888886.....78889999999999 PP

                            AAA_15 249 lkeidkklaeelk.....kil 264
                                       ++ei+ k++e+++     k++
  gi|385805837|ref|YP_005842235.1| 562 IEEIERKISENEStleimKKI 582
                                       999999998877765333222 PP

  == domain 3  score: 21.7 bits;  conditional E-value: 2e-07
                            AAA_15 103 kadlllkkkesdlkktikdkklklkknelsdekisvekkkskkelpkekeeklekekeelkidkedlkklikklees 179
                                       k  ++++k+ ++  +  +d +++++ + +++ k+ ++++ ++ +l ++k+++ e+ k+e+   k +++         
  gi|385805837|ref|YP_005842235.1| 618 KIVKEYEKLGEEYLSKTNDGNIEISIEAYNKYKKILQEISNSESLLDSKKKDMENIKNEFNSLKLEIE--------- 685
                                       22222222222333333333333333333333333333333333333333333333333333333333......... PP

                            AAA_15 180 lkkeeelknvlksaiiklllisakRnvsdedsekkssll.gklkekileealqekleeelteklkeiqeklkeidkk 255
                                            el+++++s+    +  +++R+  d  ++ +++   ++    i+ + l+++   e +ek+k+ ++ l++id+ 
  gi|385805837|ref|YP_005842235.1| 686 -----ELDKKIESLRSVEEELKKVRSEIDAVEKDIQNKQrENGELVISIDTLKKE-LAEYEEKIKSYESGLRQIDDA 756
                                       .....44444444444444555555544432222222220222222222223332.457788888888888888888 PP

                            AAA_15 256 laeelk.............................kilkkkidkikkfnykgkkneeieik................ 287
                                       +   +k                             +                        +                
  gi|385805837|ref|YP_005842235.1| 757 I---YKlnvllkvrelydkenipkwlrneaiailsN------------------------Emsntlskldltytevd 806
                                       8...55324444555555444444444444444444........................04444444555555555 PP

                            AAA_15 288 .............ddeelplnknGsGvqrllllillileaekk...dekeeknvilliEEPEahLHpqaqkvlikll 348
                                                    +  ++ l++++ G + ++ +++ +++ +        ee  ++l+++EP +hL  +  + l++ +
  gi|385805837|ref|YP_005842235.1| 807 idenlnielidknSARSVLLSQASGGESVAVAIAFVLAMQKVIqkmIAGEEVFDFLILDEPTTHLDDERVRDLVEVF 883
                                       55555566889999999******************999999998787788889************************ PP

                            AAA_15 349 kelandnkt..QviitTHSp 366
                                       + l + +++  Q+ii TH +
  gi|385805837|ref|YP_005842235.1| 884 RTLGERGEGvpQLIIVTHDE 903
                                       ******************86 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 ?   -3.0   0.5       9.7   6.7e+03      22      26 ..     110     114 ..      98     116 .. 0.78
   2 ?   -0.9   0.5       2.2   1.5e+03      31      46 ..     234     249 ..     226     254 .. 0.58
   3 ?    0.4   0.4      0.84   5.8e+02       1      19 [.     408     426 ..     408     428 .. 0.87
   4 ?   -2.3   0.5       6.1   4.2e+03      36      51 ..     441     456 ..     436     457 .. 0.72
   5 !   43.6   1.9   2.8e-14   1.9e-11       2      47 ..     461     506 ..     460     510 .. 0.93
   6 ?    0.9   0.7      0.59   4.1e+02       1      15 [.     558     572 ..     555     590 .. 0.83
   7 ?   -2.2   0.2       5.5   3.8e+03       6      19 ..     647     660 ..     645     661 .. 0.81
   8 ?    1.8   0.7      0.31   2.2e+02       4      19 ..     683     698 ..     680     700 .. 0.86
   9 ?   -2.0   0.6       4.8   3.3e+03       1      15 [.     732     746 ..     732     748 .. 0.71

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 9.7
                                       -TTT- CS
                     Rad50_zn_hook  22 CPlCg 26 
                                       C++C+
  gi|385805837|ref|YP_005842235.1| 110 CYCCD 114
                                       ****7 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.2
                                       HHHHHHHHHHHHHHHH CS
                     Rad50_zn_hook  31 eehrseLikelqskle 46 
                                        ++ seL +++++k  
  gi|385805837|ref|YP_005842235.1| 234 GKKLSELKNDYEKKKA 249
                                       4455666666666655 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.84
                                       HHHHHHHHHHHHHHHTT-S CS
                     Rad50_zn_hook   1 lhqeteelnkkieelkeak 19 
                                       l++ ++e +k++++l +++
  gi|385805837|ref|YP_005842235.1| 408 LEKYENEAKKYLNMLDSNE 426
                                       5778899*********998 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 6.1
                                       HHHHHHHHHHHHHH.. CS
                     Rad50_zn_hook  36 eLikelqsklerlpee 51 
                                       eL ++ ++k+e+l+ +
  gi|385805837|ref|YP_005842235.1| 441 ELKDQFKAKIEDLQRK 456
                                       6777888888888766 PP

  == domain 5  score: 43.6 bits;  conditional E-value: 2.8e-14
                                       HHHHHHHHHHHHHHTT-SEE-TTT--EE-HHHHHHHHHHHHHHHHH CS
                     Rad50_zn_hook   2 hqeteelnkkieelkeakgcCPlCgReldeehrseLikelqskler 47 
                                       ++  + ++++i+e+k a+g+CPlCgRel+eeh+ eLi + ++ +++
  gi|385805837|ref|YP_005842235.1| 461 ESSLKTFKEYINEIKRAEGRCPLCGRELNEEHKVELIHKFEEAINN 506
                                       788999*********************************9998887 PP

  == domain 6  score: 0.9 bits;  conditional E-value: 0.59
                                       HHHHHHHHHHHHHHH CS
                     Rad50_zn_hook   1 lhqeteelnkkieel 15 
                                       +++e+ee+++ki+e 
  gi|385805837|ref|YP_005842235.1| 558 INSEIEEIERKISEN 572
                                       578888888888875 PP

  == domain 7  score: -2.2 bits;  conditional E-value: 5.5
                                       HHHHHHHHHHTT-S CS
                     Rad50_zn_hook   6 eelnkkieelkeak 19 
                                       + ++k++ e+++++
  gi|385805837|ref|YP_005842235.1| 647 NKYKKILQEISNSE 660
                                       57999999999876 PP

  == domain 8  score: 1.8 bits;  conditional E-value: 0.31
                                       HHHHHHHHHHHHTT-S CS
                     Rad50_zn_hook   4 eteelnkkieelkeak 19 
                                       e+eel kkie l +++
  gi|385805837|ref|YP_005842235.1| 683 EIEELDKKIESLRSVE 698
                                       89**********9987 PP

  == domain 9  score: -2.0 bits;  conditional E-value: 4.8
                                       HHHHHHHHHHHHHHH CS
                     Rad50_zn_hook   1 lhqeteelnkkieel 15 
                                       l++e +e+++ki+  
  gi|385805837|ref|YP_005842235.1| 732 LKKELAEYEEKIKSY 746
                                       577888888888765 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 !   34.7  51.5   1.7e-11   1.2e-08       2     213 ..      10     917 ..       9     923 .. 0.95

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 1.7e-11
                                       EEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N   2 lkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkae 78 
                                       l+++++enF++y  ++++l+f k++t++vG+NG+GKs++++AilF L  +    lr +  ++    + + ++ k  e
  gi|385805837|ref|YP_005842235.1|  10 LSSVTLENFRNYS-ERTTLNFGKGITVLVGENGAGKSSIVEAILFALTGE---LLRGTIEQA----RTKDSKKKYFE 78 
                                       7899********7.*********************************843...344433222....23344455556 PP

                                       EEEEEEETTEE..........SSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT.......... CS
                                       xxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......... RF
                             SMC_N  79 veitfdnedkk..........lkiekeevsisrrvkrkgeseykingkevtkkevsellesagiske.......... 135
                                       ve+ +++ d++          + + ++e+ i     ++++ +    g +  +++++ell s + ske          
  gi|385805837|ref|YP_005842235.1|  79 VELELKDRDNTvikilrrrkeTGEAEDELRICYCCDEEKRFKLIARGANGVNEKIRELLLSDENSKEkdffksiirl 155
                                       666666666665666555544567788899999999999999999************99998888889********* PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|385805837|ref|YP_005842235.1| 156 siigqgelinranalqsnsaskldfidiplglssfekankklgefsirlenisdlissftykvndnslsnlcgskkl 232
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|385805837|ref|YP_005842235.1| 233 lgkklselkndyekkkaeleslekeraiverelkmmeekekelnatmenllskskeleqarskrdekearfkllknk 309
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|385805837|ref|YP_005842235.1| 310 leenearlkeleektskkddiinkvqairylllyneakncleyikeiynnykdysaslndlksvqenikqlereeke 386
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|385805837|ref|YP_005842235.1| 387 lernramlvskreqiekikadlekyeneakkylnmldsneadtlkgkdletkivelkdqfkakiedlqrkisfiess 463
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|385805837|ref|YP_005842235.1| 464 lktfkeyineikraegrcplcgrelneehkvelihkfeeainnninekkrlenelkdlkstyekayesknsplmkyl 540
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|385805837|ref|YP_005842235.1| 541 sflqheadvlkeediekinseieeierkisenestleimkkienayrnsesckrnlisigkmlefeqisaenielle 617
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|385805837|ref|YP_005842235.1| 618 kivkeyeklgeeylsktndgnieisieaynkykkilqeisnseslldskkkdmeniknefnslkleieeldkkiesl 694
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|385805837|ref|YP_005842235.1| 695 rsveeelkkvrseidavekdiqnkqrengelvisidtlkkelaeyeekiksyesglrqiddaiyklnvllkvrelyd 771
                                       ***************************************************************************** PP

                                       ........................................................CS-HHHHHHHHHHHHHH.... CS
                                       ........................................................xxxxxxxxxxxxxxxxx.... RF
                             SMC_N 136 ........................................................lLSgGektLvalaLlfA.... 152
                                                                                               + SgGe   va+a+++A    
  gi|385805837|ref|YP_005842235.1| 772 kenipkwlrneaiailsnemsntlskldltytevdidenlnielidknsarsvllsQASGGESVAVAIAFVLAmqkv 848
                                       *******************************************************999***************6666 PP

                                       ....HHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT....SEEEEE-SSHHHCCC-SCEEEEEE CS
                                       ....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 153 ....iqkvkpaplyllDeidaaLDeknvkkvaellkekskn....aQfivislreemlekadklvgvtk 213
                                           i   +   + +lDe   +LD+++v+ ++e++++  ++     Q+i+++++e++ e  d+++ v+k
  gi|385805837|ref|YP_005842235.1| 849 iqkmIAGEEVFDFLILDEPTTHLDDERVRDLVEVFRTLGERgegvPQLIIVTHDEQLKEAGDAIYEVKK 917
                                       44444445566799******************99996655433357*******************9987 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   1.4   6.8e-08   4.7e-05       1      83 [.      33     102 ..      33     241 .. 0.65
   2 ?    0.5   5.6      0.64   4.4e+02      99     234 ..     284     421 ..     252     423 .. 0.80
   3 ?   -0.8   0.7       1.5   1.1e+03      63     135 ..     501     562 ..     452     643 .. 0.61
   4 !   28.3   4.6   2.1e-09   1.5e-06     126     299 ..     652     903 ..     534     906 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 6.8e-08
                            AAA_21   1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglr 77 
                                       ++vl+G Ng+GKS++ +a+ ++              +g    + i+   + +++++ fe e+e+++ ++++++   r
  gi|385805837|ref|YP_005842235.1|  33 ITVLVGENGAGKSSIVEAILFAL-------------TGELLRGTIEQARTKDSKKKYFEVELELKDRDNTVIKILRR 96 
                                       79*****************9984.............56667788888888888888888888877777777777777 PP

                            AAA_21  78 lersqv 83 
                                        ++ + 
  gi|385805837|ref|YP_005842235.1|  97 RKETGE 102
                                       666666 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.64
                            AAA_21  99 lldkrsleeedvfnpeargirggvsvfslkelsvsepndlqfgkaltditsrawsllllldglrke...rigllnif 172
                                        + k+ +  + + + ++ +++ ++   ++ e  ++e +++ ++k+ + ++ +a ++lll ++  +     +  +n+ 
  gi|385805837|ref|YP_005842235.1| 284 SKSKELEQARSKRDEKEARFKLLKNKLEENEARLKELEEKTSKKDDIINKVQAIRYLLLYNEAKNCleyIKEIYNNY 360
                                       555666666677777888888888888888888888888888888888888888888865555444999******** PP

                            AAA_21 173 adyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrergvvflengdgqelpa 234
                                       +dy    + ++ +q+ +++l + e el+ ++++ ++  + +e ++  ++  +en+  + l++
  gi|385805837|ref|YP_005842235.1| 361 KDYSASLNDLKSVQENIKQLEREEKELERNRAMLVSKREQIEKIKA-DLEKYENEAKKYLNM 421
                                       ********************************99999999998888.888888887777765 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.5
                            AAA_21  63 eeflsqgvryryglrlersqveeklssvetllesgllldkrsleeedvfnpeargirggvsvfslkelsvsep 135
                                       ee  +++++ + +l+ e +++           +s++ + ++s++++  ++  +    ++v  ++++e++ se 
  gi|385805837|ref|YP_005842235.1| 501 EEAINNNINEKKRLENELKDL-----------KSTYEKAYESKNSPLMKYLSFLQHEADVLKEEDIEKINSEI 562
                                       333334444444444444444...........44444444444444444433333333333333333333333 PP

  == domain 4  score: 28.3 bits;  conditional E-value: 2.1e-09
                            AAA_21 126 slkelsvsepndlqfgkaltditsrawsllllldglrke...........rigllnifadyfgfakekrllqrlvrs 191
                                        l+e+s se+  + ++k+  +i+++++sl+l+ ++l k+           ++ + +i a +   ++++r  ++lv s
  gi|385805837|ref|YP_005842235.1| 652 ILQEISNSESLLDSKKKDMENIKNEFNSLKLEIEELDKKieslrsveeelKKVRSEIDAVEKDIQNKQRENGELVIS 728
                                       455666777777777888888888888888888888888999999999999999999999999999999******** PP

                            AAA_21 192 lklveielsdlgegeeliasvderlrer................................................. 219
                                       +++   el   +e++++++s  ++++++                                                 
  gi|385805837|ref|YP_005842235.1| 729 IDTLKKELAEYEEKIKSYESGLRQIDDAiyklnvllkvrelydkenipkwlrneaiailsnemsntlskldltytev 805
                                       ***********99999999999999999************************************************* PP

                            AAA_21 220 ......gvvflengdgqelparelSdGtkrllalltallralkkg.........sllliDEpEngLHPkllrrllel 281
                                             ++ + ++++ + + ++++S G   + a++  l+ +             ++l++DEp ++L+ +++r l+e+
  gi|385805837|ref|YP_005842235.1| 806 didenlNIELIDKNSARSVLLSQASGGESVAVAIAFVLAMQKVIQkmiageevfDFLILDEPTTHLDDERVRDLVEV 882
                                       *******************************8777777776666688****************************** PP

                            AAA_21 282 l.kelsr..ngaQviltTHSp 299
                                       +  + +r  +  Q+i++TH+ 
  gi|385805837|ref|YP_005842235.1| 883 FrTLGERgeGVPQLIIVTHDE 903
                                       *64444477799*******95 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   1.4e-09   9.9e-07      26      89 ..     822     884 ..     798     885 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 1.4e-09
                           SbcCD_C  26 lsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                        s   ++ SGGe+ +++++a+++a+  ++++  + e+ +++++LDE    lD+e+++ l+e+++
  gi|385805837|ref|YP_005842235.1| 822 RSVLLSQASGGES-VAVAIAFVLAMQKVIQKMIAGEEVFDFLILDEPTTHLDDERVRDLVEVFR 884
                                       4666799******.*****************864599************************997 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0   4.7e-09   3.3e-06       1      49 [.      10      58 ..      10      63 .. 0.91

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 4.7e-09
                            AAA_29  1 LkrlqlvNWgtfdg.htieidlkgatlltGpsGsGKSTllDAiqalLvpa 49
                                      L+++ l N   +++ +t+++  kg+t+l+G++G+GKS+++ Ai + L+++
  gi|385805837|ref|YP_005842235.1| 10 LSSVTLENFRNYSErTTLNFG-KGITVLVGENGAGKSSIVEAILFALTGE 58
                                      678889999999999999998.88**********************9986 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1  21.0   9.5e-05     0.066     146     261 ..     221     335 ..     212     339 .. 0.84
   2 !   10.3  15.9   0.00034      0.23     141     241 ..     377     476 ..     363     499 .. 0.70
   3 !    7.6  13.3    0.0022       1.5     164     262 ..     499     594 ..     487     598 .. 0.85
   4 !   15.4  18.3   9.5e-06    0.0065     143     268 ..     648     775 ..     644     815 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.5e-05
                              Spc7 146 enlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkel 222
                                       + l++l   k+lL k+ +el++ +++ ++e ++le+e +  +++ +   + +++eL+++ e+l + ++e+e+ + + 
  gi|385805837|ref|YP_005842235.1| 221 NSLSNLCGSKKLLGKKLSELKNDYEKKKAELESLEKERAIVERELKM-MEEKEKELNATMENLLSKSKELEQARSKR 296
                                       56777888888999999999999999999999999998888886665.44578899999999999999999999999 PP

                              Spc7 223 aelqeqleeleekieelkeqkseleeeiaeaervleeck 261
                                       +e++++ + l++k+ee +++ +elee+++++++++++ +
  gi|385805837|ref|YP_005842235.1| 297 DEKEARFKLLKNKLEENEARLKELEEKTSKKDDIINKVQ 335
                                       999999999999999999999999999999999988765 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00034
                              Spc7 141 kegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelael.kaeie 216
                                        ++le++ ++le+ +++L +++e++++++ +le++++e ++ l++l +  +e ++++ ++Le+   el+++ ka+ie
  gi|385805837|ref|YP_005842235.1| 377 IKQLEREEKELERNRAMLVSKREQIEKIKADLEKYENEAKKYLNMLDS--NEADTLKGKDLETKIVELKDQfKAKIE 451
                                       357888888888888888888888888888888888888888888887..445566666666655555544366777 PP

                              Spc7 217 ekkkelaelqeqleeleekieelke 241
                                        ++++++  ++ l++ +e i+e+k 
  gi|385805837|ref|YP_005842235.1| 452 DLQRKISFIESSLKTFKEYINEIKR 476
                                       7777777777777777777777764 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0022
                              Spc7 164 eldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelk 240
                                       +++e+ ++  +ek++le+el++l++ +e+  ++++  L ++ + l+  +a++  k++++++ ++++ee+e ki+e  
  gi|385805837|ref|YP_005842235.1| 499 KFEEAINNNINEKKRLENELKDLKSTYEKAYESKNSPLMKYLSFLQH-EADVL-KEEDIEKINSEIEEIERKISEN- 572
                                       55666666778899***************99*********9998875.55555.699****************998. PP

                              Spc7 241 eqkseleeeiaeaervleeckg 262
                                       e+  e++++i++a r  e ck+
  gi|385805837|ref|YP_005842235.1| 573 ESTLEIMKKIENAYRNSESCKR 594
                                       7888999********9999997 PP

  == domain 4  score: 15.4 bits;  conditional E-value: 9.5e-06
                              Spc7 143 gleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekk 219
                                       +++++l+++ + ++lL+++++ ++++++    e+++l+ e+e+l ++ e+l s+ +eeL+++r+e+++++++i++k+
  gi|385805837|ref|YP_005842235.1| 648 KYKKILQEISNSESLLDSKKKDMENIKN----EFNSLKLEIEELDKKIESLRSV-EEELKKVRSEIDAVEKDIQNKQ 719
                                       6778888888889999888887776655....4555666666666655555554.4678888888888888888888 PP

                              Spc7 220 ke.......laelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesev 268
                                       +e       +++l+++l+e eeki++ ++  +++ ++i + + +l+ ++  +++++
  gi|385805837|ref|YP_005842235.1| 720 REngelvisIDTLKKELAEYEEKIKSYESGLRQIDDAIYKLNVLLKVRELYDKENI 775
                                       77122221145555555555555555555555555555555555555555555555 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2  23.5      0.24   1.7e+02      32     125 ..     229     325 ..     220     339 .. 0.63
   2 ?    2.7  18.5      0.18   1.2e+02      20     113 ..     371     474 ..     354     498 .. 0.73
   3 !   25.1  15.1   2.1e-08   1.4e-05      27     118 ..     650     744 ..     646     765 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.24
                    CENP-F_leu_zip  32 elemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeL...ekelqkkqervseLeslnss 105
                                        ++ +++++++++ + E++kae+e+l++e    ++el+ +e + ++l    e+L    kel++ +++ +e e++   
  gi|385805837|ref|YP_005842235.1| 229 SKKLLGKKLSELKNDYEKKKAELESLEKERAIVERELKMMEEKEKELNATMENLlskSKELEQARSKRDEKEARFKL 305
                                       56677888888999999999999986665555555555554444444444444432245566666666666777777 PP

                    CENP-F_leu_zip 106 lenlleekEqekvqmkeesk 125
                                       l+n lee+E+  ++++e++ 
  gi|385805837|ref|YP_005842235.1| 306 LKNKLEENEARLKELEEKTS 325
                                       77777777776555555543 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.18
                    CENP-F_leu_zip  20 dsLkdkvenLerelemseenqekvil...eaEtskaevetlkeeieelaeelreleldLvalr.......sekeeLe 86 
                                        s+++ +++Lere +++e+n+  ++    + E+ ka +e+ ++e ++  + l   e+d  + +       + k++ +
  gi|385805837|ref|YP_005842235.1| 371 KSVQENIKQLEREEKELERNRAMLVSkreQIEKIKADLEKYENEAKKYLNMLDSNEADTLKGKdletkivELKDQFK 447
                                       47888999999999999999998886333566778888887777766666666666654444455566668899999 PP

                    CENP-F_leu_zip  87 kelqkkqervseLeslnsslenlleek 113
                                        ++++ q+++s  es+  ++++ ++e 
  gi|385805837|ref|YP_005842235.1| 448 AKIEDLQRKISFIESSLKTFKEYINEI 474
                                       9****************9999988764 PP

  == domain 3  score: 25.1 bits;  conditional E-value: 2.1e-08
                    CENP-F_leu_zip  27 enLerelemseenqekvileaEtskaevetlkeeieelaee...lreleldLvalrsekeeLekelqkkqervseLe 100
                                       +++ +e+ +se+ +++ + ++E+ k+e ++lk eieel ++   lr  e +L+++rse + +ek++q+kq++  eL 
  gi|385805837|ref|YP_005842235.1| 650 KKILQEISNSESLLDSKKKDMENIKNEFNSLKLEIEELDKKiesLRSVEEELKKVRSEIDAVEKDIQNKQRENGELV 726
                                       566689999*****************************986222667789*************************** PP

                    CENP-F_leu_zip 101 slnsslenlleekEqekv 118
                                        +  +l++ l e E++ +
  gi|385805837|ref|YP_005842235.1| 727 ISIDTLKKELAEYEEKIK 744
                                       ************998744 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9  10.8   0.00017      0.11     432     534 ..     219     325 ..     192     333 .. 0.74
   2 !   12.5  26.4   2.8e-05     0.019     697     924 ..     367     585 ..     352     627 .. 0.78
   3 !    6.9  12.4    0.0013      0.92     238     369 ..     675     800 ..     614     822 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00017
                           DUF3584 432 leaqkeelneeekelesrlselklrldsatateEeleqieead.ealekaqee...lekaeaevealqaeeeqlrkk 504
                                       +++  ++l   +k l ++lselk   ++ +a+ E le+ ++ + ++l+ ++e+   l++  ++  +  +e+eq+r+k
  gi|385805837|ref|YP_005842235.1| 219 NDNSLSNLCGSKKLLGKKLSELKNDYEKKKAELESLEKERAIVeRELKMMEEKekeLNATMENLLSKSKELEQARSK 295
                                       45556677778888899999999999999999998887766551455555555000444455556678889999999 PP

                           DUF3584 505 rdeadealqkaerrleqlrqaleeleeqls 534
                                       rde + +++  +++le+  ++l+elee  s
  gi|385805837|ref|YP_005842235.1| 296 RDEKEARFKLLKNKLEENEARLKELEEKTS 325
                                       999999999999999999999999998765 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 2.8e-05
                           DUF3584 697 eeqqkaaleelkedlseerlekkakwqevvgeldeqlaelkkaieaartqakarlkeleeaykreLkskdvDpetvk 773
                                       +++ k+++e++k+  +ee+  + +  +++  ++ eq++++k+ +e+ +++ak+ l+ l+ + ++ Lk kd + ++v+
  gi|385805837|ref|YP_005842235.1| 367 LNDLKSVQENIKQLEREEK--ELERNRAMLVSKREQIEKIKADLEKYENEAKKYLNMLDSNEADTLKGKDLETKIVE 441
                                       5677788888887777776..66667777778889*************************************99983 PP

                           DUF3584 774 ...elkrkieeLekkieriekrreevreYraflqetwlkvdslaeerpalkeqveelesaaeeleqeltrliedtkl 847
                                          + k+kie+L++ki+ ie+    ++ ++++++e   +     e r  l  ++ + e+++ el ++ +++i++  +
  gi|385805837|ref|YP_005842235.1| 442 lkdQFKAKIEDLQRKISFIES---SLKTFKEYINEIKRA-----EGRCPLCGRELNEEHKV-ELIHKFEEAINNNIN 509
                                       222556778888888888876...567777778875433.....44555555544445554.67788999999999* PP

                           DUF3584 848 erkklekerkalekqldqldenlrklrdllsklaelkldadaeqaegelaerlaaleelkrkrerlse..dvkkale 922
                                       e k+le+e+k l+   +++ e++    +l+++l++l+ +ad+ ++e ++++ ++ +ee+ rk + ++   ++ k++e
  gi|385805837|ref|YP_005842235.1| 510 EKKRLENELKDLKSTYEKAYESKN--SPLMKYLSFLQHEADVLKEE-DIEKINSEIEEIERKISENEStlEIMKKIE 583
                                       ***********************9..****************9999.9*********99888665554114556666 PP

                           DUF3584 923 rf 924
                                       ++
  gi|385805837|ref|YP_005842235.1| 584 NA 585
                                       55 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0013
                           DUF3584 238 aaiekvrpeieklqeefeqleslelrLsllkgelkadeerlaekqeevqeakaelkqqlrtledelkeaidelnqel 314
                                       +++++ + eie+l +++e+l s+e++L+ +  e+ a e+ +++kq e  e       +++tl++el+e +++ ++  
  gi|385805837|ref|YP_005842235.1| 675 NEFNSLKLEIEELDKKIESLRSVEEELKKVRSEIDAVEKDIQNKQRENGELVI----SIDTLKKELAEYEEKIKSYE 747
                                       24555555555555555555555555555555555555555555555444333....33333333333333333333 PP

                           DUF3584 315 saakaklaakeselealeeqkkkyedadieklkadldqlpsirseleeleeelda 369
                                       s +  +++ + ++l+ l + ++ y++++i+k     +++  +++e++++  +ld+
  gi|385805837|ref|YP_005842235.1| 748 SGL-RQIDDAIYKLNVLLKVRELYDKENIPKWL-RNEAIAILSNEMSNTLSKLDL 800
                                       322.24444555666666677777777777764.346666666777766666665 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.2   1.4e-06   0.00099       4      92 ..      11     101 ..       8     108 .. 0.74
   2 ?   -3.0   3.3       6.6   4.6e+03     158     199 ..     275     319 ..     234     327 .. 0.61
   3 ?   -0.6   0.7       1.2   8.2e+02     154     194 ..     376     415 ..     362     426 .. 0.56
   4 ?   -1.6   0.3       2.5   1.7e+03     156     180 ..     699     723 ..     651     746 .. 0.58

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.4e-06
                            AAA_27   4 erLdLeryGkftdr.sldfsaeeadlhliyGpNEAGKstalrAis.....dllfGipertkdnflhdakkLrigavl 74 
                                       ++ +Le + ++++r +l+f+   +++++++G N AGKs++++Ai      +ll G  e+++ +   ++k  +++  l
  gi|385805837|ref|YP_005842235.1|  11 SSVTLENFRNYSERtTLNFG---KGITVLVGENGAGKSSIVEAILfaltgELLRGTIEQARTK-DSKKKYFEVELEL 83 
                                       56788888888887479998...8*******************97222225555543333332.2356678899999 PP

                            AAA_27  75 eeadgeelefaRrkgrkk 92 
                                       +++d++++++ Rr++++ 
  gi|385805837|ref|YP_005842235.1|  84 KDRDNTVIKILRRRKETG 101
                                       999999999999998765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6.6
                            AAA_27 158 lrevleaLeaeadelfk...prkskkrainealeeleeakkelre 199
                                       l++++e+L ++ +el +   +r +k+++++  +++lee +++l+e
  gi|385805837|ref|YP_005842235.1| 275 LNATMENLLSKSKELEQarsKRDEKEARFKLLKNKLEENEARLKE 319
                                       444444444444433330003333335566666666666666665 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.2
                            AAA_27 154 GlaslrevleaLeaeadelfkprkskkrainealeeleeak 194
                                        +++l++  ++Le+++  l ++r++ + +i++ le++e+  
  gi|385805837|ref|YP_005842235.1| 376 NIKQLEREEKELERNRAMLVSKREQIE-KIKADLEKYENEA 415
                                       344555555555555555555555555.4554444444333 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 2.5
                            AAA_27 156 aslrevleaLeaeadelfkprkskk 180
                                       ++l++v+ +++a  +++ ++++++ 
  gi|385805837|ref|YP_005842235.1| 699 EELKKVRSEIDAVEKDIQNKQRENG 723
                                       3334444444444444444444433 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.5e-06     0.001      13      67 ..      33      87 ..      24     182 .. 0.74
   2 ?   -1.3   3.0       4.1   2.8e+03      51      98 ..     253     302 ..     222     348 .. 0.57
   3 ?   -2.0   2.2         7   4.9e+03      58      93 ..     374     423 ..     342     457 .. 0.53

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.5e-06
                                      EEEEEESTTSSHHHHHHHHTTSS--..SEEEEEETTCEGGGB-HHHCCHCEEEE-SS CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 13 kvaivGenGaGKStLlkllagllkp..teGeilldgkdlkeqeleslrkeigvlpqe 67
                                      ++++vGenGaGKS+++++++  l+     G+i  +++ +k+ +++ ++ e++    +
  gi|385805837|ref|YP_005842235.1| 33 ITVLVGENGAGKSSIVEAILFALTGelLRGTI--EQARTKDSKKKYFEVELELKDRD 87
                                      689**************999887764456777..55555554455555555555544 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 4.1
                                       G..B-HHHCCHCEEEE-SS.--S-TTSBHHHH.......HHHTCHHHHHHHSTTGGTT CS
                                       x..xxxxxxxxxxxxxxxx.xxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  51 e..qeleslrkeigvlpqe.pqlfpeltvren.......esdeeiekalsklglkelk 98 
                                       +  +e+ ++++e+++++++ ++l        n        +++e+e+a+sk + ke +
  gi|385805837|ref|YP_005842235.1| 253 SleKERAIVERELKMMEEKeKEL--------NatmenllSKSKELEQARSKRDEKEAR 302
                                       12234444444444444442222........233344675555555555554444422 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 7
                                       CHCEEEE-SS--S-TTSBHHHH.........................HHHTCHHHHHHHST CS
                                       xxxxxxxxxxxxxxxxxxxxxx.........................xxxxxxxxxxxxxx RF
                          ABC_tran  58 rkeigvlpqepqlfpeltvren.........................esdeeiekalsklg 93 
                                       +++i+ l+ e           +                         ++++e++k+l+ l+
  gi|385805837|ref|YP_005842235.1| 374 QENIKQLERE-----------EkelernramlvskreqiekikadleKYENEAKKYLNMLD 423
                                       2222222222...........0222222344442222222222222344444554444444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.2e-05    0.0084      22      63 ..      28      67 ..      13     148 .. 0.68
   2 ?   -2.6   0.5         9   6.2e+03      60      60 ..     310     310 ..     238     410 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.2e-05
                            AAA_16 22 grp.elvllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                      + + ++++l+Ge G GKss+v+++l al+++   +lrg+ +q 
  gi|385805837|ref|YP_005842235.1| 28 NFGkGITVLVGENGAGKSSIVEAILFALTGE---LLRGTIEQA 67
                                      334599*******************999999...566665555 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 9
                            AAA_16  60 c 60 
                                        
  gi|385805837|ref|YP_005842235.1| 310 L 310
                                       1 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.5       8.3   5.7e+03      48      80 ..      65      97 ..      62     100 .. 0.82
   2 ?    8.8   9.6    0.0023       1.6      57     103 ..     235     281 ..     230     288 .. 0.91
   3 ?    4.0  12.5     0.072        50      35     104 ..     279     327 ..     273     336 .. 0.53
   4 ?   15.6   8.3   1.8e-05     0.012      33     103 ..     344     417 ..     339     422 .. 0.89
   5 ?    7.4   5.1    0.0064       4.4      40     112 ..     399     471 ..     396     476 .. 0.85
   6 ?   -0.1   5.2       1.3     9e+02       8      92 ..     447     530 ..     440     534 .. 0.85
   7 ?   -1.2   6.0       2.9     2e+03       3      37 ..     554     588 ..     552     629 .. 0.71
   8 ?    7.3   2.0    0.0067       4.6      37      84 ..     648     695 ..     639     698 .. 0.88
   9 ?    9.4  12.2    0.0015         1       3      98 ..     669     747 ..     654     759 .. 0.54

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 8.3
                             DHR10 48 elakleeakkklkelrdaleekeielrelerke 80
                                      e+a+++++kkk  e + +l+++ +++ ++ r++
  gi|385805837|ref|YP_005842235.1| 65 EQARTKDSKKKYFEVELELKDRDNTVIKILRRR 97
                                      889999999999999999999999888877776 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0023
                             DHR10  57 kklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqaee 103
                                       kkl+el++ +e+k++el+ le++++ ++r l+++eek   l  ++e+
  gi|385805837|ref|YP_005842235.1| 235 KKLSELKNDYEKKKAELESLEKERAIVERELKMMEEKEKELNATMEN 281
                                       79***********************************9999888876 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.072
                             DHR10  35 lrsciklleeieaelakleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqaeek 104
                                       +++++   +e+e+   k +e +++ k l+++lee+e++l+el                     +e+ ++k
  gi|385805837|ref|YP_005842235.1| 279 MENLLSKSKELEQARSKRDEKEARFKLLKNKLEENEARLKEL---------------------EEKTSKK 327
                                       444444445555555555555555555555555555555555.....................5555555 PP

  == domain 4  score: 15.6 bits;  conditional E-value: 1.8e-05
                             DHR10  33 kdlrsciklleeieaelakleeakkklkelrdaleekeielrelerkeerl...qrqlenaeeklerlreqaee 103
                                       ++ ++c++ ++ei ++ + +  +  +lk+ +++++++e+e +eler++++l   + q+e+ +  le+++++a++
  gi|385805837|ref|YP_005842235.1| 344 NEAKNCLEYIKEIYNNYKDYSASLNDLKSVQENIKQLEREEKELERNRAMLvskREQIEKIKADLEKYENEAKK 417
                                       5789*********************************************9966667888888888888888775 PP

  == domain 5  score: 7.4 bits;  conditional E-value: 0.0064
                             DHR10  40 klleeieaelakleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqaeekreaakarl 112
                                       +++e+i+a+l+k+e + kk  +  d  e  + + ++le+k+  l+ q + + e l+r     e   +  k+ +
  gi|385805837|ref|YP_005842235.1| 399 EQIEKIKADLEKYENEAKKYLNMLDSNEADTLKGKDLETKIVELKDQFKAKIEDLQRKISFIESSLKTFKEYI 471
                                       68999******************************************99999999997776666666655555 PP

  == domain 6  score: -0.1 bits;  conditional E-value: 1.3
                             DHR10   8 keelaelErkarelqakidalqvvekdlrsciklleeieaelakleeakkklkelrdaleekeielrelerkeerlq 84 
                                       k+++++l+rk+  ++ ++++++++ ++++++      + +el+++ ++ + + + ++a++++ +e++ le++ + l+
  gi|385805837|ref|YP_005842235.1| 447 KAKIEDLQRKISFIESSLKTFKEYINEIKRAEGRCPLCGRELNEEHKV-ELIHKFEEAINNNINEKKRLENELKDLK 522
                                       788999999999999999999999999999999999999999876665.5688899999999999999999999998 PP

                             DHR10  85 rqlenaee 92 
                                          e+a e
  gi|385805837|ref|YP_005842235.1| 523 STYEKAYE 530
                                       88888766 PP

  == domain 7  score: -1.2 bits;  conditional E-value: 2.9
                             DHR10   3 slaeekeelaelErkarelqakidalqvvekdlrs 37 
                                       ++++  +e++e Erk+ e + +++ ++++e+  r+
  gi|385805837|ref|YP_005842235.1| 554 DIEKINSEIEEIERKISENESTLEIMKKIENAYRN 588
                                       45566677777777777777777777777766543 PP

  == domain 8  score: 7.3 bits;  conditional E-value: 0.0067
                             DHR10  37 sciklleeieaelakleeakkklkelrdaleekeielrelerkeerlq 84 
                                       +  k+l+ei++    l++ kk+ ++ +++ ++++ e +el++k+e l+
  gi|385805837|ref|YP_005842235.1| 648 KYKKILQEISNSESLLDSKKKDMENIKNEFNSLKLEIEELDKKIESLR 695
                                       556899999999999999999999999999999999999999999885 PP

  == domain 9  score: 9.4 bits;  conditional E-value: 0.0015
                             DHR10   3 slaeekeelaelErkarelqakidalqvvekdlrsciklleeieaelakleeakkklkelrdaleekeielrelerk 79 
                                       + ++ k+e ++l   + el +ki++l  ve++l+++   ++ +e++++                  k++e  el   
  gi|385805837|ref|YP_005842235.1| 669 DMENIKNEFNSLKLEIEELDKKIESLRSVEEELKKVRSEIDAVEKDIQN-----------------KQRENGELVIS 728
                                       3455566666666666666666666666666666666666666666554.................44444444444 PP

                             DHR10  80 eerlqrqlenaeeklerlr 98 
                                       ++ l++ l+  eek+  ++
  gi|385805837|ref|YP_005842235.1| 729 IDTLKKELAEYEEKIKSYE 747
                                       4444444444444444443 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.2      0.11        75      18      39 ..      33      54 ..      16      79 .. 0.73
   2 ?   -0.8  18.7      0.65   4.5e+02     327     460 ..     187     324 ..     160     337 .. 0.71
   3 ?   13.0  55.8   4.3e-05      0.03      92     462 ..     297     693 ..     294     697 .. 0.64
   4 ?   14.9  22.3   1.1e-05    0.0078     277     571 ..     605     903 ..     602     914 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.11
                            AAA_13 18 iNliYGwNGaGKTtLSrllrsl 39
                                      i ++ G NGaGK+++ +++   
  gi|385805837|ref|YP_005842235.1| 33 ITVLVGENGAGKSSIVEAILFA 54
                                      77888*********99888665 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.65
                            AAA_13 327 kaeaealeeqLkglqraleaKrkepfksvelesvkakie....sikklvaeineliakhNekvanlee.ekeeakkk 398
                                        + +e+ +++L + + +le+   ++ +s+++++ ++ ++    s k l +++ el +++ +k a+le+ eke+a ++
  gi|385805837|ref|YP_005842235.1| 187 LSSFEKANKKLGEFSIRLENIS-DLISSFTYKVNDNSLSnlcgSKKLLGKKLSELKNDYEKKKAELESlEKERAIVE 262
                                       5678999999********9976.788889999999988523335566678888888888888888887567788889 PP

                            AAA_13 399 lelhlveeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaa 460
                                        el ++ee e+el++ ++++ + +k++e++  + +e+ea+ k l+++ +e e++l++ ++  
  gi|385805837|ref|YP_005842235.1| 263 RELKMMEEKEKELNATMENLLSKSKELEQARSKRDEKEARFKLLKNKLEENEARLKELEEKT 324
                                       99999999999999988888888888888888888888777777777555555555444333 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 4.3e-05
                            AAA_13  92 iekqekieklkkeikkleekleaaeaqlqkaek..............ekkklekeledeawkkivkkknsalsealk 154
                                        ek+++ + lk+++++ e++l++ e++ +k+++              ++ k + e+ +e++++  k   sa  ++lk
  gi|385805837|ref|YP_005842235.1| 297 DEKEARFKLLKNKLEENEARLKELEEKTSKKDDiinkvqairylllyNEAKNCLEYIKEIYNNY-K-DYSASLNDLK 371
                                       5788888888888888888888888888888888888888888855433344444444444433.2.2223334566 PP

                            AAA_13 155 glkyeekfkerllkelkkknrkaaellsdeelkak....letvesenlpelaplslssidldalek..aeilkkkvv 225
                                       +++++ k+ er  kel+++    a l+s+ e+ +k    le+ e+e++++l+ l  +++d  + +   ++i++ k  
  gi|385805837|ref|YP_005842235.1| 372 SVQENIKQLEREEKELERN---RAMLVSKREQIEKikadLEKYENEAKKYLNMLDSNEADTLKGKDleTKIVELKDQ 445
                                       6666666666666666664...5555554444444222277777777777777655444444444444444444443 PP

                            AAA_13 226 gkdseieeLienld.ladWVkqGlelheas...sdtCpFCgqplpaerkaaLeahFddefeekq...erLekliekv 295
                                          ++ie+L+++ + +++ +k   e++++    ++ Cp Cg++l++e k +L   F+++ ++++   +rLe+ ++++
  gi|385805837|ref|YP_005842235.1| 446 F-KAKIEDLQRKISfIESSLKTFKEYINEIkraEGRCPLCGRELNEEHKVELIHKFEEAINNNInekKRLENELKDL 521
                                       3.499*****9976357788888888886445689***********9999999999888876541115666666666 PP

                            AAA_13 296 eskkselleklkavsde......asensafeedkeelkaeaealeeqLkglqraleaKrkepfksvelesvkakies 366
                                       +s+ +++ e+ +++  +       +++   eed+e++++e+e++e ++ ++++ le  +k   +  + es k ++ s
  gi|385805837|ref|YP_005842235.1| 522 KSTYEKAYESKNSPLMKylsflqHEADVLKEEDIEKINSEIEEIERKISENESTLEIMKKIENAYRNSESCKRNLIS 598
                                       555555555544444433333433344457888********************998655555555567777777755 PP

                            AAA_13 367 ikklv...aeineliakhNekvanleeekeeakkklelhlveeleseldeykkkykklekaieklekelkeeeaelk 440
                                       i k +   +   e+i+   ++v+++e+  ee  +k       ++e  +++y+ kykk+ ++i++ e  l+ ++++++
  gi|385805837|ref|YP_005842235.1| 599 IGKMLefeQISAENIELLEKIVKEYEKLGEEYLSKTND---GNIEISIEAYN-KYKKILQEISNSESLLDSKKKDME 671
                                       55544000444577888888888888888888777777...45556677776.677777777777777777777777 PP

                            AAA_13 441 kleeeikeLekqlrdekpaaee 462
                                       ++++e + L+ ++++  + +e 
  gi|385805837|ref|YP_005842235.1| 672 NIKNEFNSLKLEIEELDKKIES 693
                                       7777777777777766666655 PP

  == domain 4  score: 14.9 bits;  conditional E-value: 1.1e-05
                            AAA_13 277 FddefeekqerLekliekveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfk 353
                                       F++ ++e++e Lek+++++e+  +e+l k +++  e    +++ ++++++ +e+++ e+ L++ ++ +e+ ++e  +
  gi|385805837|ref|YP_005842235.1| 605 FEQISAENIELLEKIVKEYEKLGEEYLSKTNDGNIEI--SIEAYNKYKKILQEISNSESLLDSKKKDMENIKNEFNS 679
                                       777788999***************9999988877754..468999*************************9988888 PP

                            AAA_13 354 .svelesvkaki...esikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeykkkykklekaie 426
                                        ++e+e++++ki    s++++++++   i +  + ++n ++e  e+  ++       l++el ey++k+k+ e  + 
  gi|385805837|ref|YP_005842235.1| 680 lKLEIEELDKKIeslRSVEEELKKVRSEIDAVEKDIQNKQRENGELVISID-----TLKKELAEYEEKIKSYESGLR 751
                                       8999********333355666666666666666666666666666665555.....477888888888888888888 PP

                            AAA_13 427 klekelkeeeaelkkleee.ikeLekqlrdekpaaeeinkeLkafGlgeleLkfeee..kkgYrivrkggsqaa... 497
                                       + ++++ + +  lk +e    +++ k lr+e  a+  + +e+++  l++l L+++e   +++ +i   +++ a    
  gi|385805837|ref|YP_005842235.1| 752 QIDDAIYKLNVLLKVRELYdKENIPKWLRNEAIAI--LSNEMSNT-LSKLDLTYTEVdiDENLNIELIDKNSARsvl 825
                                       88888887777776665432666777788775555..66777777.7777777777666555555444443343113 PP

                            AAA_13 498 .etLSeGEktaIaflYFlkslkeddseigkdki...vviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHn 570
                                         + S GE  a+a+ + l+  k  ++ i  +++    ++D P   LD++ +   +   ++   + + + Ql+i TH 
  gi|385805837|ref|YP_005842235.1| 826 lSQASGGESVAVAIAFVLAMQKVIQKMIAGEEVfdfLILDEPTTHLDDERVRDLVEVFRTLGERGEGVPQLIIVTHD 902
                                       355588*********99988885555555555534489***********99999988888866889**********7 PP

                            AAA_13 571 l 571
                                        
  gi|385805837|ref|YP_005842235.1| 903 E 903
                                       5 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00038      0.26       2      63 ..      34      91 ..      33     104 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00038
                            AAA_33  2 vllvGlpGsGKstlaerllkklgavllssdtlrrrlfgtdqqsktdytrvldrlyqilnela 63
                                      ++lvG +G+GKs  +e +l +l+++ll+  ++  r + +    k++y +v+ +l+++ n ++
  gi|385805837|ref|YP_005842235.1| 34 TVLVGENGAGKSSIVEAILFALTGELLRGTIEQARTKDS----KKKYFEVELELKDRDNTVI 91
                                      689*************************99999988854....4445555555554443333 PP

>> MukB  MukB N-terminal
   #    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       8      54 ..      12      59 ..       9      80 .. 0.83
   2 ?   -1.1   2.3       1.9   1.3e+03     115     188 ..     310     378 ..     274     411 .. 0.54
   3 ?    1.8   2.0      0.25   1.7e+02     108     203 ..     684     782 ..     661     801 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00018
                                      EEEEEEETTEEEE.EE-HHHHHHHHHS--SHHHHHHHHHHHHHHS--T CS
                              MukB  8 sltlinWnGffar.tfdldelvttlsGgnGaGksttmaafvtaliPdl 54
                                      s+tl n++ +  r t ++ + +t l G nGaGks ++ a++ al  +l
  gi|385805837|ref|YP_005842235.1| 12 SVTLENFRNYSERtTLNFGKGITVLVGENGAGKSSIVEAILFALTGEL 59
                                      77888888887772578999********************99997665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.9
                                       EEEEEEEEES--TT--HHHHHEE--SSS--EE--HHHHHHHHHTSTT-EEEE-S-HHHHHHHHHHTTSBSS--- CS
                              MukB 115 vdikpfalqgleedvkltdvlleklddkkarvrelnelkekleelegvrlkkfnsvtdyhallfdlGvipkrlr 188
                                       ++ +   l++lee+++ +d +++k++     ++  ne k+ le +     +++n  +dy a l dl  +   ++
  gi|385805837|ref|YP_005842235.1| 310 LEENEARLKELEEKTSKKDDIINKVQA-IRYLLLYNEAKNCLEYI----KEIYNNYKDYSASLNDLKSVQENIK 378
                                       222333333333333333333333333.11222223333333332....3467777777777777766665555 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.25
                                       -SSTTT-EEEEEEEEES--TT--HHHHH....EE--SSS--EE--HHHHHHHHHTSTT-EEEE-S-.HHHHHHHHHH CS
                              MukB 108 vagrdkkvdikpfalqgleedvkltdvl....leklddkkarvrelnelkekleelegvrlkkfns.vtdyhallfd 179
                                       + + dkk++    + ++l++  + +d +     +k+ ++ + v+++  lk++l+e e+ ++k+++s +++   ++++
  gi|385805837|ref|YP_005842235.1| 684 IEELDKKIESLRSVEEELKKVRSEIDAVekdiQNKQRENGELVISIDTLKKELAEYEE-KIKSYESgLRQIDDAIYK 759
                                       55567776665555555555444444440000345555567899999*******9888.999999745677778888 PP

                                       TTSBSS---SHHHHHHHHHHHHHH CS
                              MukB 180 lGvipkrlrssedrskfyrlieas 203
                                       l v+  ++r+  d++ + + ++  
  gi|385805837|ref|YP_005842235.1| 760 LNVL-LKVRELYDKENIPKWLRNE 782
                                       8776.4566666666666655555 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00018      0.13      97     120 ..      29      52 ..      10      75 .. 0.81
   2 ?   -3.1   1.3       9.5   6.6e+03      35      73 ..     261     297 ..     241     348 .. 0.52
   3 ?   -1.8   0.8       3.7   2.6e+03      78      99 ..     390     410 ..     366     454 .. 0.55
   4 ?   -2.0   0.2       4.3     3e+03      56      97 ..     547     586 ..     540     592 .. 0.73
   5 ?   -1.7   0.1       3.5   2.4e+03      61      99 ..     666     703 ..     647     710 .. 0.69
   6 ?    0.0   0.3         1     7e+02      43      99 ..     719     781 ..     700     789 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00018
                                       CTTSEEEEECSTTSSHHHHHHHHC CS
                       RsgA_GTPase  97 lkdktsvlvGqSGvGKStLinall 120
                                       + + ++vlvG+ G+GKS++++a+l
  gi|385805837|ref|YP_005842235.1|  29 FGKGITVLVGENGAGKSSIVEAIL 52 
                                       55689***************9986 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 9.5
                                       HHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHH CS
                       RsgA_GTPase  35 ldrfLvlaeekgiepvivlnKiDlleeeeeleelkeele 73 
                                       ++r L ++eek+ e+   +   +ll++++ele+ +++  
  gi|385805837|ref|YP_005842235.1| 261 VERELKMMEEKEKELNATM--ENLLSKSKELEQARSKRD 297
                                       4444444444443333222..223333333333333333 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 3.7
                                       EEEE--TTTHTTHHHHHHHCTT CS
                       RsgA_GTPase  78 evllvsaktkegleelkellkd 99 
                                       +  ++ ++++e++e++k+ l++
  gi|385805837|ref|YP_005842235.1| 390 NRAML-VSKREQIEKIKADLEK 410
                                       33333.2223444444444433 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 4.3
                                       GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHC CS
                       RsgA_GTPase  56 iDlleeeeeleelkeelealgyevllvsaktkegleelkell 97 
                                       +D+l+ee+ +e++++e+e+++ ++   + +t e +++++++ 
  gi|385805837|ref|YP_005842235.1| 547 ADVLKEED-IEKINSEIEEIERKISENE-STLEIMKKIENAY 586
                                       68888888.9999999999988776654.4466666666655 PP

  == domain 5  score: -1.7 bits;  conditional E-value: 3.5
                                       HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTT CS
                       RsgA_GTPase  61 eeeeleelkeelealgyevllvsaktkegleelkellkd 99 
                                       +++++e++k+e+++l +e+  +++k  e+l++++e+lk+
  gi|385805837|ref|YP_005842235.1| 666 KKKDMENIKNEFNSLKLEIEELDKK-IESLRSVEEELKK 703
                                       3446777788888887777777655.5666666666665 PP

  == domain 6  score: 0.0 bits;  conditional E-value: 1
                                       HHTT-EEEEEEE..-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTH....TTHHHHHHHCTT CS
                       RsgA_GTPase  43 eekgiepvivln..KiDlleeeeeleelkeelealgyevllvsaktk....egleelkellkd 99 
                                       ++++ e+vi +   K +l+e ee+++++++ l++++ +++++++  k     + e++ ++l++
  gi|385805837|ref|YP_005842235.1| 719 QRENGELVISIDtlKKELAEYEEKIKSYESGLRQIDDAIYKLNVLLKvrelYDKENIPKWLRN 781
                                       555566666664449999999999*********999888877654221111455566666666 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00065      0.45       3      34 ..      35      66 ..      33     102 .. 0.79
   2 ?   -1.4   0.1       3.1   2.2e+03      83     124 ..     304     347 ..     298     355 .. 0.75
   3 ?   -0.0   0.2       1.2     8e+02      41      84 ..     521     565 ..     493     610 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00065
                                      EEE--SSSSHHHHHHHGGGGBS--EEEEE--T CS
                             AAA_5  3 lLvGppGtgKselaerlaaalnreveyvqltr 34
                                      +LvG+ G gKs+++e ++ al+ e++   + +
  gi|385805837|ref|YP_005842235.1| 35 VLVGENGAGKSSIVEAILFALTGELLRGTIEQ 66
                                      7********************87776555544 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.1
                                       HHHHHHHHSSEEE..-SSSEEE---.........-EEEEEESS-- CS
                             AAA_5  83 nsLlslleerrllleeggelvkaknddller...frviatanpld 124
                                       + L + lee++ +l e+ e +++k d ++++   +r + ++n+++
  gi|385805837|ref|YP_005842235.1| 304 KLLKNKLEENEARLKELEEKTSKKDD-IINKvqaIRYLLLYNEAK 347
                                       568889999****9999999988875.444436788888888766 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 1.2
                                       HH--B--.........--------....G-SEEEEESGGG--HHHHHH CS
                             AAA_5  41 lkgrreikngttslvdsplvraar....egeilvlDEveraesevlns 84 
                                       lk  +   ++ ++ ++spl++       e+++l  +++e+++se+ ++
  gi|385805837|ref|YP_005842235.1| 521 LKSTY---EKAYESKNSPLMKYLSflqhEADVLKEEDIEKINSEIEEI 565
                                       33333...4788889999998888999999999999999999998554 PP

>> CRPV_capsid  CRPV capsid protein like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   2.7    0.0017       1.1      55     167 ..     568     676 ..     495     684 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0017
                       CRPV_capsid  55 eakegidlvsylsylYafyrGgvryKiaaeknkllknealesrsslvdvysttdspdktgasvyiqpnlegvaefei 131
                                       + +e+ + ++++  +   yr + + K    +   +  e  ++ ++ ++  ++++++ ++ +++y  +  +g  e++i
  gi|385805837|ref|YP_005842235.1| 568 KISENESTLEIMKKIENAYRNSESCKRNLISI-GKMLEFEQISAENIELLEKIVKEYEKLGEEYLSKTNDGNIEISI 643
                                       45666666666666666666666666554444.3556778899999*******************9999******** PP

                       CRPV_capsid 132 PYYsqyrklPatstvigsesedvlr.kglvnlsiats 167
                                         Y++y+k+  +     s+se++l+ k+++ ++i+++
  gi|385805837|ref|YP_005842235.1| 644 EAYNKYKKILQE----ISNSESLLDsKKKDMENIKNE 676
                                       ******998666....378888888777777787765 PP

>> HrpB7  Bacterial type III secretion protein (HrpB7)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0  10.3      0.36   2.5e+02      18     120 ..     238     335 ..     234     337 .. 0.89
   2 ?   12.9  10.1   0.00016      0.11      13     145 ..     285     416 ..     284     417 .. 0.94
   3 ?    1.3   0.0      0.59   4.1e+02      95     139 ..     439     480 ..     431     495 .. 0.79
   4 ?    0.1   0.1       1.3   9.1e+02     101     136 ..     554     588 ..     536     594 .. 0.71
   5 ?    4.5   0.2      0.06        41     105     134 ..     690     719 ..     632     757 .. 0.66

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.36
                             HrpB7  18 erlraeleaaraalaaaeaalaaaqaqveaardavraheerlddlttgsspfsiadylacrayrdvlegrvraaeae 94 
                                        +l+++ e+++a+l+++e+++a  + +++  ++++++ ++ +++l++ s     +++ + r  rd+ e+r + ++++
  gi|385805837|ref|YP_005842235.1| 238 SELKNDYEKKKAELESLEKERAIVERELKMMEEKEKELNATMENLLSKS-----KELEQARSKRDEKEARFKLLKNK 309
                                       57899999999**********************************9999.....69999999999999999999999 PP

                             HrpB7  95 laaarqaldaaedavaatarkiaRnd 120
                                       l+  +++l++ e++ ++++  i + +
  gi|385805837|ref|YP_005842235.1| 310 LEENEARLKELEEKTSKKDDIINKVQ 335
                                       99999999999999999888877766 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00016
                             HrpB7  13 rarreerlraeleaaraalaaaeaalaaaqaqveaardavraheerlddlttgsspfsiadylacrayrdvlegrvr 89 
                                       + ++ e++r +  ++ a+ + ++++l++ +a +++ +++  + ++ ++++ + +  ++ +++  c  y++++ ++ +
  gi|385805837|ref|YP_005842235.1| 285 KSKELEQARSKRDEKEARFKLLKNKLEENEARLKELEEKTSKKDDIINKVQAIRYLLLYNEAKNCLEYIKEIYNNYK 361
                                       56777888889999999999999999*************************************************** PP

                             HrpB7  90 aaeaelaaarqaldaaedavaatarkiaRndaqidacrerierlrraaeraredaa 145
                                         +a l  ++  +++  +++++ ++++ Rn+a++   re+ie++++++e+ +++a+
  gi|385805837|ref|YP_005842235.1| 362 DYSASLNDLK-SVQENIKQLEREEKELERNRAMLVSKREQIEKIKADLEKYENEAK 416
                                       *********7.69************************************9999885 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.59
                             HrpB7  95 laaarqaldaaedavaatarkiaRndaqidacrerierlrraaer 139
                                       ++ ++++++   ++++  +rki+  ++++   +e i+ ++ra+ r
  gi|385805837|ref|YP_005842235.1| 439 IVELKDQFK---AKIEDLQRKISFIESSLKTFKEYINEIKRAEGR 480
                                       555555554...567888899999999999999999999998765 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 1.3
                             HrpB7 101 aldaaedavaatarkiaRndaqidacrerierlrra 136
                                        +++ + ++++ +rki+ n++ ++ + ++ie + r+
  gi|385805837|ref|YP_005842235.1| 554 DIEKINSEIEEIERKISENESTLEIM-KKIENAYRN 588
                                       45666778888888888888888765.456666555 PP

  == domain 5  score: 4.5 bits;  conditional E-value: 0.06
                             HrpB7 105 aedavaatarkiaRndaqidacrerierlr 134
                                       + + ++ +++++ + +++ida+++ i+  +
  gi|385805837|ref|YP_005842235.1| 690 KIESLRSVEEELKKVRSEIDAVEKDIQNKQ 719
                                       333333344444444444444443333322 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9  14.9   0.00017      0.12      46     108 ..     227     289 ..     194     292 .. 0.84
   2 ?   -2.3  12.8       8.6   5.9e+03      37      82 ..     284     329 ..     277     338 .. 0.51
   3 ?   13.0  16.7   0.00016      0.11       9     103 ..     341     431 ..     339     448 .. 0.89
   4 ?    4.1   7.0     0.088        61      11      86 ..     450     527 ..     441     534 .. 0.60
   5 ?    4.4  13.3     0.074        51      10     104 ..     496     589 ..     495     599 .. 0.89
   6 ?    0.6   0.3       1.1   7.6e+02      11      66 ..     579     630 ..     577     641 .. 0.69
   7 ?   15.2  18.7   3.5e-05     0.024      15     126 ..     636     750 ..     628     757 .. 0.83
   8 ?    6.6   0.6     0.015        10      11      45 ..     729     771 ..     726     808 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00017
                            APG6_N  46 deeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynel 108
                                         + + l ++l++l+++ e++ +eL+ leker+ +e+el+  ee++++l++  e+ +++ +el
  gi|385805837|ref|YP_005842235.1| 227 CGSKKLLGKKLSELKNDYEKKKAELESLEKERAIVERELKMMEEKEKELNATMENLLSKSKEL 289
                                       4566788899*******************************************9999998876 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 8.6
                            APG6_N  37 kekkeeekqdeeleeleeeleklekeeeelleeLkelekereelea 82 
                                       +++ke e+ +++++e e +++ l+++ ee ++ Lkele++ ++ ++
  gi|385805837|ref|YP_005842235.1| 284 SKSKELEQARSKRDEKEARFKLLKNKLEENEARLKELEEKTSKKDD 329
                                       2223333334555556666666666666666666666665555554 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 0.00016
                            APG6_N   9 lLleeldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaela 85 
                                       lL +e +++le+ ++  ++Y+++ + l++ k+ +e    ++++le+e ++le+ ++ l+++ +++ek +++le+  +
  gi|385805837|ref|YP_005842235.1| 341 LLYNEAKNCLEYIKEIYNNYKDYSASLNDLKSVQE----NIKQLEREEKELERNRAMLVSKREQIEKIKADLEKYEN 413
                                       688999**********************9977655....9************************************* PP

                            APG6_N  86 aleeelealeeeeerfwr 103
                                       ++++ l+ l+ +e+  ++
  gi|385805837|ref|YP_005842235.1| 414 EAKKYLNMLDSNEADTLK 431
                                       ***********9987664 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.088
                            APG6_N  11 leeldkqleqaekerdaYeeflkklkkekkeeek..............qdeeleeleeeleklekeeeelleeLkel 73 
                                       +e l+++++  e+  ++++e+ +++k+      +              +        e + k e++ ++ ++e k+l
  gi|385805837|ref|YP_005842235.1| 450 IEDLQRKISFIESSLKTFKEYINEIKRA-----EgrcplcgrelneehK-------VELIHKFEEAINNNINEKKRL 514
                                       5677777777777777777777777777.....1345678754443332.......344566666666666666666 PP

                            APG6_N  74 ekereeleaelaa 86 
                                       e+e ++l++  ++
  gi|385805837|ref|YP_005842235.1| 515 ENELKDLKSTYEK 527
                                       6666666555544 PP

  == domain 5  score: 4.4 bits;  conditional E-value: 0.074
                            APG6_N  10 LleeldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeellee.Lkelekereeleaela 85 
                                       L+ ++++ +++  +e++ +e+ lk lk++ +++   +++   l + l+ l+ e + l ee ++++ +e ee+e++++
  gi|385805837|ref|YP_005842235.1| 496 LIHKFEEAINNNINEKKRLENELKDLKSTYEKA--YESKNSPLMKYLSFLQHEADVLKEEdIEKINSEIEEIERKIS 570
                                       78899999999****************997775..4899999***********999876559*************** PP

                            APG6_N  86 aleeelealeeeeerfwre 104
                                       + e++le +++ e+++ ++
  gi|385805837|ref|YP_005842235.1| 571 ENESTLEIMKKIENAYRNS 589
                                       ********99999888655 PP

  == domain 6  score: 0.6 bits;  conditional E-value: 1.1
                            APG6_N  11 leeldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeel 66 
                                       ++++++ ++++e++++++ +  k l+ e+ ++e    ++e le+ +++ ek  ee 
  gi|385805837|ref|YP_005842235.1| 579 MKKIENAYRNSESCKRNLISIGKMLEFEQISAE----NIELLEKIVKEYEKLGEEY 630
                                       566778888888888888888888887766655....6666666666665555544 PP

  == domain 7  score: 15.2 bits;  conditional E-value: 3.5e-05
                            APG6_N  15 dkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeel...leeLkelekereeleaelaale 88 
                                       d  +e + +  ++Y++ l+++ ++++  +++++++e++++e+  l+ e eel   +e L+ +e+e +++++e+ a e
  gi|385805837|ref|YP_005842235.1| 636 DGNIEISIEAYNKYKKILQEISNSESLLDSKKKDMENIKNEFNSLKLEIEELdkkIESLRSVEEELKKVRSEIDAVE 712
                                       5666777777788888888888887777779**********99999887765222677888899999********** PP

                            APG6_N  89 eelealeeeeerfwreynelqlelleleeeldsleaqy 126
                                       +  +++++e+ + + +   l+ el+e ee+ +s e+ +
  gi|385805837|ref|YP_005842235.1| 713 KDIQNKQRENGELVISIDTLKKELAEYEEKIKSYESGL 750
                                       *******************************9998765 PP

  == domain 8  score: 6.6 bits;  conditional E-value: 0.015
                            APG6_N  11 leeldkqleqaekerdaYeeflkklkkekkeeek........q 45 
                                       +++l+k+l++ e+++++Ye+ l+++++   + +         +
  gi|385805837|ref|YP_005842235.1| 729 IDTLKKELAEYEEKIKSYESGLRQIDDAIYKLNVllkvrelyD 771
                                       7899999999999999999999999988777665554444441 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6  12.7   0.00016      0.11      55     121 ..     230     296 ..     225     305 .. 0.91
   2 ?    0.7   8.5      0.71   4.9e+02      73     122 ..     286     335 ..     284     338 .. 0.85
   3 ?    3.2  14.3      0.13        88      45     138 ..     370     476 ..     343     481 .. 0.68
   4 ?    2.8  10.4      0.17   1.2e+02      27     123 ..     483     581 ..     456     595 .. 0.81
   5 ?    3.2   4.1      0.12        84      60     103 ..     661     704 ..     651     713 .. 0.79
   6 ?   11.5   0.6   0.00035      0.24      57     112 ..     710     765 ..     705     769 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00016
                              ADIP  55 reslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrl 121
                                       +++l +++++l++++e+++++ e+l+++ +  erel+  ++ke++l++++++l +k k++ +  ++ 
  gi|385805837|ref|YP_005842235.1| 230 KKLLGKKLSELKNDYEKKKAELESLEKERAIVERELKMMEEKEKELNATMENLLSKSKELEQARSKR 296
                                       67888999****************************************************9987775 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.71
                              ADIP  73 qskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlk 122
                                       +++ e+   +  ++e + +l+++k+ ++e++lk+le+k+ ++ + +++ +
  gi|385805837|ref|YP_005842235.1| 286 SKELEQARSKRDEKEARFKLLKNKLEENEARLKELEEKTSKKDDIINKVQ 335
                                       567778888888999999999**************999999999998876 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.13
                              ADIP  45 lqardrdleqreslnetirkleaeierlqskierlktqleqlerelalvqa..........kerqlekklktleqkl 111
                                       l++ +++++q e  ++++++++a + +++ +ie+ k+ le++e+e++ + +          k ++le+k+ +l+++ 
  gi|385805837|ref|YP_005842235.1| 370 LKSVQENIKQLEREEKELERNRAMLVSKREQIEKIKADLEKYENEAKKYLNmldsneadtlKGKDLETKIVELKDQF 446
                                       57778888888888888888888888888888888888888888876554411111112223467888888888888 PP

                              ADIP 112 knekeelqrlknalqqi.kt..qyahelkk 138
                                       k + e+lqr  + +++  kt   y +e+k+
  gi|385805837|ref|YP_005842235.1| 447 KAKIEDLQRKISFIESSlKTfkEYINEIKR 476
                                       888888888877666431222245566665 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.17
                              ADIP  27 tekveeniaaiinviysLlqardrdleqreslnetirkleaeierl.qskierlktqleqlerela.lvqakerqle 101
                                        +++e n ++ + +i++   a   ++++++ l+ ++++l++++e+  +sk + l + l+ l+ e++ l +++  +++
  gi|385805837|ref|YP_005842235.1| 483 LCGRELNEEHKVELIHKFEEAINNNINEKKRLENELKDLKSTYEKAyESKNSPLMKYLSFLQHEADvLKEEDIEKIN 559
                                       677888889999999999999*********************99853889999*************9999999**** PP

                              ADIP 102 kklktleqklknekeelqrlkn 123
                                        ++++ e+k+ +    l+ +k+
  gi|385805837|ref|YP_005842235.1| 560 SEIEEIERKISENESTLEIMKK 581
                                       ***9999999877766665555 PP

  == domain 5  score: 3.2 bits;  conditional E-value: 0.12
                              ADIP  60 etirkleaeierlqskierlktqleqlerelalvqakerqlekk 103
                                         + +++ ++e+ ++++++lk + e+l+++++++ + e +l+k 
  gi|385805837|ref|YP_005842235.1| 661 SLLDSKKKDMENIKNEFNSLKLEIEELDKKIESLRSVEEELKKV 704
                                       45667888999999999999999999999999988888888764 PP

  == domain 6  score: 11.5 bits;  conditional E-value: 0.00035
                              ADIP  57 slnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklk 112
                                       +++++i++++ e+  l  +i+ lk++l+++e +++++++ +rq+  ++ +l+  lk
  gi|385805837|ref|YP_005842235.1| 710 AVEKDIQNKQRENGELVISIDTLKKELAEYEEKIKSYESGLRQIDDAIYKLNVLLK 765
                                       67899***************************************999999887776 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   1.5         3   2.1e+03      19      50 ..     230     261 ..     217     281 .. 0.55
   2 ?   14.3  14.9   5.4e-05     0.037      10     122 ..     368     475 ..     352     476 .. 0.67
   3 ?    1.8   9.2      0.41   2.8e+02      41     115 ..     502     580 ..     493     585 .. 0.73
   4 ?   12.7   9.9   0.00017      0.12       6      93 ..     671     757 ..     665     762 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 3
                           DUF5082  19 iaaleekIerLkeaktklsdekeslkqkkkkl 50 
                                        + l +k+++Lk  ++k ++e esl++++  +
  gi|385805837|ref|YP_005842235.1| 230 KKLLGKKLSELKNDYEKKKAELESLEKERAIV 261
                                       44455555555555555555555555544433 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 5.4e-05
                           DUF5082  10 aqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklekplnssesWkGk.eennydgirsnlessyqtyvdk 85 
                                       ++  + +++i++le   ++L++ +  l+++ e++++ k +lek++n+ + + +   +n+ d+       + +  ++k
  gi|385805837|ref|YP_005842235.1| 368 NDLKSVQENIKQLEREEKELERNRAMLVSKREQIEKIKADLEKYENEAKKYLNMlDSNEADTL------KGKDLETK 438
                                       344556666666666666666777777777777777777777777777655555233322222......34567778 PP

                           DUF5082  86 ldelidaieeEIerLenqiseaqgvldtlqsqlnslk 122
                                       + el+d+ + +Ie+L+ +is  +++l+t ++++n++k
  gi|385805837|ref|YP_005842235.1| 439 IVELKDQFKAKIEDLQRKISFIESSLKTFKEYINEIK 475
                                       8889999999999999999999999999999998876 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.41
                           DUF5082  41 eslkqkkkklekplnssesWkGkeennydgirs...nlessyqtyvdkld.elidaieeEIerLenqiseaqgvldt 113
                                       e++ +++++ +  +n+ + +k + e+ y+++ s   ++ s  q+  d l+ e i +i++EIe++e +ise ++ l+ 
  gi|385805837|ref|YP_005842235.1| 502 EAINNNINEKKRLENELKDLKSTYEKAYESKNSplmKYLSFLQHEADVLKeEDIEKINSEIEEIERKISENESTLEI 578
                                       45566666666666666688888888888888866677777777666664145789999999999999999998876 PP

                           DUF5082 114 lq 115
                                        +
  gi|385805837|ref|YP_005842235.1| 579 MK 580
                                       65 PP

  == domain 4  score: 12.7 bits;  conditional E-value: 0.00017
                           DUF5082   6 sklqaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklekplnssesWkGkeennydgirsnlessyqty 82 
                                       ++ +++  +l+ ei+ l++kIe L+++ ++l+++ +++++ +k+++++  ++ ++  +  ++ + +++++e++++ y
  gi|385805837|ref|YP_005842235.1| 671 ENIKNEFNSLKLEIEELDKKIESLRSVEEELKKVRSEIDAVEKDIQNKQRENGELVIS-IDTLKKELAEYEEKIKSY 746
                                       6889999******************************************999987644.456666677788888888 PP

                           DUF5082  83 vdkldelidai 93 
                                       ++ l+++ dai
  gi|385805837|ref|YP_005842235.1| 747 ESGLRQIDDAI 757
                                       88877777776 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   4.1       5.4   3.7e+03      17      80 ..     274     335 ..     203     379 .. 0.65
   2 ?    9.4   1.1    0.0014      0.99      51     110 ..     398     473 ..     357     477 .. 0.59
   3 ?    5.9   0.3     0.018        12      39     109 ..     503     577 ..     491     596 .. 0.59
   4 ?    7.1   2.2    0.0077       5.3      40      96 ..     663     717 ..     631     785 .. 0.57
   5 ?   -1.2   0.1       2.8   1.9e+03      75      75 ..     763     763 ..     722     824 .. 0.51

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 5.4
                      Baculo_PEP_C  17 dLtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq 80 
                                       +L+ +++ + +++ ++  q  +  d+ e +++ l+++l++  a l+ +l++ +++ +d +n++q
  gi|385805837|ref|YP_005842235.1| 274 ELNATMENLLSKSKEL-EQARSKRDEKEARFKLLKNKLEENEARLK-ELEEKTSKKDDIINKVQ 335
                                       4444444443333333.44455555555555555555555333332.45555555555555555 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0014
                      Baculo_PEP_C  51 sedlksllaeldt...............rldtll.tnLtdalnalqdtlrneLtnlnsiltnLlssvtNinstLnn 110
                                        e++++  a+l++               + dtl  + L++++ +l+d+++ +++ l+ +++ + ss+   ++ +n 
  gi|385805837|ref|YP_005842235.1| 398 REQIEKIKADLEKyeneakkylnmldsnEADTLKgKDLETKIVELKDQFKAKIEDLQRKISFIESSLKTFKEYINE 473
                                       3333333333333333444455544444444443267999999999999999999999999999998877777665 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.018
                      Baculo_PEP_C  39 lldaietqLnalsedlksllaeldtrldtlltnLtdalnalq...dtlr.neLtnlnsiltnLlssvtNinstLn 109
                                       ++++  ++ + l+++lk+l +  +++ ++  + L + l  lq   d l+ ++++ +ns++ ++  ++   +stL+
  gi|385805837|ref|YP_005842235.1| 503 AINNNINEKKRLENELKDLKSTYEKAYESKNSPLMKYLSFLQheaDVLKeEDIEKINSEIEEIERKISENESTLE 577
                                       344444444445555555555555555555555555555555554444314688888888888888887777775 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.0077
                      Baculo_PEP_C  40 ldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsiltn 96 
                                       ld+ ++ +++++++++sl  e++ +ld+ ++ L +   +l+ ++r+e++++++++ n
  gi|385805837|ref|YP_005842235.1| 663 LDSKKKDMENIKNEFNSLKLEIE-ELDKKIESLRSVEEELK-KVRSEIDAVEKDIQN 717
                                       44444444444444444333333.24444444444444443.444444444444443 PP

  == domain 5  score: -1.2 bits;  conditional E-value: 2.8
                      Baculo_PEP_C  75 a 75 
                                        
  gi|385805837|ref|YP_005842235.1| 763 L 763
                                       1 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       5.2   3.6e+03      48      66 ..     194     212 ..     184     221 .. 0.51
   2 ?   -1.8   0.0       6.3   4.4e+03      22      46 ..     253     277 ..     235     297 .. 0.51
   3 ?    6.4   1.3     0.017        12      22      66 ..     288     332 ..     274     341 .. 0.79
   4 ?    4.0   1.7     0.097        67      11      60 ..     368     417 ..     348     430 .. 0.65
   5 ?    3.8   0.1      0.12        83      23      62 ..     435     475 ..     425     477 .. 0.65
   6 ?    1.6   0.1      0.55   3.8e+02      35      61 ..     553     579 ..     538     606 .. 0.62
   7 ?    4.9   1.1     0.055        38       9      61 ..     652     704 ..     647     708 .. 0.64
   8 ?    4.6   0.7     0.064        44      10      64 ..     698     749 ..     693     776 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 5.2
                           NPV_P10  48 saqLaeletkvenIqdiLn 66 
                                       +++L e++  +enI+d+ +
  gi|385805837|ref|YP_005842235.1| 194 NKKLGEFSIRLENISDLIS 212
                                       3344444444444444333 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 6.3
                           NPV_P10  22 alqqqvddvqenlpdvtelnekLda 46 
                                       +l+++ + v+ +l+ ++e +++L+a
  gi|385805837|ref|YP_005842235.1| 253 SLEKERAIVERELKMMEEKEKELNA 277
                                       3333334444444444444444444 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.017
                           NPV_P10  22 alqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiLn 66 
                                        l+q+  + +e+   ++ l++kL++  a L+ele+k ++ +di n
  gi|385805837|ref|YP_005842235.1| 288 ELEQARSKRDEKEARFKLLKNKLEENEARLKELEEKTSKKDDIIN 332
                                       5555555556666778889****************9999999998 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.097
                           NPV_P10  11 adikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkven 60 
                                       +d k v++ ++ l+ + ++++ n   +    e+++++ a L++ e++ ++
  gi|385805837|ref|YP_005842235.1| 368 NDLKSVQENIKQLEREEKELERNRAMLVSKREQIEKIKADLEKYENEAKK 417
                                       55556666666666666666666555555556666666666655555555 PP

  == domain 5  score: 3.8 bits;  conditional E-value: 0.12
                           NPV_P10  23 lqqqvddvqenlp.dvtelnekLdaqsaqLaeletkvenIq 62 
                                       l++++ +++++++ ++++l+ k+  +  +L+++++ +++I+
  gi|385805837|ref|YP_005842235.1| 435 LETKIVELKDQFKaKIEDLQRKISFIESSLKTFKEYINEIK 475
                                       45555555555542356666777777777777777777775 PP

  == domain 6  score: 1.6 bits;  conditional E-value: 0.55
                           NPV_P10  35 pdvtelnekLdaqsaqLaeletkvenI 61 
                                       +d++++n++++++  ++ e e+++e  
  gi|385805837|ref|YP_005842235.1| 553 EDIEKINSEIEEIERKISENESTLEIM 579
                                       455555555555555555444444433 PP

  == domain 7  score: 4.9 bits;  conditional E-value: 0.055
                           NPV_P10   9 IradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenI 61 
                                       I+++i++ ++ +d+ ++ +++++++++ ++   e+Ld+  ++L ++e++++++
  gi|385805837|ref|YP_005842235.1| 652 ILQEISNSESLLDSKKKDMENIKNEFNSLKLEIEELDKKIESLRSVEEELKKV 704
                                       66666666666666666667777666666655566666666666666666655 PP

  == domain 8  score: 4.6 bits;  conditional E-value: 0.064
                           NPV_P10  10 radikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdi 64 
                                        ++ k+v + +da+++ +++ q +     el   +d + ++Lae e+k+++ ++ 
  gi|385805837|ref|YP_005842235.1| 698 EEELKKVRSEIDAVEKDIQNKQREN---GELVISIDTLKKELAEYEEKIKSYESG 749
                                       5667777777777777666555433...458888888888888888888766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (930 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3290  (0.183502); expected 358.6 (0.02)
Passed bias filter:                      708  (0.0394891); expected 358.6 (0.02)
Passed Vit filter:                       236  (0.013163); expected 17.9 (0.001)
Passed Fwd filter:                       150  (0.00836633); 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: 3.01u 0.45s 00:00:03.46 Elapsed: 00:00:00.76
# Mc/sec: 3673.98
//
Query:       gi|385805838|ref|YP_005842236.1|  [L=386]
Description: hypothetical protein FFONT_0796 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-10   39.4   0.2    1.1e-09   38.4   0.2    1.6  1  NurA      NurA domain


Domain annotation for each model (and alignments):
>> NurA  NurA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.2   6.1e-14   1.1e-09       2     242 .]      56     359 ..      55     359 .. 0.84

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 6.1e-14
                                       EEEEEEEEEEEEEETTCEEEEEEEEEEECCEEECCCEEEECEBTCCHHEEEEE......HHHHHHHHHHHHHHHHHH CS
                              NurA   2 rvaAvDGSngvvrlsggilyilsayavvgggkerleealslasvdsispsdel......errirllmetlElklgal 72 
                                       ++a++DG++  +++ g+ ly++  ya +  + ++++  ++  s ++i + d l      ++ri  +++  El+  a 
  gi|385805838|ref|YP_005842236.1|  56 KIAGIDGGSLPKSFLGFDLYFIKTYA-IRLHLNEEKNEYVRGSTYKIADIDMLippgslQDRITVYRQVTELR--AI 129
                                       69************************.777777777777888888877555559*****9*************..88 PP

                                       HCGGCCSCEEEEECSHHCCCH....................................................HHHH CS
                              NurA  73 lleekgedllllDGsligslv....................................................efde 97 
                                       l + k++   l DGs    +                                                     + +e
  gi|385805838|ref|YP_005842236.1| 130 LDSLKNNYFTLEDGSAESLISrpthirprilnglseyscedigkivnksfndeftsmgikslieeiyekekksDLNE 206
                                       888899999999**854333377799*************************************************** PP

                                       HHHHHHHHHHHHHHHHHTT-...TTCEEEEESS-SCTCCHCCC......S--HHHHCCHHCCHCH---STTS-HHHH CS
                              NurA  98 lheeleyeeylyslsrllea...glnlvgvaKsfrskellnllletlligesisDiallgallrkpgytspllkilr 171
                                       l   le +e +y++s++l++   g+ l +v K+ rs++++n     l++++ is  + ++  + +   +spl+ +  
  gi|385805838|ref|YP_005842236.1| 207 LAFKLELGEKFYYISEILKEitkGKELFFVTKTGRSNDFFNSS---LSDQYIISMKTKVAGFI-T---RSPLPLSKV 276
                                       *****************************************99...66666666555555544.2...455554333 PP

                                       TT.....-HCCHHHHHH-.EEEEEEESSTTTTEEEEEHHHHHHC........CHHHHHHHHHH..TTB-SSSBCCHH CS
                              NurA 172 ek.....pllrealidke.iyfaYvrlegggsilrleipaevst........akdedvlsllasqrlsisGYprpLa 234
                                              +  ++ l d     + Y rle +g++l++e+ ++  +        +   + l ++    +s sGYp+ L 
  gi|385805838|ref|YP_005842236.1| 277 VEesktsFCGVSDLMDEVyLLTGYARLENFGPVLKVELLLPKFKaesisdpnKFYYEKLLQIS--SISVSGYPYVLS 351
                                       33556788888888888868888**************77773346778888777777777788..9*********** PP

                                       HHHHHHCC CS
                              NurA 235 lAhelaki 242
                                       lAh++a i
  gi|385805838|ref|YP_005842236.1| 352 LAHQEAHI 359
                                       ****9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); 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: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2365.91
//
Query:       gi|385805839|ref|YP_005842237.1|  [L=552]
Description: putative ATPase [Fervidicoccus fontis Kam940]
Scores for 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-40  137.5   0.4    1.3e-39  136.6   0.4    1.5  1  DUF87       Helicase HerA, central domain
    1.7e-07   30.3   0.0    2.9e-05   22.9   0.0    2.2  2  DUF853      Bacterial protein of unknown function (DUF853)
    2.1e-06   27.8   0.1      7e-06   26.1   0.1    2.0  1  HAS-barrel  HAS barrel domain
  ------ inclusion threshold ------
      0.021   13.8   0.1       0.72    8.7   0.0    2.4  2  AAA_10      AAA-like 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 !  136.6   0.4     3e-43   1.3e-39       1     227 []     154     382 ..     154     382 .. 0.88

  Alignments for each domain:
  == domain 1  score: 136.6 bits;  conditional E-value: 3e-43
                             DUF87   1 ieiGrllsgsevpvyldlnklvtrHlAilgsTGsGKSntvavLleellekkgatililDpHGEYgkalekllsekvk 77 
                                       ++iG l +  +vpv ++++ +v+rHlAil+ TG+GKSn v++L e++    ++t+li+D+HGEY++ +    ++k +
  gi|385805839|ref|YP_005842237.1| 154 VRIGVLSNHPNVPVFVKVDPIVSRHLAILAVTGAGKSNSVSILTERITCGLNGTVLIFDIHGEYASSD--ICKDKQN 228
                                       579999999***********************************************************..9999999 PP

                             DUF87  78 vitpspsakdkelkinpwsldpeelldlleeddkpaaavqrsvleealdqaka...keekeklss.depveklleel 150
                                       ++ p         kinp sl++ el++l+ +  +++a +q+s+l+++++++k+   + + + + + +e+++k+le l
  gi|385805839|ref|YP_005842237.1| 229 IVPP---------KINPFSLSIFELFRLARI--RDDAIKQQSILRRVYKYIKDnykPSDPNTIEYkREFLNKILEVL 294
                                       9999.........9*****************..999999************99777333333333156777777777 PP

                             DUF87 151 k..............kekeelrklknqaiarlldkledllrkggsf..snsstdliallleklekegkitiidlsgv 211
                                       k                k  l   k++ i ++++kledl ++++     + ++++   +     k+++++i+dlsgv
  gi|385805839|ref|YP_005842237.1| 295 KselekklkkknnttADKGILGGFKDDEILNVINKLEDLESNYSAVltPDAPEEVKIAI-----KPNELNIVDLSGV 366
                                       79999*******99555559999***********************5555555555556.....************* PP

                             DUF87 212 delaqqlvvsvilrri 227
                                       de+ ++++vs+++rr+
  gi|385805839|ref|YP_005842237.1| 367 DENGSDVIVSYYTRRL 382
                                       *************985 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 !    5.1   0.0    0.0016       7.2      19      62 ..     174     218 ..     158     240 .. 0.79
   2 !   22.9   0.0   6.5e-09   2.9e-05     261     360 ..     403     497 ..     397     508 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0016
                            DUF853  19 lanrhGliaGatGtGktvtLqvlaeslse.aGvpvfladvkGdLs 62 
                                       ++ rh  i   tG+Gk  ++ +l+e ++     +v++ d+ G+ +
  gi|385805839|ref|YP_005842237.1| 174 IVSRHLAILAVTGAGKSNSVSILTERITCgLNGTVLIFDIHGEYA 218
                                       689**********************99641445799999999865 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 6.5e-09
                            DUF853 261 fffdeahLLfndapkall.ekveqvvrLirskGvGvyfvtqnPldlPdtvLaqLGnrvqhalraftpkdqkavkaaa 336
                                       +  +eah+L  +  ++l  + + ++ r  r  GvG+ +v+q P ++ ++ L+q  nr+   l+   p+d + ++ a+
  gi|385805839|ref|YP_005842237.1| 403 IIVEEAHILVPKDEETLTkDIIGKIAREGRKFGVGICLVSQRPKNIDENSLSQTNNRII--LKIIEPNDLQYIQRAT 477
                                       5679*****988777776266899*********************************95..8999999999999999 PP

                            DUF853 337 dtfranpefdveeaiteLgvGeal 360
                                       + + +    ++ e +  L +Gea+
  gi|385805839|ref|YP_005842237.1| 478 EQMSS----ELLELLPGLRTGEAV 497
                                       88864....566777777777776 PP

>> HAS-barrel  HAS barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.1   1.6e-09     7e-06       1      44 [.      16      56 ..      16      99 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 1.6e-09
                        HAS-barrel  1 iGevigestssslifrvegskdvkvGeyVeielpdgeivlGmvt 44
                                      +G+vigest+   +f ++   +++vGeyV i+++ ++++lGmv 
  gi|385805839|ref|YP_005842237.1| 16 LGYVIGESTPFRITFLSNS--PPRVGEYVFIKHD-EDYLLGMVD 56
                                      59****************8..9************.*******95 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.011        51      22      60 ..     177     216 ..     171     340 .. 0.81
   2 ?    8.7   0.0   0.00016      0.72     247     292 ..     406     454 ..     401     477 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.011
                            AAA_10  22 sasliiGdlGnGKSvlakllvlyisl.lggkaliiDpkke 60 
                                        + +i+  +G+GKS ++ +l   i+  l+g +li D   e
  gi|385805839|ref|YP_005842237.1| 177 RHLAILAVTGAGKSNSVSILTERITCgLNGTVLIFDIHGE 216
                                       57799999**********9999887658999999998888 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00016
                            AAA_10 247 DEawiftssae...GkkllkelvRiGRsynaavylvtqsadDvlkeelk 292
                                        Ea i+   +e    k ++ ++ R GR++   + lv+q ++ +++++l+
  gi|385805839|ref|YP_005842237.1| 406 EEAHILVPKDEetlTKDIIGKIAREGRKFGVGICLVSQRPKNIDENSLS 454
                                       56666655554222478999***********************999854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (552 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); 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: 0.67u 0.34s 00:00:01.01 Elapsed: 00:00:00.51
# Mc/sec: 3284.02
//
Query:       gi|385805840|ref|YP_005842238.1|  [L=149]
Description: putative membrane-bound metal dependent hydrolase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-22   79.5   0.8    1.4e-21   76.5   0.8    1.9  1  YdjM      LexA-binding, inner membrane-associated putative hy
  ------ inclusion threshold ------
       0.26   11.4   3.6       0.29   11.3   0.6    2.1  2  DUF2985   Protein of unknown function (DUF2985)


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 !   76.5   0.8   1.6e-25   1.4e-21       1     163 [.       1     143 [.       1     148 [. 0.84

  Alignments for each domain:
  == domain 1  score: 76.5 bits;  conditional E-value: 1.6e-25
                              YdjM   1 MdgltHallGaalglalaallgaakeavllavavlgAllPDiDhpsstlgrklgllskklaklvgHRgftHSllfla 77 
                                       M+ +tH+l+G  l+l + +l g+  + + ++++v+ +++PD+D            l++       HR ++H +++l+
  gi|385805840|ref|YP_005842238.1|   1 MQKKTHLLFGTGLSLYIISLFGQISQ-ISILFIVIFSIFPDLD------------LKN------NHRKLFHNIFALL 58 
                                       9999******************9776.999999999*******............444......4************ PP

                              YdjM  78 llalvlllllrlfgrsa.......lrlglllllgvlsHlllDlltkyGvpllwPfskkkvrlsllfiiidplltlls 147
                                       l+++++ +l+ ++           + + l+ ++++ +Hl+lD+ltk+Gv l+wP+s  +++++l+++++d+ l    
  gi|385805840|ref|YP_005842238.1|  59 LIPAIAVVLSYNYLIDYqltseseILIYLSAVISYGLHLILDMLTKMGVYLFWPLS--NKSIGLKLVRTDNNL---- 129
                                       ***********99988889998865555668889*********************9..9********999822.... PP

                              YdjM 148 rrglvalelvllvlyl 163
                                         + v l ++ ++l++
  gi|385805840|ref|YP_005842238.1| 130 -LNAV-LSIIGMLLII 143
                                       .2444.4444444443 PP

>> DUF2985  Protein of unknown function (DUF2985)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1     0.068   6.1e+02      23      47 ..      28      53 ..       8      71 .. 0.61
   2 ?   11.3   0.6   3.2e-05      0.29      11      65 ..      83     142 ..      77     148 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.068
                           DUF2985 23 amlfLlLlgaapamn.insarkkwie 47
                                       +lf+++  ++p    +n++rk + +
  gi|385805840|ref|YP_005842238.1| 28 SILFIVIFSIFPDLDlKNNHRKLFHN 53
                                      45666666666665523355555444 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 3.2e-05
                           DUF2985  11 vtiYglnvvawgamlfLlLlgaapamn.....insarkkwieidsqilnALFcvtgfgla 65 
                                       ++iY+  v+  g+ l+L +l  + +       ++s   k +  d++ lnA   ++g+ l+
  gi|385805840|ref|YP_005842238.1|  83 ILIYLSAVISYGLHLILDMLTKMGVYLfwplsNKSIGLKLVRTDNNLLNAVLSIIGMLLI 142
                                       78**************99988877766899855599999*****************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       735  (0.040995); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 971.85
//
Query:       gi|385805841|ref|YP_005842239.1|  [L=78]
Description: 4Fe-4S ferredoxin [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.6e-21   74.4   0.8    9.3e-21   74.1   0.8    1.1  1  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
    1.8e-20   73.4   1.4    2.1e-20   73.2   1.4    1.0  1  Fer4_15   4Fe-4S single cluster domain
      1e-07   32.4  10.6    9.8e-05   22.9   2.2    2.0  3  Fer4_7    4Fe-4S dicluster domain
    4.5e-07   29.4   7.4    6.7e-06   25.7   4.4    2.4  2  Fer4      4Fe-4S binding domain
    5.5e-06   26.2   2.4    5.5e-06   26.2   2.4    2.2  2  Fer4_6    4Fe-4S binding domain
    1.4e-05   25.1   4.0    5.8e-05   23.1   4.2    1.9  2  Fer4_10   4Fe-4S dicluster domain
    6.6e-05   22.8   3.5    6.6e-05   22.8   3.5    1.9  2  Fer4_2    4Fe-4S binding domain
    0.00011   22.7   0.2    0.00014   22.3   0.2    1.2  1  Fer4_17   4Fe-4S dicluster domain
    0.00039   20.7   0.8    0.00039   20.7   0.8    2.0  2  Fer4_4    4Fe-4S binding domain
      0.001   19.5   1.4     0.0017   18.8   1.4    1.4  1  Fer4_8    4Fe-4S dicluster domain
     0.0016   18.5   6.7     0.0082   16.3   6.7    2.0  1  Fer4_21   4Fe-4S dicluster domain
      0.003   18.5   3.5      0.028   15.3   0.5    2.2  2  Fer4_16   4Fe-4S double cluster binding domain
     0.0046   17.0   4.2      0.018   15.1   4.2    1.8  1  Fer4_19   Divergent 4Fe-4S mono-cluster
     0.0093   16.8   1.2      0.016   16.1   1.2    1.4  1  Fer4_22   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.015   15.4   2.2      0.015   15.4   2.2    1.9  2  Fer4_9    4Fe-4S dicluster 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 !   74.1   0.8   7.8e-24   9.3e-21       1      58 []       8      75 ..       8      75 .. 0.93

  Alignments for each domain:
  == domain 1  score: 74.1 bits;  conditional E-value: 7.8e-24
                           Fer4_13  1 VDrdtCiacgaCvelaPdvFeeddeggasvvae..........qptseeekadaeeAadaCPvesIgv 58
                                      +Dr+tCi+cg+C++l+PdvFe ++++g+s ++e          ++++e ++++a++Aa +CPv++I+v
  gi|385805841|ref|YP_005842239.1|  8 IDRNTCIGCGVCANLCPDVFELNPNDGKSSIVEkfrvggdlgaGEVDESLEECANSAAGSCPVSAIKV 75
                                      8********************************77777777777888*******************97 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.2   1.4   1.7e-23   2.1e-20       1      66 []       6      75 ..       6      75 .. 0.94

  Alignments for each domain:
  == domain 1  score: 73.2 bits;  conditional E-value: 1.7e-23
                           Fer4_15  1 VvvDrdaCigcglCvaeapevfelde.dglasvl...lddgeiaegevpddeeeaaqeAaraCPvdAIrv 66
                                      V++Dr++Cigcg+C+ ++p+vfel+  dg++s++     +g+++ gev++ +ee+a  Aa +CPv AI v
  gi|385805841|ref|YP_005842239.1|  6 VTIDRNTCIGCGVCANLCPDVFELNPnDGKSSIVekfRVGGDLGAGEVDESLEECANSAAGSCPVSAIKV 75
                                      89***********************989***999999447899999**********************87 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   1.5   6.2e-07   0.00075      30      49 ..       5      24 ..       2      26 .. 0.87
   2 !   22.9   2.2   8.2e-08   9.8e-05       1      42 [.      12      64 ..      12      72 .. 0.73
   3 ?    0.7   0.0      0.67     8e+02      11      20 ..      67      76 ..      64      78 .] 0.76

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 6.2e-07
                            Fer4_7 30 kveidpekClgCgaCvavCP 49
                                      kv+id ++C+gCg+C++ CP
  gi|385805841|ref|YP_005842239.1|  5 KVTIDRNTCIGCGVCANLCP 24
                                      78999999999999999999 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 8.2e-08
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenek............gtekveidpekClgCg 42
                                      +CigCg C++ Cp +++el++ + ++            g  +v+ + e+C +  
  gi|385805841|ref|YP_005842239.1| 12 TCIGCGVCANLCP-DVFELNPNDGKSsivekfrvggdlGAGEVDESLEECANSA 64
                                      6************.9999999877766666666666665577788888887643 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.67
                            Fer4_7 11 aCpvkaield 20
                                       Cpv+ai+++
  gi|385805841|ref|YP_005842239.1| 67 SCPVSAIKVE 76
                                      5999998876 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   4.4   5.6e-09   6.7e-06       1      19 [.       6      24 ..       6      26 .. 0.94
   2 ?    4.4   0.0     0.029        35      17      24 .]      67      74 ..      65      74 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 5.6e-09
                                      EEEETTTSSS-THHHHHST CS
                              Fer4  1 vvideekCigCGaCvevCP 19
                                      v+id + CigCG C++ CP
  gi|385805841|ref|YP_005842239.1|  6 VTIDRNTCIGCGVCANLCP 24
                                      68***************** PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.029
                                      HSTTTEEE CS
                              Fer4 17 vCPvgAIt 24
                                       CPv AI+
  gi|385805841|ref|YP_005842239.1| 67 SCPVSAIK 74
                                      6*****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 !   26.2   2.4   4.6e-09   5.5e-06       1      20 [.       5      24 ..       5      29 .. 0.94
   2 ?    0.9   0.3      0.46   5.5e+02      19      24 .]      68      73 ..      58      73 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 4.6e-09
                            Fer4_6  1 vveidpdkCigCgdCvrvCP 20
                                      +v+id++ CigCg C++ CP
  gi|385805841|ref|YP_005842239.1|  5 KVTIDRNTCIGCGVCANLCP 24
                                      79*****************9 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.46
                            Fer4_6 19 CPegai 24
                                      CP  ai
  gi|385805841|ref|YP_005842239.1| 68 CPVSAI 73
                                      999997 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   4.2   4.9e-08   5.8e-05       1      30 [.       5      41 ..       5      69 .. 0.63
   2 ?    0.4   0.2       0.6   7.2e+02      17      21 ..      62      70 ..      56      77 .. 0.59

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 4.9e-08
                           Fer4_10  1 kvvidddtCirCgkCvkaCPadl...........tsvgakg 30
                                      kv id++tCi+Cg C + CP  +                ++
  gi|385805841|ref|YP_005842239.1|  5 KVTIDRNTCIGCGVCANLCPDVFelnpndgkssiV----EK 41
                                      589*****************977777766644442....22 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.6
                           Fer4_10 17 k....aCPa 21
                                      +    +CP+
  gi|385805841|ref|YP_005842239.1| 62 NsaagSCPV 70
                                      433347888 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   3.5   5.5e-08   6.6e-05       3      21 ..       6      24 ..       4      25 .. 0.93
   2 ?   -1.4   0.2       2.8   3.3e+03      19      21 ..      67      69 ..      58      70 .. 0.61

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 5.5e-08
                            Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                      v +d+++CigCg C + CP
  gi|385805841|ref|YP_005842239.1|  6 VTIDRNTCIGCGVCANLCP 24
                                      789***************9 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.8
                            Fer4_2 19 aCP 21
                                      +CP
  gi|385805841|ref|YP_005842239.1| 67 SCP 69
                                      366 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.2   1.2e-07   0.00014       2      48 ..      13      62 ..      12      71 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.2e-07
                           Fer4_17  2 CiqCgyClpeCp.syeaydnepk.kllraakl.glleeaekeekaslCie 48
                                      Ci+Cg C++ Cp  +e ++n+ k ++++++++ g+l++ e +e  ++C++
  gi|385805841|ref|YP_005842239.1| 13 CIGCGVCANLCPdVFELNPNDGKsSIVEKFRVgGDLGAGEVDESLEECAN 62
                                      ************55777888765269***999646666666677777764 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.8   3.2e-07   0.00039       2      16 ..      11      25 ..      10      41 .. 0.91
   2 ?   -0.7   0.5       2.4   2.8e+03      13      15 ..      67      69 ..      58      71 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 3.2e-07
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      ++CigCg+C + CP+
  gi|385805841|ref|YP_005842239.1| 11 NTCIGCGVCANLCPD 25
                                      68************4 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.4
                            Fer4_4 13 aCP 15
                                      +CP
  gi|385805841|ref|YP_005842239.1| 67 SCP 69
                                      477 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   1.4   1.4e-06    0.0017       3      52 ..      11      61 ..       9      72 .. 0.58

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.4e-06
                            Fer4_8  3 ekCieCgaCqsaCpvlrrtk.khlldargeaaedvqeeqvlee.eealwsCt 52
                                      + Ci+Cg C + Cp + + + ++ +++  e+   v  + +  e +e+l++C 
  gi|385805841|ref|YP_005842239.1| 11 NTCIGCGVCANLCPDVFELNpNDGKSSIVEKFR-VGGDLGAGEvDESLEECA 61
                                      57************6666554554444444444.333333333466666663 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   6.7   6.9e-06    0.0082       2      20 ..       7      25 ..       6      75 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6.9e-06
                           Fer4_21  2 ridedkCigCgkCliaCed 20
                                      +id+++CigCg C+  C+d
  gi|385805841|ref|YP_005842239.1|  7 TIDRNTCIGCGVCANLCPD 25
                                      5999999999999999997 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   0.5   2.4e-05     0.028      53      65 ..      12      24 ..       2      40 .. 0.76
   2 ?    4.4   0.1     0.061        73      10      20 ..      66      76 ..      57      78 .] 0.79

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.4e-05
                           Fer4_16 53 aitgCdiCqdvCP 65
                                       ++gC++C++ CP
  gi|385805841|ref|YP_005842239.1| 12 TCIGCGVCANLCP 24
                                      5666666666665 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.061
                           Fer4_16 10 evCPtnaikek 20
                                       +CP++aik +
  gi|385805841|ref|YP_005842239.1| 66 GSCPVSAIKVE 76
                                      58******977 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 !   15.1   4.2   1.5e-05     0.018       5      59 ..       3      73 ..       1      78 [] 0.70

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.5e-05
                           Fer4_19  5 eitiednrelCihsgnCvkglpevFdpkrk....pwi............kpdeasteeiievverCPSGAL 59
                                      +++++ +r+ Ci+ g+C +  p+vF+++ +     ++            + de+  e + +++ +CP  A+
  gi|385805841|ref|YP_005842239.1|  3 KVKVTIDRNTCIGCGVCANLCPDVFELNPNdgksSIVekfrvggdlgagEVDESLEECANSAAGSCPVSAI 73
                                      799**********************9876521213446666666666655566666666666666666555 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   1.2   1.3e-05     0.016      73      94 ..       4      25 ..       1      27 [. 0.83

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.3e-05
                           Fer4_22 73 fkekfgesgCvGCgRCieacpv 94
                                      +k ++++++C+GCg C + cp 
  gi|385805841|ref|YP_005842239.1|  4 VKVTIDRNTCIGCGVCANLCPD 25
                                      56678999************96 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   2.2   1.3e-05     0.015      32      48 ..      10      25 ..       1      28 [. 0.73
   2 ?   10.5   6.3   0.00043      0.52       2      15 ..      13      26 ..      12      77 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.3e-05
                            Fer4_9 32 seeaCigCgaCveaCpk 48
                                      + + CigCg C++ Cp 
  gi|385805841|ref|YP_005842239.1| 10 R-NTCIGCGVCANLCPD 25
                                      3.379999999999995 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00043
                            Fer4_9  2 CtgCgaCveaCpag 15
                                      C+gCg C + Cp  
  gi|385805841|ref|YP_005842239.1| 13 CIGCGVCANLCPDV 26
                                      77777777777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 491.42
//
Query:       gi|385805842|ref|YP_005842240.1|  [L=710]
Description: ferrous iron transport protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.3e-46  157.1   0.0    4.1e-46  156.4   0.0    1.4  1  FeoB_N       Ferrous iron transport protein B
    9.4e-18   64.5  20.8    1.6e-14   54.1   2.9    3.5  4  Gate         Nucleoside recognition
    3.4e-17   62.6   0.0    7.1e-17   61.5   0.0    1.5  1  MMR_HSR1     50S ribosome-binding GTPase
    3.2e-13   50.0   2.5    3.2e-13   50.0   2.5    1.7  2  FeoB_Cyto    FeoB cytosolic helical domain
    2.4e-12   46.3   1.1    2.4e-12   46.3   1.1    3.1  4  FeoB_C       Ferrous iron transport protein B C terminus
  ------ inclusion threshold ------
      0.032   14.1   0.1         11    5.9   0.0    2.3  2  RsgA_GTPase  RsgA GTPase
      0.094   12.0   0.0       0.16   11.2   0.0    1.3  1  Septin       Septin
       0.22   11.6   0.6        1.5    8.8   0.1    2.2  2  Dynamin_N    Dynamin family
        4.4    5.9  18.1     0.0037   16.1   1.9    2.6  3  DUF2207      Predicted membrane protein (DUF2207)


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 !  156.4   0.0     2e-49   4.1e-46       2     156 .]      18     172 ..      17     172 .. 0.99

  Alignments for each domain:
  == domain 1  score: 156.4 bits;  conditional E-value: 2e-49
                                       EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHHCTS CS
                            FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardflleee 78 
                                       ++ ++G pnvGk+t+fn++tg + +v+NwpG+tvekkeg+++++g+ + + DlPG+Y+ls++s ee+++ + +l+ +
  gi|385805842|ref|YP_005842240.1|  18 KILVAGSPNVGKSTFFNTVTGESVSVANWPGTTVEKKEGRVRYNGNVLCFSDLPGTYNLSSFSPEESITLENILNGK 94 
                                       7899************************************************************************* PP

                                       SSEEEEEEEGGGHHHHHHHHHHHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBTHHHHHHH CS
                            FeoB_N  79 pdvvvnvvdatnlernLyLtlqllelgvpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkegieellka 155
                                        d+++ +vd+  l ++Ly+ +q+lel  + +la+ ++d  ++kgi+i  + ++++Lgvp +++s+ +k+gi+ellk+
  gi|385805842|ref|YP_005842240.1|  95 WDAILILVDSLDLIKSLYFAAQVLELYSNAILAFTKSDITHSKGIHIRYDGIQRELGVPLIPISSLTKSGIDELLKE 171
                                       **************************************************************************998 PP

                                       H CS
                            FeoB_N 156 i 156
                                       i
  gi|385805842|ref|YP_005842240.1| 172 I 172
                                       6 PP

>> Gate  Nucleoside recognition
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       1.9   3.7e+03      90     101 ..     304     315 ..     285     366 .. 0.65
   2 !   22.4   1.5   5.5e-08   0.00011       2     109 ..     389     481 ..     388     484 .. 0.95
   3 ?   -2.4   0.2       2.8   5.5e+03       5      20 ..     495     510 ..     490     525 .. 0.76
   4 !   54.1   2.9     8e-18   1.6e-14       1     111 [.     553     680 ..     553     681 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.9
                              Gate  90 lfvllytpcvat 101
                                       + +l+y+  +a+
  gi|385805842|ref|YP_005842240.1| 304 FSILIYFTIFAI 315
                                       333333322222 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 5.5e-08
                              Gate   2 lkagpiillasiliwflssssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtlytsalgellqg 78 
                                       l ++p+i+   +l+++l++s+l  ri+  ++ +f+ +g  l++++  +l+++++   ++v+ + +++         +
  gi|385805842|ref|YP_005842240.1| 389 LSFLPLIMTTYALLGVLEDSGLGIRIALSFDRFFKIFG--LTGRSLFPLTLSLG---CNVPGVLSTR---------S 451
                                       6789**********************************..**************...*********9.........* PP

                              Gate  79 fdtpksalafllfvllytpcvatlavivrel 109
                                        +++ ++l+++  v +  pc a+l++i+ ++
  gi|385805842|ref|YP_005842240.1| 452 LEDKNERLSLIYSVPFV-PCQARLVIIMAFV 481
                                       ****************5.9*******99876 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 2.8
                              Gate   5 gpiillasiliwflss 20 
                                       +  i ++sili +ls+
  gi|385805842|ref|YP_005842240.1| 495 MVSIYAISILIALLSA 510
                                       5567788888888875 PP

  == domain 4  score: 54.1 bits;  conditional E-value: 8e-18
                              Gate   1 llkagpiillasiliwflss............ssllgrigkllepvfaplg..qeldwkatvslltgfaakevvvgt 63 
                                       l+kag+ii+++si++wfl +            +s++++ig +l+p+ +  g      wk++  + tg++ake  + t
  gi|385805842|ref|YP_005842240.1| 553 LKKAGTIIFALSIVVWFLLNfspsgnyapsieDSIASYIGSFLSPIGKMYGmnDVTAWKTAFLFETGIVAKEGFLET 629
                                       79***********************************************9998999********************9 PP

                              Gate  64 lgtly...tsalgellqgfdtpksalafllfvllytpcvatlavivrelgs 111
                                          l     s   ++++  ++ ++a+a+ll  +ly+pc+atl v+++e++s
  gi|385805842|ref|YP_005842240.1| 630 SVLLSggnVSVNEAISALGYSAPQAYAVLLAATLYVPCIATLSVLYSETKS 680
                                       8333355546677888899*****************************975 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.5   0.0   3.5e-20   7.1e-17       1      92 [.      18     110 ..      18     130 .. 0.75

  Alignments for each domain:
  == domain 1  score: 61.5 bits;  conditional E-value: 3.5e-20
                                       EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSS..HHHHHHHHHHHHHHHHC CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGlie..gaseekglgkaflalee 75 
                                       +++++G pNvGKSt++n+ tge + v+++pgtT + +egrv+++g+ + + D+pG ++  + s e++++ +   + +
  gi|385805842|ref|YP_005842240.1|  18 KILVAGSPNVGKSTFFNTVTGESVSVANWPGTTVEKKEGRVRYNGNVLCFSDLPGTYNlsSFSPEESITLENILNGK 94 
                                       5899***************************************************8754333344455555555677 PP

                                       TSEEEEEEETTTTCSHH CS
                          MMR_HSR1  76 adlillvvdaseeklkp 92 
                                        d+il++vd s + +k 
  gi|385805842|ref|YP_005842240.1|  95 WDAILILVD-SLDLIKS 110
                                       9********.5353433 PP

>> FeoB_Cyto  FeoB cytosolic helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0         8   1.6e+04      21      45 ..      87     111 ..      82     129 .. 0.70
   2 !   50.0   2.5   1.6e-16   3.2e-13       5      90 ..     191     279 ..     189     280 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 8
                         FeoB_Cyto  21 lkaklppRwlAlklLegDeelleel 45 
                                       l++ l+ +w A+ +L +  +l+++l
  gi|385805842|ref|YP_005842240.1|  87 LENILNGKWDAILILVDSLDLIKSL 111
                                       5677888888888887766666666 PP

  == domain 2  score: 50.0 bits;  conditional E-value: 1.6e-16
                         FeoB_Cyto   5 iEkaiekleellkesnlkaklppRwlAlklLegDeelleelked...pelraeveearkeleaelgedledvIvdar 78 
                                       +E  i++le++l   ++k k+  Rw+A+klLe+De +++++ ++    e+++++ee++k++ ++++  +++v+++ r
  gi|385805842|ref|YP_005842240.1| 191 LEPFIKELENALIPFKSKLKWRLRWIAIKLLEQDELVEKYVLNAlgsDEIKKKAEELIKKYIENYNRTPREVVISRR 267
                                       788999****999999999****************9999988654447***************************** PP

                         FeoB_Cyto  79 ykfiegilrevv 90 
                                       y+f+e+i++e v
  gi|385805842|ref|YP_005842240.1| 268 YDFVEKIVKENV 279
                                       *********966 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 ?   -3.2   1.2       3.6   7.1e+03       3      13 ..     307     317 ..     295     330 .. 0.64
   2 !   46.3   1.1   1.2e-15   2.4e-12       1      52 [.     495     547 ..     495     548 .. 0.93
   3 ?   -3.8   0.7       5.4   1.1e+04       4      14 ..     560     570 ..     558     573 .. 0.68
   4 ?   -2.2   0.7       1.8   3.6e+03       7      19 ..     694     706 ..     685     709 .. 0.55

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3.6
                            FeoB_C   3 slYllgilval 13 
                                       ++Y++ +++a+
  gi|385805842|ref|YP_005842240.1| 307 LIYFTIFAIAF 317
                                       34544444444 PP

  == domain 2  score: 46.3 bits;  conditional E-value: 1.2e-15
                            FeoB_C   1 lfslYllgilvallvalllkktt.lkgep.spfvmELPpYrlPslknvliktwe 52 
                                       ++s+Y+++il+all+all+++ + lk ++ s ++ E Pp ++P +k ++ ++w+
  gi|385805842|ref|YP_005842240.1| 495 MVSIYAISILIALLSALLIRR-FiLKSKEpSEMIAEVPPIHKPIVKVIWWHVWD 547
                                       79*******************.66887666***********************7 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 5.4
                            FeoB_C   4 lYllgilvall 14 
                                       +++l+i+v +l
  gi|385805842|ref|YP_005842240.1| 560 IFALSIVVWFL 570
                                       67777777776 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 1.8
                            FeoB_C   7 lgilvallvalll 19 
                                       + i+v +++ +ll
  gi|385805842|ref|YP_005842240.1| 694 VAIVVSFISYKLL 706
                                       3445555555544 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0    0.0063        13     102     123 ..      19      40 ..       6      58 .. 0.80
   2 ?    5.9   0.0    0.0054        11      48      97 ..     123     172 ..     103     177 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0063
                                       EEEECSTTSSHHHHHHHHCTT- CS
                       RsgA_GTPase 102 svlvGqSGvGKStLinallpel 123
                                       ++++G+  vGKSt+ n++++e 
  gi|385805842|ref|YP_005842240.1|  19 ILVAGSPNVGKSTFFNTVTGES 40 
                                       5679999***********9984 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0054
                                       EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHC CS
                       RsgA_GTPase  48 epvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkell 97 
                                       + +++++K D+++++    ++    ++lg++++ +s+ tk+g++el +++
  gi|385805842|ref|YP_005842240.1| 123 NAILAFTKSDITHSKGIHIRYDGIQRELGVPLIPISSLTKSGIDELLKEI 172
                                       7899************7778889999******************998765 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0     8e-05      0.16       3      33 ..      15      45 ..      13      64 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 8e-05
                                      EEEEEEEEEBTTSSCCCCCCTTSSSS----- CS
                            Septin  3 ieftlmvvGesglGkttlintlfetdlieee 33
                                      ++f ++v+G+  +Gk+t++nt+  +++  ++
  gi|385805842|ref|YP_005842240.1| 15 CNFKILVAGSPNVGKSTFFNTVTGESVSVAN 45
                                      689******************9998877664 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1   0.00076       1.5       1      25 [.      19      43 ..      19      52 .. 0.86
   2 ?    0.5   0.0      0.28   5.6e+02      90     127 ..     217     254 ..     159     291 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00076
                                      EEEEEBTTTTHHHHHHHHHTS--S- CS
                         Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilp 25
                                      i+v Gs + GKS++ n ++ge + +
  gi|385805842|ref|YP_005842240.1| 19 ILVAGSPNVGKSTFFNTVTGESVSV 43
                                      7899*****************9865 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.28
                                       -EEEEEEETTS-SEEEEE---B-SSSGTTSHHHHHHH.S CS
                         Dynamin_N  90 villkilsllvkgltlvDlPGldsvnkrdqelvkeyi.k 127
                                        i+l  ++ lv+++ ++   G d+++k+ +el+k+yi +
  gi|385805842|ref|YP_005842240.1| 217 AIKLLEQDELVEKY-VLNALGSDEIKKKAEELIKKYIeN 254
                                       56666666666666.456789999999999999999944 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.1   1.9   1.9e-06    0.0037     303     430 ..     187     378 ..      87     406 .. 0.69
   2 ?    1.1   2.0     0.065   1.3e+02     390     435 ..     475     519 ..     455     531 .. 0.66
   3 ?   -3.2   0.6       1.3   2.7e+03     389     409 ..     559     621 ..     546     701 .. 0.50

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.9e-06
                           DUF2207 303 d..........................tltilkkndeeldpyEkalldlLfdkseegks.lkeikkyakkskk..ka 350
                                       +                             i +k  e++   Ek++l++L +++ ++ +  + ikky+++ +   + 
  gi|385805842|ref|YP_005842240.1| 187 NylslepfikelenalipfksklkwrlR-WIAIKLLEQDELVEKYVLNALGSDEIKK-KaEELIKKYIENYNRtpRE 261
                                       2555555555555555555555555531.3344444555779********9444444.2566699999999998899 PP

                           DUF2207 351 kkfkkalkkwksavkk.kergyfdkkgkkklkkls..alglgliilglilillallllvll................ 408
                                         +++ ++ +++ vk+ ++++  +kk++ +  ++   +lg+++ il+++ i++++++++++                
  gi|385805842|ref|YP_005842240.1| 262 VVISRRYDFVEKIVKEnVAQKAVEKKPSMIERIFFvpVLGFLFSILIYFTIFAIAFTINIGfplnvifkyvglekvg 338
                                       999*************9888888888866554444113444444444444445555554448888888888888888 PP

                           DUF2207 409 .................................lvfllilllillliaiivlllf 430
                                                                        +               i+ l++
  gi|385805842|ref|YP_005842240.1| 339 ellenyslsgiisegfnrlsatlfpflslyvpnW---------------IASLIC 378
                                       8888888888888888885554444444443331...............333333 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.065
                           DUF2207 390 liilglilillallllvlllvfllilllillliaiivlllfsrllg 435
                                       +ii++++ ++++   l++ +v+ +i+++ +l++++ +ll+ + +l+
  gi|385805842|ref|YP_005842240.1| 475 VIIMAFVSVFFTSPILGA-SVMVSIYAISILIALLSALLIRRFILK 519
                                       344444444444444444.888888888888887777777644443 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 1.3
                           DUF2207 389 gliilglilillallllvll............................................l 409
                                       +++ l++++ +l++++                                                +
  gi|385805842|ref|YP_005842240.1| 559 IIFALSIVVWFLLNFSP--SgnyapsiedsiasyigsflspigkmygmndvtawktaflfetgiV 621
                                       33333333333333322..1234455555444444444444444444444444444444444440 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (710 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       934  (0.0520944); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); 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: 0.79u 0.34s 00:00:01.13 Elapsed: 00:00:00.53
# Mc/sec: 4031.80
//
Query:       gi|385805843|ref|YP_005842241.1|  [L=238]
Description: HAD-superfamily hydrolase [Fervidicoccus fontis Kam940]
Scores for 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   55.1   0.0    2.4e-14   53.8   0.0    1.6  1  HAD_2           Haloacid dehalogenase-like hydrolase
    1.9e-06   28.3   0.0    3.9e-06   27.3   0.0    1.6  1  Hydrolase       haloacid dehalogenase-like hydrolase
    6.1e-06   26.2   0.0    9.9e-06   25.5   0.0    1.3  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 !   53.8   0.0     4e-18   2.4e-14      17     174 ..      11     200 ..       7     204 .. 0.87

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 4e-18
                             HAD_2  17 iqafnelleeyglselseeelrkliglslrellrklgeseeeee..........................kieellr 67 
                                       ++++ ++l+e ++ +l   ++ k++g s +e+++++ + ++                             + e+l++
  gi|385805843|ref|YP_005842241.1|  11 FDVWDTILNEDKFYQLLSINIGKKLGKSGEEVFKNIMSIDRDAIkirleggfkniiydtaeyfsnrlglkNQEDLFN 87 
                                       5677888888888888888888888999888888888876655488888889999999999999999**97888888 PP

                             HAD_2  68 kyneekkkkevk..pydgvkelLeeLkeagyklgivTsk...sreaveekleqlgiesyFdvivtsedvekkKPdpe 139
                                        + e  + +e++   +++ ++ ++e+k++g+k+g+v +        ++  l+++g+ +yFd  + +++v+ +KP+ e
  gi|385805843|ref|YP_005842241.1|  88 SVIEIIESEEICslAFEDSISSIHEIKKMGMKIGLVGNVlfwPGMITRLILKRNGLLDYFDATIFQDEVGYQKPSKE 164
                                       8888777766663369**********************96656889999**************************** PP

                             HAD_2 140 viekaleklklkkeeviyvGDsp.tDieaakkagik 174
                                       +++ a ++l+++ +e   +GDs  +D+ +a   g+ 
  gi|385805843|ref|YP_005842241.1| 165 IFQIASKRLNVSLNELGHIGDSLeNDFVGAISSGMY 200
                                       ********************************9996 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   6.4e-10   3.9e-06       1     202 [.       6     190 ..       6     198 .. 0.75

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 6.4e-10
                                       SSEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTEHHHHTHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase   1 iktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrgayaigkpewl 77 
                                       ik++ fD+  T+++      +++  +               igk+l +  +++  ++ ++ +     a+ i  +  +
  gi|385805843|ref|YP_005842241.1|   6 IKALTFDVWDTILNED-KFYQLLSIN---------------IGKKLGKSGEEVFKNIMSIDRD----AIKIRLEGGF 62 
                                       7999999999999555.555666666...............8888888888886666666551....2333333333 PP

                                       HHH..HCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEH..HHHH. CS
                                       xxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxx. RF
                         Hydrolase  78 tal..dippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnp..etae. 149
                                       +    d  + + ++ g  ++++    +   ++ +  +i      +++    ++++k++g +++l+ +      +   
  gi|385805843|ref|YP_005842241.1|  63 KNIiyDTAEYFSNRLGLKNQEDLFNSVI--EIIESEEICSL--AFEDSISSIHEIKKMGMKIGLVGNVLFwpGMITr 135
                                       3333333555666667777777777777..77777777777..899999****************987644477774 PP

                                       HHHHHTT.GGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHH.H CS
                                       xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                         Hydrolase 150 raanqlG.ddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvn.D 202
                                        ++++ G  dyfda+i +d+++  kps+e+++ a ++L+++ +e  ++GD++  D
  gi|385805843|ref|YP_005842241.1| 136 LILKRNGlLDYFDATIFQDEVGYQKPSKEIFQIASKRLNVSLNELGHIGDSLEnD 190
                                       6666699********************************************9866 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   1.7e-09   9.9e-06       2      52 ..     158     208 ..     157     222 .. 0.93

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1.7e-09
                                       .STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSS CS
                    Hydrolase_like   2 lgKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGv 52 
                                       + KP++e++  a ++l++  +e   iGD+l+ D  gA   G+ + L+++  
  gi|385805843|ref|YP_005842241.1| 158 YQKPSKEIFQIASKRLNVSLNELGHIGDSLENDFVGAISSGMYGFLIKRDL 208
                                       68********************************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1397.66
//
Query:       gi|385805844|ref|YP_005842242.1|  [L=335]
Description: mevalonate kinase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-15   57.6   0.2    3.8e-15   56.0   0.1    1.8  2  GHMP_kinases_C   GHMP kinases C terminal
    3.7e-14   52.7   0.1      8e-14   51.6   0.1    1.6  1  GHMP_kinases_N   GHMP kinases N terminal domain
    2.3e-07   30.2   0.0    5.9e-07   29.0   0.0    1.8  1  GalKase_gal_bdg  Galactokinase galactose-binding signature
  ------ inclusion threshold ------
      0.044   13.6   0.0       0.11   12.3   0.0    1.7  1  SH3_19           Myosin X N-terminal SH3 domain
       0.12   12.3   0.9        0.3   10.9   0.7    1.7  1  Transcrip_act    Transcriptional activator


Domain annotation for each model (and alignments):
>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.4   4.9e+03      55      66 ..     113     124 ..     112     143 .. 0.81
   2 !   56.0   0.1   1.1e-18   3.8e-15       2      79 ..     238     311 ..     237     316 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.4
                    GHMP_kinases_C  55 GaGgGptvfalf 66 
                                       GaG+G++ ++ +
  gi|385805844|ref|YP_005842242.1| 113 GAGLGTSAAVAV 124
                                       999999988766 PP

  == domain 2  score: 56.0 bits;  conditional E-value: 1.1e-18
                    GHMP_kinases_C   2 lealergdlellgellnlsqrselkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvara 78 
                                        +al++++l +lg  +nl++   l++ +g+++++l el+  ++++Ga+g+kl+GaGgG++v+al+  +++++ ++ a
  gi|385805844|ref|YP_005842242.1| 238 ESALLNNNLHELGSFMNLNHS--LLDALGVSTRRLNELVYVARDAGAYGSKLTGAGGGGCVIALT--PENQDVIETA 310
                                       57999****************..9****************************************9..5555555555 PP

                    GHMP_kinases_C  79 l 79 
                                       +
  gi|385805844|ref|YP_005842242.1| 311 M 311
                                       5 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 !   51.6   0.1   2.2e-17     8e-14       2      66 .]     104     170 ..     103     170 .. 0.92

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 2.2e-17
                                       EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHH..HH.HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                    GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglsl..ee.aklaleaerlaqggngsggDvaasvyGg 66 
                                       i+i+se+PvgaGLG SAA+av+++aA ++ ++ +l  ee a+l+ + e+++q g  s++D +  + Gg
  gi|385805844|ref|YP_005842242.1| 104 IEIRSEMPVGAGLGTSAAVAVSTIAAYAYVNEYELkkEEiANLGWQVEKEVQ-GIASPMDTSITAIGG 170
                                       89***************************99988964339************.********9988887 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 !   29.0   0.0   1.6e-10   5.9e-07      11      48 ..       4      41 ..       1      42 [. 0.93

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 1.6e-10
                                      -EEEEEEEEEEEE--S-TTTT-EEEEEEEEEEEEEEEE CS
                   GalKase_gal_bdg 11 pfvasAPGRvnLiGEHtDYngGfVlpmAieqdiyiavs 48
                                      +++asAPG v L GEH    g+  l ++i+++iy+++ 
  gi|385805844|ref|YP_005842242.1|  4 KVIASAPGKVTLFGEHAVVYGYPALVVSIDKRIYAIAE 41
                                      589********************************986 PP

>> SH3_19  Myosin X N-terminal SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.1e-05      0.11      14      34 ..      57      77 ..      50      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.1e-05
                            SH3_19 14 lPstVsscddgsvvlttdYGe 34
                                      +P  V s  +++vvl+tdYG 
  gi|385805844|ref|YP_005842242.1| 57 VPGIVISYIGNEVVLETDYGL 77
                                      7999****************5 PP

>> Transcrip_act  Transcriptional activator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.7   8.5e-05       0.3      33      90 ..     176     236 ..     162     253 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8.5e-05
                     Transcrip_act  33 akeeeierkklevrekveaqLgrveeetkr...LaeireeLealadPlrkevavvrkkida 90 
                                         ++ +er  +ev+e +   +g ve e++    +a++r+++e+  +   k ++ +   +++
  gi|385805844|ref|YP_005842242.1| 176 YIDKTVERTPIEVKEEIPLLIGYVERESRTkdmVAMVRKKIESYPEIYMKIMELIGNTVEK 236
                                       557789********************98853337999999999887777777766666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); 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: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2123.63
//
Query:       gi|385805845|ref|YP_005842243.1|  [L=456]
Description: hypothetical protein FFONT_0803 [Fervidicoccus fontis Kam940]
Scores for 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   90.4  40.1    1.4e-25   89.9  40.1    1.2  1  TctA      Tripartite tricarboxylate transporter TctA family
  ------ inclusion threshold ------
        5.3    6.9   7.3        7.9    6.3   1.3    2.9  3  Bap31     Bap31/Bap29 transmembrane region


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 !   89.9  40.1   1.6e-29   1.4e-25       3     405 ..      13     437 ..      12     441 .. 0.78

  Alignments for each domain:
  == domain 1  score: 89.9 bits;  conditional E-value: 1.6e-29
                              TctA   3 lvllGvllGtliGllPGlhatlavalllpltf..gldpeaalilllgiyvgaifggsipaillgvPGtpssvatvld 77 
                                       l+++  +++++iG+lPG+++t+++a ++ + +  gldp+++l+ +++ +v+  ++++ip +l g+PG  ++v+ v d
  gi|385805845|ref|YP_005842243.1|  13 LAAISSIIYIFIGILPGTDETATMAPVALALLlaGLDPIVVLAWFMASIVAFKIADAIPVALAGIPGGVMAVPQVPD 89 
                                       578999***************7666544444478******************************************* PP

                              TctA  78 gyplakqGrageAlrlaaigSfiGglvsvllllllapllakvalkf.........gpaeyfalillglvliailsek 145
                                       +    + G a   lr+   +++++++  ++++l+++ +l ++               a  f+lil g++++a+ s++
  gi|385805845|ref|YP_005842243.1|  90 ALVAKEHGLADTLLRKGNSAALVAAITVTIFVLVVSYVLMPLGAWLnttdlimsvKVARWFWLILGGVIFLAVTSKN 166
                                       **99999*****************************9999999888999999999********************** PP

                              TctA 146 sllkglialllglllgtvgldpnsgtpRftfgsielldgislvpvliGlFgis..elltsleskskip......... 211
                                       +ll  +++ ++++l++ +    ++g+p     si+l+ gi++ p++  +F     el +s+e+k k+          
  gi|385805845|ref|YP_005842243.1| 167 KLLGLFAIPAFAILVQGIRG--VYGKP----VSISLFLGITIGPIIYEIFTSLngELRKSMEKKGKKIvklskvgki 237
                                       **************997765..66677....78*****************975447888887665554788877776 PP

                              TctA 212 ....lslkdlkkslptilrgsliGtivGilPgvGasiaaflayavakrlskkpekfgkgaiegvaapeaannaaagg 284
                                            ++   +++l  ++ + + +++  ++++vG +i    +  ++kr   + +      +eg+        +++gg
  gi|385805845|ref|YP_005842243.1| 238 sinpFKNLTKEEILHIFIWSPISSILATVMSPVGLTILIGDTLRETKRNRLQGSVLAYTVREGI-----KLGTYIGG 309
                                       5543122222234445666777777777********8766666666653222222334444444.....445699** PP

                              TctA 285 aliplltlgipgsgvaavllgal..lihglqpgpeLf..t..enpelvyallasllianvlllvlgllliklfakll 355
                                       +lipll++g  + +++a   + +  +i  ++  p     t  +   +v++ + s++i+  ++++l ++ ++ ++ ++
  gi|385805845|ref|YP_005842243.1| 310 TLIPLLVIGAATGPMSAGPAAPFfqMIPTINDKPFHYilThySYSFIVLIAIYSVIISLAISYPLIVKYSRRLTLFV 386
                                       *********99887775444433112333333333223341123334444556677777777777777777777755 PP

                              TctA 356 ..kipkelLlpiilvllvigayalnnslfdvlvmlifgvlGlllrrlgvpla 405
                                         +i+ e L+ ++++++v++ay+ ++   +++ ml++ v+  +l++lgv+l 
  gi|385805845|ref|YP_005842243.1| 387 fnRISAESLYGLFVAIAVLLAYYDAGI-PGIFGMLLVSVISGALNKLGVSLG 437
                                       8**************************.********************9975 PP

>> Bap31  Bap31/Bap29 transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.2   0.2       1.6   1.4e+04      51      59 ..     115     123 ..     102     129 .. 0.49
   2 ?    3.0   0.0    0.0093        83      24      72 ..     240     286 ..     235     299 .. 0.83
   3 ?    6.3   1.3   0.00088       7.9       5      59 ..     353     406 ..     350     412 .. 0.72

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 1.6
                             Bap31  51 lkillifll 59 
                                       +++++++l+
  gi|385805845|ref|YP_005842243.1| 115 ITVTIFVLV 123
                                       222222222 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.0093
                             Bap31  24 lPlpsavrkklfksllvsklsaklqialkillifllllflDavrrvrkv 72 
                                        P+ + ++++++++ ++s++s+ l++++  + + l++l+ D++r+ ++ 
  gi|385805845|ref|YP_005842243.1| 240 NPFKNLTKEEILHIFIWSPISSILATVM--SPVGLTILIGDTLRETKRN 286
                                       58889999*************9988766..5667888899999998875 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.00088
                             Bap31   5 ytlvaalLvaeivvvllLvlPlpsavrkklfksllvsklsaklqialkillifll 59 
                                       y++++++ +  +++ l ++ Pl+ +  ++l  +++ + +sa+  ++l++ +++ll
  gi|385805845|ref|YP_005842243.1| 353 YSFIVLIAIYSVIISLAISYPLIVKYSRRLTLFVF-NRISAESLYGLFVAIAVLL 406
                                       77888888889999999999999999999877665.5566666666666655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       915  (0.0510346); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 3117.24
//
Query:       gi|385805846|ref|YP_005842244.1|  [L=84]
Description: hypothetical protein FFONT_0804 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0069   16.0   0.3     0.0079   15.8   0.3    1.1  1  Virul_fac_BrkB  Virulence factor BrkB


Domain annotation for each model (and alignments):
>> Virul_fac_BrkB  Virulence factor BrkB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.3   4.4e-07    0.0079     157     212 ..      13      69 ..       3      77 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.4e-07
                    Virul_fac_BrkB 157 l.llqllrwlvallllvlafallYrvlpnvkvrlraalpGallaallwllvkilfsl 212
                                       + +++l ++++a l+ +++ +llY+++p    r  + l+ al  +l+ ++++i+f +
  gi|385805846|ref|YP_005842244.1|  13 GeYVSLKELTIASLISIAFAFLLYYFAPYIAMRSNPSLINALKITLGAIGASIGFLI 69 
                                       35678889999999***********************99999999999999999965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 563.38
//
Query:       gi|385805847|ref|YP_005842245.1|  [L=133]
Description: hypothetical protein FFONT_0805 [Fervidicoccus fontis Kam940]
Scores for complete 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-16   58.4   0.1    8.7e-16   58.2   0.1    1.0  1  DUF296    Plants and Prokaryotes Conserved (PCC) domain


Domain annotation for each model (and alignments):
>> DUF296  Plants and Prokaryotes Conserved (PCC) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.2   0.1   4.9e-20   8.7e-16       2     104 ..       3     118 ..       2     120 .. 0.88

  Alignments for each domain:
  == domain 1  score: 58.2 bits;  conditional E-value: 4.9e-20
                                       EEEEEE-TTSBHHHHHHHHHHHHT-SSEEEEEEEEEEEEEE.EEECTTT......EE-.....S-EEEEEEEEEEEE CS
                            DUF296   2 phvlrlepGediveaieefarkrgiraacvlsaiGavsnvt.rladgee......kll.....grfeilslsGtilp 66 
                                       ++ l++++G+++ + +++f++ +g +++++  +iG +++v+ +++++++      k         +e+ls++G+++ 
  gi|385805847|ref|YP_005842245.1|   3 VIPLKIPEGSKLPDFVISFIQVNGLKGGYL-VGIGGLEEVEiGVLNRKTnqyevsK-FtrngdSTIELLSITGNYFV 77 
                                       6789*************************9.***********99999999665552.0566668************* PP

                                       ..TT...EEEEEEEEETTSEEEEEEEEEE.EEEEEEEEEEEEE CS
                            DUF296  67 ..dg...lHlhvslagedgqvvgGhlaegplvaattvevvvae 104
                                         dg   +H h+++a+++++v gGhl+   ++++  ve+++ e
  gi|385805847|ref|YP_005842245.1|  78 ksDGniaFHAHATFATGHEKVAGGHLI-S-AKVSPYVELFLVE 118
                                       7644899********************.4.6889****99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       255  (0.0142228); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.52
# Mc/sec: 774.44
//
Query:       gi|385805848|ref|YP_005842246.1|  [L=132]
Description: hypothetical protein FFONT_0806 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      5e-14   52.5   0.2    3.6e-08   33.4   0.0    2.0  2  DrsE_2     DsrE/DsrF/DrsH-like family
    4.9e-09   36.6   0.4    1.3e-08   35.2   0.4    1.6  1  DrsE       DsrE/DsrF-like family
  ------ inclusion threshold ------
      0.015   14.7   0.1      0.018   14.3   0.1    1.1  1  TAtT       TRAP transporter T-component
      0.032   14.2   0.0      0.046   13.7   0.0    1.2  1  PhaP_Bmeg  Polyhydroxyalkanoic acid inclusion protein (PhaP_B


Domain annotation for each model (and alignments):
>> DrsE_2  DsrE/DsrF/DrsH-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.1   2.1e-07   0.00095       8      55 ..       4      52 ..       1      64 [. 0.73
   2 !   33.4   0.0   8.1e-12   3.6e-08      76     153 .]      51     131 ..      46     131 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2.1e-07
                                      EE----H.HHHHHHHHHHHHHHTT-EEEEEE-GGGGGGGB-GG.G---T CS
                            DrsE_2  8 ifskgtldkalaalilAsgAaalglevtiFftFwGLnilrkee.kkkvk 55
                                       +++g  d+     +l sgA a+g+ev++F   wG+ +++k+  kk+++
  gi|385805848|ref|YP_005842246.1|  4 AVFSGSIDRLTGLAMLVSGAVAMGYEVELFLQLWGVYAFKKDVvKKNMN 52
                                      555566655555557889***********************97344444 PP

  == domain 2  score: 33.4 bits;  conditional E-value: 8.1e-12
                                       S-GGGHHHHH..HHHHHHHCT---HHHHHHHHHHTT.-EEEEEHHHHHHHT--GGGB-TT-.EEE-HHHHHHHHHC- CS
                            DrsE_2  76 mnmagigtkm..mkkvmkekgvasleeLleaakeag.vklvaCqmtmdlmglkkeelidgv.eiagaatylkeaeea 148
                                       mn+++++ k   + k ++e +v+s  +++++ake+g vk++aC  +  + ++kke+l + v  i+gaat+++++++a
  gi|385805848|ref|YP_005842246.1|  51 MNFSEFQDKApeVAKRLQELNVPSWFDIIKEAKENGsVKIYACSAAASIWNVKKEDL-ELVdDIIGAATWIEKMSKA 126
                                       5555555544114567899***************988******************97.56669************** PP

                                       SEEEE CS
                            DrsE_2 149 dvnLf 153
                                       d++Lf
  gi|385805848|ref|YP_005842246.1| 127 DITLF 131
                                       ****9 PP

>> DrsE  DsrE/DsrF-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.4     3e-12   1.3e-08      25     114 ..      21     129 ..       4     131 .. 0.88

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 3e-12
                                       HHHHTTT-EEEEEE-GGGGGGGBS...................---TGGGTS---GGGGGGCGGGT.-EEEEEHHHH CS
                              DrsE  25 laaaalghevsvffygdGvllllk...................gqtanpadeknlaellkalkeyg.vklyvCgqaa 81 
                                         a a+g+ev++f+   Gv++++k                   ++  ++ + ++  + +k++ke+g vk+y+C +aa
  gi|385805848|ref|YP_005842246.1|  21 SGAVAMGYEVELFLQLWGVYAFKKdvvkknmnfsefqdkapevAKRLQELNVPSWFDIIKEAKENGsVKIYACSAAA 97 
                                       5567899****************************88888888777777788888999******************* PP

                                       HHTT--GGGE-T--EEEE-HHHHHHHHHH-SEE CS
                              DrsE  82 kargldededlgvgvevsglgelaelqnegdrv 114
                                          +++ +edl++   + g+++++e+++++d  
  gi|385805848|ref|YP_005842246.1|  98 SIWNVK-KEDLELVDDIIGAATWIEKMSKADIT 129
                                       ******.67775688999999*********965 PP

>> TAtT  TRAP transporter T-component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   4.1e-06     0.018      83     157 ..      54     127 ..      48     130 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.1e-06
                                       HHHHHHSTTHHHHHTSS-HHHHHHHHHT--GGGHHHHHHHHHHHHHHHHTS-TTSS-HHHHHHHHHHHHHHHHH- CS
                              TAtT  83 raLetaydgltkalregeadeleaaLaklkkedvpalywaaaawasaialdkedpallaelpkvealmervlelD 157
                                       +  + ++++++k+l+e +++ +  +++++k++    +y+ ++a as  +++ked++l++++  +++ +e+  + D
  gi|385805848|ref|YP_005842246.1|  54 SEFQDKAPEVAKRLQELNVPSWFDIIKEAKENGSVKIYA-CSAAASIWNVKKEDLELVDDIIGAATWIEKMSKAD 127
                                       5667789999**********************9999996.67778899*******************99998877 PP

>> PhaP_Bmeg  Polyhydroxyalkanoic acid inclusion protein (PhaP_Bmeg)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0     1e-05     0.046      78     123 ..      42      83 ..      32      87 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1e-05
                         PhaP_Bmeg  78 lrskaGnkvednieEwtdkleevsakleklalspsKssldllkkae 123
                                       + +k  +k + n++E++dk  ev+ +l++l++    s +d++k a+
  gi|385805848|ref|YP_005842246.1|  42 F-KKDVVKKNMNFSEFQDKAPEVAKRLQELNVP---SWFDIIKEAK 83 
                                       5.4555778*********************974...5667766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); expected 358.6 (0.02)
Passed bias filter:                      611  (0.0340789); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 853.75
//
Query:       gi|385805849|ref|YP_005842247.1|  [L=443]
Description: putative DNA-binding protein (regulator) [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-28   98.9   0.0    3.6e-28   97.9   0.0    1.5  1  DUF1743          Domain of unknown function (DUF1743)
    5.7e-07   29.4   0.1    1.2e-06   28.4   0.1    1.5  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
     0.0017   18.2   2.4     0.0034   17.3   2.4    1.4  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.006   16.6   0.8      0.011   15.8   0.8    1.3  1  DZR              Double zinc ribbon
  ------ inclusion threshold ------
      0.047   13.6   0.9      0.083   12.8   0.9    1.3  1  C1_1             Phorbol esters/diacylglycerol binding domain
      0.049   13.7   0.7         13    6.0   0.0    2.4  2  Zn-ribbon_8      Zinc ribbon domain
      0.067   12.6   3.4       0.55    9.7   0.1    2.4  2  zf-ribbon_3      zinc-ribbon domain
       0.17   11.9   1.6       0.32   11.0   1.6    1.4  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
       0.31   10.5   2.0       0.82    9.1   2.0    1.6  1  zf_Rg            Reverse gyrase zinc finger
        0.4   10.4   1.4        0.8    9.4   1.4    1.4  1  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
       0.47   10.4   2.4          1    9.3   2.4    1.5  1  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit


Domain annotation for each model (and alignments):
>> DUF1743  Domain of unknown function (DUF1743)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.9   0.0   2.2e-31   3.6e-28       3     116 .]     147     258 ..     145     258 .. 0.97

  Alignments for each domain:
  == domain 1  score: 97.9 bits;  conditional E-value: 2.2e-31
                                       HHHHHHHHHH-..-TTS-EEEEEEEE-GGGTT---EEHHHHHHHHHHHTTCECTSEBTTTTCECCS-STTSSEEEEE CS
                           DUF1743   3 giiGAtaalganialedstyEllaYreperwgerevdeesvieadektypetfdnvDlshklvvlvPhtpdpvlfGi 79 
                                        iiGA+ alg+  + +dst+EllaYr+p ++ger++d+ +  ++  + y++ f+n+D ++kl+v  P++pdpvl Gi
  gi|385805849|ref|YP_005842247.1| 147 SIIGAVSALGYMYSGDDSTFELLAYRMPGETGERKIDNLTAGKVLLS-YKTLFNNFDEKRKLLVASPKGPDPVLIGI 222
                                       69*********99999*************************999765.9**************************** PP

                                       EES-HHHHHHHHHCSEE..S-EECEEEEEESTTS-TT CS
                           DUF1743  80 rgedpeallkaakeilskeeeseemavfrtnqgtdah 116
                                       rg +p+++++a+ +++  ee++ e+++f+tnq+tdah
  gi|385805849|ref|YP_005842247.1| 223 RGYEPKDMVDAFYKLKI-EEKIWEWCIFKTNQHTDAH 258
                                       *****************.9****************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 !   28.4   0.1   7.4e-10   1.2e-06       3      72 ..     275     346 ..     273     350 .. 0.92

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 7.4e-10
                                       EEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET..HHHHHHHTTS-TTSEEEEE.EEEEECTTSSEEEEEEE CS
                   tRNA_anti-codon   3 vaGrvtsisdrsggkvifidlrDgtgriqvvlfr..eeatklaenlkeGdvvrvt.Grvkrrpggelelkvee 72 
                                       + G vt++ + ++g+++ i++ Dg+g+i v++ +  + + ++a++lkeGd +++  G v++ ++g +   +e+
  gi|385805849|ref|YP_005842247.1| 275 IYGTVTKKPEVKKGGHVLIEVSDGSGTIDVIFYSetNPMNEIASRLKEGDNIGILgGAVEKKDEG-IIFEAEK 346
                                       67999999999********************************************9999999999.7777766 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 !   17.3   2.4   2.1e-06    0.0034      31      55 ..     363     387 ..     361     390 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.1e-06
                    OrfB_Zn_ribbon  31 CseCgsknkealsgrtfkCpnCgfe 55 
                                       C++Cg+++k a +g+ +kC+nCgf+
  gi|385805849|ref|YP_005842247.1| 363 CPKCGKRLKSAGKGKGYKCDNCGFK 387
                                       ***********************98 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.8   6.5e-06     0.011      14      40 ..     362     390 ..     355     393 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.5e-06
                               DZR  14 fCseCgtklkavaa..edrCpsCgekvdp 40 
                                        C++Cg++lk++ +   ++C++Cg k+++
  gi|385805849|ref|YP_005842247.1| 362 LCPKCGKRLKSAGKgkGYKCDNCGFKTSE 390
                                       7*********888899*******988765 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 ?   12.8   0.9   5.1e-05     0.083      14      37 ..     363     387 ..     358     391 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.1e-05
                                       -TTT-SB--S.SSS-EEEETTT--E CS
                              C1_1  14 CkhCgeflwg.kekqglkCswCkll 37 
                                       C +Cg+ l+  +   g+kC++C+++
  gi|385805849|ref|YP_005842247.1| 363 CPKCGKRLKSaGKGKGYKCDNCGFK 387
                                       9*******99899*********986 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0    0.0078        13      26      36 ..     359     370 ..     350     372 .. 0.75
   2 ?    5.7   0.1      0.01        17       6      20 ..     379     394 ..     378     402 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0078
                       Zn-ribbon_8  26 lta.CPeCgsev 36 
                                       l + CP+Cg+++
  gi|385805849|ref|YP_005842247.1| 359 LNPlCPKCGKRL 370
                                       4455*****976 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.01
                       Zn-ribbon_8   6 YrCeeCghefe.vlqs 20 
                                       Y+C++Cg +   +l +
  gi|385805849|ref|YP_005842247.1| 379 YKCDNCGFKTSeKLEK 394
                                       9******543335555 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1   0.00034      0.55      12      26 .]     356     370 ..     353     370 .. 0.83
   2 ?    3.0   0.6     0.043        71      18      24 ..     380     386 ..     378     388 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00034
                       zf-ribbon_3  12 lssddnvCpyCGtkl 26 
                                       +++  + Cp+CG++l
  gi|385805849|ref|YP_005842247.1| 356 VKELNPLCPKCGKRL 370
                                       5788899*****987 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.043
                       zf-ribbon_3  18 vCpyCGt 24 
                                       +C +CG 
  gi|385805849|ref|YP_005842247.1| 380 KCDNCGF 386
                                       4777775 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 ?   11.0   1.6    0.0002      0.32      19      44 ..     361     385 ..     357     387 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0002
                     Zn_Tnp_IS1595  19 fvCPhCgsrkayriktrglfqCkeCr 44 
                                       + CP+Cg+r     k+ + ++C  C+
  gi|385805849|ref|YP_005842247.1| 361 PLCPKCGKRLKSAGKG-KGYKCDNCG 385
                                       67*****994444455.66******8 PP

>> zf_Rg  Reverse gyrase zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   2.0    0.0005      0.82       8      37 ..     361     390 ..     358     401 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0005
                             zf_Rg   8 klCPNCgGdisdeRlekGLpCkrClPkegd 37 
                                        lCP Cg  +++    kG  C +C  k  +
  gi|385805849|ref|YP_005842247.1| 361 PLCPKCGKRLKSAGKGKGYKCDNCGFKTSE 390
                                       69**********************655555 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   1.4   0.00049       0.8       4      28 ..     361     385 ..     359     386 .. 0.94

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00049
                     zf-NADH-PPase   4 rFCgrCGaptepaeggwarvCpaCg 28 
                                       + C++CG + + a  g +  C++Cg
  gi|385805849|ref|YP_005842247.1| 361 PLCPKCGKRLKSAGKGKGYKCDNCG 385
                                       57**********************8 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   2.4   0.00061         1       4      28 ..     363     385 ..     362     388 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00061
                                       ESTTTSBEEEEECSCCCEEEESSSS CS
                    RNA_POL_M_15KD   4 CpkCgNlLlpkedkegknfeCrqCg 28 
                                       CpkCg  L ++++ +g  + C++Cg
  gi|385805849|ref|YP_005842247.1| 363 CPKCGKRLKSAGKGKG--YKCDNCG 385
                                       *************999..89****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 2650.60
//
Query:       gi|385805850|ref|YP_005842248.1|  [L=83]
Description: AsnC family transcriptional regulator [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      4e-15   55.5   0.7    4.4e-15   55.4   0.7    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 !   55.4   0.7   2.4e-19   4.4e-15       1      74 [.       6      76 ..       6      77 .. 0.94

  Alignments for each domain:
  == domain 1  score: 55.4 bits;  conditional E-value: 2.4e-19
                                      EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
                    AsnC_trans_reg  1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74
                                      vl++ e g+    ee+   + ++ eV+e+y+v G yd ++kv +  ++ l +++  ++++lp v++t t+iv e
  gi|385805850|ref|YP_005842248.1|  6 VLINAEIGS---EEEVFNDITKINEVTEAYVVYGVYDVIAKVEADTMDKLKEIIASHIRKLPKVRSTLTMIVVE 76
                                      567777778...899*********************************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); 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 0.26s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 541.07
//
Query:       gi|385805851|ref|YP_005842249.1|  [L=317]
Description: GHMP kinase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00017   21.9   0.1     0.0011   19.3   0.0    2.1  2  GHMP_kinases_C  GHMP kinases C terminal
  ------ inclusion threshold ------
      0.027   14.7   0.2      0.054   13.7   0.2    1.5  1  GHMP_kinases_N  GHMP kinases N terminal domain


Domain annotation for each model (and alignments):
>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.17   1.5e+03      40      64 ..     107     129 ..      99     151 .. 0.80
   2 !   19.3   0.0   1.2e-07    0.0011       5      81 ..     212     290 ..     207     295 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.17
                    GHMP_kinases_C  40 lealselGalgaklsGaGgGptvfa 64 
                                       ++++  +G   + +sG G ++++++
  gi|385805851|ref|YP_005842249.1| 107 KKIAVLAG--RGTISGIGIYGFIYG 129
                                       55555566..899999999999997 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 1.2e-07
                    GHMP_kinases_C   5 lergdlellgellnlsqrs.....elkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqva 76 
                                       l  ++++l+g+++ + q        + +  + +++e e+++e l+  G   +++ ++++Gp+ ++++ + ++ e+++
  gi|385805851|ref|YP_005842249.1| 212 LISKNIGLFGKGIEDIQKHmgeyfSKYQGGEFSSEETEKAVEVLRHSG--TVGIGQSSWGPAAYGFY-EVEKEEEIR 285
                                       5567888888888888888888874444588899**************..*****************.666667787 PP

                    GHMP_kinases_C  77 ralre 81 
                                        ++ +
  gi|385805851|ref|YP_005842249.1| 286 KKIEK 290
                                       77733 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 ?   13.7   0.2   6.1e-06     0.054       8      66 .]      76     130 ..      69     130 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.1e-06
                                       SHTTSSSCHHHHHHHHHHHHHHHHTTEHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                    GHMP_kinases_N   8 iPvgaGLGSSAAlavalvaAllallglsleeaklaleaerlaqggngsggDvaasvyGg 66 
                                        P  +GLGS + l++++++ l   +++++   +l   a  la++g  sg+ ++ ++yGg
  gi|385805851|ref|YP_005842249.1|  76 PPSQKGLGSTTQLSLSIAKGLSVICSKKI---NLKKIAV-LAGRGTISGIGIYGFIYGG 130
                                       58899********************7553...4444444.7778999***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       728  (0.0406046); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1982.17
//
Query:       gi|385805852|ref|YP_005842250.1|  [L=183]
Description: hypothetical protein FFONT_0810 [Fervidicoccus fontis Kam940]
Scores for complete 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-39  134.0   0.0    2.9e-39  133.7   0.0    1.1  1  Ribo_biogen_C  Ribosome biogenesis protein, C-terminal


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 !  133.7   0.0   1.6e-43   2.9e-39       1     127 []      50     177 ..      50     177 .. 0.93

  Alignments for each domain:
  == domain 1  score: 133.7 bits;  conditional E-value: 1.6e-43
                                       EEE-TT-SSB--GGGHHHHHHT-EEEE---TTT--GGG..TTT-E....EB--S-B--STTTTT-BS---HHHHHHH CS
                     Ribo_biogen_C   1 ivlspkakkvlspaDreiveksgiavvdcsWarleevk..fkklkakeerlLPyLvAaNpvnYgkplkLscvEAlaa 75 
                                       ivl+p+++kv+s++D + ++ +gi vvd sW+++ e    +  +k   +r+LP+++A+Np+nYg ++kLs++EAlaa
  gi|385805852|ref|YP_005842250.1|  50 IVLDPFSQKVISKDDIS-YNLNGILVVDRSWNKILEKGgeVFPFKFGVRRRLPIFIASNPINYGIAYKLSSAEALAA 125
                                       8************9955.5889***********98776335556888****************************** PP

                                       HHHHTT-HHHHHHHHTSSTTHHHHHHHCHHHHHHH.TT--HHHHHHHHHHHH CS
                     Ribo_biogen_C  76 alyilglkeeaeellskfkwgeeFlelnkelleeYakckdseevvevqkeyl 127
                                       al+ilg+ e+a+e+ls fkwge+F++ln++l+ +Y k++++++v+e+++e++
  gi|385805852|ref|YP_005842250.1| 126 ALIILGCIERAKEILSYFKWGENFFSLNSKLIIDYVKASNEKDVLEIEEEFI 177
                                       *************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1166.54
//
Query:       gi|385805853|ref|YP_005842251.1|  [L=138]
Description: hypothetical protein FFONT_0811 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.05   13.5   0.2        0.2   11.5   0.1    1.8  2  CheZ      Chemotaxis phosphatase, CheZ


Domain annotation for each model (and alignments):
>> CheZ  Chemotaxis phosphatase, CheZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   1.1e-05       0.2      35     111 ..       1      75 [.       1      79 [. 0.86
   2 ?   -0.4   0.0     0.052   9.3e+02     144     158 ..     114     128 ..     108     136 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.1e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              CheZ  35 ipdardrLeyvielTeqAAertldavekalpladklkeeakeleeewerllerelekeefrelvkeveaflkeveek 111
                                       ++d +  L+yv+e  e  ++  ++++ +a+++ ++l++++k ++ +  +++ + ++  ++r+ +k+ve++lk++ ++
  gi|385805853|ref|YP_005842251.1|   1 MSDEKADLQYVVEQIEIPSKLIFSCIHAAKAMEEALNAKSKGVSLR--NFQFEVIRRLTMRKQAKDVESLLKDIGNE 75 
                                       5788999**********************************99866..66667788888888888888888887665 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.052
                                       XXXXXXXXXXXXXXX CS
                              CheZ 144 keveskLvqllleas 158
                                       +++e+kLv+l++ +s
  gi|385805853|ref|YP_005842251.1| 114 EDIEKKLVSLIALTS 128
                                       689******998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); 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: 00:00:00.47
# Mc/sec: 873.95
//
Query:       gi|385805854|ref|YP_005842252.1|  [L=212]
Description: purine phosphoribosyltransferase [Fervidicoccus fontis Kam940]
Scores for complete 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   89.1   0.0    3.2e-25   88.5   0.0    1.2  1  Pribosyltran  Phosphoribosyl transferase domain
    0.00022   20.9   1.0      0.014   15.1   0.3    2.6  3  DUF956        Domain of unknown function (DUF956)
     0.0042   16.6   0.0     0.0058   16.1   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 !   88.5   0.0   5.4e-29   3.2e-25       8     153 ..      12     151 ..       9     156 .. 0.94

  Alignments for each domain:
  == domain 1  score: 88.5 bits;  conditional E-value: 5.4e-29
                                       ---EEEEEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE--- CS
                      Pribosyltran   8 npaildavarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlled 84 
                                       ++ i++ava ++++i+e+ n++p vvvgi+rgG+++a i ad L+++     + k++++  e++ r ++ ++ l  d
  gi|385805854|ref|YP_005842252.1|  12 WEDIENAVAAISEKIIES-NFNPNVVVGILRGGWIPARIFADFLGIKDIGAIEIKFYKGIEEKMERPVITQP-LVLD 86 
                                       455677************.**********************************************9999887.**** PP

                                       -TTSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHHHHHHH-TTS.....EEEEEEE- CS
                      Pribosyltran  85 pagkkVliVDDildtGgTllaalelLkekgpeevriavlvdkpateeevdknakrvfslspdnfvavvg 153
                                       +++k Vl+VDD+ d+G++l+ al ++  +gp+ ++++ l+ kp +++ +d+++ +++    +++v++++
  gi|385805854|ref|YP_005842252.1|  87 IRNKNVLLVDDVADSGKSLQTALSAINFYGPKNLKTVSLYVKPWSVIIPDYYYGETD----KWIVFPWE 151
                                       ***************************************************999999....88888886 PP

>> DUF956  Domain of unknown function (DUF956)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.5   0.0    0.0092        55      43      63 ..       5      25 ..       2      33 .. 0.83
   2 ?   -2.5   0.0      0.67     4e+03      33      44 ..     111     122 ..      98     134 .. 0.64
   3 !   15.1   0.3   2.4e-06     0.014      41      85 ..     141     184 ..     136     207 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.0092
                            DUF956 43 edyiqipWeevdsvvasvlfk 63
                                      ++++++ We++++ va ++ k
  gi|385805854|ref|YP_005842252.1|  5 NKFLTLKWEDIENAVAAISEK 25
                                      789*************99866 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.67
                            DUF956  33 afefyndknved 44 
                                       a++fy  kn + 
  gi|385805854|ref|YP_005842252.1| 111 AINFYGPKNLKT 122
                                       667777776654 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 2.4e-06
                            DUF956  41 nvedyiqipWeevdsvvasvlfkgklirrfaivtkkngkfsFssk 85 
                                       +++++i +pWe+ ++++a v  + k+i+r +i ++k  + +Fs k
  gi|385805854|ref|YP_005842252.1| 141 ETDKWIVFPWEKRETIEALVQAEYKIISRATIDVEK-ISKEFSDK 184
                                       56799***************************9998.56677765 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   9.7e-07    0.0058      68     155 ..      33     121 ..       3     132 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 9.7e-07
                           UPRTase  68 kialVpilRaGegmeealrellpearvghlglqree...etlepveyynkLPkkiaertvlllDpviaTGgsaaaai 141
                                         ++V ilR+G   ++ + + l    +g + ++  +   e+ e   + + L  +i++++vll+D v  +G+s+++a+
  gi|385805854|ref|YP_005842252.1|  33 PNVVVGILRGGWIPARIFADFLGIKDIGAIEIKFYKgieEKMERPVITQPLVLDIRNKNVLLVDDVADSGKSLQTAL 109
                                       56899***************987777777777653322144455567788999************************ PP

                           UPRTase 142 qlLkergvgeekIl 155
                                       + +     g ++  
  gi|385805854|ref|YP_005842252.1| 110 SAINF--YGPKNLK 121
                                       99987..4445555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      625  (0.0348597); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1445.50
//
Query:       gi|385805855|ref|YP_005842253.1|  [L=88]
Description: hypothetical protein FFONT_0813 [Fervidicoccus fontis Kam940]
Scores for complete 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   27.6   0.0      4e-06   27.4   0.0    1.1  1  ThiS      ThiS family
  ------ inclusion threshold ------
      0.011   16.0   0.1      0.019   15.3   0.1    1.6  1  Urm1      Urm1 (Ubiquitin related modifier)


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 !   27.4   0.0   4.4e-10     4e-06       1      77 []       8      88 .]       8      88 .] 0.92

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 4.4e-10
                                      EEETTCCHHHHTCEEEEESSTSBHHHHHHHHHHHTCHHG.....TTTTEEEEETTEEEGCCTTTSB--TTCEEEEEEST CS
                              ThiS  1 vllfaelrelageeelelaegstvaelleaLgerypela.....lerrvavavNgeivprlwldtelkdgDevailppV 74
                                      ++l a+l e++g +e     +++++e+l+ L  + p +       + + ++++Ng + +  ++d ++kd D+v i+p+ 
  gi|385805855|ref|YP_005842253.1|  8 ITLIANLIEKVG-SEKINVKAEKLSEALKFLIPKLPDILdlegkPSGNYIFLLNGADYRVFGDDPVVKDSDKVTIIPVS 85
                                      68999******9.5555567899************9999*****99********************************9 PP

                                      TC- CS
                              ThiS 75 aGG 77
                                       GG
  gi|385805855|ref|YP_005842253.1| 86 HGG 88
                                      998 PP

>> Urm1  Urm1 (Ubiquitin related modifier)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.1   2.2e-06     0.019      62      96 .]      55      88 .]       6      88 .] 0.83

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.2e-06
                                      EEEEETTCEHHHCTCCCSB--TTEEEEEEETTT-- CS
                              Urm1 62 ilvLindaDwellgekdyelkdkDkivFistlhGG 96
                                       + L+n aD+ + g+ d ++kd+Dk++ i   hGG
  gi|385805855|ref|YP_005842253.1| 55 YIFLLNGADYRVFGD-DPVVKDSDKVTIIPVSHGG 88
                                      589***********9.999***************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); 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:                         2  (0.000111551); expected 0.2 (1e-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: 583.88
//
Query:       gi|385805856|ref|YP_005842254.1|  [L=68]
Description: 30S ribosomal protein S17e [Fervidicoccus fontis Kam940]
Scores for complete 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   64.9   0.6    7.1e-18   64.7   0.6    1.0  1  Ribosomal_S17e  Ribosomal S17
  ------ inclusion threshold ------
        0.1   12.2   0.0       0.15   11.7   0.0    1.2  1  SSXT            SSXT protein (N-terminal region)


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 !   64.7   0.6   7.9e-22   7.1e-18       1      61 [.       1      61 [.       1      67 [. 0.95

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 7.9e-22
                                      XX----HHHHHHHHHHHHS-TTT--S-HHHHHHHHHHHS----SHHHHHHHHHHHHHHHHT CS
                    Ribosomal_S17e  1 mgrvrtktvKkaarviiekyyskltndFhtnkkvceevaiipskklrnkiaGyvthlmkri 61
                                      mg+vrt  vK++ar++i  +   +t+dF++nk+++++   ++sk++ nkiaGy+thl+k  
  gi|385805856|ref|YP_005842254.1|  1 MGKVRTAMVKRTARKLITAHPDLFTEDFEENKQLIRKLVDVNSKRVSNKIAGYITHLVKVT 61
                                      9*********************************************************964 PP

>> SSXT  SSXT protein (N-terminal region)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   1.7e-05      0.15      14      39 ..      29      54 ..      28      64 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.7e-05
                              SSXT 14 DENsqLIqtIielqnkGraeecdqyq 39
                                      +EN+qLI+  +++++k   +++  y 
  gi|385805856|ref|YP_005842254.1| 29 EENKQLIRKLVDVNSKRVSNKIAGYI 54
                                      8*************994444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 452.12
//
Query:       gi|385805857|ref|YP_005842255.1|  [L=204]
Description: nadh oxidase (noxc) [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      4e-29  101.8   0.0    4.7e-29  101.6   0.0    1.0  1  Nitroreductase  Nitroreductase family
    1.1e-06   28.4   0.0    0.00078   19.1   0.0    2.8  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 !  101.6   0.0   5.2e-33   4.7e-29       1     169 [.       7     191 ..       7     192 .. 0.91

  Alignments for each domain:
  == domain 1  score: 101.6 bits;  conditional E-value: 5.2e-33
                                       HHH--B---B-S----HHHHHHHHHHH.............HTS--GGG---EEEEEE.-CCCH..........HHHH CS
                    Nitroreductase   1 irkRrSiRkFddepvpkeelekileaa.............rraPsagnlqpwrfvvvqdkelr..........ykla 54 
                                       i++R S R F+++p++ e+l+ il+ a             r aPsag ++p++++v+  ++ +          yk+ 
  gi|385805857|ref|YP_005842255.1|   7 ILNRSSKRSFKKDPLKFEHLSIILWSAqglveskkqglakRVAPSAGATYPFEVFVAIGENSIcegpqiisgiYKYI 83 
                                       789************************************999***************44555589999999996666 PP

                                       HHHHHHHHHHHTT-SS-GGGGGGHHHHHHHHHHHHSSEEEEE---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Nitroreductase  55 eaalelllkaeaqaelaqryrkeelklkaqkalagapvlivivatldkserkaaerayryalldagaaaqnllLaAt 131
                                          ++  lk+e ++++   ++     ++ q  + +ap+ i++va+++  ++ +++r+ ry +++ag++ qn++L+At
  gi|385805857|ref|YP_005842255.1|  84 SEEHSIKLKLEGDKRDDLARA-----AYSQNSIVQAPISIILVAKYEITTQVYGDRGIRYVHFEAGHIGQNIYLMAT 155
                                       666666666666666666655.....9************************************************** PP

                                       HTT-EEEEE-GGGGGHHHHHHHHT-S..SEEEEEEEEE CS
                    Nitroreductase 132 alGlgscpiggfdeaaeevrkllglpdeeeivvliavG 169
                                       alGlg++ ig+fd++a  v ++l+l++ee++++++++G
  gi|385805857|ref|YP_005842255.1| 156 ALGLGTVAIGAFDDDA--VSEVLHLEKEEKPLYIFPIG 191
                                       ****************..*******************9 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.0   0.00067         6       2      29 ..       3      30 ..       2      46 .. 0.82
   2 ?   -1.1   0.0      0.13   1.1e+03     166     182 ..      45      61 ..      33      84 .. 0.77
   3 !   19.1   0.0   8.7e-08   0.00078      80     135 ..     139     195 ..      73     200 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.00067
                                      HHHHHHH--B---B--S---HHHHHHHH CS
                    TM1586_NiRdase  2 lyeaiekRhsvRkYkdealeeelleelk 29
                                      l eai +R s R++k+ +l+ e l+ + 
  gi|385805857|ref|YP_005842255.1|  3 LEEAILNRSSKRSFKKDPLKFEHLSIIL 30
                                      679***************9988877665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.13
                                       HHHTS--GGG----EEE CS
                    TM1586_NiRdase 166 aarlAPsAlNqqpwrfe 182
                                       a r+APsA  + p+++ 
  gi|385805857|ref|YP_005842255.1|  45 AKRVAPSAGATYPFEVF 61 
                                       56899**9999999754 PP

  == domain 3  score: 19.1 bits;  conditional E-value: 8.7e-08
                                       HHHHHHHHHHHHHHHHHHTT-EEEEES--SST............T-S-EEEEE-BS- CS
                    TM1586_NiRdase  80 leekaGYygeqlvLkltalGlgtcWvggtykk.kkakvelkkgeklvivIalGyakt 135
                                       ++ +aG +g+++ L +talGlgt  +g+  +  +++ ++l+k+ek +++  +G++k+
  gi|385805857|ref|YP_005842255.1| 139 VHFEAGHIGQNIYLMATALGLGTVAIGAFDDDaVSEVLHLEKEEKPLYIFPIGFPKS 195
                                       56789**********************87776688889***************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 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:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1304.12
//
Query:       gi|385805858|ref|YP_005842256.1|  [L=85]
Description: hypothetical protein FFONT_0816 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.013   15.6   0.8      0.013   15.6   0.8    2.4  2  Ldr_toxin  Toxin Ldr, type I toxin-antitoxin system
      0.093   12.7   1.3      0.093   12.7   1.3    3.0  2  TM_helix   Conserved TM helix


Domain annotation for each model (and alignments):
>> Ldr_toxin  Toxin Ldr, type I toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   2.4      0.14   1.3e+03      22      31 ..      23      32 ..      16      34 .. 0.81
   2 ?   15.6   0.8   1.4e-06     0.013      15      33 ..      67      85 .]      65      85 .] 0.90

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.14
                                      HHHHHHHHHH CS
                         Ldr_toxin 22 IlaaaIVnWl 31
                                      I+a aI n +
  gi|385805858|ref|YP_005842256.1| 23 IIAGAILNVW 32
                                      8999999877 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1.4e-06
                                      HHHHHHHHHHHHHHHHHHH CS
                         Ldr_toxin 15 AAPvlAGIlaaaIVnWlrk 33
                                        PvlAG +   I++Wl k
  gi|385805858|ref|YP_005842256.1| 67 IGPVLAGFIIGLIIGWLHK 85
                                      57***************86 PP

>> TM_helix  Conserved TM helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   7.4      0.88   7.9e+03      25      38 ..       4      17 ..       3      31 .. 0.66
   2 ?   12.7   1.3     1e-05     0.093      11      44 ..      52      85 .]      49      85 .] 0.89

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.88
                                      HHHHHHHHHHHHHH CS
                          TM_helix 25 lvGwiiAkfvsrlv 38
                                      l+G+i+Ak  + ++
  gi|385805858|ref|YP_005842256.1|  4 LLGYILAKAFKYII 17
                                      56777777655544 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 1e-05
                                      HTTHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          TM_helix 11 lsflPnLvgAilILlvGwiiAkfvsrlvtkllak 44
                                      ++++++   ++ ILl+G ++A f+  l+  +l+k
  gi|385805858|ref|YP_005842256.1| 52 MQYVIQFAKFLSILLIGPVLAGFIIGLIIGWLHK 85
                                      5799999999999999999999999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       872  (0.0486363); 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:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.33s 00:00:00.81 Elapsed: 00:00:00.52
# Mc/sec: 495.84
//
Query:       gi|385805859|ref|YP_005842257.1|  [L=104]
Description: translation initiation factor IF-1 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-19   67.7   0.1    6.8e-19   67.4   0.1    1.1  1  eIF-1a    Translation initiation factor 1A / IF-1


Domain annotation for each model (and alignments):
>> eIF-1a  Translation initiation factor 1A / IF-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.4   0.1   3.8e-23   6.8e-19       3      64 .]      20      81 ..      18      81 .. 0.93

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 3.8e-23
                                      EEEEEEEEETTTEEEEEE.SSSSBEEEEE-HHHHCT----TT-EEEEEE-TT-.TTEEEEES- CS
                            eIF-1a  3 vigkViealgnnlfrVelpdngkevlaeipgkfRnkiwikrGdyVlVelspyd.ltkGrIvyr 64
                                      v ++V+++lg+++f  +++d gk++l +ipg++R+k+wik+ d+VlV +++ + +tk++  y+
  gi|385805859|ref|YP_005842257.1| 20 VVCVVEKILGGDHFIAKCSD-GKKRLTRIPGRLRRKMWIKERDVVLVAPWDMQsDTKADLLYK 81
                                      79****************85.*******************************9566*998885 PP



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:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 648.63
//
Query:       gi|385805860|ref|YP_005842258.1|  [L=219]
Description: protein kinase RIO family [Fervidicoccus fontis Kam940]
Scores for complete 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-59  201.3   0.1    1.2e-59  201.1   0.1    1.0  1  RIO1             RIO1 family
     0.0012   17.7   0.6      0.002   17.0   0.6    1.3  1  Pkinase_fungal   Fungal protein kinase
     0.0069   16.3   0.0      0.058   13.3   0.0    2.1  2  APH              Phosphotransferase enzyme family
  ------ inclusion threshold ------
       0.14   11.3   0.0       0.56    9.4   0.0    1.8  2  Fructosamin_kin  Fructosamine kinase


Domain annotation for each model (and alignments):
>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.1   0.1   2.7e-63   1.2e-59       2     180 ..      21     200 ..      20     209 .. 0.95

  Alignments for each domain:
  == domain 1  score: 201.1 bits;  conditional E-value: 2.7e-63
                                       EEEEEETTTEEEEEEEE-S---SS-H.HHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEE CS
                              RIO1   2 VyhavsedgkevaiKiyktstteFkk.rkkyvsgekrfkdrksktnprklvklwaekEfrnLkrleeagvpvPkpie 77 
                                       Vy ++++++ke+aiKiy t  +eFk+ + ky+ g++rf++  +  n+ kl+  wa+kE+ nLk+++e+gv+vPkp++
  gi|385805860|ref|YP_005842258.1|  21 VYRGIDKNKKEFAIKIYLTFSSEFKQgILKYILGDPRFESI-KIGNTHKLMSFWAKKEYVNLKKMYESGVSVPKPYA 96 
                                       9*************************99***********88.5899******************************* PP

                                       EETTEEEEE--EETTEEGGBHHHCG.-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETTEEEE--GTTEE CS
                              RIO1  78 lkrhvlvmefigedgvaapklkdve.eeeeaeelyeevleemrklykeaglvHaDLSeyNvlvdedkvviIDvsQav 153
                                        +r+++vm+fige+gv+ap lk++  + e+   +y+e++e+++k++ +a+lvH+DLSeyN+++ +d ++iIDvsQav
  gi|385805860|ref|YP_005842258.1|  97 QNRNIVVMDFIGENGVRAPLLKELGaDLENPGIIYNEIIENIKKIVCRANLVHGDLSEYNIMIFNDTPFIIDVSQAV 173
                                       *************************557788889******************************************* PP

                                       ETTSTTHHHHHHHHHHHHHHHHHTTC- CS
                              RIO1 154 eldhpnalefLerDveniikfFrrkgv 180
                                       +++hpna +fL +D+ ni++fF+r + 
  gi|385805860|ref|YP_005842258.1| 174 HIKHPNAIDFLSKDIGNINRFFKRLFD 200
                                       ***********************9865 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.6   4.4e-07     0.002     316     367 ..     135     180 ..     131     192 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.4e-07
                    Pkinase_fungal 316 IkghrsLflkagiLHrDiSenNilitdskkegerkglLiDLDlakelsddss 367
                                       I+  ++ +  a+++H D Se+Ni+i       +++ ++iD+  a++++++++
  gi|385805860|ref|YP_005842258.1| 135 IENIKKIVCRANLVHGDLSEYNIMIF------NDTPFIIDVSQAVHIKHPNA 180
                                       6667778889****************......8999**********998765 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0     0.087   3.9e+02       6      59 ..      14      96 ..      12     108 .. 0.50
   2 !   13.3   0.0   1.3e-05     0.058     164     194 ..     143     170 ..     105     176 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.087
                                      --.SSCEEEEEEETT.--EEEEEE-TTS-HHHHHHHHH.............................HHHHHHHTT-B- CS
                               APH  6 sggasnrtylvttpa.gryvlrrnpparaaeeirreva.............................llrlLakagvpv 54
                                      s+g ++r+y+  +++ ++++ +++ +  + e+ +++++                              l+ + ++gv+v
  gi|385805860|ref|YP_005842258.1| 14 SAGKESRVYRGIDKNkKEFAIKIYLTF-SSEFKQGILKyilgdprfesikignthklmsfwakkeyvNLKKMYESGVSV 91
                                      666677777766666557776665554.333333333322233333333333333333333333333556666667777 PP

                                      -B-CT CS
                               APH 55 Pevla 59
                                      P+++a
  gi|385805860|ref|YP_005842258.1| 92 PKPYA 96
                                      77776 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 1.3e-05
                                       S-EEEE-SS-SGGGEEEC..TTEEEEE---T CS
                               APH 164 lptvllHgDlhpgNllvdpddgrvtGviDfe 194
                                        ++ l+HgDl+  N+++  +d+++  +iD  
  gi|385805860|ref|YP_005842258.1| 143 CRANLVHGDLSEYNIMIF-NDTPF--IIDVS 170
                                       47789*************.99**9..**965 PP

>> Fructosamin_kin  Fructosamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       0.1   4.7e+02      57      80 ..      75      97 ..      60     124 .. 0.74
   2 ?    9.4   0.0   0.00012      0.56     160     212 ..     117     168 ..      95     172 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.1
                   Fructosamin_kin 57 eaEaesLealaetqtirvPkvlav 80
                                      ++E+ +L+++ e+  + vPk++a 
  gi|385805860|ref|YP_005842258.1| 75 KKEYVNLKKMYES-GVSVPKPYAQ 97
                                      5799999999876.5899999874 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00012
                   Fructosamin_kin 160 akekglefakieelvervaellskhqpkpsllHGdLWsgNaaltkdgepvifd 212
                                       +ke g + ++   + +++ e ++k   ++ l+HGdL + N+++ +d  p+i+d
  gi|385805860|ref|YP_005842258.1| 117 LKELGADLENPGIIYNEIIENIKKIVCRANLVHGDLSEYNIMIFNDT-PFIID 168
                                       5555666677777888999999999*****************99998.99988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); 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:                         4  (0.000223102); expected 0.2 (1e-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 0.36s 00:00:00.95 Elapsed: 00:00:00.56
# Mc/sec: 1167.69
//
Query:       gi|385805861|ref|YP_005842259.1|  [L=206]
Description: KH, type 1, domain-containing protein [Fervidicoccus fontis Kam940]
Scores for complete 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   34.1  15.8    2.3e-05   24.1   1.6    2.5  2  KH_1      KH domain
  ------ inclusion threshold ------
       0.22   11.4  14.2      0.033   14.0   3.1    2.8  2  KH_2      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 !   24.1   1.6   2.5e-09   2.3e-05       5      64 ..      18      76 ..      16      78 .. 0.75
   2 !   14.8   6.7   2.2e-06     0.019      12      65 ..     118     163 ..     113     164 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 2.5e-09
                                      EEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEE....E.SHHHHHHHHHHH CS
                              KH_1  5 lvPsslvgriIGkgGsnIkeIreetgakIkvpksedegsderevtis....G.speavekAkeli 64
                                      lvP + +g++IG +G++   I++ t ++Ik++ s     +  +v i       +++++ kAke i
  gi|385805861|ref|YP_005842259.1| 18 LVPEERIGAVIGQNGKVKEMIEQATSTNIKIE-S-----NTGIVYIEprdeNtKADSIIKAKEII 76
                                      79*********************9******86.4.....45677774333343555566666655 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 2.2e-06
                                       HHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEEESHHHHHHHHHHHH CS
                              KH_1  12 griIGkgGsnIkeIreetgakIkvpksedegsderevtisGspeavekAkelie 65 
                                       +riIG  G++ k I+e tg k+++         e+ + i+G+ e+   A+++i+
  gi|385805861|ref|YP_005842259.1| 118 SRIIGEEGRTRKIIEETTGSKVVIG--------ESAIGIIGDFEQASIAERAIR 163
                                       79**************88*****53........457*************99985 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   3.1   3.7e-06     0.033      33      66 ..      21      55 ..      12     110 .. 0.82
   2 ?    2.1   3.5     0.019   1.7e+02      36      59 ..     117     140 ..     114     150 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.7e-06
                                      ESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTC..E CS
                              KH_2 33 esqpgivIGkgGsnikkigkelrkdieklegkk..V 66
                                      e++ g vIG++G+  ++i+++   +i+ +e     V
  gi|385805861|ref|YP_005842259.1| 21 EERIGAVIGQNGKVKEMIEQATSTNIK-IESNTgiV 55
                                      789*********************994.66655564 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.019
                                       HHHHHTGGGHHHHHHHHHHHHHHH CS
                              KH_2  36 pgivIGkgGsnikkigkelrkdie 59 
                                       + ++IG +G++ k i+++ + ++ 
  gi|385805861|ref|YP_005842259.1| 117 KSRIIGEEGRTRKIIEETTGSKVV 140
                                       5689******99999999999983 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 1178.40
//
Query:       gi|385805862|ref|YP_005842260.1|  [L=609]
Description: putative ATPase RIL [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-37  129.6   0.3    2.5e-17   63.7   0.0    3.0  2  ABC_tran         ABC transporter
    1.8e-12   46.9   1.4    4.3e-12   45.6   1.4    1.7  1  RLI              Possible Fer4-like domain in RNase L inhibit
      5e-12   45.7   6.4    0.00039   19.9   0.1    4.1  4  SMC_N            RecF/RecN/SMC N terminal domain
    5.5e-12   46.1  11.1     0.0066   16.3   0.1    4.5  4  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    9.4e-07   28.9   0.0    0.00094   19.1   0.0    2.9  2  NACHT            NACHT domain
    2.2e-06   28.3   0.3        0.1   13.1   0.1    2.7  2  AAA_23           AAA domain
    2.6e-06   27.4   7.9    4.9e-06   26.6   7.9    1.5  1  Fer4_21          4Fe-4S dicluster domain
      4e-06   26.4   5.4      4e-06   26.4   5.4    2.8  3  Fer4             4Fe-4S binding domain
    7.9e-06   25.7   0.3      0.034   13.9   0.0    2.4  2  AAA_24           AAA domain
      1e-05   25.4  11.6     0.0023   17.9   3.7    2.3  2  Fer4_6           4Fe-4S binding domain
    1.3e-05   25.2   9.2     0.0016   18.5   1.7    2.3  2  Fer4_10          4Fe-4S dicluster domain
    2.3e-05   24.7   0.0      0.041   14.2   0.0    2.6  2  AAA_22           AAA domain
    3.2e-05   24.3   0.0       0.18   12.3   0.0    2.6  2  AAA              ATPase family associated with various cellul
    4.3e-05   23.8   0.0      0.085   13.3   0.0    2.7  2  RNA_helicase     RNA helicase
    4.8e-05   23.2   0.4       0.27   10.9   0.0    2.6  2  AAA_15           AAA ATPase domain
    5.4e-05   22.9   0.1       0.12   12.0   0.0    2.5  2  SRP54            SRP54-type protein, GTPase domain
    0.00038   20.9   0.0       0.29   11.5   0.0    2.5  2  AAA_16           AAA ATPase domain
    0.00042   20.3   0.0       0.18   11.7   0.0    2.4  2  Rad17            Rad17 P-loop domain
    0.00053   20.5   1.4    0.00053   20.5   1.4    2.2  3  Fer4_7           4Fe-4S dicluster domain
    0.00065   19.8   8.3     0.0012   19.0   8.3    1.4  1  Fer4_9           4Fe-4S dicluster domain
    0.00078   19.4   0.1        0.3   11.0   0.0    2.6  2  MobB             Molybdopterin guanine dinucleotide synthesis
      0.001   19.1   0.5       0.59   10.2   0.0    2.9  2  AAA_14           AAA domain
     0.0011   19.9   6.1     0.0084   17.0   0.3    2.8  2  Fer4_16          4Fe-4S double cluster binding domain
     0.0011   19.5   0.1        1.5    9.3   0.0    3.1  3  AAA_18           AAA domain
     0.0012   19.0   0.0       0.86    9.8   0.0    3.3  3  AAA_33           AAA domain
     0.0013   18.6   0.1        1.8    8.4   0.0    3.0  3  RsgA_GTPase      RsgA GTPase
     0.0019   18.6   0.5        1.2    9.5   0.0    2.4  2  AAA_19           AAA domain
     0.0023   17.9   1.7        0.1   12.5   0.1    2.8  2  NTPase_1         NTPase
     0.0025   17.9   0.5        3.5    7.7   0.1    2.6  2  DUF87            Helicase HerA, central domain
     0.0042   17.1   2.7     0.0042   17.1   2.7    2.3  2  Fer4_2           4Fe-4S binding domain
     0.0077   16.0   0.0       0.43   10.3   0.0    2.2  2  VirE             Virulence-associated protein E
     0.0091   15.2   0.6       0.65    9.1   0.0    2.4  2  NB-ARC           NB-ARC domain
  ------ inclusion threshold ------
      0.012   15.9   0.0        8.1    6.7   0.0    2.8  2  AAA_28           AAA domain
      0.012   15.6   0.2        1.3    9.0   0.0    2.6  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.012   15.4   0.0       0.23   11.2   0.0    2.3  2  PRK              Phosphoribulokinase / Uridine kinase family
      0.016   14.7   0.1       0.46   10.0   0.0    2.2  2  AAA_7            P-loop containing dynein motor region
      0.017   15.2   0.6         10    6.3   0.1    3.0  2  MMR_HSR1         50S ribosome-binding GTPase
      0.024   13.6   1.3        1.6    7.7   0.1    2.2  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
      0.027   14.2   0.1        3.9    7.1   0.0    2.7  2  AAA_30           AAA domain
      0.027   14.7   0.2         18    5.6   0.0    3.0  2  SbcCD_C          Putative exonuclease SbcCD, C subunit
      0.044   13.5   2.3        6.8    6.5   0.1    2.4  2  AAA_29           P-loop containing region of AAA domain
      0.047   12.5   0.0       0.91    8.2   0.0    2.2  2  AAA_32           AAA domain
      0.051   12.9   0.0        2.7    7.2   0.0    2.2  2  Septin           Septin
      0.079   13.2   0.0          2    8.6   0.0    2.4  2  Roc              Ras of Complex, Roc, domain of DAPkinase
      0.095   12.6   1.9       0.61   10.0   0.0    2.5  2  ATPase_2         ATPase domain predominantly from Archaea
        0.1   12.6   0.1        5.5    7.0   0.0    2.7  2  AAA_5            AAA domain (dynein-related subfamily)
        0.1   11.2   0.1        2.9    6.4   0.0    2.2  2  AAA_13           AAA domain
       0.11   12.6   2.0        0.2   11.8   2.0    1.3  1  Fer4_11          4Fe-4S dicluster domain
       0.12   11.6   0.0        0.7    9.1   0.0    2.0  2  KAP_NTPase       KAP family P-loop domain
       0.12   12.1   0.0       0.85    9.3   0.0    2.3  2  ATP_bind_1       Conserved hypothetical ATP binding protein
       0.14   11.8   0.1         19    4.8   0.0    2.4  2  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
       0.14   11.8   0.1         10    5.8   0.0    2.7  2  Thymidylate_kin  Thymidylate kinase
       0.19   11.3   0.0        1.2    8.7   0.0    2.2  2  AAA_25           AAA domain
       0.44   11.1   8.2        1.9    9.1   8.3    1.9  1  Fer4_17          4Fe-4S dicluster domain
        1.1   10.3  15.3       0.14   13.2   4.2    2.3  2  Fer4_3           4Fe-4S binding domain
        5.6    7.7  13.2        1.7    9.3   3.6    2.3  2  Fer4_4           4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.4   0.0     2e-19   6.3e-17       9     136 ..      98     241 ..      97     242 .. 0.73
   2 !   63.7   0.0   7.7e-20   2.5e-17       8     137 .]     368     491 ..     364     491 .. 0.85

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 2e-19
                                       ETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEE...........EETTCEGGGB-HHHCCHCEEEE-SS..--S-T CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxx..xxxxx RF
                          ABC_tran   9 kegekvaivGenGaGKStLlkllagllkpteGei...........lldgkdlkeqeleslrkeigvlpqe..pqlfp 72 
                                       k+ge+++i+G+nG GK+t +++lag+l p+ G+            +++g++l e   ++++k+i+v ++    +l p
  gi|385805862|ref|YP_005842260.1|  98 KKGEVLGIIGKNGIGKTTTIRILAGELIPNFGDKerkasenevleRFRGTELFEYFQKVYSKKIKVAHKIqyVELVP 174
                                       68***************************888874433444444444444444433333333333333222255555 PP

                                       TSBHHHH.........HHHTC..HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxxx.........xxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  73 eltvren.........esdee..iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       ++              ++de+  + k++s+lgl+ + ++ v    +++SgG+ q++ ++++l kk++l+++DEp+
  gi|385805862|ref|YP_005842260.1| 175 RY----LsgkvstlleKADERgiAIKLASELGLSPVLERDV----KNISGGELQKILIVATLSKKADLYIFDEPS 241
                                       55....0334588896444447899**********999999....*****************************7 PP

  == domain 2  score: 63.7 bits;  conditional E-value: 7.7e-20
                                       EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS..--S-TTSBHHHH... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxx... RF
                          ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe..pqlfpeltvren... 79 
                                        ++ge+++i+G+nG GK+t++k l  + + +                e  + ++++ pq   p++f+++tv+en   
  gi|385805862|ref|YP_005842260.1| 368 ASKGEVIGILGPNGIGKTTFVKKLVSMISEDR--------------PEDEEIKFSYKPQYvsPEIFEKKTVEENlin 430
                                       589*******************9999987533..............3456667777777777889999999999887 PP

                                       .......HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       .......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  80 .......esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                              + +   e++++ +gl +l+++ v    s+LSgG+ q++ala +l+k+++l+llDEp+a
  gi|385805862|ref|YP_005842260.1| 431 anpqslsTGTWAYEDIVRPFGLYKLREREV----SELSGGELQKLALAVSLIKDAELYLLDEPSA 491
                                       7776654445559*****************....*****************************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 !   45.6   1.4   1.3e-14   4.3e-12       1      34 [.       1      31 [.       1      32 [. 0.96

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 1.3e-14
                                      --EEEES---------TTHHHHHTTSEEEESS-- CS
                               RLI  1 mrlAivdadqCdPKKCtgkkcarfcpvrlvrtgk 34
                                      mr+A++d+  C+P KC+  +c+rfcpv  +r+ +
  gi|385805862|ref|YP_005842260.1|  1 MRVAVIDYSLCKPTKCNL-ECIRFCPV--NRSRR 31
                                      9*****************.********..**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 ?    3.4   0.1      0.14        45      20      40 ..      96     116 ..      80     124 .. 0.76
   2 !   18.0   0.0   4.6e-06    0.0015     136     206 ..     213     280 ..     126     292 .. 0.71
   3 ?    5.1   0.2     0.042        14      25      44 ..     372     391 ..     354     403 .. 0.81
   4 !   19.9   0.1   1.2e-06   0.00039     136     189 ..     462     511 ..     413     537 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.14
                                       EETTSSEEEEEESTTSSHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  20 lpfsksftaivGpNGSGKsnl 40 
                                       +p + ++  i+G+NG GK+  
  gi|385805862|ref|YP_005842260.1|  96 VPKKGEVLGIIGKNGIGKTTT 116
                                       556667889*********975 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 4.6e-06
                                       CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHC.TTSEEEEE-SSHHHCCC-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                             SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeks.knaQfivislreemlekad 206
                                       ++SgGe +     L++A+ + k+a ly++De  + LD +++ ++a+l++e   k++  ivi ++  +l   +
  gi|385805862|ref|YP_005842260.1| 213 NISGGELQK---ILIVATLS-KKADLYIFDEPSSFLDVRERIRIASLIRELVpKESYSIVIEHDIALLDYLS 280
                                       899999653...35666654.6788************************98625699999998877776654 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.042
                                       SEEEEEESTTSSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAi 44 
                                       ++  i+GpNG GK+ ++  +
  gi|385805862|ref|YP_005842260.1| 372 EVIGILGPNGIGKTTFVKKL 391
                                       56789*********998766 PP

  == domain 4  score: 19.9 bits;  conditional E-value: 1.2e-06
                                       CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn 189
                                       +LSgGe + +a    +A+  +k a lyllDe  a LD +++  va+++++ +++
  gi|385805862|ref|YP_005842260.1| 462 ELSGGELQKLA----LAVSLIKDAELYLLDEPSAYLDVEERLSVAKVIRRLTES 511
                                       89***976444....45667999**************************87765 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.7   0.00016      0.05       3      32 ..     104     127 ..     102     167 .. 0.75
   2 !   11.3   0.1   0.00067      0.21     234     285 ..     211     259 ..     200     269 .. 0.78
   3 !    9.3   0.1    0.0028      0.91       2      24 ..     374     396 ..     373     433 .. 0.69
   4 !   16.3   0.1   2.1e-05    0.0066     230     285 ..     456     508 ..     419     527 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00016
                            AAA_21   3 vliGpNgsGKSnLLdaldllarldrdvegl 32 
                                       ++iG+Ng GK++ +++l      ++++++ 
  gi|385805862|ref|YP_005842260.1| 104 GIIGKNGIGKTTTIRIL------AGELIPN 127
                                       79***************......4444444 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00067
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkel 285
                                       + ++S G ++ + +++ l     k++l+++DEp ++L+ +   r++ l++el
  gi|385805862|ref|YP_005842260.1| 211 VKNISGGELQKILIVATLSK---KADLYIFDEPSSFLDVRERIRIASLIREL 259
                                       45679999999555555554...44**************8888888887664 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0028
                            AAA_21   2 nvliGpNgsGKSnLLdaldllar 24 
                                        ++ GpNg GK+++ + l  + +
  gi|385805862|ref|YP_005842260.1| 374 IGILGPNGIGKTTFVKKLVSMIS 396
                                       689***********998877754 PP

  == domain 4  score: 16.3 bits;  conditional E-value: 2.1e-05
                            AAA_21 230 qelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkel 285
                                       +e+ ++elS G ++ lal+++l+ ++    l+l+DEp + L+ +   ++++++++l
  gi|385805862|ref|YP_005842260.1| 456 REREVSELSGGELQKLALAVSLIKDA---ELYLLDEPSAYLDVEERLSVAKVIRRL 508
                                       67889999******************...9************94444444444333 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1     0.024       7.8       3      21 ..     103     121 ..     101     130 .. 0.84
   2 !   19.1   0.0   2.9e-06   0.00094       2      37 ..     373     408 ..     372     434 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.024
                                       EEEEC-TTTCHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqkla 21 
                                       + + G++G+GKTt ++ la
  gi|385805862|ref|YP_005842260.1| 103 LGIIGKNGIGKTTTIRILA 121
                                       5689*********988776 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 2.9e-06
                                       CEEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEE CS
                             NACHT   2 lvilqGeaGsGKTtLlqklalawaegklpqgafklv 37 
                                       ++ + G++G+GKTt+++kl++ + e++++ ++ k++
  gi|385805862|ref|YP_005842260.1| 373 VIGILGPNGIGKTTFVKKLVSMISEDRPEDEEIKFS 408
                                       56799**********************999876665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.1   0.00032       0.1      23     114 ..     104     205 ..      87     270 .. 0.66
   2 !   12.4   0.0   0.00053      0.17      17      39 ..     363     391 ..     346     443 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00032
                            AAA_23  23 lItGpNGaGKTTildAiklaLygetprlsrks...........grgfeksdveiese...............gkvka 73 
                                        I+G+NG GKTT ++ +   L   +++ +rk                         e               +++ +
  gi|385805862|ref|YP_005842260.1| 104 GIIGKNGIGKTTTIRILAGELIPNFGDKERKAsenevlerfrgT------------ElfeyfqkvyskkikvAHKIQ 168
                                       69*************99988877666655555222344333330............133344444444555577777 PP

                            AAA_23  74 yveltfenkdgrytrsiererelskkkgkttkkaklellei 114
                                       yvel  ++ +g+    ++   e++++ g  +k a + +l++
  gi|385805862|ref|YP_005842260.1| 169 YVELVPRYLSGK----VSTLLEKADERGIAIKLASELGLSP 205
                                       888876666664....5555555555555555555555554 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00053
                            AAA_23  17 F......skgltlItGpNGaGKTTildAi 39 
                                              +  +  I GpNG GKTT++  +
  gi|385805862|ref|YP_005842260.1| 363 VkpgsasKGEVIGILGPNGIGKTTFVKKL 391
                                       2555553335899***********98755 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   7.9   1.5e-08   4.9e-06       1      56 [.       4      66 ..       4      69 .. 0.80

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 1.5e-08
                           Fer4_21  1 AridedkC..igCg.kCliaCedt....shqaieidaktvlkvv.edeCvGCnlCssvCPvedc 56
                                      A+id + C   +C+ +C+  C+ +    s +aieid++t  +v+ e+ C+GCn+C++ CP  ++
  gi|385805862|ref|YP_005842260.1|  4 AVIDYSLCkpTKCNlECIRFCPVNrsrrSSKAIEIDSNTGKPVIyENVCIGCNICVKKCPY-NA 66
                                      677777775568984599999864333389*************86899************5.65 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       7.5   2.4e+03       2       8 ..       5      11 ..       4      12 .. 0.87
   2 ?    2.9   0.2      0.34   1.1e+02      13      21 ..      19      27 ..      18      27 .. 0.90
   3 !   26.4   5.4   1.2e-08     4e-06       1      24 []      45      68 ..      45      68 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 7.5
                                      EEETTTS CS
                              Fer4  2 videekC 8 
                                      vid+++C
  gi|385805862|ref|YP_005842260.1|  5 VIDYSLC 11
                                      8****** PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.34
                                      HHHHHSTTT CS
                              Fer4 13 aCvevCPvg 21
                                      +C+  CPv+
  gi|385805862|ref|YP_005842260.1| 19 ECIRFCPVN 27
                                      6******98 PP

  == domain 3  score: 26.4 bits;  conditional E-value: 1.2e-08
                                      EEEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  1 vvideekCigCGaCvevCPvgAIt 24
                                      +vi e+ CigC++Cv+ CP++A++
  gi|385805862|ref|YP_005842260.1| 45 PVIYENVCIGCNICVKKCPYNALE 68
                                      6899******************85 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0    0.0021      0.67       4      22 ..     102     120 ..      99     142 .. 0.83
   2 !   13.9   0.0   0.00011     0.034       4      22 ..     373     391 ..     370     402 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0021
                            AAA_24   4 kiliyGpsgiGKTtlakel 22 
                                        + i+G++giGKTt+++ l
  gi|385805862|ref|YP_005842260.1| 102 VLGIIGKNGIGKTTTIRIL 120
                                       5789***********9877 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 0.00011
                            AAA_24   4 kiliyGpsgiGKTtlakel 22 
                                        i i Gp+giGKTt++k+l
  gi|385805862|ref|YP_005842260.1| 373 VIGILGPNGIGKTTFVKKL 391
                                       689**************98 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   1.0   0.00051      0.16       1      22 [.       3      27 ..       3      35 .. 0.89
   2 !   17.9   3.7   7.1e-06    0.0023       3      24 .]      46      67 ..      44      67 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00051
                            Fer4_6  1 vveidpdkCi..gCgd.CvrvCPeg 22
                                      v++id+++C    C+  C+r CP +
  gi|385805862|ref|YP_005842260.1|  3 VAVIDYSLCKptKCNLeCIRFCPVN 27
                                      689******9888*666******86 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 7.1e-06
                            Fer4_6  3 eidpdkCigCgdCvrvCPegai 24
                                      +i ++ CigC+ Cv+ CP++a+
  gi|385805862|ref|YP_005842260.1| 46 VIYENVCIGCNICVKKCPYNAL 67
                                      566788**************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 !   17.7  11.3   8.7e-06    0.0028       2      56 .]       4      63 ..       3      63 .. 0.88
   2 !   18.5   1.7     5e-06    0.0016       2      24 ..      45      74 ..      44     101 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 8.7e-06
                           Fer4_10  2 vvidddtC..irCg.kCvkaCPadl..tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      +vid + C  ++C+ +C ++CP++   +s++a++++s+ ++  +    C+gc  Cv++CP
  gi|385805862|ref|YP_005842260.1|  4 AVIDYSLCkpTKCNlECIRFCPVNRsrRSSKAIEIDSNTGKPVIYENVCIGCNICVKKCP 63
                                      5899999*888************9887788888888888888888889***********9 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 5e-06
                           Fer4_10  2 vvidddtCirCgkCvkaCPadl.......t 24
                                      +vi ++ Ci+C+ Cvk CP+++       +
  gi|385805862|ref|YP_005842260.1| 45 PVIYENVCIGCNICVKKCPYNAleienlpD 74
                                      678899**************6655544440 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0     0.012       3.9       7      28 ..     102     123 ..      98     167 .. 0.88
   2 !   14.2   0.0   0.00013     0.041       7     103 ..     373     493 ..     368     526 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.012
                            AAA_22   7 ilvvtGesGtGKTtllrrlleq 28 
                                       +l ++G  G+GKTt++r l+ +
  gi|385805862|ref|YP_005842260.1| 102 VLGIIGKNGIGKTTTIRILAGE 123
                                       5679************988766 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 0.00013
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaee................erpevv.....fvtlpsstsskdllrellr 62 
                                       ++ + G+ G+GKTt +++l++   e+   +e                e +++v       +++s+++ +  +++++r
  gi|385805862|ref|YP_005842260.1| 373 VIGILGPNGIGKTTFVKKLVSMISEDRPEDEeikfsykpqyvspeifE-KKTVeenliNANPQSLSTGTWAYEDIVR 448
                                       56689*****************97766555589999999999999952.4444466225555555577777999999 PP

                            AAA_22  63 alglelkaerlsseell.ealeqalrarav...ielliiDEaqh.l 103
                                        +gl + + + + +el    l++ + a +     el ++DE    l
  gi|385805862|ref|YP_005842260.1| 449 PFGLYKLR-EREVSELSgGELQKLALAVSLikdAELYLLDEPSAyL 493
                                       99987777.5555555556666655555555556888888855445 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   0.00055      0.18       3      42 ..     105     157 ..     103     171 .. 0.65
   2 !    9.4   0.0    0.0042       1.4       3      22 ..     376     395 ..     374     430 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00055
                                       EESSTTSSHHHHHHHHHHHH..........THE....EEEEETTTCSSSSTTHH CS
                               AAA   3 lyGppGtGKTllakavakel..........gve....fleisgsellskyvges 42 
                                       ++G  G+GKT++++ +a el            +    + ++ g+el++ +++  
  gi|385805862|ref|YP_005842260.1| 105 IIGKNGIGKTTTIRILAGELipnfgdkerkA-SenevLERFRGTELFEYFQKVY 157
                                       68*****************866554443330.0333356667777764444444 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0042
                                       EESSTTSSHHHHHHHHHHHH CS
                               AAA   3 lyGppGtGKTllakavakel 22 
                                       + Gp G+GKT+++k +++ +
  gi|385805862|ref|YP_005842260.1| 376 ILGPNGIGKTTFVKKLVSMI 395
                                       57************999876 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0     0.014       4.4       3      30 ..     105     132 ..     103     169 .. 0.82
   2 !   13.3   0.0   0.00026     0.085       3      31 ..     376     404 ..     374     424 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.014
                      RNA_helicase   3 lyGpsgeGKStlakeLakallkklklkk 30 
                                       + G++g+GK+t+++ La +l  ++++k+
  gi|385805862|ref|YP_005842260.1| 105 IIGKNGIGKTTTIRILAGELIPNFGDKE 132
                                       78***************99997774444 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00026
                      RNA_helicase   3 lyGpsgeGKStlakeLakallkklklkkk 31 
                                       + Gp+g+GK+t++k+L++ ++++  ++++
  gi|385805862|ref|YP_005842260.1| 376 ILGPNGIGKTTFVKKLVSMISEDRPEDEE 404
                                       78******************977754444 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0    0.0018      0.58      26      43 ..     103     120 ..      89     203 .. 0.84
   2 !   10.9   0.0   0.00086      0.27      25      58 ..     373     422 ..     350     439 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0018
                            AAA_15  26 tvliGkNnsGKSsileal 43 
                                         +iGkN++GK++ +++l
  gi|385805862|ref|YP_005842260.1| 103 LGIIGKNGIGKTTTIRIL 120
                                       569************998 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00086
                            AAA_15  25 ltvliGkNnsGKSsilealdlFlnnkekkn................kkvi 58 
                                       +  + G+N++GK+++++ l  +++++++ +                ++++
  gi|385805862|ref|YP_005842260.1| 373 VIGILGPNGIGKTTFVKKLVSMISEDRPEDeeikfsykpqyvspeiFEKK 422
                                       56688*******************99555555555666666666553333 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   0.1    0.0058       1.9       5      23 ..     104     122 ..     101     132 .. 0.84
   2 !   12.0   0.0   0.00038      0.12       3      27 ..     373     397 ..     371     403 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0058
                                       EEEESTTSSHHHHHHHHHH CS
                             SRP54   5 llvGlqGaGKTttlaKLaa 23 
                                        ++G +G+GKTtt+  La 
  gi|385805862|ref|YP_005842260.1| 104 GIIGKNGIGKTTTIRILAG 122
                                       589***********99885 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00038
                                       EEEEEESTTSSHHHHHHHHHHHHHH CS
                             SRP54   3 villvGlqGaGKTttlaKLaallkk 27 
                                       vi ++G++G+GKTt + KL  ++++
  gi|385805862|ref|YP_005842260.1| 373 VIGILGPNGIGKTTFVKKLVSMISE 397
                                       77899**************999876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0     0.021       6.7      25      51 ..     101     127 ..      91     258 .. 0.77
   2 !   11.5   0.0    0.0009      0.29      19      51 ..     366     398 ..     359     479 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.021
                            AAA_16  25 elvllsGesGvGKsslvrellralekd 51 
                                       e++ ++G  G+GK++ +r l+ +l  +
  gi|385805862|ref|YP_005842260.1| 101 EVLGIIGKNGIGKTTTIRILAGELIPN 127
                                       677899***********9998777766 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.0009
                            AAA_16  19 vrsgrpelvllsGesGvGKsslvrellralekd 51 
                                        +++ +e++ + G+ G+GK++ v++l   +++d
  gi|385805862|ref|YP_005842260.1| 366 GSASKGEVIGILGPNGIGKTTFVKKLVSMISED 398
                                       5566669999**************998877776 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00056      0.18      42      74 ..      96     129 ..      71     163 .. 0.76
   2 ?    6.0   0.0     0.032        10      46      66 ..     372     392 ..     360     403 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00056
                             Rad17  42 srkkr.iLLisGPsGCgkstvvkvLskelgiklr 74 
                                         kk  +L i G  G gk+t++++L+ el +++ 
  gi|385805862|ref|YP_005842260.1|  96 VPKKGeVLGIIGKNGIGKTTTIRILAGELIPNFG 129
                                       433334999******************9988765 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.032
                             Rad17  46 riLLisGPsGCgkstvvkvLs 66 
                                       +++ i GP G gk+t vk L 
  gi|385805862|ref|YP_005842260.1| 372 EVIGILGPNGIGKTTFVKKLV 392
                                       577899************986 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   1.5      0.85   2.7e+02      32      51 ..       5      27 ..       1      28 [. 0.71
   2 !   13.8  11.6   0.00021     0.067       4      52 .]      15      66 ..      10      66 .. 0.79
   3 !   20.5   1.4   1.7e-06   0.00053       2      22 ..      52      72 ..      51      84 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.85
                            Fer4_7 32 eidpekC..lgCga.CvavCPtg 51
                                      +id++ C  + C+  C++ CP++
  gi|385805862|ref|YP_005842260.1|  5 VIDYSLCkpTKCNLeCIRFCPVN 27
                                      56667775568887799999986 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 0.00021
                            Fer4_7  4 gCg.aCvaaCpvkaieldee..enekgtekveidpekClgCgaCvavCPtga 52
                                      +C+  C + Cpv+  +   +  e ++ t k++i ++ C+gC+ Cv+ CP++a
  gi|385805862|ref|YP_005842260.1| 15 KCNlECIRFCPVNRSRRSSKaiEIDSNTGKPVIYENVCIGCNICVKKCPYNA 66
                                      78779******88777664412233466899999***************997 PP

  == domain 3  score: 20.5 bits;  conditional E-value: 1.7e-06
                            Fer4_7  2 CigCgaCvaaCpvkaieldee 22
                                      CigC+ Cv+ Cp++a+e+++ 
  gi|385805862|ref|YP_005842260.1| 52 CIGCNICVKKCPYNALEIENL 72
                                      ****************99765 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   8.3   3.6e-06    0.0012       3      50 ..      14      66 ..      11      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 3.6e-06
                            Fer4_9  3 tgCg.aCveaCpagvvvedaaerkarlraase....eaCigCgaCveaCpkga 50
                                      t+C+ +C++ Cp +  ++++++ ++  +  +     + CigC+ Cv++Cp +a
  gi|385805862|ref|YP_005842260.1| 14 TKCNlECIRFCPVNRSRRSSKAIEIDSNTGKPviyeNVCIGCNICVKKCPYNA 66
                                      679857********999999999999877666999999************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 ?    5.8   0.1     0.037        12       1      23 [.     102     124 ..     102     136 .. 0.83
   2 !   11.0   0.0   0.00093       0.3       1      25 [.     373     397 ..     373     409 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.037
                              MobB   1 vlgivgksgsGKTtLleklipel 23 
                                       vlgi+gk+g GKTt +  l  el
  gi|385805862|ref|YP_005842260.1| 102 VLGIIGKNGIGKTTTIRILAGEL 124
                                       799***********988766555 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00093
                              MobB   1 vlgivgksgsGKTtLleklipelka 25 
                                       v+gi g +g GKTt+++kl++++++
  gi|385805862|ref|YP_005842260.1| 373 VIGILGPNGIGKTTFVKKLVSMISE 397
                                       799*****************98876 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1     0.035        11       3      34 ..     101     135 ..      99     173 .. 0.64
   2 !   10.2   0.0    0.0019      0.59       2      27 ..     371     396 ..     370     434 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.035
                            AAA_14   3 kilvitGaRrvGKTtllkqlikell...vkkesil 34 
                                       ++l i G   +GKTt ++ l+ el+    +ke+  
  gi|385805862|ref|YP_005842260.1| 101 EVLGIIGKNGIGKTTTIRILAGELIpnfGDKERKA 135
                                       7899****************999985443333333 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0019
                            AAA_14   2 rkilvitGaRrvGKTtllkqlikell 27 
                                       ++++ i G+  +GKTt++k+l++   
  gi|385805862|ref|YP_005842260.1| 371 GEVIGILGPNGIGKTTFVKKLVSMIS 396
                                       57899***************986544 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   1.0      0.24        77       3      20 ..      14      32 ..      11      50 .. 0.72
   2 !   17.0   0.3   2.6e-05    0.0084       2      20 ..      52      70 ..      51      90 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.24
                           Fer4_16  3 gtCgk.CaevCPtnaikek 20
                                      ++C+  C+  CP+n  +  
  gi|385805862|ref|YP_005842260.1| 14 TKCNLeCIRFCPVNRSRRS 32
                                      5798889*****9987666 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 2.6e-05
                           Fer4_16  2 CgtCgkCaevCPtnaikek 20
                                      C++C+ C++ CP na++ +
  gi|385805862|ref|YP_005842260.1| 52 CIGCNICVKKCPYNALEIE 70
                                      ***************9865 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0      0.04        13       3      25 ..     105     146 ..     103     196 .. 0.73
   2 !    9.3   0.0    0.0048       1.5       1      44 [.     374     412 ..     374     445 .. 0.68
   3 ?   -1.0   0.0       7.4   2.4e+03      33      85 ..     479     532 ..     465     592 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.04
                            AAA_18   3 ltGtpGvGKttlakeLskrl.gf..................g 25 
                                       + G+ G GKtt  + L+ +l  +                  g
  gi|385805862|ref|YP_005842260.1| 105 IIGKNGIGKTTTIRILAGELiPNfgdkerkasenevlerfrG 146
                                       89**************87765334554444444444444444 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0048
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpe 44 
                                       I++ G+ G GKtt+ k L ++      + d   ++++ +++ p+
  gi|385805862|ref|YP_005842260.1| 374 IGILGPNGIGKTTFVKKLVSMI-----SEDRPEDEEIKFSYKPQ 412
                                       89****************9884.....55555555555555555 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 7.4
                            AAA_18  33 kenglllevdpe.aldeskrldedkldklldaleenss...aleegknlvidghlae 85 
                                       k+ +l+l ++p   ld ++rl   k   +++ l e++s      e++  +id + + 
  gi|385805862|ref|YP_005842260.1| 479 KDAELYLLDEPSaYLDVEERLSVAK---VIRRLTESRSvaaFVVEHDLSIIDYICSR 532
                                       5555555555554344444444444...44444444444446666666666666544 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0      0.13        42       4      22 ..     105     123 ..     102     163 .. 0.90
   2 ?    0.7   0.0       1.7   5.4e+02      63      95 ..     224     259 ..     209     272 .. 0.83
   3 !    9.8   0.0    0.0027      0.86       4      20 ..     376     392 ..     373     523 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.13
                            AAA_33   4 lvGlpGsGKstlaerllkk 22 
                                       ++G +G GK+t ++ l+ +
  gi|385805862|ref|YP_005842260.1| 105 IIGKNGIGKTTTIRILAGE 123
                                       79**********9988766 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.7
                            AAA_33  63 arkalsagrn.vildat..nlsrrerarflklarrl 95 
                                       +  +ls++++ +i+d +  +l+ rer r+ +l r+l
  gi|385805862|ref|YP_005842260.1| 224 IVATLSKKADlYIFDEPssFLDVRERIRIASLIREL 259
                                       556788888889**99988999****9999988865 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.0027
                            AAA_33   4 lvGlpGsGKstlaerll 20 
                                       + G++G GK+t++++l+
  gi|385805862|ref|YP_005842260.1| 376 ILGPNGIGKTTFVKKLV 392
                                       67*************98 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.026       8.3      99     123 ..     100     124 ..      93     143 .. 0.83
   2 ?   -1.2   0.0       5.1   1.6e+03      92     110 ..     274     292 ..     221     294 .. 0.85
   3 !    8.4   0.0    0.0057       1.8      98     122 ..     370     394 ..     365     408 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.026
                                       TSEEEEECSTTSSHHHHHHHHCTT- CS
                       RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpel 123
                                       +++  ++G+ G+GK+t i  l++el
  gi|385805862|ref|YP_005842260.1| 100 GEVLGIIGKNGIGKTTTIRILAGEL 124
                                       567789*************999985 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 5.1
                                       HHHHHCTTSEEEEECSTTS CS
                       RsgA_GTPase  92 elkellkdktsvlvGqSGv 110
                                       +l ++l+d+++v+ G+ Gv
  gi|385805862|ref|YP_005842260.1| 274 ALLDYLSDNIVVMYGEPGV 292
                                       5788999999999999998 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0057
                                       TTSEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpe 122
                                       k++++ ++G+ G+GK+t++++l++ 
  gi|385805862|ref|YP_005842260.1| 370 KGEVIGILGPNGIGKTTFVKKLVSM 394
                                       5678889**************9975 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.2     0.028       9.1      10      35 ..     100     125 ..      96     136 .. 0.81
   2 !    9.5   0.0    0.0036       1.2       7      38 ..     368     399 ..     365     408 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.028
                            AAA_19  10 ekvllvtaGpGtGKTrvlkhivallv 35 
                                        +vl +++  G GKT++++    +l+
  gi|385805862|ref|YP_005842260.1| 100 GEVLGIIGKNGIGKTTTIRILAGELI 125
                                       67899*************98877665 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0036
                            AAA_19   7 alkekvllvtaGpGtGKTrvlkhivallvelg 38 
                                       a+k +v+ ++++ G GKT+ +k+ v+++ e +
  gi|385805862|ref|YP_005842260.1| 368 ASKGEVIGILGPNGIGKTTFVKKLVSMISEDR 399
                                       5688999******************9988766 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.3      0.19        60       3      22 ..     104     123 ..     102     127 .. 0.82
   2 !   12.5   0.1   0.00032       0.1       2      25 ..     374     397 ..     373     400 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.19
                                       EEE--TTSSHHHHHHHHHHH CS
                          NTPase_1   3 fiTGppGvGKtTlvkkvlel 22 
                                        i G+ G+GKtT ++ ++ +
  gi|385805862|ref|YP_005842260.1| 104 GIIGKNGIGKTTTIRILAGE 123
                                       5789********99877665 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00032
                                       EEEE--TTSSHHHHHHHHHHHH.. CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellks 25 
                                       + i Gp G+GKtT+vkk+++++++
  gi|385805862|ref|YP_005842260.1| 374 IGILGPNGIGKTTFVKKLVSMISE 397
                                       6688***************99965 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1     0.011       3.5      26      48 ..     103     125 ..     101     136 .. 0.89
   2 ?    7.6   0.0     0.011       3.5      26      49 ..     374     397 ..     372     406 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.011
                             DUF87  26 lAilgsTGsGKSntvavLleell 48 
                                       l+i+g+ G GK++t+++L  el+
  gi|385805862|ref|YP_005842260.1| 103 LGIIGKNGIGKTTTIRILAGELI 125
                                       69*****************9998 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.011
                             DUF87  26 lAilgsTGsGKSntvavLleelle 49 
                                       ++ilg  G GK+++v+ L++ + e
  gi|385805862|ref|YP_005842260.1| 374 IGILGPNGIGKTTFVKKLVSMISE 397
                                       69*****************98885 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   1.9       3.1   9.8e+02       4      21 ..       5      25 ..       2      26 .. 0.66
   2 !   17.1   2.7   1.3e-05    0.0042       2      22 .]      44      64 ..      43      64 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 3.1
                            Fer4_2  4 vvdtdrC..igCg.aCvsaCP 21
                                      v+d   C  + C+  C+  CP
  gi|385805862|ref|YP_005842260.1|  5 VIDYSLCkpTKCNlECIRFCP 25
                                      666666642358678999999 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 1.3e-05
                            Fer4_2  2 pvvvdtdrCigCgaCvsaCPa 22
                                      ++v+ ++ CigC++Cv+ CP+
  gi|385805862|ref|YP_005842260.1| 44 KPVIYENVCIGCNICVKKCPY 64
                                      689999**************5 PP

>> VirE  Virulence-associated protein E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0    0.0013      0.43      47     112 ..      95     163 ..      90     170 .. 0.83
   2 ?    3.3   0.0      0.18        58      52      74 ..     371     393 ..     361     410 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0013
                              VirE  47 PgiKfDfvlvLvGkqgsgKstfleklgee...wftdslksvedkdavekiqgvliveiaEleasnkaev 112
                                       P  K  +vl + Gk g+gK+t++++l++e    f d+ ++  +++ +e  +g+ + e+     s+k++v
  gi|385805862|ref|YP_005842260.1|  95 PVPKKGEVLGIIGKNGIGKTTTIRILAGElipNFGDKERKASENEVLERFRGTELFEYFQKVYSKKIKV 163
                                       6668889999****************66657789********9**999999998888865555555555 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.18
                              VirE  52 DfvlvLvGkqgsgKstfleklge 74 
                                        +v+ + G+ g+gK+tf++kl +
  gi|385805862|ref|YP_005842260.1| 371 GEVIGILGPNGIGKTTFVKKLVS 393
                                       4677788*************954 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.4     0.094        30      22      36 ..     102     116 ..      96     124 .. 0.86
   2 !    9.1   0.0     0.002      0.65      21      43 ..     372     394 ..     364     426 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.094
                                       EEEEEESTTSSHHHH CS
                            NB-ARC  22 vvalvGmgGvGKttl 36 
                                       v+++ G+ G+GKtt 
  gi|385805862|ref|YP_005842260.1| 102 VLGIIGKNGIGKTTT 116
                                       89***********96 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.002
                                       EEEEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC  21 lvvalvGmgGvGKttlakqilnk 43 
                                        v+++ G  G+GKtt +k+ ++ 
  gi|385805862|ref|YP_005842260.1| 372 EVIGILGPNGIGKTTFVKKLVSM 394
                                       599***************99876 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0     0.025       8.1       4      25 ..     105     126 ..     103     168 .. 0.76
   2 ?    6.1   0.0     0.037        12       2      20 ..     374     392 ..     373     427 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.025
                            AAA_28   4 itGgestGKTtlleaLaargyp 25 
                                       i+G  + GKTt+++ La + +p
  gi|385805862|ref|YP_005842260.1| 105 IIGKNGIGKTTTIRILAGELIP 126
                                       8999************966444 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.037
                            AAA_28   2 ivitGgestGKTtlleaLa 20 
                                       i i+G+ + GKTt +++L 
  gi|385805862|ref|YP_005842260.1| 374 IGILGPNGIGKTTFVKKLV 392
                                       5699************996 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1      0.18        59      19      43 ..     100     124 ..      77     130 .. 0.81
   2 ?    9.0   0.0    0.0041       1.3      19      43 ..     371     395 ..     358     403 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.18
                                       TEEEEEEESTTSSHHHHHHHHHHHT CS
                              TsaE  19 gdvilLeGdLGaGKTtlvrglakal 43 
                                       g+v+ + G+ G GKTt +r la +l
  gi|385805862|ref|YP_005842260.1| 100 GEVLGIIGKNGIGKTTTIRILAGEL 124
                                       5678899************998765 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0041
                                       TEEEEEEESTTSSHHHHHHHHHHHT CS
                              TsaE  19 gdvilLeGdLGaGKTtlvrglakal 43 
                                       g+vi + G+ G GKTt+v++l++ +
  gi|385805862|ref|YP_005842260.1| 371 GEVIGILGPNGIGKTTFVKKLVSMI 395
                                       6788899*************99865 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.62     2e+02       1      20 [.     102     121 ..     102     171 .. 0.79
   2 ?   11.2   0.0   0.00072      0.23       1      33 [.     373     405 ..     373     437 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.62
                               PRK   1 vIgvagsSGaGkttvarkle 20 
                                       v+g+ g+ G Gktt+ r l 
  gi|385805862|ref|YP_005842260.1| 102 VLGIIGKNGIGKTTTIRILA 121
                                       689***********998765 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00072
                               PRK   1 vIgvagsSGaGkttvarklekifgrekvkaaei 33 
                                       vIg+ g+ G Gktt+ +kl++++ +   +  ei
  gi|385805862|ref|YP_005842260.1| 373 VIGILGPNGIGKTTFVKKLVSMISEDRPEDEEI 405
                                       8*********************99655554444 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 ?    2.3   0.0      0.32     1e+02      37      53 ..     104     120 ..      91     128 .. 0.79
   2 ?   10.0   0.0    0.0014      0.46      37      72 ..     375     410 ..     367     422 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.32
                             AAA_7  37 llvGptGtGKtviikdl 53 
                                        ++G+ G GKt++i+ l
  gi|385805862|ref|YP_005842260.1| 104 GIIGKNGIGKTTTIRIL 120
                                       479**********9865 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0014
                             AAA_7  37 llvGptGtGKtviikdllkkldkekylsltinfsaq 72 
                                        + Gp G GKt+ +k+l++ +++++     i+fs++
  gi|385805862|ref|YP_005842260.1| 375 GILGPNGIGKTTFVKKLVSMISEDRPEDEEIKFSYK 410
                                       578*********************999999999975 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.045        14       3      23 ..     104     125 ..     102     145 .. 0.81
   2 ?    6.3   0.1     0.031        10       2      22 ..     374     397 ..     373     547 .. 0.66

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.045
                                       EEEESTTSSHHHHHHHHHTS.T CS
                          MMR_HSR1   3 aivGrpNvGKStLinaltge.k 23 
                                       +i+G+   GK+t i+ l ge  
  gi|385805862|ref|YP_005842260.1| 104 GIIGKNGIGKTTTIRILAGElI 125
                                       8****************99743 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.031
                                       EEEEESTTSSHHHHHHHHHT...S CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltg...e 22 
                                       ++i+G    GK+t++++l+    e
  gi|385805862|ref|YP_005842260.1| 374 IGILGPNGIGKTTFVKKLVSmisE 397
                                       899***************963330 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 ?    4.7   0.1     0.039        12      29      54 ..     100     125 ..      94     131 .. 0.87
   2 ?    7.7   0.1     0.005       1.6      26      53 ..     368     395 ..     361     399 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.039
                                       SEEEEEEE-TTSSHHHHHHHHHHHHH CS
                              MeaB  29 aqvvGltGvPGaGkstlvealglelr 54 
                                        +v+G+ G  G Gk t++  l+ el+
  gi|385805862|ref|YP_005842260.1| 100 GEVLGIIGKNGIGKTTTIRILAGELI 125
                                       579***************99988876 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.005
                                       -S-SEEEEEEE-TTSSHHHHHHHHHHHH CS
                              MeaB  26 aGraqvvGltGvPGaGkstlvealglel 53 
                                       a + +v+G+ G  G Gk t+v++l+  +
  gi|385805862|ref|YP_005842260.1| 368 ASKGEVIGILGPNGIGKTTFVKKLVSMI 395
                                       56789******************98766 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1      0.13        43      19      39 ..     101     121 ..      96     131 .. 0.84
   2 ?    7.1   0.0     0.012       3.9      16      45 ..     369     398 ..     365     418 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.13
                            AAA_30  19 rvavltGpAGtGKttalkalr 39 
                                        v  + G  G GKtt+++ l+
  gi|385805862|ref|YP_005842260.1| 101 EVLGIIGKNGIGKTTTIRILA 121
                                       478899***********9875 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.012
                            AAA_30  16 sgdrvavltGpAGtGKttalkalreaweaa 45 
                                       s+  v  + Gp G GKtt +k+l+ ++ ++
  gi|385805862|ref|YP_005842260.1| 369 SKGEVIGILGPNGIGKTTFVKKLVSMISED 398
                                       44568999***************9988765 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 ?    5.6   0.0     0.057        18      25      47 ..     206     228 ..     191     257 .. 0.84
   2 ?    5.6   0.1      0.06        19      26      44 ..     456     474 ..     445     507 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.057
                           SbcCD_C  25 elsrssgtlSGGekqflaylala 47 
                                        l+r++++ SGGe q+++ +a +
  gi|385805862|ref|YP_005842260.1| 206 VLERDVKNISGGELQKILIVATL 228
                                       5899************9999876 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.06
                           SbcCD_C  26 lsrssgtlSGGekqflayl 44 
                                        +r++++lSGGe q+la  
  gi|385805862|ref|YP_005842260.1| 456 REREVSELSGGELQKLALA 474
                                       57999********987643 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1     0.021       6.8      19      39 ..      96     117 ..      87     127 .. 0.83
   2 ?    6.2   0.2     0.026       8.3      23      39 ..     371     388 ..     361     395 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.021
                            AAA_29  19 idlkg.atlltGpsGsGKSTll 39 
                                       +  kg +  ++G++G GK+T +
  gi|385805862|ref|YP_005842260.1|  96 VPKKGeVLGIIGKNGIGKTTTI 117
                                       556676778**********976 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.026
                            AAA_29  23 g.atlltGpsGsGKSTll 39 
                                       g ++ + Gp+G GK+T++
  gi|385805862|ref|YP_005842260.1| 371 GeVIGILGPNGIGKTTFV 388
                                       446779**********97 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.29        91      22      50 ..      92     120 ..      90     127 .. 0.89
   2 ?    8.2   0.0    0.0029      0.91      33      65 ..     374     406 ..     366     413 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.29
                            AAA_32  22 fglkikkkgYNifvlGesgtGrttlvkrl 50 
                                       fgl + kkg  + ++G++g+G+tt+++ l
  gi|385805862|ref|YP_005842260.1|  92 FGLPVPKKGEVLGIIGKNGIGKTTTIRIL 120
                                       8999********************99865 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0029
                            AAA_32  33 ifvlGesgtGrttlvkrlleeiakkeptpdDwc 65 
                                       i +lG++g+G+tt+vk+l++ i++++p  +++ 
  gi|385805862|ref|YP_005842260.1| 374 IGILGPNGIGKTTFVKKLVSMISEDRPEDEEIK 406
                                       6689********************999888765 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.13        41       9      33 ..     105     129 ..     101     163 .. 0.75
   2 ?    7.2   0.0    0.0084       2.7       9      32 ..     376     399 ..     372     434 .. 0.64

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.13
                                       EEEBTTSSCCCCCCTTSSSS----- CS
                            Septin   9 vvGesglGkttlintlfetdlieee 33 
                                       ++G++g+Gktt i+ l  + + +  
  gi|385805862|ref|YP_005842260.1| 105 IIGKNGIGKTTTIRILAGELIPNFG 129
                                       89***********988776555543 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0084
                                       EEEBTTSSCCCCCCTTSSSS---- CS
                            Septin   9 vvGesglGkttlintlfetdliee 32 
                                       + G +g+Gktt+++ l++    ++
  gi|385805862|ref|YP_005842260.1| 376 ILGPNGIGKTTFVKKLVSMISEDR 399
                                       689***********9986543333 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 ?    2.0   0.0      0.74   2.4e+02       4      19 ..     105     120 ..     103     159 .. 0.85
   2 ?    8.6   0.0    0.0063         2       3      27 ..     375     399 ..     373     430 .. 0.68

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.74
                                       EESSTTSSHHHHHHCH CS
                               Roc   4 lvGdsgvGKtsllkrf 19 
                                       ++G++g+GKt+ ++ +
  gi|385805862|ref|YP_005842260.1| 105 IIGKNGIGKTTTIRIL 120
                                       89********988755 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0063
                                       EEESSTTSSHHHHHHCHCT-CCC-E CS
                               Roc   3 vlvGdsgvGKtsllkrfvedkfsek 27 
                                        ++G +g+GKt+++k++v+   +++
  gi|385805862|ref|YP_005842260.1| 375 GILGPNGIGKTTFVKKLVSMISEDR 399
                                       589**************97554333 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.8       1.2   3.7e+02      21      43 ..     101     123 ..      97     195 .. 0.75
   2 ?   10.0   0.0    0.0019      0.61      20      46 ..     371     397 ..     367     481 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 1.2
                          ATPase_2  21 eiyfiYGpegsGKtaLlkeiien 43 
                                       e++ i G  g+GKt+ ++ ++ +
  gi|385805862|ref|YP_005842260.1| 101 EVLGIIGKNGIGKTTTIRILAGE 123
                                       566789999*****999865544 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0019
                          ATPase_2  20 neiyfiYGpegsGKtaLlkeiienled 46 
                                        e++ i Gp g+GKt+++k++++  ++
  gi|385805862|ref|YP_005842260.1| 371 GEVIGILGPNGIGKTTFVKKLVSMISE 397
                                       578889**************9987643 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 ?    2.3   0.1       0.5   1.6e+02       4      21 ..     105     122 ..     103     134 .. 0.86
   2 ?    7.0   0.0     0.017       5.5       4      24 ..     376     397 ..     374     408 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.5
                                       EE--SSSSHHHHHHHGGG CS
                             AAA_5   4 LvGppGtgKselaerlaa 21 
                                       ++G+ G+gK++ ++ la 
  gi|385805862|ref|YP_005842260.1| 105 IIGKNGIGKTTTIRILAG 122
                                       69**********999885 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.017
                                       EE--SSSSHHHHHHHGGGGB.S CS
                             AAA_5   4 LvGppGtgKselaerlaaal.n 24 
                                       ++Gp G+gK++++++l +++ +
  gi|385805862|ref|YP_005842260.1| 376 ILGPNGIGKTTFVKKLVSMIsE 397
                                       68**************999852 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.16        51      21      38 ..     105     122 ..      99     162 .. 0.84
   2 ?    6.4   0.0    0.0091       2.9      21      76 ..     376     429 ..     373     438 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.16
                            AAA_13  21 iYGwNGaGKTtLSrllrs 38 
                                       i G+NG GKTt  r+l+ 
  gi|385805862|ref|YP_005842260.1| 105 IIGKNGIGKTTTIRILAG 122
                                       66**********999986 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0091
                            AAA_13  21 iYGwNGaGKTtLSrllrslelgetepkfangsieitngeeldirVfNrdFveenls 76 
                                       i G NG GKTt+ + l s+ ++   p+ ++ ++++ + +     +f ++ veenl 
  gi|385805862|ref|YP_005842260.1| 376 ILGPNGIGKTTFVKKLVSMISED-RPEDEEIKFSY-KPQYVSPEIFEKKTVEENLI 429
                                       679**********9999985543.44445666666.447779999*******9986 PP

>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   2.0   0.00062       0.2       8      63 ..      14      71 ..       8      83 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00062
                           Fer4_11  8 eqCr.hCleppCvasapse.......aivkdeetGaVlldektkkeevrevveacPykivrkne 63
                                      ++C+ +     C++ +p++       ai  d +tG  ++ e+ +  +++ +v+ cPy++   ++
  gi|385805862|ref|YP_005842260.1| 14 TKCNlE-----CIRFCPVNrsrrsskAIEIDSNTGKPVIYENVCI-GCNICVKKCPYNALEIEN 71
                                      555434.....444454444445578**********9999****7.************987766 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 ?   -0.1   0.0       1.4   4.3e+02      19      44 ..      99     124 ..      90     228 .. 0.90
   2 ?    9.1   0.0    0.0022       0.7      18      48 ..     369     399 ..     363     487 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.4
                        KAP_NTPase  19 tpivvgLygkWGsGKssllnkledel 44 
                                       ++ v+g+ gk G GK++ +  l  el
  gi|385805862|ref|YP_005842260.1|  99 KGEVLGIIGKNGIGKTTTIRILAGEL 124
                                       66799999********9998887665 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0022
                        KAP_NTPase  18 atpivvgLygkWGsGKssllnkledelkefa 48 
                                       +++ v+g+ g+ G GK+++++kl + ++e  
  gi|385805862|ref|YP_005842260.1| 369 SKGEVIGILGPNGIGKTTFVKKLVSMISEDR 399
                                       66779******************99999885 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       2.9   9.2e+02       1      15 [.     105     119 ..     105     124 .. 0.86
   2 ?    9.3   0.0    0.0027      0.85       1      23 [.     376     398 ..     376     427 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 2.9
                        ATP_bind_1   1 vvGpaGsGKttfvga 15 
                                       ++G  G GKtt ++ 
  gi|385805862|ref|YP_005842260.1| 105 IIGKNGIGKTTTIRI 119
                                       79*********9875 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0027
                        ATP_bind_1   1 vvGpaGsGKttfvgalseilelr 23 
                                       ++Gp G GKttfv++l++++++ 
  gi|385805862|ref|YP_005842260.1| 376 ILGPNGIGKTTFVKKLVSMISED 398
                                       68**************9998765 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 ?    4.4   0.0      0.08        25      13      65 ..      99     146 ..      93     169 .. 0.71
   2 ?    4.8   0.0      0.06        19      12      38 ..     369     395 ..     366     408 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.08
                                       TT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEEESEEHHHHHHHHHHCHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  13 qGqrtlipgafgvGktvisqslskqsnsddaiiyvgiGergnevaevleefpe 65 
                                       +G+ ++i+g++g+Gkt+ ++ l+ +     +i   g  er+ + +evle+f+ 
  gi|385805862|ref|YP_005842260.1|  99 KGEVLGIIGKNGIGKTTTIRILAGE-----LIPNFGDKERKASENEVLERFRG 146
                                       79999************99888766.....23334555555555566666655 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.06
                                       BTT-EEEEEESTTSSHHHHHHHHHHHS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  12 vqGqrtlipgafgvGktvisqslskqs 38 
                                        +G+ ++i+g +g+Gkt+ +++l+   
  gi|385805862|ref|YP_005842260.1| 369 SKGEVIGILGPNGIGKTTFVKKLVSMI 395
                                       58999*************998887765 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.21        69       3      23 ..     107     127 ..     105     168 .. 0.85
   2 ?    5.8   0.0     0.032        10       3      22 ..     378     397 ..     376     410 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.21
                                       ESTTSSHHHHHHHHHHHHHHT CS
                   Thymidylate_kin   3 GlDGaGKttqaellkerlkee 23 
                                       G +G GKtt +++l+  l  +
  gi|385805862|ref|YP_005842260.1| 107 GKNGIGKTTTIRILAGELIPN 127
                                       779**********99877655 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.032
                                       ESTTSSHHHHHHHHHHHHHH CS
                   Thymidylate_kin   3 GlDGaGKttqaellkerlke 22 
                                       G +G GKtt++++l++ ++e
  gi|385805862|ref|YP_005842260.1| 378 GPNGIGKTTFVKKLVSMISE 397
                                       899***********998876 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1       2.4   7.7e+02      32      49 ..      99     116 ..      95     124 .. 0.85
   2 ?    8.7   0.0    0.0037       1.2      28      65 ..     366     403 ..     361     512 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 2.4
                            AAA_25  32 agelallaGapgtGKttl 49 
                                       +ge+  ++G  g GKtt 
  gi|385805862|ref|YP_005842260.1|  99 KGEVLGIIGKNGIGKTTT 116
                                       68888999********96 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0037
                            AAA_25  28 gllpagelallaGapgtGKttlaldlalavatGkpwlg 65 
                                       g   +ge++ + G+ g GKtt++  l+  +++++p  +
  gi|385805862|ref|YP_005842260.1| 366 GSASKGEVIGILGPNGIGKTTFVKKLVSMISEDRPEDE 403
                                       556799*******************9999999888654 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   8.3    0.0058       1.9       4      59 ..      15      65 ..      11      67 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0058
                           Fer4_17  4 qCgy.ClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPqg 59
                                      +C   C++ Cp ++ +++      +a+++ ++++ +   + + Ci+C+ C++kCP++
  gi|385805862|ref|YP_005842260.1| 15 KCNLeCIRFCPVNRSRRS-----SKAIEIDSNTG-KPVIYENVCIGCNICVKKCPYN 65
                                      566557777777776665.....33333332222.12246689************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 ?    2.7   3.3      0.95   3.1e+02       3      14 ..      15      27 ..      11      27 .. 0.82
   2 ?   13.2   4.2   0.00043      0.14       1      15 []      52      66 ..      52      66 .. 0.98

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.95
                            Fer4_3  3 gCg.aCvevCPvg 14
                                       C+  C + CPv+
  gi|385805862|ref|YP_005842260.1| 15 KCNlECIRFCPVN 27
                                      69856******97 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00043
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+gC+ Cv+ CP++A
  gi|385805862|ref|YP_005842260.1| 52 CIGCNICVKKCPYNA 66
                                      *************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 ?    3.4   2.1      0.42   1.4e+02       6      17 .]      15      27 ..       8      28 .. 0.74
   2 ?    9.3   3.6    0.0054       1.7       2      17 .]      50      65 ..      49      65 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.42
                            Fer4_4  6 gCg.sCvaaCPqg 17
                                       C   C+++CP++
  gi|385805862|ref|YP_005842260.1| 15 KCNlECIRFCPVN 27
                                      56645******75 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0054
                            Fer4_4  2 erCigCgsCvaaCPqg 17
                                      + CigC  Cv  CP++
  gi|385805862|ref|YP_005842260.1| 50 NVCIGCNICVKKCPYN 65
                                      57************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (609 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                       109  (0.00607954); expected 17.9 (0.001)
Passed Fwd filter:                        56  (0.00312343); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              56  [number of targets reported over threshold]
# CPU time: 0.78u 0.33s 00:00:01.11 Elapsed: 00:00:00.49
# Mc/sec: 3703.58
//
Query:       gi|385805863|ref|YP_005842261.1|  [L=336]
Description: hypothetical protein FFONT_0821 [Fervidicoccus fontis Kam940]
Scores for complete 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-42  144.8   0.7    2.9e-42  144.8   0.7    1.4  2  NMD3         NMD3 family
  ------ inclusion threshold ------
      0.019   15.2   0.2      0.054   13.8   0.2    1.7  1  POTRA_1      POTRA domain, FtsQ-type
       0.08   12.7   0.1        1.8    8.4   0.0    2.7  3  Rtt106_N     Histone chaperone Rtt106 N-terminal domain
        1.7    9.1   6.8       0.61   10.6   2.1    2.7  3  DUF104       Protein of unknown function DUF104
        7.3    6.6   7.5         20    5.2   2.0    3.3  3  zf-C4_ClpX   ClpX C4-type zinc finger


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 !  144.8   0.7   8.1e-46   2.9e-42       1     243 []       5     226 ..       5     226 .. 0.89
   2 ?   -3.6   0.0       1.7     6e+03      67      73 ..     270     275 ..     249     305 .. 0.47

  Alignments for each domain:
  == domain 1  score: 144.8 bits;  conditional E-value: 8.1e-46
                              NMD3   1 CcrCGkei...eelinglCedCllkevditegiekievevCkeCgrylpkgkWvkaeleseellaeclkklvekgLk 74 
                                       C+ CG+e+    + + g+C++C+l+++++   i+ i+++ Ck Cg++++k++W+    ++e+ ++e++ k+vek+ k
  gi|385805863|ref|YP_005842261.1|   5 CPICGREEsknLPFVGGICVECYLNKNPL--EIKAITLNKCKICGKIRYKNDWI---FANENFYSEIFAKEVEKNNK 76 
                                       ********544334555**********95..5788******************4...569***********888744 PP

                              NMD3  75 vseeveevkvelvdaefiwtephskrikvkvtvqgevrgenetilqqevevevkvkrqqCprCsriaggyyeaivQv 151
                                            + +++  +d +    +p  ++ kv vtvq+e+ +     ++  ++  +  k ++Cp+C ++++g+y++++Q+
  gi|385805863|ref|YP_005842261.1|  77 ----KKFIQFG-LDLK---AVP--YKEKVLVTVQNEIGK-----YETYLDPIIDYKFTICPQCLARKAGSYDSVIQI 138
                                       ....3445555.5555...566..7789*********33.....5688999999999******************** PP

                              NMD3 152 RqkrelteeehkrtfelleqlilkhdahafiskikevkeGlDfyfgsksaArklveflksevggkvkeseklvsedk 228
                                       R++++l+ e++k +++l+e+l   +d +++i++i+e+k+++D+ +  +++Ar +++fl++++gg++k++ kl+s+ k
  gi|385805863|ref|YP_005842261.1| 139 RGTNKLDFEDKKIIMNLIEKLP--YDLKQHIVTITENKDWIDVEIVGHEKARLIASFLSEKLGGETKQTFKLIST-K 212
                                       **********************..99*************************************************.7 PP

                              NMD3 229 ksgkevyrltysvrl 243
                                       k g+++ rlt+s+r+
  gi|385805863|ref|YP_005842261.1| 213 K-GERNSRLTISLRI 226
                                       7.***********98 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.7
                              NMD3  67 klvekgL 73 
                                       ++ +k++
  gi|385805863|ref|YP_005842261.1| 270 EI-RKNV 275
                                       22.1221 PP

>> POTRA_1  POTRA domain, FtsQ-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   1.5e-05     0.054      32      64 ..     264     297 ..     256     298 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.5e-05
                                       GGS-HHHHHHHHHH.-TTEEEEEEEEETTTEEEE CS
                           POTRA_1  32 fsldleaieqrlek.lpwvksasVrrqwPntlei 64 
                                       ++ldl++i+++++     +ks++V+  +P+++ +
  gi|385805863|ref|YP_005842261.1| 264 IKLDLKEIRKNVKTfEGEIKSVTVQAVLPDRVIV 297
                                       679***********999**************987 PP

>> Rtt106_N  Histone chaperone Rtt106 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       2.5   8.9e+03       4      14 ..      26      36 ..      25      37 .. 0.82
   2 ?    8.4   0.0    0.0005       1.8       6      21 ..     156     171 ..     153     173 .. 0.92
   3 ?    1.0   0.0       0.1   3.7e+02      18      36 ..     285     303 ..     280     305 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.5
                          Rtt106_N  4 SFldkLPaeLr 14
                                       +l+k P e++
  gi|385805863|ref|YP_005842261.1| 26 CYLNKNPLEIK 36
                                      689**999987 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0005
                          Rtt106_N   6 ldkLPaeLrskvskIt 21 
                                       ++kLP +L+  +++It
  gi|385805863|ref|YP_005842261.1| 156 IEKLPYDLKQHIVTIT 171
                                       89*************9 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.1
                          Rtt106_N  18 skItsvlPdSlSiFqelYn 36 
                                       +++  vlPd   + ++ Yn
  gi|385805863|ref|YP_005842261.1| 285 VTVQAVLPDRVIVIDDSYN 303
                                       78899******99999998 PP

>> DUF104  Protein of unknown function DUF104
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.1   3.8e+03      25      37 ..      92     102 ..      89     111 .. 0.77
   2 ?   -3.2   0.0       3.3   1.2e+04      30      50 ..     179     202 ..     169     208 .. 0.59
   3 ?   10.6   2.1   0.00017      0.61      17      50 ..     253     286 ..     251     291 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.1
                            DUF104  25 GeevkikIeeake 37 
                                       +e+v +++++  e
  gi|385805863|ref|YP_005842261.1|  92 KEKVLVTVQN--E 102
                                       7999999999..3 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.3
                            DUF104  30 ikIee...akeilkklkgilkead 50 
                                       ++I     a+ i+  l ++l+ ++
  gi|385805863|ref|YP_005842261.1| 179 VEIVGhekARLIASFLSEKLGGET 202
                                       444444455566666666666444 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00017
                            DUF104  17 LekvdLkEGeevkikIeeakeilkklkgilkead 50 
                                       L+  +LkE++e+k+ ++e+++ +k ++g +k+++
  gi|385805863|ref|YP_005842261.1| 253 LKLFKLKERKEIKLDLKEIRKNVKTFEGEIKSVT 286
                                       55679***********************998665 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 ?    5.2   2.0    0.0056        20       2      29 ..       4      26 ..       3      28 .. 0.88
   2 ?    1.0   0.1      0.11     4e+02       2      10 ..      42      50 ..      41      63 .. 0.75
   3 ?    1.2   0.0     0.097   3.5e+02      14      30 ..     111     125 ..     104     128 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0056
                        zf-C4_ClpX  2 rCSFCgksesevkklIagpngvyICdeC 29
                                       C  Cg++es+  + +   +g  IC eC
  gi|385805863|ref|YP_005842261.1|  4 ICPICGREESKNLPFV---GG--ICVEC 26
                                      699************9...35..99999 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.11
                        zf-C4_ClpX  2 rCSFCgkse 10
                                      +C  Cgk +
  gi|385805863|ref|YP_005842261.1| 42 KCKICGKIR 50
                                      8*****965 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.097
                        zf-C4_ClpX  14 kklIagpngvyICdeCv 30 
                                       +++I       IC +C 
  gi|385805863|ref|YP_005842261.1| 111 DPIIDYK--FTICPQCL 125
                                       5566553..57*****7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1188  (0.0662614); expected 358.6 (0.02)
Passed bias filter:                      687  (0.0383178); 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):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2358.28
//
Query:       gi|385805864|ref|YP_005842262.1|  [L=103]
Description: hypothetical protein FFONT_0822 [Fervidicoccus fontis Kam940]
Scores for complete 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   68.8   0.4    4.2e-19   68.6   0.4    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 !   68.6   0.4   2.4e-23   4.2e-19       6      90 ..      15      99 ..      11     101 .. 0.95

  Alignments for each domain:
  == domain 1  score: 68.6 bits;  conditional E-value: 2.4e-23
                                      E.EEEEEEEGGGTT-EEEETTEEEE--HHHH--EEE-HHHHHHHHHHHEEEEEESHHHHHHHHHTTSS-GGG-EEETTE CS
                            DUF424  6 llklvavcdkellgktfkegelllnvsegfyggelaseeeaikeLekatiaNivgeeavvlavkaGlvdpdsVlvidgv 84
                                        k v vcd ellgk+f+eg   l vs+++y ge a+eee+  ++++a+ ++++g+++v+l +++Glv++d++ +++gv
  gi|385805864|ref|YP_005842262.1| 15 RRKFVLVCDFELLGKKFVEGHYILDVSREYYEGECANEEEVAVQIKDADYVSLIGDQSVKLGINEGLVHKDAIVKVQGV 93
                                      4589*************************************************************************** PP

                                      EEEEEE CS
                            DUF424 85 phaqig 90
                                      p+a+ +
  gi|385805864|ref|YP_005842262.1| 94 PFAIFI 99
                                      **9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); 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: 0.31u 0.24s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 848.33
//
Query:       gi|385805865|ref|YP_005842263.1|  [L=145]
Description: translation initiation factor IF-2 [Fervidicoccus fontis Kam940]
Scores for complete 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  120.1   0.0    5.9e-35  119.7   0.0    1.1  1  eIF-5_eIF-2B     Domain found in IF2B/IF5
     0.0023   18.1   0.1      0.096   12.9   0.0    2.3  2  zf-RING_7        C4-type zinc ribbon domain
  ------ inclusion threshold ------
      0.021   15.2   0.7      0.039   14.3   0.7    1.4  1  Lar_restr_allev  Restriction alleviation protein Lar
      0.025   13.9   0.5      0.042   13.2   0.5    1.4  1  zf-TFIIB         Transcription factor zinc-finger
      0.042   13.9   0.1      0.071   13.2   0.1    1.3  1  Elf1             Transcription elongation factor Elf1 like
      0.092   12.4   1.4       0.32   10.7   1.4    1.8  1  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
       0.11   12.7   0.4        2.3    8.4   0.1    2.4  2  NOB1_Zn_bind     Nin one binding (NOB1) Zn-ribbon like
       0.25   11.2   2.4        7.4    6.6   0.0    2.6  3  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
       0.31   10.6   0.2       0.31   10.6   0.2    2.2  2  zf_C2H2_13       Zinc finger domain


Domain annotation for each model (and alignments):
>> eIF-5_eIF-2B  Domain found in IF2B/IF5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.7   0.0   2.9e-38   5.9e-35       7     116 ..      29     138 ..      24     139 .. 0.97

  Alignments for each domain:
  == domain 1  score: 119.7 bits;  conditional E-value: 2.9e-38
                                       SSS--SSTT--EEEETT.EEEETTHHHHHHHHTTSHHHHHHHHHHHHTSEEEES.ETTEEEESSSSSCCHHHHHHHH CS
                      eIF-5_eIF-2B   7 kkerykmpklqvkvegkkktvivNfeeiakaLnrdpehvlkyllkelgtqgsid.engrlilngkfeakkleklldk 82 
                                       + er++ pkl +++ g+ +tvi+Nf+e+a++L+r+pe +++y+lk l+t+g++d e+g+l+ln k + ++l+++l+k
  gi|385805865|ref|YP_005842263.1|  29 SGERFEPPKLIAHQMGN-QTVIRNFREVADKLRREPELLARYFLKGLATSGNYDrESGTLLLNSKLNVETLNNILNK 104
                                       678**************.*********************************************************** PP

                                       HHHHHTSTSSSTSTCEEECCSSSCEEEEESSSTC CS
                      eIF-5_eIF-2B  83 yieeyVlCkeCkspetelekeerllvlkCkaCga 116
                                       +ie+yV+C++C++p+t ++k++++++lkC+aCga
  gi|385805865|ref|YP_005842263.1| 105 FIESYVICPTCGRPDTVIIKKGKIWILKCEACGA 138
                                       *********************************8 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 !   12.9   0.0   4.8e-05     0.096       8      31 ..      92     117 ..      90     117 .. 0.93
   2 ?    3.0   0.0     0.057   1.1e+02      24      30 ..     131     137 ..     122     139 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.8e-05
                                       B--CCHHHHHCCS..TB-EE-TTT-- CS
                         zf-RING_7   8 elppqvlselrag..devvtCpeCGR 31 
                                       +l+ ++l+ + ++  +  v Cp CGR
  gi|385805865|ref|YP_005842263.1|  92 KLNVETLNNILNKfiESYVICPTCGR 117
                                       8999**********9999*******9 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.057
                                       EE-TTT- CS
                         zf-RING_7  24 vtCpeCG 30 
                                        +C+ CG
  gi|385805865|ref|YP_005842263.1| 131 LKCEACG 137
                                       6677776 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 ?   14.3   0.7     2e-05     0.039       6      36 ..     112     138 ..     108     144 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2e-05
                   Lar_restr_allev   6 CPfCggravlersqrvvaeigqcvyCadCga 36 
                                       CP Cg +++++  +++ +       C+ Cga
  gi|385805865|ref|YP_005842263.1| 112 CPTCGRPDTVIIKKGKIW----ILKCEACGA 138
                                       ***********9999999....9*******9 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.5   2.1e-05     0.042       2      26 ..     112     137 ..     111     137 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.1e-05
                          zf-TFIIB   2 CPkCqd.eleeserggveidyCpqCr 26 
                                       CP+C+  + +++++g++ i +C++C+
  gi|385805865|ref|YP_005842263.1| 112 CPTCGRpDTVIIKKGKIWILKCEACG 137
                                       *****96799***************7 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   3.6e-05     0.071      18      54 ..     106     139 ..      94     143 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.6e-05
                              Elf1  18 lptkFdCpfCnheksvevkldkkekiaevsCkvCges 54 
                                       ++++  Cp C+  ++v +   kk ki +++C+ Cg++
  gi|385805865|ref|YP_005842263.1| 106 IESYVICPTCGRPDTVII---KKGKIWILKCEACGAE 139
                                       777788*******99976...68899********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 ?   10.7   1.4   0.00016      0.32       5      30 ..     111     139 ..     107     140 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00016
                     zf-NADH-PPase   5 FCgrCGap..tepaeg.gwarvCpaCgle 30 
                                        C++CG p  ++ ++g  w + C+aCg+e
  gi|385805865|ref|YP_005842263.1| 111 ICPTCGRPdtVIIKKGkIWILKCEACGAE 139
                                       6*****998666666789*********97 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.15   2.9e+02      25      31 ..     111     117 ..     100     121 .. 0.81
   2 ?    8.4   0.1    0.0012       2.3       1      14 [.     123     136 ..     123     140 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.15
                      NOB1_Zn_bind  25 FCpkCGn 31 
                                        Cp+CG 
  gi|385805865|ref|YP_005842263.1| 111 ICPTCGR 117
                                       6*****8 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0012
                      NOB1_Zn_bind   1 ikrvkswvlrChaC 14 
                                       ik+ k w+l+C aC
  gi|385805865|ref|YP_005842263.1| 123 IKKGKIWILKCEAC 136
                                       78999********* 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 ?   -2.3   0.1       2.2   4.5e+03       4      12 ..      60      68 ..      58      69 .. 0.79
   2 ?    4.1   0.2     0.022        43      27      35 ..     111     119 ..     110     121 .. 0.72
   3 ?    6.6   0.0    0.0037       7.4       6      19 ..     125     138 ..     122     139 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.2
                           DUF35_N  4 aaegrLvgq 12
                                      ++e++L+++
  gi|385805865|ref|YP_005842263.1| 60 RREPELLAR 68
                                      689999986 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.022
                           DUF35_N  27 vCphCgsdd 35 
                                       +Cp Cg+ d
  gi|385805865|ref|YP_005842263.1| 111 ICPTCGRPD 119
                                       688888765 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0037
                           DUF35_N   6 egrLvgqrCpdCGt 19 
                                        g++++ +C +CG+
  gi|385805865|ref|YP_005842263.1| 125 KGKIWILKCEACGA 138
                                       69999********6 PP

>> zf_C2H2_13  Zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2   0.00016      0.31       3      26 ..      94     118 ..      92     123 .. 0.87
   2 ?    0.1   0.6      0.32   6.4e+02      20      25 ..     133     138 ..     132     143 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00016
                        zf_C2H2_13   3 ntrliedpLdtn.lnYRvCnkCGkP 26 
                                       n++ +++ L++    Y +C  CG+P
  gi|385805865|ref|YP_005842263.1|  94 NVETLNNILNKFiESYVICPTCGRP 118
                                       788899999999778*********9 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.32
                        zf_C2H2_13  20 CnkCGk 25 
                                       C++CG 
  gi|385805865|ref|YP_005842263.1| 133 CEACGA 138
                                       *****5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      673  (0.037537); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); 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 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 990.70
//
Query:       gi|385805866|ref|YP_005842264.1|  [L=339]
Description: small GTP-binding protein [Fervidicoccus fontis Kam940]
Scores for complete 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-19   68.5   1.3    7.4e-19   67.9   0.1    1.9  2  MMR_HSR1      50S ribosome-binding GTPase
    8.4e-15   54.6   0.8    1.8e-14   53.5   0.8    1.5  1  FeoB_N        Ferrous iron transport protein B
    2.9e-14   52.6   0.4    7.5e-14   51.3   0.4    1.8  1  NOG1          Nucleolar GTP-binding protein 1 (NOG1)
    5.1e-10   39.3   0.3    1.7e-09   37.5   0.3    1.9  1  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
    4.6e-08   32.8   0.1    8.9e-05   22.1   0.2    2.7  2  GTP_EFTU      Elongation factor Tu GTP binding domain
      9e-08   32.2   5.5    7.6e-05   22.7   1.2    2.7  2  RsgA_GTPase   RsgA GTPase
    2.1e-06   27.3   0.1    4.7e-06   26.1   0.1    1.6  1  SRPRB         Signal recognition particle receptor beta subun
    3.9e-05   23.2   4.3    0.00013   21.4   1.2    2.7  2  Arf           ADP-ribosylation factor family
    8.8e-05   22.5   5.0    0.00016   21.7   0.0    3.1  3  ATPase_2      ATPase domain predominantly from Archaea
    0.00011   22.3   4.7       0.16   12.0   0.2    2.9  3  Dynamin_N     Dynamin family
    0.00013   21.6   0.1    0.00027   20.6   0.1    1.6  1  Ras           Ras family
    0.00015   21.6   4.3      0.053   13.3   0.1    3.1  4  ATP_bind_1    Conserved hypothetical ATP binding protein
     0.0002   21.5   0.0    0.00066   19.9   0.0    1.9  1  Roc           Ras of Complex, Roc, domain of DAPkinase
     0.0014   18.6   0.3     0.0014   18.6   0.3    2.3  2  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
     0.0023   18.0   1.3      0.094   12.8   0.0    2.6  2  AAA_14        AAA domain
     0.0023   18.3   0.0      0.024   15.0   0.0    2.2  2  AAA_16        AAA ATPase domain
     0.0078   15.8   0.1        2.2    7.8   0.0    2.4  2  cobW          CobW/HypB/UreG, nucleotide-binding domain
  ------ inclusion threshold ------
      0.012   16.0   0.4      0.059   13.8   0.1    2.4  3  AAA           ATPase family associated with various cellular 
      0.012   16.1   0.0      0.033   14.7   0.0    1.8  1  AAA_18        AAA domain
      0.017   15.5   0.1       0.27   11.6   0.0    2.4  2  RNA_helicase  RNA helicase
      0.017   14.6   0.5       0.27   10.7   0.0    2.3  2  KTI12         Chromatin associated protein KTI12
      0.018   15.4   0.0      0.038   14.3   0.0    1.6  1  AAA_22        AAA domain
      0.022   14.2   0.0      0.069   12.6   0.0    1.8  1  TniB          Bacterial TniB protein
      0.023   14.8   0.0      0.051   13.7   0.0    1.7  1  AAA_33        AAA domain
      0.029   14.6   0.0      0.059   13.6   0.0    1.5  1  AAA_28        AAA domain
      0.031   13.5   0.0      0.056   12.6   0.0    1.5  1  NB-ARC        NB-ARC domain
      0.085   12.8   6.9        0.2   11.6   6.9    1.6  1  NOG1_N        NOG1 N-terminal helical 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 ?   -1.2   0.1       3.2   2.1e+03      83      83 ..      89      89 ..      32     161 .. 0.58
   2 !   67.9   0.1   1.1e-21   7.4e-19       2     114 .]     171     289 ..     170     289 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 3.2
                                      E CS
                          MMR_HSR1 83 v 83
                                      v
  gi|385805866|ref|YP_005842264.1| 89 V 89
                                      3 PP

  == domain 2  score: 67.9 bits;  conditional E-value: 1.1e-21
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETT.EEEEEEECGGCSS.HHHHHH.HHHHHHHHHHC CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkg.keielvDtpGlie.gaseek.glgkaflalee 75 
                                       ++ivG pN+GKStL++++ +++ iv+++p+tT++++ gr+k ++  +++++DtpG++  + se +  +++af+ l+ 
  gi|385805866|ref|YP_005842264.1| 171 IVIVGPPNSGKSTLVQKIAESRTIVASYPFTTKEVVPGRLKASQlINLTVLDTPGILRkNFSEMNiIERRAFATLKI 247
                                       79***************************************888899********8863333344466666665554 PP

                                       .TSEEEEEEETTTTCSHHHHHHH..HHHHHHTTSEEEEEEES CS
                          MMR_HSR1  76 .adlillvvdaseeklkpldeel..eelleeakkplilvlnk 114
                                          +i++v+d s+e+  +l+e+l   ++ + +  ++i+++nk
  gi|385805866|ref|YP_005842264.1| 248 fNGVIVFVMDPSKESTMNLKEQLelIKMFRVEVLNVIVAVNK 289
                                       5699******88553434433330033323355556666665 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 !   53.5   0.8   2.8e-17   1.8e-14       3     154 ..     171     329 ..     170     331 .. 0.86

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 2.8e-17
                                       EEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETT.EEEEEEE----SSSSSSSHHHHHHHHHHHCTS CS
                            FeoB_N   3 valvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkg.keveivDlPGiYslsayseeekvardflleee 78 
                                       +++vG pn+Gk+tl+ +++++++ v+ +p +t e   g+lk ++  +++++D PGi   +++se + + r+ +++ +
  gi|385805866|ref|YP_005842264.1| 171 IVIVGPPNSGKSTLVQKIAESRTIVASYPFTTKEVVPGRLKASQlINLTVLDTPGILR-KNFSEMNIIERRAFATLK 246
                                       789**************************************99989**********76.678888888888887655 PP

                                       ..SSEEEEEEE.....GGGHHHHHHHHHHHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBT CS
                            FeoB_N  79 ..pdvvvnvvd.....atnlernLyLtlqllelgvpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkeg 148
                                           v+v v+d     ++nl+ +L L+       ++v++a+n++d +e+ + ++  ++L+++   ++  +sa ++ +
  gi|385805866|ref|YP_005842264.1| 247 ifNGVIVFVMDpskesTMNLKEQLELIKMFRVEVLNVIVAVNKVDLIENFEKDVIRSELEKIGVYDIFFISALNNIN 323
                                       325789999995333345677777776665555689************************999999*********** PP

                                       HHHHHH CS
                            FeoB_N 149 ieellk 154
                                       i el++
  gi|385805866|ref|YP_005842264.1| 324 IGELVE 329
                                       999986 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 !   51.3   0.4   1.1e-16   7.5e-14       2      58 .]     237     291 ..     236     291 .. 0.98

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 1.1e-16
                              NOG1   2 IEkqAiaALkhladavlFllDpseecgysleeQlsLleeikelfankpvivvlnKiD 58 
                                       IE++A a+Lk  +++++F++Dps+e+ ++l+eQl+L++  + ++ n  viv++nK+D
  gi|385805866|ref|YP_005842264.1| 237 IERRAFATLKIFNGVIVFVMDPSKESTMNLKEQLELIKMFRVEVLN--VIVAVNKVD 291
                                       9******************************************995..********9 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.5   0.3   2.6e-12   1.7e-09       4     142 ..     171     332 ..     169     333 .. 0.72

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 2.6e-12
                         PduV-EutP   4 illiGkvgsGKttLtqalkg............eelkYkktqaiefsd.eviDtPGeylenrklys.....alivtsa 62 
                                       i+++G+ +sGK tL q++ +            +e+   + +a ++ + +v+DtPG   +n + ++     a++++ +
  gi|385805866|ref|YP_005842264.1| 171 IVIVGPPNSGKSTLVQKIAEsrtivasypfttKEVVPGRLKASQLINlTVLDTPGILRKNFSEMNiierrAFATLKI 247
                                       789***************998888888888886666555555555551469****6555544443111125666666 PP

                         PduV-EutP  63 eadvialvqdateeesvfpp...gfasvfnkeviGiit...kidlaedeenieaveelLksaGaekifevsavekeg 133
                                          vi++v+d ++e+++  +   ++ ++f+ ev+ +i    k+dl  ++ + ++ +++L++ G+  if +sa+++++
  gi|385805866|ref|YP_005842264.1| 248 FNGVIVFVMDPSKESTMNLKeqlELIKMFRVEVLNVIVavnKVDLI-ENFEKDVIRSELEKIGVYDIFFISALNNIN 323
                                       77899***99988766543311256799999998887512266666.444456789********************* PP

                         PduV-EutP 134 ieellkyle 142
                                       i el++yl+
  gi|385805866|ref|YP_005842264.1| 324 IGELVEYLK 332
                                       *******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 !    7.7   0.0    0.0034       2.3       6      29 ..     171     194 ..     167     203 .. 0.86
   2 !   22.1   0.2   1.3e-07   8.9e-05      70     190 ..     216     333 ..     196     337 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0034
                                       EEEEESTTSSHHHHHHHHHHHTTS CS
                          GTP_EFTU   6 igiighvDhGKtTLtdrLlyktga 29 
                                       i+i+g  ++GK+TL+ ++ ++  +
  gi|385805866|ref|YP_005842264.1| 171 IVIVGPPNSGKSTLVQKIAESRTI 194
                                       89***************9877665 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 1.3e-07
                                       EEEEEEEESS..SGGGHHHHH...HH...HHT-SEEEE.EEETTTBSTHHHHHHHHHHHHTTTE...EEEEEESCGS CS
                          GTP_EFTU  70 ylinliDtPG..HvdFskevi...rg...lrvlDgavl.vvdaveGvepqteevlrlalkegvp...iivfiNKmDr 134
                                        +++++DtPG   ++Fs+  i   r+   l++ +g+++ v+d ++  +++ +e l+l++  +v+   +iv++NK+D 
  gi|385805866|ref|YP_005842264.1| 216 INLTVLDTPGilRKNFSEMNIierRAfatLKIFNGVIVfVMDPSKESTMNLKEQLELIKMFRVEvlnVIVAVNKVDL 292
                                       5678899999444568764332222244488888887637799999999999999999999998888*********9 PP

                                       THHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHH CS
                          GTP_EFTU 135 lkaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealve 190
                                       +++  k +++   +k+             g   + ++f+Sal++ ++ +l+e+l e
  gi|385805866|ref|YP_005842264.1| 293 IENFEKDVIRSELEKI-------------G--VYDIFFISALNNINIGELVEYLKE 333
                                       9654444444444355.............2..4679**************999876 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.1   0.00047      0.31      50     161 ..     111     226 ..     101     232 .. 0.56
   2 !   22.7   1.2   1.1e-07   7.6e-05      18     101 ..     249     335 ..     231     337 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00047
                                       EEEEE-GGG--HHH........HHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTTSEEEEECSTTSSHHHHHHH CS
                       RsgA_GTPase  50 vivlnKiDlleeee........eleelkeelealgyevllvsaktkegleelkellkdktsvlvGqSGvGKStLina 118
                                       v  l Ki++l++++        ++ +    l + + ++l    + k++l+ +++  +   +v+vG+   GKStL+ +
  gi|385805866|ref|YP_005842264.1| 111 VYSLAKIEMLSSDDrdlrkkgiRAASRLISLVKRNKKLLEDIINIKKELQLIADTGEFPPIVIVGPPNSGKSTLVQK 187
                                       55677777777777433222222222222222333333333333334444444444445689*************** PP

                                       HCTT---..--S--------------SEEEEEETTTEEEESS-SS CS
                       RsgA_GTPase 119 llpelel..ktgevseklgrGkhTTtavellelaegglliDtPGf 161
                                       ++++ ++  +   + ++   G+   +a++l++l     + DtPG+
  gi|385805866|ref|YP_005842264.1| 188 IAESRTIvaSYPFTTKEVVPGRL--KASQLINLT----VLDTPGI 226
                                       *9975430033334555556664..667777777....8888887 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 1.1e-07
                                       EEEEEEESTTTT--HHHHHHHHHHHHHTT-...EEEEEEE-GGG--HHHHHHHHHHHHHHTT.SEEEE--TTTHTTH CS
                       RsgA_GTPase  18 qllivvslkepelslnlldrfLvlaeekgi...epvivlnKiDlleeeeeleelkeelealg.yevllvsaktkegl 90 
                                       + +iv+ ++  + s+  l+  L l++  ++   ++++++nK+Dl+e+ e  + +++ele++g y+++++sa ++ ++
  gi|385805866|ref|YP_005842264.1| 249 NGVIVFVMDPSKESTMNLKEQLELIKMFRVevlNVIVAVNKVDLIENFE-KDVIRSELEKIGvYDIFFISALNNINI 324
                                       56888888877777778887776666555422378999***********.9***********99************* PP

                                       HHHHHHCTTSE CS
                       RsgA_GTPase  91 eelkellkdkt 101
                                        el e+lk+k+
  gi|385805866|ref|YP_005842264.1| 325 GELVEYLKEKV 335
                                       ********987 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 !   26.1   0.1   7.1e-09   4.7e-06       4     139 ..     169     307 ..     167     315 .. 0.72

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 7.1e-09
                                       -EEEEE-STTSSHHHHHHHHHHS.S---B---S.S-EEETTG...GGTT-SEEEETT-GCCSHHHHHHHHHHGG... CS
                             SRPRB   4 pavllvGlsdsGKTslftrLttd.svkktvtSq.essaalkvksekgskltliDfPGheklrqklleklkakss... 75 
                                       p +++vG+ +sGK +l +++ +  ++  ++    ++ +  ++k+++  +lt++D PG   lr++++e  + +++   
  gi|385805866|ref|YP_005842264.1| 169 PPIVIVGPPNSGKSTLVQKIAESrTIVASYPFTtKEVVPGRLKASQLINLTVLDTPGI--LRKNFSEMNIIERRafa 243
                                       5699****************9874444555444466667778999************5..77777775443333122 PP

                                       .EE....EEEEEEETTS-HHHHHHHHHHHHHHHHHHHHHTT---EEEEEE-TTSTT---HHHHHHHHHH CS
                             SRPRB  76 .lk....glvfvvDStidpkevkevAEllyeilliteklkdavdiliACnKqelflakspklikdaLEk 139
                                        lk     +vfv+D + ++     +  l  ++ li++ + + +++++A nK +l    ++ +i+ +LEk
  gi|385805866|ref|YP_005842264.1| 244 tLKifngVIVFVMDPSKES-----TMNLKEQLELIKMFRVEVLNVIVAVNKVDLIENFEKDVIRSELEK 307
                                       1332222478999966543.....3344444445566667889*************************8 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1       1.1   7.5e+02     102     139 ..      70     107 ..      61     137 .. 0.64
   2 !   21.4   1.2     2e-07   0.00013      17     173 ..     171     333 ..     155     335 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.1
                                       HHHHHHCTSGCCTTSEEEEEEE-TTSTTSS-HHHHHHH CS
                               Arf 102 eeLkalleeeelkevallvlaNKqDlpealseeelrel 139
                                       ++L +l++++e  +  ll++     +++  +++ l+ +
  gi|385805866|ref|YP_005842264.1|  70 DKLYKLISKNEKVKGYLLIVLGEDAINKLKKASYLKYK 107
                                       46778888777777777766654444444444444444 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 2e-07
                                       EEEEESTTSSHHHHHHHHHHSS.CEECSSSSSEEEEEEEE......TTEEEEEEEE-S.....SGGG....GGGGGG CS
                               Arf  17 illlGLDnaGKtTilkklklee.lvttvPTigfnveelei......knlkftvwDvGG.....qekl....RplWkn 77 
                                       i+++G  n+GK+T+++k+ + + +v   P   f+++e+        + +++tv D  G      +++    R+ + +
  gi|385805866|ref|YP_005842264.1| 171 IVIVGPPNSGKSTLVQKIAESRtIVASYP---FTTKEVVPgrlkasQLINLTVLDTPGilrknFSEMniieRRAFAT 244
                                       89***************987651344555...444444332223346689******994422211221122444444 PP

                                       GCTTESEEEEEEETT-CTTHHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTSS-HHHHHHHTTGGGSSSSSSEEEE CS
                               Arf  78 YfektdavifvvDsadreRleeakeeLkalleeeelkevallvlaNKqDlpealseeelrellgleelkgkrkleiq 154
                                             +++fv+D ++++ ++  ke+L +l+++ +++   ++v  NK Dl e  +++ +r++l+   +       i+
  gi|385805866|ref|YP_005842264.1| 245 LKIFNGVIVFVMDPSKESTMNL-KEQL-ELIKMFRVEVLNVIVAVNKVDLIENFEKDVIRSELEKIGVY-----DIF 314
                                       444445789*****99998864.4444.5777788888899*******************998766555.....677 PP

                                       EEBTTTTBTHHHHHHHHHH CS
                               Arf 155 kcsavkgeglkeglewlse 173
                                         sa+++ ++ e +e l e
  gi|385805866|ref|YP_005842264.1| 315 FISALNNINIGELVEYLKE 333
                                       7777777777777666655 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   1.3      0.98   6.5e+02     100     120 ..      63      87 ..       6     146 .. 0.54
   2 !   21.7   0.0   2.5e-07   0.00016       9      44 ..     157     192 ..     154     213 .. 0.91
   3 ?   -0.4   0.0       1.3   8.7e+02      49      72 ..     311     334 ..     298     339 .] 0.72

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.98
                          ATPase_2 100 klvfkaielllekikkkgkk....i 120
                                       k+  +  ++l++ i+k+ k     +
  gi|385805866|ref|YP_005842264.1|  63 KDKIEEYDKLYKLISKNEKVkgylL 87 
                                       2222222233333333332234431 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 2.5e-07
                          ATPase_2   9 keleeilerepneiyfiYGpegsGKtaLlkeiienl 44 
                                       kel+ i+++++ ++++i Gp +sGK++L+++i+e +
  gi|385805866|ref|YP_005842264.1| 157 KELQLIADTGEFPPIVIVGPPNSGKSTLVQKIAESR 192
                                       68999****************************988 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.3
                          ATPase_2  49 kyviyyialreesiskldefieee 72 
                                       +++++++al++++i +l e+++e+
  gi|385805866|ref|YP_005842264.1| 311 YDIFFISALNNINIGELVEYLKEK 334
                                       46788999*******999997765 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       3.8   2.5e+03      36      76 ..      42      80 ..      22     101 .. 0.61
   2 !   11.7   0.1    0.0003       0.2       1      35 [.     171     205 ..     171     215 .. 0.85
   3 !   12.0   0.2   0.00024      0.16     100     167 ..     215     289 ..     202     290 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 3.8
                                      EEEEECCT---CCS...SSEEEET-EB--CHHHHHHHHHHH CS
                         Dynamin_N 36 lelqlgeeeeaseravkeelkekekkledfsevreeieket 76
                                      l+ ++g+e+ ++    +  ++  ++k+e+++++ + i+k +
  gi|385805866|ref|YP_005842264.1| 42 LKTSYGRENAIE--LLNTAYNIIKDKIEEYDKLYKLISKNE 80
                                      444444444422..233333333666666666666655544 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.0003
                                       EEEEEBTTTTHHHHHHHHHTS--S---SSS---S- CS
                         Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrrp 35 
                                       i++vG  +sGKS+++ ++ +++  + +   tT  +
  gi|385805866|ref|YP_005842264.1| 171 IVIVGPPNSGKSTLVQKIAESRTIVASYPFTTKEV 205
                                       89*******************98877777777665 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.00024
                                       S-SEEEEE---B-SSSGTTSHHHHH....HH.STTEEEEEEEETTS..-CCC-CHHHHHHHHSTTBTTEEEEEE- CS
                         Dynamin_N 100 vkgltlvDlPGldsvnkrdqelvke....yi.kkadiilavtsanh..dlsnsealflarevdpkgkrtivvltk 167
                                         +lt++D+PG+ + n  +++++++    ++   + +i++v++ ++   +  +e+l+l ++ +++  ++iv ++k
  gi|385805866|ref|YP_005842264.1| 215 LINLTVLDTPGILRKNFSEMNIIERrafaTLkIFNGVIVFVMDPSKesTMNLKEQLELIKMFRVEVLNVIVAVNK 289
                                       5689****************6665511115545578899999776622444459999999999999999998887 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.1   4.1e-07   0.00027       2     161 ..     171     336 ..     170     337 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 4.1e-07
                                       EEEEESTTSSHHHHHHHHHHSS.CSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETT..SGGGHHHHHHHHTT...E CS
                               Ras   2 lvlvGdsavGKtslllrfvkdk.FkeeyesTigvdfytkeievdgkevkleiwDTAG..qeefkslrelyyrd...a 72 
                                       +v+vG  + GK++l+ + ++++    +y  T   +    ++   ++ ++l+++DT G    +f++++    r     
  gi|385805866|ref|YP_005842264.1| 171 IVIVGPPNSGKSTLVQKIAESRtIVASYPFTT-KEVVPGRL-KASQLINLTVLDTPGilRKNFSEMNIIERRAfatL 245
                                       79***************998761566666676.45444444.45899**********66688999875544331003 PP

                                       SEE..EEEEETT.BHHHHHTHHHHHHHHHHHSTTTSEEEEEEETTTGGG..G-SS-HHHHHHHHHHHT.SEEEEEBT CS
                               Ras  73 egi..llvydit.sresfenvkkwveeikrvaeenvpivLvGnKvDlee..kravsteegeelakelg.lkfletSA 143
                                       + +  ++v+ ++ s+es  n+k+ +e ik+   e +++++  nKvDl e  ++ v     ++  +++g +  + +SA
  gi|385805866|ref|YP_005842264.1| 246 KIFngVIVFVMDpSKESTMNLKEQLELIKMFRVEVLNVIVAVNKVDLIEnfEKDVI----RSELEKIGvYDIFFISA 318
                                       332335666665378899999999999999999989999999*****984434444....444556665677779** PP

                                       TTTCTHHHHHHHHHHHHH CS
                               Ras 144 ktnenveeafeellreil 161
                                        +n n+ e++e l +++l
  gi|385805866|ref|YP_005842264.1| 319 LNNINIGELVEYLKEKVL 336
                                       ******999999888776 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 ?   -2.5   0.0       5.2   3.4e+03      70      96 ..      50      76 ..      36      79 .. 0.75
   2 ?   -0.9   0.0       1.7   1.1e+03     152     177 ..     103     129 ..      92     165 .. 0.65
   3 !    9.1   0.0    0.0015         1       1      19 [.     173     191 ..     173     198 .. 0.89
   4 !   13.3   0.1     8e-05     0.053      67     176 ..     193     297 ..     189     335 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 5.2
                        ATP_bind_1 70 valeflresldwldeelekeeddyllf 96
                                       a+e+l +  + +++++e++++ y l+
  gi|385805866|ref|YP_005842264.1| 50 NAIELLNTAYNIIKDKIEEYDKLYKLI 76
                                      578888888888899998888877665 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.7
                        ATP_bind_1 152 mlrlelPhvvvlnkfDllkek.lekel 177
                                        l+++l +v  l k+++l+++ ++ + 
  gi|385805866|ref|YP_005842264.1| 103 YLKYKLSQVYSLAKIEMLSSDdRDLRK 129
                                       577888899999999998877533222 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0015
                        ATP_bind_1   1 vvGpaGsGKttfvgalsei 19 
                                       +vGp+ sGK+t+v++++e 
  gi|385805866|ref|YP_005842264.1| 173 IVGPPNSGKSTLVQKIAES 191
                                       79*************9986 PP

  == domain 4  score: 13.3 bits;  conditional E-value: 8e-05
                        ATP_bind_1  67 alvvaleflresldwldeelekeed..dyllfDtPGQie..lfthseslakiveeLesefalvvvyLvDsqrltdpt 139
                                       ++v ++ f ++++  +  +l+   +  ++ ++DtPG ++  +  +    ++ + +L+  f+ v+v+++D+    +++
  gi|385805866|ref|YP_005842264.1| 193 TIVASYPFTTKEV--VPGRLKAS-QliNLTVLDTPGILRknFSEMNIIERRAFATLK-IFNGVIVFVMDPSKE-STM 264
                                       6667777777766..88888444.3479********887223344444455666777.7**********9754.446 PP

                        ATP_bind_1 140 kfisgllsalsamlrle.lPhvvvlnkfDllkekleke 176
                                       ++ ++  + l  m+r+e l  +v++nk+Dl++   ++e
  gi|385805866|ref|YP_005842264.1| 265 NLKEQ--LELIKMFRVEvLNVIVAVNKVDLIE---NFE 297
                                       66666..7777788887368999*******88...232 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 !   19.9   0.0   9.9e-07   0.00066       2     119 ..     171     291 ..     170     292 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 9.9e-07
                                       EEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-S..GGCTTTT-... CS
                               Roc   2 vvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaG..qerfrslh... 73 
                                       +v+vG  ++GK++l++++ e++         ++ f+tkev+   g    k+ + ++l + Dt G   ++f++++   
  gi|385805866|ref|YP_005842264.1| 171 IVIVGPPNSGKSTLVQKIAESRTI-----VASYPFTTKEVV--PGR--LKASQLINLTVLDTPGilRKNFSEMNiie 238
                                       89***************9976654.....455666777763..332..23345799********6557777765222 PP

                                       .HHHHC...TSCEEEEEEE..GHHHHCHHHHHHHHHHHCSSS.-EEEEEE-TT CS
                               Roc  74 .plylr...eaalailvyd..srssenlkeWlkelkkvagks.pvilvgnkiD 119
                                        + + +    + ++++v+d  ++s  nlke l+ +k  + +  +vi+ +nk+D
  gi|385805866|ref|YP_005842264.1| 239 rRAFATlkiFNGVIVFVMDpsKESTMNLKEQLELIKMFRVEVlNVIVAVNKVD 291
                                       2455542223456677888644455799*********988764888999***9 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 ?   -0.9   0.4       2.5   1.7e+03      67      67 ..      94      94 ..      37     154 .. 0.61
   2 !   18.6   0.3   2.2e-06    0.0014      54     100 ..     279     331 ..     239     338 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2.5
                      MMR_HSR1_Xtn 67 l 67
                                      +
  gi|385805866|ref|YP_005842264.1| 94 A 94
                                      3 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 2.2e-06
                      MMR_HSR1_Xtn  54 vYipclyvlNKiDlisleeldelare......pnsvviSaekelnldeLkeki 100
                                       + +++++++NK+Dli++ e d +++e       ++++iSa +++n+ eL+e +
  gi|385805866|ref|YP_005842264.1| 279 EVLNVIVAVNKVDLIENFEKDVIRSElekigvYDIFFISALNNINIGELVEYL 331
                                       557899****************9997778887799***********7777654 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   1.0      0.12        83      11      69 ..      30      87 ..      29     148 .. 0.71
   2 !   12.8   0.0   0.00014     0.094       3      27 ..     169     193 ..     167     245 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.12
                            AAA_14 11 RrvGKTtllkqlikellvkkesilyinldderd..kkladpekllelileklkeekktylf 69
                                      RrvGK    ++ +k+++  +e+ +++     +   +k+++++kl++li ++ k   k yl+
  gi|385805866|ref|YP_005842264.1| 30 RRVGKIIAKQKTLKTSY-GRENAIELLNTAYNIikDKIEEYDKLYKLISKNEKV--KGYLL 87
                                      99***999999999999.555555553333333113344566888888886433..33333 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00014
                            AAA_14   3 kilvitGaRrvGKTtllkqlikell 27 
                                       +++vi+G+  +GK+tl++++++++ 
  gi|385805866|ref|YP_005842264.1| 169 PPIVIVGPPNSGKSTLVQKIAESRT 193
                                       689*****************98876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0       0.9     6e+02       3      17 ..      46      60 ..      44      68 .. 0.86
   2 !   15.0   0.0   3.6e-05     0.024      20      47 ..     164     191 ..     152     221 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.9
                            AAA_16  3 vGReeeleqLlsale 17
                                      +GRe+ +e L++a++
  gi|385805866|ref|YP_005842264.1| 46 YGRENAIELLNTAYN 60
                                      9***********997 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 3.6e-05
                            AAA_16  20 rsgrpelvllsGesGvGKsslvrellra 47 
                                        +g+ + ++++G++ +GKs+lv++++++
  gi|385805866|ref|YP_005842264.1| 164 DTGEFPPIVIVGPPNSGKSTLVQKIAES 191
                                       4677799*****************9974 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0033       2.2       3      23 ..     171     191 ..     169     196 .. 0.87
   2 ?    5.4   0.1     0.018        12     109     167 ..     246     306 ..     206     311 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0033
                                       EEEEESTTCCHHHHHHHHHCT CS
                              cobW   3 tvltGflGsGKTtLlnhllen 23 
                                       +v++G++ sGK+tL++++ e 
  gi|385805866|ref|YP_005842264.1| 171 IVIVGPPNSGKSTLVQKIAES 191
                                       79**************99865 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.018
                                       CCCECEEEEEEETTTH.CCHCCHHHHHHHHH..HTSSEEE.EE-HHHHCHC..HHHHHHHHH CS
                              cobW 109 dltldavvavvDaknleaeeekieekaedql..aaadllv.lnKtDlldeeallekleerlr 167
                                       ++   ++v+v+D ++ ++ + k++ ++ +++  ++ +++v +nK+Dl+++ ++ ++++++l+
  gi|385805866|ref|YP_005842264.1| 246 KIFNGVIVFVMDPSKESTMNLKEQLELIKMFrvEVLNVIVaVNKVDLIENFEK-DVIRSELE 306
                                       555567899999988877777777777777611556666658******99855.66666555 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 ?   -2.0   0.0       6.6   4.4e+03      85     117 ..      68     100 ..      34     116 .. 0.68
   2 ?   -1.9   0.0       6.2   4.1e+03      29      99 ..     122     148 ..      94     162 .. 0.56
   3 ?   13.8   0.1     9e-05     0.059       2      53 ..     172     234 ..     171     295 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 6.6
                                       HHHHHHHHHHHTTTSSSTEEEEEEESS.GGGSTH CS
                               AAA  85 vvnqLlteldgvkkkeskvivigatnr.pdkldp 117
                                         ++L++ +++ +k ++  ++i+ + + ++kl++
  gi|385805866|ref|YP_005842264.1|  68 EYDKLYKLISKNEKVKG-YLLIVLGEDaINKLKK 100
                                       44566666666666544.5555555554555555 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 6.2
                                       EETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS CS
                               AAA  29 isgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk 99 
                                        +  +l+                                            +++ r+++ L++ +++ kk 
  gi|385805866|ref|YP_005842264.1| 122 SDDRDLR--------------------------------------------KKGIRAASRLISLVKRNKKL 148
                                       3333333............................................34444444444444444443 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 9e-05
                                       EEESSTTSSHHHHHHHHHHH.........H..THEEEEEETTTCSSSSTTHHHHHHHHHHHHH CS
                               AAA   2 llyGppGtGKTllakavake.........l..gvefleisgsellskyvgesekkirelfkea 53 
                                       +++Gpp  GK++l++ +a++         +  +v   ++++s+l++ +v +++  +r+ f+e+
  gi|385805866|ref|YP_005842264.1| 172 VIVGPPNSGKSTLVQKIAESrtivasypfTtkEVVPGRLKASQLINLTVLDTPGILRKNFSEM 234
                                       789****************96555333321222334677777777777777777777766654 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0     5e-05     0.033       1      22 [.     171     192 ..     171     232 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrl 22 
                                       I++ G+p +GK+tl + ++++ 
  gi|385805866|ref|YP_005842264.1| 171 IVIVGPPNSGKSTLVQKIAESR 192
                                       89****************9984 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.73   4.9e+02      27     101 ..      65     139 ..      42     142 .. 0.78
   2 ?   11.6   0.0   0.00041      0.27       1      20 [.     171     190 ..     171     212 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.73
                      RNA_helicase  27 klkkkdsvysrnpeddfwdgYtgqevvvidDfgqvkdee.nps.dlaelirlvsstpyplnmasleekgtlftSkvv 101
                                       k ++ d++y   ++++ ++gY    +v+ +D  ++ +++   +  l+++  l++   +  +  +l +kg+  +S+++
  gi|385805866|ref|YP_005842264.1|  65 KIEEYDKLYKLISKNEKVKGYL--LIVLGEDAINKLKKAsYLKyKLSQVYSLAKIEMLSSDDRDLRKKGIRAASRLI 139
                                       3456678888888888888888..88888888888877777777999999999999999999999999999999887 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00041
                      RNA_helicase   1 iwlyGpsgeGKStlakeLak 20 
                                       i+++Gp++ GKStl++++a+
  gi|385805866|ref|YP_005842264.1| 171 IVIVGPPNSGKSTLVQKIAE 190
                                       789**************886 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.18   1.2e+02     161     216 ..      20      76 ..       9     131 .. 0.75
   2 ?   10.7   0.0    0.0004      0.27       2      23 ..     169     190 ..     168     206 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.18
                                       -HHHHHHHHHHH.HTS--SSSTT-------HHHHHHHHHHHHHHHHHHH....HTT- CS
                             KTI12 161 pldeilkaliek.kklkpnqatlskplaeanflqeLdketseivkeileaqksavai 216
                                       +++ei+++++ +  k  ++q+tl+ +   +n ++ L+++ + i ++i e  k  + i
  gi|385805866|ref|YP_005842264.1|  20 EYEEIYNKVYRRvGKIIAKQKTLKTSYGRENAIELLNTAYNIIKDKIEEYDKLYKLI 76 
                                       679999999765156778999999999999999999888776666666655544444 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0004
                                       .EEEEE--TTSSHHHHHHHHHH CS
                             KTI12   2 pLvvltGlPssGKstrakeLak 23 
                                       p +v+ G P sGKst+++++a+
  gi|385805866|ref|YP_005842264.1| 169 PPIVIVGPPNSGKSTLVQKIAE 190
                                       569***************9986 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   5.7e-05     0.038       8      37 ..     171     200 ..     169     276 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.7e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee 37 
                                       +v++G++ +GK+tl+++++e+ +++a+   
  gi|385805866|ref|YP_005842264.1| 171 IVIVGPPNSGKSTLVQKIAESRTIVASYPF 200
                                       89******************9988766555 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0    0.0001     0.069      26      60 ..     159     193 ..     136     209 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0001
                              TniB  26 LleypkrkrmpnlllvGdsnnGKtmivekFarlhp 60 
                                       L   ++  + p +++vG++n GK+++v+k a++++
  gi|385805866|ref|YP_005842264.1| 159 LQLIADTGEFPPIVIVGPPNSGKSTLVQKIAESRT 193
                                       444566778899*****************998765 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   7.6e-05     0.051       2      25 ..     171     198 ..     171     288 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.6e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklg....a 25 
                                       +++vG+p sGKstl++++++ ++    +
  gi|385805866|ref|YP_005842264.1| 171 IVIVGPPNSGKSTLVQKIAESRTivasY 198
                                       689***************9887744444 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   8.9e-05     0.059       2      23 ..     171     197 ..     170     223 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.9e-05
                            AAA_28   2 ivitGgestGKTtlleaLaar.....g 23 
                                       ivi+G++ +GK+tl++++a+       
  gi|385805866|ref|YP_005842264.1| 171 IVIVGPPNSGKSTLVQKIAESrtivaS 197
                                       9******************86333333 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   8.4e-05     0.056      22     100 ..     170     245 ..     138     272 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.4e-05
                                       EEEEEESTTSSHHHHHHHHCCSHCCCCCCBTEEEEEEEESXXHHHHHHHXXHHHHHCCCTTSSSS-STTSHHHHHHH CS
                            NB-ARC  22 vvalvGmgGvGKttlakqilnksdevegrFdsvawvvvsktdkseeiletilkeLslseddleekeeveslkrklvr 98 
                                        + +vG + +GK+tl+++i ++  ++   ++     vv    k +++++  l +L +    +++++e + ++r+ + 
  gi|385805866|ref|YP_005842264.1| 170 PIVIVGPPNSGKSTLVQKIAES-RTIVASYPFTTKEVVPGRLKASQLIN--LTVLDTPGILRKNFSEMNIIERRAFA 243
                                       589*****************99.99999999888777777777776666..56666665566666665555555555 PP

                                       HC CS
                            NB-ARC  99 lL 100
                                        L
  gi|385805866|ref|YP_005842264.1| 244 TL 245
                                       55 PP

>> NOG1_N  NOG1 N-terminal helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   6.9    0.0003       0.2       8     154 ..      19     160 ..      14     164 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0003
                            NOG1_N   8 ptseelidkalrrakraakttkkkkneikrlrnlearkvrtasntlsdkLeeivkkfPnldelhpFyrelldvlvdk 84 
                                       p+ ee+ +k +rr  ++  + k    +++  r+  ++ ++ta n+++dk+ee+ k +  +++ ++   +ll ++++ 
  gi|385805866|ref|YP_005842264.1|  19 PEYEEIYNKVYRRVGKIIAKQKT--LKTSYGRENAIELLNTAYNIIKDKIEEYDKLYKLISKNEKVKGYLL-IVLGE 92 
                                       77899999******999766644..4566678888999**************************9999887.889*9 PP

                            NOG1_N  85 delkksLaqvkwarklirkigkeyvnklkkaddkkeakelrreafgrvasvlkkvdkaldfLedvrkkLr 154
                                       d ++ +L + + ++ +  ++++    ++  +dd + +++    a  r+ s++k+ +k l+ + +++k+L+
  gi|385805866|ref|YP_005842264.1|  93 DAIN-KLKKASYLKYKLSQVYSLAKIEMLSSDD-RDLRKKGIRAASRLISLVKRNKKLLEDIINIKKELQ 160
                                       *997.5999999999999999987777777888.669999999*************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1295  (0.0722293); expected 358.6 (0.02)
Passed bias filter:                      627  (0.0349713); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); 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: 0.76u 0.32s 00:00:01.08 Elapsed: 00:00:00.57
# Mc/sec: 1805.98
//
Query:       gi|385805867|ref|YP_005842265.1|  [L=424]
Description: proteasome-activating nucleotidase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-43  148.7   0.1    2.7e-43  147.6   0.1    1.6  1  AAA              ATPase family associated with various cellul
    8.3e-17   60.7   0.2      2e-16   59.5   0.2    1.7  1  AAA_lid_3        AAA+ lid domain
    8.5e-09   35.2   0.4      2e-08   34.1   0.4    1.7  1  Prot_ATP_ID_OB   Proteasomal ATPase OB C-terminal domain
    3.5e-07   30.5   1.2    7.7e-07   29.4   0.0    2.2  1  AAA_2            AAA domain (Cdc48 subfamily)
    9.6e-06   25.4   0.2    5.4e-05   23.0   0.0    2.2  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    1.2e-05   25.4   0.2    6.5e-05   22.9   0.2    2.3  1  AAA_5            AAA domain (dynein-related subfamily)
      3e-05   23.3   0.1    8.1e-05   21.9   0.0    1.8  1  DUF815           Protein of unknown function (DUF815)
    7.7e-05   23.1   0.2     0.0077   16.6   0.1    2.5  2  AAA_16           AAA ATPase domain
     0.0004   20.7   0.5      0.019   15.2   0.1    2.4  2  AAA_22           AAA domain
    0.00085   18.6   2.3     0.0057   15.9   0.1    2.6  2  TIP49            TIP49 P-loop domain
     0.0019   18.5   1.2     0.0024   18.1   0.0    1.8  1  AAA_28           AAA domain
     0.0034   17.4  21.9      0.065   13.3  10.8    2.9  2  bZIP_1           bZIP transcription factor
     0.0035   16.7   0.1     0.0083   15.5   0.1    1.6  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0042   16.4   2.1     0.0064   15.8   0.0    2.3  3  Zeta_toxin       Zeta toxin
     0.0043   17.6   1.1      0.025   15.1   0.0    2.5  2  AAA_18           AAA domain
     0.0057   16.3   0.3      0.019   14.6   0.3    1.9  1  Prot_ATP_OB_N    Proteasomal ATPase OB N-terminal domain
     0.0063   16.3   0.1      0.025   14.3   0.0    2.1  2  AAA_24           AAA domain
     0.0066   16.3   0.0      0.021   14.7   0.0    1.9  1  AAA_3            ATPase family associated with various cellul
     0.0071   15.3   7.4      0.016   14.1   7.4    1.5  1  Spc7             Spc7 kinetochore protein
  ------ inclusion threshold ------
      0.016   15.6   0.0      0.051   14.0   0.0    1.9  1  RNA_helicase     RNA helicase
      0.017   15.2   1.2      0.066   13.3   0.0    2.2  2  AAA_14           AAA domain
      0.017   14.9   0.0      0.035   13.9   0.0    1.5  1  IstB_IS21        IstB-like ATP binding protein
       0.02   15.1   0.0      0.039   14.1   0.0    1.5  1  AAA_33           AAA domain
      0.024   14.6   0.2       0.11   12.4   0.1    2.0  2  NACHT            NACHT domain
      0.041   13.9   2.6      0.097   12.7   1.3    2.1  2  FlxA             FlxA-like protein
      0.041   12.4   7.7      0.061   11.8   7.7    1.1  1  LCD1             DNA damage checkpoint protein
      0.042   13.2  13.2      0.041   13.2  11.8    1.8  1  GAS              Growth-arrest specific micro-tubule binding
      0.056   13.0   0.1       0.13   11.8   0.1    1.5  1  AAA_7            P-loop containing dynein motor region
      0.058   13.4   0.0       0.12   12.4   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.063   13.4   0.0        0.2   11.8   0.0    1.8  1  Torsin           Torsin
      0.074   12.8   0.3       0.27   10.9   0.0    2.0  2  Sigma54_activat  Sigma-54 interaction domain
       0.12   11.9   0.0       0.33   10.5   0.0    1.7  1  AAA_25           AAA domain
       0.13   11.6   6.3       0.19   11.0   0.1    2.6  3  ATPase           KaiC
       0.16   12.4   1.4        1.9    9.0   0.1    2.8  2  ABC_tran         ABC transporter
       0.18   10.4   8.8        7.4    5.1   0.0    2.2  2  AAA_13           AAA domain
       0.28   10.0   2.8       0.45    9.3   2.8    1.2  1  Fmp27_WPPW       RNA pol II promoter Fmp27 protein domain
       0.37   10.9  10.5        8.1    6.6   6.7    2.7  2  Cep57_CLD_2      Centrosome localisation domain of PPC89
       0.51    8.2   3.3       0.72    7.7   3.3    1.1  1  V_ATPase_I       V-type ATPase 116kDa subunit family
       0.58   10.2  14.4       0.18   11.9  10.8    2.0  1  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
       0.66   10.1   9.3        1.5    8.9   9.3    1.5  1  UPF0242          Uncharacterised protein family (UPF0242) N-t
       0.75    9.6  13.7        2.6    7.8  13.7    1.8  1  ERM              Ezrin/radixin/moesin family
       0.86    8.9  21.9        1.2    8.5   6.0    2.8  3  DUF2353          Uncharacterized coiled-coil protein (DUF2353
       0.92    9.7  13.3        2.7    8.2   9.9    3.0  2  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
        1.2    8.8  11.7        4.5    6.8  11.6    2.0  1  PI3K_P85_iSH2    Phosphatidylinositol 3-kinase regulatory sub
        1.2    9.4   5.5          3    8.0   5.5    1.6  1  Fib_alpha        Fibrinogen alpha/beta chain family
          2    9.0  17.0         35    4.9  17.0    2.4  1  APG6_N           Apg6 coiled-coil region
        5.4    7.2  16.7         10    6.3   4.2    2.7  2  bZIP_2           Basic region leucine zipper
        6.2    6.4  12.1       0.67    9.5   6.0    2.4  3  DUF4795          Domain of unknown function (DUF4795)
        7.2    6.9  13.1        7.5    6.9  11.6    1.8  1  DUF737           Protein of unknown function (DUF737)
        7.7    7.1  21.4        4.3    7.9   3.7    3.7  3  KELK             KELK-motif containing domain of MRCK Ser/Thr


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 !  147.6   0.1   7.5e-46   2.7e-43       1     132 []     202     335 ..     202     335 .. 0.97

  Alignments for each domain:
  == domain 1  score: 147.6 bits;  conditional E-value: 7.5e-46
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH... CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr... 74 
                                       +llyG pGtGKT+lakava+e++++f+++ gse+++k++ge+++ +re+f+ ak+ka p i+fiDEida+a +r   
  gi|385805867|ref|YP_005842265.1| 202 ILLYGSPGTGKTMLAKAVASETNATFIRVVGSEFVQKFIGEGARIVREVFELAKRKA-PAIIFIDEIDAIAARRidi 277
                                       69******************************************************9.*****************99 PP

                                       TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETTS CS
                               AAA  75 sgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieiel 132
                                        +s ++e +r++ qLl+e+dg++  ++ v vi+atnr+d ldpa+lr gRfdr+ie++l
  gi|385805867|ref|YP_005842265.1| 278 GTSGEREVQRTMMQLLAEMDGFDPLDN-VKVIAATNRIDILDPAILRpGRFDRIIEVPL 335
                                       88899999****************755.****************************985 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.5   0.2   5.7e-19     2e-16       1      45 []     357     401 ..     357     401 .. 0.97

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 5.7e-19
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitmedfee 45 
                                       ++d+ +L e+TeG++GAD++a+c eA+ +A+r+ ++ +tmedf++
  gi|385805867|ref|YP_005842265.1| 357 NLDIRKLSELTEGFVGADIKAVCVEAGYNAIREERDLVTMEDFIK 401
                                       689****************************************85 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 !   34.1   0.4   5.5e-11     2e-08       2      57 .]      90     144 ..      90     144 .. 0.98

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 5.5e-11
                                       EEEEEE-TTSSEEEEE-TTS-EEEEEE-GGGSSST--TTEEEEEETTTTEEEEEE- CS
                    Prot_ATP_ID_OB   2 atVsEvlddteraiVktssdeevvvslagavpremLrpgDlVavdkdtgfifEkLP 57 
                                       a+V ++l+d +r++V +s++ + +v ++g +  ++L pg+ Va++++   i+E+LP
  gi|385805867|ref|YP_005842265.1|  90 ASVLDILPD-KRVVVRSSTGPNLIVTVSGNISVDQLLPGTIVAINQRGSSIVEVLP 144
                                       68999****.*********************************************9 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   2.1e-09   7.7e-07       6     103 ..     202     293 ..     197     298 .. 0.86

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 2.1e-09
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       ill g+ g+Gkt+laka+a+  ++    ++ir+  se+ +    + + +   + ++    a+ +   i+++DEid i
  gi|385805867|ref|YP_005842265.1| 202 ILLYGSPGTGKTMLAKAVASETNA----TFIRVVGSEFVQ----KFIGEGARIVREVFELAKRKApaIIFIDEIDAI 270
                                       8999******************96....************....77777777777777777777677********** PP

                                       ------------H.HHHHHHHHHH CS
                             AAA_2  81 hpkessgadvSre.gVqrdLLqil 103
                                       ++ +++    S+e +Vqr ++q+l
  gi|385805867|ref|YP_005842265.1| 271 AA-RRIDIGTSGErEVQRTMMQLL 293
                                       **.777777787669*******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 ?   -1.1   0.1       3.9   1.4e+03      79     120 ..      58     100 ..      51     112 .. 0.80
   2 !   23.0   0.0   1.5e-07   5.4e-05      33      97 ..     199     271 ..     175     278 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 3.9
                            RuvB_N  79 ltnleekdvlfideihrlsraveevlysa.medfrldivigkG 120
                                       +++lee+++++  e+   ++++e +l +  +e   ldi+ +k 
  gi|385805867|ref|YP_005842265.1|  58 IKELEEEKLMLNREVKYYKEEMEKLLAPPlIEASVLDILPDKR 100
                                       5789999999999999999999999987526888889986665 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 1.5e-07
                            RuvB_N  33 ldhvllyGpPGlGkttlakiiakelgvk.lkitsgPvlek.agdlaallt...nl...eekdvlfideihrls 97 
                                          +llyG+PG Gkt lak +a+e +++ +++  +  ++k  g+ a ++    +l   ++  ++fidei  ++
  gi|385805867|ref|YP_005842265.1| 199 PKGILLYGSPGTGKTMLAKAVASETNATfIRVVGSEFVQKfIGEGARIVRevfELakrKAPAIIFIDEIDAIA 271
                                       5679*********************99835666666676633565555541114421134579*****98775 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.2   1.8e-07   6.5e-05       2     124 ..     202     315 ..     201     324 .. 0.67

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.8e-07
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG-- CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEverae 78 
                                       +lL G pGtgK++la+ +a+ +n+++  v ++++ ++    g r +      ++  +l  + + ++i+++DE++ + 
  gi|385805867|ref|YP_005842265.1| 202 ILLYGSPGTGKTMLAKAVASETNATFIRVVGSEFVQKFIGEGARIV------REVFELA-KRKAPAIIFIDEIDAIA 271
                                       89*****************************997655444444443......3333333.334899********888 PP

                                       HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS-- CS
                             AAA_5  79 sevlnsLlslleerrllleeggelvkaknddllerfrviatanpld 124
                                          +++  s   e ++ ++++  +++   +d l ++ via++n+ d
  gi|385805867|ref|YP_005842265.1| 272 ARRIDIGTSGEREVQRTMMQLLAEMDG--FDPLDNVKVIAATNRID 315
                                       777776655544444444444444433..22344488888888877 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   2.3e-07   8.1e-05      51     116 ..     197     267 ..     145     273 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 2.3e-07
                            DUF815  51 lpannvLLwGarGtGKSslvkallneyaeegLrli..evekedlkelpklvellr...erperfilfvDDL 116
                                       +p + +LL+G+ GtGK  l ka+ +e++++ +r++  e  ++ + e  ++v+++    +r+   i+f+D +
  gi|385805867|ref|YP_005842265.1| 197 EPPKGILLYGSPGTGKTMLAKAVASETNATFIRVVgsEFVQKFIGEGARIVREVFelaKRKAPAIIFIDEI 267
                                       57789******************************777778899999999987652226677789**9975 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   2.1e-05    0.0077      24      57 ..     199     229 ..     170     242 .. 0.79
   2 ?    4.0   0.0      0.17        60     123     149 ..     247     272 ..     241     302 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.1e-05
                            AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflr 57 
                                       p  +ll+G +G+GK+ l+++++ + +++   f+r
  gi|385805867|ref|YP_005842265.1| 199 PKGILLYGSPGTGKTMLAKAVASETNAT---FIR 229
                                       589******************9755544...444 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.17
                            AAA_16 123 lkrllallsrderplvlvlDdlqwade 149
                                       +++ ++l++r + p ++++D+++ + +
  gi|385805867|ref|YP_005842265.1| 247 VREVFELAKR-KAPAIIFIDEIDAIAA 272
                                       5666788998.778*********6654 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   5.3e-05     0.019       8      40 ..     202     225 ..     197     236 .. 0.83
   2 ?    3.2   0.1      0.28        99      80     109 ..     248     290 ..     223     311 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.3e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerp 40 
                                       ++++G +GtGKT+l++ ++++          ++
  gi|385805867|ref|YP_005842265.1| 202 ILLYGSPGTGKTMLAKAVASET---------NA 225
                                       89****************9987.........44 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.28
                            AAA_22  80 ealeqalraravielliiDEaqhlr......s........eeal 109
                                       + + + ++++a  +++ iDE++ +                 +++
  gi|385805867|ref|YP_005842265.1| 248 REVFELAKRKAP-AIIFIDEIDAIAarridiGtsgerevqRTMM 290
                                       555566677777.9********9966544330334444444454 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.4      0.37   1.3e+02     230     275 ..       6      49 ..       4      94 .. 0.69
   2 !   15.9   0.1   1.6e-05    0.0057      51      90 ..     200     237 ..     185     272 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.37
                                       XXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 230 Dvanarpqdllslllqllkskkteiteklreeinkkvakyveegka 275
                                       D++na+++++l+ + ++l+ +k  + e+ + +++k ++ y+ee + 
  gi|385805867|ref|YP_005842265.1|   6 DISNANSTNVLAHI-KYLE-EKLKVLEEEKARLEKDINSYKEEKEK 49 
                                       78999999999999.5554.55568888889999999999887654 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.6e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevys 90 
                                       +++Ll G +gtGkt la a++ e +    f+ ++gse+ +
  gi|385805867|ref|YP_005842265.1| 200 KGILLYGSPGTGKTMLAKAVASETN--ATFIRVVGSEFVQ 237
                                       89********************977..78999***99765 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   6.6e-06    0.0024       2      44 ..     202     249 ..     201     294 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 6.6e-06
                            AAA_28   2 ivitGgestGKTtlleaLaar....gypvv.pEaareileeklakged 44 
                                       i + G ++tGKT l++a a++     ++vv  E++ +++ e+++  ++
  gi|385805867|ref|YP_005842265.1| 202 ILLYGSPGTGKTMLAKAVASEtnatFIRVVgSEFVQKFIGEGARIVRE 249
                                       7899***************54444478888888888888777654444 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   5.1    0.0042       1.5      26      57 ..      17      48 ..      16      49 .. 0.93
   2 !   13.3  10.8   0.00018     0.065      24      60 ..      47      83 ..      45      85 .. 0.96

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0042
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1 26 aeieeLerrvkaLekeNksLkseleelkkeve 57
                                      a i+ Le++ k+Le+e + L + ++++k+e e
  gi|385805867|ref|YP_005842265.1| 17 AHIKYLEEKLKVLEEEKARLEKDINSYKEEKE 48
                                      67999************************987 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00018
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1 24 KqaeieeLerrvkaLekeNksLkseleelkkevekLk 60
                                      K+++i+ Le++ k+Le+e  +L  e++ +k+e+ekL+
  gi|385805867|ref|YP_005842265.1| 47 KEKYIKYLEEKIKELEEEKLMLNREVKYYKEEMEKLL 83
                                      99*********************************97 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   2.3e-05    0.0083      25      43 ..     202     220 ..     193     226 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.3e-05
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll+G+pG+GKtmlak+++
  gi|385805867|ref|YP_005842265.1| 202 ILLYGSPGTGKTMLAKAVA 220
                                       89**************976 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.2       6.7   2.4e+03     156     185 ..      44      75 ..      27      83 .. 0.68
   2 !   15.8   0.0   1.8e-05    0.0064      14      52 ..     197     233 ..     187     241 .. 0.85
   3 ?   -1.6   0.0       3.7   1.3e+03      84     118 ..     372     407 ..     351     416 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 6.7
                        Zeta_toxin 156 keehdeafeglresvealeeek..qldrvkik 185
                                       kee ++  + l+e++++leeek  +  +vk++
  gi|385805867|ref|YP_005842265.1|  44 KEEKEKYIKYLEEKIKELEEEKlmLNREVKYY 75 
                                       66677777888899999999884333344444 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1.8e-05
                        Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrldpD 52 
                                       e Pk ill G+pG GK+ la++++ e+  +  ++r+ + 
  gi|385805867|ref|YP_005842265.1| 197 EPPKGILLYGSPGTGKTMLAKAVASET--NATFIRVVGS 233
                                       679***********************8..8888888765 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 3.7
                        Zeta_toxin  84 vekllqeaiengyniiv.egtlrspdvvkklaealk 118
                                       ++ + +  +e+gyn i  e+ l + +++ k++e++k
  gi|385805867|ref|YP_005842265.1| 372 GADIKAVCVEAGYNAIReERDLVTMEDFIKAIEKIK 407
                                       455556668889999962567888888888888776 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.2       2.8     1e+03      17      66 ..      21      63 ..      10     102 .. 0.58
   2 !   15.1   0.0     7e-05     0.025       1      31 [.     202     240 ..     202     301 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 2.8
                            AAA_18 17 eLskrlgfgvnlrdvakenglllevdpealdeskrldedkldklldalee 66
                                      +L+++l       +v+ e+  +le d + ++e+k+  +++l++ +++lee
  gi|385805867|ref|YP_005842265.1| 21 YLEEKL-------KVLEEEKARLEKDINSYKEEKEKYIKYLEEKIKELEE 63
                                      555554.......3444444444444443333333333333333333333 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 7e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf........gvnlrdv 31 
                                       Ill G pG+GKt lak+++++++          ++ +++
  gi|385805867|ref|YP_005842265.1| 202 ILLYGSPGTGKTMLAKAVASETNAtfirvvgsEFVQKFI 240
                                       89****************999754677777654444444 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 !   14.6   0.3   5.3e-05     0.019      18      56 ..     105     144 ..      89     148 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.3e-05
                     Prot_ATP_OB_N  18 lvggrrmrVavsPlvdaeeLrpGqeVlLnE.alvvVealg 56 
                                       ++ g  + V+vs ++++++L pG+ V +n+ ++ +Ve+l+
  gi|385805867|ref|YP_005842265.1| 105 SSTGPNLIVTVSGNISVDQLLPGTIVAINQrGSSIVEVLP 144
                                       5679999**********************94589999987 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   7.1e-05     0.025       5      26 ..     202     225 ..     199     272 .. 0.84
   2 ?   -2.4   0.0         9   3.2e+03      32      62 ..     381     409 ..     377     415 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.1e-05
                            AAA_24   5 iliyGpsgiGKTtlakel..gpkp 26 
                                       il+yG++g+GKT+lak    + ++
  gi|385805867|ref|YP_005842265.1| 202 ILLYGSPGTGKTMLAKAVasETNA 225
                                       89*************998654444 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 9
                            AAA_24  32 ekGlksldadkfpdieswedfldevvelaae 62 
                                       e+G++++   +  d+ ++edf++++++++  
  gi|385805867|ref|YP_005842265.1| 381 EAGYNAIREER--DLVTMEDFIKAIEKIKGR 409
                                       78888888887..456899999999887544 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 !   14.7   0.0     6e-05     0.021       2      30 ..     202     230 ..     201     274 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6e-05
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                       +ll g PG++kt+l+ka+a+  +++f r+
  gi|385805867|ref|YP_005842265.1| 202 ILLYGSPGTGKTMLAKAVASETNATFIRV 230
                                       7999**********************998 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   7.4   4.3e-05     0.016     213     278 ..      17      82 ..       9      86 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.3e-05
                              Spc7 213 aeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkal 278
                                       a i+ ++++l+ l+e++++le++i++ ke+k+++ + ++e+ + lee+k + + ev+ +kee+++l
  gi|385805867|ref|YP_005842265.1|  17 AHIKYLEEKLKVLEEEKARLEKDINSYKEEKEKYIKYLEEKIKELEEEKLMLNREVKYYKEEMEKL 82 
                                       6788999*******************************************************9987 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   0.00014     0.051       1      56 [.     202     248 ..     202     271 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.00014
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevvvid 56 
                                       i+lyG++g+GK++lak +a++         ++ +++r + ++f++++ g+ + ++ 
  gi|385805867|ref|YP_005842265.1| 202 ILLYGSPGTGKTMLAKAVASE---------TNATFIRVVGSEFVQKFIGEGARIVR 248
                                       789**************5544.........45555566666666666665555555 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   1.0         4   1.4e+03      36      74 ..      36      73 ..      13      87 .. 0.57
   2 ?   13.3   0.0   0.00018     0.066       5      76 ..     202     270 ..     199     303 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 4
                            AAA_14 36 inldderdkkladpekllelileklke.ekktylflDEiq 74
                                      ++ d +++k+++  ek+++++ ek+ke e++++++  E++
  gi|385805867|ref|YP_005842265.1| 36 LEKDINSYKEEK--EKYIKYLEEKIKElEEEKLMLNREVK 73
                                      333333333322..34667777776555555555544554 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00018
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76 
                                       +++ G   +GKT+l+k +++e       ++ +   +  +k + + +++ ++++e++k++   ++f+DEi  +
  gi|385805867|ref|YP_005842265.1| 202 ILLYGSPGTGKTMLAKAVASETN---ATFIRVVGSEFVQKFIGEGARIVREVFELAKRKAPAIIFIDEIDAI 270
                                       67899999**********98887...5555555444333333344478899999876678999******877 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 ?   13.9   0.0   9.7e-05     0.035      46      73 ..     198     225 ..     185     240 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.7e-05
                         IstB_IS21  46 kkenivllGpsGvGKshlaialgveavr 73 
                                         ++i+l G +G+GK+ la a++ e+ +
  gi|385805867|ref|YP_005842265.1| 198 PPKGILLYGSPGTGKTMLAKAVASETNA 225
                                       56789*****************988655 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   0.00011     0.039       2      29 ..     202     229 ..     202     283 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 0.00011
                            AAA_33   2 vllvGlpGsGKstlaerllkklgavlls 29 
                                       +ll G pG+GK+ la+ ++ ++ a++++
  gi|385805867|ref|YP_005842265.1| 202 ILLYGSPGTGKTMLAKAVASETNATFIR 229
                                       6789***************999955544 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1    0.0003      0.11       3      23 ..     202     222 ..     200     228 .. 0.90
   2 ?   -0.7   0.0       3.3   1.2e+03      73     114 ..     250     294 ..     234     300 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0003
                                       EEEEC-TTTCHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                       ++l G +G GKT+L++ +a++
  gi|385805867|ref|YP_005842265.1| 202 ILLYGSPGTGKTMLAKAVASE 222
                                       7899*************9987 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 3.3
                                       HHHHCCSCCCEEEEEE-STT-SS-TCH............HHHHHC CS
                             NACHT  73 wavllelperlLlilDglDelvtdlgq...kekqpvrtlLselir 114
                                       + +l++++  + + +D +D +++       +++++v++ + +l+ 
  gi|385805867|ref|YP_005842265.1| 250 VFELAKRKAPAIIFIDEIDAIAARRIDigtSGEREVQRTMMQLLA 294
                                       445788888888999999999986555777777777777777765 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.3   0.00027     0.097       9      63 ..       9      63 ..       2      79 .. 0.90
   2 ?   -0.6   0.0       3.7   1.3e+03      26      39 ..     167     180 ..     164     189 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00027
                              FlxA  9 sssssgsasqiasLqkQiknlqkqLkelsesdeltkeekkkqqqliqaQIqqlqa 63
                                       ++s++  + i+ L++ +k l+++   l ++ +  keek+k ++ ++++I+ l+ 
  gi|385805867|ref|YP_005842265.1|  9 NANSTNVLAHIKYLEEKLKVLEEEKARLEKDINSYKEEKEKYIKYLEEKIKELEE 63
                                      5667778899*********************9999*****************986 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 3.7
                              FlxA  26 iknlqkqLkelses 39 
                                       i  l+kq++e+ e+
  gi|385805867|ref|YP_005842265.1| 167 IGGLSKQIQEVRET 180
                                       55566666666555 PP

>> LCD1  DNA damage checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   7.7   0.00017     0.061       6      61 ..      26      77 ..      18      96 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00017
                                      HHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHCHHTTTTT CS
                              LCD1  6 LelLeqekekeleklknskkqlkesheeelekLkkevqkleDekkFlenElrslse 61
                                      L+ L    e+e+++l++++++ ke++e+ ++ L++++++le ek+ l++E++  +e
  gi|385805867|ref|YP_005842265.1| 26 LKVL----EEEKARLEKDINSYKEEKEKYIKYLEEKIKELEEEKLMLNREVKYYKE 77
                                      4444....56788999***********************************98776 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2  11.8   0.00012     0.041      51     118 ..      14      82 ..       1      85 [. 0.72

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00012
                               GAS  51 eisqenkrlkepLkkaeeeveeLrkqlknyekdkqsl.knlkarlkelekelkdlkwehevleqrfekv 118
                                       ++ ++ k l+e+Lk +eee+++L+k+++ y+++k+++ k l++++kele+e   l  e +  ++++ek+
  gi|385805867|ref|YP_005842265.1|  14 NVLAHIKYLEEKLKVLEEEKARLEKDINSYKEEKEKYiKYLEEKIKELEEEKLMLNREVKYYKEEMEKL 82 
                                       555677888888888888888888888888888876426677777777777777777777777777765 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00035      0.13      33      60 ..     199     226 ..     189     272 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00035
                             AAA_7  33 kkpvllvGptGtGKtviikdllkkldke 60 
                                        k +ll+G+ GtGKt+++k + ++ + +
  gi|385805867|ref|YP_005842265.1| 199 PKGILLYGSPGTGKTMLAKAVASETNAT 226
                                       5789****************99988843 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00032      0.12      19      47 ..     199     229 ..     170     237 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00032
                                       TEEEEEEESTTSSHHHHHHHHHHHTT--..- CS
                              TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve..e 47 
                                        + ilL+G  G+GKT+l++++a++ + +  +
  gi|385805867|ref|YP_005842265.1| 199 PKGILLYGSPGTGKTMLAKAVASETNATfiR 229
                                       3459******************998776543 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00056       0.2      56      92 ..     202     241 ..     191     246 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00056
                                       EEEEE-TTSSHHHHHHHHH...HHHSTTGGGSTTEEEEEH CS
                            Torsin  56 lsfhGwtGtGknfvaeiia...enlyrdGlrsdyvkkfva 92 
                                       + ++G +GtGk  +a+ +a   ++++ + + s++v+kf++
  gi|385805867|ref|YP_005842265.1| 202 ILLYGSPGTGKTMLAKAVAsetNATFIRVVGSEFVQKFIG 241
                                       5689**************8333567999999*******97 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   0.00076      0.27      23      47 ..     200     224 ..     171     241 .. 0.81
   2 ?   -1.2   0.1       4.1   1.5e+03     115     115 ..     283     283 ..     250     318 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00076
                                       S-EEEECSTTSSHHHHHHHHHHHST CS
                   Sigma54_activat  23 lsvlitGesGtGKellaraiheask 47 
                                         +l+ G  GtGK++la+a+ ++++
  gi|385805867|ref|YP_005842265.1| 200 KGILLYGSPGTGKTMLAKAVASETN 224
                                       679***************9976554 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 4.1
                                       H CS
                   Sigma54_activat 115 r 115
                                       r
  gi|385805867|ref|YP_005842265.1| 283 R 283
                                       1 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00093      0.33      36      55 ..     202     221 ..     196     237 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00093
                            AAA_25  36 allaGapgtGKttlaldlal 55 
                                       +ll+G pgtGKt+la  +a 
  gi|385805867|ref|YP_005842265.1| 202 ILLYGSPGTGKTMLAKAVAS 221
                                       69************987775 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   1.1      0.21        76      78     125 ..      23      68 ..       7      95 .. 0.68
   2 ?   11.0   0.1   0.00054      0.19      13      37 ..     193     217 ..     188     228 .. 0.83
   3 ?   -2.7   0.0       8.5     3e+03     116     132 ..     255     272 ..     242     298 .. 0.50

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.21
                            ATPase  78 eeegklaiidasesaeesaeekdkedleelieelaeaikeikakrvvi 125
                                       ee  kl +++  + + e+  +++ke+ e+ i+ l+e ike++++++++
  gi|385805867|ref|YP_005842265.1|  23 EE--KLKVLEEEKARLEKDINSYKEEKEKYIKYLEEKIKELEEEKLML 68 
                                       22..46666666666666666777777777777777777777766654 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00054
                            ATPase  13 kgGipegrvvlitGepGtGKtifal 37 
                                       k Gi   + +l++G+pGtGKt++a+
  gi|385805867|ref|YP_005842265.1| 193 KIGIEPPKGILLYGSPGTGKTMLAK 217
                                       568888889**************97 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 8.5
                            ATPase 116 keikakrvviDsitgl.a 132
                                       k++    + iD i+++ a
  gi|385805867|ref|YP_005842265.1| 255 KRKAPAIIFIDEIDAIaA 272
                                       444445566666666632 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1       1.7     6e+02      56      88 ..      21      57 ..       3      99 .. 0.47
   2 ?    9.0   0.1    0.0053       1.9       8      37 ..     196     225 ..     192     238 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 1.7
                                      HCCHCEEEE-SS.--S-TTSBHHHHHHHTC...HHHH CS
                                      xxxxxxxxxxxx.xxxxxxxxxxxxxxxxx...xxxx RF
                          ABC_tran 56 slrkeigvlpqe.pqlfpeltvrenesdee...ieka 88
                                       l+++++vl++e ++l ++++ +++e+++    +e+ 
  gi|385805867|ref|YP_005842265.1| 21 YLEEKLKVLEEEkARLEKDINSYKEEKEKYikyLEEK 57
                                      3333344443333333333322222111111112222 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0053
                                       EETTSEEEEEESTTSSHHHHHHHHTTSS-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkp 37 
                                       +++ + + + G+ G+GK+ L+k++a +++ 
  gi|385805867|ref|YP_005842265.1| 196 IEPPKGILLYGSPGTGKTMLAKAVASETNA 225
                                       666677899***************999875 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   7.7     0.038        14     403     467 ..      18      79 ..       3      85 .. 0.74
   2 ?    5.1   0.0     0.021       7.4      20      41 ..     203     223 ..     200     263 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.038
                            AAA_13 403 lveeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeL 467
                                        ++ le++l+ +++++++lek+i++ +   +e+e+ +k lee+ikeLe++    ++ ++   +e+
  gi|385805867|ref|YP_005842265.1|  18 HIKYLEEKLKVLEEEKARLEKDINSYK---EEKEKYIKYLEEKIKELEEEKLMLNREVKYYKEEM 79 
                                       466688999999999999999999988...56677888999999999988776666666555555 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.021
                            AAA_13  20 liYGwNGaGKTtLSrllrslel 41 
                                       l+YG+ G+GKT L+++ +s  +
  gi|385805867|ref|YP_005842265.1| 203 LLYGSPGTGKTMLAKAVASE-T 223
                                       69*************99984.3 PP

>> Fmp27_WPPW  RNA pol II promoter Fmp27 protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   2.8    0.0013      0.45     173     240 ..      19      79 ..       5     101 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0013
                        Fmp27_WPPW 173 kelleeRleeleeqiekleekleelelksekedeelkeeieelekeikelkeklefletlledlkese 240
                                        ++lee l+ lee+ ++le++++++++++ek        i+ le++ikel+e++ +l++ ++ +ke++
  gi|385805867|ref|YP_005842265.1|  19 IKYLEEKLKVLEEEKARLEKDINSYKEEKEKY-------IKYLEEKIKELEEEKLMLNREVKYYKEEM 79 
                                       46777778888888888888888888888775.......55555555555555555555554444443 PP

>> Cep57_CLD_2  Centrosome localisation domain of PPC89
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   6.7     0.023       8.1       3      50 ..      17      68 ..      15      85 .. 0.78
   2 ?    5.1   0.0     0.066        24      19      43 ..     342     366 ..     338     369 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.023
                       Cep57_CLD_2  3 aevktLqnrLdsltrklqvheeelkrLnkERdsalrqLgvAyeelne....L 50
                                      a +k L+++L+ l+++ +  e  +++   E + +++ L +++ el+e    L
  gi|385805867|ref|YP_005842265.1| 17 AHIKYLEEKLKVLEEEKARLEKDINSYKEEKEKYIKYLEEKIKELEEeklmL 68
                                      67888999999999999999999999999*************9998733333 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.066
                       Cep57_CLD_2  19 lqvheeelkrLnkERdsalrqLgvA 43 
                                       +++  +++k++n E + ++r+L++ 
  gi|385805867|ref|YP_005842265.1| 342 IEIFKIHIKKMNVEKNLDIRKLSEL 366
                                       5566699***************985 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   3.3     0.002      0.72      34     103 ..      14      83 ..      10     104 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.002
                        V_ATPase_I  34 emerklrfleeeieklekavikeeeaeesleapeekeldeleeelekleeelkelnenleklkkelnelv 103
                                       ++  ++++lee+++ le+++++ e++ +s ++++ek+++ lee++++leee   ln++ +  k+e+++l+
  gi|385805867|ref|YP_005842265.1|  14 NVLAHIKYLEEKLKVLEEEKARLEKDINSYKEEKEKYIKYLEEKIKELEEEKLMLNREVKYYKEEMEKLL 83 
                                       566789999**9999999999999999999*********************9999999999999988876 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9  10.8   0.00049      0.18      20      85 ..      13      82 ..       7      85 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00049
                    CENP-F_leu_zip 20 dsLkdkvenLerelemseenqekvileaEtskaevet....lkeeieelaeelreleldLvalrsekeeL 85
                                       ++  +++ Le  l+ +ee++ +++ +  + k+e e+    l+e+i+el+ee   l+ +++  ++e e+L
  gi|385805867|ref|YP_005842265.1| 13 TNVLAHIKYLEEKLKVLEEEKARLEKDINSYKEEKEKyikyLEEKIKELEEEKLMLNREVKYYKEEMEKL 82
                                      5555667777777777777777777776666666666666677777777777777777776666666665 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   9.3    0.0042       1.5     104     167 ..      18      81 ..       3      85 .. 0.46

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0042
                           UPF0242 104 eldakeeelerlkeenqqLqekleaiaedfeelkleleeqLaekqellqeyqetieeqrsvlek 167
                                       ++++ ee+l+ l+ee++ L++  +  +e+ e++ + lee+++e +e    ++++++  ++++ek
  gi|385805867|ref|YP_005842265.1|  18 HIKYLEEKLKVLEEEKARLEKDINSYKEEKEKYIKYLEEKIKELEEEKLMLNREVKYYKEEMEK 81 
                                       3444444444444444444444444444444444444444444444444444444444444443 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8  13.7    0.0073       2.6      36      94 ..      20      82 ..       6      86 .. 0.52

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0073
                               ERM 36 elLaekarraeeeaelLeqkaaeaeeeiqr....lkesaekeeeekeklerklreaeleaarl 94
                                      + L+ek++++eee+ +Le++ +  +ee+++    l+e+ ++ eeek  l+r+++ +++e+++l
  gi|385805867|ref|YP_005842265.1| 20 KYLEEKLKVLEEEKARLEKDINSYKEEKEKyikyLEEKIKELEEEKLMLNREVKYYKEEMEKL 82
                                      455555555555555555554444333332111144444444555555555555555555443 PP

>> DUF2353  Uncharacterized coiled-coil protein (DUF2353)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   4.7    0.0039       1.4     196     224 ..      17      45 ..      13      52 .. 0.86
   2 ?    8.5   6.0    0.0033       1.2     199     228 ..      52      81 ..      50      90 .. 0.94
   3 ?   -1.2   0.1       2.8     1e+03     124     149 ..     392     417 ..     346     421 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0039
                           DUF2353 196 lENrYlkerlkqleeEkelakqtlskYks 224
                                       +  +Yl+e+lk leeEk  +++ ++ Yk+
  gi|385805867|ref|YP_005842265.1|  17 AHIKYLEEKLKVLEEEKARLEKDINSYKE 45 
                                       5569************************8 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0033
                           DUF2353 199 rYlkerlkqleeEkelakqtlskYksllek 228
                                       +Yl+e++k+leeEk +++++++ Yk+ +ek
  gi|385805867|ref|YP_005842265.1|  52 KYLEEKIKELEEEKLMLNREVKYYKEEMEK 81 
                                       9************************98776 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 2.8
                           DUF2353 124 saeereelvkqlEklkekiqqlerdl 149
                                        +   e+++k++Ek+k +++++e ++
  gi|385805867|ref|YP_005842265.1| 392 DLVTMEDFIKAIEKIKGRKKEVEPEV 417
                                       35566788888888888888877665 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   9.9    0.0076       2.7       3      76 ..       8      82 ..       6      85 .. 0.84
   2 ?    0.5   0.0       1.9   6.9e+02      44      79 ..     145     180 ..     124     186 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0076
                       TMF_TATA_bd  3 stssagpsvqlverlsseirrlEgElaslkeelerleaerdeareeivklmkeneelk.elkkeleelekeleel 76
                                      s++++++    +++l+ +++ lE E+a l++++++ ++e+++  + + + +ke ee k  l++e++  ++e+e+l
  gi|385805867|ref|YP_005842265.1|  8 SNANSTNVLAHIKYLEEKLKVLEEEKARLEKDINSYKEEKEKYIKYLEEKIKELEEEKlMLNREVKYYKEEMEKL 82
                                      667888888999******************************999999999887765515577788888888876 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.9
                       TMF_TATA_bd  44 eareeivklmkeneelkelkkeleelekeleelqer 79 
                                       + ++  vk m+  e+ + + k++  l+k+++e++e 
  gi|385805867|ref|YP_005842265.1| 145 QREDPYVKAMEVIERPNVKYKDIGGLSKQIQEVRET 180
                                       566778999999999999999999999999999875 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 ?    6.8  11.6     0.013       4.5      83     146 ..      12      79 ..       3      82 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.013
                     PI3K_P85_iSH2  83 ieklqenleqlksrlkelhsskekLeedlkqqkeeer....eleReinalkpellqLqkrkdkylewL 146
                                         ++  +++ l+++lk l+++k++Le+d+++ kee+      le +i +l  e l+L+++   y e +
  gi|385805867|ref|YP_005842265.1|  12 STNVLAHIKYLEEKLKVLEEEKARLEKDINSYKEEKEkyikYLEEKIKELEEEKLMLNREVKYYKEEM 79 
                                       5677889999*******************9877765544448***************99877776665 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   5.5    0.0084         3      49     121 ..      10      82 ..       2      85 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0084
                                       CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  49 nstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvlesneqkiqkL 121
                                        +++++  ++k+++++l+  +++k+  ++ i+++++e e+ i +l+e+i++ e++   L   ++  +++++kL
  gi|385805867|ref|YP_005842265.1|  10 ANSTNVLAHIKYLEEKLKVLEEEKARLEKDINSYKEEKEKYIKYLEEKIKELEEEKLMLNREVKYYKEEMEKL 82 
                                       3456677889999999999999999999**********************99999999999999999999988 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9  17.0     0.097        35      60     114 ..      16      70 ..       2      84 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.097
                            APG6_N  60 ekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlelle 114
                                        +  + l+e+Lk le+e+++le+++++++ee+e+  +  e++++e  e +l l++
  gi|385805867|ref|YP_005842265.1|  16 LAHIKYLEEKLKVLEEEKARLEKDINSYKEEKEKYIKYLEEKIKELEEEKLMLNR 70 
                                       5566678888899999999999999999999998888888888888888877664 PP

>> bZIP_2  Basic region leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   4.2     0.029        10      25      54 .]      17      46 ..      15      48 .. 0.89
   2 ?    4.8   7.3     0.085        30      19      53 ..      43      77 ..      40      78 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.029
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_2 25 akeeeleervkeLeeeNaqLrqkveqLeke 54
                                      a+ ++lee++k Leee+a+L++ + +++ e
  gi|385805867|ref|YP_005842265.1| 17 AHIKYLEEKLKVLEEEKARLEKDINSYKEE 46
                                      57899****************999888765 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.085
                                      -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_2 19 sRekkkakeeeleervkeLeeeNaqLrqkveqLek 53
                                      ++e k ++ ++lee++keLeee+  L ++v+ ++ 
  gi|385805867|ref|YP_005842265.1| 43 YKEEKEKYIKYLEEKIKELEEEKLMLNREVKYYKE 77
                                      7777888999****************999987765 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   6.0    0.0019      0.67      13      69 ..      16      81 ..       5      87 .. 0.62
   2 ?   -2.1   0.0       6.9   2.5e+03      32      55 ..     155     178 ..     125     187 .. 0.64
   3 ?   -2.3   0.0       7.8   2.8e+03      43      66 ..     392     415 ..     386     420 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0019
                           DUF4795 13 qeaieklqeelekleekvkelekr....ledkekklealkkqieelekvk.....adkeeveeela 69
                                       ++i+ l+e+l+ lee++++lek+    +e+kek ++ l+++i+ele++k     + k++ ee ++
  gi|385805867|ref|YP_005842265.1| 16 LAHIKYLEEKLKVLEEEKARLEKDinsyKEEKEKYIKYLEEKIKELEEEKlmlnrEVKYYKEEMEK 81
                                      34555555555555555555555511115678899***************8877644555555554 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 6.9
                           DUF4795  32 elekrledkekklealkkqieele 55 
                                       e+ +r + k k++ +l kqi+e +
  gi|385805867|ref|YP_005842265.1| 155 EVIERPNVKYKDIGGLSKQIQEVR 178
                                       444555555566666666665554 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 7.8
                           DUF4795  43 klealkkqieelekvkadkeevee 66 
                                       +l ++++ i++ ek k+ k+eve 
  gi|385805867|ref|YP_005842265.1| 392 DLVTMEDFIKAIEKIKGRKKEVEP 415
                                       444555566666666666666665 PP

>> DUF737  Protein of unknown function (DUF737)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9  11.6     0.021       7.5     119     174 ..      28      82 ..       9      84 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.021
                            DUF737 119 aqeelteailrerlstedErlkaqllelerkarqLeekekeLkkqdafYkeqlakL 174
                                         ee ++ ++++ +s ++E++k  ++ le k+++Lee    L++  ++Yke ++kL
  gi|385805867|ref|YP_005842265.1|  28 VLEEEKARLEKDINSYKEEKEKYIKY-LEEKIKELEEEKLMLNREVKYYKEEMEKL 82 
                                       34555667778889999******999.**************************998 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 ?    7.9   3.7     0.012       4.3       2      28 ..      19      45 ..      18      51 .. 0.89
   2 ?    3.6   6.1      0.26        93      54      80 .]      54      80 ..      46      80 .. 0.82
   3 ?    2.4   0.0      0.63   2.2e+02       9      38 ..     384     414 ..     377     423 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.012
                              KELK  2 lkeLekqlrllkqEkeelqkelaeaqE 28
                                      +k Le++l++l++Ek  l+k+++  +E
  gi|385805867|ref|YP_005842265.1| 19 IKYLEEKLKVLEEEKARLEKDINSYKE 45
                                      899******************998876 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.26
                              KELK 54 vneklselrsqkqklsRqlrdkeeEle 80
                                      ++ek++el ++k  l R+++   eE+e
  gi|385805867|ref|YP_005842265.1| 54 LEEKIKELEEEKLMLNREVKYYKEEME 80
                                      688999999999999999999888886 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.63
                              KELK   9 lrllkqEkeelq.kelaeaqErlksqkkeLk 38 
                                       + ++++E++ ++  ++  a E++k +kke  
  gi|385805867|ref|YP_005842265.1| 384 YNAIREERDLVTmEDFIKAIEKIKGRKKEVE 414
                                       66789999988768999**********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2132  (0.118913); expected 358.6 (0.02)
Passed bias filter:                     1148  (0.0640303); expected 358.6 (0.02)
Passed Vit filter:                       246  (0.0137208); expected 17.9 (0.001)
Passed Fwd filter:                        60  (0.00334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              50  [number of targets reported over threshold]
# CPU time: 0.98u 0.37s 00:00:01.35 Elapsed: 00:00:00.55
# Mc/sec: 2332.20
//
Query:       gi|385805868|ref|YP_005842266.1|  [L=171]
Description: helix-turn-helix domain-containing protein [Fervidicoccus fontis Kam940]
Scores for complete 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   37.6   3.2    2.9e-09   36.8   3.2    1.4  1  HTH_3            Helix-turn-helix
    5.9e-05   23.3   0.1     0.0001   22.6   0.1    1.3  1  HTH_31           Helix-turn-helix domain
    0.00054   19.8   0.4     0.0013   18.6   0.4    1.6  1  HTH_25           Helix-turn-helix domain
     0.0007   19.4   4.1      0.001   18.9   4.1    1.3  1  PAW              PNGase C-terminal domain, mannose-binding mo
     0.0024   17.8   2.5     0.0024   17.8   2.5    1.9  2  HTH_19           Helix-turn-helix domain
  ------ inclusion threshold ------
      0.025   14.6   0.3      0.044   13.8   0.3    1.3  1  DZR              Double zinc ribbon
       0.12   12.4   0.2       0.38   10.8   0.1    1.8  2  Lum_binding      Lumazine binding domain
        2.3    8.5   8.9       0.48   10.7   3.9    2.3  3  Rpr2             RNAse P Rpr2/Rpp21/SNM1 subunit domain
        2.4    8.5  11.6       0.39   11.1   7.5    1.7  2  DNA_pol_delta_4  DNA polymerase delta, subunit 4


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 !   36.8   3.2   1.5e-12   2.9e-09       1      53 [.      87     139 ..      87     140 .. 0.97

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 1.5e-12
                                       HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEHH CS
                             HTH_3   1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvsld 53 
                                       +k +R++lgl++  L++k+  + s ++riE G+ +Ps+e  k+l+kaLg++l 
  gi|385805868|ref|YP_005842266.1|  87 IKNAREKLGLTLLALSQKVMEKESVLRRIEQGRLRPSIELSKRLEKALGIKLL 139
                                       899*****************************999**************9985 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.1     5e-08    0.0001       8      56 ..      89     136 ..      86     141 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 5e-08
                            HTH_31   8 alReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgl 56 
                                        +Re+ GL++ ++ + +   es l+r+EqGr  rps +   +l  alg 
  gi|385805868|ref|YP_005842266.1|  89 NAREKLGLTLLALSQKVMEKESVLRRIEQGRL-RPSIELSKRLEKALGI 136
                                       68******************************.9*************96 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.4   6.3e-07    0.0013       2      35 ..      87     120 ..      86     123 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 6.3e-07
                                       HHHHHHTTT--HHHHHHHSS--HHHHHHHHCT-- CS
                            HTH_25   2 LraaRearglsleevaketkIrkdylealEeddf 35 
                                        ++aRe++gl+l +++++   ++++l+++E++++
  gi|385805868|ref|YP_005842266.1|  87 IKNAREKLGLTLLALSQKVMEKESVLRRIEQGRL 120
                                       589****************************986 PP

>> PAW  PNGase C-terminal domain, mannose-binding module PAW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   4.1   5.1e-07     0.001      20      79 ..      53     117 ..      35     118 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 5.1e-07
                                       ..-----EB---HHHHHHTEEEEEEETTTTEEEECCGTTEEE....ESGGGG-SSEESEEEEEET CS
                               PAW  20 k.kekeyvfkptekekkekllelrYsivkDkYvrvskneeei....kgwesavfevenifrkvEe 79 
                                       + k+++ + kp+ +ekk+k+ e++Y++v D Y+++++ +e++       ++ v+e e++ r+ E+
  gi|385805868|ref|YP_005842266.1|  53 DeKKNSQIQKPKMQEKKKKKEEIEYEVVDDYYIKIKNAREKLgltlLALSQKVMEKESVLRRIEQ 117
                                       2478899******************************99655444488999999999**999986 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       3.3   6.7e+03      11      21 ..      68      78 ..      66      83 .. 0.57
   2 !   17.8   2.5   1.2e-06    0.0024       3      55 ..      86     137 ..      84     148 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.3
                            HTH_19 11 lgltqeelaer 21
                                      ++ ++ee++++
  gi|385805868|ref|YP_005842266.1| 68 KKKKKEEIEYE 78
                                      55556665554 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 1.2e-06
                            HTH_19   3 rLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgid 55 
                                       ++k aRe+lglt+ +l++++    s ++ iE g+   ps+el +++ +algi 
  gi|385805868|ref|YP_005842266.1|  86 KIKNAREKLGLTLLALSQKVMEKESVLRRIEQGRL-RPSIELSKRLEKALGIK 137
                                       69*******************************99.***************98 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.3   2.2e-05     0.044      10      40 ..       5      43 ..       3      47 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.2e-05
                               DZR 10 pdarfCseCgtklkavaa........edrCpsCgekvdp 40
                                      p+a +C+ Cg++++  a          ++C +C +k  +
  gi|385805868|ref|YP_005842266.1|  5 PEALYCELCGSPIEGRAYkvnidgvsLTVCEKCYRKQIQ 43
                                      6899*********8655599*************998554 PP

>> Lum_binding  Lumazine binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00019      0.38      40      73 ..      24      51 ..      18      61 .. 0.62
   2 ?   -2.3   0.0       2.2   4.4e+03      25      25 ..      86      86 ..      59     111 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00019
                                      EEETTEEEEEEEEEE.SSEEEEEEEHHHHHHSSG CS
                       Lum_binding 40 iavnGvcLTVvteeveeeeftvdvipeTlerttl 73
                                      + ++Gv+LTV+++      ++ + i+++ ++++ 
  gi|385805868|ref|YP_005842266.1| 24 VNIDGVSLTVCEK-----CYR-KQIQKSTSKVNA 51
                                      779*******942.....233.334444444444 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.2
                                      E CS
                       Lum_binding 25 e 25
                                      +
  gi|385805868|ref|YP_005842266.1| 86 K 86
                                      1 PP

>> Rpr2  RNAse P Rpr2/Rpp21/SNM1 subunit domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       1.9   3.9e+03      47      54 ..       9      16 ..       3      30 .. 0.75
   2 ?   10.7   3.9   0.00024      0.48      43      79 ..      29      65 ..      19      86 .. 0.79
   3 ?   -1.0   0.0       1.1   2.3e+03      16      43 ..      97     124 ..      82     129 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.9
                                      B-TTT--B CS
                              Rpr2 47 vCkkCgsv 54
                                      +C+ Cgs 
  gi|385805868|ref|YP_005842266.1|  9 YCELCGSP 16
                                      78889886 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00024
                                      CCCTB-TTT--B--CTTTEEEEEE-SSS-E....... CS
                              Rpr2 43 vkrtvCkkCgsvlipgvtcsvrvenkskkkkkkkkka 79
                                      v+ tvC+kC    i+ +t++v+ e ++k+++ +k+k 
  gi|385805868|ref|YP_005842266.1| 29 VSLTVCEKCYRKQIQKSTSKVNAEDEKKNSQIQKPKM 65
                                      6779*******************88777766666554 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.1
                                       H-HHHHHHHHHHHHHHHHHCT---SSTC CS
                              Rpr2  16 aspalsrylakqlrevskkaqlrlppsv 43 
                                       ++ als+ ++++   + + +q rl ps+
  gi|385805868|ref|YP_005842266.1|  97 TLLALSQKVMEKESVLRRIEQGRLRPSI 124
                                       5567777777777777777777777776 PP

>> DNA_pol_delta_4  DNA polymerase delta, subunit 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   7.5    0.0002      0.39      12      81 ..      40     114 ..      31     132 .. 0.77
   2 ?   -1.2   0.1       1.2   2.5e+03      31      38 ..     146     153 ..     121     166 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0002
                   DNA_pol_delta_4  12 sevdk.ekkvssaekeevaetkepekleeelkaekelekqidkewkkieeerka..ppvHa..eelskvekvLre 81 
                                       ++++k ++kv++++++++ + ++p+ +e++ k+e++  + +d+++ ki+++r +   ++ a  + + + e vLr 
  gi|385805868|ref|YP_005842266.1|  40 KQIQKsTSKVNAEDEKKNSQIQKPKMQEKKKKKEEIEYEVVDDYYIKIKNAREKlgLTLLAlsQKVMEKESVLRR 114
                                       33333266777777777777899****************************988552333345788888888875 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.2
                   DNA_pol_delta_4  31 tkepekle 38 
                                       +ke+e+ e
  gi|385805868|ref|YP_005842266.1| 146 KKEEESEE 153
                                       12222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2786  (0.155391); expected 358.6 (0.02)
Passed bias filter:                      758  (0.0422779); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.54
# Mc/sec: 960.97
//
Query:       gi|385805869|ref|YP_005842267.1|  [L=342]
Description: GTPase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      4e-19   68.8   0.1    9.6e-19   67.6   0.1    1.7  1  MMR_HSR1      50S ribosome-binding GTPase
    2.6e-11   44.0   2.6    2.6e-11   44.0   2.6    1.9  1  GTP-bdg_M     GTP-binding GTPase Middle Region
    4.9e-09   36.7   0.4    9.2e-09   35.9   0.4    1.5  1  GTP-bdg_N     GTP-binding GTPase N-terminal
    1.4e-08   34.4   3.2    2.3e-08   33.7   1.0    2.4  2  FeoB_N        Ferrous iron transport protein B
    3.3e-07   30.0   0.2    0.00076   19.1   0.0    2.3  2  GTP_EFTU      Elongation factor Tu GTP binding domain
     0.0002   21.3   0.6    0.00048   20.1   0.1    1.9  2  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
     0.0016   17.9   0.1     0.0029   17.1   0.1    1.5  1  SRPRB         Signal recognition particle receptor beta subun
     0.0022   17.5   1.3     0.0062   16.0   0.2    2.2  2  Arf           ADP-ribosylation factor family
  ------ inclusion threshold ------
      0.022   15.3   0.3      0.096   13.2   0.2    2.0  2  ABC_tran      ABC transporter
      0.037   13.9   0.1        1.6    8.6   0.0    2.6  2  RsgA_GTPase   RsgA GTPase
      0.062   13.0   0.3       0.33   10.7   0.3    2.1  1  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
       0.14   12.2   1.6        0.2   11.7   0.2    2.0  2  Dynamin_N     Dynamin family
        4.7    7.5  11.7         14    6.0   1.5    3.6  3  DUF3618       Protein of unknown function (DUF3618)


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 !   67.6   0.1     7e-22   9.6e-19       2     114 .]     168     284 ..     167     284 .. 0.81

  Alignments for each domain:
  == domain 1  score: 67.6 bits;  conditional E-value: 7e-22
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHH..HHHHHHHHHHCT CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseek..glgkaflaleea 76 
                                       +ai+G+ N+GK+tL+n ltg++ ++s+kp+tT+ ++    +     + ++Dt+G++ +   e    +  ++++++ea
  gi|385805869|ref|YP_005842267.1| 168 IAIIGYANAGKTTLFNLLTGSNKETSNKPFTTISPKVSLSN---LGFLVIDTVGFVMNVPPEIieAFYSTLEEIREA 241
                                       89**********************************99665...67********7532222223356667777888* PP

                                       SEEEEEEETT......TTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                          MMR_HSR1  77 dlillvvdas......eeklkpldeeleelleeakkplilvlnk 114
                                       d++ll++d++      ee +k+   +l ++ e+  kp++++lnk
  gi|385805869|ref|YP_005842267.1| 242 DVLLLLLDSTedlfliEERVKQASVTLSNI-ESLYKPIVVALNK 284
                                       ********7788888766788888888777.46899*****998 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 !   44.0   2.6   1.9e-14   2.6e-11       2      79 .]      84     160 ..      83     160 .. 0.89

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 1.9e-14
                                       --SHHHHHHHHHHHHHHHHHHHCXXXXXXXXX..X..XXXXXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHH..... CS
                         GTP-bdg_M   2 ArtkeaklQVelAqlkyllprLeglgkelsrqgGgigtrGpGetkleldrrlireriaklkkeLekvkkkrelqrkk 78 
                                       A +keaklQ+ lA+  ++lp +++  ++ +r +   g+   G + ++ + r++r+++ak ++eLe+++ +r+ +r++
  gi|385805869|ref|YP_005842267.1|  84 AGSKEAKLQISLARSGHMLPLVREVLNNSKRGE-LPGFLAGGTYAIDKYYRQLRRQVAKTRRELEEIRIRRDILRER 159
                                       99********************65555555543.246999************************************9 PP

                                       T CS
                         GTP-bdg_M  79 R 79 
                                       R
  gi|385805869|ref|YP_005842267.1| 160 R 160
                                       8 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 !   35.9   0.4   6.7e-12   9.2e-09      14      88 ..       8      80 ..       1      81 [. 0.88

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 6.7e-12
                         GTP-bdg_N 14 aglevvgevvqkrekpdpatyiGkGkveeikelveeeeadlvifddeLspsqqrnLekelevkViDRtqLILdIF 88
                                      +gl++ ++v+ +  k + +++i   k++ei e+ e+ +a++++++ eL p+ + n+ k+++  ViDRt L L++F
  gi|385805869|ref|YP_005842267.1|  8 IGLDIQESVTIR--KNSGRYLISDYKLREIVEKKEKVKAEVILIEPELPPRDKINIIKATKADVIDRTLLLLEVF 80
                                      566666666666..56789*******************************************************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 ?   -1.2   0.0      0.95   1.3e+03      64      97 ..      37      76 ..      14      84 .. 0.56
   2 !   33.7   1.0   1.6e-11   2.3e-08       3     154 ..     168     330 ..     167     332 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.95
                                      SHHHHHHHHHHH...CTSSSEEEEEEEGGG...HHHHHHH CS
                            FeoB_N 64 seeekvardfll...eeepdvvvnvvdatn...lernLyL 97
                                       + ekv  +++l   e  p   +n++ at+   ++r+L+L
  gi|385805869|ref|YP_005842267.1| 37 EKKEKVKAEVILiepELPPRDKINIIKATKadvIDRTLLL 76
                                      3456666666553332234555555555432226666655 PP

  == domain 2  score: 33.7 bits;  conditional E-value: 1.6e-11
                                       EEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHHCTSS CS
                            FeoB_N   3 valvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardflleeep 79 
                                       +a++G  n+Gkttlfn ltg++++ +N p +t+  k    +     + ++D  G     +  + e    ++   +e+
  gi|385805869|ref|YP_005842267.1| 168 IAIIGYANAGKTTLFNLLTGSNKETSNKPFTTISPKVSLSN---LGFLVIDTVGFVMNVPPEIIEAFYSTLEEIREA 241
                                       89*******************************99876665...889999999976555555555555555555677 PP

                                       SEEEEEEEGGG........HHHHHHHHHHHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHT......S-EEEEB CS
                            FeoB_N  80 dvvvnvvdatn........lernLyLtlqllelgvpvvlalnmideaekkgieidlkkLsekLg......vpvvkts 142
                                       dv++ ++d+t+        +++  + + ++  l +p+v+aln++++  ++ ie   +kL ++ +      v   k+s
  gi|385805869|ref|YP_005842267.1| 242 DVLLLLLDSTEdlflieerVKQASVTLSNIESLYKPIVVALNKVEKTGRDDIEEKRAKLYQTCKsvfpmfVGLAKVS 318
                                       88888888775433311113333333345566789**************9999999999887543322225567888 PP

                                       TTTTBTHHHHHH CS
                            FeoB_N 143 akkkegieellk 154
                                       akk+ gi+e+++
  gi|385805869|ref|YP_005842267.1| 319 AKKGLGIDEMVN 330
                                       888888888776 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0   0.00072      0.99       6      32 ..     168     194 ..     164     205 .. 0.85
   2 !   19.1   0.0   5.5e-07   0.00076      89     192 ..     236     336 ..     197     338 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00072
                                       EEEEESTTSSHHHHHHHHHHHTTSSCH CS
                          GTP_EFTU   6 igiighvDhGKtTLtdrLlyktgaisk 32 
                                       i+iig  ++GKtTL   L+ +++++s+
  gi|385805869|ref|YP_005842267.1| 168 IAIIGYANAGKTTLFNLLTGSNKETSN 194
                                       89*************999987777665 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 5.5e-07
                                       HHHHT-SEEEEEEETTTB......STHHHHHHHHHHHHTTTEEEEEEESCGST.HHHHHHHHHHHHHHHHHHHHHHH CS
                          GTP_EFTU  89 rglrvlDgavlvvdaveG......vepqteevlrlalkegvpiivfiNKmDrl.kaelkeiveevkqklsrkeekle 158
                                       + +r +D+ +l++d++e+         q    l  + ++  pi+v++NK+ ++ +++++e   +++q+         
  gi|385805869|ref|YP_005842267.1| 236 EEIREADVLLLLLDSTEDlflieeRVKQASVTLSNIESLYKPIVVALNKVEKTgRDDIEEKRAKLYQTC-------- 304
                                       338999**********88888666667777778888889999***********9999*********999........ PP

                                       HHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHHS CS
                          GTP_EFTU 159 kygekgekevpvvfgSalkgegvktllealvell 192
                                       k ++    +v ++ +Sa+kg g++++++++ + l
  gi|385805869|ref|YP_005842267.1| 305 KSVFPM--FVGLAKVSAKKGLGIDEMVNVIWKAL 336
                                       455554..688****************9998765 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 ?   -3.2   0.1       6.2   8.6e+03      15      36 ..      27      48 ..      14      51 .. 0.64
   2 !   20.1   0.1   3.5e-07   0.00048      53     105 ..     273     337 ..     255     337 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 6.2
                      MMR_HSR1_Xtn 15 ldeetvkkilkeykihnaevli 36
                                      +++ + ++i+++   ++aev++
  gi|385805869|ref|YP_005842267.1| 27 ISDYKLREIVEKKEKVKAEVIL 48
                                      5556667777777777777765 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 3.5e-07
                      MMR_HSR1_Xtn  53 rvYipclyvlNKiDlisleeldelare........pnsvv.......iSaekelnldeLkekiweeLn 105
                                         Y+p +++lNK+ +   ++++e + +            +       +Sa+k+l++de+++ iw+ Ln
  gi|385805869|ref|YP_005842267.1| 273 SLYKPIVVALNKVEKTGRDDIEEKRAKlyqtcksvF---PmfvglakVSAKKGLGIDEMVNVIWKALN 337
                                       57***********99666655554443344444440...25556777******************996 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 !   17.1   0.1   2.1e-06    0.0029       4      87 ..     166     252 ..     163     293 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.1e-06
                                       -EEEEE-STTSSHHHHHHHHHHSS---B---SS-EEETTG...GGTT-SEEEETT-G.....CCSHHHHHHHHHHGG CS
                             SRPRB   4 pavllvGlsdsGKTslftrLttdsvkktvtSqessaalkvksekgskltliDfPGhe.....klrqklleklkakss 75 
                                       p + ++G  ++GKT+lf++Lt    k+t     ++++ kv s  +  + +iD  G +     ++   +  +l + ++
  gi|385805869|ref|YP_005842267.1| 166 PLIAIIGYANAGKTTLFNLLTGS-NKETSNKPFTTISPKV-SLSNLGFLVIDTVGFVmnvppEIIEAFYSTLEEIRE 240
                                       56889*************98755.4444443344444455.556677778887776531122233444444555555 PP

                                       EEEEEEEEETTS CS
                             SRPRB  76 lkglvfvvDSti 87 
                                       +  l+ ++DSt 
  gi|385805869|ref|YP_005842267.1| 241 ADVLLLLLDSTE 252
                                       666777777765 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.69   9.5e+02     100     161 ..      28      99 ..      20     112 .. 0.63
   2 !   16.0   0.2   4.5e-06    0.0062      17     171 ..     168     332 ..     153     336 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.69
                                       HHHHHHHHCTSGCCTTSEEEEE......EE-TTSTTSS-HHHHHHHTTGGGSS....SSSSEEEEEEBTTTT CS
                               Arf 100 akeeLkalleeeelkevallvl......aNKqDlpealseeelrellgleelk....gkrkleiqkcsavkg 161
                                       +  +L++++e++e  ++ ++++        K+ + +a +++ + ++l l e+     g+++ ++q + a +g
  gi|385805869|ref|YP_005842267.1|  28 SDYKLREIVEKKEKVKAEVILIepelppRDKINIIKATKADVIDRTLLLLEVFesnaGSKEAKLQISLARSG 99 
                                       566788888888877777666522222236888888888888888777777654555555666665555555 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 4.5e-06
                                       EEEEESTTSSHHHHHHHHHHSSCEECSSSSSEEEEEEEETTEEEEEEEE-S.SGGGGG.GGGGGC......TTESEE CS
                               Arf  17 illlGLDnaGKtTilkklkleelvttvPTigfnveeleiknlkftvwDvGG.qeklRp.lWknYf......ektdav 85 
                                       i ++G  naGKtT+ + l+  + +t        + +++  nl f v D  G   ++ p + + ++      ++ d++
  gi|385805869|ref|YP_005842267.1| 168 IAIIGYANAGKTTLFNLLTGSNKETSNKPFTTISPKVSLSNLGFLVIDTVGfVMNVPPeIIEAFYstleeiREADVL 244
                                       6799**************988888766667777889************66623444332333343111111567899 PP

                                       EEEEETT-CT.THHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTSS-HHHHHHHTTGGGSSSSSS..EEEEEEBTT CS
                               Arf  86 ifvvDsadre.RleeakeeLkalleeeelkevallvlaNKqDlpealseeelrellgleelkgkrk..leiqkcsav 159
                                       + ++Ds++    +ee  ++ +  l++ e    +++v  NK + ++  + ee r++l   + k+  +  + ++k+sa 
  gi|385805869|ref|YP_005842267.1| 245 LLLLDSTEDLfLIEERVKQASVTLSNIESLYKPIVVALNKVEKTGRDDIEEKRAKLYQ-TCKSVFPmfVGLAKVSAK 320
                                       999**997662455555555555666666677999999**999988887777777653.344344400556788899 PP

                                       TTBTHHHHHHHH CS
                               Arf 160 kgeglkeglewl 171
                                       kg g++e ++ +
  gi|385805869|ref|YP_005842267.1| 321 KGLGIDEMVNVI 332
                                       999998887766 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       1.6   2.2e+03      85      85 ..      70      70 ..       4     165 .. 0.52
   2 ?   13.2   0.2   6.9e-05     0.096      13      39 ..     167     193 ..     161     199 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.6
                                      H CS
                                      x RF
                          ABC_tran 85 i 85
                                      i
  gi|385805869|ref|YP_005842267.1| 70 I 70
                                      0 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 6.9e-05
                                       EEEEEESTTSSHHHHHHHHTTSS--SE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  13 kvaivGenGaGKStLlkllagllkpte 39 
                                       ++ai+G   aGK+tL++ll+g  k t+
  gi|385805869|ref|YP_005842267.1| 167 LIAIIGYANAGKTTLFNLLTGSNKETS 193
                                       689******************998876 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0    0.0011       1.6     100     131 ..     166     193 ..     127     221 .. 0.71
   2 ?    2.4   0.1     0.092   1.3e+02      38      74 ..     267     303 ..     242     335 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0011
                                       SEEEEECSTTSSHHHHHHHHCTT-----S--- CS
                       RsgA_GTPase 100 ktsvlvGqSGvGKStLinallpelelktgevs 131
                                        +++++G   +GK+tL n l+++++    e+s
  gi|385805869|ref|YP_005842267.1| 166 PLIAIIGYANAGKTTLFNLLTGSNK----ETS 193
                                       567899***************9843....333 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.092
                                       HHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHH CS
                       RsgA_GTPase  38 fLvlaeekgiepvivlnKiDlleeeeeleelkeelea 74 
                                        L  +e+   ++v++lnK++ + +++  e+ ++ +++
  gi|385805869|ref|YP_005842267.1| 267 TLSNIESLYKPIVVALNKVEKTGRDDIEEKRAKLYQT 303
                                       566777777789999****999999833333333333 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3   0.00024      0.33       4     140 ..     168     331 ..     166     334 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00024
                         PduV-EutP   4 illiGkvgsGKttLtqalkg..........eelkYkktqaiefsdeviDtPGeylen.....rklysalivtsaead 65 
                                       i +iG  ++GKttL + l+g             +  k    ++   viDt G  ++      + +ys+l  +  ead
  gi|385805869|ref|YP_005842267.1| 168 IAIIGYANAGKTTLFNLLTGsnketsnkpfT-TISPKVSLSNLGFLVIDTVGFVMNVppeiiEAFYSTLEEI-READ 242
                                       6789**************9866444333221.1122333334444579998877764222224688888776.699* PP

                         PduV-EutP  66 vialvqdateeesvfppgfa.........svfnkeviGiitkidlaedeenieaveelLksaGaekif.......ev 126
                                       v+ l++d+te   ++ + +          + + k+++  + k++++  +++ie  + +L +  ++++f       +v
  gi|385805869|ref|YP_005842267.1| 243 VLLLLLDSTEDLFLIEERVKqasvtlsniESLYKPIVVALNKVEKT-GRDDIEEKRAKLYQT-CKSVFpmfvglaKV 317
                                       ****999998766665544311111111145789999999999988.788888888888876.44444333444467 PP

                         PduV-EutP 127 savekegieellky 140
                                       sa +  gi+e++++
  gi|385805869|ref|YP_005842267.1| 318 SAKKGLGIDEMVNV 331
                                       78888888887766 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       2.2   3.1e+03      77     106 ..      33      62 ..      27      62 .. 0.79
   2 ?   11.7   0.2   0.00015       0.2       1      40 [.     168     206 ..     168     308 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.2
                                       HHHHTSSSS--SS-EEEEEEETTS-SEEEE CS
                         Dynamin_N  77 ekiagankgiskkvillkilsllvkgltlv 106
                                       ++i +++++++ +vil+++  + +++++++
  gi|385805869|ref|YP_005842267.1|  33 REIVEKKEKVKAEVILIEPELPPRDKINII 62 
                                       566678889999999999999999988886 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00015
                                       EEEEEBTTTTHHHHHHHHHTS--S---SSS---S-EEEEE CS
                         Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrrplelql 40 
                                       ia++G  ++GK+++ n L+g++   +++ p T    +++l
  gi|385805869|ref|YP_005842267.1| 168 IAIIGYANAGKTTLFNLLTGSN-KETSNKPFTTISPKVSL 206
                                       89*******************9.77888887766656555 PP

>> DUF3618  Protein of unknown function (DUF3618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   1.5      0.01        14       6      20 ..     134     148 ..     132     149 .. 0.91
   2 ?    1.8   2.4      0.22     3e+02       7      17 ..     151     161 ..     150     164 .. 0.88
   3 ?    3.2   0.0     0.078   1.1e+02       8      21 ..     290     303 ..     290     306 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.01
                           DUF3618   6 eIerdIertRaeLae 20 
                                       +++r+++ tR+eL e
  gi|385805869|ref|YP_005842267.1| 134 QLRRQVAKTRRELEE 148
                                       8************76 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.22
                           DUF3618   7 IerdIertRae 17 
                                       I+rdI r R++
  gi|385805869|ref|YP_005842267.1| 151 IRRDILRERRR 161
                                       9********98 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.078
                           DUF3618   8 erdIertRaeLaeT 21 
                                       + dIe+ Ra L +T
  gi|385805869|ref|YP_005842267.1| 290 RDDIEEKRAKLYQT 303
                                       67*********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); 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: 0.68u 0.29s 00:00:00.97 Elapsed: 00:00:00.50
# Mc/sec: 2040.32
//
Query:       gi|385805870|ref|YP_005842268.1|  [L=195]
Description: hypothetical protein FFONT_0828 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-46  155.7   0.0    6.1e-46  155.2   0.0    1.2  1  Trm56     tRNA ribose 2'-O-methyltransferase, aTrm56
  ------ inclusion threshold ------
       0.14   11.9   0.1       0.33   10.7   0.0    1.6  2  DUF460    Protein of unknown function (DUF460)


Domain annotation for each model (and alignments):
>> Trm56  tRNA ribose 2'-O-methyltransferase, aTrm56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.2   0.0   6.8e-50   6.1e-46       1     119 []      60     180 ..      60     180 .. 0.97

  Alignments for each domain:
  == domain 1  score: 155.2 bits;  conditional E-value: 6.8e-50
                                       H-S--E.EE.E--HHHHHHC-S....SEEEEE-TTSEEHHHHHHHHHC-SE.EEEEE------TCHHHHSSEEEESS CS
                             Trm56   1 wGgefk.vevakslkklikefkk.eggivvhltmyGenieevieeikkkekdllvvvGaekvprevyeladynvsvg 75 
                                       wG  fk v++  s+k++i+ +++  +g++vhltmyG+++e+ i+ ikk+ k++l+++G+ekvp e+y++ad+n+svg
  gi|385805870|ref|YP_005842268.1|  60 WGRGFKlVSCGLSYKDYISIWRNyMKGVIVHLTMYGLELEREIDGIKKAGKPVLIIIGSEKVPGEIYKIADFNISVG 136
                                       99999867899**********98579*************************************************** PP

                                       SS---HHHHHHHHHHHHC.--TTT---TT-SSEEE--SSS-EEE CS
                             Trm56  76 nqPhsevaalaifldrllegkelekefedaklkviPsergkkvv 119
                                       nqPhsevaalaifldrl++g+el+ +fedak+++ Ps++gkkv+
  gi|385805870|ref|YP_005842268.1| 137 NQPHSEVAALAIFLDRLYNGQELYYKFEDAKVQIEPSASGKKVI 180
                                       ******************************************95 PP

>> DUF460  Protein of unknown function (DUF460)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   3.6e-05      0.33      61     109 ..      95     143 ..      83     147 .. 0.82
   2 ?   -2.7   0.0      0.49   4.4e+03       5      18 ..     164     177 ..     161     191 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 3.6e-05
                            DUF460  61 eldreevieliselGkpvivAtDvspppetvkklarslkavlyvPeedl 109
                                       +l+ e+ i+ i+++Gkpv++    +++p  + k+a    +v  +P++++
  gi|385805870|ref|YP_005842268.1|  95 GLELEREIDGIKKAGKPVLIIIGSEKVPGEIYKIADFNISVGNQPHSEV 143
                                       5667778999************************988777777777665 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.49
                            DUF460   5 kdvkvevesvekdk 18 
                                       +d kv++e+  + k
  gi|385805870|ref|YP_005842268.1| 164 EDAKVQIEPSASGK 177
                                       67788887766544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1225.99
//
Query:       gi|385805871|ref|YP_005842269.1|  [L=180]
Description: transcription initiation factor E subunit alpha [Fervidicoccus fontis Kam940]
Scores for complete 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   75.6   2.2    2.4e-21   75.6   2.2    1.8  2  TFIIE_alpha     TFIIE alpha subunit
    7.1e-05   22.7   0.7       0.21   11.6   0.1    2.5  2  HTH_11          HTH domain
     0.0042   16.9   0.6      0.013   15.4   0.1    2.0  2  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0047   17.0   1.7       0.99    9.5   0.1    2.3  2  Mut7-C          Mut7-C RNAse domain
     0.0062   16.4   2.6      0.034   14.1   2.9    2.0  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
  ------ inclusion threshold ------
      0.019   15.3   0.2       0.13   12.6   0.0    2.2  2  Rrf2            Transcriptional regulator
       0.02   14.8   0.6      0.032   14.2   0.6    1.3  1  zinc-ribbons_6  zinc-ribbons
      0.023   14.7   1.8      0.045   13.7   1.8    1.4  1  ADK_lid         Adenylate kinase, active site lid
       0.03   14.4   0.1      0.039   14.0   0.1    1.3  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.033   15.0   1.1      0.067   14.1   1.1    1.6  1  Ima1_N          Ima1 N-terminal domain
      0.039   14.2   0.5       0.97    9.7   0.1    2.2  2  DUF1400         Alpha/beta hydrolase of unknown function (DUF
      0.081   12.6   0.0       0.12   12.1   0.0    1.3  1  FlhC            Flagellar transcriptional activator (FlhC)
        0.1   12.4   0.0       0.16   11.8   0.0    1.3  1  HTH_IclR        IclR helix-turn-helix domain
       0.11   13.0   3.5        4.4    7.9   0.4    2.5  2  zf-C2H2         Zinc finger, C2H2 type
       0.11   12.0   0.3        1.1    8.8   0.0    2.2  2  HTH_24          Winged helix-turn-helix DNA-binding
       0.15   11.8   2.0        2.7    7.8   0.2    2.3  2  A2L_zn_ribbon   A2L zinc ribbon domain
       0.22   11.1   5.9      0.078   12.5   2.3    2.0  2  TF_Zn_Ribbon    TFIIB zinc-binding
       0.25   11.0   1.3         14    5.4   0.1    2.3  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
       0.25   12.3   2.6         16    6.7   0.2    2.4  2  zf-C2H2_4       C2H2-type zinc finger
       0.39   10.9   5.6        6.9    6.9   0.4    2.4  2  Zn-ribbon_8     Zinc ribbon domain
       0.71   10.6   6.5        1.7    9.3   0.5    2.6  2  Zn_ribbon_2     Putative zinc ribbon domain
        4.6    7.6   5.8         16    5.9   0.4    2.2  2  C1_2            C1 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 !   75.6   2.2   2.9e-24   2.4e-21       4     104 ..      12     113 ..      10     114 .. 0.93
   2 ?   -0.8   0.2       1.6   1.3e+03      90     104 ..     160     174 ..     152     175 .. 0.74

  Alignments for each domain:
  == domain 1  score: 75.6 bits;  conditional E-value: 2.9e-24
                                       HHHHHHCS-HHHHHHHHHHH.CTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEECC CS
                       TFIIE_alpha   4 kevvrkfygeeavlvldvLl.ekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywrinye 79 
                                       +e + k++ +   l+   L+ e++e te+ l+++l++ +n +rklL++L ++ +v y+r rdee++ y yyw+in e
  gi|385805871|ref|YP_005842269.1|  12 EEFISKMATNPSLLIFRFLAkENSEATEDTLSEKLGMSKNLVRKLLYKLHDINVVVYRRVRDEETNYYIYYWKINWE 88 
                                       67888999999999999998358****************************************************** PP

                                       CHCCCHHHHHHHHHHHHHHHHCCCT CS
                       TFIIE_alpha  80 klvdvvkrkleevvkkLeeklekee 104
                                        l   + ++++ev+kkL+ek   ee
  gi|385805871|ref|YP_005842269.1|  89 GLAATLLERKKEVLKKLKEKAASEE 113
                                       *******************988775 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.6
                                       HHHHHHHHHHHCCCT CS
                       TFIIE_alpha  90 eevvkkLeeklekee 104
                                       ++ +kkLee+++ e+
  gi|385805871|ref|YP_005842269.1| 160 QKYIKKLEEEIKIES 174
                                       677888888888776 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.1   0.00026      0.21       5      46 ..      26      67 ..      23      72 .. 0.84
   2 !    9.1   0.1    0.0015       1.2      33      53 ..     160     179 ..     158     179 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00026
                            HTH_11  5 ilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpI 46
                                      i ++L ++++  + ++L+e+L++S+  vr+ + +L ++ v +
  gi|385805871|ref|YP_005842269.1| 26 IFRFLAKENSEATEDTLSEKLGMSKNLVRKLLYKLHDINVVV 67
                                      77888777888******************9998888877655 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0015
                            HTH_11  33 rrdIkaLeelgvpIesepgrG 53 
                                       +++Ik+Lee   +Iese++ G
  gi|385805871|ref|YP_005842269.1| 160 QKYIKKLEEEI-KIESERNYG 179
                                       79********6.******976 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   1.5e-05     0.013      19      62 ..      33      81 ..      25      88 .. 0.84
   2 ?   -1.4   0.0       2.7   2.2e+03      41      49 ..     100     108 ..      93     121 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.5e-05
                                      HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.....TTEE CS
                              TrmB 19 klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.....pklY 62
                                      ++ +at d+++e+lg +++ v + L +L d  +V  ++ r     +++Y
  gi|385805871|ref|YP_005842269.1| 33 ENSEATEDTLSEKLGMSKNLVRKLLYKLHDINVVVYRRVRdeetnYYIY 81
                                      7899*****************************9888877777776655 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.7
                                       HHHHHHHHC CS
                              TrmB  41 evLrsLedk 49 
                                       evL++L++k
  gi|385805871|ref|YP_005842269.1| 100 EVLKKLKEK 108
                                       677777776 PP

>> Mut7-C  Mut7-C RNAse domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.3    0.0081       6.6     104     133 ..      97     128 ..      91     136 .. 0.90
   2 !    9.5   0.1    0.0012      0.99      91     122 ..     138     169 ..     128     173 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0081
                            Mut7-C 104 ekeevkervpekvyeeade..ftrCekCrkvf 133
                                       +k+ev ++++ek+++e+ +  ++ C+kC++ +
  gi|385805871|ref|YP_005842269.1|  97 RKKEVLKKLKEKAASEEGKvgIYYCKKCGREY 128
                                       588999********99999999*******987 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0012
                            Mut7-C  91 srCvaCngeleevekeevkervpekvyeeade 122
                                        rC  Cn++le ++k + +e +++++++ ++e
  gi|385805871|ref|YP_005842269.1| 138 FRCKICNEPLEFTQKGKYEEFLQKYIKKLEEE 169
                                       59****************99999998887766 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   1.1    0.0042       3.4      25      35 ..     119     129 ..     106     132 .. 0.66
   2 !   14.1   2.9   4.2e-05     0.034       4      37 ..     118     150 ..     118     151 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0042
                    Zn_ribbon_SprT  25 YrCrrCkgtLr 35 
                                       Y+C++C+ + +
  gi|385805871|ref|YP_005842269.1| 119 YYCKKCGREYT 129
                                       55555554443 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 4.2e-05
                    Zn_ribbon_SprT   4 vYrCtgCgreythhlsirrhnYrCrrCkgtLrgk 37 
                                       +Y+C  Cgreyt+     +   rC++C + L+++
  gi|385805871|ref|YP_005842269.1| 118 IYYCKKCGREYTFDEALENDF-RCKICNEPLEFT 150
                                       6********999999999988.*********997 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00016      0.13      13      56 ..      26      67 ..      17      70 .. 0.81
   2 ?   -0.5   0.0         2   1.6e+03      39      59 ..     156     176 ..     151     176 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00016
                                      HHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 13 allyLakeeeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                      +  +Lake++e  ++ ++++e+ ++s++ ++k+l kL   ++v 
  gi|385805871|ref|YP_005842269.1| 26 IFRFLAKENSE--ATEDTLSEKLGMSKNLVRKLLYKLHDINVVV 67
                                      55567777775..6***********************9887775 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 2
                                       HHHHHHHHHHHHHTTSEEEET CS
                              Rrf2  39 psylekilakLrkaglvksvr 59 
                                       +++l+k ++kL+++  ++s+r
  gi|385805871|ref|YP_005842269.1| 156 EEFLQKYIKKLEEEIKIESER 176
                                       5799999***99998888876 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.6   3.9e-05     0.032      15      50 ..     117     158 ..      99     174 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.9e-05
                                       SEEE-TTT--......EEEEEEE-SSS-S---EEEETTEEEE CS
                    zinc-ribbons_6  15 eqyhCeaCqe......dlkkealCpeCeqelevlkaCgavdy 50 
                                         y C++C +       l++   C  C+++le+ ++   +++
  gi|385805871|ref|YP_005842269.1| 117 GIYYCKKCGReytfdeALENDFRCKICNEPLEFTQKGKYEEF 158
                                       568999999977777667778899999999999988666655 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 ?   13.7   1.8   5.5e-05     0.045       3      31 ..     120     147 ..     119     148 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.5e-05
                                       E-TTT--EEETTT.B--SSTTB-TTT--.- CS
                           ADK_lid   3 vCpkCGrsYhvvf.npPkveglCDkCGepL 31 
                                        C+kCGr Y   f     ++  C  C+epL
  gi|385805871|ref|YP_005842269.1| 120 YCKKCGREYT--FdEALENDFRCKICNEPL 147
                                       5********9..756789***********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 ?   14.0   0.1   4.8e-05     0.039      69      97 ..     117     148 ..      61     164 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.8e-05
                                       -EEEETTTS-EEECHH..H.HHS-TTTSSS-E CS
                              HypA  69 vkvrCreCgkefelee..k.alrCpkCgsadv 97 
                                         ++C++Cg+e++ +e  + ++rC+ C++   
  gi|385805871|ref|YP_005842269.1| 117 GIYYCKKCGREYTFDEalEnDFRCKICNEPLE 148
                                       4578*********777453689*****98644 PP

>> Ima1_N  Ima1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   1.1   8.2e-05     0.067       5      47 ..     123     165 ..     106     178 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.2e-05
                            Ima1_N   5 fCnkkskvkyeeknsfeCpsCeayNgfdedGdindeipeqeee 47 
                                        C+++ +     +n f+C+ C+    f+++G++++ +++  ++
  gi|385805871|ref|YP_005842269.1| 123 KCGREYTFDEALENDFRCKICNEPLEFTQKGKYEEFLQKYIKK 165
                                       366677777777888******************9955444333 PP

>> DUF1400  Alpha/beta hydrolase of unknown function (DUF1400)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1    0.0012      0.97      17      69 ..       7      58 ..       3      66 .. 0.89
   2 ?    2.5   0.1      0.21   1.7e+02      23      44 ..     148     169 ..     144     176 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0012
                           DUF1400 17 svedLekfaktgevsseLatylkllskeqreelreaLqaeiklspvllsqlln 69
                                      + + Le+f  +  ++++L  +   l+ke+ e  ++ L +++ +s++l+++ll+
  gi|385805871|ref|YP_005842269.1|  7 PNDPLEEFISKMATNPSLLIFRF-LAKENSEATEDTLSEKLGMSKNLVRKLLY 58
                                      55779999999999999987666.***************************98 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.21
                           DUF1400  23 kfaktgevsseLatylkllske 44 
                                       +f+++g+ ++ L++y+k l++e
  gi|385805871|ref|YP_005842269.1| 148 EFTQKGKYEEFLQKYIKKLEEE 169
                                       6999************999887 PP

>> FlhC  Flagellar transcriptional activator (FlhC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00014      0.12     129     165 ..     113     148 ..      77     156 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
                              FlhC 129 skllqlasCkrCkgefvthaedlesefvCglCqlpsR 165
                                        + + +  Ck+C+ e+ t+ e+le++f C +C+ p  
  gi|385805871|ref|YP_005842269.1| 113 EGKVGIYYCKKCGREY-TFDEALENDFRCKICNEPLE 148
                                       55667789****9999.78899**********98854 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 ?   11.8   0.0   0.00019      0.16       6      47 ..      24      65 ..      23      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00019
                                      HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                          HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGy 47
                                      l i ++la+++ e t   l++++g++k  v+ lL  L+    
  gi|385805871|ref|YP_005842269.1| 24 LLIFRFLAKENSEATEDTLSEKLGMSKNLVRKLLYKLHDINV 65
                                      56999******************************9987655 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.4    0.0054       4.4       1      13 [.     119     131 ..     119     136 .. 0.80
   2 ?    5.7   0.2     0.027        22       1      13 [.     138     152 ..     138     157 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0054
                                       EEETTTTEEESSH CS
                           zf-C2H2   1 ykCpdCgksFkrk 13 
                                       y+C++Cg+ ++  
  gi|385805871|ref|YP_005842269.1| 119 YYCKKCGREYTFD 131
                                       99*****999865 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.027
                                       EEETTTT..EEESSH CS
                           zf-C2H2   1 ykCpdCg..ksFkrk 13 
                                       ++C++C+    F++k
  gi|385805871|ref|YP_005842269.1| 138 FRCKICNepLEFTQK 152
                                       89*****66666665 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0    0.0014       1.1      13      44 ..      31      63 ..      24      67 .. 0.78
   2 ?    0.8   0.1      0.45   3.6e+02      36      44 ..     161     169 ..     159     169 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0014
                            HTH_24 13 qk.nprisqreLAerlglSpstvnrrlkrLeee 44
                                       k n+  +   L+e+lg+S++ v++ l +L + 
  gi|385805871|ref|YP_005842269.1| 31 AKeNSEATEDTLSEKLGMSKNLVRKLLYKLHDI 63
                                      44488899999************9987776665 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.45
                            HTH_24  36 rrlkrLeee 44 
                                       +++k+Leee
  gi|385805871|ref|YP_005842269.1| 161 KYIKKLEEE 169
                                       79*****96 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.2    0.0033       2.7      20      30 ..     117     127 ..     115     130 .. 0.81
   2 ?    3.5   0.1     0.074        60       6      20 ..     140     153 ..     135     156 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0033
                     A2L_zn_ribbon  20 gylvCieCgas 30 
                                       g+++C++Cg +
  gi|385805871|ref|YP_005842269.1| 117 GIYYCKKCGRE 127
                                       79999999965 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.074
                     A2L_zn_ribbon   6 CsvCggngilnseqg 20 
                                       C+ C+ + ++ + +g
  gi|385805871|ref|YP_005842269.1| 140 CKICNEPLEF-TQKG 153
                                       *********9.6655 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       2.1   1.7e+03      11      21 ..      70      80 ..      66      80 .. 0.78
   2 ?   12.5   2.3   9.6e-05     0.078       1      25 [.     119     143 ..     119     151 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.1
                                      CHEETSTTCEE CS
                      TF_Zn_Ribbon 11 lveDpergelv 21
                                       v+D+e++ ++
  gi|385805871|ref|YP_005842269.1| 70 RVRDEETNYYI 80
                                      699***99875 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 9.6e-05
                                       EEETTTTCEECHEETSTTCEEESSS CS
                      TF_Zn_Ribbon   1 ykCPnCgstnlveDpergelvCtdC 25 
                                       y C++Cg +++  ++ +++++C+ C
  gi|385805871|ref|YP_005842269.1| 119 YYCKKCGREYTFDEALENDFRCKIC 143
                                       78******9966668899*****99 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1     0.017        14       3      18 ..     119     134 ..     117     135 .. 0.80
   2 ?    4.4   0.1     0.034        28       2      16 ..     137     151 ..     136     153 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.017
                            zf_UBZ   3 ylCerCgkeipeselq 18 
                                       y C++Cg+e   +e  
  gi|385805871|ref|YP_005842269.1| 119 YYCKKCGREYTFDEAL 134
                                       89*****998777655 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.034
                            zf_UBZ   2 tylCerCgkeipese 16 
                                        + C+ C+++++ ++
  gi|385805871|ref|YP_005842269.1| 137 DFRCKICNEPLEFTQ 151
                                       699******998776 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 ?    6.7   0.2     0.019        16       1      12 [.     119     130 ..     119     136 .. 0.78
   2 ?    5.6   0.2     0.042        34       1      10 [.     138     147 ..     138     165 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.019
                         zf-C2H2_4   1 fkCpiCgksFss 12 
                                       ++C+ Cg+ ++ 
  gi|385805871|ref|YP_005842269.1| 119 YYCKKCGREYTF 130
                                       89*******954 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.042
                         zf-C2H2_4   1 fkCpiCgksF 10 
                                       f+C+iC+++ 
  gi|385805871|ref|YP_005842269.1| 138 FRCKICNEPL 147
                                       89****7765 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.7     0.015        12       6      16 ..     119     129 ..     118     135 .. 0.86
   2 ?    6.9   0.4    0.0085       6.9       5      22 ..     137     154 ..     137     161 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.015
                       Zn-ribbon_8   6 YrCeeCghefe 16 
                                       Y C++Cg+e++
  gi|385805871|ref|YP_005842269.1| 119 YYCKKCGREYT 129
                                       99*****9975 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0085
                       Zn-ribbon_8   5 eYrCeeCghefevlqsis 22 
                                       ++rC+ C++  e  q+ +
  gi|385805871|ref|YP_005842269.1| 137 DFRCKICNEPLEFTQKGK 154
                                       79**********999876 PP

>> Zn_ribbon_2  Putative zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.9      0.11        87      11      39 ..     104     132 ..     100     137 .. 0.76
   2 ?    9.3   0.5    0.0021       1.7      27      63 ..     139     173 ..     128     178 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.11
                       Zn_ribbon_2  11 keedlgteadgsksedYCkyCykdGefte 39 
                                       k ++ +  ++g+    YCk C ++ +f e
  gi|385805871|ref|YP_005842269.1| 104 KLKEKAASEEGKVGIYYCKKCGREYTFDE 132
                                       5556667788999999*****88877765 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0021
                       Zn_ribbon_2  27 YCkyCykdGeftepdltmeemiekcvkklaeenkelt 63 
                                        Ck C +  eft+ + ++ee+++k++kkl+ee k ++
  gi|385805871|ref|YP_005842269.1| 139 RCKICNEPLEFTQ-KGKYEEFLQKYIKKLEEEIK-IE 173
                                       4************.9***************9975.54 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.9      0.06        49      32      43 ..     117     131 ..     106     133 .. 0.69
   2 ?    5.9   0.4      0.02        16      16      28 ..     135     147 ..     129     156 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.06
                              C1_2  32 f.YsCseC..dfslh 43 
                                         Y+C++C  +++++
  gi|385805871|ref|YP_005842269.1| 117 GiYYCKKCgrEYTFD 131
                                       2599*9995447776 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.02
                              C1_2  16 sesfnCsaCgrki 28 
                                       +++f+C++C ++ 
  gi|385805871|ref|YP_005842269.1| 135 ENDFRCKICNEPL 147
                                       67899****9984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1420  (0.0792013); expected 358.6 (0.02)
Passed bias filter:                      738  (0.0411624); expected 358.6 (0.02)
Passed Vit filter:                       114  (0.00635841); 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: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1117.77
//
Query:       gi|385805872|ref|YP_005842270.1|  [L=319]
Description: DNA-cytosine methyltransferase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-42  145.3   0.0    1.9e-28   99.8   0.0    2.0  2  DNA_methylase    C-5 cytosine-specific DNA methylase
     0.0027   17.3   0.0     0.0045   16.6   0.0    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase


Domain annotation for each model (and alignments):
>> 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 !   99.8   0.0   2.1e-32   1.9e-28       2     165 ..       7     181 ..       6     229 .. 0.81
   2 !   44.0   0.0     2e-15   1.8e-11     279     332 ..     254     314 ..     207     317 .. 0.79

  Alignments for each domain:
  == domain 1  score: 99.8 bits;  conditional E-value: 2.1e-32
                                       EEEEES-TT-HHHHHHHHTT-EEEEEEE--TTTHHHHHHH-...-SEEEES-TTTS-....GS--.-SEEEE---GG CS
                     DNA_methylase   2 kfidLfaGiGGfrlgleaagfecvaaseidkkaaktYeanfk..kvsigDitkidkk....klpediDlLvgGfPCq 72 
                                       +++dLf+G GGf+ g++ +gf++ +a++++k++a tY+ nf    v+ +Di++++ k     l    D+++g++PC 
  gi|385805872|ref|YP_005842270.1|   7 TVVDLFCGGGGFSRGFHDVGFKVKIAIDNEKNVARTYKYNFLetIVIAEDIKEVSGKdildALGRAPDIVIGSPPCE 83 
                                       79****************************************988999*********666544445*********** PP

                                       GTECTSE.......E--TTSGGGHHHHHHHHHHHHH--SEEEEEEEGGGGGGCCSHHHHHHHHHHHHHTEE.EEEEE CS
                     DNA_methylase  73 pfSvaGk.......qkgfedtrgtLffeiiriikekkPkvfllENVkgLlkhdkgktlkvilekleelGYe.vsykl 141
                                       p+  a k        +   d+ g L+  + ri+ e kP + ++ENV+ +l+   + +l+   ++ e  GY+ +++++
  gi|385805872|ref|YP_005842270.1|  84 PYTAANKkrmnkplDRLYSDPMGILTLSFFRIVGELKPSIWIMENVPAILEDGLKDALE---KEAERSGYKeIYFNI 157
                                       ******94444444444568888***************************995544444...4556789*5489*** PP

                                       EEGGGTT-SB--EEEEEEEEEGGG CS
                     DNA_methylase 142 lnasdyGvpQnReRvfivgirkdl 165
                                       l+a++y +p +R R+fi  i+ + 
  gi|385805872|ref|YP_005842270.1| 158 LKAEEYCTPSKRTRIFISNIEIKP 181
                                       *****************8886543 PP

  == domain 2  score: 44.0 bits;  conditional E-value: 2e-15
                                       T........TTGGG--B-BHHHHHHHHT--TT-----SBHHHHHHHHTS--HHHHHHHHHH CS
                     DNA_methylase 279 p.......viekkriRrLtprEaarlqGfPddfefgskksaaykqiGnsVpvpvieaiake 332
                                       p       +++++++R +t+rE arl+G+Pd+  f + k ++y +iG+sVp+++ +aia  
  gi|385805872|ref|YP_005842270.1| 254 PtvlgssrFLHPEENRLITVREQARLMGYPDEHVFLGGKDEQYNMIGESVPPTLSKAIAAF 314
                                       1344444489************************************************975 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 !   16.6   0.0   5.1e-07    0.0045       3      80 ..       7      81 ..       5      98 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.1e-07
                   Methyltransf_15  3 vilDlfsGaGGnviqfalv.fekviaieinleklacaqhN.aevYgvsdkitlvlg.dvfellaklklekikvdlvflS 78
                                      +++Dlf+G+GG +  f  v f+  iai+ +++     + N  e   +++ i+ v g d++++l +        d+v+ S
  gi|385805872|ref|YP_005842270.1|  7 TVVDLFCGGGGFSRGFHDVgFKVKIAIDNEKNVARTYKYNfLETIVIAEDIKEVSGkDILDALGR------APDIVIGS 79
                                      589***************97777799998887776666663455556666766666223332222......35677777 PP

                   Methyltransf_15 79 pP 80
                                      pP
  gi|385805872|ref|YP_005842270.1| 80 PP 81
                                      77 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1961.88
//
Query:       gi|385805873|ref|YP_005842271.1|  [L=354]
Description: glycerol dehydrogenase [Fervidicoccus fontis Kam940]
Scores for complete 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-68  229.1   0.2    9.3e-68  228.6   0.2    1.2  1  Fe-ADH_2      Iron-containing alcohol dehydrogenase
    2.4e-28   99.0   0.2    2.7e-27   95.5   0.2    1.9  1  Fe-ADH        Iron-containing alcohol dehydrogenase
    3.9e-09   36.1   0.0    0.00065   18.9   0.0    2.8  2  DHQ_synthase  3-dehydroquinate synthase
    0.00016   21.2   0.1    0.00094   18.8   0.0    2.1  2  AIRC          AIR carboxylase
  ------ inclusion threshold ------
      0.029   13.7   0.1      0.057   12.7   0.0    1.5  2  PFK           Phosphofructokinase


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 !  228.6   0.2   2.6e-71   9.3e-68       3     250 .]      17     275 ..      15     275 .. 0.87

  Alignments for each domain:
  == domain 1  score: 228.6 bits;  conditional E-value: 2.6e-71
                          Fe-ADH_2   3 gegaleklgellk...elelkkvllvadentkkaagekveeslkeagikvevveeveeeadleeveklvealreket 76 
                                       g++ l+++ ++l    ++++kkv +v++ ++++++g+k+ee lk++++++  + +++e++++ee++++++ ++ k++
  gi|385805873|ref|YP_005842271.1|  17 GKDLLKDIIQYLPlnlSKNIKKVYVVTGPHVWDTYGKKLEEGLKSKELELY-I-KKSESPTIEEAKQIISDAKGKSI 91 
                                       555555555555311145689*************************88875.4.4799******************* PP

                          Fe-ADH_2  77 dlvvavGgGtiiDiakyvsaklnvpyvsvpTaaSvDGfaspgaslvvdgkkrtvakaaaPlaviaDldvlaeAPrrl 153
                                       dl+++ GgG+ iD+aky++++  +p++s+pT+aS+DG+asp+asl+  g  ++v ka  P++viaDl++++ +Pr+l
  gi|385805873|ref|YP_005842271.1|  92 DLIIGFGGGKSIDLAKYAASQISIPFISIPTSASHDGIASPFASLKGGGWSTSV-KAVEPICVIADLEIISSSPRKL 167
                                       *****************************************************9.9********************* PP

                          Fe-ADH_2 154 lasGvGDllgkytaladwklan........evseplaklsaamvqeaaeklvedkketealeelleal.....alsg 217
                                       l +G GD+++k+ta+ dw+la+        ++++ l++lsa+++ +  + + +   ++ea++ +leal     a+++
  gi|385805873|ref|YP_005842271.1| 168 LIAGAGDAIAKLTAVSDWRLAHllrneyygSYAAGLSLLSAKHIIKYSDIISK--TDVEATRIVLEALisssvAIGI 242
                                       **********************9999888888999999999999988887775..4444444444443333358999 PP

                          Fe-ADH_2 218 igisrpaSGsEHliSHaldmlalkqalHGeqVG 250
                                       +g++rpaSGsEHl+SHald++a+k+alHGeq G
  gi|385805873|ref|YP_005842271.1| 243 AGSTRPASGSEHLFSHALDKIAPKPALHGEQTG 275
                                       999****************************87 PP

>> Fe-ADH  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.5   0.2   7.6e-31   2.7e-27       3     345 ..      13     324 ..      12     342 .. 0.80

  Alignments for each domain:
  == domain 1  score: 95.5 bits;  conditional E-value: 7.6e-31
                                       EEEEETTGGGGHHHHHTTT...-..EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HHHHHHHHTT CS
                            Fe-ADH   3 rivfgkgaleelgellkkl...gakralivtdkgslkksglldkvlesleeagievtvfdgvepnptleeveeaaal 76 
                                       r+v+gk+ l+++ ++l      ++k++++vt++ ++ ++ + +k++e l+++  e++++ + ++ pt+ee +++++ 
  gi|385805873|ref|YP_005842271.1|  13 RVVIGKDLLKDIIQYLPLNlskNIKKVYVVTGPHVW-DT-YGKKLEEGLKSK--ELELYIKKSESPTIEEAKQIISD 85 
                                       7888888888888888432333579***********.55.99*******555..555556889************** PP

                                       S-TT.--EEEEEESHHHHHHHHHHHHHTT..................--EEEEESS-S-S-TT-SEEEEE.-TTSEE CS
                            Fe-ADH  77 areegadvviavGGGsviDtAKaialllanpevedylgegkakkkkalpliaiPTtaGtGsevtplavitdeeegek 153
                                       a+ + +d++i++GGG++iD+AK++a  ++                  +p+i iPT a+ +  ++p+a +     g  
  gi|385805873|ref|YP_005842271.1|  86 AKGKSIDLIIGFGGGKSIDLAKYAASQIS------------------IPFISIPTSASHDGIASPFASLK----GGG 140
                                       *****************************..................***********************....445 PP

                                       EEE-..SS--SEEEEEHHHHHHS-HHHHHHHHHHHHHHHHHHHHHH........T---TTSSB--HHHHHHHHHHHH CS
                            Fe-ADH 154 lsifdpellPdlaivDpeltltlPkrvtaatglDalahalEayvsk........kanplsdalaleairliaknler 222
                                       +s + + + P ++i D e++ + P+++++a+++Da+a+       +            +  +l+l +++ i+k+ + 
  gi|385805873|ref|YP_005842271.1| 141 WSTSVKAVEPICVIADLEIISSSPRKLLIAGAGDAIAKLTAVSDWRlahllrneYYGSYAAGLSLLSAKHIIKYSDI 217
                                       7777779*******************************987744444455444455567778888888899988888 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHSS---.....HHHHHHHHHHC.CGGGGGS-HHHHHHHHH..........HH CS
                            Fe-ADH 223 avadgedleareqmllastlaglafsnaglg.....avHalahalgalfgiphglanaillpavlrfnaeaaperla 294
                                       + +   d ea + +l+a + + +a++ ag +       H ++hal ++  +p+ +++++    ++          + 
  gi|385805873|ref|YP_005842271.1| 218 ISKT--DVEATRIVLEALISSSVAIGIAGSTrpasgSEHLFSHALDKI--APKPALHGEQTGVGT--------IMMS 282
                                       8766..899999999999999999988888777777999999999993..667777777777777........2355 PP

                                       HHHHT.......T--HHHHHHHHHHHHHTT---SHHHHT-TT-...HHHHHHHH CS
                            Fe-ADH 295 qlaralggesdeeaaeeliealrellkelglptsLselgvdee...dldklaea 345
                                       +l r+              +++r++lk++g+pt+ +elg++e+   ++ ++a++
  gi|385805873|ref|YP_005842271.1| 283 KLHRM------------NWKKVRRVLKKVGAPTTAKELGIPENiiiEALTIAHK 324
                                       66666............4568999999999999999999999643333555555 PP

>> DHQ_synthase  3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   9.1e-06     0.033      15      65 ..      75     123 ..      67     128 .. 0.84
   2 !   18.9   0.0   1.8e-07   0.00065      94     248 ..     149     312 ..     146     326 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.1e-06
                                       HHHHHHHHHHHTT--TT-EEEEEESHHHHHHHHHHHHHBTT--EEEEEE-S CS
                      DHQ_synthase  15 tlekildalleakleRksllialGGGvvgDlaGfvAatylRGvrfvqvPtt 65 
                                       t+e+  + + +ak +  +l+i +GGG   Dla ++A+     + f+ +Pt+
  gi|385805873|ref|YP_005842271.1|  75 TIEEAKQIISDAKGKSIDLIIGFGGGKSIDLAKYAASQIS--IPFISIPTS 123
                                       556666777777788889*******************886..********8 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 1.8e-07
                                       --SEEEEEGGGGGGS-HHHHHHHHHHHH.HHHHHT-HHHHHHHHHHHHHHHC.......................TT CS
                      DHQ_synthase  94 qPkavlidlevLktLperelraGlaEvi.Kyalikdeelfelleenaeallk.......................ee 146
                                       +P +v++dle++++ p++ l+aG +++i K ++++d +l +ll+++   + +                       e 
  gi|385805873|ref|YP_005842271.1| 149 EPICVIADLEIISSSPRKLLIAGAGDAIaKLTAVSDWRLAHLLRNEYYGSYAaglsllsakhiikysdiisktdvEA 225
                                       6999********************9965599************9999888778888888776666666553222211 PP

                                       THHHHHHHHHHHHHHHHHHHHHCCTTTTGGGGGGTTHHHHHHHHHHHTTTTS-HHHHHHHHHHHHHHHHHHTTSS-H CS
                      DHQ_synthase 147 eeealeeliarsievkaevveeDekekglralLnlGHtigHaiEallgyekllHGeaVaiGmvlaaelseklgllkk 223
                                       ++ +le+li++s+++            ++r +    H ++Ha+++++     lHGe   +G ++  +l +       
  gi|385805873|ref|YP_005842271.1| 226 TRIVLEALISSSVAIG--------IAGSTRPASGSEHLFSHALDKIAPK-PALHGEQTGVGTIMMSKLHRM------ 287
                                       1122222222222221........235667777888**********988.9*************9999843...... PP

                                       HHHHHHHHHHHHTT---STTTT..-H CS
                      DHQ_synthase 224 eeverllkllkklglpvslkel.lev 248
                                        + ++++++lkk+g p++ kel +  
  gi|385805873|ref|YP_005842271.1| 288 -NWKKVRRVLKKVGAPTTAKELgIPE 312
                                       .4678999*********999884333 PP

>> AIRC  AIR carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   2.6e-07   0.00094      39      95 ..      75     131 ..      49     140 .. 0.87
   2 ?   -1.0   0.0      0.34   1.2e+03      56      70 ..     166     181 ..     157     184 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.6e-07
                                       SHHHHHHHHHHCHTTTEEEEEEEEES.S--HHHHHHHHSSS-EEEEEE--STTCCHHH CS
                              AIRC  39 tpeelleyaeeaeerglkviIagAGg.aahLpgvvaslttlPVigvPvkskalkglds 95 
                                       t ee ++++++a+ + ++ iI   Gg + +L+   as+ ++P i++P+++ + +g+ s
  gi|385805873|ref|YP_005842271.1|  75 TIEEAKQIISDAKGKSIDLIIGFGGGkSIDLAKYAASQISIPFISIPTSA-SHDGIAS 131
                                       6789999**************98888799*******************99.5566655 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.34
                                       EEEEEEEESS.--HHH CS
                              AIRC  56 kviIagAGga.ahLpg 70 
                                       k +IagAG a a+L+ 
  gi|385805873|ref|YP_005842271.1| 166 KLLIAGAGDAiAKLTA 181
                                       789*****95367765 PP

>> PFK  Phosphofructokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.6e-05     0.057      68     133 ..      68     127 ..      49     148 .. 0.86
   2 ?   -3.6   0.0       1.5   5.4e+03      41      63 ..     278     300 ..     271     304 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.6e-05
                                       ----GGGGSHHHHHHHHHHHHHHT--EEEEEESHHHHHHHHHHHHT..T....--EEEEEEETT-- CS
                               PFK  68 saRskefkeregrkkaaenlkklgidaLvviGGdgslkganklseerkglleelkivgiPkTidND 133
                                        ++s++  + e+ k++++  k + id ++  GG +s++ a+  +++  +    ++++ iP + + D
  gi|385805873|ref|YP_005842271.1|  68 IKKSESP-TIEEAKQIISDAKGKSIDLIIGFGGGKSIDLAKYAASQI-S----IPFISIPTSASHD 127
                                       4555554.45669****************************999997.8....********99887 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.5
                                       HHHTT-EEEE-SGGGTT-TT--S CS
                               PFK  41 GlieeeiekltledvsgilsegG 63 
                                        ++ ++++++++++v+ +l++ G
  gi|385805873|ref|YP_005842271.1| 278 TIMMSKLHRMNWKKVRRVLKKVG 300
                                       44556777888888888887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2265.31
//
Query:       gi|385805874|ref|YP_005842272.1|  [L=263]
Description: short-chain dehydrogenase/reductase SDR [Fervidicoccus fontis Kam940]
Scores for complete 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-48  164.3   0.0    4.3e-48  163.9   0.0    1.1  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
    4.1e-35  121.0   0.0      5e-35  120.7   0.0    1.1  1  adh_short     short chain dehydrogenase
    6.2e-07   29.5   0.0    1.6e-06   28.1   0.0    1.6  2  KR            KR domain
  ------ inclusion threshold ------
      0.011   15.1   0.0      0.015   14.7   0.0    1.1  1  DUF1776       Fungal family of unknown function (DUF1776)
      0.038   13.9   0.0      0.074   12.9   0.0    1.4  1  3HCDH_N       3-hydroxyacyl-CoA dehydrogenase, NAD binding do
      0.071   13.2   0.0       0.16   12.1   0.0    1.6  1  Med28         Mediator complex subunit 28


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 !  163.9   0.0   1.4e-51   4.3e-48       4     233 ..      18     259 ..      14     260 .. 0.93

  Alignments for each domain:
  == domain 1  score: 163.9 bits;  conditional E-value: 1.4e-51
                                       TSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSEE..EE--TTSHHHHHHHHHHHHHHHSSEEEEEE-- CS
                      adh_short_C2   4 sgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgaev..lecDVtdeeqvealveevvekfgklDilvnna 77 
                                       +gIG++iAk l e+Ga+vv+  ++ee+  k++e+l+  +++++  + +D++++++  +lv+e ++++g+lD lv   
  gi|385805874|ref|YP_005842272.1|  18 RGIGFGIAKVLLENGAKVVINGRSEEGvIKAIEKLQYPYKNNAkgIVADISNKDEAIRLVKESAKSLGGLDSLVYVT 94 
                                       9**************************99**********988778******************************** PP

                                       ---EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC..CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHH CS
                      adh_short_C2  78 giapklkgpfletsreefdraldvnlyslfllakaalplmkeg..gsivnlssvgaervvpnynaygaaKaalealt 152
                                       g  ++  g f e++ +++++ ++  ++s++ lak+ +p +ke+   s++ l+s++ +  +pn +  ++ + ++++l+
  gi|385805874|ref|YP_005842272.1|  95 GPPKP--GYFNELNYDDWEEGVNLLINSAIVLAKESIPFLKESknPSMIFLTSIAVKEPIPNIALSNVLRISVHGLV 169
                                       *****..*******************************8887768******************************** PP

                                       HHHHHHHGGGTEEEEEEEE--BHCTGGGGSTT.........HHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGT CS
                      adh_short_C2 153 rylAvelgpkgiRvNavspgpikTlaasgikg.........fdelleelearaplgrlgtpeevaeaalfLasdeas 220
                                       ++l +el++++iRvNav pg i+T+ + ++++          +e+l+ + +++plgrlg+pee++ +++fL+s+ +s
  gi|385805874|ref|YP_005842272.1| 170 KTLSKELARYKIRVNAVLPGHIETERSLQLASdrakrenrtIEEVLNDMTKEIPLGRLGKPEEIGYTVAFLISPYSS 246
                                       ************************875444432333344445679999***************************** PP

                                       T--SEEEEESTTG CS
                      adh_short_C2 221 yitGqtlvvDgGl 233
                                       yitG+ + vDgG+
  gi|385805874|ref|YP_005842272.1| 247 YITGAFIPVDGGV 259
                                       ************7 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.7   0.0   1.7e-38     5e-35       2     190 ..      10     199 ..       9     204 .. 0.97

  Alignments for each domain:
  == domain 1  score: 120.7 bits;  conditional E-value: 1.7e-38
                                       EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT.TSEEEEEE-TTTSHHHHHHHHHHHHHHHSS CS
                         adh_short   2 vvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee.gakalaiqvDvtdreevealvekavkklgk 77 
                                        vlvt  ++GIG  iak l+++Gakvv+ +rsee + +++++l+   +++a  i +D+++++e+ +lv++ +k lg+
  gi|385805874|ref|YP_005842272.1|  10 KVLVTASTRGIGFGIAKVLLENGAKVVINGRSEEGVIKAIEKLQYPyKNNAKGIVADISNKDEAIRLVKESAKSLGG 86 
                                       69******************************************999****************************** PP

                                       ESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHH CS
                         adh_short  78 ldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKa 154
                                       ld Lv  +G  ++g f+el+ ++we+ +++ +++++ l+++ +p ++++++ + ++ +S+a k+p ++ a       
  gi|385805874|ref|YP_005842272.1|  87 LDSLVYVTGPPKPGYFNELNYDDWEEGVNLLINSAIVLAKESIPFLKESKNPSMIFLTSIAVKEPIPNIALSNVLRI 163
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHH CS
                         adh_short 155 avagltrslakelaptgirvnavaPGlvdTdmakel 190
                                        v+gl+++l+kela+++irvnav PG ++T+   +l
  gi|385805874|ref|YP_005842272.1| 164 SVHGLVKTLSKELARYKIRVNAVLPGHIETERSLQL 199
                                       ******************************976655 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   5.4e-10   1.6e-06       3     119 ..      11     124 ..       9     148 .. 0.86
   2 ?   -1.7   0.0      0.76   2.3e+03      43      85 ..     171     214 ..     162     217 .. 0.75

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 5.4e-10
                                       EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHT.T-EEEE----TT-HHHHHHHHHHHHHH CS
                                KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaeleal.gaevevvaaDvsdkdavealleeikae 78 
                                       +l+t  + g+G  +a+ l+e+ga+ +v+ +Rs   +e   + i++l+     + + + aD+s+kd+  +l++e  ++
  gi|385805874|ref|YP_005842272.1|  11 VLVTASTRGIGFGIAKVLLENGAK-VVINGRS---EEGVIKAIEKLQYPyKNNAKGIVADISNKDEAIRLVKESAKS 83 
                                       69999*****************96.7899***...56777799999986599************************* PP

                                       SS---EEEE---------TTT--HHHHHHHHTTTTHHHHHH CS
                                KR  79 eppikGvihaAgvlrdklleemtaedleqvlapKvkGawnL 119
                                        + +   +   g  + + ++e++ +d+e+ ++  ++ a +L
  gi|385805874|ref|YP_005842272.1|  84 LGGLDSLVYVTGPPKPGYFNELNYDDWEEGVNLLINSAIVL 124
                                       ***************************99877666655555 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.76
                                       HHHHHHHHTT-EEE.E----TT-HHHHHHHHHHHHHHSS---EE CS
                                KR  43 aliaelealgaeve.vvaaDvsdkdavealleeikaeeppikGv 85 
                                       +l +el+++ ++v+ v++  +  + +++ + +++k+e+++i+ v
  gi|385805874|ref|YP_005842272.1| 171 TLSKELARYKIRVNaVLPGHIETERSLQLASDRAKRENRTIEEV 214
                                       55677788888886245788888888888888888888888777 PP

>> DUF1776  Fungal family of unknown function (DUF1776)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   4.9e-06     0.015     106     203 ..     100     194 ..      66     218 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.9e-06
                           DUF1776 106 gpietiplsswaselnerllspiltlqallplltsrakqkakiivvnpsissslnlpfhapEalvssalsalfevLk 182
                                       g ++++  + w++ +n  + s i++ ++ +p l++    k   +++ +si  +  +p+ a+  ++  +++ l+++L+
  gi|385805874|ref|YP_005842272.1| 100 GYFNELNYDDWEEGVNLLINSAIVLAKESIPFLKE---SKNPSMIFLTSIAVKEPIPNIALSNVLRISVHGLVKTLS 173
                                       44889999********88888999999*******8...45555566789**************************** PP

                           DUF1776 183 relrphnidvtqikLGnldla 203
                                       +el++++i v  +  G ++  
  gi|385805874|ref|YP_005842272.1| 174 KELARYKIRVNAVLPGHIETE 194
                                       **********99988877764 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.5e-05     0.074      10      68 ..      20      78 ..      19      91 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.5e-05
                                      CHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEE CS
                           3HCDH_N 10 mGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalaris 68
                                      +G gia+v++++g +Vv+  +see + ka ek++  +++ ++   ++ ++ ++a+  ++
  gi|385805874|ref|YP_005842272.1| 20 IGFGIAKVLLENGAKVVINGRSEEGVIKAIEKLQYPYKNNAKGIVADISNKDEAIRLVK 78
                                      799*******************************9888887766666666666666555 PP

>> Med28  Mediator complex subunit 28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   5.2e-05      0.16      30      83 ..     158     208 ..     141     223 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.2e-05
                             Med28  30 rneLsasvsdlkkelerkaekykvapeellmkHlqktseqlatqlkalrekgqn 83 
                                       +n L +sv+ l k+l ++  +yk+  +++l  H++    + + ql + r k +n
  gi|385805874|ref|YP_005842272.1| 158 SNVLRISVHGLVKTLSKELARYKIRVNAVLPGHIET---ERSLQLASDRAKREN 208
                                       677888****************************99...667788888877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); 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: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 1752.03
//
Query:       gi|385805875|ref|YP_005842273.1|  [L=641]
Description: asparagine synthetase [Fervidicoccus fontis Kam940]
Scores for complete 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-67  228.8   0.0    1.9e-67  228.4   0.0    1.1  1  Asn_synthase  Asparagine synthase
    9.3e-41  138.6   0.0    1.5e-40  138.0   0.0    1.3  1  GATase_7      Glutamine amidotransferase domain
      6e-35  120.4   0.0    9.8e-35  119.7   0.0    1.3  1  GATase_6      Glutamine amidotransferase domain
      0.003   17.0   0.1     0.0061   16.0   0.1    1.4  1  DUF3700       Aluminium induced protein


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 !  228.4   0.0   4.3e-71   1.9e-67       2     354 ..     267     631 ..     266     632 .. 0.87

  Alignments for each domain:
  == domain 1  score: 228.4 bits;  conditional E-value: 4.3e-71
                      Asn_synthase   2 lrelLedaVkrrlradvpvGalLSGGlDSSliaalaarqsk...........splktFsigfee.kgsdeakyakev 66 
                                       ++e ++++V  +lr+dvp+G+  SGG+DS++++++ +++++           +++k F ++ +e  + de++ a++ 
  gi|385805875|ref|YP_005842273.1| 267 WKEKFAESVSLHLRSDVPLGFEVSGGIDSTSLVSISKEMLEksvvkergfdlKNIKLFNVKIKEnVKIDESSIAEKF 343
                                       5799**********************************************************76799********** PP

                      Asn_synthase  67 aehlgte..htelvlteeelldalpdviyhleepfadrsaiplyllsrlakrkgvkvvLsGeGaDElfgGYpyfyka 141
                                       ae+lg++   +e+ ++++++l++l+++iy+ eep  + s i  ++ls++a +k+vkv+L G+G+DEl gGY+  y +
  gi|385805875|ref|YP_005842273.1| 344 AEYLGLKdnLIEISVSPQDFLSELEKIIYFEEEPPEGLSPILHWFLSKEA-SKHVKVLLNGQGGDELLGGYH-AYIP 418
                                       *******7779******************999999***************.888******************.8988 PP

                      Asn_synthase 142 alsrsrefeklplarslrasllarklrklaellelaeardleelaelyrlkasdsae..........aelegedelh 208
                                       +++++       l+++   s +++ ++    ++   +a+++   +++y +k ++             +  ++ + l+
  gi|385805875|ref|YP_005842273.1| 419 LYIKEV------LRKKGVISAIKETWKLRYYIFD--KAKYA---LKVYIGKRESLGMsllgkdlkmhNSRDSISILN 484
                                       877532......3456666677777777776666..22222...234444444433366677775556667778899 PP

                      Asn_synthase 209 relyldlktllpgdllrk.DrasmahglEaRvPflDhrlvevalrlppelklrggieKyiLRealegylPeeileRp 284
                                       ++ly dl+      +lr  Dr smah++E RvP++ h l+e+ l++p +lk+r+g +K+i R+a+eg++P++il+ +
  gi|385805875|ref|YP_005842273.1| 485 EALYKDLTGGRLAEILRVeDRNSMAHSIEIRVPYINHILAEFTLSMPEDLKIRNGYTKWIHRKAMEGLVPKDILWSK 561
                                       ****************999*********************************************************9 PP

                      Asn_synthase 285 .Kegfsapvgewklkgelrelaeellsdsrlakeglldreaveelleehea..gkrnesrqlwslllsleawl 354
                                        K gf+ap +ew +   l++   e ls+s l k g+l+++av+ l+++ e+    r+ sr  w +   le w+
  gi|385805875|ref|YP_005842273.1| 562 kKLGFQAPEYEWLI--LLKKNFIEVLSNSELVKDGFLKADAVRGLIKNVEKekIDRELSRFYWRVF-LLEVWY 631
                                       99**********55..6*****************************99999333344445555555.777776 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.0   0.0   3.3e-44   1.5e-40       2     122 ..      75     192 ..      74     193 .. 0.96

  Alignments for each domain:
  == domain 1  score: 138.0 bits;  conditional E-value: 3.3e-44
                          GATase_7   2 rrlsi.idseagaQPmvssedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllalleaewgeealerlnGm 77 
                                       rrlsi + se+g+QP++    +++++v nGeiyNy+e+r+eLe+kg++f ++sDtev l+++++ + +eal+++ Gm
  gi|385805875|ref|YP_005842273.1|  75 RRLSIiDVSEKGHQPLFF---ENFALVLNGEIYNYREIRRELEDKGYNFYGDSDTEVALKAIAEYGFDEALKKFIGM 148
                                       89**977799*******4...89****************************************************** PP

                          GATase_7  78 fAfaiwdeeekrlllaRDrlGikPLyygedkgdallfaSelkall 122
                                       fA++++d+++++l+ aRDr+GikPL+y++d+ ++++faSe+k +l
  gi|385805875|ref|YP_005842273.1| 149 FAVLVYDKAKNTLYGARDRFGIKPLFYYNDE-ENFYFASEIKGFL 192
                                       ******************************7.7*********875 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.7   0.0   2.2e-38   9.8e-35      11     134 .]      67     187 ..      51     187 .. 0.95

  Alignments for each domain:
  == domain 1  score: 119.7 bits;  conditional E-value: 2.2e-38
                          GATase_6  11 edevalaHvRlaivglaeeegaqPfpsedgrlllvhNGeiynykelreelpalkglafrsrsDtevllalleelG.e 86 
                                       +++vala +Rl+i++ + e+g+qP+    ++++lv NGeiyny+e+r+el++ kg++f ++sDtev l++++e+G +
  gi|385805875|ref|YP_005842273.1|  67 KAKVALANRRLSIIDVS-EKGHQPL--FFENFALVLNGEIYNYREIRRELED-KGYNFYGDSDTEVALKAIAEYGfD 139
                                       4469************9.*******..999**********************.************************ PP

                          GATase_6  87 evlerlrGmfafaiwdkrentlilardrlgvkplyyavdesglafase 134
                                       e+l+++ Gmfa+ ++dk++ntl  ardr+g+kpl+y  de++++fase
  gi|385805875|ref|YP_005842273.1| 140 EALKKFIGMFAVLVYDKAKNTLYGARDRFGIKPLFYYNDEENFYFASE 187
                                       ***********************************************8 PP

>> DUF3700  Aluminium induced protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   1.4e-06    0.0061     116     162 ..     132     178 ..     127     190 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.4e-06
                           DUF3700 116 drgPypadqvvkdleGkfafvlydskaktvfvaldadgsvplyWGia 162
                                         + y  d+ +k++ G fa ++yd+ ++t++ a+d+ g  pl++  +
  gi|385805875|ref|YP_005842273.1| 132 AIAEYGFDEALKKFIGMFAVLVYDKAKNTLYGARDRFGIKPLFYYND 178
                                       55779999*********************************998655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (641 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); 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: 0.67u 0.26s 00:00:00.93 Elapsed: 00:00:00.46
# Mc/sec: 4223.03
//
Query:       gi|385805876|ref|YP_005842274.1|  [L=363]
Description: major facilitator superfamily protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-14   53.6  45.5    3.2e-07   29.6  19.8    2.0  2  MFS_1     Major Facilitator Superfamily


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6  19.8   1.8e-11   3.2e-07      37     185 ..      26     178 ..      13     212 .. 0.71
   2 !   25.9  23.3   2.4e-10   4.3e-06       6     169 ..     197     356 ..     192     362 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 1.8e-11
                             MFS_1  37 lltlyalgaavaslplGrlsdrfGrrrvlllglllfalg..lllll..fa.sslw.lllvlrvlqGlgagalfpaga 107
                                       +l++  l+a ++  + G l++++ + ++l++  ++  ++  ++  +  +a s+ w + ++l +l  +g g+  p+  
  gi|385805876|ref|YP_005842274.1|  26 MLSIGELLAYLFRAFSGILVTKYRSSSFLWFLTITGYVTnlAV--IplLAiSGNWiIAFILYMLERIGKGLRGPSRD 100
                                       56777788999************55556666555555553222..23356899999********************* PP

                             MFS_1 108 aliadwfpkeergraigllsagfslGailgpllgg.llasslgWravfyilaivsllafvlfllllpeepperkrks 183
                                       ++++++ ++   g+++g+     +lGa+ gpl+ + +la ++g+ +++++lai + +a+ l++  +   +p+ + + 
  gi|385805876|ref|YP_005842274.1| 101 IILSELIKGLGSGKGFGIHEFLDQLGAVSGPLIVAyYLAGHGGFYYAYLFLAIPATIAIALVFSAM-IQYPKIESVH 176
                                       ******************************766552777*******************88644444.3333333332 PP

                             MFS_1 184 pk 185
                                       + 
  gi|385805876|ref|YP_005842274.1| 177 TD 178
                                       22 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 2.4e-10
                             MFS_1   6 flsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa 82 
                                       ++ +  +++ + +++  ++ + gi ++ + +l++l +++ a+ ++plG l d++G + ++ + +++ ++  +lllf 
  gi|385805876|ref|YP_005842274.1| 197 IFLISVSFTQWGIISYRITLE-GIGAQYAAILYVLAMAADAAVAIPLGMLFDKYGVKTIYPIPIISIFSN-ILLLF- 270
                                       444444445555555533444.566777899999999999**************************9999.77777. PP

                             MFS_1  83 sslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyila 158
                                        ++  ll+++ +l G  +g + ++  a++a+++++ + + ++g++s+  ++++ +g ++ ++++  ++ +a+   + 
  gi|385805876|ref|YP_005842274.1| 271 ENSLfLLFLGSILWGTVTGYYESVFRAAVAELAKE-DVAGGFGVYSLVQGIAMGIGGIIIAVFY-IVSKSALIDYII 345
                                       55555****************************99.*************************999.666555555555 PP

                             MFS_1 159 ivsllafvlfl 169
                                       ++ l+a+++f+
  gi|385805876|ref|YP_005842274.1| 346 ALNLIAMLFFA 356
                                       55555555433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); 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:                         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: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2395.04
//
Query:       gi|385805877|ref|YP_005842275.1|  [L=235]
Description: Mn2+-dependent serine/threonine protein kinase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score 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   15.2   0.1      0.021   14.2   0.1    1.5  1  Kdo       Lipopolysaccharide kinase (Kdo/WaaP) family


Domain annotation for each model (and alignments):
>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   1.2e-06     0.021     118     186 ..     110     173 ..      88     185 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.2e-06
                               Kdo 118 elkrallkavgrliaklhragvnHadlyaknillqqeeeeeaeiwliDldkarlrlradrwrekdLarL 186
                                        + ++ l +vg +  ++h+ + + +d  ++n+l+ +e+     +++iD +++ +  +++  +  dLa L
  gi|385805877|ref|YP_005842275.1| 110 LKSQEDLYRVGVALGNIHNKDFCLGDTRPQNFLILNED-----MAIIDAEQSTHECKKKETKAWDLALL 173
                                       5678999****************************998.....*************9999999999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        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 0.26s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1572.45
//
Query:       gi|385805878|ref|YP_005842276.1|  [L=246]
Description: hypothetical protein FFONT_0836 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-29  103.6   0.2    1.6e-29  103.5   0.2    1.0  1  PAC2      PAC2 family
  ------ inclusion threshold ------
      0.026   15.0   0.0      0.045   14.2   0.0    1.3  1  ThiD2     ThiD2 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 !  103.5   0.2   1.8e-33   1.6e-29       1     211 [.      15     225 ..      15     227 .. 0.87

  Alignments for each domain:
  == domain 1  score: 103.5 bits;  conditional E-value: 1.8e-33
                                       EEEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETT.EEE-SEEEEEETTT.SEEEEEEE.. CS
                              PAC2   1 LilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveeg.relepprlyakdsgsrdllvlqg.. 74 
                                       Li+Gfpg+ +Vg+ ++d+Li+++++e++ e+ + +  p     ++v+v +g  +  +++ly ++  s +++vl+   
  gi|385805878|ref|YP_005842276.1|  15 LIVGFPGMALVGKATADFLISKMKLEEYVEFFPVQ-SP-----SSVIVMDGiIQPLSIKLYSSS--SLQIAVLTAsf 83 
                                       89****************************99999.89.....899999997666666667554..7********86 PP

                                       .E-HSCHHH..HHHHHHHHHHHHTTESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHHHCT....-CEEEE CS
                              PAC2  75 .repilqye..efakalldwaeelgvkevvvLggldageradvphtrpekvtgaatdeelleelees....eyggiv 144
                                        +  ++     ++a  l + + +lg+++++  +++ + e +     +  kv++aat++e+++el++      +ggi+
  gi|385805878|ref|YP_005842276.1|  84 qP--QGEEAqtALAFDLSKKLVDLGFSKIISAAAYVSPEIK-----NGRKVFVAATNKEFIDELSKVgcvpMNGGIS 153
                                       53..3333344799**********************77653.....3448**************533466688**** PP

                                       HHHHHHHHHHHHTT-EEEEEEEEEEC.CC....--HHHHHHHHHHHHHHHT---HCHHHHHHHHHHHHHHHH CS
                              PAC2 145 gitglLlsaakergipavgllaevph.yl....pdPkaaaalleflskllglevdtedLeedaeeleeqlee 211
                                       g++gl+  +a+++gi++++ll+e+++ y+    +d  a  ++l++ls +l++e+d+edL ++a+ ++e++++
  gi|385805878|ref|YP_005842276.1| 154 GLNGLIPALAEMYGIEGAVLLGETSEvYVasnvVDYMAVGEILRVLSSYLKFEIDLEDLTSKAKDIDEKIKK 225
                                       **************************8878876799*********************************987 PP

>> ThiD2  ThiD2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   5.1e-06     0.045      11      55 ..     193     236 ..     188     244 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.1e-06
                             ThiD2  11 rEGlRvlediarfvlddeelteelkelRhelaelekeleeaella 55 
                                        E lRvl  +++f +d e+lt+++k++  +++++ ++   +e+++
  gi|385805878|ref|YP_005842276.1| 193 GEILRVLSSYLKFEIDLEDLTSKAKDIDEKIKKAMEK-GFQEVAE 236
                                       588******************************9999.4455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       985  (0.0549389); expected 358.6 (0.02)
Passed bias filter:                      676  (0.0377043); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1723.77
//
Query:       gi|385805879|ref|YP_005842277.1|  [L=441]
Description: Aspartyl-tRNA synthetase [Fervidicoccus fontis Kam940]
Scores for 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-84  284.3   0.7    1.3e-84  284.0   0.7    1.1  1  tRNA-synt_2      tRNA synthetases class II (D, K and N)
    3.1e-14   52.7   1.9    3.1e-14   52.7   1.9    1.6  2  tRNA_anti-codon  OB-fold nucleic acid binding domain
  ------ inclusion threshold ------
      0.029   13.8   1.4        1.5    8.2   0.1    2.6  3  tRNA-synt_2d     tRNA synthetases class II core domain (F)
      0.041   13.3   0.0       0.07   12.6   0.0    1.4  1  DUF1593          Protein of unknown function (DUF1593)
       0.06   13.9   0.8         16    6.1   0.0    2.5  2  TetR_C_19        Tetracyclin repressor-like, C-terminal domai
        0.1   12.8   0.1       0.19   11.9   0.1    1.5  1  tRNA_anti_2      OB-fold nucleic acid binding domain
       0.23   11.1   0.1       0.23   11.1   0.1    1.9  2  YkyA             Putative cell-wall binding lipoprotein


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 !  284.0   0.7   4.9e-88   1.3e-84       3     312 ..     121     434 ..     119     436 .. 0.95

  Alignments for each domain:
  == domain 1  score: 284.0 bits;  conditional E-value: 4.9e-88
                                       CHHHHTHHHHCCSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE....-E CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xx RF
                       tRNA-synt_2   3 elrlknryldlrtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeff....aL 75 
                                       ++rl+ r+ldlr  + + ++ +  ++++a+r+++ +ngfie+ tP +++++te+ga+ F v        +f    +L
  gi|385805879|ref|YP_005842277.1| 121 NVRLDWRFLDLRATRNRLIFVVTDEAVNALREFYRSNGFIEVFTPKIVSEATEGGAEVFPV-------IYFdkpaFL 190
                                       6899*********************************************************.......34444446* PP

                                       -S-SHHHHHHHHHCTHSEEEEEEEEE--S--BTTB-S-CEEEEEEEEET-SCHH.HHHHHHHHHHHHHHHHHHCSCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  76 tqspqlylellivagidrvfqiaraFRaEdsrtdrhlaEFtqieaemsfieeed.imqvleelikslvkevlessak 151
                                       +qspqly++++++ag++rvf++++a+RaE+++t+rhl+E+ ++++emsfi+ ++ +m+++e+ + + +k+v e+  +
  gi|385805879|ref|YP_005842277.1| 191 AQSPQLYKQMMMAAGFERVFEVGPAYRAEKHHTNRHLTEYESVDIEMSFIDSHEdVMKMVENAVIYSIKKVNEKYGS 267
                                       ***************************************************9999****************999999 PP

                                       CCCHTTTTTSEE-SSS-EEEEHHHHHHHHHTS......-SS--HHHHHHHHH....HS--SEEEEEEEBGGGSTTCB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 152 diefvirrnskdlkkpfkrltykeaieklnei......gkdldkaderalvk....keknepvfvtdfPaelkpFya 218
                                        i++   r   +++++ +r+t +ea + l+++       +dld++ er+l +    + +++ +fvt++ +  +pFy+
  gi|385805879|ref|YP_005842277.1| 268 YIKQYFPRIP-EIPSNVPRITLREAHKLLENKgfkqpdPNDLDTEGERLLGEimekEYGSQLFFVTEYSWLYRPFYT 343
                                       9999998876.99999************9999999999899*******99887777999****************** PP

                                       BBSTTSTTBBSEEEEEETTEEEEEEEEB--SHHHHHHHHHHCCHHSSSGGGGHHHHHHHHCT--SEEEEEEEHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 219 rkeeddkkltesyDllingvElvgGslRiedpeeleeklkskgldeeaeekfswylealeyGapphgGlglGldRlv 295
                                        k+ +++ lt+s+Dl+++g E+v+Gs+R+++ ++le+++k+kgl+    ++f+++++ ++yG+pphgG glGl+Rlv
  gi|385805879|ref|YP_005842277.1| 344 MKKPEEPSLTRSFDLIYRGTEIVSGSQREHRADVLENQIKEKGLN---VKNFEFFIKFFRYGMPPHGGAGLGLERLV 417
                                       *********************************************...***************************** PP

                                       HHHCT-SSGGGCSSS-X CS
                                       xxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 296 mlllgsesIrdviaFPk 312
                                       +++lg+++Ir+v + P+
  gi|385805879|ref|YP_005842277.1| 418 QMMLGLKNIREVRLLPR 434
                                       ***************98 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 !   52.7   1.9   1.2e-17   3.1e-14       1      74 [.      23      99 ..      23     101 .. 0.94
   2 ?   -3.9   0.0       5.8   1.5e+04      21      48 ..     129     156 ..     128     164 .. 0.58

  Alignments for each domain:
  == domain 1  score: 52.7 bits;  conditional E-value: 1.2e-17
                                      EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET...HHHHHHHTTS-TTSEEEEEEEEEECTTS..SEEEEEEEEE CS
                   tRNA_anti-codon  1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfr...eeatklaenlkeGdvvrvtGrvkrrpgg..elelkveeie 74
                                      V +aG++ ++  r +g+vifi+lrD++g++q+v+ +   e+ ++ a++l  +dvv ++G+vk+ ++   + e++ve++ 
  gi|385805879|ref|YP_005842277.1| 23 VLIAGWIEAV--RIIGGVIFIVLRDRSGKVQAVIKKnidEKLFNEASELGSEDVVAIKGEVKEAKTSlgDREIVVEKLY 99
                                      779*******..****************************************************888888999999976 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 5.8
                                       EEEEETTEEEEEEEETHHHHHHHTTS-T CS
                   tRNA_anti-codon  21 idlrDgtgriqvvlfreeatklaenlke 48 
                                       +dlr    r+  v+++e++ +l e  + 
  gi|385805879|ref|YP_005842277.1| 129 LDLRATRNRLIFVVTDEAVNALREFYRS 156
                                       5566555666666666666666665555 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 ?   -3.0   0.0       1.6     4e+03      20      45 ..     144     169 ..     140     172 .. 0.78
   2 ?    3.9   0.0     0.013        32     101     129 ..     206     235 ..     192     296 .. 0.79
   3 ?    8.2   0.1    0.0006       1.5     214     234 ..     409     429 ..     401     434 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.6
                                       HHHHHHHHHHHHCTTCEESSTTSEEE CS
                      tRNA-synt_2d  20 tkvleeikeiflelgfeevegpeves 45 
                                       ++ ++ ++e++++ gf ev  p++ s
  gi|385805879|ref|YP_005842277.1| 144 DEAVNALREFYRSNGFIEVFTPKIVS 169
                                       56778899999999999998888765 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.013
                                       SEEEEEEEEEEBSST.-SSSB-SEEEEEEE CS
                      tRNA-synt_2d 101 pikiisigrvfRrda.vDathlaeFhqveg 129
                                         +++ +g ++R ++    +hl e+ +v+ 
  gi|385805879|ref|YP_005842277.1| 206 FERVFEVGPAYRAEKhHTNRHLTEYESVDI 235
                                       5689**********978899*****99864 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0006
                                       EEEEHHHHHHHHHT-SSGHHH CS
                      tRNA-synt_2d 214 fGlGveRlamlkygieDiRel 234
                                        GlG+eRl  +++g+++iRe+
  gi|385805879|ref|YP_005842277.1| 409 AGLGLERLVQMMLGLKNIREV 429
                                       6******************85 PP

>> DUF1593  Protein of unknown function (DUF1593)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.7e-05      0.07     141     182 ..     242     283 ..     235     331 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.7e-05
                                       -HHHHHHHHHTEEEEEES--SH.HHHHHHHH-TTSEEEEE-- CS
                           DUF1593 141 sekelakllsklrvyaisdqDdtagayirknfpdllyiesev 182
                                       s++++ k+++++++y+i + ++++g+yi++ fp++  i s+v
  gi|385805879|ref|YP_005842277.1| 242 SHEDVMKMVENAVIYSIKKVNEKYGSYIKQYFPRIPEIPSNV 283
                                       678899****************************98887774 PP

>> TetR_C_19  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.3    0.0095        24      24      93 ..     195     262 ..     190     274 .. 0.74
   2 ?    6.1   0.0    0.0062        16      48      81 ..     369     402 ..     358     404 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0095
                         TetR_C_19  24 kffkniflnmnykiekkftkefkkkkkker.lkelyelidkskLnieseeelklllkilmavtfqtiveyf 93 
                                       +++k++++   ++   ++ + ++ +k++ + +   ye +d +   i+s+e   +++k++ + ++ +i ++ 
  gi|385805879|ref|YP_005842277.1| 195 QLYKQMMMAAGFERVFEVGPAYRAEKHHTNrHLTEYESVDIEMSFIDSHE---DVMKMVENAVIYSIKKVN 262
                                       78999999999988888888888877777766777777887777776665...567777777777777665 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0062
                         TetR_C_19  48 kkkkerlkelyelidkskLnieseeelklllkil 81 
                                        ++++r + l ++i++++Ln+++ e ++++++  
  gi|385805879|ref|YP_005842277.1| 369 SQREHRADVLENQIKEKGLNVKNFEFFIKFFRYG 402
                                       556666889999*****************99875 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 ?   11.9   0.1   7.5e-05      0.19      10      79 ..      11      82 ..       3      98 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.5e-05
                       tRNA_anti_2 10 ikelleaelkkavwvrGeisnlkrkasghvYftLkDekakisavifrsraaklkft....ledGmkVlvkgrls 79
                                      i ++++++  ++v + G i  + r   g +++ L+D + k++avi ++  +kl  +    l + + V +kg+++
  gi|385805879|ref|YP_005842277.1| 11 IADVFSKNNGEKVLIAGWIEAV-RIIGGVIFIVLRDRSGKVQAVIKKNIDEKLF-NeaseLGSEDVVAIKGEVK 82
                                      667887777788**********.53499******************97776664.3344578888888888875 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   9.1e-05      0.23      34      73 ..      59      98 ..      51     114 .. 0.89
   2 ?   -1.7   0.6      0.75   1.9e+03     104     124 ..     252     272 ..     218     273 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.1e-05
                              YkyA 34 eqelyeeiielgmdefdkikklsdealenveeReelleke 73
                                      +++l++e  elg ++  +ik +++ea +++ +Re  +ek 
  gi|385805879|ref|YP_005842277.1| 59 DEKLFNEASELGSEDVVAIKGEVKEAKTSLGDREIVVEKL 98
                                      689*******************************999984 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.75
                              YkyA 104 eelieameeryeaydklykaY 124
                                       +++i ++++  e+y +++k+Y
  gi|385805879|ref|YP_005842277.1| 252 NAVIYSIKKVNEKYGSYIKQY 272
                                       445555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); 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:                         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 0.32s 00:00:00.96 Elapsed: 00:00:00.52
# Mc/sec: 2560.23
//
Query:       gi|385805880|ref|YP_005842278.1|  [L=214]
Description: hypothetical protein FFONT_0838 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.03   14.7   0.1       0.15   12.4   0.1    2.1  2  FaeA      FaeA-like protein
      0.071   13.3   0.0       0.11   12.7   0.0    1.4  1  DUF4443   Domain of unknown function (DUF4443)


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 ?   12.4   0.1   1.7e-05      0.15       6      44 ..      37      75 ..      35      83 .. 0.89
   2 ?   -1.6   0.0      0.42   3.8e+03      39      56 ..     128     145 ..     126     147 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.7e-05
                                      HHHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSS CS
                              FaeA  6 leylnsikapckTreiAdalglsaYQaRyYLeqLekegk 44
                                      + yl si+ +   ++i   +g s Y +R  L++L+ +  
  gi|385805880|ref|YP_005842278.1| 37 ILYLLSINKSIGRSQISTVFGFSEYYVRRALKCLKDKAY 75
                                      56999*****************************87655 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.42
                                       HHHHSSEEEE--SSSSS- CS
                              FaeA  39 LekegkikrspvrrGvst 56 
                                       L+   +++ s +r G+++
  gi|385805880|ref|YP_005842278.1| 128 LKETVMLRDSAIRWGAEG 145
                                       677889999999999976 PP

>> DUF4443  Domain of unknown function (DUF4443)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.3e-05      0.11      28      68 ..     131     172 ..     107     207 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.3e-05
                           DUF4443  28 sielrdeairffakgamilivkngepvfpede.rplrdtmee 68 
                                       ++ lrd air+ a+g++il   n e  +p  e   +r+ +e+
  gi|385805880|ref|YP_005842278.1| 131 TVMLRDSAIRWGAEGSIILQYCNMETNIPGIEdLSIRNEIEK 172
                                       688***********************9997551467766654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1371.53
//
Query:       gi|385805881|ref|YP_005842279.1|  [L=79]
Description: hypothetical protein FFONT_0839 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.026   15.0   0.3      0.037   14.5   0.3    1.4  1  Fungal_TACC  Fungal Transforming acidic coiled-coil (TACC) pr


Domain annotation for each model (and alignments):
>> Fungal_TACC  Fungal Transforming acidic coiled-coil (TACC) proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.3   2.1e-06     0.037       4      32 ..      23      51 ..      20      76 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.1e-06
                       Fungal_TACC  4 krlqelaedLYvqYSsKHEqKVkllkkgy 32
                                        l+e++e LY +Y  K E K ++lkk+ 
  gi|385805881|ref|YP_005842279.1| 23 DSLEEISEWLYEEYGIKAEPKEEVLKKKI 51
                                      5799**********************974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 514.96
//
Query:       gi|385805882|ref|YP_005842280.1|  [L=417]
Description: DNA/pantothenate metabolism flavoprotein [Fervidicoccus fontis Kam940]
Scores for complete 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-59  199.6   0.4    1.2e-56  191.5   0.1    2.3  2  DFP           DNA / pantothenate metabolism flavoprotein
    4.3e-38  130.5   1.0    5.1e-37  127.1   0.1    2.3  2  Flavoprotein  Flavoprotein


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 !    6.1   0.0   0.00096       8.6      31      53 ..      34      56 ..      23      75 .. 0.82
   2 !  191.5   0.1   1.3e-60   1.2e-56       2     186 .]     194     382 ..     193     382 .. 0.94

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.00096
                                      HHHHHHHHHHHTT-EEEEEE-S- CS
                               DFP 31 mGyalAeaaaarGaeVtlvsgpv 53
                                        + lA+ +++ GaeVt+v ++ 
  gi|385805882|ref|YP_005842280.1| 34 KSIDLARTLMKNGAEVTVVMSSE 56
                                      5678***************9874 PP

  == domain 2  score: 191.5 bits;  conditional E-value: 1.3e-60
                                       TT-EEEEEES-EEEECCTTEEEEE----HHHHHHHHHHHHTT-EEEEEE-S-SS--.-TT-EEEE--SHHHHHHHHH CS
                               DFP   2 egkkvlvtaGpTrEaiDpVRfisNrSSGkmGyalAeaaaarGaeVtlvsgpvslet.pegvevvkvesaeemleave 77 
                                       +g k+lvtaGpTrE iD VRfisN+SSGkmG+a+A++a+ rG +V +++gp s+e+ p+  ++++v s++eml++v 
  gi|385805882|ref|YP_005842280.1| 194 NGIKFLVTAGPTREFIDTVRFISNPSSGKMGIAIASEALYRGGKVSFIHGPLSVEKiPSFHSTISVISTDEMLNSVI 270
                                       7899***********************************************99887365678*************** PP

                                       HHHTT-..SEEEE---S--EEES-------------..----EEE---HHHHHHHC-S.S-EEEEEEE-S.S...-H CS
                               DFP  78 ealkea..divimaAAvaDyrpkeaaeeKikkeeeeeeltleleknpdilaelaekkkkkqllvGFaaet.e...el 148
                                       +++k    d++im+AA +D++p +++++Ki+    ++ ltl+le++p+il+e+ ++kk++++++ Faa t +   el
  gi|385805882|ref|YP_005842280.1| 271 SEMKMFdpDVIIMSAAPSDFKPIQTQTKKISS---DKPLTLSLEPTPKILKEIVSRKKESSVVISFAADTvDsdeEL 344
                                       99976677**********************95...568***************99999999********965788** PP

                                       HHHHHHHHHHTT-SEEEEEEGGGTTGGG-SS-EEEEE. CS
                               DFP 149 lenareklerkgldlivaNdvskeeagfgsdenevtll 186
                                       +++a+ek+e+ ++d++vaN+vs+++ gf+sd nev+++
  gi|385805882|ref|YP_005842280.1| 345 IKKATEKIEKYRVDAVVANNVSRKDIGFSSDFNEVIIV 382
                                       ***********************************985 PP

>> Flavoprotein  Flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.1   0.1   5.7e-41   5.1e-37       1     150 [.      20     179 ..      20     187 .. 0.92
   2 ?    1.9   0.1     0.018   1.7e+02      17      54 ..     314     350 ..     309     399 .. 0.79

  Alignments for each domain:
  == domain 1  score: 127.1 bits;  conditional E-value: 5.7e-41
                                       EEEEEEE-SSCGGGCHHHHHHHHHHTTEEEEEEESCHHHHCCHHGGS............TCSSHHHHHHCTTESEEE CS
                      Flavoprotein   1 kkillgiTGsvaaikalellekLkkegievqvvltkaAkkfiskeklklaa........redpilhielrrwadllv 69 
                                       kki+lg+T sv+a+k ++l + L k+g+ev+vv++ +A++fis+  +++a+         +++  hi+l++++d++v
  gi|385805882|ref|YP_005842280.1|  20 KKIVLGVTSSVSAYKSIDLARTLMKNGAEVTVVMSSEATRFISPLMFEWATgnkvyyekFGGETGHISLSEEYDAMV 96 
                                       79*****************************************887777669999999999**************** PP

                                       EEEEEHHHHHHHHTT--SSHHHHHHHT..HCCTTEEEEE.--HHCCTCSTCHHHHHHH.HT................ CS
                      Flavoprotein  70 iaPasantlakianGiadnlltlilra..takkpiliaPamnpamyenpqtlknlekl.eegvtvikPsegdigkgk 143
                                       iaPa+ant+ k+  Giad+ +tl +++  +akkp++++Pam+ ++y+ pq+++ ++kl e gv +++P+  + +k+k
  gi|385805882|ref|YP_005842280.1|  97 IAPATANTITKLSFGIADSAVTLAALSflGAKKPVMVVPAMHIQLYRAPQVQQAINKLkEYGVSLHEPI-LERDKAK 172
                                       **********************9997788*****************************77*********.6667777 PP

                                       GHHHHHH CS
                      Flavoprotein 144 maeieei 150
                                       +++++e+
  gi|385805882|ref|YP_005842280.1| 173 FPDLNEL 179
                                       7777665 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.018
                                       HHHHHHHHHTTEEEEEEESCHHHHCCHHGGS....TCS CS
                      Flavoprotein  17 lellekLkkegievqvvltkaAkkfiskeklklaared 54 
                                       +++l+++ +++ e  vv++ aA  + s+e+l ++a ++
  gi|385805882|ref|YP_005842280.1| 314 PKILKEIVSRKKESSVVISFAADTVDSDEELIKKA-TE 350
                                       788999999999***************99665544.22 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       873  (0.0486921); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.34s 00:00:00.95 Elapsed: 00:00:00.53
# Mc/sec: 2375.78
//
Query:       gi|385805883|ref|YP_005842281.1|  [L=291]
Description: GHMP kinase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); 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: 0.57u 0.34s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 1623.44
//
Query:       gi|385805884|ref|YP_005842282.1|  [L=256]
Description: hypothetical protein FFONT_0842 [Fervidicoccus fontis Kam940]
Scores for complete 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-73  244.4   1.4    6.9e-73  243.9   1.4    1.2  1  PPS_PS    Phosphopantothenate/pantothenate synthetase
  ------ inclusion threshold ------
      0.082   12.7   0.2        1.7    8.4   0.1    2.3  2  DUF4881   Domain of unknown function (DUF4881)
       0.11   12.3   0.9       0.52   10.0   0.2    2.3  2  Met_10    Met-10+ like-protein


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 !  243.9   1.4   1.2e-76   6.9e-73       1     174 [.      66     239 ..      66     241 .. 0.98

  Alignments for each domain:
  == domain 1  score: 243.9 bits;  conditional E-value: 1.2e-76
                            PPS_PS   1 lllakkpvisvNGNtaaLvaeeiveLaealgaklevNlfyrteeRvekiaellkeagaeevlgleedaripeleseR 77 
                                       lll++ pvisvNGN+aaLv++ei++L++ ++ak+evNlfyrteeRv+ki ++lke+ga+evlgle  + ip+l+seR
  gi|385805884|ref|YP_005842282.1|  66 LLLSNYPVISVNGNAAALVPDEIINLSNIIDAKIEVNLFYRTEERVKKIVDFLKERGAKEVLGLEYVEGIPGLSSER 142
                                       799************************************************************************** PP

                            PPS_PS  78 akvskeGiysaDvvlvplEDGDRaeaLvkmgKkviaiDLNPlsRtartatitivdnvvRalpnlteavkelkkkske 154
                                       +kv+ +Gi++aDvvlv lEDGDR+eaL+k+gK+viaiDLNP+sRt+++a+++i+dnv+Ra+p ++++++ +kk  ke
  gi|385805884|ref|YP_005842282.1| 143 RKVDPRGILKADVVLVMLEDGDRTEALKKIGKRVIAIDLNPFSRTSMAADVSIMDNVTRAIPLMIDKARIMKKLPKE 219
                                       ***************************************************************************** PP

                            PPS_PS 155 eleeivkefdnkkvlkealk 174
                                       el++ +++++n++ l e + 
  gi|385805884|ref|YP_005842282.1| 220 ELKKKISNYNNRRRLGEYII 239
                                       *************9988775 PP

>> DUF4881  Domain of unknown function (DUF4881)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.027   1.6e+02     138     170 ..      84     115 ..      79     120 .. 0.83
   2 ?    8.4   0.1   0.00029       1.7      88     132 ..     192     234 ..     167     246 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.027
                           DUF4881 138 vpdeaislPdstWeaGdevriaykeegqalrfm 170
                                       vpde i+l  ++ +a  ev ++y++e++  +++
  gi|385805884|ref|YP_005842282.1|  84 VPDEIINLS-NIIDAKIEVNLFYRTEERVKKIV 115
                                       899999996.5779**********999877765 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00029
                           DUF4881  88 lvdlkknvdrehPlvfdkaedaakkfPvvdkekktvtvysgrqkl 132
                                        v +++nv r  Pl+ dka    kk+P  +  kk ++ y +r++l
  gi|385805884|ref|YP_005842282.1| 192 DVSIMDNVTRAIPLMIDKAR-IMKKLPKEE-LKKKISNYNNRRRL 234
                                       5889***********99997.67999*855.5777999***9985 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.17     1e+03      89     106 ..      15      32 ..      11      41 .. 0.87
   2 ?   10.0   0.2   8.7e-05      0.52      87     171 ..     138     223 ..     118     255 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.17
                                       HHHHHHHTT--TT-EEEE CS
                            Met_10  89 aErerlaklveegevVvd 106
                                        Ere++++ +++g vV++
  gi|385805884|ref|YP_005842282.1|  15 MEREKIIEGFKNGIVVIN 32 
                                       69***********99986 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 8.7e-05
                                       GHHHHHHHHTT.--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHH.TT-TTCEEEEES-GG CS
                            Met_10  87 leaErerlakl.veegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkenikl.NkvekvvkpileDgr 161
                                       l++Er+++    + + +vV+ ++   G  + +++k   +krv+aidlnP s   +   +    +v + + p++ D +
  gi|385805884|ref|YP_005842282.1| 138 LSSERRKVDPRgILKADVVLVMLE-DGDRTEALKK--IGKRVIAIDLNPFSRTSMAADVSImDNVTRAI-PLMIDKA 210
                                       666666665554666667666665.4777777888..67889**************9998625677777.9999998 PP

                                       G---...TT-EEE CS
                            Met_10 162 evir...eqladr 171
                                        +++   ++ + +
  gi|385805884|ref|YP_005842282.1| 211 RIMKklpKEELKK 223
                                       8876444444445 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); 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: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1669.59
//
Query:       gi|385805885|ref|YP_005842283.1|  [L=184]
Description: rubrerythrin [Fervidicoccus fontis Kam940]
Scores for 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   97.2   4.0    1.4e-27   96.8   4.0    1.2  1  Rubrerythrin    Rubrerythrin
  ------ inclusion threshold ------
      0.023   14.5   1.4      0.043   13.6   1.4    1.5  1  Cys_rich_CPCC   Cysteine-rich CPCC
      0.023   14.7   0.5       0.07   13.2   0.3    1.9  2  HypA            Hydrogenase/urease nickel incorporation, meta
      0.024   14.2   2.6       0.66    9.5   2.4    2.3  2  TF_Zn_Ribbon    TFIIB zinc-binding
      0.029   14.6   0.2       0.75   10.0   0.0    2.2  2  Ferritin_2      Ferritin-like domain
      0.039   13.7   1.0      0.085   12.6   1.0    1.6  1  DUF3039         Protein of unknown function (DUF3039)
      0.045   13.8   6.0        2.7    8.1   0.2    2.4  2  Rubredoxin      Rubredoxin
      0.047   13.1   2.1        2.7    7.5   0.2    2.3  2  zf-ribbon_3     zinc-ribbon domain
      0.052   13.5   3.2       0.46   10.4   3.2    2.0  1  Ferritin        Ferritin-like domain
      0.057   12.2   0.3      0.092   11.5   0.3    1.3  1  NRDD            Anaerobic ribonucleoside-triphosphate reducta
      0.059   13.3   0.4        1.7    8.7   0.0    2.4  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.06   13.3   0.3        6.7    6.8   0.0    2.4  2  Ogr_Delta       Ogr/Delta-like zinc finger
      0.074   13.5   3.2          2    9.0   0.3    2.7  2  Zn-C2H2_12      Autophagy receptor zinc finger-C2H2 domain
      0.076   13.0   0.2       0.12   12.5   0.2    1.3  1  DZR             Double zinc ribbon
       0.12   12.4   0.0        3.8    7.6   0.0    2.2  2  Pro_3_hydrox_C  L-proline 3-hydroxylase, C-terminal
       0.14   12.2   2.7         10    6.2   0.1    2.4  2  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
       0.33   10.9   2.3       0.81    9.6   0.1    2.1  2  DUF3797         Domain of unknown function (DUF3797)
       0.37   10.6   3.5       0.98    9.2   3.4    1.7  1  zinc_ribbon_2   zinc-ribbon domain
        1.1    9.4   5.0        5.5    7.2   5.1    2.1  1  Zn-ribbon_8     Zinc ribbon domain
        2.3    8.0   7.1        1.7    8.4   0.4    2.3  2  zf-RRN7         Zinc-finger of RNA-polymerase I-specific TFII


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 !   96.8   4.0   1.5e-30   1.4e-27       2     136 ..       9     136 ..       8     137 .. 0.95

  Alignments for each domain:
  == domain 1  score: 96.8 bits;  conditional E-value: 1.5e-30
                                       HHHHHHHHHHHHHHHHHHHHHCHH.TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS-------T CS
                      Rubrerythrin   2 iLekAiagEssarrlYkelaekak.egypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakpk 77 
                                        L +A+ gEs+a+++Y+++a+ a+ eg++++++lF+ +A +E+ Ha +++++l+++++++             +++ 
  gi|385805885|ref|YP_005842283.1|   9 ALIAAFGGESMAHMRYQIFADIAEkEGFKNVSRLFRGIAYAEKVHASNHYNALREYNEDQI--------AHSGVPIG 77 
                                       6889*****************************************************9999........56667778 PP

                                       TGGHHHHHHHHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Rubrerythrin  78 flttaknLeeaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerlrkl 136
                                          t knLe ai+g++ e +emy++y ++a+++g+ ea k+f ++ +aE+ H+e+++++
  gi|385805885|ref|YP_005842283.1|  78 PGNTSKNLELAIRGEEFEVKEMYPVYIDIAKMQGENEALKSFNFALKAEEIHAELYKQA 136
                                       88999***************************************************986 PP

>> Cys_rich_CPCC  Cysteine-rich CPCC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.4   4.8e-05     0.043       1      25 [.     153     175 ..     153     182 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.8e-05
                     Cys_rich_CPCC   1 yqCpcCgyltleeeegsydiCpvCf 25 
                                       y Cp+Cgy+ + ee    + Cp+C 
  gi|385805885|ref|YP_005842283.1| 153 YVCPVCGYTYVGEE--PPERCPICG 175
                                       57*********999..578899996 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       5.8   5.2e+03      13      54 ..      26      67 ..      18      73 .. 0.58
   2 ?   13.2   0.3   7.8e-05      0.07      63      96 ..     139     178 ..      86     182 .. 0.59

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 5.8
                                      HHHHHHCCTT..EEEEEEEEEETTCT--HHHHHHHHHHHHCC CS
                              HypA 13 vveeeakeaaarkvtkvkvevGelsgvepeaLefafellaeg 54
                                      +  + a+++++++v+++   +   ++v+ +    a++ ++e+
  gi|385805885|ref|YP_005842283.1| 26 IFADIAEKEGFKNVSRLFRGIAYAEKVHASNHYNALREYNED 67
                                      555566666677777766666666666555555555555555 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 7.8e-05
                                       E......EEEE--EEEETTTS-EEECHHHHHS-TTTSSS- CS
                              HypA  63 e......ieevpvkvrCreCgkefeleekalrCpkCgsad 96 
                                       +      ++ +  ++ C +Cg+++  ee  +rCp Cg+++
  gi|385805885|ref|YP_005842283.1| 139 DvdsgkdFNLKGRVYVCPVCGYTYVGEEPPERCPICGAKR 178
                                       1444444566667889********97765579*****975 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   2.4   0.00073      0.66       1      30 [.     153     179 ..     153     180 .. 0.85
   2 ?    6.8   0.0    0.0054       4.8       2      15 ..     170     184 .]     169     184 .] 0.81

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00073
                                       EEETTTTCEEC.HEETSTTCEEESSSSBEEE CS
                      TF_Zn_Ribbon   1 ykCPnCgstnl.veDpergelvCtdCGlVle 30 
                                       y+CP+Cg t++ +e+pe    +C+ CG+  e
  gi|385805885|ref|YP_005842283.1| 153 YVCPVCGYTYVgEEPPE----RCPICGAKRE 179
                                       89*******95499999....8999998766 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0054
                                       EETTTTCEE.CHEET CS
                      TF_Zn_Ribbon   2 kCPnCgstn.lveDp 15 
                                       +CP+Cg ++ + +D+
  gi|385805885|ref|YP_005842283.1| 170 RCPICGAKReMFRDF 184
                                       6*****987788885 PP

>> Ferritin_2  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1      0.17   1.5e+02      37      54 ..      37      54 ..       5      75 .. 0.48
   2 ?   10.0   0.0   0.00084      0.75       3      28 ..     116     141 ..     114     156 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.17
                        Ferritin_2 37 aevrevaeeiakheeaHv 54
                                      ++v ++++ ia+ e+ H+
  gi|385805885|ref|YP_005842283.1| 37 KNVSRLFRGIAYAEKVHA 54
                                      233344444444444444 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00084
                        Ferritin_2   3 vdiLnfAlnlEyleaafYtaalegas 28 
                                       ++ +nfAl +E + a+ Y++a +  +
  gi|385805885|ref|YP_005842283.1| 116 LKSFNFALKAEEIHAELYKQAKKDVD 141
                                       5679****************988654 PP

>> DUF3039  Protein of unknown function (DUF3039)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.0   9.5e-05     0.085      26      54 ..     154     182 ..     144     184 .] 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.5e-05
                           DUF3039  26 VvALCGkvwvptrdpkkfPvCpeCkeiye 54 
                                       V   CG ++v +  p++ P+C + +e++ 
  gi|385805885|ref|YP_005842283.1| 154 VCPVCGYTYVGEEPPERCPICGAKREMFR 182
                                       6779*****************99888875 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   1.6    0.0041       3.7       2      12 ..     153     163 ..     152     170 .. 0.85
   2 ?    8.1   0.2     0.003       2.7      36      47 .]     170     181 ..     167     181 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0041
                                       EEETTT-BEEE CS
                        Rubredoxin   2 yeCkvCgyvYd 12 
                                       y C vCgy Y 
  gi|385805885|ref|YP_005842283.1| 153 YVCPVCGYTYV 163
                                       89*******95 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.003
                                       BBTTTB-BGGGE CS
                        Rubredoxin  36 vCPdCgvekeqF 47 
                                       +CP Cg+++e+F
  gi|385805885|ref|YP_005842283.1| 170 RCPICGAKREMF 181
                                       6********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 ?    5.2   0.1     0.016        14      13      24 ..     149     160 ..     143     161 .. 0.68
   2 ?    7.5   0.2     0.003       2.7       4      11 ..     170     177 ..     169     179 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.016
                       zf-ribbon_3  13 ssddnvCpyCGt 24 
                                       + ++ vCp CG+
  gi|385805885|ref|YP_005842283.1| 149 KGRVYVCPVCGY 160
                                       555667777775 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.003
                       zf-ribbon_3   4 rCPnCGap 11 
                                       rCP CGa+
  gi|385805885|ref|YP_005842283.1| 170 RCPICGAK 177
                                       89999985 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   3.2   0.00051      0.46       3     112 ..       9     146 ..       7     149 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00051
                                       HHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHH......HHHH.. CS
                          Ferritin   3 aLneqladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklaerilalGgtpvltra......elee.. 71 
                                       aL +++  e  a++ y  +a  ++ +g+++++ +f+  a  e  ha   ++ +++ +++ +++           +  
  gi|385805885|ref|YP_005842283.1|   9 ALIAAFGGESMAHMRYQIFADIAEKEGFKNVSRLFRGIAYAEKVHASNHYNALREYNEDQIAHSGvpigpgN--Tsk 83 
                                       66677788999**********************************************944333334444440..044 PP

                                       ......................C-SSSSCSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-H CS
                          Ferritin  72 ......................ieapkefgsveevleaalehekkvteslrelielaeeegDp 112
                                                             i++ +  +++++ +  al++e+   e ++++ + +++ +D+
  gi|385805885|ref|YP_005842283.1|  84 nlelairgeefevkemypvyidIAKMQGENEALKSFNFALKAEEIHAELYKQAKKDVDSGKDF 146
                                       444444444455555666664433333334778888888888888888888888887777776 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.3    0.0001     0.092     507     530 ..     152     179 ..     143     183 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0001
                                       EEEETT.--..EESS..SB-TTT--BE. CS
                              NRDD 507 idvCnecgy..kgei..ekCpkCgseee 530
                                       + vC+ cgy   ge   e+Cp Cg ++e
  gi|385805885|ref|YP_005842283.1| 152 VYVCPVCGYtyVGEEppERCPICGAKRE 179
                                       679******8777779999*****7765 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0    0.0018       1.7      40      56 ..     145     162 ..     134     163 .. 0.81
   2 ?    2.3   0.1      0.18   1.6e+02      30      39 ..     170     179 ..     169     183 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0018
                    OrfB_Zn_ribbon  40 e.alsgrtfkCpnCgfea 56 
                                       + +l+gr+++Cp Cg+++
  gi|385805885|ref|YP_005842283.1| 145 DfNLKGRVYVCPVCGYTY 162
                                       36899**********985 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.18
                    OrfB_Zn_ribbon  30 tCseCgsknk 39 
                                       +C+ Cg+k +
  gi|385805885|ref|YP_005842283.1| 170 RCPICGAKRE 179
                                       7*****9876 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0075       6.7      21      40 ..     148     165 ..     139     168 .. 0.84
   2 ?    4.1   0.2      0.05        45       1       8 [.     170     177 ..     170     182 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0075
                         Ogr_Delta  21 vreryyqCsnfeCgatfvaa 40 
                                       ++ r+y+C +  Cg+t+v  
  gi|385805885|ref|YP_005842283.1| 148 LKGRVYVCPV--CGYTYVGE 165
                                       56699***99..*****976 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.05
                         Ogr_Delta   1 rCPhCgap 8  
                                       rCP Cga+
  gi|385805885|ref|YP_005842283.1| 170 RCPICGAK 177
                                       7*****98 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 ?    9.0   0.3    0.0022         2       2      10 ..     154     162 ..     154     164 .. 0.93
   2 ?    4.3   0.2     0.066        59       3       7 ..     171     175 ..     170     181 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0022
                        Zn-C2H2_12   2 eCPlCseqF 10 
                                       +CP+C++++
  gi|385805885|ref|YP_005842283.1| 154 VCPVCGYTY 162
                                       7******98 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.066
                        Zn-C2H2_12   3 CPlCs 7  
                                       CP+C+
  gi|385805885|ref|YP_005842283.1| 171 CPICG 175
                                       ****8 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   0.00013      0.12      13      37 ..     153     177 ..     143     184 .] 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                               DZR  13 rfCseCgtklkavaaedrCpsCgek 37 
                                        +C+ Cg +   ++ ++rCp Cg+k
  gi|385805885|ref|YP_005842283.1| 153 YVCPVCGYTYVGEEPPERCPICGAK 177
                                       68*******988888*******997 PP

>> Pro_3_hydrox_C  L-proline 3-hydroxylase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0042       3.8      34      72 ..      25      63 ..       7      69 .. 0.89
   2 ?    2.6   0.0      0.16   1.4e+02      60      84 ..      93     117 ..      90     129 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0042
                                      HGGGGT--TTTHHHHHHHHHHHCCTBSS-TTHHHHHHHH CS
                    Pro_3_hydrox_C 34 lalsevvsranykdivflLaklhffekvpieasydWLke 72
                                        ++ + +++ +k++  l+  + + ekv++++ y+ L e
  gi|385805885|ref|YP_005842283.1| 25 QIFADIAEKEGFKNVSRLFRGIAYAEKVHASNHYNALRE 63
                                      568899999**************************9988 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.16
                                       SS-TTHHHHHHHHHHHHH--HHHHH CS
                    Pro_3_hydrox_C  60 kvpieasydWLkeicrrrGdpaLie 84 
                                       + +++++y   ++i++ +G+++ ++
  gi|385805885|ref|YP_005842283.1|  93 EFEVKEMYPVYIDIAKMQGENEALK 117
                                       667899*************987665 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.4     0.015        13       2       6 ..     155     159 ..     154     166 .. 0.87
   2 ?    6.2   0.1     0.012        10       1       8 [.     170     177 ..     170     180 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.015
                    DNA_ligase_ZBD   2 CPvCG 6  
                                       CPvCG
  gi|385805885|ref|YP_005842283.1| 155 CPVCG 159
                                       ****9 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.012
                    DNA_ligase_ZBD   1 hCPvCGsa 8  
                                       +CP+CG++
  gi|385805885|ref|YP_005842283.1| 170 RCPICGAK 177
                                       5*****86 PP

>> DUF3797  Domain of unknown function (DUF3797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1    0.0009      0.81       7      25 ..     146     164 ..     141     167 .. 0.84
   2 ?    0.6   0.2      0.59   5.3e+02      15      22 ..     170     177 ..     169     179 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0009
                           DUF3797   7 vkLdekYvqCPeCgNnkvl 25 
                                       ++L ++   CP+Cg  +v+
  gi|385805885|ref|YP_005842283.1| 146 FNLKGRVYVCPVCGYTYVG 164
                                       789999667******9997 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.59
                           DUF3797  15 qCPeCgNn 22 
                                        CP Cg +
  gi|385805885|ref|YP_005842283.1| 170 RCPICGAK 177
                                       5****976 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   3.4    0.0011      0.98       2      22 ..     155     177 ..     154     178 .. 0.95

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0011
                     zinc_ribbon_2   2 CpnCGaelqdnakF..CpyCGtp 22 
                                       Cp CG++   +++   Cp CG++
  gi|385805885|ref|YP_005842283.1| 155 CPVCGYTYVGEEPPerCPICGAK 177
                                       *********************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 ?    7.2   5.1    0.0061       5.5       6      34 ..     153     176 ..     152     180 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0061
                       Zn-ribbon_8   6 YrCeeCghefevlqsisdapltaCPeCgs 34 
                                       Y C  Cg ++       ++p++ CP Cg+
  gi|385805885|ref|YP_005842283.1| 153 YVCPVCGYTYV-----GEEPPERCPICGA 176
                                       99*****6555.....5777788*****8 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   1.5      0.11     1e+02       6      11 ..     154     159 ..     150     166 .. 0.85
   2 ?    8.4   0.4    0.0019       1.7       4      13 ..     168     178 ..     165     183 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.11
                           zf-RRN7   6 pCgvCg 11 
                                       +C+vCg
  gi|385805885|ref|YP_005842283.1| 154 VCPVCG 159
                                       8****9 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0019
                           zf-RRN7   4 gppCgvCgc.r 13 
                                        ++C++Cg+ r
  gi|385805885|ref|YP_005842283.1| 168 PERCPICGAkR 178
                                       68*******44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      611  (0.0340789); expected 358.6 (0.02)
Passed Vit filter:                       109  (0.00607954); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1245.11
//
Query:       gi|385805886|ref|YP_005842284.1|  [L=121]
Description: hypothetical protein FFONT_0844 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.7e-14   51.2   0.2    1.8e-13   50.4   0.2    1.4  1  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
     0.0043   16.5   0.1     0.0096   15.4   0.1    1.7  1  TF_Zn_Ribbon    TFIIB zinc-binding
      0.009   16.0   0.1      0.019   15.0   0.1    1.7  1  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
  ------ inclusion threshold ------
      0.016   14.6   1.9      0.043   13.2   1.9    1.7  1  zf-ribbon_3     zinc-ribbon domain
       0.12   13.1   1.0       0.25   12.1   0.1    1.9  2  DUF2043         Uncharacterized conserved protein (DUF2043)
       0.14   12.1   0.2       0.77    9.7   0.0    2.1  2  DUF723          Protein of unknown function (DUF723)


Domain annotation for each model (and alignments):
>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   0.2   5.9e-17   1.8e-13       1      40 []       8      46 ..       8      46 .. 0.93

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 5.9e-17
                     Auto_anti-p27  1 kkmgelLlkGwtMLaetCpvCgvPLmrdrkggkvyCvaCd 40
                                      kk +elL +G+tML+ tCp Cg+PL++ + +g+++C++++
  gi|385805886|ref|YP_005842284.1|  8 KKSAELLRQGATMLSLTCPICGSPLFKLK-NGDIVCPIHG 46
                                      6789************************7.79*****995 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   3.2e-06    0.0096       2      23 ..      24      43 ..      23      49 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.2e-06
                                      EETTTTCEECHEETSTTCEEES CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCt 23
                                      +CP+Cgs+  ++  ++g++vC+
  gi|385805886|ref|YP_005842284.1| 24 TCPICGSP--LFKLKNGDIVCP 43
                                      8*******..89999******7 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 !   15.0   0.1   6.3e-06     0.019       1      14 [.      24      37 ..      24      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 6.3e-06
                    DNA_ligase_ZBD  1 hCPvCGsavvReeg 14
                                      +CP+CGs++ +  +
  gi|385805886|ref|YP_005842284.1| 24 TCPICGSPLFKLKN 37
                                      7********98543 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.9   1.4e-05     0.043       4      20 ..      24      43 ..      23      49 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.4e-05
                       zf-ribbon_3  4 rCPnCGa.p..lssddnvCp 20
                                      +CP CG+ +  l+ +d+vCp
  gi|385805886|ref|YP_005842284.1| 24 TCPICGSpLfkLKNGDIVCP 43
                                      6******87899*******9 PP

>> DUF2043  Uncharacterized conserved protein (DUF2043)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   8.3e-05      0.25      86     100 ..      40      55 ..      22      59 .. 0.85
   2 ?   -1.0   0.1      0.94   2.8e+03      41      66 ..      88     113 ..      71     120 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.3e-05
                           DUF2043  86 lkCPlHGk.iipRDee 100
                                         CP+HGk ii RDe 
  gi|385805886|ref|YP_005842284.1|  40 IVCPIHGKvIIARDER 55 
                                       58*****956799985 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.94
                           DUF2043  41 eeviskekleelkqraitfageaeev 66 
                                       e +++++k++ l  + ++  ++a+++
  gi|385805886|ref|YP_005842284.1|  88 EDMENESKIADLLYKWMNIIEKAKRL 113
                                       44555555555555555555555554 PP

>> DUF723  Protein of unknown function (DUF723)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1       0.4   1.2e+03      34      60 .]      24      29 ..      17      32 .. 0.65
   2 ?    9.7   0.0   0.00026      0.77      33      45 ..      40      52 ..      35      61 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.4
                            DUF723 34 nCPlHGnvtystykalikSkyGCPeCa 60
                                                            CP C+
  gi|385805886|ref|YP_005842284.1| 24 T---------------------CPICG 29
                                      4.....................55554 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00026
                            DUF723 33 inCPlHGnvtyst 45
                                      i+CP+HG+v + +
  gi|385805886|ref|YP_005842284.1| 40 IVCPIHGKVIIAR 52
                                      99******98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1449  (0.0808188); expected 358.6 (0.02)
Passed bias filter:                      705  (0.0393218); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
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 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 789.57
//
Query:       gi|385805887|ref|YP_005842285.1|  [L=590]
Description: putative Fe-S osidoreductase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      1e-21   78.0   0.0      1e-21   78.0   0.0    1.8  2  Radical_SAM  Radical SAM superfamily
    2.4e-09   37.3   0.9    8.6e-09   35.6   0.0    2.3  2  Fer4_14      4Fe-4S single cluster domain
      1e-06   29.1   0.3    2.5e-06   27.8   0.0    1.9  1  Fer4_12      4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.021   14.6   0.6        3.1    7.7   0.3    2.6  2  zf-CHC2      CHC2 zinc finger


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 ?   -4.5   1.2         4   1.8e+04       7      17 ..     122     132 ..     117     135 .. 0.84
   2 !   78.0   0.0   2.3e-25     1e-21       1     166 [.     141     306 ..     141     307 .. 0.92

  Alignments for each domain:
  == domain 1  score: -4.5 bits;  conditional E-value: 4
                                       ESS--TTTSCC CS
                                       xxxxxxxxxxx RF
                       Radical_SAM   7 CnlrCsfCarp 17 
                                       C+++C  C+ +
  gi|385805887|ref|YP_005842285.1| 122 CPFNCGLCPMH 132
                                       ******99977 PP

  == domain 2  score: 78.0 bits;  conditional E-value: 2.3e-25
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlaklavp 76 
                                       +vvt+ C l C++C +    ++ g++++ ++e++ e+v++lk ++  +  + ++ggepl+++d+v+++++ +++   
  gi|385805887|ref|YP_005842285.1| 141 IVVTNRCDLSCWYCFFFA--EKAGYVYEPTIEQLREQVRALK-KQKvTLAIQITGGEPLMRDDIVDIIKMFKEE--G 212
                                       689**************9..5********************7.444499*************************..8 PP

                                       TEEEEEEECSSCHG..........HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSE CS
                                       xxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  77 giritvetngtlpd..........eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagik 143
                                        ++i + t ++ +            +++++l+e+gv++++++ + ++++     +n+ ++  ++   ++++r++g+ 
  gi|385805887|ref|YP_005842285.1| 213 VRHIQLNTEAIPLAelyrknpeeaIKWAKELREAGVNTIYMSFDGVSPK-----TNP-KNHWDIPFIFDAFRKSGMT 283
                                       ************99**********************************9.....655.44444447899999***** PP

                                       TEEEEEEEBTTTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 144 rvvdrivglpGendeeleellel 166
                                       +vv + ++++ +nde+l +++++
  gi|385805887|ref|YP_005842285.1| 284 SVVLVPTVIKSVNDEDLGNIVKF 306
                                       *****************999988 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.2      0.63   2.8e+03       6      17 ..     120     131 ..     115     137 .. 0.77
   2 !   35.6   0.0   1.9e-12   8.6e-09       4      90 ..     143     223 ..     141     243 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.63
                           Fer4_14   6 sgCnlsCkgCdn 17 
                                       + C+++C  C  
  gi|385805887|ref|YP_005842285.1| 120 APCPFNCGLCPM 131
                                       57*******964 PP

  == domain 2  score: 35.6 bits;  conditional E-value: 1.9e-12
                           Fer4_14   4 rlsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeype 80 
                                        +++C lsC  C+  ++++  + +  t e+l ++++ lkk+++  + + +tGGePL+    +++++++k+ kee+  
  gi|385805887|ref|YP_005842285.1| 143 VTNRCDLSCWYCFFFAEKAGYVYE-PTIEQLREQVRALKKQKVTLA-IQITGGEPLMR---DDIVDIIKMFKEEG-V 213
                                       49***********88755554444.566677788889******888.*********65...99***********9.6 PP

                           Fer4_14  81 kkiwletngt 90 
                                        +i+l+t + 
  gi|385805887|ref|YP_005842285.1| 214 RHIQLNTEAI 223
                                       7899998775 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 !   27.8   0.0   5.6e-10   2.5e-06       7      87 ..     139     216 ..     133     243 .. 0.74

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 5.6e-10
                           Fer4_12   7 rlslfvsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeek 83 
                                         ++ +++C+lsC +Cf  + +     +++ ++l e++ +  k++    + ++GGEPl+   ++++++++k +kee+
  gi|385805887|ref|YP_005842285.1| 139 ANIVVTNRCDLSCWYCFFFAEKAGYVYEPTIEQLREQVRALKKQKVTLAIQITGGEPLM---RDDIVDIIKMFKEEG 212
                                       55677899*********66666665566666777777655544555589**********...9999*********99 PP

                           Fer4_12  84 pekd 87 
                                       +   
  gi|385805887|ref|YP_005842285.1| 213 VRHI 216
                                       8533 PP

>> zf-CHC2  CHC2 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0    0.0072        32      33      66 ..      55      88 ..      39     101 .. 0.88
   2 ?    7.7   0.3   0.00069       3.1      33      83 ..     126     177 ..     113     191 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0072
                           zf-CHC2 33 valCPFHeektpsftvspekqfyyCfgCgagGda 66
                                      +++CP+ e   p++ v+ + ++y    C ++G+ 
  gi|385805887|ref|YP_005842285.1| 55 QSVCPYCERLIPAIIVERNDKLYIRKVCPEHGEF 88
                                      679**************************99985 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00069
                           zf-CHC2  33 valCPFHeektpsft.vspekqfyyCfgCgagGdaikFlmeieklsfveave 83 
                                        +lCP H+++t+  + v++++    C+ C    +   ++ e    +  e v+
  gi|385805887|ref|YP_005842285.1| 126 CGLCPMHKNHTALANiVVTNRCDLSCWYCFFFAEKAGYVYEPTIEQLREQVR 177
                                       69*********96651555666677777766666666665555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (590 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      620  (0.0345808); 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: 0.71u 0.30s 00:00:01.01 Elapsed: 00:00:00.48
# Mc/sec: 3690.22
//
Query:       gi|385805888|ref|YP_005842286.1|  [L=178]
Description: hypothetical protein FFONT_0846 [Fervidicoccus fontis Kam940]
Scores for complete 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-07   29.6   5.4    1.1e-05   25.6   5.4    2.1  1  THUMP           THUMP domain
  ------ inclusion threshold ------
      0.037   13.7   0.0      0.066   12.9   0.0    1.4  1  Ribosomal_S19e  Ribosomal protein S19e


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 !   25.6   5.4   1.2e-09   1.1e-05      42     132 ..      28     150 ..       3     154 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.2e-09
                                       HHHHTST...............................TECEEEEEEEEEESSHHHHHHHHHHHHHHHHHHCT-EEE CS
                             THUMP  42 ealekar...............................giqrvipvcevceadledileaakeivkkkfeeeketFa 87 
                                       +++e +r                                i r+ipv +v+   +++++e ++e++++k ++e+ tF+
  gi|385805888|ref|YP_005842286.1|  28 NIIENIRivdtsqsiilaivdepyatiekikslelketPILRIIPVDRVTDIFVDRVKEVIHELFNTKVKKEE-TFK 103
                                       44444444444444444555555555555555555555*******************************9986.*** PP

                                       EEEEESSSTS.........SSHHHHHHHHHHHHHHCCTT-EE-SSS-SEEEEEE CS
                             THUMP  88 Vrvkrrgkhf.........eftsreinrevGkaivektglkVdlenPdivvrve 132
                                       ++       +         ++ + e  +++++ + +     V+l++P ++v v+
  gi|385805888|ref|YP_005842286.1| 104 IKLDGH---LykrqegsieKIHKDEAIKILAEGLEN----PVNLKSPSWLVYVK 150
                                       *98763...234456556677777777777777777....9**********997 PP

>> Ribosomal_S19e  Ribosomal protein S19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   7.4e-06     0.066       2      35 ..     118     151 ..     117     159 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.4e-06
                                       SSSHHHHHHHHHS--S---S-SSS-SSSS-SS-S CS
                    Ribosomal_S19e   2 vkdVpaeelikalaeeLkksgklevPewadlvKt 35 
                                       +++++ +e ik lae L++  +l+ P+w  +vKt
  gi|385805888|ref|YP_005842286.1| 118 IEKIHKDEAIKILAEGLENPVNLKSPSWLVYVKT 151
                                       68999****************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       723  (0.0403257); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1135.13
//
Query:       gi|385805889|ref|YP_005842287.1|  [L=473]
Description: phospho-sugar mutase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-37  128.5   0.1    4.2e-37  126.9   0.0    1.8  2  PGM_PMM_I    Phosphoglucomutase/phosphomannomutase, alpha/bet
    3.6e-21   75.7   0.0    8.7e-21   74.5   0.0    1.7  1  PGM_PMM_II   Phosphoglucomutase/phosphomannomutase, alpha/bet
    5.2e-12   45.8   0.0    1.5e-11   44.3   0.0    1.7  1  PGM_PMM_IV   Phosphoglucomutase/phosphomannomutase, C-termina
    0.00012   22.2   0.0    0.00033   20.8   0.0    1.8  1  PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/bet


Domain annotation for each model (and alignments):
>> PGM_PMM_I  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.9   0.0   9.5e-41   4.2e-37       2     135 ..       6     135 ..       5     138 .. 0.96
   2 ?   -1.8   0.0      0.53   2.4e+03      30      59 ..     264     295 ..     259     324 .. 0.68

  Alignments for each domain:
  == domain 1  score: 126.9 bits;  conditional E-value: 9.5e-41
                                       GGBBTTCEEEECCHCTBSCCHHHHHHHHHHHHCHHCSTS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEEEB- CS
                         PGM_PMM_I   2 qkfgtsGlRgkvgegeltpelveklgqaiaeylkaeakkkkvvvGrDtRvssrelaealaaglaanGvevillgllp 78 
                                       ++fgt+G+Rgk+  ++++p l++ +g a+a ++     ++++ +G+D R++s+ la ++ +g+++ G ++i+lg++p
  gi|385805889|ref|YP_005842287.1|   6 RLFGTDGIRGKYL-EKVKPGLAYDIGLAVAAHVGG---RGTITIGHDIRTTSPLLALSAGSGAMSGGTDAIFLGMVP 78 
                                       68***********.559*****************8...6************************************** PP

                                       HHHHHHHHHHCCECEEEEE--TTS-TTCCCEEEEETTTCE--CHHHHHHHHHHCCT- CS
                         PGM_PMM_I  79 tPavsfairklkadagimitaSHnppeyngiKvylsnGgpispeveekIeaiiekee 135
                                       tP++++++ + k +agimitaSHnpp +ngiKv++ nG+++++ +e+++e+ii+ ++
  gi|385805889|ref|YP_005842287.1|  79 TPVLAYSVPHTKSKAGIMITASHNPPPDNGIKVFQYNGMEYTERMEDELERIIQVKS 135
                                       ****************************************************98766 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.53
                                       HHHHCHHC..STS-EEEEEE-S-TTHHHHHHH CS
                         PGM_PMM_I  30 iaeylkae..akkkkvvvGrDtRvssrelaea 59 
                                       ia y k++  ++k++++v+ D   s   + e+
  gi|385805889|ref|YP_005842287.1| 264 IALYAKEKllEGKGTIIVSVDVGNSVSDIVEK 295
                                       67778888888999999999976665555555 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 !   74.5   0.0   1.9e-24   8.7e-21       2      99 ..     156     251 ..     155     256 .. 0.90

  Alignments for each domain:
  == domain 1  score: 74.5 bits;  conditional E-value: 1.9e-24
                                       HHHHHGGGTS-HHHHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-EEEES-----TT-TTSS----TT-TTTTHHHHG CS
                        PGM_PMM_II   2 aYiealkekvdseaikksglkvvidplhGaggeilkellkelgvdvvelnaepdpdfptkapnpeekealkllielv 78 
                                       +Y+++l + ++ ++  k   +v +d+ +Ga+++++++ll+++g++v + n++pd+ fp + p+p++ ++l+ li+++
  gi|385805889|ref|YP_005842287.1| 156 DYVDELSSMMSPRTV-KYVPRVYVDCSNGAASNYTPRLLRKMGAKVFSANCHPDGYFPAHEPEPRQ-DVLEPLINVA 230
                                       788999888884333.33358*********************************************.********** PP

                                       GGGG-SEEEEE-TTS-BEEEE CS
                        PGM_PMM_II  79 kkegadlglafDgDaDRlgvv 99 
                                       +  + d++la+DgDaDRl + 
  gi|385805889|ref|YP_005842287.1| 231 QPLSPDVILAHDGDADRLSAL 251
                                       ******************886 PP

>> PGM_PMM_IV  Phosphoglucomutase/phosphomannomutase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.0   3.2e-15   1.5e-11      16      73 ..     397     453 ..     382     454 .. 0.84

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 3.2e-15
                                       CCCCCTTHHCCCCCCCCGCCEEEE.EEEETTCCEEEEEEEESSHHHHHHHHHHHHHHH CS
                        PGM_PMM_IV  16 laallkvasikeglkilledGrrlavRpSGTepllrvyvEaksdeelarlaeevaell 73 
                                       +++++      +g++ ++ d +++ +R SGTep++r+y+Ea++ ++l++l++++ +++
  gi|385805889|ref|YP_005842287.1| 397 FDGYKT-LTKVDGIRLDFDDKTWFLIRMSGTEPKIRLYAEAPTTQKLEELVDKLSKII 453
                                       555533.36779***************************************9988765 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 !   20.8   0.0   7.4e-08   0.00033       3     109 ..     261     362 ..     259     366 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 7.4e-08
                                       HHHHHHHHHHHHCHCSTTTCEEEEETTS-THHHHHHHHTT-EEEEESSSCHHHHHHHHHT.TECEEEETTCEEEETT CS
                       PGM_PMM_III   3 dqllallakylleeklkpgagvvktvmtslalervakklgiklvetkvGdkyvleemkee.gavlGgEeSghiifld 78 
                                       d+l+al ak+ l    +++++++ +v   + + ++++k+g++lv++k G     e++ e  ga+++ E    +i ++
  gi|385805889|ref|YP_005842287.1| 261 DHLIALYAKEKLL---EGKGTIIVSVDVGNSVSDIVEKYGGRLVRAKLGKL--HEKLLEYpGALFAAEP-WKLIDPK 331
                                       7777777775433...33346****************************85..5776666479999997.7899999 PP

                                       TBSS--HHHHHHHHHHHHHHHTS-HHHHHHH CS
                       PGM_PMM_III  79 eattkDGilaallvleilaetgkslsellee 109
                                          + DGi+ a+ + +++ e+g sl+ ll++
  gi|385805889|ref|YP_005842287.1| 332 WGMWVDGIYQAIYLTKLMMEEGLSLDGLLSD 362
                                       99**********************9999965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); 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: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.47
# Mc/sec: 3002.70
//
Query:       gi|385805890|ref|YP_005842288.1|  [L=126]
Description: hypothetical protein FFONT_0848 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       964  (0.0537676); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); 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: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 845.86
//
Query:       gi|385805891|ref|YP_005842289.1|  [L=337]
Description: AIR synthase related protein domain protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.1e-21   75.0   0.0    9.9e-21   74.5   0.0    1.2  1  AIRS_C    AIR synthase related protein, C-terminal domain
    4.1e-16   59.4   0.1    8.5e-16   58.4   0.1    1.5  1  AIRS      AIR synthase related protein, N-terminal domain


Domain annotation for each model (and alignments):
>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.5   0.0   1.1e-24   9.9e-21       1     151 [.     151     307 ..     151     312 .. 0.87

  Alignments for each domain:
  == domain 1  score: 74.5 bits;  conditional E-value: 1.1e-24
                                       STTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHH..HTTECEEEE--TTHHHHH CS
                            AIRS_C   1 kpGdvliltgslGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaal..kglvkaahDvTgGGLlga 75 
                                       +pGd +i+t+   l + ++++ ++++   +   s+ ++  +  + ++i v++++ +l  +gl++++hD T+GG++ +
  gi|385805891|ref|YP_005842289.1| 151 QPGDYIIMTKYAALEATALAALDHGDLLVKSGVSSDEINFAKSLIRKISVYKEAMLLseNGLANSMHDPTEGGIIAS 227
                                       79*********9999999999888887777666677777777777788888888888889***************** PP

                                       HHHHHHTTTEEEEEECGTHHHHHHHH......HHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEE CS
                            AIRS_C  76 laemapasgvgaeidldkvpifdele......splemllsensGrllvavppeeadavlaileeeglpeaavIGevt 146
                                         ema as+  ++i+ldk+p++           ++++l s +sG ll +vp+e+a++++ +l++ g+ e+++IGev 
  gi|385805891|ref|YP_005842289.1| 228 SFEMAYASRNDVRIYLDKIPVLPL-TfkilkiIGADPLTSLSSGSLLATVPKEKANEAIGLLKDNGI-ECTIIGEVL 302
                                       *****************8887743.346668889999999***************************.8******** PP

                                       ESSSE CS
                            AIRS_C 147 akeel 151
                                       +++++
  gi|385805891|ref|YP_005842289.1| 303 KGGGK 307
                                       99865 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 !   58.4   0.1   9.4e-20   8.5e-16      10      93 ..      39     138 ..      31     139 .. 0.88

  Alignments for each domain:
  == domain 1  score: 58.4 bits;  conditional E-value: 9.4e-20
                                       EEEE.EECCTCCCC.......HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......HHHHHHHHHHHHHHHTT-EE CS
                              AIRS  10 dshnrpvlvepvhf.......iGakavavnlsDlaamGArPlalllslalp......wleevvrglaeaaeelgvpl 73 
                                       d  n++v+v  v++       iG+++++v+++D+++ GArP+++l +l lp      ++ ++++g++ea++e++  l
  gi|385805891|ref|YP_005842289.1|  39 DIGNEKVIVTHVDPitsaidsIGWLSIHVVANDIVSSGARPRWFLTVLLLPvgtsydDIIKIMSGINEALKEINGTL 115
                                       444677777777777778899******************************************************** PP

                                       EEEEEEEESS...EEEEEEEEEE CS
                              AIRS  74 vgGdtsfsne...ptisvtavGl 93 
                                       vgG+t+f+++    +i +ta+G+
  gi|385805891|ref|YP_005842289.1| 116 VGGHTEFTDSvnrSVIITTAIGE 138
                                       ******99877888999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.49
# Mc/sec: 2068.46
//
Query:       gi|385805892|ref|YP_005842290.1|  [L=200]
Description: hexulose-6-phosphate isomerase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-17   63.2   0.1    3.5e-17   62.5   0.1    1.3  1  SIS       SIS domain
    8.1e-13   48.6   0.8    6.9e-08   32.6   0.5    2.2  2  SIS_2     SIS domain
    0.00034   20.5   1.5       0.39   10.5   0.1    2.2  2  PRMT5     PRMT5 arginine-N-methyltransferase
  ------ inclusion threshold ------
      0.071   12.9   0.0      0.086   12.6   0.0    1.1  1  DUF2855   Protein of unknown function (DUF2855)
       0.13   11.3   0.1          1    8.4   0.0    2.1  2  LigB      Catalytic LigB subunit of aromatic ring-opening dio


Domain annotation for each model (and alignments):
>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.5   0.1   9.6e-21   3.5e-17       4     105 ..      40     135 ..      37     141 .. 0.94

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 9.6e-21
                                       TSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHTT CS
                               SIS   4 kakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelakerg 80 
                                       ++ +i+v+GaG+s+ +++ +a+ l+++g++ ++  d+ +      + i+++d+v++is sg+t   + aa+ ak+ g
  gi|385805892|ref|YP_005842290.1|  40 SKSKILVMGAGRSGLVGRAFAMRLMHLGFNSYVLGDTIT------PSISKGDIVVAISGSGRTELIITAARAAKKTG 110
                                       455**********************************99......88****************************** PP

                                       SEEEEEESSTTSHHHHHSSEEEEEE CS
                               SIS  81 akiiaITdskgsplareadlalyin 105
                                       a+iia+T+  +spl + +dl+l+++
  gi|385805892|ref|YP_005842290.1| 111 AEIIAVTSFLNSPLGEISDLVLEVP 135
                                       *********************9987 PP

>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   6.4e-06     0.023       9      63 ..      15      68 ..       8      80 .. 0.82
   2 !   32.6   0.5   1.9e-11   6.9e-08      96     138 .]      78     118 ..      69     118 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6.4e-06
                                      HHHHHHHHSHHHHHHHHHHHHHHHHTT--EEEEESGGGHHHHHHTSSSTT-BTTE CS
                             SIS_2  9 ilerivetqaeaiekaaeliadslenggkvlvfGsGhSaalaeelaaragglaef 63
                                      i ++i e + ++++++++ ++d+ +++ k+lv+G+G S +    +a r+  l +f
  gi|385805892|ref|YP_005842290.1| 15 INKSIDELKFDEVDRVVKRLVDAYNSKSKILVMGAGRSGLVGRAFAMRLMHL-GF 68
                                      4466777799******************************999999998764.45 PP

  == domain 2  score: 32.6 bits;  conditional E-value: 1.9e-11
                                       HHHTT--TT-EEEEE-SS--SHHHHHHHHHHHHHT-EEEEEE- CS
                             SIS_2  96 lrlvrlkpgDvLlviSnsGnnavvveaaeaakergmkviAlts 138
                                         +  +++gD+ + iS sG+ + ++ aa+aak+ g+++iA+ts
  gi|385805892|ref|YP_005842290.1|  78 TPS--ISKGDIVVAISGSGRTELIITAARAAKKTGAEIIAVTS 118
                                       555..89***********************************8 PP

>> PRMT5  PRMT5 arginine-N-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.1   0.00011      0.39      62      85 ..      34      61 ..       4      73 .. 0.72
   2 !    9.4   0.2   0.00024      0.86      63      99 ..      83     116 ..      68     122 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00011
                                      C.....-EEEEEEES-TTSHHHHHHHHH CS
                             PRMT5 62 s....ekklvilvvGaGRGplvdralka 85
                                           ++k  ilv+GaGR +lv ra+ +
  gi|385805892|ref|YP_005842290.1| 34 LvdayNSKSKILVMGAGRSGLVGRAFAM 61
                                      0333356678************999875 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00024
                                       .-EEEEEEES-TTSHHHHHHHHHHHHHCCCEEEEEEE CS
                             PRMT5  63 ekklvilvvGaGRGplvdralkaleetkvtkvkivav 99 
                                       + ++v+++ G+GR  l+ +a +a+++t+    +i+av
  gi|385805892|ref|YP_005842290.1|  83 KGDIVVAISGSGRTELIITAARAAKKTG---AEIIAV 116
                                       5789********************9999...444444 PP

>> DUF2855  Protein of unknown function (DUF2855)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.4e-05     0.086      70     187 ..      11     123 ..       3     148 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.4e-05
                           DUF2855  70 hlvvspsdlklegfretsphraalmpiYnrylrvsedpay.esdeeealtallrplfetsflledflfddadlsgak 145
                                        +++  + +++ +f e+    + l   Yn+ +++    a  +    +a  + l  l   s++l d +  +   +g  
  gi|385805892|ref|YP_005842290.1|  11 IATFINKSIDELKFDEVDRVVKRLVDAYNSKSKILVMGAGrSGLVGRAFAMRLMHLGFNSYVLGDTITPSIS-KGD- 85 
                                       5555556666677888888888888888887777766665466667888999999999*********99777.455. PP

                           DUF2855 146 vvvllsASsKTAlslayllrkrrkaeegplklvglTSaknra 187
                                       +vv +s S++T l ++ + + ++       +++++TS  n+ 
  gi|385805892|ref|YP_005842290.1|  86 IVVAISGSGRTELIITAARAAKKT----GAEIIAVTSFLNSP 123
                                       9**********9998854444443....489******88874 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 ?    0.7   0.0     0.061   2.2e+02      82     108 ..       1      27 [.       1      44 [. 0.84
   2 ?    8.4   0.0   0.00028         1     153     193 ..      69     109 ..      59     146 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.061
                              LigB  82 leyelkgnpeLaekiaealkksgidla 108
                                       +eye++  +e+a  i +++++ ++d +
  gi|385805892|ref|YP_005842290.1|   1 MEYEYEAMKEIATFINKSIDELKFDEV 27 
                                       6899****************9999953 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00028
                              LigB 153 rlykLGeAlrkaveeldknvlilgsGglsHqlegdeaakad 193
                                       ++y LG+++++ +++ d  v+i gsG     +++ +aak++
  gi|385805892|ref|YP_005842290.1|  69 NSYVLGDTITPSISKGDIVVAISGSGRTELIITAARAAKKT 109
                                       6899**********************877666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       737  (0.0411066); expected 358.6 (0.02)
Passed bias filter:                      646  (0.036031); 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: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1238.11
//
Query:       gi|385805893|ref|YP_005842291.1|  [L=102]
Description: hypothetical protein FFONT_0851 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score 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   13.1   2.1        2.4    8.0   2.1    2.1  1  VHS       VHS domain
      0.067   13.7   0.2      0.085   13.3   0.2    1.1  1  DUF4497   Protein of unknown function (DUF4497)


Domain annotation for each model (and alignments):
>> VHS  VHS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   2.1   0.00026       2.4     107     137 ..      71     101 ..       4     102 .] 0.75

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00026
                                       HHHHHHHHHHHHHHTTT-TTGHHHHHHHHHH CS
                               VHS 107 kkkvlelleeWadafknkpelkkisdvykll 137
                                          +++++ee ++ +++++++++i+d+y++l
  gi|385805893|ref|YP_005842291.1|  71 AISIITAIEEIEELMNQNEKVSYIYDIYNEL 101
                                       44699999999999999**********9987 PP

>> DUF4497  Protein of unknown function (DUF4497)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   9.5e-06     0.085      11      86 ..      13      89 ..      10      96 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.5e-06
                           DUF4497 11 LFaltpedlekklkkfpleisvlkkgeepkkkliGsaeislselfnklikevkekkknepv.sktikgtfpLkdedg 86
                                      L++  +e+ ++ l+ ++l+i+v+k+ge++  +++ + ++ +++++ +l+++++ +k++ ++    i+   +L+++++
  gi|385805893|ref|YP_005842291.1| 13 LYKEAEETKKQALSTIKLSIEVYKDGEKELALVVLKESMRIAKSYLELMDKLDADKDTAISiITAIEEIEELMNQNE 89
                                      667778888999*****************************************997777664555555556665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1588  (0.0885716); expected 358.6 (0.02)
Passed bias filter:                      618  (0.0344693); 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: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 614.98
//
Query:       gi|385805894|ref|YP_005842292.1|  [L=337]
Description: glyoxylate reductase [Fervidicoccus fontis Kam940]
Scores for complete 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  233.3   0.0    1.5e-69  232.9   0.0    1.2  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    8.1e-39  132.3   0.0    9.4e-39  132.1   0.0    1.0  1  2-Hacid_dh     D-isomer specific 2-hydroxyacid dehydrogenase,
    2.4e-05   24.6   0.0    3.9e-05   23.9   0.0    1.3  1  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd
      0.001   18.4   0.0     0.0051   16.1   0.0    2.0  2  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
  ------ inclusion threshold ------
       0.02   15.2   0.0       0.04   14.3   0.0    1.6  1  Gp_dh_N        Glyceraldehyde 3-phosphate dehydrogenase, NAD 
      0.023   14.8   0.0      0.098   12.7   0.0    2.0  2  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi
       0.03   13.9   0.1      0.074   12.6   0.0    1.7  2  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
      0.032   14.1   0.0      0.051   13.4   0.0    1.3  1  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
       0.04   13.8   0.0      0.076   12.9   0.0    1.4  1  Lipocalin_7    Lipocalin / cytosolic fatty-acid binding prote
      0.067   13.6   0.0       0.15   12.5   0.0    1.6  1  NAD_binding_7  Putative NAD(P)-binding
       0.11   13.0   0.3       0.35   11.5   0.2    1.9  1  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent


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 !  232.9   0.0   9.5e-73   1.5e-69       1     178 []     110     293 ..     110     293 .. 0.98

  Alignments for each domain:
  == domain 1  score: 232.9 bits;  conditional E-value: 9.5e-73
                                       HHHHHHHHTTHHHHHHHHHTTCC......HTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHH CS
                      2-Hacid_dh_C   1 lalllallrrlaeadeevregew......ksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkk 71 
                                       +al+la++rr+ ead+ vr+g w      + +  llg el+gkt+GiiG+GrIG+ava+r+ +f+m++++yd++k +
  gi|385805894|ref|YP_005842292.1| 110 FALILAITRRIVEADKFVRDGSWersrtgWHPLMLLGMELKGKTLGIIGMGRIGRAVAQRALGFEMNILYYDVNKLP 186
                                       589********************9888888888999***************************************** PP

                                       HHCHHHHTCEECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCCE CS
                      2-Hacid_dh_C  72 eeeeeelgvelvsleellaesDivslhlpltpetrhlinaeelakmkkgailiNtaRGglvdeeaLleaLksgkiag 148
                                        eee++l+++++sleell++sD+vs+h+ l+++t+hlin+e+l++mkk+a++iN+aRG+++d++aL++aLk+g+iag
  gi|385805894|ref|YP_005842292.1| 187 PEEEKRLNAQYASLEELLEKSDVVSIHTDLNKSTYHLINEERLKRMKKTAYIINVARGPIIDTQALVKALKEGWIAG 263
                                       ***************************************************************************** PP

                                       EEES--SSSSSGTCHHHHHSTTEEE-SS-T CS
                      2-Hacid_dh_C 149 aalDvfeeeplpedspllelpnviltPHia 178
                                       a+lDvfe+eplp++++l++l+nv++ PHi+
  gi|385805894|ref|YP_005842292.1| 264 AGLDVFESEPLPSNHELTKLNNVVIVPHIG 293
                                       ****************************98 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 !  132.1   0.0   5.8e-42   9.4e-39       1     134 []       6     325 ..       6     325 .. 0.99

  Alignments for each domain:
  == domain 1  score: 132.1 bits;  conditional E-value: 5.8e-42
                                       EEEEST.CHHHHHHHHHTTE.EEEEES...CSSHHHCHHHHTTESEEEE-TTS-BSHHHHHHHTT--EEEESSSSCT CS
                                       xxxxxxxxxxxxxxxxxxxx.xxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        2-Hacid_dh   1 vlileplreeelellkeegv.evevkd...ellteellekakdadalivrsntkvtaevlealpkLkviaragvGvD 73 
                                       v i++++++ +lel+k+  + evev+    ++++e llek+k++d+l+   ++k++ae+l+++++Lk+i++++vG+D
  gi|385805894|ref|YP_005842292.1|   6 VYITREIPSVGLELIKK--YfEVEVWPeywAPPREILLEKVKNIDGLVSLLTDKIDAELLDKAKNLKIISQYAVGYD 80 
                                       678999999********..66******************************************************** PP

                                       TB-HHHHHHTT-EEEE-TTTTHHHHHHHH................................................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................................ RF
                        2-Hacid_dh  74 nvDldaakerGilVtnvpgystesvAElt................................................ 102
                                       n+Dl++a+++G+ Vtn+pg+ t+s+A+lt                                                
  gi|385805894|ref|YP_005842292.1|  81 NIDLSYATKKGVYVTNTPGVLTDSTADLTfalilaitrriveadkfvrdgswersrtgwhplmllgmelkgktlgii 157
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                        2-Hacid_dh 103 ............................................................................. 102
                                                                                                                    
  gi|385805894|ref|YP_005842292.1| 158 gmgrigravaqralgfemnilyydvnklppeeekrlnaqyasleelleksdvvsihtdlnkstyhlineerlkrmkk 234
                                       ***************************************************************************** PP

                                       ...........................................................T-BHHHHHHHHHHHHHHH CS
                                       ...........................................................xxxxxxxxxxxxxxxxxx RF
                        2-Hacid_dh 103 ...........................................................aaTeeaqeniaeeaaenl 120
                                                                                                  +aT+ea++ +a+++a+nl
  gi|385805894|ref|YP_005842292.1| 235 tayiinvargpiidtqalvkalkegwiagagldvfeseplpsnheltklnnvvivphigSATHEARNGMAMKVATNL 311
                                       ***************************************************************************** PP

                                       HHHHTTCCGTTBCS CS
                                       xxxxxxxxxxxxxx RF
                        2-Hacid_dh 121 vaflkgespanavn 134
                                       ++fl+g+ p++ vn
  gi|385805894|ref|YP_005842292.1| 312 IEFLNGRVPPDLVN 325
                                       ***********998 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 !   23.9   0.0   2.4e-08   3.9e-05       2     106 ..     154     258 ..     153     266 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 2.4e-08
                                       EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS.HC CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevieg.ll 77 
                                       +g+iG+G +G+  a++ l  ++++  y+++k   ee    +a  ++s+eel+++ dvv +    +k + ++i++  l
  gi|385805894|ref|YP_005842292.1| 154 LGIIGMGRIGRAVAQRALGFEMNILYYDVNKLPPEEEKRLNA-QYASLEELLEKSDVVSIHTDLNKSTYHLINEeRL 229
                                       79****************************988888777776.67899************************99999 PP

                                       CC--TT-EEEE-S---HHHHHHHHHHHHH CS
                     NAD_binding_2  78 ealkkgdilidgstsspedtrelakelke 106
                                       +++kk +++i+++   + dt+ l k+lke
  gi|385805894|ref|YP_005842292.1| 230 KRMKKTAYIINVARGPIIDTQALVKALKE 258
                                       9***********************99997 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   3.2e-06    0.0051      32     128 ..     155     242 ..     141     258 .. 0.85
   2 ?   -1.1   0.0      0.59   9.6e+02     102     121 ..     316     335 ..     300     335 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.2e-06
                                       EEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHHHHHH-SEE.EE---BTTSS-- CS
                       AlaDh_PNT_C  32 lviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeellaeavkeadvv.igtvlipGkkaP 107
                                        +iG G  G + ++ a g++ ++  +Dv++   e+ + l+a+         ++l+e ++++dvv i t     k++ 
  gi|385805894|ref|YP_005842292.1| 155 GIIGMGRIGRAVAQRALGFEMNILYYDVNKLPPEEEKRLNAQ--------YASLEELLEKSDVVsIHT--DLNKSTY 221
                                       59***************************9999988777777........7899999*****983333..2356778 PP

                                       -SC-HHHHHTS-TTEEEEETT CS
                       AlaDh_PNT_C 108 kLvteemvksMkpgsVivDvA 128
                                       +L++ee +k+Mk+ + i+ vA
  gi|385805894|ref|YP_005842292.1| 222 HLINEERLKRMKKTAYIINVA 242
                                       9*****************999 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.59
                                       TTSS---SC-HHHHHTS-TT CS
                       AlaDh_PNT_C 102 pGkkaPkLvteemvksMkpg 121
                                        G+  P Lv++e+v+  kpg
  gi|385805894|ref|YP_005842292.1| 316 NGRVPPDLVNKEVVNVRKPG 335
                                       69999*********988887 PP

>> Gp_dh_N  Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   2.4e-05      0.04       3      50 ..     154     202 ..     152     242 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.4e-05
                                       EEEESTSHHHHHHHHHHHHHT.TCEEEEEE-TS-HHHHHHHHHEETTTE CS
                           Gp_dh_N   3 vainGfGRIGrlvlralleek.elevvaindltdletlayllkyDsvhg 50 
                                       ++i G+GRIGr v++ +l  + ++    +n+l   e+     +y s   
  gi|385805894|ref|YP_005842292.1| 154 LGIIGMGRIGRAVAQRALGFEmNILYYDVNKLPPEEEKRLNAQYASLEE 202
                                       79************99995444888888888766666666666666555 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0     6e-05     0.098      21     111 ..     149     243 ..     145     262 .. 0.82
   2 ?   -1.8   0.0       1.8   2.9e+03      95     116 ..     278     299 ..     274     313 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6e-05
                                       -TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HHHCTTT-SEEEE-SS.SS...SSB- CS
                     AdoHcyase_NAD  21 laGkvavvaGyGdvGkGcaaslkglGarvivtevdPicalqaameGfevvtleevvkkadivvtttG.nk...diit 93 
                                       l Gk+  ++G G +G+  a+   g+   ++  +v+ +          + + lee+++k+d+v   t  nk    +i+
  gi|385805894|ref|YP_005842292.1| 149 LKGKTLGIIGMGRIGRAVAQRALGFEMNILYYDVNKLPPEEEKRLNAQYASLEELLEKSDVVSIHTDlNKstyHLIN 225
                                       689**************99999999999999999999888888888999***********997666424422269** PP

                                       HHHHCCS-TTEEEEE-SS CS
                     AdoHcyase_NAD  94 lehlkkmkddaivcniGh 111
                                        e+lk+mk++a + n+  
  gi|385805894|ref|YP_005842292.1| 226 EERLKRMKKTAYIINVAR 243
                                       ***************975 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.8
                                       HHHCCS-TTEEEEE-SSTTTTB CS
                     AdoHcyase_NAD  95 ehlkkmkddaivcniGhfdsei 116
                                       ++l+k+++ +iv  iG  ++e 
  gi|385805894|ref|YP_005842292.1| 278 HELTKLNNVVIVPHIGSATHEA 299
                                       5788999999999999888775 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.3   3.7e+03      67      94 ..      53      72 ..      42      99 .. 0.54
   2 ?   12.6   0.0   4.6e-05     0.074       2      89 ..     149     236 ..     148     256 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.3
                                      -S-HHHHHHHHHHHTGGG--TT-EEEES CS
                              IlvN 67 liPDelqkevyeeeiepnlkegkalafa 94
                                      l+ D++ +e++++         k l+  
  gi|385805894|ref|YP_005842292.1| 53 LLTDKIDAELLDK--------AKNLKII 72
                                      4455555444433........2333333 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 4.6e-05
                                       HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-H.HHHHHHHTT-EEEEHHHHHHT-SEEEE-S-.HHHHHHH CS
                              IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsk.svkkAkeegfevltvaeavkkadvvmiliP.Delqkev 76 
                                       lkgk++ +iG+G  G+a a+      +++ +  ++ +k   ++ k+ + + ++++e+ +k+dvv i +  ++   ++
  gi|385805894|ref|YP_005842292.1| 149 LKGKTLGIIGMGRIGRAVAQRALGFEMNILY--YDVNKlPPEEEKRLNAQYASLEELLEKSDVVSIHTDlNKSTYHL 223
                                       89*****************966655555555..444432556667777888999*********99876423334444 PP

                                       HHHHTGGG--TT- CS
                              IlvN  77 yeeeiepnlkegk 89 
                                       ++ee  + +k+ +
  gi|385805894|ref|YP_005842292.1| 224 INEERLKRMKKTA 236
                                       5454444555444 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   0.0   3.2e-05     0.051       2      53 ..     154     207 ..     153     242 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.2e-05
                                       EEEE--SCCHHHHHHHHHHTT-EEEEE-S......-HHHHHHHHHHHHHHHHCCTTTT CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdi......seealekalekieksleklvekg 53 
                                       +++iG G +G+ +a+ ++  ++++  +d+      +e++l++  +++e+ l    ek 
  gi|385805894|ref|YP_005842292.1| 154 LGIIGMGRIGRAVAQRALGFEMNILYYDVnklppeEEKRLNAQYASLEELL----EKS 207
                                       79***************************5544444444444444444444....333 PP

>> Lipocalin_7  Lipocalin / cytosolic fatty-acid binding protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   4.7e-05     0.076       9      66 ..      41     100 ..      37     122 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.7e-05
                                       EEEEESHHHHHHHHT..--HHHHHHHHTS-EEEEEEEETTEEEEEEEETTTEEEEEEEET CS
                       Lipocalin_7   9 leseknydefmkrlg..lpsdviekarnlkiitevkqdgqnftwsqsysgghsltnkfti 66 
                                       le  kn d ++ +l+  +  + ++ka+nlkii++     +n+  s     g  +tn+  +
  gi|385805894|ref|YP_005842292.1|  41 LEKVKNIDGLVSLLTdkIDAELLDKAKNLKIISQYAVGYDNIDLSYATKKGVYVTNTPGV 100
                                       6788999999999964588999************99999999999999999999998655 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   0.0   9.2e-05      0.15       3      81 ..     147     226 ..     145     246 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.2e-05
                     NAD_binding_7   3 ldlkgkkvlvvGgGevAarkvrklleagakvtvvapev.keeleelvklaeeelekdlegadlviaatddrelneri 78 
                                       ++lkgk+  ++G G+++   +++ l ++ ++  ++ +   +e e++++++   le+ le+ d+v + td ++   ++
  gi|385805894|ref|YP_005842292.1| 147 MELKGKTLGIIGMGRIGRAVAQRALGFEMNILYYDVNKlPPEEEKRLNAQYASLEELLEKSDVVSIHTDLNKSTYHL 223
                                       689*************************99999988764566678899999999*************9866655444 PP

                     NAD_binding_7  79 aea 81 
                                        ++
  gi|385805894|ref|YP_005842292.1| 224 INE 226
                                       443 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   0.00022      0.35       2      65 ..     154     210 ..     153     231 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00022
                                       EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEE CS
                     F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvv 65 
                                       +giiG+G++g+a+a+++l       +i+     + +k+    ee   +++  + ee++e++dvv
  gi|385805894|ref|YP_005842292.1| 154 LGIIGMGRIGRAVAQRALGFE---MNILYY---DVNKLPPE-EEKRLNAQYASLEELLEKSDVV 210
                                       8**************988766...555522...33333222.2223344445566666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      624  (0.0348039); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2188.88
//
Query:       gi|385805895|ref|YP_005842293.1|  [L=407]
Description: ORC complex protein Cdc6/Orc1 [Fervidicoccus fontis Kam940]
Scores for complete 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   0.6    1.7e-19   69.5   0.4    2.0  1  Cdc6_C          CDC6, C terminal winged helix domain
    9.5e-13   48.6   0.8    5.4e-12   46.2   0.0    2.3  2  AAA_22          AAA domain
    2.6e-12   47.5   0.3    3.5e-09   37.3   0.0    2.9  2  AAA_16          AAA ATPase domain
    2.6e-10   40.8   0.5    2.7e-09   37.6   0.2    2.7  2  AAA             ATPase family associated with various cellula
    2.5e-09   36.8   0.1    2.9e-08   33.4   0.0    2.1  2  TniB            Bacterial TniB protein
    0.00011   21.5   0.1     0.0011   18.2   0.0    2.4  3  DUF815          Protein of unknown function (DUF815)
    0.00014   21.9   1.4    0.00014   21.9   1.4    2.7  3  ATPase_2        ATPase domain predominantly from Archaea
    0.00025   20.0   0.5       0.27   10.0   0.0    2.2  2  AAA_32          AAA domain
    0.00038   19.7   0.0    0.00075   18.8   0.0    1.5  1  NB-ARC          NB-ARC domain
    0.00051   20.3   0.2     0.0016   18.7   0.2    1.8  1  AAA_assoc_2     AAA C-terminal domain
    0.00053   19.3   0.0    0.00099   18.4   0.0    1.3  1  PIF1            PIF1-like helicase
    0.00066   19.0   0.1        0.1   11.8   0.0    2.4  2  KAP_NTPase      KAP family P-loop domain
      0.009   15.9   0.0      0.017   15.0   0.0    1.5  1  NACHT           NACHT domain
  ------ inclusion threshold ------
      0.014   14.9   0.0      0.027   14.0   0.0    1.4  1  AAA_7           P-loop containing dynein motor region
      0.016   15.3   0.1      0.048   13.7   0.0    1.8  2  ResIII          Type III restriction enzyme, res subunit
      0.016   15.0   0.1       0.55   10.0   0.0    2.5  2  Bac_DnaA        Bacterial dnaA  protein
      0.017   14.2   0.0      0.035   13.2   0.0    1.5  1  T2SSE           Type II/IV secretion system protein
      0.023   15.3   1.3      0.074   13.7   0.8    2.0  1  Mg_chelatase_C  Magnesium chelatase, subunit ChlI C-terminal
      0.032   13.5   0.0      0.074   12.3   0.0    1.6  1  Zeta_toxin      Zeta toxin
      0.035   14.2   0.0        0.1   12.8   0.0    1.8  1  TIP49_C         TIP49 AAA-lid domain
      0.041   13.9   0.3       0.11   12.5   0.0    1.8  1  TsaE            Threonylcarbamoyl adenosine biosynthesis prot
      0.051   13.5   0.0       0.12   12.3   0.0    1.6  1  Microtub_bd     Microtubule binding
      0.067   13.3   0.0       0.17   12.1   0.0    1.7  1  AAA_33          AAA domain
      0.071   12.0   0.0       0.17   10.8   0.0    1.6  1  Kinesin         Kinesin motor domain
       0.14   12.3   0.2         16    5.7   0.0    2.4  2  HTH_54          ParA helix turn helix 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 !   69.5   0.4   2.4e-22   1.7e-19       1      83 [.     311     391 ..     311     392 .. 0.96

  Alignments for each domain:
  == domain 1  score: 69.5 bits;  conditional E-value: 2.4e-22
                                       HHHHHHHHCHCSSS-EEHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSS CS
                            Cdc6_C   1 LcalvlllrksgkeevttgevyevYkslCesegvdpltqrevsdllseLemlgileleksskGrregrtrkisLnvd 77 
                                       L+++v l+r +gk+++ttge++ +Y++ ++++ +++ltqr+v d++seL+m+g++++++ s+Gr +g+t+ ++L  +
  gi|385805895|ref|YP_005842293.1| 311 LASIVDLTR-RGKDSATTGEIFVEYSKKTSELRLETLTQRRVTDIISELDMMGLVSARVISRGR-YGKTKVVKLIAN 385
                                       789******.*****************************************************9.*********998 PP

                                       CHHHHH CS
                            Cdc6_C  78 pddvle 83 
                                        ++vl+
  gi|385805895|ref|YP_005842293.1| 386 LNTVLN 391
                                       888876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.0   7.5e-15   5.4e-12       6     129 ..      62     187 ..      57     195 .. 0.84
   2 ?   -0.1   0.0       1.4     1e+03      37      90 ..     290     359 ..     276     369 .. 0.61

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 7.5e-15
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseelleal 82 
                                       + ++ +G +GtGKT +++ ++++l+e+a   + + ++v+v++ +  +s  +l ++ + lg      +ls+ el+++l
  gi|385805895|ref|YP_005842293.1|  62 NNIFTYGLTGTGKTAVVKLVTKKLQERAVELKLPIQTVYVNCRQRDTSYRVLADIIESLGGHVPFTGLSLAELYRRL 138
                                       567789******************88776666****************************999999*********** PP

                            AAA_22  83 eqalraravielliiDEaqhlr..s.eealeeLrsllnlsrkgvqliLvG 129
                                          l++ + + ++i+DE+++++  + +++l +L ++ + + k+ +l ++G
  gi|385805895|ref|YP_005842293.1| 139 ISKLESLGGRFIVILDEIDFIIkkQgDDLLYKLTRINE-ELKNSSLSMIG 187
                                       *********888999*****876525888888855544.45555555555 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.4
                            AAA_22  37 e.erpevvfvtlpsstsskdllrellralglelka..............erlsseell.ealeqalrara 90 
                                       e e+++v++v  + +   k +l  ++  + +++++              ++l++e l  +++++ +++ +
  gi|385805895|ref|YP_005842293.1| 290 ElEKDKVYEVVSTLPLHAKLILASIVDLTRRGKDSattgeifveyskktSELRLETLTqRRVTDIISELD 359
                                       1466666666666666667777777777776666666666666655555557777777777777766665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.0   4.9e-12   3.5e-09       2      76 ..      38     117 ..      37     124 .. 0.83
   2 !    7.3   0.0     0.008       5.7     118     163 ..     130     176 ..     119     186 .. 0.82

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 4.9e-12
                            AAA_16   2 lvGReeeleqLlsale.rvrsgrpelvllsGesGvGKsslvrellralekd......ggiflrgkcdqlesaipysa 71 
                                       l+ Ree++++++s+l  ++r +rp++++ +G  G+GK+++v+ + + l+++       + +++ +c+q   +++y +
  gi|385805895|ref|YP_005842293.1|  38 LPFREEQIKKIASILAqALRNSRPNNIFTYGLTGTGKTAVVKLVTKKLQERavelklPIQTVYVNCRQR--DTSYRV 112
                                       789*************77888888***************************666654455566666666..899988 PP

                            AAA_16  72 laqal 76 
                                       la+++
  gi|385805895|ref|YP_005842293.1| 113 LADII 117
                                       88887 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.008
                            AAA_16 118 rllellkrllallsrderplvlvlDdlq.wadeaslqllaaLlrlle 163
                                       +l+el +rl+++l++ +  ++++lD+++  ++ +  +ll+ L r  e
  gi|385805895|ref|YP_005842293.1| 130 SLAELYRRLISKLESLGGRFIVILDEIDfIIKKQGDDLLYKLTRINE 176
                                       7899999***888888999*********8788888888998887755 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 !   37.6   0.2   3.7e-12   2.7e-09       3     122 ..      66     204 ..      64     214 .. 0.82
   2 ?   -0.9   0.0       2.8     2e+03      10      20 ..     375     385 ..     373     401 .. 0.85

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 3.7e-12
                                       EESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS.........................STTHH.HHHHHHHHHHH CS
                               AAA   3 lyGppGtGKTllakavakelgvefleisgsellsk.........................yvges.ekkirelfkea 53 
                                        yG  GtGKT+++k v k+l+ + +e++++  +                           + g s ++  r l++++
  gi|385805895|ref|YP_005842293.1|  66 TYGLTGTGKTAVVKLVTKKLQERAVELKLPIQTVYvncrqrdtsyrvladiieslgghvpFTGLSlAELYRRLISKL 142
                                       69******************9888877777666225677888889999999******99955555156667888888 PP

                                       HHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS...GGGSTHHHHST CS
                               AAA  54 kekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnr...pdkldpallrg 122
                                       ++  +  i+++DEid ++k++       +++++ +L +  +++k+  s + +ig+tn+   +d+ldp ++ +
  gi|385805895|ref|YP_005842293.1| 143 ESLGGRFIVILDEIDFIIKKQ-------GDDLLYKLTRINEELKN--SSLSMIGITNDlnfIDNLDPRIR-S 204
                                       877777***************.......9999***9999999999..479********888888888888.3 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.8
                                       SHHHHHHHHHH CS
                               AAA  10 GKTllakavak 20 
                                       GKT ++k +a+
  gi|385805895|ref|YP_005842293.1| 375 GKTKVVKLIAN 385
                                       9********98 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.0     4e-11   2.9e-08      24     170 ..      50     196 ..      39     211 .. 0.83
   2 ?    1.1   0.0      0.31   2.2e+02      36      65 ..     364     393 ..     334     406 .. 0.75

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 4e-11
                              TniB  24 eeLleypkrkrmpnlllvGdsnnGKtmivekFarlhppekdedaekvpvlvvqappkpdekrlyaaiLealgaplka 100
                                         L ++ +++r++n+  +G + +GKt++v+  +++ +++  e +  ++ ++v+++++ +  r  a i+e+lg  +  
  gi|385805895|ref|YP_005842293.1|  50 SILAQALRNSRPNNIFTYGLTGTGKTAVVKLVTKKLQERAVELKLPIQTVYVNCRQRDTSYRVLADIIESLGGHVPF 126
                                       346677899************************999999999999**************************988876 PP

                              TniB 101 ra.rvskleqqvlrllrelkvrvL.iiDEihnllagsarkqreflnalksLgnelkip.ivlvGteealralr 170
                                       +  ++++l+++ ++ l++l+ r + i+DEi+ ++    ++   +l  l ++++elk + + ++G+++ l++++
  gi|385805895|ref|YP_005842293.1| 127 TGlSLAELYRRLISKLESLGGRFIvILDEIDFII---KKQGDDLLYKLTRINEELKNSsLSMIGITNDLNFID 196
                                       654999***************966167******9...677788999999999999864156778877777774 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.31
                              TniB  36 pnlllvGdsnnGKtmivekFarlhppekde 65 
                                        ++ ++++   GKt++v+  a+l++  +  
  gi|385805895|ref|YP_005842293.1| 364 VSARVISRGRYGKTKVVKLIANLNTVLNAL 393
                                       567899999********9988888766654 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.6e-06    0.0011      33      83 ..      41      91 ..      30     110 .. 0.89
   2 ?   -0.2   0.1      0.63   4.5e+02      96     118 ..     136     158 ..     129     174 .. 0.83
   3 ?   -2.0   0.1       2.2   1.6e+03      92     119 ..     168     195 ..     154     199 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.6e-06
                            DUF815 33 idkqkealventeqfleglpannvLLwGarGtGKSslvkallneyaeegLr 83
                                       ++q +++ +  +q l++ + nn++ +G  GtGK ++vk ++++++e+ + 
  gi|385805895|ref|YP_005842293.1| 41 REEQIKKIASILAQALRNSRPNNIFTYGLTGTGKTAVVKLVTKKLQERAVE 91
                                      588999999999*********************************999854 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.63
                            DUF815  96 pklvellrerperfilfvDDLsF 118
                                        +l+++l++   rfi+ +D + F
  gi|385805895|ref|YP_005842293.1| 136 RRLISKLESLGGRFIVILDEIDF 158
                                       578999999**********9988 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 2.2
                            DUF815  92 lkelpklvellrerperfilfvDDLsFe 119
                                       l +l ++ e+l++++  +i    DL F 
  gi|385805895|ref|YP_005842293.1| 168 LYKLTRINEELKNSSLSMIGITNDLNFI 195
                                       6789999999999999999999999995 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 !   21.9   1.4     2e-07   0.00014       4     153 ..      41     179 ..      40     190 .. 0.70
   2 ?   -2.5   0.1       5.3   3.8e+03      76      95 ..     281     300 ..     265     325 .. 0.54
   3 ?   -3.3   0.0       9.4   6.8e+03      30      44 ..     373     387 ..     368     394 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 2e-07
                          ATPase_2   4 Rekelkeleeiler....epneiyfiYGpegsGKtaLlkeiienledkdk......yviyyialreesiskldefie 70 
                                       Re+ +k++ +il +    ++ + +f YG  g GKta++k + ++l++         + +y++  r++++s+      
  gi|385805895|ref|YP_005842293.1|  41 REEQIKKIASILAQalrnSRPNNIFTYGLTGTGKTAVVKLVTKKLQERAVelklpiQTVYVN-CRQRDTSYRVLA-- 114
                                       999999999987651111566789*****************999977665444553344433.333333322222.. PP

                          ATPase_2  71 eeeekkklekalgiavpkaeleeilkeksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLln 147
                                              + + lg  vp + l         l++ +  +l+ k++  g + i+i+De+  +i  + ++  +l+++L +
  gi|385805895|ref|YP_005842293.1| 115 ------DIIESLGGHVPFTGL--------SLAELY-RRLISKLESLGGRFIVILDEIDFII--K-KQGDDLLYKLTR 173
                                       ......355566666666666........665555.7889999**************9999..4.678999999999 PP

                          ATPase_2 148 lieslt 153
                                       + e+l 
  gi|385805895|ref|YP_005842293.1| 174 INEELK 179
                                       888754 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.3
                          ATPase_2  76 kklekalgiavpkaeleeil 95 
                                       k+  +++ ++++k+++ e++
  gi|385805895|ref|YP_005842293.1| 281 KEHVEKARKELEKDKVYEVV 300
                                       33333333333333333333 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 9.4
                          ATPase_2  30 gsGKtaLlkeiienl 44 
                                       + GKt+++k i++  
  gi|385805895|ref|YP_005842293.1| 373 RYGKTKVVKLIANLN 387
                                       579999999888765 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00037      0.27      31      71 ..      62     105 ..      49     114 .. 0.76
   2 !    8.2   0.2    0.0013      0.94     478     510 ..     258     290 ..     223     293 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00037
                            AAA_32  31 YNifvlGesgtGrttlvk...rlleeiakkeptpdDwcYvnnfd 71 
                                        Nif  G +gtG+t +vk   + l+e+a + + p   +Yvn  +
  gi|385805895|ref|YP_005842293.1|  62 NNIFTYGLTGTGKTAVVKlvtKKLQERAVELKLPIQTVYVNCRQ 105
                                       5*************987622255667777788888999997555 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0013
                            AAA_32 478 seiadllrEAdywakkegaevveaehVekAlee 510
                                       ++  dllr A  +a++eg+e v++ehVekA +e
  gi|385805895|ref|YP_005842293.1| 258 RKALDLLRVAGEIAEREGDEKVRKEHVEKARKE 290
                                       6789**************************887 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0     1e-06   0.00075       3     112 ..      43     156 ..      41     167 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1e-06
                                       HHHHHHHHHHHC...TTTSCSEEEEEEESTTSSHHHHHHHHCCSHCC..CCCCBT.EEEEEEEESXXHHHHHHHXXH CS
                            NB-ARC   3 ksvekviekLle...kdelqslvvalvGmgGvGKttlakqilnksde..vegrFd.svawvvvsktdkseeiletil 73 
                                       ++++k++  L +   +  ++   ++ +G  G GKt ++k + +k++e  ve + +   ++v   + d+s+++l +i+
  gi|385805895|ref|YP_005842293.1|  43 EQIKKIASILAQalrNSRPN--NIFTYGLTGTGKTAVVKLVTKKLQEraVELKLPiQTVYVNCRQRDTSYRVLADII 117
                                       55666666665542144444..89********************988224557777789999*************** PP

                                       HHHHCCCTTSSSS-STTSHHHHHHHHCCCT..TEEEEEEEE CS
                            NB-ARC  74 keLslseddleekeeveslkrklvrlLltk..rfllvlDDV 112
                                       + L+ +       +  e l r+l   L++   rf+++lD +
  gi|385805895|ref|YP_005842293.1| 118 ESLGGH-VPFTGLSLAE-LYRRLISKLESLggRFIVILDEI 156
                                       ***887.6666666555.88999999988677*******76 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 !   18.7   0.2   2.2e-06    0.0016      11      75 ..     245     302 ..     237     304 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.2e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXHHHHHHH CS
                       AAA_assoc_2  11 alealaeladGDaRkaLnlLElaaeaaeakegkieitledleealqrkalryDkagdehYdliSA 75 
                                        ++ala+  +GDaRkaL lL +a e ae+ eg++++ +e++e+a +      + ++d+ Y+++S 
  gi|385805895|ref|YP_005842293.1| 245 LCAALAAREHGDARKALDLLRVAGEIAER-EGDEKVRKEHVEKARK------ELEKDKVYEVVST 302
                                       4567888889***************9986.999********97653......2334557777775 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.4e-06   0.00099       5      49 ..      43      88 ..      40      93 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.4e-06
                                      HH.HHHHHHH......HCTS-EEEEESTTSSCHHHHHHHHHHCHCT CS
                              PIF1  5 eQ.kkvfdaiieavlnekgklfFvtGsgGtgKtflwkallkklrse 49
                                      eQ kk++    +a+ n++++++F +G  GtgKt + k ++kkl+++
  gi|385805895|ref|YP_005842293.1| 43 EQiKKIASILAQALRNSRPNNIFTYGLTGTGKTAVVKLVTKKLQER 88
                                      5525666666678889************************999876 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   0.00014       0.1       2      48 ..      46      89 ..      45     126 .. 0.81
   2 ?    4.8   0.0     0.019        14     156     183 ..     130     157 ..     121     174 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00014
                        KAP_NTPase  2 dlyasaladilseptlatpivvgLygkWGsGKssllnkledelkefa 48
                                      +++as la+ l ++ + + ++ gL+   G+GK+++++++ ++l+e+a
  gi|385805895|ref|YP_005842293.1| 46 KKIASILAQALRNSRPNNIFTYGLT---GTGKTAVVKLVTKKLQERA 89
                                      6899*****************9999...68***************96 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.019
                        KAP_NTPase 156 eveelladmektLdalqkrlVvviDdLD 183
                                       + +el+ +++++L+ l  r +v++D++D
  gi|385805895|ref|YP_005842293.1| 130 SLAELYRRLISKLESLGGRFIVILDEID 157
                                       6678999********************9 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.4e-05     0.017       3     112 ..      64     171 ..      62     209 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.4e-05
                                       EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-........-HCHHHCCCCTS--SSS-CCHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgna.....rsladllfsqlpepaapvsevwa 74 
                                       ++  G  G GKT+ ++ +  +++e+  + +      ++++r++ +s ++      sl  ++   ++ +a+  ++ ++
  gi|385805895|ref|YP_005842293.1|  64 IFTYGLTGTGKTAVVKLVTKKLQERAVELKLPIQTVYVNCRQRDTSYRVladiiESLGGHVPFTGLSLAELYRRLIS 140
                                       677899********************999874445577777777776444333333333333344555556666888 PP

                                       HHCCSCCCEEEEEE-STT-SS-TCH.........HHHH CS
                             NACHT  75 vllelperlLlilDglDelvtdlgqkekqpvrtlLsel 112
                                        l +l  r   ilD +D + ++ g        +lL +l
  gi|385805895|ref|YP_005842293.1| 141 KLESLGGRFIVILDEIDFIIKKQGD-------DLLYKL 171
                                       8888889999******998876665.......455444 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 ?   14.0   0.0   3.7e-05     0.027      33      62 ..      61      90 ..      36     119 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.7e-05
                             AAA_7 33 kkpvllvGptGtGKtviikdllkkldkeky 62
                                       ++++ +G tGtGKt+++k ++kkl+++ +
  gi|385805895|ref|YP_005842293.1| 61 PNNIFTYGLTGTGKTAVVKLVTKKLQERAV 90
                                      3568999******************96544 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   6.7e-05     0.048       2      51 ..      38      88 ..      37     103 .. 0.84
   2 ?   -2.5   0.0         6   4.3e+03      56      67 ..     148     159 ..     129     236 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.7e-05
                                      -EE-HHHHHHHHHHT.......TTSEEEEEESTTSTHHHHHHHHHHHH-S. CS
                            ResIII  2 lelreyQeeaienll.eklkskrdkrglikmaTGtGKTlvaaklierllkk 51
                                      l +re Q++ i ++l ++l + r ++++    TGtGKT v   ++++l++ 
  gi|385805895|ref|YP_005842293.1| 38 LPFREEQIKKIASILaQALRNSRPNNIFTYGLTGTGKTAVVKLVTKKLQER 88
                                      5799*********9966777677778888999********99998888775 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 6
                                       -EEEEESSHHHH CS
                            ResIII  56 kflflvprksll 67 
                                       +f+++ ++++ +
  gi|385805895|ref|YP_005842293.1| 148 RFIVILDEIDFI 159
                                       566666655433 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00077      0.55      22      67 ..      48      94 ..      40     119 .. 0.82
   2 ?    2.3   0.1      0.17   1.3e+02     100     155 ..     150     206 ..     132     266 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00077
                                      HHHHHHHS.TTT.S--EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-E CS
                          Bac_DnaA 22 aalkvaea.pgkkynPlfiygevGlGktHLlkaignevlenapelrv 67
                                      +a  +a+a  +++ n +f yg +G Gkt ++k ++++++e+a el++
  gi|385805895|ref|YP_005842293.1| 48 IASILAQAlRNSRPNNIFTYGLTGTGKTAVVKLVTKKLQERAVELKL 94
                                      4555666634458899*********************9999988875 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.17
                                       EEEEE-GGGGTT-HHHHHHHHHHHHHHHTTT-EE...EEEESS-TTT-SS--HHHHHHH CS
                          Bac_DnaA 100 vLliDDiqflagkektqeelfhtfnalleegkqv...vlssDrsPkeleeledrlrsrf 155
                                       ++++D+i f+ +k++  ++l+  ++ + ee k+    ++      + +++l+ r+rs +
  gi|385805895|ref|YP_005842293.1| 150 IVILDEIDFIIKKQG--DDLLYKLTRINEELKNSslsMIGITNDLNFIDNLDPRIRSSL 206
                                       6899*********95..444444444444444330002233333455667777777765 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 ?   13.2   0.0   4.9e-05     0.035     106     157 ..      36      89 ..      16     111 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.9e-05
                             T2SSE 106 ddlgaeealkekiaevlrkavrer..glilvsGgTgsGKttllyallkeinksd 157
                                       ++l ++e++ +kia++l++a+r+    +i   G Tg+GKt ++  + k+++++ 
  gi|385805895|ref|YP_005842293.1|  36 ENLPFREEQIKKIASILAQALRNSrpNNIFTYGLTGTGKTAVVKLVTKKLQERA 89 
                                       6788899999**********985422688888**********999999998874 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 ?   13.7   0.8    0.0001     0.074      39      89 ..     237     287 ..     226     289 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.0001
                    Mg_chelatase_C  39 eldeeaeelleeaierlglsaRaydrilkvArTiADLegseeieeehlaeA 89 
                                       +lde + +l  ++++r +  aR++  +l+vA  iA  eg+e++++eh+++A
  gi|385805895|ref|YP_005842293.1| 237 ALDEGVIDLCAALAAREHGDARKALDLLRVAGEIAEREGDEKVRKEHVEKA 287
                                       67778888899999999999*****************************99 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0    0.0001     0.074      11      50 ..      56      93 ..      46      95 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0001
                        Zeta_toxin 11 psqerPklillgGqpGAGKselaellkdelerqgnvvrld 50
                                       +++rP  i+  G +G GK+++ +l++++l  q+++v+l+
  gi|385805895|ref|YP_005842293.1| 56 LRNSRPNNIFTYGLTGTGKTAVVKLVTKKL--QERAVELK 93
                                      5789**************************..89999875 PP

>> TIP49_C  TIP49 AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00014       0.1      31      61 ..     258     288 ..     252     291 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00014
                           TIP49_C  31 RYaiqLltpasilakkrkkkevevedveeve 61 
                                       R a+ Ll +a  +a++++ ++v +e+ve++ 
  gi|385805895|ref|YP_005842293.1| 258 RKALDLLRVAGEIAEREGDEKVRKEHVEKAR 288
                                       55899***********************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 ?   12.5   0.0   0.00015      0.11       4      46 ..      42      88 ..      40     100 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00015
                                      HHHHHHHHHHHHHCH....TEEEEEEESTTSSHHHHHHHHHHHTT-- CS
                              TsaE  4 eeetealgkklakal....gdvilLeGdLGaGKTtlvrglakalgve 46
                                      ee+++++++ la+al     + i+ +G  G+GKT+ v+ + k+l+ +
  gi|385805895|ref|YP_005842293.1| 42 EEQIKKIASILAQALrnsrPNNIFTYGLTGTGKTAVVKLVTKKLQER 88
                                      7899999999999887654456*******************999765 PP

>> Microtub_bd  Microtubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00017      0.12      66     112 ..      44      91 ..      33     119 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00017
                                       CCCCCCHHHHHHHH.TT--EEEEEEES.................ST-HC CS
                       Microtub_bd  66 evfeeisqlvqsal.dgynvcifaygqTGsGKtyTmeg.eeeeagmipr 112
                                       ++ +  s l+  al +    +if+yg TG GKt  ++  +++ ++   +
  gi|385805895|ref|YP_005842293.1|  44 QIKKIASILA-QALrNSRPNNIFTYGLTGTGKTAVVKLvTKKLQERAVE 91 
                                       4444444454.455488889*************9888743333333333 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00023      0.17       2      49 ..      64     111 ..      64     152 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00023
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqsktdyt 49 
                                       +++ Gl G+GK+ +++ + kkl+  av l  +  +++++++ +q++t y 
  gi|385805895|ref|YP_005842293.1|  64 IFTYGLTGTGKTAVVKLVTKKLQerAVELKLP--IQTVYVNCRQRDTSYR 111
                                       6899*******************777777777..5888887777776443 PP

>> Kinesin  Kinesin motor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00023      0.17      61      89 ..      47      75 ..      26      92 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00023
                                      HHHHHHHHHHHTTSEEEEEEEESTTSSHH CS
                           Kinesin 61 etakplvesvleGynatifaYGqtgsGKT 89
                                      ++a+ l +++ +     if+YG tg+GKT
  gi|385805895|ref|YP_005842293.1| 47 KIASILAQALRNSRPNNIFTYGLTGTGKT 75
                                      44333444444455678***********9 PP

>> HTH_54  ParA helix turn helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.022        16      10      43 ..     282     321 ..     278     327 .. 0.68
   2 ?    5.7   0.0     0.022        16       4      56 ..     310     363 ..     306     377 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.022
                            HTH_54  10 eqiqkqkkElkedeyyqtys......kaalaklpklsrrk 43 
                                       e+++k +kEl++d+ y++ s      k  la++  l+rr 
  gi|385805895|ref|YP_005842293.1| 282 EHVEKARKELEKDKVYEVVStlplhaKLILASIVDLTRRG 321
                                       89**************997722222244555566666665 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.022
                            HTH_54   4 mLqelteqiqkqkkElkedeyyqtyskaala.klpklsrrkvdkavsemeaeGy 56 
                                       +L+++++  ++ k+  ++ e + +ysk + + +l  l++r v + +se++  G 
  gi|385805895|ref|YP_005842293.1| 310 ILASIVDLTRRGKDSATTGEIFVEYSKKTSElRLETLTQRRVTDIISELDMMGL 363
                                       677777777888888899999*****9876536789************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       993  (0.0553851); expected 358.6 (0.02)
Passed bias filter:                      719  (0.0401026); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); 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: 0.65u 0.33s 00:00:00.98 Elapsed: 00:00:00.48
# Mc/sec: 2551.75
//
Query:       gi|385805896|ref|YP_005842294.1|  [L=195]
Description: hypothetical protein FFONT_0854 [Fervidicoccus fontis Kam940]
Scores for complete 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-51  173.2   0.0    4.3e-51  172.9   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 !  172.9   0.0   2.4e-55   4.3e-51       5     182 ..       7     185 ..       5     186 .. 0.95

  Alignments for each domain:
  == domain 1  score: 172.9 bits;  conditional E-value: 2.4e-55
                                       EEEEEEEE.....-SS-EEEEEEEEETT.EEEEEEEEEE-TT-S-HHHHHHHHHCC-...TTTTEEEEEESSSEETT CS
                             DUF99   5 vlGiddsfferkkkdgksvlvGvvmradrvvdgvafgrvtvdGtDateaiielvkrl...eredirvvlldGitiag 78 
                                       ++Gidd++fe k k++++v+vGv +++ + + +++++++ vd tDate+ iel++++    +++  vv+ldG+t+ag
  gi|385805896|ref|YP_005842294.1|   7 AIGIDDGHFE-KGKNKNTVIVGVKFNGFN-PVSAFIRKIGVDRTDATERGIELIQSAtegINSKDVVVFLDGVTYAG 81 
                                       69********.578**********99886.99999********************997544667779********** PP

                                       TEE--HHHHHHHH---EEEEESS---HHHHHHCCT.TSTTHHHHHHHHHHC.---EEETT....EEEEEESS-HHHH CS
                             DUF99  79 FNvvDlerlheetglPviavtreepdlgklekaLrkhfpdeeeRlelieklgerieevektgeelyvravGieleea 155
                                       FN++D+e++ e+t++ +ia+++++p+ +k+e+aLr hf+d+e R+e+i k++++++ +++ +++ly+ ++  ++++a
  gi|385805896|ref|YP_005842294.1|  82 FNFIDPEEIKEKTKMEIIAIFSRKPNQDKIENALRLHFSDWEYRWEHIYKVIKNVRSIVNFRGKLYFFTTIENAKDA 158
                                       ***************************************************************************** PP

                                       HHHHHHC-SSSSS-HHHHHHHHHHHHH CS
                             DUF99 156 aklvrkltlegriPEPlRvAhliAsal 182
                                       + l+++++l +++PEP+RvAh+iA+++
  gi|385805896|ref|YP_005842294.1| 159 EFLIESYQLISKLPEPIRVAHIIAKEI 185
                                       ************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); 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: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 1094.32
//
Query:       gi|385805897|ref|YP_005842295.1|  [L=168]
Description: putative nucleotide kinase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-23   84.2   0.3    1.4e-23   83.8   0.3    1.1  1  AAA_18           AAA domain
    1.2e-06   29.0   0.4      4e-06   27.3   0.4    1.8  1  AAA_17           AAA domain
    3.7e-06   27.3   0.0    1.4e-05   25.3   0.0    1.8  2  AAA_28           AAA domain
    4.2e-06   27.1   0.0    4.9e-06   26.9   0.0    1.3  1  AAA_22           AAA domain
    5.8e-06   26.8   0.1    1.1e-05   25.8   0.1    1.6  1  AAA              ATPase family associated with various cellul
    8.5e-06   26.0   0.1     0.0025   18.0   0.0    2.2  2  AAA_33           AAA domain
    2.2e-05   23.9   0.1    0.00031   20.1   0.0    2.2  2  Zeta_toxin       Zeta toxin
    0.00012   21.9   0.4     0.0002   21.2   0.4    1.4  1  AAA_24           AAA domain
    0.00018   22.0   0.0    0.00027   21.5   0.0    1.2  1  ABC_tran         ABC transporter
    0.00019   21.4   2.0    0.00036   20.5   0.2    2.2  2  NTPase_1         NTPase
    0.00021   21.7   0.0    0.00026   21.4   0.0    1.3  1  AAA_16           AAA ATPase domain
    0.00022   20.6   0.1    0.00022   20.6   0.1    1.3  1  DUF2075          Uncharacterized conserved protein (DUF2075)
    0.00037   20.3   0.0    0.00054   19.7   0.0    1.3  1  AAA_30           AAA domain
    0.00038   20.8   0.1    0.00075   19.8   0.1    1.5  1  AAA_19           AAA domain
    0.00044   20.3   0.3    0.00065   19.7   0.3    1.8  1  AAA_14           AAA domain
    0.00061   19.7   2.8       0.18   11.7   0.1    2.2  2  dNK              Deoxynucleoside kinase
    0.00064   19.1   0.0    0.00067   19.0   0.0    1.2  1  KAP_NTPase       KAP family P-loop domain
    0.00072   19.3   2.0       0.31   10.7   0.1    2.4  2  Thymidylate_kin  Thymidylate kinase
    0.00081   19.4   1.2     0.0021   18.0   0.1    2.0  2  Rad17            Rad17 P-loop domain
    0.00095   19.5   0.0     0.0015   18.9   0.0    1.3  1  RNA_helicase     RNA helicase
    0.00098   18.3   0.1      0.002   17.3   0.1    1.5  1  T2SSE            Type II/IV secretion system protein
     0.0014   18.2   0.6     0.0032   17.1   0.5    1.7  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
     0.0019   18.0   0.1     0.0027   17.5   0.1    1.2  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
     0.0021   17.5   1.2       0.13   11.7   0.2    2.2  2  SRPRB            Signal recognition particle receptor beta su
     0.0021   18.0   0.0     0.0036   17.3   0.0    1.5  1  AAA_5            AAA domain (dynein-related subfamily)
     0.0022   17.6   0.1     0.0035   16.9   0.1    1.3  1  AAA_7            P-loop containing dynein motor region
     0.0025   17.3   0.0     0.0042   16.6   0.0    1.5  1  KTI12            Chromatin associated protein KTI12
     0.0045   16.4   0.4       0.79    9.0   0.2    2.2  2  FtsK_SpoIIIE     FtsK/SpoIIIE family
  ------ inclusion threshold ------
       0.01   15.1   1.9      0.012   14.9   1.9    1.1  1  TIP49            TIP49 P-loop domain
      0.012   15.6   0.1      0.016   15.1   0.1    1.4  1  NACHT            NACHT domain
      0.017   15.0   0.4      0.039   13.8   0.1    1.8  1  MobB             Molybdopterin guanine dinucleotide synthesis
      0.019   15.0   0.4      0.033   14.3   0.4    1.6  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
       0.02   14.6   0.0      0.031   14.0   0.0    1.3  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.025   14.5   0.0      0.037   13.9   0.0    1.4  1  APS_kinase       Adenylylsulphate kinase
      0.029   13.3   0.0      0.042   12.8   0.0    1.2  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
      0.032   13.2   0.2      0.061   12.3   0.0    1.5  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
      0.043   13.5   0.2      0.056   13.2   0.2    1.4  1  VirE             Virulence-associated protein E
      0.078   12.7   0.9       0.12   12.1   0.3    1.6  2  AAA_11           AAA domain
      0.086   12.6   0.3       0.16   11.8   0.3    1.4  1  AAA_29           P-loop containing region of AAA domain
      0.088   12.1   8.0        0.5    9.7   0.8    2.8  3  ATPase           KaiC
      0.098   12.6   0.0       0.42   10.5   0.0    1.8  2  Ploopntkinase3   P-loop Nucleotide Kinase3
       0.12   12.0   2.1        7.8    6.1   0.0    2.2  2  Guanylate_kin    Guanylate kinase
       0.13   12.3   0.4       0.18   11.8   0.4    1.4  1  ResIII           Type III restriction enzyme, res subunit
       0.17   11.8   0.8       0.61   10.0   0.0    2.1  2  RsgA_GTPase      RsgA GTPase
       0.45   10.6   1.9        9.1    6.4   0.0    2.5  2  ADK              Adenylate kinase


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 !   83.8   0.3   3.6e-26   1.4e-23       2     128 ..       9     131 ..       8     133 .. 0.96

  Alignments for each domain:
  == domain 1  score: 83.8 bits;  conditional E-value: 3.6e-26
                            AAA_18   2 lltGtpGvGKttlakeLskrl.gf..gvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegk 75 
                                       ++tGtpG+GKtt+ k+L+k+l ++   +  +++a +++l + +d    ++s+++d++ l++ ++++ e +s    ++
  gi|385805897|ref|YP_005842295.1|   9 IITGTPGTGKTTILKNLEKELkENalMIDAGELAIKEDLIFAYDCL--RKSLVIDIEALKEEINKIIELAS----ED 79 
                                       79******************98889*********************..**********9999999999876....99 PP

                            AAA_18  76 nlvidghlaeleseaakdikkvvLtaspeelleRlekRgyeeakikeneeaei 128
                                        +vi++h     + + ++++ +vL++spe+l++Rl++Rg+e++ki+en ++e 
  gi|385805897|ref|YP_005842295.1|  80 LIVISSHYPCIADKNKVERV-IVLRTSPEKLYDRLKNRGWEKRKIEENIDSEE 131
                                       99******999999999999.***************************99986 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.4     1e-08     4e-06       1     128 [.      11     122 ..      11     132 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1e-08
                                       EE-TTSSHHHHHHHHHHHH..TEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEE CS
                            AAA_17   1 lGgPGsGKgtqceklveky..gfthlsaGdllreeakrgglakardemrklpleekkelqkeaaekiaeeakkkgvl 75 
                                       +G PG GK+t++++l +++  +  ++ aG+l ++e     l+ a d +rk +l+++ e +ke ++ki e a+++ ++
  gi|385805897|ref|YP_005842295.1|  11 TGTPGTGKTTILKNLEKELkeNALMIDAGELAIKE----DLIFAYDCLRK-SLVIDIEALKEEINKIIELASEDLIV 82 
                                       69****************9778999******9887....78778887776.578888888888889*9999999999 PP

                                       EEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHH.TTST-T CS
                            AAA_17  76 vdghprikeqagfldglpkevleelkpdaiilleadpeeilerrlkd.rtrgrd 128
                                       +  h+               + ++ k++ +i+l ++pe++++r++++   ++r+
  gi|385805897|ref|YP_005842295.1|  83 ISSHYPC-------------IADKNKVERVIVLRTSPEKLYDRLKNRgW-EKRK 122
                                       9988743.............2345566889***************9953.3332 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   3.6e-08   1.4e-05       2      77 ..       8      82 ..       7      91 .. 0.76
   2 ?   -0.1   0.0       2.4   9.6e+02     106     157 ..      93     152 ..      83     156 .. 0.54

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 3.6e-08
                            AAA_28  2 ivitGgestGKTtlleaLaar..gypvvpEaareileeklakgedalpwvedllafaervleeqleeeaaaaankvlf 77
                                      ++itG+++tGKTt+l++L+++  +   + +a+   ++e l +  d l+++   l + ++ l+e++ +  + a++++++
  gi|385805897|ref|YP_005842295.1|  8 FIITGTPGTGKTTILKNLEKElkENALMIDAGELAIKEDLIFAYDCLRKS---LVIDIEALKEEINKIIELASEDLIV 82
                                      68*****************8875666779999999999999999878764...4555555666776665555666555 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 2.4
                            AAA_28 106 ekrydlvfllppap.....eidddgeRredlee...reaiderlrealrelgipviivps 157
                                       +++  +v++l+++p      +++ g+ + + ee    e++  +l+ea   +g++vi++++
  gi|385805897|ref|YP_005842295.1|  93 KNKVERVIVLRTSPeklydRLKNRGWEKRKIEEnidSEELSVILLEAKSCYGNKVIEINT 152
                                       556666666666664333222444444434444111444444566666668888888854 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   1.2e-08   4.9e-06       5      70 ..       5      79 ..       1     138 [. 0.74

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 1.2e-08
                            AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaee......erpevvfvtlpsst...sskdllrellralglelka 70
                                      ++i ++tG +GtGKTt l++l ++l+e a   +      +++ ++ +++  ++   + + l +e+ ++++l  ++
  gi|385805897|ref|YP_005842295.1|  5 KKIFIITGTPGTGKTTILKNLEKELKENALMIDagelaiKEDLIFAYDCLRKSlviDIEALKEEINKIIELASED 79
                                      7899*********************98888877888887666666888887777777777777777777765555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.1   2.9e-08   1.1e-05       2      56 ..       9      79 ..       8     101 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 2.9e-08
                                      EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS................STTHHHHHHHHHHHHHHHT CS
                               AAA  2 llyGppGtGKTllakavakelgvefleisgsellsk................yvgesekkirelfkeakek 56
                                      +++G+pGtGKT++ k + kel+ + l i++ el  k                 +++ +++i+++++ a+e 
  gi|385805897|ref|YP_005842295.1|  9 IITGTPGTGKTTILKNLEKELKENALMIDAGELAIKedlifaydclrkslviDIEALKEEINKIIELASED 79
                                      689******************************95558888888888887776666677777777776655 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   6.1e-06    0.0025       2      33 ..       8      50 ..       7      96 .. 0.57
   2 ?    6.7   0.0      0.02       7.8      99     123 ..      97     121 ..      88     133 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 6.1e-06
                            AAA_33  2 vllvGlpGsGKstlaerllkklg..avllssdt.........l 33
                                      +++ G pG+GK+t +++l k+l+  a  ++  +         +
  gi|385805897|ref|YP_005842295.1|  8 FIITGTPGTGKTTILKNLEKELKenALMIDAGElaikedlifA 50
                                      5789*****************9966444443335544444443 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.02
                            AAA_33  99 vrivvvetdeetlkeRlakRaangd 123
                                       +r++v++t++e+l +Rl+ R  +++
  gi|385805897|ref|YP_005842295.1|  97 ERVIVLRTSPEKLYDRLKNRGWEKR 121
                                       5999****************98753 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   7.7e-07   0.00031      15      52 ..       4      39 ..       1      42 [. 0.90
   2 ?    2.0   0.0      0.27   1.1e+02     125     159 ..      98     128 ..      62     167 .. 0.67

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 7.7e-07
                        Zeta_toxin 15 rPklillgGqpGAGKselaellkdelerqgnvvrldpD 52
                                       +k+ ++ G pG GK+++++ l++el  ++n++ +d+ 
  gi|385805897|ref|YP_005842295.1|  4 MKKIFIITGTPGTGKTTILKNLEKEL--KENALMIDAG 39
                                      67999*********************..9999999975 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.27
                        Zeta_toxin 125 evvvvavkkelSrlgvldRyeeevaegRlvpkeeh 159
                                       +v+v+ +++e  + ++++R +e+    R++++++ 
  gi|385805897|ref|YP_005842295.1|  98 RVIVLRTSPEKLYDRLKNRGWEK----RKIEENID 128
                                       56666777777777777777766....66665544 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.4   4.9e-07    0.0002       2      38 ..       5      43 ..       4     104 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 4.9e-07
                            AAA_24  2 klkiliyGpsgiGKTtlakel....gpkplfidtekGlksl 38
                                      k+ ++i+G +g+GKTt++k+l    ++++l+id  +   ++
  gi|385805897|ref|YP_005842295.1|  5 KKIFIITGTPGTGKTTILKNLekelKENALMIDAGE--LAI 43
                                      67789***************************9655..344 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   6.8e-07   0.00027      11     110 ..       5     133 ..       2     134 .. 0.63

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 6.8e-07
                                       TSEEEEEESTTSSHHHHHHHHTTSS--.....SEEEEEETTCEGGG.........B-HHHCCHCEEEE-SS--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  11 gekvaivGenGaGKStLlkllagllkp.....teGeilldgkdlke.........qeleslrkeigvlpqepqlfpe 73 
                                        ++  i+G  G+GK+t+lk l ++lk      ++Ge+ ++++ +           +++e l++ei  + + ++    
  gi|385805897|ref|YP_005842295.1|   5 KKIFIITGTPGTGKTTILKNLEKELKEnalmiDAGELAIKEDLIFAydclrkslvIDIEALKEEINKIIELASE--- 78 
                                       577899*******************9977777777776665544446655555555555555555555554222... PP

                                       SBHHHH................HHHTC........HHHHHHHSTTGGTTCBGESTTS..GGS- CS
                                       xxxxxx................xxxxx........xxxxxxxxxxxxxxxxxxxxxx..xxxx RF
                          ABC_tran  74 ltvren................esdee........iekalsklglkelkdtvvkssp..ssLS 110
                                                                 e        +ek+ ++l++ ++++++++++   ++LS
  gi|385805897|ref|YP_005842295.1|  79 -----DlivisshypciadknkV---ErvivlrtsPEKLYDRLKNRGWEKRKIEENIdsEELS 133
                                       .....123333346777554330...2345555558888888888888888887776555555 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.2   9.1e-07   0.00036       2      29 ..       8      35 ..       7      39 .. 0.89
   2 ?   -0.2   0.1         2     8e+02     124     124 ..      94      94 ..      57     135 .. 0.58

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 9.1e-07
                                      EEEE--TTSSHHHHHHHHHHHH...GGG CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvk 29
                                      ++iTG pG+GKtT++k++ ++lk++ + 
  gi|385805897|ref|YP_005842295.1|  8 FIITGTPGTGKTTILKNLEKELKENALM 35
                                      68********************998765 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 2
                                       T CS
                          NTPase_1 124 s 124
                                       +
  gi|385805897|ref|YP_005842295.1|  94 N 94 
                                       1 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   6.6e-07   0.00026      25      76 ..       6      65 ..       1     115 [. 0.68

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 6.6e-07
                            AAA_16 25 elvllsGesGvGKsslvrellralekd.............ggiflrgkcdqlesaipysalaqal 76
                                       + +++G +G+GK+++++ l ++l+++             + if++   +++     +++ ++al
  gi|385805897|ref|YP_005842295.1|  6 KIFIITGTPGTGKTTILKNLEKELKENalmidagelaikeDLIFAYDCLRKS-----LVIDIEAL 65
                                      6789**********************95555333333332233333333333.....22244444 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.1   5.5e-07   0.00022       1      27 [.       5      31 ..       5     139 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 5.5e-07
                           DUF2075  1 kavvlVtGvaGtGKtvvllnllaeled 27
                                      k+++++tG +GtGKt +l nl  el++
  gi|385805897|ref|YP_005842295.1|  5 KKIFIITGTPGTGKTTILKNLEKELKE 31
                                      789******************999933 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.4e-06   0.00054      18      44 ..       5      31 ..       1      47 [. 0.82

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.4e-06
                            AAA_30 18 drvavltGpAGtGKttalkalreawea 44
                                      +++ ++tG +GtGKtt+lk l++ +++
  gi|385805897|ref|YP_005842295.1|  5 KKIFIITGTPGTGKTTILKNLEKELKE 31
                                      6789****************9665544 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.1   1.9e-06   0.00075      10      37 ..       5      32 ..       2      45 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.9e-06
                            AAA_19 10 ekvllvtaGpGtGKTrvlkhivallvel 37
                                      +k++++t+ pGtGKT++lk   ++l+e+
  gi|385805897|ref|YP_005842295.1|  5 KKIFIITGTPGTGKTTILKNLEKELKEN 32
                                      6899***************999988876 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.3   1.6e-06   0.00065       2      49 ..       5      49 ..       4     165 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.6e-06
                            AAA_14  2 rkilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladp 49
                                      +ki +itG   +GKTt+lk+l kel    e+ l i+  +   k+   +
  gi|385805897|ref|YP_005842295.1|  5 KKIFIITGTPGTGKTTILKNLEKELK---ENALMIDAGELAIKEDLIF 49
                                      689******************88877...9999999888777665544 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.2    0.0053       2.1       2      23 ..       9      30 ..       8      40 .. 0.88
   2 !   11.7   0.1   0.00044      0.18     121     154 ..      94     130 ..      74     151 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0053
                                      EEEESTTSSHHHHHHHHHCCST CS
                               dNK  2 vveGnIgaGKstlvklLskklg 23
                                       + G+ g GK+t++k L+k+l+
  gi|385805897|ref|YP_005842295.1|  9 IITGTPGTGKTTILKNLEKELK 30
                                      689999*************986 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00044
                                       CH-SEEEEEE--HHHHHHHHHHCTTCCCT...TS-HH CS
                               dNK 121 akpdlliYLkasletclerikkRgreeek...kield 154
                                       +k++ +i L++s+e+++ r+k+Rg e+ k   +i+ +
  gi|385805897|ref|YP_005842295.1|  94 NKVERVIVLRTSPEKLYDRLKNRGWEKRKieeNIDSE 130
                                       458999*****************96664444377765 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 !   19.0   0.0   1.7e-06   0.00067      22      49 ..       7      76 ..       2     167 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.7e-06
                        KAP_NTPase 22 vvgLygkWGsGKssllnkledelkefa..........................................k 49
                                      ++ ++g  G+GK+++l++le+elke+a                                          +
  gi|385805897|ref|YP_005842295.1|  7 IFIITGTPGTGKTTILKNLEKELKENAlmidagelaikedlifaydclrkslvidiealkeeinkiielA 76
                                      5889999*******************99999999998888888888665555555555555555555551 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.1   0.00078      0.31       3      25 ..      12      34 ..      10      39 .. 0.89
   2 !    7.9   0.1    0.0054       2.2     121     185 .]      99     163 ..      89     163 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00078
                                      ESTTSSHHHHHHHHHHHHHHTTE CS
                   Thymidylate_kin  3 GlDGaGKttqaellkerlkeegi 25
                                      G  G+GKtt++++l + lke+++
  gi|385805897|ref|YP_005842295.1| 12 GTPGTGKTTILKNLEKELKENAL 34
                                      888*****************986 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0054
                                       EEEEESSHHHHHTSCCTTSSTTTSHHHHHHHHHHHHHHHHHHHH.TTSTEEEEETTS-HHHHHHHH CS
                   Thymidylate_kin 121 tflldvdpevalkRlakrdeldeeeeeqldflrkvrerylelak.ederiliidasksieevheeI 185
                                       ++ l ++pe+ + Rl+ r+ +++++ee++d  +++   +le+   + ++++ i++ + i  ++++I
  gi|385805897|ref|YP_005842295.1|  99 VIVLRTSPEKLYDRLKNRGWEKRKIEENID-SEELSVILLEAKScYGNKVIEINTDDDIATTMKKI 163
                                       789999**************8888888888.78888889999999999999999999988887776 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   5.1e-06    0.0021      43      70 ..       3      30 ..       1      39 [. 0.90
   2 ?    0.2   0.1       1.5   6.1e+02     128     174 ..      40      86 ..      29      98 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 5.1e-06
                             Rad17 43 rkkriLLisGPsGCgkstvvkvLskelg 70
                                      + k+i +i+G +G gk+t++k L kel 
  gi|385805897|ref|YP_005842295.1|  3 KMKKIFIITGTPGTGKTTILKNLEKELK 30
                                      5689*********************986 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.5
                             Rad17 128 dlrtdkklilved.lPnkfyrdsdalrevirkylrssealplilvite 174
                                       +l  +  li+  d l     +d +al+e i k +       li++ + 
  gi|385805897|ref|YP_005842295.1|  40 ELAIKEDLIFAYDcLRKSLVIDIEALKEEINKIIELASE-DLIVISSH 86 
                                       556677788876624588899999999999999988776.67766554 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   3.8e-06    0.0015       2      84 ..       9      89 ..       8     105 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 3.8e-06
                      RNA_helicase  2 wlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevvvidDfgqvkdeenps.dlaelirlvss 79
                                      +++G +g+GK+t+ k+L k+l ++  ++ ++++     ++d    Y+     ++ D+ + k+e n+  +la    +v s
  gi|385805897|ref|YP_005842295.1|  9 IITGTPGTGKTTILKNLEKELKENALMIDAGELA---IKEDLIFAYDCLRKSLVIDIEALKEEINKIiELASEDLIVIS 84
                                      689*******************999999999995...599*******************99886444355444444444 PP

                      RNA_helicase 80 tpypl 84
                                       +yp+
  gi|385805897|ref|YP_005842295.1| 85 SHYPC 89
                                      44433 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 !   17.3   0.1   4.9e-06     0.002     128     168 ..       4      40 ..       1      52 [. 0.79

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.9e-06
                             T2SSE 128 erglilvsGgTgsGKttllyallkeinksderivtvEDpvE 168
                                        +++++++G+ g+GKtt+l  l ke++++     ++ D+ E
  gi|385805897|ref|YP_005842295.1|   4 MKKIFIITGTPGTGKTTILKNLEKELKEN----ALMIDAGE 40 
                                       5899****************999999988....33335555 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 !   17.1   0.5   8.2e-06    0.0032       2      46 ..       7      48 ..       6      85 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 8.2e-06
                                      EEEEEESTTCCHHHHHHHHHCT--SS-EEEEESS-SSCHCCCCCC CS
                              cobW  2 vtvltGflGsGKTtLlnhllenraglklavivNefgevsiDaell 46
                                      ++++tG +G+GKTt+l++l ++ +++ l   + + ge++i ++l+
  gi|385805897|ref|YP_005842295.1|  7 IFIITGTPGTGKTTILKNLEKELKENAL---MIDAGELAIKEDLI 48
                                      579***************9876555444...44555555555554 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 !   17.5   0.1   6.8e-06    0.0027      37     112 ..       9      81 ..       2      97 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 6.8e-06
                            RuvB_N  37 llyGpPGlGkttlakiiakelgvklkitsgPvlekagdlaalltnleekdvlfideihrlsraveevlysamedfr 112
                                       +++G PG Gktt+ k + kel+ +  +  +  l  + dl+     l+++ v+  d i  l+++++ ++  a ed  
  gi|385805897|ref|YP_005842295.1|   9 IITGTPGTGKTTILKNLEKELKENALMIDAGELAIKEDLIFAYDCLRKSLVI--D-IEALKEEINKIIELASEDLI 81 
                                       789*************************************999999987554..4.77888999999999998865 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 !   11.7   0.2   0.00033      0.13       3      33 ..       5      35 ..       3      47 .. 0.84
   2 ?    4.8   0.1     0.042        17     135     178 ..      63     114 ..      43     116 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00033
                                      --EEEEE-STTSSHHHHHHHHHHSS---B-- CS
                             SRPRB  3 kpavllvGlsdsGKTslftrLttdsvkktvt 33
                                      k+++++ G   +GKT++++ L ++ ++++ +
  gi|385805897|ref|YP_005842295.1|  5 KKIFIITGTPGTGKTTILKNLEKELKENALM 35
                                      789******************9987776655 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.042
                                       HHHHHHHHHHHHCHHHHHH--........----T....T--------GGGSS CS
                             SRPRB 135 daLEkElnkiierrskalkel........deeedksavlakkgkdFkfdqle 178
                                       +aL +E+nkiie  s +l  +        d+++ +++ + +++ +  +d+l+
  gi|385805897|ref|YP_005842295.1|  63 EALKEEINKIIELASEDLIVIsshypciaDKNKVERVIVLRTSPEKLYDRLK 114
                                       79****************9998888888866666666666666666666666 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   8.9e-06    0.0036       2      47 ..       8      53 ..       7     102 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 8.9e-06
                                      EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B-- CS
                             AAA_5  2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrrei 47
                                      +++ G pGtgK+++ + l + l+ + +++   +   +edl+  ++ 
  gi|385805897|ref|YP_005842295.1|  8 FIITGTPGTGKTTILKNLEKELKENALMIDAGELAIKEDLIFAYDC 53
                                      6899************************999999999999888876 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 !   16.9   0.1   8.9e-06    0.0035      31      63 ..       3      35 ..       1      43 [. 0.86

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 8.9e-06
                             AAA_7 31 knkkpvllvGptGtGKtviikdllkkldkekyl 63
                                      k kk ++++G+ GtGKt+i+k+l k+l+++ ++
  gi|385805897|ref|YP_005842295.1|  3 KMKKIFIITGTPGTGKTTILKNLEKELKENALM 35
                                      6788999********************976655 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.1e-05    0.0042       5      30 ..       9      34 ..       6      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.1e-05
                                      EEE--TTSSHHHHHHHHHHHHHHTT- CS
                             KTI12  5 vltGlPssGKstrakeLakaleeekr 30
                                      ++tG P +GK+t+ k+L+k+l+e+  
  gi|385805897|ref|YP_005842295.1|  9 IITGTPGTGKTTILKNLEKELKENAL 34
                                      89********************9654 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.2     0.002      0.79      42      59 ..       8      25 ..       1      26 [. 0.87
   2 ?    5.5   0.0     0.024       9.6     118     170 ..      49     103 ..      41     119 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.002
                                      EEEE--TTSSHHHHHHHH CS
                      FtsK_SpoIIIE 42 llvaGatgsGKStalntL 59
                                       ++ G++g+GK+t l++L
  gi|385805897|ref|YP_005842295.1|  8 FIITGTPGTGKTTILKNL 25
                                      589************987 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.024
                                       HHHHHHHHTT-SSHHHHHHHHHHHHHTT---B-TT-................... CS
                      FtsK_SpoIIIE 118 eryalfreagvrsiaaydgeiaedpldifgdvflvlDnyddlaaene..ritsLs 170
                                        +y  +r++ v +i+a ++ei + ++ + +d+ +++  y  +a +n+  r+++L 
  gi|385805897|ref|YP_005842295.1|  49 FAYDCLRKSLVIDIEALKEEINKIIELASEDLIVISSHYPCIADKNKveRVIVLR 103
                                       578999*****************************************99999986 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   1.9   2.9e-05     0.012      51     174 ..       6     130 ..       1     159 [. 0.72

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.9e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XX-S-EEEEEEE CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkktevltqalrksigvri....keekevleGevv 123
                                       +  +++G +gtGkt +   + kel e+    ++ ++e+   e        + lrks+ + i     e+++++e    
  gi|385805897|ref|YP_005842295.1|   6 KIFIITGTPGTGKTTILKNLEKELKENA--LMIDAGELAIKE--DLIFAYDCLRKSLVIDIealkEEINKIIELASE 78 
                                       67899*******************9875..678899985443..233346789999999883332356788998888 PP

                                       EEEE...-SSS-..TTS--EEEEEE-SS-EEEEEE-HHHHHHHH.HHT--TT CS
                             TIP49 124 eleveeaenplskekkikevkitlktakeekklklgskiaeell.kekvkeg 174
                                       +l v +++ p+  +k++ e  i+l+t+ e+   +l+++  e+ + +e++ ++
  gi|385805897|ref|YP_005842295.1|  79 DLIVISSHYPCIADKNKVERVIVLRTSPEKLYDRLKNRGWEKRKiEENIDSE 130
                                       8888888888888999999999****99888777776654433213444433 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.1     4e-05     0.016       3      29 ..       8      34 ..       6      83 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4e-05
                                      EEEEC-TTTCHHHHHHHHHHHHCTS-S CS
                             NACHT  3 vilqGeaGsGKTtLlqklalawaegkl 29
                                       i++G +G GKTt l+ l  +++e+ l
  gi|385805897|ref|YP_005842295.1|  8 FIITGTPGTGKTTILKNLEKELKENAL 34
                                      699*******************99876 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 ?   13.8   0.1   9.9e-05     0.039       1      30 [.       7      36 ..       7      47 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.9e-05
                              MobB  1 vlgivgksgsGKTtLleklipelkarglrv 30
                                      ++ i+g+ g+GKTt+l++l +elk++ l +
  gi|385805897|ref|YP_005842295.1|  7 IFIITGTPGTGKTTILKNLEKELKENALMI 36
                                      57899*******************998876 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 ?   14.3   0.4   8.2e-05     0.033       1      38 [.       7      41 ..       7     162 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.2e-05
                                      EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEES CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpq 38
                                      i+i+ ++ G+GKTt++ nL + l++   + l++Da+  
  gi|385805897|ref|YP_005842295.1|  7 IFIITGTPGTGKTTILKNLEKELKE---NALMIDAGEL 41
                                      789999***************9999...6677776543 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 ?   14.0   0.0   7.8e-05     0.031       2      39 ..       9      40 ..       8      64 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.8e-05
                   Viral_helicase1  2 vvhGvpGcGKStlirkllrtsliltvnrptaelltegk 39
                                      ++ G pG GK+t++++l ++       +++a ++ +g 
  gi|385805897|ref|YP_005842295.1|  9 IITGTPGTGKTTILKNLEKE------LKENALMIDAGE 40
                                      799*************9999......667666665555 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   9.2e-05     0.037       4      31 ..       7      34 ..       4     101 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.2e-05
                                      EEEEESSTTSSHHHHHHHHHHHHHHTT- CS
                        APS_kinase  4 vvwltGlsgsGKstianalekkLvekgi 31
                                      ++ +tG  g+GK+ti ++lek+L+e+  
  gi|385805897|ref|YP_005842295.1|  7 IFIITGTPGTGKTTILKNLEKELKENAL 34
                                      6789*******************99764 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00011     0.042      18      42 ..       8      32 ..       2      52 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00011
                     TrwB_AAD_bind 18 ilivGttGsGKtqalekllrairar 42
                                      ++i+Gt G+GKt+ l++l +++++ 
  gi|385805897|ref|YP_005842295.1|  8 FIITGTPGTGKTTILKNLEKELKEN 32
                                      789**************98887764 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   0.00015     0.061      34      56 ..      10      32 ..       3      42 .. 0.89
   2 ?   -2.5   0.0         5     2e+03     165     183 ..      72      92 ..      61     126 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00015
                                      EEE-TTSSHHHHHHHHHHHHHCT CS
                              MeaB 34 ltGvPGaGkstlvealglelrrr 56
                                      +tG+PG+Gk t++++l  el+++
  gi|385805897|ref|YP_005842295.1| 10 ITGTPGTGKTTILKNLEKELKEN 32
                                      8*****************99886 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5
                                       CHHH-..SEEEEE---HHHHH CS
                              MeaB 165 ileia..DiivvnkaDkkeae 183
                                       i+e+a  D+iv+    +  a+
  gi|385805897|ref|YP_005842295.1|  72 IIELAseDLIVISSHYPCIAD 92 
                                       555554466666554322222 PP

>> VirE  Virulence-associated protein E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   0.00014     0.056      50     124 ..       3      74 ..       1     143 [. 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00014
                              VirE  50 KfDfvlvLvGkqgsgKstfleklgeewftdslksvedkdavekiqgvliveiaEleasnkaeveaiKafitrkkd 124
                                       K+  + +++G  g+gK+t+l++l +e   + l    +     +i++ li  ++ l++s  +++ea+K+ i +  +
  gi|385805897|ref|YP_005842295.1|   3 KMKKIFIITGTPGTGKTTILKNLEKELKENALMIDAG---ELAIKEDLIFAYDCLRKSLVIDIEALKEEINKIIE 74 
                                       888999*****************99986666655443...46899**********************99987554 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.3    0.0003      0.12      17      42 ..       5      30 ..       1      71 [. 0.84
   2 ?   -1.1   0.0       3.2   1.3e+03     163     186 ..     102     125 ..      52     153 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0003
                            AAA_11 17 seitliqGPPGtgKTktivellsqll 42
                                      ++i++i G PGtgKT+ +  l ++l 
  gi|385805897|ref|YP_005842295.1|  5 KKIFIITGTPGTGKTTILKNLEKELK 30
                                      5689************9998888873 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 3.2
                            AAA_11 163 leqerrklkkerkelskeleeaee 186
                                       l+++ +kl +  k+   e +++ee
  gi|385805897|ref|YP_005842295.1| 102 LRTSPEKLYDRLKNRGWEKRKIEE 125
                                       222222222333222333333333 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   0.3   0.00039      0.16      22      39 ..       5      22 ..       1      26 [. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00039
                            AAA_29 22 kgatlltGpsGsGKSTll 39
                                      k ++++tG+ G+GK+T+l
  gi|385805897|ref|YP_005842295.1|  5 KKIFIITGTPGTGKTTIL 22
                                      45899***********98 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.8    0.0013       0.5      19      35 ..       5      21 ..       3      40 .. 0.85
   2 ?    5.2   0.3      0.03        12      99     145 ..      57     102 ..      23     117 .. 0.70
   3 ?    2.2   0.1      0.23        93      56      83 ..     102     127 ..      97     166 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0013
                            ATPase 19 grvvlitGepGtGKtif 35
                                      +++  itG+pGtGKt++
  gi|385805897|ref|YP_005842295.1|  5 KKIFIITGTPGTGKTTI 21
                                      67899**********97 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.03
                            ATPase  99 kdkedleelieelaeaikeikakrvviDsitglayeekeavaReilr 145
                                       +   d+e+l+ee++++i+   +  +vi s  +    +k++v R i+ 
  gi|385805897|ref|YP_005842295.1|  57 SLVIDIEALKEEINKIIELASEDLIVISSHYPC-IADKNKVERVIVL 102
                                       45789**********************999888.5555555555554 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.23
                            ATPase  56 veepaedlrenakslGwdlekleeegkl 83 
                                       +  ++e+l+ + k+ Gw+ +k+ee+  +
  gi|385805897|ref|YP_005842295.1| 102 LRTSPEKLYDRLKNRGWEKRKIEEN--I 127
                                       5567899************999987..3 PP

>> Ploopntkinase3  P-loop Nucleotide Kinase3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0    0.0011      0.42       5      40 ..       6      43 ..       2      54 .. 0.73
   2 ?   -0.6   0.0       2.7   1.1e+03     161     181 ..      94     114 ..      76     116 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0011
                    Ploopntkinase3  5 liylv.GqPGaGkstlmaeltkgfdrskveqee.etvp 40
                                       i+++ G+PG+Gk+t++ +l k ++ + +  +  e++ 
  gi|385805897|ref|YP_005842295.1|  6 KIFIItGTPGTGKTTILKNLEKELKENALMIDAgELAI 43
                                      4555439**************99988776655445555 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.7
                    Ploopntkinase3 161 aekgkvkvlaGhPdelrsile 181
                                       ++  +v+vl+  P++l + l+
  gi|385805897|ref|YP_005842295.1|  94 NKVERVIVLRTSPEKLYDRLK 114
                                       33446999******9998886 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0      0.02       7.8       2      29 ..       5      32 ..       4      36 .. 0.87
   2 ?    5.6   0.5      0.03        12     117     181 ..      98     166 ..      62     167 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.02
                                      SSEEEEESTTTSSHHHHHHHHHHHSTTT CS
                     Guanylate_kin  2 rrpvvlvgpsgaGksslkkaLlselpek 29
                                      ++  ++ g  g+Gk ++ k+L +el+e+
  gi|385805897|ref|YP_005842295.1|  5 KKIFIITGTPGTGKTTILKNLEKELKEN 32
                                      5789*****************9988875 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.03
                                       EEEEEESSHHHHHHHHTTSSSSH...HHHHH.HHHHHHHHHHGGGCS.SEEEEESSHHHHHHHHHHHHHH CS
                     Guanylate_kin 117 ivFikppslkelqrrlksrgkeq...eekla.krlaaaekelqeyef.dvvivnddleealkklkellea 181
                                        v +  +s+++l +rlk+rg e+   ee++  ++l+ +  e++++ + + vi+ ++ +++ + +k+++ea
  gi|385805897|ref|YP_005842295.1|  98 RVIVLRTSPEKLYDRLKNRGWEKrkiEENIDsEELSVILLEAKSC-YgNKVIEINTDDDIATTMKKIFEA 166
                                       3445679*************8862223444324566666666666.427899888888888888888876 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   0.4   0.00046      0.18      24     122 ..       5     120 ..       1     164 [. 0.65

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00046
                                       TSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEE.ESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--... CS
                            ResIII  24 dkrglikmaTGtGKTlvaaklierllkkgkeekflfl.vprkslleqtleefkkflseaykeigkkvsgdkkka... 96 
                                       +k ++i  + GtGKT ++ +l ++l++     ++l++ + ++++ e ++ ++ ++ ++ + +i+  +++ +k++   
  gi|385805897|ref|YP_005842295.1|   5 KKIFIITGTPGTGKTTILKNLEKELKE-----NALMIdAGELAIKEDLIFAYDCLRKSLVIDIEALKEEINKIIela 76 
                                       5678899999********999999998.....455553677789999998888888777776666666655555444 PP

                                       ......................-SEEEEEHHHHHHTH....... CS
                            ResIII  97 ...............kekdstnkkilvttiqsldadseee...e 122
                                                       +++ +   +l t+ ++l+ +++++   +
  gi|385805897|ref|YP_005842295.1|  77 sedlivisshypciaDKNKVERVIVLRTSPEKLYDRLKNRgweK 120
                                       44445555555554322222233333344555555555545542 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0    0.0015      0.61      99     125 ..       5      31 ..       2      42 .. 0.86
   2 ?    0.0   0.1       1.7     7e+02      33      41 ..      94     102 ..      55     160 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0015
                                       TSEEEEECSTTSSHHHHHHHHCTT--- CS
                       RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpelel 125
                                       +k+ ++ G  G GK+t++++l  el+ 
  gi|385805897|ref|YP_005842295.1|   5 KKIFIITGTPGTGKTTILKNLEKELKE 31 
                                       58999****************998765 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.7
                                       HHHHHHHHH CS
                       RsgA_GTPase  33 nlldrfLvl 41 
                                       n ++r++vl
  gi|385805897|ref|YP_005842295.1|  94 NKVERVIVL 102
                                       333333332 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.023       9.1       1      24 [.      10      33 ..      10      47 .. 0.77
   2 ?    3.2   0.3      0.22        89     100     127 ..      93     132 ..      89     166 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.023
                                      EEESTTSSHHHHHHHHHHHHTSEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK  1 llGaPgaGKGtqaeklvkkyglah 24
                                      + G+Pg+GK t  ++l k+++ + 
  gi|385805897|ref|YP_005842295.1| 10 ITGTPGTGKTTILKNLEKELKENA 33
                                      67**************99986543 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.22
                                       TSEESEEEEEE--HHHHHHHHHT............GSHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxx............xxxxx RF
                               ADK 100 kvkldlvleldvpeevlveRltg............Dneet 127
                                       k k++ v+ l+ + e l +Rl +            D+ee 
  gi|385805897|ref|YP_005842295.1|  93 KNKVERVIVLRTSPEKLYDRLKNrgwekrkieeniDSEEL 132
                                       6688999999999999999999888888877777744443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1153  (0.0643092); expected 358.6 (0.02)
Passed bias filter:                      704  (0.039266); expected 358.6 (0.02)
Passed Vit filter:                       127  (0.0070835); expected 17.9 (0.001)
Passed Fwd filter:                        46  (0.00256568); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              45  [number of targets reported over threshold]
# CPU time: 0.72u 0.36s 00:00:01.08 Elapsed: 00:00:00.55
# Mc/sec: 918.50
//
Query:       gi|385805898|ref|YP_005842296.1|  [L=114]
Description: Ferredoxin domain containing protein [Fervidicoccus fontis Kam940]
Scores for complete 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-28   97.1   0.9    5.8e-28   96.7   0.9    1.2  1  DUF2148   Uncharacterized protein containing a ferredoxin dom


Domain annotation for each model (and alignments):
>> DUF2148  Uncharacterized protein containing a ferredoxin domain (DUF2148)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.7   0.9   3.2e-32   5.8e-28       3      68 .]      47     111 ..      45     111 .. 0.98

  Alignments for each domain:
  == domain 1  score: 96.7 bits;  conditional E-value: 3.2e-32
                           DUF2148   3 plCafkaiDlGiAlgsavkvaadlrvDnRvmysvGaaAkslgllkeasvvlgiplsvsgKsifFDR 68 
                                       p+ a+ +++lGi+lgsavk+a+ l++DnR+mys+G+aA++lgl++ a+v++gip+s++ K+i+FDR
  gi|385805898|ref|YP_005842296.1|  47 PNTACFLVNLGISLGSAVKMASLLNIDNRIMYSIGVAAIKLGLID-ADVAFGIPISAKAKNIYFDR 111
                                       899999***************************************.*******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 765.70
//
Query:       gi|385805899|ref|YP_005842297.1|  [L=228]
Description: 2, 5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine 1-reductase [Fervidicoccus fontis Kam940]
Scores for complete 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  113.2   0.0    1.7e-32  112.9   0.0    1.0  1  RibD_C    RibD C-terminal domain
  ------ inclusion threshold ------
      0.028   14.1   0.0       0.04   13.6   0.0    1.2  1  Fe-ADH_2  Iron-containing alcohol dehydrogenase


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 !  112.9   0.0   1.9e-36   1.7e-32       2     197 ..       3     206 ..       2     209 .. 0.91

  Alignments for each domain:
  == domain 1  score: 112.9 bits;  conditional E-value: 1.9e-36
                                       EEEEEEEEETTSBSSCTTSSGCTSS-HHHHHHHHHHHHTSSEEEEEHHHHHHHT--SS--SSCHSCHHHTT.G.SS- CS
                            RibD_C   2 yvilklavSlDGklaaaggeskwitgeearadvhelraeadailvGrgtvladnpsltvrwvkkreaeadaea.rqp 77 
                                       +v + +a+++DGk+a+++ge   + +++ r+++ +  + +da++vG++tvl+ n s    +           + ++p
  gi|385805899|ref|YP_005842297.1|   3 HVRISMAMTADGKTADEEGEWY-PLCQYERERFYRNIEWSDAVVVGADTVLTTNIS----FLSP-------SSlKNP 67 
                                       6899**************8877.********************************2....2222.......2349** PP

                                       EEEEEETTS-S-TTSHHHHSS.S-EEEEESSCSCHHHHHHCC.........E.......SE-HHHHHHHHHHTT--E CS
                            RibD_C  78 vrvVvdstlrvpldakvltdd.aptlvatteeadkekveklk.........v.......rvdlkelleeLkergirs 137
                                       +r V+d +l++p + kv ++   p+l+++++ea + k++k++         v       ++  ke+l+ Lk+rg+++
  gi|385805899|ref|YP_005842297.1|  68 LRAVIDPKLKTPIERKVYDTLrGPVLIFSSKEAYNAKRDKIEklnskgieiVtinekegYLSTKEILNVLKKRGCEK 144
                                       *******************99***********99999999998878887652778999******************* PP

                                       EEEEETHHHHHHHHHTTT-SEEEEEEESCE--TTSBCSSSSST-SS..EEEEEEEEEEETTE CS
                            RibD_C 138 llveGGatLagsllraglvDelrlyiaPkllGgagktlfdgegfka..lklklvksealgeg 197
                                       +lv GG+ +++ +l++glvDe+ +++ P++lG+ + + ++g gf+   +kl+l ++e++++g
  gi|385805899|ref|YP_005842297.1| 145 ILVVGGGRTNWFFLKEGLVDEFYITVTPYILGNTKYSPVSGSGFPFpgIKLELLSMEKCPCG 206
                                       *********************************888999999999899********999876 PP

>> Fe-ADH_2  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   4.4e-06      0.04      21      87 ..      91     153 ..      72     155 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.4e-06
                          Fe-ADH_2  21 kvllvadentkkaagekveeslkeagikvevveeveeeadleeveklvealreketdlvvavGgGti 87 
                                        vl+ ++++ ++a  +k+e +l+++gi++ +++e+e+  + +   +++++l++++++ ++ vGgG+ 
  gi|385805899|ref|YP_005842297.1|  91 PVLIFSSKEAYNAKRDKIE-KLNSKGIEIVTINEKEGYLSTK---EILNVLKKRGCEKILVVGGGRT 153
                                       5789999999999999996.699******9887555555555...5567778899**********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); 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: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1419.97
//
Query:       gi|385805900|ref|YP_005842298.1|  [L=62]
Description: 50S ribosomal protein L37e [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-24   85.3  10.5    2.6e-24   85.1  10.5    1.0  1  Ribosomal_L37e  Ribosomal protein L37e
  ------ inclusion threshold ------
      0.013   15.6   1.3      0.019   15.1   1.3    1.2  1  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
        5.3    7.0   9.5         40    4.2   9.5    2.0  1  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)


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 !   85.1  10.5   4.3e-28   2.6e-24       2      53 ..       3      55 ..       2      56 .. 0.98

  Alignments for each domain:
  == domain 1  score: 85.1 bits;  conditional E-value: 4.3e-28
                    Ribosomal_L37e  2 kGtssfGkrqkkktHilCrrCgkrsyhvqkktCascGy.psaklrkynWsaKa 53
                                      kGt+s+Gk+++  tHi+CrrCg++s++v k +Ca+cGy +s+++r+y+W++K+
  gi|385805900|ref|YP_005842298.1|  3 KGTTSMGKHSNGLTHIRCRRCGRHSFNVAKGYCAACGYgRSKRIRRYSWQNKK 55
                                      9**************************************************97 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   1.3   3.1e-06     0.019       9      40 ..      18      49 ..      15      60 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.1e-06
                      NOB1_Zn_bind  9 lrChaCfkvtkdmtkkFCpkCGnktLkrvavs 40
                                      +rC+ C +   +  k +C  CG    kr+  +
  gi|385805900|ref|YP_005842298.1| 18 IRCRRCGRHSFNVAKGYCAACGYGRSKRIRRY 49
                                      69********************9777776544 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   9.5    0.0067        40      13      32 ..      19      39 ..      14      42 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0067
                           DUF35_N 13 rCpdCGtvqfPPr.avCphCg 32
                                      rC+ CG++ f     +C  Cg
  gi|385805900|ref|YP_005842298.1| 19 RCRRCGRHSFNVAkGYCAACG 39
                                      9*********99999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       772  (0.0430587); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 395.87
//
Query:       gi|385805901|ref|YP_005842299.1|  [L=76]
Description: putative snRNP Sm protein [Fervidicoccus fontis Kam940]
Scores for complete 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   82.2   0.1    1.7e-23   82.1   0.1    1.0  1  LSM       LSM domain
     0.0012   18.9   0.0     0.0015   18.6   0.0    1.2  1  SM-ATX    Ataxin 2 SM domain
     0.0032   17.6   0.1      0.005   17.0   0.1    1.3  1  DUF150_C  RimP C-terminal SH3 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 !   82.1   0.1   2.9e-27   1.7e-23       2      67 .]       8      72 ..       7      72 .. 0.97

  Alignments for each domain:
  == domain 1  score: 82.1 bits;  conditional E-value: 2.9e-27
                                      HHHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTETEEEEEEEEEEEGGGEEEEEE CS
                               LSM  2 flkklinkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkkekrklglvliRGnnivlisl 67
                                       l+++++++v+v+lk+++e+rG+Lk++D ++N+vLed+ee  +d+ + rklg+v+iRG+n+++is+
  gi|385805901|ref|YP_005842299.1|  8 ILSSSMGQTVLVKLKGNKEVRGKLKSYDHHLNIVLEDAEELFPDG-QARKLGTVIIRGDNVIIISP 72
                                      58999****************************************.******************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 !   18.6   0.0   2.5e-07    0.0015       7      51 ..       8      50 ..       2      72 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.5e-07
                                      HHHTTTTSEEEEEETTS-EEEEEEEEE-T..T--EEEEEEEETTS CS
                            SM-ATX  7 lltslvGkevevtvknGevyeGifstvslekdfsvvLkmarkvkk 51
                                      +l s++G++v v++k  +  +G +++++    +++vL+ a ++ +
  gi|385805901|ref|YP_005842299.1|  8 ILSSSMGQTVLVKLKGNKEVRGKLKSYDH--HLNIVLEDAEELFP 50
                                      6889*************************..*********99988 PP

>> DUF150_C  RimP C-terminal SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   8.3e-07     0.005      10      45 ..      12      44 ..       9      50 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 8.3e-07
                          DUF150_C 10 flGelVkvklklpvegrkkftGkivevd.eetitlev 45
                                      + G++V vklk    g k+++Gk++++d   +i+le 
  gi|385805901|ref|YP_005842299.1| 12 SMGQTVLVKLK----GNKEVRGKLKSYDhHLNIVLED 44
                                      68*********....*************556688885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 483.41
//
Query:       gi|385805902|ref|YP_005842300.1|  [L=154]
Description: PUA domain containing protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-22   80.0   4.4      2e-22   79.2   4.4    1.4  1  DUF1947   Domain of unknown function (DUF1947)
    3.4e-19   68.6   0.3    4.8e-19   68.1   0.3    1.2  1  PUA       PUA domain


Domain annotation for each model (and alignments):
>> DUF1947  Domain of unknown function (DUF1947)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.2   4.4   2.2e-26     2e-22       2      66 .]       3      67 ..       2      67 .. 0.98

  Alignments for each domain:
  == domain 1  score: 79.2 bits;  conditional E-value: 2.2e-26
                                      -EE--HHHHHHHHHHHHTTT---TT--..-EEEE-SS-EEEEETTEEEEEE.SSSEEE-HHHHHHS CS
                           DUF1947  2 RHfLSkKeakeileklkekyisislesdkiEieeekkeklYlingvpilfe.eekliPtLklLlki 66
                                      RH+LSkKe++eil+++++k  +isle++k+Ei e+k++++Yl+++vp+l++ e+k++P+Lk+Llk+
  gi|385805902|ref|YP_005842300.1|  3 RHYLSKKEKDEILKEVNSKL-KISLEPEKVEILESKEFSCYLFDSVPALCKtEDKFFPHLKYLLKH 67
                                      9*******************.******************************************996 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.1   0.3   5.4e-23   4.8e-19       1      73 [.      73     146 ..      73     147 .. 0.97

  Alignments for each domain:
  == domain 1  score: 68.1 bits;  conditional E-value: 5.4e-23
                                       CEEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETT.SCEEEEEEESS-HHHHHHHCTSEEEEEEEE CS
                               PUA   1 grvvvddgAvkallsgasLlapGvvevegdfeegdvVaivded.gelvavGlanysseelakikggksveierv 73 
                                       +++ vd+gAvk ++sga+L+apG+v++egdf +gd+V + d +   ++av +a++ss+e++  k+g++++++++
  gi|385805902|ref|YP_005842300.1|  73 PKIFVDKGAVKPVSSGADLMAPGIVRIEGDFLPGDIVIVEDLEhKLPIAVMIAEMSSAEMKVTKKGRVARNIHY 146
                                       69****************************************9899*************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); 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: 00:00:00.45
# Mc/sec: 1032.54
//
Query:       gi|385805903|ref|YP_005842301.1|  [L=131]
Description: hypothetical protein FFONT_0861 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score 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   13.6   0.4       0.12   12.9   0.4    1.4  1  DUF4789   Domain of unknown function (DUF4789)


Domain annotation for each model (and alignments):
>> DUF4789  Domain of unknown function (DUF4789)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.4   6.9e-06      0.12      17      49 ..      67      98 ..      58     111 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.9e-06
                           DUF4789 17 gvCdCk.sepravyseetdkCyelytqGpCpegq 49
                                      ++C C+  + + +y e++++Cy+ly+  +C  ++
  gi|385805903|ref|YP_005842301.1| 67 SFCSCTdFSLNVIYREKRQNCYHLYS--YCLAEK 98
                                      69****878999*************7..555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 907.58
//
Query:       gi|385805904|ref|YP_005842302.1|  [L=233]
Description: ribose-5-phosphate isomerase [Fervidicoccus fontis Kam940]
Scores for complete 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-52  176.2   0.5    5.7e-52  175.8   0.5    1.1  1  Rib_5-P_isom_A  Ribose 5-phosphate isomerase A (phosphoribois
    3.7e-07   30.2   0.2     0.0014   18.5   0.0    2.1  2  DeoRC           DeoR C terminal sensor domain
     0.0014   18.5   0.0      0.002   17.9   0.0    1.2  1  PA14            PA14 domain
  ------ inclusion threshold ------
      0.051   13.0   0.0       0.09   12.2   0.0    1.3  1  Pox_F16         Poxvirus F16 protein
      0.067   12.3   0.0       0.13   11.4   0.0    1.5  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 !  175.8   0.5   1.6e-55   5.7e-52       2     171 ..      51     220 ..      50     221 .. 0.96

  Alignments for each domain:
  == domain 1  score: 175.8 bits;  conditional E-value: 1.6e-55
                                       EEESSHHHHHHHHHTT--BE-GGCCSSEEEEEE--SEEETTS-EE--TTS-HHHHHHHHHTEEEEEEEEEGGGBESS CS
                    Rib_5-P_isom_A   2 gvptSeqteelaeelgipllsldeveeidlaiDGaDevdedlnliKGgGgallrEKivaaaakkfiviadesKlvek 78 
                                       +v++S++++ ++++ g ++ls+d++e+id++iDG+D +d++ ++iKGgG+al+rEK++a+++k f+ iad sKl ++
  gi|385805904|ref|YP_005842302.1|  51 FVTSSFDSTLRLKQKGAKVLSIDSIESIDIYIDGVDAIDDNGTAIKGGGAALFREKLLASMSKYFVAIADTSKLKKE 127
                                       89*************************************************************************** PP

                                       TTSS-EEEEE-GGGHHHHHHHHHHTTT-EEEE-TE.TTTTEE-B-TTS-EEEEEESSSBSSSHHHHHHHHHTSTTEE CS
                    Rib_5-P_isom_A  79 lgkfpvPveVlpfaleavarelekllggkpelRea.kgkdgpvvTdngnlilDvkfeekiedpeelekelksipGVv 154
                                       l++  +P+eV p a+++v+++l++ +g+  ++R + +gk gpv++d+  +i+D+++++   ++eel+++lksi+GVv
  gi|385805904|ref|YP_005842302.1| 128 LNNSFIPIEVKPEAVNYVIKKLKD-IGVIGNVRYSkEGKWGPVISDSYGVIVDIQIKNWKISLEELNNTLKSITGVV 203
                                       **********************96.6*999***9955699****************66555**************** PP

                                       EESEE-S--SEEEEEET CS
                    Rib_5-P_isom_A 155 etGlFlgladkvlvgke 171
                                       etGlF+g+ d+++vg+e
  gi|385805904|ref|YP_005842302.1| 204 ETGLFIGMIDALIVGGE 220
                                       **************986 PP

>> DeoRC  DeoR C terminal sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0     4e-07    0.0014       3      66 ..       4      70 ..       2      74 .. 0.82
   2 !    9.8   0.0   0.00019      0.69      93     151 ..      78     136 ..      71     143 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 4e-07
                             DeoRC  3 aeeKrrIAkaAael..iedgdtifldaGtTtlelaraLaekk..nltvvTnslnvaeeLsekedikvi 66
                                       eeK+  A+ A +l  +++ ++i +++G+Tt +++++L+e+     + vT s++   +L++k ++kv+
  gi|385805904|ref|YP_005842302.1|  4 EEEKKIAASIATNLeeVKKAKVIGIGTGSTTSYFIDYLPEDIlkGKVFVTSSFDSTLRLKQK-GAKVL 70
                                      5777777777765444999*********************977677889*****99999998.66665 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00019
                             DeoRC  93 vdkaflgangidaegglttsdeeeaevkralieaarrvillaDssKfgkrafvriaale 151
                                       +d+ + g+++id++g +++   +    ++ l+++++  + +aD sK++k+   +++++e
  gi|385805904|ref|YP_005842302.1|  78 IDIYIDGVDAIDDNGTAIKGGGAALFREKLLASMSKYFVAIADTSKLKKELNNSFIPIE 136
                                       799999******999999999999999999999****************9998888876 PP

>> PA14  PA14 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   5.6e-07     0.002      46      87 ..      52      93 ..      39     114 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 5.6e-07
                                      CEEEEEEEEEBSSSEEEEEEETTCCCEEEEETTCCCEETT-T CS
                              PA14 46 fsarwtGylkppesGtYtFkvasddgvrlsidgelvidnngq 87
                                      +++ ++ +l+ +++G+ +++++s +++ ++idg  +id+ng 
  gi|385805904|ref|YP_005842302.1| 52 VTSSFDSTLRLKQKGAKVLSIDSIESIDIYIDGVDAIDDNGT 93
                                      678999**********************************65 PP

>> Pox_F16  Poxvirus F16 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.5e-05      0.09      34     111 ..     145     225 ..     139     229 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.5e-05
                           Pox_F16  34 vvkeikefGyinektLete.kWediinndidllvfyqvkqlsisveklYnlliknrev.plklyf.vkDnlafdGsp 107
                                       v+k++k+ G i +   ++e kW  +i+++  ++v  q+k   is e+l n+l     v +  l+  + D l+ +G p
  gi|385805904|ref|YP_005842302.1| 145 VIKKLKDIGVIGNVRYSKEgKWGPVISDSYGVIVDIQIKNWKISLEELNNTLKSITGVvETGLFIgMIDALIVGGEP 221
                                       678889999998876655439*******************************9987663555554346********* PP

                           Pox_F16 108 Psfr 111
                                       P+ +
  gi|385805904|ref|YP_005842302.1| 222 PIVK 225
                                       *877 PP

>> Sugar-bind  Putative sugar-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.7e-05      0.13      35      83 ..       6      53 ..       1      56 [. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.7e-05
                                      HHHHHHHHHHHHHHH--TTEEEEE-SSHHHHHHHHHTHHCCHTCEEEEE CS
                        Sugar-bind 35 lealgraaaqllesllkdgdvvgvgwGrtlsavaealtpkslrdvkvvq 83
                                       +++++ +a  le  +k+ +v+g+g+G t+s ++++l+++ l++  +v+
  gi|385805904|ref|YP_005842302.1|  6 EKKIAASIATNLE-EVKKAKVIGIGTGSTTSYFIDYLPEDILKGKVFVT 53
                                      5666777776665.58999******************998888777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       699  (0.0389871); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 1506.67
//
Query:       gi|385805905|ref|YP_005842303.1|  [L=120]
Description: hypothetical protein FFONT_0863 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.5e-18   65.1   0.6      6e-18   64.7   0.6    1.2  1  Elf1        Transcription elongation factor Elf1 like
  ------ inclusion threshold ------
      0.088   12.9   2.4          1    9.4   0.1    3.0  3  Rubredoxin  Rubredoxin


Domain annotation for each model (and alignments):
>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.7   0.6   6.7e-22     6e-18       1      77 [.       4      82 ..       4      83 .. 0.94

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 6.7e-22
                              Elf1  1 gkRkkkakkrkkkkkkklptkFdCpfCnheksvevkldkkek....iaevsCkvCgesfetkvnalsepvDvYskwiDa 75
                                      g+Rk+k++ + kk ++k+p+ F Cp+C++e s+++ +  k++    iae+sC+ Cg  +++ v+++ epv+ Y k+iD+
  gi|385805905|ref|YP_005842303.1|  4 GRRKRKRQ-QLKKPVRKIPKIFVCPHCSKE-SLRIVIRPKQGedkaIAEASCGECGFCARFYVPNIFEPVNAYGKVIDL 80
                                      89999996.69999999*************.999999999888999********************************9 PP

                              Elf1 76 ce 77
                                      ++
  gi|385805905|ref|YP_005842303.1| 81 YD 82
                                      86 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.1   0.00011         1      30      41 ..      19      30 ..      12      34 .. 0.86
   2 ?    0.4   0.2     0.075   6.7e+02       3      14 ..      55      66 ..      52      73 .. 0.74
   3 ?    0.5   0.0     0.071   6.4e+02      11      24 ..      81      94 ..      79      97 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00011
                                      GS-TT-BBTTTB CS
                        Rubredoxin 30 dlPddWvCPdCg 41
                                      ++P+ +vCP+C+
  gi|385805905|ref|YP_005842303.1| 19 KIPKIFVCPHCS 30
                                      79*********7 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.075
                                      EETTT-BEEETT CS
                        Rubredoxin  3 eCkvCgyvYdpa 14
                                      eC  C   Y p+
  gi|385805905|ref|YP_005842303.1| 55 ECGFCARFYVPN 66
                                      588888788776 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.071
                                      EETTTBBGGGTB-T CS
                        Rubredoxin 11 YdpakGdpdegiap 24
                                      Yd  +Gd +++ia 
  gi|385805905|ref|YP_005842303.1| 81 YDSFEGDIEKEIAS 94
                                      9******9999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.35s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 683.10
//
Query:       gi|385805906|ref|YP_005842304.1|  [L=250]
Description: PcrB-like protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.6e-60  202.2   0.4    8.5e-60  202.0   0.4    1.0  1  PcrB            PcrB family
    9.6e-05   21.9   0.2    0.00021   20.8   0.1    1.6  2  His_biosynth    Histidine biosynthesis protein
    0.00049   19.2   0.0    0.00085   18.4   0.0    1.3  1  IMPDH           IMP dehydrogenase / GMP reductase domain
     0.0015   18.0   0.3     0.0035   16.8   0.3    1.7  1  G3P_antiterm    Glycerol-3-phosphate responsive antiterminato
     0.0052   16.1   0.1      0.014   14.7   0.1    1.7  2  TMP-TENI        Thiamine monophosphate synthase
  ------ inclusion threshold ------
      0.011   15.0   0.4      0.019   14.2   0.4    1.3  1  DHO_dh          Dihydroorotate dehydrogenase
      0.011   14.6   0.8      0.017   14.0   0.3    1.5  2  Trp_syntA       Tryptophan synthase alpha chain
      0.011   15.1   0.4      0.028   13.8   0.0    1.9  2  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
      0.014   14.8   0.5      0.041   13.3   0.1    1.8  2  Aldolase        KDPG and KHG aldolase


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 !  202.0   0.4   4.3e-63   8.5e-60       7     224 ..      16     248 ..      10     250 .] 0.92

  Alignments for each domain:
  == domain 1  score: 202.0 bits;  conditional E-value: 4.3e-63
                                       S......EEEEE-TTSS-CHHHHHHH...HCTT-SEEEEECSTCHHHHHHHHHHHHHCTSSS-EEEEESSGGG--TT CS
                              PcrB   7 r......hltklDPeeenpdEiveiv...iesgtDavmigGsqsvtldntvrllkkvsriklPivlepsnvegvvry 74 
                                       r      h t++DP ++n +++ +i+    + gtDa ++gGs++v+  ++ ++  k ++++lP++++p++ +++v+ 
  gi|385805906|ref|YP_005842304.1|  16 RrkfgtlHFTLIDPHKTNAENAEKIAsilKDIGTDAFLLGGSIGVDPIEASEIALKLKETGLPVIIFPGDLTNIVKT 92 
                                       33456669*******99887655544433788***************999999999********************* PP

                                       SSEEEEEEETTBSSTTTTTHHHHHHHHHHHHHHHCTEEEEEEEEEBTTTSHHHHHTTB-.B-TTHHHHHHHHHHHHH CS
                              PcrB  75 aDalFvmsllnsanadWivgahalglkkvkklieseeilaegYlvvePdskvaavteak.vdlnkediaayallaak 150
                                       aDa+ +msllns+n++ i+ga+ +g+  vkk+   +e l+ +Y+v+  ++++++++ a+ ++ ++ +i  +++laa+
  gi|385805906|ref|YP_005842304.1|  93 ADAILFMSLLNSENPYHIIGAQVQGAFLVKKYG--LETLPTAYIVIGYGGAAGYMGMARpIPWDQVNISIAYALAAN 167
                                       *********************************..****************************************** PP

                                       HTT-SEEEEE-.TTSSS-H..HHHHHHHHHHSSSEEEEESS--SHHHHHHHHCC.SSEEEE-CHHHHHH...HCHHH CS
                              PcrB 151 llglrliYlEa.sGaledv..eevialkkklekarlivGGGirsaEkAkevvea.ADvivvGnvveekd...erkid 220
                                       +lg+r+iYlEa sG ++++  e ++ +kk + +a livGGGir +E A  v+ea AD+iv+Gn+vee+    e+ i+
  gi|385805906|ref|YP_005842304.1| 168 MLGMRYIYLEAgSGSPQHIppEVIKSIKKTVPEAFLIVGGGIRTKEAALSVAEAgADAIVTGNIVEEDIkkaEEIIK 244
                                       ******************997888899****************************************9867778888 PP

                                       HHHH CS
                              PcrB 221 aile 224
                                       ai++
  gi|385805906|ref|YP_005842304.1| 245 AIKK 248
                                       8876 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.92   1.8e+03      60      80 ..      35      55 ..       9      82 .. 0.52
   2 !   20.8   0.1   1.1e-07   0.00021      62     121 ..     188     248 ..     160     250 .] 0.84

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.92
                                      HHHHHHHHHHHH-SSEEEEES CS
                      His_biosynth 60 anldlveeiaeevfipvqvGG 80
                                      +n + ++ i++ +  +  + G
  gi|385805906|ref|YP_005842304.1| 35 ENAEKIASILKDIGTDAFLLG 55
                                      444444444444443333333 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 1.1e-07
                                       HHHHHHHHHH-S.SEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCG CS
                      His_biosynth  62 ldlveeiaeevf.ipvqvGGGIrsledveelleagadkviigtaavknpelikelaekfgs 121
                                        ++++ i ++v  + + vGGGIr+ e++ ++ eagad ++ g  + ++ +  +e+++++ +
  gi|385805906|ref|YP_005842304.1| 188 PEVIKSIKKTVPeAFLIVGGGIRTKEAALSVAEAGADAIVTGNIVEEDIKKAEEIIKAIKK 248
                                       47788888887646789***************************99999999999988765 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   4.3e-07   0.00085     133     173 ..     188     229 ..     160     230 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 4.3e-07
                                       HHHHHHHHHHTTT.SEEEEEEE-SHHHHHHHHHTT-SEEEE- CS
                                       xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 133 leavkeikkkvee.veviaGnvataegakaLieagadavkvG 173
                                        e++k+ikk+v+e   +++G + t+e+a +++eagada+  G
  gi|385805906|ref|YP_005842304.1| 188 PEVIKSIKKTVPEaFLIVGGGIRTKEAALSVAEAGADAIVTG 229
                                       4789********978899********************9766 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 !   16.8   0.3   1.8e-06    0.0035     124     169 ..     183     230 ..     180     249 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.8e-06
                                       SGGG.HHHHCTSTTS....EEEEESS--SHHHHHHHCTT.SSEEEE-- CS
                      G3P_antiterm 124 Pglv.pkvikeikkel.kipiiaGGLietkedveealkaGaiavstsn 169
                                       P  + p+vik+ikk++ +  +i GG i+tke   ++ +aGa+a+ t+n
  gi|385805906|ref|YP_005842304.1| 183 PQHIpPEVIKSIKKTVpEAFLIVGGGIRTKEAALSVAEAGADAIVTGN 230
                                       777889*********868999***********************9986 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       3.3   6.5e+03      43      58 ..      34      49 ..      20      56 .. 0.61
   2 !   14.7   0.1   6.9e-06     0.014      97     135 ..     203     241 ..     190     247 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 3.3
                          TMP-TENI 43 lelaeklaalcrkygv 58
                                      +e aek+a + ++ g+
  gi|385805906|ref|YP_005842304.1| 34 AENAEKIASILKDIGT 49
                                      4455555555555444 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 6.9e-06
                          TMP-TENI  97 liiGlSvhsleeaeeaealgadYigvGpifpTdtKkdae 135
                                       li+G  + ++e a+ ++++gad i+ G i + d Kk +e
  gi|385805906|ref|YP_005842304.1| 203 LIVGGGIRTKEAALSVAEAGADAIVTGNIVEEDIKKAEE 241
                                       79*********************************9875 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.4   9.4e-06     0.019     232     293 ..     189     248 ..     174     249 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.4e-06
                                       HHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHHHHHHHHH CS
                            DHO_dh 232 kvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpkiakkikkelee 293
                                       +vi +++k++ +   +I  GGi + e al  +eaGA ++  +  +  e+ k a++i+k +++
  gi|385805906|ref|YP_005842304.1| 189 EVIKSIKKTVPE-AFLIVGGGIRTKEAALSVAEAGADAIVTGNIV-EEDIKKAEEIIKAIKK 248
                                       667777777774.446666*******************9888776.8999999**9999986 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.3   2.7e+03      22      44 ..      33      55 ..      22      64 .. 0.68
   2 ?   14.0   0.3   8.5e-06     0.017     188     243 ..     189     245 ..     174     250 .] 0.79

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.3
                                      -HHHHHHHHHHHHHCT-SSEEEE CS
                         Trp_syntA 22 dleqsleilkalekagadviElG 44
                                      ++e+  +i + l++ g+d+  lG
  gi|385805906|ref|YP_005842304.1| 33 NAENAEKIASILKDIGTDAFLLG 55
                                      36677777788888888887777 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 8.5e-06
                                       HHHHHHHHCT.SS-EEEESSS-SHHHHHHHH.TT-SEEEE-HHHHHHHHCTTTSHHHH CS
                         Trp_syntA 188 elverlkklt.avPvavGFGistkeqvkqva.kvadGvivGSalvkkieeeaeekeqa 243
                                       e+++ +kk+  ++ + vG Gi+tke + +va ++ad+++ G  + ++i++ aee  +a
  gi|385805906|ref|YP_005842304.1| 189 EVIKSIKKTVpEAFLIVGGGIRTKEAALSVAeAGADAIVTGNIVEEDIKK-AEEIIKA 245
                                       56777777654666789**************99********988888884.4444444 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 ?   -4.0   0.1       3.9   7.8e+03     122     135 ..      87     100 ..      85     102 .. 0.82
   2 ?   13.8   0.0   1.4e-05     0.028     153     196 ..     191     231 ..     179     233 .. 0.77

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 3.9
                                       TTTCCC-SEEEEES CS
                    Ribul_P_3_epim 122 eyllekldlvllms 135
                                        +++++ d++l ms
  gi|385805906|ref|YP_005842304.1|  87 TNIVKTADAILFMS 100
                                       57889999999998 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.4e-05
                                       HHHHHHHHHHHT---EEEEESS--TT.TCHHHHHHT--EEEESHH CS
                    Ribul_P_3_epim 153 ikkvrklidekeldlkievDGGvkld.nieqiaeagadvlVagsa 196
                                       ik+++k+++e      + v GG++++ ++  +aeagad++V+g  
  gi|385805906|ref|YP_005842304.1| 191 IKSIKKTVPE----AFLIVGGGIRTKeAALSVAEAGADAIVTGNI 231
                                       4455555555....9999*****87615678***********986 PP

>> Aldolase  KDPG and KHG aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.48   9.5e+02      74     100 ..      70      96 ..      36     124 .. 0.72
   2 ?   13.3   0.1   2.1e-05     0.041      48      97 ..     189     239 ..     157     246 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.48
                                       HHHHHCT-SEEEESS--HHHHHHHHHT CS
                          Aldolase  74 aeakeaGaqfvvsPGltadllkaavdl 100
                                        + ke+G   ++ PG  ++++k+a + 
  gi|385805906|ref|YP_005842304.1|  70 LKLKETGLPVIIFPGDLTNIVKTADAI 96 
                                       455677777777777666777666554 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 2.1e-05
                                       HHHHHHHHH-TTS.EEEEES--SHHHHHHHHHCT-SEEEESS--HHHHHHH CS
                          Aldolase  48 dairvlrkerpdl.lvgaGtvlnaeqlaeakeaGaqfvvsPGltadllkaa 97 
                                       ++i+ ++k +p++ l+  G + ++e +  ++eaGa+ +v+  + ++ +k+a
  gi|385805906|ref|YP_005842304.1| 189 EVIKSIKKTVPEAfLIVGGGIRTKEAALSVAEAGADAIVTGNIVEEDIKKA 239
                                       799*9******962566777788888899***********98865444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       710  (0.0396006); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1572.92
//
Query:       gi|385805907|ref|YP_005842305.1|  [L=126]
Description: hypothetical protein FFONT_0865 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-05   24.4   0.1      4e-05   23.6   0.1    1.5  1  HTH_3            Helix-turn-helix
    0.00036   20.5   0.1    0.00067   19.6   0.1    1.4  1  Cro              Cro
    0.00046   20.2   1.1     0.0072   16.4   0.5    3.0  2  HTH_22           HTH domain
    0.00075   19.2   0.1     0.0043   16.8   0.0    2.2  2  LacI             Bacterial regulatory proteins, lacI family
     0.0049   16.8   1.2      0.069   13.1   0.1    2.7  2  HTH_11           HTH domain
     0.0052   17.1   0.0     0.0081   16.5   0.0    1.2  1  HTH_31           Helix-turn-helix domain
     0.0095   16.1   0.1      0.013   15.7   0.1    1.3  1  Phage_CII        Bacteriophage CII protein
  ------ inclusion threshold ------
      0.017   15.0   0.0      0.027   14.3   0.0    1.3  1  YdaS_antitoxin   Putative antitoxin of bacterial toxin-antito
      0.021   14.7   0.0      0.034   14.0   0.0    1.3  1  P22_Cro          DNA-binding transcriptional regulator Cro
      0.026   14.3   0.1      0.088   12.6   0.0    1.8  2  HTH_10           HTH DNA binding domain
      0.032   14.2   0.1        0.1   12.6   0.0    1.8  2  HTH_19           Helix-turn-helix domain
      0.037   14.0   1.4      0.076   13.0   1.4    1.6  1  SWIRM-assoc_1    SWIRM-associated region 1
      0.041   13.5   0.4       0.15   11.7   0.0    2.1  2  HTH_50           Helix-turn-helix domain
      0.063   13.2   0.1       0.28   11.1   0.0    2.1  2  HTH_5            Bacterial regulatory protein, arsR family
      0.068   13.4   0.0       0.24   11.6   0.0    1.8  2  FAA_hydrolase_N  Fumarylacetoacetase N-terminal
       0.07   13.4   0.1       0.12   12.6   0.1    1.4  1  KORA             TrfB plasmid transcriptional repressor
       0.15   10.8   0.0       0.21   10.4   0.0    1.1  1  Glyco_hydro_77   4-alpha-glucanotransferase


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 !   23.6   0.1   3.8e-08     4e-05      13      46 ..      29      62 ..      23      70 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 3.8e-08
                                      HHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHH CS
                             HTH_3 13 eeLAeklGvsrstisriEnGernPsletlkklak 46
                                      +++Ae lGvs+++isr+ +Ge  Ps ++l k+ +
  gi|385805907|ref|YP_005842305.1| 29 KKVAEDLGVSKAAISRYLKGEIFPSDKILSKIFE 62
                                      679*****************777********965 PP

>> Cro  Cro
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   6.4e-07   0.00067       6      34 ..      19      47 ..      14      51 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 6.4e-07
                                      HHHHHHHHHHHHHHHHHTS-HHHHHHHHH CS
                               Cro  6 LsdyvtkvGQaktAkdlgvkqsaIsKAlk 34
                                      +++ v k G +k+A+dlgv ++aIs+ lk
  gi|385805907|ref|YP_005842305.1| 19 IETIVLKRGGKKVAEDLGVSKAAISRYLK 47
                                      567799*******************9876 PP

>> HTH_22  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.5   6.9e-06    0.0072      40      63 .]      24      47 ..       4      47 .. 0.86
   2 ?   -0.5   0.0       1.2   1.3e+03      57      63 .]      98     104 ..      88     114 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.9e-06
                            HTH_22 40 lkgavekvAekLgiSraTvYryLr 63
                                      lk+  +kvAe Lg+S+a + ryL+
  gi|385805907|ref|YP_005842305.1| 24 LKRGGKKVAEDLGVSKAAISRYLK 47
                                      89999*****************96 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.2
                            HTH_22  57 TvYryLr 63 
                                       T+Y+ ++
  gi|385805907|ref|YP_005842305.1|  98 TIYKDIK 104
                                       5555543 PP

>> LacI  Bacterial regulatory proteins, lacI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       1.3   1.4e+03      27      36 ..      11      20 ..       8      23 .. 0.76
   2 !   16.8   0.0   4.1e-06    0.0043       4      37 ..      30      63 ..      29      78 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.3
                                      THHHHHHHHH CS
                              LacI 27 seetrerVea 36
                                        etr+++ +
  gi|385805907|ref|YP_005842305.1| 11 DRETRKKIIE 20
                                      579***9975 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 4.1e-06
                                      HHHHHCTS-HHHHHHHCTTSSSSTHHHHHHHHHH CS
                              LacI  4 DVArlAGVSkaTVSrvLnnkerVseetrerVeaa 37
                                       VA+  GVSka++Sr+L+++   s+++  +++++
  gi|385805907|ref|YP_005842305.1| 30 KVAEDLGVSKAAISRYLKGEIFPSDKILSKIFEI 63
                                      59*****************988888888887776 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.1   6.5e-05     0.069       2      37 ..      15      47 ..      14      48 .. 0.88
   2 ?    1.7   0.1      0.24   2.6e+02      31      37 ..      98     104 ..      93     105 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.5e-05
                            HTH_11  2 llqilelLleargpisgeeLAeeLnvSrrtvrrdIk 37
                                      +++i+e +  +rg   g++ Ae L+vS++++ r++k
  gi|385805907|ref|YP_005842305.1| 15 RKKIIETIVLKRG---GKKVAEDLGVSKAAISRYLK 47
                                      5788888888888...999***************98 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.24
                            HTH_11  31 tvrrdIk 37 
                                       t+++dIk
  gi|385805907|ref|YP_005842305.1|  98 TIYKDIK 104
                                       9*****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 !   16.5   0.0   7.7e-06    0.0081      19      49 ..      30      59 ..      26      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 7.7e-06
                            HTH_31 19 evAerlgvsestlsrlEqGrrgrpspavlea 49
                                       vAe lgvs++ +sr+  G++  ps   l +
  gi|385805907|ref|YP_005842305.1| 30 KVAEDLGVSKAAISRYLKGEI-FPSDKILSK 59
                                      79*******************.899877765 PP

>> Phage_CII  Bacteriophage CII protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   1.3e-05     0.013      18      65 ..      19      68 ..       3      94 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.3e-05
                                      HHHHHH.HHHHHHHHHHTSSTTTHHHH.HHHHHHHHHHHHHHTTTTHHHH CS
                         Phage_CII 18 Lnkiai.lgqrkvaeaiGvdeskisrw.ktDwipkasvLlavlefGvadd 65
                                      +  i + +g +kvae +Gv ++ isr+ k++  p   +L  ++e   +++
  gi|385805907|ref|YP_005842305.1| 19 IETIVLkRGGKKVAEDLGVSKAAISRYlKGEIFPSDKILSKIFEISDKEE 68
                                      4444332799****************857777777778777777655444 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   2.6e-05     0.027       8      38 ..      25      54 ..      18      68 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.6e-05
                    YdaS_antitoxin  8 vGgqkaLAealgvsqqaVsqWlkgkkqvpae 38
                                       +g k++Ae lgvs++a+s+ lkg   +p  
  gi|385805907|ref|YP_005842305.1| 25 KRGGKKVAEDLGVSKAAISRYLKG-EIFPSD 54
                                      57889*****************87.445544 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 ?   14.0   0.0   3.2e-05     0.034      13      36 ..      29      54 ..      22      58 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.2e-05
                                      HHHHHHHTS-HHHHHHH..HTC--HH CS
                           P22_Cro 13 ekvAkalgvtksAVsqW..geeiPel 36
                                      +kvA+ lgv+k+A+s+   ge  P +
  gi|385805907|ref|YP_005842305.1| 29 KKVAEDLGVSKAAISRYlkGEIFPSD 54
                                      79**************9888888876 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   8.3e-05     0.088      25      45 ..      27      47 ..      25      49 .. 0.90
   2 ?   -1.7   0.0       2.4   2.6e+03      29      38 ..      57      66 ..      54      76 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.3e-05
                            HTH_10 25 tlkeLAkelGIskstlsehLr 45
                                        k++A++lG+sk+++s +L+
  gi|385805907|ref|YP_005842305.1| 27 GGKKVAEDLGVSKAAISRYLK 47
                                      5789**************996 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.4
                            HTH_10 29 LAkelGIsks 38
                                      L+k++ Is+ 
  gi|385805907|ref|YP_005842305.1| 57 LSKIFEISDK 66
                                      7888888876 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   9.8e-05       0.1      16      50 ..      29      62 ..      24      68 .. 0.90
   2 ?   -1.1   0.0       1.9     2e+03      30      35 ..      92      97 ..      64     120 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.8e-05
                            HTH_19 16 eelaerlgisrskisaiEngkkdvpsaelllkiae 50
                                      +++ae+lg+s++ is + +g++  ps + l ki e
  gi|385805907|ref|YP_005842305.1| 29 KKVAEDLGVSKAAISRYLKGEI-FPSDKILSKIFE 62
                                      68*******************9.999998888866 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.9
                            HTH_19 30 saiEng 35
                                      s +E++
  gi|385805907|ref|YP_005842305.1| 92 SSLEKD 97
                                      444433 PP

>> SWIRM-assoc_1  SWIRM-associated region 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.4   7.2e-05     0.076      38      60 ..     102     124 ..      84     126 .] 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.2e-05
                     SWIRM-assoc_1  38 elKLkqfeelEklleaerrelek 60 
                                       ++K+k feelE+l+++ + e ++
  gi|385805907|ref|YP_005842305.1| 102 DIKMKIFEELESLVKELKSECDQ 124
                                       89*************99998776 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00015      0.15      28      45 ..      30      47 ..      13      48 .. 0.88
   2 ?   -0.8   0.1       1.2   1.2e+03       3      13 ..      86      96 ..      69     101 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00015
                            HTH_50 28 klAkrLGvShtaianklr 45
                                      k+A+ LGvS++ai + l+
  gi|385805907|ref|YP_005842305.1| 30 KVAEDLGVSKAAISRYLK 47
                                      9************88665 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.2
                            HTH_50  3 sLkeyveefEr 13
                                       +k + ++ E+
  gi|385805907|ref|YP_005842305.1| 86 EYKNLFSSLEK 96
                                      34555555555 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       5.6   5.9e+03       2       8 ..      13      19 ..      12      22 .. 0.82
   2 ?   11.1   0.0   0.00026      0.28      22      37 ..      32      47 ..      29      47 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 5.6
                                      HHHHHHH CS
                             HTH_5  2 ptRlkIL 8 
                                      +tR kI+
  gi|385805907|ref|YP_005842305.1| 13 ETRKKII 19
                                      7999998 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00026
                                      HHHHTS-HHHHHHHHH CS
                             HTH_5 22 aeelglsqstvShHLk 37
                                      ae+lg+s++++S++Lk
  gi|385805907|ref|YP_005842305.1| 32 AEDLGVSKAAISRYLK 47
                                      89*************8 PP

>> FAA_hydrolase_N  Fumarylacetoacetase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.6   1.7e+03      65      79 ..       8      22 ..       4      45 .. 0.66
   2 ?   11.6   0.0   0.00023      0.24      10      43 ..      63      96 ..      59     124 .. 0.64

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.6
                                      HHHHHHHHHHHHHHH CS
                   FAA_hydrolase_N 65 revwravRaalqelL 79
                                      r+  r++R+++ e +
  gi|385805907|ref|YP_005842305.1|  8 RKLDRETRKKIIETI 22
                                      566788888888776 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00023
                                      ESSEE.SEEEEEEETTEEEEHHHHHHTTSS-STGG CS
                   FAA_hydrolase_N 10 tkekk.eprigvaIGdqvldLsalaeaglfsqlee 43
                                       ++k+ +++i + IG++++dL +   ++lfs+le+
  gi|385805907|ref|YP_005842305.1| 63 ISDKEeREKISIIIGEYIVDLLKE-YKNLFSSLEK 96
                                      544442679***********9776.4578886633 PP

>> KORA  TrfB plasmid transcriptional repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00012      0.12      10      51 ..       4      45 ..       1      50 [. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00012
                              KORA 10 ikgleelaeqtveiargvLVegkkqadvatelgltkqavsqa 51
                                      i    +l  +t++ + + +V ++  ++va+ lg++k a+s+ 
  gi|385805907|ref|YP_005842305.1|  4 ITFFRKLDRETRKKIIETIVLKRGGKKVAEDLGVSKAAISRY 45
                                      5566778899999899999999999**************986 PP

>> Glyco_hydro_77  4-alpha-glucanotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0    0.0002      0.21     309     360 ..      13      64 ..       5      76 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0002
                                       HHHHHHHHHHHHHCT-EEEE---SS--HHHHHHHHHTT-BEEEEGGGTTSTT CS
                    Glyco_hydro_77 309 eelfevlkeelqkgkllviaEDLGvvpdevrelleelgilgmkvlqfafede 360
                                       e   ++++  + k   + +aEDLGv ++ ++++l+   +++ k+l   fe +
  gi|385805907|ref|YP_005842305.1|  13 ETRKKIIETIVLKRGGKKVAEDLGVSKAAISRYLKGEIFPSDKILSKIFEIS 64 
                                       4455566666666788899*************************98766444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1348  (0.0751855); expected 358.6 (0.02)
Passed bias filter:                      628  (0.0350271); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 806.92
//
Query:       gi|385805908|ref|YP_005842306.1|  [L=496]
Description: xanthine/uracil/vitamin C permease [Fervidicoccus fontis Kam940]
Scores for complete 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   64.3  54.1    1.7e-17   63.2  48.8    2.2  2  Xan_ur_permease  Permease family


Domain annotation for each model (and alignments):
>> Xan_ur_permease  Permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.2   0.2   0.00079        14       3      28 ..      26      51 ..      24      64 .. 0.87
   2 !   63.2  48.8   9.6e-22   1.7e-17      41     387 ..      86     454 ..      73     487 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.00079
                                      HHHHHHHHHHHHHHHHHHHHHTTTS- CS
                   Xan_ur_permease  3 llllglQhllamfaalvvvPllvgda 28
                                      ++++g++++l m + l v+P +++d 
  gi|385805908|ref|YP_005842306.1| 26 EIIAGITTFLSMAYILFVNPSILTDG 51
                                      699*******************9986 PP

  == domain 2  score: 63.2 bits;  conditional E-value: 9.6e-22
                                       HHHHHHHHHHHHHHHHTTT-----EEE-GGGHH.......HHHGGG-...............HHHHHHHHHHHHHHH CS
                   Xan_ur_permease  41 atllasGiatllqllifgirlpillgssfafvt.......almialGsa...........edieialagllgallva 99 
                                       at l+++ atl++ l+++++  ++ g++ +++             +  +           +    a+  +l++++  
  gi|385805908|ref|YP_005842306.1|  86 ATALSAATATLIMSLYAKMPFGLAPGMGENAFIgytaiplF----A--SilitshdlqgvAPAIFAIYLALVSVFFN 156
                                       78899**********************98766656644431....2..1335556777877777788889999999* PP

                                       HHHHHHHHTT-SH.HHHHH--HHHHHHHHHHHHHHHHHHHHHHTTSS-...BTT.B---HHHHHHHHHHHHHHHHHH CS
                   Xan_ur_permease 100 gvlfilisltglrgrlarlipPvvtgpvvlliGlslaqiavkkvgggwaa.vegltvvslkllllavvvllvillls 175
                                       g+lf+++s+  +r+ +    p  +  ++ ++iGl+++ i+++++g+++   + +  +    l ++a+ + l+++ ++
  gi|385805908|ref|YP_005842306.1| 157 GILFLIFSVGRIREFILNSVPESIRLGISIGIGLFITLIGFSNIGIVEPGvGTPISFNTAALKTAAFYLGLLSFFIA 233
                                       ***********************************************988777766666666677777788888888 PP

                                       HSSSTTTTTHHHHHHHHHHHHHHHHHHHTTSSHH.............HHS-SS-----------HH..H.HHHHTHH CS
                   Xan_ur_permease 176 vflkglfsqlpiLigiiagwllalfmgivnlspe.............vseapwfqlpsplkfgtplfnlgliltvla 239
                                        +l+  ++ ++  i+i++++++a+ + i+ l+p              ++++ +  lp+ +++   lf lg  +++++
  gi|385805908|ref|YP_005842306.1| 234 AVLMAKKVIGGFIIAILGSTAIAILLSITGLTPGlistssslftmpsFTTSILNDLPKSFYLYFTLFGLGF-PIAFS 309
                                       889999999*************************9988888766666555555666666666666688865.55556 PP

                                       H.HHHHHHHHHHHHHHHHHHTS-TII.IIIHHHHHHHHHHHHHHHHHHT---EEE-HHHHHHHHHHTB--HHHHHHH CS
                   Xan_ur_permease 240 valvavvesvGdiravakvvgrslkp.kpdlrralladGlatllsgllGalpvttyaeniGvvaltkvasrrvmvta 315
                                       ++lv +++ +G+++++a+ +g+  ++   ++++al+ d la+++s + G++ + +y+e++ +++++    ++ ++t 
  gi|385805908|ref|YP_005842306.1| 310 LFLVDFFDGIGTLTGLAMKAGLVKDGkVMNINKALISDALASIISPFYGTSTTVVYVESASGIEAG----GKSGLTS 382
                                       66*******************77776789*************************************....******* PP

                                       HHHHHHHT--HHHHHHHTTS-HHHHHHHHHHHHHHHHHHHHHHHHHTTS-SHHHHHHHHHHHHHHHH----- CS
                   Xan_ur_permease 316 gvilillglipklaallssIPepvlgGvllvvfgmiaasgvsnlqtvdldsarnllivavslvlGlgvatvp 387
                                        +i+il+ ++  +a+l++ IP++  gGvl++v  + ++ + +  + +dl++   ++ + v++ ++ +++t++
  gi|385805908|ref|YP_005842306.1| 383 LIIAILFFISAIFAPLFTYIPTFTTGGVLVLVGLLFLGLAGKLTSMEDLTEVIPAFFTLVAIPFTYSITTGI 454
                                       ********************************9999*****************************9999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (496 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       840  (0.0468515); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.51
# Mc/sec: 2899.36
//
Query:       gi|385805909|ref|YP_005842307.1|  [L=314]
Description: DNA methylase N-4/N-6 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-28  100.4   1.9    1.7e-14   54.1   0.0    2.1  2  N6_N4_Mtase      DNA methylase
    2.1e-06   28.3   0.0     0.0034   18.0   0.0    2.3  2  Methyltransf_11  Methyltransferase domain
    2.6e-06   27.3   0.0      4e-05   23.4   0.0    2.2  1  UPF0020          Putative RNA methylase family UPF0020
    2.8e-05   24.0   0.0      4e-05   23.5   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    0.00076   19.1   0.0     0.0012   18.5   0.0    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
     0.0049   17.6   0.0       0.04   14.6   0.0    2.2  1  Methyltransf_25  Methyltransferase domain
     0.0099   15.5   0.0      0.019   14.6   0.0    1.5  1  Cons_hypoth95    Conserved hypothetical protein 95
  ------ inclusion threshold ------
      0.069   12.9   0.0       0.16   11.7   0.0    1.6  1  DUF2286          Uncharacterized protein conserved in archaea


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 !   54.1   0.0   7.7e-18   1.7e-14     109     223 ..      35     139 ..      20     145 .. 0.78
   2 !   45.2   1.1   4.1e-15   9.2e-12       2     114 ..     178     301 ..     177     310 .. 0.85

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 7.7e-18
                                       ESSTT-..---GGGSSBSS-HHHHHHHHHHCHHHCC-B--BSEEE-SCCCTTSTTS-CHH----SS---HHHHHHHH CS
                       N6_N4_Mtase 109 sknkkyllkfnldaikvpyeekdklekrgaytskkkgkkiediWdlseiqsnekkskgdtkkkHpaqkPvallerlI 185
                                       +k kky  +   ++i+++ e  ++l+ +         ++ + +W ++e+ + + ++    ++k+      + ++ l+
  gi|385805909|ref|YP_005842307.1|  35 AKRKKY-VTIGCKKIELEIEGFKELQPKE------FVVEKTSVWSFPERGKWATHKY---NAKFRGNWSPQVARNLL 101
                                       555555.5555555555555555555544......7888999**5555555555555...689************** PP

                                       HHHS-TT-EEEETT-TTTHHHHHHHHTT-EEEEEESSH CS
                       N6_N4_Mtase 186 klstkkgdivlDpFaGSGtTavaakelgrkfiGieiee 223
                                       +l++k gd+vlDpF+GSGt +++++ l+r+++G++i+ 
  gi|385805909|ref|YP_005842307.1| 102 LLYSKSGDTVLDPFLGSGTSMIECILLKRRCYGVDINI 139
                                       ************************************96 PP

  == domain 2  score: 45.2 bits;  conditional E-value: 4.1e-15
                                       EEEEE--SSSSSCS......GCCGCCHHHHHHHHHHHHHHHHHHHEEEEEEEEEEE-CCCHHT......HHHHHHHH CS
                       N6_N4_Mtase   2 dlivtdpPYntgkdy.endeqyeeedsyeeyleflekvlkevrrvLkddgsifiniddseikk......elkalade 71 
                                       d i+  pPY    +y + ++    + s++eyle ++++++e++r+Lk+d+ + i ++d++ kk       +++++  
  gi|385805909|ref|YP_005842307.1| 178 DFILGHPPYASIIKYsKGSDGDLSKMSIQEYLEKMRRIARELYRILKKDKYLAIMVGDIRRKKhviplgYMVMKIFL 254
                                       679999********9544455556778***************************************99966666666 PP

                                       HTT-EEEEEEEEEEES.....SSTTTSTCCS-B--EEEEEEEESSTT- CS
                       N6_N4_Mtase  72 ifggffllnvivwkkp.....nsmpesnkdrltsthEyilvfsknkky 114
                                       + g f+++++i++ +        + + ++d+l   hE+i+vf+k+ + 
  gi|385805909|ref|YP_005842307.1| 255 EEG-FIIKEHIIKVQHnmigtAFWKNKKNDFLLLKHEHIFVFRKPLDS 301
                                       668.*********999899865666777789*************8655 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.5e-06    0.0034       3      66 ..     116     181 ..     112     184 .. 0.79
   2 !    8.0   0.0    0.0019       4.4      72      96 .]     207     231 ..     193     231 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.5e-06
                                       ET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-...EEEETTEECCCT.SS-TT-EEEEE CS
                   Methyltransf_11   3 vGcGtGrlaealakrgarvvgvDlskemlklakekaseegl...kvefvvadaekl.pfednsfDlvv 66 
                                       +G+Gt  + + l    +r++gvD++   + l+ +++++ +     v++ ++dae l  fed++fD+++
  gi|385805909|ref|YP_005842307.1| 116 LGSGTSMIECILL--KRRCYGVDINIDSVMLSWSRIKPIYSsdsFVKLFEGDAEYLdAFEDEKFDFIL 181
                                       5777777777777..45678888877777777777777666778899*********88********96 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0019
                                       CC-CCHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  72 hhvedpekalkeiaRvLkpgGllvi 96 
                                       +++e+++++ +e++R+Lk++ +l+i
  gi|385805909|ref|YP_005842307.1| 207 EYLEKMRRIARELYRILKKDKYLAI 231
                                       566999*************999875 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   1.8e-08     4e-05      13     164 ..      93     220 ..      83     244 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.8e-08
                                       -HHHHHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHH CS
                           UPF0020  13 ketLAaalvrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklygsDldrrvv 89 
                                       ++++A+ l+ l   k g++ lDP+ GsGt  IE  ll+++++                         + +++d+ ++
  gi|385805909|ref|YP_005842307.1|  93 SPQVARNLLLLY-SKSGDTVLDPFLGSGTSMIECILLKRRCY------------------------GVDINIDSVML 144
                                       566777777664.5899*************************........................23345667777 PP

                                       HHHHHHHHHTT-GGGEEEEE--GGG--.STTS---EEEE----------HHHH.HHHHHHHHHHHHHH-TT..-EEE CS
                           UPF0020  90 qgareNaekagvgdliefsqadaakLr.lkegevdvivtnpPYGerlgskkal.ekLYseflrelkrvlrgggrlvl 164
                                         +r +   +  + ++++ + da  L   +++++d i++ pPY   ++  k    +L +   +e  + +r+ +r ++
  gi|385805909|ref|YP_005842307.1| 145 SWSRIKP-IYSSDSFVKLFEGDAEYLDaFEDEKFDFILGHPPYASIIKYSKGSdGDLSKMSIQEYLEKMRRIARELY 220
                                       7777664.5778899999999*****9755559**********9988754433377777666666666666555444 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   1.8e-08     4e-05       2     110 ..     106     232 ..     105     285 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.8e-08
                   Methyltransf_31   2 dkglrvlD..lGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld..nveFeqgdieeleklledek 74 
                                       ++g +vlD  lG+Gt+ +   l      k + +G+Di+ +++ l+ ++ +   ++   v++ +gd+e l+  +edek
  gi|385805909|ref|YP_005842307.1| 106 KSGDTVLDpfLGSGTSMIECILL-----KRRCYGVDINIDSVMLSWSRIKPIYSSdsFVKLFEGDAEYLDA-FEDEK 176
                                       78999***888999988888888.....4579****************9999988899***********96.9**** PP

                   Methyltransf_31  75 fDlilsn..................evl...naladpdkileeiervlkpggillie 110
                                       fD+il +                    +    +l  +  i +e+ r lk++ +l+i 
  gi|385805909|ref|YP_005842307.1| 177 FDFILGHppyasiikyskgsdgdlsK-MsiqEYLEKMRRIARELYRILKKDKYLAIM 232
                                       *******8887777777666666540.155588888999999999999999988765 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 !   18.5   0.0   5.3e-07    0.0012       3     101 ..     110     208 ..     108     243 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 5.3e-07
                   Methyltransf_15   3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNae.vYgvsdkitlvlgdvfellaklklekikvdlvflS 78 
                                       ++lD+f G+G  +i+  l  ++ ++++in++ + ++    + +Y  ++ ++l  gd +  l  ++ ek   d+++  
  gi|385805909|ref|YP_005842307.1| 110 TVLDPFLGSGTSMIECILLKRRCYGVDINIDSVMLSWSRIKpIYSSDSFVKLFEGDAE-YLDAFEDEKF--DFILGH 183
                                       79*****************************999987776559*************75.6777777777..****** PP

                   Methyltransf_15  79 pPwGG.psYkkqekfdlkk.klkpl 101
                                       pP    ++Y+k  + dl k +++++
  gi|385805909|ref|YP_005842307.1| 184 PPYASiIKYSKGSDGDLSKmSIQEY 208
                                       **987369*****999955334433 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.8e-05      0.04       1      70 [.     111     182 ..     111     226 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.8e-05
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHH...TTTTEEEEESBCCGBS.SSTTTEEEEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraee...eglnvefvqgdaedlp.fedgsfDlvvs 70 
                                       vLd   G+G+ ++++     k + +gvDi+ + +    +r++    ++  v++ +gdae l+ fed++fD+++ 
  gi|385805909|ref|YP_005842307.1| 111 VLDPFLGSGTSMIECILL--KRRCYGVDINIDSVMLSWSRIKPiysSDSFVKLFEGDAEYLDaFEDEKFDFILG 182
                                       788889999999999866..49*******988888888887655434449***********879*******986 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   8.5e-06     0.019      42     126 ..     108     189 ..      99     221 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.5e-06
                                       C-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEE CS
                     Cons_hypoth95  42 garvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdivf 118
                                       g +vLD f GsG+  +E++  + ++++ v+ +   v +    ++ +  ++++ +l e ++e l+    ++e+fd++ 
  gi|385805909|ref|YP_005842307.1| 108 GDTVLDPFLGSGTSMIECILLK-RRCYGVDINIDSVMLSWSRIKPIYSSDSFVKLFEGDAEYLDAF--EDEKFDFIL 181
                                       6689***************987.89**********************9999999999999999888..7899***** PP

                                       E--SSSTT CS
                     Cons_hypoth95 119 lDPPyake 126
                                         PPya+ 
  gi|385805909|ref|YP_005842307.1| 182 GHPPYASI 189
                                       *****975 PP

>> DUF2286  Uncharacterized protein conserved in archaea (DUF2286)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   7.1e-05      0.16      24      70 ..     266     310 ..     251     313 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.1e-05
                           DUF2286  24 evvkevakealkeWnpeesDfivlrdklelelklplkpelydklkel 70 
                                       +v  +++  a   W+ ++ Df+ l+++  + + +pl+   y+k++ +
  gi|385805909|ref|YP_005842307.1| 266 KVQHNMIGTA--FWKNKKNDFLLLKHEHIFVFRKPLDSSDYEKFQYY 310
                                       4444444444..4*****************************99877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       689  (0.0384294); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); 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: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 1928.65
//
Query:       gi|385805910|ref|YP_005842308.1|  [L=110]
Description: hypothetical protein FFONT_0868 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.1e-06   26.7   0.2    6.5e-06   26.0   0.2    1.3  1  PadR           Transcriptional regulator PadR-like family
     0.0044   16.8   0.3      0.013   15.3   0.1    1.8  2  DUF4364        Domain of unknown function (DUF4364)
     0.0059   16.4   0.2      0.011   15.6   0.2    1.6  1  DUF3116        Protein of unknown function (DUF3116)
  ------ inclusion threshold ------
      0.053   13.9   0.1      0.096   13.1   0.1    1.6  1  Ribosomal_L23  Ribosomal protein L23


Domain annotation for each model (and alignments):
>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.2   1.4e-09   6.5e-06      14      73 ..      40      92 ..      29      94 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 1.4e-09
                                      HHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHH CS
                              PadR 14 eiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrel 73
                                      ei+ke+++l+ g ++++   lY +  r+e+egl+++ + +     p+ +Y++T++G+ ++
  gi|385805910|ref|YP_005842308.1| 40 EIKKEINDLF-G-IKVNTLYLYSIIYRMEEEGLIVKVEGD-----PKSTYTITPEGELTY 92
                                      899******7.7.8*********************99776.....9**********9766 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1      0.14   6.3e+02      91     124 ..      12      45 ..       3      56 .. 0.48
   2 !   15.3   0.1   2.8e-06     0.013      34      71 ..      56      93 ..      42     106 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.14
                           DUF4364  91 enkeelkkese.vkadyykkengeytVklkikekd 124
                                       ++k+++++e+  + + y+  ++g  +++ +ik + 
  gi|385805910|ref|YP_005842308.1|  12 RLKKKIENEVLwIYVSYVLIKKGALSIN-EIKKEI 45 
                                       4555555554323444444444444444.333333 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 2.8e-06
                           DUF4364 34 fdlqqalseLvesglieeeekenktlykiTekGketle 71
                                      ++l +++  ++e+gli + e + k++y+iT++G+ t +
  gi|385805910|ref|YP_005842308.1| 56 LYLYSIIYRMEEEGLIVKVEGDPKSTYTITPEGELTYK 93
                                      45678999*************************97755 PP

>> DUF3116  Protein of unknown function (DUF3116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.2   2.4e-06     0.011      42      82 ..      56      94 ..      15     100 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.4e-06
                           DUF3116 42 neLLytvYWLElkgyilRkeekannkkrYelTekGellyke 82
                                        L   +Y +E++g i++ e   + k +Y++T++Gel yk+
  gi|385805910|ref|YP_005842308.1| 56 LYLYSIIYRMEEEGLIVKVEG--DPKSTYTITPEGELTYKK 94
                                      3456679**********9999..799*************97 PP

>> Ribosomal_L23  Ribosomal protein L23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   2.2e-05     0.096      32      80 ..      39     101 ..       7     105 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.2e-05
                                       HHHHHHHHHHHT--EEE..EEEEEE--EBESSSSS......EEBE-...........-EEEEEEEESS CS
                     Ribosomal_L23  32 leikkaveklFgVkVek..Vntlnvkgkkkrvgrk......vgrrk...........syKkaiVtLke 80 
                                        eikk ++ lFg+kV+     +++++ ++     +      +g  k            yKka+V L+e
  gi|385805910|ref|YP_005842308.1|  39 NEIKKEINDLFGIKVNTlyLYSIIYRMEE-----EglivkvEGDPKstytitpegelTYKKALVFLEE 101
                                       69***********9877332333333333.....2222333343335566677788899**9999954 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); 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 0.30s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 681.67
//
Query:       gi|385805911|ref|YP_005842309.1|  [L=368]
Description: Myo-inositol-1-phosphate synthase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-28   99.4   0.0    2.4e-28   98.5   0.0    1.4  1  Inos-1-P_synth  Myo-inositol-1-phosphate synthase
     0.0003   20.3   0.0      0.005   16.3   0.0    2.2  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 !   98.5   0.0   2.7e-32   2.4e-28       1     108 [.     193     303 ..     193     304 .. 0.94

  Alignments for each domain:
  == domain 1  score: 98.5 bits;  conditional E-value: 2.7e-32
                                       SHHHHHHHHHHHHHHTT-EEEEEEEEEEE-HHHHHHTTSHHHHHHHHHHHHHHHHHHHSS--EEE....EEE...EE CS
                    Inos-1-P_synth   1 GqTklksvLaellverglkvksivslNilGnnDgknlseeerfksKkisKssvvddivkanellyvdhevvi...kY 74 
                                       G+T+l+s L+ l++ergl+++++++lNi+Gn+D++n++eeer++sK++sK+s+v +++ + +   ++  ++i   ++
  gi|385805911|ref|YP_005842309.1| 193 GATILHSSLTALMRERGLRINETYQLNIGGNTDFLNMKEEERLRSKRESKTSAVLNTLTNPKEILEKNRIRIgpsDW 269
                                       9***************************************************99988776444445789999***** PP

                                       -GGGTTEEEEEEEEEEEEGGGEEEEEEEEEEEEH CS
                    Inos-1-P_synth  75 vpylgDsKvaldeieseiflggkntielkleceD 108
                                       vp+lg++K+a++ + ++ flg+++++++kl+++D
  gi|385805911|ref|YP_005842309.1| 270 VPFLGNTKIAYIYVRATSFLGFPVELDVKLKVDD 303
                                       ********************************99 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 ?    1.9   0.0     0.013   1.2e+02       3      29 ..       6      31 ..       4      36 .. 0.84
   2 !   16.3   0.0   5.5e-07     0.005     205     301 ..     141     344 ..      94     360 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.013
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     NAD_binding_5  3 vllvGlgGnngtTlvagvlankkglsw 29
                                      v l+G+ Gn ++ +v gvl  kk+ ++
  gi|385805911|ref|YP_005842309.1|  6 VGLIGI-GNCASAIVQGVLLSKKDPNK 31
                                      7799**.*************9997655 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 5.5e-07
                                       xxxxxxxxxxxxxxxxxxxxxxxxx..xxx.xxxxxxxxxxxxxxxxxxx........................... RF
                     NAD_binding_5 205 pstiyavAailegvpyingsPqntl..vpg.lvelAekkgvfiaGdDfKt........................... 251
                                       +   ya Aai++gv++ing P        g  +e  +k g+++ GdD+K                            
  gi|385805911|ref|YP_005842309.1| 141 ATRFYAEAAIKAGVAFINGMPVFIAsdPKGeWQEKFKKAGLPVLGDDVKGqfgatilhssltalmrerglrinetyq 217
                                       3456*****************988843334245667889***********9999*****999999999999999999 PP

                                       ............................................................................. RF
                     NAD_binding_5 252 ............................................................................. 251
                                                                                                                    
  gi|385805911|ref|YP_005842309.1| 218 lniggntdflnmkeeerlrskresktsavlntltnpkeileknririgpsdwvpflgntkiayiyvratsflgfpve 294
                                       99999999999999999999999999999999999999999999999999999999999999999999998888888 PP

                                       ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     NAD_binding_5 252 ...........lLAaPlilDLvllveLaqrvevkkekkkefkklesvlsllsyflKaPlvs 301
                                                    Aa  ++D+++l+ La   +++           ++ + ++y++K P ++
  gi|385805911|ref|YP_005842309.1| 295 ldvklkvddksQYAA-AMIDVIRLAKLALDNGLS----------GAIHEASAYYMKHPPKP 344
                                       888888888864444.367888888888777777..........56666667777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 2447.43
//
Query:       gi|385805912|ref|YP_005842310.1|  [L=378]
Description: ATP-NAD/AcoX kinase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.7e-33  116.0   0.0      2e-33  115.9   0.0    1.0  1  NAD_kinase  ATP-NAD kinase
    5.2e-06   26.1   0.0    8.4e-05   22.2   0.0    2.3  2  DAGK_cat    Diacylglycerol kinase catalytic domain
     0.0068   16.0   0.1      0.054   13.1   0.0    2.3  3  PrpR_N      Propionate catabolism activator


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 !  115.9   0.0   3.3e-37     2e-33       1     292 []       5     375 ..       5     375 .. 0.91

  Alignments for each domain:
  == domain 1  score: 115.9 bits;  conditional E-value: 3.3e-37
                                       .EEEEESSC...........................GGTCSHHHHHHHHHHHCT-..EEEEECCGGCCSSSTT--HH CS
                        NAD_kinase   1 kvgivvnpi...........................kkeaieraeevarwLldalsrvlevtveeklgeslaeaaef 50 
                                       k+g+++npi                            k+a+  a  + + L++++ +v+++++++ +ge+ +++++ 
  gi|385805912|ref|YP_005842310.1|   5 KIGFLANPIaglggalalkgsddiswndlgsligpgYKKALLFALILKERLKEKIEKVEFLVPDGMMGEDIFKRFGL 81 
                                       799999999999999999999999999999999999789999************77********************* PP

                                       HHTTTT--.......EEECCC-TTTTTSSSEEEEEE-HHHHHHHHHHHHHCT-EEEEEESSS--SS-SE..EGGGHH CS
                        NAD_kinase  51 rsevisvlkkvkttddtrkaleafadagvdliivvGGDGTaldvarllqkaeiPvlgvnaGvkgfltef..epeaaa 125
                                        ++ +  ++ ++t+ dt++ + +  ++g+++  + GGDGT+ dv+++++  +iP++g++ G+k+++++f  +++aaa
  gi|385805912|ref|YP_005842310.1|  82 SYTSVCSPNYPSTNLDTKNCAMEIKKEGAEVFFISGGDGTVYDVYTQVKT-SIPIVGIPSGTKMYSSIFakSINAAA 157
                                       *************************************************6.************************** PP

                                       HHHHHHHHT-SEEEEEEEEE...........................EEEEETTE...................... CS
                        NAD_kinase 126 ellekllegeirvekrevld...........................avimrskgee.................dia 158
                                        lle+++++++ +e  e+l                            +                          +ia
  gi|385805912|ref|YP_005842310.1| 158 ILLEDFINENYVLEAGEILLvdentirengsyrelfrgiaytiesknN--------LlhqqtkdlsyseeesleEIA 226
                                       *****************8777788888888888888888777777752........133333335777777799*** PP

                                       .EEEEEEESSEEEEEESSSSS-EE....EEEEETTEEEEEEEESEE.........................EEE-TG CS
                        NAD_kinase 159 diviensvlnevviirgpgstlie....lelyvdtelleadqldgl.........................ivstPt 206
                                       ++v ++ v + v +i+gpg t+++    l+++ d+ l  a +++g+                         i+++P 
  gi|385805912|ref|YP_005842310.1| 227 EYV-NEIVNDKVPLIIGPGRTCSKiaqkLNIKKDNVLSVAAGYKGKtycsdcnslqlsnfvdsldnldllrIIVSPL 302
                                       ***.5568****************9977777778888889999999******************************* PP

                                       GGGTHHHHTT--EE-TT---EEEEEESESSS----EEE-TT-EEEEEE-SS--EEEEETTTEEEEE-TT-EEEEEEE CS
                        NAD_kinase 207 GstayslsaGgplisPgvlailivpicPhslssrpiVvssssklrirvasrseallaldGseelelspgdevrvtas 283
                                       G  +y++++G+ +i+  +l         ++  + +++v s++k++     r + ll++  +++  l+++++ r +++
  gi|385805912|ref|YP_005842310.1| 303 GNSGYLFGRGNHQITGYILS--------KITIKNLLIVGSRNKMS-----RLKSLLIDIPKSNKLLTLSGYTRAIVG 366
                                       ********************........***************99.....99************************* PP

                                       SSEEEEEE. CS
                        NAD_kinase 284 dkkfklirl 292
                                       +++  +i++
  gi|385805912|ref|YP_005842310.1| 367 YEEEVVIKV 375
                                       **9999986 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   1.4e-08   8.4e-05      42      92 ..      96     142 ..      76     156 .. 0.90
   2 ?    1.2   0.0     0.044   2.6e+02      24      60 ..     205     241 ..     195     271 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.4e-08
                                       THHHHHHHHHHHCC-SEEEEEESHHHHHHHHHHHCTHHCTTSEEEEEE-SS CS
                          DAGK_cat  42 gdakelakeakeegvdlivvaGGDGtvsevlnglleelatkpplgiiPlGt 92 
                                        d k++a e+k+eg+++ ++ GGDGtv  v  ++       +p+  iP Gt
  gi|385805912|ref|YP_005842310.1|  96 LDTKNCAMEIKKEGAEVFFISGGDGTVYDVYTQVKT----SIPIVGIPSGT 142
                                       56899****************************999....999999****9 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.044
                                       HHHHHCTCEEEEEE--STTHHHHHHHHHHHCC-SEEE CS
                          DAGK_cat  24 elleeagvelelieteepgdakelakeakeegvdliv 60 
                                       +ll+++  +l+  e e+ ++  e+++e+ +++v li+
  gi|385805912|ref|YP_005842310.1| 205 NLLHQQTKDLSYSEEESLEEIAEYVNEIVNDKVPLII 241
                                       5666666677777777777777777777777776665 PP

>> PrpR_N  Propionate catabolism activator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       1.1   6.7e+03     120     143 ..      62      86 ..      56      89 .. 0.74
   2 ?   -0.5   0.0      0.13   7.8e+02      21      54 ..     102     139 ..      94     158 .. 0.56
   3 !   13.1   0.0     9e-06     0.054      82     139 ..     196     257 ..     192     266 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.1
                            PrpR_N 120 vevvvG.dgvvadlAekaGlksvll 143
                                       ve +v  +++ +d+ +++Gl +  +
  gi|385805912|ref|YP_005842310.1|  62 VEFLVPdGMMGEDIFKRFGLSYTSV 86 
                                       5666664678899999999998776 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.13
                            PrpR_N  21 akeleaegvdvi.iSrG.gtae..llrkhvsvPVveik 54 
                                       a e+++eg++v+ iS+G gt+   + + ++s+P+v i+
  gi|385805912|ref|YP_005842310.1| 102 AMEIKKEGAEVFfISGGdGTVYdvYTQVKTSIPIVGIP 139
                                       44555555555325544212211133344567777665 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 9e-06
                            PrpR_N  82 iikglktlselldldieiytinseee...aeaavkelkaegvevvvG.dgvvadlAekaGlk 139
                                       i + +++ ++ll+ + +  ++++ee+   + + v+e+ +++v +++G + +++++A+k+++k
  gi|385805912|ref|YP_005842310.1| 196 IAYTIESKNNLLHQQTKDLSYSEEESleeIAEYVNEIVNDKVPLIIGpGRTCSKIAQKLNIK 257
                                       56666666677766666666666654333888999999999999999777888999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       772  (0.0430587); expected 358.6 (0.02)
Passed bias filter:                      629  (0.0350828); 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: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.50
# Mc/sec: 2266.83
//
Query:       gi|385805913|ref|YP_005842311.1|  [L=417]
Description: hypothetical protein FFONT_0871 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-49  168.1  35.1    5.2e-49  167.6  35.1    1.1  1  DUF401    Protein of unknown function (DUF401)
  ------ inclusion threshold ------
      0.052   13.9   1.1      0.052   13.9   1.1    2.4  2  Erg28     Erg28 like protein


Domain annotation for each model (and alignments):
>> DUF401  Protein of unknown function (DUF401)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.6  35.1   5.8e-53   5.2e-49       9     386 ..      26     413 ..      18     415 .. 0.80

  Alignments for each domain:
  == domain 1  score: 167.6 bits;  conditional E-value: 5.8e-53
                            DUF401   9 fsvivvlilikklsisllifvivailalkv..lileillvtlksladsftieivvvvllalllGyseksfGdlekvs 83 
                                         +ivvl +++k++i++  + + + ++l+   + lei +v+l ++ ++  i +  ++l ++l  +     G  ek+ 
  gi|385805913|ref|YP_005842311.1|  26 SIIIVVLLVLRKVNIAISLGSGLLFFSLLAirNPLEIGIVILYTMNKTTLITLSSLILAMFLADIYRVT-GIAEKMV 101
                                       357899******************9999987899*********88777777777776666666665555.******* PP

                            DUF401  84 eelreifskyvdllvPlliGllPmPGGalisavilknllkeerisseklalknywfrhvivtfwPlyPavvlvael. 159
                                       ++l+    k++  + P++iGllPmPGGa isav+ ++  ke  +s+e  +  nywfrh++   wPly  v+l+++l 
  gi|385805913|ref|YP_005842311.1| 102 NGLKFFGKKFTGIFTPAIIGLLPMPGGAYISAVLAESIYKELNLSPEEKSFINYWFRHIWIPTWPLYQNVILASALl 178
                                       ***987778999**************************************************************972 PP

                            DUF401 160 ..vnvdyfkva..la...lfPvfvialtlGltltr.kqerrlrksrsl....fdslinlyPliillilsvll.lldk 223
                                         +  d fk+   l+   l+   vi l+lG ++++ +  +  + ++++    + +++ ++Pli ++ils+++  l  
  gi|385805913|ref|YP_005842311.1| 179 kmSTTDIFKMNweLTvsgLLGGAVILLLLGSYYKKsEIDKDNKDNKNIekarLKNILHIWPLICIVILSLVFgILLP 255
                                       2245567776522331113444678889995554413333333333321111588999*******999977625667 PP

                            DUF401 224 llalvvlllavsiyavakledllkilkrvvdkkvilllfavyvykvvvensGvaesl.aedvrlnlsapillilltl 299
                                       ++ l+ ++l +++y   k ++l + lk  ++  +i+l+   +++  ++   Gv+  l a + ++ +   +++  +++
  gi|385805913|ref|YP_005842311.1| 256 VSILISIFLYIAVYHPTK-KHLYDALKYSFNLTIIVLVVETLIFGNMITFGGVTKELtAIFSSYAF---LAVTTIPF 328
                                       899999999999999887.57999********************************9677777765...56677899 PP

                            DUF401 300 lvGiatGieqaavsialPlltevtssgivvakylvlviaaaviGvilsPvhlcvvlsakyfevevfdilkklllil. 375
                                       ++G+atG e ++v++a+P l++++      + ++ + ++ +++Gv+lsP h c++l+ +y++ e+ ++++ l+  + 
  gi|385805913|ref|YP_005842311.1| 329 IIGFATGTELTYVALAFPPLINIFNQ---SSLFIPVAFLSGYMGVMLSPSHSCLILTVQYYKAELPKVYRYLIPSVi 402
                                       **********************9987...45667778899******************************9875430 PP

                            DUF401 376 vltlilvalvl 386
                                       v+ ++ v l++
  gi|385805913|ref|YP_005842311.1| 403 VVFAVAVLLIY 413
                                       34444455555 PP

>> Erg28  Erg28 like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.24   2.2e+03      49      76 ..     163     190 ..     129     197 .. 0.78
   2 ?   13.9   1.1   5.8e-06     0.052      53      98 ..     258     303 ..     245     315 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.24
                             Erg28  49 gtwtllsaivrlyaaynienkalyqlal 76 
                                        tw l++ ++   a ++++   ++++ +
  gi|385805913|ref|YP_005842311.1| 163 PTWPLYQNVILASALLKMSTTDIFKMNW 190
                                       5899999999999999999999988865 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 5.8e-06
                             Erg28  53 llsaivrlyaaynienkalyqlalltyvialvhflsEllvfktakl 98 
                                       +l +i   +a y+ ++k+ly+    ++ ++++  ++E+l+f+ +  
  gi|385805913|ref|YP_005842311.1| 258 ILISIFLYIAVYHPTKKHLYDALKYSFNLTIIVLVVETLIFGNMIT 303
                                       45677788899******************************99754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1258  (0.0701657); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 2641.78
//
Query:       gi|385805914|ref|YP_005842312.1|  [L=271]
Description: radical SAM protein [Fervidicoccus fontis Kam940]
Scores for complete 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-09   37.1   0.0    1.2e-08   35.5   0.0    1.7  2  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
      0.016   15.0   6.1        2.3    7.9   0.0    2.3  2  DUF1848      Domain of unknown function (DUF1848)
       0.12   12.5   0.5       0.34   11.1   0.2    1.9  2  Fer4_14      4Fe-4S single cluster domain
       0.13   11.7   0.0       0.19   11.2   0.0    1.2  1  DUF5131      Protein of unknown function (DUF5131)


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 !   35.5   0.0   2.8e-12   1.2e-08       2     165 ..      30     199 ..      29     201 .. 0.78
   2 ?   -1.1   0.0      0.47   2.1e+03     121     142 ..     224     245 ..     202     250 .. 0.70

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 2.8e-12
                                       EEESEESS--TTTSCCTT.....HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpet.....vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakl 73 
                                       +++ gC+++C++C+ +        ++++   +l + +++e +k+  +++ +k+++ +g   ++y +++ +++  ++ 
  gi|385805914|ref|YP_005842312.1|  30 NPYLGCSHGCIYCYARLYtkderASKNWGKVVLVKTNLVEVLKKE-VKRKKKGIVGVGTITDAYQPLEAIYKLTRRS 105
                                       5778************99*****8888888888888888888888.5553555555555555555555555555554 PP

                                       C....CCTEEEEEEECSSCHGHHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSET CS
                                       x....xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  74 a....vpgiritvetngtlpdeeklerllelg.vdrvslgleaaddekvlklmn.rghtfeevlealeklreagikr 144
                                            ++g+ +++ t  +l+  +  e ll+++    v +++ ++ +  v k ++   + +  + +a+++l + gik 
  gi|385805914|ref|YP_005842312.1| 106 VkillESGFYLSFQTKNPLI-LRDKEILLNYReKVDVGFTITSLKSS-VSKFIEpNAPFPISRANAIRALSKEGIKT 180
                                       4999****************.88888888888778888888999998.******8888889999************5 PP

                                       EEEEEEEBTTTSHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 145 vvdrivglpGendeeleelle 165
                                        ++  +++p  nd+  +e+++
  gi|385805914|ref|YP_005842312.1| 181 WIFYGPIIPRINDD--RETAD 199
                                       44445888889988..56665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.47
                                       HTCTSHHHHHHHHHHHHHHTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 121 mnrghtfeevlealeklreagi 142
                                       +n+++ + e++++++k+r +++
  gi|385805914|ref|YP_005842312.1| 224 LNDTYPLNEIIRTFDKARVKNF 245
                                       4467777888888888887765 PP

>> DUF1848  Domain of unknown function (DUF1848)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   3.6   0.00059       2.7     253     265 .]      32      44 ..      29      44 .. 0.91
   2 ?    7.9   0.0    0.0005       2.3      46     122 ..     111     188 ..      84     261 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00059
                           DUF1848 253 yntClhgCvYCYA 265
                                       y  C+hgC+YCYA
  gi|385805914|ref|YP_005842312.1|  32 YLGCSHGCIYCYA 44 
                                       778*********9 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0005
                           DUF1848  46 edvdlivFwtknpkpllkkleelkergiklyfqfTltdyeke....lepnvpsleerietfkelseklgkerviwRy 118
                                       e+   + F tknp  l +k e l + + k+ + fT+t+ +++    +epn p   +r +++++ls++  k  +   y
  gi|385805914|ref|YP_005842312.1| 111 ESGFYLSFQTKNPLILRDK-EILLNYREKVDVGFTITSLKSSvskfIEPNAPFPISRANAIRALSKEGIKTWIF--Y 184
                                       5556788******966655.44555567777888888765432224999999999999*****99985444333..6 PP

                           DUF1848 119 DPil 122
                                        Pi+
  gi|385805914|ref|YP_005842312.1| 185 GPII 188
                                       6666 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 ?   11.1   0.2   7.5e-05      0.34       7      55 ..      34      86 ..      31     141 .. 0.65
   2 ?   -2.4   0.0       1.2   5.2e+03      66      86 ..     241     261 ..     236     267 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 7.5e-05
                           Fer4_14  7 gCnlsCkgCd.....nketwkselgkpq.teelleqilkdlkkseikiqglvltG 55
                                      gC++ C  C+     + e  ++++gk+  ++  l+++l  +k+ + k++g+v +G
  gi|385805914|ref|YP_005842312.1| 34 GCSHGCIYCYarlytKDERASKNWGKVVlVKTNLVEVL--KKEVKRKKKGIVGVG 86
                                      8*********9888755666778887642566677777..444444445555444 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.2
                           Fer4_14  66 ellklvkrlkeeypekkiwle 86 
                                        + ++++ lk++++e  i ++
  gi|385805914|ref|YP_005842312.1| 241 RVKNFLNFLKKRCEEEGIICK 261
                                       566677777888877777665 PP

>> DUF5131  Protein of unknown function (DUF5131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   4.1e-05      0.19       8      84 ..      26      92 ..      20     127 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.1e-05
                           DUF5131  8 datwnpvtGCtkvspgCdnCyaerlakrlkaakaekyglkltgkkaervrlseekleeplrwkkprrvfvnslsDlf 84
                                      d + np  GC   s gC  Cya+  +k  +a k+         k    ++   e l++ +++kk+  v v +++D +
  gi|385805914|ref|YP_005842312.1| 26 DYALNPYLGC---SHGCIYCYARLYTKDERASKNWG-------KVVLVKTNLVEVLKKEVKRKKKGIVGVGTITDAY 92
                                      6678******...68*******98776555554333.......3333344445566666666666666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1935.40
//
Query:       gi|385805915|ref|YP_005842313.1|  [L=407]
Description: hypothetical protein FFONT_0873 [Fervidicoccus fontis Kam940]
Scores for 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-106  353.6   0.1   1.7e-105  352.7   0.1    1.4  1  Nre_N     Archaeal Nre, N-terminal
    3.7e-34  116.9   0.1    7.1e-34  116.0   0.1    1.5  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 !  352.7   0.1  1.9e-109  1.7e-105       2     270 .]      17     283 ..      16     283 .. 1.00

  Alignments for each domain:
  == domain 1  score: 352.7 bits;  conditional E-value: 1.9e-109
                             Nre_N   2 cglkkcpileklravekakkkisskeleGsspPsvfVGrygYPkVsvgplvppvegdasvldspekwlglslediik 78 
                                       cgl +cpi+ + +a++k+k  +++ke++GsspPsvfVGr gYPkV++gp+ pp +gd+++++ pe+wl+l++edi++
  gi|385805915|ref|YP_005842313.1|  17 CGLAYCPIIARNTALTKLKGLTEKKEIYGSSPPSVFVGRIGYPKVRIGPSSPPLSGDTQIYELPESWLKLRIEDILD 93 
                                       ***************************************************************************** PP

                             Nre_N  79 lrlslvrgekkvkvkkakedklleeiqelalsekpvdvevelekkpkaklkfdevlaPvGpsaeleklkvaenpkvp 155
                                       +r+sl++g++ ++v++++ +k+++e++ +a+s kpv++e++l k+p + + fde+++P+Gps+++e++k+++np++p
  gi|385805915|ref|YP_005842313.1|  94 YRYSLITGYNYASVNQVN-EKFVNEVRDIAMSIKPVEIEMKLIKPPVPIVIFDEEQPPFGPSSPIERFKIVNNPSIP 169
                                       *****************8.********************************************************** PP

                             Nre_N 156 rkveklveDtdlkAeeavveLyrsgvdvykiqrlLSvGlLGekkkrrlVPTrWsITAvddivgkelkkeikdlpeid 232
                                       + ++ l++D ++kA++a+++Ly++++ v++i++++S+G++Ge++krrlVPTrWsITAvd+++++el+k++k ++ei+
  gi|385805915|ref|YP_005842313.1| 170 KIIDSLYYD-EIKAKDAIIYLYERNFPVSYISKVMSIGTFGEREKRRLVPTRWSITAVDSTISEELLKKVKGFQEIS 245
                                       *********.******************************************************************* PP

                             Nre_N 233 evevfsgeylgNrflviLaPgkwsfelvEawapgslwn 270
                                       e+ev++ ++++N f+ iL+P++wsfe++Eaw+pgs+wn
  gi|385805915|ref|YP_005842313.1| 246 EIEVYELKIHDNLFISILFPRSWSFEWMEAWWPGSTWN 283
                                       *************************************8 PP

>> Nre_C  Archaeal Nre, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.0   0.1     8e-38   7.1e-34       1     110 []     296     406 ..     296     406 .. 0.98

  Alignments for each domain:
  == domain 1  score: 116.0 bits;  conditional E-value: 8e-38
                             Nre_C   1 egyegrkeyseiaGaYyaarlavleaLekikrqakvivlreitpeYwaPvGvWqvReavrkalekkp.kefesleea 76 
                                       e y+grk+y++i+G+Yy+arla++e L ++krqa++++lrei+p++++P+GvW+vRe++r+++++ p +++ +++e+
  gi|385805915|ref|YP_005842313.1| 296 EYYRGRKNYPSIGGCYYSARLATAELLLNKKRQATAVLLREIYPGFNVPIGVWFVRESIREMYKRGPvMKTYDINEV 372
                                       6799************************************************************99889******** PP

                             Nre_C  77 leevseklklplkkllkkskllkelkkqktLddF 110
                                       ++++++++kl ++k++++sk+++ ++++k+++++
  gi|385805915|ref|YP_005842313.1| 373 VSFLNKETKLGSAKWIASSKIIQLIMTEKKITEY 406
                                       ******************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 2757.44
//
Query:       gi|385805916|ref|YP_005842314.1|  [L=362]
Description: exopeptidase, family M24B [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-49  168.0   0.0    2.7e-49  167.7   0.0    1.1  1  Peptidase_M24  Metallopeptidase family M24
    3.6e-18   66.5   0.0    1.2e-16   61.6   0.0    2.5  3  Creatinase_N   Creatinase/Prolidase N-terminal domain
  ------ inclusion threshold ------
      0.015   15.4   0.7       0.27   11.3   0.0    2.4  2  THUMP          THUMP domain
      0.098   12.7   0.0       0.15   12.1   0.0    1.2  1  Talin_middle   Talin, middle 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 !  167.7   0.0     6e-53   2.7e-49       2     209 .]     145     346 ..     144     346 .. 0.96

  Alignments for each domain:
  == domain 1  score: 167.7 bits;  conditional E-value: 6e-53
                                       HHHHHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBCSSSB--TTEEEE CS
                     Peptidase_M24   2 lirkaariasaaleavleaikpgvterelaaeieattlkrhgarglafppivasgenaavlhytpndrvlkegdlvl 78 
                                       +i+ka++i s+++e + e i pg++e+e+   + ++  ++ ga  + f   ++sgen+a++h++ ++r++++gdl++
  gi|385805916|ref|YP_005842314.1| 145 NIEKASNILSKIFETAQESISPGISEAEVRFNLMKK-ASELGASSYDFI-AIQSGENTAIPHHEFSSRKIRRGDLIV 219
                                       689***************************999977.799999999996.89***********9999********** PP

                                       EEEEEEETTEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTBCCGBSSCSEE CS
                     Peptidase_M24  79 idagaeydgyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesaglakffphglGH 155
                                       ida + y+ y +D tr++++Gk+++e   +y +v++aq+ +i+     vt++ id+++r++++++++ +ff h++GH
  gi|385805916|ref|YP_005842314.1| 220 IDAVVSYNWYNADLTRVFSLGKPNEEVLSIYSFVRQAQKIGIESSISNVTAKSIDEKVRNYFKEREIDQFFIHRTGH 296
                                       *******************************************999******************************* PP

                                       EESSSSSEEEEEESSSTTCSSB--TTBEEEEEEEEEEETTTEEEEEBEEEEEES CS
                     Peptidase_M24 156 gvGlevhdegpsvsresndgrkleeGmvftiEpgiyfapgeggvriedtvlvte 209
                                       g+G++ h++ p++s  s +++++e+G+vftiEpg+y  pg++g+r+e +v+++e
  gi|385805916|ref|YP_005842314.1| 297 GLGIDAHEK-PFIS--STSNDVIENGQVFTIEPGLY-FPGKFGIRLEVDVVIKE 346
                                       *******99.***9..5779****************.58999*********986 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 !   61.6   0.0   2.6e-20   1.2e-16      12     132 .]      15     137 ..       7     137 .. 0.85
   2 ?    1.5   0.0       0.1   4.5e+02      80     114 ..     248     277 ..     218     289 .. 0.73
   3 ?    0.4   0.0      0.21   9.3e+02       3      21 ..     275     293 ..     274     296 .. 0.91

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 2.6e-20
                                       TT-SEEEEECCHHHHHHHSS...-SSSEEEEEEESSCEEEEEECTTHHHHHHHH.TTSEEEEEST...HSSHHHHHH CS
                      Creatinase_N  12 kgldallvtspenlrYltGfatetgsrglalvvtadgalllvdalryteaaeesatveevveydd...pvealadll 85 
                                        gld+++vts +n++YltG + et++r+l+l+ ++d ++ll ++l++++       v e + ydd   p    ++++
  gi|385805916|ref|YP_005842314.1|  15 YGLDSIVVTSGSNFFYLTGLKIETFERPLLLFMSEDYSFLLAPKLEMERLGDLN--VTESLFYDDatdP----FKII 85 
                                       69*****************************9999999************9999..7777778885552....4444 PP

                                       HHH......HHHT-EEEE-TTSSBHHHHHHHHHHCTTSEEEETHHHHHHHHSC CS
                      Creatinase_N  86 kel......lesekrvgveldaltvafyealkealpdaelvdaselieelRvv 132
                                       +++      l ++ ++gv+++ l ++f+ +l + ++d+++vdase i+  R++
  gi|385805916|ref|YP_005842314.1|  86 ESTptlkniLRKGVKIGVDPN-LRFSFFYKLNNIFKDVNFVDASEEIQLARMI 137
                                       44433333266669******9.8*****************************8 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.1
                                       HHHHHHHHHHHHT-EEEE-TTSSBHHHHHHHHHHC CS
                      Creatinase_N  80 aladllkellesekrvgveldaltvafyealkeal 114
                                       +++++++++    +++g+e++ +++ ++++++e++
  gi|385805916|ref|YP_005842314.1| 248 SIYSFVRQA----QKIGIESS-ISNVTAKSIDEKV 277
                                       556666666....99****98.6888888888887 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.21
                                       HHHHHHHHHTT-SEEEEEC CS
                      Creatinase_N   3 erlralmeekgldallvts 21 
                                       e++r+  +e+++d +++++
  gi|385805916|ref|YP_005842314.1| 275 EKVRNYFKEREIDQFFIHR 293
                                       799*************986 PP

>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.2     0.043   1.9e+02      15      69 ..     128     180 ..      92     193 .. 0.64
   2 ?   11.3   0.0   6.1e-05      0.27      35      89 ..     241     292 ..     231     316 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.043
                                       SEEEEETTEEEEECTEEEEEETHHHHHHHHHTSTTECEEEEEEEEEESSHHHHHH CS
                             THUMP  15 erveagkgrivvelkgekpeedeellkealekargiqrvipvcevceadledile 69 
                                       +++++  + i  e+  +++e++ ++l +++e a   ++++p+ ++ e +++ +++
  gi|385805916|ref|YP_005842314.1| 128 SEEIQLARMIKEEEEIKNIEKASNILSKIFETAQ--ESISPGISEAEVRFNLMKK 180
                                       4444444444444444455555555555555555..7777776666666665555 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 6.1e-05
                                       ETHHHHHHHHHTSTTECEEEEEEEEEESSHHHHHHHHHHHHHHHHHHCT-EEEEE CS
                             THUMP  35 edeellkealekargiqrvipvcevceadledileaakeivkkkfeeeketFaVr 89 
                                       +++e++ ++++++r +q++ ++ ++ + + ++i e++++++k++ ++    F ++
  gi|385805916|ref|YP_005842314.1| 241 KPNEEVLSIYSFVRQAQKIGIESSISNVTAKSIDEKVRNYFKEREID---QFFIH 292
                                       368999**************************************999...67766 PP

>> Talin_middle  Talin, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.3e-05      0.15      95     160 ..     123     190 ..     119     192 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.3e-05
                      Talin_middle  95 nlkelsknvrllaaLdddesgdkLleAareLadAfsdLlkaaepes..kedrqnLleAAsrvGeasqq 160
                                       n  ++s++++l   ++++e+ +++ +A+  L++ f    ++  p    +e r nL++ As+ G +s +
  gi|385805916|ref|YP_005842314.1| 123 NFVDASEEIQLARMIKEEEEIKNIEKASNILSKIFETAQESISPGIseAEVRFNLMKKASELGASSYD 190
                                       88899**************************************98655889*************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); 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: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 2199.78
//
Query:       gi|385805917|ref|YP_005842315.1|  [L=938]
Description: DNA polymerase I [Fervidicoccus fontis Kam940]
Scores for complete 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-51  175.3   2.8    3.6e-51  174.3   2.8    1.4  1  DNA_pol_B       DNA polymerase family B
    2.3e-34  119.0   6.9    7.1e-34  117.4   6.9    1.8  1  DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
    8.1e-09   35.7   0.7    5.5e-08   33.0   0.7    2.4  1  RNase_H_2       RNase_H superfamily
    8.7e-06   25.6   0.5    2.3e-05   24.2   0.0    1.9  2  DNA_pol_B_exo2  Predicted 3'-5' exonuclease related to the ex
  ------ inclusion threshold ------
       0.11   12.9   0.0       0.41   11.1   0.0    2.0  1  FDX-ACB         Ferredoxin-fold anticodon binding domain
       0.39   11.2   3.7       0.18   12.2   0.3    2.2  2  LIAS_N          N-terminal domain of lipoyl synthase of Radic
        1.6    9.0   4.9          1    9.6   1.1    2.6  2  XhlA            Haemolysin XhlA


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 !  174.3   2.8   1.4e-54   3.6e-51      14     429 ..     519     897 ..     510     924 .. 0.83

  Alignments for each domain:
  == domain 1  score: 174.3 bits;  conditional E-value: 1.4e-54
                                       HHHHHHHHHHHHTTBE-B-----.--SS...........-S----BE----EEESS-EEEEEETTHHHHHHHHTT-S CS
                         DNA_pol_B  14 rveslLlrlakeegfilpdrtekkgkeee..........gYqGatVlePkkglydkpvlvlDFaSLYPsiiqahNlc 80 
                                        ++ + + +++++++i+p++++  ++++e          +Y+Ga Vl+P  g++  +v+vlDFaSLYPsii   Nl+
  gi|385805917|ref|YP_005842315.1| 519 WIKNMFYWEHRKRNYIIPKQEDILAHKKEikskavikgkKYAGAIVLNPPVGVFF-NVVVLDFASLYPSIIKVWNLS 594
                                       577888999*********8444434444466677777757*************97.5889***************** PP

                                       TTTCE-HCCHCCT--BTT...TEEE-TCC-EEE-TTS---HHHHHHHHHHHHHHH.HHHHHH.CS--HHHHHHHHHH CS
                         DNA_pol_B  81 yttlvaseeeakeleaedeyleveveprlvefvkksvregllpklLkdllakRka.ikkelk.eekdefekalldkq 155
                                       y+t+  +   +ke +       +   +++v f    +r+g+ p+++  + + R + +kk+ k ++ +e++k+ +++ 
  gi|385805917|ref|YP_005842315.1| 595 YETVNPHYPCNKERT-------IPDVGHKVCF----DRRGMTPIMIGAMRDLRVKvYKKKSKdKSISEERKEWYNAV 660
                                       ***998877766433.......3333444444....789**************7725777776777888******** PP

                                       HHHHHHHHHHHHHHHTSTTSTT--HHHHHHHHHHHHHHHHHHHHHHHHT...SSGGGT-SS.....T-EEEEEBSSE CS
                         DNA_pol_B 156 QlalKvtaNsvYGftGvansrlpclalAasvTtiGRemLektkelvekkaellskllalpeeaeeeklkviYGDTDS 232
                                       Q alKv+ N+ YG+ G  n +l++ ++A+svT+ GR+++++t e  ++                  +l++ YGDTDS
  gi|385805917|ref|YP_005842315.1| 661 QSALKVLLNASYGVFGSDNFALYAPPVAESVTAVGRYTITNTVEKAKSL-----------------GLRILYGDTDS 720
                                       ****************************************998887766.................9********** PP

                                       EEEE-S-SSHHHHHHHHHHHHHHHHT.TSTTT--EEEEEEEEEEEEEE.TTEEEEEEEEESSTTSEEEEESSGGGST CS
                         DNA_pol_B 233 vfielkvkdveellkigkelaeevseklfkkplklefekvykkllLis.KKkYaglkvektskanklliKGvdlvRr 308
                                       +fi    k++       +e+ + v++  f   l le++k +  + +   KK Y g++       ++++iKG+   +r
  gi|385805917|ref|YP_005842315.1| 721 MFIWSPSKEA------LQEIIASVEK-EF--GLDLEVDKEFRYVAFSGlKKNYLGVTSL-----GEVIIKGLLGKKR 783
                                       ***8776543......3455566666.23..368999******999865999*****99.....99*********** PP

                                       TS-HHHHHHHHHHHHHHSSS....S-HHHHHHHHHHHHHHHHHHHHTT-S-GGGG-EEEEESS.CCCSSGCCSHHHH CS
                         DNA_pol_B 309 dncklvkevikkvlelllkdeteersleeglealksilkdvleeleenkvplekfvlskelskepenyksknlphle 385
                                       ++ ++ k+  ++v+++l +  ++ ++  e  +++k+ +k+++ +l++++ +l+++ ++ +l+k+  +yk+++  h++
  gi|385805917|ref|YP_005842315.1| 784 NQPEFLKQAFSDVIKRLSEI-NKPNDFLETQDKIKENVKKIYLKLKNMEYNLDELAFNVMLNKDVLEYKKNTPQHVK 859
                                       ****************9999.7788899999********************************************** PP

                                       HHHHHHHHCSS---TTCEEEEEEBETSS.....SS-GGGTEEEH CS
                         DNA_pol_B 386 vakrlkkrneeapevgdrisYvivekkkevkkknllaseraedp 429
                                       +a +lk  n +a   gd isYv v+ k+ v     ++ e+a+ +
  gi|385805917|ref|YP_005842315.1| 860 AALQLKPFN-KALARGDIISYVKVKGKDGV-----KTVELAKLS 897
                                       ***999885.88899***********9855.....444444333 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 !  117.4   6.9   2.8e-37   7.1e-34      10     332 ..     147     433 ..     138     435 .. 0.81

  Alignments for each domain:
  == domain 1  score: 117.4 bits;  conditional E-value: 2.8e-37
                                       EEEEE---EEEEEESSCGGHHHHHHHHHHHCCTTCCCEEEEEEEECCCCEECCTSSCCHHCEEEEEESSTCHHHHHH CS
                    DNA_pol_B_exo1  10 vnvfgfkpyfYceapdgkeleevkeelkelyeelskkvtkivkvelvlkkslygyekkpvpylkvsvsnpnelkkir 86 
                                       ++++++kpyf+++ +        +ee++++ ++  k  +k+ + ++vlk + +  ++++  y+k++v++p ++k++r
  gi|385805917|ref|YP_005842315.1| 147 YDKTDHKPYFLAKES--------PEEIDKILNGSLK--QKVISKDIVLKINPLTMKNEH--YTKITVTDPLAVKEMR 211
                                       567788888888777........6777777776654..357888999999999999997..**************** PP

                                       HHHHHCCCCCCCCSSS--HHHHHHHHCTS-TTCEEEEE...........TEEEEGCC--C-.SEEEEEETTTSCEET CS
                    DNA_pol_B_exo1  87 kelspleeivdvyeydvdylerflidnkivgfgwysvk...........kylvraegkisncdveidcdvddliakp 152
                                       +++       d +e++++y+ +f+ d+++ +++ y+v              + + e+  sn d e  + v+d+ +  
  gi|385805917|ref|YP_005842315.1| 212 DKF------RDSWESNIKYHHNFIFDRQLIPGAKYNVLgknlalafegnSIPKEIEQSFSNEDEETLKFVRDVYP-L 281
                                       **9......79***************************8888888886555556667777778787777777777.5 PP

                                       TTCC.S-EEEEEEEEEETEETTS.EETTTT..--EEEEEEEE.CCTC.SS.SEEEEEEECCCTSS----EE--SSTC CS
                    DNA_pol_B_exo1 153 kese.pplrvlsFDIeckskkgk.fpdaensedpiiqIscvl.dglgekepearklftlrecaseeeedfeltpkpe 226
                                       +e++ p+++++++DIe+ s +++  pd+++   pi++Is+   dg++        ++t      +    ++   k+e
  gi|385805917|ref|YP_005842315.1| 282 FEQSpPQPKMAAIDIEVFSPYQNrVPDVSQALYPIVAISISTtDGKK-------IVLTSAYPL-S----SKDPIKSE 346
                                       55667****************999******************55544.......222222222.2....22233566 PP

                                       STTEEEEEESSHHHHHHHHHHHHHHH--SEEEESSTTTTHHHHHHHHHHHCCTCCHCG.SCCSCTCEECCCCESEEE CS
                    DNA_pol_B_exo1 227 ypgvkvlefdsEkelLqaflefikqydPdvitgYNidnFDlpYilnRakelykvklsklgrlnkggrskvseigfsk 303
                                       +++ +v  fd+E+ l+q+f++++k+y   v++++N+dnFDlpYi nRa  l            +  ++ ++e++   
  gi|385805917|ref|YP_005842315.1| 347 TKDIEVHVFDDEYSLIQEFFSILKDY--PVVYTFNGDNFDLPYIRNRAIILGM----------REEEIPIEEFQ--- 408
                                       66779999******************..*********************2222..........45555555555... PP

                                       EEECEEEETTSEEEEHHHHHHHHSSSSG- CS
                    DNA_pol_B_exo1 304 qarekvkisgrihlDlyrvvkrklklpsY 332
                                          + ++ ++ ih+Dly+v+++k  l+ Y
  gi|385805917|ref|YP_005842315.1| 409 ---DFYTFKNAIHIDLYHVFNNKA-LKTY 433
                                       ...55****************997.6665 PP

>> RNase_H_2  RNase_H superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.7   2.1e-11   5.5e-08      42     116 ..     357     454 ..     343     490 .. 0.82

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 2.1e-11
                         RNase_H_2  42 eeekailelflellekkkalvtfngksFDvpflkrlf.......kkyklde.......eefrhiDLlkelrkkkl.. 102
                                       +e + i+e+f ++l++++ ++tfng +FD+p++++++       ++++++e       ++  hiDL++++++k l  
  gi|385805917|ref|YP_005842315.1| 357 DEYSLIQEFF-SILKDYPVVYTFNGDNFDLPYIRNRAiilgmreEEIPIEEfqdfytfKNAIHIDLYHVFNNKALkt 432
                                       4566677766.**************************777775444444449888887788*********8888877 PP

                         RNase_H_2 103 ........esysLksveke.lgi 116
                                               e+  L s++++ +gi
  gi|385805917|ref|YP_005842315.1| 433 yafggeyrEN-TLNSIAEAiIGI 454
                                       8889988888.899998875555 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 !   24.2   0.0   8.9e-09   2.3e-05      34     111 ..     355     424 ..     310     462 .. 0.68
   2 ?   -2.4   0.1       1.3   3.2e+03     169     207 ..     823     859 ..     822     863 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 8.9e-09
                    DNA_pol_B_exo2  34 essekelikkffegvekkkpqlVsfngrgfDlpvleyralkhgvsapkyfdegdedrekkwnnylsrystrhlDLmd 110
                                        ++e +li++ff++++ + p + +fng +fDlp +  ra++ g++ ++   e+       ++++ +  +  h+DL+ 
  gi|385805917|ref|YP_005842315.1| 355 FDDEYSLIQEFFSILKDY-PVVYTFNGDNFDLPYIRNRAIILGMREEEIPIEE-------FQDFYTFKNAIHIDLYH 423
                                       35699********99877.8999********************9887653322.......33333333333555555 PP

                    DNA_pol_B_exo2 111 l 111
                                       +
  gi|385805917|ref|YP_005842315.1| 424 V 424
                                       4 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.3
                    DNA_pol_B_exo2 169 vylrlellrgklseeeyaeeiaqvrellekekeekehlk 207
                                       +yl+l+ ++ +l+e +++ ++   +++le +k++ +h+k
  gi|385805917|ref|YP_005842315.1| 823 IYLKLKNMEYNLDELAFNVML--NKDVLEYKKNTPQHVK 859
                                       799******999999996555..5678877777666665 PP

>> FDX-ACB  Ferredoxin-fold anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00016      0.41      34      93 ..     687     746 ..     681     747 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00016
                                       TEEEEEEEEEEESTTS-SSEEEEEEEEEE--SSS---HHHHHHHHHHHHHHHHTT.T-BE CS
                           FDX-ACB  34 llesvqlfDvYrgkklaegkkSlalrltlqskertLtdeevnaaiekvvealekklgael 93 
                                       + esv+ + +Y+  +  e+ kSl lr+ + +++     +  ++a +++++++ek++g  l
  gi|385805917|ref|YP_005842315.1| 687 VAESVTAVGRYTITNTVEKAKSLGLRILYGDTDSMFIWSPSKEALQEIIASVEKEFGLDL 746
                                       668999999***999999**************************************9865 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 ?   12.2   0.3   7.1e-05      0.18      32      71 ..       7      46 ..       2      50 .. 0.88
   2 ?   -2.2   0.3       2.2   5.6e+03      64      64 ..     828     828 ..     784     871 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.1e-05
                            LIAS_N 32 kkelleeGPdlqDFvsgdkedkseweeykgnlkrekgerl 71
                                      k+++ e+GP+l DF++  +++++++++++++l+ ++++ l
  gi|385805917|ref|YP_005842315.1|  7 KRDRKENGPTLFDFINSSNKKEKTANNFAEDLTYNQDKEL 46
                                      78999*************99999*******9998887765 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.2
                            LIAS_N  64 k 64 
                                       k
  gi|385805917|ref|YP_005842315.1| 828 K 828
                                       1 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.93   2.4e+03      10      23 ..      43      56 ..      35      58 .. 0.86
   2 ?    9.6   1.1   0.00041         1       4      45 ..     798     838 ..     795     841 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.93
                              XhlA 10 etkldnleervdkl 23
                                      +++l+++e++v+kl
  gi|385805917|ref|YP_005842315.1| 43 DKELKDHEDEVQKL 56
                                      688999*9999997 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00041
                              XhlA   4 erlerietkldnleervdkleekaaeaeekiknleedlkkle 45 
                                       +rl +i++  d le++ dk++e+  + + k+kn+e +l++l 
  gi|385805917|ref|YP_005842315.1| 798 KRLSEINKPNDFLETQ-DKIKENVKKIYLKLKNMEYNLDELA 838
                                       7899999999999998.9*********************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (938 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       996  (0.0555525); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); 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: 0.79u 0.29s 00:00:01.08 Elapsed: 00:00:00.48
# Mc/sec: 5823.19
//
Query:       gi|385805918|ref|YP_005842316.1|  [L=546]
Description: Lysine-specific permease [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-29  103.5  58.9    1.1e-29  103.5  58.9    1.9  2  AA_permease_2   Amino acid permease
    9.1e-06   24.7  23.8    9.1e-06   24.7  23.8    2.5  2  Spore_permease  Spore germination protein
     0.0025   16.9  35.0     0.0029   16.7  23.7    2.3  2  Trp_Tyr_perm    Tryptophan/tyrosine permease family


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 !  103.5  58.9   1.9e-33   1.1e-29       1     420 [.      30     490 ..      30     495 .. 0.77
   2 ?    0.1   1.4     0.047   2.8e+02      25      56 ..     503     533 ..     493     537 .. 0.57

  Alignments for each domain:
  == domain 1  score: 103.5 bits;  conditional E-value: 1.9e-33
                     AA_permease_2   1 lsllsafalvigsvigsgifvkn..laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkk 75 
                                       l++++ ++l ig++igsgi+  +  +aa++gp+ ++++++a + + l+v+l+y  l  + p sgG++ y ++  g +
  gi|385805918|ref|YP_005842316.1|  30 LGFWDNVMLNIGTMIGSGILLLPfvVAAYAGPYEWISWLVAGIFI-LPVILIYSLLVELYPVSGGMSRYPYYSHGGL 105
                                       79**********************99999****888877766655.8*********999****************99 PP

                     AA_permease_2  76 vaflsawfn.wfayvpvlasilsvaasyllnalgp.dlqgntwltylia...iaililvalinirgikesakiqnil 147
                                       v fl++  + +++ ++ +++ + +++ yl  ++ p  l+++ ++t+l +   +++++lv +i ++g++ +++ ++++
  gi|385805918|ref|YP_005842316.1| 106 VSFLASVNAiFYFSMIIIPIEAQAIVRYLNLFW-PvLLEPSGYPTILGYiveVILTVLVSVIVYLGVRSVSTSNFVI 181
                                       999988776233444444444455555555555.4455555555544443338899999999*************** PP

                     AA_permease_2 148 gilkillpliiliilglitv.dgggfsslstetdtffpngwpgvllgllivlwsfdGfesaanvseevkk...kdvp 220
                                       + +k   +++++ ++ ++++ +++ f+   +    ++p g pg++++ ++++++++Gf   a ++ e+k+   k++ 
  gi|385805918|ref|YP_005842316.1| 182 TAIKSG-LILLFGLTMFLFFwSPKNFT---DPSIAVMPMGIPGIFAAAGASIFAYTGFRRTAIFAGEAKEeivKKLN 254
                                       *****5.66666655555552555555...345559999*****************************987888999 PP

                     AA_permease_2 221 kaifigllivlvlyllvniaflgvvpddei................anlsnlgsvaalffeavggk...vvaiivvi 278
                                          +++++ivlv+y+++++a++g++ ++++                a ++nl    ++f++++ g    ++ +++ +
  gi|385805918|ref|YP_005842316.1| 255 WSEIVAWAIVLVIYVFMSVAIVGAIDWEKLapiaakmginlypgnwAGIANL---SGPFAAMALGYgliWMYYLFLL 328
                                       999***************************8888877777776544334443...55555555432245******** PP

                     AA_permease_2 279 lialsllgaintavigssrvlealardgvlPrffakvn.kfgspiraiiltaivslillllfllassaaynfllsvs 354
                                        +++s +g  +    g +r+++a+a+ +++P+ f kv+ k+g+pi ++i ++i  +i l+++ l+ s +++++++ s
  gi|385805918|ref|YP_005842316.1| 329 DGIISPFGVSIVEQGGLPRLFYAAAKAKYMPKAFLKVDkKTGTPIWGLIASLIGEIIYLFVIRLY-SQSVDVVVASS 404
                                       **************************************9****************6666666566.7999******* PP

                     AA_permease_2 355 slgliisyllliigalilrkkrphl...kr...........pgkilvaiigalfllfllvalffp.pkgpa...tqs 413
                                       ++++    +++i  +   ++k+  +                ++ ++ ++ g++ l+++l +++++  kg a   +++
  gi|385805918|ref|YP_005842316.1| 405 NILYATGPAAVIGILARKKIKSTFYsilAPvamvssslifyWATYPYTLWGTIALFIFLPLFIYYvAKGEArgdIKN 481
                                       99999988888866666667766664442267778888876666777777766655555555544233332445*** PP

                     AA_permease_2 414 sliyt..ii 420
                                       +++y+  ii
  gi|385805918|ref|YP_005842316.1| 482 GIWYLtyII 490
                                       *99995333 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.047
                     AA_permease_2  25 aasggpalilwvwiavligslavllvy.aElss 56 
                                       ++  g++++ w +++++i+  a++++y a +s+
  gi|385805918|ref|YP_005842316.1| 503 FGGKGILSFPWDFVVIIIV--ALIFTYwAKISA 533
                                       4555666666666666665..555555566655 PP

>> Spore_permease  Spore germination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7  23.8   1.5e-09   9.1e-06       9     238 ..      37     283 ..      32     289 .. 0.78
   2 ?   -6.5   6.7         3   1.8e+04     140     170 ..     405     435 ..     363     508 .. 0.48

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.5e-09
                    Spore_permease   9 vlivsfqlGvgiltlprsvaeqatpdgWisvllagiiililvllmlkllkkfpek.tliellkkilgkwLGsllsil 84 
                                       +l + +++G+gil lp +va+ a+p  Wis l+agi+il ++l+++ l++ +p +  +  +     g ++++l s+ 
  gi|385805918|ref|YP_005842316.1|  37 MLNIGTMIGSGILLLPFVVAAYAGPYEWISWLVAGIFILPVILIYSLLVELYPVSgGMSRYPYYSHGGLVSFLASVN 113
                                       677899*****************************************999999651455666666777777777777 PP

                    Spore_permease  85 filyFlllaa....felRefse.....liqvflledtplwiiilllllvilYlvvkGieslar.eflfiivilliil 151
                                        i yF ++++      +  + +     l++ + ++++  +i+ ++l +++  +v+ G++s++  +f++ ++   +il
  gi|385805918|ref|YP_005842316.1| 114 AIFYFSMIIIpieaQAIVRYLNlfwpvLLEPSGYPTILGYIVEVILTVLVSVIVYLGVRSVSTsNFVITAIKSGLIL 190
                                       7777766543211134444444111113444456777778999999999999**********976666666666777 PP

                    Spore_permease 152 llillfslklaeiknlr.P...vlgngikpvlkslkttslsflgveillllvpflkdk..kkvkkaallgvlistll 222
                                       l+ l ++l +  +kn + P   v+  gi  ++ ++   +++++g+    ++    k++  kk  +  +++ +i+ ++
  gi|385805918|ref|YP_005842316.1| 191 LFGLTMFLFFWSPKNFTdPsiaVMPMGIPGIFAAAGASIFAYTGFRRTAIFAGEAKEEivKKLNWSEIVAWAIVLVI 267
                                       77777777777777764355559******************************99997669999************* PP

                    Spore_permease 223 yllttlivilvlsveq 238
                                       y+++ +  +++ + e+
  gi|385805918|ref|YP_005842316.1| 268 YVFMSVAIVGAIDWEK 283
                                       ***9999888877666 PP

  == domain 2  score: -6.5 bits;  conditional E-value: 3
                    Spore_permease 140 flfiivilliilllillfslklaeiknlrPv 170
                                       ++++++   +++ ++    +k+     l Pv
  gi|385805918|ref|YP_005842316.1| 405 NILYATGPAAVIGILARKKIKSTFYSILAPV 435
                                       2222222222222222222222223333333 PP

>> Trp_Tyr_perm  Tryptophan/tyrosine permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7  23.7   4.8e-07    0.0029       5     255 ..      32     291 ..      28     296 .. 0.76
   2 !    5.6   3.4    0.0012       6.9      80     186 ..     379     489 ..     367     508 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.8e-07
                      Trp_Tyr_perm   5 llggvlliagtviGaGmlalPvatagagfipsllllilswvlmlasgl...lllEvllaakeeasfttlakkllGkk 78 
                                       ++  v+l +gt+iG+G+l lP + a     +  +  +++ +++l  +l   ll+E++      + +   ++  l + 
  gi|385805918|ref|YP_005842316.1|  32 FWDNVMLNIGTMIGSGILLLPFVVAAYAGPYEWISWLVAGIFILPVILiysLLVELYPVSGGMSRYPYYSHGGLVSF 108
                                       78899****************98887554444444444444444444311156777777777777777777777777 PP

                      Trp_Tyr_perm  79 gniivalvllfllyiLlvA.yisggGsilselleeasgialsa.rlavliftlvlgalvvlstkavdrinrvllflk 153
                                          ++a+ + +++ i + A  i    ++   +l e sg++++   ++ +i+t++++++v l+ + v+  n v+  +k
  gi|385805918|ref|YP_005842316.1| 109 LASVNAIFYFSMIIIPIEAqAIVRYLNLFWPVLLEPSGYPTILgYIVEVILTVLVSVIVYLGVRSVSTSNFVITAIK 185
                                       788888888777777666635778888999999999997666515667889*******************9998765 PP

                      Trp_Tyr_perm 154 ...lvafvlllalllskvksdvLls..aksdtskvslvlsalPvlllsf.GFhgivpslvkyldknvkkvkkailiG 224
                                          ++ f l+++l++++   ++  +      ++ ++ ++ a+   + ++ GF+    +  +  ++ vkk++++ ++ 
  gi|385805918|ref|YP_005842316.1| 186 sglILLFGLTMFLFFWS--PKNFTDpsIAVMPMGIPGIFAAAGASIFAYtGFRRTAIFAGEAKEEIVKKLNWSEIVA 260
                                       32155556666665655..5555554466678999999999999888877*************************** PP

                      Trp_Tyr_perm 225 tliaLvlyllWelivlGnlpreelariiakg 255
                                        +i Lv+y++  ++++G+++ e+la+i ak 
  gi|385805918|ref|YP_005842316.1| 261 WAIVLVIYVFMSVAIVGAIDWEKLAPIAAKM 291
                                       ***************************9986 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0012
                      Trp_Tyr_perm  80 niivalvllfl..lyiLlvAyisggGsilselleeasgialsarlavliftlvlgalvvlstkavdrinrv..llfl 152
                                        +i  + +lf+  ly+  v  + ++++il+ + + a    l ++ +  +f  +l+++ ++s++++ +  +    l +
  gi|385805918|ref|YP_005842316.1| 379 SLIGEIIYLFVirLYSQSVDVVVASSNILYATGPAAVIGILARKKIKSTFYSILAPVAMVSSSLIFYWATYpyTLWG 455
                                       55666777777457*********************9988899999******************99887765213444 PP

                      Trp_Tyr_perm 153 klvafvlllalllskvksdvLlsaksdtskvslv 186
                                        +  f++l  ++   +k++   + k+  +++ ++
  gi|385805918|ref|YP_005842316.1| 456 TIALFIFLPLFIYYVAKGEARGDIKNGIWYLTYI 489
                                       4555555545555555555555566666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (546 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       847  (0.0472419); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.48
# Mc/sec: 3422.33
//
Query:       gi|385805919|ref|YP_005842317.1|  [L=222]
Description: peptidase, family C15 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-69  233.4   0.0    3.1e-69  233.2   0.0    1.0  1  Peptidase_C15  Pyroglutamyl peptidase


Domain annotation for each model (and alignments):
>> Peptidase_C15  Pyroglutamyl peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  233.2   0.0   1.7e-73   3.1e-69       2     201 ..       5     211 ..       4     212 .. 0.94

  Alignments for each domain:
  == domain 1  score: 233.2 bits;  conditional E-value: 1.7e-73
                                       EEEEEEE---TT-S--HHHHHHHHHTT-EET....TEEEEEEEE-SSTTHHHHHHHHHHHHH--SEEEEEEE-TT-- CS
                     Peptidase_C15   2 kvLvtGfdPfgkekinPaleavkeLdgaeia....eativkrevPtvfkksadvlkkaiaeikpdivlaiGqagGrs 74 
                                       k+LvtGf+Pfg+ k nP++ ++++L+ ++i+    + ++++ ++P+ +kk++d l   +++ kpdivl++G  +G s
  gi|385805919|ref|YP_005842317.1|   5 KILVTGFEPFGGYKQNPSQIIAEHLP-EKIEkempNVELQTAILPVAYKKAKDKLLTLLDSYKPDIVLSMGLWAGIS 80 
                                       9************************9.666511114678999*********************************** PP

                                       SEEEE-EEES-BE-SS--TTS---ESB-SSTTS-SEEE--S-HHHHHHHHHHTT--EEEES---SSHHHHHHHHHHH CS
                     Peptidase_C15  75 aitvervainldDaripDnegkqlidepispdgeaaYfstlPvkamvkalkeaGvPaavsntaGtfvCnhllYqvly 151
                                        +t+erva+n+ DaripDn+g+q+idepi ++g++aYfstlP+k +vk+lke G+Pa+vsntaGtf+Cn+++Y +l+
  gi|385805919|ref|YP_005842317.1|  81 YVTMERVAVNIMDARIPDNDGYQPIDEPIYTEGPNAYFSTLPIKSIVKRLKESGIPASVSNTAGTFLCNYVMYIALH 157
                                       ***************************************************************************** PP

                                       HHHHHS--SEEEEEEE-B-GGGTHHHHHT....-B--HHHHHHHHHHHHHHHHH CS
                     Peptidase_C15 152 lldkklpevraGfihiPylpeqvidkpet....pslsldkevagvkaaieaive 201
                                        +++k+++ r+G++h+P lpeq+++ +      ps+sl++ +++  +++++ ve
  gi|385805919|ref|YP_005842317.1| 158 SRATKGYPRRSGYMHVPLLPEQTASVKSEfgipPSMSLENMIRAAIITLKVTVE 211
                                       ***********************9877667999*********999888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); 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: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1461.22
//
Query:       gi|385805920|ref|YP_005842318.1|  [L=446]
Description: Pyridoxal phosphate-dependent aminotransferase [Fervidicoccus fontis Kam940]
Scores for complete 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-98  327.8   0.0      9e-98  327.6   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 !  327.6   0.0    5e-102     9e-98       6     406 .]      19     426 ..      13     426 .. 0.93

  Alignments for each domain:
  == domain 1  score: 327.6 bits;  conditional E-value: 5e-102
                                       B--SCEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHH CS
                       Aminotran_3   6 ednlllvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllkl 82 
                                       ++ ++l+++k eG++++dv+gk+y+D++ss a  n G ++ +vv  + e ++++ h   + l +e+++klae+l ++
  gi|385805920|ref|YP_005842318.1|  19 YKYFPLIVKKIEGSRIVDVNGKEYIDFLSSAALYNAGLNNDEVVTSLLEELKNMLHYT-QYLYHEKSIKLAEILKEI 94 
                                       444559***************************************************9.****************** PP

                                       CT-..S.EEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEE CS
                       Aminotran_3  83 apkgld.kvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevv 158
                                       +p+ ++ kv +  sG  Av  Al+ +           k+ + +f++++HG t++++sv+gs  +  ++  +  p v+
  gi|385805920|ref|YP_005842318.1|  95 TPGTFEkKVAFELSGGAAVDIALRSSLY------FSGKKLLGSFENSYHGTTYLSISVSGSFRPEIREKLNAYPYVY 165
                                       *****98899999***************......99*************************66666666666999** PP

                                       EE-TTBGGGTB-HHHHHH...HHHHHHHHHH..CHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEE CS
                       Aminotran_3 159 rlkypdeevlkeneeeea...alleeleale..kkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvlli 230
                                       ++kypd+++ +   e e+    ll e+e+    ++  +  aA+i+Epiqg+gGv v++++f+ +lr+++++++++li
  gi|385805920|ref|YP_005842318.1| 166 FFKYPDTFRRPRGIEPEEygeILLGEIERTLqvDAYGKGFAAIIFEPIQGDGGVLVPPKSFIVGLRKIADEYGIVLI 242
                                       ********99877655550005555666555788999**************************************** PP

                                       EE-TTTTTTTTSSSSGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTSB--TTTT-HHHHHHHHHHHHH CS
                       Aminotran_3 231 vDEvqtGfGrTGklfAlehagvspDlmtlaKaltgGlplsavlataevmqalapgshgsTfgGnplacavalavlei 307
                                        DE+qtGfGrTGk+fA+eh+g++pD+++l+K+l++G+p+sav++++e+ +  +p    sT++   l c +a+a +e 
  gi|385805920|ref|YP_005842318.1| 243 DDEIQTGFGRTGKMFAIEHFGIEPDIIVLGKSLGSGMPISAVIGRREILDSPEPMTYMSTYSPHYLSCIAAMAGIEY 319
                                       ***************************************************************************** PP

                                       HHHTTHHHHHHHHHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTC......HHHHHHHHHCTEE-EEET CS
                       Aminotran_3 308 ieeekllenaqelgaalkegLeelqkkyevikevRgkGlmiaielkeeaevke......keilkkakekGvlilsaG 378
                                       i ++ l ++a+ +g++l ++L+el++ +e +++vRgkGlmi++e++++++  +      ++i+ +a e+G++++++G
  gi|385805920|ref|YP_005842318.1| 320 IIKNRLHDRAELMGEYLMKRLNELKDGHEIVGDVRGKGLMIGVEIVDDKDSLKpsskkaQKIIWRAYENGLIMMTFG 396
                                       ***********************************************99976689999999**************** PP

                                       T..TEEEE---TT--HHHHHHHHHHHHHHH CS
                       Aminotran_3 379 d..nvirllppliitdeeidelleilkkal 406
                                       +  nv+r++ppl+i+ eeid+++ei++ka+
  gi|385805920|ref|YP_005842318.1| 397 KygNVLRIAPPLTIEREEIDKAVEIMEKAI 426
                                       ***************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); 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: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.52
# Mc/sec: 2585.78
//
Query:       gi|385805921|ref|YP_005842319.1|  [L=258]
Description: exopeptidase, family M15B [Fervidicoccus fontis Kam940]
Scores for complete 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   85.7   0.0    7.1e-24   84.7   0.0    1.5  1  Peptidase_M15  D-ala-D-ala dipeptidase
    3.9e-06   26.7   0.3    2.3e-05   24.2   0.3    1.9  1  VanY           D-alanyl-D-alanine carboxypeptidase


Domain annotation for each model (and alignments):
>> Peptidase_M15  D-ala-D-ala dipeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.7   0.0   7.9e-28   7.1e-24      44     191 ..      75     238 ..      63     245 .. 0.71

  Alignments for each domain:
  == domain 1  score: 84.7 bits;  conditional E-value: 7.9e-28
                     Peptidase_M15  44 valalaeaaavaaiagqqlvlwdayrpksaqdglllwavvPedklviekqvyqieavenin............vatd 108
                                       v l l++a + + ++ ++lv+ da+rp+ +q +  l++   e    i k+ + i+++e i+            +  +
  gi|385805921|ref|YP_005842319.1|  75 VLLRLLKASS-RLPSEYKLVILDAWRPITVQQS--LFDTLKE---RIMKENPLISEEEAIKetlkfvalpskdPNKP 145
                                       5566666655.55688***************33..3333322...2222222222222222223344444444999* PP

                     Peptidase_M15 109 sshsrgaaldltlrddegelvdmGsefDelseRslatak.qtv.........epaaqrnRklLraimesgGflsysg 175
                                       s+h +g a+dlt+ d++g  ++mG+++D+  e++  t+  + v         e +a +nR+lL +im  +Gf++y  
  gi|385805921|ref|YP_005842319.1| 146 SPHNTGGAIDLTIADENGLFLNMGTDYDDTTEKARTTYFeEKVrrgeklseeEEEALKNRRLLYNIMIDAGFTNYFD 222
                                       ******************************9998777641335333333322455668******************* PP

                     Peptidase_M15 176 EWWHfelpdaasawly 191
                                       EWWH++ +++ +awl 
  gi|385805921|ref|YP_005842319.1| 223 EWWHYDYGNQNWAWLS 238
                                       **************85 PP

>> VanY  D-alanyl-D-alanine carboxypeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.3   2.5e-09   2.3e-05      22      86 ..      88     196 ..      73     236 .. 0.68

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 2.5e-09
                                       TT--EEEEE----HHHHHHHH.HHHHH..........HHHHHHHHHHS--TTT.....-GGGGTSEEEEEEGGGTT. CS
                              VanY  22 egielalvsgfRsverQeelfekksvk..........eeklkeilrvsalpGa.....SeHhtGlaiDisdkeaeet 83 
                                        +++l ++ ++R ++ Q++lf++ + +          ee++ke+l+++alp +     S H+tG aiD++ ++++  
  gi|385805921|ref|YP_005842319.1|  88 SEYKLVILDAWRPITVQQSLFDTLKERimkenpliseEEAIKETLKFVALPSKdpnkpSPHNTGGAIDLTIADENGL 164
                                       467999***************555555999*******999*********9986566669**********99988764 PP

                                       --.............................S CS
                              VanY  84 kl.............................e 86 
                                        l                             e
  gi|385805921|ref|YP_005842319.1| 165 FLnmgtdyddttekarttyfeekvrrgeklsE 196
                                       44557777776666666666544444443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); 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: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1489.54
//
Query:       gi|385805922|ref|YP_005842320.1|  [L=178]
Description: Appr-1-p processing protein [Fervidicoccus fontis Kam940]
Scores for complete 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-38  129.0   0.2    1.1e-37  128.6   0.2    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 !  128.6   0.2   6.3e-42   1.1e-37       1     118 []      27     141 ..      27     141 .. 0.98

  Alignments for each domain:
  == domain 1  score: 128.6 bits;  conditional E-value: 6.3e-42
                                       EEEEETTSS-CSHHHHHHHHHHHHHHHHHHHHHHHHHHS--TTSEEEEE-TTSSSSEEEEEESE-TTTSTSTTHHHH CS
                             Macro   1 VnAaNsrllggggvagaihraagkalkeeckelekkqggcllGeavvtpaynlpakyvihtvgplftsskskeeeel 77 
                                       +nAaNs+l++gggva ai r++g  +++e++e+ kk g++++G ++vt+a++l++kyvih+vgp+f   ++++ +++
  gi|385805922|ref|YP_005842320.1|  27 ANAANSYLEHGGGVALAIVRKGGYIIQKESREFVKKFGPVPTGGVAVTNAGKLKCKYVIHAVGPRF---GEENGDKK 100
                                       5*****************************************************************...699***** PP

                                       HHHHHHHHHHHHHHTT-SEEEEE-TTSSTTSBTHHHHHHHH CS
                             Macro  78 lakayknalelaeekgiksvafPaistGifgvpweeaarva 118
                                       la+a+ +al++aee +i+s+afPaistGifg+p e+aa+++
  gi|385805922|ref|YP_005842320.1| 101 LASAVASALNKAEELKINSIAFPAISTGIFGYPYERAAEIM 141
                                       **************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); 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: 00:00:00.45
# Mc/sec: 1196.33
//
Query:       gi|385805923|ref|YP_005842321.1|  [L=140]
Description: YjgH/F family protein - putative translation initiation inhibitor [Fervidicoccus fontis Kam940]
Scores for complete 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-32  110.5   0.0    2.8e-31  108.1   0.0    1.8  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 !  108.1   0.0   1.5e-35   2.8e-31       2     120 ..      12     137 ..      11     138 .. 0.90

  Alignments for each domain:
  == domain 1  score: 108.1 bits;  conditional E-value: 1.5e-35
                                       TTSTTTSSS-BSEEE..........ETTEEEEEEE-SB-TTTSCB.-SSHHHHHHHHHHHHHHHHHHTT--GGGEEE CS
                     Ribonuc_L-PSP   2 eaapaaaapYsqavk..........agnlvyvsGqlpldpetgelvegdveeqtrqalenlkavLaaagaslsdvVk 68 
                                       ++ap++++pYsq++              ++++sG +p+dpetg+ veg veeq+r++l n+kav++aag  l+d+ k
  gi|385805923|ref|YP_005842321.1|  12 DKAPKPVGPYSQGIVarkilcsegkECSILFISGMIPVDPETGKPVEGGVEEQARRCLLNIKAVVEAAGGRLEDIAK 88 
                                       689*********887345555433334579*********************************************** PP

                                       EEEEESSGGGHHHHHHHHHHHSSSSTS--EEEEEE-SBSGGG-SEEEEEEEE CS
                     Ribonuc_L-PSP  69 vtvFladiedfaevnevyaeafdelkeaParsaveVaaLpkgakvEIeaiav 120
                                       vtvFl di++f  +n+vy e+f+++k  Pars+++++  p+g++vE+eaiav
  gi|385805923|ref|YP_005842321.1|  89 VTVFLSDISNFDSFNKVYSEFFKDHK--PARSVIGAKP-PRGYEVEVEAIAV 137
                                       *************************8..*******875.89**********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 997.17
//
Query:       gi|385805924|ref|YP_005842322.1|  [L=565]
Description: major facilitator superfamily protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-47  161.8  96.3      2e-38  132.2  60.0    3.2  2  MFS_1     Major Facilitator Superfamily
    1.7e-06   27.2  14.0    1.7e-06   27.2  14.0    3.6  4  Sugar_tr  Sugar (and other) transporter
  ------ inclusion threshold ------
      0.089   11.9   0.0       0.15   11.2   0.0    1.2  1  DUF1749   Protein of unknown function (DUF1749)


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 !  132.2  60.0   3.4e-42     2e-38       2     352 ..      20     435 ..      19     436 .. 0.87
   2 !   43.9  28.3   2.5e-15   1.5e-11       2     224 ..     289     546 ..     289     554 .. 0.75

  Alignments for each domain:
  == domain 1  score: 132.2 bits;  conditional E-value: 3.4e-42
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispse......igllltlyalgaavaslplGrlsdrfGrrrvlllglllf 72 
                                       +l++++s+++++il+++lp a+ + lgi+p +      + ++l +y++  a   + lGr+sd +Gr r + lg+++f
  gi|385805924|ref|YP_005842322.1|  20 SLGVIMSSMNMNILMISLP-AIFRGLGINPFApgefayLLWVLMGYSIILATILVTLGRISDMHGRERAYTLGFIIF 95 
                                       6899***************.9*9****99999888998999************************************ PP

                             MFS_1  73 alglllllfa....sslwl..llvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggl 143
                                       ++++++l+f+     ++ +  l++lr++q++g+g+l+ ++ ali+d fp +erg+a+gl +++f +G+ lg ++ggl
  gi|385805924|ref|YP_005842322.1|  96 SIASIALSFIpsnsGNFGAliLIILRMVQAIGGGLLMVNSTALITDAFPLTERGKALGLNQVMFIVGTFLGLIAGGL 172
                                       ***666668554533333246**************************************************999999 PP

                             MFS_1 144 lasslgWravfyilaivsllafvlfllllpeepperkrkspkeee................................ 188
                                       ++  + W+ vf++  ++++ + +   + ++  ++++++ ++  +                                 
  gi|385805924|ref|YP_005842322.1| 173 VV-GIDWHMVFILSVPFGVAGSL---WSVFKLRKTKGTGKTSLDIpgnvtlaggllaislgltyalmpygnsqmgwg 245
                                       99.889***************88...44433333333333333334579**************************** PP

                             MFS_1 189 .....................kgtgpaplvpawkallkdpvlw...illialllfffgfsglltllplylqevlgls 241
                                                            +++++apl++ +++++ +p+ +   +l++ +l  ++++++++++l  +    +g+s
  gi|385805924|ref|YP_005842322.1| 246 npwvitafiigvalfivfveiEKKAKAPLFQ-LSLFKIRPFTYgllALFFNALARGAVMFLITIWLQGIYLPLHGYS 321
                                       *******************************.********8863334444444445555555555555458889999 PP

                             MFS_1 242 ...glllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGfglg 315
                                          + + ag+++  ++l+++++a+++g l d++g+r++ +l+++++++++ g+ ll+   + +++ ++l++ G+g g
  gi|385805924|ref|YP_005842322.1| 322 weeTPFWAGIYMIPMMLGMVVMAPFSGILTDKYGARTFATLGMIIIAITFYGMTLLPYNFDRTWFEILLFINGLGNG 398
                                       99*6699998888888888888******************************************************* PP

                             MFS_1 316 fvfpsllalasdlappeeagtasglfntagslggalg 352
                                       +++++ ++++++ ++ + +++ +g  +t++++g++++
  gi|385805924|ref|YP_005842322.1| 399 LFSAPNTTAIMNALSSKDRAAGNGMRQTFNNIGSSIS 435
                                       **********************************997 PP

  == domain 2  score: 43.9 bits;  conditional E-value: 2.5e-15
                             MFS_1   2 llaaflsalarsilgpalplalaed....lgispseigllltlyal....gaavaslplGrlsdrfGrrrvlllgll 70 
                                       lla+f++alar++++++++++l+      +g+s  e  + +++y++    g++v++++ G l+d++G+r +  lg++
  gi|385805924|ref|YP_005842322.1| 289 LLALFFNALARGAVMFLITIWLQGIylplHGYSWEETPFWAGIYMIpmmlGMVVMAPFSGILTDKYGARTFATLGMI 365
                                       5899***************888777444334444444446666555333488************************* PP

                             MFS_1  71 lfalglllll.fa...sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailg.pllgg 142
                                       + a++++ ++ ++      w + +l ++ Glg g++ +   ++i    + ++r+ ++g+ ++++++G+ +  +++  
  gi|385805924|ref|YP_005842322.1| 366 IIAITFYGMTlLPynfDRTW-FEILLFINGLGNGLFSAPNTTAIMNALSSKDRAAGNGMRQTFNNIGSSISmAIFFT 441
                                       *****666664334444455.99***********99999999999999999*****************888688888 PP

                             MFS_1 143 llasslg.................Wrav.fyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvp... 198
                                       +l++ l+                  +++ f+   +vs l+f   +++l ++p +  ++s + +     p+++v+   
  gi|385805924|ref|YP_005842322.1| 442 ILLTFLSkylptqisttlssyglpQEVIkFISSIPVSGLLF---GAFLGVDPASAIPSSLISL----LPSNVVEiln 511
                                       99999999999999999988777544447777777777765...5999999999999999999....7777777543 PP

                             MFS_1 199 ...........awkallkdpvlwillialllfffgfs 224
                                                   +k  l++     + ial+l++++fs
  gi|385805924|ref|YP_005842322.1| 512 sraflptvlgpSFKTALTNSLY--ISIALVLIGAVFS 546
                                       4433334444455555555533..5555555555554 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.6      0.15   9.2e+02     251     289 ..      11      49 ..       4      73 .. 0.75
   2 !   27.2  14.0   2.8e-10   1.7e-06      56     190 ..      65     198 ..      53     203 .. 0.86
   3 ?   -1.4   0.5      0.14   8.3e+02     404     435 ..     233     263 ..     217     272 .. 0.45
   4 !    2.5   5.6    0.0088        52      48     150 ..     329     431 ..     289     468 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.15
                                       ...HHHHHHHHHHHHHHTTHHHHHHHTTTHHHHSS-THH CS
                          Sugar_tr 251 vrqrlligvvlqifqqltGinaimyysptifenlglsks 289
                                       +++ +li   l ++     +n++m+  p if+ lg+++ 
  gi|385805924|ref|YP_005842322.1|  11 YKWTVLINTSLGVIMSSMNMNILMISLPAIFRGLGINPF 49 
                                       788999999999999999999999999999999999876 PP

  == domain 2  score: 27.2 bits;  conditional E-value: 2.8e-10
                                       HHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTT...SS-TGGGGGHHHHHHHHHHHHHHHHHHHHT CS
                          Sugar_tr  56 lvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgk...nsvevlivgRvlvGigvGlasvlvPmyisE 129
                                       +++ +   +++g ++d+ GR  ++  + ++f+i+++   +++++   +   +li+ R++  ig Gl  v ++ +i  
  gi|385805924|ref|YP_005842322.1|  65 SIILATILVTLGRISDMHGRERAYTLGFIIFSIASIALSFIPSNsgnFGALILIILRMVQAIGGGLLMVNSTALITD 141
                                       55555556789****************99999999999999977866777778888********************* PP

                                       TS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGG CS
                          Sugar_tr 130 iApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilllf 190
                                         p + Rg+  +l+q++ ++G +++ i g  +  +     w++ + l++ + ++ +++ +f
  gi|385805924|ref|YP_005842322.1| 142 AFPLTERGKALGLNQVMFIVGTFLGLIAGGLVVGI----DWHMVFILSVPFGVAGSLWSVF 198
                                       *************************9998665433....4999999999999999999877 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.14
                                       HHHHHHHCHHHT-HHHHHHHHHHHHHHHHHHH CS
                          Sugar_tr 404 llfpiiteaigggyvflvfaglavlfiifvff 435
                                        l+p+  +++g ++  +v +++ + +++f++f
  gi|385805924|ref|YP_005842322.1| 233 ALMPYGNSQMG-WGNPWVITAFIIGVALFIVF 263
                                       33344444444.33333333333333333333 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.0088
                                       HHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHH CS
                          Sugar_tr  48 sglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvP 124
                                        g+ +  +++G ++ + f+g+l+d++G +     + ++  i    + + + ++    + +  ++ G+g Gl+s+  +
  gi|385805924|ref|YP_005842322.1| 329 AGIYMIPMMLGMVVMAPFSGILTDKYGARTFATLGMIIIAITFYGMTLLPYNFDRTWFEILLFINGLGNGLFSAPNT 405
                                       55556667777778888888888888888877777777777777777766554444444445777777777776655 PP

                                       HHHHTTS-SCCHHHHHHHHHHHHHHH CS
                          Sugar_tr 125 myisEiApkklRgalvslyqlaitfG 150
                                       + i      k R a  ++ q++  +G
  gi|385805924|ref|YP_005842322.1| 406 TAIMNALSSKDRAAGNGMRQTFNNIG 431
                                       55555555555555555555555555 PP

>> DUF1749  Protein of unknown function (DUF1749)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   2.4e-05      0.15      31      59 ..     387     415 ..     368     420 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.4e-05
                           DUF1749  31 kallFigGLgdGlltvpyvkelanaldea 59 
                                       + llFi GLg+Gl + p +  + nal   
  gi|385805924|ref|YP_005842322.1| 387 EILLFINGLGNGLFSAPNTTAIMNALSSK 415
                                       569***********************765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (565 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       705  (0.0393218); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); 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):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.38
# Mc/sec: 4436.22
//
Query:       gi|385805925|ref|YP_005842323.1|  [L=65]
Description: putative flavoredoxin [Fervidicoccus fontis Kam940]
Scores for complete 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-08   32.8   0.0    6.3e-08   32.8   0.0    1.1  1  Flavin_Reduct  Flavin reductase like domain
  ------ inclusion threshold ------
      0.094   12.5   0.0       0.15   11.9   0.0    1.3  1  N36            36-mer N-terminal peptide of the N protein (N3


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 !   32.8   0.0     7e-12   6.3e-08      23      63 ..       1      41 [.       1      64 [. 0.91

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 7e-12
                                      EEESSEEEEETTTTEEEEEEETTSHHHHHHHHHSEEEEEEE CS
                     Flavin_Reduct 23 atlssftslsldPplvafslrlpsstadalkeagefvinll 63
                                      + +s+ t++s +P l+++s+ ++++t++ lk+++ f+in+l
  gi|385805925|ref|YP_005842323.1|  1 MVASWWTQISVNPLLIGVSVSPERYTYKLLKKSSTFAINFL 41
                                      789************************************98 PP

>> N36  36-mer N-terminal peptide of the N protein (N36)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.6e-05      0.15      20      31 ..      11      22 ..       3      24 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.6e-05
                                      TSCCGCCSS--T CS
                               N36 20 AnPLLvGvsAKP 31
                                       nPLL+Gvs  P
  gi|385805925|ref|YP_005842323.1| 11 VNPLLIGVSVSP 22
                                      6********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      184  (0.0102627); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 439.25
//
Query:       gi|385805926|ref|YP_005842324.1|  [L=335]
Description: pyruvate dehydrogenase [Fervidicoccus fontis Kam940]
Scores for complete 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-90  301.1   0.0    7.4e-90  300.9   0.0    1.0  1  E1_dh           Dehydrogenase E1 component
    2.2e-06   27.6   0.3    1.9e-05   24.5   0.3    2.2  1  TPP_enzyme_C    Thiamine pyrophosphate enzyme, C-terminal TPP
  ------ inclusion threshold ------
      0.011   15.4   0.0      0.017   14.7   0.0    1.2  1  TPP_enzyme_N    Thiamine pyrophosphate enzyme, N-terminal TPP
      0.031   13.5   0.0       0.19   10.9   0.0    1.9  2  DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
      0.085   12.6   0.1       0.24   11.2   0.1    1.7  1  SpoVS           Stage V sporulation protein S (SpoVS)
       0.16   12.3   2.9       0.71   10.2   0.2    2.5  2  FAM25           FAM25 family


Domain annotation for each model (and alignments):
>> E1_dh  Dehydrogenase E1 component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  300.9   0.0   2.5e-93   7.4e-90       2     300 .]      17     315 ..      15     315 .. 0.96

  Alignments for each domain:
  == domain 1  score: 300.9 bits;  conditional E-value: 2.5e-93
                                       HHHHHHHHHHHHHHHHHTTSS-S-----TT-HHHHHHHHHTS-TTSEEEESS--HHHHHHTT--HHHHHHHHTT-T. CS
                             E1_dh   2 klvllrrvedaldalykrkkrigfyhlsagqealkvgiaaalekeDliiteYReagvllarglsleeilaeltgkv. 77 
                                       ++ l+r+ e+a++  y   k+ g  hl++g+ea++vg+ a l++eD+i +++R++g++la+g sl+++ ael gk+ 
  gi|385805926|ref|YP_005842324.1|  17 TMLLIRKNEEAVEKYYRIGKIPGSLHLYIGEEAVAVGVVANLNREDVITSTHRGHGHFLAKGGSLKKLWAELLGKRt 93 
                                       4566777888888888889999******************************************************* PP

                                       ...TTSSGTT-.-E..BTT..BEEE-SSTTTHHHHHHHHHHHHHHHTS---EEEEEEGGGTT-HHHHHHHHHHHHTT CS
                             E1_dh  78 ...kgkggsrhelmyaekesrilggngivgaqvplvaGialaakiegkkevailliGDgAanqGdvyealnlaalwk 151
                                          kgkggs+h + +++     lg ngivg   p++ G+al  k  + k+va+ ++G+gA+nq +++e+lnla++wk
  gi|385805926|ref|YP_005842324.1|  94 gacKGKGGSMHLFDFENC---NLGSNGIVGGGIPHAVGAALSFKLSESKNVAVSFFGEGATNQQNFHEGLNLASIWK 167
                                       ***********5554444...59****************************************************** PP

                                       --EEEEEEEESEETTEEHHHH-S---GGG..TTTTS-EEEEETTSHHHHHHHHHHHHHHHHTTT--EEEEEEE--SS CS
                             E1_dh 152 lpvifvveNNkygisTeaekasaskeladrargvgipglrVdgnDplavyeAvkfAaeraregkgpllielvtYRyg 228
                                       lpvifv+eNN+y is +++k++a + +a+r+  +gip ++Vdg+D++avye+vk A+erar+ +gp+lie++tYR++
  gi|385805926|ref|YP_005842324.1| 168 LPVIFVCENNQYQISLHYSKQQAIEGVAKRGISYGIPAVEVDGQDVVAVYEVVKRAVERARSREGPTLIEAKTYRFT 244
                                       ***************************************************************************** PP

                                       -SSTTSHSHSSSHHHHHHHHHHHH-HHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHHHHHHHHS----GG CS
                             E1_dh 229 gHsesDdpstyrtreeveevrkkkdpiqrlkelLvkkgvvseeelkeiekevrkeveeavkkaeskkelepe 300
                                       gH+ +D    yr r+eve ++k+kdp+++++++++++ +  +e+l++i + v+ke+ee++k ae+++++epe
  gi|385805926|ref|YP_005842324.1| 245 GHTIDD-NELYRNRDEVEWWKKNKDPLAIFERKIIEEKIFGKEVLEKIAEDVEKEIEETIKFAEESPYPEPE 315
                                       **9866.999**********************************************************9985 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 !   24.5   0.3   6.5e-09   1.9e-05      26     152 ..     115     237 ..     107     238 .. 0.68

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 6.5e-09
                                       TTS-TTTHHHHHHHHHH...H.STTSEEEEEEEHHHHHHT.GGG.HHHHHHTT-SEEEEEEE-SBCCCHHHHHHHHT CS
                      TPP_enzyme_C  26 glgtmGyglpaAiGakl...a.kpdrevvaivGDGgflmi.lqe.latavrrnlpitvvvlnNegygmtggqqepfg 96 
                                         g  G g+p A+Ga+l   + + ++  v++ G G++    ++e l  a   +lp+++v+ nN++       ++++ 
  gi|385805926|ref|YP_005842324.1| 115 SNGIVGGGIPHAVGAALsfkLsESKNVAVSFFGEGATNQQnFHEgLNLASIWKLPVIFVCENNQYQISLHYSKQQAI 191
                                       57899************776334567899*******765556551555555688******99999866666644333 PP

                                       CCTTTTSBB.BS----HHHHHHHTTSEEE.EESSH.HHHHHHHHHHHHCSSSEEEEE CS
                      TPP_enzyme_C  97 gkrksgpagkdlkpvdfaklaealGakga.rvekadveeleealkealekkgpalie 152
                                       ++     a   ++ +++   + a++++g  +v ++  e +++a+++a++++gp+lie
  gi|385805926|ref|YP_005842324.1| 192 EGV----A---KRGISYG--IPAVEVDGQdVVAVY--EVVKRAVERARSREGPTLIE 237
                                       322....1...2233332..223333333455578..88999999999********8 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 ?   14.7   0.0   5.7e-06     0.017      50     159 ..     125     238 ..     124     245 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.7e-06
                                       HHHHHHHHHHHHH.TS-EEEEE-CHH.HHHHCHHHHHHHHHHT--EEEEEEE--CCCHHS..TC--T...-CCHHHC CS
                      TPP_enzyme_N  50 gaafaAdgyarat.gkpgvvlvtsgp.GatnaltalaeAkvdriPllvlsgdrptslrgqgvlqqel...dqlalfr 121
                                       +a++aA  +  +  ++++v +   g  +  n   +l  A+  ++P+++++ +++++   ++  qq++      ++  
  gi|385805926|ref|YP_005842324.1| 125 HAVGAALSFKLSEsKNVAVSFFGEGAtNQQNFHEGLNLASIWKLPVIFVCENNQYQISLHYSKQQAIegvAKRGISY 201
                                       5899999999877688888888775559999****************************999998885554555544 PP

                                       CCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EEEEEE CS
                      TPP_enzyme_N 122 pvtkyaervtspeelpealrrAirtalsgrpgPvylel 159
                                        +    +  +++ ++ e+++rA++ a  +r gP+++e 
  gi|385805926|ref|YP_005842324.1| 202 GIPAVEVDGQDVVAVYEVVKRAVERA-RSREGPTLIEA 238
                                       5555588888999999**********.*******9985 PP

>> DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   6.3e-05      0.19     116     176 ..     122     182 ..     110     194 .. 0.92
   2 ?   -0.8   0.0      0.24   7.3e+02     245     271 ..     208     238 ..     187     240 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6.3e-05
                    DXP_synthase_N 116 sisaalGlavardlkgekkkvvaviGDgaltgGmafealnnigelkkkllvilNdNemsis 176
                                        i  a+G a + +l+++k+ +v+  G+ga      +e+ln ++  k  ++ +  +N+  is
  gi|385805926|ref|YP_005842324.1| 122 GIPHAVGAALSFKLSESKNVAVSFFGEGATNQQNFHEGLNLASIWKLPVIFVCENNQYQIS 182
                                       678899**************************************************99887 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.24
                    DXP_synthase_N 245 idGhdleelikvle....evkklkgpvllhv 271
                                       +dG+d+ ++ +v++    ++++ +gp+l+  
  gi|385805926|ref|YP_005842324.1| 208 VDGQDVVAVYEVVKraveRARSREGPTLIEA 238
                                       8999998887776511115566788888866 PP

>> SpoVS  Stage V sporulation protein S (SpoVS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1     8e-05      0.24      11      40 ..     124     153 ..     118     155 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 8e-05
                                       HHHHHHHHHHHHHHTSEEEEEE-SHHHHHH CS
                             SpoVS  11 pnkvagAiagvlrekgkvevqaiGagAvnq 40 
                                       p++v++A+  +l+e+++v+v+  G gA+nq
  gi|385805926|ref|YP_005842324.1| 124 PHAVGAALSFKLSESKNVAVSFFGEGATNQ 153
                                       99***************************9 PP

>> FAM25  FAM25 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.3      0.12   3.6e+02       2      17 ..     213     228 ..     212     232 .. 0.84
   2 ?   10.2   0.2   0.00024      0.71      10      34 ..     285     309 ..     276     326 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.12
                             FAM25   2 vhaveevvkevveHaK 17 
                                       v av evvk  ve a+
  gi|385805926|ref|YP_005842324.1| 213 VVAVYEVVKRAVERAR 228
                                       56899****9999886 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00024
                             FAM25  10 kevveHaKeaGEKAiadalKkAqes 34 
                                       kev+e + e  EK i +++K A+es
  gi|385805926|ref|YP_005842324.1| 285 KEVLEKIAEDVEKEIEETIKFAEES 309
                                       9***********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       842  (0.046963); 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:                         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 0.33s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 2017.39
//
Query:       gi|385805927|ref|YP_005842325.1|  [L=336]
Description: Pyruvate dehydrogenase, beta subunit (lipoamide), (pdhB-2) [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-50  171.3   0.0    2.3e-50  170.8   0.0    1.2  1  Transket_pyr     Transketolase, pyrimidine binding domain
    1.4e-39  134.7   0.0    3.3e-39  133.6   0.0    1.6  1  Transketolase_C  Transketolase, C-terminal domain
    6.1e-07   29.7   0.0    1.6e-06   28.3   0.0    1.7  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
  ------ inclusion threshold ------
      0.049   12.8   0.2       0.13   11.4   0.0    1.8  2  NanE             Putative N-acetylmannosamine-6-phosphate epi
       0.19   10.1   0.1        0.3    9.5   0.1    1.2  1  DUF4503          Domain of unknown function (DUF4503)


Domain annotation for each model (and alignments):
>> Transket_pyr  Transketolase, pyrimidine binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.8   0.0   6.3e-54   2.3e-50       3     176 ..      13     187 ..      11     189 .. 0.98

  Alignments for each domain:
  == domain 1  score: 170.8 bits;  conditional E-value: 6.3e-54
                                       EEHHHHHHHHHHHHHCTTTTEEEEESSTH..HHHTTCHCCHHEGGTTEGEEE--S-HHHHHHHHHHHHHHCTTEEEE CS
                      Transket_pyr   3 iawrkaeaealaellkedpevvligaDva..ggtfsvrkgllhdqgegrvidsgisEqavlgfavGaalagpllviv 77 
                                       i++r+a++eal+++++e+ +v+lig+D++  gg f+v+k l ++ ge+rv d + +E++++g+a+Gaa+ g ++++v
  gi|385805927|ref|YP_005842325.1|  13 ITFREAINEALDQEMQENAKVILIGEDIGryGGIFGVTKRLIDKYGEERVRDAPTAESGFIGAAIGAAMMG-YRPVV 88 
                                       899**************************99****************************************.8**** PP

                                       EEEEHHHHGGG..HHGGHHHHHCHHHHHT--EEEEESBSGGGSTTGTTTSBSSHHHHHHTSTTEEEE--SSHHHHHH CS
                      Transket_pyr  78 eaqFgdFangA..qiyadqairsgeakgklkvgvvtrlpigvgedGpehqsaeleaflrlipglkvvrPsdpaetkh 152
                                       e++F dF+ +A  qi++++a+++++++g++ v++v+r+  g+g++G +++s++l ++l +ipglkvv+Ps+p ++k+
  gi|385805927|ref|YP_005842325.1|  89 ELMFIDFIGVAfdQIINQAAKIRYMSGGGISVPIVIRTVSGAGFSGGAQHSQSLHSILLHIPGLKVVMPSNPFDAKG 165
                                       ***************************************************************************** PP

                                       HHHHHHHSSS.SEEEEEE-SSEEC CS
                      Transket_pyr 153 llrrairredrkPvvlrlpksllr 176
                                       ll   i+  d++Pvv++++k+l++
  gi|385805927|ref|YP_005842325.1| 166 LLISSIE--DDDPVVFIEHKGLYE 187
                                       *******..899**********97 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.6   0.0   9.2e-43   3.3e-39       1     124 []     202     324 ..     202     324 .. 0.98

  Alignments for each domain:
  == domain 1  score: 133.6 bits;  conditional E-value: 9.2e-43
                                       TEEEEEETTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHH CS
                   Transketolase_C   1 gkaeilregkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGig 77 
                                       g a+i++ gkdvt++a+  m++  l ++e+L++egis+eV+d+r+++plD+eti++svkktgrlvvv+e ++r++++
  gi|385805927|ref|YP_005842325.1| 202 GVADIKKAGKDVTVIATAVMLHKTLSVVEKLREEGISVEVIDPRSLRPLDTETIANSVKKTGRLVVVDESYPRCSFA 278
                                       56899************************************************************************ PP

                                       HHHHHHHHHCCCTTCSSEEEEEEE-SSSSSSGHHHHHHHTT-SHHHH CS
                   Transketolase_C  78 sevaaalaeeafdgldapvkrvggpdviepgsaeelekafgldaeki 124
                                       +++a+++a ++f++l+ap+k v+ pd+++p+s   le+a++++ eki
  gi|385805927|ref|YP_005842325.1| 279 TDIASFIASKYFEYLEAPIKIVTPPDTPVPYS-LPLERAWIPNEEKI 324
                                       ********************************.88*********998 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 !   28.3   0.0   4.5e-10   1.6e-06       2      79 ..     212     286 ..     211     298 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 4.5e-10
                                       SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHHT CS
                           PFOR_II   2 evvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaal 78 
                                       +v ++a++ +  ++ s+v++lReegi+v ++ +r+lrP  +e +++ +kk+ ++vv+d ++    +   ++++++ +
  gi|385805927|ref|YP_005842325.1| 212 DVTVIATAVMLHKTLSVVEKLREEGISVEVIDPRSLRPLDTETIANSVKKTGRLVVVDESY---PRCSFATDIASFI 285
                                       78899999999*************************************************9...3467777777766 PP

                                       G CS
                           PFOR_II  79 k 79 
                                        
  gi|385805927|ref|YP_005842325.1| 286 A 286
                                       5 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.38   1.4e+03     109     123 ..      75      84 ..      17     131 .. 0.62
   2 ?   11.4   0.0   3.7e-05      0.13      47     101 ..     219     272 ..     192     299 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.38
                                       HHTT-SEEE-TTTTS CS
                              NanE 109 kklGvdivGttlsGy 123
                                        +     +G+++ Gy
  gi|385805927|ref|YP_005842325.1|  75 AA-----IGAAMMGY 84 
                                       33.....33444444 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 3.7e-05
                                       ---BS-SHHHHHHHHTTT-SEEEEE--SS--T--HHHHHHHHHHH--EEEEE-SS CS
                              NanE  47 evritatlkdideLaaagadiialDatdrerpvtieelikkikekyqllmaDist 101
                                        v++  tl+ +++L ++g+ +  +D  +  rp++ e++++++k+++ l++ D s 
  gi|385805927|ref|YP_005842325.1| 219 AVMLHKTLSVVEKLREEGISVEVIDPRS-LRPLDTETIANSVKKTGRLVVVDESY 272
                                       3444556788***************865.79******************999875 PP

>> DUF4503  Domain of unknown function (DUF4503)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1   8.2e-05       0.3     213     283 ..     207     275 ..     199     280 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 8.2e-05
                           DUF4503 213 rekgrivcvertvlllq..kpllssasg.aeskelpePvkldeLdsatkvnsiCsvqGvvvgvdestafsWPvC 283
                                       ++ g+ v v  t ++l+   +++++  +   s e+ +P  l +Ld++t +ns+   +G +v vdes    +P C
  gi|385805927|ref|YP_005842325.1| 207 KKAGKDVTVIATAVMLHktLSVVEKLREeGISVEVIDPRSLRPLDTETIANSVKK-TGRLVVVDES----YPRC 275
                                       5566666666665555501444444444245778******************965.899999**95....4555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      589  (0.0328518); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 2266.90
//
Query:       gi|385805928|ref|YP_005842326.1|  [L=374]
Description: hypothetical protein FFONT_0886 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       728  (0.0406046); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2364.65
//
Query:       gi|385805929|ref|YP_005842327.1|  [L=398]
Description: aminotransferase [Fervidicoccus fontis Kam940]
Scores for complete 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-51  174.4   0.0    4.5e-51  174.1   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
     0.0032   16.0   0.0     0.0053   15.3   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
     0.0071   15.3   0.0     0.0096   14.8   0.0    1.2  1  Alliinase_C      Allinase
  ------ inclusion threshold ------
      0.034   14.3   0.3          1    9.5   0.1    2.4  2  SspH             Small acid-soluble spore protein H family
       0.18   11.1   0.0       0.27   10.5   0.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
       0.19   11.8   0.0       0.31   11.1   0.0    1.3  1  Octopine_DH      NAD/NADP octopine/nopaline dehydrogenase, al


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 !  174.1   0.0   1.5e-54   4.5e-51       5     359 ..      35     388 ..      31     391 .. 0.91

  Alignments for each domain:
  == domain 1  score: 174.1 bits;  conditional E-value: 1.5e-54
                                       ESSSSSTTSTTSSHHHHHHHHHHHH.HHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHH CS
                     Aminotran_1_2   5 nLgsneylgdsgkptlpevakaeke.galaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagal 80 
                                       n++++++ +     + ++++ka+ e  +  + +  +y+p++glpel++++ + l++s +++++++ ++vv+sG  ++
  gi|385805929|ref|YP_005842327.1|  35 NFTQGQPGFP----PDENIIKATFEhALKNSFDHYRYLPTQGLPELRTDISDELKESGGISIDPS-NIVVTSGGIEA 106
                                       7788888777....***********444444455689****************************.99999999888 PP

                                       HHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS CS
                     Aminotran_1_2  81 iealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesp 157
                                       + + + ++  +pgd+ +  dpty+ y +i++++ ++v +++ ++ edf+ d e l+e++++       t +ilv+sp
  gi|385805929|ref|YP_005842327.1| 107 LHLTFYAT-TDPGDRAFFLDPTYSVYWDIANMYNLKVDSCE-QNGEDFQPDPECLKEKINR------NTSLILVTSP 175
                                       88888888.69******************************.668****************......899******* PP

                                       -TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTT....EEEEEESSSTTSSGGG-E CS
                     Aminotran_1_2 158 hNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepn....llivgslsKafGlaGeRv 230
                                        NPt  +++++  + ++dla  + ++l+ DeaY    ++ +     +++++++      l+ + ++sK+++++G+R+
  gi|385805929|ref|YP_005842327.1| 176 DNPTSRILSEDIFKLIADLAVDNDVWLLYDEAYRNIIYEGK-----HVWIQKYSRtlekLVGLDTFSKDLAIPGLRL 247
                                       ***************************************76.....4555555444459****************** PP

                                       EEEEE.EHHHHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS..TEEEECC CS
                     Aminotran_1_2 231 Gyilg.naavvsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLael..glkvlas 302
                                       Gy+++ n+++++ + kl+  + +  +s++q+++  als   lk+ +l++   ++ +rr+  ++ ++e   + kv+++
  gi|385805929|ref|YP_005842327.1| 248 GYLYAeNKDLIKEVLKLKGIVSIssDSSAQWMAHIALSSGMLKI-YLSKVIPKYRSRRDAAYETIREFlpEAKVTKP 323
                                       ********************999877777777777777777665.********************999********* PP

                                       SCSSEEEEEETHH......CHHHHHHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHH CS
                     Aminotran_1_2 303 qsgmflltdlsae......takelskkLleevgvyvtpgtsftv..pgrlRitvAglteeeleel 359
                                        +gm+l+ dls++      ++++++ kL ee+gv v+pg++f++  +g++Rit+ ++ ee +++ 
  gi|385805929|ref|YP_005842327.1| 324 IAGMYLFPDLSPYlskkgmDDTSFAIKLSEEKGVGVLPGSIFGKagKGHVRITFVTMQEERIKKG 388
                                       *******************99*********************************99999998875 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.8e-06    0.0053      69     173 ..      96     205 ..      91     210 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.8e-06
                                       EEEEESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHH.TTCEEEEEST.TSHHHHHHHCCTTEEEEEE CS
                   Cys_Met_Meta_PP  69 aalavssGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkk.lgievkfvdt.sdleelekaikentklvyl 143
                                       + +++s G  A+++++ a    Gd+    d  Y+   ++ + +  k  + e +  d   d+e l+++i+ nt+l+++
  gi|385805929|ref|YP_005842327.1|  96 NIVVTSGGIEALHLTFYATTDPGDRAFFLDPTYSVYWDIANMYNLKvDSCEQNGEDFqPDPECLKEKINRNTSLILV 172
                                       56889999*****************999988887777766655444233444444433589**************** PP

                                       ESS-TTTT---..-H.HHHHHHHHHTT-EEEEE CS
                   Cys_Met_Meta_PP 144 Etptnpllkvv..Di.ekiaklakkagvlvvvD 173
                                        +p np+ +++  Di + ia+la +++v ++ D
  gi|385805929|ref|YP_005842327.1| 173 TSPDNPTSRILseDIfKLIADLAVDNDVWLLYD 205
                                       *******99964476244666776666666666 PP

>> Alliinase_C  Allinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   3.2e-06    0.0096     103     219 ..     125     263 ..      74     291 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.2e-06
                                       SS--THHHHHTTTT-BTTEEEEEESTT-........--S..S-EEEEEESS-TTT---.-----.......-TT-EE CS
                       Alliinase_C 103 vPyysvykeqtslldsklykweGdaaayv.......kkknpeefielvtsPnnPdgll.reavv.......kgseak 164
                                        P ysvy + +++++ k    e + ++++       +k n +  + lvtsP+nP +++  e +         ++++ 
  gi|385805929|ref|YP_005842327.1| 125 DPTYSVYWDIANMYNLKVDSCEQNGEDFQpdpeclkEKINRNTSLILVTSPDNPTSRIlSEDIFkliadlaVDNDVW 201
                                       699****************999999999988888765667778889********99761555544445544456667 PP

                                       EEEE-TT....-STTTS---S-B...--SEEEEEHHHHHS-GGG-EEEEEES-HHHHHHHHH CS
                       Alliinase_C 165 viyDlay....YWPhytpitska...dedimLftlskltGhaGsrlGWalvkdkevakklve 219
                                       ++yD ay    Y  ++  i++ +   ++ + L t+sk     G rlG+    +k++ k +++
  gi|385805929|ref|YP_005842327.1| 202 LLYDEAYrniiYEGKHVWIQKYSrtlEKLVGLDTFSKDLAIPGLRLGYLYAENKDLIKEVLK 263
                                       78888875555555555565432111445667788888888888888877777777666655 PP

>> SspH  Small acid-soluble spore protein H family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1   0.00035         1      17      31 ..     210     224 ..     204     229 .. 0.86
   2 ?    2.2   0.0     0.068     2e+02       6      41 ..     258     293 ..     254     296 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00035
                              SspH  17 eVtYngkpVwIehvd 31 
                                       ++ Y+gk VwI++ +
  gi|385805929|ref|YP_005842327.1| 210 NIIYEGKHVWIQKYS 224
                                       799*********986 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.068
                              SspH   6 akeIlnskemieVtYngkpVwIehvdeenetAtVhf 41 
                                       +ke+l+ k  + ++ +++  w+ h+  ++++ +++ 
  gi|385805929|ref|YP_005842327.1| 258 IKEVLKLKGIVSISSDSSAQWMAHIALSSGMLKIYL 293
                                       799****************************99986 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   8.9e-05      0.27      41     118 ..      97     173 ..      91     207 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 8.9e-05
                                       EEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEEE CS
                   DegT_DnrJ_EryC1  41 aiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpaaieaaitertkaIlp 117
                                        + +s G +Alhl+  a   +pgd       t+   +  +   ++k+  ++ + +++++dp+ ++++i+++t+ Il+
  gi|385805929|ref|YP_005842327.1|  97 IVVTSGGIEALHLTFYAT-TDPGDRAFFLDPTYSVYWDIANMYNLKVDSCEQNGEDFQPDPECLKEKINRNTSLILV 172
                                       57788899******9995.5789**************************************************9997 PP

                                       B CS
                   DegT_DnrJ_EryC1 118 V 118
                                        
  gi|385805929|ref|YP_005842327.1| 173 T 173
                                       5 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 ?   11.1   0.0    0.0001      0.31      60     118 ..     133     187 ..     106     200 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0001
                       Octopine_DH  60 aiakalglevlplaerlldaYgdeikdksslaevirtneaykgikaPmsldhRyltEDi 118
                                       +ia+ ++l+v ++++   ++++    d++ l+e+i+ n ++  +++P+++ +R+l+EDi
  gi|385805929|ref|YP_005842327.1| 133 DIANMYNLKVDSCEQN-GEDFQ---PDPECLKEKINRNTSLILVTSPDNPTSRILSEDI 187
                                       5666677777666666.44443...59*******************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2497.69
//
Query:       gi|385805930|ref|YP_005842328.1|  [L=464]
Description: dihydrolipoamide dehydrogenase [Fervidicoccus fontis Kam940]
Scores for 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-65  219.4   0.6    8.5e-65  218.9   0.6    1.1  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    4.8e-21   75.1   0.0      2e-20   73.1   0.0    2.0  2  Pyr_redox_dim   Pyridine nucleotide-disulphide oxidoreductase
    2.9e-19   69.4   2.8    2.1e-16   60.2   0.2    2.8  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    5.8e-16   58.6   6.5    6.2e-15   55.2   6.5    2.0  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    1.4e-09   37.2   0.3     0.0013   17.6   0.0    3.1  3  HI0933_like     HI0933-like protein
    3.2e-08   33.1   9.6    4.1e-06   26.1   1.5    4.1  3  GIDA            Glucose inhibited division protein A
    2.3e-06   27.1   0.1      0.053   12.8   0.0    2.2  2  FAD_binding_3   FAD binding domain
    7.1e-06   25.4   1.2    1.5e-05   24.4   0.1    2.1  3  Thi4            Thi4 family
    8.5e-06   25.8   2.4      0.019   14.9   0.0    2.6  3  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
    5.1e-05   23.3   1.3       0.12   12.3   0.0    3.8  4  NAD_binding_9   FAD-NAD(P)-binding
      6e-05   22.6   0.1    0.00064   19.2   0.0    2.2  2  FAD_oxidored    FAD dependent oxidoreductase
    6.5e-05   22.2   4.0    0.00013   21.2   0.4    2.9  4  FAD_binding_2   FAD binding domain
    0.00035   19.8   0.2      0.012   14.8   0.0    2.4  3  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
    0.00062   19.1   0.1      0.048   12.9   0.0    2.3  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
    0.00078   19.1   8.5       0.13   11.9   1.2    3.9  4  DAO             FAD dependent oxidoreductase
     0.0018   18.5   0.4      0.048   13.9   0.1    2.5  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
     0.0052   17.2   0.2        4.4    7.8   0.0    3.1  2  NAD_binding_7   Putative NAD(P)-binding
  ------ inclusion threshold ------
      0.054   13.1   3.5        3.1    7.3   0.5    2.4  2  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
        0.1   12.9   1.4        2.3    8.5   0.1    3.1  3  TrkA_N          TrkA-N domain
       0.12   11.7   0.1       0.68    9.3   0.0    2.0  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
       0.26   10.3   4.5         19    4.2   0.1    3.6  4  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 !  218.9   0.6   9.9e-68   8.5e-65       1     291 [.      11     319 ..      11     322 .. 0.95

  Alignments for each domain:
  == domain 1  score: 218.9 bits;  conditional E-value: 9.9e-68
                                       CSEEEE--SHHHHHHHHHHHHHTS-EEEEE...TTHCHHHCSHHHHCHHHHHHHHHHHHH................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx................. RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve...legtclnggcllskallgvaedaeias................. 57 
                                       +dv++iG+G +G+  a++laq+g+kv+++e    +g+c n gc++ska+ ++ae  ++++                 
  gi|385805930|ref|YP_005842328.1|  11 FDVAIIGSGTGGYPGAIYLAQKGLKVAVIEenlTGGECTNYGCVPSKAIYQFAESIRTLKnisanssyewekliewa 87 
                                       69***************************999********************************************* PP

                                       .HHHHCHHHHCCCCHCCT.CEEEEESCEEEEETEEEC...TCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSE CS
                                       .xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  58 .evvkklnqgielllgee.vvkidpgkkkvklekkke...gdeekiaydklvlAtGssprdlgipGvaenvgklvrt 129
                                        + vk +++gie l ++   +++ +gk+ +k ++k +   +++ +i++++++lAtG  p ++++    +++     +
  gi|385805930|ref|YP_005842328.1|  88 dNSVKGVRNGIESLFDSYdNIAYFKGKGVLKAKNKISiieENNSEIDAKNVILATGTDPSKIPVADFDKKG-----I 159
                                       *999************6566666677777777777669999999*****************9999885555.....6 PP

                                       CHHHHHHCCSS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 130 ldsaealklkllpkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsv 206
                                       + + e ++lk++p+++++vGgG+iGvElA ++++lg +++lve  +r+l+ ldk++s+a++ +l ++Gv+v+ +ts 
  gi|385805930|ref|YP_005842328.1| 160 ISNREVFSLKEKPNSMLIVGGGVIGVELANMFSSLGIQTYLVELKERILPFLDKDVSQAIKGYLVEKGVKVMERTSL 236
                                       89*************************************************************************** PP

                                       EEEEETTEEEEEEETTSCEEEESEEEE-S-EEES-HHCS.HCCT-EEEETTEEE--TTSBESSTTEEE-GGGCTECC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 207 keidgngeklevvledgeeidadlvvvavGvrpstelle.eklglelderggivvdeflrtnvpgiyaiGDvaggkg 282
                                       k + + +e+++v l++ e++++d v++++G++p+t+ ++ e+lg+++derg+i+v+e+l+tn  giya GDv+   g
  gi|385805930|ref|YP_005842328.1| 237 KGVSKVSENYQVLLSNDEKLEVDKVIISTGRSPKTKNIGlENLGIKIDERGFIKVNEKLETNASGIYATGDVV---G 310
                                       ********999**************************************************************...* PP

                                       SS--HHHHH CS
                                       xxxxxxxxx RF
                       Pyr_redox_2 283 gpelaqaAv 291
                                       gp la++A+
  gi|385805930|ref|YP_005842328.1| 311 GPLLAHKAI 319
                                       ******997 PP

>> Pyr_redox_dim  Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       4.6   3.9e+03      59      80 ..     174     195 ..     168     198 .. 0.83
   2 !   73.1   0.0   2.4e-23     2e-20       1     107 [.     342     448 ..     342     451 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 4.6
                                       TTBEEEEEEECTTHHHHHHHHH CS
                     Pyr_redox_dim  59 tgkvlGahivGpgageliqela 80 
                                       +  ++G  ++G + + +++ l 
  gi|385805930|ref|YP_005842328.1| 174 SMLIVGGGVIGVELANMFSSLG 195
                                       6779********9999998765 PP

  == domain 2  score: 73.1 bits;  conditional E-value: 2.4e-23
                                       BEEEEESSSEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTHTEEEEEEEEETTTTBEEEEEEECTTHHHHHH CS
                     Pyr_redox_dim   1 iptvvftdpevasvGlteeeAkaagieikvgkfpfkangralayaetkgfvKlvadaktgkvlGahivGpgageliq 77 
                                       ip+v+f+ +e+a++G++e+e++ +gi+++ +k+p+  ++  ++ +e++ f+Kl+ d++++k+ G+ iv+p+a+e+i+
  gi|385805930|ref|YP_005842328.1| 342 IPQVIFSGLEIAWIGMGENELNSKGINYEKIKLPIYYLAAVRIRNERRSFIKLLLDKESKKIYGIEIVAPHASEVIS 418
                                       79*************************************************************************** PP

                                       HHHHHHHTTSBHHHHHTSBSSSSSTGGGGH CS
                     Pyr_redox_dim  78 elavaikagltvedladtihihPtlsealk 107
                                        +  +  +++t+e++ +   +h t+se+++
  gi|385805930|ref|YP_005842328.1| 419 SYLPLYLNKITIEEASKITYPHLTVSESIR 448
                                       ***************************997 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.2    0.0034       2.9       2      30 ..      13      41 ..      12      44 .. 0.95
   2 !   60.2   0.2   2.4e-19   2.1e-16       2      78 ..     175     250 ..     174     254 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0034
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEES CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvver 30
                                      v+++G+G+ g   A +la+ g kV v+e 
  gi|385805930|ref|YP_005842328.1| 13 VAIIGSGTGGYPGAIYLAQKGLKVAVIEE 41
                                      89*************************97 PP

  == domain 2  score: 60.2 bits;  conditional E-value: 2.4e-19
                                       EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEEE CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedgvesvkl 78 
                                       +++vGgG+ig+ElA++++ lg ++++ve ++++l+ lD+++s++++ +l ++g++v+  t+++ + + +++ ++v l
  gi|385805930|ref|YP_005842328.1| 175 MLIVGGGVIGVELANMFSSLGIQTYLVELKERILPFLDKDVSQAIKGYLVEKGVKVMERTSLKGVSKVSEN-YQVLL 250
                                       79***************************************************************988875.55665 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 !   55.2   6.5   7.3e-18   6.2e-15       2     305 .]      15     306 ..      14     306 .. 0.79

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 7.3e-18
                       Pyr_redox_3   2 IiGaGPaGlaaaielkkagledylilEkgnignsiyrypk.emtfispsftsekleipdlnaiseetspafs..lke 75 
                                       IiG G  G   ai l ++gl ++ ++E +  g   ++y     + i  +f +    i  l++is ++s ++   ++ 
  gi|385805930|ref|YP_005842328.1|  15 IIGSGTGGYPGAIYLAQKGL-KVAVIEENLTGGECTNYGCvPSKAIY-QFAES---IRTLKNISANSSYEWEklIEW 86 
                                       9*******************.79***************761445554.44444...444445555555333321344 PP

                       Pyr_redox_3  76 eklsrkealeYlrevaksfelpiklfeeVesvkk.edegfevetsketyeAkkviiAtGefdkPnklnipGeek.lv 150
                                          s k + +  +++ +s++ +i +f+  + v k +++  ++e +++++ Ak+vi+AtG    P k  +   +k   
  gi|385805930|ref|YP_005842328.1|  87 ADNSVKGVRNGIESLFDSYD-NIAYFKG-KGVLKaKNKISIIEENNSEIDAKNVILATGT--DPSKIPVADFDKkGI 159
                                       44455566777788888877.5777766.555551667778888889************9..788777766665156 PP

                       Pyr_redox_3 151 khyskvkefhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeeki 227
                                       + +++v ++ k + + ++++Gg+  +v+ A  + + g +  +v  ++ i          l  d+ + ++ ++ e+ +
  gi|385805930|ref|YP_005842328.1| 160 ISNREVFSL-KEKPNSMLIVGGGVIGVELANMFSSLGIQTYLVELKERILPF-------LDKDVSQAIKGYLVEKGV 228
                                       688888888.677899****************************99976665.......677777777777777679 PP

                       Pyr_redox_3 228 kvlfnaevkeikekeeeykvktedgkkvevkddvvlatGykpdlsf..lkkslfeldedgrpvlteeteetnvpglf 302
                                       kv++++++k +++ +e+y+v  ++ +k+ev d+v++ tG +p+++   l++ ++++de g+++++e+  etn +g++
  gi|385805930|ref|YP_005842328.1| 229 KVMERTSLKGVSKVSENYQVLLSNDEKLEV-DKVIISTGRSPKTKNigLENLGIKIDERGFIKVNEK-LETNASGIY 303
                                       ************************999998.899*********998566779************975.79******* PP

                       Pyr_redox_3 303 laG 305
                                         G
  gi|385805930|ref|YP_005842328.1| 304 ATG 306
                                       988 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   1.4e-05     0.012       1      33 [.      11      43 ..      11      90 .. 0.90
   2 ?    1.7   0.0     0.099        85     136     164 ..     117     144 ..     109     150 .. 0.77
   3 !   17.6   0.0   1.5e-06    0.0013      82     165 ..     187     268 ..     184     298 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.4e-05
                                      -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekak 33
                                      +dv++iG G  G  +Ai +a++g +V+++e++ 
  gi|385805930|ref|YP_005842328.1| 11 FDVAIIGSGTGGYPGAIYLAQKGLKVAVIEENL 43
                                      59****************************985 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.099
                                       ECETTE.EEEEE.TTEEEEESEEEE---- CS
                       HI0933_like 136 ekeedgkfrvktkseeeleadklvlAtGG 164
                                        k +++ +++  ++++e+ a++++lAtG 
  gi|385805930|ref|YP_005842328.1| 117 LKAKNK-ISIIEENNSEIDAKNVILATGT 144
                                       455555.4444459*************96 PP

  == domain 3  score: 17.6 bits;  conditional E-value: 1.5e-06
                                       HHHHHHHTT--E.EE-STTEEEETT.-CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESE CS
                       HI0933_like  82 lialveelgvel.keedsgrlFpvsdkaedivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadk 157
                                       l +++++lg+++  +e + r+ p     +d+ +a++  l e+gvk++ +t++k+v+k +++ ++v ++++e+le dk
  gi|385805930|ref|YP_005842328.1| 187 LANMFSSLGIQTyLVELKERILPFL--DKDVSQAIKGYLVEKGVKVMERTSLKGVSKVSEN-YQVLLSNDEKLEVDK 260
                                       6789999999751578899999988..57999***********************886666.999999********* PP

                                       EEE----S CS
                       HI0933_like 158 lvlAtGGl 165
                                       ++++tG  
  gi|385805930|ref|YP_005842328.1| 261 VIISTGRS 268
                                       ****9954 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   1.5   4.8e-09   4.1e-06       1     150 [.      12     144 ..      12     168 .. 0.75
   2 !    6.5   0.3    0.0045       3.9       3      31 ..     176     204 ..     174     239 .. 0.82
   3 ?    2.2   0.1     0.092        78      97     150 ..     215     267 ..     210     280 .. 0.72

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 4.8e-09
                                       CEEEE-SSHHHHHHHHHHHHTT--EEEE..ES-GGGTT--SSSSEEE-TTHHHHHHHHHHHT-SHHHHHHH.HEEEE CS
                              GIDA   1 dviViGgGhAGceAAlaaarlGakvlLi..thkldtiaelsCnpsiggiakgllvrEidalggliikaadk.agiqf 74 
                                       dv +iG G  G+  A+ +a++G+kv+ i      +++ + +C ps    a ++  + i+ l+ + ++   +  ++  
  gi|385805930|ref|YP_005842328.1|  12 DVAIIGSGTGGYPGAIYLAQKGLKVAVIeeNLTGGECTNYGCVPSK---AIYQFAESIRTLKNISANSSYEwEKLIE 85 
                                       799*************************55555679999*9*9985...8899999999999777765544144434 PP

                                       EEESTTS-..CCC-EEEEEE-HHHHHHHHHHHHHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--T CS
                              GIDA  75 rilNrskG..pavralraqvdrelyskevteklenepnleiieeeveeliveekkvkgvvtedgetikakavviatG 149
                                          N+ kG  + +++l  ++d  +y k  + +l+++++++iiee+ +e+ +                 ak+v++atG
  gi|385805930|ref|YP_005842328.1|  86 WADNSVKGvrNGIESLFDSYDNIAYFK-GKGVLKAKNKISIIEENNSEI-D-----------------AKNVILATG 143
                                       566888884345666767777777765.477888888888888888888.3.................688888888 PP

                                       T CS
                              GIDA 150 t 150
                                       t
  gi|385805930|ref|YP_005842328.1| 144 T 144
                                       8 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0045
                                       EEE-SSHHHHHHHHHHHHTT--EEEEES- CS
                              GIDA   3 iViGgGhAGceAAlaaarlGakvlLithk 31 
                                        ++GgG  G+e A   + lG+++ L+  k
  gi|385805930|ref|YP_005842328.1| 176 LIVGGGVIGVELANMFSSLGIQTYLVELK 204
                                       69***********************9433 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.092
                                       HHHHHHHHHHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT CS
                              GIDA  97 yskevteklenepnleiieeeveeliveekkvkgvvtedgetikakavviatGt 150
                                       +s++++ +l + + ++++e++  + + + ++   v+++++e+++ ++v+i+tG 
  gi|385805930|ref|YP_005842328.1| 215 VSQAIKGYLVE-KGVKVMERTSLKGVSKVSENYQVLLSNDEKLEVDKVIISTGR 267
                                       45566666655.77888877665555656777889******************7 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   6.2e-05     0.053       2      32 ..      11      41 ..      10      82 .. 0.92
   2 !   12.3   0.1   8.6e-05     0.074       4      32 ..     175     203 ..     173     210 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.2e-05
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEES CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvek 32
                                       dV+I+G+G  G   a  L+++G +v ++e 
  gi|385805930|ref|YP_005842328.1| 11 FDVAIIGSGTGGYPGAIYLAQKGLKVAVIEE 41
                                      79***************************96 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 8.6e-05
                                       EEEE--SHHHHHHHHHHHHTTHHEEEEES CS
                     FAD_binding_3   4 VlIVGaGpaGlmlallLseaGvrvvlvek 32 
                                        lIVG+G  G+ la++ s+ G+++ lve 
  gi|385805930|ref|YP_005842328.1| 175 MLIVGGGVIGVELANMFSSLGIQTYLVEL 203
                                       59*************************95 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.1   1.8e-08   1.5e-05      17      60 ..      10      52 ..       2      80 .. 0.84
   2 ?   -4.0   0.0       8.4   7.2e+03     157     174 ..     133     150 ..     129     172 .. 0.71
   3 ?   -1.9   0.1       1.9   1.6e+03      20      48 ..     175     202 ..     159     205 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.8e-08
                                      EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTT CS
                              Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlG 60
                                      e Dv+i+G+G+ G   a yla+k +lkva++e++++ G  +  G
  gi|385805930|ref|YP_005842328.1| 10 EFDVAIIGSGTGGYPGAIYLAQK-GLKVAVIEENLTGGECTNYG 52
                                      78*********************.***********877666555 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 8.4
                                       EEEEEEEE--GSSSTTTT CS
                              Thi4 157 irakvvvdatGhdgeiva 174
                                       i+ak v+ atG d + + 
  gi|385805930|ref|YP_005842328.1| 133 IDAKNVILATGTDPSKIP 150
                                       788899999999865444 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.9
                                       EEEE--SHHHHHHHHHHHHCTTS-EEEEE CS
                              Thi4  20 vvivGaGssGLtaayylakkpdlkvaile 48 
                                       ++ivG+G  G+  a +++   ++++ ++e
  gi|385805930|ref|YP_005842328.1| 175 MLIVGGGVIGVELANMFSSL-GIQTYLVE 202
                                       6899******9999999888.88887777 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 !   10.2   0.3   0.00061      0.52       2      31 ..      13      42 ..      12      54 .. 0.93
   2 ?   -2.6   0.0       5.2   4.4e+03      73     112 ..     129     142 ..      82     156 .. 0.56
   3 !   14.9   0.0   2.2e-05     0.019       4      63 ..     177     236 ..     174     262 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00061
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S- CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdis 31
                                      va+iG+Gt G   a  +a++gl+V +++ +
  gi|385805930|ref|YP_005842328.1| 13 VAIIGSGTGGYPGAIYLAQKGLKVAVIEEN 42
                                      9*************************9865 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5.2
                                       HHHHHC-SEEEE-S-SSHHHHHHHHHHHHCCS-TTSEEEE CS
                           3HCDH_N  73 leeavdadlviEavvEnlelKrkvfaelekiakpdailas 112
                                        ++ +d                           +++ila+
  gi|385805930|ref|YP_005842328.1| 129 NNSEID--------------------------AKNVILAT 142
                                       333333..........................34444444 PP

  == domain 3  score: 14.9 bits;  conditional E-value: 2.2e-05
                                       EE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCC CS
                           3HCDH_N   4 viGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaa 63 
                                       ++G G++G ++a++f s g+++ lv+ +e++l    + +++ ++    ++ +k  e+ ++
  gi|385805930|ref|YP_005842328.1| 177 IVGGGVIGVELANMFSSLGIQTYLVELKERILPFLDKDVSQAIKGYLVEKGVKVMERTSL 236
                                       8*******************************9999999998887766666664444444 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.19   1.6e+02       1      41 [.      14      48 ..      14     101 .. 0.77
   2 ?    4.8   0.0     0.029        25     130     155 ..     119     144 ..     114     145 .. 0.84
   3 ?   -1.1   0.3       1.9   1.6e+03       2      15 ..     177     190 ..     176     199 .. 0.85
   4 !   12.3   0.0   0.00014      0.12     115     155 ..     226     267 ..     209     268 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.19
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsepgagrv 41
                                      ai+G G  G   +  L+++      l++ +++++ +g g +
  gi|385805930|ref|YP_005842328.1| 14 AIIGSGTGGYPGAIYLAQK-----GLKVAVIEENLTG-GEC 48
                                      89************99999.....599*****99998.554 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.029
                     NAD_binding_9 130 radgqavlladgaslaadaVvLAlGh 155
                                       ++++  ++++++++++a++V+LA+G 
  gi|385805930|ref|YP_005842328.1| 119 AKNKISIIEENNSEIDAKNVILATGT 144
                                       4566688999***************6 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.9
                     NAD_binding_9   2 ivGaGprGlavler 15 
                                       ivG+G+ G+ +++ 
  gi|385805930|ref|YP_005842328.1| 177 IVGGGVIGVELANM 190
                                       9*******999876 PP

  == domain 4  score: 12.3 bits;  conditional E-value: 0.00014
                     NAD_binding_9 115 vtvevh.raevvdleeradgqavlladgaslaadaVvLAlGh 155
                                         v+v+ r++   +++  ++++vll+++++l++d+V++ +G 
  gi|385805930|ref|YP_005842328.1| 226 KGVKVMeRTSLKGVSKVSENYQVLLSNDEKLEVDKVIISTGR 267
                                       3456653779999***************************96 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   7.5e-07   0.00064       1      45 [.      12      55 ..      12      86 .. 0.88
   2 ?    0.7   0.0      0.31   2.6e+02       3      30 ..     176     203 ..     175     207 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 7.5e-07
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvat 45
                                      Dv ++G+g++G+  Ai  a++G kv+++ee+   GG  t+ +  +
  gi|385805930|ref|YP_005842328.1| 12 DVAIIGSGTGGYPGAIYLAQKGLKVAVIEEN-LTGGECTNYGCVP 55
                                      9***************************986.6799999877665 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.31
                      FAD_oxidored   3 vVvGGgpaGvaAAiaAaraGakvlLvee 30 
                                       ++vGGg+ Gv  A      G ++ Lve 
  gi|385805930|ref|YP_005842328.1| 176 LIVGGGVIGVELANMFSSLGIQTYLVEL 203
                                       79************************95 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.4   1.5e-07   0.00013       1      30 [.      12      41 ..      12      50 .. 0.93
   2 ?   -0.2   0.0      0.48   4.1e+02     183     203 ..     126     146 ..      59     156 .. 0.77
   3 ?   -1.8   0.1       1.4   1.2e+03       3      32 ..     176     205 ..     174     207 .. 0.88
   4 ?   -1.2   0.0      0.97   8.3e+02     376     404 ..     281     311 ..     279     313 .. 0.66

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.5e-07
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEES CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvek 30
                                      Dv +iGsG +G+  A+ +a++Glkvav+e 
  gi|385805930|ref|YP_005842328.1| 12 DVAIIGSGTGGYPGAIYLAQKGLKVAVIEE 41
                                      9***************************96 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.48
                                       TTTCEEEEEESEEEE-----G CS
                     FAD_binding_2 183 esgrevrirakavvlatgGfg 203
                                        ++++ +i ak+v+latg  +
  gi|385805930|ref|YP_005842328.1| 126 IEENNSEIDAKNVILATGTDP 146
                                       56677899999*****99755 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.4
                                       EEE--SHHHHHHHHHHHHTTT-EEEEESSS CS
                     FAD_binding_2   3 iViGsGlAGLaAAleaaeaGlkvavvekeq 32 
                                       +++G+G+ G   A   +  G ++ +ve ++
  gi|385805930|ref|YP_005842328.1| 176 LIVGGGVIGVELANMFSSLGIQTYLVELKE 205
                                       89*******999999999999999999766 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 0.97
                                       EEBETTSBE..STTEEESSBTEEE-STCEES CS
                     FAD_binding_2 376 vetdengrv..ldadgqpipGLYAaGevaag 404
                                       +++de+g     ++ +++ +G YA G v +g
  gi|385805930|ref|YP_005842328.1| 281 IKIDERGFIkvNEKLETNASGIYATGDVVGG 311
                                       555555533225555559********99854 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 ?   -3.8   0.0       6.3   5.4e+03     192     201 ..      11      20 ..       7      32 .. 0.76
   2 !   14.8   0.0   1.4e-05     0.012     132     212 ..     116     193 ..      69     224 .. 0.68
   3 ?    2.6   0.0      0.07        60     292     339 ..     225     266 ..     212     268 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 6.3
                       K_oxygenase 192 kriaVvGsGq 201
                                        ++a++GsG 
  gi|385805930|ref|YP_005842328.1|  11 FDVAIIGSGT 20 
                                       5688888885 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.4e-05
                       K_oxygenase 132 lltveskd..aegeeeelearnlvlgvGtepk.iPevleklegkervvHsseylerkeellakkriaVvGsGqSaae 205
                                       +l+ ++k    e++++e+ a+n++l++Gt p+ iP  ++ ++ k+ ++ + e+ + k   ++++++++vG+G  + e
  gi|385805930|ref|YP_005842328.1| 116 VLKAKNKIsiIEENNSEIDAKNVILATGTDPSkIPV-AD-FD-KKGIISNREVFSLK---EKPNSMLIVGGGVIGVE 186
                                       4555444334577899************99962664.44.55.46788888888777...7999*********9999 PP

                       K_oxygenase 206 ifedllr 212
                                       +++   +
  gi|385805930|ref|YP_005842328.1| 187 LANMFSS 193
                                       9876555 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.07
                       K_oxygenase 292 eerlrllpnrevesaeaegkgeveltlrneesgeeetlevdavvlATG 339
                                       e+ ++++++++++++++ ++ ++++ l+n     +e+levd v+++TG
  gi|385805930|ref|YP_005842328.1| 225 EKGVKVMERTSLKGVSKVSE-NYQVLLSN-----DEKLEVDKVIISTG 266
                                       66789999**********96.9***9999.....899**********9 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.031        27      20      62 ..       4      44 ..       1      78 [. 0.84
   2 !   12.9   0.0   5.6e-05     0.048      27      69 ..     171     213 ..     167     266 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.031
                                      TCEETCB---EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHH CS
                       AlaDh_PNT_C 20 aGgvpgvepakvlviGgGvaGlqAiatakglgakVtvlDvrpa 62
                                      +++++  ++  v +iG G+ G   +   ++ g kV v++ + +
  gi|385805930|ref|YP_005842328.1|  4 LSTIK--KEFDVAIIGSGTGGYPGAIYLAQKGLKVAVIEENLT 44
                                      66777..7889************99999999****99998876 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 5.6e-05
                                       ---EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH CS
                       AlaDh_PNT_C  27 epakvlviGgGvaGlqAiatakglgakVtvlDvrparleqles 69 
                                       +p  +l++GgGv G++ +++ ++lg ++++++++++ l  l++
  gi|385805930|ref|YP_005842328.1| 171 KPNSMLIVGGGVIGVELANMFSSLGIQTYLVELKERILPFLDK 213
                                       57789**************************999888777666 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   1.2   0.00015      0.13       1      37 [.      12      49 ..      12      89 .. 0.85
   2 ?    0.6   0.0      0.39   3.3e+02     172     203 ..     119     145 ..     106     169 .. 0.65
   3 ?    2.7   0.2     0.089        76       3      15 ..     176     188 ..     174     204 .. 0.82
   4 ?    5.4   0.0     0.014        12     150     201 ..     217     266 ..     212     292 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00015
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGG CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaS 37
                                      dv+iiG+G  G   A +La++g  V+++e +   g +++
  gi|385805930|ref|YP_005842328.1| 12 DVAIIGSGTGGYPGAIYLAQKGlkVAVIEEN-LTGGECT 49
                                      8*****************************9.5553554 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.39
                                       EEEEETCEEEEEEECTEEEEEEEE..EEE--GGG CS
                               DAO 172 leeedgkvwgverttpgendaada..vVnaaGaw 203
                                        +   +k++ + ++++   +++da  v++a+G  
  gi|385805930|ref|YP_005842328.1| 119 AK---NKISII-EENN---SEIDAknVILATGTD 145
                                       33...356677.2222...2345555******54 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.089
                                       EEECTSHHHHHHH CS
                               DAO   3 viiGGGiiGlstA 15 
                                       +i+GGG+iG+  A
  gi|385805930|ref|YP_005842328.1| 176 LIVGGGVIGVELA 188
                                       8********8655 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.014
                                       HHHHHHHHHTT-EEEESECEEEEEEEETCEEEEE..EECTEEEEEEEEEEE--G CS
                               DAO 150 aalaraaealGveilegtevtgleeedgkvwgve..rttpgendaadavVnaaG 201
                                       +a+   + ++Gv++ e+t  +g+++ ++  ++v   ++++    ++d+v++++G
  gi|385805930|ref|YP_005842328.1| 217 QAIKGYLVEKGVKVMERTSLKGVSKVSEN-YQVLlsNDEK---LEVDKVIISTG 266
                                       67788899**************9774433.5554544333...247*******9 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.1   5.6e-05     0.048       1      38 [.      15      51 ..      15      70 .. 0.91
   2 ?    2.1   0.0      0.26   2.2e+02       1      30 [.     177     206 ..     177     234 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.6e-05
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EE CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasy 38
                                      I+G+G +G   A +La++g++v ++e  + +GG ++ y
  gi|385805930|ref|YP_005842328.1| 15 IIGSGTGGYPGAIYLAQKGLKVAVIEE-NLTGGECTNY 51
                                      9************************98.5889988876 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.26
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSS CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdr 30 
                                       IvG+G+ G  +A   +  g++  l+e  +r
  gi|385805930|ref|YP_005842328.1| 177 IVGGGVIGVELANMFSSLGIQTYLVELKER 206
                                       9*******9999988888888777777666 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0051       4.4       7      53 ..      10      89 ..       6     160 .. 0.68
   2 ?    5.9   0.0      0.02        17       8      40 ..     173     205 ..     166     274 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0051
                     NAD_binding_7  7 gkkvlvvGgGevAarkvrklleagakvtvvapev....keele................................elvk 49
                                      +  v ++G G+ ++  +  l+++g kv v+ +++    +                                    +l++
  gi|385805930|ref|YP_005842328.1| 10 EFDVAIIGSGTGGYPGAIYLAQKGLKVAVIEENLtggeC---TnygcvpskaiyqfaesirtlknisanssyeweKLIE 85
                                      56899*************************999865440...2344444445555555555554444444444444444 PP

                     NAD_binding_7 50 laee 53
                                      +a++
  gi|385805930|ref|YP_005842328.1| 86 WADN 89
                                      4444 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.02
                     NAD_binding_7   8 kkvlvvGgGevAarkvrklleagakvtvvapev 40 
                                        ++l+vGgG ++ + ++ + + g +  +v  + 
  gi|385805930|ref|YP_005842328.1| 173 NSMLIVGGGVIGVELANMFSSLGIQTYLVELKE 205
                                       689*************99999999988887663 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 ?    7.3   0.5    0.0036       3.1       3      32 ..      13      42 ..      11      53 .. 0.93
   2 ?    6.2   0.1    0.0083         7       4      72 ..     176     244 ..     173     250 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0036
                                      EEEE--STTHHHHHHHHHHCTSEEEEE-S- CS
                    UDPG_MGDP_dh_N  3 isviGlGYvGlvtaavlaeighevigvDid 32
                                      +++iG+G  G + a+ la++g +v ++  +
  gi|385805930|ref|YP_005842328.1| 13 VAIIGSGTGGYPGAIYLAQKGLKVAVIEEN 42
                                      89**********************999765 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0083
                                       EEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS--TTHHHHHHHHCHTTTEEEES-HHH CS
                    UDPG_MGDP_dh_N   4 sviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiyepgLeelvkkavesgrlsfttdvek 72 
                                        ++G G +G+  a +++++g++  +v   e+    l ++ ++ +   L e   k++e + l++ ++v++
  gi|385805930|ref|YP_005842328.1| 176 LIVGGGVIGVELANMFSSLGIQTYLVELKERILPFLDKDVSQAIKGYLVEKGVKVMERTSLKGVSKVSE 244
                                       59************************9999999999988888887777777777777777777777766 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.39   3.4e+02       1      30 [.      13      42 ..      13      75 .. 0.87
   2 ?   -1.4   0.0       3.1   2.6e+03      19      36 ..     119     135 ..     114     154 .. 0.64
   3 ?    8.5   0.1    0.0027       2.3       2      48 ..     176     222 ..     175     229 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.39
                                      EEEES-SHHHHHHHHHHHHTTEEEEEEESS CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLseggkdvvvidkd 30
                                      ++iiG G+ G+  a +L ++g +v vi+ +
  gi|385805930|ref|YP_005842328.1| 13 VAIIGSGTGGYPGAIYLAQKGLKVAVIEEN 42
                                      68*****************6646****987 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.1
                                       HTTEEEEEEESSHHHHHH CS
                            TrkA_N  19 eggkdvvvidkdeervee 36 
                                       +++ ++++i+ + + ++ 
  gi|385805930|ref|YP_005842328.1| 119 AKN-KISIIEENNSEIDA 135
                                       344.58888888776654 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0027
                                       EEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES- CS
                            TrkA_N   2 iiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgd 48 
                                       +i+G G +G +la+ +s+ g++ ++++ +e+ +  l ++  ++++g 
  gi|385805930|ref|YP_005842328.1| 176 LIVGGGVIGVELANMFSSLGIQTYLVELKERILPFLDKDVSQAIKGY 222
                                       79****************6668********99999999988898885 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1       0.9   7.6e+02      38      70 ..      12      44 ..       5      66 .. 0.81
   2 ?    9.3   0.0   0.00079      0.68      35      68 ..     171     204 ..     152     218 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.9
                                      EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHH CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmkviaydrskk 70
                                       v+iiG G  G   a +l++ g+kv +++ + +
  gi|385805930|ref|YP_005842328.1| 12 DVAIIGSGTGGYPGAIYLAQKGLKVAVIEENLT 44
                                      689****************99999999987766 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00079
                                       TTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSS CS
                      2-Hacid_dh_C  35 sgktvGiiGlGrIGqavakrlkafgmkviaydrs 68 
                                       +   + i+G G IG ++a++++++g++ + ++ +
  gi|385805930|ref|YP_005842328.1| 171 KPNSMLIVGGGVIGVELANMFSSLGIQTYLVELK 204
                                       556789*********************9988765 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1     0.022        19       1      32 [.      12      41 ..      12      53 .. 0.92
   2 ?   -2.2   0.0       1.9   1.6e+03     117     142 ..     121     144 ..     112     152 .. 0.75
   3 ?    3.1   0.1     0.047        40       3      35 ..     176     206 ..     174     211 .. 0.88
   4 ?    2.6   0.0     0.067        57      89     152 ..     215     276 ..     209     284 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.022
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvliea 32
                                      Dv++iG+G  g   A  l  a++glkv +ie 
  gi|385805930|ref|YP_005842328.1| 12 DVAIIGSGTGGYPGAIYL--AQKGLKVAVIEE 41
                                      9*****************..9********974 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.9
                     Lycopene_cycl 117 ageslvvleggrkirarlvvdargla 142
                                       + + +++ e++ +i+a+ v+ a+g  
  gi|385805930|ref|YP_005842328.1| 121 N-KISIIEENNSEIDAKNVILATG-T 144
                                       4.5667778888**********99.3 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.047
                     Lycopene_cycl   3 vviGaGpAglslAarlteakpglkvvlieasps 35 
                                       +++G+G  g+ lA+    +  g++  l+e  + 
  gi|385805930|ref|YP_005842328.1| 176 LIVGGGVIGVELANMF--SSLGIQTYLVELKER 206
                                       89**************..99****999997665 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.067
                     Lycopene_cycl  89 lkeellerlvengvklleakves.veeeeageslvvleggrkirarlvvdarglaslkkarrlgl 152
                                         + ++  lve+gvk +e +  + v ++++ + +v l++++k++   v+ ++g  +++k +++gl
  gi|385805930|ref|YP_005842328.1| 215 VSQAIKGYLVEKGVKVMERTSLKgVSKVSE-NYQVLLSNDEKLEVDKVIISTG--RSPKTKNIGL 276
                                       566778889999999998776551666666.999*******************..6666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); 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: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 3396.96
//
Query:       gi|385805931|ref|YP_005842329.1|  [L=120]
Description: hypothetical protein FFONT_0889 [Fervidicoccus fontis Kam940]
Scores for complete 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-20   72.1   0.0    4.5e-20   71.6   0.0    1.2  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
    3.1e-05   24.2   0.0    6.9e-05   23.1   0.0    1.4  1  Acetyltransf_1   Acetyltransferase (GNAT) family
     0.0025   18.2   0.0     0.0031   17.9   0.0    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
     0.0089   16.0   0.0      0.013   15.4   0.0    1.3  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.012   15.1   0.1      0.019   14.5   0.0    1.4  1  Acetyltransf_15  Putative acetyl-transferase


Domain annotation for each model (and alignments):
>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.6   0.0   1.2e-23   4.5e-20       8      80 .]      21      94 ..      13      94 .. 0.89

  Alignments for each domain:
  == domain 1  score: 71.6 bits;  conditional E-value: 1.2e-23
                   Acetyltransf_CG  8 egeevafleYe.vrkegvldfthTeVpeelrGkGiAkkLvkaalddareeglkvvptCsyvaaylekhpeyadl 80
                                      e+ e+ fl+Ye ++k+ v+++  T++p++lrG+GiA+kLv++a+++a+e++lk+ p+Csy+  y+ kh e +dl
  gi|385805931|ref|YP_005842329.1| 21 EEGEKPFLRYEiDEKNRVIKLIETYTPPKLRGRGIAEKLVDEAVKFAKENELKIEPICSYAIYYFIKHSEKRDL 94
                                      345789****84566669**************************************************998875 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   1.9e-08   6.9e-05      55      95 ..      31      73 ..      25      82 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.9e-08
                                      T..TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTES CS
                    Acetyltransf_1 55 d..ekggvayieslaVspeyrgkGlGsaLlealeerareegik 95
                                      +  ek++v+ +++ +  p+ rg+G++ +L+++++++a+e+++k
  gi|385805931|ref|YP_005842329.1| 31 EidEKNRVIKLIETYTPPKLRGRGIAEKLVDEAVKFAKENELK 73
                                      3446899999******************************764 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   8.6e-07    0.0031       3      49 ..      10      68 ..       8     103 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 8.6e-07
                                      EEEEEEEETTEEEEEEEEEEES.............TCTEE......EEE-GGGTTSSHHHHHHHH.....T CS
                    Acetyltransf_7  3 gevfVaeddgkivGfialslld.............aeitr......laVdpeyrgkGiGraLlea.....a 49
                                      ++vfVa  ++++         +                 r       ++ p+ rg+Gi+ +L++      +
  gi|385805931|ref|YP_005842329.1| 10 KTVFVAIVGNEE---------EgekpflryeidekN---RviklieTYTPPKLRGRGIAEKLVDEavkfaK 68
                                      568888443333.........223334444453341...243444479***************95233331 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   3.6e-06     0.013      53      86 ..      38      73 ..       6      82 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.6e-06
                   Acetyltransf_10 53 hisll..fVdpeyrgqGigkaLleaveeeaekdgik 86
                                       i l+  +  p+ rg+Gi+++L++++ + a+++++k
  gi|385805931|ref|YP_005842329.1| 38 VIKLIetYTPPKLRGRGIAEKLVDEAVKFAKENELK 73
                                      4444444899********************888665 PP

>> Acetyltransf_15  Putative acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   5.2e-06     0.019      67     102 ..      33      68 ..       5      93 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.2e-06
                   Acetyltransf_15  67 lieknvleiYtlyvsekyrgkGlakklLeeslkelk 102
                                        +++ v+++ + y+++k rg+G+a kl+ e++k  k
  gi|385805931|ref|YP_005842329.1|  33 DEKNRVIKLIETYTPPKLRGRGIAEKLVDEAVKFAK 68 
                                       5688999***********************987654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       956  (0.0533214); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); 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: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 829.54
//
Query:       gi|385805932|ref|YP_005842330.1|  [L=321]
Description: carbamate kinase-like carbamoyl phosphate synthetase [Fervidicoccus fontis Kam940]
Scores for 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-30  103.9   0.3    3.3e-29  102.2   0.3    1.7  1  AA_kinase  Amino acid kinase family
  ------ inclusion threshold ------
       0.15   12.7   0.0         27    5.4   0.0    3.2  3  MucBP_2    Mucin binding domain
       0.17   11.1   0.0       0.35   10.0   0.0    1.5  2  DUF4556    Domain of unknown function (DUF4556)


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 !  102.2   0.3   5.6e-33   3.3e-29       2     240 ..       8     301 ..       7     302 .. 0.85

  Alignments for each domain:
  == domain 1  score: 102.2 bits;  conditional E-value: 5.6e-33
                                       EEEEEE-TTCCCCTCC........HHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHH....TCCCCCHHHC... CS
                         AA_kinase   2 rvVvKlGGssltdkee........aslrrlaeqiaalkesgnklvvVhGggsftdgllal....ksglssgelaa.. 64 
                                       ++V++lGG+++ +k+e        +++  +a++i  l ++g+k+vv hG+g+++ + ++     k ++++   ++  
  gi|385805932|ref|YP_005842330.1|   8 LIVIALGGNAFLQKGEkgtveeqwKNVYVAAKEIVGLIKRGYKVVVTHGNGPQVGNVMEWiealKDKIPPLTMDIag 84 
                                       79*******99977777*******************************************55443333333333355 PP

                                       ..........E..HHHHHHHHH..HHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE................. CS
                         AA_kinase  65 .......glrstleeagevatr..dalaslgerlvaallaaglpavglsaaaldateagr................. 115
                                              g  +++++++ ++++  d      + +++ ++++  pa + + +++++   +                  
  gi|385805932|ref|YP_005842330.1|  85 amtqgwiGYMLQQAIQNVLIEEglDHHYRAVTLINQVIVKKDDPAWNNPTKYVGPYYYNEeeieklkkergwvikpd 161
                                       55555666666666666666668866666666666667777777777777777777666688888************ PP

                                       .........HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEETTTE........EEEE-HHHHHHHHHHHCTSSEEE CS
                         AA_kinase 116 .......degsdgnvesvdaeaieelleagvvpvltgfigldeege........lgrgssDtiaallAealgAdkli 177
                                               + s+++v +v++eai+ l e++++++ +g++g+++  +         +++++D    llA  ++Ad  i
  gi|385805932|ref|YP_005842330.1| 162 prggyrrVVASPDVVDNVEKEAIKLLYENDFIVIASGGGGIPVVADeigrlegrEAVIDKDLGGQLLASVVDADIFI 238
                                       *************************************9977777777777999988********************* PP

                                       EEESSSSCESSTTTTCCTTCECCEEEHHHCHH..CSSS.TTTHHHHCHHHHHHHHHCTT-EEEEE CS
                         AA_kinase 178 iltdVdGVydadpkkvpdarllpeisvdeaee..saselatgGmkvkhpaalaaarrggipvvIt 240
                                       iltdV+G y + +k +   +ll+e++v+ea++  +++ ++ g+m +k++aa+++a++ g p++I 
  gi|385805932|ref|YP_005842330.1| 239 ILTDVEGAYINYGKPD--QKLLKELKVSEAKKllEQGIFGAGSMGPKVKAAIRFAEKTGKPAYIG 301
                                       ************9776..8**************************************99****96 PP

>> MucBP_2  Mucin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0    0.0045        27      30      51 ..      29      55 ..      16      65 .. 0.72
   2 ?    2.2   0.0     0.044   2.6e+02       7      36 ..     218     256 ..     217     273 .. 0.80
   3 ?    0.5   0.0      0.15   9.1e+02       2      29 ..     285     318 ..     284     319 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0045
                           MucBP_2 30 s.....YstadtikaleaqgYvlvssd 51
                                            Y +a++i  l+++gY++v + 
  gi|385805932|ref|YP_005842330.1| 29 EqwknvYVAAKEIVGLIKRGYKVVVTH 55
                                      344455989999**********98444 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.044
                           MucBP_2   7 yiDdt.tnktltd.......dtltGktgetisY.stadt 36 
                                       +iD++ +++ l++         lt+  g+ i+Y + +++
  gi|385805932|ref|YP_005842330.1| 218 VIDKDlGGQLLASvvdadifIILTDVEGAYINYgKPDQK 256
                                       58999999999998999999999**********665553 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.15
                           MucBP_2   2 katvtyiDdt.tnktltd.....dtltGktgeti 29 
                                       ka +++  +t + + +       d l+Gk+g++i
  gi|385805932|ref|YP_005842330.1| 285 KAAIRFAEKTgKPAYIGHlyklqDILEGKSGTKI 318
                                       68899999997777666666799999*****998 PP

>> DUF4556  Domain of unknown function (DUF4556)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0      0.72   4.3e+03     123     135 ..      38      50 ..      28      52 .. 0.76
   2 ?   10.0   0.0   5.9e-05      0.35      42      90 ..     223     270 ..     204     316 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.72
                           DUF4556 123 pkqrlgLvkrGsy 135
                                        k+ +gL+krG +
  gi|385805932|ref|YP_005842330.1|  38 AKEIVGLIKRGYK 50 
                                       578899****975 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 5.9e-05
                           DUF4556  42 LrGeLvasLeDasLiglevdinattitvqsprqelLqrvevlnteaell 90 
                                       L G+L as+ Da +  +  d++ ++i    p q+lL+  +v++++ +ll
  gi|385805932|ref|YP_005842330.1| 223 LGGQLLASVVDADIFIILTDVEGAYINYGKPDQKLLKELKVSEAK-KLL 270
                                       78***************************************8884.444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); 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: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2361.04
//
Query:       gi|385805933|ref|YP_005842331.1|  [L=190]
Description: hypothetical protein FFONT_0891 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-16   59.5  10.3    3.8e-16   59.2  10.3    1.1  1  DUF998    Protein of unknown function (DUF998)
  ------ inclusion threshold ------
       0.54   10.9   0.2       0.54   10.9   0.2    2.8  4  Renin_r   Renin receptor-like protein
       0.64    9.9   3.4        1.7    8.6   0.0    2.4  2  UPF0139   Uncharacterised protein family (UPF0139)


Domain annotation for each model (and alignments):
>> DUF998  Protein of unknown function (DUF998)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.2  10.3   6.3e-20   3.8e-16       1     170 [.      17     171 ..      17     185 .. 0.83

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 6.3e-20
                            DUF998   1 vaaallalavilaaallrpgydplrhaiSeLgaeggpggwlfnaglvllgllvlalavgllraargragragrllla 77 
                                       ++a l+a+++il+a+ l+p +d+ ++a+S+Lg  g     +fn +l+++ l+++ +  ++l+  +++ g++++++ +
  gi|385805933|ref|YP_005842331.1|  17 IIAFLIAFIGILIAVKLNPWFDVSKNALSDLGRIGLKYSSIFNITLIISSLFAISYIPYMLKLLSNKFGAFSVGVYT 93 
                                       6999**********************************************************9************** PP

                            DUF998  78 vaglglvlagvfptdpgggspslsglvHglasavaflalavavlllasaarrrawallrlvggvallllvaalvwll 154
                                       v+++ l+l+g fp+++           H+++s+ +f+++ +++ll++         l r++++ ++l+l+++ +++ 
  gi|385805933|ref|YP_005842331.1|  94 VGAFHLFLIGMFPEGTK---------FHWFVSLEFFILMSISLLLFS----ITMLTLKRKTSFFLFLILFLLSLLGS 157
                                       *****************.........9********************....33333333333333333333333333 PP

                            DUF998 155 aaaldgslllGlaerl 170
                                       +   +++++++l+e+ 
  gi|385805933|ref|YP_005842331.1| 158 L--FVRWPSTALLEIY 171
                                       3..3677777777765 PP

>> Renin_r  Renin receptor-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       1.8   1.1e+04      63      74 ..      18      29 ..      13      36 .. 0.47
   2 ?   10.9   0.2   9.1e-05      0.54      48      76 ..      51      79 ..      37      89 .. 0.84
   3 ?   -0.3   0.6      0.28   1.7e+03      58      79 ..     116     137 ..     111     140 .. 0.77
   4 ?   -3.3   0.8       2.4   1.4e+04      54      67 ..     170     183 ..     168     185 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.8
                           Renin_r 63 vvlvlaliaivv 74
                                      +++++a i i +
  gi|385805933|ref|YP_005842331.1| 18 IAFLIAFIGILI 29
                                      333333333333 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 9.1e-05
                           Renin_r 48 ssdYpaiFniiLwlvvvlvlaliaivval 76
                                        +Y++iFni L ++ +++++ i  +++l
  gi|385805933|ref|YP_005842331.1| 51 GLKYSSIFNITLIISSLFAISYIPYMLKL 79
                                      568**************999988666655 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.28
                           Renin_r  58 iLwlvvvlvlaliaivvalasm 79 
                                        L + +++ ++l++ +++++++
  gi|385805933|ref|YP_005842331.1| 116 SLEFFILMSISLLLFSITMLTL 137
                                       5778888888888888888765 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 2.4
                           Renin_r  54 iFniiLwlvvvlvl 67 
                                       i+ni +++  +l+l
  gi|385805933|ref|YP_005842331.1| 170 IYNITIYFFGFLIL 183
                                       89999999888876 PP

>> UPF0139  Uncharacterised protein family (UPF0139)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0   0.00029       1.7      29      55 ..      13      39 ..       4      46 .. 0.89
   2 ?    1.1   1.1      0.06   3.6e+02      31      62 ..     123     154 ..     118     175 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00029
                           UPF0139 29 dymnllgmifsllglmlklkwcaWval 55
                                       y ++++++++++g+++ +k+  W+ +
  gi|385805933|ref|YP_005842331.1| 13 KYQGIIAFLIAFIGILIAVKLNPWFDV 39
                                      6999********************876 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.06
                           UPF0139  31 mnllgmifsllglmlklkwcaWvalvcslisf 62 
                                       m++  ++fs++ l+lk k +  + l++ l s+
  gi|385805933|ref|YP_005842331.1| 123 MSISLLLFSITMLTLKRKTSFFLFLILFLLSL 154
                                       55566889999999999999988888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       974  (0.0543254); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); 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):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1138.59
//
Query:       gi|385805934|ref|YP_005842332.1|  [L=88]
Description: hypothetical protein FFONT_0892 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.05   13.7   1.2      0.049   13.8   1.2    1.0  1  GWT1      GWT1
        7.4    6.8   6.9         19    5.4   2.1    2.1  2  DUF872    Eukaryotic protein of unknown function (DUF872)


Domain annotation for each model (and alignments):
>> GWT1  GWT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.2   5.5e-06     0.049      62     110 ..      12      71 ..       1      88 [] 0.62

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.5e-06
                              GWT1  62 illlllllllelyvef..........vSRrlaNlpYvlwvvalnltllllflliel.lfv 110
                                       +ll+ ++l++++++++           S  ++N +Y l+++a ++++l +++ i+  ++ 
  gi|385805934|ref|YP_005842332.1|  12 LLLFSFILAYNSFTNYtlaipsnysdLSSAIINSSYELIILAAKIAFLGIMVWISGiFIK 71 
                                       112222233344444466666666667*************************99994443 PP

>> DUF872  Eukaryotic protein of unknown function (DUF872)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   2.1    0.0021        19      50      70 ..       3      23 ..       1      31 [. 0.87
   2 ?    4.6   0.2    0.0039        35      34      68 ..      38      72 ..      23      77 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0021
                            DUF872 50 llLlllGlvLlllgvvilvep 70
                                      ++Ll +G++Lll +++++ + 
  gi|385805934|ref|YP_005842332.1|  3 IILLSIGIILLLFSFILAYNS 23
                                      89*************998775 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0039
                            DUF872 34 lkhPkvkknrkvvlaallLlllGlvLlllgvvilv 68
                                      l++  +++ +  +++a  + +lG+++ + g++i+ 
  gi|385805934|ref|YP_005842332.1| 38 LSSAIINSSYELIILAAKIAFLGIMVWISGIFIKY 72
                                      56667888889999999999999999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); 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: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 561.51
//
Query:       gi|385805935|ref|YP_005842333.1|  [L=130]
Description: hypothetical protein FFONT_0893 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       818  (0.0456244); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 843.91
//
Query:       gi|385805936|ref|YP_005842334.1|  [L=148]
Description: hypothetical protein FFONT_0894 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        4.5    7.6  13.0       0.64   10.3   8.0    1.9  2  DUF3938   Protein of unknown function (DUF3938)


Domain annotation for each model (and alignments):
>> DUF3938  Protein of unknown function (DUF3938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.4     0.078   1.4e+03      56      72 ..      35      51 ..       5      66 .. 0.57
   2 ?   10.3   8.0   3.6e-05      0.64      20      89 ..      70     142 ..      57     147 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.078
                           DUF3938 56 itnyalvlqlssaffhg 72
                                         +++  ++s  f+  
  gi|385805936|ref|YP_005842334.1| 35 TISFPILKEISPLFYFN 51
                                      23445555555555555 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 3.6e-05
                           DUF3938  20 lllgrlvlflldseesaqktvlltmigivggclsysitnyalvlqlssaf...fhglwawfiafcladvfnll 89 
                                        +l + v+ ++    s    +++ +     g +sysit+ + ++++   f   ++ ++a fi+f l d f ++
  gi|385805936|ref|YP_005842334.1|  70 EILEGTVYSFIVKAISKIIVLMIIFTSFNNGFISYSITQGNSIVNIEINFnplLYLFFAIFITFILLDFFSMI 142
                                       567777777776655555555556667899********88877777776622245667899*********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1029  (0.0573931); 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:                         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 0.32s 00:00:00.78 Elapsed: 00:00:00.50
# Mc/sec: 893.20
//
Query:       gi|385805937|ref|YP_005842335.1|  [L=177]
Description: putative deoxycytidine triphosphate deaminase (dCTP deaminase) [Fervidicoccus fontis Kam940]
Scores for complete 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   74.9   0.0    7.5e-21   74.2   0.0    1.3  1  dUTPase   dUTPase
    9.3e-10   37.8   0.0    1.6e-09   37.0   0.0    1.4  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 !   74.2   0.0   8.3e-25   7.5e-21      16     125 ..      63     168 ..      58     169 .. 0.93

  Alignments for each domain:
  == domain 1  score: 74.2 bits;  conditional E-value: 8.3e-25
                                       EEEE-SSSEEEETTEEEEEEEEEEEE--TTEEEEEEE-HHHHHHHEEEEEEEEETTBTSEEEEEEEE-SSS.-EEE- CS
                           dUTPase  16 yDlsaakdltvkpgetvlvptdisiklpdglaalilpRSglaakglivvpgvidsdyrGevkvvlfnltkk.dvkik 91 
                                       y +++ + ++++p+e+vl+ t  ++klpd+l+a+++ RS +a++gli +p+++d+ ++G  ++++ + +++ +vk++
  gi|385805937|ref|YP_005842335.1|  63 YTIEKGESFVIQPNERVLLNTLEYVKLPDDLMAFVNLRSTFARLGLIAPPTIVDAGFEG--NITIEVVGGAfPVKLH 137
                                       88999******************************************************..99999999999***** PP

                                       TT-EEEEEEEEEBECGEEEEESST.TTESSBTTXT CS
                           dUTPase  92 kgdRiAqLifariltaeleevetl.katergeggf 125
                                       +gdR+ +Lifa++l     +ve++ +  ++g++g+
  gi|385805937|ref|YP_005842335.1| 138 VGDRFIHLIFAKLLS----PVEKPySGDYQGQKGV 168
                                       ***********9998....7777778899999886 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 !   37.0   0.0   1.8e-13   1.6e-09       4     162 ..       2     149 ..       1     170 [. 0.90

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 1.8e-13
                               DCD   4 ilpdqeiealieegaikaeepleeeqiqPaslDLrLgkkayrvrasFlpgkgekvaekleelklheldLtegavlek 80 
                                       il d++++  i+++ i   ep++ee +  + lDLrL+++  r ++   p   ++ a+ l+ +++++++  e+ v++ 
  gi|385805937|ref|YP_005842335.1|   2 ILGDRDLKYYIKTKRI-VIEPFDEEIVRENGLDLRLSNEIARFKSNSEPV--DSKANFLDPFQYYTIEKGESFVIQP 75 
                                       7888999999999999.5689************************98884..566899******************* PP

                               DCD  81 gcvYivplleslaLpadlsaaanpksstGRlDvftRvitdkgeefdeveagYkGplyleisprsFsilvrkGsrLsq 157
                                       +   +++ le ++Lp+dl a +n +s+  Rl ++    +        v+ag++G++ +e++  +F+++++ G+r   
  gi|385805937|ref|YP_005842335.1|  76 NERVLLNTLEYVKLPDDLMAFVNLRSTFARLGLI----APP----TIVDAGFEGNITIEVVGGAFPVKLHVGDRFIH 144
                                       *******************************865....444....35899************************999 PP

                               DCD 158 irfrr 162
                                       + f +
  gi|385805937|ref|YP_005842335.1| 145 LIFAK 149
                                       98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       239  (0.0133304); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1245.29
//
Query:       gi|385805938|ref|YP_005842336.1|  [L=248]
Description: nucleotidyltransferase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-31  108.9   0.0    3.4e-31  108.7   0.0    1.0  1  NTP_transferase  Nucleotidyl transferase
    2.1e-08   34.7   0.0    2.5e-08   34.4   0.0    1.1  1  NTP_transf_3     MobA-like NTP transferase domain


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 !  108.7   0.0   3.8e-35   3.4e-31       1     243 [.       4     234 ..       4     239 .. 0.90

  Alignments for each domain:
  == domain 1  score: 108.7 bits;  conditional E-value: 3.8e-35
                                       EEEEE--S--GGGTTCCTTSSGGGSEETTET.ETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEE CS
                   NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgke.rliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevl 76 
                                       k+vILaGG+G+RLwP++  ++k ++p + +e +l+++ +  l  +gi++ iv+l  ++   +++++++g++f+v++ 
  gi|385805938|ref|YP_005842336.1|   4 KGVILAGGEGKRLWPISYYIQKTMIPLGPEEkPLLEFIIRLLKLNGIND-IVILIGYKGNQIKNYFGNGERFNVNID 79 
                                       79***************************999*****************.999999********************* PP

                                       EEEESS--.BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEE CS
                   NTP_transferase  77 ialepegk.gtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvie 152
                                       ++  +e+  g+A+A+++a      ++  e+vl+  gD+l + +++e++ ++ +++a  ++t++++++ +    G+++
  gi|385805938|ref|YP_005842336.1|  80 YSEDDENYkGSAGALLKAYINGLFND-TENVLIYYGDILGDFNLKEMMMFHSSRNA--DATLMVTEKYN-VPVGIAK 152
                                       **9988766******99876555555.579**************************..78888776655.567**** PP

                                       ECTTSBEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-E CS
                   NTP_transferase 153 adeegrverfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyW 229
                                       +++ +++++++EKP  +     a  Gi + +++ +  + k  +  k+++d ++d++p +++e +  l ++fkd  +W
  gi|385805938|ref|YP_005842336.1| 153 IEN-DKIIELKEKPWLEL---NATIGILTMKTNLISLI-K--KIHKKETDIMSDFIPFLIKENYLILPYFFKD--KW 220
                                       *98.69**********98...5999*999999999988.5..5778889999*********************..6* PP

                                       EEXSSHHHHHHHHH CS
                   NTP_transferase 230 sDvGtldslleane 243
                                        D+G+++ + ++ +
  gi|385805938|ref|YP_005842336.1| 221 YDIGSIERYEKIDK 234
                                       *******9988765 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 !   34.4   0.0   2.8e-12   2.5e-08       1      97 [.       5     117 ..       5     165 .. 0.78

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 2.8e-12
                                       EEEEEESS-TTTTT.....THHHHCC..CCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHH...TTC..TS-EE CS
                      NTP_transf_3   1 aviLAGGrSsRmgg.....dKallpl..ggkpllervldalraagvdevvvvggd..eevlaal...arl..gvrvv 63 
                                       +viLAGG+++R+        K ++pl   +kplle +++ l+  g++++v+  g+  +++++++   +r+  ++++ 
  gi|385805938|ref|YP_005842336.1|   5 GVILAGGEGKRLWPisyyiQKTMIPLgpEEKPLLEFIIRLLKLNGINDIVILIGYkgNQIKNYFgngERFnvNIDYS 81 
                                       79**********6333678*******88899**********************995557777663334444457789 PP

                                       E-TTSS-SHHHHHHHHHHH..H.SSSCEEEEETT-T CS
                      NTP_transf_3  64 ededpgkgplaslaaalra..aadadavlvlacDmP 97 
                                       ed++ +kg +++l+ a  +   +d++ vl+  +D+ 
  gi|385805938|ref|YP_005842336.1|  82 EDDENYKGSAGALLKAYINglFNDTENVLIYYGDIL 117
                                       999999******999997767669********9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1623.89
//
Query:       gi|385805939|ref|YP_005842337.1|  [L=373]
Description: tryptophanyl-tRNA synthetase [Fervidicoccus fontis Kam940]
Scores for complete 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-42  144.3   0.0    5.8e-42  144.0   0.0    1.1  1  tRNA-synt_1b  tRNA synthetases class I (W and Y)


Domain annotation for each model (and alignments):
>> tRNA-synt_1b  tRNA synthetases class I (W and Y)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.0   0.0   3.2e-46   5.8e-42       3     292 ..      68     349 ..      66     350 .. 0.91

  Alignments for each domain:
  == domain 1  score: 144.0 bits;  conditional E-value: 3.2e-46
                                       HS--EEEEEEETSSS-BGGGHHHHHHHHHHHHTTSEEEEEEEHHHHHTTTTT-SSHHHHHHHHHHHHHHHHHHHHHT CS
                      tRNA-synt_1b   3 erplrvysGidPTgklHlGylvplkklvelqkaghevffliaDlhAiigdpskaeerklrkreevlenaikaqlakg 79 
                                        +++++++G++P+gklH G+   + ++++ qk+g ++ + +aD +A+ +++  +  +++r + e++++     +a g
  gi|385805939|ref|YP_005842337.1|  68 GKKVTLLTGFMPSGKLHFGHKALFDQIIYYQKQGFHINLALADIEAYSVRKV-ERKETIRLAIEEYVAN---AIALG 140
                                       67899***********************************************.7899************...***** PP

                                       CHTTTEEEEETHHHHTTHHHHHHHHHHHTTCBHHHHHHHHH..CCHHCSSSC--BHHHHHHHHHHHHHHHHTCHSEE CS
                      tRNA-synt_1b  80 ldpekaevvlqsewlehlelaellrdlgklgslnrmlqfks..vkkrleegegislgeftYplLqaaDilllkadlv 154
                                       l+ +++++++qs+   +  +  l++++++ +++++m+++       ++ +    +++++++p+L +   +  +  +v
  gi|385805939|ref|YP_005842337.1| 141 LEKKNLRIYFQSAT--KPAYYRLIQMFSQKVTMAEMTAIYGdlTPGKIVS-VFTQAADILHPMLEEFGGY--DYVFV 212
                                       ************75..7788888888888888888888887554445544.245899*******987765..888** PP

                                       EEEGGGHHHHHHHHHHHHHHHHHSTTSS-EEEEET-BBSTTSSSBTTCETTCGC-BTTCCHHHHHHHHHHCHCSTTC CS
                      tRNA-synt_1b 155 pgGsDQkqnielgrdlarrfnkkevfkkpegltvplltgldGekKmSKSagnsaIfLddekesvkkkiqkavtdsde 231
                                       p+G DQ+ +i+++rd+ +rf ++  f+ p +++++++tgldG+ KmS+S ++saIfL+d +e v+kk ++a+t  ++
  gi|385805939|ref|YP_005842337.1| 213 PVGADQDPHIRFTRDISDRFSSELGFRRPASTYHRFMTGLDGG-KMSSSRPESAIFLSDPPEIVVKKLNNALTGGRA 288
                                       *******************************************.********************************* PP

                                       ..SHHHHHHHHHTHHHCHHHHHHHHCCSEEESSHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH CS
                      tRNA-synt_1b 232 ..evekllklktelsnelierleavsgkkpkreaeellaeevtklvhggdlkkalaealnell 292
                                         e +k l + +  +  ++e + +++  ++ +++ ++  +++++++ +g+ kk + e++ ++l
  gi|385805939|ref|YP_005842337.1| 289 tiEEQKRLGGEPLKCA-IYEMYLYHLMPND-KDLLDIFMRCRRGELLCGEDKKLAIEKTLKFL 349
                                       8888888888999999.9999999988887.9***********************99998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); 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 0.26s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2448.26
//
Query:       gi|385805940|ref|YP_005842338.1|  [L=57]
Description: hypothetical protein FFONT_0898 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); 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 0.31s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 351.46
//
Query:       gi|385805941|ref|YP_005842339.1|  [L=191]
Description: hypothetical protein FFONT_0899 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       926  (0.0516482); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1256.52
//
Query:       gi|385805942|ref|YP_005842340.1|  [L=231]
Description: triosephosphate isomerase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-11   43.5   0.4    1.1e-07   31.5   0.1    2.0  2  TIM           Triosephosphate isomerase
      1e-06   28.3   0.1    1.5e-06   27.7   0.1    1.3  1  ThiG          Thiazole biosynthesis protein ThiG
      1e-05   24.5   0.2      2e-05   23.6   0.2    1.4  1  Trp_syntA     Tryptophan synthase alpha chain
    1.9e-05   24.2   0.1    3.5e-05   23.4   0.1    1.4  1  His_biosynth  Histidine biosynthesis protein
    9.1e-05   22.0   0.1    0.00013   21.5   0.1    1.3  1  PcrB          PcrB family
    0.00012   21.2   0.0    0.00019   20.6   0.0    1.3  1  FMN_dh        FMN-dependent dehydrogenase
    0.00017   21.1   0.1    0.00021   20.8   0.1    1.2  1  NMO           Nitronate monooxygenase
     0.0034   16.6   0.0     0.0045   16.2   0.0    1.3  1  IGPS          Indole-3-glycerol phosphate synthase
  ------ inclusion threshold ------
      0.021   14.0   0.0       0.04   13.1   0.0    1.4  1  NanE          Putative N-acetylmannosamine-6-phosphate epimer
      0.032   13.2   0.5      0.041   12.9   0.1    1.4  2  IMPDH         IMP dehydrogenase / GMP reductase domain
       0.06   12.8   0.5       0.14   11.6   0.2    1.7  2  G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
       0.11   11.8   0.1       0.18   11.1   0.1    1.3  1  TMP-TENI      Thiamine monophosphate synthase


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 !   31.5   0.1   7.1e-11   1.1e-07       2     122 ..       8     123 ..       7     130 .. 0.81
   2 !   10.5   0.0   0.00018      0.27     158     235 ..     139     211 ..     125     215 .. 0.82

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 7.1e-11
                                       EEEEE-TBTS-HHHHHHHHHH.HHHHCHG.CTSEEEEE--GGGHHHHHHHHTTSSECEEES--BSSSSBS-TT--BH CS
                               TIM   2 liagNwKmnktleeakellkk.lkaklke.ekvevviappflylekvkklleesklklgaqnvsaeksGafTGevsa 76 
                                       +++ N+K + t    ++ll + +++k +   +++++ia+pf+++ +++k +   ++ ++aq v+    G+ TG ++a
  gi|385805942|ref|YP_005842340.1|   8 IFVINYKAYETSYGHQALLIAkASEKAELeFSIKTIIAVPFTEIWRISKEV---SIDVIAQHVDPIIPGQGTGFITA 81 
                                       6788******9998888877634444444689*************988888...5********************** PP

                                       HHHHHTT-SEEEES-HHHHHHST--HHHHHHHHHHHHHTT-EEEEE CS
                               TIM  77 emlkdlgvkyviiGHsErrqlfkEtdelvakKvkaalksglkpilC 122
                                       em++  g k  i+ HsE +  + E     +k +++++ ++l  i+C
  gi|385805942|ref|YP_005842340.1|  82 EMIAGSGGKGSILNHSEHKLKIFEI----EKGIERLKLNNLYSIVC 123
                                       *****************99766654....44455555556666666 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00018
                                       EEEEE--GGGSSSS----HHHHHHHHHHHHHHHHHHSTHHHHTTSEEEEE.SS--TTTHHHHHTSTT--EEEESGGG CS
                               TIM 158 vviAYePvWAiGtgktatpeqaqevhaairkelaekvskevaekirilYG.GsvnkenakellkqkdidGlLvGgas 233
                                        ++A eP   iGtg ++++++ + v +++ k+      ++  +ki+il G G v ke+a++ +k    dG+Lv +  
  gi|385805942|ref|YP_005842340.1| 139 DIVAMEPPDLIGTGVSVSKSKPELVTKTVEKI-----RNSGFKKIPILVGaGIVDKEDARKAIKLG-ADGILVSSII 209
                                       589***************99999999988877.....4556799*****97888999999988765.6999998766 PP

                                       CS CS
                               TIM 234 lk 235
                                       +k
  gi|385805942|ref|YP_005842340.1| 210 MK 211
                                       55 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.1     1e-09   1.5e-06     166     215 ..     166     217 ..     123     227 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1e-09
                                       HHHHHHHH-..SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHH CS
                              ThiG 166 alkiiieea..kvPvivDAGigspsdaaqamelGadavllntavaeakdpva 215
                                       +++ i+++   k+P++v AGi   +da +a++lGad++l+ + + ++k+p +
  gi|385805942|ref|YP_005842340.1| 166 TVEKIRNSGfkKIPILVGAGIVDKEDARKAIKLGADGILVSSIIMKSKEPEK 217
                                       444555443369************************************9965 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.2   1.3e-08     2e-05     178     234 ..     155     214 ..     149     228 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.3e-08
                                       TTSSB-TTHHHHHHHHHHCT..SS-EEEESSS-SHHHHHHHH.TT-SEEEE-HHHHHHHH CS
                         Trp_syntA 178 aenavaaevdelverlkklt..avPvavGFGistkeqvkqva.kvadGvivGSalvkkie 234
                                       ++++  + v ++ve++++    + P++vG Gi +ke++++++  +adG++v S ++k  e
  gi|385805942|ref|YP_005842340.1| 155 VSKSKPELVTKTVEKIRNSGfkKIPILVGAGIVDKEDARKAIkLGADGILVSSIIMKSKE 214
                                       44566778999*****9965549***************9999899********9998765 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.1   2.4e-08   3.5e-05      58     116 ..     160     220 ..     148     226 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 2.4e-08
                                       HHHHHHHHHHHHHH-S..SEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHH CS
                      His_biosynth  58 reanldlveeiaeevf..ipvqvGGGIrsledveelleagadkviigtaavknpelikela 116
                                        e  ++ ve+i+++ f  ip+ vG GI + ed+++++++gad + +++  +k++e  k+++
  gi|385805942|ref|YP_005842340.1| 160 PELVTKTVEKIRNSGFkkIPILVGAGIVDKEDARKAIKLGADGILVSSIIMKSKEPEKKIF 220
                                       455567888888887788*********************************9998777666 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.1   8.6e-08   0.00013     165     224 ..     157     224 ..     121     226 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 8.6e-08
                                       SS-HHHHHHHHHHH.....SSSEEEEESS--SHHHHHHHHCC.SSEEEE-CHHHHHH..HCHHHHHHH CS
                              PcrB 165 ledveevialkkkl.....ekarlivGGGirsaEkAkevvea.ADvivvGnvveekd..erkidaile 224
                                       + ++e+v +++ k+     +k+ ++vG Gi ++E+A++ ++  AD i+v  ++ +++  e+ki +++e
  gi|385805942|ref|YP_005842340.1| 157 KSKPELVTKTVEKIrnsgfKKIPILVGAGIVDKEDARKAIKLgADGILVSSIIMKSKepEKKIFELAE 224
                                       445577777766652222256789*****************************998867788877766 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   1.3e-07   0.00019     198     244 ..     157     206 ..     105     207 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.3e-07
                                       HB-TC--HHHHHHHHHH..HSSEEEE.EEE-SHHHHHHHHHTTESEEEE- CS
                            FMN_dh 198 qldpsltwddikwlreq..tklplvv.KGvltaedakraveaGvdgivvS 244
                                        ++p+l  ++++++r+    k+p++v  G++++eda++a+++G+dgi+vS
  gi|385805942|ref|YP_005842340.1| 157 KSKPELVTKTVEKIRNSgfKKIPILVgAGIVDKEDARKAIKLGADGILVS 206
                                       4578889999999998633579999945*********************9 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   1.4e-07   0.00021     128     231 ..     109     215 ..      39     224 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.4e-07
                               NMO 128 vvarlkeagvvliptissvkearkvearGaDalivqGpeaGGhqGtpevgdkglfaLvp.qvldavd.....iPviA 198
                                        ++rlk  ++  i+ + +     +v+++GaD++ ++ p+  G     +v  k+  +Lv  +v +  +     iP++ 
  gi|385805942|ref|YP_005842340.1| 109 GIERLKLNNLYSIVCAETPRSSLAVANLGADIVAMEPPDLIGTGV--SVS-KSKPELVTkTVEKIRNsgfkkIPILV 182
                                       57788888999999999999999***************9988544..554.344444440444444477789***** PP

                               NMO 199 aGGiidrrgvaaaLalGAsgvqigtrfLltkes 231
                                         Gi+d+++   a+ lGA g+ + +  +  ke 
  gi|385805942|ref|YP_005842340.1| 183 GAGIVDKEDARKAIKLGADGILVSSIIMKSKEP 215
                                       **********************99988888875 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0     3e-06    0.0045     198     254 .]     166     222 ..     125     222 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3e-06
                                       HHHHHCHCC-TTSEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC-TTHHHHHHHH CS
                              IGPS 198 tteeLaklvpkdvllvaeSGiktredveklkeegvnafLvGeslmrqedvekairel 254
                                       t+e+++++  k++ +    Gi ++ed++k  + g++++Lv + +m++++ ek+i el
  gi|385805942|ref|YP_005842340.1| 166 TVEKIRNSGFKKIPILVGAGIVDKEDARKAIKLGADGILVSSIIMKSKEPEKKIFEL 222
                                       4455555555677777889********************************999765 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 ?   13.1   0.0   2.7e-05      0.04      79     181 ..     104     214 ..      93     223 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.7e-05
                                       --HHHHHHHHHHH--EEEEE-SSHHHHHHHHHTT-SEEE-...TTTTSSTTS-.SS--H..HHHHHHHHTT--...E CS
                              NanE  79 vtieelikkikekyqllmaDistleeglvakklGvdivGt...tlsGytkeeekaepDf..alvkalseaglk...v 147
                                        +ie+ i+++k + +  +    t   +l+  +lG+div      l G   + +k++p++  + v+++ ++g+k   +
  gi|385805942|ref|YP_005842340.1| 104 FEIEKGIERLKLNNLYSIVCAETPRSSLAVANLGADIVAMeppDLIGTGVSVSKSKPELvtKTVEKIRNSGFKkipI 180
                                       56777788888777777777778899999999***999863335888877777788876336899999999877668 PP

                                       EEES---SHHHHHHHHTT--SEEEE-HHHH-HHH CS
                              NanE 148 iaeGrintPekakkaieiGvdavvvGsaitrlee 181
                                       ++   i   e a+kai++G+d + v s i + +e
  gi|385805942|ref|YP_005842340.1| 181 LVGAGIVDKEDARKAIKLGADGILVSSIIMKSKE 214
                                       888889999******************9998776 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   0.1       1.9   2.8e+03     168     189 ..      68      88 ..      56     114 .. 0.59
   2 ?   12.9   0.1   2.8e-05     0.041     128     237 ..     159     207 ..     123     225 .. 0.64

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.9
                                       SEEEE-SS-STTBHHHHHCSB- CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 168 davkvGiGpGsiCttrvvagvG 189
                                       d +  G G+G i t  ++ag G
  gi|385805942|ref|YP_005842340.1|  68 DPIIPGQGTGFI-TAEMIAGSG 88 
                                       555555555544.334444443 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 2.8e-05
                                       SSHHHHHHHHHHHHH.TTTSEEEEEEE-SHHHHHHHHHTT-SEEEE-SS-STTBHHHHHCSB---HHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 128 hsekvleavkeikkk.veeveviaGnvataegakaLieagadavkvGiGpGsiCttrvvagvGvpqltAvaevaeaa 203
                                       + e v+++v++i+++ +++                                                          
  gi|385805942|ref|YP_005842340.1| 159 KPELVTKTVEKIRNSgFKK---------------------------------------------------------- 177
                                       4445555555555441233.......................................................... PP

                                       CTCT-EEEEES---SHHHHHHHHHTT-SEEEESC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 204 kkagvpviaDGGikysgdivkAlaaGadavmlGs 237
                                           +p++   Gi  ++d  kA+ +Gad +++ s
  gi|385805942|ref|YP_005842340.1| 178 ----IPILVGAGIVDKEDARKAIKLGADGILVSS 207
                                       ....555555555555555555555555555555 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 ?   -3.1   0.0         3   4.5e+03      29      55 ..      60      86 ..      51      96 .. 0.57
   2 ?   11.6   0.2   9.3e-05      0.14     124     168 ..     160     206 ..     152     209 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3
                                      TTTHHHHHHHHHHTT-EEEEEGGGEET CS
                      G3P_antiterm 29 ilnlkeiveklkkagkkvfvhiDlieG 55
                                      i  + + v+ +   + + f+ +++i G
  gi|385805942|ref|YP_005842340.1| 60 IDVIAQHVDPIIPGQGTGFITAEMIAG 86
                                      344444444444445555555666655 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 9.3e-05
                                       SGGGHHHHCTSTTS.....EEEEESS--SHHHHHHHCTT.SSEEEE- CS
                      G3P_antiterm 124 Pglvpkvikeikke..lkipiiaGGLietkedveealkaGaiavsts 168
                                       P lv k++++i+++   kipi+ G  i +ked ++a+k Ga+++ +s
  gi|385805942|ref|YP_005842340.1| 160 PELVTKTVEKIRNSgfKKIPILVGAGIVDKEDARKAIKLGADGILVS 206
                                       8899999****9996459******9999***************9888 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00012      0.18     112     180 ..     141     208 ..     128     209 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00012
                          TMP-TENI 112 aealgadYigvGpifpTdtKkdaeplgleglkelaealeiPvvaiGGi.tlenvaevleagadgvavvsa 180
                                       ++++ +d ig G    +++K++  +  +e++++   + +iP+ + +Gi ++e++ ++++ gadg+ v s 
  gi|385805942|ref|YP_005842340.1| 141 VAMEPPDLIGTGVS-VSKSKPELVTKTVEKIRNSGFK-KIPILVGAGIvDKEDARKAIKLGADGILVSSI 208
                                       55666777777744.6777777766666666654333.48988888864899*************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); 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: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1532.84
//
Query:       gi|385805943|ref|YP_005842341.1|  [L=466]
Description: Pyridoxal phosphate-dependent aminotransferase [Fervidicoccus fontis Kam940]
Scores for complete 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-109  365.3   0.0   3.6e-109  365.1   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 !  365.1   0.0    2e-113  3.6e-109       8     405 ..      39     446 ..      31     447 .. 0.95

  Alignments for each domain:
  == domain 1  score: 365.1 bits;  conditional E-value: 2e-113
                                       -SCEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT CS
                       Aminotran_3   8 nlllvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklap 84 
                                        ++++itk+eG+ ++d+dg++y+D++ s av n+Gh+hP+vv+a+keq +k+    ++ + +e+ +kla++l++++p
  gi|385805943|ref|YP_005842341.1|  39 YFPIAITKTEGSKVWDADGNEYIDFLTSAAVYNIGHRHPNVVNAIKEQTEKVLNYTIAYFYEENPVKLAKYLIEITP 115
                                       3459************************************************99999******************** PP

                                       -..S.EEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE CS
                       Aminotran_3  85 kgld.kvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrl 160
                                       ++++ kv +  sGs++v  AlK+ar+      +++k+ ii+f g++HG t+gals+tg  ++  ++    + +v ++
  gi|385805943|ref|YP_005842341.1| 116 GSFEkKVAFGFSGSDSVDIALKVARA------YKKKKGIISFYGSYHGTTYGALSATGIIDPQLKDTVFPSKDVLFV 186
                                       ***98999******************......8999**********************97766666666699***** PP

                                       -TTBGGGTB-HH.......HHHHHHHHHHHHHHCHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEE CS
                       Aminotran_3 161 kypdeevlkene.......eeeaalleelealekkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvlli 230
                                       +ypd+++ + n        e ++ +le +e+ +k  +++v+Avi+Epiqg++Gv+v++++f+++lr+l++++++lli
  gi|385805943|ref|YP_005842341.1| 187 EYPDPYRNPWNIdgyedplELSNIALENIEKKIKNVNEDVSAVIFEPIQGDAGVIVPPKGFIEGLRKLAQNYNILLI 263
                                       ********9998788767666777777888877999***************************************** PP

                                       EE-TTTTTTTTSSSSGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTSB--TTTT-HHHHHHHHHHHHH CS
                       Aminotran_3 231 vDEvqtGfGrTGklfAlehagvspDlmtlaKaltgGlplsavlataevmqalapgshgsTfgGnplacavalavlei 307
                                         Evq+G+GrTGk++A+eh++++pD++++aKal+gG+p+sav++++e+ + + p     T +G  + +++a+a++e+
  gi|385805943|ref|YP_005842341.1| 264 DEEVQSGMGRTGKWWAIEHYNIEPDILISAKALGGGMPISAVIGKKEIIDSIPPPLLVFTHTGHAINASAAIATIET 340
                                       ***************************************************************************** PP

                                       HHHTTHHHHHHHHHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTC......HHHHHHHHHCTEE-EEET CS
                       Aminotran_3 308 ieeekllenaqelgaalkegLeelqkkyevikevRgkGlmiaielkeeaevke......keilkkakekGvlilsaG 378
                                       i++e l+++a elg++  ++ +e+++k   i+++RgkGlmi+i+++++ + ke       +i+ +a ekG++++++G
  gi|385805943|ref|YP_005842341.1| 341 IKKEGLIKKAYELGNYAIKRFREMSEKFSIIGDIRGKGLMIGIDIVKNTKLKEpdkslaLKICWRAWEKGLILITFG 417
                                       **************************************************9999*****99**************** PP

                                       T..TEEEE---TT--HHHHHHHHHHHHHH CS
                       Aminotran_3 379 d..nvirllppliitdeeidelleilkka 405
                                       +  nv+r++ppl i  +e+d+++ei+++ 
  gi|385805943|ref|YP_005842341.1| 418 KygNVLRIAPPLNIDINELDKGIEIIEES 446
                                       **************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.50
# Mc/sec: 2776.45
//
Query:       gi|385805944|ref|YP_005842342.1|  [L=332]
Description: dihydrodipicolinate reductase [Fervidicoccus fontis Kam940]
Scores for complete 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-09   36.6   0.2    8.3e-09   35.6   0.2    1.5  1  DapB_N         Dihydrodipicolinate reductase, N-terminus
     0.0016   18.7   0.7     0.0086   16.4   0.5    2.3  2  Gp_dh_N        Glyceraldehyde 3-phosphate dehydrogenase, NAD 
     0.0017   17.8   0.2     0.0031   16.9   0.2    1.3  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
  ------ inclusion threshold ------
      0.019   15.6   1.6      0.062   14.0   1.6    2.0  1  PglD_N         PglD N-terminal domain
      0.072   13.7   0.3       0.18   12.4   0.3    1.7  1  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent


Domain annotation for each model (and alignments):
>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.2   2.3e-12   8.3e-09       1      95 [.       4      96 ..       4     101 .. 0.87

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 2.3e-12
                                      EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH-SEEEE-S..-H CS
                            DapB_N  1 ikvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavtddleevlekadvliDFT..tp 77
                                      ik++++G+ G +Gk v++++ e +++e+++avd ++ e+ +kd+ge++g++k+g +vt++l+ +le++dv+i  T    
  gi|385805944|ref|YP_005842342.1|  4 IKLGIYGF-GAIGKLVANVALE-RGYEISGAVDVNK-EILDKDIGEIVGKEKIGAKVTNNLN-ILENSDVIIHTTgsFL 78
                                      799*****.**********999.***********98.9********************9995.7889*****9983334 PP

                                      HHHHHHHHHHHHTT-EEE CS
                            DapB_N 78 eavlenlklalekgvklV 95
                                      ++v e l+ +++ g ++V
  gi|385805944|ref|YP_005842342.1| 79 DSVFEQLANIIKLGLPIV 96
                                      677777777777777776 PP

>> Gp_dh_N  Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.5   2.4e-06    0.0086       1      33 [.       4      39 ..       4      72 .. 0.77
   2 ?   -0.9   0.0       0.6   2.1e+03      87     100 ..      66      79 ..      48      80 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.4e-06
                                      CEEEEESTSHHHHHHHHHHHHHT.TCE.EEEEE-.T CS
                           Gp_dh_N  1 vkvainGfGRIGrlvlralleek.ele.vvaind.l 33
                                      +k++i+GfG IG+lv+ ++le+  e++  v +n+ +
  gi|385805944|ref|YP_005842342.1|  4 IKLGIYGFGAIGKLVANVALERGyEISgAVDVNKeI 39
                                      699*****************7765443267777744 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.6
                                       TSSEEEE-SSS--S CS
                           Gp_dh_N  87 gvdlVvestGvftd 100
                                       + d+++ +tG f d
  gi|385805944|ref|YP_005842342.1|  66 NSDVIIHTTGSFLD 79 
                                       56999*****9976 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 !   16.9   0.2   8.6e-07    0.0031      38      96 ..       5      71 ..       3      76 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 8.6e-07
                                      EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH........CHHHHTCEECSHHHHHHH-SEEE CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmkviaydrskkkee........eeeelgvelvsleellaesDivs 96
                                      ++Gi G+G+IG+ va+++ + g ++ +    +k+           +e+ g+++++  ++l++sD+++
  gi|385805944|ref|YP_005842342.1|  5 KLGIYGFGAIGKLVANVALERGYEISGAVDVNKEILdkdigeivGKEKIGAKVTNNLNILENSDVII 71
                                      79***********************986555553223345666677888999999999999999987 PP

>> PglD_N  PglD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.6   1.7e-05     0.062       1      46 [.       5      55 ..       5      76 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.7e-05
                            PglD_N  1 kivIiGaGGhgkvvadiieangeyeiigflDdnkkteveg......ypvlgk 46
                                      k+ I+G G  gk va+++  +g yei g +D nk+   ++       + +g 
  gi|385805944|ref|YP_005842342.1|  5 KLGIYGFGAIGKLVANVALERG-YEISGAVDVNKEILDKDigeivgKEKIGA 55
                                      577*******************.*********99743332112122444443 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 ?   12.4   0.3   5.1e-05      0.18       1      67 [.       5      72 ..       5      97 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.1e-05
                                      EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC....-EEECECHHHHHHH-SEEEE CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg....vkvtavdneeaaeeadvvvl 67
                                      k+gi G+G +g+ +a+ +l++g   +ei  a + n+e +++   e+     ++++ ++n   +e++dv++ 
  gi|385805944|ref|YP_005842342.1|  5 KLGIYGFGAIGKLVANVALERG---YEISGAVDVNKEILDKDIGEIVgkekIGAKVTNNLNILENSDVIIH 72
                                      68999*****************...****77777777776655444468888888888**********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 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:                        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: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2194.21
//
Query:       gi|385805945|ref|YP_005842343.1|  [L=349]
Description: exopeptidase, family M19 [Fervidicoccus fontis Kam940]
Scores for complete 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-77  260.7   0.0      2e-77  260.5   0.0    1.0  1  Peptidase_M19  Membrane dipeptidase (Peptidase family M19)


Domain annotation for each model (and alignments):
>> Peptidase_M19  Membrane dipeptidase (Peptidase family M19)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  260.5   0.0   1.1e-81     2e-77       4     318 ..      10     345 ..       7     346 .. 0.92

  Alignments for each domain:
  == domain 1  score: 260.5 bits;  conditional E-value: 1.1e-81
                                       CCS.EEEEEE-HHHHHHHCTTTTT....-TTTHCTSSS-HHHHHHHTEEEEEEEEE--C.................. CS
                     Peptidase_M19   4 kkliviDghndlplklrqekkesl....llekdselqtdlerlraggvsavlfaifvpe.................. 58 
                                       ++l++iD h d++ ++   ++  +    + e+    + d++++++g+v +v+ aif+                    
  gi|385805945|ref|YP_005842343.1|  10 ESLPIIDHHEDVSSYFLYPGEGGApygnFGEDIPGREADIPKYKRGKVRCVFSAIFPGIetfrpeeskelekiygkw 86 
                                       7899***********99999988899977777788899******************44477**************** PP

                                       ..CCCCCCHHHHHHHHHHHHHHHHHHGTTTEEE-SSHHHHHHHHHTT-EEEEEEEESCGGGTT-HHHHHHHHHTTEE CS
                     Peptidase_M19  59 ..dasyeeavkatleqidlirrlvrknpeqlklvrtaddierakkegkiavllgiegaealgddlallrafyalGvr 133
                                         ++ y+       e ++++++l  +++  +k+v++++d+e+  ke+++ ++l++egaeal d+   l  +++ G+r
  gi|385805945|ref|YP_005842343.1|  87 lpATGYRVPQALLWEHVSIYYKLSDAYK--IKIVERVEDVESCIKEERLCFVLHLEGAEAL-DEPYDLVLLKKIGLR 160
                                       *655555555556677777777777666..9******************************.7888899******** PP

                                       EEES-SSS-BSSB-BCCGTT.SSSSB-HHHHHHHHHHHHHT-EEE-TTB-HHHHHHHHHH-SSE.EECCEEBTTTS- CS
                     Peptidase_M19 134 vlgltynrnnkfAdgaleekdedgGLsefGkelVrelNrlgiliDlShlsektfldvlelSkaPvvaSHSnaralcd 210
                                       ++g+t+n+ nk+++g+  +  +d GLse+G+elV+ +Nrlgi++Dl+h+s+kt+ +++e+Sk+Pv++SH+n+r+l d
  gi|385805945|ref|YP_005842343.1| 161 SIGITWNYVNKYGTGCGAK--KDTGLSEMGEELVKMANRLGIIVDLAHASKKTSVEAIEISKRPVMISHANVRKLID 235
                                       ******************9..******************************************************** PP

                                       -TTSB-HHHHHHHHHTT-EEEE-SSHHHCTTTS--BHHHHHHHHHHHHHHT-GGGEEE---T...TTTSS-BBTBSS CS
                     Peptidase_M19 211 hpRNltDeqlkaiaesgGvvgvtfvpaflkekaeatledvvdhidyivelaGidhVGlGsDf...dgggelpegled 284
                                        +RN++De l+++ ++gG++g  +++  +++ +++tl+++vdh+ y+ e +G++++++G+Df    g +  pegle+
  gi|385805945|ref|YP_005842343.1| 236 RSRNVDDELLELLHKNGGILGFSVIGPLISNRPRPTLDELVDHVMYVYENYGAENIAIGTDFlglMGLP-SPEGLES 311
                                       **************************************************************5533333.49***** PP

                                       GGGHHHHHHHHHHTTS-HHHHHHHHTHHHHHHHH CS
                     Peptidase_M19 285 vsklpnltaeLlrrgyseadiekilggNflrvle 318
                                       v+klpnl+++L+++g +++d++k++++N lr+++
  gi|385805945|ref|YP_005842343.1| 312 VDKLPNLLEKLAEKGMNDSDVRKVAYENSLRLMR 345
                                       *******************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2207.01
//
Query:       gi|385805946|ref|YP_005842344.1|  [L=486]
Description: amino acid transporter [Fervidicoccus fontis Kam940]
Scores for complete 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-35  122.4  54.6    2.6e-35  122.1  54.6    1.0  1  AA_permease_2  Amino acid permease
    2.4e-26   92.4  49.2    3.2e-26   92.0  49.2    1.1  1  AA_permease    Amino acid permease


Domain annotation for each model (and alignments):
>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.1  54.6   2.9e-39   2.6e-35       1     423 [.       9     440 ..       9     446 .. 0.86

  Alignments for each domain:
  == domain 1  score: 122.1 bits;  conditional E-value: 2.9e-39
                     AA_permease_2   1 lsllsafalvigsvig.sgifvkn...laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafg 73 
                                       ls+ +++al    +ig s  ++ +   +++ +g +++ + +++ +++   v+l+yaE++s++p+ gG++ ++  + g
  gi|385805946|ref|YP_005842344.1|   9 LSWPQLLALGAAGIIGtSWAYMNTrfySIYGPGGVILGYAIGTLMAF--LVALAYAEMGSTIPKAGGEVAFVFPTLG 83 
                                       7899999999999999444565558888999**99999999888887..6********777**************** PP

                     AA_permease_2  74 kkvaflsawfnwfayvpvlasilsvaasyllnalgpdlqgn..........twltyliaiaililvalinirgikes 140
                                       ++  f+++w++ ++ v++ a+  ++++s ll+++ p+l++             +++l++i   il+ ++n+r+++ +
  gi|385805946|ref|YP_005842344.1|  84 PLGSFFVGWMFILSSVLAGAAFYVIGISLLLSWWLPSLYTIpiysiagvpvYLPALLLGITSAILILILNYRSVSLT 160
                                       ************************************88766888889998844555555666666679********* PP

                     AA_permease_2 141 akiqnilgilkillpliiliilglitvdgggfsslstetdtffpngwpgvllgl...livlwsfdGfesaanvseev 214
                                       + +q i++i+ + l  ++++i++l+ ++++ f      + + fp+g +   lgl   li++ +++Gfe+    +ee+
  gi|385805946|ref|YP_005842344.1| 161 GQAQLIMFIMLL-LAGATILITALFKGSISNFA-----NPSPFPQGENPLGLGLrfgLISIGYLSGFEGLPALAEEI 231
                                       ************.68899999999999888887.....889****9997666554456789999************7 PP

                     AA_permease_2 215 k.k.kdvpkaifigllivlvlyllvniaflgvvpddeianlsnlgsvaalffeavggk.vvaiivvilialsllgai 288
                                       k k +++ ++i  ++l+++ +y+ +++a    vp+ +   ++  g +++l+ +    + ++  i++++ +l+l+ + 
  gi|385805946|ref|YP_005842344.1| 232 KiKpRTFGLVIAGSVLVAGAFYMTMMFAGSLFVPWQQSYAIAHRG-TIELMSRY---SiWLGLIAWLASFLGLVTSW 304
                                       75569******************************9995555433.45555555...44****************** PP

                     AA_permease_2 289 ntavigssrvlealardgvlPrffakvn.kfgspiraiiltaivslillllfllassaaynfllsvsslgliisyll 364
                                       +  v+++sr+++alar+g +P+ f +++ k+g+p+ a+i++ i+s+i++  +l+  +  + + l++s +gl  ++ll
  gi|385805946|ref|YP_005842344.1| 305 IPTVMTTSRMVFALAREGLFPSQFERIHpKYGTPTIALIFVTIISIIFG--SLG--EQGLIWFLDISGVGLGTCWLL 377
                                       *********************************************7765..433..89******************* PP

                     AA_permease_2 365 liigalilrkkrphlkr....pgkilvaiigalfllfllvalffppkgpatqssliytiiltv 423
                                         +++++ r+k p+ +r    p+ +lv+i+g  ++l ++ + ++p+  ++   +  y+i++++
  gi|385805946|ref|YP_005842344.1| 378 STLSMILTRRKYPNIPRyfkvPAGYLVGILGSGITLTVILVSIIPGTSLSLVWPYEYMILILW 440
                                       ***************9976666669********************999987666666644443 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.0  49.2   3.6e-30   3.2e-26       8     470 ..      20     456 ..      13     464 .. 0.81

  Alignments for each domain:
  == domain 1  score: 92.0 bits;  conditional E-value: 3.6e-30
                       AA_permease   8 ggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGlnylf 84 
                                       +g+iGt     +    s  Gp+g++l+y++++++ flv+l+ +e+ + +pk+gg  +++  +lgp  +f++G+++ +
  gi|385805946|ref|YP_005842344.1|  20 AGIIGTSWAYMNTRFYSIYGPGGVILGYAIGTLMAFLVALAYAEMGSTIPKAGGEVAFVFPTLGPLGSFFVGWMFIL 96 
                                       6788888888888888889*******************************************************877 PP

                       AA_permease  85 swi.tvlaleltaasiliqfwelvtdlpkawvt..............gavflvvlliinlvgvkvygeaefilalik 146
                                       s++ +++a+ ++++s l+++w  +++l ++ ++              g+   +++li+n+ +v + g+a++i+++++
  gi|385805946|ref|YP_005842344.1|  97 SSVlAGAAFYVIGISLLLSWW--LPSLYTIPIYsiagvpvylpalllGITSAILILILNYRSVSLTGQAQLIMFIML 171
                                       77615678899999*******..888887777789***********9988899999****************99999 PP

                       AA_permease 147 iiaiiafiivgiillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiag 223
                                       ++a +  +i     l++g  +++       +n s     +p+g   e+   +   +++++i ++  +G+e ++++a+
  gi|385805946|ref|YP_005842344.1| 172 LLAGATILITA---LFKGSISNF-------ANPS----PFPQG---ENPLGLGLRFGLISIGYL--SGFEGLPALAE 229
                                       99888777777...455555555.......3444....58888...555556666777777765..6********** PP

                       AA_permease 224 EvkdPeksiPkailqvviritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaa 300
                                       E+k   ++   +i   v+  + fY  ++++ +l vp++    +++         i ++++ ++ l+ +  +++++ +
  gi|385805946|ref|YP_005842344.1| 230 EIKIKPRTFGLVIAGSVLVAGAFYMTMMFAGSLFVPWQQSYAIAHRG------TIELMSRYSIWLGLIAWLASFLGL 300
                                       ***************************************99999655......345666677788888899999*** PP

                       AA_permease 301 lssansslysasRvlyslakdglaP.kvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisalig 376
                                       + s +  ++++sR++++la++gl+P  + + + k+g P  a+++++iis ++  l +  l+      ++l is++  
  gi|385805946|ref|YP_005842344.1| 301 VTSWIPTVMTTSRMVFALAREGLFPsQFERIHPKYGTPTIALIFVTIISIIFGSLGEQGLI------WFLDISGVGL 371
                                       *************************8888899*********************99999999......********** PP

                       AA_permease 377 livwlliilsylrfRkalkyqgrsieelgfkaallplgvilvlaaliiillilalyayltvkkgpkdwgaasfaaay 453
                                         +wll+ ls +  R+++    r    +++ a +      lv ++ + i+l++ l+ +++       w ++++++  
  gi|385805946|ref|YP_005842344.1| 372 GTCWLLSTLSMILTRRKYPNIPR---YFKVPAGY------LVGILGSGITLTVILVSIIPGTSLSLVWPYEYMILIL 439
                                       ************99999443333...33333333......3333333333333344444433333347888888777 PP

                       AA_permease 454 livllfliilvgvklhv 470
                                        ivl ++i+ +++  + 
  gi|385805946|ref|YP_005842344.1| 440 WIVLGMIIYPFAKRRMN 456
                                       77777777666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (486 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       842  (0.046963); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.45
# Mc/sec: 3236.56
//
Query:       gi|385805947|ref|YP_005842345.1|  [L=280]
Description: exopeptidase, family M55 [Fervidicoccus fontis Kam940]
Scores for complete 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-78  261.4   0.0    9.6e-78  261.2   0.0    1.0  1  Peptidase_M55  D-aminopeptidase


Domain annotation for each model (and alignments):
>> Peptidase_M55  D-aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  261.2   0.0   5.4e-82   9.6e-78       2     263 ..       3     265 ..       1     266 [. 0.99

  Alignments for each domain:
  == domain 1  score: 261.2 bits;  conditional E-value: 5.4e-82
                     Peptidase_M55   2 kvyISaDiEGvagvvsweqvepgeaeyerarrlmteevnaaiegalaagatevlVnDsHgsmrNllpeeLdervrli 78 
                                       k ++S+D+EG+  +v++ q+++g++ +e++rr+  e   aa+++++++g++ev+V+DsH++m N+ +e+L++ + l+
  gi|385805947|ref|YP_005842345.1|   3 KAFLSVDLEGLPFIVNRGQLSTGNPLWEEGRRIASELTYAAVKAIHDEGFDEVIVADSHADMINIYYERLPKYAYLV 79 
                                       78*************************************************************************** PP

                     Peptidase_M55  79 sGkpkplsmmegldesfdavlfvGyHaragtekgvlaHTysgsaieevrlngkevgEfglnaalagelgVPvvlvsG 155
                                       +G+p+p sm++g  e++ a++f+GyHa  gt++++ +H++s+++i+e+rln ++++Ef +n+++ ge+g+Pv++v+G
  gi|385805947|ref|YP_005842345.1|  80 RGYPRPRSMITGA-EGCSAAFFLGYHAGVGTKDATYDHSFSSATIKELRLNSEKTSEFIFNTLALGEIGIPVIFVAG 155
                                       ************5.9************************************************************** PP

                     Peptidase_M55 156 Ddalceeakellpevetvavkeglgrfaakslspeeaeeaireavkeavekake..akplkleepvelevefkstal 230
                                       D+al e++++++p++++v++k+++gr++++s s+e+++e++ ++vkeav++ ++  a++ ++++pv+++++f  + +
  gi|385805947|ref|YP_005842345.1| 156 DEALREDVEKFAPWAVFVPLKKSYGRYSSISPSIEKLNEDLAQGVKEAVRRMSNgeANVASIDKPVNVKIDFLYSGY 232
                                       ***************************************************999889******************** PP

                     Peptidase_M55 231 Adaaslvpgveridartvefeaedveellrale 263
                                       A++a+++p v+r++a+ +e+ +++v e+++++e
  gi|385805947|ref|YP_005842345.1| 233 AEVAEYLPFVKRVSATAIEYISNSVLEAYNIME 265
                                       *****************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); 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 0.31s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1647.75
//
Query:       gi|385805948|ref|YP_005842346.1|  [L=432]
Description: amidinotransferase [Fervidicoccus fontis Kam940]
Scores for complete 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  172.1   0.3    3.3e-50  171.1   0.3    1.5  1  Amidinotransf  Amidinotransferase
  ------ inclusion threshold ------
       0.01   15.1   0.2       0.18   11.0   0.2    2.3  1  PAD_porph      Porphyromonas-type peptidyl-arginine deiminase


Domain annotation for each model (and alignments):
>> Amidinotransf  Amidinotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.1   0.3   3.7e-54   3.3e-50       1     340 []      15     431 ..      15     431 .. 0.87

  Alignments for each domain:
  == domain 1  score: 171.1 bits;  conditional E-value: 3.7e-54
                                       E----HHHHT--TTTTTTTT-SS---HHHHHHHHHHHHHHH.HTTT-EEEEHHHHHHHHCTSHHHHHHHHHHHSSTT CS
                     Amidinotransf   1 mvrPgrflenltetasdnllqddeiilekaqkEHdafvqvL.rekGveVlvledllaealeaeearkekldeklles 76 
                                       m+rPg +++    ++   l+ d+++ +++a +EH+ +   L  e  v+V+ l+d   +  e+++++ke+l ++  e+
  gi|385805948|ref|YP_005842346.1|  15 MHRPGIEMFFSLIEPYASLY-DRAFSQNEALREHERLEHILmHEFRVDVIRLKDFILQEAERSSKVKEELVKM-AEE 89 
                                       9*********9999999999.****************99872678*********7553333333333333222.222 PP

                                       TTITTT...........................GGGS-S-HHHHHHHHHHHHH----EEE---GGGG-TTTTEEEEB CS
                     Amidinotransf  77 elgikl...........................gvklseeikiekleladkatsnnsflipplpnlvFtrdwfstig 126
                                       +++  +                           + +l++++  ++++  ++a   n  + +pl nl+F+rd+++ ++
  gi|385805948|ref|YP_005842346.1|  90 RVE--FrgdeedvkmakdefsrykdiydsefffNLILLSPKVTLERGRGERAIYYNVTVREPLGNLYFMRDQQAVTD 164
                                       222..2446788********************9888888888888888888889999999***************** PP

                                       SEEEE---SSGGGHHHHHHHHHHHHHSHTSB-EEEEE-TTS--TT----GGGEEEEETTEEEEEESSSS-HHHHHHH CS
                     Amidinotransf 127 ggvvlnpmaapnRrrErllaeliykkhpgvkvakvldisgkeeesktlEGGdfvvlskgvvaigvssRtdeegieel 203
                                       +g++l +m +p+RrrE++++++ +k       + v++i++    ++t+EGGdf++++++ ++ g + Rt++egie++
  gi|385805948|ref|YP_005842346.1| 165 KGIILSRMSKPQRRRETQVTKFLWKL---MGEEIVHEIKE----PGTFEGGDFIPMKDFALI-GTGDRTNQEGIEQI 233
                                       **************************...66788999996....************998776.************** PP

                                       HHHHHHT...TS-SEEEEEE--GGSS....TS-GGGTEEEEETTEEEE-HHHH.TT-E.............SS-HHH CS
                     Amidinotransf 204 akklfyk...tvafkviaieipkgra....imHldtvftvvdddavvclpsildaegv.............kakere 260
                                        k+  +     v+++     ip ++      mHldt f+v +++ v+ ++  l+++++             + +++ 
  gi|385805948|ref|YP_005842346.1| 234 LKHGVSFdevAVVHQPAHPLIPGDQTdpmiNMHLDTYFNVPSSNVVIGCDTLLKRAKIdvyikesegnyrkEEERNL 310
                                       *985443336777777777777666544446**********************99977***********98888888 PP

                                       HHHHHTT-SS-EEEE-CS-SS-B---S-EEEETTEEEEETTGHHHHHHHHHT......................... CS
                     Amidinotransf 261 avaqaLkekgleiIeigeeeqwnfggNvLelkpgvvvaydrntvtnekleea......................... 312
                                        +++ +kekg+eiI i+  eq+ +++N+L++k+g ++a +     +++l                            
  gi|385805948|ref|YP_005842346.1| 311 NLYDYIKEKGFEIINITTLEQMSYASNFLTIKDGTILAIETERIVKRTLANLeasarlnperygklleqakkdyehl 387
                                       9***********************************9998888888888777778999999999999999******* PP

                                       ................T-EEEEE-HTTTGGGS--TTTT-EEEEE CS
                     Amidinotransf 313 ................gievievpiselerGgGgarCmsaplfr 340
                                                       gi+v +v++++l+ G+Gga+Cm+++l+r
  gi|385805948|ref|YP_005842346.1| 388 knegqffphkkemyknGIDVYTVDLTNLTGGYGGAHCMTCSLRR 431
                                       *****************************************987 PP

>> PAD_porph  Porphyromonas-type peptidyl-arginine deiminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2     2e-05      0.18     160     316 ..     225     427 ..     220     429 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 2e-05
                                       S-HHHHHHHHHHHHT-SEEEEESS-....STTTT....SSS-GGGTEEEEETTEEEEEE..........-S-TTSTT CS
                         PAD_porph 160 lskeeieaeLkellgvekviwlkeG....lagdd....tdgHiDtlarfvapgtvllar..........eddeeden 218
                                        ++e ie+ Lk+ +  ++v +++++    + gd+     + H Dt+ ++ ++++v+ +             +e++ n
  gi|385805948|ref|YP_005842346.1| 225 TNQEGIEQILKHGVSFDEVAVVHQPahplIPGDQtdpmINMHLDTYFNVPSSNVVIGCDtllkrakidvYIKESEGN 301
                                       56888999999999999999997653335566765566677999999999999999888788766654433344444 PP

                                       HHHHHHHHHHHHTTB-TTSSB-EEEEEEB-S--EEEE--BTT.--EEETTEEEEEE-SST................. CS
                         PAD_porph 219 yealkealeiLkaatdakgrklevvelplpeevrerlpasYa.Nflivngavlvptfgde................. 277
                                       y+  ke ++ L+     k++ +e++++ + e      ++sYa Nfl+++++ ++    ++                 
  gi|385805948|ref|YP_005842346.1| 302 YR--KEEERNLNLYDYIKEKGFEIINITTLE------QMSYAsNFLTIKDGTILAIETERivkrtlanleasarlnp 370
                                       44..455556666666777888888888764......3455446665555544444444445555555666666666 PP

                                       ..........TCHHHHHHHHHHHSTTS........EEEEEETTTGGGGS--TGGGEE CS
                         PAD_porph 278 ..........ekDekAleilqelfpdr........evvgvdaralvlggGsiHCitq 316
                                                 +kD + l+   + fp++        +v +vd ++l  g+G+ HC+t 
  gi|385805948|ref|YP_005842346.1| 371 erygklleqaKKDYEHLKNEGQFFPHKkemykngiDVYTVDLTNLTGGYGGAHCMTC 427
                                       6666667777889999999999999887777777799*****************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 2685.98
//
Query:       gi|385805949|ref|YP_005842347.1|  [L=336]
Description: ornithine carbamoyltransferase [Fervidicoccus fontis Kam940]
Scores for 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  194.6   0.0    1.6e-57  193.9   0.0    1.3  1  OTCace           Aspartate/ornithine carbamoyltransferase, As
    5.2e-53  179.0   0.0    8.2e-53  178.4   0.0    1.3  1  OTCace_N         Aspartate/ornithine carbamoyltransferase, ca
  ------ inclusion threshold ------
      0.068   12.6   0.0       0.12   11.8   0.0    1.3  1  Glyco_hydro_101  Endo-alpha-N-acetylgalactosaminidase


Domain annotation for each model (and alignments):
>> OTCace  Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.9   0.0   2.8e-61   1.6e-57       1     155 [.     179     332 ..     179     334 .. 0.99

  Alignments for each domain:
  == domain 1  score: 193.9 bits;  conditional E-value: 2.8e-61
                                       CC.EEEEESSTTSHHHHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEEE CS
                            OTCace   1 kglkiafvGdkknnvanslikllarlgmdvvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvyt 77 
                                       +gl+++f+Gd+ nn++ns++ + a++gm+++++ Pkg+ pd+++l++a ++akk+g++i+i +d++ea+k+aD++yt
  gi|385805949|ref|YP_005842347.1| 179 EGLNFVFIGDG-NNMCNSWLLGSAIVGMNMTAAIPKGYYPDQKILDKALEIAKKTGSKIKIVNDPKEAAKDADILYT 254
                                       5899*******.***************************************************************** PP

                                       --SSETTCCGGHHHHHHHHCCCSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHHHHHHHH CS
                            OTCace  78 dvwvsmgeekereerlkklkdyqvteellklakkdaivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlhtikAll 154
                                       dvwvsmg+eke e+r+k++++yq+++ell+lakkd++v+HcLPa+rg E+td+V+++++s+v+ qaeN+l+ ++A+l
  gi|385805949|ref|YP_005842347.1| 255 DVWVSMGQEKETEKRMKDFQGYQINKELLRLAKKDVVVMHCLPAHRGLEITDDVIEGEQSIVWVQAENKLYGAAAVL 331
                                       ****************************************************************************9 PP

                                       H CS
                            OTCace 155 v 155
                                        
  gi|385805949|ref|YP_005842347.1| 332 E 332
                                       6 PP

>> OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.4   0.0   1.4e-56   8.2e-53       1     148 []      33     173 ..      33     173 .. 0.98

  Alignments for each domain:
  == domain 1  score: 178.4 bits;  conditional E-value: 1.4e-56
                                       S-BSSGGGS-HHHHHHHHHHHHHHHHHHHTTT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTTTS CS
                          OTCace_N   1 rhllsledlskeeieelldlaaelkekvkkekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseaedi 77 
                                       ++lls++dlsk+ei+e+ld+a+elk+++k++++ ++lk+k+++llFe+pStRTr+SfevAa rlGg++++ls a+++
  gi|385805949|ref|YP_005842347.1|  33 KSLLSVADLSKDEINEILDRAKELKKSIKSRQELNILKNKVVGLLFEKPSTRTRTSFEVAALRLGGSAVYLS-ANEL 108
                                       689*********************************************************************.889* PP

                                       CTTTGGSTTSSCHHHHHHHHHHHTSEEEEEESSHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHHHHHH CS
                          OTCace_N  78 qlssvskgrkEsleDtarvlsryvdaiviRhpgaeeleelakyasvpviNagdgdgeHPtQaLaDlltire 148
                                       qls     r+E+++Dtar+l+++ daiv+R+++++++ elakya+vpviN++ +d eHPtQ+L D+lti e
  gi|385805949|ref|YP_005842347.1| 109 QLS-----RGEPIKDTARILGSFLDAIVARVYSHNTVVELAKYANVPVINGL-SDLEHPTQILSDMLTIIE 173
                                       **9.....77************************9*****************.***************986 PP

>> Glyco_hydro_101  Endo-alpha-N-acetylgalactosaminidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0     2e-05      0.12     151     214 ..     232     294 ..     215     301 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2e-05
                                       TT.HHHHHHHHHHHH-.T--EEEEESTSTTSHHHHHHHHHHHCTT-EEEES-TTS-TTT-SBBH CS
                   Glyco_hydro_101 151 sgkllkRfkelreelgeeldfiYvDvyresgwaskklskelnkqGwrvasewaealeedstwsh 214
                                       +g++ k +++ +e+  ++ d++Y Dv+ + g++ +  +++   qG+++ +e+ +  ++d +  h
  gi|385805949|ref|YP_005842347.1| 232 TGSKIKIVNDPKEA-AKDADILYTDVWVSMGQEKETEKRMKDFQGYQINKELLRLAKKDVVVMH 294
                                       45555555555555.5599************8877655555568*******9988888877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1117  (0.0623013); expected 358.6 (0.02)
Passed bias filter:                      759  (0.0423336); 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: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 1997.11
//
Query:       gi|385805950|ref|YP_005842348.1|  [L=177]
Description: NTPase [Fervidicoccus fontis Kam940]
Scores for 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-46  155.5   0.0    1.1e-45  155.4   0.0    1.0  1  NTPase_I-T  Protein of unknown function DUF84


Domain annotation for each model (and alignments):
>> NTPase_I-T  Protein of unknown function DUF84
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.4   0.0   6.1e-50   1.1e-45       1     162 [.       7     170 ..       7     171 .. 0.97

  Alignments for each domain:
  == domain 1  score: 155.4 bits;  conditional E-value: 6.1e-50
                                       S---HHHHHHHHHHHHHHCTTEEEEEEE---SS-SS-BSHHHHHHHHHHHHHHHHHHSTTSSEEEEEEEEEET.... CS
                        NTPase_I-T   1 gSkNpvKveAvkeafeklfkdvevegvsvpsgvsdqPmgdeetlkGAinRaknaleaaeeadygvGlEgGveeleek 77 
                                       g+kN  K+ ++++af++++++v++ +++ + + ++qP+g +e++ GA++Rak+a+++ e +++gvG+E+G+ ++ee+
  gi|385805950|ref|YP_005842348.1|   7 GTKNVSKITGIERAFSSFYEEVQLLAIDLSYKLPPQPIGIKEIMSGAEKRAKEAIKSSEMCEFGVGVEAGLIKIEES 83 
                                       89*******************************************************999***************** PP

                                       TEEEEEE.EEEESS-EEEEE---EE--HHHHHHHCTT-..-HHHHHHHHHTHCCHHHTTHHHHHHTTTSS-HHHHHH CS
                        NTPase_I-T  78 lldvawaavvdkegrvsvgrsasfelPeevveevkege..elgevmdelfgtenikqkeGaigllTkglvtRedlye 152
                                       ++d++  +v++k+gr  +g+s+sf +P+++ e + +++  el+ev+d++f+ten+++k+G+i+llTkg+vtRedl+ 
  gi|385805950|ref|YP_005842348.1|  84 YYDIQASFVINKDGRGYFGFSPSFIIPKSFSEGIITKKyrELEEVTDAYFNTENVGEKGGVIKLLTKGRVTREDLTY 160
                                       **********************************754445************************************* PP

                                       HHHHHHTHHH CS
                        NTPase_I-T 153 qavilAlipf 162
                                        av++ lipf
  gi|385805950|ref|YP_005842348.1| 161 YAVMMSLIPF 170
                                       *********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 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:                        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: 00:00:00.41
# Mc/sec: 1287.44
//
Query:       gi|385805951|ref|YP_005842349.1|  [L=608]
Description: formaldehyde:ferredoxin oxidoreductase [Fervidicoccus fontis Kam940]
Scores for complete 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-104  347.9   0.0   8.3e-104  347.6   0.0    1.1  1  AFOR_C    Aldehyde ferredoxin oxidoreductase, domains 2 & 3
    5.7e-74  248.3   0.1    8.4e-74  247.7   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 !  347.6   0.0  9.2e-108  8.3e-104       4     382 .]     221     594 ..     218     594 .. 0.95

  Alignments for each domain:
  == domain 1  score: 347.6 bits;  conditional E-value: 9.2e-108
                                       HHHHHHHHHSH.HHHHHHHH-GGGHHHHHHHTT---BTTTTBS--TTGGGGSHHHHHHHTEEEE.E-TT-SS--EEE CS
                            AFOR_C   4 kkiqkeiksspqvtaelrkyGTaelvnianetgalptknfqegtfekaekisgealeekylvknegCfsCpiaCgre 80 
                                       ++++++i +++  ++ +   GT+ ++ +++++++lpt nf+egt++ +e+isg+ +e+ ++v+++gC +C+++Cg+ 
  gi|385805951|ref|YP_005842349.1| 221 AEAYEKILKDS-NYKFWISQGTMTTIAWSHKNSVLPTMNFKEGTWDSYESISGDFMEK-IKVGRRGCPYCNMQCGNI 295
                                       56666666666.455999***************************************9.*****99*********** PP

                                       EE......ETEE---HHHHHHHTGGGT---HHHHHHHHHHHHHHTB-HHHHHHHHHHHHHHHHTTSS-HHHHTS--- CS
                            AFOR_C  81 vkveegkkvkvegpeyetlaalGsnlgiddleailklnelcdelGlDtisaGntiafamelyekGllkkedtdglel 157
                                       ++ ++g+    +  +ye++a+lGsnl iddl ++ +ln+l+d  GlDtis+Gn i+f++e+ ek ++ +      ++
  gi|385805951|ref|YP_005842349.1| 296 IEDNTGE---LSELDYENVAMLGSNLLIDDLRKVGELNRLADMFGLDTISLGNSIGFYIEAGEKRMVGE------KV 363
                                       **88888...5778*****************************************************88......78 PP

                                       -TT-THHHHHHHHHHHTT-TTHHHHTT-HHHHHHCTT..-GGG--EETTEE--SS-GGG-HHHHHHHHH-TTSS-SG CS
                            AFOR_C 158 efgdaeallellekiAkregigdllAeGvkrlaeklg..aeelamhvkGlelpaydprgakgmalaYatsnrGacHl 232
                                       e+gd + ++el+e++A+r+gig+ +A+Gv r++  lg  +e +amhvkGle++ay++  ++gmal+Y +s+ Ga+H 
  gi|385805951|ref|YP_005842349.1| 364 EWGDFKRIRELIEEVAERRGIGNFIADGVMRMSMNLGreSESFAMHVKGLEVSAYNCYSTPGMALSYGVSPIGAHHK 440
                                       ***************************************************************************** PP

                                       GG-THHHHS---TT--.HHHHHHHHHHHH.HHHHHHHHT--GGGG-HHH......HHHHHHHHHT----HHHHHHHH CS
                            AFOR_C 233 raylialeekvdplet.egkaelvkwfqd.ltalvdslglCkftseaeerldlelyakllsavtGidvteeellkaG 307
                                       ++++ia e   d+l++ ++k+e v+  q+ +  +++sl++C+f+   e+ ldl+ y+k+l+a+tG+++t +++  + 
  gi|385805951|ref|YP_005842349.1| 441 DSFVIAQEVLRDRLSYsREKVEKVVALQNmRGGMFESLTTCRFPP-YEVSLDLNYYPKMLNAATGLSITLDDFKIVT 516
                                       ********999*****88999999888886889************.999**************************** PP

                                       HHHHHHHHHHHHHHT.--.HHHS---HHHHHS---SSTTTT---...-HHHHHHHHHHHHT--TTS---HHHHHHCT CS
                            AFOR_C 308 eRiynleRlfnlreG.lt.rkddtlperlleeplkegpakgkvl.edeleemldeyYelrGWdetGvPtketlkrLg 381
                                       +Riy l R+f++re   + r+ d  p+r++++ +++gp +g ++  ++++eml+ yYelrGW+++G+P++etl  Lg
  gi|385805951|ref|YP_005842349.1| 517 DRIYSLIRAFWIREFgYWsRELDLPPKRWTTQSMSKGPYAGVKIdIEKYDEMLSYYYELRGWNDRGIPKRETLNSLG 593
                                       **************42333688**********************9999***************************** PP

                                       - CS
                            AFOR_C 382 L 382
                                       L
  gi|385805951|ref|YP_005842349.1| 594 L 594
                                       8 PP

>> AFOR_N  Aldehyde ferredoxin oxidoreductase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  247.7   0.1   9.4e-78   8.4e-74       1     198 []       6     205 ..       6     205 .. 0.97

  Alignments for each domain:
  == domain 1  score: 247.7 bits;  conditional E-value: 9.4e-78
                                       SEEEEEETTTTEEEEEE--HHHHHHH-SCHHHHHHHHHHHS-TTS-TTSTTS-EEEEE-TTTTSSSTTB-EEEEEEE CS
                            AFOR_N   1 gkilrvdLstgkieveelpeelaekylGgrglaakllldevppgvdplspenplvfatGpltgtpapgsgrlvvvak 77 
                                       gk l +dL ++ki+  +++++++ +++Ggrgla+kll+d vp g+dplsp+n+l++a Gpl+g+p+p+sg+lvv++k
  gi|385805951|ref|YP_005842349.1|   6 GKALFIDLGERKIKFMSIDQDVYTNFIGGRGLAIKLLWDLVPLGADPLSPKNVLIIASGPLSGMPLPSSGKLVVASK 82 
                                       689************************************************************************** PP

                                       -TTTSSEEEEEEETCHHHHHHHCT-SEEEEES--SS-EEEEEETTEEEEEE-TTTTTS-HHHHHHHHHHHHTS..EE CS
                            AFOR_N  78 sPltgtlgesnaGgrfgaelkraGydaivieGkaekpvylvieddkveiedaedlwgldtyettealkeelgd..kv 152
                                       sPlt ++g+ + G  ++++l+r+G+dai i+G+++kpvyl+ie+dkv+i +a+dlwg+dt+et+++lke++g+   v
  gi|385805951|ref|YP_005842349.1|  83 SPLTFGYGDGSLGTMASHHLRRSGFDAITITGASDKPVYLYIENDKVQIFSADDLWGKDTFETEDKLKERHGKdvGV 159
                                       *************************************************************************5555 PP

                                       EEE-HHHHTT-TTB-E.EE.TTEEE-SSSHHHHHHHTTEEEEEEE-- CS
                            AFOR_N 153 aviGpaGenlvrfAsisvd.dgraagrgGlGavmgsKnlkaivvrgt 198
                                       ++iG+aGenlvr+A+i ++ +gr+ gr G+GavmgsK+lkaiv+rgt
  gi|385805951|ref|YP_005842349.1| 160 LSIGKAGENLVRYATI-TSlKGRSGGRPGIGAVMGSKKLKAIVIRGT 205
                                       5***************.555*************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (608 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.49
# Mc/sec: 3718.45
//
Query:       gi|385805952|ref|YP_005842350.1|  [L=633]
Description: oligopeptide transporter [Fervidicoccus fontis Kam940]
Scores for complete 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-95  318.9  55.5    9.5e-95  318.5  55.5    1.1  1  OPT       OPT oligopeptide transporter protein


Domain annotation for each model (and alignments):
>> OPT  OPT oligopeptide transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  318.5  55.5   5.3e-99   9.5e-95       2     615 ..      20     592 ..      19     593 .. 0.95

  Alignments for each domain:
  == domain 1  score: 318.5 bits;  conditional E-value: 5.3e-99
                               OPT   2 lTlRavvlGillgvlgsavnmyfglrtglvsissipaallafplgkalarilpklslnpgpftikEnvliqtmasaa 78 
                                       l lR ++lGi+l+ l++a+n+y+gl +g+++++sipaa++a ++++a+           +  +i+ n+++qt+a a+
  gi|385805952|ref|YP_005842350.1|  20 LSLRYLILGIILALLFAATNAYLGLYSGMTISASIPAAIIAIAVFRAM-----------RTRNILGNNIVQTIACAG 85 
                                       789********************************************8...........468**********99999 PP

                               OPT  79 atlalatglivvipalelygqsag..fgylillslsvqllGvgfagplRkflvypeklifPsglataellkalhkpe 153
                                       ++l  a+g+i+++pal++++  ++  f+++ +l+ + + lG  ++ ++Rk  + +ekl+fP+g a ae+l +++k++
  gi|385805952|ref|YP_005842350.1|  86 EAL--AAGAIFTLPALIIINIYMNlpFWTTTALVAIAGTLGAALTTIIRKPYIKEEKLPFPEGKAGAEVLIVGDKGG 160
                                       988..*************88888888*************************************************** PP

                               OPT 154 geeksrlkfflivflgsfvwglfplylfpalssfswltwiapknvvlanlfglgllpltfdwnviaayiGsglivpl 230
                                            + k +l    g++++g     +f++l +++ +  +++       ++ lg   + f  ++++a+   g+iv++
  gi|385805952|ref|YP_005842350.1| 161 A----STKPLLT---GGIIGG-----IFKFLEGIGLWPGTVEA------ATKLGSSLFYFGSDLSTALAAIGYIVGI 219
                                       8....8999999...******.....6999*******888887......5588888899****************** PP

                               OPT 231 wvavnmliGavlswgiliPllyysngwypaylpydvteildedgvldyekyigyglmllaalvallylvqfaaitll 307
                                       +vav +++G +l+w iliP+l+ +  ++ + l+      +   +++++++yig+g+mll++l+++          + 
  gi|385805952|ref|YP_005842350.1| 220 NVAVLIFLGGILGWIILIPILATHTALTGSALD------MAYSIWSSQIRYIGVGTMLLGGLWTI----------FR 280
                                       *********************9999********......99************************..........** PP

                               OPT 308 ivhtilkhgkdikaalksarsprteeddrhrrlmrkykdvpmwwylallvlslvigiivvealf..tqlpvwgllla 382
                                       +   i++++k+  +a+++            + + r+++++p  ++++l++++ ++++ v++++   ++l  +  +l 
  gi|385805952|ref|YP_005842350.1| 281 LRGAIARGIKSGISAARKR---------SSEGIERTERELPLNVAFILVAIFDMVLMGVFYYITraLGLSILLGILT 348
                                       *****99999999999998.........78889999*************998888888888888779999999**** PP

                               OPT 383 lllafllaivsaiiaGltgl..npvsgigkltqlifgallpg.......rpvanlvfgavvyaaaaqagdfmqDLKt 450
                                       l+l+fl + ++++++Gl+g+   pvsgi+++  li++++l         + + +l+++a+ + + a+agd+mq L +
  gi|385805952|ref|YP_005842350.1| 349 LILSFLGVSIAGYLTGLVGSsnLPVSGITIMNLLIAALILRLlgiggveGSLGTLLVAAMICMGSAVAGDMMQTLFI 425
                                       ********************988*****************99999988889************************** PP

                               OPT 451 GhllkasPraqfvaqliGtlvgavvniavlkllvkaygdict..adasnaftaPqakvfaavavllvggkkglpwaf 525
                                       G++++ +P++q+v+ ++G++++a++ +++l+ll++ayg+ +t  a++s a++aPqa+++  +++ +++++  l+w +
  gi|385805952|ref|YP_005842350.1| 426 GYVVGGTPWKQQVGMIVGSFASAFIIAPILNLLINAYGIAGTptAKGSMALAAPQATLMSKLTE-AIFTG-TLNWTM 500
                                       ******************************************99999*****************.*****.9***** PP

                               OPT 526 llgavapfilllllkkfpkkstarklplplafavgfylppslsialligglianlwlk..rrdaewakkynyvlaaG 600
                                       l++++a++i+l++ +++ ++++ +   +++ +a+g+ylp sls+++++ggl+ +l+ k  +r++++    +++ aaG
  gi|385805952|ref|YP_005842350.1| 501 LFIGFAIAIVLIITDEILARKKSKFRTPVMPVAIGIYLPFSLSVPIFVGGLVNWLVGKkiKRASDESTDAGTIGAAG 577
                                       ****************99888888889*******************************9999999************ PP

                               OPT 601 LiaGealmgviiafl 615
                                       LiaGe+++g++ a+l
  gi|385805952|ref|YP_005842350.1| 578 LIAGESIIGIVFAAL 592
                                       ***********9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (633 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       948  (0.0528752); 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:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.78u 0.34s 00:00:01.12 Elapsed: 00:00:00.56
# Mc/sec: 3384.89
//
Query:       gi|385805953|ref|YP_005842351.1|  [L=213]
Description: Nitrate transport ATP-binding protein [Fervidicoccus fontis Kam940]
Scores for complete 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-29  103.0   0.0    3.1e-29  102.2   0.0    1.4  1  ABC_tran     ABC transporter
    1.3e-08   35.1   1.7    0.00084   19.2   0.3    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    2.3e-06   27.2   0.6      0.034   13.6   0.1    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
     0.0023   18.5   0.5     0.0033   18.0   0.5    1.6  1  AAA_23       AAA domain
     0.0038   17.6   0.0     0.0099   16.3   0.0    1.7  1  AAA_16       AAA ATPase domain
     0.0058   17.1   2.7       0.14   12.6   2.7    2.6  1  AAA          ATPase family associated with various cellular a
     0.0065   16.4   0.1      0.014   15.3   0.1    1.5  1  RsgA_GTPase  RsgA GTPase
  ------ inclusion threshold ------
      0.011   16.1   0.1      0.025   14.8   0.1    1.7  1  AAA_22       AAA domain
      0.013   15.1   0.1      0.022   14.3   0.1    1.4  1  cobW         CobW/HypB/UreG, nucleotide-binding domain
      0.013   15.4   1.9      0.022   14.7   0.1    2.1  3  ATPase_2     ATPase domain predominantly from Archaea
      0.015   14.0   0.8        1.4    7.5   0.0    2.1  2  AAA_13       AAA domain
      0.016   14.1   1.5       0.62    8.8   0.3    2.8  2  ABC_ATPase   Predicted ATPase of the ABC class
      0.025   14.5   0.4       0.26   11.2   0.1    2.1  2  NACHT        NACHT domain
      0.026   14.5   0.8      0.058   13.3   0.0    1.8  2  Rad17        Rad17 P-loop domain
      0.038   13.2   0.2      0.087   12.0   0.1    1.6  2  NB-ARC       NB-ARC domain
      0.039   13.6   0.1      0.049   13.3   0.1    1.3  1  ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-bindi
      0.044   13.8   0.1      0.087   12.9   0.1    1.5  1  AAA_14       AAA domain
      0.076   11.8   0.0       0.54    9.0   0.0    1.9  2  DLIC         Dynein light intermediate chain (DLIC)
      0.086   12.6   0.1       0.15   11.8   0.1    1.4  1  AAA_29       P-loop containing region of AAA domain
       0.15   11.8   0.1       0.53   10.0   0.0    1.8  2  AAA_24       AAA domain
       0.16   12.0   0.4        2.3    8.2   0.1    2.3  2  AAA_5        AAA domain (dynein-related subfamily)
       0.16   12.3   0.4       0.39   11.0   0.3    1.9  1  AAA_19       AAA domain
       0.16   11.7   0.1       0.19   11.4   0.1    1.3  1  AAA_30       AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.2   0.0     4e-32   3.1e-29       2     136 ..      21     151 ..      20     152 .. 0.97

  Alignments for each domain:
  == domain 1  score: 102.2 bits;  conditional E-value: 4e-32
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       +n+s+kl++ge+++i+G+nG+GK+t+l++++gl+++++Ge+             + r +ig++pq++ l p l++re
  gi|385805953|ref|YP_005842351.1|  21 SNISFKLNRGEVLGIMGPNGCGKTTMLRTILGLENKDSGEV-------------KIRGKIGYVPQDNLLLPWLKLRE 84 
                                       79***************************************.............899******************** PP

                                       H.........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       n         + ++eie+ ls ++     ++++++ p+ +SgG  ++ ++aral+  p++l+lDEp 
  gi|385805953|ref|YP_005842351.1|  85 NiviglkisgAGEREIEERLSYVSELLSLNDHLDKYPNRVSGGTARKASIARALIIMPDILILDEPY 151
                                       *********999999*******9999999*************************************5 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   0.1   1.4e-05     0.011       3      43 ..      34      64 ..      32      78 .. 0.74
   2 !   19.2   0.3   1.1e-06   0.00084     215     302 ..     117     188 ..      79     189 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.4e-05
                            AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggir 43
                                      ++ GpNg+GK++ L+++ +l           +++sg ++ir
  gi|385805953|ref|YP_005842351.1| 34 GIMGPNGCGKTTMLRTILGL----------ENKDSGEVKIR 64
                                      688**************888..........34444444444 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 1.1e-06
                            AAA_21 215 rlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.nga 290
                                       ++++               ++ +S Gt r + ++ al+  +   ++l++DEp +gL+ + ++ l +llk+l++  + 
  gi|385805953|ref|YP_005842351.1| 117 LDKY---------------PNRVSGGTARKASIARALIIMP---DILILDEPYTGLDSSSISILQTLLKNLKKeIRL 175
                                       4444...............6779*******98888888888...9*************9999999999777665568 PP

                            AAA_21 291 QviltTHS.plll 302
                                        +i+++H+  +l+
  gi|385805953|ref|YP_005842351.1| 176 GIIIVSHQvDELM 188
                                       89*****966655 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 !   13.6   0.1   4.3e-05     0.034      25      50 ..      31      53 ..       4      66 .. 0.70
   2 !   12.3   0.0   0.00011     0.082     161     213 ..     144     199 ..      81     206 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.3e-05
                                      SEEEEEESTTSSHHHHHHHHHHHCTT CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnlldAilFvLGe 50
                                      ++  i+GpNG+GK+ +l  i   LG 
  gi|385805953|ref|YP_005842351.1| 31 EVLGIMGPNGCGKTTMLRTI---LGL 53
                                      3457*************999...554 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00011
                                       EEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SS.HHHCCC-SCEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxx.xxxxxxxxxxxxxxx RF
                             SMC_N 161 lyllDeidaaLDeknvkkvaellkekskn..aQfivislr.eemlekadklvgvtk 213
                                       + +lDe    LD + ++++ +llk+ +k+    +i++s++ +e++e +d+++ +t+
  gi|385805953|ref|YP_005842351.1| 144 ILILDEPYTGLDSSSISILQTLLKNLKKEirLGIIIVSHQvDELMEISDRIIVLTH 199
                                       679*********************99999446689999983456666688887776 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.5   4.2e-06    0.0033      15      39 ..      23      50 ..      11     194 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4.2e-06
                            AAA_23 15 idF..sk.gltlItGpNGaGKTTildAi 39
                                      i F  ++  +  I GpNG+GKTT l+ i
  gi|385805953|ref|YP_005842351.1| 23 ISFklNRgEVLGIMGPNGCGKTTMLRTI 50
                                      455544425778************9877 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.3e-05    0.0099      23      76 ..      29      83 ..      24     180 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.3e-05
                            AAA_16 23 rpelvllsGesGvGKsslvrellralekdggif.lrgkcdqlesaipysalaqal 76
                                      r+e++ + G+ G+GK++++r++l   +kd g + +rgk    +++  +++++++ 
  gi|385805953|ref|YP_005842351.1| 29 RGEVLGIMGPNGCGKTTMLRTILGLENKDSGEVkIRGKIGYVPQDNLLLPWLKLR 83
                                      5578889****************65555557777888877776665555666655 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   2.7   0.00018      0.14       3     115 ..      35     187 ..      33     209 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00018
                                       EESSTTSSHHHHHHHHHHH.......HTHE..................................EEEEETTTCSSS. CS
                               AAA   3 lyGppGtGKTllakavake.......lgve..................................fleisgsellsk. 37 
                                       ++Gp G+GKT++ + +          +  +                                               
  gi|385805953|ref|YP_005842351.1|  35 IMGPNGCGKTTMLRTILGLenkdsgeV--KirgkigyvpqdnlllpwlklreniviglkisgagE----------Re 99 
                                       68**************98833333331..133444455555555555555555544333333330..........12 PP

                                       ................STTHHHHHHHHHHHHHHHTS.....TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHH CS
                               AAA  38 ................yvgesekkirelfkeakeka.....kpsilfiDEidalaksrsgseseeeervvnqLltel 93 
                                                       ++ + ++++++  ++  + a      p il++DE +    s+       + +++++Ll+ l
  gi|385805953|ref|YP_005842351.1| 100 ieerlsyvsellslndHLDKYPNRVSGGTARKASIAraliiMPDILILDEPYTGLDSS-------SISILQTLLKNL 169
                                       3444554444444444444444444433333222223445777888888888877777.......666666666666 PP

                                       HHTTTSSSTEEEEEEESSGGGS CS
                               AAA  94 dgvkkkeskvivigatnrpdkl 115
                                       +++ +    + +i++++++d+l
  gi|385805953|ref|YP_005842351.1| 170 KKEIR----LGIIIVSHQVDEL 187
                                       66655....4455555555554 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   1.8e-05     0.014      82     133 ..      12      64 ..       3      69 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.8e-05
                                       --TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S----- CS
                       RsgA_GTPase  82 vsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpelelktgevsek 133
                                        s +++  +++++ +l+  ++  ++G+ G GK+t++ ++l+ ++   gev+ +
  gi|385805953|ref|YP_005842351.1|  12 KSFSDGPVISNISFKLNRgEVLGIMGPNGCGKTTMLRTILGLENKDSGEVKIR 64 
                                       556667778899999988799********************989999988765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   3.2e-05     0.025       8     112 ..      33     165 ..      28     188 .. 0.53

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.2e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee................erpevvfvtlpsstsskdllrellralglel 68 
                                       l ++G+ G+GKTt lr++l   ++++   e                               + +l+++++  l+ ++
  gi|385805953|ref|YP_005842351.1|  33 LGIMGPNGCGKTTMLRTILGLENKDS--GEvkirgkigyvpqdnllL-------------PWLKLRENIVIGLKISG 94 
                                       6699*************999864332..2233444444444444440.............44444444444444444 PP

                            AAA_22  69 ka.......................erlsseellealeqalrarav.ielliiDEaqh.lr..seealeeL 112
                                        +                       ++++ +   ++ +  +ra    + +li+DE    l+  s  +l++L
  gi|385805953|ref|YP_005842351.1|  95 AGereieerlsyvsellslndhldkYPNRVSGGTARKASIARALIImPDILILDEPYTgLDssSISILQTL 165
                                       44444443333333333333334444555555555555555555557777777776666654334444444 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   2.8e-05     0.022       2      26 ..      32      58 ..      31      92 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.8e-05
                                      EEEEEESTTCCHHHHHHHHH..CT--S CS
                              cobW  2 vtvltGflGsGKTtLlnhll..enrag 26
                                      v+++ G+ G GKTt+l+++l  en+++
  gi|385805953|ref|YP_005842351.1| 32 VLGIMGPNGCGKTTMLRTILglENKDS 58
                                      7899****************8655444 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   0.1   2.9e-05     0.022      19      44 ..      29      54 ..      20      64 .. 0.78
   2 ?   -3.3   0.0       9.1   7.1e+03     136     153 ..     101     118 ..      95     124 .. 0.70
   3 ?   -0.6   0.2       1.3     1e+03     105     130 ..     161     190 ..     135     197 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.9e-05
                          ATPase_2 19 pneiyfiYGpegsGKtaLlkeiienl 44
                                      + e++ i Gp g+GKt++l+ i+   
  gi|385805953|ref|YP_005842351.1| 29 RGEVLGIMGPNGCGKTTMLRTILGLE 54
                                      467889**************998765 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 9.1
                          ATPase_2 136 ngaellvkeLlnlieslt 153
                                       ++  ++v+eLl+l ++l 
  gi|385805953|ref|YP_005842351.1| 101 EERLSYVSELLSLNDHLD 118
                                       556678888888877765 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.3
                          ATPase_2 105 aielllekikkkgkk.iiii...iDelqkl 130
                                        ++ ll+++kk+ +  iii+   +Del ++
  gi|385805953|ref|YP_005842351.1| 161 ILQTLLKNLKKEIRLgIIIVshqVDELMEI 190
                                       455566666666555555543444555555 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    0.0018       1.4      21      45 ..      35      59 ..      30      86 .. 0.83
   2 ?    5.1   0.3    0.0094       7.4     527     580 ..     142     193 ..     133     210 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0018
                            AAA_13 21 iYGwNGaGKTtLSrllrslelgete 45
                                      i G NG GKTt+ r +  le++   
  gi|385805953|ref|YP_005842351.1| 35 IMGPNGCGKTTMLRTILGLENKDSG 59
                                      77****************9987654 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0094
                            AAA_13 527 dkivviDDPvSSLDsnslfivfsliksrllkkkkak.QlfiLTHnleffkevkkn 580
                                         i ++D P   LDs s+ i  +l+k+     k+++  ++i  H ++ + e++++
  gi|385805953|ref|YP_005842351.1| 142 PDILILDEPYTGLDSSSISILQTLLKNLK---KEIRlGIIIVSHQVDELMEISDR 193
                                       5799************************7...55332455556655555444443 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1     0.076        60     243     264 ..      28      50 ..      23      58 .. 0.88
   2 ?    8.8   0.3    0.0008      0.62     370     414 ..     156     199 ..     105     212 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.076
                                       -SS.EEEEEE-TTSSHHHHHHHH CS
                        ABC_ATPase 243 pkG.vtlIvGggfhGKsTLLeAl 264
                                        +G v  I+G++  GK+T+L+ +
  gi|385805953|ref|YP_005842351.1|  28 NRGeVLGIMGPNGCGKTTMLRTI 50 
                                       5677899*************987 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0008
                                       G--B--HHHCHHHHHHHH--EEEEEESS-GCCTTT-SEEEEEETT CS
                        ABC_ATPase 370 kepitplvdrvrelykklgvstilvvggsgdyldvAdtvilmeey 414
                                       +  i  l  ++++l k++ + +i+v+  ++++++++d++i++  +
  gi|385805953|ref|YP_005842351.1| 156 SSSISILQTLLKNLKKEIRLGIIIVSHQVDELMEISDRIIVLT-H 199
                                       55788899999*****************************996.3 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00033      0.26       3      21 ..      33      51 ..      31      60 .. 0.86
   2 ?    1.2   0.0      0.41   3.2e+02      49      83 ..     170     204 ..     155     205 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00033
                                      EEEEC-TTTCHHHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqkla 21
                                      + + G++G+GKTt+l+ + 
  gi|385805953|ref|YP_005842351.1| 33 LGIMGPNGCGKTTMLRTIL 51
                                      5689************996 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.41
                                       -...-HCHHHCCCCTS--SSS-CCHHHHCCSCCCE CS
                             NACHT  49 gnarsladllfsqlpepaapvsevwavllelperl 83 
                                       +++ +l  +++s++ ++ +++s  ++vl+ +p r+
  gi|385805953|ref|YP_005842351.1| 170 KKEIRLGIIIVSHQVDELMEISDRIIVLTHRPARI 204
                                       4445888899***********99999999999886 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   7.4e-05     0.058      45      64 ..      30      49 ..      20      59 .. 0.83
   2 ?   -1.3   0.1       2.2   1.7e+03     143     179 ..     152     188 ..     135     193 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.4e-05
                             Rad17 45 kriLLisGPsGCgkstvvkv 64
                                       ++L i GP GCgk+t+++ 
  gi|385805953|ref|YP_005842351.1| 30 GEVLGIMGPNGCGKTTMLRT 49
                                      46999***********9985 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.2
                             Rad17 143 nkfyrdsdalrevirkylrssealplilviteiesle 179
                                            +s ++ + ++k l+ +  l +i+v  +++ l 
  gi|385805953|ref|YP_005842351.1| 152 TGLDSSSISILQTLLKNLKKEIRLGIIIVSHQVDELM 188
                                       4455555566666777777777778888877777665 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00011     0.087      21      41 ..      31      51 ..      18      66 .. 0.84
   2 ?   -1.8   0.0       1.8   1.4e+03      83     110 ..     117     148 ..      85     173 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                                      EEEEEEESTTSSHHHHHHHHC CS
                            NB-ARC 21 lvvalvGmgGvGKttlakqil 41
                                       v++++G  G+GKtt+++ il
  gi|385805953|ref|YP_005842351.1| 31 EVLGIMGPNGCGKTTMLRTIL 51
                                      599**************9996 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.8
                                       SSSS-STTS....HHHHHHHHCCCTTEEEEEE CS
                            NB-ARC  83 leekeeves....lkrklvrlLltkrfllvlD 110
                                       l++ +++ s    +k  + r+L+    +l+lD
  gi|385805953|ref|YP_005842351.1| 117 LDKYPNRVSggtaRKASIARALIIMPDILILD 148
                                       44444443345556666666666666666666 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   6.3e-05     0.049       9      45 ..      25      63 ..      19     153 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.3e-05
                                      S-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTS..SEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxx RF
                       ATP-synt_ab  9 fpivqGqrtlipgafgvGktvisqslskqsnsd..daii 45
                                      f + +G+ ++i+g +g+Gkt+++++++   n+d  ++ i
  gi|385805953|ref|YP_005842351.1| 25 FKLNRGEVLGIMGPNGCGKTTMLRTILGLENKDsgEVKI 63
                                      66789*********************9998888332444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   0.00011     0.087       3      23 ..      31      51 ..      29      77 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                            AAA_14  3 kilvitGaRrvGKTtllkqli 23
                                      ++l i+G+  +GKTt+l++++
  gi|385805953|ref|YP_005842351.1| 31 EVLGIMGPNGCGKTTMLRTIL 51
                                      7899*************9987 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00069      0.54      19      54 ..      24      59 ..      14      64 .. 0.87
   2 ?    0.5   0.0      0.27   2.1e+02     122     170 ..      78     125 ..      72     155 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00069
                              DLIC 19 ssklPsgksvlvlGedgsGkttliaklqGveeekkG 54
                                      s kl  g  + ++G +g+Gktt++  + G+e++  G
  gi|385805953|ref|YP_005842351.1| 24 SFKLNRGEVLGIMGPNGCGKTTMLRTILGLENKDSG 59
                                      66888898899********************98877 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.27
                              DLIC 122 kwasvlrehidklkiepeekreleqrlvkefqeyvepeedlpgsPqrrt 170
                                        w ++ ++ +  lki     re+e+rl     e +  +++l+  P r +
  gi|385805953|ref|YP_005842351.1|  78 PWLKLRENIVIGLKISGAGEREIEERLSY-VSELLSLNDHLDKYPNRVS 125
                                       69999999999***************964.4667777777777777754 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   0.1    0.0002      0.15      17      39 ..      25      47 ..      19      53 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0002
                            AAA_29 17 ieidlkgatlltGpsGsGKSTll 39
                                      +++++ ++  ++Gp+G GK+T+l
  gi|385805953|ref|YP_005842351.1| 25 FKLNRGEVLGIMGPNGCGKTTML 47
                                      5666555888***********98 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   0.00067      0.53       4      22 ..      32      50 ..      29      61 .. 0.85
   2 ?   -0.9   0.0       1.5   1.1e+03     113     135 ..     160     187 ..     149     200 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00067
                            AAA_24  4 kiliyGpsgiGKTtlakel 22
                                       + i+Gp+g GKTt+++++
  gi|385805953|ref|YP_005842351.1| 32 VLGIMGPNGCGKTTMLRTI 50
                                      5789***********9987 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.5
                            AAA_24 113 rllkk.lqelrk....nvifiahektrk 135
                                       ++l++ l++l+k     +i+++h+  + 
  gi|385805953|ref|YP_005842351.1| 160 SILQTlLKNLKKeirlGIIIVSHQVDEL 187
                                       5555547777777778899999986665 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 ?    8.2   0.1    0.0029       2.3       4      23 ..      35      54 ..      32      67 .. 0.82
   2 ?    1.5   0.0      0.34   2.7e+02      51      92 ..     127     169 ..     116     209 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0029
                                      EE--SSSSHHHHHHHGGGGB CS
                             AAA_5  4 LvGppGtgKselaerlaaal 23
                                      + Gp G+gK+++ + ++ + 
  gi|385805953|ref|YP_005842351.1| 35 IMGPNGCGKTTMLRTILGLE 54
                                      68************998765 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.34
                                       ......--------G-SEEEEESGGG--.HHHHHHHHHHHHSS CS
                             AAA_5  51 ttslvdsplvraaregeilvlDEverae.sevlnsLlslleer 92 
                                       +t+++ s++   +  ++il+lDE  +   s+ +++L++ll + 
  gi|385805953|ref|YP_005842351.1| 127 GTARKASIARALIIMPDILILDEPYTGLdSSSISILQTLLKNL 169
                                       5555555555445588999999976665599999999998775 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.3    0.0005      0.39      10      34 ..      30      54 ..      22     180 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0005
                            AAA_19 10 ekvllvtaGpGtGKTrvlkhivall 34
                                       +vl ++++ G+GKT++l++i+ l 
  gi|385805953|ref|YP_005842351.1| 30 GEVLGIMGPNGCGKTTMLRTILGLE 54
                                      578899*************998764 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00024      0.19      19      48 ..      31      60 ..      24     149 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00024
                            AAA_30 19 rvavltGpAGtGKttalkalreaweaaggr 48
                                       v  + Gp G GKtt+l+++  + +++ g+
  gi|385805953|ref|YP_005842351.1| 31 EVLGIMGPNGCGKTTMLRTILGLENKDSGE 60
                                      488899************998877776444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); 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: 0.60u 0.35s 00:00:00.95 Elapsed: 00:00:00.53
# Mc/sec: 1214.49
//
Query:       gi|385805954|ref|YP_005842352.1|  [L=241]
Description: putative transporter [Fervidicoccus fontis Kam940]
Scores for complete 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   50.4  14.2    2.2e-13   50.4  14.2    1.9  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
        9.1    6.5  20.4        8.8    6.6   4.2    3.6  3  Papilloma_E5  Papillomavirus E5


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   3.5      0.33   2.9e+03      43      57 ..      16      59 ..       1      74 [. 0.38
   2 !   50.4  14.2   2.5e-17   2.2e-13       6     170 ..      68     223 ..      63     229 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.33
                      BPD_transp_1 43 f.............................vilsilghlilpvi 57
                                      +                              +++ l +++l+ +
  gi|385805954|ref|YP_005842352.1| 16 AlertypyaipslssvalyieiqgiisiarNVFKTLENTFLGFA 59
                                      12333333444333333444444444444433333444444433 PP

  == domain 2  score: 50.4 bits;  conditional E-value: 2.5e-17
                      BPD_transp_1   6 ilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrslpkd 82 
                                       +l+a++ n  l+ +++ l  +++s+ ++v+ i++v    i+ +++++  p++++++ ++ p+ + i  ++++s++  
  gi|385805954|ref|YP_005842352.1|  68 SLIAYHINLHLRSFITALNTFIQSISVLVWSIIFV----IIYGVTSGLPPIFVVSA-TSYPILLSIGISGMQSIEGK 139
                                       567789999************************99....44566655555555555.56677777778899****** PP

                      BPD_transp_1  83 lveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseisnggvl 159
                                       ++e++++ Ga++++ + + ++P +lp++i g + a+g++l  +v++e lg+++G+g++ll    +yd+ + + g+++
  gi|385805954|ref|YP_005842352.1| 140 YRELFKVFGAKKRHELLYLIIPGTLPYLIGGSRAAIGSALRITVVAEALGASGGIGYMLLY---SYDLGYKQ-GVFA 212
                                       *********************************************************9975...67777777.4444 PP

                      BPD_transp_1 160 alviavlllnl 170
                                         +++vll++l
  gi|385805954|ref|YP_005842352.1| 213 WSILLVLLMIL 223
                                       44444444444 PP

>> Papilloma_E5  Papillomavirus E5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   4.2     0.013   1.1e+02       1      67 [.       7      73 ..       3      82 .. 0.83
   2 ?    6.6   4.2   0.00098       8.8      20      51 ..      87     117 ..      78     128 .. 0.81
   3 ?    4.6   0.1    0.0041        37      27      41 ..     210     224 ..     203     230 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.013
                      Papilloma_E5  1 lvlvFllcfcvllllcllvpLllsvsvyaallllvlvlwvvvtsplevFlvyllflylPllllhlha 67
                                      ++++F+l++ +       +p l sv +y  +  ++ +   v  +  ++Fl + l + l ++ l ++ 
  gi|385805954|ref|YP_005842352.1|  7 IIFLFILWIALERTYPYAIPSLSSVALYIEIQGIISIARNVFKTLENTFLGFALSFALAMISLIAYH 73
                                      5677788888888888999999999999999999999998888999999999999999888776665 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.00098
                      Papilloma_E5  20 pLllsvsvyaallllvlvlwvvvtsplevFlv 51 
                                         ++s+sv ++ +++v+++ v+++ p  +F+v
  gi|385805954|ref|YP_005842352.1|  87 TFIQSISVLVWSIIFVIIYGVTSGLP-PIFVV 117
                                       679****************9988766.35655 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.0041
                      Papilloma_E5  27 vyaallllvlvlwvv 41 
                                       v+a+ +llvl+++++
  gi|385805954|ref|YP_005842352.1| 210 VFAWSILLVLLMILL 224
                                       99********99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       868  (0.0484132); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1603.44
//
Query:       gi|385805955|ref|YP_005842353.1|  [L=326]
Description: putative ABC transporter [Fervidicoccus fontis Kam940]
Scores for complete 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   36.8   0.1    1.1e-08   35.1   0.1    1.7  1  NMT1_2           NMT1-like family
    1.7e-05   24.3   0.4    7.1e-05   22.3   0.4    1.9  1  SBP_bac_3        Bacterial extracellular solute-binding prote
     0.0021   18.0   0.5      0.014   15.3   0.1    2.1  3  NMT1             NMT1/THI5 like
     0.0034   17.0   0.1     0.0047   16.6   0.1    1.3  1  Phosphonate-bd   ABC transporter, phosphonate, periplasmic su
  ------ inclusion threshold ------
       0.02   14.5   0.2      0.042   13.4   0.1    1.6  1  OpuAC            Substrate binding domain of ABC-type glycine
      0.047   14.1   0.0       0.14   12.5   0.0    1.9  1  Phage_holin_5_1  Bacteriophage A118-like holin, Hol118
       0.17   11.2   0.0       0.29   10.5   0.0    1.3  1  HEM4             Uroporphyrinogen-III synthase HemD
       0.31   11.4   3.1       0.35   11.2   0.2    2.4  2  Phage_holin_5_2  Phage holin family Hol44, in holin superfami


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 !   35.1   0.1   5.1e-12   1.1e-08      20     249 ..      45     265 ..      37     270 .. 0.85

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 5.1e-12
                            NMT1_2  20 plvvakekglfakeGltvelekqaswaelrdkllagelDaahvltpapllidlGiggakadmkvlaslnlnGqaitl 96 
                                        l ++++ +l +k+G ++++ ++  ++ + ++l++g++D+a++  +++  + l        +k++a+  l+ qai+ 
  gi|385805955|ref|YP_005842353.1|  45 TLDIMQYYNLSEKYGYELQVYRFDKTTDIINALASGSIDVAVIPSEMAANMLLQN----ISVKIIAPEMLQNQAILT 117
                                       67899999***********************************888877776665....89**************99 PP

                            NMT1_2  97 snklkdkkvsdakalkdlvakkkaskplkiavtfpgsthdlllrywLaaaGldp......eadvklvvvpppqmvan 167
                                        ++      ++a++l          k+ ++a+   ++t  +   y  +  ++ +      ++ +  + + p +    
  gi|385805955|ref|YP_005842353.1| 118 VKG-----NISAQEL----------KGKTVATLLSTGTYMMFKAYMKYIYNITVseqgkgNDTIYAINTLPGSFLDV 179
                                       753.....2444444..........56677777777777777777777777777778888999************** PP

                            NMT1_2 168 lkagtidgfcvgePwnaqavaegiGvtaltsqelwkdh.....PekvlgvredfveknpntaralvkalleAtkwld 239
                                       +++ +i + ++ eP+ + av +    ++++ q+ wk+      P+  + v +  + +n+++ + ++k+  +A ++++
  gi|385805955|ref|YP_005842353.1| 180 MRENDIYAIIAWEPFVSEAVVNYNASIIADYQTFWKEAnmsgePVMLIWVASPSASNNKELINSFLKTREDAVNIWN 256
                                       ********************777779*********987778789999****************************** PP

                            NMT1_2 240 akkenraeaa 249
                                         +en  ++a
  gi|385805955|ref|YP_005842353.1| 257 -GNENETISA 265
                                       .666655554 PP

>> SBP_bac_3  Bacterial extracellular solute-binding proteins, family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.4   3.2e-08   7.1e-05      31     174 ..      53     206 ..      27     247 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 3.2e-08
                                       HHHHHCT-EEEEEE-.SGGGHHHHHHTTSSSEEESSEB--HHH..HT.TEEEESESEEEEEEEEEEETTSHGTCCHS CS
                                       xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx..xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SBP_bac_3  31 aiakrlgvkvefvpv.swdelipalksgkvDiaiaaititpeR..ee.kvdFsqpyfsagqvllvrkkdaskissik 103
                                       ++ ++ g+++++ ++ + +++i+al+sg +D+a+ +  + +    +   v    p +  +q++l+ k++      i 
  gi|385805955|ref|YP_005842353.1|  53 NLSEKYGYELQVYRFdKTTDIINALASGSIDVAVIPSEMAANMllQNiSVKIIAPEMLQNQAILTVKGN------I- 122
                                       577888999998888899*************998666665555213346999999999999*9999763......5. PP

                                       SCGCGTTSEEEEETTSHHHHHHHHHHHC............TSEEEEESSHHHHHHH.HHTTSSSEEEEEHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx............xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                         SBP_bac_3 104 sladLkgkkvgvqagstaeellkeelkk............gaeivefdtleealqa.Lkngrvdavvadspvlaylv 167
                                       s ++Lkgk+v++  ++ +  ++k ++k+            + +i   +tl+  +++  +++ + a++a +p + ++v
  gi|385805955|ref|YP_005842353.1| 123 SAQELKGKTVATLLSTGTYMMFKAYMKYiynitvseqgkgNDTIYAINTLPGSFLDvMRENDIYAIIAWEPFVSEAV 199
                                       3669*******999988887888888777755555555533233457899988777789999999999999888888 PP

                                       HHCCGCC CS
                                       xxxxxxx RF
                         SBP_bac_3 168 kknpdkk 174
                                        ++++  
  gi|385805955|ref|YP_005842353.1| 200 VNYNASI 206
                                       7777655 PP

>> NMT1  NMT1/THI5 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   6.3e-06     0.014      20     113 ..      59     149 ..      55     159 .. 0.87
   2 ?   -2.2   0.0       1.4   3.2e+03     185     206 ..     231     252 ..     214     262 .. 0.78
   3 ?    0.0   0.0      0.31   6.9e+02      96     144 ..     252     299 ..     234     305 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.3e-06
                                       TEEEEEE--SSTTHHHHHHHCTS-SEEEE-HHHHHHHHHTT--EEEEEEEE-S--EEEEEECCC--SSGGGGTTSEE CS
                              NMT1  20 GldVeivepadpsdatelvasgkadfgvsyqesllaarakglpvvsvaallqeplsglivlkdsgikspkDLkGkri 96 
                                       G ++++     ++d ++++asg  d++v  +e  +    +++ v+ +a  + ++   l+v+ +    s ++LkGk++
  gi|385805955|ref|YP_005842353.1|  59 GYELQVYRFDKTTDIINALASGSIDVAVIPSEMAANMLLQNISVKIIAPEMLQNQAILTVKGN---ISAQELKGKTV 132
                                       5567777778899***********************************999777666666554...689******** PP

                                       EE-S-TTHHHHHHHHHH CS
                              NMT1  97 gyvgspfekallkalla 113
                                       ++  s  + +++ka ++
  gi|385805955|ref|YP_005842353.1| 133 ATLLSTGTYMMFKAYMK 149
                                       *****99****999987 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.4
                                       HHHHHH-HHHHHHHHHHHHHHH CS
                              NMT1 185 ekllkenpelvkkFlrAlkkGy 206
                                          +++n+el+ +Fl+  + ++
  gi|385805955|ref|YP_005842353.1| 231 SPSASNNKELINSFLKTREDAV 252
                                       4557789999999999777665 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.31
                                       EEE-S-TTHHHHHHHHHHHTT--GGG-EEEE-.TT-HHHHHHCTSSSEE CS
                              NMT1  96 igyvgspfekallkallakdggdpsdvtlvnvggtslakalltgkvDaa 144
                                       + +++ ++e+ +++al++ ++++++  + +   +t l + l +g +D +
  gi|385805955|ref|YP_005842353.1| 252 VNIWN-GNENETISALMSIYNLNEKTAEYLYSRVTVLDNNLSQGVIDGI 299
                                       55677.7888999999999999999999888888888889999988855 PP

>> Phosphonate-bd  ABC transporter, phosphonate, periplasmic substrate-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   2.1e-06    0.0047      23     126 ..      54     148 ..      51     251 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.1e-06
                                       HHHHHSSEEEEE--SSHHHHHHHHHTTS-SEEE--HHHHHHHHHHS.-EEEEEEEEETT--SEEEEEEEEETTSS-- CS
                    Phosphonate-bd  23 LseelGvevelvvatdyaavvealragqvDiaflgplayvqardqa.gveplatrvrsdGsasyrsviivradsdiq 98 
                                       Lse+ G+e ++  ++  ++++ al++g++D+a + ++ ++++  q+  v+ +a +        ++ + i +   +i 
  gi|385805955|ref|YP_005842353.1|  54 LSEKYGYELQVYRFDKTTDIINALASGSIDVAVIPSEMAANMLLQNiSVKIIAPE-------MLQNQAILTVKGNI- 122
                                       99****************************************9987344444444.......47888888888889. PP

                                       SHHHHGG-EEEE--TT-TTTTHHHHHHT CS
                    Phosphonate-bd  99 sledLkgktiafvspsStsGylvpaalL 126
                                       s ++Lkgkt+a     St+ y++ +a++
  gi|385805955|ref|YP_005842353.1| 123 SAQELKGKTVAT--LLSTGTYMMFKAYM 148
                                       999999999998..67888888888877 PP

>> OpuAC  Substrate binding domain of ABC-type glycine betaine transport system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   1.9e-05     0.042      23     107 ..      54     134 ..      47     170 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.9e-05
                                       HHHHTTEEEEEEEEESHHHHHHHHHTTSSSEEEEEEHHHHHHHHHHHHHHHHEEEEEEEESEEECEEEEEEHHHHHH CS
                             OpuAC  23 llekkGykveltnlgstavlfaalasGdiDvypeewtgtayeaykkaveekkglevlgplgagnteglavpkyvaek 99 
                                       l ek Gy+ ++ ++++t+ +++alasG+iDv++   +  a++ + ++++    +++ +p   +n+  l+v+ ++  +
  gi|385805955|ref|YP_005842353.1|  54 LSEKYGYELQVYRFDKTTDIINALASGSIDVAV-IPSEMAANMLLQNIS----VKIIAPEMLQNQAILTVKGNISAQ 125
                                       44666***************************9.444444444444444....555578888888888888877666 PP

                                       .HTTTBHHH CS
                             OpuAC 100 .ygiksisD 107
                                         + k+++ 
  gi|385805955|ref|YP_005842353.1| 126 eLKGKTVAT 134
                                       666666665 PP

>> Phage_holin_5_1  Bacteriophage A118-like holin, Hol118
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.3e-05      0.14      33      90 ..       3      60 ..       1      63 [. 0.92

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.3e-05
                   Phage_holin_5_1 33 skwlptvsilvgailgalatsldgsgslatmiwagalagaggtglfeqftnrakkygk 90
                                      +k++  + ++v   lga  ++     s   +i ag+l g   t  + q+ n + kyg 
  gi|385805955|ref|YP_005842353.1|  3 TKYILIIIVVVAVALGASYAFYREKESSPMIIRAGTLQGGISTLDIMQYYNLSEKYGY 60
                                      67888888999999******************************************96 PP

>> HEM4  Uroporphyrinogen-III synthase HemD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00013      0.29     145     213 ..      61     129 ..      31     139 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00013
                                       EE-SEEEEE-HHHHHHHHHHHHTT--SEEEESSHHHHHHHHHH-S-HH....HHHCTSEEEEESHHHHHHHHH CS
                              HEM4 145 evevYetvpaeeepeelkealkagevdavvftSpstvrnllellkdeg....delkevkvaaiGptTaealkk 213
                                       e+ vY+     ++  ++ +al +g++d+ v+ S  +++ ll++++ +     + ++++ + + G++ a++lk 
  gi|385805955|ref|YP_005842353.1|  61 ELQVYRF----DKTTDIINALASGSIDVAVIPSEMAANMLLQNISVKIiapeMLQNQAILTVKGNISAQELKG 129
                                       6789999....9999****************************996558887788888888888888888875 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 ?   11.2   0.2   0.00016      0.35      19      62 ..       2      45 ..       1      47 [. 0.72
   2 ?   -0.4   0.2      0.68   1.5e+03      44      73 ..     110     145 ..      79     147 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00016
                   Phage_holin_5_2 19 kdkyIPlilgiiGiilgvvivftadfqaedilifgaiiqGilsg 62
                                      + kyI +i++++ ++lg+ + f  + + + ++i + ++qG +s+
  gi|385805955|ref|YP_005842353.1|  2 NTKYILIIIVVVAVALGASYAFYREKESSPMIIRAGTLQGGIST 45
                                      569**************666666666666677655666665554 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.68
                   Phage_holin_5_2  44 fqaedilifg......aiiqGilsggastglnQliK 73 
                                       +q+++il+ +       +    +++++stg++ ++K
  gi|385805955|ref|YP_005842353.1| 110 LQNQAILTVKgnisaqELKGKTVATLLSTGTYMMFK 145
                                       555555554455444333333577888898888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       919  (0.0512577); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); 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: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2125.40
//
Query:       gi|385805956|ref|YP_005842354.1|  [L=266]
Description: hypothetical protein FFONT_0914 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.094   12.7   0.3         24    5.0   0.0    2.7  3  Cdc6_C    CDC6, C terminal winged helix 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 ?   -2.4   0.0      0.28     5e+03      59      70 ..      95     106 ..      89     111 .. 0.75
   2 ?    4.8   0.0    0.0015        27      24      64 ..     160     202 ..     157     206 .. 0.84
   3 ?    5.0   0.0    0.0014        24       5      31 ..     216     242 ..     210     248 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.28
                                       EEE-CC.C-EEE CS
                            Cdc6_C  59 ksskGrregrtr 70 
                                       k s Gr+++rt 
  gi|385805956|ref|YP_005842354.1|  95 KASLGRKYKRTC 106
                                       567788888875 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0015
                                       HHHHHHHHT.T-----H.HHHHHHHHHHHHTTSEEEEEEE-CC CS
                            Cdc6_C  24 vYkslCese.gvdpltq.revsdllseLemlgileleksskGr 64 
                                        Y+  +es+ ++d l +  +++++l + +++gi+e  + s++r
  gi|385805956|ref|YP_005842354.1| 160 IYEYYTESLgHIDSLEEtIRFLSMLFQISSWGIIEEYEISENR 202
                                       5777788887789999966***************998887665 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.0014
                                       HHHHCHCSSS-EEHHHHHHHHHHHHHH CS
                            Cdc6_C   5 vlllrksgkeevttgevyevYkslCes 31 
                                       +++ ++s+k+  t+g ++  Y+sl+++
  gi|385805956|ref|YP_005842354.1| 216 LKEKQSSDKPKLTLGVIEGFYSSLTKR 242
                                       3334499*****************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); 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: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1544.13
//
Query:       gi|385805957|ref|YP_005842355.1|  [L=187]
Description: nicotinamide-nucleotide adenylyltransferase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-13   49.5   0.1      9e-13   48.6   0.1    1.5  1  CTP_transf_like  Cytidylyltransferase-like
    1.7e-05   24.2   0.0     0.0054   16.0   0.0    2.1  2  HIGH_NTase1      HIGH Nucleotidyl Transferase
     0.0014   18.3   0.1       0.41   10.3   0.0    2.2  2  Citrate_ly_lig   Citrate lyase ligase C-terminal domain


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 !   48.6   0.1   1.5e-16     9e-13       1      61 [.       8      66 ..       8     139 .. 0.70

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 1.5e-16
                                      EEEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-SCSSTHHHHHHHHHHHTTC CS
                   CTP_transf_like  1 lagGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkkkplasaeeRlemlelakev 61
                                      ++ G+F+p+H+GHl ++e+++k+ ee ++ +v  + +++ + +++++a eR+em++la ++
  gi|385805957|ref|YP_005842355.1|  8 IFFGRFQPFHKGHLYVAENILKEYEE-IVFLVGMSTESHTE-RNPFTAGERIEMIRLAMKE 66
                                      689***********************.9999********99.****************333 PP

>> HIGH_NTase1  HIGH Nucleotidyl Transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0     9e-07    0.0054      10      40 ..      13      43 ..      12      72 .. 0.87
   2 !    6.4   0.0   0.00073       4.4     201     240 ..     128     165 ..     114     185 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 9e-07
                       HIGH_NTase1 10 YNPfHnGHlyhlekakeltgadvviavmSGn 40
                                      + PfH+GHly  e++ +++++ v  + mS++
  gi|385805957|ref|YP_005842355.1| 13 FQPFHKGHLYVAENILKEYEEIVFLVGMSTE 43
                                      67**************************984 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.00073
                       HIGH_NTase1 201 eeiaSAtaiRkalkeekkleelkklvPestleilkeelkk 240
                                       +ei   t iR++++e+  +++ ++lvP+s++e+l++  ++
  gi|385805957|ref|YP_005842355.1| 128 REIYNGTLIRRYMAEQ--NDKWRELVPKSVAEFLDSIKAT 165
                                       4688899******777..689***********99876333 PP

>> Citrate_ly_lig  Citrate lyase ligase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   6.9e-05      0.41       9      55 ..      14      65 ..      10      94 .. 0.76
   2 !    6.3   0.0    0.0012       7.1     116     182 .]      96     159 ..      78     159 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 6.9e-05
                    Citrate_ly_lig  9 nPftlGhryLvekaakendvvhlfv.v....kedkslfsyeerlklvkkGik 55
                                       Pf +Gh y+ e+  ke + +   v +    +++++ f++ er+++++  +k
  gi|385805957|ref|YP_005842355.1| 14 QPFHKGHLYVAENILKEYEEIVFLVgMstesHTERNPFTAGERIEMIRLAMK 65
                                      6****************98764443232221235567899999999986655 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0012
                    Citrate_ly_lig 116 eplsevtaaYnqalkevlekaeievveierkekeeelisaskvrkllkeknleklaelvPkttleyl 182
                                        p se   + n +++++l++a+ +v  i  k ++ e+   + +r+ ++e+n +k +elvPk+  e+l
  gi|385805957|ref|YP_005842355.1|  96 SPHSEAIFIGNPIVSQILREAGFNV--IVPKPYKREIYNGTLIRRYMAEQN-DKWRELVPKSVAEFL 159
                                       6777778888999999999997665..4456788899999*******9987.789******999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); 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: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 1234.49
//
Query:       gi|385805958|ref|YP_005842356.1|  [L=141]
Description: hypothetical protein FFONT_0916 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 919.57
//
Query:       gi|385805959|ref|YP_005842357.1|  [L=217]
Description: peroxiredoxin [Fervidicoccus fontis Kam940]
Scores for complete 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-34  116.8   0.0    7.7e-34  116.3   0.0    1.3  1  AhpC-TSA    AhpC/TSA family
    7.4e-14   51.7   0.0    9.8e-14   51.3   0.0    1.1  1  Redoxin     Redoxin
    2.6e-09   36.8   0.0    4.4e-09   36.0   0.0    1.4  1  1-cysPrx_C  C-terminal domain of 1-Cys peroxiredoxin
  ------ inclusion threshold ------
       0.19   11.7   0.1       0.99    9.3   0.0    2.0  2  SCO1-SenC   SCO1/SenC


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.3   0.0   1.7e-37   7.7e-34       1     123 [.      11     141 ..      11     142 .. 0.96

  Alignments for each domain:
  == domain 1  score: 116.3 bits;  conditional E-value: 1.7e-37
                                       TTSB----EEESTTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHH CS
                          AhpC-TSA   1 vgdkapdfelknadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfi 77 
                                       +g+kap+fe+ ++ g+ +  +d+kgk+vvlf +p+d++pvCt e  a++k++++f+e++v++ig+svd+++sh k+ 
  gi|385805959|ref|YP_005842357.1|  11 IGEKAPSFEASTTYGRIKFPDDFKGKWVVLFSHPADFTPVCTSEFVAFQKRIKQFEELNVQLIGLSVDQVFSHIKWD 87 
                                       89**********99777666********************************************************9 PP

                                       HH-H.......SSEEEE-TTSHHHHHTT-EETT..TTECSCEEEEE-TTSBEEE CS
                          AhpC-TSA  78 ekes......lnfpllsDeegkvakaygvlkee..kglalratfvidkegkiry 123
                                       e ++      ++fp++ D++g va  +g+l+ +     ++ra+f+id+eg+ir+
  gi|385805959|ref|YP_005842357.1|  88 EWIRekfgieITFPIIGDNTGRVASLFGMLHAQaeGSSTVRAVFIIDPEGIIRA 141
                                       9999999***********************99998899**************97 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.3   0.0   2.2e-17   9.8e-14       2     135 ..      11     147 ..      10     157 .. 0.81

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 2.2e-17
                                       TTSBB---ECCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHH... CS
                           Redoxin   2 agdkaPdftlplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndaf... 75 
                                        g+kaP+f+  +  t g     ++fkgk vv+++ p+ f+P+C+ e ++++k  ++++e +v+ +++++d+      
  gi|385805959|ref|YP_005842357.1|  11 IGEKAPSFEAST--TYGRIKFPDDFKGKWVVLFSHPADFTPVCTSEFVAFQKRIKQFEELNVQLIGLSVDQVFShik 85 
                                       599******644..8887777778************************999999999**********9987655554 PP

                                       HHHHHHH...TT-TSEEEE-TTSHHHHHTT-TTEEE.GGG.EEE-EEEEEEETTEEEEEEESSS CS
                           Redoxin  76 vkefwgk...eglkfpvlsDgsaaftkalGlrleedaseg.lrtpryavidedgkvvylevepe 135
                                         e++ +    +++fp++ D ++ +++ +G+    +++eg    +++++id +g ++++ + p 
  gi|385805959|ref|YP_005842357.1|  86 WDEWIREkfgIEITFPIIGDNTGRVASLFGML--HAQAEGsSTVRAVFIIDPEGIIRAILYYPQ 147
                                       4444444888566*****************55..55555556**************99866665 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 !   36.0   0.0   9.9e-13   4.4e-09       2      37 ..     163     202 ..     162     205 .. 0.85

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 9.9e-13
                                       HHHHHHHT-BB-TTT.T.....BT-EEE---SSHHHHHHHH CS
                        1-cysPrx_C   2 LQladkhgvatPAnWkp.....GdkvivpPpateedavkry 37 
                                       LQ++dk+gva+PAnW p     Gdkvi++P    +d+ +r+
  gi|385805959|ref|YP_005842357.1| 163 LQTSDKYGVAIPANW-PnneliGDKVILSPVDNKNDIPERL 202
                                       9**************.99*********99966666665555 PP

>> SCO1-SenC  SCO1/SenC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00022      0.99       3      66 ..      17      78 ..      15      81 .. 0.75
   2 ?   -0.9   0.0      0.32   1.4e+03      61      77 ..     188     204 ..     183     206 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00022
                         SCO1-SenC  3 pFelvdqdgeavteedlegkpslvffgFthCpdvCpttlanmaevldalgeea.ekvqplfiTvD 66
                                      +Fe  ++ g+    +d++gk++++f   +h  d  p+ +++  + ++++++ +  +vq++  +vD
  gi|385805959|ref|YP_005842357.1| 17 SFEASTTYGRIKFPDDFKGKWVVLF---SHPADFTPVCTSEFVAFQKRIKQFEeLNVQLIGLSVD 78
                                      79999999999999*******9985...6666666666666666666666543358999999998 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.32
                         SCO1-SenC  61 lfiTvDPerDtpevlke 77 
                                       +   vD ++D pe+lk+
  gi|385805959|ref|YP_005842357.1| 188 ILSPVDNKNDIPERLKK 204
                                       55669**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); 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:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 1390.04
//
Query:       gi|385805960|ref|YP_005842358.1|  [L=455]
Description: udp-n-acetyl-d-mannosaminuronic acid dehydrogenase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-35  122.7   0.3    2.4e-35  121.8   0.3    1.5  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
    4.1e-22   78.6   0.0      1e-20   74.1   0.0    2.3  2  UDPG_MGDP_dh_C   UDP-glucose/GDP-mannose dehydrogenase family
    7.4e-20   71.0   0.0      2e-19   69.6   0.0    1.8  1  UDPG_MGDP_dh     UDP-glucose/GDP-mannose dehydrogenase family
    5.4e-08   33.2   0.0    2.3e-07   31.1   0.1    2.0  2  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
    2.2e-07   31.0   0.0    6.2e-05   23.0   0.1    3.1  3  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
    0.00019   21.4   0.2    0.00039   20.3   0.2    1.6  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
     0.0045   16.4   0.0       0.22   10.8   0.1    2.8  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
     0.0047   17.4   0.0        0.8   10.2   0.0    2.5  2  NAD_binding_7    Putative NAD(P)-binding
  ------ inclusion threshold ------
      0.035   14.0   0.0        8.1    6.3   0.0    2.7  3  Methyltransf_23  Methyltransferase domain
      0.053   13.9   0.0       0.32   11.4   0.0    2.4  2  Mur_ligase       Mur ligase family, catalytic domain
       0.24   12.0   1.5       0.74   10.4   0.2    2.5  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent


Domain annotation for each model (and alignments):
>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.8   0.3   1.5e-38   2.4e-35       2     179 ..      21     197 ..      20     205 .. 0.93

  Alignments for each domain:
  == domain 1  score: 121.8 bits;  conditional E-value: 1.5e-38
                                       EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS.--TTHHHHHHHHCHTTTEEEES-HHHHHHC- CS
                    UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipi.yepgLeelvkkavesgrlsfttdvekaveea 77 
                                       ++sv+GlG +Gl+ a+v+a++g +v gvD +e+ v+++n+g+ pi +epg  el++kav+++rl++ td   a +++
  gi|385805960|ref|YP_005842358.1|  21 TVSVFGLGKMGLPLALVFASKGAKVYGVDLNENVVEMVNRGENPIsFEPGVGELLEKAVKEKRLTAVTDGALASSKS 97 
                                       69*******************************************66****************************** PP

                                       SEEEE-----B-TTTTCB-THHHHHHHHHHHHHHHCEEEEEE-S---TTHHHHCHHHHHHHHCSS-TTCEEEEE--- CS
                    UDPG_MGDP_dh_N  78 dvifiaVgTPskkkgkaaDlkyvesaarsiaealkkgkvvvvkSTvpvgtaeelvkkileeaskkkgvdfdvvsnPE 154
                                       d+i++ V+  ++ kg  + ++ +e+a++++++ ++kg +vv++ T p+gt+e ++ ki +    k g+df++++ PE
  gi|385805960|ref|YP_005842358.1|  98 DLIVLLVPVYANAKG--IRMELMEKAIDEVSNGIRKGAIVVTETTLPPGTTESFIPKIENVSGFKAGIDFGIAHAPE 172
                                       *******98888855..56*********************************99999988888888*********** PP

                                       ---TTSHHHHHHS-S-EEEEESSCH CS
                    UDPG_MGDP_dh_N 155 flregsavkdllnpdrvviGveekk 179
                                       +   g ++kd+ +    +iG+ +++
  gi|385805960|ref|YP_005842358.1| 173 RTMSGRVIKDITESYPKIIGAINEA 197
                                       ***********99877777766655 PP

>> UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.16   2.5e+02      32      75 ..      63     105 ..      41     124 .. 0.78
   2 !   74.1   0.0   6.3e-24     1e-20       2     103 ..     336     430 ..     335     432 .. 0.95

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.16
                                       EEEEE-SSTHHCCCCHHGGBTCCEEES-CHHHHTT-SEEEE-S- CS
                    UDPG_MGDP_dh_C  32 evkiyDPkvkeeaveaeleekgvevvdsleealkgadaivilte 75 
                                       +   ++P v e  ++a + ek+++ v++ + a++++d+iv+l++
  gi|385805960|ref|YP_005842358.1|  63 NPISFEPGVGELLEKAVK-EKRLTAVTDGALASSKSDLIVLLVP 105
                                       555556666665555544.699*******************986 PP

  == domain 2  score: 74.1 bits;  conditional E-value: 6.3e-24
                                       EE-SSSSTT-S--TT-HHHHHHHHHHHCTSEEEEE-SSTHHCCCCHHGGBTCCEEES-CHHHHTT-SEEEE-S--GG CS
                    UDPG_MGDP_dh_C   2 ilGlafKkdtdDlReSpaldiieeLleegaevkiyDPkvkeeaveaeleekgvevvdsleealkgadaiviltehde 78 
                                       ++Gl+++ +++++ +Sp++ +i+e l+ ga+v++yDP++++e+++ ++        ++++  ++gada+v++t+h++
  gi|385805960|ref|YP_005842358.1| 336 VFGLSYRGGIKETINSPSFPLINEFLKWGANVEVYDPYFSNEEIMSYG-------FKPFNGNFEGADAVVVVTDHPQ 405
                                       89*****************************************99844.......56889***************** PP

                                       GGGS-HHHHHHCCSS-EEEESSS-C CS
                    UDPG_MGDP_dh_C  79 fkeldlaklkelmkpavvfDgrnvl 103
                                       fke+dl +lk++m++++++Dgr ++
  gi|385805960|ref|YP_005842358.1| 406 FKEVDLRDLKDKMATPIIIDGRYIY 430
                                       **********************987 PP

>> UDPG_MGDP_dh  UDP-glucose/GDP-mannose dehydrogenase family, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.6   0.0   1.2e-22     2e-19       2      93 ..     222     308 ..     221     309 .. 0.92

  Alignments for each domain:
  == domain 1  score: 69.6 bits;  conditional E-value: 1.2e-22
                      UDPG_MGDP_dh   2 tAEliKlaaNaflatkIsfiNelanlcealgidveeVieavgldprigpkflkpglGvGGsclpkDvkaLvalaeel 78 
                                        AE++K+++ ++++++I+++Nela + e+lgi+v+e i+ ++++p   +++++pg+GvGG+c+ + +++L++   el
  gi|385805960|ref|YP_005842358.1| 222 VAEAVKVFEGVYRDVNIALANELALISERLGINVNEAIDSANTQPY--SHIHRPGAGVGGHCIGVYTWFLIHSFPEL 296
                                       7*********************************************..8**************************99 PP

                      UDPG_MGDP_dh  79 gleaelleavrevNe 93 
                                           ++++ +re+N+
  gi|385805960|ref|YP_005842358.1| 297 ---SKIMKIARETND 308
                                       ...566666666665 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 !   31.1   0.1   1.4e-10   2.3e-07       2     105 ..      22     154 ..      21     178 .. 0.79
   2 ?   -2.0   0.0       2.3   3.7e+03      13      47 ..     355     388 ..     354     426 .. 0.66

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 1.4e-10
                                       EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT......................EEE-SSHHHHHHHC CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg......................akaaesieelvasl 56 
                                       + + GlG+MG ++al ++++g kv++++++ e+v e+v++g                      ++a+++ + + ++ 
  gi|385805960|ref|YP_005842358.1|  22 VSVFGLGKMGLPLALVFASKGAKVYGVDLN-ENVVEMVNRGenpisfepgvgellekavkekrLTAVTDGALASSKS 97 
                                       7899*************************9.566666777779*999999999998877766555555555555555 PP

                                       SEEEE-SSSHHHHHHHHHS........HCCC--TT-EEEE-S---HHHHHHHHHHHH CS
                     NAD_binding_2  57 dvvitmvkagkavdevieg........llealkkgdilidgstsspedtrelakelk 105
                                       d+++++v+  ++ + +  +        + + ++kg+i++  +t  p +t+ +  +++
  gi|385805960|ref|YP_005842358.1|  98 DLIVLLVPVYANAKGIRMElmekaideVSNGIRKGAIVVTETTLPPGTTESFIPKIE 154
                                       ********999888777774444555566777*************999998877665 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.3
                                       HHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-S CS
                     NAD_binding_2  13 nmalnllkagykvavynrtkekveelvaegakaae 47 
                                       ++++++lk g +v vy+   +  ee+++ g+k+++
  gi|385805960|ref|YP_005842358.1| 355 PLINEFLKWGANVEVYDPYFS-NEEIMSYGFKPFN 388
                                       577788899999999996543.3555556655554 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.1   3.8e-08   6.2e-05       2      84 ..      22     111 ..      21     140 .. 0.81
   2 ?    3.5   0.0      0.04        64      31      78 ..     293     340 ..     277     350 .. 0.86
   3 ?   -0.3   0.0      0.56   9.2e+02      67     107 ..     391     437 ..     387     442 .. 0.68

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 3.8e-08
                                       EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHSSBTTTBTT-.......---TTEEEES-HHHHHTT-- CS
                    NAD_Gly3P_dh_N   2 iavlGaGswGtalAkvlaenghevrlwvreeelieeineehenvkyLpgi.......klpenlvattdlaealkgad 71 
                                       ++v+G G+ G  lA v+a++g +v     +e+++e +n+ ++   + pg+         ++ l+a+td a a +++d
  gi|385805960|ref|YP_005842358.1|  22 VSVFGLGKMGLPLALVFASKGAKVYGVDLNENVVEMVNRGENPISFEPGVgellekaVKEKRLTAVTDGALASSKSD 98 
                                       89***********************************998888777555322111116678899************* PP

                                       EEEE---HHHHHH CS
                    NAD_Gly3P_dh_N  72 iivlvvPsqalre 84 
                                       +ivl vP  a ++
  gi|385805960|ref|YP_005842358.1|  99 LIVLLVPVYANAK 111
                                       *******977554 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.04
                                       -HHHHHHHHHHSSBTTTBTT----TTEEEES-HHHHHTT--EEEE--- CS
                    NAD_Gly3P_dh_N  31 eeelieeineehenvkyLpgiklpenlvattdlaealkgadiivlvvP 78 
                                        +el + ++ ++e ++ +p + ++ +++a + +++ ++ga+iiv+ ++
  gi|385805960|ref|YP_005842358.1| 293 FPELSKIMKIARETNDSMPLHIVELTVKALNLVRKPVNGARIIVFGLS 340
                                       3588999999***********************************876 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.56
                                       HTT--EEEE---HHHHHHH.HHHHCCC--TT-EEEE......---SEE CS
                    NAD_Gly3P_dh_N  67 lkgadiivlvvPsqalrev.lkklkgllkkkailvs......liKGie 107
                                        +gad +v+v  +  ++ev l++lk+++++   ++       ++KGie
  gi|385805960|ref|YP_005842358.1| 391 FEGADAVVVVTDHPQFKEVdLRDLKDKMATPI-IIDgryiyaTAKGIE 437
                                       579999*****999999986777777763322.221333334777776 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.2   2.4e-07   0.00039       1      40 [.      21      60 ..      21     143 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.4e-07
                                      EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHH CS
                           3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdiseealekale 40
                                      +v v G G mG  +a vfas+g +V  vd +e+ +e +++
  gi|385805960|ref|YP_005842358.1| 21 TVSVFGLGKMGLPLALVFASKGAKVYGVDLNENVVEMVNR 60
                                      699****************************998876654 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.1   0.00014      0.22      36      73 ..      19      56 ..       6     122 .. 0.88
   2 ?    1.8   0.0     0.083   1.4e+02      55      99 ..     360     401 ..     356     408 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00014
                                      TSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH CS
                      2-Hacid_dh_C 36 gktvGiiGlGrIGqavakrlkafgmkviaydrskkkee 73
                                      + tv ++GlG++G  +a ++++ g+kv+++d +++  e
  gi|385805960|ref|YP_005842358.1| 19 ELTVSVFGLGKMGLPLALVFASKGAKVYGVDLNENVVE 56
                                      579****************************9988665 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.083
                                       HHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S CS
                      2-Hacid_dh_C  55 lkafgmkviaydrskkkeeeeeelgvelvsleellaesDivslhl 99 
                                       + ++g++v +yd++ ++ee    + + +  ++  ++ +D v++++
  gi|385805960|ref|YP_005842358.1| 360 FLKWGANVEVYDPYFSNEE---IMSYGFKPFNGNFEGADAVVVVT 401
                                       55789*********99665...44556689999999999999876 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1      0.03        49       8      39 ..      20      51 ..      17     141 .. 0.75
   2 !   10.2   0.0   0.00049       0.8      23      76 ..     357     408 ..     356     422 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.03
                     NAD_binding_7  8 kkvlvvGgGevAarkvrklleagakvtvvape 39
                                       +v v+G G++++  +  ++++gakv  v+ +
  gi|385805960|ref|YP_005842358.1| 20 LTVSVFGLGKMGLPLALVFASKGAKVYGVDLN 51
                                      5799**********************877766 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00049
                     NAD_binding_7  23 vrklleagakvtvvapevkeeleelvklaeeelekdlegadlviaatddrelne 76 
                                       ++ +l+ ga+v v++p +    ee++++  + +++++egad v+++td+++ +e
  gi|385805960|ref|YP_005842358.1| 357 INEFLKWGANVEVYDPYF--SNEEIMSYGFKPFNGNFEGADAVVVVTDHPQFKE 408
                                       5789*************3..4458888999******************998776 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0    0.0049       8.1      35      62 ..      33      76 ..      25     140 .. 0.76
   2 ?   -0.9   0.0      0.79   1.3e+03      82     107 ..     280     305 ..     216     318 .. 0.82
   3 ?    4.2   0.0     0.021        34      38      62 ..     358     400 ..     348     436 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0049
                   Methyltransf_23 35 illevlrengfsvtgvDlspeaveiae................k 62
                                       l+ v++ +g++v+gvDl+++ ve++                 +
  gi|385805960|ref|YP_005842358.1| 33 PLALVFASKGAKVYGVDLNENVVEMVNrgenpisfepgvgellE 76
                                      56889999*************99998666655555555544441 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.79
                   Methyltransf_23  82 kfdlIvlrevlehvpdppellrqiat 107
                                       ++  ++ +++++++p + + ++ +++
  gi|385805960|ref|YP_005842358.1| 280 HCIGVYTWFLIHSFPELSKIMKIARE 305
                                       55568999999999999999998765 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.021
                   Methyltransf_23  38 evlrengfsvtgvDlspeaveiae..................k 62 
                                       +++ ++g++v+++D+++ + ei +                   
  gi|385805960|ref|YP_005842358.1| 358 NEFLKWGANVEVYDPYFSNEEIMSygfkpfngnfegadavvvV 400
                                       567899***************9988888777777766664443 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 ?   11.4   0.0    0.0002      0.32      13      39 ..      31      61 ..      28      84 .. 0.85
   2 ?   -3.2   0.0       6.7   1.1e+04      34      49 ..     430     445 ..     423     447 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0002
                                      H.HHHHHHHHTTSEEEEEESSHC...HHHTT CS
                        Mur_ligase 13 s.agalflalkGykvdGsdfies...lialG 39
                                      + ++al++a kG+kv G d++e+   ++++G
  gi|385805960|ref|YP_005842358.1| 31 GlPLALVFASKGAKVYGVDLNENvveMVNRG 61
                                      5599******************977766666 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 6.7
                                       CHHHTT-EEEES-HGG CS
                        Mur_ligase  34 slialGaaavvghdaa 49 
                                       ++ a+G++ ++  +++
  gi|385805960|ref|YP_005842358.1| 430 YATAKGIENFIYASPG 445
                                       4889999999887776 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   0.00045      0.74       2      77 ..      22     112 ..      21     138 .. 0.74
   2 ?   -2.7   0.1       5.7   9.4e+03      62      93 ..     394     425 ..     391     425 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00045
                                       EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.....................-EEECECHHH CS
                     F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.....................vkvtavdnee 57 
                                       + + G G+mg  la+ ++++g    +++ +    +e + e+ ++ +                      ++ + d + 
  gi|385805960|ref|YP_005842358.1|  22 VSVFGLGKMGLPLALVFASKG---AKVY-G-VDLNENVVEMVNRGEnpisfepgvgellekavkekrLTAVT-DGAL 92 
                                       6789*****************...7777.6.44444555555555556777777779999999996444444.6667 PP

                                       HHHH-SEEEE-S-HHHHHHH CS
                     F420_oxidored  58 aaeeadvvvlavkpedveev 77 
                                       a +++d +vl v+ ++ ++ 
  gi|385805960|ref|YP_005842358.1|  93 ASSKSDLIVLLVPVYANAKG 112
                                       7779*********9986654 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.7
                                       -SEEEE-S-HHHHHHH.HHHCGHHHHTTSEEEE CS
                     F420_oxidored  62 advvvlavkpedveev.lselakdalkgklvis 93 
                                       ad vv+     +++ev l++l kd+ +  ++i+
  gi|385805960|ref|YP_005842358.1| 394 ADAVVVVTDHPQFKEVdLRDL-KDKMATPIIID 425
                                       555555544444444426777.77777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (455 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 3057.34
//
Query:       gi|385805961|ref|YP_005842359.1|  [L=496]
Description: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase [Fervidicoccus fontis Kam940]
Scores for complete 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-136  454.6   0.0   3.3e-136  454.3   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 !  454.3   0.0  1.9e-140  3.3e-136       1     405 [.      14     430 ..      14     431 .. 0.97

  Alignments for each domain:
  == domain 1  score: 454.3 bits;  conditional E-value: 1.9e-140
                                       HHHCCCTTSEEEEESEB-TBTHHHHHHHHHHHHT--EEEEEEBTTB.TT-EEEE-TTS-HCHHHHHHTS-GHHHHHH CS
                              UbiD   1 lealekagelvrikeevdpelEiaeiarrvleeggpallFenvkgkgskfpvltnlfgtrervalalglssleeile 77 
                                       +e+le+++ lvr+ke+++p lEi+  +r+v+ + gpa+lFe+vkg  ++++v +nlf +   +  alg++s+eei e
  gi|385805961|ref|YP_005842359.1|  14 VEWLEERELLVRVKEPLSPILEIPYFLRKVMYSSGPAVLFESVKGF-EGWRVCGNLFPSVFTISSALGINSFEEISE 89 
                                       689***************************99***********976.68**************************** PP

                                       HHHHHHHS..-..................---EE--GCG-GGGSEEECCCCC--HHHS---BSSTTSSS-EEECEEE CS
                              UbiD  78 klaellepkpp..................ippkvvesekapcqeevvlegddvdLskLPvltlwpgDgGpyitlglv 136
                                       +l +l+++++                   ++pk+v+  ka ++e+v +eg+d  L+k+P++++wp+DgG+y t ++v
  gi|385805961|ref|YP_005842359.1|  90 RLISLITHQQAqgitekikafsdaskllgYFPKKVN--KAEFEEKV-IEGKDNPLDKIPFFKTWPMDGGRYATFPMV 163
                                       *******8775699*********************5..69999888.69**************************** PP

                                       EEE-TTTT-EEEEEEEEEEEETTEEEE--TTTHCHHHHHHHHHHCCT--EEEEEEES--HHHHHHCTS--TTT-TCH CS
                              UbiD 137 itrdpetgkrnlgiyRmqvldknklglhwqihkggaehlrkakkkggeplpvavaiGvdPaltlaAvaplPeglsEl 213
                                       it+dp +g  n+g+yR+++++ +k ++hwq hk+ga+ +   k+++ +++pva++iG dP ++++Av p+P+ ++++
  gi|385805961|ref|YP_005842359.1| 164 ITKDPAKGIINMGVYRVMIVNGRKGIIHWQVHKRGAMAYSVTKEMKAKEMPVAIIIGSDPGTMISAVSPVPYPIDKM 240
                                       **********************************************99***************************** PP

                                       HHHHHHHTS--EEEE-SSSSSEEETT-SEEEEEEEECCEEEECTTTC-TTSCEEC--CCEEEEEEEEEEE-TT-EEE CS
                              UbiD 214 efaGalrgepvelvkcetvdlevpadAEivleGeidpgetapEGPfgdhtGyysevrdefpvfkVtaithRkdpiyp 290
                                       +faG++rg+ vel++ + ++++vp+++Eiv+eG +  +e+a EGPfgdh Gyy+++ + +pvf+V+++++R++piy+
  gi|385805961|ref|YP_005842359.1| 241 LFAGMVRGRGVELFELD-NGIPVPSNSEIVIEGSVRVDELASEGPFGDHWGYYDTPTEMYPVFTVERVYMRENPIYY 316
                                       **************995.69********************************************************* PP

                                       E-SSSCCSHHHHCHHHHHHHHHHHHHHCCSTTEEEEEE-GGGTTTCEEEEECHHHTCCHHHHHHHHHHCCTTGGC-S CS
                              UbiD 291 ttvvgkppeedallgkalealflpllkkqvpevkdvhlpeeggfhllavvsikkrypghakkvmealwalkqqlslt 367
                                         v+g pp eda++gk +e++f p++k  +pev+d+  p  g f+ ++vvsikkrypg+akkvm+alw+l q  slt
  gi|385805961|ref|YP_005842359.1| 317 GSVTGLPPLEDAVMGKIVEKMFKPFIKLLLPEVVDISYPVYGIFQGMVVVSIKKRYPGQAKKVMNALWGLAQ-SSLT 392
                                       555*******************************************************************76.9*** PP

                                       EEEEEEETTS-TTSHHHHHHHHHHC--CCCCEEEECCC CS
                              UbiD 368 KlvivvDedvdvrdlkevlwaiatrvdpdrDlviiegt 405
                                       K+vivvDed+dv++l++v+wa++ +v+p+rD+v+i+ t
  gi|385805961|ref|YP_005842359.1| 393 KIVIVVDEDIDVNNLDKVIWAVSSNVEPQRDVVVIPYT 430
                                       **********************************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (496 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); 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 0.35s 00:00:01.06 Elapsed: 00:00:00.58
# Mc/sec: 2591.56
//
Query:       gi|385805962|ref|YP_005842360.1|  [L=299]
Description: prenyltransferase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-37  129.7  19.6    1.4e-37  129.4  19.6    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 !  129.4  19.6   7.9e-42   1.4e-37       2     232 ..      32     266 ..      32     284 .. 0.88

  Alignments for each domain:
  == domain 1  score: 129.4 bits;  conditional E-value: 7.9e-42
                              UbiA   2 lipalvglalaaggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivlli 78 
                                       l+++++g+al+ + +++l+ ++l++++++ +++a++++N+++D++iD++++rt++RPl +G +s + a+i++++  +
  gi|385805962|ref|YP_005842360.1|  32 LPFTYAGMALT-HYPITLREVVLATFAVIGLRIAGMTYNNIADADIDRKNPRTARRPLLTGDVSFRDAWILVALGSL 107
                                       57899*****9.6678999********************************************************** PP

                              UbiA  79 lgllllalllnpltallgllalllyvvYtglrlKrrtllgtvvggiafglppllgwaavtgsl........sllall 147
                                       + ++ + ++l++++++l+ +  ++   Y+  + Kr+++++++ +g++ +l++++g+ a++g+            ++ 
  gi|385805962|ref|YP_005842360.1| 108 IYFASA-FFLSFYAFILSPILYIVIMTYP--FAKRFHPFPHLHLGLSLALIVFGGAIATSGEYvnnlmeaiESVPWT 181
                                       ******.***************99*****..******************************999*******9999** PP

                              UbiA 148 lalavflltwaialandlrdregDrkagiktlpvvlGrkaarillalllavlllallllllalllllylllalllaa 224
                                       +++av+++  +++ ++++ d e D+   + + ++++G + a+ ++++ +++ +l+ll+++ ++ l+l++l+++++ +
  gi|385805962|ref|YP_005842360.1| 182 YFFAVLFWGSGFDAIYSIMDEEFDKSMKLGSVAARFGSRGALMFSLANYIISSLFLLIAWRLYNLGLLTLASMIISI 258
                                       *******************************************8555555555554455555555555555555555 PP

                              UbiA 225 lallraar 232
                                       +++++++ 
  gi|385805962|ref|YP_005842360.1| 259 FIMFYQVA 266
                                       55555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       845  (0.0471303); 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:                         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: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1930.46
//
Query:       gi|385805963|ref|YP_005842361.1|  [L=251]
Description: hypothetical protein FFONT_0921 [Fervidicoccus fontis Kam940]
Scores for complete 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-67  225.6  12.7    7.8e-67  225.3  12.7    1.0  1  DUF2208   Predicted membrane protein (DUF2208)
  ------ inclusion threshold ------
      0.022   15.2   6.2      0.022   15.2   6.2    2.1  2  DUF4199   Protein of unknown function (DUF4199)
      0.084   12.7   0.0       0.17   11.7   0.0    1.5  1  KdpC      K+-transporting ATPase, c chain


Domain annotation for each model (and alignments):
>> DUF2208  Predicted membrane protein (DUF2208)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.3  12.7   1.3e-70   7.8e-67       1     229 [.       9     242 ..       9     243 .. 0.98

  Alignments for each domain:
  == domain 1  score: 225.3 bits;  conditional E-value: 1.3e-70
                           DUF2208   1 kmilisqvsiilfalvlafl...pqylflviilYiivimvimsvltsrsllrerkkleevesgktLfeEknalklie 74 
                                       ++i+i+q+sii+f++ ++fl    ++++l+iilY+i++m+im+++++++ l +++k++ +++gk+LfeE++a+++++
  gi|385805963|ref|YP_005842361.1|   9 RQIAIGQASIIIFSIAAGFLgrsGAVYWLFIILYFILYMIIMTKFGQPK-LPNTAKADLISKGKVLFEENKAMEVAS 84 
                                       589******************999************************9.99************************* PP

                           DUF2208  75 kDeelqkelkeqlkasmitllllliviilffllyryiiplassllgevleeklarflaflalFealflismflrlla 151
                                       +D+++++e+++qlk++ +t+l++++v+i+ff+   +i+p++s ++ ++++ek+   +++++lFe+ fl+s+f ++l+
  gi|385805963|ref|YP_005842361.1|  85 TDRQYVVEMQDQLKMLQFTTLFSFLVLIYFFI---AIGPVTSLIAPKFSNEKIGYSVSYFILFEGSFLLSIFGQYLS 158
                                       ********************************...8999999999999****************************9 PP

                           DUF2208 152 ....rrvlkklvmlimatsykvtekGivlk...krtgikfplkenieiklneerkfVElrstkqklktriRLYtkdp 221
                                           +r+ kk v+++m++++ vt++Givlk   ++tg+kfpl+ +++i+lneerkfVEl++++qk+ ++iRLYtk+p
  gi|385805963|ref|YP_005842361.1| 159 vrnySRSGKKFVTINMPRTFFVTSEGIVLKgmmSSTGLKFPLT-AYKIVLNEERKFVELVNETQKAINKIRLYTKSP 234
                                       999889999**********************************.9******************************** PP

                           DUF2208 222 eklyeile 229
                                       +klye+++
  gi|385805963|ref|YP_005842361.1| 235 NKLYEVIS 242
                                       ******97 PP

>> DUF4199  Protein of unknown function (DUF4199)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   6.2   3.7e-06     0.022      72     161 ..      31     125 ..      21     128 .. 0.79
   2 ?    0.4   0.3      0.13   7.6e+02      32      57 ..     139     164 ..     128     178 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.7e-06
                           DUF4199  72 fgflislvagllsavfqyiyfnfidpdfienyiaeilekleeakeesaeeenaemseeeikealesls.....piiv 143
                                        g ++ l++ l ++++++i  +f +p + ++++a +++k + + ee++++e+a+ ++++  e+ ++l+     +++ 
  gi|385805963|ref|YP_005842361.1|  31 SGAVYWLFIILYFILYMIIMTKFGQPKLPNTAKADLISKGKVLFEENKAMEVASTDRQYVVEMQDQLKmlqftTLFS 107
                                       688999***********************************999999998888877777755555444322534444 PP

                           DUF4199 144 alqsflgnliiGlilsli 161
                                       +l  + + + iG ++sli
  gi|385805963|ref|YP_005842361.1| 108 FLVLIYFFIAIGPVTSLI 125
                                       777777777777777777 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.13
                           DUF4199  32 llgllallllllvpflvylalkkyrk 57 
                                          +l+  ++ll++f+ yl++++y +
  gi|385805963|ref|YP_005842361.1| 139 SYFILFEGSFLLSIFGQYLSVRNYSR 164
                                       33444566777778899999998833 PP

>> KdpC  K+-transporting ATPase, c chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.9e-05      0.17       7      47 ..      34      73 ..      29      92 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.9e-05
                                      HHHHHHHHHHTHHHHHHHHHHHHH-HHHHTT-EEE.ETEEE CS
                              KdpC  7 lllvltvllgliYplavtgiaqllfpeqAnGslieadgkvv 47
                                      +  ++++l  ++Y +++t ++q  +p+ A+++li+ +gkv+
  gi|385805963|ref|YP_005842361.1| 34 VYWLFIILYFILYMIIMTKFGQPKLPNTAKADLIS-KGKVL 73
                                      5678899999************************9.79886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1122  (0.0625802); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1632.64
//
Query:       gi|385805964|ref|YP_005842362.1|  [L=281]
Description: hypothetical protein FFONT_0922 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     0.0001   22.1   0.7     0.0011   18.9   0.1    2.5  2  TrmB        Sugar-specific transcriptional regulator TrmB
     0.0087   15.9   0.6       0.78    9.6   0.1    3.1  2  DUF1495     Winged helix DNA-binding domain (DUF1495)
  ------ inclusion threshold ------
      0.015   14.8   0.3       0.21   11.1   0.0    2.6  2  Sigma70_r4  Sigma-70, region 4
      0.015   15.6   0.2        5.9    7.3   0.1    2.5  2  Rrf2        Transcriptional regulator
       0.15   12.6   0.2       0.56   10.7   0.0    2.1  3  HTH_27      Winged helix DNA-binding domain


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   2.9e-07    0.0011      13      58 ..      33      78 ..      17      94 .. 0.86
   2 ?    1.0   0.1      0.11   4.1e+02      11      43 ..     137     169 ..     134     171 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.9e-07
                                      HCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB 13 vYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                      v+l L+    +t +ei+e ++  r  v ++Lr+L  kG+V+++ ++
  gi|385805964|ref|YP_005842362.1| 33 VFLFLIYGRDLTPTEISESANERRKAVLDALRKLQLKGIVKKVGEK 78
                                      67888888999******************************99776 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.11
                                       CCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHH CS
                              TrmB  11 akvYlaLlklgpatadeiaeelgvprskvYevL 43 
                                       a +Yla  k + ++ ++i++ l++++ ++ e+L
  gi|385805964|ref|YP_005842362.1| 137 AICYLATSKDQTLSLKTISRLLNLSEERAKEYL 169
                                       6678888888899999*********99998887 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 !    9.6   0.1   0.00022      0.78       8      89 ..      26      96 ..      21      97 .. 0.74
   2 ?   -0.1   0.0      0.23   8.4e+02       3      39 ..     156     192 ..     154     202 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00022
                           DUF1495  8 SkvRkkvllyLysiypeksnlqeisrrvrskpsnvkGaleGmgkrynsessLielGLveeeeeseglklYklteeGiei 86
                                      S+v  ++ ++L+ iy +  +++eis++ + +++ v  al            L  +G+v+++ e++g  lY l+eeG+++
  gi|385805964|ref|YP_005842362.1| 26 SSVQIEI-VFLFLIYGRDLTPTEISESANERRKAVLDALR----------KLQLKGIVKKVGEKDGEPLYGLSEEGKKY 93
                                      5555444.35555788888888888888888777777775..........344579999999999999********999 PP

                           DUF1495 87 vev 89
                                       e+
  gi|385805964|ref|YP_005842362.1| 94 SEE 96
                                      886 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.23
                           DUF1495   3 rslnkSkvRkkvllyLysiypeksnlqeisrrvrskp 39 
                                       r ln S+ R k +l++ys  pe+ + + i  ++r  +
  gi|385805964|ref|YP_005842362.1| 156 RLLNLSEERAKEYLDIYSRPPERLFRKIIKPDTRETY 192
                                       5678899999999999999888877777766666654 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.091   3.3e+02      15      30 ..      37      52 ..      34      67 .. 0.82
   2 ?   11.1   0.0   5.9e-05      0.21      17      38 ..     140     166 ..     119     169 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.091
                                      HHHTTT--HHHHHHHH CS
                        Sigma70_r4 15 lrfgeglTleEIgerl 30
                                      l +g++lT  EI+e  
  gi|385805964|ref|YP_005842362.1| 37 LIYGRDLTPTEISESA 52
                                      6799999999999875 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 5.9e-05
                                       H.....TTT--HHHHHHHHTS-HHHHH CS
                        Sigma70_r4  17 f.....geglTleEIgerlgiSrerVr 38 
                                       +     ++ l+l+ I++ l++S+er++
  gi|385805964|ref|YP_005842362.1| 140 YlatskDQTLSLKTISRLLNLSEERAK 166
                                       155666899****************98 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0    0.0047        17      24      58 ..      42      75 ..      25      83 .. 0.86
   2 ?    7.3   0.1    0.0016       5.9       8      43 ..     132     166 ..     129     171 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0047
                                      C-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              Rrf2 24 epvsseeiaerqnispsylekilakLrkaglvksv 58
                                        ++ +ei+e+ n  ++ +   l+kL+ +g+vk v
  gi|385805964|ref|YP_005842362.1| 42 D-LTPTEISESANERRKAVLDALRKLQLKGIVKKV 75
                                      3.7889**************************965 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0016
                                       HHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHH CS
                              Rrf2   8 eyalhallyLakeeeeepvsseeiaerqnispsyle 43 
                                       +y   a++yLa+ ++++ +s+++i++  n+s++ ++
  gi|385805964|ref|YP_005842362.1| 132 NYIYNAICYLATSKDQT-LSLKTISRLLNLSEERAK 166
                                       688899*********88.***********9998665 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0         5   1.8e+04      33      45 ..       5      17 ..       4      24 .. 0.70
   2 ?   10.7   0.0   0.00016      0.56       5      68 .]      31      90 ..      28      90 .. 0.89
   3 ?   -2.9   0.0       2.9     1e+04      31      43 ..     145     158 ..     137     164 .. 0.57

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 5
                            HTH_27 33 shisyslkkLtek 45
                                      s+i + l+ L + 
  gi|385805964|ref|YP_005842362.1|  5 SSIEEKLRTLKRL 17
                                      6677778888877 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00016
                            HTH_27  5 qalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      +++ L+li+  +r  + +++++  n    ++  +l+kL  kG v++ g +  ++e ++ l+++G
  gi|385805964|ref|YP_005842362.1| 31 EIVFLFLIY--GRDLTPTEISESANERRKAVLDALRKLQLKGIVKKVGEK--DGEPLYGLSEEG 90
                                      677899999..999999***************************999998..778888888877 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 2.9
                            HTH_27  31 edshis.yslkkLt 43 
                                        d++ s + +++L 
  gi|385805964|ref|YP_005842362.1| 145 KDQTLSlKTISRLL 158
                                       45555555665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       915  (0.0510346); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); 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: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 1955.06
//
Query:       gi|385805965|ref|YP_005842363.1|  [L=122]
Description: hypothetical protein FFONT_0923 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 831.92
//
Query:       gi|385805966|ref|YP_005842364.1|  [L=224]
Description: Flagellin (FlaB) [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.3e-33  114.5   9.7    1.2e-32  113.3   9.7    1.5  1  Arch_flagellin  Archaebacterial flagellin


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.3   9.7   6.8e-37   1.2e-32       1     164 []       6     210 ..       6     210 .. 0.84

  Alignments for each domain:
  == domain 1  score: 113.3 bits;  conditional E-value: 6.8e-37
                                       X--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEEEEE-SSSSSEEEEEEE--T CS
                    Arch_flagellin   1 GfvgigtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvgdsatngtineitiyvklna 77 
                                       G vgi+++Iv+IA+V+VAA++a v++n++ f++qka++t +++  ++s++le++g v+++++ +t+n+++i ++++a
  gi|385805966|ref|YP_005842364.1|   6 GIVGIEAAIVLIAFVIVAAALAFVALNMGLFTTQKAKETISQGLGEASTALEVDGYVVGISNGTTVNTVSIPIRTSA 82 
                                       779************************************************************************** PP

                                       TS--EEGGG-EEE..EEESS..--EE--E................................................ CS
                    Arch_flagellin  78 Gsspidlnkttis..vtddg..qetlltad...................................efgivvisdtdg 115
                                       G s++dl+ +++s   ++ +  +e+ +  +                                   e+ +        
  gi|385805966|ref|YP_005842364.1|  83 GVSSVDLAPSRTSidAIVGNqsFENIY--KaifyvypngtlayanngtltnlttdfsthnltadiESVLG------- 150
                                       *******88776655555552344443..33588888888888888888888885555555554444444....... PP

                                       .....................T-EE-TT-EEEEEEE--TTT---TT-EEEEEEE-SSS--EEEEE CS
                    Arch_flagellin 116 sltng................devlekgekvelevnvneddgitagdevsvevvpenGasttief 164
                                           +                + vle gek+ + +++ e++g++++++ sve++p++Ga++t+e+
  gi|385805966|ref|YP_005842364.1| 151 ----SpstptayvviiqnvnyNSVLETGEKAVVLIDL-ENNGLGPYGQLSVEIRPPEGAPLTVER 210
                                       ....25555555555599999****************.7***********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1507.01
//
Query:       gi|385805967|ref|YP_005842365.1|  [L=227]
Description: methyl-accepting chemotaxis sensory transducer [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00096   19.2   6.2    0.00098   19.1   0.2    2.4  2  Focal_AT       Focal adhesion targeting region
  ------ inclusion threshold ------
      0.024   13.5  10.5      0.043   12.7  10.5    1.4  1  Spc7           Spc7 kinetochore protein
      0.061   13.1   0.0          5    7.0   0.0    2.5  2  WIYLD          Ubiquitin-binding WIYLD domain
      0.064   13.1   0.1        2.5    7.9   0.0    2.2  2  PhageMin_Tail  Phage-related minor tail protein
      0.089   12.8   7.1        0.2   11.7   4.8    2.2  2  DUF1664        Protein of unknown function (DUF1664)
       0.11   11.4   5.0       0.12   11.1   5.0    1.1  1  ALMT           Aluminium activated malate transporter
       0.12   12.1   0.3       0.17   11.6   0.3    1.2  1  zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
       0.13   12.4  10.2       0.23   11.6  10.2    1.3  1  UPF0242        Uncharacterised protein family (UPF0242) N-ter
       0.24   11.6  10.9       0.42   10.8  10.9    1.5  1  ATG16          Autophagy protein 16 (ATG16)
       0.28   11.8   6.1       0.37   11.4   5.0    1.7  2  Syntaxin-6_N   Syntaxin 6, N-terminal
        0.3   11.0   5.8      0.075   13.0   2.9    1.4  2  EspB           Enterobacterial EspB protein
       0.32   10.0   8.2       0.58    9.2   8.2    1.4  1  Atg14          Vacuolar sorting 38 and autophagy-related subu
       0.44   10.4   6.3       0.56   10.0   1.2    2.9  2  DivIC          Septum formation initiator
       0.71   10.6   7.3       0.49   11.1   3.6    2.3  2  DUF2203        Uncharacterized conserved protein (DUF2203)
        4.3    6.5   8.1        6.7    5.9   8.1    1.4  1  TMPIT          TMPIT-like protein
        5.7    7.2  17.1        7.5    6.8   4.2    2.5  2  Seryl_tRNA_N   Seryl-tRNA synthetase N-terminal domain
          6    7.0  11.9        8.8    6.5   9.4    2.5  2  Fib_alpha      Fibrinogen alpha/beta chain family


Domain annotation for each model (and alignments):
>> Focal_AT  Focal adhesion targeting region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   1.6      0.17   1.8e+02      39      79 ..      48      73 ..      19     116 .. 0.49
   2 !   19.1   0.2   9.3e-07   0.00098       5      78 ..     120     193 ..     116     202 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.17
                          Focal_AT 39 slvksvglelrkLltsvdellsslpasarreielaekvlsk 79
                                      +  k+v ++l++ +++ + ++  l+               +
  gi|385805967|ref|YP_005842365.1| 48 DSLKEVVDALKESVAELKATIGDLS---------------N 73
                                      3333333333333333333333322...............2 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 9.3e-07
                          Focal_AT   5 drtdDkvyeatlsvvkavvelsqevetakaeeyvslvksvglelrkLltsvdellsslpasarreielaekvls 78 
                                        r++   +++t+++ k + +ls+++   + ++y+sl+k++g++  k l  +  l +++++  + +i l+ ++ls
  gi|385805967|ref|YP_005842365.1| 120 KRREPVLFKETVKMLKILYSLSEKMPGDMIDDYISLMKEIGISEEKTLDVIRLLNQIVQKGIKSNISLQDQLLS 193
                                       57777889***********************************9999999999999999999999999999986 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7  10.5   4.1e-05     0.043     168     278 ..      20     134 ..      16     141 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.1e-05
                              Spc7 168 llpeleeekaeleeeleklqeaaeelesid..keeLeelreelaelkaeieekkkelaelqeqleeleek.ieelke 241
                                       ++  l ++k++++e++ek+ ++ +e +sid  ke + +l+e++aelka+i  +++ l +l ++ +++e+k +e+ +e
  gi|385805967|ref|YP_005842365.1|  20 IVYPLLKKKKKVKEKVEKEPTQ-NEKNSIDslKEVVDALKESVAELKATIGDLSNPLFSLSSEAKQKEAKeVEKSTE 95 
                                       5566777888888888888774.445777766778888888888888888888888888888777776542554444 PP

                              Spc7 242 .qkseleeeiaeaervleeck.gwsesevsrlkeevkal 278
                                        q +  +eei+e ++ +ee k  +++ e    ke+vk+l
  gi|385805967|ref|YP_005842365.1|  96 kQVQMPKEEIRENKEEVEEVKtPVKRREPVLFKETVKML 134
                                       044555778887766666554145556655666666655 PP

>> WIYLD  Ubiquitin-binding WIYLD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0048         5      12      32 ..     153     173 ..     146     178 .. 0.84
   2 ?    3.4   0.0     0.062        66      16      34 ..     199     217 ..     198     222 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0048
                             WIYLD  12 idamkelGfskeqvrpvlkkL 32 
                                       i  mke+G+s+e++  v++ L
  gi|385805967|ref|YP_005842365.1| 153 ISLMKEIGISEEKTLDVIRLL 173
                                       778**************9855 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.062
                             WIYLD  16 kelGfskeqvrpvlkkLLk 34 
                                       k++Gfs++++++ + ++L 
  gi|385805967|ref|YP_005842365.1| 199 KAMGFSEPEIEEEVAQILI 217
                                       68*********99999885 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 ?    3.1   0.2     0.071        75     160     190 ..      40      65 ..      19     100 .. 0.70
   2 ?    7.9   0.0    0.0024       2.5      49     116 ..     141     207 ..     127     226 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.071
                     PhageMin_Tail 160 tkdaqgkmksldeiledlsealkkltdaqra 190
                                       t++ ++ + sl+e+ + l+e++++l     +
  gi|385805967|ref|YP_005842365.1|  40 TQNEKNSIDSLKEVVDALKESVAEL-----K 65 
                                       4444566677777777777777766.....2 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0024
                     PhageMin_Tail  49 ggaddleeaaeilstalnafglsaadaeeaaDvlaaaanngatsvedlaealkevgavakaaGlsfee 116
                                       ++ + ++++ +  +++++  g+s++++ ++  +l++++++g  s   l + l  +    ka+G+s  e
  gi|385805967|ref|YP_005842365.1| 141 SEKM-PGDMIDDYISLMKEIGISEEKTLDVIRLLNQIVQKGIKSNISLQDQLLSIYILSKAMGFSEPE 207
                                       4545.888999999999999999778888888888888888888888888888887788888877655 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.2    0.0069       7.3      76     120 ..      36      78 ..      23      82 .. 0.59
   2 ?   11.7   4.8   0.00019       0.2      41     112 ..      48     121 ..      43     128 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0069
                           DUF1664  76 deqkeiskeikeevtevredlseigedvesvkeavegleskleri 120
                                       +  ke +++ k+ +++++e +++++e v ++k+++ +l + l ++
  gi|385805967|ref|YP_005842365.1|  36 E--KEPTQNEKNSIDSLKEVVDALKESVAELKATIGDLSNPLFSL 78 
                                       3..344555566677777777777777777777777766666555 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00019
                           DUF1664  41 davesvskqleqvseslaatkrhLssridrvd..kkldeqkeiskeikeevtevredlseigedvesvkeaveg 112
                                       d +++v   l++  ++l+at  +Ls+ + ++   +k++e ke+ k+++++v+  +e+++e +e+ve+vk+ v+ 
  gi|385805967|ref|YP_005842365.1|  48 DSLKEVVDALKESVAELKATIGDLSNPLFSLSseAKQKEAKEVEKSTEKQVQMPKEEIRENKEEVEEVKTPVKR 121
                                       667778888888888888888999999998862268999*****************************998875 PP

>> ALMT  Aluminium activated malate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   5.0   0.00012      0.12     309     397 ..      30     123 ..      18     177 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00012
                              ALMT 309 vlrelaesvkkmkklsk...veellkevkvaaeeLqskl.dskskLlvnsekweaakkkekaeeveekkeeekeses 381
                                       +++e+ e+  +++++++    +e+++ +k ++ eL++++ d +  L+  s++ ++++ ke ++++e++ +  ke+  
  gi|385805967|ref|YP_005842365.1|  30 KVKEKVEKEPTQNEKNSidsLKEVVDALKESVAELKATIgDLSNPLFSLSSEAKQKEAKEVEKSTEKQVQMPKEEIR 106
                                       44444443333333332113678999999999*******99888899877774544444444444444444444333 PP

                              ALMT 382 kkeea.eaveeaesese 397
                                       +++e+ e+v++  ++ e
  gi|385805967|ref|YP_005842365.1| 107 ENKEEvEEVKTPVKRRE 123
                                       33333233333333333 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3   0.00016      0.17      18      32 .]       8      22 ..       3      22 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00016
                     zf-NADH-PPase 18 ggwarvCpaCglehY 32
                                      g+w + Cp C++++Y
  gi|385805967|ref|YP_005842365.1|  8 GEWVCSCPICRRIVY 22
                                      7************99 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 ?   11.6  10.2   0.00022      0.23      73     168 ..      27     122 ..      19     134 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00022
                           UPF0242  73 keaklteld..eglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkleleeqLaek 147
                                       k++k++e+   e+ +++++++  l+e  + Lke +++ + ++  l +   +L+++  a +++ +e+ +  e+q++  
  gi|385805967|ref|YP_005842365.1|  27 KKKKVKEKVekEPTQNEKNSIDSLKEVVDALKESVAELKATIGDLSNPLFSLSSE--AKQKEAKEVEKSTEKQVQMP 101
                                       4555555443466677777777777777777777777777777776666566544..44477777777777777777 PP

                           UPF0242 148 qellqeyqetieeqrsvlekr 168
                                       +e + e +e++ee +  +++r
  gi|385805967|ref|YP_005842365.1| 102 KEEIRENKEEVEEVKTPVKRR 122
                                       777777777777777666655 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8  10.9    0.0004      0.42      55     143 ..      29     116 ..      19     169 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0004
                             ATG16  55 kksakekeasasqsnskqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkede..erlaele 129
                                       kk++++ e++++q   +++++i sl++ + +l+e +ael  + g+l++ l +l++e +++e+k  e++  ++++  +
  gi|385805967|ref|YP_005842365.1|  29 KKVKEKVEKEPTQ---NEKNSIDSLKEVVDALKESVAELKATIGDLSNPLFSLSSEAKQKEAKEVEKSteKQVQMPK 102
                                       3334444444444...78889**********************************9999988766554113344444 PP

                             ATG16 130 aeraaletklkdre 143
                                       +e+++ ++++++ +
  gi|385805967|ref|YP_005842365.1| 103 EEIRENKEEVEEVK 116
                                       44444444443333 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   5.0   0.00035      0.37      29      96 ..      40     120 ..      18     122 .. 0.62
   2 ?   -1.9   0.0       4.8   5.1e+03      10      21 ..     177     188 ..     150     213 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00035
                      Syntaxin-6_N  29 edtssstseeldetrteLrkalrsiewdledLeetv............riveknpsk.fkidekelsrrrafveevr 92 
                                       +++++++ ++l+e  + L++++ +++ ++ dL +              + vek+ +k +++ ++e+++ ++ veev+
  gi|385805967|ref|YP_005842365.1|  40 TQNEKNSIDSLKEVVDALKESVAELKATIGDLSNPLfslsseakqkeaKEVEKSTEKqVQMPKEEIRENKEEVEEVK 116
                                       22222334444444455555555555555555554488888888877777888888889999999999999999999 PP

                      Syntaxin-6_N  93 eevk 96 
                                         vk
  gi|385805967|ref|YP_005842365.1| 117 TPVK 120
                                       8876 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.8
                      Syntaxin-6_N  10 Vqkslnkaesly 21 
                                       Vqk ++++ sl 
  gi|385805967|ref|YP_005842365.1| 177 VQKGIKSNISLQ 188
                                       444444444443 PP

>> EspB  Enterobacterial EspB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   2.9   7.1e-05     0.075     109     184 ..      48     120 ..      25     135 .. 0.76
   2 ?   -3.7   0.0       9.5     1e+04     167     189 ..     157     179 ..     154     190 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.1e-05
                              EspB 109 vsvkAlvkasEsiadaagetvgklqqgiasvaaaaktrneqrakavedlqesnleeykktvresqDkiasvlqdlr 184
                                        s k +v+a  + + +   t+g+l++  +s++++ak+++++    ve   e+ ++  k+++re ++++ +v   ++
  gi|385805967|ref|YP_005842365.1|  48 DSLKEVVDALKESVAELKATIGDLSNPLFSLSSEAKQKEAK---EVEKSTEKQVQMPKEEIRENKEEVEEVKTPVK 120
                                       4566777776444445689*************999887655...5788888999999999**99999998876555 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 9.5
                              EspB 167 ktvresqDkiasvlqdlrstard 189
                                       k+++ s++k ++v++ l +++++
  gi|385805967|ref|YP_005842365.1| 157 KEIGISEEKTLDVIRLLNQIVQK 179
                                       67777888888888777777665 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   8.2   0.00055      0.58      42     165 ..      28     159 ..      21     199 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00055
                             Atg14  42 kkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklk...... 112
                                       kkk+++++e++  ++++++ i+++k+ ++ lk  +a+l++ +  l+  l +l +e ++k +k  ++s +        
  gi|385805967|ref|YP_005842365.1|  28 KKKVKEKVEKEP-TQNEKNSIDSLKEVVDALKESVAELKATIGDLSNPLFSLSSEAKQKEAKEVEKSTEKQvqmpke 103
                                       455555555555.4555777777777777777777777777777777777777666666554333333322467777 PP

                             Atg14 113 ...kRrsdleslqneleerrkkqiaklqdaikrieqklsslssktlesrsslcsel 165
                                          + +++ e +++ ++ r+  +++++++++k      +++  ++++  +sl++e+
  gi|385805967|ref|YP_005842365.1| 104 eirENKEEVEEVKTPVKRREPVLFKETVKMLKILYSLSEKMPGDMIDDYISLMKEI 159
                                       77777777888888888888888888888888888888888888888777777765 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.2   0.00053      0.56      23      62 ..      44      88 ..      38     103 .. 0.76
   2 ?    0.3   3.0      0.58   6.1e+02      29      50 ..      94     115 ..      76     122 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00053
                                      HHHHHHHHHHHHHHHHHHHHHHHHHCC-XX.....XXXXXXXXXX CS
                             DivIC 23 kqeiaalqaelaklkaeneeLeaevkdLks.....dedyieerAR 62
                                      k+ i+ l++ +++lk+  +eL+a + dL++     + ++ ++ A+
  gi|385805967|ref|YP_005842365.1| 44 KNSIDSLKEVVDALKESVAELKATIGDLSNplfslSSEAKQKEAK 88
                                      677889999999999999999999999976777777777777777 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.58
                                       HHHHHHHHHHHHHHHHHHHCC- CS
                             DivIC  29 lqaelaklkaeneeLeaevkdL 50 
                                        +++++  k+e++e ++ev++ 
  gi|385805967|ref|YP_005842365.1|  94 TEKQVQMPKEEIRENKEEVEEV 115
                                       3444444455555555555554 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.2     0.023        25      35      77 ..      27      69 ..      15      79 .. 0.47
   2 ?   11.1   3.6   0.00046      0.49       9      83 ..      51     126 ..      44     133 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.023
                           DUF2203 35 eleeakaeaekseaaeleaeleeleaeieelveeieelGvevk 77
                                      + ++ k++ ek+  +++++++++l++ +++l e + el++ + 
  gi|385805967|ref|YP_005842365.1| 27 KKKKVKEKVEKEPTQNEKNSIDSLKEVVDALKESVAELKATIG 69
                                      2233333333333444444444444444444444444444444 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00046
                           DUF2203   9 nalLpllkelleelralrkeleeleeeleeakaeaekse.aaeleaeleeleaeieelveeieelGvevkdleagl 83 
                                       ++++  lke ++el+a+  +l +   +l+++ +++e++e +++ e++++  ++ei+e  ee+ee++  vk  e++l
  gi|385805967|ref|YP_005842365.1|  51 KEVVDALKESVAELKATIGDLSNPLFSLSSEAKQKEAKEvEKSTEKQVQMPKEEIRENKEEVEEVKTPVKRREPVL 126
                                       456666666666666666666666657776666666666799999*************************998877 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   8.1    0.0064       6.7       2      83 ..      45     127 ..      24     140 .. 0.52

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0064
                             TMPIT   2 eeweelekefkeleetakeykqkleelsklqskcskeik.kqkkrlkelksslkklkksvkeeeeeeveelkeelke 77 
                                       +++++l++ +++l+e+  e+k+++ +ls+   ++s+e+k k+ k++++ +++  ++ k+  +e++eevee+k+ +k+
  gi|385805967|ref|YP_005842365.1|  45 NSIDSLKEVVDALKESVAELKATIGDLSNPLFSLSSEAKqKEAKEVEKSTEKQVQMPKEEIRENKEEVEEVKTPVKR 121
                                       34445555555555555555555555555444443333202233333333333333333335666666666666666 PP

                             TMPIT  78 rkkvlk 83 
                                       r+ vl+
  gi|385805967|ref|YP_005842365.1| 122 REPVLF 127
                                       665554 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   4.2    0.0071       7.5      49      93 ..      25      71 ..      17      80 .. 0.61
   2 ?    6.1   4.9     0.012        13      46     104 ..      81     140 ..      76     143 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0071
                                      HHHHHHHHHHCCCCCCTT..S-TCCCCCCCHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N 49 qaerNelskeIgkakkkk..edaeeliaevkelkeelkaleaelkel 93
                                       ++++++ ++++k   ++  + +++l++ v++lke +++l+a+  +l
  gi|385805967|ref|YP_005842365.1| 25 LKKKKKVKEKVEKEPTQNekNSIDSLKEVVDALKESVAELKATIGDL 71
                                      55666666666666555544556666666666666666666655544 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.012
                                       HHHHHHHHHHHHHCCCCCCTT.S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCTS CS
                      Seryl_tRNA_N  46 eelqaerNelskeIgkakkkk.edaeeliaevkelkeelkaleaelkeleaeleklllai 104
                                       e+ q+e +e+ k+ +k  +   e++ e ++ev+e+k+ +k+ e  l + + ++ k+l ++
  gi|385805967|ref|YP_005842365.1|  81 EAKQKEAKEVEKSTEKQVQMPkEEIRENKEEVEEVKTPVKRREPVLFKETVKMLKILYSL 140
                                       566777777777776655544699****************99999999999999999887 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   9.4    0.0084       8.8      11     126 ..       9     120 ..       3     143 .. 0.73
   2 ?   -0.7   3.5       1.4   1.5e+03      30      61 ..      91     122 ..      85     195 .. 0.57

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0084
                                       CCEEEEE-CCHHHHCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  11 efgslCPtgCglqdlllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskele 87 
                                       e+   CP   ++   llk++k+vk+++ek  +  ++ +ns  + +e+v ++k+s++e +++  d +n + ++s+e +
  gi|385805967|ref|YP_005842365.1|   9 EWVCSCPICRRIVYPLLKKKKKVKEKVEK--EPTQNEKNSIDSLKEVVDALKESVAELKATIGDLSNPLFSLSSEAK 83 
                                       67778888888888889999999988885..5667778888888888888888888888888887666666666655 PP

                                       HCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  88 eeilrlketidaqesnirvLqnvlesneqkiqkLeqdid 126
                                         + + ke  +++e++++  ++ +++n++++++ ++ ++
  gi|385805967|ref|YP_005842365.1|  84 --QKEAKEVEKSTEKQVQMPKEEIRENKEEVEEVKTPVK 120
                                       ..3333333344456777777777777777777776655 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.4
                                       CCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHH CS
                         Fib_alpha  30 ekdvkkdlekleneleeisnstkeaeelvkei 61 
                                       ek+++k+++  ++e++e++++ +e+++ vk+ 
  gi|385805967|ref|YP_005842365.1|  91 EKSTEKQVQMPKEEIRENKEEVEEVKTPVKRR 122
                                       33333333333333333333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2869  (0.16002); expected 358.6 (0.02)
Passed bias filter:                      999  (0.0557198); expected 358.6 (0.02)
Passed Vit filter:                       143  (0.0079759); 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: 0.71u 0.31s 00:00:01.02 Elapsed: 00:00:00.49
# Mc/sec: 1402.00
//
Query:       gi|385805968|ref|YP_005842366.1|  [L=162]
Description: archaeal flagellar protein FlaG [Fervidicoccus fontis Kam940]
Scores for complete 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   40.3   5.8    4.1e-10   40.1   5.8    1.1  1  Arch_flagellin  Archaebacterial flagellin


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   5.8   2.3e-14   4.1e-10       3     150 ..       5     148 ..       2     159 .. 0.77

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 2.3e-14
                                       -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEEEEE-SSSSSEEEEEEE--TTS CS
                    Arch_flagellin   3 vgigtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvgdsatngtineitiyvklnaGs 79 
                                       ++i ++ + IA++ +A+++a v+i     + +++++  ++ ++ ++s+++i+  +++s+      +  iyvk n G 
  gi|385805968|ref|YP_005842366.1|   5 TTITHALLTIAAITIASIFAFVMISKISAINSSITQMISSNVNNMESSITIIDFFYNSSGG----SFVIYVK-NVGT 76 
                                       66******************************************************55555....59*****.**** PP

                                       --EEGGG-EEE.EEESS.--EE--E...................T-EE-TT-EEEEEEE--TTT---TT-EEEE CS
                    Arch_flagellin  80 spidlnkttis.vtddg.qetlltadefgivvisdtdgsltng.devlekgekvelevnvneddgitagdevsv 150
                                       s+i l+  + + v + +  + l+ ++ ++   +  ++ +l  g ++ ++ g ++ + + +  +++i +  +v++
  gi|385805968|ref|YP_005842366.1|  77 SDISLSALQNTdVYIGTyNSPLTLYTYLSSAYPGHWNYTLAIGgSNSWSAGSTIIIYLYN--QTSISPPYYVKI 148
                                       ****98766553555554555666655666666666666655578888888888888776..355555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1129  (0.0629706); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1214.40
//
Query:       gi|385805969|ref|YP_005842367.1|  [L=171]
Description: archaeal flagellar protein FlaF, putative [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0092   16.2   2.9      0.011   15.9   2.9    1.1  1  Arch_flagellin  Archaebacterial flagellin
  ------ inclusion threshold ------
       0.22   11.4   3.3          3    7.7   2.9    2.1  2  DUF4811         Domain of unknown function (DUF4811)


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   2.9   1.2e-06     0.011       3     164 .]       4     167 ..       2     167 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.2e-06
                                       -H.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEEEEE-SSSSSEEEEEEE--TT CS
                    Arch_flagellin   3 vg.igtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvgdsatngtineitiyvklnaG 78 
                                       ++ ++ +Iv+ ++++     ++v+ +  g+++++++ +   + ++v+s+l+it ++   + n+++ ++t+    n G
  gi|385805969|ref|YP_005842367.1|   4 SVtASGIIVMAVLIISVLSMVSVIMKGYGMITSSIERK---ALSSVRSSLSITYITN-VTVNQNNLTMTFIFS-NNG 75 
                                       5547888888888888889999**********999875...6778899999999998.444555557899999.999 PP

                                       S-.-EEGGG-EEEEEESS--EE--E...................................T-EE-TT-EEEEEEE-- CS
                    Arch_flagellin  79 ss.pidlnkttisvtddgqetlltad.......efgivvisdtdgsltng..........devlekgekvelevnvn 137
                                       s    d++  + ++++   +t+  ++       +          + +t+           + v++++e + +   + 
  gi|385805969|ref|YP_005842367.1|  76 SWsFWDFDHFDFILIYTSNKTNSESSkvlvygrD----------WNITAIlingglverfNGVVDPSESGIVYASLP 142
                                       973579***9999999993333333234555542..........333333344455555577********9999996 PP

                                       TTT---TT-EEEEEEE-SSS--EEEEE CS
                    Arch_flagellin 138 eddgitagdevsvevvpenGasttief 164
                                          +i  ++ +++++v ++G +++++f
  gi|385805969|ref|YP_005842367.1| 143 --PDISFSQPITIVFVNQYGFKASYTF 167
                                       ..9999999999999999999999886 PP

>> DUF4811  Domain of unknown function (DUF4811)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   2.9   0.00034         3       8      50 ..       8      49 ..       3      74 .. 0.78
   2 ?    2.1   0.0     0.017   1.6e+02      55      74 ..      88     108 ..      81     113 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00034
                           DUF4811  8 lglisllllvaSvllivandsdHfGmkkvtttktqkiysaads 50
                                       g+i +++l++Svl +v  + + +Gm ++   +++ + s+ +s
  gi|385805969|ref|YP_005842367.1|  8 SGIIVMAVLIISVLSMVSVIMKGYGMITSSI-ERKALSSVRSS 49
                                      6899**********************87654.44556666555 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.017
                           DUF4811  55 lllyqeiGtkgke.kvylYkt 74 
                                       +l+y++++t+++  kv++Y  
  gi|385805969|ref|YP_005842367.1|  88 ILIYTSNKTNSESsKVLVYGR 108
                                       689999999776679***965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       785  (0.0437838); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1180.31
//
Query:       gi|385805970|ref|YP_005842368.1|  [L=234]
Description: archaeal flagellar protein FlaH [Fervidicoccus fontis Kam940]
Scores for complete 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   83.3   0.1      2e-23   83.0   0.1    1.1  1  ATPase    KaiC
    1.1e-07   31.4   0.6    9.6e-05   21.7   0.1    2.1  2  PAXNEB    PAXNEB protein
     0.0018   17.6   0.0      0.003   16.9   0.0    1.3  1  Rad51     Rad51
  ------ inclusion threshold ------
       0.16   11.5   0.0       0.22   11.1   0.0    1.2  1  AAA_25    AAA domain


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.0   0.1   4.4e-27     2e-23       1     227 [.       5     227 ..       5     230 .. 0.81

  Alignments for each domain:
  == domain 1  score: 83.0 bits;  conditional E-value: 4.4e-27
                            ATPase   1 vktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekl 77 
                                       v+tg  +lD  l+gG+p  + +li Ge Gt Kt++a+qF++  +++ g +g+   +e p++d+ +++k l +d+ ++
  gi|385805970|ref|YP_005842368.1|   5 VSTGNDELDVRLQGGLPYPSLILIEGEQGTSKTVLAQQFVYGALRD-GLRGIVLETEMPSVDFLRKMKLLKMDIVDY 80 
                                       689999***********************************88777.****************************** PP

                            ATPase  78 eeegklaiidasesaeesaeekdkedleelieelaeaikeika..krvviDsitglayeekeavaReilrqlvrvlk 152
                                         +gk+ +  + +++ e++       l++ ++ ++++i+++      + iDs++ l + +k     +++ ++++ lk
  gi|385805970|ref|YP_005842368.1|  81 VIKGKVRLHSILSKNLEIN----DVVLSNALTVFEKYINSKLDnfDFLAIDSLSMLVKFAKY----SEVLEFFSNLK 149
                                       ************9988754....566777777777777776444589*********444444....45666777776 PP

                            ATPase 153 klgvTailvsekss..seeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskk.ehpfeIte.egik 225
                                       k+ +   l+    +    ++    ++    +dg i+L    i ++ v++++ivk+Rg+++s + ++ f++++  gik
  gi|385805970|ref|YP_005842368.1| 150 KISTSGKLIFATMHssILSEDILTKLRA-FCDGYIKLGISNIGGRSVKVMNIVKLRGAPTSFDsVISFDVDPaFGIK 225
                                       6666553333322212345566678888.89****************************997525678888877887 PP

                            ATPase 226 vl 227
                                        +
  gi|385805970|ref|YP_005842368.1| 226 LV 227
                                       65 PP

>> PAXNEB  PAXNEB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1   2.1e-08   9.6e-05      17      59 ..       3      44 ..       1      70 [. 0.82
   2 !    8.4   0.1   0.00023         1     228     281 ..     135     185 ..     114     189 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.1e-08
                            PAXNEB 17 lltStGtpsLDklLgGGLplGsillieEdgttdfakvLlkyFl 59
                                      +++StG+++LD  L GGLp  s++lie ++  + ++vL++ F+
  gi|385805970|ref|YP_005842368.1|  3 TTVSTGNDELDVRLQGGLPYPSLILIEGEQG-TSKTVLAQQFV 44
                                      79*************************6543.34677777775 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00023
                            PAXNEB 228 eskpedllkFLhsLrallrssnlvalitlplsliarssslvrkieqlvDtvieL 281
                                        +k +++l+F+  L+ +  s +  +++t+ +s++  s+ +++k++  +D+ i+L
  gi|385805970|ref|YP_005842368.1| 135 FAKYSEVLEFFSNLKKISTSGK-LIFATMHSSIL--SEDILTKLRAFCDGYIKL 185
                                       567799*********9876665.579********..99**************98 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   6.7e-07     0.003      18      57 ..       4      43 ..       2      49 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.7e-07
                                      EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHH CS
                             Rad51 18 qlttGskklDelLgGGietgsiteifGefrsGktqlchtl 57
                                      +++tG+ +lD  L+GG++  s+  i Ge ++ kt l++++
  gi|385805970|ref|YP_005842368.1|  4 TVSTGNDELDVRLQGGLPYPSLILIEGEQGTSKTVLAQQF 43
                                      589*******************************999886 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   4.8e-05      0.22      25     153 ..      15     131 ..       6     165 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.8e-05
                            AAA_25  25 lvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal...r 98 
                                        ++g lp  +l+l+ G +gt Kt+la + ++  +++            + +++ +E++  ++ r+++ +  ++    
  gi|385805970|ref|YP_005842368.1|  15 RLQGGLPYPSLILIEGEQGTSKTVLAQQFVYGALRDG----------LRGIVLETEMPSVDFLRKMKLLKMDIvdyV 81 
                                       5677789999********************9999633..........477899999999999999986665554333 PP

                            AAA_25  99 ddarllvldlagveslpLfakdrggtlltadvdaleaaieeveg.vrlvviDplsr 153
                                        +++++++++ ++       ++ ++ +l  ++   e+ i++  +  +++ iD+ls 
  gi|385805970|ref|YP_005842368.1|  82 IKGKVRLHSILSK------NLEINDVVLSNALTVFEKYINSKLDnFDFLAIDSLSM 131
                                       3444444444332......2222344444444455555555333466666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); 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: 0.38u 0.20s 00:00:00.58 Elapsed: 00:00:00.36
# Mc/sec: 1969.55
//
Query:       gi|385805971|ref|YP_005842369.1|  [L=845]
Description: archaeal flagellar protein FlaI [Fervidicoccus fontis Kam940]
Scores for complete 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-40  138.9   0.0    1.1e-35  123.1   0.0    2.2  2  T2SSE            Type II/IV secretion system protein
    4.1e-18   65.6   0.0      1e-17   64.4   0.0    1.7  1  Intein_splicing  Intein splicing domain
    1.5e-05   24.6   0.1    3.5e-05   23.5   0.1    1.6  1  AAA_29           P-loop containing region of AAA domain
     0.0079   15.7   0.0      0.017   14.7   0.0    1.4  1  Hint             Hint module
  ------ inclusion threshold ------
      0.056   14.0   0.0       0.18   12.3   0.0    1.8  2  ABC_tran         ABC transporter
      0.078   12.2   0.0        2.4    7.4   0.0    2.2  2  Zeta_toxin       Zeta toxin
      0.085   13.1   0.0        0.5   10.6   0.0    2.3  2  AAA_22           AAA domain


Domain annotation for each model (and alignments):
>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.1   0.0   4.3e-39   1.1e-35       4     221 ..     182     404 ..     179     406 .. 0.94
   2 !   13.5   0.0   1.1e-05     0.028     221     257 ..     679     714 ..     676     726 .. 0.84

  Alignments for each domain:
  == domain 1  score: 123.1 bits;  conditional E-value: 4.3e-39
                             T2SSE   4 lleallddekvsdihvekper.vkvrervdgielreveelekaalerlisriaalakldiseerplqdarlpekgvr 79 
                                       +le++l+d+   d+  +  ++ ++v++  ++   +++ +l +++l  +i ++    ++ is+ rp++da+lp +g r
  gi|385805971|ref|YP_005842369.1| 182 ILEPFLRDPYLEDVSASGIGNiFVVHKIFGS-LESNMGFLGDEELDEFIIKLGEKIGKPISSARPVVDATLP-DGSR 256
                                       78999****************7777777777.889999**********************************.**** PP

                             T2SSE  80 lrvvllPvvag..ealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkein 154
                                       +++v+   v     +++iR+ s++ +++ +l+  ++++++ia+ +   +re +++ v G T sGKtt+l+a+  +i+
  gi|385805971|ref|YP_005842369.1| 257 INIVFGSDVSLrgSNFTIRRVSKSPISVTQLVDWGTFDARIAAYVWMMLREGMSLFVCGETASGKTTSLNAISVFIK 333
                                       ***997644433599*************************************************************9 PP

                             T2SSE 155 ksderivtvEDpvEiqleganqvqlnak.....kakvtfadllraaLRlrPDrimvGEiRdketleilkAvn 221
                                        +  +iv +ED++E+   ++n ++  ++     + +vt+ dllraaLR+rP  i+vGEiR++e   + +A++
  gi|385805971|ref|YP_005842369.1| 334 PN-AKIVSIEDTAEVVFPHPNWTRELTRdtgrpESSVTMFDLLRAALRQRPNYIIVGEIRGAEGNIAFQAMQ 404
                                       99.********************9888889*********************************988899987 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 1.1e-05
                             T2SSE 221 nTGHlgslsTlHansaagalerLeqlgaeveaaelks 257
                                       nTGH++ +sT Ha +  + ++rL +    ++++++ +
  gi|385805971|ref|YP_005842369.1| 679 NTGHPV-MSTFHAADISKLIQRLTNPPISIPKTNMDN 714
                                       9*****.****************98776677776665 PP

>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.4   0.0   3.9e-21     1e-17      10     134 .]     424     679 ..     412     679 .. 0.88

  Alignments for each domain:
  == domain 1  score: 64.4 bits;  conditional E-value: 3.9e-21
                                       EEHHHHCC......ECTTEEEEEETTTTEEEEEE......EEEEEEEEEEEEEEEEETTS-EEEEETT-EEEECCT. CS
                                       xxxxxxxx......xxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                   Intein_splicing  10 vkieelve......kegeevlslnledlklevks......vkkliklklkelyeiklesgrkikaTpeHkllvvrd. 73 
                                       ++i+++v+      + + ++ + +++ l+l  +       ++ l +++ +e+y+i le+g+++k+T+ H+l+v++  
  gi|385805971|ref|YP_005842369.1| 424 TNIGDFVDsyykegE-EGKKFVKDVSVLSLSPNGkiifspIEYLLRHRAEEIYTIILENGSNLKVTGSHSLFVFDPs 499
                                       567777777775532.222222333333333333566666**********************************889 PP

                                       .TEEEEEECCC--TT-EEEEE........................................................ CS
                                       .xxxxxxxxxxxxxxxxxxxx........................................................ RF
                   Intein_splicing  74 .egivEkradeLkegdliavp........................................................ 93 
                                         +iv k + +Lkegd+++++                                                        
  gi|385805971|ref|YP_005842369.1| 500 tVQIVPKPVYKLKEGDYLIKAelkkerpllrksggeirggvlvferdlgvsskieelwkeslrvrrmnsirlsilnk 576
                                       899************************************************************************** PP

                                       ............................................................HSCEEEEEEEEEEEEEC CS
                                       ............................................................xxxxxxxxxxxxxxxxx RF
                   Intein_splicing  94 ............................................................dadvvwdkvksievede 110
                                                                                                   ++d+ +  vk+i++e++
  gi|385805971|ref|YP_005842369.1| 577 iferfniiaseitrfagensselydveipvngimklflsslfnklkgqarekmkrlfyllESDLELVMVKEIRKEKY 653
                                       ***************************************************************************** PP

                                       EEEEEEEEETTT-EEEE.CTTE.EE- CS
                                       xxxxxxxxxxxxxxxxx.xxxx.xxx RF
                   Intein_splicing 111 eeyVYdltvednhNFva.ngii.vHN 134
                                       e+ VYd++v++++ F++ +  + +HN
  gi|385805971|ref|YP_005842369.1| 654 EGFVYDVSVPGTQLFLGgERPFaLHN 679
                                       ****************9855444888 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 !   23.5   0.1   1.3e-08   3.5e-05       4      51 ..     285     337 ..     282     340 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.3e-08
                            AAA_29   4 lqlvNWgtfdgh....tieidlkg.atlltGpsGsGKSTllDAiqalLvpakk 51 
                                        qlv+Wgtfd +    ++++ ++g + ++ G++ sGK+T l Ai++ + p+ k
  gi|385805971|ref|YP_005842369.1| 285 TQLVDWGTFDARiaayVWMMLREGmSLFVCGETASGKTTSLNAISVFIKPNAK 337
                                       69********85334467888899888999****************9999875 PP

>> Hint  Hint module
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   6.5e-06     0.017      37     112 ..     448     517 ..     438     530 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6.5e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              Hint  37 kVlavdesgevvfsevllfldrdseqraefveietengekltlTpaHLvfvsenekssseeeeavfaskvregdyv 112
                                        Vl+++ +g+++fs++ + l ++ e   e ++i +eng++l++T +H +fv ++++ +     +    k +egdy+
  gi|385805971|ref|YP_005842369.1| 448 SVLSLSPNGKIIFSPIEYLLRHRAE---EIYTIILENGSNLKVTGSHSLFVFDPSTVQI---VPKPVYKLKEGDYL 517
                                       599**************99977655...689999*****************99886655...45555666666665 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   7.1e-05      0.18       7      47 ..     304     344 ..     300     373 .. 0.84
   2 ?   -3.9   0.0         7   1.8e+04      30      51 ..     386     408 ..     385     417 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.1e-05
                                       EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkpteGeilldgk 47 
                                        l+eg  + + Ge+ +GK+t l++++   kp++  + ++++
  gi|385805971|ref|YP_005842369.1| 304 MLREGMSLFVCGETASGKTTSLNAISVFIKPNAKIVSIEDT 344
                                       67899999***********************9999988743 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 7
                                       HHTTSS--SEEEEEET.TCEGGG CS
                                       xxxxxxxxxxxxxxxx.xxxxxx RF
                          ABC_tran  30 llagllkpteGeilld.gkdlke 51 
                                       ++ g+ + +eG+i ++ ++++++
  gi|385805971|ref|YP_005842369.1| 386 IIVGEIRGAEGNIAFQaMQSVSR 408
                                       68899999999999985555554 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0   0.00092       2.4      18      54 ..     310     345 ..     306     388 .. 0.80
   2 ?    2.5   0.0      0.03        77     121     197 ..     742     828 ..     732     830 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00092
                        Zeta_toxin  18 lillgGqpGAGKselaellkdelerqgnvvrldpDdl 54 
                                       ++++ G +++GK++ ++++   ++++ ++v ++ D+ 
  gi|385805971|ref|YP_005842369.1| 310 SLFVCGETASGKTTSLNAISVFIKPNAKIVSIE-DTA 345
                                       5799*******************9999999995.444 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.03
                        Zeta_toxin 121 GYevevvvvavkkelSrlgvldRyeeevae...........gRlvpkeehdeafeglresvealeeekqldrvkik. 185
                                       GY+    ++a+ + +++  v+dR++ ++++            R +p  +++e++e+l+   + ++   +l+   ++ 
  gi|385805971|ref|YP_005842369.1| 742 GYDPASDAIATMPVFTWDPVADRFLFSGKGssylleekiavMRGIPRGRINEIYEELETRRRYIQDLVDLK---VFd 815
                                       788888899****************9955556888899*866***************99999988755555...441 PP

                        Zeta_toxin 186 .drdgktvlydnn 197
                                        dr  k+v+y +n
  gi|385805971|ref|YP_005842369.1| 816 yDRVFKAVIYAEN 828
                                       1666677777766 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0    0.0002       0.5       5      29 ..     308     332 ..     304     392 .. 0.61
   2 ?   -2.0   0.0       1.5   3.9e+03      38      83 ..     595     637 ..     574     645 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0002
                            AAA_22   5 agilvvtGesGtGKTtllrrlleql 29 
                                         +l+v+Ge+ +GKTt+l+ +    
  gi|385805971|ref|YP_005842369.1| 308 GMSLFVCGETASGKTTSLNAISVFI 332
                                       56899*************9887665 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.5
                            AAA_22  38 erpevvfvtlpsstsskdllrellralglelkaerlsseelleale 83 
                                       +++e++ v++p+ +  k +l+ l+++l+ ++ +   + ++l+ +le
  gi|385805971|ref|YP_005842369.1| 595 NSSELYDVEIPVNGIMKLFLSSLFNKLKGQARE---KMKRLFYLLE 637
                                       677888899999999999999999999987777...6666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (845 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.81u 0.34s 00:00:01.15 Elapsed: 00:00:00.50
# Mc/sec: 5074.61
//
Query:       gi|385805972|ref|YP_005842370.1|  [L=546]
Description: archaeal flagellar protein FlaJ [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-12   46.7   0.3    1.5e-06   28.2   0.0    3.9  4  T2SSF     Type II secretion system (T2SS), protein F


Domain annotation for each model (and alignments):
>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -5.4   3.3         1   1.8e+04     116     118 ..      23      25 ..       8      50 .. 0.60
   2 !   28.2   0.0   8.3e-11   1.5e-06       2     121 ..      72     196 ..      71     197 .. 0.94
   3 ?   -4.9   4.4         1   1.8e+04     102     120 ..     215     233 ..     210     236 .. 0.46
   4 !   24.9   0.1   8.4e-10   1.5e-05      26     117 ..     343     437 ..     318     447 .. 0.78

  Alignments for each domain:
  == domain 1  score: -5.4 bits;  conditional E-value: 1
                                       XXX CS
                             T2SSF 116 lli 118
                                       +l+
  gi|385805972|ref|YP_005842370.1|  23 VLF 25 
                                       222 PP

  == domain 2  score: 28.2 bits;  conditional E-value: 8.3e-11
                                       HHHHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTS.SHHHHHC....T-TT.TS-HHHHHHHHHHHH CS
                             T2SSF   2 lrqlatllsaGvplveaLellaeeaengplaeelkriarrlraGg.slseale....rtpssefpelvvqliragee 73 
                                       l++l + + +  p    +e +++e  ++++++++ +i++  +++g s+++a +    + ++++++e++++l+ + + 
  gi|385805972|ref|YP_005842370.1|  72 LQHLLSVSTGNPPRSSLFEVVSKENIYPKYSPIFLKIYKLGKEWGySFPQACRlvgkEVGNKVLKEFLSRLSIVLSV 148
                                       677888888888899999**********************9998889******99998888899************* PP

                                       HT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXX CS
                             T2SSF  74 ggnLaevLerlaeyleeerelrrkllaallepllllvvallvllilla 121
                                       g +++++L+   + + + +e+++ +  + + + l +++ ll ++++++
  gi|385805972|ref|YP_005842370.1| 149 GEDVEQFLRTELSSILNIYETQYMRTIEAMNVFLGIYTSLLAASVFML 196
                                       *******************************************99996 PP

  == domain 3  score: -4.9 bits;  conditional E-value: 1
                                       HHTTXXXXXXXXXXXXXXX CS
                             T2SSF 102 llepllllvvallvllill 120
                                       + +  +++ ++++ l++++
  gi|385805972|ref|YP_005842370.1| 215 MSYAFVIATIGIVALVLYI 233
                                       4444444444444444443 PP

  == domain 4  score: 24.9 bits;  conditional E-value: 8.4e-10
                                       HSSHHHHHHHHHHHHHHHTTSSHHHHHC....T-TT.TS.-HHHHHHHHHHHHHT-HHHHHHHHHHHHHHHHHHHHH CS
                             T2SSF  26 aengplaeelkriarrlraGgslseale....rtpssef.pelvvqlirageeggnLaevLerlaeyleeerelrrk 97 
                                          g+l+++lk++++rl +G+++  a+     +t s e+ ++++  +  ++e+gg++++v   ++ +++    lrr+
  gi|385805972|ref|YP_005842370.1| 343 E-LGKLSKILKNLYARLMNGINPQIAWMmmaaETRS-ELaRRFLKIFEDTIEKGGKISQVGASISGHYNTIVGLRRN 417
                                       4.89************************99986666.555*****************************99999977 PP

                                       HHHHHHTTXXXXXXXXXXXX CS
                             T2SSF  98 llaallepllllvvallvll 117
                                       +l       ++ +++   ++
  gi|385805972|ref|YP_005842370.1| 418 RLQVAKTFEMTTYIMQGAIV 437
                                       66444333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (546 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       923  (0.0514808); 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:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.69u 0.32s 00:00:01.01 Elapsed: 00:00:00.52
# Mc/sec: 3143.69
//
Query:       gi|385805973|ref|YP_005842371.1|  [L=568]
Description: methionyl-tRNA synthetase [Fervidicoccus fontis Kam940]
Scores for complete 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-152  508.0   0.0   1.7e-152  507.7   0.0    1.1  1  tRNA-synt_1g   tRNA synthetases class I (M)
    6.5e-14   51.1   0.8    2.5e-05   22.8   0.0    4.0  3  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    8.9e-05   22.5   0.0    0.00017   21.6   0.0    1.4  1  Anticodon_1    Anticodon-binding domain of tRNA
  ------ inclusion threshold ------
      0.036   14.1   1.9      0.073   13.1   1.9    1.5  1  DZR            Double zinc ribbon
      0.042   12.8   0.0      0.082   11.8   0.0    1.4  1  tRNA-synt_1f   tRNA synthetases class I (K)
      0.072   13.1   3.4      0.076   13.0   0.5    2.1  2  zf-C2HC5       Putative zinc finger motif, C2HC5-type
        3.4    7.2  11.3         11    5.6   1.5    3.2  3  zf-ribbon_3    zinc-ribbon domain
        3.7    7.4   7.5        5.1    6.9   0.7    2.7  2  zinc_ribbon_2  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 !  507.7   0.0  7.7e-156  1.7e-152       2     391 .]       5     397 ..       4     397 .. 0.99

  Alignments for each domain:
  == domain 1  score: 507.7 bits;  conditional E-value: 7.7e-156
                                       EEEE--B--SS---HHHHH.HHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHHH CS
                      tRNA-synt_1g   2 lvttalpYangklHlGhll.evisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvheeikel 77 
                                       +v +a+pY+n+++HlG ++ + +s+D++ ++ +l ge+ ++v+g+DehG pie++A+k+g++p+ +++ +h+ +++l
  gi|385805973|ref|YP_005842371.1|   5 VVCAAWPYVNNVPHLGTMIgSLLSGDVYFKFLKLLGEDAVYVSGSDEHGSPIEVEAKKKGIEPKLMTDAMHSYVTKL 81 
                                       7999************************************************************************* PP

                                       HHHTT---SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG-EE........-TTS-EE-T CS
                      tRNA-synt_1g  78 fkklnisfdkygrttseehkelvqeifkklkekgliyekeieqlycpkderflpdryvegtCPkckseeargdqcee 154
                                        ++++i+f++y+rt++  h ++v++++ kl+e+g+i +k+    ycp d+ fl+dr++egtCP+c++e+argdqc++
  gi|385805973|ref|YP_005842371.1|  82 INDWEITFTNYSRTHNPVHINFVRDFVMKLYENGYIVKKKELLPYCPVDKIFLADRFIEGTCPYCGYEKARGDQCDN 158
                                       ***************************************************************************** PP

                                       TSSB-E................EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS- CS
                      tRNA-synt_1g 155 cgkkleptelinpksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdl 231
                                       cg+ l+ptelinp+++ +gskp++keteh+ffk++ ++++l ew+ +++ el +nvk+++ +w+ egLk+++i+rd+
  gi|385805973|ref|YP_005842371.1| 159 CGRLLTPTELINPHCVFCGSKPIYKETEHWFFKMDMLQNELLEWL-KNNDELDDNVKNYSINWVAEGLKERSITRDV 234
                                       *********************************************.88889************************** PP

                                       SSS-EET..TECCEEE-HHHHHHHHHHHTTTTT-...TTSGGGG.G--S......EEEEEGGGHHHHHTHHHHHHHH CS
                      tRNA-synt_1g 232 dwGipvP..gaekkvlYVWldAligYisatkelakkkgeeekwkeyWakdkevelvhfigkdiikFHtifwPaillg 306
                                       +wG+p P  gae+k++YVW+dAl+gYisa+ke ++k g++++++++W kdk+++ ++figkd+i+FH+i++P++l++
  gi|385805973|ref|YP_005842371.1| 235 SWGVPAPfpGAEGKTIYVWFDALLGYISAVKEHFEKIGRSDEFEKWW-KDKNTKTIYFIGKDNIPFHAIIFPSMLIA 310
                                       *****9888**************************************.99*************************** PP

                                       ..TT----S-EEEE--EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHHHHHHHHHHCCC CS
                      tRNA-synt_1g 307 ..aelklpkkvvaheyltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswedfvervNseLad 381
                                         +++ lp k++a+eyl ++++K+SkSrg++v+a+eale l+ad++R+ l++ +pe kD++fsw++f + +NseL+d
  gi|385805973|ref|YP_005842371.1| 311 srEGYPLPWKISATEYLLFQEEKFSKSRGIGVWADEALEILPADYWRFALIRMRPEAKDTNFSWSEFYRIINSELND 387
                                       999************************************************************************** PP

                                       HHHHHHHHH. CS
                      tRNA-synt_1g 382 klgnlvnRvl 391
                                       ++gnlv+Rvl
  gi|385805973|ref|YP_005842371.1| 388 DIGNLVHRVL 397
                                       ********85 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 !   22.8   0.0   1.1e-08   2.5e-05      24     112 ..       3      90 ..       1     141 [. 0.74
   2 !   20.6   0.5   4.9e-08   0.00011     358     433 ..     166     242 ..     154     297 .. 0.77
   3 ?    2.3   0.0     0.017        39     519     602 .]     289     373 ..     248     373 .. 0.67

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.1e-08
                       tRNA-synt_1  24 efilvdgPPyvtGslHiGhalaktlk.divirykrmkGkevlyvpGwDhaGlaieakvekklgakekkerkklgree 99 
                                       ++++ +  Pyv+  +H+G ++ + l  d+  ++ ++ G+++ yv G D +G +ie + +kk g++ k   ++  +  
  gi|385805973|ref|YP_005842371.1|   3 KYVVCAAWPYVNNVPHLGTMIGSLLSgDVYFKFLKLLGEDAVYVSGSDEHGSPIEVEAKKK-GIEPK-LMTDAMHSY 77 
                                       79999999****************976999*************************999988.56554.333333333 PP

                       tRNA-synt_1 100 frekvrewkaeya 112
                                        ++ + +w  +++
  gi|385805973|ref|YP_005842371.1|  78 VTKLINDWEITFT 90 
                                       3444444444443 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 4.9e-08
                       tRNA-synt_1 358 iehsvpfcerskkpiiyrateqWfvrvkeladaalkavekvqfvpkskekryaswlen.iqdWciSRqrwWGhripl 433
                                       +e+  p+c   +   iy+ te Wf +++ l++++l+ +++     +  ++   +w+++  ++  i R+  WG++ p+
  gi|385805973|ref|YP_005842371.1| 166 TELINPHCVFCGSKPIYKETEHWFFKMDMLQNELLEWLKNNDELDDNVKNYSINWVAEgLKERSITRDVSWGVPAPF 242
                                       556679999999999************************9999999988888999976489*************996 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.017
                       tRNA-synt_1 519 mlleGlDiirgWvarlillslaltgse....PfkevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltli 591
                                       ++  G D i +  + +i+ s+ +  +e    P+k   ++ l+ +e   K SKs g  +  ++ ++ + ad  R++li
  gi|385805973|ref|YP_005842371.1| 289 IYFIGKDNIPF--HAIIFPSMLIASREgyplPWKISATEYLLFQE--EKFSKSRGIGVWADEALEILPADYWRFALI 361
                                       55556666654..34455555554444555577766677676665..59**************************** PP

                       tRNA-synt_1 592 .lsdvgrdinls 602
                                        + +  +d+n+s
  gi|385805973|ref|YP_005842371.1| 362 rMRPEAKDTNFS 373
                                       999999999985 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 !   21.6   0.0   7.4e-08   0.00017       3     109 ..     420     538 ..     418     566 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 7.4e-08
                       Anticodon_1   3 wilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkra..aqevllevletllrll 77 
                                        +l+ ++++ +e+ +ay + +++ a +++ e       + yl++  p+   +++ ++ a  + +++l +++ l+ ll
  gi|385805973|ref|YP_005842371.1| 420 KLLNDMERFYNEAIAAYSNAKLKLASDKILEM--ARRGNQYLNSQAPWDEIKESRER-AgtIIYNMLNYVNVLMTLL 493
                                       6899999************************7..8899**********977766554.33355************** PP

                       Anticodon_1  78 aPfmPfitEelwqr..............eeeelgkkesimlaewpe 109
                                        P++P  +E  +                 +e+l++ +si +++ p 
  gi|385805973|ref|YP_005842371.1| 494 WPITPSSSEAFYSIlningpkegglrriIQEKLESGKSI-RQPQPI 538
                                       ************546676666666666633344555555.444443 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.9   3.2e-05     0.073      15      48 ..     143     173 ..     131     185 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.2e-05
                               DZR  15 CseCgtklkavaaedrCpsCgekvdpearfCpeC 48 
                                       C++Cg +     + d+C++Cg+ ++p++ + p+C
  gi|385805973|ref|YP_005842371.1| 143 CPYCGYEKA---RGDQCDNCGRLLTPTELINPHC 173
                                       666655533...2556666666655555553333 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.7e-05     0.082     262     316 ..     314     368 ..     278     383 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.7e-05
                      tRNA-synt_1f 262 ggeaPekvvYelillkggekmssSkGnvltledwlevaepevlrflilrrkPkka 316
                                       g++ P k+     ll ++ek s+S+G ++  +++le+++ +  rf ++r +P+ +
  gi|385805973|ref|YP_005842371.1| 314 GYPLPWKISATEYLLFQEEKFSKSRGIGVWADEALEILPADYWRFALIRMRPEAK 368
                                       5555655555445566777********************************9854 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 ?    0.4   0.1       0.3   6.8e+02      34      42 ..     140     148 ..     125     155 .. 0.78
   2 ?   13.0   0.5   3.4e-05     0.076      19      49 ..     155     186 ..     150     188 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.3
                          zf-C2HC5  34 skpCsfCgs 42 
                                       +++C++Cg 
  gi|385805973|ref|YP_005842371.1| 140 EGTCPYCGY 148
                                       579****95 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 3.4e-05
                          zf-C2HC5  19 nClnCGkiiCakeglskpCsfCg.spllssee 49 
                                       +C nCG  +   e ++ +C fCg +p+++++e
  gi|385805973|ref|YP_005842371.1| 155 QCDNCGRLLTPTELINPHCVFCGsKPIYKETE 186
                                       6**********************677777665 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   1.5    0.0049        11      18      24 ..     142     148 ..     141     150 .. 0.84
   2 ?    4.4   2.4     0.012        27       4      23 ..     155     177 ..     152     179 .. 0.68
   3 ?    2.2   0.4     0.057   1.3e+02       4      11 ..     172     180 ..     170     183 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0049
                       zf-ribbon_3  18 vCpyCGt 24 
                                       +CpyCG+
  gi|385805973|ref|YP_005842371.1| 142 TCPYCGY 148
                                       5999998 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.012
                       zf-ribbon_3   4 rCPnCGaplssdd...nvCpyCG 23 
                                       +C nCG +l++     ++C  CG
  gi|385805973|ref|YP_005842371.1| 155 QCDNCGRLLTPTElinPHCVFCG 177
                                       7******8899862224566666 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.057
                       zf-ribbon_3   4 rCPnCGa.p 11 
                                       +C  CG+ p
  gi|385805973|ref|YP_005842371.1| 172 HCVFCGSkP 180
                                       799999866 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   0.7    0.0023       5.1      16      22 ..     143     149 ..     137     150 .. 0.86
   2 ?    3.1   1.0     0.036        82       2      21 ..     156     178 ..     155     179 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0023
                     zinc_ribbon_2  16 CpyCGtp 22 
                                       CpyCG++
  gi|385805973|ref|YP_005842371.1| 143 CPYCGYE 149
                                       9***996 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.036
                     zinc_ribbon_2   2 CpnCGaelqdnakF...CpyCGt 21 
                                       C nCG+ l +++     C  CG+
  gi|385805973|ref|YP_005842371.1| 156 CDNCGRLLTPTELInphCVFCGS 178
                                       89999999998888888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (568 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); 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: 0.72u 0.33s 00:00:01.05 Elapsed: 00:00:00.53
# Mc/sec: 3210.88
//
Query:       gi|385805974|ref|YP_005842372.1|  [L=374]
Description: 2-oxoacid:ferredoxin oxidoreductase, fused gamma and delta subunits [Fervidicoccus fontis Kam940]
Scores for complete 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   49.9  15.8    1.1e-07   31.3   5.6    2.3  2  Fer4      4Fe-4S binding domain
    6.8e-09   35.4  15.7    1.9e-05   24.5   5.1    2.3  2  Fer4_6    4Fe-4S binding domain
      7e-09   36.5   4.7    0.00015   22.6   0.2    2.6  2  Fer4_16   4Fe-4S double cluster binding domain
    2.7e-08   33.8   6.2    4.5e-05   23.5   0.3    2.4  2  Fer4_10   4Fe-4S dicluster domain
    3.9e-08   33.8  22.3      3e-06   27.7  12.0    2.2  2  Fer4_7    4Fe-4S dicluster domain
    3.9e-08   33.3   9.4    7.2e-08   32.4   9.4    1.5  1  Fer4_21   4Fe-4S dicluster domain
    2.3e-07   30.5  13.2    0.00012   22.0   3.1    2.3  2  Fer4_2    4Fe-4S binding domain
      4e-06   27.2   1.4      0.055   13.9   0.2    2.4  2  Fer4_8    4Fe-4S dicluster domain
    5.5e-06   26.5  12.6      0.002   18.5   3.4    2.2  2  Fer4_4    4Fe-4S binding domain
    2.2e-05   24.9   4.0      0.044   14.3   0.3    2.4  2  Fer4_17   4Fe-4S dicluster domain
    2.5e-05   24.3  11.1    9.7e-05   22.5  11.4    1.8  2  Fer4_9    4Fe-4S dicluster domain
     0.0027   18.4   6.5      0.043   14.6   0.3    2.7  2  Fer4_15   4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.043   14.4  11.8        0.8   10.3   1.2    2.7  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
      0.055   13.5   0.1       0.15   12.1   0.1    1.7  1  POR       Pyruvate ferredoxin/flavodoxin oxidoreductase
        8.6    7.6  17.3        6.4    8.0   6.5    2.3  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 !   24.2   2.5   1.6e-08     2e-05       1      24 []     297     320 ..     297     320 .. 0.95
   2 !   31.3   5.6   9.4e-11   1.1e-07       1      24 []     324     347 ..     324     347 .. 0.95

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.6e-08
                                       EEEETTTSSS-THHHHHSTTTEEE CS
                              Fer4   1 vvideekCigCGaCvevCPvgAIt 24 
                                       ++id+ +C+ C++C   CP gAI+
  gi|385805974|ref|YP_005842372.1| 297 PIIDYKRCTDCKLCHYYCPDGAIS 320
                                       68********************96 PP

  == domain 2  score: 31.3 bits;  conditional E-value: 9.4e-11
                                       EEEETTTSSS-THHHHHSTTTEEE CS
                              Fer4   1 vvideekCigCGaCvevCPvgAIt 24 
                                       ++id++ C gCG+C++vCP  AI+
  gi|385805974|ref|YP_005842372.1| 324 IKIDYDYCKGCGICANVCPAKAIS 347
                                       68********************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 !   16.6   2.8     5e-06     0.006       2      24 .]     297     319 ..     296     319 .. 0.93
   2 !   24.5   5.1   1.6e-08   1.9e-05       2      24 .]     324     346 ..     323     346 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5e-06
                            Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                       + id+ +C++C  C   CP gai
  gi|385805974|ref|YP_005842372.1| 297 PIIDYKRCTDCKLCHYYCPDGAI 319
                                       569*******************8 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 1.6e-08
                            Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                       + id+d C gCg C++vCP++ai
  gi|385805974|ref|YP_005842372.1| 324 IKIDYDYCKGCGICANVCPAKAI 346
                                       789******************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 !   14.9   0.7   3.1e-05     0.037       1      20 [.     303     322 ..     303     329 .. 0.86
   2 !   22.6   0.2   1.2e-07   0.00015       2      21 ..     331     350 ..     330     370 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.1e-05
                           Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                       rC++C+ C   CP +ai+ +
  gi|385805974|ref|YP_005842372.1| 303 RCTDCKLCHYYCPDGAISFN 322
                                       6****************977 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 1.2e-07
                           Fer4_16   2 CgtCgkCaevCPtnaikekk 21 
                                       C++Cg Ca+vCP++ai++ +
  gi|385805974|ref|YP_005842372.1| 331 CKGCGICANVCPAKAISMVS 350
                                       ****************9883 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   1.3   9.3e-05      0.11       2      21 ..     297     316 ..     296     322 .. 0.88
   2 !   23.5   0.3   3.7e-08   4.5e-05       2      40 ..     324     362 ..     323     366 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.3e-05
                           Fer4_10   2 vvidddtCirCgkCvkaCPa 21 
                                       ++id ++C+ C+ C   CP 
  gi|385805974|ref|YP_005842372.1| 297 PIIDYKRCTDCKLCHYYCPD 316
                                       5899**************96 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 3.7e-08
                           Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrk 40 
                                       ++id d C +Cg C ++CPa++ s++ + e  e+ ++r+
  gi|385805974|ref|YP_005842372.1| 324 IKIDYDYCKGCGICANVCPAKAISMVSELEHLEGLKDRE 362
                                       689*****************8877777777766666665 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  12.0   2.5e-09     3e-06       1      52 []     303     345 ..     303     345 .. 0.96
   2 !   19.5   2.6   9.5e-07    0.0011       2      22 ..     331     351 ..     330     363 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 2.5e-09
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       rC+ C+ C  +Cp +ai++++         ++id+++C gCg C++vCP++a
  gi|385805974|ref|YP_005842372.1| 303 RCTDCKLCHYYCPDGAISFNP---------IKIDYDYCKGCGICANVCPAKA 345
                                       8******************99.........69*****************986 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 9.5e-07
                            Fer4_7   2 CigCgaCvaaCpvkaieldee 22 
                                       C gCg C+++Cp+kai++  e
  gi|385805974|ref|YP_005842372.1| 331 CKGCGICANVCPAKAISMVSE 351
                                       ****************99865 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   9.4   6.1e-11   7.2e-08       2      59 .]     298     348 ..     297     348 .. 0.90

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 6.1e-11
                           Fer4_21   2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedciem 59 
                                       +id ++C +C++C+  C+d    ai++++   +k+  d C GC +C++vCP  ++i+m
  gi|385805974|ref|YP_005842372.1| 298 IIDYKRCTDCKLCHYYCPD---GAISFNP---IKIDYDYCKGCGICANVCPA-KAISM 348
                                       6999**************9...7899975...67799**************5.99998 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   2.6   3.6e-05     0.043       2      21 ..     296     315 ..     295     316 .. 0.92
   2 !   22.0   3.1   9.6e-08   0.00012       2      22 .]     323     343 ..     322     343 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.6e-05
                            Fer4_2   2 pvvvdtdrCigCgaCvsaCP 21 
                                       ++ +d  rC+ C+ C   CP
  gi|385805974|ref|YP_005842372.1| 296 RPIIDYKRCTDCKLCHYYCP 315
                                       5789***********999*9 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 9.6e-08
                            Fer4_2   2 pvvvdtdrCigCgaCvsaCPa 22 
                                       p+++d d C gCg+C ++CPa
  gi|385805974|ref|YP_005842372.1| 323 PIKIDYDYCKGCGICANVCPA 343
                                       6899****************8 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.1   0.00017       0.2      46      63 ..     299     316 ..     248     318 .. 0.81
   2 !   13.9   0.2   4.6e-05     0.055       3      63 ..     329     343 ..     325     371 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00017
                            Fer4_8  46 ealwsCttcgaCtevCpv 63 
                                          ++Ct c+ C   Cp 
  gi|385805974|ref|YP_005842372.1| 299 IDYKRCTDCKLCHYYCPD 316
                                       557899999999999996 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 4.6e-05
                            Fer4_8   3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63 
                                       ++C +Cg C + Cp                                               
  gi|385805974|ref|YP_005842372.1| 329 DYCKGCGICANVCP----------------------------------------------A 343
                                       45666666666666..............................................3 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   3.4   1.6e-06     0.002       2      17 .]     302     317 ..     301     317 .. 0.92
   2 !   13.2   1.8   8.5e-05       0.1       2      16 ..     329     343 ..     328     350 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.6e-06
                            Fer4_4   2 erCigCgsCvaaCPqg 17 
                                       +rC++C+ C+++CP+g
  gi|385805974|ref|YP_005842372.1| 302 KRCTDCKLCHYYCPDG 317
                                       8*************86 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 8.5e-05
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       + C gCg C ++CP 
  gi|385805974|ref|YP_005842372.1| 329 DYCKGCGICANVCPA 343
                                       89************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 !   14.3   0.3   3.7e-05     0.044      43      59 ..     301     317 ..     280     318 .. 0.85
   2 !   11.3   0.3   0.00032      0.38       2      15 ..     331     344 ..     328     369 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.7e-05
                           Fer4_17  43 aslCieCgeCerkCPqg 59 
                                        ++C+ C++C ++CP g
  gi|385805974|ref|YP_005842372.1| 301 YKRCTDCKLCHYYCPDG 317
                                       689************76 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00032
                           Fer4_17   2 CiqCgyClpeCpsy 15 
                                       C +Cg C+++Cp  
  gi|385805974|ref|YP_005842372.1| 331 CKGCGICANVCPAK 344
                                       88888888888864 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   2.0   7.7e-05     0.092      33      51 .]     294     319 ..     280     319 .. 0.70
   2 !   22.5  11.4   8.1e-08   9.7e-05       1      51 []     303     346 ..     303     346 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.7e-05
                            Fer4_9  33 e.......eaCigCgaCveaCpkgai 51 
                                       +       ++C++C+ C   Cp gai
  gi|385805974|ref|YP_005842372.1| 294 WqrpiidyKRCTDCKLCHYYCPDGAI 319
                                       24445555789999999999998876 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 8.1e-08
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                       +Ct+C+ C++ Cp g+++    +    +       C gCg C+++Cp +ai
  gi|385805974|ref|YP_005842372.1| 303 RCTDCKLCHYYCPDGAISFNPIKIDYDY-------CKGCGICANVCPAKAI 346
                                       6*****************9999999887.......************9987 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   1.4     0.018        22       3      20 ..     299     316 ..     298     319 .. 0.92
   2 !   14.6   0.3   3.6e-05     0.043       1      19 [.     324     342 ..     324     358 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.018
                           Fer4_15   3 vDrdaCigcglCvaeape 20 
                                       +D ++C+ c lC   +p+
  gi|385805974|ref|YP_005842372.1| 299 IDYKRCTDCKLCHYYCPD 316
                                       8*************9997 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 3.6e-05
                           Fer4_15   1 VvvDrdaCigcglCvaeap 19 
                                       +++D d C gcg C+ ++p
  gi|385805974|ref|YP_005842372.1| 324 IKIDYDYCKGCGICANVCP 342
                                       79****************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 ?   10.3   1.2   0.00067       0.8       1      18 [.     299     316 ..     299     317 .. 0.94
   2 ?    9.2   2.5    0.0014       1.7       1      18 [.     326     343 ..     326     344 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00067
                           Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                       +D ++C++c++C   +Pd
  gi|385805974|ref|YP_005842372.1| 299 IDYKRCTDCKLCHYYCPD 316
                                       7899*************8 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0014
                           Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                       +D d C +cg+C++++P 
  gi|385805974|ref|YP_005842372.1| 326 IDYDYCKGCGICANVCPA 343
                                       79999************5 PP

>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00013      0.15      70     160 ..     111     194 ..      34     205 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                                       H.HHGGGEEEEEEEEEECTCGTT-CCHHHCTS-HHHHHHHT-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHT. CS
                               POR  70 s.ehldglkpggiiiynseelkpdelkkakeeerelkerlgvrvygvdatkiakeiggneraaNtvmlGalaallg. 144
                                           +dg k++ i+++n++  ++d++k  k  + ++++    rv++++a +i   i+         mlGa+a + + 
  gi|385805974|ref|YP_005842372.1| 111 RaLLFDGAKKNAILVVNTSISPDDVVKLVKKYNLAQDW--FGRVVTISAARIDSAIA-------YPMLGAVASAWDr 178
                                       2456899***********98888888888876655555..67777777777765555.......599****999999 PP

                                       S-HHHHHHHHHCCS-C CS
                               POR 145 lplealeeaikkrfpk 160
                                       ++l++l++a     ++
  gi|385805974|ref|YP_005842372.1| 179 VDLDSLLAAADIFGKE 194
                                       9999999886544444 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   3.1     0.036        43       1      15 []     304     318 ..     304     318 .. 0.93
   2 ?    8.0   6.5    0.0053       6.4       1      15 []     331     345 ..     331     345 .. 0.94

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.036
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       Ct C +C   CP gA
  gi|385805974|ref|YP_005842372.1| 304 CTDCKLCHYYCPDGA 318
                                       99**********877 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0053
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C gCg C +vCP +A
  gi|385805974|ref|YP_005842372.1| 331 CKGCGICANVCPAKA 345
                                       9***********887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); 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:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2855.56
//
Query:       gi|385805975|ref|YP_005842373.1|  [L=412]
Description: 2-oxoacid:ferredoxin oxidoreductase subunit alpha [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-46  157.7   0.5    4.9e-46  157.3   0.5    1.1  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    3.3e-22   78.7   0.0    6.4e-22   77.8   0.0    1.5  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
     0.0016   18.3   0.0      0.013   15.4   0.0    2.5  2  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 !  157.3   0.5   8.2e-50   4.9e-46       2     203 ..      30     227 ..      29     255 .. 0.91

  Alignments for each domain:
  == domain 1  score: 157.3 bits;  conditional E-value: 8.2e-50
                                       HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCC CS
                             POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmien 78 
                                       a++ a+vdvi+aYPI P + i+++la+++a+ge   ++vv + sE+++++ v +A+a Gar+++ +Sg Gl+++ e+
  gi|385805975|ref|YP_005842373.1|  30 AVKVADVDVISAYPIRPYTGIMNALASMIANGEF-IADVVIADSEHSQFEIVKHASAVGARTFVGSSGVGLAYAAEA 105
                                       77889****************************8.89**************************************** PP

                                       HHHHHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHHS---EEEE-SSHHHHHHHHHHHHHHHHH..CTSEEEEEE CS
                             POR_N  79 lglaageelPvvivvvaRalpstglsirtdqsDlmaardtglivlasenvqeafdlalvAfnlAek..vrvPvivlf 153
                                       ++++a ++lPvv ++ +Ral+++  +   ++sD+++ rd+g+++ ++++vqea+d++lvA+++Ae+  v +P +v++
  gi|385805975|ref|YP_005842373.1| 106 IIVTALSQLPVVGAIGTRALDDP-GNFGMEWSDVLMFRDYGWLISWAKTVQEAHDMTLVAYRVAEDkrVLLPHFVVL 181
                                       ***********************.9****************************************999********* PP

                                       EHHHH.HEEEEEEC-SGG.GS-----SBXXXXXXXXSXXX.BXXTXXTSSX CS
                             POR_N 154 Dgfllshevekvelpdeedelklikekleeyerkeyaldp.ekpiargtaa 203
                                       Dg  l+h + ++   ++e     ++++l++y++ +  +dp + p++  +  
  gi|385805975|ref|YP_005842373.1| 182 DGAALTHVATPIVPVTKE----QATDFLPPYKPPY-RIDPiDGPVTKAQHI 227
                                       ************999999....8999999999866.888856666655544 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 !   77.8   0.0   1.1e-25   6.4e-22       1     101 [.     278     382 ..     278     383 .. 0.96

  Alignments for each domain:
  == domain 1  score: 77.8 bits;  conditional E-value: 1.1e-25
                                       -SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G...-HHHHHH CS
                           PFOR_II   1 AevvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgse...Gqlveev 74 
                                       A++++++mG+ +++++ +++++Re+g+k+G +rlr++rPFP+e+l +++++vk+  v++  +sfgs+   G l++e+
  gi|385805975|ref|YP_005842373.1| 278 ADFALIGMGAYMKDIEIVAKRMREKGVKIGTIRLRYVRPFPAEDLLRVIDGVKAAGVIEFGYSFGSPfgtGSLYHEI 354
                                       89****************************************************************9999******* PP

                                       HHHTGGG..TSEEEEEE--GGG----HHH CS
                           PFOR_II  75 kaalkks..kvkvvnfvaglgGrditved 101
                                       +++l++   ++++++f+  lgGr+++ve+
  gi|385805975|ref|YP_005842373.1| 355 ATSLYETntRPELLDFLF-LGGREPKVEH 382
                                       *****9998888888876.6****99998 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.28   1.7e+03       3      17 ..     151     165 ..     150     167 .. 0.90
   2 !   15.4   0.0   2.1e-06     0.013       8      62 ..     276     330 ..     272     366 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.28
                                       EEEEETTSSEEEEEE CS
                   Transketolase_C   3 aeilregkdvtlvay 17 
                                       a++++e +d+tlvay
  gi|385805975|ref|YP_005842373.1| 151 AKTVQEAHDMTLVAY 165
                                       688999********8 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 2.1e-06
                                       TTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHS CS
                   Transketolase_C   8 egkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktg 62 
                                       e  d +l+++G+ ++    +a++ +++g+++  + lr v+p+  e++l ++   +
  gi|385805975|ref|YP_005842373.1| 276 EDADFALIGMGAYMKDIEIVAKRMREKGVKIGTIRLRYVRPFPAEDLLRVIDGVK 330
                                       567899*************************************999987666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 2490.69
//
Query:       gi|385805976|ref|YP_005842374.1|  [L=319]
Description: 2-oxoacid:ferredoxin oxidoreductase subunit beta [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-20   72.7   0.1    4.1e-20   72.1   0.1    1.3  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
  ------ inclusion threshold ------
      0.028   14.2   0.0       0.04   13.7   0.0    1.1  1  PBC           PBC 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 !   72.1   0.1   4.6e-24   4.1e-20       2     153 .]      52     224 ..      51     224 .. 0.85

  Alignments for each domain:
  == domain 1  score: 72.1 bits;  conditional E-value: 4.6e-24
                                       SSHHHH.HHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHH..........ST.TSEEEEEEEHHHHHHT.GGGH CS
                      TPP_enzyme_C   2 iGcltl.waarllkvkrprsyltsgglgtmGyglpaAiGakla..........kp.drevvaivGDGgflmi.lqel 65 
                                       +Gc+ +  a+++  +++p+s+  +  ++ +G g +aAiG++ a          kp d +v+++ GDG++++i l+ l
  gi|385805976|ref|YP_005842374.1|  52 TGCMYVaNAHQF--LTSPYSV--PWHHTQLGGGGAAAIGIASAlrtlmlkgkrKPeDINVIVMGGDGAMADIgLSGL 124
                                       688887223333..2335443..458***************94455566677678678******************* PP

                                       HHHHHTT-.SEEEEEEE-SBCCCHHHH...HHHHTCCTTTTSBB.......BS----HHHHHHHT.TSE.EEEESSH CS
                      TPP_enzyme_C  66 atavrrnl.pitvvvlnNegygmtggq...qepfggkrksgpagk......dlkpvdfaklaeal.Gak.garveka 130
                                       +    ++   ++++v++Negy++tg q   ++p+g+ ++++p+gk      + +++++a +a+++  +k +a+ +  
  gi|385805976|ref|YP_005842374.1| 125 SMGLSYDYqRLLYIVYDNEGYMNTGVQassTTPWGATTTFTPSGKvkplgnTRYKKNVALIAASHpNVKyVATATLW 201
                                       *******99*****************************************889999********9999999955555 PP

                                       .HHHHHHHHHHHHCSSSEEEEEE CS
                      TPP_enzyme_C 131 dveeleealkealekkgpaliev 153
                                        + +l +++ +al+++gp++i++
  gi|385805976|ref|YP_005842374.1| 202 PPLDLMNKVVRALNSGGPSVIHA 224
                                       55*******************95 PP

>> PBC  PBC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.5e-06      0.04     134     175 ..     272     313 ..     265     315 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.5e-06
                               PBC 134 ehvrnllreqsetRPisekeiermvsiiskkfsaiqiqlkqs 175
                                       +hvr+ l  q+++R    ++i++m ++i+++  + ++  kq+
  gi|385805976|ref|YP_005842374.1| 272 KHVREYLSLQGRFRHLKDEDIDKMDKMIEEEWFYWNESAKQE 313
                                       79***************************9988888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); 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: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1928.20
//
Query:       gi|385805977|ref|YP_005842375.1|  [L=418]
Description: multiple substrate aminotransferase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-42  145.3   0.0    2.9e-42  145.1   0.0    1.1  1  Aminotran_1_2   Aminotransferase class I and II
    1.2e-10   40.8   0.0    2.2e-10   39.9   0.0    1.3  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 !  145.1   0.0   3.2e-46   2.9e-42      30     363 .]      70     405 ..      42     405 .. 0.89

  Alignments for each domain:
  == domain 1  score: 145.1 bits;  conditional E-value: 3.2e-46
                                       HHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THH CS
                     Aminotran_1_2  30 galaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasy 106
                                       + +   ++ +yg++ g   l++a+ +++++++ +++ ++ +++ ++G++++++++ +++ +npgd++++ +pty s 
  gi|385805977|ref|YP_005842375.1|  70 IKNHAAQALQYGTTNGFTPLRNAIVEWMKKKYSIQISKD-NLIITTGSQQALDLIGRVF-INPGDVVIAEAPTYLSA 144
                                       346777899******************************.*******************.***************** PP

                                       HHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-.TTT--B--HHHHHHHHHHHHHTTE CS
                     Aminotran_1_2 107 knilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesph.NPtGtvatleeleklldlakkynl 182
                                        +++++++ e+v++pl+   d ++ ++ lee+lke++++ k +k++++ s++ NP G+ ++++  +++l+la +y +
  gi|385805977|ref|YP_005842375.1| 145 LQAFEYYKPEFVQIPLD---DEGIRIDLLEEKLKELKSQGKSVKFVYTISIFqNPAGVTMSEKRRKEILELASQYDF 218
                                       ***************77...889***************************966************************ PP

                                       EEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTS..SHHHH CS
                     Aminotran_1_2 183 llfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlrklsrpfls..ssllq 257
                                       +++ D  Y+++ +  +   + +   +++  +l +g+lsK + ++G+R+G+i+g++++++ l+++++++    s+  q
  gi|385805977|ref|YP_005842375.1| 219 IIIEDNPYGELRYSGSPIRP-IKSWDDDGRVLYLGTLSKVL-APGFRIGWIAGDPRFINKLEIAKQSVDLctSTFNQ 293
                                       ************99764444.6666666678********88.6*******************999998665488888 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS...TEEEECCSCSSEEEEEETHH.CHHHHHHHHHHTCTE CS
                     Aminotran_1_2 258 aavaaalsdallkqseleemrqrlqkrrkelrdeLael...glkvlasqsgmflltdlsae.takelskkLleevgv 330
                                        ++ + ++   l ++++ + ++ ++ rr+ + ++L++    g+k++++++gmf ++  ++  + k +++k + + gv
  gi|385805977|ref|YP_005842375.1| 294 VIAWKYIEGGYL-DKQIPKIVEFYKPRRDAMLKALEDFmpeGVKWTKPEGGMFIWVTAPEGiDTKLMFEKAVAK-GV 368
                                       888888888775.45********************777*****************7666668888888999999.** PP

                                       EEEEGGGGTS....TTEEEEECTTS-HHHHHHHHHHH CS
                     Aminotran_1_2 331 yvtpgtsftv....pgrlRitvAglteeeleelveal 363
                                       + +pg+ f++    ++  R+++  ++ee+++e +++l
  gi|385805977|ref|YP_005842375.1| 369 AYVPGEAFYAhrevKNAMRLNFTYVSEEKIREGISRL 405
                                       **************999*****99*******999886 PP

>> Aminotran_MocR  Alanine-glyoxylate amino-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.0   2.4e-14   2.2e-10     127     410 ..     134     410 ..     125     417 .. 0.84

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 2.4e-14
                                       EEEEES--HHHHHHHHHHT-EEEEEEEETTEE-HHHHH....HHHHC-TTEEEEEE-SSS-TTT-----HHHHHHHH CS
                    Aminotran_MocR 127 llvtvpGydrhfllleelGielltvdlqddGpdvdave....klvaedasvkGilavpkysnptGetiseevarrla 199
                                       ++  +p y   +   e +  e++ ++l+d+G  +d +e    +l ++  svk ++++  + np+G t+se++ +++ 
  gi|385805977|ref|YP_005842375.1| 134 VIAEAPTYLSALQAFEYYKPEFVQIPLDDEGIRIDLLEeklkELKSQGKSVKFVYTISIFQNPAGVTMSEKRRKEIL 210
                                       567788898889999999999**********9998654222179999**********************99888888 PP

                                       T---SSTT-EEEEE-TTSS-BS.SSSS----HHHHHHHHT-TTSEEEEEESTTTS-TTSS-EEEEE-HHHHHHHHHH CS
                    Aminotran_MocR 200 alkaaapdfrifaddayavhdlvaeedkdanivalardaGhpdrafvlastskitfaGaGvafvassedniawlkky 276
                                        l a+  df i  d+ y        +      +   ++     r + l + sk+   G  ++ +a  +  i+ l+  
  gi|385805977|ref|YP_005842375.1| 211 EL-ASQYDFIIIEDNPYGELRY--SGS----PIRPIKSWDDDGRVLYLGTLSKVLAPGFRIGWIAGDPRFINKLEIA 280
                                       87.5678**********75554..332....23344555666799****************************9998 PP

                                       HHHC-S---HHHHHHHHHHHHHSTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTSSEEE---SBSS-EEEEESSS- CS
                    Aminotran_MocR 277 lGlqsiGpdkveqlrhvkflkdyeGlealmrdhaeliapkfeavlevleaelggaevatwteprGGyfisldtldgv 353
                                            +    ++q+   k++++   l  ++ +  e+ +p+ +a+l++le+ +  +    wt+p+GG fi + + +g+
  gi|385805977|ref|YP_005842375.1| 281 KQSVDLCTSTFNQVIAWKYIEGG-YLDKQIPKIVEFYKPRRDAMLKALEDFMPEG--VKWTKPEGGMFIWVTAPEGI 354
                                       88888999**********99864.599999*******************998743..68*****************9 PP

                                       HHH.HHHHHHHCTEE---TTTTSSTT--SSS-EEEE--SSS-HHHHHHHHHHHHHHHH CS
                    Aminotran_MocR 354 akr.vvklaeeaGvsltaaGatypaGedpkdrnirlaptlppleevetamdvvatcvk 410
                                         + + + a + Gv+  +  a y +  + k+  +rl  t  + e++++ ++ +a  +k
  gi|385805977|ref|YP_005842375.1| 355 DTKlMFEKAVAKGVAYVPGEAFYAHR-EVKN-AMRLNFTYVSEEKIREGISRLAETIK 410
                                       877256889999******99988875.4555.599999*9999999999998887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       754  (0.0420548); expected 358.6 (0.02)
Passed bias filter:                      613  (0.0341904); 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 0.27s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2778.25
//
Query:       gi|385805978|ref|YP_005842376.1|  [L=519]
Description: lysyl-tRNA synthetase [Fervidicoccus fontis Kam940]
Scores for complete 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-69  234.5   0.0      2e-69  234.1   0.0    1.1  1  tRNA-synt_2      tRNA synthetases class II (D, K and N)
    3.1e-16   59.1   0.0    1.1e-15   57.4   0.0    2.0  2  tRNA_anti-codon  OB-fold nucleic acid binding domain
    9.9e-05   22.2   0.2    0.00032   20.6   0.2    1.9  1  Rho_N            Rho termination factor, N-terminal domain
     0.0045   16.5   0.0      0.017   14.6   0.0    1.9  2  tRNA-synt_2d     tRNA synthetases class II core domain (F)
  ------ inclusion threshold ------
      0.012   15.8   0.0      0.021   15.0   0.0    1.5  1  tRNA_anti_2      OB-fold nucleic acid binding domain


Domain annotation for each model (and alignments):
>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  234.1   0.0   5.4e-73     2e-69       2     311 ..     151     491 ..     150     493 .. 0.91

  Alignments for each domain:
  == domain 1  score: 234.1 bits;  conditional E-value: 5.4e-73
                                       CCHHHHTHHHHC.CSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE-E-S CS
                                       xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2   2 eelrlknryldl.rtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeffaLtq 77 
                                        e r+++ryld+  ++kv+k l    ++ + +r +l++++f+e++tP ++   +++ a++F++k ++  +++ +L +
  gi|385805978|ref|YP_005842376.1| 151 PEQRYRERYLDIlLNSKVRKALVDLYKIEMTMRLILDKKNFVEVHTPKIQPIYGGALAKPFVTKIEAL-DRMGYLSI 226
                                       5889********9**************************************************99999.56667*** PP

                                       -SHHHHHHHHHCTHSEEEEEEEEE--S--BTTB-S-CEEEEEEEEET-SCHHHHHHHHHHHHHHHHHHHHCSCCCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  78 spqlylellivagidrvfqiaraFRaEdsrtdrhlaEFtqieaemsfieeedimqvleelikslvkevlessakdie 154
                                       +p+ yl++l+vag++rv++ia +FR+Ed++ ++ + EF+q+ea+ +f + +di++++eel+ + vk v  + + +i+
  gi|385805978|ref|YP_005842376.1| 227 APETYLKRLVVAGLHRVYEIAVCFRNEDIDVTHYP-EFIQLEAYKAFGDWNDILDLTEELVAESVKAVYGDYKVEIT 302
                                       ***********************************.********************************988877776 PP

                                       HTT.TTTSEE-SSS-EEEEHHHHHHHHHTS............-SS--HHHHHHHHH..................... CS
                                       xxx.xxxxxxxxxxxxxxxxxxxxxxxxxx............xxxxxxxxxxxxxx..................... RF
                       tRNA-synt_2 155 fvi.rrnskdlkkpfkrltykeaieklnei............gkdldkaderalvk..................... 197
                                       +   ++++ d+++pfk++t +ea+e + +i                                               
  gi|385805978|ref|YP_005842376.1| 303 KPDgEKETLDFSRPFKKMTLEEAVETYGGIniknktheelveI------------Akqlgvgiddprkgklvenife 367
                                       654145559*****************88884444444444440............3556666666666666669999 PP

                                       ....HS--SEEEEEEEBGGGSTTCBBBSTTSTTBBSEEEEEETTEEEEEEEEB--SHHHHHHHHHHCCHH....... CS
                                       ....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....... RF
                       tRNA-synt_2 198 ....keknepvfvtdfPaelkpFyarkeeddkkltesyDllingvElvgGslRiedpeeleeklkskgld....... 263
                                           k+  +p+f+t fP+ ++p++++ + d ++ +e+++l+i g+E+++G++++++p +++  +k+++         
  gi|385805978|ref|YP_005842376.1| 368 kvaeKKLRNPTFITLFPRDISPLARPYRVD-PNYAERFELYIAGMEVGNGYSELNNPIIQYMAFKEEEELrkkagrg 443
                                       99888999**********************.9*********************************999888999999 PP

                                       SSSGGGGHHHHHHHHCT--SEEEEEEEHHHHHHHHCT-SSGGGCSSS- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 264 eeaeekfswylealeyGapphgGlglGldRlvmlllgsesIrdviaFP 311
                                        e++  ++++++aleyG+pp+gG g+Gl Rl+++l g++sI+dvi+F 
  gi|385805978|ref|YP_005842376.1| 444 TETHPMDKDFIRALEYGLPPTGGTGIGLYRLIQILSGLPSIKDVIPFT 491
                                       99********************************************95 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.8   6.3e+03      31      49 ..      32      50 ..      29      51 .. 0.85
   2 !   57.4   0.0   3.1e-19   1.1e-15       1      75 [.      57     133 ..      57     134 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.8
                                      EEEEETHHHHHHHTTS-TT CS
                   tRNA_anti-codon 31 qvvlfreeatklaenlkeG 49
                                       v++f+e+ ++ +++l++G
  gi|385805978|ref|YP_005842376.1| 32 DVTAFSEDIKNKYSHLQPG 50
                                      6899999999999999998 PP

  == domain 2  score: 57.4 bits;  conditional E-value: 3.1e-19
                                       EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET....HHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEEEEE CS
                   tRNA_anti-codon   1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfr....eeatklaenlkeGdvvrvtGrvkrrpggelelkveei 73 
                                       V+vaGr+  i  r +g+++fidl D  griq+vl r      +++l++ +++Gd+++++Gr+ r++ ge+++ +e++
  gi|385805978|ref|YP_005842376.1|  57 VSVAGRIWHI--RRHGGILFIDLYDQMGRIQIVLRRdtvkPPKDALLDLIDKGDFLGIKGRIIRTKAGEISILAEDF 131
                                       89********..**************************************************************998 PP

                                       EE CS
                   tRNA_anti-codon  74 el 75 
                                        l
  gi|385805978|ref|YP_005842376.1| 132 DL 133
                                       66 PP

>> Rho_N  Rho termination factor, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.2   8.9e-08   0.00032       3      41 ..     335     372 ..     333     373 .. 0.95

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 8.9e-08
                                       HHS-HHHHHHHHHHTT-TTGGGS-HHHHHHHHHHGGGSS CS
                             Rho_N   3 kektlseLraiAkelgienysrlRKqdLIfaIlkaqaek 41 
                                       k+kt +eL++iAk+lg+ ++   RK+ L++ I ++ aek
  gi|385805978|ref|YP_005842376.1| 335 KNKTHEELVEIAKQLGV-GIDDPRKGKLVENIFEKVAEK 372
                                       9****************.*****************9998 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 !   14.6   0.0   4.9e-06     0.017     104     130 ..     243     269 ..     238     302 .. 0.84
   2 ?   -2.7   0.0      0.89   3.2e+03     214     234 ..     467     487 ..     463     489 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.9e-06
                                       EEEEEEEEBSST-SSSB-SEEEEEEEE CS
                      tRNA-synt_2d 104 iisigrvfRrdavDathlaeFhqvegl 130
                                       +  i  +fR++++D th +eF q+e  
  gi|385805978|ref|YP_005842376.1| 243 VYEIAVCFRNEDIDVTHYPEFIQLEAY 269
                                       556778******************975 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.89
                                       EEEEHHHHHHHHHT-SSGHHH CS
                      tRNA-synt_2d 214 fGlGveRlamlkygieDiRel 234
                                        G+G+ Rl  +  g++ i+++
  gi|385805978|ref|YP_005842376.1| 467 TGIGLYRLIQILSGLPSIKDV 487
                                       69************9999986 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 ?   15.0   0.0   5.8e-06     0.021       3      92 ..      33     129 ..      31     132 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.8e-06
                       tRNA_anti_2   3 Vseltraikell.....eaelkkavwvrGeisnlkrkasghvYftLkDekakisavifrsraaklkft....ledGm 70 
                                       V+++++ ik++       +e +++v v G i+ + r++ g ++++L D+  +i++v+ r +++  k      +++G+
  gi|385805978|ref|YP_005842376.1|  33 VTAFSEDIKNKYshlqpGEETNDTVSVAGRIWHI-RRHGGILFIDLYDQMGRIQIVLRRDTVKPPKDAlldlIDKGD 108
                                       666677777766666664567789**********.55699*******************999888744444679999 PP

                       tRNA_anti_2  71 kVlvkgrlsvYeprGsyqlive 92 
                                        + +kgr+   ++ G++++ +e
  gi|385805978|ref|YP_005842376.1| 109 FLGIKGRII-RTKAGEISILAE 129
                                       999999874.455666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (519 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); 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 0.34s 00:00:01.05 Elapsed: 00:00:00.54
# Mc/sec: 2885.61
//
Query:       gi|385805979|ref|YP_005842377.1|  [L=482]
Description: prolyl-tRNA synthetase [Fervidicoccus fontis Kam940]
Scores for complete 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-27   95.8   0.1    7.7e-27   94.4   0.0    1.8  2  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
      2e-18   66.3   1.0    5.1e-18   65.0   1.0    1.7  1  HGTP_anticodon  Anticodon binding domain
    3.8e-12   46.2   0.1    1.2e-11   44.7   0.1    1.8  1  ProRS-C_1       Prolyl-tRNA synthetase, C-terminal
  ------ inclusion threshold ------
       0.21   11.0   1.5        2.7    7.4   0.0    2.5  3  SpoIIP          Stage II sporulation protein P (SpoIIP)


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 !   94.4   0.0   1.7e-30   7.7e-27       2     176 ..      93     271 ..      92     274 .. 0.88
   2 ?   -1.7   0.0      0.56   2.5e+03     127     152 ..     377     402 ..     294     417 .. 0.50

  Alignments for each domain:
  == domain 1  score: 94.4 bits;  conditional E-value: 1.7e-30
                                       EEE....ETTSEEEEE-SSSHHHHHHHHHHHEEEB.GGSSEEEEEEEEEEBTTTSTBCTTTB-SEE.EEEEEEEEES CS
                                       xxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                      tRNA-synt_2b   2 kle....drndreyiLkPtneetfvelirdevlrs.krLPlklyqiqtkyRdEksdsrGLlRvreF.hqkdgyvfha 72 
                                       ++     d+ d +++L+Pt+e+ +  + + + l+s k+LP k+yqi +++R+E++++r ++R+re  + k+++  h+
  gi|385805979|ref|YP_005842377.1|  93 WVThgglDELDVKLALRPTSETSISLMESYW-LNSyKQLPKKFYQIVSIFRYETKATRAMIRLREVsTFKEAHTAHS 168
                                       5555565888999*******99887777755.***777***************************93469******* PP

                                       .GGGHHHHHHHHHHHHHHHHHHTT.SCEEEEEE..GTTSCBTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTT CS
                                       .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  73 .easlddslrdlikaisriferlglefraiiel..msaksadykdkkefeavsesltkgieigtiqklgtrlserlg 146
                                         +++d ++r+ i+ +s+if +lg++ ++i +    + k a + ++  f+ v++  +k++++gt++ lg+++s+ l+
  gi|385805979|ref|YP_005842377.1| 169 tFEDADRQVREAIEIYSTIFDQLGIP-YVISKRpdFD-KFAGALYTIAFDTVMP-DGKVLQVGTVHHLGQNFSKSLD 242
                                       7699**********************.7788885433.3378889*********.9********************* PP

                                       EEEECTTSSEEEEEEEEEEEEHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b 147 atvldennreksvimicaaigveRllsail 176
                                       ++vl+en+++  v  + ++++  R+++  +
  gi|385805979|ref|YP_005842377.1| 243 VKVLQENGENDYVWQTSYGLS-DRVIASTI 271
                                       ********************9.99998655 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.56
                                       EEEEEEEEEEEETHHHHHTTEEEECT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b 127 kgieigtiqklgtrlserlgatvlde 152
                                       ++  + ++ k g++  +rl+ +++++
  gi|385805979|ref|YP_005842377.1| 377 REKICESVRKEGEEIDKRLRERAKKK 402
                                       22224455555555555555555544 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.0   1.0   1.1e-21   5.1e-18       1      93 [.     290     386 ..     290     387 .. 0.93

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 1.1e-21
                                       SEEEEESSSS...HHHHHHHHHHHHHHHHTTTSEEEEES.SSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEE CS
                    HGTP_anticodon   1 qvvviplnek...aeeleeyakklaeeLraagirveldd.snesigkkireadllgipfavvvGekelekgtvtvrd 73 
                                       +vv+ip+  +   ++ + ey +++++eL++ gir+++d   + ++gkk+ +++l g+p+++++G++e+ ++tv + +
  gi|385805979|ref|YP_005842377.1| 290 KVVIIPIYFNdeeKKGVIEYSEEIRNELENCGIRTVIDTrTELTPGKKFYDWELRGVPIRLEIGKREISSKTVVIVT 366
                                       79*******955544455*********************9999********************************** PP

                                       TTTCEEEEEETTHHHHHHHH CS
                    HGTP_anticodon  74 rdtreqervsldelveklke 93 
                                       rd+ ++ +++++++ e +++
  gi|385805979|ref|YP_005842377.1| 367 RDELKKKSIAREKICESVRK 386
                                       ************99998876 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 !   44.7   0.1   2.6e-15   1.2e-11      12      69 .]     425     482 .]     416     482 .] 0.94

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 2.6e-15
                                       -EEEEEESSGHHHHHHHHHHHS-EEEEEESSB-SSCCCSB-TTT-SB-SEEEEEE-B- CS
                         ProRS-C_1  12 gfvlapWcgeeecEekIkeetgakslcipfdqepseegtkCivcgkpakkwvlfgrsY 69 
                                       g++ +pWcg+e+c  kI+e+tg  +l+ p+++++  +g++C vcg++a +    +++Y
  gi|385805979|ref|YP_005842377.1| 425 GIIEVPWCGSEDCALKIQERTGIRVLGSPIEKPEWIKGKTCPVCGRNAVTSLRLAKTY 482
                                       699****************************98889*******************999 PP

>> SpoIIP  Stage II sporulation protein P (SpoIIP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.031   1.4e+02     106     153 ..     223     272 ..     212     280 .. 0.83
   2 ?    7.4   0.0    0.0006       2.7     100     131 ..     299     330 ..     295     343 .. 0.86
   3 ?   -2.8   0.7      0.75   3.4e+03      36      54 ..     385     403 ..     351     420 .. 0.39

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.031
                            SpoIIP 106 nvveVGe..eLaeeL.ekygisvihdktvhdlesynksYkrsretvkeilk 153
                                       +v++VG+  +L +++ ++ +++v++++   d+  ++ sY  s +++ + ++
  gi|385805979|ref|YP_005842377.1| 223 KVLQVGTvhHLGQNFsKSLDVKVLQENGENDYV-WQTSYGLSDRVIASTIS 272
                                       67788852269999988899************9.9********99988776 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0006
                            SpoIIP 100 stdeeknvveVGeeLaeeLekygisvihdktv 131
                                       +++e+k v+e +ee+ +eLe+ gi ++ d++ 
  gi|385805979|ref|YP_005842377.1| 299 NDEEKKGVIEYSEEIRNELENCGIRTVIDTRT 330
                                       567899**********************9976 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 0.75
                            SpoIIP  36 eeeeeekeeeeeeeikkee 54 
                                        +e ee ++   e +kk+ 
  gi|385805979|ref|YP_005842377.1| 385 RKEGEEIDKRLRERAKKKM 403
                                       1111111111111111111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (482 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1284  (0.0716158); expected 358.6 (0.02)
Passed bias filter:                      826  (0.0460706); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.34s 00:00:01.04 Elapsed: 00:00:00.50
# Mc/sec: 2926.85
//
Query:       gi|385805980|ref|YP_005842378.1|  [L=82]
Description: hypothetical protein FFONT_0938 [Fervidicoccus fontis Kam940]
Scores for complete 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   0.4    0.00071   19.7   0.4    1.4  1  Ribosomal_L24e  Ribosomal protein L24e
  ------ inclusion threshold ------
      0.012   16.2   0.1      0.018   15.7   0.1    1.3  1  DUF971          Protein of unknown function (DUF971)


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 !   19.7   0.4     8e-08   0.00071       5      43 ..      11      48 ..       8      50 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 8e-08
                                      B-TTT-SB--SS--EEEE-TTS-EEEESSHHHHHHHHTT CS
                    Ribosomal_L24e  5 kCsFsgykiyPGhGkrfvrnDgkvfrFlssKceklfkqk 43
                                      +C  +g+  y G+G+r +++ g ++ F ssKc++lf ++
  gi|385805980|ref|YP_005842378.1| 11 ECVVCGKVFYEGQGIR-IKREGLQLDFHSSKCAALFFKR 48
                                      7**************9.7889*************99876 PP

>> DUF971  Protein of unknown function (DUF971)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   0.1     2e-06     0.018       6      48 ..      28      71 ..      24      81 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2e-06
                            DUF971  6 kgkrLeiewddgkesslpaelLRdacpcaecrkp.gqrllqsgk 48
                                      k++ L++ ++  k ++l ++ L +++p+aec+++  ++l+++ k
  gi|385805980|ref|YP_005842378.1| 28 KREGLQLDFHSSKCAALFFKRLIEESPSAECVSEtAKKLIDEFK 71
                                      67789***************************654666777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1123  (0.062636); expected 358.6 (0.02)
Passed bias filter:                      720  (0.0401584); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 556.03
//
Query:       gi|385805981|ref|YP_005842379.1|  [L=296]
Description: hypothetical protein FFONT_0939 [Fervidicoccus fontis Kam940]
Scores for complete 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-08   33.6  17.5    4.1e-06   26.8   2.5    3.0  3  VIT1             VIT family
    1.8e-07   31.6  11.0    5.5e-07   30.1  11.0    1.7  1  Rubrerythrin     Rubrerythrin
    0.00043   20.5   1.4       0.03   14.5   0.0    2.6  2  Ferritin_2       Ferritin-like domain
  ------ inclusion threshold ------
      0.012   15.4   3.4      0.021   14.6   0.3    2.2  2  CbtA             Probable cobalt transporter subunit (CbtA)
      0.025   13.4   0.2      0.047   12.5   0.2    1.4  1  FA_desaturase_2  Fatty acid desaturase
      0.071   12.6   0.9       0.18   11.3   0.1    1.9  2  DUF455           Protein of unknown function (DUF455)
      0.085   11.6   3.9       0.16   10.7   3.9    1.5  1  Presenilin       Presenilin
       0.51   10.2  11.8        0.7    9.8   8.1    2.1  2  7TMR-DISM_7TM    7TM diverse intracellular signalling
       0.55    9.7   5.7       0.28   10.7   0.1    2.2  3  E1-E2_ATPase     E1-E2 ATPase


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 ?   -0.6   0.5       0.5     1e+03      78     119 ..      13      54 ..       3     132 .. 0.63
   2 !   19.9   7.3   2.8e-07   0.00056       4      59 ..     144     198 ..     141     200 .. 0.92
   3 !   26.8   2.5   2.1e-09   4.1e-06     131     214 ..     199     283 ..     194     284 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.5
                              VIT1  78 pe.egeaeelaeilearglseelaqevaaellknpdallelml 119
                                       +e e e   l ++++++  ++e  +++++ ++k+++   ++  
  gi|385805981|ref|YP_005842379.1|  13 CEqEYEDSMLYAYIASK-EKDENRRKILEAIAKDEEGHYKFWK 54 
                                       44344433344444444.4666666777777777776544443 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 2.8e-07
                              VIT1   4 avlGanDGLvspfalvaGlsaaslgssktvllaGlaellAGaiSMgiGeYlsvkse 59 
                                       ++lG++D +v + ++ aG  +++ +s+ +  +aG+   ++ aiSM+  +Yl +k e
  gi|385805981|ref|YP_005842379.1| 144 IILGLADAIVEINGVHAGFLGVT-ESTIVTGIAGMVVGVSAAISMASAAYLQAKHE 198
                                       79******************888.698999999999999*************9987 PP

  == domain 3  score: 26.8 bits;  conditional E-value: 2.1e-09
                              VIT1 131 l.asplkaAlssalsfliGgliPllpylfvesvglalvvsiavtllalllfGavkalltgssklvsalrmlliGalA 206
                                       + +sp ++Al+++l+++    +  lpy+++ ++ +a++vsi +++l+++ f + ++ l ++   ++ ++ +l+ +++
  gi|385805981|ref|YP_005842379.1| 199 AgKSPRTSALMTGLAYISAVSVLALPYFLIRKMLTAFLVSISIAILMIASFTYYGSTLQEKDFKREFIESTLLMLGT 275
                                       34799************************************************************************ PP

                              VIT1 207 aaaaylig 214
                                       a ++y++g
  gi|385805981|ref|YP_005842379.1| 276 AFVTYFFG 283
                                       *****987 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1  11.0   2.8e-10   5.5e-07       2     131 ..       5     127 ..       4     129 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 2.8e-10
                                       HHHHH...HHHHHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS------ CS
                      Rubrerythrin   2 iLekA...iagEssarrlYkelaekakegypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeak 75 
                                       iLekA   +  E+++ +lY ++a+k k   ++ ++++e++A++E+ H k+ +kl++k  +++   ++ k   +++ +
  gi|385805981|ref|YP_005842379.1|   5 ILEKArefCEQEYEDSMLYAYIASKEK--DENRRKILEAIAKDEEGHYKFWKKLYGKDCKTES--INSKMLFFLFLR 77 
                                       66666555789**************99..55559***********************666666..888999999999 PP

                                       -TTGGHHH..HHHHHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHH CS
                      Rubrerythrin  76 pkflttak..nLeeaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHee 131
                                       + f +t +  +Le        +e++++++y++++++ + e  ++++ k++++E+ He+
  gi|385805981|ref|YP_005842379.1|  78 KLFGITFTlkYLE-------NKEKKAIESYKKMLSELKGE-DAQVLMKIIQDEEIHEK 127
                                       8886554323777.......899999999******99888.56666789*******97 PP

>> Ferritin_2  Ferritin-like 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      0.03      15      64 ..      18      59 ..       4      75 .. 0.77
   2 ?    4.5   0.3     0.018        37      11      61 ..      91     133 ..      78     199 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.5e-05
                        Ferritin_2 15 leaafYtaalegaslddkalldaevrevaeeiakheeaHveflkaaleGa 64
                                           Y++ +       ++  d++ r+++e iak+ee+H++f+k+   G+
  gi|385805981|ref|YP_005842379.1| 18 EDSMLYAYIA-------SKEKDENRRKILEAIAKDEEGHYKFWKKLY-GK 59
                                      3333333333.......6789999********************987.54 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.018
                        Ferritin_2  11 nlEyleaafYtaalegaslddkalldaevrevaeeiakheeaHveflkaal 61 
                                       n E  +++ Y+++l        + l+ e+ +v+ +i ++ee H ++  + l
  gi|385805981|ref|YP_005842379.1|  91 NKEKKAIESYKKML--------SELKGEDAQVLMKIIQDEEIHEKTEIQSL 133
                                       34444444444444........47899999999999999999988766665 PP

>> CbtA  Probable cobalt transporter subunit (CbtA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.3     1e-05     0.021      62     121 ..     160     218 ..     118     226 .. 0.79
   2 ?    1.4   0.2      0.11   2.3e+02      80     119 ..     236     279 ..     228     294 .. 0.50

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1e-05
                              CbtA  62 elvsrgvqrtlgtvlanvltgvalglllaavfallegrlgklsaralalllalagflavv 121
                                       +++   +++t++t++a++++gv+ +  +a +++l  ++  + s+r +al+ +la +++ v
  gi|385805981|ref|YP_005842379.1| 160 AGFLGVTESTIVTGIAGMVVGVSAAISMASAAYLQAKHEAGKSPRTSALMTGLA-YISAV 218
                                       556667899****************99998888777666677677766666655.44433 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.11
                              CbtA  80 ltgvalglllaavfallegrlgklsara....lalllalagfla 119
                                       l++++++ l++a f+++++ l++ + ++    ++ll+ + +f++
  gi|385805981|ref|YP_005842379.1| 236 LVSISIAILMIASFTYYGSTLQEKDFKRefieSTLLMLGTAFVT 279
                                       55555555555555555555544332222222333333344443 PP

>> FA_desaturase_2  Fatty acid desaturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   2.4e-05     0.047     173     214 ..      24      65 ..      21     135 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.4e-05
                   FA_desaturase_2 173 aklakeagdellakicgaiaadEkrHeaaYtrvvekllevdp 214
                                       a +a++++de   ki++aia+dE+ H+++++++  k  ++++
  gi|385805981|ref|YP_005842379.1|  24 AYIASKEKDENRRKILEAIAKDEEGHYKFWKKLYGKDCKTES 65 
                                       5678999************************99888766665 PP

>> DUF455  Protein of unknown function (DUF455)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   9.2e-05      0.18     172     225 ..      29      82 ..      21     103 .. 0.84
   2 ?   -0.8   0.2      0.45   8.9e+02     169     191 ..     103     125 ..      92     129 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9.2e-05
                            DUF455 172 aagdeesaeiLevIledEitHVaaGvrWfrylcekegldpvetFrelvreyfrg 225
                                       + +de+  +iLe I +dE +H ++ ++ + + c+ e+ +    F   +r+ f  
  gi|385805981|ref|YP_005842379.1|  29 KEKDENRRKILEAIAKDEEGHYKFWKKLYGKDCKTESINSKMLFFLFLRKLFGI 82 
                                       6799*********************************99999998888888764 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.45
                            DUF455 169 klraagdeesaeiLevIledEit 191
                                        l++ + e++  ++++I ++Ei+
  gi|385805981|ref|YP_005842379.1| 103 MLSELKGEDAQVLMKIIQDEEIH 125
                                       44555555566666777777774 PP

>> Presenilin  Presenilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   3.9   8.2e-05      0.16      57     136 ..     199     278 ..     162     282 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 8.2e-05
                        Presenilin  57 llnsllnalililvivvvtfllvlLykyrcykvikgwlilsslllLflvsglllaevlkaynipldyitlllllwnf 133
                                       +++s  +++ + ++  +  + +++L ++   k+++++l+  s+ +L++ s++++ + l++ ++  ++i  +ll++  
  gi|385805981|ref|YP_005842379.1| 199 AGKSPRTSALMTGLAYISAVSVLALPYFLIRKMLTAFLVSISIAILMIASFTYYGSTLQEKDFKREFIESTLLMLGT 275
                                       444444555555555566666778999999*********************************99999999999887 PP

                        Presenilin 134 gvv 136
                                       ++v
  gi|385805981|ref|YP_005842379.1| 276 AFV 278
                                       776 PP

>> 7TMR-DISM_7TM  7TM diverse intracellular signalling
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1     0.095   1.9e+02      64      94 ..      66      95 ..      59     105 .. 0.63
   2 ?    9.8   8.1   0.00035       0.7      74     176 ..     184     285 ..     135     292 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.095
                     7TMR-DISM_7TM 64 lnnkllyltlllllilfllFarsflelkkkp 94
                                      +n+k+l++++l  l + + F+ ++le k+k+
  gi|385805981|ref|YP_005842379.1| 66 INSKMLFFLFLRKL-FGITFTLKYLENKEKK 95
                                      45555554444444.5555*****9996653 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00035
                     7TMR-DISM_7TM  74 llllilfllFarsflelkkkprllklllllavllsllllllpllpyteslslaqllallvillllligikaw.rkgn 149
                                       ++++ +++++++  +e  k+pr   l+ +la + ++ +l+lp ++  ++l+ +++ + ++il+++ + ++   ++ +
  gi|385805981|ref|YP_005842379.1| 184 AISM-ASAAYLQAKHEAGKSPRTSALMTGLAYISAVSVLALPYFLIRKMLTAFLVSISIAILMIASFTYYGStLQEK 259
                                       3333.5555888888887788*******************************9999999999999999998889999 PP

                     7TMR-DISM_7TM 150 kparyfliawlllligvlidilsllg.l 176
                                          r f+ + ll+l +++++   ++g l
  gi|385805981|ref|YP_005842379.1| 260 DFKREFIESTLLMLGTAFVTY--FFGdL 285
                                       999999999999999999966..55545 PP

>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00014      0.28     101     169 ..     119     191 ..     110     202 .. 0.85
   2 ?   -0.2   2.0      0.31   6.1e+02     125     166 ..     212     246 ..     200     257 .. 0.51
   3 ?    0.2   1.5      0.24   4.7e+02     112     148 ..     229     265 ..     214     279 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00014
                                       S----.----HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTT...HHHHHHHHHHHHHS-TTHHHHHHH CS
                      E1-E2_ATPase 101 veeak.skktplqkkldklgkvlvpvvlliallvflialllgksla...eallralallvaaiPcaLplavpl 169
                                       +++++ ++kt++q   +k+++++++++l +a +++ i+ ++ ++l     +++ ++a +v+ +  a+ +a   
  gi|385805981|ref|YP_005842379.1| 119 IQDEEiHEKTEIQSLDEKVVRYMSFIILGLADAIVEINGVHAGFLGvteSTIVTGIAGMVVGVSAAISMASAA 191
                                       55555699******************************9999998899888999********99999988654 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.31
                                       HHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHHHS-TTHHHH CS
                      E1-E2_ATPase 125 vvlliallvflialllgkslaeallralallvaaiPcaLpla 166
                                       ++ + a+ v+++ ++l ++  +a+l ++++++ +       +
  gi|385805981|ref|YP_005842379.1| 212 LAYISAVSVLALPYFLIRKMLTAFLVSISIAILM-------I 246
                                       4444444444444444444444444444444443.......3 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.24
                                       HHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHH CS
                      E1-E2_ATPase 112 qkkldklgkvlvpvvlliallvflialllgkslaeal 148
                                        k+l+ +   +++++l+ia +++    l +k+  + +
  gi|385805981|ref|YP_005842379.1| 229 RKMLTAFLVSISIAILMIASFTYYGSTLQEKDFKREF 265
                                       4555666666666666666666666666666555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1707  (0.0952089); expected 358.6 (0.02)
Passed bias filter:                      722  (0.04027); 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):               9  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 1771.19
//
Query:       gi|385805982|ref|YP_005842380.1|  [L=419]
Description: glycosyltransferase, family 4 [Fervidicoccus fontis Kam940]
Scores for complete 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-15   55.5   0.0    1.2e-14   54.9   0.0    1.3  1  Glyco_trans_1_4  Glycosyl transferases group 1
      1e-13   51.2   0.1    2.5e-13   49.9   0.1    1.6  1  Glycos_transf_1  Glycosyl transferases group 1
     0.0023   18.3   0.0     0.0046   17.3   0.0    1.4  1  Glyco_trans_1_2  Glycosyl transferases group 1
  ------ inclusion threshold ------
      0.031   14.3   0.0      0.057   13.4   0.0    1.4  1  Glyco_transf_4   Glycosyltransferase Family 4
      0.067   13.2   0.0       0.12   12.4   0.0    1.4  1  ALG11_N          ALG11 mannosyltransferase N-terminus
       0.21   10.4   0.0       0.33    9.7   0.0    1.2  1  Epimerase_2      UDP-N-acetylglucosamine 2-epimerase


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 !   54.9   0.0   3.9e-18   1.2e-14       2     134 .]     230     385 ..     229     385 .. 0.82

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 3.9e-18
                                       EEEEEES---GG.GTHHHHHHHH.HHHH.H..HEEEEEES---........HHHHHHHTT-..........T.TEEE CS
                   Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleav.pllrkk..dvrlvivGdgp.rp.....eeleelaagl..........eervef 59 
                                       + i+ +Gr+  ++k+ ++++e++ p++ ++  d ++++vG ++ r+     +el + +++l          ++rv +
  gi|385805982|ref|YP_005842380.1| 230 NSIVLLGRF-SREKRYHWVIENIvPKVVNEvgDSKFYFVGYSKgRRsasyvNELVSILNKLnisysfdirkNARVYL 305
                                       6799*****.566***************99766*******7666444555544433333225566666654567*** PP

                                       E---.TH.HHHHHHH-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGT.TT--..TTSSEE--TT-HHHHHHHHH CS
                   Glyco_trans_1_4  60 tGfv.ed.laellaaadvfvaPs..egfglkllEamaaglpvVatdvggi.aevv..gengllvppgdpealaeail 129
                                       +  + ++ ++e+l++++v++  +  e +g+++ E m++glpvV  + gg+ +++   g++g+  +  ++e+ +++i+
  gi|385805982|ref|YP_005842380.1| 306 LENLdKEiVNEVLRRSKVLLHATinEHWGISIAEGMSFGLPVVIHKSGGLwSDLAlaGKSGVGYE--NAEEAIQEIV 380
                                       ****6447***************999*********************9955998899****8888..9********* PP

                                       HHHH- CS
                   Glyco_trans_1_4 130 rLled 134
                                       +L++d
  gi|385805982|ref|YP_005842380.1| 381 KLIND 385
                                       **997 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 !   49.9   0.1   8.4e-17   2.5e-13      12     163 ..     226     390 ..     220     397 .. 0.82

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 8.4e-17
                                       TTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.......STTHHHHHHHHHHHCTT........CG CS
                   Glycos_transf_1  12 nekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaG......ngeeekelkklaeelels........dn 74 
                                        ++++ i+ +gr+++eK+++ +i+ +     ++  + k+ ++G      + ++ +el +   +l++s        ++
  gi|385805982|ref|YP_005842380.1| 226 SSRENSIVLLGRFSREKRYHWVIENIVPKVVNEVGDSKFYFVGyskgrrSASYVNELVSILNKLNISysfdirknAR 302
                                       56789999****************976544567****************7777777777777776642222222266 PP

                                       GGEEECCHSSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEET.TTTHCHHCHTTTSEEEE-TT-HHHHHH CS
                   Glycos_transf_1  75 viflgevsredleellknadifvlpsisEgfGivllEAmaaglpviasn.aggpaevvkdgetGllvkpnnaealae 150
                                       v +l ++++e + e+l++++++++  i+E++Gi++ E m++glpv++++  g  +++   g++G+ +++   e++++
  gi|385805982|ref|YP_005842380.1| 303 VYLLENLDKEIVNEVLRRSKVLLHATINEHWGISIAEGMSFGLPVVIHKsGGLWSDLALAGKSGVGYENA--EEAIQ 377
                                       777778888888999999*******************************555569999999999887766..***** PP

                                       HHHHHHHSHHHHH CS
                   Glycos_transf_1 151 airklledeelre 163
                                       +i kl++de++ +
  gi|385805982|ref|YP_005842380.1| 378 EIVKLINDEKTWR 390
                                       ********97655 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.5e-06    0.0046      14      76 ..     336     399 ..     318     416 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.5e-06
                   Glyco_trans_1_2  14 rlfEaaacGafaltdda.egleelftpgkevilfedleelaekiryllanpeerraiaeaarer 76 
                                        + E + +G +++  ++     +l   gk+++ +e+ ee+++ i +l+++++ +r  +    +r
  gi|385805982|ref|YP_005842380.1| 336 SIAEGMSFGLPVVIHKSgGLWSDLALAGKSGVGYENAEEAIQEIVKLINDEKTWRHYSSMSLRR 399
                                       5789***********9966668999******************************998877776 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.9e-05     0.057      56     166 ..      84     212 ..      41     216 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.9e-05
                    Glyco_transf_4  56 rslaflrrlrrllkrekpDvvHahspaalgaallalrrrlgiplVltvHglye................krllkarl 116
                                        ++  +r + +++k  +p  + + sp++ g      r+  gi+++ ++H++ e                +++ ++++
  gi|385805982|ref|YP_005842380.1|  84 MRILLRREINKVIKSTDPEFLFVDSPFYDGNK---VRK-NGIKVIEYIHFPIEayfmslndrkinlngdPYIKENYN 156
                                       456677889999*************9998655...455.9***************************9955555666 PP

                    Glyco_transf_4 117 kplsrllralerrl.........lrradrviavSeatadelrerygvppekitVipnGv 166
                                       +    l++ +  ++         +++a+ v+++Se++a+ + + y    +k  V+ +++
  gi|385805982|ref|YP_005842380.1| 157 GIIGSLYFSMFGKIsskfkrenpFDSAHLVLVNSEYVAKIVSSIYS---QKPKVLNPPI 212
                                       555444444444444666777799***************9999665...5556666655 PP

>> ALG11_N  ALG11 mannosyltransferase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.9e-05      0.12     129     209 .]     119     201 ..      93     201 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.9e-05
                           ALG11_N 129 agvkvvaYvHYPtistdmlkrvkereakynnkeavakskllsllkllYyklfallYslvgs.....ladvvmvnssW 200
                                       +g+kv+ Y+H+P+     + ++++r+ + n + ++++ ++  ++  lY+++f ++ s +++     +a++v+vns +
  gi|385805982|ref|YP_005842380.1| 119 NGIKVIEYIHFPIEAY--FMSLNDRKINLNGDPYIKE-NYNGIIGSLYFSMFGKISSKFKRenpfdSAHLVLVNSEY 192
                                       579*********9655..5579999999999888865.789999********999887754222226889*****99 PP

                           ALG11_N 201 Tknhikslw 209
                                         + ++s++
  gi|385805982|ref|YP_005842380.1| 193 VAKIVSSIY 201
                                       998888875 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 ?    9.7   0.0   0.00011      0.33     237     326 ..     298     392 ..     276     400 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00011
                                       HH-TTEEEE----HHHHHHHHHC-SEEEES-.....H.HHHHHHHHCT--EEESSSS-S-THHHHTTSEEE-TT-HH CS
                       Epimerase_2 237 eelenvtlieplgyldflsllknaklvltdS.....g.GiqeEapslgvpvvnlReeteRpegveagtnvlvgtdke 307
                                       ++ ++v+l+e+l+++   ++l+++k++l        g  i  E +s+g+pvv   + + + +   ag++ +  +++e
  gi|385805982|ref|YP_005842380.1| 298 RKNARVYLLENLDKEIVNEVLRRSKVLLHATinehwGiSIA-EGMSFGLPVVIHKSGGLWSDLALAGKSGVGYENAE 373
                                       44458999999999999999999999886433333355566.*****************************666666 PP

                                       HHHHHHHHHCT-..--... CS
                       Epimerase_2 308 eIvaaleklledkkelekm 326
                                       e ++++ kl++d+k++++ 
  gi|385805982|ref|YP_005842380.1| 374 EAIQEIVKLINDEKTWRHY 392
                                       6667777777675655544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      568  (0.0316805); 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: 0.65u 0.33s 00:00:00.98 Elapsed: 00:00:00.52
# Mc/sec: 2428.72
//
Query:       gi|385805983|ref|YP_005842381.1|  [L=49]
Description: hypothetical protein FFONT_0941 [Fervidicoccus fontis Kam940]
Scores for complete 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   25.0   0.1    2.2e-05   24.8   0.1    1.0  1  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 !   24.8   0.1   1.2e-09   2.2e-05       2      43 ..       6      47 ..       5      48 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.2e-09
                                      HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEE CS
                               CBS  2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklv 43
                                      +d  +++ ++++ d++  +al+ m ++++s+lPV+d+d+++v
  gi|385805983|ref|YP_005842381.1|  6 KDCESTKELVINSDDDANKALNVMLKHRLSSLPVIDKDDNFV 47
                                      555577788**************************9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); 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 0.29s 00:00:00.80 Elapsed: 00:00:00.52
# Mc/sec: 282.59
//
Query:       gi|385805984|ref|YP_005842382.1|  [L=42]
Description: chloride channel protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       170  (0.00948185); expected 358.6 (0.02)
Passed bias filter:                      143  (0.0079759); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.45
# Mc/sec: 280.01
//
Query:       gi|385805985|ref|YP_005842383.1|  [L=43]
Description: hypothetical protein FFONT_0943 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       154  (0.00858944); expected 358.6 (0.02)
Passed bias filter:                      131  (0.0073066); 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: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 304.83
//
Query:       gi|385805986|ref|YP_005842384.1|  [L=39]
Description: hypothetical protein FFONT_0944 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.1   0.0       0.13   12.0   0.0    1.1  1  DUF3094   Protein of unknown function (DUF3094)


Domain annotation for each model (and alignments):
>> DUF3094  Protein of unknown function (DUF3094)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.2e-06      0.13      24      47 ..      10      33 ..       4      38 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.2e-06
                           DUF3094 24 ERqPFrpWlllvvvlavvigLGll 47
                                      E  P+  W +l ++l+v  gL  l
  gi|385805986|ref|YP_005842384.1| 10 EISPYTKWYILGIILGVAAGLSAL 33
                                      568***************999766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.46
# Mc/sec: 255.01
//
Query:       gi|385805987|ref|YP_005842385.1|  [L=378]
Description: peptide chain release factor 1 [Fervidicoccus fontis Kam940]
Scores for complete 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-40  136.6   0.0    1.1e-39  135.8   0.0    1.4  1  eRF1_2          eRF1 domain 2
    3.6e-18   66.1   0.2    2.2e-16   60.4   0.1    2.8  2  eRF1_3          eRF1 domain 3
    2.7e-16   60.0   0.0    5.6e-16   59.0   0.0    1.5  1  acVLRF1         Actinobacteria/chloroflexi VLRF1 release fact
    1.3e-13   51.4   0.0    2.2e-13   50.7   0.0    1.4  1  baeRF_family10  Bacterial archaeo-eukaryotic release factor f
    9.2e-06   25.7   0.0    1.8e-05   24.8   0.0    1.4  1  eRF1_1          eRF1 domain 1
  ------ inclusion threshold ------
      0.017   14.7   0.0      0.033   13.7   0.0    1.6  1  LIDHydrolase    Lipid-droplet associated hydrolase


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 !  135.8   0.0   3.6e-43   1.1e-39       2     133 .]     150     283 ..     149     283 .. 0.98

  Alignments for each domain:
  == domain 1  score: 135.8 bits;  conditional E-value: 3.6e-43
                                       EEEEEEETTEEEEEEEESSCEEEEEEEE------BSTTBSCCCCHHHHHHHHHHHHHHHHHHHHHHHHH.HCHTTTE CS
                            eRF1_2   2 vglivldegeAtigllkgsrtevlkkievsvPkKhkrGgqsarrfeRlreekleeflkkvaeaankafl.lvdkdkl 77 
                                       +gli+++++eAtigllkg+++++l+++ + +P+Kh +Ggqs+rrf+R++e+++e f+k vae a++ f  l+ ++kl
  gi|385805987|ref|YP_005842385.1| 150 YGLILIERDEATIGLLKGTTIQMLDNFMSYIPGKHTKGGQSQRRFDRIIEQMVEDFYKTVAERAKQLFEpLLLEGKL 226
                                       89******************************************************************9999***** PP

                                       SEEEEEESSTHHHHHHHHHHHHHHHHTCCEE.EEE-S-TSCHHHHHHHHCCHHHHCC CS
                            eRF1_2  78 kgiilagpgfvkeefldkdlldaelkkkvik.lvdvsyggesglnevlekaaevlkd 133
                                       kgi+++gpg+ k++f+++++l+++ ++ vi  l+dv+y+ge+gl+e++ ka++vl+d
  gi|385805987|ref|YP_005842385.1| 227 KGILIGGPGYSKQDFVTGEYLEKRFRDLVINkLIDVGYQGEAGLRELVLKAEDVLQD 283
                                       ***************************98877***********************97 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       3.1   9.2e+03      70      77 ..     197     204 ..     169     215 .. 0.58
   2 !   60.4   0.1   7.2e-20   2.2e-16       6     113 .]     291     377 ..     286     377 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.1
                                       HHHHHHHH CS
                            eRF1_3  70 lieelven 77 
                                       +ie++ve+
  gi|385805987|ref|YP_005842385.1| 197 IIEQMVED 204
                                       33333333 PP

  == domain 2  score: 60.4 bits;  conditional E-value: 7.2e-20
                                       HHHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSHHHHHS-HHH-HHHHHHHHHHHHHHHHHTT CS
                            eRF1_3   6 klleefleelakdtgkavYGveevlkalemgAvetLLvseelersrdtlkekvketgeelelvelieelvenveesg 82 
                                       k  ee+  ++ak +g++v+G+eev++a+e+gA++tLL++e+  +                      +e+   +++s+
  gi|385805987|ref|YP_005842385.1| 291 KKAEELKLHMAKADGLYVFGIEEVKHAAEIGALQTLLIIESHPNI---------------------DEMEAVAKKSN 346
                                       56688999****99**************************98875.....................5667789**** PP

                                       -EEEEE-TTSHHHHHHHHHTTTEEEEESS-- CS
                            eRF1_3  83 akveiisseseeGeqlvkafgGiaaiLRykv 113
                                       a+++i++++++eGe+l+++fgG+a+iLRyk+
  gi|385805987|ref|YP_005842385.1| 347 AEIVIVPEDTPEGEWLKSSFGGVAGILRYKL 377
                                       *****************************96 PP

>> acVLRF1  Actinobacteria/chloroflexi VLRF1 release factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.0   0.0   1.9e-19   5.6e-16       2     127 ..     149     280 ..     148     282 .. 0.90

  Alignments for each domain:
  == domain 1  score: 59.0 bits;  conditional E-value: 1.9e-19
                           acVLRF1   2 rlgvllvrrggfavgvveggelvaskvgtrdvqgrtaaGGwSqqRfaRrrenqadalleavaeaaarllaeesae.. 76 
                                       ++g++l+ r+  ++g+++g+++++  ++ +++ g++ +GG+Sq+Rf+R +e+ +++ +++vae+a++l+++   e  
  gi|385805987|ref|YP_005842385.1| 149 YYGLILIERDEATIGLLKGTTIQMLDNFMSYIPGKHTKGGQSQRRFDRIIEQMVEDFYKTVAERAKQLFEPLLLEgk 225
                                       6899*****************************************************************65555555 PP

                           acVLRF1  77 ...vvlgGdrslvaevledar.laplatlareelldvpdprravLedavrrarav 127
                                          +++gG+    +++ + +   ++ ++l+ ++l+dv+   +a L++ v +a++v
  gi|385805987|ref|YP_005842385.1| 226 lkgILIGGPGYSKQDFVTGEYlEKRFRDLVINKLIDVGYQGEAGLRELVLKAEDV 280
                                       567**************997725569999999**************999888776 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 !   50.7   0.0   7.3e-17   2.2e-13       3     137 ..     137     279 ..     136     285 .. 0.86

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 7.3e-17
                    baeRF_family10   3 lapLlealdeyerygvvlvdreraRlfevylgeleeveevegevpgrtktggwksqdrfqrreeeqaerhlkevAel 79 
                                       ++ L + + e + yg++l++r++a +    +  ++  + + + +pg++ +gg+ sq+rf r  e+++e ++k vAe 
  gi|385805987|ref|YP_005842385.1| 137 VEYLEDMISEKDYYGLILIERDEATIGLLKGTTIQMLDNFMSYIPGKHTKGGQ-SQRRFDRIIEQMVEDFYKTVAER 212
                                       7779999***************************************9999999.*********************** PP

                    baeRF_family10  80 laklleerg....verlvlgGd..eeetaalldrlpkalrarvvgt.lplpv..dasaaaVlekaee 137
                                       +++l+e+      ++ +++gG+   + + +  + l k+ r++v+ + ++++   +a  ++++ kae+
  gi|385805987|ref|YP_005842385.1| 213 AKQLFEPLLlegkLKGILIGGPgySKQDFVTGEYLEKRFRDLVINKlIDVGYqgEAGLRELVLKAED 279
                                       ****99765555699*******555555566689***********9877776425577777666665 PP

>> eRF1_1  eRF1 domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   5.9e-09   1.8e-05      12     128 ..      38     143 ..      26     144 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 5.9e-09
                                       SCCEEEEEE-SCHHHHHHHHHCHTTHEEEEEEEECHHH.......--CEEEEEEEEEEEEEEECTT...SSEEEEEE CS
                            eRF1_1  12 gsgsvtLipeddedlwhlynliapgdsvrastvrkvqresstgsreservklkLtikvekvdfdkd...agvlrisG 85 
                                        + +++L++++   ++++ n+++++ s+  +++ k ++           v++ L + + ++   ++   +g++ ++G
  gi|385805987|ref|YP_005842385.1|  38 ATTLLSLYIPPGRPISDVVNMLREELSITDNIKLKRTK---------DAVQTSLSMAIDRLSSINKvpeNGLVLFCG 105
                                       57889*****************************9877.........7899999998888877666666******** PP

                                       EEEEGGGG--TTSEEEEEE-TTSEEEEEECE.ESHHHHHHHHHH CS
                            eRF1_1  86 kvieenehvklgafhtldlelkrpftiikee.wdsfalerLkea 128
                                       k+ + n+       + l + +++p++i+ ++ ++ f++e L+++
  gi|385805987|ref|YP_005842385.1| 106 KNSDTNK------EICLMFSPPEPVKIYFYRtDKWFHVEYLEDM 143
                                       ******9......69**************998999******987 PP

>> LIDHydrolase  Lipid-droplet associated hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.1e-05     0.033     180     249 ..      65     147 ..       4     161 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.1e-05
                      LIDHydrolase 180 vettlkfvkspevvrqalhlakdEmeeikeddeeedvllkknkeka.............lvfyfgkkDhWvpeetrd 243
                                       +   +k+ + +++v+  l +a d +  i++  e+  vl+  +++++             +++yf ++D+W ++e+ +
  gi|385805987|ref|YP_005842385.1|  65 ITDNIKLKRTKDAVQTSLSMAIDRLSSINKVPENGLVLFCGKNSDTnkeiclmfsppepVKIYFYRTDKWFHVEYLE 141
                                       455667777899999***************99997766554444445899*************************** PP

                      LIDHydrolase 244 elkell 249
                                       +++ + 
  gi|385805987|ref|YP_005842385.1| 142 DMISEK 147
                                       **9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); 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: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2791.25
//
Query:       gi|385805988|ref|YP_005842386.1|  [L=316]
Description: Transcription initiation factor IIB (TFIIB) [Fervidicoccus fontis Kam940]
Scores for 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  116.9   4.6    4.6e-17   61.8   0.4    2.3  2  TFIIB          Transcription factor TFIIB repeat
    1.4e-08   34.1   0.0    2.6e-08   33.2   0.0    1.5  1  TF_Zn_Ribbon   TFIIB zinc-binding
    5.9e-05   22.5   0.1    0.00021   20.8   0.1    2.0  1  Sigma70_r4     Sigma-70, region 4
    9.7e-05   21.7   0.2     0.0038   16.6   0.1    2.4  2  HTH_Tnp_ISL3   Helix-turn-helix domain of transposase family 
    0.00036   20.6   0.0        1.1    9.4   0.0    2.3  2  Cyclin_C       Cyclin, C-terminal domain
    0.00046   20.2   0.8    0.00099   19.1   0.4    1.7  2  RB_B           Retinoblastoma-associated protein B domain
     0.0013   18.5   0.0     0.0049   16.7   0.0    2.1  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain
     0.0019   17.9   0.5      0.036   13.8   0.3    2.1  2  Cyclin_N       Cyclin, N-terminal domain
     0.0095   15.5   0.5      0.027   14.0   0.1    2.0  2  HTH_24         Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.019   14.6   0.0      0.073   12.8   0.0    2.0  1  Sigma70_r4_2   Sigma-70, region 4
      0.025   14.7   0.1      0.064   13.4   0.1    1.7  1  IL8            Small cytokines (intecrine/chemokine), interle
      0.048   13.6   0.2       0.12   12.3   0.2    1.7  1  HTH_11         HTH domain
      0.054   13.8   1.5       0.11   12.8   0.0    2.2  2  UPF0253        Uncharacterised protein family (UPF0253)
       0.12   12.3   0.2         18    5.2   0.0    3.0  3  HxlR           HxlR-like helix-turn-helix
       0.26   11.3   4.5       0.91    9.6   1.2    2.3  2  TFIIB_C_1      Transcription factor IIB C-terminal module 1


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 !   56.9   0.3   1.3e-18   1.6e-15       2      69 ..     134     201 ..     133     203 .. 0.92
   2 !   61.8   0.4   3.8e-20   4.6e-17       1      71 []     227     297 ..     227     297 .. 0.98

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 1.3e-18
                                       HHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SH CS
                             TFIIB   2 krfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsek 69 
                                        r++++l L   V+++A  ++++a+e++++ Grs ++++AA++y+Acr++++ rt+ eis  ++ + k
  gi|385805988|ref|YP_005842386.1| 134 DRLSNQLHLNRAVREEAAVIYRKAVEKGLVRGRSIESVIAASVYVACRLKKLPRTLDEISLHTRANRK 201
                                       58999******************************************************977666555 PP

  == domain 2  score: 61.8 bits;  conditional E-value: 3.8e-20
                                       HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                       i+r+ + l+L+ k  + A  ++k a+++ +++G+ pag+aAA++y+A+++e++krtqkei++++ V+e+t+
  gi|385805988|ref|YP_005842386.1| 227 IPRMGSLLDLSGKAMNIAARIVKIAKQKALTAGKDPAGLAAAAIYVATLLENEKRTQKEIANIAGVTEVTV 297
                                       89999****************************************************************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 !   33.2   0.0   2.2e-11   2.6e-08       9      43 .]      23      58 ..      20      58 .. 0.93

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 2.2e-11
                                      EE.CHEETSTTCEEESSSSBEEEECCCCCCCHHHHH CS
                      TF_Zn_Ribbon  9 tn.lveDpergelvCtdCGlVlednsidegpewref 43
                                      +n +v+Dperge++Ct+ G+Vle   +  gpewr+f
  gi|385805988|ref|YP_005842386.1| 23 PNaIVFDPERGEYICTETGEVLEQKLVNQGPEWRAF 58
                                      4669******************************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 !   20.8   0.1   1.7e-07   0.00021      18      49 ..     278     309 ..     269     310 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.7e-07
                                       TTT--HHHHHHHHTS-HHHHHHHHHHHHHHHH CS
                        Sigma70_r4  18 geglTleEIgerlgiSrerVrqiekrAlrkLR 49 
                                        e++T++EI+++ g+++ +Vr + k+ ++ L+
  gi|385805988|ref|YP_005842386.1| 278 NEKRTQKEIANIAGVTEVTVRNRYKELVNELK 309
                                       689**********************9998887 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      0.08        95      23      39 ..     194     209 ..     192     210 .. 0.78
   2 !   16.6   0.1   3.1e-06    0.0038      18      52 .]     270     305 ..     266     305 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.08
                      HTH_Tnp_ISL3  23 lllesrsvkavArqlgv 39 
                                       l+++ +++k++Ar++++
  gi|385805988|ref|YP_005842386.1| 194 LHTR-ANRKEIARCYRL 209
                                       4444.5********996 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 3.1e-06
                      HTH_Tnp_ISL3  18 ayilellles.rsvkavArqlgvSwtTVwrildryv 52 
                                        y+++ll +  r+ k++A++ gv++ TV+++++++v
  gi|385805988|ref|YP_005842386.1| 270 IYVATLLENEkRTQKEIANIAGVTEVTVRNRYKELV 305
                                       699****************************99876 PP

>> Cyclin_C  Cyclin, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0   0.00091       1.1      45      90 ..     170     214 ..     167     219 .. 0.87
   2 !    8.9   0.0    0.0013       1.6      42      88 ..     260     306 ..     223     313 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00091
                                       HHHHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHHHHHH CS
                          Cyclin_C  45 SliAaaalllarstlnspewtetlehytgyskedlkpcvelilell 90 
                                       S+iAa++++++r   + p   +++  +t+++ +++  c++l+++ l
  gi|385805988|ref|YP_005842386.1| 170 SVIAASVYVACRLK-KLPRTLDEISLHTRANRKEIARCYRLLVKEL 214
                                       88998887777777.899999********************99865 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0013
                                       S-HHHHHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHHHH CS
                          Cyclin_C  42 yppSliAaaalllarstlnspewtetlehytgyskedlkpcvelile 88 
                                        +p  +Aaaa+++a+   n++  ++++ ++ g+++  +++ ++ +++
  gi|385805988|ref|YP_005842386.1| 260 KDPAGLAAAAIYVATLLENEKRTQKEIANIAGVTEVTVRNRYKELVN 306
                                       568889*********9999999****************999998876 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 !   19.1   0.4   8.3e-07   0.00099      10      94 ..     126     208 ..     118     218 .. 0.85
   2 ?   -2.4   0.0       3.8   4.6e+03      61      78 ..     269     286 ..     247     305 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 8.3e-07
                              RB_B  10 yklaavrlrdLcerLklsselrekiwtlfehvlveetellkdRhlDqillcavYvvakvtkeelsFkeiikaYrkqp 86 
                                       +  a+  l +L ++L+l++ +re++  + ++++  e+ l++ R ++ ++ ++vYv ++++k  +++ ei  + r + 
  gi|385805988|ref|YP_005842386.1| 126 LAQAMNELDRLSNQLHLNRAVREEAAVIYRKAV--EKGLVRGRSIESVIAASVYVACRLKKLPRTLDEISLHTRANR 200
                                       56788999****************988888876..578**********************99999999988888777 PP

                              RB_B  87 qasskvyr 94 
                                       ++ ++ yr
  gi|385805988|ref|YP_005842386.1| 201 KEIARCYR 208
                                       77766665 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.8
                              RB_B  61 avYvvakvtkeelsFkei 78 
                                       a+Yv + +++e+++ kei
  gi|385805988|ref|YP_005842386.1| 269 AIYVATLLENEKRTQKEI 286
                                       455555555555555544 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   4.1e-06    0.0049      12      41 ..     275     304 ..     272     305 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.1e-06
                     HTH_AsnC-type  12 LqedaRisyaeLAervGlSestvlrRvrrL 41 
                                       L e+ +++ +e+A   G++e tv++R++ L
  gi|385805988|ref|YP_005842386.1| 275 LLENEKRTQKEIANIAGVTEVTVRNRYKEL 304
                                       78999**********************988 PP

>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.3     3e-05     0.036      38     124 ..     133     216 ..     106     218 .. 0.86
   2 ?    2.0   0.0      0.14   1.6e+02      35     103 ..     224     291 ..     221     312 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3e-05
                                       HHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSSS---HHHHHHHTTTSS-HHHHHHH CS
                          Cyclin_N  38 lvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKveeisppkledlvyitdeafteeeilem 114
                                       l +++++++l++ +   a++++ + ++k  v+ + ++ v a+++++A+++++  p +l+++   t    +++ei + 
  gi|385805988|ref|YP_005842386.1| 133 LDRLSNQLHLNRAVREEAAVIYRKAVEKGLVRGRSIESVIAASVYVACRLKKL-PRTLDEISLHTR--ANRKEIARC 206
                                       6678999999999999**********************************998.888888888865..889999999 PP

                                       HHHHHHHTTT CS
                          Cyclin_N 115 ErliLetLnf 124
                                        rl++++L+ 
  gi|385805988|ref|YP_005842386.1| 207 YRLLVKELQL 216
                                       9999999985 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSSS---HHHHHHHTT CS
                          Cyclin_N  35 idwlvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKveeisppkledlvyitd 103
                                       id++ ++ + ++l+ + + +a++++    +k  +  ++   ++a+++++A+ +e+ +  + ++++ i++
  gi|385805988|ref|YP_005842386.1| 224 IDYIPRMGSLLDLSGKAMNIAARIVKIAKQKALTAGKDPAGLAAAAIYVATLLENEK-RTQKEIANIAG 291
                                       67888888888888888889999998888888888889999999*****99997774.66666666654 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 ?   -2.9   0.1       4.5   5.4e+03       9      25 ..     189     205 ..     187     205 .. 0.75
   2 !   14.0   0.1   2.3e-05     0.027      11      44 ..     274     307 ..     270     307 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.5
                            HTH_24   9 LelLqknprisqreLAe 25 
                                       L ++  + r + +e+A+
  gi|385805988|ref|YP_005842386.1| 189 LDEISLHTRANRKEIAR 205
                                       66677777889999996 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 2.3e-05
                            HTH_24  11 lLqknprisqreLAerlglSpstvnrrlkrLeee 44 
                                       +L +n + +q+e+A   g++  tv+ r k+L++e
  gi|385805988|ref|YP_005842386.1| 274 TLLENEKRTQKEIANIAGVTEVTVRNRYKELVNE 307
                                       799****************************985 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   6.1e-05     0.073      27      48 ..     281     302 ..     274     304 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.1e-05
                                       --HHHHHHHHT--HHHHHHHHH CS
                      Sigma70_r4_2  27 lsykEIAellgisegtVksrls 48 
                                        ++kEIA + g++e+tV++r++
  gi|385805988|ref|YP_005842386.1| 281 RTQKEIANIAGVTEVTVRNRYK 302
                                       689*****************95 PP

>> IL8  Small cytokines (intecrine/chemokine), interleukin-8 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   5.4e-05     0.064      15      56 ..       7      48 ..       2      51 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.4e-05
                                      GGEEEEEEE.CSTTSSS-EEEEEETTSSCEEEETTSHHHHHH CS
                               IL8 15 kriksyriqetsssCpkpavifttkkgkevCadpkekwVqkl 56
                                      k+ ++ r+ e  s+Cp +a++f   +g  +C    e   qkl
  gi|385805988|ref|YP_005842386.1|  7 KKKEEARKSENESGCPPNAIVFDPERGEYICTETGEVLEQKL 48
                                      55567788899********************98766655555 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2    0.0001      0.12       9      40 ..     275     306 ..     269     312 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0001
                            HTH_11   9 LleargpisgeeLAeeLnvSrrtvrrdIkaL.e 40 
                                       Lle+++  + +e+A   +v++ tvr++ k+L +
  gi|385805988|ref|YP_005842386.1| 275 LLENEK-RTQKEIANIAGVTEVTVRNRYKELvN 306
                                       667777.7******************9999844 PP

>> UPF0253  Uncharacterised protein family (UPF0253)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   8.9e-05      0.11      12      52 ..     111     151 ..     102     154 .. 0.89
   2 ?   -2.4   0.9         5     6e+03      36      59 ..     249     271 ..     239     274 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.9e-05
                           UPF0253  12 yaqIgsgdlgYipdAiscalktLdevaanealpeevrekAA 52 
                                         qI s  ++ i+  ++ a++ Ld++ ++ +l+++vre+AA
  gi|385805988|ref|YP_005842386.1| 111 KWQIRSRIQSSIDRNLAQAMNELDRLSNQLHLNRAVREEAA 151
                                       5688899999999***************************9 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5
                           UPF0253  36 evaanealpeevrekAAyAAANLl 59 
                                       ++a+++al +  ++ A  AAA + 
  gi|385805988|ref|YP_005842386.1| 249 KIAKQKALTA-GKDPAGLAAAAIY 271
                                       5777777765.4889999998765 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.015        18      57      77 ..      29      49 ..      21      61 .. 0.86
   2 ?   -1.2   0.0       1.6   1.9e+03      34      58 ..     124     151 ..     107     176 .. 0.51
   3 ?    3.2   0.0     0.065        77      11      45 ..     272     306 ..     268     311 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.015
                                      SS-EEEEEE-TCGGGGHHHHH CS
                              HxlR 57 vPpkveYsltekGrslepvlq 77
                                       P++ eY  te+G+ le+ l 
  gi|385805988|ref|YP_005842386.1| 29 DPERGEYICTETGEVLEQKLV 49
                                      699*************98775 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.6
                                       HHHHHHHHHH...HHTTSEEEEEESSSS CS
                              HxlR  34 kmLaqrLreL...eqdglierevypevP 58 
                                       + Laq + eL    ++  ++r v +e  
  gi|385805988|ref|YP_005842386.1| 124 RNLAQAMNELdrlSNQLHLNRAVREEAA 151
                                       5555544444000444455555555443 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.065
                                       HHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHH CS
                              HxlR  11 lvellkgkkRfselkralpkisqkmLaqrLreLeq 45 
                                       + +ll+ +kR+++  +++ ++++ +  +r +eL +
  gi|385805988|ref|YP_005842386.1| 272 VATLLENEKRTQKEIANIAGVTEVTVRNRYKELVN 306
                                       678999999*998888999*************986 PP

>> TFIIB_C_1  Transcription factor IIB C-terminal module 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.2   0.00077      0.91       6      93 ..     130     215 ..     125     219 .. 0.78
   2 ?    2.5   0.1      0.13   1.5e+02      24      94 ..     238     310 ..     231     314 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00077
                         TFIIB_C_1   6 rnalevllklsrrdeavleealelakrfvGkrrergervekqeevaaaclmlaaerlrqPvPLaelrvl.dpslkdv 81 
                                        n l+ l ++ + + av+eea  + ++ v k   rg+ +e    v+aa++ +a+   + P  L e+     +  k++
  gi|385805988|ref|YP_005842386.1| 130 MNELDRLSNQLHLNRAVREEAAVIYRKAVEKGLVRGRSIE---SVIAASVYVACRLKKLPRTLDEISLHtRANRKEI 203
                                       5778889999999*******************99999887...69***********999999999864303344555 PP

                         TFIIB_C_1  82 elrrkevvrevk 93 
                                           + +v+e++
  gi|385805988|ref|YP_005842386.1| 204 ARCYRLLVKELQ 215
                                       555555555555 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.13
                         TFIIB_C_1  24 eealelakrfvGkrrergervekqee.vaaaclmlaaerlrqPvPLaelrvldpslk.dvelrrkevvrevkl 94 
                                        +a+++a r v   ++++    k     aaa++ +a+   ++    +e+  +++  +  v  r ke+v+e+kl
  gi|385805988|ref|YP_005842386.1| 238 GKAMNIAARIVKIAKQKALTAGKDPAgLAAAAIYVATLLENEKRTQKEIANIAGVTEvTVRNRYKELVNELKL 310
                                       5789999999998888888888776416777888888777777788888888775432677788999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       954  (0.0532099); expected 358.6 (0.02)
Passed bias filter:                      644  (0.0359195); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 1869.54
//
Query:       gi|385805989|ref|YP_005842387.1|  [L=104]
Description: translation initiation factor Sui1 [Fervidicoccus fontis Kam940]
Scores for complete 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   75.8   1.5    3.7e-21   75.4   1.5    1.2  1  SUI1        Translation initiation factor SUI1
     0.0034   17.6   0.8     0.0047   17.2   0.8    1.4  1  Img2        Mitochondrial large subunit ribosomal protein (Im
  ------ inclusion threshold ------
      0.014   15.6   0.0      0.017   15.3   0.0    1.1  1  ExbD        Biopolymer transport protein ExbD/TolR
       0.15   12.5   0.3       0.33   11.3   0.1    1.8  2  E3_binding  e3 binding domain


Domain annotation for each model (and alignments):
>> SUI1  Translation initiation factor SUI1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.4   1.5   8.2e-25   3.7e-21       2      77 .]      25      96 ..      24      96 .. 0.95

  Alignments for each domain:
  == domain 1  score: 75.4 bits;  conditional E-value: 8.2e-25
                              SUI1  2 kpkihirleqrggrKkvTtvsgleafgidlkklakelkkkfacsgsvvkdggeeiqvQGdqrkkvaelLtekygvp 77
                                      ++ i+irle+r+ +K vT+++g++ +++d+kkla++lk+k+a++g+  k+g   i++QGd+r +++e+L++  g+p
  gi|385805989|ref|YP_005842387.1| 25 QQLIKIRLEKRKFGKEVTIIEGIDEKEVDIKKLASQLKTKLATGGTA-KNG--RIELQGDHRSALKEILIQF-GFP 96
                                      789*******************************************6.999..8****************95.876 PP

>> Img2  Mitochondrial large subunit ribosomal protein (Img2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.8     1e-06    0.0047      25      80 .]      39      95 ..      16      95 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1e-06
                              Img2 25 kkltvirki...eGDiaalredLrkaleelvkvnevtgkieikGdrveevkkfLeskgF 80
                                      k++t+i  i   e Di++l+++L++ l+  +  + ++g+ie++Gd+++ +k++L + gF
  gi|385805989|ref|YP_005842387.1| 39 KEVTIIEGIdekEVDIKKLASQLKTKLA--TGGTAKNGRIELQGDHRSALKEILIQFGF 95
                                      5666666662224699***********9..79999********************9998 PP

>> ExbD  Biopolymer transport protein ExbD/TolR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0   3.7e-06     0.017      40     103 ..      13      84 ..       4      91 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.7e-06
                              ExbD  40 lPsssstqkeveekelirisisad..gs.iy....ldkkavsveelaqklkerkakppdk..ltvaikadkdv 103
                                       lP   ++q  ++e++li+i+++++  g+ +     +d+k+v++++la +lk + a+  ++    + +++d + 
  gi|385805989|ref|YP_005842387.1|  13 LPPELCEQ-LAKEQQLIKIRLEKRkfGKeVTiiegIDEKEVDIKKLASQLKTKLATGGTAknGRIELQGDHRS 84 
                                       78888899.79***********884422322567899****************99988887788888888766 PP

>> E3_binding  e3 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       2.2   9.8e+03      10      15 ..      21      26 ..      20      27 .. 0.76
   2 ?   11.3   0.1   7.4e-05      0.33       8      30 ..      55      76 ..      47      79 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.2
                                      HHHHCT CS
                        E3_binding 10 lAkelG 15
                                      lAke+ 
  gi|385805989|ref|YP_005842387.1| 21 LAKEQQ 26
                                      999975 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 7.4e-05
                                      HHHHHHCT--TTTS-..--CTTTBE CS
                        E3_binding  8 RklAkelGidLsdvk..GtGpgGRI 30
                                      +klA +l   L   +  Gt ++GRI
  gi|385805989|ref|YP_005842387.1| 55 KKLASQLKTKL---AtgGTAKNGRI 76
                                      67888888844...3569******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       835  (0.0465726); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); 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: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 623.58
//
Query:       gi|385805990|ref|YP_005842388.1|  [L=110]
Description: V-type ATP synthase subunit K [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.5e-15   57.2  18.3    1.5e-15   57.2  18.3    1.9  2  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 ?   -1.2   0.5      0.15   2.6e+03      14      23 ..      30      39 ..      17      44 .. 0.53
   2 !   57.2  18.3   8.5e-20   1.5e-15       1      59 [.      47     105 ..      47     106 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.15
                                      HHHHHHHHHH CS
                        ATP-synt_C 14 sGigiGkags 23
                                      +++++ ++gs
  gi|385805990|ref|YP_005842388.1| 30 MAYAQTTTGS 39
                                      4555555555 PP

  == domain 2  score: 57.2 bits;  conditional E-value: 8.5e-20
                                       HHHHHHH.GGGHHHHHHHHHHHHHHHHHHHHSGHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        ATP-synt_C   1 lgaglavGlsalgsGigiGkagsagiravarnpklftksliilafaeaialygLivali 59 
                                       +gagla+Gl+++g Gi++G +g+ag++ ++++p++f+++l+i+a+ e ia+ygLi+a++
  gi|385805990|ref|YP_005842388.1|  47 IGAGLAIGLAGIGGGIAVGRTGAAGLSVLSEKPEAFGTVLLIVALGEGIAIYGLIIAIL 105
                                       7********************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 752.91
//
Query:       gi|385805991|ref|YP_005842389.1|  [L=124]
Description: hypothetical protein FFONT_0949 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.094   13.2   0.1       0.13   12.7   0.1    1.3  1  Telomere_reg-2  Telomere length regulation protein


Domain annotation for each model (and alignments):
>> Telomere_reg-2  Telomere length regulation protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   7.5e-06      0.13      24      51 ..      46      75 ..      30      89 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.5e-06
                    Telomere_reg-2 24 LksaeeLirrkad..eveenaveLataLlt 51
                                      L++ae+Lir+k++  +v+e+  eL+  +++
  gi|385805991|ref|YP_005842389.1| 46 LDYAEKLIREKKTrlKVSEIIDELVAKIIN 75
                                      99*******888889*********998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 813.89
//
Query:       gi|385805992|ref|YP_005842390.1|  [L=209]
Description: V-type ATP synthase subunit D [Fervidicoccus fontis Kam940]
Scores for complete 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-42  143.8   9.1    6.3e-42  143.6   9.1    1.0  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 !  143.6   9.1   3.5e-46   6.3e-42       1     196 []      14     204 ..      14     204 .. 0.93

  Alignments for each domain:
  == domain 1  score: 143.6 bits;  conditional E-value: 3.5e-46
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSTSTTSTSHHHHHHHSSS.SS-. CS
                        ATP-synt_D   1 eLirlkkrlklaqrghslLkkKrdaLilefreilkelkelreeleeelkeayfslaeafaaggeediesavlesvkl 77 
                                       +Li+lk+ l l++r++++L++Kr+aL+l + +++ke+++l +e   elk+ay++l+   ++ g ++ ++++   ++ 
  gi|385805992|ref|YP_005842390.1|  14 NLIKLKRDLTLIRRVREVLEEKRSALLLYLNTMIKEYEKLYNETSSELKKAYDTLQASLLTIGYNRSKEISDIVPS- 89 
                                       79******************************************************77888889989988885554. PP

                                       .TSS-SEEEEEEBTTSEEEEEEE-..S.SSTSSSSS.SSSTCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        ATP-synt_D  78 akvvkvelktenvaGVkvpvfeleeeksdstelygl.lrtgaqldeavealrellellvelasletslelLdeeikk 153
                                          ++v++k + ++ Vkvp +++ e   +s++ + + ++ +++l e +e+l+e++e+l++l ++e++l ++ +e+k+
  gi|385805992|ref|YP_005842390.1|  90 --TLRVNVKIRALFAVKVPYISIAE---NSFPKMDFpSDVPPSLIESREKLKEVFEKLLRLIEVENTLFTIINELKT 161
                                       ..5********************66...445555444999************************************* PP

                                       HHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        ATP-synt_D 154 tnrRvNaLekvvIPrleetikyIkseLdEqereeffrlkkvkk 196
                                       t+r +N +++ +IP++e+ti+yI+  LdE+ereef+rlk++kk
  gi|385805992|ref|YP_005842390.1| 162 TQRLINSIDYSIIPNYEKTIRYISLVLDEREREEFSRLKMIKK 204
                                       *****************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1272  (0.0709465); expected 358.6 (0.02)
Passed bias filter:                      611  (0.0340789); 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: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1430.25
//
Query:       gi|385805993|ref|YP_005842391.1|  [L=474]
Description: V-type ATP synthase subunit B [Fervidicoccus fontis Kam940]
Scores for complete 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-66  221.9   0.0    9.6e-66  221.5   0.0    1.2  1  ATP-synt_ab    ATP synthase alpha/beta family, nucleotide-bin
    7.3e-12   45.6   1.2    1.5e-11   44.6   1.2    1.6  1  ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel do
    2.2e-05   24.5   0.5    0.00014   22.0   0.5    2.1  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 !  221.5   0.0   1.6e-69   9.6e-66       1     213 []     142     360 ..     142     360 .. 0.98

  Alignments for each domain:
  == domain 1  score: 221.5 bits;  conditional E-value: 1.6e-69
                                       SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTS....S.EEEEEEESEEHHHHHHHHHHCHHSSGGGGE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsd....d.aiiyvgiGergnevaevleefpegtimkrt 72 
                                       G++++D++ ++v+Gq++ i+++ g++++++++++++q+  +    + a++++++G + ++   + + f+e+++ +++
  gi|385805993|ref|YP_005842391.1| 142 GVSAIDVMNTLVRGQKLPIFSGGGLPHNMLAAQIARQAVVRgeeeEfAVVFAAVGIKYDDFLFFKRFFEESGAKNKV 218
                                       899**********************************8776888768****************************** PP

                                       EEEEEETTS-HHHHHHHHHHHHHHHHHHHH.TTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  73 vlvantsnepvaareasiytgitlAEyfrd.qgknvlliadslsrwaeAlreislrlgempadqgypaylgaklasl 148
                                        +++n +nep++ r++++++++tlAEy+++ +++++l i+++++++aeAlreis++ +e+p++qgyp+y++++ as+
  gi|385805993|ref|YP_005842391.1| 219 AMFVNLANEPAMIRLITPRVALTLAEYLAYeKDMHILAIITDMTNYAEALREISAAREEIPGRQGYPGYMYSDFASI 295
                                       *****************************9999******************************************** PP

                                       HTTSEEETSSEEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab 149 yERagkapdrtGsvtivaavspaggDfsdpvttatlgitdgfivLdkklaqrkhfPainvlvSvS 213
                                       yERag+a  ++Gs+t+++++s++++D+++p+++ t +it+g+ivLd+ l++++++P+invl+S+S
  gi|385805993|ref|YP_005842391.1| 296 YERAGRAIGKKGSITQMPILSMPNDDITHPIPDLTGYITEGQIVLDRGLFNKGIYPPINVLMSLS 360
                                       *******99******************************************************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 !   44.6   1.2   2.6e-15   1.5e-11       3      69 .]      21      85 ..      19      85 .. 0.95

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 2.6e-15
                                      EEETTEEEEESSTSCETCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBT.TSEEEEES CS
                     ATP-synt_ab_N  3 qviGpvvdvefgigrlpgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsr.GteVkrTG 69
                                       + Gp++ v+  +g   + ++++evel++ g++++g +l ++ + ++++++++t+G+   Gt+V+++G
  gi|385805993|ref|YP_005842391.1| 21 MIRGPLLFVKVSSG--VAFDEVVEVELQD-GEKRRGRVLDVSKNLAVIQIFEGTTGIGSlGTTVRFLG 85
                                      588***********..9999999999999.************************************98 PP

>> HAS-barrel  HAS barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.5   2.3e-08   0.00014      11      89 ..      23      86 ..      17      89 .. 0.89
   2 ?   -0.9   0.0      0.32   1.9e+03      24      50 ..     241     265 ..     230     280 .. 0.69

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.3e-08
                        HAS-barrel 11 sslifrvegskdvkvGeyVeielpdgeivlGmvtdirrgnselsndlalvlsleeleeangddevalatedt....... 82
                                      ++++ +v+ s +v + e Ve+el+dge++ G+v+d+++                       +++v++++e+t       
  gi|385805993|ref|YP_005842391.1| 23 RGPLLFVKVSSGVAFDEVVEVELQDGEKRRGRVLDVSK-----------------------NLAVIQIFEGTtgigslg 78
                                      567778888889**************************.......................9*******9999888888 PP

                        HAS-barrel 83 .gvkvlGe 89
                                       +v+ lGe
  gi|385805993|ref|YP_005842391.1| 79 tTVRFLGE 86
                                      88888887 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.32
                        HAS-barrel  24 kvGeyVeielpdgeivlGmvtdirrgn 50 
                                        + ey+ +e +   ++l ++td+ ++ 
  gi|385805993|ref|YP_005842391.1| 241 TLAEYLAYEKD--MHILAIITDMTNYA 265
                                       55578888866..899999**999964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.50
# Mc/sec: 2833.21
//
Query:       gi|385805994|ref|YP_005842392.1|  [L=574]
Description: V-type ATP synthase subunit A [Fervidicoccus fontis Kam940]
Scores for complete 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-90  301.8   0.0    3.5e-90  301.3   0.0    1.2  1  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
    1.7e-45  153.8   0.0      3e-45  153.0   0.0    1.4  1  ATP-synt_ab_Xtn  ATPsynthase alpha/beta subunit N-term extens
    7.8e-09   35.9   2.3    1.8e-08   34.7   0.9    2.5  2  ATP-synt_ab_N    ATP synthase alpha/beta family, beta-barrel 
    0.00088   19.0   0.2        1.8    8.3   0.1    3.2  3  AAA_30           AAA domain
  ------ inclusion threshold ------
      0.094   12.9   0.1         15    5.9   0.0    2.5  2  Peptidase_M23    Peptidase family M23


Domain annotation for each model (and alignments):
>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  301.3   0.0   9.7e-94   3.5e-90       1     213 []     197     420 ..     197     420 .. 0.98

  Alignments for each domain:
  == domain 1  score: 301.3 bits;  conditional E-value: 9.7e-94
                                       SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEEESEEHHHHHHHHHHCHH......SS.GGG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xx.xxx RF
                       ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsddaiiyvgiGergnevaevleefpe......gt.imk 70 
                                       G+r++D++fpi++G++ +ipg+fg+Gktv ++ ++++s+++ ++iy+g+Gergne++evle+fp+      g+ +m+
  gi|385805994|ref|YP_005842392.1| 197 GLRIIDTFFPIAKGGTAAIPGGFGTGKTVTLHGIAQWSEAK-VVIYIGCGERGNEMTEVLEKFPHykdpwtGRpLME 272
                                       89***********************************9888.***********************777765228*** PP

                                       GEEEEEEETTS-HHHHHHHHHHHHHHHHHHHHTTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  71 rtvlvantsnepvaareasiytgitlAEyfrdqgknvlliadslsrwaeAlreislrlgempadqgypaylgaklas 147
                                       rt+l+antsn+pvaareasiy+g+tlAEy+rdqg++vll+ads+srwaeAlrei++rl+empa++gyp+yl+++la+
  gi|385805994|ref|YP_005842392.1| 273 RTILIANTSNMPVAAREASIYVGVTLAEYYRDQGYDVLLVADSTSRWAEALREIGGRLEEMPAEEGYPSYLASRLAE 349
                                       ***************************************************************************** PP

                                       HHTTSEEE.....TSSEEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                                       xxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab 148 lyERagka.....pdrtGsvtivaavspaggDfsdpvttatlgitdgfivLdkklaqrkhfPainvlvSvS 213
                                       +yERag++     p+r Gsvt   avsp+ggDf++pvt++t++++ +f+ Ld++la ++h+Pain+l+S+S
  gi|385805994|ref|YP_005842392.1| 350 FYERAGRVialgdPKRIGSVTLGGAVSPPGGDFTEPVTSHTRRFVRVFWALDTTLAYSRHYPAINWLTSYS 420
                                       *************99*******************************************************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 !  153.0   0.0   8.3e-49     3e-45       1     121 []      66     188 ..      66     188 .. 0.98

  Alignments for each domain:
  == domain 1  score: 153.0 bits;  conditional E-value: 8.3e-49
                                       EETTS-BHHHHHHHHTS.BE-TT----SS-SSS-EEEEE..SS-TT-EEETT-EEEEEECTTCEEEEEE--TT-EEE CS
                   ATP-synt_ab_Xtn   1 yDGiqrpLekiaeksgs.fierGvkvpaldrekkwefkp..kvkvgdkvsggdilGtvqeteliehkimvppkvegk 74 
                                       yDGiqrpLe i+eksgs fi+rG+k pal r+kkw+f p  ++k+gd+vs+g++lG+v+etelieh+i+vpp+++gk
  gi|385805994|ref|YP_005842392.1|  66 YDGIQRPLEVIKEKSGSiFIRRGIKSPALPRNKKWHFMPnkELKTGDEVSSGTVLGSVKETELIEHRILVPPNISGK 142
                                       9**************************************999*********************************** PP

                                       EEEE--EEEE-TTSECEEECETT.ECEEEESSEEEETTS---ESEEE CS
                   ATP-synt_ab_Xtn  75 vkeiaeegeytvedtiaeveteegkekeltllqkwPvrkprpvkekl 121
                                       ++ +a+e +y+ved+ia+v++e+ +e+el+l+++wPvr prp+kekl
  gi|385805994|ref|YP_005842392.1| 143 LTFLAKEDDYSVEDVIAKVTKEN-EERELKLYHNWPVRIPRPFKEKL 188
                                       ********************988.7********************97 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 !   34.7   0.9   5.2e-12   1.8e-08      19      69 .]       4      50 ..       1      50 [. 0.93
   2 ?   -3.3   0.0       3.8   1.4e+04      11      24 ..     154     167 ..     153     172 .. 0.81

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 5.2e-12
                                      TCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBTTSEEEEES CS
                     ATP-synt_ab_N 19 pgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsrGteVkrTG 69
                                       ++y+++ev+     ++++g++ ++ +d + ++v++st+G+++G+ V++ G
  gi|385805994|ref|YP_005842392.1|  4 VKMYEVVEVG--S--DGIIGEVTRIVGDDAYIQVYESTSGIKPGDIVVSSG 50
                                      789*******..7..9*******************************9876 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.8
                                       EESSTSCETCTTEE CS
                     ATP-synt_ab_N  11 vefgigrlpgiyna 24 
                                       ve++i+++ ++++ 
  gi|385805994|ref|YP_005842392.1| 154 VEDVIAKVTKENEE 167
                                       99999999999886 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.1    0.0005       1.8      20      45 ..     212     237 ..     206     260 .. 0.80
   2 ?    0.9   0.0     0.089   3.2e+02      38      64 ..     298     325 ..     293     337 .. 0.79
   3 !    5.6   0.0    0.0032        11     106     138 ..     345     376 ..     339     426 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0005
                            AAA_30  20 vavltGpAGtGKttalkalreaweaa 45 
                                       +a++ G+ GtGKt +l ++++  ea+
  gi|385805994|ref|YP_005842392.1| 212 TAAIPGGFGTGKTVTLHGIAQWSEAK 237
                                       68899**************9988876 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.089
                            AAA_30  38 lreaweaaggrviglA.ptgkaAkvLae 64 
                                       l+e ++++g++v+++A +t++ A++L+e
  gi|385805994|ref|YP_005842392.1| 298 LAEYYRDQGYDVLLVAdSTSRWAEALRE 325
                                       689999*******999446788998985 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.0032
                            AAA_30 106 aallkaaekagakvilvGDerQlasVeaGgvlr 138
                                        +l++  e+   +vi +GD++  +sV+ Gg+++
  gi|385805994|ref|YP_005842392.1| 345 SRLAEFYER-AGRVIALGDPKRIGSVTLGGAVS 376
                                       567777777.89*****************9976 PP

>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1     0.014        50      24      63 ..       9      46 ..       5      55 .. 0.86
   2 ?    5.9   0.0    0.0042        15      54      76 ..     105     127 ..      97     140 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.014
                                      EEEEEEETTTEEEEEEEECTCEEEEEEEESEESS-TTEEE CS
                     Peptidase_M23 24 VvfagkkegyGnvviidhgdgystlyahlskisvkegqkV 63
                                      Vv++g ++ +G+v++i  +d y+++y   s   +k+g+ V
  gi|385805994|ref|YP_005842392.1|  9 VVEVGSDGIIGEVTRIVGDDAYIQVYESTSG--IKPGDIV 46
                                      8999998566*****************9999..8888876 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0042
                                       EESS-TTEEE-TTCEEEEEBSTS CS
                     Peptidase_M23  54 kisvkegqkVkaGqvIGtvgstg 76 
                                       + ++k+g++V+ G+v+G v +t+
  gi|385805994|ref|YP_005842392.1| 105 NKELKTGDEVSSGTVLGSVKETE 127
                                       55699**************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (574 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 3925.82
//
Query:       gi|385805995|ref|YP_005842393.1|  [L=205]
Description: V-type ATP synthase subunit E [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00015   21.8   1.8    0.00035   20.6   1.8    1.7  1  FliH           Flagellar assembly protein FliH
    0.00084   18.8  16.3      0.017   14.5  16.3    2.4  1  vATP-synt_E    ATP synthase (E/31 kDa) subunit
     0.0056   17.2   3.9     0.0068   17.0   0.8    2.4  2  Vac14_Fab1_bd  Vacuolar 14 Fab1-binding region
     0.0068   16.4   0.8       0.01   15.8   0.7    1.4  1  DUF1804        Protein of unknown function (DUF1804)
  ------ inclusion threshold ------
      0.042   13.3   1.6      0.056   12.9   1.6    1.1  1  HBM            Helical bimodular sensor domain
      0.056   13.3   0.0       0.11   12.4   0.0    1.5  1  Whirly         Whirly transcription factor
      0.061   13.3   0.2       0.16   11.9   0.2    1.7  2  Peptidase_S49  Peptidase family S49
       0.13   11.5   8.4      0.051   12.9   5.2    1.8  2  CorA           CorA-like Mg2+ transporter protein
        4.9    7.6  12.4          3    8.3   9.4    2.0  3  Imm42          Immunity protein 42
        5.6    7.0   7.4          4    7.5   1.4    3.1  3  DASH_Dad4      DASH complex subunit Dad4
        5.9    6.3   9.2         18    4.7   9.3    1.7  1  Z1             Z1 domain
        8.9    6.9  11.1    1.2e+03    0.1  11.0    3.0  1  YtxH           YtxH-like protein


Domain annotation for each model (and alignments):
>> FliH  Flagellar assembly protein FliH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   1.8   2.3e-07   0.00035      13     115 ..      57     172 ..      13     182 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.3e-07
                                       HHHHHHHHH...........HHHHHHHHHHHHHHHHHHHHHHS--.S-HHHHHHHHHHHHTTSCHHHS-EEEEE-HH CS
                              FliH  13 elenslael...........deeledqlvqlaldiarkvikkels.vdpekilalvrealaklpvdekkitlrvnpd 77 
                                       +  +s+ +l            +e + ++v+lal+ ++k i  el+ +++++i +++   l k+ ++ ++  +++  +
  gi|385805995|ref|YP_005842393.1|  57 NYVESVNNLrslrqyeikikTQEKKAEIVDLALKEVEKKIFYELDkEEKKIIYEAILSKL-KESIKLTNGEIHIEKE 132
                                       44444444455555556665888999********99999997776155666778999999.999************* PP

                                       HHHHHHHHHHHHHHHCT-..EEEE-TTS-TT-EEEEESSC CS
                              FliH  78 Dlelvrehlgeelsargw..rlvaDsslsrGgcrieseeg 115
                                       D +lv + ++++l++ +   +++ D     Gg++  s++g
  gi|385805995|ref|YP_005842393.1| 133 DKDLVSKIIKKKLEDSKEkiKIIDDLPSGTGGIKFVSQDG 172
                                       **********999888876799999888888988887776 PP

>> vATP-synt_E  ATP synthase (E/31 kDa) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5  16.3   1.1e-05     0.017      55     199 .]      66     200 ..      13     200 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.1e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHTTSHHCCCCHHHHHHCCCCCCC-SSCEEEEECCCCHHCCCCT CS
                       vATP-synt_E  55 iSnalnkarlkvLkareevleevfeeaekkLa.eveedkdeYkellkkLivqalvkleepevivrarkeDaelveea 130
                                        S    + ++k  + + e+++ +++e+ekk+  e++++  e k + + ++ +  ++++  +  +   keD++lv+++
  gi|385805995|ref|YP_005842393.1|  66 RSLRQYEIKIKTQEKKAEIVDLALKEVEKKIFyELDKE--EKKIIYEAILSKLKESIKLTNGEIHIEKEDKDLVSKI 140
                                       45556677888888899***********9985155554..477777777777777788788888999*********8 PP

                                       HCCCCCCHHCCSSSS--SEEEEESSEBTTSSSEEEECCSSSCEEECCCHHHCHHHHHHHHHHCCCCCHC CS
                       vATP-synt_E 131 ldkaaeeykaktkkktvevagdeedfledvlGGvvleaadgkikvnnTlearLelvleqllpeirkaLF 199
                                          ++++++   +k    +++d    l +  GG+  +++dg    + Tl  ++el + +l + + + LF
  gi|385805995|ref|YP_005842393.1| 141 ---IKKKLEDSKEKI---KIIDD---LPSGTGGIKFVSQDGSTVYDFTLKKIFELSKFELASIVYNVLF 200
                                       ...555555543333...55566...69999****************************9999999998 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 !   17.0   0.8   4.6e-06    0.0068      20      77 ..       5      62 ..       2      91 .. 0.91
   2 ?    0.8   0.3       0.5   7.5e+02      28      48 ..      92     112 ..      62     156 .. 0.54

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.6e-06
                     Vac14_Fab1_bd 20 kikeyleeivkpvlkcfsDkdsrvRyyacEslyniakvakgevlkllneifdalvklv 77
                                      +i++ le +++ v++ f+D+ +++R  a E l    k +k++++k l+++++  v+ v
  gi|385805995|ref|YP_005842393.1|  5 NIESLLEYVINKVINEFKDTVEELRKDAHELLDDAYKNTKNSLVKELSDLYENYVESV 62
                                      588999*********************************************9887665 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.5
                     Vac14_Fab1_bd  28 ivkpvlkcfsDkdsrvRyyac 48 
                                       + k ++  ++ +++++ y a+
  gi|385805995|ref|YP_005842393.1|  92 VEKKIFYELDKEEKKIIYEAI 112
                                       445555555555555555443 PP

>> DUF1804  Protein of unknown function (DUF1804)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.7   6.8e-06      0.01      59     148 ..       1      94 [.       1     110 [. 0.84

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.8e-06
                           DUF1804  59 laeggieevakqlledfvvqvqetleelrent.....elsaedkveiLasLsdsfsktvaaakrldPelsklavale 130
                                       + eg+ie++ + ++++++  ++ t+eelr++      +   ++k +++ +Lsd ++  v+++++    l + ++ ++
  gi|385805995|ref|YP_005842393.1|   1 MEEGNIESLLEYVINKVINEFKDTVEELRKDAhelldDAYKNTKNSLVKELSDLYENYVESVNN-LRSLRQYEIKIK 76 
                                       6799*************************99877776777899******************966.778888888888 PP

                           DUF1804 131 vlellaefvrekfpehae 148
                                       + e+ ae+v     e+ +
  gi|385805995|ref|YP_005842393.1|  77 TQEKKAEIVDLALKEVEK 94 
                                       888877777666555555 PP

>> HBM  Helical bimodular sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.6   3.7e-05     0.056      46     148 ..      21     122 ..      15     128 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.7e-05
                                       HHHHHHHHHHHHHHHHHH--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               HBM  46 vqkkldelkaqlqklkakfkspenvrlLqeqlalvqeyrksfnelraayesrnaaRqeldsaaeraleaideleaev 122
                                        +++++el++   +l +   +     l++e  +l ++y +s+n+lr+ ++ + +++ + +++ae ++ a+ e+e+++
  gi|385805995|ref|YP_005842393.1|  21 FKDTVEELRKDAHELLDDAYKNTKNSLVKELSDLYENYVESVNNLRSLRQYEIKIKTQ-EKKAEIVDLALKEVEKKI 96 
                                       5789999999999999999999999****************************99987.677889999********* PP

                                       HCS-S-HHHHHHHHHHHHHHHHHHHH CS
                               HBM 123 lqtpeadserlaqlqaiaelkrqvql 148
                                         +++++++++     +++lk+ ++l
  gi|385805995|ref|YP_005842393.1|  97 FYELDKEEKKIIYEAILSKLKESIKL 122
                                       *****987777666667888887765 PP

>> Whirly  Whirly transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   7.1e-05      0.11      35      65 ..     165     195 ..     140     202 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.1e-05
                                       EEEEEEEETTEE-GGG-EEEEE-HHHHHHHH CS
                            Whirly  35 LefapavgerqYdwekkqvfaLSatElgell 65 
                                       ++f++  g+  Yd++ k++f LS  El++++
  gi|385805995|ref|YP_005842393.1| 165 IKFVSQDGSTVYDFTLKKIFELSKFELASIV 195
                                       57888889999*****************997 PP

>> Peptidase_S49  Peptidase family S49
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.66   9.8e+02      90     110 ..      12      31 ..       8      39 .. 0.75
   2 ?   11.9   0.2   0.00011      0.16      71     118 ..      30      77 ..      19      84 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.66
                                       HHHHHHHHHHHHHHHHHHTS- CS
                     Peptidase_S49  90 rlldetyqqFvqtVaknRnls 110
                                         ++++ ++F++tV + R+ +
  gi|385805995|ref|YP_005842393.1|  12 YVINKVINEFKDTVEELRK-D 31 
                                       5789999999999999997.4 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00011
                                       CCCCCTTSS--HHHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHCHH CS
                     Peptidase_S49  71 ksavslrrelteeereilqrlldetyqqFvqtVaknRnlsveqvdkiA 118
                                       k+a  l ++  ++ ++ l ++l ++y+++v++V + R+l   +++  +
  gi|385805995|ref|YP_005842393.1|  30 KDAHELLDDAYKNTKNSLVKELSDLYENYVESVNNLRSLRQYEIKIKT 77 
                                       667788899999**************************9988887655 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   5.2   3.4e-05     0.051     107     183 ..       5      81 ..       1     123 [. 0.83
   2 ?   -1.0   0.2      0.59   8.8e+02     123     155 ..     109     142 ..     104     157 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.4e-05
                              CorA 107 spgellyrlldeivdrlfellekleeeldeledeledstkkeilrelaqlrrrlvklrralapnrevlkrllakadd 183
                                       + ++ll+ +++++++++ +++e+l ++ +el d   ++tk+++++el++l +++v+    l+ +r+   ++++++ +
  gi|385805995|ref|YP_005842393.1|   5 NIESLLEYVINKVINEFKDTVEELRKDAHELLDDAYKNTKNSLVKELSDLYENYVESVNNLRSLRQYEIKIKTQEKK 81 
                                       67899**********************************************99999888888877765455554444 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.59
                              CorA 123 lfellekleeeldeledel.edstkkeilrelaq 155
                                       ++++l+kl+e ++    e+  ++++k++++++++
  gi|385805995|ref|YP_005842393.1| 109 YEAILSKLKESIKLTNGEIhIEKEDKDLVSKIIK 142
                                       5666677777777777777656666666666654 PP

>> Imm42  Immunity protein 42
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   9.4     0.002         3      29     152 ..      10     127 ..       3     146 .. 0.82
   2 ?   -0.7   0.1       1.1   1.7e+03     126     133 ..     148     155 ..     124     186 .. 0.53
   3 ?   -1.8   0.0       2.6   3.9e+03      68      85 ..     181     198 ..     174     203 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.002
                             Imm42  29 fvfcIdgeiypdykltttLrsevnslkdnksalinkkidkelfnldakeafkllvdaegaekgddeddleedeeesy 105
                                       + ++I+  i   +++   Lr + ++l d+  ++ + +  kel +l ++ + + +++ +++ +++ + +++e++ e +
  gi|385805995|ref|YP_005842393.1|  10 LEYVINKVINEFKDTVEELRKDAHELLDDAYKNTKNSLVKELSDLYENYVES-VNNLRSLRQYEIKIKTQEKKAEIV 85 
                                       5677777777778889999999999999999999999999999887776666.666679999999999999988888 PP

                             Imm42 106 rydlspeeifDdgfyiFlvsndeniriiwekdkkeniseviLkkgev 152
                                       +  l+     + + +iF+  ++e+ +ii+e + ++  +++ L+ ge+
  gi|385805995|ref|YP_005842393.1|  86 DLALK-----EVEKKIFYELDKEEKKIIYEAILSKLKESIKLTNGEI 127
                                       88777.....44558****************9888777788888876 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.1
                             Imm42 126 ndenirii 133
                                       ++e+i+ii
  gi|385805995|ref|YP_005842393.1| 148 SKEKIKII 155
                                       23333444 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 2.6
                             Imm42  68 kelfnldakeafkllvda 85 
                                       k++f+l + e+++++++ 
  gi|385805995|ref|YP_005842393.1| 181 KKIFELSKFELASIVYNV 198
                                       689999999999998885 PP

>> DASH_Dad4  DASH complex subunit Dad4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   1.4    0.0027         4      37      59 ..      41      63 ..       5      72 .. 0.73
   2 ?    1.4   0.2      0.21   3.1e+02      36      67 ..      74     105 ..      63     107 .. 0.84
   3 ?   -0.7   0.1      0.97   1.5e+03       6      17 ..     130     141 ..     112     152 .. 0.60

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0027
                         DASH_Dad4 37 inkkNknvelvsqlwenYqrnvq 59
                                       n+kN+ v+ +s+l enY ++v+
  gi|385805995|ref|YP_005842393.1| 41 KNTKNSLVKELSDLYENYVESVN 63
                                      3899999***********99996 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.21
                         DASH_Dad4  36 einkkNknvelvsqlwenYqrnvqfnLeatge 67 
                                       +i+++ k+ e+v   +++ ++ + ++L++ ++
  gi|385805995|ref|YP_005842393.1|  74 KIKTQEKKAEIVDLALKEVEKKIFYELDKEEK 105
                                       7899999******999*999999999998765 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.97
                         DASH_Dad4   6 eeqqsalLsRIi 17 
                                       e++ ++l s Ii
  gi|385805995|ref|YP_005842393.1| 130 EKEDKDLVSKII 141
                                       444444555555 PP

>> Z1  Z1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   9.3     0.012        18      36     127 ..      15     103 ..       8     157 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.012
                                Z1  36 kdeqekvaelieelleelkkelkesaeekkeellkeleklwekekts.......tkseeeelsfeevkeelkealek 105
                                       +++ +++++ +eel ++ ++ l+++ +++k++l+kel++l+e+  +s                  + + ++k   +k
  gi|385805995|ref|YP_005842393.1|  15 NKVINEFKDTVEELRKDAHELLDDAYKNTKNSLVKELSDLYENYVESvnnlrslR----------QYEIKIKTQEKK 81 
                                       5667788888888888888888888999****************44344555541..........444444444444 PP

                                Z1 106 ievvvvNsskkkerldYeeeee 127
                                        e+v +  ++ ++++ Ye ++e
  gi|385805995|ref|YP_005842393.1|  82 AEIVDLALKEVEKKIFYELDKE 103
                                       4444444443334444443322 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1  11.0      0.82   1.2e+03      28      53 ..      19      62 ..      14     154 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.82
                              YtxH 28 kdlkekaddlkekakelleeakeka..................k 53
                                      ++ k+++++l+++a ell++a++++                  +
  gi|385805995|ref|YP_005842393.1| 19 NEFKDTVEELRKDAHELLDDAYKNTknslvkelsdlyenyvesV 62
                                      56678888888888888888887776555444422223333220 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2774  (0.154721); expected 358.6 (0.02)
Passed bias filter:                      785  (0.0437838); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 1316.93
//
Query:       gi|385805996|ref|YP_005842394.1|  [L=81]
Description: hypothetical protein FFONT_0954 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.9e-09   35.6   0.4      1e-08   35.3   0.4    1.0  1  ATP-synt_F   ATP synthase (F/14-kDa) subunit
  ------ inclusion threshold ------
      0.044   13.7   1.2      0.052   13.5   0.3    1.6  2  GnsAB_toxin  GnsA/GnsB toxin of bacterial toxin-antitoxin sys
      0.064   13.4   0.0      0.072   13.2   0.0    1.1  1  IF-2         Translation-initiation factor 2


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 !   35.3   0.4   1.8e-12     1e-08      16      90 ..       2      74 ..       1      75 [. 0.91

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 1.8e-12
                                      TTCEEEECSSHHHHHHHHHHHHHHTTEEEEEEEHHHHCCCHHHHHHCTCSSSSEEEEESCSCCGGSHHCHHHHHH CS
                        ATP-synt_F 16 aGvgevevtdeeeieealkelleredigiilitekiaeeirelideykeealPaileIPskegpydeekdsvrkk 90
                                      +G +++e+ ++++i+++++++++r+di +il+++++ e i+++i+++++++  +i  +Ps ++ +++   ++rk+
  gi|385805996|ref|YP_005842394.1|  2 IGCEGIEERNPDNIAQIIETYAKRQDISVILVEKELGELISSDIENIRKKTGKIIFYLPSPSSAMEP--TDIRKM 74
                                      7999*********************************************************997655..566665 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 ?   -2.6   0.0      0.91   5.4e+03      12      18 ..      13      19 ..       4      24 .. 0.59
   2 ?   13.5   0.3   8.8e-06     0.052      11      31 ..      34      54 ..      31      58 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.91
                                      HHHHHHH CS
                       GnsAB_toxin 12 eeiaeli 18
                                      ++ia+ i
  gi|385805996|ref|YP_005842394.1| 13 DNIAQII 19
                                      4555554 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 8.8e-06
                                      HHHHHHHHHHHHHHHHHHHSS CS
                       GnsAB_toxin 11 EeeiaeliakKiaELkKkTGk 31
                                      E+e+ eli+  i  ++KkTGk
  gi|385805996|ref|YP_005842394.1| 34 EKELGELISSDIENIRKKTGK 54
                                      99******************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 ?   13.2   0.0   1.2e-05     0.072      29      80 ..      14      66 ..      11      76 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.2e-05
                                      HHHHHHHCTT..SSTEEEECEEEESSB-HHHHHHHHHSTEEEEEESSSCTHHH CS
                              IF-2 29 AlkeaLekles.eevkvkvihsgvGaitesDvelasasnaiiigFnvkvskka 80
                                       +++++e++ + ++++v  ++++ G++  sD+e  +++ + ii +  ++s+++
  gi|385805996|ref|YP_005842394.1| 14 NIAQIIETYAKrQDISVILVEKELGELISSDIENIRKKTGKIIFYLPSPSSAM 66
                                      588999999889*************************9999998866666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       723  (0.0403257); expected 358.6 (0.02)
Passed bias filter:                      589  (0.0328518); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 557.54
//
Query:       gi|385805997|ref|YP_005842395.1|  [L=667]
Description: V-type ATP synthase subunit I [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.5e-36  123.4  19.2    1.9e-24   85.7   0.8    3.2  4  V_ATPase_I      V-type ATPase 116kDa subunit family
  ------ inclusion threshold ------
      0.017   15.1   0.4      0.041   13.8   0.4    1.6  1  SPATA24         Spermatogenesis-associated protein 24
      0.024   14.8   0.1         12    6.2   0.1    2.5  2  Med2            Mediator complex subunit 2
       0.03   14.6   1.4       0.03   14.6   1.4    2.6  2  ABC_tran_CTD    ABC transporter C-terminal domain
      0.036   14.4   2.7        1.2    9.5   0.3    2.5  2  BLOC1_2         Biogenesis of lysosome-related organelles com
        0.1   12.2   5.8      0.085   12.5   1.2    2.4  2  PI3K_P85_iSH2   Phosphatidylinositol 3-kinase regulatory subu
       0.16   12.7   0.8         22    5.8   0.2    2.6  2  DUF2203         Uncharacterized conserved protein (DUF2203)
        0.2   11.2   1.6       0.66    9.5   1.6    1.7  1  DUF4795         Domain of unknown function (DUF4795)
       0.21   11.7   2.9        2.5    8.2   0.8    3.1  3  DUF1192         Protein of unknown function (DUF1192)
       0.22   11.9   1.5        1.9    8.9   0.0    2.3  2  Tli4_N          Tle cognate immunity protein 4 N-terminal dom
       0.29   11.1   8.0        5.2    7.1   2.9    2.4  2  Prefoldin_2     Prefoldin subunit
        0.6   10.1   6.3        7.5    6.6   0.4    2.4  2  CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein C
       0.64   10.5   5.0        5.1    7.6   0.1    3.4  3  FlaC_arch       Flagella accessory protein C (FlaC)
        1.1    7.9   3.6       0.41    9.3   0.3    1.8  2  Tektin          Tektin family
        1.7    9.2   5.9        7.7    7.0   0.7    2.5  2  ZapB            Cell division protein ZapB
        2.4    7.1   6.4        3.2    6.7   0.2    2.1  2  TelA            Toxic anion resistance protein (TelA)
        2.5    8.3   6.2          6    7.1   0.2    2.5  2  Seryl_tRNA_N    Seryl-tRNA synthetase N-terminal domain
        3.4    8.2   6.0         12    6.5   0.2    2.3  2  APG6_N          Apg6 coiled-coil region
        4.4    7.5   5.5         11    6.2   0.7    2.5  2  Swi5            Swi5
        9.9    5.7   7.7       0.96    9.0   2.0    2.0  2  Snf7            Snf7


Domain annotation for each model (and alignments):
>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       0.6   5.3e+02      25     101 ..      45     127 ..      42     135 .. 0.61
   2 !   85.7   0.8   2.2e-27   1.9e-24     193     421 ..     179     390 ..      82     434 .. 0.76
   3 ?   -0.9   0.8      0.32   2.9e+02     515     556 ..     451     492 ..     447     501 .. 0.84
   4 !   47.2   4.0     9e-16     8e-13     705     810 ..     560     657 ..     552     659 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.6
                        V_ATPase_I  25 fvkevrrc.demerklrfleeeieklekavikeeea.....eesleapeekeldeleeelekleeelkelnenlekl 95 
                                       + +e+ r+ +e+e k++ +++ +++ +   i++  +       +++++ ++e d le+e+e + +elk+ ++  ek+
  gi|385805997|ref|YP_005842395.1|  45 YNNEILRYsQEIEGKVNKFSSILSDINIYGIRNGGEikvskWIETAKSISAEYDMLEKEIEPIISELKSSKSDREKI 121
                                       66666554257777777777777776666665555445543333444455667777777777777777777777777 PP

                        V_ATPase_I  96 kkelne 101
                                        + l+e
  gi|385805997|ref|YP_005842395.1| 122 DAFLKE 127
                                       665555 PP

  == domain 2  score: 85.7 bits;  conditional E-value: 2.2e-27
                        V_ATPase_I 193 eepledpetgekveksvfiiffqgeqlkekikkicesfgaklyelpes.eeereeklkeveeriedlekvleqteea 268
                                       ee             +v +i+++ e  ++ i+ki    g +   +p++ +++ + +++e++++i++ +k +e+ ee+
  gi|385805997|ref|YP_005842395.1| 179 EE------------SNVAVILYKKED-EKEIEKILAESGFSEVVIPKDlPSNFHLAYEELKKKISEFDKKIEELEEK 242
                                       33............566677776655.6789***99888888888766368889999*****************999 PP

                        V_ATPase_I 269 lkevleeiakeleewklkvkkekaiyhtLnlfnldvtkkvliaegWvpkeeleeiqkalkeateess.ssvpsilne 344
                                       +k+  e + k+l++ + +vk    iy+++        + + + +g++p+ e e+i + +k+a +++     ++i+ +
  gi|385805997|ref|YP_005842395.1| 243 IKAK-EVYLKDLYSRMYTVKEALRIYSQIKNT-----DYFSYVRGYIPAYEAEKIISFIKKALDNRIlVIWEEITLK 313
                                       9875.667889999999**********98777.....457799******************9977753333333333 PP

                        V_ATPase_I 345 ietketpPTyfrtnkfteafQeivdaYGiarYrEvNpalftiitFPFlFavMFGDiGHGlllllfalllvlkekklk 421
                                         ++e+ PT +++nk+ + f  +v+ YG +  +E+ p  f+ itFP +F++MF D+GHGll+llf+++++  +k  +
  gi|385805997|ref|YP_005842395.1| 314 AVKEEKLPTEIKVNKLLKPFSMLVENYGYPLPHEIVPIYFMAITFPIIFGIMFPDLGHGLLVLLFGIYMIKASKGRE 390
                                       3346889***************************************************************8877544 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.32
                        V_ATPase_I 515 lsvilGviqMlfgvllslvNalyfkkkldiilefiPqllfll 556
                                       +s  +G i ++ g l+ l+N+l+ ++++d ++  +P++l + 
  gi|385805997|ref|YP_005842395.1| 451 ISLKIGSILLISGTLFGLINSLMAREYFDAVAIKLPKFLAFS 492
                                       5777899999**************************988554 PP

  == domain 4  score: 47.2 bits;  conditional E-value: 9e-16
                        V_ATPase_I 705 qvIhtIEfvLgciSnTASYLRLWALSLAHaqLseVlwemvlkkallksksvlgvillvilfavfavltvavLllmeg 781
                                       ++I+t E  +  i nTAS+LR+  LS AH     V++  ++   ll  k+++g+i   i++++f  l       +eg
  gi|385805997|ref|YP_005842395.1| 560 SFIETFETGIMLIGNTASFLRILGLSVAHI---GVMYAFTIMA-LLVWKGTIGAI-AGITIYIFGNLLA---AALEG 628
                                       68***************************8...699*999999.65667777766.3444444544443...468** PP

                        V_ATPase_I 782 lsafLHaLRLhWVEfqsKFykgdGykFep 810
                                       +  f H++RLh  E  +KFy+g+G++F+p
  gi|385805997|ref|YP_005842395.1| 629 IVVFAHTMRLHYYEWFTKFYSGTGIPFKP 657
                                       ****************************9 PP

>> SPATA24  Spermatogenesis-associated protein 24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.4   4.6e-05     0.041     112     154 ..     223     265 ..     217     276 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.6e-05
                           SPATA24 112 dqLkekCseveseierqeDilnakeneikeLkqrlskqkevhr 154
                                       ++Lk+k se +++ie +e+ + ake+ +k+L  r+   ke+ r
  gi|385805997|ref|YP_005842395.1| 223 EELKKKISEFDKKIEELEEKIKAKEVYLKDLYSRMYTVKEALR 265
                                       689*********************************9999976 PP

>> Med2  Mediator complex subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.017        15      19      63 ..      25      72 ..      21      97 .. 0.82
   2 ?    6.2   0.1     0.013        12      44      78 ..     222     256 ..     206     271 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.017
                              Med2 19 emlvqeqlktiqldsnvvtGfnnql...qksLkekikkFhsiLDdlei 63
                                       +++ e  +  +l+     ++nn+    ++ ++ k++kF siL d++i
  gi|385805997|ref|YP_005842395.1| 25 SLMLTEKFHPAELSIAYPGSYNNEIlrySQEIEGKVNKFSSILSDINI 72
                                      5566777777777777667778877788999*************9976 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.013
                              Med2  44 qksLkekikkFhsiLDdleiklndaksyveqlvei 78 
                                       ++ Lk+ki++F++ + +le k++  + y++ l++ 
  gi|385805997|ref|YP_005842395.1| 222 YEELKKKISEFDKKIEELEEKIKAKEVYLKDLYSR 256
                                       678*************************9998764 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.7      0.16   1.4e+02      18      54 ..      98     132 ..      88     138 .. 0.82
   2 ?   14.6   1.4   3.3e-05      0.03      10      47 ..     222     261 ..     218     269 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.16
                      ABC_tran_CTD  18 eaLEeeiaeleaeladpelysdpeklaelsaeleele 54 
                                       + LE+ei+ +  el +    sd ek+ +  +e+e l+
  gi|385805997|ref|YP_005842395.1|  98 DMLEKEIEPIISELKSSK--SDREKIDAFLKEIEPLK 132
                                       669999999999999998..99999999999988765 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 3.3e-05
                      ABC_tran_CTD  10 leeleaeIeaLEeeiaeleaeladpely.sdp.eklaels 47 
                                       +eel ++I + +++i+ele+++ + e+y +d   ++  + 
  gi|385805997|ref|YP_005842395.1| 222 YEELKKKISEFDKKIEELEEKIKAKEVYlKDLySRMYTVK 261
                                       899***********************99444345554444 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.057        51      30      70 ..      91     131 ..      81     134 .. 0.89
   2 ?    9.5   0.3    0.0013       1.2      61      94 ..     223     256 ..     214     258 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.057
                           BLOC1_2  30 eaasekykklkdvaaslekkleklnekyeelqpylqqidqi 70 
                                       ++ s++y+ l+++++ + ++l+  ++  e+++ +l++i+ +
  gi|385805997|ref|YP_005842395.1|  91 KSISAEYDMLEKEIEPIISELKSSKSDREKIDAFLKEIEPL 131
                                       6678999*****************************99876 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0013
                           BLOC1_2  61 qpylqqidqiekqvteLeeavseLDeyskeLEak 94 
                                       ++++++i +++k+++eLee +++ + y k+L ++
  gi|385805997|ref|YP_005842395.1| 223 EELKKKISEFDKKIEELEEKIKAKEVYLKDLYSR 256
                                       6788999999999999999999999998888665 PP

>> PI3K_P85_iSH2  Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.2      0.25   2.3e+02      80     112 ..      94     126 ..      47     143 .. 0.75
   2 ?   12.5   1.2   9.5e-05     0.085      84     132 ..     216     264 ..     175     274 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.25
                     PI3K_P85_iSH2  80 ehEieklqenleqlksrlkelhsskekLeedlk 112
                                       ++E + l++ +e + s lk+ +s +ek++  lk
  gi|385805997|ref|YP_005842395.1|  94 SAEYDMLEKEIEPIISELKSSKSDREKIDAFLK 126
                                       678888888888888888888888888887776 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 9.5e-05
                     PI3K_P85_iSH2  84 eklqenleqlksrlkelhsskekLeedlkqqkeeereleReinalkpel 132
                                       ++++  +e+lk++++e+ ++ e+Lee++k++  + + l  +++++k  l
  gi|385805997|ref|YP_005842395.1| 216 SNFHLAYEELKKKISEFDKKIEELEEKIKAKEVYLKDLYSRMYTVKEAL 264
                                       478899*******************************999999999766 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.047        42      47     107 ..      96     157 ..      47     161 .. 0.81
   2 ?    5.8   0.2     0.025        22      48      79 ..     222     253 ..     182     272 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.047
                           DUF2203  47 eaaeleaeleeleaeieelveeieelGvevkdleagl.vDFpakldgeevllCWklgEeeie 107
                                       e+  le+e+e + +e+++  +  e++ + +k++e++  +DF  + +++ ++l  k+g  +ie
  gi|385805997|ref|YP_005842395.1|  96 EYDMLEKEIEPIISELKSSKSDREKIDAFLKEIEPLKdLDFDLNEEKKYGYLGFKVGYIDIE 157
                                       36778899999999999999999999999999998745999999999999999999877765 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.025
                           DUF2203  48 aaeleaeleeleaeieelveeieelGvevkdl 79 
                                       ++el+++++e +++ieel e+i++  v +kdl
  gi|385805997|ref|YP_005842395.1| 222 YEELKKKISEFDKKIEELEEKIKAKEVYLKDL 253
                                       77888888888888888888888888888887 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   1.6   0.00073      0.66      25     151 ..      85     266 ..      80     277 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00073
                           DUF4795  25 kleekvkelekrledkekklealkkqieelekvkadkeeveeelaekadkeaLatkvsrdq....fDeakkeLe.km 96 
                                       k  e++k+++ +   +ek++e +   i+el+++k d+e+++  l+e  + ++L+   ++++    + +++  ++ +m
  gi|385805997|ref|YP_005842395.1|  85 KWIETAKSISAEYDMLEKEIEPI---ISELKSSKSDREKIDAFLKEIEPLKDLDFDLNEEKkygyLGFKVGYIDiEM 158
                                       55566666666666666666654...889******************************99****888888886467 PP

                           DUF4795  97 leellekle.......................eqeealkkaldtLq..................eelkekld..rle 130
                                       + + lek+                        e e++++k+l +                    eelk+k+    + 
  gi|385805997|ref|YP_005842395.1| 159 IPSFLEKMRkfncyifvekgeesnvavilykkEDEKEIEKILAESGfsevvipkdlpsnfhlayEELKKKISefDKK 235
                                       78888888888888888888899999999999999999999999989888888888888888888888888777777 PP

                           DUF4795 131 lepLkeqle..........erlkelqkelqe 151
                                       +e+L e+++          +r+  ++++l+ 
  gi|385805997|ref|YP_005842395.1| 236 IEELEEKIKakevylkdlySRMYTVKEALRI 266
                                       8888888876666666666666666655555 PP

>> DUF1192  Protein of unknown function (DUF1192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.71   6.4e+02      34      49 ..      47      62 ..      44      65 .. 0.87
   2 ?   -0.0   0.1       1.1   9.5e+02      32      56 ..     100     124 ..      94     126 .. 0.87
   3 ?    8.2   0.8    0.0028       2.5      19      47 ..     219     247 ..     193     250 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.71
                           DUF1192 34 aEIaRleaaiakkkas 49
                                       EI R +++i+ k ++
  gi|385805997|ref|YP_005842395.1| 47 NEILRYSQEIEGKVNK 62
                                      7**********99875 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.1
                           DUF1192  32 LeaEIaRleaaiakkkasraAAeal 56 
                                       Le+EI+ +  ++++ k+ r+  +a+
  gi|385805997|ref|YP_005842395.1| 100 LEKEIEPIISELKSSKSDREKIDAF 124
                                       999****999999999999888887 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0028
                           DUF1192  19 lLSveELeerIalLeaEIaRleaaiakkk 47 
                                       +L  eEL++ I+++ + I+ le++i++k+
  gi|385805997|ref|YP_005842395.1| 219 HLAYEELKKKISEFDKKIEELEEKIKAKE 247
                                       5889***********************96 PP

>> Tli4_N  Tle cognate immunity protein 4 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0021       1.9      30      74 ..      86     133 ..      73     153 .. 0.78
   2 ?    1.6   0.3      0.36   3.2e+02      27      64 ..     240     276 ..     212     302 .. 0.56

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0021
                            Tli4_N  30 ki.eskrvsp..eafrqriakreqeLkaekrikekdepllkkavslpd 74 
                                       +i ++k +s   +  +++i+ +++eLk++k++ ek  ++lk++++l+d
  gi|385805997|ref|YP_005842395.1|  86 WIeTAKSISAeyDMLEKEIEPIISELKSSKSDREKIDAFLKEIEPLKD 133
                                       676777777656889*****************************9988 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.36
                            Tli4_N  27 gdvkieskrvspeafrqriakreqeLkaekrikekdep 64 
                                       ++ ki++k+v+ ++   r+ + +++L+   +ik++d+ 
  gi|385805997|ref|YP_005842395.1| 240 EE-KIKAKEVYLKDLYSRMYTVKEALRIYSQIKNTDYF 276
                                       22.45555555555555555555555555555444444 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.2    0.0091       8.2       5      43 ..      95     133 ..      91     135 .. 0.91
   2 ?    7.1   2.9    0.0058       5.2      60      93 ..     225     258 ..     219     269 .. 0.50

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0091
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-T CS
                       Prefoldin_2   5 nkfqqlqqqlqqlaqqikqletqlkelelvleelellde 43 
                                       +++  l+++++ + +++k+ + + ++++  l+e+e l++
  gi|385805997|ref|YP_005842395.1|  95 AEYDMLEKEIEPIISELKSSKSDREKIDAFLKEIEPLKD 133
                                       6888999****************************9986 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0058
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  60 keevkeeLeerketlekeiktlekqleklekele 93 
                                       +++ ++e ++++e+le++ik+ e  l++l  ++ 
  gi|385805997|ref|YP_005842395.1| 225 LKKKISEFDKKIEELEEKIKAKEVYLKDLYSRMY 258
                                       2333344445555555555555555555555555 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.9     0.014        13      27      76 ..      91     139 ..      82     143 .. 0.74
   2 ?    6.6   0.4    0.0084       7.5      45      82 ..     220     257 ..     213     271 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.014
                    CENP-F_leu_zip  27 enLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLv 76 
                                       +++ +e  m+e++ e +i e  +sk   e++ + ++e+ e l++l  dL+
  gi|385805997|ref|YP_005842395.1|  91 KSISAEYDMLEKEIEPIISELKSSKSDREKIDAFLKEI-EPLKDLDFDLN 139
                                       55667888888888888888888888888888888885.56777777776 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0084
                    CENP-F_leu_zip  45 leaEtskaevetlkeeieelaeelreleldLvalrsek 82 
                                       l  E+ k++++++ ++ieel+e+ +  e+ L++l s  
  gi|385805997|ref|YP_005842395.1| 220 LAYEELKKKISEFDKKIEELEEKIKAKEVYLKDLYSRM 257
                                       66778888888888888888888888887777776654 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0         2   1.8e+03       4      17 ..      55      68 ..      54      73 .. 0.82
   2 ?    2.5   0.4      0.21   1.9e+02       3      34 ..      98     129 ..      90     133 .. 0.84
   3 ?    7.6   0.1    0.0056       5.1      17      38 ..     223     244 ..     215     271 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 2
                         FlaC_arch  4 elEnklsklstele 17
                                      e+E k++k+s+ l+
  gi|385805997|ref|YP_005842395.1| 55 EIEGKVNKFSSILS 68
                                      89******999766 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.21
                         FlaC_arch   3 delEnklsklsteletvkkeneelsksveelk 34 
                                       d lE++++ + +el++ k++ e++   ++e++
  gi|385805997|ref|YP_005842395.1|  98 DMLEKEIEPIISELKSSKSDREKIDAFLKEIE 129
                                       56899999999999999999999987777665 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0056
                         FlaC_arch  17 etvkkeneelsksveelkenVk 38 
                                       e +kk+++e  k++eel+e++k
  gi|385805997|ref|YP_005842395.1| 223 EELKKKISEFDKKIEELEEKIK 244
                                       6789999999999999999994 PP

>> Tektin  Tektin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.3      0.93   8.4e+02      57      91 ..      95     129 ..      88     133 .. 0.74
   2 ?    9.3   0.3   0.00046      0.41     267     303 ..     222     258 ..     212     266 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.93
                            Tektin  57 fwkeeLekeleelkeeieaLeeekrrlekaleale 91 
                                          ++Leke+e +++e ++ ++ +++++  l+++e
  gi|385805997|ref|YP_005842395.1|  95 AEYDMLEKEIEPIISELKSSKSDREKIDAFLKEIE 129
                                       45567888888888888888888888888877765 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00046
                            Tektin 267 lkkvleeiaeleknieeLekairdkeaplklaqtRle 303
                                        ++++++i+e +k+ieeLe++i++ke +lk   +R+ 
  gi|385805997|ref|YP_005842395.1| 222 YEELKKKISEFDKKIEELEEKIKAKEVYLKDLYSRMY 258
                                       5678999999999999999999999999997777765 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.5     0.073        66      10      45 ..      80     115 ..      80     142 .. 0.76
   2 ?    7.0   0.7    0.0086       7.7      20      47 ..     222     249 ..     221     269 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.073
                              ZapB  10 EskiqkaidtitlLqmeieeLkeeneelkeenrele 45 
                                       E k++k i+t ++ + e++ L++e e   +e +  +
  gi|385805997|ref|YP_005842395.1|  80 EIKVSKWIETAKSISAEYDMLEKEIEPIISELKSSK 115
                                       779******************999865555444444 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0086
                              ZapB  20 itlLqmeieeLkeeneelkeenreleee 47 
                                       +++L+++i+e  ++ eel+e++++ e  
  gi|385805997|ref|YP_005842395.1| 222 YEELKKKISEFDKKIEELEEKIKAKEVY 249
                                       6788888888888888888888877644 PP

>> TelA  Toxic anion resistance protein (TelA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.2    0.0036       3.2      56     114 ..      66     120 ..      49     145 .. 0.74
   2 ?    2.8   1.7     0.057        51      87     156 ..     218     287 ..     189     293 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0036
                              TelA  56 elkeldpdelkeekklgllplfkkaknkieklfakYekaeeqidkIvkeLekgqdellk 114
                                       +l+++++  +++    g ++ ++k  ++++++ a+Y+ +e++i+ I+ eL++++++  k
  gi|385805997|ref|YP_005842395.1|  66 ILSDINIYGIRNG---GEIK-VSKWIETAKSISAEYDMLEKEIEPIISELKSSKSDREK 120
                                       5555555555443...3344.44566788999********************9987655 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.057
                              TelA  87 lfakYekaeeqidkIvkeLekgqdellkdnaaLdqlyeknleyfkeLekyiaaGekkleeldekllpele 156
                                       +   Ye+++++i +  k++e+ +++++     L++ly ++++  ++L+ y ++ ++      + ++p++e
  gi|385805997|ref|YP_005842395.1| 218 FHLAYEELKKKISEFDKKIEELEEKIKAKEVYLKDLYSRMYTVKEALRIYSQIKNTDYFSYVRGYIPAYE 287
                                       5567999999999999999999999999999999999999999999999998877666666666666655 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 ?    2.9   1.5      0.14   1.3e+02      55      99 ..      83     127 ..      79     143 .. 0.56
   2 ?    7.1   0.2    0.0067         6      70     101 ..     223     254 ..     210     260 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.14
                                       HHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  55 lskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelek 99 
                                       +sk I+ ak   ++ + l +e++ +  elk  + + ++++a l++
  gi|385805997|ref|YP_005842395.1|  83 VSKWIETAKSISAEYDMLEKEIEPIISELKSSKSDREKIDAFLKE 127
                                       455555555555555555555555555555555555555544443 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0067
                                       CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  70 eeliaevkelkeelkaleaelkeleaelekll 101
                                       eel+++++e  +++++le++ k+ e  l++l 
  gi|385805997|ref|YP_005842395.1| 223 EELKKKISEFDKKIEELEEKIKAKEVYLKDLY 254
                                       56777777777777777777777777777665 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.2     0.013        12      48      88 ..      89     129 ..      51     144 .. 0.86
   2 ?    3.9   1.3     0.081        73      64      92 ..     223     251 ..     175     270 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.013
                            APG6_N  48 eleeleeeleklekeeeelleeLkelekereeleaelaale 88 
                                         +++  e++ leke e  ++eLk  ++ re+++a l+++e
  gi|385805997|ref|YP_005842395.1|  89 TAKSISAEYDMLEKEIEPIISELKSSKSDREKIDAFLKEIE 129
                                       55778899999999999999999999999999999999876 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.081
                            APG6_N  64 eelleeLkelekereeleaelaaleeele 92 
                                       eel +++ e +k+ eele++++a e  l+
  gi|385805997|ref|YP_005842395.1| 223 EELKKKISEFDKKIEELEEKIKAKEVYLK 251
                                       33444444444444444444444443333 PP

>> Swi5  Swi5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.4      0.12   1.1e+02       5      36 ..      90     121 ..      87     133 .. 0.77
   2 ?    6.2   0.7     0.012        11       6      30 ..     223     247 ..     219     271 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.12
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHH CS
                              Swi5   5 ikeleeqleelekelaelkeelkekkdpeetv 36 
                                        k++ ++++ leke++ + +elk+ k   e +
  gi|385805997|ref|YP_005842395.1|  90 AKSISAEYDMLEKEIEPIISELKSSKSDREKI 121
                                       57788999***************877444444 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.012
                                       HHHHHHHHHHHHHHHHHHHHHHHHH CS
                              Swi5   6 keleeqleelekelaelkeelkekk 30 
                                       +el+++++e +k+++el+e+ k+k+
  gi|385805997|ref|YP_005842395.1| 223 EELKKKISEFDKKIEELEEKIKAKE 247
                                       6788888888888888888888665 PP

>> Snf7  Snf7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.3       1.7   1.5e+03      12      37 ..      92     117 ..      87     129 .. 0.57
   2 ?    9.0   2.0    0.0011      0.96       4      39 ..     223     258 ..     221     274 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.7
                                       HHHHHHHHHHHHHHHHHHHHHHHHCT CS
                              Snf7  12 kldkkqeslekkikkleaelkklakk 37 
                                       +++ + + lek+i+ + +elk  + +
  gi|385805997|ref|YP_005842395.1|  92 SISAEYDMLEKEIEPIISELKSSKSD 117
                                       45555555566666555555555444 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0011
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTT- CS
                              Snf7   4 rsLrkaerkldkkqeslekkikkleaelkklakkgn 39 
                                        +L+k++ + dkk+e+le+kik  e  lk+l+  + 
  gi|385805997|ref|YP_005842395.1| 223 EELKKKISEFDKKIEELEEKIKAKEVYLKDLYSRMY 258
                                       589999*****************9999999887654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (667 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1752  (0.0977188); expected 358.6 (0.02)
Passed bias filter:                     1030  (0.0574488); expected 358.6 (0.02)
Passed Vit filter:                       182  (0.0101512); 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: 0.85u 0.33s 00:00:01.18 Elapsed: 00:00:00.52
# Mc/sec: 3891.19
//
Query:       gi|385805998|ref|YP_005842396.1|  [L=221]
Description: hypothetical protein FFONT_0956 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.6e-07   31.1   0.0    5.1e-07   30.1   0.0    1.6  1  NERD       Nuclease-related domain
    3.6e-05   23.7   0.0    6.2e-05   23.0   0.0    1.4  1  Mrr_cat    Restriction endonuclease
    6.8e-05   23.0   0.1    0.00013   22.1   0.1    1.5  1  UPF0102    Uncharacterised protein family UPF0102
     0.0001   22.2   0.0    0.00019   21.4   0.0    1.6  1  Hjc        Archaeal holliday junction resolvase (hjc)
  ------ inclusion threshold ------
      0.012   15.8   0.0      0.023   14.9   0.0    1.5  1  MTES_1575  REase_MTES_1575


Domain annotation for each model (and alignments):
>> NERD  Nuclease-related domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0   1.4e-10   5.1e-07       5      60 ..      78     131 ..      74     200 .. 0.70

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 1.4e-10
                              NERD   5 gEravakeLkelkedeylvlhdvrlrpg.tgeiDhlvispkgifviEvKnwsGwifg 60 
                                        E+++ + L+   + +y vl+++r+r+  ++eiD+++i ++  +++++K+ws +  +
  gi|385805998|ref|YP_005842396.1|  78 FEKELSEILE---QYGYEVLRNYRIRKPsRAEIDIVAIKTGLALIVDCKHWSPRSAS 131
                                       4555555555...44**********888555*********************42222 PP

>> Mrr_cat  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   1.7e-08   6.2e-05       4      62 ..      73     131 ..      70     150 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.7e-08
                                       T-TTCHHHHHHHHHHHHSSS..EEE---B-TTSSB--EEEETTEEEEEEEEEEE--T.S-B- CS
                           Mrr_cat   4 mspkeFeklvaellealGyk..eveltgrsgDggiDliakkdplgserilvqaKryk.nkvg 62 
                                       +s+k+Fek + e+le++Gy+  + ++ ++ +   iD++a k +     ++v +K+++ ++ +
  gi|385805998|ref|YP_005842396.1|  73 LSWKDFEKELSEILEQYGYEvlRNYRIRKPSRAEIDIVAIKTG---LALIVDCKHWSpRSAS 131
                                       79******************88446777788899*****9977...56********753433 PP

>> UPF0102  Uncharacterised protein family UPF0102
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.1   3.6e-08   0.00013       2      55 ..      79     142 ..      78     156 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 3.6e-08
                                       HHHHHHHHHHTT-EEEEEEEEETT...EEEEEEE..TTEEEEEEEEE-............----- CS
                           UPF0102   2 EelaaeyLekkgyeilernwrcra...gEiDiia..tevlvfvEVKtRssekfg......spaea 55 
                                       E+   e+Le+ gye+l rn+r r     EiDi+a  t   ++v+ K  s ++        ++ ++
  gi|385805998|ref|YP_005842396.1|  79 EKELSEILEQYGYEVL-RNYRIRKpsrAEIDIVAikTGLALIVDCKHWSPRSASrgriefAANKQ 142
                                       778899********99.89999777778*******988999*****9744333311233333333 PP

>> Hjc  Archaeal holliday junction resolvase (hjc)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   5.3e-08   0.00019       2      49 ..      78     125 ..      77     167 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 5.3e-08
                                       HHHHHHHHHHHTT-EEEEBSCSSSSSSSS-SEEEEETTEEEEEEEEEE CS
                               Hjc   2 yERelvkiLrergfavvRsagSggatkplpDviAirgdvvlviEvKss 49 
                                       +E+el +iL++ g++v+R     + ++   D++Ai+ +  l++ +K  
  gi|385805998|ref|YP_005842396.1|  78 FEKELSEILEQYGYEVLRNYRIRKPSRAEIDIVAIKTGLALIVDCKHW 125
                                       8*******************999999999*****************74 PP

>> MTES_1575  REase_MTES_1575
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   6.4e-06     0.023       1      51 [.      78     130 ..      78     152 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6.4e-06
                         MTES_1575   1 FeeeVaeaLrergykvkpqvgvg...gfriDlvvedpgkyllaIecdgdkyhss 51 
                                       Fe+e+ e L++ gy+v +++++    + +iD+v ++  +  l + c   +  s+
  gi|385805998|ref|YP_005842396.1|  78 FEKELSEILEQYGYEVLRNYRIRkpsRAEIDIVAIKT-GLALIVDCKHWSPRSA 130
                                       9********************98444689*******9.8888888877665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1390.81
//
Query:       gi|385805999|ref|YP_005842397.1|  [L=272]
Description: thymidylate synthase [Fervidicoccus fontis Kam940]
Scores for complete 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-67  225.9   2.1    5.2e-67  225.3   2.1    1.3  1  Thy1      Thymidylate synthase complementing protein
  ------ inclusion threshold ------
      0.044   13.9   0.7       0.15   12.2   0.7    1.9  1  LPD11     Large polyvalent protein-associated domain 11
      0.059   13.4   8.6       0.21   11.6   1.0    2.2  2  DUF600    Protein of unknown function, DUF600
       0.22   11.8   6.3        2.2    8.6   0.3    3.5  3  DUF4358   Domain of unknown function (DUF4358)
       0.82   10.2   6.5        1.1    9.8   4.3    2.3  2  DUF3106   Protein of unknown function (DUF3106)


Domain annotation for each model (and alignments):
>> Thy1  Thymidylate synthase complementing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.3   2.1   1.4e-70   5.2e-67       1     187 [.       4     196 ..       4     197 .. 0.93

  Alignments for each domain:
  == domain 1  score: 225.3 bits;  conditional E-value: 1.4e-70
                                       EEEEEE.CHHHHHHHHHHHHHTTCSSHHHH..S.GCCHHHHHHHHHHTTGGGGGGG-EEEEEEEEEEHHHHHHHTT- CS
                              Thy1   1 kLldyt.dpeklvaaaarvcygsseeaeele.e.eekkeklikkllkhghgsplehasftfeiegvSravlrqlvrH 74 
                                       +L++yt + ekl+a aa+++  ++e +e++  + e++k++++k+ +++gh+sp+eh+++tf+ie+vSr++++qlvrH
  gi|385805999|ref|YP_005842397.1|   4 TLISYTkECEKLIAVAAKQTITQKEFSESWNeMkEDEKKEWLKETMSRGHTSPWEHCTYTFLIEDVSRVLTHQLVRH 80 
                                       69*******************876444444464578899************************************** PP

                                       TTSEEEE--TTTSGCCC.TC.BS--GGGCC..HHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHGGGSBTTBEEEEEE CS
                              Thy1  75 RiasfsqqSqRYvessk.ea.fvippeieqk.eeleelyeeamekaleaykelleagvarEdaryvLPlatktklvv 148
                                       R+as+sq SqRY++ ++ e+ +vip++i +k +++ e+y ++++k++e+y+el+++g+++EdaryvLP+a+ktk+vv
  gi|385805999|ref|YP_005842397.1|  81 RLASYSQLSQRYKRIKEiENyYVIPKSILKKgDKALEKYINSIKKSFEEYQELINMGMPPEDARYVLPQAVKTKIVV 157
                                       **************999877788898988745899999*************************************** PP

                                       EEEHHHHHHHHHHHSSTTS-HHHHHHHHHHHHHHHHHSH CS
                              Thy1 149 tmNlrsLlhflelracsrAqwEirelaeemleelkkvaP 187
                                       tmN+r+Ll+f+ lr+c +AqwEir+la++++ ++k ++P
  gi|385805999|ref|YP_005842397.1| 158 TMNARELLNFFGLRMCMKAQWEIRALAWNIYYIVKSIHP 196
                                       **************************************9 PP

>> LPD11  Large polyvalent protein-associated domain 11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.7   4.1e-05      0.15      28      58 ..      14      46 ..       5      51 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.1e-05
                             LPD11 28 hLwagsveeqi..eemkelynslpedeKPewlt 58
                                      +L a + +++i  +e  e +n+++edeK ewl 
  gi|385805999|ref|YP_005842397.1| 14 KLIAVAAKQTItqKEFSESWNEMKEDEKKEWLK 46
                                      466666677763367899*************96 PP

>> DUF600  Protein of unknown function, DUF600
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.0   5.8e-05      0.21      47      98 ..      11      64 ..       5      70 .. 0.84
   2 ?    5.8   1.3    0.0037        13      46      87 ..      90     131 ..      82     136 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.8e-05
                                      -EEEGGGGGGT--S-HHHHHHHHHHHHH..HHHHHHHHHHHHHSS--SEEEEEE CS
                            DUF600 47 kliysheipekynvseeeykkllkeLye..likeLreefkkeeqeaWtnltltl 98
                                      ++ + + +  k ++ ++e++++++e++e  + + L+e++++ ++ +W+ +t t+
  gi|385805999|ref|YP_005842397.1| 11 ECEKLIAVAAKQTITQKEFSESWNEMKEdeKKEWLKETMSRGHTSPWEHCTYTF 64
                                      6677788999****************86225566****************9886 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0037
                                       T-EEEGGGGGGT--S-HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            DUF600  46 ekliysheipekynvseeeykkllkeLyelikeLreefkkee 87 
                                       + + +  ei + y +++++ kk  k L++ i+++++ f++ +
  gi|385805999|ref|YP_005842397.1|  90 QRYKRIKEIENYYVIPKSILKKGDKALEKYINSIKKSFEEYQ 131
                                       5788899*******************************9876 PP

>> DUF4358  Domain of unknown function (DUF4358)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.6     0.057     2e+02      41      74 ..      11      44 ..       3      48 .. 0.90
   2 ?    8.6   0.3   0.00062       2.2      60      78 ..     113     131 ..     106     136 .. 0.87
   3 ?    1.3   0.0      0.12   4.1e+02      46      81 ..     232     267 ..     227     270 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.057
                           DUF4358 41 sadevlivkakdeedaeevkkaleerledqkksf 74
                                      ++++++ v ak + + +e  +  +e +ed kk++
  gi|385805999|ref|YP_005842397.1| 11 ECEKLIAVAAKQTITQKEFSESWNEMKEDEKKEW 44
                                      68999**************************998 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00062
                           DUF4358  60 kkaleerledqkksfedYl 78 
                                        kale++++++kksfe+Y 
  gi|385805999|ref|YP_005842397.1| 113 DKALEKYINSIKKSFEEYQ 131
                                       589***************3 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.12
                           DUF4358  46 livkakdeedaeevkkaleerledqkksfedYlpeq 81 
                                       +i k+ ++ + e++k  +++ l+d+++  e+ +p++
  gi|385805999|ref|YP_005842397.1| 232 IIEKCPEGVARENIKLCVRTALNDIREFLESANPNN 267
                                       66678888889********************99997 PP

>> DUF3106  Protein of unknown function (DUF3106)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   4.3   0.00029       1.1       9      92 ..      22     102 ..      17     111 .. 0.77
   2 ?   -1.8   0.0       1.3   4.5e+03      83      94 ..     122     133 ..     116     136 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00029
                           DUF3106   9 rqaLa.plaeewnelspeqreklleiaerykkltpeeqkrlqermeewakLspeqreqarenyqklkqLppeereel 84 
                                       +++ + +++e+wne+++++++++l+ + +  + +p e  +    +e+ ++     ++ +r+++++++qL++  + + 
  gi|385805999|ref|YP_005842397.1|  22 QTITQkEFSESWNEMKEDEKKEWLKETMSRGHTSPWEHCTYTFLIEDVSRVLT--HQLVRHRLASYSQLSQRYK-R- 94 
                                       33333499*****************9999999999999999999999888765..4588899999999988777.3. PP

                           DUF3106  85 rekweeyq 92 
                                        ++ e+y 
  gi|385805999|ref|YP_005842397.1|  95 IKEIENYY 102
                                       34455565 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.3
                           DUF3106  83 elrekweeyqkL 94 
                                       ++++++eeyq+L
  gi|385805999|ref|YP_005842397.1| 122 SIKKSFEEYQEL 133
                                       578899999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1071  (0.0597356); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); 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: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 1824.64
//
Query:       gi|385806000|ref|YP_005842398.1|  [L=138]
Description: CopG family transcriptional regulator [Fervidicoccus fontis Kam940]
Scores for complete 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   87.7   3.5      6e-25   87.2   3.5    1.2  1  NikR_C       NikR C terminal nickel binding domain
    0.00041   20.2   0.0     0.0012   18.8   0.0    1.8  1  RHH_3        Ribbon-helix-helix domain
  ------ inclusion threshold ------
      0.059   14.0   0.0        0.1   13.2   0.0    1.4  1  Hemerythrin  Hemerythrin HHE cation binding domain


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 !   87.2   3.5     1e-28     6e-25       1      76 [.      58     133 ..      58     134 .. 0.98

  Alignments for each domain:
  == domain 1  score: 87.2 bits;  conditional E-value: 1e-28
                                       EEEEEEEEETTSTTHHHHHHHHHHHHSSEEEEEEEEEESSSEEEEEEEEEE-HHHHHHHHHHHHTSTTEEEEEEEE CS
                            NikR_C   1 vGvitivydhhqrelserltdiqheyhdliisslhvhldhdncLevivlkGeaeeikelaeklralkgVkhvkltl 76 
                                       +G+i+++y+h++ +l+e++tdiqhey d+i+s+lhvh+++++cL +i++kGe+++ik+l ++l++l gV+++++++
  gi|385806000|ref|YP_005842398.1|  58 AGAIIMLYNHETGRLEEKITDIQHEYMDVIVSALHVHVSKEECLLIIAIKGEVSRIKRLYQSLSGLHGVMQIQYSI 133
                                       699*********************************************************************9987 PP

>> RHH_3  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.9e-07    0.0012       3      27 ..       7      31 ..       6      40 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.9e-07
                             RHH_3  3 trttvsidpelaekLkaLSekTrIp 27
                                      ++++vs++ el+++L+++S++++I+
  gi|385806000|ref|YP_005842398.1|  7 VKFGVSFPYELYKELEEVSKELGIN 31
                                      68**********************7 PP

>> Hemerythrin  Hemerythrin HHE cation binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.7e-05       0.1      34      83 ..      77     127 ..      58     130 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.7e-05
                                       HCCHHHHHHHHHHHHHHHHHHHHHHCHHHHH..CCC.HHHHHHHHHHHHHH CS
                       Hemerythrin  34 lrklaelldelvdeleaHhaaEEellfPlle.drpggravldvlereHdei 83 
                                        +  +e++d +v +l+ H  +EE ll  +++ ++++++  + +l++ H ++
  gi|385806000|ref|YP_005842398.1|  77 TDIQHEYMDVIVSALHVHVSKEECLLIIAIKgEVSRIKRLYQSLSGLHGVM 127
                                       4556789999*************************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.32s 00:00:00.83 Elapsed: 00:00:00.52
# Mc/sec: 804.81
//
Query:       gi|385806001|ref|YP_005842399.1|  [L=157]
Description: hypothetical protein FFONT_0959 [Fervidicoccus fontis Kam940]
Scores for 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-27   93.7   0.0      1e-26   93.4   0.0    1.1  1  DUF2122    RecB-family nuclease (DUF2122)
  ------ inclusion threshold ------
      0.041   13.3   0.1      0.047   13.1   0.1    1.1  1  SAC3_GANP  SAC3/GANP family


Domain annotation for each model (and alignments):
>> DUF2122  RecB-family nuclease (DUF2122)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.4   0.0   1.1e-30     1e-26       1     104 [.      41     147 ..      41     149 .. 0.98

  Alignments for each domain:
  == domain 1  score: 93.4 bits;  conditional E-value: 1.1e-30
                           DUF2122   1 GaAAqsGipevlklalklgksllvlpdlkDalellkpekvlllskeegeelleeeel..eekgrvllvfsgadegfs 75 
                                       GaAAq Gi+e++k  +k++ ++l+l+d+ D+l+++++ k++ +++ +g e ++ e+l  ++++r+ll+fsg+d gf 
  gi|385806001|ref|YP_005842399.1|  41 GAAAQYGIAEISKALFKSNVNFLILQDIGDFLQFFQGYKIFQFTQAYGVEFKSLEQLglKDNDRILLIFSGNDVGFG 117
                                       89*****************************************************9999****************** PP

                           DUF2122  76 kke.lelgetvkvegveadvgelaelavvl 104
                                       k+e l +++++k++g+e+++++  e+++++
  gi|385806001|ref|YP_005842399.1| 118 KNElLPNATYLKISGIEKELPPQVEFGIFM 147
                                       ****************************98 PP

>> SAC3_GANP  SAC3/GANP family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   5.3e-06     0.047     204     292 ..       2      92 ..       1      93 [. 0.92

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.3e-06
                                       HHHHHHHHHHH--TTHHHHHHHHT.TS-HHHHHHHGGGHHHHHHHHHHHHHHHS.-TT---EEHHHHHHHTT-SSHH CS
                         SAC3_GANP 204 vqlalklvaalqennyvrffklvk.evsylqacllerhfnevRrkalkalsray.kskskkvpleeLaelLlfddee 278
                                       v++++ l+ + ++  ++ ffk+v+   +++++ +++r      ++ +  +s+a+ ks+ + + l+++ ++L f +  
  gi|385806001|ref|YP_005842399.1|   2 VEIVVGLHDISSTYRLSDFFKTVQaYKKFINTFAISRVTGAAAQYGIAEISKALfKSNVNFLILQDIGDFLQFFQGY 78 
                                       6677888999999999********8899**************************888888888************** PP

                                       HHHHHHHHTT--EE CS
                         SAC3_GANP 279 eaeefceayglevs 292
                                       ++ +f +ayg+e++
  gi|385806001|ref|YP_005842399.1|  79 KIFQFTQAYGVEFK 92 
                                       ***********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 961.94
//
Query:       gi|385806002|ref|YP_005842400.1|  [L=58]
Description: hypothetical protein FFONT_0960 [Fervidicoccus fontis Kam940]
Scores for complete 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-15   54.8   2.8    8.1e-15   54.6   2.8    1.1  1  Sec61_beta  Sec61beta family
     0.0056   16.7   0.1     0.0058   16.6   0.1    1.0  1  Calcyon     D1 dopamine receptor-interacting protein (calcyon


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 !   54.6   2.8   9.1e-19   8.1e-15       1      40 [.      17      56 ..      17      57 .. 0.97

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 9.1e-19
                                      XXXXXXXXXX----SS-B-THHHHHHHHHHHHHHHHHTSS CS
                        Sec61_beta  1 SsaGLlryyeedapgikidPkvVlvlsvafiasVilLhil 40
                                      S+aGL+ +ye+ + +i i+P++++++s+afi++V++L++l
  gi|385806002|ref|YP_005842400.1| 17 SAAGLISFYEDTSAKITITPTTIIIISIAFIGIVVALRVL 56
                                      89************************************97 PP

>> Calcyon  D1 dopamine receptor-interacting protein (calcyon)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   6.4e-07    0.0058      57     101 ..       4      53 ..       1      57 [. 0.71

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.4e-07
                           Calcyon  57 keksklkvp...kikeltisleegvserlkvt..llillalAllacvvlL 101
                                       k+k+k+k p     +   is++e+ s ++ +t  ++i++++A+++ vv L
  gi|385806002|ref|YP_005842400.1|   4 KSKEKKKKPsglMSAAGLISFYEDTSAKITITptTIIIISIAFIGIVVAL 53 
                                       3344444443334456679*********99954389***********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       771  (0.043003); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.50
# Mc/sec: 350.27
//
Query:       gi|385806003|ref|YP_005842401.1|  [L=366]
Description: fructose-1,6-bisphosphate phosphatase (type V) [Fervidicoccus fontis Kam940]
Scores for complete 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-189  628.7   0.0   3.8e-189  628.4   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 !  628.4   0.0  2.1e-193  3.8e-189       1     359 [.       6     364 ..       6     365 .. 1.00

  Alignments for each domain:
  == domain 1  score: 628.4 bits;  conditional E-value: 2.1e-193
                          FBPase_3   1 kvtlsvikaDvGslaGhtkvheellekveevleeakkkgllidfyvtkvGDDielimthtkgvdneevhklawdafk 77 
                                       kvtls+ikaDvG+laGh+ vh++l+++++++l+eak++g+++dfyvt+vGDD++limth +gvd+++vh+lawd+fk
  gi|385806003|ref|YP_005842401.1|   6 KVTLSIIKADVGGLAGHHVVHPDLIATATRMLSEAKESGIIEDFYVTNVGDDLQLIMTHYRGVDSKDVHSLAWDTFK 82 
                                       89*************************************************************************** PP

                          FBPase_3  78 eatevakelklygaGqDlLkdafsGnvkGlGPgvaelefeeRksepvvvfaaDktepgafnlplykifadpfntaGl 154
                                       eat+va++l+lygaGqDlL+dafsGnv+G+GPgvae+ef eR+sepvv f+aDktepgafnlp+yki+adpfntaGl
  gi|385806003|ref|YP_005842401.1|  83 EATKVAQKLGLYGAGQDLLSDAFSGNVRGMGPGVAEMEFIERTSEPVVAFMADKTEPGAFNLPFYKIYADPFNTAGL 159
                                       ***************************************************************************** PP

                          FBPase_3 155 vidpklheGfkfevlDvieekkillsapeelydllallgakeryvikrvyskkdeeiaavvsterlsliaGkYvGkD 231
                                       vidpklh+Gfkfe++D+ie+k++ l+ape++yd+lal+g+++r++ikrvy+k+++eiaa+vs+erl+liaGkYvGkD
  gi|385806003|ref|YP_005842401.1| 160 VIDPKLHSGFKFEIWDLIEHKQYFLNAPEDSYDILALIGTTGRFTIKRVYRKDNNEIAAAVSSERLNLIAGKYVGKD 236
                                       ***************************************************************************** PP

                          FBPase_3 232 DPvaivRaqsglPavgevlepfalphlvaGwmrGshngplmPvslkdakptrfdgpprvvalgfqlkegklvgpvDl 308
                                       DPvai Raqsg+Pa+ge+lepf++phlvaGwmrGshngplmPvs+kda++trfdgppr++algf++k+gkl+gp+Dl
  gi|385806003|ref|YP_005842401.1| 237 DPVAIARAQSGFPALGEILEPFSFPHLVAGWMRGSHNGPLMPVSQKDARCTRFDGPPRIIALGFNIKDGKLIGPTDL 313
                                       ***************************************************************************** PP

                          FBPase_3 309 fddpafdeaRekaaeiadelRrqGpfephrlpeeeleYttlpevleklker 359
                                       fddpafde+R++a+ iad++Rr+Gpf+phrl +ee+eYttlp+vl+kl+e+
  gi|385806003|ref|YP_005842401.1| 314 FDDPAFDETRRTAQIIADYMRRHGPFMPHRLGPEEMEYTTLPQVLKKLEEK 364
                                       ************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 2390.58
//
Query:       gi|385806004|ref|YP_005842402.1|  [L=362]
Description: RNA 3'-terminal-phosphate cyclase [Fervidicoccus fontis Kam940]
Scores for complete 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-80  267.7   0.1    6.3e-80  267.5   0.1    1.0  1  RTC         RNA 3'-terminal phosphate cyclase
    7.6e-21   74.6   0.1    1.8e-20   73.4   0.1    1.7  2  RTC_insert  RNA 3'-terminal phosphate cyclase (RTC), insert d


Domain annotation for each model (and alignments):
>> RTC  RNA 3'-terminal phosphate cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  267.5   0.1     7e-84   6.3e-80       2     222 .]      12     339 ..      11     339 .. 0.99

  Alignments for each domain:
  == domain 1  score: 267.5 bits;  conditional E-value: 7e-84
                                       TTTSTHHHHHHHHHHHHH---EEEESTTTTSSS-S--HHHHHHHHHHHHHHT-EEE--STT-SEEEEE------SEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               RTC   2 gegGgqiLRtalaLsaltgkpvrIenIRanRkkPGLraqhltavrllakitnaevegaeigsteleFkPgeikagey 78 
                                       gegGgqiLRt+laLsa++g p+++ nIRa+R++PGL++qh+tav+++++++na++eg  +gs+el F P+++++g++
  gi|385806004|ref|YP_005842402.1|  12 GEGGGQILRTSLALSAILGMPLKVINIRAKRENPGLQHQHITAVKVVSALSNAKTEGLYLGSKELLFYPNKLSGGNF 88 
                                       8**************************************************************************** PP

                                       EEEEESSEBHHHHHHHHHHHHTTSSS-EEEEEEEBSBBTTS--HHHHHHTHHHHHHHHT.-EEEEEEEE--BTTTB- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               RTC  79 evdigtAGsitlllqtllplllfakkpseltlkGgTnvsaapsvdylktvllpllkrfgvlelelelkkrGfypkGg 155
                                       e+d+gtAGs++l+lq++lp+l+f ++++++ lkGgT+v+ ap++dy+k+v+l+llkr+g +++++++k+rG+ypkGg
  gi|385806004|ref|YP_005842402.1|  89 EFDVGTAGSVMLVLQAILPILPFLETSTKIVLKGGTDVPGAPTFDYFKNVTLELLKRIG-IDMKANIKRRGYYPKGG 164
                                       ***********************************************************.7**************** PP

                                       EEEEEEEE-.-S.---EB........................................................... CS
                                       xxxxxxxxxxxx.xxxxx........................................................... RF
                               RTC 156 Gevelevepskk.lkpie........................................................... 172
                                       G v + +e +k  lk+ie                                                           
  gi|385806004|ref|YP_005842402.1| 165 GIVDIFIESPKGrLKNIElvkrgelkkikifsvahklpshiakrqalsaqsfleerlqgilyeteieddeknhelas 241
                                       *******877756**************************************************************** PP

                                       ................................................BSS-HHHHHHHHHHHHHHT.-EEEEESS- CS
                                       ................................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               RTC 173 ................................................acvDehlqdqlilfmaLakgksrirvael 201
                                                                                       +++D+++ d++i+f+aLakgks++  ++l
  gi|385806004|ref|YP_005842402.1| 242 fspgtsisiiaeakesilggdslgkkgkpaekvgedaakvliedistqMALDRFMSDMIIPFLALAKGKSKVGGSRL 318
                                       ***************************************************************************** PP

                                       -HHHHHHHHHHHHHSS-EEEE CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                               RTC 202 tlhtetairvieqflgvkfkv 222
                                       tlh++t+i vie++l++k kv
  gi|385806004|ref|YP_005842402.1| 319 TLHAITNILVIEKILNIKAKV 339
                                       *****************9886 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 !   73.4   0.1     2e-24   1.8e-20       1     103 []     184     287 ..     184     287 .. 0.90
   2 ?   -3.6   0.0       1.8   1.6e+04      54      69 ..     310     325 ..     297     330 .. 0.77

  Alignments for each domain:
  == domain 1  score: 73.4 bits;  conditional E-value: 2e-24
                                       -S----SEEEEEEEEESS-THHHHHHHHHHHHHHTTTSS....EEEEEEE.EE-CGGC-SS-EEEEEEEEE-T.TS- CS
                        RTC_insert   1 vdrGrvkrirGvafaarvspsvanrmveaargvLnkllp....dvyiytdvvkegkesgkspGfgisLvaetttegv 73 
                                       v+rG++k+i+++++a ++++++a+r++ +a++ L++ l+    + +i+ d +k+++ ++ spG+ is++ae +  + 
  gi|385806004|ref|YP_005842402.1| 184 VKRGELKKIKIFSVAHKLPSHIAKRQALSAQSFLEERLQgilyETEIEDD-EKNHELASFSPGTSISIIAEAK--ES 257
                                       589**********************************9966666665566.6667779**************6..59 PP

                                       EEEEEEEE-TT--HHHHHHHHHHHHHHHHH CS
                        RTC_insert  74 llgaealgekgvppedvGeeaaeeLleeie 103
                                       +lg+++lg+kg+p+e+vGe+aa+ L+e+i+
  gi|385806004|ref|YP_005842402.1| 258 ILGGDSLGKKGKPAEKVGEDAAKVLIEDIS 287
                                       ***************************985 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.8
                                       C-SS-EEEEEEEEE-T CS
                        RTC_insert  54 sgkspGfgisLvaett 69 
                                       ++k  G+ ++L a t+
  gi|385806004|ref|YP_005842402.1| 310 KSKVGGSRLTLHAITN 325
                                       4556799999998874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); 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: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 2146.12
//
Query:       gi|385806005|ref|YP_005842403.1|  [L=327]
Description: putative thiamine-monophosphate kinase [Fervidicoccus fontis Kam940]
Scores for 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   45.3   0.0    1.7e-11   44.6   0.0    1.3  1  AIRS      AIR synthase related protein, N-terminal domain
    2.1e-05   24.7   0.0    2.7e-05   24.3   0.0    1.2  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 !   44.6   0.0   1.9e-15   1.7e-11       6      93 ..      47     144 ..      36     145 .. 0.86

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 1.9e-15
                                       EEEEEEEE.EECCTCCCC........HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......HHHHHHHHHHHHHHH CS
                              AIRS   6 vvttdshnrpvlvepvhf........iGakavavnlsDlaamGArPlalllslalp......wleevvrglaeaaee 68 
                                        +++d      ++e++           G++a+++++sDl+a G +P ++++sl lp      +le++  g+++a++e
  gi|385806005|ref|YP_005842403.1|  47 SIKID-----GYCEKYSRypwerwsnWGWRAITGTVSDLYAKGYTPFGVVYSLGLPknfplsKLEDISIGIKKAMRE 118
                                       56666.....55555555666668889************************************************** PP

                                       TT-EEEEEEEEEESS.EEEEEEEEEE CS
                              AIRS  69 lgvplvgGdtsfsne.ptisvtavGl 93 
                                       ++ + +gGd+++s +   i v+a+G+
  gi|385806005|ref|YP_005842403.1| 119 YDLSFLGGDLNVSYKyAWIDVAALGT 144
                                       ***********996658899999986 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 !   24.3   0.0     3e-09   2.7e-05      43     150 ..     195     305 ..     157     310 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 3e-09
                                       HHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHHHHHHHTTTEEEEEECGTHHHHHHHH........HHHHHHHCST CS
                            AIRS_C  43 leptliyvkralaalkglvkaahDvTgGGLlgalaemapasgvgaeidldkvpifdele........splemllsen 111
                                        +p+ +++ ++   +  +v++  D ++ GL+ +l  +a+ s   ++i++d++pi  ++         + +e +l   
  gi|385806005|ref|YP_005842403.1| 195 YTPRAVKEFPLVSKA-IKVNSSIDSSD-GLAKSLWILAKSS--NVVIHIDNIPIHGKVIsylknfnlNIEEFALYGG 267
                                       555555666666665.89999999999.8***********9..7777777778888887777788898888888888 PP

                                       TTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEESSS CS
                            AIRS_C 112 sGrllvavppeeadavlaileeeglpeaavIGevtakee 150
                                       ++  +++  +e++d+v+++++++g+ e+  IG+v++k +
  gi|385806005|ref|YP_005842403.1| 268 EEYEVIFTTSEKEDRVIRVCKSAGI-ECIKIGKVIEKSD 305
                                       9999999******************.8*********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 2161.30
//
Query:       gi|385806006|ref|YP_005842404.1|  [L=201]
Description: hypothetical protein FFONT_0964 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-33  116.2   0.0      2e-33  115.5   0.0    1.2  1  TYW3      Methyltransferase TYW3


Domain annotation for each model (and alignments):
>> TYW3  Methyltransferase TYW3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.5   0.0   1.1e-37     2e-33       3     212 ..      13     194 ..      11     195 .. 0.93

  Alignments for each domain:
  == domain 1  score: 115.5 bits;  conditional E-value: 1.1e-37
                                       HHHHHHHH....HHHHHCCHC-GGGHHHHHHHHC-SSEEEEEEES-EEEEE............EESSTT-STT-EEE CS
                              TYW3   3 KakiLeeLsvpdtdkspkGsvDekirelideinsledlvTtSSCsGRvsvflegrksaeaeeeaaksggkkgggkwl 79 
                                       K+ +++++    + + + G++D++i e +++in++e+ +TtSSCsGR+s++            +++  +k+++   +
  gi|385806006|ref|YP_005842404.1|  13 KTMFIKRI----ESDREIGYLDPGIDETLSLINKREKSYTTSSCSGRISIV------------DTDYLWKRNELPLI 73 
                                       55566666....677899*********************************............89999********* PP

                                       EEESS---HHHHHHHHCS--..............SSEEEEEEE--EEEEEESSHHHHHHHHHHHHHCT-TT-EEEEE CS
                              TYW3  80 fvsHdpvkeeellaelfgleeeegsaksseseeeerlilfkfePmILHvlcrslesAqkllsaAleaGfreSGivsl 156
                                       f++H++v++eel++ ++++               +++ ++ +  +ILHv++ ++e+A  +l+a++eaGf++SGi+s 
  gi|385806006|ref|YP_005842404.1|  74 FKKHSEVSSEELISIFKKEP--------------MNTFWLIVSGPILHVRTLDIEEALFILNAGREAGFKHSGIMSY 136
                                       ********999998888876..............789**************************************** PP

                                       CTTEEEEEEE---EEEEEEE.ST.S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHC- CS
                              TYW3 157 kkkkvivairsglklevpig.ke.llvseeylkllvklanerfeenkkrierfeealk 212
                                       +++ ++v++ sg++++ pi  k+  l++ e++++++klan+ +   ++++e++++ lk
  gi|385806006|ref|YP_005842404.1| 137 SEDGYLVELISGTQFNFPIKnKNgYLINIEKIDYIAKLANSALVDGRRKLEKLNQFLK 194
                                       ********************9556*****************************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1250.39
//
Query:       gi|385806007|ref|YP_005842405.1|  [L=211]
Description: proteasome subunit Beta [Fervidicoccus fontis Kam940]
Scores for complete 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-50  171.8   0.1    1.2e-50  171.7   0.1    1.0  1  Proteasome  Proteasome subunit


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.7   0.1   6.7e-55   1.2e-50       3     190 .]      18     197 ..      16     197 .. 0.97

  Alignments for each domain:
  == domain 1  score: 171.7 bits;  conditional E-value: 6.7e-55
                                       HS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGT CS
                        Proteasome   3 kGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrpi 79 
                                       +Gtt+vG+ +kd v+laad+ratag  ++ ++t +Ki ki+d++++++aGl+aDa++l+++++ +++   ++ ++p+
  gi|385806007|ref|YP_005842405.1|  18 HGTTTVGLIAKDAVILAADRRATAGTFIAHRKT-RKILKITDKMALTTAGLVADAQVLADWLNTQMNYLTITKKQPV 93 
                                       8***************************88886.******************************************* PP

                                       CHHHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHHST CS
                        Proteasome  80 pverlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekeyke 156
                                       +v+    ++a +l+  ++r++  pf+v+l+++g+d   +p+L+++d  Gs++eek ++++Gsgs  a+++le+ y+e
  gi|385806007|ref|YP_005842405.1|  94 TVR----EAAHLLSLLLYRYKLFPFYVQLILGGYD--TAPRLFSLDLYGSLVEEK-YTSTGSGSPIAIGVLEDGYRE 163
                                       ***....999999999999999*************..55***************8.********************* PP

                                       TBSHHHHHHHHHHHHHHHHHHBTTSCSSEEEEEE CS
                        Proteasome 157 dltleeavelavkalkealerdklsgknievavi 190
                                       +++ eea +lavka++ al+rd+++g++++ ++i
  gi|385806007|ref|YP_005842405.1| 164 NMSPEEARKLAVKAVQMALKRDSATGDGVDSVII 197
                                       *****************************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); 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 0.29s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1393.67
//
Query:       gi|385806008|ref|YP_005842406.1|  [L=521]
Description: Carboxyl transferase, catalytic subunit [Fervidicoccus fontis Kam940]
Scores for 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-186  618.2   0.4   1.1e-185  618.0   0.4    1.0  1  Carboxyl_trans  Carboxyl transferase domain
     0.0024   17.4   0.3     0.0056   16.2   0.0    1.7  2  MdcE            Malonate decarboxylase gamma subunit (MdcE)


Domain annotation for each model (and alignments):
>> Carboxyl_trans  Carboxyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  618.0   0.4  1.2e-189  1.1e-185       1     492 [.      28     517 ..      28     519 .. 0.97

  Alignments for each domain:
  == domain 1  score: 618.0 bits;  conditional E-value: 1.2e-189
                                       SSCTTCEEEEEEEEHTTSGGGEBEHHHHHHHHHHHHHHH.HHT..EEEEEEEESBETTEEHHHHTTEEEEESSTTSG CS
                    Carboxyl_trans   1 kehprGkltareridllldpgsFgeledlffhrvtelgr.kkklprdgvvtgsGaviGravevvaqdktvlggslgp 76 
                                       k+h++Gkltareridll+dpgsF+e+ +++ hr+t +g+  kk  +dgv+tg+G+++Gr+v++ +qd+t++ggslg+
  gi|385806008|ref|YP_005842406.1|  28 KQHEKGKLTARERIDLLVDPGSFVEIGAFVTHRATGFGLeTKKQLGDGVITGYGKINGRTVFIASQDFTFMGGSLGE 104
                                       69*************************************98899********************************* PP

                                       GGCEEECHHHHHHHHHTEEEEEEEEE-ESSSGHHSSHHHHHHHHHHHHHHHHHHHCS-EEEEESSEEETHHHHHHHH CS
                    Carboxyl_trans  77 akgekllkaqeeaikagepligindsgGaegriqegveslrgsGkifgenskasgeIpqislvtgrcaGggaYlpal 153
                                       a++ek++++ ++aik+g p+i +ndsgGa  riqegv+sl+g+G+if+ n+kasg Ipqi+ ++g++aGg++Y+pal
  gi|385806008|ref|YP_005842406.1| 105 AHAEKIVRVLDLAIKSGSPMIFLNDSGGA--RIQEGVDSLKGYGDIFYLNVKASGFIPQIAAILGPAAGGAVYSPAL 179
                                       *****************************..********************************************** PP

                                       TSEEEEETTEEEEESSTHHHHHHHHSSCC-SSCHHHHSHHHHTTTTSSSEEESSHHHHHHHHHHHHTTS-SSTTSGG CS
                    Carboxyl_trans 154 gdrvimveetskifltGpdvikkvlgreevtseelgGatqhmtksGvahltaeddeealelirkllsylPkkasnnr 230
                                        d++im +++s++f+tGp+v+k+++g eev++ +lgGa++h +ksGva l+ e++eeal+li+kllsylP   snnr
  gi|385806008|ref|YP_005842406.1| 180 MDFIIMSRKNSYMFVTGPKVVKAAIG-EEVDEYSLGGAEIHEQKSGVASLVGETEEEALNLIKKLLSYLP---SNNR 252
                                       **************************.*******************************************...9999 PP

                                       SS----ECSSGSSSH.....HCS-CTTTS---HHHHHHCEECTTC-EEESTTSSTTEEEEEEEETTEEEEEEEE--S CS
                    Carboxyl_trans 231 esaPivetadepdrd...lieivPdnakkpyDvreviarlvdegeFlEikegyAktvVvGfArlgGipvGvvAnetr 304
                                       e++P v++ d+++r    l++i+P+++++pyDv+evi+r+ d++ F+Ei++++A++ V+Gf+r+gG+ vG++An++ 
  gi|385806008|ref|YP_005842406.1| 253 EDPPYVKSEDPVERAdkeLDSIIPTDPNAPYDVKEVITRVLDKDTFFEIQPNWAQNAVIGFGRIGGRVVGIIANQPM 329
                                       **************999899********************************************************* PP

                                       EEETTEE-HHHHHHHHHHHHHHHHTT--EEEEE-BSEE--SHHHHHTTHHHHHHHHHHHHHT--S-EEEEE-TEEEH CS
                    Carboxyl_trans 305 veaGqvlfidsavKaarfirlcdaenlPlviladvrGflvGqrqeyggilkhGaklvdalaeakvPkitvilrkayG 381
                                         aG +l+ids++K +rfir++da+n+ +++++dv+Gfl+G+ qeygg+++hGak+++a++ea+ Pkitvi+rkayG
  gi|385806008|ref|YP_005842406.1| 330 YLAG-SLDIDSSDKISRFIRFLDAFNISIITFVDVPGFLPGTVQEYGGVIRHGAKVIYAYSEATSPKITVIMRKAYG 405
                                       ****.************************************************************************ PP

                                       HHHHTTTGGGSTTTTEEETTT-EEESS-HHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Carboxyl_trans 382 GayvvmdskingadlvaawptariaVlgpegaveilfrkekaaaemerkdlaaerkkklkeyeeellnpyvaaargf 458
                                       Gay++m+sk++gad+v+a p a+iaV+gp gaveil+ ke+a  +    ++++++++  key+e+++npyvaa+rg+
  gi|385806008|ref|YP_005842406.1| 406 GAYIAMGSKHLGADYVLAYPFAEIAVMGPRGAVEILYGKELASLK-DMSEKQEFLNRVAKEYRENITNPYVAASRGY 481
                                       ****************************************98776.44578999*********************** PP

                                       HHTTSSHHHHHHTTSSSEEEHGGGHH..HHHHHHHH CS
                    Carboxyl_trans 459 aDavidpsetraklvialelewkkar..klparkrr 492
                                       +D+vi psetr++l++ale+ ++k++    +++k++
  gi|385806008|ref|YP_005842406.1| 482 IDDVIFPSETRTYLARALEAFASKKKeeRQINKKHG 517
                                       ******************987766654467888887 PP

>> MdcE  Malonate decarboxylase gamma subunit (MdcE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.33     3e+03      86      86 ..     144     144 ..      63     184 .. 0.53
   2 !   16.2   0.0   6.2e-07    0.0056      66     150 ..     356     440 ..     331     459 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.33
                                       T CS
                              MdcE  86 G 86 
                                       G
  gi|385806008|ref|YP_005842406.1| 144 G 144
                                       1 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 6.2e-07
                                       EEEEEEEE--B--SHHHHHHTHHHHHHHHHHHHHHHHHHT--EEEEEEEEEEHHHHHHTT...TT-SEEEEEET-EE CS
                              MdcE  66 pilvlvDvasQrlgrrdEllGihealahlakalarArlaGhpvigllvGkavsGaflahg...lqanrlialpgvqv 139
                                       +i+  vDv++   g  +E  G+    a ++ a+  A     p i++++ ka  Ga++a+g   l a+ ++a p +++
  gi|385806008|ref|YP_005842406.1| 356 SIITFVDVPGFLPGTVQEYGGVIRHGAKVIYAYSEAT---SPKITVIMRKAYGGAYIAMGskhLGADYVLAYPFAEI 429
                                       6899999999999999999999888888888888875...7*****************9966567************ PP

                                       ESS-HHHHHHH CS
                              MdcE 140 avmdkasaArv 150
                                       avm+ + a  +
  gi|385806008|ref|YP_005842406.1| 430 AVMGPRGAVEI 440
                                       ****9887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (521 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      618  (0.0344693); 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: 0.71u 0.29s 00:00:01.00 Elapsed: 00:00:00.48
# Mc/sec: 3270.40
//
Query:       gi|385806009|ref|YP_005842407.1|  [L=70]
Description: Carboxyl transferase, biotin-binding subunit [Fervidicoccus fontis Kam940]
Scores for 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-18   64.5   4.6    7.1e-18   64.2   4.6    1.2  1  Biotin_lipoyl    Biotin-requiring enzyme
    1.1e-14   54.0   1.6    9.1e-09   35.0   0.9    2.0  2  Biotin_lipoyl_2  Biotin-lipoyl like
    7.6e-08   31.8   0.1     0.0009   18.5   0.1    2.0  2  HlyD_D23         Barrel-sandwich domain of CusB or HlyD membr
    1.1e-06   29.3   0.1      0.012   16.3   0.0    2.0  2  HlyD_3           HlyD family secretion protein
    0.00014   21.6   0.8      0.022   14.5   0.2    2.1  2  PTS_EIIA_1       phosphoenolpyruvate-dependent sugar phosphot
    0.00055   19.9   0.1     0.0068   16.4   0.1    2.0  2  QRPTase_N        Quinolinate phosphoribosyl transferase, N-te
    0.00061   19.7   0.3     0.0021   18.0   0.1    1.7  2  RnfC_N           RnfC Barrel sandwich hybrid domain
     0.0025   17.7   0.3     0.0026   17.6   0.3    1.2  1  GCV_H            Glycine cleavage H-protein
     0.0084   15.7   0.2        1.3    8.8   0.1    2.1  2  PYNP_C           Pyrimidine nucleoside phosphorylase C-termin
  ------ inclusion threshold ------
      0.022   14.2   0.8      0.029   13.8   0.8    1.4  1  NQRA             Na(+)-translocating NADH-quinone reductase s


Domain annotation for each model (and alignments):
>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.2   4.6     4e-21   7.1e-18      15      73 .]      10      69 ..       1      69 [. 0.91

  Alignments for each domain:
  == domain 1  score: 64.2 bits;  conditional E-value: 4e-21
                                      ..ECSESSSTTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESSTTTEEE-TTCEEEEE CS
                     Biotin_lipoyl 15 g.vvevlvkvGdkVkagqvlaeveamKmemeieapkaGvvkeilvkeGdtvevgdllaki 73
                                      g +v +lvk+Gd+Vk++qvl+ +e+mKm +e  +pk+G+v++i v++Gd v+ +++l++i
  gi|385806009|ref|YP_005842407.1| 10 GkIVDILVKDGDEVKKNQVLLKIESMKMIIETRSPKDGKVEKIFVSKGDFVQKDKPLLEI 69
                                      35777****************************************************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 !   35.0   0.9   5.1e-12   9.1e-09       3      35 ..       2      34 ..       2      37 .. 0.93
   2 !   17.9   0.0   1.1e-06     0.002       7      33 ..      43      69 ..      39      70 .] 0.92

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 5.1e-12
                   Biotin_lipoyl_2  3 vsIaapvsGrVaqlnVkdGqrVkaGdvLaelDs 35
                                      v ++++v+G+++ ++VkdG++Vk+ +vL+ ++s
  gi|385806009|ref|YP_005842407.1|  2 VVVTSKVPGKIVDILVKDGDEVKKNQVLLKIES 34
                                      5689***************************98 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 1.1e-06
                   Biotin_lipoyl_2  7 apvsGrVaqlnVkdGqrVkaGdvLael 33
                                      +p +G+V++++V  G+ V++   L+e+
  gi|385806009|ref|YP_005842407.1| 43 SPKDGKVEKIFVSKGDFVQKDKPLLEI 69
                                      788*****************9999998 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 !   18.5   0.1     5e-07    0.0009      20      57 ..       2      38 ..       1      42 [. 0.92
   2 !   12.7   0.0     3e-05     0.053     109     139 ..      39      69 ..      35      70 .] 0.63

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 5e-07
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          HlyD_D23 20 arvsarveGwveklyvnatgdkVkkGqpLaelyspelv 57
                                      ++v+++v G + ++ v+  gd+Vkk+q L++++s +++
  gi|385806009|ref|YP_005842407.1|  2 VVVTSKVPGKIVDILVK-DGDEVKKNQVLLKIESMKMI 38
                                      6899*************.****************9875 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 3e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          HlyD_D23 109 vtvkapisGvVteknvreGqyvqpgdtlfti 139
                                       ++ ++p +G V +  v +G++vq++++l++i
  gi|385806009|ref|YP_005842407.1|  39 IETRSPKDGKVEKIFVSKGDFVQKDKPLLEI 69 
                                       4556666666666666666666666666666 PP

>> HlyD_3  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.1   0.00017       0.3       1      32 [.       3      34 ..       3      42 .. 0.89
   2 !   16.3   0.0   6.6e-06     0.012       3      30 ..      42      69 ..      40      70 .] 0.95

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00017
                            HlyD_3  1 tlrApvdGvvvelnveegevvqagdelleiip 32
                                      ++++ v G++v++ v+ g+ v ++++ll+i  
  gi|385806009|ref|YP_005842407.1|  3 VVTSKVPGKIVDILVKDGDEVKKNQVLLKIES 34
                                      589**************************974 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 6.6e-06
                            HlyD_3  3 rApvdGvvvelnveegevvqagdellei 30
                                      r+p dG+v ++ v++g++vq+ ++llei
  gi|385806009|ref|YP_005842407.1| 42 RSPKDGKVEKIFVSKGDFVQKDKPLLEI 69
                                      9**************************9 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 !   14.5   0.2   1.2e-05     0.022      76     108 ..       5      37 ..       2      45 .. 0.86
   2 !    6.8   0.0     0.003       5.4      80     103 ..      46      69 ..      34      70 .] 0.68

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.2e-05
                                       TTTTTTTTEEES----SEE-SEEEEEEE-HHHH CS
                        PTS_EIIA_1  76 tvklkgegFellvkegdkVkagdklvevdleai 108
                                       t k+ g+  ++lvk+gd+Vk+++ l++++  ++
  gi|385806009|ref|YP_005842407.1|   5 TSKVPGKIVDILVKDGDEVKKNQVLLKIESMKM 37 
                                       778899*********************986654 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.003
                                       TTTTEEES----SEE-SEEEEEEE CS
                        PTS_EIIA_1  80 kgegFellvkegdkVkagdklvev 103
                                       +g++ +++v++gd V++ ++l+e+
  gi|385806009|ref|YP_005842407.1|  46 DGKVEKIFVSKGDFVQKDKPLLEI 69 
                                       456667788888888888888775 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 !   16.4   0.1   3.8e-06    0.0068      44      68 ..       9      33 ..       1      39 [. 0.85
   2 ?    2.4   0.0     0.088   1.6e+02      45      67 ..      46      69 ..      33      70 .] 0.73

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.8e-06
                                      TTTEEEESS-TT-EEETTEEEEEEE CS
                         QRPTase_N 44 pglevellvkDGervekgdvlleie 68
                                      pg  v++lvkDG++v+k++vll+ie
  gi|385806009|ref|YP_005842407.1|  9 PGKIVDILVKDGDEVKKNQVLLKIE 33
                                      677799*****************98 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.088
                                      TTEEE.ESS-TT-EEETTEEEEEE CS
                         QRPTase_N 45 gleve.llvkDGervekgdvllei 67
                                      + +ve ++v+ G+ v+k + llei
  gi|385806009|ref|YP_005842407.1| 46 DGKVEkIFVSKGDFVQKDKPLLEI 69
                                      556666899999*****9999998 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 !   18.0   0.1   1.2e-06    0.0021      32      80 ..       3      52 ..       1      55 [. 0.85
   2 ?    2.7   0.0     0.066   1.2e+02      39      57 ..      47      65 ..      46      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.2e-06
                            RnfC_N 32 lplsqhiGapakplvkvgdkVlkGqkiaeaeg.fvsapvhasvsGtVkai 80
                                      +  s+  G+  ++lvk gd+V+k+q++ + e+  +  +  ++  G+V +i
  gi|385806009|ref|YP_005842407.1|  3 VVTSKVPGKIVDILVKDGDEVKKNQVLLKIESmKMIIETRSPKDGKVEKI 52
                                      556667799999****************9998556778899*****9998 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.066
                            RnfC_N 39 GapakplvkvgdkVlkGqk 57
                                      G+  k+ v++gd V+k + 
  gi|385806009|ref|YP_005842407.1| 47 GKVEKIFVSKGDFVQKDKP 65
                                      6677999*******99876 PP

>> GCV_H  Glycine cleavage H-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.3   1.5e-06    0.0026      29      73 ..       8      51 ..       1      66 [. 0.87

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.5e-06
                                      HH-SEEEEE---TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEE CS
                             GCV_H 29 elgdvvfvelpevgtkvkkgeslaavEsvKaasevyapvsGevve 73
                                        g++v + ++ +g++vkk++ l  +Es K++ e  +p +G+v +
  gi|385806009|ref|YP_005842407.1|  8 VPGKIVDILVK-DGDEVKKNQVLLKIESMKMIIETRSPKDGKVEK 51
                                      55888888665.6*****************************976 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 !    8.8   0.1   0.00071       1.3      35      53 ..      14      32 ..      13      44 .. 0.86
   2 !    5.3   0.0    0.0085        15      37      53 ..      53      69 ..      51      69 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00071
                                      EES--TT-EEBTTSEEEEE CS
                            PYNP_C 35 elhkklGdkVkkGeplati 53
                                      ++ +k Gd+Vkk+++l+ i
  gi|385806009|ref|YP_005842407.1| 14 DILVKDGDEVKKNQVLLKI 32
                                      678999**********998 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0085
                                      S--TT-EEBTTSEEEEE CS
                            PYNP_C 37 hkklGdkVkkGeplati 53
                                      ++  Gd V+k++pl+ i
  gi|385806009|ref|YP_005842407.1| 53 FVSKGDFVQKDKPLLEI 69
                                      6778**********987 PP

>> NQRA  Na(+)-translocating NADH-quinone reductase subunit A (NQRA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.8   1.6e-05     0.029      40      79 ..      12      52 ..       1      62 [. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.6e-05
                              NQRA 40 kpklkvkegdkVkkGqvlfedKknpgvlft.spasGevvei 79
                                         ++vk gd+Vkk qvl++  +++ ++ t sp +G+v +i
  gi|385806009|ref|YP_005842407.1| 12 IVDILVKDGDEVKKNQVLLKIESMKMIIETrSPKDGKVEKI 52
                                      56789***************999999886659******998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 495.45
//
Query:       gi|385806010|ref|YP_005842408.1|  [L=54]
Description: hypothetical protein FFONT_0968 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.036   14.0   0.6       0.04   13.9   0.6    1.1  1  DUF771    Domain of unknown function (DUF771)


Domain annotation for each model (and alignments):
>> DUF771  Domain of unknown function (DUF771)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.6   2.2e-06      0.04      29      74 ..       4      52 ..       1      54 [] 0.77

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.2e-06
                            DUF771 29 lekkls.kssewikeniLenprfrkeldi..ekggfvlypkgkgkkwlf 74
                                      lek+     ++++keni e+  +r  ++i  + + + +y k+kgk+++f
  gi|385806010|ref|YP_005842408.1|  4 LEKYARrTIKNMLKENINEHVGYRYWISIdkKRNLIYVYDKKKGKRYVF 52
                                      56666645577888899999888888888557789999*********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       785  (0.0437838); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); 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: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 367.18
//
Query:       gi|385806011|ref|YP_005842409.1|  [L=389]
Description: hypothetical protein FFONT_0969 [Fervidicoccus fontis Kam940]
Scores for complete 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   30.8  35.8    1.4e-07   30.8  35.8    2.1  2  MFS_1     Major Facilitator Superfamily


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8  35.8   7.7e-12   1.4e-07       2     329 ..       4     334 ..       3     350 .. 0.72
   2 ?    0.8   7.6      0.01   1.9e+02     106     166 ..     326     385 ..     322     387 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 7.7e-12
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalgll 77 
                                       ++a+++ +l +++ + +++ +++ ++++sp ++g+++++ +l +++++ ++G l+d+ G  + ++l++l+  +++ +
  gi|385806011|ref|YP_005842409.1|   4 FIAILFLSLLSFLDLGIFT-YIGYSFNVSPLVYGIIAATWSLIYIISNKLFGNLADK-GENKlLMLISLINIFVA-T 77 
                                       6667777777777777888.9************************************.77775888888888888.6 PP

                             MFS_1  78 lllfasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailg.pllggllasslgWra 152
                                       +l+ + ++  +++++ ++ ++  ++++ ++ + i +++  e   ++ +   + + l    +  l++  ++s+  +++
  gi|385806011|ref|YP_005842409.1|  78 FLF-SRGSLaYIAIAYMFHAISVSTANLSVSSSIFELTDSESWWKYSAAQRLLVYLIRGTTlLLISTGILSLSIFQV 153
                                       666.655555***************************************9998877553332555555554555888 PP

                             MFS_1 153 vfyilaivsllafvlfllllpeepperkrkspkeee.....................kgtgpaplvpawkallkdpv 208
                                       ++++ ai+++ a+vl  + +  e++ +  ++ +                           ++++l    + + +++ 
  gi|385806011|ref|YP_005842409.1| 154 LMIATAIAAISAIVLPSIGVNIERKLHLINKNVSNVieysnmkslaainlenptglqGVLEGFKL--KEGGVSSKN- 227
                                       88888888888888866666555555555555555577777776776655555553222222222..235566666. PP

                             MFS_1 209 lwillialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllalllll 285
                                          +l++l+++ ++  +++t +pl+++ +  l+  l ++   +++++v+ i+ +l +++++  +++ ++++ ll +l
  gi|385806011|ref|YP_005842409.1| 228 ---ILLSLFFAIAMGDFMFTIMPLLIKGDISLN-TLWIS--HGITGIVIGISLVLMSKILK-GSKKSATFFVLLRGL 297
                                       ...88888888778888*******999999999.78888..***********999999994.467888888888888 PP

                             MFS_1 286 laalglallavtssavllllvlvliGfglgfvfpsllalasdla 329
                                        +alg+ ll  +s  +l+l++++l        ++++ ++  +l+
  gi|385806011|ref|YP_005842409.1| 298 WLALGIPLLFKPSGLILYLIIMYL-------SSSAIDTIFYNLY 334
                                       888888888888333333333333.......3333344444443 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.01
                             MFS_1 106 gaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafv 166
                                       + +++  ++++++ g +   + +   +G+++g l++g+++  +g +a+ + la+++ +a++
  gi|385806011|ref|YP_005842409.1| 326 IDTIFYNLYSETNSGYGANNYFIVREMGTLFGSLIAGMIM-TFGLTAIIISLALMCTIALI 385
                                       556666777777777777777777889*************.999************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       975  (0.0543812); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); 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):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2509.05
//
Query:       gi|385806012|ref|YP_005842410.1|  [L=44]
Description: hypothetical protein FFONT_0970 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       187  (0.01043); expected 358.6 (0.02)
Passed bias filter:                      182  (0.0101512); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 308.17
//
Query:       gi|385806013|ref|YP_005842411.1|  [L=537]
Description: hypothetical protein FFONT_0971 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (537 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); 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: 0.63u 0.34s 00:00:00.97 Elapsed: 00:00:00.49
# Mc/sec: 3267.46
//
Query:       gi|385806014|ref|YP_005842412.1|  [L=44]
Description: hypothetical protein FFONT_0972 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00032   20.5   0.3    0.00038   20.3   0.3    1.1  1  RHH_1     Ribbon-helix-helix protein, copG family
  ------ inclusion threshold ------
      0.038   13.5   0.1       0.86    9.1   0.0    2.0  2  ArfA      Alternative ribosome-rescue factor A
      0.074   13.2   0.0      0.079   13.1   0.0    1.0  1  RHH_8     Ribbon-Helix-Helix transcriptional regulator family
       0.15   12.1   0.0       0.16   11.9   0.0    1.0  1  MtlR      Mannitol repressor


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.3   8.6e-08   0.00038      10      33 ..       1      25 [.       1      29 [. 0.93

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 8.6e-08
                                      HHHHHHHHHHHHT.SSHHHHHHHHH CS
                             RHH_1 10 llerLdelarrrg.rSrSelIReAl 33
                                      ++ ++d+l+++   +SrSe+IR A+
  gi|385806014|ref|YP_005842412.1|  1 MASAIDRLVEDKIfQSRSEAIRYAI 25
                                      6889******************998 PP

>> ArfA  Alternative ribosome-rescue factor A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0   0.00019      0.86      12      28 ..       3      19 ..       1      23 [. 0.87
   2 ?    2.8   0.0     0.018        81      30      36 ..      34      40 ..      30      42 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00019
                              ArfA 12 NalkAlvtskLFrqrve 28
                                      +a+  lv +k+F++r e
  gi|385806014|ref|YP_005842412.1|  3 SAIDRLVEDKIFQSRSE 19
                                      68888**********88 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.018
                              ArfA 30 akKGKGS 36
                                      +kKGK S
  gi|385806014|ref|YP_005842412.1| 34 NKKGKES 40
                                      8****77 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 ?   13.1   0.0   1.8e-05     0.079      17      47 ..       4      34 ..       2      41 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.8e-05
                             RHH_8 17 qiDlLveeGfYsnRtDlirtairaqLakhdd 47
                                       iD Lve+  + +R++ ir ai + +++h +
  gi|385806014|ref|YP_005842412.1|  4 AIDRLVEDKIFQSRSEAIRYAIGSLISTHFN 34
                                      69********************999988855 PP

>> MtlR  Mannitol repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.7e-05      0.16      27      55 ..       2      31 ..       1      34 [. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.7e-05
                              MtlR 27 eeavdqLie.rvFrkddfavkyvvepLlek 55
                                      ++a+d+L+e ++F    +a++y++ +L+++
  gi|385806014|ref|YP_005842412.1|  2 ASAIDRLVEdKIFQSRSEAIRYAIGSLIST 31
                                      6899***9758****************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.46
# Mc/sec: 288.53
//
Query:       gi|385806015|ref|YP_005842413.1|  [L=92]
Description: hypothetical protein FFONT_0973 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.067   13.3   0.0        0.1   12.7   0.0    1.3  1  SBDS      Shwachman-Bodian-Diamond syndrome (SBDS) protein


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 ?   12.7   0.0   5.7e-06       0.1      45      81 ..      32      68 ..      25      72 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.7e-06
                                      EETTTTEE--HHHHHHHHS---HHHHHHHHHHHSEEE CS
                              SBDS 45 tnaskGetaskselekafgteskdeiikeILkkGeiq 81
                                      tn s Ge     ele ++g ++ +++i++ + kG ++
  gi|385806015|ref|YP_005842413.1| 32 TNLSVGEILAVRELERVYGIKNPESVIEILISKGLLE 68
                                      567999999*************************765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 707.03
//
Query:       gi|385806016|ref|YP_005842414.1|  [L=454]
Description: glycerate kinase [Fervidicoccus fontis Kam940]
Scores for complete 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-75  252.4   0.8    1.2e-74  250.7   0.1    2.0  3  DUF4147     Domain of unknown function (DUF4147)
    1.3e-27   96.1   0.2    2.5e-27   95.2   0.2    1.5  1  MOFRL       MOFRL family
  ------ inclusion threshold ------
      0.017   15.5   0.1      0.056   13.8   0.1    1.9  1  E3_binding  e3 binding domain
      0.023   15.0   0.5       0.27   11.5   0.4    2.6  3  3H          3H domain


Domain annotation for each model (and alignments):
>> DUF4147  Domain of unknown function (DUF4147)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  250.7   0.1   2.8e-78   1.2e-74       2     228 ..      13     257 ..      12     258 .. 0.90
   2 ?   -0.8   0.0      0.21   9.3e+02      78     135 ..     274     331 ..     264     339 .. 0.83
   3 ?   -2.6   0.1      0.73   3.3e+03      31      51 ..     344     364 ..     304     375 .. 0.73

  Alignments for each domain:
  == domain 1  score: 250.7 bits;  conditional E-value: 2.8e-78
                                       HHHHHHHHHHTTSHHHHHHTTHHH...........H--........-SEEEEEESTTHHHHHHHHH....HHHGEEE CS
                           DUF4147   2 lraifeaaveavdpeklvkralsl...........keeeldls.kkkrvvvvgaGKAaaamaaalee...ealksgv 63 
                                       l++i+++ v+ +d +  +k+ ++l           +++e++++ k+krv+++++GKA+ +ma+ + +   +++ +g+
  gi|385806016|ref|YP_005842414.1|  13 LETILKESVRLADIQYYMKKRVRLegecliiknekENKEYKITiKNKRVHLISFGKASQKMAEFALNllgSRIIDGI 89 
                                       6889999999***********9998888877665433367776779****************777644665566888 PP

                                       EEE...ETT-----TT-EEEEE-SSS--HHHHHHHHHHHHHHSS--TT-EEEEEE-TTHHHHS--B-TT--HHHHHH CS
                           DUF4147  64 vvv...kkghaeekerievleaahplPdeesveaarkilelaeklkeddlvlvliSGGgSAllaaPaegitledkqa 137
                                       vv     ++ +e  ++i+v+ea+hp+Pd+ s+eaa++il+l+++++eddl+l+liSGGgSA++++P+++itled ++
  gi|385806016|ref|YP_005842414.1|  90 VVKlkfAEKISEFPQNIKVIEANHPVPDSGSIEAAKSILNLISNASEDDLMLFLISGGGSAMVELPIDPITLEDAEK 166
                                       7775333455556678************************************************************* PP

                                       HHHHHHHCT--HHHHHHHHHTTBSSTTTHHHHHHTTSEEEEEEE--STT--TTTGGG-TTS-----HHHHHHHHHHT CS
                           DUF4147 138 ltkaLlasGasIqelNtVRkhlsaikGGrLaraaaparvvsLilSDVvgddldvIASGPtvpdsstfadalaileky 214
                                         ++L++sGa+I+e+N+VRkh+s+ikGG+La+ a+pa+vvsLi SDV+g+ +dvIASGPt+pd st++da +ile+y
  gi|385806016|ref|YP_005842414.1| 167 AFSLLIRSGATIHEINAVRKHISQIKGGKLAKKAYPAEVVSLIASDVPGNYIDVIASGPTAPDMSTYSDAYRILEQY 243
                                       ***************************************************************************** PP

                                       T---..-HHHHHHH CS
                           DUF4147 215 kleeklpesvrelL 228
                                       ++ +k+p+sv e++
  gi|385806016|ref|YP_005842414.1| 244 EILDKIPKSVLEVI 257
                                       **********9987 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.21
                                       EEEEE-SSS--HHHHHHHHHHHHHHSS--TT-EEEEEE-TTHHHHS--B-TT--HHHH CS
                           DUF4147  78 evleaahplPdeesveaarkilelaeklkeddlvlvliSGGgSAllaaPaegitledk 135
                                       +v+e ah+   ++  + a+++ ++++k++ +  vl  i  G S  +a    +i ++ k
  gi|385806016|ref|YP_005842414.1| 274 KVFERAHNFLIAAPSDLAKEVSSYVSKIGYNSYVLTSILQGESGEVAKALSSIAIDTK 331
                                       678888888888899999*****************99999999888777777777665 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.73
                                       .....-SEEEEEESTTHHHHH CS
                           DUF4147  31 dlskkkrvvvvgaGKAaaama 51 
                                        l+ +++v v g GK   am 
  gi|385806016|ref|YP_005842414.1| 344 ILAGETNVKVKGSGKGGRAME 364
                                       455678889999999988885 PP

>> MOFRL  MOFRL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.2   0.2   5.7e-31   2.5e-27       2     108 ..     342     446 ..     341     447 .. 0.94

  Alignments for each domain:
  == domain 1  score: 95.2 bits;  conditional E-value: 5.7e-31
                                       EEEEEE--B----S-----HHHHHHHHHHH...HTTT-TTEEEEEEETTS--SSSS--EEEEETTHHHHHHH.TT-- CS
                             MOFRL   2 vllsgGEttvtvkgkGkGGrnqelalalalelkelegaeevvllsagtDGiDGptdaaGaivdaetleraea.agld 77 
                                       +l+++GEt v+vkg+GkGGr++el+  +++e++ +   +++++++++tDG+DG+t+ aGa++d +t++++ +  gl+
  gi|385806016|ref|YP_005842414.1| 342 ALILAGETNVKVKGSGKGGRAMELVAYFSREIAGI---DGISIFAIDTDGMDGSTTSAGAFADCNTWRKIFKkYGLK 415
                                       799***************************66666...9*****************************9876378** PP

                                       HHHHHHTT-HHHHHHHTT-EE-----S---- CS
                             MOFRL  78 akeaLanndsyeffeklgallktgpTgtNVn 108
                                       a + L+nn+sye++++lg ++ tgpTg N+n
  gi|385806016|ref|YP_005842414.1| 416 AFDELRNNNSYELLDSLGYTIYTGPTGSNLN 446
                                       *****************************98 PP

>> E3_binding  e3 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   1.3e-05     0.056       2      29 ..     337     361 ..     337     364 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.3e-05
                                       BE-HHHHHHHHHCT--TTTS---CTTTB CS
                        E3_binding   2 lAsPaaRklAkelGidLsdvkGtGpgGR 29 
                                       +A P a  lA e ++   +vkG+G+gGR
  gi|385806016|ref|YP_005842414.1| 337 FALPTALILAGETNV---KVKGSGKGGR 361
                                       57788888*******...*********9 PP

>> 3H  3H domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.4   6.1e-05      0.27       6      65 ..       5      65 ..       1      97 [. 0.81
   2 ?   -0.5   0.0      0.35   1.6e+03       8      38 ..     162     192 ..     160     197 .. 0.78
   3 ?   -1.8   0.0      0.91   4.1e+03      60      81 ..     268     289 ..     254     295 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.1e-05
                                      -GGGHHHHHHHHHHTT-EEEEEEEEETTTEEEEEE.EEE-SHHHHHHHHHHHHH--S--ST CS
                                3H  6 teeeieeeleiivdnggtvedvivehpvygeltak.lnissredvkkfieklkkskaslLs 65
                                      t +++ e+le+i++  +++ d+ ++++   +l+++ l i+++++ k++  ++k+++ +l+s
  gi|385806016|ref|YP_005842414.1|  5 TGKKMPEKLETILKESVRLADIQYYMKKRVRLEGEcLIIKNEKENKEYKITIKNKRVHLIS 65
                                      567899***************************984699**********999999888744 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.35
                                       GGHHHHHHHHHHTT-EEEEEEEEETTTEEEE CS
                                3H   8 eeieeeleiivdnggtvedvivehpvygelt 38 
                                       e+ e+ ++++++ g+t++++    + + +++
  gi|385806016|ref|YP_005842414.1| 162 EDAEKAFSLLIRSGATIHEINAVRKHISQIK 192
                                       7788889999999999999987766666665 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.91
                                       -S--STTGGGGEEEEEEEESSH CS
                                3H  60 kaslLseltsgvHlHtieapse 81 
                                         ++L ++ +  H + i+aps+
  gi|385806016|ref|YP_005842414.1| 268 TPKPLDKVFERAHNFLIAAPSD 289
                                       4567999999999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.65u 0.34s 00:00:00.99 Elapsed: 00:00:00.53
# Mc/sec: 2580.67
//
Query:       gi|385806017|ref|YP_005842415.1|  [L=221]
Description: hypothetical protein FFONT_0975 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); 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: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1320.67
//
Query:       gi|385806018|ref|YP_005842416.1|  [L=151]
Description: Universal stress protein UspA [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.5e-25   89.2   0.0    3.9e-25   89.0   0.0    1.0  1  Usp            Universal stress protein family
  ------ inclusion threshold ------
      0.066   12.9   0.0      0.077   12.7   0.0    1.1  1  Peptidase_M22  Glycoprotease 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 !   89.0   0.0   4.3e-29   3.9e-25       2     140 ..       5     144 ..       4     145 .. 0.91

  Alignments for each domain:
  == domain 1  score: 89.0 bits;  conditional E-value: 4.3e-29
                                       -SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCT CS
                               Usp   2 ykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeag 78 
                                       y++I++++Dgs +s+ Al++A el +++g+el ++ vi+p + ++    ++ +  +++e + +  e+++ k aa+ +
  gi|385806018|ref|YP_005842416.1|   5 YEKIVIGFDGSASSRLALQKACELGERFGSELNVVLVIEPLDVYYGEPIPDVEISKQKEAANMIIEKAK-KIAANYK 80 
                                       89*****************************************99999988888888888888877765.9****** PP

                                       TCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTT.CSSBHHHHHHHHHTS.SEEEEE CS
                               Usp  79 gvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsr.lllGSvseyvlrhap.cpVlvV 140
                                       +++v   v+ g pa ei ++a +++adliVvG++ ++gl + +llGSvs+++++ ++ ++Vl++
  gi|385806018|ref|YP_005842416.1|  81 IKNVNYMVKYGVPANEIMKTATDIKADLIVVGRKSKKGLLEkVLLGSVSQSIVNLSKdIDVLIT 144
                                       **********************************97766666************9963577775 PP

>> Peptidase_M22  Glycoprotease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   8.6e-06     0.077     196     244 ..      53     103 ..      12     113 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.6e-06
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCTBSEE..EEESGGGGXHHHHHCHC CS
                     Peptidase_M22 196 vedlaasfqeavvdhlvekteralklpkakel..vilGGvaankrLreale 244
                                       + d+  s q++++++++ek++++++++k+k++  ++  Gv an+ +++a  
  gi|385806018|ref|YP_005842416.1|  53 IPDVEISKQKEAANMIIEKAKKIAANYKIKNVnyMVKYGVPANEIMKTATD 103
                                       77888999****************99666666555666******9888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       868  (0.0484132); 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: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 1201.50
//
Query:       gi|385806019|ref|YP_005842417.1|  [L=231]
Description: uridylate kinase [Fervidicoccus fontis Kam940]
Scores for complete 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   87.3   0.1      6e-24   85.0   0.1    1.8  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 !   85.0   0.1   3.3e-28     6e-24       3     237 ..       6     203 ..       4     207 .. 0.84

  Alignments for each domain:
  == domain 1  score: 85.0 bits;  conditional E-value: 3.3e-28
                                       EEEEE-TTCCC.CTCCHHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC....E..HHHHHHHH CS
                         AA_kinase   3 vVvKlGGsslt.dkeeaslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaaglrstleeagevat 78 
                                       +V+K+ Gs +  dk  +++r++ + + +l esg++++vV+Ggg++++ +++++++l  +e+ +              
  gi|385806019|ref|YP_005842417.1|   6 IVIKISGSFIQpDKP-DAIRNFSNVLIELWESGYRPAVVVGGGNTARDYINAARKLGGNESVL-------------- 67 
                                       8**********6555.59**********************************99999999885.............. PP

                                       HHHHHHHHHHHHHHHHHTTHGEEEE-G..GGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEETTT CS
                         AA_kinase  79 rdalaslgerlvaallaaglpavglsa..aaldateagrdegsdgnvesvdaeaieelleagvvpvltgfigldeeg 153
                                        d++++  +rl+a+ll   l ++ ++   ++++ +             +v+     + le+  ++v++g++    +g
  gi|385806019|ref|YP_005842417.1|  68 -DLIGIEVTRLNAYLLILSLGSYAVPYplESINDIL------------KVK----DDPLER--IIVMGGLQ----PG 121
                                       .***************99996666654003333222............222....333444..89999999....99 PP

                                       EEEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHH..CSSS.TTTHHHHCHHHHHH CS
                         AA_kinase 154 elgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaee..saselatgGmkvkhpaala 228
                                       +    s+  ++a+lAe +gA+ +i++t VdG+yd+dp  ++da+l+++i+  +++e  ++     g  + ++p  l 
  gi|385806019|ref|YP_005842417.1| 122 Q----STNAVSAILAEVIGAKNIINVTKVDGIYDKDPLLNKDAKLIKKITTLQLREllKQHSSEAGKYELFDPLSLS 194
                                       9....9**************************************************987777777777778888888 PP

                                       HHHCTT-EE CS
                         AA_kinase 229 aarrggipv 237
                                       +++r++  v
  gi|385806019|ref|YP_005842417.1| 195 IIERSKLIV 203
                                       888886544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1449.86
//
Query:       gi|385806020|ref|YP_005842418.1|  [L=63]
Description: hypothetical protein FFONT_0978 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       804  (0.0448435); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 397.13
//
Query:       gi|385806021|ref|YP_005842419.1|  [L=167]
Description: histidine triad (HIT) protein [Fervidicoccus fontis Kam940]
Scores for complete 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   51.1   0.0    3.4e-13   50.1   0.0    1.4  1  HIT       HIT domain
    2.3e-09   37.7   0.0    3.7e-09   37.1   0.0    1.3  1  DcpS_C    Scavenger mRNA decapping enzyme C-term binding
    2.8e-09   36.9   0.2    4.5e-09   36.2   0.2    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 !   50.1   0.0   5.7e-17   3.4e-13       4      95 ..      39     131 ..      36     132 .. 0.95

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 5.7e-17
                                       C-CCEEEE-SSEEEEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEESGG CS
                               HIT   4 ipstvvyeddlvlafldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqkkfknkglrvvinngah 80 
                                       +++ vv++ ++++++ ++ p   ghl v+p kh+s++++l++eel +l +++ + +k+l + ++ +g+++ +n g++
  gi|385806021|ref|YP_005842419.1|  39 NKNLVVFRGNKTFVIMNKYPYNSGHLMVVPYKHVSRIENLDNEELLELSTLIVRSVKVLTELYRPDGFNIGMNIGRA 115
                                       677899999******************************************************************** PP

                                       GT-SS.SS-EEEEEEC CS
                               HIT  81 agqsv.ahlHiHvipr 95 
                                       ag  +  h+H+H++pr
  gi|385806021|ref|YP_005842419.1| 116 AGAGIeDHIHVHIVPR 131
                                       ***9945*******97 PP

>> DcpS_C  Scavenger mRNA decapping enzyme C-term binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.0   6.2e-13   3.7e-09       1     100 [.      26     129 ..      26     132 .. 0.83

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 6.2e-13
                                       T-HHHHHHTTSS.-B-E.EEE-SSEEEEE-SS-SSSEEEEEEESS---SGGG--TTTTTHHHHHHHHHHHHHHHTT- CS
                            DcpS_C   1 kwvfnilakgke.perv.vyedekfvvlkDikpkaklhllvipkrdikslrdLtkehlpllkemrekakkvieekyn 75 
                                       +++f++++ +k+ ++++ v++ +k+ v+  ++p ++ hl+v+p+++++ +++L++e+l  l ++     kv+ e y 
  gi|385806021|ref|YP_005842419.1|  26 SCIFCKVIAEKDdNKNLvVFRGNKTFVIMNKYPYNSGHLMVVPYKHVSRIENLDNEELLELSTLIVRSVKVLTELY- 101
                                       699***9999886444448899999999*************************99999999999999999999988. PP

                                       T-EEEEE--SCCCT-.....-S-S--EEEE CS
                            DcpS_C  76 evdaeelrvgvhyqP.....svyhlHlHvi 100
                                         +++ +++g+++         +h+H+H++
  gi|385806021|ref|YP_005842419.1| 102 --RPDGFNIGMNIGRaagagIEDHIHVHIV 129
                                       ..456666666655544446679*****97 PP

>> CwfJ_C_1  Protein similar to CwfJ C-terminus 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.2   7.5e-13   4.5e-09       5      72 ..      18      87 ..      16     131 .. 0.86

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 7.5e-13
                                      HHHHHHHHH-S--..--SS---SS--S-B-SSEEEE---S-SSTT-EEEEESS--SSTTSS-HHHHHHHH CS
                          CwfJ_C_1  5 krikasldsClfC..lsnpklekhlivsignkvYlalpkgpLssgHvliipieHisallsldeevldeir 72
                                      +++k++ +sC fC  + +++ +k+l+v  gnk+++ + k p +sgH++++p +H+s   +ld+e+l e++
  gi|385806021|ref|YP_005842419.1| 18 EISKEEKGSCIFCkvIAEKDDNKNLVVFRGNKTFVIMNKYPYNSGHLMVVPYKHVSRIENLDNEELLELS 87
                                      5678899******8778899999****************************************9887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); 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: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1091.69
//
Query:       gi|385806022|ref|YP_005842420.1|  [L=547]
Description: dihydropteroate synthase-like protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.5e-05   23.5   0.8    0.00035   20.6   0.1    2.3  2  DUF4346         Domain of unknown function (DUF4346)
  ------ inclusion threshold ------
      0.053   14.3   0.6       0.14   12.9   0.4    1.8  2  Complex1_LYR_2  Complex1_LYR-like


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 ?    0.6   0.1      0.06   5.4e+02      13      31 ..     445     463 ..     443     469 .. 0.86
   2 !   20.6   0.1   3.9e-08   0.00035      68     118 .]     474     521 ..     465     521 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.06
                           DUF4346  13 lDpaGYflikvdreakliv 31 
                                       +D + Y li vd+e++li+
  gi|385806022|ref|YP_005842420.1| 445 MDKGIYVLIFVDHEKRLIY 463
                                       78888**********9996 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 3.9e-08
                           DUF4346  68 yrgrtakelcvkileeeeelpvtkldhaaYlGRelqraeaaLlsgkeYiqD 118
                                       y +   k+l  k++ +  +      +ha Y+G el +ae++L+ gk+Y qD
  gi|385806022|ref|YP_005842420.1| 474 YASDNGKDLYKKLTRSGVKF---SNEHASYIGYELAKAEFSLKLGKQYEQD 521
                                       55555566666665543322...347************************9 PP

>> Complex1_LYR_2  Complex1_LYR-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0         2   1.8e+04      35      57 ..     107     129 ..     102     145 .. 0.70
   2 ?   12.9   0.4   1.6e-05      0.14       3      60 ..     481     539 ..     480     545 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2
                    Complex1_LYR_2  35 khlknpeeialflknqreYaell 57 
                                       ++l+ ++e + f+++ +    ++
  gi|385806022|ref|YP_005842420.1| 107 RDLSLLKELINFVSSGKKLSSTI 129
                                       46677778888888877666555 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 1.6e-05
                    Complex1_LYR_2   3 sLYrrllrel.relppelrslgdayvraefrrhkhlknpeeialflknqreYaellery 60 
                                        LY+ l r+  +++ ++    g++  +aef  +  ++ ++++ +f+   + Y+++l++y
  gi|385806022|ref|YP_005842420.1| 481 DLYKKLTRSGvKFSNEHASYIGYELAKAEFSLKLGKQYEQDFSSFVEPKEKYFDILKYY 539
                                       69********544577888999**********66666777******************* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (547 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.52
# Mc/sec: 3141.60
//
Query:       gi|385806023|ref|YP_005842421.1|  [L=385]
Description: iron-containing alcohol dehydrogenase [Fervidicoccus fontis Kam940]
Scores for complete 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-77  261.2   0.0    1.3e-77  261.1   0.0    1.0  1  Fe-ADH        Iron-containing alcohol dehydrogenase
    3.6e-13   49.8   0.9    2.7e-10   40.4   0.1    2.2  2  Fe-ADH_2      Iron-containing alcohol dehydrogenase
  ------ inclusion threshold ------
      0.099   11.8   0.0        0.2   10.8   0.0    1.4  1  DHQ_synthase  3-dehydroquinate synthase
       0.15   11.1   0.1       0.23   10.5   0.1    1.2  1  T2SSE         Type II/IV secretion system protein


Domain annotation for each model (and alignments):
>> Fe-ADH  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  261.1   0.0   2.9e-81   1.3e-77       2     346 ..      14     357 ..      13     377 .. 0.93

  Alignments for each domain:
  == domain 1  score: 261.1 bits;  conditional E-value: 2.9e-81
                                       SEEEEETTGGGGHHHHHTTT-..EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HHHHHHHHTTS- CS
                            Fe-ADH   2 trivfgkgaleelgellkklgakralivtdkgslkksglldkvlesleeagievtvfdgvepnptleeveeaaalar 78 
                                       t+++fg +++e++ + +k +  +ralivt+k s+kksg+ld++l+ l+e++ie+t++d v++npt++++ee+++  +
  gi|385806023|ref|YP_005842421.1|  14 TTLYFGINSTERISRSIKGF--RRALIVTGKTSAKKSGALDDILKILNENDIEYTIYDSVTSNPTVDKIEEITEKGK 88 
                                       5789*************888..6****************************************************** PP

                                       TT.--EEEEEESHHHHHHHHHHHHHTT...................--EEEEESS-S-S-TT-SEEEEE.-TTSEEE CS
                            Fe-ADH  79 eegadvviavGGGsviDtAKaialllanpe.vedylgegkakkkkalpliaiPTtaGtGsevtplavitdeeegekl 154
                                        ++ d++ia+GGGsviD AK ++++l+ ++ + dy+ ++k k+ +   l+ai  t GtG ev ++av t +e++ekl
  gi|385806023|ref|YP_005842421.1|  89 IFDTDLIIAIGGGSVIDSAKFASVILSIGGnPVDYI-KRKIKPVSHTFLVAINLTHGTGTEVDRYAVATISETKEKL 164
                                       ***************************88569****.66666777799*********************99998888 PP

                                       EE-..SS--SEEEEEHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHT---TTSSB--HHHHHHHHHHHHHHHHHHHHH CS
                            Fe-ADH 155 sifdpellPdlaivDpeltltlPkrvtaatglDalahalEayvskkanplsdalaleairliaknleravadgedle 231
                                       + +    +P++++ +p+++++l +++t +t +Da+ halE+ + + +np+ + l+++++  i ++++ a+++++d+e
  gi|385806023|ref|YP_005842421.1| 165 GSS--IAYPNISVDNPRYMVSLSPQQTLFTSIDAFYHALESSIVESSNPYVQDLSEKSAYYIKTYIQVAMKNPSDIE 239
                                       777..89********************************************************************** PP

                                       HHHHHHHHHHHHHHHHHSS---HHHHHHHHHHC.C.GGGGGS-HHHHHHHHH..........HHHHHHT........ CS
                            Fe-ADH 232 areqmllastlaglafsnaglgavHalahalgalf.giphglanaillpavlrfnaeaaperlaqlaralgge..sd 305
                                       ar  +l+as+lag+++  ag+++ H+++h+l++    ++hg+++ai+ p  l   ++a pe   ++ + l      +
  gi|385806023|ref|YP_005842421.1| 240 ARYWLLYASMLAGISIDLAGTSIIHGMEHGLSGVNpSLEHGAGLAIIGPLFLPLLYKAFPENSWKVMKVLDPSlrPT 316
                                       *********************************777899*************99998889*********9888**99 PP

                                       .T--HHHHHHHHHHHHHTT---SHHHHT-TT-HHHHHHHHH CS
                            Fe-ADH 306 eeaaeeliealrellkelglptsLselgvdeedldklaeaa 346
                                        e ae++ + l+e+ k++g+   L+++g+d+e l++ +ea 
  gi|385806023|ref|YP_005842421.1| 317 PEDAEKAGKILDEFQKSIGFNYALKDYGFDKEWLKDAVEAG 357
                                       9******************************8777777765 PP

>> Fe-ADH_2  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.1   6.1e-14   2.7e-10      17      96 ..      31     112 ..      19     117 .. 0.88
   2 !    8.0   0.1   0.00047       2.1     172     237 ..     207     272 ..     191     283 .. 0.79

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 6.1e-14
                          Fe-ADH_2  17 lelkkvllvadentkka..agekveeslkeagikvevveeveeeadleeveklvealreketdlvvavGgGtiiDia 91 
                                       ++++++l+v++++  k   a +++ + l+e++i+ +++++v+ +++++++e++ e+ +  +tdl++a+GgG++iD a
  gi|385806023|ref|YP_005842421.1|  31 KGFRRALIVTGKTSAKKsgALDDILKILNENDIEYTIYDSVTSNPTVDKIEEITEKGKIFDTDLIIAIGGGSVIDSA 107
                                       3689********9766545889******************************************************* PP

                          Fe-ADH_2  92 kyvsa 96 
                                       k++s 
  gi|385806023|ref|YP_005842421.1| 108 KFASV 112
                                       ***97 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00047
                          Fe-ADH_2 172 klanevseplaklsaamvqeaaeklvedkketealeellealalsgigisrpaSGsEHliSHaldm 237
                                       + +n + + l+++sa  +++ ++ +++++ ++ea   ll a++l+gi+i  ++    H + H l  
  gi|385806023|ref|YP_005842421.1| 207 ESSNPYVQDLSEKSAYYIKTYIQVAMKNPSDIEARYWLLYASMLAGISIDLAGTSIIHGMEHGLSG 272
                                       45567788999**************************************88885555555555544 PP

>> DHQ_synthase  3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   4.4e-05       0.2      15      53 ..      76     114 ..      67     123 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 4.4e-05
                                       HHHHHHHHHHHTT--TT-EEEEEESHHHHHHHHHHHHHB CS
                      DHQ_synthase  15 tlekildalleakleRksllialGGGvvgDlaGfvAaty 53 
                                       t+ ki +   + k+  ++l+ia+GGG v D a f++ ++
  gi|385806023|ref|YP_005842421.1|  76 TVDKIEEITEKGKIFDTDLIIAIGGGSVIDSAKFASVIL 114
                                       567777777777888899****************98776 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   0.1     5e-05      0.23     110     172 ..      18      76 ..       4      97 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 5e-05
                             T2SSE 110 aeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderivtvEDpvEiqle 172
                                       +  + +e+i++ ++     r  ++v+G T+  K+  l  +lk++n++ +   t+ D+v  ++ 
  gi|385806023|ref|YP_005842421.1|  18 FGINSTERISRSIKGF---RRALIVTGKTSAKKSGALDDILKILNEN-DIEYTIYDSVTSNPT 76 
                                       5555667778888888...999************************9.555777777766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); 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 0.33s 00:00:00.99 Elapsed: 00:00:00.54
# Mc/sec: 2144.62
//
Query:       gi|385806024|ref|YP_005842422.1|  [L=335]
Description: putative phosphohydrolase, DHH superfamily [Fervidicoccus fontis Kam940]
Scores for complete 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   28.4   0.0    4.5e-06   27.1   0.0    1.6  1  DHHA1     DHHA1 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 !   27.1   0.0   2.5e-10   4.5e-06      56     123 ..     240     295 ..     197     299 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 2.5e-10
                                       HHHHHHHHHTHGBT.TCEEEEEEEECTEEEEEEEESSHSS-HHHHHHHHHHHTTCCEEEETCEEEEEEE CS
                             DHHA1  56 lgiaadklksklkk.pvivfvakeegdkvkvsarskkdgvdagelakeaaaklgggGGGHdlAaGagip 123
                                          +  +l+s  k  + iv+++ e g    +s+rsk  +vd++ +a+        gGGGH+lA+Ga i+
  gi|385806024|ref|YP_005842422.1| 240 ASLLGHYLLS--KTgADIVVIYRESG---VLSFRSK--QVDVSSIARC------IGGGGHKLASGAEIK 295
                                       5556678888..88899999999866...*******..9*********......************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); 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: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 1928.55
//
Query:       gi|385806025|ref|YP_005842423.1|  [L=276]
Description: inositol monophosphatase [Fervidicoccus fontis Kam940]
Scores for complete 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  112.6   0.0    2.8e-32  112.3   0.0    1.0  1  Inositol_P  Inositol monophosphatase family
    1.7e-05   24.4   0.1    3.2e-05   23.5   0.1    1.4  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 !  112.3   0.0   3.2e-36   2.8e-32       3     243 ..       9     254 ..       6     273 .. 0.81

  Alignments for each domain:
  == domain 1  score: 112.3 bits;  conditional E-value: 3.2e-36
                                       HHHHHHHHHHHHHHHHHHHHHTT.TSEEEESTTTCCHHHHHHHHHHHHHHHHHHHHHHHHSTTSEEEHHCHHHHCCC CS
                        Inositol_P   3 eevtkaavelaakagevlreefs.enelvieekskegeedlvtaadeaveelilealaekfpshkilgeetlakgek 78 
                                       ee+++++ ++a +a++ l++  + e+++ + +k+    ++++ +ad+ +e+li+e l+ +  + +i++ee+  + e 
  gi|385806025|ref|YP_005842423.1|   9 EELMNISRKIAEEASKELAKISQdERSFEHLDKG----KETI-KADKLSEDLIIEMLKNEGIRGTIVTEESEVIKE- 79 
                                       5666666777777777777766634444444333....5566.8**************************999988. PP

                                       T.SSSSSEEEEEEEEETHHHHHHT-SG-EEEEEEEE.....TTEEEEEEEEETTTTEEECEETTTEEEETCEEEEEC CS
                        Inositol_P  79 seltedgltwivDPiDGTknFvrgipqvaVsigllv.....egkpvlGviaqPllgqlysaakgkGaflngeklpls 150
                                          ++++ + i+DP+DG kn++rgi ++ Vsi++++        +v+G +  ++ ++++s +k  G f+n+ek +++
  gi|385806025|ref|YP_005842423.1|  80 ---GNENIIAIIDPLDGSKNYARGIKWCSVSIAFAEqrgngINDIVAGTVKPVFFNESFSFYKRGGVFVNNEKYYIK 153
                                       ...5555*****************************866333369******************************** PP

                                       TTSEGGGTEEEEEESSSSSSHHHHCHHHHHHHCCCCCH...EEEBESSHHHHHHHHHHTSTSEEEEEC..EBHHHHH CS
                        Inositol_P 151 rappiseallvtlfavssrkdtseasllekvesavsae...gvrsvgssalklaavaeGkadaylefg.rekkWDhA 223
                                       ++p i+++   + + +++++ ++   + +  e++ ++     +rs+gs+al+la+v  Gk+d +++++ ++ + D A
  gi|385806025|ref|YP_005842423.1| 154 KQPGIDKEKY-YAVYFDNDNAIET--VKNIREKLINRGyiaTFRSLGSAALELALVSIGKIDGFIDARsKLRIVDAA 227
                                       ***8877754.4466666666666..6666666666667778*************************99******** PP

                                       HHHHHHHHTTEEEEESSSC.......S CS
                        Inositol_P 224 AGeaileeaGGvvtdakge.......g 243
                                       AG+  + e GGvv  ++ge       +
  gi|385806025|ref|YP_005842423.1| 228 AGIGMIIENGGVVRGLDGEdfldidlK 254
                                       ******************955544443 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 !   23.5   0.1   3.6e-09   3.2e-05      57     117 ..      41      97 ..       9     114 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 3.6e-09
                            FBPase  57 tGdeqkklDvladeiliealkaseevkvlvSEEeeelivlerekegkyvvafDPlDGSSni 117
                                       +G e  k D l+++++ie+lk++++  ++v EE+e ++    e + +++ ++DPlDGS n 
  gi|385806025|ref|YP_005842423.1|  41 KGKETIKADKLSEDLIIEMLKNEGIRGTIVTEESEVIK----EGNENIIAIIDPLDGSKNY 97 
                                       699999**************************998654....3466789999******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1639.80
//
Query:       gi|385806026|ref|YP_005842424.1|  [L=986]
Description: isoleucyl-tRNA synthetase [Fervidicoccus fontis Kam940]
Scores for complete 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-165  550.2   0.4   6.9e-165  549.7   0.4    1.1  1  tRNA-synt_1     tRNA synthetases class I (I, L, M and V)
    2.6e-25   89.2   0.3    2.6e-25   89.2   0.3    2.0  2  Anticodon_1     Anticodon-binding domain of tRNA
    7.3e-23   80.9   2.8    3.6e-07   29.3   0.0    4.2  4  tRNA-synt_1g    tRNA synthetases class I (M)
    3.3e-10   39.8   1.1    2.9e-06   26.8   0.0    3.2  3  tRNA-synt_1e    tRNA synthetases class I (C) catalytic domain
    1.5e-08   34.3   0.1    5.6e-08   32.5   0.0    2.0  2  tRNA-synt_1_2   Leucyl-tRNA synthetase, Domain 2
    4.2e-05   22.6   0.0    0.00011   21.2   0.0    1.7  1  tRNA-synt_1f    tRNA synthetases class I (K)
    0.00062   19.7   0.7        1.5    8.9   0.3    3.6  2  DZR             Double zinc ribbon
     0.0037   16.6   4.3        5.7    6.4   0.1    4.3  4  zf-TFIIB        Transcription factor zinc-finger
     0.0098   15.9   6.2        1.5    8.9   0.3    3.8  3  zf-ACC          Acetyl-coA carboxylase zinc finger domain
  ------ inclusion threshold ------
      0.018   14.4   0.5       0.81    8.9   0.0    2.6  2  tRNA-synt_1b    tRNA synthetases class I (W and Y)
      0.029   13.8  13.2        4.1    6.9   0.1    4.3  4  zf-ribbon_3     zinc-ribbon domain
       0.03   13.8   0.2        5.7    6.5   0.1    2.8  2  DUF2688         Protein of unknown function (DUF2688)
        0.1   13.1   1.5         56    4.2   0.1    3.7  3  zf-IS66         zinc-finger binding domain of transposase IS6
       0.14   12.5   1.1        5.3    7.3   0.7    3.0  3  PSII_Pbs27      Photosystem II Pbs27
       0.18   12.2   0.5         21    5.6   0.0    3.1  2  DUF983          Protein of unknown function (DUF983)
       0.19   11.2  11.7       0.44   10.0   0.2    3.7  4  Mu-like_Com     Mu-like prophage protein Com
       0.19   11.5  16.2        5.1    6.9   0.9    4.4  4  zinc_ribbon_2   zinc-ribbon domain
       0.33   11.1   6.9        7.1    6.8   0.1    3.7  3  Zn-ribbon_8     Zinc ribbon domain
       0.52   10.3   6.1          3    7.9   0.2    3.4  3  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
       0.52   10.5   2.6        3.2    8.0   2.6    2.5  1  Bac_small_YrzI  Probable sporulation protein (Bac_small_yrzI)
       0.94    9.2   9.9         16    5.3   0.0    4.1  4  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
        1.1    9.2   9.1         19    5.4   0.1    3.9  3  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
        7.2    6.7   9.9         15    5.7   0.1    3.9  4  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
        8.1    6.5   7.1         52    3.9   0.1    3.6  3  zinc_ribbon_4   zinc-ribbon domain


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  549.7   0.4  9.2e-168  6.9e-165       5     600 ..      21     638 ..      18     640 .. 0.93

  Alignments for each domain:
  == domain 1  score: 549.7 bits;  conditional E-value: 9.2e-168
                       tRNA-synt_1   5 kWeeedvfkkele....kekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaie 77 
                                        W+e+++ kk l+    +++  + f++  gPP  +G +H Gha  ++ kd++iry+ +kG++v  + GwD+ Gl++e
  gi|385806026|ref|YP_005842424.1|  21 YWTENGIRKKVLKevwdSREGSEIFSFLEGPPTTNGYMHAGHARGRIYKDVMIRYHMIKGFRVWAQGGWDTQGLPVE 97 
                                       577766655544311115666888***************************************************** PP

                       tRNA-synt_1  78 akvekklgakekke.rkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladk 153
                                        +vekk+  k kke  +k+g+e+f+e++++ +++y++e+ ++ +rl v++D+++ y T ++++ e+v+   ++ +++
  gi|385806026|ref|YP_005842424.1|  98 LEVEKKFKVKSKKEiEEKIGVEKFIEECKKSVDHYISEWISDNERLAVWLDYEDAYQTRNPKYLETVWSFVKNAYEE 174
                                       *******98887762679*********************************************************** PP

                       tRNA-synt_1 154 gliyrgkklvnwstklktalselEv..eykdkkdalihvafpladkeevklviaTTtPeTllgdtavavnpeldyv. 227
                                       gl+y++  +v+ ++++ tals+ E     + +kd++++++ +  d++  ++ ++TTtP+T+++++a+avnp+ dyv 
  gi|385806026|ref|YP_005842424.1| 175 GLLYKSYSVVPRCPRCGTALSNHELslGSEIVKDPSLYFKVKSLDGDF-YFAVWTTTPWTIIANRALAVNPQSDYVl 250
                                       ************************965677799*****9999999988.**************************** PP

                       tRNA-synt_1 228 ..itkeklilaeallkslvkke..sekkiledergkeLegkevelpl..........vnrkipiiaddyvdkeaGtG 290
                                         i++ekl++ae ll+sl+ k   ++ ki+ +++g+eL+gk++ +pl             ++++++ dyv++ +GtG
  gi|385806026|ref|YP_005842424.1| 251 veIKGEKLLIAEPLLNSLLSKLqvKDAKITAKYKGSELVGKRYVHPLseevpknsncSPPECTVVSADYVTMTEGTG 327
                                       *****************9999864555*************************9998888999*************** PP

                       tRNA-synt_1 291 vVkiaPahdedDyevgkkynlevinildedgtlteeaaefeglkvfdarkkvveelkekglllkaekiehsvpfcer 367
                                       +V++aPah+++D+e++kky+lev ++l+++g + e+a+ f+g+  +da k+vve+lkekgl l+ e+ieh++p+c+r
  gi|385806026|ref|YP_005842424.1| 328 IVHTAPAHGPEDFETAKKYGLEVWTPLKDNGYFGEDAGIFSGMWFKDASKAVVEALKEKGLVLHYEEIEHEYPHCWR 404
                                       ***************************************************************************** PP

                       tRNA-synt_1 368 skkpiiyrateqWfvrvkeladaalkavekvqfvpkskekryaswleniqdWciSRqrwWGhriplfvsketeevvv 444
                                        ++p+iy+ t+qWf++ +++++ + + +++v+f p ++ +r+  w+e  +dWciSR+r+WG+++p+++  + + + v
  gi|385806026|ref|YP_005842424.1| 405 CGTPLIYYPTSQWFIKTTAIVNRMREYLKNVKFRPSWGYNRMDAWVEASRDWCISRERYWGTPLPIWICPKCGHIEV 481
                                       *************************************************************************9999 PP

                       tRNA-synt_1 445 reelkelvagreeeeaekkalekeakdkl....kkekgelekdedvlDvWFsSgswpfstlgypeedteelkkffpa 517
                                         +++el +   +  +  k+ +k  +d+l     k  +e+++++ v+DvW +Sg  +++ l+  ++ ++  k  fp 
  gi|385806026|ref|YP_005842424.1| 482 FGSIEELSK---AAGVDVKDPHKPYIDQLhikcPKCGEEMKREPFVMDVWADSGVAHTAALKQLNK-QHLHKYIFPY 554
                                       888888877...556666677778888887744444589***********************5555.5555668*** PP

                       tRNA-synt_1 518 dmlleGlDiirgWvarlillslaltgsePfkevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltli.ls 593
                                       ++ le   ++rgW+++l+++s+ l++s+Pfk + +hgl++d+eG+KmSKs+gNv+   + +kk+gad lRl+++  +
  gi|385806026|ref|YP_005842424.1| 555 SFALEPPEQVRGWFYTLLITSTVLNDSSPFKMLGMHGLILDAEGQKMSKSKGNVVFAREALKKHGADQLRLFMCyRN 631
                                       **************************************************************************878 PP

                       tRNA-synt_1 594 dvgrdin 600
                                       +  +di+
  gi|385806026|ref|YP_005842424.1| 632 SPWQDIR 638
                                       8888876 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 !   89.2   0.3   3.5e-28   2.6e-25       1     151 [.     686     839 ..     686     841 .. 0.89
   2 ?   -2.0   0.1       4.1   3.1e+03     121     150 ..     900     929 ..     872     932 .. 0.73

  Alignments for each domain:
  == domain 1  score: 89.2 bits;  conditional E-value: 3.5e-28
                       Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkra.aqevllevletllrl 76 
                                       d+wil++ +++ k+v e++e+++++ a +al++f+++d+++ y+ +v+pr ++e+++++++ a+++++++l+  + l
  gi|385806026|ref|YP_005842424.1| 686 DKWILTKEESVMKSVYESIENFDLHSASKALFDFLVEDVSRRYIVAVRPRVWTEENTKDKRaAYATIFTLLKHSIPL 762
                                       9*****************************************************99888555*************** PP

                       Anticodon_1  77 laPfmPfitEelwqr..eeeelgkkesimlae.wpekaeelekeleeeevellkeivkairklrselkikpsselkv 150
                                       +  f+Pfi+E+++q   ++  ++ kes+ml+   p  +++l++++  e ve + +++ +i ++r+e +ik++ +lk+
  gi|385806026|ref|YP_005842424.1| 763 IGIFTPFIAEYIYQTvwRKVGIEPKESVMLEVaKPLPKDYLDNTA-FENVEEAMKVIDTIVSYRGERGIKRRMPLKK 838
                                       ****************977788999****9873443444554444.4689998999999999**********99765 PP

                       Anticodon_1 151 v 151
                                       +
  gi|385806026|ref|YP_005842424.1| 839 I 839
                                       4 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.1
                       Anticodon_1 121 eevellkeivkairklrselkikpsselkv 150
                                        e+ l+ke+++ i+ +r+e+++  s +++v
  gi|385806026|ref|YP_005842424.1| 900 YELGLAKEVIRRIQIMRKENNLEYSDKVNV 929
                                       366788999999999999999988877655 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 !   27.8   0.1   1.4e-09     1e-06      10     100 ..      54     144 ..      50     202 .. 0.59
   2 !   20.4   0.1   2.4e-07   0.00018     159     238 ..     392     469 ..     375     478 .. 0.88
   3 ?   -2.9   0.0       2.9   2.2e+03     136     148 ..     508     520 ..     502     546 .. 0.79
   4 !   29.3   0.0   4.8e-10   3.6e-07     321     373 ..     594     646 ..     567     652 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 1.4e-09
                                       -SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHT.TS-HHHHHHHHHHHHHHHHHHTT--- CS
                      tRNA-synt_1g  10 angklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAeke.gvtpeelvekvheeikelfkklnisf 85 
                                       +ng +H Gh++  i  D+++Ry+  +g  v+  +g D+ G p+el+ ek+ +v+ ++ + + +  +++  ++++ s 
  gi|385806026|ref|YP_005842424.1|  54 TNGYMHAGHARGRIYKDVMIRYHMIKGFRVWAQGGWDTQGLPVELEVEKKfKVKSKKEI-EEKIGVEKFIEECKKSV 129
                                       79******************************************998875233333333.33444555666666666 PP

                                       SEEEETTSHHHHHHH CS
                      tRNA-synt_1g  86 dkygrttseehkelv 100
                                       d+y++   +++++l+
  gi|385806026|ref|YP_005842424.1| 130 DHYISEWISDNERLA 144
                                       666655544444443 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 2.4e-07
                                       -E................EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS- CS
                      tRNA-synt_1g 159 leptelinpksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdldwGi 235
                                       +e  e + p++  +g+  ++  t+++f k  ++ ++++e++ ++ k  ++   + + +w+++  +d++isr+  wG 
  gi|385806026|ref|YP_005842424.1| 392 YEEIEHEYPHCWRCGTPLIYYPTSQWFIKTTAIVNRMREYL-KNVKFRPSWGYNRMDAWVEA-SRDWCISRERYWGT 466
                                       555566779********************************.777778899999999***99.8************* PP

                                       EET CS
                      tRNA-synt_1g 236 pvP 238
                                       p+P
  gi|385806026|ref|YP_005842424.1| 467 PLP 469
                                       *99 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 2.9
                                       EE........-TT CS
                      tRNA-synt_1g 136 egtCPkckseear 148
                                       + +CPkc++e +r
  gi|385806026|ref|YP_005842424.1| 508 HIKCPKCGEEMKR 520
                                       6689999888766 PP

  == domain 4  score: 29.3 bits;  conditional E-value: 4.8e-10
                                       EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHHHHH CS
                      tRNA-synt_1g 321 ltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswedfve 373
                                       l  eg+K+SkS+g+vv+a+eal++  ad+lR ++++ ++  +D+ +  +++ e
  gi|385806026|ref|YP_005842424.1| 594 LDAEGQKMSKSKGNVVFAREALKKHGADQLRLFMCYRNSPWQDIRYVDKEISE 646
                                       5789******************************************9988765 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.1   0.00057      0.43      17     124 ..      52     180 ..      38     184 .. 0.70
   2 !   26.8   0.0   3.9e-09   2.9e-06     240     283 ..     587     630 ..     572     648 .. 0.81
   3 ?   -2.5   0.0       3.3   2.4e+03      52      68 ..     680     696 ..     655     751 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00057
                                       EBTTS--BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTTS-...................HHH CS
                      tRNA-synt_1e  17 ptvydashlGhaRslvafDilrrilqalgYdvqfvqnvtDidDkiikrareeeks...................vke 74 
                                       pt   ++h GhaR  +  D++ r+   +g+ v   q   D +   ++  +e++ +                   +k+
  gi|385806026|ref|YP_005842424.1|  52 PTTNGYMHAGHARGRIYKDVMIRYHMIKGFRVW-AQGGWDTQGLPVELEVEKKFKvkskkeieekigvekfieeCKK 127
                                       68999*******************999999884.4444444333333222222223334444557888888888888 PP

                                       HHHHHHHHHHHHHHHTT--...--SB--BGGGGHHHHHHHHHHHHHTTSEEE- CS
                      tRNA-synt_1e  75 laekfieefkkdleaLnvl...kptleprvsekvdeiielvekliekgyaYav 124
                                        ++++i+e+ +d e L v    +  +++r  ++++ +  +v++  e+g  Y++
  gi|385806026|ref|YP_005842424.1| 128 SVDHYISEWISDNERLAVWldyEDAYQTRNPKYLETVWSFVKNAYEEGLLYKS 180
                                       88888888888888888852224567888888888888888888888887765 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 3.9e-09
                                       EEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS CS
                      tRNA-synt_1e 240 yflhnghlkiegekmsksLknfitikdvlkkfdprqlRllllsa 283
                                         +h  +l  eg+kmsks +n+++ +++lkk+ + qlRl++   
  gi|385806026|ref|YP_005842424.1| 587 LGMHGLILDAEGQKMSKSKGNVVFAREALKKHGADQLRLFMCYR 630
                                       45899999*******************************99754 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 3.3
                                       EEBB--SHHHHHHHHHT CS
                      tRNA-synt_1e  52 qnvtDidDkiikraree 68 
                                       +n+t++d  i+++ ++ 
  gi|385806026|ref|YP_005842424.1| 680 KNITNVDKWILTKEESV 696
                                       56666665555554444 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 ?   -2.4   0.1       3.8   2.9e+03      52      68 ..     112     128 ..     101     137 .. 0.76
   2 !   32.5   0.0   7.5e-11   5.6e-08      13     137 ..     212     351 ..     208     380 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3.8
                     tRNA-synt_1_2  52 aekkkelaafieevkkk 68 
                                        e+k  +++fiee+kk+
  gi|385806026|ref|YP_005842424.1| 112 IEEKIGVEKFIEECKKS 128
                                       56677799999999986 PP

  == domain 2  score: 32.5 bits;  conditional E-value: 7.5e-11
                     tRNA-synt_1_2  13 efkvees..eeklevfttrpdtlfGvtfvalapehplvekl.aekkkelaa.fieevkkksesereletkekeGv.f 84 
                                        fkv++   +  + v+tt p t++    +a+ p+++ v    + +k  +a+ +++++ +k + + ++ t++ +G   
  gi|385806026|ref|YP_005842424.1| 212 YFKVKSLdgDFYFAVWTTTPWTIIANRALAVNPQSDYVLVEiKGEKLLIAEpLLNSLLSKLQVKDAKITAKYKGSeL 288
                                       56776662234689*******************99987655255555554437788777777777777888888868 PP

                     tRNA-synt_1_2  85 tglkaihPitgek..........ipiwvanyvlmeygtgavmavPahdqrDfeFakkynlpik 137
                                        g   +hP+++e             +  a+yv m+ gtg v + Pah  +Dfe akky+l++ 
  gi|385806026|ref|YP_005842424.1| 289 VGKRYVHPLSEEVpknsncsppeCTVVSADYVTMTEGTGIVHTAPAHGPEDFETAKKYGLEVW 351
                                       9*********998889999999999***********************************985 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 !   21.2   0.0   1.5e-07   0.00011     259     319 ..     576     639 ..     570     664 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.5e-07
                      tRNA-synt_1f 259 eilggeaPekv..vYelillkggekmssSkGnvltledwlevaepevlrfli.lrrkPkkakkl 319
                                        +l+ + P k+  +  lil+ +g+kms+SkGnv+  +++l+    + lr+++ +r+ P + ++ 
  gi|385806026|ref|YP_005842424.1| 576 TVLNDSSPFKMlgMHGLILDAEGQKMSKSKGNVVFAREALKKHGADQLRLFMcYRNSPWQDIRY 639
                                       67788888776557899***********************999988888655278888887764 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.071        53      30      40 ..     186     196 ..     123     200 .. 0.82
   2 !    8.9   0.3     0.002       1.5      15      39 ..     402     519 ..     392     523 .. 0.57

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.071
                               DZR  30 rCpsCgekvdp 40 
                                       rCp+Cg+++++
  gi|385806026|ref|YP_005842424.1| 186 RCPRCGTALSN 196
                                       56666666554 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.002
                               DZR  15 CseCgtklkavaa................................................................ 27 
                                       C +Cgt+l  +++                                                                
  gi|385806026|ref|YP_005842424.1| 402 CWRCGTPLIYYPTsqwfikttaivnrmreylknvkfrpswgynrmdawveasrdwcisrerywgtplpiwicpkcgh 478
                                       55555555555555555555555555555555555555555555555555555555555555555555444444444 PP

                               DZR  28 .............................edrCpsCgekvd 39 
                                                                    +++Cp+Cge+++
  gi|385806026|ref|YP_005842424.1| 479 ievfgsieelskaagvdvkdphkpyidqlHIKCPKCGEEMK 519
                                       44445555555566677777777888888888888888765 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.012       8.6       2      15 ..     187     200 ..     186     206 .. 0.82
   2 ?    2.6   0.1      0.11        83      18      26 ..     469     477 ..     462     480 .. 0.78
   3 !    6.4   0.1    0.0077       5.7       1      10 [.     510     519 ..     510     531 .. 0.89
   4 ?   -1.5   0.0       2.2   1.7e+03      29      38 ..     661     670 ..     660     673 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.012
                          zf-TFIIB   2 CPkCqdeleeserg 15 
                                       CP+C+++l  +e++
  gi|385806026|ref|YP_005842424.1| 187 CPRCGTALSNHELS 200
                                       ********999884 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.11
                          zf-TFIIB  18 eidyCpqCr 26 
                                       +i+ Cp+C+
  gi|385806026|ref|YP_005842424.1| 469 PIWICPKCG 477
                                       677777775 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0077
                          zf-TFIIB   1 kCPkCqdele 10 
                                       kCPkC+ e++
  gi|385806026|ref|YP_005842424.1| 510 KCPKCGEEMK 519
                                       8*******98 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 2.2
                          zf-TFIIB  29 Wldrgelekl 38 
                                       +++++el+k+
  gi|385806026|ref|YP_005842424.1| 661 FISYAELDKW 670
                                       8899****** PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.018        13       3      16 ..     186     199 ..     186     200 .. 0.89
   2 ?    1.7   0.3      0.37   2.8e+02       4       9 ..     473     478 ..     471     479 .. 0.74
   3 !    8.9   0.3    0.0021       1.5       2      14 ..     509     521 ..     509     523 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.018
                            zf-ACC   3 KCpsCgemlykkeL 16 
                                       +Cp+Cg+ l + eL
  gi|385806026|ref|YP_005842424.1| 186 RCPRCGTALSNHEL 199
                                       6********99887 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.37
                            zf-ACC   4 CpsCge 9  
                                       Cp+Cg+
  gi|385806026|ref|YP_005842424.1| 473 CPKCGH 478
                                       888886 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0021
                            zf-ACC   2 tKCpsCgemlykk 14 
                                       +KCp+Cge + ++
  gi|385806026|ref|YP_005842424.1| 509 IKCPKCGEEMKRE 521
                                       8*******98875 PP

>> tRNA-synt_1b  tRNA synthetases class I (W and Y)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0011      0.81     188     214 ..     590     614 ..     576     710 .. 0.79
   2 ?    2.9   0.0     0.074        56      76     113 ..     830     867 ..     804     886 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0011
                                       ET-BBSTTSSSBTTCETTCGC-BTTCC CS
                      tRNA-synt_1b 188 vplltgldGekKmSKSagnsaIfLdde 214
                                       + l+ +++G+ KmSKS+gn ++f  + 
  gi|385806026|ref|YP_005842424.1| 590 HGLILDAEGQ-KMSKSKGN-VVFAREA 614
                                       33888999**.********.7775544 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.074
                                       HHHTCHTTTEEEEETHHHHTTHHHHHHHHHHHTTCBHH CS
                      tRNA-synt_1b  76 lakgldpekaevvlqsewlehlelaellrdlgklgsln 113
                                       +++ ++++k+ +++ +e+ e++e++ l++++++++s++
  gi|385806026|ref|YP_005842424.1| 830 IKRRMPLKKIVILWSNEIKEKEEYISLISTMANITSVE 867
                                       67778999*************************99987 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.4     0.043        32       4      10 ..     186     192 ..     185     196 .. 0.80
   2 ?    4.1   0.2     0.044        33       4      11 ..     401     408 ..     398     410 .. 0.84
   3 ?    5.3   0.3     0.019        14       5      11 ..     473     479 ..     472     481 .. 0.73
   4 ?    6.9   0.1    0.0055       4.1       3      10 ..     509     516 ..     504     519 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.043
                       zf-ribbon_3   4 rCPnCGa 10 
                                       rCP+CG+
  gi|385806026|ref|YP_005842424.1| 186 RCPRCGT 192
                                       7999998 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.044
                       zf-ribbon_3   4 rCPnCGap 11 
                                       +C++CG+p
  gi|385806026|ref|YP_005842424.1| 401 HCWRCGTP 408
                                       8*****96 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.019
                       zf-ribbon_3   5 CPnCGap 11 
                                       CP+CG++
  gi|385806026|ref|YP_005842424.1| 473 CPKCGHI 479
                                       8888875 PP

  == domain 4  score: 6.9 bits;  conditional E-value: 0.0055
                       zf-ribbon_3   3 vrCPnCGa 10 
                                       ++CP+CG+
  gi|385806026|ref|YP_005842424.1| 509 IKCPKCGE 516
                                       56666664 PP

>> DUF2688  Protein of unknown function (DUF2688)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1    0.0076       5.7       6      24 ..     183     201 ..     179     207 .. 0.83
   2 ?    4.1   0.0     0.044        33       9      18 ..     401     410 ..     398     416 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0076
                           DUF2688   6 VtTqCrRCGkslstlsrSL 24 
                                       V  +C RCG++ls  + SL
  gi|385806026|ref|YP_005842424.1| 183 VVPRCPRCGTALSNHELSL 201
                                       6679*********988887 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.044
                           DUF2688   9 qCrRCGksls 18 
                                       +C RCG++l 
  gi|385806026|ref|YP_005842424.1| 401 HCWRCGTPLI 410
                                       9*******95 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.32   2.4e+02       3      11 ..     186     194 ..     185     215 .. 0.77
   2 ?    2.8   0.0      0.21   1.6e+02       3      11 ..     472     482 ..     471     504 .. 0.76
   3 ?    4.2   0.1     0.075        56       3      14 ..     510     521 ..     509     525 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.32
                           zf-IS66   3 tCpcCGgll 11 
                                        Cp CG++l
  gi|385806026|ref|YP_005842424.1| 186 RCPRCGTAL 194
                                       6*****954 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.21
                           zf-IS66   3 tCpcCGg.l.l 11 
                                       +Cp+CG+ +  
  gi|385806026|ref|YP_005842424.1| 472 ICPKCGHiEvF 482
                                       6*****97754 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.075
                           zf-IS66   3 tCpcCGgllkpi 14 
                                       +Cp+CG ++k+ 
  gi|385806026|ref|YP_005842424.1| 510 KCPKCGEEMKRE 521
                                       6*****999875 PP

>> PSII_Pbs27  Photosystem II Pbs27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.7    0.0071       5.3      50      89 ..      99     138 ..      96     153 .. 0.83
   2 ?    1.5   0.0      0.46   3.5e+02      42      84 ..     415     457 ..     365     462 .. 0.83
   3 ?   -2.4   0.0       7.4   5.5e+03      36      49 ..     794     807 ..     743     840 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0071
                        PSII_Pbs27  50 evvktlresleldkkddakreraakaakesireyvskYrs 89 
                                       ev k+ +   + +++++  +e+++++ k+s+  y+s++ s
  gi|385806026|ref|YP_005842424.1|  99 EVEKKFKVKSKKEIEEKIGVEKFIEECKKSVDHYISEWIS 138
                                       6777777778888889999*******************43 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.46
                        PSII_Pbs27  42 kaYlkdarevvktlresleldkkddakreraakaakesireyv 84 
                                       +++  ++ ++v+ +re+l+  k   +  +++++a +e++r++ 
  gi|385806026|ref|YP_005842424.1| 415 SQWFIKTTAIVNRMREYLKNVKFRPSWGYNRMDAWVEASRDWC 457
                                       56677899************99888999999999999999995 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 7.4
                        PSII_Pbs27  36 adkalpkaYlkdar 49 
                                         k+lpk+Yl ++ 
  gi|385806026|ref|YP_005842424.1| 794 VAKPLPKDYLDNTA 807
                                       44556666665442 PP

>> DUF983  Protein of unknown function (DUF983)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.029        21       6      22 ..     182     198 ..     178     206 .. 0.86
   2 ?    3.2   0.1      0.15   1.2e+02       8      21 ..     508     521 ..     505     527 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.029
                            DUF983   6 kvadaCeaCgldlshar 22 
                                       +v+++C++Cg+ ls ++
  gi|385806026|ref|YP_005842424.1| 182 SVVPRCPRCGTALSNHE 198
                                       689**********9987 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.15
                            DUF983   8 adaCeaCgldlsha 21 
                                       + +C++Cg++++++
  gi|385806026|ref|YP_005842424.1| 508 HIKCPKCGEEMKRE 521
                                       669*******9987 PP

>> Mu-like_Com  Mu-like prophage protein Com
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0059       4.4      26      33 ..     186     193 ..     180     206 .. 0.76
   2 ?   -2.6   1.3       5.2   3.9e+03      27      32 ..     402     407 ..     400     408 .. 0.89
   3 ?   -0.7   0.1       1.3   9.8e+02      27      32 ..     473     478 ..     470     482 .. 0.84
   4 ?   10.0   0.2   0.00059      0.44      20      31 ..     504     515 ..     502     517 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0059
                       Mu-like_Com  26 KCPRCGtL 33 
                                       +CPRCGt 
  gi|385806026|ref|YP_005842424.1| 186 RCPRCGTA 193
                                       7******5 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5.2
                       Mu-like_Com  27 CPRCGt 32 
                                       C RCGt
  gi|385806026|ref|YP_005842424.1| 402 CWRCGT 407
                                       99***9 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.3
                       Mu-like_Com  27 CPRCGt 32 
                                       CP+CG 
  gi|385806026|ref|YP_005842424.1| 473 CPKCGH 478
                                       ****96 PP

  == domain 4  score: 10.0 bits;  conditional E-value: 0.00059
                       Mu-like_Com  20 lDeltiKCPRCG 31 
                                       +D+l iKCP+CG
  gi|385806026|ref|YP_005842424.1| 504 IDQLHIKCPKCG 515
                                       699********9 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1    0.0086       6.5       1      11 [.     186     196 ..     184     198 .. 0.71
   2 ?    1.9   0.2      0.27     2e+02       2       9 ..     402     409 ..     401     409 .. 0.78
   3 ?    4.5   0.4     0.039        30      16      21 ..     473     478 ..     472     479 .. 0.60
   4 ?    6.9   0.9    0.0069       5.1       1       8 [.     510     517 ..     510     520 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0086
                     zinc_ribbon_2   1 fCpnCGaelqd 11 
                                       +Cp+CG+ l++
  gi|385806026|ref|YP_005842424.1| 186 RCPRCGTALSN 196
                                       57888777665 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.27
                     zinc_ribbon_2   2 CpnCGael 9  
                                       C++CG++l
  gi|385806026|ref|YP_005842424.1| 402 CWRCGTPL 409
                                       99999875 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.039
                     zinc_ribbon_2  16 CpyCGt 21 
                                       Cp+CG+
  gi|385806026|ref|YP_005842424.1| 473 CPKCGH 478
                                       566655 PP

  == domain 4  score: 6.9 bits;  conditional E-value: 0.0069
                     zinc_ribbon_2   1 fCpnCGae 8  
                                       +Cp+CG+e
  gi|385806026|ref|YP_005842424.1| 510 KCPKCGEE 517
                                       79999988 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1      0.15   1.1e+02      27      36 ..     185     194 ..     178     196 .. 0.77
   2 ?    2.8   0.0      0.18   1.3e+02      29      35 ..     473     480 ..     466     492 .. 0.76
   3 ?    6.8   0.1    0.0095       7.1      26      38 ..     508     520 ..     494     521 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.15
                       Zn-ribbon_8  27 taCPeCgsev 36 
                                       + CP+Cg ++
  gi|385806026|ref|YP_005842424.1| 185 PRCPRCGTAL 194
                                       45****9865 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.18
                       Zn-ribbon_8  29 CPeCgs.e 35 
                                       CP+Cg+ e
  gi|385806026|ref|YP_005842424.1| 473 CPKCGHiE 480
                                       88887655 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0095
                       Zn-ribbon_8  26 ltaCPeCgsevrr 38 
                                        ++CP+Cg+e++r
  gi|385806026|ref|YP_005842424.1| 508 HIKCPKCGEEMKR 520
                                       567******9998 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1       1.1   8.6e+02       3       9 ..     185     191 ..     180     193 .. 0.84
   2 ?    7.9   0.2    0.0041         3      19      27 ..     470     478 ..     466     478 .. 0.93
   3 ?    2.9   0.1      0.15   1.1e+02      21      28 ..     510     517 ..     501     519 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 1.1
                    PhnA_Zn_Ribbon   3 pkCplCa 9  
                                       p Cp C+
  gi|385806026|ref|YP_005842424.1| 185 PRCPRCG 191
                                       8899995 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0041
                    PhnA_Zn_Ribbon  19 llvCpeCah 27 
                                       +++Cp+C+h
  gi|385806026|ref|YP_005842424.1| 470 IWICPKCGH 478
                                       8*******9 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.15
                    PhnA_Zn_Ribbon  21 vCpeCahE 28 
                                        Cp+C++E
  gi|385806026|ref|YP_005842424.1| 510 KCPKCGEE 517
                                       47777776 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 ?    8.0   2.6    0.0043       3.2      14      43 ..     102     133 ..     100     135 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0043
                    Bac_small_YrzI  14 KRk..yseeEiereqqiekieeemkdrqlkYy 43 
                                       K++  +s+ Eie ++ +ek+ ee k+++ +Y 
  gi|385806026|ref|YP_005842424.1| 102 KKFkvKSKKEIEEKIGVEKFIEECKKSVDHYI 133
                                       666679*********************99997 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 ?    4.6   0.5     0.034        26       6      12 ..     187     193 ..     185     197 .. 0.85
   2 ?    0.1   0.1      0.91   6.8e+02       5      13 ..     401     409 ..     398     410 .. 0.78
   3 ?    2.2   0.2      0.19   1.5e+02      24      29 ..     473     478 ..     472     480 .. 0.62
   4 ?    5.3   0.0     0.021        16       6      15 ..     511     520 ..     499     522 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.034
                     zf-NADH-PPase   6 CgrCGap 12 
                                       C+rCG++
  gi|385806026|ref|YP_005842424.1| 187 CPRCGTA 193
                                       *****97 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.91
                     zf-NADH-PPase   5 FCgrCGapt 13 
                                        C rCG+p 
  gi|385806026|ref|YP_005842424.1| 401 HCWRCGTPL 409
                                       6779***95 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.19
                     zf-NADH-PPase  24 CpaCgl 29 
                                       Cp Cg+
  gi|385806026|ref|YP_005842424.1| 473 CPKCGH 478
                                       666666 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.021
                     zf-NADH-PPase   6 CgrCGaptep 15 
                                       C++CG ++++
  gi|385806026|ref|YP_005842424.1| 511 CPKCGEEMKR 520
                                       8888888876 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 ?    4.2   0.0     0.056        42      19      27 ..     185     193 ..     173     201 .. 0.81
   2 ?    5.4   0.1     0.025        19      14      28 ..     463     480 ..     460     489 .. 0.74
   3 ?    3.0   0.1      0.13        99      19      27 ..     509     517 ..     505     524 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.056
                     Zn_Tnp_IS1595  19 fvCPhCgsr 27 
                                       ++CP+Cg +
  gi|385806026|ref|YP_005842424.1| 185 PRCPRCGTA 193
                                       79*****76 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.025
                     Zn_Tnp_IS1595  14 rWpng...fvCPhCgsrk 28 
                                        W++     +CP+Cg+ +
  gi|385806026|ref|YP_005842424.1| 463 YWGTPlpiWICPKCGHIE 480
                                       6888886667*****874 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.13
                     Zn_Tnp_IS1595  19 fvCPhCgsr 27 
                                         CP+Cg +
  gi|385806026|ref|YP_005842424.1| 509 IKCPKCGEE 517
                                       56*****87 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1      0.02        15       1      10 [.     186     195 ..     186     206 .. 0.86
   2 ?   -1.4   0.0       3.3   2.5e+03       1      10 [.     401     410 ..     401     412 .. 0.83
   3 ?   -0.3   0.8       1.5   1.1e+03       2       7 ..     473     478 ..     473     479 .. 0.91
   4 ?    4.6   0.1     0.045        33       1      13 [.     510     522 ..     510     535 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.02
                    DNA_ligase_ZBD   1 hCPvCGsavv 10 
                                       +CP CG+a+ 
  gi|385806026|ref|YP_005842424.1| 186 RCPRCGTALS 195
                                       5******986 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.3
                    DNA_ligase_ZBD   1 hCPvCGsavv 10 
                                       hC  CG++++
  gi|385806026|ref|YP_005842424.1| 401 HCWRCGTPLI 410
                                       7778***985 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.5
                    DNA_ligase_ZBD   2 CPvCGs 7  
                                       CP CG+
  gi|385806026|ref|YP_005842424.1| 473 CPKCGH 478
                                       ****96 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.045
                    DNA_ligase_ZBD   1 hCPvCGsavvRee 13 
                                       +CP CG +  Re+
  gi|385806026|ref|YP_005842424.1| 510 KCPKCGEEMKREP 522
                                       6*****9988875 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.2      0.21   1.5e+02      27      33 ..     186     192 ..     184     194 .. 0.61
   2 ?    1.9   0.3      0.29   2.2e+02      28      34 ..     473     479 ..     472     479 .. 0.88
   3 ?    3.9   0.1      0.07        52      26      33 ..     509     516 ..     505     519 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.21
                     zinc_ribbon_4  27 rCskCgh 33 
                                       rC++Cg+
  gi|385806026|ref|YP_005842424.1| 186 RCPRCGT 192
                                       4555554 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.29
                     zinc_ribbon_4  28 CskCghv 34 
                                       C+kCgh+
  gi|385806026|ref|YP_005842424.1| 473 CPKCGHI 479
                                       9999996 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.07
                     zinc_ribbon_4  26 vrCskCgh 33 
                                       ++C+kCg+
  gi|385806026|ref|YP_005842424.1| 509 IKCPKCGE 516
                                       78888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (986 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       869  (0.048469); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                        35  (0.00195214); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.88u 0.34s 00:00:01.22 Elapsed: 00:00:00.56
# Mc/sec: 5338.81
//
Query:       gi|385806027|ref|YP_005842425.1|  [L=270]
Description: nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase [Fervidicoccus fontis Kam940]
Scores for 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-26   90.7   0.0    1.2e-25   90.4   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 !   90.4   0.0   6.6e-30   1.2e-25       5     258 ..      10     241 ..       8     244 .. 0.88

  Alignments for each domain:
  == domain 1  score: 90.4 bits;  conditional E-value: 6.6e-30
                                       EEBB-STTHHHHHHHHHHHHHHHHHHTTESEEEEETTTTTBSSSHHHHHHHHBHSSSHHHHHHHHHHHHHTEEEEEE CS
                      CN_hydrolase   5 vQlpqkaadleanlqklleliaeAarkgadLivlPElfitgykeeahfleaAeaglgetlallaalarkngiavvig 81 
                                       vQ +    dle+nl +l + +++++ ++ ++ivlPE+++t  ke  ++    +  l  +l +l  l+++ g++ v g
  gi|385806027|ref|YP_005842425.1|  10 VQHKR-EDDLEKNLMRLIKNLRAIKIEKNSIIVLPEVWLT--KEILEYS---T--LKSFLTQLEILSNELGVWMVPG 78 
                                       55555.579**************9999*************..5555555...5..789******************* PP

                                       EEEEECCTTEEEEEEEEEEEETTSEEEEEEE-SS--EECTTSCECCGHHTSCS-SSS-EEEETTEEEEEEEGGGGGS CS
                      CN_hydrolase  82 liereltngklqayntavlldldgklvgkyrKlhLfpgeprpptaverelfepgdgipvfdtpvgkiGaaiCyeigf 158
                                        ++ + +ngk   + + ++++++g+  +++ K+      +   +++e +  +    ++v d+ ++kiG+ iC +  +
  gi|385806027|ref|YP_005842425.1|  79 AFYVR-ENGKA--LSKSYIISPKGESKAISEKIFP---SYPMKERNEISPGSF---LKVEDLGFTKIGVIICVDAMY 146
                                       99987.9****..*******************993...455555555555555...44669**************** PP

                                       HHHHHHHHHTT-SEEEE.BH.GCCCTCHHHHHHHHHHHHHHHHHHTSEEEEEEBEEEHCETTEEEE--EEEE-TTS- CS
                      CN_hydrolase 159 pellralalkgaeilvn.lserapvpksmgppqwellgraralengcfviaanqvggyeqlilwpvghSaiidpdGr 234
                                       pel+r la +gae+++n        p+++ + + e ++ +ra en ++ + +  +g+  ++++  +g+S ++dp Gr
  gi|385806027|ref|YP_005842425.1| 147 PELSRLLAIRGAELILNpS----SIPENRVQLW-ESISVTRASENTVYWASVILTGTSYPDGRKVLGGSIVVDPGGR 218
                                       *****************42....6899999998.***********************99****************** PP

                                       EEEECCSSSTEEEEEEEEHHHHHH CS
                      CN_hydrolase 235 ilaglgeeeegvliaeidladvra 258
                                       i+ + g  ee ++ +++d + ++ 
  gi|385806027|ref|YP_005842425.1| 219 IILKSGASEE-IVRVTLDKNVLEN 241
                                       *******997.9999999877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); 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: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 1601.92
//
Query:       gi|385806028|ref|YP_005842426.1|  [L=203]
Description: hypothetical protein FFONT_0986 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-05   23.4   5.9      0.044   13.6   4.0    2.1  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 !    9.9   0.0   3.4e-05      0.61       3      69 ..      29      96 ..      27     117 .. 0.74
   2 !   13.6   4.0   2.5e-06     0.044     141     213 ..     124     197 ..     110     198 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 3.4e-05
                              VIT1  3 davlGanDGLvspfalvaGlsaaslgssktvllaGlaell.AGaiSMgiGeYlsvkserdlekaerkr 69
                                       +v+   DGL++ +++++G   ++ +++ + + a + +++  G +S  iG Y+  ++er  e +e ++
  gi|385806028|ref|YP_005842426.1| 29 LFVMNSFDGLLTSIGVIIGTHISGSKDPIVYIWAIVGGIItVGIFSNFIGVYMTERAERINEVKEIEK 96
                                      5888899*************9766544444444445555525999***********999666665554 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 2.5e-06
                              VIT1 141 salsfliGgliPllpylf.vesvglalvvsiavtllalllfGavkalltgssklvsalrmlliGalAaaaayli 213
                                       ++++f + +++Pl+  l  v   +  l+ s++++ + ++++Ga  +++++ s++++a r  liG+ A+a  y++
  gi|385806028|ref|YP_005842426.1| 124 MGALFSLISILPLILSLKgVILLDHSLISSVVMSNIQIAFIGAYLGKISKESVIKEAARFSLIGLSATAFLYIV 197
                                       45556666666666665434469999*****************************************9988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1082  (0.0603492); expected 358.6 (0.02)
Passed bias filter:                      590  (0.0329076); 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: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1186.85
//
Query:       gi|385806029|ref|YP_005842427.1|  [L=95]
Description: 30S ribosomal protein S26e [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-25   88.7   3.2    3.6e-25   88.5   3.2    1.0  1  Ribosomal_S26e  Ribosomal protein S26e
     0.0063   16.7   0.4       0.14   12.4   0.2    2.5  2  zf-RING_7       C4-type zinc ribbon domain
  ------ inclusion threshold ------
      0.023   14.9   2.1       0.22   11.7   2.6    1.9  2  Yippee-Mis18    Yippee zinc-binding/DNA-binding /Mis18, centr
        4.9    7.2   9.2       0.65   10.0   1.1    2.4  2  zf-dskA_traR    Prokaryotic dksA/traR C4-type zinc finger


Domain annotation for each model (and alignments):
>> Ribosomal_S26e  Ribosomal protein S26e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.5   3.2   7.9e-29   3.6e-25       1      97 [.       1      93 [.       1      95 [] 0.96

  Alignments for each domain:
  == domain 1  score: 88.5 bits;  conditional E-value: 7.9e-29
                                      X--S-SSTT----S-S---EEE-TTT--EEES----EEEEEEESS-SSSHHHHTTSBSSSS----EEEEEEE--HHHHH CS
                    Ribosomal_S26e  1 mtkKRrnngrnkkgrghvkivrCsncarlvpkdKaikrfvvrniveaaavrdlseasvyeeyalPklYiklaycvscai 79
                                      m+kKR ++gr+k g+g+v+ ++C+nc+rl+p dKai     ++ +e + +++l+++      ++ ++ +k++ycvscai
  gi|385806029|ref|YP_005842427.1|  1 MPKKRESRGRHKGGKGYVERIQCDNCGRLIPEDKAICVERYYSPIEPQLAKELEKK----GAIITRYPVKKCYCVSCAI 75
                                      9*****************************************************99....678889999********** PP

                                      HTTSS----TTTTS--S- CS
                    Ribosomal_S26e 80 hskvvrvRsredrknrep 97
                                      h  +v+vR++e+rk +++
  gi|385806029|ref|YP_005842427.1| 76 HLGIVKVRAEEERKAKQN 93
                                      **************9975 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 !   12.4   0.2     3e-05      0.14      24      32 ..      21      29 ..       5      30 .. 0.80
   2 ?    2.0   0.0     0.055   2.4e+02      10      25 ..      46      61 ..      45      64 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3e-05
                                      EE-TTT--E CS
                         zf-RING_7 24 vtCpeCGRI 32
                                      ++C++CGR+
  gi|385806029|ref|YP_005842427.1| 21 IQCDNCGRL 29
                                      89******8 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.055
                                      -CCHHHHHCCSTB-EE CS
                         zf-RING_7 10 ppqvlselragdevvt 25
                                       pq+ +el +++ ++t
  gi|385806029|ref|YP_005842427.1| 46 EPQLAKELEKKGAIIT 61
                                      69******99988765 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 ?    3.4   0.1     0.019        85      49      65 ..      14      30 ..       3      33 .. 0.71
   2 ?   11.7   2.6   4.9e-05      0.22       3      81 ..      21      93 ..      19      95 .] 0.73

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.019
                                      TTEEEEEEEETTT--EE CS
                      Yippee-Mis18 49 gkctystlsCkgCnsvl 65
                                      gk  +++++C +C+  +
  gi|385806029|ref|YP_005842427.1| 14 GKGYVERIQCDNCGRLI 30
                                      34678899999999765 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 4.9e-05
                                      EEETTTS-EEEECCCEEEEECCCEEEES---CCCEEEECEEEETTSTTEEEEEEEETTT--EEEEEEEECSCCCCCCCT CS
                      Yippee-Mis18  3 fqCkkCktilgdslqlvsegralnivvlkkvtrnvvvgkelvtdeegkctystlsCkgCnsvlGwkYksteeelkykrg 81
                                      +qC +C + +    +++ e+ +      ++++ ++  + e++    +++ +++ +C +C+ +lG + +++eee k+k++
  gi|385806029|ref|YP_005842427.1| 21 IQCDNCGRLIPEDKAICVERYY------SPIEPQLAKELEKKGAIITRYPVKKCYCVSCAIHLGIVKVRAEEERKAKQN 93
                                      6888888888888888886555......4555555444444444334499999********************998876 PP

>> zf-dskA_traR  Prokaryotic dksA/traR C4-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.1   0.00014      0.65       4      17 ..      20      34 ..      17      39 .. 0.87
   2 ?    1.3   1.6     0.077   3.5e+02      26      31 ..      69      74 ..      67      76 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00014
                      zf-dskA_traR  4 gs.CeeCGEpIpeaR 17
                                      ++ C+ CG  Ipe +
  gi|385806029|ref|YP_005842427.1| 20 RIqCDNCGRLIPEDK 34
                                      678**********87 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.077
                      zf-dskA_traR 26 lCveCq 31
                                      +Cv+C+
  gi|385806029|ref|YP_005842427.1| 69 YCVSCA 74
                                      8****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 608.51
//
Query:       gi|385806030|ref|YP_005842428.1|  [L=280]
Description: endonuclease IV [Fervidicoccus fontis Kam940]
Scores for 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-21   75.1   0.0    6.2e-21   74.8   0.0    1.1  1  AP_endonuc_2  Xylose isomerase-like TIM barrel
     0.0046   16.2   0.3      0.018   14.3   0.3    1.8  1  UvdE          UV-endonuclease UvdE
  ------ inclusion threshold ------
      0.011   13.7   0.2      0.014   13.3   0.2    1.1  1  PolC_DP2      DNA polymerase II large subunit DP2
      0.048   13.0   0.0      0.083   12.2   0.0    1.4  1  Amidohydro_1  Amidohydrolase family
       0.12   12.5   0.0       0.22   11.6   0.0    1.4  1  DUF3627       Protein of unknown function (DUF3627)


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 !   74.8   0.0   1.7e-24   6.2e-21       4     209 ..      28     239 ..      26     240 .. 0.92

  Alignments for each domain:
  == domain 1  score: 74.8 bits;  conditional E-value: 1.7e-24
                                       HHHCT-SEEEEECCTCSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCS.HHHHHHHHHHHHHHH CS
                      AP_endonuc_2   4 aaeaGfdgvElfgrdlvpvselsdeelrelrkaldelglriaslslftrfgypdederear.reesvdalkraiela 79 
                                       ++++G d++E+    +v++se   ++++e+ k+++e+++ ++++ +++ + +      +++  e+s+++l +ai+++
  gi|385806030|ref|YP_005842428.1|  28 LKKIGLDAMEYEAVRGVNISE---SKAKEFGKIAEENDVLLSMHAPYYINLSAQ----QKDtIEKSKERLLDAIRAS 97 
                                       799****************95...8*************************9954....455789************* PP

                                       HHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHT...SEEEEE--TTTTSSSTCHHHHHHHHHHTT CS
                      AP_endonuc_2  80 aaLGapllvlhpGtagagpkgseeeawerlaeslneladyaekeg...vklalEtlagsgvelgdeelarlldavds 153
                                       + +   ++v+hpG   ++ +++ + a+e+++e+l+++ ++a  +g    +l+ Et+ ++ +    +++ ++++ v+ 
  gi|385806030|ref|YP_005842428.1|  98 EWMKSYVVVFHPG---YYLDWGVKKAVELVIEALKDVREEANSKGwkyTWLGPETTGKKKQVGSIDDTIEICRNVEK 171
                                       *************...*******************************9************98888***********5 PP

                                       TTEEEEEEHHHHHHH........TTTHHHHHHHHHGG.......EEEEEE.EESSTTTTSSTTEESTTSSS CS
                      AP_endonuc_2 154 pnvgvclDtgHllia........eedvddalraladr.......ikhvHikDakgdlgagrdrhvpigeGe 209
                                         ++ + D++Hl+++        ++ v ++++++++          h H++ ++  +++g+ +h+ ++e e
  gi|385806030|ref|YP_005842428.1| 172 --CRPVVDWAHLYARslgmsiksKDEVVKIIDTIEKElgnesvhPLHTHFSKIEY-NSGGEKEHHTLDENE 239
                                       ..*********************99999999999999999997777777777777.899999999888865 PP

>> UvdE  UV-endonuclease UvdE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.3     5e-06     0.018      86     237 ..      48     207 ..      36     238 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5e-06
                              UvdE  86 aeeleevGelakelglRltfHPeqftllnSdrkevtesairdlayHdklldalklaeqqdavliiHvGGkfg..dke 160
                                       +++ +e G++a+e ++ l++H   ++ l++++k+  e++       ++llda++  e  ++++++   G +   +++
  gi|385806030|ref|YP_005842428.1|  48 ESKAKEFGKIAEENDVLLSMHAPYYINLSAQQKDTIEKS------KERLLDAIRASEWMKSYVVVFHPGYYLdwGVK 118
                                       567899**************************9999987......68999**9999999666655445566413578 PP

                              UvdE 161 aalerfkenikrlpdsvker......lvLENDdk...sytvadlLpvceeln.iPlVlDyHHhnvld..lreeslde 225
                                       +a+e   e +k++ ++  ++      l  E   k     +++d++++c + +    V+D+ H ++       +s de
  gi|385806030|ref|YP_005842428.1| 119 KAVELVIEALKDVREEANSKgwkytwLGPETTGKkkqVGSIDDTIEICRNVEkCRPVVDWAHLYARSlgMSIKSKDE 195
                                       88898899888888877664434333555654431114589999999987542556789999999865555666666 PP

                              UvdE 226 slplveriveTW 237
                                       +++++++i +  
  gi|385806030|ref|YP_005842428.1| 196 VVKIIDTIEKEL 207
                                       666555555443 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   0.2   3.8e-06     0.014     404     539 ..      53     195 ..      48     222 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.8e-06
                          PolC_DP2 404 ayGeflennhpLvp..asyveewwiqelekaaakkeaeekpsaeealelseeldvpLhPkytylwhdisvee..lek 476
                                       ++G   e+n  L++  a+y  +  +q+ +  + +k++e+  +a +a e+ +++ v +hP y + w   ++ e  +e+
  gi|385806030|ref|YP_005842428.1|  53 EFGKIAEENDVLLSmhAPYYINLSAQQKD--TIEKSKERLLDAIRASEWMKSYVVVFHPGYYLDWGVKKAVElvIEA 127
                                       58999999999964227888888777744..4555556689999*********************644433311345 PP

                          PolC_DP2 477 Laeavaekkkl......eeeklvleleeevkeiLekllvehkvkeekivieealallkslgldleeekl 539
                                       L+++ +e++++        +  ++ ++++v +i +++ +  +v++ + v++ a+  ++slg+++++++ 
  gi|385806030|ref|YP_005842428.1| 128 LKDVREEANSKgwkytwL-GPETTGKKKQVGSIDDTIEICRNVEKCRPVVDWAHLYARSLGMSIKSKDE 195
                                       555555554445434421.222334456688888999999999999999999999999**999885543 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.3e-05     0.083     129     213 ..      46     131 ..      37     164 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.3e-05
                                       SHHHHHHHHHHHHHHHTTEEEEEE...TSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEE... CS
                      Amidohydro_1 129 fsdeelkealkeakkrdlpvaiHa...letkgevedaeaafgetiehgthlevaeslglldeiklilahgvhlt... 199
                                       +s++  ke  k a++ d+ +++Ha    ++++ ++d++++ +   e+  +l+        +++ ++++ g +l+   
  gi|385806030|ref|YP_005842428.1|  46 ISESKAKEFGKIAEENDVLLSMHApyyINLSAQQKDTIEKSK---ER--LLDAIRASEWMKSYVVVFHPGYYLDwgv 117
                                       6777889999***************99999999999999999...88..999999999999**************96 PP

                                       HHHHHHHHHHHHHH CS
                      Amidohydro_1 200 pteaellkerlkea 213
                                        + +el++e+lk++
  gi|385806030|ref|YP_005842428.1| 118 KKAVELVIEALKDV 131
                                       55899999997765 PP

>> DUF3627  Protein of unknown function (DUF3627)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   6.2e-05      0.22      29      89 ..      29      87 ..      18      90 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.2e-05
                           DUF3627 29 krndkeryeYyaiRgqdkyikkrlkrykkeypdleiildikyqPNprnlfnriKeklkskk 89
                                      k+   + +eY a+Rg +++ +k++   k    + + +l +   P+ +nl  + K+ ++++k
  gi|385806030|ref|YP_005842428.1| 29 KKIGLDAMEYEAVRGVNISESKAKEFGKIA--EENDVLLSMHAPYYINLSAQQKDTIEKSK 87
                                      44446789*******999988887655555..7788888999***************7665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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 0.30s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 1649.73
//
Query:       gi|385806031|ref|YP_005842429.1|  [L=261]
Description: ribonuclease Z [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-22   80.4   0.0    1.6e-22   80.0   0.0    1.1  1  Lactamase_B_2  Beta-lactamase superfamily domain
    2.7e-10   40.6   0.1    5.5e-10   39.6   0.0    1.5  2  Lactamase_B    Metallo-beta-lactamase superfamily
    1.4e-06   27.9   0.0    2.9e-06   26.9   0.0    1.5  1  Lactamase_B_4  tRNase Z endonuclease
     0.0055   16.6   0.0      0.025   14.5   0.0    1.8  1  Lactamase_B_3  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.088   12.2   0.1       0.17   11.3   0.0    1.6  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 !   80.0   0.0   4.4e-26   1.6e-22      24     201 .]      49     228 ..      33     228 .. 0.84

  Alignments for each domain:
  == domain 1  score: 80.0 bits;  conditional E-value: 4.4e-26
                                       SS--..SEEEEE-SS--HHHHGGGGCCCC.....C--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSE CS
                     Lactamase_B_2  24 lrdelppidaVllthaHyDHlaglltlre.....lrpkklplyapkgvlavleanfvylaleeepavnvheldwges 95 
                                           +++id +l++h H DH+ gl+ + +     +r++kl ++ p+g+ ++l+a ++    + e   +++ ++++++
  gi|385806031|ref|YP_005842429.1|  49 NGIGVNRIDHILISHLHGDHIFGLPGIIQtmsmeGRERKLSIISPEGIEKILNAASQITSYQLE--FPIEIIKPEGE 123
                                       345789*********************999987777777****************999998888..9********** PP

                                       EEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEE....CTTEE......EEEESS-S---HHHHHHHCT-SEEEE CS
                     Lactamase_B_2  96 felgdggleitatparhksgrrldrnagdtlGlrie....gggkr......vyyigDtgyipeeigerlggadllll 162
                                       ++l++  +++ ++   h+  +         +G++i+    g  k       ++y+gDt+ ++e i+ +++gad+l++
  gi|385806031|ref|YP_005842429.1| 124 ISLEQ-YISVYPFKTCHTNIE--------SFGYIIKafgtG--KEkkerfsLAYTGDTAPCEELIE-KIKGADVLIH 188
                                       ***85.577888888888887........*******99551..33456677***********7765.********** PP

                                       E-S-SSTTHHHH...HHT---STSHHHHCTTSSSSEEEEESB CS
                     Lactamase_B_2 163 ditayeddemir...hmgHltpeeaveaaadlgakrlvliHi 201
                                       d t+ ++    +     gH+t + a+++a+++g+k l+l+Hi
  gi|385806031|ref|YP_005842429.1| 189 DSTFDSSMV--EkaiAFGHSTSSIAAKVAKMAGVKSLILFHI 228
                                       *99777744..446***************************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 !   39.6   0.0   1.5e-13   5.5e-10       8      67 ..      24      78 ..      20      98 .. 0.95
   2 ?   -3.3   0.0       2.1   7.4e+03     145     157 ..     164     176 ..     163     194 .. 0.61

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 1.5e-13
                                      EEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTH CS
                       Lactamase_B  8 syliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglvea 67
                                      s+l++  g+ iL D G ++++++++     +g++ +++d+++++HlH DHi+gl+g++++
  gi|385806031|ref|YP_005842429.1| 24 SILLQYRGKYILLDIGEGSQRSLIK-----NGIGVNRIDHILISHLHGDHIFGLPGIIQT 78
                                      789999******************8.....9*************************9875 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.1
                                       EEEECTTTSSHHC CS
                       Lactamase_B 145 vlftGDallaget 157
                                       +++tGD+ + +e 
  gi|385806031|ref|YP_005842429.1| 164 LAYTGDTAPCEEL 176
                                       6788888773333 PP

>> Lactamase_B_4  tRNase Z endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0     8e-10   2.9e-06      12      59 ..      21      67 ..      11      71 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 8e-10
                     Lactamase_B_4 12 g.PlllLqldskrYlfGkvgEgtQRavneqkvrlsklesiFLtgkvsws 59
                                      g P++lLq++ k  l+ ++gEg+QR ++++++ ++++++i +++ +  +
  gi|385806031|ref|YP_005842429.1| 21 GlPSILLQYRGKYILL-DIGEGSQRSLIKNGIGVNRIDHILISHLH-GD 67
                                      55*******9977777.*************************9988.44 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 !   14.5   0.0     7e-06     0.025       8     133 ..      23     187 ..      19     189 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7e-06
                     Lactamase_B_3   8 nsflletagarilvDPfkanlgyeppa....eeaDlvlisqaledHahletlkql...................... 58 
                                        s+ll+ +g+ il+D +++++   +++     ++D +lis+ + dH     l+++                      
  gi|385806031|ref|YP_005842429.1|  23 PSILLQYRGKYILLDIGEGSQRSLIKNgigvNRIDHILISHLHGDHIF--GLPGIiqtmsmegrerklsiispegie 97 
                                       5899***********9977655555557788************99964..334433337777776666666665554 PP

                     Lactamase_B_3  59 ..............aenvkvleegeslevg.gleiravatshdavggsergenngflleq........dgltiyhlG 112
                                                     +  ++++++++++ ++  +++  ++t h++       e  g++++         +  ++++ G
  gi|385806031|ref|YP_005842429.1|  98 kilnaasqitsyqlEFPIEIIKPEGEISLEqYISVYPFKTCHTN------IESFGYIIKAfgtgkekkERFSLAYTG 168
                                       44444444444444333344444555555423344444444432......333444444433222223377777887 PP

                     Lactamase_B_3 113 hlahelsseelkelgrvDvvl 133
                                       ++a    +e +++++ +Dv++
  gi|385806031|ref|YP_005842429.1| 169 DTAP--CEELIEKIKGADVLI 187
                                       7775..677777777777776 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 ?   11.3   0.0   4.9e-05      0.17       1      59 [.      26      79 ..      26     110 .. 0.81
   2 ?   -3.4   0.0       1.5   5.5e+03     160     173 ..     230     243 ..     226     250 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.9e-05
                     Lactamase_B_6  1 lLeldnvkiLlDvGwdeskvslesalkelekviptvdliLLshatlehlGayallyakf 59
                                      lL++ +  iLlD+G  +++      l +    ++++d+iL+sh   +h+ +++ +++++
  gi|385806031|ref|YP_005842429.1| 26 LLQYRGKYILLDIGEGSQRS-----LIKNGIGVNRIDHILISHLHGDHIFGLPGIIQTM 79
                                      67788889******998633.....33344469****************9998777665 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.5
                     Lactamase_B_6 160 vdwnhakeshLnga 173
                                        ++n ++e +L++a
  gi|385806031|ref|YP_005842429.1| 230 NRYNDKSEMILDNA 243
                                       57999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1594.13
//
Query:       gi|385806032|ref|YP_005842430.1|  [L=336]
Description: putative DNA modification methylase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-20   73.4   0.0    7.3e-19   68.2   0.0    2.2  1  UPF0020          Putative RNA methylase family UPF0020
    6.6e-05   22.6   0.0    0.00012   21.8   0.0    1.4  1  Cons_hypoth95    Conserved hypothetical protein 95
    0.00093   19.9   0.0     0.0019   18.9   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
     0.0049   17.5   0.0      0.017   15.8   0.0    1.9  1  Methyltransf_11  Methyltransferase domain
     0.0053   16.2   0.0        1.1    8.6   0.0    2.2  2  AviRa            RRNA methyltransferase AviRa
  ------ inclusion threshold ------
       0.02   14.6   0.0       0.24   11.1   0.0    2.0  2  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran
      0.042   13.5   0.0        3.2    7.4   0.0    2.2  2  N6_N4_Mtase      DNA methylase
      0.051   12.8   0.0       0.13   11.5   0.0    1.7  1  N6_Mtase         N-6 DNA Methylase
       0.19   11.6   0.3         20    5.1   0.0    3.0  3  PASTA            PASTA domain


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 !   68.2   0.0   3.7e-22   7.3e-19       5     170 ..     160     301 ..     156     328 .. 0.89

  Alignments for each domain:
  == domain 1  score: 68.2 bits;  conditional E-value: 3.7e-22
                                       -SS---SS-HHHHHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEE CS
                           UPF0020   5 efngpapLketLAaalvrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklyg 81 
                                       +f +p++L+   A+ lv+l+  k+g++++DP+CG+G++++ a   ++ i                          ++
  gi|385806032|ref|YP_005842430.1| 160 PFYKPGALNFWFARLLVNLSISKEGRVFYDPFCGTGSLPLSALNDWEFIS-------------------------IC 211
                                       7889************************************8877777776.........................8* PP

                                       EES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE----------HHHH.HHHHHHHHHHHHHH-T CS
                           UPF0020  82 sDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYGerlgskkal.ekLYseflrelkrvlr 157
                                       sD+ + +  ga++N++     ++ e+  ada++L+ +e +++ ++t+pPYG++++s  +   +L +  l+el+++l+
  gi|385806032|ref|YP_005842430.1| 212 SDIRKDMCYGAKRNLKTLSKVNEFEIIRADARHLPIRERSIGFVATDPPYGRSVKSLFSDsTNLSQDSLKELANILD 288
                                       ***********************************9999*****************977769*************** PP

                                       T..-EEEEEESSH CS
                           UPF0020 158 gggrlvlltsenk 170
                                        gg++v+ +  n 
  gi|385806032|ref|YP_005842430.1| 289 FGGKIVFSLDRNI 301
                                       *999988766655 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   6.1e-08   0.00012      42     127 ..     184     265 ..     170     287 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 6.1e-08
                                       C-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEE CS
                     Cons_hypoth95  42 garvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdivf 118
                                       g  + D f+G+G+l l Al      +++ +  k ++   k+nl++l   +e+++++ da +   ++    +++ +v 
  gi|385806032|ref|YP_005842430.1| 184 GRVFYDPFCGTGSLPLSALNDWEFISICSDIRKDMCYGAKRNLKTLSKVNEFEIIRADARHLPIRE----RSIGFVA 256
                                       56688***************999999***********************99999999988776666....6799*** PP

                                       E--SSSTTC CS
                     Cons_hypoth95 119 lDPPyakel 127
                                        DPPy ++ 
  gi|385806032|ref|YP_005842430.1| 257 TDPPYGRSV 265
                                       *****9874 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   9.6e-07    0.0019       5      69 ..     191     256 ..     188     291 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 9.6e-07
                                       T-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHH.TTT.TEEEEESBCCGBSSSTTTEEEEE CS
                   Methyltransf_25   5 GcGtGrltlalakrlgkakvtgvDiseemleaareraee.egl.nvefvqgdaedlpfedgsfDlvv 69 
                                        cGtG l l +++ + +   ++ Di ++m+  a+++++  +++ ++e++++da++lp  ++s+ +v 
  gi|385806032|ref|YP_005842430.1| 191 FCGTGSLPLSALNDW-EFISICSDIRKDMCYGAKRNLKTlSKVnEFEIIRADARHLPIRERSIGFVA 256
                                       5********999998.68889****************9965558**************999998875 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   8.4e-06     0.017       5      96 .]     192     295 ..     189     295 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8.4e-06
                                       -TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES....-CCC- CS
                   Methyltransf_11   5 cGtGrlaealakrg.arvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvsse....vlhhv 74 
                                       cGtG+l     +      ++ D+ k m   ak++ ++     ++e+++ada++lp+++ s+ +v        ++  +
  gi|385806032|ref|YP_005842430.1| 192 CGTGSLPLSALNDWeFISICSDIRKDMCYGAKRNLKTLSKvnEFEIIRADARHLPIRERSIGFVATDPpygrSVKSL 268
                                       89998877777666688999***********9999999989999********************8765666633333 PP

                                       .....CCHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  75 .....edpekalkeiaRvLkpgGllvi 96 
                                            +  ++ lke+a +L  gG++v+
  gi|385806032|ref|YP_005842430.1| 269 fsdstNLSQDSLKELANILDFGGKIVF 295
                                       333447778888888888888888875 PP

>> AviRa  RRNA methyltransferase AviRa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0   0.00057       1.1      52     104 ..     182     231 ..     170     233 .. 0.81
   2 !    5.8   0.0    0.0041       8.1     148     208 ..     234     294 ..     228     305 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00057
                             AviRa  52 gapltlyDpCCGgayLltvlgllhgkkikkvlasDvdeevlelakkNLsLLtk 104
                                       +++   yDp CG++ L   l+ l   ++ ++  sD+ +++   ak+NL+ L+k
  gi|385806032|ref|YP_005842430.1| 182 KEGRVFYDPFCGTGSLP--LSALNDWEFISI-CSDIRKDMCYGAKRNLKTLSK 231
                                       446779********994..677888888886.69**************99976 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0041
                             AviRa 148 eievfkaditekeeeaekevdivitDlPYGelvswqge.seepvkqlleslaavldpeesvv 208
                                       e e+++ad   + +  e+++  v tD PYG  v+   + s++  ++ l++la++ld    +v
  gi|385806032|ref|YP_005842430.1| 234 EFEIIRADAR-HLPIRERSIGFVATDPPYGRSVKSLFSdSTNLSQDSLKELANILDFGGKIV 294
                                       5556666665.4445556699*********99875444388888999999999998766665 PP

>> MethyltransfD12  D12 class N6 adenine-specific DNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00012      0.24      16      41 ..     180     204 ..     174     244 .. 0.76
   2 ?    1.2   0.0      0.12   2.4e+02     180     207 ..     254     279 ..     222     306 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00012
                                       S-..--SEEEETT-TTSCCHHCS... CS
                   MethyltransfD12  16 ipkdkgktfvepFaGggaVffeakkq 41 
                                       i+k  g++f++pF+G+g++ ++a+++
  gi|385806032|ref|YP_005842430.1| 180 ISK-EGRVFYDPFCGTGSLPLSALND 204
                                       556.789************9999763 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.12
                                       EEEE--S-T.S...TS--GGGG.CS-HH CS
                   MethyltransfD12 180 ivYlDPPYnprqytanytlyetlafsde 207
                                       +v  DPPY    ++ + ++ +t++ +d 
  gi|385806032|ref|YP_005842430.1| 254 FVATDPPYGR--SVKSLFSDSTNLSQDS 279
                                       7778****96..6666666666554443 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0016       3.2     180     204 ..     171     196 ..     101     220 .. 0.82
   2 ?    4.3   0.0     0.014        28       3      63 ..     254     304 ..     252     335 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0016
                                       HHHHHHHHH.S-TT-EEEETT-TTTH CS
                       N6_N4_Mtase 180 llerlIkls.tkkgdivlDpFaGSGt 204
                                       +++ l++ls +k+g +  DpF+G+G+
  gi|385806032|ref|YP_005842430.1| 171 FARLLVNLSiSKEGRVFYDPFCGTGS 196
                                       577888666156688889*******8 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.014
                                       EEEE--SSSSSCS.....GCCGCCHHHHHHHHHHHHHHHHHHHEEEEEEEEEEE-CCCHHT CS
                       N6_N4_Mtase   3 livtdpPYntgkdyendeqyeeedsyeeyleflekvlkevrrvLkddgsifiniddseikk 63 
                                        + tdpPY+ + +          + +++  ++ +  lke+  +L  +g i+ + d++ ++k
  gi|385806032|ref|YP_005842430.1| 254 FVATDPPYGRSVK----------SLFSDSTNLSQDSLKELANILDFGGKIVFSLDRNIAEK 304
                                       5889******999..........77888888888899999999999999999877776665 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   6.6e-05      0.13      35      89 ..     172     228 ..     160     285 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.6e-05
                          N6_Mtase  35 sklivellepksgesvyDpacGsggllvqaekvlkee..dgktkelsiyGqeknett 89 
                                        +l+v+l  +k+g++ yDp cG+g+l ++a +  +      ++++   yG   n +t
  gi|385806032|ref|YP_005842430.1| 172 ARLLVNLSISKEGRVFYDPFCGTGSLPLSALNDWEFIsiCSDIRKDMCYGAKRNLKT 228
                                       4678888899****************9888764322122666666677777766665 PP

>> PASTA  PASTA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.054   1.1e+02      30      50 ..      55      75 ..      31      76 .. 0.75
   2 ?    5.1   0.0      0.01        20      33      45 ..     144     156 ..     132     158 .. 0.90
   3 ?   -1.0   0.0      0.82   1.6e+03      41      52 ..     255     266 ..     255     268 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.054
                                      EECTCCGTTBEEEECS-TTSE CS
                             PASTA 30 etsddvpeGtVisQsPeaGte 50
                                       +s  ++ G+Vi+ +P++G+ 
  gi|385806032|ref|YP_005842430.1| 55 RSSTIKEVGRVIGIIPSKGEP 75
                                      37888999**********985 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.01
                                       TCCGTTBEEEECS CS
                             PASTA  33 ddvpeGtVisQsP 45 
                                       +d ++G++isQ+P
  gi|385806032|ref|YP_005842430.1| 144 SDRGKGDIISQNP 156
                                       7899********9 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.82
                                       EEECS-TTSEEC CS
                             PASTA  41 isQsPeaGtevs 52 
                                       ++++P++G +v+
  gi|385806032|ref|YP_005842430.1| 255 VATDPPYGRSVK 266
                                       579*****9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 2140.76
//
Query:       gi|385806033|ref|YP_005842431.1|  [L=292]
Description: ribose-phosphate pyrophosphokinase [Fervidicoccus fontis Kam940]
Scores for complete 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   85.7   0.0      1e-22   80.2   0.0    2.3  2  Pribosyltran_N  N-terminal domain of ribose phosphate pyropho
    1.4e-14   54.0   0.5    5.6e-14   52.0   0.1    2.1  3  Pribosyltran    Phosphoribosyl transferase domain
    3.2e-08   33.8   0.4    6.6e-08   32.8   0.4    1.4  1  Pribosyl_synth  Phosphoribosyl synthetase-associated domain
    0.00012   21.6   0.1    0.00048   19.6   0.0    1.9  2  UPRTase         Uracil phosphoribosyltransferase
     0.0017   17.9   0.0     0.0024   17.4   0.0    1.2  1  PRTase_2        Phosphoribosyl transferase
  ------ inclusion threshold ------
      0.035   13.7   0.1      0.087   12.4   0.0    1.7  2  Tsp45I          Tsp45I type II restriction enzyme
      0.055   13.4   0.1       0.11   12.5   0.1    1.4  1  Kinase-PolyVal  Serine/Threonine/Tyrosine Kinase found in pol


Domain annotation for each model (and alignments):
>> Pribosyltran_N  N-terminal domain of ribose phosphate pyrophosphokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.2   0.0     4e-26     1e-22       3     116 .]       4     118 ..       3     118 .. 0.98
   2 ?    3.2   0.0     0.032        83       9      57 ..     173     219 ..     166     266 .. 0.70

  Alignments for each domain:
  == domain 1  score: 80.2 bits;  conditional E-value: 4e-26
                    Pribosyltran_N   3 ifagssskeLaekiakrlgvelgkakvsrfadgEikveieesvrgkdvfiiqslskpvndnlmelllmidalrrasa 79 
                                       i+ g++s  + ++++k l+++  k+  + f+dgE+++++ e+v gk+v++ +sls+p nd++ el+l+++alr+   
  gi|385806033|ref|YP_005842431.1|   4 ILCGTKSDWFCDNLSKSLNIKSLKVFHKVFPDGETYIRVPEEVSGKKVILAHSLSPPQNDSIWELILILEALRELDI 80 
                                       77889999999****************************************************************** PP

                    Pribosyltran_N  80 kritaViPylgysrqdrk.ksrepisaklvaklLeaaG 116
                                       k+i+  iPy +ysrqd+   + epis k ++++L+++G
  gi|385806033|ref|YP_005842431.1|  81 KEINGYIPYVAYSRQDKIfLNGEPISIKALLQILSQMG 118
                                       ******************9******************9 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.032
                    Pribosyltran_N   9 skeLaekiakrlgvelgkakvsrfadgEikveiee.svrgkdvfiiqsls 57 
                                       ++ La++++   +    k       +g i+++++e +++++dv+i+ ++ 
  gi|385806033|ref|YP_005842431.1| 173 ARRLANELSTDFDYMEKKR---DVYTGKIEISFHEvNLKDRDVVIVDDII 219
                                       4444444444444443333...3457999999999899********9987 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.65   1.7e+03      79      92 ..      38      53 ..      15      57 .. 0.73
   2 ?   -2.3   0.0       1.1   2.8e+03     103     124 ..      68      89 ..      68      99 .. 0.78
   3 !   52.0   0.1   2.2e-17   5.6e-14      21     144 ..     151     269 ..     140     281 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.65
                                      ...EE----TTSEEEE CS
                      Pribosyltran 79 s..rlledpagkkVli 92
                                      +  r +e++ gkkV++
  gi|385806033|ref|YP_005842431.1| 38 TyiRVPEEVSGKKVIL 53
                                      1447889999999997 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.1
                                       HHHHHHHHHCC-BSEEEEEEEE CS
                      Pribosyltran 103 llaalelLkekgpeevriavlv 124
                                       l+ +le+L+e + +e+    ++
  gi|385806033|ref|YP_005842431.1|  68 LILILEALRELDIKEINGYIPY 89 
                                       6779999*99999999877665 PP

  == domain 3  score: 52.0 bits;  conditional E-value: 2.2e-17
                                       EEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----TTSEEEEE-SEE CS
                      Pribosyltran  21 eileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlledpagkkVliVDDil 97 
                                       + +++   k + v+ ++ g++ +a +la+eL   ++y++k++    g+ e++         + +++++ V+iVDDi+
  gi|385806033|ref|YP_005842431.1| 151 NMIRN-MAKHPFVISPDIGALERARRLANELSTDFDYMEKKRDVYTGKIEISF-------HEVNLKDRDVVIVDDII 219
                                       45555.6799**********************999999999999999999974.......789************** PP

                                       SSSHHHHHHHHHHHCC-BSEEEEEEEE...E-HHHHHHHHHH-TTS.... CS
                      Pribosyltran  98 dtGgTllaalelLkekgpeevriavlv...dkpateeevdknakrvfsls 144
                                       +tGgT+ +a++ + + g+++v +av++   +  a  + +++n+++v+s +
  gi|385806033|ref|YP_005842431.1| 220 STGGTVAEAAKKIYSLGAKKVFVAVSHallAGDAINKLKEANVYSVLSAN 269
                                       *************************9977766666777777777777655 PP

>> Pribosyl_synth  Phosphoribosyl synthetase-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.4   2.6e-11   6.6e-08      84     148 ..     210     274 ..     204     283 .. 0.93

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 2.6e-11
                                       SEEEEEEEEE-S-HHHHHHHHHHHHTT--EEEEEEEEE---TTHHHHHHHSS--EEEEESSS--H CS
                    Pribosyl_synth  84 riaiivddliddvesfvaaaevlkerGaykiyvlathGllssdaprlleesaidevvvtntiphe 148
                                       r  +ivdd+i    ++ +aa+ +   Ga k++v ++h ll+ da ++l+e+++  v+ +nt+p +
  gi|385806033|ref|YP_005842431.1| 210 RDVVIVDDIISTGGTVAEAAKKIYSLGAKKVFVAVSHALLAGDAINKLKEANVYSVLSANTLPPK 274
                                       5679**********************************************************976 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.48   1.2e+03     109     128 ..      36      55 ..      15      58 .. 0.75
   2 !   19.6   0.0   1.9e-07   0.00048     118     171 ..     206     259 ..     181     269 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.48
                           UPRTase 109 veyynkLPkkiaertvlllD 128
                                        e y ++P++++ ++v+l  
  gi|385806033|ref|YP_005842431.1|  36 GETYIRVPEEVSGKKVILAH 55 
                                       478999*****999999975 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 1.9e-07
                           UPRTase 118 kiaertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegvkrlae 171
                                       ++++r v+++D +i+TGg++a+a +++ + g+++  + v   l +  ++++l e
  gi|385806033|ref|YP_005842431.1| 206 NLKDRDVVIVDDIISTGGTVAEAAKKIYSLGAKKVFVAVSHALLAGDAINKLKE 259
                                       458899***********************9998888888888888888887766 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   9.3e-07    0.0024     115     157 ..     203     245 ..     161     266 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 9.3e-07
                          PRTase_2 115 eellaaakelvLvDDEistGktalnliralqeklprkryvvvs 157
                                       +e+  +++ +v+vDD istG t+++ ++++ +   +k +v vs
  gi|385806033|ref|YP_005842431.1| 203 HEVNLKDRDVVIVDDIISTGGTVAEAAKKIYSLGAKKVFVAVS 245
                                       556668899*********************9998888887776 PP

>> Tsp45I  Tsp45I type II restriction enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.4e-05     0.087      55     105 ..      72     124 ..      24     163 .. 0.82
   2 ?   -2.2   0.0      0.93   2.4e+03      86     107 ..     223     244 ..     205     260 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.4e-05
                            Tsp45I  55 ikellkldlfpikd..syiaflrkdktaidrnpetvnrlcgrlyelGldkiye 105
                                       ++ l  ld+  i     y+a+ r+dk  ++ +p +++ l + l ++G+  iy 
  gi|385806033|ref|YP_005842431.1|  72 LEALRELDIKEINGyiPYVAYSRQDKIFLNGEPISIKALLQILSQMGMSSIYT 124
                                       3445556665555433599999*****************************96 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.93
                            Tsp45I  86 etvnrlcgrlyelGldkiyeki 107
                                        tv   + ++y lG +k++  +
  gi|385806033|ref|YP_005842431.1| 223 GTVAEAAKKIYSLGAKKVFVAV 244
                                       5788888999999999987655 PP

>> Kinase-PolyVal  Serine/Threonine/Tyrosine Kinase found in polyvalent proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   4.2e-05      0.11      27     137 ..      88     205 ..      75     221 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.2e-05
                    Kinase-PolyVal  27 eylseGaEqkVYlkddksViKlndaiyyaswldylnslllh..N..llFpntayellGfakseeklvavvkQpfika 99 
                                        y++ +   k++l+ +   iK   +i ++  ++ ++ + +h  N   +F+ t+y+++ f+   + ++   k pf+ +
  gi|385806033|ref|YP_005842431.1|  88 PYVAYSRQDKIFLNGEPISIKALLQILSQMGMSSIYTIDIHkpNtlSYFNGTSYNIIPFKSMANMIRNMAKHPFVIS 164
                                       567777888999977778899999999999999999999995544458****************************9 PP

                    Kinase-PolyVal 100 deevdleevkeflek..ngfe.ntrnndyinkelgliledl 137
                                        +  +le  +++ ++  + f+ +++++d ++ ++++ + ++
  gi|385806033|ref|YP_005842431.1| 165 PDIGALERARRLANElsTDFDyMEKKRDVYTGKIEISFHEV 205
                                       87766666555544311556623455677777777777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); 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: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1905.95
//
Query:       gi|385806034|ref|YP_005842432.1|  [L=676]
Description: DNA topoisomerase III [Fervidicoccus fontis Kam940]
Scores for complete 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  360.2   0.1     2e-107  359.8   0.1    1.2  1  Topoisom_bac  DNA topoisomerase
    1.8e-14   53.8   1.0    1.1e-13   51.3   0.0    2.8  3  Toprim        Toprim domain


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 !  359.8   0.1  2.3e-111    2e-107       3     412 ..     162     569 ..     160     570 .. 0.92

  Alignments for each domain:
  == domain 1  score: 359.8 bits;  conditional E-value: 2.3e-111
                      Topoisom_bac   3 nenlvdaaeaRrelDwliGinlsrlltk...klkg..kkvlsaGRVqtptLaliveRereienFvpeeyweveatlk 74 
                                       + ++++a+ +R+elDw++Gin sr+l++   +  +  + vls GRVq+p+L  + +R+ e ++F + + ++++a + 
  gi|385806034|ref|YP_005842432.1| 162 DYDMIEAGICRHELDWIWGINTSRALMHiykQ-ASgkNIVLSSGRVQSPALIEVFDRYIEERSFFSPPKFQLTAVFS 237
                                       67899***********************8743.33468899*********************************995 PP

                      Topoisom_bac  75 kekkekekkkkkkkerikdkeeaeaileklkk.keakvesvekkekkkppplpfdtttLqkeasrklglsakktlsi 150
                                       k++ ++   +++ ++ ++ k++ae++ ++  + k+ +v+++++++++ ppp pf++++Lq easr++g+s++ t++i
  gi|385806034|ref|YP_005842432.1| 238 KDSYKF--SSSHISSPFEYKKDAEEAKKRALNvKRGNVSDIKEEKERIPPPPPFNLSDLQYEASRIYGFSPSYTQKI 312
                                       555555..4899999*************9989669*************9999************************* PP

                      Topoisom_bac 151 aqkLYekaglitYpRTdstrlseeaelkailealakkygkeylefaekllkktkkks..vvknkkveaHeAIrPtee 225
                                       a++LY +  li+YpRT+s++l+++   k+ile+l+    key++  e+++k++ +     +++k++ aH+AI+Pt++
  gi|385806034|ref|YP_005842432.1| 313 AEDLYLD-VLISYPRTNSQKLPPSIPHKNILENLSVL--KEYEKQIEEVKKRNPS-YipRQGRKEDPAHPAIYPTGK 385
                                       ******7.****************7789******986..7899988888875544.2566666677*********** PP

                      Topoisom_bac 226 lpklkelsddekklYelIvrrflaslmkdakyeettvklev.eeeefkasgktilekGfkkvykeekkeeeeeelpe 301
                                       +p  k+l++d+ klY+lIvrr++ ++m+d +  +++vk++v e++ f+++g++i +kG++k+yk    e+    +p+
  gi|385806034|ref|YP_005842432.1| 386 IP--KDLKGDKLKLYDLIVRRYISTFMDDLVLIKRRVKINVgERDVFETNGTIIESKGWLKAYKFYTIEKA---IPS 457
                                       **..79*********************************9966689*****************87777654...9** PP

                      Topoisom_bac 302 lkegeevkvkeveleekkTkppkryteasLikamekagiGtpaTraeiieklvergYverkkkslvptelGkalvel 378
                                       lk +++v+++++++ +   ++pk +t++sL+k+me+ +iGt+aTra+iie+l++rgY+++ +k ++pt+lG+++  +
  gi|385806034|ref|YP_005842432.1| 458 LKLNDIVSIESIKIASYYPSKPKLHTKTSLLKWMESQNIGTEATRAQIIETLFKRGYLKSTSKGIIPTKLGIVVSLA 534
                                       ************************************************************99*************** PP

                      Topoisom_bac 379 lekf.kdlvspelTaeleekLdeIaegkadakevl 412
                                       l+k+ ++l++++lT+++e +L+eI+e+k+++++v+
  gi|385806034|ref|YP_005842432.1| 535 LKKYvSELTDVSLTRSFEVRLQEIRENKKSRSDVV 569
                                       *8888****************************98 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.3   0.0   1.2e-17   1.1e-13       1     102 [.      14     145 ..      14     146 .. 0.90
   2 ?   -2.5   0.0      0.66   5.9e+03      22      54 ..     426     459 ..     416     475 .. 0.69
   3 ?   -1.4   0.1      0.32   2.8e+03      37      66 ..     535     579 ..     500     600 .. 0.55

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 1.2e-17
                                       EEEEESSHHHHHHHHHTHT...................STEEEEEEESSSSEEEHS..........TTEEEEEECTT CS
                            Toprim   1 elvivEgpsdaktiakalg...................sgfqavtaslGhildlet..........efkpvyeeied 48 
                                       +l+i E+p++ak+ia+al+                   ++++++ ++ Gh+++l t          e+ p + + ++
  gi|385806034|ref|YP_005842432.1|  14 TLIISEKPKAAKAIAEALSykpisckdnnityyvinnnEKTTVIASTAGHLFTLSTnskdypvfdyEWVPRWLVEKG 90 
                                       59***********************************999**********************999999999995555 PP

                                       THHHHHH...HHHHHHHHSEEEEECSSSHHHHHHHHHHHHHHTHHHTTTEEEEEESS CS
                            Toprim  49 kkkvlka...lkelakradeiilatDpDreGeaiawellevlkellenkigrvefse 102
                                       +    k    l +l+kra+e + a+D D eG+ i++ ++++l+  +e k++r++fs 
  gi|385806034|ref|YP_005842432.1|  91 AFHLKKYyylLSKLSKRASEYVNACDYDIEGSVIGYMIIKLLG--NETKGKRMKFST 145
                                       5544444454*****************************9998..55667****985 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.66
                                       EEEEEEESSSSEEEHSTTEEEEE..ECTTTHHHHH CS
                            Toprim  22 fqavtaslGhildletefkpvye..eiedkkkvlk 54 
                                       +  v+ + G+i++ +  + ++y+   ie+++  lk
  gi|385806034|ref|YP_005842432.1| 426 ERDVFETNGTIIESKG-WLKAYKfyTIEKAIPSLK 459
                                       5678888999999988.888888553333333333 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.32
                                       S..............TTEEEEE.....ECTTTHHHHHHHHHHHHHHSEE CS
                            Toprim  37 t..............efkpvye.....eiedkkkvlkalkelakradei 66 
                                                      +f    e     ++e+kk+  +++ke ++  ++i
  gi|385806034|ref|YP_005842432.1| 535 LkkyvseltdvsltrSF----EvrlqeIRENKKSRSDVVKEAREVMSKI 579
                                       24333333345333322....2333344444444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (676 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1468  (0.0818785); expected 358.6 (0.02)
Passed bias filter:                      842  (0.046963); 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: 0.78u 0.34s 00:00:01.12 Elapsed: 00:00:00.51
# Mc/sec: 3987.77
//
Query:       gi|385806035|ref|YP_005842433.1|  [L=98]
Description: DNA-directed RNA polymerase subunit K [Fervidicoccus fontis Kam940]
Scores for complete 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-14   51.5   0.0    9.2e-14   51.1   0.0    1.2  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 !   51.1   0.0   5.1e-18   9.2e-14       4      49 .]      15      66 ..      13      66 .. 0.88

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 5.1e-18
                                      TSS--HHHHHHHHHHHHHHH....HT...........SS-SSSSTTCHHHHTT-S-- CS
                      RNA_pol_Rpb6  4 skvltrYelvriaakRArQieegesl...........etqkpvviAlrEiaegkipi 49
                                      +k+ltr+e +ri+++RA+Q+    s+             ++p+ iA++E++ g +p+
  gi|385806035|ref|YP_005842433.1| 15 PKKLTRFERARIIGARALQL----SMgappfidvsnlP-KDPIIIAEKELEMGVLPL 66
                                      599*****************....88888888777543.6*************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); 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 0.36s 00:00:00.87 Elapsed: 00:00:00.55
# Mc/sec: 539.35
//
Query:       gi|385806036|ref|YP_005842434.1|  [L=554]
Description: thermosome [Fervidicoccus fontis Kam940]
Scores for 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-178  594.0  19.6   2.3e-178  593.8  19.6    1.0  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  593.8  19.6  1.3e-182  2.3e-178       1     490 [.      33     528 ..      33     529 .. 0.98

  Alignments for each domain:
  == domain 1  score: 593.8 bits;  conditional E-value: 1.3e-182
                                       HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHH CS
                        Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleea 77 
                                       la+i+kt+lGP+G+dKmlv+++g+v+vTnDG+ti+ke+e++hPaakllve+a++qd evGDGTtt+v+Lag+Lle+a
  gi|385806036|ref|YP_005842434.1|  33 LAEILKTSLGPRGLDKMLVDSFGDVTVTNDGVTIVKEMEVNHPAAKLLVEVAKAQDAEVGDGTTTAVVLAGALLEKA 109
                                       79*************************************************************************** PP

                                       HHHHHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTS..SXXSTHHHHHHHHHHHHHC CS
                        Cpn60_TCP1  78 ekliaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslssk..ltskeaeelsklvvdAvkl 152
                                       e l+++++hpt+i++g+  a++kale+L++i  +++++ +d+e L+k+++ts+ssk   + ++ e+l++l+v+A kl
  gi|385806036|ref|YP_005842434.1| 110 EALLDQNIHPTVIMDGFSLAMHKALEILDSI--AVEVKPEDTELLKKLVKTSISSKyiGSGETLEKLTDLIVEAAKL 184
                                       *******************************..7777788****************66567889***********88 PP

                                       HCCCS.....EECSCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCC CS
                        Cpn60_TCP1 153 ieene.....keldlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvl 224
                                       + e +     +el l++ik++k++g+sl+ds l++G+vldk+v++p mpk++enak++lld +Lei+k+e+++++++
  gi|385806036|ref|YP_005842434.1| 185 VAEPKpqgkgYELRLDNIKIEKKKGESLNDSMLIKGIVLDKEVVHPGMPKRVENAKIALLDAPLEIKKPEISAKINI 261
                                       8777779********************************************************************** PP

                                       CSCCHHHHHHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCG CS
                        Cpn60_TCP1 225 sdaeeleklekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssl 301
                                       +++e++++++++e+k l+e+++ki++ g+nvv++qkgidd+a+hflak+gila+rrvk++d+e+l +atG+++v+s+
  gi|385806036|ref|YP_005842434.1| 262 TSPEQMKSFLDEETKLLKEMVDKIAEVGANVVIAQKGIDDVAQHFLAKRGILAVRRVKRSDMEKLERATGGRIVTSI 338
                                       ***************************************************************************** PP

                                       GGGGCGC-EEEEEEEECCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTC CS
                        Cpn60_TCP1 302 edltpeelGtakkveeekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGa 378
                                        dl pe+lG+a+ vee+k+g+ek++++e+vk++k++tillrga+d +lde+er+i+dAl+v++n+++d+k+v GGGa
  gi|385806036|ref|YP_005842434.1| 339 RDLRPEDLGEASLVEERKVGNEKMLFVEGVKNAKSVTILLRGANDIILDEAERSINDALHVLRNVMKDPKIVGGGGA 415
                                       ***************************************************************************** PP

                                       HHHHHHHHHHCCCCTSXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEE.C CS
                        Cpn60_TCP1 379 telelakklkeyaksvsgeeqlaieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesgeiid.l 454
                                        e+ela +l+++a++v g++qlaieafa+A+e+ip++Lae +G+d+ e l klr+ h ++++ +g+++ +++ii+  
  gi|385806036|ref|YP_005842434.1| 416 PEIELALQLRKFATTVGGKKQLAIEAFADAMETIPMILAETSGIDALEALMKLRQLHTENKIFAGVNALTEKIIEnT 492
                                       ************************************************************************65549 PP

                                       CCCTXEEEHHHHHHHHHHHHHHHHHHHCEEEEEXXX CS
                        Cpn60_TCP1 455 veagvvDplkvkrqalksAteaastiLrideiikak 490
                                       +e+++++p+ vk+qa+ksA+ea  tiL+id+ i a+
  gi|385806036|ref|YP_005842434.1| 493 FEENIIEPIIVKKQAVKSASEATITILKIDDLIAAQ 528
                                       *********************************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (554 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        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 0.27s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 3968.57
//
Query:       gi|385806037|ref|YP_005842435.1|  [L=93]
Description: alkylhydroperoxidase [Fervidicoccus fontis Kam940]
Scores for complete 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   60.5   0.1    1.3e-16   60.4   0.1    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 !   60.4   0.1   7.2e-21   1.3e-16      17      78 ..       9      70 ..       1      77 [. 0.92

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 7.2e-21
                                      GSSTS-HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHSHHHHHH CS
                               CMD 17 reggLdpkereLialavsaangceyCvdaHtraAleaGvteeeiaevlaqaaayagwpaara 78
                                      ++g+Ld+k++eLial + ++ +ce C+ +H+++A++ G+++eei e++ +a+ ++g+p + +
  gi|385806037|ref|YP_005842435.1|  9 KNGALDAKTKELIALSIGIVKNCETCIYYHLNEAMKLGASREEILEAAWVAVLMDGGPSLAH 70
                                      489*******************************************************8765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.41
# Mc/sec: 685.56
//
Query:       gi|385806038|ref|YP_005842436.1|  [L=43]
Description: hypothetical protein FFONT_0996 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); 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 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 280.86
//
Query:       gi|385806039|ref|YP_005842437.1|  [L=322]
Description: hypothetical protein FFONT_0997 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.046   13.3   0.8      0.046   13.3   0.8    2.3  2  RecR             RecR protein
      0.092   12.7   4.7        2.4    8.1   1.8    2.3  2  zf-RING_9        Putative zinc-RING and/or ribbon
        4.7    6.8   9.8       0.23   11.1   3.6    1.9  2  zf-SNAP50_C      snRNA-activating protein of 50kDa MW C termi


Domain annotation for each model (and alignments):
>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   2.1       0.6   3.6e+03      12      23 ..      15      26 ..      13      27 .. 0.79
   2 ?   13.3   0.8   7.7e-06     0.046      16      35 ..     282     301 ..     280     302 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.6
                                      HHHH-EE-TTT- CS
                              RecR 12 akekvrhCsrCg 23
                                       k +   C +Cg
  gi|385806039|ref|YP_005842437.1| 15 IKANCMKCTKCG 26
                                      577888999998 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 7.7e-06
                                       -EE-TTT--EESSSS-CCCC CS
                              RecR  16 vrhCsrCgnlteedlCaICs 35 
                                       ++ C+ Cg  + +++C++C+
  gi|385806039|ref|YP_005842437.1| 282 LKKCKYCGGTSSSEVCRFCK 301
                                       689****************6 PP

>> zf-RING_9  Putative zinc-RING and/or ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   1.8    0.0004       2.4     152     187 ..      16      51 ..       2      62 .. 0.79
   2 ?    5.2   0.1     0.003        18     132     163 ..     269     302 ..     223     314 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0004
                         zf-RING_9 152 kakgfiCelCkseellfpfqlktverCekCkavfHk 187
                                       ka+ + C  C ++e +f+   +++  C +C +++  
  gi|385806039|ref|YP_005842437.1|  16 KANCMKCTKCGKKEAIFKVPYTNYFLCADCYSTYFY 51 
                                       445567889**********999999*****998765 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.003
                         zf-RING_9 132 ekleklvelleeHvekCelCkakg..fiCelCks 163
                                       ++l+ l++   +  +kC+ C +     +C++Ck+
  gi|385806039|ref|YP_005842437.1| 269 KSLSWLYKERGSMLKKCKYCGGTSssEVCRFCKT 302
                                       4566667777778899****76543389****96 PP

>> zf-SNAP50_C  snRNA-activating protein of 50kDa MW C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   3.6   3.8e-05      0.23     140     197 ..      10      64 ..       7      67 .. 0.83
   2 ?   -1.4   0.4      0.25   1.5e+03     145     162 ..     281     298 ..     274     311 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.8e-05
                       zf-SNAP50_C 140 fkkklrrkkCkvCekfsakwvvlndkllpedpsyfCdkCfrslhydkngeklgdfkay 197
                                       +++++ + +C+ C k   k  ++    +p++ +++C +C+  + y++ ++ l+++++ 
  gi|385806039|ref|YP_005842437.1|  10 IRNSHIKANCMKCTKCGKKEAIF---KVPYTNYFLCADCYSTYFYKRLKRNLSRSNVL 64 
                                       56677888999999999999999...689999*************9998888766665 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.25
                       zf-SNAP50_C 145 rrkkCkvCekfsakwvvl 162
                                         kkCk C   s + v++
  gi|385806039|ref|YP_005842437.1| 281 MLKKCKYCGGTSSSEVCR 298
                                       567788887776666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       920  (0.0513135); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2062.97
//
Query:       gi|385806040|ref|YP_005842438.1|  [L=86]
Description: hypothetical protein FFONT_0998 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       409  (0.0228122); 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:                         0  (0); expected 0.2 (1e-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: 00:00:00.50
# Mc/sec: 512.47
//
Query:       gi|385806041|ref|YP_005842439.1|  [L=106]
Description: hypothetical protein FFONT_0999 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); 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 0.28s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 693.37
//
Query:       gi|385806042|ref|YP_005842440.1|  [L=853]
Description: ribonucleotide reductase [Fervidicoccus fontis Kam940]
Scores for complete 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-181  602.4   0.0   3.6e-180  600.0   0.0    1.9  2  Ribonuc_red_lgC  Ribonucleotide reductase, barrel domain
    2.7e-26   91.4   0.5    5.8e-26   90.3   0.5    1.6  1  Ribonuc_red_lgN  Ribonucleotide reductase, all-alpha domain
      2e-10   41.1   0.6      2e-10   41.1   0.6    2.5  2  ATP-cone         ATP cone domain
  ------ inclusion threshold ------
        0.1   12.6   0.0       0.18   11.7   0.0    1.3  1  CHAD             CHAD domain
       0.13   12.3   0.3        1.7    8.7   0.1    2.5  2  DUF1451          Zinc-ribbon containing domain


Domain annotation for each model (and alignments):
>> Ribonuc_red_lgC  Ribonucleotide reductase, barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.08   2.9e+02     237     267 ..      32      62 ..      22      64 .. 0.81
   2 !  600.0   0.0  9.9e-184  3.6e-180       1     524 []     206     788 ..     206     788 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.08
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 237 LakfvkkdeegkkefdwdelkkviqlvvraL 267
                                       L++ vkk ++g +e+d +++k+v++ v++ L
  gi|385806042|ref|YP_005842440.1|  32 LMQSVKKAANGFNEIDEEQIKEVVESVIKDL 62 
                                       4455589999999************999866 PP

  == domain 2  score: 600.0 bits;  conditional E-value: 9.9e-184
                                       EEE.....BSS-.....EEEE-X..............XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC   1 ssCfvlsvedsl.....esIletvkeaallskaggGvGlnlsklRakgslvkgtegaasGpvsfmklidavadvvkq 72 
                                       s+C+v+ v+dsl     ++I+++v+++al+ ++ggG+G+++s+lR++g++v++t+g asGp+sfm+l+d +++v+kq
  gi|385806042|ref|YP_005842440.1| 206 SACYVIPVRDSLttrnnDGIMDAVRAQALIQQQGGGTGFDFSELRPEGDIVGSTQGVASGPLSFMRLFDVTTEVIKQ 282
                                       79**************9************************************************************ PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.......... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......... RF
                   Ribonuc_red_lgC  73 gGkRrGAamvylevwHpDiekfidaKekntgeeenrlsnlnisvgvpdlFmeavkedkdwtLfsPrt.......... 139
                                       gGkRrGA+m++l+vwHpDi  fi+aK+ + +  ++ l+n+nisvgv d Fm+av++d+ ++L++Pr+          
  gi|385806042|ref|YP_005842440.1| 283 GGKRRGANMGVLHVWHPDIKRFIKAKTGELK--DVFLQNFNISVGVYDSFMRAVENDGIFPLINPRKtwlkntldid 357
                                       **************************99888..9********************************87877776665 PP

                                       ....XXX...........................................................XXXXXXXXXXX CS
                                       ....xxxxxxxxx.....................xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 140 ....vvkleklyg.....................ee.............feeeyeeleekakikkkevkakeLfeei 178
                                           +                             ++             +ee+++ +e++++i  + vka++Lf+e+
  gi|385806042|ref|YP_005842440.1| 358 skfyA-------VnlmrysieeewvqeelikeleKNdwsiplheskiitWEEALAIAENEKAIV-NYVKARDLFKEM 426
                                       55552.......0444444444443333333333113444444444554555555555555554.69********** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 179 aesawetgePgvlfkDtiNrrnvlekakggkIratNlCgEiplleyesvavCnLasinLakfvkkdeegkkefdwde 255
                                         sawe g+Pgvlf+DtiNr++++++   gkI+atN+CgE+plle+e+   CnL+sinL+k++  +e+gk +++w  
  gi|385806042|ref|YP_005842440.1| 427 TDSAWEGGDPGVLFIDTINRKHPTWYL--GKINATNPCGEEPLLEWEN---CNLGSINLTKYL-VEENGKYKINWVA 497
                                       ************************776..6******************...************.788********** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 256 lkkviqlvvraLdnvidvnkyplpeiekntkktRriGlGvmgladalaklgipydseealkfarkitelltyyayka 332
                                       l + +++++r+Ldnvid+n+ pl +i+k++ ktR+iGlGvmg+a++la+++ipyds ea+ +a k+ e ++y ay +
  gi|385806042|ref|YP_005842440.1| 498 LGNDVKIAIRFLDNVIDANRHPLSQITKANLKTRKIGLGVMGWAHLLAMMKIPYDSVEAIVLAYKLSEWIAYNAYLE 574
                                       ***************************************************************************** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..........................XXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................xxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 333 SvelAkergpfplfekskyskgilpvdefeeke....................kedweeLreeikkyGlrnamvtal 389
                                       S+elAke+gpfp+f+   y+  +   +++e+                      + dw++L ee +kyGlrna+vt++
  gi|385806042|ref|YP_005842440.1| 575 SIELAKEKGPFPEFKPDLYRPIWRDARKIEDLLsianiehgniesiikafdtpEIDWNKLEEEYRKYGLRNATVTSI 651
                                       ****************9999998777777322255556677788899999999************************ PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 390 aPTgsiSliagtssgiePifalvykksvtvgeflevnpvfeeeLkklglwseellkki..lesvqgleeipeeikrv 464
                                       aPTg+iS+i gtss+ieP+fal++++ v+vg f+e+++vf++eL+klgl++ +l +ki  ++s+qg++ei+ee+krv
  gi|385806042|ref|YP_005842440.1| 652 APTGTISIIGGTSSSIEPLFALAFMRIVSVGTFIEIDKVFLKELEKLGLDTPNLISKIaeTGSIQGMDEISEELKRV 728
                                       **********************************************************77677************** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 465 fktaldidqedhikaqaaiqkwidqsiSktinlpneatvedvkelyllAwklGlKgvtyY 524
                                       fkta+did+ +h+ +qa++q w+d ++Sktinl+ +++ e+v ++yllAwklG+Kg+t+Y
  gi|385806042|ref|YP_005842440.1| 729 FKTAHDIDPIWHMLQQASWQVWVDAGTSKTINLRRDEPPETVYNIYLLAWKLGIKGITVY 788
                                       ***********************************************************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 !   90.3   0.5   1.6e-29   5.8e-26       2      83 .]     123     203 ..     122     203 .. 0.95

  Alignments for each domain:
  == domain 1  score: 90.3 bits;  conditional E-value: 1.6e-29
                   Ribonuc_red_lgN   2 kltynalkvledrYllkdeng.eivEspqqmfmRvAlalaiaealydkleedkdlaeefydlmssqkflpasPtlmn 77 
                                       ++t+nalkvle+rYllk+ ++ +  E+p  mf+RvA++la  e  y   ++ + + +efy+ ms++kf+p+sPtlmn
  gi|385806042|ref|YP_005842440.1| 123 SFTFNALKVLEARYLLKNTESlRFTETPSMMFKRVARHLASVEGRY--NNNTEVYEREFYKIMSELKFIPNSPTLMN 197
                                       69*****************999*********************987..688888999******************** PP

                   Ribonuc_red_lgN  78 aGtelg 83 
                                       aGt++g
  gi|385806042|ref|YP_005842440.1| 198 AGTRNG 203
                                       ***986 PP

>> ATP-cone  ATP cone domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.6   5.5e-14     2e-10       1      81 [.      15     103 ..      15     107 .. 0.78
   2 ?   -1.7   0.4       1.2   4.4e+03      14      46 ..     790     822 ..     784     842 .. 0.69

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 5.5e-14
                                       -EEE-TTS-EEE--HHHHHHHHHHHHHH....-HHHHHHHHHHHHHHHHHHHIIT-BHHHHHHHHHHHHH....HSS CS
                          ATP-cone   1 ikViKRdGtvepfdvekIkraiekAceg....seeeideiaeeveaevrkrlrdgisteeIqdlvektli....ehp 69 
                                       i+V+KR+G++e f+ ek+ ++++kA++g    +ee+i+e++e v++++   + ++++++ I dlvek        +p
  gi|385806042|ref|YP_005842440.1|  15 IVVKKRNGSTEQFNLEKLMQSVKKAANGfneiDEEQIKEVVESVIKDLT-LKGKEVPSSVISDLVEKHFVsrilISP 90 
                                       68**************************777777777777777776663.34567************9988888666 PP

                                       -H.HHHHHHHHHH CS
                          ATP-cone  70 dy.avaaayilyr 81 
                                        + +va++y+l r
  gi|385806042|ref|YP_005842440.1|  91 IWeEVAKRYVLAR 103
                                       6634444444444 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.2
                                       -HHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHH CS
                          ATP-cone  14 dvekIkraiekAcegseeeideiaeeveaevrk 46 
                                       d++k ++ +ek  +++++++d+ ++e + e+ +
  gi|385806042|ref|YP_005842440.1| 790 DKSKSIQVLEKGIKKENKTVDNHVKEAVGELHE 822
                                       677888888888888888888887777666633 PP

>> CHAD  CHAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0     5e-05      0.18     128     185 ..     747     831 ..     716     836 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5e-05
                                       HHHHHT--S--.................................TSBHHHHHHHHHHHHHHHH.HHHH--------T CS
                              CHAD 128 ldallaaerle.................................aepaaaalekrlrkayrklekraakaeadesde 171
                                       ++ +++a+  +                                 + ++ ++lek ++k  +++++  ++a       
  gi|385806042|ref|YP_005842440.1| 747 WQVWVDAGTSKtinlrrdeppetvyniyllawklgikgitvyrdKSKSIQVLEKGIKKENKTVDNHVKEA------V 817
                                       44445333333666666666667777888888888888888888889999*************6666655......9 PP

                                       HHHHHHHHHHHHHH CS
                              CHAD 172 ealHelRkaaKrlR 185
                                        +lHe Rk++K++R
  gi|385806042|ref|YP_005842440.1| 818 GELHETRKSVKKIR 831
                                       ************99 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.1   0.00047       1.7       8      59 ..      23      74 ..      17      97 .. 0.76
   2 ?    0.3   0.0      0.19   6.7e+02      67     103 ..     607     643 ..     598     647 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00047
                           DUF1451  8 ekseeeleelvekakeklseaeeltkeelelvaeylkrDleeaarsleeske 59
                                      ++++ +le+l++++k+ ++  +e+++e++++v e + +Dl   ++++ +s  
  gi|385806042|ref|YP_005842440.1| 23 STEQFNLEKLMQSVKKAANGFNEIDEEQIKEVVESVIKDLTLKGKEVPSSVI 74
                                      566779**********************************987777766655 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.19
                           DUF1451  67 ldlelieesllealasiaDktqvelaelaedlehagv 103
                                       l ++ ie+  +e++ +  D  ++++++l+e+ ++ g+
  gi|385806042|ref|YP_005842440.1| 607 LSIANIEHGNIESIIKAFDTPEIDWNKLEEEYRKYGL 643
                                       5678899999999*****************9987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (853 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1123  (0.062636); expected 358.6 (0.02)
Passed bias filter:                      840  (0.0468515); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.85u 0.34s 00:00:01.19 Elapsed: 00:00:00.54
# Mc/sec: 4753.37
//
Query:       gi|385806043|ref|YP_005842441.1|  [L=295]
Description: beta-lactamase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-18   67.1   0.0    4.9e-18   65.8   0.0    1.6  1  Lactamase_B    Metallo-beta-lactamase superfamily
     0.0029   17.1   0.0     0.0049   16.4   0.0    1.5  1  Lactamase_B_2  Beta-lactamase superfamily domain
     0.0061   16.0   0.1      0.016   14.6   0.0    1.7  2  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.025   14.7   0.8       0.06   13.5   0.1    1.9  2  KaiA           KaiA C-terminal 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 !   65.8   0.0   1.1e-21   4.9e-18       6     186 ..      14     189 ..      11     216 .. 0.82

  Alignments for each domain:
  == domain 1  score: 65.8 bits;  conditional E-value: 1.1e-21
                                       SEEEEEE.ETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHC CS
                       Lactamase_B   6 vnsylie.gdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapa 81 
                                       +n+ +++ +++++i++DtG++++ +r+    + l  + + + a+i++H+H+DHiGg+ +l +++++ ++  + e + 
  gi|385806043|ref|YP_005842441.1|  14 TNVLIVTnDNKEAIIVDTGIDEDSGRKI--AKFLNQNSLTPVAIINSHSHADHIGGNSYLEKKFKIQSYSTKNECAF 88 
                                       7899999777****************97..7********************************************** PP

                                       CHCHHHHHHHHHCCHH.TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEE.TTCCEEEECTTTSSHH CS
                       Lactamase_B  82 lfmeeaddaasrkgll.lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvvey.gggkvlftGDallage 156
                                        +++ +++ + ++  +      +    ++     ++++ + ++++  + ++gh+   +++  gg +lft Da++  +
  gi|385806043|ref|YP_005842441.1|  89 IENPLLEPLYLYEAFPpESLTIKTLAAEPSSCNSIEEFNINEFGIEIIRLPGHSIDMIGLkIGGELLFTADAFFGID 165
                                       ************99999444444555555555556666666666666666666666666634678*********999 PP

                                       CCCCCC.TTCEEE-SHCHHHHHHHHHHHHH CS
                       Lactamase_B 157 tgridltlrgaevrdpsdaekyldsllkla 186
                                       t+  ++       ++++ ++++  +ll+l+
  gi|385806043|ref|YP_005842441.1| 166 TLIKHK------IPYHVNVKNSYLTLLMLK 189
                                       999999......888888888887777765 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 !   16.4   0.0   1.1e-06    0.0049       3      69 ..      27      93 ..      25     171 .. 0.56

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.1e-06
                                      EEES--TT......HHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC.C--EEEEEEEEHHHHH.....H CS
                     Lactamase_B_2  3 iLiDagpd......lrqqalralqPvelrdelppidaVllthaHyDHlaglltlre.lrpkklplyapkgvla.....v 69
                                      i++D+g d      +   a+ +       ++l p++ ++ +h+H+DH+ g   l + +   k++ y +k   a      
  gi|385806043|ref|YP_005842441.1| 27 IIVDTGIDedsgrkI---AKFL-----NQNSLTPVA-IINSHSHADHIGGNSYLEKkF---KIQSYSTKNECAfienpL 93
                                      788999995543221...2222.....355777887.***********8877777732...244554443333344443 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 !   14.6   0.0   3.7e-06     0.016       4      62 ..      21      78 ..      18      88 .. 0.82
   2 ?   -2.1   0.0      0.49   2.2e+03      28      45 ..     187     204 ..     178     224 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.7e-06
                     Lactamase_B_6  4 ld.nvkiLlDvGwdeskvslesalkelekviptvdliLLshatlehlGayallyakfksk 62
                                       d +  i++D G de   s +++ k+l++   t  +i+ sh+ ++h+G+ ++l +kfk +
  gi|385806043|ref|YP_005842441.1| 21 NDnKEAIIVDTGIDED--SGRKIAKFLNQNSLTPVAIINSHSHADHIGGNSYLEKKFKIQ 78
                                      563468********97..45789999*99999999**************99999988643 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.49
                     Lactamase_B_6  28 elekviptvdliLLshat 45 
                                        l++ +++ +++L sh +
  gi|385806043|ref|YP_005842441.1| 187 MLKEEVKKFNAVLPSHGD 204
                                       577788888888888866 PP

>> KaiA  KaiA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.1   4.9e+03      61      90 ..     159     189 ..     156     197 .. 0.69
   2 ?   13.5   0.1   1.3e-05      0.06      27      86 ..     214     275 ..     203     288 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.1
                                       HHHH.TT--HHHHHHHHHHHHHHHHHHHHCC CS
                              KaiA  61 kaff.adlsvskileihmelldefskqlkle 90 
                                        aff  d  + + +  h+++ +++   l+l+
  gi|385806043|ref|YP_005842441.1| 159 DAFFgIDTLIKHKIPYHVNVKNSYLTLLMLK 189
                                       4555247777778888888888888777776 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 1.3e-05
                                       HHHHHHHHH..HHHHHHHHCTSTTSSHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHH CS
                              KaiA  27 kelleelks..eyreivleyfkddsevnqkidefvnkaffadlsvskileihmelldefskq 86 
                                       + +l+++++  e r+++++ f++++ev++ i +++n+  f+++++++   ++  ++  f+  
  gi|385806043|ref|YP_005842441.1| 214 DAILKNINAilEVRDLIVNSFESKKEVESVISQVLNHYGFSNVPLAQYFLLKSAIMSYFAWL 275
                                       4566666542278**********************************999999999998755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); 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:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.48
# Mc/sec: 1829.35
//
Query:       gi|385806044|ref|YP_005842442.1|  [L=349]
Description: membrane protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.2e-35  120.9   0.3    1.2e-34  119.8   0.1    1.7  2  ABC_tran     ABC transporter
    9.7e-09   35.4  10.0    2.4e-05   24.3   1.4    2.7  3  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    1.9e-06   27.5   1.3    8.8e-06   25.3   1.3    2.0  1  SMC_N        RecF/RecN/SMC N terminal domain
    4.1e-05   24.2   1.1    4.1e-05   24.2   1.1    1.9  1  AAA_23       AAA domain
    4.5e-05   23.1   0.3     0.0001   21.9   0.3    1.6  1  AAA_29       P-loop containing region of AAA domain
    0.00023   21.4   0.2     0.0041   17.3   0.2    2.3  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
     0.0003   20.6   2.6     0.0016   18.3   2.6    2.2  1  AAA_15       AAA ATPase domain
    0.00037   19.4   1.4       0.23   10.2   0.2    2.5  2  ABC_ATPase   Predicted ATPase of the ABC class
     0.0004   20.1   0.1    0.00065   19.4   0.1    1.3  1  AAA_27       AAA domain
     0.0018   18.6   0.2     0.0042   17.4   0.2    1.7  1  AAA_22       AAA domain
     0.0073   16.2   0.1      0.023   14.6   0.1    1.8  1  RsgA_GTPase  RsgA GTPase
     0.0075   16.0   0.0      0.023   14.4   0.0    1.7  2  AAA_30       AAA domain
  ------ inclusion threshold ------
      0.012   14.8   0.0      0.017   14.2   0.0    1.4  1  T2SSE        Type II/IV secretion system protein
      0.071   11.9   0.3       0.11   11.3   0.3    1.2  1  Adeno_IVa2   Adenovirus IVa2 protein
      0.082   13.3   0.0       0.14   12.5   0.0    1.4  1  AAA_16       AAA ATPase domain
      0.092   13.3   0.0        0.2   12.2   0.0    1.6  1  AAA_18       AAA domain
       0.27   11.8   1.0       0.57   10.8   1.0    1.5  1  DUF4236      Protein of unknown function (DUF4236)


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   0.1   1.1e-37   1.2e-34       3     136 ..      28     168 ..      26     169 .. 0.98
   2 ?   -2.8   0.0       7.9   8.3e+03      31      45 ..     305     322 ..     304     342 .. 0.64

  Alignments for each domain:
  == domain 1  score: 119.8 bits;  conditional E-value: 1.1e-37
                                       EEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   3 nvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren 79 
                                        ++l+lk++ +  i+G+nGaGKStLlk+++gl + + G+i l+g+++++  l+  +++ig++pq   lf+++tvren
  gi|385806044|ref|YP_005842442.1|  28 PINLNLKKNGVGLIIGPNGAGKSTLLKVILGLIDAKRGNIILNGREITK--LPTEKRNIGYVPQSYALFENMTVREN 102
                                       689**********************************************..9************************* PP

                                       .............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       .............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  80 .............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                    e++e++ +++++l++++l +++v    s LSgGqkqrvalaral+  p+llllDEp+
  gi|385806044|ref|YP_005842442.1| 103 iefglkvrkiplnERNERVLNLARELKIEDLLNKKV----SILSGGQKQRVALARALAILPDLLLLDEPF 168
                                       ************9999********************....*****************************7 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 7.9
                                       HTTSS--SEEEE...EET CS
                                       xxxxxxxxxxxx...xxx RF
                          ABC_tran  31 lagllkpteGei...lld 45 
                                       l+g+l+ +eG+i   +++
  gi|385806044|ref|YP_005842442.1| 305 LYGELEIEEGTIikaRIQ 322
                                       688888889988444333 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   1.4   2.3e-08   2.4e-05       3      26 ..      40      68 ..      38     120 .. 0.69
   2 !   16.0   0.7   7.6e-06     0.008     197     294 ..     130     197 ..      90     198 .. 0.66
   3 ?   -1.0   0.0       1.1   1.2e+03      13      83 ..     202     276 ..     202     313 .. 0.71

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 2.3e-08
                            AAA_21  3 vliGpNgsGKSnLLdaldllarl.....d 26
                                      ++iGpNg+GKS+LL+ + +l ++     +
  gi|385806044|ref|YP_005842442.1| 40 LIIGPNGAGKSTLLKVILGLIDAkrgniI 68
                                      79*****************9774322221 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 7.6e-06
                            AAA_21 197 ielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPk 273
                                       ie+ ++++++                              lS G+k+  al+ al+ ++   +lll+DEp ++L+P+
  gi|385806044|ref|YP_005842442.1| 130 IEDLLNKKVSI-----------------------------LSGGQKQRVALARALAILP---DLLLLDEPFSNLDPQ 174
                                       33333333322.............................399**99999999999999...9*************5 PP

                            AAA_21 274 llrrllellkelsr..ngaQvil 294
                                            ++ll+++ +  +++ +i+
  gi|385806044|ref|YP_005842442.1| 175 SFVNAIDLLDRTVAriGLSTIIV 197
                                       55555555544444667777776 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.1
                            AAA_21  13 SnLLdaldllarl.....drdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrlersqv 83 
                                       SnLL++   ++++     +  +++++  +++++ ++ i   +d+  + ++++ + +  +s+  + ++ l l  +++
  gi|385806044|ref|YP_005842442.1| 202 SNLLKIATDVFFMkngkmLYLGDPDKALRDPKVLEAAIYLGFDNFIKLSDVKKHAN-IFSDIQEKDGYLALRSNDI 276
                                       78888888888888888888888888888888888888888888887777777777.6666666555555555555 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   1.3   8.4e-09   8.8e-06      24     196 ..      36     198 ..      27     219 .. 0.65

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 8.4e-09
                                       SSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--.....BTTCSSTTEEEEEEEEEETTEESSSSSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  24 ksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk.....skekasvkkaeveitfdnedkklkieke 95 
                                       +++  i+GpNG+GKs ll  i   LG  +a      k  ++i +     +   ++ + ++v   +   ++ ++ e+ 
  gi|385806044|ref|YP_005842442.1|  36 NGVGLIIGPNGAGKSTLLKVI---LGLIDA------KRGNIILNgreitKLPTEKRNIGYVPQSYALFENMTVRENI 103
                                       56789****************...884444......33444444332222334455666776666666666566666 PP

                                       CEEEEEEEET.TSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS CS
                                       xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  96 evsisrrvkr.kgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaL 171
                                       e+ +++r++  ++++e  +n   +++ ++++ll+++    + LSgG+k+ vala  +Ai       l llDe  ++L
  gi|385806044|ref|YP_005842442.1| 104 EFGLKVRKIPlNERNERVLN--LARELKIEDLLNKK---VSILSGGQKQRVALARALAILP----DLLLLDEPFSNL 171
                                       66666554440344555555..34555666666653...568****************984....48999******* PP

                                       -HHHHHHHHHHHHHHCTT..SEEEEE- CS
                                       xxxxxxxxxxxxxxxxxx..xxxxxxx RF
                             SMC_N 172 Deknvkkvaellkekskn..aQfivis 196
                                       D +   +  +ll+++  +     i++s
  gi|385806044|ref|YP_005842442.1| 172 DPQSFVNAIDLLDRTVARigLSTIIVS 198
                                       *99999999998877666223333333 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   1.1   3.9e-08   4.1e-05      15      40 ..      29      57 ..      11     265 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 3.9e-08
                            AAA_23 15 idF...skgltlItGpNGaGKTTildAik 40
                                      i++   ++g+ lI+GpNGaGK+T+l  i 
  gi|385806044|ref|YP_005842442.1| 29 INLnlkKNGVGLIIGPNGAGKSTLLKVIL 57
                                      44455788*****************9885 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.3   9.9e-08    0.0001      17      43 ..      31      57 ..      22      71 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 9.9e-08
                            AAA_29 17 ieidlkgatlltGpsGsGKSTllDAiq 43
                                      ++++ +g+ l++Gp+G+GKSTll  i 
  gi|385806044|ref|YP_005842442.1| 31 LNLKKNGVGLIIGPNGAGKSTLLKVIL 57
                                      5677788***************96555 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.2   3.9e-06    0.0041      26      89 ..     134     184 ..      95     185 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.9e-06
                           SbcCD_C  26 lsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                       l+++++ lSGG+kq    +ala ala            ++l++LDE Fs+lD++s  ++++ll+
  gi|385806044|ref|YP_005842442.1| 134 LNKKVSILSGGQKQ---RVALARALA----I------LPDLLLLDEPFSNLDPQSFVNAIDLLD 184
                                       77888888888884...344444443....3......3789*******************9986 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   2.6   1.5e-06    0.0016      18      80 ..      30     129 ..      26     348 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.5e-06
                            AAA_15  18 eidlsee.ltvliGkNnsGKSsilealdlFlnnkekkn.....................................kk 56 
                                        ++l+++ + ++iG+N++GKS++l+++  +++ k + n                                     ++
  gi|385806044|ref|YP_005842442.1|  30 NLNLKKNgVGLIIGPNGAGKSTLLKVILGLIDAK-RGNiilngreitklptekrnigyvpqsyalfenmtvreniEF 105
                                       5778888899******************999988.555577777777777776666666666666655555555544 PP

                            AAA_15  57 vikiekedleifeniseskdikId 80 
                                        +k+ k  l++ +++  +   +++
  gi|385806044|ref|YP_005842442.1| 106 GLKVRKIPLNERNERVLNLARELK 129
                                       444445555554444444444444 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 !   10.2   0.2   0.00022      0.23     243     264 ..      35      56 ..      31      84 .. 0.87
   2 !    8.0   0.1    0.0011       1.1     377     417 ..     180     220 ..     142     236 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00022
                                       -SSEEEEEE-TTSSHHHHHHHH CS
                        ABC_ATPase 243 pkGvtlIvGggfhGKsTLLeAl 264
                                       ++Gv lI+G++  GKsTLL+ +
  gi|385806044|ref|YP_005842442.1|  35 KNGVGLIIGPNGAGKSTLLKVI 56 
                                       679****************987 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0011
                                       HHCHHHHHHHH--EEEEEESS-GCCTTT-SEEEEEETTEEE CS
                        ABC_ATPase 377 vdrvrelykklgvstilvvggsgdyldvAdtvilmeeykpk 417
                                       +d++ + ++++g+sti+v+  ++++l++A  v  m++ k+ 
  gi|385806044|ref|YP_005842442.1| 180 IDLLDRTVARIGLSTIIVSQNASNLLKIATDVFFMKNGKML 220
                                       56777788999************************987665 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   6.1e-07   0.00065       7      49 ..      16      59 ..      11      60 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 6.1e-07
                            AAA_27  7 dLery.GkftdrsldfsaeeadlhliyGpNEAGKstalrAisdl 49
                                       Le+y G f    ++++ +++++ li+GpN AGKst+l+ i  l
  gi|385806044|ref|YP_005842442.1| 16 GLEAYlGGFHLGPINLNLKKNGVGLIIGPNGAGKSTLLKVILGL 59
                                      5777778899999999999*******************988765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.2     4e-06    0.0042       4      99 ..      35     166 ..      31     207 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4e-06
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee............erpevvfvtlpsst..sskdllrellralgl 66 
                                       + g+++++G+ G+GK+tll+ +l   d+     +             +++ + + ++s    +  ++++++   l++
  gi|385806044|ref|YP_005842442.1|  35 KNGVGLIIGPNGAGKSTLLKVILGLIDAKR--GNiilngreitklpTEKRNIGYVPQSYAlfENMTVRENIEFGLKV 109
                                       7899****************9998876433..225588888888876666666666666667777777777777777 PP

                            AAA_22  67 elka....................erlsseell.ealeqalrarav...ielliiDE 99 
                                       ++                       +++ + l   + ++ + ara    + ll++DE
  gi|385806044|ref|YP_005842442.1| 110 RKIPlnernervlnlarelkiedlLNKKVSILSgGQKQRVALARALailPDLLLLDE 166
                                       777777777777777744444444333344444444444444444477777777777 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   2.2e-05     0.023      96     130 ..      32      67 ..      17      76 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.2e-05
                                       HCTT.SEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                       RsgA_GTPase  96 llkd.ktsvlvGqSGvGKStLinallpelelktgev 130
                                       +lk+  + +++G+ G+GKStL++++l+  ++k g++
  gi|385806044|ref|YP_005842442.1|  32 NLKKnGVGLIIGPNGAGKSTLLKVILGLIDAKRGNI 67 
                                       555547889****************99888877766 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   2.2e-05     0.023      17      50 ..      35      68 ..      30      77 .. 0.86
   2 ?   -2.2   0.0       2.8   2.9e+03     103     141 ..     199     239 ..     193     281 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.2e-05
                            AAA_30 17 gdrvavltGpAGtGKttalkalreaweaaggrvi 50
                                      ++ v ++ Gp G+GK+t+lk++  +++a+ g++i
  gi|385806044|ref|YP_005842442.1| 35 KNGVGLIIGPNGAGKSTLLKVILGLIDAKRGNII 68
                                      456899*****************99999977776 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.8
                            AAA_30 103 kqlaallkaaeka....gakvilvGDerQlasVeaGgvlrdlv 141
                                       +++ +llk+a++     + k++ +GD++  ++    +vl+  +
  gi|385806044|ref|YP_005842442.1| 199 QNASNLLKIATDVffmkNGKMLYLGDPD--KALRDPKVLEAAI 239
                                       5677777777775555578888888887..5555555555554 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.6e-05     0.017     125     162 ..      32      69 ..      11     139 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.6e-05
                             T2SSE 125 avrerglilvsGgTgsGKttllyallkeinksderivt 162
                                        ++++g+ l+ G+ g GK+tll ++l  i+++  +i++
  gi|385806044|ref|YP_005842442.1|  32 NLKKNGVGLIIGPNGAGKSTLLKVILGLIDAKRGNIIL 69 
                                       5667788899**********************999986 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.3    0.0001      0.11      81     108 ..      31      57 ..      22      84 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0001
                        Adeno_IVa2  81 lnyglqPviGviyGPtGsGksqllrnli 108
                                       ln++++  +G+i GP G+Gks ll+ ++
  gi|385806044|ref|YP_005842442.1|  31 LNLKKNG-VGLIIGPNGAGKSTLLKVIL 57 
                                       4555554.7***************9876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00013      0.14      27      60 ..      39      73 ..      31     166 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                            AAA_16 27 vllsGesGvGKsslvrellralekdg.giflrgkc 60
                                       l++G+ G GKs+l++ +l  + +++  i l+g+ 
  gi|385806044|ref|YP_005842442.1| 39 GLIIGPNGAGKSTLLKVILGLIDAKRgNIILNGRE 73
                                      69***************998888885244455554 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00019       0.2       2      69 ..      40     130 ..      40     153 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00019
                            AAA_18   2 lltGtpGvGKttlakeL.....skrlgf..................gvnlrdvakenglllevdpealdeskrlded 55 
                                       l+ G+ G+GK+tl k +     +kr+++                   v  +  ++en+++ e+ ++ l+  k+   +
  gi|385806044|ref|YP_005842442.1|  40 LIIGPNGAGKSTLLKVIlglidAKRGNIilngreitklptekrnigYVPQSYALFENMTVRENIEFGLKVRKIPLNE 116
                                       689**************999998887668998888888888888844444444556666666666677777777777 PP

                            AAA_18  56 kldklldaleenss 69 
                                       + +++l++ +e   
  gi|385806044|ref|YP_005842442.1| 117 RNERVLNLARELKI 130
                                       77777776666544 PP

>> DUF4236  Protein of unknown function (DUF4236)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.0   0.00054      0.57       7      31 ..      24      47 ..      21      51 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00054
                           DUF4236  7 ikigPgvrlNlSksGiSvSvGvrga 31
                                      + +gP ++lNl k G+++ +G+ ga
  gi|385806044|ref|YP_005842442.1| 24 FHLGP-INLNLKKNGVGLIIGPNGA 47
                                      679**.*****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 2351.32
//
Query:       gi|385806045|ref|YP_005842443.1|  [L=266]
Description: binding-protein-dependent transport system inner membrane protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.4e-16   59.2  17.0    4.4e-16   59.2  17.0    2.1  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   8.8      0.36   6.4e+03      19      67 ..      14      65 ..       4      68 .. 0.69
   2 !   59.2  17.0   2.4e-20   4.4e-16       1     173 [.      69     258 ..      69     263 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.36
                      BPD_transp_1 19 llrpliivllslPsfvlaillvlvf...vilsilghlilpviillllsaapy 67
                                      +l+++  +++s P+ v++ + +  +   + ++ +  + l  ii++ l a++ 
  gi|385806045|ref|YP_005842443.1| 14 ILSGILLLFFSYPIAVIFAVGISGAlssFKITQFELGLLITIIASSLAALAS 65
                                      6778888888999999888877666666666666666666666666655554 PP

  == domain 2  score: 59.2 bits;  conditional E-value: 2.4e-20
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf...........vilsilghlilpviillllsaap 66 
                                       gi+l++++a ++n+++++++ ++++++ ++P+++++i++vl f            +  ++ ++i+++++++l+ +  
  gi|385806045|ref|YP_005842443.1|  69 GIPLAYILA-RYNFRFKEVIETIVDIPIAVPHMIVGIMIVLSFaqyygfgallqTLGIKVIDTIFGAVLAVLYVSST 144
                                       89*******.****************************************999955556789999************ PP

                      BPD_transp_1  67 yvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllle 143
                                       y+++i+++a++ l+ + +++a+ lGa+r  +f+ vv+Pn++  ++  ++ +++++  +a +l++++         ++
  gi|385806045|ref|YP_005842443.1| 145 YAVRIIESAIKGLDPEIENVALSLGAPRAITFFSVVIPNIKKALANAILTSWARASSEAGALLIVA-------YQVN 214
                                       *****************************************************************9.......4455 PP

                      BPD_transp_1 144 ailgydyseis..............nggvlalviavlllnlvad 173
                                       +  ++ y++                +  ++a++i++l + l+++
  gi|385806045|ref|YP_005842443.1| 215 FAGNFVYPASVaiyeayvglgvleaARFSVAMLILILGIYLATR 258
                                       55555555444555566677778855555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       986  (0.0549947); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); 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):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1712.31
//
Query:       gi|385806046|ref|YP_005842444.1|  [L=378]
Description: ABC-type molybdate transport system periplasmic component-like protein [Fervidicoccus fontis Kam940]
Scores for complete 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  101.1   0.0    9.2e-29  100.8   0.0    1.1  1  SBP_bac_11    Bacterial extracellular solute-binding protein
  ------ inclusion threshold ------
      0.049   13.8   2.4        0.1   12.8   2.4    1.5  1  ATPase_gene1  Putative F0F1-ATPase subunit Ca2+/Mg2+ transpor


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 !  100.8   0.0     1e-32   9.2e-29       2     229 ..      45     340 ..      44     341 .. 0.90

  Alignments for each domain:
  == domain 1  score: 100.8 bits;  conditional E-value: 1e-32
                                       EEEE-SSTHHHHHHHHHHHHHH.H-.--EEEEESSHHHHHHHHHHH..-SEEEESSH.HHHH.HHHHGGGGGGG-EE CS
                        SBP_bac_11   2 tvaaagslaaalrelaaaFeah.tg.vkvevsaggsgklarqiadgarpDvwipassawlel.laaaglvqaesavp 75 
                                       +v aag+l++ +++l   ++++ ++  +    ++gsg++a++   ++ + ++++a++  + + l  a+l +   + +
  gi|385806046|ref|YP_005842444.1|  45 NVGAAGTLKFSFSQLLSIYSNYfPSvQQGSPFFAGSGEVAQKEVTTKSYSIVAAADTSTIPSvLFPANLSD--YEIA 119
                                       799****************9987774677***************************777666379999999..**** PP

                                       EEEEEEEEEESTT-T................T---SHHHHHHS.........S--EEEE--T-TTTTHH.HHHHGGG CS
                        SBP_bac_11  76 lassplviavpkgnp................kkikgwadLlkp.........glklavadPttspsGlaalalleaa 127
                                       + ++++ i+v  ++p                  +++w+d +++         ++ ++v++P t+psG++a+++l+ a
  gi|385806046|ref|YP_005842444.1| 120 FGYTQMTIIVDLNTPygrevyslwnqsiqqiPYSDTWNDTWRKifniialnpNTVVGVSNPFTDPSGYQAQCMLKLA 196
                                       **************87777777777666554457799998888888887777889********************** PP

                                       --......HHHHHHHHHTEEEE..ESSHHHHHHHHHTTT.-SEEE.EEHHHH.....H..HSTTSSEEEE--TTT-- CS
                        SBP_bac_11 128 ga......qellkalekkvvkl..gessrqlltaveage.adagi.vyesea.....kaaengdkleavylpeglnl 189
                                       g       ++l+ a++++  k+  ++++++ll+ + a++ ++ ++ +y+s+a     ++++ng ++++++lp  +nl
  gi|385806046|ref|YP_005842444.1| 197 GLtfygnsSYLWSAIYSNPSKYimRNTETDLLSLMTANNtVQFILsAYLSNAipqvqYYQQNGYNITYITLPSAINL 273
                                       9999999***********9998878899******88755389777699****666665569**************** PP

                                       ..............................EEEEEEEE-TT--HHHHHHHHHTTSHHHHHHHHHTT- CS
                        SBP_bac_11 190 .d..........................pldypaavlkkaakreaAraFlafLrspeaqailrkyGf 229
                                        d                          p+ y+++++++ ++++a  +F+ +++sp +q++l++yG 
  gi|385806046|ref|YP_005842444.1| 274 gDlsyvnyykqvnvtwtqlgttktfsckPVIYTITIPSNVQNKQASIDFILLIYSPIGQQVLKSYGI 340
                                       99****************************************************************6 PP

>> ATPase_gene1  Putative F0F1-ATPase subunit Ca2+/Mg2+ transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   2.4   1.1e-05       0.1      32      52 ..       6      26 ..       3      28 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.1e-05
                      ATPase_gene1 32 spwfliiglllGlaaGfynvy 52
                                      ++w+l+ig+++Gla+G+ +vy
  gi|385806046|ref|YP_005842444.1|  6 KYWYLTIGIIIGLAIGGVLVY 26
                                      79******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); 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: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.53
# Mc/sec: 2133.50
//
Query:       gi|385806047|ref|YP_005842445.1|  [L=373]
Description: pelota-like protein [Fervidicoccus fontis Kam940]
Scores for 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   73.1   0.2    3.9e-20   72.2   0.2    1.5  1  eRF1_1       eRF1 domain 1
    2.4e-15   57.0   0.2      2e-14   54.0   0.0    2.5  3  eRF1_3       eRF1 domain 3
    3.4e-08   33.9   0.1    6.2e-08   33.0   0.1    1.4  1  eRF1_2       eRF1 domain 2
  ------ inclusion threshold ------
      0.017   14.6   0.1      0.027   14.0   0.1    1.2  1  BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
       0.21   11.7   3.6        2.1    8.5   0.8    2.7  2  Smoothelin   Smoothelin cytoskeleton protein


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 !   72.2   0.2   1.1e-23   3.9e-20       8     127 ..       5     123 ..       1     124 [. 0.90

  Alignments for each domain:
  == domain 1  score: 72.2 bits;  conditional E-value: 1.1e-23
                                       TBTTSCCEEEEEE-SCHHHHHHHHHCHTTHEEEEEEEECHHH.......--CEEEEEEEEEEEEEEECTTSSEEEEE CS
                            eRF1_1   8 lekdgsgsvtLipeddedlwhlynliapgdsvrastvrkvqresstgsreservklkLtikvekvdfdkdagvlris 84 
                                       +  +++ ++++ +e+ +dlw ly ++++gd +  +t r v+++ + g  +s+r  ++Lti+   ++f++ ++ lri+
  gi|385806047|ref|YP_005842445.1|   5 FIDNKKTVLKIKIENIDDLWLLYTILQKGDLITMKTLRDVKQS-EGG--KSRRLPMTLTISLSHMEFQPFTNKLRIR 78 
                                       55789999********************************773.333..369************************* PP

                                       EEEEEGGGG.--TTSEEEEEE-TTSEEEEEECE.ESHHHHHHHHH CS
                            eRF1_1  85 Gkvieeneh.vklgafhtldlelkrpftiikee.wdsfalerLke 127
                                       G v e+ ++   lg++htl +  ++++ +++ee wd+  ++r+++
  gi|385806047|ref|YP_005842445.1|  79 GIVKEGPDKfGILGSHHTLSVGEGDELIVFREEgWDQSTIKRMEK 123
                                       ******9986789*****************9888******99985 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.94   3.4e+03      73      94 ..     119     140 ..      92     146 .. 0.78
   2 ?   -1.6   0.0         1   3.7e+03       6      30 ..     215     239 ..     209     242 .. 0.75
   3 !   54.0   0.0   5.5e-18     2e-14       6     113 .]     258     352 ..     253     352 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.94
                                       HHHHHHHHTT-EEEEE-TTSHH CS
                            eRF1_3  73 elvenveesgakveiissesee 94 
                                       + +e++++s ++v i+  + +e
  gi|385806047|ref|YP_005842445.1| 119 KRMEKYKKSFGSVLIVAVDYDE 140
                                       4578899999999998877665 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1
                                       HHHHHHHHHHHCTCSSEEESHHHHH CS
                            eRF1_3   6 klleefleelakdtgkavYGveevl 30 
                                       + +++++  l++ +   vYG++e+ 
  gi|385806047|ref|YP_005842445.1| 215 NSINKLTIVLENTSMGGVYGIKETI 239
                                       5677777777777777899999985 PP

  == domain 3  score: 54.0 bits;  conditional E-value: 5.5e-18
                                       HHHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSHHHHHS-HHH-HHHHHHHHHHHHHHHHHTT CS
                            eRF1_3   6 klleefleelakdtgkavYGveevlkalemgAvetLLvseelersrdtlkekvketgeelelvelieelvenveesg 82 
                                       +lle+ l +l+  +++++ G ee ++a e+gAv+++L+++el +++d +++k             iee+++nve++g
  gi|385806047|ref|YP_005842445.1| 258 QLLENILIKLSVKPEQVAIGLEECKNASEIGAVSDILILDELLSNQDLERRK------------EIEEVLNNVESFG 322
                                       78999999*************************************9996666............39*********** PP

                                       -EEEEE-TTSHHHHHHHHHTTTEEEEESS-- CS
                            eRF1_3  83 akveiisseseeGeqlvkafgGiaaiLRykv 113
                                       ++v+i++s se+ e+l  ++g i+++LR+++
  gi|385806047|ref|YP_005842445.1| 323 GRVVILPSCSEASEKL-YGLGSIVCLLRFPI 352
                                       ****************.************96 PP

>> eRF1_2  eRF1 domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.1   1.7e-11   6.2e-08       4     127 ..     133     244 ..     130     250 .. 0.80

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 1.7e-11
                                       EEEEETTEEEEEEEESSCEEEEEEEE------BSTTBSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCHTTTESEE CS
                            eRF1_2   4 livldegeAtigllkgsrtevlkkievsvPkKhkrGgqsarrfeRlreekleeflkkvaeaankafllvdkdklkgi 80 
                                       ++ +d +e  i+l +++  ++l + + ++P+K      s++       +++ e ++++a+ + +  + + ++++ gi
  gi|385806047|ref|YP_005842445.1| 133 IVAVDYDEYSIALFRRQGYKILVSNDLHIPGKGD---ESRE-------KAITEAINEIASLVLSI-I-NREKDIFGI 197
                                       6789999************************985...4544.......55566666666555555.3.4559***** PP

                                       EEEESSTHHHHHHHHHHHHHHHHTCCEEEEE-S-TSCHHHHHHHHC..C CS
                            eRF1_2  81 ilagpgfvkeefldkdlldaelkkkviklvdvsyggesglnevlek..a 127
                                       ++ gpgf+ke   +    ++  +k  i+l ++s gg +g++e + k   
  gi|385806047|ref|YP_005842445.1| 198 VISGPGFFKEVVSE--AIKNSINKLTIVLENTSMGGVYGIKETIAKgkP 244
                                       **********8765..568999999*******************98443 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 ?   14.0   0.1   7.5e-06     0.027     180     246 ..     158     219 ..     148     233 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.5e-06
                                       HHHHHHHTT--HHHHHHHHHHHHHHHHHHHHHTT---SS.EEEES.GGGG-HHHHHHH.....HHHH- CS
                       BcrAD_BadFG 180 elrdalsggekaedIlaglhraialrvialisrsggvtdevtltG.Gvakneaavkelrklvkenyge 246
                                       +l    +g+e++e+ + ++ ++ia++v ++i+r++++   +++ G G++k+  + +++    k+++++
  gi|385806047|ref|YP_005842445.1| 158 DLHIPGKGDESREKAITEAINEIASLVLSIINREKDIFG-IVISGpGFFKE-VVSEAI----KNSINK 219
                                       55555689*****************************98.66666488887.555555....555554 PP

>> Smoothelin  Smoothelin cytoskeleton protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1     0.035   1.2e+02       5      29 ..       8      32 ..       6      34 .. 0.87
   2 ?    8.5   0.8   0.00058       2.1      10      39 ..     283     311 ..     278     311 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.035
                        Smoothelin  5 aaskltseeLeaIeDeevLdkmLeq 29
                                      ++++ ++ ++e I D+ +L + L++
  gi|385806047|ref|YP_005842445.1|  8 NKKTVLKIKIENIDDLWLLYTILQK 32
                                      67788999***********999986 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00058
                        Smoothelin  10 tseeLeaIeDeevLdkmLeqasdyEeRrrI 39 
                                       ++ e+ a+ D+ +Ld +L + +d E+R+ I
  gi|385806047|ref|YP_005842445.1| 283 NASEIGAVSDILILDELLSN-QDLERRKEI 311
                                       6789**************76.9******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); 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: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 2247.05
//
Query:       gi|385806048|ref|YP_005842446.1|  [L=348]
Description: radical SAM protein [Fervidicoccus fontis Kam940]
Scores for complete 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   55.0   0.2    2.8e-13   50.6   0.1    2.3  2  Radical_SAM  Radical SAM superfamily
    1.1e-08   35.2   0.1      3e-08   33.8   0.0    1.7  2  Fer4_14      4Fe-4S single cluster domain
    7.6e-07   29.5   0.1    1.8e-06   28.3   0.1    1.6  1  Fer4_12      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6   0.1   4.7e-17   2.8e-13       4     108 ..      34     140 ..      31     161 .. 0.90
   2 ?    2.3   0.0     0.033     2e+02      94     150 ..     179     246 ..     146     259 .. 0.65

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 4.7e-17
                                       ESEESS--TTTSCCTT..HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC.CCT CS
                                       xxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                       Radical_SAM   4 trgCnlrCsfCarpet..vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla.vpg 77 
                                       t  Cn +C +C++++    ++  ++ ++ +e+ +e+++e+ ++ g+k   ++ggepl   d + ++ +l k    ++
  gi|385806048|ref|YP_005842446.1|  34 TGLCNEKCFYCPVSYLrrNKDLIYVNERKIENFEEIFEEI-ERSGAKSASITGGEPLIVFDRTTKIIELLKQNfGSN 109
                                       667***********9999999*******************.9****************9999988888888888*** PP

                                       EEEEEEECSSCHGHHHHHHHHHTT-SEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  78 iritvetngtlpdeeklerllelgvdrvslg 108
                                       ++i++ tng+l++e++l++l ++g+d + ++
  gi|385806048|ref|YP_005842446.1| 110 FHIHLYTNGILINEDVLKKLEKAGLDELRIH 140
                                       ************************8877665 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.033
                                       HHHHHHTT-SEEEEEEBSSSHH..........HHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxx..........xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  94 lerllelgvdrvslgleaadde..........kvlklmn.rghtfeevlealeklreagikrvvdriv 150
                                       +e l+++g d ++++   a++           ++ +     ++++e  ++++e+++++ +k  +++++
  gi|385806048|ref|YP_005842446.1| 179 AEFLDKAGADFLNINELEANETniknlringfVISDNGIvVNGSRETAMKVIEYAKKHSLKIPIHFCP 246
                                       55566666666666666666664433333333111111124456699999999999999886556555 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 !   33.8   0.0   5.1e-12     3e-08       2      92 ..      32     121 ..      31     140 .. 0.79
   2 ?   -3.0   0.0       1.3   7.8e+03      65      84 ..     224     243 ..     194     245 .. 0.69

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 5.1e-12
                           Fer4_14   2 fvrlsgCnlsCkgCd...nketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlk 75 
                                       f+ ++ Cn +C  C     + +++  + ++ + e  e+i+++ + s  k +  ++tGGePL+    +   k+++ lk
  gi|385806048|ref|YP_005842446.1|  32 FL-TGLCNEKCFYCPvsyLRRNKDLIYVNERKIENFEEIFEEIERSGAKSA--SITGGEPLIV--FDRTTKIIELLK 103
                                       66.899****99997666556677888888888888899988888888666..********76..677788888888 PP

                           Fer4_14  76 eey.pekkiwletngtle 92 
                                       +++  +++i+l+tng l 
  gi|385806048|ref|YP_005842446.1| 104 QNFgSNFHIHLYTNGILI 121
                                       888777********9875 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.3
                           Fer4_14  65 kellklvkrlkeeypekkiw 84 
                                       ++ +k++++ k++  +++i+
  gi|385806048|ref|YP_005842446.1| 224 ETAMKVIEYAKKHSLKIPIH 243
                                       45567777777777666666 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 !   28.3   0.1     3e-10   1.8e-06       5     105 ..      26     131 ..      24     157 .. 0.72

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 3e-10
                           Fer4_12   5 Gvrlslfvsg.CnlsCkgCfnketwsfk...sgkeftkelleeiiedlkkesiegltllGGEPllpena.eallelv 76 
                                       G+ +++f++g Cn +C +C    +++ k   + +e + e  eei+e+++ +  +  +++GGEPl  + +  +++el+
  gi|385806048|ref|YP_005842446.1|  26 GIKAVIFLTGlCNEKCFYCPVSYLRRNKdliYVNERKIENFEEIFEEIERSGAKSASITGGEPLIVFDRtTKIIELL 102
                                       77888886666*******98555555442224444457778899999999999************887657889999 PP

                           Fer4_12  77 kevkeekpekdiwlytgytl.eelskkeke 105
                                       k+    ++   ++ ++g  + e+++kk  +
  gi|385806048|ref|YP_005842446.1| 103 KQNFGSNF-HIHLYTNGILInEDVLKKLEK 131
                                       99998888.478888887551445544333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 1957.84
//
Query:       gi|385806049|ref|YP_005842447.1|  [L=241]
Description: putative nucleotidyltransferase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-07   31.2   0.4    4.9e-07   30.0   0.4    2.1  1  NTP_transf_2     Nucleotidyltransferase domain
    3.2e-05   23.9   0.1    8.8e-05   22.5   0.1    1.8  1  Polbeta          Polymerase beta, Nucleotidyltransferase
     0.0071   15.8   0.0     0.0097   15.3   0.0    1.2  1  Put_Phosphatase  Putative Phosphatase


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 !   30.0   0.4   8.2e-11   4.9e-07       2      53 ..      30      79 ..      29     228 .. 0.85

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 8.2e-11
                                      HHHHHHHHHHTT.TSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHH CS
                      NTP_transf_2  2 kklleelkelep.vakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegl 53
                                      kk+++++  le+ +++ +l+GS+arG+ ++ SD+D++++ + +++   + e +
  gi|385806049|ref|YP_005842447.1| 30 KKARNIMGILESkNIRSFLHGSVARGDVHSKSDVDIVILQDIPSY---VIELT 79
                                      567777777777799************************999977...33333 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.1   1.5e-08   8.8e-05       6      40 ..      38      70 ..      33      85 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.5e-08
                                      THHHHHHHHSTTEEEEEE-S------EEEEEEEES CS
                           Polbeta  6 ilekekeielaylFGSrakgkareeSDiDlavllk 40
                                      ile++ +i+  +l+GS+a+g+ +++SD+D+ +l +
  gi|385806049|ref|YP_005842447.1| 38 ILESK-NIR-SFLHGSVARGDVHSKSDVDIVILQD 70
                                      56666.554.58******************99865 PP

>> Put_Phosphatase  Putative Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.6e-06    0.0097      31     124 ..       4      98 ..       1     112 [. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.6e-06
                   Put_Phosphatase  31 eelretlrkglwnelmdrvlkelheqgvseadikkvlrsiplspglveli.kslakkkleldliiiSDaNsffieei 106
                                       e++ +++  +++ e+ ++ lk l+e+ ++ ++i  +l+s  + + l   + +   ++k+ +d++i+ D  s+ ie +
  gi|385806049|ref|YP_005842447.1|   4 EKVSKNYD-EFYFEYGEKELKILNEKRKKARNIMGILESKNIRSFLHGSVaRGDVHSKSDVDIVILQDIPSYVIELT 79 
                                       56666776.899*******************************99976551555577899***************** PP

                   Put_Phosphatase 107 leaagledlFseif.tNPa 124
                                       le  g+  + ++i  + P+
  gi|385806049|ref|YP_005842447.1|  80 LESFGILPVLKRIVqATPS 98 
                                       ******9999996415555 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:                      381  (0.0212505); 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 0.29s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1468.87
//
Query:       gi|385806050|ref|YP_005842448.1|  [L=164]
Description: hypothetical protein FFONT_1008 [Fervidicoccus fontis Kam940]
Scores for complete 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-43  146.4   6.7    5.4e-43  146.1   6.7    1.2  1  DUF2286   Uncharacterized protein conserved in archaea (DUF22


Domain annotation for each model (and alignments):
>> DUF2286  Uncharacterized protein conserved in archaea (DUF2286)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.1   6.7     3e-47   5.4e-43       3     137 ..       9     145 ..       7     161 .. 0.97

  Alignments for each domain:
  == domain 1  score: 146.1 bits;  conditional E-value: 3e-47
                           DUF2286   3 lvikaeegkiaskeivegdleevvkevakeal.keWnpeesDfivlrdklelelklplkpelydklkelsl.sregn 77 
                                       ++i+a++gk+++k+iveg++eevvk++ ke+l +eW p+ sDf++lrd +e+elk++l++e+++k+ke++l +++++
  gi|385806050|ref|YP_005842448.1|   9 IIINAHSGKVKDKKIVEGEFEEVVKNAGKEFLlNEWLPSFSDFMILRDIFEVELKSSLPKEVISKYKEYNLkRKDKD 85 
                                       89****************************988**************************************889999 PP

                           DUF2286  78 eaivklPvyvisfdnewidedtyvdkkvyvvapyiddeakkeleeeaaevtkeekeeeae 137
                                       +++++lPvy+i++++ +i+ed+y+d+ v vvapyi++e ++ l+e ++e+tk+++ ee e
  gi|385806050|ref|YP_005842448.1|  86 TLVATLPVYLIVYESLKISEDSYHDRGVSVVAPYIREEDAQLLSELLIETTKKPTLEEIE 145
                                       9*****************************************************998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1115  (0.0621897); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1104.47
//
Query:       gi|385806051|ref|YP_005842449.1|  [L=406]
Description: aminotransferase [Fervidicoccus fontis Kam940]
Scores for complete 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-39  134.7   0.0    4.8e-39  134.6   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    1.6e-13   50.2   0.0    2.5e-13   49.6   0.0    1.2  1  Aminotran_MocR   Alanine-glyoxylate amino-transferase
     0.0043   15.8   0.0      0.006   15.3   0.0    1.2  1  Aminotran_3      Aminotransferase class-III
  ------ inclusion threshold ------
      0.038   13.7   0.6       0.53   10.0   0.0    2.4  2  Fis1_TPR_N       Fis1 N-terminal tetratricopeptide repeat
      0.038   13.3   0.0      0.056   12.7   0.0    1.2  1  Beta_elim_lyase  Beta-eliminating lyase
       0.14   10.9   0.0       0.22   10.2   0.0    1.2  1  DPPIV_N          Dipeptidyl peptidase IV (DPP IV) N-terminal 


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 !  134.6   0.0   1.6e-42   4.8e-39       6     360 ..      34     391 ..      29     394 .. 0.88

  Alignments for each domain:
  == domain 1  score: 134.6 bits;  conditional E-value: 1.6e-42
                                       SSSSSTTSTTSSHHHHHHHHHHHH.HHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHH CS
                     Aminotran_1_2   6 Lgsneylgdsgkptlpevakaeke.galaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagali 81 
                                       ++++ + +   + +l++++   +e    + +t  +y+pi+g pel ++l k++ +   lk + ++  +  sG+++++
  gi|385806051|ref|YP_005842449.1|  34 FSEGRPNFS--RFPLDKALPYVQEvFKTEYQTMLQYPPIKGNPELMKELRKLMEKYVSLKGTEDDDMIIMSGSQQAL 108
                                       555555554..33555555555555556778***********************77789999999************ PP

                                       HHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEE.ESS CS
                     Aminotran_1_2  82 ealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilv.esp 157
                                        ++ ++l ++pgd i+v +pty + + ++ ++++++  ++   +++ ++  ++le++l++++++ k++k++++  + 
  gi|385806051|ref|YP_005842449.1| 109 YMVSRIL-VDPGDYIVVERPTYLEAIFAFTYNKAKMLGVN---QDENGMKTDELETLLRKLKSEGKRIKFVYTvPNY 181
                                       *******.9*******************************...78889***********************9637** PP

                                       -TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEE CS
                     Aminotran_1_2 158 hNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyil 234
                                       +NP+G+ ++ e  + l++la +y +l+f D+aY  + ++ + a +++  +++e  ++ +++lsK + ++G+R+G+++
  gi|385806051|ref|YP_005842449.1| 182 QNPSGATLPMERRKHLYELASQYDFLIFEDDAYCYLSYEGK-ALPAIKSLDTEGRVIFTSTLSKIL-SPGLRIGWVF 256
                                       ***************************************65.5566999999999*********88.6********* PP

                                       EEHHHHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS...TEEEECCSCSS CS
                     Aminotran_1_2 235 gnaavvsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLael...glkvlasqsgm 306
                                       +n+++v++l  ++  +    s + q++++ +l++   ++++l+ +   ++++r+ + + L+el   +  ++++++g+
  gi|385806051|ref|YP_005842449.1| 257 ANKEIVKALLAAKEVIDLgvSGISQYLATIWLRNGI-HEEFLKIAIPWYKQKRDIMLEMLDELfrnDAHWTKPKGGL 332
                                       *************99988978888888888888877.5679999999****************************** PP

                                       EEEEEETHHCHHHHHHHHHHT...CTEEEEEGGGGTS....TTEEEEECTTS-HHHHHHHH CS
                     Aminotran_1_2 307 flltdlsaetakelskkLlee...vgvyvtpgtsftv....pgrlRitvAglteeeleelv 360
                                       f ++ ++++  k   +kLle+   +gv+ + g++f+      + +R++++  te+e++e +
  gi|385806051|ref|YP_005842449.1| 333 FIYVQFNNK--KVNTQKLLEYakkKGVLFVSGQPFYHdfsvLNTIRLNFSMPTEDEIKEGI 391
                                       *********..55556666554447************9999888*****888999998866 PP

>> Aminotran_MocR  Alanine-glyoxylate amino-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   0.0   8.5e-17   2.5e-13     128     403 ..     123     392 ..     115     397 .. 0.78

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 8.5e-17
                                       EEEES--HHHHHHHHHHT-EEEEEEEETTEE-HHHHH....HHHHC-TTEEEEEE-SSS-TTT-----HHHHHHHHT CS
                    Aminotran_MocR 128 lvtvpGydrhfllleelGielltvdlqddGpdvdave....klvaedasvkGilavpkysnptGetiseevarrlaa 200
                                       +v  p y            ++l v+ +++G   d +e    kl +e   +k +++vp+y np+G t+  e+ ++l  
  gi|385806051|ref|YP_005842449.1| 123 VVERPTYLEAIFAFTYNKAKMLGVNQDENGMKTDELEtllrKLKSEGKRIKFVYTVPNYQNPSGATLPMERRKHLYE 199
                                       566677755544444556799*********9999887222256677889**************************99 PP

                                       ---SSTT-EEEEE-TTSS-BS.SSSS----HHHHHHHHT-TTSEEEEEESTTTS-TTSS-EEEEE-HHHHHHHHHHH CS
                    Aminotran_MocR 201 lkaaapdfrifaddayavhdlvaeedkdanivalardaGhpdrafvlastskitfaGaGvafvassedniawlkkyl 277
                                       l  +  df if dday   +   e++  + i +l        r +  ++ ski   G  ++ v + ++ ++ l    
  gi|385806051|ref|YP_005842449.1| 200 LA-SQYDFLIFEDDAYCYLSY--EGKALPAIKSL----DTEGRVIFTSTLSKILSPGLRIGWVFANKEIVKALLAAK 269
                                       95.678**********86554..77666555555....444566655556***********************9999 PP

                                       HHC-S---HHHHHHHHHHHHHSTHHHHHHHHHHHHHHHHHHHHHHHHHHHHT..TTSSEEE---SBSS-EEEEESS. CS
                    Aminotran_MocR 278 GlqsiGpdkveqlrhvkflkdyeGlealmrdhaeliapkfeavlevleaelg..gaevatwteprGGyfisldtld. 351
                                        +  +G   + q     +l++  G++    +  ++  p +++  +++ + l     + a wt+p+GG fi ++  + 
  gi|385806051|ref|YP_005842449.1| 270 EVIDLGVSGISQYLATIWLRN--GIH---EEFLKIAIPWYKQKRDIMLEMLDelFRNDAHWTKPKGGLFIYVQFNNk 341
                                       9*********99877777764..554...56778889999999999999998767899***********98876651 PP

                                       .S-HHHHHHHHHHCTEE---TTTTSSTT--SSS-EEEE--SSS-HHHHHHHHH CS
                    Aminotran_MocR 352 .gvakrvvklaeeaGvsltaaGatypaGedpkdrnirlaptlppleevetamd 403
                                          +++ ++ a++ Gv +  +G  + +      + irl  ++p+ +e+++ ++
  gi|385806051|ref|YP_005842449.1| 342 kVNTQKLLEYAKKKGVLFV-SGQPFYHDFSV-LNTIRLNFSMPTEDEIKEGIR 392
                                       155789999******9765.56555444333.345999999999999988765 PP

>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0     2e-06     0.006     157     376 ..     133     361 ..     124     397 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2e-06
                                       EEEE-TTBGGGTB-HHHHHHHHHHHHHHHH...CHTCCCEEEEEE-S.CETTTTSEB--CCHHHHHHHHHHHHT-EE CS
                       Aminotran_3 157 vvrlkypdeevlkeneeeeaalleeleale...kkkkdevaAvivEp.iqgegGvvvaspeflaklrelckkhdvll 229
                                       +  + y+   +l +n++e+ + + ele l    k + + +  v + p  q   G + + +   ++l el+ ++d l+
  gi|385806051|ref|YP_005842449.1| 133 IFAFTYNKAKMLGVNQDENGMKTDELETLLrklKSEGKRIKFVYTVPnYQNPSGATLPMER-RKHLYELASQYDFLI 208
                                       5567788888888888888888888888887777778889988888888888998887665.688999999999999 PP

                                       EEE-TTTTTTTTSSSS.GGGGCTS--SEE...EE-GGGGTTSS-EEEEEEHHHHTTS-TTSB--TTTT-HHHHHHHH CS
                       Aminotran_3 230 ivDEvqtGfGrTGklf.AlehagvspDlm...tlaKaltgGlplsavlataevmqalapgshgsTfgGnplacaval 302
                                         D   + ++  Gk   A+++++++  ++   tl+K l+ Gl +  v+a++e+++al   +     g   +   +a 
  gi|385806051|ref|YP_005842449.1| 209 FEDDAYCYLSYEGKALpAIKSLDTEGRVIftsTLSKILSPGLRIGWVFANKEIVKALLAAKEVIDLGVSGISQYLAT 285
                                       99999999999999764788888888877333567**********************99985555555555555555 PP

                                       HHHHHHHHTTHHHHH....HHHHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTCHHHHHHHHHCTEE-E CS
                       Aminotran_3 303 avleiieeekllena....qelgaalkegLeelqkkyevikevRgkGlmiaielkeeaevkekeilkkakekGvlil 375
                                         l+   +e++l+ a    +++++++ e L el  ++    + ++ Gl+i + + +++  +++++l+ ak+kGvl+ 
  gi|385806051|ref|YP_005842449.1| 286 IWLRNGIHEEFLKIAipwyKQKRDIMLEMLDELFRND-AHWTKPKGGLFIYVQFNNKKV-NTQKLLEYAKKKGVLFV 360
                                       5555555555554432333899999999999999887.44555777******8877777.6699**********976 PP

                                       E CS
                       Aminotran_3 376 s 376
                                       s
  gi|385806051|ref|YP_005842449.1| 361 S 361
                                       5 PP

>> Fis1_TPR_N  Fis1 N-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1     0.081   2.4e+02      24      33 .]     313     322 ..     312     322 .. 0.88
   2 ?   10.0   0.0   0.00018      0.53      17      32 ..     385     400 ..     382     400 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.081
                        Fis1_TPR_N  24 aLLeelyrds 33 
                                       ++L el+r++
  gi|385806051|ref|YP_005842449.1| 313 EMLDELFRND 322
                                       8*******96 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00018
                        Fis1_TPR_N  17 edqqeGiaLLeelyrd 32 
                                       ++++eGi+LL e y++
  gi|385806051|ref|YP_005842449.1| 385 DEIKEGIRLLKEAYDE 400
                                       79**********9986 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.9e-05     0.056      65     168 ..     113     212 ..      74     217 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.9e-05
                                       HHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTT CS
                   Beta_elim_lyase  65 killqrgeevivtepahihfdetgaiaelagvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntag 141
                                       +il+ +g+ ++v++p      e+  + +++ +k+  ++++e + m+ ++le ++++ ++  ++ik++++    +   
  gi|385806051|ref|YP_005842449.1| 113 RILVDPGDYIVVERPTYL---EAIFAFTYNKAKMLGVNQDE-NGMKTDELETLLRKLKSEGKRIKFVYTVPNYQNPS 185
                                       566666666666666433...22233355888888889999.89********9999777789********999999* PP

                                       TB---HHHHHHHHHHHHHCT-EEEEEE CS
                   Beta_elim_lyase 142 GqvvsleelrevaaiakkygiplhlDg 168
                                       G  +++e  + ++++a +y+  ++ D 
  gi|385806051|ref|YP_005842449.1| 186 GATLPMERRKHLYELASQYDFLIFEDD 212
                                       *******************98887775 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 ?   10.2   0.0   7.3e-05      0.22      97     138 ..     316     356 ..     314     368 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 7.3e-05
                                       HHTSSSSBEEEE-TTSSEEEEEEEECTTS-EEEEEESSSSC- CS
                           DPPIV_N  97 EEvlgsnsavwWspdgsrlaylrfdeseVpeitlpsytdees 138
                                       +E l +n a+w  p+g    y++f+ ++V++++l +y++++ 
  gi|385806051|ref|YP_005842449.1| 316 DE-LFRNDAHWTKPKGGLFIYVQFNNKKVNTQKLLEYAKKKG 356
                                       57.8899******************************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       740  (0.0412739); expected 358.6 (0.02)
Passed bias filter:                      643  (0.0358637); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 2901.15
//
Query:       gi|385806052|ref|YP_005842450.1|  [L=309]
Description: ABC transporter [Fervidicoccus fontis Kam940]
Scores for complete 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  109.1   0.0    4.4e-31  108.2   0.0    1.5  1  ABC_tran      ABC transporter
      1e-11   45.2   0.2    3.5e-05   23.8   0.0    2.4  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    8.9e-11   42.4   1.3    1.9e-10   41.3   1.3    1.6  1  DUF4162       Domain of unknown function (DUF4162)
    0.00021   21.9   0.7     0.0014   19.2   0.0    2.1  2  AAA_23        AAA domain
    0.00045   19.9   0.0    0.00087   19.0   0.0    1.5  1  AAA_29        P-loop containing region of AAA domain
     0.0013   18.7   0.0     0.0027   17.7   0.0    1.6  1  Rad17         Rad17 P-loop domain
     0.0051   17.1   0.2      0.015   15.6   0.1    2.0  2  AAA_22        AAA domain
     0.0054   17.1   0.0      0.012   16.0   0.0    1.6  2  AAA_16        AAA ATPase domain
  ------ inclusion threshold ------
      0.018   14.6   0.0      0.051   13.2   0.0    1.7  2  AAA_27        AAA domain
      0.025   15.0   0.4       0.14   12.5   0.4    2.4  1  AAA           ATPase family associated with various cellular 
      0.029   14.8   0.0      0.062   13.7   0.0    1.6  1  RNA_helicase  RNA helicase
      0.038   13.9   0.1       0.11   12.4   0.0    1.7  1  RsgA_GTPase   RsgA GTPase
      0.063   12.7   0.0        1.1    8.6   0.0    2.5  3  SMC_N         RecF/RecN/SMC N terminal domain
      0.064   13.0   0.0       0.14   11.8   0.0    1.5  1  AAA_30        AAA domain
      0.073   12.9   0.0       0.17   11.7   0.0    1.6  1  CLP1_P        mRNA cleavage and polyadenylation factor CLP1 P
      0.083   12.5   0.1       0.17   11.5   0.1    1.5  1  SRP54         SRP54-type protein, GTPase domain
      0.091   13.0   0.9       0.29   11.4   0.4    2.0  2  AAA_28        AAA domain
       0.12   12.1   0.5         11    5.7   0.0    2.8  3  IstB_IS21     IstB-like ATP binding protein
       0.14   12.1   0.1        4.5    7.2   0.0    2.3  2  MutS_V        MutS domain V
       0.15   12.2   0.2       0.94    9.6   0.0    2.3  2  MMR_HSR1      50S ribosome-binding GTPase
       0.16   11.9   0.0       0.28   11.1   0.0    1.4  1  NACHT         NACHT domain
       0.21   11.1   3.0       0.44   10.1   0.3    2.7  3  cobW          CobW/HypB/UreG, nucleotide-binding domain
       0.22   11.0   3.1        1.2    8.6   3.1    1.9  1  DUF2117       Uncharacterized protein conserved in archaea (D
       0.24   11.4   0.7       0.38   10.8   0.7    1.2  1  Band_7        SPFH domain / Band 7 family


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 !  108.2   0.0   5.9e-34   4.4e-31       4     136 ..       1     141 [.       1     142 [. 0.95

  Alignments for each domain:
  == domain 1  score: 108.2 bits;  conditional E-value: 5.9e-34
                                       EEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                          ABC_tran   4 vslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                       +s++++e +++a++G+nGaGK+tL+++l+ +l+pt+G+  + g d+++ + +++r  +g++pqe +l+ +lt +en 
  gi|385806052|ref|YP_005842450.1|   1 MSFDVEEESIHALLGPNGAGKTTLIRILTTQLTPTKGTAYIFGLDVRK-NPQQARGMLGYVPQEVSLWTDLTGYENl 76 
                                       69*********************************************9.999************************* PP

                                       ............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       ............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  80 ............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                   e+ ++ie+al+ ++lk+   + v    +++SgG+ +r+++a+al+ +pk+l+lDEpt
  gi|385806052|ref|YP_005842450.1|  77 liyskiyeipksERVKRIEEALDFMDLKDASRRLV----KTYSGGMFRRLEIAAALMVRPKILILDEPT 141
                                       *********87666677999999999999888888....*****************************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 !   19.2   0.2   1.2e-06   0.00089       2      20 ..      11      29 ..      10      50 .. 0.81
   2 !   23.8   0.0   4.7e-08   3.5e-05     236     297 ..     113     172 ..      66     176 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.2e-06
                            AAA_21  2 nvliGpNgsGKSnLLdald 20
                                       +l GpNg+GK++L+++l 
  gi|385806052|ref|YP_005842450.1| 11 HALLGPNGAGKTTLIRILT 29
                                      689**************93 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 4.7e-08
                            AAA_21 236 elSdGtkrllalltallralkkgsllliDEpEngLHPkllrrll.ellkelsrngaQviltTH 297
                                         S G+ r l +++al  ++   ++l++DEp  gL+P +   ++ ++++++++ g+ v+++TH
  gi|385806052|ref|YP_005842450.1| 113 TYSGGMFRRLEIAAALMVRP---KILILDEPTIGLDPIARNNVWeRVISYKKEFGTTVLFATH 172
                                       4599999999*******999...9********************6666888889********* PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   1.3   2.5e-13   1.9e-10       1      80 [.     196     282 ..     196     283 .. 0.86

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 2.5e-13
                                       E-HHHHHTTS-SSEEEEE.-------......---EEEE-TTS-EEEEE--.-----------.----EEEEEEEE- CS
                           DUF4162   1 GtleeiKrsygknrieve.adaeellee....pgveeveeeggelelkled.eeaanellkal.tsgveirsFeeee 70 
                                       G++e++K  +g++r++++ +++e+++++     g+ ++ee+ + l++ +e+ + + +++l+al ++++e+++++ +e
  gi|385806052|ref|YP_005842450.1| 196 GKPEDLKMIIGGDRVTLKvDNKEKVKAIiaenFGIDIIEENSDVLTFLVEKsQLVLPRILSALeAEKIEVKELRIRE 272
                                       99****************73344444334443669999*999********99***********77************ PP

                                       --HHHHHHHH CS
                           DUF4162  71 PsLndIFiek 80 
                                       +sLnd+Fi++
  gi|385806052|ref|YP_005842450.1| 273 ASLNDVFIKL 282
                                       ********86 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.9e-06    0.0014      21      45 ..      10      34 ..       2     124 .. 0.90
   2 ?    1.2   0.5      0.62   4.6e+02     114     176 ..     217     287 ..     143     306 .. 0.50

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.9e-06
                            AAA_23 21 ltlItGpNGaGKTTildAiklaLyg 45
                                      + ++ GpNGaGKTT+++ ++  L+ 
  gi|385806052|ref|YP_005842450.1| 10 IHALLGPNGAGKTTLIRILTTQLTP 34
                                      66789************99988875 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.62
                            AAA_23 114 ideleqfisellgskki..ilnlilflgqer........feefelkdkkerleel.ekeleeledekkllekle 176
                                       +++ + +i e++g++ i  +++++ fl +++            +l+++k +++el ++e   +  ++kl+ k++
  gi|385806052|ref|YP_005842450.1| 217 KEKVKAIIAENFGIDIIeeNSDVLTFLVEKSqlvlprilS---ALEAEKIEVKELrIREASLNDVFIKLMGKRI 287
                                       2444445555555443332333443333333233332221...1112222222221111111222333333333 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 !   19.0   0.0   1.2e-06   0.00087      17      53 ..       3      39 ..       1      40 [. 0.83

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.2e-06
                            AAA_29 17 ieidlkgatlltGpsGsGKSTllDAiqalLvpakkvr 53
                                      +++++++++ l Gp+G+GK+Tl+  +++ L+p+k ++
  gi|385806052|ref|YP_005842450.1|  3 FDVEEESIHALLGPNGAGKTTLIRILTTQLTPTKGTA 39
                                      455655699**********************998655 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   3.6e-06    0.0027      45     123 ..       8      86 ..       1     137 [. 0.83

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.6e-06
                             Rad17  45 kriLLisGPsGCgkstvvkvLskelgi.klrewlnpvslkepdnqksdfkgltekesrflsqiesfkeleLkdakyl 120
                                       + i  + GP G gk+t +++L+ +l++ k   ++ ++ +++ + q   ++g + +e ++ + +  +++l+   +k  
  gi|385806052|ref|YP_005842450.1|   8 ESIHALLGPNGAGKTTLIRILTTQLTPtKGTAYIFGLDVRKNPQQARGMLGYVPQEVSLWTDLTGYENLL-IYSKIY 83 
                                       4577789***************99987266899***********************99999999999994.444444 PP

                             Rad17 121 klq 123
                                        + 
  gi|385806052|ref|YP_005842450.1|  84 EIP 86 
                                       554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1     2e-05     0.015       4      38 ..       7      48 ..       5     173 .. 0.77
   2 ?   -2.4   0.0       7.3   5.4e+03      53      70 ..     247     264 ..     219     291 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2e-05
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleqldeeakaee.......e 38
                                      +++i ++ G+ G+GKTtl+r l+ ql+  +  ++       +
  gi|385806052|ref|YP_005842450.1|  7 EESIHALLGPNGAGKTTLIRILTTQLTPTKGTAYifgldvrK 48
                                      5788899******************97655544455555551 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 7.3
                            AAA_22  53 skdllrellralglelka 70 
                                       s+ +l ++l+al+ e+ +
  gi|385806052|ref|YP_005842450.1| 247 SQLVLPRILSALEAEKIE 264
                                       445567777777766665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.6e-05     0.012      26     106 ..      10     115 ..       4     182 .. 0.68
   2 ?   -2.0   0.0       5.3     4e+03     116     127 ..     263     283 ..     186     292 .. 0.59

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.6e-05
                            AAA_16  26 lvllsGesGvGKsslvrellralekd.........ggiflrgkcdqlesa.....................ipysal 72 
                                       +  l G+ G GK++l+r l ++l+ +         +   +r + +q  ++                     + ys +
  gi|385806052|ref|YP_005842450.1|  10 IHALLGPNGAGKTTLIRILTTQLTPTkgtayifglD---VRKNPQQA-RGmlgyvpqevslwtdltgyenlLIYSKI 82 
                                       56799*******************996543333330...33333333.22444444444444444444444556667 PP

                            AAA_16  73 aqalareellrqlldeaesaeleawrekleeala 106
                                        ++  ++e ++ ++++++  +l +++++l ++++
  gi|385806052|ref|YP_005842450.1|  83 YEIP-KSERVKRIEEALDFMDLKDASRRLVKTYS 115
                                       7777.44777777777777777777777777666 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 5.3
                            AAA_16 116 a.........srllellkrll 127
                                                  +l++++ +l+
  gi|385806052|ref|YP_005842450.1| 263 IevkelrireASLNDVFIKLM 283
                                       112222233456666666665 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   6.9e-05     0.051      20      47 ..       2      29 ..       1      39 [. 0.89
   2 ?   -2.1   0.0       3.3   2.5e+03      59      95 ..     240     276 ..     221     291 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.9e-05
                            AAA_27 20 dfsaeeadlhliyGpNEAGKstalrAis 47
                                      +f+ ee+++h ++GpN AGK+t++r ++
  gi|385806052|ref|YP_005842450.1|  2 SFDVEEESIHALLGPNGAGKTTLIRILT 29
                                      788999****************998665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.3
                            AAA_27  59 dnflhdakkLrigavleeadgeelefaRrkgrkktll 95 
                                         fl ++++L +  +l++ + e++e++  + r+++l 
  gi|385806052|ref|YP_005842450.1| 240 LTFLVEKSQLVLPRILSALEAEKIEVKELRIREASLN 276
                                       4577777788777777777777777777776666665 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.4   0.00019      0.14       3      23 ..      13      33 ..      11     181 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00019
                                      EESSTTSSHHHHHHHHHHHHT CS
                               AAA  3 lyGppGtGKTllakavakelg 23
                                      l Gp G GKT+l++ + ++l 
  gi|385806052|ref|YP_005842450.1| 13 LLGPNGAGKTTLIRILTTQLT 33
                                      89**************99984 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   8.4e-05     0.062       3      60 ..      13      72 ..      11      93 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.4e-05
                      RNA_helicase  3 lyGpsgeGKStlakeLakallkkl..klkkkdsvysrnpeddfwdgYtgqevvvidDfgq 60
                                      l Gp+g GK+tl++ L+++l+ +    ++   +v  ++ +   + gY  qev ++ D+  
  gi|385806052|ref|YP_005842450.1| 13 LLGPNGAGKTTLIRILTTQLTPTKgtAYIFGLDVRKNPQQARGMLGYVPQEVSLWTDLTG 72
                                      78******************9555223444444544555666789999999999999865 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00014      0.11      99     123 ..       8      32 ..       2      41 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
                                       TSEEEEECSTTSSHHHHHHHHCTT- CS
                       RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpel 123
                                       +++ +l+G+ G+GK+tLi  l+ +l
  gi|385806052|ref|YP_005842450.1|   8 ESIHALLGPNGAGKTTLIRILTTQL 32 
                                       57899**************999875 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 ?    8.6   0.0    0.0015       1.1      24      42 ..       8      26 ..       3      36 .. 0.86
   2 ?    0.5   0.0      0.44   3.3e+02     154     206 ..     128     178 ..     121     196 .. 0.66
   3 ?   -1.7   0.1       2.1   1.6e+03      79     135 ..     210     266 ..     197     278 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0015
                                      SSEEEEEESTTSSHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxx RF
                             SMC_N 24 ksftaivGpNGSGKsnlld 42
                                      +s+ a++GpNG+GK+ l+ 
  gi|385806052|ref|YP_005842450.1|  8 ESIHALLGPNGAGKTTLIR 26
                                      67899**********9985 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.44
                                       HCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 154 qkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekad 206
                                        +v+p+ + +lDe    LD   +++v e++ + +k++   v   ++  + +ad
  gi|385806052|ref|YP_005842450.1| 128 LMVRPK-ILILDEPTIGLDPIARNNVWERVISYKKEFGTTVLFATH-YMDEAD 178
                                       555555.6689**999****99999999999888886555543333.333333 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2.1
                                       EEEEEEETTEESSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  79 veitfdnedkklkiekeevsisrrvkrkgeseykingkevtkkevsellesagiske 135
                                       v++ +dn++k   i +e++ i    ++++  ++ +++++     + + le ++i+ +
  gi|385806052|ref|YP_005842450.1| 210 VTLKVDNKEKVKAIIAENFGIDIIEENSDVLTFLVEKSQLVLPRILSALEAEKIEVK 266
                                       777778888888888888888888888888888888888888888888888888766 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00019      0.14      18      45 ..       8      35 ..       4      54 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00019
                            AAA_30 18 drvavltGpAGtGKttalkalreaweaa 45
                                      + +++l Gp G+GKtt+++ l+  ++  
  gi|385806052|ref|YP_005842450.1|  8 ESIHALLGPNGAGKTTLIRILTTQLTPT 35
                                      458899*************997666544 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 ?   11.7   0.0   0.00023      0.17       1      45 [.      15      59 ..      15      76 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00023
                            CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGqseispPgtisl 45
                                      Gp+ +GK+Tl+r+L  +++  + +  +  lDv ++     g+++ 
  gi|385806052|ref|YP_005842450.1| 15 GPNGAGKTTLIRILTTQLTPTKGTAYIFGLDVRKNPQQARGMLGY 59
                                      899*******************9*99******9987777776665 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00023      0.17       3      38 ..      10      45 ..       8      49 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00023
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                      + +l+G++GaGKTt +  L  +l+  + ++ +  +D
  gi|385806052|ref|YP_005842450.1| 10 IHALLGPNGAGKTTLIRILTTQLTPTKGTAYIFGLD 45
                                      6789************99999998888777777777 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.4   0.00038      0.29       3      22 ..      12      31 ..      10      43 .. 0.81
   2 ?   -1.9   0.0       4.7   3.5e+03      80     106 ..      71      97 ..      66     103 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00038
                            AAA_28  3 vitGgestGKTtlleaLaar 22
                                      +++G+ ++GKTtl++ L+ +
  gi|385806052|ref|YP_005842450.1| 12 ALLGPNGAGKTTLIRILTTQ 31
                                      799**************976 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.7
                            AAA_28  80 rglldtlaYarayggeaeaeleaaare 106
                                       +g+ + l+Y++ y++++++ +++++++
  gi|385806052|ref|YP_005842450.1|  71 TGYENLLIYSKIYEIPKSERVKRIEEA 97 
                                       567788899999999977777775554 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.014        11      46      70 ..       7      31 ..       2      44 .. 0.78
   2 ?    3.4   0.0     0.078        58      98     129 ..     121     151 ..      91     182 .. 0.68
   3 ?   -1.9   0.0       3.3   2.4e+03      97     129 ..     208     240 ..     199     248 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.014
                         IstB_IS21 46 kkenivllGpsGvGKshlaialgve 70
                                      ++   +llGp G+GK+ l   l ++
  gi|385806052|ref|YP_005842450.1|  7 EESIHALLGPNGAGKTTLIRILTTQ 31
                                      5555689*********998777665 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.078
                         IstB_IS21  98 klaralkrllkvdllilDd..lgllpldqaeael 129
                                       +l+ a++ ++++++lilD+  +gl p+ ++   +
  gi|385806052|ref|YP_005842450.1| 121 RLEIAAALMVRPKILILDEptIGLDPIARN---N 151
                                       455567778999******944566665444...3 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 3.3
                         IstB_IS21  97 gklaralkrllkvdllilDdlgllpldqaeael 129
                                       ++++ ++++  kv+ +i  ++g+  +++++  l
  gi|385806052|ref|YP_005842450.1| 208 DRVTLKVDNKEKVKAIIAENFGIDIIEENSDVL 240
                                       566666777777777888888877777766544 PP

>> MutS_V  MutS domain V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.15   1.1e+02       3      17 ..      13      27 ..      11      37 .. 0.86
   2 ?    7.2   0.0     0.006       4.5      56     136 ..     112     189 ..     103     245 .. 0.65

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.15
                                      EE-STTSSHHHHHHH CS
                            MutS_V  3 itGpnmaGkstylrq 17
                                      + Gpn aGk t++r 
  gi|385806052|ref|YP_005842450.1| 13 LLGPNGAGKTTLIRI 27
                                      56***********96 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.006
                                       -SS-HHHHHHHHHHHHHTT--TTSEEEEESTS-SS-HHHHHHHHHHHHHHHHHTT--EEEEEES-GGGGGHHHHSTT CS
                            MutS_V  56 kgkstFmvEmlEtasilknatekslvilDElGRGtstydGlaialavaeyllekikaktlfatHyheltklaeklee 132
                                       k+ s  m+  lE+a+ l    +  ++ilDE   G        +   v+ y  ++  +++lfatHy++ ++  + + +
  gi|385806052|ref|YP_005842450.1| 112 KTYSGGMFRRLEIAAALM--VRPKILILDEPTIGLDPIARNNVWERVISYK-KEFGTTVLFATHYMDEADKYADMIT 185
                                       555555555566665554..3344666676655555555555555555554.458899*******987766665555 PP

                                       EEEE CS
                            MutS_V 133 vknl 136
                                       + n 
  gi|385806052|ref|YP_005842450.1| 186 IINK 189
                                       5444 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0    0.0013      0.94       3      23 ..      12      32 ..      11     113 .. 0.81
   2 ?    0.2   0.2       1.1   7.9e+02      74      86 ..     234     247 ..     133     285 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0013
                                      EEEESTTSSHHHHHHHHHTST CS
                          MMR_HSR1  3 aivGrpNvGKStLinaltgek 23
                                      a++G   +GK+tLi+ lt + 
  gi|385806052|ref|YP_005842450.1| 12 ALLGPNGAGKTTLIRILTTQL 32
                                      789**************9863 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.1
                                       HC.TSEEEEEEETT CS
                          MMR_HSR1  74 ee.adlillvvdas 86 
                                       ee +d++ ++v+ s
  gi|385806052|ref|YP_005842450.1| 234 EEnSDVLTFLVEKS 247
                                       22366666666644 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00037      0.28       4      48 ..      12      52 ..       9      64 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00037
                                      EEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS CS
                             NACHT  4 ilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrs 48
                                      +l G++G GKTtL++ l +++   k       ++F l +r+ +++
  gi|385806052|ref|YP_005842450.1| 12 ALLGPNGAGKTTLIRILTTQLTPTKGT----AYIFGLDVRKNPQQ 52
                                      689************999998776632....47777777766665 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 ?   10.1   0.3   0.00059      0.44       4      23 ..      12      32 ..       9      43 .. 0.75
   2 ?   -1.5   0.0       2.2   1.6e+03     143     167 ..      75      99 ..      64     104 .. 0.84
   3 ?   -0.5   0.1       1.1   7.9e+02      65     102 ..     212     259 ..     181     296 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00059
                                      EEEESTTCCHHHHHHHHH.CT CS
                              cobW  4 vltGflGsGKTtLlnhll.en 23
                                       l G+ G+GKTtL++ l+ + 
  gi|385806052|ref|YP_005842450.1| 12 ALLGPNGAGKTTLIRILTtQL 32
                                      6889**********9988544 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.2
                                       SEEEEE-HHHHCHC..HHHHHHHHH CS
                              cobW 143 dllvlnKtDlldeeallekleerlr 167
                                       +ll+ +K+  +++++ ++++ee l+
  gi|385806052|ref|YP_005842450.1|  75 NLLIYSKIYEIPKSERVKRIEEALD 99 
                                       79999*********99999998765 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1.1
                                       CTT-HHHHHHHHHHHH.........TT-SEEEEEECTTTTHHHH.HTT CS
                              cobW  65 lredllkelealeere.........erldviliEttGlaePapv.aft 102
                                       l+ d  ++++a+ +++         +++   l+E++ l+ P  + a++
  gi|385806052|ref|YP_005842450.1| 212 LKVDNKEKVKAIIAENfgidiieenSDVLTFLVEKSQLVLPRILsALE 259
                                       555555666666666655555553334444467777777777765444 PP

>> DUF2117  Uncharacterized protein conserved in archaea (DUF2117)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   3.1    0.0016       1.2      49     132 ..     207     297 ..     158     302 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0016
                           DUF2117  49 n.......ekaeklakklseelglkivkpeevekeiveskgkrvvrkiagvspgenilvnGiviGkaeseevtivae 118
                                               +++ek+ + ++e++g++i+++++ + +   +k++ v  +i +  + e+i v  + i +a+ ++v i   
  gi|385806052|ref|YP_005842450.1| 207 GdrvtlkvDNKEKVKAIIAENFGIDIIEENSDVLTFLVEKSQLVLPRILSALEAEKIEVKELRIREASLNDVFIKLM 283
                                       14555544788889999*********988777766666789999999999*************************** PP

                           DUF2117 119 dgkivdikggeiKe 132
                                       + +i + + g++Ke
  gi|385806052|ref|YP_005842450.1| 284 GKRIEEEEEGRMKE 297
                                       ******99999997 PP

>> Band_7  SPFH domain / Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.7    0.0005      0.38     100     169 ..     219     297 ..     212     304 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0005
                            Band_7 100 alrevisemtleellsnreelaeelkneln.......eqlrkyGvevldvritdidpppevaqalaakqaaeaea.. 167
                                       +++++i+e+ +++++++ +++   l ++ +       ++l+   +ev ++ri++ ++++ +++ + ++++ e+e   
  gi|385806052|ref|YP_005842450.1| 219 KVKAIIAENFGIDIIEENSDVLTFLVEKSQlvlprilSALEAEKIEVKELRIREASLNDVFIKLMGKRIEEEEEGrm 295
                                       67888888888888888666666666666655555558899999***************************999844 PP

                            Band_7 168 qa 169
                                       ++
  gi|385806052|ref|YP_005842450.1| 296 KE 297
                                       43 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 1818.07
//
Query:       gi|385806053|ref|YP_005842451.1|  [L=256]
Description: ABC transporter [Fervidicoccus fontis Kam940]
Scores for complete 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  118.4  16.5    2.7e-34  118.4  16.5    1.6  2  ABC2_membrane    ABC-2 type transporter
    1.3e-16   60.7  21.9    1.5e-16   60.5  21.9    1.1  1  ABC2_membrane_3  ABC-2 family transporter protein
    1.3e-10   41.0  17.9    1.3e-10   41.0  17.9    1.4  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 !  118.4  16.5   4.5e-38   2.7e-34       3     209 ..      12     222 ..      10     223 .. 0.94
   2 ?   -2.0   1.0      0.33     2e+03     105     118 ..     233     246 ..     226     252 .. 0.48

  Alignments for each domain:
  == domain 1  score: 118.4 bits;  conditional E-value: 4.5e-38
                     ABC2_membrane   3 ikallkreflqrwrdpslgllwrliqplllalvfgtvfgnlg...nsedglnr..pgllffsvlflafsaltsvapv 74 
                                       i+a+   e++++ +dp+ + ++r iqp+l+  vfg+v  ++    ++ d++++  pg++  s +f++  +  ++++v
  gi|385806053|ref|YP_005842451.1|  12 IFAMAEMELRRIRHDPVEI-FTRAIQPILWVAVFGSVMAKVRafpSTGDYVTFisPGVILQSSTFIS--LSYGIMLV 85 
                                       78999999********999.********************888778888887789************..99****** PP

                     ABC2_membrane  75 ferergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldls....rfflflllllltalaassl 147
                                       fere gvl+r+l+sp+ ++s +v+++ l+ +++s  q +i+l+ + ++ g +l+      +l +++l + ++ ++++
  gi|385806053|ref|YP_005842451.1|  86 FERESGVLKRLLSSPM-PRSYIVIGRSLAGALRSSTQYIIVLVAAALV-GAKLTtdplDLILGYFILTFASMGFTAI 160
                                       ****************.**************************99997.99999866555999999999999***** PP

                     ABC2_membrane 148 gllisalapsfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrsnl 209
                                       +++i++ +++ e ++ +++++++pl++ s +++pi+ mp+ +q i+ +nPlty+v+alr  l
  gi|385806053|ref|YP_005842451.1| 161 SIVIASTLKTRERFMGIVGAITMPLFFASNALYPIQVMPRPIQVISFVNPLTYTVSALRTLL 222
                                       ***************************************9*******************875 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.33
                     ABC2_membrane 105 lpvsllqaliflli 118
                                       ++++++++l+ ++i
  gi|385806053|ref|YP_005842451.1| 233 MLIITIFVLVSMFI 246
                                       33333333333333 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 !   60.5  21.9   2.5e-20   1.5e-16     153     344 ..      54     248 ..       6     249 .. 0.88

  Alignments for each domain:
  == domain 1  score: 60.5 bits;  conditional E-value: 2.5e-20
                   ABC2_membrane_3 153 eeelsnvasflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll.. 227
                                       + ++ +++ f+ + +++ ++++++++   ++v+E+es++++++l+s++ ++ +++++ l+ +l + +q++++l+   
  gi|385806053|ref|YP_005842451.1|  54 FPSTGDYVTFISPGVILQSSTFISLSYGIMLVFERESGVLKRLLSSPMPRSYIVIGRSLAGALRSSTQYIIVLVAaa 130
                                       567789999999988888877777778889*****************************************998435 PP

                   ABC2_membrane_3 228 afglgipfgnlglllllfllf..glayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifs 302
                                       ++g  ++ + l l+l +f+l   ++ ++a++ ++ s  k+ e  ++++++++++l++++ +l+p++ +p ++++i++
  gi|385806053|ref|YP_005842451.1| 131 LVGAKLTTDPLDLILGYFILTfaSMGFTAISIVIASTLKTRERFMGIVGAITMPLFFASNALYPIQVMPRPIQVISF 207
                                       66668999977666655555533788999999********************************************* PP

                   ABC2_membrane_3 303 iiPffapglgllrlitgdplweillsliilalfavvylllal 344
                                       ++P+++   +l +l+ +     i+ +++i  +f++v + +a+
  gi|385806053|ref|YP_005842451.1| 208 VNPLTYTVSALRTLLVQS-SLYIGSDMLIITIFVLVSMFIAI 248
                                       **************9877.5699*************999998 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 !   41.0  17.9   2.2e-14   1.3e-10      97     282 ..      84     250 ..      74     253 .. 0.77

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 2.2e-14
                   ABC2_membrane_2  97 iagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalgivlaledllllvvasvllll 173
                                       ++ E+e+g lk+lLs+P++R+ i++g  ++g++       +  ++vl+a a++   g  l+++ l l++  ++l+++
  gi|385806053|ref|YP_005842451.1|  84 LVFERESGVLKRLLSSPMPRSYIVIGRSLAGALR----SSTQYIIVLVAAALV---GAKLTTDPLDLILGYFILTFA 153
                                       566******************************9....333333334433443...444444444444444444444 PP

                   ABC2_membrane_2 174 lvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqeindflsllsptsayntllneil 250
                                        + f+a++++++s+++++++ + ++ ++ + l ++ +++ly++  ++ + +v       +s+++p  +   +l+++l
  gi|385806053|ref|YP_005842451.1| 154 SMGFTAISIVIASTLKTRERFMGIVGAITMPL-FFASNALYPIQVMPRPIQV-------ISFVNPLTYTVSALRTLL 222
                                       4447************8888887777766555.9**************9999.......****************** PP

                   ABC2_membrane_2 251 agsdlnalgstatnllilllllavllvlgyvl 282
                                         s+    ++ ++ +li+ +  +v++ +++ l
  gi|385806053|ref|YP_005842451.1| 223 VQSS----LYIGSDMLIITIFVLVSMFIAIKL 250
                                       9996....999999999999999998888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); 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: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1637.47
//
Query:       gi|385806054|ref|YP_005842452.1|  [L=770]
Description: hydrogenase maturation protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-47  161.8   0.0    1.9e-47  161.1   0.0    1.4  1  Sua5_yciO_yrdC   Telomere recombination
    2.8e-27   95.4   0.0    5.7e-27   94.4   0.0    1.5  1  HypF_C           HypF Kae1-like domain
    1.1e-25   89.1   8.9      1e-12   47.6   1.5    2.3  2  zf-HYPF          HypF finger
    3.2e-21   75.5   0.1    8.5e-21   74.2   0.1    1.8  1  Acylphosphatase  Acylphosphatase
  ------ inclusion threshold ------
       0.97    9.4   6.8         21    5.1   0.0    3.5  3  DUF4428          Domain of unknown function (DUF4428)


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 !  161.1   0.0   5.4e-51   1.9e-47       2     178 ..     212     386 ..     211     387 .. 0.97

  Alignments for each domain:
  == domain 1  score: 161.1 bits;  conditional E-value: 5.4e-51
                                       HHHTTSEEEEE-SSSEEEEEETTSHHHHHHHHHHHTSHCCC--EEEESSCCCCCCCC-.TC--HHHHHHHHCT-SSS CS
                    Sua5_yciO_yrdC   2 alrkGgivaiptetvYgLacdatneeaverlreiKgrpsdkplavlvasledlkklae.seveeealkllerfwPGp 77 
                                       +l +G+i+ai+++++Y++a  a+++++v++lr+iK+rp ++p+a++++++e++k++a  +e+ e+++ +++r    p
  gi|385806054|ref|YP_005842452.1| 212 MLLEGKILAIKGVGGYHIASIASDDKVVRKLRKIKNRP-SQPFAIMAKDIETVKTIAYlDEIGEKIILSPQR----P 283
                                       6889**********************************.*********************************....* PP

                                       CEEEEE..E-TS-HHHHTTTTEEEEEE-SSHHHHHHHHHCTS-...EEEEES-STTS-S-SSHHHHHHHC-TTSECB CS
                    Sua5_yciO_yrdC  78 itlllkrskeklpkevapglktvGvrlPdtplarlLlealgep...lvaTSanlsgepsitdaeeveeelgeivdli 151
                                       i +l kr+++k+++ vapgl+t+G++lP+t + +lLle++  p   l++TS+n++g+p+++d e + +elg+ivd+i
  gi|385806054|ref|YP_005842452.1| 284 ILILPKRDSSKVSELVAPGLSTIGIMLPYTGFQHLLLEKI--PdgfLIMTSGNIHGRPMCKDLECALNELGSIVDFI 358
                                       *******9999****************************8..4445******************************* PP

                                       -SS-.--SSS---EEEETTSSTSSECEX CS
                    Sua5_yciO_yrdC 152 ldgg.eiavgvdstVvdltegkpkilRr 178
                                       ++++ +i ++vd++V+++t+g+p +lRr
  gi|385806054|ref|YP_005842452.1| 359 IEHErKIVHRVDDSVIRFTDGEPVFLRR 386
                                       ***************************9 PP

>> HypF_C  HypF Kae1-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.4   0.0   1.6e-30   5.7e-27       4     102 .]     402     500 ..     400     500 .. 0.98

  Alignments for each domain:
  == domain 1  score: 94.4 bits;  conditional E-value: 1.6e-30
                            HypF_C   4 kevLAlGaelkntfalakggqallsqhlGdlenletleayeealeeleklleikpevivcDlhpdylstklaeelae 80 
                                       ke++AlGael+++ a++ +++++ +q++Gdl+++ tle++e++le + k++eikp++i++D+hp y ++kla++l +
  gi|385806054|ref|YP_005842452.1| 402 KEIVALGAELQTAGAVSFENKIIPTQFIGDLDDIGTLEDLERELEWFIKTYEIKPKAIAIDMHPLYKNRKLAHKLKS 478
                                       689************************************************************************** PP

                            HypF_C  81 keklelievqHHhAHllavlae 102
                                        +++e+ievqHHh Hl+++++e
  gi|385806054|ref|YP_005842452.1| 479 IYGAEIIEVQHHHSHLASLMVE 500
                                       ********************98 PP

>> zf-HYPF  HypF finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   1.1     1e-15   3.6e-12       1      33 [.     108     140 ..     108     141 .. 0.97
   2 !   47.6   1.5   2.9e-16     1e-12       1      31 [.     158     189 ..     158     192 .. 0.94

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 1e-15
                                       --HHHHHHHC-TTSTTTT-TT---TTTS--EEE CS
                           zf-HYPF   1 lCedClrEykdpldRRfhaqfisCtnCGPrlsl 33 
                                       +C++Cl E++ p++R++ +  +sC +CGPr+s+
  gi|385806054|ref|YP_005842452.1| 108 ICDNCLSEIRSPSSRFYKYHWNSCAWCGPRFSM 140
                                       7******************************98 PP

  == domain 2  score: 47.6 bits;  conditional E-value: 2.9e-16
                                       --HHHHHHHC-TTS.TTTT-TT---TTTS--E CS
                           zf-HYPF   1 lCedClrEykdpld.RRfhaqfisCtnCGPrl 31 
                                       lC+dC+ +ykd ++ RRfhaq+isC+ CGP+ 
  gi|385806054|ref|YP_005842452.1| 158 LCKDCECDYKDVSNlRRFHAQGISCPVCGPKT 189
                                       7*****************************86 PP

>> Acylphosphatase  Acylphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.2   0.1   2.4e-24   8.5e-21       2      85 .]       6      89 ..       5      89 .. 0.94

  Alignments for each domain:
  == domain 1  score: 74.2 bits;  conditional E-value: 2.4e-24
                   Acylphosphatase  2 rllvtGrVQgvgFRkfvrrlAkelglkGyvrNlsdgsVeivaegeeekvekfleelksgppk.arvdeveveeleeeee 79
                                      r+ + G VQgvgFR+fv+rlA++l+l Gyv N+   +Vei +ege+++vekf e l++++p+ a  +e++++++e ++ 
  gi|385806054|ref|YP_005842452.1|  6 RIKIVGVVQGVGFRPFVYRLATNLNLFGYVVNKGGAEVEIFIEGEKRNVEKFTELLEKEKPPpAIFEEISISNEEPKGF 84
                                      6899******************************************************66666**********888777 PP

                   Acylphosphatase 80 fkdFei 85
                                       ++F+i
  gi|385806054|ref|YP_005842452.1| 85 -TEFKI 89
                                      .99987 PP

>> DUF4428  Domain of unknown function (DUF4428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0    0.0058        21      19      33 ..     105     120 ..      98     129 .. 0.78
   2 ?    3.0   0.9     0.027        96       2      26 ..     131     162 ..     130     168 .. 0.80
   3 ?    2.3   0.3     0.045   1.6e+02       2      22 ..     182     198 ..     181     201 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0058
                           DUF4428  19 DgyvCkdClkKl.sef 33 
                                       D  +C++Cl+++ s++
  gi|385806054|ref|YP_005842452.1| 105 DIGICDNCLSEIrSPS 120
                                       6779*******96544 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.027
                           DUF4428   2 CaiCgkKigll.......krlkleDgyvCkdC 26 
                                       Ca Cg   +++       +++  eD+ +CkdC
  gi|385806054|ref|YP_005842452.1| 131 CAWCGPRFSMMysvpydrENTSMEDFPLCKDC 162
                                       777888888877777765558899******** PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.045
                           DUF4428   2 CaiCgkKigllkrlkleDgyv 22 
                                       C++Cg K+ ++k    +Dg++
  gi|385806054|ref|YP_005842452.1| 182 CPVCGPKTIVIK----NDGTI 198
                                       *******99999....77765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (770 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.72u 0.29s 00:00:01.01 Elapsed: 00:00:00.51
# Mc/sec: 4502.23
//
Query:       gi|385806055|ref|YP_005842453.1|  [L=352]
Description: hydrogenase expression/formation protein HypE [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-23   83.4   0.3    2.7e-23   82.8   0.3    1.3  1  AIRS_C    AIR synthase related protein, C-terminal domain
    7.9e-17   61.7   0.1      2e-16   60.4   0.1    1.7  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 !   82.8   0.3     3e-27   2.7e-23       1     151 [.     172     324 ..     172     328 .. 0.83

  Alignments for each domain:
  == domain 1  score: 82.8 bits;  conditional E-value: 3e-27
                                       STTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTTTSE.HHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHH CS
                            AIRS_C   1 kpGdvliltgslGlggagtslkrkileeeglddsavq.lgdvlleptliyvkralaalkglvkaahDvTgGGLlgal 76 
                                       k+Gd++i+tg+l  +g+ +sl r +le+++ +      l +   +p   y+ ++    +++++aa+D T+GGL++ l
  gi|385806055|ref|YP_005842453.1| 172 KVGDKIIVTGNLAEHGVLISLYRLGLEDKAGN----AgLLQSDVMPLSKYLLPIFEKYGEKINAARDPTRGGLSEVL 244
                                       69*********************999999998....324444444444444444444499***************** PP

                                       HHHHHTTTEEEEEECGTHHHHHHHH.....HHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEES CS
                            AIRS_C  77 aemapasgvgaeidldkvpifdele.....splemllsensGrllvavppeeadavlaileeeglpeaavIGevtak 148
                                       +e+a ++++ +eid++ +p+++++      +++++l+ +++G+ +++v++  ++++l++l++ gl +a++IGev ++
  gi|385806055|ref|YP_005842453.1| 245 NEWALQNKLIIEIDEKSIPLREPVVkytemLGIDPLHLASEGVAVLSVEESVSEEILDELQKNGLSDAKIIGEVKKE 321
                                       ****************9999999994444555555555****99999999999************99********99 PP

                                       SSE CS
                            AIRS_C 149 eel 151
                                       +++
  gi|385806055|ref|YP_005842453.1| 322 AKE 324
                                       875 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 !   60.4   0.1   2.3e-20     2e-16       1      94 []      50     163 ..      50     163 .. 0.92

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 2.3e-20
                                       SSSE.........EEEEEEEEE.EECCTCCCC....HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......HHHHH CS
                              AIRS   1 dDaa.........vvvttdshnrpvlvepvhf....iGakavavnlsDlaamGArPlalllslalp......wleev 58 
                                       dD a         vv++td    ++ v+p  f    iG++a+a+ ++D+++mG+rP+a+l+s+ ++      +le++
  gi|385806055|ref|YP_005842453.1|  50 DDGAtipigdlgyVVISTD----SYTVKPLFFpggdIGKLAAAGSINDVVMMGGRPVAILDSIVVQegfeinELEKI 122
                                       677766666655679****....888999999********************************************* PP

                                       HHHHHHHHHHTT-EEEEEEEEEESS.....EEEEEEEEEEE CS
                              AIRS  59 vrglaeaaeelgvplvgGdtsfsne.....ptisvtavGlv 94 
                                       ++++ + ++e +v+++gGd ++ ++     ++i++ta+G++
  gi|385806055|ref|YP_005842453.1| 123 MESFISTLKEEKVSIIGGDFKVLPReeldgIIITTTAIGIA 163
                                       *********************997778999*********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.48
# Mc/sec: 2225.97
//
Query:       gi|385806056|ref|YP_005842454.1|  [L=78]
Description: hydrogenase expression/formation protein HypC [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.8e-15   55.8   0.0    4.3e-15   55.6   0.0    1.0  1  HupF_HypC      HupF/HypC family
  ------ inclusion threshold ------
      0.058   13.3   0.3      0.065   13.1   0.3    1.2  1  DNA_ligase_OB  NAD-dependent DNA ligase OB-fold domain


Domain annotation for each model (and alignments):
>> HupF_HypC  HupF/HypC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.6   0.0   4.8e-19   4.3e-15       1      65 []       1      69 [.       1      69 [. 0.93

  Alignments for each domain:
  == domain 1  score: 55.6 bits;  conditional E-value: 4.8e-19
                                      CCEEEEEEEEEEET..TEEEEECT.TEEEEEEGTTC.TTB-TT-EEEEETTEEEEEE-HHHHHHHHHHH CS
                         HupF_HypC  1 MCLaiPgkvveied..elAlvdvg.Gvrrevslalv.eevkvGdyVLvhvGfAiekideeeaeetlell 65
                                      MC+a P+ v +++     A+vd+g G++rev  a+  e+++ Gd VLvh+G+ i+kid++e ee +e+l
  gi|385806056|ref|YP_005842454.1|  1 MCWATPALVKSVSSdnLKAIVDYGdGIQREVINAIPdENIQAGDTVLVHAGVIISKIDKNELEEQIEFL 69
                                      ***********999655*******9******99999888*************************99875 PP

>> DNA_ligase_OB  NAD-dependent DNA ligase OB-fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.3   7.3e-06     0.065      42      74 ..      33      64 ..       8      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.3e-06
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                     DNA_ligase_OB 42 deierkdirigdtVvvekaGdvIPevvgvvlek 74
                                      + i + +i+ gdtV+v+ aG +I ++ +  le+
  gi|385806056|ref|YP_005842454.1| 33 NAIPDENIQAGDTVLVH-AGVIISKIDKNELEE 64
                                      567889********995.9*******9988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 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:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 524.18
//
Query:       gi|385806057|ref|YP_005842455.1|  [L=387]
Description: hydrogenase formation HypD protein [Fervidicoccus fontis Kam940]
Scores for complete 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-125  417.3   0.0   5.6e-125  417.1   0.0    1.0  1  HypD      Hydrogenase formation hypA family


Domain annotation for each model (and alignments):
>> HypD  Hydrogenase formation hypA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  417.1   0.0  3.1e-129  5.6e-125       3     350 ..      22     378 ..      20     379 .. 0.96

  Alignments for each domain:
  == domain 1  score: 417.1 bits;  conditional E-value: 3.1e-129
                                       HHHHHHHHHHHHHTSS-EEEEE--HHHHHHHHHTTHHHHS-TTEEEEE-S--TTTTS-HHHHHHHHHHHHH--EEEE CS
                              HypD   3 akkllekikkeakkerelkimevCGghthaivryglrslLpenielisGPGCpVCvtpeeeidkaielaekeevila 79 
                                       +++l +kik++  +e+++kim++CG+h+++ivryg+r l+p+n+eli+GPGCpVCvtp+ +i++ai+la + ++ ++
  gi|385806057|ref|YP_005842455.1|  22 IEELSKKIKAKFGEEKKIKIMNFCGTHEWSIVRYGIRALMPKNVELIAGPGCPVCVTPSYYIEEAIKLALE-GYKIY 97 
                                       78999*****************************************************************9.***** PP

                                       E-CCHHG---T.....T--HHHHHHTT-EEEE-SSHHHHHHHHHH-TTSEEEEEEEE-HHHHHHHHHHHHHHHHHT- CS
                              HypD  80 tfgDmlrvpgs.....kksLleakaegadvrivyspldalkiakenpdkevvflavGFEttapatalalleakkegl 151
                                       t+gD++r+ +       ksL e+k+ g+dv++v+s+lda k+a+++ +ke +fl++GFEt ap +a+a+ +  +  +
  gi|385806057|ref|YP_005842455.1|  98 TYGDTYRLMAVknisgVKSLSEVKSLGGDVQVVTSILDASKYANSD-SKESIFLGIGFETVAPGYAIAISS--NLIP 171
                                       *******99886777769*************************998.99********************99..999* PP

                                       SSEEEEEEEE-HHHHHHHHHH...TT.---SEEEEEHHHHHHHTTHHHHHHHHHH---EEEE-SSHHHHHHHHHHHH CS
                              HypD 152 knfsvlsshklvppalealle...seelkidgfiapghvstviGlkayeelaeeykvpvvvaGFepldilqailmlv 225
                                       k +s++s  kl+ppa+ + ++   +ee ++ g+iapghvs viG++++++l+++y++p+v++GFep+dil +i++++
  gi|385806057|ref|YP_005842455.1| 172 KKMSIMSLLKLTPPAMLYTIKgltEEEKSVFGIIAPGHVSSVIGANSWKFLSNDYNIPTVISGFEPIDILVSIMEIL 248
                                       ****************988652226779************************************************* PP

                                       HHHHTT---EEETTTTT--TT--HHHHHHHHHHEEEEEEEETTTEEEEEEEEEE-GGGGGGBGGGT---.....-S- CS
                              HypD 226 kqleegeaeveneYkrvvkeegnkkaqklieevfevrdaewRglgvipksglklreeyaefdaekkfel.....eke 297
                                       kq+ +++ae  +eYkr+v++egnk a++li+evf ++d++wRg+g +pksgl++re+++++d  kk+ +      + 
  gi|385806057|ref|YP_005842455.1| 249 KQIVRKRAETVIEYKRAVNWEGNKFAKNLINEVFYPSDDAWRGIGILPKSGLRIREKFEDYDSFKKLGIreidpLNW 325
                                       *******************************************************************8877776678 PP

                                       --SS-TT--HHHHHTTS--GGGSTTBTTTB-SSS-SSHHHHSTT-HHHHHHHT CS
                              HypD 298 eekekkackcgevlkGkakPedCklFgkaCtpenpvGacmvSsEGaCaayyky 350
                                       ++++ ++c+c+ev+ Gk+kP +C+lF+k+Ctpenp+G+cmvS EG+C ++ ++
  gi|385806057|ref|YP_005842455.1| 326 KDEKLPGCRCSEVIIGKIKPIECPLFMKKCTPENPYGPCMVSMEGTCYIWARF 378
                                       899999********************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       805  (0.0448993); expected 358.6 (0.02)
Passed bias filter:                      693  (0.0386525); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2626.81
//
Query:       gi|385806058|ref|YP_005842456.1|  [L=347]
Description: Sulfhydrogenase subunit beta [Fervidicoccus fontis Kam940]
Scores for complete 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   92.6   9.6    2.1e-26   92.6   9.6    2.1  2  Fer4_22   4Fe-4S dicluster domain
    2.9e-07   30.5  11.0     0.0011   19.0   0.2    2.6  2  Fer4_10   4Fe-4S dicluster domain
    5.1e-07   29.9   3.0     0.0038   17.4   0.0    2.5  2  Fer4_18   4Fe-4S dicluster domain
    6.3e-07   29.4  10.0     0.0018   18.4   3.9    2.4  2  Fer4_21   4Fe-4S dicluster domain
    8.9e-07   29.4   4.6     0.0078   16.7   1.0    2.6  2  Fer4_17   4Fe-4S dicluster domain
    1.8e-06   28.0   7.6    6.9e-06   26.1   7.6    2.0  1  Fer4_9    4Fe-4S dicluster domain
      1e-05   25.3  11.4     0.0045   17.0   1.5    2.6  2  Fer4_2    4Fe-4S binding domain
    1.2e-05   24.9  15.2     0.0089   15.8   3.7    2.4  2  Fer4      4Fe-4S binding domain
    1.6e-05   25.7   7.0      0.021   15.7   1.6    2.6  2  Fer4_16   4Fe-4S double cluster binding domain
     0.0003   21.2  11.2      0.004   17.6  11.9    2.3  3  Fer4_8    4Fe-4S dicluster domain
    0.00094   19.5   1.1    0.00094   19.5   1.1    2.6  2  Fer4_4    4Fe-4S binding domain
     0.0072   16.9  16.9        0.2   12.3  17.9    2.3  2  Fer4_7    4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.042   13.9  19.6       0.18   11.9   3.9    2.4  2  Fer4_6    4Fe-4S binding domain
       0.12   13.2   0.3       0.24   12.2   0.3    1.5  1  FIVAR     FIVAR domain
          2    9.0  12.7        4.6    7.9   0.4    2.5  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I


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 ?    0.0   0.2       1.3   1.6e+03       6      21 ..     131     146 ..     126     155 .. 0.81
   2 !   92.6   9.6   1.8e-29   2.1e-26       1      94 [.     238     329 ..     238     331 .. 0.96

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 1.3
                           Fer4_22   6 gaCtlvCptCsCfdve 21 
                                       ++Ct+    C+C +v 
  gi|385806058|ref|YP_005842456.1| 131 QECTIPGKYCFCSKVG 146
                                       6899999*****9875 PP

  == domain 2  score: 92.6 bits;  conditional E-value: 1.8e-29
                           Fer4_22   1 rClsCgaCtlvCptCsCfdvedetkeeskegervrvwdsClleeftkvaggenvrkekkerlrqrllhklsefkekf 77 
                                       +C++C++C++vCptC+C+++ d+++  + ++er r+w  Cl+  + ++ag  ++rke+  r+r+ +lhk+   k+++
  gi|385806058|ref|YP_005842456.1| 238 DCIGCSNCNMVCPTCTCTEFIDDIR-MNGNAERKRIWVGCLSPVYGQIAGM-HFRKEQYMRYRHFVLHKFLFSKKEI 312
                                       5***********************6.55899*******************9.9************************ PP

                           Fer4_22  78 gesgCvGCgRCieacpv 94 
                                       g++ CvGCgRCi+ cp 
  gi|385806058|ref|YP_005842456.1| 313 GTKICVGCGRCIAFCPL 329
                                       ***************96 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   5.5   3.2e-05     0.038       5      40 ..     235     270 ..     231     278 .. 0.68
   2 !   19.0   0.2   9.2e-07    0.0011       3      22 ..     311     330 ..     309     346 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.2e-05
                           Fer4_10   5 dddtCirCgkCvkaCPadltsvgakgeaseeeavrk 40 
                                        ++ Ci+C +C+ +CP++  +    +++++++a+rk
  gi|385806058|ref|YP_005842456.1| 235 ISKDCIGCSNCNMVCPTCTCTEFIDDIRMNGNAERK 270
                                       5688*************8744444444444444444 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 9.2e-07
                           Fer4_10   3 vidddtCirCgkCvkaCPad 22 
                                       +i ++ C++Cg+C ++CP  
  gi|385806058|ref|YP_005842456.1| 311 EIGTKICVGCGRCIAFCPLR 330
                                       567899************93 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   1.8   0.00031      0.37      54      74 ..     232     252 ..     214     263 .. 0.80
   2 !   17.4   0.0   3.2e-06    0.0038      46      81 ..     302     337 ..     277     342 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00031
                           Fer4_18  54 kekgagdcidcescvkvcPtg 74 
                                        ++ + dci c+ c  vcPt 
  gi|385806058|ref|YP_005842456.1| 232 WKEISKDCIGCSNCNMVCPTC 252
                                       456789*************95 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 3.2e-06
                           Fer4_18  46 alkekeerkekgagdcidcescvkvcPtgidirkGl 81 
                                        +k   ++ke g+  c+ c+ c++ cP  +d+rk l
  gi|385806058|ref|YP_005842456.1| 302 LHKFLFSKKEIGTKICVGCGRCIAFCPLRLDLRKTL 337
                                       445555677778889******************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 !   18.4   3.9   1.5e-06    0.0018      29      57 ..     227     255 ..     217     257 .. 0.83
   2 !   14.2   0.4     3e-05     0.036      38      53 ..     314     329 ..     303     333 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.5e-06
                           Fer4_21  29 daktvlkvvedeCvGCnlCssvCPvedci 57 
                                       ++++ +k ++++C+GC  C  vCP+  c 
  gi|385806058|ref|YP_005842456.1| 227 NDAELWKEISKDCIGCSNCNMVCPTCTCT 255
                                       5667788999**************98875 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 3e-05
                           Fer4_21  38 edeCvGCnlCssvCPv 53 
                                       ++ CvGC  C++ CP+
  gi|385806058|ref|YP_005842456.1| 314 TKICVGCGRCIAFCPL 329
                                       5668888888888885 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   1.0   6.5e-06    0.0078      26      57 ..     208     250 ..     190     253 .. 0.63
   2 !   13.4   0.1   7.4e-05     0.089      24      61 .]     293     332 ..     275     332 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.5e-06
                           Fer4_17  26 lraakl...........glleeaekeekaslCieCgeCerkCP 57 
                                        +++ l           ++++++  +e  ++Ci+C +C+++CP
  gi|385806058|ref|YP_005842456.1| 208 EKNFPLdvkdiegalekSINDAELWKEISKDCIGCSNCNMVCP 250
                                       444444554444222223444444557889************* PP

  == domain 2  score: 13.4 bits;  conditional E-value: 7.4e-05
                           Fer4_17  24 kllraakl..glleeaekeekaslCieCgeCerkCPqgld 61 
                                       +++r  ++  +++   +ke   + C++Cg+C + CP  ld
  gi|385806058|ref|YP_005842456.1| 293 QYMRYRHFvlHKFLFSKKEIGTKICVGCGRCIAFCPLRLD 332
                                       445544443333333344568899************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 !   26.1   7.6   5.7e-09   6.9e-06       1      47 [.     238     328 ..     238     331 .. 0.97

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 5.7e-09
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase............................................ 33 
                                       +C+gC +C  +Cp+++++e      ++ +a+++                                            
  gi|385806058|ref|YP_005842456.1| 238 DCIGCSNCNMVCPTCTCTEFIDDIRMNGNAERKriwvgclspvygqiagmhfrkeqymryrhfvlhkflfskkeigt 314
                                       5**************************9999999******************************************* PP

                            Fer4_9  34 eaCigCgaCveaCp 47 
                                       + C+gCg+C++ Cp
  gi|385806058|ref|YP_005842456.1| 315 KICVGCGRCIAFCP 328
                                       99***********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 !   12.7   2.8   8.7e-05       0.1      10      22 .]     239     251 ..     233     251 .. 0.88
   2 !   17.0   1.5   3.8e-06    0.0045       5      21 ..     312     328 ..     309     329 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.7e-05
                            Fer4_2  10 CigCgaCvsaCPa 22 
                                       CigC+ C  +CP+
  gi|385806058|ref|YP_005842456.1| 239 CIGCSNCNMVCPT 251
                                       ************7 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 3.8e-06
                            Fer4_2   5 vdtdrCigCgaCvsaCP 21 
                                       + t +C+gCg C+  CP
  gi|385806058|ref|YP_005842456.1| 312 IGTKICVGCGRCIAFCP 328
                                       67889***********9 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   3.7   2.1e-05     0.025       7      20 ..     238     251 ..     234     251 .. 0.91
   2 !   15.8   3.7   7.5e-06    0.0089       7      19 ..     316     328 ..     311     330 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.1e-05
                                       TSSS-THHHHHSTT CS
                              Fer4   7 kCigCGaCvevCPv 20 
                                       +CigC +C +vCP+
  gi|385806058|ref|YP_005842456.1| 238 DCIGCSNCNMVCPT 251
                                       7************7 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 7.5e-06
                                       TSSS-THHHHHST CS
                              Fer4   7 kCigCGaCvevCP 19 
                                        C+gCG+C+  CP
  gi|385806058|ref|YP_005842456.1| 316 ICVGCGRCIAFCP 328
                                       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 !   15.7   1.6   1.8e-05     0.021      37      65 ..     222     250 ..     187     252 .. 0.72
   2 !   12.3   0.3   0.00021      0.25       2      13 ..     317     328 ..     302     335 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.8e-05
                           Fer4_16  37 ekkdlaedeekckkqeaitgCdiCqdvCP 65 
                                        +k++++ e  +++ ++++gC +C++vCP
  gi|385806058|ref|YP_005842456.1| 222 LEKSINDAELWKEISKDCIGCSNCNMVCP 250
                                       45667777777778899***********9 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00021
                           Fer4_16   2 CgtCgkCaevCP 13 
                                       C++Cg+C+  CP
  gi|385806058|ref|YP_005842456.1| 317 CVGCGRCIAFCP 328
                                       888888888888 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   3.8   0.00027      0.32      44      63 ..     223     251 ..     191     252 .. 0.63
   2 !   17.6  11.9   3.3e-06     0.004       3      63 ..     237     329 ..     234     331 .. 0.70
   3 !   11.3   0.9    0.0003      0.36       5      23 ..     317     335 ..     314     341 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00027
                            Fer4_8  44 e.........eealwsCttcgaCtevCpv 63 
                                       e         +e+ + C +c +C+ vCp+
  gi|385806058|ref|YP_005842456.1| 223 EksindaelwKEISKDCIGCSNCNMVCPT 251
                                       12233334558899999999999999996 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 3.3e-06
                            Fer4_8   3 ekCieCgaCqsaCpvlrrtkkhlldargeaae......................dvqeeqvlee............. 44 
                                       ++Ci+C+ C+  Cp++ +t  ++ d r + ++                      +        +             
  gi|385806058|ref|YP_005842456.1| 237 KDCIGCSNCNMVCPTCTCTE-FIDDIRMNGNAerkriwvgclspvygqiagmhfR--------Keqymryrhfvlhk 304
                                       68************999996.3333333333324566666666666665554441........03444456677788 PP

                            Fer4_8  45 ......eealwsCttcgaCtevCpv 63 
                                             e + + C++cg+C   Cp 
  gi|385806058|ref|YP_005842456.1| 305 flfskkEIGTKICVGCGRCIAFCPL 329
                                       999998999***************6 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.0003
                            Fer4_8   5 CieCgaCqsaCpvlrrtkk 23 
                                       C++Cg+C + Cp+  + +k
  gi|385806058|ref|YP_005842456.1| 317 CVGCGRCIAFCPLRLDLRK 335
                                       9999999999998776665 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   9.6       2.7   3.2e+03       2      16 ..     237     251 ..     236     257 .. 0.90
   2 !   19.5   1.1   7.9e-07   0.00094       4      16 ..     317     329 ..     310     335 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2.7
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       + CigC  C  +CP+
  gi|385806058|ref|YP_005842456.1| 237 KDCIGCSNCNMVCPT 251
                                       56************6 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 7.9e-07
                            Fer4_4   4 CigCgsCvaaCPq 16 
                                       C+gCg+C+a+CP 
  gi|385806058|ref|YP_005842456.1| 317 CVGCGRCIAFCPL 329
                                       ************5 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   5.5   0.00046      0.55      35      50 ..     236     251 ..     213     253 .. 0.77
   2 !   12.3  17.9   0.00017       0.2       2      49 ..     239     328 ..     238     331 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00046
                            Fer4_7  35 pekClgCgaCvavCPt 50 
                                       + +C+gC +C  vCPt
  gi|385806058|ref|YP_005842456.1| 236 SKDCIGCSNCNMVCPT 251
                                       5678888888888886 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00017
                            Fer4_7   2 CigCgaCvaaC...................pvkaieldeeenek............gtekv................ 31 
                                       CigC +C  +C                                k            +   +                
  gi|385806058|ref|YP_005842456.1| 239 CIGCSNCNMVCptctctefiddirmngnaeR------------KriwvgclspvygQ---Iagmhfrkeqymryrhf 300
                                       ***********22222222222222222220............12333333333330...03333333344455566 PP

                            Fer4_7  32 ..........eidpekClgCgaCvavCP 49 
                                                 ei    C+gCg+C+a CP
  gi|385806058|ref|YP_005842456.1| 301 vlhkflfskkEIGTKICVGCGRCIAFCP 328
                                       6666677766999999************ PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   7.8    0.0043       5.2       9      21 ..     239     251 ..     236     253 .. 0.95
   2 ?   11.9   3.9   0.00015      0.18       8      20 ..     316     328 ..     314     329 .. 0.94

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0043
                            Fer4_6   9 CigCgdCvrvCPe 21 
                                       CigC +C +vCP+
  gi|385806058|ref|YP_005842456.1| 239 CIGCSNCNMVCPT 251
                                       ************7 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00015
                            Fer4_6   8 kCigCgdCvrvCP 20 
                                        C+gCg+C++ CP
  gi|385806058|ref|YP_005842456.1| 316 ICVGCGRCIAFCP 328
                                       6***********9 PP

>> FIVAR  FIVAR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.3    0.0002      0.24      23      62 ..     187     224 ..     182     230 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0002
                                       CC-CCHHHHHHHHHHHHHHHC...TSTT.TTCCCHHHHHHH CS
                             FIVAR  23 nydqdkkdaynnalsaAnailnktnnpn.atveqVnqalan 62 
                                       +++++ ++ yn+++++A+ +++   ++  ++v++++ al++
  gi|385806058|ref|YP_005842456.1| 187 EANEEEVKLYNEKIKNAKDTIE---KNFpLDVKDIEGALEK 224
                                       5788999**************4...4455999999998864 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 ?    4.2   6.5     0.053        64       5      18 ..     238     251 ..     235     252 .. 0.89
   2 ?    7.9   0.4    0.0038       4.6       6      17 ..     317     328 ..     314     341 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.053
                           Fer4_13   5 tCiacgaCvelaPd 18 
                                        Ci+c +C +++P 
  gi|385806058|ref|YP_005842456.1| 238 DCIGCSNCNMVCPT 251
                                       6************6 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0038
                           Fer4_13   6 CiacgaCvelaP 17 
                                       C++cg C +++P
  gi|385806058|ref|YP_005842456.1| 317 CVGCGRCIAFCP 328
                                       ************ PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       735  (0.040995); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); 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):              15  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 2037.35
//
Query:       gi|385806059|ref|YP_005842457.1|  [L=279]
Description: Sulfhydrogenase subunit gamma [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.3e-16   58.8   0.0    1.4e-15   57.8   0.0    1.5  1  NAD_binding_1    Oxidoreductase NAD-binding domain
    3.9e-11   42.6   2.2    8.1e-11   41.6   2.2    1.6  1  DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydr
      4e-06   27.1   0.0    7.1e-06   26.3   0.0    1.4  1  FAD_binding_6    Oxidoreductase FAD-binding domain
  ------ inclusion threshold ------
       0.19   11.9   0.0          7    6.7   0.0    2.4  2  NAD_binding_6    Ferric reductase NAD 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 !   57.8   0.0   3.2e-19   1.4e-15       3     108 ..     120     220 ..     117     221 .. 0.92

  Alignments for each domain:
  == domain 1  score: 57.8 bits;  conditional E-value: 3.2e-19
                                       EEGGGGHHHHHHHHHHHHHCTTCSEEEEEEEESSGCGSTTHHHHHHHHHHCTTEEEEEEEESSCTTTSSSEESSHHH CS
                     NAD_binding_1   3 agGtGiaPvrsvlraileeakdktkvvlvyGnrteedllyreeleelakklpgrlkvvavvsreeagweggkgrvqd 79 
                                       +gG G+aP+r vlr + ++ ++ +++v++yG+r+ +d++y+ e+ee+ kk pg ++++ + ++++++w+ + g+v d
  gi|385806059|ref|YP_005842457.1| 120 GGGIGFAPLRPVLRFVSNNRQKFGRLVVIYGARSPNDIIYKYEIEEY-KKIPG-IELFLTIDKPAEDWKWNVGFVPD 194
                                       5789***************9999************************.89999.8899999***************9 PP

                                       HHHHHHHHHSSTTEEEEEECSHHHHHHHH CS
                     NAD_binding_1  80 alleellslkkeethvyvCGppgMikavr 108
                                        l +++    +++  ++vCGp+ M+k ++
  gi|385806059|ref|YP_005842457.1| 195 ML-DKVKL--DGDFKYFVCGPEIMMKITA 220
                                       88.55555..89**************986 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 !   41.6   2.2   1.8e-14   8.1e-11       1      41 [.     238     270 ..     238     271 .. 0.95

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 1.8e-14
                                       ----SSSSSSS-TTEEEETTCTT.CEEETTTT-CEEECCCB CS
                   DHODB_Fe-S_bind   1 eerMaCGvGaClgCvvktkggdggeykrvCkdGPvFdadev 41 
                                       e+rM CGvG+C+ C +           +vCkdGPvF  d+v
  gi|385806059|ref|YP_005842457.1| 238 ERRMRCGVGICGTCQLGH--------YYVCKDGPVFSFDQV 270
                                       89*************999........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 !   26.3   0.0   1.6e-09   7.1e-06       3      96 ..      13     104 ..      11     106 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.6e-09
                                       EEEEEEECCTTEEEEEEEESTTTS-----TT-EEEEEECETTCCEEEEEE.BSSTTECCEEEEEEE--TT-HHHHHH CS
                     FAD_binding_6   3 kltekeevsedtrifrfklpsekqklglpvGqhvflrlkikgeaviRsYtpissenekGelellvkvypgGkmsqaL 79 
                                       +++e  + ++d++++++  ++e +  ++ +Gq+v+++lk  ge v  s + +  e++ G l +   +   G +++++
  gi|385806059|ref|YP_005842457.1|  13 NVKEIINETSDIKTYKLFSNAE-KAQKFKPGQFVMVYLKGFGE-VPISLSDLVYEEDGGSL-ITLTIRGTGTVTKYM 86 
                                       5677788899999999977754.4589************9998.55566666666665554.44455578******9 PP

                                       .HCS-TT-EEEEEEEE-S CS
                     FAD_binding_6  80 .delkigdtleikGPlGk 96 
                                        + ++igd++ i+GP+G+
  gi|385806059|ref|YP_005842457.1|  87 lSTVNIGDKIGIRGPYGN 104
                                       788**************7 PP

>> NAD_binding_6  Ferric reductase NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0016         7       4      39 ..     116     174 ..     113     200 .. 0.71
   2 ?    2.7   0.0     0.028   1.2e+02     139     152 ..     207     220 ..     192     225 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0016
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.......................xxxxxxxxxxx RF
                     NAD_binding_6   4 vllvagGiGitpfisilkdllkksk.......................kealktkkikl 39 
                                       +l+ +gGiG++p+ ++l+ + ++ +                       +e  k++ i+l
  gi|385806059|ref|YP_005842457.1| 116 ILIAGGGIGFAPLRPVLRFVSNNRQkfgrlvviygarspndiiykyeiEEYKKIPGIEL 174
                                       788899**************999996666666666666666666555555555555554 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.028
                                       xxxxxxxxxxxxxx RF
                     NAD_binding_6 139 vfvCGppklvkevk 152
                                        fvCGp++++k ++
  gi|385806059|ref|YP_005842457.1| 207 YFVCGPEIMMKITA 220
                                       69*******98654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1776.82
//
Query:       gi|385806060|ref|YP_005842458.1|  [L=260]
Description: Sulfhydrogenase subunit delta [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      8e-22   77.5   0.0    1.2e-21   76.9   0.0    1.3  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 !   76.9   0.0   6.8e-26   1.2e-21       1     130 [.      14     151 ..      14     152 .. 0.84

  Alignments for each domain:
  == domain 1  score: 76.9 bits;  conditional E-value: 6.8e-26
                                       -SHHHHHHT-TTTTHHHHHHTEEEEEETTT-S--HHHHHHTHTTTSEEEEEESBE...EEEHHHHHHHHGGGSSEEE CS
                       Oxidored_q6   1 CtGcsisllaleedlldllelielryhetlladskeeeieakekeadvlvveGavtrkpkealellkelaekakavi 77 
                                       C+Gc  ++  +  +  +++e i+++y  + l+d++     + e + d+++veG+v   +ke++e+l+e+++k ++v 
  gi|385806060|ref|YP_005842458.1|  14 CSGCINEIVYALLSDPQIMEKIQIDY-FPELQDKN-----NFEGKFDIFLVEGSV--VNKEQIERLREIRSKTRFVL 82 
                                       9***99995555555677799*****.55556666.....34569**********..99****************** PP

                                       EESHHHHH-TGGGSTT-TEE................-HHHHHHHC.S-E.EEE-SSS--HHHHHHHHHH CS
                       Oxidored_q6  78 avGtCAafGGipaaannpsv................geevgellevvpvdinipGCPphpeailetlla 130
                                       avGtC+a+GGi+++++  +v                  +v+ ++e ++ d+ +pGCP++ +++l  l +
  gi|385806060|ref|YP_005842458.1|  83 AVGTCSAYGGIQSLRDRTNVedvkksvyikpeyidiEGDVYSVSEIIKPDFIVPGCPVNGDKLLTLLRK 151
                                       ****************885566788888877776651577889999*****************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       758  (0.0422779); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); 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: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1650.91
//
Query:       gi|385806061|ref|YP_005842459.1|  [L=423]
Description: Sulfhydrogenase subunit alpha [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.5e-27   95.1   0.0    8.2e-13   48.1   0.0    3.2  3  NiFeSe_Hases    Nickel-dependent hydrogenase
  ------ inclusion threshold ------
      0.065   12.3   0.0        1.1    8.3   0.0    2.2  2  Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd s


Domain annotation for each model (and alignments):
>> NiFeSe_Hases  Nickel-dependent hydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   0.0   9.2e-17   8.2e-13       1      87 [.      39     125 ..      39     142 .. 0.92
   2 !    4.7   0.0    0.0013        12     164     210 ..     144     187 ..     131     202 .. 0.74
   3 !   38.9   0.0   5.7e-14   5.1e-10     410     505 .]     326     423 .]     295     423 .] 0.81

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 9.2e-17
                                       --HHHHTTTS-GGGHHHHHHTT-SSSTTHHHHHHHHHHHHHHT----HHHHHHHHHHHHHHHHHHHHHHHHHTTGGG CS
                      NiFeSe_Hases   1 RGlElilkgrdprdawalvqRiCGVCttvHalasvravedAlgikipknarlirnliaaalllhdhivhFYhLhalD 77 
                                       R +E  lkgr+p +a  +++RiCG+C ++ ++as++a e  +gi++p + + +r+ i   +++++ ++h   L+  D
  gi|385806061|ref|YP_005842459.1|  39 RFIEFGLKGRKPIEAPEITSRICGICSVSYQMASAKAFEYGMGIEVPYEEEEMRKAIFINEHIKSNVLHVLYLQLPD 115
                                       568999*****************************************************************9*9999 PP

                                       TS-THGGGGS CS
                      NiFeSe_Hases  78 wvdvvsalka 87 
                                        ++  s l+ 
  gi|385806061|ref|YP_005842459.1| 116 LLNASSSLEV 125
                                       9998888765 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0013
                                       THHHHHHHSSSSS--.EBTTBESSGBGSBSHHHHHHHHHHHHHHHHH CS
                      NiFeSe_Hases 164 akivaifggknPhpqslvvGGvtcaidllnaerlaevkslikevkef 210
                                        k++ ++gg+  ++ ++ vGGv ++ +   ++++++++s  +++ ++
  gi|385806061|ref|YP_005842459.1| 144 RKLMKVLGGRFHNIVNIRVGGVYSMPE---KKEVEALSSQSERAITY 187
                                       6899******************99955...44444444444444433 PP

  == domain 3  score: 38.9 bits;  conditional E-value: 5.7e-14
                                       -TT-SGGGS-.SEEEEEEEEEETTEEEEEEEEE.ETTEEEEEEEE-HHHHHH--S-TT----HHHHHHTT-B-SSTT CS
                      NiFeSe_Hases 410 eekldkkevp.keakGvglveapRGaLsHwiki.kdgkienYqavvPsTWnasPrdakgqkgayEaaLigtpvadpe 484
                                         ++++k+++ ke + +g veapRG L H  ++ k g ie+ +++ P+  n+   +a          Li++  + ++
  gi|385806061|ref|YP_005842459.1| 326 YVQVNEKSFEiKEGTYYGAVEAPRGILYHRYTVnKRGLIEDANIIPPTSQNLISMEAFSMYHLEKIGLINKAEQLEK 402
                                       34556777777789999************999956789****99999999*99998877766666679999888888 PP

                                       S-HHHHHHHHHT--BHHHHH- CS
                      NiFeSe_Hases 485 kPleilrtihSfDPClACavH 505
                                          e+ ++i+ fDPC++C+vH
  gi|385806061|ref|YP_005842459.1| 403 AHQEVQKIIRLFDPCISCSVH 423
                                       999****************** PP

>> Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.014   1.3e+02      22      73 ..     146     198 ..     139     206 .. 0.77
   2 ?    8.3   0.0   0.00012       1.1     184     221 ..     318     358 ..     291     388 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.014
                                       HHHHHSSSSS-T.TBESSBBSS---TTHHHHHHHHHHHHHHHHHHHHHHHHSS CS
                    Complex1_49kDa  22 leevtGaRltas.yiriGGvarDlpegllekikeflkelekkldeleklltkn 73 
                                       l +v G R+++   ir+GGv+   +++ +e +++  ++  +  ++l++ + +n
  gi|385806061|ref|YP_005842459.1| 146 LMKVLGGRFHNIvNIRVGGVYSMPEKKEVEALSSQSERAITYARKLSEFVLDN 198
                                       568899999975169*****998888888887777777777777777666666 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00012
                                       HHHHHHHHHHH...S-----SEEEEEEEEETTEEEEEEEEE CS
                    Complex1_49kDa 184 ealihhfklvt...egfkvpkgevyaavEapkGelgvylvs 221
                                       +++i ++ +v+   + f++++g +y avEap+G l +  + 
  gi|385806061|ref|YP_005842459.1| 318 TDFIDNYRYVQvneKSFEIKEGTYYGAVEAPRGILYHRYTV 358
                                       556666655554458899***************99775554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); 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: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.51
# Mc/sec: 2507.24
//
Query:       gi|385806062|ref|YP_005842460.1|  [L=227]
Description: cytidyltransferase [Fervidicoccus fontis Kam940]
Scores for complete 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-24   84.1   0.4    8.9e-24   83.4   0.4    1.4  1  DUF357           Protein of unknown function (DUF357)
    3.7e-16   59.6   0.0    7.4e-16   58.6   0.0    1.5  1  CTP_transf_like  Cytidylyltransferase-like
    4.5e-05   23.4   0.0     0.0073   16.2   0.0    2.3  2  FAD_syn          FAD synthetase
    0.00021   20.6   0.0    0.00036   19.8   0.0    1.4  1  Pantoate_ligase  Pantoate-beta-alanine ligase


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 !   83.4   0.4     2e-27   8.9e-24       2      72 ..       8      75 ..       7      76 .. 0.98

  Alignments for each domain:
  == domain 1  score: 83.4 bits;  conditional E-value: 2e-27
                                      HHHHHHHHHHHHH.....TS---HHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTST CS
                            DUF357  2 YirlleealekvkiapdeesplgeaaeevlemaesYleDakyflekgdlvnAlasfsYaeGwLDagarlgl 72
                                      Yi+++e+ale+ +    ++s+l++++++++++a+ YleD+ky+lek+dlv++la +sYaeG+LDa+arlg 
  gi|385806062|ref|YP_005842460.1|  8 YIKMVENALEQTE---CQKSSLNKEESDLINLAKLYLEDSKYYLEKEDLVTSLATISYAEGLLDALARLGK 75
                                      *************...99***************************************************96 PP

>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.6   0.0   1.7e-19   7.4e-16       2     118 ..      90     200 ..      89     222 .. 0.85

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 1.7e-19
                                       EEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-..SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHHHH CS
                   CTP_transf_like   2 agGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkk..kplasaeeRlemlelakevdevisvdpweltrev 76 
                                       + GtFD++H GH+rl+e+a kl++  ++v+v  d+++kk+k  + +++++ Rl+ +  +k v+ ++  d+ +  ++v
  gi|385806062|ref|YP_005842460.1|  90 ITGTFDILHEGHIRLIEEASKLGD--VYVIVSRDVNAKKNKgrEVIFPENSRLKIVSSIKNVKMAMLGDENDYLKKV 164
                                       68**********************..69999*********669*******************************988 PP

                                       HHHTTTTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEE CS
                   CTP_transf_like  77 lkklkpdklylvigadvledfsewkeleeilgnvklvvvsrp 118
                                       ++   pd  ++v+g d+      +++l+e l++++l  v++ 
  gi|385806062|ref|YP_005842460.1| 165 IEVS-PD--IIVLGPDQKFG---EEQLKEELKKRGLNNVEVI 200
                                       8877.**..*******8776...899*********9998666 PP

>> FAD_syn  FAD synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.6e-06    0.0073       3      34 ..      82     113 ..      80     156 .. 0.79
   2 !    5.2   0.0     0.004        18      94     125 ..     157     186 ..     148     208 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.6e-06
                           FAD_syn   3 eedegavvtlGnFDGvHlGHqallkkaveaak 34 
                                       +e++++v+  G FD +H GH  l+++a ++ +
  gi|385806062|ref|YP_005842460.1|  82 REKRKKVLITGTFDILHEGHIRLIEEASKLGD 113
                                       578999*********************99875 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.004
                           FAD_syn  94 aeeFiekllveklkvkavvvGfdfrfGkkreg 125
                                       ++++++k++   +    +v+G d +fG+++  
  gi|385806062|ref|YP_005842460.1| 157 ENDYLKKVIE--VSPDIIVLGPDQKFGEEQLK 186
                                       5678889777..9999***********98654 PP

>> Pantoate_ligase  Pantoate-beta-alanine ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0     8e-08   0.00036      12      58 ..      76     124 ..      66     133 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 8e-08
                                       HHHHHHHT.T-EEEEEEE-SS-GHHHHHHHHHHHHHSS.EEEEEEEEEG CS
                   Pantoate_ligase  12 llkelrke.gkkvglVpTmGaLHeGHlsLvkaakeend.vvvvSiFvNp 58 
                                       l  e+++e +kkv +  T   LHeGH++L+++a +  d +v+vS  vN 
  gi|385806062|ref|YP_005842460.1|  76 LKIEWKREkRKKVLITGTFDILHEGHIRLIEEASKLGDvYVIVSRDVNA 124
                                       444565552667*********************9998835778877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       840  (0.0468515); 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:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 1450.78
//
Query:       gi|385806063|ref|YP_005842461.1|  [L=277]
Description: diphthine synthase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.4e-18   65.7   0.0    7.4e-18   65.3   0.0    1.2  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
  ------ inclusion threshold ------
        0.2   12.0   0.0       0.29   11.4   0.0    1.3  1  DUF4976       Domain of unknown function (DUF4976)


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 !   65.3   0.0   8.2e-22   7.4e-18       2     210 ..      19     240 ..      18     242 .. 0.75

  Alignments for each domain:
  == domain 1  score: 65.3 bits;  conditional E-value: 8.2e-22
                      TP_methylase   2 lylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeel..eleapmgkekepleea.yeeiaealaea 75 
                                       l +VG+G+ +  ++++++++ lk++d ++ ++ +++  + ++ a  +   +  + +k    ++++  e+  + ++++
  gi|385806063|ref|YP_005842461.1|  19 LSFVGLGL-SLSHISIEGIKKLKSSDFIFLEG-YTSFYFPEINAAMKviGIKSDRFKI--ISRRDiEEKSGQEIIDL 91 
                                       789*****.99*****************9999.5444443333332244344444444..333333566777789** PP

                      TP_methylase  76 lragkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl...lpglake 149
                                       l +gk++ ++v+GDP++++t+  l + +++  +g++v  iPG+ +++ a +++g+  +++g + +++   +  l+  
  gi|385806063|ref|YP_005842461.1|  92 LLKGKNISMAVIGDPFIATTHLSLKNYAKE--KGCKVNYIPGINIFSYAMSATGLFNYKFGPSATIVykrEGILSVY 166
                                       *************************99999..9**********************************8763334444 PP

                      TP_methylase 150 eereleallan.gdtlvll....kaprk....laelaelL....kea...lyddttpvavveragtedervvrgtle 210
                                       ++  l+  l++  +t ++l    +   +    ++e+++lL    ke+   +  ++t+++v er+g++de+++ g+++
  gi|385806063|ref|YP_005842461.1| 167 PYLVLSGNLSRgLHTFFFLdidaE---RgplnASEAIKLLiemeKEErlgIITPETKIVVLERLGWPDEKIYYGKIS 240
                                       555555555554556666644331...25556888888886666333579666688****************88775 PP

>> DUF4976  Domain of unknown function (DUF4976)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.2e-05      0.29      28      91 ..      50     116 ..      27     127 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.2e-05
                           DUF4976  28 YhyyeyPaehavkrhygvrteryklihf..ykdidewelyDlkkDpkel.knlyddpeyeevvkelk 91 
                                       Y+ + +P+ +a+ + +g++ +r+k+i     +++   e++Dl    k++   +++dp  ++   +lk
  gi|385806063|ref|YP_005842461.1|  50 YTSFYFPEINAAMKVIGIKSDRFKIISRrdIEEKSGQEIIDLLLKGKNIsMAVIGDPFIATTHLSLK 116
                                       555669********************75114566667888876554444145666666665555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        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: 00:00:00.43
# Mc/sec: 1916.67
//
Query:       gi|385806064|ref|YP_005842462.1|  [L=203]
Description: Indolepyruvate:ferredoxin oxidoreductase subunit beta [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.2e-33  113.9   0.1    9.6e-33  113.7   0.1    1.0  1  POR           Pyruvate ferredoxin/flavodoxin oxidoreductase
  ------ inclusion threshold ------
      0.052   13.6   1.2        1.3    9.2   0.0    2.4  2  Cullin_Nedd8  Cullin protein neddylation domain


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 !  113.7   0.1   1.1e-36   9.6e-33       1     176 [.      12     193 ..      12     194 .. 0.95

  Alignments for each domain:
  == domain 1  score: 113.7 bits;  conditional E-value: 1.1e-36
                                       CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEE CS
                               POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglk 77 
                                       GGqGv+t++++++ aa+++G+++   + +g ++r g++++hvri++++ ++ ++ g+ dll+ l+a +  ++l+++k
  gi|385806064|ref|YP_005842462.1|  12 GGQGVITIANLIGLAAFKQGIKARVGEIHGLSQRFGSVFTHVRIGEDVYSSIVPLGRGDLLISLEAIETLRYLKYMK 88 
                                       9**********************************************999****************5555******* PP

                                       EEEEEEEECTCGTT-CCHHHCTS-HHHHHHH.......T-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHTS-H CS
                               POR  78 pggiiiynseelkpdelkkakeeerelkerl.......gvrvygvdatkiakeiggneraaNtvmlGalaallglpl 147
                                       ++g+i++n+  ++p      ++  ++ +e +       + +++ ++ +++ +++++ ++++Nt+++G+++ + g+pl
  gi|385806064|ref|YP_005842462.1|  89 KDGLILMNTLMTEPFKTISVDPKIADINEIKkmmksafDGKILIINGNELTEKLKN-SLLLNTAIIGIALTIPGFPL 164
                                       **********9999999999999988888889*******************99888.*****************777 PP

                                       ..HHHHHHHHCCS-CH.HHHHHHHHHHHHHH CS
                               POR 148 ..ealeeaikkrfpkkkeviekNlkafragy 176
                                         e++++ i+++f +k   +e+N++a++ g+
  gi|385806064|ref|YP_005842462.1| 165 keESIKASIEEMFDRK--YVELNIRALEVGM 193
                                       77************95..9*********997 PP

>> Cullin_Nedd8  Cullin protein neddylation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.3     0.013   1.2e+02      12      45 ..      85     116 ..      82     126 .. 0.80
   2 ?    9.2   0.0   0.00014       1.3      35      58 ..     160     183 ..     135     186 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.013
                      Cullin_Nedd8  12 RiMKsrktlshneLvsevieqlskrftpsiadik 45 
                                       + MK+   + +n+L++e  + +  ++ p+iadi 
  gi|385806064|ref|YP_005842462.1|  85 KYMKKDGLILMNTLMTEPFKTI--SVDPKIADIN 116
                                       68999999*********99999..6777776664 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00014
                      Cullin_Nedd8  35 krftpsiadikkrIesLiekeYle 58 
                                       + f+++ + ik +Ie++ ++ Y+e
  gi|385806064|ref|YP_005842462.1| 160 PGFPLKEESIKASIEEMFDRKYVE 183
                                       47999*****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1242.69
//
Query:       gi|385806065|ref|YP_005842463.1|  [L=636]
Description: Indolepyruvate:ferredoxin oxidoreductase subunit alpha [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.6e-30  104.4   0.1    9.2e-30  103.4   0.1    1.5  1  TPP_enzyme_C    Thiamine pyrophosphate enzyme, C-terminal TPP
    2.6e-16   60.1   0.0    3.8e-16   59.5   0.0    1.2  1  POR_N           Pyruvate flavodoxin/ferredoxin oxidoreductase
      5e-10   38.8  17.6    4.2e-08   32.7   1.5    2.7  2  Fer4            4Fe-4S binding domain
    1.6e-09   37.4   9.5      8e-06   25.7   1.8    2.6  2  Fer4_6          4Fe-4S binding domain
    5.5e-08   32.8   7.6    1.1e-07   31.9   7.6    1.5  1  Fer4_21         4Fe-4S dicluster domain
    1.7e-07   31.3   8.5    3.6e-07   30.2   8.5    1.6  1  Fer4_9          4Fe-4S dicluster domain
    2.8e-07   31.0   8.7    2.6e-05   24.7   9.3    2.6  2  Fer4_7          4Fe-4S dicluster domain
    4.3e-07   29.6   8.8    0.00016   21.5   1.4    2.9  2  Fer4_2          4Fe-4S binding domain
    5.1e-07   29.7  19.0    3.2e-05   24.0  10.6    2.6  2  Fer4_10         4Fe-4S dicluster domain
    0.00012   21.4   0.2     0.0036   16.6   0.1    2.3  2  DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
    0.00018   22.4  10.3     0.0043   18.0   1.6    2.8  4  Fer4_16         4Fe-4S double cluster binding domain
  ------ inclusion threshold ------
      0.017   15.6   3.1      0.017   15.6   3.1    2.7  2  Fer4_4          4Fe-4S binding domain
      0.046   13.3   0.1        9.6    5.8   0.0    2.5  2  TPP_enzyme_N    Thiamine pyrophosphate enzyme, N-terminal TPP
       0.13   12.8   9.0       0.41   11.2   1.4    2.5  2  Fer4_17         4Fe-4S dicluster domain
       0.31   11.8  10.1        2.7    8.8   0.8    3.2  2  Fer4_15         4Fe-4S single cluster domain
       0.31   11.6  11.8        1.9    9.1   2.1    2.8  2  Fer4_13         4Fe-4S single cluster domain of Ferredoxin I
        2.3    8.8  11.9    1.6e+02    2.9  11.9    2.4  1  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 !  103.4   0.1   8.7e-33   9.2e-30       1     152 [.     411     556 ..     411     557 .. 0.93

  Alignments for each domain:
  == domain 1  score: 103.4 bits;  conditional E-value: 8.7e-33
                                       ESSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHH....STTSEEEEEEEHHHHHHT.GGGHHHHHHTT CS
                      TPP_enzyme_C   1 diGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGakla....kpdrevvaivGDGgflmi.lqelatavrrn 72 
                                       diGc+tl      ++++p ++++  + ++mG +++ A+G++ a    + +++++a++GD++f++  l++la+a++++
  gi|385806065|ref|YP_005842463.1| 411 DIGCYTL------GYYPPMKLVD--TSTHMGSSIGLAHGISKAlegsASKKPIIATIGDSTFFHAgLPALANAIYNR 479
                                       89*****......999*******..99**************9655545689************************** PP

                                       -SEEEEEEE-SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSE CS
                      TPP_enzyme_C  73 lpitvvvlnNegygmtggqqepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkgp 148
                                        +++++vl+N++++mtg+q++p +g + s+ +   +k+++++ +a+a+Ga+ + +v+++d++ +e+al++al+ +g+
  gi|385806065|ref|YP_005842463.1| 480 SNFILFVLDNRTTAMTGHQPHPGTGYSISN-N---GKEIKIEDIAKAMGADyVEVVDPYDMKATEQALRKALSVNGV 552
                                       ************************977766.4...79**************889*********************** PP

                                       EEEE CS
                      TPP_enzyme_C 149 alie 152
                                       ++i+
  gi|385806065|ref|YP_005842463.1| 553 SFIV 556
                                       **97 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 !   59.5   0.0   3.6e-19   3.8e-16       2     170 ..      30     193 ..      29     223 .. 0.89

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 3.6e-19
                                       HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCC CS
                             POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmien 78 
                                       +a+++++ ++aaYP TPssei++++++ +++ +v   +v    +E  a +a++GA+++G r++T     Gl  + ++
  gi|385806065|ref|YP_005842463.1|  30 GALEGNISFFAAYPGTPSSEILDTFSAIAKDAGV---YVEVSSNEKIAYEAALGASWSGLRSMTSMKHVGLNVAADA 103
                                       89999************************99996...6666678********************************* PP

                                       HHHHHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHHS---EEEE-SSHHHHHHHHHHHHHHHHHCTSEEEEEEEH CS
                             POR_N  79 lglaageelPvvivvvaRalpstglsirtdqsDlmaardtglivlasenvqeafdlalvAfnlAekvrvPvivlfDg 155
                                       ++ +a++ +   +v+v    ps  +s +++q   ++a   +l v+ +++  ea  +a + f l+ek+ ++v+ l   
  gi|385806065|ref|YP_005842463.1| 104 FMSTAMNGVKGGFVIVVADDPSM-WSSQNEQDTRLFAKLANLPVVEPSSPDEARLFAKELFELSEKFDTAVV-LRST 178
                                       *******9988888888789999.*********************************************986.5678 PP

                                       HHH.HEEEEEEC-SG CS
                             POR_N 156 fllshevekvelpde 170
                                       ++lsh++ +v + + 
  gi|385806065|ref|YP_005842463.1| 179 TRLSHMRGEVVFGPL 193
                                       9999***99876554 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   2.3   3.3e-06    0.0035       1      15 [.     579     593 ..     579     594 .. 0.93
   2 !   32.7   1.5   3.9e-11   4.2e-08       3      23 ..     612     632 ..     610     633 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.3e-06
                                       EEEETTTSSS-THHH CS
                              Fer4   1 vvideekCigCGaCv 15 
                                       +videekC+gC++C+
  gi|385806065|ref|YP_005842463.1| 579 YVIDEEKCTGCKTCI 593
                                       69************7 PP

  == domain 2  score: 32.7 bits;  conditional E-value: 3.9e-11
                                       EETTTSSS-THHHHHSTTTEE CS
                              Fer4   3 ideekCigCGaCvevCPvgAI 23 
                                       i e++C gCG Cv+vCP++AI
  gi|385806065|ref|YP_005842463.1| 612 IQEDLCYGCGSCVSVCPFNAI 632
                                       789*****************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 !   15.6   1.1   1.2e-05     0.013       3      21 ..     580     600 ..     580     603 .. 0.89
   2 !   25.7   1.8   7.6e-09     8e-06       1      24 []     609     632 ..     609     632 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.2e-05
                            Fer4_6   3 eidpdkCigCgdCvrv..CPe 21 
                                       +id++kC+gC  C+    CP+
  gi|385806065|ref|YP_005842463.1| 580 VIDEEKCTGCKTCILTfgCPA 600
                                       69***********88888997 PP

  == domain 2  score: 25.7 bits;  conditional E-value: 7.6e-09
                            Fer4_6   1 vveidpdkCigCgdCvrvCPegai 24 
                                       ++ i++d+C gCg Cv+vCP++ai
  gi|385806065|ref|YP_005842463.1| 609 KAFIQEDLCYGCGSCVSVCPFNAI 632
                                       5789*******************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 !   31.9   7.6     1e-10   1.1e-07       2      57 ..     580     632 ..     579     634 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 1e-10
                           Fer4_21   2 ridedkCigCgkClia..Cedtshqaieidaktvlkvv.edeCvGCnlCssvCPvedci 57 
                                       +ide+kC gC+ C+++  C+     ai+ +++++ + + ed C GC  C+svCP  ++i
  gi|385806065|ref|YP_005842463.1| 580 VIDEEKCTGCKTCILTfgCP-----AISWNSDKKKAFIqEDLCYGCGSCVSVCPF-NAI 632
                                       69************973355.....9998876665554399*************7.777 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   8.5   3.4e-10   3.6e-07       1      51 []     585     632 ..     585     632 .. 0.88

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 3.4e-10
                            Fer4_9   1 kCtgCgaCvea..CpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                       kCtgC++C+    Cpa  ++ d+++ +++ +      C+gCg+Cv +Cp +ai
  gi|385806065|ref|YP_005842463.1| 585 KCTGCKTCILTfgCPAISWNSDKKKAFIQED-----LCYGCGSCVSVCPFNAI 632
                                       7*******55445***********9999974.....6************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 !   11.8   1.6   0.00026      0.28      26      46 ..     574     594 ..     557     602 .. 0.77
   2 !   24.7   9.3   2.5e-08   2.6e-05       1      52 []     585     631 ..     585     631 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00026
                            Fer4_7  26 kgtekveidpekClgCgaCva 46 
                                       +++++++id+ekC+gC+ C+ 
  gi|385806065|ref|YP_005842463.1| 574 QKFKRYVIDEEKCTGCKTCIL 594
                                       356899*************86 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 2.5e-08
                            Fer4_7   1 rCigCgaCvaa..CpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       +C+gC+ C  +  Cp  ai+++ +     ++k+ i+++ C+gCg+Cv+vCP++a
  gi|385806065|ref|YP_005842463.1| 585 KCTGCKTCILTfgCP--AISWNSD-----KKKAFIQEDLCYGCGSCVSVCPFNA 631
                                       7*******9654499..9999987.....56799******************97 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   1.4   1.5e-07   0.00016       2      22 .]     578     600 ..     577     600 .. 0.84
   2 !   20.9   1.0   2.5e-07   0.00026       3      21 ..     610     628 ..     608     629 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.5e-07
                            Fer4_2   2 pvvvdtdrCigCgaCv.sa.CPa 22 
                                       ++v+d+++C+gC++C+ +  CPa
  gi|385806065|ref|YP_005842463.1| 578 RYVIDEEKCTGCKTCIlTFgCPA 600
                                       689************64446**8 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 2.5e-07
                            Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                       +++ +d C gCg+Cvs+CP
  gi|385806065|ref|YP_005842463.1| 610 AFIQEDLCYGCGSCVSVCP 628
                                       567799************* PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0  10.6     3e-08   3.2e-05       2      56 .]     579     628 ..     578     628 .. 0.93
   2 !   19.3   1.2   8.4e-07   0.00088       2      23 ..     610     631 ..     609     636 .] 0.84

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 3e-08
                           Fer4_10   2 vvidddtCirCgkCvka..CPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                        vid+++C++C++C     CPa       +  +s++++  +  + C gcg+Cv++CP
  gi|385806065|ref|YP_005842463.1| 579 YVIDEEKCTGCKTCILTfgCPA-------ISWNSDKKKAFIQEDLCYGCGSCVSVCP 628
                                       589***********98556***.......99999999999999*************9 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 8.4e-07
                           Fer4_10   2 vvidddtCirCgkCvkaCPadl 23 
                                       + i++d C +Cg Cv++CP+++
  gi|385806065|ref|YP_005842463.1| 610 AFIQEDLCYGCGSCVSVCPFNA 631
                                       67999**************954 PP

>> DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   3.4e-06    0.0036     110     174 ..     429     492 ..     425     498 .. 0.89
   2 ?    2.1   0.0     0.088        92     232     268 ..     518     554 ..     506     558 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.4e-06
                    DXP_synthase_N 110 agHsstsisaalGlavardlkgekkkvvaviGDgal.tgGmafealnnigelkkkllvilNdNems 174
                                       ++H ++si  a+G+++a + + +kk ++a iGD+++  +G  + al n+  +++++++ + dN+ +
  gi|385806065|ref|YP_005842463.1| 429 STHMGSSIGLAHGISKALEGSASKKPIIATIGDSTFfHAG--LPALANAIYNRSNFILFVLDNRTT 492
                                       579******************************9972566..679************999999875 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.088
                    DXP_synthase_N 232 tlfeelgfkYlGpidGhdleelikvleevkklkgpvl 268
                                        + +++g +Y+  +d  d+++ +++l+++ +++g  +
  gi|385806065|ref|YP_005842463.1| 518 DIAKAMGADYVEVVDPYDMKATEQALRKALSVNGVSF 554
                                       57789***********************999888655 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 ?    0.8   3.2       0.9   9.5e+02      52      61 ..     584     593 ..     559     600 .. 0.70
   2 ?    0.3   3.2       1.3   1.4e+03       1      14 [.     585     600 ..     585     615 .. 0.68
   3 !   17.8   1.8   4.6e-06    0.0048      41      67 .]     603     630 ..     599     630 .. 0.74
   4 !   18.0   1.6   4.1e-06    0.0043       2      20 ..     617     635 ..     616     636 .] 0.88

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.9
                           Fer4_16  52 eaitgCdiCq 61 
                                       e++tgC++C 
  gi|385806065|ref|YP_005842463.1| 584 EKCTGCKTCI 593
                                       5677777774 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.3
                           Fer4_16   1 rCgtCgkCaev..CPt 14 
                                       +C++C+ C+ +  CP+
  gi|385806065|ref|YP_005842463.1| 585 KCTGCKTCILTfgCPA 600
                                       5999999974333776 PP

  == domain 3  score: 17.8 bits;  conditional E-value: 4.6e-06
                           Fer4_16  41 laedeekckkq.eaitgCdiCqdvCPan 67 
                                       ++ d++k  +q   ++gC+ C+ vCP+n
  gi|385806065|ref|YP_005842463.1| 603 WNSDKKKAFIQeDLCYGCGSCVSVCPFN 630
                                       555666655441556************9 PP

  == domain 4  score: 18.0 bits;  conditional E-value: 4.1e-06
                           Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                       C +Cg C++vCP nai+e 
  gi|385806065|ref|YP_005842463.1| 617 CYGCGSCVSVCPFNAIHEG 635
                                       9999999999999999875 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.6   0.00083      0.88       2      15 ..     584     599 ..     583     606 .. 0.88
   2 ?   15.6   3.1   1.6e-05     0.017       2      17 .]     615     630 ..     613     630 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00083
                            Fer4_4   2 erCigCgsCvaa..CP 15 
                                       e+C+gC+ C+ +  CP
  gi|385806065|ref|YP_005842463.1| 584 EKCTGCKTCILTfgCP 599
                                       89*******9887777 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1.6e-05
                            Fer4_4   2 erCigCgsCvaaCPqg 17 
                                       + C gCgsCv++CP++
  gi|385806065|ref|YP_005842463.1| 615 DLCYGCGSCVSVCPFN 630
                                       6799**********86 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 ?    5.1   0.0     0.015        16       5      74 ..      25      97 ..      21     175 .. 0.77
   2 ?    5.8   0.0    0.0091       9.6      53     154 ..     437     552 ..     423     564 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.015
                                      HHHHHHHHHCT--EEEE---CCCHHHHCCHHCT....TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHH CS
                      TPP_enzyme_N  5 ealvraLkalgvehvfgvpGsrilplldalseeq...girvvlarhEqgaafaAdgyaratgkpgvvlvtsgp 74
                                      ea+vr   + ++  + ++pG+ + ++ld +s+     g+ v ++++E  a  aA g + +  + +  + ++g 
  gi|385806065|ref|YP_005842463.1| 25 EAIVRGALEGNISFFAAYPGTPSSEILDTFSAIAkdaGVYVEVSSNEKIAYEAALGASWSGLRSMTSMKHVGL 97
                                      6777777777888888999999998888887766667999999***********9987666555555555555 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0091
                                       HHHHHHHH.....HHTS-EEEEE-CHHHHHHCHHHHHHHHHHT--EEEEEEE--CCCHH............S..TC- CS
                      TPP_enzyme_N  53 faAdgyar.....atgkpgvvlvtsgpGatnaltalaeAkvdriPllvlsgdrptslrg............qgvlqq 112
                                       + A+g+++     a++kp ++     + +  +l+ala+A ++r+  ++++ d+ t+                +   +
  gi|385806065|ref|YP_005842463.1| 437 GLAHGISKalegsASKKPIIATIGDSTFFHAGLPALANAIYNRSNFILFVLDNRTTAMTghqphpgtgysiSN-NGK 512
                                       556666665555555666666666666667789*****************99999888867777777777433.333 PP

                                       -T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--E CS
                      TPP_enzyme_N 113 eldqlalfrpvtkyaervtspeelpealrrAirtalsgrpgP 154
                                       e++++++++ +  + ++v +p ++ +a ++A+r+a  + +g+
  gi|385806065|ref|YP_005842463.1| 513 EIKIEDIAKAMGADYVEVVDPYDM-KATEQALRKA-LSVNGV 552
                                       667777788888777777777774.4567777777.444455 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   0.5     0.015        15       1      26 [.     585     612 ..     585     616 .. 0.83
   2 ?   11.2   1.4   0.00038      0.41      44      58 ..     615     629 ..     603     632 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.015
                           Fer4_17   1 rCiqCgyClp..eCpsyeaydnepkkll 26 
                                       +C++C+ C+    Cp   ++++++k ++
  gi|385806065|ref|YP_005842463.1| 585 KCTGCKTCILtfGCPAISWNSDKKKAFI 612
                                       6*******98778999999999888765 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00038
                           Fer4_17  44 slCieCgeCerkCPq 58 
                                       +lC +Cg C+++CP 
  gi|385806065|ref|YP_005842463.1| 615 DLCYGCGSCVSVCPF 629
                                       789999999999996 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   0.6    0.0055       5.8       2      16 ..     580     594 ..     580     608 .. 0.91
   2 ?    8.8   0.8    0.0026       2.7       3      19 ..     612     628 ..     611     634 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0055
                           Fer4_15   2 vvDrdaCigcglCva 16 
                                       v+D+++C+gc  C+ 
  gi|385806065|ref|YP_005842463.1| 580 VIDEEKCTGCKTCIL 594
                                       69***********86 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0026
                           Fer4_15   3 vDrdaCigcglCvaeap 19 
                                       + +d+C gcg Cv ++p
  gi|385806065|ref|YP_005842463.1| 612 IQEDLCYGCGSCVSVCP 628
                                       6689***********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 ?    7.1   2.6    0.0074       7.8       1      19 [.     581     601 ..     581     615 .. 0.73
   2 ?    9.1   2.1    0.0018       1.9       3      17 ..     614     628 ..     612     630 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0074
                           Fer4_13   1 VDrdtCiacgaCvel..aPdv 19 
                                       +D+++C++c++C  +  +P +
  gi|385806065|ref|YP_005842463.1| 581 IDEEKCTGCKTCILTfgCPAI 601
                                       89**********976556655 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0018
                           Fer4_13   3 rdtCiacgaCvelaP 17 
                                       +d C +cg+Cv+++P
  gi|385806065|ref|YP_005842463.1| 614 EDLCYGCGSCVSVCP 628
                                       689***********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 ?    2.9  11.9      0.15   1.6e+02       4      64 ..     585     630 ..     582     631 .. 0.65

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.15
                            Fer4_8   4 kCieCgaCqsa..CpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                       kC++C  C  +  Cp+++       d+++  ++      +       + C +cg+C++vCp +
  gi|385806065|ref|YP_005842463.1| 585 KCTGCKTCILTfgCPAISWN----SDKKKAFIQ------E-------DLCYGCGSCVSVCPFN 630
                                       78888888744447766544....334444333......3.......6799*********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (636 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.74u 0.34s 00:00:01.08 Elapsed: 00:00:00.52
# Mc/sec: 3709.87
//
Query:       gi|385806066|ref|YP_005842464.1|  [L=457]
Description: Acyl-CoA synthetase (NDP forming), alpha subunit [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-46  157.6   0.6    2.3e-45  153.8   0.1    2.6  3  Succ_CoA_lig     Succinyl-CoA ligase like flavodoxin domain
    8.3e-29  100.4   0.1    2.6e-26   92.4   0.1    2.5  2  CoA_binding_2    CoA binding domain
    1.6e-15   57.5   2.5    4.6e-15   56.1   2.1    2.0  2  CoA_binding      CoA binding domain
  ------ inclusion threshold ------
      0.055   13.5   0.7          2    8.5   0.1    2.7  2  Antimicrobial17  Alpha/beta enterocin family


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 !  153.8   0.1   5.1e-49   2.3e-45       1     137 [.     151     287 ..     151     288 .. 0.98
   2 ?    0.9   0.0     0.081   3.6e+02       3      30 ..     297     324 ..     294     326 .. 0.91
   3 ?   -2.9   0.0       1.2   5.3e+03      69      88 ..     393     412 ..     389     427 .. 0.73

  Alignments for each domain:
  == domain 1  score: 153.8 bits;  conditional E-value: 5.1e-49
                      Succ_CoA_lig   1 pGkialisqSGalalalldwaasrglgfskvvslGneadvdvadlleylaedpetkvillylEsirdgrkflsaarr 77 
                                       +G++ +isqSGal+  ++ ++ ++++gf+k+vs+Gn++dvd++dl+ey+++dp+t +illylE+++ g++fl+++++
  gi|385806066|ref|YP_005842464.1| 151 KGSVTFISQSGALGGGIVYKTIKENIGFAKFVSVGNMSDVDFSDLIEYFSRDPDTASILLYLEGVKSGKRFLEVLKE 227
                                       599************************************************************************** PP

                      Succ_CoA_lig  78 aarkkpvvvlksGrseagaraaashtgalagsdavvdaafrqaGvlrvdsleelfdaael 137
                                        +++kp+++lk G  ++gara++shtg++ag+ +++ +a++q G++ +++++e +++a+ 
  gi|385806066|ref|YP_005842464.1| 228 HSKEKPIIALKGGIYSTGARAVSSHTGSIAGNAEIFMTALKQGGAIKAKTIDEALSMARS 287
                                       ********************************************************9975 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.081
                      Succ_CoA_lig   3 kialisqSGalalalldwaasrglgfsk 30 
                                       ++++i+  G+ ++ + d  +++gl++sk
  gi|385806066|ref|YP_005842464.1| 297 RVGVITNAGGAGVLISDLIEENGLEMSK 324
                                       59**********************9997 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.2
                      Succ_CoA_lig  69 rkflsaarraarkkpvvvlk 88 
                                       +  ++a+ +   kkp++++ 
  gi|385806066|ref|YP_005842464.1| 393 EGIVKAINESEVKKPILAMF 412
                                       56678888888899999874 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.4   0.1   5.7e-30   2.6e-26       1     115 [.      12     136 ..      12     137 .. 0.97
   2 !    5.4   0.0    0.0054        24      63     105 ..     387     432 ..     359     436 .. 0.87

  Alignments for each domain:
  == domain 1  score: 92.4 bits;  conditional E-value: 5.7e-30
                                       --EEEET--S-TTSHHHHHHHHHHH.HT--EEEESSS-SEETTEES----T....T--EEEE-S-HHHHGGGHHHHH CS
                     CoA_binding_2   1 rtiaVvGasdnpgkfgykvlrylle.hglpvvpVnpkeeeilgekvyaslaedpepvdlvdvftppeatpeivkeal 76 
                                       ++iaV+Gas+n++k g++v+++ll+ +g +v+pVn kee+i g+k+y+++++ + ++dl ++++p  a+ + v e +
  gi|385806066|ref|YP_005842464.1|  12 KSIAVIGASNNETKLGHQVFKNLLSyKG-KVFPVNVKEESIMGVKAYKTIKDIQDEIDLSVIVVPKPAVKQAVIESG 87 
                                       79***********************677.**********************858*********************** PP

                                       HH--SEEEE-TT..........---HHHHHHHHHTT-EEE.ES-HHHHH CS
                     CoA_binding_2  77 algakavwlqpg..........sedeeaaelaeeagirvvgdrCilveg 115
                                       ++gak++++  +          +e++e++++a+++g+rv+g++C++v++
  gi|385806066|ref|YP_005842464.1|  88 EKGAKGIIIITAgfgetgergkEEERELVRVAHDYGMRVIGPNCVGVMN 136
                                       *********9999**********************************86 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0054
                                       S-HHHHGGGHHHHHHH...--SEEEE-TT---HHHHHHHHHTT-EE CS
                     CoA_binding_2  63 tppeatpeivkealal...gakavwlqpgsedeeaaelaeeagirv 105
                                       t+ e+++ ivk++ +    ++  +++++g  +e+a +++e++gi+ 
  gi|385806066|ref|YP_005842464.1| 387 TRTEHAEGIVKAINESevkKPILAMFMAGDISEDAKRFLESNGIPT 432
                                       78899999999997774556999********************975 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.1   2.1     1e-18   4.6e-15       2      96 .]      10     100 ..       9     100 .. 0.95
   2 ?   -3.0   0.0       2.7   1.2e+04      10      29 ..     385     405 ..     385     442 .. 0.55

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 1e-18
                                       TTEEEEEETTTSHHHHHH.HHHHHHHHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHH CS
                       CoA_binding   2 kdtkviviGagglgiagl.yhfkeklkygikavfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqe 77 
                                       ++++++viGa++++++++  +fk+ l+y+  +vf+vn +   + + g+++yk+++++ ++  +d +vi+vP++++++
  gi|385806066|ref|YP_005842464.1|  10 EPKSIAVIGASNNETKLGhQVFKNLLSYKG-KVFPVNVK--EESIMGVKAYKTIKDIQDE--IDLSVIVVPKPAVKQ 81 
                                       6789**************999999999886.69******..9******************..*************** PP

                                       HHHHHHHTT-SEEEEESST CS
                       CoA_binding  78 avdelveagikgiviiteg 96 
                                       av+e  e+g kgi+iit+g
  gi|385806066|ref|YP_005842464.1|  82 AVIESGEKGAKGIIIITAG 100
                                       *****************86 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.7
                                       TTTSHHHHHH.HHHHHHHHEC CS
                       CoA_binding  10 Gagglgiagl.yhfkeklkyg 29 
                                       G++++++a++ ++ +++ +++
  gi|385806066|ref|YP_005842464.1| 385 GMTRTEHAEGiVKAINESEVK 405
                                       566666666655555555444 PP

>> Antimicrobial17  Alpha/beta enterocin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1   0.00044         2      16      52 ..     163     196 ..     159     199 .. 0.85
   2 ?    2.3   0.1     0.038   1.7e+02       5      16 ..     397     408 ..     395     414 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00044
                   Antimicrobial17  16 iGGesvfskiGnavGPaayWilkGlGnmsdvnqadri 52 
                                       +GG  v+  i + +G a +     +Gnmsdv+ +d i
  gi|385806066|ref|YP_005842464.1| 163 LGGGIVYKTIKENIGFAKFV---SVGNMSDVDFSDLI 196
                                       79999999999999998874...78*******99987 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.038
                   Antimicrobial17   5 kvlnekemkkti 16 
                                       k +ne e+kk+i
  gi|385806066|ref|YP_005842464.1| 397 KAINESEVKKPI 408
                                       889********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 2622.86
//
Query:       gi|385806067|ref|YP_005842465.1|  [L=331]
Description: Proliferating-cell nucleolar antigen p120-like protein [Fervidicoccus fontis Kam940]
Scores for complete 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-54  182.9   0.0    7.1e-54  182.5   0.0    1.1  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
    2.4e-10   40.4   0.1    5.2e-10   39.3   0.0    1.6  2  Methyltransf_31  Methyltransferase domain
    1.9e-08   34.7   0.0      1e-07   32.4   0.0    2.1  2  Methyltr_RsmF_N  N-terminal domain of 16S rRNA methyltransfer
    4.1e-05   23.8   0.0    6.3e-05   23.2   0.0    1.3  1  FtsJ             FtsJ-like methyltransferase
     0.0001   22.1   0.0    0.00017   21.4   0.0    1.4  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    0.00018   21.0   0.1    0.00072   19.1   0.0    2.0  3  Methyltransf_4   Putative methyltransferase
    0.00034   21.2   0.0     0.0014   19.3   0.0    2.0  1  Methyltransf_25  Methyltransferase domain
      0.001   18.4   0.1      0.016   14.5   0.1    2.1  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
  ------ inclusion threshold ------
      0.012   15.4   0.1      0.072   12.8   0.0    2.2  3  Met_10           Met-10+ like-protein
      0.031   13.8   0.0       0.24   10.9   0.0    2.0  2  MTS              Methyltransferase small domain
       0.15   12.2   0.2       0.15   12.2   0.2    2.0  3  TssO             Type VI secretion system, TssO


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 !  182.5   0.0   4.4e-57   7.1e-54       3     198 ..     124     327 ..     122     329 .. 0.95

  Alignments for each domain:
  == domain 1  score: 182.5 bits;  conditional E-value: 4.4e-57
                                       HH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC.. CS
                   Methyltr_RsmB-F   3 lLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggel 79 
                                       +L p e+++++D++aaPGgKTth+a+lmknkg ++ +d+n+eR+ ++  n++rL+ +n+ vl++Da ki+    +e 
  gi|385806067|ref|YP_005842465.1| 124 VLSPVEDDKVVDMAAAPGGKTTHMAQLMKNKGIILSIDINRERIWKLRVNIERLNAKNVYVLRTDALKING--LDEY 198
                                       79*******************************************************************44..4469 PP

                                       EEEEEEEE--CCGGGTTT-TCHHHH--HHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEES--STTTTHHHHHHHHHH CS
                   Methyltr_RsmB-F  80 fDriLlDaPCsgtgvirrdpdvklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaLkk 156
                                       fD+++lDaPC+g g i  +++ k+++  +d +++  lq  +l+ a++llk+gG ++YsTCs+++eEne vi ++L++
  gi|385806067|ref|YP_005842465.1| 199 FDKVMLDAPCTGEGLIVYKKERKFSKGIEDYKKMIPLQISMLKKAFKLLKRGGKILYSTCSIAPEENEYVISQVLNE 275
                                       ***************************************************************************** PP

                                       -TTEEEESSBSTTSTTSSECEEC..........TSEEE-TTTTSS-SEEEEE CS
                   Methyltr_RsmB-F 157 redvelvetelsepkglklgeea..........gtlrllPhtenkdgffiak 198
                                        +d+e+ +t++++ kg +   e+          + lrl+P+t++++gff+  
  gi|385806067|ref|YP_005842465.1| 276 LKDIEILPTRYNGVKGNEGLPEYndiffgdelkNCLRLYPNTDKTEGFFLCL 327
                                       *********99998877766666899*****9999**************876 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       5.3   8.6e+03      33      46 ..       9      22 ..       4      27 .. 0.73
   2 !   39.3   0.0   3.2e-13   5.2e-10       4     114 ..     130     268 ..     127     300 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 5.3
                   Methyltransf_31 33 GiDiseeaielAre 46
                                       i i++ea+e A++
  gi|385806067|ref|YP_005842465.1|  9 DIQITKEAVEIAEK 22
                                      56678888888875 PP

  == domain 2  score: 39.3 bits;  conditional E-value: 3.2e-13
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlils 80 
                                       + +v+D +++ G +t  +a+++  k+ + +iDi+ e i + r n ++l+ +nv + + d+ +++ l  de fD ++ 
  gi|385806067|ref|YP_005842465.1| 130 DDKVVDMAAAPGGKTTHMAQLMKNKGIILSIDINRERIWKLRVNIERLNAKNVYVLRTDALKINGL--DEYFDKVML 204
                                       679****************99999999***********************************9976..899****** PP

                   Methyltransf_31  81 nevl......................naladpdkileeiervlkpggilliedpr........l 114
                                       ++++                        ++ + + l++++++lk gg +l ++++        +
  gi|385806067|ref|YP_005842465.1| 205 DAPCtgeglivykkerkfskgiedykKMIPLQISMLKKAFKLLKRGGKILYSTCSiapeeneyV 268
                                       *666666666777777777777777799***************************433322221 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 !   32.4   0.0   6.1e-11     1e-07       8      90 .]      32     119 ..      27     119 .. 0.84
   2 ?   -0.9   0.0       1.5   2.4e+03      25      45 ..     163     183 ..     144     207 .. 0.64

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 6.1e-11
                                       HHHHHHGG.GHHHHHHHHH-----EEE--TTS..TTHHHHHHH...-SS--B-TT-TTEEES---....TTSHHHHT CS
                   Methyltr_RsmF_N   8 kmkellge.eaeaflaaleeprkkglRvNtlKisveeleklse...efelepvpwceeGfyleeee.rpgkhplhea 79 
                                       ++  ++g+ ea ++l + e+  +k++R+N + +++ ++ + s    +f le+ p+ + ++y+++e+ + g +++h +
  gi|385806067|ref|YP_005842465.1|  32 RYIMFMGDkEAIEYLISAEKGIEKSFRCNSILVKDCNVVERSLtekGFILEKTPYLNYAYYIKREPfSIGSTVEHLS 108
                                       5566788879999*****************99876655443323589****************997466******** PP

                                       TS-EE--TTTH CS
                   Methyltr_RsmF_N  80 GlyYiQEpSam 90 
                                       G +Y+Q   +m
  gi|385806067|ref|YP_005842465.1| 109 GKIYVQGVGSM 119
                                       ******99998 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.5
                                       H-----EEE--TTS..TTHHH CS
                   Methyltr_RsmF_N  25 eeprkkglRvNtlKisveele 45 
                                       +++r   lRvN  +++ +++ 
  gi|385806067|ref|YP_005842465.1| 163 NRERIWKLRVNIERLNAKNVY 183
                                       556666677776666655543 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   3.8e-08   6.3e-05      21     157 ..     129     281 ..      93     294 .. 0.69

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 3.8e-08
                                       TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS...HHHTTEEEE.CS-CCCSSHHHHHCHCHHHSSEEEEEE CS
                              FtsJ  21 pgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm...aplpgvtti.qgditdpetiekikealserkvdlvvs 93 
                                       ++++vvD +aaPGg +  ++q +++kg ++++D++     +++ +++ +   ++   +t  +  + l ++++d v+ 
  gi|385806067|ref|YP_005842465.1| 129 EDDKVVDMAAAPGGKTTHMAQLMKNKGIILSIDINREriwKLRVNIERLnAKNVYVLRTDALKINGL-DEYFDKVML 204
                                       4578*******************999********887566333333333344443333333333333.357899999 PP

                                       --S-.............SS-CHHHHHHHHHC.CCCHHHHCCHCCCCECCCEEEECCCH..CCCHHHHHHHHHCCEEE CS
                              FtsJ  94 Dgap.............dvsgvhdldeylqs.qLllaalelalkllkpggtfvlkifr..geeteallkqlkkfFek 154
                                       D                + +g++d   y+++  L  + l+ a+kllk+gg ++  ++    ee e +++q+ +  ++
  gi|385806067|ref|YP_005842465.1| 205 DAPCtgeglivykkerkFSKGIED---YKKMiPLQISMLKKAFKLLKRGGKILYSTCSiaPEENEYVISQVLNELKD 278
                                       975455566666554444444333...333336888889999999*****999888887555555777775555566 PP

                                       EEE CS
                              FtsJ 155 vsv 157
                                       +++
  gi|385806067|ref|YP_005842465.1| 279 IEI 281
                                       555 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 !   21.4   0.0   1.1e-07   0.00017      65     133 ..     121     189 ..      76     206 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.1e-07
                                       HHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-G CS
                              PCMT  65 alellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDG 133
                                       a e l+  + ++v+++ +  G +t  +a+l+++kg ++si+  +e +++ + n+++l+++nv v  +D 
  gi|385806067|ref|YP_005842465.1| 121 ASEVLSPVEDDKVVDMAAAPGGKTTHMAQLMKNKGIILSIDINRERIWKLRVNIERLNAKNVYVLRTDA 189
                                       44666667789*****************************************************99986 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       3.4   5.6e+03     103     124 ..      70      91 ..      67      94 .. 0.83
   2 !   19.1   0.0   4.4e-07   0.00072       5      70 ..     133     201 ..     129     206 .. 0.83
   3 ?   -1.9   0.0       1.2     2e+03      98     117 ..     238     257 ..     235     282 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3.4
                                       HHHHEEEEEEEEEEESHHHHHH CS
                    Methyltransf_4 103 larvLkkgGvlelaTDveeyae 124
                                       ++r L ++G++  +T   +ya+
  gi|385806067|ref|YP_005842465.1|  70 VERSLTEKGFILEKTPYLNYAY 91 
                                       6788999999999999998875 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 4.4e-07
                                       EEEET-TTSHHHHHHHHHS.TTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-C..CCHHHHCS-T CS
                    Methyltransf_4   5 vleiGcGkGeflvalAkkn.PdknflGiEirvkvvakvlkkiealelkNlrilrgda..lkvllelled 70 
                                       v+++  + G+ + ++A+    +  +l i+i+++++ k+  +ie+l++kN+++lr+da  ++ l e++ +
  gi|385806067|ref|YP_005842465.1| 133 VVDMAAAPGGKTTHMAQLMkNKGIILSIDINRERIWKLRVNIERLNAKNVYVLRTDAlkINGLDEYFDK 201
                                       7899999999999***9650555789*******************************555568888876 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.2
                                       HHHHHHHHHEEEEEEEEEEE CS
                    Methyltransf_4  98 ellkelarvLkkgGvlelaT 117
                                        +lk++ + Lk gG +   T
  gi|385806067|ref|YP_005842465.1| 238 SMLKKAFKLLKRGGKILYST 257
                                       67888999999999998777 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   8.8e-07    0.0014       1      70 [.     133     204 ..     133     251 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 8.8e-07
                                       EEEET-TTSHHHHHHHCTS.TSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrl.gkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvs 70 
                                       v+d+++ +G  t ++a+ + +k+ ++ +Di+ e + + r ++e+ ++ nv +++ da +++  d+ fD v++
  gi|385806067|ref|YP_005842465.1| 133 VVDMAAAPGGKTTHMAQLMkNKGIILSIDINRERIWKLRVNIERLNAkNVYVLRTDALKINGLDEYFDKVML 204
                                       89****************9659999*****************998888********************9987 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   9.9e-06     0.016      44     120 ..     126     202 ..     118     206 .. 0.92
   2 ?    1.5   0.0     0.096   1.6e+02     134     150 ..     238     254 ..     225     269 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 9.9e-06
                                       -S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEE CS
                   Ubie_methyltran  44 avkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvv 120
                                       ++ +  kv+D+a+  g  + ++++ +++kg +  +Din + +   +  +++   +n+  l ++a +++  d+ fD v
  gi|385806067|ref|YP_005842465.1| 126 SPVEDDKVVDMAAAPGGKTTHMAQLMKNKGIILSIDINRERIWKLRVNIERLNAKNVYVLRTDALKINGLDEYFDKV 202
                                       5567789***********************************999****************************9987 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.096
                                       HHHHHHHHHEEEEEEEE CS
                   Ubie_methyltran 134 kaLkeayrvlkpGGrlv 150
                                         Lk+a++ lk GG+++
  gi|385806067|ref|YP_005842465.1| 238 SMLKKAFKLLKRGGKIL 254
                                       579***********986 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       2.1   3.4e+03     166     188 ..      27      50 ..      11      59 .. 0.70
   2 ?   12.8   0.0   4.4e-05     0.072     100     178 ..     129     208 ..     122     223 .. 0.84
   3 ?   -1.2   0.0      0.91   1.5e+03      19      57 ..     263     301 ..     248     309 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.1
                                       TT-EEEEEE--T.TTGGGGHHHHH CS
                            Met_10 166 eqladrvvmnlp.ksaieFldkvl 188
                                       + +a+r++m +  k+aie+l ++ 
  gi|385806067|ref|YP_005842465.1|  27 PFMAQRYIMFMGdKEAIEYLISAE 50 
                                       557889999775246888886655 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 4.4e-05
                                       TT-EEEETT-TTTCCHHHCCHHTTSS.EEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---.TT-EEEEEE CS
                            Met_10 100 egevVvdvfAGiGpfaipiakyskak.rvlaidlnPesvkylkeniklNkvekvvkpileDgrevir.eqladrvvm 174
                                       e++ Vvd+ A  G  +  +a++ k+k ++l+id+n e +  l+ ni++ + ++v  ++ +D+ ++   ++ +d+v++
  gi|385806067|ref|YP_005842465.1| 129 EDDKVVDMAAAPGGKTTHMAQLMKNKgIILSIDINRERIWKLRVNIERLNAKNV-YVLRTDALKINGlDEYFDKVML 204
                                       56889******9999999999877653789****************87665554.4799999999888999999998 PP

                                       --TT CS
                            Met_10 175 nlpk 178
                                       ++p 
  gi|385806067|ref|YP_005842465.1| 205 DAPC 208
                                       8875 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.91
                                       SHHHHHHHHHHHHHSS-SCEEEE-S-SBTTTTB--EEEE CS
                            Met_10  19 keykkvigevildktkvktvlrkvsevegefRtfelevl 57 
                                       +e ++vi++v+ + ++++ + ++++ v+g+   +e++ +
  gi|385806067|ref|YP_005842465.1| 263 EENEYVISQVLNELKDIEILPTRYNGVKGNEGLPEYNDI 301
                                       556789999999999999999999999998877777654 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00015      0.24      19     106 ..     117     207 ..     114     224 .. 0.84
   2 ?    0.5   0.0      0.24   3.9e+02     120     136 ..     238     254 ..     226     279 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00015
                                       HHHHHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.E.EEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTS CS
                               MTS  19 GsklLletlpkelsgkvlDlGcGaGvlgaalakespeae.vtlvdvdarAlesakenleankle.vevvasdvleev 93 
                                       Gs l  e l+  +++kv+D+++  G  ++++a+  ++   +  +d++ + +   + n+e+ +++ v v+ +d+l+  
  gi|385806067|ref|YP_005842465.1| 117 GSMLASEVLSPVEDDKVVDMAAAPGGKTTHMAQLMKNKGiILSIDINRERIWKLRVNIERLNAKnVYVLRTDALKIN 193
                                       666666778888999*****************999888768899***************999998999999998754 PP

                                       T.TS-EEEEEE--- CS
                               MTS  94 e.ekkfdlivsNPP 106
                                         ++ fd ++   P
  gi|385806067|ref|YP_005842465.1| 194 GlDEYFDKVMLDAP 207
                                       44688888877655 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.24
                                       HHHHHHHHHEEEEEEEE CS
                               MTS 120 eliaeAkeaLkegGeLl 136
                                        ++++A + Lk gG++l
  gi|385806067|ref|YP_005842465.1| 238 SMLKKAFKLLKRGGKIL 254
                                       799***********987 PP

>> TssO  Type VI secretion system, TssO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   9.1e-05      0.15      86     141 ..       2      57 ..       1      61 [. 0.96
   2 ?   -2.7   0.1       3.5   5.8e+03     123     138 ..     163     178 ..     148     182 .. 0.78
   3 ?   -3.1   0.1       4.6   7.4e+03      55      67 ..     221     233 ..     215     247 .. 0.44

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.1e-05
                              TssO  86 eIkkdlndikntygknssdeRykmyaqiakfykmlledKkelksvseniklfkkqL 141
                                       +I+k+l di+ t +  +  e++ + + +a+ y m++ dK+ + ++ + +k ++k++
  gi|385806067|ref|YP_005842465.1|   2 YINKKLFDIQITKEAVEIAEKFGISPFMAQRYIMFMGDKEAIEYLISAEKGIEKSF 57 
                                       79*************999999*******************************9987 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.5
                              TssO 123 dKkelksvseniklfk 138
                                       +++++++++ ni++++
  gi|385806067|ref|YP_005842465.1| 163 NRERIWKLRVNIERLN 178
                                       6788888888888776 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 4.6
                              TssO  55 ekqkelkkkvdsi 67 
                                       +++k +++  + i
  gi|385806067|ref|YP_005842465.1| 221 KFSKGIEDYKKMI 233
                                       3333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); 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: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1983.38
//
Query:       gi|385806068|ref|YP_005842466.1|  [L=178]
Description: hypothetical protein FFONT_1026 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-05   24.5   0.2    5.2e-05   23.4   0.2    1.6  1  UPF0113   UPF0113 PUA domain


Domain annotation for each model (and alignments):
>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.2   2.9e-09   5.2e-05      13      75 ..     121     173 ..     109     174 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 2.9e-09
                           UPF0113  13 LYGrdvlkesilkitesvkenqvvvVlnengeplGiGkirkdtkaspgkivvknlaDiGeYlR 75 
                                        +G+ +  ++i  i+++   ++  +Vl +++++lG+G++        +++++ +laDiG YlR
  gi|385806068|ref|YP_005842466.1| 121 SFGKTISLNEIALIKRNE--SGIYLVLLQDETFLGWGIL--------KRKILVPLADIGLYLR 173
                                       589999999999999554..58888888999********........889************* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.55
# Mc/sec: 972.42
//
Query:       gi|385806069|ref|YP_005842467.1|  [L=258]
Description: Peptidyl-prolyl cis-trans isomerase, FKBP-type rotamase [Fervidicoccus fontis Kam940]
Scores for complete 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   56.8   5.0    3.6e-15   55.8   5.0    1.5  1  FKBP26_C  FKBP26_C-terminal
    1.3e-13   51.1   0.2    3.5e-13   49.7   0.0    1.8  2  FKBP_C    FKBP-type peptidyl-prolyl cis-trans isomerase
  ------ inclusion threshold ------
       0.14   12.7   0.3       0.54   10.7   0.2    1.9  2  Tex_YqgF  Tex protein YqgF-like domain


Domain annotation for each model (and alignments):
>> FKBP26_C  FKBP26_C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.8   5.0     6e-19   3.6e-15       1      71 [.     158     230 ..     158     231 .. 0.87

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 6e-19
                                       HHHHHHHHHHHH-..TT--..--EEEEETTEEEEE--TTGGGSTTHHHHHHHHHHHHHHH-TTEEEEEEEEEE CS
                          FKBP26_C   1 dkekikelIkryi..PnidlekfkieiedktvtIelpeeakFieniqlaklrIAkdilkrieevekVkFvdef 71 
                                       d ek+k+l kr++   nid  ++ki+ e++ v+I++pe+     +iqlak+++A++i+++ie+++kV+F++e+
  gi|385806069|ref|YP_005842467.1| 158 DDEKVKALLKRRLrpKNIDDYNIKISKEEGFVQIKIPETEMINPDIQLAKRALAREIFNYIEGIKKVEFIEEI 230
                                       57**********843456655555555699*****************************************97 PP

>> FKBP_C  FKBP-type peptidyl-prolyl cis-trans isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7   0.0   5.8e-17   3.5e-13       6      93 ..       7     151 ..       4     152 .. 0.74
   2 ?   -3.1   0.0       1.7     1e+04      65      76 ..     182     193 ..     177     229 .. 0.61

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 5.8e-17
                                       -TTCEEEEEEEEEET.TSSEEEEH.............CCHTSEEEEETTSSSSCHHHHHHHTTSBTT-EEEEEEEGG CS
                            FKBP_C   6 kegdtVtvhykgkle.dgkvfdss.............rsrakplefkvGsgqvikGfeealegmkvGekrtltippe 68 
                                       ke+d++ ++y+++++  ++v+d++              + ++p  + +G+g+v+kG+eeal++m+ Ge++ ++ pp+
  gi|385806069|ref|YP_005842467.1|   7 KEKDFILIDYTATVKeTNTVVDTTnsekakesniydeNKTYEPTLVIIGEGRVVKGLEEALQEMNEGEQKVIELPPS 83 
                                       78999*********8779999999889988888855445999999******************************** PP

                                       GTTTT.......................TTBCTTTB.TT.............................SEEEEEEEE CS
                            FKBP_C  69 laYge.......................kglaggvippn.............................atLvFeveL 93 
                                        aYge                                 +                             +t+v+ev++
  gi|385806069|ref|YP_005842467.1|  84 KAYGErdpnrlrripirefkkgdvepvpG---------KvveingvpalirdvtggrvlvdfnhplagKTIVYEVKV 151
                                       *****555555555555555444444440.........144444555555555555555555555566888888887 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.7
                                       EEGGGTTTTTTB CS
                            FKBP_C  65 ippelaYgekgl 76 
                                       i +e+++ + + 
  gi|385806069|ref|YP_005842467.1| 182 ISKEEGFVQIKI 193
                                       555555555333 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 ?   10.7   0.2   9.1e-05      0.54      18      82 ..      13      75 ..       9      81 .. 0.83
   2 ?   -1.4   0.0      0.53   3.1e+03      19      52 ..     134     167 ..     128     176 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 9.1e-05
                                      EE-TTS-EEEEEEE--STTT--HHHHHHHHHHHHHHTT--EEEEESSTTHHHHHHHHHHHHHHGG CS
                          Tex_YqgF 18 vvdetgkvletaviyphepkkkveeakkklkklvkkykveliaiGnGtasreteklvaelikeee 82
                                      ++d t++v et+++  +++++k    ++++ +  k+y+ +l+ iG+G   +  e+ ++e+ + e+
  gi|385806069|ref|YP_005842467.1| 13 LIDYTATVKETNTVVDTTNSEKA--KESNIYDENKTYEPTLVIIGEGRVVKGLEEALQEMNEGEQ 75
                                      699999******99998766654..456899999*******************999999876654 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.53
                                       E-TTS-EEEEEEE--STTT--HHHHHHHHHHHHH CS
                          Tex_YqgF  19 vdetgkvletaviyphepkkkveeakkklkklvk 52 
                                       vd +  +  ++++y  +  k +++  +k+k+l+k
  gi|385806069|ref|YP_005842467.1| 134 VDFNHPLAGKTIVYEVKVIKYLQNDDEKVKALLK 167
                                       6666667778889998888888888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1102  (0.0614647); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); 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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1975.71
//
Query:       gi|385806070|ref|YP_005842468.1|  [L=459]
Description: seryl-tRNA synthetase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-33  115.5   0.0    5.3e-33  114.5   0.0    1.5  1  tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, 
      2e-15   57.0  11.5    1.7e-14   53.9  11.7    2.2  2  Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
     0.0032   18.0   3.8     0.0067   17.0   3.8    1.5  1  DUF2408       Protein of unknown function (DUF2408)
  ------ inclusion threshold ------
       0.04   14.1   3.5      0.073   13.2   3.5    1.3  1  CREPT         Cell-cycle alteration and expression-elevated p
       0.08   12.6   6.2       0.14   11.9   6.2    1.3  1  DUF4391       Domain of unknown function (DUF4391)
      0.098   12.5   3.4       0.17   11.7   3.4    1.3  1  PCRF          PCRF domain
       0.23   11.7   2.1       0.29   11.4   0.5    2.0  1  EB1           EB1-like C-terminal motif
       0.61   10.4   6.1        1.2    9.5   6.1    1.4  1  OmpH          Outer membrane protein (OmpH-like)
       0.66    7.7   9.5        0.9    7.3   9.5    1.1  1  Nup88         Nuclear pore component
          1    9.8   8.0        5.2    7.6   8.6    1.9  1  Cep57_MT_bd   Centrosome microtubule-binding domain of Cep57
        1.3    9.4   8.2          4    7.8   8.2    1.9  1  DUF349        Domain of Unknown Function (DUF349)
        2.5    7.8   4.7          4    7.1   4.7    1.2  1  AAA_11        AAA domain
        3.8    6.5   6.4        5.1    6.0   6.4    1.1  1  eIF-4B        Plant specific eukaryotic initiation factor 4B


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 !  114.5   0.0   3.8e-36   5.3e-33       6     178 ..     248     425 ..     243     426 .. 0.94

  Alignments for each domain:
  == domain 1  score: 114.5 bits;  conditional E-value: 3.8e-36
                                       TTSEEEEE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEEEBTTTS....TBCTTTB-SEEEEEEEEEEESGGGHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b   6 rndreyiLkPtneetfvelirdevlrskrLPlklyqiqtkyRdEks....dsrGLlRvreFhqkdgyvfhaeasldd 78 
                                       +n +++ L+ t+e++++ l  d+ +r+++LPlkl+  ++++R+E+     d++G++Rv++Fh+ +++vf ++++++ 
  gi|385806070|ref|YP_005842468.1| 248 EN-EDLNLIGTAEHPLMGLAYDNPIREQDLPLKLVGWSPCFRREAGagnrDLKGIFRVHQFHKVEQFVFAHPDNSWK 323
                                       55.89****************************************778899************************** PP

                                       HHHHHHHHHHHHHHHTT.SCEEEEEEGTTSCBTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEEC.TTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                      tRNA-synt_2b  79 slrdlikaisriferlglefraiielmsaksadykdkkefeavsesltkgieigtiqklgtrlserlgatvld.enn 154
                                        l +++  +++i++ lgl++r++  + ++  + +++k+++e++++ ++k++ei++i++  + ++ r ++t+++ +++
  gi|385806070|ref|YP_005842468.1| 324 FLDEMVANTEEILQGLGLPYRVVNVVSGELGLPAAKKYDIEVWMPAQGKYREIASISQVLDWQAFRANLTYIKaSDG 400
                                       *********************9999999999****************************9****9999988761566 PP

                                       SEEEEEEEEEE.EEHHHHHHHHHHH CS
                                       xxxxxxxxxxx.xxxxxxxxxxxxx RF
                      tRNA-synt_2b 155 reksvimicaa.igveRllsaileq 178
                                       r++  ++++ + i ++R +sai+e+
  gi|385806070|ref|YP_005842468.1| 401 RREYLHTLNGTgIPTTRAISAIVEN 425
                                       999999999999***********98 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 !   53.9  11.7   1.2e-17   1.7e-14       5     107 ..       8     109 ..       7     110 .. 0.97
   2 ?   -0.3   0.0      0.92   1.3e+03       1      21 [.     382     402 ..     382     408 .. 0.85

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 1.2e-17
                                       HHHHH-HHHHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHH CS
                      Seryl_tRNA_N   5 klirenpeavkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelke 81 
                                        ++r+np+++ + +k+Rg d++ v e +e+d++ r+   e+e+l++e+N+l+ke +k  ++ e+++el+ ++ke+ +
  gi|385806070|ref|YP_005842468.1|   8 EYLRNNPDEYMQMVKRRGLDESIVREAIEIDKAYRSKLREVENLRREHNSLTKELSKENNQ-EKKNELLRKAKEILQ 83 
                                       68******************************************************99987.6999*********** PP

                                       HHHHHHHHHHHHHHHHHHHHCTS--- CS
                      Seryl_tRNA_N  82 elkaleaelkeleaeleklllaiPNi 107
                                        l+++e+e++e+e +  + l ++PNi
  gi|385806070|ref|YP_005842468.1|  84 LLEEKEKEVSEAERNWYDSLKKLPNI 109
                                       *************************9 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.92
                                       ---HHHHHH-HHHHHHHHCCC CS
                      Seryl_tRNA_N   1 MLDiklirenpeavkeklkkR 21 
                                       +LD + +r n+  +k++  +R
  gi|385806070|ref|YP_005842468.1| 382 VLDWQAFRANLTYIKASDGRR 402
                                       69************9986655 PP

>> DUF2408  Protein of unknown function (DUF2408)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   3.8   4.8e-06    0.0067      45     120 ..      39     108 ..      13     111 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.8e-06
                           DUF2408  45 kelkeeLkkieskrdeegkFkseegkevvekgqavlngLlddcfdlvedlkaqdgeekkvasslqpiYdrLleikt 120
                                       k+++++L+++e+ r e++  ++e    ++e++q+  n+Ll++  ++++ l+++   ek+v+++ ++ Yd+L ++ +
  gi|385806070|ref|YP_005842468.1|  39 KAYRSKLREVENLRREHNSLTKEL---SKENNQEKKNELLRKAKEILQLLEEK---EKEVSEAERNWYDSLKKLPN 108
                                       67899***********77774444...68999*********************...589************99866 PP

>> CREPT  Cell-cycle alteration and expression-elevated protein in tumour
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   3.5   5.3e-05     0.073      52     140 ..      30     125 ..      21     127 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.3e-05
                             CREPT  52 qveealellaeYnkrLeaeleeRkklakmledf.....leaqkellakaeekleelkeklekvksvrkelkshiqsL 123
                                        v+ea+e+ + Y ++L +  + R++ +++ +++     +e ++ell+ka+e l+ l+ek ++v++++++  + ++ L
  gi|385806070|ref|YP_005842468.1|  30 IVREAIEIDKAYRSKLREVENLRREHNSLTKELskennQEKKNELLRKAKEILQLLEEKEKEVSEAERNWYDSLKKL 106
                                       689999999*******9877777766555555411111456678999****************************** PP

                             CREPT 124 PdLt..elpdvtgglapLP 140
                                       P++   ++p+ t+ ++ LP
  gi|385806070|ref|YP_005842468.1| 107 PNILapDVPYGTSDEDNLP 125
                                       **97345555677777777 PP

>> DUF4391  Domain of unknown function (DUF4391)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   6.2   9.9e-05      0.14     197     239 ..      40      82 ..      29      85 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.9e-05
                           DUF4391 197 errerlaeieelekeiaklkkklkkekqfnrkvelnaelkkle 239
                                       + r +l+e+e l++e ++l+k+l+ke + ++k+el  + k++ 
  gi|385806070|ref|YP_005842468.1|  40 AYRSKLREVENLRREHNSLTKELSKENNQEKKNELLRKAKEIL 82 
                                       56899******************************99999875 PP

>> PCRF  PCRF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   3.4   0.00013      0.17      18      96 ..      42     116 ..      26     126 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                                       TTTGGGSSSTTHHHHHTHHHHHHHHHHHHHTTTHHH...HT....-S-..-GGGTHHHHHHHHHH..HHHHHT-..S CS
                              PCRF  18 wedqekakklskelaeleeivealeeleealedleeakelleedeelaelaeeeleelekeleeleeelkklLlpkd 94 
                                        ++ +++++l +e+++l++ +++ ++ e+++e l++ake+l    +l e++e+e++e+e++  +  ++l ++L p+ 
  gi|385806070|ref|YP_005842468.1|  42 RSKLREVENLRREHNSLTKELSKENNQEKKNELLRKAKEIL----QLLEEKEKEVSEAERNWYDSLKKLPNILAPDV 114
                                       44556788888899999999999999999999999999998....888888999999999998888*******9988 PP

                                       SS CS
                              PCRF  95 en 96 
                                       ++
  gi|385806070|ref|YP_005842468.1| 115 PY 116
                                       76 PP

>> EB1  EB1-like C-terminal motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.5   0.00021      0.29       8      39 ..      41      82 ..      40      82 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00021
                                      HHHHHHHHHHHHHH..........TT----HHHHHHHHHHHH CS
                               EB1  8 YFsKLRdIEilcqt..........epeleedlpivkkikkIL 39
                                      Y sKLR++E l  +          e+++e++++++ k k+IL
  gi|385806070|ref|YP_005842468.1| 41 YRSKLREVENLRREhnsltkelskENNQEKKNELLRKAKEIL 82
                                      559*********8899******99888888999*******98 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   6.1   0.00086       1.2      23      93 ..      36     102 ..      21     111 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00086
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS.-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH  23 qlekkfkklqaeleakekelqklqeelqkkakklekeekeqelqkkeqelqqkqqqkaqelqkkqqellkp 93 
                                       +++k +++   e+e++++e ++l +el    k++ ++ek++el +k +e+ q++++k++e+ ++++  +++
  gi|385806070|ref|YP_005842468.1|  36 EIDKAYRSKLREVENLRREHNSLTKELS---KEN-NQEKKNELLRKAKEILQLLEEKEKEVSEAERNWYDS 102
                                       6788888888999999999999999998...554.88999**9999999999999999*999999877664 PP

>> Nup88  Nuclear pore component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   9.5   0.00065       0.9     547     638 ..      21     107 ..      10     111 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00065
                             Nup88 547 kkqelvreeiekrvkllkkqkeqqleelqsleeerkslseraeklAekyeeikdkQeklvrrvkkvlkrlnsklpvl 623
                                        k+    e i +    + k+ + +l+e+++l+ e +sl+ +  k     e+ ++k ++l+r++k++l+ l++k+  +
  gi|385806070|ref|YP_005842468.1|  21 VKRRGLDESIVREAIEIDKAYRSKLREVENLRREHNSLTKELSK-----ENNQEKKNELLRKAKEILQLLEEKEKEV 92 
                                       455666777888888888999999***************99888.....7889************************ PP

                             Nup88 624 seaeremkkelekik 638
                                       seaer+    l+k+ 
  gi|385806070|ref|YP_005842468.1|  93 SEAERNWYDSLKKLP 107
                                       ******999998875 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 ?    7.6   8.6    0.0038       5.2      23      73 ..      47      94 ..      45      97 .. 0.95

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0038
                       Cep57_MT_bd 23 EfehlklelqelaaqynaldpslgkrkRkdLaeeleelvkrlEaKadqIyk 73
                                      E+e l+ e+  l +++ + +   +++k+++L ++ +e+++ lE+K++ +++
  gi|385806070|ref|YP_005842468.1| 47 EVENLRREHNSLTKELSKEN---NQEKKNELLRKAKEILQLLEEKEKEVSE 94
                                      8999****************...***********************99986 PP

>> DUF349  Domain of Unknown Function (DUF349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   8.2    0.0029         4       4      66 ..      39      99 ..      36     107 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0029
                            DUF349  4 krFraacdafferrkahfee.qdaereenlekKealieeaealaksttdwksatkrlkelqeeW 66
                                      k +r+   ++++ r++h++  ++  +e+n ekK++l+ +a+++++     +++ k++ e    W
  gi|385806070|ref|YP_005842468.1| 39 KAYRSKLREVENLRREHNSLtKELSKENNQEKKNELLRKAKEILQLL---EEKEKEVSEAERNW 99
                                      66666677777778888775145567999**************8764...67777777766666 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   4.7    0.0029         4     121     183 ..      39     105 ..      11     112 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0029
                            AAA_11 121 e....kaqlakeiskeleklakelrafeeeeekeklkkskekskskleqerrklkkerkelskelee 183
                                       +    k + ++++++e ++l kel++++++e+k++l++++++  + le+++++++++ +++ ++l++
  gi|385806070|ref|YP_005842468.1|  39 KayrsKLREVENLRREHNSLTKELSKENNQEKKNELLRKAKEILQLLEEKEKEVSEAERNWYDSLKK 105
                                       1444478888999999999999999999999999999999999999999999999999999998876 PP

>> eIF-4B  Plant specific eukaryotic initiation factor 4B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   6.4    0.0037       5.1     349     431 ..      21     101 ..      11     141 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0037
                            eIF-4B 349 leekGkdWrkidlelehrrvdrpeteeekllkeeieelkkelekeaaenkesqqessedqnslkelisekekdlell 425
                                       ++ +G d   +   +e  +  r++  e   l+ e ++l kel ke  +n+e+++e   +++++ +l++ekek++   
  gi|385806070|ref|YP_005842468.1|  21 VKRRGLDESIVREAIEIDKAYRSKLREVENLRREHNSLTKELSKE--NNQEKKNELLRKAKEILQLLEEKEKEVSEA 95 
                                       566788877777888888999999999999**************9..89999999999***************9877 PP

                            eIF-4B 426 ireldd 431
                                        r+  d
  gi|385806070|ref|YP_005842468.1|  96 ERNWYD 101
                                       777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1794  (0.100061); expected 358.6 (0.02)
Passed bias filter:                      885  (0.0493614); expected 358.6 (0.02)
Passed Vit filter:                       141  (0.00786435); 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: 0.71u 0.33s 00:00:01.04 Elapsed: 00:00:00.49
# Mc/sec: 2835.59
//
Query:       gi|385806071|ref|YP_005842469.1|  [L=196]
Description: hypothetical protein FFONT_1029 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 1229.71
//
Query:       gi|385806072|ref|YP_005842470.1|  [L=155]
Description: hypothetical protein FFONT_1030 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.8e-06   25.6   0.4    1.7e-05   24.6   0.3    1.4  1  Acid_phosphat_B  HAD superfamily, subfamily IIIB (Acid phosph
    0.00033   20.7   0.1     0.0034   17.5   0.1    2.2  1  Hydrolase_6      Haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
       0.03   13.6   0.0      0.071   12.4   0.0    1.5  1  DUF4849          Putative glycoside hydrolase Family 18, chit
      0.053   13.8   0.1      0.066   13.5   0.1    1.2  1  HAD_SAK_2        HAD domain in Swiss Army Knife RNA repair pr
        0.2   11.9   0.1       0.62   10.3   0.1    1.8  1  Hydrolase        haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> Acid_phosphat_B  HAD superfamily, subfamily IIIB (Acid phosphatase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.3   4.6e-09   1.7e-05      76     196 ..       8     122 ..       3     134 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 4.6e-09
                                       EEE--BTTTEEHHHHHHHCHHHTCHH-TTH.HHHHHHTTGGCCECCHH..HHHHHHHHTTEEEEEEEEEECCCHHHH CS
                   Acid_phosphat_B  76 vvfDiDeTvLsnspYqkyqglgkkkfdpek.fdewvnkgeakaipgal..elikkvverGvkiffvsgRseeqkaaT 149
                                       ++fDiD  +++n++  ++ gl+ +   +e+ +++ +    a+  p +l  +l+++ ++  +ki+ v+gR e  +++T
  gi|385806072|ref|YP_005842470.1|   8 IIFDIDGVIIDNTERIEKYGLNEN---KEDfYSDRLM---AFDKPRELgiKLLEEKKKV-GKIVIVTGRPERVRKKT 77 
                                       89**********999777776442...2330333333...3333444433888876665.59*************** PP

                                       HHHHHHCT-T.TBSCCEEECCSTTC---HHHHHHHHHHHHHHTTEEEE CS
                   Acid_phosphat_B 150 venLkkagfs.sweklilkgkkdkqkksvvsyKeerrqklekkGyniv 196
                                        ++L + g++ ++ k+i++ ++  +k    + K ++  +l + G ni 
  gi|385806072|ref|YP_005842470.1|  78 TQELSSFGVElKEIKIIFRPNNI-DK--IEEWKVKKILELRDSGCNIC 122
                                       ********984445677777664.55..8899**********999996 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   9.5e-07    0.0034       1      64 [.       8      94 ..       8     102 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 9.5e-07
                                      EEEESTTTSE........................ETTEE-TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHHHHHHTT CS
                       Hydrolase_6  1 flfDidGvLw........................rgdkaipgaaealnalraagkpvvllTNnsskseeeyakkleklg 55
                                      ++fDidGv++                         +dk+ +   ++l+  ++   ++v++T +  + +++  ++l+++g
  gi|385806072|ref|YP_005842470.1|  8 IIFDIDGVIIdnteriekyglnenkedfysdrlmAFDKPRELGIKLLEEKKKV-GKIVIVTGRPERVRKKTTQELSSFG 85
                                      69********7777777777666666666554444555555555555544444.6799********************* PP

                                      ----GGGEE CS
                       Hydrolase_6 56 vditeeqvv 64
                                      v+++e +++
  gi|385806072|ref|YP_005842470.1| 86 VELKEIKII 94
                                      ***996665 PP

>> DUF4849  Putative glycoside hydrolase Family 18, chitinase_18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0     2e-05     0.071     133     203 ..       3      81 ..       1      90 [. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2e-05
                           DUF4849 133 ilaladkynyDGiiidyegkskiylseeelae.ykarqkiFlkalkew......kksntdklLvlqgepqslvdeni 202
                                       +l+ +  ++ DG+iid + + ++y  +e+++  y++r   F ++  e       +k++ +k+ ++ g+p+ + +++ 
  gi|385806072|ref|YP_005842470.1|   3 QLDCCIIFDIDGVIIDNTERIEKYGLNENKEDfYSDRLMAF-DKPRELgiklleEKKKVGKIVIVTGRPERVRKKTT 78 
                                       7899999**************99977776666155555555.44333333355577899*************99998 PP

                           DUF4849 203 ..l 203
                                         l
  gi|385806072|ref|YP_005842470.1|  79 qeL 81 
                                       444 PP

>> HAD_SAK_2  HAD domain in Swiss Army Knife RNA repair proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   1.8e-05     0.066       2      95 ..       8     111 ..       7     129 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.8e-05
                         HAD_SAK_2   2 iFLDiDGVLnpekskkrregeedea..........ldp..e.averlkriveatgakiVlsstWrrredeelkallk 65 
                                       i++DiDGV+ +++++ ++ g ++++          +d+  e  ++ l++  ++   kiV+ +   +r++++  + l+
  gi|385806072|ref|YP_005842470.1|   8 IIFDIDGVIIDNTERIEKYGLNENKedfysdrlmaFDKprElGIKLLEE--KKKVGKIVIVTGRPERVRKKTTQELS 82 
                                       899**********99999888777799*999999955533336777777..888889***********999999999 PP

                         HAD_SAK_2  66 aag.rpriigvtpdlpeeeseeekksRaqei 95 
                                       + g + + i +  +   ++ ++ +++++++i
  gi|385806072|ref|YP_005842470.1|  83 SFGvELKEIKIIFR--PNNIDKIEEWKVKKI 111
                                       98863333322222..222233333555555 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00017      0.62       3      53 ..       7      47 ..       7     137 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00017
                                      EEEEESBTTTBCHHHHHHH.HHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  3 tvvfDkdGTLttgepsved.vivsaalalaaaletgsehpigkalvaaakar 53
                                      +++fD+dG++++ + ++e+  ++++            e  +  +l a+ k r
  gi|385806072|ref|YP_005842470.1|  7 CIIFDIDGVIIDNTERIEKyGLNEN-----------KEDFYSDRLMAFDKPR 47
                                      69*********99977777323333...........2233333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       770  (0.0429472); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 990.07
//
Query:       gi|385806073|ref|YP_005842471.1|  [L=177]
Description: hypothetical protein FFONT_1031 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0016   18.5   2.4     0.0026   17.8   2.4    1.4  1  DUF2730          Protein of unknown function (DUF2730)
     0.0059   16.6   5.0     0.0087   16.1   3.6    1.8  2  Laminin_II       Laminin Domain II
  ------ inclusion threshold ------
       0.01   15.7   2.7      0.024   14.5   2.7    1.6  1  Shugoshin_N      Shugoshin N-terminal coiled-coil region
       0.01   15.5   3.9      0.015   15.0   3.9    1.2  1  Laminin_I        Laminin Domain I
      0.016   15.5   3.1      0.033   14.5   3.1    1.6  1  DUF5082          Domain of unknown function (DUF5082)
      0.022   15.0   5.0      0.035   14.4   3.5    2.0  2  Lzipper-MIP1     Leucine-zipper of ternary complex factor MIP
      0.022   15.1   4.3        3.8    7.8   0.5    3.0  3  DNA_ligase_A_N   DNA ligase N terminus
      0.023   14.8   3.2      0.075   13.1   3.2    1.9  1  bZIP_2           Basic region leucine zipper
      0.027   14.7   8.1      0.027   14.7   8.1    2.6  2  XhlA             Haemolysin XhlA
      0.032   13.6   0.5      0.045   13.1   0.5    1.3  1  TraF_2           F plasmid transfer operon, TraF, protein
      0.041   14.1   5.6       0.15   12.3   5.6    2.1  1  ABC_tran_CTD     ABC transporter C-terminal domain
      0.048   13.1   6.0      0.066   12.7   6.0    1.2  1  Golgin_A5        Golgin subfamily A member 5
      0.051   11.8  10.8      0.077   11.2  10.7    1.5  1  Cast             RIM-binding protein of the cytomatrix active
       0.06   12.9   1.6       0.09   12.3   1.6    1.4  1  Fzo_mitofusin    fzo-like conserved region
      0.062   13.5   2.9       0.12   12.6   2.9    1.6  1  Spc24            Spc24 subunit of Ndc80
      0.077   13.6   2.5       0.21   12.2   1.7    2.2  1  SlyX             SlyX
      0.091   12.6   3.2      0.063   13.1   1.0    1.8  2  ACCA             Acetyl co-enzyme A carboxylase carboxyltrans
      0.093   13.2   0.4       0.24   11.9   0.4    1.8  1  NPV_P10          Nucleopolyhedrovirus P10 protein
       0.11   13.0   5.3       0.26   11.8   5.3    1.7  1  GPS2_interact    G-protein pathway suppressor 2-interacting d
       0.11   12.6   3.0        0.4   10.8   1.8    2.1  2  ApoLp-III        Apolipophorin-III precursor (apoLp-III)
       0.11   12.5   0.0       0.35   10.9   0.0    1.7  2  DUF2065          Uncharacterized protein conserved in bacteri
       0.11   12.9   7.4       0.24   11.9   6.7    2.1  1  ZapB             Cell division protein ZapB
       0.11   12.4   7.7       0.19   11.6   7.7    1.4  1  Ax_dynein_light  Axonemal dynein light chain
       0.12   12.1   3.5        1.4    8.6   0.0    2.3  2  FANCI_S3         FANCI solenoid 3
       0.14   12.1   4.7       0.19   11.7   4.3    1.4  1  DUF4446          Protein of unknown function (DUF4446)
       0.16   12.1   0.7        0.2   11.8   0.7    1.1  1  MutS_III         MutS domain III
       0.17   11.8   4.9       0.16   11.8   3.1    1.9  2  HSBP1            Heat shock factor binding protein 1
       0.23   12.0   6.3       0.34   11.4   5.9    1.5  1  DUF16            Protein of unknown function DUF16
       0.27   11.4  11.5       0.46   10.6  11.5    1.5  1  Tropomyosin_1    Tropomyosin like
       0.37   11.2   8.5        1.4    9.4   8.5    2.1  1  FlaC_arch        Flagella accessory protein C (FlaC)
       0.53   10.6   6.8       0.64   10.4   5.0    2.0  1  BLOC1_2          Biogenesis of lysosome-related organelles co
       0.71    9.1   3.3       0.84    8.8   3.3    1.2  1  TMPIT            TMPIT-like protein
       0.72    9.8   7.8       0.51   10.3   3.5    2.6  2  Prefoldin        Prefoldin subunit
       0.83   10.3   5.2        2.2    9.0   4.4    2.1  2  YabA             Initiation control protein YabA
        1.1    9.5  10.6        1.3    9.3   8.5    2.2  2  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
        1.1    9.3   6.4       0.77    9.9   3.4    2.3  3  Med9             RNA polymerase II transcription mediator com
        1.2    8.7   5.8       0.59    9.7   1.4    2.5  2  YvrJ             YvrJ protein family
        1.5    8.6   9.8        7.9    6.3   8.0    2.1  2  DUF724           Protein of unknown function (DUF724)
        1.8    9.0   5.4        4.3    7.8   2.9    2.2  2  UPF0184          Uncharacterised protein family (UPF0184)
        2.6    8.6  11.6        2.8    8.5   8.7    2.1  2  APG6_N           Apg6 coiled-coil region
          3    6.8   6.1        4.2    6.4   6.0    1.3  1  Atg14            Vacuolar sorting 38 and autophagy-related su
        4.9    7.6   8.6        7.7    6.9   4.1    2.3  2  DUF1690          Protein of Unknown function (DUF1690)


Domain annotation for each model (and alignments):
>> DUF2730  Protein of unknown function (DUF2730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   2.4   6.2e-06    0.0026      34      95 ..      16      78 ..       6      86 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 6.2e-06
                           DUF2730 34 dleklaekveendkrlteletkvenLPta.kdlekLkllladlrgelkaleaevrqlshqvdL 95
                                      + e+ ++++ee+ kr++ le+kv++L  + ++l +   +++++ g++k+++ +++q++ ++d 
  gi|385806073|ref|YP_005842471.1| 16 EEETHNDEIEEIIKRMDILEMKVSELEKKiEELREKINEIENVFGRSKEASGKIEQINMLLDK 78
                                      34455689******************765356777777899999*************988775 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   3.6     2e-05    0.0087      41     103 ..      18      80 ..       3      83 .. 0.85
   2 ?   -1.1   0.0         4   1.7e+03      70      98 ..     128     154 ..     123     155 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHHHHHHHHHHHHHHH CS
                        Laminin_II  41 eetnekvkdankairdArrsvkkLeklapqLldklkelkqleeassslsdniseikelIaqAR 103
                                       e  n+++++  k ++  + +v++Lek++++L +k++e+++    s+  s +i++i  l  + R
  gi|385806073|ref|YP_005842471.1|  18 ETHNDEIEEIIKRMDILEMKVSELEKKIEELREKINEIENVFGRSKEASGKIEQINMLLDKLR 80 
                                       4557889999******************************9999999********99988777 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 4
                                       TTGGGHHHHHHHHHH...HHHHHHHHHHH CS
                        Laminin_II  70 qLldklkelkqleeassslsdniseikel 98 
                                       + l+kl+++    + s    ++i  +kel
  gi|385806073|ref|YP_005842471.1| 128 EFLEKLSSISDSDPSS--AAEKIGDLKEL 154
                                       5678888888777774..47888888887 PP

>> Shugoshin_N  Shugoshin N-terminal coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   2.7   5.6e-05     0.024      10      39 ..      25      53 ..      21      58 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.6e-05
                       Shugoshin_N 10 reLAKsNsalslkirelekevseLlsENln 39
                                       e++K+  +l +k++elek+++eL +E++n
  gi|385806073|ref|YP_005842471.1| 25 EEIIKRMDILEMKVSELEKKIEEL-REKIN 53
                                      68999999****************.77776 PP

>> Laminin_I  Laminin Domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   3.9   3.5e-05     0.015      70     142 ..      17      88 ..       3      98 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.5e-05
                         Laminin_I  70 aqkvnaesertlnnakeLaekikkladnikeilekvatlneneealpssklseelaeaqrlLeelrsRd.ftkq 142
                                        ++ n e+e+++++   L++k+ +l+++i+e+ ek+ ++++      s++ s + ++++ lL +lr++  +++ 
  gi|385806073|ref|YP_005842471.1|  17 EETHNDEIEEIIKRMDILEMKVSELEKKIEELREKINEIEN--VFGRSKEASGKIEQINMLLDKLRNKGyLKES 88 
                                       5677899*****************************55555..444456677888999*******999855554 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   3.1   7.8e-05     0.033      58     122 ..       9      80 ..       1      81 [. 0.80

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.8e-05
                           DUF5082  58 esWkGk.eennydgirs.......nlessyqtyvdkldelidaieeEIerLenqiseaqgvldtlqsqlnslk 122
                                       + +kG+ ee++++++ +        le ++++ ++k++el  +i+ EIe+     +ea+g+++++++ l++l 
  gi|385806073|ref|YP_005842471.1|   9 DFLKGEkEEETHNDEIEeiikrmdILEMKVSELEKKIEELREKIN-EIENVFGRSKEASGKIEQINMLLDKLR 80 
                                       568888788888877777888886778889999999999999985.899999999999999999999999986 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 ?   14.4   3.5   8.1e-05     0.035      50      82 ..      21      53 ..       2      54 .. 0.85
   2 ?   -1.2   0.0       6.2   2.6e+03      56      61 ..     129     134 ..     120     154 .. 0.53

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8.1e-05
                      Lzipper-MIP1 50 pkkakellkeiallEeevvkLEqkllsLyrklf 82
                                       ++++e +k + +lE+ v++LE+k+++L+ k++
  gi|385806073|ref|YP_005842471.1| 21 NDEIEEIIKRMDILEMKVSELEKKIEELREKIN 53
                                      46899************************9986 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 6.2
                      Lzipper-MIP1  56 llkeia 61 
                                        l+ ++
  gi|385806073|ref|YP_005842471.1| 129 FLEKLS 134
                                       444332 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 ?    3.9   0.1      0.14        60     120     150 ..       9      38 ..       2      40 .. 0.81
   2 ?    7.8   0.5     0.009       3.8      71     133 ..      38      91 ..      36     113 .. 0.66
   3 ?    5.0   0.0     0.064        27      56     100 ..     118     162 ..     107     174 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.14
                                       HHHH-STTHHHHHHHHHHHHHHHS-HHHHHH CS
                    DNA_ligase_A_N 120 klaaagkgsedekkkilkkllkraspeEaky 150
                                       +    g+++e++  + +++++kr++ +E+k+
  gi|385806073|ref|YP_005842471.1|   9 DFL-KGEKEEETHNDEIEEIIKRMDILEMKV 38 
                                       442.278899999***************996 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.009
                                       HHT--HHHHHHHHHHHS-HHHHHHHHHCCHHHH------BHHHHHHHHHHHHH-STTHHHHHH CS
                    DNA_ligase_A_N  71 alglskkkikdalakvgDlgevaeevlskrstlakkspltieevnelLdklaaagkgsedekk 133
                                       ++ l kk i++  +k++++  v  +++        + +  ie++n lLdkl + g  +e e  
  gi|385806073|ref|YP_005842471.1|  38 VSELEKK-IEELREKINEIENVFGRSK--------EASGKIEQINMLLDKLRNKGYLKESEDL 91 
                                       5667766.8888888999999966644........56688***********877544443332 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.064
                                       -----HHHHHHHHHHHHT--HHHHHHHHHHHS-HHHHHHHHHCCH CS
                    DNA_ligase_A_N  56 eygigesllakalaealglskkkikdalakvgDlgevaeevlskr 100
                                       +y i +++  + l +++++s  +   a +k+gDl e  +e+l++ 
  gi|385806073|ref|YP_005842471.1| 118 RYLIYPRKWKEFLEKLSSISDSDPSSAAEKIGDLKELFFELLKEG 162
                                       677777788888888888886655556788999999999988765 PP

>> bZIP_2  Basic region leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   3.2   0.00017     0.075      26      52 ..      30      56 ..      29      57 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00017
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_2 26 keeeleervkeLeeeNaqLrqkveqLe 52
                                      ++  le++v eLe+++++Lr+k+ + e
  gi|385806073|ref|YP_005842471.1| 30 RMDILEMKVSELEKKIEELREKINEIE 56
                                      67789*****************98876 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   8.1   6.3e-05     0.027       7      46 ..      18      57 ..      14      59 .. 0.86
   2 ?   -0.8   0.5       4.4   1.9e+03       7      19 ..      70      82 ..      63     109 .. 0.52

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6.3e-05
                              XhlA  7 erietkldnleervdkleekaaeaeekiknleedlkkles 46
                                      e+++ +++++ +r+d le+k +e e+ki++l e+++++e+
  gi|385806073|ref|YP_005842471.1| 18 ETHNDEIEEIIKRMDILEMKVSELEKKIEELREKINEIEN 57
                                      456666666666**************************97 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 4.4
                              XhlA  7 erietkldnleer 19
                                      e+i+  ld+l ++
  gi|385806073|ref|YP_005842471.1| 70 EQINMLLDKLRNK 82
                                      4444444444442 PP

>> TraF_2  F plasmid transfer operon, TraF, protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.5   0.00011     0.045      32      86 ..      37      87 ..      16     110 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00011
                            TraF_2 32 dvdnlvDkiDdlsdildgleaavnaasadetq.vdeaaddlnalLedlggdgylka 86
                                       v++l  ki++l ++++++e++  +    + + ++ +++++n lL++l+++gylk 
  gi|385806073|ref|YP_005842471.1| 37 KVSELEKKIEELREKINEIENVFGR----S-KeASGKIEQINMLLDKLRNKGYLKE 87
                                      3455555555555555544444433....3.249*******************985 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   5.6   0.00035      0.15       9      60 ..      30      79 ..      12      82 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00035
                      ABC_tran_CTD  9 eleeleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeel 60
                                      +++ le +  +LE++i+el +++++ e  + + + +e+s ++e+++  L++l
  gi|385806073|ref|YP_005842471.1| 30 RMDILEMKVSELEKKIEELREKINEIE--NVFGRSKEASGKIEQINMLLDKL 79
                                      556699999999999999999999887..67799999999999999888875 PP

>> Golgin_A5  Golgin subfamily A member 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   6.0   0.00015     0.066      37     110 ..      12      87 ..       2     106 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00015
                         Golgin_A5  37 eglesstalsaeldelkqerdllreelqklnqqieqlrtelqdleaqq..qaeaeslreqlqeleeqleeerkake 110
                                       +g + +++ ++e++e+ ++ d+l+ ++ +l+++ie+lr +++++e+ +  ++ea+   eq++ l ++l+++   ke
  gi|385806073|ref|YP_005842471.1|  12 KGEKEEETHNDEIEEIIKRMDILEMKVSELEKKIEELREKINEIENVFgrSKEASGKIEQINMLLDKLRNKGYLKE 87 
                                       34445667899**********************************9752278888888999988888876655544 PP

>> Cast  RIM-binding protein of the cytomatrix active zone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2  10.7   0.00018     0.077     364     426 ..       6      68 ..       1     154 [. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00018
                              Cast 364 ktkqlqdlteekstlageirdlkdmldvkeRkvnvlqkkienLqeqlrdkdkqlaelkervks 426
                                         k++ + ++e  t++ ei+++ + +d+ e kv  l+kkie+L+e++ + ++++   ke+  +
  gi|385806073|ref|YP_005842471.1|   6 TLKDFLKGEKEEETHNDEIEEIIKRMDILEMKVSELEKKIEELREKINEIENVFGRSKEASGK 68 
                                       3466777788999**************************************999999987655 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.6   0.00021      0.09     111     157 ..      35      81 ..      10      86 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00021
                     Fzo_mitofusin 111 detekeleeeikelekeiekleevqkkakllrnkaslleseLekfee 157
                                       ++  +ele++i+el+++i+++e+v  ++k    k ++++  L+k ++
  gi|385806073|ref|YP_005842471.1|  35 EMKVSELEKKIEELREKINEIENVFGRSKEASGKIEQINMLLDKLRN 81 
                                       556689********************************999998765 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   2.9   0.00029      0.12       5      43 ..      23      61 ..      19      98 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00029
                             Spc24  5 ekfriakelsdleselesleselaelkeeleeleeesee 43
                                      e  +i+k ++ le+++++le++ +el+e+++e+e+   +
  gi|385806073|ref|YP_005842471.1| 23 EIEEIIKRMDILEMKVSELEKKIEELREKINEIENVFGR 61
                                      556799***************************986555 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.7    0.0005      0.21       3      34 ..      29      60 ..      27      93 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0005
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              SlyX  3 erleeLEiklafqedtieeLndvvaeqqqqid 34
                                      +r++ LE+k++ +e+ ieeL + + e +    
  gi|385806073|ref|YP_005842471.1| 29 KRMDILEMKVSELEKKIEELREKINEIENVFG 60
                                      69999***************999888766554 PP

>> ACCA  Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       5.1   2.2e+03      25      43 ..      16      34 ..       3      41 .. 0.50
   2 ?   13.1   1.0   0.00015     0.063       3      73 ..      40     105 ..      34     115 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 5.1
                              ACCA 25 sevdlseeieklekklekl 43
                                      +e + ++eie++ k+++ l
  gi|385806073|ref|YP_005842471.1| 16 EEETHNDEIEEIIKRMDIL 34
                                      2333345555554444443 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00015
                              ACCA   3 dfekpiaeleekieelkklaeesevdlseeieklekkleklkkeiyknltpwqkvqlaRhpeRpktldyie 73 
                                       + ek+i+el+eki+e++++  +s+ + s +ie+++  l+kl+++ y +    +   laR +++  + d i+
  gi|385806073|ref|YP_005842471.1|  40 ELEKKIEELREKINEIENVFGRSK-EASGKIEQINMLLDKLRNKGYLK----ESEDLARVKDKDFVADRIK 105
                                       789999999999999999977664.56999999999999999988744....3334566666555555555 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.4   0.00056      0.24      12      51 ..      37      76 ..      18      96 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00056
                           NPV_P10 12 dikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqL 51
                                       ++++++k++ l ++++++++ +   +e + k+++++  L
  gi|385806073|ref|YP_005842471.1| 37 KVSELEKKIEELREKINEIENVFGRSKEASGKIEQINMLL 76
                                      2333333333333333333333333333333344333333 PP

>> GPS2_interact  G-protein pathway suppressor 2-interacting domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   5.3   0.00061      0.26      29      76 ..      24      71 ..       7      81 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00061
                     GPS2_interact 29 KdeLlqnidkvDREiakveqqiskLkkkqkeleeeaakpkeeekpvep 76
                                       +e+++ +d     ++  e++i++L++k +e+e+   + ke++ ++e+
  gi|385806073|ref|YP_005842471.1| 24 IEEIIKRMDILEMKVSELEKKIEELREKINEIENVFGRSKEASGKIEQ 71
                                      599*******************************99999998888776 PP

>> ApoLp-III  Apolipophorin-III precursor (apoLp-III)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.8   0.00093       0.4      55     111 ..      15      70 ..       2      91 .. 0.71
   2 ?    0.7   0.0       1.2   5.3e+02      32      62 ..     127     157 ..     124     161 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00093
                         ApoLp-III  55 eleealkevkkkieetadklseenPevkkkaqelqekvQsgvqslvkesqklaeslk 111
                                       + ee+ ++  ++i + +d l+ + +e++kk++el+ek+   +++++  s+++  +++
  gi|385806073|ref|YP_005842471.1|  15 KEEETHNDEIEEIIKRMDILEMKVSELEKKIEELREKIN-EIENVFGRSKEASGKIE 70 
                                       456677777777777777777788888888888888874.46777766666666665 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.2
                         ApoLp-III  32 enlvdqlkqvikslqeelkkksdeleealke 62 
                                       ++++++l+++++s  +++++k++ l+e++ e
  gi|385806073|ref|YP_005842471.1| 127 KEFLEKLSSISDSDPSSAAEKIGDLKELFFE 157
                                       6899999999999999999999999998866 PP

>> DUF2065  Uncharacterized protein conserved in bacteria (DUF2065)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00083      0.35      16      36 ..     119     139 ..     118     140 .. 0.92
   2 ?   -1.8   0.0       7.9   3.4e+03      12      17 ..     161     166 ..     158     174 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00083
                           DUF2065  16 pflaPerwrralrqlaelpdr 36 
                                       ++++P++w+++l++l++++d+
  gi|385806073|ref|YP_005842471.1| 119 YLIYPRKWKEFLEKLSSISDS 139
                                       899*************99985 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 7.9
                           DUF2065  12 EGllpf 17 
                                       EGl++f
  gi|385806073|ref|YP_005842471.1| 161 EGLIYF 166
                                       9**999 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   6.7   0.00056      0.24      13      70 ..      24      80 ..      21     107 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00056
                              ZapB 13 iqkaidtitlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlkkLLgkle 70
                                      i++ i +++ L m+++eL+++ eel e+++e+e    + ke   ++ e ++ LL+kl+
  gi|385806073|ref|YP_005842471.1| 24 IEEIIKRMDILEMKVSELEKKIEELREKINEIENVFGRSKEASGKI-EQINMLLDKLR 80
                                      67889999999999*****999*****9999996665555544444.45666666665 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 ?   11.6   7.7   0.00045      0.19     117     171 ..      20      74 ..       4      93 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00045
                   Ax_dynein_light 117 aeqgkselekkikeLeeekeelekqvaelkaklealekrekerrqeeekkheeei 171
                                        +++ +e+ k++  Le +++elek+++el++k++++e+ + + +++  k ++ ++
  gi|385806073|ref|YP_005842471.1|  20 HNDEIEEIIKRMDILEMKVSELEKKIEELREKINEIENVFGRSKEASGKIEQINM 74 
                                       334445555556669***********************99999999999888776 PP

>> FANCI_S3  FANCI solenoid 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   2.2      0.24     1e+02     117     177 ..       5      78 ..       2      88 .. 0.45
   2 ?    8.6   0.0    0.0032       1.4     114     154 ..     121     162 ..     119     172 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.24
                          FANCI_S3 117 sklseFLkaigeeedlteklkelikqlqrvlvnflsedeedesi..............sKlallLveilelLskk 177
                                       + l++FLk  +eee  + +++e+ik++ ++l+  +se e + +               sK+a   +e + +L++k
  gi|385806073|ref|YP_005842471.1|   5 KTLKDFLKGEKEEETHNDEIEEIIKRM-DILEMKVSELEKKIEElrekineienvfgrSKEASGKIEQINMLLDK 78 
                                       556666666644444445555555443.22222222222222211111222333333356665555555555555 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0032
                          FANCI_S3 114 lyesklseFLkaigeeedlt.eklkelikqlqrvlvnflsed 154
                                       +y++k +eFL+++++ +d + + ++e i  l++++ ++l+e+
  gi|385806073|ref|YP_005842471.1| 121 IYPRKWKEFLEKLSSISDSDpSSAAEKIGDLKELFFELLKEG 162
                                       69***********74444445999***************996 PP

>> DUF4446  Protein of unknown function (DUF4446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   4.3   0.00044      0.19      26      77 ..       2      54 ..       1      63 [. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00044
                           DUF4446 26 klkkkykklmkgk.dgksleellkekleeveelkeeseelekeieeleeklkk 77
                                      k kk +k ++kg+ ++++ ++ ++e +++++ l+ +++elek+ieel+ek+++
  gi|385806073|ref|YP_005842471.1|  2 KAKKTLKDFLKGEkEEETHNDEIEEIIKRMDILEMKVSELEKKIEELREKINE 54
                                      678999*****886889999*****************************9986 PP

>> MutS_III  MutS domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.7   0.00047       0.2      48     145 ..      24     147 ..      22     173 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00047
                                       HHHHHHHHHHHHH.T..TT.HHHHHHHHTT---HHHHHHHHHTT---HHHHHHHHHHHHHHHTTTTT---SSTHHHH CS
                                       xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          MutS_III  48 leeInaRldaVee.leneelreelrellrrlpDleRllsrislgkakardlkallealkaleelvallekeklaese 123
                                       +eeI +R d+ e  +  +el++++ el +++  +e +  r +  ++k ++++ ll++l++ +   +  e+  +   +
  gi|385806073|ref|YP_005842471.1|  24 IEEIIKRMDILEMkV--SELEKKIEELREKINEIENVFGRSKEASGKIEQINMLLDKLRN-KGYLKESEDLAR--VK 95 
                                       799*********866..776666665555599*********9999998888889999995.332222222222..22 PP

                                       H..............................HHHHHHHHHHB-SS--SSGGG CS
                                       x..............................xxxxxxxxxxxxxxxxxxxxx RF
                          MutS_III 124 e..............................eslaelleeaideeplaleke 145
                                       +                              +++ e l++  d++p+++ ++
  gi|385806073|ref|YP_005842471.1|  96 DkdfvadrikklgaievigtkdryliyprkwKEFLEKLSSISDSDPSSAAEK 147
                                       2234555555666666666666666666555444455555444454444444 PP

>> HSBP1  Heat shock factor binding protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   3.1   0.00038      0.16      23      48 ..      25      50 ..      24      53 .. 0.92
   2 ?   -1.9   0.0       7.3   3.1e+03      28      37 ..      68      77 ..      53      82 .. 0.49

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00038
                             HSBP1 23 dqilsriDdMssriDdLEksiadlmt 48
                                      ++i++r+D ++ ++ +LEk i++l +
  gi|385806073|ref|YP_005842471.1| 25 EEIIKRMDILEMKVSELEKKIEELRE 50
                                      68*********************987 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 7.3
                             HSBP1 28 riDdMssriD 37
                                      +i+++   +D
  gi|385806073|ref|YP_005842471.1| 68 KIEQINMLLD 77
                                      3333333333 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   5.9   0.00079      0.34      26      89 ..       8      76 ..       3      84 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00079
                                      HHB-........BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHH CS
                             DUF16 26 nefkds......nkqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetlelil 89
                                      ++f +        + ++++i +++d l+ ++++le+k+e++ eki+e+++     +e      e ++++l
  gi|385806073|ref|YP_005842471.1|  8 KDFLKGekeeetHNDEIEEIIKRMDILEMKVSELEKKIEELREKINEIENVFGRSKE-ASGKIEQINMLL 76
                                      444333333343455566666666677777777777777777777666654433333.222223344444 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6  11.5    0.0011      0.46      20      84 ..       7      71 ..       1     109 [. 0.56

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0011
                     Tropomyosin_1 20 eekvKeleqenlekeqeiksLtkknqqleeevekleeklkeakekaeesekkktnnealtrkiql 84
                                       ++  + e+e++ +++ei+++ k+++ le +v +le+k++e +ek +e e+    + + + ki++
  gi|385806073|ref|YP_005842471.1|  7 LKDFLKGEKEEETHNDEIEEIIKRMDILEMKVSELEKKIEELREKINEIENVFGRSKEASGKIEQ 71
                                      22333345555555556666666666666666666666666666655555544444444444444 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   8.5    0.0033       1.4       2      35 ..      24      57 ..      22      82 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0033
                         FlaC_arch  2 idelEnklsklsteletvkkeneelsksveelke 35
                                      i+e+ ++++ l+++++ ++k++eel+++++e++ 
  gi|385806073|ref|YP_005842471.1| 24 IEEIIKRMDILEMKVSELEKKIEELREKINEIEN 57
                                      6777788888999******************985 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 ?   10.4   5.0    0.0015      0.64      48      93 ..      12      57 ..       1      60 [. 0.75

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0015
                           BLOC1_2 48 kkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLEa 93
                                      k  ++ +  ++e+++ ++++d +e +v+eLe+ ++eL e + e+E+
  gi|385806073|ref|YP_005842471.1| 12 KGEKEEETHNDEIEEIIKRMDILEMKVSELEKKIEELREKINEIEN 57
                                      4445556667799999999999999999999999999999999887 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   3.3     0.002      0.84       9      76 ..       8      77 ..       1     113 [. 0.59

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.002
                             TMPIT  9 kefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk..eeeeeeveelkeelk 76
                                      k+f + e+++++ + ++ee+ k  + +  ++++ +k+++el+++++++++  +  +e + ++e+++  l+
  gi|385806073|ref|YP_005842471.1|  8 KDFLKGEKEEETHNDEIEEIIKRMDILEMKVSELEKKIEELREKINEIENVFGrsKEASGKIEQINMLLD 77
                                      4455555555556666666666666666666666666666666666666554322333444554444433 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1       1.3   5.4e+02      24      42 ..       2      20 ..       1      22 [. 0.82
   2 ?   10.3   3.5    0.0012      0.51      81     113 ..      26      58 ..      17      65 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 1.3
                                      HHHHHHHHHTT.-TT-EEE CS
                         Prefoldin 24 ktletlktlkkedegkevl 42
                                      k+++tlk++ k+++++e++
  gi|385806073|ref|YP_005842471.1|  2 KAKKTLKDFLKGEKEEETH 20
                                      7899*****9977777775 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0012
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  81 llkkkleelekqlekleeeleklkdqittlean 113
                                        + k+++ le  + +le+++e+l+++i+++e+ 
  gi|385806073|ref|YP_005842471.1|  26 EIIKRMDILEMKVSELEKKIEELREKINEIENV 58 
                                       455889999999999999999999999999976 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   4.4     0.005       2.2       8      81 ..       8      84 ..       1     103 [. 0.62
   2 ?   -0.4   0.0       4.4   1.9e+03       6      37 ..     129     161 ..     125     171 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.005
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              YabA  8 dkleeleeqleelleeleelkeelaelleenaeLeleneklrerl...eeeekkekekkkelsegkenLarlYeeGF 81
                                      + + + e++ e+ ++e+ee+ +++  l  + +eLe   e+lre++   e+   ++ke + ++++ +  L +l ++G+
  gi|385806073|ref|YP_005842471.1|  8 KDFLKGEKEEETHNDEIEEIIKRMDILEMKVSELEKKIEELREKIneiENVFGRSKEASGKIEQINMLLDKLRNKGY 84
                                      55555566666666677777777777767777777777777777633322333444555555555555666655555 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 4.4
                                       HHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHH CS
                              YabA   6 lfdkleelee.qleelleeleelkeelaellee 37 
                                       +++kl+++++ + ++  e++++lke + ell+e
  gi|385806073|ref|YP_005842471.1| 129 FLEKLSSISDsDPSSAAEKIGDLKELFFELLKE 161
                                       555555554313456677788888887777766 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   8.5     0.003       1.3      23      75 ..      23      75 ..       6      99 .. 0.72
   2 ?   -1.3   0.0       5.8   2.5e+03      12      48 ..      98     136 ..      90     154 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.003
                                      CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCC CS
                      Seryl_tRNA_N 23 edkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliae 75
                                      e ++ ++++  l+ k  el++++eel+++ Ne+ + +g+ k++  ++e++   
  gi|385806073|ref|YP_005842471.1| 23 EIEEIIKRMDILEMKVSELEKKIEELREKINEIENVFGRSKEASGKIEQINML 75
                                      55667777777899999999999999999999999999999776444443333 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 5.8
                                       HHHHHHHCCCT..CCCHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  12 eavkeklkkRg..edkadvdelleldekrrelqveleel 48 
                                       + v++++kk g  e   + d++l   +k++e   +l ++
  gi|385806073|ref|YP_005842471.1|  98 DFVADRIKKLGaiEVIGTKDRYLIYPRKWKEFLEKLSSI 136
                                       556666665555555555666666666666666666554 PP

>> Med9  RNA polymerase II transcription mediator complex subunit 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       5.4   2.3e+03      38      66 ..       3      31 ..       2      35 .. 0.66
   2 ?    9.9   3.4    0.0018      0.77      24      62 ..      34      72 ..      20      85 .. 0.68
   3 ?   -1.9   0.0       8.9   3.8e+03      39      51 ..     127     139 ..     124     153 .. 0.61

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 5.4
                              Med9 38 arelirelpgidrsveeqeaeieeleeql 66
                                      a++ ++     ++  e+ ++eiee  +++
  gi|385806073|ref|YP_005842471.1|  3 AKKTLKDFLKGEKEEETHNDEIEEIIKRM 31
                                      55555555556777778888888876665 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0018
                              Med9 24 letktgelrhkLkkarelirelpgidrsveeqeaeieel 62
                                      le k++el +k+++ re i+e++++    +e   +ie+ 
  gi|385806073|ref|YP_005842471.1| 34 LEMKVSELEKKIEELREKINEIENVFGRSKEASGKIEQI 72
                                      677999999999999999999999543333333333333 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 8.9
                              Med9  39 relirelpgidrs 51 
                                       +e +++l+ i+ s
  gi|385806073|ref|YP_005842471.1| 127 KEFLEKLSSISDS 139
                                       6666666666554 PP

>> YvrJ  YvrJ protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.4    0.0014      0.59      19      35 ..      41      57 ..      29      58 .. 0.91
   2 ?    0.4   0.2       1.1   4.8e+02      21      35 ..      67      81 ..      66      82 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0014
                              YvrJ 19 iEkkLdeLtksIeeLse 35
                                      +Ekk++eL + I+e  +
  gi|385806073|ref|YP_005842471.1| 41 LEKKIEELREKINEIEN 57
                                      8************9865 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.1
                              YvrJ 21 kkLdeLtksIeeLse 35
                                      +k+++ ++  ++L++
  gi|385806073|ref|YP_005842471.1| 67 GKIEQINMLLDKLRN 81
                                      79******9999987 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   8.0     0.019       7.9     108     172 ..       7      71 ..       1      90 [. 0.73
   2 ?    2.2   0.0      0.33   1.4e+02      49      84 ..     127     162 ..     118     170 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.019
                            DUF724 108 leerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaeklee 172
                                       l+   k ek+ e++++e +++ + +d le+k++ele++ + l+ek ++ ++   r+k    k+e+
  gi|385806073|ref|YP_005842471.1|   7 LKDFLKGEKEEETHNDEIEEIIKRMDILEMKVSELEKKIEELREKINEIENVFGRSKEASGKIEQ 71 
                                       34444456666666677777777778888888888888888888888887777777777777765 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.33
                            DUF724  49 vsfagllekvkklsiddsrseleslkeslaeLekhG 84 
                                         f + l ++++      ++++ +lke + eL k+G
  gi|385806073|ref|YP_005842471.1| 127 KEFLEKLSSISDSDPSSAAEKIGDLKELFFELLKEG 162
                                       567777888888888889999**********99988 PP

>> UPF0184  Uncharacterised protein family (UPF0184)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   2.9      0.01       4.3      19      59 ..      15      55 ..       5      65 .. 0.79
   2 ?    1.1   0.0       1.2   5.3e+02      35      47 ..      69      81 ..      62      90 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.01
                           UPF0184 19 eedefgeeEyeainsmLDqinsaLDalEernDdlnskLrEL 59
                                      +e+e  ++E+e+i   +D ++  + +lE++ ++l  k++E+
  gi|385806073|ref|YP_005842471.1| 15 KEEETHNDEIEEIIKRMDILEMKVSELEKKIEELREKINEI 55
                                      35677788888888888888888888888888888888886 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 1.2
                           UPF0184 35 LDqinsaLDalEe 47
                                      ++qin  LD+l +
  gi|385806073|ref|YP_005842471.1| 69 IEQINMLLDKLRN 81
                                      5667777776655 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   8.7    0.0066       2.8      24      91 ..       3      66 ..       1      89 [. 0.79
   2 ?    0.6   0.0       1.8   7.7e+02      29      62 ..     127     154 ..     115     162 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0066
                            APG6_N 24 erdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeel 91
                                       ++++++flk  k+e+++    ++e+ee+ ++++ le + +el+++++el ++  e+e+     +e +
  gi|385806073|ref|YP_005842471.1|  3 AKKTLKDFLKGEKEEETH----NDEIEEIIKRMDILEMKVSELEKKIEELREKINEIENVFGRSKEAS 66
                                      577888888877777444....5699999999999999999999999999999888887666665555 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.8
                            APG6_N  29 eeflkklkkekkeeekqdeeleeleeelekleke 62 
                                       +efl+kl + +++      +  ++ e++ +l++ 
  gi|385806073|ref|YP_005842471.1| 127 KEFLEKLSSISDS------DPSSAAEKIGDLKEL 154
                                       6788888877544......555666666666554 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   6.0    0.0098       4.2      60     101 ..      15      56 ..       2     107 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0098
                             Atg14  60 dkiknkkakleelksliadlrerlqelkdklsqlkkeieekk 101
                                       ++++++++ +ee+ +++ +l+ +++el++k+++l+++i+e  
  gi|385806073|ref|YP_005842471.1|  15 KEEETHNDEIEEIIKRMDILEMKVSELEKKIEELREKINEIE 56 
                                       355555556666666666666666666666666666665543 PP

>> DUF1690  Protein of Unknown function (DUF1690)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   4.1     0.018       7.7      51      99 ..       4      52 ..       1      58 [. 0.53
   2 ?    2.5   0.3      0.42   1.8e+02      78     112 ..      62      96 ..      53     102 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.018
                           DUF1690 51 eetlkkfeeklekellkdeadakdelsskalnekieeLrkkleefkkke 99
                                      ++tlk+f +  ++e+ ++++ ++  +  + l+ k++eL+kk+ee+++k 
  gi|385806073|ref|YP_005842471.1|  4 KKTLKDFLKGEKEEETHNDEIEEIIKRMDILEMKVSELEKKIEELREKI 52
                                      6677777777777766666444444444444555555555555544443 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.42
                           DUF1690  78 skalnekieeLrkkleefkkkeeeklpeeveeare 112
                                       sk+ + kie+++  l+++++k   k++e+++++++
  gi|385806073|ref|YP_005842471.1|  62 SKEASGKIEQINMLLDKLRNKGYLKESEDLARVKD 96 
                                       67889999999999999999999888888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2172  (0.121145); expected 358.6 (0.02)
Passed bias filter:                     1165  (0.0649785); expected 358.6 (0.02)
Passed Vit filter:                       263  (0.014669); 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):              42  [number of targets reported over threshold]
# CPU time: 0.74u 0.37s 00:00:01.10 Elapsed: 00:00:00.52
# Mc/sec: 1021.85
//
Query:       gi|385806074|ref|YP_005842472.1|  [L=288]
Description: hypothetical protein FFONT_1032 [Fervidicoccus fontis Kam940]
Scores for complete 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   26.1   0.0    0.00015   21.5   0.0    2.3  2  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 !   21.5   0.0   8.2e-09   0.00015       6     230 ..      18     239 ..      15     248 .. 0.80
   2 !    2.1   0.1     0.007   1.3e+02     265     281 .]     254     270 ..     249     270 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 8.2e-09
                                       XXXXXXXXXXXXXXXXXXXXXX..XXXXHHHHHHHHHTTHHHHHHHH...........HH--HHHHHHHHHHHH..- CS
                              CitG   6 lAlllEvsatpKPGlVdrrdsgahdDmdfetFlaSaealapyfeeaaaaGleakalfeelrsiGelaekamlaa..t 80 
                                       l+++lE + +   G+V+r ++    D ++++ +     + +++ +           ++    +Ge + k m      
  gi|385806074|ref|YP_005842472.1|  18 LSMMLEPTGWGIGGNVSRMKDH--LDKTLQDYIYIGFLSGDILIDNI---------LRFNSDLGEGFLKSMKSIieK 83 
                                       6777777777777888888887..77777777777777777766666.........3444679************99 PP

                                       -----HHHHHHHHHHHHTTTTS-.......SHHHHHHHHHHHHHT--HHHHHHHHHHHHH--.......---..... CS
                              CitG  81 ggvNThkGaifllgllaaaagrraaeeeeasleelveeaaevlaeltvedavafrairlakv.......eel..... 145
                                        g+NT +G++fl+   aa++ ++    ++++l+e+ e a + l +++   +++f+ + l++        + +     
  gi|385806074|ref|YP_005842472.1|  84 TGTNTSFGTVFLIFFNAASIILK----NKRDLNEIGEGAFSYLISIKP--SIYFKSLMLTNSsflhrfsS-Slypsl 153
                                       9*************999999966....7899************99966..77889999988878876651.145555 PP

                                       .....HHHHHH.TT--HHHHHHTS-TT-HHHHHHHHTSHHHHHHHH........HH-SSHHHHHHHHHHHHHHS--H CS
                              CitG 146 .....kdelvekksltlgevlelsygvdgirgeaasgFpsvfeialpalrealasgadlndalvqallallaelpDt 217
                                            +    + ++ +l + l+l+  +d +++ea++ F  +++ a + ++e++  +  +++ + +++  + ++++D 
  gi|385806074|ref|YP_005842472.1| 154 tdvftN--YEKWDDKKLIDFLRLNI-FDPVSQEASTCFTNSIREAEKLIKEEH-CSIPTSEEIDKLFRSFCCKYNDY 226
                                       555431..22234678888888877.8****************9999999874.567889999************** PP

                                       HHHHHHHHHHHHH CS
                              CitG 218 nilrrgGaegaee 230
                                        ++r++G e  e 
  gi|385806074|ref|YP_005842472.1| 227 IVYRKYGLERSES 239
                                       *******998776 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.007
                                       ---HHHHHHHHHHHHHH CS
                              CitG 265 isPGgsADllaatlfla 281
                                        s G+  Dl+a+tlf++
  gi|385806074|ref|YP_005842472.1| 254 CSMGSLSDLVALTLFFY 270
                                       589************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.48
# Mc/sec: 1813.68
//
Query:       gi|385806075|ref|YP_005842473.1|  [L=211]
Description: hypothetical protein FFONT_1033 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0052   16.6   0.0     0.0073   16.1   0.0    1.5  1  DUF447    Protein of unknown function (DUF447)
  ------ inclusion threshold ------
      0.055   13.8   0.2        0.1   12.9   0.2    1.5  1  DUF5497   Family of unknown function (DUF5497)


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 !   16.1   0.0   8.1e-07    0.0073      80     166 ..     103     192 ..      23     203 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.1e-07
                                       T..EETT-SEEEEEEEEEECTCECCEEEEEEEEEEEEET.TB---B-HHHHHHHHHHHHHHCCCC.SHHHHHHHHHH CS
                            DUF447  80 ia.vlksaeawveveveevegdsealelelepvkeeile.ervkpfnRgdaaviEaaVlatRldi.edkeklleeie 153
                                       ++ + ++++  +  ++ee++ ++ ++ l+l++++ + ++ e+  p  R  +++iEa +  +Rl +   + +  + i+
  gi|385806075|ref|YP_005842473.1| 103 VPpHTNRSYFLIPTTIEEITLKDGLIYLKLSIEENVWIKiENLLPPYRPVNLLIEAIISHSRLYLgISDSEEINYIK 179
                                       44567777777888888999999999999999999988866666669****************99955555568899 PP

                                       HHHHHHHHH--HH CS
                            DUF447 154 ylssvikktgger 166
                                       +l s i++t  ++
  gi|385806075|ref|YP_005842473.1| 180 RLLSNIRRTTENE 192
                                       9999999998776 PP

>> DUF5497  Family of unknown function (DUF5497)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   1.1e-05       0.1      38      76 ..     157     195 ..     129     205 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.1e-05
                           DUF5497  38 emqieeeikyievddgeeintiktfllnsmstseqrdly 76 
                                       e  i     y+ + d eein ik +l n   t+e+  l 
  gi|385806075|ref|YP_005842473.1| 157 EAIISHSRLYLGISDSEEINYIKRLLSNIRRTTENERLL 195
                                       33444555699******************9999987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1357.37
//
Query:       gi|385806076|ref|YP_005842474.1|  [L=304]
Description: hypothetical protein FFONT_1034 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0027   18.0   0.1     0.0055   17.0   0.1    1.5  1  NTP_transf_2   Nucleotidyltransferase domain
  ------ inclusion threshold ------
       0.12   12.7   0.2        1.9    8.8   0.1    2.5  2  SpoU_sub_bind  RNA 2'-O ribose methyltransferase substrate bi


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 !   17.0   0.1   6.2e-07    0.0055       2      67 ..     101     179 ..     100     207 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.2e-07
                                       HHHHHHHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHH................HHHEHHHHHHHHCCC CS
                      NTP_transf_2   2 kklleelkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsre................kkeegleklaeiikf 62 
                                       +kll el+e   ++++ ++G    G+  ++SDiD++v++++  + e                +    l+++ ++ + 
  gi|385806076|ref|YP_005842474.1| 101 MKLLSELREHTNSVDIGITGGILVGK--RTSDIDVIVYGRKTCE-EvykflmesktlekygrNEVLNLLENRREKYY 174
                                       689999**9999*************9..88************54.35777666665555555222233333344444 PP

                                       EEECT CS
                      NTP_transf_2  63 leell 67 
                                        e++ 
  gi|385806076|ref|YP_005842474.1| 175 NELIV 179
                                       44444 PP

>> SpoU_sub_bind  RNA 2'-O ribose methyltransferase substrate binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0     0.072   6.5e+02       1      12 [.     134     145 ..     134     147 .. 0.87
   2 ?    8.8   0.1   0.00021       1.9       3      35 ..     157     186 ..     157     194 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.072
                     SpoU_sub_bind   1 liyGlhaVleaL 12 
                                       ++yG+++++e+ 
  gi|385806076|ref|YP_005842474.1| 134 IVYGRKTCEEVY 145
                                       69*******986 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00021
                     SpoU_sub_bind   3 yGlhaVleaLksgrr..iekllvtegradkrleel 35 
                                       yG++ Vl +L+++r+   ++l+v+++     +e++
  gi|385806076|ref|YP_005842474.1| 157 YGRNEVLNLLENRREkyYNELIVKRE-----MEKI 186
                                       9***********9888******9998.....4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1851.40
//
Query:       gi|385806077|ref|YP_005842475.1|  [L=262]
Description: hypothetical protein FFONT_1035 [Fervidicoccus fontis Kam940]
Scores for complete 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-61  205.5   0.1    7.4e-61  205.2   0.1    1.0  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 !  205.2   0.1   4.1e-65   7.4e-61       3     204 ..      48     259 ..      46     260 .. 0.96

  Alignments for each domain:
  == domain 1  score: 205.2 bits;  conditional E-value: 4.1e-65
                                       ---SEEEEEEEEE-TT---EEEEE--B-SS-.-TTSS-TT-B--B-HHHHHHHHHHHHGGG...GGSTT-EEEE--S CS
                    tRNA_deacylase   3 edvdliiflSrHssesgkplLTvHvtGnlge.aelGGkpeelapaaPrllkallralkkia...ekleefevtlEat 75 
                                       ++++++i+lS H se+g p+LTvH+tGnl++ a lGG+p+e++++ Prl   l+++++++    ++ e+++v++Eat
  gi|385806077|ref|YP_005842475.1|  48 KEYNAFIVLSMHMSEAGIPCLTVHHTGNLTSkALLGGRPREISVSFPRLSGFLIKKIHSLVsyyGLAEKMKVSYEAT 124
                                       57899**************************9**************************99999999*********** PP

                                       -SS-----S-EEEEEEEESHHHHT-HHHHHHHHHHHHHHHH--....----EEEEEE-S-TT-HHHHHHHHHBSEEE CS
                    tRNA_deacylase  76 HHGPtelkvPslFvEiGSteeeWkdedaaeavaeavlellese....eekekvlvgiGGgHYaprftklvletevav 148
                                       HHGPt+++ P+++vEiGS+e+eWkd++ ++++aeav+++          ++++++g+GGgHY++r+tk+ +e++v++
  gi|385806077|ref|YP_005842475.1| 125 HHGPTNITRPLVYVEIGSSEKEWKDKELQKLMAEAVYDAYMLLkedrLPDCEKAIGFGGGHYSERHTKISIENNVCF 201
                                       **************************************9877766777799************************** PP

                                       EEEE-GGGGGG.--HHHHHHHHHHH..T-SEEEE-TTT--HHHHHHHHHHHHHHT-EE CS
                    tRNA_deacylase 149 Ghilskyalee.lkeevikqaleks.egadvalidkkslkseqkeaieelleelgiev 204
                                       Gh+++kya++e +++ v++q+++k+ eg++ ++ +kk  ++e +e+ie+ ++e+++++
  gi|385806077|ref|YP_005842475.1| 202 GHLVPKYAIKEgIDSFVLDQIYDKNyEGINSVYAEKKIGTREFREEIEKKAKERNVKF 259
                                       *******998868888***************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); 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 0.28s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1610.22
//
Query:       gi|385806078|ref|YP_005842476.1|  [L=143]
Description: hypothetical protein FFONT_1036 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.036   14.1   1.3      0.036   14.1   1.3    3.0  3  Ac76      Orf76 (Ac76)
        2.5    8.2   9.9      0.057   13.4   1.7    2.2  2  DUF997    Protein of unknown function (DUF997)


Domain annotation for each model (and alignments):
>> Ac76  Orf76 (Ac76)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   1.4     0.083   7.5e+02      23      41 ..       3      21 ..       1      40 [. 0.71
   2 ?    2.7   0.1     0.014   1.3e+02      35      55 ..      49      70 ..      32      74 .. 0.64
   3 ?   14.1   1.3     4e-06     0.036       4      66 ..      83     143 .]      80     143 .] 0.81

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.083
                              Ac76 23 lsellltllllfvlFiill 41
                                      +s+++  l +lf+  ++++
  gi|385806078|ref|YP_005842476.1|  3 ISNIMWGLSILFLAMFFIM 21
                                      5777766666666544444 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.014
                              Ac76 35 vlFiillnvyyi.kteStpadl 55
                                      +  i+ll  yy  + eS+p+++
  gi|385806078|ref|YP_005842476.1| 49 FSLILLLVAYYQnELESHPKKI 70
                                      3344555555551568988877 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 4e-06
                              Ac76   4 illlialivlafildkneklsellltllllfvlFiillnvyyikteStpadlytekakkikKk 66 
                                         ll  l++ ++ l ++     l++ +l+lf lFi +l+  y+k+  ++ +l+ ek +k kK+
  gi|385806078|ref|YP_005842476.1|  83 AWLLSSLALYSLFLYRFGFPIGLVVSILILFPLFISILQ--YTKKMIKTIELHYEKNQKKKKR 143
                                       55677788888888888888899*************998..6788888889988888887764 PP

>> DUF997  Protein of unknown function (DUF997)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   1.5      0.21   1.9e+03      19      30 ..      13      24 ..       5      60 .. 0.50
   2 ?   13.4   1.7   6.4e-06     0.057      19      65 ..      78     126 ..      68     136 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.21
                            DUF997 19 wwllfaYglgsk 30
                                      ++l+++++++s+
  gi|385806078|ref|YP_005842476.1| 13 LFLAMFFIMSSN 24
                                      334444444433 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 6.4e-06
                            DUF997  19 wwllfaYglgskeveey..yilglPlWfflscillpilfivlvillvkf 65 
                                       +  + a++l+s    ++  y +g+P  +++s+++l++lfi ++ +  k+
  gi|385806078|ref|YP_005842476.1|  78 LVAYIAWLLSSLALYSLflYRFGFPIGLVVSILILFPLFISILQYTKKM 126
                                       4445566666555444467*********************998776554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1127  (0.0628591); 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:                         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: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 884.26
//
Query:       gi|385806079|ref|YP_005842477.1|  [L=499]
Description: peptidase M32, carboxypeptidase Taq metallopeptidase [Fervidicoccus fontis Kam940]
Scores for complete 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-162  540.9   0.4   3.3e-162  540.6   0.4    1.0  1  Peptidase_M32  Carboxypeptidase Taq (M32) metallopeptidase


Domain annotation for each model (and alignments):
>> Peptidase_M32  Carboxypeptidase Taq (M32) metallopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  540.6   0.4  1.9e-166  3.3e-162       5     488 .]      16     498 ..      12     498 .. 0.97

  Alignments for each domain:
  == domain 1  score: 540.6 bits;  conditional E-value: 1.9e-166
                     Peptidase_M32   5 llkkvsalesasallewDketvmpkkgaearaeqlatLselahelltseevaellekleeekeeldekekavveelk 81 
                                       ++k +++++ a++llewD+et+mpk+g+ +r+ +  +Ls l h+ll ++e+ +l+ek+++ +  l++ ek vv+ l 
  gi|385806079|ref|YP_005842477.1|  16 RYKFIWSIDYAMGLLEWDMETYMPKEGIIERSIANRHLSVLEHRLLLDPELVSLVEKAKSIET-LNDYEKGVVRVLD 91 
                                       56778999**************************************************98777.5567********* PP

                     Peptidase_M32  82 reykkakkvpaelvealakasakaeaaWreareandfalfepsLeevielkreiaelledlkkspYdaLldeyepgl 158
                                       re++kakk+p++l ++l + + +a++aW++ re+ndf++f+p+Le+++el++++a++l ++ ++pYdaL+d ye+g 
  gi|385806079|ref|YP_005842477.1|  92 REITKAKKIPESLIAELREVTIRAHEAWVTSREKNDFSIFKPYLEKIVELEKRMADYL-GYVEHPYDALIDYYEEGW 167
                                       **********************************************************.****************** PP

                     Peptidase_M32 159 tvekidalFeelkealvpllkkikeskekekkdksflereipeekqrelsrellkalgfdfdrgrldeseHPFttsf 235
                                       t+++++++++++  +l+ +l+k+ +++   +k + + + ++++ k  e++++ll+ lgf  +r+r+d+seHPFt++f
  gi|385806079|ref|YP_005842477.1| 168 TTKDVERMYDSIIPELKSILEKVMSDSRY-PKCHYLESYKYDITKAVEINNRLLDILGFPRTRARIDVSEHPFTINF 243
                                       ************************99984.445558899************************************** PP

                     Peptidase_M32 236 srkDvRittryeednllsslfsvlHEaGHalYeqnlpeelsktplgggvslgihEsqSrlyEniigrskeFwevllp 312
                                       + +D+Rittrye  +++++++s++HE+GHa Ye++++e+ls+tpl++gvs+gihEsqSr++En++gr+ +F++ + +
  gi|385806079|ref|YP_005842477.1| 244 GIRDARITTRYEGYDIKRTIYSAVHEFGHATYELQIDESLSGTPLARGVSMGIHESQSRFWENVVGRNFAFTKIVGS 320
                                       ***************************************************************************** PP

                     Peptidase_M32 313 klkeafpeqlddvsleefyeavnkvepsliRveADEltYslHillRyelEkeliegklsvkdlpeaWnekykeyLgi 389
                                        ++e+fpe ++ +s e++y ++n+v+psliRv+ADEltY++H+ lR+++Ek li ++++v+d+p++Wn+ ++eyLgi
  gi|385806079|ref|YP_005842477.1| 321 LIREYFPELKN-FSDEDIYYYINTVKPSLIRVDADELTYNFHVALRFRIEKMLIGNEIKVSDVPDIWNNTMEEYLGI 396
                                       ********666.***************************************************************** PP

                     Peptidase_M32 390 dppddaeGvLQDvHWssgafGYFPtYalGniyaaqlfeamekdl.pel..eiakgefseikkWLkenihqkGslyss 463
                                       +p+d ++GvLQD+HWs+g++GYFPtY+lG+i++aq+  a+ekdl ++l  +i +++f eik+WLk++ih+ G++y +
  gi|385806079|ref|YP_005842477.1| 397 RPKDYKSGVLQDIHWSQGSIGYFPTYSLGTIISAQVGYAIEKDLgKKLgdIIDSRNFAEIKEWLKRKIHRFGATYAP 473
                                       ********************************************65558889************************* PP

                     Peptidase_M32 464 eellkkatgeslnaeyyidyLkeky 488
                                       +el+++   e++n+eyyi+yLk+ky
  gi|385806079|ref|YP_005842477.1| 474 KELIRRNLNEDVNPEYYISYLKNKY 498
                                       ************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (499 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); 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 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 3076.91
//
Query:       gi|385806080|ref|YP_005842478.1|  [L=626]
Description: D-fructose-6-phosphate amidotransferase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.3e-45  152.2   1.3    4.1e-26   91.4   0.7    2.4  2  SIS         SIS domain
    8.6e-21   74.5   0.0    1.6e-20   73.6   0.0    1.4  1  GATase_6    Glutamine amidotransferase domain
    4.8e-16   58.8   0.0    8.7e-16   58.0   0.0    1.5  1  GATase_7    Glutamine amidotransferase domain
  ------ inclusion threshold ------
       0.02   14.9   0.0      0.064   13.3   0.0    1.8  1  bact-PGI_C  Bacterial phospho-glucose isomerase C-terminal SI
      0.086   11.7   0.0       0.14   11.0   0.0    1.3  1  GATase_4    Glutamine amidotransferases class-II
       0.11   12.5   0.1        0.3   11.1   0.1    1.9  1  SIS_2       SIS domain


Domain annotation for each model (and alignments):
>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.4   0.7   1.4e-29   4.1e-26       1     130 [.     307     435 ..     307     436 .. 0.97
   2 !   59.1   0.0   1.3e-19   3.9e-16       2      90 ..     481     569 ..     480     608 .. 0.93

  Alignments for each domain:
  == domain 1  score: 91.4 bits;  conditional E-value: 1.4e-29
                                       HHCTSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHH CS
                               SIS   1 lLakakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelak 77 
                                       l++k+++i++ +aGtsy++++  ++ +e+i+g++v    +se+k+    l+d+d+ +i+is+sget d+++a +  k
  gi|385806080|ref|YP_005842478.1| 307 LISKKDKIFIAAAGTSYHAGLVTKYFIEKITGRAVYTFISSEYKNI-EYLVDNDTAIIVISQSGETIDTIKAMRSSK 382
                                       588999************************************7666.9***************************** PP

                                       HTTSEEEEEESSTTSHHHHHSSEEEEEEEECHCSSSHCHHHHHHHHHHHHHHH CS
                               SIS  78 ergakiiaITdskgsplareadlalyinaepetlvastksltaqlaaldalav 130
                                       +rg+ i aIT+  gs++ rea +++ ++a+pe++va+tk++++q +++++lav
  gi|385806080|ref|YP_005842478.1| 383 NRGGVIFAITNVIGSTIGREANYVVPMRAGPEIGVAATKTFLTQVLVGSMLAV 435
                                       **************************************************986 PP

  == domain 2  score: 59.1 bits;  conditional E-value: 1.3e-19
                                       HCTSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHH CS
                               SIS   2 LakakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelake 78 
                                       ++++++iy+lG+G   ++a e+alk++ei++i++e+++a+e khg++ali++d +v+++ + +   + + ++ ++++
  gi|385806080|ref|YP_005842478.1| 481 FSSKNSIYFLGRGLGVPLAYEAALKMKEITYIHAEAYPAGESKHGPIALIEKDFPVFFVVTKDTYEEIASNIAEMNA 557
                                       57899************************************************************************ PP

                                       TTSEEEEEESST CS
                               SIS  79 rgakiiaITdsk 90 
                                       r+a +ia+++++
  gi|385806080|ref|YP_005842478.1| 558 RDAYTIALASEE 569
                                       *******99765 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.6   0.0   5.5e-24   1.6e-20      10     133 ..      84     214 ..      72     215 .. 0.89

  Alignments for each domain:
  == domain 1  score: 73.6 bits;  conditional E-value: 5.5e-24
                          GATase_6  10 vedevalaHvRlaivglaeeegaqPfpsedgrlllvhNGeiynykelreelpalkglafrsrsDtevllalleelG. 85 
                                       + + ++++H+R+a++g +++  a+P +  +g ++lvhNG i+n+ +l++ l +  g++f+s++Dtev+++l+eel+ 
  gi|385806080|ref|YP_005842478.1|  84 TPGCIGIGHTRWATHGAPTNINAHPHTDCKGDIALVHNGIIKNFLSLKKMLLN-SGHTFKSDTDTEVVAHLIEELAs 159
                                       45679*************99999*****************************9.******************99999 PP

                          GATase_6  86 .........eevlerlrGmfafaiwdk.rentlilardrlgvkplyyavdesglafas 133
                                                ++ ++ l+G fa a+++  +++++++a     ++pl+++ ++s    as
  gi|385806080|ref|YP_005842478.1| 160 tssnfyegfKKSISMLEGSFALAVVTTyEPEKIFFA---KKESPLIIGLSKSSNFLAS 214
                                       9999999999999**********************9...4568888887766555555 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.0   0.0   2.9e-19   8.7e-16      13     122 ..     106     220 ..      92     221 .. 0.90

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 2.9e-19
                          GATase_7  13 aQPmvssedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllallea.........ewgeealerlnGmfAf 80 
                                       a P + + +g++++v+nG i N+ +l++ L ++gh+f++++Dtev+++l+e+         e+ ++ +++l+G+fA+
  gi|385806080|ref|YP_005842478.1| 106 AHPHT-DCKGDIALVHNGIIKNFLSLKKMLLNSGHTFKSDTDTEVVAHLIEElastssnfyEGFKKSISMLEGSFAL 181
                                       56777.57899****************************************************************** PP

                          GATase_7  81 aiwdeeek.rlllaRDrlGikPLyygedkgdallfaSelkall 122
                                       a++++ e  +++ a+    + PL++g +k ++ ++aS + a+l
  gi|385806080|ref|YP_005842478.1| 182 AVVTTYEPeKIFFAKK---ESPLIIGLSK-SSNFLASDIPAML 220
                                       ***9766548999998...79*******7.6999999999876 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 ?   13.3   0.0   2.1e-05     0.064      19     141 ..     489     615 ..     474     621 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.1e-05
                                       EE-..TT-THHHHHHHHHHHHTT----B---.SSHHHHHHHTTSS-GGGGTTEEEEEESSHH.............HH CS
                        bact-PGI_C  19 iygssellevaArRfknqlnenAKipafagvlpeanhneivgleaeeelkkrlrlvllrdeeeh.....prvkkrae 90 
                                       ++g  +l  ++A+ ++ +++e+  i+a a    e++h  i+++    e+  ++ +v+ +d+ e+      ++++r  
  gi|385806080|ref|YP_005842478.1| 489 FLG-RGLGVPLAYEAALKMKEITYIHAEAYPAGESKHGPIALI----EKDFPVFFVVTKDTYEEiasniAEMNARDA 560
                                       556.777889999999999************************....566777777777777666777855555555 PP

                                       HHHHHHTTTS....SEEEEE---SSSHHHHHHHHHHHHHHHHHHHHHHCT---S- CS
                        bact-PGI_C  91 ivkelaeerg....vrvtevkaegesplerlaslillgDfvSvylAllrgvDPtp 141
                                        +  la+e++     +  +++  +  +l + +sli  + + S+y A+ rg+DP +
  gi|385806080|ref|YP_005842478.1| 561 YTIALASEEKlenlQPRLTITVPKVDLLLEPYSLIPPIQLLSYYTAVVRGLDPDK 615
                                       555555554411115667888889999**************************86 PP

>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   4.7e-05      0.14      75     145 ..      90     161 ..      52     180 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.7e-05
                          GATase_4  75 vaHiRkatqGevklenthpFvRelwgrewifAHnGdlkeykpkl....egrfePvGsTDsElafCelleelasrf 145
                                       + H R at+G+ ++ n+hp +    + ++ + HnG +k++        +  ++   +TD+E++  +l+eelas+ 
  gi|385806080|ref|YP_005842478.1|  90 IGHTRWATHGAPTNINAHPHTD--CKGDIALVHNGIIKNFLSLKkmllNSGHTFKSDTDTEVV-AHLIEELASTS 161
                                       89*****************986..45578999*****99643332346444555679999965.78888888776 PP

>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1    0.0001       0.3     102     137 ..     357     392 ..     302     393 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0001
                                       -TT-EEEEE-SS--SHHHHHHHHHHHHHT-EEEEEE CS
                             SIS_2 102 kpgDvLlviSnsGnnavvveaaeaakergmkviAlt 137
                                       ++  +++viS+sG+    ++a++  k+rg  + A+t
  gi|385806080|ref|YP_005842478.1| 357 DNDTAIIVISQSGETIDTIKAMRSSKNRGGVIFAIT 392
                                       5555789***************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (626 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); 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: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.47
# Mc/sec: 4011.58
//
Query:       gi|385806081|ref|YP_005842479.1|  [L=385]
Description: sugar phosphate nucleotidyltransferase [Fervidicoccus fontis Kam940]
Scores for complete 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-15   54.2   6.0    8.1e-07   28.5   0.2    5.0  6  Hexapep     Bacterial transferase hexapeptide (six repeats)
    9.3e-10   38.1   2.8    0.00056   19.6   0.0    4.4  4  Hexapep_2   Hexapeptide repeat of succinyl-transferase
     0.0042   16.1   0.1       0.07   12.1   0.0    2.3  2  Fucokinase  L-fucokinase
  ------ inclusion threshold ------
       0.01   14.0   0.1       0.02   13.1   0.1    1.4  1  DUF4954     Domain of unknown function (DUF4954)


Domain annotation for each model (and alignments):
>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0         2   9.1e+03      22      29 ..      66      73 ..      66      74 .. 0.75
   2 !   28.5   0.2   1.8e-10   8.1e-07       2      36 .]     254     288 ..     253     288 .. 0.94
   3 !   13.5   0.0     1e-05     0.045       2      30 ..     278     306 ..     277     307 .. 0.93
   4 !   13.4   0.1   1.1e-05     0.047       2      28 ..     296     321 ..     289     323 .. 0.81
   5 !   13.5   0.0     1e-05     0.046       3      33 ..     308     337 ..     306     340 .. 0.87
   6 !    8.8   0.1   0.00031       1.4       2      23 ..     358     379 ..     353     381 .. 0.67

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2
                                      E-TTEEEE CS
                           Hexapep 22 IGdnvkIg 29
                                      IG++vk++
  gi|385806081|ref|YP_005842479.1| 66 IGKRVKLE 73
                                      78888876 PP

  == domain 2  score: 28.5 bits;  conditional E-value: 1.8e-10
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36 
                                       + I+++++I++++vi g+V IG+++ Iga++ +++
  gi|385806081|ref|YP_005842479.1| 254 VLIEDGAVIDHYTVIKGPVYIGKRSFIGAHSLVRN 288
                                       679****************************9985 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 1e-05
                                       EEEETTEEE-TTEEEETTEEE-TTEEEET CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIga 30 
                                       ++IG ++l+++++ + +  ++G++v + +
  gi|385806081|ref|YP_005842479.1| 278 SFIGAHSLVRNYVSLEESSVLGSGVEVKR 306
                                       79***********************9865 PP

  == domain 4  score: 13.4 bits;  conditional E-value: 1.1e-05
                                       EEEETTEEE-TTEEEETTEEE-TTEEE CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkI 28 
                                       +v+Gs+v +   ++ig+ V+IG+n+ +
  gi|385806081|ref|YP_005842479.1| 296 SVLGSGVEVK-RSYIGPRVTIGSNCLV 321
                                       6778888888.8899999999999864 PP

  == domain 5  score: 13.5 bits;  conditional E-value: 1e-05
                                       EEETTEEE-TTEEEETTEEE-TTEEEETTEE CS
                           Hexapep   3 vIGsnvlIgpfaviggnVkIGdnvkIgagvv 33 
                                        IG  v+Ig+++ +  + ++G+n++  ++vv
  gi|385806081|ref|YP_005842479.1| 308 YIGPRVTIGSNCLV-TDSILGENATFKPFVV 337
                                       79999999999999.9999999999999998 PP

  == domain 6  score: 8.8 bits;  conditional E-value: 0.00031
                                       EEEETTEEE-TTEEEETTEEE- CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIG 23 
                                       +++G+++lI  ++v+ ++++I 
  gi|385806081|ref|YP_005842479.1| 358 VILGKGSLINGGSVLKPGTIIE 379
                                       5667777777777777777764 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 ?   -0.2   0.0      0.19   8.6e+02      17      26 ..     253     262 ..     246     263 .. 0.73
   2 !   19.6   0.0   1.3e-07   0.00056       1      30 [.     271     302 ..     271     306 .. 0.92
   3 !    8.7   0.2   0.00031       1.4       4      24 ..     309     330 ..     306     332 .. 0.74
   4 !    6.1   0.0    0.0021       9.5      16      32 ..     354     372 ..     352     374 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.19
                                       SEEE-TT-EE CS
                         Hexapep_2  17 GvslGdncvv 26 
                                       +v ++d++v+
  gi|385806081|ref|YP_005842479.1| 253 PVLIEDGAVI 262
                                       4889999998 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 1.3e-07
                                       .EEE-TT-EE-TT-EE..SEEE-TT-EE-TT- CS
                         Hexapep_2   1 pviIGdnCliGanagi..GvslGdncvvgaGv 30 
                                       pv IG++++iGa + +   vsl++ +v+g+Gv
  gi|385806081|ref|YP_005842479.1| 271 PVYIGKRSFIGAHSLVrnYVSLEESSVLGSGV 302
                                       8***************866************9 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.00031
                                       E-TT-EE-TT-EE.SEEE-TT- CS
                         Hexapep_2   4 IGdnCliGanagi.GvslGdnc 24 
                                       IG ++ iG+n+ +   +lG+n+
  gi|385806081|ref|YP_005842479.1| 309 IGPRVTIGSNCLVtDSILGENA 330
                                       7888888888886577788876 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.0021
                                       E..SEEE-TT-EE-TT-EE CS
                         Hexapep_2  16 i..GvslGdncvvgaGvvi 32 
                                       i  Gv+lG+++ +  G+v+
  gi|385806081|ref|YP_005842479.1| 354 IkrGVILGKGSLINGGSVL 372
                                       666**************98 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0      0.74   3.3e+03     229     282 ..      52     105 ..      48     111 .. 0.56
   2 !   12.1   0.0   1.6e-05      0.07     271     320 ..     276     331 ..     206     371 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.74
                        Fucokinase 229 kFyHlgttaeylehltkdaslkeelsltstafsaiknkkekkkesavvinSvle 282
                                       + y+ + ++e+ e + k+++l+e+ +l+   + +++ ++++ +e ++v+ S+l 
  gi|385806081|ref|YP_005842479.1|  52 SVYYSNISSEVYELIGKRVKLEETGKLDFLNSLKNAVENSNSQEIILVLGSFLL 105
                                       556667777777776666666666544444444444444455566666666665 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 1.6e-05
                        Fucokinase 271 kesavvinSvlessvsvgegsvie......hsslkgnvsigsnsivsglelessee 320
                                       k+s + ++S++ ++vs++e+sv+        s ++++v+igsn++v +  l ++++
  gi|385806081|ref|YP_005842479.1| 276 KRSFIGAHSLVRNYVSLEESSVLGsgvevkRSYIGPRVTIGSNCLVTDSILGENAT 331
                                       5566667899999999999999776777779***************9988887755 PP

>> DUF4954  Domain of unknown function (DUF4954)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   4.4e-06      0.02     189     271 ..     240     332 ..     230     340 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.4e-06
                           DUF4954 189 kNvkigdyatiegasklengtinSsk...eapveiGe......gViledfiiss.GskikdgavisrcfvGqavklk 255
                                       k +k+ ++a++eg   +e+g+++ +    + pv+iG+         +++ +  +  s +  g+ ++r+++G  v+++
  gi|385806081|ref|YP_005842479.1| 240 KEAKVSPTAVLEGPVLIEDGAVIDHYtviKGPVYIGKrsfigaHSLVRNYVSLEeSSVLGSGVEVKRSYIGPRVTIG 316
                                       66788888888888888888887765222568887762111114456777755415566789*************** PP

                           DUF4954 256 kqfsaedsllfaNcqg 271
                                        +  ++ds+l++N+++
  gi|385806081|ref|YP_005842479.1| 317 SNCLVTDSILGENATF 332
                                       *************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); 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: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 2313.18
//
Query:       gi|385806082|ref|YP_005842480.1|  [L=267]
Description: 3-methyl-2-oxobutanoate hydroxymethyltransferase [Fervidicoccus fontis Kam940]
Scores for complete 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-108  362.5   0.1   1.3e-108  362.4   0.1    1.0  1  Pantoate_transf  Ketopantoate hydroxymethyltransferase
    1.6e-05   24.5   0.6    8.4e-05   22.1   0.3    2.1  2  PEP_mutase       Phosphoenolpyruvate phosphomutase


Domain annotation for each model (and alignments):
>> Pantoate_transf  Ketopantoate hydroxymethyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  362.4   0.1  1.4e-112  1.3e-108       1     258 [.       7     262 ..       7     263 .. 0.99

  Alignments for each domain:
  == domain 1  score: 362.4 bits;  conditional E-value: 1.4e-112
                   Pantoate_transf   1 kvtvkdlrkmkeegekiamlTaydattAklvdeagvdviLVGDslgmvvlgyestlpvtleemiyhtkaVargakra 77 
                                       k+t++++ k+ke +eki+m+Tayd+++A+++d+agvd iLVGDsl+mvvlg+e+t++v+l +mi h+kaVar+++ra
  gi|385806082|ref|YP_005842480.1|   7 KITMRKFIKKKELKEKIVMITAYDTPFARIADKAGVDSILVGDSLAMVVLGMENTINVSLRTMIDHVKAVARAKPRA 83 
                                       689************************************************************************** PP

                   Pantoate_transf  78 lvvadlPfgsyeaskeqalenAarllkeggadavKleggaevaetvkalveagipVmgHiGltPqsvnalggykvqg 154
                                       l+v+d+Pf+sye+s++qal+nA  ++k  ga+avKlegg+e++e+vk lv+agipVmgHiGltPq+  +lggy++ g
  gi|385806082|ref|YP_005842480.1|  84 LIVGDMPFMSYEVSSKQALKNASLMIKG-GAEAVKLEGGEEIIEQVKSLVRAGIPVMGHIGLTPQRFLRLGGYRMIG 159
                                       **********************999996.************************************************ PP

                   Pantoate_transf 155 kteeeaeklledakaleeaGafalvlEavpaelakeiteklsiptIGIGAGaacdGqvlvlhDllgltekfkpkfvk 231
                                       k+  e+e+ll+da+al+eaG+f++v+E + +e+a++iteklsiptI+IG+G++cdGqvlvlhDllglt ++ p+f+k
  gi|385806082|ref|YP_005842480.1| 160 KKPFEEEQLLRDAEALQEAGVFSIVVEYTLSEVARKITEKLSIPTICIGSGPYCDGQVLVLHDLLGLT-EKPPSFAK 235
                                       *******************************************************************9.668***** PP

                   Pantoate_transf 232 kyaelaesieeavkaYaeevkegsFPa 258
                                       kya+l++++eea+++Ya+ev++g FP 
  gi|385806082|ref|YP_005842480.1| 236 KYADLSKIAEEAISKYASEVRNGIFPG 262
                                       **************************7 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.3   9.4e-09   8.4e-05       4     107 ..      19     121 ..      11     136 .. 0.83
   2 ?    1.3   0.0     0.021   1.9e+02     156     196 ..      99     139 ..      90     201 .. 0.60

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 9.4e-09
                        PEP_mutase   4 LhakgeplvlpnawDalsakiveeagfkalatsSlavaaslGvpDgeelpleellaavraiaevvslPliv.Dle.d 78 
                                       L+   e +v++ a+D   a+i+ +ag++ + ++      +lG++ + +++l +++++v+a+a++    liv D+   
  gi|385806082|ref|YP_005842480.1|  19 LK---EKIVMITAYDTPFARIADKAGVDSILVGDSLAMVVLGMENTINVSLRTMIDHVKAVARAKPRALIVgDMPfM 92 
                                       33...459*************************999999*************************9988876466435 PP

                        PEP_mutase  79 GygespeevaetvrrliaaGvvgvniEDk 107
                                        y+ s ++  ++   +i+ G+ +v +E  
  gi|385806082|ref|YP_005842480.1|  93 SYEVSSKQALKNASLMIKGGAEAVKLEGG 121
                                       67777777777777888888888877765 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.021
                        PEP_mutase 156 eeaieRaraYaeAGAdgvfvpglqkdae.iaelvaavdvpln 196
                                       ++a++ a +  + GA++v   g+++  e +++lv+a  +p++
  gi|385806082|ref|YP_005842480.1|  99 KQALKNASLMIKGGAEAVKLEGGEEIIEqVKSLVRAG-IPVM 139
                                       5677777777777777777777776644477777553.3333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1699.13
//
Query:       gi|385806083|ref|YP_005842481.1|  [L=299]
Description: 2-dehydropantoate 2-reductase [Fervidicoccus fontis Kam940]
Scores for complete 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-32  110.4   0.1    9.1e-32  109.9   0.1    1.2  1  ApbA_C    Ketopantoate reductase PanE/ApbA C terminal
    1.6e-11   44.0   0.1    3.5e-11   43.0   0.1    1.6  1  ApbA      Ketopantoate reductase PanE/ApbA
  ------ inclusion threshold ------
       0.13   12.2   0.4       0.86    9.5   0.0    2.4  3  DUF3198   Protein of unknown function (DUF3198)


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 !  109.9   0.1   1.5e-35   9.1e-32       1     125 []     170     293 ..     170     293 .. 0.98

  Alignments for each domain:
  == domain 1  score: 109.9 bits;  conditional E-value: 1.5e-35
                            ApbA_C   1 dirlarweKllinaainpltalldckngellespelralvrallkEalavaeaegvelseerleeaveavlektaan 77 
                                       di+   w K +in+ainp+t+ll++kn++++e+  ++ l+ + +kE  +va a+g++l+ +  e+++ ++++kt +n
  gi|385806083|ref|YP_005842481.1| 170 DIMPYLWLKAIINSAINPITTLLGSKNKAVIENDFAQSLALKTIKEGEKVASALGIKLPSD-PEKMLFEIATKTGEN 245
                                       689999*******************************************************.*************** PP

                            ApbA_C  78 rsSMlqDveagrktEidyinGavvklAeklgvetPvnellyellkale 125
                                       +sSMlqD++++++tEidyinG+++  +ekl +++ +n++ly ++kale
  gi|385806083|ref|YP_005842481.1| 246 YSSMLQDIKNKKRTEIDYINGYIALQGEKLSLNVETNKTLYLMVKALE 293
                                       ********************************************9976 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   0.1   5.9e-15   3.5e-11       2     150 ..       7     142 ..       6     144 .. 0.83

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 5.9e-15
                                       EEES-SHHHHHHHHHHHHHTHCEEEE-SCHHHHHHHHHCEEEEETTCEEEEEECEEECCHSCCCCS-ESEEEE-SSG CS
                              ApbA   2 ailGaGaiGsllaakLakagadvtlilrsrrlealkknGlrltseggeeilrppealsaeekselepidlvivtvKa 78 
                                       +i+GaG iG ll + L   ++dv +i +++  e    + l+ +++++++ ++++ + ++        +   ++++Ka
  gi|385806083|ref|YP_005842481.1|   7 CIIGAGNIGILLSYFL--RNEDVAIIKKNN-SEITYVRLLNGEKSWEQRFVSFEIENNFF-------CRKALIATKA 73 
                                       8***************..567787777777.44333344444444455555555555555.......999******* PP

                                       GGHHHHHHHHGGGECTCEEEEEESSSSCHHHHHTTTSTTSEEEEEEEE-EEEEEETTEEEECS--EEEEEES CS
                              ApbA  79 yqteealeeikplldpntvvlllqNGlgheeelrealpkprvlggvtthgatregpgevhhagkgeikigel 150
                                       y +ee++++ik   ++   v ++qNGlg  e+l   ++ ++ +g  +t g+ + g+   + +g gei +g+l
  gi|385806083|ref|YP_005842481.1|  74 YNVEEVVSKIKGKAEN---VFSFQNGLGIIEILVNNFGVKNSFGSSITYGVSSCGKYCTEIKGLGEIIVGQL 142
                                       ***********98876...9***********************************************99986 PP

>> DUF3198  Protein of unknown function (DUF3198)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.35   2.1e+03      26      38 ..     136     148 ..     129     151 .. 0.81
   2 ?   -2.4   0.0      0.77   4.6e+03      20      33 ..     211     224 ..     210     226 .. 0.84
   3 ?    9.5   0.0   0.00014      0.86      23      46 ..     233     256 ..     231     259 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.35
                                       HHHHHHH-SHHHH CS
                           DUF3198  26 ekiarklGssYqq 38 
                                       e+i  +lG++Y +
  gi|385806083|ref|YP_005842481.1| 136 EIIVGQLGKKYDE 148
                                       6777899***986 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.77
                                       HHHHHHHHHHHHH- CS
                           DUF3198  20 knlkeLekiarklG 33 
                                       k +ke ek+a  lG
  gi|385806083|ref|YP_005842481.1| 211 KTIKEGEKVASALG 224
                                       678999****9998 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00014
                                       HHHHHHHHHH-SHHHHHHHHHHHH CS
                           DUF3198  23 keLekiarklGssYqqrLeeakek 46 
                                       k L +ia k G+ Y ++L++ k+k
  gi|385806083|ref|YP_005842481.1| 233 KMLFEIATKTGENYSSMLQDIKNK 256
                                       56789**************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 2108.60
//
Query:       gi|385806084|ref|YP_005842482.1|  [L=375]
Description: hypothetical protein FFONT_1042 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.2e-05   22.5   0.0    0.00015   21.6   0.0    1.5  1  Polysacc_deac_1  Polysaccharide deacetylase
  ------ inclusion threshold ------
       0.16   11.8   0.0       0.28   10.9   0.0    1.4  1  Novirhabdo_Nv    Viral hemorrhagic septicemia virus non-virio
       0.24   10.4   0.2       0.35    9.8   0.2    1.1  1  Miga             Mitoguardin


Domain annotation for each model (and alignments):
>> Polysacc_deac_1  Polysaccharide deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   2.6e-08   0.00015      47     123 ..      99     190 ..      49     191 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.6e-08
                                       -..................HHHHHHHHHTT.EEEEE--SS--EGGGSHHHHHHHHHHHHHHHHHHHHS----EEE-G CS
                   Polysacc_deac_1  47 y..................pdevremaasG.veignHtinhsnlkrlseeevrreierakdalrkalgreprlfryP 104
                                                          +++ re++++  +e+++Ht  h+      ++++++ +++ kd+  ++ g +++++ +P
  gi|385806084|ref|YP_005842482.1|  99 RlvfgivtsdnsgenntyiWNLYREVVEEYgWEAASHTRYHQP----PPRNITDILGSLKDIEGNISGYTVHTYIPP 171
                                       3555666666666678888*******99866**********98....6666776677777777777899******** PP

                                       GGEE-HHHHHHHHHTT.EE CS
                   Polysacc_deac_1 105 ygsasatvlevarelgfay 123
                                       yg+ +++ l ++re g++ 
  gi|385806084|ref|YP_005842482.1| 172 YGKVTKNELSILRENGIKI 190
                                       ****************986 PP

>> Novirhabdo_Nv  Viral hemorrhagic septicemia virus non-virion protein
   #    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      48     114 ..     197     266 ..     181     274 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.7e-05
                     Novirhabdo_Nv  48 lettlprildd....lrastrlpylhvldmrisllerthyllrnvpsspattgrrsdpelviishaevkll 114
                                       +e tlp+   d    l+ s rlp++ +l + +sl + t+     + + p+      dpe +i +++e+  +
  gi|385806084|ref|YP_005842482.1| 197 FEITLPKNWYDvhisLKMSDRLPWIDILRLELSLAKYTKNGCIIIYTHPTSF-DWKDPEQMIKAFNEMLNI 266
                                       78888886555222278999******************99998888888655.578999999999998543 PP

>> Miga  Mitoguardin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.2   5.9e-05      0.35     361     391 ..     251     281 ..     247     288 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 5.9e-05
                              Miga 361 kdpkkFleayeemleflekeenwektelele 391
                                       kdp + ++a++eml+ +ek +nw +t  el 
  gi|385806084|ref|YP_005842482.1| 251 KDPEQMIKAFNEMLNIVEKGNNWITTPYELY 281
                                       9*************************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       759  (0.0423336); expected 358.6 (0.02)
Passed bias filter:                      617  (0.0344135); 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: 0.58u 0.36s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 2211.20
//
Query:       gi|385806085|ref|YP_005842483.1|  [L=488]
Description: family 2 glycosyltransferase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-12   47.0   0.0    8.1e-09   35.7   0.0    2.1  2  Glyco_tranf_2_3  Glycosyltransferase like family 2
    3.9e-12   46.3   0.2    2.1e-06   27.7   0.1    2.4  2  Glycos_transf_2  Glycosyl transferase family 2
    5.7e-12   46.0   0.5    5.7e-12   46.0   0.5    1.9  2  Glyco_trans_2_3  Glycosyl transferase family group 2
    5.5e-08   32.5   0.0    9.2e-08   31.7   0.0    1.3  1  Glyco_transf_21  Glycosyl transferase family 21
     0.0098   14.6   0.2      0.014   14.1   0.2    1.2  1  Osmo_MPGsynth    Mannosyl-3-phosphoglycerate synthase (osmo_M
  ------ inclusion threshold ------
       0.04   14.4   0.0      0.097   13.2   0.0    1.6  1  Glyco_tranf_2_4  Glycosyl transferase family 2
       0.11   11.5   0.4       0.17   10.9   0.4    1.2  1  FAM199X          Protein family FAM199X
       0.39   11.2   2.8          1    9.8   0.8    2.3  2  BRCT_2           BRCT domain, a BRCA1 C-terminus domain


Domain annotation for each model (and alignments):
>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0    0.0004      0.91       3      51 ..      71     119 ..      69     136 .. 0.88
   2 !   35.7   0.0   3.6e-12   8.1e-09      59     229 ..     152     329 ..     144     330 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0004
                   Glyco_tranf_2_3   3 dlavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaee 51 
                                       +++vl+p+ n e ++ + + s+ +q+ p+  +++  d+s++ t++ ++ 
  gi|385806085|ref|YP_005842483.1|  71 KISVLIPARNSENYIISSILSAFNQSVPPKSIYILNDNSTDNTIKKVMN 119
                                       589*************************************999986654 PP

  == domain 2  score: 35.7 bits;  conditional E-value: 3.6e-12
                   Glyco_tranf_2_3  59 vrvrvvvnarnlgstgksralnealravk..sdlvllvDdDtvvePdtlkrllqff.ltpkvgavg.tpvfllnrs. 130
                                       v+++vv  ++ +   gk  ++ne+l+  +   d+vl++D+Dt++e ++++++l f+ +++k + v  t  +++ ++ 
  gi|385806085|ref|YP_005842483.1| 152 VEINVVDFKE-H--MGKPSMINEVLPSLNdkVDYVLILDSDTIIERRYIEKMLVFLnRDSKLAGVNgTILLWKPEKe 225
                                       4566664433.3..489*********9885577***********************988899999845557776554 PP

                   Glyco_tranf_2_3 131 ...tl.....vsalgalefaerhlrflaarral..gvltlnGsgslirrevlkelegldplflltdDyelglrlrra 197
                                          ++     ++ l        +l +l++++++  +v  lnGs+s +  + l e++g       ++D +++  l   
  gi|385806085|ref|YP_005842483.1| 226 grfSWffakaFRNLA----SLYYLLTLRFSETVfnSVNSLNGSCSIYKLKPLLEIGGIPT-DTYVEDSSTSWHLQLL 297
                                       444334322222222....34455667777666545999****************99988.99************** PP

                   Glyco_tranf_2_3 198 gfrtayvpgaavrevfpsslkayikqrnRwvy 229
                                       g+ +ay p a   +v+pss+k+++    R ++
  gi|385806085|ref|YP_005842483.1| 298 GYSVAYIPTAYSFTVDPSSPKRFFSKVLRITV 329
                                       ***********************999888765 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 !   27.7   0.1   9.4e-10   2.1e-06       1      52 [.      73     127 ..      73     136 .. 0.86
   2 !   16.2   0.0   3.1e-06    0.0069      56     111 ..     154     210 ..     147     258 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 9.4e-10
                                       EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCH....C CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelak....e 52 
                                       sv ip+ N e+++  ++ s+ +q   p + i++++D+StD+t + + ++ +    +
  gi|385806085|ref|YP_005842483.1|  73 SVLIPARNSENYIISSILSAFNQ-SVPPKSIYILNDNSTDNTIKKVMNFISqkngK 127
                                       8**********************.******************99998888766333 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 3.1e-06
                                       EEEEEESSS-HHHHHHHHHHHH--SS..EEEEEESSEEE-TTHHHHHHHHHHH.TTCE CS
                   Glycos_transf_2  56 vrvirreenvGkagalnaglraatgd..yilflDaDdepdpdwleklvealekdgadv 111
                                       + v+  +e  Gk + +n+ l   + +  y+l+lD+D+++++ ++ek++ +l++d  ++
  gi|385806085|ref|YP_005842483.1| 154 INVVDFKEHMGKPSMINEVLPSLNDKvdYVLILDSDTIIERRYIEKMLVFLNRD-SKL 210
                                       6677778888899999999999988888***********************995.434 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 ?   -3.7   0.4       4.2   9.3e+03     172     192 ..      23      43 ..      15      49 .. 0.58
   2 !   46.0   0.5   2.6e-15   5.7e-12       1     181 [.     182     374 ..     182     480 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 4.2
                   Glyco_trans_2_3 172 allllfsllalalvlllllll 192
                                       ++ll+ + +++++++ ++ l+
  gi|385806085|ref|YP_005842483.1|  23 IILLIKYTFYTIWIVPAYRLA 43 
                                       455555666666666555444 PP

  == domain 2  score: 46.0 bits;  conditional E-value: 2.6e-15
                   Glyco_trans_2_3   1 iilllDaDtvlppdclreiaaela.spevaivqgpvlvm..nvanwleelaalffaedhgkdilvrealgrvvp... 71 
                                       ++l+lD+Dt + + ++++ + +l  + + a v g +l +  ++   ++++ a  f +      l + +++++v+   
  gi|385806085|ref|YP_005842483.1| 182 YVLILDSDTIIERRYIEKMLVFLNrDSKLAGVNGTILLWkpEKEGRFSWFFAKAFRNLASLYYLLTLRFSETVFnsv 258
                                       79**********************559**********9777778888888888888888888888888888888888 PP

                   Glyco_trans_2_3  72 ..svGsgaflrrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkekspltlraalrQrkRwayGc.e 145
                                         + Gs+++  ++ l e+gg++  +++  ED + +  lq +Gy v ++p +  +++ p++ + ++    R + G+ +
  gi|385806085|ref|YP_005842483.1| 259 nsLNGSCSIYKLKPLLEIGGIP--TDTYVEDSSTSWHLQLLGYSVAYIPTAYSFTVDPSSPKRFFSKVLRITVGIqK 333
                                       8788******************..9*************************************************852 PP

                   Glyco_trans_2_3 146 l....eklillvrllgy.lgsllwsa..lplhlallllfslla 181
                                       l     +++++ + + + l s+ +s   lp+ l  ++   +++
  gi|385806085|ref|YP_005842483.1| 334 LfltrLPKLIKKKKYNLlLTSIYTSFgsLPFIL--MIANTINS 374
                                       233332222222222220222222221122222..22222222 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 !   31.7   0.0   4.1e-11   9.2e-08      26     170 ..     175     326 ..     152     328 .. 0.75

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 4.1e-11
                   Glyco_transf_21  26 leaakydllvisDsdvrvkpdyLeellaaled.pkvglVtslpvgsdakg...laaaleaafl..ntlagvlqa... 93 
                                           k d+++i+Dsd+++++ y+e++l  l + +k + V ++++  ++++   +   +++af   + l+++l+    
  gi|385806085|ref|YP_005842483.1| 175 SLNDKVDYVLILDSDTIIERRYIEKMLVFLNRdSKLAGVNGTILLWKPEKegrFSWFFAKAFRnlASLYYLLTLrfs 251
                                       345799*********************9997659999****999887774455444456666532233444444222 PP

                   Glyco_transf_21  94 ..klsglgfavGksmalrreaLeaiGGfealadeLAeDyalgkllraaGlkvvlspapiaqtsvprrsslrallaRq 168
                                          +  ++  +G++ +++ + L +iGG+    d+  eD +++++l+  G++v+  p++  +  v+  ss + +++++
  gi|385806085|ref|YP_005842483.1| 252 etVFNSVNSLNGSCSIYKLKPLLEIGGIPT--DTYVEDSSTSWHLQLLGYSVAYIPTAY-SFTVD-PSSPKRFFSKV 324
                                       2234699**********************9..*********************999974.33444.45666666666 PP

                   Glyco_transf_21 169 lr 170
                                       lr
  gi|385806085|ref|YP_005842483.1| 325 LR 326
                                       65 PP

>> Osmo_MPGsynth  Mannosyl-3-phosphoglycerate synthase (osmo_MPGsynth)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.2   6.1e-06     0.014      43     103 ..      62     123 ..      42     205 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.1e-06
                     Osmo_MPGsynth  43 eeeleevesklaivvpiknEelkvlegvlsg....iPhdclvilvSnssreevdkykaevellke 103
                                       +ee++ +e k+++++p +n e  ++ ++ls+    +P +++ il  ns+    ++ k+ ++ +++
  gi|385806085|ref|YP_005842483.1|  62 AEEIKTIEGKISVLIPARNSENYIISSILSAfnqsVPPKSIYILNDNSTD---NTIKKVMNFISQ 123
                                       489**************************8544449************98...444444444444 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 ?   13.2   0.0   4.3e-05     0.097       2      83 ..      80     191 ..      79     198 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.3e-05
                   Glyco_tranf_2_4   2 neadiLpeflahhlalgf..drilvydndstDgtrailke...lpevkllhvd........................ 49 
                                       n ++++ + +  + +  +  + i++++++stD+t + + +   +++ kl +v                         
  gi|385806085|ref|YP_005842483.1|  80 NSENYIISSILSAFNQSVppKSIYILNDNSTDNTIKKVMNfisQKNGKLKRVIykdkyifisydvkrsdgikveinv 156
                                       5555555555555555554489************8888555545555533333334677777667766666665555 PP

                   Glyco_tranf_2_4  50 ksyederrqvellkallaryaea.dwvlvvDaDEf 83 
                                        ++++   + ++++++l + +++ d+vl +D+D +
  gi|385806085|ref|YP_005842483.1| 157 VDFKEHMGKPSMINEVLPSLNDKvDYVLILDSDTI 191
                                       455655555789999999988766********966 PP

>> FAM199X  Protein family FAM199X
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.4   7.6e-05      0.17     118     213 ..      54     150 ..      49     156 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 7.6e-05
                           FAM199X 118 samtndeqveyieylsrkvstemglreqld..iikiidpsaqisptdsefiielncltdeklkqvrnyikehsprqr 192
                                       s  + +e  e i+ +  k+s  +  r+  +  i  i+    q  p  s +i++ n  td+ +k+v n+i +++ +++
  gi|385806085|ref|YP_005842483.1|  54 SFYSVQELAEEIKTIEGKISVLIPARNSENyiISSILSAFNQSVPPKSIYILNDNS-TDNTIKKVMNFISQKNGKLK 129
                                       5566778889999999999999998865442155799999************9886.9****************999 PP

                           FAM199X 193 asstreswkrssyssastsgv 213
                                         + ++++   sy+   + g+
  gi|385806085|ref|YP_005842483.1| 130 RVIYKDKYIFISYDVKRSDGI 150
                                       999999998888877766665 PP

>> BRCT_2  BRCT domain, a BRCA1 C-terminus domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.42   9.3e+02      19      44 ..      56      84 ..      43      97 .. 0.71
   2 ?    9.8   0.8   0.00046         1       7      64 ..      99     157 ..      92     160 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.42
                            BRCT_2 19 psreklkklIeknGGevveti...tsavy 44
                                      +s ++l++ I++  G+++  i   +s++y
  gi|385806085|ref|YP_005842483.1| 56 YSVQELAEEIKTIEGKISVLIparNSENY 84
                                      46789999999999999665533243444 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00046
                            BRCT_2   7 glrFYindaeps.psreklkklIeknGGevvetitsavyiviaesneeelaekrkrrvv 64 
                                       + + Yi +++   ++++k+   I + +G+++++i +++yi+i+   + ++  k + +vv
  gi|385806085|ref|YP_005842483.1|  99 PKSIYILNDNSTdNTIKKVMNFISQKNGKLKRVIYKDKYIFISYDVKRSDGIKVEINVV 157
                                       5689**8555555**********************999999988877766666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (488 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       905  (0.0504769); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.69u 0.36s 00:00:01.04 Elapsed: 00:00:00.55
# Mc/sec: 2681.57
//
Query:       gi|385806086|ref|YP_005842484.1|  [L=421]
Description: SufS subfamily cysteine desulfurase [Fervidicoccus fontis Kam940]
Scores for 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-140  468.9   0.2   1.2e-140  468.8   0.2    1.0  1  Aminotran_5      Aminotransferase class-V
      5e-09   35.9   0.1    7.7e-09   35.3   0.1    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    1.5e-08   34.2   0.1    8.8e-08   31.7   0.1    1.9  2  Aminotran_1_2    Aminotransferase class I and II
      2e-07   29.9   0.2    3.7e-07   29.0   0.2    1.5  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    1.3e-06   27.9   0.0    1.5e-06   27.7   0.0    1.2  1  Beta_elim_lyase  Beta-eliminating lyase
    8.8e-05   21.7   0.1    0.00016   20.8   0.1    1.4  1  SelA             L-seryl-tRNA selenium transferase
  ------ inclusion threshold ------
      0.021   13.4   0.3      0.035   12.6   0.3    1.4  1  Met_gamma_lyase  Methionine gamma-lyase
      0.033   12.9   0.0      0.071   11.8   0.0    1.7  1  Pyridoxal_deC    Pyridoxal-dependent decarboxylase conserved 


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 !  468.8   0.2  5.2e-144  1.2e-140       1     371 []      25     395 ..      25     395 .. 1.00

  Alignments for each domain:
  == domain 1  score: 468.8 bits;  conditional E-value: 5.2e-144
                                       EEEBTTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHH CS
                       Aminotran_5   1 iyldsaAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlv 77 
                                       +y+d+aAttq p++V++a++++y  ynanvhr+ h+l++ea++ +ee  e++a++in +  ee+i t +tt+ain+v
  gi|385806086|ref|YP_005842484.1|  25 VYFDNAATTQRPKQVVEAIAKFYLYYNANVHRGFHTLSQEASQLFEESYEEIAKFINGNM-EETILTINTTDAINIV 100
                                       7**********************************************************7.**************** PP

                                       HHHCCCC.-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTT CS
                       Aminotran_5  78 alslars.lkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtG 153
                                       a++++ + lk+gdeiv+t++ehh+n++pw+ela+ tgak+k++ ++e+gel+ ++le++++e+tk+va+t +snv G
  gi|385806086|ref|YP_005842484.1| 101 AYGWGLRnLKKGDEIVTTVMEHHSNMLPWRELAELTGAKIKYVDITEDGELNYKDLESKITERTKIVAFTLASNVVG 177
                                       ****9999********************************************************************* PP

                                       EB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTTTTSSTT-EEEEEEHHHHHTS..SS.STTS CS
                       Aminotran_5 154 tiqpveeigklakkkgalvlvDaaqavghipidvkklgvDflafsghKllgPtGiGvlyvrkellekleplllggem 230
                                       ti++ ++i++la+ ++a+v++D+aq v+h + dvkk++vDflafsghK+lgPtGiG+l+++ke+le+++p+ +gg++
  gi|385806086|ref|YP_005842484.1| 178 TINDYKKIVNLAHSVEAIVIADGAQYVPHVETDVKKMDVDFLAFSGHKMLGPTGIGILWGKKEILEEMKPFRVGGDT 254
                                       ***************************************************************************** PP

                                       EEEEETTEEEEHCTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CT CS
                       Aminotran_5 231 veevsleettfaeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyllerlkslpgvrlygpdkaer 307
                                       +++v+l++ ++++ p++f aGTp++ag+igl++a++yl++ig++ +++h+ el +++ + +k++++++++gp + e+
  gi|385806086|ref|YP_005842484.1| 255 IKDVTLDNVVWHDLPWRFDAGTPHIAGVIGLAEAVRYLKKIGMDGVRAHDIELVKHTIKLMKEIDDIEILGPLDPEK 331
                                       ***************************************************************************** PP

                                       CBSEEEEEETTCSHHHHHHHHHHTTEEEEEE-TTTHHHHHHTT.S-EEEEE--TTS-HHHHHHH CS
                       Aminotran_5 308 rasivsfnfkgvhaedvatlLdeegIavrsGhhcaqplmkrlalegtvRaSlyiynteeevdrl 371
                                       r+++v+fn+kg+h++ va++Ld +gIavrsG hca+pl+ rl+ +g+vRaS yiynt+eevd++
  gi|385806086|ref|YP_005842484.1| 332 RTGLVAFNIKGLHHHIVAKALDMYGIAVRSGGHCAHPLHYRLNYQGSVRASYYIYNTKEEVDYF 395
                                       **************************************************************87 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 !   35.3   0.1   3.4e-12   7.7e-09      22     147 ..      63     202 ..      47     233 .. 0.82

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 3.4e-12
                                       SHHHHHHHH...HHHHHHT..-SEEEEESSHHHHHHHHHHHTTTT...TT-EEEEESSS-THHH....HHHHHTT-E CS
                   DegT_DnrJ_EryC1  22 gpeveeFEk...afaaylg..vkhaiavssGtaAlhlaLralgvg...pgdeVIvpsltFvata....navlelgak 86 
                                        +  + FE+   ++a++++  ++  i + + t+A+ ++    g+    +gde++++ +   + +    + +  +gak
  gi|385806086|ref|YP_005842484.1|  63 QEASQLFEEsyeEIAKFINgnMEETILTINTTDAINIVAYGWGLRnlkKGDEIVTTVMEHHSNMlpwrELAELTGAK 139
                                       55566666422268888876789999*********9988775544555********999999872223557778*** PP

                                       EEEE-B-TTTSSB-GGGCGGG--TTEEEE...EEB-GGGB---HHHHHHHHHHCT-EEEEE-TT CS
                   DegT_DnrJ_EryC1  87 pvfvDvdpdtynidpaaieaaitertkaI...lpVhlyGqvadmdalkaiaakhglkvieDaAh 147
                                         +vD++ ++  ++ +++e++itertk +   l+ +++G ++d +++ ++a++ + +vi D A+
  gi|385806086|ref|YP_005842484.1| 140 IKYVDIT-EDGELNYKDLESKITERTKIVaftLASNVVGTINDYKKIVNLAHSVEAIVIADGAQ 202
                                       ******9.89****************7763336789**************************98 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.1   3.9e-11   8.8e-08      44     244 ..      67     246 ..      26     251 .. 0.76
   2 ?    0.1   0.0      0.16   3.6e+02     318     363 .]     345     399 ..     307     399 .. 0.83

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 3.9e-11
                                       THHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHH..HTTT-EEEEEESS-TH....HHHHHHHTT CS
                     Aminotran_1_2  44 dglpeleealakflgrseklklkreaavvvgsGagaliealifllk..lnpgdeilvpdptyas....yknilrlsg 114
                                       ++  e  e++akf++       + e ++++++ ++a++ ++       l +gdei+     + s      + ++l g
  gi|385806086|ref|YP_005842484.1|  67 QLFEESYEEIAKFIN------GNMEETILTINTTDAINIVAYGWGLrnLKKGDEIVTTVMEHHSnmlpWRELAELTG 137
                                       446677789999999......88999**********99998654322378******99988754333357899999* PP

                                       SEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTT CS
                     Aminotran_1_2 115 gevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYa 191
                                       +++ ++ ++  ed +l+ ++le +++e      +tk+++++ ++N  Gt+ + ++++ l   a++ +++++ D a  
  gi|385806086|ref|YP_005842484.1| 138 AKIKYVDIT--EDGELNYKDLESKITE------RTKIVAFTLASNVVGTINDYKKIVNL---AHSVEAIVIADGAQY 203
                                       *******99..****************......***************99888888888...888889*****9843 PP

                                       TCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHH CS
                     Aminotran_1_2 192 gfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlr 244
                                       +   +         +v++ + ++++ s  K +G +G  +G++ g++++++ ++
  gi|385806086|ref|YP_005842484.1| 204 VPHVE--------TDVKKMDVDFLAFSGHKMLGPTG--IGILWGKKEILEEMK 246
                                       33333........46777777888888888888888..888888888888776 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.16
                                       HHHHHHHHHTCTEEEEEGGGGTS........TTEEEEEC.TTS-HHHHHHHHHHH CS
                     Aminotran_1_2 318 kelskkLleevgvyvtpgtsftv........pgrlRitv.Aglteeeleelveal 363
                                       + +  k l+ +g++v+ g ++          +g++R ++    t+ee++++ve+l
  gi|385806086|ref|YP_005842484.1| 345 HHIVAKALDMYGIAVRSGGHCAHplhyrlnyQGSVRASYyIYNTKEEVDYFVEKL 399
                                       4566678889999999999998888999999999999999999999999999986 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 !   29.0   0.2   1.6e-10   3.7e-07      54     200 ..      81     227 ..      29     248 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 1.6e-10
                                       HHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEEST.....T CS
                   Cys_Met_Meta_PP  54 rsvleeriaaLeggeaalavssGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdt.....s 125
                                       + ++ee+i +++ ++a  +v+ G +       + lk+Gdeiv++   + +     +++++ +g ++k+vd       
  gi|385806086|ref|YP_005842484.1|  81 NGNMEETILTINTTDAINIVAYGWGL------RNLKKGDEIVTTVMEHHSNMLPWRELAELTGAKIKYVDItedgeL 151
                                       55555555555555555555555543......36899******9999999999999**************9554445 PP

                                       SHHHHHHHCCTTEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGTTTHTTTS-GG.GGT-SEEEEETTTTT CS
                   Cys_Met_Meta_PP 126 dleelekaikentklvylEtptnpllkvvDiekiaklakkagvlvvvDntfaspllqrpl.klgaDivvhSaTKyl 200
                                       + ++le++i+e+tk+v +   +n +  + D +ki++la++++++v+ D + + p +   + k+++D    S+ K l
  gi|385806086|ref|YP_005842484.1| 152 NYKDLESKITERTKIVAFTLASNVVGTINDYKKIVNLAHSVEAIVIADGAQYVPHVETDVkKMDVDFLAFSGHKML 227
                                       67899*********************************************99995555441678888888887776 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0   6.9e-10   1.5e-06      68     216 ..     109     282 ..      53     405 .. 0.75

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 6.9e-10
                                       --TTEEEEEETT.-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB CS
                   Beta_elim_lyase  68 lqrgeevivtep.ahihfdetgaiaelagvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGq 143
                                       l++g+e++ t    h  +   + +ael g+k + +++ e+G+++ ++le++i+e      ++k++  t + n+    
  gi|385806086|ref|YP_005842484.1| 109 LKKGDEIVTTVMeHHSNMLPWRELAELTGAKIKYVDITEDGELNYKDLESKITE------RTKIVAFTLASNV---- 175
                                       466777766654345555556999******************************......589*********8.... PP

                                       ---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHHTTSSEEEEESSSTT--SS-.EEEEE-HH...... CS
                   Beta_elim_lyase 144 vvsleelrevaaiakkygiplhlDgARfanaakslgeivkemfsyvDsvtmslkKdllanvG.gvlafrddel.... 215
                                       v +++  +++ ++a++ +  ++ DgA ++    +++ +vk+m   vD + +s+ K  l + G g+l ++++ l    
  gi|385806086|ref|YP_005842484.1| 176 VGTINDYKKIVNLAHSVEAIVIADGAQYVP---HVETDVKKM--DVDFLAFSGHKM-LGPTGiGILWGKKEILeemk 246
                                       778899999*****************9986...56999**99..8**********7.568999******99556666 PP

                                       .................................... CS
                   Beta_elim_lyase 216 ...................................e 216
                                                                           
  gi|385806086|ref|YP_005842484.1| 247 pfrvggdtikdvtldnvvwhdlpwrfdagtphiagV 282
                                       666666666666666666666666655555555552 PP

>> SelA  L-seryl-tRNA selenium transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   7.2e-08   0.00016     191     234 ..     202     246 ..     131     251 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 7.2e-08
                                       ----BHHHHHHT.T-SEEEEETTSTT-SSS-EEEEE-HHHHHHHH CS
                              SelA 191 skePtvqealae.GvdlvsfsGDkllGgpqaGiivGkkelieklk 234
                                       ++ P+v+  +++  vd ++fsG k+lG    Gi+ Gkke++e++k
  gi|385806086|ref|YP_005842484.1| 202 QYVPHVETDVKKmDVDFLAFSGHKMLGPTGIGILWGKKEILEEMK 246
                                       445666655543279****************************98 PP

>> Met_gamma_lyase  Methionine gamma-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.3   1.6e-05     0.035      80     226 ..      91     228 ..      69     255 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.6e-05
                   Met_gamma_lyase  80 vsGthaiatalfg....vlrpgdellaitGkPydtleeviGlrgegqgslkdfgikykevdlleegkvdieavkeai 152
                                       ++ t ai ++ +g    +l+ gde+++ + + +  +   +  r  +   l   +iky  vd++e+g+++++ ++++i
  gi|385806086|ref|YP_005842484.1|  91 INTTDAINIVAYGwglrNLKKGDEIVTTVMEHHSNM---LPWR--ELAELTGAKIKY--VDITEDGELNYKDLESKI 160
                                       566666666666544444666666666554444333...3333..334466666666..999*************** PP

                   Met_gamma_lyase 153 kektkliliqrskGyserkslsieeieeiiklvkeinedvivfvdncyGefveekePtevGadliaGsliknpG 226
                                       +e+tk+++       ++    +i++ ++i++l ++++  +++     y   ve+ +  ++ +d++a s  k  G
  gi|385806086|ref|YP_005842484.1| 161 TERTKIVAFTL----ASNVVGTINDYKKIVNLAHSVEA-IVIADGAQYVPHVET-DVKKMDVDFLAFSGHKMLG 228
                                       *******9865....44566789999999999888754.333333456666665.3456677777777666665 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 ?   11.8   0.0   3.2e-05     0.071     157     288 ..     128     245 ..     113     341 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.2e-05
                                       HHHHHHHHHT-EEEEE--BTTTBB-HHHHHHHHHHHHCTT.EEEEEEEEBS-TTT-BB--HHHHHHHHHHCT-EEEE CS
                     Pyridoxal_deC 157 svekaalvlgvklrvipldengklrgaalekaieedkekGlipffvvatlGttvlgaFddlkelgdicekydlwlHv 233
                                        +++ a+++g k++++ ++e+g+l  ++le +i e+ +       v+ tl + v+g  +d k++ ++ +  +  +  
  gi|385806086|ref|YP_005842484.1| 128 PWRELAELTGAKIKYVDITEDGELNYKDLESKITERTKI------VAFTLASNVVGTINDYKKIVNLAHSVEAIVIA 198
                                       48999****************************998765......788999999***9*****99999998888777 PP

                                       E-TTGGGGGGSGGGGGGGTTGGGESEEEEECCCCTS--SS-EEEEESSCCGCHHH CS
                     Pyridoxal_deC 234 DAAyaGsaficpeirhllkgieradSitvnphKlllvlldcsalivkdkealqqa 288
                                       D A        p++ + +k+++ +d +++++hK+l+ + +++ l+ k+ e+l++ 
  gi|385806086|ref|YP_005842484.1| 199 DGAQ-----YVPHVETDVKKMD-VDFLAFSGHKMLG-PTGIGILWGKK-EILEEM 245
                                       7554.....4599999888887.7999999999765.78999888765.555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       914  (0.0509789); expected 358.6 (0.02)
Passed bias filter:                      705  (0.0393218); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); 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 0.31s 00:00:01.02 Elapsed: 00:00:00.53
# Mc/sec: 2393.02
//
Query:       gi|385806087|ref|YP_005842485.1|  [L=90]
Description: hypothetical protein FFONT_1045 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       722  (0.04027); 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:                         0  (0); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 573.13
//
Query:       gi|385806088|ref|YP_005842486.1|  [L=121]
Description: hypothetical protein FFONT_1046 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); 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 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 786.48
//
Query:       gi|385806089|ref|YP_005842487.1|  [L=108]
Description: hypothetical protein FFONT_1047 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       234  (0.0130515); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); 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: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 699.84
//
Query:       gi|385806090|ref|YP_005842488.1|  [L=505]
Description: Queuine/archaeosine tRNA-ribosyltransferase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-67  227.7   0.0    3.1e-67  227.2   0.0    1.1  1  TGT              Queuine tRNA-ribosyltransferase
    8.4e-05   22.5   0.2     0.0003   20.7   0.2    2.0  1  DUF5591          Domain of unknown function (DUF5591)
  ------ inclusion threshold ------
      0.023   14.9   0.0       0.06   13.6   0.0    1.7  1  DNA_Packaging_2  DNA packaging protein
      0.039   13.6   0.0      0.093   12.4   0.0    1.6  1  40S_S4_C         40S ribosomal protein S4 C-terminus


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 !  227.2   0.0   6.9e-71   3.1e-67       3     349 ..      10     329 ..       6     330 .. 0.94

  Alignments for each domain:
  == domain 1  score: 227.2 bits;  conditional E-value: 6.9e-71
                                       EEEEEEEETTEEEEESEEEEBETTSSBTTB-HHHHH.HTTES-EEEEHHHHHHTTTHHHHHHTTHHHHHHT--S..- CS
                               TGT   3 aRlGklelphgtietPafmpvgtqgtvkgltpdelkeelgaqiilsntyhlelrpgeelvakagglhkflgwdk..p 77 
                                       +R+G+++++++tietP ++pv   +t +++    +k ++g + +++n+y  + + g +      ++h+++g d+   
  gi|385806090|ref|YP_005842488.1|  10 GRIGRIKIKGKTIETPYLFPV-IDPTRQEVPISSIK-SMGFNGVITNAYLAY-KRGWNR-----DIHELIG-DGelV 77 
                                       8********************.9999999******5.89**********888.444444.....79*****.55366 PP

                                       EEEE-SHHHHHHHEEEESSEEEEE-TTTS-EEEE-HHHHHHHHHHHT-SEEE-------SS--HHHHHHHHHHHHHH CS
                               TGT  78 iltdsggfqvfslkkiteegvsfqsridGskvlltpeesieiqeklgsDiimalddvvpspaskkrveksverTlrw 154
                                       ++tdsg++q++++                + +++++ee+i+iq+ l+sDi+++ld ++  + ++++++   e+Tlr+
  gi|385806090|ref|YP_005842488.1|  78 VMTDSGAYQLMQY---------------NN-IEVSNEEIIKIQKGLNSDIAVILDVPTGDSLDQNYAKWTAEETLRR 138
                                       *********7764...............45.9************************999999*************** PP

                                       HHHHHHHH....SEEEEEE--TT-HHHHHHHHHHHHHH--SEEEE-S.SSSSS..HHHHHHHHHHHHGGGS-TTS-E CS
                               TGT 155 ldrcleah....qalfgivqGglyedlreesaeelakrdfdgyaigG.lsvge..ekeellevveavtellpedkpr 224
                                       + ++ +       +++ ++qGg++ +  ees ++ +++++d yaig+  +++e  +++ +l+++  v+e++ +d p 
  gi|385806090|ref|YP_005842488.1| 139 ASEAQKIIdrdnRMWVLPIQGGIHLSILEESSKKSSQLEYDIYAIGSpTKFMEryRYDVVLDMIRIVRENIRADVPL 215
                                       **999776888666*********************************888***8999******************** PP

                                       EETTB-SHHHHHHHHHTT--EEEESHHHHHHHTTEEEETTEEEETTSGGGTT--SBSSSS--SHHHHH-BHHHHHHH CS
                               TGT 225 ylmGvgtPedlleavalGvDmfdcvyptrtarngraltsegelnlknakyaedfspldegCsCytCknytraylhhl 301
                                       +l+G+g+P+ +  ava+GvD+fd++ +++ ar+gr++++ g+l+l++ +y     p    CsC++C++yt+++l+++
  gi|385806090|ref|YP_005842488.1| 216 HLFGAGHPMIIPFAVAMGVDLFDSASYILFARDGRYMIEGGTLRLEDIEYF----P----CSCPICSRYTPKELKNM 284
                                       ***************************************************....9....******99********* PP

                                       HHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHT CS
                               TGT 302 lktkemlgaiLltiHNlhyylelfkriReaIkegtfeefveefarkye 349
                                        k ++   ++Ll++HNl+++++ ++++++aI+eg+++e+ +++ rk++
  gi|385806090|ref|YP_005842488.1| 285 NKDER---TRLLAEHNLYMIKKILNEVKQAINEGRLWELLQSYSRKHP 329
                                       99888...*************************************997 PP

>> DUF5591  Domain of unknown function (DUF5591)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.2   6.7e-08    0.0003      50     108 ..     408     464 ..     373     498 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 6.7e-08
                                       ..SEEEEE-SS-.EEEGGGTT----------------HHHHHHHHHHHHHHHHHHT-SE CS
                           DUF5591  50 akvheviltsPlGvvPreleevYPaaqYdiavtgewseeeiefvaellakylektkyek 108
                                       +  h + +   +G++P+el  +YP  q    ++++ s e+++ +a+ + ky+ek++ + 
  gi|385806090|ref|YP_005842488.1| 408 EGKHYIYYAPGIGLIPQELSGTYPWGQNV--IPSKISYETMQSIANDVVKYIEKFSDKY 464
                                       35688889999***************965..5566999***************987643 PP

>> DNA_Packaging_2  DNA packaging protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.3e-05      0.06      21      73 ..     319     368 ..     303     374 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.3e-05
                   DNA_Packaging_2  21 adLsdherrsnqlylainkLkDkhkeqiGklqPDvtilGGlaGvLeeykekvg 73 
                                         L  + r+ + ly a n++k+kh e + k  P v+   G + +++ + ++ +
  gi|385806090|ref|YP_005842488.1| 319 ELLQSYSRKHPSLYSAFNNIKNKHVEWMEKYTPRVK---GEQKAIYLFDNDSM 368
                                       5577889**************************886...66677777777766 PP

>> 40S_S4_C  40S ribosomal protein S4 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.1e-05     0.093      21      46 ..     150     174 ..     145     175 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.1e-05
                                       TS-SS---SS-S----HHHHHHHHHH CS
                          40S_S4_C  21 nkpwvsLPkgkGiklsiaeerdkrla 46 
                                       n+ wv LP + Gi+lsi+ee  k+ +
  gi|385806090|ref|YP_005842488.1| 150 NRMWV-LPIQGGIHLSILEESSKKSS 174
                                       56666.99*************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (505 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       955  (0.0532657); expected 358.6 (0.02)
Passed bias filter:                      633  (0.0353059); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 3251.42
//
Query:       gi|385806091|ref|YP_005842489.1|  [L=88]
Description: hypothetical protein FFONT_1049 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.31s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 556.28
//
Query:       gi|385806092|ref|YP_005842490.1|  [L=702]
Description: cationic amino acid transporter (cat-1) [Fervidicoccus fontis Kam940]
Scores for complete 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-37  127.3  61.2    8.6e-37  127.0  61.2    1.1  1  AA_permease_2  Amino acid permease
    1.2e-34  119.8  58.0    1.6e-34  119.3  58.0    1.1  1  AA_permease    Amino acid permease
    3.8e-05   24.2   0.0    8.4e-05   23.1   0.0    1.5  1  Usp            Universal stress protein family
  ------ inclusion threshold ------
      0.029   14.4   0.8        0.1   12.7   0.8    1.9  1  DUF1106        Protein of unknown function (DUF1106)


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 !  127.0  61.2   1.9e-40   8.6e-37       2     408 ..       5     421 ..       4     434 .. 0.77

  Alignments for each domain:
  == domain 1  score: 127.0 bits;  conditional E-value: 1.9e-40
                     AA_permease_2   2 sllsafalvigsvigsgifvkn...laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkk 75 
                                       + l +f++ +g+++g  i+v      ++sg   +i++++ +++i  +  +l+y E++sa+p  gG + ++k +++++
  gi|385806092|ref|YP_005842490.1|   5 GNLHTFFIGLGAIVGGSIVVLIgpiIYLSGSLGAIIVLIMSAIIA-TLTALIYSEITSAIPEVGGGFLWAKLTMPRP 80 
                                       567899999999988555554445756666666777777777777.689*******777****************** PP

                     AA_permease_2  76 vaflsawfnwfayvpvlasilsvaasyllnalgp......dlqgntwltyliaiaililvalinirgikesakiqni 146
                                       + f+s+w nw+a + + ++++ ++ s++l++l++      +l +  +  +liai+++i +a +n+ g+++++++  +
  gi|385806092|ref|YP_005842490.1|  81 FPFISGWVNWMAHMMGGTFYALSFSSMFLQFLAEigfnipFLPP-YISERLIAIILIIAFAYLNYSGVSKTGRFSIV 156
                                       *******************************9985555544433.4566**************************** PP

                     AA_permease_2 147 lgilkillpliiliilglitvdgggfsslstetdt.ffpngwpgvllgllivlwsfdGfesaanvsee..vkkkdvp 220
                                       +gi+ +   ++++  +g++ + ++g   +   ++   f+++++ ++ ++  v+ +f G+e  a+ +ee  +++k++p
  gi|385806092|ref|YP_005842490.1| 157 IGIFFVA-SILLFSTIGIFSGIKSGELINGLLNSPaKFTSVSS-FFIAMISVVIAFEGYEILAQTAEEtkAPTKNLP 231
                                       ******5.8889999******9999986633333313444444.5666667999**************555569*** PP

                     AA_permease_2 221 kaifigllivlvlyllvniaflgvvpddeianlsn.lgsvaalffeavggkvvaiivvilialsllgaintavigss 296
                                       +ai+  l+++++ly+ v+i+ +g+++ +  + +    ++++   +  ++ + + iiv++++   +l +in+ ++++s
  gi|385806092|ref|YP_005842490.1| 232 RAIMETLIVATILYISVTISTIGILGTKAYSLSTIwGPDTVIRTASLAF-RYGGIIVAAGGLATVLSSINSIMYSAS 307
                                       ***************************8876544413445566666666.788999999****************** PP

                     AA_permease_2 297 rvlealardgvlPrffakvn.kfgspiraiiltaivslillllfllassaaynfllsvsslgliisylllii..gal 370
                                       rvl a++r g++P +f+ ++ k+ +p+++i +t+ v +i++l++        ++ ls++ +g+++ +l++i+  +++
  gi|385806092|ref|YP_005842490.1| 308 RVLLAMSRAGEFPIVFSEIHkKYRTPSNSILFTMAVMIIMSLIL--------DLTLSAFIVGVLFNVLFIIVnyTGI 376
                                       ********************9***************86665444........4444444444444444443300444 PP

                     AA_permease_2 371 ilrkkrphlkr.....pgk..ilvaiigalfllfllvalffppkg 408
                                       +lr    ++ +     p++  i+++ +++ ++lf+ +++++p+++
  gi|385806092|ref|YP_005842490.1| 377 KLREFYGEKLKykfltPYYplIPLTGLIIKVFLFFAALIIYPSAT 421
                                       444333333222345544455677777777777777888888654 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.3  58.0   3.6e-38   1.6e-34       1     457 [.       8     430 ..       8     448 .. 0.87

  Alignments for each domain:
  == domain 1  score: 119.3 bits;  conditional E-value: 3.6e-38
                       AA_permease   1 hvlvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfv 77 
                                       h ++i lg ++G  + v +g ++   G lga+++++++ ++ +l++l+ +ei +++p++gg   +a+ ++ + + f 
  gi|385806092|ref|YP_005842490.1|   8 HTFFIGLGAIVGGSIVVLIGPIIYLSGSLGAIIVLIMSAIIATLTALIYSEITSAIPEVGGGFLWAKLTMPRPFPFI 84 
                                       7789*****************************************************8888889************* PP

                       AA_permease  78 iGlnylfswitvlal.eltaasiliqfwelvtdlpkawvt........gavflvvlliinlvgvkvygeaefilali 145
                                        G+  ++   ++ ++ +l  +s+++qf+  +  ++  +          ++++++++  +n+ gv   g++++++ ++
  gi|385806092|ref|YP_005842490.1|  85 SGWVNWMAHMMGGTFyALSFSSMFLQFLAEIGFNI-PFLPpyiserliAIILIIAFAYLNYSGVSKTGRFSIVIGIF 160
                                       ****8888888777635667888999997776666.66668999999899999999*************99999999 PP

                       AA_permease 146 kiiaiiafiivg.iillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaii 221
                                        + +i+ f  +g ++++ +g++ +g     l++++      +++         +++f+++++ vv af G+e++a +
  gi|385806092|ref|YP_005842490.1| 161 FVASILLFSTIGiFSGIKSGELING----LLNSPAK-----FTS---------VSSFFIAMISVVIAFEGYEILAQT 219
                                       9999999999997777778888888....6666666.....444.........589********************* PP

                       AA_permease 222 agEvkdPeksiPkailqvviritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinavilt 298
                                       a+E+k P k++P+ai+ ++i  ti+Y+ ++++ + ++++++ +l +  + + +  vi + ++  ++ + +++a+ l+
  gi|385806092|ref|YP_005842490.1| 220 AEETKAPTKNLPRAIMETLIVATILYISVTISTIGILGTKAYSLST--IWG-PDTVIRTASLAFRYGGIIVAAGGLA 293
                                       *****************************************99988..655.689999******************* PP

                       AA_permease 299 aalssansslysasRvlyslakdglaP.kvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisal 374
                                       ++lss+ns++ysasRvl ++++ g +P  + + ++k++ P ++il++m++  ++ l+  l+l+          i+++
  gi|385806092|ref|YP_005842490.1| 294 TVLSSINSIMYSASRVLLAMSRAGEFPiVFSEIHKKYRTPSNSILFTMAVMIIMSLILDLTLS--------AFIVGV 362
                                       ***************************88889999****************************........456677 PP

                       AA_permease 375 iglivwlliilsylrfRkalkyqgrsieelgfkaallplgvilvlaaliiillilalyayltvkkgpkdwgaasfaa 451
                                        + +++++++++ +++R     +g ++ + +f ++++pl++ ++l++ ++++ ++ ++++ +           + +a
  gi|385806092|ref|YP_005842490.1| 363 LFNVLFIIVNYTGIKLREF---YGEKL-KYKFLTPYYPLIPLTGLIIKVFLFFAALIIYPSA-----------TLFA 424
                                       7777788888888877776...66666.899**************99999888877776554...........2333 PP

                       AA_permease 452 aylivl 457
                                       + liv+
  gi|385806092|ref|YP_005842490.1| 425 LLLIVI 430
                                       333333 PP

>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   1.9e-08   8.4e-05       4     139 ..     463     583 ..     462     589 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.9e-08
                                       EEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTC CS
                               Usp   4 rIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggv 80 
                                       rI+V +   e  +++++ A + aka+++e+ ll +i+++ + +v+d++ ea ++   + ++  + +      e g+ 
  gi|385806092|ref|YP_005842490.1| 463 RIMVLL-PPEIRTNLIQLASDIAKAKNGEINLLKIIKTPYQLSVKDYRNEAVKKDVRSLKDIIDHL-----NETGIH 533
                                       688888.888899***********************************************999865.....588999 PP

                                       EEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEE CS
                               Usp  81 kvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlv 139
                                       ++  +    ++ e+i+   +ee +dl+++ + +  +l  ++  S+         c+ l+
  gi|385806092|ref|YP_005842490.1| 534 ARYSIKAARSKTEAIIASIDEERIDLLIMSAEDAMKLNSVMRLST---------CDILI 583
                                       999999999**********************99555555444444.........44444 PP

>> DUF1106  Protein of unknown function (DUF1106)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.8   2.2e-05       0.1      62      87 ..     602     627 ..     580     632 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.2e-05
                           DUF1106  62 llynkkeyvfdklkelfpdeaiefsi 87 
                                       +l +  +y++d +ke+fpd  ie  i
  gi|385806092|ref|YP_005842490.1| 602 ILSEDEKYIVDEVKEIFPDREIEEII 627
                                       5778899************9997433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (702 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1200  (0.0669307); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); 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):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 4722.75
//
Query:       gi|385806093|ref|YP_005842491.1|  [L=83]
Description: hypothetical protein FFONT_1051 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0035   16.8   2.0     0.0059   16.1   2.0    1.5  1  YvrJ          YvrJ protein family
     0.0075   15.7   2.5     0.0077   15.6   1.3    1.6  2  Helo_like_N   Fungal N-terminal domain of STAND proteins
      0.009   16.6   0.9      0.009   16.6   0.9    2.2  2  SlyX          SlyX
  ------ inclusion threshold ------
       0.02   14.8   0.6      0.023   14.6   0.6    1.1  1  SMC_Nse1      Nse1 non-SMC component of SMC5-6 complex
      0.048   14.0   2.1      0.059   13.7   2.1    1.2  1  BLOC1_2       Biogenesis of lysosome-related organelles compl
      0.069   12.0   5.4      0.078   11.9   5.4    1.0  1  Spc7          Spc7 kinetochore protein
      0.092   12.3   5.8        0.1   12.1   5.8    1.1  1  TMCO5         TMCO5 family
      0.096   13.3   1.0       0.11   13.0   1.0    1.1  1  Syntaxin-6_N  Syntaxin 6, N-terminal
       0.19   12.0   4.1       0.13   12.5   1.1    1.9  2  Spc24         Spc24 subunit of Ndc80
       0.21   11.7   2.1       0.32   11.2   2.1    1.3  1  Fib_alpha     Fibrinogen alpha/beta chain family
       0.34   10.9   2.2       0.38   10.8   2.2    1.3  1  DUF730        Protein of unknown function (DUF730)
       0.38   10.8   2.8       0.49   10.4   2.8    1.2  1  DUF1664       Protein of unknown function (DUF1664)
        1.8    8.9   9.4       0.46   10.8   3.1    2.1  2  ABC_tran_CTD  ABC transporter C-terminal domain
        5.2    6.7   7.3        8.4    6.0   7.3    1.4  1  TPD52         Tumour protein D52 family


Domain annotation for each model (and alignments):
>> YvrJ  YvrJ protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   2.0   4.6e-06    0.0059      16      35 ..      64      83 .]      57      83 .] 0.95

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.6e-06
                              YvrJ 16 LvRiEkkLdeLtksIeeLse 35
                                      +vRiE+kL  L k I+eL++
  gi|385806093|ref|YP_005842491.1| 64 IVRIEEKLALLEKKINELNK 83
                                      59****************85 PP

>> Helo_like_N  Fungal N-terminal domain of STAND proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.51   6.5e+02     191     198 ..      19      26 ..       2      45 .. 0.47
   2 !   15.6   1.3     6e-06    0.0077     144     181 ..      42      79 ..      32      83 .] 0.84

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.51
                       Helo_like_N 191 lqrlkeEr 198
                                       +q++ +E 
  gi|385806093|ref|YP_005842491.1|  19 IQKVVDEV 26 
                                       22222222 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 6e-06
                       Helo_like_N 144 taevleeykeliedttsdLeehLedideklealtekse 181
                                       + e l ey + i+++ + Leeh+ +i+ekl+ l +k +
  gi|385806093|ref|YP_005842491.1|  42 EGEELVEYMQAIAHALEHLEEHIVRIEEKLALLEKKIN 79 
                                       5577889************************9997655 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.2      0.36   4.6e+02      38      57 ..      17      36 ..       5      61 .. 0.56
   2 !   16.6   0.9     7e-06     0.009       1      24 [.      60      83 .]      60      83 .] 0.96

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.36
                                      HHHHHHHHT-XXXXXXXXXX CS
                              SlyX 38 rqlrllaerlkeleessgas 57
                                      + ++++++++ +  ++++ +
  gi|385806093|ref|YP_005842491.1| 17 QDIQKVVDEVMSTHPEMAHE 36
                                      44444444444444444322 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 7e-06
                                      HHHHHHHHHHHHHHHHHHHHHHHH CS
                              SlyX  1 leerleeLEiklafqedtieeLnd 24
                                      lee+++++E+kla +e+ i+eLn+
  gi|385806093|ref|YP_005842491.1| 60 LEEHIVRIEEKLALLEKKINELNK 83
                                      699********************6 PP

>> SMC_Nse1  Nse1 non-SMC component of SMC5-6 complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.6   1.8e-05     0.023      15      68 ..      15      71 ..       8      81 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.8e-05
                          SMC_Nse1 15 teeelkkvlaailsae...eevspeditqedleeyiakinealspldyeirsvrhql 68
                                      +e++++kv  +++s +    ++++ +++ e+l ey+++i+ al+ l+  i++++++l
  gi|385806093|ref|YP_005842491.1| 15 NEQDIQKVVDEVMSTHpemAHEHHHEEEGEELVEYMQAIAHALEHLEEHIVRIEEKL 71
                                      6899*********9998765555588999******************9999998765 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   2.1   4.6e-05     0.059      35      95 ..      18      78 ..       8      82 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.6e-05
                           BLOC1_2 35 kykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLEakf 95
                                       ++k+ d++ s++ ++ +    +ee +++++ +++i   +++Lee + +++e    LE+k+
  gi|385806093|ref|YP_005842491.1| 18 DIQKVVDEVMSTHPEMAHEHHHEEEGEELVEYMQAIAHALEHLEEHIVRIEEKLALLEKKI 78
                                      56788888999999999999999999999***********************999999998 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   5.4   6.1e-05     0.078     158     226 ..      12      82 ..       4      83 .] 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.1e-05
                              Spc7 158 Lekqeeeldellpeleeekaeleeeleklqeaaeelesid..keeLeelreelaelkaeieekkkelaelq 226
                                       + k+e+ ++++++e+ + + e+ +e+++++e +e +e ++     Le l e +++++++++ ++k+++el+
  gi|385806093|ref|YP_005842491.1|  12 MPKNEQDIQKVVDEVMSTHPEMAHEHHHEEEGEELVEYMQaiAHALEHLEEHIVRIEEKLALLEKKINELN 82 
                                       678999************************97777776665588999999999999999999999999987 PP

>> TMCO5  TMCO5 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   5.8     8e-05       0.1      24      91 ..      17      82 ..       3      83 .] 0.73

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8e-05
                             TMCO5 24 rkiqekeetiqslereitkldsllereedeeenfsenekedalkeLeletaklekkneiLlkevveLq 91
                                      + iq+  +++ s   e+++  + +++ee ee+   ++   +al  Le+  +++e+k ++L k+++eL+
  gi|385806093|ref|YP_005842491.1| 17 QDIQKVVDEVMSTHPEMAH--EHHHEEEGEELVEYMQAIAHALEHLEEHIVRIEEKLALLEKKINELN 82
                                      3344444555555555555..5556666777777777788999***********************97 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.0   8.9e-05      0.11       7      70 ..      16      77 ..      13      83 .] 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.9e-05
                      Syntaxin-6_N  7 keeVqkslnkaeslyrrwerlledtssstseeldetrteLrkalrsiewdledLeetvrivekn 70
                                      ++++qk ++++ s++ ++ +  e  ++++ eel e ++ +  al+ +e+ +  +ee  + +ek+
  gi|385806093|ref|YP_005842491.1| 16 EQDIQKVVDEVMSTHPEMAH--EHHHEEEGEELVEYMQAIAHALEHLEEHIVRIEEKLALLEKK 77
                                      57899999999999999965..233344589999999999999999999999999998888875 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.38   4.9e+02       5      36 ..       8      39 ..       4      50 .. 0.58
   2 ?   12.5   1.1    0.0001      0.13       6      38 ..      50      82 ..      45      83 .] 0.91

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.38
                             Spc24  5 ekfriakelsdleselesleselaelkeelee 36
                                      +++++ k+ +d+++ ++++ s+  e+ +e + 
  gi|385806093|ref|YP_005842491.1|  8 LRMTMPKNEQDIQKVVDEVMSTHPEMAHEHHH 39
                                      55566666666666666666666555555443 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.0001
                             Spc24  6 kfriakelsdleselesleselaelkeeleele 38
                                       ++ia +l++le+ + ++e++la l+++++el+
  gi|385806093|ref|YP_005842491.1| 50 MQAIAHALEHLEEHIVRIEEKLALLEKKINELN 82
                                      5789***************************98 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   2.1   0.00025      0.32      40     114 ..       8      81 ..       3      83 .] 0.49

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00025
                                       CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHH CS
                         Fib_alpha  40 leneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvlesn 114
                                       l+ ++ ++++  +++ + v +++  ++++ +++++  + + ++ + + +  + l+e i++ e+++  L + ++++
  gi|385806093|ref|YP_005842491.1|   8 LRMTMPKNEQDIQKVVDEVMSTHPEMAHEHHHEEE-GEELVEYMQAIAHALEHLEEHIVRIEEKLALLEKKINEL 81 
                                       55555555555555555555555555555544443.333344444444455555555555555555555555544 PP

>> DUF730  Protein of unknown function (DUF730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   2.2   0.00029      0.38      77     120 ..      40      83 .]       6      83 .] 0.91

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00029
                            DUF730  77 keektemkkdleaakkrvesqaekiflmekkfetlekkyeslnk 120
                                        ee  e+ + ++a  + +e   e+i+ +e+k+  lekk + lnk
  gi|385806093|ref|YP_005842491.1|  40 EEEGEELVEYMQAIAHALEHLEEHIVRIEEKLALLEKKINELNK 83 
                                       5778889999999999999999****************999986 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   2.8   0.00038      0.49      49     109 ..      18      77 ..       3      83 .] 0.44

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00038
                           DUF1664  49 qleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkea 109
                                       ++++v +++ +t  +++++ ++ +++ +e  e  ++i++ +++++e++ +i+e++  +++ 
  gi|385806093|ref|YP_005842491.1|  18 DIQKVVDEVMSTHPEMAHE-HHHEEEGEELVEYMQAIAHALEHLEEHIVRIEEKLALLEKK 77 
                                       3444444444444444443.22233344444444444444444444444444444444444 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   2.4     0.012        15      14      62 ..      16      62 ..       5      63 .. 0.79
   2 ?   10.8   3.1   0.00036      0.46       9      33 ..      56      80 ..      54      83 .] 0.90

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.012
                      ABC_tran_CTD 14 eaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeelye 62
                                      e++I++   e  + + e+a++    ++e+  el + ++++ ++Le l+e
  gi|385806093|ref|YP_005842491.1| 16 EQDIQKVVDEVMSTHPEMAHEH--HHEEEGEELVEYMQAIAHALEHLEE 62
                                      7888888888888888999887..5568888888888888888888887 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00036
                      ABC_tran_CTD  9 eleeleaeIeaLEeeiaeleaelad 33
                                       le+le++I ++Ee++a le+++++
  gi|385806093|ref|YP_005842491.1| 56 ALEHLEEHIVRIEEKLALLEKKINE 80
                                      79******************99875 PP

>> TPD52  Tumour protein D52 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   7.3    0.0066       8.4       9      61 ..      30      82 ..      14      83 .] 0.64

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0066
                             TPD52  9 tsedaaesvsasep.tlteeereeLkseLakleeeivtLrqvLaakekhlaelk 61
                                        e a+e+++++e  +l e   + + + L  lee+iv +++ La  ek++ el 
  gi|385806093|ref|YP_005842491.1| 30 HPEMAHEHHHEEEGeELVEYM-QAIAHALEHLEEHIVRIEEKLALLEKKINELN 82
                                      233333333333333444443.346778999******************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1848  (0.103073); expected 358.6 (0.02)
Passed bias filter:                      826  (0.0460706); expected 358.6 (0.02)
Passed Vit filter:                       129  (0.00719505); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 583.26
//
Query:       gi|385806094|ref|YP_005842492.1|  [L=118]
Description: hypothetical protein FFONT_1052 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-15   56.5   0.5    3.1e-15   56.3   0.5    1.0  1  RNA_pol_RpbG  DNA-directed RNA polymerase, subunit G


Domain annotation for each model (and alignments):
>> RNA_pol_RpbG  DNA-directed RNA polymerase, subunit G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3   0.5   1.7e-19   3.1e-15       6     118 ..       6     117 ..       2     118 .] 0.93

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 1.7e-19
                      RNA_pol_RpbG   6 ckvksieksklkdlkivkikcqneeielDiiselni.fkeedkveviisrekPeyldgkdFcghGylvtekeeen.k 80 
                                       +++ + ++s ++ ++i+ +++++ e+++++ ++  i  k+++k+ ++ srek + ++++ Fcg+ +l++ kee++ +
  gi|385806094|ref|YP_005842492.1|   6 LEIVDTKPSIIPTITIITARNEKIELTFEVSEKFGIsYKKGEKIFLEFSREKIKPSSSFAFCGKTTLFSIKEEKDnS 82 
                                       689999***************************966389*****************************999877669 PP

                      RNA_pol_RpbG  81 iitliSlfGllvkisskkdllnelglkvmdkvYlcvrk 118
                                        + l S  G++++  s ++l   +gl++++ +++c+ k
  gi|385806094|ref|YP_005842492.1|  83 KVYLFSSGGFIIRLVSRQEL---QGLNITEDYFFCIDK 117
                                       999**********9999999...9************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); 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: 00:00:00.47
# Mc/sec: 758.02
//
Query:       gi|385806095|ref|YP_005842493.1|  [L=146]
Description: Like-Sm ribonucleoprotein, core [Fervidicoccus fontis Kam940]
Scores for complete 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   92.7   0.1    8.7e-27   92.7   0.1    1.6  2  Lsm_C            Lsm C-terminal
    6.5e-14   51.4   0.0    1.4e-13   50.4   0.0    1.5  1  LSM              LSM domain
    7.4e-05   22.8   0.0    0.00018   21.6   0.0    1.7  1  SM-ATX           Ataxin 2 SM domain
     0.0063   17.1   0.1      0.017   15.8   0.0    1.6  2  RFX_DNA_binding  RFX DNA-binding domain
  ------ inclusion threshold ------
      0.054   13.7   0.0      0.082   13.1   0.0    1.3  1  CytadhesinP1     Trypsin-sensitive surface-exposed protein
       0.06   13.0   0.0       0.11   12.2   0.0    1.4  1  Hfq              Hfq protein


Domain annotation for each model (and alignments):
>> Lsm_C  Lsm C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.2       3.7   1.1e+04      54      60 ..      60      66 ..      59      67 .. 0.82
   2 !   92.7   0.1   2.9e-30   8.7e-27       1      63 []      78     140 ..      78     140 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 3.7
                                      HHHHHHH CS
                             Lsm_C 54 lyeeYie 60
                                      +y +Yi+
  gi|385806095|ref|YP_005842493.1| 60 IYSDYIA 66
                                      8999996 PP

  == domain 2  score: 92.7 bits;  conditional E-value: 2.9e-30
                                       HHHHHHHHHHHS...TTTEEEETTTTEEEETTTEEEETTEEE--SHHHHHHHHHHHHHHH-.. CS
                             Lsm_C   1 areFaelvekelnlrpglVkvieeanvvvvldrikVsekGVeGsGplAervyelyeeYiekkk 63 
                                       ++eFa+l++++ln+r++++k+++ea+v+v+l++i+Vs+kGVeGsGplA+++y ly+eYie+kk
  gi|385806095|ref|YP_005842493.1|  78 PDEFARLIVSKLNIREADIKTYPEAGVLVILNNIRVSDKGVEGSGPLAHKIYGLYTEYIENKK 140
                                       68***********************************************************97 PP

>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   0.0   4.5e-17   1.4e-13       2      65 ..       9      68 ..       8      70 .. 0.88

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 4.5e-17
                                      HHHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTETEEEEEEEEEEEGGGEEEE CS
                               LSM  2 flkklinkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkkekrklglvliRGnnivli 65
                                       l+ l++k+vt++lk+gr+++GtL gfD+ +N+ L++++e       + ++ ++li  + i+++
  gi|385806095|ref|YP_005842493.1|  9 ELNALLDKQVTIKLKDGRTIKGTLYGFDDKLNILLKNATENE----GNSSVPTMLIYSDYIAYL 68
                                      6899************************************88....566888888888777776 PP

>> SM-ATX  Ataxin 2 SM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   5.9e-08   0.00018       8      69 ..      10      59 ..       3      71 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 5.9e-08
                                      HHTTTTSEEEEEETTS-EEEEEEEEE-T..T--EEEEEEEETTS...........-EEEEEE CS
                            SM-ATX  8 ltslvGkevevtvknGevyeGifstvslekdfsvvLkmarkvkkanskssspssgeipdtli 69
                                      l++l  k+v++++k+G +++G +++++   ++++ Lk+a + +           ++ ++t++
  gi|385806095|ref|YP_005842493.1| 10 LNALLDKQVTIKLKDGRTIKGTLYGFDD--KLNILLKNATENEG----------NSSVPTML 59
                                      56666689********************..*********98877..........33344555 PP

>> RFX_DNA_binding  RFX DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   5.6e-06     0.017       7      50 ..      42      85 ..      38      90 .. 0.86
   2 ?   -2.3   0.1       2.4   7.2e+03      25      36 ..     128     139 ..     126     143 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.6e-06
                   RFX_DNA_binding  7 wlnanfeeaedvsvprqevYaeYlsicsklklkplnaasFgKli 50
                                      +l++  e++ ++svp   +Y++Y+++ s  +  + n+ +F++li
  gi|385806095|ref|YP_005842493.1| 42 LLKNATENEGNSSVPTMLIYSDYIAYLSAIEAPIFNPDEFARLI 85
                                      45555666666*******************************98 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.4
                   RFX_DNA_binding  25 vYaeYlsicskl 36 
                                       +Y  Y+++ +++
  gi|385806095|ref|YP_005842493.1| 128 IYGLYTEYIENK 139
                                       555566555544 PP

>> CytadhesinP1  Trypsin-sensitive surface-exposed protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.7e-05     0.082      21      58 ..      33      70 ..      15      73 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.7e-05
                      CytadhesinP1 21 FglsgtdnkkdgfqkeneskksapiaLpfeayfaNlgn 58
                                      +g ++  n   ++  ene+++s+p  L ++ y+a+l +
  gi|385806095|ref|YP_005842493.1| 33 YGFDDKLNILLKNATENEGNSSVPTMLIYSDYIAYLSA 70
                                      444444444445666777779**************976 PP

>> Hfq  Hfq 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      15      55 ..      17      66 ..      10      75 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.7e-05
                                      EEEEEETTS-EEEEEEEEE-S.SEEEEEETT....E....EEEEEGGGEE CS
                               Hfq 15 pvtifLvnGiklkGviksfDn.ftvlLesdg....k....qqlvYKhais 55
                                      +vti L  G  +kG++ +fD+   +lL++      +    ++l+Y   i+
  gi|385806095|ref|YP_005842493.1| 17 QVTIKLKDGRTIKGTLYGFDDkLNILLKNATenegNssvpTMLIYSDYIA 66
                                      89*****************8616688865543333134446677777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 919.78
//
Query:       gi|385806096|ref|YP_005842494.1|  [L=408]
Description: iron ABC transporter substrate-binding protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-34  119.5   0.0    2.3e-34  119.0   0.0    1.2  1  Peripla_BP_2     Periplasmic binding protein
  ------ inclusion threshold ------
      0.011   15.7   1.3      0.022   14.7   1.3    1.5  1  Rsd_AlgQ         Regulator of RNA polymerase sigma(70) subuni
      0.019   14.9   2.8      0.036   14.0   2.8    1.4  1  DUF4446          Protein of unknown function (DUF4446)
      0.031   14.3   2.0      0.048   13.7   1.0    1.9  2  DUF1664          Protein of unknown function (DUF1664)
      0.031   13.6   5.7      0.053   12.8   5.7    1.3  1  DUF3450          Protein of unknown function (DUF3450)
      0.048   13.4   2.8       0.11   12.2   2.8    1.6  1  Lectin_N         Hepatic lectin, N-terminal domain
      0.058   12.9   9.1       0.11   12.1   9.1    1.4  1  4HB_MCP_1        Four helix bundle sensory module for signal 
       0.12   11.9   0.1       0.18   11.4   0.1    1.2  1  HAUS6_N          HAUS augmin-like complex subunit 6 N-terminu
       0.12   12.0   3.4       0.22   11.2   3.4    1.3  1  BAR_3            BAR domain of APPL family
        0.2   11.7   3.4       0.44   10.7   3.4    1.5  1  Med9             RNA polymerase II transcription mediator com
       0.25   11.3   0.7        0.5   10.3   0.4    1.5  1  Phage_Mu_Gam     Bacteriophage Mu Gam like protein
       0.29   10.9   3.3       0.47   10.3   3.3    1.3  1  SKA1             Spindle and kinetochore-associated protein 1
       0.59   10.2   4.6       0.82    9.7   2.8    2.1  3  LOH1CR12         Tumour suppressor protein
        0.7    9.0   9.6       0.17   11.0   6.3    1.5  2  AI-2E_transport  AI-2E family transporter
        1.2    9.7   9.6        1.1    9.7   6.2    2.8  2  NPV_P10          Nucleopolyhedrovirus P10 protein
        1.7    8.7   6.9        4.3    7.4   1.8    2.5  2  DivIVA           DivIVA protein
        2.1    7.6   6.2        3.5    6.9   6.2    1.2  1  DUF4763          Domain of unknown function (DUF4763)
        2.6    7.9   4.9        5.4    6.9   0.5    2.5  2  DivIC            Septum formation initiator
        5.6    7.0  19.5         23    5.0  19.5    2.0  1  FlxA             FlxA-like protein
        8.2    5.5   7.8        1.9    7.6   4.4    1.5  2  DUF2232          Predicted membrane protein (DUF2232)


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 !  119.0   0.0   2.6e-37   2.3e-34       1     236 [.     119     354 ..     119     356 .. 0.96

  Alignments for each domain:
  == domain 1  score: 119.0 bits;  conditional E-value: 2.6e-37
                                       EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT....TS-BSBESSSB-HHHHHHH--SEEEE-GGG...GGG CS
                      Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadklee..aivevgadgeidvEklaalkPDlvilskglgltded 75 
                                       i+sl+ps+te+l+ +Ga + vvgvd  +++p   ++l    +i  vg+ ++i++Ek++ lkPDlv++s+g  +++ +
  gi|385806096|ref|YP_005842494.1| 119 IVSLAPSTTEMLFDIGAGNLVVGVDDNSNYPPIVNELVIngTIQRVGGFDSISLEKVISLKPDLVVGSTGV-QFKYI 194
                                       9*********************************99999********************************.***** PP

                                       HHHHHHHS-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT.-EEEEEEEETTE..EE CS
                      Peripla_BP_2  76 eellksgiptvivessntgeslkeqiralgellgledeaeklvaeidsklaaaksaidsekpkpvlvfggadeggyv 152
                                       ++l + gi  +  +  +  +++ + i  lg+++g+ ++a  l + +++++ ++ s+++  ++kp+++f+ + + +y+
  gi|385806096|ref|YP_005842494.1| 195 YQLSQYGITALSLNDESI-SDILTDILLLGKITGHYQQALNLTNNLKNEIISIYSKVSGSQNKPTVLFIVWVN-PYY 269
                                       ****************97.****************************************************99.*** PP

                                       EE-TTSTTTHHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEH..HHHT-S--HHHHT-SHHHHTSHHHH CS
                      Peripla_BP_2 153 vagsnsyigdlldalgieniaaeskkseyeeisaEqilasdpdvifvsgr..aeadnktgleflkenpllaelpAvk 227
                                        ag +s+++dl++  g+ n +++  ++++  is+E +++ +p+vi+ +      +++++    l+++p+ a++ Av+
  gi|385806096|ref|YP_005842494.1| 270 AAGGSSFWNDLISLSGGLNSLENV-SQAWPAISWEDVVKLNPQVIIATEYagGFSNATQLINWLESQPGGANISAVE 345
                                       **************9999999999.*************************54445666778999************* PP

                                       TT-EEEE-H CS
                      Peripla_BP_2 228 ngrVyalds 236
                                       +grVy l+ 
  gi|385806096|ref|YP_005842494.1| 346 TGRVYMLHG 354
                                       *****9975 PP

>> Rsd_AlgQ  Regulator of RNA polymerase sigma(70) subunit, Rsd/AlgQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   1.3   2.5e-05     0.022      87     149 ..      33      96 ..      28      97 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.5e-05
                          Rsd_AlgQ  87 elelakelypkieatTeaaldfndkyee.aadedeleeldedLsklgeaLeeRfelEDkLievl 149
                                       +++ ++++ + ie+ T+  l++ +++++ +++ +e++ +++++s+l ++L + ++   ++i+++
  gi|385806096|ref|YP_005842494.1|  33 NTRGISQINNDIEKMTQITLNLSNQIDSiQQSLNEYKLMSQQISSLNQSLSQQIQSLNNMIAQM 96 
                                       5667899*********************999999999****************99999988876 PP

>> DUF4446  Protein of unknown function (DUF4446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   2.8   4.1e-05     0.036       1      89 [.      14     105 ..      14     109 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.1e-05
                           DUF4446   1 iiilvlavlvvillillivllvklkklkkkykklmkgk.dgksleellkekleeveelkeeseelekeieeleeklk 76 
                                       +++++++++++  +i+   +++ +++++++++k+++ + + ++  + +++ l+e++ ++++ ++l++++++  ++l+
  gi|385806096|ref|YP_005842494.1|  14 YVLILVGIIAIGSIIISYQNTRGISQINNDIEKMTQITlNLSNQIDSIQQSLNEYKLMSQQISSLNQSLSQQIQSLN 90 
                                       6889999999999***********************66588888888888888888888888887777777777777 PP

                           DUF4446  77 kslqkvg..lvrYdA 89 
                                       +++ +++  +  YdA
  gi|385806096|ref|YP_005842494.1|  91 NMIAQMNypIQVYDA 105
                                       777665422455555 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.0   5.4e-05     0.048      68     121 ..      37      90 ..      14     114 .. 0.58
   2 ?   -2.9   0.0       7.1   6.4e+03      75      97 ..     229     251 ..     222     256 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.4e-05
                           DUF1664  68 idrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                       i ++++ ++++++i+ +++++++++++ l+e +  +++++++ ++l +++++++
  gi|385806096|ref|YP_005842494.1|  37 ISQINNDIEKMTQITLNLSNQIDSIQQSLNEYKLMSQQISSLNQSLSQQIQSLN 90 
                                       444444455555555555555555555555555444444444444444444443 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 7.1
                           DUF1664  75 ldeqkeiskeikeevtevredls 97 
                                        ++  ++++++k+e+ ++ +++s
  gi|385806096|ref|YP_005842494.1| 229 YQQALNLTNNLKNEIISIYSKVS 251
                                       56666777777777777777665 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   5.7     6e-05     0.053      33      91 ..      38      96 ..      30     106 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6e-05
                           DUF3450 33 aqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieei 91
                                      +q+++ i+k+++ + +l++++ ++++ l++ ++  +q ++l +s+ q+i+sl++ i+++
  gi|385806096|ref|YP_005842494.1| 38 SQINNDIEKMTQITLNLSNQIDSIQQSLNEYKLMSQQISSLNQSLSQQIQSLNNMIAQM 96
                                      688999************************************************99987 PP

>> Lectin_N  Hepatic lectin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   2.8   0.00012      0.11      35     115 ..      13     101 ..       8     109 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
                          Lectin_N  35 lsllLLVvvcVigs.....qn....sqLqreLetLketfsnfssstlaeiqalssqggslsekvtsleaklekkqqd 102
                                       l +l+LV +  igs     qn    sq+ +++e + +   n+s+++   iq+   + + +s++++sl+  l ++ q+
  gi|385806096|ref|YP_005842494.1|  13 LYVLILVGIIAIGSiiisyQNtrgiSQINNDIEKMTQITLNLSNQID-SIQQSLNEYKLMSQQISSLNQSLSQQIQS 88 
                                       678888888766653333366888999******99999999988775.57777778899****************** PP

                          Lectin_N 103 lkadhselllhvk 115
                                       l++  +++   ++
  gi|385806096|ref|YP_005842494.1|  89 LNNMIAQMNYPIQ 101
                                       **99999877776 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 ?   12.1   9.1   0.00012      0.11      10     103 ..      17     108 ..      10     111 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00012
                         4HB_MCP_1  10 llflllallliivGvvGlyslkkinknletmYedrllpikdlgeikanlrelradlleliltkdkaekdellkdiee 86 
                                       +l++++a+  ii++  + +++++in+ +e+m +  l   +++ +i+++l+e++    ++    +++  +++++ +++
  gi|385806096|ref|YP_005842494.1|  17 ILVGIIAIGSIIISYQNTRGISQINNDIEKMTQITLNLSNQIDSIQQSLNEYKLMSQQISSL-NQSLSQQIQS-LNN 91 
                                       679999999*******************************************9877776655.8888888877.999 PP

                         4HB_MCP_1  87 leaeidkllekyektil 103
                                         a+++  ++ y+ ++ 
  gi|385806096|ref|YP_005842494.1|  92 MIAQMNYPIQVYDALNR 108
                                       99999999999998776 PP

>> HAUS6_N  HAUS augmin-like complex subunit 6 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1    0.0002      0.18     137     199 ..      39     101 ..      11     124 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0002
                           HAUS6_N 137 aaskkaqdlsklvaahrvslrrflrekaaadrarqkyqenaqllekkerelraeleelqaelk 199
                                        ++ + ++++++++  ++++  +++ +++   + q+++++ q+l++++++l++++++++  ++
  gi|385806096|ref|YP_005842494.1|  39 QINNDIEKMTQITLNLSNQIDSIQQSLNEYKLMSQQISSLNQSLSQQIQSLNNMIAQMNYPIQ 101
                                       456677788999999999**************************************9987665 PP

>> BAR_3  BAR domain of APPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   3.4   0.00024      0.22      30      90 ..      36      96 ..      32     111 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00024
                             BAR_3 30 klkkllKlckrlieagkaysaaqkqfaqsLrelkkeskgdeetdesLkkfsellqeleneh 90
                                       + ++ ++++++++ + ++s++  ++ qsL+e+k  s++ + +++sL + +++l++++ + 
  gi|385806096|ref|YP_005842494.1| 36 GISQINNDIEKMTQITLNLSNQIDSIQQSLNEYKLMSQQISSLNQSLSQQIQSLNNMIAQM 96
                                      6889999*************************************************99764 PP

>> Med9  RNA polymerase II transcription mediator complex subunit 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   3.4   0.00049      0.44       8      66 ..      39      96 ..      35     108 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00049
                              Med9  8 dilksiekdpnlsskdletktgelrhkLkkarelirelpgidrsveeqeaeieeleeql 66
                                      +i ++iek + + + +l+++++++++ L++ + + ++++ ++ s  +q + ++++  q+
  gi|385806096|ref|YP_005842494.1| 39 QINNDIEKMT-QITLNLSNQIDSIQQSLNEYKLMSQQISSLNQSLSQQIQSLNNMIAQM 96
                                      5667788888.888899***********************************9987776 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 ?   10.3   0.4   0.00055       0.5      10      64 ..      57     110 ..      53     127 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00055
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHCTHHH CS
                      Phage_Mu_Gam  10 kiaelkreleeieaeaneeiaaikekleaeleplkkeieylesllkqYaeankde 64 
                                       +i  ++++l+e++  + ++i  +++ l +++++l++ i++++  ++ Y   n+  
  gi|385806096|ref|YP_005842494.1|  57 QIDSIQQSLNEYK-LMSQQISSLNQSLSQQIQSLNNMIAQMNYPIQVYDALNRTV 110
                                       7888999999996.89*******************************98888855 PP

>> SKA1  Spindle and kinetochore-associated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   3.3   0.00053      0.47      12      80 ..      38      99 ..      27     128 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00053
                                      ............XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX......XXXXXXXXXXX CS
                              SKA1 12 rainqdpallkedlskieaevsaleellnklkkelqeeeeaikklkkeieaslkqqek.lqhlkenlpsh 80
                                      ++i       ++d++k+ +    l ++++++++ l+e + + +++   +++sl qq + l+++ ++++  
  gi|385806096|ref|YP_005842494.1| 38 SQI-------NNDIEKMTQITLNLSNQIDSIQQSLNEYKLMSQQIS-SLNQSLSQQIQsLNNMIAQMNYP 99
                                      444.......455555555555666666666666665555555555.55555555555566666666543 PP

>> LOH1CR12  Tumour suppressor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   2.8   0.00091      0.82      58     116 ..      37      92 ..      30     109 .. 0.76
   2 ?   -2.8   0.0       6.7     6e+03      71     100 ..     218     247 ..     207     253 .. 0.65
   3 ?   -2.3   0.0       4.6   4.1e+03     105     121 ..     366     382 ..     347     383 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00091
                          LOH1CR12  58 ikevdakiitllaelrekqkqyasyaealskvnelsdqlsriqiiledivpllEtlnel 116
                                       i +++++i+++ + + +  +q +s  ++l++ + +s+q+s++++ l +++++l++   +
  gi|385806096|ref|YP_005842494.1|  37 ISQINNDIEKMTQITLNLSNQIDSIQQSLNEYKLMSQQISSLNQSLSQQIQSLNN---M 92 
                                       5667788888888888888888888888888888888888888888888876543...3 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 6.7
                          LOH1CR12  71 elrekqkqyasyaealskvnelsdqlsriq 100
                                       ++    k    y +al+  n+l++++ +i 
  gi|385806096|ref|YP_005842494.1| 218 DILLLGKITGHYQQALNLTNNLKNEIISIY 247
                                       555555555667777777788888777775 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 4.6
                          LOH1CR12 105 divpllEtlnelLdede 121
                                        iv++ E l  +L++++
  gi|385806096|ref|YP_005842494.1| 366 RIVEMQEVLAAILHPED 382
                                       57999999999999887 PP

>> AI-2E_transport  AI-2E family transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   6.3   0.00019      0.17      55     132 ..      13      96 ..       5     112 .. 0.62
   2 ?   -3.1   0.1       3.8   3.4e+03     124     135 ..     234     245 ..     194     282 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00019
                   AI-2E_transport  55 lvlllllvllvllvlllvplliaqltqlvkslp...ayidslqnilnelpslleele.n..liqalkqslskilsni 125
                                       l +l+l++++++  +++  +   +++q+ ++++   +++  l+n++ +++++l+e + +  +i+ l+qsls++++++
  gi|385806096|ref|YP_005842494.1|  13 LYVLILVGIIAIGSIIISYQNTRGISQINNDIEkmtQITLNLSNQIDSIQQSLNEYKlMsqQISSLNQSLSQQIQSL 89 
                                       33444444444444444444455555555555511155555555555555555555544999999**********99 PP

                   AI-2E_transport 126 lssilns 132
                                        + i+++
  gi|385806096|ref|YP_005842494.1|  90 NNMIAQM 96 
                                       9998765 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.8
                   AI-2E_transport 124 nilssilnslls 135
                                       n+++++ n ++s
  gi|385806096|ref|YP_005842494.1| 234 NLTNNLKNEIIS 245
                                       222222222222 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   6.2    0.0013       1.1      15      56 ..      53      94 ..      37     116 .. 0.75
   2 ?   -1.8   0.1       5.1   4.6e+03      61      66 ..     212     217 ..     202     250 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0013
                           NPV_P10 15 avddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaelet 56
                                      ++++++d++qq++++ +  +++++ ln+ L +q ++L+++ +
  gi|385806096|ref|YP_005842494.1| 53 NLSNQIDSIQQSLNEYKLMSQQISSLNQSLSQQIQSLNNMIA 94
                                      578888888888888888888888888888777777776654 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 5.1
                           NPV_P10  61 IqdiLn 66 
                                       I+diL+
  gi|385806096|ref|YP_005842494.1| 212 ISDILT 217
                                       555555 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   1.8    0.0048       4.3      28      66 ..      38      76 ..      36      82 .. 0.91
   2 ?    4.2   0.2     0.049        44      41      75 ..      79     116 ..      74     123 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0048
                                      HHHHHHHHHHHHHHHHHHHHHHCCCCTXXXXXXXXXXXX CS
                            DivIVA 28 dqvakdyeallkeneelkekvkeleeklkeykeleetLk 66
                                       q+ +d+e++ +   +l ++++  +++l+eyk + ++++
  gi|385806096|ref|YP_005842494.1| 38 SQINNDIEKMTQITLNLSNQIDSIQQSLNEYKLMSQQIS 76
                                      6999****************************9998875 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.049
                                       HHHHHHHHHCCCCTXXXXX...XXXXXXXXXXXXXXXX CS
                            DivIVA  41 neelkekvkeleeklkeyk...eleetLkktlvvaqet 75 
                                       n++l ++++ l++ +++++   ++ ++L++t+v +q+ 
  gi|385806096|ref|YP_005842494.1|  79 NQSLSQQIQSLNNMIAQMNypiQVYDALNRTVVITQQP 116
                                       788888888888877777644489999*****999985 PP

>> DUF4763  Domain of unknown function (DUF4763)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   6.2    0.0039       3.5      96     152 ..      38      97 ..      32     108 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0039
                           DUF4763  96 tseqpeileLqrnnhkLrqqlaelqqhl...kasrkslkelreslcqekkrlrklqkrln 152
                                       ++ + +i ++ + +  L  q++++qq+l   k + ++++ l++sl+q+ + l+++ +++n
  gi|385806096|ref|YP_005842494.1|  38 SQINNDIEKMTQITLNLSNQIDSIQQSLneyKLMSQQISSLNQSLSQQIQSLNNMIAQMN 97 
                                       56788999999999***********98622267999*******************99987 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.5     0.006       5.4       5      51 ..      16      62 ..      13      69 .. 0.65
   2 ?    2.8   1.3      0.11     1e+02      14      48 ..      63      94 ..      60     105 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.006
                                      XXXXXXXXXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-X CS
                             DivIC  5 fllllifgkkgllaykqlkqeiaalqaelaklkaeneeLeaevkdLk 51
                                      ++l+ i+  +++   +q  + i +++++++k+++   +L  +++  +
  gi|385806096|ref|YP_005842494.1| 16 LILVGIIAIGSIIISYQNTRGISQINNDIEKMTQITLNLSNQIDSIQ 62
                                      56666666677777777777777777777777777777777776654 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.11
                                      XXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                             DivIC 14 kgllaykqlkqeiaalqaelaklkaeneeLeaevk 48
                                      ++l+ yk + q+i  l++    l++++++L+  ++
  gi|385806096|ref|YP_005842494.1| 63 QSLNEYKLMSQQISSLNQS---LSQQIQSLNNMIA 94
                                      6777777788888777654...5555555555544 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0  19.5     0.026        23      15      68 ..      40      96 ..      23     101 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.026
                              FlxA 15 sasqiasLqkQiknlqkqLkelses...deltkeekkkqqqliqaQIqqlqaQIaql 68
                                      ++++i+++++   nl++q++++++s    +l  ++ +   q +++QIq+l++ Iaq+
  gi|385806096|ref|YP_005842494.1| 40 INNDIEKMTQITLNLSNQIDSIQQSlneYKLMSQQISSLNQSLSQQIQSLNNMIAQM 96
                                      344444444444444444444444443323335557799999************998 PP

>> DUF2232  Predicted membrane protein (DUF2232)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   4.4    0.0021       1.9      82     161 ..       7      93 ..       2     108 .. 0.61
   2 ?   -3.3   0.1       4.4   3.9e+03     100     136 ..     216     250 ..     194     260 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0021
                           DUF2232  82 ksaertliagtlafllgillafallalllg.......vnllaqvekeikesveealklyeeaGmsedelkelqklle 151
                                       k+   tl++ +l+ +++i  +++ ++   g       ++ + q++ ++++ ++ +++++ e  + +++ + l+++l 
  gi|385806096|ref|YP_005842494.1|   7 KESKTTLYVLILVGIIAIGSIIISYQNTRGisqinndIEKMTQITLNLSNQIDSIQQSLNEYKLMSQQISSLNQSLS 83 
                                       56666777777777777777777777777733333334445555555555555555555555445566666666666 PP

                           DUF2232 152 eevslllrll 161
                                       +++++l +++
  gi|385806096|ref|YP_005842494.1|  84 QQIQSLNNMI 93 
                                       6666666665 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.4
                           DUF2232 100 llafallalllgvnllaqvekeikesveealklyeea 136
                                       l+ ++ll + +g    +q+ +  ++  +e++++y++ 
  gi|385806096|ref|YP_005842494.1| 216 LTDILLLGKITGHY--QQALNLTNNLKNEIISIYSKV 250
                                       44555555555544..666677777777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1884  (0.105081); expected 358.6 (0.02)
Passed bias filter:                     1067  (0.0595125); expected 358.6 (0.02)
Passed Vit filter:                       214  (0.011936); 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: 0.78u 0.31s 00:00:01.09 Elapsed: 00:00:00.47
# Mc/sec: 2607.21
//
Query:       gi|385806097|ref|YP_005842495.1|  [L=329]
Description: HutC protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.9e-65  218.9  35.9    9.7e-65  218.6  35.9    1.1  1  FecCD            FecCD transport family


Domain annotation for each model (and alignments):
>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.6  35.9   5.4e-69   9.7e-65       3     312 .]      26     324 ..      16     324 .. 0.93

  Alignments for each domain:
  == domain 1  score: 218.6 bits;  conditional E-value: 5.4e-69
                             FecCD   3 llllllslllgavkispsevfeallgkadsleaeivlelrlprvlaallvGaaLavaGallQtvtrNpLadPsilGi 79 
                                       l++ llsl lg++   + +         + + +++++++r+ r+l+++++   La+ G++lQt++ NpL+d+silGi
  gi|385806097|ref|YP_005842495.1|  26 LVSSLLSLYLGSSGSIAFD---------EWKWENVIFQIRMYRTLTVIFTSETLAIIGLILQTIFSNPLVDSSILGI 93 
                                       3444444444444322223.........3334679****************************************** PP

                             FecCD  80 ssgaalgavlalllllgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsallsaltslllllln 156
                                       ssg++lgav++lll+ + ++  a+ +++f+++lla++++l+l+ k +g ++++++L+G+++s+l++++  ll ++ +
  gi|385806097|ref|YP_005842495.1|  94 SSGSSLGAVIGLLLV-SRMGYSAIFIFSFIFSLLAFIVILFLS-KITGYKTISMVLSGVIISTLFNSFLYLLFMTNT 168
                                       **************8.***************************.*****************************9978 PP

                             FecCD 157 eealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrllllllvallta 233
                                         a    + w++G+++  + s+++ +++ +l+++++l++   +l+ l +gd+ A + G +++ +r  +l+++++ ++
  gi|385806097|ref|YP_005842495.1| 169 ILARVHSVSWMFGTFEFSNSSSFYASFISFLIVFVFLYVKGPRLRQLLYGDDFAIARGADPKNLRREVLIVTSISIS 245
                                       88888999********************************************************************* PP

                             FecCD 234 vavalvGpigFvGLivPhiarllvgadhrkllplsallGallllladllarlllsptelpvgivtaliGapffiyll 310
                                       ++ ++ GpigF+GLivPhiar+++g d +   + s +++ ++lll+d++ar+ll+p+e+p+gi+t+liGapff++ll
  gi|385806097|ref|YP_005842495.1| 246 LISVYEGPIGFIGLIVPHIARMMLGGDISVASLGSLFISPVILLLSDVVARVLLAPSEIPIGIITSLIGAPFFLMLL 322
                                       ****************************************************************************9 PP

                             FecCD 311 lr 312
                                       ++
  gi|385806097|ref|YP_005842495.1| 323 VK 324
                                       97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1172  (0.065369); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2416.29
//
Query:       gi|385806098|ref|YP_005842496.1|  [L=250]
Description: Iron (III) ABC transporter, ATPase component [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-19   70.7   0.0    3.4e-19   69.7   0.0    1.5  1  ABC_tran      ABC transporter
    9.1e-10   38.8   2.2    0.00073   19.4   0.1    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    3.4e-07   29.9   0.4     0.0012   18.4   0.1    2.1  2  SMC_N         RecF/RecN/SMC N terminal domain
    0.00027   21.5   0.6    0.00049   20.7   0.3    1.5  1  AAA_23        AAA domain
     0.0019   17.8   0.0     0.0031   17.1   0.0    1.3  1  AAA_27        AAA domain
     0.0027   16.8   0.0     0.0042   16.2   0.0    1.2  1  T2SSE         Type II/IV secretion system protein
     0.0071   16.1   0.7      0.028   14.1   0.0    1.9  2  AAA_15        AAA ATPase domain
     0.0085   15.8   0.0      0.013   15.2   0.0    1.3  1  AAA_24        AAA domain
  ------ inclusion threshold ------
      0.012   15.4   0.0      0.027   14.2   0.0    1.7  1  AAA_29        P-loop containing region of AAA domain
      0.016   15.4   0.4      0.098   12.9   0.4    2.1  1  AAA_22        AAA domain
      0.018   14.4   0.0      0.033   13.6   0.0    1.4  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
       0.06   13.3   0.2       0.12   12.3   0.2    1.4  1  NACHT         NACHT domain
      0.079   13.0   0.3          1    9.4   0.0    2.6  3  AAA_14        AAA domain
      0.083   12.9   1.4       0.32   11.0   1.0    1.9  2  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
      0.087   13.2   0.0       0.22   11.9   0.0    1.7  1  AAA_16        AAA ATPase domain
       0.09   12.5   0.0       0.14   11.8   0.0    1.2  1  AAA_30        AAA domain
      0.091   12.7   0.0       0.19   11.6   0.0    1.5  1  RsgA_GTPase   RsgA GTPase
       0.12   12.3   0.3       0.36   10.7   0.1    1.9  2  Rad17         Rad17 P-loop domain
       0.14   12.3   0.0       0.23   11.6   0.0    1.4  1  AAA_33        AAA domain
       0.14   11.3   0.0       0.24   10.5   0.0    1.3  1  PIF1          PIF1-like helicase
       0.18   12.2   0.5       0.63   10.5   0.5    2.1  1  AAA           ATPase family associated with various cellular 
       0.24   11.1   0.6        8.3    6.1   0.1    2.2  2  IstB_IS21     IstB-like ATP binding protein


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.7   0.0   4.2e-22   3.4e-19       2     136 ..      17     158 ..      16     159 .. 0.80

  Alignments for each domain:
  == domain 1  score: 69.7 bits;  conditional E-value: 4.2e-22
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.........B-HHHCCHCEEEE-SS-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.........qeleslrkeigvlpqepq 69 
                                       k+v+l++keg++  ++G+nGaGK+t+lk+lag   p eG++ +++ + k           +l++ +  + ++  + +
  gi|385806098|ref|YP_005842496.1|  17 KRVELEIKEGKLFCVLGPNGAGKTTFLKTLAGIIPPFEGKVSVEDSSKKLyispdppylPSLRIIDVILNFIIGDRK 93 
                                       7899*************************************888444444677777666666666777777777755 PP

                                       S-TTSBHHHH..HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  70 lfpeltvren..esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       +f  +   +n  +++  +e++l+++glk+     ++++ + LS G+k++v+l  al+++++ll+lDEp 
  gi|385806098|ref|YP_005842496.1|  94 FFLYSISDDNvtKRTIMAEEILNTFGLKY----GMDYEYEYLSTGEKSKVMLTGALVSEANLLFLDEPN 158
                                       55555345555455555***********9....455555*****************************5 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 !   19.4   0.1   8.9e-07   0.00073       2      32 ..      29      56 ..      28      75 .. 0.74
   2 !   18.4   0.2   1.8e-06    0.0015     237     295 ..     131     184 ..     126     189 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 8.9e-07
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdvegl 32
                                       ++ GpNg+GK+++L++l ++   ++ +eg 
  gi|385806098|ref|YP_005842496.1| 29 FCVLGPNGAGKTTFLKTLAGI---IPPFEGK 56
                                      6799**************988...4444444 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 1.8e-06
                            AAA_21 237 lSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQvilt 295
                                       lS G k+   l  al + +    ll++DEp ++L+ +    l++llk++s+    +il 
  gi|385806098|ref|YP_005842496.1| 131 LSTGEKSKVMLTGALVSEA---NLLFLDEPNSHLDLRSRIILYQLLKNESN--RRIILI 184
                                       5778888888888888888...89**************************9..777765 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 !    9.8   0.0    0.0006      0.49      16      44 ..      17      46 ..      11      50 .. 0.76
   2 !   18.4   0.1   1.4e-06    0.0012     110     199 ..      96     188 ..      81     207 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0006
                                      EEEEEETTS.SEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 16 ktvilpfsk.sftaivGpNGSGKsnlldAi 44
                                      k+v+l++++ ++ +++GpNG+GK+ +l  +
  gi|385806098|ref|YP_005842496.1| 17 KRVELEIKEgKLFCVLGPNGAGKTTFLKTL 46
                                      6666666651467899********998765 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 1.4e-06
                                       EEEETTEEE-HHHH..HHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHH CS
                                       xxxxxxxxxxxxxx..xxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 110 eykingkevtkkev..sellesagiske......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkk 178
                                        y i + +vtk+ +  +e+l++ g++        +LS Gek+ v+l        v+ a l +lDe +++LD + + +
  gi|385806098|ref|YP_005842496.1|  96 LYSISDDNVTKRTImaEEILNTFGLKYGmdyeyeYLSTGEKSKVMLTG----ALVSEANLLFLDEPNSHLDLRSRII 168
                                       57777777777666224567777776545555559******9888754....3578999****************** PP

                                       HHHHHHHHCTTSEEEEE-SSH CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 179 vaellkeksknaQfivislre 199
                                       + +llk++s n  +i isl++
  gi|385806098|ref|YP_005842496.1| 169 LYQLLKNES-NRRIILISLHD 188
                                       *******99.88899999864 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.3     6e-07   0.00049      11      39 ..      17      46 ..       2      50 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 6e-07
                            AAA_23 11 rdqeidF.skgltlItGpNGaGKTTildAi 39
                                      +++e++  + +l+++ GpNGaGKTT+l  +
  gi|385806098|ref|YP_005842496.1| 17 KRVELEIkEGKLFCVLGPNGAGKTTFLKTL 46
                                      45566666669***************9765 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   3.8e-06    0.0031      10      47 ..      10      47 ..       1      57 [. 0.87

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.8e-06
                            AAA_27 10 ryGkftdrsldfsaeeadlhliyGpNEAGKstalrAis 47
                                       yGk   ++++++ +e +l  ++GpN AGK+t l+ + 
  gi|385806098|ref|YP_005842496.1| 10 GYGKAITKRVELEIKEGKLFCVLGPNGAGKTTFLKTLA 47
                                      6999999**************************99876 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   5.1e-06    0.0042     117     166 ..      14      62 ..       3      66 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.1e-06
                             T2SSE 117 kiaevlrkavrerglilvsGgTgsGKttllyallkeinksderivtvEDp 166
                                       +i + ++  ++e +l+ v G+ g GKtt+l +l  +i+   e  v vED+
  gi|385806098|ref|YP_005842496.1|  14 AITKRVELEIKEGKLFCVLGPNGAGKTTFLKTLAGIIPPF-EGKVSVEDS 62 
                                       56666777888899*************************9.666889997 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   3.4e-05     0.028      15      43 ..      17      46 ..      13      72 .. 0.88
   2 ?    0.1   0.2      0.64   5.2e+02     324     353 ..     149     178 ..      81     189 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.4e-05
                            AAA_15 15 kdveidlsee.ltvliGkNnsGKSsileal 43
                                      k ve++++e  l ++ G+N++GK+++l+ l
  gi|385806098|ref|YP_005842496.1| 17 KRVELEIKEGkLFCVLGPNGAGKTTFLKTL 46
                                      4489999998899**************988 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.64
                            AAA_15 324 nvilliEEPEahLHpqaqkvlikllkelan 353
                                        ++l+++EP  hL      +l++llk+ +n
  gi|385806098|ref|YP_005842496.1| 149 ANLLFLDEPNSHLDLRSRIILYQLLKNESN 178
                                       378999999999877777777777776655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.6e-05     0.013       5      38 ..      29      66 ..      25      89 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.6e-05
                            AAA_24  5 iliyGpsgiGKTtlakel....gpkplfidtekGlksl 38
                                      +++ Gp+g+GKTt++k+l    +p    + +e+++k+l
  gi|385806098|ref|YP_005842496.1| 29 FCVLGPNGAGKTTFLKTLagiiPPFEGKVSVEDSSKKL 66
                                      79***************965554444445666666655 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   3.4e-05     0.027      15      45 ..      19      49 ..       5      65 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.4e-05
                            AAA_29 15 htieidlkgatlltGpsGsGKSTllDAiqal 45
                                       ++ei++   + + Gp+G+GK+T+l  ++ +
  gi|385806098|ref|YP_005842496.1| 19 VELEIKEGKLFCVLGPNGAGKTTFLKTLAGI 49
                                      556777444999************9766655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.4   0.00012     0.098       4      66 ..      25     120 ..      21     193 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00012
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee....................................erpevvf 44 
                                       + ++ +v G+ G+GKTt l++l+   +                                            ++++++
  gi|385806098|ref|YP_005842496.1|  25 EGKLFCVLGPNGAGKTTFLKTLAGIIPP-----FegkvsvedsskklyispdppylpslriidvilnfiiGDRKFFL 96 
                                       6678899**************9876532.....01234455555566666666666666666666666653333334 PP

                            AAA_22  45 vtlpsst.sskdl.lrellralgl 66 
                                       + ++ ++ + +++ ++e+l+ +gl
  gi|385806098|ref|YP_005842496.1|  97 YSISDDNvTKRTImAEEILNTFGL 120
                                       444444443333336666666665 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   4.1e-05     0.033      24      57 ..      28      61 ..       9      69 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.1e-05
                      Mg_chelatase 24 nlllvGppGsGKtmlakrlpsllpplseeealev 57
                                       + ++Gp G+GKt   k l++++pp + + ++e 
  gi|385806098|ref|YP_005842496.1| 28 LFCVLGPNGAGKTTFLKTLAGIIPPFEGKVSVED 61
                                      56789********************999888775 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   0.00014      0.12       2      21 ..      28      47 ..      27      50 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                                      CEEEEC-TTTCHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqkla 21
                                      l ++ G++G GKTt+l+ la
  gi|385806098|ref|YP_005842496.1| 28 LFCVLGPNGAGKTTFLKTLA 47
                                      5799*************997 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0    0.0013         1       3      23 ..      27      47 ..      25     147 .. 0.78
   2 ?    1.2   0.1      0.42   3.5e+02      64      80 ..     148     164 ..     103     192 .. 0.62
   3 ?   -0.3   0.0       1.3   1.1e+03      18      43 ..     168     191 ..     166     204 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0013
                            AAA_14  3 kilvitGaRrvGKTtllkqli 23
                                      k+ ++ G+  +GKTt+lk+l+
  gi|385806098|ref|YP_005842496.1| 27 KLFCVLGPNGAGKTTFLKTLA 47
                                      77899*************997 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.42
                            AAA_14  64 kktylflDEiqevpewe 80 
                                       + ++lflDE     +++
  gi|385806098|ref|YP_005842496.1| 148 EANLLFLDEPNSHLDLR 164
                                       56677777755544443 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.3
                            AAA_14  18 llkqlikellvkkesilyinldderd 43 
                                       +l+ql+k++   +++i+ i+l d ++
  gi|385806098|ref|YP_005842496.1| 168 ILYQLLKNES--NRRIILISLHDLNE 191
                                       6889998888..89999999998765 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.64   5.2e+02      22      34 ..       3      15 ..       2      22 .. 0.82
   2 ?   11.0   1.0   0.00039      0.32      16      40 ..      17      47 ..       8      57 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.64
                                      EEEEESTTSSHHH CS
                              TsaE 22 ilLeGdLGaGKTt 34
                                      ++++G LG GK  
  gi|385806098|ref|YP_005842496.1|  3 LAFSGTLGYGKAI 15
                                      5799*******75 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00039
                                      HCH......TEEEEEEESTTSSHHHHHHHHH CS
                              TsaE 16 kal......gdvilLeGdLGaGKTtlvrgla 40
                                      k +      g++++  G+ GaGKTt+ + la
  gi|385806098|ref|YP_005842496.1| 17 KRVeleikeGKLFCVLGPNGAGKTTFLKTLA 47
                                      3333333557889***************987 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   0.00027      0.22      24      76 ..      26      81 ..      14     184 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00027
                            AAA_16 24 pelvllsGesGvGKsslvrellralekdggif.lrgkcdql..esaipysalaqal 76
                                      + l  + G+ G GK++ +++l+  +   +g + ++   ++l  + + py++ ++++
  gi|385806098|ref|YP_005842496.1| 26 GKLFCVLGPNGAGKTTFLKTLAGIIPPFEGKVsVEDSSKKLyiSPDPPYLPSLRII 81
                                      47788****************96555544444333333333334447776666666 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00018      0.14      18      42 ..      26      50 ..      17      59 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                            AAA_30 18 drvavltGpAGtGKttalkalreaw 42
                                       ++ ++ Gp G+GKtt lk+l+ ++
  gi|385806098|ref|YP_005842496.1| 26 GKLFCVLGPNGAGKTTFLKTLAGII 50
                                      458999*************998765 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   0.00023      0.19      93     122 ..      19      49 ..       8      65 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00023
                                       HHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  93 lkellkd.ktsvlvGqSGvGKStLinallpe 122
                                       ++ ++k+ k+ +++G+ G+GK+t++++l++ 
  gi|385806098|ref|YP_005842496.1|  19 VELEIKEgKLFCVLGPNGAGKTTFLKTLAGI 49 
                                       5556666699*****************9875 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00045      0.36      39      68 ..      20      49 ..      13      58 .. 0.86
   2 ?   -2.9   0.0       6.7   5.5e+03     126     145 ..     100     118 ..      78     122 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00045
                             Rad17 39 vLesrkkriLLisGPsGCgkstvvkvLske 68
                                       Le ++ ++  + GP G gk+t +k L+ +
  gi|385806098|ref|YP_005842496.1| 20 ELEIKEGKLFCVLGPNGAGKTTFLKTLAGI 49
                                      47778888999****************965 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.7
                             Rad17 126 GddlrtdkklilvedlPnkf 145
                                        dd +  k+ i+ e++ n f
  gi|385806098|ref|YP_005842496.1| 100 SDD-NVTKRTIMAEEILNTF 118
                                       333.3456778888888887 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   0.00028      0.23       2      20 ..      29      47 ..      28      89 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00028
                            AAA_33  2 vllvGlpGsGKstlaerll 20
                                      + + G++G+GK+t+++ l+
  gi|385806098|ref|YP_005842496.1| 29 FCVLGPNGAGKTTFLKTLA 47
                                      5678************997 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0    0.0003      0.24      17      53 ..      21      57 ..      12      63 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0003
                                      ...HCTS-EEEEESTTSSCHHHHHHHHHHCHCTCCCE CS
                              PIF1 17 vlnekgklfFvtGsgGtgKtflwkallkklrsegkiv 53
                                      +  ++gklf v G  G+gKt ++k+l  ++ + + +v
  gi|385806098|ref|YP_005842496.1| 21 LEIKEGKLFCVLGPNGAGKTTFLKTLAGIIPPFEGKV 57
                                      34589**********************9998854444 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 ?   10.5   0.5   0.00078      0.63       2      22 ..      30      50 ..      29     186 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00078
                                      EEESSTTSSHHHHHHHHHHHH CS
                               AAA  2 llyGppGtGKTllakavakel 22
                                      ++ Gp G GKT++ k +a  +
  gi|385806098|ref|YP_005842496.1| 30 CVLGPNGAGKTTFLKTLAGII 50
                                      789*************99874 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1      0.01       8.3      44      66 ..      23      45 ..      12      49 .. 0.83
   2 ?    3.2   0.0      0.08        65     107     146 ..     147     185 ..     132     194 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.01
                         IstB_IS21 44 iekkenivllGpsGvGKshlaia 66
                                      i++ + +++lGp G+GK+ +  +
  gi|385806098|ref|YP_005842496.1| 23 IKEGKLFCVLGPNGAGKTTFLKT 45
                                      5667789**********987655 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.08
                         IstB_IS21 107 lkvdllilDdlgllpldqaeaellfeviekryerrsiiit 146
                                        +++ll lD+    +ld  ++  l++++++  +rr i+i+
  gi|385806098|ref|YP_005842496.1| 147 SEANLLFLDEPN-SHLDLRSRIILYQLLKNESNRRIILIS 185
                                       567899999975.67999*****************99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); 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: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 1665.45
//
Query:       gi|385806099|ref|YP_005842497.1|  [L=354]
Description: exonuclease of the beta-lactamase fold involved in RNA processing-like protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-05   24.8   0.0    2.2e-05   24.1   0.0    1.3  1  Lactamase_B_2  Beta-lactamase superfamily domain
     0.0066   16.6   0.8      0.012   15.8   0.1    1.7  2  DRMBL          DNA repair metallo-beta-lactamase


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 !   24.1   0.0   2.4e-09   2.2e-05      35     174 ..      40     157 ..      32     176 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 2.4e-09
                                       E-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE- CS
                     Lactamase_B_2  35 llthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleeepavnvheldwgesfelgdggleitatpar 111
                                       ++th H DH+     l + + ++  ++a++ +l+ l+  +  l      + ++ +l  ++++++ d+  +it++   
  gi|385806099|ref|YP_005842497.1|  40 VVTHMHSDHTL---YLSKSKRHSTYILATQPTLDSLTVLGEKLP-----ENKTIPLGYNKPLRIVDE--TITFVKST 106
                                       79********5...4555333335588**********9975443.....346799*********875..69999999 PP

                                       EE--CTCCE-TTTSEEEEEE.CTTEEEEEESS-S---HHHHHHHCT-SEEEEE-S-SSTTHHHH CS
                     Lactamase_B_2 112 hksgrrldrnagdtlGlrie.gggkrvyyigDtgyipeeigerlggadllllditayeddemir 174
                                       h  g          + +++e ++g r+ y+ D + +p+   + + ++d+l++d+t y ++ mir
  gi|385806099|ref|YP_005842497.1| 107 HVIGS---------AQVVVEtKEGFRLGYTSDFK-FPGT--KIMSDLDVLVIDAT-YGQEHMIR 157
                                       99998.........888888899***********.6755..468**********9.55556664 PP

>> DRMBL  DNA repair metallo-beta-lactamase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       1.2   1.1e+04      28      49 ..      47      68 ..      38      68 .. 0.65
   2 !   15.8   0.1   1.3e-06     0.012      31     103 ..     250     314 ..     238     317 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.2
                             DRMBL 28 klekylkalkekfdsvlafrPt 49
                                      + + yl++ k++ + +la +Pt
  gi|385806099|ref|YP_005842497.1| 47 DHTLYLSKSKRHSTYILATQPT 68
                                      4455777777787888877776 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1.3e-06
                             DRMBL  31 kylkalkekfdsvlafrPtGWtkkekkkkdlekikessksrekisiyrvpYSeHSSfrELkefvkslkpkkii 103
                                       +++++ k + ++   ++ +GW ++++ kk +e        ++k++ + v +S+H  f+++ + v+  kpk  i
  gi|385806099|ref|YP_005842497.1| 250 QHMNSKKGTLSQTADLILSGWFFESPIKKIIE--------KNKYEKWLVAFSDHGDFQDVFAYVSESKPKMLI 314
                                       556666666888888999*******9877777........589******************999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2391.01
//
Query:       gi|385806100|ref|YP_005842498.1|  [L=258]
Description: hypothetical protein FFONT_1058 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score 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   14.0   0.1       0.28   11.3   0.0    2.3  3  ApoA-II   Apolipoprotein A-II (ApoA-II)


Domain annotation for each model (and alignments):
>> ApoA-II  Apolipoprotein A-II (ApoA-II)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   1.6e-05      0.28      10      57 ..     100     146 ..      97     151 .. 0.87
   2 ?   -2.7   0.0      0.38   6.8e+03      32      49 ..     195     212 ..     191     212 .. 0.77
   3 ?   -1.6   0.0      0.17   3.1e+03      44      67 ..     225     248 ..     222     252 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.6e-05
                           ApoA-II  10 lfsQYfqtltdyGKdlveKvkaselqaQakaYfektqeqlvPLvkkag 57 
                                       l+sQ  ++l ++ K+l+eK ka e    a  +++   e lv L k a 
  gi|385806100|ref|YP_005842498.1| 100 LISQSSKSLEEVAKNLLEKGKAVERML-AIEFLQSQSEDLVFLMKMAF 146
                                       89********************99655.55899999999999998775 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.38
                           ApoA-II  32 selqaQakaYfektqeql 49 
                                       +e+   ++a++++ + +l
  gi|385806100|ref|YP_005842498.1| 195 KEIYGDVEAFLKNEKSRL 212
                                       588888999999888765 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.17
                           ApoA-II  44 ktqeqlvPLvkkagtdlvnflssl 67 
                                       k++e+l+ +  k + d  +++ + 
  gi|385806100|ref|YP_005842498.1| 225 KSRERLIDVLFKIKEDFASIYEYY 248
                                       789999999999999988887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); 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 0.27s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1633.41
//
Query:       gi|385806101|ref|YP_005842499.1|  [L=235]
Description: ERCC4-type nuclease [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.4e-17   62.4   0.0    7.8e-17   61.9   0.0    1.2  1  ERCC4            ERCC4 domain
    2.9e-10   40.1   0.1    4.9e-10   39.3   0.1    1.4  1  HHH_2            Helix-hairpin-helix motif
    2.5e-07   31.2   0.2    7.8e-07   29.6   0.2    1.8  1  HHH_5            Helix-hairpin-helix domain
    0.00032   20.4   0.4     0.0014   18.4   0.1    2.4  3  HHH              Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.099   12.5   0.0          2    8.3   0.0    2.8  3  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
       0.11   13.2   0.8       0.63   10.7   0.1    2.6  2  5_3_exonuc       5'-3' exonuclease, C-terminal SAM fold
       0.15   12.1   0.0       0.31   11.1   0.0    1.5  1  AARP2CN          AARP2CN (NUC121) domain


Domain annotation for each model (and alignments):
>> ERCC4  ERCC4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.9   0.0   3.1e-20   7.8e-17      17     153 ..      31     144 ..      14     146 .. 0.80

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 3.1e-20
                                       TTTSEEEEE--SSSSE.EE...CTT...............EEEEEEEHHHHHHHHCCSHHHHHHHHHHH..H-SE.. CS
                             ERCC4  17 elgvevvietlpigdyilwrrkvkaeynleldieepceekvlverksaddlvasikdgrleeqvsrlkr.ngykk.. 90 
                                       + +++v++++l+ gdy+l+   +k+        e p    +lverk+a+d+v+si+dgr+++q + lk+ ++  +  
  gi|385806101|ref|YP_005842499.1|  31 KGKLSVAVKQLEAGDYLLL---SKK-------GELP----ILVERKTAEDFVNSIIDGRIWKQSATLKKiKE--Rge 91 
                                       4457899*********888...666.......3334....***************************99544..355 PP

                                       ..EEEEEES.-GGGTT................THHH.HHHHHHHHHHHHS-EEEEESSHHHHHHHH CS
                             ERCC4  91 ..pillveg.ldqykrknknsrnkqykakvrqinrktiesaLvqlqldfgvsilttesanetaewl 153
                                         p++++eg l+  ++k k             i++ +i   + +l l+ ++++++t s++ t+ wl
  gi|385806101|ref|YP_005842499.1|  92 alPVIVLEGnLSYTLEKRK-------------ISETAILRTIDELVLNRDIPVIYTLSKSSTISWL 144
                                       8899999**5444443322.............*********************************8 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   0.1   1.9e-13   4.9e-10       2      56 ..     174     227 ..     173     233 .. 0.91

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 1.9e-13
                             HHH_2   2 llfaLGIrhVGektAklLakrFksldaLkkasleeLlevddiGeeiAqsivefFe 56 
                                       +l++L+I   G +tA++L ++F+++ ++++ ++ eL ++++iGe+ A++i+e F+
  gi|385806101|ref|YP_005842499.1| 174 VLLSLSII-TGTQTARKLLTKFGTIRNIANLTVGELMQIEGIGEVKAKKIYELFN 227
                                       66667775.4******************************************997 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.2   3.1e-10   7.8e-07      11      53 ..     183     224 ..     173     225 .. 0.93

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 3.1e-10
                                       -HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHH CS
                             HHH_5  11 GpktAlallsaGiesvedlaaadveeLakipGiGkktAeriil 53 
                                       G +tA++ll + ++++  +a+++v eL +i GiG+ +A++i +
  gi|385806101|ref|YP_005842499.1| 183 GTQTARKLLTK-FGTIRNIANLTVGELMQIEGIGEVKAKKIYE 224
                                       778********.*****************************85 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       3.3   8.6e+03      21      26 ..      61      66 ..      61      68 .. 0.80
   2 ?   -2.7   0.0       2.6   6.7e+03       8      13 ..     118     123 ..     115     124 .. 0.80
   3 !   18.4   0.1   5.6e-07    0.0014       3      29 ..     198     224 ..     196     225 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.3
                                      HHHHHH CS
                               HHH 21 pktAea 26
                                      +ktAe 
  gi|385806101|ref|YP_005842499.1| 61 RKTAED 66
                                      79**96 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.6
                                       SSHHHH CS
                               HHH   8 asreeL 13 
                                       ++++eL
  gi|385806101|ref|YP_005842499.1| 118 RTIDEL 123
                                       799*99 PP

  == domain 3  score: 18.4 bits;  conditional E-value: 5.6e-07
                                       HHHHTSSHHHHHTSTT-SHHHHHHHHH CS
                               HHH   3 eglipasreeLlalPGVGpktAeaIls 29 
                                        ++ + ++ eL++++G+G+ +A +I++
  gi|385806101|ref|YP_005842499.1| 198 RNIANLTVGELMQIEGIGEVKAKKIYE 224
                                       577777888****************86 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 ?   -2.2   0.0       1.5   3.7e+03      11      19 ..      61      69 ..      59      70 .. 0.84
   2 ?    0.2   0.0      0.26   6.8e+02      10      20 ..     183     193 ..     181     204 .. 0.78
   3 ?    8.3   0.0   0.00078         2       2      19 ..     207     224 ..     206     225 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.5
                   DNA_pol_lambd_f 11 pktAkkwya 19
                                      +ktA+++++
  gi|385806101|ref|YP_005842499.1| 61 RKTAEDFVN 69
                                      68****997 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.26
                   DNA_pol_lambd_f  10 GpktAkkwyak 20 
                                       G++tA+k+  k
  gi|385806101|ref|YP_005842499.1| 183 GTQTARKLLTK 193
                                       88*****9876 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.00078
                   DNA_pol_lambd_f   2 lFtkvyGVGpktAkkwya 19 
                                       +++++ G+G ++Akk y+
  gi|385806101|ref|YP_005842499.1| 207 ELMQIEGIGEVKAKKIYE 224
                                       69*************996 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 ?   -0.4   0.0      0.72   1.9e+03      83      83 ..     132     132 ..      58     182 .. 0.64
   2 ?   10.7   0.1   0.00025      0.63      27      47 ..     183     210 ..     180     233 .. 0.66

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.72
                        5_3_exonuc  83 e 83 
                                        
  gi|385806101|ref|YP_005842499.1| 132 I 132
                                       1 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00025
                        5_3_exonuc  27 GektAakLlkeygsleeile.......n 47 
                                       G +tA kLl+++g++ +i +       +
  gi|385806101|ref|YP_005842499.1| 183 GTQTARKLLTKFGTIRNIANltvgelmQ 210
                                       899***************9833333322 PP

>> AARP2CN  AARP2CN (NUC121) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00012      0.31      41      82 ..     172     224 ..     134     227 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00012
                           AARP2CN  41 e.........eeskedrtlsve.GyvrG.splsanqlvHipglGDfqiekiek 82 
                                       e         +  ++ r+l  + G++r  ++l +++l+ i g+G+++ +ki +
  gi|385806101|ref|YP_005842499.1| 172 ErvllslsiiTGTQTARKLLTKfGTIRNiANLTVGELMQIEGIGEVKAKKIYE 224
                                       03335556665666667776666*****8899******************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1682.12
//
Query:       gi|385806102|ref|YP_005842500.1|  [L=355]
Description: Sua5/YciO/YrdC/YwlC family protein [Fervidicoccus fontis Kam940]
Scores for complete 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-61  206.8   0.0    2.8e-61  206.1   0.0    1.4  1  Sua5_yciO_yrdC   Telomere recombination
      8e-28   97.7   0.0    1.3e-27   97.0   0.0    1.3  1  SUA5             Putative GTP-binding controlling metal-bindi
  ------ inclusion threshold ------
      0.063   13.5   0.1       0.19   11.9   0.0    1.8  2  TPM_phosphatase  TPM domain
       0.16   11.9   0.1        0.5   10.3   0.0    1.8  2  SPA              Stabilization of polarity axis


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 !  206.1   0.0   6.3e-65   2.8e-61       2     179 .]      23     198 ..      22     198 .. 0.98

  Alignments for each domain:
  == domain 1  score: 206.1 bits;  conditional E-value: 6.3e-65
                                       HHHTTSEEEEE-SSSEEEEEETTSHHHHHHHHHHHTSHCCC--EEEESSCCCCCCCC-TC--HHHHHHHHCT-SSSC CS
                    Sua5_yciO_yrdC   2 alrkGgivaiptetvYgLacdatneeaverlreiKgrpsdkplavlvasledlkklaeseveeealkllerfwPGpi 78 
                                       ++++Gg+va+ptetvYgL+++a ne a ++++++Kgrpsd+p++v+++s+e+l+k+a  +v+e a+kl++++wPGp+
  gi|385806102|ref|YP_005842500.1|  23 IIKNGGLVAFPTETVYGLGANALNEHATRKIYQVKGRPSDNPIIVHISSIEMLEKIAV-NVPEIAYKLIKKLWPGPL 98 
                                       79*******************************************************9.****************** PP

                                       EEEEE..E-TS-HHHHTTTTEEEEEE-SSHHHHHHHHHCTS-EEEEES-STTS-S-SSHHHHHHHC-TTSECB-SS- CS
                    Sua5_yciO_yrdC  79 tlllkrskeklpkevapglktvGvrlPdtplarlLlealgeplvaTSanlsgepsitdaeeveeelgeivdlildgg 155
                                       tl+lkrs++ +pk v++gl+tv+vr+P++p+a++L+e+++ p++a+San+sg+ps+t+ae+v ++l +++++i+dgg
  gi|385806102|ref|YP_005842500.1|  99 TLILKRSNA-VPKLVTGGLDTVAVRMPAHPIAQNLIEQAELPIAAPSANISGKPSPTRAEHVIKDLYGKIEAIIDGG 174
                                       *****9766.******************************************************************* PP

                                       --SSS---EEEETTSSTSSECEXX CS
                    Sua5_yciO_yrdC 156 eiavgvdstVvdltegkpkilRrG 179
                                       e+  gv+stV+++++++p +lR+G
  gi|385806102|ref|YP_005842500.1| 175 EVLYGVESTVINVLSEEPILLRPG 198
                                       **********************98 PP

>> SUA5  Putative GTP-binding controlling metal-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.0   0.0   2.8e-31   1.3e-27       2     134 .]     201     350 ..     200     350 .. 0.76

  Alignments for each domain:
  == domain 1  score: 97.0 bits;  conditional E-value: 2.8e-31
                                       -HHHHHHHS-...--............-------------S-SSEEEEE--GGGHHHH.........HHHHHTTS-E CS
                              SUA5   2 tleeleevld...avek........keekpraPGmkyrHYaPkapvvlveaeeeeeaake....ekleekkksgkkv 63 
                                       ++e +e+++d   +           + ek  aPG++yrHYaP+a+++l+e+++  e++ +    +  + +++ +++v
  gi|385806102|ref|YP_005842500.1| 201 SVEIIESIIDrkvK--IphfakgigEAEKAIAPGTRYRHYAPEAKLILIEPSTFTEDEIKkmisKIKDIANQYKNEV 275
                                       57888888854321..12234457788999*********************99888877789944444444555555 PP

                                       EEEEEGGGTGG.....TSEEEEE......E-TT-HHHHHHHHHHHHHHHHHS--SEEEEE----STTHHHHHHHHHH CS
                              SUA5  64 gvlatseskea.....assvlsls....lgsrsdleeaarnLFaaLrelDeegvdlilvegvpeeglglAvmnRLrk 131
                                        ++++se+  +     ++     +    lgsr++l e+a+n+F++Lr++De g+++ + e+++e+glglAvmnRLrk
  gi|385806102|ref|YP_005842500.1| 276 CIITSSENYYEysrilDE-----KrlfvLGSRNNLFEIAKNVFDVLRKIDEYGCKVAISESFEERGLGLAVMNRLRK 347
                                       555544444445554433.....245559************************************************ PP

                                       HTT CS
                              SUA5 132 AAg 134
                                       A++
  gi|385806102|ref|YP_005842500.1| 348 ASS 350
                                       *96 PP

>> TPM_phosphatase  TPM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.1   4.7e+03      89     108 ..     200     220 ..     198     230 .. 0.64
   2 ?   11.9   0.0   4.2e-05      0.19       7      39 ..     251     283 ..     247     323 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.1
                                       --HHHHHHHHHHTHH.HHHHH CS
                   TPM_phosphatase  89 ltdaraesildetil.palkd 108
                                       ++ +++esi+d++++ p++++
  gi|385806102|ref|YP_005842500.1| 200 YSVEIIESIIDRKVKiPHFAK 220
                                       566788999998664245544 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 4.2e-05
                                       -S-HHHHHHHHHHHHHHHHTT--EEEEEEESB- CS
                   TPM_phosphatase   7 lLsdeeeaeleeklaalekktgvqivvvtvdsl 39 
                                       +++++e++++ +k++++++++++++ ++t +  
  gi|385806102|ref|YP_005842500.1| 251 TFTEDEIKKMISKIKDIANQYKNEVCIITSSEN 283
                                       79***************************9855 PP

>> SPA  Stabilization of polarity axis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       0.8   3.6e+03      67      80 ..      64      78 ..      45      84 .. 0.76
   2 ?   10.3   0.0   0.00011       0.5      39     108 ..     256     322 ..     241     328 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.8
                               SPA 67 Py.vdlseldalekv 80
                                      P+ v++s++++lek+
  gi|385806102|ref|YP_005842500.1| 64 PIiVHISSIEMLEKI 78
                                      444899999999987 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00011
                               SPA  39 evsefvLalsnlispagdvlrgfknnsfPyvdlseldalekvpgyIvGvtNPiFeeqeqlWDvlydldsg 108
                                       e+ +++  +  +++   + + ++ ++s  y + s +  l +   +++G  N +Fe  ++++Dvl  +d+ 
  gi|385806102|ref|YP_005842500.1| 256 EIKKMISKIKDIANQ-YKNEVCIITSSENYYEYSRI--LDEKRLFVLGSRNNLFEIAKNVFDVLRKIDEY 322
                                       555555555555554.33333444444666667765..888888***********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       740  (0.0412739); expected 358.6 (0.02)
Passed bias filter:                      610  (0.0340231); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 2271.56
//
Query:       gi|385806103|ref|YP_005842501.1|  [L=532]
Description: Fe-S oxidoreductase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.1e-15   56.5   0.0    3.5e-14   53.5   0.0    2.3  2  Radical_SAM  Radical SAM superfamily
    1.1e-14   54.6   0.0    2.7e-14   53.2   0.0    1.7  2  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      0.11   9.5e+02      91     111 ..      83     104 ..      46     149 .. 0.69
   2 !   53.5   0.0   3.9e-18   3.5e-14       2     166 ..     200     367 ..     199     368 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.11
                                       HHHHHHHHHTT.-SEEEEEEBS CS
                                       xxxxxxxxxxx.xxxxxxxxxx RF
                       Radical_SAM  91 eeklerllelg.vdrvslglea 111
                                        +++++l+e+g v +v  g ++
  gi|385806103|ref|YP_005842501.1|  83 IKIAKKLKEAGnVKYVVAGGHH 104
                                       5555666666655555444444 PP

  == domain 2  score: 53.5 bits;  conditional E-value: 3.9e-18
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC.... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.... RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla.... 74 
                                       +++rgC+++C +C+++++  ++g++r++sv+++++e++++ +e g k v++  ++ +   +++ + + +   +    
  gi|385806103|ref|YP_005842501.1| 200 ETSRGCPFNCEYCSVTKM--WGGTWRFKSVDRVIKELERV-KELGYKWVFFIDDNFIIPIKKIIDERLILLDKiaks 273
                                       689**************8..********************.799********9999998655555555555556777 PP

                                       .......CCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET CS
                                       .......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  75 .......vpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikr 144
                                                 +r  +++   +    ++ +l e g+    lg+e++d+e +lk m+++  + +   a+ +l +agi +
  gi|385806103|ref|YP_005842501.1| 274 slkklklIVQLRADFVAKNQW----IVNKLYEGGIRLTFLGIESGDPE-TLKNMRKNLVPNDSALAVSLLSKAGIIV 345
                                       755555555555555555555....69*****99**************.*****999999***************** PP

                                       EEEEEEEBTTTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 145 vvdrivglpGendeeleellel 166
                                          +i+g p e+++ ++ ++++
  gi|385806103|ref|YP_005842501.1| 346 HAGFILGAPYETEKAMNRTISF 367
                                       ***************9999987 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.2   0.0   3.1e-18   2.7e-14       8     120 ..      19     132 ..      15     133 .. 0.94
   2 ?   -3.8   0.0       1.4   1.2e+04      22      49 ..     297     324 ..     293     327 .. 0.76

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 3.1e-18
                       B12-binding   8 vggdlhplGlavlaaalrdagfeVqllganven...edivaairaekpdvvglSalltsqleavkelvellkrirpr 81 
                                       +g  ++pl +a+la + +++g++ ++ +a + n   e++++ i a +pd+ ++ +  +++ +   ++++ lk++++ 
  gi|385806103|ref|YP_005842501.1|  19 FGISMPPLSAAYLASVAKERGYDAKFFDAFALNaneEKLAELISAYDPDIAAFLINASTYANPSIKIAKKLKEAGNV 95 
                                       56679***********************99999999*****************9999*****************999 PP

                       B12-binding  82 vkvvvGGahpsldpeetleaklgiddvvvgegedaleal 120
                                         vv+GG+h+++++ ++l+  +g+d++ + ege ++ ++
  gi|385806103|ref|YP_005842501.1|  96 KYVVAGGHHATFTYSLLLK--NGFDVIFLREGEVTFSNF 132
                                       999***************8..9************99876 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 1.4
                       B12-binding  22 aalrdagfeVqllganvenedivaaira 49 
                                       + l + g++ ++lg++  ++++++++r+
  gi|385806103|ref|YP_005842501.1| 297 NKLYEGGIRLTFLGIESGDPETLKNMRK 324
                                       5566779999999999998888887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (532 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 3464.70
//
Query:       gi|385806104|ref|YP_005842502.1|  [L=550]
Description: thermosome [Fervidicoccus fontis Kam940]
Scores for complete 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-179  597.2  17.2   2.8e-179  596.9  17.2    1.1  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family
  ------ inclusion threshold ------
      0.027   14.9   0.0        1.9    8.9   0.0    3.3  4  DUF2710     Protein of unknown function (DUF2710)


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 !  596.9  17.2  3.1e-183  2.8e-179       1     490 [.      36     527 ..      36     528 .. 0.97

  Alignments for each domain:
  == domain 1  score: 596.9 bits;  conditional E-value: 3.1e-183
                                       HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHH CS
                        Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleea 77 
                                       ++++++tt+GPkGmdKmlv++ g++++TnDGatil +++i+hP ak++v++a+ qdeevGDGT t+viLageLl+++
  gi|385806104|ref|YP_005842502.1|  36 ISEALRTTYGPKGMDKMLVDSLGDITITNDGATILDKMDIQHPGAKMMVQIAKGQDEEVGDGTKTAVILAGELLRQS 112
                                       789************************************************************************** PP

                                       HHHHHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHH.HCH CS
                        Cpn60_TCP1  78 ekliaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAv.kli 153
                                       e+l+++g+hpt+i++gy+ka+e+a +++kei++ i+   +++e+L+k+a+tsl sk ++ ++++l++++v+A  ++ 
  gi|385806104|ref|YP_005842502.1| 113 EDLLDKGIHPTVIVSGYKKAAEEAEKIIKEISEPID--INNKEILKKIATTSLYSKAVQGSRDKLAEIAVEAAtRVA 187
                                       *******************************66666..559********************************5555 PP

                                       CCCS...EECSCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSC CS
                        Cpn60_TCP1 154 eene...keldlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsda 227
                                       e ++   + +dl++i+++k+ ggsl d+ l++G+v+dk+v++p mpk++enak++lld +Leiek+e++++++++d+
  gi|385806104|ref|YP_005842502.1| 188 E-KRgdsYFVDLDSIQIIKKYGGSLLDTMLIDGVVIDKEVVHPGMPKRVENAKIALLDAPLEIEKPEIDAEIRINDP 263
                                       5.55599********************************************************************** PP

                                       CHHHHHHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGG CS
                        Cpn60_TCP1 228 eeleklekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledl 304
                                       +++ k++++ee++l+++++ki++ g+nvv++qkgidd+a+hflak+gila+rrvk++d+e+l +atG+++vs+++dl
  gi|385806104|ref|YP_005842502.1| 264 TQMRKFLQEEEEMLKRMVDKIAEVGANVVIAQKGIDDVAQHFLAKRGILAVRRVKRSDMEKLERATGGRIVSNIDDL 340
                                       ***************************************************************************** PP

                                       GCGC-EEEEEEEECCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHH CS
                        Cpn60_TCP1 305 tpeelGtakkveeekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatel 381
                                       +p++lG+a  vee+kig++k++++e+ ks+k++til+r+  +  +de era++dAl++v+ ai+  k+v+GGGate+
  gi|385806104|ref|YP_005842502.1| 341 QPSDLGEAALVEERKIGEDKMVFVEGAKSAKSVTILIRAGFERLVDEGERALRDALSAVADAIKMAKIVAGGGATEV 417
                                       ***************************************************************************** PP

                                       HHHHHHHCCCCTSXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTX.TTEEEETTTTCEEECCCC CS
                        Cpn60_TCP1 382 elakklkeyaksvsgeeqlaieafakALevipktLaeNaGldpievlaklraahnkge.kelgidvesgeiidlvea 457
                                       e+ak+lke+a ++ g++qla+eafa+ALe++p t+aeNaG+d+ e++ klraah++++ k +gidv +g+i+++++ 
  gi|385806104|ref|YP_005842502.1| 418 EVAKRLKEIAPKIGGKQQLAVEAFARALETLPSTIAENAGYDALEIMMKLRAAHANSNgKFMGIDVYTGNIVNMKDI 494
                                       ******************************************************555547***************** PP

                                       TXEEEHHHHHHHHHHHHHHHHHHHCEEEEEXXX CS
                        Cpn60_TCP1 458 gvvDplkvkrqalksAteaastiLrideiikak 490
                                       g+++p+++k +a+k+Ateaa++iLrid+ i a 
  gi|385806104|ref|YP_005842502.1| 495 GIIEPAAIKLNAIKAATEAATMILRIDDFIAAS 527
                                       ****************************99875 PP

>> DUF2710  Protein of unknown function (DUF2710)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.17   1.5e+03      60      81 ..     114     137 ..     108     152 .. 0.69
   2 ?    8.9   0.0   0.00021       1.9      25      91 ..     175     243 ..     161     254 .. 0.82
   3 ?    0.3   0.0       0.1   9.2e+02      50      95 ..     466     512 ..     440     518 .. 0.69
   4 ?   -1.6   0.0      0.41   3.7e+03      27      59 ..     499     531 ..     493     532 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.17
                           DUF2710  60 rlleltlhpgv.vsdyays.elae 81 
                                        ll+  +hp+v vs+y  + e ae
  gi|385806104|ref|YP_005842502.1| 114 DLLDKGIHPTViVSGYKKAaEEAE 137
                                       588899999973577765314444 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00021
                           DUF2710  25 lseaaekwealvaeaetvtysvdlgdvravansdgrlleltlhpgvvsd..yayselaerlnlvitalr 91 
                                       l e a    + vae    +y vdl  ++ + +  g ll+  l  gvv d    +  + +r++ +  al 
  gi|385806104|ref|YP_005842502.1| 175 LAEIAVEAATRVAEKRGDSYFVDLDSIQIIKKYGGSLLDTMLIDGVVIDkeVVHPGMPKRVENAKIALL 243
                                       777777778889999999***************************998722467788888877766665 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.1
                           DUF2710  50 dvr.avansdgrlleltlhpgvvsdyayselaerlnlvitalreeve 95 
                                        +r a ans+g+++ + ++ g + +     + e   + + a++  +e
  gi|385806104|ref|YP_005842502.1| 466 KLRaAHANSNGKFMGIDVYTGNIVNMKDIGIIEPAAIKLNAIKAATE 512
                                       4451579******9999999888877777777766666666666655 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 0.41
                           DUF2710  27 eaaekwealvaeaetvtysvdlgdvravansdg 59 
                                        aa k +a+ a +e++t  + + d  a ++s g
  gi|385806104|ref|YP_005842502.1| 499 PAAIKLNAIKAATEAATMILRIDDFIAASKSTG 531
                                       5888999999999*9999999999999888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (550 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.45
# Mc/sec: 3654.01
//
Query:       gi|385806105|ref|YP_005842503.1|  [L=53]
Description: hypothetical protein FFONT_1063 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       269  (0.0150036); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 395.26
//
Query:       gi|385806106|ref|YP_005842504.1|  [L=294]
Description: putative transcriptional regulator [Fervidicoccus fontis Kam940]
Scores for complete 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-31  106.3   1.3    1.4e-30  104.8   0.4    2.2  2  HrcA_DNA-bdg     Winged helix-turn-helix transcription repres
    3.3e-26   91.5   4.5      3e-13   50.0   2.1    2.7  2  CBS              CBS domain
    9.8e-09   35.5   0.2    2.6e-08   34.1   0.2    1.8  1  Rrf2             Transcriptional regulator
     0.0002   21.3   0.4    0.00057   19.8   0.4    1.8  1  HTH_11           HTH domain
    0.00029   20.7   0.2    0.00063   19.7   0.2    1.6  1  HTH_36           Helix-turn-helix domain
     0.0038   17.0   0.0     0.0085   15.9   0.0    1.7  1  HTH_IclR         IclR helix-turn-helix domain
     0.0093   15.5   1.7      0.032   13.8   1.7    2.0  1  HTH_24           Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.015   15.3   0.0       0.17   12.0   0.0    2.4  2  HTH_29           Winged helix-turn helix
      0.015   15.2   0.1      0.042   13.7   0.1    1.8  1  TrmB             Sugar-specific transcriptional regulator Trm
      0.018   14.7   0.1        1.3    8.8   0.0    2.8  2  GntR             Bacterial regulatory proteins, gntR family
      0.025   14.5   0.0      0.068   13.1   0.0    1.8  1  MarR_2           MarR family
      0.028   14.2   0.3      0.091   12.5   0.3    1.9  1  HTH_38           Helix-turn-helix domain
      0.041   14.2   0.1       0.13   12.6   0.0    1.8  2  Penicillinase_R  Penicillinase repressor
      0.044   13.9   0.2       0.21   11.7   0.0    2.2  3  LAGLIDADG_WhiA   WhiA LAGLIDADG-like domain
      0.052   13.7   0.6       0.28   11.3   0.0    2.3  2  Arc_PepC         Archaeal Peptidase A24 C-terminal Domain
       0.11   12.4   0.0       0.28   11.2   0.0    1.7  1  Dimerisation2    Dimerisation domain
       0.13   12.1   0.0        6.2    6.7   0.0    3.0  3  TusA             Sulfurtransferase TusA
       0.13   12.5   0.0          2    8.7   0.0    2.6  2  PaaX             PaaX-like protein


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 !  104.8   0.4   1.4e-33   1.4e-30       1      74 [.       3      76 ..       3      79 .. 0.98
   2 ?   -1.4   0.0       1.9   1.8e+03      23      51 ..     230     260 ..     217     264 .. 0.65

  Alignments for each domain:
  == domain 1  score: 104.8 bits;  conditional E-value: 1.4e-33
                      HrcA_DNA-bdg  1 eLtsvqkeilqaLielyrkkkravKgeeiAevlkrneGtvRNqlqsLkalgLvegvpGPkGGYkPtlkayealk 74
                                      eLt++q+e+l aLi+ly++++r vK+ eiA++++++eGtvRN+++sL++lgL+e+++GP+GGY+Ptlka e +k
  gi|385806106|ref|YP_005842504.1|  3 ELTQTQREVLLALIKLYEQNNRLVKSIEIAQQIGKDEGTVRNIISSLRSLGLLESKTGPSGGYMPTLKAKELIK 76
                                      69*******************************************************************99987 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.9
                      HrcA_DNA-bdg  23 avKgeeiAevlkrneGtvRN...qlqsLkalg 51 
                                        vK+ ++ + ++++  t+R    ++ +++ ++
  gi|385806106|ref|YP_005842504.1| 230 NVKA-KVEDYMRKHVVTIREdedIMDAVRIME 260
                                       4554.377888888888885222455555555 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.0   1.8e-13   1.7e-10       1      55 [.     173     226 ..     173     228 .. 0.93
   2 !   50.0   2.1     3e-16     3e-13       1      56 [.     235     290 ..     235     291 .. 0.94

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 1.8e-13
                                       HHHHSBSSCEEEETTSBHHHHHHH.HHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   1 Vgdimtrdvvtvppdttleealel.mrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       Vg++ t+++vt++ +++l+ea  l + ++++++ PV+ e++++vGi+t +D+++a 
  gi|385806106|ref|YP_005842504.1| 173 VGEVATKNLVTLTSQMPLREASSLlF-REKIRGAPVI-ENERIVGIITTTDIAKAY 226
                                       89**********************77.777*******.899************986 PP

  == domain 2  score: 50.0 bits;  conditional E-value: 3e-16
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                       V+d+m++ vvt+++d+++ +a+++m+ +gv+rl VV+  g++ Givt++D+l+ ++
  gi|385806106|ref|YP_005842504.1| 235 VEDYMRKHVVTIREDEDIMDAVRIMELHGVGRLIVVNAVGEPKGIVTRTDILKRIS 290
                                       89***********************5588****999****************9885 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.2   2.7e-11   2.6e-08       3      66 ..       4      66 ..       1      81 [. 0.90

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 2.7e-11
                                      --HHHHHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCEE CS
                              Rrf2  3 lsskteyalhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGkgGGyr 66
                                      l++  + +l al+ L +++++  v+s eia++ +  +  ++ i++ Lr  gl++s+ G++GGy+
  gi|385806106|ref|YP_005842504.1|  4 LTQTQREVLLALIKLYEQNNRL-VKSIEIAQQIGKDEGTVRNIISSLRSLGLLESKTGPSGGYM 66
                                      66777778999999*9999986.****************************************7 PP

>> HTH_11  HTH 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   0.00057       6      54 ..      15      65 ..      10      66 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5.7e-07
                            HTH_11  6 lelLleargp.isgeeLAeeLnvSrrtvrrdIkaLeelgvpIesepgr..GY 54
                                      l+ L+e+++  + + e+A++++  + tvr+ I +L++lg  +es+ g+  GY
  gi|385806106|ref|YP_005842504.1| 15 LIKLYEQNNRlVKSIEIAQQIGKDEGTVRNIISSLRSLG-LLESKTGPsgGY 65
                                      45566777777****************************.********9999 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.2   6.3e-07   0.00063       2      55 .]       3      55 ..       2      55 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 6.3e-07
                            HTH_36  2 rLspsaklllgslasfanknggcfpsqetlakrlglsknTvsraikeLeqlGyi 55
                                      +L+ +++ +l+ l +++ +n+    s   +a++ g+++ Tv+++i +L+ lG++
  gi|385806106|ref|YP_005842504.1|  3 ELTQTQREVLLALIKLYEQNNRLVKSI-EIAQQIGKDEGTVRNIISSLRSLGLL 55
                                      79999*****************77776.5***********************97 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   8.5e-06    0.0085      19      50 ..      26      57 ..      10      59 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 8.5e-06
                                      -BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 19 ltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      ++  e+A+++g    tv++++++L  lG++e 
  gi|385806106|ref|YP_005842504.1| 26 VKSIEIAQQIGKDEGTVRNIISSLRSLGLLES 57
                                      4778**************************95 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   1.7   3.2e-05     0.032       2      47 ..       5      55 ..       4      56 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.2e-05
                            HTH_24  2 detdrkILelLqk....npr.isqreLAerlglSpstvnrrlkrLeeeGlI 47
                                       +t+r++L +L k    n r     e+A+++g   +tv+  +  L + Gl+
  gi|385806106|ref|YP_005842504.1|  5 TQTQREVLLALIKlyeqNNRlVKSIEIAQQIGKDEGTVRNIISSLRSLGLL 55
                                      567788888887778888888**************************9997 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00017      0.17      15      52 ..      28      65 ..      12      73 .. 0.80
   2 ?    0.3   0.0      0.73   7.3e+02       2      25 ..     241     262 ..     240     262 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00017
                            HTH_29 15 vsqiAkllglsrrtvyrwlkrfeegGlaalldrrrsgr 52
                                        +iA++ g ++ tv++++   +  Gl   + ++++g 
  gi|385806106|ref|YP_005842504.1| 28 SIEIAQQIGKDEGTVRNIISSLRSLGLLESKTGPSGGY 65
                                      569***********************777777776665 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.73
                            HTH_29   2 aqallllaeGvstvsqiAkllgls 25 
                                       ++++  ++e ++ ++++++++ l+
  gi|385806106|ref|YP_005842504.1| 241 KHVVT-IREDED-IMDAVRIMELH 262
                                       55555.778888.********985 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   4.2e-05     0.042       4      58 ..       2      61 ..       1      73 [. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.2e-05
                                      CHHHHHCCCHCHHHHHHCCCHHC.....HHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB  4 lGLseyEakvYlaLlklgpatad.....eiaeelgvprskvYevLrsLedkGlVerekgr 58
                                      + L+++  +v laL+kl + + +     eia+++g ++ +v ++++sL + Gl e + g 
  gi|385806106|ref|YP_005842504.1|  2 YELTQTQREVLLALIKLYEQNNRlvksiEIAQQIGKDEGTVRNIISSLRSLGLLESKTGP 61
                                      67999999999999955444433333449*************************998876 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0    0.0013       1.3      29      59 ..      30      60 ..      17      63 .. 0.92
   2 ?    2.7   0.0     0.099        99      37      52 ..     186     201 ..     184     202 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0013
                                      HHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                              GntR 29 eLaaefgVsrttvReALrrLeaeglverrqg 59
                                      e+a+++g +  tvR  ++ L + gl+e++ g
  gi|385806106|ref|YP_005842504.1| 30 EIAQQIGKDEGTVRNIISSLRSLGLLESKTG 60
                                      89*************************9987 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.099
                                       -HHHHHHHHHHHHHTT CS
                              GntR  37 srttvReALrrLeaeg 52 
                                       s +++ReA + L +e+
  gi|385806106|ref|YP_005842504.1| 186 SQMPLREASSLLFREK 201
                                       89******99998887 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   6.9e-05     0.068       3      57 ..       4      61 ..       2      64 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.9e-05
                                      --HHHHHHHHHHHCTTTS..EE.EHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESS CS
                            MarR_2  3 ltpaqarvLaaLgrrpgr..dl.tvgelarrlglsksavsrilkrLvaaGLverrpgp 57
                                      lt +q+ vL+aL    ++  +l    e+a+  g + ++v +i+  L + GL+e ++gp
  gi|385806106|ref|YP_005842504.1|  4 LTQTQREVLLALIKLYEQnnRLvKSIEIAQQIGKDEGTVRNIISSLRSLGLLESKTGP 61
                                      78999999999666555567566999****************************9997 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.3   9.1e-05     0.091       5      41 ..       4      46 ..       3      47 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.1e-05
                            HTH_38  5 LsleeReeIerlla.eGlslr.....eIArrLgrspsTIsREl 41
                                      L+ ++Re++ +l++    ++r     eIA+++g++ +T+ + +
  gi|385806106|ref|YP_005842504.1|  4 LTQTQREVLLALIKlYEQNNRlvksiEIAQQIGKDEGTVRNII 46
                                      888999999988653445555669***************9976 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00013      0.13       1      73 [.       4      76 ..       4      79 .. 0.89
   2 ?   -2.1   0.0       4.8   4.8e+03      77     109 ..     220     252 ..     206     257 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00013
                                      ---S-SHHHHHHHHHS-EEHHHHHHT.--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE----XXXXXX CS
                   Penicillinase_R  1 lgelEaevmeilwekgeatvkevvee.leeekelaysTVktllrrLvkKgllsrekegrafiYsplvseeeava 73
                                      l++ ++ev+ +l ++ e++ + v +  ++++    + TV+ +++ L   gll++++ g +  Y p+++ +e+++
  gi|385806106|ref|YP_005842504.1|  4 LTQTQREVLLALIKLYEQNNRLVKSIeIAQQIGKDEGTVRNIISSLRSLGLLESKT-GPSGGYMPTLKAKELIK 76
                                      57889999999999999998888887688999999*****************9987.***********999876 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.8
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                   Penicillinase_R  77 kqlldklfegsvkelvaafveeeklseddleeL 109
                                        ++ + + eg+vk+ v + ++++ ++  + e++
  gi|385806106|ref|YP_005842504.1| 220 TDIAKAYSEGNVKAKVEDYMRKHVVTIREDEDI 252
                                       556666777777777777777776666655555 PP

>> LAGLIDADG_WhiA  WhiA LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       3.4   3.4e+03      30      47 ..      38      55 ..       3      78 .. 0.60
   2 ?   -2.5   0.0       5.6   5.5e+03      64      78 ..     101     115 ..      84     127 .. 0.67
   3 ?   11.7   0.0   0.00021      0.21      36      77 ..     221     262 ..     217     265 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.4
                    LAGLIDADG_WhiA 30 deelaeqlqkllnefele 47
                                      de +++++ + l++++l 
  gi|385806106|ref|YP_005842504.1| 38 DEGTVRNIISSLRSLGLL 55
                                      444455555555555444 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.6
                    LAGLIDADG_WhiA  64 aeqIvdlLkiigahe 78 
                                       + +I+d+L+  ga+ 
  gi|385806106|ref|YP_005842504.1| 101 SIEIMDVLNPAGAKA 115
                                       446788888777765 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00021
                    LAGLIDADG_WhiA  36 qlqkllnefeleakilerrkkyvvylKkaeqIvdlLkiigah 77 
                                       +++k+ +e +++ak+ +  +k vv++++ e+I+d  +i++ h
  gi|385806106|ref|YP_005842504.1| 221 DIAKAYSEGNVKAKVEDYMRKHVVTIREDEDIMDAVRIMELH 262
                                       788889999******************************976 PP

>> Arc_PepC  Archaeal Peptidase A24 C-terminal Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00028      0.28       4      40 ..      97     133 ..      94     155 .. 0.89
   2 ?   -0.2   0.1       1.1   1.1e+03      15      62 ..     243     289 ..     228     292 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00028
                          Arc_PepC   4 vsitelkliskvikaltkeelsdkkkveeLkEGdila 40 
                                       v+ + ++++ ++  a  k+ l+ + +++eLkEGdi++
  gi|385806106|ref|YP_005842504.1|  97 VTAYSIEIMDVLNPAGAKAILKANGNLDELKEGDIIR 133
                                       67788888888888889999***************98 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.1
                          Arc_PepC  15 vikaltkeelsdkkkveeLkE.Gdila.diilekeddevtvddksllkrl 62 
                                       v+++   e + d +++ eL+  G ++  + + e  ++   v + ++lkr+
  gi|385806106|ref|YP_005842504.1| 243 VVTIREDEDIMDAVRIMELHGvGRLIVvNAVGEP-KG--IVTRTDILKRI 289
                                       4444456778888888888853443330333333.33..56667777776 PP

>> Dimerisation2  Dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00028      0.28      30      83 ..      23      74 ..      11      79 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00028
                     Dimerisation2 30 eeplsaeevaeelgasvkGterLldacvaLgLLerekkeekkalYsntelasty 83
                                      ++ +++ e+a+++g +   ++ ++  + +LgLLe++  ++ +++Y  t  a++ 
  gi|385806106|ref|YP_005842504.1| 23 NRLVKSIEIAQQIGKDEGTVRNIISSLRSLGLLESK--TGPSGGYMPTLKAKEL 74
                                      56778899**************************55..5545899988877765 PP

>> TusA  Sulfurtransferase TusA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0063       6.2      15      52 ..      16      54 ..      13      68 .. 0.77
   2 ?   -1.2   0.0       1.8   1.8e+03      12      24 ..      66      78 ..      64     100 .. 0.80
   3 ?    1.4   0.0      0.29   2.9e+02      14      32 ..     116     134 ..     112     140 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0063
                                      HHHHHHHCCC.GCT-EEEEEESSCHHHHHHHHHHHHHTE CS
                              TusA 15 lklkkalekl.eegevlevladdpaatediprfakklgh 52
                                      +kl ++ ++l ++ e+ + +  d++++++i  ++++lg+
  gi|385806106|ref|YP_005842504.1| 16 IKLYEQNNRLvKSIEIAQQIGKDEGTVRNIISSLRSLGL 54
                                      555555566656667778899****************97 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.8
                                      CCHHHHHHHHCCC CS
                              TusA 12 ePllklkkalekl 24
                                      +P lk+k+ ++++
  gi|385806106|ref|YP_005842504.1| 66 MPTLKAKELIKSY 78
                                      8999999999987 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.29
                                       HHHHHHHHCCCGCT-EEEE CS
                              TusA  14 llklkkalekleegevlev 32 
                                       +lk+   l++l+eg+++++
  gi|385806106|ref|YP_005842504.1| 116 ILKANGNLDELKEGDIIRL 134
                                       6899999********9975 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0     0.002         2      26      56 ..      28      58 ..      12      66 .. 0.85
   2 ?    0.3   0.0      0.84   8.4e+02      17      37 ..     172     192 ..     165     204 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.002
                              PaaX 26 LirllaelGiseslvRaalsRlakaGwlvre 56
                                       i++ +++G +e++vR  +s l   G+l ++
  gi|385806106|ref|YP_005842504.1| 28 SIEIAQQIGKDEGTVRNIISSLRSLGLLESK 58
                                      599***********************99875 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.84
                              PaaX  17 rggaiwlgsLirllaelGise 37 
                                       + g++  ++L+ l++++ + e
  gi|385806106|ref|YP_005842504.1| 172 NVGEVATKNLVTLTSQMPLRE 192
                                       569999*******99886665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); 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: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 1670.62
//
Query:       gi|385806107|ref|YP_005842505.1|  [L=248]
Description: 3-oxoacyl-[acyl-carrier-protein] reductase FabG (short chain dehydrogenase SDR family) [Fervidicoccus fontis Kam940]
Scores for complete 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-74  248.0   0.0    9.9e-74  247.8   0.0    1.0  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
    3.3e-61  206.2   0.1    3.8e-61  205.9   0.1    1.1  1  adh_short     short chain dehydrogenase
    4.9e-16   59.2   0.0    7.2e-16   58.6   0.0    1.2  1  KR            KR domain
     0.0096   15.3   0.0      0.014   14.8   0.0    1.1  1  DUF1776       Fungal family of unknown function (DUF1776)
  ------ inclusion threshold ------
      0.042   12.8   0.0      0.051   12.6   0.0    1.2  1  3Beta_HSD     3-beta hydroxysteroid dehydrogenase/isomerase f
      0.061   13.2   0.0       0.24   11.2   0.0    1.8  2  3HCDH_N       3-hydroxyacyl-CoA dehydrogenase, NAD binding do


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  247.8   0.0   3.3e-77   9.9e-74       1     234 []      15     246 ..      15     246 .. 0.95

  Alignments for each domain:
  == domain 1  score: 247.8 bits;  conditional E-value: 3.3e-77
                                       TTTTSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEE..EE--TTSHHHHHHHHHHHHHHHSSEEEEEE CS
                      adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneeakkrveelaeelgaev..lecDVtdeeqvealveevvekfgklDilvn 75 
                                       G a gIG++iA++la+ G +++l d++++  ++++e++  l+ ev  ++ DVt++e+ve+ vee  +kfgk+Dilvn
  gi|385806107|ref|YP_005842505.1|  15 GSAMGIGKGIAQKLASLGSNLILFDISDKIFETAKEIEH-LEVEVlpFKGDVTNKEDVERSVEEGISKFGKIDILVN 90 
                                       7799**************************777777765.8988779****************************** PP

                                       -----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSC.CEEEEEEEGGGTSBSTTTTHHHHHHHHHHH CS
                      adh_short_C2  76 nagiapklkgpfletsreefdraldvnlyslfllakaalp.lmkeg.gsivnlssvgaervvpnynaygaaKaalea 150
                                       nagi p+  +pf+e++++++dr+l++nl+s+fl++ka+lp +mk++ g+ivn+ss++a +++p+  +y+a+K+++++
  gi|385806107|ref|YP_005842505.1|  91 NAGIYPS--KPFIEMTESDWDRVLNINLKSMFLFSKAVLPnMMKNSyGRIVNISSIAAIVGFPGLIHYSASKGGVVG 165
                                       *******..*******************************9999989****************************** PP

                                       HHHHHHHHHGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEE CS
                      adh_short_C2 151 ltrylAvelgpkgiRvNavspgpikTlaasgikgfdelleelearaplgrlgtpeevaeaalfLasdeasyitGqtl 227
                                       +t++lA e+++ gi+vNa++pgpi+T  ++     ++  e  ++ +p+gr+g+pe++a+a++fLas+e+++itG+ l
  gi|385806107|ref|YP_005842505.1| 166 FTKALALEVAKFGITVNAIAPGPIETSGTK---VDEQTAEIYKRLIPVGRMGKPEDIANAVAFLASEESQFITGHLL 239
                                       *************************86654...446888888999******************************** PP

                                       EESTTGG CS
                      adh_short_C2 228 vvDgGlt 234
                                       vvDgG+t
  gi|385806107|ref|YP_005842505.1| 240 VVDGGYT 246
                                       ******8 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.9   0.1   1.3e-64   3.8e-61       3     190 ..      11     197 ..       9     202 .. 0.96

  Alignments for each domain:
  == domain 1  score: 205.9 bits;  conditional E-value: 1.3e-64
                                       EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSES CS
                         adh_short   3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkld 79 
                                        +vtG + GIG+ ia++la+ G +++++d+s +k+ e+ake++ ++ ++l++++Dvt++e+ve+ ve+ ++k+gk+d
  gi|385806107|ref|YP_005842505.1|  11 SIVTGSAMGIGKGIAQKLASLGSNLILFDIS-DKIFETAKEIEHLEVEVLPFKGDVTNKEDVERSVEEGISKFGKID 86 
                                       58*****************************.5577***************************************** PP

                                       EEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHH CS
                         adh_short  80 vLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaav 156
                                       +LvnNAGi  s+pf e++e++w+rv+++Nl+++fl ++avlp+m+k+s GrIvn+sS+a+ v+++g++ YsAsK++v
  gi|385806107|ref|YP_005842505.1|  87 ILVNNAGIYPSKPFIEMTESDWDRVLNINLKSMFLFSKAVLPNMMKNSYGRIVNISSIAAIVGFPGLIHYSASKGGV 163
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHH CS
                         adh_short 157 agltrslakelaptgirvnavaPGlvdTdmakel 190
                                       +g+t++la e+a+ gi+vna+aPG+++T  +k  
  gi|385806107|ref|YP_005842505.1| 164 VGFTKALALEVAKFGITVNAIAPGPIETSGTKVD 197
                                       ***************************9887655 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.6   0.0   2.4e-19   7.2e-16       3     153 ..      11     160 ..      10     191 .. 0.84

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 2.4e-19
                                       EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHS CS
                                KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaee 79 
                                        ++tG + g+G+ +a+ la+ g  +l+l+  s    ++  ++ +e+e+l++ev  ++ Dv++k++ve+ +ee  +++
  gi|385806107|ref|YP_005842505.1|  11 SIVTGSAMGIGKGIAQKLASLGS-NLILFDIS----DKIFETAKEIEHLEVEVLPFKGDVTNKEDVERSVEEGISKF 82 
                                       58******************996.67777666....445568899******************************** PP

                                       S---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT....S--SEEEEEEEHHHHH--TT-HHHHHH CS
                                KR  80 ppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled....esldffvlfSSiagllgsagqanYaaa 152
                                       ++i   ++ Ag+   k++ emt++d+++vl+  +k +    +++ +    +s   +v +SSia+++g +g  +Y+a 
  gi|385806107|ref|YP_005842505.1|  83 GKIDILVNNAGIYPSKPFIEMTESDWDRVLNINLKSMFLFSKAVLPnmmkNSYGRIVNISSIAAIVGFPGLIHYSAS 159
                                       **************************************99999877566678889********************97 PP

                                       H CS
                                KR 153 N 153
                                        
  gi|385806107|ref|YP_005842505.1| 160 K 160
                                       5 PP

>> DUF1776  Fungal family of unknown function (DUF1776)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   4.7e-06     0.014     102     212 ..      94     200 ..      87     209 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.7e-06
                           DUF1776 102 syptgpietiplsswaselnerllspiltlqallplltsrakqkakiivvnpsissslnlpfhapEalvssalsalf 178
                                        yp+ p+ ++++s w  +ln +l s++l+++a lp + +   ++   iv   si + +  p     +   + +  ++
  gi|385806107|ref|YP_005842505.1|  94 IYPSKPFIEMTESDWDRVLNINLKSMFLFSKAVLPNMMK---NSYGRIVNISSIAAIVGFPGLIHYSASKGGVVGFT 167
                                       6999**********************************8...667777888899999999999999999999999** PP

                           DUF1776 179 evLkrelrphnidvtqikLGnldlangsqsnski 212
                                       ++L+ e+++ +i v  i  G ++ + g +  ++ 
  gi|385806107|ref|YP_005842505.1| 168 KALALEVAKFGITVNAIAPGPIETS-GTKVDEQT 200
                                       *******999999999999999998.55444444 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.7e-05     0.051       1      66 [.      12      77 ..      12     150 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.7e-05
                         3Beta_HSD  1 vvtGgaGFlGralvkeLvrlee.lkevrvlDlrespelleelskvnvkk.viegDvtdkdkleealeg 66
                                      +vtG+a  +G+ + ++L +l++ l    + D+ +++ +  e+++++v+    +gDvt+k+++e+ +e+
  gi|385806107|ref|YP_005842505.1| 12 IVTGSAMGIGKGIAQKLASLGSnLILFDISDKIFETAK--EIEHLEVEVlPFKGDVTNKEDVERSVEE 77
                                      69999999*************74455555555555555..56666666559************99986 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   8.2e-05      0.24      10      61 ..      20      72 ..      13      91 .. 0.82
   2 ?   -0.7   0.0      0.38   1.1e+03      14      56 ..     170     214 ..     161     236 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 8.2e-05
                                      CHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-.HHHHC CS
                           3HCDH_N 10 mGagiaavfasagleVvlvdiseealekalekieksleklvekgklk.eeeve 61
                                      +G+gia+ +as g +  l+dis+++ e+a+e  + ++e l  kg ++ +e+ve
  gi|385806107|ref|YP_005842505.1| 20 IGKGIAQKLASLGSNLILFDISDKIFETAKEIEHLEVEVLPFKGDVTnKEDVE 72
                                      79*************************99987777777777777776444444 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.38
                                       HHHHHHHTT-EEEEE-S..-HHHHHHHHHHHHHHHHCCTTTTSS- CS
                           3HCDH_N  14 iaavfasagleVvlvdi..seealekalekieksleklvekgklk 56 
                                       +a  +a+ g++V+ +     e + +k+ e+ ++ +++l+  g++ 
  gi|385806107|ref|YP_005842505.1| 170 LALEVAKFGITVNAIAPgpIETSGTKVDEQTAEIYKRLIPVGRMG 214
                                       555666777777776654333444455555555556666656655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); 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: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1503.51
//
Query:       gi|385806108|ref|YP_005842506.1|  [L=239]
Description: hypothetical protein FFONT_1066 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-34  119.9   0.0    1.8e-34  119.6   0.0    1.0  1  PAC2         PAC2 family
  ------ inclusion threshold ------
       0.11   12.6   0.0        2.7    8.1   0.0    2.2  2  tRNA-Thr_ED  Archaea-specific editing domain of threonyl-tRNA


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 !  119.6   0.0     2e-38   1.8e-34       3     212 ..      23     225 ..      22     226 .. 0.89

  Alignments for each domain:
  == domain 1  score: 119.6 bits;  conditional E-value: 2e-38
                                       EESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETTEEE-SEEEEEE.TTT.SEEEEEEE...E CS
                              PAC2   3 lGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveegrelepprlyak.dsgsrdllvlqg...r 75 
                                        Gf g G Vg +++ +L++sl++e++g i ++y +p      +v+ ++ +   p++++a+ +   ++l+v++    +
  gi|385806108|ref|YP_005842506.1|  23 SGFKGFGAVGIISALHLVNSLKMERIGIITTKY-HP-----EYVYRDDYGIAYPFEIFASkE---NKLVVFVTreiP 90 
                                       79*******************************.99.....88666666********98854...788888886544 PP

                                       -HSCHHHHHHHHHHHHHHHTTESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHH.HCT..-CEEEEHHHHH CS
                              PAC2  76 epilqyeefakalldwaeelgvkevvvLggldageradvphtrpekvtgaatdeelleel.ees..eyggivgitgl 149
                                       +  ++  e++ +++++a ++g++  v++ggld  +++    ++ ek+ +  ++ ++ e++  e+  ++  i+g+ +l
  gi|385806108|ref|YP_005842506.1|  91 DERIRD-EYVYEITKFAAKYGISPLVLIGGLDKKFKN----KEDEKMRWLKNSYYRGESIdAEEleKGLLIIGPLAL 162
                                       444444.6************************88775....677799****999999999533367999******** PP

                                       HHHHHHHTT-EEEEEEEEEECCC--HHHHHHHHHHHHHHHT---HCHHHHHHHHHHHHHHHHH CS
                              PAC2 150 LlsaakergipavgllaevphylpdPkaaaalleflskllglevdtedLeedaeeleeqleel 212
                                        l+ ++  ++pa++ll++++ + pdP+aaa+++e+l++l+ l++d ++L+e+ +++ee++++l
  gi|385806108|ref|YP_005842506.1| 163 QLMYSELLKVPAIVLLPYANAETPDPAAAATAIEALNRLFSLSIDNSKLIEEGKMIEEEIKKL 225
                                       ************************************************************997 PP

>> 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 ?    8.1   0.0    0.0003       2.7      32      76 ..      76     116 ..      69     118 .. 0.88
   2 ?    2.3   0.0     0.018   1.6e+02      68      99 ..     169     201 ..     142     213 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0003
                                       EESSEEEEEEE-BTT--H...HHHHHHHHHHHHHHHHHT-SEEEE CS
                       tRNA-Thr_ED  32 rleealvvFiavEkeDeeekekvvekavkeikkvakkvkakkvvl 76 
                                       + e+ lvvF++ E  De+    + ++ v ei+k+a k +++ +vl
  gi|385806108|ref|YP_005842506.1|  76 SKENKLVVFVTREIPDER----IRDEYVYEITKFAAKYGISPLVL 116
                                       6799************99....88999999999999999888776 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.018
                                       HHT-SEEEEEE-STS.-SSB--HHHHHHHHHHH CS
                       tRNA-Thr_ED  68 kvkakkvvlypyaHL.ssslaspevakeilkkl 99 
                                        +k+ ++vl pya   + + a++ +a+e+l++l
  gi|385806108|ref|YP_005842506.1| 169 LLKVPAIVLLPYANAeTPDPAAAATAIEALNRL 201
                                       578899******975245667777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); 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 0.30s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 1438.60
//
Query:       gi|385806109|ref|YP_005842507.1|  [L=160]
Description: 7-cyano-7-deazaguanine tRNA-ribosyltransferase (Archaeal tRNA-guanine transglycosylase) [Fervidicoccus fontis Kam940]
Scores for complete 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   66.2   0.0    5.6e-18   64.8   0.0    1.6  2  TGT_C2    Patch-forming domain C2 of tRNA-guanine transglycos
    3.1e-13   49.5   0.1    6.5e-13   48.5   0.1    1.5  1  PUA       PUA domain
  ------ inclusion threshold ------
      0.014   15.6   0.0      0.028   14.7   0.0    1.5  1  UPF0113   UPF0113 PUA domain


Domain annotation for each model (and alignments):
>> TGT_C2  Patch-forming domain C2 of tRNA-guanine transglycosylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.8   0.0   9.4e-22   5.6e-18       3      69 ..      16      84 ..      15      86 .. 0.93
   2 ?   -2.4   0.0      0.92   5.5e+03      40      56 ..     119     135 ..     109     138 .. 0.66

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 9.4e-22
                            TGT_C2  3 lraiadYqFGagagdaLfpedvtitrs..atgrirqvlvdgerlatlraqdgrltLsleGarrlheslp 69
                                      l+++++YqFG++a +++f+ + +i++s  +tgrir+v+++ge  + ++++ g+++Ls++Ga+++  s+p
  gi|385806109|ref|YP_005842507.1| 16 LKSVIAYQFGKEAVESIFKSNNSIEVSrySTGRIRTVYINGEEALYFNPKIGLFSLSMYGASLIFPSIP 84
                                      899***************99977777777***********************************98877 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.92
                            TGT_C2  40 dgerlatlraqdgrltL 56 
                                       dg+ ++ ++++  +l L
  gi|385806109|ref|YP_005842507.1| 119 DGDEVFIVNENGELLAL 135
                                       56666666666666665 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   0.1   1.1e-16   6.5e-13      16      72 ..     102     158 ..      89     159 .. 0.94

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 1.1e-16
                                       T-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEE CS
                               PUA  16 gasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveier 72 
                                       ++ Llap v     d++ gd+V iv+e+gel+a+G+a++  ee++kik+gk++ i+r
  gi|385806109|ref|YP_005842507.1| 102 KKTLLAPAVAWSTNDIRDGDEVFIVNENGELLALGKALLCHEEIKKIKRGKVALIKR 158
                                       789************************************************998886 PP

>> UPF0113  UPF0113 PUA 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     0.028      22      53 ..     109     140 ..     101     158 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.6e-06
                           UPF0113  22 silkitesvkenqvvvVlnengeplGiGkirk 53 
                                        + + t ++++++ v+++nenge+l++Gk+  
  gi|385806109|ref|YP_005842507.1| 109 AVAWSTNDIRDGDEVFIVNENGELLALGKALL 140
                                       57778899********************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); 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: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.56
# Mc/sec: 867.58
//
Query:       gi|385806110|ref|YP_005842508.1|  [L=235]
Description: putative transcription regulator, containing DNA-binding HTH domain [Fervidicoccus fontis Kam940]
Scores for complete 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-05   23.1   0.1     0.0006   19.8   0.0    2.6  3  HTH_3           Helix-turn-helix
     0.0001   22.3   0.1    0.00077   19.4   0.1    2.5  3  HTH_19          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.041   14.2   0.0       0.15   12.4   0.0    2.0  2  HTH_31          Helix-turn-helix domain
       0.14   12.3   0.0       0.26   11.4   0.0    1.4  1  MqsA_antitoxin  Antitoxin component of bacterial toxin-antito


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 !   19.8   0.0   1.3e-07    0.0006       2      43 ..      29      70 ..      28      73 .. 0.91
   2 ?   -0.9   0.0       0.4   1.8e+03      10      26 ..      85     101 ..      85     105 .. 0.71
   3 ?   -3.5   0.0       2.6   1.2e+04      34      43 ..     219     228 ..     218     228 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.3e-07
                                      HHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHH CS
                             HTH_3  2 kelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkk 43
                                      k++R   + +q e+++k+Gv  s +s++E+G+r+P  + + k
  gi|385806110|ref|YP_005842508.1| 29 KKWRRIFNVTQLEISKKMGVFSSVLSDYEKGRRSPGSKFIRK 70
                                      778888999**************************9888877 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.4
                                       HHHHHHHHHHTSSHHHH CS
                             HTH_3  10 lsqeeLAeklGvsrsti 26 
                                       ++ +eLA+ l ++ +++
  gi|385806110|ref|YP_005842508.1|  85 ITVKELARNLRLPATAL 101
                                       57788888877776665 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 2.6
                                       SCSBHHHHHH CS
                             HTH_3  34 rnPsletlkk 43 
                                       r+P++ tl+k
  gi|385806110|ref|YP_005842508.1| 219 RAPDVNTLIK 228
                                       7899999997 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   1.7e-07   0.00077       1      57 [.      25      81 ..      25     103 .. 0.85
   2 ?    0.6   0.0      0.13   5.8e+02       9      23 ..      80      95 ..      74     120 .. 0.81
   3 ?   -3.4   0.0       2.3     1e+04      44      55 ..     203     214 ..     198     215 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.7e-07
                            HTH_19  1 GerLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaell.lkiaealgidle 57
                                      Ge  k+ R+ ++ tq e++++ g+  s +s +E+g++  p+++ + +++  +l+id++
  gi|385806110|ref|YP_005842508.1| 25 GEAMKKWRRIFNVTQLEISKKMGVFSSVLSDYEKGRR-SPGSKFIrKFVISLLEIDEK 81
                                      8899*********************************.**977776555566666654 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.13
                            HTH_19  9 eelgl.tqeelaerlg 23
                                      e++g+ t +ela++l+
  gi|385806110|ref|YP_005842508.1| 80 EKRGWiTVKELARNLR 95
                                      6777779999998775 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 2.3
                            HTH_19  44 lllkiaealgid 55 
                                       l  k+a+  gi+
  gi|385806110|ref|YP_005842508.1| 203 LTIKLAQSDGIP 214
                                       567999999997 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.4e-05      0.15       7      50 ..      29      71 ..      25     104 .. 0.78
   2 ?   -0.4   0.0      0.34   1.5e+03      16      30 ..      86     100 ..      80     150 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.4e-05
                            HTH_31  7 ralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavleal 50
                                      + +R+  +++q e  +  gv  s ls++E Grr  p   +++++
  gi|385806110|ref|YP_005842508.1| 29 KKWRRIFNVTQLEISKKMGVFSSVLSDYEKGRR-SPGSKFIRKF 71
                                      5566666899***********************.5966655554 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.34
                            HTH_31  16 sqeevAerlgvsest 30 
                                       + +e+A+ l++ ++ 
  gi|385806110|ref|YP_005842508.1|  86 TVKELARNLRLPATA 100
                                       555666665544443 PP

>> MqsA_antitoxin  Antitoxin component of bacterial toxin-antitoxin system, MqsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   5.8e-05      0.26      67     115 ..      21      69 ..       4      80 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.8e-05
                    MqsA_antitoxin  67 elvdpafiarvrkkleldqreaaeifGgGvnafsryekGkvrpplalvk 115
                                       +   ++ +++ r+ ++++q e+++ +G+    +s yekG+  p    ++
  gi|385806110|ref|YP_005842508.1|  21 SENPGEAMKKWRRIFNVTQLEISKKMGVFSSVLSDYEKGRRSPGSKFIR 69 
                                       4456788999******************************999887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); 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: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1436.95
//
Query:       gi|385806111|ref|YP_005842509.1|  [L=433]
Description: putative 3-octaprenyl-4-hydroxybenzoate carboxylase [Fervidicoccus fontis Kam940]
Scores for complete 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  267.9   0.0    1.6e-79  267.7   0.0    1.0  1  UbiD      3-octaprenyl-4-hydroxybenzoate carboxy-lyase
  ------ inclusion threshold ------
       0.18   11.6   0.0       0.35   10.7   0.0    1.4  1  RMI2      RecQ-mediated genome instability protein 2


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 !  267.7   0.0   1.7e-83   1.6e-79       2     405 ..      11     393 ..      10     394 .. 0.91

  Alignments for each domain:
  == domain 1  score: 267.7 bits;  conditional E-value: 1.7e-83
                                       HHCCCTTSEEEE.ESEB-TBTHHHHHHHHHHHHT--EEEEEEBTTB.TT-EEEE-TTS-HCHHHHHHTS-GHHHHHH CS
                              UbiD   2 ealekagelvri.keevdpelEiaeiarrvleeggpallFenvkgkgskfpvltnlfgtrervalalglssleeile 77 
                                       ++l++ +++++  ++e + e+Ei+ +++++   g   +lF   +   + fp+++nlf tre++ +++g+++le++++
  gi|385806111|ref|YP_005842509.1|  11 NKLRESENIREYnDREYNEEFEIPLLIKKNQ--GSSTVLFRASR---TPFPIISNLFETREKFLKVFGFKNLEDFYR 82 
                                       5666666666652569999**********88..999******93...57**************************** PP

                                       HHHHHHHS..----EE--GCG-GGGSEEECCCCC--HHHS---BSSTTSSS-EEECEEEEEE-TTTT-EEEEEEEEE CS
                              UbiD  78 klaellepkppippkvvesekapcqeevvlegddvdLskLPvltlwpgDgGpyitlglvitrdpetgkrnlgiyRmq 154
                                        +++l+ +k   p ++ +        +   e+++  LskL +l+++++DgG y+t++++i+++  +   n++i+R +
  gi|385806111|ref|YP_005842509.1|  83 LVTDLKPEKD--PYVEFDF-----D-KY-YEKSNYGLSKLGALKYYEKDGGFYFTSTIFIAKT--ELSYNASIHRTM 148
                                       *****88744..3444432.....2.22.357899***************************7..5679******** PP

                                       EEETTEEEE--TTTHCHHHHHHHHHHCCT--EEEEEEES--HHHHHHCTS--TTT-TCHHHHHHHHTS--EEEE-SS CS
                              UbiD 155 vldknklglhwqihkggaehlrkakkkggeplpvavaiGvdPaltlaAvaplPeglsElefaGalrgepvelvkcet 231
                                       v+d+ +++ ++++++   + +++ k  g ++ +v++ +G++P++ l+++++ P++  E+e++  l g+++++vk++ 
  gi|385806111|ref|YP_005842509.1| 149 VIDDYSAVARIVPRHL-YRIIENNKSLG-KDTKVTILLGAHPIIELVSSISPPYNQFEFELIPNLLGKKLPIVKSPL 223
                                       ************7754.44466666666.9*********************************************** PP

                                       SSSEEETT-SEEEEEEEECCEEEECTTTC-TTSCEEC--CCEEEEEEEEEE.E-TT-EEE.E-SSSCCSHHHHCHHH CS
                              UbiD 232 vdlevpadAEivleGeidpgetapEGPfgdhtGyysevrdefpvfkVtait.hRkdpiyp.ttvvgkppeedallgk 306
                                        + +vp    i++e +i+  e++ EGPf+d++G+y++ r+ +p++k++ i+  +++pi   ++++g   e+++l+g+
  gi|385806111|ref|YP_005842509.1| 224 WNNPVPLGTSIIIEATITN-EMVNEGPFVDIMGTYDRIRK-QPLIKINGIYtLKEKPIAVhAILPGGG-EHQLLMGI 297
                                       ******************8.79**************9999.6********96899***9999999999.******** PP

                                       HHHHHHHHHHHCCSTTEEEEEE-GGGTTTCEEEEECHHHTCCHHHHHHHHHHCCTTGGC-SEEEEEEETTS-TTSHH CS
                              UbiD 307 alealflpllkkqvpevkdvhlpeeggfhllavvsikkrypghakkvmealwalkqqlsltKlvivvDedvdvrdlk 383
                                         ea ++++++  vp+v++v+l+++gg++l+a++si+k+++g+ k+++ a++++++  sl K+v+vvD dvd++d++
  gi|385806111|ref|YP_005842509.1| 298 TKEAQIYKAVSLVVPKVHKVRLTQAGGGWLHAAISIDKNHDGDGKNAILAAFGAHP--SL-KHVVVVDGDVDIDDPN 371
                                       ********************************************************..99.**************** PP

                                       HHHHHHHHC--CCCCEEEECCC CS
                              UbiD 384 evlwaiatrvdpdrDlviiegt 405
                                        ++waiatr+++dr l++++++
  gi|385806111|ref|YP_005842509.1| 372 MIEWAIATRFQADRGLIVVKNA 393
                                       *******************997 PP

>> RMI2  RecQ-mediated genome instability protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   3.9e-05      0.35      76     116 ..     239     279 ..     230     283 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 3.9e-05
                              RMI2  76 pktkkclkeGkYVmVvGvvqssspepvlkavKvvdLsenpd 116
                                       + t++ ++eG +V ++G++ + +++p++k+  +  L e+p+
  gi|385806111|ref|YP_005842509.1| 239 TITNEMVNEGPFVDIMGTYDRIRKQPLIKINGIYTLKEKPI 279
                                       5567899***********************99999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2732.01
//
Query:       gi|385806112|ref|YP_005842510.1|  [L=400]
Description: hypothetical protein FFONT_1070 [Fervidicoccus fontis Kam940]
Scores for 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-132  441.1   0.0   3.7e-132  440.8   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 !  440.8   0.0  2.1e-136  3.7e-132       1     397 [.       1     390 [.       1     393 [. 0.96

  Alignments for each domain:
  == domain 1  score: 440.8 bits;  conditional E-value: 2.1e-136
                            DUF521   1 mkLtkeeeamlnGeeGealqkameilvalGeilgAerLvpvtsahvsgvsyktigdaglefleelaekgakvrvptt 77 
                                       m Ltkeee++lnG++Ge+++ a+++++++Ge l+AerLv+v+++h sg sy tigdagl f+e++++k+akv+v +t
  gi|385806112|ref|YP_005842510.1|   1 MFLTKEEESILNGAHGEIKALALKTIIKIGESLNAERLVDVSHVHASGLSYLTIGDAGLVFIESVVSKNAKVKVFST 77 
                                       99*************************************************************************** PP

                            DUF521  78 lnpigvdlerweelgvdeefaekqeriieayeklGveltftCtpyllgnapkkGehlawsESsavvyaNSvlGarTn 154
                                       lnp+g+dl++w+++g++e+faekq+ri+e + klG+++tftCtpyl+ ++p  Gehlaw+ESsav +aN+++Ga Tn
  gi|385806112|ref|YP_005842510.1|  78 LNPVGMDLDDWKKMGISEDFAEKQKRIVELVLKLGFDPTFTCTPYLI-RKPFPGEHLAWGESSAVGMANTYYGAYTN 153
                                       **********************************************9.***************************** PP

                            DUF521 155 reggpsalaaAitGrtpeyGlhldenRkptvlveveae..sedeadygalGylvGkkvgeriPvlkglekpsedelK 229
                                       reggp+ +++Ai+G+++e+Glhl+enR+ptv + ++ e    d +  galG++vG+k++++iP++k ++ +s +++K
  gi|385806112|ref|YP_005842510.1| 154 REGGPITILSAIVGKIYEAGLHLKENRVPTVEIIIDGEidLTDPSISGALGIIVGEKIKSGIPLFKRNRLTSFEAIK 230
                                       *******************************9999999878889999*******************98888****** PP

                            DUF521 230 algAalaasgavalfhiegvTPeaetleealgekekaekititkedleevleelskakeekvdlvalGcPhlsleEl 306
                                       + +Aa++a+g +a+ +i+g+TPe ++l +++    + ek++i++++l+e++++     +  +d+v++GcPh+ leE+
  gi|385806112|ref|YP_005842510.1| 231 SYTAAVGANGDIAMSVIDGITPEYKDLIKKA---GELEKVHIDANELKEIVKDS---IDYIPDVVLMGCPHADLEEI 301
                                       ***********************66655554...579***************77...8899**************** PP

                            DUF521 307 relaellkgkkkkvkvelwvttsrevkeeaerlglveklekaGvkvlsdtCmvvsplikkkevkkvatnSgKaahYl 383
                                        +++ ++ ++ kk +v++++ tsr+v ++++++gl+++le++Gv +++dtC+vvsp+++ k +k+++t SgK ++Yl
  gi|385806112|ref|YP_005842510.1| 302 LNFSIQI-KDCKKINVPVIISTSRYVSNKLNEMGLLQQLEEKGVIFIKDTCPVVSPFVSLK-FKNIVTVSGKSLFYL 376
                                       *******.88999**********************************************86.*************** PP

                            DUF521 384 pgltgvkvalgsle 397
                                       p+++ vkva+  ++
  gi|385806112|ref|YP_005842510.1| 377 PRMHDVKVAIVPFN 390
                                       ********997665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 2613.57
//
Query:       gi|385806113|ref|YP_005842511.1|  [L=129]
Description: putative aconitase, subunit [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-28   98.5   0.1    1.8e-28   98.1   0.1    1.2  1  DUF126    Aconitase X swivel 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 !   98.1   0.1     1e-32   1.8e-28       1      79 [.      24      99 ..      24     100 .. 0.98

  Alignments for each domain:
  == domain 1  score: 98.1 bits;  conditional E-value: 1e-32
                                      --TTS-B-TTT-BB-S.-SSSTT-B-TTSEEEES--S--SS-TTHHHHHHHHT-S-SEEEESS--HHHHHHHHHHT--E CS
                            DUF126  1 lSflggvdpetGkvidkghplegqsiagkiLvlpsgkGStvgsyvllelakngtaPaAlilreadpilalGaivadiPl 79
                                      +Sflg+v++++G++i k++++   si++kiL++p+++GStvgsyv+++l+++++aP+A+i+++a+pil++G+++++iPl
  gi|385806113|ref|YP_005842511.1| 24 ISFLGEVNAKNGEIIFKDKKI---SIKDKILIFPNTRGSTVGSYVIYALKYYNNAPKAIIVEKAEPILIAGCVLSGIPL 99
                                      8*****************998...******************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 922.20
//
Query:       gi|385806114|ref|YP_005842512.1|  [L=214]
Description: cobalamin (vitamin B12) biosynthesis protein CbiM [Fervidicoccus fontis Kam940]
Scores for complete 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-63  214.4  10.5    1.6e-63  214.3  10.5    1.0  1  CbiM             Cobalt uptake substrate-specific transmembra
    0.00062   19.9  12.3    0.00062   19.9  12.3    2.8  3  ECF_trnsprt      ECF transporter, substrate-specific componen
  ------ inclusion threshold ------
       0.11   12.3   0.3        1.4    8.7   0.2    2.0  2  Pam17            Mitochondrial import protein Pam17
        2.7    7.5  16.6          1    8.8   9.8    2.2  2  ABC2_membrane_5  ABC-2 family transporter protein


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 !  214.3  10.5   3.6e-67   1.6e-63       1     207 []       2     211 ..       2     211 .. 0.98

  Alignments for each domain:
  == domain 1  score: 214.3 bits;  conditional E-value: 3.6e-67
                              CbiM   1 HipdgiLspavllaayavalallalalrrlrkeldear..vpllallaafifaaqminipip.ggtslHllgavlaa 74 
                                       Hipdg+L+ +v+++ y+++l++++++  rlr++l++++  + ++a+++a++fa+qm+n p+  ggt++Hl+g+ l+ 
  gi|385806114|ref|YP_005842512.1|   2 HIPDGYLTESVWITCYVISLPIIIFSYIRLRSKLKKEElsTSFFAVITAAVFALQMVNYPLGpGGTTAHLIGTPLLS 78 
                                       *********************************996666899********************999************ PP

                              CbiM  75 iLlGpwaaflavavvlllqallfgdGGitaLGaNilnmavigvllaylvyrllsrlasskkrvalaaflaallsvvl 151
                                       i++Gp a+++ +++vll+qallfgdGGit++GaN+lnmav +++++++ y ll++l++++k + +a++++++l++v 
  gi|385806114|ref|YP_005842512.1|  79 IIFGPEAGIVGLSIVLLIQALLFGDGGITTYGANTLNMAVTASVVSFFSYVLLRKLYKNEKGRIVAGAISGWLGIVS 155
                                       *****************************************************999999****************** PP

                              CbiM 152 aallvalelalsgleaslsltaalaamllvhlpvgilEgviTaaivkalkkvrpel 207
                                       aa++++lel+ls++++ ++l +++++m++ h+++gi+Eg++T++++ a+ k+rp+l
  gi|385806114|ref|YP_005842512.1| 156 AAFMCGLELGLSKSTFGYGLSVTIPVMVISHAILGIVEGLVTGFAIYAIGKYRPDL 211
                                       ************99999*************************************97 PP

>> ECF_trnsprt  ECF transporter, substrate-specific component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.7     0.012        52      69     113 ..      12      54 ..       6      61 .. 0.74
   2 !   19.9  12.3   1.4e-07   0.00062       4     118 ..      47     157 ..      44     162 .. 0.69
   3 ?    1.4   6.9     0.066     3e+02      40      95 ..     148     206 ..     144     212 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.012
                                       THHHHHHHHHHHHCHHHHHHHHHHCCCHTTHHHHHHHHHHHHCCC CS
                       ECF_trnsprt  69 lssfvpiaflsriligliagllykkgkkknlkeivvsfilagvlg 113
                                       +++   ++++s  +i++ +  l+ k kk  l++ ++++i a+v+ 
  gi|385806114|ref|YP_005842512.1|  12 VWI--TCYVISLPIIIFSYIRLRSKLKKEELSTSFFAVITAAVFA 54 
                                       455..7888888888888888888888888888888888777764 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 1.4e-07
                                       HHHHHHHHHHHHHHHHHEEE.STSEEESHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHCHT-SSTTHHHH...HHHH CS
                       ECF_trnsprt   4 vitglliAisivlsllgyiplpnikitiihipvllggllfGpikGailgiitsvlkailtggtgalssfv...piaf 77 
                                       vit+  +A+++v       pl++  +t+  i ++l +++fGp +G++   i  +++a+l+g +g+++  +   + ++
  gi|385806114|ref|YP_005842512.1|  47 VITAAVFALQMVNY-----PLGPGGTTAHLIGTPLLSIIFGPEAGIVGLSIVLLIQALLFGDGGITT-YGantLNMA 117
                                       66677777777777.....888889**********************************98887776.467965555 PP

                                       HHHHCHHHHHH.HHHHCCCHTTHHHHHHHHHHHHCCCCCHHH CS
                       ECF_trnsprt  78 lsriligliag.llykkgkkknlkeivvsfilagvlgtivat 118
                                       +++ ++ +  + ll+k +k  n k+ +v+ +++g lg + a 
  gi|385806114|ref|YP_005842512.1| 118 VTASVVSFFSYvLLRKLYK--NEKGRIVAGAISGWLGIVSAA 157
                                       5555555555524443333..344445555555555554444 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.066
                                       HHCTTCHHHHHHHHH.....HHHHHHHCHT-SSTTHHHHHHHHHHHHCHHHHHH.HHHHCCC CS
                       ECF_trnsprt  40 gllfGpikGailgii.....tsvlkailtggtgalssfvpiaflsriligliag.llykkgk 95 
                                       + ++G +++a++ ++     +s++++ l   t++++   +  ++ +i+ gl++g  +y +gk
  gi|385806114|ref|YP_005842512.1| 148 SGWLGIVSAAFMCGLelglsKSTFGYGL-SVTIPVMV--ISHAILGIVEGLVTGfAIYAIGK 206
                                       5678999999999998777788888888.66666655..66777777777777754555554 PP

>> Pam17  Mitochondrial import protein Pam17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.049   2.2e+02      23      55 ..      27      59 ..      22      90 .. 0.81
   2 ?    8.7   0.2   0.00032       1.4      16      99 ..     120     204 ..     107     210 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.049
                             Pam17 23 effklrkkrrrielvasivtallglllgaavls 55
                                      ++++lr k ++ el +s ++ ++++++++++++
  gi|385806114|ref|YP_005842512.1| 27 SYIRLRSKLKKEELSTSFFAVITAAVFALQMVN 59
                                      689999999999999999888888888877765 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00032
                             Pam17  16 ekkltwneffklrkkrr..rielvasivtallglllgaavlstleidptqqilglDplvvlglatlasgalGwllGp 90 
                                       ++ +++ +++ lrk  +  +   va+ +++ lg +++aa++  le+  ++  +g    v++ +++++ ++lG + G 
  gi|385806114|ref|YP_005842512.1| 120 ASVVSFFSYVLLRKLYKneKGRIVAGAISGWLG-IVSAAFMCGLELGLSKSTFGYGLSVTIPVMVISHAILGIVEGL 195
                                       566788899999985441034455555555555.5677888889********************************* PP

                             Pam17  91 vlgsavfkl 99 
                                       v g a++++
  gi|385806114|ref|YP_005842512.1| 196 VTGFAIYAI 204
                                       ***999986 PP

>> ABC2_membrane_5  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.5     0.016        72      91     158 ..      15      52 ..       5      63 .. 0.33
   2 ?    8.8   9.8   0.00023         1      91     189 ..      84     183 ..      76     203 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.016
                   ABC2_membrane_5  91 liailitlllliiavlikgnvtisevllsiliglvialiflaivlPlyfkfgvekgrivliiiifgii 158
                                       + +++ + ++++ +  +++++  +e+ +s+++++                               +++
  gi|385806114|ref|YP_005842512.1|  15 TCYVISLPIIIFSYIRLRSKLKKEELSTSFFAVIT------------------------------AAV 52 
                                       22222222222222222222332222222222222..............................222 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00023
                   ABC2_membrane_5  91 liailitlllliiavlikgnvtisevllsiliglvialiflaivlPlyfk.fgvekgrivliiiifgiifllvaifs 166
                                        ++i+ ++++l+i+ l+ g   i +     l++ v a++++ ++++l+ k +++ekgriv+ +i+  + +++ a++ 
  gi|385806114|ref|YP_005842512.1|  84 EAGIVGLSIVLLIQALLFGDGGITTYGANTLNMAVTASVVSFFSYVLLRKlYKNEKGRIVAGAISGWLGIVSAAFMC 160
                                       5678888888999*******99999********************999874799****9999999999777777666 PP

                   ABC2_membrane_5 167 lsklelslidlsnyilliillvi 189
                                          l ls +++ + +++ i +++
  gi|385806114|ref|YP_005842512.1| 161 GLELGLSKSTFGYGLSVTIPVMV 183
                                       66777776666665433333222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); 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):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.36s 00:00:00.91 Elapsed: 00:00:00.56
# Mc/sec: 1144.55
//
Query:       gi|385806115|ref|YP_005842513.1|  [L=86]
Description: hypothetical protein FFONT_1073 [Fervidicoccus fontis Kam940]
Scores for complete 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   31.7   0.1    1.8e-07   31.0   0.1    1.5  1  PDGLE        PDGLE domain
  ------ inclusion threshold ------
        0.2   11.4   6.2       0.31   10.7   6.2    1.4  1  Yip1         Yip1 domain
        3.5    8.0   5.9       0.34   11.2   0.2    1.9  2  Sigma_reg_N  Sigma factor regulator N-terminal
        7.1    6.7   8.7          1    9.4   0.3    2.2  2  OppC_N       N-terminal TM domain of oligopeptide transport p


Domain annotation for each model (and alignments):
>> PDGLE  PDGLE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.1   3.9e-11   1.8e-07      49      87 ..      41      81 ..       6      83 .. 0.83

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 3.9e-11
                             PDGLE 49 ek...talLpDYsfkgaeekkagtsvAgivGvlltlalagli 87
                                      +k   ++++p+Y+++g++e+ +g +++givG+++++++++++
  gi|385806115|ref|YP_005842513.1| 41 SKsiiQSPFPEYTVPGISEW-IGGIISGIVGMAMIFLILMVL 81
                                      225679**************.*************99998875 PP

>> Yip1  Yip1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   6.2   6.9e-05      0.31      24      86 ..       6      84 ..       1      86 [] 0.53

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 6.9e-05
                              Yip1 24 lallllalltlllgllaslnlgqtlasgeevqgltlssllga................iiggylglllgllllalllhl 86
                                       ++ll+ +++++lg  +++  + +l+   e+ +lt++s++ +                ii+g++g+ +++l+l +ll+l
  gi|385806115|ref|YP_005842513.1|  6 IIILLISIIAIFLGSTIFSYSYEPLDKVAEELNLTSKSIIQSpfpeytvpgisewiggIISGIVGMAMIFLILMVLLKL 84
                                      4555555555555555554444444444444455555555554444444444452222777777777777777777776 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 ?   11.2   0.2   7.6e-05      0.34      15      49 ..       5      41 ..       2      56 .. 0.70
   2 ?   -0.8   1.2      0.44     2e+03      20      31 ..      69      80 ..      63      85 .. 0.49

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.6e-05
                       Sigma_reg_N 15 ivlislivlllifvil.vvtllyl.aekegnklrevl 49
                                      +++i li++++if+ + +++++y  ++k  ++l+ + 
  gi|385806115|ref|YP_005842513.1|  5 TIIILLISIIAIFLGStIFSYSYEpLDKVAEELNLTS 41
                                      6778888888888888888888876666666665555 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.44
                       Sigma_reg_N 20 livlllifvilv 31
                                      +++++++++++v
  gi|385806115|ref|YP_005842513.1| 69 VGMAMIFLILMV 80
                                      333444444443 PP

>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.3   0.00023         1      20      41 ..       5      27 ..       4      48 .. 0.68
   2 ?    0.6   3.2      0.12   5.5e+02      15      25 ..      71      81 ..      67      84 .. 0.53

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00023
                            OppC_N 20 lvilllllliaif.aPliaPydp 41
                                       +i+ll+ +iaif +  i  y++
  gi|385806115|ref|YP_005842513.1|  5 TIIILLISIIAIFlGSTIFSYSY 27
                                      58888899999886555544554 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.12
                            OppC_N 15 lAvvglvilll 25
                                      +A++ l++ +l
  gi|385806115|ref|YP_005842513.1| 71 MAMIFLILMVL 81
                                      34444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       926  (0.0516482); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 553.99
//
Query:       gi|385806116|ref|YP_005842514.1|  [L=238]
Description: hypothetical protein FFONT_1074 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.014   15.0   2.5      0.014   15.0   2.5    2.0  2  DUF1182   Protein of unknown function (DUF1182)
      0.072   12.7  15.4       0.11   12.1  12.6    2.5  1  CbiQ      Cobalt transport protein


Domain annotation for each model (and alignments):
>> DUF1182  Protein of unknown function (DUF1182)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   2.5   1.6e-06     0.014      36      79 ..      53      95 ..      26     132 .. 0.88
   2 ?   -2.7   0.1       0.4   3.6e+03     115     126 ..     221     232 ..     202     237 .. 0.52

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.6e-06
                           DUF1182 36 svlfslllvifvilrkallrslkstivfvtlgsfllslplillq 79
                                       ++fs +lv f+ ++++llr lk+t++f+ l s+ +++p ++++
  gi|385806116|ref|YP_005842514.1| 53 VIIFSSFLVAFL-MKESLLRQLKNTLFFIPLFSLAVAVPRYFID 95
                                      689*****9987.6899**********************99875 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.4
                           DUF1182 115 vlplavalyryr 126
                                       ++p+ ++++  +
  gi|385806116|ref|YP_005842514.1| 221 IVPFMLTIFILF 232
                                       333333333333 PP

>> CbiQ  Cobalt transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1  12.6   1.2e-05      0.11      22     210 ..      39     208 ..      24     217 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.2e-05
                                       HHHHS-HHHHHHHHHHHHHHHHHTTS---HHHHHHHCCCHCHHHHHHHHHHE.......EECTTEEE...E-TTHHH CS
                              CbiQ  22 lalvlapnlvtlliiiallllllllvilprvlaqalilpllflllgllillfqlittegefvfagggqisitseGll 98 
                                        +lv++++ ++  ++i++  +l+++  + ++l q      lf+++ + +++     ++  f+   +        G+ 
  gi|385806116|ref|YP_005842514.1|  39 PILVVLSKDIRFSLVIIFSSFLVAFLMKESLLRQLKN--TLFFIPLFSLAVA----VPRYFIDPSF--------GIY 101
                                       3444455555555666666666666666655555555..5555555555555....3333333333........567 PP

                                       HHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHCCCSS--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTS..SH CS
                              CbiQ  99 rglllalRiltllslllllalTTppeeltsslerlgvPlelalillLayRfiflLleevqrikqAqklRlgdsklgi 175
                                         l++++++ ++ls+ +l+a    +e l+s++ ++g+P+ ++ +l+L+   i  L+  ++ ++++    +++s+ g+
  gi|385806116|ref|YP_005842514.1| 102 GLLEFFFKVWAALSFPTLMARCYGVERLASGFASIGIPSGFSSLLALT--SIDALIS-TRMLWNSVL--MLRSRGGL 173
                                       7789***********************************999876665..7888885.677788763..23345578 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS-S CS
                              CbiQ 176 rrslrslgkliaalflralkraervalAmeaRGYt 210
                                       + sl+++g  ++  flr+++r+er++lA  +RG  
  gi|385806116|ref|YP_005842514.1| 174 KVSLKEIGYFVGFQFLRSFERGERINLAYLSRGGM 208
                                       899******************************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.50
# Mc/sec: 1435.22
//
Query:       gi|385806117|ref|YP_005842515.1|  [L=221]
Description: cobalt transport ATP-binding protein (cbiO) [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.4e-31  108.6   0.0    4.6e-31  108.2   0.0    1.2  1  ABC_tran      ABC transporter
    7.7e-15   55.5   1.5    1.3e-06   28.4   0.1    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    1.2e-08   34.7   1.0    3.3e-07   30.0   1.0    2.1  1  SMC_N         RecF/RecN/SMC N terminal domain
    1.1e-06   29.3   0.2    1.6e-06   28.8   0.2    1.5  1  AAA_23        AAA domain
    3.1e-06   26.8   0.0    5.6e-06   26.0   0.0    1.3  1  AAA_29        P-loop containing region of AAA domain
    4.2e-05   23.4   0.7    0.00021   21.1   0.5    1.9  2  AAA_15        AAA ATPase domain
     0.0014   18.7   0.0     0.0029   17.6   0.0    1.5  1  AAA_5         AAA domain (dynein-related subfamily)
     0.0014   18.6   0.0     0.0016   18.4   0.0    1.3  1  ATPase_2      ATPase domain predominantly from Archaea
     0.0018   18.7   0.0     0.0028   18.1   0.0    1.4  1  AAA_16        AAA ATPase domain
     0.0033   17.4   0.0     0.0058   16.6   0.0    1.4  1  Rad17         Rad17 P-loop domain
     0.0039   17.7   0.6     0.0087   16.6   0.6    1.9  1  AAA_18        AAA domain
     0.0052   16.5   0.0     0.0057   16.4   0.0    1.2  1  AAA_30        AAA domain
     0.0053   15.9   0.0     0.0086   15.2   0.0    1.3  1  T2SSE         Type II/IV secretion system protein
     0.0094   15.9   0.0      0.022   14.7   0.0    1.7  1  NACHT         NACHT domain
  ------ inclusion threshold ------
      0.012   15.8   0.0      0.022   15.0   0.0    1.4  1  AAA_28        AAA domain
      0.012   15.8   0.1      0.026   14.8   0.1    1.8  1  AAA_22        AAA domain
      0.013   15.5   0.0       0.03   14.4   0.0    1.6  2  AAA_14        AAA domain
      0.016   14.8   0.0      0.025   14.1   0.0    1.3  1  AAA_25        AAA domain
      0.027   14.3   0.0      0.047   13.6   0.0    1.4  1  APS_kinase    Adenylylsulphate kinase
      0.032   14.6   0.0       0.06   13.7   0.0    1.5  1  RNA_helicase  RNA helicase
      0.037   13.6   0.0      0.061   12.9   0.0    1.2  1  AAA_27        AAA domain
      0.041   13.3   0.0      0.066   12.7   0.0    1.2  1  PhoH          PhoH-like protein
      0.045   13.6   0.0      0.069   13.1   0.0    1.3  1  RsgA_GTPase   RsgA GTPase
      0.057   12.4   0.0      0.088   11.8   0.0    1.3  1  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
      0.076   11.8   0.0       0.13   11.1   0.0    1.3  1  ABC_ATPase    Predicted ATPase of the ABC class
      0.086   11.5   0.0      0.098   11.3   0.0    1.2  1  AAA_13        AAA domain
      0.086   12.8   0.0       0.15   12.0   0.0    1.4  1  NTPase_1      NTPase
       0.09   12.5   0.0       0.12   12.0   0.0    1.2  1  AAA_24        AAA domain
        0.1   12.9   0.0        0.2   11.9   0.0    1.5  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
        0.1   12.5   0.0       0.16   11.8   0.0    1.4  1  dNK           Deoxynucleoside kinase
       0.14   11.7   0.0       0.24   10.9   0.0    1.4  1  cobW          CobW/HypB/UreG, nucleotide-binding domain
       0.15   12.5   0.1       0.37   11.2   0.1    1.9  1  AAA           ATPase family associated with various cellular 
       0.18   11.4   0.0       0.27   10.8   0.0    1.3  1  SRP54         SRP54-type protein, GTPase domain
       0.23   11.4   0.3       0.51   10.3   0.0    1.7  1  MutS_V        MutS domain V


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 !  108.2   0.0   8.7e-34   4.6e-31       1     137 []      21     167 ..      21     167 .. 0.86

  Alignments for each domain:
  == domain 1  score: 108.2 bits;  conditional E-value: 8.7e-34
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS..--S-TTSB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe..pqlfpelt 75 
                                       +knvsl+l++g+++ i+G+nG+GKStLl++la l  p+eGe+ l gk++++++ +++rk+ig+l+q+  + lf+ + 
  gi|385806117|ref|YP_005842515.1|  21 VKNVSLELRRGNVICITGPNGSGKSTLLMILAALIFPQEGEVYLFGKKIDKKNASEVRKKIGFLFQNpdDMLFNPSV 97 
                                       59*****************************************************************9877888885 PP

                                       HHHH.......HHHTCHHHHHHHSTTGGTTCBGESTTS.GGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  76 vren.......esdeeiekalsklglkelkdtvvkssp.ssLSgGqkqrvalarallkkpkllllDEpta 137
                                       ++e          ++ei++ l+  ++k+lk +++ ++  + LS Gq++ v+la +l+++p+llllDEpt+
  gi|385806117|ref|YP_005842515.1|  98 IEEIsfgliakGVNREISNNLALEEMKKLKIENLAYKVpHRLSFGQRRLVSLASILVTDPSLLLLDEPTS 167
                                       6666****9884555555555555555555444444445*****************************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 !   26.4   0.2   1.1e-08   5.7e-06       2      63 ..      34      98 ..      33     108 .. 0.84
   2 !   28.4   0.1   2.6e-09   1.3e-06     233     302 ..     135     204 ..     105     204 .. 0.71

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 1.1e-08
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarl...drdvegltdelsggggirkipslldlydpeipfefeie 63
                                       +++GpNgsGKS+LL +l  l +      +++g ++++ + ++ rk +++l+ + +++ f+ +++
  gi|385806117|ref|YP_005842515.1| 34 ICITGPNGSGKSTLLMILAALIFPqegEVYLFGKKIDKKNASEVRKKIGFLFQNPDDMLFNPSVI 98
                                      689***************99987799988888888888888888888888888888888777766 PP

  == domain 2  score: 28.4 bits;  conditional E-value: 2.6e-09
                            AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHP....kllrrllell.kelsrngaQviltTHSplll 302
                                        ++ lS G++rl  l+++l  ++   slll+DEp ++L+      +++rl+e++ +++ ++ga   ++TH+++l+
  gi|385806117|ref|YP_005842515.1| 135 VPHRLSFGQRRLVSLASILVTDP---SLLLLDEPTSNLDEknreLIIERLMEFFgNRKDDWGA--AIATHDNELI 204
                                       45557***************999...**************55444446666666755555555..4688888775 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 !   30.0   1.0   6.3e-10   3.3e-07      24     202 ..      31     204 ..      16     217 .. 0.63

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 6.3e-10
                                       SSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  24 ksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsis 100
                                        ++ +i+GpNGSGKs ll  +  ++  ++        + + i   k++as  + ++  +f+n+d+ l   +   +is
  gi|385806117|ref|YP_005842515.1|  31 GNVICITGPNGSGKSTLLMILAALIFPQEG---EVYLFGKKID--KKNASEVRKKIGFLFQNPDDMLFNPSVIEEIS 102
                                       35789**********987554322222222...2223333344..456666677899999*****965555545555 PP

                                       EEEETTSE...EEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HH CS
                                       xxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 101 rrvkrkge...seykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDek 174
                                         ++ kg     +  +  +e++k ++++l  ++   ++ LS G++ Lv+la ++    v   +l llDe  ++LDek
  gi|385806117|ref|YP_005842515.1| 103 FGLIAKGVnreISNNLALEEMKKLKIENLAYKV---PHRLSFGQRRLVSLASIL----VTDPSLLLLDEPTSNLDEK 172
                                       555555540013333444455555555555443...679***********9885....4456799************ PP

                                       HHHHHHHHHH....HHCTTSEEEEE-SSHHHC CS
                                       xxxxxxxxxx....xxxxxxxxxxxxxxxxxx RF
                             SMC_N 175 nvkkvaellk....eksknaQfivislreeml 202
                                       n++ + e+l     +++++    + ++++e++
  gi|385806117|ref|YP_005842515.1| 173 NRELIIERLMeffgNRKDDWGAAIATHDNELI 204
                                       **999888772222444555566666666655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.2   3.1e-09   1.6e-06      11      46 ..      22      58 ..      16     183 .. 0.73

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 3.1e-09
                            AAA_23 11 rdqeidF.skgltlItGpNGaGKTTildAiklaLyge 46
                                      +++++++   ++ +ItGpNG+GK+T+l  +    + +
  gi|385806117|ref|YP_005842515.1| 22 KNVSLELrRGNVICITGPNGSGKSTLLMILAALIFPQ 58
                                      78888995559****************9998887764 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   1.1e-08   5.6e-06      15      50 ..      24      59 ..      19      63 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 1.1e-08
                            AAA_29 15 htieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                       ++e+++ +++ +tGp+GsGKSTll  ++al+ p++
  gi|385806117|ref|YP_005842515.1| 24 VSLELRRGNVICITGPNGSGKSTLLMILAALIFPQE 59
                                      56777766699**************98999988876 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.5     4e-07   0.00021      12      50 ..      19      58 ..      19     135 .. 0.75
   2 ?    0.4   0.7      0.78   4.1e+02     295     365 ..     137     200 ..      67     204 .. 0.63

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 4e-07
                            AAA_15 12 Rslkdveidlsee.ltvliGkNnsGKSsilealdlFlnnk 50
                                      ++ k+v+++l    + ++ G+N+sGKS++l++l  ++  +
  gi|385806117|ref|YP_005842515.1| 19 KAVKNVSLELRRGnVICITGPNGSGKSTLLMILAALIFPQ 58
                                      6789999999998899*****************8877655 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.78
                            AAA_15 295 nknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnkt..QviitTHS 365
                                       ++ ++G++rl++l+  +          +++ +ll++EP  +L  ++ + +i+ l e   + k+     i TH 
  gi|385806117|ref|YP_005842515.1| 137 HRLSFGQRRLVSLASIL--V-------TDPSLLLLDEPTSNLDEKNRELIIERLMEFFGNRKDdwGAAIATHD 200
                                       45566666666654322..2.......2356778888877777777777777777777766666656666665 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 !   17.6   0.0   5.4e-06    0.0029       2      36 ..      34      69 ..      33      78 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 5.4e-06
                                      EEEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT- CS
                             AAA_5  2 vlLvGppGtgKselaerlaaal.nreveyvqltrdt 36
                                      +++ Gp G+gKs+l + laa++  +e e++++ +++
  gi|385806117|ref|YP_005842515.1| 34 ICITGPNGSGKSTLLMILAALIfPQEGEVYLFGKKI 69
                                      699********************9999999988776 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 !   18.4   0.0   3.1e-06    0.0016      15      75 ..      26      89 ..      17     188 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3.1e-06
                          ATPase_2 15 lerepneiyfiYGpegsGKtaLlkeiienl.edkdkyviyyialreesiskldefie...eeeek 75
                                      le  + +++ i+Gp gsGK++Ll+ ++     + ++  ++  ++ +++ s+++++i+   + + +
  gi|385806117|ref|YP_005842515.1| 26 LELRRGNVICITGPNGSGKSTLLMILAALIfPQEGEVYLFGKKIDKKNASEVRKKIGflfQ-NPD 89
                                      5566789****************99999886777777888899999999999999887752.222 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   0.0   5.3e-06    0.0028      23      88 ..      30     112 ..      19     188 .. 0.58

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 5.3e-06
                            AAA_16  23 rpelvllsGesGvGKsslvrellralekd.....................ggiflrgkcdqlesaipysa.laqala 77 
                                       r++++ ++G+ G+GKs+l+  l+  +  +                     ++ fl ++ d+      + + +++ ++
  gi|385806117|ref|YP_005842515.1|  30 RGNVICITGPNGSGKSTLLMILAALIFPQegevylfgkkidkknasevrkKIGFLFQNPDDM----LFNPsVIEEIS 102
                                       45899**************9999988887554444444444444444443344444444443....33333555553 PP

                            AAA_16  78 reellrqllde 88 
                                       + +l+++  ++
  gi|385806117|ref|YP_005842515.1| 103 F-GLIAKGVNR 112
                                       3.555555555 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.1e-05    0.0058      33      69 ..      19      55 ..      16      79 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.1e-05
                             Rad17 33 ewlkadvLesrkkriLLisGPsGCgkstvvkvLskel 69
                                      +++k  +Le r+ +++ i+GP G gkst + +L+   
  gi|385806117|ref|YP_005842515.1| 19 KAVKNVSLELRRGNVICITGPNGSGKSTLLMILAALI 55
                                      5778899****999*******************9765 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.6   1.6e-05    0.0087       1      22 [.      34      55 ..      34     204 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.6e-05
                            AAA_18  1 IlltGtpGvGKttlakeLskrl 22
                                      I++tG+ G+GK+tl   L+ + 
  gi|385806117|ref|YP_005842515.1| 34 ICITGPNGSGKSTLLMILAALI 55
                                      9**************9998773 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.1e-05    0.0057      17      68 ..      31      83 ..      19     171 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.1e-05
                            AAA_30 17 gdrvavltGpAGtGKttalkalreaweaaggrviglAp..tgkaAkvLaeelgi 68
                                      g  v ++tGp G+GK+t+l  l++++  ++g+v ++     +k A ++++++g+
  gi|385806117|ref|YP_005842515.1| 31 G-NVICITGPNGSGKSTLLMILAALIFPQEGEVYLFGKkiDKKNASEVRKKIGF 83
                                      3.4999****************99998887788777652256777778877776 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.6e-05    0.0086     126     156 ..      28      58 ..       7      65 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.6e-05
                             T2SSE 126 vrerglilvsGgTgsGKttllyallkeinks 156
                                       +r+  +i ++G+ gsGK+tll +l + i  +
  gi|385806117|ref|YP_005842515.1|  28 LRRGNVICITGPNGSGKSTLLMILAALIFPQ 58 
                                       45566788*************9988777555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   4.3e-05     0.022       2      23 ..      33      54 ..      32      65 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.3e-05
                                      CEEEEC-TTTCHHHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqklala 23
                                      +++++G++GsGK+tLl  la +
  gi|385806117|ref|YP_005842515.1| 33 VICITGPNGSGKSTLLMILAAL 54
                                      79**************988865 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   4.1e-05     0.022       2      22 ..      34      54 ..      33      79 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.1e-05
                            AAA_28  2 ivitGgestGKTtlleaLaar 22
                                      i+itG+ ++GK+tll  Laa 
  gi|385806117|ref|YP_005842515.1| 34 ICITGPNGSGKSTLLMILAAL 54
                                      9****************9975 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   4.9e-05     0.026       4      27 ..      30      53 ..      27     190 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.9e-05
                            AAA_22  4 tagilvvtGesGtGKTtllrrlle 27
                                      + +++++tG+ G+GK+tll  l+ 
  gi|385806117|ref|YP_005842515.1| 30 RGNVICITGPNGSGKSTLLMILAA 53
                                      6789*************9976655 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   5.7e-05      0.03       3      48 ..      32      76 ..      30     101 .. 0.75
   2 ?   -2.2   0.0       7.2   3.8e+03      64      72 ..     156     164 ..     111     185 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.7e-05
                            AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkklad 48
                                      ++++itG+  +GK+tll  l+  l+ ++e  +y+  ++ ++k++++
  gi|385806117|ref|YP_005842515.1| 32 NVICITGPNGSGKSTLLMILAA-LIFPQEGEVYLFGKKIDKKNASE 76
                                      799*************988874.44588888887777766665544 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 7.2
                            AAA_14  64 kktylflDE 72 
                                       + ++l+lDE
  gi|385806117|ref|YP_005842515.1| 156 DPSLLLLDE 164
                                       345555555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   4.8e-05     0.025      30      57 ..      28      55 ..      19      70 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.8e-05
                            AAA_25 30 lpagelallaGapgtGKttlaldlalav 57
                                      l++g ++ ++G+ g+GK+tl++ la+ +
  gi|385806117|ref|YP_005842515.1| 28 LRRGNVICITGPNGSGKSTLLMILAALI 55
                                      5799******************999865 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   8.9e-05     0.047       1      38 [.      30      66 ..      30      90 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.9e-05
                                      S-EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEH CS
                        APS_kinase  1 rgvvvwltGlsgsGKstianalekkLvekgisvylLdG 38
                                      rg v+ +tG  gsGKst+ + l+  ++ +  +vyl  G
  gi|385806117|ref|YP_005842515.1| 30 RGNVICITGPNGSGKSTLLMILAALIFPQEGEVYLF-G 66
                                      6889*******************9999888888753.4 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   0.00011      0.06       1      36 [.      34      64 ..      34      91 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00011
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallkklklkkkdsvys 36
                                      i+++Gp+g GKStl   La+ +      +++++vy 
  gi|385806117|ref|YP_005842515.1| 34 ICITGPNGSGKSTLLMILAALIF-----PQEGEVYL 64
                                      799**************877666.....66677776 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00011     0.061      18      51 ..      25      56 ..      18      63 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                            AAA_27 18 sldfsaeeadlhliyGpNEAGKstalrAisdllf 51
                                      sl+++  + ++  i GpN +GKst+l  + +l+f
  gi|385806117|ref|YP_005842515.1| 25 SLELR--RGNVICITGPNGSGKSTLLMILAALIF 56
                                      45555..778899***************999999 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00012     0.066      14      68 ..      26      84 ..      17      97 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                                      HHHHH-SEEEEE--TTSSTTHHHHHHHHHHH.HTTS-S...EEEEEE-S--TT----SS CS
                              PhoH 14 ealkkndivfaiGpaGtGKtylavalaveal.kkkkvk...riiltrpaveageelGfl 68
                                        l++ ++++++Gp G+GK+ l + la+ ++ ++++v    + i  ++a e+ +++Gfl
  gi|385806117|ref|YP_005842515.1| 26 LELRRGNVICITGPNGSGKSTLLMILAALIFpQEGEVYlfgKKIDKKNASEVRKKIGFL 84
                                      5677889************7776666665551556654233778899999999999987 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   0.00013     0.069      88     120 ..      19      52 ..       4      81 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00013
                                       TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHC CS
                       RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLinall 120
                                       +++++++ +l+  +++++ G+ G GKStL+  l+
  gi|385806117|ref|YP_005842515.1|  19 KAVKNVSLELRRgNVICITGPNGSGKSTLLMILA 52 
                                       45666666777669***************98876 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 ?   11.8   0.0   0.00017     0.088      11      51 ..      13      53 ..       4      63 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00017
                                      -SHHHHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHH CS
                              MeaB 11 erpeakellerllakaGraqvvGltGvPGaGkstlvealgl 51
                                       +p+ ++ +++++ +  r +v+ +tG  G+Gkstl+  l++
  gi|385806117|ref|YP_005842515.1| 13 AYPDGTKAVKNVSLELRRGNVICITGPNGSGKSTLLMILAA 53
                                      567778888889999999*****************987765 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 ?   11.1   0.0   0.00024      0.13     240     266 ..      26      53 ..       6      59 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00024
                                       EEE-SS.EEEEEE-TTSSHHHHHHHHHH CS
                        ABC_ATPase 240 mgipkG.vtlIvGggfhGKsTLLeAlek 266
                                       + +++G v+ I+G++  GKsTLL  l++
  gi|385806117|ref|YP_005842515.1|  26 LELRRGnVICITGPNGSGKSTLLMILAA 53 
                                       5678999****************88766 PP

>> AAA_13  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     0.098      11      39 ..      24      54 ..      14     125 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00019
                            AAA_13 11 eledfkriNliY..GwNGaGKTtLSrllrsl 39
                                         +++r N+i   G NG+GK+tL ++l+ l
  gi|385806117|ref|YP_005842515.1| 24 VSLELRRGNVICitGPNGSGKSTLLMILAAL 54
                                      45679999986444*************9987 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00028      0.15       2      23 ..      34      55 ..      33      88 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00028
                                      EEEE--TTSSHHHHHHHHHHHH CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlell 23
                                      ++iTGp G+GK+Tl+  ++ l+
  gi|385806117|ref|YP_005842515.1| 34 ICITGPNGSGKSTLLMILAALI 55
                                      79************98776655 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   0.00024      0.12       2      22 ..      31      51 ..      30      80 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00024
                            AAA_24  2 klkiliyGpsgiGKTtlakel 22
                                      ++ i+i+Gp+g+GK+tl+  l
  gi|385806117|ref|YP_005842515.1| 31 GNVICITGPNGSGKSTLLMIL 51
                                      578*************98766 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 ?   11.9   0.0   0.00037       0.2      62      86 ..     155     179 ..     137     183 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00037
                           SbcCD_C  62 palrlvfLDEAFsklDeesiatlle 86 
                                       ++++l++LDE  s+lDe++++ ++e
  gi|385806117|ref|YP_005842515.1| 155 TDPSLLLLDEPTSNLDEKNRELIIE 179
                                       5789****************98887 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00031      0.16       1      21 [.      34      54 ..      34      90 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00031
                                      EEEEESTTSSHHHHHHHHHCC CS
                               dNK  1 ivveGnIgaGKstlvklLskk 21
                                      i++ G+ g+GKstl+ +L+  
  gi|385806117|ref|YP_005842515.1| 34 ICITGPNGSGKSTLLMILAAL 54
                                      9****************9865 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   0.00046      0.24       2      19 ..      33      50 ..      32      61 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00046
                                      EEEEEESTTCCHHHHHHH CS
                              cobW  2 vtvltGflGsGKTtLlnh 19
                                      v+ +tG+ GsGK+tLl  
  gi|385806117|ref|YP_005842515.1| 33 VICITGPNGSGKSTLLMI 50
                                      789************975 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 ?   11.2   0.1    0.0007      0.37       1      61 [.      34      97 ..      34     213 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0007
                                      EEEESSTTSSHHHHHHHHHHHH..THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS.TSEE CS
                               AAA  1 vllyGppGtGKTllakavakel..gvefleisgsellskyvgesekkirelfkeakeka.kpsi 61
                                      ++++Gp G GK++l   +a  +  +   + + g+++ +k  +e  kki  lf++   +  +ps+
  gi|385806117|ref|YP_005842515.1| 34 ICITGPNGSGKSTLLMILAALIfpQEGEVYLFGKKIDKKNASEVRKKIGFLFQNPDDMLfNPSV 97
                                      5899***************997542333555566666666777777777777765555555554 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00051      0.27       2      34 ..      32      64 ..      31      77 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00051
                                      EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEE CS
                             SRP54  2 nvillvGlqGaGKTttlaKLaallkkegkkvll 34
                                      nvi + G++G+GK t l  Laal+  ++ +v l
  gi|385806117|ref|YP_005842515.1| 32 NVICITGPNGSGKSTLLMILAALIFPQEGEVYL 64
                                      7999*****************999888777766 PP

>> MutS_V  MutS domain V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00096      0.51       2      19 ..      35      52 ..      34      68 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00096
                                      EEE-STTSSHHHHHHHHH CS
                            MutS_V  2 litGpnmaGkstylrqva 19
                                       itGpn +Gkst+l   a
  gi|385806117|ref|YP_005842515.1| 35 CITGPNGSGKSTLLMILA 52
                                      69**********997665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                       115  (0.00641419); expected 17.9 (0.001)
Passed Fwd filter:                        34  (0.00189637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              34  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.49
# Mc/sec: 1350.67
//
Query:       gi|385806118|ref|YP_005842516.1|  [L=205]
Description: hypothetical protein FFONT_1076 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       788  (0.0439511); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); 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: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1375.03
//
Query:       gi|385806119|ref|YP_005842517.1|  [L=306]
Description: anion transporting atpase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-44  152.5   4.0    6.6e-44  150.3   4.0    1.7  1  ArsA_ATPase    Anion-transporting ATPase
    1.3e-09   38.1   0.0      4e-09   36.6   0.0    1.9  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
    5.7e-09   36.1   0.2    5.7e-09   36.1   0.2    1.8  2  AAA_31         AAA domain
    5.6e-05   22.8   0.0    0.00012   21.8   0.0    1.5  1  AAA_25         AAA domain
      0.002   17.6   1.6      0.071   12.6   0.1    2.6  3  ParA           NUBPL iron-transfer P-loop NTPase
  ------ inclusion threshold ------
      0.012   15.4   3.8       0.21   11.3   3.8    2.3  1  AAA_24         AAA domain
       0.03   14.9   0.8      0.085   13.4   0.0    2.3  3  AAA_18         AAA domain
       0.04   13.6   1.7       0.12   12.0   0.1    2.4  2  SRP54          SRP54-type protein, GTPase domain
      0.046   13.9   0.0      0.089   13.0   0.0    1.6  1  AAA_33         AAA domain
      0.058   13.2   0.8        2.2    8.0   0.1    2.6  2  AAA_26         AAA domain
      0.059   13.4   0.2       0.18   11.9   0.1    1.9  2  SRP1_TIP1      Seripauperin and TIP1 family
      0.072   12.9   0.3       0.55   10.0   0.0    2.3  3  ATP_bind_1     Conserved hypothetical ATP binding protein
      0.074   12.8   1.4       0.97    9.2   0.0    2.7  3  PduV-EutP      Ethanolamine utilisation - propanediol utilisa
       0.17   12.1   5.3       0.15   12.3   2.0    2.1  2  Cortex-I_coil  Cortexillin I, coiled coil
       0.18   11.5   0.0       0.27   10.9   0.0    1.4  1  AAA_30         AAA domain
       0.27   11.7   4.7        3.7    8.1   0.3    2.8  3  PhoU           PhoU domain


Domain annotation for each model (and alignments):
>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.3   4.0   5.9e-47   6.6e-44       3     301 ..      13     301 ..      11     304 .. 0.89

  Alignments for each domain:
  == domain 1  score: 150.3 bits;  conditional E-value: 5.9e-47
                                       EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHTS--BSS-EEETSSEEEEE--HHHHHHHHHCC CS
                       ArsA_ATPase   3 vilvgGKGGVGKttvsaatavklsekgkkvllistDPAhslsDsfdqklgkeptkvkeNLsavEidpeveleeakqe 79 
                                       ++++ GKGGVGKtt sa ++++ s++   + + s DPAh l D++  kl++ ++++ eNL a E d+++ ++e+ ++
  gi|385806119|ref|YP_005842517.1|  13 LVMIVGKGGVGKTTFSAILSIYASKQ-LPTFVTSIDPAHHLGDVLGYKLEHREKRIAENLIANEADIDELIREYLSK 88 
                                       5899*****************98875.67999************************************989988887 PP

                                       HHGGGSCCH...HHHHHHHHHHHHHTSSTTHHHHHHHHHHHHHHH.CSSSSEEEEESBSCCHTCGGGGHHHHHHHHH CS
                       ArsA_ATPase  80 vqkeeeall...gleeledvlaeelaslPGideilsfeellkyvk.eeeydvvvlDtaPTGhtlrllslpevlekll 152
                                        ++  +++    ++  l++ ++    s PGi+  + +++++ +v+  +ey ++++Dt+ T  t rl+ lp v + ++
  gi|385806119|ref|YP_005842517.1|  89 SINLLKNSYkdiTALNLDKYFDTLKDS-PGIEIEAMLHYIVSLVRkVDEYKYIIVDTPATSITSRLIGLPWVQGVWV 164
                                       766554443222889999*********.****99999999998875799**************************** PP

                                       HHHHHHHHHHHHHHHHHCCCSHCHHHHHH.HHHHHHHHHHHHHHHHHHHHTSTTTEEEEEEEESSHHHHHHHHHHHH CS
                       ArsA_ATPase 153 eklvklkeklsplakqlvkllglggvsie.ealeeleetkeeikkveeiltdpertsfrlVvipEklslkEteRaik 228
                                       ++l++l+ k+  l++ +  +    +v+i+ + l+el ++ eei++ ++ +++ + t ++ V+++Ekl++ + eR+ +
  gi|385806119|ref|YP_005842517.1| 165 DNLIDLRSKIAGLKEVIESVKAGKKVTIDdKILKELIQMREEIERNKKLFMNSDFTKIIGVTTTEKLPIVDLERLSN 241
                                       ****************9887777777888899********************************************* PP

                                       HHHHTT-EEEEEEEEEE-TTCSSSTSHHHHHHHHHHHHHHHHHHHHTTTSEEEEEE--SS-S-SHHHHHHHHH CS
                       ArsA_ATPase 229 eLkkygikvdavivNkllpeeeqenCeflearkkiqkkylkeieelfedlevvklplleeEvvGlekleklse 301
                                       +Lk+ gik+ +v++Nk+  +e+                +++ ++e+f +  ++ +p ++ Ev  +ek+ek+ e
  gi|385806119|ref|YP_005842517.1| 242 SLKNRGIKISSVVINKYKKDENG-------------LSVINYLKEKFPEARLILVPQMNYEVISIEKIEKVIE 301
                                       ****************8555544.............5677888888888888888888888888888888766 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.0   3.6e-12     4e-09       3     101 ..      15     275 ..      13     304 .. 0.88

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 3.6e-12
                                       EEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH....HTTEB-HHHH..................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxx..................... RF
                              CbiA   3 iastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai....leglendiep..................... 54 
                                       ++ +kGGvGKTt++a L ++ ++ +l +++   Dp   +  +    le  e    +                     
  gi|385806119|ref|YP_005842517.1|  15 MIVGKGGVGKTTFSAILSIYASK-QLPTFVTSIDPAHHLGDVlgykLEHRE----Kriaenlianeadidelireyl 86 
                                       5679******************9.************555554544434444....14666***************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|385806119|ref|YP_005842517.1|  87 sksinllknsykditalnldkyfdtlkdspgieieamlhyivslvrkvdeykyiivdtpatsitsrliglpwvqgvw 163
                                       ***************************************************************************** PP

                                       .......................................................................CCHCCC CS
                                       .......................................................................xxxxxx RF
                              CbiA  55 .......................................................................dlkrll 60 
                                                                                                              dl+rl+
  gi|385806119|ref|YP_005842517.1| 164 vdnlidlrskiaglkeviesvkagkkvtiddkilkeliqmreeiernkklfmnsdftkiigvttteklpivDLERLS 240
                                       ******************************************************99999999988888888888888 PP

                                       HHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  61 ellealgkkkalllkiagvvlnrvdgeneetllkealeelk 101
                                       ++l++ g      +ki +vv+n+++++++  + ++ l+e  
  gi|385806119|ref|YP_005842517.1| 241 NSLKNRG------IKISSVVINKYKKDENGLSVINYLKEKF 275
                                       8887777......569***********88877777777643 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.2   5.1e-12   5.7e-09       5     126 ..      14     145 ..      10     156 .. 0.82
   2 ?   -1.6   0.1       1.9   2.1e+03      79      79 ..     260     260 ..     185     304 .. 0.60

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 5.1e-12
                            AAA_31   5 aianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekneiektlyevli.eeknikeaiiktkven 80 
                                       +++  KGGvGKTT s  l+   a+++  + +  +Dp   +   lg++ +++ek++ e li +e++i+e+i +  +++
  gi|385806119|ref|YP_005842517.1|  14 VMIVGKGGVGKTTFSAILSIY-ASKQLPTFVTSIDPAHHLGDVLGYKLEHREKRIAENLIaNEADIDELIREYLSKS 89 
                                       56778***********99986.5667899****************************9987**********888899 PP

                            AAA_31  81 ldlipss.id..Laeaeielvelekk.....eeilkellekvk..deYDyiiiDcp 126
                                       ++l+  s  d    ++++ + +l+++     e +l+ +++ v+  deY yii+D+p
  gi|385806119|ref|YP_005842517.1|  90 INLLKNSyKDitALNLDKYFDTLKDSpgieiEAMLHYIVSLVRkvDEYKYIIVDTP 145
                                       99887541441155778889999988888777778888777762268*******98 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.9
                            AAA_31  79 e 79 
                                       +
  gi|385806119|ref|YP_005842517.1| 260 K 260
                                       0 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     1e-07   0.00012      32     150 ..      10     144 ..       4     149 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1e-07
                            AAA_25  32 agelallaGapgtGKttlaldlalavatGkpwlg....pvapeqgkVlyvsaEdsedelrrRlravgeal....... 97 
                                       +++l++++G +g+GKtt+   l++  ++  p +     p a+  g Vl + +E +e+++++ l a  +++       
  gi|385806119|ref|YP_005842517.1|  10 EKGLVMIVGKGGVGKTTFSAILSIYASKQLPTFVtsidP-AHHLGDVLGYKLEHREKRIAENLIANEADIdelirey 85 
                                       6899***********************999999998854.5799*************************95555555 PP

                            AAA_25  98 .........rddarllvldlagveslpLfakdrggtl.ltadvdaleaaieevegvrlvviDp 150
                                                +  ++ ++l+l++  +   + kd+ g + ++a ++ +   +++v +++ +++D+
  gi|385806119|ref|YP_005842517.1|  86 lsksinllkNSYKDITALNLDKYFD---TLKDSPG-IeIEAMLHYIVSLVRKVDEYKYIIVDT 144
                                       5555554442233333333322211...1112222.235666666666666666666666665 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 !   12.6   0.1   6.3e-05     0.071       6      29 ..      13      36 ..       9      53 .. 0.84
   2 ?   -2.3   0.0       2.2   2.5e+03     110     120 ..     135     145 ..     119     149 .. 0.61
   3 ?    3.4   0.0     0.039        44     135     173 ..     218     256 ..     207     272 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.3e-05
                              ParA  6 iavlSgKGGVGKStvavnlAlaLa 29
                                      ++++ gKGGVGK+t+++ l++  +
  gi|385806119|ref|YP_005842517.1| 13 LVMIVGKGGVGKTTFSAILSIYAS 36
                                      56778************9998655 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.2
                              ParA 110 gelDyLiiDlP 120
                                       +e  y+i+D+P
  gi|385806119|ref|YP_005842517.1| 135 DEYKYIIVDTP 145
                                       45567777776 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.039
                              ParA 135 plagaviVttpqevaladvkkaiemfkkvkvkvlGvveN 173
                                       + ++++ Vtt +++ + d ++  + +k+  +k+ +vv N
  gi|385806119|ref|YP_005842517.1| 218 DFTKIIGVTTTEKLPIVDLERLSNSLKNRGIKISSVVIN 256
                                       5678999*****************************988 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   3.8   0.00019      0.21       5      73 ..      14     144 ..      11     149 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00019
                            AAA_24   5 iliyGpsgiGKTtlakel.....gpkplfi............................................... 29 
                                       ++i+G+ g+GKTt+ + l     ++ p f+                                               
  gi|385806119|ref|YP_005842517.1|  14 VMIVGKGGVGKTTFSAILsiyasKQLPTFVtsidpahhlgdvlgyklehrekriaenlianeadidelireylsksi 90 
                                       79**************9999999666666677999999999999988877777777777777777777777666666 PP

                            AAA_24  30 .dtekGlksldadkfpdie.........swedfldevvelaaeladyktlviDt 73 
                                         + +++k++ a ++++            +e++l+++v+l ++ ++yk +++Dt
  gi|385806119|ref|YP_005842517.1|  91 nLLKNSYKDITALNLDKYFdtlkdspgiEIEAMLHYIVSLVRKVDEYKYIIVDT 144
                                       6333344444444433333666677777889999999999*************8 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   7.6e-05     0.085       1      61 [.      14      82 ..      14     146 .. 0.68
   2 ?   -2.8   0.0       7.5   8.4e+03      78      83 ..     180     185 ..     158     214 .. 0.50
   3 ?   -1.8   0.0       3.9   4.4e+03      19      37 ..     240     264 ..     236     302 .. 0.47

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.6e-05
                            AAA_18  1 IlltGtpGvGKttlakeL....skrl.gfgvnlrdvakenglllevdpe...aldeskrldedkldkll 61
                                      +++ G+ GvGKtt++  L    sk l  f++ +   +  ++ l +  ++    + e+++++e   d+l+
  gi|385806119|ref|YP_005842517.1| 14 VMIVGKGGVGKTTFSAILsiyaSKQLpTFVTSIDPAHHLGDVLGYKLEHrekRIAENLIANEADIDELI 82
                                      799***************888766664444444444444444444444433344444444444444444 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 7.5
                            AAA_18  78 vidghl 83 
                                       vi+++ 
  gi|385806119|ref|YP_005842517.1| 180 VIESVK 185
                                       333332 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 3.9
                            AAA_18  19 skrlgf......gvnlrdvakengl 37 
                                       s++l++      +v+++++ k+++ 
  gi|385806119|ref|YP_005842517.1| 240 SNSLKNrgikisSVVINKYKKDENG 264
                                       4444223223444444444444333 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00011      0.12       3      28 ..      13      38 ..      11      48 .. 0.84
   2 ?   -0.0   0.2      0.51   5.8e+02      96     124 ..     191     219 ..     185     273 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                                      EEEEEESTTSSHHHHHHHHHHHHHHT CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkke 28
                                      ++++vG  G+GKTt  a L+ + +k+
  gi|385806119|ref|YP_005842517.1| 13 LVMIVGKGGVGKTTFSAILSIYASKQ 38
                                      68*****************9888776 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.51
                                       TTHHHHHHHHHHHHHHHSSSEEEEEEETT CS
                             SRP54  96 qndkelmeelkkikkvvkpdevllvldat 124
                                        +d+++++el ++++ ++ +++l+  +  
  gi|385806119|ref|YP_005842517.1| 191 TIDDKILKELIQMREEIERNKKLFMNSDF 219
                                       56888888888888888777777665444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   7.9e-05     0.089       1      39 [.      13      57 ..      13     155 .. 0.50

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.9e-05
                            AAA_33  1 lvllvGlpGsGKstlaerl....lkklgavllssdt....lrrrlfg 39
                                      lv++vG  G+GK+t++  l     k+l++++ s d         + g
  gi|385806119|ref|YP_005842517.1| 13 LVMIVGKGGVGKTTFSAILsiyaSKQLPTFVTSIDPahhlG--DVLG 57
                                      89**************9887776666665555555533330..3333 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.079        89      95     123 ..       7      35 ..       1      45 [. 0.61
   2 ?    8.0   0.1     0.002       2.2     150     190 ..     241     285 ..     220     292 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.079
                            AAA_26  95 lekdadivvVEGagglgvpiteellnadi 123
                                       l+k++ +v + G gg+g+ +++  l ++ 
  gi|385806119|ref|YP_005842517.1|   7 LPKEKGLVMIVGKGGVGKTTFSAILSIYA 35 
                                       56666666666666666666665554444 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.002
                            AAA_26 150 ealrqknvrvlGvilNkvrnpe....nvetlekksgipvlGvvPy 190
                                       ++l+++++++  v++Nk +++e     +  l++k++   l  vP+
  gi|385806119|ref|YP_005842517.1| 241 NSLKNRGIKISSVVINKYKKDEnglsVINYLKEKFPEARLILVPQ 285
                                       6789*************9998656668888888888777777776 PP

>> SRP1_TIP1  Seripauperin and TIP1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00016      0.18      11      81 ..      89     158 ..      73     161 .. 0.88
   2 ?   -2.7   0.0       5.6   6.3e+03      37      72 ..     188     222 ..     177     228 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00016
                         SRP1_TIP1  11 evaelevllnDvks.nlkeYlslakansgfslPsgvlsvyaalatatddsYttllseidfaevssmitglPW 81 
                                        ++ l+   +D+++ nl +Y+   k+++g+++ + +  ++  +  ++ d+Y  ++ + + ++++s + glPW
  gi|385806119|ref|YP_005842517.1|  89 SINLLKNSYKDITAlNLDKYFDTLKDSPGIEIEAMLHYIVSLV--RKVDEYKYIIVDTPATSITSRLIGLPW 158
                                       567788889999877****************988877777655..77899********************** PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.6
                         SRP1_TIP1  37 sgfslPsgvlsvyaalatatddsYttllseidfaev 72 
                                       +++++ +++l+   ++  ++ +    l+ + df+++
  gi|385806119|ref|YP_005842517.1| 188 KKVTIDDKILKELIQMR-EEIERNKKLFMNSDFTKI 222
                                       55666666666666653.333444556666666665 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 ?   10.0   0.0   0.00049      0.55       1      36 [.      16      50 ..      16      62 .. 0.85
   2 ?   -1.4   0.0       1.4   1.6e+03      16      53 ..      89     126 ..      83     131 .. 0.79
   3 ?   -1.4   0.0       1.4   1.6e+03      86      99 ..     131     145 ..     121     146 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00049
                        ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrsvavvNLDPAa 36
                                      +vG  G+GKttf   ls +++++  +  v  +DPA 
  gi|385806119|ref|YP_005842517.1| 16 IVGKGGVGKTTFSAILSIYASKQ-LPTFVTSIDPAH 50
                                      79**********88777777666.9999999***96 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.4
                        ATP_bind_1  16 lseilelrgrsvavvNLDPAaeelpYeaavdirelitl 53 
                                        +++l+++ +++  +NLD   ++l+ ++ ++i+ ++++
  gi|385806119|ref|YP_005842517.1|  89 SINLLKNSYKDITALNLDKYFDTLKDSPGIEIEAMLHY 126
                                       55566667778889999999999999999999998875 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.4
                        ATP_bind_1  86 lekeed.dyllfDtP 99 
                                       ++k ++ +y+++DtP
  gi|385806119|ref|YP_005842517.1| 131 VRKVDEyKYIIVDTP 145
                                       44555559******9 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00087      0.97       4      72 ..      14      84 ..      11     101 .. 0.75
   2 ?   -1.2   0.0       1.3   1.5e+03      41      52 ..     113     124 ..      83     156 .. 0.49
   3 ?    1.8   0.1      0.16   1.8e+02      72     122 ..     202     250 ..     163     273 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00087
                         PduV-EutP  4 illiGkvgsGKttLtqalkgeelkYkktq..aiefsdeviDtPGeylenrklysalivtsaeadvialvqd 72
                                      ++++Gk g+GKtt +  l+  + k   t   +i+  +++ D  G  le+r+   a + ++ ead+  l+ +
  gi|385806119|ref|YP_005842517.1| 14 VMIVGKGGVGKTTFSAILSIYASKQLPTFvtSIDPAHHLGDVLGYKLEHREKRIAENLIANEADIDELIRE 84
                                      8**************99987555554444114555666788888888888888888888888888777665 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.3
                         PduV-EutP  41 iDtPGeylenrk 52 
                                        D+PG  +e   
  gi|385806119|ref|YP_005842517.1| 113 KDSPGIEIEAML 124
                                       455553333322 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.16
                         PduV-EutP  72 dateeesvfppgfasvfnkeviGiitkidlaedeenieaveelLksaGaek 122
                                       ++ ee +   + f++    ++iG+ t   l+    ++e   + Lk+ G++ 
  gi|385806119|ref|YP_005842517.1| 202 QMREEIERNKKLFMNSDFTKIIGVTTTEKLP--IVDLERLSNSLKNRGIKI 250
                                       4444444444455555555688888888887..778888888888888864 PP

>> Cortex-I_coil  Cortexillin I, coiled coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1      0.84   9.4e+02      54      72 ..      61      83 ..      51     113 .. 0.63
   2 ?   12.3   2.0   0.00013      0.15      13      97 ..     169     248 ..     166     252 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.84
                                      HHHHHHHHH.H...HHHHHHHHH CS
                     Cortex-I_coil 54 aerekrlre.l...eakldealk 72
                                      ++rekr++e l   ea +de ++
  gi|385806119|ref|YP_005842517.1| 61 EHREKRIAEnLianEADIDELIR 83
                                      45555555421222444554444 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00013
                                       XHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Cortex-I_coil  13 elanklaglenslesekvsreelikqkdelesllasleseaaerekrlreleakldealknleleklarlelesrls 89 
                                       +l +k+agl++ +es k  ++  i  k  l++l++ ++ e+ er+k+l  +++ + +++     ekl  ++le rls
  gi|385806119|ref|YP_005842517.1| 169 DLRSKIAGLKEVIESVKAGKKVTIDDK-ILKELIQ-MR-EEIERNKKLF-MNSDFTKIIGVTTTEKLPIVDLE-RLS 240
                                       7899**************998877654.5777765.44.5578999886.8999******************9.999 PP

                                       HHHHHCHH CS
                     Cortex-I_coil  90 ktekdkai 97 
                                          k++ i
  gi|385806119|ref|YP_005842517.1| 241 NSLKNRGI 248
                                       99999876 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00024      0.27      11      81 ..       4      75 ..       2     143 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00024
                            AAA_30 11 ealltsgdrvavltGpAGtGKttalkalreaweaa.ggrviglAptgkaAkvLaeelgieastiakllkrlk 81
                                       ++l +++ +++++G  G GKtt  + l   + ++    v  + p +   +vL+ +l+ + ++ia+ l +++
  gi|385806119|ref|YP_005842517.1|  4 SQILPKEKGLVMIVGKGGVGKTTFSAILSIYASKQlPTFVTSIDPAHHLGDVLGYKLEHREKRIAENLIANE 75
                                      578888999**************9888876666665777888888888888888888888777777766555 PP

>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.3    0.0033       3.7      19      57 ..      60      99 ..      52     116 .. 0.79
   2 ?   -2.1   0.0         5   5.6e+03       8      23 ..     120     135 ..     117     141 .. 0.76
   3 ?    4.5   0.2     0.044        49      21      52 ..     191     222 ..     177     246 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0033
                                      HHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HGG CS
                              PhoU 19 leekdtelarevierddeidrlekeiersllealak.rqp 57
                                      le++++ +a+ +i+++ +id+l +e   + +++l++ ++ 
  gi|385806119|ref|YP_005842517.1| 60 LEHREKRIAENLIANEADIDELIREYLSKSINLLKNsYKD 99
                                      6888999***************999988889988663443 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5
                                       HHHHHHHHHHHHHCT- CS
                              PhoU   8 veemlddalealeekd 23 
                                       +e ml++ ++++++ d
  gi|385806119|ref|YP_005842517.1| 120 IEAMLHYIVSLVRKVD 135
                                       5778888888888777 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.044
                                       CT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              PhoU  21 ekdtelarevierddeidrlekeierslleal 52 
                                       + d+++++e+i++++ei+r  k++ +s ++++
  gi|385806119|ref|YP_005842517.1| 191 TIDDKILKELIQMREEIERNKKLFMNSDFTKI 222
                                       4466999************9999977766666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1156  (0.0644765); expected 358.6 (0.02)
Passed bias filter:                      630  (0.0351386); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); 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: 0.66u 0.33s 00:00:00.99 Elapsed: 00:00:00.49
# Mc/sec: 1876.78
//
Query:       gi|385806120|ref|YP_005842518.1|  [L=97]
Description: hypothetical protein FFONT_1078 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score 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   0.1       0.25   11.5   0.1    1.3  1  Flagellin_IN  Flagellin hook IN motif


Domain annotation for each model (and alignments):
>> Flagellin_IN  Flagellin hook IN motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   1.4e-05      0.25      20      31 ..      83      94 ..      81      96 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.4e-05
                                      TTBCHHHHHHHH CS
                      Flagellin_IN 20 gdtlddiadaIN 31
                                      +dtl+di+daIN
  gi|385806120|ref|YP_005842518.1| 83 DDTLGDIIDAIN 94
                                      7*********** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); 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: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 665.98
//
Query:       gi|385806121|ref|YP_005842519.1|  [L=583]
Description: carbon starvation protein CstA [Fervidicoccus fontis Kam940]
Scores for complete 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-105  351.2  26.9     1e-104  350.5  26.9    1.3  1  CstA      Carbon starvation protein CstA
    2.2e-23   82.8   4.4    2.2e-23   82.8   4.4    2.9  3  CstA_5TM  5TM C-terminal transporter carbon starvation CstA


Domain annotation for each model (and alignments):
>> CstA  Carbon starvation protein CstA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  350.5  26.9  1.1e-108    1e-104       5     361 ..       7     358 ..       3     371 .. 0.95

  Alignments for each domain:
  == domain 1  score: 350.5 bits;  conditional E-value: 1.1e-108
                              CstA   5 llvvvavvvfviayrfYgkfiakkvlklddkraTPaerledgkdyvptnklvlfghhFasiagagPlvGpvlAaqfG 81 
                                       l++++  v +++ y+fYg + +k++ +++d++ TPa+++ dg dyvp+nk++l+ghh  +iag+gP+ Gp++A+ +G
  gi|385806121|ref|YP_005842519.1|   7 LILLLLGVWYILFYKFYGGYFHKRIAEAKDENITPAHKYFDGIDYVPANKYILYGHHVGAIAGTGPIAGPTMAMAWG 83 
                                       444555578999***************************************************************** PP

                              CstA  82 ylPgllWilvGavfagavhDfvvlvasvrrkgkslgelakkelgkvakllallaillililvlavlalvvvkalaes 158
                                       +lPg+lWi + +v+ gavhD+++l+as+r++gk+++ +  + l+k+++ ++   il+ lil++a++++  v+ ++++
  gi|385806121|ref|YP_005842519.1|  84 WLPGILWIAIANVVLGAVHDYLALIASIRHEGKTIAFVSGQVLSKRTQYIFQWYILFALILIIAAFVIFDVQVFMST 160
                                       ***************************************************************************** PP

                              CstA 159 paavfsviltipialllGvllrklrkgvleasvigvvllllavvvgseveealaelltlsketlaivlivYvfvAsv 235
                                       p+++++++ ++pia+++Gvl++kl+ ++  a v gvvlllla+++g ++      l+  + ++++++l++Y+ +A  
  gi|385806121|ref|YP_005842519.1| 161 PSTATAILWFMPIAIFVGVLIYKLNFKLPYAIVTGVVLLLLAMYAGYKL-----PLVINNFNAWITILLIYGWMAGW 232
                                       *************************************************.....78888999*************** PP

                              CstA 236 lPvwlllaPrdYlstflligtivllalgilvvapelklpavtefvdgegpvfagslfPllfitiACGaiSGFHslvs 312
                                       lP+w +l+Prd+l+ +++ g+i+l ++g+++++  ++l+a+++f+        ++++P++ ++iACGa+SGFHslv+
  gi|385806121|ref|YP_005842519.1| 233 LPLWYFLQPRDFLNVYIMWGGIILGVIGLILARTPIQLDALSSFTWKVVGGQPSPVYPTIVLVIACGALSGFHSLVA 309
                                       ********************************************5555555689*********************** PP

                              CstA 313 sgttskllekesdarlvgygamllEslvailalvaaavlepaayfalns 361
                                       sgtt+++l+ e dar +gyg+ml+E+lva+ + +++a++ p ay+  n+
  gi|385806121|ref|YP_005842519.1| 310 SGTTARQLNSELDARAIGYGGMLTEGLVAMTVALSVATMIPFAYSYYNN 358
                                       ***************************************9*99987765 PP

>> CstA_5TM  5TM C-terminal transporter carbon starvation CstA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   2.1      0.57   5.1e+03      78     109 ..     144     176 ..      97     183 .. 0.61
   2 ?   -5.8   5.4         2   1.8e+04      42      42 ..     183     183 ..     144     251 .. 0.53
   3 !   82.8   4.4   2.4e-27   2.2e-23       2     116 .]     400     524 ..     399     524 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.57
                          CstA_5TM  78 QlLAalaLlvvtvwll.ktgrkalvtliPmvfm 109
                                        ++Aa++++ v v++   +   a+++++P+++ 
  gi|385806121|ref|YP_005842519.1| 144 LIIAAFVIFDVQVFMStPSTATAILWFMPIAIF 176
                                       345555555555555533333666666666655 PP

  == domain 2  score: -5.8 bits;  conditional E-value: 2
                          CstA_5TM  42 a 42 
                                       +
  gi|385806121|ref|YP_005842519.1| 183 K 183
                                       1 PP

  == domain 3  score: 82.8 bits;  conditional E-value: 2.4e-27
                          CstA_5TM   2 avaytfailfvalfalTtlDtatRlaRyilqellgelk......kkaltnkyvatliavalavllllwggintlWpl 72 
                                       a+++ fa l++a+f    lDt++RlaR++++e+++ l+      +k l+n+y+++l+a++++ +l+ +g++n ++p+
  gi|385806121|ref|YP_005842519.1| 400 AIGTLFAGLWFATFDFAVLDTTNRLARFTWNEIVEPLRiraptaHKILSNRYLGSLVALLIGGSLAYTGALNYVYPA 476
                                       57899********************************9877776666****************************** PP

                          CstA_5TM  73 FGaaNQlLAalaLlvvtvwll.ktgr...kalvtliPmvfmlvvtlta 116
                                       F+ aNQlLAalaL++++ +++ + +r   + l+ ++P++f+++++++a
  gi|385806121|ref|YP_005842519.1| 477 FAGANQLLAALALITTSSYVYyELRRslkQSLLAFVPAFFLWITVTSA 524
                                       *********************88888898889999********99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (583 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1012  (0.0564449); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); 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):               2  [number of targets reported over threshold]
# CPU time: 0.72u 0.32s 00:00:01.04 Elapsed: 00:00:00.50
# Mc/sec: 3541.11
//
Query:       gi|385806122|ref|YP_005842520.1|  [L=109]
Description: hypothetical protein FFONT_1080 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score 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   0.2      0.023   14.8   0.2    1.1  1  DUF872    Eukaryotic protein of unknown function (DUF872)


Domain annotation for each model (and alignments):
>> DUF872  Eukaryotic protein of unknown function (DUF872)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.2   1.3e-06     0.023      41      91 ..      27      79 ..       7      84 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.3e-06
                            DUF872 41 knrkvvlaallLlllGlvLlllgvvilvep..seGvssavf.lvlGlllfi..PGv 91
                                       n k + a +++++lG++L++ +++   +    +G+   ++ +v+G +l++  PG+
  gi|385806122|ref|YP_005842520.1| 27 MNLKQI-AGMIMTFLGIILMFYSYLANWKNgmIAGD--DAYtFVAGTILLLagPGF 79
                                      466666.56889************999887434444..455578998888834555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       796  (0.0443973); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 739.55
//
Query:       gi|385806123|ref|YP_005842521.1|  [L=619]
Description: beta-lactamase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-26   92.6   0.0    3.8e-26   91.5   0.0    1.6  1  Beta-Casp      Beta-Casp domain
    1.4e-21   76.3   3.5    1.6e-18   66.4   0.2    3.0  3  KH_7           KH domain
    5.8e-16   58.2   0.1    1.3e-15   57.1   0.1    1.6  1  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
    1.9e-15   56.8   0.0    1.5e-14   53.9   0.0    2.2  2  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
    3.2e-13   50.1   0.4    9.6e-13   48.6   0.4    1.8  1  Lactamase_B    Metallo-beta-lactamase superfamily
    7.4e-10   38.7   0.0    1.4e-09   37.8   0.0    1.4  1  Lactamase_B_2  Beta-lactamase superfamily domain
      0.006   16.5   0.0      0.015   15.2   0.0    1.6  1  Lactamase_B_3  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.015   15.1   1.0      0.015   15.1   1.0    2.4  2  KH_2           KH 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 !   91.5   0.0   1.7e-29   3.8e-26       2     110 .]     399     521 ..     398     521 .. 0.86

  Alignments for each domain:
  == domain 1  score: 91.5 bits;  conditional E-value: 1.7e-29
                                       HHHHHHH..HCTT..TTS-S-EEEEE-HHHHHHHHHGGGGGG........................E-SHH....HH CS
                         Beta-Casp   2 qellylLeelwkekkledlklpiyldsplaskatevYkeyae........................veakslewmes 54 
                                       qe++++L+e+ ++++l  +++p+y+ + +++++t+++++y+e                        v  +s    ++
  gi|385806123|ref|YP_005842521.1| 399 QEIMLILSEAFSKGQL--QDIPVYIEG-MVTEVTALHTHYPElmsqsvekaihlgenpfmnknfvvV--QS----KD 466
                                       9***********9774..457******.************999999999999999999766666322..23....33 PP

                                       HH..HHHS-SSEEEEES-TTSSSSHHHHHHHHHTTSTTSEEEESS---TTSHHHHH CS
                         Beta-Casp  55 kkeelnsskgpkvilassgmlegGrsrellkklledprntvilvgyqaegTlgrkl 110
                                       k++e + ++gp++ila+sgml+gG+s+e+lk+l+edp+n++i+v+yq+egTlgrk+
  gi|385806123|ref|YP_005842521.1| 467 KRSE-ALEPGPCIILATSGMLNGGPSVEYLKSLAEDPKNSLIFVSYQVEGTLGRKI 521
                                       3333.4567*********************************************97 PP

>> KH_7  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.4   0.2   7.3e-22   1.6e-18      21      68 .]       2      49 ..       1      49 [. 0.97
   2 !    9.7   0.1   0.00035      0.79       5      26 ..      53      74 ..      50     100 .. 0.92
   3 ?   -3.8   0.0       5.9   1.3e+04       5      18 ..     275     288 ..     273     293 .. 0.81

  Alignments for each domain:
  == domain 1  score: 66.4 bits;  conditional E-value: 7.3e-22
                              KH_7 21 itdveFEGPelViYtknpklfaengdlirklAkelrkRiviRpDpsvl 68
                                      +t++eFEGPe++iY+knp +++e+  +ir +Ak++rkR+viR+Dps++
  gi|385806123|ref|YP_005842521.1|  2 MTSIEFEGPEIAIYVKNPGILMEQMGIIRDIAKTIRKRVVIRTDPSIR 49
                                      589*******************************************86 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00035
                              KH_7  5 eelkekieeklPkevkitdveF 26
                                      ee k+ i e++Pke++i+ +eF
  gi|385806123|ref|YP_005842521.1| 53 EEAKKIILETVPKEAEIKAIEF 74
                                      799******************9 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 5.9
                              KH_7   5 eelkekieeklPke 18 
                                       +e+k+ + +++P e
  gi|385806123|ref|YP_005842521.1| 275 KEVKKAVLHTIPVE 288
                                       78999999999965 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 !   57.1   0.1   5.6e-19   1.3e-15       1      56 [.     539     596 ..     539     610 .. 0.86

  Alignments for each domain:
  == domain 1  score: 57.1 bits;  conditional E-value: 5.6e-19
                             RMMBL   1 tipvkarieeid.fSgHadknellelirklkprn..vilvHGeeeatsalarllkeeeg 56 
                                       ti+++++i+ i+ fSgH+dknel+ +i+ ++p++  +il+HGe  a+ +l + + e+++
  gi|385806123|ref|YP_005842521.1| 539 TIKINMEIHSIEgFSGHSDKNELISFIENIEPKPknIILNHGELSAIMSLYNSI-EKRK 596
                                       699***********************************************9999.4443 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 !   53.9   0.0   6.8e-18   1.5e-14       1     174 [.     176     344 ..     176     358 .. 0.78
   2 ?   -0.1   0.0      0.24   5.4e+02      21      59 ..     557     592 ..     549     611 .. 0.73

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 6.8e-18
                     Lactamase_B_6   1 lLeldnvkiLlDvGwdeskvsles...alkelekviptvdliLLshatlehlGayallyakfksklllnipvyatlp 74 
                                       l+e ++ kiLlD G++  + s+ s    ++  e  i+++d+i+++ha l+h+G +++l+     k++ n pvy t++
  gi|385806123|ref|YP_005842521.1| 176 LVETNESKILLDAGVNPGSSSFPSiapRFDVDEFKIEELDAIVITHAHLDHVGMLPFLF-----KYGYNGPVYMTKA 247
                                       688999**********7766665511144444557******************877666.....468899***8876 PP

                     Lactamase_B_6  75 vvk...LGrvslldlyaskgllgpedseeleledideafdkiktlkYsQklelkskldgltitaynaGhtlGGtiWk 148
                                       +     L ++  ld ++++g + p+     + +++++a  + +++ Y   +++     ++ +t y aGh lG ++ +
  gi|385806123|ref|YP_005842521.1| 248 TRDimvLSQLDFLDIMTKEGKIPPY-----TQKEVKKAVLHTIPVEYGDVTDIAP---DIRLTLYDAGHILGSAMAH 316
                                       6550005666666666666666555.....55799**************999985...89*************9866 PP

                     Lactamase_B_6 149 i..skesekivYavdwnhakeshLngaa 174
                                       +   +++++ivY  d+  a+ ++Ln+a+
  gi|385806123|ref|YP_005842521.1| 317 LhiGNGLHNIVYTGDFKYAHTKLLNKAT 344
                                       52278999****************9974 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.24
                     Lactamase_B_6  21 slesalkelekviptvdliLLshatlehlGayallyakf 59 
                                       + ++ ++++e++ p+   i+L h +l+ + ++   y+++
  gi|385806123|ref|YP_005842521.1| 557 DKNELISFIENIEPKPKNIILNHGELSAIMSL---YNSI 592
                                       45679999***************999888764...4433 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   0.4   4.3e-16   9.6e-13       5     162 ..     171     343 ..     168     450 .. 0.84

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 4.3e-16
                                       SSEEEEEEETTCEEEES--SCHHHHHHHH...HHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHH CS
                       Lactamase_B   5 pvnsyliegdggviLiDtGtsteaaraal...elaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaee 78 
                                       + +++l+e++++ iL D+G+ +  + + +   +    ++k++++da+++TH+HlDH+G l+ l +   + +++  ++
  gi|385806123|ref|YP_005842521.1| 171 GRSAILVETNESKILLDAGVNPGSSSFPSiapRFDVDEFKIEELDAIVITHAHLDHVGMLPFLFKYGYNGPVYMTKA 247
                                       67899************************9999999**************************999999988888888 PP

                                       HHCCHCHHHHHHHHHCCHH...............TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSC.CEEEEE CS
                       Lactamase_B  79 apalfmeeaddaasrkgll...............lagvsadkpdvdeeeldgnaggrralyvtggpghgh.ghgvve 139
                                       ++        d       +               +++v +  p++  +++d+  + r++ly  g+ + ++  h++++
  gi|385806123|ref|YP_005842521.1| 248 TRDIMVLSQLDFLD----ImtkegkippytqkevKKAVLHTIPVEYGDVTDIAPDIRLTLYDAGHILGSAmAHLHIG 320
                                       88777666644333....12335799******99999999999999999999999999999887766555269**** PP

                                       ETTCCEEEECTTTSSHHCCCCCC CS
                       Lactamase_B 140 ygggkvlftGDallagetgridl 162
                                       +g  ++++tGD+ +a+  ++   
  gi|385806123|ref|YP_005842521.1| 321 NGLHNIVYTGDFKYAHTKLLNKA 343
                                       **************988887776 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 !   37.8   0.0   6.2e-13   1.4e-09       3     173 ..     184     366 ..     182     391 .. 0.74

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 6.2e-13
                                       EEES--TTHHHHHTCGGS--S..SS--..SEEEEE-SS--HHHHGGGGCCCC.C--EEEEEEEEHHHHH........ CS
                     Lactamase_B_2   3 iLiDagpdlrqqalralqPve..lrdelppidaVllthaHyDHlaglltlre.lrpkklplyapkgvla........ 68 
                                       iL+Dag +      +   P+      +++++da+++thaH DH+  l++l + ++  + p+y +k +++        
  gi|385806123|ref|YP_005842521.1| 184 ILLDAGVNPGSSSFPSIAPRFdvDEFKIEELDAIVITHAHLDHVGMLPFLFKyGY--NGPVYMTKATRDimvlsqld 258
                                       888998885444444443433244556789**************88888888543..46899999998877666666 PP

                                       ....HCCTTCGHHHCHTT.............TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEE CS
                     Lactamase_B_2  69 ....vleanfvylaleee.............pavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGl 128
                                             ++         e             + +++ +++ g+ ++++ +++++t+  a h  g         ++ l
  gi|385806123|ref|YP_005842521.1| 259 fldiM-TK---------EgkippytqkevkkAVLHTIPVEYGDVTDIA-PDIRLTLYDAGHILGS-------AMAHL 317
                                       66642.22.........12233333334678889999999*******9.69999*9999999999.......8999* PP

                                       EEECTTEEEEEESS-S---....HHHHHHHCT-SEEEEE-S-SSTTHHH CS
                     Lactamase_B_2 129 riegggkrvyyigDtgyip....eeigerlggadllllditayeddemi 173
                                        i++g ++++y+gD +y +     ++ +++  ++ l+++ t+ e ++++
  gi|385806123|ref|YP_005842521.1| 318 HIGNGLHNIVYTGDFKYAHtkllNKATDKFPRLETLIMESTYGETKQPS 366
                                       *****************99544444557777788888888876666655 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 !   15.2   0.0   6.9e-06     0.015       5      50 ..     170     227 ..     168     233 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6.9e-06
                     Lactamase_B_3   5 lghnsflletagarilvDPf....kanlgyeppa..........eeaDlvlisqaledHa 50 
                                       +g +++l+et++ +il+D +    +    +   a          ee D+++i++a+ dH 
  gi|385806123|ref|YP_005842521.1| 170 VGRSAILVETNESKILLDAGvnpgS--SSFPSIAprfdvdefkiEELDAIVITHAHLDHV 227
                                       5889*************98744331..22332225688888888***************7 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       1.2   2.8e+03      47      58 ..      29      40 ..       8      53 .. 0.71
   2 ?   15.1   1.0   6.9e-06     0.015       8      44 ..      61      96 ..      54     102 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.2
                                      HHHHHHHHHHHH CS
                              KH_2 47 ikkigkelrkdi 58
                                      i+ i k++rk++
  gi|385806123|ref|YP_005842521.1| 29 IRDIAKTIRKRV 40
                                      677777888777 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 6.9e-06
                                      HHT.ECETEEEEEEECCSCEEEEEEEESCHHHHHTGGG CS
                              KH_2  8 vei.kkagvskveIertanrviiviresqpgivIGkgG 44
                                      +++ k+a+++ +e ++      ++i++++pg+vIGkgG
  gi|385806123|ref|YP_005842521.1| 61 ETVpKEAEIKAIEFDD--VLGDVIIKAEKPGLVIGKGG 96
                                      4555899999999977..5668999************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (619 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); 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: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.46
# Mc/sec: 4044.87
//
Query:       gi|385806124|ref|YP_005842522.1|  [L=83]
Description: hypothetical protein FFONT_1082 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0041   17.2   6.7      0.011   15.8   6.7    1.9  1  Ribosomal_L38e  Ribosomal L38e protein family
  ------ inclusion threshold ------
      0.094   13.7   1.6       0.11   13.5   1.6    1.1  1  IL1_propep      Interleukin-1 propeptide


Domain annotation for each model (and alignments):
>> Ribosomal_L38e  Ribosomal L38e protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   6.7   1.2e-06     0.011      23      50 ..      28      54 ..      11      79 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.2e-06
                    Ribosomal_L38e 23 kikknkkdntKfKvRcsryLYTLvvkdk 50
                                       ik nk +n+K+K+R +  LYTLv++ +
  gi|385806124|ref|YP_005842522.1| 28 LIKVNK-ENVKLKIRDKNKLYTLVFSKE 54
                                      588888.99***************9866 PP

>> IL1_propep  Interleukin-1 propeptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.6   1.2e-05      0.11      29      90 ..      14      75 ..       4      82 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.2e-05
                        IL1_propep 29 plslkksfqdldlcslkedlvdkgiqlkiseqsksksfkesvvvvvAveklkkrrlslnqsf 90
                                      ++++kk +++ dlc  k + ++ +++ +  ++ ++  f +  v v+ ve+lkk ++ + +++
  gi|385806124|ref|YP_005842522.1| 14 NEKVKKLVKEPDLCLIKVNKENVKLKIRDKNKLYTLVFSKENVGVSSVEELKKVATDIATKI 75
                                      456779999*****97777665555555556666669****************998887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       951  (0.0530426); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 528.27
//
Query:       gi|385806125|ref|YP_005842523.1|  [L=428]
Description: putative exonuclease [Fervidicoccus fontis Kam940]
Scores for complete 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-17   62.5   0.0    7.5e-17   61.6   0.0    1.5  1  Beta-Casp      Beta-Casp domain
    8.8e-17   60.8   0.0    1.8e-16   59.8   0.0    1.6  1  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
    1.2e-10   41.1   0.0    2.1e-10   40.4   0.0    1.3  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
    1.5e-08   34.9   0.4    8.2e-08   32.5   0.4    2.0  1  Lactamase_B    Metallo-beta-lactamase superfamily
    9.4e-08   31.8   0.0    1.7e-07   30.9   0.0    1.5  1  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.052   13.4   0.1       0.11   12.3   0.1    1.7  1  Lactamase_B_3  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Beta-Casp  Beta-Casp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.6   0.0   2.5e-20   7.5e-17      12     110 .]     246     344 ..     235     344 .. 0.73

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 2.5e-20
                                       CTT..TTS-S-EEEEE-HHHHHHHHHGGGGGG...........E-SHH....HHHH..HH...........HS-SSE CS
                         Beta-Casp  12 wkekkledlklpiyldsplaskatevYkeyae...........veakslewmeskkeeln...........sskgpk 66 
                                               +  p+y+d+ ++++ate+  e++                      s+    +             k+p+
  gi|385806125|ref|YP_005842523.1| 246 D-------V-SPVYIDG-MVKQATEIMLENKVflknsellekaY---------SE----QiflkgwqdrrkVWKKPC 300
                                       2.......2.49*****.********666655754444443321.........22....0223344444445579** PP

                                       EEEES-TTSSSSHHHHHHHHHTTSTTSEEEESS---TTSHHHHH CS
                         Beta-Casp  67 vilassgmlegGrsrellkklledprntvilvgyqaegTlgrkl 110
                                       vi++ssgml+gG+sr++l+k+++d++n+v+lv++q ++T+gr++
  gi|385806125|ref|YP_005842523.1| 301 VIVSSSGMLKGGPSRYYLRKIADDEKNAVFLVSFQGKNTPGRSI 344
                                       ******************************************86 PP

>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.8   0.0   6.2e-20   1.8e-16       3      62 .]     356     416 ..     354     416 .. 0.94

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 6.2e-20
                             RMMBL   3 pvkarieeidfSgHadknellelirklkprn.vilvHGeeeatsalarllkeeegidvfiP 62 
                                       pvkar+e++dfS Ha+kn+l+e+i+++++   +ilvHGe+e++  la+ +k+++gi  +iP
  gi|385806125|ref|YP_005842523.1| 356 PVKARVEWMDFSSHAGKNGLIEIIKSIRNLEkIILVHGEPESQNVLADEIKQQTGIVPVIP 416
                                       8****************************999***********************866665 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 !   40.4   0.0     7e-14   2.1e-10       2     177 ..      25     184 ..      24     195 .. 0.86

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 7e-14
                     Lactamase_B_6   2 LeldnvkiLlDvGwdeskvslesalkelekviptvdliLLshatlehlGayallyakfksklllnipvyatlpvvkL 78 
                                       +e++n  +LlD G++    + ++ + +l+    ++d ++Lsh  l+h+Ga +lly ++      + ++++t  + +L
  gi|385806125|ref|YP_005842523.1|  25 VEYNNRSVLLDYGVNFD--ENDNPVMPLHISPIKLDGVVLSHVHLDHIGAAPLLYSSV------KPKAFSTRVTRHL 93 
                                       5788999********65..345677777777789****************99999775......5789********* PP

                     Lactamase_B_6  79 GrvslldlyaskgllgpedseeleledideafdkiktlkYsQklelkskldgltitaynaGhtlGGtiWkiskesek 155
                                       +r++l d  + +g         +e+++++   ++i+++k    ++l++     ++  y +Gh +G    k+s+   +
  gi|385806125|ref|YP_005842523.1|  94 ARLMLEDFLKLSGYYL-----DFEINEVNSLLSSIQDVKAGDFVKLSE---FFSLDFYHSGHIPGSLSVKVSTPDGS 162
                                       ******9988776652.....36789**************99999996...678999******************** PP

                     Lactamase_B_6 156 ivYavdwnhakeshLngaalld 177
                                       ++Y  d+n    +++++a++ +
  gi|385806125|ref|YP_005842523.1| 163 LIYTADINSIDTKLVESAKIDG 184
                                       **********999999998765 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.4   2.8e-11   8.2e-08      11     152 ..      25     170 ..      17     212 .. 0.73

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 2.8e-11
                                       EEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHH CS
                       Lactamase_B  11 iegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeea 87 
                                       +e +++ +L D G+  ++++       l++ p ++d v+l+H HlDHiG+++ l +  + + +  + + +  +   +
  gi|385806125|ref|YP_005842523.1|  25 VEYNNRSVLLDYGVNFDENDNP--VMPLHISPIKLDGVVLSHVHLDHIGAAPLLYSSVKPKAFSTRVTRHLARLMLE 99 
                                       7889999999999999999999..899***************************99888888776666555544444 PP

                                       HHHHHHCCHH.....TTCHCGCCEEEEETTTEECCCTEEEEEHECTTST..SCCEEEEEETTCCEEEECTTT CS
                       Lactamase_B  88 ddaasrkgll.....lagvsadkpdvdeeeldgnaggrralyvtggpgh..ghghgvveygggkvlftGDal 152
                                       d+    +  +      +  s  +++ d   +d+  ++  +   +++ gh  g++++ v+ ++g++++t D  
  gi|385806125|ref|YP_005842523.1| 100 DFLKLSGY-YldfeiNEVNSLLSSIQDVKAGDFVKLSEFFSLDFYHSGHipGSLSVKVSTPDGSLIYTADIN 170
                                       44333333.247888555555555555555555555555555555555411555666677999999999875 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 !   30.9   0.0   5.8e-11   1.7e-07       2     174 ..      31     204 ..      30     229 .. 0.71

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 5.8e-11
                                       EEEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC.C--EEEEEEEEHHHHHHCCTTCGHH CS
                     Lactamase_B_2   2 riLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlre.lrpkklplyapkgvlavleanfvyl 77 
                                        +L+D g ++ ++ ++ + P +   ++ ++d+V+l+h H DH+  ++ l    +pk      + +v ++l++ +  +
  gi|385806125|ref|YP_005842523.1|  31 SVLLDYGVNFDENDNPVM-PLH--ISPIKLDGVVLSHVHLDHIGAAPLLYSsVKPKA----FSTRVTRHLARLMLED 100
                                       578888888888877776.654..66779**************77777777655543....4678888888888888 PP

                                       HCHTT.............TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEES CS
                     Lactamase_B_2  78 aleee.............pavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyig 141
                                       +l+                  +++++++g+ ++l     e+      h++           l++ + +++ ++ y++
  gi|385806125|ref|YP_005842523.1| 101 FLKLSgyyldfeinevnsLLSSIQDVKAGDFVKLS----EFFSLDFYHSGHI------PGSLSVKVSTPDGSLIYTA 167
                                       88888777555444555555556666677777775....4666666666666......456888888********** PP

                                       S-S---HHHH..HHHCT..-SEEEEE-S-SSTTHHHH CS
                     Lactamase_B_2 142 Dtgyipeeig..erlgg..adllllditayeddemir 174
                                       D + i+ ++   ++++g  ad+l+++ t+ + + ++r
  gi|385806125|ref|YP_005842523.1| 168 DINSIDTKLVesAKIDGaeADVLIIESTYGNANHPER 204
                                       ******55442255555669******99888877766 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 ?   12.3   0.1   3.8e-05      0.11       6      55 ..      19      75 ..      17     192 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.8e-05
                     Lactamase_B_3  6 ghnsflletagarilvDPf.......kanlgyeppaeeaDlvlisqaledHahletl 55
                                      g +++ +e ++ ++l+D++       ++ + + +++ + D v++s+ + dH  +++l
  gi|385806125|ref|YP_005842523.1| 19 GRAAISVEYNNRSVLLDYGvnfdendNPVMPLHISPIKLDGVVLSHVHLDHIGAAPL 75
                                      7889999***********966665532255666666***************987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.49
# Mc/sec: 2620.08
//
Query:       gi|385806126|ref|YP_005842524.1|  [L=124]
Description: nascent polypeptide-associated complex protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-15   57.4   1.3    1.8e-15   56.6   1.3    1.3  1  NAC            NAC domain
  ------ inclusion threshold ------
      0.023   14.5   0.1      0.035   13.9   0.1    1.3  1  UBA_4          UBA-like domain
       0.03   14.6   1.5      0.036   14.3   1.5    1.2  1  Med21          Subunit 21 of Mediator complex
      0.037   14.1   0.6      0.044   13.9   0.6    1.1  1  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi
      0.046   13.8   0.2        0.1   12.7   0.2    1.5  1  UPF0004        Uncharacterized protein family UPF0004
      0.058   13.4   1.0       0.13   12.2   1.1    1.7  1  HOIP-UBA       HOIP UBA domain pair
      0.098   13.0   0.5        1.4    9.3   0.1    2.5  3  DUF1456        Protein of unknown function (DUF1456)
       0.11   12.4   0.0       0.24   11.4   0.0    1.5  1  UBA            UBA/TS-N domain
       0.28   12.0   2.2        1.3    9.9   1.4    2.0  2  Histone_HNS    H-NS histone family


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 !   56.6   1.3     9e-19   1.8e-15       2      56 ..       7      67 ..       6      67 .. 0.97

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 9e-19
                               NAC  2 kKlrkalkklgl....keipgieeVtirksdgkvlvfdnPkVq..kspgsntyvvfGeaee 56
                                       +++k++k++g+    +e++++e+V i++s++k++v+++P+V+  k++g+++++v+G+ +e
  gi|385806126|ref|YP_005842524.1|  7 SDMKKMMKRMGInvdvEEVKDAERVLIETSGDKNFVVEQPSVTflKMKGQTIIYVIGSLKE 67
                                      57*******************************************************9986 PP

>> UBA_4  UBA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   1.8e-05     0.035      11      33 ..      94     116 ..      85     118 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.8e-05
                             UBA_4  11 TGadeekArqlLeannWdLerAi 33 
                                       +G++ e+Ar+ Le +n+d+ +Ai
  gi|385806126|ref|YP_005842524.1|  94 AGVSLEEARKALEITNGDIAQAI 116
                                       58899*****************8 PP

>> Med21  Subunit 21 of Mediator complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   1.5   1.8e-05     0.036      79     134 ..      51     107 ..      22     115 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.8e-05
                             Med21  79 lilkeqqIeyLIssLPgigsse.eeqeerikeLeeelreveeereekvkekeellkk 134
                                       l +k q I y I sL +i+ +e  +q+++++ Le++++ v++e    ++e+++ l+ 
  gi|385806126|ref|YP_005842524.1|  51 LKMKGQTIIYVIGSLKEIEKEEtTHQKRELEILEDDVQLVAAEAGVSLEEARKALEI 107
                                       66799*************99651689999**********************999875 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.6   2.2e-05     0.044      70     143 ..      20      95 ..       7     110 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.2e-05
                                       --HHHCTTT-SEEEE-SSSSSSB-HH...HHCCS-TTEEEEE-SSTTTTBTHHHHHTTT-EEEEEETTEEEEE-TTS CS
                     AdoHcyase_NAD  70 vtleevvkkadivvtttGnkdiitle...hlkkmkddaivcniGhfdseidvaaleanalkkeevkpqvdrvtlkdg 143
                                       v +eev +   +++ t+G k+ +  +   ++ kmk ++i+  iG   +ei+ ++ ++++ + e +  +v+ v  + g
  gi|385806126|ref|YP_005842524.1|  20 VDVEEVKDAERVLIETSGDKNFVVEQpsvTFLKMKGQTIIYVIGSL-KEIEKEETTHQKRELEILEDDVQLVAAEAG 95 
                                       4699*****************88765333799************76.689988888887777777777776665555 PP

>> UPF0004  Uncharacterized protein family UPF0004
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2     5e-05       0.1      11      94 ..       4      81 ..       2      84 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5e-05
                                      CCCHHHHHHHHHTTTSSS--.--SSS--SEEEEEE--SSSSHHHHTHHHHHHHHTTST.--EEEEEEHHHHS-HHHHHH CS
                           UPF0004 11 mNevdseelaslLkkegyel.vedeeeAdvvlvnTCavrekaekkviqalrelkalkkpekkvvvlGCmaqrekeellk 88
                                      mN +d++++++++   g+++ ve+ ++A+ vl++T + ++   ++   +  ++k +     +++v+G + + ekee  +
  gi|385806126|ref|YP_005842524.1|  4 MNPSDMKKMMKRM---GINVdVEEVKDAERVLIETSGDKNFVVEQPSVTFLKMKGQT----IIYVIGSLKEIEKEETTH 75
                                      6777777766666...6665266779*********9888877777777776666655....99***********99999 PP

                                      H-TTS- CS
                           UPF0004 89 eepevd 94
                                      +++e +
  gi|385806126|ref|YP_005842524.1| 76 QKRELE 81
                                      887765 PP

>> HOIP-UBA  HOIP UBA domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.1   6.7e-05      0.13      53      94 ..      67     117 ..       9     123 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.7e-05
                          HOIP-UBA  53 evaalaaseqkekke...............nevgklsraEakealleagGdvekAvk 94 
                                       e+ ++ ++      +               +    +s +Ea++al  ++Gd+ +A+ 
  gi|385806126|ref|YP_005842524.1|  67 EIEKEETT------HqkreleileddvqlvAAEAGVSLEEARKALEITNGDIAQAIM 117
                                       33333333......234446688888877766667899***************9986 PP

>> DUF1456  Protein of unknown function (DUF1456)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1   0.00069       1.4      11      37 ..       1      27 [.       1      47 [. 0.89
   2 ?   -0.9   0.0       1.1   2.2e+03      12      33 ..      80     101 ..      76     107 .. 0.79
   3 ?    1.1   0.0      0.25   4.9e+02       7      23 ..     100     116 ..      96     121 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00069
                           DUF1456 11 aLdlkdedmveifklggvevtkeelsa 37
                                      +++++ +dm +++k  g++v+ ee+++
  gi|385806126|ref|YP_005842524.1|  1 MFKMNPSDMKKMMKRMGINVDVEEVKD 27
                                      68999*******************986 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.1
                           DUF1456  12 Ldlkdedmveifklggvevtke 33 
                                       L++ ++d+  + + +gv+++++
  gi|385806126|ref|YP_005842524.1|  80 LEILEDDVQLVAAEAGVSLEEA 101
                                       6777888888888898888765 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.25
                           DUF1456   7 rlRyaLdlkdedmveif 23 
                                         R aL++++ d+ + +
  gi|385806126|ref|YP_005842524.1| 100 EARKALEITNGDIAQAI 116
                                       5699*******998765 PP

>> UBA  UBA/TS-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00012      0.24      17      34 ..      99     116 ..      97     119 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                                       HHHHHHHHHTTTSHHHHH CS
                               UBA  17 eevveALratgnNeErAv 34 
                                       ee+++AL+ t++++ +A+
  gi|385806126|ref|YP_005842524.1|  99 EEARKALEITNGDIAQAI 116
                                       89*************997 PP

>> Histone_HNS  H-NS histone family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.47   9.3e+02      27      40 ..       8      21 ..       5      42 .. 0.76
   2 ?    9.9   1.4   0.00064       1.3       6      44 ..      65     103 ..      63     117 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.47
                                      XXXXXXXXXX---- CS
                       Histone_HNS 27 eirelaaeyGltle 40
                                      ++++++++ G++++
  gi|385806126|ref|YP_005842524.1|  8 DMKKMMKRMGINVD 21
                                      68999999997765 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00064
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX----SSS- CS
                       Histone_HNS   6 ieelekqeealeaeerkealaeirelaaeyGltleelaa 44 
                                       ++e+ek+e++ +++e + + ++++ +aae G++lee  +
  gi|385806126|ref|YP_005842524.1|  65 LKEIEKEETTHQKRELEILEDDVQLVAAEAGVSLEEARK 103
                                       6899*******************************9844 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1207  (0.0673211); expected 358.6 (0.02)
Passed bias filter:                      652  (0.0363657); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 817.90
//
Query:       gi|385806127|ref|YP_005842525.1|  [L=414]
Description: hypothetical protein FFONT_1085 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.1e-32  110.5   0.0    1.3e-31  109.9   0.0    1.3  1  CLP1_P         mRNA cleavage and polyadenylation factor CLP1 
  ------ inclusion threshold ------
       0.01   16.0   0.1      0.019   15.0   0.1    1.4  1  Torsin         Torsin
      0.014   15.2   0.2      0.026   14.3   0.2    1.4  1  ATP_bind_1     Conserved hypothetical ATP binding protein
      0.067   12.9   0.1       0.13   12.0   0.1    1.5  1  PduV-EutP      Ethanolamine utilisation - propanediol utilisa
       0.09   12.5   0.9       0.24   11.1   0.3    2.0  2  AAA_24         AAA domain
       0.13   11.0   0.0       0.21   10.3   0.0    1.2  1  Peptidase_M29  Thermophilic metalloprotease (M29)


Domain annotation for each model (and alignments):
>> 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 !  109.9   0.0   4.4e-35   1.3e-31       1     184 [.     108     279 ..     108     283 .. 0.93

  Alignments for each domain:
  == domain 1  score: 109.9 bits;  conditional E-value: 4.4e-35
                            CLP1_P   1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGqseispPgtislalverpidveegfsldaplvyffGdtspsdnp 77 
                                       G++dsGK+T++ +++N+a  kg+++ yvD+D+Gq+ +++Pg++ +++ + ++ +++  ++d+ +  f+G+ sp ++ 
  gi|385806127|ref|YP_005842525.1| 108 GKVDSGKTTFSSMIANTAYLKGMETYYVDTDLGQKTFGYPGSVTISKNSGKLFWSTASKSDKFI--FIGKLSPVGKE 182
                                       899***************************************************9998888855..*********** PP

                            CLP1_P  78 slylalvkelareveekleenkkakasgliIntpGwvkgl.gaellleliealepdvvvvldq.eellnelkrdlpl 152
                                       s ++++++el+  +e          ++++iI+t+Gw  +   ++++ ++i+ ++pd+ v++++ ++ + ++k+ +p+
  gi|385806127|ref|YP_005842525.1| 183 SDVIQATEELIAGIE----------KGIIIIDTDGWFGDPlSLNYKFRMIQKIKPDYTVIIRSgQKIDLFVKSIFPI 249
                                       ***************..........89**********88549*********************99999999999998 PP

                            CLP1_P 153 skvkvvklpkspgvvqrsreerrelreerire 184
                                       +k+ ++++p +++  +rs+ er+++r +++ +
  gi|385806127|ref|YP_005842525.1| 250 TKIITLNTPPNKA--SRSKIERKMIRGDKVLS 279
                                       8888888888766..5**********999876 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   6.4e-06     0.019      50     107 ..      98     155 ..      88     173 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 6.4e-06
                                       -SS-EEEEEEE-TTSSHHHHHHHHHHHHSTTGGGSTTEEEEEHHHHS--GGGHHHHHH CS
                            Torsin  50 pkkpLvlsfhGwtGtGknfvaeiiaenlyrdGlrsdyvkkfvatadfPkkkkveeyke 107
                                        +k+  + + G+  +Gk   +++ia+  y +G+++ yv + ++++ f  + +v+  k+
  gi|385806127|ref|YP_005842525.1|  98 KEKTCKVIVLGKVDSGKTTFSSMIANTAYLKGMETYYVDTDLGQKTFGYPGSVTISKN 155
                                       4455555566999****************************99999977777665554 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   8.7e-06     0.026       1      47 [.     106     152 ..     106     155 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.7e-06
                        ATP_bind_1   1 vvGpaGsGKttfvgalseilelrgrsvavvNLDPAaeelpYeaavdi 47 
                                       v+G + sGKttf + +++++ l+g + ++v  D + +++ Y+ +v i
  gi|385806127|ref|YP_005842525.1| 106 VLGKVDSGKTTFSSMIANTAYLKGMETYYVDTDLGQKTFGYPGSVTI 152
                                       899**************************************988876 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   4.3e-05      0.13       3      56 ..     103     159 ..     101     194 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.3e-05
                         PduV-EutP   3 killiGkvgsGKttLtqalkg.eelkYkktqaiefs..deviDtPGeylenrklysa 56 
                                       k++++Gkv+sGKtt +  + +   lk   t +++    +++   PG    +++  + 
  gi|385806127|ref|YP_005842525.1| 103 KVIVLGKVDSGKTTFSSMIANtAYLKGMETYYVDTDlgQKTFGYPGSVTISKNSGKL 159
                                       89***************9988345777777776543225666666666666655555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.15   4.4e+02      47      70 ..      79     106 ..      46     107 .. 0.57
   2 ?   11.1   0.3   7.9e-05      0.24       4      47 ..     103     153 ..     100     228 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.15
                            AAA_24  47 e...swedfldevvel.aaeladyktlv 70 
                                       e    w++  + +ve  a +++++k++v
  gi|385806127|ref|YP_005842525.1|  79 EvytDWKKYSSLIVEEcANKEKTCKVIV 106
                                       2222333333333333566666666666 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 7.9e-05
                            AAA_24   4 kiliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdie 47 
                                       k+++ G+  +GKTt+ +++       g ++ ++dt+ G k       ++i+
  gi|385806127|ref|YP_005842525.1| 103 KVIVLGKVDSGKTTFSSMIantaylkGMETYYVDTDLGQKTFGYPGSVTIS 153
                                       899****************66666666666666999988877666655555 PP

>> Peptidase_M29  Thermophilic metalloprotease (M29)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   6.9e-05      0.21       4      57 ..      83     138 ..      81     155 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 6.9e-05
                                       HHHHHHHHHHHTTT---TT-EEEEEEETT..-HHHHHHHHHHHHHTT-SEEEEEEE CS
                     Peptidase_M29   4 klekyAellvkvglnlqkgqevvinaeve..alelarlvaeeaykagakkvvvews 57 
                                       + +ky  l+v+ ++n +k  +v++  +v+  +  +  ++a+ ay +g++  +v+ +
  gi|385806127|ref|YP_005842525.1|  83 DWKKYSSLIVEECANKEKTCKVIVLGKVDsgKTTFSSMIANTAYLKGMETYYVDTD 138
                                       579*********************8777522789***************9999654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); 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: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 2651.12
//
Query:       gi|385806128|ref|YP_005842526.1|  [L=205]
Description: hypothetical protein FFONT_1086 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.045   13.6   0.2      0.063   13.2   0.2    1.2  1  DEDD_Tnp_IS110  Transposase
      0.047   13.7   0.7        0.1   12.6   0.5    1.6  1  MinE            Septum formation topological specificity fact
      0.072   12.8   0.2       0.19   11.4   0.2    1.7  2  DUF460          Protein of unknown function (DUF460)


Domain annotation for each model (and alignments):
>> DEDD_Tnp_IS110  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   1.1e-05     0.063       1     104 [.      88     191 ..      88     198 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.1e-05
                    DEDD_Tnp_IS110   1 vGiDvakdkhdacvidaegkvllservpndeegleallek.laakagevlvvv...eatghygallvaflleagitv 73 
                                       vGiDv+ +  ++++   +gk++ + +v +de  + ++l+k +   ++++ v +     +++ + l  ++l++   ++
  gi|385806128|ref|YP_005842526.1|  88 VGIDVGREIGYVVLA--DGKIIGKGKVIQDE--IISVLKKyENVPHDNMIVKIgdyNDNNRLWNLTSTILENVSAEL 160
                                       8*****999888877..5********99999..77777775777888888887322445557999999********* PP

                    DEDD_Tnp_IS110  74 vvvnplavkrlrklylrkaKtDakDAkvIAd 104
                                        +v  ++++++++ +l ++  D k A++IA+
  gi|385806128|ref|YP_005842526.1| 161 ELVDEYKTSKIKRKQLEEKDPDVKAAYIIAN 191
                                       *************99999999********96 PP

>> MinE  Septum formation topological specificity factor MinE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.5   1.7e-05       0.1      28      53 ..     113     139 ..     110     157 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.7e-05
                                       HHHHHHHHHHHHH-..-SEEEEEEE.- CS
                              MinE  28 lkeeileviskYveideekvevkle.k 53 
                                       +++ei+ v++kY ++  +++ vk+   
  gi|385806128|ref|YP_005842526.1| 113 IQDEIISVLKKYENVPHDNMIVKIGdY 139
                                       89*********************9843 PP

>> DUF460  Protein of unknown function (DUF460)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.83     5e+03       3      23 ..       8      28 ..       7      33 .. 0.81
   2 ?   11.4   0.2   3.2e-05      0.19      23      48 ..      77     102 ..      61     125 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.83
                            DUF460  3 kskdvkvevesvekdkiefep 23
                                      +skd+ + v++ ++++i+f++
  gi|385806128|ref|YP_005842526.1|  8 SSKDYYLFVKNLREESIDFKS 28
                                      578888999999999999964 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 3.2e-05
                            DUF460  23 plkkkrkkklivGiDPGittgiavld 48 
                                        + k++ k++ivGiD G ++g  vl 
  gi|385806128|ref|YP_005842526.1|  77 IDGKEKYKEIIVGIDVGREIGYVVLA 102
                                       45578899*************98874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       828  (0.0461822); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 1329.16
//
Query:       gi|385806129|ref|YP_005842527.1|  [L=200]
Description: Rad51 domain containing protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-08   34.2   1.7    4.9e-06   26.0   1.7    3.3  1  Rad51         Rad51
    9.6e-08   32.0   0.0    1.3e-07   31.5   0.0    1.2  1  AAA_24        AAA domain
    3.4e-07   30.4   4.0    3.3e-05   23.9   4.0    2.1  1  ATPase_2      ATPase domain predominantly from Archaea
    3.1e-05   24.0   0.4      6e-05   23.1   0.4    1.5  1  AAA_14        AAA domain
    4.4e-05   23.8   0.1    8.8e-05   22.8   0.1    1.5  1  AAA_22        AAA domain
    7.9e-05   22.1   1.6     0.0012   18.2   1.6    2.1  1  ATPase        KaiC
    0.00017   21.6   0.1      0.071   13.0   0.0    2.2  2  NACHT         NACHT domain
    0.00039   20.3   0.2    0.00059   19.7   0.2    1.2  1  Bac_DnaA      Bacterial dnaA  protein
      0.002   18.5   0.0     0.0025   18.2   0.0    1.4  1  AAA_16        AAA ATPase domain
     0.0033   17.1   0.0     0.0038   16.9   0.0    1.1  1  Zot           Zonular occludens toxin (Zot)
     0.0088   16.0   0.0      0.055   13.5   0.0    2.1  2  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
     0.0088   15.6   0.2       0.16   11.6   0.2    2.2  1  AAA_25        AAA domain
  ------ inclusion threshold ------
      0.012   15.7   0.5      0.035   14.1   0.5    1.9  1  ResIII        Type III restriction enzyme, res subunit
      0.019   14.6   0.0      0.023   14.3   0.0    1.2  1  Ras           Ras family
       0.02   15.3   0.0       0.03   14.8   0.0    1.3  1  AAA           ATPase family associated with various cellular 
      0.022   14.3   0.0      0.029   13.9   0.0    1.1  1  RecA          recA bacterial DNA recombination protein
      0.023   15.1   0.0      0.045   14.1   0.0    1.5  1  RNA_helicase  RNA helicase
      0.026   15.0   0.3      0.081   13.4   0.1    1.9  2  ABC_tran      ABC transporter
      0.034   13.8   0.0      0.084   12.5   0.0    1.7  1  KRAB          KRAB box
      0.035   13.6   0.0      0.054   12.9   0.0    1.2  1  KTI12         Chromatin associated protein KTI12
      0.045   13.5   0.3      0.083   12.7   0.1    1.5  2  ATP_bind_1    Conserved hypothetical ATP binding protein
      0.078   12.7   0.0       0.15   11.8   0.0    1.5  1  AAA_29        P-loop containing region of AAA domain
      0.079   12.4   0.1      0.087   12.3   0.1    1.1  1  Elong_Iki1    Elongator subunit Iki1
        0.1   12.9   0.0       0.16   12.2   0.0    1.3  1  Roc           Ras of Complex, Roc, domain of DAPkinase
        0.1   11.7   0.6       0.35   10.0   0.6    1.8  1  NB-ARC        NB-ARC domain
       0.15   11.7   0.0       0.39   10.3   0.0    1.8  1  CobU          Cobinamide kinase / cobinamide phosphate guanyl
       0.21   11.5   0.1       0.66    9.9   0.0    1.8  2  MobB          Molybdopterin guanine dinucleotide synthesis pr
       0.27   10.0   0.9        3.3    6.5   0.1    2.0  2  DUF2791       P-loop Domain of unknown function (DUF2791)
       0.29    9.7   2.6        1.3    7.5   2.6    1.9  1  GvpD          GvpD gas vesicle protein


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 !   26.0   1.7     8e-09   4.9e-06      41     172 ..      24     134 ..      19     176 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 8e-09
                                       EEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEESSS---GGGGHHHH.HHTT--HHHHGGGEEEEE--STTH CS
                             Rad51  41 eifGefrsGktqlchtlcvtvqlplelgGgegkavyidtegtfrperlveia.erykldkeevlenvayaRaytieh 116
                                        i+Ge +sGkt +c t+     l        +ka+yi+teg+++ erl++i  e +++   +v             +
  gi|385806129|ref|YP_005842527.1|  24 TIYGEAGSGKTTFCLTFI--KNL-------FNKAIYINTEGSVNKERLLQILgENFDIMFIDVF------------S 79 
                                       49************8864..333.......479*****************97688877555554............3 PP

                                       HHHHHHHTHHHHHHS-EEEEEEETTTGGGCH-------THHHHHHH.HHHHHHHHHH CS
                             Rad51 117 qeellqqaaallaedkfallivDsvtalyRtdfsgrgelakRqqkl.gkllrtLrkl 172
                                         ellq++   l +d   l++vDs+  lyR  fs+ ++++++   l + ll++ +kl
  gi|385806129|ref|YP_005842527.1|  80 EWELLQAVLRSLYKD--VLIVVDSINYLYRLSFSQNEDISSKLFMLiNSLLKENSKL 134
                                       467888877777766..69********************987644315555555554 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.0   2.2e-10   1.3e-07       5      84 ..      23     112 ..      19     120 .. 0.74

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 2.2e-10
                            AAA_24   5 iliyGpsgiGKTtlakel....gpkplfidtekGlksldadkfpdie...swedfldevvel.......aaeladyk 67 
                                       + iyG++g+GKTt+++++     +k+++i+te++++     ++ +i      ++f+d + e+       +   + yk
  gi|385806129|ref|YP_005842527.1|  23 VTIYGEAGSGKTTFCLTFiknlFNKAIYINTEGSVN---KERLLQILgenFDIMFIDVFSEWellqavlR---SLYK 93 
                                       78*****************9999**********664...4444444444333577777777777784433...3444 PP

                            AAA_24  68 ..tlviDtideleelclae 84 
                                          +v+D+i+ l++l + +
  gi|385806129|ref|YP_005842527.1|  94 dvLIVVDSINYLYRLSFSQ 112
                                       33789********998765 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   4.0   5.3e-08   3.3e-05      23     161 ..      23     136 ..      17     147 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 5.3e-08
                          ATPase_2  23 yfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekalgiavpkaeleeilkeks 99 
                                       + iYG  gsGKt++   +i+nl +   + iy++   +++              ++l + lg+++    +        
  gi|385806129|ref|YP_005842527.1|  23 VTIYGEAGSGKTTFCLTFIKNLFN---KAIYINTEGSVNK-------------ERLLQILGENFDIMFI-------- 75 
                                       67********************44...4677765443333.............4567778888888777........ PP

                          ATPase_2 100 klvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLlnliesltkekhlcvv 161
                                        +vf+ +ell + ++   k + i++D + +l  l + ++e+  ++L+ li sl+ke+ +   
  gi|385806129|ref|YP_005842527.1|  76 -DVFSEWELLQAVLRSLYKDVLIVVDSINYLYRLSFSQNEDISSKLFMLINSLLKENSKLSP 136
                                       .99****************************************************9887655 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.4   9.6e-08     6e-05       4      90 ..      22      95 ..      19     135 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 9.6e-08
                            AAA_14  4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevpeweka 82
                                       ++i G   +GKTt++ ++ik+l+   ++ +yin +   +k+ +    ll+++ e++      ++f+D  +e + ++ +
  gi|385806129|ref|YP_005842527.1| 22 YVTIYGEAGSGKTTFCLTFIKNLF---NKAIYINTEGSVNKE-R----LLQILGENF-----DIMFIDVFSEWELLQAV 87
                                      68999999****************...*********966653.2....345666643.....46899999999999999 PP

                            AAA_14 83 lkslvdeg 90
                                      l+sl+++ 
  gi|385806129|ref|YP_005842527.1| 88 LRSLYKDV 95
                                      99998854 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.1   1.4e-07   8.8e-05       4     105 ..      19     109 ..      18     142 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.4e-07
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseelle 80 
                                       ++g ++++Ge+G+GKTt + ++ ++l           + ++++  +s + + ll+ l ++++    +   s+    e
  gi|385806129|ref|YP_005842527.1|  19 KKGYVTIYGEAGSGKTTFCLTFIKNL---------FNKAIYINTEGSVNKERLLQILGENFDIMFID-VFSEW---E 82 
                                       578899********************.........89999********9999999999999965555.44444...4 PP

                            AAA_22  81 aleqalraravielliiDEaqhlr..s 105
                                       +l+  lr+ ++ +l+++D + +l   s
  gi|385806129|ref|YP_005842527.1|  83 LLQAVLRSLYKDVLIVVDSINYLYrlS 109
                                       444555555554678899888876563 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   1.6     2e-06    0.0012      21      59 ..      22      56 ..      16     161 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2e-06
                            ATPase 21 vvlitGepGtGKtifalqFlikgaekygepgvfvtveep 59
                                       v i+Ge+G+GKt+f+l+F+ +  +k     +++ +e +
  gi|385806129|ref|YP_005842527.1| 22 YVTIYGEAGSGKTTFCLTFIKNLFNK----AIYINTEGS 56
                                      689*****************998666....888888765 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   0.00012     0.071       2      23 ..      22      43 ..      21      51 .. 0.84
   2 !    6.7   0.0      0.01       6.2      74     125 ..      86     135 ..      68     158 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00012
                                      CEEEEC-TTTCHHHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqklala 23
                                      +v + GeaGsGKTt+   ++  
  gi|385806129|ref|YP_005842527.1| 22 YVTIYGEAGSGKTTFCLTFIKN 43
                                      5889**********98777665 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.01
                                       HHHCCSCCCEEEEEE-STT-SS-TCH.........HHHHHCTTTTT--EEEE CS
                             NACHT  74 avllelperlLlilDglDelvtdlgqkekqpvrtlLselirkkllpeaslll 125
                                       avl +l + +L+++D++++l + l++++++ +   L  li+  ll+e+s l 
  gi|385806129|ref|YP_005842527.1|  86 AVLRSLYKDVLIVVDSINYLYR-LSFSQNEDISSKLFMLINS-LLKENSKLS 135
                                       4667788999**********98.7776788888888888887.777777665 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.2   9.5e-07   0.00059      37     133 ..      23     134 ..      14     142 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 9.5e-07
                                       EEEE-SSSSSHHHH.H........HHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHTT-SEEE.E CS
                          Bac_DnaA  37 lfiygevGlGktHL.l........kaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklrkvDvLl.i 103
                                       + iyge G Gkt   l        kai  +++ + ++ r++ + +e+F   +++   + ++ +   +    DvL+ +
  gi|385806129|ref|YP_005842527.1|  23 VTIYGEAGSGKTTFcLtfiknlfnKAIYINTEGSVNKERLLQILGENFDIMFIDVFSEWELLQAVLRSLYKDVLIvV 99 
                                       579********964232222222346666677788999******************997776655555566777626 PP

                                       E-GGGG.....TT-HHHHHHHHHHHHHHHTTT-EE CS
                          Bac_DnaA 104 DDiqfl.....agkektqeelfhtfnalleegkqv 133
                                       D i++l     ++ e++  +lf ++n+ll+e+ ++
  gi|385806129|ref|YP_005842527.1| 100 DSINYLyrlsfSQNEDISSKLFMLINSLLKENSKL 134
                                       99999733333567888899*********999876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0     4e-06    0.0025      25      85 ..      21      87 ..       9     180 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 4e-06
                            AAA_16 25 elvllsGesGvGKsslvrellralekdggiflrgkcdqlesa.ipy......sa.laqalareellrql 85
                                      ++v ++Ge+G+GK++   ++ + l  + +i+++++   +++  +        ++ +++++++ ell+++
  gi|385806129|ref|YP_005842527.1| 21 GYVTIYGEAGSGKTTFCLTFIKNLFNK-AIYINTEGSVNKERlL-QilgenfDImFIDVFSEWELLQAV 87
                                      7899*************9999999999.8888888888833321.012222322244444444444444 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   6.2e-06    0.0038       6      99 ..      26     112 ..      22     153 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.2e-06
                               Zot   6 tGapGsgKtsgavkkdllpalkegRkiitnidG.lrlerieqvlgekvstarliridnpegaetlkefakwatid.k 80 
                                       +G+ GsgKt   + + +++     + i+ n +G  ++er+ q+lge++    +++id    ++ ++ ++   +   k
  gi|385806129|ref|YP_005842527.1|  26 YGEAGSGKTTFCLTF-IKNLF--NKAIYINTEGsVNKERLLQILGENFD---IMFID---VFSEWELLQAVLRSLyK 93 
                                       8*************9.66655..5678889998456*************...99998...66666666665553349 PP

                               Zot  81 gallviDEcqeifpvrake 99 
                                       + l+v+D  ++++  +  +
  gi|385806129|ref|YP_005842527.1|  94 DVLIVVDSINYLYRLSFSQ 112
                                       ***********99877664 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   8.9e-05     0.055      13      43 ..      14      44 ..       2      53 .. 0.72
   2 ?   -0.3   0.0       1.7     1e+03      16      32 ..     136     153 ..     113     162 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.9e-05
                                      HHHHCHTEEEEEEESTTSSHHHHHHHHHHHT CS
                              TsaE 13 klakalgdvilLeGdLGaGKTtlvrglakal 43
                                       +  + +  ++++G+ G+GKTt++  ++k+l
  gi|385806129|ref|YP_005842527.1| 14 VFFPNKKGYVTIYGEAGSGKTTFCLTFIKNL 44
                                      3333225569**************9999988 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.7
                                       HCH.TEEEEEEESTTSSH CS
                              TsaE  16 kal.gdvilLeGdLGaGK 32 
                                        +l ++ ++LeGd+ +G 
  gi|385806129|ref|YP_005842527.1| 136 PVLsTAQVYLEGDIPSGY 153
                                       333345699999998885 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.2   0.00025      0.16      33     165 ..      20     116 ..      16     130 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00025
                            AAA_25  33 gelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgealrddarllvldla 109
                                       ++ + ++G  g+GKtt++l     +               k +y+++E+s    ++Rl +++ ++    +  ++d+ 
  gi|385806129|ref|YP_005842527.1|  20 KGYVTIYGEAGSGKTTFCLTFIKNLF------N-------KAIYINTEGSV--NKERLLQILGEN---FDIMFIDV- 77 
                                       6678899**********998765555......3.......78999999998..688888888776...67777775. PP

                            AAA_25 110 gveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralggdensnsdv 165
                                        +                ++++ l+a++++ ++ +l+v+D+++ +++ +   n+d+
  gi|385806129|ref|YP_005842527.1|  78 -F----------------SEWELLQAVLRSLYKDVLIVVDSINYLYRLSFSQNEDI 116
                                       .2................67888999999999999999999999999988888887 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 ?   14.1   0.5   5.6e-05     0.035      23      82 ..      18      78 ..       3     181 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.6e-05
                                      TTSEEE.EEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG.. CS
                            ResIII 23 rdkrgl.ikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseay 82
                                      ++k ++ i  + G+GKT  ++ +i++l++k+ + ++   v+++ ll+ + e+f  ++ + +
  gi|385806129|ref|YP_005842527.1| 18 NKKGYVtIYGEAGSGKTTFCLTFIKNLFNKAIYINTEGSVNKERLLQILGENFDIMFIDVF 78
                                      44544458999******************98877776667777777666677755555554 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.7e-05     0.023       3      54 ..      24      76 ..      22     128 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.7e-05
                                      EEEESTTSSHHHHHHHHHHSSCSSS.CTTTSSEEEEEEEEEETTEEEEEEEEE CS
                               Ras  3 vlvGdsavGKtslllrfvkdkFkee.yesTigvdfytkeievdgkevkleiwD 54
                                       + G+ + GKt++ l f+k+ F++  y++T g  ++++ +++ g++  +   D
  gi|385806129|ref|YP_005842527.1| 24 TIYGEAGSGKTTFCLTFIKNLFNKAiYINTEGSVNKERLLQILGENFDIMFID 76
                                      578*******************9864889999888888888877777666655 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   4.8e-05      0.03       2      98 ..      24     129 ..      23     149 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.8e-05
                                       EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS..............STTHHHHHHHHHHHHHHHTS....... CS
                               AAA   2 llyGppGtGKTllakavakelgvefleisgsellsk..............yvgesekkirelfkeakeka....... 57 
                                        +yG  G GKT+++   +k+l  + + i+    ++k              +         ++f+e +  +       
  gi|385806129|ref|YP_005842527.1|  24 TIYGEAGSGKTTFCLTFIKNLFNKAIYINTEGSVNKerllqilgenfdimF--------IDVFSEWELLQavlrsly 92 
                                       68*******************888888888888877777775444444431........333333222223334443 PP

                                       TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTT CS
                               AAA  58 kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkk 98 
                                       k + +++D i  l + +     +++e++ ++L+  ++ + k
  gi|385806129|ref|YP_005842527.1|  93 KDVLIVVDSINYLYRLS----FSQNEDISSKLFMLINSLLK 129
                                       45788888888888777....23334444444444444433 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.6e-05     0.029      55     143 ..      22     105 ..      12     127 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.6e-05
                                       EEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEESS----HH.HHHHTT--GGG-EEE--SSHHHHHHHHHHHHTTT CS
                              RecA  55 iieiyGpessGkttlalhaiaeaqkkggvaafidaehaldpk.yakklGvdidellvsqpdtGeqaleiadalvrsg 130
                                        + iyG   sGktt++l  i +  +    a +i++e +++ +   + lG + d +++          e+++a++rs 
  gi|385806129|ref|YP_005842527.1|  22 YVTIYGEAGSGKTTFCLTFIKNLFN---KAIYINTEGSVNKErLLQILGENFDIMFIDVFS----EWELLQAVLRSL 91 
                                       578****************988765...589*******99762567899999999886654....467788888888 PP

                                       --SE.EEEE-TTT- CS
                              RecA 131 aidl.ivvdsvaal 143
                                         d+ ivvds+  l
  gi|385806129|ref|YP_005842527.1|  92 YKDVlIVVDSINYL 105
                                       88853788998765 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   7.3e-05     0.045       1      26 [.      23      48 ..      23      65 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.3e-05
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallkkl 26
                                      + +yG++g GK+t++ +++k+l +k 
  gi|385806129|ref|YP_005842527.1| 23 VTIYGEAGSGKTTFCLTFIKNLFNKA 48
                                      579*****************998655 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   0.00013     0.081      13      42 ..      22      57 ..      15     143 .. 0.75
   2 ?   -1.1   0.0         4   2.5e+03      25      46 ..     160     180 ..     159     192 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00013
                                      EEEEEESTTSSHHHHHHHHTTSS--......SEEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxx......xxxxx RF
                          ABC_tran 13 kvaivGenGaGKStLlkllagllkp......teGei 42
                                       v i Ge G+GK+t++ +++++l +      teG++
  gi|385806129|ref|YP_005842527.1| 22 YVTIYGEAGSGKTTFCLTFIKNLFNkaiyinTEGSV 57
                                      689************999988776623333344444 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 4
                                       HHHHHHHTTSS--SEEEEEETT CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  25 StLlkllagllkpteGeilldg 46 
                                       StLl+l  g ++  eGe+lld+
  gi|385806129|ref|YP_005842527.1| 160 STLLRLSKGSSR-SEGEVLLDD 180
                                       888887766665.899998885 PP

>> KRAB  KRAB box
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00014     0.084      15      30 ..      80      95 ..      70      97 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                              KRAB 15 EWelLdpaQreLYrdV 30
                                      EWelL    r+LY+dV
  gi|385806129|ref|YP_005842527.1| 80 EWELLQAVLRSLYKDV 95
                                      9**************9 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   8.8e-05     0.054       4      82 ..      23     105 ..      21     109 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.8e-05
                                       EEEE--TTSSHHHHHHHHHHHHHH....TT--EEEE-THHHH.TTSSS--GGGHHHHHHHHHHHHHHHHTT.SEEEE CS
                             KTI12   4 vvltGlPssGKstrakeLakalee....ekrsvvviddeslgiekdsykdsakekalRsslrsavkrdLskekvVIv 76 
                                       v++ G   sGK+t+  ++ k l +     + +  v ++  l+i  ++++ +        +l +av r+L k+ +++v
  gi|385806129|ref|YP_005842527.1|  23 VTIYGEAGSGKTTFCLTFIKNLFNkaiyINTEGSVNKERLLQILGENFDIMFIDVFSEWELLQAVLRSLYKDVLIVV 99 
                                       78999999*****9988777766646666677778888888899999999999999999****************** PP

                                       -S---S CS
                             KTI12  77 Dslnyi 82 
                                       Ds+ny 
  gi|385806129|ref|YP_005842527.1| 100 DSINYL 105
                                       *****6 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   0.00013     0.083       1      20 [.      25      44 ..      25      58 .. 0.81
   2 ?   -2.3   0.0       5.1   3.1e+03     180     180 ..      98      98 ..      70     141 .. 0.48

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00013
                        ATP_bind_1  1 vvGpaGsGKttfvgalseil 20
                                      + G aGsGKttf+ ++++ l
  gi|385806129|ref|YP_005842527.1| 25 IYGEAGSGKTTFCLTFIKNL 44
                                      67***********9887765 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.1
                        ATP_bind_1 180 f 180
                                       +
  gi|385806129|ref|YP_005842527.1|  98 V 98 
                                       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 ?   11.8   0.0   0.00025      0.15       9      38 ..       8      36 ..       7      48 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00025
                            AAA_29  9 WgtfdghtieidlkgatlltGpsGsGKSTl 38
                                      W  f    ++ + kg + + G+ GsGK+T+
  gi|385806129|ref|YP_005842527.1|  8 WNAFASVFFPNK-KGYVTIYGEAGSGKTTF 36
                                      677776655555.8899************7 PP

>> Elong_Iki1  Elongator subunit Iki1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00014     0.087      91     150 ..      93     161 ..      46     181 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                        Elong_Iki1  91 kkalviiDslnplas......likeeslaaflssllsspsvslvavYHtdv....eyapspltlLkylAt 150
                                       k +l+++Ds+n l +       + +++l ++++sll+  ++ l  v+ t         ps +++L++ +t
  gi|385806129|ref|YP_005842527.1|  93 KDVLIVVDSINYLYRlsfsqnEDISSKLFMLINSLLK-ENSKLSPVLSTAQvyleGDIPSGYNILSHYST 161
                                       789********99999976554446678888888885.66666666665555666666777777777765 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00026      0.16       2      29 ..      23      50 ..      22      77 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00026
                                      EEEESSTTSSHHHHHHCHCT-CCC-EEE CS
                               Roc  2 vvlvGdsgvGKtsllkrfvedkfsekek 29
                                      v + G++g+GKt+++  f+++ f++   
  gi|385806129|ref|YP_005842527.1| 23 VTIYGEAGSGKTTFCLTFIKNLFNKAIY 50
                                      5688*******************98743 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.6   0.00056      0.35      22      40 ..      22      40 ..      15     100 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00056
                                      EEEEEESTTSSHHHHHHHH CS
                            NB-ARC 22 vvalvGmgGvGKttlakqi 40
                                       v+++G +G+GKtt     
  gi|385806129|ref|YP_005842527.1| 22 YVTIYGEAGSGKTTFCLTF 40
                                      79***********976443 PP

>> CobU  Cobinamide kinase / cobinamide phosphate guanyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00064      0.39       2      43 ..      24      65 ..      23     143 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00064
                              CobU  2 lvtGgarSGKSefAeklaeeskekvvYiATaealDeemaeRi 43
                                       + G a SGK +f  + +++  +k +Yi T  + ++e   +i
  gi|385806129|ref|YP_005842527.1| 24 TIYGEAGSGKTTFCLTFIKNLFNKAIYINTEGSVNKERLLQI 65
                                      5899**************************999988866555 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 ?    9.9   0.0    0.0011      0.66       2      31 ..      23      52 ..      22      54 .. 0.89
   2 ?   -1.7   0.0         4   2.5e+03      78     103 ..      56      82 ..      48      90 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0011
                              MobB  2 lgivgksgsGKTtLleklipelkarglrvg 31
                                      ++i g  gsGKTt+    i+ l ++ + ++
  gi|385806129|ref|YP_005842527.1| 23 VTIYGEAGSGKTTFCLTFIKNLFNKAIYIN 52
                                      6899******************99988776 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4
                              MobB  78 elsleellarl.sevDlvlvEGfkkea 103
                                       +++ e+ll+ l ++ D++++  f + +
  gi|385806129|ref|YP_005842527.1|  56 SVNKERLLQILgENFDIMFIDVFSEWE 82 
                                       567788899996779999998887665 PP

>> DUF2791  P-loop Domain of unknown function (DUF2791)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1    0.0053       3.3      53      92 ..      24      64 ..      18      80 .. 0.87
   2 ?    2.7   0.1     0.073        45     228     278 ..      83     131 ..      64     148 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0053
                           DUF2791 53 firGeYGsGKt.FllqllreralergfvvaeadlsperrLh 92
                                       i Ge GsGKt F l ++++   +  ++ +e ++++er L+
  gi|385806129|ref|YP_005842527.1| 24 TIYGEAGSGKTtFCLTFIKNLFNKAIYINTEGSVNKERLLQ 64
                                      589*******54999**************999999999887 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.073
                           DUF2791 228 llaafvrkaGykGLlvvlDElvnlyklsnsdaReknyekllqilndvlqgk 278
                                       ll a++r+  yk  l+v+D +  ly+l + ++ e   +kl  ++n +l+ +
  gi|385806129|ref|YP_005842527.1|  83 LLQAVLRSL-YKDVLIVVDSINYLYRL-SFSQNEDISSKLFMLINSLLKEN 131
                                       444555544.999**************.55556666788999999888765 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   2.6    0.0021       1.3       4      44 ..      15      52 ..      12     146 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0021
                              GvpD  4 ffdgeaGktllikGaPGtGktlftlrgldvlrresdvlyvs 44
                                      ff ++ G  + i G+ G+Gkt+f l +++ l ++   +y+ 
  gi|385806129|ref|YP_005842527.1| 15 FFPNKKGY-VTIYGEAGSGKTTFCLTFIKNLFNKA--IYIN 52
                                      77777775.6799**************99987653..4554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); 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: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 1351.04
//
Query:       gi|385806130|ref|YP_005842528.1|  [L=173]
Description: hypothetical protein FFONT_1088 [Fervidicoccus fontis Kam940]
Scores for 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  123.8   5.8    9.9e-36  123.3   5.8    1.2  1  CarS-like     CDP-archaeol synthase
    1.5e-06   28.2   1.3    2.2e-06   27.6   1.3    1.3  1  CTP_transf_1  Cytidylyltransferase family


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 !  123.3   5.8   1.1e-39   9.9e-36       1     175 []       3     173 .]       3     173 .] 0.89

  Alignments for each domain:
  == domain 1  score: 123.3 bits;  conditional E-value: 1.1e-39
                         CarS-like   1 lldlilksiylllpayvanasavlvG...GGtpvdlGktlvdGrrliGdGvtyrGtvaGvlvGvlvgliqgllekls 74 
                                       +l++++  + + +p  van   v+v     G+p+d Gk l dG+r++GdG+t  Gt + +l+G+l+g i g+l   +
  gi|385806130|ref|YP_005842528.1|   3 ILRILIDFLKIYIPPMVANGIPVVVSkfiKGRPLDRGKYLSDGKRILGDGKTVEGTTFAILTGTLMGAIIGIL---N 76 
                                       5788888899999*******9999763337******************************************9...2 PP

                         CarS-like  75 ilaldssgsvlefvilalllafGallGdavGsfikrrlkierGkpalildqldfvlgalllayp...vkllpielii 148
                                             + s l++  +++l ++G +lGd++ sf krr++ierG   +++dqldf lg+ l+ y     +  ++++ +
  gi|385806130|ref|YP_005842528.1|  77 ------YYS-LQYCFTGFLGSLGGILGDITKSFFKRRIGIERGGMLPLVDQLDFYLGSTLFIYLcpiCAHPSLDVFL 146
                                       ......222.456789******************************************9999864434555689999 PP

                         CarS-like 149 livlitlvlhlsaniiayklglkdvwy 175
                                       + ++i ++lhls+n+ia+kl lk v++
  gi|385806130|ref|YP_005842528.1| 147 FGIIIIPLLHLSTNYIAFKLHLKSVPW 173
                                       99************************9 PP

>> CTP_transf_1  Cytidylyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   1.3   2.5e-10   2.2e-06     170     240 ..      52     116 ..      49     137 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 2.5e-10
                                       --BHHHHHHHHHHHHHHHHHHHHHHHCTS---TTSHHHHHHHHHHHHHHHHHHHHHHHHHHT-SSS-S-SS CS
                      CTP_transf_1 170 kKTveGfigGlvaavvvglllalvlskalalsllhllllslllslvavfGDLveSglKRafgiKDsGkliP 240
                                       +KTveG   ++++ +++g ++  +         l+  + ++l sl +++GD+++S +KR++gi   G ++P
  gi|385806130|ref|YP_005842528.1|  52 GKTVEGTTFAILTGTLMGAIIGILNYY-----SLQYCFTGFLGSLGGILGDITKSFFKRRIGIE-RGGMLP 116
                                       6*****************999988775.....5899999***********************94.455565 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1122.33
//
Query:       gi|385806131|ref|YP_005842529.1|  [L=64]
Description: Nucleolar RNA-binding protein Nop10p [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.7e-25   86.5   1.7    1.1e-24   86.2   1.7    1.1  1  Nop10p          Nucleolar RNA-binding protein, Nop10p family
     0.0023   18.0   1.8     0.0032   17.5   1.8    1.2  1  DUF1272         Protein of unknown function (DUF1272)
  ------ inclusion threshold ------
      0.014   15.4   0.2      0.018   15.0   0.2    1.1  1  zinc-ribbons_6  zinc-ribbons
      0.017   15.3   0.6      0.024   14.8   0.6    1.2  1  FANCL_C         FANCL C-terminal domain
      0.019   14.8   1.4      0.032   14.1   1.4    1.4  1  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
       0.12   12.4   0.3       0.14   12.2   0.3    1.2  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.17   11.3   7.1        3.5    7.2   7.1    2.1  1  zf-ribbon_3     zinc-ribbon domain
        1.4    8.9   8.5        7.7    6.6   1.4    2.3  2  zf-C2HC_2       zinc-finger of a C2HC-type


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 !   86.2   1.7     5e-28   1.1e-24       1      49 [.       5      54 ..       5      56 .. 0.98

  Alignments for each domain:
  == domain 1  score: 86.2 bits;  conditional E-value: 5e-28
                                      .----EE-TTT--EESS.SB-TTT-SB-B-SS--S--TT-TTCHHHHHCH CS
                            Nop10p  1 mksylrkcgkcrvYTLk.kvcpecggptksahPaRFSPdDkyskyRralK 49
                                      mk+ +rkc+kc++YTL+  +cp+cgg+++++hP RFSP+Dky kyR+a+K
  gi|385806131|ref|YP_005842529.1|  5 MKWLMRKCSKCKRYTLEtGRCPYCGGELFVPHPHRFSPEDKYAKYRIAIK 54
                                      9****************99******************************9 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   1.8   1.4e-06    0.0032      32      57 .]      12      39 ..       9      39 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.4e-06
                           DUF1272 32 CaeCaeevl.envCPncgGel.vkRPir 57
                                      C++C   +l +++CP cgGel v+ P r
  gi|385806131|ref|YP_005842529.1| 12 CSKCKRYTLeTGRCPYCGGELfVPHPHR 39
                                      99***9999678********73566765 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.2   7.9e-06     0.018      17      39 ..      10      32 ..       2      36 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7.9e-06
                                      EE-TTT--EEEEEEE-SSS-S-- CS
                    zinc-ribbons_6 17 yhCeaCqedlkkealCpeCeqel 39
                                       +C++C++   ++  Cp C+ el
  gi|385806131|ref|YP_005842529.1| 10 RKCSKCKRYTLETGRCPYCGGEL 32
                                      68*****************9988 PP

>> FANCL_C  FANCL C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.6   1.1e-05     0.024      39      65 ..       6      32 ..       3      36 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.1e-05
                                      HHHHHHHSSS-TTT--EEE-TTT-SEE CS
                           FANCL_C 39 eWlrslkesrqsfdvlfGeCPyCkkki 65
                                       Wl+   +  + +++  G+CPyC   +
  gi|385806131|ref|YP_005842529.1|  6 KWLMRKCSKCKRYTLETGRCPYCGGEL 32
                                      6***999999*************8765 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   1.4   1.4e-05     0.032      10      33 ..       8      30 ..       6      35 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.4e-05
                           DUF35_N 10 vgqrCpdCGtvqfPPravCphCgs 33
                                      + ++C++C ++    +  Cp+Cg+
  gi|385806131|ref|YP_005842529.1|  8 LMRKCSKCKRYTL-ETGRCPYCGG 30
                                      6789*******96.8899****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 ?   12.2   0.3   6.3e-05      0.14      69      95 ..       8      31 ..       1      36 [. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.3e-05
                                      -EEEETTTS-EEECHHHHHS-TTTSSS CS
                              HypA 69 vkvrCreCgkefeleekalrCpkCgsa 95
                                      +  +C++C+ +++le+   rCp Cg++
  gi|385806131|ref|YP_005842529.1|  8 LMRKCSKCK-RYTLET--GRCPYCGGE 31
                                      5679****9.777674..48****986 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   7.1    0.0015       3.5       2      26 .]       9      32 ..       8      32 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0015
                       zf-ribbon_3  2 tvrCPnCGa.plssddnvCpyCGtkl 26
                                      +++C++C+   l+++   CpyCG++l
  gi|385806131|ref|YP_005842529.1|  9 MRKCSKCKRyTLETGR--CPYCGGEL 32
                                      7899999997788886..*****986 PP

>> zf-C2HC_2  zinc-finger of a C2HC-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   1.4    0.0034       7.7       2      10 ..       9      17 ..       9      17 .. 0.92
   2 ?    6.5   0.9    0.0036       8.1       1       9 [.      21      29 ..      21      29 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0034
                         zf-C2HC_2  2 lvpCpkCgR 10
                                      +++C kC+R
  gi|385806131|ref|YP_005842529.1|  9 MRKCSKCKR 17
                                      689*****9 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0036
                         zf-C2HC_2  1 elvpCpkCg 9 
                                      e+  Cp+Cg
  gi|385806131|ref|YP_005842529.1| 21 ETGRCPYCG 29
                                      5779****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       812  (0.0452898); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); 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 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 438.29
//
Query:       gi|385806132|ref|YP_005842530.1|  [L=264]
Description: translation initiation factor IF-2 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.7e-22   77.8   3.1    3.8e-21   75.3   0.0    2.4  3  EIF_2_alpha      Eukaryotic translation initiation factor 2 a
    3.3e-14   53.0   1.6    5.8e-14   52.2   0.3    2.0  2  S1               S1 RNA binding domain
     0.0097   15.7   1.6     0.0097   15.7   1.6    2.2  2  DUF2247          Uncharacterized protein conserved in bacteri
  ------ inclusion threshold ------
      0.025   14.9   0.9      0.025   14.9   0.9    1.8  2  Pox_polyA_pol_N  Poxvirus poly(A) polymerase N-terminal domai
        2.3    8.0   6.0        1.5    8.5   0.3    3.2  3  DUF4325          STAS-like domain of unknown function (DUF432


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 ?    2.9   0.1     0.032   1.2e+02      72      99 ..      51      82 ..      37      86 .. 0.65
   2 !   75.3   0.0   1.1e-24   3.8e-21       1     116 []     121     232 ..     121     232 .. 0.94
   3 ?   -4.0   0.1       4.3   1.5e+04      76      87 ..     240     251 ..     237     259 .. 0.43

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.032
                                      HHHHHHHHHHHST.S......TTSSSEEEEEE CS
                       EIF_2_alpha 72 veaIkeaLkageeasne....eeveeeeevki 99
                                      v++Ike+Lk++e+   +    ++++++++v++
  gi|385806132|ref|YP_005842530.1| 51 VKNIKEVLKENEKIVVKvirvNKQKKQVDVSL 82
                                      89999999966664333554433444444444 PP

  == domain 2  score: 75.3 bits;  conditional E-value: 1.1e-24
                                       HHHCTHHHHTTTTS-HHHHH.HHHHSTTHHHHHTTS-TTTHHHHHHCTHHHHHHT-EEEEEEEEEEE-STTHHHHHH CS
                       EIF_2_alpha   1 lyeevgwklyekyghaydaF.klaitdeevldkleipeeveeaLveiikkklkpqkvkiradieltcftkdGveaIk 76 
                                       +y+++gw+l ++y ++y a+  +++ +++ l+  + +ee++  + e+++k++k+++vk++  i+l ++++ G+e I+
  gi|385806132|ref|YP_005842530.1| 121 AYNDIGWPLLDHYSDLYTALeTAVMLGPDTLRVPNAKEEWIMPVYEEANKHIKIKQVKVTRIINLWSTSPSGIEDIR 197
                                       599*****************9999***************************************************** PP

                                       HHHHHHST.S..TTSSSEEEEEEEESSSSEEEEEEEES.. CS
                       EIF_2_alpha  77 eaLkageeasneeeveeeeevkikliapPeYvltvetldk 116
                                       ++L + ++      +e++ +v+i++i++P+Y+++v ++d+
  gi|385806132|ref|YP_005842530.1| 198 SVLLNMKNI-----SEDNSSVNIYTIGAPKYKIEVISEDY 232
                                       ****55554.....456799***************99996 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 4.3
                                       HHHHHHHST.S. CS
                       EIF_2_alpha  76 keaLkageeasn 87 
                                        ++L+++e++++
  gi|385806132|ref|YP_005842530.1| 240 NSILEKAEKDAQ 251
                                       445554444322 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2   0.3   1.6e-17   5.8e-14       4      75 .]      11      83 ..       8      83 .. 0.96
   2 ?   -1.3   0.1      0.81   2.9e+03      32      62 ..     201     244 ..     197     253 .. 0.68

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 1.6e-17
                                      TTCEEEEEEEEEETTEEEEEET..TTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEEEEEEC CS
                                S1  4 kgevveGeVtsvtkgGafVelg..ngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrriilsik 75
                                      ++e v ++V+++ ++Ga+Vel+  ng+++f+p se++ +  v++++evlk+++++ vkv++v+k+++ +++s+k
  gi|385806132|ref|YP_005842530.1| 11 ANELVIATVKEIFDYGAYVELDeyNGMRAFLPWSEVATK-WVKNIKEVLKENEKIVVKVIRVNKQKKQVDVSLK 83
                                      688899*********************************.******************************9986 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.81
                                       EEGGGSSSS.............CEESCHHHCEETTEEEEEEEEE CS
                                S1  32 vpaselsrd.............arvedpdevlkvGdevkvkvlk 62 
                                       +  +++s d             +++e+++e +k  +++   +l+
  gi|385806132|ref|YP_005842530.1| 201 LNMKNISEDnssvniytigapkYKIEVISEDYKSAERIINSILE 244
                                       55667777766666667777677777888888777777666655 PP

>> DUF2247  Uncharacterized protein conserved in bacteria (DUF2247)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   1.6   2.7e-06    0.0097      21      97 ..      38     114 ..      25     130 .. 0.82
   2 ?    0.2   0.4      0.16   5.7e+02      30      79 ..     165     215 ..     156     248 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.7e-06
                           DUF2247  21 knlisadevieyaekll.ekgeaseelileLafleekeeeelknllkklaseekkideeleerkwlyvvLkelkels 96 
                                       + ++ ++ev +   k++ e  +++e+++++++ +++++ +++++ lk +++ ekk+ ++ ++r+ ++++++el +++
  gi|385806132|ref|YP_005842530.1|  38 RAFLPWSEVATKWVKNIkEVLKENEKIVVKVIRVNKQK-KQVDVSLKRVYDSEKKKKMHWYKRNQRAEKILELAAQK 113
                                       5578899999998888866677799******8877776.99*****************************9998876 PP

                           DUF2247  97 k 97 
                                        
  gi|385806132|ref|YP_005842530.1| 114 L 114
                                       4 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.16
                           DUF2247  30 ieyaekllekgeaseelileLafleekeeeelknllkklase.ekkideel 79 
                                        e a+k ++ ++ +  +i++L + +++  e++ ++l ++ ++ e++++ ++
  gi|385806132|ref|YP_005842530.1| 165 YEEANKHIKIKQVKVTRIINLWSTSPSGIEDIRSVLLNMKNIsEDNSSVNI 215
                                       566777777777777788888888888888887777666666444444444 PP

>> Pox_polyA_pol_N  Poxvirus poly(A) polymerase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.9     7e-06     0.025       9      84 ..      31     108 ..      26     124 .. 0.79
   2 ?   -1.6   0.1      0.98   3.5e+03      33      71 ..     204     244 ..     171     256 .. 0.53

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 7e-06
                                       HHHHHTS---HHHHHHHGGGHHHHHHHHHS-HHHHHHHHHHHHHHH-TTSSS-..THHHHHHHHHHTTGGGC---HH CS
                   Pox_polyA_pol_N   9 leeyLGrtpsleeyvvlksqvrniqkilnfdkdiflsLlkknkkkffkdlkls..eseikkrileyfskqkktkkiG 83 
                                       l+ey G ++ l    v  + v+ni+ +l+ +++i +++++ nk+k   d++l    +  kk+ ++++ + ++++ki 
  gi|385806132|ref|YP_005842530.1|  31 LDEYNGMRAFLPWSEVATKWVKNIKEVLKENEKIVVKVIRVNKQKKQVDVSLKrvYDSEKKKKMHWYKRNQRAEKIL 107
                                       68899999999999999999*******************99988877666543114555666667777777777775 PP

                                       H CS
                   Pox_polyA_pol_N  84 k 84 
                                       +
  gi|385806132|ref|YP_005842530.1| 108 E 108
                                       5 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.98
                                       HHHHHS-HHHHHHHH..HHHHHHH-TTSSS-THHHHHHHHH CS
                   Pox_polyA_pol_N  33 qkilnfdkdiflsLl..kknkkkffkdlklseseikkrile 71 
                                       ++i   +  + +  +   k k   +++  +s++ i ++ile
  gi|385806132|ref|YP_005842530.1| 204 KNISEDNSSVNIYTIgaPKYKIEVISEDYKSAERIINSILE 244
                                       33333333333333311233344445555555555555555 PP

>> DUF4325  STAS-like domain of unknown function (DUF4325)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.2      0.12   4.3e+02       7      22 ..      52      66 ..      47      86 .. 0.83
   2 ?   -1.3   0.0      0.52   1.9e+03      49      60 ..     166     177 ..     162     180 .. 0.79
   3 ?    8.5   0.3   0.00043       1.5       1      27 [.     234     260 ..     234     262 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.12
                           DUF4325  7 dkilkpllkegekvel 22
                                      ++i++ l ke+ek+++
  gi|385806132|ref|YP_005842530.1| 52 KNIKEVL-KENEKIVV 66
                                      5677755.99999986 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.52
                           DUF4325  49 eeiskklkiknl 60 
                                       ee +k++kik +
  gi|385806132|ref|YP_005842530.1| 166 EEANKHIKIKQV 177
                                       688999999975 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.00043
                           DUF4325   1 sGerfrdkilkpllkegekvelDFdgv 27 
                                       s+er+ + il+++ k+ +k+ ++F+ v
  gi|385806132|ref|YP_005842530.1| 234 SAERIINSILEKAEKDAQKLKVNFEVV 260
                                       69**********************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2358  (0.131519); expected 358.6 (0.02)
Passed bias filter:                      710  (0.0396006); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 1732.31
//
Query:       gi|385806133|ref|YP_005842531.1|  [L=66]
Description: 30S ribosomal protein S27e [Fervidicoccus fontis Kam940]
Scores for complete 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   75.9   1.5    1.6e-21   75.8   1.5    1.0  1  Ribosomal_S27e   Ribosomal protein S27
     0.0014   17.9   1.4      0.087   12.3   0.1    2.2  2  zf-ribbon_3      zinc-ribbon domain
     0.0015   18.5   1.7       0.32   11.0   0.0    2.2  2  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger doma
     0.0044   16.9   0.2       0.03   14.2   0.2    1.9  2  DUF3797          Domain of unknown function (DUF3797)
  ------ inclusion threshold ------
      0.013   15.0   0.4      0.022   14.3   0.4    1.4  1  TF_Zn_Ribbon     TFIIB zinc-binding
      0.014   15.7   0.1      0.017   15.5   0.1    1.2  1  Lar_restr_allev  Restriction alleviation protein Lar
      0.026   14.5   1.4      0.051   13.6   1.4    1.6  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.032   14.3   0.0      0.036   14.1   0.0    1.1  1  HypA             Hydrogenase/urease nickel incorporation, met
      0.033   13.8   1.5       0.83    9.4   0.5    2.4  2  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
      0.038   14.1   1.1       0.11   12.6   1.2    1.7  2  Zn-ribbon_8      Zinc ribbon domain
      0.038   13.7   0.4        1.3    8.9   0.1    2.2  2  zinc_ribbon_2    zinc-ribbon domain
      0.039   14.3   1.5       0.82   10.0   0.1    2.1  2  RNA_pol_N        RNA polymerases N / 8 kDa subunit
      0.048   13.7   0.4      0.094   12.8   0.4    1.5  1  DZR              Double zinc ribbon
      0.094   12.5   0.8        0.3   10.9   0.0    1.8  2  PADR1            PADR1 (NUC008) domain
       0.11   12.2   1.1        3.5    7.4   0.2    2.1  2  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
       0.16   11.7   4.2        3.5    7.4   4.2    2.2  1  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
       0.41   10.6   3.4        1.5    8.7   1.5    2.4  2  TFIIS_C          Transcription factor S-II (TFIIS)


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 !   75.8   1.5   1.5e-24   1.6e-21       1      54 [.      12      65 ..      12      66 .] 0.96

  Alignments for each domain:
  == domain 1  score: 75.8 bits;  conditional E-value: 1.5e-24
                                      -S--EEEEE-TTTS-EEEEESS-SS-EEESSSTCEEEEECSSSEEESSCEEEEE CS
                    Ribosomal_S27e  1 prskFldvkCpdCenetvvFshaatvvkCisCgkvLvePtGGkaklkaqilerl 54
                                      pr+kF+ v+Cp C+ne+v+Fsha   v C++Cg+ Lv+PtGG+a+l+aq + ++
  gi|385806133|ref|YP_005842531.1| 12 PRTKFILVRCPACGNEQVIFSHATFPVRCLICGSQLVKPTGGRARLQAQFIKVV 65
                                      89***********************************************98765 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.1   8.3e-05     0.087       3      11 ..      19      28 ..      17      32 .. 0.86
   2 ?    4.9   0.2     0.017        18       3      14 ..      38      50 ..      37      51 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.3e-05
                       zf-ribbon_3  3 vrCPnCGa.p 11
                                      vrCP+CG+ +
  gi|385806133|ref|YP_005842531.1| 19 VRCPACGNeQ 28
                                      89*****966 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.017
                       zf-ribbon_3  3 vrCPnCGa.plss 14
                                      vrC  CG+ ++++
  gi|385806133|ref|YP_005842531.1| 38 VRCLICGSqLVKP 50
                                      6899999977876 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 !    6.9   0.4    0.0058       6.2       1       7 [.      20      26 ..      20      29 .. 0.84
   2 !   11.0   0.0   0.00031      0.32       2      15 ..      40      53 ..      39      57 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0058
                    DNA_ligase_ZBD  1 hCPvCGs 7 
                                      +CP+CG 
  gi|385806133|ref|YP_005842531.1| 20 RCPACGN 26
                                      5*****6 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00031
                    DNA_ligase_ZBD  2 CPvCGsavvReege 15
                                      C +CGs +v++ g+
  gi|385806133|ref|YP_005842531.1| 40 CLICGSQLVKPTGG 53
                                      99********9887 PP

>> DUF3797  Domain of unknown function (DUF3797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.2   2.8e-05      0.03      14      30 ..      19      35 ..      13      40 .. 0.85
   2 ?    1.1   0.0      0.36   3.8e+02      14      32 ..      38      56 ..      35      61 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.8e-05
                           DUF3797 14 vqCPeCgNnkvlNsegk 30
                                      v CP CgN++v  s ++
  gi|385806133|ref|YP_005842531.1| 19 VRCPACGNEQVIFSHAT 35
                                      79*********988887 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.36
                           DUF3797 14 vqCPeCgNnkvlNsegkvi 32
                                      v C  Cg + v   +g+ +
  gi|385806133|ref|YP_005842531.1| 38 VRCLICGSQLVKPTGGRAR 56
                                      67999*9999998888765 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.4   2.1e-05     0.022       2      29 ..      20      47 ..      19      50 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.1e-05
                                      EETTTTCEECHEETSTTCEEESSSSBEE CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlVl 29
                                      +CP Cg++++++ +++  ++C  CG+ l
  gi|385806133|ref|YP_005842531.1| 20 RCPACGNEQVIFSHATFPVRCLICGSQL 47
                                      7************************865 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.1   1.6e-05     0.017       3      39 ..      18      46 ..      17      64 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.6e-05
                   Lar_restr_allev  3 LkpCPfCggravlersqrvvaeigqcvyCadCgastp 39
                                      L  CP Cg+++v++ +   +      v C  Cg   +
  gi|385806133|ref|YP_005842531.1| 18 LVRCPACGNEQVIFSHATFP------VRCLICGS--Q 46
                                      568************98877......67888887..3 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.4   4.9e-05     0.051      19      46 .]      19      46 ..      12      58 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.9e-05
                     Zn_Tnp_IS1595 19 fvCPhCgsrkayriktrglfqCkeCrkq 46
                                      ++CP+Cg++++++  + +  +C  C+ q
  gi|385806133|ref|YP_005842531.1| 19 VRCPACGNEQVIFSHATFPVRCLICGSQ 46
                                      57*******8888877788888888765 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   0.0   3.5e-05     0.036      70     103 ..      18      54 ..       7      63 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.5e-05
                                       EEEETTTS-EEECHHH...HHS-TTTSSS-EEEEESS CS
                              HypA  70 kvrCreCgkefeleek...alrCpkCgsadveivsGe 103
                                        vrC  Cg+e  + ++    +rC  Cgs+ v+ ++G+
  gi|385806133|ref|YP_005842531.1|  18 LVRCPACGNEQVIFSHatfPVRCLICGSQLVKPTGGR 54 
                                       689*****9988554323456**********999997 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.5   0.00079      0.83      23      31 ..      20      28 ..      19      29 .. 0.90
   2 ?    3.5   0.0     0.056        59       9      22 ..      43      56 ..      30      57 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00079
                     zf-NADH-PPase 23 vCpaCgleh 31
                                      +CpaCg+e+
  gi|385806133|ref|YP_005842531.1| 20 RCPACGNEQ 28
                                      8******97 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.056
                     zf-NADH-PPase  9 CGaptepaeggwar 22
                                      CG+  ++  gg+ar
  gi|385806133|ref|YP_005842531.1| 43 CGSQLVKPTGGRAR 56
                                      66666666667666 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.3    0.0041       4.3      27      34 ..      19      26 ..      11      30 .. 0.71
   2 ?   12.6   1.2    0.0001      0.11       7      38 ..      20      49 ..      18      50 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0041
                       Zn-ribbon_8 27 taCPeCgs 34
                                      + CP+Cg 
  gi|385806133|ref|YP_005842531.1| 19 VRCPACGN 26
                                      56999997 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.0001
                       Zn-ribbon_8  7 rCeeCghefevlqsisdaplta.CPeCgsevrr 38
                                      rC +Cg+e  ++     a  ++ C  Cgs++ +
  gi|385806133|ref|YP_005842531.1| 20 RCPACGNEQVIFSH---ATFPVrCLICGSQLVK 49
                                      8*****77666654...457788******8765 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.1    0.0012       1.3       1       8 [.      20      27 ..       9      28 .. 0.71
   2 ?    3.2   0.0     0.071        75       2       9 ..      40      47 ..      32      50 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0012
                     zinc_ribbon_2  1 fCpnCGae 8 
                                      +Cp CG+e
  gi|385806133|ref|YP_005842531.1| 20 RCPACGNE 27
                                      46666665 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.071
                     zinc_ribbon_2  2 CpnCGael 9 
                                      C  CG +l
  gi|385806133|ref|YP_005842531.1| 40 CLICGSQL 47
                                      44455554 PP

>> RNA_pol_N  RNA polymerases N / 8 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.2      0.07        73       3      12 ..      17      26 ..      16      33 .. 0.87
   2 ?   10.0   0.1   0.00078      0.82       3      13 ..      36      46 ..      35      59 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.07
                                      --SS-TTT-- CS
                         RNA_pol_N  3 iPVrCFtCGk 12
                                      i VrC  CG+
  gi|385806133|ref|YP_005842531.1| 17 ILVRCPACGN 26
                                      78*******7 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00078
                                      --SS-TTT--B CS
                         RNA_pol_N  3 iPVrCFtCGkv 13
                                      +PVrC  CG  
  gi|385806133|ref|YP_005842531.1| 36 FPVRCLICGSQ 46
                                      7********75 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.4   8.9e-05     0.094      15      40 ..      21      50 ..      11      53 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.9e-05
                               DZR 15 CseCgtklkavaa...edrCpsCgek.vdp 40
                                      C++Cg++    ++   + rC  Cg++ v+p
  gi|385806133|ref|YP_005842531.1| 21 CPACGNEQVIFSHatfPVRCLICGSQlVKP 50
                                      999999855455567899999999985555 PP

>> PADR1  PADR1 (NUC008) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00029       0.3      13      30 ..      18      35 ..      17      38 .. 0.86
   2 ?   -0.1   0.1      0.77   8.1e+02      15      25 ..      39      48 ..      37      52 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00029
                             PADR1 13 lekCpeCkegqlvfdssg 30
                                      l +Cp C++ q++f++ +
  gi|385806133|ref|YP_005842531.1| 18 LVRCPACGNEQVIFSHAT 35
                                      568***********9875 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.77
                             PADR1 15 kCpeCkegqlv 25
                                      +C  C+ +qlv
  gi|385806133|ref|YP_005842531.1| 39 RCLICG-SQLV 48
                                      7999*9.8775 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.2    0.0033       3.5       6      13 ..      20      29 ..      18      32 .. 0.76
   2 ?    4.0   0.1     0.039        41       5      13 ..      38      46 ..      34      53 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0033
                           zf-RRN7  6 pCgvCgc..r 13
                                      +C++Cg+  +
  gi|385806133|ref|YP_005842531.1| 20 RCPACGNeqV 29
                                      8*****9444 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.039
                           zf-RRN7  5 ppCgvCgcr 13
                                       +C +Cg+ 
  gi|385806133|ref|YP_005842531.1| 38 VRCLICGSQ 46
                                      68*****95 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   4.2    0.0033       3.5       3      27 ..      21      47 ..      20      48 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0033
                                      -SSS--B----SSS..----SSS---- CS
                    DNA_RNApol_7kD  3 CgeCgaevslkkgd..piRCkeCGhRi 27
                                      C  Cg+e  + + +  p+RC  CG+ +
  gi|385806133|ref|YP_005842531.1| 21 CPACGNEQVIFSHAtfPVRCLICGSQL 47
                                      88999999986665459*******976 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       5.3   5.6e+03      23      28 ..      11      16 ..      11      17 .. 0.84
   2 ?    8.7   1.5    0.0015       1.5       2      14 ..      20      32 ..      19      47 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 5.3
                           TFIIS_C 23 Epmtvf 28
                                      Ep t f
  gi|385806133|ref|YP_005842531.1| 11 EPRTKF 16
                                      899999 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0015
                           TFIIS_C  2 kCpkCgsreayff 14
                                      +Cp Cg+++++f 
  gi|385806133|ref|YP_005842531.1| 20 RCPACGNEQVIFS 32
                                      7********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); 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 0.28s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 410.98
//
Query:       gi|385806134|ref|YP_005842532.1|  [L=72]
Description: 50S ribosomal protein L44e [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-22   80.3  10.4    1.2e-22   80.2  10.4    1.0  1  Ribosomal_L44   Ribosomal protein L44
  ------ inclusion threshold ------
      0.044   14.3   0.0      0.051   14.1   0.0    1.2  1  SRCR_2          Scavenger receptor cysteine-rich domain
      0.076   13.1   0.0      0.088   12.9   0.0    1.1  1  PHD_4           PHD-finger
       0.12   12.3   0.2        0.2   11.5   0.2    1.4  1  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit


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 !   80.2  10.4   2.6e-26   1.2e-22      10      76 .]       3      69 ..       1      69 [. 0.98

  Alignments for each domain:
  == domain 1  score: 80.2 bits;  conditional E-value: 2.6e-26
                                      -------SSSHHHHHHHH.H-SSSGGGGS----.--SSBB--EEEEETTT--EEE----BBS--EEE CS
                     Ribosomal_L44 10 ykkgkdselaqgkRrydrkqsgygGqtkpvfkkkaKttKKivlrleCteCkkkrlkalkRakkfelv 76
                                      yk+gk++ l+ g+Rry rkq+gyg+++kp +k+ aKttKK v++l+C+eC++ +++++ R+kk+el+
  gi|385806134|ref|YP_005842532.1|  3 YKAGKRRALSIGQRRYVRKQEGYGSKRKPEQKRYAKTTKKQVIKLKCSECGYIQHRKGLRLKKLELT 69
                                      9****************************************************************95 PP

>> SRCR_2  Scavenger receptor cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.1e-05     0.051      73      96 ..      31      54 ..       3      56 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.1e-05
                            SRCR_2 73 ealqssesCssgsvvslrcsecGl 96
                                         ++  +++ ++v++l+csecG 
  gi|385806134|ref|YP_005842532.1| 31 PEQKRYAKTTKKQVIKLKCSECGY 54
                                      44455678999************6 PP

>> PHD_4  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     2e-05     0.088      16      49 ..      32      65 ..      20      71 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2e-05
                             PHD_4 16 edevveeesetpsslmeCsvCyeivHpeClkeke 49
                                      e++  +++++++   + Cs C  i H++ l+ k+
  gi|385806134|ref|YP_005842532.1| 32 EQKRYAKTTKKQVIKLKCSECGYIQHRKGLRLKK 65
                                      3444466677888889***********9998765 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 ?   11.5   0.2   4.6e-05       0.2      14      31 ..      38      56 ..      36      58 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.6e-05
                                      EECSCCCE.EEESSSS-EE CS
                    RNA_POL_M_15KD 14 kedkegkn.feCrqCgYee 31
                                      k+ k+ ++ + C+ CgY++
  gi|385806134|ref|YP_005842532.1| 38 KTTKKQVIkLKCSECGYIQ 56
                                      566677788********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       881  (0.0491383); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); 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: 0.47u 0.32s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 430.66
//
Query:       gi|385806135|ref|YP_005842533.1|  [L=149]
Description: hypothetical protein FFONT_1093 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       837  (0.0466841); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); 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: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1024.55
//
Query:       gi|385806136|ref|YP_005842534.1|  [L=389]
Description: DNA primase small subunit [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.3e-18   65.0   0.0    2.1e-16   60.5   0.0    2.5  2  DNA_primase_S  DNA primase small subunit
  ------ inclusion threshold ------
      0.054   13.2   0.2      0.088   12.5   0.2    1.3  1  TackOD1        Thaumarchaeal output domain 1
       0.13   12.3   1.2       0.27   11.3   1.2    1.4  1  Zn_Tnp_IS91    Transposase zinc-binding domain
       0.14   11.8   0.0       0.27   10.8   0.0    1.4  1  RE_MamI        MamI restriction endonuclease
        1.5    8.6   4.9       0.66    9.8   0.9    2.4  2  A2L_zn_ribbon  A2L zinc ribbon domain


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 ?    1.6   0.1     0.072   2.6e+02       1      22 [.     105     126 ..     105     130 .. 0.86
   2 !   60.5   0.0   5.8e-20   2.1e-16      28     170 ..     165     319 ..     153     322 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.072
                                       EEEEEETTT-.TT--HHHHHHH CS
                     DNA_primase_S   1 FDiDmddyddcseatvcekcwk 22 
                                       FDiD+d+ ++c++ +   +c++
  gi|385806136|ref|YP_005842534.1| 105 FDIDADEVPGCESIEQLHACLN 126
                                       9*********998888888865 PP

  == domain 2  score: 60.5 bits;  conditional E-value: 5.8e-20
                                       HHHHHHHH-----GGGEEEEE--SEEEEEE.E--TTEEES-HHHHHHHHHH.......................... CS
                     DNA_primase_S  28 vkvldellredfgfkdilwvfsgrrGfHcw.vsdkdarpltdeeraaivnylnlyrplhpflsrsmlkivkpvveei 103
                                       +k+l ++lr+dfgf++i+++fsg+rGfH++  +d++   lt+eer+ i +y++  +   + + ++  ++ k +   i
  gi|385806136|ref|YP_005842534.1| 165 AKKLIKVLRKDFGFEKIKIYFSGNRGFHVHpKCDDEWLKLTSEERSMIIKYITGSGVNIERIIGL-GESIKGKNMYI 240
                                       45556799*********************945666666************988888899999998.66666666666 PP

                                       ..............HCHHHHCT--------.............................-----------------. CS
                     DNA_primase_S 104 ileeqdpf......eikkllrllpdkslrekkkw...........eakedivlvllyprldeqvtkgikhllkapfc 163
                                           ++ +         k ++l        +kk+           ++  ++++++  +++de+vt ++++l+++p++
  gi|385806136|ref|YP_005842534.1| 241 PNPKEPGWrgrlgeILYKKMNLND------EKKItfgeaevllgeKINLNDIMKMASISIDEKVTVDVHRLIRIPGS 311
                                       666666666644433333333333......3344455555689999999**************************** PP

                                       ...---.- CS
                     DNA_primase_S 164 ihgktg.n 170
                                       i+gk g +
  gi|385806136|ref|YP_005842534.1| 312 INGKLGlP 319
                                       ***97755 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   2.4e-05     0.088      30     101 ..      78     150 ..      58     157 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.4e-05
                           TackOD1  30 dpkskelysypllealskekeeseelleelvkrglleeelvdrirlCpsCksghl.nvrevCpkCkSidieeq 101
                                        + s+ +y++p ++ ++k+    +e++ ++ ++++   e ++++++C +C s    + ++ C kC+S ++ e 
  gi|385806136|ref|YP_005842534.1|  78 LYYSSAIYTFPEIDDMEKKGMIGSEIIFDIDADEVPGCESIEQLHACLNCGSLLYgKSIKKCTKCGSQNVIEV 150
                                       4555677888888888777667777777777777777888999999999999776467889999999988765 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.2   7.5e-05      0.27      21      51 ..     118     148 ..     110     158 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.5e-05
                       Zn_Tnp_IS91  21 rkavekilrCrtaalGfaryeCeeCghekiv 51 
                                       ++++++ l+C++  +G +  +C++Cg+++++
  gi|385806136|ref|YP_005842534.1| 118 IEQLHACLNCGSLLYGKSIKKCTKCGSQNVI 148
                                       6889**********************99887 PP

>> RE_MamI  MamI restriction endonuclease
   #    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      42      82 ..     108     149 ..      99     176 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 7.6e-05
                           RE_MamI  42 DgsevksankldavDkcnatapRvn.rlidkgtdastadile 82 
                                       D  ev ++  ++++  c ++++ +  + i+k+t++++ + +e
  gi|385806136|ref|YP_005842534.1| 108 DADEVPGCESIEQLHACLNCGSLLYgKSIKKCTKCGSQNVIE 149
                                       889*****************997651689********99976 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.2      0.45   1.6e+03      24      29 ..     124     129 ..     122     130 .. 0.85
   2 ?    9.8   0.9   0.00018      0.66       2      15 ..     135     148 ..     134     149 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.45
                     A2L_zn_ribbon  24 CieCga 29 
                                       C +Cg+
  gi|385806136|ref|YP_005842534.1| 124 CLNCGS 129
                                       999996 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00018
                     A2L_zn_ribbon   2 nlkvCsvCggngil 15 
                                       ++k+C++Cg+++++
  gi|385806136|ref|YP_005842534.1| 135 SIKKCTKCGSQNVI 148
                                       79*********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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 0.28s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2566.58
//
Query:       gi|385806137|ref|YP_005842535.1|  [L=229]
Description: DNA polymerase sliding clamp B2 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.8e-13   48.7   0.0    1.2e-12   47.6   0.0    1.6  1  PCNA_N         Proliferating cell nuclear antigen, N-terminal
    7.3e-07   29.4   0.1      1e-05   25.7   0.0    2.2  2  PCNA_C         Proliferating cell nuclear antigen, C-terminal
    0.00015   20.9   0.2       0.27   10.2   0.1    2.1  2  Rad1           Repair protein Rad1/Rec1/Rad17
     0.0039   16.7   0.0      0.022   14.2   0.0    2.0  1  Rad9           Rad9
  ------ inclusion threshold ------
      0.014   15.5   0.3      0.035   14.2   0.2    1.7  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 !   47.6   0.0   3.4e-16   1.2e-12      19     104 ..       3      87 ..       1     111 [. 0.89

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 3.4e-16
                                       HTTTCSEEEEEEETTEEEEEEE-TTSSEEEEEEEEGGGSSEEEESS-EEEEEEHHHHHHHHTTSTTTSEEEEEEETT CS
                            PCNA_N  19 ikdlvneanfdcddsGislqalDsshvaLvslelrsegfekyrCDrnlalgvnlnslskilkcannedsvtlkaede 95 
                                       i  +++e+++++d++Gi+l+a+D shv L+ l + s++fe+y  + ++ +g+nl++ls +lk a++ d++ + +e +
  gi|385806137|ref|YP_005842535.1|   3 ISKILEEVAIKADKDGIRLRAMDPSHVMLIDLFFPSSSFESYEANSEI-IGINLENLSDMLKRAKKGDKLEIVTEGN 78 
                                       678999*************************************99886.8************************999 PP

                                       SSEEEEEEE CS
                            PCNA_N  96 adtlalvfe 104
                                       + +l+++ +
  gi|385806137|ref|YP_005842535.1|  79 KFQLKFIGK 87 
                                       999888754 PP

>> PCNA_C  Proliferating cell nuclear antigen, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.12   4.2e+02      25      45 ..       3      23 ..       2      26 .. 0.88
   2 !   25.7   0.0   2.9e-09     1e-05       5     127 ..     109     226 ..     104     227 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.12
                                      HTTT-SEEEEEEETTEEEEEE CS
                            PCNA_C 25 lsqlsdsvvisvtkegvkfsa 45
                                      +s++ ++v i++ k+g++ +a
  gi|385806137|ref|YP_005842535.1|  3 ISKILEEVAIKADKDGIRLRA 23
                                      578899************987 PP

  == domain 2  score: 25.7 bits;  conditional E-value: 2.9e-09
                                       SS-SEEEEEEHHHHHHHHHHHTTT-SEEEEEEETTEEEEEEEETTEEEEEEE--BEESSSGGGCBEEEESS-EEEEE CS
                            PCNA_C   5 seydavvklpssefaricrdlsqlsdsvvisvtkegvkfsasGdiGsasivlkqvkdvdkeeeavklelkepvtltf 81 
                                       +e++a ++l+++ f+  + d+  l+d++   +         + +iG+a + l      +++ + + l  +   +  +
  gi|385806137|ref|YP_005842535.1| 109 LEFKADIRLSAQIFKDSIEDVEFLGDNIYFIANESKFTILNESEIGKAIVELD-----KDSGNIISLVCEGEQKSLY 180
                                       699**************************999999999999*******44443.....467789999999999999* PP

                                       EHHHHHHHGGGGGC-SEEEEEEETTSEEEEEEEETTCEEEEEEE-B CS
                            PCNA_C  82 alkYlaeftkatsLservtlslssevPlvveykikdvgllayllak 127
                                       +l+Yl ++  ++ +++ v++++ss +P ++ ++  ++  l  ++a+
  gi|385806137|ref|YP_005842535.1| 181 GLEYLESLLYSAEVADIVSIQFSSGIPTKITFEFPQGARLVSYIAP 226
                                       **********************************999999999887 PP

>> Rad1  Repair protein Rad1/Rec1/Rad17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0    0.0002      0.72      24      62 ..       9      48 ..       3      84 .. 0.85
   2 !   10.2   0.1   7.6e-05      0.27     164     262 ..     110     201 ..      70     205 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0002
                              Rad1 24 kalvqissdGlkfi.vednrvlqaqafldkalFtsYtfen 62
                                      ++ +++++dG+++   + ++v+ + +f++++ F+sY+ ++
  gi|385806137|ref|YP_005842535.1|  9 EVAIKADKDGIRLRaMDPSHVMLIDLFFPSSSFESYEANS 48
                                      67899********625789*****************9854 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 7.6e-05
                              Rad1 164 evvlkvilkselLhsalteLdatskklkilassekkapvfalsakgelgssevefpneksvlekfevsslsessess 240
                                       e  + + l ++++++ +++ +   ++++++a+++     f++  ++e+g++ ve+ +++  + ++++    + ++s 
  gi|385806137|ref|YP_005842535.1| 110 EFKADIRLSAQIFKDSIEDVEFLGDNIYFIANES----KFTILNESEIGKAIVELDKDSGNIISLVCE---GEQKSL 179
                                       45567889999******************99995....7*****************************...999999 PP

                              Rad1 241 YkfallkkaakalalssKvslr 262
                                       Y +++l+ +  + +++  vs++
  gi|385806137|ref|YP_005842535.1| 180 YGLEYLESLLYSAEVADIVSIQ 201
                                       ***********99999999987 PP

>> Rad9  Rad9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   6.2e-06     0.022       8      64 ..       3      56 ..       1     211 [. 0.77

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.2e-06
                              Rad9  8 lsrigdelyleisedglelrtvnssrSayalvtlkksfFdkyekevseqirckilvK 64
                                      +s+i +e+ +++ +dg++lr+++ s+     + + +s F++ye ++    ++ i++ 
  gi|385806137|ref|YP_005842535.1|  3 ISKILEEVAIKADKDGIRLRAMDPSHVMLIDLFFPSSSFESYEANS---EIIGINLE 56
                                      8*****************************************4432...23344444 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 ?   14.2   0.2   9.9e-06     0.035      29     114 ..       6      99 ..       3     110 .. 0.75
   2 ?   -1.8   0.0      0.92   3.3e+03      68     100 ..     115     148 ..     102     156 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.9e-06
                                       GGGEEEEEEETTEEEEEEE-......SSEEEEEEEESEEEEE-EEEEEEHHHHHHHHHHSSTTSEEEEEEETTEEEE CS
                     DNA_pol3_beta  29 iLsgvllevkdsqlsltgtD......leisiestisaeseeeegkvlvparllldivkaLpndkkvkisvneqklli 99 
                                       iL  v ++++++++ l + D       ++++ s+   + e+++  + ++  +l+d++k+  ++ k +i+++++k ++
  gi|385806137|ref|YP_005842535.1|   6 ILEEVAIKADKDGIRLRAMDpshvmlIDLFFPSSSFESYEANSEIIGINLENLSDMLKRAKKGDKLEIVTEGNKFQL 82 
                                       8999****************432222234455544444456666778*************************99888 PP

                                       EEETT..EEEEEE-BEG CS
                     DNA_pol3_beta 100 iksgs..srfslstlsa 114
                                       +  g+    f++st+++
  gi|385806137|ref|YP_005842535.1|  83 KFIGKfsRIFTESTVDV 99 
                                       77776546688888753 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.92
                                       EEEEHHHHHHHHHHSST.TSEEEEEEETTEEEEE CS
                     DNA_pol3_beta  68 vlvparllldivkaLpn.dkkvkisvneqkllii 100
                                       + ++a+ + d +   ++ + ++ +  ne+k +i 
  gi|385806137|ref|YP_005842535.1| 115 IRLSAQIFKDSIEDVEFlGDNIYFIANESKFTIL 148
                                       4556666666655555423456666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); 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: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 1482.62
//
Query:       gi|385806138|ref|YP_005842536.1|  [L=104]
Description: DNA-directed RNA polymerase subunit M [Fervidicoccus fontis Kam940]
Scores for complete 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   8.9    1.9e-21   75.6   3.9    2.1  2  TFIIS_C          Transcription factor S-II (TFIIS)
    4.1e-07   29.9   3.2    0.00015   21.6   0.8    2.2  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
    5.7e-06   25.7   5.5     0.0029   17.1   0.4    2.8  2  TF_Zn_Ribbon     TFIIB zinc-binding
    1.7e-05   24.4   9.8       0.13   12.1   0.2    3.4  3  zinc_ribbon_2    zinc-ribbon domain
      6e-05   22.9   4.6       0.16   11.9   0.1    3.0  3  Prok-RING_1      Prokaryotic RING finger family 1
    8.1e-05   22.7   4.1        2.9    8.1   0.1    3.3  3  Zn-ribbon_8      Zinc ribbon domain
    0.00012   21.7   7.4      0.036   13.8   0.1    3.3  3  A2L_zn_ribbon    A2L zinc ribbon domain
    0.00048   20.0   6.1       0.24   11.3   2.9    3.0  2  Nudix_N_2        Nudix N-terminal
    0.00063   19.6   8.0          1    9.3   0.2    3.2  3  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
    0.00068   19.5   7.6       0.56   10.2   0.4    3.6  3  zinc_ribbon_4    zinc-ribbon domain
     0.0008   19.5   5.7        0.4   10.8   1.7    2.2  2  DUF2387          Probable metal-binding protein (DUF2387)
     0.0012   18.7   4.2       0.24   11.3   1.7    2.6  3  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
     0.0016   18.5   7.9       0.55   10.4   0.3    3.2  3  UPF0547          Uncharacterised protein family UPF0547
     0.0028   17.7   3.5       0.24   11.5   1.0    2.4  2  DZR              Double zinc ribbon
      0.003   17.9   7.1      0.092   13.1   7.1    2.2  1  Lar_restr_allev  Restriction alleviation protein Lar
     0.0054   16.9   9.1        1.5    9.0   0.1    3.2  3  zinc_ribbon_13   Nucleic-acid-binding protein containing Zn-r
     0.0059   16.0  13.4       0.24   10.9   0.5    3.2  3  zf-ribbon_3      zinc-ribbon domain
  ------ inclusion threshold ------
      0.022   14.9   3.7       0.49   10.6   1.5    2.8  3  NOB1_Zn_bind     Nin one binding (NOB1) Zn-ribbon like
       0.03   14.0   4.5       0.25   11.1   0.0    3.0  3  Baculo_LEF5_C    Baculoviridae late expression factor 5 C-ter
       0.03   14.1   4.6        1.6    8.6   0.0    3.1  3  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
      0.033   14.2   7.5       0.22   11.5   0.1    2.9  2  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
      0.035   14.0   3.4         24    4.9   0.1    3.1  3  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
      0.035   13.8   7.3        4.8    7.0   0.0    3.4  3  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
      0.036   14.1  11.4        1.7    8.8   1.6    3.5  3  zf-ACC           Acetyl-coA carboxylase zinc finger domain
       0.04   13.5   6.8        8.7    6.1   0.1    3.2  3  zf-tcix          Putative treble-clef, zinc-finger, Zn-bindin
      0.048   13.9   2.5         26    5.2   0.0    3.1  3  Methyltransf_13  Putative zinc binding domain
      0.048   13.6  12.3       0.26   11.2   0.1    3.1  2  Zn_ribbon_SprT   SprT-like zinc ribbon domain
      0.048   13.6   2.3        6.4    6.8   0.2    3.0  3  HalOD2           Halobacterial output domain 2
      0.053   13.5   2.7          1    9.4   2.9    2.3  2  HypA             Hydrogenase/urease nickel incorporation, met
       0.06   11.9   2.7      0.097   11.2   1.0    1.8  2  Terminase_GpA    Phage terminase large subunit (GpA)
      0.065   12.8  10.9       0.68    9.5   0.3    3.4  3  zf_C2H2_10       C2H2 type zinc-finger
      0.066   12.8   4.9       0.16   11.6   0.8    2.1  2  DpnI             Dam-replacing family
      0.067   13.5   4.3        5.8    7.3   0.1    2.7  2  C1_2             C1 domain
      0.087   12.4   2.8        2.1    8.0   0.1    2.9  3  RecR             RecR protein
      0.091   12.8   3.2         11    6.1   0.5    2.9  3  Zn_Tnp_IS91      Transposase zinc-binding domain
       0.11   12.5  10.4        7.5    6.7   0.1    3.3  3  Rubredoxin       Rubredoxin
       0.13   12.3  10.0        1.4    8.9   0.6    3.1  3  DUF1610          Domain of unknown function (DUF1610)
       0.13   12.8   5.3        3.5    8.2   3.1    2.5  2  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
       0.13   12.3   3.6         27    4.9   0.1    3.3  3  YhfH             YhfH-like protein
       0.13   11.9   4.3         14    5.5   0.1    3.5  3  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
       0.14   12.5   2.6          7    7.0   0.1    2.9  3  zinc_ribbon_9    zinc-ribbon
       0.15   11.5   9.2        4.4    6.7   0.1    2.9  2  zf-TFIIB         Transcription factor zinc-finger
       0.17   11.8   0.9        7.2    6.4   0.2    2.2  2  zf-ZPR1          ZPR1 zinc-finger domain
       0.25   11.8  15.4        1.7    9.2   1.0    3.4  3  zf-H2C2_2        Zinc-finger double domain
       0.26   11.0   3.5        3.6    7.4   1.0    2.9  2  Ribosomal_S27e   Ribosomal protein S27
       0.27   11.1  16.4       0.14   12.1   6.4    3.0  2  DUF3797          Domain of unknown function (DUF3797)
       0.29   11.5   5.4         11    6.4   2.2    2.2  2  DUF3268          zinc-finger-containing domain
        0.3   10.9   2.8         21    5.0   0.0    3.0  3  HscB_4_cys       Co-chaperone HscB tetracysteine metal bindin
       0.33    9.8   2.9        2.5    6.9   0.1    2.0  2  tRNA-synt_1f     tRNA synthetases class I (K)
       0.33   10.8   4.2       0.14   12.0   0.7    2.0  2  eIF-5_eIF-2B     Domain found in IF2B/IF5
       0.41   10.8   0.2       0.41   10.8   0.2    2.6  3  Acetone_carb_G   Acetone carboxylase gamma subunit
       0.42   10.9   3.0         32    4.9   0.1    3.0  3  Ribosomal_L32p   Ribosomal L32p protein family
       0.47   10.7   6.8        2.2    8.6   0.5    3.0  3  zf-RING_7        C4-type zinc ribbon domain
       0.73    9.6   5.6        6.4    6.6   2.4    2.8  2  Zn_Tnp_IS1       InsA N-terminal domain
       0.79    9.4   8.3        4.4    7.0   0.1    3.2  3  zf_UBZ           Ubiquitin-Binding Zinc Finger
       0.81    9.5   8.6        5.8    6.7   0.1    3.1  2  zinc_ribbon_10   Predicted integral membrane zinc-ribbon meta
       0.89    9.5   5.3         22    5.1   1.9    2.8  2  PHD              PHD-finger
        1.2    8.3   8.6        1.4    8.1   3.7    2.2  2  Baculo_ME53      Baculoviridae ME53
        1.3    9.8   4.8        5.2    7.8   0.2    2.6  2  FYDLN_acid       Protein of unknown function (FYDLN_acid)
        1.3    9.1  10.4        8.3    6.6   0.7    3.0  2  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
        1.7    8.5  13.9        2.4    8.0   0.4    3.2  3  Rubredoxin_2     Rubredoxin metal binding domain
        1.7    9.3   7.9        7.1    7.4   0.7    3.0  3  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
        1.9    8.3   0.0        1.9    8.3   0.0    2.6  2  Cys_rich_KTR     Cysteine-rich KTR
          2    8.1  11.0        3.5    7.3   0.3    3.2  3  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
        2.2    9.1   7.4        7.7    7.3   1.8    2.6  2  zinc_ribbon_15   zinc-ribbon family
        3.5    7.7   8.8        4.2    7.4   0.2    3.0  2  CpXC             CpXC protein
        3.8    7.6  10.1         11    6.1   0.1    3.0  2  ADK_lid          Adenylate kinase, active site lid
        5.1    7.1   8.2         11    6.1   0.6    2.6  2  DUF2719          Protein of unknown function (DUF2719)
        7.1    7.8   8.5         44    5.3   0.5    3.2  3  zf-C2H2_4        C2H2-type zinc finger


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 ?    6.0   0.2     0.041        11       2       9 ..      13      20 ..      11      23 .. 0.55
   2 !   75.6   3.9   7.3e-24   1.9e-21       3      39 .]      65     101 ..      63     101 .. 0.98

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.041
                           TFIIS_C  2 kCpkCgsr 9 
                                       CpkCg +
  gi|385806138|ref|YP_005842536.1| 13 VCPKCGYT 20
                                      35555544 PP

  == domain 2  score: 75.6 bits;  conditional E-value: 7.3e-24
                           TFIIS_C   3 CpkCgsreayffqlQtRsaDEpmtvfykCtkCghrWr 39 
                                       CpkCg++e+y++++QtR+aDEp+t+fykCtkCg+ Wr
  gi|385806138|ref|YP_005842536.1|  65 CPKCGNNEVYYWTMQTRAADEPPTRFYKCTKCGYVWR 101
                                       ************************************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 !    8.7   0.1    0.0067       1.7      19      27 ..      12      20 ..       7      30 .. 0.81
   2 !   21.6   0.8   5.9e-07   0.00015      19      45 ..      63      98 ..      54      99 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0067
                     Zn_Tnp_IS1595 19 fvCPhCgsr 27
                                       vCP+Cg++
  gi|385806138|ref|YP_005842536.1| 12 YVCPKCGYT 20
                                      58*****98 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 5.9e-07
                     Zn_Tnp_IS1595 19 fvCPhCgsr..kayrikt.......rglfqCkeCrk 45
                                      + CP+Cg+    +++++t        + ++C +C++
  gi|385806138|ref|YP_005842536.1| 63 VYCPKCGNNevYYWTMQTraadeppTRFYKCTKCGY 98
                                      44*******655566666*******9********97 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.6    0.0018      0.48       1      19 [.      12      29 ..      12      31 .. 0.59
   2 !   17.1   0.4   1.1e-05    0.0029       2      30 ..      64     101 ..      63     103 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0018
                                      EEETTTTCEECHEETSTTC CS
                      TF_Zn_Ribbon  1 ykCPnCgstnlveDperge 19
                                      y+CP+Cg t+ +++p+ +e
  gi|385806138|ref|YP_005842536.1| 12 YVCPKCGYTE-EVEPKKNE 29
                                      5677777666.55555555 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 1.1e-05
                                       EETTTTCEEC.........HEETSTTCEEESSSSBEEE CS
                      TF_Zn_Ribbon   2 kCPnCgstnl.........veDpergelvCtdCGlVle 30 
                                        CP+Cg+ ++           +p +  + Ct+CG+V+ 
  gi|385806138|ref|YP_005842536.1|  64 YCPKCGNNEVyywtmqtraADEPPTRFYKCTKCGYVWR 101
                                       6******99669****996666999999********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 !   10.7   0.2    0.0013      0.34       8      21 ..       5      19 ..       4      20 .. 0.72
   2 !   12.1   0.2   0.00048      0.13      12      21 ..      61      70 ..      59      71 .. 0.73
   3 ?    6.6   0.6     0.026       6.7       1       7 [.      92      98 ..      89      99 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0013
                     zinc_ribbon_2  8 elqdnakF.CpyCGt 21
                                      +++ ++++ Cp+CG+
  gi|385806138|ref|YP_005842536.1|  5 KIDGKDVYvCPKCGY 19
                                      677667777999997 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00048
                     zinc_ribbon_2 12 nakFCpyCGt 21
                                      ++++Cp+CG 
  gi|385806138|ref|YP_005842536.1| 61 DVVYCPKCGN 70
                                      6778888885 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.026
                     zinc_ribbon_2  1 fCpnCGa 7 
                                      +C++CG+
  gi|385806138|ref|YP_005842536.1| 92 KCTKCGY 98
                                      5777774 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 !   11.4   0.2   0.00092      0.24      16      28 ..       7      19 ..       3      43 .. 0.76
   2 !   11.9   0.1   0.00062      0.16      15      27 ..      57      69 ..      52      72 .. 0.82
   3 ?   -0.1   0.1       3.5     9e+02      23      27 ..      93      97 ..      90     101 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00092
                       Prok-RING_1 16 eedDiVvCpeCgt 28
                                      +++D+ vCp+Cg 
  gi|385806138|ref|YP_005842536.1|  7 DGKDVYVCPKCGY 19
                                      578********96 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00062
                       Prok-RING_1 15 keedDiVvCpeCg 27
                                       + +D+V Cp+Cg
  gi|385806138|ref|YP_005842536.1| 57 PKLKDVVYCPKCG 69
                                      5668********9 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 3.5
                       Prok-RING_1 23 CpeCg 27
                                      C++Cg
  gi|385806138|ref|YP_005842536.1| 93 CTKCG 97
                                      55555 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.1     0.011       2.9       6      33 ..      12      18 ..       2      31 .. 0.65
   2 ?    8.0   0.0     0.012       3.1      26      35 ..      61      72 ..      50      74 .. 0.76
   3 ?    6.9   0.1     0.026       6.8       6      14 ..      91      99 ..      79     102 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.011
                       Zn-ribbon_8  6 YrCeeCghefevlqsisdapltaCPeCg 33
                                      Y                      CP+Cg
  gi|385806138|ref|YP_005842536.1| 12 YV---------------------CPKCG 18
                                      55.....................55555 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.012
                       Zn-ribbon_8 26 lta.CPeCgs.e 35
                                      +++ CP+Cg  e
  gi|385806138|ref|YP_005842536.1| 61 DVVyCPKCGNnE 72
                                      5666*****855 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.026
                       Zn-ribbon_8  6 YrCeeCghe 14
                                      Y+C++Cg +
  gi|385806138|ref|YP_005842536.1| 91 YKCTKCGYV 99
                                      9******65 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   0.00014     0.036      19      32 ..       9      22 ..       6      23 .. 0.87
   2 ?    7.0   0.1     0.018       4.7      23      32 ..      64      73 ..      59      81 .. 0.70
   3 ?    3.5   0.8      0.23        60       4      10 ..      91      97 ..      90      99 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00014
                     A2L_zn_ribbon 19 qgylvCieCgasfp 32
                                      ++ +vC++Cg++++
  gi|385806138|ref|YP_005842536.1|  9 KDVYVCPKCGYTEE 22
                                      578********987 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.018
                     A2L_zn_ribbon 23 vCieCgasfp 32
                                      +C++Cg+ ++
  gi|385806138|ref|YP_005842536.1| 64 YCPKCGNNEV 73
                                      6777776544 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.23
                     A2L_zn_ribbon  4 kvCsvCg 10
                                      ++C++Cg
  gi|385806138|ref|YP_005842536.1| 91 YKCTKCG 97
                                      5677775 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.1    0.0097       2.5      23      31 ..      12      20 ..       4      21 .. 0.86
   2 !   11.3   2.9   0.00093      0.24       2      31 ..      64      99 ..      63     101 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0097
                                      EEETTTTEE CS
                         Nudix_N_2 23 lvCpaCgti 31
                                      +vCp+Cg++
  gi|385806138|ref|YP_005842536.1| 12 YVCPKCGYT 20
                                      79*****96 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00093
                                      B-TTT--B.-E...EE--.TT-SS-EEE.ETTTTEE CS
                         Nudix_N_2  2 FCsqCGtp.ve...lrip.dgDnreRlv.CpaCgti 31
                                      +C++CG+  v    +++  +++  +R+  C++Cg++
  gi|385806138|ref|YP_005842536.1| 64 YCPKCGNNeVYywtMQTRaADEPPTRFYkCTKCGYV 99
                                      9******9554766455515666679644*****98 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.2    0.0039         1      21      34 ..      11      24 ..       1      26 [. 0.76
   2 ?    6.8   0.4     0.024       6.2       3       9 ..      64      70 ..      62      71 .. 0.90
   3 ?    7.4   0.1     0.015         4      20      30 ..      88      99 ..      78     100 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0039
                                      EEEESSSS-EEESS CS
                    RNA_POL_M_15KD 21 nfeCrqCgYeepad 34
                                      ++ C +CgY e+ +
  gi|385806138|ref|YP_005842536.1| 11 VYVCPKCGYTEEVE 24
                                      366********976 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.024
                                      BESTTTS CS
                    RNA_POL_M_15KD  3 FCpkCgN 9 
                                       CpkCgN
  gi|385806138|ref|YP_005842536.1| 64 YCPKCGN 70
                                      6*****9 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.015
                                      CE.EEESSSS-E CS
                    RNA_POL_M_15KD 20 kn.feCrqCgYe 30
                                      ++ + C +CgY+
  gi|385806138|ref|YP_005842536.1| 88 TRfYKCTKCGYV 99
                                      55699******7 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1      0.15        39       5      10 ..      14      19 ..       8      33 .. 0.75
   2 ?    7.9   0.3     0.011       2.9      17      33 ..      54      70 ..      47      71 .. 0.75
   3 !   10.2   0.4    0.0021      0.56      27      36 .]      92     101 ..      87     101 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.15
                     zinc_ribbon_4  5 CpsCka 10
                                      Cp+C+ 
  gi|385806138|ref|YP_005842536.1| 14 CPKCGY 19
                                      666654 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.011
                     zinc_ribbon_4 17 eklpakgvkvrCskCgh 33
                                      e lp+ +  v C+kCg+
  gi|385806138|ref|YP_005842536.1| 54 ETLPKLKDVVYCPKCGN 70
                                      35777777888****97 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.0021
                     zinc_ribbon_4  27 rCskCghvFr 36 
                                       +C+kCg v+r
  gi|385806138|ref|YP_005842536.1|  92 KCTKCGYVWR 101
                                       8********7 PP

>> DUF2387  Probable metal-binding protein (DUF2387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.1    0.0019      0.51      26      50 ..       7      31 ..       4      52 .. 0.75
   2 !   10.8   1.7    0.0016       0.4      10      39 ..      64      99 ..      62     103 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0019
                           DUF2387 26 deveyrECvsCgftdelsekgqsva 50
                                      d++++  C +Cg+t+e + k+++ +
  gi|385806138|ref|YP_005842536.1|  7 DGKDVYVCPKCGYTEEVEPKKNEYK 31
                                      7888899*********999954433 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0016
                           DUF2387 10 vCPrCsemD......kirmweedeveyrECvsCgft 39
                                       CP+C +        ++r+ +e ++++  C++Cg++
  gi|385806138|ref|YP_005842536.1| 64 YCPKCGNNEvyywtmQTRAADEPPTRFYKCTKCGYV 99
                                      6*****9998888666666666669999*******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 ?    6.9   0.0     0.022       5.7      31      39 ..      14      22 ..       4      34 .. 0.65
   2 ?    3.6   0.2      0.25        64      45      54 ..      61      70 ..      55      74 .. 0.72
   3 !   11.3   1.7   0.00093      0.24      30      56 ..      64     100 ..      63     101 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.022
                    OrfB_Zn_ribbon 31 CseCgsknk 39
                                      C++Cg++ +
  gi|385806138|ref|YP_005842536.1| 14 CPKCGYTEE 22
                                      555555555 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.25
                    OrfB_Zn_ribbon 45 rtfkCpnCgf 54
                                      ++++Cp+Cg 
  gi|385806138|ref|YP_005842536.1| 61 DVVYCPKCGN 70
                                      5667777775 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.00093
                    OrfB_Zn_ribbon  30 tCseCgsknke..........alsgrtfkCpnCgfea 56 
                                        C++Cg +  +          ++ +r +kC++Cg+++
  gi|385806138|ref|YP_005842536.1|  64 YCPKCGNNEVYywtmqtraadEPPTRFYKCTKCGYVW 100
                                       6******99999999999999999**********986 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.3     0.014       3.6      16      22 ..      13      19 ..      10      20 .. 0.82
   2 ?    4.0   0.1      0.21        55      14      21 ..      62      69 ..      60      70 .. 0.76
   3 !   10.4   0.3    0.0021      0.55      16      25 ..      92     101 ..      87     102 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.014
                           UPF0547 16 fCphCGy 22
                                      +Cp CGy
  gi|385806138|ref|YP_005842536.1| 13 VCPKCGY 19
                                      7*****9 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.21
                           UPF0547 14 aqfCphCG 21
                                      ++ Cp CG
  gi|385806138|ref|YP_005842536.1| 62 VVYCPKCG 69
                                      56688888 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.0021
                           UPF0547  16 fCphCGyvFq 25 
                                       +C  CGyv+ 
  gi|385806138|ref|YP_005842536.1|  92 KCTKCGYVWR 101
                                       7*99*****6 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1     0.034       8.9      28      37 ..      11      20 ..       2      29 .. 0.70
   2 !   11.5   1.0   0.00091      0.24      13      37 ..      63      99 ..      54     104 .] 0.75

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.034
                               DZR 28 edrCpsCgek 37
                                       ++Cp+Cg+ 
  gi|385806138|ref|YP_005842536.1| 11 VYVCPKCGYT 20
                                      5788888875 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00091
                               DZR 13 rfCseCgtk......lkavaa..........edrCpsCgek 37
                                       +C++Cg++      +    +           ++C +Cg+ 
  gi|385806138|ref|YP_005842536.1| 63 VYCPKCGNNevyywtM----QtraadepptrFYKCTKCGYV 99
                                      69*****997665442....0456688999999*****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 !   13.1   7.1   0.00035     0.092       2      43 ..      10      77 ..       9     104 .] 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00035
                   Lar_restr_allev  2 eLkpCPfCggravlersqrvvaeigq..........................cvyCadCgastpwfki 43
                                      +++ CP Cg  +++e  ++ ++ + +                          +vyC +Cg ++  + +
  gi|385806138|ref|YP_005842536.1| 10 DVYVCPKCGYTEEVEPKKNEYKIVNKikhgekdkliivdenkipetlpklkdVVYCPKCGNNEVYYWT 77
                                      7899*******999988777654444888******************************993333333 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 ?    8.0   0.2     0.012       3.2      37      52 ..      13      28 ..      10      36 .. 0.74
   2 !    9.0   0.1    0.0059       1.5      36      48 ..      63      75 ..      61      84 .. 0.58
   3 ?    4.4   0.6      0.16        41      37      44 ..      92      99 ..      88     101 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.012
                    zinc_ribbon_13 37 sCknCgYtelYkaets 52
                                       C +CgYte  +++++
  gi|385806138|ref|YP_005842536.1| 13 VCPKCGYTEEVEPKKN 28
                                      6999999996666655 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0059
                    zinc_ribbon_13 36 vsCknCgYtelYk 48
                                      v+C +Cg  e+Y 
  gi|385806138|ref|YP_005842536.1| 63 VYCPKCGNNEVYY 75
                                      5555565555554 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.16
                    zinc_ribbon_13 37 sCknCgYt 44
                                       C++CgY+
  gi|385806138|ref|YP_005842536.1| 92 KCTKCGYV 99
                                      69999996 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.5     0.005       1.3      16      24 ..      11      19 ..       8      20 .. 0.74
   2 !   10.9   0.5   0.00091      0.24       3      11 ..      63      71 ..      62      73 .. 0.85
   3 ?    4.3   1.0      0.11        28      18      25 ..      92      99 ..      91      99 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.005
                       zf-ribbon_3 16 dnvCpyCGt 24
                                      + vCp+CG+
  gi|385806138|ref|YP_005842536.1| 11 VYVCPKCGY 19
                                      558999986 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00091
                       zf-ribbon_3  3 vrCPnCGap 11
                                      v+CP+CG++
  gi|385806138|ref|YP_005842536.1| 63 VYCPKCGNN 71
                                      79*****96 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.11
                       zf-ribbon_3 18 vCpyCGtk 25
                                      +C++CG++
  gi|385806138|ref|YP_005842536.1| 92 KCTKCGYV 99
                                      6*****96 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 ?    3.3   0.0      0.37        95      25      31 ..      13      19 ..       4      37 .. 0.85
   2 ?   10.6   1.5    0.0019      0.49      22      42 ..      61      81 ..      54      96 .. 0.77
   3 ?   -0.5   0.2       5.7   1.5e+03      26      30 ..      93      97 ..      82     100 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.37
                      NOB1_Zn_bind 25 FCpkCGn 31
                                       CpkCG 
  gi|385806138|ref|YP_005842536.1| 13 VCPKCGY 19
                                      5****97 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0019
                      NOB1_Zn_bind 22 tkkFCpkCGnktLkrvavsvd 42
                                      + ++CpkCGn+ +   +++++
  gi|385806138|ref|YP_005842536.1| 61 DVVYCPKCGNNEVYYWTMQTR 81
                                      668*******99877666665 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 5.7
                      NOB1_Zn_bind 26 CpkCG 30
                                      C kCG
  gi|385806138|ref|YP_005842536.1| 93 CTKCG 97
                                      88887 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 ?    0.2   0.4       2.4   6.3e+02      36      41 ..      13      18 ..      11      19 .. 0.82
   2 ?    2.7   0.3       0.4     1e+02      35      41 ..      63      69 ..      61      70 .. 0.85
   3 ?   11.1   0.0   0.00095      0.25      22      41 ..      78      97 ..      76      98 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 2.4
                     Baculo_LEF5_C 36 yCskCg 41
                                      +C kCg
  gi|385806138|ref|YP_005842536.1| 13 VCPKCG 18
                                      7****9 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.4
                     Baculo_LEF5_C 35 ryCskCg 41
                                       yC kCg
  gi|385806138|ref|YP_005842536.1| 63 VYCPKCG 69
                                      69****9 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00095
                     Baculo_LEF5_C 22 iQnRagDEivsfvryCskCg 41
                                       Q+Ra DE       C kCg
  gi|385806138|ref|YP_005842536.1| 78 MQTRAADEPPTRFYKCTKCG 97
                                      5*******9988889****9 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.2     0.051        13       4       8 ..      14      18 ..      11      31 .. 0.76
   2 ?    8.6   0.0    0.0061       1.6       2      10 ..      63      71 ..      62      76 .. 0.78
   3 ?    0.2   0.1       2.6   6.8e+02       3       8 ..      92      97 ..      90      99 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.051
                                      -SSS- CS
                    zf-C4_Topoisom  4 CPkCg 8 
                                      CPkCg
  gi|385806138|ref|YP_005842536.1| 14 CPKCG 18
                                      99998 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0061
                                      EE-SSS--E CS
                    zf-C4_Topoisom  2 ekCPkCggd 10
                                      + CPkCg++
  gi|385806138|ref|YP_005842536.1| 63 VYCPKCGNN 71
                                      78*****54 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 2.6
                                      E-SSS- CS
                    zf-C4_Topoisom  3 kCPkCg 8 
                                      kC kCg
  gi|385806138|ref|YP_005842536.1| 92 KCTKCG 97
                                      899998 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00085      0.22      17      27 ..       9      19 ..       7      19 .. 0.88
   2 ?    2.6   4.2      0.53   1.4e+02       5      25 ..      65      96 ..      55     101 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00085
                    PhnA_Zn_Ribbon 17 gallvCpeCah 27
                                      ++++vCp+C++
  gi|385806138|ref|YP_005842536.1|  9 KDVYVCPKCGY 19
                                      79*******96 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.53
                    PhnA_Zn_Ribbon  5 CplCaSeytY...........edgallvCpeC 25
                                      Cp+C+  ++Y             +  + C +C
  gi|385806138|ref|YP_005842536.1| 65 CPKCGNNEVYywtmqtraadePPTRFYKCTKC 96
                                      77777666666666666555444455555555 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 ?    3.9   0.1       0.2        52      27      32 ..      13      18 ..      11      22 .. 0.71
   2 ?    4.9   0.1     0.091        24      27      32 ..      64      69 ..      62      73 .. 0.68
   3 ?    4.8   0.1       0.1        27      10      20 ..      89      99 ..      81     100 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.2
                           DUF35_N 27 vCphCg 32
                                      vCp+Cg
  gi|385806138|ref|YP_005842536.1| 13 VCPKCG 18
                                      566665 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.091
                           DUF35_N 27 vCphCg 32
                                      +Cp+Cg
  gi|385806138|ref|YP_005842536.1| 64 YCPKCG 69
                                      677777 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.1
                           DUF35_N 10 vgqrCpdCGtv 20
                                      ++ +C++CG v
  gi|385806138|ref|YP_005842536.1| 89 RFYKCTKCGYV 99
                                      56799999965 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 ?    5.2   0.1     0.066        17      12      25 ..       6      19 ..       2      27 .. 0.73
   2 ?    7.0   0.0     0.018       4.8      15      25 ..      60      70 ..      54      74 .. 0.82
   3 ?    3.9   0.8      0.17        43      19      25 ..      92      98 ..      89      99 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.066
                                      --SSS----SSS-- CS
                    DNA_RNApol_7kD 12 lkkgdpiRCkeCGh 25
                                      ++ +d+  C +CG+
  gi|385806138|ref|YP_005842536.1|  6 IDGKDVYVCPKCGY 19
                                      56667777888886 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.018
                                      SS----SSS-- CS
                    DNA_RNApol_7kD 15 gdpiRCkeCGh 25
                                      +d++ C +CG 
  gi|385806138|ref|YP_005842536.1| 60 KDVVYCPKCGN 70
                                      89********6 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.17
                                      --SSS-- CS
                    DNA_RNApol_7kD 19 RCkeCGh 25
                                      +C++CG+
  gi|385806138|ref|YP_005842536.1| 92 KCTKCGY 98
                                      5777775 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   1.6    0.0064       1.7      19      26 .]      10      17 ..       9      17 .. 0.88
   2 ?    5.7   0.3     0.062        16       3       9 ..      64      70 ..      63      71 .. 0.80
   3 ?    5.0   0.1     0.097        25       2       8 ..      91      97 ..      90      99 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0064
                            zf-ACC 19 nlyVCPkC 26
                                      + yVCPkC
  gi|385806138|ref|YP_005842536.1| 10 DVYVCPKC 17
                                      68****** PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.062
                            zf-ACC  3 KCpsCge 9 
                                       Cp+Cg+
  gi|385806138|ref|YP_005842536.1| 64 YCPKCGN 70
                                      6999996 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.097
                            zf-ACC  2 tKCpsCg 8 
                                       KC++Cg
  gi|385806138|ref|YP_005842536.1| 91 YKCTKCG 97
                                      59****8 PP

>> zf-tcix  Putative treble-clef, zinc-finger, Zn-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.2      0.07        18      13      17 ..      14      18 ..       9      20 .. 0.85
   2 ?    6.1   0.1     0.034       8.7      12      18 ..      64      70 ..      56      72 .. 0.81
   3 ?    5.1   0.2     0.067        17      12      17 ..      92      97 ..      88      99 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.07
                           zf-tcix 13 CpkCG 17
                                      CpkCG
  gi|385806138|ref|YP_005842536.1| 14 CPKCG 18
                                      ***** PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.034
                           zf-tcix 12 kCpkCGt 18
                                       CpkCG 
  gi|385806138|ref|YP_005842536.1| 64 YCPKCGN 70
                                      5*****6 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.067
                           zf-tcix 12 kCpkCG 17
                                      kC+kCG
  gi|385806138|ref|YP_005842536.1| 92 KCTKCG 97
                                      9***** PP

>> Methyltransf_13  Putative zinc binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.099        26      40      49 ..      10      19 ..       8      30 .. 0.82
   2 ?    3.0   0.2      0.49   1.3e+02      40      48 ..      61      69 ..      47      73 .. 0.85
   3 ?    4.8   0.1      0.13        34      37      50 ..      86      99 ..      75     104 .] 0.82

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.099
                   Methyltransf_13 40 rlvvCedCgl 49
                                      +++vC++Cg 
  gi|385806138|ref|YP_005842536.1| 10 DVYVCPKCGY 19
                                      69******96 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.49
                   Methyltransf_13 40 rlvvCedCg 48
                                      ++v+C++Cg
  gi|385806138|ref|YP_005842536.1| 61 DVVYCPKCG 69
                                      699*****8 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.13
                   Methyltransf_13 37 yplrlvvCedCglv 50
                                       p r + C++Cg v
  gi|385806138|ref|YP_005842536.1| 86 PPTRFYKCTKCGYV 99
                                      58999*******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 ?   11.2   0.1     0.001      0.26       2      13 ..       9      20 ..       9      28 .. 0.81
   2 ?    1.8   7.6      0.88   2.3e+02       6      31 ..      64      97 ..      59      99 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.001
                    Zn_ribbon_SprT  2 kyvYrCtgCgre 13
                                      k vY+C+ Cg +
  gi|385806138|ref|YP_005842536.1|  9 KDVYVCPKCGYT 20
                                      689*******55 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.88
                    Zn_ribbon_SprT  6 rCtgCgreythhlsirrhn........YrCrrCk 31
                                      +C+ Cg++  +  + ++ +        Y C +C+
  gi|385806138|ref|YP_005842536.1| 64 YCPKCGNNEVYYWTMQTRAadepptrfYKCTKCG 97
                                      7888888888888887766788888888888885 PP

>> HalOD2  Halobacterial output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0      0.16        42      28      40 ..       8      20 ..       5      25 .. 0.86
   2 ?    0.8   0.1       1.8   4.7e+02      33      39 ..      64      70 ..      60      84 .. 0.72
   3 ?    6.8   0.2     0.025       6.4      32      40 ..      91      99 ..      87     103 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.16
                            HalOD2 28 GayvWkCtrCGev 40
                                      G +v+ C +CG +
  gi|385806138|ref|YP_005842536.1|  8 GKDVYVCPKCGYT 20
                                      78999******87 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1.8
                            HalOD2 33 kCtrCGe 39
                                       C +CG+
  gi|385806138|ref|YP_005842536.1| 64 YCPKCGN 70
                                      4666664 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.025
                            HalOD2 32 WkCtrCGev 40
                                      +kCt+CG v
  gi|385806138|ref|YP_005842536.1| 91 YKCTKCGYV 99
                                      577777766 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   2.9    0.0039         1      71      98 ..      12      74 ..       4      98 .. 0.86
   2 ?    1.8   0.2      0.93   2.4e+02      71      81 ..      91     101 ..      82     104 .] 0.74

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0039
                                      EEETTTS-EEECHHH..HH.................................S-TTTSSS-EE CS
                              HypA 71 vrCreCgkefeleek..al.................................rCpkCgsadve 98
                                      + C +Cg++ e+e k  ++                                  CpkCg+++v 
  gi|385806138|ref|YP_005842536.1| 12 YVCPKCGYTEEVEPKknEYkivnkikhgekdkliivdenkipetlpklkdvvYCPKCGNNEVY 74
                                      689****998876642333889999**************************9******99875 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.93
                                       EEETTTS-EEE CS
                              HypA  71 vrCreCgkefe 81 
                                       ++C++Cg+ ++
  gi|385806138|ref|YP_005842536.1|  91 YKCTKCGYVWR 101
                                       57999998776 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 ?    0.3   0.0      0.77     2e+02     228     241 ..      12      25 ..       4      45 .. 0.64
   2 ?   11.2   1.0   0.00037     0.097     199     239 ..      63     102 ..      61     104 .] 0.85

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.77
                     Terminase_GpA 228 yvCphcgslieehh 241
                                       yvCp+cg   e + 
  gi|385806138|ref|YP_005842536.1|  12 YVCPKCGYTEEVEP 25 
                                       66666665444333 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00037
                     Terminase_GpA 199 vpCphCgelqelsferlkwpegeaeekaryvCphcgsliee 239
                                       v Cp+Cg+  +  +   +  ++ ++ +  y C +cg ++ e
  gi|385806138|ref|YP_005842536.1|  63 VYCPKCGNNEVYYWTMQTRAAD-EPPTRFYKCTKCGYVWRE 102
                                       78*********99987444555.9***************88 PP

>> zf_C2H2_10  C2H2 type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.3    0.0026      0.68       3      10 ..      12      19 ..      11      21 .. 0.86
   2 ?    5.6   0.5     0.045        12       5      10 ..      65      70 ..      63      72 .. 0.86
   3 ?    3.4   0.3      0.21        55       4      11 ..      92      99 ..      90     100 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0026
                        zf_C2H2_10  3 fsCPKCqe 10
                                      + CPKC++
  gi|385806138|ref|YP_005842536.1| 12 YVCPKCGY 19
                                      67*****9 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.045
                        zf_C2H2_10  5 CPKCqe 10
                                      CPKC+ 
  gi|385806138|ref|YP_005842536.1| 65 CPKCGN 70
                                      ****85 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.21
                        zf_C2H2_10  4 sCPKCqek 11
                                       C KC+++
  gi|385806138|ref|YP_005842536.1| 92 KCTKCGYV 99
                                      6*****97 PP

>> DpnI  Dam-replacing family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.2      0.19        50      54      82 ..      12      42 ..       7      56 .. 0.70
   2 ?   11.6   0.8   0.00062      0.16      29      59 ..      60      96 ..      55     104 .] 0.78

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.19
                                      EE-TTT-..-EEEEEEEESS--SEEEEEEHH CS
                              DpnI 54 fyCesck..eefeLkskksklskkivdgays 82
                                      + C +c   ee e k ++ k+ +ki+ g+ +
  gi|385806138|ref|YP_005842536.1| 12 YVCPKCGytEEVEPKKNEYKIVNKIKHGEKD 42
                                      4588886446777777777888888888755 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00062
                                      HHH---TTT--SS-EE--------E.....EE.-TTT CS
                              DpnI 29 aknlyCpkCgskklsefennkpvaD.....fy.Cesc 59
                                      ++ +yCpkCg++++  ++  +++aD     fy C++c
  gi|385806138|ref|YP_005842536.1| 60 KDVVYCPKCGNNEVYYWTMQTRAADepptrFYkCTKC 96
                                      6779*********999999999988555554447776 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.1     0.022       5.8      26      41 ..       4      20 ..       3      23 .. 0.86
   2 ?    7.0   0.1     0.027       7.1      31      41 ..      89      99 ..      82     102 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.022
                              C1_2 26 rkidgff.YsCseCdfs 41
                                      +kidg++ Y C++C ++
  gi|385806138|ref|YP_005842536.1|  4 KKIDGKDvYVCPKCGYT 20
                                      57899999******985 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.027
                              C1_2 31 ffYsCseCdfs 41
                                       fY+C++C ++
  gi|385806138|ref|YP_005842536.1| 89 RFYKCTKCGYV 99
                                      45******997 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1       0.3        77      16      29 ..      11      24 ..       9      25 .. 0.75
   2 ?    8.0   0.1    0.0081       2.1      14      24 ..      60      70 ..      54      72 .. 0.88
   3 ?    0.1   0.1       2.4   6.2e+02      18      24 ..      92      98 ..      88     102 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.3
                                      -EE-TTT--EESSS CS
                              RecR 16 vrhCsrCgnlteed 29
                                      v  C++Cg   e +
  gi|385806138|ref|YP_005842536.1| 11 VYVCPKCGYTEEVE 24
                                      667****9877766 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0081
                                      HH-EE-TTT-- CS
                              RecR 14 ekvrhCsrCgn 24
                                      ++v +C++Cgn
  gi|385806138|ref|YP_005842536.1| 60 KDVVYCPKCGN 70
                                      5799******9 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 2.4
                                      E-TTT-- CS
                              RecR 18 hCsrCgn 24
                                       C +Cg 
  gi|385806138|ref|YP_005842536.1| 92 KCTKCGY 98
                                      6****96 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.074        19      36      50 ..       8      22 ..       3      52 .. 0.81
   2 ?    6.1   0.5     0.042        11      59      75 ..      64      80 ..      60      94 .. 0.72
   3 ?    0.6   0.2       2.3     6e+02      40      47 ..      91      98 ..      85     103 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.074
                       Zn_Tnp_IS91 36 GfaryeCeeCgheki 50
                                      G  +y C++Cg ++ 
  gi|385806138|ref|YP_005842536.1|  8 GKDVYVCPKCGYTEE 22
                                      778889999987654 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.042
                       Zn_Tnp_IS91 59 hCpsCqkkateewlekq 75
                                       Cp+C++++   w  ++
  gi|385806138|ref|YP_005842536.1| 64 YCPKCGNNEVYYWTMQT 80
                                      48888888887777554 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 2.3
                       Zn_Tnp_IS91 40 yeCeeCgh 47
                                      y+C++Cg 
  gi|385806138|ref|YP_005842536.1| 91 YKCTKCGY 98
                                      77888875 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1     0.029       7.5      34      43 ..      11      20 ..       9      24 .. 0.76
   2 ?    4.3   0.1      0.15        40      35      44 ..      63      72 ..      51      75 .. 0.77
   3 ?    6.1   2.1     0.044        12       2      13 ..      91     102 ..      90     104 .] 0.87

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.029
                                      T-BBTTTB-B CS
                        Rubredoxin 34 dWvCPdCgve 43
                                       +vCP+Cg +
  gi|385806138|ref|YP_005842536.1| 11 VYVCPKCGYT 20
                                      5899999876 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.15
                                      -BBTTTB-BG CS
                        Rubredoxin 35 WvCPdCgvek 44
                                        CP+Cg + 
  gi|385806138|ref|YP_005842536.1| 63 VYCPKCGNNE 72
                                      57****9765 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.044
                                       EEETTT-BEEET CS
                        Rubredoxin   2 yeCkvCgyvYdp 13 
                                       y+C+ Cgyv+ +
  gi|385806138|ref|YP_005842536.1|  91 YKCTKCGYVWRE 102
                                       9*******9876 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.2    0.0097       2.5      17      23 ..      12      18 ..      11      19 .. 0.87
   2 ?    8.9   0.6    0.0055       1.4      18      24 .]      64      70 ..      62      70 .. 0.90
   3 ?   -0.3   0.2       4.1   1.1e+03       1       5 [.      93      97 ..      92      99 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0097
                           DUF1610 17 FpCPNCG 23
                                      + CP+CG
  gi|385806138|ref|YP_005842536.1| 12 YVCPKCG 18
                                      78****9 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0055
                           DUF1610 18 pCPNCGE 24
                                      +CP+CG+
  gi|385806138|ref|YP_005842536.1| 64 YCPKCGN 70
                                      7*****7 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 4.1
                           DUF1610  1 CtSCG 5 
                                      Ct CG
  gi|385806138|ref|YP_005842536.1| 93 CTKCG 97
                                      77787 PP

>> Zn_ribbon_recom  Recombinase zinc beta ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0      0.21        53       7      24 ..      13      30 ..       8      52 .. 0.75
   2 ?    8.2   3.1     0.013       3.5       2      31 ..      59      95 ..      58      98 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.21
                   Zn_ribbon_recom  7 rCgeCGspmtrrkrkgkr 24
                                      +C +CG +  +  +k+++
  gi|385806138|ref|YP_005842536.1| 13 VCPKCGYTEEVEPKKNEY 30
                                      8*****987777666544 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.013
                   Zn_ribbon_recom  2 LsGllrCgeCGsp...mtrrkrk.gkr....hyYrCst 31
                                      L+ +++C +CG++   ++  +++   +    + Y+C +
  gi|385806138|ref|YP_005842536.1| 59 LKDVVYCPKCGNNevyYWTMQTRaA-DepptRFYKCTK 95
                                      7889*********776444444321.234558899987 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1      0.42   1.1e+02      15      20 ..      13      18 ..      10      28 .. 0.88
   2 ?    4.1   0.1      0.17        45      15      21 ..      64      70 ..      54      72 .. 0.88
   3 ?    4.9   0.1       0.1        27      15      22 ..      92      99 ..      90     104 .] 0.80

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.42
                              YhfH 15 kCteCG 20
                                      +C++CG
  gi|385806138|ref|YP_005842536.1| 13 VCPKCG 18
                                      6****9 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.17
                              YhfH 15 kCteCGk 21
                                       C++CG+
  gi|385806138|ref|YP_005842536.1| 64 YCPKCGN 70
                                      5*****8 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.1
                              YhfH 15 kCteCGke 22
                                      kCt+CG +
  gi|385806138|ref|YP_005842536.1| 92 KCTKCGYV 99
                                      7*****76 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1     0.058        15      24      29 ..      14      19 ..      13      36 .. 0.64
   2 ?    5.5   0.1     0.053        14       5      10 ..      64      69 ..      62      71 .. 0.83
   3 ?   -0.1   0.1       2.9   7.7e+02      24      29 ..      93      98 ..      92      99 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.058
                     zf-NADH-PPase 24 CpaCgl 29
                                      Cp Cg+
  gi|385806138|ref|YP_005842536.1| 14 CPKCGY 19
                                      555554 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.053
                     zf-NADH-PPase  5 FCgrCG 10
                                      +C++CG
  gi|385806138|ref|YP_005842536.1| 64 YCPKCG 69
                                      788888 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 2.9
                     zf-NADH-PPase 24 CpaCgl 29
                                      C  Cg+
  gi|385806138|ref|YP_005842536.1| 93 CTKCGY 98
                                      888886 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1      0.17        44      21      28 ..      10      18 ..       4      21 .. 0.75
   2 ?    7.0   0.1     0.027         7      19      29 ..      60      70 ..      53      73 .. 0.76
   3 ?   -0.9   0.1       7.9   2.1e+03      21      28 ..      91      97 ..      77      98 .. 0.64

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.17
                     zinc_ribbon_9 21 dv.lCPhCg 28
                                      dv +CP Cg
  gi|385806138|ref|YP_005842536.1| 10 DVyVCPKCG 18
                                      3446****8 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.027
                     zinc_ribbon_9 19 dsdvlCPhCgg 29
                                       + v+CP Cg+
  gi|385806138|ref|YP_005842536.1| 60 KDVVYCPKCGN 70
                                      56679****97 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 7.9
                     zinc_ribbon_9 21 dvlCPhCg 28
                                       + C  Cg
  gi|385806138|ref|YP_005842536.1| 91 YK-CTKCG 97
                                      24.88886 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1     0.017       4.4      13      26 ..       5      18 ..       1      18 [. 0.75
   2 ?    5.0   5.3     0.057        15       1      29 [.      64     100 ..      64     100 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.017
                          zf-TFIIB 13 erggveidyCpqCr 26
                                      + +g  +++Cp+C+
  gi|385806138|ref|YP_005842536.1|  5 KIDGKDVYVCPKCG 18
                                      567778999***97 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.057
                          zf-TFIIB   1 kCPkCqdele.....eser....ggveidyCpqCrGvW 29 
                                       +CPkC+++ +     +  r        +++C++C+ vW
  gi|385806138|ref|YP_005842536.1|  64 YCPKCGNNEVyywtmQ-TRaadePPTRFYKCTKCGYVW 100
                                       7****99766688642.335654558999999998555 PP

>> zf-ZPR1  ZPR1 zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0      0.13        33      31      56 ..      12      42 ..      10      59 .. 0.63
   2 ?    6.4   0.2     0.028       7.2       2      41 ..      64     101 ..      63     104 .] 0.80

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.13
                           zf-ZPR1 31 feCehCgy......knnevksageieekGkri 56
                                      ++C++Cgy      k+ne k+ ++i++ G++ 
  gi|385806138|ref|YP_005842536.1| 12 YVCPKCGYteevepKKNEYKIVNKIKH-GEKD 42
                                      57*****93333333466666666654.5555 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.028
                           zf-ZPR1   2 lCpsCgkengetrllltkiPyfkeviimsfeCehCgyknn 41 
                                        Cp+Cg  n e + ++++     e     ++C +Cgy  +
  gi|385806138|ref|YP_005842536.1|  64 YCPKCG--NNEVYYWTMQTRAADEPPTRFYKCTKCGYVWR 101
                                       5****8..457777777888899999999*******9655 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   1.0    0.0066       1.7      11      23 ..       8      20 ..       2      20 .. 0.83
   2 ?    3.1   1.4      0.54   1.4e+02      15      21 ..      63      69 ..      35      71 .. 0.79
   3 ?    8.4   0.5     0.012       3.1      12      22 ..      88      98 ..      82      99 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0066
                         zf-H2C2_2 11 gekpyeCplCdka 23
                                      g+  y Cp+C+++
  gi|385806138|ref|YP_005842536.1|  8 GKDVYVCPKCGYT 20
                                      5667*******96 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.54
                         zf-H2C2_2 15 yeCplCd 21
                                      + Cp+C+
  gi|385806138|ref|YP_005842536.1| 63 VYCPKCG 69
                                      68****7 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.012
                         zf-H2C2_2 12 ekpyeCplCdk 22
                                       ++y+C +C++
  gi|385806138|ref|YP_005842536.1| 88 TRFYKCTKCGY 98
                                      356******99 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1         1   2.6e+02      10      15 ..      14      19 ..       9      38 .. 0.66
   2 ?    7.4   1.0     0.014       3.6       8      34 ..      63      98 ..      61     102 .. 0.59

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 1
                                      -TTTS- CS
                    Ribosomal_S27e 10 CpdCen 15
                                      Cp+C+ 
  gi|385806138|ref|YP_005842536.1| 14 CPKCGY 19
                                      555543 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.014
                                      EE-TTTS-EEEEE.........SS-SS-EEESSSTC CS
                    Ribosomal_S27e  8 vkCpdCenetvvF.........shaatvvkCisCgk 34
                                      v Cp+C+n+ v +         + + +  kC +Cg 
  gi|385806138|ref|YP_005842536.1| 63 VYCPKCGNNEVYYwtmqtraadEPPTRFYKCTKCGY 98
                                      789***999987722222222112334567777775 PP

>> DUF3797  Domain of unknown function (DUF3797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   2.5      0.26        68       9      21 ..       6      19 ..       3      51 .. 0.84
   2 ?   12.1   6.4   0.00053      0.14      11      46 ..      60      98 ..      50      99 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.26
                           DUF3797  9 Ldek..YvqCPeCgN 21
                                      +d+k  Y  CP+Cg 
  gi|385806138|ref|YP_005842536.1|  6 IDGKdvY-VCPKCGY 19
                                      6778544.4****95 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00053
                           DUF3797 11 ekYvqCPeCgNnkvlNsegkviiedd...tfyreCkCgf 46
                                      +  v+CP+CgNn v     + +  d+    fy+  kCg+
  gi|385806138|ref|YP_005842536.1| 60 KDVVYCPKCGNNEVYYWTMQTRAADEpptRFYKCTKCGY 98
                                      5579**********9988888777653335888888886 PP

>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1     0.043        11      26      45 ..       7      26 ..       2      37 .. 0.77
   2 ?    6.4   2.2     0.043        11       3      37 ..      63      97 ..      61     102 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.043
                           DUF3268 26 kgkllylCpkCdayvgvhkg 45
                                       gk +y+CpkC+    v+++
  gi|385806138|ref|YP_005842536.1|  7 DGKDVYVCPKCGYTEEVEPK 26
                                      67899******976666554 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.043
                           DUF3268  3 trCpyCGekvilvsaseiYkerskgkllylCpkCd 37
                                      ++Cp CG++ ++    +   + +  + +y C+kC+
  gi|385806138|ref|YP_005842536.1| 63 VYCPKCGNNEVYYWTMQTRAADEPPTRFYKCTKCG 97
                                      68********9999999999999999********8 PP

>> HscB_4_cys  Co-chaperone HscB tetracysteine metal binding motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0      0.14        36      14      23 ..       8      17 ..       2      18 .. 0.82
   2 ?    5.0   0.0     0.083        21      14      23 ..      59      68 ..      55      69 .. 0.84
   3 ?   -0.2   0.5       3.6   9.3e+02       3       8 ..      93      98 ..      92     102 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.14
                                      -S---B-TTT CS
                        HscB_4_cys 14 rgdefFCpqC 23
                                      + d++ Cp+C
  gi|385806138|ref|YP_005842536.1|  8 GKDVYVCPKC 17
                                      579999**** PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.083
                                      -S---B-TTT CS
                        HscB_4_cys 14 rgdefFCpqC 23
                                        d+ +Cp+C
  gi|385806138|ref|YP_005842536.1| 59 LKDVVYCPKC 68
                                      57999***** PP

  == domain 3  score: -0.2 bits;  conditional E-value: 3.6
                                      -SSS-- CS
                        HscB_4_cys  3 CWnCGg 8 
                                      C +CG 
  gi|385806138|ref|YP_005842536.1| 93 CTKCGY 98
                                      889996 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 ?    6.9   0.1    0.0095       2.5     199     227 ..      11      39 ..       3      52 .. 0.85
   2 ?    3.6   0.4     0.099        26     175     208 ..      63      99 ..      49     102 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0095
                      tRNA-synt_1f 199 eYkceecGeeeevdiregngKLqWkvdwa 227
                                        Y+c +cG++eev+ ++ + K+  k+  +
  gi|385806138|ref|YP_005842536.1|  11 VYVCPKCGYTEEVEPKKNEYKIVNKIKHG 39 
                                       599******************99888766 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.099
                      tRNA-synt_1f 175 pvcekcgr..vdttevvevd.aeeeeieYkceecGee 208
                                       ++c+kcg   v + +++    +e  +  Ykc++cG+ 
  gi|385806138|ref|YP_005842536.1|  63 VYCPKCGNneVYYWTMQTRAaDEPPTRFYKCTKCGYV 99 
                                       68888876224444444444035567779*****975 PP

>> eIF-5_eIF-2B  Domain found in IF2B/IF5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.3       2.7     7e+02      89      99 ..      13      23 ..       9      41 .. 0.69
   2 ?   12.0   0.7   0.00055      0.14      74     116 ..      50      98 ..      27      99 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 2.7
                                      STSSSTSTCEE CS
                      eIF-5_eIF-2B 89 lCkeCkspete 99
                                      +C++C+  e  
  gi|385806138|ref|YP_005842536.1| 13 VCPKCGYTEEV 23
                                      48888876644 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00055
                                       CHHHHHHHHHHHHHTSTSSSTSTCEEECC.......SSSCEEEEESSSTC CS
                      eIF-5_eIF-2B  74 kkleklldkyieeyVlCkeCkspetelek.......eerllvlkCkaCga 116
                                       +k+ ++l k +++ V C++C++ e+   +       e  + + kC++Cg 
  gi|385806138|ref|YP_005842536.1|  50 NKIPETLPK-LKDVVYCPKCGNNEVYYWTmqtraadEPPTRFYKCTKCGY 98 
                                       555566655.5788********998765555566666778899*****95 PP

>> Acetone_carb_G  Acetone carboxylase gamma subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2    0.0016      0.41      78     102 ..      12      36 ..       9      44 .. 0.89
   2 ?    1.6   0.5       1.1   2.9e+02      79      85 ..      64      70 ..      54      78 .. 0.85
   3 ?   -1.3   0.1       9.1   2.4e+03      75      85 ..      88      98 ..      69     103 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0016
                                       EE-TTT--EEEEEEE-TT------E CS
                    Acetone_carb_G  78 yycPecgtllevEaltpgyPvihdf 102
                                       y+cP+cg   evE     y ++  +
  gi|385806138|ref|YP_005842536.1|  12 YVCPKCGYTEEVEPKKNEYKIVNKI 36 
                                       9************999999998876 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 1.1
                                      E-TTT-- CS
                    Acetone_carb_G 79 ycPecgt 85
                                      ycP+cg+
  gi|385806138|ref|YP_005842536.1| 64 YCPKCGN 70
                                      9****97 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 9.1
                                      EEEEE-TTT-- CS
                    Acetone_carb_G 75 irEyycPecgt 85
                                       r y c +cg 
  gi|385806138|ref|YP_005842536.1| 88 TRFYKCTKCGY 98
                                      34566777764 PP

>> Ribosomal_L32p  Ribosomal L32p protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1      0.12        32      41      50 ..      13      22 ..       7      28 .. 0.80
   2 ?    4.7   0.1      0.14        37      23      34 ..      59      70 ..      55      74 .. 0.82
   3 ?    0.2   0.0       3.6   9.5e+02      28      47 ..      92      98 ..      82     101 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.12
                                      -BTTTTBSSS CS
                    Ribosomal_L32p 41 vcpscGyYkg 50
                                      vcp+cGy + 
  gi|385806138|ref|YP_005842536.1| 13 VCPKCGYTEE 22
                                      8999998765 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.14
                                      ---EEEETTTCC CS
                    Ribosomal_L32p 23 apnlvecpncge 34
                                       +++v cp+cg+
  gi|385806138|ref|YP_005842536.1| 59 LKDVVYCPKCGN 70
                                      568999****96 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 3.6
                                      EETTTCCEECTTC-BTTTTB CS
                    Ribosomal_L32p 28 ecpncgelklpHrvcpscGy 47
                                      +c++c             Gy
  gi|385806138|ref|YP_005842536.1| 92 KCTKC-------------GY 98
                                      45555.............54 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1      0.13        33      17      30 ..       6      18 ..       4      18 .. 0.77
   2 ?    8.6   0.5    0.0084       2.2      21      30 ..      60      69 ..      32      69 .. 0.75
   3 ?   -1.1   0.1       8.6   2.2e+03      23      30 ..      90      97 ..      78      97 .. 0.61

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.13
                                      HCCSTB-EE-TTT- CS
                         zf-RING_7 17 lragdevvtCpeCG 30
                                      ++++ +v  Cp CG
  gi|385806138|ref|YP_005842536.1|  6 IDGK-DVYVCPKCG 18
                                      5566.59******9 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0084
                                      TB-EE-TTT- CS
                         zf-RING_7 21 devvtCpeCG 30
                                      ++vv+Cp CG
  gi|385806138|ref|YP_005842536.1| 60 KDVVYCPKCG 69
                                      459******9 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 8.6
                                      -EE-TTT- CS
                         zf-RING_7 23 vvtCpeCG 30
                                        +C  CG
  gi|385806138|ref|YP_005842536.1| 90 FYKCTKCG 97
                                      46777777 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 ?    2.8   0.1      0.38     1e+02       8      15 ..      14      21 ..       9      24 .. 0.79
   2 ?    6.6   2.4     0.025       6.4       6      17 ..      63      74 ..      62      97 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.38
                        Zn_Tnp_IS1  8 CPrCsstd 15
                                      CP+C  t+
  gi|385806138|ref|YP_005842536.1| 14 CPKCGYTE 21
                                      ****8776 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.025
                        Zn_Tnp_IS1  6 ihCPrCsstdVy 17
                                      + CP+C  ++Vy
  gi|385806138|ref|YP_005842536.1| 63 VYCPKCGNNEVY 74
                                      78*********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 ?    7.0   0.1     0.017       4.4       2       9 ..      11      18 ..      10      29 .. 0.85
   2 ?    3.6   0.2      0.19        49       3      10 ..      63      70 ..      61      71 .. 0.80
   3 ?    2.7   0.4      0.36        94       3       9 ..      91      97 ..      89      99 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.017
                            zf_UBZ  2 tylCerCg 9 
                                       y+C++Cg
  gi|385806138|ref|YP_005842536.1| 11 VYVCPKCG 18
                                      69*****9 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.19
                            zf_UBZ  3 ylCerCgk 10
                                      + C++Cg 
  gi|385806138|ref|YP_005842536.1| 63 VYCPKCGN 70
                                      57****96 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.36
                            zf_UBZ  3 ylCerCg 9 
                                      y C +Cg
  gi|385806138|ref|YP_005842536.1| 91 YKCTKCG 97
                                      99****8 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 ?    6.7   0.1     0.022       5.8      44      52 ..      11      19 ..       3      21 .. 0.86
   2 ?    1.9   5.1       0.7   1.8e+02      25      52 ..      65      98 ..      54     100 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.022
                    zinc_ribbon_10 44 kyrCpkCga 52
                                       y+CpkCg 
  gi|385806138|ref|YP_005842536.1| 11 VYVCPKCGY 19
                                      59*****97 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.7
                    zinc_ribbon_10 25 CskChshnGlap......keeleevkyrCpkCga 52
                                      C+kC ++  ++        +e+ +  y+C kCg 
  gi|385806138|ref|YP_005842536.1| 65 CPKCGNNEVYYWtmqtraADEPPTRFYKCTKCGY 98
                                      6666665555544444433444455799999996 PP

>> PHD  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1      0.11        28      42      49 ..       9      17 ..       1      20 [. 0.66
   2 ?    5.1   1.9     0.084        22      13      49 ..      60      96 ..      51      98 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.11
                                      S.TBSSTTT CS
                               PHD 42 g.ewlCekC 49
                                      +  ++C+kC
  gi|385806138|ref|YP_005842536.1|  9 KdVYVCPKC 17
                                      248****** PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.084
                                      SCEEEETTTSCEEETTTSSSTHSHHSHHSSTBSSTTT CS
                               PHD 13 eelvqCdgCkrwfHqkClkppleseekpegewlCekC 49
                                      +++v+C +C++    +    +   +e p++ + C+kC
  gi|385806138|ref|YP_005842536.1| 60 KDVVYCPKCGNNEVYYWTMQTRAADEPPTRFYKCTKC 96
                                      6889999998877666666666666777778999999 PP

>> Baculo_ME53  Baculoviridae ME53
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.2      0.13        33     277     295 ..       4      22 ..       1      48 [. 0.74
   2 ?    8.1   3.7    0.0053       1.4     265     304 ..      39      93 ..      26     103 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.13
                       Baculo_ME53 277 klytknPvlscskcGftnv 295
                                       k + ++ v+ c kcG+t+ 
  gi|385806138|ref|YP_005842536.1|   4 KKIDGKDVYVCPKCGYTEE 22 
                                       5556788999999999975 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0053
                       Baculo_ME53 265 edkeycklckktkly....tknPvlscskcGftnvyyft...........eysky 304
                                        +k+   + ++ k+       + v++c kcG  +vyy+t            ++k+
  gi|385806138|ref|YP_005842536.1|  39 GEKDKLIIVDENKIPetlpKLKDVVYCPKCGNNEVYYWTmqtraadepptRFYKC 93 
                                       5555555555666653333446799*************97777777776644444 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 ?    7.8   0.2      0.02       5.2      25      58 ..      10      42 ..       8      63 .. 0.63
   2 ?    4.1   0.3      0.29        75      25      38 ..      61      74 ..      56      94 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.02
                        FYDLN_acid 25 dPivcpkcgeefepeevlksraaaaeaeeakkkk 58
                                      d  vcpkcg + e+e+  k++ +  ++ ++ +k+
  gi|385806138|ref|YP_005842536.1| 10 DVYVCPKCGYTEEVEPK-KNEYKIVNKIKHGEKD 42
                                      5679*****99999988.4444444444443333 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.29
                        FYDLN_acid 25 dPivcpkcgeefep 38
                                      d + cpkcg+    
  gi|385806138|ref|YP_005842536.1| 61 DVVYCPKCGNNEVY 74
                                      6689****986444 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.7     0.032       8.3      16      25 ..      11      20 ..       3      51 .. 0.88
   2 ?    5.3   3.9     0.082        21       1      25 [.      64      99 ..      25     102 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.032
                          zf-Mss51 16 dfeCpdCGip 25
                                       + Cp+CG+ 
  gi|385806138|ref|YP_005842536.1| 11 VYVCPKCGYT 20
                                      599*****96 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.082
                          zf-Mss51  1 lCPvpkhkqt...........apkhvdfeCpdCGip 25
                                      +CP + +++            +p    ++C +CG++
  gi|385806138|ref|YP_005842536.1| 64 YCPKCGNNEVyywtmqtraadEPPTRFYKCTKCGYV 99
                                      5888876666888888888888888889*****986 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.4    0.0092       2.4       1       9 [.      12      20 ..      12      22 .. 0.91
   2 ?    2.2   0.6      0.57   1.5e+02      17      21 ..      65      69 ..      64      72 .. 0.77
   3 ?    6.2   1.4     0.032       8.4       1       9 [.      91      99 ..      91     103 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0092
                      Rubredoxin_2  1 YvCsqCGfe 9 
                                      YvC +CG++
  gi|385806138|ref|YP_005842536.1| 12 YVCPKCGYT 20
                                      9*******8 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.57
                      Rubredoxin_2 17 CpsCg 21
                                      Cp Cg
  gi|385806138|ref|YP_005842536.1| 65 CPKCG 69
                                      88887 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.032
                      Rubredoxin_2  1 YvCsqCGfe 9 
                                      Y C +CG++
  gi|385806138|ref|YP_005842536.1| 91 YKCTKCGYV 99
                                      99*****97 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.7     0.027       7.1       4      19 ..      13      31 ..      10      45 .. 0.71
   2 ?    5.5   0.1      0.11        28       5      14 ..      65      74 ..      61      81 .. 0.82
   3 ?   -0.6   0.2       8.5   2.2e+03       4       9 ..      92      97 ..      89     102 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.027
                           zf-ISL3  4 rCPnCgsktv...vkhgkk 19
                                      +CP+Cg +     +k+ +k
  gi|385806138|ref|YP_005842536.1| 13 VCPKCGYTEEvepKKNEYK 31
                                      7******954366555554 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.11
                           zf-ISL3  5 CPnCgsktvv 14
                                      CP+Cg+  v+
  gi|385806138|ref|YP_005842536.1| 65 CPKCGNNEVY 74
                                      *****98665 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 8.5
                           zf-ISL3  4 rCPnCg 9 
                                      +C +Cg
  gi|385806138|ref|YP_005842536.1| 92 KCTKCG 97
                                      466676 PP

>> Cys_rich_KTR  Cysteine-rich KTR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.8      0.11        29      30      50 ..      14      34 ..      11      37 .. 0.81
   2 ?    8.3   0.0    0.0074       1.9      28      36 ..      63      71 ..      44      86 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.11
                      Cys_rich_KTR 30 CPKCkqetlinvkqlkievik 50
                                      CPKC +   ++ k+ + ++++
  gi|385806138|ref|YP_005842536.1| 14 CPKCGYTEEVEPKKNEYKIVN 34
                                      ****99998888888877776 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0074
                      Cys_rich_KTR 28 LfCPKCkqe 36
                                      ++CPKC ++
  gi|385806138|ref|YP_005842536.1| 63 VYCPKCGNN 71
                                      689999665 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.5      0.12        32       4      14 ..       9      19 ..       7      24 .. 0.82
   2 ?    2.6   0.4       0.4     1e+02       4      14 ..      60      70 ..      57      74 .. 0.78
   3 ?    7.3   0.3     0.013       3.5       6      14 ..      90      98 ..      87     100 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.12
                                      T-EEE-TTT-- CS
                   Desulfoferrod_N  4 levYkCevCGn 14
                                       +vY C  CG 
  gi|385806138|ref|YP_005842536.1|  9 KDVYVCPKCGY 19
                                      58********5 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.4
                                      T-EEE-TTT-- CS
                   Desulfoferrod_N  4 levYkCevCGn 14
                                       +v  C  CGn
  gi|385806138|ref|YP_005842536.1| 60 KDVVYCPKCGN 70
                                      57777*****9 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.013
                                      EEE-TTT-- CS
                   Desulfoferrod_N  6 vYkCevCGn 14
                                       YkC+ CG 
  gi|385806138|ref|YP_005842536.1| 90 FYKCTKCGY 98
                                      6*******6 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   3.3     0.072        19      35      73 ..       9      70 ..       4      74 .. 0.60
   2 ?    7.3   1.8      0.03       7.7      34      74 ..      59      99 ..      51     103 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.072
                    zinc_ribbon_15 35 kpylacskCkslleaskelgkeiekkesse........................kkeCknCgk 73
                                      k +++c kC+++ e + ++++  +  ++++                        + +C++Cg+
  gi|385806138|ref|YP_005842536.1|  9 KDVYVCPKCGYTEEVEPKKNE-YKIVNKIKhgekdkliivdenkipetlpklkdVVYCPKCGN 70
                                      567788888877666553322.22222222344555888887777777777777777777765 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.03
                    zinc_ribbon_15 34 kkpylacskCkslleaskelgkeiekkessekkeCknCgke 74
                                       k +++c kC+++     +++++  ++  ++ ++C +Cg +
  gi|385806138|ref|YP_005842536.1| 59 LKDVVYCPKCGNNEVYYWTMQTRAADEPPTRFYKCTKCGYV 99
                                      46788999998877777767777777788889999999865 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.2     0.016       4.2      38      50 ..      12      24 ..       9      55 .. 0.85
   2 ?    0.6   0.3       2.1   5.5e+02      38      45 ..      91      98 ..      84     102 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.016
                              CpXC 38 atCpkCgatakle 50
                                      ++CpkCg+t ++e
  gi|385806138|ref|YP_005842536.1| 12 YVCPKCGYTEEVE 24
                                      78*****998887 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 2.1
                              CpXC 38 atCpkCga 45
                                      ++C kCg+
  gi|385806138|ref|YP_005842536.1| 91 YKCTKCGY 98
                                      78999997 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 ?    6.1   0.1     0.042        11       3       9 ..      13      19 ..      12      42 .. 0.87
   2 ?    2.0   6.4      0.83   2.2e+02       3      28 ..      64      97 ..      63     101 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.042
                                      E-TTT-- CS
                           ADK_lid  3 vCpkCGr 9 
                                      vCpkCG 
  gi|385806138|ref|YP_005842536.1| 13 VCPKCGY 19
                                      9****95 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.83
                                      E-TTT--..EE.....ETT.T.B--SSTTB-TTT- CS
                           ADK_lid  3 vCpkCGr..sY.....hvv.f.npPkveglCDkCG 28
                                       CpkCG   +Y       +    pP    +C kCG
  gi|385806138|ref|YP_005842536.1| 64 YCPKCGNneVYywtmqT-RaAdEPPTRFYKCTKCG 97
                                      5****976688555541.13358999999999999 PP

>> DUF2719  Protein of unknown function (DUF2719)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.5     0.052        13      19      33 ..       8      22 ..       2      52 .. 0.78
   2 ?    6.1   0.6      0.04        11      18      28 ..      58      68 ..      49      78 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.052
                           DUF2719 19 eedvvlcPkcyfvap 33
                                       +dv +cPkc +   
  gi|385806138|ref|YP_005842536.1|  8 GKDVYVCPKCGYTEE 22
                                      478*******88655 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.04
                           DUF2719 18 reedvvlcPkc 28
                                      + +dvv cPkc
  gi|385806138|ref|YP_005842536.1| 58 KLKDVVYCPKC 68
                                      5689******* PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.2      0.45   1.2e+02       1       7 [.      12      18 ..      12      24 .. 0.80
   2 ?    2.7   0.1       1.1     3e+02       2       8 ..      64      70 ..      63      80 .. 0.79
   3 ?    5.3   0.5      0.17        44       1      11 [.      91     101 ..      91     104 .] 0.82

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.45
                         zf-C2H2_4  1 fkCpiCg 7 
                                      + Cp Cg
  gi|385806138|ref|YP_005842536.1| 12 YVCPKCG 18
                                      89****5 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 1.1
                         zf-C2H2_4  2 kCpiCgk 8 
                                      +Cp Cg 
  gi|385806138|ref|YP_005842536.1| 64 YCPKCGN 70
                                      7****75 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.17
                         zf-C2H2_4   1 fkCpiCgksFs 11 
                                       +kC+ Cg +++
  gi|385806138|ref|YP_005842536.1|  91 YKCTKCGYVWR 101
                                       89****98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1045  (0.0582855); expected 358.6 (0.02)
Passed bias filter:                      680  (0.0379274); expected 358.6 (0.02)
Passed Vit filter:                       131  (0.0073066); expected 17.9 (0.001)
Passed Fwd filter:                        74  (0.00412739); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              69  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 603.23
//
Query:       gi|385806139|ref|YP_005842537.1|  [L=115]
Description: hypothetical protein FFONT_1097 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 780.99
//
Query:       gi|385806140|ref|YP_005842538.1|  [L=98]
Description: RNA polymerase, dimerization [Fervidicoccus fontis Kam940]
Scores for complete 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   78.2   0.1    3.6e-22   77.9   0.1    1.1  1  RNA_pol_L_2  RNA polymerase Rpb3/Rpb11 dimerisation domain
    2.7e-08   33.1   0.0    4.5e-08   32.4   0.0    1.4  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 !   77.9   0.1     4e-26   3.6e-22       1      74 [.      18      91 ..      18      92 .. 0.97

  Alignments for each domain:
  == domain 1  score: 77.9 bits;  conditional E-value: 4e-26
                                      EEEEEEES--HHHHHHHHHHHTTSTTEEEEEEECSSTTTSEEEEEEEESTSS-HHHHHHHHHHHHHHHHHHHHH CS
                       RNA_pol_L_2  1 eltfeingEDhTLgnlLrhlllknpsVefagYkipHPlepkmnlriqtkssnnpleaLkkalkdlldicdelee 74
                                      el++ +++EDhT+gnl+ + l+k ++V +  Y+i+HPl+++m l  +t++s++p+eaLkk++  l+d++ ele 
  gi|385806140|ref|YP_005842538.1| 18 ELEIVLYDEDHTFGNLMAKTLMKIDGVVMSYYRIDHPLKNEMVLYLKTDGSIKPVEALKKGIGLLKDEIRELET 91
                                      6899******************************************************************9986 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 !   32.4   0.0     5e-12   4.5e-08       3      68 ..      22      85 ..      20      86 .. 0.92

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 5e-12
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         RNA_pol_L  3 llrgvdhtlgNaLRrillsevpgvaiea.....pvvkvntdkdklilevetdgslkPeealkeAlkiLkek 68
                                      +l ++dht+gN + ++l+ ++ gv +       p       k++++l  +tdgs+kP ealk+++  Lk+ 
  gi|385806140|ref|YP_005842538.1| 22 VLYDEDHTFGNLMAKTLM-KIDGVVMSYyridhPL------KNEMVLYLKTDGSIKPVEALKKGIGLLKDE 85
                                      56689*************.**99999999888899......99***********************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       946  (0.0527637); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); 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: 0.46u 0.32s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 617.62
//
Query:       gi|385806141|ref|YP_005842539.1|  [L=213]
Description: hypothetical protein FFONT_1099 [Fervidicoccus fontis Kam940]
Scores for complete 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-44  149.6   0.8    8.8e-44  149.3   0.8    1.1  1  DUF2067   Uncharacterized protein conserved in archaea (DUF20


Domain annotation for each model (and alignments):
>> DUF2067  Uncharacterized protein conserved in archaea (DUF2067)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.3   0.8   4.9e-48   8.8e-44       2     186 .]      14     201 ..      13     201 .. 0.98

  Alignments for each domain:
  == domain 1  score: 149.3 bits;  conditional E-value: 4.9e-48
                           DUF2067   2 klndeeeleeflekise.kiksaeevkievegnrllievyGtekeikdiirrikellre.....klkkekrglfkys 72 
                                       ++++++++e+fl++i+  +i  a++v+++++gn++ i+++G++ +++++i+ri++++++      ++ke+rg++ ++
  gi|385806141|ref|YP_005842539.1|  14 RIPKNADVERFLDAIMGsTI--ATQVMYRIKGNSVEIRIIGDPVSVENSIHRIRSAVEDfaikmGYPKEGRGITVFG 88 
                                       799**************888..******************************************************* PP

                           DUF2067  73 lsdllreagapvppdvLvdaLkllGykaelre.envlktnapleevvelaerlseiykelrfknlskaakrvvavvs 148
                                        s+l +++++pvp++ ++++L+l++++++++e e+ l+++ +lee+++la++l + yk++r+ ++     +++av+s
  gi|385806141|ref|YP_005842539.1|  89 -SMLAKSLEVPVPLEGFKRLLELENIDFSYDEkEDLLVIYDDLEELKSLAKDLFDSYKSAREIAR-GIGAEIIAVLS 163
                                       .***************************************************************9.8999******* PP

                           DUF2067 149 vltgldpdevieellekGlLeeeegkivlrkewkkalk 186
                                       v++gl+p+e+++ + e+G++e+ e++++l+ +++kal+
  gi|385806141|ref|YP_005842539.1| 164 VYSGLSPMEIASIGEEEGVFEKIEDMYMLKADKDKALN 201
                                       ***********************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1458.18
//
Query:       gi|385806142|ref|YP_005842540.1|  [L=191]
Description: exosome complex RNA-binding protein Csl4 [Fervidicoccus fontis Kam940]
Scores for complete 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   21.9   0.5    0.00019   21.3   0.5    1.3  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    0.00015   21.5   0.0     0.0025   17.6   0.0    2.7  3  ECR1_N          Exosome complex exonuclease RRP4 N-terminal r
     0.0053   16.6   0.6       0.79    9.7   0.1    2.6  2  zinc_ribbon_4   zinc-ribbon domain
     0.0055   17.0   0.0      0.016   15.5   0.0    1.7  2  S1              S1 RNA binding domain
     0.0065   16.5   0.1       0.01   15.9   0.1    1.3  1  HypA            Hydrogenase/urease nickel incorporation, meta
  ------ inclusion threshold ------
      0.019   14.6   1.2      0.031   13.9   1.2    1.3  1  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
      0.026   14.7   0.8       0.05   13.7   0.8    1.4  1  Zn-ribbon_8     Zinc ribbon domain
      0.032   14.2   1.3      0.054   13.5   1.3    1.3  1  zf-C2HC5        Putative zinc finger motif, C2HC5-type
      0.043   14.4   0.1         10    6.8   0.1    2.4  2  EXOSC1          Exosome component EXOSC1/CSL4
      0.045   13.9   1.3      0.075   13.2   1.3    1.3  1  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
      0.064   13.3   0.2       0.28   11.2   0.0    2.0  2  Med26           TFIIS helical bundle-like domain
      0.068   12.6   6.0       0.58    9.6   6.4    2.1  2  zf-ribbon_3     zinc-ribbon domain
       0.08   13.0   0.4       0.13   12.3   0.4    1.3  1  DZR             Double zinc ribbon
      0.085   13.0   0.2       0.22   11.7   0.2    1.6  1  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
       0.17   11.9   0.3       0.28   11.2   0.3    1.3  1  Zn_Tnp_IS91     Transposase zinc-binding domain
        0.2   11.4   2.2        1.5    8.6   2.2    2.1  1  A2L_zn_ribbon   A2L zinc ribbon domain
       0.44   10.1   3.4         36    4.0   0.1    2.6  1  TF_Zn_Ribbon    TFIIB zinc-binding
       0.67    9.7   6.9        8.1    6.3   2.1    2.4  1  zinc_ribbon_2   zinc-ribbon domain
        1.1    9.4   5.2        3.2    7.9   0.6    2.5  2  zf-ACC          Acetyl-coA carboxylase zinc finger 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 !   21.3   0.5     2e-07   0.00019      30      59 ..     150     178 ..     149     187 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2e-07
                    OrfB_Zn_ribbon  30 tCseCgsknkealsgrtfkCpnCgfeadrD 59 
                                       +Cs+Cg+++++ l++ ++kCp+Cg   +r 
  gi|385806142|ref|YP_005842540.1| 150 SCSKCGAIMQK-LENGKLKCPKCGNIENRK 178
                                       6**********.************999985 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 !   17.6   0.0   2.6e-06    0.0025       2      36 ..       8      43 ..       7      45 .. 0.91
   2 ?   -0.4   0.0       1.1     1e+03      27      37 ..      94     104 ..      84     105 .. 0.66
   3 ?   -0.5   0.0       1.2   1.1e+03       2       8 ..     118     124 ..     118     127 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.6e-06
                                      E-TT-EEEETTTSEE-TTEEE.ETTEEEESSSEEEE CS
                            ECR1_N  2 VtPGevlttdeefmrGhGTYv.rggtiyAsvaGtve 36
                                      + PG+ l+  eef++  G+Y  ++g++++++ G v 
  gi|385806142|ref|YP_005842540.1|  8 AFPGDELAILEEFIPVSGVYSdENGKLRSTLIGKVV 43
                                      67******************55***********995 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.1
                                       EEESSSEEEEE CS
                            ECR1_N  27 iyAsvaGtvev 37 
                                       i A +aG+++v
  gi|385806142|ref|YP_005842540.1|  94 ISAPLAGFLHV 104
                                       36779***997 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1.2
                                       E-TT-EE CS
                            ECR1_N   2 VtPGevl 8  
                                       V+PG+ +
  gi|385806142|ref|YP_005842540.1| 118 VLPGDLV 124
                                       89***87 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.034        32      26      34 ..     149     157 ..     144     159 .. 0.78
   2 !    9.7   0.1   0.00084      0.79      24      34 ..     164     174 ..     161     174 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.034
                     zinc_ribbon_4  26 vrCskCghv 34 
                                       + CskCg++
  gi|385806142|ref|YP_005842540.1| 149 ASCSKCGAI 157
                                       569999987 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00084
                     zinc_ribbon_4  24 vkvrCskCghv 34 
                                       +k++C+kCg++
  gi|385806142|ref|YP_005842540.1| 164 GKLKCPKCGNI 174
                                       79*******86 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       8.1   7.6e+03      29      40 ..      18      29 ..      17      44 .. 0.66
   2 !   15.5   0.0   1.7e-05     0.016      27      62 ..      97     130 ..      94     133 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 8.1
                                      EEEEEGGGSSSS CS
                                S1 29 egfvpaselsrd 40
                                      e f+p+s + +d
  gi|385806142|ref|YP_005842540.1| 18 EEFIPVSGVYSD 29
                                      568888877666 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.7e-05
                                       TEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEE CS
                                S1  27 gvegfvpaselsrdarvedpdevlkvGdevkvkvlk 62 
                                       +  gf+++s+++ +  ++++++ + +Gd vk+k++ 
  gi|385806142|ref|YP_005842540.1|  97 PLAGFLHVSQVDEE--GKNISDYVLPGDLVKAKIIS 130
                                       677*********88..******************85 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   1.1e-05      0.01      71     104 ..     149     183 ..     128     190 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.1e-05
                                       EEETTTS-EEECHHH.HHS-TTTSSS-EEEEESSS CS
                              HypA  71 vrCreCgkefeleek.alrCpkCgsadveivsGee 104
                                       + C++Cg+ +++ e+ +l+CpkCg+ + + +s + 
  gi|385806142|ref|YP_005842540.1| 149 ASCSKCGAIMQKLENgKLKCPKCGNIENRKLSSDY 183
                                       68********96555689******98776666655 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 ?   13.9   1.2   3.3e-05     0.031       6      30 ..     151     174 ..     151     175 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.3e-05
                     zf-NADH-PPase   6 CgrCGaptepaeggwarvCpaCgle 30 
                                       C++CGa +++ e+g ++ Cp Cg++
  gi|385806142|ref|YP_005842540.1| 151 CSKCGAIMQKLENG-KLKCPKCGNI 174
                                       *************8.********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 ?   13.7   0.8   5.3e-05      0.05       8      38 ..     151     178 ..     148     179 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.3e-05
                       Zn-ribbon_8   8 CeeCghefevlqsisdapltaCPeCgs.evrr 38 
                                       C +Cg    +l     + + +CP+Cg  e r+
  gi|385806142|ref|YP_005842540.1| 151 CSKCGAIMQKLE----NGKLKCPKCGNiENRK 178
                                       *****8888776....34677*****988777 PP

>> zf-C2HC5  Putative zinc finger motif, C2HC5-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.3   5.7e-05     0.054      16      42 ..     147     173 ..     140     179 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.7e-05
                          zf-C2HC5  16 aapnClnCGkiiCakeglskpCsfCgs 42 
                                       ++  C +CG i+ + e+ + +C+ Cg+
  gi|385806142|ref|YP_005842540.1| 147 ILASCSKCGAIMQKLENGKLKCPKCGN 173
                                       5678*********************85 PP

>> EXOSC1  Exosome component EXOSC1/CSL4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1     0.011        10       2      44 ..      63     109 ..      62     112 .. 0.79
   2 ?    6.5   0.0     0.013        12      85     108 ..     107     130 ..     103     131 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.011
                                       S-TT-EEEEEEEEEESSEEEEEEEEECTB....SBCCCEEECCCTTS CS
                            EXOSC1   2 PkegdvVLarvtrlrkkqalveilsvege....nnvlsdsgvgange 44 
                                       P+  +vV++ v  ++  +al+ il   +      +  + ++v++++e
  gi|385806142|ref|YP_005842540.1|  63 PRLKSVVIGYVNSVKSDIALITILYDGNLkpisAPLAGFLHVSQVDE 109
                                       8899********************98655555555566677777765 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.013
                                       CSSSTT-GGCTEECTTEEEEEEEE CS
                            EXOSC1  85 tekdrvkviemfrpGDIvraqviS 108
                                       ++ +   + + + pGD+v+a++iS
  gi|385806142|ref|YP_005842540.1| 107 VDEEGKNISDYVLPGDLVKAKIIS 130
                                       56666779999************9 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.3   7.9e-05     0.075      17      40 .]     150     172 ..     146     172 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.9e-05
                     Auto_anti-p27  17 tCpvCgvPLmrdrkggkvyCvaCd 40 
                                       +C++Cg+++ +  ++gk+ C+ C+
  gi|385806142|ref|YP_005842540.1| 150 SCSKCGAIMQKL-ENGKLKCPKCG 172
                                       5********999.689*******6 PP

>> Med26  TFIIS helical bundle-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0003      0.28      14      29 ..      31      47 ..      15      61 .. 0.84
   2 ?   -0.7   0.0       1.6   1.5e+03      18      41 ..     151     179 ..     141     184 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0003
                                      H.HHHHHSHHHHHHHHH CS
                             Med26 14 e.tLkstgIGkvVnalr 29
                                      + +L+st IGkvV+ + 
  gi|385806142|ref|YP_005842540.1| 31 NgKLRSTLIGKVVKDII 47
                                      668***********985 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.6
                                       HHSHHHHHHHHH....H-TTS.-HHHHHH CS
                             Med26  18 stgIGkvVnalr....khkhe.taevktl 41 
                                        ++ G ++ +l     k++++ + e+++l
  gi|385806142|ref|YP_005842540.1| 151 CSKCGAIMQKLEngklKCPKCgNIENRKL 179
                                       57778888888766666777666666666 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   6.4   0.00062      0.58       4      23 ..     150     172 ..     148     173 .. 0.85
   2 ?    7.2   1.3    0.0036       3.4       4      10 ..     167     173 ..     164     176 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00062
                       zf-ribbon_3   4 rCPnCGa.p..lssddnvCpyCG 23 
                                       +C++CGa    l+ +  +Cp+CG
  gi|385806142|ref|YP_005842540.1| 150 SCSKCGAiMqkLENGKLKCPKCG 172
                                       8******7458899999****** PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0036
                       zf-ribbon_3   4 rCPnCGa 10 
                                       +CP+CG+
  gi|385806142|ref|YP_005842540.1| 167 KCPKCGN 173
                                       7999987 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.4   0.00014      0.13      14      36 ..     150     173 ..     144     179 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                               DZR  14 fCseCgtklkavaa.edrCpsCge 36 
                                        Cs+Cg+ +++ ++ + +Cp+Cg 
  gi|385806142|ref|YP_005842540.1| 150 SCSKCGAIMQKLENgKLKCPKCGN 173
                                       599999998877778899999986 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   0.00023      0.22       9      33 ..     149     175 ..     144     184 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00023
                      NOB1_Zn_bind   9 lrChaCfkvtkd..mtkkFCpkCGnkt 33 
                                         C  C  ++++  + k  CpkCGn  
  gi|385806142|ref|YP_005842540.1| 149 ASCSKCGAIMQKleNGKLKCPKCGNIE 175
                                       57********887799********955 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.3    0.0003      0.28      31      71 ..     140     179 ..     136     185 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0003
                       Zn_Tnp_IS91  31 rtaalGfaryeCeeCghekivyfsCksrhCpsCqkkateew 71 
                                       + ++lG+    C++Cg   +     ++  Cp+C++ ++++ 
  gi|385806142|ref|YP_005842540.1| 140 KHSSLGVILASCSKCGAI-MQKLENGKLKCPKCGNIENRKL 179
                                       56789***********74.4555566677*****9998876 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 ?    8.6   2.2    0.0016       1.5       6      31 ..     151     175 ..     148     176 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0016
                     A2L_zn_ribbon   6 CsvCggngiln.seqgylvCieCgasf 31 
                                       Cs+Cg   i++  e g l C++Cg+++
  gi|385806142|ref|YP_005842540.1| 151 CSKCGA--IMQkLENGKLKCPKCGNIE 175
                                       999996..5665999*********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 ?    4.0   0.1     0.038        36      21      30 ..     150     159 ..     149     165 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.038
                                       EESSSSBEEE CS
                      TF_Zn_Ribbon  21 vCtdCGlVle 30 
                                        C++CG++++
  gi|385806142|ref|YP_005842540.1| 150 SCSKCGAIMQ 159
                                       6*****9986 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   2.1    0.0085       8.1       1       7 [.     167     173 ..     167     174 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0085
                     zinc_ribbon_2   1 fCpnCGa 7  
                                       +Cp+CG+
  gi|385806142|ref|YP_005842540.1| 167 KCPKCGN 173
                                       7999997 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.4       0.1        94       4      11 ..     151     158 ..     150     161 .. 0.87
   2 ?    7.9   0.6    0.0034       3.2       3      10 ..     167     174 ..     166     178 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.1
                            zf-ACC   4 CpsCgeml 11 
                                       C +Cg+++
  gi|385806142|ref|YP_005842540.1| 151 CSKCGAIM 158
                                       *****997 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0034
                            zf-ACC   3 KCpsCgem 10 
                                       KCp+Cg++
  gi|385806142|ref|YP_005842540.1| 167 KCPKCGNI 174
                                       9*****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); expected 358.6 (0.02)
Passed Vit filter:                       111  (0.00619109); 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: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1355.13
//
Query:       gi|385806143|ref|YP_005842541.1|  [L=212]
Description: putative DNA methylase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-08   34.7   0.0      4e-08   33.8   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    3.2e-07   30.0   0.0    4.6e-07   29.5   0.0    1.2  1  MTS              Methyltransferase small domain
    5.1e-07   30.3   0.0    9.6e-07   29.4   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    1.5e-06   28.1   0.0    2.1e-06   27.6   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    1.8e-05   24.4   0.0    2.4e-05   24.0   0.0    1.2  1  Cons_hypoth95    Conserved hypothetical protein 95
    0.00012   21.9   0.0    0.00017   21.4   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
     0.0032   17.2   0.0      0.004   16.9   0.0    1.3  1  UPF0020          Putative RNA methylase family UPF0020
     0.0034   16.8   0.1     0.0048   16.3   0.1    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
  ------ inclusion threshold ------
      0.024   13.8   0.0      0.034   13.3   0.0    1.2  1  Methyltransf_3   O-methyltransferase
      0.028   14.0   0.0      0.047   13.3   0.0    1.4  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
       0.19   11.6   0.0       0.21   11.4   0.0    1.2  1  Methyltransf_23  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 !   33.8   0.0   2.5e-11     4e-08       1      94 [.      54     148 ..      54     149 .. 0.92

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 2.5e-11
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEEST.G CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssga.l 74 
                                       +Ld+G GtGrl+l  + + g+ + + ++i++e +e+  + a++ g+  +ve++++d  ++p+ d+s D+ +++   +
  gi|385806143|ref|YP_005842541.1|  54 ILDIGSGTGRLCLGSLIA-GANECVSIEIDDEEIEEQIKYAKKLGIecKVEIIKADGASVPLRDSSLDVTLMN-PpF 128
                                       8***********998888.68***************999999988888************************5.669 PP

                                       GGSSHHHHHHHHHHHHHHEE CS
                   Methyltransf_25  75 hhlsdedlekalkeiarvLk 94 
                                         +++    k+lke+ rv++
  gi|385806143|ref|YP_005842541.1| 129 GSVKRGIDWKFLKEALRVTR 148
                                       9999888889*******987 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0   2.8e-10   4.6e-07      27     127 ..      44     145 ..      33     153 .. 0.80

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 2.8e-10
                                       CHCC..TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTT.TSTTS-E CS
                               MTS  27 lpke..lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvle.eveekkf 98 
                                       l++   +++k+lD+G+G+G l +  + +  + e + +++d + +e   + +++ ++e  ve+++ d+ +  + + ++
  gi|385806143|ref|YP_005842541.1|  44 LQHGliINKKILDIGSGTGRLCLGSLIAGAN-ECVSIEIDDEEIEEQIKYAKKLGIEckVEIIKADGASvPLRDSSL 119
                                       5555557899*********998877776655.678888888889999999999988888999999998735679*** PP

                                       EEEEE---STTTCHCHHHHHHHHHHHHHH CS
                               MTS  99 dlivsNPPfhagkatelavaeeliaeAke 127
                                       d+ ++NPPf + k     + +++++eA +
  gi|385806143|ref|YP_005842541.1| 120 DVTLMNPPFGSVKR---GIDWKFLKEALR 145
                                       *********98777...788888888866 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   5.9e-10   9.6e-07       1      89 [.      55     148 ..      55     149 .. 0.85

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 5.9e-10
                                       EEET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES-CCC- CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg.arvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvssevlhhv 74 
                                       Ld+G+GtGrl+     +g  ++v +++++e ++   + a++ g+  kve+++ad  ++p++d+s D+ +++  +  v
  gi|385806143|ref|YP_005842541.1|  55 LDIGSGTGRLCLGSLIAGaNECVSIEIDDEEIEEQIKYAKKLGIecKVEIIKADGASVPLRDSSLDVTLMNPPFGSV 131
                                       8*********998886778***********99555555555555677*************************99999 PP

                                       ..CCHHHHHHHHHHHEE CS
                   Methyltransf_11  75 ..edpekalkeiaRvLk 89 
                                             k+lke+ Rv +
  gi|385806143|ref|YP_005842541.1| 132 krGIDWKFLKEALRVTR 148
                                       553467999**999986 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   1.3e-09   2.1e-06       4      86 ..      51     136 ..      50     171 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 1.3e-09
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDlil 79 
                                       ++++lD+G+GtG+l++     +    e v+i+i+ e ie   + a+klg++  ve  ++d  + +  l d++ D+ l
  gi|385806143|ref|YP_005842541.1|  51 NKKILDIGSGTGRLCLGSL--IAGANECVSIEIDDEEIEEQIKYAKKLGIEcKVEIIKADGASVP--LRDSSLDVTL 123
                                       689************9766..444577**************************************..99******99 PP

                   Methyltransf_31  80 snevl......na 86 
                                        n ++       +
  gi|385806143|ref|YP_005842541.1| 124 MNPPFgsvkrgID 136
                                       9865544344444 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   1.5e-08   2.4e-05      33     127 ..      41     132 ..      26     167 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.5e-08
                                       HHHHCCC.HCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS- CS
                     Cons_hypoth95  33 Fnilaae.iegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallkla 108
                                          l++  i ++++LD+ +G+G l l  l  ga+++v +e d+e ++   +  ++l++e +++++k d ++  l+  
  gi|385806143|ref|YP_005842541.1|  41 WFALQHGlIINKKILDIGSGTGRLCLGSLIAGANECVSIEIDDEEIEEQIKYAKKLGIECKVEIIKADGASVPLRD- 116
                                       4445555588899*********************************999999*****9998888888888777666. PP

                                       -SS-EEEEEEE--SSSTTC CS
                     Cons_hypoth95 109 kkkeefdivflDPPyakel 127
                                          +++d+  ++PP+ +++
  gi|385806143|ref|YP_005842541.1| 117 ---SSLDVTLMNPPFGSVK 132
                                       ...689*********9876 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 !   21.4   0.0   1.1e-07   0.00017      70     134 ..      46     110 ..      21     117 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.1e-07
                                       T.--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC.SEEEEES-GG CS
                              PCMT  70 e.lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle.nvivvvgDGr 134
                                       + l   +++L++GsG+G l  +l  l+      vsie   e +ee  +  kkl++e +v ++ +DG 
  gi|385806143|ref|YP_005842541.1|  46 HgLIINKKILDIGSGTGRL--CLGSLIAGANECVSIEIDDEEIEEQIKYAKKLGIEcKVEIIKADGA 110
                                       23444589*********86..99999999999************************9*********6 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.5e-06     0.004      79     133 ..      76     130 ..      68     186 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.5e-06
                                       EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE------ CS
                           UPF0020  79 lygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYGe 133
                                        + +++d + ++   + a+k g++ ++e+ +ad a+++l++++ dv + npP+G 
  gi|385806143|ref|YP_005842541.1|  76 CVSIEIDDEEIEEQIKYAKKLGIECKVEIIKADGASVPLRDSSLDVTLMNPPFGS 130
                                       567899999999999***********************9999************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 !   16.3   0.1   2.9e-06    0.0048     161     216 ..      50     105 ..      39     125 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.9e-06
                              PrmA 161 egeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveakleva 216
                                        ++++lD+G G+G L ++++  ga++ v + iD+  ++   + a++ ++e k+e++
  gi|385806143|ref|YP_005842541.1|  50 INKKILDIGSGTGRLCLGSLIAGANECVSIEIDDEEIEEQIKYAKKLGIECKVEII 105
                                       5789******************************9999888888777777777664 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.1e-05     0.034      44     111 ..      47     112 ..      12     119 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.1e-05
                                       HHHT--EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-GGGEEEEES-HHHH CS
                    Methyltransf_3  44 klvnakrvleiGvftGyslLatalalPeDGkilaididreayeialkfiqkagvaekieliegdalkv 111
                                        l+  k++l+iG  tG   L +   +    + ++i+id e+ e   k+ +k g++ k+e+i++d+ +v
  gi|385806143|ref|YP_005842541.1|  47 GLIINKKILDIGSGTGR--LCLGSLIAGANECVSIEIDDEEIEEQIKYAKKLGIECKVEIIKADGASV 112
                                       56678999****98885..5556667777889******************************998765 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 ?   13.3   0.0   2.9e-05     0.047       2      84 ..      52     131 ..      51     163 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.9e-05
                   Methyltransf_15   2 rvilDlfsGaG....GnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdl 74 
                                       + ilD+ sG+G    G  i+ a   ++ ++iei+ e+++   + a+  g++ k+ ++++d  ++   l+ +++  d+
  gi|385806143|ref|YP_005842541.1|  52 KKILDIGSGTGrlclGSLIAGA---NECVSIEIDDEEIEEQIKYAKKLGIECKVEIIKADGASV--PLRDSSL--DV 121
                                       5799*****9944444444444...4679*******************************8764..3344444..99 PP

                   Methyltransf_15  75 vflSpPwGGp 84 
                                        ++ pP G +
  gi|385806143|ref|YP_005842541.1| 122 TLMNPPFGSV 131
                                       9999999976 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00013      0.21      23      59 ..      51      88 ..      21     162 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00013
                   Methyltransf_23 23 ggrvLdiGcGtGillevlrengf.svtgvDlspeavei 59
                                      ++++LdiG GtG+l+      g+ +++ +++++e +e+
  gi|385806143|ref|YP_005842541.1| 51 NKKILDIGSGTGRLCLGSLIAGAnECVSIEIDDEEIEE 88
                                      689***********987777777778888887766654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       788  (0.0439511); expected 358.6 (0.02)
Passed bias filter:                      591  (0.0329634); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1294.02
//
Query:       gi|385806144|ref|YP_005842542.1|  [L=342]
Description: diphthamide synthesis protein [Fervidicoccus fontis Kam940]
Scores for 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-81  274.7   0.0    1.3e-81  274.4   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 !  274.4   0.0     7e-86   1.3e-81       1     295 [.      29     335 ..      29     340 .. 0.91

  Alignments for each domain:
  == domain 1  score: 274.4 bits;  conditional E-value: 7e-86
                   Diphthamide_syn   1 fPegllpdsaeiadileef..gaevvilgDttYGaCcvdevaaehlgadllvHyGhsclspvd......rlpvlYvf 69 
                                       fP+g++ +s +iad l+++  +++++i+++ t+G C++   +a+ lga+l+vH+Gh+++s  +      ++pv+Yv+
  gi|385806144|ref|YP_005842542.1|  29 FPDGFKLFSIAIADYLKNYlkDVKIYISAESTWGGCDIAIEEAKMLGAELIVHFGHTPYSLAEyksileKVPVIYVP 105
                                       9***************999899**************************************655668999*******9 PP

                   Diphthamide_syn  70 veie..ldvehlvetlkknf.kekkkivlvstiqyahaleevkeeleeegyevvkvpqsekplspgevlgctspklk 143
                                       ++ +  l+ ++l++ l +      +k +lvstiq+++al+++++ l+e+g++ + +p+s   +++g+++gc+++ l 
  gi|385806144|ref|YP_005842542.1| 106 GKFKkeLSKSSLISLLFELNkIGASKPALVSTIQHVDALKQIRDFLNERGISAT-IPKS-PLMEEGQIVGCDYSPLI 180
                                       98661155555555555544434788*********************9999888.9999.889************98 PP

                   Diphthamide_syn 144 eeeeevdailyigdgrfhllslmlsnpklpvyrydpyskklteesydakkllrrRyaaiekakdakkvGiivgtlgv 220
                                       + e+++d+++++++g fh+ ++ l + k p++++dpy++k+++ ++++kk+l++Rya++e++k+a+++Gii+gt ++
  gi|385806144|ref|YP_005842542.1| 181 N-EKNYDSVVVVSGGYFHAFGAGLMTMK-PTIKIDPYTDKVENVTENVKKILKKRYATMERSKSAEVWGIIIGTRTG 255
                                       7.589*********************77.************************************************ PP

                   Diphthamide_syn 221 qgrlelverlkkllkeagkksylvlvgelnpakLanfae..idafVlvaCprlsidd..gkeFekPvltpyEleval 293
                                       q+r+ +++ l++l+k++gkk+yl++ + l+ ++L+n+++  ida+V+++Cpr++idd   keFekPvltp E++++l
  gi|385806144|ref|YP_005842542.1| 256 QYRPITIRALESLIKNKGKKYYLFFSKSLTINELRNIDQpkIDAYVVTSCPRIPIDDisEKEFEKPVLTPGEAFMVL 332
                                       *************************************6455***************844689*************** PP

                   Diphthamide_syn 294 g.e 295
                                       + e
  gi|385806144|ref|YP_005842542.1| 333 KgE 335
                                       943 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); 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: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.51
# Mc/sec: 2001.69
//
Query:       gi|385806145|ref|YP_005842543.1|  [L=395]
Description: citrate transporter [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.4e-32  111.5  28.6    1.6e-29  103.0  26.9    2.0  2  CitMHS         Citrate transporter
    1.5e-05   24.3  27.6     0.0073   15.4  11.2    2.9  2  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 !  103.0  26.9   1.8e-33   1.6e-29      22     275 ..       8     312 ..       1     329 [. 0.78
   2 !    8.8   0.1   9.2e-05      0.82     117     168 ..     328     389 ..     310     395 .] 0.84

  Alignments for each domain:
  == domain 1  score: 103.0 bits;  conditional E-value: 1.8e-33
                                       x....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS  22 l....vltieealsgiaspiillllgamiigaaleetGlfdrlaakllrlaggkrdllvllvlltallsafvsndgv 94 
                                            ++ iee+ s+i+ ++i++l+g++ i+a+ e++Gl d l+  +++++++  + ++ ++++ +ll++++ nd++
  gi|385806145|ref|YP_005842543.1|   8 SvaggLVNIEEIPSAIDLNVIFFLIGMFSIIALAESSGLLDLLSHYVISKFKSTYAAIIGTFAFFGLLTSVAVNDTM 84 
                                       1335799*********************************************97778888999999999******** PP

                                       xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................. RF
                            CitMHS  95 vlimipivlslakrlkklppl.lliplalaaniggaltpiGtpttraaarpglslpnlll................. 153
                                       +++  piv  + k   k+p + lli+la++  ig+++tp+G+p            +n+l+                 
  gi|385806145|ref|YP_005842543.1|  85 AVMAPPIVYFISKH-LKIPYRqLLILLAFSITIGSVMTPMGNP------------QNVLIaigsgmsapfiyfieyl 148
                                       99999999999996.8999999*********************............9999988888888888888887 PP

                                       ....xxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxx........... RF
                            CitMHS 154 ....lalllvgllplvllfmfgvalalpvnap........kvkkqkaiieaiarsllpvatillla........... 207
                                           ++ l++  + ++ ++ + +                 k k++k+ i a    +++  +i++++           
  gi|385806145|ref|YP_005842543.1| 149 flptIINLVITSFLVIKIYKIPNNS------IdigtipeeKIKNKKDAILAAIG-IFS--VIVAMIvndilrvmgkp 216
                                       7544333444445555555333333......25555657654444444444444.332..22222246789999999 PP

                                       ..........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx...xxxxxxxxxx RF
                            CitMHS 208 ..........................ykkveWsvlllfaGvfllvgaleqtGilealadll.ga...ggplvalalv 254
                                                                 +k+v+W+++++f+ +f++++++ ++G++  l  ++  +   +   ++  ++
  gi|385806145|ref|YP_005842543.1| 217 sieqigfipfiiasslyffvseprslIKEVDWGTIIFFITMFIAMDGVWKSGVASELLRVFiPSkpsD---TIAPVL 290
                                       9999999999999999999*********************************9999999994445431...333456 PP

                                       xxxxxx.xxxxxxxxxxxxxxx RF
                            CitMHS 255 lglial.lsafisnvavaalma 275
                                       +++i++ ls+++snv+++ l++
  gi|385806145|ref|YP_005842543.1| 291 ISIISIiLSQLFSNVPFVKLFM 312
                                       8888888**********97766 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 9.2e-05
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......................xxxxxxxxxxxxxxx RF
                            CitMHS 117 liplalaaniggaltpiGtpttraaarpglslpnlll......................lalllvgllplvllf 168
                                        i la+++ i g lt++G               n+++                      ++ ll++ ++l++++
  gi|385806145|ref|YP_005842543.1| 328 WISLAMSSTIAGNLTLFGAA------------SNIIIleisesryketipfseffkigfPVTLLNLTIYLFYIY 389
                                       36799***************............*****9999999999999999999999888999889998888 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 !   15.4  11.2   8.1e-07    0.0073     323     458 ..      26     159 ..      21     170 .. 0.74
   2 !    9.3  13.1   5.6e-05       0.5     309     462 ..     236     388 ..     130     393 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.1e-07
                     Na_sulph_symp 323 ntllllgglialakllersgliewlgnklttslsglspavaiiiilslfvlvhylfaSatAttaall.pillavaqa 398
                                       n++++l g+ ++  l e sgl++ l++ ++++ +    + a ii  ++f+ + +  a +  + a+++ pi+  +++ 
  gi|385806145|ref|YP_005842543.1|  26 NVIFFLIGMFSIIALAESSGLLDLLSHYVISKFK---STYAAIIGTFAFFGLLTSVAVNDTM-AVMApPIVYFISKH 98 
                                       788999999999999**************99888...4555555566666777777777655.55551666677777 PP

                     Na_sulph_symp 399 ipgappllvalllalatslagfllpyatgpnp.ivfgagylk.vkdywrlGfilsiigllil 458
                                       + ++p  ++ +lla+++ ++++++p++ ++n+ i+ g+g       +    f+ +ii+l+i 
  gi|385806145|ref|YP_005842543.1|  99 L-KIPYRQLLILLAFSITIGSVMTPMGNPQNVlIAIGSGMSApFIYFIEYLFLPTIINLVIT 159
                                       7.9****************************8356788865414445555566677777665 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 5.6e-05
                     Na_sulph_symp 309 vldWkDivkqktaWntllllgglialakllersgliewlgnklttslsglspavaiiiilslfvlvhylfaSatAtt 385
                                       v +    + ++  W+t++++ ++     +  +sg+ + l  ++++s    s ++a  +++s++ ++  +  S++  +
  gi|385806145|ref|YP_005842543.1| 236 VSEPR-SLIKEVDWGTIIFFITMFIAMDGVWKSGVASELLRVFIPSKP--SDTIA-PVLISIISIILSQLFSNVPFV 308
                                       44444.5566789******999998889999***99999999999988..44443.4444544444455569***** PP

                     Na_sulph_symp 386 aallpillavaqaipgappllvalllalatslagfllpyatgpnpivfga......gylkvkdywrlGfilsiigll 456
                                         ++  +  ++ ++   + ++  ++la+++ +ag l+ ++++ n i++ +      ++++  ++ ++Gf++++++l+
  gi|385806145|ref|YP_005842543.1| 309 KLFMDYMRELGYTA---NNIVPWISLAMSSTIAGNLTLFGAASNIIILEIsesrykETIPFSEFFKIGFPVTLLNLT 382
                                       ******99999998...77899999**********************9863333335788899************** PP

                     Na_sulph_symp 457 illllg 462
                                       i+l  +
  gi|385806145|ref|YP_005842543.1| 383 IYLFYI 388
                                       999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       722  (0.04027); 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):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.50
# Mc/sec: 2381.15
//
Query:       gi|385806146|ref|YP_005842544.1|  [L=170]
Description: 50S ribosomal protein L10e [Fervidicoccus fontis Kam940]
Scores for complete 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  116.0   0.0    1.3e-33  115.8   0.0    1.0  1  Ribosomal_L16  Ribosomal protein L16p/L10e


Domain annotation for each model (and alignments):
>> Ribosomal_L16  Ribosomal protein L16p/L10e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.8   0.0   7.2e-38   1.3e-33       3     131 ..      14     162 ..      12     163 .. 0.95

  Alignments for each domain:
  == domain 1  score: 115.8 bits;  conditional E-value: 7.2e-38
                                       SSXXBSSSXXSSTSXX.XSXXXXXESX........EEEEESSXEEEEHHHHHHHHHHHCTCCCCTSXC...EEXXSX CS
                     Ribosomal_L16   3 rkkyrKsrkryirgvs.tkgtklefgd........ygLvalekgqltaealeaariainrylkkkrgk...klwirv 67 
                                        ++y++++  yi gv+ +k+tk+e+g+        ++L++le+gq++++alea+r+a+++yl+ + g+    l++  
  gi|385806146|ref|YP_005842544.1|  14 SPPYTRKE--YIPGVPqPKITKFEMGNpkldadyiLSLIVLEDGQIRHNALEAMRVAAHKYLTANVGEgnyYLKVTR 88 
                                       679*****..***********************9999**************************999999999***** PP

                                       XXXEEEEE-.....SS-TTTSSSS....XEEEEEEEEEXSSCEEEEE.TTXXXSHHHHHHHHHHHHTSSSXEEE CS
                     Ribosomal_L16  68 fphhpvtkk.....agedRmgkGk....Gkpegwvarvkigqiifei.kagvneeiakealrraasKlpiktki 131
                                       +phh+++++     ag+dR+++G+    Gkp g+++rv++g  ++ +  ++ + e+ak+al++++sK+p++t i
  gi|385806146|ref|YP_005842544.1|  89 YPHHVLRENkmmafAGADRLQDGMrlsfGKPIGTAVRVYKGYDVLVVkVKKEHLEHAKKALKVCSSKIPFPTMI 162
                                       ******************************************999996333599*****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1047.44
//
Query:       gi|385806147|ref|YP_005842545.1|  [L=379]
Description: aminotransferase [Fervidicoccus fontis Kam940]
Scores for 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-45  153.4   0.0      1e-44  153.3   0.0    1.0  1  Aminotran_1_2   Aminotransferase class I and II
    3.8e-07   29.3   0.0    2.1e-06   26.8   0.0    1.9  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 !  153.3   0.0   1.1e-48     1e-44       2     363 .]      12     373 ..      11     373 .. 0.90

  Alignments for each domain:
  == domain 1  score: 153.3 bits;  conditional E-value: 1.1e-48
                                       EEEESSSSSTTSTTSSHHHHHHHHHHHH.HHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHH CS
                     Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaeke.galaggtlneygpidglpeleealakflgrseklklkreaavvvgsGa 77 
                                       +vi ++++e++       + ++  +  +  +++ + + +y+p dg+ el+e++akf+++   +k++++  +vv+ G 
  gi|385806147|ref|YP_005842545.1|  12 EVISFAAGEPDPS---VLPRKIFGELMKeVFEKVELVGNYTPADGAFELREEIAKFMKKYDDVKTDPN-KIVVTIGG 84 
                                       5677777777666...3444444444446777888899********************999*******.88888888 PP

                                       HHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEE CS
                     Aminotran_1_2  78 galiealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilv 154
                                       ++++++l +++ l++gd  ++ +p+y +   +++ +g+ +v +p++   d ++  ++le+ +k+++ ++k++k++++
  gi|385806147|ref|YP_005842545.1|  85 SQALDLLGRIF-LDAGDIAISESPSYVNTLIDWKQYGARIVGVPVD---DSGMITDELEKTVKKLKGERKRVKLVYT 157
                                       88889999999.99******************************66...889***********************85 PP

                                       .ESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-E CS
                     Aminotran_1_2 155 .esphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRv 230
                                         + +NP+G+ + +e  + ll++a +y l+l+ D aY ++ ++ + + +t+  +++e  ++  g++sK +G +G+R+
  gi|385806147|ref|YP_005842545.1| 158 iPTGQNPSGVTMIEERRKHLLEIASQYDLILVEDTAYNHLLYEGQPP-KTLRSMDKEGRVIYSGTFSKILG-TGLRI 232
                                       3799***************************************7654.55888999999************.8**** PP

                                       EEEEEEHHHHHHHHHHHHH..HTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS..TEEEECCS CS
                     Aminotran_1_2 231 Gyilgnaavvsqlrklsrp..flsssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLael..glkvlasq 303
                                       G++ g ++v + ++ ++ p  ++ s+++q++v ++l+   ++ +  +++ + ++ +r+ + ++++e+  glk++++ 
  gi|385806147|ref|YP_005842545.1| 233 GWLEGPSEVMDLIKMVKGPtdMCASTPMQYLVIESLRRGIFE-DAKKKALENYKMKRDIMIKSIEEKlkGLKFTKPI 308
                                       ************999998733666****************86.6999*****************999********** PP

                                       CSSEEEEEETHH.CHHHHHHHHHHTCTEEEEEGGGGTS....TTEEEEECTTS-HHHHHHHHHHH CS
                     Aminotran_1_2 304 sgmflltdlsae.takelskkLleevgvyvtpgtsftv....pgrlRitvAglteeeleelveal 363
                                       +gmf l+ l++  +  +++++Lle++gv+v+p   f++    ++ +R++++ +++e++e+ ++++
  gi|385806147|ref|YP_005842545.1| 309 AGMFILVWLKKGmDGYAFAEELLEKKGVAVVPAAAFYTddsgKEVIRLNFSMVPPEKIEKGISSI 373
                                       ******99999888899*************************99***************998876 PP

>> Aminotran_MocR  Alanine-glyoxylate amino-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0   2.4e-10   2.1e-06     128     406 ..     103     374 ..      98     378 .. 0.71

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 2.4e-10
                                       EEEES--HHHHHHHHHHT-EEEEEEEETTEE-HH....HHHHHHHC-TTEEEEEE-SSS-TTT-----HHHHHHHHT CS
                    Aminotran_MocR 128 lvtvpGydrhfllleelGielltvdlqddGpdvd....aveklvaedasvkGilavpkysnptGetiseevarrlaa 200
                                       +  +p y   ++  +++G +++ v+++d G   d    +v+kl +e   vk ++++p+  np+G t+ ee+ ++l  
  gi|385806147|ref|YP_005842545.1| 103 ISESPSYVNTLIDWKQYGARIVGVPVDDSGMITDelekTVKKLKGERKRVKLVYTIPTGQNPSGVTMIEERRKHLLE 179
                                       567899999999999***************8776222257889999************************9999988 PP

                                       ---SSTT-EEEEE-TTSS-BS.SSSS----HHHHHHHHT-TTSEEEEEESTTTS-TTSS-EEEEE-HHHHHHHHHHH CS
                    Aminotran_MocR 201 lkaaapdfrifaddayavhdlvaeedkdanivalardaGhpdrafvlastskitfaGaGvafvassedniawlkkyl 277
                                       + a+  d+ +  d ay+ h l  e++  + +    r+     r +   + ski  +G  ++ +   ++ +  +k   
  gi|385806147|ref|YP_005842545.1| 180 I-ASQYDLILVEDTAYN-HLL-YEGQPPKTL----RSMDKEGRVIYSGTFSKILGTGLRIGWLEGPSEVMDLIKMVK 249
                                       7.456899999999996.555.566655544....344445588877888999999999999987776665555555 PP

                                       HHC-S---HHHHHHHHHHHHHSTHHHHHHHHHH.HHHHHHHHHHHHHHHHHHTTTSSEEE---SBSS-EEEEESSS- CS
                    Aminotran_MocR 278 GlqsiGpdkveqlrhvkflkdyeGlealmrdha.eliapkfeavlevleaelggaevatwteprGGyfisldtldgv 353
                                       G + +      q   +  l+   G+    +++a e  + k + + + +e++l g     +t+p  G fi +   +g+
  gi|385806147|ref|YP_005842545.1| 250 GPTDMCASTPMQYLVIESLR--RGIFEDAKKKAlENYKMKRDIMIKSIEEKLKGL---KFTKPIAGMFILVWLKKGM 321
                                       55555554444433333332..244333332221333333344455566666655...5789999999987665555 PP

                                       HHH..HHHHHHHCTEE---TTTTSSTT--SSS-EEEE--SSS-HHHHHHHHHHHH CS
                    Aminotran_MocR 354 akr..vvklaeeaGvsltaaGatypaGedpkdrnirlaptlppleevetamdvva 406
                                              +l e+ Gv++ +a a y   +d  +  irl  ++ p e++e+ ++++a
  gi|385806147|ref|YP_005842545.1| 322 DGYafAEELLEKKGVAVVPAAAFYT--DDSGKEVIRLNFSMVPPEKIEKGISSIA 374
                                       4431145799999999999999985..6788889999999999999999888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); 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: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 2469.95
//
Query:       gi|385806148|ref|YP_005842546.1|  [L=56]
Description: hypothetical protein FFONT_1106 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      152  (0.00847788); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 397.83
//
Query:       gi|385806149|ref|YP_005842547.1|  [L=453]
Description: 4-aminobutyrate aminotransferase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.7e-102  343.1   0.0   2.1e-102  342.8   0.0    1.0  1  Aminotran_3    Aminotransferase class-III
  ------ inclusion threshold ------
       0.22   10.6   0.0       0.37    9.9   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 !  342.8   0.0  2.3e-106  2.1e-102       9     406 .]      29     433 ..      24     433 .. 0.94

  Alignments for each domain:
  == domain 1  score: 342.8 bits;  conditional E-value: 2.3e-106
                                       SCEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT- CS
                       Aminotran_3   9 lllvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapk 85 
                                       +++vi+k++G++++d +g++y+D++ s a+ n+Gh + +vvka+k++++++     + l +ep+++lae l++++p+
  gi|385806149|ref|YP_005842547.1|  29 FPIVIKKSKGCRIWDIEGREYIDFLTSAASFNIGHTNDEVVKAIKQAIDDMIDYD-QYLYHEPSIRLAEMLVNIVPG 104
                                       459************************************************8888.********************* PP

                                       ..S.EEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB.-TSEEEE CS
                       Aminotran_3  86 gld.kvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpf.lpevvrl 160
                                       +++ kv++  sG  A+  AlK+a +       t +++i +f++++HG  ++ ls +gs  k +t ++ +  p v+++
  gi|385806149|ref|YP_005842547.1| 105 SYEkKVLYELSGGAANDMALKVALA------FTGRKYIGSFEDSYHGTHYLVLSSSGS-FKPETRYKYNaYPYVYFF 174
                                       **98899999***************......***************************.55566666554999**** PP

                                       -TTBGGGTB-HHHHHH...HHHHHHHHHH..CHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE CS
                       Aminotran_3 161 kypdeevlkeneeeea...alleeleale..kkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivD 232
                                       kypd+++ +   e e+    ll e+e+    ++  +  aA+i+Epiqg+gGv v++++f+ +lr+++++++++li D
  gi|385806149|ref|YP_005842547.1| 175 KYPDTFRRPRGIEPEEygeILLGEIERTLqvDAYGKGFAAIIFEPIQGDGGVLVPPKSFIVGLRKIADEYGIVLIDD 251
                                       ******99877655550005555666555788999****************************************** PP

                                       -TTTTTTTTSSSSGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTSB--TTTT-HHHHHHHHHHHHHHH CS
                       Aminotran_3 233 EvqtGfGrTGklfAlehagvspDlmtlaKaltgGlplsavlataevmqalapgshgsTfgGnplacavalavleiie 309
                                       E+qtGfGrTGk+fA+eh+g++pD++tl+K l++G+p+sav++++e+ +   p+  gs  +G  l   +a+a +e i 
  gi|385806149|ref|YP_005842547.1| 252 EIQTGFGRTGKMFAIEHFGIEPDVVTLGKNLGAGFPMSAVVGRKEIIDSGPPNTLGSNASGHYLGSIAAMAGIEYII 328
                                       ***************************************************************************** PP

                                       HTTHHHHHHHHHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTC......HHHHHHHHHCTEE-EEETT. CS
                       Aminotran_3 310 eekllenaqelgaalkegLeelqkkyevikevRgkGlmiaielkeeaevke......keilkkakekGvlilsaGd. 379
                                       ++ l ++a+ +g++l ++L+el++ +e +++vRgkGlmi++e++++++  +      ++i+ +a e+G++++++G+ 
  gi|385806149|ref|YP_005842547.1| 329 KNRLHDRAELMGEYLMKRLNELKDGHEIVGDVRGKGLMIGVEIVDDKDSLKpsskkaQKIIWRAYENGLIMMTFGKy 405
                                       *********************************************99976689999999****************** PP

                                       .TEEEE---TT--HHHHHHHHHHHHHHH CS
                       Aminotran_3 380 .nvirllppliitdeeidelleilkkal 406
                                        nv+r++ppl+i+ eeid+++ei++ka+
  gi|385806149|ref|YP_005842547.1| 406 gNVLRIAPPLTIEREEIDKAVEIMEKAI 433
                                       *************************997 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   4.1e-05      0.37     164     241 ..     228     299 ..     188     428 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 4.1e-05
                                       B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHH CS
                     Aminotran_1_2 164 vatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavv 240
                                       v+++  ++ l ++a++y+++l+ De+  gf  + + ++  ++++e+++      +l+K++G+ G+ + +++g ++++
  gi|385806149|ref|YP_005842547.1| 228 VPPKSFIVGLRKIADEYGIVLIDDEIQTGFGRTGKMFAIEHFGIEPDVV-----TLGKNLGA-GFPMSAVVGRKEII 298
                                       5667778888888*******************98877555999999855.....******95.77888888877776 PP

                                       H CS
                     Aminotran_1_2 241 s 241
                                       +
  gi|385806149|ref|YP_005842547.1| 299 D 299
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 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:                        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: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 2663.37
//
Query:       gi|385806150|ref|YP_005842548.1|  [L=101]
Description: 50S ribosomal protein L21e [Fervidicoccus fontis Kam940]
Scores for complete 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  120.2   1.2    3.2e-35  120.0   1.2    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 !  120.0   1.2   1.8e-39   3.2e-35       2      99 ..       3      97 ..       2      99 .. 0.97

  Alignments for each domain:
  == domain 1  score: 120.0 bits;  conditional E-value: 1.8e-39
                                      --S-STTTT-TTTTS--GGG-S.S--SHHHH----TT-EEEE---TT--SS---GGGTT-EEEE..EEEETTEEEEEEE CS
                    Ribosomal_L21e  2 knskglrrgtrklfskkfrkkg.vpplstylreykkGdkVdikidpsvqkgmphkryhGktgrvynvtkravgvivnkk 79
                                      k++kg+r++trklf+k++r++g vp+ls ++ +y++GdkV i i+ps++kgmph+r+hG+tg++  v++r++++iv+  
  gi|385806150|ref|YP_005842548.1|  3 KAPKGYRHRTRKLFKKDIRERGgVPSLSLLMIKYNVGDKVMIYINPSIHKGMPHRRFHGRTGVI--VGRRGRAYIVELY 79
                                      789******************9999***************************************..************* PP

                                      ETTE..EEEEEE-GGGEEE- CS
                    Ribosomal_L21e 80 vggkileKriivriehlkks 99
                                       g+   +++++vr+eh++++
  gi|385806150|ref|YP_005842548.1| 80 EGSV--KRTLFVRPEHIRPL 97
                                      *999..************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 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:                        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 0.26s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 692.02
//
Query:       gi|385806151|ref|YP_005842549.1|  [L=108]
Description: hypothetical protein FFONT_1109 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-07   30.9   4.1    4.7e-07   30.2   4.1    1.4  1  RNA_pol_Rpb4  RNA polymerase Rpb4
     0.0059   15.6   1.2     0.0062   15.5   1.2    1.0  1  mTERF         mTERF
  ------ inclusion threshold ------
      0.011   15.5   0.3      0.013   15.2   0.3    1.2  1  IL31          Interleukin 31
      0.037   13.7   0.4       0.29   10.8   0.0    2.2  2  Nucleolin_bd  Nucleolin binding domain
      0.057   14.0   0.9      0.087   13.4   0.9    1.5  1  NPA           Nematode polyprotein allergen ABA-1
      0.077   13.4   0.0        0.1   13.0   0.0    1.3  1  Radical_SAM   Radical SAM superfamily


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 !   30.2   4.1   1.6e-10   4.7e-07      42     122 ..      29     107 ..       7     108 .] 0.91

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 1.6e-10
                                       CHHHHHHHHHHHCTHHTTSSHHHHHHHHHHHTTSTSTHHHHHHHHHCSTSSHHHHHHHSTTGTTTSTSHHHHHHHHH CS
                      RNA_pol_Rpb4  42 nkilkktleyltnkfsrlkneekfnelvellksfeLtkaEklqlvnlkPesavelktlieeleerfedeqleeiLde 118
                                       + i+kk+ eyl+    ++k +e+++e++e+lk+ ++ +  +++++n +P++ +el++l ++  + +  e++e+ +++
  gi|385806151|ref|YP_005842549.1|  29 SIIIKKVEEYLSA-VRKCK-AENIKEILEELKKLSIPEELAVMIINVLPTESAELRALLPQQYQSLPSETVEKAVEI 103
                                       568889889***9.88888.9*******************************************************9 PP

                                       HHHH CS
                      RNA_pol_Rpb4 119 lkev 122
                                       ++++
  gi|385806151|ref|YP_005842549.1| 104 VSKC 107
                                       9986 PP

>> mTERF  mTERF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   1.2   2.1e-06    0.0062      58     132 ..       2      81 ..       1     107 [. 0.69

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.1e-06
                             mTERF  58 PkiLskkleeslsksvdflkeikvdkss..igellrslplilgskvenkiknlvevLrelGvpkkllarllisrpq. 131
                                       P+i+  k   s s+  ++lk+ + dk s  i++++  l+ + ++k en ik++ e L++l +p++l + ++   p  
  gi|385806151|ref|YP_005842549.1|   2 PRIIVSKEYLSNSQLEELLKSSSFDKDSiiIKKVEEYLSAVRKCKAEN-IKEILEELKKLSIPEELAVMIINVLPTe 77 
                                       999999999999999999999955554411566666778888888888.***************9988877655544 PP

                             mTERF 132 ...v 132
                                          +
  gi|385806151|ref|YP_005842549.1|  78 saeL 81 
                                       4442 PP

>> IL31  Interleukin 31
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.3   4.4e-06     0.013      58     108 ..      28      78 ..       7      92 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.4e-06
                              IL31  58 nninssailaylkaikplldnksdideiieqLkklklqnepevni..svPtns 108
                                       + i +  +  yl a+++     ++i+ei+e+Lkkl++ +e+ v i  + Pt+s
  gi|385806151|ref|YP_005842549.1|  28 DSIIIKKVEEYLSAVRKC--KAENIKEILEELKKLSIPEELAVMIinVLPTES 78 
                                       33446899*********9..7889****************9998733357766 PP

>> Nucleolin_bd  Nucleolin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   9.8e-05      0.29       3      40 ..      22      59 ..      20      60 .. 0.91
   2 ?    0.4   0.1      0.18   5.2e+02      56      66 ..      96     106 ..      94     107 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9.8e-05
                      Nucleolin_bd  3 rsgsfsDkrLvqRveqyLesnedseyvDvdamaaeLqr 40
                                      +s++  D+ +++ ve+yL++ ++++  +++++ +eL++
  gi|385806151|ref|YP_005842549.1| 22 SSSFDKDSIIIKKVEEYLSAVRKCKAENIKEILEELKK 59
                                      567779******************************97 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.18
                      Nucleolin_bd  56 qVekayeiile 66 
                                        Veka+ei+++
  gi|385806151|ref|YP_005842549.1|  96 TVEKAVEIVSK 106
                                       69*****9986 PP

>> NPA  Nematode polyprotein allergen ABA-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.9   2.9e-05     0.087      13      61 ..       9      56 ..       7     107 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.9e-05
                               NPA 13 kWlteeqkaeikalkeagasseeiekkvlefyealeadkkeeareklkg 61
                                      ++l++ q++e+ +  +  ++s  i kkv+e+++a+ + k e+++e l++
  gi|385806151|ref|YP_005842549.1|  9 EYLSNSQLEELLKSSSFDKDS-IIIKKVEEYLSAVRKCKAENIKEILEE 56
                                      689*******99888888888.99******************9998875 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.4e-05       0.1     116     158 ..      37      80 ..       5      85 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.4e-05
                                       HHHHHHTCTSHHHHHHHHHHHHHHTTSET..EEEEEEEBTTTSHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx RF
                       Radical_SAM 116 kvlklmnrghtfeevlealeklreagikr..vvdrivglpGende 158
                                       ++l  + r+   e ++e le l+++ i++   v +i +lp e+ e
  gi|385806151|ref|YP_005842549.1|  37 EYLSAV-RKCKAENIKEILEELKKLSIPEelAVMIINVLPTESAE 80 
                                       377888.99**********************9********99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1277  (0.0712254); expected 358.6 (0.02)
Passed bias filter:                      708  (0.0394891); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 703.43
//
Query:       gi|385806152|ref|YP_005842550.1|  [L=227]
Description: hypothetical protein FFONT_1110 [Fervidicoccus fontis Kam940]
Scores for 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-57  192.1   0.2    9.8e-57  191.8   0.2    1.1  1  DUF655    Protein of unknown function (DUF655)
     0.0016   18.7   0.1     0.0049   17.1   0.1    1.8  1  HHH_6     Helix-hairpin-helix motif
  ------ inclusion threshold ------
       0.18   12.4   0.8        2.9    8.6   0.4    2.5  2  HHH_5     Helix-hairpin-helix domain


Domain annotation for each model (and alignments):
>> DUF655  Protein of unknown function (DUF655)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.8   0.2   1.6e-60   9.8e-57       3     180 ..      24     206 ..      22     207 .. 0.95

  Alignments for each domain:
  == domain 1  score: 191.8 bits;  conditional E-value: 1.6e-60
                                       -EEEEEEEETT--TT--S-GGG---EEEEEETTT--EEEEEE-TT----TT-EEE-SSS--SS..EEEEEEE--GGG CS
                            DUF655   3 eeaivLDylpeGypddkhrehrdkpvvqalgereltLlelvplkevdilkldevaigkgksdk..ivkikreisyed 77 
                                       ++a+vLD+lp+G+p dkh ehr+ p++q++g +++tL+elv+ +  ++++ ++++ g +  +k  i++i  +isyed
  gi|385806152|ref|YP_005842550.1|  24 DVAVVLDFLPHGNPFDKHVEHRRVPLAQVVGYKYFTLFELVVPEGENFEVGEKIYAGPDYVGKgpIKSIFGPISYED 100
                                       689*******************************************************9866555************ PP

                                       S-HHHHHHHHHHHHHHHHTTHHHHHHHH-----B-SSSBGGGGSTT--HHHHHHHHHHHHHS---SHHHHHHHST.. CS
                            DUF655  78 LtdvaraeLpdvvekivkekEdrfveffneaepitiRlHaLelLpgvgkklarkileeRerrrFesFedvkkrvk.. 152
                                       Lt va+++L  v+ +i+ke+E+ f +ffn+a +it+R+H LelLpg+gk++++ +l+eR+r++FesFed+ +r+   
  gi|385806152|ref|YP_005842550.1| 101 LTTVAKENLVSVLSQIIKENEKYFLKFFNNAGSITLRMHMLELLPGIGKRTLNVMLDERKRKPFESFEDIVQRLTir 177
                                       ************************************************************************98633 PP

                                       ..T---HHHHHHHHHHHHHH-TTSS--SS- CS
                            DUF655 153 ..glkdpaeilverileEiedktekYylFv 180
                                          +++ +++++eri++E+ +  e+YylF+
  gi|385806152|ref|YP_005842550.1| 178 gvKIHNIEKVIAERIVKELIGG-ERYYLFI 206
                                       334899**************99.9*****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 !   17.1   0.1   8.1e-07    0.0049      30      75 ..     142     188 ..     128     202 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 8.1e-07
                             HHH_6  30 aaikglgeaaaerivaeRekegpfksledlarrvds..lnkrqleaLa 75 
                                       + + g+g+++++ +++eR+ ++pf+s+ed+++r+    ++ +++e+ +
  gi|385806152|ref|YP_005842550.1| 142 ELLPGIGKRTLNVMLDERK-RKPFESFEDIVQRLTIrgVKIHNIEKVI 188
                                       55679*************9.8************997788888887766 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.9   1.1e+04      24      39 ..      96     111 ..      90     117 .. 0.68
   2 ?    8.6   0.4   0.00049       2.9       7      55 ..     144     196 ..     139     196 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.9
                                       -SHHHHHHS-HHHHHT CS
                             HHH_5  24 esvedlaaadveeLak 39 
                                        s+edl   ++e L +
  gi|385806152|ref|YP_005842550.1|  96 ISYEDLTTVAKENLVS 111
                                       5777777666666655 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00049
                                       STT--HHHHHHHHTT...T.--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHH CS
                             HHH_5   7 vsGiGpktAlallsa...G.iesvedlaaadveeLakipGiGkktAeriilel 55 
                                       ++GiG++t   +l+      +es+ed+++  + +  ki+ i k  Aeri+ el
  gi|385806152|ref|YP_005842550.1| 144 LPGIGKRTLNVMLDErkrKpFESFEDIVQRLTIRGVKIHNIEKVIAERIVKEL 196
                                       68888888888888754423568889988888888999999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 1419.71
//
Query:       gi|385806153|ref|YP_005842551.1|  [L=288]
Description: dimethyladenosine transferase [Fervidicoccus fontis Kam940]
Scores for 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  122.2   1.1    2.3e-35  122.0   1.1    1.0  1  RrnaAD          Ribosomal RNA adenine dimethylase
      0.005   16.3   0.3      0.011   15.2   0.0    1.6  2  Methyltransf_4  Putative methyltransferase
  ------ inclusion threshold ------
      0.057   13.2   0.0      0.098   12.4   0.0    1.3  1  PCMT            Protein-L-isoaspartate(D-aspartate) O-methylt


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 !  122.0   1.1   3.8e-39   2.3e-35       3     261 ..      31     280 ..      29     284 .. 0.91

  Alignments for each domain:
  == domain 1  score: 122.0 bits;  conditional E-value: 3.8e-39
                                       CCXXGCG--EE--HHHHHHHHHHH-GG.TTSEEEEES-TTTCCHHHHHCC-..SEEEEE-S-HHHHHHHHCHTTTCC CS
                            RrnaAD   3 klrksygqnflknkkvineIldklnle.ekltvleigpGkGilTeeLakra..kqvvvlElderLakllqkklskde 76 
                                       k +k+++qnf+++++ i+  +++l l  +   ++eig+G G lT+ +   +   +   +E+d +L+ + +  ++ ++
  gi|385806153|ref|YP_005842551.1|  31 KPKKKLSQNFTIDPNYIETFIKELSLIdNLEWMVEIGTGIGTLTKAVSYAFssSNIITIEKDASLFSIISSIIE-ER 106
                                       5689*********************9945556***************7777789*****************665.** PP

                                       CEEEE-S-CCGHHHHHHHCTTTCCCCEEEEEEE--TTTHHHHHHHHHHGGGGCEEEEEEEEEHHHHHHHH--TTSTT CS
                            RrnaAD  77 klkvvhqDflkfetpeevtekdsihqeflvvanlPyeistqlvkqlleesrfglvkmllwlqkefarrllarpgskk 153
                                       ++ ++ +D+l               +   v++++P  i+++++ +    + +  ++m+l +qke+a+rl+a+ gsk+
  gi|385806153|ref|YP_005842551.1| 107 NVYLILADALGIVPSI---------KTSVVFSSTPFSITSPIIIKACRNNNI--KNMILGMQKEVAERLVAATGSKS 172
                                       **********986655.........6779******************85555..*********************** PP

                                       -SHHHHHHHHHEEEEEEEEC-GGCECS--SSSEEEEEEEE-SS-S--S-HHHHHHHHHHHHCTTTSBCCCHCCCTST CS
                            RrnaAD 154 rsrlsvlreaftdvklvakveksifsPppkvdsalvelerkdedlpqkdlkkyesvvrkllnrkrktlstslksllp 230
                                       ++rls+l+++++++++v    +++f P+pkv  ++v l+rk++  + k    +e+++++++ +++k+ ++++k+ l+
  gi|385806153|ref|YP_005842551.1| 173 YGRLSILAQLLFEIRIVRSFTPKSFFPEPKVSVSIVSLKRKKNY-DTKVHFLLEKLTSCVFSQRNKNSRKVFKQCLE 248
                                       *******************************************7.9999999**********************999 PP

                                       CHHHHHCTT..T--TTTCCCCSGHHHHHHHHH CS
                            RrnaAD 231 ggelqalsst.gindnalvkklsaeqtldifk 261
                                         +l+ +    ++ +n++v +ls+ ++ +i+ 
  gi|385806153|ref|YP_005842551.1| 249 TLKLNCIDYIeKLLENKRVRELSPWEMEEISR 280
                                       99988885556999999999999988877765 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.8e-06     0.011       5      64 ..      63     119 ..      59     127 .. 0.86
   2 ?   -2.9   0.0      0.69   4.1e+03      51      74 ..     245     268 ..     231     271 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.8e-06
                                       EEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCHH CS
                    Methyltransf_4   5 vleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgdalkvl 64 
                                       ++eiG+G G+++ a + ++ + n++ iE+  ++   + + ie+   +N++++  dal ++
  gi|385806153|ref|YP_005842551.1|  63 MVEIGTGIGTLTKAVSYAFSSSNIITIEKDASLFSIISSIIEE---RNVYLILADALGIV 119
                                       79***************************99998877777776...58888888887655 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.69
                                       SSEEEEES-CCCHHHHCS-TTSEE CS
                    Methyltransf_4  51 kNlrilrgdalkvllelledgsle 74 
                                       + l+ l+ + ++++++lle+++++
  gi|385806153|ref|YP_005842551.1| 245 QCLETLKLNCIDYIEKLLENKRVR 268
                                       446666777777777777777665 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 ?   12.4   0.0   1.6e-05     0.098      49     120 ..      35     105 ..      15     119 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.6e-05
                                       EEETTEEE--HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHH CS
                              PCMT  49 sigynatiSaphmvalalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkk 120
                                       ++++n ti   ++ +++ el  +++ + ++e+G+G G lt  ++  + ++  +++ie+ ++l +  +  +++
  gi|385806153|ref|YP_005842551.1|  35 KLSQNFTIDPNYIETFIKELSLIDNLEWMVEIGTGIGTLTKAVSYAFSSSN-IITIEKDASLFSIISSIIEE 105
                                       6788899998888888888888*******************9999998887.*******9998876666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       749  (0.0417759); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); 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: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1712.96
//
Query:       gi|385806154|ref|YP_005842552.1|  [L=211]
Description: putative methylase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.3e-11   41.8   0.0    1.1e-10   41.4   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    1.3e-09   37.8   0.0    2.9e-08   33.4   0.0    2.0  1  MTS              Methyltransferase small domain
    1.4e-05   24.8   0.0      2e-05   24.4   0.0    1.1  1  Cons_hypoth95    Conserved hypothetical protein 95
     0.0007   19.5   0.0     0.0018   18.1   0.0    1.7  1  Methyltransf_23  Methyltransferase domain
      0.003   17.4   0.0      0.013   15.3   0.0    1.9  1  Methyltransf_31  Methyltransferase domain
     0.0062   16.3   0.0     0.0088   15.8   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
  ------ inclusion threshold ------
      0.011   15.7   0.0       0.02   14.8   0.0    1.4  1  Methyltransf_18  Methyltransferase domain
      0.028   15.1   0.0      0.072   13.8   0.0    1.7  2  Methyltransf_25  Methyltransferase domain
      0.083   12.6   0.1       0.12   12.1   0.1    1.2  1  Methyltransf_16  Lysine methyltransferase
      0.085   12.3   0.0       0.11   11.9   0.0    1.3  1  TehB             Tellurite resistance protein TehB
       0.16   10.9   0.0       0.22   10.4   0.0    1.2  1  Methyltransf_9   Protein of unknown function (DUF1698)


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 !   41.4   0.0     7e-14   1.1e-10     148     233 ..      27     118 ..      25     119 .. 0.80

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 7e-14
                              PrmA 148 Tklclealekl..vkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNael.Nkveaklevalseel 221
                                       T + le l ++  + ++++vlD+GtGSGi+a+ ++ Lga++vva+D++ +A  ++  N++   k +++++v + +++
  gi|385806154|ref|YP_005842552.1|  27 TYMILEYLSSHpeIVKNKKVLDIGTGSGIIALHSLVLGASDVVATDVNCLASYSTCLNLSSfDKQQERFSVVIGNKV 103
                                       678888888876666889****************************************9761556669998654444 PP

                              PrmA 222 l...keekadvivaN 233
                                       +   +++ +d i+ N
  gi|385806154|ref|YP_005842552.1| 104 TflrSRSGFDTIIIN 118
                                       434336788888877 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   1.8e-11   2.9e-08      20     107 ..      27     121 ..      19     193 .. 0.76

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 1.8e-11
                                       HHHHHHHCHCC....TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC...EEEEE-ST CS
                               MTS  20 sklLletlpke....lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle...vevvasdv 89 
                                       + ++le+l+++    +++kvlD+G+G G+++++ +    + +v+++dv+  A  s+  nl++ + +    +vv  + 
  gi|385806154|ref|YP_005842552.1|  27 TYMILEYLSSHpeivKNKKVLDIGTGSGIIALHSLVLGAS-DVVATDVNCLASYSTCLNLSSFDKQqerFSVVIGNK 102
                                       5678888988888888999**************9998777.8*************9999987665555766666666 PP

                                       TTTST.TS-EEEEEE---S CS
                               MTS  90 leeve.ekkfdlivsNPPf 107
                                       +  +     fd+i+ NPP+
  gi|385806154|ref|YP_005842552.1| 103 VTFLRsRSGFDTIIINPPY 121
                                       655552678********97 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   1.2e-08     2e-05      39     123 ..      39     121 ..      29     129 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.2e-08
                                       C.HCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--T.TTEEEEES-HHHHCTS--SS-E CS
                     Cons_hypoth95  39 e.iegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelklee.etaelkedaleallklakkkee 113
                                       e +++++vLD+  GsG ++l  l  ga+ +v+ + +  a      nl++++ ++ ++++++ +++  l+++    + 
  gi|385806154|ref|YP_005842552.1|  39 EiVKNKKVLDIGTGSGIIALHSLVLGASDVVATDVNCLASYSTCLNLSSFDKQQeRFSVVIGNKVTFLRSR----SG 111
                                       25899**********************************999999*****999867777777777777655....57 PP

                                       EEEEEE--SS CS
                     Cons_hypoth95 114 fdivflDPPy 123
                                       fd + ++PPy
  gi|385806154|ref|YP_005842552.1| 112 FDTIIINPPY 121
                                       ********** 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   1.1e-06    0.0018      21      91 ..      41     103 ..      28     182 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.1e-06
                   Methyltransf_23  21 raggrvLdiGcGtGillevlrengf.svtgvDlspeaveiaekakkaqkdqfdeqeaaepqgkfdlIvlrev 91 
                                        ++++vLdiG+G+Gi + +    g+ +v++ D ++ a+       + + ++f     +++q++f +++ + v
  gi|385806154|ref|YP_005842552.1|  41 VKNKKVLDIGTGSGIIALHSLVLGAsDVVATDVNCLASYS----TCLNLSSF-----DKQQERFSVVIGNKV 103
                                       5799**********8777666667669******9976664....45555555.....667777777766655 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   7.8e-06     0.013       3     119 ..      42     175 ..      40     208 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 7.8e-06
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseea.ielArenaq.klgldnveFeqgdiee.leklledekfD 76 
                                       k+++vlD+G+G+G ++  l++++   ++vv  D ++ a  + + + ++ +++ +++++ +g+  + l    +++ fD
  gi|385806154|ref|YP_005842552.1|  42 KNKKVLDIGTGSGIIA--LHSLVLGASDVVATDVNCLAsYSTCLNLSSfDKQQERFSVVIGNKVTfLR---SRSGFD 113
                                       89**********8665..5555778899*****99854234444432213344477788888888555...3599** PP

                   Methyltransf_31  77 lilsn.............evl........naladpdkileeiervlkpggilliedprllaelp 119
                                        i+ n               +          + ++ +il ei++ l++gg ll+ + + l +l 
  gi|385806154|ref|YP_005842552.1| 114 TIIINppylpiepknandP-FelqwaggkEGIDFSLSILDEIPEILSSGGTLLLVSSS-LGNLE 175
                                       *****87777766666640.266677888999999******************99998.44433 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   5.4e-06    0.0088      64     132 ..      29     101 ..      23     120 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.4e-06
                                       HHHHHTT....--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC..SEEEEES- CS
                              PCMT  64 lalelle....lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle..nvivvvgD 132
                                       ++le+l+    + k ++vL++G+GsG+ + + + ++g++  vv+ +       ++  nl   d +  + +vv+g 
  gi|385806154|ref|YP_005842552.1|  29 MILEYLSshpeIVKNKKVLDIGTGSGIIA-LHSLVLGAS-DVVATDVNCLASYSTCLNLSSFDKQqeRFSVVIGN 101
                                       6789998888899*************975.344444444.36665544433344445555544443355555555 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.2e-05      0.02      11      88 ..      40     117 ..      32     118 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.2e-05
                   Methyltransf_18  11 lvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniek.agledkievrlsdGleklkeee.vdt 85 
                                       +v k+++v+DiGt  g+++++ +  g a+ v+a+D+n  +  +   n+++  + +++ +v++++ ++ l++++ +dt
  gi|385806154|ref|YP_005842552.1|  40 IV-KNKKVLDIGTGSGIIALHSLVLG-ASDVVATDVNCLASYSTCLNLSSfDKQQERFSVVIGNKVTFLRSRSgFDT 114
                                       34.589**************999766.569*******98888877777773556889*************9988*** PP

                   Methyltransf_18  86 vvi 88 
                                       ++i
  gi|385806154|ref|YP_005842552.1| 115 III 117
                                       *99 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.4e-05     0.072       1      70 [.      46     117 ..      46     131 .. 0.68
   2 ?   -2.2   0.0       4.5   7.3e+03      29      43 ..     146     160 ..     142     197 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.4e-05
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHH...TTTTEEEEESBCCGBSSSTTTEEEEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraee...eglnvefvqgdaedlpfedgsfDlvvs 70 
                                       vLd+G+G+G ++l+ +   g+++v+++D++  +   +  ++++   ++ ++++v g+  ++    + fD +++
  gi|385806154|ref|YP_005842552.1|  46 VLDIGTGSGIIALHSLVL-GASDVVATDVNCLASYSTCLNLSSfdkQQERFSVVIGNKVTFLRSRSGFDTIII 117
                                       9***********999987.79*******985554443333333221333666666666555556667777766 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.5
                                       SSHHHHHHHHHHHHH CS
                   Methyltransf_25  29 iseemleaareraee 43 
                                       +s + l+++ e +++
  gi|385806154|ref|YP_005842552.1| 146 FSLSILDEIPEILSS 160
                                       555555444443332 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   7.6e-05      0.12      31      79 ..      33      74 ..      24      87 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.6e-05
                   Methyltransf_16 31 ylekklakelganelsklsvlELGsGtGlvGlavaellpeakviltDle 79
                                      yl+       + + +++++vl++G G+G++ l    l +  +v+ tD++
  gi|385806154|ref|YP_005842552.1| 33 YLSS------HPEIVKNKKVLDIGTGSGIIALHSLVL-GASDVVATDVN 74
                                      4444......677899*************76655444.99999999987 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   6.6e-05      0.11      24      62 ..      36      75 ..      13     104 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.6e-05
                                      HHCCCS-S-EEEEES-TTSHHHHHHHHTT.-EEEEEES-H CS
                              TehB 24 eavkivkpgkvldlgcgqgrnslylsllg.ydvtawdkne 62
                                      +  +ivk  kvld+g g+g  +l+  +lg  dv a d n 
  gi|385806154|ref|YP_005842552.1| 36 SHPEIVKNKKVLDIGTGSGIIALHSLVLGaSDVVATDVNC 75
                                      55689******************97766636999999884 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 ?   10.4   0.0   0.00014      0.22     108     167 ..      35      92 ..      29     118 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00014
                                       GGGS.--TT-EEEEET-TTSHHHHHHHHCT-SEEEEE---HHHHHHHHHHHCCTTTTSSE CS
                    Methyltransf_9 108 lphlsdlkgrtildvGcgnGyhlwrmvgegaklvvGidPselfliqfeavrkllgedqra 167
                                       + h   +k++++ld+G g+G      +  ga+ vv  d + l    + +  +l++ d+++
  gi|385806154|ref|YP_005842552.1|  35 SSHPEIVKNKKVLDIGTGSGIIALHSLVLGASDVVATDVNCL--ASYSTCLNLSSFDKQQ 92 
                                       5566679***************************99997765..3444444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); 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: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1396.71
//
Query:       gi|385806155|ref|YP_005842553.1|  [L=236]
Description: rRNA methylase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-30  105.6   0.0    3.5e-30  105.0   0.0    1.3  1  SpoU_methylase  SpoU rRNA Methylase family


Domain annotation for each model (and alignments):
>> SpoU_methylase  SpoU rRNA Methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.0   0.0   1.9e-34   3.5e-30       2     142 .]       3     152 ..       2     152 .. 0.90

  Alignments for each domain:
  == domain 1  score: 105.0 bits;  conditional E-value: 1.9e-34
                                       EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHH.EEEESSHHHHHHHHCCCTEE CS
                    SpoU_methylase   2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevle.lkvvdsleealkelkeegfa 77 
                                       +++vlv+ie   NlG+i+R+a++f+++++vlv pr+   + +ea+r++a+a   l+ l+v+++l+eal+ ++ + ++
  gi|385806155|ref|YP_005842553.1|   3 IRLVLVGIEGGANLGMIMRLAENFEVDDVVLVYPREL--DMDEARRFSAKAVGRLDnLVVYKNLDEALSPCDVRVCT 77 
                                       799********************************97..778899***********9***************99666 PP

                                       EEEESTT-SEGC....CSHHH......TTEEEEEEBTTTBS-HHHHCTSSEEEE----TTSSS--HHHHHHHHHH CS
                    SpoU_methylase  78 lvatslkgksls....eidlk......ekvalvfGnEdkGlsnelleladrlvkIpmsgeveSLNvavAvailly 142
                                       +  +sl+g+ l+     +dl+      +k ++vfG+E++Gl++++l+++d + +Ip s e++ LN+a++v+i ly
  gi|385806155|ref|YP_005842553.1|  78 TAKFSLDGDILRstipSYDLPsfleryKKPCIVFGRESSGLTRDELSKCDFVSTIPSSSEYSALNLANSVSIYLY 152
                                       6666668887775333445557778899*********************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        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 0.30s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 1332.73
//
Query:       gi|385806156|ref|YP_005842554.1|  [L=422]
Description: putative pseudouridine synthase PsuX [Fervidicoccus fontis Kam940]
Scores for complete 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-07   29.2   1.0    8.2e-07   29.2   1.0    2.0  2  THUMP          THUMP domain
  ------ inclusion threshold ------
      0.034   14.5   0.0       0.81   10.1   0.0    2.7  2  DUF1456        Protein of unknown function (DUF1456)
      0.056   13.3   0.7       0.13   12.2   0.0    2.0  2  DUF3198        Protein of unknown function (DUF3198)
       0.16   11.9   2.2         12    5.9   0.0    2.8  3  DUF4428        Domain of unknown function (DUF4428)


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 !   29.2   1.0   1.8e-10   8.2e-07       2     140 ..      25     191 ..      24     195 .. 0.81
   2 ?   -0.2   0.2      0.21   9.4e+02      25      75 ..     291     338 ..     280     368 .. 0.67

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 1.8e-10
                                       HHHHHHHHTT.H-SEEEEETTEEEEECTEEEEEETHHHHHHHHHTST.........TECEEEEE.....EEEEESSH CS
                             THUMP   2 eieellkegkvnverveagkgrivvelkgekpeedeellkealekar.........giqrvipv.....cevceadl 64 
                                       ++++ + +g  n+er++a k  i +el ++ ++  ee++ ++le +          +++ v +      c+ c+ +l
  gi|385806156|ref|YP_005842554.1|  25 RMFSSFLKGFTNEERGKAIKIAIAMELIKK-LKSGEEEAGKKLEAISqslgpefdkTLEEVNIKrrtgeCYLCGGKL 100
                                       566777777778888888888888887755.5555555555555555588888888777777778888899999999 PP

                                       HHHHHHHHHHHHHHHHHCT-EEEEEEEESSSTS...............SSHHHHHHHHHHHHHHCCTT-EE-SSS-S CS
                             THUMP  65 edileaakeivkkkfeeeketFaVrvkrrgkhf...............eftsreinrevGkaivektglkVdlenPd 126
                                       ++   + ke+v   +++  e+F V+++  ++ +               e ++ e++revGk+i ++tg    +++P 
  gi|385806156|ref|YP_005842554.1| 101 KKWVSLYKEAVPILKKKSVESFVVGITGSKEIEtkedellrefsidtaESIKSELRREVGKLITSSTGIDAGFTDPG 177
                                       98777777777777777777***********99******************************************** PP

                                       EEEEEEEETTEEEE CS
                             THUMP 127 ivvrveiikdkayi 140
                                        v+ +++  +++ +
  gi|385806156|ref|YP_005842554.1| 178 AVIYIDLKSENLRV 191
                                       *******9998765 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.21
                                       EEECTEEEEEETHHHHHHHHHTSTTECEEEEEEEEEESSHHHHHHHHHHHH CS
                             THUMP  25 vvelkgekpeedeellkealekargiqrvipvcevceadledileaakeiv 75 
                                       ++e+kg+   +d +++ke+ +k r i r++++  +++ + +d    ++e++
  gi|385806156|ref|YP_005842554.1| 291 ILEEKGK--RKDVREIKELDSKKRKIYRIVVA-GDVPLNEKDADTIVRELK 338
                                       4555544..57888888888888888888888.555555555444444444 PP

>> DUF1456  Protein of unknown function (DUF1456)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00018      0.81      42      68 .]      14      40 ..       3      40 .. 0.80
   2 ?    1.0   0.0      0.12   5.4e+02      12      41 ..     307     336 ..     304     380 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00018
                           DUF1456 42 edeegyeeckdqvLesFLnGliikkRG 68
                                      e+ + +  c  ++++sFL+G+++++RG
  gi|385806156|ref|YP_005842554.1| 14 EKYPLCDSCLGRMFSSFLKGFTNEERG 40
                                      55555667999***************9 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.12
                           DUF1456  12 LdlkdedmveifklggvevtkeelsalLkk 41 
                                       Ld k+ ++ +i+ +g+v++++++ + + ++
  gi|385806156|ref|YP_005842554.1| 307 LDSKKRKIYRIVVAGDVPLNEKDADTIVRE 336
                                       78899999***********99999988887 PP

>> DUF3198  Protein of unknown function (DUF3198)
   #    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      23      42 ..      64      83 ..      61      89 .. 0.92
   2 ?   -2.9   0.1       1.5   6.5e+03      19      26 ..     301     308 ..     296     313 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.8e-05
                                      HHHHHHHHHH-SHHHHHHHH CS
                           DUF3198 23 keLekiarklGssYqqrLee 42
                                      k+Le+i++ lG+ + + Lee
  gi|385806156|ref|YP_005842554.1| 64 KKLEAISQSLGPEFDKTLEE 83
                                      89*****************9 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.5
                                       HHHHHHHH CS
                           DUF3198  19 vknlkeLe 26 
                                       v+ +keL+
  gi|385806156|ref|YP_005842554.1| 301 VREIKELD 308
                                       77788887 PP

>> DUF4428  Domain of unknown function (DUF4428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0    0.0027        12      15      34 ..      10      31 ..       4      42 .. 0.75
   2 ?    4.8   0.2    0.0058        26       1      11 [.      92     102 ..      92     110 .. 0.85
   3 ?   -4.0   0.0       3.4   1.5e+04      33      46 ..     214     226 ..     210     227 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0027
                           DUF4428 15 lkleDgy.vCkdClkKl.sefl 34
                                      + + + y +C++Cl++  s+fl
  gi|385806156|ref|YP_005842554.1| 10 ISIMEKYpLCDSCLGRMfSSFL 31
                                      67778888********965543 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0058
                           DUF4428   1 iCaiCgkKigl 11 
                                       +C++Cg+K+++
  gi|385806156|ref|YP_005842554.1|  92 ECYLCGGKLKK 102
                                       6*******987 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 3.4
                           DUF4428  33 flsdvkikkiltle 46 
                                       +++d+k k++l ++
  gi|385806156|ref|YP_005842554.1| 214 WFDDDK-KQQLSVK 226
                                       565665.5888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       816  (0.0455129); expected 358.6 (0.02)
Passed bias filter:                      684  (0.0381505); 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):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2699.92
//
Query:       gi|385806157|ref|YP_005842555.1|  [L=453]
Description: signal recognition 54 kDa protein [Fervidicoccus fontis Kam940]
Scores for complete 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-71  239.4   0.1    3.5e-71  238.9   0.1    1.2  1  SRP54            SRP54-type protein, GTPase domain
      3e-24   85.5   0.6      3e-24   85.5   0.6    2.9  2  SRP_SPB          Signal peptide binding domain
    2.4e-18   66.1   0.3    2.4e-16   59.7   0.0    3.1  3  SRP54_N          SRP54-type protein, helical bundle domain
    9.8e-06   25.6   0.0      3e-05   24.1   0.0    2.0  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
    4.1e-05   23.2   0.2    0.00053   19.6   0.2    2.2  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
    4.6e-05   23.2   0.1    0.00015   21.6   0.0    1.8  2  AAA_30           AAA domain
    7.2e-05   22.1   0.0    0.00012   21.4   0.0    1.4  1  Zeta_toxin       Zeta toxin
    0.00029   20.9   1.0     0.0024   17.9   0.1    2.6  3  ResIII           Type III restriction enzyme, res subunit
    0.00034   20.8   0.0    0.00072   19.7   0.0    1.6  1  AAA_33           AAA domain
    0.00043   20.2   0.0    0.00096   19.1   0.0    1.6  1  MobB             Molybdopterin guanine dinucleotide synthesis
    0.00048   20.5   0.0     0.0012   19.2   0.0    1.7  1  AAA_16           AAA ATPase domain
    0.00052   19.9   0.1     0.0015   18.5   0.0    1.7  1  APS_kinase       Adenylylsulphate kinase
    0.00057   20.2   0.0     0.0046   17.2   0.0    2.3  2  AAA_22           AAA domain
    0.00093   18.3   0.0     0.0021   17.1   0.0    1.5  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
     0.0016   18.5   0.3     0.0092   16.1   0.2    2.3  1  MMR_HSR1         50S ribosome-binding GTPase
     0.0037   17.8   0.0     0.0098   16.4   0.0    1.8  1  AAA_18           AAA domain
     0.0039   16.6   0.1      0.013   14.9   0.1    1.9  1  ATPase           KaiC
     0.0045   17.4   0.1       0.03   14.7   0.0    2.5  1  AAA              ATPase family associated with various cellul
     0.0071   15.8   0.0      0.013   14.9   0.0    1.4  1  ParA             NUBPL iron-transfer P-loop NTPase
     0.0074   16.0   0.2      0.035   13.8   0.0    2.3  3  AAA_24           AAA domain
  ------ inclusion threshold ------
      0.012   15.6   1.4       0.11   12.4   0.0    2.8  3  NTPase_1         NTPase
      0.014   15.8   3.2      0.029   14.8   0.1    2.7  3  AAA_17           AAA domain
      0.014   15.6   0.0      0.033   14.5   0.0    1.6  1  AAA_28           AAA domain
      0.018   14.4   0.0      0.039   13.2   0.0    1.5  1  6PF2K            6-phosphofructo-2-kinase
      0.024   14.7   0.0      0.061   13.3   0.0    1.7  1  AAA_5            AAA domain (dynein-related subfamily)
      0.045   13.4   0.0       0.14   11.8   0.0    1.9  1  Thymidylate_kin  Thymidylate kinase
      0.046   13.6   0.0       0.14   12.1   0.0    1.8  1  AAA_31           AAA domain
      0.048   13.5   0.0        5.1    6.9   0.0    2.6  2  CLP1_P           mRNA cleavage and polyadenylation factor CLP
      0.052   12.7   0.0       0.18   10.9   0.0    1.9  2  G-alpha          G-protein alpha subunit
      0.059   13.1   0.1       0.69    9.6   0.0    2.2  2  VirE             Virulence-associated protein E
      0.059   12.6   0.1      0.084   12.1   0.1    1.3  1  KAP_NTPase       KAP family P-loop domain
      0.067   12.6   0.0       0.15   11.5   0.0    1.6  1  KTI12            Chromatin associated protein KTI12
       0.12   12.1   0.1          6    6.6   0.0    2.4  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
       0.14   12.8   0.1       0.67   10.6   0.0    2.2  1  CdiI_2           CdiI immunity protein
       0.14   11.4   0.0        2.5    7.3   0.0    2.4  1  MipZ             ATPase MipZ
       0.16   11.9   0.1       0.32   10.9   0.1    1.5  1  NACHT            NACHT domain
        0.7   10.4   3.8          8    6.9   1.4    2.7  1  AAA_23           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 !  238.9   0.1   7.1e-74   3.5e-71       2     196 .]     100     296 ..      99     296 .. 0.98

  Alignments for each domain:
  == domain 1  score: 238.9 bits;  conditional E-value: 7.1e-74
                                       EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHH CS
                             SRP54   2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeavek 78 
                                        vi+lvG+qG+GKTtt+aKLa ++k++g++v l+aaDtfRa+A+eQLk+laek+gv++ + k  +dpa++ ++++e 
  gi|385806157|ref|YP_005842555.1| 100 YVIMLVGVQGSGKTTTAAKLAWYYKNRGYRVGLIAADTFRAGAYEQLKQLAEKVGVEFWGDKGLNDPAEISRKGLEY 176
                                       79*************************************************************************** PP

                                       HHHTTSSEEEEEE--SST..THHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSS CS
                             SRP54  79 akeekidvvlvDTaGrlq..ndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltklDgd 153
                                         ++k++++++DTaGr+   ++++l++e+k+i+++vkpdev+lvlda++gq+a+  ak+F+ea+ i+++i+tklDg+
  gi|385806157|ref|YP_005842555.1| 177 HLSKKAEIIIIDTAGRHGygEESKLIDEMKAIADAVKPDEVILVLDASIGQKAYDLAKKFHEATPIGSIIITKLDGT 253
                                       ****************97225789***************************************************** PP

                                       SSTTHHHHHHHHHTS-EEEEE-SSSTTGEEE--HHHHHHHHHT CS
                             SRP54 154 akgGaalsiaaelklPikfigvGekiedleefdperlvsrllg 196
                                       akgG+a+s+ a+++  +kf+g+Gek++++e+f+p++++sr+lg
  gi|385806157|ref|YP_005842555.1| 254 AKGGGAISAIAATGAKVKFVGTGEKVDEIEPFRPKNFASRILG 296
                                       *****************************************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 ?   -0.2   0.1       3.3   1.6e+03      13      37 ..     293     317 ..     288     325 .. 0.63
   2 !   85.5   0.6   6.2e-27     3e-24       3      98 ..     329     429 ..     327     430 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 3.3
                                       HHHCCCCCCHHHHCCC.....H... CS
                           SRP_SPB  13 qikkmGplskllsmiPgmsaeakae 37 
                                       +i  mG+++ +l+ +  ++++++ e
  gi|385806157|ref|YP_005842555.1| 293 RILGMGDIEAILERVYSTMSQNELE 317
                                       6778888888888876655443222 PP

  == domain 2  score: 85.5 bits;  conditional E-value: 6.2e-27
                                       CTHHHHHHHHHHHCCCCCCHHHHCCC.........H.....CCCCCHHHHHHHHHTTSBHHHHHSGCG-...H.HHH CS
                           SRP_SPB   3 tlrdlleqlqqikkmGplskllsmiPgmsae....akae..eeaekklkrieaiidSMTkeErdspekllk.e.sRk 71 
                                       +++ +++q++qi++mGp+ k+l miPg+s +    +     + +ekk++ +  ii+SMT eE+++pe ll+ e sR+
  gi|385806157|ref|YP_005842555.1| 329 NMKLIYKQIKQIRSMGPIGKILRMIPGLSMSlpedE--GalKVSEKKMDMWLNIINSMTYEEMEKPE-LLErEkSRI 402
                                       78889**********************776676443..1568899**********************.555336*** PP

                                       HHHHHHTTS-HHHHHHHHHHHHHHHHH CS
                           SRP_SPB  72 rRiArGsGtsvqevnellkqfeqmkkm 98 
                                       rRiA G+G+  ++v+ell+ ++ +kk+
  gi|385806157|ref|YP_005842555.1| 403 RRIAIGAGVAQEDVRELLNYYNYIKKL 429
                                       *********************999986 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 !   59.7   0.0   4.9e-19   2.4e-16       3      75 .]       6      81 ..       4      81 .. 0.95
   2 ?    2.8   0.0      0.29   1.4e+02      16      52 ..     309     341 ..     298     345 .. 0.79
   3 ?   -1.7   0.0       7.2   3.5e+03      44      56 ..     426     438 ..     423     452 .. 0.55

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 4.9e-19
                                      HHHHHHHHHHCCSSCGHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTS...S-HHHHHHHHHHHHH CS
                           SRP54_N  3 kklnsalkklsgkskideedleealkeleeaLleaDVgvkvvkklienvkkkavgekk...lkpkqqvkkivkdeL 75
                                      +++++a+kk+ ++++  e+ +ee+++el+++L+++DV+vkvv +++++++k+a++ek    +++++ ++kiv++eL
  gi|385806157|ref|YP_005842555.1|  6 SGIKEAIKKFLSSTSPYEQSVEEFIRELQRILIKSDVNVKVVFEFTSKIRKRALEEKPpqgVSRRDWFIKIVYEEL 81
                                      7899***********************************************9999555*****************8 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.29
                                       SCGHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHH CS
                           SRP54_N  16 skideedleealkeleeaLleaDVgvkvvkklienvk 52 
                                       s+ ++  lee    + ++L++ ++++k+  k i++++
  gi|385806157|ref|YP_005842555.1| 309 STMSQNELEE----MADSLMSGNLNMKLIYKQIKQIR 341
                                       5566667777....**************999888886 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 7.2
                                       HHHHHHHHHHHHH CS
                           SRP54_N  44 vkklienvkkkav 56 
                                        kkl++++k+++ 
  gi|385806157|ref|YP_005842555.1| 426 IKKLLKQLKRRKS 438
                                       5566666655443 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 !   24.1   0.0   6.2e-08     3e-05       9      99 ..     109     265 ..     102     374 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 6.2e-08
                                       TSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH............................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................... RF
                              CbiA   9 GvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep............................... 54 
                                       G+GKTt+aa+La + ++rg+rV l+ aD+ +  +   e+l+    +                               
  gi|385806157|ref|YP_005842555.1| 109 GSGKTTTAAKLAWYYKNRGYRVGLIAADTFRAGAY--EQLK----Qlaekvgvefwgdkglndpaeisrkgleyhls 179
                                       99**************************9955543..2222....23335778889999999999999999999999 PP

                                       ..........................................CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS... CS
                                       ..........................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ..........................................dlkrllellealgkkkalllkiagvvlnrvdgene 89 
                                                                                 d+ ++++ + +l kk+  +  i ++++++ dg + 
  gi|385806157|ref|YP_005842555.1| 180 kkaeiiiidtagrhgygeesklidemkaiadavkpdevilvlDA-SIGQKAYDLAKKFHEATPIGSIIITKLDGTAK 255
                                       99999999999999999999999999999999999999998866.44666666666666667777777777777655 PP

                                       -TTCHHHHHH CS
                                       xxxxxxxxxx RF
                              CbiA  90 etllkealee 99 
                                           ++a++ 
  gi|385806157|ref|YP_005842555.1| 256 GGGAISAIAA 265
                                       5555555444 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 !   19.6   0.2   1.1e-06   0.00053       2     155 ..     101     255 ..     100     271 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.1e-06
                                       EEEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCCCCHCCCT.EEEETTTTECCHCTT-HHHHHHHH CS
                              cobW   2 vtvltGflGsGKTtLlnhll..enraglklavivNefgevsiDaellretgveivelenGciCctlredllkeleal 76 
                                       v++l+G  GsGKTt   +l    +++g+++ +i  +    +  ++l + +++  ve+   +       +++++  ++
  gi|385806157|ref|YP_005842555.1| 101 VIMLVGVQGSGKTTTAAKLAwyYKNRGYRVGLIAADTFRAGAYEQLKQLAEKVGVEFWGDKGLND-PAEISRKGLEY 176
                                       789****************999999************9888887777666655677765555555.45555555555 PP

                                       HHHHTT-SEEEEEECT.TTTHHHH.HTT.SHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-H CS
                              cobW  77 eereerldviliEttG.laePapv.aft.eeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKt 150
                                          + + ++i+i t G      ++ ++   + ++++++ d v+ v+Da  + ++  + ++k+++     + ++++K 
  gi|385806157|ref|YP_005842555.1| 177 HLSK-KAEIIIIDTAGrHGYGEESkLIDeMKAIADAVKPDEVILVLDA-SIGQKAYDLAKKFHEATPIGS-IIITKL 250
                                       5555.69*********98888888644459999***************.555788888888888777665.678899 PP

                                       HHHCH CS
                              cobW 151 Dllde 155
                                       D   +
  gi|385806157|ref|YP_005842555.1| 251 DGTAK 255
                                       87655 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0     3e-07   0.00015      20     114 ..     101     207 ..      92     224 .. 0.67
   2 ?   -1.9   0.0       4.6   2.2e+03     110     131 ..     261     282 ..     252     341 .. 0.65

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 3e-07
                            AAA_30  20 vavltGpAGtGKttalkalreaweaaggrviglAptgkaA......kvLaeelgi.....eastiakllkrlk.... 81 
                                       v +l+G+ G+GKtt+ ++l+  ++++g+rv ++A     A      k+Lae++g+     ++ +        +    
  gi|385806157|ref|YP_005842555.1| 101 VIMLVGVQGSGKTTTAAKLAWYYKNRGYRVGLIAADTFRAgayeqlKQLAEKVGVefwgdKGLNDPA-----Eisrk 172
                                       7899**************************9777655444122222345567776334443333333.....24444 PP

                            AAA_30  82 ..grarlepg.tllivDEagmvdtkqlaallkaaek 114
                                         +  +l+++ +++i+D ag  +  +  +l++++++
  gi|385806157|ref|YP_005842555.1| 173 glE-YHLSKKaEIIIIDTAGRHGYGEESKLIDEMKA 207
                                       453.34555559*****9999987777777776655 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.6
                            AAA_30 110 kaaekagakvilvGDerQlasV 131
                                       +a++++gakv +vG  +  + +
  gi|385806157|ref|YP_005842555.1| 261 SAIAATGAKVKFVGTGEKVDEI 282
                                       5566668888888865555544 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   2.6e-07   0.00012      11      62 ..      94     144 ..      87     207 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.6e-07
                        Zeta_toxin  11 psqerPklillgGqpGAGKselaellkdele.rqgnvvrldpDdlRelhPeye 62 
                                        ++++P +i+l+G +G+GK+++a++l+ + + r+ +v  + +D++R+    ye
  gi|385806157|ref|YP_005842555.1|  94 LPKKKPYVIMLVGVQGSGKTTTAAKLAWYYKnRGYRVGLIAADTFRAGA--YE 144
                                       5679*************************99555566678899999854..44 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 ?   -0.9   0.0       3.1   1.5e+03      69     118 ..      10      58 ..       6      74 .. 0.75
   2 !   17.9   0.1   4.9e-06    0.0024      22      61 ..      97     134 ..      74     189 .. 0.78
   3 ?   -0.5   0.0       2.3   1.1e+03     127     159 ..     176     214 ..     141     224 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 3.1
                                       HHHHHGGGGTGG....GEEEESSS-B--.......-SEEEEEHHHHHHTH CS
                            ResIII  69 qtleefkkflseaykeigkkvsgdkkkakekdstnkkilvttiqsldads 118
                                        ++++f + +s++ +++++++++ +++   k++ n k++++ ++++ ++ 
  gi|385806157|ref|YP_005842555.1|  10 EAIKKFLSSTSPYEQSVEEFIRELQRIL-IKSDVNVKVVFEFTSKIRKRA 58 
                                       4667788888888888899998888888.778888899999888888776 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 4.9e-06
                                       .TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEE CS
                            ResIII  22 krdkrglikmaTGtGKTlvaaklierllkkgkeekflflv 61 
                                       k+   ++++   G+GKT +aakl++++++ g+  ++ +++
  gi|385806157|ref|YP_005842555.1|  97 KKPYVIMLVGVQGSGKTTTAAKLAWYYKNRGY--RVGLIA 134
                                       45556779999******************988..555554 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 2.3
                                       HHHTTT-SEEEEETGGGTTS.T......TTHHHHHT--- CS
                            ResIII 127 ellrdrfdviiiDEaHrlgakk......swreilekfke 159
                                         l+++ ++iiiD a r g+ +      ++++i++++k+
  gi|385806157|ref|YP_005842555.1| 176 YHLSKKAEIIIIDTAGRHGYGEesklidEMKAIADAVKP 214
                                       456677779999*99888877333445588888887765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.5e-06   0.00072       1      43 [.     101     148 ..     101     222 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.5e-06
                            AAA_33   1 lvllvGlpGsGKstlaerl...lkklg..avllssdtlrrrlfgtdqq 43 
                                       +++lvG++GsGK+t a +l   +k++g  + l++ dt+r   +++ +q
  gi|385806157|ref|YP_005842555.1| 101 VIMLVGVQGSGKTTTAAKLawyYKNRGyrVGLIAADTFRAGAYEQLKQ 148
                                       89****************977677888777779999999877754443 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 !   19.1   0.0     2e-06   0.00096       1      34 [.     101     134 ..     101     142 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2e-06
                              MobB   1 vlgivgksgsGKTtLleklipelkarglrvgtiK 34 
                                       v+ +vg +gsGKTt   kl    k+rg+rvg+i 
  gi|385806157|ref|YP_005842555.1| 101 VIMLVGVQGSGKTTTAAKLAWYYKNRGYRVGLIA 134
                                       6899***************************995 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   0.0   2.5e-06    0.0012      23     142 ..      98     222 ..      79     224 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.5e-06
                            AAA_16  23 rpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawre 99 
                                        p +++l+G +G+GK++ + +l+ +++ +      g  + l       + a+++ r + ++ql++ ae+  +e w +
  gi|385806157|ref|YP_005842555.1|  98 KPYVIMLVGVQGSGKTTTAAKLAWYYKNR------GYRVGL-------IAADTF-RAGAYEQLKQLAEKVGVEFWGD 160
                                       556799*****************666655......444444.......444555.5577777777777777777777 PP

                            AAA_16 100 kleeala....................avpelagaea....srllellkrllallsrderplvlvlD 142
                                       k +   a                    +++  +        s l +++k++++  ++ ++ ++lvlD
  gi|385806157|ref|YP_005842555.1| 161 KGLNDPAeisrkgleyhlskkaeiiiiDTAGRH---GygeeSKLIDEMKAIADAVKP-DE-VILVLD 222
                                       777666666666666666777777655444444...14558***********99998.76.999999 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0     3e-06    0.0015       2      51 ..      99     148 ..      98     153 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 3e-06
                                       -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT--S CS
                        APS_kinase   2 gvvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLgf 51 
                                       + v++l G+ gsGK+t a +l+ + +++g++v l+  d+ R g +++L +
  gi|385806157|ref|YP_005842555.1|  99 PYVIMLVGVQGSGKTTTAAKLAWYYKNRGYRVGLIAADTFRAGAYEQLKQ 148
                                       789***************************************99998865 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       2.8   1.3e+03      74     134 ..      25      55 ..       3      58 .. 0.53
   2 !   17.2   0.0   9.6e-06    0.0046       4     101 ..      98     191 ..      96     222 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 2.8
                            AAA_22  74 sseellealeqalraravielliiDEaqhlrseealeeLrsllnlsrkgvqliLvGtpelr 134
                                       s ee+++ l++ l +                              s+ +v++++  t ++r
  gi|385806157|ref|YP_005842555.1|  25 SVEEFIRELQRILIK------------------------------SDVNVKVVFEFTSKIR 55 
                                       333333333333333..............................5555555555555555 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 9.6e-06
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevv...fvtlpsstsskdllrellralglelkaerlssee 77 
                                       + ++++++G  G+GKTt++++l+  ++++      r++++   ++ + + + +k+l++++  ++  ++   ++  e 
  gi|385806157|ref|YP_005842555.1|  98 KPYVIMLVGVQGSGKTTTAAKLAWYYKNRG----YRVGLIaadTFRAGAYEQLKQLAEKVGVEFWGDKGL-NDPAEI 169
                                       56899*****************99886554....588888555555555557777777776666544444.345555 PP

                            AAA_22  78 llealeqalraravielliiDEaq 101
                                        ++ le +l+++a   ++iiD a 
  gi|385806157|ref|YP_005842555.1| 170 SRKGLEYHLSKKAE--IIIIDTAG 191
                                       55777777777666..99999775 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   4.3e-06    0.0021      31      66 ..     101     136 ..      94     142 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.3e-06
                                       EEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE- CS
                              MeaB  31 vvGltGvPGaGkstlvealglelrrrGkrvavlavD 66 
                                       v+ l Gv G+Gk t+  +l+  +++rG+rv+++a D
  gi|385806157|ref|YP_005842555.1| 101 VIMLVGVQGSGKTTTAAKLAWYYKNRGYRVGLIAAD 136
                                       78899*****************************98 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.2   1.9e-05    0.0092       2      99 ..     102     234 ..     101     249 .. 0.55

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.9e-05
                                       EEEEESTTSSHHHHHHHHH....TSTEEESSSTTSSSSE.EEEEEE...ETTEE....................... CS
                          MMR_HSR1   2 vaivGrpNvGKStLinalt....gekaivsdkpgtTrdi.negrvk...lkgke....................... 47 
                                       +++vG   +GK+t   +l     ++  +v+ ++  T     ++++k   +   +                       
  gi|385806157|ref|YP_005842555.1| 102 IMLVGVQGSGKTTTAAKLAwyykNRGYRVGLIAADTFRAgAYEQLKqlaE---Kvgvefwgdkglndpaeisrkgle 175
                                       67788888888888888864443234566666666655545555542221...123333333344444444444555 PP

                                       ........EEEEECGGCSSHHHHHH...HHHHHHHHHHCTSEEEEEEETT..TTCSHHHHHHHHH CS
                          MMR_HSR1  48 ........ielvDtpGliegaseek...glgkaflaleeadlillvvdas..eeklkpldeelee 99 
                                               i+++Dt+G  +g  ee    ++ ka+++  + d ++lv+das  +     +  +l++
  gi|385806157|ref|YP_005842555.1| 176 yhlskkaeIIIIDTAG-RHGYGEESkliDEMKAIADAVKPDEVILVLDASigQ-----KAYDLAK 234
                                       55555555********.65344444113666666666667********88543.....3333333 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     2e-05    0.0098       1      67 [.     102     184 ..     102     231 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2e-05
                            AAA_18   1 IlltGtpGvGKttlakeL....skrlgf..............gvnlrdvakenglllevdpealdeskrldedkldk 59 
                                       I+l G++G+GKtt a  L    ++r g+               ++l+++a + g +++ d+  l++  ++ ++ l++
  gi|385806157|ref|YP_005842555.1| 102 IMLVGVQGSGKTTTAAKLawyyKNR-GYrvgliaadtfragaYEQLKQLAEKVGVEFWGDKG-LNDPAEISRKGLEY 176
                                       99****************7764333.557788888888888888888888888888888888.77777777777666 PP

                            AAA_18  60 lldaleen 67 
                                       +l++  e+
  gi|385806157|ref|YP_005842555.1| 177 HLSKKAEI 184
                                       66665554 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   2.7e-05     0.013      21      74 ..     101     157 ..      94     219 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.7e-05
                            ATPase  21 vvlitGepGtGKtifalqFlikgaekygepgvfvtveepa....edlrenakslGwdl 74 
                                       v+ ++G+ G+GKt+ a++ ++   ++ g+++ +++ +       e+l++ a+++G+++
  gi|385806157|ref|YP_005842555.1| 101 VIMLVGVQGSGKTTTAAKLAWYYKNR-GYRVGLIAADTFRagayEQLKQLAEKVGVEF 157
                                       78899****************99666.**********987777899999999999887 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 !   14.7   0.0   6.2e-05      0.03       1      64 [.     102     221 ..     102     296 .. 0.49

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6.2e-05
                                       EEEESSTTSSHHHHHHHHHHHHTHE......................EEEEETTTCS.SS................. CS
                               AAA   1 vllyGppGtGKTllakavakelgve......................fleisgsell.sk................. 37 
                                       ++l+G  G GKT++a  +a   + +                      + e  g e++ +k                 
  gi|385806157|ref|YP_005842555.1| 102 IMLVGVQGSGKTTTAAKLAWYYKNRgyrvgliaadtfragayeqlkqLAEKVGVEFWgDKglndpaeisrkgleyhl 178
                                       689******************86433334444444444444444444333334444433344444444444444444 PP

                                       ...............STTHHHHHHHHHHHHHHHTSTS..EEEEE CS
                               AAA  38 ...............yvgesekkirelfkeakekakp..silfi 64 
                                                        ge +k i e+ + a + + p  +il++
  gi|385806157|ref|YP_005842555.1| 179 skkaeiiiidtagrhGYGEESKLIDEMKAIADAVK-PdeVILVL 221
                                       44444444444444444555555555444444443.22133333 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.8e-05     0.013       8      42 ..     103     137 ..      97     165 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.8e-05
                              ParA   8 vlSgKGGVGKStvavnlAlaLakkglkvgllDaDi 42 
                                       +l g  G GK+t+a++lA+  +++g++vgl+ aD 
  gi|385806157|ref|YP_005842555.1| 103 MLVGVQGSGKTTTAAKLAWYYKNRGYRVGLIAADT 137
                                       55667799***********************9996 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       6.8   3.3e+03     101     135 ..      18      56 ..       7      65 .. 0.61
   2 !   13.8   0.0   7.2e-05     0.035       2      23 ..      99     124 ..      98     212 .. 0.66
   3 ?   -2.7   0.0       8.4   4.1e+03     156     174 ..     312     330 ..     305     340 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 6.8
                            AAA_24 101 gkG.ygelaeefrrllkk.lqelrk..nvifiahektrk 135
                                        +  y +  eef+r l++ l + +    v+f   +k+rk
  gi|385806157|ref|YP_005842555.1|  18 STSpYEQSVEEFIRELQRiLIKSDVnvKVVFEFTSKIRK 56 
                                       445577777888888888444444445666666666665 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 7.2e-05
                            AAA_24   2 klkiliyGpsgiGKTtlakel....g 23 
                                       ++ i+++G +g+GKTt+a++l    +
  gi|385806157|ref|YP_005842555.1|  99 PYVIMLVGVQGSGKTTTAAKLawyyK 124
                                       689****************9944331 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 8.4
                            AAA_24 156 tanelkeevDlvlranlkr 174
                                       ++nel+e++D ++  nl++
  gi|385806157|ref|YP_005842555.1| 312 SQNELEEMADSLMSGNLNM 330
                                       68999****9999888774 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1       1.4   6.7e+02     107     135 ..      22      50 ..      20      63 .. 0.72
   2 ?   12.4   0.0   0.00022      0.11       2      39 ..     102     139 ..     101     145 .. 0.86
   3 ?   -0.9   0.0       2.8   1.4e+03      94     107 ..     180     193 ..     166     240 .. 0.67

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.4
                                       TGGG-HHHHHHHHHHHTTTSEEEEE--SS CS
                          NTPase_1 107 mElkskkfkeaveevLksekpvlavihrr 135
                                        E ++++f+++++++L ++ + + v+ + 
  gi|385806157|ref|YP_005842555.1|  22 YEQSVEEFIRELQRILIKSDVNVKVVFEF 50 
                                       589999*********99666666666554 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00022
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE- CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgGfyteevr 39 
                                       +++ G +G+GKtT   k++   k++g++vg + +   r
  gi|385806157|ref|YP_005842555.1| 102 IMLVGVQGSGKTTTAAKLAWYYKNRGYRVGLIAADTFR 139
                                       7899*************************877666666 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 2.8
                                       HHH-EEEE---STT CS
                          NTPase_1  94 seadviviDEiGkm 107
                                       ++a++i+iD  G+ 
  gi|385806157|ref|YP_005842555.1| 180 KKAEIIIIDTAGRH 193
                                       78999999988875 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       4.9   2.4e+03      72     123 ..      13      62 ..       6      71 .. 0.69
   2 ?   14.8   0.1     6e-05     0.029       1     110 [.     105     223 ..     105     234 .. 0.65
   3 ?   -0.1   0.1       2.5   1.2e+03      35     122 ..     312     401 ..     304     419 .. 0.59

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 4.9
                                       SEEEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHT CS
                            AAA_17  72 kgvlvdghprikeqagfldglpkevleelkpdaiilleadpeeilerrlkdr 123
                                       k++l  + p  +  ++f+ +l++ +l + ++++ +++e   + i++r l+++
  gi|385806157|ref|YP_005842555.1|  13 KKFLSSTSPYEQSVEEFIRELQR-ILIKSDVNVKVVFEFTSK-IRKRALEEK 62 
                                       56777777777777888888876.444556777777777775.888888764 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 6e-05
                                       EE-TTSSHHHHHHHHHHHH...TEEE.EEHHHHHHHHHHTTTSHSSHHHHC.....TSHHHHHHHHHHHHHHHHHHH CS
                            AAA_17   1 lGgPGsGKgtqceklveky...gfth.lsaGdllreeakrgglakardemr.....klpleekkelqkeaaekiaee 68 
                                       +G+ GsGK+t ++kl+  y   g+ + l a d +r+ a ++ l++  +++      +  l++  e+ ++  e    +
  gi|385806157|ref|YP_005842555.1| 105 VGVQGSGKTTTAAKLAWYYknrGYRVgLIAADTFRAGAYEQ-LKQLAEKVGvefwgDKGLNDPAEISRKGLEYHLSK 180
                                       79*************96554346766567788888887544.43444444445666455555555555555544443 PP

                                       HHSSEEEEEE-SEE..EETTEEEESSHHHHHHHH..SEEEE.EE- CS
                            AAA_17  69 akkkgvlvdghpri..keqagfldglpkevleelkpdaiil.lea 110
                                        k + +++d+  r    e+++++d++++ + + +kpd +il l+a
  gi|385806157|ref|YP_005842555.1| 181 -KAEIIIIDTAGRHgyGEESKLIDEMKA-IADAVKPDEVILvLDA 223
                                       .567899998876422455566666654.6788899888773555 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 2.5
                                       HTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHH.HSSEE.EEEE-S.EEEETTEEEESSHHHHHHHH...SEEEE CS
                            AAA_17  35 krgglakardemrklpleekkelqkeaaekiaeea.kkkgv.lvdghp.rikeqagfldglpkevleelkp.daiil 107
                                       ++++l++  d ++ ++l+ k     + +++i+ +    k + ++ g   ++ e++g+l+  +k++   l++ + +++
  gi|385806157|ref|YP_005842555.1| 312 SQNELEEMADSLMSGNLNMKL--IYKQIKQIRSMGpIGKILrMIPGLSmSLPEDEGALKVSEKKMDMWLNIiNSMTY 386
                                       555555555555555544333..333344555554322222355555413456677777778888777777677888 PP

                                       EE--HHHHHHHHHHH CS
                            AAA_17 108 leadpeeilerrlkd 122
                                        e ++ e+ler +++
  gi|385806157|ref|YP_005842555.1| 387 EEMEKPELLEREKSR 401
                                       888887777775544 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   6.7e-05     0.033       2      38 ..     102     145 ..     101     194 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.7e-05
                            AAA_28   2 ivitGgestGKTtlleaLa....argypvv...pEaareileek 38 
                                       i+++G +++GKTt++++La    +rgy+v    ++++r    e+
  gi|385806157|ref|YP_005842555.1| 102 IMLVGVQGSGKTTTAAKLAwyykNRGYRVGliaADTFRAGAYEQ 145
                                       899****************9987779996411355554444444 PP

>> 6PF2K  6-phosphofructo-2-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   8.1e-05     0.039      10      53 ..      96     144 ..      89     160 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.1e-05
                                       ..S-EEEEEESSTTSSHHHHHHHHHHHHHHTT--.....EEEEEHHHHH CS
                             6PF2K  10 knsklvivlvGLpargKtyiskkltrylkwlgvr.....tkvFnvgkyr 53 
                                       k+++ vi+lvG    gKt+++ kl  y k  g+r     + +F +g y 
  gi|385806157|ref|YP_005842555.1|  96 KKKPYVIMLVGVQGSGKTTTAAKLAWYYKNRGYRvgliaADTFRAGAYE 144
                                       57899***********************976665111114555555554 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 ?   13.3   0.0   0.00013     0.061       2      72 ..     102     188 ..     101     193 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00013
                                       EEEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT-....-HHHHH--B--.........--------......... CS
                             AAA_5   2 vlLvGppGtgKselaerlaaal.nreveyvqltrdt....teedlkgrreikngttslvdsplvraar......... 64 
                                       ++LvG +G+gK++ a +la  + nr + + ++ +dt     +e+lk+  e k g + + d+ l + a+         
  gi|385806157|ref|YP_005842555.1| 102 IMLVGVQGSGKTTTAAKLAWYYkNRGYRVGLIAADTfragAYEQLKQLAE-KVGVEFWGDKGLNDPAEisrkgleyh 177
                                       69********************9999999999999844445677777777.57777777777777776666666666 PP

                                       ...G-SEEEEE CS
                             AAA_5  65 ...egeilvlD 72 
                                          ++ei+++D
  gi|385806157|ref|YP_005842555.1| 178 lskKAEIIIID 188
                                       66666666666 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00028      0.14       3      27 ..     106     130 ..     104     137 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00028
                                       ESTTSSHHHHHHHHHHHHHHTTE.E CS
                   Thymidylate_kin   3 GlDGaGKttqaellkerlkeegikv 27 
                                       G+ G+GKtt a++l+ ++k++g++v
  gi|385806157|ref|YP_005842555.1| 106 GVQGSGKTTTAAKLAWYYKNRGYRV 130
                                       99********************985 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00029      0.14      12      40 ..     109     137 ..     101     156 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00029
                            AAA_31  12 GvGKTTtsvnlaaalaklgkkvLlvDlDp 40 
                                       G GKTTt+ +la    ++g++v l+ +D+
  gi|385806157|ref|YP_005842555.1| 109 GSGKTTTAAKLAWYYKNRGYRVGLIAADT 137
                                       89***********************9997 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 ?    3.8   0.0      0.09        44       1      31 [.     106     136 ..     106     140 .. 0.90
   2 ?    6.9   0.0      0.01       5.1      99     141 ..     178     227 ..     163     254 .. 0.64

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.09
                            CLP1_P   1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlD 31 
                                       G + sGK+T a+ L+ y  ++g+++ ++ +D
  gi|385806157|ref|YP_005842555.1| 106 GVQGSGKTTTAAKLAWYYKNRGYRVGLIAAD 136
                                       5689********************9988777 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.01
                            CLP1_P  99 kkakasgliIntpGwvkglg..aell...leliealepdvvv.vldq..ee 141
                                        + ka+++iI+t G  +g+g   +l+   +++++a++pd v+ vld    +
  gi|385806157|ref|YP_005842555.1| 178 LSKKAEIIIIDTAGR-HGYGeeSKLIdemKAIADAVKPDEVIlVLDAsiGQ 227
                                       45589********95.45551134443326789999**6555055554434 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00037      0.18      20      50 ..      96     126 ..      87     240 .. 0.86
   2 ?   -1.2   0.0       1.8   8.6e+02     132     148 ..     409     431 ..     275     452 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00037
                                       E..EEEEEEEESTTSSHHHHHHHHHHHCS-- CS
                           G-alpha  20 kkrevkllllGqseSGKsTilkqlkllykkg 50 
                                       kk+++ ++l+G ++SGK+T+  +l  +yk+ 
  gi|385806157|ref|YP_005842555.1|  96 KKKPYVIMLVGVQGSGKTTTAAKLAWYYKNR 126
                                       567999*****************99999765 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.8
                                       H.....HHHHHCCSH.HHHHHHC CS
                           G-alpha 132 e.....dikaLwndp.giqelye 148
                                             d+++L n +  i++l++
  gi|385806157|ref|YP_005842555.1| 409 AgvaqeDVRELLNYYnYIKKLLK 431
                                       12233355555543325555555 PP

>> VirE  Virulence-associated protein E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.83     4e+02     115     141 ..       8      33 ..       3      41 .. 0.73
   2 ?    9.6   0.0    0.0014      0.69      50      75 ..      97     122 ..      93     128 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.83
                              VirE 115 iKafitrkkdkfrapygrkvedfpres 141
                                       iK++i  k  +   py++ ve+f re 
  gi|385806157|ref|YP_005842555.1|   8 IKEAIK-KFLSSTSPYEQSVEEFIREL 33 
                                       566653.44566789********9974 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0014
                              VirE  50 KfDfvlvLvGkqgsgKstfleklgee 75 
                                       K  +v++LvG qgsgK+t+ +kl+ +
  gi|385806157|ref|YP_005842555.1|  97 KKPYVIMLVGVQGSGKTTTAAKLAWY 122
                                       6679*****************99643 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 ?   12.1   0.1   0.00017     0.084      18     140 ..      97     299 ..      78     404 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00017
                        KAP_NTPase  18 atpivvgLygkWGsGKssllnkledelkefa.............................................. 48 
                                       ++p+v++L g  GsGK++  +kl  ++k++                                               
  gi|385806157|ref|YP_005842555.1|  97 KKPYVIMLVGVQGSGKTTTAAKLAWYYKNRGyrvgliaadtfragayeqlkqlaekvgvefwgdkglndpaeisrkg 173
                                       789***************************99********************************************* PP

                        KAP_NTPase  49 ......kpvrflfaefnawsfkggddavaellaaLadaleeeygqlatkllrakklkalkikgkiklrkacaiplvl 119
                                             k+ ++++++       g+++ + + ++a+ada++ +  +l  +  +++k ++l  k+   +  +++i+++l
  gi|385806157|ref|YP_005842555.1| 174 leyhlsKKAEIIIIDTAGRHGYGEESKLIDEMKAIADAVKPDEVILVLDASIGQKAYDLAKKFHEATPIGSIIITKL 250
                                       ****9988888888888888889999999999999999999999999999999999999999998888999999999 PP

                        KAP_NTPase 120 ilevalflliegasll.avls...........................r 140
                                        +  + +++i++++++ a+++                            
  gi|385806157|ref|YP_005842555.1| 251 DGTAKGGGAISAIAATgAKVKfvgtgekvdeiepfrpknfasrilgmgD 299
                                       8888888877665554133335555555555555555555555555551 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00032      0.15       4      42 ..     102     140 ..      99     154 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00032
                                       EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH. CS
                             KTI12   4 vvltGlPssGKstrakeLakaleeekrsvvviddeslgi 42 
                                       ++l G+  sGK+t a++La + ++++++v +i  ++++ 
  gi|385806157|ref|YP_005842555.1| 102 IMLVGVQGSGKTTTAAKLAWYYKNRGYRVGLIAADTFRA 140
                                       7899****************************9999873 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.012         6       4      21 ..     102     119 ..      99     125 .. 0.89
   2 ?    2.9   0.0      0.17        82      24     102 ..     172     253 ..     166     283 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.012
                         PduV-EutP   4 illiGkvgsGKttLtqal 21 
                                       i+l+G  gsGKtt + +l
  gi|385806157|ref|YP_005842555.1| 102 IMLVGVQGSGKTTTAAKL 119
                                       9************88776 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.17
                         PduV-EutP  24 eelkYkktqaiefsdeviDtPGe..ylenrklysalivt..saeadvialvqdateeesvf..ppgfasvfnkeviG 94 
                                       + l+Y+  +  e+   +iDt G   y e+ kl   ++++  +++ d + lv+da+  ++ +  +++f +      iG
  gi|385806157|ref|YP_005842555.1| 172 KGLEYHLSKKAEII--IIDTAGRhgYGEESKLIDEMKAIadAVKPDEVILVLDASIGQKAYdlAKKFHEAT---PIG 243
                                       55666666666654..89**996558999999988877622578899999999987777661134444333...345 PP

                         PduV-EutP  95 ..iitkidla 102
                                         iitk+d +
  gi|385806157|ref|YP_005842555.1| 244 siIITKLDGT 253
                                       4478888865 PP

>> CdiI_2  CdiI immunity protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0    0.0014      0.67      19      86 ..       3      75 ..       1      79 [. 0.72

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0014
                            CdiI_2 19 legdsieeiledYvssesp..eevaelideieellassldee.leeaflael...gaefdpeawgltarefLee 86
                                       ++++i+e++++++ss+sp  + v+e i+e++++l +s+ +  +  +f +++     e +p+ +g + r+++ +
  gi|385806157|ref|YP_005842555.1|  3 NIFSGIKEAIKKFLSSTSPyeQSVEEFIRELQRILIKSDVNVkVVFEFTSKIrkrALEEKPP-QGVSRRDWFIK 75
                                      57899************9744779*********99988877556666655552223344566.67777777765 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0051       2.5      11      42 ..     109     140 ..     100     224 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0051
                                       TSSHHHHHHHHHHHHHTTT--EEEEE--TTT- CS
                              MipZ  11 GsGksttavhvavaLlkkGarvaaidldlrqr 42 
                                       GsGk+tta  +a    ++G rv+ i  d+ ++
  gi|385806157|ref|YP_005842555.1| 109 GSGKTTTAAKLAWYYKNRGYRVGLIAADTFRA 140
                                       99*********************999997554 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00066      0.32       2      22 ..     101     121 ..     100     131 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00066
                                       CEEEEC-TTTCHHHHHHHHHH CS
                             NACHT   2 lvilqGeaGsGKTtLlqklal 22 
                                       +++l G +GsGKTt ++kla 
  gi|385806157|ref|YP_005842555.1| 101 VIMLVGVQGSGKTTTAAKLAW 121
                                       689***************986 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   1.4     0.017         8      18      41 ..      98     121 ..      75     452 .. 0.50

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.017
                            AAA_23  18 skgltlItGpNGaGKTTildAikl 41 
                                       ++ +  ++G  G+GKTT    + +
  gi|385806157|ref|YP_005842555.1|  98 KPYVIMLVGVQGSGKTTTAAKLAW 121
                                       566777888888888886554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       952  (0.0530983); expected 358.6 (0.02)
Passed bias filter:                      742  (0.0413855); expected 358.6 (0.02)
Passed Vit filter:                       129  (0.00719505); expected 17.9 (0.001)
Passed Fwd filter:                        37  (0.0020637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              37  [number of targets reported over threshold]
# CPU time: 0.72u 0.32s 00:00:01.04 Elapsed: 00:00:00.49
# Mc/sec: 2771.77
//
Query:       gi|385806158|ref|YP_005842556.1|  [L=132]
Description: translation initiation factor IF-5A [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-07   30.3   0.1    5.7e-07   29.6   0.1    1.4  1  eIF-5a    Eukaryotic elongation factor 5A hypusine, DNA-bindi
    9.1e-05   22.4   0.1    0.00017   21.5   0.1    1.4  1  EFP_N     Elongation factor P (EF-P) KOW-like domain
     0.0066   16.5   0.3      0.014   15.4   0.3    1.5  1  EFP       Elongation factor P (EF-P) OB domain


Domain annotation for each model (and alignments):
>> eIF-5a  Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.1   9.5e-11   5.7e-07       1      69 []      69     131 ..      69     131 .. 0.90

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 9.5e-11
                                       --EEEEEEEEEE-SS.EEEEEE.TT--EEE.EEGG...GB-HHHHTT--TT-E..EEEEEETTEEEEEEE- CS
                            eIF-5a   1 nVkrkeyqLidIqdDgflsLmd.ddgetkeDlklp.egelgkqikekfeegkdvlVtVlsamGeekiiavK 69 
                                       ++++k +q+i+  ++   +Lmd +++et+e ++ p + el  +i     +gk+  V+++++mG+  i++++
  gi|385806158|ref|YP_005842556.1|  69 IIEKKVAQVIADLGN-SYQLMDmESYETFE-VQKPnDPELLSKI----APGKE--VEYWEVMGQRIIVRMR 131
                                       5899********999.99************.****555776666....79***..************9986 PP

>> EFP_N  Elongation factor P (EF-P) KOW-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.1   2.9e-08   0.00017       3      33 ..       9      39 ..       7      43 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.9e-08
                                      GG--TT-EEEETTEEEEEEEEEEEEETTS-- CS
                             EFP_N  3 selkkGlvieidgklyvVlefehvkpGkGqa 33
                                       ++k G+ i i++++++V+e+   k Gk ++
  gi|385806158|ref|YP_005842556.1|  9 GDVKIGTYIIIENEPCRVVEITKAKTGKHGS 39
                                      699************************9875 PP

>> EFP  Elongation factor P (EF-P) OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.3   2.4e-06     0.014      10      28 ..      82     100 ..      79     103 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.4e-06
                                       TTEEEEEETTT--EEEEEH CS
                               EFP  10 gdeyvFMdnetYeqielpk 28 
                                       g++y +Md+e+Ye +e++k
  gi|385806158|ref|YP_005842556.1|  82 GNSYQLMDMESYETFEVQK 100
                                       899*************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); 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: 0.52u 0.35s 00:00:00.87 Elapsed: 00:00:00.55
# Mc/sec: 724.34
//
Query:       gi|385806159|ref|YP_005842557.1|  [L=168]
Description: hypothetical protein FFONT_1117 [Fervidicoccus fontis Kam940]
Scores for complete 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   19.7   0.0     0.0013   19.3   0.0    1.4  1  ASCH      ASCH domain
  ------ inclusion threshold ------
      0.025   14.6   0.0      0.053   13.6   0.0    1.6  1  DUF3850   Domain of unknown function (DUF3850)


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 !   19.3   0.0   1.5e-07    0.0013       2      55 ..      22      74 ..      21     134 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.5e-07
                                      EE-TTHHHHHHTTS--EEEESSTTTGGGT-CEEEEEECCCCTSEEEEEEEEEEE CS
                              ASCH  2 sfhqelaslivsGkKtaeirvwdeelpkvrgdllilaalkptgralgivevtkv 55
                                      s+++e+a++i+sG+K+ e r ++ +   ++g+l i++++   + + g++++ ++
  gi|385806159|ref|YP_005842557.1| 22 SIRPEYAEAIFSGRKKFELRRGKGK-DLIKGGLAIVYVSGRVKAISGEFTIGRI 74
                                      6899****************99999.7789******888766666666666555 PP

>> DUF3850  Domain of unknown function (DUF3850)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   5.9e-06     0.053       5      25 ..      22      42 ..      18      51 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.9e-06
                           DUF3850  5 kilpeyfeaVvsGkKtfeirk 25
                                       i pey ea+ sG+K+fe+r+
  gi|385806159|ref|YP_005842557.1| 22 SIRPEYAEAIFSGRKKFELRR 42
                                      589****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1065.30
//
Query:       gi|385806160|ref|YP_005842558.1|  [L=313]
Description: spermidine synthase [Fervidicoccus fontis Kam940]
Scores for 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-53  181.5   0.0    1.6e-53  181.0   0.0    1.2  1  Spermine_synth   Spermine/spermidine synthase domain
    7.6e-06   25.8   0.0    1.1e-05   25.3   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    1.6e-05   24.7   0.0    3.8e-05   23.5   0.0    1.6  1  Spermine_synt_N  Spermidine synthase tetramerisation domain
    2.4e-05   25.0   0.0    4.1e-05   24.2   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    0.00013   21.7   0.0     0.0002   21.0   0.0    1.3  1  Cons_hypoth95    Conserved hypothetical protein 95
    0.00025   21.7   0.0    0.00055   20.6   0.0    1.7  1  Methyltransf_12  Methyltransferase domain
    0.00026   20.3   0.0    0.00038   19.8   0.0    1.2  1  DUF43            Branched-chain polyamine synthase A C-termin
     0.0026   17.6   0.0     0.0049   16.7   0.0    1.5  1  Methyltransf_30  S-adenosyl-L-methionine-dependent methyltran
     0.0051   16.4   0.0      0.008   15.7   0.0    1.3  1  MTS              Methyltransferase small domain
     0.0056   17.3   0.0      0.011   16.3   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
  ------ inclusion threshold ------
      0.031   13.8   0.0      0.049   13.1   0.0    1.2  1  Methyltransf_5   MraW methylase family


Domain annotation for each model (and alignments):
>> Spermine_synth  Spermine/spermidine synthase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.0   0.0   9.6e-57   1.6e-53       1     181 [.      66     249 ..      66     258 .. 0.94

  Alignments for each domain:
  == domain 1  score: 181.0 bits;  conditional E-value: 9.6e-57
                                       THHHHHHHHHHHHCCSSST-EEEEESSTTSHHHHHHTTSTT-SEEEEEES-HHHHHHHHHHSHHHHTTCGGCTTEEE CS
                    Spermine_synth   1 efaykemiahvplmlhknpkevLiiGGgDGgvlrevvkhntvekitlvdiDqkvidfskkflpslaisafndarvkl 77 
                                       ef+y+e ++h pl++h np++vLi+GGg G +lrev++++tv+k+++vdiD+kv++fskk+l++ + ++f d+r ++
  gi|385806160|ref|YP_005842558.1|  66 EFVYHESLVHPPLLAHGNPERVLILGGGEGATLREVLRYKTVKKAVMVDIDEKVVEFSKKYLQEWHHNSFFDKRAEV 142
                                       799************************************************************************** PP

                                       EESTCHHHHCTCSS...-EEEEEEECCSTTCSSCG..CSSHHHHHHHHHTEEEEEEEEEEEEETTTCHHHHHHHHHH CS
                    Spermine_synth  78 vlgdgfkflkayek...kfdvvivdsldpvgpaen..lFskeffdllkkvlkedGviilqaekpelekelvinvdks 149
                                       v++dg k+l++  k   kfd+++ d++dp   + +  l+++ef++l+k +lke+Gv+++qa +p l +e++ +++ +
  gi|385806160|ref|YP_005842558.1| 143 VIEDGRKYLENAGKsdeKFDAIVIDLVDPLAGSPAvkLYTREFYQLVKGALKEGGVMVTQATSPVLYQEMFATIHST 219
                                       ************9999************997777667**************************************** PP

                                       HHTTSSCEEEEEEEETTTSCSCEEEEEEEESS CS
                    Spermine_synth 150 gkqvfalqvepsavlvPtylsgminfvveskk 181
                                       +k+vf+ +++p+av++++y + +++fv  s++
  gi|385806160|ref|YP_005842558.1| 220 IKSVFK-IARPYAVYMRSYNG-LWGFVFGSEE 249
                                       *****9.************76.5566655554 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   6.5e-09   1.1e-05       6     122 ..      86     216 ..      81     257 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 6.5e-09
                   Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielAre....naqklgld.nveFeqgdiee.lekl.ledekf 75 
                                       rvl lG G+G+ + e   +  + ++ v +Di+e+++e++++       + ++d ++e+ ++d  + le++  +dekf
  gi|385806160|ref|YP_005842558.1|  86 RVLILGGGEGATLREVL-RYKTVKKAVMVDIDEKVVEFSKKylqeWHHNSFFDkRAEVVIEDGRKyLENAgKSDEKF 161
                                       67779***********9.666678899**************6665233566778*********************** PP

                   Methyltransf_31  76 Dlilsn..evlnalad....pdkileeiervlkpggilliedpr..llaelpakv 122
                                       D i+ +  ++l+  ++      ++++ ++ +lk+gg+++++  +  l +e+ a +
  gi|385806160|ref|YP_005842558.1| 162 DAIVIDlvDPLAGSPAvklyTREFYQLVKGALKEGGVMVTQATSpvLYQEMFATI 216
                                       *****95555555555111145566688889999999988766654444444444 PP

>> Spermine_synt_N  Spermidine synthase tetramerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   2.3e-08   3.8e-05       2      52 ..      12      62 ..      11      62 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 2.3e-08
                                      EEEEEEETTEEEEEEEEEEEEE.EEESSSEEEEEEETTTEEEEEETTEEEEE CS
                   Spermine_synt_N  2 WfteisdpglalelkVekvLye.ekSeyQdieifesktfGkvLvLDgvvqlt 52
                                      W+ e +d+g   ++k  + Ly  ek++yQ++ ++   t Gk L++Dg+vq t
  gi|385806160|ref|YP_005842558.1| 12 WYVEWIDDGD-ASFKAANQLYAmEKTPYQEVFVVNLLTLGKALIIDGKVQST 62
                                      8888888554.4788888888659**************************76 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   2.5e-08   4.1e-05       1      93 [.      87     189 ..      87     197 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 2.5e-08
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT......TEEEEESBCCG.BS...SSTTTEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl......nvefvqgdaed.lp...fedgsfDl 67 
                                       vL lG G+G +++++++    +k ++vDi+e+ +e  ++ ++e +       ++e+v  d ++ l+     d++fD+
  gi|385806160|ref|YP_005842558.1|  87 VLILGGGEGATLREVLRYKTVKKAVMVDIDEKVVEFSKKYLQEWHHnsffdkRAEVVIEDGRKyLEnagKSDEKFDA 163
                                       7889************995589*******************99544556999*********77333333799***** PP

                                       EEEESTGGGSSHHHHHHHHHHHHHHE CS
                   Methyltransf_25  68 vvssgalhhlsdedlekalkeiarvL 93 
                                       +v+  +  +   + ++ + +e+++++
  gi|385806160|ref|YP_005842558.1| 164 IVIDLVDPLAGSPAVKLYTREFYQLV 189
                                       **943322344455555555555544 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.2e-07    0.0002      40     160 ..      82     211 ..      56     226 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.2e-07
                                       HCC-EEEETT-TTSHHHHHHHH.TT-SEEEEEES-HHHHHHHHHHHCCCT--T....TTEEEEES-HHHHCTS--SS CS
                     Cons_hypoth95  40 iegarvLDlfaGsGalglEAlS.Rgakkavlvekdkeavkilkenleelklee....etaelkedaleallklakkk 111
                                       ++ +rvL l +G Ga   E l    +kkav+v+ d+++v+  k+ l+e + ++    ++++++ed  + l++ +k +
  gi|385806160|ref|YP_005842558.1|  82 GNPERVLILGGGEGATLREVLRyKTVKKAVMVDIDEKVVEFSKKYLQEWHHNSffdkRAEVVIEDGRKYLENAGKSD 158
                                       77888999999999999999853679**********************9988899989999**************** PP

                                       -EEEEEEE-..-SSSTTCH....HHHHHHHHHTT-EEEEEEEEEEEECCSSS-- CS
                     Cons_hypoth95 112 eefdivflD..PPyakell...ieevlelleekkllkenalvvvetekekelpe 160
                                       e+fd + +D   P a + +   + + + +l  k++lke++++v++  + +   e
  gi|385806160|ref|YP_005842558.1| 159 EKFDAIVIDlvDPLAGSPAvklYTREFYQLV-KGALKEGGVMVTQATSPVLYQE 211
                                       ******9875546665544344555666666.5999999999999877655554 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   3.3e-07   0.00055       2      74 ..      89     168 ..      88     199 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.3e-07
                   Methyltransf_12   2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.........ssfDl 69 
                                        +G+G G++lr++l++   ++ + vDi+++++e  k+ l++++ n+  +++ +a+ ++++  +         ++fD+
  gi|385806160|ref|YP_005842558.1|  89 ILGGGEGATLREVLRYKTVKKAVMVDIDEKVVEFSKKYLQEWHHNS--FFDKRAEVVIEDGRKylenagksdEKFDA 163
                                       68******************************99999999999755..5555555555444447889********** PP

                   Methyltransf_12  70 vvasn 74 
                                       +v+  
  gi|385806160|ref|YP_005842558.1| 164 IVIDL 168
                                       99744 PP

>> DUF43  Branched-chain polyamine synthase A C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   2.3e-07   0.00038      47     152 ..      86     203 ..      78     238 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2.3e-07
                                       EEEEES-TT-HHHHHHHH.T--SEEEEE-S-HHHHHHHHHHHHHHT-....-..EEEE---TTS---T..TTSS-BS CS
                             DUF43  47 eilvlGdDDLtslalaLt.glpkkvvvvDiDeRlikfiervakelgl....k..ieaivyDlrkplpe..elkekFd 114
                                       ++l+lG  +  +l   L  +  kk v+vDiDe++++f ++  +e       +  +e+++ D rk l +  +  ekFd
  gi|385806160|ref|YP_005842558.1|  86 RVLILGGGEGATLREVLRyKTVKKAVMVDIDEKVVEFSKKYLQEWHHnsffDkrAEVVIEDGRKYLENagKSDEKFD 162
                                       68888888888888888625679999**************9998654222223589********9987224668*** PP

                                       EEEE...---SSHHHHHHHHHHHHHTB-STT-EEEEEE-TT CS
                             DUF43 115 vfit...DPpetvealkaFlgRGiaaLkgegcagYlgltrr 152
                                        ++    DP  +  a+k++     + +kg+   g + +t+ 
  gi|385806160|ref|YP_005842558.1| 163 AIVIdlvDPLAGSPAVKLYTREFYQLVKGALKEGGVMVTQA 203
                                       99862226888888899886655555566655565555555 PP

>> Methyltransf_30  S-adenosyl-L-methionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0     3e-06    0.0049      24      91 ..     133     204 ..     109     218 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3e-06
                                       EEETTTTEEEEEEES-HHHHHHHC-...T-EEEEEE-SS-T...TTSGGGCSHHHHHHHHHHEEEEEEEEES-- CS
                   Methyltransf_30  24 lelaaeevtlklligdarealkeld...ekadawFlDgFsP...aknPelwseellkelarllkkkgtlatyss 91 
                                        ++   + + +++i+d r+ l++     ek+da+  D   P   + + +l++ e++++++ +lk++g+++t + 
  gi|385806160|ref|YP_005842558.1| 133 NSF--FDKRAEVVIEDGRKYLENAGksdEKFDAIVIDLVDPlagSPAVKLYTREFYQLVKGALKEGGVMVTQAT 204
                                       333..3567899******9999876666******887555521166779*********************9765 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   4.9e-06     0.008      33     160 ..      85     224 ..      74     234 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4.9e-06
                                       SEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC......EEEEE-STTTTST.....TS-E CS
                               MTS  33 gkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle......vevvasdvleeve.....ekkf 98 
                                       ++vl lG G G+   ++++ +   + ++vd+d + +e++k+ l++ +++      +evv +d+ + +e     ++kf
  gi|385806160|ref|YP_005842558.1|  85 ERVLILGGGEGATLREVLRYKTVKKAVMVDIDEKVVEFSKKYLQEWHHNsffdkrAEVVIEDGRKYLEnagksDEKF 161
                                       57899*******9999999999999*****************99988878889999******9776543333479** PP

                                       EEEEE-..--STTTCHCHHHHHHHHHHHHHHHEEEEEEEEEEEETTSCHHHHHHHHHS--EEEE CS
                               MTS  99 dlivsN..PPfhagkatelavaeeliaeAkeaLkegGeLliVanrklgyeslleelfgnvevva 160
                                       d+iv     P+  + a  +  ++e+ +  k aLkegG ++  a + + y+++ +++ ++++ v 
  gi|385806160|ref|YP_005842558.1| 162 DAIVIDlvDPLAGSPA-VKLYTREFYQLVKGALKEGGVMVTQATSPVLYQEMFATIHSTIKSVF 224
                                       ***9864468766655.67789999999*********999999999999998777777666554 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   6.9e-06     0.011       3      86 ..      90     187 ..      88     201 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6.9e-06
                                       ET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-......EEEETTEECCC....TSS-TT-EEEEEE CS
                   Methyltransf_11   3 vGcGtGrlaealakrg..arvvgvDlskemlklakekaseegl......kvefvvadaek....lpfednsfDlvvs 67 
                                       +G G G+ ++++ ++   ++ v vD+++++++ +k+  +e ++      + e+v +d +k        d++fD++v+
  gi|385806160|ref|YP_005842558.1|  90 LGGGEGATLREVLRYKtvKKAVMVDIDEKVVEFSKKYLQEWHHnsffdkRAEVVIEDGRKylenAGKSDEKFDAIVI 166
                                       799**********55566*****************99999999999999888888888865332568999*****99 PP

                                       ES-CCC-..CCHHHHHHHHHH CS
                   Methyltransf_11  68 sevlhhv..edpekalkeiaR 86 
                                         v      + ++ + +e+++
  gi|385806160|ref|YP_005842558.1| 167 DLVDPLAgsPAVKLYTREFYQ 187
                                       876333343444444444444 PP

>> Methyltransf_5  MraW methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     3e-05     0.049      30     100 ..      93     168 ..      78     169 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3e-05
                                       TTSHHHHHHHTT--TTEEEEEES-HHHHHHHTT.....---..EEEEES-G.GGHHHHHHHTT..TT-EEEEEEE- CS
                    Methyltransf_5  30 GaggHsealLeqlselrligidrDksalarakerLkefekr..ltlvkgnf.kelkealaean..vtkvdgillDL 100
                                       G+g   +++L+ ++ ++++++d+D+++++ +k+ L+e++++  +    +   ++ +++l++a+   +k+d+i++DL
  gi|385806160|ref|YP_005842558.1|  93 GEGATLREVLRYKTVKKAVMVDIDEKVVEFSKKYLQEWHHNsfFDKRAEVViEDGRKYLENAGksDEKFDAIVIDL 168
                                       6777778999999999*********************9876442222222234444555555543479*******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); 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: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 1803.78
//
Query:       gi|385806161|ref|YP_005842559.1|  [L=275]
Description: short-chain dehydrogenase/reductase SDR [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.5e-41  140.4   0.1    4.4e-23   82.1   0.0    2.1  2  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    1.5e-25   89.9   0.8    7.7e-18   64.7   0.9    2.1  2  adh_short        short chain dehydrogenase
    1.3e-09   38.2   0.4    2.1e-09   37.5   0.4    1.4  1  KR               KR domain
    4.2e-06   26.4   0.0    5.4e-06   26.0   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    1.9e-05   23.8   0.0    2.1e-05   23.7   0.0    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    0.00012   21.6   0.2    0.00022   20.7   0.2    1.4  2  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    0.00024   21.4   0.2    0.00054   20.2   0.2    1.6  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
    0.00085   18.5   0.3     0.0013   18.0   0.3    1.2  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
     0.0043   15.9   0.0     0.0046   15.9   0.0    1.1  1  COX1             Cytochrome C and Quinol oxidase polypeptide 
  ------ inclusion threshold ------
      0.026   13.7   0.5      0.034   13.3   0.5    1.3  1  NAD_binding_4    Male sterility protein
      0.076   12.5   1.3       0.32   10.5   0.8    2.1  2  Hpr_kinase_C     HPr Serine kinase C-terminal domain
       0.13   13.0   0.0        0.3   11.8   0.0    1.7  1  Methyltransf_25  Methyltransferase 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 !   56.5   0.1   1.9e-18   2.8e-15       5     145 ..      18     150 ..      14     157 .. 0.89
   2 !   82.1   0.0   2.9e-26   4.4e-23     139     233 ..     171     265 ..     158     266 .. 0.94

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 1.9e-18
                                       SHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEE..EE--TTSHHHHHHHHHHHHHHHSSEEEEEE---- CS
                      adh_short_C2   5 gIGraiAkalaeeGaevvltdlneeakkrveelaeelgaev..lecDVtdeeqvealveevvekfgklDilvnnagi 79 
                                       gIG+a+Ak+la++G  +++  + e++kk   el+ e++ ++  + +DV++e +v++l++++  ++g l  +v+ agi
  gi|385806161|ref|YP_005842559.1|  18 GIGKATAKLLAKKGSLLLADIVPEALKKVESELKGEVNGSIetMVTDVSNERDVKELAKKAS-ELGDLGAIVHTAGI 93 
                                       9*************76655555555588888999999988677*****************76.58************ PP

                                       -EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSCCEEEEEEEGGGTSBSTTTTHHHHHH CS
                      adh_short_C2  80 apklkgpfletsreefdraldvnlyslfllakaalplmkeggsivnlssvgaervvpnynaygaaK 145
                                       +p+          ++ +r++dvnl ++++++k++ +++++g+  v ++s++a +v  ++n+ +  K
  gi|385806161|ref|YP_005842559.1|  94 SPT---------MADAKRIFDVNLVGTAYVLKHFHNIATSGSVGVMIASMSAYMVPRDTNVSNLLK 150
                                       **9.........7899************************************99999998887777 PP

  == domain 2  score: 82.1 bits;  conditional E-value: 2.9e-26
                                       THHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHC CS
                      adh_short_C2 139 naygaaKaalealtrylAvelgpkgiRvNavspgpikTlaasgikgfdelleelearaplgrlgtpeevaeaalfLa 215
                                        ay+ +K +++ l+   A  +++kg R  ++spg+i+T++ ++  +++  +++l +++pl r+g+pee+a+++ fL+
  gi|385806161|ref|YP_005842559.1| 171 MAYSLSKLGVILLVEDQAEAWAKKGARLVSISPGIIDTTMGRRELEMQPAMRQLLQMTPLSRMGRPEEIANVIEFLV 247
                                       39**************************************9999999999*************************** PP

                                       SGGGTT--SEEEEESTTG CS
                      adh_short_C2 216 sdeasyitGqtlvvDgGl 233
                                       s+++syi+G+++ vDgG+
  gi|385806161|ref|YP_005842559.1| 248 SEKSSYINGTDILVDGGV 265
                                       *****************7 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.7   0.9   5.1e-21   7.7e-18       1     139 [.       8     136 ..       8     144 .. 0.89
   2 !   23.2   0.0   2.6e-08   3.8e-05     146     192 ..     170     216 ..     162     219 .. 0.90

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 5.1e-21
                                       SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT.TSEEEEEE-TTTSHHHHHHHHHHHHHHHS CS
                         adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee.gakalaiqvDvtdreevealvekavkklg 76 
                                       kv ++tG+++GIG+a+ak lak+G  ++ +d+ +e+l++v +elk e + ++ ++ +Dv+++++v++l +ka ++lg
  gi|385806161|ref|YP_005842559.1|   8 KVYVITGGGGGIGKATAKLLAKKGSLLL-ADIVPEALKKVESELKGEvNGSIETMVTDVSNERDVKELAKKA-SELG 82 
                                       7889*******************98765.5*****************************************9.99** PP

                                       SESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGG CS
                         adh_short  77 kldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvag 139
                                        l ++v+ AGi       + + ++ +r+++vNl+g+  + +++ +   ++s G  v ++S+ +
  gi|385806161|ref|YP_005842559.1|  83 DLGAIVHTAGI-------SPTMADAKRIFDVNLVGTAYVLKHFHNIATSGSVG--VMIASMSA 136
                                       ***********.......4678899*****************99995555555..55566554 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 2.6e-08
                                       BHHHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHHCT CS
                         adh_short 146 vaaYsAsKaavagltrslakelaptgirvnavaPGlvdTdmakelre 192
                                       + aYs sK +v+ l++  a+ +a++g r +++ PG++dT m +++ e
  gi|385806161|ref|YP_005842559.1| 170 GMAYSLSKLGVILLVEDQAEAWAKKGARLVSISPGIIDTTMGRRELE 216
                                       579**************************************987665 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.5   0.4   1.4e-12   2.1e-09       2      93 ..       9      95 ..       8     146 .. 0.79

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 1.4e-12
                                      EEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHT.T-EEEE----TT-HHHHHHHHHHHHHHS CS
                                KR  2 tylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaeleal.gaevevvaaDvsdkdavealleeikaee 79
                                      +y+itGG Gg+G+++a+ la+kg   l+ +  +  a ++     +el+   + ++e++  Dvs++ +v++l ++++ e 
  gi|385806161|ref|YP_005842559.1|  9 VYVITGGGGGIGKATAKLLAKKGSLLLADIVPE--ALKKV---ESELKGEvNGSIETMVTDVSNERDVKELAKKAS-EL 81
                                      7**********************9877777777..33333...35666654779*********************8.56 PP

                                      S---EEEE------ CS
                                KR 80 ppikGvihaAgvlr 93
                                      + +  ++h+Ag++ 
  gi|385806161|ref|YP_005842559.1| 82 GDLGAIVHTAGISP 95
                                      6**********964 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   3.6e-09   5.4e-06       2     159 ..      11     190 ..      10     213 .. 0.72

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 3.6e-09
                                       EEETTTSHHHHHHHHHHHHCT....SEEEEEES-STTTTCHHCHHC....EEEE--TT-HHHHHHHHHHH....T-S CS
                         Epimerase   2 lVtGatGfiGsalvkallekg....yevigldrlssasntarledl....elveldltdrsalerlfkee....qpd 66 
                                       ++tG+ G iG+a++k l++kg     + i+   l ++ +++++ ++    e +  d+ ++ ++++l k+     +  
  gi|385806161|ref|YP_005842559.1|  11 VITGGGGGIGKATAKLLAKKGslllAD-IVPEAL-KKVESELKGEVngsiETMVTDVSNERDVKELAKKAselgDLG 85 
                                       79*******************543222.222222.334444444447889999999999998888887532124567 PP

                                       EEEE--S---HHHHHHSHHHHHHHHTHHHHHHHHHHHHH....TCTEEEEEEEGGGGTSCSS......SS....BST CS
                         Epimerase  67 avihlAavggvaassedpadfieknlqgtlnlleaarka....gvkrllflsSsevYGkdae......qp....kee 129
                                       a++h A   g++ ++ d++++++ nl+gt  +l+  +       v  ++   S+ + ++d++       p     +e
  gi|385806161|ref|YP_005842559.1|  86 AIVHTA---GISPTMADAKRIFDVNLVGTAYVLKHFHNIatsgSVGVMIASMSAYMVPRDTNvsnllkDPlsqgFSE 159
                                       788885...56666668888999************9955223344489999999****8888666653357656556 PP

                                       CSTTS--.--SSHHHHHHHHHHHHHHHHHHH CS
                         Epimerase 130 ttltgpl.kpnspYaaaKlageklveayaaq 159
                                       ++       p  +Y+++Kl +  lve+ a++
  gi|385806161|ref|YP_005842559.1| 160 KLSVIAKsDPGMAYSLSKLGVILLVEDQAEA 190
                                       6644444799999999999888888876665 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 !   23.7   0.0   1.4e-08   2.1e-05       1     112 [.      11     131 ..      11     243 .. 0.65

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.4e-08
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlresp.elleelskvnvkk...viegDvtdkdkleealegvd..... 68 
                                       v+tGg+G +G+a  k L + ++   +  +D++ +  ++ e+  k +v+    ++ +Dv ++ +++e  ++++     
  gi|385806161|ref|YP_005842559.1|  11 VITGGGGGIGKATAKLLAKKGS---LLLADIVPEAlKKVESELKGEVNGsieTMVTDVSNERDVKELAKKASelgdl 84 
                                       79*************9999997...5566644332122233333333323348889999999998866544323333 PP

                         3Beta_HSD  69 .vvihlaslvdvagkltedeimkvnvkGTrnvlea....cvkagvrvlv 112
                                        +++h+a++++ +     ++i +vn+ GT  vl+     +++ +v v++
  gi|385806161|ref|YP_005842559.1|  85 gAIVHTAGISPTMA--DAKRIFDVNLVGTAYVLKHfhniATSGSVGVMI 131
                                       389*******9988..6778************97511114445555555 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 !   20.7   0.2   1.5e-07   0.00022       2     130 ..      12     135 ..      11     137 .. 0.82
   2 ?   -4.1   0.0       5.4     8e+03     149     169 ..     169     189 ..     166     201 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.5e-07
                                       EETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SE CS
                     GDP_Man_Dehyd   2 iTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpde 78 
                                       iTG+ G iG  +a+lL +kg      +        + +++++++ k e++++++ +  D+++++ +++l +++   e
  gi|385806161|ref|YP_005842559.1|  12 ITGGGGGIGKATAKLLAKKGSLLLADIVP------EALKKVESELKGEVNGSIETMVTDVSNERDVKELAKKA--SE 80 
                                       9******************9977653333......3444444455567899********************99..68 PP

                                       EEE--S---...HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEG CS
                     GDP_Man_Dehyd  79 vynLAAqsh...VdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaSts 130
                                          L+A  h   ++  + ++++ ++vn++Gt+ +L+   ++  + +v +++aS s
  gi|385806161|ref|YP_005842559.1|  81 LGDLGAIVHtagISPTMADAKRIFDVNLVGTAYVLKHFHNIATSGSVGVMIASMS 135
                                       88888887755566789999****************9999988888888888866 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 5.4
                                       --SHHHHHHHHHHHHHHHHHH CS
                     GDP_Man_Dehyd 149 PrsPYaaaKlyadwivvnyre 169
                                       P   Y+ +Kl    +v++  e
  gi|385806161|ref|YP_005842559.1| 169 PGMAYSLSKLGVILLVEDQAE 189
                                       566788888877777665554 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.2   3.6e-07   0.00054       4      70 ..      13      78 ..      10     102 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 3.6e-07
                                      E--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH...TTTCEEEEE--TTTHHHHHHHHHTTS CS
                   Sacchrp_dh_NADP  4 iGa.GsvGqavaellarhfdvdaeitvadrskeklealaaka...lgvrfeaialdaenyeavLaallkeg 70
                                       G+ G++G+a+a+lla+++++     +ad   e l+++ +++    + ++e++  d++n+++ +++l k++
  gi|385806161|ref|YP_005842559.1| 13 TGGgGGIGKATAKLLAKKGSL----LLADIVPEALKKVESELkgeVNGSIETMVTDVSNERD-VKELAKKA 78
                                      4555**************976....777777777777776666669999*************.99999987 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.3   8.4e-07    0.0013       2     114 ..      11     117 ..      10     139 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 8.4e-07
                                       EEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT.... CS
                   Polysacc_synt_2   2 lvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleel.. 76 
                                       ++tG+gG iG++  + ++kk   +++l +    +l ++e+el+ e++      +i ++++dv +++ ++++ ++   
  gi|385806161|ref|YP_005842559.1|  11 VITGGGGGIGKATAKLLAKK--GSLLLADIVPEALKKVESELKGEVNG-----SIETMVTDVSNERDVKELAKKAse 80 
                                       69*********998877765..689*****************776665.....445779999999999888875422 PP

                                       ..T-SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHH CS
                   Polysacc_synt_2  77 ..kvdvvfhaAAlKhVPlveenpleaiktNvlgtenviea 114
                                         +  +++h+A +   P++   +   ++ N +gt  v++ 
  gi|385806161|ref|YP_005842559.1|  81 lgDLGAIVHTAGIS--PTMA-DAKRIFDVNLVGTAYVLKH 117
                                       22466788888763..5553.4556777788888777765 PP

>> COX1  Cytochrome C and Quinol oxidase polypeptide I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   3.1e-06    0.0046     324     367 ..      99     143 ..      84     230 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.1e-06
                                       HTSHHHHHHHTTBHHHHHHHHHHH.TTHHHHHHHHHHHHHHHHHH CS
                              COX1 324 lalpsvnyvvhntywvvaHfHlvl.lgavvfllfaaiyyllpklt 367
                                        a +++++ + +t +v  HfH ++  g v++++  +  y++p+ t
  gi|385806161|ref|YP_005842559.1|  99 DAKRIFDVNLVGTAYVLKHFHNIAtSGSVGVMIASMSAYMVPRDT 143
                                       477899***************765167777777778899999876 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.5   2.3e-05     0.034      57     208 ..      53     208 ..      12     261 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.3e-05
                                       HHTTTEEEEE--TTSGGGG--H..HHHHHHHHH--EEEE--SS-S.STTSSEEHHHHHHHHHHHHHHHTSSS--..- CS
                     NAD_binding_4  57 elaerikvveGDlseprlGLse..edlqelaeevdviihsaAtvnfdepykellrvNveGtrevlelakklkkl.kv 130
                                       e+   i+ +++D+s++r  ++e  +++ e    + +i+h a+    +++ k++++vN+ Gt  vl+  ++++    v
  gi|385806161|ref|YP_005842559.1|  53 EVNGSIETMVTDVSNER-DVKElaKKASE-LGDLGAIVHTAGISPTMADAKRIFDVNLVGTAYVLKHFHNIATSgSV 127
                                       55666677777777666.33330022233.47789***************************999877765555333 PP

                                       EEEEEE..GGGTTS-TTT--SSS-H......HHH--EEEETTTCCCHHHHHHH....HHHHHHHHHHHHH---EEEE CS
                     NAD_binding_4 131 llhvST..ayvngeregeveekvyeegekeekldederaklkglpntYeqsKa....laEklvrearrrsglpvviv 201
                                        + + +  ay+ + ++ +v  ++++ + ++   ++++   + +   +Y+ sK     l E+  ++++++ g ++v +
  gi|385806161|ref|YP_005842559.1| 128 GVMIASmsAYMVPRDT-NV-SNLLKDPLSQGFSEKLSVIAKSDPGMAYSLSKLgvilLVEDQAEAWAKK-GARLVSI 201
                                       3444444477766666.44.5677777888888888888888888899999963333566666777755.7777777 PP

                                       EE-EEE- CS
                     NAD_binding_4 202 Rpsiitg 208
                                        p+ii +
  gi|385806161|ref|YP_005842559.1| 202 SPGIIDT 208
                                       7777755 PP

>> 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 ?   10.5   0.8   0.00022      0.32      19      72 ..       9      61 ..       2      65 .. 0.84
   2 ?   -0.6   0.0      0.57   8.4e+02      29      74 ..     164     211 ..     161     219 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00022
                                      EEEEEEESTCHHHHHHHHHHHTTT-EEEEESSEEEEEETTE.EEEEE-TTTTTE CS
                      Hpr_kinase_C 19 vGvLitGesgvGKselaleLikrghrLvaDDaveikridektlvGrapellkhl 72
                                      v v+  G  g+GK+ +a  L k+g  L+aD + e  ++ e++l G+ +  ++ +
  gi|385806161|ref|YP_005842559.1|  9 VYVITGGGGGIGKA-TAKLLAKKGSLLLADIVPEALKKVESELKGEVNGSIETM 61
                                      557777899****8.6777***************99999999****99888876 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.57
                                       HHHHH..HHHHHHTTT-EEEEESSEEEEEETTE.EEEEE-TTTTTEEE CS
                      Hpr_kinase_C  29 vGKse..laleLikrghrLvaDDaveikridektlvGrapellkhlle 74 
                                       + Ks+  +a  L k g  L+  D+ e   ++ ++lv  +p +++  + 
  gi|385806161|ref|YP_005842559.1| 164 IAKSDpgMAYSLSKLGVILLVEDQAEAWAKKGARLVSISPGIIDTTMG 211
                                       556653367889999999999999999999999999999999988876 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    0.0002       0.3       5      57 ..      16      67 ..      12     102 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0002
                                      T-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCG CS
                   Methyltransf_25  5 GcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaed 57
                                      G G G+ t++l+++  k++++  Di +e+l++++++++ e   ++e ++ d+++
  gi|385806161|ref|YP_005842559.1| 16 GGGIGKATAKLLAK--KGSLLLADIVPEALKKVESELKGEVNgSIETMVTDVSN 67
                                      67888888888877..49*******************87543799999998854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); 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: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 1645.73
//
Query:       gi|385806162|ref|YP_005842560.1|  [L=211]
Description: uracil phosphoribosyltransferase [Fervidicoccus fontis Kam940]
Scores for complete 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-43  146.6   0.4    7.4e-43  146.4   0.4    1.0  1  UPRTase       Uracil phosphoribosyltransferase
    2.8e-08   33.4   0.6    3.9e-08   33.0   0.6    1.2  1  Pribosyltran  Phosphoribosyl transferase domain


Domain annotation for each model (and alignments):
>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.4   0.4   8.3e-47   7.4e-43       8     206 ..       2     210 ..       1     211 [] 0.91

  Alignments for each domain:
  == domain 1  score: 146.4 bits;  conditional E-value: 8.3e-47
                           UPRTase   8 kakltilRdastsrkdfrelvdriarllaeealsallpveevtvttplgkeysg.elldeekialVpilRaGegmee 83 
                                       +a lt+lRd++ts+ +fr+ + +++r l+ e++++ ++ eev+v+tplg++ +g +  d +k++++ +lRaG +++e
  gi|385806162|ref|YP_005842560.1|   2 QAVLTTLRDKNTSQIEFRKSLVKLGRALGIEITRE-MEKEEVEVETPLGAKAKGlKFRDMDKVIIITVLRAGTPLTE 77 
                                       789********************************.******************7778889**************** PP

                           UPRTase  84 alrellpearvghlglqreeet.......lepveyynkLPkkiaertvlllDpviaTGgsaaaaiqlLkergvgeek 153
                                       +l +++ +a+ g +   r +e         e +  y +LPk   e+ v++ Dp++aTG+++ ++ ++++e  ++ +k
  gi|385806162|ref|YP_005842560.1|  78 GLIKIFYNAKQGVVSARRMDELgmgsgknFEIEVNYIRLPKISGENIVIISDPMLATGSTISKVTNIVLE-RARPKK 153
                                       **********9999888877557777777888899******99***************************.5789** PP

                           UPRTase 154 Ilvlsvlaseegvkrlae...efp.kvkvvtaavDeeldekgyivpGlGDfGDRlFg 206
                                       I+++  +a + +++++ e   + + +v+v++a++D+e++ +gyivpGlGD+GDR Fg
  gi|385806162|ref|YP_005842560.1| 154 IIIVGAIATKVAIEKIREierNSEvDVSVYIASIDPEINSRGYIVPGLGDAGDRAFG 210
                                       ********99998766541114446899****************************8 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.6   4.4e-12   3.9e-08      30     134 ..      62     170 ..      48     190 .. 0.79

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 4.4e-12
                                       GEEEEEEETTTHHHHHHHHHHS.TT-EE-EEEEEE-TTT--EE.............EE----TTSEEEEE-SEESSS CS
                      Pribosyltran  30 pdvvvgiargGvpfakiladeL.evplayvrkvkyrpdgseeaargssdes.....rlledpagkkVliVDDildtG 100
                                       ++++++++r G p+   l++ + +++  +v++++ ++ g+++ + +++  +     rl+++   ++V+i D +l+tG
  gi|385806162|ref|YP_005842560.1|  62 KVIIITVLRAGTPLTEGLIKIFyNAKQGVVSARRMDELGMGSGK-NFE--IevnyiRLPKISGENIVIISDPMLATG 135
                                       6899******************5444455555555555555554.343..334788********************* PP

                                       HHHHHHHH.HHHCC-BSEEEEEEEEE-HHHHHHHH CS
                      Pribosyltran 101 gTllaale.lLkekgpeevriavlvdkpateeevd 134
                                       +T+ ++++  L++++p++++i+  ++ +   e+ +
  gi|385806162|ref|YP_005842560.1| 136 STISKVTNiVLERARPKKIIIVGAIATKVAIEKIR 170
                                       *******************9998887777666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.51
# Mc/sec: 1245.97
//
Query:       gi|385806163|ref|YP_005842561.1|  [L=242]
Description: HAD-superfamily hydrolase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-09   37.1   0.1      8e-05   22.5   0.1    2.1  2  Hydrolase_3      haloacid dehalogenase-like hydrolase
    9.8e-06   24.9   0.0    1.3e-05   24.5   0.0    1.2  1  Trehalose_PPase  Trehalose-phosphatase
  ------ inclusion threshold ------
      0.024   15.1   0.1         11    6.4   0.0    2.9  3  HAD              haloacid dehalogenase-like hydrolase
      0.056   13.7   0.1        6.1    7.1   0.0    2.4  2  Hydrolase        haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   7.9e-06     0.036       1      74 [.      17      87 ..      17     115 .. 0.74
   2 !   22.5   0.1   1.8e-08     8e-05     115     231 ..      98     214 ..      81     221 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.9e-06
                                      EEEEIIIII..S-TTS---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEEEGGGTEEECTTTEEE CS
                       Hydrolase_3  1 ialDlDGTL..lnsdkkisektkeaikklkekgikvviATGRslravlpvleelgldlpvialNGaliddekgkil 74
                                      +++D DGTL  + s+  +s +  ++++ lk + +k+++A+ R  r+   ++e++g+  +++++NG       + ++
  gi|385806163|ref|YP_005842561.1| 17 LVFDYDGTLspIGSEAGVSRELLDILNLLK-NMYKLIVASTRDCRF---LMEKIGFFDAFVCSNGLEA-IIGDVVV 87
                                      689******55557777*********9998.99*******997776...5677777779******655.3344444 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 1.8e-08
                                       HHHHHHHHCHCTCEEEESHHHHHCHCSESEEE..EES-HHHHHHHHHHHHHHCTTTEEEEEESTTEEEEEETT-SHH CS
                       Hydrolase_3 115 ekkkkeeektkkkkeeidseeeledeeiakil..ilkdkekldelekelksklnklltitssskgyleimpkgvsKg 189
                                        kk +e +k + +++ + +e+   d +++ +        ek + + + +++ +  +l i  +++ ++e++  ++ K 
  gi|385806163|ref|YP_005842561.1|  98 TKKLEELKKMADEECLKVEEKMSLDGKLIGLGisWRRCGEKPNCIDEIIREAIRGELVIEWYQRPFVEVYVDKAGKM 174
                                       4444444444444444444444444455444435555567777788888888888889******************* PP

                                       HHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS CS
                       Hydrolase_3 190 talkklakelnisleeviafGDgeNDieMLeaaglgvAmgna 231
                                       ++lk     lni  e+ + fGD+e D+e L+ a ++v ++n+
  gi|385806163|ref|YP_005842561.1| 175 EGLKIANAILNI--ERFAYFGDSESDLESLKNASISVFVRNS 214
                                       ****98888877..6899**********************98 PP

>> Trehalose_PPase  Trehalose-phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   2.8e-09   1.3e-05       2      58 ..      19      70 ..      18     119 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 2.8e-09
                                      EETBTTTB---SSGGG--B-TTHHHHHHHHHTTS-..EEEE-SS-HHHHHHHH---S CS
                   Trehalose_PPase  2 lDydGTlspivedpdaavpssellslLkkLasdpknvvaivSGrslkeeellvkvpe 58
                                      +DydGTlspi +   +a +s+ell++L+ L + +k  +++ S r++++  +  +  +
  gi|385806163|ref|YP_005842561.1| 19 FDYDGTLSPIGS---EAGVSRELLDILNLLKNMYK--LIVASTRDCRFLMEKIGFFD 70
                                      8***********...9*******************..**********9555444444 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0    0.0067        30       2      12 ..      18      28 ..      17      41 .. 0.84
   2 ?   -0.1   0.0      0.24   1.1e+03     114     160 ..      61     103 ..      35     118 .. 0.51
   3 ?    6.4   0.0    0.0025        11     170     188 .]     185     203 ..     130     203 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0067
                               HAD  2 lfDfDgTLldg 12
                                      +fD+DgTL + 
  gi|385806163|ref|YP_005842561.1| 18 VFDYDGTLSPI 28
                                      9*******876 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.24
                               HAD 114 lvepllaelg.adevlatelevdd..rltgelglegkpvrgegkvaalre 160
                                       ++    ++ g +d+++++    ++   + g + ++ k v + ++ ++l+e
  gi|385806163|ref|YP_005842561.1|  61 FLM---EKIGfFDAFVCS----NGleAIIGDVVVHKKGVLQIERTKKLEE 103
                                       333...333556677777....2233555555555555555444444444 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0025
                               HAD 170 dleevvayGDspsDlpllr 188
                                        +e+  ++GDs+sDl+ l+
  gi|385806163|ref|YP_005842561.1| 185 NIERFAYFGDSESDLESLK 203
                                       44555677*******9875 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0      0.01        47       2      12 ..      15      25 ..      14      45 .. 0.85
   2 ?    7.1   0.0    0.0014       6.1     183     209 ..     177     205 ..     140     206 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.01
                                      SEEEEESBTTT CS
                                      xxxxxxxxxxx RF
                         Hydrolase  2 ktvvfDkdGTL 12
                                      +++vfD dGTL
  gi|385806163|ref|YP_005842561.1| 15 EALVFDYDGTL 25
                                      79********9 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0014
                                       HHHHT..STGGGEEEEESSHHHHHHHHHT CS
                                       xxxxx..xxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 183 ireLq..gkpeevamVGDgvnDaaalaaA 209
                                       ++  +   ++e+ a +GD+  D++ l++A
  gi|385806163|ref|YP_005842561.1| 177 LKIANaiLNIERFAYFGDSESDLESLKNA 205
                                       333335578999***************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); 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: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 1417.67
//
Query:       gi|385806164|ref|YP_005842562.1|  [L=247]
Description: putative replication protein [Fervidicoccus fontis Kam940]
Scores for complete 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   22.2   0.0    0.00019   21.6   0.0    1.2  1  RepB_primase  RepB DNA-primase from phage plasmid
  ------ inclusion threshold ------
      0.061   13.1   0.1       0.16   11.7   0.0    1.8  1  NIF           NLI interacting factor-like phosphatase


Domain annotation for each model (and alignments):
>> RepB_primase  RepB DNA-primase from phage plasmid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   2.2e-08   0.00019      81     146 ..     171     235 ..     156     246 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.2e-08
                      RepB_primase  81 lePaavletSPgnyqawlrvkaplshalrtaaakaLaeryGgDpaaadvsrfgRlPGfnnrKpkka 146
                                       ++++ ++  S + y++   +++  s      + + + e +GgD++++d  r +RlPG++n+K +k+
  gi|385806164|ref|YP_005842562.1| 171 FRLPDIVVDSGNGYHLYFELNKEESALKILSLEENVVELLGGDEKSKDLARILRLPGTVNQK-NKR 235
                                       4455577777777888877775555555556677777888**********************.444 PP

>> NIF  NLI interacting factor-like phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   1.8e-05      0.16      21      51 ..     142     172 ..     112     180 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.8e-05
                               NIF  21 klkvegekvevsvlkRpgldefLkelsklye 51 
                                        ++++++k+ ++v kRp l e+L++++k + 
  gi|385806164|ref|YP_005842562.1| 142 FCTYRKNKYSWYVVKRPALAEILEKAAKSFR 172
                                       446668999*****************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); 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 0.30s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1532.78
//
Query:       gi|385806165|ref|YP_005842563.1|  [L=304]
Description: 5-carboxymethyl-2-hydroxymuconate delta-isomerase [Fervidicoccus fontis Kam940]
Scores for complete 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-69  231.5   0.0      1e-68  231.3   0.0    1.1  1  FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family
  ------ inclusion threshold ------
      0.039   13.7   0.0       0.16   11.7   0.0    2.1  2  DUF348         G5-linked-Ubiquitin-like domain
      0.086   13.1   1.8       0.22   11.9   1.8    1.7  1  DUF1947        Domain of unknown function (DUF1947)


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 !  231.3   0.0   1.7e-72     1e-68       2     217 ..      94     300 ..      93     301 .. 0.96

  Alignments for each domain:
  == domain 1  score: 231.3 bits;  conditional E-value: 1.7e-72
                                       EEEEEEE--SHHHHHTTT.-SS-EEEEEEGGGE.EETTE..EE-TTSSSS-EE......EEEEEEEESS-B--T--H CS
                     FAA_hydrolase   2 ivcdglnyaehvreagkaaeeppdrhiplepvfflkrasslvgpgdpirrPagsekldyEvELavvigkplrevlsv 78 
                                       ++c+++ny++h +e g    +pp      +p+ff k ++slvg++d+i+ P+ sek+d+EvEL+vvigk+ + + + 
  gi|385806165|ref|YP_005842563.1|  94 FLCVAVNYKQHGQESG---LKPPS-----RPYFFPKFPTSLVGHEDNILKPKVSEKVDWEVELGVVIGKAGKYI-KK 161
                                       68************98...66777.....899******************************************.9* PP

                                       HHHHTTEEEEEEEEEEE-SBGGG---.HH..HHHHTGGGEEEEEE-B--B-.STT---SS-EEEEEETTEEEEEEEG CS
                     FAA_hydrolase  79 eeAedaiaGytllnDvsaRdlqaeekapl..gwflgksfdtftpiGpwivtpdeledpedlelrlrvngeevqdsnt 153
                                       ++A+++i+Gyt++nD++ Rd+q++   +l  +w+ gk +d +tp+Gp ivt+de+++p++l+l lrvng   q+++t
  gi|385806165|ref|YP_005842563.1| 162 DDADEHIFGYTIVNDITMRDWQFPPLGSLglDWIGGKTMDLSTPVGPYIVTKDEIDNPNNLKLYLRVNGSIEQNGST 238
                                       ************************9966677********************************************** PP

                                       GGTTTSHHHHHHHHHHHH-B-TT-EEEEEES.......S--EE--TT-EEEEEETTTEEEEEEE CS
                     FAA_hydrolase 154 kdmifspaeliahlsagltLepGdliltGTpsgvgaeeeslkflkdgDeveveieglGelrnrV 217
                                       +d+if+++eli++ s+g+tL+pGd+i+tGTpsgvg   +++k+lk gDeve+e+e++G lrn V
  gi|385806165|ref|YP_005842563.1| 239 NDLIFNVEELIEWSSKGITLRPGDIISTGTPSGVG--HSKNKYLKGGDEVEAEVEKIGILRNFV 300
                                       *********************************99..689*********************987 PP

>> DUF348  G5-linked-Ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0         1     6e+03       5      14 ..     195     204 ..     195     205 .. 0.84
   2 ?   11.7   0.0   2.7e-05      0.16      18      37 ..     244     265 ..     244     267 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1
                                       ETTEEEEE-- CS
                            DUF348   5 vDGktvtvrT 14 
                                       ++Gkt+ ++T
  gi|385806165|ref|YP_005842563.1| 195 IGGKTMDLST 204
                                       58***99998 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 2.7e-05
                                       SHHHHHH..HTT----TT-EEE CS
                            DUF348  18 TVgdlLe..eagitlgeqDkVs 37 
                                       +V++l+e  ++gitl++ D++s
  gi|385806165|ref|YP_005842563.1| 244 NVEELIEwsSKGITLRPGDIIS 265
                                       69******************98 PP

>> DUF1947  Domain of unknown function (DUF1947)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.8   3.6e-05      0.22       4      31 ..      49      75 ..      46      84 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.6e-05
                                      E--HHHHHHHHHHHHTTT---TT--..- CS
                           DUF1947  4 fLSkKeakeileklkekyisislesdki 31
                                      +L +Keak+++e+++ k+++++le++ i
  gi|385806165|ref|YP_005842563.1| 49 ILMEKEAKKLIEEIEAKSLDLDLEGN-I 75
                                      6889*********************8.5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2137.35
//
Query:       gi|385806166|ref|YP_005842564.1|  [L=207]
Description: methyltransferase small [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-15   57.5   0.0    4.1e-15   55.7   0.0    1.8  1  MTS              Methyltransferase small domain
    1.8e-11   44.0   0.0    2.4e-11   43.6   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    1.6e-10   41.0   0.0    2.4e-10   40.4   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    2.1e-10   41.2   0.0    4.3e-10   40.2   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    6.9e-09   36.3   0.0    2.8e-08   34.4   0.0    1.8  2  Methyltransf_12  Methyltransferase domain
    2.6e-07   31.2   0.0    6.5e-07   29.9   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
    2.6e-06   27.3   0.3      1e-05   25.4   0.3    1.8  1  UPF0020          Putative RNA methylase family UPF0020
    1.1e-05   25.3   0.0    2.1e-05   24.4   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
    1.9e-05   24.6   0.0    7.2e-05   22.8   0.0    1.7  2  Methyltransf_18  Methyltransferase domain
    0.00021   21.1   0.2    0.00073   19.3   0.0    1.8  2  Methyltransf_16  Lysine methyltransferase
    0.00038   20.6   0.0      0.001   19.2   0.0    1.6  1  FtsJ             FtsJ-like methyltransferase
     0.0004   19.8   0.0    0.00055   19.3   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
    0.00058   18.9   0.0    0.00075   18.6   0.0    1.1  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
     0.0014   18.2   0.0     0.0023   17.5   0.0    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
     0.0034   17.2   0.0     0.0047   16.7   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
     0.0062   15.8   0.0     0.0087   15.4   0.0    1.1  1  N6_Mtase         N-6 DNA Methylase
       0.01   15.3   0.0      0.013   14.9   0.0    1.3  1  TehB             Tellurite resistance protein TehB
  ------ inclusion threshold ------
      0.013   14.8   0.0       0.02   14.3   0.0    1.3  1  Methyltransf_10  RNA methyltransferase
      0.019   14.5   0.0      0.034   13.7   0.0    1.3  1  MetW             Methionine biosynthesis protein MetW
       0.02   14.2   0.0       0.03   13.6   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
      0.021   14.6   0.0       0.03   14.1   0.0    1.2  1  DUF938           Protein of unknown function (DUF938)
       0.06   13.0   0.0        0.1   12.2   0.0    1.4  1  Cons_hypoth95    Conserved hypothetical protein 95
       0.09   11.8   0.0       0.12   11.4   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
       0.12   11.8   0.0        0.2   11.1   0.0    1.3  1  Methyltransf_4   Putative 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 !   55.7   0.0   5.5e-18   4.1e-15       9     107 ..      25     122 ..      18     181 .. 0.82

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 5.5e-18
                                       TSTTTTS--HHHHHHHHHCHCC.TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..E CS
                               MTS   9 gvFskdklDkGsklLletlpke.lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..v 82 
                                       gvF    +   ++l++++l++   +gkvl +GcG+G++++ +ak+    +  ++d++  Al+ ak n + n++e  +
  gi|385806166|ref|YP_005842564.1|  25 GVFNP-TFTLSTSLIIDYLNEFkPKGKVLEIGCGTGAISIYIAKKFGL-KSYCTDISEVALATAKINSKINGVEknI 99 
                                       56643.4567899*******988999******************9876.899**********************999 PP

                                       EEEE-STTTTSTTS-EEEEEE---S CS
                               MTS  83 evvasdvleeveekkfdlivsNPPf 107
                                       ev++++ l  v+  +fdl+++NPP+
  gi|385806166|ref|YP_005842564.1| 100 EVLKTEKLRYVA--SFDLVITNPPY 122
                                       999999999999..**********7 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   0.0   3.3e-14   2.4e-11     148     233 ..      35     119 ..      29     121 .. 0.85

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 3.3e-14
                              PrmA 148 TklclealeklvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellke 224
                                       T+l +  l+++ k++ +vl +G+G+G ++i  ak    k + +Di evA+  ak N ++N+ve+++ev  +e+l   
  gi|385806166|ref|YP_005842564.1|  35 TSLIIDYLNEF-KPKGKVLEIGCGTGAISIYIAKKFGLKSYCTDISEVALATAKINSKINGVEKNIEVLKTEKLRYV 110
                                       66666666665.67779*************877766677899**************************666666657 PP

                              PrmA 225 ekadvivaN 233
                                       +++d+++ N
  gi|385806166|ref|YP_005842564.1| 111 ASFDLVITN 119
                                       99*****99 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.0   3.2e-13   2.4e-10       4     113 ..      48     167 ..      45     188 .. 0.79

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 3.2e-13
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDlil 79 
                                       + +vl++GCGtG++++ +a++ g   + +  Dise a+  A+ n++ +g++ n+e+ +   e+l   +  ++fDl++
  gi|385806166|ref|YP_005842564.1|  48 KGKVLEIGCGTGAISIYIAKKFG--LKSYCTDISEVALATAKINSKINGVEkNIEVLK--TEKLR--YV-ASFDLVI 117
                                       568****************8765..688999*******************95665554..44555..66.89***** PP

                   Methyltransf_31  80 sn.......evl..........naladpdkileeiervlkpggilliedpr 113
                                       +n         +           +l+ +++++    ++l+++g+++i+  +
  gi|385806166|ref|YP_005842564.1| 118 TNppylpleP-IdsldlnwcggRDLNLLKEAILLGRKALRKKGEMIITLSS 167
                                       **88777750.2555777878877777777777779**********99888 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.0   5.8e-13   4.3e-10       1      71 [.      51     119 ..      51     131 .. 0.91

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 5.8e-13
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvss 71 
                                       vL++GcGtG +++++ak++g  k +++Dise +l++a+ + + +g++ ++++ + e+l + + sfDlv+ +
  gi|385806166|ref|YP_005842564.1|  51 VLEIGCGTGAISIYIAKKFG-LKSYCTDISEVALATAKINSKINGVEKNIEVLKTEKLRYVA-SFDLVITN 119
                                       9******************8.******************99999999999999999999886.*****984 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.0   3.7e-11   2.8e-08       1      72 [.      52     118 ..      52     121 .. 0.86
   2 ?   -0.9   0.0       3.8   2.9e+03      58      72 ..     173     200 ..     145     203 .. 0.62

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 3.7e-11
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvva 72 
                                       LeiGcGtG+++ ++++k  +++ +++Dis+ a+  a +k+++++n   +n+e+ +++ l     +sfDlv+ 
  gi|385806166|ref|YP_005842564.1|  52 LEIGCGTGAISIYIAKK-FGLKSYCTDISEVAL--ATAKINSKINGVEKNIEVLKTEKLRY--VASFDLVIT 118
                                       8****************.89*************..88888888888888888877775443..47*****96 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 3.8
                   Methyltransf_12  58 lldldgg.............ssfDlvva 72 
                                       lld++ +             s fDlv++
  gi|385806166|ref|YP_005842564.1| 173 LLDDFLKkqgffmvgikrrvSPFDLVFL 200
                                       3333333445778888888889999986 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0   8.7e-10   6.5e-07       1      67 [.      52     118 ..      52     120 .. 0.88

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 8.7e-10
                                       EEET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEE CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg.arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvs 67 
                                       L++GcGtG+++ ++ak++  + +++D+s+ +l++ak +++ +g++ ++ v   ekl +   sfDlv+ 
  gi|385806166|ref|YP_005842564.1|  52 LEIGCGTGAISIYIAKKFgLKSYCTDISEVALATAKINSKINGVEKNIEVLKTEKLRYVA-SFDLVIT 118
                                       89*************6666*****************999999985567788888888876.****986 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.3   1.3e-08     1e-05      77     132 ..      71     123 ..      39     125 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 1.3e-08
                                       --EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE----- CS
                           UPF0020  77 lklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYG 132
                                       lk y+ D+ + ++++a+ N +  gv++ ie+ +    kLr   +++d+++tnpPY 
  gi|385806166|ref|YP_005842564.1|  71 LKSYCTDISEVALATAKINSKINGVEKNIEVLK--TEKLR-YVASFDLVITNPPYL 123
                                       5689************************99877..88999.7779**********5 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   2.9e-08   2.1e-05      20      62 ..      45      94 ..      36     121 .. 0.70

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 2.9e-08
                   Methyltransf_23 20 lraggrvLdiGcGtGillevl.rengfsvtgvDlspeaveiae......k 62
                                       +++g+vL+iGcGtG  + ++ +++g + +  D+s++a + a+      +
  gi|385806166|ref|YP_005842564.1| 45 FKPKGKVLEIGCGTGAISIYIaKKFGLKSYCTDISEVALATAKinskinG 94
                                      57899****************666799********998887754443331 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   9.7e-08   7.2e-05      13      78 ..      46     110 ..      37     118 .. 0.85
   2 ?   -0.9   0.0       1.9   1.4e+03     100     135 ..     149     185 ..     143     187 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 9.7e-08
                   Methyltransf_18  13 ekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGlekl 78 
                                       +++ +v+ iG+  g ++iy++k+    k + +Di+e +l++ak n + +g+e++iev  ++ l  +
  gi|385806166|ref|YP_005842564.1|  46 KPKGKVLEIGCGTGAISIYIAKKFGL-KSYCTDISEVALATAKINSKINGVEKNIEVLKTEKLRYV 110
                                       456799***************87777.7899**************************988877666 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.9
                   Methyltransf_18 100 Leeakeklkkikk.lilqpnseaeelRkylvengfki 135
                                       L  +k   kk +  + l++ ++   l ++l ++gf +
  gi|385806166|ref|YP_005842564.1| 149 LLGRKALRKKGEMiITLSSLTDLTLLDDFLKKQGFFM 185
                                       4444445555554245889999999999999999976 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   9.7e-07   0.00073      48     102 ..      49     101 ..      31     119 .. 0.76
   2 ?   -0.7   0.0       1.4     1e+03     139     170 ..     171     202 ..     161     206 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 9.7e-07
                   Methyltransf_16  48 lsvlELGsGtGlvGlavaellpeakviltDlee.llellkknielnknalkskvkv 102
                                        +vlE+G GtG + + +a++  ++k + tD++e +l   k n ++n+  ++++++v
  gi|385806166|ref|YP_005842564.1|  49 GKVLEIGCGTGAISIYIAKK-FGLKSYCTDISEvALATAKINSKING--VEKNIEV 101
                                       58*****************9.78899999999855666677777754..6665543 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.4
                   Methyltransf_16 139 LvkvLkellkkeskvlvaykkr.reaekkFfkl 170
                                       L ++L++ lkk++ ++v +k+r +  +  F+ +
  gi|385806166|ref|YP_005842564.1| 171 L-TLLDDFLKKQGFFMVGIKRRvSPFDLVFLYH 202
                                       3.5789999999999999999944556666655 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.4e-06     0.001      17     152 ..      43     183 ..      37     193 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.4e-06
                                       T-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS....HHH.TTEEEECS-CCCSSHHHHHCHCHHHSSE CS
                              FtsJ  17 klfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm....apl.pgvttiqgditdpetiekikealserkv 88 
                                       + fkp ++v+++g+++G+ s ++++++g   k +  D+ ++    a++ ++++ ++ +i   +t+++    +  + +
  gi|385806166|ref|YP_005842564.1|  43 NEFKPKGKVLEIGCGTGAISIYIAKKFG--LKSYCTDISEValatAKInSKINGVEKNIEVLKTEKLRY--V--ASF 113
                                       448899********************97..699********7766455789999999998888777333..2..359 PP

                                       EEEEE--S-SS-CHHHHHHHHH.......CCCCHHHHCCHCCCCECCCEEEECCCHCCCHHHHHHHHH.CCE CS
                              FtsJ  89 dlvvsDgapdvsgvhdldeylq.......sqLllaalelalkllkpggtfvlkifrgeeteallkqlk.kfF 152
                                       dlv+          + +d++         ++Ll+ a+ l+ k l+++g +++ +   ++ + l  +lk ++F
  gi|385806166|ref|YP_005842564.1| 114 DLVITNPP--YLPLEPIDSLDLnwcggrdLNLLKEAILLGRKALRKKGEMIITLSSLTDLTLLDDFLKkQGF 183
                                       99998753..3333444444445557777999*************999999988776666655555443555 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   7.3e-07   0.00055      60     120 ..      45     105 ..      33     118 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 7.3e-07
                                       --TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES- CS
                              CMAS  60 lkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklld 120
                                        kp  ++L+iGcG G++ ++ +++++ k     +S+   ++ak + +  ++e++ ev+ ++
  gi|385806166|ref|YP_005842564.1|  45 FKPKGKVLEIGCGTGAISIYIAKKFGLKSYCTDISEVALATAKINSKINGVEKNIEVLKTE 105
                                       688889******************************9999999998888888888887654 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 !   18.6   0.0     1e-06   0.00075     201     254 ..      47     102 ..      18     112 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1e-06
                   tRNA_U5-meth_tr 201 skgdllelycGnGnfslalarnfe.kvlateiakssveaaqyniaankid.nvqii 254
                                        kg +le+ cG G  s+ +a++f  k   t+i+  ++++a++n + n ++ n++++
  gi|385806166|ref|YP_005842564.1|  47 PKGKVLEIGCGTGAISIYIAKKFGlKSYCTDISEVALATAKINSKINGVEkNIEVL 102
                                       46799*****************95499********************996477775 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0     3e-06    0.0023       3      65 ..      50     113 ..      48     127 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3e-06
                   Methyltransf_15   3 vilDlfsGaGGnviqfalvf.ekviaieinleklacaqhNaevYgvsdkitlvlgdvfellakl 65 
                                        +l + +G+G  +i +a++f  k ++ +i++  la a+ N ++ gv+++i + + + +  +a++
  gi|385806166|ref|YP_005842564.1|  50 KVLEIGCGTGAISIYIAKKFgLKSYCTDISEVALATAKINSKINGVEKNIEVLKTEKLRYVASF 113
                                       589999************972589***************************9998877766654 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   6.3e-06    0.0047      63     104 ..      36      78 ..      18     112 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.3e-06
                                       HHHHHHTT.--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEE CS
                              PCMT  63 alalelle.lkkgarvLevGsGsGyltavlarlvgekgrvvsi 104
                                       +l++++l+ +k++ +vLe+G+G+G  +  +a+ +g k     i
  gi|385806166|ref|YP_005842564.1|  36 SLIIDYLNeFKPKGKVLEIGCGTGAISIYIAKKFGLKSYCTDI 78 
                                       57899**99***************9999999988887744444 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.2e-05    0.0087      36     135 ..      36     122 ..      21     126 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.2e-05
                          N6_Mtase  36 klivell.epksgesvyDpacGsggllvqaekvlkeedgktkelsiyGqeknettyrLakmNlllhgieykkvkirl 111
                                       +li++ l e k++ +v+   cG+g++ +  +k++         l+ y  ++ e + + ak+N  + g+e++      
  gi|385806166|ref|YP_005842564.1|  36 SLIIDYLnEFKPKGKVLEIGCGTGAISIYIAKKF--------GLKSYCTDISEVALATAKINSKINGVEKN------ 98 
                                       677777766677778999******9999888876........6999***********************99...... PP

                          N6_Mtase 112 gdtlekpkfekdkkfdvvvaNppf 135
                                        + l+++k +   +fd v++Npp+
  gi|385806166|ref|YP_005842564.1|  99 IEVLKTEKLRYVASFDLVITNPPY 122
                                       35678888888999*********9 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.8e-05     0.013      20      92 ..      36     109 ..      25     146 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.8e-05
                                       HHHHHHCCCS-S.-EEEEES-TTSHHHHHHHH.TT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG--- CS
                              TehB  20 sevveavkivkp.gkvldlgcgqgrnslylsl.lgydvtawdknensiafleeikekenlknistalydineakl 92 
                                       s +++  +  kp gkvl++gcg g  s+y++   g +  + d  e ++a  + i++k n  + + ++++ ++++ 
  gi|385806166|ref|YP_005842564.1|  36 SLIIDYLNEFKPkGKVLEIGCGTGAISIYIAKkFGLKSYCTDISEVALATAK-INSKINGVEKNIEVLKTEKLRY 109
                                       55667777777768***************98525777777777776666543.3333332224444444455555 PP

>> Methyltransf_10  RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   2.6e-05      0.02      94     167 ..      43     110 ..       6     125 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.6e-05
                                       TGGGSGTTS--EEEEES-TTTTHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHHT.T-TTTEEEEE--TT-SC CS
                   Methyltransf_10  94 gkadsdisaqvraldiGvGanCiyPllGvteyGWrfvgsevddvslasakaivesnsklsdaiklrkqkekkai 167
                                        + +++   +v  +  G+Ga  iy    ++++G +   +++++v+la+ak + + n  +++ i++ k ++ + +
  gi|385806166|ref|YP_005842564.1|  43 NEFKPKG--KVLEIGCGTGAISIY---IAKKFGLKSYCTDISEVALATAKINSKIN-GVEKNIEVLKTEKLRYV 110
                                       3333332..344445556666666...4789*********************9999.9*******998776554 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.6e-05     0.034      10      80 ..      44     117 ..      37     121 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.6e-05
                              MetW  10 likpgsrvldlGcGdGellellkeekqvdgrGleldeegvaec.vakGlsviqgdld..kdlenfedksfdyvv 80 
                                         kp+ +vl++GcG G +  +++++ +++++  +++e ++a + ++  ++ ++++++  k  +     sfd+v+
  gi|385806166|ref|YP_005842564.1|  44 EFKPKGKVLEIGCGTGAISIYIAKKFGLKSYCTDISEVALATAkINSKINGVEKNIEvlKTEKLRYVASFDLVI 117
                                       56899*****************************9998887653667788888887632222223345777777 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0     4e-05      0.03      46     106 ..      46     105 ..      32     118 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4e-05
                                       --TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS.TEEEEE-- CS
                   Ubie_methyltran  46 krgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki.nieflqan 106
                                       k+  kvl++ +Gtg +++ ++++ g k      Di+e  L +++   k +g+  nie l+++
  gi|385806166|ref|YP_005842564.1|  46 KPKGKVLEIGCGTGAISIYIAKKFGLKS--YCTDISEVALATAKINSKINGVEkNIEVLKTE 105
                                       44459****************9998765..678***********999999987799998764 PP

>> DUF938  Protein of unknown function (DUF938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   4.1e-05      0.03      21      54 ..      44      76 ..      34     104 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.1e-05
                            DUF938 21 ylakttervLEiasGtGqHAvffApalpnlkwqp 54
                                       ++ +++ vLEi+ GtG   +++A+++    + +
  gi|385806166|ref|YP_005842564.1| 44 EFKPKGK-VLEIGCGTGAISIYIAKKFGLKSYCT 76
                                      4666775.******************98887765 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00014       0.1      34     123 ..      40     122 ..      14     130 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                                       HHHCCCHCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--S CS
                     Cons_hypoth95  34 nilaaeiegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakk 110
                                       + l++   + +vL++ +G+Ga+++  +     k+++ + ++ a+++ k n +  ++e+++++lk ++l+ +      
  gi|385806166|ref|YP_005842564.1|  40 DYLNEFKPKGKVLEIGCGTGAISIYIAKKFGLKSYCTDISEVALATAKINSKINGVEKNIEVLKTEKLRYV------ 110
                                       56666677889***************99999********************99999987777777666555...... PP

                                       S-EEEEEEE--SS CS
                     Cons_hypoth95 111 keefdivflDPPy 123
                                        ++fd+v  +PPy
  gi|385806166|ref|YP_005842564.1| 111 -ASFDLVITNPPY 122
                                       .469********* PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00016      0.12      27      84 ..      44     105 ..      30     125 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00016
                                       -GGTTSEEEEES-TTTCCHHHHHCC-..SEEEE..E-S-HHHHHHHHCHTT.TCCCEEEE-S- CS
                            RrnaAD  27 nleekltvleigpGkGilTeeLakra..kqvvv..lElderLakllqkkls.kdeklkvvhqD 84 
                                       + ++k +vleig G+G+ +  +ak +  k++     E   + ak+ + k++  +++++v++++
  gi|385806166|ref|YP_005842564.1|  44 EFKPKGKVLEIGCGTGAISIYIAKKFglKSYCTdiSEVALATAKI-NSKINgVEKNIEVLKTE 105
                                       356999******************999888764112333333333.33355677777777765 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00026       0.2       5      63 ..      51     109 ..      47     114 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00026
                                       EEEET-TTSHHHHHHHHHSTTSEEEE.EES-HHHHHHHHHHHHHCTTSSEEEEES-CCCH CS
                    Methyltransf_4   5 vleiGcGkGeflvalAkknPdknflG.iEirvkvvakvlkkiealelkNlrilrgdalkv 63 
                                       vleiGcG G + + +Akk+  k++   i      +ak+++ki+    kN+++l+++ l++
  gi|385806166|ref|YP_005842564.1|  51 VLEIGCGTGAISIYIAKKFGLKSYCTdISEVALATAKINSKINGV-EKNIEVLKTEKLRY 109
                                       89****************998887542333334445555555544.37888888776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); 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 0.28s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1237.51
//
Query:       gi|385806167|ref|YP_005842565.1|  [L=479]
Description: major facilitator superfamily protein [Fervidicoccus fontis Kam940]
Scores for complete 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-48  164.0  54.9    6.7e-48  163.4  54.2    1.8  1  MFS_1       Major Facilitator Superfamily
    2.4e-10   39.9  41.3    6.9e-10   38.4  18.2    3.0  3  Sugar_tr    Sugar (and other) transporter
    5.6e-06   25.5  29.7     0.0043   15.9  12.1    2.2  2  MFS_1_like  MFS_1 like family
    4.7e-05   21.9   0.4    4.7e-05   21.9   0.4    3.5  4  OATP        Organic Anion Transporter Polypeptide (OATP) fami
  ------ inclusion threshold ------
        4.2    6.9   6.6        9.7    5.8   0.9    2.7  2  PIRT        Phosphoinositide-interacting protein family


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.4  54.2   1.9e-51   6.7e-48       2     352 ..      17     403 ..      16     404 .. 0.91

  Alignments for each domain:
  == domain 1  score: 163.4 bits;  conditional E-value: 1.9e-51
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglll 78 
                                        la f++++++ ++ + lp ++a + g+++ ++ +++ +++lg+ +++l++Grl+d +Gr r++ +g+ +f +g+ll
  gi|385806167|ref|YP_005842565.1|  17 TLASFIAGFNARLAVVGLP-TIAGEIGADVWSMIWIIQGFMLGSTIFQLIIGRLTDLYGRVRLFTIGIGIFTIGALL 92 
                                       5899***************.******************************************************555 PP

                             MFS_1  79 llfasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravf 154
                                         + ss + +l+++r +qG+g+++l+++++++++d +p+++ g  +g+ ++++ +Ga+lg  l+g+++++l+W+++f
  gi|385806167|ref|YP_005842565.1|  93 SGL-SSNPaFLIISRTVQGIGGAFLMSISITILTDNVPPSRLGTWLGVNQVAWRIGALLGLTLSGFIIDLLSWHWIF 168
                                       557.88898******************************************************************** PP

                             MFS_1 155 yilaivsllafvlfllllpeepperkrkspkeee........................................... 188
                                       +i  ++++++  lf+  ++ +++ +++++   +                                            
  gi|385806167|ref|YP_005842565.1| 169 LIQVPIGVIV--LFWTRIRLKEVYKPKENIFIDIkgftfftlsltlsligltmvgygyrdysyillalsvaflaifv 243
                                       **********..98999999999999999999999999999999999999999999999998888886666665555 PP

                             MFS_1 189 ..kgtgpaplvpawkallkdpvl.....w...illialllfffgfsglltllplylqevlglsglllaglllallal 255
                                         + +  +p+++          l     w     +i+ ll ++gf + ltll +y+q+vlg+s   ++g+ll  + +
  gi|385806167|ref|YP_005842565.1| 244 ysELKTTHPALD----------LrlfkiWqfsGGIISQLLYSIGFGASLTLLAIYMQSVLGYS-PSETGILLVPYEA 309
                                       554444444444..........033333566679999999999********************.8************ PP

                             MFS_1 256 vgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGfglgfvfpsllalasdlappe 332
                                        ++++++++grlsd lg   +  +++++l++++++l+ll+++ s ++++++ v++G+g g+++++ ++ ++ ++pp+
  gi|385806167|ref|YP_005842565.1| 310 SFLVFGIIGGRLSDILG---FAPVTVAGLAVGSISLFLLSLAGSIPMIIFAEVILGVGTGLFVSPNTSSIMTSVPPD 383
                                       ***************88...7999999999999999999999999******************************** PP

                             MFS_1 333 eagtasglfntagslggalg 352
                                       ++g as++ ++ +++g a++
  gi|385806167|ref|YP_005842565.1| 384 RRGVASSIRTVSFNVGFAIS 403
                                       ***************99986 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4  18.2   1.9e-13   6.9e-10      47     187 ..      47     181 ..      12     185 .. 0.93
   2 ?    0.4   2.9     0.063   2.3e+02      66     151 ..     215     316 ..     204     317 .. 0.75
   3 !   11.3   7.2   3.1e-05      0.11      62     157 ..     314     406 ..     288     426 .. 0.87

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 1.9e-13
                                       HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHH CS
                          Sugar_tr  47 lsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlv 123
                                        + +i   f++G++i +l++g l+d +GR   + i++ +f iga+l++++    +   li++R + Gig  +   ++
  gi|385806167|ref|YP_005842565.1|  47 SMIWIIQGFMLGSTIFQLIIGRLTDLYGRVRLFTIGIGIFTIGALLSGLSS---NPAFLIISRTVQGIGGAFLMSIS 120
                                       57899999*******************************************...9**************99999999 PP

                                       HHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHH CS
                          Sugar_tr 124 PmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllil 187
                                        + +  + p++  g+  +++q+a+ +G l++ ++  ++ +  +   w++ + +q+ + +++l++
  gi|385806167|ref|YP_005842565.1| 121 ITILTDNVPPSRLGTWLGVNQVAWRIGALLGLTLSGFIIDLLS---WHWIFLIQVPIGVIVLFW 181
                                       9999999999999****************************99...************998876 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.063
                                       HHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTT..........SS-TGGGGG...HHHHHHHHHHHHHHHHHHHHT CS
                          Sugar_tr  66 agllgdrfGRkkslliaavlfvigavlqaaakgk..........nsvevlivg...RvlvGigvGlasvlvPmyisE 129
                                       +gl +  +G+++   i  +l+v+  ++ + ++ k          ++++++  g   ++l  ig G+  +l  +y++ 
  gi|385806167|ref|YP_005842565.1| 215 IGLTMVGYGYRDYSYILLALSVAFLAIFVYSELKtthpaldlrlFKIWQFSGGiisQLLYSIGFGASLTLLAIYMQS 291
                                       4555666999*999999**********9999998999999****666666444444***********9999999875 PP

                                       T...S-SCCHHHHHHHHHHHHHHHH CS
                          Sugar_tr 130 i...ApkklRgalvslyqlaitfGi 151
                                       +   +p +    lv +  ++++fGi
  gi|385806167|ref|YP_005842565.1| 292 VlgySPSETGILLVPYEASFLVFGI 316
                                       4222455555555555555666665 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 3.1e-05
                                       HHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHH CS
                          Sugar_tr  62 GslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRga 138
                                        ++++g l+d++G  ++ +++ ++ +i+ +l  +a    s+ ++i++ v++G+g Gl+    +  i    p++ Rg 
  gi|385806167|ref|YP_005842565.1| 314 FGIIGGRLSDILGFAPVTVAGLAVGSISLFLLSLAG---SIPMIIFAEVILGVGTGLFVSPNTSSIMTSVPPDRRGV 387
                                       57899*******************************...*******************999999999999******* PP

                                       HHHHHHHHHHHHHHHHHHH CS
                          Sugar_tr 139 lvslyqlaitfGilvaaif 157
                                         s+  ++  +G+ ++  +
  gi|385806167|ref|YP_005842565.1| 388 ASSIRTVSFNVGFAISLNI 406
                                       ************9776554 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 !   15.9  12.1   1.2e-06    0.0043     261     384 ..      45     169 ..      39     170 .. 0.91
   2 !   15.4   9.6   1.8e-06    0.0065     165     352 ..     208     390 ..     201     406 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.2e-06
                        MFS_1_like 261 llGslvalg..vvaeiplfffaeklleklGhvklliiallayilrfllyaiienawlvlpievLhgisfgllwaaav 335
                                       +++++++++  ++++ ++ ++  +l++ +G v+l +i++ ++++  ll ++ +n+ ++++  + +gi  + l ++ +
  gi|385806167|ref|YP_005842565.1|  45 VWSMIWIIQgfMLGSTIFQLIIGRLTDLYGRVRLFTIGIGIFTIGALLSGLSSNPAFLIISRTVQGIGGAFLMSISI 121
                                       6888888873345578888999******************************************************* PP

                        MFS_1_like 336 eyvskiapksleatgqgllsglyfglGralGsliGGllwdlksaiflFr 384
                                       +   + +p+s  +t  g+ + + + +G  lG  ++G+++dl s +++F 
  gi|385806167|ref|YP_005842565.1| 122 TILTDNVPPSRLGTWLGVNQVA-WRIGALLGLTLSGFIIDLLSWHWIFL 169
                                       *****************98766.******************99999986 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.8e-06
                        MFS_1_like 165 tGilidhysvnllp..ysallyvlaallvisllvvlilnetekesklkvtkslqvllnilknpeviifllvalilgm 239
                                       +++ +  +  ++++  y+   y+l+al v+ l++++  + ++ +++l+++        ++k  +  + ++  l+  +
  gi|385806167|ref|YP_005842565.1| 208 LSLTLSLIGLTMVGygYRDYSYILLALSVAFLAIFVYSELKTTHPALDLR--------LFKIWQFSGGIISQLLYSI 276
                                       55555555555555666677777777777777777777777777777666........7788888888999999999 PP

                        MFS_1_like 240 swgiienFlflYL.kelgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaiienawl 315
                                        +g+  + l +Y+ + lg+s +  G+l++   ++ +++ +++ +l ++lG+  + +++l +  + ++l+++  +  +
  gi|385806167|ref|YP_005842565.1| 277 GFGASLTLLAIYMqSVLGYSPSETGILLVPYEASFLVFGIIGGRLSDILGFAPVTVAGLAVGSISLFLLSLAGSIPM 353
                                       9999999******8889************************************************************ PP

                        MFS_1_like 316 vlpievLhgisfgllwaaaveyvskiapksleatgqg 352
                                       ++++ev+ g+ +gl+ +  ++ +   +p+  ++   +
  gi|385806167|ref|YP_005842565.1| 354 IIFAEVILGVGTGLFVSPNTSSIMTSVPPDRRGVASS 390
                                       **************98777777777777666665555 PP

>> OATP  Organic Anion Transporter Polypeptide (OATP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.7     0.092   3.3e+02      37      83 ..      47      93 ..      13      99 .. 0.77
   2 !   21.9   0.4   1.3e-08   4.7e-05     134     193 ..     101     160 ..      93     166 .. 0.92
   3 ?    0.4   4.0     0.043   1.6e+02     289     375 ..     257     342 ..     244     357 .. 0.78
   4 ?   -0.1   0.2     0.059   2.1e+02     134     506 ..     353     397 ..     343     413 .. 0.55

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.092
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 37 tsgliassneignillilfvsYfggrghrPrwigigallmalgslll 83
                                      ++ +i  ++ +g++++ l+++ + +   r r+  ig+ ++++g+ll 
  gi|385806167|ref|YP_005842565.1| 47 SMIWIIQGFMLGSTIFQLIIGRLTDLYGRVRLFTIGIGIFTIGALLS 93
                                      56788888889999999999999999999999999999999999886 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 1.3e-08
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 134 lfflaqlllGiGatpiytlGisYidDnvkkknsplylgilyalrilGpalGfllGslllk 193
                                       +++++ +++GiG++ ++++ i+ + Dnv +++  + lg+ ++++ +G  lG +l+++++ 
  gi|385806167|ref|YP_005842565.1| 101 FLIISRTVQGIGGAFLMSISITILTDNVPPSRLGTWLGVNQVAWRIGALLGLTLSGFIID 160
                                       6899***************************************************99875 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.043
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 289 rllknpifllvilssvfeillvaGfitFlpkylEtqFslsaseAnlltGvvvipgaalGillgGllvkklklsakkl 365
                                       rl+k   f   i+s+ ++++++ +  t l  y+++  + s+se  +l+ ++   + ++Gi +gG l   l + + ++
  gi|385806167|ref|YP_005842565.1| 257 RLFKIWQFSGGIISQLLYSIGFGASLTLLAIYMQSVLGYSPSETGILLVPYEASFLVFGI-IGGRLSDILGFAPVTV 332
                                       6667777777899**********************************9999999999997.5888887777777777 PP

                                       xxxxxxxxxx RF
                              OATP 366 aklvlvvsll 375
                                       a l++ +  l
  gi|385806167|ref|YP_005842565.1| 333 AGLAVGSISL 342
                                       7666554433 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 0.059
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 134 lfflaqlllGiGatpiytlGisYidDnvkkknsplylgilyalrilGpalGfllGslllklyvdidseisltpkdpr 210
                                       ++++a+++lG+G+ ++++  +s i  +v + +                                             
  gi|385806167|ref|YP_005842565.1| 353 MIIFAEVILGVGTGLFVSPNTSSIMTSVPPDRR-------------------------------------------- 385
                                       566666666666666666555555555555554............................................ PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 211 WvgaWWlgflilgvllllaaiplffFPkelpkkkeerakkkseeesaekkeekkkkeksksseeeelkslkdfpkal 287
                                                                                                                    
  gi|385806167|ref|YP_005842565.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 288 krllknpifllvilssvfeillvaGfitFlpkylEtqFslsaseAnlltGvvvipgaalGillgGllvkklklsakk 364
                                                                                                                    
  gi|385806167|ref|YP_005842565.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 365 laklvlvvsllsllllllllflgCetskvagvtvsyeelnqvenltssCnsdCsssseakkksttettncscaaeke 441
                                                                                                                    
  gi|385806167|ref|YP_005842565.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 442 gesesavaGkCdsdCkkklllflillflvsflgalgrvpallvilRcVkkedksfalGlqlllir 506
                                                                                             +a ++ ++ ++
  gi|385806167|ref|YP_005842565.1| 386 -----------------------------------------------------GVASSIRTVSFN 397
                                       .....................................................333333333332 PP

>> PIRT  Phosphoinositide-interacting protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.9    0.0027       9.7      52      98 ..      78     124 ..      70     128 .. 0.90
   2 ?    3.2   0.5     0.017        59      66     105 ..     181     220 ..     161     223 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0027
                              PIRT  52 vlsvGgavfllGvvittlsrnstlknkdkevfklsGpaflslGlmll 98 
                                       ++++G  +f +G +++ ls n ++   +++v  + G  ++s+ + +l
  gi|385806167|ref|YP_005842565.1|  78 LFTIGIGIFTIGALLSGLSSNPAFLIISRTVQGIGGAFLMSISITIL 124
                                       6789********************************9999*999887 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.017
                              PIRT  66 ittlsrnstlknkdkevfklsGpaflslGlmllvcGlvwv 105
                                        t +  +++ k k++    + G +f++l l l ++Gl  v
  gi|385806167|ref|YP_005842565.1| 181 WTRIRLKEVYKPKENIFIDIKGFTFFTLSLTLSLIGLTMV 220
                                       244556677777777777******************9866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (479 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.52
# Mc/sec: 2792.97
//
Query:       gi|385806168|ref|YP_005842566.1|  [L=37]
Description: hypothetical protein FFONT_1126 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       197  (0.0109878); 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:                         0  (0); expected 0.2 (1e-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: 00:00:00.49
# Mc/sec: 227.08
//
Query:       gi|385806169|ref|YP_005842567.1|  [L=235]
Description: 50S ribosomal protein L15e [Fervidicoccus fontis Kam940]
Scores for complete 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-78  261.6   6.2    3.7e-78  261.6   6.2    1.4  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 !  261.6   6.2   2.1e-82   3.7e-78       1     182 [.      14     194 ..      14     203 .. 0.96

  Alignments for each domain:
  == domain 1  score: 261.6 bits;  conditional E-value: 2.1e-82
                                       -SHHHHHHHTTSTTSHHHHHHHHHHHHHHTTS-SEEEESS-SSHHHHHHHT--SSTTEEEEEEEEE-SS---..--- CS
                    Ribosomal_L15e   1 gaykylrelwkkkqsdvlrellrerlweyrqepavvrverptrldrArrLGYkakqGivvvrvrvrrGgrkkkvskg 77 
                                       ++y y++ +wk++ s  + +l+r r++++r+epavvr+++ptrl++Ar+LGYkakqGi+vvrvr+r+Gg+++  ++ 
  gi|385806169|ref|YP_005842567.1|  14 SMYYYMARVWKRPYSGDHLQLMRARMIRWRREPAVVRINKPTRLNKARMLGYKAKQGIIVVRVRIRKGGQRR--QRP 88 
                                       79**********************************************************************..*** PP

                                       SS---GGGG-SSS---SS-HHHHHHHHHHHHSTTSEEEEEEEEEEESSEEEEEEEEE-TTSHHHHT-TTTGGGGSGG CS
                    Ribosomal_L15e  78 ktgrkpkrqgvnklkpakslqaiaeervgrklpnlrvLnSYwvgeDgtykyyEvilvDpshkairndkkinwickkv 154
                                       ++gr+pkr+gv+ + paks++ iaeer++rk+pnl+vLnSY+vgeDg + +yEvi+vDp+h+ai +d++++wi++++
  gi|385806169|ref|YP_005842567.1|  89 NKGRRPKRMGVYGYAPAKSIRLIAEERAARKYPNLEVLNSYYVGEDGVHEWYEVIMVDPHHPAILSDPELKWIAEPQ 165
                                       ***************************************************************************** PP

                                       GTTGGGGT-SHHHHHHTT-S-SS..TT-T CS
                    Ribosomal_L15e 155 hkhRelrGltsagkksRGlrkkg.lkgae 182
                                       +++R++rGltsagkk+RGl+ ++ l+g+ 
  gi|385806169|ref|YP_005842567.1| 166 NRGRVFRGLTSAGKKMRGLKASRgLRGTM 194
                                       *******************8654266655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1428.47
//
Query:       gi|385806170|ref|YP_005842568.1|  [L=145]
Description: hypothetical protein FFONT_1128 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.1e-27   94.8   3.0      5e-27   94.6   3.0    1.1  1  RNA_binding   RNA binding
     0.0091   15.4   0.1      0.014   14.8   0.1    1.3  1  UBM           Ubiquitin binding region
  ------ inclusion threshold ------
      0.027   14.8   0.1      0.041   14.2   0.1    1.3  1  Blt1          Blt1 N-terminal domain
      0.049   14.2   0.1      0.078   13.5   0.1    1.3  1  3-dmu-9_3-mt  3-demethylubiquinone-9 3-methyltransferase


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 !   94.6   3.0   1.1e-30     5e-27       1     118 [.       5     124 ..       5     125 .. 0.97

  Alignments for each domain:
  == domain 1  score: 94.6 bits;  conditional E-value: 1.1e-30
                                       EEEEEEEE-TTC-HHHHHHHHHTTSTTS...E---EEEEEE-CCC-EEEEEEEEESSHHHHHHHHHHHHHHCCCCHH CS
                       RNA_binding   1 kievrafvhaTEdeekVlealsnllpee...eveieeeeaeGhygnpitileaelekkkakkvlkkllellreeeik 74 
                                       +ie+r++ h TE+e++Vl++l n lpe+   +v+    +++Ghyg+ i+++++ lek++a+k+++++++++++  + 
  gi|385806170|ref|YP_005842568.1|   5 QIELRVIQHMTEEEDRVLRSLLNALPEDlreKVKPVAVSSKGHYGDTIIFYKVVLEKEDAEKAAEFIIRSFDKCSVF 81 
                                       59************************99*88777799**************************************** PP

                                       HHHHCCHCCB-TTSEEEEEEEHHHHHTT---BESSSSEEEEEEE CS
                       RNA_binding  75 eLlkeleervdekgklylrldKQaaylgklslvegddvIkvkik 118
                                       e+++++ +r++ +++++lrldK +++++k+ ++++ddv+k++ik
  gi|385806170|ref|YP_005842568.1|  82 EIKNTFYNRFS-DNSFHLRLDKFKLLENKFIISNSDDVVKIVIK 124
                                       ***********.9*****************************98 PP

>> UBM  Ubiquitin binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   3.1e-06     0.014       5      23 ..      17      35 ..      14      37 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.1e-06
                               UBM  5 ppegiDpsFLaaLPpdLRe 23
                                      +++ +  s L+aLP+dLRe
  gi|385806170|ref|YP_005842568.1| 17 EEDRVLRSLLNALPEDLRE 35
                                      5667889***********9 PP

>> Blt1  Blt1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   9.1e-06     0.041      83     131 ..      76     126 ..      58     136 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.1e-06
                              Blt1  83 attsvkdlkeavqervkeaetkvpldkikiLykkkPv..sgktlaevlase 131
                                        + sv ++k+++ +r  +++ ++ ldk k+L +k  +  s+ +++ v++++
  gi|385806170|ref|YP_005842568.1|  76 DKCSVFEIKNTFYNRFSDNSFHLRLDKFKLLENKFIIsnSDDVVKIVIKES 126
                                       589******************************999954446666666553 PP

>> 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 ?   13.5   0.1   1.7e-05     0.078       9      66 ..      60     118 ..      51     131 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.7e-05
                      3-dmu-9_3-mt   9 fdgeaeeAaefYvsvfenseilsvarypeee.pskegkvltveFtlagqefvalnggpe 66 
                                        +++ae+Aaef ++ f++ ++ +++++  +   +++ ++   +F+l +++f+  n+   
  gi|385806170|ref|YP_005842568.1|  60 EKEDAEKAAEFIIRSFDKCSVFEIKNTFYNRfSDNSFHLRLDKFKLLENKFIISNSDDV 118
                                       3699*******************99988877477999999************9998754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       834  (0.0465168); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 876.85
//
Query:       gi|385806171|ref|YP_005842569.1|  [L=204]
Description: RNase P subunit p30 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-10   39.8   0.2    5.6e-10   39.0   0.2    1.3  1  RNase_P_p30    RNase P subunit p30
  ------ inclusion threshold ------
      0.078   12.7   0.0       0.29   10.9   0.0    2.1  2  FAD_binding_4  FAD binding 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 !   39.0   0.2   6.3e-14   5.6e-10       9     212 ..      13     195 ..       8     198 .. 0.88

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 6.3e-14
                                       .........HHHHHHHHH-SEEEEEEEEEESS---HHHHH.......HHHHHHHH..HHSSEEEEEEES-H..HHHH CS
                       RNase_P_p30   9 sddskkksrtiktlaelgytgvainftveaekekkpnasepikeelkelkkelsglkllsRvtlvvsdpskl.qrls 84 
                                       +d+++ k+ ++k +++l+y+ + i+ +++   +k+ +               +++lk+l+   +++ d ++  ++l 
  gi|385806171|ref|YP_005842569.1|  13 KDEEELKK-IVKVAQSLNYSLIGIDEKYS---TKISSLA-------------SEQLKVLTSRRVEAFDEREAkNKLH 72 
                                       55555555.88888888888888888888...3333322.............3568999999999999997669*** PP

                                       HHHHH--EEEEE--SHHHHHHHHHT.T-SEEE-TTTTSSS-S--HHHHHHHHHHT-EEEEESHHHHHS-HHHHHHHH CS
                       RNase_P_p30  85 kvrqkfdllavrPttekalraacenldvDiisidltsrlpfglkhktiraAvergvafEinyspllrdsglaRrnfi 161
                                          +k+ +     +   alr+  +n  vDii i    +l+ +++++++ +  + ++++ in+++++r+       +i
  gi|385806171|ref|YP_005842569.1|  73 AAGKKVSITIGVAKGASALRFFSKNKSVDIIEISP--KLHRVMDKNQADLMKQGKTSIGINLGEIVRKLE-----LI 142
                                       ********************************999..9*****************************999.....9* PP

                                       HHHHHHHHHHHH..--EEEE--BSSGGG---HHHHHHHHHHHT--HHHHHHTT CS
                       RNase_P_p30 162 snarkllrltrg..kgvviSSgAesplelRnpydiinLlktlGLeedrakeav 212
                                         a  l++ + +    + + SgAe+  el++p+ +  Llkt+G++e  ak++v
  gi|385806171|ref|YP_005842569.1| 143 PFAEFLIKYALKydIKIAFYSGAEKYSELWHPRSVFHLLKTFGITERVAKSIV 195
                                       ********99999999999*******************************987 PP

>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   3.2e-05      0.29       2      28 ..       7      33 ..       6      87 .. 0.77
   2 ?   -1.8   0.0      0.26   2.4e+03      17      36 ..     149     168 ..     147     173 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.2e-05
                                      EEEEEESSHHHHHHHHHHHHHCTSCEE CS
                     FAD_binding_4  2 aavvrpeseeevaaalrlaneaglpvl 28
                                      +++++p++eee+++++++a++ +  ++
  gi|385806171|ref|YP_005842569.1|  7 DYYIFPKDEEELKKIVKVAQSLNYSLI 33
                                      799****************98776654 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.26
                                       HHHHHHCTSCEEEESSSTTE CS
                     FAD_binding_4  17 lrlaneaglpvlvrGgGssl 36 
                                       +++a ++++++ +++g  ++
  gi|385806171|ref|YP_005842569.1| 149 IKYALKYDIKIAFYSGAEKY 168
                                       899*********99998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       816  (0.0455129); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.32s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1289.60
//
Query:       gi|385806172|ref|YP_005842570.1|  [L=168]
Description: ribonuclease P protein subunit Rpp14 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-14   53.0   0.1    4.5e-14   52.5   0.1    1.2  1  RNase_P_Rpp14  Rpp14/Pop5 family
  ------ inclusion threshold ------
      0.043   13.9   0.7      0.094   12.8   0.7    1.5  1  IGR            IGR protein motif
      0.063   13.3   0.3       0.25   11.4   0.3    2.0  2  WhiA_N         WhiA N-terminal LAGLIDADG-like domain
       0.22   11.4   1.8       0.28   11.1   0.5    1.8  2  DUF5370        Family of unknown function (DUF5370)


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     1e-17   4.5e-14       1     101 [.      69     164 ..      69     166 .. 0.93

  Alignments for each domain:
  == domain 1  score: 52.5 bits;  conditional E-value: 1e-17
                                       EEEEEEEEESS......-HHHHHHHHHHHHHHHHHHHHHHH--..EEEEEETTTTEEEEEEEGGGHHHHHHHHHT-- CS
                     RNase_P_Rpp14   1 RYllveilypdeeeelteksllkairesvqelfGdyglgklgsslsvkyfspatstaiiRcsresyrlvwaaLtlit 77 
                                       RY++++i ++    +++ +++++ i +++ +++G+  ++k g  + ++y+s+  + +i+R+ re+ ++++a++++ +
  gi|385806172|ref|YP_005842570.1|  69 RYIVFSITSDA---DIDYSEIADSILTALGKIYGEPFISKSGYHF-IVYYSD-IKKGIVRVYREYADNIIAIFPFAR 140
                                       9*********9...4789*************************64.677776.699********************* PP

                                       EETTEEEEEEEEEEESSHHHHHHH CS
                     RNase_P_Rpp14  78 kiegrpvvfrvvrvsGTikkaeee 101
                                       ++ ++++++ +v+v GT+kka+++
  gi|385806172|ref|YP_005842570.1| 141 RYAKKDFMIVPVKVCGTVKKAKKF 164
                                       *********************997 PP

>> IGR  IGR protein motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.7   2.1e-05     0.094       4      45 ..      29      71 ..      29      74 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.1e-05
                               IGR  4 LkkIGRnceehaekfeswekLfelsskqlkelGipvr.qRRYi 45
                                      +kkI R++ +  +kf  + +L +++++++ ++  +v+ ++RYi
  gi|385806172|ref|YP_005842570.1| 29 FKKIERGLTTLNKKFSLISSLENWNKEEMVKKEAKVKrKKRYI 71
                                      589*******************************775167898 PP

>> WhiA_N  WhiA N-terminal LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.3   5.7e-05      0.25      41      75 ..      43      77 ..      36      91 .. 0.85
   2 ?   -0.7   0.0      0.33   1.5e+03      29      49 ..      79      99 ..      73     101 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.7e-05
                            WhiA_N 41 ykllkelYgieaellvrkknklkknnvYivrvkeg 75
                                      ++l+  l + + e +v+k+ k k++++Yiv+ +++
  gi|385806172|ref|YP_005842570.1| 43 FSLISSLENWNKEEMVKKEAKVKRKKRYIVFSITS 77
                                      78888888999*******************96655 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.33
                            WhiA_N 29 vqtenaaiARriykllkelYg 49
                                      + ++  +iA  i + l ++Yg
  gi|385806172|ref|YP_005842570.1| 79 ADIDYSEIADSILTALGKIYG 99
                                      66788999999**99999997 PP

>> DUF5370  Family of unknown function (DUF5370)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.1     5e+03      14      38 ..       5      29 ..       3      30 .. 0.79
   2 ?   11.1   0.5   6.3e-05      0.28       4      29 ..     103     127 ..     102     147 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.1
                           DUF5370 14 EySvikqkGAiHVyrkgkfieeikF 38
                                      Ey  i +  Ai     g fi  i+F
  gi|385806172|ref|YP_005842570.1|  5 EYLAIAEAVAILLLSLGIFIIYIRF 29
                                      7888888888888888888888887 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 6.3e-05
                           DUF5370   4 iernGyrFepEySvikqkGAiHVyrk 29 
                                       i ++Gy F + yS ik kG + Vyr+
  gi|385806172|ref|YP_005842570.1| 103 ISKSGYHFIVYYSDIK-KGIVRVYRE 127
                                       789***********96.7******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1308  (0.0729544); expected 358.6 (0.02)
Passed bias filter:                      777  (0.0433376); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1102.24
//
Query:       gi|385806173|ref|YP_005842571.1|  [L=426]
Description: phosphoglycerate mutase [Fervidicoccus fontis Kam940]
Scores for complete 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-46  157.3   0.0    4.5e-46  156.8   0.0    1.2  1  PhosphMutase   2,3-bisphosphoglycerate-independent phosphogly
    3.7e-26   92.0   0.0    4.6e-26   91.7   0.0    1.0  1  Metalloenzyme  Metalloenzyme superfamily
  ------ inclusion threshold ------
      0.026   14.1   0.0       0.04   13.5   0.0    1.3  1  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 !  156.8   0.0   7.6e-50   4.5e-46       1     170 []      34     224 ..      34     224 .. 0.96

  Alignments for each domain:
  == domain 1  score: 156.8 bits;  conditional E-value: 7.6e-50
                                       HHTSEEEEEE-----------TCHHHHTT--HHCH---HHHHHHHHTT----TT-.EEEEEEEEEEC..TTCEEETT CS
                      PhosphMutase   1 AkkGetGlldtvpegiapgSdvAnlsilGydpkkyytGRGplEAlgiGlelkpgd.vafRcnlvtvdeedgiiidrr 76 
                                       A k+++Gl++ + +giap+Sd A+l++lGydp + ++GRGp+EAlg+++elk+++ vafR+n++tvd+ +++iidrr
  gi|385806173|ref|YP_005842571.1|  34 AYKSKCGLMYVIGKGIAPESDAAVLALLGYDPINEHPGRGPIEALGVDIELKEEKeVAFRGNFATVDPLTKKIIDRR 110
                                       6789***********************************************99877***********99******** PP

                                       GGG-..-TTHHHHHHHT-EEE...TTEEEEEEE-STTEEEEEE......--S-B--S--..SSTTS..........- CS
                      PhosphMutase  77 agri.steeakeLikalneel..eegvevkfypgveyrhllvl......lsdkitdtdpphdkegk..........e 134
                                       agr  ++eea+eL++ +++    + + ++k++++v++r+++vl      l+d++++tdp++++ gk           
  gi|385806173|ref|YP_005842571.1| 111 AGRGiNKEEANELASLIDGIQllNGKGYAKVKATVGHRVVVVLghkekqLGDEVSNTDPAYERRGKvsvalenfdaT 187
                                       ***77**************989757899************************************************* PP

                                       -----BS..SGGGHHHHHHHHHHHHHHHHHHHHSHHH CS
                      PhosphMutase 135 ikellpl.kseeaketaellnelieksqeiLedhpvN 170
                                       ik++ pl ++e+++ t+el+ne++e++ +iL++ +vN
  gi|385806173|ref|YP_005842571.1| 188 IKPCIPLnQDEKNRITCELVNEFTERAIKILSSSKVN 224
                                       *******888899*********************999 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.7   0.0   7.6e-30   4.6e-26       2     236 ..       2     409 ..       1     417 [. 0.94

  Alignments for each domain:
  == domain 1  score: 91.7 bits;  conditional E-value: 7.6e-30
                                       EEEEEEETTBB----GGGTTHHHS--HHHHHHHHH.......SEEEEEESSSTT----HHHHHHHH........... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........... RF
                     Metalloenzyme   2 kvvlvvlDGlGeapadelnaihvAktPtldkLkkeaPerwlikahgtavglpeddmgnsevgHlel........... 67 
                                       k+v +vlDG +  p+    a  +A++P+ld+L+ +       +++g+++ + +++ + s+ + l+l           
  gi|385806173|ref|YP_005842571.1|   2 KLVYLVLDGAAGDPNLGKTAYMIADKPNLDSLAYK-------SKCGLMYVIGKGIAPESDAAVLALlgydpinehpg 71 
                                       67889**********999***************99.......89********************************* PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Metalloenzyme  68 ............................................................................. 67 
                                                                                                                    
  gi|385806173|ref|YP_005842571.1|  72 rgpiealgvdielkeekevafrgnfatvdpltkkiidrragrginkeeanelaslidgiqllngkgyakvkatvghr 148
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Metalloenzyme  68 ............................................................................. 67 
                                                                                                                    
  gi|385806173|ref|YP_005842571.1| 149 vvvvlghkekqlgdevsntdpayerrgkvsvalenfdatikpciplnqdeknritcelvnefteraikilssskvne 225
                                       ***************************************************************************** PP

                                       HHHHTT-----EEEEEEEE-.S---SS.HHHHHT--EEEE--SHH....................STT--HHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxx.xxxxxx.xxxxxxxxxxxxxxxxx....................xxxxxxxxxxxx RF
                     Metalloenzyme  68 lrisetvkfahvtffwnggr.sgyfnp.leereeipsdtvitfdl....................qpemkavevaek 122
                                        r++++  +a+ ++++++g+ + +++     + +++   ++++ +                    ++++ +++ a k
  gi|385806173|ref|YP_005842571.1| 226 SRLKNGMLPANAILLRDAGTgKAKMKDiSAMYSNLKFSALTEMPVekgiakaagmkmidvssisgERKHVYEQWALK 302
                                       999*************9987355777767788899999999999999*****************999999******* PP

                                       HHHHH.CC.-SEEEEEE-HHHHHHHTT-HHHHHHHHHHHHH.HHHHHHTTS-TTTEEEEEE-SSB--TTTSS..... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme 123 aldailsgkfdlvvvniknaDmvGHtgdleatiaaieaaDe.avkeildaieqvdgilvvtADHgnaedmvkrdkqp 198
                                       +++a+ s   d+v+v++k +D+ GH+g+l+ + + ie++D+  ++ i++ +e++d  ++vt+DH ++ + +      
  gi|385806173|ref|YP_005842571.1| 303 TIEAL-SV-SDVVYVHLKGPDEPGHEGNLKLKTKIIEDIDKyYLGSIVKYLEKEDIAILVTSDHATPCEKKA----- 372
                                       *****.44.7*******************************99**************************999..... PP

                                       ...-----EEEEEESTT----S.--S.SHHHHTT-TTEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxx.xxx.xxxxxxxxxxxxx RF
                     Metalloenzyme 199 lTsHtlepVPilivgkglapdk.vke.gakfrekggLanv 236
                                          H+  pVP+l+++k++   + +k+ ++ ++++g+++ +
  gi|385806173|ref|YP_005842571.1| 373 ---HSDSPVPFLLYSKNFSDGDrIKRfDEVECKSGSFGLI 409
                                       ...**************98755145566777778888776 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   6.7e-06      0.04     171     233 ..     308     365 ..     233     390 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.7e-06
                                       SSESEEEEEECCCHHHHHHH-TTSHHHHHHHHHHHH.HHHHHHHHHHHTTGTTTEEEEEEES-- CS
                      Phosphodiest 171 ekpdlllvyleetDtvgHkfGpdspevedalrrvDk.aigdLlealderglsaetniilvSDHG 233
                                          d+++v+l ++D  gH+   + +  ++ ++++Dk ++g ++++l+++    + +i+++SDH 
  gi|385806173|ref|YP_005842571.1| 308 SVSDVVYVHLKGPDEPGHEG--NLKLKTKIIEDIDKyYLGSIVKYLEKE----DIAILVTSDHA 365
                                       556***************55..4333478899999945***********....**********5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); 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: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2680.84
//
Query:       gi|385806174|ref|YP_005842572.1|  [L=515]
Description: carbohydrate kinase [Fervidicoccus fontis Kam940]
Scores for complete 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-44  152.0   0.0    3.1e-44  151.3   0.0    1.3  1  Carb_kinase  Carbohydrate kinase
      2e-41  141.7   0.0    3.3e-41  141.0   0.0    1.4  1  YjeF_N       YjeF-related protein N-terminus


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 !  151.3   0.0   3.4e-48   3.1e-44       1     240 [.     251     501 ..     251     505 .. 0.88

  Alignments for each domain:
  == domain 1  score: 151.3 bits;  conditional E-value: 3.4e-48
                                       EEEEE-BTTCHHHHHHHHHHHHCTT-SEEEEEESSTTTCCCCTTTTTCEECCTT....HTTTS....--SSS-SEEE CS
                       Carb_kinase   1 vlvigGsedytGAallaalaalrlgaglvsvateseaiavlksylpevivhpll....edeqa.kileklerldavv 72 
                                       v vigGs++y+GA+ l+ala lr+ga+lv  ++ ++ ++ + s +p +iv  ++    + e+  +i +  +r d vv
  gi|385806174|ref|YP_005842572.1| 251 VTVIGGSKEYYGAPTLSALAVLRAGADLVYLIVPEKIKQIVSSFTPSLIVIGTEndyhSPEEIsSIDKYISRSDSVV 327
                                       689***********************************************999977774455558888999****** PP

                                       E-TT-SSSHCHHHHCHHHCCCCS-......EEEEGGGGGSGGGG...TTTTSSEEEE--HHHHHHHCTTTCHHCC.S CS
                       Carb_kinase  73 iGpGLgrdekikklleevlekdep......lviDAdgLnllaqknelserkaeviLTPhkkEfkrLlkaivkked.d 142
                                       +GpGLg +e++ +++ e  ++ ++      +++DAd+L+ +a++  ++  +++ +LTPh +E   Ll + ++ +d d
  gi|385806174|ref|YP_005842572.1| 328 VGPGLGFNETTCNFVSELIDHLKSkypdakVIVDADALKCIAKN--KKTLNENFVLTPHRGELDLLLRSYDITGDnD 402
                                       ************988877777666666899*************9..599**********************955515 PP

                                       HHHHHHHHHHHHT.TEEEEESTTSEEEECTTEEEEE----GGG-STTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHH CS
                       Carb_kinase 143 rlelarelaqkln.avvllkgekdvivspegevlinstgssalakGGsGDvLaGligalLaqneasyeaaiaaawlh 218
                                       r +   +l++kl+ a+v+ kg  d i s +  +     g++++  GG+GD+L+Gli+a+     + + a + a++++
  gi|385806174|ref|YP_005842572.1| 403 REKNSLNLSNKLGgAIVVSKGPIDYICSAKYGCREKRCGNPGMSIGGTGDILTGLIAAFYKRTGSLFYASCIASFVN 479
                                       5556667888886268889********************************************************** PP

                                       HHHHHHHCCCT-TS-HCHHHHH CS
                       Carb_kinase 219 gaasdeaaekkgvgmlatelsk 240
                                       + a+d + +++   ++++++++
  gi|385806174|ref|YP_005842572.1| 480 SLAGDYLLNNYNEFYTSEDVLN 501
                                       *********9998555555544 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 !  141.0   0.0   3.6e-45   3.3e-41       4     171 .]      28     201 ..      25     201 .. 0.91

  Alignments for each domain:
  == domain 1  score: 141.0 bits;  conditional E-value: 3.6e-45
                            YjeF_N   4 Lmenagravaevlrallg.nspaekkvlvlvGsgnnGgdglaaArhLaqegakVtvllleeee.kldedaerale.l 77 
                                       Lmenag++vae   ++l+    ++ kv+v++G+g n gdg++aArhL+ +g++V+vlll ++e   ++da+++l+ l
  gi|385806174|ref|YP_005842572.1|  28 LMENAGKCVAEESYKALEtLGKENGKVVVVAGRGGNAGDGFVAARHLRAMGVSVDVLLLYQKElINHNDARTNLDyL 104
                                       9**********666666657889999******************************999898878899******945 PP

                            YjeF_N  78 lkkaggkvveekpeedleeklsapvdlviDAllGiglrgelreelaeliewlnsseapvlavDiPSGldadtGavs. 153
                                       lk ++++++++++ + ++    +++d++iDA+lG+g+rgelr ++ ++ie +nss+++v+avDiPSG+d+dtG+++ 
  gi|385806174|ref|YP_005842572.1| 105 LKDFQINIFHWDEISPHSFL--KNYDIIIDAILGTGVRGELRYPIPQAIEAINSSGSYVVAVDIPSGIDPDTGELAs 179
                                       688*********99998654..57****************************************************8 PP

                            YjeF_N 154 ....gtavkadvtvtfgapkrg 171
                                           ++avka++tv +++ k+g
  gi|385806174|ref|YP_005842572.1| 180 yrdeKIAVKANTTVVMHYRKKG 201
                                       8888888*********999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (515 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); 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: 0.68u 0.35s 00:00:01.03 Elapsed: 00:00:00.66
# Mc/sec: 2336.08
//
Query:       gi|385806175|ref|YP_005842573.1|  [L=525]
Description: PilT protein domain-containing protein [Fervidicoccus fontis Kam940]
Scores for complete 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   43.0   0.2    1.4e-10   40.7   0.0    1.9  2  T2SSE            Type II/IV secretion system protein
    3.7e-05   24.2   0.0      9e-05   22.9   0.0    1.7  1  AAA_16           AAA ATPase domain
    0.00035   21.1   0.0     0.0042   17.6   0.0    2.6  2  AAA_18           AAA domain
    0.00071   19.6   0.0     0.0025   17.9   0.0    1.9  1  AAA_14           AAA domain
    0.00075   19.3   0.2      0.053   13.2   0.0    2.4  2  AAA_30           AAA domain
     0.0022   17.7   0.0     0.0082   15.9   0.0    1.8  2  IstB_IS21        IstB-like ATP binding protein
     0.0025   18.1   0.0      0.015   15.5   0.0    2.2  2  AAA_22           AAA domain
     0.0025   17.2   0.1     0.0068   15.8   0.0    1.7  2  DnaB_C           DnaB-like helicase C terminal domain
     0.0029   17.4   0.1      0.011   15.4   0.0    2.0  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
     0.0043   16.7   0.1      0.014   15.1   0.0    1.9  2  Thymidylate_kin  Thymidylate kinase
     0.0044   17.5   0.0      0.019   15.5   0.0    2.0  2  ABC_tran         ABC transporter
      0.006   16.6   0.0      0.014   15.4   0.0    1.6  1  AAA_5            AAA domain (dynein-related subfamily)
     0.0065   16.9   0.4      0.024   15.0   0.0    2.3  1  AAA              ATPase family associated with various cellul
      0.009   16.7   0.1         15    6.3   0.0    4.0  4  PTS_IIB          PTS system, Lactose/Cellobiose specific IIB 
     0.0092   16.2   0.0      0.025   14.8   0.0    1.8  1  AAA_28           AAA domain
     0.0093   16.1   0.0      0.042   14.0   0.0    2.1  2  Sigma54_activ_2  Sigma-54 interaction domain
  ------ inclusion threshold ------
       0.01   15.4   0.1      0.023   14.3   0.1    1.7  1  AAA_25           AAA domain
      0.012   15.6   0.1      0.026   14.4   0.1    1.6  1  NACHT            NACHT domain
      0.013   15.2   1.0      0.023   14.3   0.1    1.9  2  SRP54            SRP54-type protein, GTPase domain
      0.014   15.6   0.0      0.063   13.4   0.0    2.1  1  AAA_33           AAA domain
      0.015   14.3   0.0      0.032   13.2   0.0    1.5  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
      0.017   14.5   0.1      0.065   12.7   0.0    2.0  2  KTI12            Chromatin associated protein KTI12
      0.019   14.9   0.0      0.053   13.4   0.0    1.8  1  NTPase_1         NTPase
      0.021   14.1   0.0      0.052   12.8   0.0    1.6  1  Zeta_toxin       Zeta toxin
      0.022   14.8   0.1      0.069   13.1   0.0    1.9  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.025   14.3   0.0      0.052   13.3   0.0    1.5  1  ATP_bind_1       Conserved hypothetical ATP binding protein
      0.036   14.1   0.0      0.078   13.0   0.0    1.5  1  ResIII           Type III restriction enzyme, res subunit
      0.048   12.8   0.0      0.098   11.8   0.0    1.4  1  DUF815           Protein of unknown function (DUF815)
      0.053   13.3   0.1        8.1    6.2   0.0    2.4  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
      0.055   13.2   0.6       0.16   11.7   0.1    2.1  2  AAA_24           AAA domain
      0.078   12.8   0.0       0.57   10.0   0.0    2.5  3  AAA_3            ATPase family associated with various cellul
      0.098   12.4   0.0       0.22   11.2   0.0    1.5  1  Sigma54_activat  Sigma-54 interaction domain
       0.11   12.8   0.0       0.37   11.1   0.0    1.8  1  AAA_19           AAA domain
       0.12   11.7   0.0       0.23   10.8   0.0    1.4  1  FtsK_SpoIIIE     FtsK/SpoIIIE family


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 ?   -0.2   0.2       0.8   4.2e+02      23      95 ..      80     149 ..      70     165 .. 0.76
   2 !   40.7   0.0   2.6e-13   1.4e-10      78     245 ..     227     383 ..     182     402 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.8
                             T2SSE  23 er.vkvrervdgielreveelekaalerlisriaalakldiseerplqdarlpekgvrlrvvllPvvagealvi 95 
                                       er + v e v++ ++r  ++++  +l+r+++++a+++++ + ++ ++ + ++  +++ ++ + +P++a ++l +
  gi|385806175|ref|YP_005842573.1|  80 ERnIEV-EIVGD-SQRVFSQVDILELSRIVRELAISTESVLITSDKIAS-QIA-QATGIKTLYVPASASKRLKL 149
                                       444788.88888.899999999999999999999999887777666554.666.78888888888887776655 PP

  == domain 2  score: 40.7 bits;  conditional E-value: 2.6e-13
                             T2SSE  78 vrlrvvllPvvag.ealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkei 153
                                       +r+ +v +P+  +    ++  k   +l+l+d++  e+l e+++   ++       il++G+ g GKtt++ al ++ 
  gi|385806175|ref|YP_005842573.1| 227 YRIVIVRPPLGSKwMITAV--KPLVKLSLEDYMLPEKLLERFK---KR----AEGILIAGAPGMGKTTFAQALAEFY 294
                                       5565666665555333333..3455667777776665554444...33....4789********************* PP

                             T2SSE 154 nksderivtvEDpvEiqleganqvqlnakkakvtfadllraa.LRlrPDrimvGEiRdketlei.lkAvnTGHlgsl 228
                                       +k+ + + t+E p+ ++l+ ++ vq  ++      +d +  + L  rPD  +  E+R+ + +++ +     G    +
  gi|385806175|ref|YP_005842573.1| 295 QKEGKIVTTIESPRDMRLS-PQIVQYSKH---FAEKDEIHDIlLLSRPDYTFFDELRGDDDFKLyVDLRLAGIGM-V 366
                                       ***888889********97.455555555...55566666651568******************99888899766.9 PP

                             T2SSE 229 sTlHansaagalerLeq 245
                                       + lHa s+++a++r  +
  gi|385806175|ref|YP_005842573.1| 367 GVLHATSPIDAIQRFIN 383
                                       9*************755 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   1.7e-07     9e-05      15      76 ..     262     320 ..     253     406 .. 0.62

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.7e-07
                            AAA_16  15 alervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysa.laqal 76 
                                       +ler +  r e +l+ G++G+GK++ +++l++ ++k+g i+++ +  +    +++s+ ++q+ 
  gi|385806175|ref|YP_005842573.1| 262 LLERFK-KRAEGILIAGAPGMGKTTFAQALAEFYQKEGKIVTTIESPRD---MRLSPqIVQYS 320
                                       455444.45599*************************966655555555...33333333332 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1       2.5   1.3e+03     103     115 ..     259     271 ..     257     272 .. 0.89
   2 !   17.6   0.0   7.9e-06    0.0042       1      31 [.     273     304 ..     273     356 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 2.5
                            AAA_18 103 peelleRlekRgy 115
                                       pe+lleR++kR +
  gi|385806175|ref|YP_005842573.1| 259 PEKLLERFKKRAE 271
                                       79*********75 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 7.9e-06
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf...gvnlrdv 31 
                                       Il++G+pG GKtt+a++L++   +   g +++ +
  gi|385806175|ref|YP_005842573.1| 273 ILIAGAPGMGKTTFAQALAEF--YqkeGKIVTTI 304
                                       99****************663..22234444444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   4.7e-06    0.0025       5      82 ..     273     355 ..     270     361 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 4.7e-06
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe..kllelileklke........ekktylflD 71 
                                       ++i Ga  +GKTt+++ l+ e + +ke  +  +++++rd +l+ p+  ++ + + ek  +        ++  y f+D
  gi|385806175|ref|YP_005842573.1| 273 ILIAGAPGMGKTTFAQALA-EFY-QKEGKIVTTIESPRDMRLS-PQivQYSKHFAEK--DeihdilllSRPDYTFFD 344
                                       6899**********98888.666.799999*********7766.4323445555555..123458888899****** PP

                            AAA_14  72 Eiqevpeweka 82 
                                       E    ++++ +
  gi|385806175|ref|YP_005842573.1| 345 ELRGDDDFKLY 355
                                       *9887777665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.088        46      98     126 ..      64      92 ..      63     136 .. 0.92
   2 !   13.2   0.0    0.0001     0.053      21      49 ..     273     301 ..     261     310 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.088
                            AAA_30  98 gmvdtkqlaallkaaekagakvilvGDer 126
                                       g++++++l+++ + a++++++v +vGD +
  gi|385806175|ref|YP_005842573.1|  64 GLAGIEELQRIRELAKERNIEVEIVGDSQ 92 
                                       78999**********************86 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.0001
                            AAA_30  21 avltGpAGtGKttalkalreaweaaggrv 49 
                                        ++ G++G GKtt  +al+e ++++g+ v
  gi|385806175|ref|YP_005842573.1| 273 ILIAGAPGMGKTTFAQALAEFYQKEGKIV 301
                                       5799*********************9655 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 ?   -1.8   0.1       4.1   2.2e+03     123     157 ..      96     131 ..      70     138 .. 0.67
   2 !   15.9   0.0   1.6e-05    0.0082      42      78 ..     265     301 ..     255     332 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 4.1
                         IstB_IS21 123 dqaeaellfeviek.ryerrsiiitsnlpfaewdev 157
                                       +q +  +l +++ + +  ++s++its++  ++  + 
  gi|385806175|ref|YP_005842573.1|  96 SQVDILELSRIVRElAISTESVLITSDKIASQIAQA 131
                                       555555566666552467889999999887776665 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.6e-05
                         IstB_IS21  42 sfiekkenivllGpsGvGKshlaialgveavraglsv 78 
                                        f +++e+i++ G +G+GK+ +a al+    ++g+ v
  gi|385806175|ref|YP_005842573.1| 265 RFKKRAEGILIAGAPGMGKTTFAQALAEFYQKEGKIV 301
                                       577899********************98777777666 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0         3   1.6e+03      80     114 ..      72     105 ..      47     139 .. 0.72
   2 !   15.5   0.0   2.9e-05     0.015       5      34 ..     270     299 ..     265     331 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 3
                            AAA_22  80 ealeqalraravielliiDEaqhlrs.eealeeLrs 114
                                       +++++ +++r   e+ i+ + q+++s  ++le   +
  gi|385806175|ref|YP_005842573.1|  72 QRIRELAKERNI-EVEIVGDSQRVFSqVDILELS-R 105
                                       556666666666.888888888865414444333.3 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 2.9e-05
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeak 34 
                                       a  +++ G +G+GKTt ++ l+e +++e k
  gi|385806175|ref|YP_005842573.1| 270 AEGILIAGAPGMGKTTFAQALAEFYQKEGK 299
                                       66689*******************987633 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 ?   -3.1   0.1       7.4   3.9e+03     141     172 ..      74      85 ..      53     121 .. 0.57
   2 !   15.8   0.0   1.3e-05    0.0068      19      50 ..     270     301 ..     260     321 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 7.4
                                       TBTSCSSSCCCHHHHHHHHHHHHHHHHCTSXE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C 141 megseekenreqevseisrsLkalakelnvpv 172
                                       ++                    +lake n+ v
  gi|385806175|ref|YP_005842573.1|  74 IR--------------------ELAKERNIEV 85 
                                       33....................2222222222 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1.3e-05
                                       TXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  19 gdliiiAarpsmGktalalniaenaavkeklp 50 
                                       ++ i+iA+ p+mGkt++a  +ae   ++ k+ 
  gi|385806175|ref|YP_005842573.1| 270 AEGILIAGAPGMGKTTFAQALAEFYQKEGKIV 301
                                       55699*****************9887755543 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 !   15.4   0.0   2.2e-05     0.011      32      74 ..     269     309 ..     261     334 .. 0.75
   2 ?   -2.3   0.0       6.4   3.3e+03      90     130 ..     375     413 ..     372     416 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.2e-05
                            RuvB_N  32 aldhvllyGpPGlGkttlakiiakelgvklkitsgPvlekagd 74 
                                         + +l++G+PG+Gktt+a+ +a+  + + ki ++  +e ++d
  gi|385806175|ref|YP_005842573.1| 269 RAEGILIAGAPGMGKTTFAQALAEFYQKEGKIVTT--IESPRD 309
                                       55679******************988887777653..455554 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 6.4
                            RuvB_N  90 ideihrlsraveevlysamedfrldivigkGpsarsikldl 130
                                       id i r+ + ve  + +++ d    i i++G+ ++  ++++
  gi|385806175|ref|YP_005842573.1| 375 IDAIQRFINRVELGVIPSIIDTV--IFIDRGQISKVYEITI 413
                                       78899999999988888888876..5778888888777765 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.6e-05     0.014       3      59 ..     277     334 ..     275     339 .. 0.78
   2 ?   -1.3   0.0       2.8   1.5e+03     115     126 ..     334     346 ..     327     351 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.6e-05
                                       ESTTSSHHHHHHHHHHHHHHTTE.EEEESSSTTSHHHHHHHHHHH.TCS---HHHHHH CS
                   Thymidylate_kin   3 GlDGaGKttqaellkerlkeegikvvltrepggteiGekirelll.keeeleeqteal 59 
                                       G  G GKtt+a++l+e +++eg+ v +   p++ ++  +i ++ + ++e++e + ++l
  gi|385806175|ref|YP_005842573.1| 277 GAPGMGKTTFAQALAEFYQKEGKIVTTIESPRDMRLSPQIVQYSKhFAEKDEIHDILL 334
                                       7789******************645555558999999999999886666666555555 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.8
                                       TS.E-SEEEEEES CS
                   Thymidylate_kin 115 ll.kPdltflldv 126
                                       ll +Pd+tf+ ++
  gi|385806175|ref|YP_005842573.1| 334 LLsRPDYTFFDEL 346
                                       4479******886 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       7.4   3.9e+03      29      79 ..      30      81 ..      28     147 .. 0.51
   2 !   15.5   0.0   3.6e-05     0.019      12      46 ..     271     304 ..     267     343 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 7.4
                                      HHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSB.HHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                          ABC_tran 29 kllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpelt.vren 79
                                      kl++ ++ p+  +i + ++ ++ +e+e ++ +   l   ++l++  + ++e+
  gi|385806175|ref|YP_005842573.1| 30 KLILSNEIPELSKIYIHKTLVSFIEKEAFEGKAVGLAGIEELQRIRElAKER 81
                                      5666666666666666666666644444433333222222222222213333 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 3.6e-05
                                       SEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  12 ekvaivGenGaGKStLlkllagllkpteGeilldg 46 
                                       e + i G  G GK+t++++la+ ++ +eG+i    
  gi|385806175|ref|YP_005842573.1| 271 EGILIAGAPGMGKTTFAQALAEFYQ-KEGKIVTTI 304
                                       66889*******************9.699994332 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 !   15.4   0.0   2.6e-05     0.014       2      36 ..     273     310 ..     272     345 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.6e-05
                                       EEEE--SSSSHHHHHHHGGGGB...S--EEEEE--TT- CS
                             AAA_5   2 vlLvGppGtgKselaerlaaal...nreveyvqltrdt 36 
                                       +l+ G+pG gK+++a+ la+++   ++ v+++  +rd+
  gi|385806175|ref|YP_005842573.1| 273 ILIAGAPGMGKTTFAQALAEFYqkeGKIVTTIESPRDM 310
                                       7999******************6555555666666665 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   4.6e-05     0.024       1      22 [.     273     294 ..     273     345 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.6e-05
                                       EEEESSTTSSHHHHHHHHHHHH CS
                               AAA   1 vllyGppGtGKTllakavakel 22 
                                       +l+ G pG+GKT++a+a+a+  
  gi|385806175|ref|YP_005842573.1| 273 ILIAGAPGMGKTTFAQALAEFY 294
                                       6899**************9865 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 ?    4.0   0.1      0.16        83      18      37 ..      72      91 ..      71     136 .. 0.76
   2 ?    0.7   0.0       1.7   8.9e+02      43      89 ..     223     264 ..     198     265 .. 0.71
   3 ?    6.3   0.0     0.029        15       2      33 ..     273     305 ..     272     337 .. 0.83
   4 ?   -1.4   0.0       7.6     4e+03      17      34 ..     506     523 ..     477     525 .] 0.80

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.16
                                      HHHHHHHHHCTEEEEETTEE CS
                           PTS_IIB 18 eklekaakelgieaegeagv 37
                                      +++++ ake++ie+e++  +
  gi|385806175|ref|YP_005842573.1| 72 QRIRELAKERNIEVEIVGDS 91
                                      5799*******888887666 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.7
                                       HHHHT-SEEEEEESSGGCTHHHHTTSEEEEECTTHHHCCHCHHHHHH CS
                           PTS_IIB  43 eiaddaDlvllapqvrvkdlarfagkpvavinikdalgimdgekvlk 89 
                                       + ++ + +v++ p +  k +  +++ p+++ +++d +  m +ek+l+
  gi|385806175|ref|YP_005842573.1| 223 QLGA-YRIVIVRPPLGSKWMITAVK-PLVKLSLED-Y--MLPEKLLE 264
                                       5555.99*******99877777777.999999999.7..88888886 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.029
                                       EEEEESSSHHHHHHHHHHHHHHHHHCT..EEEEE CS
                           PTS_IIB   2 illaCgaGmatSlmaaeklekaakelg..ieaeg 33 
                                       il+a + Gm+ ++ a ++l ++ +++g  + ++ 
  gi|385806175|ref|YP_005842573.1| 273 ILIAGAPGMGKTTFA-QALAEFYQKEGkiVTTIE 305
                                       89*************.*********998644443 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 7.6
                                       HHHHHHHHHHCTEEEEET CS
                           PTS_IIB  17 aeklekaakelgieaege 34 
                                       a++l+++a+++g + ++e
  gi|385806175|ref|YP_005842573.1| 506 AKRLKRIAQKMGYDLRIE 523
                                       578889999998555444 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   4.8e-05     0.025       2      29 ..     273     305 ..     272     331 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.8e-05
                            AAA_28   2 ivitGgestGKTtlleaLaar.....gypvvpE 29 
                                       i i G+++ GKTt ++aLa+      ++++  E
  gi|385806175|ref|YP_005842573.1| 273 ILIAGAPGMGKTTFAQALAEFyqkegKIVTTIE 305
                                       789****************63333434444455 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0     8e-05     0.042      14      55 ..     263     304 ..     260     321 .. 0.84
   2 ?   -2.5   0.0       9.8   5.2e+03       3      20 ..     498     515 ..     486     519 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8e-05
                                       HHHHHT-SS-EEEEEETT--HHHHHHCC--TTS-EE--SSTT CS
                   Sigma54_activ_2  14 LeqaaqsklpvfltGekGsgkelvArlLhknsgpwleifvve 55 
                                       Le  +++   ++++G++G gk+++A++L+++ ++  +i++ +
  gi|385806175|ref|YP_005842573.1| 263 LERFKKRAEGILIAGAPGMGKTTFAQALAEFYQKEGKIVTTI 304
                                       7888889999*********************99998887653 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 9.8
                                       --HHHHHHHHHHHHHHT- CS
                   Sigma54_activ_2   3 asaaiqelkerLeqaaqs 20 
                                       +s++i + ++rL+ +aq+
  gi|385806175|ref|YP_005842573.1| 498 NSRLIMKRAKRLKRIAQK 515
                                       355555555555555554 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   4.4e-05     0.023      23      58 ..     260     295 ..     258     415 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.4e-05
                            AAA_25  23 rwlvkgllpagelallaGapgtGKttlaldlalava 58 
                                       ++l++++  + e +l+aGapg GKtt+a  la  + 
  gi|385806175|ref|YP_005842573.1| 260 EKLLERFKKRAEGILIAGAPGMGKTTFAQALAEFYQ 295
                                       67888888889999***************9996655 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1     5e-05     0.026       3      23 ..     273     293 ..     271     301 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5e-05
                                       EEEEC-TTTCHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                       +++ G++G+GKTt++q la+ 
  gi|385806175|ref|YP_005842573.1| 273 ILIAGAPGMGKTTFAQALAEF 293
                                       789**************9975 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       9.6     5e+03      79     108 ..      78     106 ..      68     131 .. 0.49
   2 ?   14.3   0.1   4.3e-05     0.023       4      32 ..     273     301 ..     270     306 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 9.6
                                       HHHTTSSEEEEEE--SSTTHHHHHHHHHHH CS
                             SRP54  79 akeekidvvlvDTaGrlqndkelmeelkki 108
                                       ake++i+v +v  + r  ++ +++ el++i
  gi|385806175|ref|YP_005842573.1|  78 AKERNIEVEIVGDSQRVFSQVDIL-ELSRI 106
                                       445555555555555555544444.33333 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 4.3e-05
                                       EEEEESTTSSHHHHHHHHHHHHHHTTS-E CS
                             SRP54   4 illvGlqGaGKTttlaKLaallkkegkkv 32 
                                       il++G  G+GKTt +  La+ ++kegk v
  gi|385806175|ref|YP_005842573.1| 273 ILIAGAPGMGKTTFAQALAEFYQKEGKIV 301
                                       89***********************9876 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   0.00012     0.063       2      21 ..     273     292 ..     273     337 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00012
                            AAA_33   2 vllvGlpGsGKstlaerllk 21 
                                       +l+ G+pG+GK+t+a+ l++
  gi|385806175|ref|YP_005842573.1| 273 ILIAGAPGMGKTTFAQALAE 292
                                       5789*************954 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 ?   13.2   0.0     6e-05     0.032      27      63 ..     268     304 ..     249     307 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6e-05
                                       S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEE CS
                              MeaB  27 GraqvvGltGvPGaGkstlvealglelrrrGkrvavl 63 
                                        ra+ + + G PG Gk t+ +al++ ++++Gk v+ +
  gi|385806175|ref|YP_005842573.1| 268 KRAEGILIAGAPGMGKTTFAQALAEFYQKEGKIVTTI 304
                                       4789999************************999765 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00012     0.065       4      36 ..     273     305 ..     272     330 .. 0.81
   2 ?   -3.4   0.1       9.8   5.2e+03     206     245 ..     470     511 ..     468     512 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                                       EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE- CS
                             KTI12   4 vvltGlPssGKstrakeLakaleeekrsvvvid 36 
                                       +++ G P  GK+t+a+ La+  ++e++ v+ i+
  gi|385806175|ref|YP_005842573.1| 273 ILIAGAPGMGKTTFAQALAEFYQKEGKIVTTIE 305
                                       799*********************999998876 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 9.8
                                       HHH....HTT--HHH..................HHHHHHHHH CS
                             KTI12 206 ileaqksavaidkltlpgsseslelpak..kltlaeLsrlrr 245
                                       i++++++ v++ ++++ g++ +++l+ +  +l +++ +rl+r
  gi|385806175|ref|YP_005842573.1| 470 IIRQIETLVPGAEVEILGKTATVKLSGEnsRLIMKRAKRLKR 511
                                       788889999999999999999999987766788888888887 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0    0.0001     0.053       2      31 ..     273     302 ..     272     311 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.0001
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvg 31 
                                       ++i G pG+GKtT+ + ++e  +++g  v+
  gi|385806175|ref|YP_005842573.1| 273 ILIAGAPGMGKTTFAQALAEFYQKEGKIVT 302
                                       789*******************99998876 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   9.8e-05     0.052      15      48 ..     269     302 ..     259     319 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.8e-05
                        Zeta_toxin  15 rPklillgGqpGAGKselaellkdelerqgnvvr 48 
                                       r   il++G+pG GK++ a++l++  +++g++v+
  gi|385806175|ref|YP_005842573.1| 269 RAEGILIAGAPGMGKTTFAQALAEFYQKEGKIVT 302
                                       55669*******************9999999986 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00013     0.069      12      51 ..     264     307 ..     253     308 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00013
                                       HHHHHCHTEEEEEEESTTSSHHHHHHHHHHHTT--.....----T CS
                              TsaE  12 kklakalgdvilLeGdLGaGKTtlvrglakalgve.....evkSP 51 
                                       ++++k  ++ il+ G  G+GKTt++++la+ ++ e     +++SP
  gi|385806175|ref|YP_005842573.1| 264 ERFKK-RAEGILIAGAPGMGKTTFAQALAEFYQKEgkivtTIESP 307
                                       33333.23459******************9886554333456665 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   9.9e-05     0.052       1      29 [.     275     303 ..     275     305 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.9e-05
                        ATP_bind_1   1 vvGpaGsGKttfvgalseilelrgrsvav 29 
                                       ++G +G GKttf +al+e+++++g+ v +
  gi|385806175|ref|YP_005842573.1| 275 IAGAPGMGKTTFAQALAEFYQKEGKIVTT 303
                                       68********************9987766 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00015     0.078      13      54 ..     260     300 ..     250     328 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00015
                                       HHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.... CS
                            ResIII  13 enlleklkskrdkrglikmaTGtGKTlvaaklierllkkgke 54 
                                       e+lle +k kr + +li+ a G+GKT  a +l+e ++k+gk+
  gi|385806175|ref|YP_005842573.1| 260 EKLLERFK-KRAEGILIAGAPGMGKTTFAQALAEFYQKEGKI 300
                                       57889998.9*****************999999999887764 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00019     0.098      51     101 ..     268     319 ..     260     331 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00019
                            DUF815  51 lpannvLLwGarGtGKSslvkallneyaeeg..Lrlievekedlkelpklvel 101
                                       ++a+ +L+ Ga G+GK +  +al + y++eg  +  ie  + d++  p++v+ 
  gi|385806175|ref|YP_005842573.1| 268 KRAEGILIAGAPGMGKTTFAQALAEFYQKEGkiVTTIESPR-DMRLSPQIVQY 319
                                       67999************************996666666444.46666666665 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.053        28      76     139 ..       8      73 ..       4      76 .. 0.82
   2 ?    6.2   0.0     0.015       8.1       4      23 ..     273     292 ..     270     309 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.053
                         PduV-EutP  76 eesvfppgfasvfnkeviGiitkidlaedeeniea..veelLksaGaekifevsavekegieellk 139
                                       e++ fp++f+   +  + Gi+tk+ l+++  ++++   +++L s   ++ fe +av   gieel++
  gi|385806175|ref|YP_005842573.1|   8 ENKKFPDNFVPDHSSLIGGIVTKLILSNEIPELSKiyIHKTLVSFIEKEAFEGKAVGLAGIEELQR 73 
                                       6788999**999999999******999988888751246788888888999999999999999964 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.015
                         PduV-EutP   4 illiGkvgsGKttLtqalkg 23 
                                       il+ G+ g GKtt +qal +
  gi|385806175|ref|YP_005842573.1| 273 ILIAGAPGMGKTTFAQALAE 292
                                       8999*************986 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       7.2   3.8e+03     156     175 ..     189     208 ..     176     223 .. 0.72
   2 ?   11.7   0.1    0.0003      0.16       5      22 ..     273     290 ..     269     306 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 7.2
                            AAA_24 156 tanelkeevDlvlranlkre 175
                                       t +e+++++D++++   +re
  gi|385806175|ref|YP_005842573.1| 189 TRAEIQSIFDEIVETAKSRE 208
                                       56789999999888665544 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.0003
                            AAA_24   5 iliyGpsgiGKTtlakel 22 
                                       ili G +g+GKTt+a  l
  gi|385806175|ref|YP_005842573.1| 273 ILIAGAPGMGKTTFAQAL 290
                                       89*************987 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       7.7   4.1e+03      60      72 ..      26      38 ..      22      57 .. 0.59
   2 ?   -2.3   0.0       7.2   3.8e+03     117     129 ..     254     266 ..     232     267 .. 0.66
   3 ?   10.0   0.0    0.0011      0.57       2      26 ..     273     297 ..     272     323 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 7.7
                             AAA_3 60 pvfanllladein 72
                                       ++++l+l++ei 
  gi|385806175|ref|YP_005842573.1| 26 GIVTKLILSNEIP 38
                                      5666666666663 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 7.2
                             AAA_3 117 Gtyplpeaqldrf 129
                                         y lpe  l+rf
  gi|385806175|ref|YP_005842573.1| 254 EDYMLPEKLLERF 266
                                       4699*****9999 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.0011
                             AAA_3   2 vllegvPGlaktllvkalakaldle 26 
                                       +l+ g+PG++kt++++ala+  + e
  gi|385806175|ref|YP_005842573.1| 273 ILIAGAPGMGKTTFAQALAEFYQKE 297
                                       799****************987765 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00042      0.22      16      54 ..     264     302 ..     255     316 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00042
                                       HHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EE CS
                   Sigma54_activat  16 kkvaktdlsvlitGesGtGKellaraiheaskrkekpfv 54 
                                       +++ k    +li G  G GK+++a+a+ e  +++ k + 
  gi|385806175|ref|YP_005842573.1| 264 ERFKKRAEGILIAGAPGMGKTTFAQALAEFYQKEGKIVT 302
                                       5666667789*****************998887766554 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00071      0.37      10      39 ..     270     299 ..     263     308 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00071
                            AAA_19  10 ekvllvtaGpGtGKTrvlkhivallvelgg 39 
                                       ++ +l+ + pG+GKT+  ++  + ++++g+
  gi|385806175|ref|YP_005842573.1| 270 AEGILIAGAPGMGKTTFAQALAEFYQKEGK 299
                                       556899999**********99999999886 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00043      0.23      35      59 ..     267     290 ..     245     291 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00043
                                       GGGS-.SEEEE--TTSSHHHHHHHH CS
                      FtsK_SpoIIIE  35 lkkmashllvaGatgsGKStalntL 59 
                                        k ++  +l+aGa+g GK+t+ ++L
  gi|385806175|ref|YP_005842573.1| 267 KKRAE-GILIAGAPGMGKTTFAQAL 290
                                       44444.89*************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (525 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       828  (0.0461822); expected 358.6 (0.02)
Passed bias filter:                      711  (0.0396564); expected 358.6 (0.02)
Passed Vit filter:                       125  (0.00697194); expected 17.9 (0.001)
Passed Fwd filter:                        34  (0.00189637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              34  [number of targets reported over threshold]
# CPU time: 0.71u 0.32s 00:00:01.03 Elapsed: 00:00:00.49
# Mc/sec: 3228.28
//
Query:       gi|385806176|ref|YP_005842574.1|  [L=295]
Description: putative (S)-2,3-Di-O-farnesylgeranylglyceryl synthase [Fervidicoccus fontis Kam940]
Scores for complete 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  128.4  18.8    3.7e-37  128.0  18.8    1.2  1  UbiA      UbiA prenyltransferase family
  ------ inclusion threshold ------
        2.1    7.6   8.8        2.1    7.6   6.9    1.9  2  DUF4407   Domain of unknown function (DUF4407)


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.0  18.8   4.2e-41   3.7e-37       4     244 ..      34     273 ..      32     292 .. 0.85

  Alignments for each domain:
  == domain 1  score: 128.0 bits;  conditional E-value: 4.2e-41
                              UbiA   4 palvglalaaggspdl....llllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivl 76 
                                       ++lvg+++a +  +      l++l  ++++++++a+++++Ndy DreiD +  + p RP++s ri  +eal ++i+l
  gi|385806176|ref|YP_005842574.1|  34 AVLVGVLIANHEYFLNfrnyLTILSGFATGFFLTASSMVFNDYNDREIDLI--NQPSRPIPSKRIGEREALSYGILL 108
                                       5789988888877755566677777777888********************..************************ PP

                              UbiA  77 lilgllllalllnpltallgllalllyvvYtglrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavf 153
                                        ++g++ + l+++++t+++++l++ ++++Y+ ++ K+++l+g++ ++ + ++p++ g+++++ + ++ ++++a +vf
  gi|385806176|ref|YP_005842574.1| 109 SLIGIISS-LYTGLYTFAIAILTFGIALLYN-FWGKKTGLIGNFMVSYSVTIPLIYGAVMINSF-TFKIMIFASMVF 182
                                       ********.**********************.9***************************9775.9*********** PP

                              UbiA 154 lltwaialandlrdregDrkagiktlpvvlGrkaaril.lalllavlllallllllalllllylllalllaalallr 229
                                       l  ++  +++ + d+ gD   gi+t++v++G+k+a i+ ++++l++++l+++ + + +++lly++l+l++ ++++  
  gi|385806176|ref|YP_005842574.1| 183 LTNTGREIIKGIADIAGDSVKGIRTIAVKYGAKRASIVaSWFILVAVFLSFIPTITRMTGLLYFILVLAVDGILISS 259
                                       *************************************9877777777777666767777777776666666666655 PP

                              UbiA 230 aarlvrrrdakkaak 244
                                        +  + ++ +k++a 
  gi|385806176|ref|YP_005842574.1| 260 -VLTILNKADKEIAL 273
                                       .44444444444444 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.17   1.5e+03      86      96 ..      32      42 ..      26      50 .. 0.83
   2 ?    7.6   6.9   0.00023       2.1      28      94 ..     224     288 ..     208     289 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.17
                           DUF4407 86 llAvligvvis 96
                                       lAvl+gv+i+
  gi|385806176|ref|YP_005842574.1| 32 GLAVLVGVLIA 42
                                      68899999887 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00023
                           DUF4407  28 alsgayAlytvlksplllallvGllwgllIfnlDRfivssi.kkrakkrrelalal.pRlllAvligvv 94 
                                       ++ +a++l++      ++  + Gll+ +l++++D  ++ss+ +  +k  +e+al++  R+l+A+ +g++
  gi|385806176|ref|YP_005842574.1| 224 FILVAVFLSF----IPTITRMTGLLYFILVLAVDGILISSVlTILNKADKEIALLVkKRILFAMFLGLI 288
                                       2333333222....2227889********************76666777777776636********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       962  (0.0536561); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.33s 00:00:00.93 Elapsed: 00:00:00.54
# Mc/sec: 1645.77
//
Query:       gi|385806177|ref|YP_005842575.1|  [L=139]
Description: hypothetical protein FFONT_1135 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 891.49
//
Query:       gi|385806178|ref|YP_005842576.1|  [L=77]
Description: hypothetical protein FFONT_1136 [Fervidicoccus fontis Kam940]
Scores for complete 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   63.4   2.7    1.6e-17   63.3   2.7    1.0  1  HTH_45         Winged helix-turn-helix
     0.0024   17.6   0.3     0.0024   17.6   0.3    1.1  1  DUF4364        Domain of unknown function (DUF4364)
     0.0085   16.2   0.0      0.011   15.9   0.0    1.2  1  Mrr_N          Mrr N-terminal domain
  ------ inclusion threshold ------
      0.011   15.2   0.0        4.1    6.9   0.0    2.3  2  Adeno_E1B_19K  Adenovirus E1B 19K protein / small t-antigen


Domain annotation for each model (and alignments):
>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.3   2.7   3.5e-21   1.6e-17       8      76 ..       1      69 [.       1      70 [. 0.97

  Alignments for each domain:
  == domain 1  score: 63.3 bits;  conditional E-value: 3.5e-21
                            HTH_45  8 iadILeaisegeakkTkimykanLsykllnkYLdmLvekglikkskekYvlTekGlelleklkeleela 76
                                      +++IL +i+e+++k+T++  k+ L+yk+++kYL++L++++l+k+ ++k ++TekG+e+le++k+l++l+
  gi|385806178|ref|YP_005842576.1|  1 MVSILANIKEDGTKPTHLSNKSMLDYKVMKKYLSYLIQEELVKQLDGKIYITEKGREFLEEYKRLRNLI 69
                                      689**************************************************************9985 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.3   5.4e-07    0.0024      26      74 ..      19      63 ..       5      76 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 5.4e-07
                           DUF4364 26 leneytnYfdlqqalseLvesglieeeekenktlykiTekGketlelfe 74
                                       ++ +++Y  ++++ls L++++l+++     +  + iTekG+e le+ +
  gi|385806178|ref|YP_005842576.1| 19 SNKSMLDYKVMKKYLSYLIQEELVKQ----LDGKIYITEKGREFLEEYK 63
                                      567899*******************6....668888*********9865 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.4e-06     0.011      32      86 ..       7      60 ..       2      61 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.4e-06
                             Mrr_N 32 glseeeraellpsgkqtrfknrvgWartyLkkagllespkrgvwkiTekGrevlk 86
                                      +++e+  + ++ s+k+ +  + +  +++yL +++l+++   g++ iTekGre+l+
  gi|385806178|ref|YP_005842576.1|  7 NIKEDGTKPTHLSNKSMLDYKVMKKYLSYLIQEELVKQL-DGKIYITEKGREFLE 60
                                      666777777777776633333446689**********99.9************97 PP

>> Adeno_E1B_19K  Adenovirus E1B 19K protein / small t-antigen
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0   0.00092       4.1      93     125 ..       2      34 ..       1      45 [. 0.83
   2 ?    6.4   0.0    0.0013       5.9       5      24 ..      57      76 ..      53      77 .] 0.90

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00092
                     Adeno_E1B_19K  93 lallvfildkwskeshlsedylldllavplwrk 125
                                       +++l+ i ++  k +hls+  +ld+ +++ +  
  gi|385806178|ref|YP_005842576.1|   2 VSILANIKEDGTKPTHLSNKSMLDYKVMKKYLS 34 
                                       78999999*****************99876655 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0013
                     Adeno_E1B_19K  5 kkledlkslrrllegasnrt 24
                                      + le++k lr+l++ ++n+t
  gi|385806178|ref|YP_005842576.1| 57 EFLEEYKRLRNLIQFSTNKT 76
                                      569**************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       782  (0.0436165); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 479.00
//
Query:       gi|385806179|ref|YP_005842577.1|  [L=145]
Description: holliday junction resolvase [Fervidicoccus fontis Kam940]
Scores for complete 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   81.3   0.1      5e-23   80.9   0.1    1.2  1  Hjc          Archaeal holliday junction resolvase (hjc)
    2.7e-06   26.9   0.1    1.2e-05   24.9   0.1    2.0  1  AHJR-like    REase_AHJR-like
     0.0027   18.2   0.0     0.0033   17.9   0.0    1.3  1  NERD         Nuclease-related domain
      0.006   16.8   0.4      0.009   16.2   0.3    1.5  1  UPF0102      Uncharacterised protein family UPF0102
  ------ inclusion threshold ------
       0.13   12.1   0.0       0.24   11.2   0.0    1.5  1  L_protein_N  L protein N-terminus


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 !   80.9   0.1   1.4e-26     5e-23       2      92 ..      18     114 ..      17     115 .. 0.91

  Alignments for each domain:
  == domain 1  score: 80.9 bits;  conditional E-value: 1.4e-26
                                       HHHHHHHHHHHTT-EEEEBSCSSSSSS..SS-SEEEEETTEEEEEEEEEESSS.EEEEEHHHHHHHHHHHHHHT..C CS
                               Hjc   2 yERelvkiLrergfavvRsagSggatk..plpDviAirgdvvlviEvKsskke.riylkkeqvekllefarkag..g 73 
                                       +ER+lv+ L+e gfa +R+++Sg++ k  ++pD+iA +++ + viEvK+++ + ++y+++ qv kl e++++ag  +
  gi|385806179|ref|YP_005842577.1|  18 KERDLVRKLWEMGFATIRAPASGAKAKktYQPDIIAAKNNRIFVIEVKTRRATdTVYVDSFQVSKLKEWSSRAGsnA 94 
                                       7**********************9988899*******************99877*******************7225 PP

                                       EEEEEEEE.TTTEEEEEEGG CS
                               Hjc  74 elllavkl.qgkewkllvve 92 
                                       + ++av + ++  wk++++e
  gi|385806179|ref|YP_005842577.1|  95 RCFIAVYFdRKIGWKFVPLE 114
                                       6689999977779***9987 PP

>> AHJR-like  REase_AHJR-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.1   3.2e-09   1.2e-05      19      66 ..      25      70 ..      16     141 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 3.2e-09
                         AHJR-like 19 qyrekGyevllhPnredlPdfLksYrpDliarkdeeaviiEvksrrss 66
                                      ++ e G+  + +P +    +  k Y+pD+ia k++   +iEvk+rr +
  gi|385806179|ref|YP_005842577.1| 25 KLWEMGFATIRAPASGA--KAKKTYQPDIIAAKNNRIFVIEVKTRRAT 70
                                      55566666666666655..34489*********************973 PP

>> NERD  Nuclease-related domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   9.2e-07    0.0033      32      62 ..      39      82 ..      14     118 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 9.2e-07
                              NERD 32 g.....tg.eiDhlvispkgifviEvKnwsG..wifgd.....k 62
                                            ++ + D+++  +++ifviEvK ++   +++ d     k
  gi|385806179|ref|YP_005842577.1| 39 SgakakKTyQPDIIAAKNNRIFVIEVKTRRAtdTVYVDsfqvsK 82
                                      344343236*******************9965677776443333 PP

>> UPF0102  Uncharacterised protein family UPF0102
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.3   2.5e-06     0.009      29      49 ..      50      72 ..      19     104 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.5e-06
                                      EEEE..TTEEEEEEEEE-..... CS
                           UPF0102 29 Diia..tevlvfvEVKtRssekf 49
                                      Diia  ++++ ++EVKtR+++++
  gi|385806179|ref|YP_005842577.1| 50 DIIAakNNRIFVIEVKTRRATDT 72
                                      9*****889********965542 PP

>> L_protein_N  L protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   6.8e-05      0.24      62      85 ..      48      71 ..      32      79 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.8e-05
                       L_protein_N 62 tPDniiiengklyiiefkvsvsne 85
                                       PD+i  +n+++++ie k++++++
  gi|385806179|ref|YP_005842577.1| 48 QPDIIAAKNNRIFVIEVKTRRATD 71
                                      6*******************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); 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: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 895.88
//
Query:       gi|385806180|ref|YP_005842578.1|  [L=132]
Description: phenylacetic acid degradation protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.6e-19   68.4   0.0    1.6e-17   63.5   0.0    2.0  2  FeS_assembly_P  Iron-sulfur cluster assembly protein
  ------ inclusion threshold ------
      0.025   14.4   0.1      0.052   13.4   0.1    1.5  1  DUF384          Domain of unknown function (DUF384)


Domain annotation for each model (and alignments):
>> FeS_assembly_P  Iron-sulfur cluster assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.5   0.0   1.7e-21   1.6e-17       1      64 [.      11      76 ..      11      80 .. 0.95
   2 ?    3.3   0.0     0.011        96      35      68 ..      83     114 ..      75     117 .. 0.81

  Alignments for each domain:
  == domain 1  score: 63.5 bits;  conditional E-value: 1.7e-21
                                      HHHHHHHHTT-B-TTTSSBCCCCT---EEEE-T.-EEEEEE--SSTT-TTHHHHHHHHHHHHC..S CS
                    FeS_assembly_P  1 keavlaaLrtVtDPelgvdlvslglvreidieg.gkVsvditltypacslaeairadaeaalr.al 64
                                      +e++ +aL+ V+DPe++v++++lgl++ei++++  +V++ + lt+p c++++ i + +e+ ++ +l
  gi|385806180|ref|YP_005842578.1| 11 REKIIEALKGVYDPEIPVNIYDLGLIYEIQVNDdMSVYIRMGLTTPFCPMVSSIVSVVEEEVEkKL 76
                                      589******************************99*************************998555 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.011
                                       EEEEEE--SSTT-T.THHHHHHHHHHHHC.STT-- CS
                    FeS_assembly_P  35 kVsvditltypacs.laeairadaeaalralpgve 68 
                                       kV+vdi +    ++ +a +i ++ +++l+++ g +
  gi|385806180|ref|YP_005842578.1|  83 KVYVDIDIS---KPwSAKMITKEGREQLKSIYGYD 114
                                       799999987...7777899******9999998855 PP

>> DUF384  Domain of unknown function (DUF384)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   5.8e-06     0.052       8      33 ..     100     125 ..      98     131 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.8e-06
                            DUF384   8 trhgReyLRskgvYpilRelhkaekd 33 
                                       t++gRe L+s   Y i+ e+ k e++
  gi|385806180|ref|YP_005842578.1| 100 TKEGREQLKSIYGYDIVEEMIKREEE 125
                                       9*******************999965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       807  (0.0450109); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); 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: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.52
# Mc/sec: 759.87
//
Query:       gi|385806181|ref|YP_005842579.1|  [L=78]
Description: hypothetical protein FFONT_1139 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0018   18.4   1.9     0.0022   18.1   1.9    1.1  1  DUF3784       Domain of unknown function (DUF3784)
      0.002   17.6   0.9      0.002   17.6   0.9    1.1  1  Jiraiya       Jiraiya
     0.0024   16.7   2.3     0.0025   16.6   2.3    1.0  1  DUF2207       Predicted membrane protein (DUF2207)
     0.0046   16.9   0.4     0.0051   16.8   0.4    1.1  1  RseC_MucC     Positive regulator of sigma(E), RseC/MucC
  ------ inclusion threshold ------
      0.012   15.9   1.7      0.015   15.6   1.7    1.2  1  DUF3267       Putative zincin peptidase
      0.065   13.4   0.1      0.065   13.4   0.1    2.1  2  DUF4519       Domain of unknown function (DUF4519)
      0.069   13.2   0.0      0.072   13.1   0.0    1.1  1  Hpr_kinase_N  HPr Serine kinase N terminus
       0.14   11.7   1.0       0.15   11.6   1.0    1.0  1  E1-E2_ATPase  E1-E2 ATPase
       0.49   10.6   7.5       0.61   10.3   7.5    1.1  1  TMEM238       TMEM238 protein family
       0.79   10.3  10.2       0.55   10.8   0.6    2.2  2  DUF3899       Domain of unknown function (DUF3899)
        1.5    9.0   6.8        1.9    8.7   6.8    1.2  1  SdpI          SdpI/YhfL protein family
        3.2    7.4   7.0          4    7.1   7.0    1.2  1  Tetraspanin   Tetraspanin family


Domain annotation for each model (and alignments):
>> DUF3784  Domain of unknown function (DUF3784)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   1.9   1.5e-06    0.0022      29      86 ..       5      59 ..       4      72 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.5e-06
                           DUF3784 29 mskeekekydekklsrfmgivllligilflllgll...saiesealliialiviiiiviyl 86
                                      +s+ +k++  + kl   + i +++igi++++++++   +   ++  + +++i   ++vi++
  gi|385806181|ref|YP_005842579.1|  5 LSDRKKREKEIFKLFFSYQIPFFIIGIALIIFSVFlnvE---TSLGMFLFII---GAVIIV 59
                                      57889999999************************4221...2222222222...222222 PP

>> Jiraiya  Jiraiya
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.9   1.3e-06     0.002     109     164 ..      20      75 ..       8      78 .] 0.89

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.3e-06
                           Jiraiya 109 FflsipvfltalilytlllfestpaivtsiilgvGivllllalvhnvyvwqrekkk 164
                                       F   ip+f+++++l ++ +f      ++  + ++G+v++++a   ++y+ +r+ +k
  gi|385806181|ref|YP_005842579.1|  20 FSYQIPFFIIGIALIIFSVFLNVETSLGMFLFIIGAVIIVIAPPLSIYLVKRKISK 75 
                                       5578**************************************99999998887666 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   2.3   1.7e-06    0.0025     374     425 ..      10      61 ..       3      77 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.7e-06
                           DUF2207 374 kkgkkklkklsalglgliilglilillallllvlllvfllilllillliaii 425
                                       k++k+++k +  + + ++i+g++li+++++l v ++ ++++++++ ++i+i+
  gi|385806181|ref|YP_005842579.1|  10 KREKEIFKLFFSYQIPFFIIGIALIIFSVFLNVETSLGMFLFIIGAVIIVIA 61 
                                       5667788888889999999999999999999887644444444444444333 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 !   16.8   0.4   3.4e-06    0.0051      65     122 ..      16      77 ..       8      78 .] 0.85

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.4e-06
                         RseC_MucC  65 kaallvYllPllllilgallgsall....gssellaalgallglvlgflivrllskrlkkks 122
                                          ++ Y +P++++ ++++++s++l      + +l ++ga++++++  l ++l++++++k++
  gi|385806181|ref|YP_005842579.1|  16 FKLFFSYQIPFFIIGIALIIFSVFLnvetSLGMFLFIIGAVIIVIAPPLSIYLVKRKISKDK 77 
                                       457999******************99887777888888899999999999999999988875 PP

>> DUF3267  Putative zincin peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   1.7     1e-05     0.015      55      89 ..      23      57 ..      12      77 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1e-05
                           DUF3267 55 laPfvllgilllllalllpsstlllllllalnaag 89
                                        Pf+++gi+l++ +++l+  t l ++l+++ a++
  gi|385806181|ref|YP_005842579.1| 23 QIPFFIIGIALIIFSVFLNVETSLGMFLFIIGAVI 57
                                      57****************95555444444444433 PP

>> DUF4519  Domain of unknown function (DUF4519)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   4.4e-05     0.065      18      52 ..       7      41 ..       2      45 .. 0.92
   2 ?   -0.4   0.3      0.91   1.4e+03      38      45 ..      53      60 ..      47      72 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.4e-05
                           DUF4519 18 eRrkenkeaqekvttvVlPvlavlillivvfvYlk 52
                                      +R+k  ke+ + +++  +P++++ i+li++ v+l 
  gi|385806181|ref|YP_005842579.1|  7 DRKKREKEIFKLFFSYQIPFFIIGIALIIFSVFLN 41
                                      6999999**************************97 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.91
                           DUF4519 38 lavlilli 45
                                      ++++i++i
  gi|385806181|ref|YP_005842579.1| 53 IGAVIIVI 60
                                      33333333 PP

>> Hpr_kinase_N  HPr Serine kinase N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.8e-05     0.072      66     108 ..       9      51 ..       4      68 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.8e-05
                                       HHHH..HHHHHHTT--S-EEEETTT---HHHHHHHHHH---EE CS
                      Hpr_kinase_N  66 eeerkerleklfskkipciiltrgleppeellelaeeygvpll 108
                                       ++++ke+++ +fs++ip++i+   l + + +l++ +  g+ l+
  gi|385806181|ref|YP_005842579.1|   9 KKREKEIFKLFFSYQIPFFIIGIALIIFSVFLNVETSLGMFLF 51 
                                       4567899999************999999999999888888777 PP

>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.0    0.0001      0.15     107     163 ..       7      66 ..       1      70 [. 0.51

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0001
                                       ---HHHHHHHHHHHH..HHHHHHHHHHHHHHS-STTTSSTT.HHHHHHHHHHHHHS-TTH CS
                      E1-E2_ATPase 107 kktplqkkldklgkv..lvpvvlliallvflialllgksla.eallralallvaaiPcaL 163
                                       ++++ +k++ kl+    + ++++ ial++f ++l ++ sl  + ++ + +++v+a P  +
  gi|385806181|ref|YP_005842579.1|   7 DRKKREKEIFKLFFSyqIPFFIIGIALIIFSVFLNVETSLGmFLFIIGAVIIVIAPPLSI 66 
                                       555556666655444024445555555555555555555534444445555566656555 PP

>> TMEM238  TMEM238 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   7.5   0.00041      0.61       4      45 ..      17      60 ..      15      68 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00041
                           TMEM238  4 kvflalavvfdvvGlvlLlvGifael..lfgDllvytGaliifl 45
                                      k+f+   + f ++G++l++  +f ++  + g +l  +Ga+ii++
  gi|385806181|ref|YP_005842579.1| 17 KLFFSYQIPFFIIGIALIIFSVFLNVetSLGMFLFIIGAVIIVI 60
                                      6899999*******************988999999******986 PP

>> DUF3899  Domain of unknown function (DUF3899)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.6   0.00037      0.55      56      82 ..      10      40 ..       2      42 .. 0.73
   2 ?    4.1   3.3     0.043        65       7      21 ..      46      60 ..      41      62 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00037
                           DUF3899 56 kkkes....skkstrplliiGlllivlsivl 82
                                      k++++    ++ +  p++iiG+ li++s++l
  gi|385806181|ref|YP_005842579.1| 10 KREKEifklFFSYQIPFFIIGIALIIFSVFL 40
                                      3333356788999999999999999999987 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.043
                           DUF3899  7 lglllliigillivl 21
                                      lg++l+iig+++iv+
  gi|385806181|ref|YP_005842579.1| 46 LGMFLFIIGAVIIVI 60
                                      799*******99997 PP

>> SdpI  SdpI/YhfL protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   6.8    0.0012       1.9      33      60 ..      26      60 ..      17      66 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0012
                              SdpI 33 wiiaGlilllla.......lgavvlvllvlvlllv 60
                                      ++i+G++l++++         +++l+++++v++++
  gi|385806181|ref|YP_005842579.1| 26 FFIIGIALIIFSvflnvetSLGMFLFIIGAVIIVI 60
                                      79***********9986542223333333333333 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   7.0    0.0026         4       4      64 ..      18      61 ..      15      73 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0026
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXX.....................XXXXXXXXXXXX CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Tetraspanin  4 llfffnllfwligivllavGvwlrlkhaeaalacllsesaedpailaillivvGvllfllg 64
                                      l+f + + f++igi+l++++v l                 + +++l ++l+++G+++++++
  gi|385806181|ref|YP_005842579.1| 18 LFFSYQIPFFIIGIALIIFSVFL-----------------NVETSLGMFLFIIGAVIIVIA 61
                                      56777777************999.................456678899******999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1180  (0.0658152); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 466.04
//
Query:       gi|385806182|ref|YP_005842580.1|  [L=280]
Description: competence damage-inducible protein A [Fervidicoccus fontis Kam940]
Scores for complete 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-31  107.0   0.0    1.1e-30  106.2   0.0    1.3  1  MoCF_biosynth  Probable molybdopterin binding domain
     0.0011   19.1   0.4     0.0027   17.8   0.4    1.7  1  CinA_KH        Damage-inducible protein CinA KH 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 !  106.2   0.0   1.2e-34   1.1e-30       2     138 ..      23     183 ..      22     188 .. 0.94

  Alignments for each domain:
  == domain 1  score: 106.2 bits;  conditional E-value: 1.2e-34
                                       EEEE-HHHHTTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTS.SEEEEESS-SSSTT--HHHH CS
                     MoCF_biosynth   2 vitvGdellsgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleea.dviittGGtGptpdDvtpea 77 
                                       +i +G+ell+g +++tn+++la++l+ lg++v+++ vvpD+ ee++++l++ale++  ++ittGG+Gpt dD t   
  gi|385806182|ref|YP_005842580.1|  23 IINTGTELLNGITVNTNASWLARKLSFLGFKVKRIIVVPDEFEEFSNELKRALENKaGIVITTGGLGPTYDDNTLLF 99 
                                       899**********************************************66666666******************** PP

                                       HHHHHSEE-HHHHHHHHHHHHHHCC........................TTSHGGGGGGE.EETTEEEEE-SSHHHH CS
                     MoCF_biosynth  78 laklfekelegfeeafrrvslkpgk........................pvgvapgailsravgktiigLPGspkav 130
                                       ++k ++ + e +e a+++v++ +++                        pvg+apg++l  + g+ ii LPG+p+++
  gi|385806182|ref|YP_005842580.1| 100 ISKSLKIPYEVNEDALNMVKKVYEAmsepltkerekmakmpkgsiplknPVGTAPGMMLYYS-GSYIISLPGVPSEM 175
                                       **********************999**********************************865.666*********** PP

                                       HHHHHHHH CS
                     MoCF_biosynth 131 kealeeil 138
                                       k+++ee l
  gi|385806182|ref|YP_005842580.1| 176 KAIFEEDL 183
                                       ****9866 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 !   17.8   0.4     3e-07    0.0027       3      67 ..     199     269 ..     197     274 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3e-07
                                       EEEE-S--HHHHHHHHGGGS-B.SSSEEEEEEETTE.....EEEEEE...EEHHHHHHHHH....HHHHHT CS
                           CinA_KH   3 vLktfGigESavaekladlidr.enptlAiyakege.....vtvRltakaaneeeaealiapveeeirerl 67 
                                       ++k+ Gi ESa+a  ++   ++  n  + + +k +e     +++++ a +++eeea++l+++++  i + +
  gi|385806182|ref|YP_005842580.1| 199 IIKVRGIMESAIAPLIEKASKKyLNAYIKTHPKGKEsnepyIEIQILATGNTEEEANKLASEITSDIINEI 269
                                       79******************9988889999999875444559********************999987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); 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: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 1637.69
//
Query:       gi|385806183|ref|YP_005842581.1|  [L=436]
Description: serine hydroxymethyltransferase [Fervidicoccus fontis Kam940]
Scores for complete 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-65  220.3   0.2      4e-65  220.0   0.2    1.0  1  SHMT             Serine hydroxymethyltransferase
    1.5e-10   40.8   0.0    2.2e-10   40.3   0.0    1.3  1  Beta_elim_lyase  Beta-eliminating lyase
    1.1e-09   38.0   0.0    2.7e-09   36.7   0.0    1.5  1  Aminotran_1_2    Aminotransferase class I and II
    0.00083   18.5   0.0     0.0014   17.7   0.0    1.3  1  SelA             L-seryl-tRNA selenium transferase
    0.00083   18.8   0.0     0.0012   18.3   0.0    1.3  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
     0.0014   17.7   0.0     0.0022   17.0   0.0    1.3  1  Aminotran_5      Aminotransferase class-V
  ------ inclusion threshold ------
       0.12   11.0   0.0       0.21   10.3   0.0    1.3  1  Pyridoxal_deC    Pyridoxal-dependent decarboxylase conserved 


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 !  220.0   0.2   1.6e-68     4e-65      14     399 .]      22     389 ..      10     389 .. 0.92

  Alignments for each domain:
  == domain 1  score: 220.0 bits;  conditional E-value: 1.6e-68
                                       HHHHHHHHSEE-STT-----HHHHHHHTSGGGG----EETTEESSST-HHHHHHHHHHHHHHHHHCT-STTTEEEE- CS
                              SHMT  14 kekerqkeeieliasenftskavlealGsvltnkyaeGyPGkryyGGcefvdeveelaqdrakelfkldpakwgvnv 90 
                                        ++ r+k++i+liasen++s+ +  +  s +  +yaeG P kryy G++++de+e +  +   ++ +++    +++ 
  gi|385806183|ref|YP_005842581.1|  22 ANEWRRKKSINLIASENVMSPLAEAVYLSDFMSRYAEGKPKKRYYQGTKYIDELEIMLAELMGKILNIQ----YIET 94 
                                       3445999**************************************************************....**** PP

                                       --SSHHHHHHHHHHHHT-TT-EEEEESCTTTSTGGGT-BTSS-B-SHHHHHSEEEEE-B-TTTSSB-HHHHHHHHHH CS
                              SHMT  91 qplsGsqanlavytallepgdrilgldladGGhlthGakveskkisassklfesveykvdketglidydelekkake 167
                                       +p sG+ an++v++ l epgdr l   + +G h++h        + a +++   ++y   +e   +d d+  k  ke
  gi|385806183|ref|YP_005842581.1|  95 RPISGTIANASVFKELGEPGDRALVAPVQAGSHVSHTKFGT---LGALGMTQVYLPYD--EERMNVDVDKAIKMIKE 166
                                       ************************************76554...58888888788885..56889************ PP

                                       H--SEEEEE-SST-S---HHHHHHHHHHTT-EEEEE-GGGHHHHHTTSS--GCC.TSSEEEEESSSTT-S-S-EEEE CS
                              SHMT 168 fkPklivaGtsaysrlidyarlreiadevgayllvdmahiaGlvaagvipsPfe.yadvvtttthktlrGprgglil 243
                                        k k++v G s y      + l +  +e ga ++ d ah+ Gl+++gv  +P++  adv+t+ thkt+ Gp+ggli 
  gi|385806183|ref|YP_005842581.1| 167 EKFKFLVLGGSVYLFPHPVKELADAVKERGAKIVYDAAHVFGLIVGGVWRNPLReGADVMTASTHKTFPGPQGGLIA 243
                                       ****************************************************96269******************** PP

                                       EC-SEEEEETTTEEEEHHHHHHHHHHHTTTT-SS--HHHHHHHHHHHHHCTSHHHHHHHHHHHHHHHHHHHHHHHTT CS
                              SHMT 244 lrkgvksvdktgkevleelekkinsavfPglqGGPlnhviaakavalkealepefkvyqkqvlknakalaealkekg 320
                                       ++             +e l+k++ +++fP      + h i a+ v+  e ++    +y+k v++nak++aeal e+g
  gi|385806183|ref|YP_005842581.1| 244 FS-------------DEGLYKQVSKTIFPYFLSNHHLHRIPATLVTTLEMMKY-GEQYAKAVVENAKKFAEALAEEG 306
                                       *9.............689*************************9998887764.479******************** PP

                                       -EEGGGS...-SSSEEEEEGGGGTS-HHHHHHHHHHTTEE-EEE--TTS..STTTT-SEEEEESHHHHHTT--HHHH CS
                              SHMT 321 yklvsgG...tdnhlvlvdlrekgldGkraekvlekvnitankntvPgd..ksalvtsGlrlGtpaltsrgfkeedl 392
                                       +k++ +    t +h v+vd+ ++g  G+++ ++le++ni +nkn +P+d  ++   +sGlrlGt  +t+ g++++++
  gi|385806183|ref|YP_005842581.1| 307 FKVLGENlgyTMSHQVVVDVAKQG-GGAKCATLLESANIITNKNLLPYDppENVQNPSGLRLGTQEMTRYGMGKQEM 382
                                       ***985333499*******98766.89**********************9888889********************* PP

                                       HHHHHHH CS
                              SHMT 393 ekvakfi 399
                                        ++a+++
  gi|385806183|ref|YP_005842581.1| 383 YEIAHLM 389
                                       ***9875 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.0   8.7e-14   2.2e-10      27     242 ..      65     322 ..      49     417 .. 0.81

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 8.7e-14
                                       CCT--HHHHHHHHHHHHHTT-SEEEE.....ES-HHHHHHHHHHHH--TTEEEEEETT...-HHHHSSTTHHHHCC- CS
                   Beta_elim_lyase  27 sYgedktvnrLedavaelfgkeaalf.....vpqGtaAnsillkillqrgeevivtep...ahihfdetgaiaelag 95 
                                        Y++ k + +Le  +ael+gk   +        +Gt An+  +k l ++g+  +v      +h+  +  g + +l+ 
  gi|385806183|ref|YP_005842581.1|  65 YYQGTKYIDELEIMLAELMGKILNIQyietrPISGTIANASVFKELGEPGDRALVAPVqagSHVSHTKFGTLGALGM 141
                                       5888899999999999999999888546665569******************9987556677777777777777777 PP

                                       -EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---.HHHHHHHHHHHHHCT-EEEEEETTH CS
                   Beta_elim_lyase  96 vklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvs.leelrevaaiakkygiplhlDgARf 171
                                        ++   + +e  ++d++k  ++ike     ek k+++l       gG v+  +  ++e+a+ +k++g ++++D+A +
  gi|385806183|ref|YP_005842581.1| 142 TQVYLPYDEERMNVDVDKAIKMIKE-----EKFKFLVL-------GGSVYLfPHPVKELADAVKERGAKIVYDAAHV 206
                                       7666666666688999998888888.....78999987.......67777515679********************* PP

                                       HHHHHHHTS-CHHHHTTSSEEEEESSSTT--SS-EEEEE-HH................................... CS
                   Beta_elim_lyase 172 anaakslgeivkemfsyvDsvtmslkKdllanvGgvlafrddel................................. 215
                                       +      g+    + +++D++t+s  K    + Gg++af+d++l                                 
  gi|385806183|ref|YP_005842581.1| 207 FGLI-VGGVWRNPLREGADVMTASTHKTFPGPQGGLIAFSDEGLykqvsktifpyflsnhhlhripatlvttlemmk 282
                                       *877.67888888889***************************9********************************* PP

                                       ....HHHHHHHHHHHHT---SSTHHHHH............ CS
                   Beta_elim_lyase 216 ..edylaerveqrkylggglrqagvlaa...........l 242
                                         e+y +  ve +k+ ++ l + g+++            +
  gi|385806183|ref|YP_005842581.1| 283 ygEQYAKAVVENAKKFAEALAEEGFKVLgenlgytmshqV 322
                                       *****9999***************9988544444444440 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 !   36.7   0.0     1e-12   2.7e-09      39     306 ..      65     316 ..      56     353 .. 0.81

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 1e-12
                                       ST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEE...ESS-THHHHH..H CS
                     Aminotran_1_2  39 eygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvp...dptyasykni..l 110
                                        y+ ++  +ele  la+++g  + l+++   +   +sG+ a++++++ l +  pgd+ lv    + ++ s+++   l
  gi|385806183|ref|YP_005842581.1|  65 YYQGTKYIDELEIMLAELMG--KILNIQYI-ETRPISGTIANASVFKELGE--PGDRALVApvqAGSHVSHTKFgtL 136
                                       699999**************..66666677.77889**************8..999988751225689999986225 PP

                                       HHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEE CS
                     Aminotran_1_2 111 rlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvD 187
                                        + g++ v+ p y+ee +++d+++ ++ +ke      k k++++ +      + + +  +++l+d +k++++ ++ D
  gi|385806183|ref|YP_005842581.1| 137 GALGMTQVYLP-YDEERMNVDVDKAIKMIKEE-----KFKFLVLGGS-----VYLFPHPVKELADAVKERGAKIVYD 202
                                       66788888888.88****************94.....5689999863.....45667779***************** PP

                                       ETTTTCBSSSSHTHHH.HGGSTTSTTEEEEEESSSTT.SSGGG-EEEEEE.EHHHHHHHHHHHHHHTSSHHHHHHHH CS
                     Aminotran_1_2 188 eaYagfvfgsldavat.ranveeepnllivgslsKaf.GlaGeRvGyilg.naavvsqlrklsrpflsssllqaava 261
                                        a+  +         + r  + e+ + + + s  K f G  G   G i+  ++ + +q+ k   p+  s++  + + 
  gi|385806183|ref|YP_005842581.1| 203 AAHVFGLIVG----GVwRNPLREGAD-VMTASTHKTFpGPQG---GLIAFsDEGLYKQVSKTIFPYFLSNHHLHRIP 271
                                       ***8665542....333666777767.666666677779999...****97889***********999777777777 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSS CS
                     Aminotran_1_2 262 aalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgm 306
                                       a l ++l+++++ e+ ++ + +++k++ ++Lae g+kvl+++ g+
  gi|385806183|ref|YP_005842581.1| 272 ATLVTTLEMMKYGEQYAKAVVENAKKFAEALAEEGFKVLGENLGY 316
                                       7777778899*****************************998665 PP

>> SelA  L-seryl-tRNA selenium transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   5.6e-07    0.0014     188     329 ..     207     346 ..     185     355 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 5.6e-07
                                       GT-----BHHHHHHTT-SEEEEETTSTT-SSS-EEEEE-HH.HHHHHHHSTHHHHTB--HHHHHHHHHHHHHHH..T CS
                              SelA 188 yglskePtvqealaeGvdlvsfsGDkllGgpqaGiivGkke.lieklkknplkraLrvDkltlaaleatlrlyldpe 263
                                       +gl      ++ l+eG+d+++ s  k + gpq G+i    e l +++ k  +   L      l  + atl   l+  
  gi|385806183|ref|YP_005842581.1| 207 FGLIVGGVWRNPLREGADVMTASTHKTFPGPQGGLIAFSDEgLYKQVSKTIFPYFLSNHH--LHRIPATLVTTLEMM 281
                                       677777888999************************876652667777777777776555..556666666666554 PP

                                       T-GGGSHHHHHHH--HHHHHHHHHHHHHHHTTSTT..EEEEEEEEEE-TCSSS-SS--EEEEEEEE CS
                              SelA 264 klaeklptlrlltqkleelrakaerlqkelkealgselevkvvkslsqvGsGslPveelpsaalti 329
                                       k  e+  + +++ + ++  +a ae+  k l e+lg +++ +vv ++++ G+G+   + l+sa +  
  gi|385806183|ref|YP_005842581.1| 282 KYGEQY-AKAVVENAKKFAEALAEEGFKVLGENLGYTMSHQVVVDVAKQGGGAKCATLLESANIIT 346
                                       444443.446678888899999999999*******************************9998765 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 !   18.3   0.0   4.6e-07    0.0012      82     195 ..     138     254 ..      62     291 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 4.6e-07
                                       HTT-EEEEE-B-TTTSSB-GGGCGGG--TTE.EE.EEEB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETT. CS
                   DegT_DnrJ_EryC1  82 elgakpvfvDvdpdtynidpaaieaaitert.ka.IlpVhlyGqvadmdalkaiaakhglkvieDaAhAlGatykg. 155
                                        lg++ v++  d++ +n+d++++ + i e+  k  +l   +y  +  +++l +  ++ g k++ DaAh +G  + g 
  gi|385806183|ref|YP_005842581.1| 138 ALGMTQVYLPYDEERMNVDVDKAIKMIKEEKfKFlVLGGSVYLFPHPVKELADAVKERGAKIVYDAAHVFGLIVGGv 214
                                       689999*********************9988755266678899999******************************9 PP

                                       ..EECCCSSSEEEEE-BTTSSS-SSS-EEEEESTHHHHHHHH CS
                   DegT_DnrJ_EryC1 156 ..kkvGalgdaavfSFyptKnlttGeGGavvtndeelaekar 195
                                          ++ + +d+ + S +  K++    GG++ + de l ++++
  gi|385806183|ref|YP_005842581.1| 215 wrNPLREGADVMTASTH--KTFPGPQGGLIAFSDEGLYKQVS 254
                                       99899999999999977..8899**************99987 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   8.4e-07    0.0022      86     215 ..     112     246 ..      78     259 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 8.4e-07
                                       TTTSEEEEE..TTSHGGGTHHHHHHHHHHTEEEEEEEBETT.SCBEGGGHHHH--.TTEEEEEEESBETTTTEB--H CS
                       Aminotran_5  86 kpgdeivvt..eaehhanlvpwqelakrtgakvkvipldee.geldldeleklln.ektklvaithvsnvtGtiqpv 158
                                       +pgd+++v   +a+ h  +     l  + g++ +++p dee  ++d+d++ k ++ ek k +      +v    +pv
  gi|385806183|ref|YP_005842581.1| 112 EPGDRALVApvQAGSHVSHTKFGTLG-ALGMTQVYLPYDEErMNVDVDKAIKMIKeEKFKFLV--LGGSVYLFPHPV 185
                                       56666666411334444444455555.455555566555441467777777777534444443..3445555679** PP

                                       HHHHHHHHHTT-EEEEE-TTTTTTS--....-HHHHTESEEEEETTT.TTSSTT-EEEEEEH CS
                       Aminotran_5 159 eeigklakkkgalvlvDaaqavghipi....dvkklgvDflafsghK.llgPtGiGvlyvrk 215
                                       +e+++++k++ga ++ Daa  +g i      +  + g+D++++s+hK + gP+G G++ +++
  gi|385806183|ref|YP_005842581.1| 186 KELADAVKERGAKIVYDAAHVFGLIVGgvwrNPLREGADVMTASTHKtFPGPQG-GLIAFSD 246
                                       ********************9887765111155678***********999***9.5555555 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 ?   10.3   0.0   8.2e-05      0.21     147     267 ..     119     233 ..     106     267 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 8.2e-05
                                       EEEEETTS-HHHHHHHHHHT-EEEEE--BTTTBB-HHHHHHHHHHHHCTT.EEEEEEEEBS-TTT-BB--HHHHHHH CS
                     Pyridoxal_deC 147 vlytsdqahssvekaalvlgvklrvipldengklrgaalekaieedkekGlipffvvatlGttvlgaFddlkelgdi 223
                                       v+   + +h+s  k++ ++ +++  + l  + + +  +  kai++ ke+          lG +v+     +kel+d+
  gi|385806183|ref|YP_005842581.1| 119 VAPVQAGSHVSHTKFGTLGALGMTQVYLPYDEERMNVDVDKAIKMIKEE-KFK---FLVLGGSVYLFPHPVKELADA 191
                                       55555678**************99876655556788899******9999.444...45699999999999******* PP

                                       HHHCT-EEEEE-TTGGGGGGSGGGGGGGTTGGGESEEEEECCCC CS
                     Pyridoxal_deC 224 cekydlwlHvDAAyaGsaficpeirhllkgieradSitvnphKl 267
                                       +++ +  +  DAA   ++++    r+ l+  e ad +t++ hK 
  gi|385806183|ref|YP_005842581.1| 192 VKERGAKIVYDAAHVFGLIVGGVWRNPLR--EGADVMTASTHKT 233
                                       *************9988888888887655..5677777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.33s 00:00:01.01 Elapsed: 00:00:00.53
# Mc/sec: 2492.88
//
Query:       gi|385806184|ref|YP_005842582.1|  [L=142]
Description: hypothetical protein FFONT_1142 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.6e-08   33.1   0.2    6.8e-08   32.8   0.2    1.1  1  RNA_binding  RNA binding


Domain annotation for each model (and alignments):
>> RNA_binding  RNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.2   3.8e-12   6.8e-08       6     114 ..       3     106 ..       1     111 [. 0.85

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 3.8e-12
                                       EEE-TTC-HHHHHHHHHTTSTTSE---EEEEEE-CCC-EEEEEEEEESSHHHHHHHHHHHHHHCCCCH.....HHHH CS
                       RNA_binding   6 afvhaTEdeekVlealsnllpeeeveieeeeaeGhygnpitileaelekkkakkvlkkllellreeei.....keLl 77 
                                       + v++TE e+  +  +++++++ee           y+++  i +  + ++k   +lkk++ llr+e+i     ++L+
  gi|385806184|ref|YP_005842582.1|   3 IPVKPTESEKNLALLVEKIMEPEE----------IYSEDLGIEKKIVARSKCISSLKKMHYLLRSERIldsarRYLK 69 
                                       67999***************9997..........799999999988888888****************966666666 PP

                                       HCCHCCB-TTSEEEEEEEHHHHHTT---BESSSS.....EEE CS
                       RNA_binding  78 keleervdekgklylrldKQaaylgklslvegdd.....vIk 114
                                       +++ +     ++++++l+KQa+++g++s+v+++      ++k
  gi|385806184|ref|YP_005842582.1|  70 EGVAD-----KMIVVMLHKQALAAGRISFVSEEResplgAVK 106
                                       66666.....99******************998766666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); 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 0.34s 00:00:00.88 Elapsed: 00:00:00.54
# Mc/sec: 790.48
//
Query:       gi|385806185|ref|YP_005842583.1|  [L=195]
Description: Dephospho-CoA kinase, CoaE [Fervidicoccus fontis Kam940]
Scores for complete 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-14   52.9   0.0    8.7e-14   52.1   0.0    1.4  1  AAA_17           AAA domain
      8e-12   45.8   0.0    1.5e-11   45.0   0.0    1.5  1  AAA_18           AAA domain
    0.00075   18.9   0.7      0.014   14.7   0.1    2.1  2  ATPase           KaiC
     0.0099   16.1   0.0      0.015   15.6   0.0    1.3  1  AAA_28           AAA domain
  ------ inclusion threshold ------
      0.019   14.6   0.0      0.045   13.4   0.0    1.6  2  CoaE             Dephospho-CoA kinase
      0.022   15.0   0.1      0.046   14.0   0.1    1.5  1  AAA_22           AAA domain
      0.029   13.8   0.0      0.052   13.0   0.0    1.4  1  KTI12            Chromatin associated protein KTI12
       0.03   14.5   0.0      0.039   14.1   0.0    1.3  1  AAA_33           AAA domain
       0.05   12.8   0.0      0.052   12.8   0.0    1.2  1  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.067   12.5   0.0       0.11   11.7   0.0    1.5  1  Zeta_toxin       Zeta toxin
      0.073   13.2   0.0       0.12   12.4   0.0    1.5  1  Sigma54_activ_2  Sigma-54 interaction domain
       0.16   12.3   0.0       0.25   11.7   0.0    1.4  1  AAA_16           AAA ATPase domain


Domain annotation for each model (and alignments):
>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1   0.0   5.8e-17   8.7e-14       1     129 [.      12     134 ..      12     141 .. 0.79

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 5.8e-17
                                       EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHH....HHHHHHHHHHHHSSE CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemrklpleekkelq....keaaekiaeeakkkg 73 
                                       +G+PGsGK+ ++    +  g+t++s+Gd++r+ a+++g +k+ +++    +e+++++     ++++  i e++k+++
  gi|385806185|ref|YP_005842583.1|  12 TGMPGSGKSIVS-SYFKSRGYTVYSMGDIVRNIAEERGVEKTLENLLSIAQEIRNKYGpsgvAKLMIPILEKEKSET 87 
                                       7********998.888999***************************988888877664444478888899999**** PP

                                       EEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHTTST-TS CS
                            AAA_17  74 vlvdghprikeqagfldglpkevleelkpdaiilleadpeeilerrlkdrtrgrdd 129
                                       v++dg  +i+e  + ++++     + +    ii ++ +p   +er+l  r+r  d 
  gi|385806185|ref|YP_005842583.1|  88 VVIDGVRSINEIGE-FKKVS----KCI---NIIAVYSPPYMRFERLLY-RGRPGDP 134
                                       ********966444.34433....444...899999999877777776.4554444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   0.0   9.8e-15   1.5e-11       1     116 [.       9     131 ..       9     146 .. 0.80

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 9.8e-15
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpealdeskrldedk.ldklldaleenssal 71 
                                       Il+tG+pG+GK+ ++ + ++r g+     g+++r +a e+g + + ++  l+  ++++ ++    + +++  +    
  gi|385806185|ref|YP_005842583.1|   9 ILITGMPGSGKSIVSSYFKSR-GYtvysmGDIVRNIAEERGVEKTLENL-LSIAQEIRNKYgPSGVAKLMIPIL-EK 82 
                                       99****************999.67789**********************.333333333330333333333333.47 PP

                            AAA_18  72 eegknlvidghlaeleseaakdikk....vvLtaspeelleRlekRgye 116
                                       e+ +++vidg+++ +e  ++k+  k    + ++ +p +++eRl  Rg+ 
  gi|385806185|ref|YP_005842583.1|  83 EKSETVVIDGVRSINEIGEFKKVSKciniIAVYSPPYMRFERLLYRGRP 131
                                       899******************9999*********************954 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   9.4e-06     0.014      19      44 ..       6      31 ..       4      39 .. 0.87
   2 ?    2.6   0.1     0.049        74      99     134 ..      64      99 ..      33     112 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 9.4e-06
                            ATPase 19 grvvlitGepGtGKtifalqFlikga 44
                                      ++ +litG pG+GK+i++  F  +g 
  gi|385806185|ref|YP_005842583.1|  6 RKLILITGMPGSGKSIVSSYFKSRGY 31
                                      689****************9988775 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.049
                            ATPase  99 kdkedleelieelaeaikeikakrvviDsitglaye 134
                                       ++k+ ++ +++ +  ++++ k + vviD + +++++
  gi|385806185|ref|YP_005842583.1|  64 RNKYGPSGVAKLMIPILEKEKSETVVIDGVRSINEI 99 
                                       56677777777788889999999*****99999554 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0     1e-05     0.015       2      43 ..       9      52 ..       8      68 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1e-05
                            AAA_28  2 ivitGgestGKTtlleaLaargypvv..pEaareileeklakge 43
                                      i itG +++GK+ +++ +++rgy+v+   +++r i ee++ +++
  gi|385806185|ref|YP_005842583.1|  9 ILITGMPGSGKSIVSSYFKSRGYTVYsmGDIVRNIAEERGVEKT 52
                                      89**********************99899******999885443 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     3e-05     0.045       3      40 ..       9      46 ..       7      71 .. 0.79
   2 ?   -2.1   0.0       1.7   2.6e+03     118     142 ..     104     128 ..      71     130 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3e-05
                                      EEEEESTTSSHHHHHHHHHHTT-EEEEHHHHHHHTTCC CS
                              CoaE  3 vgltGgiasGKstvanlfadlgvpivDaDlvArqvvep 40
                                      + +tG  +sGKs v+++f++ g+++     + r++ e+
  gi|385806185|ref|YP_005842583.1|  9 ILITGMPGSGKSIVSSYFKSRGYTVYSMGDIVRNIAEE 46
                                      679*******************9998877777777654 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.7
                                       GGGGSSEEEEEE--HHHHHHHHHHC CS
                              CoaE 118 lekliervlvvdvelelqveRlvar 142
                                         +++ +++ v  ++  + eRl+ r
  gi|385806185|ref|YP_005842583.1| 104 KVSKCINIIAVYSPPYMRFERLLYR 128
                                       4456677777777888888887766 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   3.1e-05     0.046       5     103 ..       6      96 ..       4     116 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.1e-05
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevv.....fvtlpsstsskdllrellralglelkaerlsse 76 
                                       ++++++tG +G+GK+ +   ++++            +v+       +++++ + ++ l++ll++ ++ +++     +
  gi|385806185|ref|YP_005842583.1|   6 RKLILITGMPGSGKSIVSSYFKSRG----------YTVYsmgdiVRNIAEERGVEKTLENLLSIAQEIRNK--YGPS 70 
                                       6899**************9999984..........333333332445555556677777777777766666..6677 PP

                            AAA_22  77 ellealeqalraravielliiDEaqhl 103
                                        + +++   l++ +  e ++iD +  +
  gi|385806185|ref|YP_005842583.1|  71 GVAKLMIPILEKEKS-ETVVIDGVRSI 96 
                                       777777777777777.77777766555 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.5e-05     0.052       3      34 ..       8      35 ..       6      64 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.5e-05
                                      EEEEE--TTSSHHHHHHHHHHHHHHTT--EEE CS
                             KTI12  3 LvvltGlPssGKstrakeLakaleeekrsvvv 34
                                      L+++tG+P sGKs +++    ++++++++v+ 
  gi|385806185|ref|YP_005842583.1|  8 LILITGMPGSGKSIVSS----YFKSRGYTVYS 35
                                      9************9986....55555555555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.6e-05     0.039       1      45 [.       8      51 ..       8     147 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.6e-05
                            AAA_33  1 lvllvGlpGsGKstlaerllkklgavllssdtlrrrlfgtdqqsk 45
                                      l+l+ G+pGsGKs ++  + k +g+++ s  ++ r+++++    k
  gi|385806185|ref|YP_005842583.1|  8 LILITGMPGSGKSIVSS-YFKSRGYTVYSMGDIVRNIAEERGVEK 51
                                      7999*********9887.799999999999888888877433322 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.5e-05     0.052       1      20 [.       6      25 ..       6     106 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.5e-05
                           DUF2075  1 kavvlVtGvaGtGKtvvlln 20
                                      ++++l+tG +G+GK++v + 
  gi|385806185|ref|YP_005842583.1|  6 RKLILITGMPGSGKSIVSSY 25
                                      589************99765 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   7.5e-05      0.11      17      39 ..       7      29 ..       3      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.5e-05
                        Zeta_toxin 17 klillgGqpGAGKselaellkde 39
                                      klil+ G pG+GKs +++++k +
  gi|385806185|ref|YP_005842583.1|  7 KLILITGMPGSGKSIVSSYFKSR 29
                                      89****************99876 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   8.3e-05      0.12      24      61 ..       9      46 ..       4     103 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.3e-05
                                      EEEEEETT--HHHHHHCC--TTS-EE--SSTTHHHH-H CS
                   Sigma54_activ_2 24 vfltGekGsgkelvArlLhknsgpwleifvverlaklp 61
                                      +++tG +Gsgk++v+ ++++ + ++ ++ ++ r +++ 
  gi|385806185|ref|YP_005842583.1|  9 ILITGMPGSGKSIVSSYFKSRGYTVYSMGDIVRNIAEE 46
                                      79******************999999888876666544 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00017      0.25      25      45 ..       7      27 ..       2      74 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
                            AAA_16 25 elvllsGesGvGKsslvrell 45
                                       l+l++G++G+GKs +   ++
  gi|385806185|ref|YP_005842583.1|  7 KLILITGMPGSGKSIVSSYFK 27
                                      689***********8876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       705  (0.0393218); expected 358.6 (0.02)
Passed bias filter:                      602  (0.0335769); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1128.99
//
Query:       gi|385806186|ref|YP_005842584.1|  [L=385]
Description: hypothetical protein FFONT_1144 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.24s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2569.33
//
Query:       gi|385806187|ref|YP_005842585.1|  [L=47]
Description: hypothetical protein FFONT_1145 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); 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 0.34s 00:00:00.74 Elapsed: 00:00:00.49
# Mc/sec: 288.69
//
Query:       gi|385806188|ref|YP_005842586.1|  [L=254]
Description: Ser/Thr protein kinase-like protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score 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   15.0   0.3      0.034   14.1   0.3    1.4  1  TMCCDC2   Transmembrane and coiled-coil domain-containing pro


Domain annotation for each model (and alignments):
>> TMCCDC2  Transmembrane and coiled-coil domain-containing protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.3   1.9e-06     0.034     101     153 ..     183     236 ..     155     241 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.9e-06
                           TMCCDC2 101 aelkiqdnknlllslg.lqekilkklqmvenkvkdlegliiaqkpatkrdcsse 153
                                       ++  +q ++ l+ls + ++e+i k +++ e k ++l +l+i +k+  k+ c  e
  gi|385806188|ref|YP_005842586.1| 183 NSNFLQISSALFLSKSrINERITKSFKIDEIKQNKLRELLILYKNCFKKRCMQE 236
                                       2233488899999975399********************************887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       900  (0.050198); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1641.50
//
Query:       gi|385806189|ref|YP_005842587.1|  [L=485]
Description: 2-5 oligoadenylate synthetase, ubiquitin domain protein region [Fervidicoccus fontis Kam940]
Scores for 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-39  132.6   0.1    2.4e-38  130.8   0.0    1.9  2  tRNA_NucTransf2  tRNA nucleotidyltransferase, second domain
    1.1e-10   41.6   0.3    3.6e-10   40.0   0.3    1.9  1  NTP_transf_2     Nucleotidyltransferase domain
    9.8e-07   29.1   0.4    1.9e-06   28.1   0.4    1.5  1  SMODS            Second Messenger Oligonucleotide or Dinucleo


Domain annotation for each model (and alignments):
>> tRNA_NucTransf2  tRNA nucleotidyltransferase, second domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.83     5e+03      75      88 ..      14      27 ..       7      42 .. 0.79
   2 !  130.8   0.0   4.1e-42   2.4e-38       1     112 [.     154     269 ..     154     270 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.83
                                      EETTEEEEETTTTS CS
                   tRNA_NucTransf2 75 iDPvDpkRNvaaal 88
                                      i P+D++R  a a+
  gi|385806189|ref|YP_005842587.1| 14 IKPTDEDRAKANAI 27
                                      78999999988876 PP

  == domain 2  score: 130.8 bits;  conditional E-value: 4.1e-42
                                       HHHHHHHHHHHHTT-BSSSTTT-SB-HHHHHHHHHHHSSHHHHHHHHTT--TTEEEE.........EEE...-SS-E CS
                   tRNA_NucTransf2   1 devrllKkflkgigvYGselkvkGfsGYlaEllvleygsfeevleaaakwkpkvvidleekea...llkkf.deplv 73 
                                       de+r+ Kkf+++igvYG+e+k++GfsGYl+Ell+++yg+f+e+l++a++w+ +++i  +++e+   ll+k+ + p++
  gi|385806189|ref|YP_005842587.1| 154 DEIRVAKKFARSIGVYGAETKIEGFSGYLIELLTIKYGGFRELLNKASEWRIPIKISFSSSESikrLLSKYeNCPMI 230
                                       89******************************************************877766655666666577*** PP

                                       EEETTEEEEETTTTS-HHHHHHHHHHHHHHHHS--GGGG CS
                   tRNA_NucTransf2  74 viDPvDpkRNvaaalsleklaefilaareflkkpseeff 112
                                       v DP+D++RNvaaa+s++k+ ef+ a++ +lkkp++ ff
  gi|385806189|ref|YP_005842587.1| 231 VEDPTDSERNVAAAVSKRKIFEFSSASKLYLKKPTLYFF 269
                                       ************************************999 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.3     6e-14   3.6e-10       3      94 ..      34     139 ..      32     140 .. 0.93

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 6e-14
                                       HHHHHHHHHTTTSEEEEEHHHHCTTSCTT.SSEEEEEEESTTCHHH.............HHHEHHHHHHHHCCCEEE CS
                      NTP_transf_2   3 klleelkelepvakvvlfGSyarGtalkg.SDiDllvvlpeevsre.............kkeegleklaeiikflee 65 
                                       k++e lk  + + +v l GS a++t+l++  ++D+++v+++e ++              + +e ++ +ae+++ + +
  gi|385806189|ref|YP_005842587.1|  34 KIIEGLKASNEKFEVLLEGSIAKDTWLRTsPEMDVFIVFENELDKKdfesivnklasilNEYEPAKQYAEHPYLTIK 110
                                       89999999999******************88***********7777*************888899************ PP

                                       CTTEEEEEECEEECCCCTEEEEEECEEEH CS
                      NTP_transf_2  66 llglevdlvtrekledpllvksileerpl 94 
                                       +  ++vd+v+  k e+ ++ k++++++pl
  gi|385806189|ref|YP_005842587.1| 111 VDEYNVDIVPAIKYEKGKRTKTAVDRTPL 139
                                       *********99999988999999999887 PP

>> SMODS  Second Messenger Oligonucleotide or Dinucleotide Synthetase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.4   3.2e-10   1.9e-06       1     136 [.       1     127 [.       1     137 [. 0.84

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 3.2e-10
                             SMODS   1 MkvssqFkeflsnielsqttkdsissrvkaitkrLnkdfrelkskiaesllvGSyardTaikpvsdkdmlfeldvdl 77 
                                       M++ss   e l++i++ ++++++++   + +++++ +   + +++  e ll GS a+dT ++ +       e+dv +
  gi|385806189|ref|YP_005842587.1|   1 MTLSSIEVEILKKIKPTDEDRAKANAIFNIVKNKIIEGL-KASNEKFEVLLEGSIAKDTWLRTSP------EMDV-F 69 
                                       67777777899**************************99.7777888999************433......3566.5 PP

                             SMODS  78 lvvvnevegdepsdlleklkkalkktyksseirqdrqvvvvelneikidvvPavenkdg 136
                                       +v  ne ++++ +++++kl ++l+++ +  +   +++ ++++++e+++d+vPa++ ++g
  gi|385806189|ref|YP_005842587.1|  70 IVFENELDKKDFESIVNKLASILNEYEPA-KQYAEHPYLTIKVDEYNVDIVPAIKYEKG 127
                                       6666777888999******9888665555.999*********************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (485 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); 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: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.51
# Mc/sec: 2856.39
//
Query:       gi|385806190|ref|YP_005842588.1|  [L=184]
Description: 2'-5' RNA ligase [Fervidicoccus fontis Kam940]
Scores for complete 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   95.3   0.0    2.7e-15   56.3   0.0    2.1  2  LigT_PEase       LigT like Phosphoesterase
    4.5e-14   52.8   0.4      7e-14   52.2   0.4    1.3  1  AKAP7_NLS        AKAP7 2'5' RNA ligase-like domain
    8.1e-13   48.5   0.0    9.9e-13   48.3   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 !   56.3   0.0   4.6e-19   2.7e-15      23      87 .]      24      86 ..       6      86 .. 0.88
   2 !   37.4   0.0   3.6e-13   2.2e-09       9      87 .]      95     173 ..      87     173 .. 0.87

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 4.6e-19
                                      CCTTEEETSGGGSEEEEEEEEEESHHHHHHHHHHHHHHHHTSBEEEEEEEEEEEEEECCSCCEEE CS
                        LigT_PEase 23 aklglkpvrpfnpHiTLaflgevdeekvpellealaeiasgaepfelkvdgvglfpsrlrprviy 87
                                       k   k+v+++n+HiTLaf+ge++e+++++++ea++ei++   +++ k++g+g+fp+ ++prv++
  gi|385806190|ref|YP_005842588.1| 24 LKVPMKVVEKENLHITLAFIGEISEDTLQDAIEAIKEIEHT--KIKAKLKGIGAFPNSNSPRVVW 86
                                      55677899******************************766..566******************9 PP

  == domain 2  score: 37.4 bits;  conditional E-value: 3.6e-13
                                       HHHHHHHHHHHHHHCCTTEEET..SGGGSEEEEEEEEEES.HHHHHHHHHHHHHHHHTSBEEEEEEEEEEEEEECC. CS
                        LigT_PEase   9 eelarlaaeleralaklglkpv..rpfnpHiTLaflgevd.eekvpellealaeiasgaepfelkvdgvglfpsrl. 81 
                                         + +l +++ + l + +++++  ++f+pH+T+a+++  +  ++++  ++++++i+ g  +  + +d++ l +s+l 
  gi|385806190|ref|YP_005842588.1|  95 ISIMELYKKVSSSLVAHKVPFEreKDFTPHLTIARIKGREnIKRLASFINEFSSIEIG--E--VVFDKLKLKKSTLt 167
                                       567788888888888889999988*************98889*************777..4..************** PP

                                       SCCEEE CS
                        LigT_PEase  82 rprviy 87 
                                       ++++iy
  gi|385806190|ref|YP_005842588.1| 168 PKGPIY 173
                                       *****9 PP

>> AKAP7_NLS  AKAP7 2'5' RNA ligase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2   0.4   1.2e-17     7e-14       6     189 ..       2     164 ..       1     176 [. 0.84

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 1.2e-17
                                       EEE---HHHHHHHHHHHHHHHHH-GGGGGGB.--TT--EEEEEEE---SHHHHHHHHHHHHHHHHHHHHHHTTS--E CS
                         AKAP7_NLS   6 siplnsnklrkklekfqesvlsklpgldeslfikpeklHlTllvlkLknkeeiaaakevLkevkeeikdaldnkpls 82 
                                       +i +n+++++ k+ ++ e++ls   ++  ++ +++e+lH+Tl  +   +++ +++a e++ke++        +++++
  gi|385806190|ref|YP_005842588.1|   2 AIEVNDPNVVSKIINIEEQMLS--LKVPMKV-VEKENLHITLAFIGEISEDTLQDAIEAIKEIE--------HTKIK 67 
                                       799******************9..5567778.9*********9987656666666655555553........57889 PP

                                       EEEEEEEEE.....TTTEEEEEE--SHHHHHHHHHHHHHHHHHHTTT--B--SS-.---EEEEEEGGG-THHHHTT- CS
                         AKAP7_NLS  83 lrlkGletfnddpakarVlYakveeesneekLqeladriikafeeaglvlekdkkkvklHaTlmnsrkrkkkqaksk 159
                                        +lkG++ f +   + rV++++v++++ +  + el +++   +++ ++  e++k+ +++H+T++ ++ r+++++  +
  gi|385806190|ref|YP_005842588.1|  68 AKLKGIGAFPN-SNSPRVVWIGVDDKA-SISIMELYKKVSSSLVAHKVPFEREKD-FTPHLTIARIKGRENIKRLAS 141
                                       9********65.5559*******9666.99**********************999.**********99988887555 PP

                                       -S--GG.GGGGGTT-EEEEEE--EEEEEES CS
                         AKAP7_NLS 160 esfdareilkqfkdfefgeekineihLsql 189
                                              ++++f++ e ge+ + +++L + 
  gi|385806190|ref|YP_005842588.1| 142 -------FINEFSSIEIGEVVFDKLKLKKS 164
                                       .......99999999999999999999765 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 !   48.3   0.0   1.6e-16   9.9e-13      21     126 ..      31     140 ..      16     162 .. 0.85

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 1.6e-16
                   2_5_RNA_ligase2  21 yprwppHitLlypfvededl.adlaellsrlaketepfevrldgfgvFeh.kks.vvylsv..sdsealqalraall 92 
                                       +++  +HitL++ ++++ed  +d+ e+++++  e++++++ l+g+g F+   +  vv++ v  + s ++ +l +++ 
  gi|385806190|ref|YP_005842588.1|  31 VEKENLHITLAFIGEISEDTlQDAIEAIKEI--EHTKIKAKLKGIGAFPNsNSPrVVWIGVddKASISIMELYKKVS 105
                                       78899************99889999999999..8999*************96667******888888999******* PP

                   2_5_RNA_ligase2  93 ealpeagdkeds.geftPHlTiaqsadstsaaell 126
                                       + l +++   ++ ++ftPHlTia+ + ++  ++l 
  gi|385806190|ref|YP_005842588.1| 106 SSLVAHKVPFEReKDFTPHLTIARIKGRENIKRLA 140
                                       **99995444445**********988777666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1150.03
//
Query:       gi|385806191|ref|YP_005842589.1|  [L=150]
Description: tRNA-splicing endonuclease subunit beta [Fervidicoccus fontis Kam940]
Scores for complete 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-09   37.0   1.2    4.2e-09   36.3   0.1    1.8  2  tRNA_int_endo    tRNA intron endonuclease, catalytic C-termin
  ------ inclusion threshold ------
      0.038   13.7   0.1      0.084   12.6   0.1    1.7  1  tRNA_int_endo_N  tRNA intron endonuclease, N-terminal domain
      0.078   12.2   0.0      0.098   11.9   0.0    1.2  1  SdiA-regulated   SdiA-regulated


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 ?   -1.0   0.1      0.31   1.8e+03      31      31 ..      27      27 ..       2      57 .. 0.50
   2 !   36.3   0.1   7.1e-13   4.2e-09       2      85 .]      65     143 ..      64     143 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.31
                                      E CS
                     tRNA_int_endo 31 Y 31
                                      Y
  gi|385806191|ref|YP_005842589.1| 27 Y 27
                                      2 PP

  == domain 2  score: 36.3 bits;  conditional E-value: 7.1e-13
                                       HHHHHHHHHHHHTT-EEEECGGGTSSEEEETSCTTTSSCSEEEEEEETTSEEEHHHHHHHHHHHHHTTSEEEEEEET CS
                     tRNA_int_endo   2 alkyavyrdLrekGyvvrsGlkFGadFrvYqrrpslehseylVvvvsedeeldwpdlsaavrlahsvkKklilaivd 78 
                                       ++ + vy dLre+G +++ G  F   F +Y    ++ +  +lV+v++e+ e++++ l++ +  a+  ++++ila+vd
  gi|385806191|ref|YP_005842589.1|  65 WILFSVYYDLRERGRILKYG-PFQNSFTLY----QNNKPISLVFVYEETFEFKVSTLLDLLDAAKRLNREAILAVVD 136
                                       67789***************.*********....55666789*********************************** PP

                                       TTSCEEE CS
                     tRNA_int_endo  79 aegdvty 85 
                                       + gdv y
  gi|385806191|ref|YP_005842589.1| 137 KHGDVSY 143
                                       ****988 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 ?   12.6   0.1   1.4e-05     0.084      38      61 ..      24      48 ..       9      54 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.4e-05
                                      EEHHHHHHHHHTTSEEEE.TTSEEE CS
                   tRNA_int_endo_N 38 LslvEAlYLlekGklevv.kggepl 61
                                      L+++E++Y ++kGk+ ++ +++++l
  gi|385806191|ref|YP_005842589.1| 24 LDFYETVYMCKKGKIIITdEDQKTL 48
                                      99****************7777766 PP

>> SdiA-regulated  SdiA-regulated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.6e-05     0.098      68     166 ..      27     121 ..      19     141 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.6e-05
                    SdiA-regulated  68 pEaveylgdgrlaivdEreqalvvvkvdadtksldaadlkklelglkkakNkGfEGvaydaredrLlvakErkPvkl 144
                                        E+v + ++g+++i+dE +++l  +++  d+++l+ ++   +++ ++  + +G   + y + ++++ + +  kP+ l
  gi|385806191|ref|YP_005842589.1|  27 YETVYMCKKGKIIITDEDQKTLEWYDIVLDRSQLENNAWILFSVYYD-LRERG-RILKYGPFQNSFTLYQNNKPISL 101
                                       59999****************************99999888886666.55566.4699****************999 PP

                    SdiA-regulated 145 yevkgvlskeelkvsekeklle 166
                                       + v    +  e kvs+  +ll+
  gi|385806191|ref|YP_005842589.1| 102 VFVYE--ETFEFKVSTLLDLLD 121
                                       88877..666666666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 947.82
//
Query:       gi|385806192|ref|YP_005842590.1|  [L=95]
Description: hypothetical protein FFONT_1150 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score 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   15.2   5.1      0.055   13.5   0.8    2.2  2  Sigma70_r1_1  Sigma-70 factor, region 1.1
       0.12   11.7   0.0       0.12   11.7   0.0    1.1  1  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain


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 ?   13.5   0.8   6.1e-06     0.055      25      58 ..      10      43 ..       4      52 .. 0.80
   2 ?    3.8   0.8    0.0064        58      10      38 ..      52      79 ..      42      85 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.1e-06
                                      HHHHGCCSS--HHHHHHHHHHHHCCT-EEE-SS- CS
                      Sigma70_r1_1 25 indaLpddeldseqiediiemLedmgIdvveeae 58
                                      i d   ++++++  +ed+i++L+++gId+   ++
  gi|385806192|ref|YP_005842590.1| 10 IKDEIIESIISAGLLEDLISYLSKNGIDIDGIKK 43
                                      66677788999*****************965555 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.0064
                                      HHHHHHHHSCEEHHHHHHHGCCSS--HHH CS
                      Sigma70_r1_1 10 LikkgKkkGyLtyeEindaLpddeldseq 38
                                      L+k +K+kG L  ++ +++L+ +  + e 
  gi|385806192|ref|YP_005842590.1| 52 LLKYAKEKGLLFESDPSQVLE-KTDEYED 79
                                      99********99999999997.3333343 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 ?   11.7   0.0   1.3e-05      0.12      39      81 ..      29      72 ..      16      92 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.3e-05
                                      HHHHHTT-EEEEEEEBB--SHHHHHH.HHHTTS-HHHHHHHHHH CS
                      tRNA-synt_1e 39 rilqalgYdvqfvqnvtDidDkiikr.areeeksvkelaekfie 81
                                       +l + g d+  ++ +tDid+ ++++ a+e+++ +++ ++++ e
  gi|385806192|ref|YP_005842590.1| 29 SYLSKNGIDIDGIKKITDIDEEVLLKyAKEKGLLFESDPSQVLE 72
                                      588999**************998765277777777666655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 738.65
//
Query:       gi|385806193|ref|YP_005842591.1|  [L=360]
Description: Linocin_M18 bacteriocin protein [Fervidicoccus fontis Kam940]
Scores for complete 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-27   95.5   0.0    5.2e-27   94.8   0.0    1.3  1  Linocin_M18     Encapsulating protein for peroxidase
    6.8e-09   36.2   2.5    6.8e-09   36.2   2.5    1.8  1  Rubrerythrin    Rubrerythrin
    0.00012   22.0   0.5    0.00032   20.6   0.3    1.8  2  Ferritin        Ferritin-like domain
     0.0015   18.9   0.3     0.0015   18.9   0.3    2.0  3  DUF2383         Domain of unknown function (DUF2383)
     0.0071   16.0   1.2      0.011   15.3   0.5    1.7  2  DUF3231         Protein of unknown function (DUF3231)
     0.0091   15.5   2.8      0.012   15.2   2.8    1.1  1  UvrD-helicase   UvrD/REP helicase N-terminal domain
  ------ inclusion threshold ------
      0.029   14.6   0.5      0.077   13.3   0.5    1.7  1  T3RM_EcoP15I_C  Type III R-M EcoP15I C-terminal domain
      0.036   14.1   0.6        0.1   12.6   0.4    1.8  2  DUF892          Domain of unknown function (DUF892)
      0.064   13.0   0.0       0.55   10.0   0.1    2.1  2  COQ7            Ubiquinone biosynthesis protein COQ7
      0.097   12.6   0.2       0.17   11.9   0.2    1.4  1  SeqA            SeqA protein C-terminal domain


Domain annotation for each model (and alignments):
>> Linocin_M18  Encapsulating protein for peroxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.8   0.0   2.9e-30   5.2e-27      66     254 ..     165     344 ..     146     345 .. 0.94

  Alignments for each domain:
  == domain 1  score: 94.8 bits;  conditional E-value: 2.9e-30
                                       EEEEEEEEE-EEEEEEEEEEHHHHHHHHHT-SS---HHHHHHHHHHHHHHHHHHHT--TTTT---STT-GG.GBE-- CS
                       Linocin_M18  66 kakvrkvlplvelrkdFtLsrrdleavergaedldlsavaeAArklAlaEdrlifeGlaeagieGlleakgkkklkl 142
                                       + ++r++ pl e+++ F +s   ++++++ + +l+  ++ ++A +l++ Edrli+e         +l+ +g+ kl++
  gi|385806193|ref|YP_005842591.1| 165 EKGEREIIPLNEIESYFIVSQMSIDSIDK-NGELEAPDLYRSALELSNNEDRLILET--------ILNREGTIKLPV 232
                                       56789***********************9.7789********************986........77********** PP

                                       -..SSHHHHHHHHHHHHHHHHTT---SSEEEEEEHHHHHHHHHHSSS.SS-HHHHHHHHTS-EEEEESS-SS..EEE CS
                       Linocin_M18 143 sdwakagnileavleAlekLreaGvegpyalvlspelYtklfrvsentgypeiehikelvdggvikapalkgd.avl 218
                                        +w+++++ ++++++A +++ ++G ++p+al +sp++Y kl  +s++tg++ +e+ik  + ++++  p+l ++ +++
  gi|385806193|ref|YP_005842591.1| 233 DEWNEPSQSVNDIANAFTEILRSGATKPFALFISPKKYVKLLAISDKTGTTDLERIKAFI-DNIVILPILPDNvTII 308
                                       ***********************************************************9.9*************** PP

                                       EETTSSSEEEEESS-SEEEEEEE-SSEEEEEEEEEE CS
                       Linocin_M18 219 vstrggdfeLtvgqDlsigYlsheaenvelrltEsl 254
                                       vs ++  +eL++g D +i Yl+ e+ ++++r  E l
  gi|385806193|ref|YP_005842591.1| 309 VSLQPRILELVIGIDSEIRYLGPEKGYHNFRAREKL 344
                                       *******************************99987 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   2.5   3.8e-12   6.8e-09       1      96 [.      22     114 ..      22     143 .. 0.78

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 3.8e-12
                                       HHHHHHHHHHHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS-------T CS
                      Rubrerythrin   1 eiLekAiagEssarrlYkelaekakegypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakpk 77 
                                       + L  +i++E +a++lY  l++ ++   ++++++Fe++A+eE+ H + +  ll++l+ e++ + +e   ++++  ++
  gi|385806193|ref|YP_005842591.1|  22 DALRLSIIAELDAINLYLQLSKSVE--DENVKKVFEDVAKEEKTHVGEFLALLNSLDAEQK-SELEAGLKEVKELTS 95 
                                       6799*********************..9999**************************9999.555555555555555 PP

                                       TGGHHHHHHHHHHHHHHHH CS
                      Rubrerythrin  78 flttaknLeeaiegayaee 96 
                                       + ++++    + + + +ee
  gi|385806193|ref|YP_005842591.1|  96 MNIKDDPSNLVSNEEKKEE 114
                                       5555543332234444333 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.3   1.8e-07   0.00032       3      72 ..      23      87 ..      21     142 .. 0.75
   2 ?   -2.0   0.0       1.8   3.2e+03      51      87 ..     217     251 ..     202     255 .. 0.64

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.8e-07
                                      HHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHH.C CS
                          Ferritin  3 aLneqladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklaerilalGgtpvltraelee.i 72
                                      aL+  + +el+a+++yl+++  v++++ +++   f++ a+ee +h  +++  ++ l++    +++ele+ +
  gi|385806193|ref|YP_005842591.1| 23 ALRLSIIAELDAINLYLQLSKSVEDENVKKV---FEDVAKEEKTHVGEFLALLNSLDA---EQKSELEAgL 87
                                      67777789*****************998877...***********************9...4444444442 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.8
                                       HHHHHHHTTS....SHHHHHHC-SSSSCSSHHHHHHH CS
                          Ferritin  51 laerilalGgtpvltraeleeieapkefgsveevlea 87 
                                       ++e il ++gt  l   e+ e    ++++++ +++ +
  gi|385806193|ref|YP_005842591.1| 217 ILETILNREGTIKLPVDEWNEP--SQSVNDIANAFTE 251
                                       6788999999555555555552..2224455555555 PP

>> DUF2383  Domain of unknown function (DUF2383)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.3   8.3e-07    0.0015       5      63 ..      23      81 ..      19     100 .. 0.88
   2 ?   -3.5   0.0       7.3   1.3e+04     101     111 .]     128     138 ..     127     138 .. 0.83
   3 ?   -2.9   0.0       4.7   8.4e+03      82      99 ..     209     226 ..     205     230 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 8.3e-07
                                      HHHHHHHHHHHHHHHHHHHHHT--SHHHHHHHHHHHHHHHHHHHHHHHHHHHCT----- CS
                           DUF2383  5 aLndLietlkdgeegykeaaekvkdpqlktlleriaeereeaaeeLqseiralggeped 63
                                      aL   i ++ d+++ y +  + v+d+++k+++e++a+e + ++ e+ + +++l  e ++
  gi|385806193|ref|YP_005842591.1| 23 ALRLSIIAELDAINLYLQLSKSVEDENVKKVFEDVAKEEKTHVGEFLALLNSLDAEQKS 81
                                      5555567789************************************9999999877665 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 7.3
                                       HHHHHHHHHHS CS
                           DUF2383 101 aleeyeealek 111
                                       +++ey++ale+
  gi|385806193|ref|YP_005842591.1| 128 VVNEYQKALEE 138
                                       68999999985 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 4.7
                                       -----HHHHHHHHHHHHH CS
                           DUF2383  82 ltsndeeaileeleegEd 99 
                                       l++n+++ ile + + E 
  gi|385806193|ref|YP_005842591.1| 209 LSNNEDRLILETILNREG 226
                                       678888899999998886 PP

>> DUF3231  Protein of unknown function (DUF3231)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.5   6.3e-06     0.011       8      71 ..      10      74 ..       7      92 .. 0.92
   2 ?   -2.6   0.0         2   3.7e+03      53      73 ..     205     226 ..     196     251 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.3e-06
                           DUF3231  8 gkkrpLtasEias.lwssyianslgialitgFlqvaedkeikelleralelsnkhikelkelLke 71
                                      + +r+L a Eia+ l  s+ia+  +i l+ + ++++ed+++k+++e + +  + h+ e+  lL++
  gi|385806193|ref|YP_005842591.1| 10 PMDRKLKANEIADaLRLSIIAELDAINLYLQLSKSVEDENVKKVFEDVAKEEKTHVGEFLALLNS 74
                                      5689********747789*************************************9999999986 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2
                           DUF3231  53 ralelsn.khikelkelLkeen 73 
                                        alelsn +   +l+++L+ e+
  gi|385806193|ref|YP_005842591.1| 205 SALELSNnEDRLILETILNREG 226
                                       5777865144567888888886 PP

>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   2.8   6.6e-06     0.012     128     244 ..      47     254 ..       2     270 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6.6e-06
                                       HCCHHHHHHHHHSCHSHTTTTHHHHHHHHHHHHHHCCCCCHHHHCCCHHHHHCHHHHHHHHHHHTTCCTTHHCHSST CS
                     UvrD-helicase 128 dlkqqellkelleksaddslnldkkkleklikelsksrnikkeelslskskaeelrelvskakekqlspkelkkafe 204
                                       d +++++++++ +    ++ ++   ++ +l    s++ + k+e + + k ++e +++ +++ +++++s++e+k++++
  gi|385806193|ref|YP_005842591.1|  47 DENVKKVFEDVAK----EE-KTHVGEFLAL--LNSLDAEQKSELEAGLKEVKELTSMNIKDDPSNLVSNEEKKEENK 116
                                       4445555555554....21.2222222222..2355666669999******************************** PP

                                       SCSHHHHHHHHHHHHHHHHHHHHTC.................................................... CS
                     UvrD-helicase 205 kasdlqkkiaeflkeyqeqkkeena.................................................... 229
                                        ++ + +++  + +eyq+ ++e+++                                                    
  gi|385806193|ref|YP_005842591.1| 117 VKNSNGDFLSIVVNEYQKALEEMRIfrkylpikriekgtqaifveksdekgereiiplneiesyfivsqmsidsidk 193
                                       ************************99999999999999999999999999999999999999999999999999999 PP

                                       ..............................................EEHHHHHHHHHHHHH CS
                     UvrD-helicase 230 ..............................................lDfsdllhallelle 244
                                                                                     +  +d+++a++e+l+
  gi|385806193|ref|YP_005842591.1| 194 ngeleapdlyrsalelsnnedrliletilnregtiklpvdewnepsQSVNDIANAFTEILR 254
                                       9996666666666666666666666666666666666666666666666666666666655 PP

>> T3RM_EcoP15I_C  Type III R-M EcoP15I C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.5   4.3e-05     0.077      36      93 ..      34      92 ..      18      96 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.3e-05
                    T3RM_EcoP15I_C 36 ekkLYl.iekglesealkaLiekldedkefniekivlfgysfeskelreleenlkqlkn 93
                                        +LYl + k +e+e++k+++e + ++++ ++ +  ++ +s++ ++++ele +lk++k+
  gi|385806193|ref|YP_005842591.1| 34 AINLYLqLSKSVEDENVKKVFEDVAKEEKTHVGEFLALLNSLDAEQKSELEAGLKEVKE 92
                                      5579998899*********************************************9986 PP

>> DUF892  Domain of unknown function (DUF892)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.4   5.8e-05       0.1       9      91 ..      23     101 ..      19     107 .. 0.87
   2 ?   -1.9   0.0       1.7   3.1e+03     118     140 ..     204     226 ..     202     235 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.8e-05
                                       HHHHHHHHHHHHHHHHHHHHHH-SSHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-------.-HHHHTTT------- CS
                            DUF892   9 eLrDlyaaEkqllkalpkmakaaespeLkaaleqHleeTegqierLeqvferlgesasekkcdamegliaegqelie 85 
                                       +Lr    aE  ++++  +++k++e++++k+ +e+  +e ++++ +   ++++l+++++ +     e  ++e++el  
  gi|385806193|ref|YP_005842591.1|  23 ALRLSIIAELDAINLYLQLSKSVEDENVKKVFEDVAKEEKTHVGEFLALLNSLDAEQKSEL----EAGLKEVKELTS 95 
                                       6666778999*******************************************99988887....666788888888 PP

                                       ----TH CS
                            DUF892  86 eaaede 91 
                                       ++++d+
  gi|385806193|ref|YP_005842591.1|  96 MNIKDD 101
                                       777776 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.7
                                       HHHHCTT-HHHHHHHHHHHHHHH CS
                            DUF892 118 alAeqlgekeaaklLeqtleeek 140
                                       + A +l+++e++ +Le++l+ e 
  gi|385806193|ref|YP_005842591.1| 204 RSALELSNNEDRLILETILNREG 226
                                       66889999**********99885 PP

>> COQ7  Ubiquinone biosynthesis protein COQ7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00031      0.55       2      60 ..      20      76 ..      19      84 .. 0.86
   2 ?    0.4   0.0      0.27   4.9e+02       8      38 ..     191     218 ..     188     227 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00031
                              COQ7  2 ldrllRvdhaGElgAvaiYkgqlavlakkdpelkpllkemleqEkeHlatfeellkerr 60
                                      ++ +lR     El A  +Y      +  +d+++k+++++++++Ek H+  f +ll++ +
  gi|385806193|ref|YP_005842591.1| 20 IADALRLSIIAELDAINLYLQLSKSV--EDENVKKVFEDVAKEEKTHVGEFLALLNSLD 76
                                      67789999999********9888775..788889**************99999988765 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.27
                              COQ7   8 vdhaGElgAvaiYkgqlavlakkdpelkpll 38 
                                       +d+ GEl A  +Y++ l   +++d     +l
  gi|385806193|ref|YP_005842591.1| 191 IDKNGELEAPDLYRSALELSNNEDR---LIL 218
                                       6999***********9998533333...344 PP

>> SeqA  SeqA protein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   9.4e-05      0.17       9      74 ..      55     120 ..      48     134 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.4e-05
                              SeqA   9 seefaeekkavnrFlliLsalyradpeaFakatekvkGrtRvYfakdeetllasgkstkpkqipet 74 
                                       ++  +eek  v+ Fl++L++l  +++++ ++ +++vk  t +   +d ++l++++++ +  ++ ++
  gi|385806193|ref|YP_005842591.1|  55 EDVAKEEKTHVGEFLALLNSLDAEQKSELEAGLKEVKELTSMNIKDDPSNLVSNEEKKEENKVKNS 120
                                       5778999*******************************9999999999999999988777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       957  (0.0533772); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.61u 0.34s 00:00:00.95 Elapsed: 00:00:00.50
# Mc/sec: 2162.61
//
Query:       gi|385806194|ref|YP_005842592.1|  [L=158]
Description: hypothetical protein FFONT_1152 [Fervidicoccus fontis Kam940]
Scores for complete 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   3.1    0.00048   20.4   3.1    1.6  1  FCH              Fes/CIP4, and EFC/F-BAR homology domain
     0.0085   16.6   3.5     0.0085   16.6   3.5    1.4  2  TFIIS_M          Transcription factor S-II (TFIIS), central d
  ------ inclusion threshold ------
      0.011   16.1   9.4      0.032   14.6   8.7    2.0  1  Rubrerythrin     Rubrerythrin
       0.02   13.8   0.4       0.25   10.1   0.0    2.0  2  FA_desaturase_2  Fatty acid desaturase
      0.022   13.3   4.4      0.026   13.1   4.4    1.0  1  Vps35            Vacuolar protein sorting-associated protein 
      0.047   14.0   1.6       0.17   12.2   0.3    2.2  2  Cas_Cmr5         CRISPR-associated protein (Cas_Cmr5)
      0.052   13.6   3.7      0.066   13.3   2.2    1.7  2  Cnd1             non-SMC mitotic condensation complex subunit
      0.093   11.4   3.2       0.11   11.1   3.2    1.0  1  Peptidase_S46    Peptidase S46
        4.6    7.0   8.3         24    4.7   8.3    2.0  1  YkuI_C           EAL-domain associated signalling protein dom


Domain annotation for each model (and alignments):
>> FCH  Fes/CIP4, and EFC/F-BAR homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   3.1   2.4e-07   0.00048      17      66 ..       4      62 ..       2      65 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.4e-07
                                      HHHHHHHHHHHHHHHHHHHHHHHHCT----T........T-.........HHHHHHHHHHHH CS
                               FCH 17 edlqeflkeRaeiEkeYakkLqkLakkylkr........rkkks....eestlvtawtvlle 66
                                      e++++ +ke a +EkeYak L  L+kk++++            s    +++tl+++ ++ll+
  gi|385806194|ref|YP_005842592.1|  4 EEIKKEVKEFAILEKEYAKILLELSKKIKHKalssifesL---SkdseKHATLYETISELLS 62
                                      6889999***********************7555555531...0333466777777777766 PP

>> TFIIS_M  Transcription factor S-II (TFIIS), central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.2       4.9   9.7e+03      94     103 ..       3      12 ..       1      22 [. 0.57
   2 !   16.6   3.5   4.3e-06    0.0085       2     100 ..      30     139 ..      29     142 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 4.9
                                       -HHHHHHHHH CS
                           TFIIS_M  94 seelkeerek 103
                                       +ee+k+e ++
  gi|385806194|ref|YP_005842592.1|   3 EEEIKKEVKE 12 
                                       5555555444 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 4.3e-06
                                       HHHHHHHHHHHHHTT---...-..........--THHHHHHH............HHHHHHHHT------HHHHHHHH CS
                           TFIIS_M   2 kvRdkcrelLaealeedsseaee.........eedveelaae............iEealfekekkstdkkykqkvrs 57 
                                       k++ k+++ ++e+l +ds+++ +         +        +            iE+ + e  + +t+ k  +  r+
  gi|385806194|ref|YP_005842592.1|  30 KIKHKALSSIFESLSKDSEKHATlyetisellS--------NeqpfiseedfrlIERTINE--HITTEAKMIEESRK 96 
                                       6889999**********9544436544444440........23555444555567777655..567899******** PP

                                       HHHHHS-TT-HHHHHTSSSS--STTTTS---TTTSS-HHHHHH CS
                           TFIIS_M  58 lvfNLkdkkNpeLrrrvlsgeispeklvkmspeElaseelkee 100
                                       ++ N+kd++   L+  +++ e +  kl+   +e+ a +e+ +e
  gi|385806194|ref|YP_005842592.1|  97 ILNNIKDPRVRLLAAIIYEDEEKHHKLLLTVKEDIAKKETFSE 139
                                       ************************************9998665 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   8.7   1.6e-05     0.032      10     134 ..      17     125 ..       9     128 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.6e-05
                                       HHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS-------TTGGHHHHHH CS
                      Rubrerythrin  10 EssarrlYkelaekakegypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakpkflttaknLe 86 
                                       E +  ++  el++k+k   + ++ +Fe l+++ ++Ha  l++ +++l  +++          +  +++f + +    
  gi|385806194|ref|YP_005842592.1|  17 EKEYAKILLELSKKIK--HKALSSIFESLSKDSEKHAT-LYETISELLSNEQ---------PFISEEDFRLIE---- 77 
                                       777778889*******..99****************97.6677777777777.........344445554444.... PP

                                       HHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHH CS
                      Rubrerythrin  87 eaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerlr 134
                                         i+  ++ e +m+++  +++++ ++++++ l + + e+E+kH ++l 
  gi|385806194|ref|YP_005842592.1|  78 RTINEHITTEAKMIEESRKILNNIKDPRVRLLAAIIYEDEEKHHKLLL 125
                                       455566666677777778888888889888888889999999998876 PP

>> FA_desaturase_2  Fatty acid desaturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00013      0.25     175     239 ..      27      94 ..      22      99 .. 0.79
   2 ?    2.3   0.1     0.031        61     176     209 ..      98     131 ..      92     140 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00013
                   FA_desaturase_2 175 lakeagdellakicgaiaadEkrHeaaYtrvvekllevdp...deavlaladmmrkkitmPaallrdg 239
                                       l k+ + ++l+ i + +++d ++H++ Y++++e l + +p   +e  + +++ ++++it  a++++++
  gi|385806194|ref|YP_005842592.1|  27 LSKKIKHKALSSIFESLSKDSEKHATLYETISELLSNEQPfisEEDFRLIERTINEHITTEAKMIEES 94 
                                       56788999***********************9988777764446667777777777777777777665 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.031
                   FA_desaturase_2 176 akeagdellakicgaiaadEkrHeaaYtrvvekl 209
                                        ++ +d+ +  + ++i +dE++H++   +v e +
  gi|385806194|ref|YP_005842592.1|  98 LNNIKDPRVRLLAAIIYEDEEKHHKLLLTVKEDI 131
                                       5677899999999**********99877776665 PP

>> Vps35  Vacuolar protein sorting-associated protein 35
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   4.4   1.3e-05     0.026     400     502 ..      15     135 ..       2     144 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.3e-05
                             Vps35 400 vlklenykellsllsyktrkkvaleivdaileeketkietleevekllellsvlikdek.d..........keeeef 465
                                       +l  ++y+++l  ls+k ++k   +i +++ +++e++ + +e +++ll+  +++i++e+ +          +     
  gi|385806194|ref|YP_005842592.1|  15 IL-EKEYAKILLELSKKIKHKALSSIFESLSKDSEKHATLYETISELLSNEQPFISEEDfRliertinehiT----- 85 
                                       33.379************************9888899*******************8776356666545441..... PP

                             Vps35 466 aeeqelvaklvhli..............knddldkqfklllllrkkllkgg 502
                                        +e +++    +++                +d +k+ klll++++ + k++
  gi|385806194|ref|YP_005842592.1|  86 -TEAKMIEESRKILnnikdprvrllaaiIYEDEEKHHKLLLTVKEDIAKKE 135
                                       .33333333333332222222222222256778999999999999887765 PP

>> Cas_Cmr5  CRISPR-associated protein (Cas_Cmr5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.3   8.5e-05      0.17      54     104 ..      35      90 ..       3     103 .. 0.67
   2 ?    0.6   0.1      0.32   6.4e+02      57      76 ..     115     134 ..     107     146 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.5e-05
                                       C.......SSCCCHHHHHHHHHHHHHHHHCTSS...STTTCHHHHHHHHSTHHHHHHH CS
                          Cas_Cmr5  54 g.......kkkkedahkkllehlaewlkkeksaskkkkgendllkelleadlseymra 104
                                       +        +k++++h+ l+e ++e l++e  ++  ++++  l+++ ++ + ++   +
  gi|385806194|ref|YP_005842592.1|  35 AlssifesLSKDSEKHATLYETISELLSNE--QPFISEEDFRLIERTINEHITTEAKM 90 
                                       1333333346789*****************..77788888888888887776555544 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.32
                                       CCCHHHHHHHHHHHHHHHHC CS
                          Cas_Cmr5  57 kkedahkkllehlaewlkke 76 
                                       ++e++h+kll  ++e ++k+
  gi|385806194|ref|YP_005842592.1| 115 EDEEKHHKLLLTVKEDIAKK 134
                                       46888888888888888777 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 ?   13.3   2.2   3.3e-05     0.066      60     134 ..      17      91 ..       6     104 .. 0.84
   2 ?    3.2   0.2     0.041        82      49     103 ..      80     134 ..      78     144 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.3e-05
                              Cnd1  60 lselaklleDenprVvanalaalteiseksenaiynllpdiisklsdalnecsewgqitilefLlsyipkdkqea 134
                                        +e ak+l + ++++   al+++ e ++k++++  +l  +i   ls+++  +se++++ i +++ ++i+ +++ +
  gi|385806194|ref|YP_005842592.1|  17 EKEYAKILLELSKKIKHKALSSIFESLSKDSEKHATLYETISELLSNEQPFISEEDFRLIERTINEHITTEAKMI 91 
                                       567789999999*****************9899999988888888888778******************999843 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.041
                              Cnd1  49 ilndmvkekgflselaklleD.enprVvanalaalteiseksenaiynllpdiisk 103
                                       i++ +  e ++++e +k+l++ ++prV+ +a ++  e  ek  +++++++ di++k
  gi|385806194|ref|YP_005842592.1|  80 INEHITTEAKMIEESRKILNNiKDPRVRLLAAII-YEDEEKHHKLLLTVKEDIAKK 134
                                       5666777888999999999653778888777655.555555559999999999876 PP

>> Peptidase_S46  Peptidase S46
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   3.2   5.5e-05      0.11     411     531 ..      11     133 ..       2     140 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.5e-05
                                       HHHHHHHHHCHHHHCS--HHHHHHHHHHHHHHHHHHS-GGG--S----SS.........-S-SHHCCCCC-TTSSCH CS
                     Peptidase_S46 411 ralealekeleridkdldaevdkavlaallkeyreklkaerlpavdkvlgkes...kgdlealvdrlvakskladea 484
                                       ++ + leke+++i  +l++++ ++ l   ++++ +  +++  +++++++++     +  +++   rl++++  +  +
  gi|385806194|ref|YP_005842592.1|  11 KEFAILEKEYAKILLELSKKIKHKALSSIFESLSKDSEKH--ATLYETISELLsneQPFISEEDFRLIERTINEHIT 85 
                                       4555566666666666666666666666666666555533..455555554442112445666668*********** PP

                                       HHHHHT-SHHCHHHHCC-HHHHHHHHH.HHHHHHTHHHHHHHHHHHHH CS
                     Peptidase_S46 485 krkalleeakaaveaskDplielaval.adaraalekaekelegklek 531
                                       + ++++ee+++ +++ kDp ++l +a+ ++ +++++k   +++++++k
  gi|385806194|ref|YP_005842592.1|  86 TEAKMIEESRKILNNIKDPRVRLLAAIiYEDEEKHHKLLLTVKEDIAK 133
                                       **************************9888888888877777777666 PP

>> YkuI_C  EAL-domain associated signalling protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   8.3     0.012        24       7      59 ..       2      55 ..       1     135 [. 0.83

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.012
                            YkuI_C  7 lkdklkkefhqfiayekkklealyelseklkkr.lkellkklkkaedydelllk 59
                                      + +++kke+++f   ek+  ++l+els+k+k++ l++++++l k+++ +  l++
  gi|385806194|ref|YP_005842592.1|  2 VEEEIKKEVKEFAILEKEYAKILLELSKKIKHKaLSSIFESLSKDSEKHATLYE 55
                                      5689*************************9865378888887777666544433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1588  (0.0885716); expected 358.6 (0.02)
Passed bias filter:                      683  (0.0380947); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); 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 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1125.07
//
Query:       gi|385806195|ref|YP_005842593.1|  [L=78]
Description: cysteine synthase B [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-13   49.7   0.0    3.4e-13   49.6   0.0    1.0  1  PALP      Pyridoxal-phosphate dependent enzyme


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   0.0   1.9e-17   3.4e-13      52     111 ..       9      69 ..       1      77 [. 0.82

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 1.9e-17
                                       T..TTTSEEEEEBSSHHHHHHHHHHHHHT-EEEEEEETTS-HHHHHHHHHTT-EEEEECCHH CS
                              PALP  52 g..tgaktvveassGNhgralAaaaallGlkvtivvpadaspekvallrllGaevvevggdy 111
                                       +  + ++ +veassGN+++ +A++a++lGl  +ivv++ +s +kv+l++ lGae+    +d 
  gi|385806195|ref|YP_005842593.1|   9 HnlKLGEYIVEASSGNTAIYVAFVARKLGLNPIIVVSRQTSVAKVKLIKILGAEIFYG-SDD 69 
                                       34457889**********************************************9765.333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.49
# Mc/sec: 481.32
//
Query:       gi|385806196|ref|YP_005842594.1|  [L=60]
Description: Cysteine synthase B [Fervidicoccus fontis Kam940]
Scores for complete 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   41.1   0.0    1.5e-10   41.0   0.0    1.0  1  PALP      Pyridoxal-phosphate dependent enzyme


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   0.0   8.6e-15   1.5e-10     119     169 ..       9      59 ..       5      60 .] 0.93

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 8.6e-15
                                       HHHHHHSTTCEE--TTTSHHHHHH.HHTHHHHHHHHTTTTEEEEEEE-SSSH CS
                              PALP 119 aelaaegegaylvsqfdnptvieg.ygtiglEileqlggkpdavvvpvGgGg 169
                                       +++a+e +g ++++q+++  ++ + y+t+g+Ei++q++gk+da+v+++G+ g
  gi|385806196|ref|YP_005842594.1|   9 KKIAEE-KGGVFLNQYEDKNNFRAhYETTGPEIWSQMNGKIDAFVMGIGTRG 59 
                                       589999.******************************************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 409.37
//
Query:       gi|385806197|ref|YP_005842595.1|  [L=54]
Description: hypothetical protein FFONT_1155 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); 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: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.47
# Mc/sec: 348.36
//
Query:       gi|385806198|ref|YP_005842596.1|  [L=585]
Description: metal dependent phosphohydrolase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-06   27.6   0.1    1.1e-05   25.7   0.1    2.2  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 !   25.7   0.1   5.9e-10   1.1e-05       1      72 [.      72     181 ..      72     248 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 5.9e-10
                                       HHHHHHHHHHHHHHHHHHHHH...................HHHHHHHHHHHHHTTTTHHHHTS..HHH......... CS
                                HD   1 rleHsleVaklarrlaedlge...................eedrellllaaLlHDiGkgpfgdafekk......... 49 
                                       r+eHsl+ +++a+++  +                       ++   +++ aLlHD+G+ p ++  e +         
  gi|385806198|ref|YP_005842596.1|  72 RFEHSLGAMHVAGMIWTSFMNnspgiiselfptsssrkdqSAFYLATRISALLHDVGHLPYSHVTESAletayenge 148
                                       799***********999876699*************9999999999*****************99999777666665 PP

                                       .........HHH..CTCCHHHHHHHHHHHHHHHH CS
                                HD  50 .........eee..fekflaHekvgaeilrevek 72 
                                                e +  ++k++ He +g    ++++k
  gi|385806198|ref|YP_005842596.1| 149 lpeemneifE-KaeKRKLKLHEYYGCIFSEKLLK 181
                                       5544444430.14466666666666655554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (585 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 4147.75
//
Query:       gi|385806199|ref|YP_005842597.1|  [L=425]
Description: MiaB family RNA modification protein [Fervidicoccus fontis Kam940]
Scores for complete 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-25   87.5   0.0    9.5e-25   86.5   0.0    1.6  1  UPF0004      Uncharacterized protein family UPF0004
    4.8e-20   72.6   0.1    1.3e-19   71.2   0.0    1.7  2  Radical_SAM  Radical SAM superfamily
    1.1e-06   28.5   0.6    2.2e-06   27.6   0.6    1.5  1  TRAM         TRAM domain
     0.0015   18.7   0.6      0.018   15.2   0.6    2.4  1  TRAM_2       TRAM domain


Domain annotation for each model (and alignments):
>> UPF0004  Uncharacterized protein family UPF0004
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.5   0.0   2.1e-28   9.5e-25       1      92 [.       2      92 ..       2      97 .. 0.94

  Alignments for each domain:
  == domain 1  score: 86.5 bits;  conditional E-value: 2.1e-28
                                      XEEEE--S-CCCCHHHHHHHHHTTTSSS----SSS--SEEEEEE--SSSSHHHHTHHHHHHHHTTST.--EEEEEEHHH CS
                           UPF0004  1 kvaietlGCqmNevdseelaslLkkegyelvedeeeAdvvlvnTCavrekaekkviqalrelkalkkpekkvvvlGCma 79
                                      k++i+t+GC  N++dse + ++L ++g+e++++ e+Adv++vnTC+vr+++++k+i+ ++++k+l+ +++k+vv+GC++
  gi|385806199|ref|YP_005842597.1|  2 KFFIKTFGCALNRSDSELMREILISRGFEEIDNLENADVIIVNTCTVRKDSDQKAIEYIEKVKQLN-KNSKIVVAGCIP 79
                                      789***************************************************************.79********** PP

                                      HS-HHHHHHH-TT CS
                           UPF0004 80 qrekeellkeepe 92
                                        ++  ++++ p 
  gi|385806199|ref|YP_005842597.1| 80 GSQPYLIKSRFPD 92
                                      9999888888774 PP

>> 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     130     141 ..      56      67 ..      21      98 .. 0.60
   2 !   71.2   0.0   2.8e-23   1.3e-19       5     165 ..     140     309 ..     136     311 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHTT CS
                                       xxxxxxxxxxxx RF
                       Radical_SAM 130 vlealeklreag 141
                                        +e +ek ++++
  gi|385806199|ref|YP_005842597.1|  56 AIEYIEKVKQLN 67 
                                       333333333332 PP

  == domain 2  score: 71.2 bits;  conditional E-value: 2.8e-23
                                       SEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS..........TTHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxx RF
                       Radical_SAM   5 rgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly..........pdfvellerla 71 
                                        gC  +C+fC+++     ++r  s+ +  il+ +k l +e+gv e+ l++++ ++y          pd+ve + +++
  gi|385806199|ref|YP_005842597.1| 140 DGCLSNCNFCITKV---ARRRLLSRMPKVILKAIKDL-VENGVYEIQLSSQDASVYgidfkgrpllPDLVETINQEI 212
                                       79***********9...8*******************.8999*******9999999999999988888888888888 PP

                                       HTCCCTEEEEEEECSSCHG.HHHHHHHHHTT..-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET. CS
                                       xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       Radical_SAM  72 klavpgiritvetngtlpd.eeklerllelg..vdrvslgleaaddekvlklmnrghtfeevlealeklreagikr. 144
                                       k +   +ri++  + ++    e   ++ e++  +  ++l+++++dde vlk+m+r +++e+ l ++  +r++ ik+ 
  gi|385806199|ref|YP_005842597.1| 213 KGE-YMLRIAMMNPDGVKKdLENFVKIFEYEhvFKFLHLPIQSGDDE-VLKIMGRDYSIEDALYVVNEFRSR-IKDl 286
                                       875.6666666666666446666666777778***************.************************.**** PP

                                       ..EEEEEEEBTTTSHHHHHHHHH CS
                                       ..xxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 145 ..vvdrivglpGendeeleelle 165
                                          +d+ivg+pGe++e +e++l+
  gi|385806199|ref|YP_005842597.1| 287 riATDIIVGHPGESEEAFENTLK 309
                                       ********************997 PP

>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.6   4.8e-10   2.2e-06       2      62 .]     364     425 .]     363     425 .] 0.92

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 4.8e-10
                                       XXXXXEEE.EEEEEE-.TTSEEEEEET.TEEEEETT--T...TEEEEEEEEEE-SSEEEEEEE CS
                              TRAM   2 syvGstqe.VlveglsksegegiGrtdngkvvfvpgdlpg.IGdfVeVkItkvkrqyLrGell 62 
                                       +yvG+ +e V ve+   +    i+rt+n+  ++++g+++  +G +V+++It+ +++ LrG +l
  gi|385806199|ref|YP_005842597.1| 364 KYVGKIIEgVVVEKDE-KRESYIARTKNYISIVLKGGKKVsLGMKVNIEITDYTPYDLRGIAL 425
                                       7999999878999998.999*****************8888*******************886 PP

>> TRAM_2  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.6     4e-06     0.018       1      61 [.     366     422 ..     366     424 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4e-06
                                       BTSEEEEEEEE..EETTEEEEEETTS-TTTS--EEEES---T...T-EEEEEEEEEETTEEEE CS
                            TRAM_2   1 iGktvevlvdg..eeeglyvGRsyadAPEvDgevyvtgaeklskvGdfvkvkItdadeyDLiG 61 
                                       +Gk +e +v +  e+++ y++R++         ++++g++k+ + G  v+++Itd++ yDL G
  gi|385806199|ref|YP_005842597.1| 366 VGKIIEGVVVEkdEKRESYIARTKNY-----ISIVLKGGKKV-SLGMKVNIEITDYTPYDLRG 422
                                       67777755555466666788888877.....46888887775.48****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1182  (0.0659267); expected 358.6 (0.02)
Passed bias filter:                      806  (0.0449551); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.29s 00:00:00.94 Elapsed: 00:00:00.47
# Mc/sec: 2705.48
//
Query:       gi|385806200|ref|YP_005842598.1|  [L=85]
Description: hypothetical protein FFONT_1158 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.16   11.9   0.0       0.17   11.7   0.0    1.1  1  FCP1_C    FCP1, C-terminal


Domain annotation for each model (and alignments):
>> FCP1_C  FCP1, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   9.6e-06      0.17      53      76 ..      20      43 ..      10      59 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.6e-06
                                      XXXXXXXXXXXXXXXXXXXXXX.. CS
                            FCP1_C 53 apevRiYDsvtGkLiRkgaqasrp 76
                                      ++e+ +YD +tGk++R+   + ++
  gi|385806200|ref|YP_005842598.1| 20 SAEISLYDESTGKMVRREELGKEK 43
                                      689*************98776554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 581.45
//
Query:       gi|385806201|ref|YP_005842599.1|  [L=108]
Description: hypothetical protein FFONT_1159 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.056   13.8   0.0       0.28   11.5   0.0    2.1  2  WG_beta_rep      WG containing repeat
       0.14   12.1   0.0       0.21   11.5   0.0    1.2  1  Lep_receptor_Ig  Ig-like C2-type domain


Domain annotation for each model (and alignments):
>> WG_beta_rep  WG containing repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.23   2.1e+03       9      22 ..       9      22 ..       7      28 .. 0.69
   2 ?   11.5   0.0   3.1e-05      0.28       3      20 ..      55      72 ..      55      81 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.23
                       WG_beta_rep  9 kivippkYddagsF 22
                                      k+ i+ kY + + F
  gi|385806201|ref|YP_005842599.1|  9 KEKITTKYRKGEAF 22
                                      56677777766655 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 3.1e-05
                       WG_beta_rep  3 yiDknGkivippkYddag 20
                                      +i++nG +v+++ Y +++
  gi|385806201|ref|YP_005842599.1| 55 VINNNGDVVLECVYRKMK 72
                                      69************9875 PP

>> Lep_receptor_Ig  Ig-like C2-type domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   2.4e-05      0.21       3      56 ..      46     103 ..      44     106 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.4e-05
                   Lep_receptor_Ig   3 cgvisvespvvslGsnvtasCilkenC.shlsveakiivWklkn...e.lvpgeqytvl 56 
                                       +g+is   +v++ +  v   C++++   +    ++++i W +k+   + +vp ++y+v 
  gi|385806201|ref|YP_005842599.1|  46 KGHISGRIKVINNNGDVVLECVYRKMKvRRVRGSSHLI-WAVKKlleKlKVPVKRYNVK 103
                                       79***********************7745555555555.*8774222467888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); 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:                         2  (0.000111551); expected 0.2 (1e-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: 758.81
//
Query:       gi|385806202|ref|YP_005842600.1|  [L=119]
Description: putative transcriptional regulator consisting of an HTH domain fused to a Zn-ribbon [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0012   18.9   1.8     0.0021   18.1   1.8    1.3  1  Zn-ribbon_8      Zinc ribbon domain
     0.0018   18.1   1.5     0.0028   17.5   1.5    1.3  1  Zn_ribbon_SprT   SprT-like zinc ribbon domain
     0.0024   17.9   1.1     0.0042   17.1   1.0    1.3  1  HypA             Hydrogenase/urease nickel incorporation, met
  ------ inclusion threshold ------
      0.025   14.5   0.5      0.041   13.8   0.5    1.4  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.034   14.0   0.2      0.047   13.5   0.2    1.2  1  MCM_OB           MCM OB domain
       0.11   12.6   0.1       0.17   12.0   0.1    1.3  1  Ribosomal_L37ae  Ribosomal L37ae protein family
       0.15   11.8   0.0       0.17   11.6   0.0    1.0  1  HGD-D            2-hydroxyglutaryl-CoA dehydratase, D-compone
       0.16   11.9   1.5        7.4    6.5   0.0    2.2  2  TFIIS_C          Transcription factor S-II (TFIIS)
       0.33   10.7   2.1       0.63    9.8   2.1    1.4  1  DUF3039          Protein of unknown function (DUF3039)
       0.93    9.3   3.8        9.1    6.1   0.2    2.2  2  Rubredoxin_2     Rubredoxin metal binding domain


Domain annotation for each model (and alignments):
>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   1.8   1.2e-06    0.0021       7      35 ..      71      98 ..      71     100 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.2e-06
                       Zn-ribbon_8  7 rCeeCghefevlqsisdapltaCPeCgs.e 35
                                      rC +Cg +f   +++++  + +CP+C+s +
  gi|385806202|ref|YP_005842600.1| 71 RCLNCGYTFKDNRKAKR--PSKCPKCKSfR 98
                                      8*********9998774..446****9866 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 !   17.5   1.5   1.6e-06    0.0028       5      33 ..      70      98 ..      69     103 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.6e-06
                    Zn_ribbon_SprT  5 YrCtgCgreythhlsi.rrhnYrCrrCk.gt 33
                                      +rC +Cg +++ +++  r+ +  C++Ck  +
  gi|385806202|ref|YP_005842600.1| 70 ARCLNCGYTFKDNRKAkRP-S-KCPKCKsFR 98
                                      79**************555.5.5*****555 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   1.0   2.3e-06    0.0042      71      98 ..      70     100 ..      64     109 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.3e-06
                                       EEETTTS-EEECHH..H.HHS-TTTSSS-EE CS
                              HypA  71 vrCreCgkefelee..k.alrCpkCgsadve 98 
                                       +rC +Cg++f+ ++  k   +CpkC+s ++e
  gi|385806202|ref|YP_005842600.1|  70 ARCLNCGYTFKDNRkaKrPSKCPKCKSFRIE 100
                                       79*********6663324559*****98764 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 ?   13.8   0.5   2.3e-05     0.041      30      53 ..      71      95 ..      51      98 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.3e-05
                    OrfB_Zn_ribbon 30 tCseCgsknke.alsgrtfkCpnCg 53
                                      +C +Cg++ k+ ++++r  kCp+C+
  gi|385806202|ref|YP_005842600.1| 71 RCLNCGYTFKDnRKAKRPSKCPKCK 95
                                      7**********99***********7 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   2.6e-05     0.047      23      73 ..      58     111 ..      53     116 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.6e-05
                                       E---EEEEEEEEEEETTT-.-EE.E.S----SB-..TTT-...HHH-EEE-GGGSE CS
                            MCM_OB  23 asevkpklkkavfeckkcgktve.v.eleePrkCeekeCe...skdpfkleteksk 73 
                                       +s+ k+++  +  +c +cg+t +   + ++P+kC  ++C+    ++p+   te+s+
  gi|385806202|ref|YP_005842600.1|  58 RSNGKERIAILPARCLNCGYTFKdNrKAKRPSKC--PKCKsfrIEGPWFYITESSS 111
                                       5677788888999*******9885347889****..99*94443457777666654 PP

>> Ribosomal_L37ae  Ribosomal L37ae protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   9.3e-05      0.17      35      79 ..      71     116 ..      55     118 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.3e-05
                                       EESSSSSS.EEEEEETTEEEETTTTEEEE-BSSSSS-HHHHHHHH- CS
                   Ribosomal_L37ae  35 tCpfcgkt.kvkRkavgiwkCkkcgktvaGgAytpettsaktvksa 79 
                                       +C +cg t k +Rka    kC kc+     g + + t+s  ++k +
  gi|385806202|ref|YP_005842600.1|  71 RCLNCGYTfKDNRKAKRPSKCPKCKSFRIEGPWFYITESSSSMKGS 116
                                       69*****999****************************99998866 PP

>> HGD-D  2-hydroxyglutaryl-CoA dehydratase, D-component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   9.7e-05      0.17     131     187 ..      11      68 ..       9      89 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.7e-05
                                       HHHHHHHTTSSS-SS-HHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHT..STS-EEE CS
                             HGD-D 131 lkelytllpqspapihgfdllllakvvflgkeeatealeelleeleersk.seriRll 187
                                       ++++y +l++sp p++++d+++++  ++ +k++  e +e+l+ +l+ rs  +eri +l
  gi|385806202|ref|YP_005842600.1|  11 REKIYLILKNSPIPLTVEDIINMLGYSVREKRKVEEDIEHLALSLKSRSNgKERIAIL 68 
                                       67899999****************99999*************9999963224666555 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0    0.0042       7.4      29      39 .]      70      80 ..      66      80 .. 0.87
   2 ?    4.4   0.4     0.019        33       2       8 ..      90      96 ..      89      99 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0042
                           TFIIS_C 29 ykCtkCghrWr 39
                                       +C++Cg++++
  gi|385806202|ref|YP_005842600.1| 70 ARCLNCGYTFK 80
                                      58******997 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.019
                           TFIIS_C  2 kCpkCgs 8 
                                      kCpkC+s
  gi|385806202|ref|YP_005842600.1| 90 KCPKCKS 96
                                      8****97 PP

>> DUF3039  Protein of unknown function (DUF3039)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   2.1   0.00035      0.63      30      51 ..      75      96 ..      68      98 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00035
                           DUF3039 30 CGkvwvptrdpkkfPvCpeCke 51
                                      CG ++  +r++k+   Cp+Ck 
  gi|385806202|ref|YP_005842600.1| 75 CGYTFKDNRKAKRPSKCPKCKS 96
                                      ********************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 ?    6.1   0.2    0.0051       9.1       2      10 ..      71      79 ..      71      82 .. 0.86
   2 ?    4.2   0.5     0.021        37      16      23 ..      90      97 ..      90      97 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0051
                      Rubredoxin_2  2 vCsqCGfes 10
                                      +C +CG+++
  gi|385806202|ref|YP_005842600.1| 71 RCLNCGYTF 79
                                      7******97 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.021
                      Rubredoxin_2 16 rCpsCgsW 23
                                      +Cp C+s+
  gi|385806202|ref|YP_005842600.1| 90 KCPKCKSF 97
                                      7****985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      604  (0.0336884); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); 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 0.31s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 705.80
//
Query:       gi|385806203|ref|YP_005842601.1|  [L=398]
Description: nicotinate phosphoribosyltransferase [Fervidicoccus fontis Kam940]
Scores for complete 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-28   98.0   0.0      7e-28   97.5   0.0    1.2  1  QRPTase_C   Quinolinate phosphoribosyl transferase, C-termina
    5.8e-05   23.5   0.0    0.00012   22.5   0.0    1.5  1  NAPRTase_C  Nicotinate phosphoribosyltransferase C-terminal d
    8.6e-05   22.5   0.0    0.00015   21.7   0.0    1.4  1  QRPTase_N   Quinolinate phosphoribosyl transferase, N-termina
     0.0052   17.2   0.0        3.5    8.0   0.0    2.3  2  NAPRTase_N  Nicotinate phosphoribosyltransferase (NAPRTase) N


Domain annotation for each model (and alignments):
>> QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.5   0.0   1.6e-31     7e-28       1     169 []     120     308 ..     120     308 .. 0.94

  Alignments for each domain:
  == domain 1  score: 97.5 bits;  conditional E-value: 1.6e-31
                                       HHHHHHHHHHHHHCTSSEEEE-S---TTTHHHHHHHHHHTTSB.......--TSSTTTSEEE-HHHHHHHSSHHHHH CS
                         QRPTase_C   1 iAtltarmveaaksakvrildTRkttPglrllekyAvliGGgd.......nhrlgLsdmvlikdnhiaaagsiveav 70 
                                       iAt+tar++ aa +++v +++ R  +P+l++l+ +A+liGG+d       +++lg++   ++++  ++++g++ +a+
  gi|385806203|ref|YP_005842601.1| 120 IATKTARIKYAAGNKQVLFFGLRSLHPALAPLADRAALIGGADsvsgvlsKKYLGVEPSGTMPHSLMIIVGDQAKAW 196
                                       9**************************************************************************** PP

                                       HHHHHHHTTTSE..EEEEESSHHHHHHHHHHT.....-SEEEEES--H..HHHHHHHHHH.HHHSTT....SEEEEE CS
                         QRPTase_C  71 ksvreavdkevk..ievevesleeleevleae.....adiimLDnfsv..eelkkaveel.keknkr....vlievS 133
                                       k ++e++d+ v+  i v++  +e +e  l+++       +++LD++s+   +++k++ee+ ++ + +    v+i +S
  gi|385806203|ref|YP_005842601.1| 197 KLFDENIDESVPriILVDTFWDERIETELAMKtlgkkLYGVRLDTPSSrrGNFRKIIEEVrWALDLNgfknVKIIAS 273
                                       **********999*******99999887775444555899******997799*******988888878899****** PP

                                       SS--TTTHHHHHCTT-SEEEECHHCHTB----EEEE CS
                         QRPTase_C 134 GgvtlenveeyaksgvdvisvgalthsvkalDislk 169
                                       Gg+++e+++e+++++ d+++vg+ +   +++Dis++
  gi|385806203|ref|YP_005842601.1| 274 GGLNEEDINELKDIV-DAFGVGTSIAFPPSVDISMD 308
                                       ************998.******************97 PP

>> NAPRTase_C  Nicotinate phosphoribosyltransferase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   2.7e-08   0.00012      53      87 ..     360     394 ..     346     397 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 2.7e-08
                        NAPRTase_C  53 ekLlkkvfkdGklvyelpsleeireyvkeqlaelr 87 
                                       + Llkk++++Gkl+++lp+l+eir+ v +ql+el 
  gi|385806203|ref|YP_005842601.1| 360 KLLLKKYIENGKLIEPLPDLKEIRKLVLSQLNELA 394
                                       679*****************************986 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 !   21.7   0.0   3.4e-08   0.00015      22      88 ..      53     117 ..      35     118 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 3.4e-08
                                       EEESSSEEE-SHHHHHHHHHHHTTTEEEESS-TT-EEETTEEEEEEEEEHHHHHHHHHHHHHHHHHH CS
                         QRPTase_N  22 iiakeegvvaGlevaeevfellpglevellvkDGervekgdvlleieGnarallsaERvaLnllqrl 88 
                                        +  +++++aGle+a +v+e   ++ v +l ++G  +++ + ++ ieG++ ++  +E ++L +l ++
  gi|385806203|ref|YP_005842601.1|  53 PKDYSWAIFAGLEEALNVLENH-KVDVYAL-PEGILFREREPVMLIEGEYYDFALYESIILGILRHY 117
                                       5567899*************99.7777665.*********************************996 PP

>> NAPRTase_N  Nicotinate phosphoribosyltransferase (NAPRTase) N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0     0.001       4.6       3      55 ..      22      75 ..      21      78 .. 0.90
   2 !    8.0   0.0   0.00077       3.5      88     124 ..      78     114 ..      73     115 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.001
                        NAPRTase_N  3 tDlYkltmaqavfkkgp.dvevvfelffRkkpfkgeyaivagleevieylenlr 55
                                      tD+Y     +++ + g  d++v+ e+     p++++ ai+aglee+++ len +
  gi|385806203|ref|YP_005842601.1| 22 TDVYFTRVEKILESAGLkDKKVRAEFHTYGLPKDYSWAIFAGLEEALNVLENHK 75
                                      7888888888888888889*******************************9976 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00077
                        NAPRTase_N  88 evaveeeev.vfpgepeirveGpwieaillEtplLaiv 124
                                       ++a++e+ + + ++ep + +eG  ++  l+E  +L i+
  gi|385806203|ref|YP_005842601.1|  78 VYALPEG-IlFREREPVMLIEGEYYDFALYESIILGIL 114
                                       4455555.549999********************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); 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: 0.58u 0.36s 00:00:00.94 Elapsed: 00:00:00.54
# Mc/sec: 2230.35
//
Query:       gi|385806204|ref|YP_005842602.1|  [L=198]
Description: hypothetical protein FFONT_1162 [Fervidicoccus fontis Kam940]
Scores for complete 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   38.0   3.9    1.2e-09   38.0   3.9    2.7  3  HTH_45          Winged helix-turn-helix
     0.0073   16.1   0.2     0.0073   16.1   0.2    1.7  2  DUF4364         Domain of unknown function (DUF4364)
  ------ inclusion threshold ------
      0.012   15.0   0.4      0.022   14.1   0.4    1.4  1  RNA_pol_Rpc34   RNA polymerase Rpc34 subunit
      0.029   14.3   1.9      0.073   13.0   0.7    2.1  2  TBPIP           TBPIP/Hop2 winged helix domain
      0.053   13.3   0.0       0.14   11.9   0.0    1.8  1  MutL_C          MutL C terminal dimerisation domain
      0.066   13.4   0.6       0.15   12.2   0.3    1.8  2  B-block_TFIIIC  B-block binding subunit of TFIIIC
      0.099   13.0   2.6       0.56   10.5   0.0    2.5  3  DUF5603         Domain of unknown function (DUF5603)
        0.1   11.7   0.1       0.14   11.3   0.1    1.3  1  FBPase_3        Fructose-1,6-bisphosphatase
       0.11   12.6   1.7         18    5.4   1.0    2.7  3  HydF_dimer      Hydrogen maturase F dimerization domain


Domain annotation for each model (and alignments):
>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   3.9   6.2e-13   1.2e-09      20      73 ..      12      69 ..       2      73 .. 0.85
   2 ?    1.7   0.0      0.13   2.5e+02      28      45 ..      60      77 ..      58      91 .. 0.82
   3 ?   -1.1   0.1      0.97   1.9e+03      36      46 ..     142     152 ..     133     164 .. 0.62

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 6.2e-13
                            HTH_45 20 akkTkimykanLsykllnkYLdmLvekgli....kkskekYvlTekGlelleklkele 73
                                       kkT++myk nL+ k+l+kYLd+L+ +gli    k +++  ++T kG+  + +lk + 
  gi|385806204|ref|YP_005842602.1| 12 IKKTHLMYKTNLNSKMLQKYLDILQRNGLIieesKGKQKIIKMTPKGKSAYFSLKMFS 69
                                      69***************************99775446777889****99888887765 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.13
                            HTH_45 28 kanLsykllnkYLdmLve 45
                                      +a+ s k++++YL++ + 
  gi|385806204|ref|YP_005842602.1| 60 SAYFSLKMFSSYLNIVQT 77
                                      688999*******98765 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.97
                            HTH_45  36 lnkYLdmLvek 46 
                                       l +Y+ m+++ 
  gi|385806204|ref|YP_005842602.1| 142 LMQYIIMMLDT 152
                                       34566666554 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.2   3.6e-06    0.0073      35      70 ..      27      62 ..      15     100 .. 0.84
   2 ?   -2.4   0.1       1.7   3.4e+03      76      77 ..     164     165 ..     138     194 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.6e-06
                           DUF4364 35 dlqqalseLvesglieeeekenktlykiTekGketl 70
                                       lq++l+ L  +gli ee+k +++++k+T+kGk + 
  gi|385806204|ref|YP_005842602.1| 27 MLQKYLDILQRNGLIIEESKGKQKIIKMTPKGKSAY 62
                                      69*******************************973 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.7
                           DUF4364  76 ri 77 
                                       +i
  gi|385806204|ref|YP_005842602.1| 164 SI 165
                                       22 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 ?   14.1   0.4   1.1e-05     0.022      93     132 ..       2      41 ..       1      50 [. 0.93

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.1e-05
                                       HHHHHHXSSXEEHHHHHHTTGXXHHHHHHHHHHHHHTTXX CS
                     RNA_pol_Rpc34  93 siIeesGneGIwsrtiksklnLhksvvkkcLksLeskkyi 132
                                       ++I + G  GI +  + +k+nL+ ++++k L +L   ++i
  gi|385806204|ref|YP_005842602.1|   2 NVISSGGDFGIKKTHLMYKTNLNSKMLQKYLDILQRNGLI 41 
                                       6899******************************999988 PP

>> TBPIP  TBPIP/Hop2 winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.7   3.7e-05     0.073      29      58 ..      22      51 ..      15      54 .. 0.89
   2 ?   -1.0   0.0      0.85   1.7e+03       8      28 ..      70      90 ..      65      97 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.7e-05
                             TBPIP 29 klgKtavqkaLdeLvdegkiieKeyGKqki 58
                                      +l  +  qk Ld L+ +g+iie   GKqki
  gi|385806204|ref|YP_005842602.1| 22 NLNSKMLQKYLDILQRNGLIIEESKGKQKI 51
                                      6677789**********************9 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.85
                             TBPIP  8 eylqeqnrPfsvqdvvanlqk 28
                                       yl+    P+ + ++++ l++
  gi|385806204|ref|YP_005842602.1| 70 SYLNIVQTPQEIVEIYERLRG 90
                                      688888889999999998865 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 ?   11.9   0.0   6.9e-05      0.14      66     110 ..      25      69 ..      18     105 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.9e-05
                                       HHHHHHCHHHHHHCT-EEEE-STTEEEEEEEECCCTTTSHHHHHH CS
                            MutL_C  66 aalleehkeeLaklGfeleefgpnslivravPallrqqnleelir 110
                                        ++l+++ ++L+++G+ +ee ++++ i++++P  ++  +  +++ 
  gi|385806204|ref|YP_005842602.1|  25 SKMLQKYLDILQRNGLIIEESKGKQKIIKMTPKGKSAYFSLKMFS 69 
                                       6789****************9999999999998777766655555 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.3   7.5e-05      0.15      10      53 ..       3      46 ..       1      72 [. 0.88
   2 ?   -2.0   0.0         2     4e+03      19      34 ..     110     125 ..     106     147 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.5e-05
                    B-block_TFIIIC 10 lIassRysGitqsdLakeskqdprslfyrlksLekkgLIvkqsi 53
                                      +I+s ++ Gi  + L   ++  +++l + l+ L+++gLI   s 
  gi|385806204|ref|YP_005842602.1|  3 VISSGGDFGIKKTHLMYKTNLNSKMLQKYLDILQRNGLIIEESK 46
                                      6999***********************************97765 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2
                    B-block_TFIIIC  19 itqsdLakeskqdprs 34 
                                       i    L+ ++k + r 
  gi|385806204|ref|YP_005842602.1| 110 IEYAALVVITKEKDRY 125
                                       4444444444444444 PP

>> DUF5603  Domain of unknown function (DUF5603)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00028      0.56      10      45 ..      28      63 ..      20      81 .. 0.88
   2 ?    1.8   0.3      0.15     3e+02      45      82 ..     103     143 ..      74     160 .. 0.54
   3 ?   -1.8   0.0       1.9   3.8e+03      65      83 ..     164     181 ..     141     194 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00028
                                      HHHHHHHHHHTT---EE-TTHHHH...HHCTSSSEE CS
                           DUF5603 10 lnklleelkkeglrveedkekeeklkdeelgkiafv 45
                                      l+k l+ l+++gl +ee+k+k++ +k   +gk a+ 
  gi|385806204|ref|YP_005842602.1| 28 LQKYLDILQRNGLIIEESKGKQKIIKMTPKGKSAYF 63
                                      6788999*************************9985 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.15
                                       EEES..SSEEEE--SHHHHH...HHHHHHHHHHHTTSSEEE CS
                           DUF5603  45 vlvgkneksykiygsleeqk...kvskvldklslegkielv 82 
                                       +l+gk+   y+    + ++k   +v +vl+k +l+  ++l+
  gi|385806204|ref|YP_005842602.1| 103 MLLGKSGIEYAALVVITKEKdryVVGHVLSKNKLDMVVDLM 143
                                       44444444444333333222111345555555555444444 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.9
                                       HHHHHHHHHHHTTSSEEEE CS
                           DUF5603  65 kvskvldklslegkielvy 83 
                                        +sk++ + +le +i+++ 
  gi|385806204|ref|YP_005842602.1| 164 SISKIIPE-KLENDIKIIP 181
                                       45555544.3455555554 PP

>> FBPase_3  Fructose-1,6-bisphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1     7e-05      0.14     116     212 ..      42     139 ..      23     149 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7e-05
                          FBPase_3 116 feeRksepvvvfaaDktepgafnlplykifadpfntaGlvid.pklheGfkfevlDvieekkillsapeelydllal 191
                                       +ee k +  ++ ++ k +++ f+l+++  + + ++t+  +++  +  +G k e +++  ++++l ++  e   l+++
  gi|385806204|ref|YP_005842602.1|  42 IEESKGKQKIIKMTPKGKSAYFSLKMFSSYLNIVQTPQEIVEiYERLRGLKGENVNISYNSMLLGKSGIEYAALVVI 118
                                       677777888999999*********************987776245679*************999999999999**** PP

                          FBPase_3 192 lgakeryvikrvyskkdeeia 212
                                        ++k+ryv+ +v sk++ +++
  gi|385806204|ref|YP_005842602.1| 119 TKEKDRYVVGHVLSKNKLDMV 139
                                       **************9776655 PP

>> HydF_dimer  Hydrogen maturase F dimerization domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.015        31      49      84 ..      24      58 ..      16      71 .. 0.83
   2 ?   -1.0   0.0      0.91   1.8e+03      63      94 ..      71     105 ..      57     108 .. 0.62
   3 ?    5.4   1.0    0.0093        18      34      87 ..     126     179 ..     114     182 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.015
                        HydF_dimer 49 keseleaalkslkrkpklvitDsqvvkkvaeivpkd 84
                                      +++ l+++l+ l+ +  l+i +s+  +k+ +++pk 
  gi|385806204|ref|YP_005842602.1| 24 NSKMLQKYLDILQ-RNGLIIEESKGKQKIIKMTPKG 58
                                      5677899999999.789****************985 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.91
                        HydF_dimer  63 kpklvitDs...qvvkkvaeivpkdvklttfsilf 94 
                                         ++v t     +++++++   +++v++   s+l+
  gi|385806204|ref|YP_005842602.1|  71 YLNIVQTPQeivEIYERLRGLKGENVNISYNSMLL 105
                                       44444444300045677777888888888888777 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.0093
                        HydF_dimer  34 viRdilDekaiavvvkeseleaalkslkrkpklvitDsqvvkkvaeivpkdvkl 87 
                                       v+ ++l ++ + +vv   ++  ++  ++ k+ l+++D  + k + e++ +d+k+
  gi|385806204|ref|YP_005842602.1| 126 VVGHVLSKNKLDMVVDLMQYIIMMLDTNSKIILIVSDESISKIIPEKLENDIKI 179
                                       566778888888888888877777777788999999999999888888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       857  (0.0477997); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 1132.81
//
Query:       gi|385806205|ref|YP_005842603.1|  [L=96]
Description: hypothetical protein FFONT_1163 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score 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   14.0   0.1      0.059   13.5   0.0    1.3  1  KaiA      KaiA C-terminal domain


Domain annotation for each model (and alignments):
>> KaiA  KaiA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.3e-06     0.059      50      85 ..      20      55 ..       2      71 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.3e-06
                                      SHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHH CS
                              KaiA 50 evnqkidefvnkaffadlsvskileihmelldefsk 85
                                       ++++  +++++a+f+d  vski+ei  +l +e ++
  gi|385806205|ref|YP_005842603.1| 20 MIDENPSNWIKAAYFSDSEVSKIMEILYKLWEENNE 55
                                      4666677899*******************9998654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1209  (0.0674327); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 586.98
//
Query:       gi|385806206|ref|YP_005842604.1|  [L=282]
Description: stomatin [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      5e-35  121.1   1.0    6.3e-35  120.8   1.0    1.1  1  Band_7    SPFH domain / Band 7 family
     0.0011   18.7   0.3     0.0021   17.8   0.1    1.5  2  Band_7_1  SPFH domain-Band 7 family
  ------ inclusion threshold ------
       0.15   12.0   0.4       0.26   11.2   0.4    1.3  1  ProSAAS   ProSAAS precursor


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 !  120.8   1.0   1.1e-38   6.3e-35       2     178 .]      30     200 ..      29     200 .. 0.99

  Alignments for each domain:
  == domain 1  score: 120.8 bits;  conditional E-value: 1.1e-38
                            Band_7   2 iieegevgvvvrfGklsrvlepGlhfilPfgrsvtvvsvrvqtldvsvsltvptkDglpvtidvtviyrvpddapkl 78 
                                       +++e e++vv+r G+l + ++pGl fi+Pf++++ +v++r++ +dv+  +  +t+D+++v++d++++y+v  d+ k+
  gi|385806206|ref|YP_005842604.1|  30 VVREYERAVVFRLGRLLGAKGPGLFFIIPFVDRLLKVDLRIVAVDVPE-QRSVTRDNVSVGVDAVIYYKV-LDPVKA 104
                                       799*********************************************.*********************.****** PP

                            Band_7  79 vaaveresanldnlirrvlesalrevisemtleellsnreelaeelknelneqlrkyGvevldvritdidpppevaq 155
                                       + av    +n+   +  +++ +lr vi++ +l++lls+reel+++++  l    + +G+ v+ v+++++++p++  +
  gi|385806206|ref|YP_005842604.1| 105 IMAV----ENYSYAVLMLAQTTLRDVIGQVELDDLLSKREELNKRIQGILDVLTDPWGIKVTAVTLKEVKLPDTMLR 177
                                       ****....********************************************************************* PP

                            Band_7 156 alaakqaaeaeaqaeiaraeaea 178
                                       ala+ ++ae+ ++a+i +ae+e+
  gi|385806206|ref|YP_005842604.1| 178 ALAKQAEAERFRRARIIEAEGER 200
                                       *********999********995 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 ?   -3.1   0.0      0.87   5.2e+03      18      41 ..      30      53 ..      27      56 .. 0.81
   2 !   17.8   0.1   3.6e-07    0.0021     145     209 ..     123     185 ..     104     187 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.87
                          Band_7_1 18 ivregqeavfvneGqiaDvfapGt 41
                                      +vre  +av  + G++    +pG 
  gi|385806206|ref|YP_005842604.1| 30 VVREYERAVVFRLGRLLGAKGPGL 53
                                      899999999999999987777776 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 3.6e-07
                          Band_7_1 145 lsdvlaeskipvldlaakseelaeklkealkeelaeyGlelekleienislpeevekaldkrasm 209
                                       l dv++  ++ + dl +k eel ++++  l+   +  G+++++++++++ lp+ + +al k+a++
  gi|385806206|ref|YP_005842604.1| 123 LRDVIG--QVELDDLLSKREELNKRIQGILDVLTDPWGIKVTAVTLKEVKLPDTMLRALAKQAEA 185
                                       555555..466789***********************************************9976 PP

>> ProSAAS  ProSAAS precursor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.4   4.4e-05      0.26      75     108 ..     175     208 ..     165     220 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.4e-05
                           ProSAAS  75 laralahlleaerqeraraeaqeaedqqarvlaq 108
                                       + rala+  eaer  rar    e e q a ++++
  gi|385806206|ref|YP_005842604.1| 175 MLRALAKQAEAERFRRARIIEAEGERQSASIMSE 208
                                       67*****************999*******99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       981  (0.0547158); expected 358.6 (0.02)
Passed bias filter:                      599  (0.0334096); 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: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 1801.98
//
Query:       gi|385806207|ref|YP_005842605.1|  [L=446]
Description: membrane-bound serine peptidase Nfed [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-14   54.1   3.0    2.9e-13   50.0   0.5    2.7  2  NfeD          NfeD-like C-terminal, partner-binding
     0.0001   22.3   0.3    0.00016   21.6   0.3    1.4  1  CLP_protease  Clp protease
    0.00072   18.6   1.3    0.00072   18.6   1.3    1.7  2  SDH_sah       Serine dehydrogenase proteinase


Domain annotation for each model (and alignments):
>> NfeD  NfeD-like C-terminal, partner-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1     0.017     1e+02       3      42 ..      10      43 ..       7      57 .. 0.56
   2 !   50.0   0.5   4.9e-17   2.9e-13       2      84 .]     360     442 ..     359     442 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.017
                                      XXXXXXXXXXXXXXS---SSS--S.S---GGTTSEEEEEE CS
                              NfeD  3 avvsvlllvllrplllkklkkkekktnaealiGkegvvle 42
                                      ++v +lll+ll+     k+ +     +++++iG +++v++
  gi|385806207|ref|YP_005842605.1| 10 FIVVFLLLFLLF--SESKI-S---YAQSNNVIGNRVIVIT 43
                                      333333333333..22222.1...1333479999999988 PP

  == domain 2  score: 50.0 bits;  conditional E-value: 4.9e-17
                                       XXXXXXXXXXXXXXXS---SSS--S.S---.GGTTSEEEEEE-B..S.-EEEEETTEEEEEE-.SS.B-TT-EEEEE CS
                              NfeD   2 favvsvlllvllrplllkklkkkekktnae.aliGkegvvledi..g.tGrvkvdGeeWsarsege.iekgerVrVv 73 
                                        +v+++++ +++++++  +++k       + +l G+ g+++++i  + +G v +dGe+W+a+se+e i++g++V Vv
  gi|385806207|ref|YP_005842605.1| 360 GVVLGAITAFIIYKIIAVRRRK----P-FSwKLEGALGKAVDPIspDnEGFVVIDGEYWKAKSESEsISPGDEVIVV 431
                                       6788899999999886665634....2.234799**********98458**************9888********** PP

                                       EE-SSSEEEEE CS
                              NfeD  74 eveGltliVep 84 
                                       + eG  liV++
  gi|385806207|ref|YP_005842605.1| 432 KKEGPILIVRK 442
                                       *********98 PP

>> CLP_protease  Clp protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.3   2.7e-08   0.00016      12     109 ..      33     129 ..      22     201 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.7e-08
                                       HHHTTTEEEE..ES-BSHHHHHHHHHHHHHHHHH-SSS-EEEEEEE--B-HHHHHHHH.HHHHHSSS-EEEEEEEEE CS
                      CLP_protease  12 rllkeriifl..gseiddevankiiaqLllLeaedpdkdillyinspGGsvtaglaIy.dtmqyikpdvsticlGla 85 
                                       +++ +r+i++  ++ id++v + + + + ++e  +++  +++y+n+pGG +++++ I+ d+ +   p +  ++  +a
  gi|385806207|ref|YP_005842605.1|  33 NVIGNRVIVItvSGVIDSAVEEYVSNAIAVAE--KEHAILVIYLNTPGGLLDSAMNIAiDIDKSTIPVIGFVVDKWA 107
                                       45555555441145567777777777777775..555569*****************835555556666777779** PP

                                       ETHHHHHHHTS-TTGEEEETTEEE CS
                      CLP_protease  86 aSmgslllaagekgkRfalpnari 109
                                        S+g+l++++ +    ++ p + i
  gi|385806207|ref|YP_005842605.1| 108 ESAGTLIFVCTHIA--AMQPGTII 129
                                       ********998776..45555555 PP

>> SDH_sah  Serine dehydrogenase proteinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1      0.29   1.8e+03      11      28 ..       9      26 ..       4      41 .. 0.54
   2 !   18.6   1.3   1.2e-07   0.00072      72     157 ..      47     134 ..      26     153 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.29
                           SDH_sah 11 ssllwfllflylllapql 28
                                      + ++ fll+++l+   ++
  gi|385806207|ref|YP_005842605.1|  9 FFIVVFLLLFLLFSESKI 26
                                      333444444444444444 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 1.2e-07
                           SDH_sah  72 fitiedseevlrairltpkdkpidli.ihtpGGlvlaatqiakalkehkakt.rvivphyamsGGtlialaadeiil 146
                                        i+    e v  ai ++ k++ i +i + tpGGl  +a +ia  + +   ++   +v ++a s Gtli + +    +
  gi|385806207|ref|YP_005842605.1|  47 VIDSAVEEYVSNAIAVAEKEHAILVIyLNTPGGLLDSAMNIAIDIDKSTIPViGFVVDKWAESAGTLIFVCTHIAAM 123
                                       556666788999*********99877468****************9998886257899**************999** PP

                           SDH_sah 147 denavlGpvdp 157
                                       ++ +++G ++p
  gi|385806207|ref|YP_005842605.1| 124 QPGTIIGSMQP 134
                                       *****999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       932  (0.0519828); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 3059.85
//
Query:       gi|385806208|ref|YP_005842606.1|  [L=729]
Description: AAA ATPase [Fervidicoccus fontis Kam940]
Scores for complete 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-100  331.5   0.0    2.9e-50  170.1   0.0    2.5  2  AAA              ATPase family associated with various cellul
    4.2e-34  116.1   1.2    1.5e-16   59.9   0.1    2.7  2  AAA_lid_3        AAA+ lid domain
    1.4e-28   98.9   0.1    5.9e-28   96.9   0.5    1.9  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
    1.1e-16   61.0   0.0    1.7e-08   34.3   0.0    2.9  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    1.1e-15   58.4   0.1    4.4e-07   30.5   0.0    3.6  3  AAA_16           AAA ATPase domain
    4.7e-15   56.1   0.0    6.3e-08   32.9   0.0    2.5  2  AAA_2            AAA domain (Cdc48 subfamily)
    6.7e-13   48.8   0.8    5.3e-06   26.5   0.1    4.0  2  AAA_5            AAA domain (dynein-related subfamily)
      2e-12   47.0   0.0    8.6e-05   21.9   0.0    2.9  2  TIP49            TIP49 P-loop domain
      1e-11   45.3   1.4     0.0019   18.5   0.2    4.3  3  AAA_22           AAA domain
    2.2e-11   44.1   0.0    5.8e-05   23.3   0.0    2.6  2  AAA_33           AAA domain
    4.3e-10   39.7   0.0    0.00029   20.9   0.0    2.7  2  AAA_14           AAA domain
    4.5e-10   39.2   0.7    4.5e-10   39.2   0.7    2.1  2  CDC48_2          Cell division protein 48 (CDC48), domain 2
    1.9e-08   34.2   0.0     0.0093   15.7   0.0    2.6  2  IstB_IS21        IstB-like ATP binding protein
    3.5e-08   33.9   0.0     0.0033   17.7   0.0    2.6  2  AAA_28           AAA domain
    5.5e-08   32.4   0.4     0.0087   15.5   0.0    2.5  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    6.4e-08   33.2   0.0      0.006   17.1   0.0    2.6  2  AAA_18           AAA domain
      2e-07   30.8   2.7       0.14   11.7   0.3    4.2  3  AAA_25           AAA domain
    2.1e-07   31.3   0.0     0.0049   17.3   0.0    2.6  2  RNA_helicase     RNA helicase
    1.6e-06   28.0   0.5     0.0042   17.0   0.0    3.0  2  Vps4_C           Vps4 C terminal oligomerisation domain
    2.5e-06   27.3   0.0       0.14   11.8   0.0    3.4  2  Sigma54_activat  Sigma-54 interaction domain
      3e-06   27.1   0.0      0.049   13.4   0.0    2.7  2  AAA_24           AAA domain
    3.9e-06   26.9   0.5       0.31   11.0   0.0    4.0  3  NACHT            NACHT domain
    4.5e-06   26.5   0.0       0.19   11.4   0.0    3.4  3  AAA_30           AAA domain
    5.6e-06   26.0   0.0      0.093   12.2   0.0    2.7  2  AAA_7            P-loop containing dynein motor region
    6.5e-06   25.5   0.0      0.094   11.9   0.0    2.5  2  DUF815           Protein of unknown function (DUF815)
    6.7e-06   26.1   0.0     0.0021   17.9   0.0    2.7  2  Bac_DnaA         Bacterial dnaA  protein
    7.8e-06   25.4   1.5       0.38   10.1   0.0    3.6  3  ATPase           KaiC
    9.2e-06   26.2   0.0       0.24   11.9   0.0    2.5  2  ABC_tran         ABC transporter
    9.5e-06   25.6   0.0      0.092   12.8   0.0    2.6  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    1.2e-05   25.1   0.0      0.089   12.7   0.0    2.5  2  AAA_3            ATPase family associated with various cellul
    1.7e-05   24.1   0.1      0.042   12.9   0.0    2.2  2  Parvo_NS1        Parvovirus non-structural protein NS1
    2.2e-05   24.0   0.0       0.28   10.6   0.0    2.7  2  PhoH             PhoH-like protein
    4.5e-05   22.8   0.0       0.23   10.7   0.0    2.7  2  Zeta_toxin       Zeta toxin
    0.00012   22.2   0.0       0.23   11.6   0.0    2.6  2  Sigma54_activ_2  Sigma-54 interaction domain
    0.00016   21.7   0.1       0.36   10.7   0.0    3.6  3  ATPase_2         ATPase domain predominantly from Archaea
    0.00042   20.2   0.0       0.95    9.2   0.0    2.3  2  AAA_11           AAA domain
    0.00049   20.5   0.4        1.8    8.9   0.0    2.9  3  AAA_19           AAA domain
     0.0005   19.4   0.0       0.12   11.5   0.0    2.4  2  DUF2075          Uncharacterized conserved protein (DUF2075)
     0.0011   18.4   0.0        2.5    7.5   0.0    3.8  4  TniB             Bacterial TniB protein
     0.0013   17.8   0.0       0.11   11.4   0.0    2.5  2  AAA_6            Hydrolytic ATP binding site of dynein motor 
     0.0014   19.1   0.0        1.7    9.1   0.0    3.0  2  AAA_17           AAA domain
     0.0021   17.0   0.0        1.4    7.8   0.0    2.8  3  AFG1_ATPase      AFG1-like ATPase
     0.0025   17.8   0.0        8.2    6.3   0.0    3.3  3  Rad17            Rad17 P-loop domain
     0.0027   17.6   1.1        7.1    6.5   0.0    4.0  3  NTPase_1         NTPase
     0.0058   16.3   0.2        8.1    6.1   0.0    3.9  4  Guanylate_kin    Guanylate kinase
     0.0075   15.5   0.0        4.9    6.3   0.0    2.6  2  NB-ARC           NB-ARC domain
  ------ inclusion threshold ------
      0.014   14.8   0.1        4.1    6.7   0.0    2.3  2  IPT              Isopentenyl transferase
      0.015   15.8   0.8        2.1    8.9   0.3    3.1  2  ADSL_C           Adenylosuccinate lyase C-terminus
      0.018   14.8   0.1          5    6.8   0.0    2.5  2  Cytidylate_kin   Cytidylate kinase
      0.034   13.9   0.0        8.2    6.2   0.0    2.5  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
      0.037   14.1   0.0        4.6    7.4   0.0    2.6  2  SKI              Shikimate kinase
       0.05   12.6   0.0        5.9    5.9   0.0    2.5  2  T2SSE            Type II/IV secretion system protein
      0.066   13.0   0.0         14    5.5   0.0    2.4  2  AAA_29           P-loop containing region of AAA domain
      0.082   12.5   0.1        7.3    6.1   0.0    2.5  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
       0.14   11.9   0.0          5    6.8   0.0    2.2  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.14   11.5   0.0         15    4.9   0.0    2.5  2  KTI12            Chromatin associated protein KTI12
       0.15   11.2   0.0         10    5.3   0.0    2.8  3  KAP_NTPase       KAP family 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 !  170.1   0.0   9.2e-53   2.9e-50       1     130 [.     226     354 ..     226     356 .. 0.98
   2 !  159.0   0.0   2.5e-49   7.8e-47       1     131 [.     500     631 ..     500     632 .. 0.98

  Alignments for each domain:
  == domain 1  score: 170.1 bits;  conditional E-value: 9.2e-53
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTC CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgs 77 
                                       vllyGppGtGKTllaka+a+e+g++f+ i+g+e++sk+ gese+++re+f++a+e+a p i+fiDEid++a++r++ 
  gi|385806208|ref|YP_005842606.1| 226 VLLYGPPGTGKTLLAKALANEIGAYFVAINGPEIMSKFYGESEQRLREIFQQAQENA-PAIIFIDEIDSIAPKREEV 301
                                       79******************************************************9.******************* PP

                                       CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEET CS
                               AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkiei 130
                                       + e+e+rvv+qLlt +dg+k++ ++v+vigatnrpd ldpal+r gRfdr+iei
  gi|385806208|ref|YP_005842606.1| 302 TGEVERRVVAQLLTLMDGLKER-GRVVVIGATNRPDALDPALRRpGRFDREIEI 354
                                       *********************6.77***************************98 PP

  == domain 2  score: 159.0 bits;  conditional E-value: 2.5e-49
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH..T CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr..s 75 
                                       vll+GppGtGKT+lakava+e++++f+ + g+e+lsk+vgesek ire+f++a++ a p+++f+DEid+++++r  +
  gi|385806208|ref|YP_005842606.1| 500 VLLFGPPGTGKTMLAKAVATESEANFIAVRGPEVLSKWVGESEKAIREIFRRARQVA-PTVIFFDEIDSITPARglR 575
                                       79******************************************************9.****************999 PP

                                       TCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  76 gseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                        ++s++++r+vnqLlte+dg +   s+v+vigatnrpd ldpallr gRfdr ++i+
  gi|385806208|ref|YP_005842606.1| 576 YDSSGVTDRIVNQLLTEIDGIQPL-SNVVVIGATNRPDILDPALLRpGRFDRLVYIP 631
                                       99*********************6.66**************************9997 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.4   0.1   2.5e-17   7.8e-15       1      37 [.     378     414 ..     378     424 .. 0.90
   2 !   59.9   0.1   4.6e-19   1.5e-16       1      39 [.     654     694 ..     654     700 .. 0.89

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 2.5e-17
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgike 37 
                                       dvdl++LA+ T+G++GADlaal++eAa++++rr i+e
  gi|385806208|ref|YP_005842606.1| 378 DVDLDKLAAITHGFTGADLAALVKEAAMNTIRRFIEE 414
                                       9********************************9885 PP

  == domain 2  score: 59.9 bits;  conditional E-value: 4.6e-19
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgike..it 39 
                                       dvdl++LA +TeGy+GADl+al+reA++lAlr+++++  ++
  gi|385806208|ref|YP_005842606.1| 654 DVDLEKLADMTEGYTGADLEALVREAVMLALREKLEArpVE 694
                                       9*********************************9843466 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 !   96.9   0.5   1.9e-30   5.9e-28       3      84 ..       8      90 ..       6      91 .. 0.97

  Alignments for each domain:
  == domain 1  score: 96.9 bits;  conditional E-value: 1.9e-30
                                      EEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEEC.CCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEEE CS
                           CDC48_N  3 rVaeapqedvgrgivridpedmeelglepgdvveieg.krkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkVtV 80
                                      +Vaea+++dvg++++r++   m++lg+ +gd++eieg k +T ++vwpa+pede+k++Ir+dgv+R+ +gvs+G++Vt+
  gi|385806208|ref|YP_005842606.1|  8 IVAEAKSRDVGKKRARVSFRLMSKLGVTSGDFIEIEGrKGTTLVQVWPAYPEDEDKDYIRIDGVIRNAIGVSVGETVTI 86
                                      7************************************8888************************************** PP

                                      EEE- CS
                           CDC48_N 81 rkae 84
                                      rkae
  gi|385806208|ref|YP_005842606.1| 87 RKAE 90
                                      **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 !   34.3   0.0   5.5e-11   1.7e-08      34     104 ..     224     302 ..     216     350 .. 0.82
   2 !   23.4   0.0   1.3e-07     4e-05      35      98 ..     499     570 ..     490     625 .. 0.69

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 5.5e-11
                            RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsravee 102
                                         vllyGpPG Gkt lak +a+e+g+ + +  gP +      e ++ l  ++++ +e+   ++fidei  ++++ ee
  gi|385806208|ref|YP_005842606.1| 224 KGVLLYGPPGTGKTLLAKALANEIGAYFVAINGPEImskfygESEQRLREIFQQAQENapAIIFIDEIDSIAPKREE 300
                                       569*******************************994444434567899999998876336**************99 PP

                            RuvB_N 103 vl 104
                                       v 
  gi|385806208|ref|YP_005842606.1| 301 VT 302
                                       85 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 1.3e-07
                            RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsr 98 
                                        vll+GpPG Gkt lak +a+e ++++ +  gP +      e ++ +  ++ + ++    v+f dei  +++
  gi|385806208|ref|YP_005842606.1| 499 GVLLFGPPGTGKTMLAKAVATESEANFIAVRGPEVlskwvgESEKAIREIFRRARQVapTVIFFDEIDSITP 570
                                       59******************************9663322223345556666555443226888888887765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.0   1.4e-09   4.4e-07      24     140 ..     223     329 ..     207     337 .. 0.74
   2 !   18.4   0.0   7.1e-06    0.0022      24      58 ..     497     530 ..     487     539 .. 0.82
   3 ?    5.1   0.0     0.086        27     122     149 ..     544     570 ..     540     605 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 1.4e-09
                            AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaes.aeleawre 99 
                                       p  vll+G++G+GK+ l+++l++++    ++f++ +  +      +s +      e+ lr++ ++a++ a +  + +
  gi|385806208|ref|YP_005842606.1| 223 PKGVLLYGPPGTGKTLLAKALANEIG---AYFVAINGPEI-----MSKFYGES--EQRLREIFQQAQEnAPAIIFID 289
                                       589*******************9777...88999999999.....33333333..3555555555444044455555 PP

                            AAA_16 100 kleealaavpelagaeasrllellkrllallsrderplvlv 140
                                       ++++ +    e++g+ ++r+ ++l  l++ l++++r +v++
  gi|385806208|ref|YP_005842606.1| 290 EIDSIAPKREEVTGEVERRVVAQLLTLMDGLKERGR-VVVI 329
                                       56666668888888888**************99787.5543 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 7.1e-06
                            AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrg 58 
                                       p+ vll G++G+GK+ l+++++++ e++ +i++rg
  gi|385806208|ref|YP_005842606.1| 497 PRGVLLFGPPGTGKTMLAKAVATESEAN-FIAVRG 530
                                       499*******************988887.555555 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.086
                            AAA_16 122 llkrllallsrderplvlvlDdlqwade 149
                                       +++++++++++   p+v+++D+++ + +
  gi|385806208|ref|YP_005842606.1| 544 AIREIFRRARQ-VAPTVIFFDEIDSITP 570
                                       67888999999.778*********6654 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.0     2e-10   6.3e-08       6     105 ..     226     319 ..     222     323 .. 0.90
   2 !   20.5   0.0   1.3e-06    0.0004       6     100 ..     500     590 ..     495     597 .. 0.77

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 2e-10
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       +ll gp g+Gkt+lakala+ + +     ++ ++  e++     + + ++++  ++  ++a+e+   i+++DEid i
  gi|385806208|ref|YP_005842606.1| 226 VLLYGPPGTGKTLLAKALANEIGA----YFVAINGPEIMS----KFYGESEQRLREIFQQAQENApaIIFIDEIDSI 294
                                       6889******************96....************....99999999999999999999999********** PP

                                       ---.---------HHHHHHHHHHHH- CS
                             AAA_2  81 hpk.essgadvSregVqrdLLqileg 105
                                       +pk e+ + +v r  V+  LL +++g
  gi|385806208|ref|YP_005842606.1| 295 APKrEEVTGEVERR-VVAQLLTLMDG 319
                                       **988888888886.66678888887 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 1.3e-06
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       +ll gp g+Gkt+laka+a   ++    ++i +   e+l     + + ++++  ++   +a +    ++++DEid i
  gi|385806208|ref|YP_005842606.1| 500 VLLFGPPGTGKTMLAKAVATESEA----NFIAVRGPEVLS----KWVGESEKAIREIFRRARQVAptVIFFDEIDSI 568
                                       6788***************99985....9*********99....66666667777777777777788********** PP

                                       ------------..HHHHHHHH CS
                             AAA_2  81 hpkessgadvSr..egVqrdLL 100
                                       +p +  + d S+  + +++ LL
  gi|385806208|ref|YP_005842606.1| 569 TPARGLRYDSSGvtDRIVNQLL 590
                                       **96666666642234555555 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.1   1.7e-08   5.3e-06       1     136 [.     225     344 ..     225     345 .. 0.73
   2 !   17.6   0.1   9.3e-06    0.0029       1      78 [.     499     569 ..     499     621 .. 0.71

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1.7e-08
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEve 75 
                                       +vlL GppGtgK+ la+ la  +++ ++ +++++ +++  + g+ e        +  ++ ++a+   ++i+++DE++
  gi|385806208|ref|YP_005842606.1| 225 GVLLYGPPGTGKTLLAKALANEIGAYFVAINGPEIMSK--FYGESE-------QRLREIFQQAQenAPAIIFIDEID 292
                                       59********************************8875..555555.......244566666666789********* PP

                                       G--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHT CS
                             AAA_5  76 raesevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrs 136
                                        + ++  ++     e +r+ ++++ +l++  ++    r+ vi+++n++d     l+palr+
  gi|385806208|ref|YP_005842606.1| 293 SIAPKREEVT-G--EVERRVVAQLLTLMDGLKE--RGRVVVIGATNRPD----ALDPALRR 344
                                       8876543333.2..2233333466666655442..23399*******99....88999986 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 9.3e-06
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEve 75 
                                       +vlL GppGtgK++la+ +a   ++++  v +++      ++ ++    g+ +    ++ r ar   + ++++DE++
  gi|385806208|ref|YP_005842606.1| 499 GVLLFGPPGTGKTMLAKAVATESEANFIAVRGPE------VLSKWV---GESEKAIREIFRRARqvAPTVIFFDEID 566
                                       59****************9998888888887776......444555...2333333334444444666777777776 PP

                                       G-- CS
                             AAA_5  76 rae 78 
                                        + 
  gi|385806208|ref|YP_005842606.1| 567 SIT 569
                                       665 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   2.7e-07   8.6e-05      51      97 ..     224     268 ..     219     307 .. 0.87
   2 !   21.8   0.0     3e-07   9.3e-05      51     108 ..     498     554 ..     489     559 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 2.7e-07
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte 97 
                                       ++vLl Gp+gtGkt la a+++e+g    fva++g e+ s     +e
  gi|385806208|ref|YP_005842606.1| 224 KGVLLYGPPGTGKTLLAKALANEIG--AYFVAINGPEIMSKFYGESE 268
                                       89***********************..79*********997665555 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 3e-07
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte.vltqalrksig 108
                                       r+vLl Gp+gtGkt la a++ e  ++  f+a+ g ev s  v  +e ++ + +r++ +
  gi|385806208|ref|YP_005842606.1| 498 RGVLLFGPPGTGKTMLAKAVATE--SEANFIAVRGPEVLSKWVGESEkAIREIFRRARQ 554
                                       89*******************98..5689**************9998578899999865 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.2     6e-06    0.0019       8      84 ..     226     277 ..     221     338 .. 0.57
   2 !   16.4   0.0   2.6e-05    0.0083       8      30 ..     500     522 ..     495     542 .. 0.80
   3 ?    0.8   0.0       1.8   5.6e+02      82     112 ..     545     589 ..     538     614 .. 0.61

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 6e-06
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.....sskdllrellralglelkaerlsseell 79 
                                       ++++G++GtGKT+l++ l+++          ++ +v ++ p+ +     +s+                     ++l+
  gi|385806208|ref|YP_005842606.1| 226 VLLYGPPGTGKTLLAKALANEI---------GAYFVAINGPEIMskfygESE---------------------QRLR 272
                                       689*****************98.........333333333332211122222.....................2222 PP

                            AAA_22  80 ealeq 84 
                                       e ++q
  gi|385806208|ref|YP_005842606.1| 273 EIFQQ 277
                                       22222 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 2.6e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqld 30 
                                       ++++G++GtGKT+l++ ++ + +
  gi|385806208|ref|YP_005842606.1| 500 VLLFGPPGTGKTMLAKAVATESE 522
                                       689***************99863 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 1.8
                            AAA_22  82 leqalrarav..ielliiDEaqhlr.....s.......eealeeL 112
                                       +++ +r+++   + ++  DE++ ++     +       ++++++L
  gi|385806208|ref|YP_005842606.1| 545 IREIFRRARQvaPTVIFFDEIDSITparglRydssgvtDRIVNQL 589
                                       55555555556779********99655433133345555555554 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   1.8e-07   5.8e-05       2      79 ..     226     333 ..     226     377 .. 0.72
   2 !   18.2   0.0   6.7e-06    0.0021       2      47 ..     500     577 ..     500     631 .. 0.69

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1.8e-07
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt............................dy 48 
                                       vll G+pG+GK+ la+ l+++ g  +v ++ ++++++ +g+ +q+++                              
  gi|385806208|ref|YP_005842606.1| 226 VLLYGPPGTGKTLLAKALANEIGayFVAINGPEIMSKFYGESEQRLReifqqaqenapaiifideidsiapkreeVT 302
                                       7899*******************98889************8888888777777777777888877777777555433 PP

                            AAA_33  49 trvldrlyqilnelarkalsagrnvildatn 79 
                                        +v+ r+ ++l  l +   ++gr v++ atn
  gi|385806208|ref|YP_005842606.1| 303 GEVERRVVAQLLTLMDGLKERGRVVVIGATN 333
                                       3455566667767777777777777777774 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 6.7e-06
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt.............................. 46 
                                       vll G+pG+GK+ la+ ++ +    ++ ++ ++++++ +g+ ++ ++                              
  gi|385806208|ref|YP_005842606.1| 500 VLLFGPPGTGKTMLAKAVATESEanFIAVRGPEVLSKWVGESEKAIReifrrarqvaptviffdeidsitparglry 576
                                       7899***************999999999999*999888887766666444444444444555555555555555544 PP

                            AAA_33  47 d 47 
                                       d
  gi|385806208|ref|YP_005842606.1| 577 D 577
                                       4 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   9.4e-07   0.00029       5     101 ..     226     332 ..     223     358 .. 0.76
   2 !   15.9   0.0   3.3e-05      0.01       5      77 ..     500     569 ..     497     597 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 9.4e-07
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev..... 76 
                                       +++ G+  +GKT l+k l++e       ++ in  +   k + ++e+ l++i+++++e+   ++f+DEi  +     
  gi|385806208|ref|YP_005842606.1| 226 VLLYGPPGTGKTLLAKALANEIG---AYFVAINGPEIMSKFYGESEQRLREIFQQAQENAPAIIFIDEIDSIapkre 299
                                       7899***************8888...888999988887766666665666666665667999*********988887 PP

                            AAA_14  77 .......pewekalkslvd.egknldvivtGSn 101
                                              +++   l  l+d  +++++v+v G  
  gi|385806208|ref|YP_005842606.1| 300 evtgeveRRVVAQLLTLMDgLKERGRVVVIGAT 332
                                       777777766666777777742356777777765 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 3.3e-05
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevp 77 
                                       +++ G+  +GKT+l+k ++ e+     +++ +   +   k   ++ek +++i++++++   t++f+DEi  ++
  gi|385806208|ref|YP_005842606.1| 500 VLLFGPPGTGKTMLAKAVATESE---ANFIAVRGPEVLSKWVGESEKAIREIFRRARQVAPTVIFFDEIDSIT 569
                                       6899***************9888...89999998888888777777777777776555688********9875 PP

>> CDC48_2  Cell division protein 48 (CDC48), domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       7.9   2.5e+03      31      57 ..      73      99 ..      34     104 .. 0.69
   2 !   39.2   0.7   1.4e-12   4.5e-10       8      63 ..     117     175 ..     113     176 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 7.9
                                      CCCEEEEEEEECCCCSCEEECTSCCEE CS
                           CDC48_2 31 gqeiklvVvstePkgpvgitetTeiel 57
                                       ++i   V +t ++ ++ ++++T+i l
  gi|385806208|ref|YP_005842606.1| 73 RNAIGVSVGETVTIRKAEASPATKIVL 99
                                      556777777788888888888888876 PP

  == domain 2  score: 39.2 bits;  conditional E-value: 1.4e-12
                                       H.HHHCCCTTEEE-TTEEEEE..CCTCCCEEEEEEEECCCCSCEEECTSCCEEESTTCC CS
                           CDC48_2   8 a.ylkrqFlgrpvtkGdlvvf..efkgqeiklvVvstePkgpvgitetTeielgtkpve 63 
                                       +  lk  + g+p+  G+++ +  +f+g e+++vV++t+P   v +t +Tei+++++pv+
  gi|385806208|ref|YP_005842606.1| 117 EnLLKEELSGKPLKRGETIIVplSFFGSELTFVVTNTQPTTNVFVTSSTEIQVREEPVK 175
                                       4479999************6622667*******************************98 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0     3e-05    0.0093      46      70 ..     222     246 ..     206     294 .. 0.89
   2 !   15.6   0.0   3.2e-05    0.0099      48      72 ..     498     522 ..     487     565 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3e-05
                         IstB_IS21  46 kkenivllGpsGvGKshlaialgve 70 
                                         ++++l Gp+G+GK+ la al+ e
  gi|385806208|ref|YP_005842606.1| 222 PPKGVLLYGPPGTGKTLLAKALANE 246
                                       56789*****************976 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 3.2e-05
                         IstB_IS21  48 enivllGpsGvGKshlaialgveav 72 
                                        +++l+Gp+G+GK+ la a+++e  
  gi|385806208|ref|YP_005842606.1| 498 RGVLLFGPPGTGKTMLAKAVATESE 522
                                       5799****************98865 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.1e-05    0.0033       2      49 ..     226     274 ..     225     310 .. 0.72
   2 !   13.6   0.0   0.00019     0.059       2      35 ..     500     538 ..     499     561 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.1e-05
                            AAA_28   2 ivitGgestGKTtlleaLaar.gypvvpEaareileeklakgedalpwv 49 
                                       + + G+++tGKT l++aLa++ g   v+  + ei+++ + + e+ l++ 
  gi|385806208|ref|YP_005842606.1| 226 VLLYGPPGTGKTLLAKALANEiGAYFVAINGPEIMSKFYGESEQRLREI 274
                                       6799***************988766664444444444444444444433 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 0.00019
                            AAA_28   2 ivitGgestGKTtlleaLaar...gypvv..pEaareil 35 
                                       + ++G+++tGKT l++a a +   ++  v  pE+  + +
  gi|385806208|ref|YP_005842606.1| 500 VLLFGPPGTGKTMLAKAVATEseaNFIAVrgPEVLSKWV 538
                                       6799***************55434433333666655554 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1     6e-05     0.019      25      43 ..     226     244 ..     222     251 .. 0.90
   2 !   15.5   0.0   2.8e-05    0.0087      25      43 ..     500     518 ..     497     524 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6e-05
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll+GppG+GKt+lak+l+
  gi|385806208|ref|YP_005842606.1| 226 VLLYGPPGTGKTLLAKALA 244
                                       89**************996 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 2.8e-05
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll+GppG+GKtmlak+++
  gi|385806208|ref|YP_005842606.1| 500 VLLFGPPGTGKTMLAKAVA 518
                                       79*************9875 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.9e-05     0.006       1      25 [.     226     268 ..     226     332 .. 0.66
   2 !   13.4   0.0   0.00026     0.082       1      22 [.     500     521 ..     500     603 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.9e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.................g 25 
                                       +ll G+pG+GKt lak+L+++  ++                  
  gi|385806208|ref|YP_005842606.1| 226 VLLYGPPGTGKTLLAKALANEIgAYfvaingpeimskfygesE 268
                                       799***************9998555777776644444444442 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00026
                            AAA_18   1 IlltGtpGvGKttlakeLskrl 22 
                                       +ll G+pG+GKt lak+++ + 
  gi|385806208|ref|YP_005842606.1| 500 VLLFGPPGTGKTMLAKAVATES 521
                                       799**************96553 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0    0.0015      0.47      36      54 ..     226     244 ..     210     248 .. 0.90
   2 ?    4.9   0.1     0.056        18     128     176 ..     269     317 ..     257     330 .. 0.85
   3 !   11.7   0.3   0.00044      0.14      36      94 ..     500     556 ..     481     606 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0015
                            AAA_25  36 allaGapgtGKttlaldla 54 
                                       +ll+G+pgtGKt la  la
  gi|385806208|ref|YP_005842606.1| 226 VLLYGPPGTGKTLLAKALA 244
                                       69************98887 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.056
                            AAA_25 128 advdaleaaieevegvrlvviDplsralggdensnsdv.galvealeria 176
                                       + ++++ ++++e + ++ + iD ++++ +  e+   +v +++v++l  + 
  gi|385806208|ref|YP_005842606.1| 269 QRLREIFQQAQE-NAPAIIFIDEIDSIAPKREEVTGEVeRRVVAQLLTLM 317
                                       556788899999.77***************99999999999999997765 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00044
                            AAA_25  36 allaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravg 94 
                                       +ll+G+pgtGKt+la  +a +     ++   + pe    ++   E +  e+ rR+r+v 
  gi|385806208|ref|YP_005842606.1| 500 VLLFGPPGTGKTMLAKAVATESE--ANFIAVRGPEVLSKWVGESEKAIREIFRRARQVA 556
                                       589**********9876554322..2232233346666666666666666666666655 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.5e-05    0.0049       1      34 [.     226     259 ..     226     302 .. 0.77
   2 !   11.4   0.0     0.001      0.33       1      25 [.     500     524 ..     500     570 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.5e-05
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsv 34 
                                       ++lyGp+g+GK++lak La+++   +  ++ +++
  gi|385806208|ref|YP_005842606.1| 226 VLLYGPPGTGKTLLAKALANEIGAYFVAINGPEI 259
                                       689******************9987744444443 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.001
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkk 25 
                                       ++l+Gp+g+GK++lak +a++ + +
  gi|385806208|ref|YP_005842606.1| 500 VLLFGPPGTGKTMLAKAVATESEAN 524
                                       679**************88876654 PP

>> Vps4_C  Vps4 C terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.1    0.0095         3      19      44 ..     423     448 ..     413     452 .. 0.81
   2 !   17.0   0.0   1.3e-05    0.0042      22      56 ..     686     720 ..     676     724 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0095
                            Vps4_C  19 ipsdkllePpvtlkDflkalkkarpt 44 
                                       i+++ l+  +vt +Df++alk + p+
  gi|385806208|ref|YP_005842606.1| 423 IKPELLKDVKVTWSDFMNALKDVNPS 448
                                       555666667***************99 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 1.3e-05
                            Vps4_C  22 dkllePpvtlkDflkalkkarptVskeDLekheeF 56 
                                       +kl ++pv++k flka++++ p+ + e++ek+e+ 
  gi|385806208|ref|YP_005842606.1| 686 EKLEARPVEFKYFLKAMETVGPSLTREEVEKYERL 720
                                       799999**************************975 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00046      0.14      23      61 ..     224     259 ..     208     335 .. 0.80
   2 !   11.0   0.0    0.0008      0.25      23      52 ..     498     524 ..     486     536 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00046
                                       S-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS CS
                   Sigma54_activat  23 lsvlitGesGtGKellaraiheaskrkekpfvavncaai 61 
                                         vl+ G  GtGK+lla+a+ ++     + fva+n  +i
  gi|385806208|ref|YP_005842606.1| 224 KGVLLYGPPGTGKTLLAKALANEIG---AYFVAINGPEI 259
                                       579****************987654...77888887655 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0008
                                       S-EEEECSTTSSHHHHHHHHHHHSTTTTS- CS
                   Sigma54_activat  23 lsvlitGesGtGKellaraiheaskrkekp 52 
                                         vl+ G  GtGK++la+a+ ++s+   ++
  gi|385806208|ref|YP_005842606.1| 498 RGVLLFGPPGTGKTMLAKAVATESE---AN 524
                                       579****************998876...44 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   0.00015     0.049       5      22 ..     226     243 ..     223     301 .. 0.75
   2 !   10.8   0.0   0.00097      0.31       5      22 ..     500     517 ..     497     535 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00015
                            AAA_24   5 iliyGpsgiGKTtlakel 22 
                                       +l+yGp+g+GKT lak l
  gi|385806208|ref|YP_005842606.1| 226 VLLYGPPGTGKTLLAKAL 243
                                       89**************98 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00097
                            AAA_24   5 iliyGpsgiGKTtlakel 22 
                                       +l++Gp+g+GKT+lak  
  gi|385806208|ref|YP_005842606.1| 500 VLLFGPPGTGKTMLAKAV 517
                                       79*************987 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.1    0.0018      0.58       3      24 ..     226     247 ..     224     250 .. 0.90
   2 ?    0.4   0.0       1.7   5.4e+02      62     115 ..     264     319 ..     257     369 .. 0.62
   3 !   11.0   0.0   0.00098      0.31       3      23 ..     500     520 ..     498     525 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0018
                                       EEEEC-TTTCHHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklalaw 24 
                                       v+l G++G GKT L++ la ++
  gi|385806208|ref|YP_005842606.1| 226 VLLYGPPGTGKTLLAKALANEI 247
                                       799***************9876 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.7
                                       CTS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH.............HHHHHCT CS
                             NACHT  62 lpepaapvsevwavllelperlLlilDglDelvtdlgq....kekqpvrtlLselirk 115
                                       + e++++ +e+++  +e++  + + +D +D ++ + ++     e++ v + L +l+ +
  gi|385806208|ref|YP_005842606.1| 264 YGESEQRLREIFQQAQENAPAIIF-IDEIDSIAPKREEvtgeVERRVVAQ-LLTLMDG 319
                                       566777777877777777777766.5888888887777777433333333.3355554 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00098
                                       EEEEC-TTTCHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                       v+l G++G GKT+L++ +a++
  gi|385806208|ref|YP_005842606.1| 500 VLLFGPPGTGKTMLAKAVATE 520
                                       7899************99986 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0    0.0006      0.19       5      40 ..     210     245 ..     206     256 .. 0.87
   2 ?    1.1   0.0      0.85   2.7e+02     126     163 ..     382     417 ..     379     432 .. 0.84
   3 !    9.3   0.0    0.0026      0.83      21      44 ..     500     523 ..     489     557 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0006
                            AAA_30   5 eQaaavealltsgdrvavltGpAGtGKttalkalre 40 
                                        Q +++++l  ++ + ++l Gp+GtGKt + kal++
  gi|385806208|ref|YP_005842606.1| 210 RQPQLFRHLGIEPPKGVLLYGPPGTGKTLLAKALAN 245
                                       6899999999999999**************999976 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.85
                            AAA_30 126 rQlasVeaGgvlrdlveaagigtaeLtevvRqkeseer 163
                                       + la+++ G + +dl  aa  + a +++++R+ e++  
  gi|385806208|ref|YP_005842606.1| 382 DKLAAITHGFTGADL--AALVKEAAMNTIRRFIEEKKV 417
                                       66899**********..789************776554 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0026
                            AAA_30  21 avltGpAGtGKttalkalreawea 44 
                                       ++l Gp+GtGKt++ ka++   ea
  gi|385806208|ref|YP_005842606.1| 500 VLLFGPPGTGKTMLAKAVATESEA 523
                                       6788************99876665 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   0.00029     0.093      30      58 ..     220     248 ..     209     302 .. 0.81
   2 !   10.7   0.0   0.00087      0.27      34      58 ..     498     522 ..     489     529 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00029
                             AAA_7  30 lknkkpvllvGptGtGKtviikdllkkld 58 
                                       ++  k vll+Gp GtGKt+++k l +++ 
  gi|385806208|ref|YP_005842606.1| 220 IEPPKGVLLYGPPGTGKTLLAKALANEIG 248
                                       566689****************9998876 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00087
                             AAA_7  34 kpvllvGptGtGKtviikdllkkld 58 
                                       + vll Gp GtGKt+++k + ++ +
  gi|385806208|ref|YP_005842606.1| 498 RGVLLFGPPGTGKTMLAKAVATESE 522
                                       679**************99777665 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0    0.0003     0.094      47      84 ..     217     254 ..     167     333 .. 0.69
   2 !   11.1   0.0   0.00052      0.16      24     102 ..     459     548 ..     435     567 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0003
                            DUF815  47 fleglpannvLLwGarGtGKSslvkallneyaeegLrl 84 
                                       +l  +p + vLL+G  GtGK  l kal ne+ +  +++
  gi|385806208|ref|YP_005842606.1| 217 HLGIEPPKGVLLYGPPGTGKTLLAKALANEIGAYFVAI 254
                                       445578899*********************98877554 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00052
                            DUF815  24 evklddLvgidkqkealvente.........qfleglpannvLLwGarGtGKSslvkallneyaeeg..Lrlievek 89 
                                       +vk++d+ g+++ k++l e +e         + +  +p + vLL+G  GtGK  l ka+ +e +++   +r  ev  
  gi|385806208|ref|YP_005842606.1| 459 NVKWSDIGGLEEAKQQLREAVEwplkypeiyEKMGVRPPRGVLLFGPPGTGKTMLAKAVATESEANFiaVRGPEVLS 535
                                       56777777777777777776652221111112233467889*******************99998873344456655 PP

                            DUF815  90 edlkelpklvell 102
                                       + + e +k ++++
  gi|385806208|ref|YP_005842606.1| 536 KWVGESEKAIREI 548
                                       5555555544444 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   6.7e-06    0.0021      37     180 ..     226     371 ..     221     419 .. 0.79
   2 ?    5.2   0.0     0.054        17      37      64 ..     500     527 ..     493     545 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 6.7e-06
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHTT-.SEEEEE-GGGGTT- CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklrkv.DvLliDDiqflagk 112
                                       +++yg+ G Gkt L ka++ne+ + +     v +++ e ++++    +++  e f++   ++  ++ iD+i  +a k
  gi|385806208|ref|YP_005842606.1| 226 VLLYGPPGTGKTLLAKALANEIGAYF-----VAINGPEIMSKFYGESEQRLREIFQQAQENApAIIFIDEIDSIAPK 297
                                       79*****************9997655.....678999999999999999999999998886625778*******988 PP

                                       H.........HHHHHHHHHHHHHHTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHHHHHH CS
                          Bac_DnaA 113 e.........ktqeelfhtfnalleegkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailkkkie 180
                                                 ++  +l+++++ l e g+ vv+ +   P +l+    r   rf++   ++i ppd + r +il+ + +
  gi|385806208|ref|YP_005842606.1| 298 ReevtgeverRVVAQLLTLMDGLKERGRVVVIGATNRPDALDPAL-RRPGRFDR--EIEIAPPDVKARKEILMVHTR 371
                                       522222111123457899999999**************9987644.33568877..68999**********986554 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.054
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSSS CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenape 64 
                                       ++++g+ G Gkt L ka++ e ++n+ +
  gi|385806208|ref|YP_005842606.1| 500 VLLFGPPGTGKTMLAKAVATESEANFIA 527
                                       799****************999888765 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0    0.0012      0.38      14      37 ..     218     241 ..     212     250 .. 0.84
   2 ?    2.9   0.0      0.19        59     121     154 ..     284     320 ..     255     329 .. 0.64
   3 !    8.7   0.0    0.0032         1      15      40 ..     493     518 ..     486     528 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0012
                            ATPase  14 gGipegrvvlitGepGtGKtifal 37 
                                        Gi   + vl++G pGtGKt++a+
  gi|385806208|ref|YP_005842606.1| 218 LGIEPPKGVLLYGPPGTGKTLLAK 241
                                       577788889*************97 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.19
                            ATPase 121 krvviDsitgl...ayeekeavaReilrqlvrvlkkl 154
                                         + iD i+++    +e + +v R+ + ql++ + +l
  gi|385806208|ref|YP_005842606.1| 284 AIIFIDEIDSIapkREEVTGEVERRVVAQLLTLMDGL 320
                                       4455555555532166667788999999999999765 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0032
                            ATPase  15 GipegrvvlitGepGtGKtifalqFl 40 
                                       G+   r vl+ G pGtGKt++a+  +
  gi|385806208|ref|YP_005842606.1| 493 GVRPPRGVLLFGPPGTGKTMLAKAVA 518
                                       66777889*************98755 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00089      0.28       6      67 ..     218     277 ..     216     327 .. 0.76
   2 !   11.9   0.0   0.00077      0.24       8      73 ..     494     558 ..     491     604 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00089
                                       EEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   6 lklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe 67 
                                       l +++ + v + G+ G+GK+ L+k+la++       + ++g ++ ++   +++++++ ++q+
  gi|385806208|ref|YP_005842606.1| 218 LGIEPPKGVLLYGPPGTGKTLLAKALANEIGAY--FVAINGPEIMSKFYGESEQRLREIFQQ 277
                                       6678888899*****************998654..344466666666666666666666666 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00077
                                       EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                          ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpe 73 
                                       +++ + v ++G+ G+GK+ L+k++a +++  +  i ++g ++ ++   +++k i+ ++    q+ p+
  gi|385806208|ref|YP_005842606.1| 494 VRPPRGVLLFGPPGTGKTMLAKAVATESE--ANFIAVRGPEVLSKWVGESEKAIREIFRRaRQVAPT 558
                                       556667899****************9986..577777888888777777777777777664555555 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   0.00029     0.092      19      51 ..     223     257 ..     193     270 .. 0.77
   2 !    9.9   0.0    0.0022      0.68      21      49 ..     499     529 ..     469     533 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00029
                                       TEEEEEEESTTSSHHHHHHHHHHHTT--..----T CS
                              TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve..evkSP 51 
                                        + +lL+G+ G+GKT l+++la+++g    +++ P
  gi|385806208|ref|YP_005842606.1| 223 PKGVLLYGPPGTGKTLLAKALANEIGAYfvAINGP 257
                                       3449********************99765556555 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0022
                                       EEEEEESTTSSHHHHHHHHHHHTT--..--- CS
                              TsaE  21 vilLeGdLGaGKTtlvrglakalgve..evk 49 
                                        +lL G+ G+GKT+l++++a + + +  +v+
  gi|385806208|ref|YP_005842606.1| 499 GVLLFGPPGTGKTMLAKAVATESEANfiAVR 529
                                       499*****************99877666665 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   0.00028     0.089       2      31 ..     226     255 ..     225     315 .. 0.75
   2 !   10.1   0.0    0.0018      0.57       2      31 ..     500     529 ..     499     611 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00028
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkriq 31 
                                       vll g PG++ktll+kala+ +++ f  i 
  gi|385806208|ref|YP_005842606.1| 226 VLLYGPPGTGKTLLAKALANEIGAYFVAIN 255
                                       7999*******************9998775 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0018
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkriq 31 
                                       vll g PG++kt+l+ka+a+  +++f  ++
  gi|385806208|ref|YP_005842606.1| 500 VLLFGPPGTGKTMLAKAVATESEANFIAVR 529
                                       7999****************9999997765 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   0.00013     0.042     117     141 ..     226     250 ..     221     256 .. 0.90
   2 !    8.7   0.0    0.0026      0.82     117     136 ..     500     519 ..     493     526 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00013
                         Parvo_NS1 117 vwfyGpantGktnlaeaIakavply 141
                                       v++yGp+ tGkt la+a+a+ +  y
  gi|385806208|ref|YP_005842606.1| 226 VLLYGPPGTGKTLLAKALANEIGAY 250
                                       89*****************988766 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0026
                         Parvo_NS1 117 vwfyGpantGktnlaeaIak 136
                                       v+++Gp+ tGkt+la+a a+
  gi|385806208|ref|YP_005842606.1| 500 VLLFGPPGTGKTMLAKAVAT 519
                                       7899*************997 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0     0.001      0.32      20      40 ..     224     244 ..     204     249 .. 0.78
   2 !   10.6   0.0    0.0009      0.28      22      42 ..     500     520 ..     494     529 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.001
                                       SEEEEE--TTSSTTHHHHHHH CS
                              PhoH  20 divfaiGpaGtGKtylavala 40 
                                       + v   Gp GtGKt+la ala
  gi|385806208|ref|YP_005842606.1| 224 KGVLLYGPPGTGKTLLAKALA 244
                                       568899***********9998 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0009
                                       EEEE--TTSSTTHHHHHHHHH CS
                              PhoH  22 vfaiGpaGtGKtylavalave 42 
                                       v  +Gp GtGKt+la a+a e
  gi|385806208|ref|YP_005842606.1| 500 VLLFGPPGTGKTMLAKAVATE 520
                                       6789************99976 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00074      0.23      14      51 ..     221     256 ..     213     281 .. 0.87
   2 !    9.1   0.0    0.0023      0.72      16      49 ..     497     528 ..     488     533 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00074
                        Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrldp 51 
                                       e Pk +ll G pG GK+ la++l++e+  +  +v +++
  gi|385806208|ref|YP_005842606.1| 221 EPPKGVLLYGPPGTGKTLLAKALANEI--GAYFVAING 256
                                       56999*********************9..777777776 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0023
                        Zeta_toxin  16 PklillgGqpGAGKselaellkdelerqgnvvrl 49 
                                       P  +ll G pG GK+ la+++++e   + n++ +
  gi|385806208|ref|YP_005842606.1| 497 PRGVLLFGPPGTGKTMLAKAVATES--EANFIAV 528
                                       78899*******************8..6777665 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   0.00072      0.23      24      83 ..     226     296 ..     221     335 .. 0.73
   2 ?    7.8   0.0     0.011       3.3      24      48 ..     500     524 ..     494     572 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00072
                                       EEEEEETT--HHHHHHCC--TTS-E.E--SSTTHHHH-H.........HHHHHHT...TTSEEEEEE-TT--H CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpw.leifvverlaklp.........ldlleqa...kggtLylkdiadlsk 83 
                                       v+l G++G+gk+l A++L+++ g   ++i   e  +             ++++qa    ++++++ +i+++ +
  gi|385806208|ref|YP_005842606.1| 226 VLLYGPPGTGKTLLAKALANEIGAYfVAINGPEIMS--KfygeseqrlREIFQQAqenAPAIIFIDEIDSIAP 296
                                       9******************98765312322222222..02233333448888887555678888888888765 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.011
                                       EEEEEETT--HHHHHHCC--TTS-E CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpw 48 
                                       v+l G++G+gk++ A++ + +s+ +
  gi|385806208|ref|YP_005842606.1| 500 VLLFGPPGTGKTMLAKAVATESEAN 524
                                       9****************99988764 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 !   10.7   0.0    0.0012      0.36      18     121 ..     221     328 ..     213     331 .. 0.64
   2 ?    6.2   0.0     0.027       8.6      20      45 ..     497     522 ..     486     530 .. 0.80
   3 ?   -1.1   0.0       4.8   1.5e+03     107     130 ..     542     568 ..     525     575 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0012
                          ATPase_2  18 epneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekal............ 82 
                                       ep + +++YGp g GKt L k ++++         y+ a+++ +i ++       e++++l++ +            
  gi|385806208|ref|YP_005842606.1| 221 EPPKGVLLYGPPGTGKTLLAKALANEI------GAYFVAINGPEIMSKFYG----ESEQRLREIFqqaqenapaiif 287
                                       6677789**************999988......456666666666665555....3333333333333566666666 PP

                          ATPase_2  83 ..giavpkaeleeilkeksklvfkaielllekikkkgkkii 121
                                          i+    + ee+  e  + v +++  l++ +k++g+ ++
  gi|385806208|ref|YP_005842606.1| 288 idEIDSIAPKREEVTGEVERRVVAQLLTLMDGLKERGRVVV 328
                                       66444444445556667777777777777777777777555 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.027
                          ATPase_2  20 neiyfiYGpegsGKtaLlkeiienle 45 
                                        + ++++Gp g GKt L k +++++e
  gi|385806208|ref|YP_005842606.1| 497 PRGVLLFGPPGTGKTMLAKAVATESE 522
                                       556789*************9998875 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 4.8
                          ATPase_2 107 elllekikkkgkk...iiiiiDelqkl 130
                                       e+++++i +++++    +i++De+  +
  gi|385806208|ref|YP_005842606.1| 542 EKAIREIFRRARQvapTVIFFDEIDSI 568
                                       567778888888878789999*99876 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0     0.003      0.95      19      41 ..     225     247 ..     210     285 .. 0.76
   2 !    8.6   0.0    0.0046       1.4      20      73 ..     500     551 ..     475     560 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.003
                            AAA_11  19 itliqGPPGtgKTktivellsql 41 
                                        +l+ GPPGtgKT    +l +++
  gi|385806208|ref|YP_005842606.1| 225 GVLLYGPPGTGKTLLAKALANEI 247
                                       4799*********8887777776 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0046
                            AAA_11  20 tliqGPPGtgKTktivellsqllsrrkseeeksakpriLv..CapSNaAvDeller 73 
                                       +l+ GPPGtgKT    ++  +     + +  + ++p++L    ++S++A+ e+  r
  gi|385806208|ref|YP_005842606.1| 500 VLLFGPPGTGKTMLAKAVATES----EANFIAVRGPEVLSkwVGESEKAIREIFRR 551
                                       6889********8888887777....334566677777643367777777777666 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.1      0.01       3.2      11      34 ..     224     247 ..     220     285 .. 0.73
   2 ?   -1.3   0.0       8.1   2.6e+03      97     121 ..     277     301 ..     262     319 .. 0.67
   3 !    8.9   0.0    0.0057       1.8      12      33 ..     499     520 ..     492     600 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.01
                            AAA_19  11 kvllvtaGpGtGKTrvlkhivall 34 
                                       k +l+ ++pGtGKT + k+  +++
  gi|385806208|ref|YP_005842606.1| 224 KGVLLYGPPGTGKTLLAKALANEI 247
                                       56899*********9888776655 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 8.1
                            AAA_19  97 ekklqeeellivDEfqdvdelqyrL 121
                                       + + ++ +++++DE+  + +   ++
  gi|385806208|ref|YP_005842606.1| 277 QAQENAPAIIFIDEIDSIAPKREEV 301
                                       33333456999***99988766555 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0057
                            AAA_19  12 vllvtaGpGtGKTrvlkhival 33 
                                        +l+ ++pGtGKT + k++ ++
  gi|385806208|ref|YP_005842606.1| 499 GVLLFGPPGTGKTMLAKAVATE 520
                                       5899*********987766554 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   0.00039      0.12       4      44 ..     226     259 ..     223     306 .. 0.67
   2 ?    5.6   0.0     0.026       8.1       6      25 ..     502     521 ..     498     567 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00039
                           DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplv 44 
                                       vl  G +GtGKt+++ +l++e+        a ++  N+p++
  gi|385806208|ref|YP_005842606.1| 226 VLLYGPPGTGKTLLAKALANEI-------GAYFVAINGPEI 259
                                       6789*****************9.......333444444433 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.026
                           DUF2075   6 VtGvaGtGKtvvllnllael 25 
                                         G +GtGKt+++ ++++e 
  gi|385806208|ref|YP_005842606.1| 502 LFGPPGTGKTMLAKAVATES 521
                                       5699*********9999987 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.051        16      25      56 ..     213     244 ..     199     253 .. 0.85
   2 ?   -0.2   0.0       1.8   5.7e+02     112     150 ..     275     317 ..     253     350 .. 0.64
   3 !    7.5   0.0    0.0079       2.5      33      59 ..     495     521 ..     468     533 .. 0.77
   4 ?   -0.7   0.0       2.6   8.2e+02     107     132 ..     544     569 ..     535     575 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.051
                              TniB  25 eLleypkrkrmpnlllvGdsnnGKtmivekFa 56 
                                       +L+++   + ++ +ll+G++ +GKt +++  a
  gi|385806208|ref|YP_005842606.1| 213 QLFRHLGIEPPKGVLLYGPPGTGKTLLAKALA 244
                                       5777777788899*************998765 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.8
                              TniB 112 lrllrelkvrvLiiDEihnll....agsarkqreflnalksLg 150
                                        +  +e  + ++ iDEi+++     + + +  r+++++l +L+
  gi|385806208|ref|YP_005842606.1| 275 FQQAQENAPAIIFIDEIDSIApkreEVTGEVERRVVAQLLTLM 317
                                       3334445578999****99861111333444455555555555 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0079
                              TniB  33 krmpnlllvGdsnnGKtmivekFarlh 59 
                                         ++ +ll+G++ +GKtm+++  a + 
  gi|385806208|ref|YP_005842606.1| 495 RPPRGVLLFGPPGTGKTMLAKAVATES 521
                                       334789*************99877665 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 2.6
                              TniB 107 leqqvlrllrelkvrvLiiDEihnll 132
                                       + +++ r  r++ + v+ +DEi+++ 
  gi|385806208|ref|YP_005842606.1| 544 AIREIFRRARQVAPTVIFFDEIDSIT 569
                                       455667778999**********9986 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 !   11.4   0.0   0.00036      0.11      36      68 ..     227     259 ..     220     267 .. 0.88
   2 ?    3.5   0.0     0.092        29     290     327 .]     472     511 ..     428     521 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00036
                             AAA_6  36 apaGpagtGKtEtvkdLakalakqvvvfncsdq 68 
                                        ++Gp gtGKt   k La++++ ++v +n  + 
  gi|385806208|ref|YP_005842606.1| 227 LLYGPPGTGKTLLAKALANEIGAYFVAINGPEI 259
                                       679************************997665 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.092
                             AAA_6 290 ekklqleekfvekviqlyetlkvr..hgvmlvGetgsgKt 327
                                       +++l    ++  k  ++ye + vr  +gv+l G++g+gKt
  gi|385806208|ref|YP_005842606.1| 472 KQQLREAVEWPLKYPEIYEKMGVRppRGVLLFGPPGTGKT 511
                                       4556667778888889999998885568999999999987 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0    0.0053       1.7       1      25 [.     229     255 ..     229     301 .. 0.77
   2 ?    6.7   0.0      0.03       9.5       1      23 [.     503     527 ..     503     559 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0053
                                       EE-TTSSHHHHHHHHHHHHT..EEEEE CS
                            AAA_17   1 lGgPGsGKgtqceklvekyg..fthls 25 
                                       +G+PG GK+ +++ l+ ++g  f  ++
  gi|385806208|ref|YP_005842606.1| 229 YGPPGTGKTLLAKALANEIGayFVAIN 255
                                       7*****************972244445 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.03
                                       EE-TTSSHHHHHHHHHHHH..TEEE CS
                            AAA_17   1 lGgPGsGKgtqceklveky..gfth 23 
                                       +G+PG GK+ +++ ++ +   +f  
  gi|385806208|ref|YP_005842606.1| 503 FGPPGTGKTMLAKAVATESeaNFIA 527
                                       6***********9998765225544 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.017       5.5      58      79 ..     219     240 ..     188     249 .. 0.82
   2 ?   -1.9   0.0       3.7   1.2e+03     302     336 ..     307     341 ..     284     354 .. 0.68
   3 !    7.8   0.0    0.0043       1.4      58      79 ..     493     514 ..     468     522 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.017
                       AFG1_ATPase  58 svepvrglYlwGgvGrGKtylm 79 
                                         ep++g+ l+G+ G GKt l 
  gi|385806208|ref|YP_005842606.1| 219 GIEPPKGVLLYGPPGTGKTLLA 240
                                       568****************985 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.7
                       AFG1_ATPase 302 edaarRfiaLvDelYdadvklvvsaevaleelyea 336
                                       + +   + +L+D l ++++ +v+ a   +  l  a
  gi|385806208|ref|YP_005842606.1| 307 RRVVAQLLTLMDGLKERGRVVVIGATNRPDALDPA 341
                                       44445566788888888888888777766665554 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0043
                       AFG1_ATPase  58 svepvrglYlwGgvGrGKtylm 79 
                                        v+p+rg+ l G+ G GKt+l 
  gi|385806208|ref|YP_005842606.1| 493 GVRPPRGVLLFGPPGTGKTMLA 514
                                       578*****************96 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.026       8.2      47      71 ..     225     249 ..     197     258 .. 0.84
   2 ?    3.3   0.0      0.22        69     140     178 ..     258     294 ..     250     300 .. 0.82
   3 ?    4.1   0.0      0.12        39      46      76 ..     498     528 ..     483     570 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.026
                             Rad17  47 iLLisGPsGCgkstvvkvLskelgi 71 
                                        +L+ GP+G gk+   k L+ e g 
  gi|385806208|ref|YP_005842606.1| 225 GVLLYGPPGTGKTLLAKALANEIGA 249
                                       46899***************99986 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.22
                             Rad17 140 dlPnkfyrds.dalrevirkylrssealplilviteiesl 178
                                       ++ +kfy++s ++lre+ +++       p i+ i ei+s+
  gi|385806208|ref|YP_005842606.1| 258 EIMSKFYGESeQRLREIFQQAQENA---PAIIFIDEIDSI 294
                                       6779****9989*****99986544...568899999876 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.12
                             Rad17  46 riLLisGPsGCgkstvvkvLskelgiklrew 76 
                                       r +L+ GP+G gk+   k ++ e   +++  
  gi|385806208|ref|YP_005842606.1| 498 RGVLLFGPPGTGKTMLAKAVATESEANFIAV 528
                                       557899********99999998877766655 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.069        22       2      25 ..     226     249 ..     225     260 .. 0.81
   2 ?    1.7   0.1      0.67   2.1e+02      81     118 ..     267     305 ..     258     323 .. 0.74
   3 ?    6.5   0.0     0.023       7.1       2      32 ..     500     530 ..     499     565 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.069
                                       EEEE--TTSSHHHHHHHHHHHH.. CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellks 25 
                                       v++ GppG+GKt l k +++++  
  gi|385806208|ref|YP_005842606.1| 226 VLLYGPPGTGKTLLAKALANEIGA 249
                                       6788**********9999998855 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.67
                                       HHHHHHHHHHHHH.HHH-EEEE---STTGGG-HHHHHHH CS
                          NTPase_1  81 feelalealrkal.seadviviDEiGkmElkskkfkeav 118
                                        e+   e++++a+ + + +i iDEi ++  k +++  +v
  gi|385806208|ref|YP_005842606.1| 267 SEQRLREIFQQAQeNAPAIIFIDEIDSIAPKREEVTGEV 305
                                       577777888888845556*******77766666555555 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.023
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                       v++ GppG+GKt l k v+ + + + + v+G
  gi|385806208|ref|YP_005842606.1| 500 VLLFGPPGTGKTMLAKAVATESEANFIAVRG 530
                                       6788************999988776666666 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0      0.12        37       4      31 ..     225     252 ..     223     258 .. 0.87
   2 ?    0.7   0.0       1.1   3.6e+02      75      96 ..     260     284 ..     254     302 .. 0.78
   3 ?    6.1   0.0     0.026       8.1       3      30 ..     498     525 ..     496     533 .. 0.87
   4 ?   -1.3   0.0       4.7   1.5e+03      77      96 ..     536     555 ..     528     563 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.12
                                       EEEEESTTTSSHHHHHHHHHHHSTTTEE CS
                     Guanylate_kin   4 pvvlvgpsgaGksslkkaLlselpekfg 31 
                                        v l gp g+Gk  l kaL +e   +f 
  gi|385806208|ref|YP_005842606.1| 225 GVLLYGPPGTGKTLLAKALANEIGAYFV 252
                                       6899***************999888885 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.1
                                       TTEEEEEEHHHHHHHHHTTSE...E CS
                     Guanylate_kin  75 sgnlygtsveaieevlekgki...v 96 
                                        ++ yg+s +  +e+++++++   +
  gi|385806208|ref|YP_005842606.1| 260 MSKFYGESEQRLREIFQQAQEnapA 284
                                       5789************999875554 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.026
                                       SEEEEESTTTSSHHHHHHHHHHHSTTTE CS
                     Guanylate_kin   3 rpvvlvgpsgaGksslkkaLlselpekf 30 
                                       r v l gp g+Gk +l ka+ +e + +f
  gi|385806208|ref|YP_005842606.1| 498 RGVLLFGPPGTGKTMLAKAVATESEANF 525
                                       6789****************99988887 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 4.7
                                       EEEEEEHHHHHHHHHTTSEE CS
                     Guanylate_kin  77 nlygtsveaieevlekgkiv 96 
                                       +  g+s +ai+e++  +++v
  gi|385806208|ref|YP_005842606.1| 536 KWVGESEKAIREIFRRARQV 555
                                       66799**********99986 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.017       5.2      23      43 ..     226     246 ..     213     253 .. 0.86
   2 ?    6.3   0.0     0.016       4.9      23      44 ..     500     521 ..     490     550 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.017
                                       EEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC  23 valvGmgGvGKttlakqilnk 43 
                                       v l+G +G GKt lak   n+
  gi|385806208|ref|YP_005842606.1| 226 VLLYGPPGTGKTLLAKALANE 246
                                       789************998876 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.016
                                       EEEEESTTSSHHHHHHHHCCSH CS
                            NB-ARC  23 valvGmgGvGKttlakqilnks 44 
                                       v l G +G GKt lak +  +s
  gi|385806208|ref|YP_005842606.1| 500 VLLFGPPGTGKTMLAKAVATES 521
                                       6789************999874 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0     0.013       4.1       5      32 ..     227     254 ..     224     258 .. 0.91
   2 ?    5.4   0.0     0.032        10       5      31 ..     501     527 ..     498     530 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.013
                               IPT   5 lifGatttGKtaeaiklaketgapvivl 32 
                                       l++G+ +tGKt  a +la+e ga  +++
  gi|385806208|ref|YP_005842606.1| 227 LLYGPPGTGKTLLAKALANEIGAYFVAI 254
                                       89*******************9988775 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.032
                               IPT   5 lifGatttGKtaeaiklaketgapviv 31 
                                       l+fG+ +tGKt  a ++a e  a  i+
  gi|385806208|ref|YP_005842606.1| 501 LLFGPPGTGKTMLAKAVATESEANFIA 527
                                       89****************999888776 PP

>> ADSL_C  Adenylosuccinate lyase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0      0.32     1e+02      10      40 ..     385     415 ..     383     445 .. 0.71
   2 ?    8.9   0.3    0.0068       2.1      12      57 ..     663     718 ..     659     727 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.32
                                       HHHHHTH-HHHHHHHHHHHHHHHHHCHHHHH CS
                            ADSL_C  10 laLvkglgReeAyelVqeaamkaweellelL 40 
                                        a ++g +  +  +lV+eaam + ++++e  
  gi|385806208|ref|YP_005842606.1| 385 AAITHGFTGADLAALVKEAAMNTIRRFIEEK 415
                                       4555788889999***********9955543 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0068
                                       HHHTH-HHHHHHHHHHHHHHHHHC........HHHHHHT-HHHH.C.HHCHHHHHT CS
                            ADSL_C  12 LvkglgReeAyelVqeaamkawee........llelLaadpevk.k.seeeldalf 57 
                                       +++g +  +  +lV+ea m a +e        ++  L+a ++v    ++ee+++  
  gi|385806208|ref|YP_005842606.1| 663 MTEGYTGADLEALVREAVMLALREklearpveFKYFLKAMETVGpSlTREEVEKYE 718
                                       556667778899********************************669888998765 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0     0.016         5       4      27 ..     229     252 ..     226     256 .. 0.89
   2 ?    5.4   0.0     0.043        13       5      27 ..     504     526 ..     500     529 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.016
                                       E-STTSSHHHHHHHHHHHHT-EEE CS
                    Cytidylate_kin   4 DGPagsGKssvaralaeklglkyl 27 
                                        GP g+GK  +a+ala+++g+ ++
  gi|385806208|ref|YP_005842606.1| 229 YGPPGTGKTLLAKALANEIGAYFV 252
                                       6******************99775 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.043
                                       -STTSSHHHHHHHHHHHHT-EEE CS
                    Cytidylate_kin   5 GPagsGKssvaralaeklglkyl 27 
                                       GP g+GK  +a+a+a++ +++++
  gi|385806208|ref|YP_005842606.1| 504 GPPGTGKTMLAKAVATESEANFI 526
                                       9***************9999887 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.026       8.2       2      24 ..     224     246 ..     223     252 .. 0.88
   2 ?    5.1   0.0     0.055        17       4      24 ..     500     520 ..     497     524 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.026
                         PduV-EutP   2 kkilliGkvgsGKttLtqalkge 24 
                                       k +ll G+ g+GKt L++al +e
  gi|385806208|ref|YP_005842606.1| 224 KGVLLYGPPGTGKTLLAKALANE 246
                                       5699****************987 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.055
                         PduV-EutP   4 illiGkvgsGKttLtqalkge 24 
                                       +ll+G+ g+GKt L++a+  e
  gi|385806208|ref|YP_005842606.1| 500 VLLFGPPGTGKTMLAKAVATE 520
                                       89**************98765 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0     0.015       4.6       1      44 [.     232     280 ..     232     282 .. 0.68
   2 ?    4.1   0.0      0.15        46       1      22 [.     506     527 ..     506     554 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.015
                                       TTSSHHHHHHHHHHHHTSEEEEHHH..HHHHHHT...S-HHHHHHHHHH CS
                               SKI   1 mGaGKstvGkllAkklglefiDlDe..liekrtg...ksiaeifeeege 44 
                                       +G+GK+ ++k+lA+++g  f+ +    +++k  g   ++ +eif++  e
  gi|385806208|ref|YP_005842606.1| 232 PGTGKTLLAKALANEIGAYFVAINGpeIMSKFYGeseQRLREIFQQAQE 280
                                       69******************87653314455444223556666666655 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.15
                                       TTSSHHHHHHHHHHHHTSEEEE CS
                               SKI   1 mGaGKstvGkllAkklglefiD 22 
                                       +G+GK+ ++k++A + + +fi 
  gi|385806208|ref|YP_005842606.1| 506 PGTGKTMLAKAVATESEANFIA 527
                                       69**************999985 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.019       5.9     130     156 ..     224     250 ..     193     258 .. 0.83
   2 ?    4.2   0.0     0.062        20     130     152 ..     498     520 ..     364     529 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.019
                             T2SSE 130 glilvsGgTgsGKttllyallkeinks 156
                                       + +l+ G+ g+GKt l+ al +ei ++
  gi|385806208|ref|YP_005842606.1| 224 KGVLLYGPPGTGKTLLAKALANEIGAY 250
                                       568999***************999876 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.062
                             T2SSE 130 glilvsGgTgsGKttllyallke 152
                                         +l+ G+ g+GKt l+ a+ +e
  gi|385806208|ref|YP_005842606.1| 498 RGVLLFGPPGTGKTMLAKAVATE 520
                                       457899**********9998776 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.076        24      21      39 ..     223     240 ..     214     245 .. 0.77
   2 ?    5.5   0.0     0.046        14      21      42 ..     497     517 ..     488     519 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.076
                            AAA_29  21 lkgatlltGpsGsGKSTll 39 
                                       +kg +ll Gp G+GK+ l 
  gi|385806208|ref|YP_005842606.1| 223 PKG-VLLYGPPGTGKTLLA 240
                                       466.9**********8765 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.046
                            AAA_29  21 lkgatlltGpsGsGKSTllDAi 42 
                                       ++g +ll Gp G+GK+ l  A+
  gi|385806208|ref|YP_005842606.1| 497 PRG-VLLFGPPGTGKTMLAKAV 517
                                       456.9**********9887666 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 ?    3.5   0.0      0.15        47       4      23 ..     227     246 ..     225     263 .. 0.78
   2 ?    6.1   0.0     0.023       7.3       4      31 ..     501     528 ..     499     535 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.15
                                       EEEESTTCCHHHHHHHHHCT CS
                              cobW   4 vltGflGsGKTtLlnhllen 23 
                                       +l G++G+GKT L ++l ++
  gi|385806208|ref|YP_005842606.1| 227 LLYGPPGTGKTLLAKALANE 246
                                       688*******9887777655 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.023
                                       EEEESTTCCHHHHHHHHHCT--SS-EEE CS
                              cobW   4 vltGflGsGKTtLlnhllenraglklav 31 
                                       +l G++G+GKT+L +++ ++++ + +av
  gi|385806208|ref|YP_005842606.1| 501 LLFGPPGTGKTMLAKAVATESEANFIAV 528
                                       688************9999988888887 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 ?    2.8   0.0      0.26        80       5      71 ..     230     291 ..     226     295 .. 0.67
   2 ?    6.8   0.0     0.016         5       4      71 ..     503     565 ..     500     571 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.26
                   Viral_helicase1   5 GvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                       G pG GK+ l + l+++    +++++   e+ ++   +++++  + ++++++++       i+++DE+
  gi|385806208|ref|YP_005842606.1| 230 GPPGTGKTLLAKALANEIgAYFVAING-PEIMSKFYGESEQRLREIFQQAQENAP-----AIIFIDEI 291
                                       78*************996655555554.455555545566665666666655543.....47888886 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.016
                   Viral_helicase1   4 hGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                        G pG GK+ l + ++ +s  ++ ++r   e+l++++ ++++   + ++ + +   ++    ++++DE+
  gi|385806208|ref|YP_005842606.1| 503 FGPPGTGKTMLAKAVATESeANFIAVRG-PEVLSKWVGESEKAIREIFRRARQV--AP---TVIFFDEI 565
                                       588*************999988888888.9*******77777766666654443..22...37888886 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.049        15       4      27 ..     226     249 ..     225     321 .. 0.74
   2 ?    4.0   0.0     0.088        28       4      27 ..     500     523 ..     499     554 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.049
                                       EEEE--TTSSHHHHHHHHHHHHHH CS
                             KTI12   4 vvltGlPssGKstrakeLakalee 27 
                                       v+l G P +GK+ +ak La+++ +
  gi|385806208|ref|YP_005842606.1| 226 VLLYGPPGTGKTLLAKALANEIGA 249
                                       899***************998765 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.088
                                       EEEE--TTSSHHHHHHHHHHHHHH CS
                             KTI12   4 vvltGlPssGKstrakeLakalee 27 
                                       v+l+G P +GK+ +ak +a++ e+
  gi|385806208|ref|YP_005842606.1| 500 VLLFGPPGTGKTMLAKAVATESEA 523
                                       89**************99877655 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.31        96      19      44 ..     222     247 ..     211     250 .. 0.86
   2 ?    5.3   0.0     0.032        10     167     196 ..     277     305 ..     257     312 .. 0.73
   3 ?   -1.3   0.0       3.1   9.8e+02     171     187 ..     554     570 ..     491     574 .. 0.65

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.31
                        KAP_NTPase  19 tpivvgLygkWGsGKssllnkledel 44 
                                       +p  v Lyg+ G+GK+ l + l +e+
  gi|385806208|ref|YP_005842606.1| 222 PPKGVLLYGPPGTGKTLLAKALANEI 247
                                       566799*************9999886 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.032
                        KAP_NTPase 167 tLdalqkrlVvviDdLDrceteevlqllea 196
                                         + ++ + +++iD++D++ +++   + e+
  gi|385806208|ref|YP_005842606.1| 277 QAQ-ENAPAIIFIDEIDSIAPKREEVTGEV 305
                                       333.58999**********99987776666 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 3.1
                        KAP_NTPase 171 lqkrlVvviDdLDrcet 187
                                       +  + V++ D++D++++
  gi|385806208|ref|YP_005842606.1| 554 QVAPTVIFFDEIDSITP 570
                                       45566777777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (729 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                       102  (0.00568911); 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):              57  [number of targets reported over threshold]
# CPU time: 0.98u 0.34s 00:00:01.32 Elapsed: 00:00:00.54
# Mc/sec: 4032.09
//
Query:       gi|385806209|ref|YP_005842607.1|  [L=40]
Description: hypothetical protein FFONT_1167 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       140  (0.00780858); expected 358.6 (0.02)
Passed bias filter:                      115  (0.00641419); 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: 0.45u 0.32s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 245.51
//
Query:       gi|385806210|ref|YP_005842608.1|  [L=826]
Description: putative P-loop ATPase fused to an acetyltransferase [Fervidicoccus fontis Kam940]
Scores for complete 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  173.1   0.0      9e-51  172.2   0.0    1.5  1  Helicase_RecD    Helicase
    6.8e-45  153.2   0.1      1e-31  110.1   0.0    2.7  3  GNAT_acetyltr_2  GNAT acetyltransferase 2
    1.3e-29  101.9   0.0    1.2e-28   98.8   0.0    2.8  2  DUF1726          Domain of unknown function (DUF1726)
    5.4e-09   36.1   0.7    1.6e-08   34.6   0.7    1.8  1  tRNA_bind_2      Possible tRNA binding domain
     0.0011   18.8   0.0     0.0022   17.8   0.0    1.5  1  AAA_30           AAA domain
     0.0014   18.9   0.1     0.0086   16.3   0.0    2.2  2  Acetyltransf_1   Acetyltransferase (GNAT) family
  ------ inclusion threshold ------
      0.051   14.0   0.1       0.72   10.3   0.0    2.7  3  Acetyltransf_7   Acetyltransferase (GNAT) domain
       0.14   12.5   0.1        1.4    9.3   0.1    2.5  2  AAA_19           AAA domain


Domain annotation for each model (and alignments):
>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.2   0.0     4e-54     9e-51       1     177 []     284     463 ..     284     463 .. 0.97

  Alignments for each domain:
  == domain 1  score: 172.2 bits;  conditional E-value: 4e-54
                     Helicase_RecD   1 vltAdRGRGKSaalGlalaaliaegk.....snilvtapskenvktlfeflakglealglkeeekkkkaekaelrvr 72 
                                       v+t++RGRGKS++lG+ + al+++ +     ++ilvtap+ +nv++lf+ +  + +++gl+ +  kk +  +e++ +
  gi|385806210|ref|YP_005842608.1| 284 VITSNRGRGKSSVLGIGVIALANHMSqfkhkVRILVTAPEITNVQSLFDLAYLSAKSIGLNVKLLKKGGMIIEIQGQ 360
                                       79**************9999998877788999******************************9999****9****** PP

                     Helicase_RecD  73 kqrieyiapdellklkeqadllvvDEAAaiplpllkkllekfkrvvlatTvhGYEGtGrgfslkflkqlkkekkrel 149
                                       + +iey++p ++ k k   d++vvDEA+ i +pll k+l+++kr++++ T+hGYEG+Grgfs++fl  l+k+ + el
  gi|385806210|ref|YP_005842608.1| 361 NFSIEYWEPINIPKIKG--DVVVVDEASGISVPLLLKILKTHKRLIFSATIHGYEGAGRGFSVRFLGSLRKDPNVEL 435
                                       **************875..********************************************************** PP

                     Helicase_RecD 150 releleepiRyaegdplEkwlndlLlLd 177
                                       + +e+++piRy egdp+Ekwl+++LlLd
  gi|385806210|ref|YP_005842608.1| 436 STCEMKTPIRYGEGDPIEKWLYRALLLD 463
                                       **************************97 PP

>> GNAT_acetyltr_2  GNAT acetyltransferase 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0         3   6.8e+03     160     187 ..     107     134 ..      83     136 .. 0.49
   2 !  110.1   0.0   4.5e-35     1e-31       2     125 ..     504     621 ..     503     624 .. 0.92
   3 !   41.9   0.0   3.3e-14   7.5e-11     174     227 .]     619     672 ..     617     672 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 3
                   GNAT_acetyltr_2 160 kprkelpplllklseekpekldylgvsf 187
                                       k +++  + + +  ++  ++  ylg+s+
  gi|385806210|ref|YP_005842608.1| 107 KMARKKLQNIERNIDVYEKSDRYLGTSY 134
                                       2223333333334444445556888888 PP

  == domain 2  score: 110.1 bits;  conditional E-value: 4.5e-35
                   GNAT_acetyltr_2   2 lvallvssHYknsPnDLqllsDaPahklfvLlapkkekkklpevlcvvqvalEGkiskesvknslsrgkrasGdlip 78 
                                       l++++v +HY+n+P+DL++++DaP+h + + + + +      +++c +q+a+EG +++++v+    rg++ +G++ip
  gi|385806210|ref|YP_005842608.1| 504 LFGIFVLAHYRNQPDDLAMMADAPHHMIRAVMIKGT-----NKIVCSLQIAVEGGLDSQTVDTL-LRGNKIQGNIIP 574
                                       789**************************9998554.....69***************988765.5677******** PP

                   GNAT_acetyltr_2  79 wtlsqqfqdeefaslsGaRivRiAvhpelqkmGYGsralellekyye 125
                                       + + ++ +  e++ l G RivRiA+hpe+q++G Gs ale+l ++  
  gi|385806210|ref|YP_005842608.1| 575 DRIIKHLRIWEMGWLRGYRIVRIATHPEVQNLGIGSFALERLYEEAR 621
                                       ******************************************98765 PP

  == domain 3  score: 41.9 bits;  conditional E-value: 3.3e-14
                   GNAT_acetyltr_2 174 eekpekldylgvsfGltseLlkFWkragfspvylrqtaneltGEhsaimlrsle 227
                                       e++ ++ d++g +fG   +Ll+FW +++f pv+++  +n ++GE+++i++r+++
  gi|385806210|ref|YP_005842608.1| 619 EARQKSFDWIGSGFGANYSLLNFWIKNKFIPVHISPDKNPISGEYTVIVIRPIN 672
                                       6678899********************************************985 PP

>> DUF1726  Domain of unknown function (DUF1726)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.8   0.0   5.5e-32   1.2e-28       1      93 []     123     214 ..     123     214 .. 0.98
   2 ?   -2.2   0.0       1.9   4.2e+03      21      42 ..     334     355 ..     330     359 .. 0.86

  Alignments for each domain:
  == domain 1  score: 98.8 bits;  conditional E-value: 5.5e-32
                           DUF1726   1 ykesekvLGqtydllvldlfealtPnalgrlvetVrGGGliilllppleelkqlytdfhkklvveplteevkkrfnk 77 
                                       y++s+++LG++yd+l+ldl+++l+Pn++g+lve+V+GGGlii+l+p+le+++ ++t+f++klvv+ ++ e ++ f++
  gi|385806210|ref|YP_005842608.1| 123 YEKSDRYLGTSYDVLILDLTNDLRPNDIGKLVEIVNGGGLIIFLTPDLEKWDRWMTAFKQKLVVPGFN-EPRHIFIR 198
                                       89*****************************************************************6.******** PP

                           DUF1726  78 rfirklkehegilivd 93 
                                       +f++++ ++++++++d
  gi|385806210|ref|YP_005842608.1| 199 WFKETILDSDSTYVYD 214
                                       **********999987 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.9
                           DUF1726  21 ealtPnalgrlvetVrGGGlii 42 
                                         l++  +g  v + + GG+ii
  gi|385806210|ref|YP_005842608.1| 334 AYLSAKSIGLNVKLLKKGGMII 355
                                       56888999999*********98 PP

>> tRNA_bind_2  Possible tRNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.7     7e-12   1.6e-08      59     148 ..     722     811 ..     686     823 .. 0.84

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 7e-12
                                       ---HHHHHHHHHHHHS---HHHHHSSSSHHHHHHHH--SSTTTS-SSSSSSHHHHHHTT---HHHHHHHHT--SSHH CS
                       tRNA_bind_2  59 llspfDlkRLesYannllDYhvilDllptlaklyFsgrlkeevkLsavqsaiLlaiGLQrksvddlekeLnlpsnQv 135
                                        l p D+ RL  Y    + Y+ i D+  +la  yF g +++ v+L++ ++ iLla  LQ k+ ++++k L   +  +
  gi|385806210|ref|YP_005842608.1| 722 KLHPIDVDRLWIYVYGPMTYEAISDVFLDLAIYYFLGDMEKLVELNNEEKIILLAKVLQGKDWSEMSKMLRRRRIDL 798
                                       589*******************************************************************9999999 PP

                                       HHHHHHHHHHHHH CS
                       tRNA_bind_2 136 lalFvkiirkvsk 148
                                       + ++ +i +++ +
  gi|385806210|ref|YP_005842608.1| 799 MLILKDIAKRMLN 811
                                       9999999988754 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   9.7e-07    0.0022      15     111 ..     277     399 ..     258     410 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 9.7e-07
                            AAA_30  15 tsgdrvavltGpAGtGKttalkalreaweaag......grviglAptgkaAkvLaeelgieastiakllkrlk.... 81 
                                       t++++v v+t   G GK+ +l+  + a++++        r+++ Ap+ +  + L + + + a++i   +k lk    
  gi|385806210|ref|YP_005842608.1| 277 TKKKKVLVITSNRGRGKSSVLGIGVIALANHMsqfkhkVRILVTAPEITNVQSLFDLAYLSAKSIGLNVKLLKkggm 353
                                       466789***************977666666633678889999*************9888999999888777778889 PP

                            AAA_30  82 ....................grarlepgtllivDEagmvdtkqlaallka 111
                                                           +     +g++++vDEa+ ++   l ++lk 
  gi|385806210|ref|YP_005842608.1| 354 iieiqgqnfsieywepinipK----IKGDVVVVDEASGISVPLLLKILKT 399
                                       999**********98875532....567*************999999986 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.2   2.8e+03      41      55 ..      54      68 ..      15      93 .. 0.63
   2 !   16.3   0.0   3.8e-06    0.0086      43      92 ..     576     623 ..     557     629 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.2
                                      TTEEEEEEEEEEEET CS
                    Acetyltransf_1 41 dgeliGfisllkipd 55
                                      d++  Gfis+++ ++
  gi|385806210|ref|YP_005842608.1| 54 DEKKQGFISGYITYH 68
                                      366778888888888 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 3.8e-06
                                       EEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHT CS
                    Acetyltransf_1  43 eliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeeraree 92 
                                       ++i +++++   +   + + i ++a +pe ++ G+Gs  le l e+ar++
  gi|385806210|ref|YP_005842608.1| 576 RIIKHLRIWEMGW--LRGYRIVRIATHPEVQNLGIGSFALERLYEEARQK 623
                                       5666667777777..4788999**************************97 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       7.3   1.6e+04      28      42 ..     280     294 ..     260     315 .. 0.70
   2 ?   -0.5   0.0      0.76   1.7e+03      29      39 ..     502     516 ..     472     516 .. 0.67
   3 ?   10.3   0.0   0.00032      0.72      24      47 ..     587     614 ..     561     648 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 7.3
                                       EEEEE-GGGTTSSHH CS
                    Acetyltransf_7  28 trlaVdpeyrgkGiG 42 
                                       +++ V ++ rg+G  
  gi|385806210|ref|YP_005842608.1| 280 KKVLVITSNRGRGKS 294
                                       347777777777754 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.76
                                       E....EEE-GGGTTS CS
                    Acetyltransf_7  29 r....laVdpeyrgk 39 
                                       r    ++V+ +yr++
  gi|385806210|ref|YP_005842608.1| 502 RqlfgIFVLAHYRNQ 516
                                       244459*******98 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00032
                                       S....TCTEEEEE-GGGTTSSHHHHHHH CS
                    Acetyltransf_7  24 d....aeitrlaVdpeyrgkGiGraLle 47 
                                       +    + i r+a++pe ++ GiG+  le
  gi|385806210|ref|YP_005842608.1| 587 GwlrgYRIVRIATHPEVQNLGIGSFALE 614
                                       2444356778*************98776 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.87   1.9e+03      71     126 ..     101     158 ..      26     166 .. 0.57
   2 ?    9.3   0.1   0.00062       1.4       8     125 ..     278     400 ..     271     405 .. 0.63

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.87
                            AAA_19  71 TiHrlalldfddlltealelle........eaeeekklqeee.llivDEfqdvd.elqyrLlkall 126
                                       T+ ++        +++a + l+        ++++++ l   + +li D + d+    + +L++ + 
  gi|385806210|ref|YP_005842608.1| 101 TFRQF--------MKMARKKLQniernidvYEKSDRYLGTSYdVLILDLTNDLRpNDIGKLVEIVN 158
                                       22222........22222222233355667667777777777799999988888777777776665 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00062
                            AAA_19   8 lkekvllvtaGpGtGKTrvlk.hivallvelggvkp.eeillvaftgrAakelrerlaalgaeatTiHrlal..... 77 
                                        k+kvl++t   G GK+ vl  +++al++++ + k   +il+ a+    ++ l +      ++a+ i    +     
  gi|385806210|ref|YP_005842608.1| 278 KKKKVLVITSNRGRGKSSVLGiGVIALANHMSQFKHkVRILVTAPEITNVQSLFDLA---YLSAKSIGLN-Vkllkk 350
                                       578999999999****99996245566555555543267888888888888888755...4455555411.111222 PP

                            AAA_19  78 ....ldfddlltealelle.........eaeeekklqeeellivDEfqdvd.elqyrLlkal 125
                                           +++           +         e  +  k+ ++++++vDE++ ++ +l  ++lk+ 
  gi|385806210|ref|YP_005842608.1| 351 ggmiIEI-----------QgqnfsieywEPINIPKI-KGDVVVVDEASGISvPLLLKILKTH 400
                                       2223222...........133344444422334566.889***********99999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (826 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1044  (0.0582297); expected 358.6 (0.02)
Passed bias filter:                      678  (0.0378158); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.81u 0.34s 00:00:01.15 Elapsed: 00:00:00.51
# Mc/sec: 4848.08
//
Query:       gi|385806211|ref|YP_005842609.1|  [L=340]
Description: Threonine synthase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-48  164.9   0.0    3.4e-48  164.6   0.0    1.0  1  PALP            Pyridoxal-phosphate dependent enzyme
    0.00018   21.6   1.3    0.00035   20.6   1.3    1.5  1  Zn-ribbon_8     Zinc ribbon domain
    0.00078   19.4   0.1       0.62   10.1   0.1    2.4  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
     0.0041   17.1   7.3     0.0046   17.0   3.6    2.2  2  Rubredoxin      Rubredoxin
     0.0048   16.9   0.4       0.01   15.8   0.4    1.5  1  HypA            Hydrogenase/urease nickel incorporation, meta
     0.0077   16.2   0.4      0.014   15.4   0.4    1.3  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.013   14.9   5.2      0.041   13.3   5.2    1.8  1  zf-ribbon_3     zinc-ribbon domain
      0.028   14.4   0.5      0.059   13.3   0.5    1.5  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.04   13.5   2.4        0.3   10.7   0.3    2.3  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
      0.053   13.4   0.1        0.1   12.5   0.1    1.4  1  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)
      0.074   13.0   0.3       0.14   12.1   0.3    1.4  1  zinc-ribbons_6  zinc-ribbons
      0.076   12.7   0.4       0.16   11.7   0.4    1.5  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
      0.082   12.8   0.4       0.18   11.8   0.4    1.5  1  Prok-RING_1     Prokaryotic RING finger family 1
       0.12   11.9   6.0        1.5    8.4   0.1    3.0  3  TF_Zn_Ribbon    TFIIB zinc-binding
       0.12   12.4   1.2       0.28   11.2   1.2    1.7  1  ADK_lid         Adenylate kinase, active site lid
       0.12   13.2   2.0        6.5    7.9   0.2    2.5  2  zf-C2H2_4       C2H2-type zinc finger
       0.15   12.7   0.4       0.31   11.7   0.4    1.4  1  FYDLN_acid      Protein of unknown function (FYDLN_acid)
       0.19   11.8   1.0        4.7    7.4   1.7    2.7  2  zf-Sec23_Sec24  Sec23/Sec24 zinc finger
       0.19   12.2   1.8        5.1    7.8   0.2    2.5  2  zf-C2H2         Zinc finger, C2H2 type
       0.26   11.6   2.7        7.5    6.9   0.1    2.3  2  zf-Di19         Drought induced 19 protein (Di19), zinc-bindi
       0.27   11.0   8.0        2.3    8.0   7.2    2.3  2  zinc_ribbon_2   zinc-ribbon domain
       0.34   10.9   3.6         17    5.5   4.5    2.3  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
       0.49   10.4   5.6       0.22   11.5   0.8    2.4  2  DUF1610         Domain of unknown function (DUF1610)
       0.92    9.6   2.4         23    5.1   0.1    2.5  2  CpXC            CpXC protein
       0.95    9.5   2.9        2.9    8.0   0.5    2.2  2  zf-C2H2_6       C2H2-type zinc finger
        1.3    8.8   3.8         14    5.5   3.8    2.3  1  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
        2.7    8.6   4.8         32    5.2   0.3    2.4  2  zf-H2C2_2       Zinc-finger double 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 !  164.6   0.0     5e-51   3.4e-48       4     294 .]      46     331 ..      44     331 .. 0.89

  Alignments for each domain:
  == domain 1  score: 164.6 bits;  conditional E-value: 5e-51
                                       CSSS--EEEECCTCCCCCCE.EEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT- CS
                              PALP   4 gigpTPlvrlprlskelgvp.lflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGl 79 
                                       g+g+TPlv+      ++g++ lf+KlE+lnptgSfKdRg +  +++  ++ +    +e ssGN+g+++A +a++ + 
  gi|385806211|ref|YP_005842609.1|  46 GEGNTPLVKE-----KIGGKeLFFKLEYLNPTGSFKDRGTSATVQYFLKK-KCSSFIEDSSGNTGISTAVYARRVNR 116
                                       799****655.....567777*************************8888.89************************ PP

                                       EEEEEEETTS-HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHH.HHTT CS
                              PALP  80 kvtivvpadaspekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEil.eqlg 155
                                       +++i+ p++  ++k++ll llGa+++ +++  +ea ++a ++a++ e+a ++ +  np    g++ ++ E+l + +g
  gi|385806211|ref|YP_005842609.1| 117 ESYIFSPKTIAESKKKLLNLLGAKLTITET-REEAFNLAVKMAKKYENACYIGHMVNPIFNYGMSFLVEEVLkKTIG 192
                                       ****************************55.9******99*****99999999999***************955555 PP

                                       TTEEEEEEE-SSSHHHHHHHHHHHH....HSTT.-EEEEEEECTTCGGTTCCS..S.SS..B....SSS.CCSTCS. CS
                              PALP 156 gkpdavvvpvGgGgliaGiaaglke....rrpd.vrvigvepegsdalarslragrrvtvpvs...dtiadglavg. 223
                                         ++ v+vp+ +G l+ Gi  g+k     ++   +++ +v+p++   l + ++  ++     s   +  ad+l v+ 
  gi|385806211|ref|YP_005842609.1| 193 --ITDVIVPLASGTLLLGIFEGFKRnidkNG-GlPKIWAVQPTRTGYLRGKVKIVHE-----SqgrSDSADALVVSn 261
                                       ..777*******************9766444.26*********99999999933333.....233477777777776 PP

                                       .CGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHCCTTCEEEEEEE-B CS
                              PALP 224 .spselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaalklreagelkegdrvvviltg 294
                                        +  ++ + ++ ++ + ++ v+de++ e+mr l+   g +vepss ++  a +l++++el ++ ++++ ltg
  gi|385806211|ref|YP_005842609.1| 262 pARINDIINAINETKGGGIIVDDEDIKEGMRNLY-SRGFIVEPSSSVVWKAFELLNREELIGS-KILIPLTG 331
                                       6889999***************************.99***************99999999999.89999997 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   1.3   5.3e-07   0.00035       4      35 ..       4      30 ..       1      36 [. 0.82

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 5.3e-07
                       Zn-ribbon_8  4 YeYrCeeCghefevlqsisdaplta.CPeCgse 35
                                      Y + C +Cg+efe      dap+   CP Cgs 
  gi|385806211|ref|YP_005842609.1|  4 YTFICPKCGKEFE------DAPKDWkCPYCGSS 30
                                      99***********......5666666*****94 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.1   0.00094      0.62      19      30 .]       5      16 ..       2      16 .. 0.87
   2 !    7.0   0.0    0.0083       5.5       4      15 ..      23      34 ..      19      53 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00094
                    PhnA_Zn_Ribbon 19 llvCpeCahEwe 30
                                       ++Cp+C+ E+e
  gi|385806211|ref|YP_005842609.1|  5 TFICPKCGKEFE 16
                                      59********97 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0083
                    PhnA_Zn_Ribbon  4 kCplCaSeytYe 15
                                      kCp C+S+ +++
  gi|385806211|ref|YP_005842609.1| 23 KCPYCGSSLNLA 34
                                      9*******9995 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.5       0.2   1.3e+02      34      41 ..       5      12 ..       4      14 .. 0.83
   2 !   17.0   3.6   6.9e-06    0.0046      25      42 ..      12      29 ..      10      33 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.2
                                      T-BBTTTB CS
                        Rubredoxin 34 dWvCPdCg 41
                                      +++CP+Cg
  gi|385806211|ref|YP_005842609.1|  5 TFICPKCG 12
                                      689****8 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 6.9e-06
                                      T--GGGS-TT-BBTTTB- CS
                        Rubredoxin 25 gTkFedlPddWvCPdCgv 42
                                      g +Fed P+dW+CP Cg 
  gi|385806211|ref|YP_005842609.1| 12 GKEFEDAPKDWKCPYCGS 29
                                      779*************96 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.4   1.6e-05      0.01      70      95 ..       5      30 ..       2      37 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.6e-05
                                      EEEETTTS-EEECHHHHHS-TTTSSS CS
                              HypA 70 kvrCreCgkefeleekalrCpkCgsa 95
                                      ++ C +Cgkefe + k+ +Cp Cgs+
  gi|385806211|ref|YP_005842609.1|  5 TFICPKCGKEFEDAPKDWKCPYCGSS 30
                                      689*********8877899*****95 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.4   2.1e-05     0.014      15      39 ..       8      32 ..       4      40 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.1e-05
                               DZR 15 CseCgtklkavaaedrCpsCgekvd 39
                                      C++Cg++ + +++  +Cp Cg++++
  gi|385806211|ref|YP_005842609.1|  8 CPKCGKEFEDAPKDWKCPYCGSSLN 32
                                      7777777776666777777776654 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   5.2   6.1e-05     0.041       3      24 ..       6      29 ..       5      31 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.1e-05
                       zf-ribbon_3  3 vrCPnCGa.p.lssddnvCpyCGt 24
                                        CP+CG+    ++ d +CpyCG+
  gi|385806211|ref|YP_005842609.1|  6 FICPKCGKeFeDAPKDWKCPYCGS 29
                                      57********8889999******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 ?   13.3   0.5   8.9e-05     0.059      30      56 ..       7      31 ..       5      33 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.9e-05
                    OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgfea 56
                                       C++Cg++ ++  +++ +kCp Cg ++
  gi|385806211|ref|YP_005842609.1|  7 ICPKCGKEFED--APKDWKCPYCGSSL 31
                                      5**********..***********876 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3   0.00045       0.3       2      14 ..       5      17 ..       4      21 .. 0.88
   2 ?    2.5   0.1      0.17   1.1e+02       2      16 ..      21      35 ..      20      37 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00045
                            zf_UBZ  2 tylCerCgkeipe 14
                                      t++C++Cgke+++
  gi|385806211|ref|YP_005842609.1|  5 TFICPKCGKEFED 17
                                      89********986 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.17
                            zf_UBZ  2 tylCerCgkeipese 16
                                       + C+ Cg+++  ++
  gi|385806211|ref|YP_005842609.1| 21 DWKCPYCGSSLNLAK 35
                                      589*****9987765 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00015       0.1      21      46 ..       3      30 ..       3      33 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00015
                                      EEEEE-HHHHHHHHH..TT-B-TTT--B CS
                        zf-C3HC4_3 21 gHlvlCeeCaekllk..rkkkCpiCrrp 46
                                      g++++C +C +++++  ++ kCp+C ++
  gi|385806211|ref|YP_005842609.1|  3 GYTFICPKCGKEFEDapKDWKCPYCGSS 30
                                      56789********999*********876 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.3   0.00022      0.14       2      28 ..       7      33 ..       4      38 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00022
                                      --SSS-S--EE-SSEEE-TTT--EEEE CS
                    zinc-ribbons_6  2 kCpeCqqelekrgeqyhCeaCqedlkk 28
                                      +Cp+C +e e   +  +C  C ++l+ 
  gi|385806211|ref|YP_005842609.1|  7 ICPKCGKEFEDAPKDWKCPYCGSSLNL 33
                                      599999999988889999999887654 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.4   0.00024      0.16       2      25 ..       7      29 ..       6      31 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00024
                                      B-SSS--B----SSS----SSS-- CS
                    DNA_RNApol_7kD  2 iCgeCgaevslkkgdpiRCkeCGh 25
                                      iC +Cg+e+++ ++d  +C +CG+
  gi|385806211|ref|YP_005842609.1|  7 ICPKCGKEFEDAPKDW-KCPYCGS 29
                                      9*************86.******6 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 ?   11.8   0.4   0.00026      0.18       6      29 ..       7      30 ..       3      33 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00026
                       Prok-RING_1  6 kCpvCgkelkeedDiVvCpeCgtp 29
                                      +Cp Cgke++++     Cp Cg++
  gi|385806211|ref|YP_005842609.1|  7 ICPKCGKEFEDAPKDWKCPYCGSS 30
                                      7***********77789*****86 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1    0.0022       1.5      19      32 ..       5      18 ..       1      21 [. 0.77
   2 ?    5.9   0.2     0.014       9.1       2       9 ..      23      30 ..      22      37 .. 0.88
   3 ?   -3.0   0.2       8.3   5.5e+03      27      37 ..     280     290 ..     279     290 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0022
                                      CEEESSSSBEEEEC CS
                      TF_Zn_Ribbon 19 elvCtdCGlVledn 32
                                      +++C++CG   ed 
  gi|385806211|ref|YP_005842609.1|  5 TFICPKCGKEFEDA 18
                                      68999999888875 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.014
                                      EETTTTCE CS
                      TF_Zn_Ribbon  2 kCPnCgst 9 
                                      kCP+Cgs+
  gi|385806211|ref|YP_005842609.1| 23 KCPYCGSS 30
                                      8*****96 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 8.3
                                       BEEEECCCCCC CS
                      TF_Zn_Ribbon  27 lVlednsideg 37 
                                        +++d++i+eg
  gi|385806211|ref|YP_005842609.1| 280 IIVDDEDIKEG 290
                                       57999999986 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 ?   11.2   1.2   0.00042      0.28       3      31 ..       7      31 ..       6      38 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00042
                                      E-TTT--EEETTTB--SSTTB-TTT--.- CS
                           ADK_lid  3 vCpkCGrsYhvvfnpPkveglCDkCGepL 31
                                      +CpkCG+ +      P ++ +C  CG+ L
  gi|385806211|ref|YP_005842609.1|  7 ICPKCGKEFE---DAP-KDWKCPYCGSSL 31
                                      8*********...446.7********987 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.2    0.0098       6.5       1      12 [.       6      17 ..       6      20 .. 0.88
   2 ?    4.5   0.1      0.12        81       1       9 [.      22      30 ..      22      36 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0098
                         zf-C2H2_4  1 fkCpiCgksFss 12
                                      f+Cp Cgk F +
  gi|385806211|ref|YP_005842609.1|  6 FICPKCGKEFED 17
                                      89********76 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.12
                         zf-C2H2_4  1 fkCpiCgks 9 
                                      +kCp+Cg s
  gi|385806211|ref|YP_005842609.1| 22 WKCPYCGSS 30
                                      59****865 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 ?   11.7   0.4   0.00047      0.31      11      41 ..       7      36 ..       3      51 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00047
                        FYDLN_acid 11 iCpscgakFYDLnkdPivcpkcgeefepeev 41
                                      iCp+cg+ F D  kd   cp+cg++ ++++ 
  gi|385806211|ref|YP_005842609.1|  7 ICPKCGKEFEDAPKD-WKCPYCGSSLNLAKK 36
                                      8**********9999.79*****99887765 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 ?    7.4   1.7     0.007       4.7      10      32 ..       6      30 ..       1      35 [. 0.74
   2 ?   -1.4   0.0       3.9   2.6e+03      10      21 ..      68      79 ..      67      83 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.007
                    zf-Sec23_Sec24 10 ylNpfc..kidfggkrwiCnfCnhk 32
                                      +++p c  ++ ++ k w+C+ C+++
  gi|385806211|ref|YP_005842609.1|  6 FICPKCgkEFEDAPKDWKCPYCGSS 30
                                      6666663346677899******987 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.9
                    zf-Sec23_Sec24 10 ylNpfckidfgg 21
                                      ylNp  ++ ++g
  gi|385806211|ref|YP_005842609.1| 68 YLNPTGSFKDRG 79
                                      9***99998877 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.2    0.0077       5.1       1      12 [.       6      17 ..       6      19 .. 0.88
   2 ?    3.5   0.1      0.17   1.1e+02       2       7 ..      23      28 ..      22      43 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0077
                                      EEETTTTEEESS CS
                           zf-C2H2  1 ykCpdCgksFkr 12
                                      + Cp+Cgk F +
  gi|385806211|ref|YP_005842609.1|  6 FICPKCGKEFED 17
                                      78*******975 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.17
                                      EETTTT CS
                           zf-C2H2  2 kCpdCg 7 
                                      kCp+Cg
  gi|385806211|ref|YP_005842609.1| 23 KCPYCG 28
                                      8****9 PP

>> zf-Di19  Drought induced 19 protein (Di19), zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.7     0.064        42       2      14 ..       5      17 ..       4      19 .. 0.87
   2 ?    6.9   0.1     0.011       7.5       3      13 ..      22      32 ..      20      36 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.064
                           zf-Di19  2 sftCPyCgkeltv 14
                                      +f CP Cgke+++
  gi|385806211|ref|YP_005842609.1|  5 TFICPKCGKEFED 17
                                      699******9987 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.011
                           zf-Di19  3 ftCPyCgkelt 13
                                       +CPyCg +l+
  gi|385806211|ref|YP_005842609.1| 22 WKCPYCGSSLN 32
                                      69****98765 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   1.8    0.0071       4.7       2       8 ..       8      14 ..       2      15 .. 0.58
   2 ?    8.0   7.2    0.0035       2.3       2      23 .]       8      31 ..       7      31 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0071
                     zinc_ribbon_2  2 CpnCGae 8 
                                      Cp+CG+e
  gi|385806211|ref|YP_005842609.1|  8 CPKCGKE 14
                                      5555554 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0035
                     zinc_ribbon_2  2 CpnCGaelqdnakF..CpyCGtpl 23
                                      Cp+CG+e +d  k   CpyCG+ l
  gi|385806211|ref|YP_005842609.1|  8 CPKCGKEFEDAPKDwkCPYCGSSL 31
                                      *******977666677*****876 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 ?    5.5   4.5     0.026        17      18      44 ..       5      28 ..       2      30 .. 0.71
   2 ?    5.0   0.3     0.037        25      20      27 ..      23      30 ..      19      42 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.026
                     Zn_Tnp_IS1595 18 gfvCPhCgsrkayrikt.rglfqCkeCr 44
                                      +f+CP+Cg++    +++ ++ ++C  C+
  gi|385806211|ref|YP_005842609.1|  5 TFICPKCGKE----FEDaPKDWKCPYCG 28
                                      489*****43....33337889998886 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.037
                     Zn_Tnp_IS1595 20 vCPhCgsr 27
                                       CP+Cgs+
  gi|385806211|ref|YP_005842609.1| 23 KCPYCGSS 30
                                      6*****87 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.8   0.00033      0.22      16      24 .]       5      13 ..       2      13 .. 0.86
   2 ?    0.4   0.3      0.97   6.4e+02      19      23 ..      24      28 ..      22      29 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00033
                           DUF1610 16 vFpCPNCGE 24
                                       F+CP+CG+
  gi|385806211|ref|YP_005842609.1|  5 TFICPKCGK 13
                                      5*******8 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.97
                           DUF1610 19 CPNCG 23
                                      CP CG
  gi|385806211|ref|YP_005842609.1| 24 CPYCG 28
                                      ****9 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.3      0.07        47      38      47 ..       6      15 ..       3      20 .. 0.74
   2 ?    5.1   0.1     0.034        23      36      51 ..      20      35 ..      15      43 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.07
                              CpXC 38 atCpkCgata 47
                                      + CpkCg+++
  gi|385806211|ref|YP_005842609.1|  6 FICPKCGKEF 15
                                      6788888765 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.034
                              CpXC 36 featCpkCgataklea 51
                                       +++Cp+Cg +  l  
  gi|385806211|ref|YP_005842609.1| 20 KDWKCPYCGSSLNLAK 35
                                      5799*****9988765 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 ?    8.0   0.5    0.0043       2.9       2      12 ..       6      16 ..       5      16 .. 0.91
   2 ?    1.3   0.1      0.55   3.6e+02       3      10 ..      23      30 ..      22      32 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0043
                         zf-C2H2_6  2 heCsvCsksFp 12
                                      ++C+ C+k+F+
  gi|385806211|ref|YP_005842609.1|  6 FICPKCGKEFE 16
                                      9*********6 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.55
                         zf-C2H2_6  3 eCsvCsks 10
                                      +C++C+ s
  gi|385806211|ref|YP_005842609.1| 23 KCPYCGSS 30
                                      7****976 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 ?    5.5   3.8      0.02        14      21      52 ..       4      29 ..       1      31 [. 0.79

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.02
                    zinc_ribbon_10 21 yalICskChshnGlapkeeleevkyrCpkCga 52
                                      y  IC+kC + +  a      +  ++Cp+Cg+
  gi|385806211|ref|YP_005842609.1|  4 YTFICPKCGKEFEDA------PKDWKCPYCGS 29
                                      678999999988777......55799999997 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.6     0.064        43      17      24 ..       8      15 ..       6      17 .. 0.92
   2 ?    5.2   0.3     0.047        32      12      22 ..      19      29 ..      18      31 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.064
                         zf-H2C2_2 17 CplCdkaF 24
                                      Cp+C+k F
  gi|385806211|ref|YP_005842609.1|  8 CPKCGKEF 15
                                      ******99 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.047
                         zf-H2C2_2 12 ekpyeCplCdk 22
                                      +k ++Cp+C+ 
  gi|385806211|ref|YP_005842609.1| 19 PKDWKCPYCGS 29
                                      5779*****86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                       117  (0.00652574); 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):              27  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 1960.85
//
Query:       gi|385806212|ref|YP_005842610.1|  [L=81]
Description: hypothetical protein FFONT_1170 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       703  (0.0392102); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); 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: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 515.72
//
Query:       gi|385806213|ref|YP_005842611.1|  [L=401]
Description: thiamine biosynthesis protein ThiI [Fervidicoccus fontis Kam940]
Scores for complete 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-48  163.4   0.0    6.8e-48  162.9   0.0    1.2  1  ThiI           Thiamine biosynthesis protein (ThiI)
    3.1e-19   69.5   0.8    3.1e-19   69.5   0.8    1.6  2  THUMP          THUMP domain
      6e-07   29.2   0.0     0.0017   17.9   0.0    2.6  2  QueC           Queuosine biosynthesis protein QueC
  ------ inclusion threshold ------
       0.12   11.2   0.0        0.2   10.4   0.0    1.3  1  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 !  162.9   0.0   1.5e-51   6.8e-48       2     189 ..     181     366 ..     180     373 .. 0.93

  Alignments for each domain:
  == domain 1  score: 162.9 bits;  conditional E-value: 1.5e-51
                              ThiI   2 tqgkvlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlke 78 
                                       ++ k+l+L+SgG+DSpVaa++l+kRG  v+++++  + g +e+++  + ++ +l+  ++ + + ++++v+++ +   
  gi|385806213|ref|YP_005842611.1| 181 SELKILSLVSGGFDSPVAAWMLMKRGSPVDILFF--NIGGKEHKEYFLDVAKKLICGWSYGPNQNVYIVEHRWIFPY 255
                                       56689*****************************..68888888888888888999999999*************** PP

                              ThiI  79 ilekvkekltivllkrkmlriAekvaeeegakalvtGesLgqVaSqtleNlrvisavvnllilrPLigldKeeiikl 155
                                       + +  +e++++v lk +m+  Ae +a+  g+ka+ tGe+L+qV+Sqt++Nl v+++ ++++++rPLig+dKeeii+l
  gi|385806213|ref|YP_005842611.1| 256 LFNYFPEGYRTVALKVSMYVGAEALAKSLGIKAISTGENLAQVSSQTVHNLAVTESFIDIPVFRPLIGFDKEEIIEL 332
                                       ***************************************************************************** PP

                              ThiI 156 AkeigtyeisiekedkCsvlakhPttkakleeve 189
                                        k++gtye+s + ++ C++ + + +t+   +++e
  gi|385806213|ref|YP_005842611.1| 333 SKKVGTYEVSSRVPEFCAIASSKASTAVDGKKLE 366
                                       *******************998888876666555 PP

>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.5   0.8     7e-23   3.1e-19       1     142 [.      35     168 ..      35     170 .. 0.92
   2 ?   -2.7   0.1       1.3   5.8e+03      12     101 ..     337     353 ..     324     388 .. 0.51

  Alignments for each domain:
  == domain 1  score: 69.5 bits;  conditional E-value: 7e-23
                                       HHHHHHHHHTT.H-SEEEEETTEEEEECTEEEEEETHHHHHHHHHTSTTECEEEEEEEEEESSHHHHHHHHHHHHHH CS
                             THUMP   1 geieellkegkvnverveagkgrivvelkgekpeedeellkealekargiqrvipvcevceadledileaakeivkk 77 
                                       ++ie++lk ++ +++ v+   gr++v +  e+   +++++ e++++++g+ + +p++++ ++dl+d+ ++++e+  +
  gi|385806213|ref|YP_005842611.1|  35 KNIENALKSNGFERSIVRVIPGRVLVTTP-ED---PRKEA-ELISRVFGVTSSSPALMGEYRDLDDLVDKVSEASIE 106
                                       69******************999999986.43...44444.66699******************************* PP

                                       HHHHCT-EEEEEEEESSSTSSSHHHHHHHHHHHHHHCCTT-EE-SSS-SEEEEEEEETTEEEEEE CS
                             THUMP  78 kfeeeketFaVrvkrrgkhfeftsreinrevGkaivektglkVdlenPdivvrveiikdkayisi 142
                                         +++   F Vr +r +++  fts++i+r +G+ + e +  kV+le+P+i + ve +k  ++++ 
  gi|385806213|ref|YP_005842611.1| 107 DVRGK--VFMVRGRRADEN-RFTSKDIERRIGAKLQEMGAGKVNLESPEISIYVEARKGLFFVYK 168
                                       **998..9***********.***************************************999985 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.3
                                       .H-SEEEEETTEEEEECTEEEEEETHHHHHHHHHTSTTECEEEEEEEEEESSHHHHHHHHHHHHHHHHHHCT-EEEE CS
                             THUMP  12 vnverveagkgrivvelkgekpeedeellkealekargiqrvipvcevceadledileaakeivkkkfeeeketFaV 88 
                                       +                                                                        t+ V
  gi|385806213|ref|YP_005842611.1| 337 G------------------------------------------------------------------------TYEV 341
                                       2........................................................................4444 PP

                                       EEEESSSTSSSHH CS
                             THUMP  89 rvkrrgkhfefts 101
                                        ++++  +  + s
  gi|385806213|ref|YP_005842611.1| 342 SSRVPEFC-AIAS 353
                                       44444443.3322 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   3.7e-07    0.0017       2      47 ..     185     232 ..     184     247 .. 0.86
   2 !    8.4   0.0   0.00031       1.4     113     175 ..     285     338 ..     270     349 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.7e-07
                                       EEEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-TTSHH..HHHHHHH CS
                              QueC   2 avvllSGGlDSttvlalakkegkevealtfdYgqrhkke..leaakki 47 
                                       ++ l+SGG DS +++++ +k+g  v +l f+ g +++ke  l++akk+
  gi|385806213|ref|YP_005842611.1| 185 ILSLVSGGFDSPVAAWMLMKRGSPVDILFFNIGGKEHKEyfLDVAKKL 232
                                       7899*******************************8887334666665 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00031
                                       T-SEEEE---S-STT--GGGSHHHHHHHHHHHHHHHTS--EEE-TTTT--HHHHHHHHHHTTH CS
                              QueC 113 gaeaiiiGvneedfsgYPDcrdefvkalnkalnlgedkkieieaPlidlsKaeivklgkelgv 175
                                       g++ai +G n  ++s      +++v++l ++ ++    +i +  Pli ++K+ei++l+k++g 
  gi|385806213|ref|YP_005842611.1| 285 GIKAISTGENLAQVS------SQTVHNLAVTESF---IDIPVFRPLIGFDKEEIIELSKKVGT 338
                                       555555555555433......3444444433333...358999*****************994 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   4.4e-05       0.2       2      37 ..     184     219 ..     183     232 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 4.4e-05
                     tRNA_Me_trans   2 kvvvalSgGVDSsvaaallkeqgyevigvflklwee 37 
                                       k++ ++SgG DS vaa +l ++g  v  +f+++  +
  gi|385806213|ref|YP_005842611.1| 184 KILSLVSGGFDSPVAAWMLMKRGSPVDILFFNIGGK 219
                                       68899******************9998888776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); 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: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2591.88
//
Query:       gi|385806214|ref|YP_005842612.1|  [L=194]
Description: hypothetical protein FFONT_1172 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.094   12.6   0.1       0.14   12.0   0.1    1.2  1  Claudin_3  Tight junction protein, Claudin-like


Domain annotation for each model (and alignments):
>> Claudin_3  Tight junction protein, Claudin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   8.1e-06      0.14      89     140 ..       9      60 ..       7      71 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.1e-06
                         Claudin_3  89 svrklffliallslliviltviaviliavnvskfndsfndsslqLGYsawls 140
                                       + rk+f+++ ++ ll+vi+++ a++  +++  + +  + +  l+L Y + +s
  gi|385806214|ref|YP_005842612.1|   9 RSRKIFYILGISGLLAVIFLIGAIVYAEIDTPSLKPMYSQPGLKLDYLMNVS 60 
                                       579***************************9998888877778888876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.49
# Mc/sec: 1179.66
//
Query:       gi|385806215|ref|YP_005842613.1|  [L=63]
Description: acylphosphatase [Fervidicoccus fontis Kam940]
Scores for complete 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   60.9   0.1    1.3e-16   60.8   0.1    1.0  1  Acylphosphatase  Acylphosphatase
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.012   15.4   0.0    1.0  1  T2SSM_b          Type II secretion system (T2SS), protein M s
      0.062   12.8   0.0      0.066   12.7   0.0    1.0  1  Acyl_transf_1    Acyl transferase domain


Domain annotation for each model (and alignments):
>> Acylphosphatase  Acylphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.8   0.1   2.1e-20   1.3e-16      25      85 .]       1      61 [.       1      61 [. 0.98

  Alignments for each domain:
  == domain 1  score: 60.8 bits;  conditional E-value: 2.1e-20
                   Acylphosphatase 25 lglkGyvrNlsdgsVeivaegeeekvekfleelksgppkarvdeveveeleeeeefkdFei 85
                                      +++kG+vrN  dgsVeivaegee+++ k+++e+k+gpp+a v++v+v+++e+++ef+dF i
  gi|385806215|ref|YP_005842613.1|  1 MNVKGWVRNCIDGSVEIVAEGEEDALFKLINEVKKGPPAAVVENVDVSWEEYRGEFDDFVI 61
                                      689********************************************************87 PP

>> T2SSM_b  Type II secretion system (T2SS), protein M subtype b
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.0   2.1e-06     0.012      52      86 ..      14      48 ..      11      58 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.1e-06
                           T2SSM_b 52 avrvslegeleaLqklLasLeaqrPflfVDelsvq 86
                                      +v++ +ege++aL+kl+ ++ ++ P+ +V++++v 
  gi|385806215|ref|YP_005842613.1| 14 SVEIVAEGEEDALFKLINEVKKGPPAAVVENVDVS 48
                                      68999****************************97 PP

>> Acyl_transf_1  Acyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.1e-05     0.066     151     192 ..      10      51 ..       3      55 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.1e-05
                                       EEEECCCCECCEEHHHHHHHHHHHHHCC.CCEEECCCEECTT CS
                     Acyl_transf_1 151 vansprrvvisgsqealrelvervskegvgalvenvnvavhs 192
                                       +  +  ++v++g+++al +l+++v+k   +a venv+v  + 
  gi|385806215|ref|YP_005842613.1|  10 CIDGSVEIVAEGEEDALFKLINEVKKGPPAAVVENVDVSWEE 51 
                                       56667789*****************************98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 393.31
//
Query:       gi|385806216|ref|YP_005842614.1|  [L=335]
Description: Dehydrogenase (flavoprotein)-like protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.14   12.1   0.0       0.25   11.3   0.0    1.4  1  NAD_binding_9  FAD-NAD(P)-binding


Domain annotation for each model (and alignments):
>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   1.4e-05      0.25       2      35 ..       4      35 ..       3      70 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.4e-05
                     NAD_binding_9  2 ivGaGprGlavlerLlarakkkspleitlfdpse 35
                                      ivG+Gp+G++++   l ++  +++ +i+++d + 
  gi|385806216|ref|YP_005842614.1|  4 IVGGGPSGISFAISYLINS--RKDEKIKVYDGER 35
                                      9***********9999887..8889999998754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2141.04
//
Query:       gi|385806217|ref|YP_005842615.1|  [L=115]
Description: hypothetical protein FFONT_1175 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); 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 0.27s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 749.39
//
Query:       gi|385806218|ref|YP_005842616.1|  [L=820]
Description: valyl-tRNA synthetase [Fervidicoccus fontis Kam940]
Scores for complete 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-113  380.0   0.1   4.7e-112  375.2   0.1    2.1  1  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    3.8e-27   95.0   1.5    8.4e-14   51.1   0.0    4.4  3  tRNA-synt_1g   tRNA synthetases class I (M)
    2.5e-25   89.2   3.1      7e-25   87.8   3.1    1.8  1  Anticodon_1    Anticodon-binding domain of tRNA
    4.6e-05   23.0   0.0       0.01   15.3   0.0    2.8  2  tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
  ------ inclusion threshold ------
      0.065   13.4   0.0       0.22   11.7   0.0    1.9  1  AhpC-TSA_2     AhpC/TSA antioxidant enzyme
      0.066   12.9   1.9         21    4.7   0.0    3.4  3  TackOD1        Thaumarchaeal output domain 1
      0.081   13.2   2.6      0.085   13.2   0.2    2.4  2  DUF2175        Uncharacterized protein conserved in archaea (
       0.14   12.2   0.6         16    5.6   0.3    3.2  2  DZR            Double zinc ribbon
       0.38   10.7   8.1        5.9    6.9   0.1    3.6  3  zf-FPG_IleRS   Zinc finger found in FPG and IleRS
        0.4   10.5   0.0        0.4   10.5   0.0    2.7  2  HscB_4_cys     Co-chaperone HscB tetracysteine metal binding 
       0.72   10.0   5.9        2.8    8.1   1.5    3.4  3  Zn-ribbon_8    Zinc ribbon domain
        2.5    8.3   8.0         18    5.5   0.1    4.5  4  zf-ACC         Acetyl-coA carboxylase zinc finger domain
        3.3    7.4   4.7         30    4.3   0.1    3.5  3  zf_UBZ         Ubiquitin-Binding Zinc Finger
        3.7    7.0   5.1        6.5    6.2   0.0    3.2  3  zf-TFIIB       Transcription factor 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 !  375.2   0.1  3.7e-115  4.7e-112       2     601 ..      23     584 ..      22     585 .. 0.94

  Alignments for each domain:
  == domain 1  score: 375.2 bits;  conditional E-value: 3.7e-115
                       tRNA-synt_1   2 lyekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaiea 78 
                                       + e+W++e++ k  +e   +k++ ++  +PPy  G+ H+  a + + +d++ r+ rm G++vl  +  D  Gl++e 
  gi|385806218|ref|YP_005842616.1|  23 IIERWKKENIGKFRKEDLGRKPTLVIDTPPPYPSGKWHVAGAAHYVHHDMIARFFRMIGYNVLLPFYADRNGLPVEV 99 
                                       6899*****98888778888********************************************************* PP

                       tRNA-synt_1  79 kvekklgakekk.erkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkg 154
                                        vekk g++ ++ + +  gre+f + +++  +   ee+ k ++rlG s+D+ ++  T ++e+ + ++ +f +l +kg
  gi|385806218|ref|YP_005842616.1| 100 SVEKKTGINPHEvSSTPEGREKFLALCKKELDSIEEEMVKLLERLGCSYDYWKN-GTDSEEYRKLTQATFRELWKKG 175
                                       *******98764155678*********************************886.5889****************** PP

                       tRNA-synt_1 155 liyrgkklvnwstklktalselEveykdkkdalihvafpladkeevklviaTTtPeTllgdtavavnpeldyvitke 231
                                       liy ++++vnw++++kt+ls++E eyk+ + +l++++f++ + ++ ++ +aTT+Pe l + +a+  +p         
  gi|385806218|ref|YP_005842616.1| 176 LIYVAERPVNWCPRCKTTLSDAELEYKELETYLYYIKFKIRETND-YVTVATTRPELLSSCKALIYHPS-------- 243
                                       *********************************************.***********************........ PP

                       tRNA-synt_1 232 klilaeallkslvkkesekkiledergkeLegkevelplvnrkipiiaddyvdkeaGtGvVkiaPahdedDyevgkk 308
                                                              d+r++ Legk+++ p+ +++++i +++ +d ++GtG+V i  + dedD ++ ++
  gi|385806218|ref|YP_005842616.1| 244 -----------------------DPRYSGLEGKTAISPIYEKELKIYKNENADPNFGTGLVMICSYGDEDDIKMFRE 297
                                       .......................9***************************************************** PP

                       tRNA-synt_1 309 ynlevinildedgtlteeaaefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrateqWfvrvk 385
                                        +le+  ++d dg+l+e+a+  +g+k  +ar k+ eel+++gl++k+ek +h+vp+c+r ++pi++  +  +f ++ 
  gi|385806218|ref|YP_005842616.1| 298 LGLEPEIVVDRDGRLNEKAGFLKGMKTHEARTKIAEELEKRGLMVKKEKLMHKVPVCWRCGTPIEFIHVREYFLKQI 374
                                       ***************************************************************************** PP

                       tRNA-synt_1 386 eladaalkavekvqfvpkskekryaswleniq.dWciSRqrwWGhriplfvsketeevvvreelkelvagreeeeae 461
                                       e++d++l+a++k++f+p++++++  +w++ i+ dW iSR+r++ + ip ++ k+ + + v e+ k++   + e   e
  gi|385806218|ref|YP_005842616.1| 375 EFKDKLLEAIDKMKFYPEMHKQKLIDWINSIKtDWPISRDRYYATEIPTWRCKKCNSILVPEDFKYYRPWKDEPPFE 451
                                       ******************************955***********************999966666665533333332 PP

                       tRNA-synt_1 462 kkalekeakdklkkekgelekdedvlDvWFsSgswpfstlgypeedteelkkffpadmll.eGlDiirgWvarlill 537
                                       k           + +k  le ++ v+D+WF+S+ +   + gy     +el +    d+l  +G+ iir W++ +il 
  gi|385806218|ref|YP_005842616.1| 452 KCP-------VCGADKSYLEGEKKVFDTWFDSSISSLYITGYMRD--NELYEKLKNDILRpQGYEIIRTWLYYSILR 519
                                       222.......247788899**********************9887..666667888888649*************** PP

                       tRNA-synt_1 538 slaltgsePfkevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltli.lsdvgrdinl 601
                                         +ltg+  fk v ++g+ +de+G  m Ks+gNvidp  vi++ygada R++ +  ++vg d ++
  gi|385806218|ref|YP_005842616.1| 520 VYQLTGRPAFKYVRITGMGLDEKGEAMHKSKGNVIDPFPVIESYGADAFRFWAAsAAKVGYDYRF 584
                                       *****************************************************977788777765 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 !   51.1   0.0   6.5e-17   8.4e-14       2     136 ..      47     200 ..      46     203 .. 0.84
   2 !   20.8   0.3     1e-07   0.00013     150     239 ..     333     423 ..     322     433 .. 0.84
   3 !   17.1   0.0   1.5e-06    0.0019     240     368 ..     465     586 ..     454     592 .. 0.76

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 6.5e-17
                                       EEEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHH.TTS-HHHH........... CS
                      tRNA-synt_1g   2 lvttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAek.egvtpeel........... 66 
                                       ++ t+ pY++gk H+  +++++  D++aR+ r+ g++vl     D  G p+e++ ek  g++p+e+           
  gi|385806218|ref|YP_005842616.1|  47 VIDTPPPYPSGKWHVAGAAHYVHHDMIARFFRMIGYNVLLPFYADRNGLPVEVSVEKkTGINPHEVsstpegrekfl 123
                                       688999***********************************************987526999988622222222222 PP

                                       ..H....HHHHHHHHHHHHHTT---SEEEE.TTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG-E CS
                      tRNA-synt_1g  67 ..v....ekvheeikelfkklnisfdkygr.ttseehkelvqeifkklkekgliyekeieqlycpkderflpdryve 136
                                         +    ++++ee+ +l+++l+ s+d++++ t+see ++l+q+ f++l +kgliy  e  + +cp+++++l+d ++e
  gi|385806218|ref|YP_005842616.1| 124 alCkkelDSIEEEMVKLLERLGCSYDYWKNgTDSEEYRKLTQATFRELWKKGLIYVAERPVNWCPRCKTTLSDAELE 200
                                       223222245778888999**********8748889999***********************************9875 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 1e-07
                                       -EE-TTSSB-E..................EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT---- CS
                      tRNA-synt_1g 150 dqceecgkkleptelin..pksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkd 224
                                       ++ e+ g  ++ ++l+   p++  +g+  e+ + +++f+k  +f++kl e i  + k  +e  k+++ +w+++  +d
  gi|385806218|ref|YP_005842616.1| 333 EELEKRGLMVKKEKLMHkvPVCWRCGTPIEFIHVREYFLKQIEFKDKLLEAI-DKMKFYPEMHKQKLIDWINSIKTD 408
                                       556777777777777654499*******************************.55557999999999******999* PP

                                       EE-ESS-SSS-EETT CS
                      tRNA-synt_1g 225 laisrdldwGipvPg 239
                                       + isrd  ++ ++P 
  gi|385806218|ref|YP_005842616.1| 409 WPISRDRYYATEIPT 423
                                       *************94 PP

  == domain 3  score: 17.1 bits;  conditional E-value: 1.5e-06
                                       ECCEEE-HHHHHHHHHHHTTTTT-...TTSGGGG.G--S......EEEEEGGGHHHHHTHHHHHHHH...TT----S CS
                      tRNA-synt_1g 240 aekkvlYVWldAligYisatkelakkkgeeekwkeyWakdkevelvhfigkdiikFHtifwPaillg...aelklpk 313
                                        ekkv+  W+d  i  + +t+++     ++e +++   +    ++    g +ii+  t ++ +il     ++  + k
  gi|385806218|ref|YP_005842616.1| 465 GEKKVFDTWFDSSISSLYITGYMR----DNELYEKLK-N----DILRPQGYEIIR--TWLYYSILRVyqlTGRPAFK 530
                                       578888888888888888888875....566777665.3....577777777776..33333444442344445667 PP

                                       -EEEE--.EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-H CS
                      tRNA-synt_1g 314 kvvahey.ltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfsw 368
                                        v  +++ l  +g+ + kS+g+v+++  ++e++ ad++R++ a++a+   D  f+ 
  gi|385806218|ref|YP_005842616.1| 531 YVRITGMgLDEKGEAMHKSKGNVIDPFPVIESYGADAFRFWAASAAKVGYDYRFNP 586
                                       777777657889**********************************9999999975 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 !   87.8   3.1   5.5e-28     7e-25       1     150 [.     623     775 ..     623     777 .. 0.89

  Alignments for each domain:
  == domain 1  score: 87.8 bits;  conditional E-value: 5.5e-28
                       Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedk...ra.aqevllevletl 73 
                                       d+ il  +  +++++  +++e++ ++  + +y+f+w+ ++++y+elvk+r y+ ++e +   ++ a ++l+ vl+t+
  gi|385806218|ref|YP_005842616.1| 623 DKAILEYTKMTLRKYISSFKEMDTYEPSNLVYSFTWDIFASNYIELVKQRAYNLNNEWSkedQEsAWATLHLVLRTI 699
                                       899****************************************************999999877799********** PP

                       Anticodon_1  74 lrllaPfmPfitEelwqreeeelgkkesimlaewpekaeel...ekeleeeevellkeivkairklrselkikpsse 147
                                       l + aP+mPfi++e+w    +++++  si+ a+  ++ + +   +++l  + ++l+ ++++ i k+++++++k s e
  gi|385806218|ref|YP_005842616.1| 700 LLMTAPIMPFISDEIW----RLMKNCGSIHQASLTQEINAEegiNDKL-TQIIDLMVKVNSDIWKYKKQNGLKFSDE 771
                                       ****************....999999*******775332222354444.89**********************9998 PP

                       Anticodon_1 148 .lkv 150
                                        +kv
  gi|385806218|ref|YP_005842616.1| 772 iAKV 775
                                       4444 PP

>> tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.019        25      11      37 ..     210     236 ..     209     246 .. 0.86
   2 !   15.3   0.0   8.2e-06      0.01      85     146 ..     251     312 ..     243     346 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.019
                     tRNA-synt_1_2  11 eiefkveeseeklevfttrpdtlfGvt 37 
                                        i+fk++e+++ ++v ttrp+ l + +
  gi|385806218|ref|YP_005842616.1| 210 YIKFKIRETNDYVTVATTRPELLSSCK 236
                                       599******************998766 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 8.2e-06
                     tRNA-synt_1_2  85 tglkaihPitgekipiwvanyvlmeygtgavmavPahdqrDfeFakkynlpikqvikpedee 146
                                       +g +ai Pi ++++ i+  +    ++gtg vm +   d+ D +  ++ +l+ + v+  +++ 
  gi|385806218|ref|YP_005842616.1| 251 EGKTAISPIYEKELKIYKNENADPNFGTGLVMICSYGDEDDIKMFRELGLEPEIVVDRDGRL 312
                                       6889***************************************************9976543 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 ?   11.7   0.0   0.00017      0.22      12      84 ..     276     349 ..     265     397 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
                        AhpC-TSA_2  12 agvklvaig.igdp.sakkFvkltgfpfelyvDpsaklyqalglkrglklklaplslqkalenllkrlkeigipg 84 
                                        g++lv+i   gd+ ++k F+ + g   e++vD+++ l ++ g+ +g+k + a+ ++++ le+  +++k+ +  +
  gi|385806218|ref|YP_005842616.1| 276 FGTGLVMICsYGDEdDIKMFR-ELGLEPEIVVDRDGRLNEKAGFLKGMKTHEARTKIAEELEKRGLMVKKEKLMH 349
                                       68899999879***66*****.999************************99999999999999888888876554 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0      0.03        39     126     144 ..     187     205 ..     178     208 .. 0.77
   2 ?    4.7   0.0     0.016        21      48      81 ..     324     359 ..     299     368 .. 0.84
   3 ?    1.1   0.2      0.21   2.7e+02     124     146 ..     424     446 ..     414     466 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.03
                           TackOD1 126 CpkCktkLrhiGvDYdrpl 144
                                       Cp+Ckt+L+    +Y++++
  gi|385806218|ref|YP_005842616.1| 187 CPRCKTTLSDAELEYKELE 205
                                       8888888888888887764 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.016
                           TackOD1  48 ekeeseelleelvkrglle..eelvdrirlCpsCks 81 
                                       ++e  ++++eel+krgl+   e+l+ ++ +C +C +
  gi|385806218|ref|YP_005842616.1| 324 THEARTKIAEELEKRGLMVkkEKLMHKVPVCWRCGT 359
                                       44578899********9866789***********75 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.21
                           TackOD1 124 leCpkCktkLrhiGvDYdrplev 146
                                         C kC++ L   +  Y rp ++
  gi|385806218|ref|YP_005842616.1| 424 WRCKKCNSILVPEDFKYYRPWKD 446
                                       57889999998888888888764 PP

>> DUF2175  Uncharacterized protein conserved in archaea (DUF2175)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.2       7.9     1e+04       2      10 ..     423     431 ..     423     438 .. 0.79
   2 ?   13.2   0.2   6.7e-05     0.085      13      90 ..     710     790 ..     707     796 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 7.9
                           DUF2175   2 kwkCyiCgk 10 
                                       +w+C+ C+ 
  gi|385806218|ref|YP_005842616.1| 423 TWRCKKCNS 431
                                       5******76 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 6.7e-05
                           DUF2175  13 vegekFTft.kkgvvHyeClvekarkklkesedaaaLleleevlneeivklkelervaedeevkkv..leqkrkelE 86 
                                       +++e + ++ + g++H++ l+++++ +   + + + + +l   +n+ i k k+ + ++ ++e+ kv  + q  ke+E
  gi|385806218|ref|YP_005842616.1| 710 ISDEIWRLMkNCGSIHQASLTQEINAEEGINDKLTQIIDLMVKVNSDIWKYKKQNGLKFSDEIAKVvyIPQELKEAE 786
                                       677888888678*******************9999**********************98899888723578999999 PP

                           DUF2175  87 kaaa 90 
                                       k   
  gi|385806218|ref|YP_005842616.1| 787 KDLK 790
                                       9765 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.13   1.7e+02      14      23 ..     186     195 ..     172     212 .. 0.81
   2 ?    5.6   0.3     0.013        16      15      49 .]     354     457 ..     344     462 .. 0.63

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.13
                               DZR  14 fCseCgtklk 23 
                                        C++C+t+l+
  gi|385806218|ref|YP_005842616.1| 186 WCPRCKTTLS 195
                                       5777777776 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.013
                               DZR  15 CseCgtklkavaa.........................................................edrCpsC 34 
                                       C +Cgt+++   +                                                           rC +C
  gi|385806218|ref|YP_005842616.1| 354 CWRCGTPIE-FIHvreyflkqiefkdklleaidkmkfypemhkqklidwinsiktdwpisrdryyateipTWRCKKC 429
                                       666666654.2223555666666666666666666666666666666666666666666666666666666677778 PP

                               DZR  35 gek.vdpearf............CpeCG 49 
                                       ++  v++++++            Cp CG
  gi|385806218|ref|YP_005842616.1| 430 NSIlVPEDFKYyrpwkdeppfekCPVCG 457
                                       7776777777677777777777777776 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 ?    6.9   0.1    0.0046       5.9      22      27 ..     185     190 ..     179     200 .. 0.63
   2 ?    1.2   0.9      0.27   3.4e+02       3      12 ..     353     362 ..     352     363 .. 0.85
   3 ?    5.0   0.1     0.017        22       2       8 ..     451     457 ..     450     459 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0046
                                       EE-TTT CS
                      zf-FPG_IleRS  22 yfCprC 27 
                                       ++CprC
  gi|385806218|ref|YP_005842616.1| 185 NWCPRC 190
                                       566666 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.27
                                       B-TTT--BBE CS
                      zf-FPG_IleRS   3 pCpRCwryie 12 
                                       +C RC+++ie
  gi|385806218|ref|YP_005842616.1| 353 VCWRCGTPIE 362
                                       5889**9997 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.017
                                       SB-TTT- CS
                      zf-FPG_IleRS   2 epCpRCw 8  
                                       e+Cp+C+
  gi|385806218|ref|YP_005842616.1| 451 EKCPVCG 457
                                       9*****9 PP

>> HscB_4_cys  Co-chaperone HscB tetracysteine metal binding motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.2       1.1   1.4e+03      19      23 ..     186     190 ..     184     192 .. 0.83
   2 ?   10.5   0.0   0.00032       0.4       1      14 [.     352     365 ..     352     371 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.1
                                       B-TTT CS
                        HscB_4_cys  19 FCpqC 23 
                                        Cp+C
  gi|385806218|ref|YP_005842616.1| 186 WCPRC 190
                                       5**** PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00032
                                       -B-SSS--B--SS- CS
                        HscB_4_cys   1 PrCWnCGgpgapgr 14 
                                       P CW CG p +   
  gi|385806218|ref|YP_005842616.1| 352 PVCWRCGTPIEFIH 365
                                       89******998665 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.28   3.5e+02      23      35 ..     181     193 ..     176     196 .. 0.71
   2 ?   -1.3   0.0       1.9   2.5e+03      28      35 ..     353     360 ..     345     366 .. 0.62
   3 ?    8.1   1.5    0.0022       2.8       7      34 ..     425     458 ..     423     461 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.28
                       Zn-ribbon_8  23 dapltaCPeCgse 35 
                                       ++p   CP+C+ +
  gi|385806218|ref|YP_005842616.1| 181 ERPVNWCPRCKTT 193
                                       455455****875 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.9
                       Zn-ribbon_8  28 aCPeCgse 35 
                                       +C +Cg +
  gi|385806218|ref|YP_005842616.1| 353 VCWRCGTP 360
                                       35555543 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0022
                       Zn-ribbon_8   7 rCeeCghefe.....vlqsis.dapltaCPeCgs 34 
                                       rC++C++          ++ + ++p ++CP Cg+
  gi|385806218|ref|YP_005842616.1| 425 RCKKCNSILVpedfkYYRPWKdEPPFEKCPVCGA 458
                                       7888886555555556677776888888*****8 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.014        18       4      17 ..     187     200 ..     186     201 .. 0.95
   2 ?   -0.7   0.0       1.2   1.5e+03       6      13 ..     234     241 ..     233     242 .. 0.88
   3 ?    3.3   0.1     0.071        91       2      12 ..     424     434 ..     424     439 .. 0.79
   4 ?    0.2   0.3      0.66   8.5e+02       3       9 ..     452     458 ..     450     458 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.014
                            zf-ACC   4 CpsCgemlykkeLe 17 
                                       Cp+C+++l   eLe
  gi|385806218|ref|YP_005842616.1| 187 CPRCKTTLSDAELE 200
                                       ********999998 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.2
                            zf-ACC   6 sCgemlyk 13 
                                       sC++++y 
  gi|385806218|ref|YP_005842616.1| 234 SCKALIYH 241
                                       8*****95 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.071
                            zf-ACC   2 tKCpsCgemly 12 
                                       ++C +C+++l 
  gi|385806218|ref|YP_005842616.1| 424 WRCKKCNSILV 434
                                       58******985 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 0.66
                            zf-ACC   3 KCpsCge 9  
                                       KCp Cg+
  gi|385806218|ref|YP_005842616.1| 452 KCPVCGA 458
                                       9999996 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.023        30       5      17 ..     187     199 ..     186     200 .. 0.90
   2 ?    0.1   0.1      0.49   6.3e+02       4      13 ..     353     362 ..     353     365 .. 0.88
   3 ?    2.0   0.1      0.12   1.6e+02       2      13 ..     423     434 ..     422     439 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.023
                            zf_UBZ   5 CerCgkeipesel 17 
                                       C+rC+++++++el
  gi|385806218|ref|YP_005842616.1| 187 CPRCKTTLSDAEL 199
                                       ********99987 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.49
                            zf_UBZ   4 lCerCgkeip 13 
                                       +C rCg++i+
  gi|385806218|ref|YP_005842616.1| 353 VCWRCGTPIE 362
                                       699****996 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.12
                            zf_UBZ   2 tylCerCgkeip 13 
                                       t+ C++C++ + 
  gi|385806218|ref|YP_005842616.1| 423 TWRCKKCNSILV 434
                                       799*****8665 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0    0.0051       6.5       2      14 ..     187     199 ..     186     207 .. 0.83
   2 ?   -0.6   0.1      0.68   8.7e+02      15      25 ..     419     429 ..     414     434 .. 0.86
   3 ?    0.2   0.5      0.37   4.8e+02       1       7 [.     452     458 ..     452     462 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0051
                          zf-TFIIB   2 CPkCqdeleeser 14 
                                       CP+C+++l ++e+
  gi|385806218|ref|YP_005842616.1| 187 CPRCKTTLSDAEL 199
                                       ********98876 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.68
                          zf-TFIIB  15 ggveidyCpqC 25 
                                        +++ ++C +C
  gi|385806218|ref|YP_005842616.1| 419 TEIPTWRCKKC 429
                                       57999****** PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.37
                          zf-TFIIB   1 kCPkCqd 7  
                                       kCP+C++
  gi|385806218|ref|YP_005842616.1| 452 KCPVCGA 458
                                       8****86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (820 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       976  (0.0544369); expected 358.6 (0.02)
Passed bias filter:                      716  (0.0399353); 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):              14  [number of targets reported over threshold]
# CPU time: 0.81u 0.33s 00:00:01.14 Elapsed: 00:00:00.54
# Mc/sec: 4602.80
//
Query:       gi|385806219|ref|YP_005842617.1|  [L=267]
Description: metal dependent phosphohydrolase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00049   20.3   0.0     0.0011   19.2   0.0    1.6  1  HD              HD domain
     0.0023   18.1   0.1     0.0046   17.1   0.1    1.5  1  Clavanin        Clavanin
  ------ inclusion threshold ------
      0.069   13.8   0.0       0.63   10.7   0.0    2.0  2  Mannosidase_ig  Mannosidase Ig/CBM-like 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 !   19.2   0.0   1.8e-07    0.0011      21     120 ..      92     181 ..      60     183 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.8e-07
                                       H..HHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHH............HHHHHH CS
                                HD  21 e..eedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgld............ledvak 83 
                                          ee++ ++ll+ L+HDiG+  ++              +He++g  +   ++ r   +             e+v++
  gi|385806219|ref|YP_005842617.1|  92 QktEEAKLVVLLGSLFHDIGNSIHRI-------------NHEFIGMLMSASILDRILSSifpndkrkailmREEVLH 155
                                       1557999****************775.............45555554444444444222555566779999999999 PP

                                       HHHTTCCHHHHHHHHHHHHCCTSCHHHHHHHHHHHHH CS
                                HD  84 lirehheswegkkrprglaerqlslearivklaDrla 120
                                       +i + +   +           +l++ea +vk+ D ++
  gi|385806219|ref|YP_005842617.1| 156 AIYATSYTVP-----------ALTIEAGCVKVGDGTD 181
                                       9999999999...........99********999776 PP

>> Clavanin  Clavanin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   7.8e-07    0.0046      23      52 ..      92     121 ..      72     124 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 7.8e-07
                          Clavanin  23 rkaeeekvlrllgkvihgvgnlvygisvvl 52 
                                       +k+ee k++ llg++ h++gn ++ i++ +
  gi|385806219|ref|YP_005842617.1|  92 QKTEEAKLVVLLGSLFHDIGNSIHRINHEF 121
                                       79************************9976 PP

>> Mannosidase_ig  Mannosidase Ig/CBM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.15     9e+02      31      85 ..      54     116 ..      33     121 .. 0.66
   2 ?   10.7   0.0    0.0001      0.63      16      90 ..     166     240 ..     154     242 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.15
                    Mannosidase_ig  31 laetsttpvtvgansstevaeidvdellaat........ggadpravvlvarledatgevlat 85 
                                        +++ +t +++   ss e++   ++  ++ t        ++++++ vvl  +l+++ g+ +++
  gi|385806219|ref|YP_005842617.1|  54 YNDHGPTHAKIVSGSSLEIFDRIFSAGIEPTtikdgifqKTEEAKLVVLLGSLFHDIGNSIHR 116
                                       555556666666666666666666444444455566666678888899999999888888887 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0001
                    Mannosidase_ig  16 qgtlelrlidl.tgkllaets.ttpvtvgansstevaeidvdellaatggadpravvlvarledatgevlatnvywp 90 
                                        +t+e  ++++ +g++++e + + p ++g n    +  +++d+++ +   +d  +vv+  +++   g +  ++v +p
  gi|385806219|ref|YP_005842617.1| 166 ALTIEAGCVKVgDGTDMSEGRaRIPYRLGKNDIHAISALSIDKVTIS--SEDETPVVITIYMKERAGVFQVEQVLYP 240
                                       568888899999********9999********************997..7*************99999999999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1586.99
//
Query:       gi|385806220|ref|YP_005842618.1|  [L=175]
Description: putative adenylyl cyclase CyaB [Fervidicoccus fontis Kam940]
Scores for complete 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   77.6   0.9    1.3e-21   77.3   0.9    1.0  1  CYTH      CYTH domain
  ------ inclusion threshold ------
        0.2   11.6   0.1       0.25   11.3   0.1    1.2  1  DUF3108   Protein of unknown function (DUF3108)


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 !   77.3   0.9   1.4e-25   1.3e-21       1     165 [.       1     161 [.       1     168 [. 0.89

  Alignments for each domain:
  == domain 1  score: 77.3 bits;  conditional E-value: 1.4e-25
                                       EEEEEEEEEE-HHHHHHHHHH.HHHCTCEEEEEEEEEEEEEE-TTTHHHHTTEEEEEE...EETTTEEE.EEEEEEC CS
                              CYTH   1 miEvEvKflvsaaeyedlelr.laelrakeettveqrdtYydtpdrdlartdeaLRiR...raegdgee.ltlKgpg 72 
                                       miE+EvK++++ ++ +  ++r  ae++    ++v + d+Y+ +p+ d+++tdea+RiR   +a g +++ +t+Kg  
  gi|385806220|ref|YP_005842618.1|   1 MIETEVKIKIDDNDEK--RIRdFAESSCIFREKVSINDIYLIHPCIDFSKTDEAVRIRiesTA-GIEKVkITYKGKR 74 
                                       89********744444..467889999*******************************77655.777889******9 PP

                                       SSST....EEEEEEEECCCEEECCCCHHHHHHHHHHHTT-EEEEEEEEEEEEEEETTEEEEEEEETTTTEEEEEEEE CS
                              CYTH  73 vdge....reevegevsreEyeeplsdaaeaaelldglglepvasvkklRrkyklegvevalDaveflegeevEiEl 145
                                         ++    ree+e+ev+        + ++++++++ ++  +++  ++k R++y+++g+ + +D v++l g+++E+E 
  gi|385806220|ref|YP_005842618.1|  75 NKDTdfkkREEIEFEVK--------ASPNDVISFFLRNRYRVLCNIEKDREIYECKGFYLMIDNVKDL-GKYIELEQ 142
                                       8888999********99........45899999***********************************.******** PP

                                       EESSHHHHHHHHHHHHHHHH CS
                              CYTH 146 evedeeevkeaaekllallr 165
                                        +++e+  + ++e  ++l++
  gi|385806220|ref|YP_005842618.1| 143 IGKNEKSIQIFLES-FNLKE 161
                                       *****999888888.55544 PP

>> DUF3108  Protein of unknown function (DUF3108)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   2.8e-05      0.25      92     166 ..      64     131 ..      45     143 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.8e-05
                           DUF3108  92 kveevtfargakkerdvepekdrtislpagvqDplsalyylrtsklkvgdsitlpvfdgrkrydlklkvlgretv 166
                                       +++++t++++++k++d +++++ + +++a   D++s++++ r        ++  ++  +r++y+ k  +l  ++v
  gi|385806220|ref|YP_005842618.1|  64 EKVKITYKGKRNKDTDFKKREEIEFEVKASPNDVISFFLRNR-------YRVLCNIEKDREIYECKGFYLMIDNV 131
                                       467889999999999999999999999999999999999444.......45666666666666666666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.62
# Mc/sec: 851.47
//
Query:       gi|385806221|ref|YP_005842619.1|  [L=325]
Description: Thioredoxin reductase (trxB-3) [Fervidicoccus fontis Kam940]
Scores for complete 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-54  183.9   0.8    4.6e-54  183.7   0.8    1.0  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    1.3e-26   93.6   2.2    7.4e-25   87.8   0.5    2.1  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
      7e-15   55.4   4.1    2.5e-14   53.6   0.8    2.6  3  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    2.3e-07   29.8   2.4     0.0029   16.4   0.0    3.7  4  HI0933_like    HI0933-like protein
      6e-06   25.6   0.1      0.015   14.4   0.0    3.1  3  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
      1e-05   24.8   1.0       0.29   10.1   0.1    3.4  4  FAD_binding_2  FAD binding domain
    5.6e-05   22.4   3.7        4.8    6.2   0.0    4.3  5  GIDA           Glucose inhibited division protein A
    0.00012   21.4   0.6      0.015   14.6   0.0    2.4  2  Thi4           Thi4 family
     0.0005   19.4   0.1       0.26   10.5   0.0    2.5  2  FAD_binding_3  FAD binding domain
    0.00076   19.7   0.3       0.48   10.7   0.1    2.5  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
  ------ inclusion threshold ------
      0.013   14.6   0.1        3.8    6.4   0.1    2.6  3  Lycopene_cycl  Lycopene cyclase protein
       0.02   14.9   0.3       0.18   11.8   0.0    2.5  3  NAD_binding_9  FAD-NAD(P)-binding
      0.031   13.6   0.1        4.2    6.6   0.0    2.9  3  FAD_oxidored   FAD dependent oxidoreductase


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.7   0.8   3.3e-57   4.6e-54       1     294 []      17     307 ..      17     307 .. 0.89

  Alignments for each domain:
  == domain 1  score: 183.7 bits;  conditional E-value: 3.3e-57
                                       CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH........HHHHCHHHHCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxx RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias........evvkklnqgiel 69 
                                       +dv++iG+GpA l++ l+ a++ +k++++   g + +g+  l+++++++ ++++i +        ++v+++   +e+
  gi|385806221|ref|YP_005842619.1|  17 YDVAIIGSGPASLSCGLYSARYRMKTIII---GDTIGGQLNLTNIVENYLGFPKITAtdlisrfkKHVEEYD--VEF 88 
                                       69***************************...77889*****************999*99987776666665..555 PP

                                       CHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-TSEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  70 llgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllpkriv 146
                                        l+  v +i ++   + +  ++  ++++i+++++vlA+G + r+l++pG++e +gk+v+++  ++a   k     ++
  gi|385806221|ref|YP_005842619.1|  89 NLD-RVNSIKKEGSYFII-RTV--NGKEIKAKSIVLAIGLKRRKLNVPGENEFAGKGVSYCSICDAAFFKDAA-AVA 160
                                       566.46777555555555.444..6779******************************************998.9** PP

                                       EES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHH.HHHHHHHTTEEEEESCEEEEEEETTE....EEE. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx....xxx. RF
                       Pyr_redox_2 147 vvGgGyiGvElAaalaklgkevtlveardrllraldkelsaa.leealekeGvevklgtsvkeidgnge....kle. 217
                                       +vGgG  ++E A  l++++k+v+l+++rd++        + + ++++  ++++e++ ++ vkei+g+++    k++ 
  gi|385806221|ref|YP_005842619.1| 161 IVGGGDSALEGALLLSEYAKKVYLIHRRDQFR------GQPIlVNAVKSRKNIEIVYNSIVKEIKGDKKvnsvKIKn 231
                                       *******************************8......33440455555569*******************77666* PP

                                       EEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGCTECCSS--HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 218 vvledgeeidadlvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDvaggkggpelaqaAvqqG 294
                                       vv ++++e+++  +++ +G++p+ el  +++g+elde+g+i+v+e++ tnv+g++a+GD+++  +g++++ +A  qG
  gi|385806221|ref|YP_005842619.1| 232 VVSGEERELQVNGIFIEIGFEPDIELP-RSIGIELDENGFIKVNEYMSTNVEGVFAAGDCTNMWKGFRQIITATVQG 307
                                       **************************7.*********************************9999999999998776 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.7   0.1    0.0055       7.6       2      27 ..      21      45 ..      20      62 .. 0.84
   2 !   87.8   0.5   5.3e-28   7.4e-25      78     305 .]      68     288 ..      50     288 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0055
                       Pyr_redox_3  2 IiGaGPaGlaaaielkkagledylil 27
                                      IiG GPa l++++   +  +++ +i+
  gi|385806221|ref|YP_005842619.1| 21 IIGSGPASLSCGLYSARYRMKT-III 45
                                      9************999999965.454 PP

  == domain 2  score: 87.8 bits;  conditional E-value: 5.3e-28
                       Pyr_redox_3  78 lsrkealeYlrevaksfelpiklfeeVesvkkedegfevetske.tyeAkkviiAtGefdkPnklnipGeek...lv 150
                                       +++ ++ + +++ +++++++ +l+ +V+s+kke++ f+++t ++ +++Ak++++A+G   k +kln+pGe++   + 
  gi|385806221|ref|YP_005842619.1|  68 ITATDLISRFKKHVEEYDVEFNLD-RVNSIKKEGSYFIIRTVNGkEIKAKSIVLAIGL--KRRKLNVPGENEfagKG 141
                                       566666667777788888888775.7***************98769***********9..999********864456 PP

                       Pyr_redox_3 151 khyskvkefhkya.gqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeek 226
                                       + y  + +++ ++    v+++Gg++Sa + Al l ++ ++V +++r+++ +          +p+  n +++    ++
  gi|385806221|ref|YP_005842619.1| 142 VSYCSICDAAFFKdAAAVAIVGGGDSALEGALLLSEYAKKVYLIHRRDQFRG---------QPILVNAVKSR---KN 206
                                       6777777777677456799****************************85433.........69999999984...45 PP

                       Pyr_redox_3 227 ikvlfnaevkeikekeeeykvk...tedgkkvevkddvvla.tGykpdlsflkkslfeldedgrpvlteeteetnvp 299
                                       i++++n+ vkeik +++   vk     +g++ e + + +++ +G++pd+++ ++ ++elde+g+++++e  ++tnv+
  gi|385806221|ref|YP_005842619.1| 207 IEIVYNSIVKEIKGDKKVNSVKiknVVSGEERELQVNGIFIeIGFEPDIELPRSIGIELDENGFIKVNE-YMSTNVE 282
                                       ************966655445411444567777777888888*************************85.8****** PP

                       Pyr_redox_3 300 glflaG 305
                                       g+f aG
  gi|385806221|ref|YP_005842619.1| 283 GVFAAG 288
                                       ****99 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.21   2.9e+02       2      28 ..      19      45 ..      18      53 .. 0.90
   2 ?   -3.2   0.0       9.7   1.3e+04      44      60 ..      75      91 ..      70     101 .. 0.65
   3 !   53.6   0.8   1.8e-17   2.5e-14       2      79 ..     159     230 ..     158     237 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.21
                                      EEEECSSHHHHHHHHHHHHTTSEEEEE CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvv 28
                                      v+++G+G   l ++ + a+++ k+ ++
  gi|385806221|ref|YP_005842619.1| 19 VAIIGSGPASLSCGLYSARYRMKTIII 45
                                      89************9999999998887 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 9.7
                                      HHHHHHHHHTTEEEECS CS
                         Pyr_redox 44 kilqeklekngievlln 60
                                      +++++++e+  +e+ l+
  gi|385806221|ref|YP_005842619.1| 75 SRFKKHVEEYDVEFNLD 91
                                      56677888888888765 PP

  == domain 3  score: 53.6 bits;  conditional E-value: 1.8e-17
                                       EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHT.TEEEECSEEEEEEEEETTSEEEEE CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekn.gievllntkveeiegsedgvesvk 77 
                                       v++vGgG+++lE A  l+e++kkV++++r+d+++       + il + ++ + +ie+++n+ v+ei+g+++ v+svk
  gi|385806221|ref|YP_005842619.1| 159 VAIVGGGDSALEGALLLSEYAKKVYLIHRRDQFR------GQPILVNAVKSRkNIEIVYNSIVKEIKGDKK-VNSVK 228
                                       89********************************......999******7777**************9998.***** PP

                                       EE CS
                         Pyr_redox  78 lk 79 
                                       +k
  gi|385806221|ref|YP_005842619.1| 229 IK 230
                                       98 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.1    0.0027       3.8       1      30 [.      17      46 ..      17      64 .. 0.84
   2 !   16.4   0.0   2.1e-06    0.0029     102     163 ..      65     123 ..      60     126 .. 0.90
   3 !    5.3   0.0    0.0049       6.7       2      35 ..     158     191 ..     157     199 .. 0.91
   4 ?   -3.2   0.0       1.8   2.5e+03     369     384 ..     276     290 ..     271     294 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0027
                                      -SEEEE--SHHHHHHHHHHHHTT--EEEE- CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVllle 30
                                      +dv++iG G+A l + +  a+   +++++ 
  gi|385806221|ref|YP_005842619.1| 17 YDVAIIGSGPASLSCGLYSARYRMKTIIIG 46
                                      59**************99999999988875 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 2.1e-06
                                       EETT.-CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE--- CS
                       HI0933_like 102 FpvsdkaedivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtG 163
                                       Fp+  +a+d+++ ++k+++e +v+++l+ +v+s++k e++ f ++t +++e++a+++vlA+G
  gi|385806221|ref|YP_005842619.1|  65 FPKI-TATDLISRFKKHVEEYDVEFNLD-RVNSIKK-EGSYFIIRTVNGKEIKAKSIVLAIG 123
                                       7777.9*******************996.7****76.5555999999*************99 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.0049
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakkl 35 
                                        v+++GgG + l +A+ +++  k+V l+ + +++
  gi|385806221|ref|YP_005842619.1| 158 AVAIVGGGDSALEGALLLSEYAKKVYLIHRRDQF 191
                                       599*************************988765 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 1.8
                                       T-BBTTSTTEEE-GGG CS
                       HI0933_like 369 tmeskkvpgLffaGEv 384
                                        m s +v+g+f aG +
  gi|385806221|ref|YP_005842619.1| 276 YM-STNVEGVFAAGDC 290
                                       45.999********87 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.017        23       3      20 ..      17      34 ..      15      46 .. 0.79
   2 !   14.4   0.0   1.1e-05     0.015     119     229 ..      93     192 ..      72     196 .. 0.67
   3 ?    3.2   0.0     0.028        39     113     160 ..     209     253 ..     200     280 .. 0.62

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.017
                       K_oxygenase  3 lDligiGiGpsnLsLail 20
                                      +D+++iG Gp++Ls  + 
  gi|385806221|ref|YP_005842619.1| 17 YDVAIIGSGPASLSCGLY 34
                                      9************96555 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 1.1e-05
                       K_oxygenase 119 veevepdeeeeeelltveskdaegeeeelearnlvlgvGtep...kiPevleklegkervvHsseylerkeellakk 192
                                       v++++ +     +++ +++     + +e++a+++vl++G ++   ++P   e     + v   s         +++ 
  gi|385806221|ref|YP_005842619.1|  93 VNSIKKEG----SYFIIRT----VNGKEIKAKSIVLAIGLKRrklNVPGENEFAG--KGVSYCSICDAAF--FKDAA 157
                                       33333333....4677776....35689***********6652225777766433..5666666666666..67899 PP

                       K_oxygenase 193 riaVvGsGqSaaeifedllrrqkkvelklvtrseale 229
                                        +a+vG+G Sa e +  l +   ++++ l+ r+++++
  gi|385806221|ref|YP_005842619.1| 158 AVAIVGGGDSALEGALLLSEY--AKKVYLIHRRDQFR 192
                                       9***********976655444..45888899988875 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.028
                       K_oxygenase 113 vrfgeeveevepdeeeeeelltveskd.aegeeeelearnlvlgvGtep 160
                                       + +++ v+e++ d++ +   ++++  +  +gee+el+ + + + +G ep
  gi|385806221|ref|YP_005842619.1| 209 IVYNSIVKEIKGDKKVN--SVKIK--NvVSGEERELQVNGIFIEIGFEP 253
                                       44666666666666432..23333..22566666666666666666666 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.1   0.00021      0.29       1      28 [.      18      45 ..      18      53 .. 0.93
   2 !    6.2   0.0    0.0033       4.5       2      37 ..     159     194 ..     158     201 .. 0.95
   3 ?   -2.2   0.0       1.2   1.6e+03     147     191 ..     197     241 ..     194     250 .. 0.82
   4 !    5.0   0.0    0.0075        10     375     410 ..     262     298 ..     222     304 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00021
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEE CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavv 28
                                      Dv +iGsG A L+++l  a+   k++++
  gi|385806221|ref|YP_005842619.1| 18 DVAIIGSGPASLSCGLYSARYRMKTIII 45
                                      9******************999999987 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0033
                                       EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSG CS
                     FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqefgga 37 
                                       v ++G+G + L  Al ++e  +kv ++   ++f+g+
  gi|385806221|ref|YP_005842619.1| 159 VAIVGGGDSALEGALLLSEYAKKVYLIHRRDQFRGQ 194
                                       89*******************************997 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.2
                                       HHHHHHTCT.EEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEE CS
                     FAD_binding_2 147 lvesarkag.vdfqerteadeLivedgrvtGavvenpesgrevrir 191
                                       lv+++++++ +++  +  ++e+   d++v+ + ++n  sg+e++++
  gi|385806221|ref|YP_005842619.1| 197 LVNAVKSRKnIEIVYNSIVKEI-KGDKKVNSVKIKNVVSGEERELQ 241
                                       6788888888999999999999.55889999999999998888765 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.0075
                                       EEEBETTSBE..STTEEESSBTEEE-STCEESSSSTTS CS
                     FAD_binding_2 375 Gvetdengrv..ldadgqpipGLYAaGevaaggvhgan 410
                                       G+e deng     +   ++++G +AaG ++  + +g++
  gi|385806221|ref|YP_005842619.1| 262 GIELDENGFIkvNEYMSTNVEGVFAAGDCT-NMWKGFR 298
                                       666666664433556677***********9.7777665 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.1   0.0    0.0071       9.8       1      29 [.      18      52 ..      18      62 .. 0.82
   2 !    6.2   0.0    0.0035       4.8     103     153 ..      79     126 ..      69     149 .. 0.77
   3 ?    4.0   0.1     0.016        22       2      35 ..     159     191 ..     158     219 .. 0.81
   4 ?   -1.6   0.0       0.8   1.1e+03     102     134 ..     198     230 ..     186     240 .. 0.71
   5 !    5.0   0.1    0.0077        11     348     390 ..     275     320 ..     267     322 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0071
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEE......E CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi......t 29
                                      dv +iG G A + + l +ar  +k+++i      +
  gi|385806221|ref|YP_005842619.1| 18 DVAIIGSGPASLSCGLYSARYRMKTIIIgdtiggQ 52
                                      799***********************995544443 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0035
                                       HHHHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT-BT CS
                              GIDA 103 eklenepnleiieeeveeliveekkvkgvvtedgetikakavviatGtflk 153
                                       + +e+  ++e   ++v+++  +e++   ++t +g++ikak++v+a G   +
  gi|385806221|ref|YP_005842619.1|  79 KHVEE-YDVEFNLDRVNSI-KKEGSYFIIRTVNGKEIKAKSIVLAIGL-KR 126
                                       55555.6788888899999.55999999*******************7.33 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.016
                                       EEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGT CS
                              GIDA   2 viViGgGhAGceAAlaaarlGakvlLithkldti 35 
                                       v ++GgG + +e Al +++   kv Li h+ d++
  gi|385806221|ref|YP_005842619.1| 159 VAIVGGGDSALEGALLLSEYAKKVYLI-HRRDQF 191
                                       89************************9.666665 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 0.8
                                       HHHHHTSTTEEEEES-.EEEEEECTTEEEEEEET CS
                              GIDA 102 teklenepnleiieee.veeliveekkvkgvvte 134
                                        +++++ +n+ei+ ++ v+e+   +kkv+ v+ +
  gi|385806221|ref|YP_005842619.1| 198 VNAVKSRKNIEIVYNSiVKEI-KGDKKVNSVKIK 230
                                       578899999999877614555.557777777665 PP

  == domain 5  score: 5.0 bits;  conditional E-value: 0.0077
                                       TTSBBSSSBTEEE-CGGGTB.-SH...HHHHHHHHHHHHHHHHHHCT CS
                              GIDA 348 ntLetkkvkgLflAGqinGt.eGY...eEaaaqGllAGinaarkakg 390
                                       + ++t+ v+g+f+AG+ + + +G+   + a+ qG +A+  a +++ +
  gi|385806221|ref|YP_005842619.1| 275 EYMSTN-VEGVFAAGDCTNMwKGFrqiITATVQGAVAAYSAYKYLSE 320
                                       455555.**********999889722256788*******99988776 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.1e-05     0.015      16      50 ..      15      48 ..       6      62 .. 0.88
   2 ?    4.5   0.1     0.013        17      19      50 ..     158     188 ..     149     197 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.1e-05
                                      TEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESS CS
                              Thi4 16 aesDvvivGaGssGLtaayylakkpdlkvailers 50
                                       e Dv+i+G+G++ L+++ y a+   +k++i+   
  gi|385806221|ref|YP_005842619.1| 15 TEYDVAIIGSGPASLSCGLYSARY-RMKTIIIGDT 48
                                      689********************9.9****99765 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.013
                                       EEEEE--SHHHHHHHHHHHHCTTS-EEEEESS CS
                              Thi4  19 DvvivGaGssGLtaayylakkpdlkvailers 50 
                                        v+ivG+G s L  a  l++    kv ++ r+
  gi|385806221|ref|YP_005842619.1| 158 AVAIVGGGDSALEGALLLSEY-AKKVYLIHRR 188
                                       699****************99.8899998876 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.0    0.0028       3.9       1      29 [.      16      44 ..      16      48 .. 0.80
   2 !   10.5   0.0   0.00019      0.26       3      36 ..     158     191 ..     156     239 .. 0.94

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0028
                                      EEEEEEE--SHHHHHHHHHHHHTTHHEEE CS
                     FAD_binding_3  1 etdVlIVGaGpaGlmlallLseaGvrvvl 29
                                      e+dV+I+G+Gpa l+ +l  +++  ++++
  gi|385806221|ref|YP_005842619.1| 16 EYDVAIIGSGPASLSCGLYSARYRMKTII 44
                                      589*********99999877777666665 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00019
                                       EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSS CS
                     FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrstt 36 
                                        V+IVG+G + l  allLse+  +v l+ +r++ 
  gi|385806221|ref|YP_005842619.1| 158 AVAIVGGGDSALEGALLLSEYAKKVYLIHRRDQF 191
                                       79****************************9875 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 !   10.7   0.1   0.00035      0.48       1      35 [.      21      53 ..      21      63 .. 0.90
   2 !    6.6   0.0    0.0065       8.9       1      33 [.     161     193 ..     161     195 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00035
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGra 35
                                      I+G+G ++l++  + a+++ +  ++  +d +GG++
  gi|385806221|ref|YP_005842619.1| 21 IIGSGPASLSCGLYSARYRMKTIII--GDTIGGQL 53
                                      9****************99998888..88888886 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0065
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSG CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrlGG 33 
                                       IvG+G s+l  A lL+++ ++v l+ +rd++ G
  gi|385806221|ref|YP_005842619.1| 161 IVGGGDSALEGALLLSEYAKKVYLIHRRDQFRG 193
                                       9************************99999876 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1    0.0028       3.8       1      30 [.      18      45 ..      18      53 .. 0.87
   2 ?    5.3   0.0    0.0061       8.5      80     145 ..      64     128 ..      52     144 .. 0.85
   3 ?   -2.2   0.0       1.1   1.6e+03       2      31 ..     159     186 ..     159     192 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0028
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvli 30
                                      Dv++iG+GpA ls    +  a++++k ++i
  gi|385806221|ref|YP_005842619.1| 18 DVAIIGSGPASLSCGLYS--ARYRMKTIII 45
                                      9************99999..8888888887 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0061
                     Lycopene_cycl  80 aYgrvsskrlkeellerlvengvklleakvesveeeeageslvvleggrkirarlvvdarglaslk 145
                                        + +++ ++l ++ ++++ e  v++   +v+s+++e      + + +g++i+a+ +v a gl ++k
  gi|385806221|ref|YP_005842619.1|  64 GFPKITATDLISRFKKHVEEYDVEFNLDRVNSIKKEGS-YFIIRTVNGKEIKAKSIVLAIGLKRRK 128
                                       57789999999***********************9998.99999*****************76655 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.1
                     Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlie 31 
                                       v+++G+G   l  A  l  ++++ kv li 
  gi|385806221|ref|YP_005842619.1| 159 VAIVGGGDSALEGALLL--SEYAKKVYLIH 186
                                       79*******99999999..88888888885 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       1.1   1.5e+03       1      12 [.      20      31 ..      20      35 .. 0.88
   2 ?   11.8   0.0   0.00013      0.18     105     154 ..      75     123 ..      69     125 .. 0.84
   3 ?   -1.0   0.0       1.1   1.5e+03       1      18 [.     160     177 ..     160     193 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.1
                     NAD_binding_9  1 aivGaGprGlav 12
                                      ai+G Gp+ l++
  gi|385806221|ref|YP_005842619.1| 20 AIIGSGPASLSC 31
                                      8******99875 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00013
                     NAD_binding_9 105 eellarlpegvtvevhraevvdleeradgqavlladgaslaadaVvLAlG 154
                                       +++ + + e+ +ve+  ++v +++++++ + +++ +g++++a+++vLA+G
  gi|385806221|ref|YP_005842619.1|  75 SRFKKHV-EEYDVEFNLDRVNSIKKEGSYFIIRTVNGKEIKAKSIVLAIG 123
                                       4444444.346899999*******************************99 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.1
                     NAD_binding_9   1 aivGaGprGlavlerLla 18 
                                       aivG+G ++l  +  L +
  gi|385806221|ref|YP_005842619.1| 160 AIVGGGDSALEGALLLSE 177
                                       89****999876665555 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0031       4.2       1      38 [.      18      53 ..      18     100 .. 0.82
   2 ?    1.0   0.0      0.15   2.1e+02       2      33 ..     159     190 ..     158     196 .. 0.91
   3 ?    2.2   0.1     0.068        93      96     128 ..     200     232 ..     192     241 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0031
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGll 38
                                      Dv ++G+gpa + + + +ar   k++++   + +GG+l
  gi|385806221|ref|YP_005842619.1| 18 DVAIIGSGPASLSCGLYSARYRMKTIIIG--DTIGGQL 53
                                      9***************************6..5689986 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.15
                      FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakvlLveergv 33 
                                       v +vGGg + +  A+   +  +kv L+++r+ 
  gi|385806221|ref|YP_005842619.1| 159 VAIVGGGDSALEGALLLSEYAKKVYLIHRRDQ 190
                                       89**************************9975 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.068
                      FAD_oxidored  96 ml.aeagvtvllntrlvevekegkriesvtvesk 128
                                        + +++++++++n+ ++e++ ++ +++sv++++ 
  gi|385806221|ref|YP_005842619.1| 200 AVkSRKNIEIVYNSIVKEIKGDK-KVNSVKIKNV 232
                                       444679**************985.9****99874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.71u 0.36s 00:00:01.06 Elapsed: 00:00:00.57
# Mc/sec: 1722.45
//
Query:       gi|385806222|ref|YP_005842620.1|  [L=460]
Description: putative Dehydrogenase [Fervidicoccus fontis Kam940]
Scores for complete 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-08   33.0   0.0     0.0058   16.3   0.0    2.2  2  DAO             FAD dependent oxidoreductase
    1.1e-05   24.8   0.0      0.038   13.1   0.0    2.7  3  FAD_binding_2   FAD binding domain
    2.8e-05   23.5   0.1    0.00033   20.0   0.0    2.6  4  Thi4            Thi4 family
    6.2e-05   23.2   0.0    0.00013   22.1   0.0    1.5  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    0.00013   21.3   0.0      0.058   12.6   0.0    2.9  3  FAD_binding_3   FAD binding domain
    0.00079   18.7   0.0      0.011   15.0   0.0    2.1  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
     0.0027   17.1   0.1     0.0099   15.3   0.1    1.9  1  FAD_oxidored    FAD dependent oxidoreductase
     0.0036   16.2   0.0        2.7    6.8   0.0    3.1  3  Trp_halogenase  Tryptophan halogenase
  ------ inclusion threshold ------
      0.018   15.6   0.1         13    6.5   0.0    3.6  4  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   9.4e-06     0.019       1      29 [.       8      39 ..       8      48 .. 0.92
   2 !   16.3   0.0   2.9e-06    0.0058     137     202 ..      92     159 ..      71     179 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.4e-06
                                      EEEEECTSHHHHHHHHHHHHTT...EEEEESS CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg...Vtllekg 29
                                      dv+i G+G  G++ Ay+L++++   V++++++
  gi|385806222|ref|YP_005842620.1|  8 DVIIAGSGPSGSTLAYFLSQKKsykVAVFDSR 39
                                      8******************986799*****98 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 2.9e-06
                                       ETTEEEEEHHHHHHHHHHHHHHTT-EEEESECEEE.EEEEETCEEEEE...EECTEEEEEEEEEEE--GG CS
                               DAO 137 ypdtgqvdpakltaalaraaealGveilegtevtg.leeedgkvwgve...rttpgendaadavVnaaGa 202
                                       y ++ ++d  k+   l+++a ++Gve++ +t+v g +  e+ k++g++   +++ +e ++ + +V a+G 
  gi|385806222|ref|YP_005842620.1|  92 YGEGYIIDRKKFGTRLLKTAVDNGVEFYPRTQVLGpV-FENAKLAGIKvkiNDKIEE-FKGKIIVDATGT 159
                                       6677788****************************54.5566788886654333232.34466****994 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0   0.00045       0.9       1      29 [.       8      37 ..       8      40 .. 0.93
   2 !   13.1   0.0   1.9e-05     0.038     145     205 ..     105     166 ..      83     189 .. 0.88
   3 ?   -1.8   0.0      0.62   1.2e+03      27      53 ..     248     275 ..     248     285 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00045
                                      SEEEE--SHHHHHHHHHHHHTTT.-EEEEE CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGl.kvavve 29
                                      Dvi+ GsG +G + A+ ++++   kvav +
  gi|385806222|ref|YP_005842620.1|  8 DVIIAGSGPSGSTLAYFLSQKKSyKVAVFD 37
                                      9*******************9888***986 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 1.9e-05
                                       HHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG.... CS
                     FAD_binding_2 145 arlvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgr...a 205
                                        rl+++a ++gv+f++rt+++  + e+ +  G+ v+   + ++++++ k +v+atg +g     
  gi|385806222|ref|YP_005842620.1| 105 TRLLKTAVDNGVEFYPRTQVLGPVFENAKLAGIKVK--INDKIEEFKGKIIVDATGTAGVirrY 166
                                       68999999****************************..*******************9974432 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.62
                                       EEESSSGGGS.GGGG--S-EE-TT..SS CS
                     FAD_binding_2  27 vvekeqefgg.atawsqGgidavlspeq 53 
                                       +++k +e ++   ++s+Gg++++ +++ 
  gi|385806222|ref|YP_005842620.1| 248 LLSKRPEIRSkKEVISSGGAQVPTRRPL 275
                                       57899999998999*********97775 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   1.7e-07   0.00033      17      50 ..       6      39 ..       1      58 [. 0.93
   2 ?   -0.7   0.0      0.36   7.1e+02     158     182 ..     149     173 ..     140     204 .. 0.71
   3 ?   -1.4   0.0      0.56   1.1e+03      38      58 ..     197     217 ..     190     219 .. 0.76
   4 ?   -3.5   0.0       2.4   4.8e+03     174     205 ..     364     394 ..     359     404 .. 0.62

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.7e-07
                                      EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESS CS
                              Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailers 50
                                      + Dv+i G+G+sG t ay l++k   kva+++++
  gi|385806222|ref|YP_005842620.1|  6 DYDVIIAGSGPSGSTLAYFLSQKKSYKVAVFDSR 39
                                      57****************************9875 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.36
                                       EEEEEEE--GSSSTTTTHHHHHHHH CS
                              Thi4 158 rakvvvdatGhdgeivavvvkkikl 182
                                       + k++vdatG  g i   + k    
  gi|385806222|ref|YP_005842620.1| 149 KGKIIVDATGTAGVIRRYLPKEWPV 173
                                       568999***9999887777666544 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.56
                                       HCTTS-EEEEESSSS--TTTT CS
                              Thi4  38 kkpdlkvailersvspGGGaw 58 
                                       k+p +  + l+++vspGG  w
  gi|385806222|ref|YP_005842620.1| 197 KEPSILKIYLNQKVSPGGYWW 217
                                       45566566789******9888 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 2.4
                                       THHHHHHHHCTTTS-----ECB-HHHHHHHHH CS
                              Thi4 174 avvvkkikleakiekvkgeksldaekaedaiv 205
                                        +++kki++e+ + ++ g k+   e a ++ v
  gi|385806222|ref|YP_005842620.1| 364 FIMEKKIVDEN-DVDILGRKGELNESAIEKSV 394
                                       56778888877.55667777766665544444 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   6.8e-08   0.00013       1      29 [.      11      40 ..      11      41 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 6.8e-08
                                      EE--SHHHHHHHHHHHCC.TEEEEEE-SSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLaka.gfdvlllekrd 29
                                      I G+G sG+++Ay+L+++  ++v ++++r+
  gi|385806222|ref|YP_005842620.1| 11 IAGSGPSGSTLAYFLSQKkSYKVAVFDSRS 40
                                      67**************97699******985 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   0.0   2.9e-05     0.058       2      23 ..       7      28 ..       6      50 .. 0.83
   2 ?    1.5   0.0      0.07   1.4e+02     110     180 ..     106     175 ..      86     186 .. 0.85
   3 ?    3.2   0.0     0.021        42     284     312 ..     281     309 ..     271     324 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.9e-05
                                      EEEEEE--SHHHHHHHHHHHHT CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLsea 23
                                      +dV+I G+Gp+G +la +Ls++
  gi|385806222|ref|YP_005842620.1|  7 YDVIIAGSGPSGSTLAYFLSQK 28
                                      79*****************986 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.07
                                       HHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE--GTT-HHHHHHTGGEEEEE CS
                     FAD_binding_3 110 iLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrakYlvGaDGgrStvrktlgiefegee 180
                                        L++ a+  g++++  t+v++   ++ +  a ++ k ++++e+++ k +v a G  + +r+ l+ e + +e
  gi|385806222|ref|YP_005842620.1| 106 RLLKTAVDNGVEFYPRTQVLGPVFENAK-LAGIKVKINDKIEEFKGKIIVDATGTAGVIRRYLPKEWPVSE 175
                                       5788889999999999999987777666.6888999999*********************99998766555 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.021
                                       TTEEE-GGGTEEE-STTSHHHHHHHHHHH CS
                     FAD_binding_3 284 grvflaGDAaHihpPtgGqGlNtaiqDav 312
                                       ++   +GD+a ++ P++G G+  a+  a+
  gi|385806222|ref|YP_005842620.1| 281 DNFIAIGDSAFAVNPVHGGGMGYAMISAY 309
                                       556678***************99998777 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   5.4e-06     0.011       1     108 [.       7     158 ..       7     160 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.4e-06
                                       CSEEEE--SHHHHHHHHHHHH.HTS-EEEEE...............TTHCHHHCSHHHHCHHHHHHHHHHHHH.... CS
                                       xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx...............xxxxxxxxxxxxxxxxxxxxxxxxxxx.... RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaq.agakvtlve...............legtclnggcllskallgvaedaeias.... 57 
                                       +dv++ G+Gp G ++a +l+q +++kv++++                +++++++  ++ +   ++++    +s    
  gi|385806222|ref|YP_005842620.1|   7 YDVIIAGSGPSGSTLAYFLSQkKSYKVAVFDsrswedlwgkpcgnaIGKHHFFELGIPEPQGDEIKQTVTGISiisp 83 
                                       69*******************77*******65555555555555555555555555554433333333333335557 PP

                                       .........................HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEEC.TCEEEEEESEEEE--- CS
                                       .........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  58 .........................evvkklnqgielllgeevvkidpgkkkvklekkke.gdeekiaydklvlAtG 108
                                                                +  + + +g+e++ +++v++  ++++k+   k k  ++ e+++ + +v AtG
  gi|385806222|ref|YP_005842620.1|  84 sehvefriygegyiidrkkfgtrllK--TAVDNGVEFYPRTQVLGPVFENAKLAGIKVKInDKIEEFKGKIIVDATG 158
                                       77777777777777777777776441..3455667777777777777777777776655335556666666666666 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   4.9e-06    0.0099      88     148 ..     103     162 ..       8     165 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.9e-06
                      FAD_oxidored  88 vakavleemlaeagvtvllntrlvevekegkriesvtveskegrktirAkvfiDATgdGdl 148
                                       + +++l+  +++ gv+ +  t++ +++ e+ ++ +++v+ +++ +++++k+++DATg + +
  gi|385806222|ref|YP_005842620.1| 103 FGTRLLKTAVDN-GVEFYPRTQVLGPVFENAKLAGIKVKINDKIEEFKGKIIVDATGTAGV 162
                                       445555556655.****************999******99889**************9876 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.9   0.0    0.0098        19       1      30 [.       8      35 ..       8      44 .. 0.81
   2 !    6.8   0.0    0.0013       2.7     148     213 ..      95     163 ..      72     187 .. 0.84
   3 ?    1.6   0.0      0.05     1e+02     316     343 ..     281     308 ..     262     333 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.0098
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEE CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtl 30
                                      +++i+G G++G++ A  l++  +  ++v +
  gi|385806222|ref|YP_005842620.1|  8 DVIIAGSGPSGSTLAYFLSQKKS--YKVAV 35
                                      699***************99874..44444 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0013
                                       EEEE-HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETT...S-EEE-SEEEE-SGGG-II CS
                    Trp_halogenase 148 AyhldaalyakfLrrvaearGvtrvegkvvevqldedgrveslrled...greveadlfiDcsGfrgll 213
                                       +y +d++++   L + a ++Gv+    + v   + e+ + ++++++     +e+++ +++D++G +g +
  gi|385806222|ref|YP_005842620.1|  95 GYIIDRKKFGTRLLKTAVDNGVEFYPRTQVLGPVFENAKLAGIKVKIndkIEEFKGKIIVDATGTAGVI 163
                                       799*********************99888888888888888877765334577899********99975 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.05
                                       TTEEE-CCCTEE--CCCS-HHHHHHHHH CS
                    Trp_halogenase 316 knvvalGlasgfvePlestsihliqaal 343
                                        n++a+G+++ +v+P+ + ++  ++ ++
  gi|385806222|ref|YP_005842620.1| 281 DNFIAIGDSAFAVNPVHGGGMGYAMISA 308
                                       69**************999987777655 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0    0.0064        13       2      32 ..       9      40 ..       8      59 .. 0.87
   2 ?    3.5   0.0     0.052     1e+02      42      78 ..     103     139 ..      99     145 .. 0.77
   3 ?   -1.3   0.0       1.7   3.3e+03      50      68 ..     132     150 ..     127     151 .. 0.79
   4 ?    0.4   0.1      0.51     1e+03      28      51 ..     347     372 ..     331     398 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0064
                                      EEEECSSHHHHHHHHHHHHTT.SEEEEEESSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelg.kkVtvversd 32
                                      v++ G+G +g  lA +l++ +  kV v++ ++
  gi|385806222|ref|YP_005842620.1|  9 VIIAGSGPSGSTLAYFLSQKKsYKVAVFDSRS 40
                                      89***************886636999998775 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.052
                                       HHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEEE CS
                         Pyr_redox  42 askilqeklekngievllntkveeiegsedgvesvkl 78 
                                       ++++l +   +ng+e++  t+v   + ++ ++ ++k+
  gi|385806222|ref|YP_005842620.1| 103 FGTRLLKTAVDNGVEFYPRTQVLGPVFENAKLAGIKV 139
                                       6788899999***********9877655545666666 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.7
                                       HHHTTEEEECSEEEEEEEE CS
                         Pyr_redox  50 lekngievllntkveeieg 68 
                                        +  gi+v  n k+ee++g
  gi|385806222|ref|YP_005842620.1| 132 AKLAGIKVKINDKIEEFKG 150
                                       45569******99999987 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 0.51
                                       EESSSSSS.TTSSHHHHHHHHHHH.H CS
                         Pyr_redox  28 versdkll.rllDeeaskilqekl.e 51 
                                       +e   ++l rl Dee+  i+++k+  
  gi|385806222|ref|YP_005842620.1| 347 LELTRMFLqRLSDEELDFIMEKKIvD 372
                                       44455566666677776666666633 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 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:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.68u 0.32s 00:00:01.00 Elapsed: 00:00:00.51
# Mc/sec: 2696.78
//
Query:       gi|385806223|ref|YP_005842621.1|  [L=199]
Description: hypothetical protein FFONT_1181 [Fervidicoccus fontis Kam940]
Scores for complete 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-50  169.9  22.7    5.9e-50  169.8  22.7    1.0  1  DUF981       Protein of unknown function (DUF981)


Domain annotation for each model (and alignments):
>> DUF981  Protein of unknown function (DUF981)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.8  22.7   3.3e-54   5.9e-50       1     186 [.       1     190 [.       1     191 [. 0.98

  Alignments for each domain:
  == domain 1  score: 169.8 bits;  conditional E-value: 3.3e-54
                            DUF981   1 Ma..FidyltlmlitlgagllllayyvlkaleerekkeankalaapflivGllalitGlhmtltWPlpgsYnilfgd 75 
                                       Ma  ++d+lt++l+ ++ +++l+ay++l++++ ++ k++ k+l+ap+l++G++++++Gl++ ++WPlpgsY+ilf+d
  gi|385806223|ref|YP_005842621.1|   1 MAitYTDPLTAQLFGITGSTILVAYAMLRMAMGQDIKTVLKGLYAPLLAMGVYVFFSGLYGYFIWPLPGSYDILFYD 77 
                                       67779************************************************************************ PP

                            DUF981  76 pallfGvllllaavalykkaklkalgilalflGlilivygvailklgLtaePlaalllyilvGLagllsplvllkld 152
                                       +++++Gv l+++a+++++++kl+++g+lal++G+i+i yg+++++lg+t+eP+ +++ly+lvGL+++++++v +  d
  gi|385806223|ref|YP_005842621.1|  78 MYAVLGVGLIAIALCIKHDTKLEYIGFLALIYGVITIFYGYSGYSLGMTKEPAGMFALYALVGLSSIVFYFVSFGID 154
                                       **************************************************************************999 PP

                            DUF981 153 ksrs..vllvlaavlliiagllalliGieavyeHla 186
                                       + +    ll+++a+lli++gl+a++i+ +av++Hl+
  gi|385806223|ref|YP_005842621.1| 155 SGKVnkPLLYIEALLLILGGLAAAYIAGSAVPSHLK 190
                                       998778****************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1368.82
//
Query:       gi|385806224|ref|YP_005842622.1|  [L=411]
Description: SufS subfamily cysteine desulfurase [Fervidicoccus fontis Kam940]
Scores for complete 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-125  418.5   0.2   2.4e-125  418.3   0.2    1.0  1  Aminotran_5      Aminotransferase class-V
    7.9e-06   25.3   0.0    1.1e-05   24.8   0.0    1.3  1  Aminotran_1_2    Aminotransferase class I and II
    2.7e-05   23.6   0.0    3.6e-05   23.2   0.0    1.2  1  Beta_elim_lyase  Beta-eliminating lyase
    0.00022   20.6   0.2    0.00054   19.4   0.1    1.6  2  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    0.00064   18.4   0.0     0.0011   17.6   0.0    1.3  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
  ------ inclusion threshold ------
      0.013   15.8   0.5       0.14   12.5   0.1    2.2  2  Gp-FAR-1         Nematode fatty acid retinoid binding protein
      0.014   14.4   1.1      0.033   13.2   0.3    2.1  2  SelA             L-seryl-tRNA selenium transferase
      0.017   14.0   0.0      0.027   13.3   0.0    1.2  1  GDC-P            Glycine cleavage system P-protein
      0.077   13.3   0.5       0.27   11.5   0.1    2.1  2  TetR_C_10        Tetracyclin repressor-like, C-terminal domai
       0.15   11.7   0.5        5.9    6.7   0.0    3.4  4  TFA2_Winged_2    TFA2 Winged helix domain 2


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 !  418.3   0.2  1.3e-128  2.4e-125       1     371 []      25     399 ..      25     399 .. 0.99

  Alignments for each domain:
  == domain 1  score: 418.3 bits;  conditional E-value: 1.3e-128
                                       EEEBTTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHH CS
                       Aminotran_5   1 iyldsaAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlv 77 
                                       +y+d+aAt+q p +V++a+++y ++ n+nvhr+ h l+k+ t+ +eea+e va+ ina+s +eiif  +t+ a+nl+
  gi|385806224|ref|YP_005842622.1|  25 VYFDNAATSQRPIQVINAIKKYNEELNSNVHRGHHYLSKKSTELYEEAHEIVAKHINADSWQEIIFSLNTSYAVNLM 101
                                       7**************************************************************************** PP

                                       HHHCCCC.-TTT.SEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTT CS
                       Aminotran_5  78 alslars.lkpg.deivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvt 152
                                       a+ l  + lk+g d+iv+te+ehh+n++pw+++ak  ga+v+++++d++g +d+++l ++l+ekt+++aith+snvt
  gi|385806224|ref|YP_005842622.1| 102 AYPLVMRgLKEGrDKIVITEMEHHSNMLPWRNAAKIFGARVEYARVDKDGYIDVKRLINKLDEKTSVLAITHASNVT 178
                                       ***998897766489************************************************************** PP

                                       TEB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTTTTSSTT-EEEEEEHHHHHTS..SS.STT CS
                       Aminotran_5 153 GtiqpveeigklakkkgalvlvDaaqavghipidvkklgvDflafsghKllgPtGiGvlyvrkellekleplllgge 229
                                       G+i+p+e+i k akk+g+ v++D aq+++h  idvkklg+Df++fsghK+lgP GiGvly++ e+l ++ p+ +gg+
  gi|385806224|ref|YP_005842622.1| 179 GIINPIENISKEAKKYGITVFADVAQSIPHLSIDVKKLGADFIVFSGHKMLGPLGIGVLYGKLEMLREIDPFIVGGG 255
                                       ***************************************************************************** PP

                                       SEEEEETTEEEEHCTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-C CS
                       Aminotran_5 230 mveevsleettfaeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyllerlkslpgvrlygpdkae 306
                                       ++++v+le+  ++e+p+kfeaGTpnv +++gl +a++yle++g ++i +he+ l  +++++l+++++++ly +d + 
  gi|385806224|ref|YP_005842622.1| 256 TIKDVTLESVMYDEPPYKFEAGTPNVSAAVGLMEAVKYLEKVGKDNIIQHERMLLMKARKGLSEVEKIKLYPKDLKS 332
                                       ***************************************************************************** PP

                                       TCBSEEEEEETTCSHHHHHHHHHHT.TEEEEEE-TTTHHHHHHTT.S.-EEEEE--TTS-HHHHHHH CS
                       Aminotran_5 307 rrasivsfnfkgvhaedvatlLdee.gIavrsGhhcaqplmkrlale.gtvRaSlyiynteeevdrl 371
                                       +++++++fn++g +++ v+++L++  +Iavr+G hca+p++  ++ + gt+RaS+y+ynte e++++
  gi|385806224|ref|YP_005842622.1| 333 ESTGTLAFNIDGANPHIVGSVLNDFyAIAVRTGLHCAHPYHYAIGANeGTIRASFYLYNTESEIEYF 399
                                       ************************99******************9999****************986 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 !   24.8   0.0   6.1e-09   1.1e-05      86     189 ..     108     203 ..      28     250 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 6.1e-09
                                       HHHHHTTT-EEEEEESS-TH....HHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS- CS
                     Aminotran_1_2  86 fllklnpgdeilvpdptyas....yknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesph 158
                                       + l ++  d+i++ +  + s      n++++ g+ v + +++  +d  +d++ l+++l+e      kt v++++ ++
  gi|385806224|ref|YP_005842622.1| 108 RGL-KEGRDKIVITEMEHHSnmlpWRNAAKIFGARVEYARVD--KDGYIDVKRLINKLDE------KTSVLAITHAS 175
                                       445.46677777777766432222467788888888888866..****************......*********** PP

                                       TTT--B--HHHHHHHHHHHHHTTEEEEEEET CS
                     Aminotran_1_2 159 NPtGtvatleeleklldlakkynlllfvDea 189
                                       N tG + + e + k    akky++ +f D a
  gi|385806224|ref|YP_005842622.1| 176 NVTGIINPIENISKE---AKKYGITVFADVA 203
                                       ***************...***********88 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0     2e-08   3.6e-05      74     214 ..     118     243 ..      93     345 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 2e-08
                                       EEEETT-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHH CS
                   Beta_elim_lyase  74 vivtepahihfdetgaiaelagvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleel 150
                                       vi + + h  +   +++a + g+++  ++ +++G++d+++l ++++e      k++++ +t + n+  G + ++e+ 
  gi|385806224|ref|YP_005842622.1| 118 VITEMEHHSNMLPWRNAAKIFGARVEYARVDKDGYIDVKRLINKLDE------KTSVLAITHASNV-TGIINPIEN- 186
                                       444445666677779999999999******************99999......699*********7.898888776. PP

                                       HHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHHTTSSEEEEESSSTT--SS-.EEEEE-HH. CS
                   Beta_elim_lyase 151 revaaiakkygiplhlDgARfanaakslgeivkemfsyvDsvtmslkKdllanvG.gvlafrdde 214
                                         +++ akkygi+++ D A       +l+ +vk++  ++D +++s+ K  l + G gvl ++ + 
  gi|385806224|ref|YP_005842622.1| 187 --ISKEAKKYGITVFADVAQ---SIPHLSIDVKKL--GADFIVFSGHKM-LGPLGiGVLYGKLEM 243
                                       ..57899**********875...556788889987..689999999996.557888888888774 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 ?   -1.9   0.0      0.86   1.5e+03     301     348 ..      53      98 ..      23     111 .. 0.68
   2 !   19.4   0.1     3e-07   0.00054      53     159 ..     105     217 ..      97     228 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.86
                                       CEE-B-SGSCHGGGSCCHHHHHHCCCHC-HHHHHHHHHEEEEEGGTTG CS
                   DegT_DnrJ_EryC1 301 gigtrvhypnplhrqpvyaerkeeasgdlpnaerlaervlsLplypel 348
                                       ++    hy    +++++y+e +e   ++  na+++ e ++sL ++ ++
  gi|385806224|ref|YP_005842622.1|  53 NVHRGHHY-LSKKSTELYEEAHEIV-AKHINADSWQEIIFSLNTSYAV 98 
                                       55555666.4666777888887665.4788999999988888776555 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 3e-07
                                       HHHHHTTTTTT-EEEEESSS-THHH....HHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEEEB-...GGG CS
                   DegT_DnrJ_EryC1  53 laLralgvgpgdeVIvpsltFvata....navlelgakpvfvDvdpdtynidpaaieaaitertkaIlpVh...lyG 122
                                       l++r l+ g+ d+++++ +   + +    na+   ga++ ++ vd ++  id++++ +++ e+t+   + h   + G
  gi|385806224|ref|YP_005842622.1| 105 LVMRGLKEGR-DKIVITEMEHHSNMlpwrNAAKIFGARVEYARVD-KDGYIDVKRLINKLDEKTSVLAITHasnVTG 179
                                       5566666663.444444444433322222788889**********.6778**************7666666223689 PP

                                       B---HHHHHHHHHHCT-EEEEE-TT-TT.-EETTEECC CS
                   DegT_DnrJ_EryC1 123 qvadmdalkaiaakhglkvieDaAhAlG.atykgkkvG 159
                                        ++ ++++ + a+k+g+ v+ D A+++   +++ kk+G
  gi|385806224|ref|YP_005842622.1| 180 IINPIENISKEAKKYGITVFADVAQSIPhLSIDVKKLG 217
                                       999***********************983444446665 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   5.9e-07    0.0011      92     201 ..     115     230 ..      96     237 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 5.9e-07
                                       EEEEEESTSSHHHHHHHHHTHHHTTCEEEE..ESTTSHHHHHHHCCT...TEEEEEEESS-TTTT----HHHHHHHH CS
                   Cys_Met_Meta_PP  92 deivvsddlYggtqrllkkvlkklgievkf..vdtsdleelekaike...ntklvylEtptnpllkvvDiekiakla 163
                                       d+iv+++  + +     ++ +k +g +v++  vd++   ++++ i++   +t+++ +   +n +  +  ie+i+k a
  gi|385806224|ref|YP_005842622.1| 115 DKIVITEMEHHSNMLPWRNAAKIFGARVEYarVDKDGYIDVKRLINKldeKTSVLAITHASNVTGIINPIENISKEA 191
                                       44555555555555555666666665554411676655555555443333*************************** PP

                                       HHTT-EEEEEGTTTHT.TTS-GGGGT-SEEEEETTTTTT CS
                   Cys_Met_Meta_PP 164 kkagvlvvvDntfasp.llqrplklgaDivvhSaTKylg 201
                                       kk g++v+ D + + p l +   klgaD +v S+ K lg
  gi|385806224|ref|YP_005842622.1| 192 KKYGITVFADVAQSIPhLSIDVKKLGADFIVFSGHKMLG 230
                                       ****************44556668*********999875 PP

>> Gp-FAR-1  Nematode fatty acid retinoid binding protein (Gp-FAR-1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   7.8e-05      0.14      31      84 ..      28      81 ..       6      91 .. 0.83
   2 ?    1.0   0.0      0.27   4.8e+02      62      84 ..     178     200 ..     143     216 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.8e-05
                          Gp-FAR-1 31 knykgyknedellaalKkkspaLyekaeklqaklkekvdkLspeakeFvkklia 84
                                       n ++ +   ++++a+Kk +++L +++ + + +l +k  +L +ea e v k i+
  gi|385806224|ref|YP_005842622.1| 28 DNAATSQRPIQVINAIKKYNEELNSNVHRGHHYLSKKSTELYEEAHEIVAKHIN 81
                                      555555556689**********************************99988664 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.27
                          Gp-FAR-1  62 aklkekvdkLspeakeFvkklia 84 
                                       + + + ++++s eak++   ++a
  gi|385806224|ref|YP_005842622.1| 178 TGIINPIENISKEAKKYGITVFA 200
                                       44444455555555554433333 PP

>> SelA  L-seryl-tRNA selenium transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       2.4   4.3e+03     265     300 ..      33      68 ..      25      82 .. 0.67
   2 ?   13.2   0.3   1.8e-05     0.033     198     233 ..     212     247 ..     152     250 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.4
                                       -GGGSHHHHHHH--HHHHHHHHHHHHHHHTTSTT.. CS
                              SelA 265 laeklptlrlltqkleelrakaerlqkelkealgse 300
                                        ++ + +++ +++ +eel+++ +r ++ l+++ ++ 
  gi|385806224|ref|YP_005842622.1|  33 SQRPIQVINAIKKYNEELNSNVHRGHHYLSKKSTEL 68 
                                       345577888888888888888888777777766654 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1.8e-05
                                       HHHHTT-SEEEEETTSTT-SSS-EEEEE-HHHHHHH CS
                              SelA 198 ealaeGvdlvsfsGDkllGgpqaGiivGkkeliekl 233
                                       ++ + G+d + fsG k+lG    G++ Gk e++ ++
  gi|385806224|ref|YP_005842622.1| 212 DVKKLGADFIVFSGHKMLGPLGIGVLYGKLEMLREI 247
                                       34467**************************99887 PP

>> GDC-P  Glycine cleavage system P-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.5e-05     0.027     143     267 ..     103     235 ..      93     240 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.5e-05
                                       HHHHHHH-SSS--EEEEETTS-HHHHHHHHHHHGGGT-EEEEE-GGG--S-............S-EEEEEEEES-TT CS
                             GDC-P 143 vllaaraskkkakkvvvdkkvhpqtlevlktrakglgieivevdlteekvtd.........kekevagvlvqypnte 210
                                         l++r  k+ ++k+v+ +  h  ++   +  ak +g  ++ + + +++  d         ++++v + +    n++
  gi|385806224|ref|YP_005842622.1| 103 YPLVMRGLKEGRDKIVITEMEHHSNMLPWRNAAKIFGARVEYARVDKDGYIDvkrlinkldEKTSVLA-ITHASNVT 178
                                       557889999999******************************99999999888999997533333333.467899** PP

                                       SB----HHHHHHHHHTT-EEEEEE-TTGGGTB--HHHHT-SEEEEE-TTTT---GGG CS
                             GDC-P 211 GriedlkelvekakkkkslvvvaadllaLtllkpPgelgaDivvGsaqrfGvPlgyG 267
                                       G i+++++++++akk+ ++v + +      l     +lgaD +v s+ ++  Plg G
  gi|385806224|ref|YP_005842622.1| 179 GIINPIENISKEAKKYGITVFADVAQSIPHLSIDVKKLGADFIVFSGHKMLGPLGIG 235
                                       ****************99887544433333444567999999999999987788876 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 ?   11.5   0.1   0.00015      0.27      48     100 ..      53     105 ..      42     126 .. 0.88
   2 ?   -2.4   0.0         3   5.3e+03      73     117 ..     157     201 ..     154     207 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00015
                         TetR_C_10  48 ethkdakyLdeeskelfeelmdfltdliekGkekGvirslpskaliaivygal 100
                                       + h+  +yL+++s el+ee  +++ + i++   +  i sl+++  + ++  +l
  gi|385806224|ref|YP_005842622.1|  53 NVHRGHHYLSKKSTELYEEAHEIVAKHINADSWQEIIFSLNTSYAVNLMAYPL 105
                                       8899************************************9988887766555 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3
                         TetR_C_10  73 dliekGkekGvirslpskaliaivygallklyklletgkieatkd 117
                                        li+k  ek  +  +   + ++ + +++++++k  +   i+   d
  gi|385806224|ref|YP_005842622.1| 157 RLINKLDEKTSVLAITHASNVTGIINPIENISKEAKKYGITVFAD 201
                                       567777788888888888888888889999988777766666555 PP

>> TFA2_Winged_2  TFA2 Winged helix domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.96   1.7e+03      45      58 ..     105     118 ..     105     120 .. 0.91
   2 ?    6.7   0.0    0.0033       5.9      25      48 ..     149     172 ..     149     201 .. 0.87
   3 ?    0.7   0.0      0.25   4.4e+02      15      40 ..     192     218 ..     184     227 .. 0.78
   4 ?   -3.8   0.0         6   1.1e+04      30      43 ..     286     299 ..     283     304 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.96
                     TFA2_Winged_2  45 lvlrtkkdgqpkiV 58 
                                       lv+r+ k+g+ kiV
  gi|385806224|ref|YP_005842622.1| 105 LVMRGLKEGRDKIV 118
                                       799**9***99998 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0033
                     TFA2_Winged_2  25 kdswpdveealeeLeaegeilvlr 48 
                                       kd++ dv+  +++L ++  +l + 
  gi|385806224|ref|YP_005842622.1| 149 KDGYIDVKRLINKLDEKTSVLAIT 172
                                       8*******************9985 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.25
                     TFA2_Winged_2  15 kaeGikv.kdLkdswpdveealeeLea 40 
                                       k+ Gi v +d+  s+p+ + ++++L a
  gi|385806224|ref|YP_005842622.1| 192 KKYGITVfADVAQSIPHLSIDVKKLGA 218
                                       555666548999************988 PP

  == domain 4  score: -3.8 bits;  conditional E-value: 6
                     TFA2_Winged_2  30 dveealeeLeaege 43 
                                       + +ea++ Le+ g+
  gi|385806224|ref|YP_005842622.1| 286 GLMEAVKYLEKVGK 299
                                       56788998988654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       841  (0.0469072); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.68u 0.34s 00:00:01.02 Elapsed: 00:00:00.53
# Mc/sec: 2324.84
//
Query:       gi|385806225|ref|YP_005842623.1|  [L=364]
Description: tyrosyl-tRNA synthetase [Fervidicoccus fontis Kam940]
Scores for complete 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-41  140.8   0.1    1.3e-39  136.3   0.1    2.0  1  tRNA-synt_1b   tRNA synthetases class I (W and Y)
  ------ inclusion threshold ------
      0.092   13.5   0.1       0.66   10.8   0.0    2.5  2  PSK_trans_fac  Rv0623-like transcription factor


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 !  136.3   0.1   1.5e-43   1.3e-39       5     292 ..      32     334 ..      29     335 .. 0.90

  Alignments for each domain:
  == domain 1  score: 136.3 bits;  conditional E-value: 1.5e-43
                                       --EEEEEEETSSS-BGGGHHHHHHHHHHHHTTSEEEEEEEHHHHHTTTTT-SSHHHHHHHHHHHHHHHHHHHHHTCH CS
                      tRNA-synt_1b   5 plrvysGidPTgklHlGylvplkklvelqkaghevffliaDlhAiigdpskaeerklrkreevlenaikaqlakgld 81 
                                       +l  y+G +P+g +H+G++v   k  +l +ag+++ +l a +hA ++d+ + +++ +++++++   +   + a+g++
  gi|385806225|ref|YP_005842623.1|  32 KLEGYLGYEPSGLFHIGWMVWAYKAKDLVEAGVNLRLLEATWHAWVNDKFNGNMQVIKDDAKYIRHS---LKAIGIP 105
                                       6778**********************************************99***************...******* PP

                                       TTTEEEEETHHHHTTHHHHHHHHHHHTTCBHHHHHHHHHCCHHCSSSC--BHHHHHHHHHHHHHHHHTCHSEEEEEG CS
                      tRNA-synt_1b  82 pekaevvlqsewlehlelaellrdlgklgslnrmlqfksvkkrleegegislgeftYplLqaaDilllkadlvpgGs 158
                                       +ek++++   +  + ++++ ll +++k ++l+r  +  +++ r ee+ ++  + ++Yp +qa Di+++  ++ +gG 
  gi|385806225|ref|YP_005842623.1| 106 VEKIKFIDAEDLVSDKDYWALLLKVAKNTTLARAKRTLTIMGRKEEEAELDSSKIIYPFMQATDIYYMGLNIALGGI 182
                                       **********************************************889**************************** PP

                                       GGHHHHHHHHHHHHHHHHHSTTSS-EEEEET-BBSTTS...............SSBTTCETTCGC-BTTCCHHHHHH CS
                      tRNA-synt_1b 159 DQkqnielgrdlarrfnkkevfkkpegltvplltgldG...............ekKmSKSagnsaIfLddekesvkk 220
                                       DQ++   l r+la++++ k    k +++ +plltgl+G               e KmSKS+++s+I + d++e++++
  gi|385806225|ref|YP_005842623.1| 183 DQRKVHMLVRELAEKVGAK----KIVAIHTPLLTGLQGsgragggsskdeimsEVKMSKSKPESTIIIHDSPEDIRE 255
                                       ******************9....88888888888888744444444444444347********************** PP

                                       HHHHCHCSTTC........SHHHHHHHHHTHHHCHHHHHHHHCCSEEESSHHHHHHHHHCCCCHHHHHHHHHHHHHH CS
                      tRNA-synt_1b 221 kiqkavtdsde........evekllklktelsnelierleavsgkkpkreaeellaeevtklvhggdlkkalaealn 289
                                       ki +a++  +          +++ll+ +   s   +er ++++g  +  ++ el+  + ++++h+ dlkka+a+al+
  gi|385806225|ref|YP_005842623.1| 256 KIMNAYCPKQVvefnpiieINKYLLFSQDNFSL-YVERPSEYGGPIEIYSYDELERMYLKGEIHPLDLKKATADALI 331
                                       ********9998777776333444444555555.99***********78**************************99 PP

                                       HHH CS
                      tRNA-synt_1b 290 ell 292
                                       + l
  gi|385806225|ref|YP_005842623.1| 332 KKL 334
                                       866 PP

>> PSK_trans_fac  Rv0623-like transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   7.4e-05      0.66       5      38 ..     182     215 ..     173     241 .. 0.83
   2 ?   -1.1   0.1      0.39   3.5e+03       7      18 ..     344     355 ..     320     361 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 7.4e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                     PSK_trans_fac   5 IkdpeverlareLarltgeskteAvrrAleerle 38 
                                       I+  +v+ l+reLa+  g+ k+ A+++ l   l+
  gi|385806225|ref|YP_005842623.1| 182 IDQRKVHMLVRELAEKVGAKKIVAIHTPLLTGLQ 215
                                       67889********************987766665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.39
                                       XXXXXXXXXXXX CS
                     PSK_trans_fac   7 dpeverlareLa 18 
                                       ++e+++la ++a
  gi|385806225|ref|YP_005842623.1| 344 NKEAKELALKIA 355
                                       455555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); 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: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 2078.27
//
Query:       gi|385806226|ref|YP_005842624.1|  [L=410]
Description: DNA primase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.5e-11   42.8   0.1      2e-10   41.0   0.1    2.0  1  Toprim_4         Toprim domain
      4e-08   33.6   0.1    1.8e-07   31.5   0.0    2.2  2  Toprim_2         Toprim-like
    1.4e-07   31.7   0.7    7.5e-07   29.3   0.1    2.4  2  Toprim           Toprim domain
  ------ inclusion threshold ------
      0.037   13.6   1.2        6.7    6.2   0.2    2.5  2  DUF1188          Protein of unknown function (DUF1188)
       0.13   11.1   0.2       0.18   10.6   0.2    1.2  1  Glyco_transf_54  N-Acetylglucosaminyltransferase-IV (GnT-IV) 
       0.17   10.3   1.9       0.38    9.2   0.2    2.0  2  Aldedh           Aldehyde dehydrogenase family


Domain annotation for each model (and alignments):
>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   0.1   6.8e-14     2e-10       2      76 ..     166     230 ..     165     242 .. 0.82

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 6.8e-14
                          Toprim_4   2 eiiiVEgyaDvlalekagiknvvavlg..galspldgirpeklktenlveaekkvkevilaldgDaeGeataerlae 76 
                                       ++iiVEg+aDvl+l ++g++n++a  g  g +  ++ ++  +l +        k ++vi ++dgD++Ge     l++
  gi|385806226|ref|YP_005842624.1| 166 TLIIVEGRADVLNLLRYGYNNAIALEGakGTI--PESVK--QLAS--------KKQKVIAFTDGDHAGELILRTLLN 230
                                       79*************************77777..66666..5666........238************987776665 PP

>> Toprim_2  Toprim-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.0   5.9e-11   1.8e-07       1      88 [.     168     248 ..     168     250 .. 0.87
   2 ?   -2.9   0.0       3.2   9.6e+03       8      42 ..     350     380 ..     349     385 .. 0.62

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 5.9e-11
                          Toprim_2   1 vvfEgaiDalSlaqlgikektnvvalgGt.alteaalkllerypekkvvlalDnDkaGrkaakrlaellreagvrek 76 
                                       +++Eg  D+l l+++g +   n++al G  +  ++ +k+l+++ ++kv+  +D D aG+   ++l + ++     + 
  gi|385806226|ref|YP_005842624.1| 168 IIVEGRADVLNLLRYGYN---NAIALEGAkGTIPESVKQLASK-KQKVIAFTDGDHAGELILRTLLNNVK----IDL 236
                                       69***************8...********98888999999999.6779999**********999998884....367 PP

                          Toprim_2  77 irelpegkDwne 88 
                                       ++++p+gk + +
  gi|385806226|ref|YP_005842624.1| 237 VAKTPQGKEVED 248
                                       888888887766 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.2
                          Toprim_2   8 DalSlaqlgikektnvvalgGtalteaalkllery 42 
                                       D lS +++++   ++ v   G  +t++++++ +++
  gi|385806226|ref|YP_005842624.1| 350 DTLSKLEANK---VKTVVFDGI-ITQRLIDIASQK 380
                                       5555555554...477777777.777777665554 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.47   1.4e+03      38      61 ..     118     143 ..      64     148 .. 0.59
   2 !   29.3   0.1   2.5e-10   7.5e-07       1      93 [.     166     239 ..     166     249 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.47
                                       TTEEEEE..ECTTTHHHHHHHHHHHH CS
                            Toprim  38 efkpvye..eiedkkkvlkalkelak 61 
                                       e+ + ++  e +d k+ lk++++++k
  gi|385806226|ref|YP_005842624.1| 118 ELLKTWQsaEAPDVKDLLKEIQSSLK 143
                                       33333336666666666666666655 PP

  == domain 2  score: 29.3 bits;  conditional E-value: 2.5e-10
                                       EEEEESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHSTTEEEEEECTTTHHHHHHHHHHHHHHSEEEEECSSSHHHH CS
                            Toprim   1 elvivEgpsdaktiakalgsgfqavtaslGhildletefkpvyeeiedkkkvlkalkelakradeiilatDpDreGe 77 
                                       +l+ivEg +d+ ++ ++   g+++++a+ G   ++++                 ++k+la++ +++i  tD+D +Ge
  gi|385806226|ref|YP_005842624.1| 166 TLIIVEGRADVLNLLRY---GYNNAIALEGAKGTIPE-----------------SVKQLASKKQKVIAFTDGDHAGE 222
                                       59***************...9*********9999999.................8********************** PP

                                       HHHHHHHHHHT.HHHTT CS
                            Toprim  78 aiawellevlk.ellen 93 
                                        i   ll+++k +l+ +
  gi|385806226|ref|YP_005842624.1| 223 LILRTLLNNVKiDLVAK 239
                                       *******9998765555 PP

>> DUF1188  Protein of unknown function (DUF1188)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1    0.0022       6.7     142     195 ..     280     331 ..     201     340 .. 0.79
   2 ?    6.2   0.2    0.0022       6.7      14      75 ..     342     407 ..     334     410 .] 0.73

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0022
                                       -HHHHHGGTTTSEEEEEEETTS--SB--HHHHHHHHHHHHHHHHHTSTTEEEEE CS
                           DUF1188 142 ntekrlesveaekkgiLktkglesKTSGtmTLtvdvlrdalneaeelegvLYav 195
                                        t+k le  ++e+k   +++ +e +   +m L++++ ++++++++el+g+L a+
  gi|385806226|ref|YP_005842624.1| 280 VTQKELE--KKEEKLAPQITVTEEQQKPSMPLSIEIPENVMKDMNELKGTLEAI 331
                                       3444445..33333333334444444556********************99776 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0022
                                       SSBHHHHHHHHHHHHHHHHHHHHTT--E..EEEEEES....-CCCHHHHHHHHCCCEEEEEEESSG CS
                           DUF1188  14 kvklvdivkeiaekKaeavleyleeeeleeknvlviG....aYltGaaiakkLskkeevtlvDiep 75 
                                       +v + d+ +++++  a++v++++ +  ++++ + +      +Yl Ga i + L+++e+v+l+ +++
  gi|385806226|ref|YP_005842624.1| 342 RVPVRDLYDTLSKLEANKVKTVVFDGIITQRLIDIASqknvSYLIGARIGNVLKRDEKVVLLSMYD 407
                                       677778888888888888888877666644444443333336*******************98876 PP

>> Glyco_transf_54  N-Acetylglucosaminyltransferase-IV (GnT-IV) conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2   6.2e-05      0.18      13     125 ..     273     384 ..     255     402 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 6.2e-05
                   Glyco_transf_54  13 lkltnilevlphlqkneeslkpavllgkgrtgvs..lvlGiptvkrekksylldTlesllselseeekkdlvvvvfi 87 
                                        + ++ + + ++l k+ee+l+p++++++++++ s  l + ip    +  + l+ Tle++l +    ++ ++v  v +
  gi|385806226|ref|YP_005842624.1| 273 KREEKEEVTQKELEKKEEKLAPQITVTEEQQKPSmpLSIEIPENVMKDMNELKGTLEAILYD----DNWNVVARVPV 345
                                       344455568899*******************99966778888888889999****9999974....55666667777 PP

                   Glyco_transf_54  88 aetdeeyvksvveeikk.kfkkevesgllevisppasyY 125
                                        +   +  k  ++++k+  f+  ++ +l+++ s ++ +Y
  gi|385806226|ref|YP_005842624.1| 346 RDLYDTLSKLEANKVKTvVFDGIITQRLIDIASQKNVSY 384
                                       777777777777777652466667777777776666666 PP

>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.2   0.00013      0.38       8      65 ..      85     143 ..      80     150 .. 0.87
   2 ?   -0.6   0.1      0.12   3.5e+02      22     126 ..     245     344 ..     238     346 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00013
                                       EEEEEETT.TCEEEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHH CS
                            Aldedh   8 tievinPa.tgeviakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlle 65 
                                       t++++ P+  + +++++ +   e++++av++Ake  k+w++ +a++ +++L+++++ l+
  gi|385806226|ref|YP_005842624.1|  85 TVDKVGPYnAKVQVTRIVDLRIEKLKKAVERAKELLKTWQSAEAPDVKDLLKEIQSSLK 143
                                       67888899455568899999********************************9988775 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.12
                                       EEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH---HHHHHH.HHHHHHHHH CS
                            Aldedh  22 kvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaeletletGkplaeara.eveeaidvl 97 
                                       +v++ t ++++ a+++A   ++  +  ++e+R+e  + +++ le+++e+la  +t       +e ++  ++ +i++ 
  gi|385806226|ref|YP_005842624.1| 245 EVEDLTGKEIEMALQNAVPPQQFLS--ELEKREEKEEVTQKELEKKEEKLAPQITVT-----EEQQKpSMPLSIEIP 314
                                       6778888999999999998888554..566777777778899999999999877652.....222222555555555 PP

                                       HHHHHHHHHHSEEEEEE.CTTEEEEEEEEE CS
                            Aldedh  98 ryyaelaeklegevlps.segklalvrreP 126
                                       + +++ +++l+g+  ++  +++ ++v r P
  gi|385806226|ref|YP_005842624.1| 315 ENVMKDMNELKGTLEAIlYDDNWNVVARVP 344
                                       555556666555544444455555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1723  (0.0961013); expected 358.6 (0.02)
Passed bias filter:                      821  (0.0457917); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.47
# Mc/sec: 2640.08
//
Query:       gi|385806227|ref|YP_005842625.1|  [L=242]
Description: dTMP kinase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-38  132.1   0.1    2.3e-38  131.8   0.1    1.1  1  Thymidylate_kin  Thymidylate kinase
    1.8e-06   28.0   1.0      2e-05   24.5   1.0    2.2  1  dNK              Deoxynucleoside kinase
    1.5e-05   25.3   0.0    1.9e-05   25.0   0.0    1.1  1  AAA_28           AAA domain
    0.00048   20.6   0.2       0.51   10.8   0.0    2.6  2  AAA_17           AAA domain
     0.0031   18.1   0.2     0.0061   17.1   0.2    1.5  1  AAA_18           AAA domain
      0.004   16.4   0.3      0.011   14.9   0.0    1.7  2  NB-ARC           NB-ARC domain
     0.0043   17.0   0.0     0.0096   15.9   0.0    1.6  2  NACHT            NACHT domain
     0.0095   15.6   0.0       0.02   14.5   0.0    1.4  1  SRP54            SRP54-type protein, GTPase domain
  ------ inclusion threshold ------
      0.015   15.4   0.1       0.54   10.4   0.0    2.4  2  SKI              Shikimate kinase
       0.03   14.2   0.2      0.069   13.1   0.1    1.7  2  NTPase_1         NTPase
      0.049   13.8   0.0      0.072   13.3   0.0    1.5  1  AAA_33           AAA domain
      0.056   13.3   0.0       0.11   12.4   0.0    1.4  1  APS_kinase       Adenylylsulphate kinase
      0.072   13.2   0.1       0.19   11.8   0.0    1.6  2  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
      0.092   11.7   0.0       0.15   11.0   0.0    1.3  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
      0.099   12.3   0.0       0.16   11.7   0.0    1.2  1  AAA_30           AAA domain
       0.12   12.2   0.0       0.27   11.1   0.0    1.6  1  MobB             Molybdopterin guanine dinucleotide synthesis
       0.13   12.7   0.0        0.2   12.2   0.0    1.4  1  ABC_tran         ABC transporter


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 !  131.8   0.1   2.1e-41   2.3e-38       1     185 []      55     235 ..      55     235 .. 0.96

  Alignments for each domain:
  == domain 1  score: 131.8 bits;  conditional E-value: 2.1e-41
                                       EEESTTSSHHHHHHHHHHHHHHTTE.EEEESSSTTSHHHHHHHHHHHTCS---HHHHHHHHHHHHHHTTHHHHHHHH CS
                   Thymidylate_kin   1 iEGlDGaGKttqaellkerlkeegikvvltrepggteiGekirelllkeeeleeqteallfaadriehleekikpal 77 
                                       iEG+DG+GKtt+ae++ + l + g++ +l rep +      i++ll+++ ++++  ea+lfa dr    +++i  al
  gi|385806227|ref|YP_005842625.1|  55 IEGIDGSGKTTIAEKVCNLLMQGGKRCILVREPWTL----EIKKLLENNPKIDPVVEAFLFATDRMILNYNVISNAL 127
                                       8***********************99******9955....5788889999*************************** PP

                                       HTT-EEEEES-HHHHHHHHHTTTTTTCHHHHHHGGGTTSE-SEEEEEESSHHHHHTSCCTTSSTTTSHHHHHHHHHH CS
                   Thymidylate_kin  78 kqgktvivdRylfSslaYqgakegvdldlvlslnedvllkPdltflldvdpevalkRlakrdeldeeeeeqldflrk 154
                                       k+++ vi+dR+++Ssl+Yq + +  + +++  ln  ++ kPd++flldv++e++lkRl+++++++ +  e  +fl+k
  gi|385806227|ref|YP_005842625.1| 128 KEDTYVISDRCYLSSLVYQYIRG-AEESIIFALNSLII-KPDAIFLLDVSVETGLKRLMEKKKRELTHLEGFEFLKK 202
                                       ********************855.799*********99.************************************** PP

                                       HHHHHHHHHH..TTSTEEEEETTS-HHHHHHHH CS
                   Thymidylate_kin 155 vrerylelak..ederiliidasksieevheeI 185
                                       v+eryle+ +  +d++i+ id + + ee+ e+I
  gi|385806227|ref|YP_005842625.1| 203 VKERYLEISNtlKDQKIFKIDGEAKPEEISEAI 235
                                       *********998999*************99987 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   1.0   1.9e-08     2e-05       2     198 ..      54     238 ..      53     242 .] 0.80

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.9e-08
                                       EEEESTTSSHHHHHHHHHCCST..CEEEE-HHHHCCSSSSHHHHHHHH.SHHHHHHHHHHHHHHHHHHHHHCHHSSS CS
                               dNK   2 vveGnIgaGKstlvklLskklg..vkvfeEpvdkwtnvqknlLekfYk.dpsrwsfalqtyvllsrlkqqlealatk 75 
                                       ++eG  g+GK+t+++   + l    k +  + + wt   k+lLe+  k dp   +f + t  +   ++++ +al+++
  gi|385806227|ref|YP_005842625.1|  54 AIEGIDGSGKTTIAEKVCNLLMqgGKRCILVREPWTLEIKKLLENNPKiDPVVEAFLFATDRMILNYNVISNALKED 130
                                       79***********99766665222344444677899999999998766599999*********************** PP

                                       -EEEEES-HHHHHHTHHHHHHHTTSS-HHHHHHHHHHHHHHHHHCCH-SEEEEEE--HHHHHHHHHHC.TTCCCTTS CS
                               dNK  76 qvvvleRsiysdryiFakalaekgtlseeelkiykelldnlleelakpdlliYLkasletclerikkR.greeekki 151
                                         v+ +R+  s+  ++        ++   e  i  +l + ++    kpd +  L++s+et l+r+ ++ +re  +  
  gi|385806227|ref|YP_005842625.1| 131 TYVISDRCYLSSL-VYQ-------YIRGAEESIIFALNSLII----KPDAIFLLDVSVETGLKRLMEKkKRELTHLE 195
                                       **********999.664.......566666666666766666....7*****************8655055555577 PP

                                       -HHHHHHHHHHHHHHHTSGGCS-EEEEETSS.-TTTHCCHHHHHHHH CS
                               dNK 152 eldYlekLhekyeewlkklnevpvlvidveeldlvaeeekredvvee 198
                                        +++l+k++e+y e  ++l+   + +id+e     + ee +e + ++
  gi|385806227|ref|YP_005842625.1| 196 GFEFLKKVKERYLEISNTLKDQKIFKIDGEA----KPEEISEAIFNK 238
                                       89****************************9....556666666555 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   1.8e-08   1.9e-05       2     138 ..      53     193 ..      52     217 .. 0.68

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.8e-08
                            AAA_28   2 ivitGgestGKTtlleaLaar....gypvv..pEaareileeklakgedalpwv.edllafaervleeqleeeaaa. 70 
                                       ++i G  ++GKTt++e+  +     g +++  +E+ +  ++++l+++ ++ p v + l a  +++l+       +a 
  gi|385806227|ref|YP_005842625.1|  53 VAIEGIDGSGKTTIAEKVCNLlmqgGKRCIlvREPWTLEIKKLLENNPKIDPVVeAFLFATDRMILNY--NVISNAl 127
                                       789999*********99886656666666556***************998888844444444555555..5555555 PP

                            AAA_28  71 aankvlfcDrglldtlaYarayggeaeae...leaaarekrydlvfllppapeidddgeRredleereaid 138
                                       +++ ++++Dr++l +l+Y   +g e e     l++     + d++fll+++ e+     R  + ++re ++
  gi|385806227|ref|YP_005842625.1| 128 KEDTYVISDRCYLSSLVYQYIRGAE-ESIifaLNSL--IIKPDAIFLLDVSVET--GLKRLMEKKKRELTH 193
                                       89****************9999888.4431113332..2335888888887776..333334445555555 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0    0.0059       6.2       2      16 ..      57      71 ..      56      76 .. 0.90
   2 !   10.8   0.0   0.00048      0.51      99     126 ..     163     190 ..     115     198 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0059
                                      E-TTSSHHHHHHHHH CS
                            AAA_17  2 GgPGsGKgtqceklv 16
                                      G+ GsGK+t++ek+ 
  gi|385806227|ref|YP_005842625.1| 57 GIDGSGKTTIAEKVC 71
                                      899*********986 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00048
                                       HH..SEEEEEE--HHHHHHHHHHHTTST CS
                            AAA_17  99 elkpdaiilleadpeeilerrlkdrtrg 126
                                        +kpdai+ll+++ e+ l+r++++++r+
  gi|385806227|ref|YP_005842625.1| 163 IIKPDAIFLLDVSVETGLKRLMEKKKRE 190
                                       679********************98886 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.2   5.8e-06    0.0061       1     117 [.      53     190 ..      53     200 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.8e-06
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.............gvnlrdvakenglllevdpealdeskrldedkldklldal 64 
                                       +++ G+ G+GKtt+a+ + ++l +               ++++++ +n   ++v ++ l  ++r+  ++ +++++al
  gi|385806227|ref|YP_005842625.1|  53 VAIEGIDGSGKTTIAEKVCNLL-MqggkrcilvrepwTLEIKKLLENNPKIDPVVEAFLFATDRMILNY-NVISNAL 127
                                       689***************6665.3456655666777444444444444434444444222222222222.3444555 PP

                            AAA_18  65 eenssaleegknlvidghlaeleseaakdikk............vvLtaspeelleRlekRgyee 117
                                       +e   ++   + +++++++ +++  a   i +            + L++s e+ l+Rl + +++e
  gi|385806227|ref|YP_005842625.1| 128 KED--TYVISDRCYLSSLVYQYIRGAEESIIFalnsliikpdaiFLLDVSVETGLKRLMEKKKRE 190
                                       554..456666666666666666666666666888888888888999999999999998887765 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.1e-05     0.011      13      43 ..      43      73 ..      33      80 .. 0.85
   2 ?   -1.5   0.0       1.1   1.1e+03      59     103 ..     174     217 ..     158     232 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.1e-05
                                      HCTTTSCSEEEEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC 13 lekdelqslvvalvGmgGvGKttlakqilnk 43
                                      l++de +   va+ G  G+GKtt+a+++ n 
  gi|385806227|ref|YP_005842625.1| 43 LKSDEKKGRYVAIEGIDGSGKTTIAEKVCNL 73
                                      4578888899*****************9985 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.1
                                       EESXXHHHHHHHXXHHHHHCCCTTSSSS-STTSHHHHHHHHCCCT CS
                            NB-ARC  59 vsktdkseeiletilkeLslseddleekeeveslkrklvrlLltk 103
                                       vs +   ++++e+  +eL +  +  e  ++v+++  ++ + L+++
  gi|385806227|ref|YP_005842625.1| 174 VSVETGLKRLMEKKKRELTHL-EGFEFLKKVKERYLEISNTLKDQ 217
                                       555555555555555555333.44444444444555555555554 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   9.1e-06    0.0096       1      31 [.      51      81 ..      51     113 .. 0.81
   2 ?   -2.6   0.0       4.2   4.4e+03     119     151 ..     166     198 ..     152     207 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9.1e-06
                                      SCEEEEC-TTTCHHHHHHHHHHHHCTS-SCC CS
                             NACHT  1 rlvilqGeaGsGKTtLlqklalawaegklpq 31
                                      r+v+++G  GsGKTt ++k++ ++ +g   +
  gi|385806227|ref|YP_005842625.1| 51 RYVAIEGIDGSGKTTIAEKVCNLLMQGGKRC 81
                                      789*********************9998655 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.2
                                       T--EEEEEEECCCHHHHCTTSSCE....EEEE--T CS
                             NACHT 119 peasllltvrpralrdleeqleea..ivlevegfs 151
                                       p a +ll v+ ++   l++++e++  + +++egf+
  gi|385806227|ref|YP_005842625.1| 166 PDAIFLLDVSVETG--LKRLMEKKkrELTHLEGFE 198
                                       55555555555555..6666666655566676665 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   1.9e-05      0.02       4      35 ..      53      84 ..      51      86 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.9e-05
                                      EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEE CS
                             SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvllv 35
                                      +++ G+ G+GKTt + K+ +ll++ gk+++lv
  gi|385806227|ref|YP_005842625.1| 53 VAIEGIDGSGKTTIAEKVCNLLMQGGKRCILV 84
                                      6788***********************99987 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.099     1e+02       2      14 ..      60      72 ..      59      76 .. 0.84
   2 ?   10.4   0.0   0.00051      0.54      85     155 ..     166     237 ..     120     241 .. 0.68

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.099
                                      TSSHHHHHHHHHH CS
                               SKI  2 GaGKstvGkllAk 14
                                      G+GK+t+++++ +
  gi|385806227|ref|YP_005842625.1| 60 GSGKTTIAEKVCN 72
                                      9******998866 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00051
                                       HSEEEEEE--HHHHHHHHHHTTSSGGGCSCHHHHHHHHHHH...HHHHHHCCSSCEEEECTSSHHHHHHHHHHH CS
                               SKI  85 kgiviyLdvsleellerlkadkeRPllqekskeeelleela...ereplyeeaadvvvdeseeskeevaeeile 155
                                          +++Ldvs+e+ l+rl+++k+R l + +    e l++ +    + ++  + ++++  + e+++ee+ e i++
  gi|385806227|ref|YP_005842625.1| 166 PDAIFLLDVSVETGLKRLMEKKKRELTHLEGF--EFLKKVKeryLEISNTLKDQKIFKIDGEAKPEEISEAIFN 237
                                       566889*****************988887777..4444444102222222222333333333333666666655 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   6.6e-05     0.069       2      27 ..      53      78 ..      52      85 .. 0.88
   2 ?   -2.7   0.0       4.4   4.7e+03     142     156 ..     209     223 ..     178     235 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.6e-05
                                      EEEE--TTSSHHHHHHHHHHHH...G CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssg 27
                                      v+i G  G+GKtT+ +kv++ll + g
  gi|385806227|ref|YP_005842625.1| 53 VAIEGIDGSGKTTIAEKVCNLLMQGG 78
                                      688999****************8766 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.4
                                       HHHHT-TT-EEEE-- CS
                          NTPase_1 142 eeirerkdvkvfevt 156
                                       e  +  kd k+f+++
  gi|385806227|ref|YP_005842625.1| 209 EISNTLKDQKIFKID 223
                                       222233444555555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   6.8e-05     0.072       3      32 ..      54      88 ..      53     190 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.8e-05
                            AAA_33  3 llvGlpGsGKstlaerllkklg.....avllssdt 32
                                       + G  GsGK+t ae++++ l      ++l++++ 
  gi|385806227|ref|YP_005842625.1| 54 AIEGIDGSGKTTIAEKVCNLLMqggkrCILVREPW 88
                                      578*************9865555667888888775 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0    0.0001      0.11       3      35 ..      51      83 ..      49      86 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0001
                                      EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEE CS
                        APS_kinase  3 vvvwltGlsgsGKstianalekkLvekgisvyl 35
                                        v + G+ gsGK+tia+++ + L++ g++++l
  gi|385806227|ref|YP_005842625.1| 51 RYVAIEGIDGSGKTTIAEKVCNLLMQGGKRCIL 83
                                      567899******************999998865 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00018      0.19       9      33 ..      60      84 ..      53      86 .. 0.90
   2 ?   -1.6   0.0       2.5   2.7e+03      94      94 ..     181     181 ..      90     213 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                                      TSSHHHHHHHHHHHHHHTT--EEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  9 GvGKTtlaanLaralarrglrVllv 33
                                      G+GKTt+a + + +l ++g+r +lv
  gi|385806227|ref|YP_005842625.1| 60 GSGKTTIAEKVCNLLMQGGKRCILV 84
                                      89******************98876 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.5
                                       H CS
                                       x RF
                              CbiA  94 k 94 
                                       k
  gi|385806227|ref|YP_005842625.1| 181 K 181
                                       1 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 ?   11.0   0.0   0.00014      0.15      29      61 ..      50      82 ..      39      87 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00014
                                      SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EE CS
                              MeaB 29 aqvvGltGvPGaGkstlvealglelrrrGkrva 61
                                       + v + G+ G+Gk t+ e++   l++ Gkr  
  gi|385806227|ref|YP_005842625.1| 50 GRYVAIEGIDGSGKTTIAEKVCNLLMQGGKRCI 82
                                      567899********************9999964 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   0.00015      0.16      17      51 ..      49      83 ..      44      88 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00015
                            AAA_30 17 gdrvavltGpAGtGKttalkalreaweaaggrvig 51
                                      + r+++++G  G+GKtt+ +++ +++ + g+r i+
  gi|385806227|ref|YP_005842625.1| 49 KGRYVAIEGIDGSGKTTIAEKVCNLLMQGGKRCIL 83
                                      55799*******************99999988775 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00025      0.27       2      32 ..      53      83 ..      52      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00025
                              MobB  2 lgivgksgsGKTtLleklipelkarglrvgt 32
                                      ++i g  gsGKTt+ ek+ + l + g r  +
  gi|385806227|ref|YP_005842625.1| 53 VAIEGIDGSGKTTIAEKVCNLLMQGGKRCIL 83
                                      678899****************999988655 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00019       0.2       9      36 ..      48      75 ..      43     155 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00019
                                      ETTSEEEEEESTTSSHHHHHHHHTTSS- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  9 kegekvaivGenGaGKStLlkllagllk 36
                                      k+g+ vai G  G+GK+t+++ +++ll 
  gi|385806227|ref|YP_005842625.1| 48 KKGRYVAIEGIDGSGKTTIAEKVCNLLM 75
                                      7899****************99998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        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 0.31s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1499.02
//
Query:       gi|385806228|ref|YP_005842626.1|  [L=206]
Description: hypothetical protein FFONT_1186 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.14   12.3   0.1         26    5.1   0.0    2.3  2  SelB-wing_2  Elongation factor SelB, winged helix


Domain annotation for each model (and alignments):
>> 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 ?    5.0   0.0    0.0016        28      32      53 ..     147     168 ..     135     169 .. 0.91
   2 ?    5.1   0.0    0.0015        26      31      56 ..     179     204 ..     172     205 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0016
                                       HCCHHHHHHHHHHTTSEEE-SS CS
                       SelB-wing_2  32 aklfqallealvargilavegd 53 
                                       +k++  ll+++++ g++ +e++
  gi|385806228|ref|YP_005842626.1| 147 EKAYKVLLDSMLEFGEITLEDA 168
                                       699***************9986 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0015
                                       -HCCHHHHHHHHHHTTSEEE-SSEEE CS
                       SelB-wing_2  31 paklfqallealvargilavegdwvh 56 
                                       + + + +ll +l++r++l+  g+++h
  gi|385806228|ref|YP_005842626.1| 179 SKNEAKKLLYELIKRKKLEFKGGILH 204
                                       5677899***************9999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       778  (0.0433934); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.50
# Mc/sec: 1227.60
//
Query:       gi|385806229|ref|YP_005842627.1|  [L=492]
Description: glycosyltransferase, family 39 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.2e-06   26.5  15.2    6.2e-06   26.5  15.2    2.5  2  PMT_2     Dolichyl-phosphate-mannose-protein mannosyltransfer


Domain annotation for each model (and alignments):
>> PMT_2  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5  15.2   3.5e-10   6.2e-06       2     158 ..     157     308 ..     156     309 .. 0.73
   2 !    2.3   0.5    0.0099   1.8e+02      25      82 ..     366     422 ..     347     435 .. 0.53

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 3.5e-10
                             PMT_2   2 hPPliawllalftklfgfselairlvsalagvltilllyllarrlfgkraallaalllavvplfvalsa.lftpdap 77 
                                       hPPl  +++al   l+g++    rl+ ++ g+  +++  l   rl g    +++++l+++ ++f  l++ +  +  +
  gi|385806229|ref|YP_005842627.1| 157 HPPLGKYIIALAIYLLGDKPICWRLPGIIEGAAIVIIAALAGWRLAG----IFGMILASTAAFFDPLTTnMASVAML 229
                                       9*****************************99999999888888855....55555555555444444423333444 PP

                             PMT_2  78 lvllwalalylllraleknklkywllagvlfGlgflsKytaallliaall.yllisarrilke.kkpyl.alllall 151
                                        + l  ++++ +l ++ ++k     ++ ++f l+  +Ky  ++l++ +l+ +l+ +++ i+   +k+ l  l++a++
  gi|385806229|ref|YP_005842627.1| 230 DIHLAFFTALGSLFYIYDKKN----FSLLFFSLASTIKYSGLFLIP-FLIlFLYKKENDIIGAfFKVALaQLIVAII 301
                                       455555555666666666663....899******************.777366666555777745666668888899 PP

                             PMT_2 152 lfspvli 158
                                       +f+p +i
  gi|385806229|ref|YP_005842627.1| 302 VFLPYII 308
                                       9999876 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.0099
                             PMT_2  25 rlvsalagvltilllyllarrlfgkraallaal.llavvplfvalsalftpdaplvllw 82 
                                       +++ + a++lt  ++++ + +  +k+   +a l ll+++++f+++ + f  + +l+ ++
  gi|385806229|ref|YP_005842627.1| 366 YIPVFFASLLTFPVYFFKISE--NKNLEKFAGLsLLSFFFFFFYYITYFAGNKTLYSFY 422
                                       455444444444333333333..444444444413333444444444555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (492 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       951  (0.0530426); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); 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: 0.68u 0.32s 00:00:01.00 Elapsed: 00:00:00.52
# Mc/sec: 2866.60
//
Query:       gi|385806230|ref|YP_005842628.1|  [L=161]
Description: AsnC family transcriptional regulator [Fervidicoccus fontis Kam940]
Scores for complete 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-16   58.3   0.0      1e-15   57.4   0.0    1.4  1  AsnC_trans_reg   Lrp/AsnC ligand binding domain
    3.1e-13   49.0   0.5    5.4e-13   48.3   0.5    1.4  1  HTH_24           Winged helix-turn-helix DNA-binding
    6.8e-09   35.4   0.0      1e-08   34.8   0.0    1.3  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
    1.9e-06   27.7   0.1    3.1e-06   27.0   0.1    1.4  1  MarR             MarR family
    4.5e-06   26.4   0.1    7.2e-06   25.8   0.1    1.4  1  HTH_5            Bacterial regulatory protein, arsR family
    0.00021   21.1   0.0    0.00033   20.5   0.0    1.3  1  TrmB             Sugar-specific transcriptional regulator Trm
    0.00029   20.8   0.0    0.00048   20.1   0.0    1.3  1  HTH_20           Helix-turn-helix domain
    0.00041   20.3   0.1    0.00073   19.4   0.1    1.4  1  HTH_11           HTH domain
    0.00043   20.1   0.0    0.00085   19.1   0.0    1.5  1  HxlR             HxlR-like helix-turn-helix
     0.0013   18.5   0.0     0.0021   17.8   0.0    1.2  1  HTH_IclR         IclR helix-turn-helix domain
     0.0016   18.6   0.0     0.0035   17.5   0.0    1.6  1  B-block_TFIIIC   B-block binding subunit of TFIIIC
     0.0027   17.8   0.1     0.0048   17.0   0.1    1.4  1  DUF2250          Uncharacterized protein conserved in archaea
     0.0039   17.7   0.4     0.0086   16.6   0.4    1.5  1  Mga              Mga helix-turn-helix domain
     0.0055   16.6   0.0     0.0099   15.7   0.0    1.4  1  MarR_2           MarR family
     0.0086   16.3   0.1      0.042   14.0   0.1    2.0  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
  ------ inclusion threshold ------
      0.014   15.4   0.0      0.021   14.8   0.0    1.4  1  HTH_Crp_2        Crp-like helix-turn-helix domain
      0.026   14.7   0.0      0.043   14.0   0.0    1.4  1  AsnC_trans_reg2  AsnC-like ligand binding domain
      0.028   14.2   0.0      0.047   13.4   0.0    1.4  1  HTH_DeoR         DeoR-like helix-turn-helix domain
      0.031   14.2   0.4      0.068   13.1   0.2    1.7  2  RuvB_C           RuvB C-terminal winged helix domain
      0.069   13.3   0.0      0.095   12.8   0.0    1.2  1  DprA_WH          DprA winged helix domain
      0.098   12.9   0.0       0.19   11.9   0.0    1.5  1  HTH_34           Winged helix DNA-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 !   57.4   0.0   1.2e-18     1e-15       1      74 [.      78     147 ..      78     148 .. 0.97

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 1.2e-18
                                       EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
                    AsnC_trans_reg   1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74 
                                       ++ s+e++h   +eefe+++ ++p+V+ +y +tGd+d ++  ++r++e+l+ f+++ + ++p v+rt t+i+l+
  gi|385806230|ref|YP_005842628.1|  78 INFSVEGSH---IEEFEKQISNHPNVLFLYDITGDFDVIAVTRFRNIEELDYFIKN-VLKNPYVKRTITNIALR 147
                                       56799*999...********************************************.**************997 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.5   6.3e-16   5.4e-13       1      47 [.      12      58 ..      12      59 .. 0.98

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 6.3e-16
                            HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      lde+d+kIL  L   +++s ++L+  lg+++stv +r+k+Lee+G+I
  gi|385806230|ref|YP_005842628.1| 12 LDEIDLKILTHLSNSSKTSLNQLSNILGIPVSTVFARIKKLEEKGII 58
                                      7*********************************************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 !   34.8   0.0   1.2e-11     1e-08       1      42 []      12      53 ..      12      53 .. 0.99

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 1.2e-11
                     HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                      LDeiD+kIL +L   +++s  +L+  +G+  stv +R+++Le
  gi|385806230|ref|YP_005842628.1| 12 LDEIDLKILTHLSNSSKTSLNQLSNILGIPVSTVFARIKKLE 53
                                      8****************************************8 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.1   3.6e-09   3.1e-06       6      55 ..      17      66 ..      12      70 .. 0.92

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 3.6e-09
                                      HHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTS CS
                              MarR  6 fviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRskspeD 55
                                      ++iL+ l+++   s+ +L + lg+  stv   +++Le+kG i+++    D
  gi|385806230|ref|YP_005842628.1| 17 LKILTHLSNSSKTSLNQLSNILGIPVSTVFARIKKLEEKGIIDKYTLSVD 66
                                      68*****************************************9987666 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.1   8.5e-09   7.2e-06       5      47 .]      17      60 ..      13      60 .. 0.93

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 8.5e-09
                                      HHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5  5 lkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                      lkIL  L++ ++++  +l+++lg++ stv    kkL+e G+++k
  gi|385806230|ref|YP_005842628.1| 17 LKILTHLSNsSKTSLNQLSNILGIPVSTVFARIKKLEEKGIIDK 60
                                      8********777*****************************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 !   20.5   0.0   3.9e-07   0.00033       4      54 ..      10      60 ..       7      70 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 3.9e-07
                                      CHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEE CS
                              TrmB  4 lGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVer 54
                                      + L e + k+ + L ++ + + ++++++lg+p s+v   +++Le+kG++++
  gi|385806230|ref|YP_005842628.1| 10 YQLDEIDLKILTHLSNSSKTSLNQLSNILGIPVSTVFARIKKLEEKGIIDK 60
                                      678999******************************************987 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   5.6e-07   0.00048      13      55 ..      17      59 ..      12      63 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 5.6e-07
                                      HHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20 13 rrilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55
                                      ++il +L+     ++++l   l+++ +t+  ++++Lee g+++
  gi|385806230|ref|YP_005842628.1| 17 LKILTHLSNSSKTSLNQLSNILGIPVSTVFARIKKLEEKGIID 59
                                      89***************************************97 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   8.6e-07   0.00073       3      44 ..      17      61 ..      16      72 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 8.6e-07
                            HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg....v 44
                                      l+il+ L ++ ++ s ++L+  L++  +tv  +Ik+Lee+g    +
  gi|385806230|ref|YP_005842628.1| 17 LKILTHL-SNSSKTSLNQLSNILGIPVSTVFARIKKLEEKGiidkY 61
                                      58999**.666679***************************54444 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   9.9e-07   0.00085       9      67 ..      18      76 ..      14      94 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 9.9e-07
                                      HHHHHHTT.S-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-T CS
                              HxlR  9 lilvellk.gkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYslte 67
                                       il++l +  k   ++l+++l +i+ ++  +r+++Le++g+i++ +++  P+k  +++t+
  gi|385806230|ref|YP_005842628.1| 18 KILTHLSNsSKTSLNQLSNIL-GIPVSTVFARIKKLEEKGIIDKYTLSVDPKKLGFNVTA 76
                                      589999995666789999888.9******************************9999885 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.4e-06    0.0021       6      48 ..      17      58 ..      16      60 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.4e-06
                                      HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyv 48
                                      l iL +l+      +l +l++ +g+p Stv+  ++ L+e G++
  gi|385806230|ref|YP_005842628.1| 17 LKILTHLSNSSKT-SLNQLSNILGIPVSTVFARIKKLEEKGII 58
                                      6799999999997.9*************************987 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   4.1e-06    0.0035      22      69 ..      32     103 ..      29     105 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.1e-06
                    B-block_TFIIIC  22 sdLakeskqdprslfyrlksLekkgLIvkqsii........................dsatkksistsllvl 69 
                                       ++L++++++ ++ +f r+k+Le+kg I k ++                         + +++ s++ ++l+l
  gi|385806230|ref|YP_005842628.1|  32 NQLSNILGIPVSTVFARIKKLEEKGIIDKYTLSvdpkklgfnvtaiinfsvegshieEFEKQISNHPNVLFL 103
                                       68999***************************7666666666666666666666666666666666666665 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   5.6e-06    0.0048       4      56 ..      10      62 ..       7      66 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.6e-06
                           DUF2250  4 leedelalkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlerve 56
                                      ++ de +lk+l hl +       ++++ l ip++ v   +kkLee G++++++
  gi|385806230|ref|YP_005842628.1| 10 YQLDEIDLKILTHLSNSSKTSLNQLSNILGIPVSTVFARIKKLEEKGIIDKYT 62
                                      678999*********************************************98 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.4     1e-05    0.0086      15      65 ..      13      65 ..       3      73 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1e-05
                                      HSHHHHHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHHHH..HCHCCT-EE CS
                               Mga 15 eslkyqllkflfeeeevsieelaqelyiSestlkrkikelnk..lLkefdlel 65
                                      + +++++l++l ++ ++s+ +l++ l i  st++  ik+l++   + ++ l++
  gi|385806230|ref|YP_005842628.1| 13 DEIDLKILTHLSNSSKTSLNQLSNILGIPVSTVFARIKKLEEkgIIDKYTLSV 65
                                      4789************************************8733577888887 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.2e-05    0.0099      10      54 ..      19      61 ..      12      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.2e-05
                                      HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      +L +L ++     + ++l   lg++ s+v  ++k+L+++G + + 
  gi|385806230|ref|YP_005842628.1| 19 ILTHLSNSSK--TSLNQLSNILGIPVSTVFARIKKLEEKGIIDKY 61
                                      7888888888..899**************************9875 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.1   4.9e-05     0.042      14      53 ..      20      59 ..       7      62 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.9e-05
                                      HHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                    Fe_dep_repress 14 YtlseekkvvktkdlaerLnvspssVsemlkkLekdGyve 53
                                      +t   ++++ +  +l+ +L++  s+V   +kkLe++G ++
  gi|385806230|ref|YP_005842628.1| 20 LTHLSNSSKTSLNQLSNILGIPVSTVFARIKKLEEKGIID 59
                                      4444466777889***********************9765 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 ?   14.8   0.0   2.5e-05     0.021      23      55 ..      30      62 ..       9      71 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.5e-05
                                      HHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETE CS
                         HTH_Crp_2 23 tqeelAsmlGltretvsrilseLkreglisrgr 55
                                      +  +l+++lG+  +tv   +++L+++g+i++ +
  gi|385806230|ref|YP_005842628.1| 30 SLNQLSNILGIPVSTVFARIKKLEEKGIIDKYT 62
                                      6689*************************9653 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 ?   14.0   0.0     5e-05     0.043       1      66 [.      69     134 ..      69     148 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5e-05
                   AsnC_trans_reg2   1 klGfkanalvawkvpeerveevaevvaelpevtHcYeRewpynlyfmvharseeeveevlaeiaaa 66 
                                       klGf+ +a + ++v+ +++ee+ ++++++p+v   Y    ++ + +++  r+ ee++ +++++ ++
  gi|385806230|ref|YP_005842628.1|  69 KLGFNVTAIINFSVEGSHIEEFEKQISNHPNVLFLYDITGDFDVIAVTRFRNIEELDYFIKNVLKN 134
                                       79********************************99998899888888888888888888887665 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   5.5e-05     0.047       4      46 ..      18      60 ..      16      62 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.5e-05
                          HTH_DeoR  4 qilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltR 46
                                      +il  l ++ k s+++l++ lg+   T+   +++Lee+g++ +
  gi|385806230|ref|YP_005842628.1| 18 KILTHLSNSSKTSLNQLSNILGIPVSTVFARIKKLEEKGIIDK 60
                                      7999************************999*********976 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 ?   13.1   0.2   7.9e-05     0.068       4      42 ..      12      47 ..      10      60 .. 0.91
   2 ?   -2.6   0.0       6.3   5.4e+03      53      64 ..     136     142 ..     130     150 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.9e-05
                                      --HHHHHHHHHHHHT.TT--B-HHHHHHHTT--HHHHHH CS
                            RuvB_C  4 LdeldikyLkllkekfkggpvglktlaailgeeketied 42
                                      Lde+d k+L  l    + ++++l+ l++ilg++ +t+  
  gi|385806230|ref|YP_005842628.1| 12 LDEIDLKILTHLS---NSSKTSLNQLSNILGIPVSTVFA 47
                                      89**********9...689****************9965 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6.3
                                       SEEEETTEEEE- CS
                            RuvB_C  53 lIertsrGRilT 64 
                                       +++rt     +T
  gi|385806230|ref|YP_005842628.1| 136 YVKRT-----IT 142
                                       55554.....44 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00011     0.095       8      53 ..      10      56 ..       3      61 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00011
                           DprA_WH  8 pplddlerrvLaaLgp.ePvhvDqLvrrtglpaaevsaaLleLELaG 53
                                       +ld+   ++L++L++ + +++ qL+  +g+p+++v a    LE +G
  gi|385806230|ref|YP_005842628.1| 10 YQLDEIDLKILTHLSNsSKTSLNQLSNILGIPVSTVFARIKKLEEKG 56
                                      57899999******98469******************9998888666 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00023      0.19       2      44 ..      16      58 ..      15      71 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00023
                            HTH_34  2 RlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYi 44
                                       l++l+ L+  ++ + ++l++ l++  +   + +kkLe++g i
  gi|385806230|ref|YP_005842628.1| 16 DLKILTHLSNSSKTSLNQLSNILGIPVSTVFARIKKLEEKGII 58
                                      699*************************************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       870  (0.0485247); expected 358.6 (0.02)
Passed bias filter:                      635  (0.0354175); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 937.47
//
Query:       gi|385806231|ref|YP_005842629.1|  [L=264]
Description: SPP-like hydrolase [Fervidicoccus fontis Kam940]
Scores for complete 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   83.8   1.6    3.7e-15   56.4   0.5    2.1  2  Hydrolase_3  haloacid dehalogenase-like hydrolase
    9.1e-08   31.9   0.0    1.2e-07   31.6   0.0    1.2  1  S6PP         Sucrose-6F-phosphate phosphohydrolase
     0.0045   17.4   0.2        4.3    7.7   0.0    3.0  3  HAD          haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
       0.11   12.7   0.0        1.5    9.1   0.0    2.2  1  Hydrolase    haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0   8.7e-10   3.9e-06       1      71 [.      20      93 ..      20     124 .. 0.86
   2 !   56.4   0.5   8.3e-19   3.7e-15     152     252 ..     147     247 ..     115     249 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 8.7e-10
                                      EEEEIIIII.S-TTS-.--HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEEEGGGTEE..ECTTT CS
                       Hydrolase_3  1 ialDlDGTL.lnsdkk.isektkeaikklkekgikvviATGRslravlpvleelgldlpvialNGali..ddekg 71
                                      ia+D+DGT+  n d+  i+ + +e i+++++ +i +++ +++ +  +  +++ +g + ++++ NG++i    e+g
  gi|385806231|ref|YP_005842629.1| 20 IATDVDGTItANRDGYfIPSEVIECIREIRKYNIMLIFVSANAFPVLYGLARYIGAK-AIVSENGCIIasLNEHG 93
                                      89*******66788889**************************************88.**********7633444 PP

  == domain 2  score: 56.4 bits;  conditional E-value: 8.3e-19
                                       HHHHHHHHHHHHHCTTTE....EEEEESTTEEEEEETT-SHHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSE CS
                       Hydrolase_3 152 ekldelekelksklnkll....titssskgyleimpkgvsKgtalkklakelnisleeviafGDgeNDieMLeaagl 224
                                       e    l++++k+ + k+      ++++s++ + i+pk+  K  +lkk+ + l+i+l++++ +GD+  D+e ++ +g+
  gi|385806231|ref|YP_005842629.1| 147 E----LIQKIKKIVIKNGydskVNVNYSGYAFHITPKEGGKSVGLKKISEILGIELKNTLGIGDSYMDLEFIQLTGV 219
                                       2....334444433333334448899*************************************************** PP

                                       EEEETTS-HHHHHHSSEEE--GGGTHHH CS
                       Hydrolase_3 225 gvAmgnaseevkkaAdyvtksnnedGVa 252
                                        vA++na+e +k + d +t+  +  G a
  gi|385806231|ref|YP_005842629.1| 220 KVAVRNADEDLKRNVDIITDEESGYGFA 247
                                       *******************987766655 PP

>> S6PP  Sucrose-6F-phosphate phosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   2.6e-11   1.2e-07       6     215 ..      21     231 ..      18     257 .. 0.76

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 2.6e-11
                                       EE-TBTTTB..S-HHHH.HHHHHHHH.GGGGGEEEEEE-SS-HHHHHHHHHHHT----SEEEETTTTEEEE..TTEE CS
                              S6PP   6 vsdLDntlv.dgdneal.arlnelleaeerkdvllvfaTGRsldsakellkeknllkPdvlitsvGteiyygeelvp 80 
                                       ++d+D+t++ ++d   +  +  e++++ ++ +++l+f+++  +     l    + +  ++++++ G  i++ +e  +
  gi|385806231|ref|YP_005842629.1|  21 ATDVDGTITaNRDGYFIpSEVIECIREIRKYNIMLIFVSANAFPVLYGL---ARYIGAKAIVSENGCIIASLNEHGR 94 
                                       6677777764222222212333333336666777777766555544444...3445667899999999999999999 PP

                                       -HHHHHHHHTT--H..HHHHHHHHT-TTEEE--GGG-BTTBEEEEE-TTS-THHHHHHHHHHHTTTS-EEEEEE.TT CS
                              S6PP  81 dkaweeildekwdr..qavvealaklpeLtlQpeeeqrehKvSyfvdkekaaevlkeleqlLekreldvkviys.sg 154
                                       + +  ei  + +++   ++v++++++ +   Q+++++  + +    ++    e++++++++  k++ d kv  + sg
  gi|385806231|ref|YP_005842629.1|  95 EMNIYEICGRGYRElvSKIVSEMGDFLKESWQNDYRKYDFALIQKDNRVSHIELIQKIKKIVIKNGYDSKVNVNySG 171
                                       9999999999998777888888888888888888887777766666666667889***********99998654268 PP

                                       TEEEEEETT-SHHHHHHHHHHHHT--GGGEEEEE-SGGGHHHHTSSSEEEE-TT--HHHHH CS
                              S6PP 155 kdlDvlPkraskgeAlryLakkleleleqilvcGdsgnDeellignvlgVvVgnaqeellq 215
                                        ++ + Pk+++k+  l+ +++ l++el+++l  Gds  D e ++ +   V V+na+e  l+
  gi|385806231|ref|YP_005842629.1| 172 YAFHITPKEGGKSVGLKKISEILGIELKNTLGIGDSYMDLEFIQLTGVKVAVRNADED-LK 231
                                       89*****************************************999999*******99.43 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1     0.039   1.8e+02       2      17 ..      21      36 ..      20      37 .. 0.77
   2 ?    4.0   0.0     0.013        58      88     130 ..      38      81 ..      32     100 .. 0.87
   3 !    7.7   0.0   0.00095       4.3     137     186 ..     168     213 ..     147     215 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.039
                               HAD  2 lfDfDgTLldgdslel 17
                                        D+DgT++++  +++
  gi|385806231|ref|YP_005842629.1| 21 ATDVDGTITANRDGYF 36
                                      57*******9965554 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.013
                               HAD  88 p.galellaahraaGdrvvvvSgglrplvepllaelgadevlat 130
                                       p ++ e +++ r+ ++ ++ vS++  p++  l++  ga++++++
  gi|385806231|ref|YP_005842629.1|  38 PsEVIECIREIRKYNIMLIFVSANAFPVLYGLARYIGAKAIVSE 81 
                                       55788899999999***********************9999887 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.00095
                               HAD 137 rltgelglegkpvrgegkvaalrewlaaegegidleevvayGDspsDlpl 186
                                        ++g ++++ +   g  k   l++    e  gi+l+++  +GDs+ Dl++
  gi|385806231|ref|YP_005842629.1| 168 NYSGYAFHITPKEGG--KSVGLKK--ISEILGIELKNTLGIGDSYMDLEF 213
                                       566666666655555..6666666..99999*****************86 PP

>> Hydrolase  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   0.00033       1.5       2     205 ..      18     213 ..      17     218 .. 0.44

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00033
                                       SEEEEESBTTTBCHH......HHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTEHHHHT CS
                                       xxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase   2 ktvvfDkdGTLttge......psvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrgayaig 72 
                                       + ++ D+dGT+t  +      ++v ++i+++ ++ +  l ++                    + +a       ++ g
  gi|385806231|ref|YP_005842629.1|  18 DSIATDVDGTITANRdgyfipSEVIECIREI-RKYNIMLIFV--------------------SANAF-----PVLYG 68 
                                       6688899999994444447777777777777.3333333333....................22222.....22222 PP

                                       HHHHHHHHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHH.HH..HTTEEEEEEESSEH. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx..xxxxxxxxxxxxxx. RF
                         Hydrolase  73 kpewltaldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavas.Lk..aagievvlltgdnp. 145
                                         +++ a  i ++ g  i s++++gr+  +   ++++    +   k+  e+ +++++ ++   ++++ +l+  dn+ 
  gi|385806231|ref|YP_005842629.1|  69 LARYIGAKAIVSENGCIIASLNEHGREMNIY--EICGRGYRELVSKIVSEMGDFLKEsWQndYRKYDFALIQKDNRv 143
                                       2222222222222244444444444444444..33333333333334444444444321111112234444444443 PP

                                       ...HHHHHHHHHTTGGGESEEEEHHCES.......STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHH CS
                                       ...xxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 146 ...etaeraanqlGddyfdaviasdiet.......vakpspegkvaaireLqgkpeevamVGDgvnDaaa 205
                                          e  +++ + + ++ +d ++++  ++         + +  g++++ + L+++ ++++ +GD+  D+++
  gi|385806231|ref|YP_005842629.1| 144 shiELIQKIKKIVIKNGYDSKVNVNYSGyafhitpKEGGKSVGLKKISEILGIELKNTLGIGDSYMDLEF 213
                                       3332222222221111122222222222222223377778888888888888999999999999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       749  (0.0417759); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 1704.43
//
Query:       gi|385806232|ref|YP_005842630.1|  [L=303]
Description: phosphoesterase, DHHA1 [Fervidicoccus fontis Kam940]
Scores for complete 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-07   30.8   0.0    6.8e-07   29.8   0.0    1.5  1  DHHA1          DHHA1 domain
    1.3e-06   28.6   0.0    2.1e-06   27.9   0.0    1.3  1  DHH            DHH family
  ------ inclusion threshold ------
      0.016   15.4   0.2      0.016   15.4   0.2    1.8  2  Kindlin_2_N    Kindlin-2 N-terminal domain
      0.016   15.7   0.0      0.032   14.7   0.0    1.5  1  CoA_binding_2  CoA binding domain
      0.018   14.9   0.1      0.034   14.0   0.1    1.4  1  DUF4897        Domain of unknown function (DUF4897)
      0.051   13.8   0.5       0.13   12.5   0.5    1.6  1  DUF1799        Phage related hypothetical protein (DUF1799)
       0.18   12.1   0.2       0.28   11.5   0.2    1.6  1  PHP            PHP 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 !   29.8   0.0   2.6e-10   6.8e-07      21     124 ..     192     291 ..     179     302 .. 0.62

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 2.6e-10
                                       HHHHHHHHHHHHTCEEEC...TCEEEEEECHCCHHHHHHHHHHHHHHTHGBT.TCEEEEEEEECTEEEEEEEESSHS CS
                             DHHA1  21 alaklkaeellekaeevk...gvkvlvaevgeewdagalgiaadklksklkk.pvivfvakeegdkvkvsarskkdg 93 
                                       + +kl +++++++ e v+   gv  +++ + e+ ++   g ++ +l s+ k+ +   +++ ++g    +s+rs   +
  gi|385806232|ref|YP_005842630.1| 192 EYKKLIKSAIEAS-EYVQteqGVIAFISSS-EKLHP---GDIVRELESEGKRpADLYVFIYDKG----ISLRSH--K 257
                                       3333332222222.2222556999999999.99999...4455666666666344444444555....******..9 PP

                                       S-HHHHHHHHHHHTTCCEEEETCEEEEEE.E........H CS
                             DHHA1  94 vdagelakeaaaklgggGGGHdlAaGagi.p........a 124
                                       +++  +a++      +gGGGH+ AaG ++ +        +
  gi|385806232|ref|YP_005842630.1| 258 INVLQIASA------LGGGGHPYAAGISLiDdvqdkesiK 291
                                       *********......***********99844454444444 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   8.1e-10   2.1e-06       8     100 ..       7     137 ..       4     138 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 8.1e-10
                                       CSSSHHHHHHHHHHHH................................CECS--TCGGCGCCH...HCCCSEEEEEE CS
                                       xxxxxxxxxxxxxxxx................................xxxxxxxxxxxxxxx...xxxxxxxxxxx RF
                               DHH   8 knpDtDsigSaialan................................llvDhneksqavege...akeeaedviii 49 
                                        + D+D+i+Sa+ l+                                 ++ D n + q +e+    a++++ +++ i
  gi|385806232|ref|YP_005842630.1|   7 SHWDIDGIASAVILSInygiptrniklsstikidkyfneisknkvqnvFITDLNPSFQIAENIikiAEKKKIKLVWI 83 
                                       689*******999999899999999999998888888888888888887999998877776667768999999**** PP

                                       E-S---S....S---SS--EEEE-SSS-HHHHHHHHHHHTT----HHHHHHHHHH CS
                                       xxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DHH  50 DHHrlge....efetlapilflnepvgstaeivaelleekkeeiskeiaellllg 100
                                       DHH+  e     ++t    ++++e+++++ae+v ++l + ++++++ i ++l l+
  gi|385806232|ref|YP_005842630.1|  84 DHHAWDEeaknFLKTRGAEIIVDEKASCAAELVKNYL-YGEQRPPSYIEDVLKLA 137
                                       *****998887667777778999**********9885.45555566666666555 PP

>> Kindlin_2_N  Kindlin-2 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.2   6.2e-06     0.016      16      67 ..      47      99 ..      33     118 .. 0.78
   2 ?   -5.4   3.0         7   1.8e+04      45      56 ..     167     178 ..     151     190 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6.2e-06
                       Kindlin_2_N 16 eikkevelkir.vkgdlhiGgvmlklvekldikkdwsDyalWWekkkkWLkkt 67
                                      + +k  ++ i+ ++  ++i + ++k++ek +ik  w D++ W e++k++Lk  
  gi|385806232|ref|YP_005842630.1| 47 SKNKVQNVFITdLNPSFQIAENIIKIAEKKKIKLVWIDHHAWDEEAKNFLKTR 99
                                      444555566666788899*******************************9864 PP

  == domain 2  score: -5.4 bits;  conditional E-value: 7
                       Kindlin_2_N  45 dikkdwsDyalW 56 
                                       ++ ++w D  +W
  gi|385806232|ref|YP_005842630.1| 167 KTLESWIDGYIW 178
                                       334455555555 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.2e-05     0.032      66     108 ..      64     106 ..      33     111 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.2e-05
                                       HHHGGGHHHHHHH--SEEEE-TT---HHHHHHHHHTT-EEE.E CS
                     CoA_binding_2  66 eatpeivkealalgakavwlqpgsedeeaaelaeeagirvvgd 108
                                       +++++i+k a+++++k vw+  +++deea ++++ +g +++ d
  gi|385806232|ref|YP_005842630.1|  64 QIAENIIKIAEKKKIKLVWIDHHAWDEEAKNFLKTRGAEIIVD 106
                                       5667899999999**********************99998865 PP

>> DUF4897  Domain of unknown function (DUF4897)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   1.3e-05     0.034      48      89 ..      38      79 ..      24      97 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.3e-05
                           DUF4897 48 tfekylsqlseevgreikvvslessateregileveEkavlk 89
                                      +  ky++++s++  +++ +++l+ s++  e+i+++ Ek ++k
  gi|385806232|ref|YP_005842630.1| 38 KIDKYFNEISKNKVQNVFITDLNPSFQIAENIIKIAEKKKIK 79
                                      678***********************************9987 PP

>> DUF1799  Phage related hypothetical protein (DUF1799)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.5   4.9e-05      0.13      28      64 ..     148     185 ..     143     198 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.9e-05
                           DUF1799  28 rvgtqWrv.gpaGavgLdYealfavldrlgldkeekdd 64 
                                       ++  +Wrv   +G ++++Y++l+ ++d + ++k ++++
  gi|385806232|ref|YP_005842630.1| 148 EMTYKWRVlLRWGDWSIRYKTLESWIDGYIWPKWAQRE 185
                                       57889***999****************99999877776 PP

>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   0.00011      0.28      11      60 ..      33      80 ..      28     215 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00011
                                      -.S-H..HHHHHHHHHCT-SEEEEEEEEBTTHHHHHHHHHHHHTTTTSEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               PHP 11 ldgalsieelvkkakelglkaiaiTDhgnlfgyvefykaakkkykagikp 60
                                      l+++++i++++++  + + + + iTD ++ f++ e + ++ +k+  +ik+
  gi|385806232|ref|YP_005842630.1| 33 LSSTIKIDKYFNEISKNKVQNVFITDLNPSFQIAENIIKIAEKK--KIKL 80
                                      45899**************************9999998885554..6876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       746  (0.0416086); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); 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: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2006.01
//
Query:       gi|385806233|ref|YP_005842631.1|  [L=319]
Description: NAD-dependent epimerase/dehydratase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-23   82.1   0.0    5.1e-23   81.8   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    2.3e-22   79.8   0.1    5.9e-22   78.5   0.1    1.6  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    1.1e-13   51.0   0.0      2e-13   50.1   0.0    1.3  1  RmlD_sub_bind    RmlD substrate binding domain
    1.2e-06   27.9   0.0      1e-05   24.9   0.0    2.4  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    1.9e-06   27.3   0.0    4.5e-06   26.0   0.0    1.6  1  NAD_binding_4    Male sterility protein
     0.0012   17.9   0.0      0.002   17.2   0.0    1.4  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
  ------ inclusion threshold ------
      0.012   15.5   0.0      0.023   14.6   0.0    1.4  1  Cry1Ac_D5        Insecticidal delta-endotoxin CryIA(c) 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 !   81.8   0.0     2e-26   5.1e-23       1     228 [.       4     226 ..       4     239 .. 0.81

  Alignments for each domain:
  == domain 1  score: 81.8 bits;  conditional E-value: 2e-26
                                       EEEETTTSHHHHHHHHHHHHCT.SEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S.-- CS
                         Epimerase   1 ilVtGatGfiGsalvkallekg.yevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAa.vg 75 
                                       +lV+Ga+G+iG  lv  l +    e +    ++++   ++++     ++d+++ + +e ++k++++d++++lAa  +
  gi|385806233|ref|YP_005842631.1|   4 ALVIGANGQIGFELVPVLRKLYgSENVIAGYYPEKIDIKLEA--PREYIDVLNVDLVESVVKKYDVDEIYNLAAiLS 78 
                                       59*****************99865544444444455544444..788***************************888 PP

                                       -HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHH CS
                         Epimerase  76 gvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlagekl 152
                                         ++  ++p+  +++nl g+ n+le+ark+g  r+   sS +v+G+ ++  k +t + + ++p++ Y+++K+age l
  gi|385806233|ref|YP_005842631.1|  79 ATGE--KNPQLAFKTNLLGVFNVLEVARKYGT-RVFWPSSIAVFGPTTP--KYSTPQHTIIEPTTMYGITKYAGELL 150
                                       8887..89999*********************.************9999..4555544455**************** PP

                                       HHHHHHHHT-EEEEEEESEEESTT..S-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHH CS
                         Epimerase 153 veayaaqyglnaiilrlfnlyGpr..ngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvle 227
                                        ++y ++y+l++  +r   +++     g g+ +  +  +   i egk + t +   +   + +y  D+++ i+ +++
  gi|385806233|ref|YP_005842631.1| 151 SRYYVNKYDLDVRGVRWPGIISSEalPGGGTTDYAVEIFYYAI-EGK-KYTCYLHEDTMLPMMYMPDAIKSIIQLMN 225
                                       ****************999999996444444444444444444.566.67777778888888888888888888887 PP

                                       H CS
                         Epimerase 228 h 228
                                       +
  gi|385806233|ref|YP_005842631.1| 226 A 226
                                       7 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 !   78.5   0.1   2.3e-25   5.9e-22       1     332 []       5     304 ..       5     304 .. 0.79

  Alignments for each domain:
  == domain 1  score: 78.5 bits;  conditional E-value: 2.3e-25
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       L+ G +G+iG  l+  L +     +g  +  + ++ ++i+   + p+          + D+ + + +e++++++++d
  gi|385806233|ref|YP_005842631.1|   5 LVIGANGQIGFELVPVLRKL----YGSENVIAGYYPEKIDIKLEAPR---------EYIDVLNVDLVESVVKKYDVD 68 
                                       89999*******99999876....33344446778888987777665.........489****************** PP

                                       EEEE--S-.--HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSS.B-TTS-----SH CS
                     GDP_Man_Dehyd  78 evynLAAq.shVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevp.qtEttpfyPrsP 152
                                       e+ynLAA  s+ ++  ++P+  +++n+lG++++Le++r++g    +r++  S+  v+G ++       +t ++P+  
  gi|385806233|ref|YP_005842631.1|  69 EIYNLAAIlSATGE--KNPQLAFKTNLLGVFNVLEVARKYG----TRVFWPSSIAVFGPTTPKYsTPQHTIIEPTTM 139
                                       *******8455555..89**********************9....69************9855515578999***** PP

                                       HHHHHHHHHHHHHHHHHHH---EEE....EEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEE CS
                     GDP_Man_Dehyd 153 YaaaKlyadwivvnyreayglfavn....gilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwgh 225
                                       Y+++K + + + + y ++y+l +      gi++    p  g    t   +++   + +gk+ + yl + d      +
  gi|385806233|ref|YP_005842631.1| 140 YGITKYAGELLSRYYVNKYDLDVRGvrwpGIISSEALPGGGT---TDYAVEIFYYAIEGKKYTCYL-HEDTMLPMMY 212
                                       *********************887612225666666666544...455555666666777666655.566788899* PP

                                       HHHHHHHHHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--S.S CS
                     GDP_Man_Dehyd 226 vkDyveamwlmlqqdkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrp.g 301
                                         D ++ + +++++dk+    ++t   ++v  f   + ++l k+i++               + +ve++p y+++ +
  gi|385806233|ref|YP_005842631.1| 213 MPDAIKSIIQLMNADKS---KLETFVGYNVSAFS-FTPKQLEKEIKKY------------IPEFQVEYKPDYRQQiA 273
                                       *************9985...47777777776443.4445555554433............34567899999988867 PP

                                       --SB--B-THHHHHHH----SS-HHHHHHHH CS
                     GDP_Man_Dehyd 302 evdlllgdaskakeeLgWkpkvsfeelvrem 332
                                       +   + +d   a++e gW+p++ fe++v++m
  gi|385806233|ref|YP_005842631.1| 274 DSWPRTIDDCVARKEWGWSPEWVFESMVKDM 304
                                       888999***********************98 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1   0.0   7.9e-17     2e-13       2     135 ..       3     150 ..       2     160 .. 0.86

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 7.9e-17
                                       EEEEESTTSHHHHHHHHHCTT..TSEEEEEE-TT............T--TTSHHHHHHHHHHH--SEEEE------H CS
                     RmlD_sub_bind   2 kilvtGanGqlGseLakqlae..eglevlaltre............eldltdaeavaellkeakpdvvvnaAAytav 64 
                                       + lv+GanGq+G eL+  l++     +v+a   +             +d+ + + v++++k+ + d ++n+AA    
  gi|385806233|ref|YP_005842631.1|   3 RALVIGANGQIGFELVPVLRKlyGSENVIAGYYPekidikleapreYIDVLNVDLVESVVKKYDVDEIYNLAAILSA 79 
                                       679************98887754334666665446899******999**************************9876 PP

                                       HHHHHSHHHHHHHHTHHHHHHHHHHHHCT-EEEEEEEGGGS-S-TTS-B-T..TS----SSHHHHHHHHHHHH CS
                     RmlD_sub_bind  65 DkaEseeeaayavnaeavealAeaaaavgalLihvStDyVFdGekkrpYee..ddetsPlnvYGrtKlaGEqa 135
                                          E+++++a++ n  +v ++ e+a+++g  +   S+  VF  ++++ Y++  +   +P ++YG tK+aGE  
  gi|385806233|ref|YP_005842631.1|  80 -TGEKNPQLAFKTNLLGVFNVLEVARKYGTRVFWPSSIAVFGPTTPK-YSTpqHTIIEPTTMYGITKYAGELL 150
                                       .67**************************************999777.5541144569*************75 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   3.9e-09     1e-05      58     156 ..      47     158 ..       4     237 .. 0.71

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 3.9e-09
                                       ..E--TT-HHHHHHHTT..T-SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEE....EEE.... CS
                   Polysacc_synt_2  58 pvigdvrdkerlekaleelkvdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkv....vli.... 126
                                           dv + + +e+++++++vd +++ AA+    + e+np  a+ktN lg  nv+e+a ++g + +    +++    
  gi|385806233|ref|YP_005842631.1|  47 REYIDVLNVDLVESVVKKYDVDEIYNLAAILS-ATGEKNPQLAFKTNLLGVFNVLEVARKYGTRVFwpssIAVfgpt 122
                                       33569************************976.589*************************9987633333333332 PP

                                       ....EEGG..GSS--SHHHHHHHHHHHHHHHGGG-- CS
                   Polysacc_synt_2 127 ....StDK..AvnPtnvmGatKrlaekllqalakes 156
                                           St     ++Pt ++G+tK + e+l   + ++ 
  gi|385806233|ref|YP_005842631.1| 123 tpkySTPQhtIIEPTTMYGITKYAGELLSRYYVNKY 158
                                       222244323357889999999998888876665554 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   1.8e-09   4.5e-06      87     241 ..      66     205 ..      53     217 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 1.8e-09
                                       H--EEEE--SS-S.STTSSE..EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H......HH CS
                     NAD_binding_4  87 evdviihsaAtvnfdepyke..llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegekeekl 161
                                        vd i++ aA ++ +++ +   ++++N++G+ +vle a+k     v+   S a++ ++                  +
  gi|385806233|ref|YP_005842631.1|  66 DVDEIYNLAAILSATGEKNPqlAFKTNLLGVFNVLEVARKYGTR-VFWPSSIAVFGPTTP----------------K 125
                                       6899*******9998754443499***************99888.666666599999999................4 PP

                                       H--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEE.E-EEE--SSST---TTSHHHHHHHHHHHH-EEES- CS
                     NAD_binding_4 162 dederaklkglpntYeqsKalaEklvrearrrsglpvvivR.psiitgesktGwingsdlgirgllgliakgvlpei 237
                                       +++ + +  + ++ Y  +K+++E l r + ++ +l v  vR p+ii +e  +G   ++   ++ + ++i+ +++++ 
  gi|385806233|ref|YP_005842631.1| 126 YSTPQHTIIEPTTMYGITKYAGELLSRYYVNKYDLDVRGVRwPGIISSEALPGGGTTDY-AVEIFYYAIEGKKYTCY 201
                                       6677888888999************************88876999999****9998888.99999999999999988 PP

                                       SB-- CS
                     NAD_binding_4 238 lgdk 241
                                       l ++
  gi|385806233|ref|YP_005842631.1| 202 LHED 205
                                       7774 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 !   17.2   0.0   7.8e-07     0.002       2     123 ..       6     122 ..       5     148 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 7.8e-07
                         3Beta_HSD   2 vtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdv..vihlasl 76 
                                       v+G+ G +G +lv  L +l   ++v +      pe+ +   +  ++   + Dv++ d +e ++++ dv  +  la++
  gi|385806233|ref|YP_005842631.1|   6 VIGANGQIGFELVPVLRKLYGSENVIA---GYYPEKIDIKLEAPRE---YIDVLNVDLVESVVKKYDVdeIYNLAAI 76 
                                       666666666666666666555444432...2333443444444444...679999999999999766544899**** PP

                         3Beta_HSD  77 vdvagkltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpn 123
                                          +g+ + +   k n+ G  nvle ++k g rv+ + Ss+ v gp 
  gi|385806233|ref|YP_005842631.1|  77 LSATGEKNPQLAFKTNLLGVFNVLEVARKYGTRVF-WPSSIAVFGPT 122
                                       *******************************8876.99****99994 PP

>> Cry1Ac_D5  Insecticidal delta-endotoxin CryIA(c) domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   8.9e-06     0.023      57     114 ..     225     284 ..     209     290 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.9e-06
                         Cry1Ac_D5  57 kidesklkpytryqvrgfvgsskdlglvvtrygkevnvvmnpeyntpvtdgy..tsdtcs 114
                                       + d+skl+ +  y+v  f  + k+l   + +y  e +v  +p+y   ++d +  t d c 
  gi|385806233|ref|YP_005842631.1| 225 NADKSKLETFVGYNVSAFSFTPKQLEKEIKKYIPEFQVEYKPDYRQQIADSWprTIDDCV 284
                                       5799**********************************************9733555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 2036.37
//
Query:       gi|385806234|ref|YP_005842632.1|  [L=396]
Description: pyridoxal phosphate-dependent acyltransferase [Fervidicoccus fontis Kam940]
Scores for complete 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-66  224.3   0.0      3e-66  224.1   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    1.1e-06   27.4   0.0    1.6e-06   26.9   0.0    1.1  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    3.7e-05   22.9   0.0     0.0013   17.8   0.0    2.1  2  Aminotran_5      Aminotransferase class-V
    4.7e-05   22.3   0.0       0.56    8.9   0.0    2.9  2  OKR_DC_1         Orn/Lys/Arg decarboxylase, major domain
      0.001   17.8   0.0     0.0034   16.0   0.0    1.8  1  SHMT             Serine hydroxymethyltransferase
     0.0023   17.3   0.0     0.0065   15.8   0.0    1.8  1  Beta_elim_lyase  Beta-eliminating lyase


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  224.1   0.0   9.9e-70     3e-66       2     360 ..      43     383 ..      42     385 .. 0.95

  Alignments for each domain:
  == domain 1  score: 224.1 bits;  conditional E-value: 9.9e-70
                                       EEEESSSSSTTSTTSSHHHHHHHHHHHH..HHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESH CS
                     Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaeke..galaggtlneygpidglpeleealakflgrseklklkreaavvvgsG 76 
                                       +vi +++n+yl +++   l+ +a +++e  g + g  +++ g  ++l ele+++a+f +        +ea + + +G
  gi|385806234|ref|YP_005842632.1|  43 EVIMFATNNYLNLANDQRLKQAAVEAIEkyGWGPGAVWAIAGFHEILSELEKKIAEFKR--------TEAGIFFPTG 111
                                       7999*********9997777777777777******************************........999******* PP

                                       HHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEE CS
                     Aminotran_1_2  77 agaliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvil 153
                                       +  +  ++++l +  +gd il+++++++s+++++rls++e + y+       h+d+ +le++l++a+ +   + +i+
  gi|385806234|ref|YP_005842632.1| 112 YATNVGTIPTLVE--TGDLILSDQLNHGSIIDGIRLSRAEKIVYN-------HCDVADLEDKLRKAHGKYN-KILII 178
                                       ************8..******************************.......*************987766.78999 PP

                                       EESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-E CS
                     Aminotran_1_2 154 vesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRv 230
                                       + ++++++G++a+l+++ kl   a++yn++++vD+a++++v+g+ + ++++++v+++++ + +g++sKa+G+ G   
  gi|385806234|ref|YP_005842632.1| 179 TDGVFSMDGDIAPLKDISKL---AEEYNAIVYVDDAHGEGVLGEGRGTPAHFGVDDKID-IHMGTFSKALGSSG--- 248
                                       ********************...********************9977777*********.**************... PP

                                       EEEEEEHHHHHHHHHHHHHHTS.SHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCS CS
                     Aminotran_1_2 231 Gyilgnaavvsqlrklsrpfls.ssllqaavaaalsdallkqs.eleemrqrlqkrrkelrdeLaelglkvlasqsg 305
                                       G++ ++ ++++++r+ +r++l  + + + a+aa l++ + ++s e +e+++rl++++ ++r+eL+++g++  +s++ 
  gi|385806234|ref|YP_005842632.1| 249 GMVGSDREIIEYVRNTARSWLLsTGPSPGAIAANLKALEIVMSqEGKERVRRLHENANYFRKELQSIGFNTGKSETP 325
                                       *********************98899999999999999999999********************************* PP

                                       SEEEEEETHHCHHHHHHHHHHTCTEEEEEGGGGTS...TTEEEEEC.TTS-HHHHHHHH CS
                     Aminotran_1_2 306 mflltdlsaetakelskkLleevgvyvtpgtsftv...pgrlRitv.Aglteeeleelv 360
                                       m+++  ++ ++a el+k+L +  g+ v+p+ ++ v   ++r R  v Ag+t+e+l++ +
  gi|385806234|ref|YP_005842632.1| 326 MIPVIIGDTKKARELAKALFDD-GIFVVPIVYPMVprgTERTRNEVsAGHTREDLDKTL 383
                                       **********************.***************9****************9876 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   5.4e-10   1.6e-06      56     182 ..      91     218 ..      88     260 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 5.4e-10
                                       HHHHHHHHHHT-SEEEEESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEESTTSHHH.HH CS
                   Cys_Met_Meta_PP  56 vleeriaaLeggeaalavssGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdtsdlee.le 131
                                        le++ia+ +++ea++ +++G a+   +i +l+++Gd i++++  +g+  + ++ + +  +i ++++d++dle+ l+
  gi|385806234|ref|YP_005842632.1|  91 ELEKKIAEFKRTEAGIFFPTGYATNVGTIPTLVETGDLILSDQLNHGSIIDGIR-LSRAEKIVYNHCDVADLEDkLR 166
                                       79***********************************98887777777777765.5566779999999988765266 PP

                                       HHCCT.TEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGTTTHTTTS CS
                   Cys_Met_Meta_PP 132 kaike.ntklvylEtptnpllkvvDiekiaklakkagvlvvvDntfaspllq 182
                                       ka  + n  l+ ++ + +   +++ +++i+kla + +++v vD +   ++l 
  gi|385806234|ref|YP_005842632.1| 167 KAHGKyNKILIITDGVFSMDGDIAPLKDISKLAEEYNAIVYVDDAHGEGVLG 218
                                       6665535555666778888889**********************99988875 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   4.2e-07    0.0013      41     177 ..      85     211 ..      56     216 .. 0.81
   2 ?    2.9   0.0     0.015        43     237     333 ..     259     349 ..     238     352 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4.2e-07
                                       HHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEE CS
                       Aminotran_5  41 atkaveearekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvk 117
                                       +++++ e ++k+ae+  +e    i f  G ++ + +++  +    ++gd i+  +++h + +          g+++ 
  gi|385806234|ref|YP_005842632.1|  85 FHEILSELEKKIAEFKRTEA--GIFFPTGYATNVGTIPTLV----ETGDLILSDQLNHGSII---------DGIRLS 146
                                       78899999999***999996..9999888776777766655....99*************99.........577777 PP

                                       EEEBETTSCBEGGGHHHH-....-TTEEEEEEE.SBETTTTEB--HHHHHHHHHHTT-EEEEE-T CS
                       Aminotran_5 118 vipldeegeldldelekll....nektklvait.hvsnvtGtiqpveeigklakkkgalvlvDaa 177
                                        +++    + d+ +le++l     +  k+++it  v ++ G i p+++i kla +++a+v vD a
  gi|385806234|ref|YP_005842632.1| 147 RAEKIVYNHCDVADLEDKLrkahGKYNKILIITdGVFSMDGDIAPLKDISKLAEEYNAIVYVDDA 211
                                       77777777777777777774333466678888725789*************************87 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.015
                                       TEEEEHCTTGGGS.SS--HHHHHHHH.HHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBSEE CS
                       Aminotran_5 237 eettfaeapskfeaGTpnvagiiglg.aaleyleeigleaiekhekelaeyllerlkslpgvrlygpdkaerrasiv 312
                                       e+   +  ++ +   T + +g+i+ + +ale++++++ ++  ++ +e a+y +++l+s++  +       + ++ ++
  gi|385806234|ref|YP_005842632.1| 259 EYVRNTARSWLLS--TGPSPGAIAANlKALEIVMSQEGKERVRRLHENANYFRKELQSIGFNTG------KSETPMI 327
                                       4455455556666..666666666553799**97777777778889999********9986544......3344444 PP

                                       EEEE.TTCSHHHHHHHHHHTTE CS
                       Aminotran_5 313 sfnf.kgvhaedvatlLdeegI 333
                                        + + ++ +a+++a++L + gI
  gi|385806234|ref|YP_005842632.1| 328 PVIIgDTKKARELAKALFDDGI 349
                                       4444355555666666666666 PP

>> OKR_DC_1  Orn/Lys/Arg decarboxylase, major domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.1   0.00032      0.96     103     207 ..     123     213 ..      89     217 .. 0.69
   2 !    8.9   0.0   0.00019      0.56     265     341 ..     263     360 ..     240     385 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00032
                                       --TTEEEEEESS--HHHHHHHHHS-EEEEEE--EB-TTS-BE---GGGGSHHHHHHHHHHSTTTGSESEEEEESS-T CS
                          OKR_DC_1 103 ltpgdlvlvdRNcHKSiehalvlsgatPvylepernalgiiggidlkefeeetlkekikevpdakaprlavitnsTY 179
                                       ++ gdl+l d  +H Si  ++ ls a+ +            ++ d      + l+ k+++ ++ k  + ++it + +
  gi|385806234|ref|YP_005842632.1| 123 VETGDLILSDQLNHGSIIDGIRLSRAEKIV----------YNHCDV-----ADLEDKLRK-AHGKYNKILIITDGVF 183
                                       556666666666666666666666555432..........122222.....334445543.3344457899999876 PP

                                       ..TSEEE-HHHHHHHHTTSESEEEEE-TT- CS
                          OKR_DC_1 180 ..dGvlynakeivdkleklsdrilfDeAwv 207
                                         dG ++ +k i +++e+++  +++D+A++
  gi|385806234|ref|YP_005842632.1| 184 smDGDIAPLKDISKLAEEYNAIVYVDDAHG 213
                                       558999999999999999999999999996 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00019
                                       HHHHHHTS-SS--HHHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHH..HSSS---EESS-SEEESTS.... CS
                          OKR_DC_1 265 neafmmhattSpsYpllAsldvaakmlegesgrrlleevveraielrkeikr..ldnaelikpvnpevvdeke.... 335
                                       n a + + +t ps   +A++  a +++ +++g++ +++  e+a+ +rke+++   + ++  +p++p ++ +++    
  gi|385806234|ref|YP_005842632.1| 263 NTARSWLLSTGPSPGAIAANLKALEIVMSQEGKERVRRLHENANYFRKELQSigFNTGKSETPMIPVIIGDTKkare 339
                                       5666778899999999999999*****************************9999999999********98885555 PP

                                       ...............GEEE-T CS
                          OKR_DC_1 336 ...............ffklep 341
                                                      ++++ p
  gi|385806234|ref|YP_005842632.1| 340 lakalfddgifvvpiVYPMVP 360
                                       555555555555555444444 PP

>> SHMT  Serine hydroxymethyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.1e-06    0.0034     105     323 ..     121     319 ..      97     339 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.1e-06
                                       HHT-TT-EEEEESCTTTSTGGGT-BTSS-B-S.HHHHHSEEEEE-B-TTTSSB-HHHHHHHHHHH--SEEEEE-SST CS
                              SHMT 105 allepgdrilgldladGGhlthGakveskkis.assklfesveykvdketglidydelekkakefkPklivaGtsay 180
                                       +l+e+gd il+ +l +      G+ ++  ++s a  ++++        + ++ d+++  +ka+    k+++     +
  gi|385806234|ref|YP_005842632.1| 121 TLVETGDLILSDQLNH------GSIIDGIRLSrAEKIVYN--------HCDVADLEDKLRKAHGKYNKILIITDGVF 183
                                       5555555555544443......333333222202333333........33456776666778888888888888888 PP

                                       -S---HHHHHHH...HHHTT-EEEEE-GGGHHHHHTTS.S--GC...CTSSEEEEESSSTT-S-S-EEEEEC-SEEE CS
                              SHMT 181 srlidyarlrei...adevgayllvdmahiaGlvaagv.ipsPf...eyadvvtttthktlrGprgglillrkgvks 250
                                       s   d a l++i   a+e +a++ vd ah  G++  g  +p+ f   +  d+   t  k+l G+ gg++ +      
  gi|385806234|ref|YP_005842632.1| 184 SMDGDIAPLKDIsklAEEYNAIVYVDDAHGEGVLGEGRgTPAHFgvdDKIDIHMGTFSKAL-GSSGGMVGSD----- 254
                                       88877776665422289***************99876426776633345678888888888.899***9988..... PP

                                       EETTTEEEEHHHHHHHHHHHTTTT-SS--HHHHHHHHHHHHHCTSHHHHHHHHHHHHHHHHHHHHHHHTT-EE CS
                              SHMT 251 vdktgkevleelekkinsavfPglqGGPlnhviaakavalkealepefkvyqkqvlknakalaealkekgykl 323
                                            +e+ e + +   s     l  GP   +iaa   al+ ++++e k+  +++ +na+ + ++l++ g++ 
  gi|385806234|ref|YP_005842632.1| 255 -----REIIEYVRNTARSW---LLSTGPSPGAIAANLKALEIVMSQEGKERVRRLHENANYFRKELQSIGFNT 319
                                       .....56666665554444...4568******************************************99974 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   2.2e-06    0.0065      35     169 ..      90     211 ..      83     324 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.2e-06
                                       HHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-H CS
                   Beta_elim_lyase  35 nrLedavaelfgkeaalfvpqGtaAnsillkillqrgeevivtepahihfdetgaiaelagvklrdlknkeaGkmdl 111
                                        +Le+++ae   +ea++f+p+G a n   + +l++ g+ ++ ++ +h+            g++l  +++   +  d+
  gi|385806234|ref|YP_005842632.1|  90 SELEKKIAEFKRTEAGIFFPTGYATNVGTIPTLVETGDLILSDQLNHGSII--------DGIRLSRAEKIVYNHCDV 158
                                       689*******************************66666666666665443........6666666666666778** PP

                                       HHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEET CS
                   Beta_elim_lyase 112 ekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgA 169
                                       ++le+++++  ah +  k++++t  + ++ G + +l+    ++++a++y+  + +D A
  gi|385806234|ref|YP_005842632.1| 159 ADLEDKLRK--AHGKYNKILIITDGVFSMDGDIAPLK---DISKLAEEYNAIVYVDDA 211
                                       ********9..7889999999999999999*998865...678889999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); 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: 0.69u 0.35s 00:00:01.04 Elapsed: 00:00:00.53
# Mc/sec: 2243.52
//
Query:       gi|385806235|ref|YP_005842633.1|  [L=88]
Description: hypothetical protein FFONT_1193 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score 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   2.4      0.019   14.9   2.4    1.3  1  Glycos_transf_4  Glycosyl transferase family 4


Domain annotation for each model (and alignments):
>> Glycos_transf_4  Glycosyl transferase family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   2.4   1.1e-06     0.019      94     145 ..      26      84 ..       8      88 .] 0.78

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.1e-06
                   Glycos_transf_4  94 vsiiialalvvlaavd.grsellllalallgallGfllfNryp......AkvFmGDsgs 145
                                         +i++l+ v++ +++ ++ e+++l +++ ga++ f+l+ + +       k+F+G   s
  gi|385806235|ref|YP_005842633.1|  26 FIAITFLMKVIFLYIQsENVEVVILRFVVFGAFVVFWLYSWWKftvyykKKIFVGQKLS 84 
                                       4455566666666666588999999999999******9998666777779****98666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       913  (0.0509231); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 572.63
//
Query:       gi|385806236|ref|YP_005842634.1|  [L=46]
Description: hypothetical protein FFONT_1194 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-09   37.2   1.5    2.6e-09   37.1   1.5    1.1  1  Ribosomal_S30  Ribosomal protein S30


Domain annotation for each model (and alignments):
>> Ribosomal_S30  Ribosomal protein S30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   1.5   1.5e-13   2.6e-09       6      48 ..       1      42 [.       1      46 [] 0.78

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 1.5e-13
                                      STTTTHHHHHS-------.------THHHHHHHHHHHTTSSS-- CS
                     Ribosomal_S30  6 LarAGKVrnqTPKveKqe.kkKkptGRakkRlqYnrRfvnvvvg 48
                                      +++AGKVrnqTPK+e +  k K p  R   R+ Y  R v+ + +
  gi|385806236|ref|YP_005842634.1|  1 MTKAGKVRNQTPKIEPKGrKNKPPIVR--NRIEYFVRVVKPTLS 42
                                      58***************5488888766..788999999994444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       192  (0.0107089); expected 358.6 (0.02)
Passed bias filter:                      133  (0.00741815); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 309.30
//
Query:       gi|385806237|ref|YP_005842635.1|  [L=361]
Description: membrane protein [Fervidicoccus fontis Kam940]
Scores for complete 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-79  265.8  11.2    7.5e-79  265.6  11.2    1.1  1  DUF373    Domain of unknown function (DUF373)


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 !  265.6  11.2   4.2e-83   7.5e-79       1     320 [.       5     329 ..       5     350 .. 0.90

  Alignments for each domain:
  == domain 1  score: 265.6 bits;  conditional E-value: 4.2e-83
                            DUF373   1 ktLvlcvDrDdDlgrkagvktPvvGreavleaavklaladPeDSDvNalfgaikvydeLkaegedvevavvtGdekv 77 
                                       k+L l+vDrD+D+ r +g +tP+ G+++v + av++al+ PeDSD+N++f a+++y++L++eg dve+avv+G+e  
  gi|385806237|ref|YP_005842635.1|   5 KVLLLVVDRDNDIERVTGKSTPIFGKDDVFKIAVEFALKSPEDSDLNVMFSALQLYEKLRNEGMDVEIAVVGGHETD 81 
                                       6899************************************************************************* PP

                            DUF373  78 gveadrkiaeqldevlskleadsaivVsDGaeDesvlpiiqsrvkvdsvkrVvVkqsrniEstyyll....kkalkd 150
                                        ++ad+ki++ ++ + +k+ ++++i+VsDG eDe  lp+i+  ++v+s+krVvV+q r++E+ty+l+    kka+ +
  gi|385806237|ref|YP_005842635.1|  82 SIKADMKIRDAVKFLKEKTGVTGIIMVSDGTEDELTLPVIETILPVISIKRVVVEQWRGVEETYILIgkylKKAIFE 158
                                       ***************************************************************************** PP

                            DUF373 151 pelrktiLvplGlllliyalllllglpelalaiillllGlylllrGfgldelleelleklkesleegritfvtyvva 227
                                       p+++k++L+++G+++l + +l ++g++++ +++  +l+G+++++rGf+l++       k+ e + ++ i+f+++++a
  gi|385806237|ref|YP_005842635.1| 159 PRFSKIFLGLPGAIILAFVILDFFGYIQYGVMVAGFLIGGAMIIRGFNLES-------KIYELWASSPIMFISSTIA 228
                                       ***************************************************.......99***************99 PP

                            DUF373 228 llllligiisgyislesvssasvssglltlilafiygavewlalailtaslgkiideylkreekdiarllllpflvl 304
                                       +++l+ g++   ++l s ++       + +    +++a++++ l+i+ +++gk i ++++r + +i+r +l ++++l
  gi|385806237|ref|YP_005842635.1| 229 TIFLISGAVIFGYTLYSEYN-------IRSWGEALQSATPLIGLSIFSIYIGKGIVKIIER-NIRIWRDVLGMIVTL 297
                                       99999987766666555555.......3344445567888*******************55.59999***9999999 PP

                            DUF373 305 aiglvlygasaylls................l 320
                                       ++ + + ++ +yl                   
  gi|385806237|ref|YP_005842635.1| 298 IFIIAFLRLGQYLTTypggtaldilrsslfdS 329
                                       99999999999996678888877777776642 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); 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 0.25s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2482.58
//
Query:       gi|385806238|ref|YP_005842636.1|  [L=212]
Description: DNA-(apurinic or apyrimidinic site) lyase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score 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   12.7   0.3       0.48   10.3   0.2    2.0  2  HEPN_Toprim_N  HEPN/Toprim N-terminal domain 1
       0.18   12.1   1.3        9.7    6.5   0.1    2.8  3  TetR_C_24      Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> HEPN_Toprim_N  HEPN/Toprim N-terminal domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.2   5.4e-05      0.48      64     106 ..      76     118 ..      72     127 .. 0.86
   2 ?    1.4   0.0     0.029   2.6e+02     153     219 ..     122     189 ..     110     191 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 5.4e-05
                     HEPN_Toprim_N  64 vkpRLellGytleaaeaeyeeyvkeaieeresfqeaedearee 106
                                       + +RL  lG+ +++ +aey   +++ ++  +++ +++de+r  
  gi|385806238|ref|YP_005842636.1|  76 LARRLRELGHRYPEKRAEYIVKARKFKDKICELVKNSDEDRSK 118
                                       789****************************999999885443 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.029
                     HEPN_Toprim_N 153 kialdr.ddlaysessvlgsllpildpysmlrallenpnldaevvwdygdlveaGwaeeeeflpearr 219
                                       k++ d+ ++ +y ess++  +  ++++ ++   +l +  + + +  ++  l +  ++e e++l++++ 
  gi|385806238|ref|YP_005842636.1| 122 KWMADNiYGIGYKESSHFLRNTGFFNLAIIDFHILDILKKYKLLKQEFKTLTRKRYEEIEKVLEKIAT 189
                                       33333358999999999999988888888888888888888888888888888888888888888766 PP

>> TetR_C_24  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.1     1e+04       5      13 ..      13      21 ..      10      24 .. 0.79
   2 ?    6.5   0.1    0.0011       9.7      29      65 ..      79     115 ..      68     124 .. 0.86
   3 ?    3.7   0.0    0.0078        70      67      96 ..     179     209 ..     154     211 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.1
                                      HHHHHHHHH CS
                         TetR_C_24  5 aerLralvr 13
                                      +e+Lr+l+ 
  gi|385806238|ref|YP_005842636.1| 13 DEKLRELIN 21
                                      799999986 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0011
                                       HHHHGGGS-HHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                         TetR_C_24  29 llrelraLspehreeiralrreyerllrdlieeGvaa 65 
                                        lrel +  pe+r+e++ + r++++ + +l++   ++
  gi|385806238|ref|YP_005842636.1|  79 RLRELGHRYPEKRAEYIVKARKFKDKICELVKNSDED 115
                                       58999*************************9987766 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.0078
                                       SB-SS-HHHHHHHHHHHHH.CHHHC--TTSS CS
                         TetR_C_24  67 efedldpklaalailgmln.wvyrWyrpdGp 96 
                                       e+e++  k+a+ +il++   ++y Wy ++G+
  gi|385806238|ref|YP_005842636.1| 179 EIEKVLEKIATTSILSLGElDLYLWYMETGK 209
                                       5667778999999999987579999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1375  (0.0766914); expected 358.6 (0.02)
Passed bias filter:                      807  (0.0450109); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 1363.37
//
Query:       gi|385806239|ref|YP_005842637.1|  [L=85]
Description: hypothetical protein FFONT_1197 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score 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      0.064   13.5   0.0    1.0  1  MPM1      Mitochondrial peculiar membrane protein 1
       0.14   12.3   0.0       0.17   12.0   0.0    1.1  1  Fer4_11   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> MPM1  Mitochondrial peculiar membrane protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   7.1e-06     0.064      57     113 ..      15      72 ..      11      84 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.1e-06
                              MPM1  57 vendkkhkyGlFFkeftdyLnW..ksemkelikekreeeikkkkeeekkkkesektked 113
                                       v nd k+   +FF++ ++ ++W   ++mke +++ re+e k ++e ++++ ++   +e+
  gi|385806239|ref|YP_005842637.1|  15 VSNDRKKIFAVFFEDSEGVITWieNRKMKEALQKIREAESKGYREATQDELDNL-AREK 72 
                                       6788888899************5556899999**9******9999999888876.4444 PP

>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.9e-05      0.17      12      53 ..       5      52 ..       2      71 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.9e-05
                           Fer4_11 12 hCleppCvasapse.....aivkdeetGaVll.dektkkeevrevvea 53
                                       C eppC++++ ++     a++ ++++G++   +++++ke +++++ea
  gi|385806239|ref|YP_005842637.1|  5 YCKEPPCIHVVSNDrkkifAVFFEDSEGVITWiENRKMKEALQKIREA 52
                                      6*********9998999**99999999998761444555788887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1004  (0.0559987); expected 358.6 (0.02)
Passed bias filter:                      606  (0.0338); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 548.70
//
Query:       gi|385806240|ref|YP_005842638.1|  [L=657]
Description: threonyl-tRNA synthetase [Fervidicoccus fontis Kam940]
Scores for complete 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-42  143.7   0.1      1e-41  142.9   0.1    1.4  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
      1e-11   44.8   0.4    3.4e-11   43.1   0.1    2.1  2  HGTP_anticodon  Anticodon binding domain


Domain annotation for each model (and alignments):
>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.9   0.1   1.1e-45     1e-41       8     179 .]     323     532 ..     317     532 .. 0.94

  Alignments for each domain:
  == domain 1  score: 142.9 bits;  conditional E-value: 1.1e-45
                                       SEEEEE-SSSHHHHHHHHHHHEEEB.GGSSEEEEEEEEEEBTTTS.TBCTTTB-SEEEEEEEEEEESGGGHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b   8 dreyiLkPtneetfvelirdevlrs.krLPlklyqiqtkyRdEks.dsrGLlRvreFhqkdgyvfhaeaslddslrd 82 
                                       ++e ++kP+n++ ++ +++ +   s k+LP+++++++ ++R+E+   ++GL+Rvr+F+q+d+++f  e++++++++ 
  gi|385806240|ref|YP_005842638.1| 323 EKEHAIKPMNCPFHIIIFKRK-KWSyKELPVRYFELGNVHRYERAgTLHGLTRVRGFTQDDAHIFAREDQIEEEISG 398
                                       4799**************999.555488****************88999**************************** PP

                                       HHHHHHHHHHHTT.SCEEEEEEGTTSC.....................................BTTSEEEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx.....................................xxxxxxxxxxxxx RF
                      tRNA-synt_2b  83 likaisriferlglefraiielmsaks.....................................adykdkkefeavs 122
                                       ++k++++i+ ++gl+ ++ i++ ++ s                                     a+y++k ++  ++
  gi|385806240|ref|YP_005842638.1| 399 VLKLTKEIYDTMGLKDYKFILSLRDPSdkesymgseeiwqkaevalenalkslnvqytksigdaAFYGPKIDVIFTD 475
                                       ****************999999555556678999999***************************************9 PP

                                       TTTSEEEEEEEEEEEETHHHHHTTEEEECTTSSEEEEEEEEEE.EE.HHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.xxxxxxxxxxxx RF
                      tRNA-synt_2b 123 esltkgieigtiqklgtrlserlgatvldennreksvimicaa.ig.veRllsaileqn 179
                                         l+++++++tiq + ++l+er+++t++d++n+ek+ +mi++a +g +eR+++++leq+
  gi|385806240|ref|YP_005842638.1| 476 A-LGREWQCATIQLD-FNLPERFDLTYIDKDNKEKRLVMIHRAiLGsIERFIGILLEQY 532
                                       9.*************.****************************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 ?   -2.0   0.0      0.46   4.1e+03      30      42 ..     133     146 ..     106     160 .. 0.57
   2 !   43.1   0.1   3.8e-15   3.4e-11       1      84 [.     544     635 ..     544     648 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.46
                                       SEEEEES.SSSTHH CS
                    HGTP_anticodon  30 irveldd.snesig 42 
                                        rve+d+ + +++ 
  gi|385806240|ref|YP_005842638.1| 133 SRVEVDEiERSRVE 146
                                       23444444444444 PP

  == domain 2  score: 43.1 bits;  conditional E-value: 3.8e-15
                                       SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEET... CS
                    HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdr... 74 
                                       qv+v+p+ e + +  + a+++ + L + gir+ l   +++++ ++r+a+ll ip++ v+G+ ele+g++tv+ +   
  gi|385806240|ref|YP_005842638.1| 544 QVAVLPVEESDPQQVKRAEEINNYLMQSGIRTQLM-VEGRLNARLRDARLLRIPLIAVIGKSELENGSLTVSYLtyg 619
                                       8*********9999********************7.9***********************************99555 PP

                                       .TTCEE.....EEEET CS
                    HGTP_anticodon  75 .dtreq.....ervsl 84 
                                        d++++     e++s+
  gi|385806240|ref|YP_005842638.1| 620 eDSDKRykpkeEKLSF 635
                                       4222223344445555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (657 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); 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: 0.74u 0.33s 00:00:01.07 Elapsed: 00:00:00.50
# Mc/sec: 3962.95
//
Query:       gi|385806241|ref|YP_005842639.1|  [L=247]
Description: TatD-related deoxyribonuclease [Fervidicoccus fontis Kam940]
Scores for complete 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-48  164.4   0.1    3.6e-48  164.2   0.1    1.0  1  TatD_DNase    TatD related DNase
  ------ inclusion threshold ------
      0.036   13.4   0.1       0.62    9.3   0.0    2.0  2  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 !  164.2   0.1     4e-52   3.6e-48       1     253 [.      10     243 ..      10     245 .. 0.92

  Alignments for each domain:
  == domain 1  score: 164.2 bits;  conditional E-value: 4e-52
                                       EEEEE-TTSCCCTTTHHHHHHHHHHTTEEEEEEE-SSGGGHHHHHHHHTT.TTTEEEEE---GGGGGCC.CCHHHHH CS
                        TatD_DNase   1 iDaHcHldskefeedreeileraeeagvaavvvvgtsskdskavlelakkypnkvyavlGiHPnevdeasedlleel 77 
                                       iDaH+H  +  +   +e+ l++ e+     ++ v+ + ++sk++++l++ ++  vy+++GiHP++v + s ++++++
  gi|385806241|ref|YP_005842639.1|  10 IDAHTHAYE--Y---EEKSLSNYEK--EFLLIAVSDDAESSKRTVKLSEDFKA-VYPCVGIHPWNVSRSSREDIKTI 78 
                                       8*******9..6...4444444443..3356778999999************9.*********************** PP

                                       HHHHHCCCTSEEEEEEEEEET-CCCCCGHHHHHHHHHHHHHHHHHTTEEEEEEEES-HHHHHHHHHHCGGCCSEEEE CS
                        TatD_DNase  78 kelanvkhskvvaiGeiGLDyysreestkeaqeevFeeqlrlAkelklplviHlrkaeedlleilkeaaeakakvvl 154
                                       +++  +++s+  ++Ge+GLD  +  ++t e+q+e+F  +l++A+e++ +l iH+ +a+e ++e++++++  + + ++
  gi|385806241|ref|YP_005842639.1|  79 ENM--LENSESPCLGEVGLDA-RMHPETFERQKEFFASFLDIAREYDAILNIHTLDAWELVYELITKKEI-N-RAIF 150
                                       ***..****************.8888****************************************9864.3.68** PP

                                       TT--S-HHHHHHHHHTTEEEEE-GGGGTTTTHHHHHHHHHS-GGGEEE---TTSSEECCCTTSE--GGGHHHHHHHH CS
                        TatD_DNase 155 HsfsgsaeeakkflklgyyislsglltfknakelrelvkavpldrlLiETDaPyltpkpyrgkrnepanvayvvekl 231
                                       H+++g +e ++k+ ++gyyis++ +l    +k++ e++++ +l++lL+E+D Py+ +    g+  + +++++ +++l
  gi|385806241|ref|YP_005842639.1| 151 HWYNGPIELMQKIQETGYYISINVALKM--QKKHEEVARKADLKKLLTESDGPYIYK----GTLLKTEMIPEAIKYL 221
                                       ***********************98888..7899*********************99....99************** PP

                                       HHHHTS-HHHHHHHHHHHHHHH CS
                        TatD_DNase 232 aelkaltleelaeitaeNakrl 253
                                       ae+k++ +  l e+++eN+  l
  gi|385806241|ref|YP_005842639.1| 222 AEIKGVGENYLREKIYENFFDL 243
                                       ******************9766 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0    0.0086        77       6      20 ..       9      23 ..       8      50 .. 0.67
   2 ?    9.3   0.0   6.9e-05      0.62     119     207 ..      96     180 ..      43     223 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.0086
                                      EEEEEEECETTECSS CS
                      Amidohydro_1  6 lIDaHvHleqsllrg 20
                                       IDaH+H++ ++ ++
  gi|385806241|ref|YP_005842639.1|  9 YIDAHTHAYEYEEKS 23
                                      59******9886544 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 6.9e-05
                                       EEEEECGTCCSHHHHHHHHHHHHHHHTTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCT CS
                      Amidohydro_1 119 valapheapafsdeelkealkeakkrdlpvaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahg 195
                                        a + +e ++ ++e  +  l+ a+++d+ + iH+l+  + v + + +     +   +++++ +   ++ ++ i ++g
  gi|385806241|ref|YP_005842639.1|  96 DARMHPETFERQKEFFASFLDIAREYDAILNIHTLDAWELVYELITKKE---INRAIFHWYNG--PIELMQKIQETG 167
                                       5677888999999*********************999999988777777...55566777665..444455568888 PP

                                       CEEEHH.HHHHHH CS
                      Amidohydro_1 196 vhltpt.eaellk 207
                                        +++ +  +++ k
  gi|385806241|ref|YP_005842639.1| 168 YYISINvALKMQK 180
                                       8888443333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       710  (0.0396006); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1555.64
//
Query:       gi|385806242|ref|YP_005842640.1|  [L=235]
Description: metallophosphoesterase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-11   45.0   0.1    2.1e-11   44.7   0.1    1.1  1  Metallophos    Calcineurin-like phosphoesterase
    5.9e-06   26.6   0.0    0.00012   22.4   0.0    2.0  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
  ------ inclusion threshold ------
      0.076   13.1   0.3       0.17   12.0   0.3    1.6  1  Skp1           Skp1 family, dimerisation domain


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   0.1   3.5e-15   2.1e-11      29     203 ..      15     190 ..       4     191 .. 0.66

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 3.5e-15
                                       HHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHH.TSEEEEEC-TTSCHHHHHHHHHHHHHHHHHHHEHH...HCE CS
                       Metallophos  29 lreekpdlvllaGDlvdrgdlekellellaalvky.pipvylllGNHegfeeellnkygylgifsepwrsd...aev 101
                                       +ree+  + ++aGD++drg +++ + ++++   k   ++++ + GN e +ee   +k ++++ +  +w +d   +  
  gi|385806242|ref|YP_005842640.1|  15 NREEEFEVAMFAGDIIDRGKIQH-FSDFFSIIKKCkFKKIISIFGNDE-YEE-EREKVKKEYSW-VIWLDDenvQLN 87 
                                       66778899999********8888.8888644444343467********.444.33333333333.333433222344 PP

                                       EETSEEEEEETTEEEEEEEESECEEE.THHHHHHHHHHHSCHHHHCCHHHHHHHHHHTTCSEEEEEESSESS..... CS
                       Metallophos 102 fnnlplaslgsgslkvlllhGgspel.lvsldklgslnleleapepgdewlkdlekrekadwvivlgHsply..... 172
                                        +n+ + +lg++   vl ++     +  +++ +++    ++ +    +++lk   ++++++ +i+l+H p++     
  gi|385806242|ref|YP_005842640.1|  88 IENYTVTVLGTT--GVLDVPTK---WqYKNIPNIREKYERRLVLI--EKFLKA--EKRERELKILLTHYPPTfktlq 155
                                       466666667777..78888887...32222333333333332222..666666..********************98 PP

                                       ...CSSSCSCCHHHHHHH.HHHTTESEEEEESSSS CS
                       Metallophos 173 ...rgsgylfgdealedl.lkkygvdlvisGHtHv 203
                                            + +++g+e++e+l ++   +d+vi+GH H 
  gi|385806242|ref|YP_005842640.1| 156 gelPFAWPQMGSERAERLiKDLDTLDYVIHGHAHN 190
                                       888777788888888899455555*********96 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 !   22.4   0.0     2e-08   0.00012      26     142 ..      18     205 ..       8     213 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 2e-08
                     Metallophos_2  26 vgvdaiihaGDl.eeeepevleellela......pvlaVrGNnD................................. 62 
                                       ++ +  ++aGD+   ++ +   +++++       +++ ++GN +                                 
  gi|385806242|ref|YP_005842640.1|  18 EEFEVAMFAGDIiDRGKIQHFSDFFSIIkkckfkKIISIFGNDEyeeerekvkkeyswviwlddenvqlnienytvt 94 
                                       4459999****98666666777777776778899********99999999999999999999999999999888888 PP

                     Metallophos_2  63 ................eevveedvlreaaelgtdl......peeaelelagekvlliHgdpl..............g 103
                                                       +      + +  ++++++l       ++++ e ++ k+ll+H+ p                
  gi|385806242|ref|YP_005842640.1|  95 vlgttgvldvptkwqyK-----NIPNIREKYERRLvliekfLKAEKRE-RELKILLTHYPPTfktlqgelpfawpqM 165
                                       88777777665444332.....33333333333333221112333333.5667******988**********99999 PP

                     Metallophos_2 104 vkdalaellkeaeegsdvvvcGHtHvpeveke..ggvlvvn 142
                                       ++++ ++l+k+  ++ d+v++GH H  ++ ++  g+++v n
  gi|385806242|ref|YP_005842640.1| 166 GSERAERLIKD-LDTLDYVIHGHAHNGKILDTeiGNTRVFN 205
                                       99999999999.88888********9977555336887777 PP

>> Skp1  Skp1 family, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.3   2.8e-05      0.17      21      47 ..      51      75 ..      43      76 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.8e-05
                              Skp1 21 eeiReiFnIenDftpEEeeeirkEneW 47
                                       +i  iF+  nD  +EE e+++kE++W
  gi|385806242|ref|YP_005842640.1| 51 KKIISIFG--NDEYEEEREKVKKEYSW 75
                                      56777777..9967999999******* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1633.71
//
Query:       gi|385806243|ref|YP_005842641.1|  [L=96]
Description: hypothetical protein FFONT_1201 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.5e-05   24.0   1.4    4.9e-05   23.5   1.4    1.3  1  Glu-tRNAGln  Glu-tRNAGln amidotransferase C subunit
  ------ inclusion threshold ------
      0.014   14.4   0.5      0.014   14.3   0.5    1.1  1  Baculo_p48   Baculovirus P48 protein
      0.023   15.0   0.3      0.025   14.9   0.3    1.3  1  DUF4358      Domain of unknown function (DUF4358)


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 !   23.5   1.4   8.3e-09   4.9e-05       1      45 [.      23      75 ..      23      90 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 8.3e-09
                                      --HHHHHHHHHHHHHHHHHHTTCGCS--TT----S....-EB-S--......H CS
                       Glu-tRNAGln  1 lseeEleklakelnsildyveqLqevdttgveplthp..vlReDev......r 45
                                      l+e+E+ek+ ++l+ i  y++++ ++++++    +    +lReDev      +
  gi|385806243|ref|YP_005842641.1| 23 LDEDEVEKMIEDLKMIKSYIDEVLSIEVEDEGEIYLTtgRLREDEVtnqminP 75
                                      79*************************885544343368*****984444432 PP

>> Baculo_p48  Baculovirus P48 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.5   2.4e-06     0.014     302     342 ..       8      49 ..       2      73 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.4e-06
                        Baculo_p48 302 dlelrnvCrflfr.eyaeekiealiekLkaikedlseelskn 342
                                       + e +n   fl r ++ e+++e +ie+Lk+ik  + e+ls +
  gi|385806243|ref|YP_005842641.1|   8 NREIINHLSFLSRiKLDEDEVEKMIEDLKMIKSYIDEVLSIE 49 
                                       557788889**************************9999866 PP

>> DUF4358  Domain of unknown function (DUF4358)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.3   4.1e-06     0.025      19      56 ..      19      56 ..       3      90 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.1e-06
                           DUF4358 19 klygldkddvedyvayvsassasadevlivkakdeeda 56
                                      + ++ld+d+ve+ +    +++++ devl +++ de++ 
  gi|385806243|ref|YP_005842641.1| 19 SRIKLDEDEVEKMIEDLKMIKSYIDEVLSIEVEDEGEI 56
                                      5789******************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1050  (0.0585643); expected 358.6 (0.02)
Passed bias filter:                      679  (0.0378716); 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):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 588.92
//
Query:       gi|385806244|ref|YP_005842642.1|  [L=480]
Description: glutamyl-tRNA(Gln) amidotransferase subunit A [Fervidicoccus fontis Kam940]
Scores for 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-110  367.6   0.0   1.2e-109  367.3   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 !  367.3   0.0  6.5e-114  1.2e-109      41     451 .]      55     467 ..      39     467 .. 0.93

  Alignments for each domain:
  == domain 1  score: 367.3 bits;  conditional E-value: 6.5e-114
                                       ......TTTT-EEEEETTB--TTSB--TTSGGGTT-B-SS--HHHHHHHHTT-EEEEEE--SGGG-SSSSTT-TT-- CS
                           Amidase  41 rgkekgpLhGvPisvKDnidvkgvpttaGskalenypaekDatvverLkkaGavilgkTnmdefamgsstensvfgp 117
                                       +  +kg L G+Pi+vKDni++kg++tt++sk+le+y++ + atvver++++G +i+gkTnmdefamg+ + +s+fgp
  gi|385806244|ref|YP_005842642.1|  55 SIFKKGKLSGIPIAVKDNISTKGIRTTCASKILEDYVPGYSATVVERIEAEGGIIFGKTNMDEFAMGALGTTSAFGP 131
                                       45799************************************************************************ PP

                                       -BBTTCTCCB--SSSHHHHHHHHTTSSSCEEEEESSSTTHHHHHHCTSEEEE--TTSC--TTB--SSTTT-EEEEEE CS
                           Amidase 118 trNPwdksrtpGGSSGGsAAavAaglvplaiGtDtGGSiRiPAsfcglvGlKPtygrvSragvvalessldvvGpla 194
                                       t N ++ + +pGGSS+GsA+av++g v la+G+DtGGSiR+PA+++g++G+KPtyg vSr+g+++++ s+d++Gpla
  gi|385806244|ref|YP_005842642.1| 132 TLNNLNIELSPGGSSSGSAVAVSSGTVKLALGSDTGGSIRLPAAWTGIYGFKPTYGFVSRYGLISYADSMDQIGPLA 208
                                       ***************************************************************************** PP

                                       SSHHHHHHHHHHHBS--TT-TTS----......HHHHHHHHCTT---TT-EEEEEGGGC.SS---CCHHHHHHHHHH CS
                           Amidase 195 rsvedlalllrvilgedpkdstssvip......eesedlaeelkkslkglriGvvkedg.vasldpevqravekalk 264
                                       ++++dl+ll++ i+g+d++d+ts+  p        + +++e+    lk+l+  v+k++  + ++d+ + + + k lk
  gi|385806244|ref|YP_005842642.1| 209 TNISDLILLFSIISGSDERDPTSQF-PginkekMLKLAYSEADVDILKKLKLIVIKNLIeHPQADEGLINEFWKDLK 284
                                       ***********************96.669876544567788888889**********999***************** PP

                                       HHHCTT-EEEEEE-CCGGGHHHHHHHHHHHHHHHHTTT-SSSSS.---SS-SCCCCCCCHHHH.CCS-HHHHHHHHH CS
                           Amidase 265 aLeeaGhevvevelpsleealslyylilvaeassnlarylgvry.erlsetkvlsellpksra.ellgeevkrriel 339
                                        Le+ G+ ++ ++ p + ++ ++yy+i+++eassnlar++g ry +r+s+ ++ +   + +    l+g evkrri l
  gi|385806244|ref|YP_005842642.1| 285 MLESYGASIELIDEPLILKIPQIYYIIAFSEASSNLARFDGLRYgKRISNVEKNDYDSFYMENrTLFGWEVKRRILL 361
                                       *********************************************8888877766665555542679********** PP

                                       HHHHCSCCCCCCCHHHHHHHHHHHHHHHHHHCCC.BSEEEEESSSSS--BCCCCCHHHCSHHHHHGCCTTT...HHH CS
                           Amidase 340 gnyalsaeasskyylkaqkvrrllrrefakafee.lDvllsPtaptpaprlgekdktidsytvlynlldftavvvpv 415
                                       g++ ls++++++yy ka k+r+ lr++++++++e   ++++P + + + +l++  +   + + l+++++ +   +++
  gi|385806244|ref|YP_005842642.1| 362 GTFILSKGYYETYYVKALKARTYLRKRIDRILNEeTKFIVTPGSLIRPLPLKYDAR---DLSKLNAVDAPL---MLA 432
                                       **********************************9*****************9974...446666666666...*** PP

                                       HHTT--EEEEECCCCT.TECEEEEEEESTT-HHHHH CS
                           Amidase 416 nlaglpalsvpagksedglPvGvqvigkafqeetlL 451
                                       nl g pa+ +p g+s+   P ++q+ig+ +++ tlL
  gi|385806244|ref|YP_005842642.1| 433 NLIGSPAIVIPTGFSQ-SSPKSLQLIGRVWSDYTLL 467
                                       **************96.89***************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (480 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); 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: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.89
# Mc/sec: 1637.11
//
Query:       gi|385806245|ref|YP_005842643.1|  [L=474]
Description: aspartyl/glutamyl-tRNA amidotransferase subunit B [Fervidicoccus fontis Kam940]
Scores for complete 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-91  304.5   0.0    8.1e-91  304.2   0.0    1.1  1  GatB_N     GatB/GatE catalytic domain
    7.4e-28   97.3   2.4    7.4e-28   97.3   2.4    2.2  3  GatB_Yqey  GatB domain
  ------ inclusion threshold ------
      0.012   15.2   0.2      0.012   15.2   0.2    1.7  2  DDRGK      DDRGK domain


Domain annotation for each model (and alignments):
>> GatB_N  GatB/GatE catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  304.2   0.0   1.4e-94   8.1e-91      14     272 ..       5     276 ..       1     277 [. 0.93

  Alignments for each domain:
  == domain 1  score: 304.2 bits;  conditional E-value: 1.4e-94
                                       SB-SSSSSBSSSSCESTTSS--TTTTTSTT..--EEHHHHHHHHHHHHHTTEEE-SEE-EEEEE-TCTTCTTSEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N  14 ksKlFssasteeegeepnsevsevdlalPGtlPvlnkeavelaikaalalnceiaeeskfdRKnyfypdlpkgyQit 90 
                                       k+KlF+++s+   ++ pn++v++v+l+lPG+lP++nk+ave+ai++a+aln+ei+++++++RK+yfypdlpk+yQit
  gi|385806245|ref|YP_005842643.1|   5 KTKLFCGCSSDYRNSPPNTNVCPVCLGLPGSLPMINKKAVEKAIQVAIALNMEISKTLSWTRKHYFYPDLPKNYQIT 81 
                                       89*******6656666************************************************************* PP

                                       ESS....S.SEEEEEEEE.....TEEE..EEEEEEEEE---EEEE.....EETTEEEEETTSTT-EEEEEEE-STB- CS
                                       xxx....xxxxxxxxxxx.....xxxx..xxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N  91 qke....eplakeGslel.....ekkv..rierihlEeDaaksvh.....eekeeslvdlnRaGvpLiEivtepdlr 151
                                       q++    + +ak+G+++      +  +  ri+ri++EeD +k ++      ++++ l+d+nR+G++L+Eivtepd++
  gi|385806245|ref|YP_005842643.1|  82 QYDgkgvSTIAKNGYVSYtvngnS--YvaRIRRINIEEDPGKILYpsgsmITSDYILIDYNRSGIALLEIVTEPDFK 156
                                       *9977767899******6555533..056****************999873566*********************** PP

                                       SHHHHHHHHHHHHHHHHHHTSB--SGGGTTEEEEEEEEECTSETTSSS.--EEEEEE-SHHHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N 152 speearavveklrellralgvsdgnmeeGslRcDvNvSvreeekgeeegtrvEiKnlnslksiekaieyeierqiel 228
                                       + ++++++++klr++l++lg++d ++ eGs+R+DvN+S+         g+rvE+Kn++s+ +ie+ai yei+rq +l
  gi|385806245|ref|YP_005842643.1| 157 THQQVSSFLKKLRSILEHLGIADFSL-EGSMRVDVNISIGG-------GKRVELKNISSIAEIENAIVYEITRQRTL 225
                                       **************************.7************4.......49*************************** PP

                                       H.......-EEEEEETTTTEEEEECC----...-EEE-TTS--EE--HHHH CS
                                       x.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N 229 l.......qeTrkfdedkgetvslRskeeaedYryfpepdlppleiseeli 272
                                       l        eTr++d++++ t++ R ke++edYryfp+p+lp +eiseel+
  gi|385806245|ref|YP_005842643.1| 226 LnlgreveMETRHWDQERKVTFATRAKETEEDYRYFPDPNLPSIEISEELV 276
                                       ************************************************997 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1      0.36   2.1e+03      88     107 ..      39      57 ..      35      63 .. 0.75
   2 ?   -3.7   0.1       1.7   9.9e+03      57      85 ..     271     300 ..     269     303 .. 0.68
   3 !   97.3   2.4   1.2e-31   7.4e-28       1     148 []     316     463 ..     316     463 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.36
                                       XXXSSXHHHHHHHHHHTXHH CS
                         GatB_Yqey  88 isdeeeleklveeviaenpk 107
                                       i+ ++++ek+++ +ia n +
  gi|385806245|ref|YP_005842643.1|  39 IN-KKAVEKAIQVAIALNME 57 
                                       44.58999999999998854 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 1.7
                                       SGHHHHHHHHHHHHHH.TXXHHHHHHHCTX CS
                         GatB_Yqey  57 Iskkiakevleellee.gkspeeiieekgL 85 
                                       Is++ +k++ e l e  +k  e  i+ ++L
  gi|385806245|ref|YP_005842643.1| 271 ISEELVKKIRESLPELpDKRKERFIKDYKL 300
                                       777777777777776667777777777666 PP

  == domain 3  score: 97.3 bits;  conditional E-value: 1.2e-31
                                       HHHHHHHHHS.S.HHHHHHHHHTCHHHHHHHHTXXTTCSSTTHHHHHHHHHHHHTTSSGHHHHHHHHHHHHHHTXXH CS
                         GatB_Yqey   1 dffeevvkeg.adaklaanwllnellgelnkegleieelkltpeqlaellkliaegkIskkiakevleelleegksp 76 
                                       d+feev+k++  d ++aa+ ++n++lg + + + +  +  ++p+++aell+++ egkI+ k+ake+++el+ +gks 
  gi|385806245|ref|YP_005842643.1| 316 DYFEEVMKSTsIDTQKAASFIVNDVLGWIPSGDTNELNKYIPPQKIAELLEMLREGKITIKMAKELIPELI-NGKSL 391
                                       89******99567****************99988777778*******************************.8**** PP

                                       HHHHHHCTXXXXX.XSSXHHHHHHHHHHTXHHHHHHHTTXXTTSTHHHHHHHHHTTSSXSXHHHHHHHHHHHS CS
                         GatB_Yqey  77 eeiieekgLkqis.deeeleklveeviaenpkavedyksgkekalkflvGqvMkktkGkadpklvnellkekL 148
                                       + ++eekg + +  +eee+ k++e +++e p+av+d  + k ka++flvG+v  +t+ +adpk+v +l+ +k+
  gi|385806245|ref|YP_005842643.1| 392 KGAVEEKGWFEVIySEEEILKVIESIMNEYPEAVKDSIKDK-KAVQFLVGKVLEATNKRADPKKVYDLICKKI 463
                                       *******96655449*********************99998.7*************************99886 PP

>> DDRGK  DDRGK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.3         1   6.2e+03      42      58 ..     239     255 ..     223     260 .. 0.42
   2 ?   15.2   0.2     2e-06     0.012     102     168 ..     350     417 ..     320     420 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1
                                       XXXXXXXXXXXXXXXXX CS
                             DDRGK  42 rkekeekeeekekkkee 58 
                                       ++++++  ++ ++k++e
  gi|385806245|ref|YP_005842643.1| 239 WDQERKVTFATRAKETE 255
                                       22222222222222222 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 2e-06
                                       HHHHHHHHH-SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE-.--XXXXXXXXXX CS
                             DDRGK 102 eefinyikekKvvlleelavkfklktqevierikeLeeqgsltGvlDdrGkyiyi.tdeEleavakyi 168
                                       +e+ +yi  +K+ +l e+  + k++ + + e i eL + +sl+G + ++G +  i ++eE+ +v++ i
  gi|385806245|ref|YP_005842643.1| 350 NELNKYIPPQKIAELLEMLREGKITIKMAKELIPELINGKSLKGAVEEKGWFEVIySEEEILKVIESI 417
                                       67889*********************************************995443889999999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       962  (0.0536561); expected 358.6 (0.02)
Passed bias filter:                      611  (0.0340789); 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: 0.63u 0.36s 00:00:00.99 Elapsed: 00:00:00.54
# Mc/sec: 2649.12
//
Query:       gi|385806246|ref|YP_005842644.1|  [L=318]
Description: 2-oxoacid:ferredoxin oxidoreductase subunit beta [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-24   86.3   0.5    2.4e-24   85.9   0.5    1.2  1  TPP_enzyme_C    Thiamine pyrophosphate enzyme, C-terminal TPP
  ------ inclusion threshold ------
       0.13   12.2   0.4       0.31   11.0   0.4    1.6  1  GnsAB_toxin     GnsA/GnsB toxin of bacterial toxin-antitoxin 
       0.17   11.1   1.1       0.23   10.6   0.1    1.7  2  DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase


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 !   85.9   0.5     4e-28   2.4e-24       2     153 .]      53     222 ..      52     222 .. 0.90

  Alignments for each domain:
  == domain 1  score: 85.9 bits;  conditional E-value: 4e-28
                                       SSHHHHHHHHHHTTSSSSEEEC.ETTTS-TTTHHHHHHHHHHH............STTSEEEEEEEHHHHHHT.GGG CS
                      TPP_enzyme_C   2 iGcltlwaarllkvkrprsylt.sgglgtmGyglpaAiGakla............kpdrevvaivGDGgflmi.lqe 64 
                                       +Gcl++ +  +     p++ ++ + +++++ ++ ++A+G++ a            +++ +++a++GDGg+++i +q+
  gi|385806246|ref|YP_005842644.1|  53 TGCLEVSTTSF-----PYTAWKvPWIHVAFENTGAVASGVESAikamkmkgildpNEEINIIAVAGDGGTFDIgFQA 124
                                       79999966666.....888777699****************944456667777444467****************** PP

                                       HHHHHHTT-SEEEEEEE-SBCCCHHHH...HHHHTCCTTTTSBB......BS----HHHHHHHTTSE.EEEESSH.H CS
                      TPP_enzyme_C  65 latavrrnlpitvvvlnNegygmtggq...qepfggkrksgpagk.....dlkpvdfaklaealGak.garvekadv 132
                                       l+ + +r++++ +v+++Ne+y++tg q    +pfg++++++p  k       +++d+  ++ a+G+k +a+ ++a++
  gi|385806246|ref|YP_005842644.1| 125 LSGMLERGHKVMYVLYDNEAYMNTGVQrsgGTPFGAWTTTTPVTKrirgeWRNKKDIFDIVIAHGVKyAAVANPAYT 201
                                       ******************************9***********999***9769999************888999**** PP

                                       HHHHHHHHHHHCSSSEEEEEE CS
                      TPP_enzyme_C 133 eeleealkealekkgpaliev 153
                                        ++ +++k+ le++gp++ +v
  gi|385806246|ref|YP_005842644.1| 202 VDMMNKFKKGLEQEGPSFMHV 222
                                       ******************997 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 ?   11.0   0.4   5.1e-05      0.31      14      33 ..     293     312 ..     286     314 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5.1e-05
                                       HHHHHHHHHHHHHHHHSSEE CS
                       GnsAB_toxin  14 iaeliakKiaELkKkTGkEV 33 
                                       i e + kK+ E++Kk G+EV
  gi|385806246|ref|YP_005842644.1| 293 IQEQVNKKVEEVNKKVGREV 312
                                       678899*************9 PP

>> DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   3.9e-05      0.23     121     177 ..      92     148 ..      76     177 .. 0.79
   2 ?   -4.0   0.0       1.1   6.7e+03     185     211 ..     284     310 ..     281     313 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 3.9e-05
                    DXP_synthase_N 121 lGlavardlkg.ekkkvvaviGDgaltgGmafealnnigelkkkllvilNdNemsisk 177
                                       + +++   l+  e+ +++av GDg+ t  + f+al  + e  +k++ +l dNe  +++
  gi|385806246|ref|YP_005842644.1|  92 KAMKMKGILDPnEEINIIAVAGDGG-TFDIGFQALSGMLERGHKVMYVLYDNEAYMNT 148
                                       3333333332225789********9.88999*********************987665 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 1.1
                    DXP_synthase_N 185 ylskllsskayeklkkevkkllkkigk 211
                                       +l+++  s   e+++k+v+++ kk+g+
  gi|385806246|ref|YP_005842644.1| 284 HLNDVEISYIQEQVNKKVEEVNKKVGR 310
                                       556666666666666666666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       787  (0.0438954); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 2032.10
//
Query:       gi|385806247|ref|YP_005842645.1|  [L=408]
Description: 2-oxoacid:ferredoxin oxidoreductase subunit alpha [Fervidicoccus fontis Kam940]
Scores for complete 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-68  229.8   3.3    4.7e-68  229.4   3.3    1.1  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    7.4e-23   80.8   0.0    1.5e-22   79.8   0.0    1.5  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
     0.0044   16.9   0.0      0.011   15.6   0.0    1.7  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 !  229.4   3.3   7.8e-72   4.7e-68       2     228 ..      28     249 ..      27     252 .. 0.95

  Alignments for each domain:
  == domain 1  score: 229.4 bits;  conditional E-value: 7.8e-72
                                       HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCC CS
                             POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmien 78 
                                       a++ a+vdv+aaYPITP++ ++e+lael+ +ge+ ++e++ +esE++a saviGA+a Gar++TaT++qGl+Lm+e 
  gi|385806247|ref|YP_005842645.1|  28 AVKDADVDVVAAYPITPQTIVVETLAELIGNGEL-NAEMIHVESEHSALSAVIGASAVGARVFTATASQGLALMHEV 103
                                       7899*****************************9.7***************************************** PP

                                       HHHHHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHHS---EEEE-SSHHHHHHHHHHHHHHHHH..CTSEEEEEE CS
                             POR_N  79 lglaageelPvvivvvaRalpstglsirtdqsDlmaardtglivlasenvqeafdlalvAfnlAek..vrvPvivlf 153
                                       l++++g +lPvv+ v++Ral+++ +si++dqsD+m  r+tg+i ++++++qea+d +l+A+++Ae+  v +Pv+v  
  gi|385806247|ref|YP_005842645.1| 104 LHITSGLRLPVVMSVAMRALSAP-ISIFNDQSDIMNQRNTGWITIIASSAQEAYDSILQAYKIAENpkVLLPVMVSY 179
                                       ***********************.***************************************************** PP

                                       EHHHH.HEEEEEEC-SGG.GS-----SBXXXXXXXXSXXXBXXTXXTSSXXEEESBXBXTTSXBXXXXHHHHHHH CS
                             POR_N 154 Dgfllshevekvelpdeedelklikekleeyerkeyaldpekpiargtaanpdtglehrekgneaedaaekvvee 228
                                       Dg++lsh++e+ve   +     +++e  +++ + +  ld++ pi++gt + p++++e+++++++a ++  +v+++
  gi|385806247|ref|YP_005842645.1| 180 DGYVLSHTIERVETVGKS----VVEEYIPKKVTWN-TLDVKDPITMGTITSPEYYYEFKYAQERALEESLSVIKS 249
                                       ***************999....6666555555555.9***************************99988777776 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 !   79.8   0.0   2.5e-26   1.5e-22       1     101 [.     273     377 ..     273     378 .. 0.96

  Alignments for each domain:
  == domain 1  score: 79.8 bits;  conditional E-value: 2.5e-26
                                       -SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G..-HHHHHHH CS
                           PFOR_II   1 AevvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgse..Gqlveevk 75 
                                       Aev+++a+ s   ++k a d +R+eg+kvG ++lr++rPFP+eel +++k+++ + v+dr+i+fg++  G+++++++
  gi|385806247|ref|YP_005842645.1| 273 AEVALLATSSYYTNLKVATDLARKEGLKVGTIKLRVFRPFPREELYSMIKDLQVLGVIDRAIAFGQKpsGPIANDIA 349
                                       9*****************************************************************99********* PP

                                       HHTGGG..TSEEEEEE--GGG----HHH CS
                           PFOR_II  76 aalkks..kvkvvnfvaglgGrditved 101
                                       +al+ +  k+ + +++ag+g+r + +ed
  gi|385806247|ref|YP_005842645.1| 350 SALQYKkdKPIIQSIIAGIGQRRMLIED 377
                                       ***988877778899*******999988 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.9e-06     0.011       8      68 ..     271     331 ..     268     366 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.9e-06
                                       TTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEE CS
                   Transketolase_C   8 egkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvve 68 
                                       e  +v+l+a++s   +   A + ++keg+++  + lr ++p+ +e + +++k  + l v++
  gi|385806247|ref|YP_005842645.1| 271 EDAEVALLATSSYYTNLKVATDLARKEGLKVGTIKLRVFRPFPREELYSMIKDLQVLGVID 331
                                       5679********999999999999999*******************996666655554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); 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: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2520.61
//
Query:       gi|385806248|ref|YP_005842646.1|  [L=107]
Description: 2-oxoacid:ferredoxin oxidoreductase subunit delta [Fervidicoccus fontis Kam940]
Scores for complete 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-15   54.7  14.3    2.1e-07   30.5   3.0    2.2  2  Fer4         4Fe-4S binding domain
    1.8e-11   44.5  32.6    2.4e-07   31.2  12.0    1.8  3  Fer4_7       4Fe-4S dicluster domain
      8e-10   38.7   6.8    1.2e-09   38.1   6.8    1.3  1  Fer4_21      4Fe-4S dicluster domain
    2.1e-09   38.2   8.4    0.00042   21.2   3.0    2.2  2  Fer4_16      4Fe-4S double cluster binding domain
    5.7e-09   35.6  13.3    0.00025   20.9   3.1    2.2  2  Fer4_2       4Fe-4S binding domain
    1.8e-08   34.1  14.2    0.00019   21.4   2.4    2.2  2  Fer4_6       4Fe-4S binding domain
    2.4e-08   34.0  19.5    2.9e-06   27.3  11.0    1.9  2  Fer4_9       4Fe-4S dicluster domain
    2.6e-08   33.9  20.6      3e-07   30.4   9.9    1.7  2  Fer4_10      4Fe-4S dicluster domain
    1.1e-06   29.0   7.1    1.8e-06   28.3   7.1    1.3  1  Fer4_8       4Fe-4S dicluster domain
    0.00013   22.4   9.6     0.0083   16.6   0.5    2.4  2  Fer4_13      4Fe-4S single cluster domain of Ferredoxin I
    0.00081   19.9  11.2       0.04   14.5  12.2    2.1  3  Fer4_17      4Fe-4S dicluster domain
    0.00096   19.8  10.0       0.43   11.4   0.3    2.8  3  Fer4_15      4Fe-4S single cluster domain
     0.0018   18.6  11.8      0.064   13.8   0.9    2.2  2  Fer4_4       4Fe-4S binding domain
  ------ inclusion threshold ------
      0.023   15.5  10.9      0.034   15.0   1.6    2.1  2  Fer4_22      4Fe-4S dicluster domain
      0.041   14.1   0.6      0.041   14.1   0.6    1.4  2  DDE_Tnp_1_6  Transposase DDE domain
        9.3    7.4  16.7        3.5    8.8   5.9    2.3  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 !   30.5   3.0   1.9e-10   2.1e-07       1      23 [.      34      56 ..      34      57 .. 0.96
   2 !   30.2   3.6   2.3e-10   2.6e-07       2      24 .]      76      98 ..      75      98 .. 0.93

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 1.9e-10
                                      EEEETTTSSS-THHHHHSTTTEE CS
                              Fer4  1 vvideekCigCGaCvevCPvgAI 23
                                      ++id ekC++C +C   CP gAI
  gi|385806248|ref|YP_005842646.1| 34 PIIDLEKCVRCRICWTYCPEGAI 56
                                      68********************9 PP

  == domain 2  score: 30.2 bits;  conditional E-value: 2.3e-10
                                      EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  2 videekCigCGaCvevCPvgAIt 24
                                       +d+  C gCG+C++ CPv AI+
  gi|385806248|ref|YP_005842646.1| 76 AVDYQHCKGCGICANECPVKAIQ 98
                                      699******************95 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   2.1   1.3e-05     0.015      29      52 .]      32      55 ..      17      55 .. 0.81
   2 !   31.2  12.0   2.1e-10   2.4e-07       1      52 []      40      96 ..      40      96 .. 0.80
   3 !   20.6   3.1   4.5e-07    0.0005       1      23 [.      81     103 ..      81     105 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.3e-05
                            Fer4_7 29 ekveidpekClgCgaCvavCPtga 52
                                      e++ id ekC+ C+ C + CP ga
  gi|385806248|ref|YP_005842646.1| 32 ERPIIDLEKCVRCRICWTYCPEGA 55
                                      56678999************9987 PP

  == domain 2  score: 31.2 bits;  conditional E-value: 2.1e-10
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenek.....gtekveidpekClgCgaCvavCPtga 52
                                      +C+ C+ C  +Cp +ai   ++e++       + ++++d++ C gCg C+++CP++a
  gi|385806248|ref|YP_005842646.1| 40 KCVRCRICWTYCPEGAILELDKEYKTssgrvYKVTYAVDYQHCKGCGICANECPVKA 96
                                      7************9999766665666344332266689999*************987 PP

  == domain 3  score: 20.6 bits;  conditional E-value: 4.5e-07
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeee 23 
                                       +C gCg C++ Cpvkai++ +ee
  gi|385806248|ref|YP_005842646.1|  81 HCKGCGICANECPVKAIQMVPEE 103
                                       6*****************99875 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   6.8   1.1e-12   1.2e-09       2      59 .]      35      99 ..      34      99 .. 0.78

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 1.1e-12
                           Fer4_21  2 ridedkCigCgkCliaCedtshqaieidakt....vl....kvvedeCvGCnlCssvCPvedciem 59
                                      +id +kC+ C  C + C+++++  ++++ kt    v+    +v  ++C GC +C++ CPv ++i+m
  gi|385806248|ref|YP_005842646.1| 35 IIDLEKCVRCRICWTYCPEGAILELDKEYKTssgrVYkvtyAVDYQHCKGCGICANECPV-KAIQM 99
                                      6999**************9888888555444233322343366789*************9.99998 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 !   20.3   0.3   7.1e-07   0.00079       1      24 [.      40      64 ..      40      79 .. 0.75
   2 !   21.2   3.0   3.7e-07   0.00042       1      22 [.      81     102 ..      81     107 .] 0.86

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 7.1e-07
                           Fer4_16  1 rCgtCgkCaevCPtnaikek.keke 24
                                      +C++C+ C   CP++ai e  ke++
  gi|385806248|ref|YP_005842646.1| 40 KCVRCRICWTYCPEGAILELdKEYK 64
                                      6***************987623433 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 3.7e-07
                           Fer4_16   1 rCgtCgkCaevCPtnaikekke 22 
                                       +C++Cg Ca+ CP++ai++  e
  gi|385806248|ref|YP_005842646.1|  81 HCKGCGICANECPVKAIQMVPE 102
                                       7****************98744 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   2.6   3.7e-07   0.00041       2      22 .]      33      53 ..      32      53 .. 0.88
   2 !   20.9   3.1   2.3e-07   0.00025       3      21 ..      75      93 ..      73      94 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 3.7e-07
                            Fer4_2  2 pvvvdtdrCigCgaCvsaCPa 22
                                      ++ +d ++C++C++C + CP+
  gi|385806248|ref|YP_005842646.1| 33 RPIIDLEKCVRCRICWTYCPE 53
                                      799************777**5 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 2.3e-07
                            Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                      ++vd ++C gCg+C + CP
  gi|385806248|ref|YP_005842646.1| 75 YAVDYQHCKGCGICANECP 93
                                      679**************** PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   2.4   1.7e-07   0.00019       2      24 .]      34      56 ..      33      56 .. 0.94
   2 !   18.4   4.1   1.4e-06    0.0016       4      24 .]      77      97 ..      76      97 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.7e-07
                            Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                      + id +kC+ C+ C + CPegai
  gi|385806248|ref|YP_005842646.1| 34 PIIDLEKCVRCRICWTYCPEGAI 56
                                      5699******************8 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 1.4e-06
                            Fer4_6  4 idpdkCigCgdCvrvCPegai 24
                                      +d++ C gCg C++ CP +ai
  gi|385806248|ref|YP_005842646.1| 77 VDYQHCKGCGICANECPVKAI 97
                                      78899*************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 !   17.8   1.3   2.5e-06    0.0028      28      51 .]      24      56 ..      13      56 .. 0.72
   2 !   27.3  11.0   2.6e-09   2.9e-06       1      51 []      40      97 ..      40      97 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.5e-06
                            Fer4_9 28 lraase.........eaCigCgaCveaCpkgai 51
                                      +++ ++         e+C+ C+ C   Cp+gai
  gi|385806248|ref|YP_005842646.1| 24 NDMSGWrserpiidlEKCVRCRICWTYCPEGAI 56
                                      34444455677788899*************997 PP

  == domain 2  score: 27.3 bits;  conditional E-value: 2.6e-09
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase.......eaCigCgaCveaCpkgai 51
                                      kC++C+ C + Cp g++ e ++e+k +  +  +       + C gCg C++ Cp +ai
  gi|385806248|ref|YP_005842646.1| 40 KCVRCRICWTYCPEGAILELDKEYKTSSGRVYKvtyavdyQHCKGCGICANECPVKAI 97
                                      7****************6666666655544444699****99************9987 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   9.9   2.7e-10     3e-07       2      56 .]      34      93 ..      33      93 .. 0.96
   2 !   15.1   2.9   1.6e-05     0.018       4      23 ..      77      96 ..      74     106 .. 0.77

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 2.7e-10
                           Fer4_10  2 vvidddtCirCgkCvkaCPadl.....tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      ++id ++C+rC+ C + CP  +     ++++++  + ++ +  +++++C gcg C+ +CP
  gi|385806248|ref|YP_005842646.1| 34 PIIDLEKCVRCRICWTYCPEGAileldKEYKTSSGRVYKVTYAVDYQHCKGCGICANECP 93
                                      689*****************99****999999999999*********************9 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.6e-05
                           Fer4_10  4 idddtCirCgkCvkaCPadl 23
                                      +d + C +Cg C + CP+++
  gi|385806248|ref|YP_005842646.1| 77 VDYQHCKGCGICANECPVKA 96
                                      57889************944 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   7.1   1.6e-09   1.8e-06       1      64 [.      37      95 ..      37      96 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 1.6e-09
                            Fer4_8  1 elekCieCgaCqsaCp..vlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                                      +lekC++C  C + Cp  ++ + +k+ +++ g++ + v            ++C +cg C+++Cpv+
  gi|385806248|ref|YP_005842646.1| 37 DLEKCVRCRICWTYCPegAILELDKEYKTSSGRVYK-VTYAVD------YQHCKGCGICANECPVK 95
                                      589*************88888888999999999888.444444......799************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 !   16.6   0.5   7.4e-06    0.0083       1      18 [.      36      53 ..      36      67 .. 0.86
   2 !    9.7   2.8    0.0011       1.2       1      17 [.      77      93 ..      77      95 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 7.4e-06
                           Fer4_13  1 VDrdtCiacgaCvelaPd 18
                                      +D ++C+ c +C+  +P+
  gi|385806248|ref|YP_005842646.1| 36 IDLEKCVRCRICWTYCPE 53
                                      899**************8 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0011
                           Fer4_13  1 VDrdtCiacgaCvelaP 17
                                      VD + C +cg+C++ +P
  gi|385806248|ref|YP_005842646.1| 77 VDYQHCKGCGICANECP 93
                                      8999************9 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   1.5   0.00011      0.12      42      59 ..      37      54 ..      13      56 .. 0.78
   2 !   14.5  12.2   3.5e-05      0.04       1      57 [.      40      93 ..      40      97 .. 0.81
   3 !   10.7   3.2   0.00055      0.61       2      15 ..      82      95 ..      81     103 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00011
                           Fer4_17 42 kaslCieCgeCerkCPqg 59
                                        ++C+ C+ C ++CP+g
  gi|385806248|ref|YP_005842646.1| 37 DLEKCVRCRICWTYCPEG 54
                                      6789************86 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 3.5e-05
                           Fer4_17  1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCP 57
                                      +C +C+ C   Cp +++ + +++   +++++g++ ++      + C +Cg C+ +CP
  gi|385806248|ref|YP_005842646.1| 40 KCVRCRICWTYCPEGAILELDKE---YKTSSGRVYKVTYAVDYQHCKGCGICANECP 93
                                      6*************999776544...55555666676666799************** PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00055
                           Fer4_17  2 CiqCgyClpeCpsy 15
                                      C +Cg C++eCp  
  gi|385806248|ref|YP_005842646.1| 82 CKGCGICANECPVK 95
                                      99999999999975 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   0.3   0.00038      0.43       3      20 ..      36      53 ..      35      69 .. 0.82
   2 !   11.1   3.3   0.00045      0.51       3      19 ..      77      93 ..      76      95 .. 0.93
   3 ?    6.3   0.1     0.015        17      56      65 ..      89      98 ..      89      99 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00038
                           Fer4_15  3 vDrdaCigcglCvaeape 20
                                      +D ++C  c  C++ +pe
  gi|385806248|ref|YP_005842646.1| 36 IDLEKCVRCRICWTYCPE 53
                                      89**************87 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00045
                           Fer4_15  3 vDrdaCigcglCvaeap 19
                                      vD + C gcg C+ e+p
  gi|385806248|ref|YP_005842646.1| 77 VDYQHCKGCGICANECP 93
                                      8***************8 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.015
                           Fer4_15 56 araCPvdAIr 65
                                      a +CPv+AI+
  gi|385806248|ref|YP_005842646.1| 89 ANECPVKAIQ 98
                                      789******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 !   13.8   0.9   5.7e-05     0.064       2      16 ..      39      53 ..      38      67 .. 0.91
   2 !    9.5   4.2    0.0013       1.5       2      16 ..      80      94 ..      79      95 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.7e-05
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      e+C++C+ C  +CP 
  gi|385806248|ref|YP_005842646.1| 39 EKCVRCRICWTYCPE 53
                                      89************5 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0013
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      + C gCg C + CP+
  gi|385806248|ref|YP_005842646.1| 80 QHCKGCGICANECPV 94
                                      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 ?    7.1   1.6    0.0089        10       1      25 [.      40      64 ..      40      75 .. 0.76
   2 ?   15.0   1.6     3e-05     0.034      69      95 ..      69      95 ..      57      96 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0089
                           Fer4_22  1 rClsCgaCtlvCptCsCfdvedetk 25
                                      +C++C  C + Cp     ++ +e k
  gi|385806248|ref|YP_005842646.1| 40 KCVRCRICWTYCPEGAILELDKEYK 64
                                      7************988887777664 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 3e-05
                           Fer4_22 69 klsefkekfgesgCvGCgRCieacpvk 95
                                      ++++++  ++ ++C GCg C + cpvk
  gi|385806248|ref|YP_005842646.1| 69 RVYKVTYAVDYQHCKGCGICANECPVK 95
                                      56677778899*************986 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 ?   -3.4   0.1       9.4   1.1e+04      31      36 ..      39      44 ..      24      47 .. 0.62
   2 ?   14.1   0.6   3.6e-05     0.041       1      45 [.      50      95 ..      50     106 .. 0.70

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 9.4
                       DDE_Tnp_1_6 31 kdCrgC 36
                                      ++C +C
  gi|385806248|ref|YP_005842646.1| 39 EKCVRC 44
                                      444444 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 3.6e-05
                       DDE_Tnp_1_6  1 vCPagkkltlsteskekgngykrevavyrl..kdCrgCpl.reqCtkk 45
                                      +CP+g  l+l++e+k++ +g++ +v+ y+   ++C+gC   +++C+ k
  gi|385806248|ref|YP_005842646.1| 50 YCPEGAILELDKEYKTS-SGRVYKVT-YAVdyQHCKGCGIcANECPVK 95
                                      5**********998776.44444443.444339999997514667655 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   3.0     0.076        85       1      15 []      41      55 ..      41      55 .. 0.95
   2 ?    8.8   5.9    0.0031       3.5       1      15 []      82      96 ..      82      96 .. 0.97

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.076
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+ C+ C   CP+gA
  gi|385806248|ref|YP_005842646.1| 41 CVRCRICWTYCPEGA 55
                                      999*99********9 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0031
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C gCg C + CPv+A
  gi|385806248|ref|YP_005842646.1| 82 CKGCGICANECPVKA 96
                                      9************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); 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: 00:00:00.51
# Mc/sec: 637.25
//
Query:       gi|385806249|ref|YP_005842647.1|  [L=198]
Description: 2-oxoacid:ferredoxin oxidoreductase subunit gamma [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-36  124.3   0.3    6.2e-36  124.1   0.3    1.0  1  POR       Pyruvate ferredoxin/flavodoxin oxidoreductase
  ------ inclusion threshold ------
      0.026   14.8   0.0       0.28   11.5   0.0    2.4  2  POTRA_1   POTRA domain, FtsQ-type


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 !  124.1   0.3   6.9e-40   6.2e-36       1     176 [.      22     192 ..      22     193 .. 0.91

  Alignments for each domain:
  == domain 1  score: 124.1 bits;  conditional E-value: 6.9e-40
                                       CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-S.SS--TTSEEEEEESSHHHHH..HHGG CS
                               POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepiv.psievgeadllvaldaetls..ehld 74 
                                       GGqG+vta+++ a +a ++G+++ a +e+g+e+rG ++ ++ r+s+e +     ++ ++d+ v ld+++ls  +++ 
  gi|385806249|ref|YP_005842647.1|  22 GGQGAVTASELVAMSAIKEGKNAIAIPEFGAERRGVPVRAYTRVSKELKEiHKTPIVNPDIFVLLDPSLLSkaKNYI 98 
                                       9*********************************************5443478888**************889**** PP

                                       GEEEEEEEEEECTCGTT-CCHHHCTS-HHHHHHHT-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHT.S-HHHH CS
                               POR  75 glkpggiiiynseelkpdelkkakeeerelkerlgvrvygvdatkiakeiggneraaNtvmlGalaallg.lpleal 150
                                       +lk++g++i+n+   k++ +k      +e+      +++++da+ i+ +i+g +++ Ntvm+Ga++a+   ++le++
  gi|385806249|ref|YP_005842647.1|  99 DLKDDGVVIANTQLSKDEAIKVMGIKVKEE------NFFVIDAKSIVMRILG-RPIYNTVMVGAFIAIVPiVKLETV 168
                                       ************876666666655544433......7***************.************************ PP

                                       HHHHHCCS-CH.HHHHHHHHHHHHHH CS
                               POR 151 eeaikkrfpkkkeviekNlkafragy 176
                                       +e ++++f++k  + ++N +++++gy
  gi|385806249|ref|YP_005842647.1| 169 LESVRETFKGK--LGDLNAQVIEEGY 192
                                       *********95..************9 PP

>> POTRA_1  POTRA domain, FtsQ-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       0.1   9.4e+02      11      33 ..      24      46 ..      21      55 .. 0.81
   2 ?   11.5   0.0   3.1e-05      0.28      10      47 ..     108     146 ..     105     154 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.1
                                      -SS--HHHHHHHHHTTSTT-GGG CS
                           POTRA_1 11 nkhlsseeiikalgiekgtslfs 33
                                         +++ e+ + ++i++g++ + 
  gi|385806249|ref|YP_005842647.1| 24 QGAVTASELVAMSAIKEGKNAIA 46
                                      667999**********9998765 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 3.1e-05
                                       S-SS--HHHHHHHHHTTS.TT-GGGS-HHHHHHHHHH-T CS
                           POTRA_1  10 Gnkhlsseeiikalgiek.gtslfsldleaieqrleklp 47 
                                        n++ls++e ik++gi+  ++++f +d++ i  r++  p
  gi|385806249|ref|YP_005842647.1| 108 ANTQLSKDEAIKVMGIKVkEENFFVIDAKSIVMRILGRP 146
                                       599*************************99877776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.51
# Mc/sec: 1174.53
//
Query:       gi|385806250|ref|YP_005842648.1|  [L=378]
Description: endopeptidase, family M48B [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-38  131.7   0.0    4.6e-38  131.0   0.0    1.3  1  Peptidase_M48    Peptidase family M48
    0.00038   19.7   0.0    0.00087   18.6   0.0    1.5  1  Peptidase_M56    BlaR1 peptidase M56
  ------ inclusion threshold ------
      0.027   14.5   1.7      0.027   14.5   1.7    3.4  3  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
       0.39   10.0   1.6        1.2    8.4   1.6    1.8  1  DUF4191          Domain of unknown function (DUF4191)
       0.64   10.1   3.4         25    5.0   0.0    3.0  2  DUF962           Protein of unknown function (DUF962)


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 !  131.0   0.0   1.3e-41   4.6e-38       3     195 ..     114     372 ..     112     373 .. 0.86

  Alignments for each domain:
  == domain 1  score: 131.0 bits;  conditional E-value: 1.3e-41
                                       -SSHHHHHHHHHHHHTT-..-EEEEEEE-GGGT-EEEEESSS-E.EEEEEHHHH-SSB-HHHHHHHHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48   3 reaelkevveelakeaglpkpltkvyvvnspkrNAFalgggknk.rivltdgLlkqllseeelaaVlGHElGHikhr 78 
                                       +e ++ e+v ++ak agl k  +k ++++ p  NAFa g      ++++t+gLl ql  +ee++aV GHElGH+khr
  gi|385806250|ref|YP_005842648.1| 114 EESWVSEMVTKMAKDAGL-KSIPKAVIAEVPAPNAFAFGSPIAGnYVAITRGLL-QLFPKEEIEAVVGHELGHLKHR 188
                                       6789**************.8889****************999988*********.********************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHTT-SHHHHHTT--S---HHHHHHHHHHTT..........HHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxxxx RF
                     Peptidase_M48  79 hsvvslivsllasillllglallisraeedaagafldalavliglliillfl..........alSRkrEyqADeagv 145
                                       ++++ l +sll+s ++++g++ll     + ++   ++ ++++ +l++++lf+           +SR rEy AD +++
  gi|385806250|ref|YP_005842648.1| 189 DVATLLAISLLPSAIYFIGRMLLAWGWLAGDSRERGGGAMFY-VLIGAILFVagflfqflvtHFSRLREYFADYHSA 264
                                       *******************98775433333333333333333.2333333333556666788*************** PP

                                       HTTT.HHHHHHHHHHHHHHTT--S---HHHH.............................................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............................................. RF
                     Peptidase_M48 146 ellkrakdlvraliklakdlerqdvsaslrs.............................................. 176
                                       +l+ +++ l+ral++l   +e++++ + + +                                              
  gi|385806250|ref|YP_005842648.1| 265 KLTGNPRMLQRALARLTLIYESNPNVSNQINksaamlfivnyfvsmsggmayenidywfpyskkpyipkdinideav 341
                                       **********************8877777667899999999999999999999999999999999999999999999 PP

                                       ............HHS-SS--HHHHHHHHHH- CS
                                       ............xxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48 177 ............ellstHPplleRiqalkel 195
                                                   el+stHP++++R++ l++l
  gi|385806250|ref|YP_005842648.1| 342 ekimnrkesaflELFSTHPSTPKRLRFLENL 372
                                       999999999999***************9975 PP

>> Peptidase_M56  BlaR1 peptidase M56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   2.4e-07   0.00087     102     220 ..      83     198 ..      75     214 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.4e-07
                     Peptidase_M56 102 lkillliWivgalilllyliaallvlkkrfvrklgklraeelkeaLkeakeemqlkrnikirlsssidsPavlgllk 178
                                       +  l++i++++  +l+ y+i+a+         ++ k +++   e + ++ ++ +lk  +k  + +++  P  ++   
  gi|385806250|ref|YP_005842648.1|  83 TVGLVAIFMILQWLLSPYMIKAVY------RASEPKPEESWVSEMVTKMAKDAGLKSIPKA-VIAEVPAPNAFAFGS 152
                                       444444444444454555555544......4456677777778889999999997666555.556688898888766 PP

                     Peptidase_M56 179 p....rIvlPadflkklsdeeleyillHElaHlkrkDllvnllvav 220
                                       p    ++ +   +l+ + +ee+e ++ HEl Hlk++D+   l + +
  gi|385806250|ref|YP_005842648.1| 153 PiagnYVAITRGLLQLFPKEEIEAVVGHELGHLKHRDVATLLAISL 198
                                       5333379******************************987665544 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 ?    1.8   1.8     0.068   2.4e+02      66     109 ..      11      50 ..       1      53 [. 0.57
   2 ?   14.5   1.7   7.5e-06     0.027      40     102 ..      50     117 ..      41     120 .. 0.81
   3 ?   -1.3   6.0       0.6   2.2e+03      31      57 ..     221     247 ..     189     304 .. 0.68

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.068
                   Phage_holin_3_6  66 wlaalivaavllvlagvlalvglkklkkakplpertieelkedv 109
                                        ++ li  ++ + + g+la+ + k +++    p +++  lk  +
  gi|385806250|ref|YP_005842648.1|  11 FFGMLIASLLTAGIIGILAVSADKIVRG----PPKSLTGLKTSM 50 
                                       3455666677777777777777666666....556777777665 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 7.5e-06
                   Phage_holin_3_6  40 lgaagvlallalllllval.alala.a.lwlaali.vaavllvlagvlalvglkklkkakp.lperti 102
                                       +++++++++l+ ++l+ ++ +++l+   +wl +++ + a++++l ++l   ++k++ +a+  +pe+++
  gi|385806250|ref|YP_005842648.1|  50 MAVTAIVTFLGSISLIYLVgVYFLGyGfSWLYFTVgLVAIFMILQWLLSPYMIKAVYRASEpKPEESW 117
                                       5778888888888888888788887558*******999999999999998888888887766999875 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.6
                   Phage_holin_3_6  31 kragsgagllgaagvlallalllllva 57 
                                       +  g ga++ ++ g+++++a +l+ ++
  gi|385806250|ref|YP_005842648.1| 221 RERGGGAMFYVLIGAILFVAGFLFQFL 247
                                       333444444444444444444444443 PP

>> DUF4191  Domain of unknown function (DUF4191)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   1.6   0.00033       1.2      26      85 ..      51     113 ..      45     127 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00033
                           DUF4191  26 lwlllaaflvvvvvfvvlglll.g.s.lilllilgillgllvalivltrraekaayaqiegqp 85 
                                        ++++++fl+ + ++ ++g+ + g +  +l+  +g+++ +++  ++l+  + ka+y+  e +p
  gi|385806250|ref|YP_005842648.1|  51 AVTAIVTFLGSISLIYLVGVYFlGyGfSWLYFTVGLVAIFMILQWLLSPYMIKAVYRASEPKP 113
                                       556788999*9*9999999998534359999999**********************9988766 PP

>> DUF962  Protein of unknown function (DUF962)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   2.1     0.023        83      28      60 ..      48      80 ..      45      84 .. 0.92
   2 ?    5.0   0.0     0.007        25      43      90 ..     207     276 ..      80     319 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.023
                            DUF962 28 vplilltvlllllraklklllalfvvgyifafv 60
                                      +++++ +++++l +++l +l+ +  +gy+f ++
  gi|385806250|ref|YP_005842648.1| 48 TSMAVTAIVTFLGSISLIYLVGVYFLGYGFSWL 80
                                      67889999999*********************6 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.007
                            DUF962  43 k.......................lklllalfvvgyifafvGHfvfEkrkPAlfknplqsllidplmvlle 90 
                                                               + +++ lfv+g+ f+f+  + f + +  + ++   +l ++p+m+   
  gi|385806250|ref|YP_005842648.1| 207 GrmllawgwlagdsrergggamfyVLIGAILFVAGFLFQFLVTH-FSRLREYFADYHSAKLTGNPRMLQRA 276
                                       04444444555555555666665556777889999999997655.57777777777777777777777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       862  (0.0480785); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); 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):               5  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.51
# Mc/sec: 2241.28
//
Query:       gi|385806251|ref|YP_005842649.1|  [L=270]
Description: HSR1-like GTP-binding protein [Fervidicoccus fontis Kam940]
Scores for complete 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-10   38.7   0.2      4e-08   33.3   0.0    2.3  2  MMR_HSR1     50S ribosome-binding GTPase
    6.4e-09   35.9   0.0    1.1e-08   35.2   0.0    1.3  1  RsgA_GTPase  RsgA GTPase
    1.3e-07   31.2   0.5     0.0029   17.2   0.0    2.2  2  FeoB_N       Ferrous iron transport protein B
     0.0043   16.6   0.2      0.023   14.2   0.1    2.1  2  GTP_EFTU     Elongation factor Tu GTP binding domain
  ------ inclusion threshold ------
      0.017   14.7   0.5      0.041   13.5   0.1    1.7  2  cobW         CobW/HypB/UreG, nucleotide-binding domain
      0.027   13.4   0.3       0.11   11.5   0.1    1.9  2  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
       0.08   13.5   0.0       0.37   11.3   0.0    2.0  2  AAA_18       AAA domain
      0.093   12.2   0.2       0.77    9.2   0.0    2.1  2  Arf          ADP-ribosylation factor family
       0.65   10.0   2.7          3    7.9   0.7    2.8  2  Dynamin_N    Dynamin 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 ?    3.4   0.1      0.04        80      68     114 .]      11      57 ..       2      57 .. 0.71
   2 !   33.3   0.0     2e-11     4e-08       3      69 ..     113     178 ..     111     240 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.04
                                       HHHHH.HHCTSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                          MMR_HSR1  68 kafla.leeadlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                       +++l+ ++e+d +l  vda+ ++l     +le+l  + +k++ ++lnk
  gi|385806251|ref|YP_005842649.1|  11 EKMLEmIRESDFVLETVDAR-NSLGTRSIKLEKLAFQLNKQFAILLNK 57 
                                       4444525569********99.446666677777777778898888887 PP

  == domain 2  score: 33.3 bits;  conditional E-value: 2e-11
                                       EEEESTTSSHHHHHHHHHTS.TEEESSST...TSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHH CS
                          MMR_HSR1   3 aivGrpNvGKStLinaltge.kaivsdkp...gtTrdinegrvklkgkeielvDtpGliegaseekglgka 69 
                                       +i+G p +GKS++in l ++  a +s  p   g T+ +  ++++   + i+++DtpG++ +a++    +k+
  gi|385806251|ref|YP_005842649.1| 113 MIAGVPKTGKSSVINMLKKKdSANISPLPgkpGYTKSTSIYKIS---SGIYIYDTPGVFPDARDYI--EKT 178
                                       699***************98667777655333999999999998...57********876333332..222 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.0   5.6e-12   1.1e-08      45     161 ..      47     167 ..      30     169 .. 0.82

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 5.6e-12
                                       TT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTH.......TTHHHHHHHCTT.S.EEEEECSTTSSH CS
                       RsgA_GTPase  45 kgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktk.......egleelkellkd.k.tsvlvGqSGvGK 112
                                        + +  i+lnKiD++  e  + e  + +++ g+ v+ +sa+++       + l e+ke+l + k + +++G    GK
  gi|385806251|ref|YP_005842649.1|  47 LNKQFAILLNKIDIVPAEV-VAECIKYFKDKGIIVIPISAEKNigrgevvNFLLEIKEKLGKeKiVGMIAGVPKTGK 122
                                       566789*************.********************98833322222345778888774414478999999** PP

                                       HHHHHHHCTT-----S--------------SEEEEEETTTEEEESS-SS CS
                       RsgA_GTPase 113 StLinallpelelktgevseklgrGkhTTtavellelaegglliDtPGf 161
                                       S++in+l+ +++++++ +  k g     T++++++++++g ++ DtPG+
  gi|385806251|ref|YP_005842649.1| 123 SSVINMLKKKDSANISPLPGKPGY----TKSTSIYKISSGIYIYDTPGV 167
                                       **********99999988887654....78889***************7 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 !   12.3   0.2   4.4e-05     0.087      77     153 ..      18      95 ..       9      98 .. 0.84
   2 !   17.2   0.0   1.4e-06    0.0029       4      59 ..     113     169 ..     110     212 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.4e-05
                                       TSSSEEEEEEEGGGH..HHHHHHHHHHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBTHHH CS
                            FeoB_N  77 eepdvvvnvvdatnl..ernLyLtlqllelgvpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkegiee 151
                                       +e d v++ vda n    r++ L    ++l++++ + ln+id + ++ +   +k +++  g+ v+++sa+k+ g  e
  gi|385806251|ref|YP_005842649.1|  18 RESDFVLETVDARNSlgTRSIKLEKLAFQLNKQFAILLNKIDIVPAEVVAECIKYFKD-KGIIVIPISAEKNIGRGE 93 
                                       57899*******9964579*************************99887766666655.5***********999877 PP

                                       HH CS
                            FeoB_N 152 ll 153
                                       ++
  gi|385806251|ref|YP_005842649.1|  94 VV 95 
                                       65 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 1.4e-06
                                       EEEESTTSSHHHHHHHHHTTS.EEEEESTTSSSEEEEEEEEETTEEEEEEE----SS CS
                            FeoB_N   4 alvGnpnvGkttlfnaltgak.qkvgNwpGvtvekkegklklkgkeveivDlPGiYs 59 
                                       +++G p +Gk++++n l +++  +++  pG+    k++++   ++ + i+D PG++ 
  gi|385806251|ref|YP_005842649.1| 113 MIAGVPKTGKSSVINMLKKKDsANISPLPGKPGYTKSTSIYKISSGIYIYDTPGVFP 169
                                       579**************9876379*******9999999998899**********996 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 !   14.2   0.1   1.2e-05     0.023      86     139 ..      12      65 ..       6     104 .. 0.80
   2 ?   -1.1   0.0      0.59   1.2e+03      61      89 ..     150     180 ..     119     184 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.2e-05
                                       HHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHHH CS
                          GTP_EFTU  86 evirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrlkael 139
                                       ++ + +r  D+++  vda++   +++ ++ +la +++ ++ +++NK+D + ae+
  gi|385806251|ref|YP_005842649.1|  12 KMLEMIRESDFVLETVDARNSLGTRSIKLEKLAFQLNKQFAILLNKIDIVPAEV 65 
                                       567778999***************************************995543 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.59
                                       EEEETTCSSEEEEEEEESS....SGGGHHHHHH CS
                          GTP_EFTU  61 isleketkkylinliDtPG....HvdFskevir 89 
                                       +s++  + +  i + DtPG     +d+++++ir
  gi|385806251|ref|YP_005842649.1| 150 TSIY--KISSGIYIYDTPGvfpdARDYIEKTIR 180
                                       4555..556778888999833333566666666 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 ?   13.5   0.1   2.1e-05     0.041     108     167 ..      16      74 ..       3      77 .. 0.83
   2 ?   -1.6   0.0      0.87   1.7e+03       4      23 ..     113     132 ..     110     137 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.1e-05
                                       HCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHHHCHC..HHHHHHHHH CS
                              cobW 108 sdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtDlldeeallekleerlr 167
                                          + d+v+  vDa+n    ++ + ek+  ql++   ++lnK+D +++e  ++++ ++ +
  gi|385806251|ref|YP_005842649.1|  16 MIRESDFVLETVDARNSLGTRSIKLEKLAFQLNKQFAILLNKIDIVPAE-VVAECIKYFK 74 
                                       4556799999******98888888999*********************9.5689988765 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.87
                                       EEEESTTCCHHHHHHHHHCT CS
                              cobW   4 vltGflGsGKTtLlnhllen 23 
                                       +++G + +GK++++n l ++
  gi|385806251|ref|YP_005842649.1| 113 MIAGVPKTGKSSVINMLKKK 132
                                       68899999*****9987644 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   5.3e-05      0.11      14      50 ..      93     130 ..      83     137 .. 0.86
   2 ?   -0.1   0.0      0.18   3.7e+02      32      50 ..     138     156 ..     127     160 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.3e-05
                                       HHHHHHHHHGGG-S-SEEEE.EEE-TTSSHHHHHHHHH CS
                              MeaB  14 eakellerllakaGraqvvG.ltGvPGaGkstlvealg 50 
                                       e  ++l ++ +k G+ + vG + GvP +Gks +++ l 
  gi|385806251|ref|YP_005842649.1|  93 EVVNFLLEIKEKLGKEKIVGmIAGVPKTGKSSVINMLK 130
                                       6678899*************558***********9886 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.18
                                       EEEEE-TTSSHHHHHHHHH CS
                              MeaB  32 vGltGvPGaGkstlvealg 50 
                                         l G PG  kst + ++ 
  gi|385806251|ref|YP_005842649.1| 138 SPLPGKPGYTKSTSIYKIS 156
                                       55789*********98876 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   0.00019      0.37       2      27 ..     113     136 ..     113     172 .. 0.81
   2 ?   -1.0   0.0       1.2   2.4e+03      49      82 ..     224     256 ..     192     264 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00019
                            AAA_18   2 lltGtpGvGKttlakeLskrlgfgvn 27 
                                       +++G+p +GK+++ + L+k+   + n
  gi|385806251|ref|YP_005842649.1| 113 MIAGVPKTGKSSVINMLKKKD--SAN 136
                                       69***************9997..333 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.2
                            AAA_18  49 skrldedkldklldaleenssaleegknlvidgh 82 
                                       ++++  +k+  + ++ +e +   e + +++id +
  gi|385806251|ref|YP_005842649.1| 224 FLEALAKKRGWIERKSKEPII-DEAARTIIIDYL 256
                                       444444444444444444333.455555566555 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.15     3e+02     116     136 ..      49      69 ..      23      89 .. 0.79
   2 ?    9.2   0.0   0.00039      0.77      13      46 ..     108     141 ..      94     164 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.15
                                       SEEEEEEE-TTSTTSS-HHHH CS
                               Arf 116 vallvlaNKqDlpealseeel 136
                                        ++ +l NK+D+  a   +e 
  gi|385806251|ref|YP_005842649.1|  49 KQFAILLNKIDIVPAEVVAEC 69 
                                       4678999****9887666655 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00039
                                       TEEEEEEEESTTSSHHHHHHHHHHSSCEECSSSS CS
                               Arf  13 kelrilllGLDnaGKtTilkklkleelvttvPTi 46 
                                        ++  ++ G  ++GK+ ++++lk+++ ++++P  
  gi|385806251|ref|YP_005842649.1| 108 EKIVGMIAGVPKTGKSSVINMLKKKDSANISPLP 141
                                       44445788*********************99965 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       1.7   3.5e+03     123     167 ..      14      57 ..       9      58 .. 0.70
   2 ?    7.9   0.7    0.0015         3       5      28 ..     116     139 ..     113     227 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.7
                                       HHHHSTTEEEEEEEETTS-CCC-CHHHHHHHHSTTBTTEEEEEE- CS
                         Dynamin_N 123 keyikkadiilavtsanhdlsnsealflarevdpkgkrtivvltk 167
                                        e+i+++d++l  ++a ++l  +++ +l++++ + +k + ++l+k
  gi|385806251|ref|YP_005842649.1|  14 LEMIRESDFVLETVDARNSLG-TRSIKLEKLAFQLNKQFAILLNK 57 
                                       567888899998888888887.56666777666666666666665 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0015
                                       EBTTTTHHHHHHHHHTS--S---S CS
                         Dynamin_N   5 GsqSsGKSSvlnaLlgedilprgp 28 
                                       G  + GKSSv+n L ++d   ++p
  gi|385806251|ref|YP_005842649.1| 116 GVPKTGKSSVINMLKKKDSANISP 139
                                       77789*********9888665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); 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: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 1598.48
//
Query:       gi|385806252|ref|YP_005842650.1|  [L=45]
Description: hypothetical protein FFONT_1210 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       137  (0.00764125); expected 358.6 (0.02)
Passed bias filter:                      125  (0.00697194); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.47
# Mc/sec: 286.77
//
Query:       gi|385806253|ref|YP_005842651.1|  [L=375]
Description: hypothetical protein FFONT_1211 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.2e-06   26.2   1.3    0.00029   20.3   0.1    2.7  2  HTH_24         Winged helix-turn-helix DNA-binding
     0.0013   18.5   0.1      0.092   12.6   0.0    2.4  2  HTH_AsnC-type  AsnC-type helix-turn-helix domain
     0.0058   16.5   0.3       0.48   10.3   0.0    2.9  3  HTH_5          Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
      0.011   15.7   0.0        1.4    9.0   0.0    2.6  2  HTH_36         Helix-turn-helix domain
      0.012   15.4   0.0      0.081   12.7   0.0    2.1  2  HTH_IclR       IclR helix-turn-helix domain
      0.026   14.5   0.2       0.97    9.4   0.0    2.7  2  HTH_11         HTH domain
       0.18   12.3   1.9       0.92   10.0   0.1    2.9  5  HTH_40         Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1     0.015        38      10      46 ..      20      57 ..      11      57 .. 0.85
   2 !   20.3   0.1   1.1e-07   0.00029       1      39 [.     196     234 ..     196     239 .. 0.96

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.015
                            HTH_24 10 elLqk.nprisqreLAerlglSpstvnrrlkrLeeeGl 46
                                      e +++ +p i ++ +Ae l+ ++s ++r + +L + G+
  gi|385806253|ref|YP_005842651.1| 20 EQIMRtDPPIRISKIAEDLNEPISQIRRKISKLYNLGY 57
                                      556666***********************999988887 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 1.1e-07
                            HTH_24   1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlk 39 
                                       ld +d  IL   qk++ ++ + +A  l lS+s +nr+lk
  gi|385806253|ref|YP_005842651.1| 196 LDLIDVLILASYQKDAFTPVSKIASDLKLSISKINRHLK 234
                                       799***********************************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 ?    3.4   0.0     0.026        68      11      41 ..      22      52 ..      16      53 .. 0.91
   2 !   12.6   0.0   3.6e-05     0.092       1      36 [.     196     231 ..     196     234 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.026
                     HTH_AsnC-type 11 aLqedaRisyaeLAervGlSestvlrRvrrL 41
                                      +++ d+ i  +++Ae ++   s+++r + +L
  gi|385806253|ref|YP_005842651.1| 22 IMRTDPPIRISKIAEDLNEPISQIRRKISKL 52
                                      67889*******************9999998 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 3.6e-05
                     HTH_AsnC-type   1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlr 36 
                                       LD iD  IL+  q+da ++++++A  + lS s + r
  gi|385806253|ref|YP_005842651.1| 196 LDLIDVLILASYQKDAFTPVSKIASDLKLSISKINR 231
                                       899***************************887765 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.036        92      17      44 ..      30      57 ..      17      57 .. 0.89
   2 !   10.3   0.0   0.00019      0.48      18      37 ..     215     234 ..     203     235 .. 0.94
   3 ?   -3.0   0.0       2.7   6.9e+03       5      14 ..     259     268 ..     257     274 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.036
                                      EHHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                             HTH_5 17 cvcelaeelglsqstvShHLkkLreaGL 44
                                       ++ +ae+l+ + s +++  +kL+++G+
  gi|385806253|ref|YP_005842651.1| 30 RISKIAEDLNEPISQIRRKISKLYNLGY 57
                                      6899**********************97 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00019
                                       HHHHHHHHTS-HHHHHHHHH CS
                             HTH_5  18 vcelaeelglsqstvShHLk 37 
                                       v+ +a +l+ls s++ +HLk
  gi|385806253|ref|YP_005842651.1| 215 VSKIASDLKLSISKINRHLK 234
                                       899****************9 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 2.7
                                       HHHHHHHTTS CS
                             HTH_5   5 lkILklLaeg 14 
                                        +I++lL  +
  gi|385806253|ref|YP_005842651.1| 259 NRIMMLLIGK 268
                                       5899999874 PP

>> HTH_36  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     0.021        54      28      54 ..      31      57 ..      27      57 .. 0.93
   2 ?    9.0   0.0   0.00054       1.4      13      47 ..     203     234 ..     201     238 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.021
                            HTH_36 28 qetlakrlglsknTvsraikeLeqlGy 54
                                       + +a++l++  ++++r i +L  lGy
  gi|385806253|ref|YP_005842651.1| 31 ISKIAEDLNEPISQIRRKISKLYNLGY 57
                                      5789**********************9 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00054
                            HTH_36  13 slasfanknggcfpsqetlakrlglsknTvsraik 47 
                                       +las+      +f  ++ +a++l+ls +++ r++k
  gi|385806253|ref|YP_005842651.1| 203 ILASYQ---KDAFTPVSKIASDLKLSISKINRHLK 234
                                       677777...348999******************98 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.1e-05     0.081       8      47 ..      18      57 ..      17      57 .. 0.96
   2 ?   -0.3   0.0      0.38   9.7e+02      20      41 ..     214     235 ..     203     237 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.1e-05
                                      HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                          HTH_IclR  8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGy 47
                                      +++++ +++++ ++s +A+ +  p S  +R ++ L +lGy
  gi|385806253|ref|YP_005842651.1| 18 LIEQIMRTDPPIRISKIAEDLNEPISQIRRKISKLYNLGY 57
                                      689********************************99998 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.38
                                       BHHHHHHHHTS-HHHHHHHHHH CS
                          HTH_IclR  20 tlselArrtglpkStvhRlLqt 41 
                                        +s +A  + l+ S+  R+L+t
  gi|385806253|ref|YP_005842651.1| 214 PVSKIASDLKLSISKINRHLKT 235
                                       5899**************9988 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00038      0.97       4      44 ..      17      57 ..      15      62 .. 0.90
   2 ?    1.9   0.1     0.087   2.2e+02      11      38 ..     208     235 ..     199     235 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00038
                            HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                       ++e+++++++pi ++++Ae Ln   + +rr I +L  lg+
  gi|385806253|ref|YP_005842651.1| 17 LLIEQIMRTDPPIRISKIAEDLNEPISQIRRKISKLYNLGY 57
                                      5899*******************999999999999988885 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.087
                            HTH_11  11 eargpisgeeLAeeLnvSrrtvrrdIka 38 
                                       +++ + + +++A  L++S + + r++k+
  gi|385806253|ref|YP_005842651.1| 208 QKDAFTPVSKIASDLKLSISKINRHLKT 235
                                       455558899****************996 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.96   2.5e+03      15      35 ..      31      51 ..      15      91 .. 0.61
   2 ?   -2.6   0.0       3.1   7.9e+03      46      62 ..     174     190 ..     165     196 .. 0.67
   3 ?   10.0   0.1   0.00036      0.92      15      61 ..     215     265 ..     210     287 .. 0.80
   4 ?   -2.8   0.0       3.6   9.2e+03      68      78 ..     317     327 ..     308     335 .. 0.74
   5 ?   -2.5   0.0       2.9   7.5e+03      24      48 ..     333     357 ..     328     374 .. 0.63

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.96
                            HTH_40 15 ieeIAkerglkesTIegHLae 35
                                      i +IA+  +   s I + + +
  gi|385806253|ref|YP_005842651.1| 31 ISKIAEDLNEPISQIRRKISK 51
                                      333333333333333333333 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.1
                            HTH_40  46 erlvseeeekeIeeaie 62 
                                       ++l +ee+e++I+e+++
  gi|385806253|ref|YP_005842651.1| 174 NDLKKEEDEENIKEILK 190
                                       55556677777776654 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00036
                            HTH_40  15 ieeIAkerglkesTIegHLaeliee...geeidlerlvse.eeekeIeeai 61 
                                       + +IA   +l+ s I +HL   ie+    +  ++++l+s+ +++++I+  +
  gi|385806253|ref|YP_005842651.1| 215 VSKIASDLKLSISKINRHLKTHIEKrkiFNGCSIKQLISKlDIQNRIMMLL 265
                                       679**********************44413457799999989999997655 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 3.6
                            HTH_40  68 klkpikealpe 78 
                                        +k++ke+l+e
  gi|385806253|ref|YP_005842651.1| 317 FIKNVKEYLGE 327
                                       47999999965 PP

  == domain 5  score: -2.5 bits;  conditional E-value: 2.9
                            HTH_40  24 lkesTIegHLaelieegeeidlerl 48 
                                       l++sTI ++ + ++  ++ei+  ++
  gi|385806253|ref|YP_005842651.1| 333 LNPSTIKSYTIPFLAYNREIKNWDF 357
                                       6778888877776666655555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       758  (0.0422779); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.32s 00:00:00.96 Elapsed: 00:00:00.53
# Mc/sec: 2124.32
//
Query:       gi|385806254|ref|YP_005842652.1|  [L=87]
Description: hypothetical protein FFONT_1212 [Fervidicoccus fontis Kam940]
Scores for 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   21.9   0.0    0.00016   21.1   0.0    1.4  1  HTH_24        Winged helix-turn-helix DNA-binding
    0.00024   20.9   0.1    0.00033   20.5   0.1    1.3  1  TrmB          Sugar-specific transcriptional regulator TrmB
    0.00076   19.6   0.0     0.0008   19.5   0.0    1.0  1  Replic_Relax  Replication-relaxation
     0.0062   16.6   0.0      0.038   14.0   0.0    2.0  2  HicA_toxin    HicA toxin of bacterial toxin-antitoxin,
  ------ inclusion threshold ------
      0.013   15.3   0.0      0.019   14.9   0.0    1.3  1  MarR_2        MarR family
      0.033   14.1   0.0        6.2    6.8   0.0    2.2  2  MarR          MarR family
      0.037   14.4   0.0      0.069   13.5   0.1    1.5  2  Rrf2          Transcriptional regulator
      0.054   13.3   0.0       0.14   12.0   0.0    1.7  2  HTH_IclR      IclR helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   7.3e-08   0.00016       2      48 .]       7      53 ..       7      53 .. 0.96

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 7.3e-08
                            HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      d t +k+L++L +++  +  e+A  +gl++  v++  + L+e G+++
  gi|385806254|ref|YP_005842652.1|  7 DGTIKKLLKTLDEKGTANPGEIASITGLPRYYVLAAFQILKELGYVE 53
                                      66899****************************************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 !   20.5   0.1   1.5e-07   0.00033      14      64 ..      14      66 ..       4      69 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.5e-07
                                      CHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST..TTEEEE CS
                              TrmB 14 YlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr..pklYra 64
                                       ++L ++g a+  eia+++g+pr  v  + + L++ G+Ve + ++   k+Y+ 
  gi|385806254|ref|YP_005842652.1| 14 LKTLDEKGTANPGEIASITGLPRYYVLAAFQILKELGYVELIYSKgsHKVYKL 66
                                      4556699*********************************9998877889985 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   3.6e-07    0.0008       1      70 [.      14      75 ..      14      87 .] 0.84

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 3.6e-07
                      Replic_Relax  1 LrlLaehrvlTtrqiarllfashratarrrLarLrelgllsrlrkrvggarggsepyvYaLtpkGarlla 70
                                      L++L+e++ ++   ia ++   + + +  + ++L+elg+++ ++ +    ++   + vY L +kG  +l+
  gi|385806254|ref|YP_005842652.1| 14 LKTLDEKGTANPGEIASITGLPRYY-VLAAFQILKELGYVELIYSK----GS---HKVYKLSEKGSSILE 75
                                      8999*********************.****************7777....23...78*********9992 PP

>> HicA_toxin  HicA toxin of bacterial toxin-antitoxin,
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.36   8.1e+02      44      55 ..       5      16 ..       2      18 .. 0.80
   2 !   14.0   0.0   1.7e-05     0.038       7      32 ..      45      71 ..      42      80 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.36
                                      --CCCHHHHHHH CS
                        HicA_toxin 44 lkpgtlksIlkq 55
                                      +  gt+k++lk 
  gi|385806254|ref|YP_005842652.1|  5 IADGTIKKLLKT 16
                                      667999999996 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 1.7e-05
                                      HHHHTT-EEE.EEETTEEEEE-TTSS- CS
                        HicA_toxin  7 lLeklGfevv.rqkGSHvrfkhpdkrg 32
                                      +L+ lG+++   +kGSH ++k  +k+ 
  gi|385806254|ref|YP_005842652.1| 45 ILKELGYVELiYSKGSHKVYKLSEKGS 71
                                      89*****999999*********87765 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   8.3e-06     0.019      10      53 ..      13      54 ..       4      62 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 8.3e-06
                                      HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                      +L  L   +    ++ge+a  +gl++ +v  + + L + G+ve 
  gi|385806254|ref|YP_005842652.1| 13 LLKTLDEKGT--ANPGEIASITGLPRYYVLAAFQILKELGYVEL 54
                                      5556666666..79****************************96 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0028       6.2       8      29 ..      13      34 ..      11      53 .. 0.82
   2 ?    5.9   0.0    0.0055        12       8      26 ..      51      69 ..      46      72 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0028
                                      HHHHHHHSTTEEHHHHHHHHTS CS
                              MarR  8 iLrilyeqgplsvseLakklgv 29
                                      +L +l+e+g ++  e+a+  g+
  gi|385806254|ref|YP_005842652.1| 13 LLKTLDEKGTANPGEIASITGL 34
                                      89***************97766 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0055
                                      HHHHHHHSTTEEHHHHHHH CS
                              MarR  8 iLrilyeqgplsvseLakk 26
                                       ++++y++g+++v +L +k
  gi|385806254|ref|YP_005842652.1| 51 YVELIYSKGSHKVYKLSEK 69
                                      5689************998 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.34   7.6e+02      36      53 ..       4      21 ..       2      26 .. 0.82
   2 ?   13.5   0.1   3.1e-05     0.069      18      74 ..      15      73 ..      10      81 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.34
                                      TS-HHHHHHHHHHHHHTT CS
                              Rrf2 36 nispsylekilakLrkag 53
                                      +i +  ++k+l++L ++g
  gi|385806254|ref|YP_005842652.1|  4 GIADGTIKKLLKTLDEKG 21
                                      66677899******9998 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 3.1e-05
                                      HHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE..TTT-TCEEESSHCCCS CS
                              Rrf2 18 akeeeeepvsseeiaerqnispsylekilakLrkaglvksv..rGkgGGyrLakppeeI 74
                                      ++ +e+++++  eia+ +++++ y+   ++ L++ g+v+ +  +G +  y+L+++ ++I
  gi|385806254|ref|YP_005842652.1| 15 KTLDEKGTANPGEIASITGLPRYYVLAAFQILKELGYVELIysKGSHKVYKLSEKGSSI 73
                                      566677778899**************************964338888888888887777 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.19   4.4e+02      30      46 ..       5      21 ..       4      25 .. 0.80
   2 ?   12.0   0.0   6.2e-05      0.14       8      49 ..      13      53 ..      12      55 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.19
                                      S-HHHHHHHHHHHHHTT CS
                          HTH_IclR 30 lpkStvhRlLqtLvelG 46
                                      ++  t   lL+tL e G
  gi|385806254|ref|YP_005842652.1|  5 IADGTIKKLLKTLDEKG 21
                                      566788899***98877 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 6.2e-05
                                      HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR  8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      +L+ l e + + +  e+A  tglp+  v    q L elGyve
  gi|385806254|ref|YP_005842652.1| 13 LLKTLDEKGTA-NPGEIASITGLPRYYVLAAFQILKELGYVE 53
                                      67778888886.99***************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); 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: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 538.39
//
Query:       gi|385806255|ref|YP_005842653.1|  [L=238]
Description: Acyl-CoA synthetase (NDP forming), beta subunit [Fervidicoccus fontis Kam940]
Scores for complete 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-77  258.9   0.8    3.7e-77  258.7   0.8    1.0  1  ATP-grasp_5  ATP-grasp domain
      3e-05   23.7   1.2    0.00041   20.0   1.2    2.2  1  ATP-grasp_2  ATP-grasp domain
    0.00089   18.9   0.0     0.0016   18.0   0.0    1.5  1  ATP-grasp    ATP-grasp domain
      0.004   16.8   0.1     0.0089   15.6   0.1    1.6  1  RimK         RimK-like ATP-grasp domain
  ------ inclusion threshold ------
      0.052   13.3   0.4        0.1   12.3   0.1    1.7  2  GARS_A       Phosphoribosylglycinamide synthetase, ATP-grasp 


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 !  258.7   0.8     1e-80   3.7e-77       2     221 ..      18     237 ..      17     238 .] 0.99

  Alignments for each domain:
  == domain 1  score: 258.7 bits;  conditional E-value: 1e-80
                       ATP-grasp_5   2 alaegrtlLteaeakelleaygipvvetrlassaeeaveaaeeigypvvlKivspdilhKtdvgGvrlnlkdaeevr 78 
                                       a+++gr+ L e+e+ ++leay+ipv++  +a++++ea + +++ig+pvv+Kivspdi+hK+dvgGv +n+++++e+ 
  gi|385806255|ref|YP_005842653.1|  18 AKSSGRKKLLEHESLAVLEAYNIPVAPYFFAKDENEAQRNIDKIGFPVVVKIVSPDIVHKSDVGGVIVNVNSKDELV 94 
                                       7899************************************************************************* PP

                       ATP-grasp_5  79 aaaeeilervkekspeariegvlVqemakrggrElivgvteDpvFGpvilfGlGGtavevlkdvavalpplnstlar 155
                                       +a+++i+++v++++p+a+++g+lVq+m ++gg E+ivg  +DpvF   ++fGlGG+ vevlkdv+++++p+++++a 
  gi|385806255|ref|YP_005842653.1|  95 NAIKSIRANVQKNAPSAEVTGFLVQKMMPKGGLEVIVGGIRDPVFDATVMFGLGGIFVEVLKDVSFRIAPITKEEAL 171
                                       ***************************888*********************************************** PP

                       ATP-grasp_5 156 eliertkaskllkgvrgekkadlaaleellvrlsqLvvdlpeIreldinPllveeegvvalDarir 221
                                       e+i+++ka k+l+g+rge++ d +a+++++v++s+L+ + +e++e+d+nP++v+e+g+ a+Dar  
  gi|385806255|ref|YP_005842653.1| 172 EMINEIKARKILEGYRGEAPRDKEAIADIIVKVSKLLYENQELKEMDVNPVIVYEKGAYAVDARFI 237
                                       ***************************************************************986 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   1.2   1.1e-07   0.00041       1     201 [.      25     223 ..      25     224 .. 0.67

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.1e-07
                                       BE-HHHHHHHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE.--SSSTCCCTTCEEE.ESSHHHHHHHHHCC CS
                       ATP-grasp_2   1 nlhEyqakeilakygvkvpegevaesaeeaeeaakklgekelvvKa.QvlaGGRGKagGvkl.vkskeeakeaakel 75 
                                       +l E+++  +l+ y+++v+  + a++++ea++ ++k+g  + vvK     +  +   gGv + v+sk+e+ +a+k++
  gi|385806255|ref|YP_005842653.1|  25 KLLEHESLAVLEAYNIPVAPYFFAKDENEAQRNIDKIGFPV-VVKIvSPDIVHKSDVGGVIVnVNSKDELVNAIKSI 100
                                       589***********************************999.88851223444555578754389999999999887 PP

                                       TTSEEE-TTS-TT-EEE--EEEEE---E.CEEEEEEEEEETTTTEEEEEEESSTTS-HHHHHHH-GGGEEEEEEBTT CS
                       ATP-grasp_2  76 lgkelvtkqtgkeGkkvekvlveealdi.kkElYlsivlDraskkvvviaSseGGvdiEevaakkPekiikvaidpa 151
                                         +  +    ++   +v   lv+++++    E+ ++ + D   +  v+     GG+ +E v +    +i+ ++ + a
  gi|385806255|ref|YP_005842653.1| 101 RANVQK----NAPSAEVTGFLVQKMMPKgGLEVIVGGIRDPVFDATVM--FGLGGIFVE-VLKDVSFRIAPITKEEA 170
                                       544333....44445555555555554313477778777766655443..346888886.44555566666655554 PP

                                       .TB--HHHHHHHHHHCT--C.HHHHHHHHHHHHHHHHHH.HTTEEEEEEEEEE CS
                       ATP-grasp_2 152 .kglkeeqareiakklglek.elvkkaakiikklyklfv.eldatlvEiNPLv 201
                                        + ++e +ar+i++  + e+ +  + +a+ii+k+ kl+  +++++ +++NP++
  gi|385806255|ref|YP_005842653.1| 171 lEMINEIKARKILEGYRGEApRDKEAIADIIVKVSKLLYeNQELKEMDVNPVI 223
                                       04556778888888776665245666788888888865415678888888875 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   4.5e-07    0.0016       2      35 ..      36      69 ..      35     116 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4.5e-07
                                      HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEE CS
                         ATP-grasp  2 eklglpvprflaveskeeleeaaeelglpvvvKa 35
                                      e+ ++pv+++ ++++++e+++ ++++g+pvvvK 
  gi|385806255|ref|YP_005842653.1| 36 EAYNIPVAPYFFAKDENEAQRNIDKIGFPVVVKI 69
                                      6789*****************************4 PP

>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   2.5e-06    0.0089       6      71 ..      30      99 ..      23     120 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.5e-06
                                      HHHHHHHHTT-----EEEESS-S-HHHHHHTT-.-SSEEEEE-......TTTT--EEEEE-SHHHHHHHHHH CS
                              RimK  6 kslklLakakikvpntalardeedaekliekiklrfPvvvKsv......egsqGikvvlakkeqklkqvlea 71
                                       sl++L   +i+v    +a+de++a++ i+ki  +fPvvvK v      ++ +G  +v  + +++l++ +++
  gi|385806255|ref|YP_005842653.1| 30 ESLAVLEAYNIPVAPYFFAKDENEAQRNIDKI--GFPVVVKIVspdivhKSDVGGVIVNVNSKDELVNAIKS 99
                                      6899999999**********************..6******8722222234455555555666666665555 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 ?   12.3   0.1   2.9e-05       0.1       9      71 ..      34     101 ..      30     130 .. 0.76
   2 ?   -2.8   0.0       1.2   4.5e+03      59      72 ..     166     179 ..     161     187 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.9e-05
                                       HHHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEE...ESC-..GGGT-EEEE.SSHHHHHHHHHHHC CS
                            GARS_A   9 llkkagiptaeyeaftdpeeakeyieeatakalVvK...adgl..aagKgviva.kseeealkavkeil 71 
                                       +l++++ip a y   +d +ea+  i++ ++++ VvK   +d +  +   gviv  +s++e ++a+k+i 
  gi|385806255|ref|YP_005842653.1|  34 VLEAYNIPVAPYFFAKDENEAQRNIDKIGFPV-VVKivsPDIVhkSDVGGVIVNvNSKDELVNAIKSIR 101
                                       7899****************************.877221333311223466665467777777777775 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.2
                                       SHHHHHHHHHHHCT CS
                            GARS_A  59 seeealkavkeile 72 
                                       ++eeal++++ei  
  gi|385806255|ref|YP_005842653.1| 166 TKEEALEMINEIKA 179
                                       67888888888754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       741  (0.0413297); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); 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: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1481.67
//
Query:       gi|385806256|ref|YP_005842654.1|  [L=294]
Description: hypothetical protein FFONT_1214 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.4e-06   26.0  16.2     0.0013   18.9   0.7    3.9  3  DUF948          Bacterial protein of unknown function (DUF948
    1.1e-05   25.7  20.2      0.054   13.9   0.1    5.9  5  LPP             Lipoprotein leucine-zipper
    0.00011   22.3   5.3    0.00011   22.3   5.3    6.0  2  ABC_tran_CTD    ABC transporter C-terminal domain
    0.00034   20.7  12.1    0.00091   19.3   2.1    3.4  2  Baculo_PEP_C    Baculovirus polyhedron envelope protein, PEP,
    0.00042   20.5  29.0       0.25   11.5   1.4    4.4  4  COG5            Golgi transport complex subunit 5
    0.00074   18.5  13.3    0.00074   18.5  13.3    3.0  3  Spc7            Spc7 kinetochore protein
     0.0017   18.8   2.2        1.2    9.6   0.1    3.6  3  HsbA            Hydrophobic surface binding protein A
      0.002   18.1  36.4       0.34   10.8   1.4    3.3  3  YscO            Type III secretion protein YscO
     0.0034   16.7  34.9       0.02   14.2   6.7    3.6  3  DUF3450         Protein of unknown function (DUF3450)
      0.004   17.6  19.3      0.025   15.0   2.6    4.5  3  NPV_P10         Nucleopolyhedrovirus P10 protein
     0.0051   17.4   3.7       0.18   12.5   0.7    3.2  2  Hemerythrin     Hemerythrin HHE cation binding domain
     0.0074   15.9  12.7     0.0074   15.9  12.7    3.0  2  MscS_porin      Mechanosensitive ion channel porin domain
     0.0095   15.8  18.6      0.012   15.4   3.9    3.0  3  MCPsignal       Methyl-accepting chemotaxis protein (MCP) sig
  ------ inclusion threshold ------
      0.017   15.6  16.5      0.017   15.6  16.5    3.8  3  APG6_N          Apg6 coiled-coil region
       0.02   15.0   0.6       0.97    9.6   0.0    3.5  3  MbeD_MobD       MbeD/MobD like
      0.024   15.3  46.9       0.44   11.2   3.7    4.4  4  YabA            Initiation control protein YabA
      0.026   14.8  44.6       0.16   12.1   8.7    4.0  3  ATG16           Autophagy protein 16 (ATG16)
      0.028   14.3   3.4      0.028   14.3   3.4    4.2  4  Sec34           Sec34-like family
      0.031   14.8   6.9      0.031   14.8   6.9    4.2  4  Spectrin        Spectrin repeat
      0.033   14.2  37.3       0.68   10.0   7.0    4.7  4  DUF1664         Protein of unknown function (DUF1664)
      0.039   14.1  23.2      0.096   12.9   0.3    4.2  4  PI_PP_I         Phosphoinositide phosphatase insertion domain
      0.048   13.5   1.9        4.9    7.1   0.1    2.9  2  HTH_Tnp_Tc3_1   Tc3 transposase
       0.05   14.1  30.7       0.36   11.3  11.8    3.3  3  T3SSipB         Type III cell invasion protein SipB
       0.07   11.3  56.0        0.1   10.7  24.8    2.1  2  EzrA            Septation ring formation regulator, EzrA
      0.087   13.3  45.7       0.76   10.2  23.0    2.2  2  Fez1            Fez1
       0.12   13.0  20.6       0.46   11.1   3.4    4.9  4  SlyX            SlyX
       0.13   11.5  30.5        2.9    7.2  13.5    2.8  2  DUF4407         Domain of unknown function (DUF4407)
       0.25   10.9  51.3        6.2    6.4  29.5    2.7  2  DUF4795         Domain of unknown function (DUF4795)
       0.26   11.3  41.3       0.98    9.4  12.2    3.4  3  Laminin_II      Laminin Domain II
       0.34    9.0  37.9      0.021   13.1   5.7    3.3  3  COG6            Conserved oligomeric complex COG6
       0.35   11.6  35.6        4.7    7.9   7.8    3.9  3  DUF2203         Uncharacterized conserved protein (DUF2203)
       0.37   10.1  62.4       0.19   11.1  17.1    3.6  4  GAS             Growth-arrest specific micro-tubule binding
       0.38   10.7   7.4       0.96    9.4   0.4    3.5  5  ApoO            Apolipoprotein O
       0.88    8.8  47.5       0.69    9.1   9.9    3.1  3  TMPIT           TMPIT-like protein
        1.3    9.3  51.8       0.16   12.2  18.2    2.4  2  zf-C4H2         Zinc finger-containing protein
        1.4    9.4  62.2       0.17   12.4   9.3    5.7  6  ZapB            Cell division protein ZapB
        1.5    6.3  44.3       0.53    7.7  25.9    1.9  2  DUF3584         Protein of unknown function (DUF3584)
        1.7    8.9   9.2        6.1    7.1   0.2    4.6  6  WXG100          Proteins of 100 residues with WXG
        1.8    8.3  58.9      0.042   13.7  19.3    2.4  2  KASH_CCD        Coiled-coil region of CCDC155 or KASH
        2.4    7.2  57.0        0.6    9.1  28.8    3.3  2  Atg14           Vacuolar sorting 38 and autophagy-related sub
        3.2    7.8  33.9       0.41   10.7   8.7    4.3  4  COG2            COG (conserved oligomeric Golgi) complex comp
        3.3    7.2  47.9         16    4.9  21.0    4.1  3  DegS            Sensor protein DegS
        3.3    7.4  23.5        0.3   10.8  10.8    2.7  2  DUF745          Protein of unknown function (DUF745)
        3.4    7.2  35.5       0.44   10.1  15.7    2.2  2  Exonuc_VII_L    Exonuclease VII, large subunit
        3.5    7.1  50.0          1    8.8  29.3    2.5  2  Leu_zip         Leucine zipper
        3.6    7.2  54.3        4.2    7.0  25.0    2.3  2  Lebercilin      Ciliary protein causing Leber congenital amau
        4.3    5.9  48.6         12    4.4  48.6    1.7  1  AAA_13          AAA domain
        4.3    7.0  42.4       0.59    9.8  16.9    2.7  2  Laminin_I       Laminin Domain I
        5.4    7.2  50.9        0.4   10.9  11.3    3.4  3  Jnk-SapK_ap_N   JNK_SAPK-associated protein-1
        6.1    5.7  46.8       0.72    8.8  21.8    3.0  2  IFT57           Intra-flagellar transport protein 57
        6.5    6.5  54.3        1.6    8.5   6.4    3.9  3  TACC_C          Transforming acidic coiled-coil-containing pr
        6.9    4.9   7.7        2.2    6.5   3.4    1.9  2  SpecificRecomb  Site-specific recombinase
        7.2    6.7  52.2        3.7    7.7  10.7    4.5  4  Mod_r           Modifier of rudimentary (Mod(r)) protein
        9.1    6.4  52.1        0.3   11.1  17.3    4.8  5  TPR_MLP1_2      TPR/MLP1/MLP2-like protein


Domain annotation for each model (and alignments):
>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   1.6   0.00082      0.27      29      81 ..      17      76 ..       3      84 .. 0.76
   2 ?    3.8   0.7      0.21        69      25      68 ..     106     161 ..      89     171 .. 0.71
   3 !   18.9   0.7     4e-06    0.0013      21      82 ..     188     249 ..     183     253 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00082
                            DUF948 29 deaaatieele.......kqvdpilkevedllakvnelledvneklekvdplteavadlg 81
                                       ++++ i++l+       +++++i +e ++l++ ++ + e++n+k ++ +++ e++++l 
  gi|385806256|ref|YP_005842654.1| 17 YNLKQEIATLKeerigliEDLKKIKEEKRNLIESSKSVFEEINKKKDEKNAILEEIKKLK 76
                                      3333333334366666669************************************99986 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.21
                            DUF948  25 kktldeaaatieele..........kqvdpilkevedllakvnelle..dvnekle 68 
                                       ++ l++++++ie+l+          ++ +++++e+++l++  n+l +  d ++kl 
  gi|385806256|ref|YP_005842654.1| 106 GQSLSSLKKRIEQLTwkqqttpmsiDEEKKLMQEIDRLTQLYNRLKDarDAESKLM 161
                                       56778888889999888877778887778888888888888877432114444555 PP

  == domain 3  score: 18.9 bits;  conditional E-value: 4e-06
                            DUF948  21 llklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlge 82 
                                       + ++kk ++++++ i+++ +++d+  ke++++ +  n+l + + ek e++++l e+ a++ e
  gi|385806256|ref|YP_005842654.1| 188 FESIKKEISSLREKINGISQKIDQANKEITEISNRLNQLKASIDEKYEHLKKLQEESAKIKE 249
                                       5578999********************************************99998888765 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.1   0.00016     0.054       2      36 ..       9      43 ..       8      45 .. 0.96
   2 ?    1.9   0.1       0.9     3e+02       7      27 ..      70      90 ..      56      98 .. 0.79
   3 ?    1.0   0.6       1.7   5.6e+02      32      32 ..     132     132 ..     107     183 .. 0.63
   4 !   10.2   0.2    0.0024      0.78       1      31 [.     187     217 ..     187     219 .. 0.86
   5 !   10.5   0.9    0.0019      0.64       2      36 ..     216     250 ..     215     253 .. 0.96

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00016
                               LPP  2 ldeLssqVsqLkskvdqlssdvnsakaaaqaakeE 36
                                      l+++s+++ +Lk++++ l+++   + ++++++keE
  gi|385806256|ref|YP_005842654.1|  9 LEKISEDIYNLKQEIATLKEERIGLIEDLKKIKEE 43
                                      689******************************99 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.9
                               LPP  7 sqVsqLkskvdqlssdvnsak 27
                                      +++++Lks+ d+++++++++k
  gi|385806256|ref|YP_005842654.1| 70 EEIKKLKSEKDEIAKKIEELK 90
                                      678888888888888887765 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 1.7
                               LPP  32 a 32 
                                       +
  gi|385806256|ref|YP_005842654.1| 132 E 132
                                       1 PP

  == domain 4  score: 10.2 bits;  conditional E-value: 0.0024
                               LPP   1 kldeLssqVsqLkskvdqlssdvnsakaaaq 31 
                                       k + + +++s+L +k++ +s+++++a++++ 
  gi|385806256|ref|YP_005842654.1| 187 KFESIKKEISSLREKINGISQKIDQANKEIT 217
                                       56788999****************9999876 PP

  == domain 5  score: 10.5 bits;  conditional E-value: 0.0019
                               LPP   2 ldeLssqVsqLkskvdqlssdvnsakaaaqaakeE 36 
                                       ++e+s+ ++qLk+ +d+  + +++++++++++keE
  gi|385806256|ref|YP_005842654.1| 216 ITEISNRLNQLKASIDEKYEHLKKLQEESAKIKEE 250
                                       789*******************************9 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.9      0.94   3.1e+02      23      54 ..     142     171 ..     119     175 .. 0.69
   2 !   22.3   5.3   3.5e-07   0.00011       8      68 ..     186     241 ..     178     242 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.94
                      ABC_tran_CTD  23 eiaeleaeladpelysdp.eklaelsaeleele 54 
                                       ++++l ++l d+    d   kl+e+ ae++ l+
  gi|385806256|ref|YP_005842654.1| 142 RLTQLYNRLKDAR---DAeSKLMEVKAEYTSLK 171
                                       3444555666664...44488888888888775 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 3.5e-07
                      ABC_tran_CTD   8 releeleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeelyerWeeLe 68 
                                       +++e + +eI +L e+i  + +++ +++     ++++e+s++l++l+a ++e+ye    L+
  gi|385806256|ref|YP_005842654.1| 186 KKFESIKKEISSLREKINGISQKIDQAN-----KEITEISNRLNQLKASIDEKYEHLKKLQ 241
                                       56***********************998.....99********************877665 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   5.1      0.55   1.8e+02      45      80 ..     107     151 ..       1     182 [. 0.60
   2 !   19.3   2.1   2.7e-06   0.00091      18     133 ..     146     262 ..     141     269 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.55
                      Baculo_PEP_C  45 tqLnalsedlksllaeldt.........rldtlltnLtdalnalq 80 
                                       ++L++l++++++l  +++t         +l + +++Lt+  n+l+
  gi|385806256|ref|YP_005842654.1| 107 QSLSSLKKRIEQLTWKQQTtpmsideekKLMQEIDRLTQLYNRLK 151
                                       345555555555555555555555555566666666666666666 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 2.7e-06
                      Baculo_PEP_C  18 LtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq...dtlrneLtnln 91 
                                       L n L++ r  ++++  ++++  ++++ +++++++++++ +++++  +++ ++ L +++n ++   d+ ++e+t + 
  gi|385806256|ref|YP_005842654.1| 146 LYNRLKDARDAESKL-MEVKAEYTSLKIKFKDIKNSMQEKIKKFE-SIKKEISSLREKINGISqkiDQANKEITEIS 220
                                       567777777788888.78999999999999999999999888876.699999**********988889999****** PP

                      Baculo_PEP_C  92 siltnLlssvtNinstLnnllqalnnldlgalsqeledaldt 133
                                       + l++L +s+    + L+ l +  + +++++ +++ +++l++
  gi|385806256|ref|YP_005842654.1| 221 NRLNQLKASIDEKYEHLKKLQEESAKIKEEESKKKESEILEK 262
                                       *********988888888777777777777766666666666 PP

>> COG5  Golgi transport complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.8     0.038        13      31      76 ..       5      50 ..       3      59 .. 0.77
   2 !   10.7   4.0    0.0014      0.45      19      78 ..      56     117 ..      49     124 .. 0.86
   3 !    8.7   1.8    0.0057       1.9      55     114 ..     141     200 ..     128     204 .. 0.89
   4 !   11.5   1.4   0.00076      0.25      73     113 ..     208     248 ..     200     252 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.038
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXX CS
                              COG5 31 lstplkrlnydiqeldkrlrqlitsnhleLlehlskskslss.vlse 76
                                      +  +l+++++di +l++++ +l +++   L+e l+k+k+++  + ++
  gi|385806256|ref|YP_005842654.1|  5 VGETLEKISEDIYNLKQEIATL-KEERIGLIEDLKKIKEEKRnLIES 50
                                      5678999999999999999875.677789999999999988755554 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0014
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              COG5  19 katnnnddteldlstplkrlnydiqeldkrlrq..litsnhleLlehlskskslssvlselk 78 
                                        + n+++d++  +  ++k+l++  +e+ k++++  l+ ++++eL++++ + +slss+ + ++
  gi|385806256|ref|YP_005842654.1|  56 EEINKKKDEKNAILEEIKKLKSEKDEIAKKIEElkLVIKRYEELINKTPNGQSLSSLKKRIE 117
                                       56789999***********************9633699**********99999998887776 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0057
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-TTHHHHHHHHHHHHHHHHHHH CS
                              COG5  55 snhleLlehlskskslssvlselksslesLsasyerlkskvlepyeeaeklqsalkrlhq 114
                                       ++ ++L ++l++ + ++s l e+k +  sL+  ++ +k+   e++++ e+ ++++++l++
  gi|385806256|ref|YP_005842654.1| 141 DRLTQLYNRLKDARDAESKLMEVKAEYTSLKIKFKDIKNSMQEKIKKFESIKKEISSLRE 200
                                       4678999*******************************************9999999876 PP

  == domain 4  score: 11.5 bits;  conditional E-value: 0.00076
                                       XXXXXXXXXXXXXXXXXXXX-TTHHHHHHHHHHHHHHHHHH CS
                              COG5  73 vlselksslesLsasyerlkskvlepyeeaeklqsalkrlh 113
                                         ++ ++++ ++s+ +++lk  + e+ye+++klq++ +++ 
  gi|385806256|ref|YP_005842654.1| 208 KIDQANKEITEISNRLNQLKASIDEKYEHLKKLQEESAKIK 248
                                       5567788999*************************999986 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1  20.2    0.0064       2.1     167     290 ..       7     131 ..       3     134 .. 0.69
   2 !   18.5  13.3   2.2e-06   0.00074     157     257 ..     111     216 ..     105     218 .. 0.88
   3 !   12.2  31.1   0.00018      0.06     142     270 ..     144     273 ..     134     286 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0064
                              Spc7 167 ellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqk 243
                                       e l++++e   +l++e+++l+e++        e+L++++ee ++l +  ++  +e+++++++++++ e+i++lk++k
  gi|385806256|ref|YP_005842654.1|   7 ETLEKISEDIYNLKQEIATLKEERIG--L--IEDLKKIKEEKRNLIESSKSVFEEINKKKDEKNAILEEIKKLKSEK 79 
                                       55667777777888888888884332..2..3445555555555555555555899999999999999999999999 PP

                              Spc7 244 seleeeiaeaervlee.....ckgwsesevsrlkeevkaleeltgwkivsls 290
                                       +e+ ++i+e + v+++     +k  + + +s+lk++ ++l  + + + +s++
  gi|385806256|ref|YP_005842654.1|  80 DEIAKKIEELKLVIKRyeeliNKTPNGQSLSSLKKRIEQLTWKQQTTPMSID 131
                                       9999999999988875222336777788899999999998887777777665 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 2.2e-06
                              Spc7 157 lLekqeeel...dellpeleeekaeleeeleklqeaaeeles.id.keeLeelreelaelkaeieekkkelaelqeq 228
                                        L+k+ e+l   ++  p    e+++l++e+++l + ++ l++  d + +L e++ e ++lk + +  k+ ++e+ ++
  gi|385806256|ref|YP_005842654.1| 111 SLKKRIEQLtwkQQTTPMSIDEEKKLMQEIDRLTQLYNRLKDaRDaESKLMEVKAEYTSLKIKFKDIKNSMQEKIKK 187
                                       57777777766678999999***************99999985346899**************************** PP

                              Spc7 229 leeleekieelkeqkseleeeiaeaervl 257
                                        e+++++i++l+e+++ + ++i +a++ +
  gi|385806256|ref|YP_005842654.1| 188 FESIKKEISSLREKINGISQKIDQANKEI 216
                                       ***********************999865 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 0.00018
                              Spc7 142 egleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieek 218
                                       ++l ++l++ ++ +++L++ ++e ++l+ +++  k++++e+++k ++ ++e++s+ +e+++ + ++++++++ei e 
  gi|385806256|ref|YP_005842654.1| 144 TQLYNRLKDARDAESKLMEVKAEYTSLKIKFKDIKNSMQEKIKKFESIKKEISSL-REKINGISQKIDQANKEITEI 219
                                       4788888888899999999999999999999999999999999999988887664.688888888888888888888 PP

                              Spc7 219 kkelaelqeqleeleekieelkeqkseleeeiaeae..rvleeckgwsesevsr 270
                                       +++l++l++ ++e+ e +++l+e+ ++++ee ++++  ++le++k++ e+ +++
  gi|385806256|ref|YP_005842654.1| 220 SNRLNQLKASIDEKYEHLKKLQEESAKIKEEESKKKesEILEKKKKIAEEKLKK 273
                                       888888888888888888888888888877655443115777777777766654 PP

>> HsbA  Hydrophobic surface binding protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1       1.3   4.4e+02       6      42 ..       7      48 ..       2      78 .. 0.62
   2 ?    5.3   0.1     0.077        26      10      79 ..      81     149 ..      75     180 .. 0.79
   3 !    9.6   0.1    0.0035       1.2       6      55 ..     186     240 ..     181     254 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 1.3
                                      HHHHHHHHHHHHHHHHHHH--S...H....HHHHHHHHHHHH CS
                              HsbA  6 sdittistavtaldtavnafnG...g..asalpilsasnalv 42
                                      + ++ is+++ +l++ +++ +    g   ++ +i++   +l+
  gi|385806256|ref|YP_005842654.1|  7 ETLEKISEDIYNLKQEIATLKEeriGliEDLKKIKEEKRNLI 48
                                      557778888888888887776555522334444444444444 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.077
                                       HHHHHHHHHHHHHHH--S..H..HHHHHHHHHHHHHHHHHHHHHHHTS----HHHHHHHHHHHHHCHHHHHH CS
                              HsbA  10 tistavtaldtavnafnG..gasalpilsasnalvsaikkattdaqasapltdeealalaqavqtLepdvka 79 
                                        i ++++ l+  ++ +    +   +p  ++ ++l++ i++ t + q ++p++ +e ++l+q++ +L+   + 
  gi|385806256|ref|YP_005842654.1|  81 EIAKKIEELKLVIKRYEEliN--KTPNGQSLSSLKKRIEQLTWKQQ-TTPMSIDEEKKLMQEIDRLTQLYNR 149
                                       578888888888888866652..57888999999999999777755.5567************999876655 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0035
                                       HHHHHHHHHHHHHHHHHHH--S....H...HHHHHHHHHHHHHHHHHHHHHHHTS CS
                              HsbA   6 sdittistavtaldtavnafnG....g.asalpilsasnalvsaikkattdaqas 55 
                                       + +++i++ +++l + +n+ ++    + +++++i +  n+l+++i++   + ++ 
  gi|385806256|ref|YP_005842654.1| 186 KKFESIKKEISSLREKINGISQkidqAnKEITEISNRLNQLKASIDEKYEHLKKL 240
                                       56677888888888888888777887678899***********999877766655 PP

>> YscO  Type III secretion protein YscO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   7.1     0.004       1.3      66     142 ..      14      90 ..      12      91 .. 0.94
   2 !   10.8   1.4     0.001      0.34      54     126 ..      95     166 ..      93     171 .. 0.94
   3 !    9.9  12.4     0.002      0.66      65     137 ..     185     257 ..     173     277 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.004
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YscO  66 kelekvkqqvalLrekeaelekqveeakqqleaerealrqarkelqearraveKfaelarlvraeasrqqerkEeqe 142
                                       +++ ++kq++a L+e+   l ++++++k++ ++ +e +++  +e+ + + +++ + e+ +++++e+   +++ Ee+ 
  gi|385806256|ref|YP_005842654.1|  14 EDIYNLKQEIATLKEERIGLIEDLKKIKEEKRNLIESSKSVFEEINKKKDEKNAILEEIKKLKSEKDEIAKKIEELK 90 
                                       578889***********************************************************999999999875 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.001
                                       HHHHHHTTT--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YscO  54 lyaeiigklvllkelekvkqqvalLrekeaelekqveeakqqleaerealrqarkelqearraveKfaelarl 126
                                       +y+e+i+k+ + + l  +k+++  L  k++     ++e +++l +e+++l+q+ + l+ ar a++K+ e+++ 
  gi|385806256|ref|YP_005842654.1|  95 RYEELINKTPNGQSLSSLKKRIEQLTWKQQTTPMSIDE-EKKLMQEIDRLTQLYNRLKDARDAESKLMEVKAE 166
                                       79**********************************99.7899***********************9998875 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.002
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YscO  65 lkelekvkqqvalLrekeaelekqveeakqqleaerealrqarkelqearraveKfaelarlvraeasrqqer 137
                                        k  e +k+++++Lrek +   +++++a+++ ++  ++l+q+++ + e    ++K++e+ ++ ++e+s+++e+
  gi|385806256|ref|YP_005842654.1| 185 IKKFESIKKEISSLREKINGISQKIDQANKEITEISNRLNQLKASIDEKYEHLKKLQEESAKIKEEESKKKES 257
                                       688899********************************************************99999988775 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   6.7   6.1e-05      0.02      16      83 ..      35     102 ..      23     120 .. 0.89
   2 ?    0.7   2.2      0.79   2.6e+02      52      92 ..     108     151 ..     101     163 .. 0.57
   3 !   13.4  10.1    0.0001     0.035      17      94 ..     173     250 ..     165     256 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.1e-05
                           DUF3450  16 atldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeias 83 
                                       ++l+++++e+++ +++++++ ++i+k +dek+ +l+e+++lk+e+++++++ e+l+ +++  e+ i++
  gi|385806256|ref|YP_005842654.1|  35 EDLKKIKEEKRNLIESSKSVFEEINKKKDEKNAILEEIKKLKSEKDEIAKKIEELKLVIKRYEELINK 102
                                       68999***************************************************999998887765 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.79
                           DUF3450  52 eyralkeeleslevyneqlerlvasqe...qeiasleeqieeie 92 
                                        + +lk+++e+l+++++    ++++ +   qei++l++  ++++
  gi|385806256|ref|YP_005842654.1| 108 SLSSLKKRIEQLTWKQQTTPMSIDEEKklmQEIDRLTQLYNRLK 151
                                       56677777777777777777777665511134444444444444 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 0.0001
                           DUF3450  17 tldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeiee 93 
                                       +++++++  ++ +++ +++ k+i++l ++ + +++++ ++++e+ +++   +ql++++++  + +++l+e+ ++i+e
  gi|385806256|ref|YP_005842654.1| 173 KFKDIKNSMQEKIKKFESIKKEISSLREKINGISQKIDQANKEITEISNRLNQLKASIDEKYEHLKKLQEESAKIKE 249
                                       678999999****************************************************************9997 PP

                           DUF3450  94 i 94 
                                        
  gi|385806256|ref|YP_005842654.1| 250 E 250
                                       5 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   5.3      0.31     1e+02       6      66 ..       9      70 ..       4     122 .. 0.78
   2 ?    3.6   0.1      0.27        91      26      65 ..     142     181 ..     129     189 .. 0.79
   3 !   15.0   2.6   7.6e-05     0.025      23      66 ..     181     224 ..     179     252 .. 0.65

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.31
                           NPV_P10  6 LlvIradikavddkVdalqqqvddvqenlpdvtelnekL.daqsaqLaeletkvenIqdiLn 66
                                      L  I +di ++++ +  l+++   + e+l++++e + +L ++     +e+++k ++ + iL 
  gi|385806256|ref|YP_005842654.1|  9 LEKISEDIYNLKQEIATLKEERIGLIEDLKKIKEEKRNLiESSKSVFEEINKKKDEKNAILE 70
                                      67899999999999999999998888888888877766514444455777776666666665 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.27
                           NPV_P10  26 qvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiL 65 
                                       +++++ + l+d  + ++kL +  a+ ++l+ k ++I++ +
  gi|385806256|ref|YP_005842654.1| 142 RLTQLYNRLKDARDAESKLMEVKAEYTSLKIKFKDIKNSM 181
                                       4677788888888889999999999999999999998765 PP

  == domain 3  score: 15.0 bits;  conditional E-value: 7.6e-05
                           NPV_P10  23 lqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiLn 66 
                                       +q+++++ ++  ++++ l ek++++s+++++ ++++++I++ Ln
  gi|385806256|ref|YP_005842654.1| 181 MQEKIKKFESIKKEISSLREKINGISQKIDQANKEITEISNRLN 224
                                       56666666666666777777777777777777777777766666 PP

>> Hemerythrin  Hemerythrin HHE cation binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.7   0.00053      0.18      60      99 ..      55     103 ..      41     192 .. 0.86
   2 ?    3.4   0.1      0.33   1.1e+02       4      47 ..     207     243 ..     204     261 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00053
                                       HHHHH.....CCC.HHHHHHHHHHHHHHHHHHHHHHHHCHTCG.....G CS
                       Hemerythrin  60 fPlle....drpggravldvlereHdeirelleelrellkgle.....e 99 
                                       f ++     +++++ ++++ l+ e dei++++eel+ ++k++e     +
  gi|385806256|ref|YP_005842654.1|  55 FEEINkkkdEKNAILEEIKKLKSEKDEIAKKIEELKLVIKRYEelinkT 103
                                       5555566677899****************************99555553 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.33
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHCCHHHHHHHHHHH CS
                       Hemerythrin   4 ealdeeHralrallerlraladaaaevhgalrklaelldelvde 47 
                                       + +d+ ++++ +  +rl +l ++       +++  e+l++l++e
  gi|385806256|ref|YP_005842654.1| 207 QKIDQANKEITEISNRLNQLKAS-------IDEKYEHLKKLQEE 243
                                       5689999**********999999.......55555666665555 PP

>> MscS_porin  Mechanosensitive ion channel porin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5  14.7      0.26        87      17     127 ..      43     155 ..      34     160 .. 0.71
   2 !   15.9  12.7   2.2e-05    0.0074      51     164 ..     138     250 ..     134     274 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.26
                        MscS_porin  17 allqdLeqalnlLdkidkskkkaeelqkaiddaPkelrelqqeleal...qkkkeeaskeilaklsleeLeqrllqt 90 
                                       + +  +e++ ++ ++i+k k++ ++  + i++   e +e+ +++e+l    k  ee  +++++ +sl+ L +r++q 
  gi|385806256|ref|YP_005842654.1|  43 EKRNLIESSKSVFEEINKKKDEKNAILEEIKKLKSEKDEIAKKIEELklvIKRYEELINKTPNGQSLSSLKKRIEQL 119
                                       444555666666666666666666666666666666666666666665555555999******************** PP

                        MscS_porin  91 ssqlqelqeqlaqlnsqlvelqtrperaqqqltearq 127
                                         ++q++   + +++++ +e+ +r++++ ++l +ar 
  gi|385806256|ref|YP_005842654.1| 120 TWKQQTTPMSIDEEKKLMQEI-DRLTQLYNRLKDARD 155
                                       ****99999998888888887.677888888877775 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 2.2e-05
                        MscS_porin  51 kelrelqqelealqkkkeeaskeilaklsleeLeqrllqtssqlqelqeqlaqlnsqlvelqtrperaqqqltearq 127
                                       +e++ l+q  ++l+++ +++sk    k   + L  + ++ ++ +qe  ++  ++++++ +l+  ++ + q++ +a++
  gi|385806256|ref|YP_005842654.1| 138 QEIDRLTQLYNRLKDARDAESKLMEVKAEYTSLKIKFKDIKNSMQEKIKKFESIKKEISSLREKINGISQKIDQANK 214
                                       78888889999999999999********************************************************* PP

                        MscS_porin 128 rlqeirnrLnstaaagealsqaqrtalqaelaaleaq 164
                                       +++ei+nrLn+++a+  +   +   +lq e+a ++ +
  gi|385806256|ref|YP_005842654.1| 215 EITEISNRLNQLKASI-DEKYEHLKKLQEESAKIKEE 250
                                       ************5443.88888888888888877654 PP

>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   3.6    0.0096       3.2      89     168 ..      14      96 ..       4     104 .. 0.71
   2 ?    7.2   1.4     0.012       4.1      75     150 ..      70     153 ..      66     165 .. 0.66
   3 !   15.4   3.9   3.7e-05     0.012      90     163 ..     162     235 ..     149     244 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0096
                                       HHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHH CS
                         MCPsignal  89 keiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqei...aaaseeqsasieevn 162
                                       ++i +l +ei    ++ +  +e+ ++  ee  +l+e+++++++ei ++ +e +++++ei   ++  +e+++ iee  
  gi|385806256|ref|YP_005842654.1|  14 EDIYNLKQEIATLKEERIGLIEDLKKIKEEKRNLIESSKSVFEEINKKKDEKNAILEEIkklKSEKDEIAKKIEELK 90 
                                       56667777777788888899999999999999999999999999988776655555555111556667777777776 PP

                                       HHHHHH CS
                         MCPsignal 163 qaveev 168
                                         +++ 
  gi|385806256|ref|YP_005842654.1|  91 LVIKRY 96 
                                       666655 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.012
                                       HHHHHHHHHHHHHHHHHHHH...H................HHHHHHHHHHHHHHHHHCCHH...HHHHHHHHHHHHH CS
                         MCPsignal  75 dEVrkLAersaqaakeieal...iieiqkeinds..vesleetrqrveegselveetgeal...keiveavaevadl 143
                                       +E++kL ++  + ak+ie+l   i++ ++ in++   +sl++ ++r+e+ + + ++t +++   k++ ++++++++l
  gi|385806256|ref|YP_005842654.1|  70 EEIKKLKSEKDEIAKKIEELklvIKRYEELINKTpnGQSLSSLKKRIEQLTWKQQTTPMSIdeeKKLMQEIDRLTQL 146
                                       8***************9986221333333345442247899999999999999999998882223455555555555 PP

                                       HHHHHHH CS
                         MCPsignal 144 vqeiaaa 150
                                        + ++ a
  gi|385806256|ref|YP_005842654.1| 147 YNRLKDA 153
                                       5555555 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 3.7e-05
                                       HHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  90 eiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieevnq 163
                                       e++a  + ++ + +d  +s++e  ++ e+  +++++ +e+++ i++++++ +++++ei+   +++ asi+e  +
  gi|385806256|ref|YP_005842654.1| 162 EVKAEYTSLKIKFKDIKNSMQEKIKKFESIKKEISSLREKINGISQKIDQANKEITEISNRLNQLKASIDEKYE 235
                                       5566566667778899999999999****9*****************************999999999988655 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6  16.5   5.1e-05     0.017      13      90 ..      18      92 ..      14     102 .. 0.90
   2 ?    4.7  12.3      0.12        40      46     131 ..     130     214 ..      93     216 .. 0.60
   3 ?    5.4  19.0     0.075        25      12      88 ..     203     275 ..     201     278 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.1e-05
                            APG6_N 13 eldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleee 90
                                      +l+++++++++er  + e lkk+k+ek++     e+ ++  ee+ k ++e+++ lee+k+l++e++e+++++++l+  
  gi|385806256|ref|YP_005842654.1| 18 NLKQEIATLKEERIGLIEDLKKIKEEKRNLI---ESSKSVFEEINKKKDEKNAILEEIKKLKSEKDEIAKKIEELKLV 92
                                      89************************87755...7889***********************************99865 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.12
                            APG6_N  46 deeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlelleleeeldsl 122
                                        +e+++l +e+++l +  ++l +  +++e++  e++ae  +l+ + +++++  +++++++ + + e ++l e+ + +
  gi|385806256|ref|YP_005842654.1| 130 IDEEKKLMQEIDRLTQLYNRL-KDARDAESKLMEVKAEYTSLKIKFKDIKNSMQEKIKKFESIKKEISSLREKINGI 205
                                       445556666666665555543.4455566666666666666666666666666666666666666666666666666 PP

                            APG6_N 123 eaqyehaqn 131
                                         ++++a++
  gi|385806256|ref|YP_005842654.1| 206 SQKIDQANK 214
                                       666665554 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.075
                            APG6_N  12 eeldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaale 88 
                                       +++ ++++qa+ke+ + ++ l++lk++ +e+    e l++l+ee +k+++ee++  +e + lek+++  e++l++ e
  gi|385806256|ref|YP_005842654.1| 203 NGISQKIDQANKEITEISNRLNQLKASIDEKY---EHLKKLQEESAKIKEEESK-KKESEILEKKKKIAEEKLKKKE 275
                                       67889999999999999999999999977754...7999999999999877765.5778889999998888888876 PP

>> MbeD_MobD  MbeD/MobD like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0       2.1   6.8e+02      20      67 ..      42      95 ..      23      98 .. 0.61
   2 ?   -0.0   0.1       2.9   9.6e+02      46      56 ..     135     145 ..     106     155 .. 0.55
   3 ?    9.6   0.0    0.0029      0.97      28      69 ..     179     220 ..     158     221 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 2.1
                         MbeD_MobD 20 eqrlqeWesafaelqrmfeltqrena......aLseqvtgLsqQVesLseqvrR 67
                                      e +++  es+   + ++ + +  +na      +L+   +++++ +e+L   ++R
  gi|385806256|ref|YP_005842654.1| 42 EEKRNLIESSKSVFEEINKKKDEKNAileeikKLKSEKDEIAKKIEELKLVIKR 95
                                      555555555555555555566666665555556666677777777777766666 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 2.9
                         MbeD_MobD  46 aLseqvtgLsq 56 
                                       +L + +++L+q
  gi|385806256|ref|YP_005842654.1| 135 KLMQEIDRLTQ 145
                                       33333333333 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0029
                         MbeD_MobD  28 safaelqrmfeltqrenaaLseqvtgLsqQVesLseqvrRls 69 
                                       ++ +e  + fe  ++e + L+e+++g+sq +++ ++++  +s
  gi|385806256|ref|YP_005842654.1| 179 NSMQEKIKKFESIKKEISSLREKINGISQKIDQANKEITEIS 220
                                       5555666779999********************999988776 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   3.7    0.0049       1.6       8      61 ..       7      60 ..       2      66 .. 0.76
   2 ?    4.2   9.4      0.21        68      15      78 ..      63     148 ..      50     150 .. 0.53
   3 ?   11.2   3.7    0.0013      0.44       3      64 ..     153     214 ..     151     218 .. 0.82
   4 ?    8.2  11.8     0.011       3.8       6      61 ..     205     270 ..     202     289 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0049
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....XXXXXXXXX CS
                              YabA  8 dkleeleeqleelleeleelkeelaelleenaeLeleneklrerl....eeeekkeke 61
                                      ++le+++e++ +l++e+++lkee   l+e+ ++++ e+++l e      e    + ++
  gi|385806256|ref|YP_005842654.1|  7 ETLEKISEDIYNLKQEIATLKEERIGLIEDLKKIKEEKRNLIESSksvfE----EINK 60
                                      689999999**************************999999888733331....2222 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.21
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH......................XXXXXXXXXXXXXXXXX CS
                              YabA  15 eqleelleeleelkeelaelleenaeLeleneklrerl......................eeeekkekekkkelseg 69 
                                       ++ +++lee+++lk+e  e+ ++ +eL+l  ++  e++                      ++++  + +++k+l + 
  gi|385806256|ref|YP_005842654.1|  63 DEKNAILEEIKKLKSEKDEIAKKIEELKLVIKRYEELInktpngqslsslkkrieqltwkQQTTPMSIDEEKKLMQE 139
                                       55555555555555555555555555555433333333333444444444444466667555556666777778888 PP

                                       XXXXXXXXX CS
                              YabA  70 kenLarlYe 78 
                                        + L++lY+
  gi|385806256|ref|YP_005842654.1| 140 IDRLTQLYN 148
                                       888888886 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.0013
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXX CS
                              YabA   3 kkelfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkk 64 
                                        ++  +kl+e++ + ++l+ +++++k++++e +++ ++++ e ++lre+++  ++k ++ +k
  gi|385806256|ref|YP_005842654.1| 153 ARDAESKLMEVKAEYTSLKIKFKDIKNSMQEKIKKFESIKKEISSLREKINGISQKIDQANK 214
                                       5677789999****************************************554444444444 PP

  == domain 4  score: 8.2 bits;  conditional E-value: 0.011
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..........XXXXXXXXX CS
                              YabA   6 lfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerl..........eeeekkeke 61 
                                       + +k+++ +++++e++++l++lk+++ e +e+ ++L+ e  k++e+           ++++ +e++
  gi|385806256|ref|YP_005842654.1| 205 ISQKIDQANKEITEISNRLNQLKASIDEKYEHLKKLQEESAKIKEEEskkkeseileKKKKIAEEK 270
                                       667899999999999999999999999999999999999999999884443333332222222222 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   8.6    0.0013      0.43      74     157 ..       7      90 ..       2      94 .. 0.94
   2 ?   12.1   8.7   0.00049      0.16     100     180 ..     136     215 ..     102     218 .. 0.82
   3 ?    3.4  14.5      0.24        79      75     152 ..     201     277 ..     199     280 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0013
                             ATG16  74 akiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelreke 150
                                       +++++ ++ ++ l++e a+l  +r  l + l++ +ee + l e++k+  e++++ ++e++a+ +++k+++ e  e +
  gi|385806256|ref|YP_005842654.1|   7 ETLEKISEDIYNLKQEIATLKEERIGLIEDLKKIKEEKRNLIESSKSVFEEINKKKDEKNAILEEIKKLKSEKDEIA 83 
                                       5677788999******************************************************************* PP

                             ATG16 151 klvqdlq 157
                                       k +++l+
  gi|385806256|ref|YP_005842654.1|  84 KKIEELK 90 
                                       **99986 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00049
                             ATG16 100 laqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlqlnqaEeklrk 176
                                       l q + +l++   +l + ++  e++l e++ae ++l+ k kd ++ ++ek k  + ++ E+s+L+ + n + +k ++
  gi|385806256|ref|YP_005842654.1| 136 LMQEIDRLTQLYNRL-KDARDAESKLMEVKAEYTSLKIKFKDIKNSMQEKIKKFESIKKEISSLREKINGISQKIDQ 211
                                       556666665555554.45678889999********************************************999999 PP

                             ATG16 177 lekE 180
                                        +kE
  gi|385806256|ref|YP_005842654.1| 212 ANKE 215
                                       9888 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.24
                             ATG16  75 kiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekek 151
                                       ki+  +qk+ q ++e +e   + ++l+ ++ e+ e l+kl+e++ + +e+ ++ ++e + le+k k  ee+l+ ke+
  gi|385806256|ref|YP_005842654.1| 201 KINGISQKIDQANKEITEISNRLNQLKASIDEKYEHLKKLQEESAKIKEE-ESKKKESEILEKKKKIAEEKLKKKER 276
                                       67777899999999999999999999999999999999999988776666.55677788899999999999999988 PP

                             ATG16 152 l 152
                                       l
  gi|385806256|ref|YP_005842654.1| 277 L 277
                                       7 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   6.1     0.032        11       9      68 ..      27      86 ..       4      94 .. 0.73
   2 ?    4.3   1.0       0.1        33       3      65 ..      87     151 ..      85     156 .. 0.71
   3 ?   14.3   3.4   8.4e-05     0.028       4      69 ..     159     224 ..     156     228 .. 0.94
   4 ?    4.2   5.6      0.11        37      12      57 ..     209     254 ..     206     279 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.032
                             Sec34  9 eeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekL 68
                                      +ee   l+e++++++e+ ++l e+ ksv e+ ++ +++ + +lee k+l++ ++ei +k+
  gi|385806256|ref|YP_005842654.1| 27 KEERIGLIEDLKKIKEEKRNLIESSKSVFEEINKKKDEKNAILEEIKKLKSEKDEIAKKI 86
                                      455556777777777777777777777777777777777777777777777777777765 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.1
                             Sec34   3 dqLeskeeecdelleqtde..aleqLeeleekfksvsektsslheaceqlleeqkrleelaeeie 65 
                                       ++L+   ++++el+++t +   l++L++  e+ +  ++ t    ++ ++l++e +rl++l++ ++
  gi|385806256|ref|YP_005842654.1|  87 EELKLVIKRYEELINKTPNgqSLSSLKKRIEQLTWKQQTTPMSIDEEKKLMQEIDRLTQLYNRLK 151
                                       67888889999999999761144455555555555555555556778899999999999998876 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 8.4e-05
                             Sec34   4 qLeskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLk 69 
                                       +L + ++e+++l  + ++++++++e  +kf+s++++ ssl+e+ + + ++ ++ ++   ei+++L+
  gi|385806256|ref|YP_005842654.1| 159 KLMEVKAEYTSLKIKFKDIKNSMQEKIKKFESIKKEISSLREKINGISQKIDQANKEITEISNRLN 224
                                       68888999********************************************************97 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.11
                             Sec34  12 cdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrl 57 
                                       +d+  ++++e+ + L++l+ + ++  e  ++l+e++ ++ ee+++ 
  gi|385806256|ref|YP_005842654.1| 209 IDQANKEITEISNRLNQLKASIDEKYEHLKKLQEESAKIKEEESKK 254
                                       5555666777777777777777777777777777777776666554 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   4.1       1.4   4.7e+02      37      96 ..      17      76 ..       5      82 .. 0.71
   2 ?    8.4   5.7    0.0091         3       4      93 ..      80     171 ..      77     179 .. 0.72
   3 ?   14.8   6.9   9.2e-05     0.031       7      95 ..     150     240 ..     143     241 .. 0.90
   4 ?    4.7   6.9      0.12        41      39      87 ..     219     268 ..     213     272 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 1.4
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin 37 qallkkhkaleaelaaqqervkalnelaeklldeghsaseeieerleelnerWeeLkela 96
                                       +l ++  +l++e     e +k+++e +++l+++++s  eei+++ +e n   ee+k+l 
  gi|385806256|ref|YP_005842654.1| 17 YNLKQEIATLKEERIGLIEDLKKIKEEKRNLIESSKSVFEEINKKKDEKNAILEEIKKLK 76
                                      455666666666666677778888899999988888888888888888777666666655 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0091
                                       HHHHHHHHHHHHHHHHHHHHHCCSSCSSSHHHHHHHHH....HHHHHHHHHHHHHHHHHHHH...HHHHHHHHTTHT CS
                          Spectrin   4 qqfaqdadeleeWieekeellssedlgkdleevqallk....khkaleaelaaqqervkaln...elaeklldeghs 73 
                                        ++a++++el+  i+  eel++++  g++l+++++ ++    k ++    ++++++ +++++   +l      +  +
  gi|385806256|ref|YP_005842654.1|  80 DEIAKKIEELKLVIKRYEELINKTPNGQSLSSLKKRIEqltwKQQTTPMSIDEEKKLMQEIDrltQLY-----NRLK 151
                                       57899*********************************565566666666666666555555222333.....3456 PP

                                       THHHHHHHHHHHHHHHHHHH CS
                          Spectrin  74 aseeieerleelnerWeeLk 93 
                                       ++ + e++l e+   + +Lk
  gi|385806256|ref|YP_005842654.1| 152 DARDAESKLMEVKAEYTSLK 171
                                       66777777777777776665 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 9.2e-05
                                       HHHHHHHHHHHHHHHHHHCCSSC.SSSHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHHHHH CS
                          Spectrin   7 aqdadeleeWieekeellssedl.gkdle.evqallkkhkaleaelaaqqervkalnelaeklldeghsaseeieer 81 
                                        +da++ e+ + e +++ +s  +  kd+  ++q+++kk++ +++e+++ +e+++ + +  ++  +e  + s ++++ 
  gi|385806256|ref|YP_005842654.1| 150 LKDARDAESKLMEVKAEYTSLKIkFKDIKnSMQEKIKKFESIKKEISSLREKINGISQKIDQANKEITEISNRLNQL 226
                                       579*****************9999899963799************************88888888888899999999 PP

                                       HHHHHHHHHHHHHH CS
                          Spectrin  82 leelnerWeeLkel 95 
                                        + ++e++e+Lk+l
  gi|385806256|ref|YP_005842654.1| 227 KASIDEKYEHLKKL 240
                                       999*******9986 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.12
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHTTHTTHHHHHHHHHHHHH CS
                          Spectrin  39 llkkhkaleaelaaqqervkalnelaekl.ldeghsaseeieerleelne 87 
                                         +++ +l+a ++++ e++k+l+e + k+ ++e+++++ ei e+ +++ e
  gi|385806256|ref|YP_005842654.1| 219 ISNRLNQLKASIDEKYEHLKKLQEESAKIkEEESKKKESEILEKKKKIAE 268
                                       5568899**********************888889999999999988865 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1      0.27        90      46     113 ..       5      26 ..       2      37 .. 0.47
   2 ?   10.0   7.0    0.0021      0.68      55     119 ..      38     102 ..      33     107 .. 0.93
   3 ?    8.0  10.6    0.0087       2.9      56     121 ..     162     227 ..     106     228 .. 0.83
   4 ?    7.2   7.7     0.015       4.8      44      98 ..     196     253 ..     190     276 .. 0.56

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.27
                           DUF1664  46 vskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegl 113
                                       v++ le++se++ + k+                                               + +l
  gi|385806256|ref|YP_005842654.1|   5 VGETLEKISEDIYNLKQ----------------------------------------------EIATL 26 
                                       44444444444444443..............................................33333 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0021
                           DUF1664  55 eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskler 119
                                       +++++ kr+L +  ++v +++++ k+ +++i ee+++++++ +ei +++e++k +++  e+ +++
  gi|385806256|ref|YP_005842654.1|  38 KKIKEEKRNLIESSKSVFEEINKKKDEKNAILEEIKKLKSEKDEIAKKIEELKLVIKRYEELINK 102
                                       6899****************************************************999988876 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0087
                           DUF1664  56 slaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                       +++a    L+ + + + ++++e ++  ++ik+e++++re+++ i++++++ ++ ++++ ++l++++
  gi|385806256|ref|YP_005842654.1| 162 EVKAEYTSLKIKFKDIKNSMQEKIKKFESIKKEISSLREKINGISQKIDQANKEITEISNRLNQLK 227
                                       334444456667888999999999999999999999999999999999999999999999999875 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.015
                           DUF1664  44 esvskqleqvseslaatkrh...Lssridrvdkkldeqkeiskeikeevtevredlse 98 
                                       +s+ ++++ +s+++ ++ ++   +s+r++++ +++de  e  k+++ee ++++e+ s+
  gi|385806256|ref|YP_005842654.1| 196 SSLREKINGISQKIDQANKEiteISNRLNQLKASIDEKYEHLKKLQEESAKIKEEESK 253
                                       4555555555555555554411145577777777777777777777777777665443 PP

>> PI_PP_I  Phosphoinositide phosphatase insertion domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   0.00029     0.096      24      64 ..       7      47 ..       2      49 .. 0.92
   2 ?    3.1   1.6      0.32   1.1e+02       6      59 ..      45      98 ..      44     133 .. 0.72
   3 ?    8.4   2.8    0.0073       2.4      22      95 ..     129     201 ..     109     203 .. 0.87
   4 ?    3.3   1.4      0.27        91      19      61 ..     209     251 ..     203     255 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00029
                                      -SHHHHHHHHHHHHHHHHHHHHH-SSHHHHHHHHHCT-SS- CS
                           PI_PP_I 24 aslkklkqdlnqfllkWeeikktslsLeedLnkiannktpl 64
                                      ++l+k+  d++++ ++ +++k++ + L edL+ki+++k +l
  gi|385806256|ref|YP_005842654.1|  7 ETLEKISEDIYNLKQEIATLKEERIGLIEDLKKIKEEKRNL 47
                                      6789********************************99776 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.32
                                      HCS-HHHHHHHHC--TT--SHHHHHHHHHHHHHHHHHHHHH-SSHHHHHHHHHC CS
                           PI_PP_I  6 rkLeeyqqaYflnleskeaslkklkqdlnqfllkWeeikktslsLeedLnkian 59
                                      r+L e  +  f ++++k+++ + +  ++ ++  + +ei k+  +L+  +++ ++
  gi|385806256|ref|YP_005842654.1| 45 RNLIESSKSVFEEINKKKDEKNAILEEIKKLKSEKDEIAKKIEELKLVIKRYEE 98
                                      77888889999999********************99999998888776666655 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0073
                                       T--SHHHHHHHHHHHHHHHHHHHHH-SSHHHHHHHHHCT-SS--HHHHTS-HHHHHHHHHHT.T..SCCCHHHH CS
                           PI_PP_I  22 keaslkklkqdlnqfllkWeeikktslsLeedLnkiannktplPsWfnelskaqqellrvlaeaklsveeidsk 95 
                                       + ++ kkl+q++ ++++ ++ +k+   + e+ L +++++ t+l   f++++++ qe ++ + + k +++++ +k
  gi|385806256|ref|YP_005842654.1| 129 SIDEEKKLMQEIDRLTQLYNRLKDAR-DAESKLMEVKAEYTSLKIKFKDIKNSMQEKIKKFESIKKEISSLREK 201
                                       5567799***************9765.99*******************************99887777777665 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.27
                                       --TT--SHHHHHHHHHHHHHHHHHHHHH-SSHHHHHHHHHCT- CS
                           PI_PP_I  19 leskeaslkklkqdlnqfllkWeeikktslsLeedLnkiannk 61 
                                       +++ +++++++   lnq+  + +e  ++  +L+e+  ki++++
  gi|385806256|ref|YP_005842654.1| 209 IDQANKEITEISNRLNQLKASIDEKYEHLKKLQEESAKIKEEE 251
                                       678889999*************99999999*****99999876 PP

>> HTH_Tnp_Tc3_1  Tc3 transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1     0.015       4.9       7      40 ..      63      96 ..      62     101 .. 0.91
   2 ?    5.0   0.1     0.067        22      11      38 ..     204     231 ..     193     247 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.015
                                      HHHHHHHHHHHHTT--HHHHHHHHT--HHHHHHH CS
                     HTH_Tnp_Tc3_1  7 DtEraillvmkllnvklsEiarklsRsRnCIrry 40
                                      D   ail+ +k+l ++  Eia+k+   +  I+ry
  gi|385806256|ref|YP_005842654.1| 63 DEKNAILEEIKKLKSEKDEIAKKIEELKLVIKRY 96
                                      66789*******************9999999888 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.067
                                       HHHHHHHHTT--HHHHHHHHT--HHHHH CS
                     HTH_Tnp_Tc3_1  11 aillvmkllnvklsEiarklsRsRnCIr 38 
                                       +i   + + n ++ Ei+ +l+  +  I 
  gi|385806256|ref|YP_005842654.1| 204 GISQKIDQANKEITEISNRLNQLKASID 231
                                       55566678899**********8877765 PP

>> T3SSipB  Type III cell invasion protein SipB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   1.7     0.027       8.9      39      87 ..      42      90 ..      16     106 .. 0.76
   2 ?    8.1   4.6     0.011       3.6      18      92 ..     107     183 ..      98     195 .. 0.79
   3 ?   11.3  11.8    0.0011      0.36      46     136 ..     179     274 ..     173     282 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.027
                                      TTT----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           T3SSipB 39 eaasklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaq 87
                                      e++ +l +  + +++e ++ +d+ +a  e+++++ks+ d+  kk++e +
  gi|385806256|ref|YP_005842654.1| 42 EEKRNLIESSKSVFEEINKKKDEKNAILEEIKKLKSEKDEIAKKIEELK 90
                                      4555666777888899999999999999999999999999999998864 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.011
                                       HCHHHHHHHHH..HHHHHHHH.TTTTT----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                           T3SSipB  18 kSLsqLenrla..awkamska.qqeaasklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlk 91 
                                       +SLs L++r++  +wk++      ++ +kl +e+ ++++  + ++d+  +a  k+ ++k+++  ++ k ++++++++
  gi|385806256|ref|YP_005842654.1| 107 QSLSSLKKRIEqlTWKQQTTPmSIDEEKKLMQEIDRLTQLYNRLKDA-RDAESKLMEVKAEYTSLKIKFKDIKNSMQ 182
                                       7*********8558999987615688999*******99999888876.56677788888888888888888888777 PP

                                       T CS
                           T3SSipB  92 e 92 
                                       e
  gi|385806256|ref|YP_005842654.1| 183 E 183
                                       6 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.0011
                                       STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----.-----CHHH.HHHHHH...HHHHHH CS
                           T3SSipB  46 delqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeLaPd.ePekaklea.aeqQagaa.adalqa 119
                                       + +q+ +++ + +++++    ek++ + +++d+a+k ++e+ +rl++L+   + ++ +l++ +e+ a+++  ++ ++
  gi|385806256|ref|YP_005842654.1| 179 NSMQEKIKKFESIKKEISSLREKINGISQKIDQANKEITEISNRLNQLKASiDEKYEHLKKlQEESAKIKeEESKKK 255
                                       568899999999999999******************************76524445555551334455555555555 PP

                                       HHHH.HHHHHHH.HHHHHH CS
                           T3SSipB 120 deal.qKkldaa.sklsek 136
                                       +  + +Kk  +a +kl++k
  gi|385806256|ref|YP_005842654.1| 256 ESEIlEKKKKIAeEKLKKK 274
                                       4443465555541566655 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9  23.7    0.0045       1.5     101     240 ..       7     152 ..       3     156 .. 0.84
   2 ?   10.7  24.8   0.00031       0.1     309     420 ..     154     261 ..     151     277 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0045
                                       HHHHHHHHHHHHHHHHHHHHHHH....HTHHHHTTTTTHHHHHHHHHHHHHHHHT--TTT......THHHHHHHHHH CS
                              EzrA 101 kklaeleeeldeveekikkilee....lkelteseeknreeieklkekYrelrkkllanr......fsygealeele 167
                                       ++l+++ e++++++++i++++ee    +++l++ +e++r+ ie+ k+ ++e++kk  +++      +++++ ++e+ 
  gi|385806256|ref|YP_005842654.1|   7 ETLEKISEDIYNLKQEIATLKEEriglIEDLKKIKEEKRNLIESSKSVFEEINKKKDEKNaileeiKKLKSEKDEIA 83 
                                       68999****************9999999************************9987666611111155555678999 PP

                                       HHHHHH----------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTTSHHHHHHHHHHHHHSTT CS
                              EzrA 168 kqleniekefsefeeltengdyveakeilkkleeeideleevieeiPelleelkkelpkqleelkegykemke 240
                                       k++e+++  ++ +eel ++       + l++l+++i++l+ + ++ P  ++e +k+l ++++ l++ y+++k+
  gi|385806256|ref|YP_005842654.1|  84 KKIEELKLVIKRYEELINKT---PNGQSLSSLKKRIEQLTWKQQTTPMSIDE-EKKLMQEIDRLTQLYNRLKD 152
                                       99999999999999999875...45789*******************99988.5667789*******999987 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00031
                                       SSSSHHHHT--HHHHTTGGG-TTTS-GGGSSTTTSTTHHHHHHHHHHHHHHHHHHHHHHS-SS---STTGGGTHHHH CS
                              EzrA 309 kelkeklehlekqnkelkeeldrlkqsYeLseeeleklrelekelkelekdyeeleekleekkvaYSelqeeleele 385
                                       +  ++kl +++++++ lk + +++k+s    +e+++k+++++ke+++l+++++ + +k+++ +   +e++++l++l+
  gi|385806256|ref|YP_005842654.1| 154 RDAESKLMEVKAEYTSLKIKFKDIKNSM---QEKIKKFESIKKEISSLREKINGISQKIDQANKEITEISNRLNQLK 227
                                       67789999******************94...79******************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              EzrA 386 ekleeieekqeeileslkslrkdEkrAreqldeik 420
                                        +++e  e +++++e+ ++++++E++ +e+ + ++
  gi|385806256|ref|YP_005842654.1| 228 ASIDEKYEHLKKLQEESAKIKEEESKKKES-EILE 261
                                       **********************99986664.2233 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3  17.3    0.0088       2.9      22     150 ..      19     156 ..       9     163 .. 0.74
   2 ?   10.2  23.0    0.0023      0.76      37     159 ..     157     280 ..     144     292 .. 0.42

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0088
                              Fez1  22 sqaevtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelke 98 
                                        ++e+++  +e + l  +l+ ++++ ++  e+ k++ e++++k++e + + +e+++ kse++ + +k+e+l+  +k+
  gi|385806256|ref|YP_005842654.1|  19 LKQEIATLKEERIGLIEDLKKIKEEKRNLIESSKSVFEEINKKKDEKNAILEEIKKLKSEKDEIAKKIEELKLVIKR 95 
                                       678999999999***************************************************************99 PP

                              Fez1  99 lreelselsleeeeaa.....lesdeakaqrqe.....aeeleelkreverlra...eLkeerqk 150
                                         e ++++  + ++ +     +e+ + k+   +      +e ++l +e++rl +   +Lk  r++
  gi|385806256|ref|YP_005842654.1|  96 YEELINKTP-NGQSLSslkkrIEQLTWKQ---QttpmsIDEEKKLMQEIDRLTQlynRLKDARDA 156
                                       998666643.3333323444422222222...134455667777888888877622255555444 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0023
                              Fez1  37 kaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelselsleeeea 113
                                        ++l e++a+ ++   + k++++s++ek ++ e +++e++  +++ + +++k++++++e++e+ ++l++l+++ +e+
  gi|385806256|ref|YP_005842654.1| 157 ESKLMEVKAEYTSLKIKFKDIKNSMQEKIKKFESIKKEISSLREKINGISQKIDQANKEITEISNRLNQLKASIDEK 233
                                       34444555555555555555555555555555555555555555555555555555555555555555544444444 PP

                              Fez1 114 alesdeakaqrqeaeeleelkreverl..raeLkeerqkkeeqassFe 159
                                        ++ ++ +++ ++ +e e+ k+e e l  +++++ee+ kk+ ++ +Fe
  gi|385806256|ref|YP_005842654.1| 234 YEHLKKLQEESAKIKEEESKKKESEILekKKKIAEEKLKKK-ERLTFE 280
                                       43333333333332222222222222200333444443322.224444 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.2     0.013       4.3      17      54 ..       7      44 ..       5      53 .. 0.91
   2 ?    0.7   0.1       2.6   8.5e+02      31      50 ..      80      99 ..      67     114 .. 0.57
   3 ?    1.7   1.1       1.2     4e+02      31      52 ..     138     155 ..     112     168 .. 0.70
   4 ?   11.1   3.4    0.0014      0.46       4      60 ..     194     250 ..     191     257 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.013
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXX CS
                              SlyX 17 dtieeLndvvaeqqqqidrlqrqlrllaerlkeleess 54
                                      +t+e+ ++ +++  q+i+ l+++   l e lk+++e++
  gi|385806256|ref|YP_005842654.1|  7 ETLEKISEDIYNLKQEIATLKEERIGLIEDLKKIKEEK 44
                                      699****************************9999886 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 2.6
                                      HHHHHHHHHHHHHHHT-XXX CS
                              SlyX 31 qqidrlqrqlrllaerlkel 50
                                      ++i++  ++l+l+ +r +el
  gi|385806256|ref|YP_005842654.1| 80 DEIAKKIEELKLVIKRYEEL 99
                                      34444444444444444444 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHHHHT-XXXXX CS
                              SlyX  31 qqidrlqrqlrllaerlkelee 52 
                                       q+idrl++  ++l+    ++++
  gi|385806256|ref|YP_005842654.1| 138 QEIDRLTQLYNRLK----DARD 155
                                       55555555555554....4444 PP

  == domain 4  score: 11.1 bits;  conditional E-value: 0.0014
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXXXX CS
                              SlyX   4 rleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkeleessgaseae 60 
                                        +  L +k+    + i++ n++++e   ++ +l++ +++ +e+lk+l+e+s++ ++e
  gi|385806256|ref|YP_005842654.1| 194 EISSLREKINGISQKIDQANKEITEISNRLNQLKASIDEKYEHLKKLQEESAKIKEE 250
                                       567777888888899**********************************98755433 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2  13.5    0.0087       2.9     130     241 ..      61     189 ..       3     195 .. 0.80
   2 ?    7.1  11.9    0.0088       2.9     119     211 ..     184     276 ..     175     291 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0087
                           DUF4407 130 a......ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk.............gtgttgvaGkgpaake 187
                                       +        +e+++l+++ +++ ++i++++  +++ ++  +k  +g++             +++   ++   ++ k+
  gi|385806256|ref|YP_005842654.1|  61 KkdeknaILEEIKKLKSEKDEIAKKIEELKLVIKRYEELINKTPNGQSlsslkkrieqltwKQQ--TTPMSIDEEKK 135
                                       1333344788999999999999999999999999999999999999999999999888865333..35667778888 PP

                           DUF4407 188 kkaqldaaqaelaelkakldatarlaalraelaeleaerakeraasqaaaaadd 241
                                         +++d++++  + lk+ +da+++l + +ae+++l+ + ++++++ q++++++ 
  gi|385806256|ref|YP_005842654.1| 136 LMQEIDRLTQLYNRLKDARDAESKLMEVKAEYTSLKIKFKDIKNSMQEKIKKFE 189
                                       999999999999999999999999999999999999999999999999888765 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0088
                           DUF4407 119 eakelkeqlaaa...ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaql 192
                                       ++k++ e+++++   l+++++ + ++i+++++ei++ ++rl++l+a  +++++  k+ +++  + k+++ k+k++++
  gi|385806256|ref|YP_005842654.1| 184 KIKKF-ESIKKEissLREKINGISQKIDQANKEITEISNRLNQLKASIDEKYEHLKKLQEESAKIKEEESKKKESEI 259
                                       33333.22222244577777777777777777777777777777777777777655444444445556666666666 PP

                           DUF4407 193 daaqaelaelkakldatar 211
                                        ++++++ae k k  +++r
  gi|385806256|ref|YP_005842654.1| 260 LEKKKKIAEEKLK--KKER 276
                                       6666666665544..4444 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9  30.9     0.026       8.5       7     146 ..       7     189 ..       3     196 .. 0.72
   2 ?    6.4  29.5     0.019       6.2      16     159 ..     109     250 ..      95     269 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.026
                           DUF4795   7 ellkklqeaieklqeelekleek....vkelekrledkekklealkkqieelekvkadkeeveeel.aekadkeaLa 78 
                                       e+l+k+ e+i +l++e++ l+e+     ++l+k +e+k+  +e+ k+  ee +k+k++k+ + ee+ ++k+ k+ +a
  gi|385806256|ref|YP_005842654.1|   7 ETLEKISEDIYNLKQEIATLKEEriglIEDLKKIKEEKRNLIESSKSVFEEINKKKDEKNAILEEIkKLKSEKDEIA 83 
                                       67999999999999999999987333357888888899999*********************9999679******** PP

                           DUF4795  79 tkvsrdq..............fDeakkeLekmleellekle......eqeealkkaldtLq..............ee 121
                                       +k+++ +                ++++ L+k +e+l  k +       +e++l + +d L               + 
  gi|385806256|ref|YP_005842654.1|  84 KKIEELKlvikryeelinktpNGQSLSSLKKRIEQLTWKQQttpmsiDEEKKLMQEIDRLTqlynrlkdardaesKL 160
                                       ***99999888888888887756666666666666666633555556555555555555554444444886666655 PP

                           DUF4795 122 lkekld....rlelepLkeqleerlkelq 146
                                       ++ k +    ++ ++++k+ ++e++k+ +
  gi|385806256|ref|YP_005842654.1| 161 MEVKAEytslKIKFKDIKNSMQEKIKKFE 189
                                       66666677777777777777776666554 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.019
                           DUF4795  16 ieklqeelekleekvkelekrledkekklealkkqieelekvkadkeeveeelaekadkeaLatkvsrdq..fDeak 90 
                                       ++ l++++e+l  k++ ++ ++ +++k ++ +   ++  +  k+ ++  ++ +++ka    L++k  + +  ++e++
  gi|385806256|ref|YP_005842654.1| 109 LSSLKKRIEQLTWKQQTTPMSIDEEKKLMQEIDRLTQLYNRLKDARDAESKLMEVKAEYTSLKIKFKDIKnsMQEKI 185
                                       45566666666666666666666655555665555555666666666688999*************77668899988 PP

                           DUF4795  91 keLe...kmleellekleeqeealkkaldtLqeelkekldrlelepLkeqleerlkelqkelqeamekedke 159
                                       k++e   k +++l+ek+++ ++++++a +++  e+ ++     l++Lk  ++e+ + l+ +lqe ++k+++e
  gi|385806256|ref|YP_005842654.1| 186 KKFEsikKEISSLREKINGISQKIDQANKEIT-EISNR-----LNQLKASIDEKYEHLK-KLQEESAKIKEE 250
                                       87651115679999999999999999999999.88888.....6788888887777777.556555555542 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4  12.2     0.003      0.98       7     101 ..       4      95 ..       1     103 [. 0.73
   2 ?    7.8   7.2    0.0092       3.1      27     100 ..     131     203 ..     105     205 .. 0.69
   3 ?    7.5   9.9     0.012         4      27      90 ..     189     249 ..     186     277 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.003
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHH CS
                        Laminin_II   7 eanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqlee 83 
                                       ++ et++++ e++ +l+q++  +ke+  ++ +++++++e+ +++ +  +++ +++ k + + + +l+ +k+lk  ++
  gi|385806256|ref|YP_005842654.1|   4 SVGETLEKISEDIYNLKQEIATLKEERIGLIEDLKKIKEEKRNLIESSKSVFEEINKKKDEKNAILEEIKKLKSEKD 80 
                                       45567777777777777777777777777777777777777777777777777777777777777777666666666 PP

                                       H...HHHHHHHHHHHHHH CS
                        Laminin_II  84 assslsdniseikelIaq 101
                                       +   + ++i+e+k  I++
  gi|385806256|ref|YP_005842654.1|  81 E---IAKKIEELKLVIKR 95 
                                       6...**********9986 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0092
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH.......HHHHHHHHHHHH CS
                        Laminin_II  27 entkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeasss....lsdniseikelI 99 
                                       +++k+ ++ei+r     ++ + +  k  rdA+++  +++ +   L  k+k +k+  +++      ++++is ++e I
  gi|385806256|ref|YP_005842654.1| 131 DEEKKLMQEIDRL----TQ-LYNRLKDARDAESKLMEVKAEYTSLKIKFKDIKNSMQEKIKkfesIKKEISSLREKI 202
                                       3333333333333....22.33556778999999999999999**********988776556677999999999988 PP

                                       H CS
                        Laminin_II 100 a 100
                                       +
  gi|385806256|ref|YP_005842654.1| 203 N 203
                                       6 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.012
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHH CS
                        Laminin_II  27 entkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeassslsd 90 
                                       e +k+++s+++++++ + +k+++ank i + ++   +L+  +++  +    lk+l+e+s+ +++
  gi|385806256|ref|YP_005842654.1| 189 ESIKKEISSLREKINGISQKIDQANKEITEISNRLNQLKASIDEKYEH---LKKLQEESAKIKE 249
                                       556666777777777777777777777777776666666655544444...4444444333444 PP

>> COG6  Conserved oligomeric complex COG6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   5.7   6.3e-05     0.021      42     105 ..      33      96 ..       6      98 .. 0.93
   2 ?    3.2   5.6      0.06        20      33      95 ..     147     209 ..     120     214 .. 0.84
   3 ?    4.8  12.7     0.021       6.9      38     119 ..     208     289 ..     205     293 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.3e-05
                              COG6  42 vaeqLkriesdveklnelcdemkkklssakeetsdlleeaeeLkeekkklelkqkllkaflkkF 105
                                       + e Lk+i+++  +l e+++++ ++++++k+e + +lee+++Lk+ek+++ +k + lk   k++
  gi|385806256|ref|YP_005842654.1|  33 LIEDLKKIKEEKRNLIESSKSVFEEINKKKDEKNAILEEIKKLKSEKDEIAKKIEELKLVIKRY 96 
                                       5689**************************************************9999988887 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.06
                              COG6  33 eefleefqpvaeqLkriesdveklnelcdemkkklssakeetsdlleeaeeLkeekkklelkq 95 
                                        + l++ + ++ +L +++++ ++l+   +++k++++++ ++ +++ +e+++L+e+ + +++k 
  gi|385806256|ref|YP_005842654.1| 147 YNRLKDARDAESKLMEVKAEYTSLKIKFKDIKNSMQEKIKKFESIKKEISSLREKINGISQKI 209
                                       5668999999999***************************************99999999885 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.021
                              COG6  38 efqpvaeqLkriesdveklnelcdemkkklssakeetsdlleeaeeLkeekkklelkqkllka.flkkFtLseeEea 113
                                       + +++++++ +i++++++l++++de  ++l++ +ee++++ ee e+ k+e++ le+k+k++++ ++kk  L+ e++ 
  gi|385806256|ref|YP_005842654.1| 208 KIDQANKEITEISNRLNQLKASIDEKYEHLKKLQEESAKIKEE-ESKKKESEILEKKKKIAEEkLKKKERLTFEDLL 283
                                       67899********************************998777.5669999*********97526677777777777 PP

                              COG6 114 aLtsge 119
                                       aL+ +e
  gi|385806256|ref|YP_005842654.1| 284 ALYGEE 289
                                       777666 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   7.8     0.014       4.7      12      81 ..      34      98 ..       5     105 .. 0.69
   2 ?    7.4   4.5     0.021       7.1       7      79 ..     132     205 ..     107     212 .. 0.65
   3 ?    6.8   8.6     0.031        10       5      64 ..     209     268 ..     207     280 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.014
                           DUF2203 12 LpllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvevkdlea 81
                                      +  lk++ ee r+l +  +++ ee++++k+e     +++  +e+++l++e +e+ ++ieel+ ++k  e+
  gi|385806256|ref|YP_005842654.1| 34 IEDLKKIKEEKRNLIESSKSVFEEINKKKDE-----KNAILEEIKKLKSEKDEIAKKIEELKLVIKRYEE 98
                                      3333444444444444444444444444444.....89999************************99875 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.021
                           DUF2203   7 eAnalLpllkelleelralrkeleeleeeleeakaeaekse..aaeleaeleeleaeieelveeieelGvevkdl 79 
                                       e ++l++++++l++ +++l k+++++e++l e kae+++ +  ++  +++++e  +++e++ +ei++l  ++ ++
  gi|385806256|ref|YP_005842654.1| 132 EEKKLMQEIDRLTQLYNRL-KDARDAESKLMEVKAEYTSLKikFKDIKNSMQEKIKKFESIKKEISSLREKINGI 205
                                       5566666666655544443.3455556666666666555555566666666666666666666666665555544 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.031
                           DUF2203   5 leeAnalLpllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeiee 64 
                                       +++An+ +++++++l++l+a  +e  e  ++l+e++a+ +++e +++e+e+ e +++i e
  gi|385806256|ref|YP_005842654.1| 209 IDQANKEITEISNRLNQLKASIDEKYEHLKKLQEESAKIKEEESKKKESEILEKKKKIAE 268
                                       689999999999999999988888888888888888888888877777777776666654 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1  17.1   0.00057      0.19      86     171 ..       8      95 ..       4     119 .. 0.89
   2 ?    0.4   8.2       1.1   3.5e+02      56     127 ..      72     145 ..      71     150 .. 0.75
   3 ?    6.6  12.3     0.013       4.3      61     128 ..     134     201 ..     101     201 .. 0.73
   4 ?    2.9  22.6      0.18        61      27     104 ..     194     274 ..     193     283 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00057
                               GAS  86 slknlkarlkelekelkdlkwehevleqrfekvekerdelykkfeaaiqevqqktglknllLe..kklkalqeelEk 160
                                        l+++ + + +l++e+ +lk+e   l + ++k+++e+ +l ++ +++++e+ +k + kn +Le  kklk+ ++e+ k
  gi|385806256|ref|YP_005842654.1|   8 TLEKISEDIYNLKQEIATLKEERIGLIEDLKKIKEEKRNLIESSKSVFEEINKKKDEKNAILEeiKKLKSEKDEIAK 84 
                                       577888899999**************************************************977799999999999 PP

                               GAS 161 keaqleevlaa 171
                                       k ++l+ v+++
  gi|385806256|ref|YP_005842654.1|  85 KIEELKLVIKR 95 
                                       99999988875 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.1
                               GAS  56 nkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrf...ekvekerdelyk 127
                                        k+lk +  +  +++eeL+  +k+ye+  ++  n  + l++l+k +++l+w+++   + +   +k+ +e+d+l++
  gi|385806256|ref|YP_005842654.1|  72 IKKLKSEKDEIAKKIEELKLVIKRYEELINKTPNG-QSLSSLKKRIEQLTWKQQTTPMSIdeeKKLMQEIDRLTQ 145
                                       67777777888899999999999999988877765.679999999999999999888777222456667776665 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.013
                               GAS  61 epLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekvekerdelykk 128
                                       ++L +    + +L ++lk+ +   ++l+++ka++++l+ ++kd+k + + + ++fe+++ke+  l++k
  gi|385806256|ref|YP_005842654.1| 134 KKLMQEIDRLTQLYNRLKDARDAESKLMEVKAEYTSLKIKFKDIKNSMQEKIKKFESIKKEISSLREK 201
                                       33444444556677788888888889999999999999999999999999999999999999998875 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.18
                               GAS  27 lIkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrk...qlknyekdkqslknlkarlkeleke 100
                                        I sl+e+i+ + +k ++++ke+ eis++ ++lk  + +  e +++L++   ++k+ e++k++ + l+++ k +e++
  gi|385806256|ref|YP_005842654.1| 194 EISSLREKINGISQKIDQANKEITEISNRLNQLKASIDEKYEHLKKLQEesaKIKEEESKKKESEILEKKKKIAEEK 270
                                       599********************************************996667888999999999999999999999 PP

                               GAS 101 lkdl 104
                                       lk+ 
  gi|385806256|ref|YP_005842654.1| 271 LKKK 274
                                       9875 PP

>> ApoO  Apolipoprotein O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       6.6   2.2e+03      38      63 ..       5      30 ..       2      40 .. 0.72
   2 ?   -0.6   0.1       3.7   1.2e+03      45      45 ..      68      68 ..      18     105 .. 0.60
   3 ?   -0.7   0.1         4   1.3e+03      38      38 ..     104     104 ..      61     160 .. 0.58
   4 ?    3.8   0.2      0.15        51      17      58 ..     147     187 ..     122     195 .. 0.75
   5 ?    9.4   0.4    0.0029      0.96      15      64 ..     190     242 ..     186     246 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 6.6
                              ApoO 38 lnkvkskvetaeqsvtdtiasLkepp 63
                                      + ++ +k+ +   +++++ia+Lke++
  gi|385806256|ref|YP_005842654.1|  5 VGETLEKISEDIYNLKQEIATLKEER 30
                                      56667777788888888888888876 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 3.7
                              ApoO 45 v 45
                                      +
  gi|385806256|ref|YP_005842654.1| 68 I 68
                                      2 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 4
                              ApoO  38 l 38 
                                        
  gi|385806256|ref|YP_005842654.1| 104 P 104
                                       1 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.15
                              ApoO  17 eegvrslRkslepytsavqdelnkvkskvetaeqsvtdtias 58 
                                        +  + +R  +e+++ +v++e++++k k+++ ++s++++i+ 
  gi|385806256|ref|YP_005842654.1| 147 YNRLKDAR-DAESKLMEVKAEYTSLKIKFKDIKNSMQEKIKK 187
                                       33444444.368899999999999999999999999999876 PP

  == domain 5  score: 9.4 bits;  conditional E-value: 0.0029
                              ApoO  15 rLeegvrslRksl...epytsavqdelnkvkskvetaeqsvtdtiasLkeppe 64 
                                       ++++ ++slR+ +   +++++++++e++++++++++++ s+ ++++ Lk+ +e
  gi|385806256|ref|YP_005842654.1| 190 SIKKEISSLREKIngiSQKIDQANKEITEISNRLNQLKASIDEKYEHLKKLQE 242
                                       577889999987522269999***************************98765 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   9.9    0.0021      0.69       2      84 ..      21     102 ..      20     108 .. 0.90
   2 ?    3.6   6.0     0.095        32      20      92 ..     111     184 ..     105     188 .. 0.79
   3 ?    8.5  16.2    0.0032       1.1       3      84 ..     187     268 ..     185     283 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0021
                             TMPIT   2 eeweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelker 78 
                                       +e+++l++e   l e  k++k++ ++l ++ +++ +ei+k+k + +++ +++kklk++ k+e ++++eelk  +k+ 
  gi|385806256|ref|YP_005842654.1|  21 QEIATLKEERIGLIEDLKKIKEEKRNLIESSKSVFEEINKKKDEKNAILEEIKKLKSE-KDEIAKKIEELKLVIKRY 96 
                                       7899999999999999****************************************99.578889999999999988 PP

                             TMPIT  79 kkvlke 84 
                                       ++ +++
  gi|385806256|ref|YP_005842654.1|  97 EELINK 102
                                       887765 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.095
                             TMPIT  20 eykqkleelsklqskcskeikkqkkrlkelksslkklkksvk.eeeeeeveelkeelkerkkvlkevesllpkk 92 
                                       ++k+++e+l+  q+++  +i+++kk ++e+++  + +++ ++ ++ e+++ e+k+e  + k  +k++++++ +k
  gi|385806256|ref|YP_005842654.1| 111 SLKKRIEQLTWKQQTTPMSIDEEKKLMQEIDRLTQLYNRLKDaRDAESKLMEVKAEYTSLKIKFKDIKNSMQEK 184
                                       67889999999999999999999999999887666666654435667789999999999999999999998877 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0032
                             TMPIT   3 eweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerk 79 
                                       ++e+++ke+ +l+e+ + + qk+++ +k ++++s+++++ k  + e  ++lkkl++++ + +eee ++ ++e+ e+k
  gi|385806256|ref|YP_005842654.1| 187 KFESIKKEISSLREKINGISQKIDQANKEITEISNRLNQLKASIDEKYEHLKKLQEESAKIKEEESKKKESEILEKK 263
                                       67889999999999999999999999999999999999999999999999999999988777778888788877777 PP

                             TMPIT  80 kvlke 84 
                                       k ++e
  gi|385806256|ref|YP_005842654.1| 264 KKIAE 268
                                       77764 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2  18.2   0.00049      0.16      25     131 ..       8     111 ..       4     146 .. 0.72
   2 ?    0.8  27.5       1.5   5.1e+02       2     125 ..     150     272 ..     134     288 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00049
                           zf-C4H2  25 alekeekcleeykkelelLeqEkmaHveeLrlIhaDinalEsvikeaeeekekslekakklyeeykklkeevnelrs 101
                                       +lek ++ + + k+e+ +L++E+   +e+L++I++ + +l +  k+  ee +k++++ + ++ee+kklk+e +e+ +
  gi|385806256|ref|YP_005842654.1|   8 TLEKISEDIYNLKQEIATLKEERIGLIEDLKKIKEEKRNLIESSKSVFEEINKKKDEKNAILEEIKKLKSEKDEIAK 84 
                                       67889999*******************************99999******************************998 PP

                           zf-C4H2 102 elglekledleeeeeellkeeifekqklka 131
                                       ++   +l+   +  eel++++  + q l++
  gi|385806256|ref|YP_005842654.1|  85 KIE--ELKLVIKRYEELINKTP-NGQSLSS 111
                                       843..34444444444555554.2222222 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1.5
                           zf-C4H2   2 ikeirektleleklknklakevealekeekcleeykkelelLeqEkmaHveeLrlIhaDinalEsvikeaeeekeks 78 
                                       +k++r+  ++l ++k++ ++    +++ ++ ++e  k+ e +++E  +  e++  I + i++  + i e  +  ++ 
  gi|385806256|ref|YP_005842654.1| 150 LKDARDAESKLMEVKAEYTSLKIKFKDIKNSMQEKIKKFESIKKEISSLREKINGISQKIDQANKEITEISNRLNQL 226
                                       57777777777777777777777777777777777777777777777777777777777777777777777777777 PP

                           zf-C4H2  79 lekakklyeeykklkeevnelrselglekledleeeeeellkeeife 125
                                       ++++ ++ye +kkl+ee  ++++e   +k ++  e+++++ +e++ +
  gi|385806256|ref|YP_005842654.1| 227 KASIDEKYEHLKKLQEESAKIKEEESKKKESEILEKKKKIAEEKL-K 272
                                       777777777777777777777777666666665555555555444.2 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   9.3    0.0005      0.17      18      65 ..      14      75 ..       4      75 .. 0.79
   2 ?    4.4   9.7      0.16        53      17      64 ..      34      88 ..      33      90 .. 0.55
   3 ?    1.8   9.8         1   3.3e+02      35      65 ..      59      89 ..      56     126 .. 0.61
   4 ?    2.6   8.2      0.56   1.9e+02      10      64 ..     133     187 ..     107     188 .. 0.64
   5 ?    8.9   4.2    0.0062       2.1      13      62 ..     181     230 ..     173     232 .. 0.71
   6 ?    2.8  16.5      0.49   1.6e+02       6      62 ..     223     277 ..     220     284 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0005
                              ZapB 18 dtitlLqmeieeLkeeneelkeenrele..............eeneqlkeereawqerlkkL 65
                                      + i  L++ei+ Lkee   l e  ++++              ee+++ k+e++a+ e +kkL
  gi|385806256|ref|YP_005842654.1| 14 EDIYNLKQEIATLKEERIGLIEDLKKIKeekrnliessksvfEEINKKKDEKNAILEEIKKL 75
                                      567778888888888886666666666666666669***********************998 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.16
                              ZapB 17 idtitlLqmeieeLkeeneelkeenrele.......eeneqlkeereawqerlkk 64
                                      i+ +++ ++e + L e +++  ee+++ +       ee+++lk e+ ++ ++++ 
  gi|385806256|ref|YP_005842654.1| 34 IEDLKKIKEEKRNLIESSKSVFEEINKKKdeknailEEIKKLKSEKDEIAKKIEE 88
                                      5555556666666665554444444444444444447777777777777777776 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 1
                              ZapB 35 eelkeenreleeeneqlkeereawqerlkkL 65
                                      ++ k+e++++ ee+++lk e+ ++ ++++ L
  gi|385806256|ref|YP_005842654.1| 59 NKKKDEKNAILEEIKKLKSEKDEIAKKIEEL 89
                                      5555666666666666666666665555544 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.56
                              ZapB  10 EskiqkaidtitlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlkk 64 
                                       E+k  + id++t+L +++++ +   ++l e ++e ++   ++k+ ++++qe++kk
  gi|385806256|ref|YP_005842654.1| 133 EKKLMQEIDRLTQLYNRLKDARDAESKLMEVKAEYTSLKIKFKDIKNSMQEKIKK 187
                                       4444555555555555555555555555555555555555666777888887776 PP

  == domain 5  score: 8.9 bits;  conditional E-value: 0.0062
                              ZapB  13 iqkaidtitlLqmeieeLkeeneelkeenreleeeneqlkeereawqerl 62 
                                        q+ i + ++ ++ei+ L+e+ +  ++++++ ++e+ +  +  +++++ +
  gi|385806256|ref|YP_005842654.1| 181 MQEKIKKFESIKKEISSLREKINGISQKIDQANKEITEISNRLNQLKASI 230
                                       56667777777788888888887777777777777777777777777666 PP

  == domain 6  score: 2.8 bits;  conditional E-value: 0.49
                              ZapB   6 LeqLEskiqkaidtitlLqmeieeLkeeneelkeenreleeeneqlkeereawqerl 62 
                                       L+qL ++i++  + +++Lq+e ++ kee ++ ke   e+ e+ ++  ee+ + +erl
  gi|385806256|ref|YP_005842654.1| 223 LNQLKASIDEKYEHLKKLQEESAKIKEEESKKKE--SEILEKKKKIAEEKLKKKERL 277
                                       89**************************999999..99***********99999998 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1  12.2     0.019       6.4     681     785 ..      11     122 ..       3     127 .. 0.64
   2 ?    7.7  25.9    0.0016      0.53     590     745 ..     122     275 ..     103     280 .. 0.66

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.019
                           DUF3584 681 qaeeqlqkldaqlkqleeqqkaaleelkedlseerl..ekkakwqevvgeldeqlaelkkaieaartqa...karlk 752
                                       ++ e + +l++++  l+e++  ++e lk+ ++e+r+  e ++ + e++ +++++ +++ ++i++ ++++   +++++
  gi|385806256|ref|YP_005842654.1|  11 KISEDIYNLKQEIATLKEERIGLIEDLKKIKEEKRNliESSKSVFEEINKKKDEKNAILEEIKKLKSEKdeiAKKIE 87 
                                       66777888888888888888888887777777666422344444444444444444555555555444400055666 PP

                           DUF3584 753 elee..aykreLkskdvDpetvkelkrkieeLekk 785
                                       el+   ++ +eL +k ++++ +++lk++ie+L+ k
  gi|385806256|ref|YP_005842654.1|  88 ELKLviKRYEELINKTPNGQSLSSLKKRIEQLTWK 122
                                       6664335567999****************999855 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0016
                           DUF3584 590 eridvpdyaaseeeLrerlqaleealqsaeakqkqaeeelkqlnaeleeakravaeaatalknardtlerlqnekes 666
                                       ++   p ++++e++L ++++ l++ l +  + +  ae++l +++ae++ +k + ++ +++++++ ++ e +++e  s
  gi|385806256|ref|YP_005842654.1| 122 KQQTTPMSIDEEKKLMQEIDRLTQ-LYNRLKDARDAESKLMEVKAEYTSLKIKFKDIKNSMQEKIKKFESIKKEISS 197
                                       444456677777777777777754.4445555667777777888888888888888888888888888888887777 PP

                           DUF3584 667 ekdklekaiaerkqqaeeqlqkldaqlkqleeqqkaaleelkedlseerlekkakwqevvgeldeqlaelkkaieaa 743
                                       +++k++  i ++ +qa+++++++ + l+ql++ +++  e+lk+  +e    k+++ ++ ++e+ e+ +++ +++ ++
  gi|385806256|ref|YP_005842654.1| 198 LREKIN-GISQKIDQANKEITEISNRLNQLKASIDEKYEHLKKLQEESAKIKEEESKKKESEILEKKKKIAEEKLKK 273
                                       777776.4667777778888888888888888777777777776666666666666666666666655555555544 PP

                           DUF3584 744 rt 745
                                       ++
  gi|385806256|ref|YP_005842654.1| 274 KE 275
                                       43 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       9.5   3.2e+03      18      37 ..       7      26 ..       3      30 .. 0.57
   2 ?   -0.2   0.0       3.6   1.2e+03      63      72 ..      65      74 ..      49      99 .. 0.56
   3 ?    1.1   0.2       1.4   4.7e+02      40      76 ..     120     156 ..     105     167 .. 0.60
   4 ?    2.3   0.2      0.62   2.1e+02      60      69 ..     174     183 ..     129     203 .. 0.51
   5 ?    6.8   0.4     0.024       7.9      52      81 ..     187     216 ..     151     219 .. 0.84
   6 ?    7.1   0.2     0.018       6.1       9      35 ..     205     231 ..     198     235 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 9.5
                                      HHHHHHHHHHHHHHHHHHHC CS
                            WXG100 18 kqaeeledelqrlkaevdal 37
                                      ++ e++++ + +lk+e++ l
  gi|385806256|ref|YP_005842654.1|  7 ETLEKISEDIYNLKQEIATL 26
                                      44455555566666666655 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 3.6
                                      HHHHHHHHHH CS
                            WXG100 63 lvdaLeeise 72
                                       ++ Leei +
  gi|385806256|ref|YP_005842654.1| 65 KNAILEEIKK 74
                                      3333333332 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 1.4
                                       GCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  40 gWsGaaadafqaefeewkqaaqklvdaLeeisealkq 76 
                                       +W+ ++     +e ++++q++++l ++++ + +a ++
  gi|385806256|ref|YP_005842654.1| 120 TWKQQTTPMSIDEEKKLMQEIDRLTQLYNRLKDARDA 156
                                       5555555555555566666666666666666666555 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.62
                                       HHHHHHHHHH CS
                            WXG100  60 aqklvdaLee 69 
                                       ++++++ ++e
  gi|385806256|ref|YP_005842654.1| 174 FKDIKNSMQE 183
                                       3333333333 PP

  == domain 5  score: 6.8 bits;  conditional E-value: 0.024
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  52 efeewkqaaqklvdaLeeisealkqaanaf 81 
                                        fe +k+++  l ++ ++is++++qa+++ 
  gi|385806256|ref|YP_005842654.1| 187 KFESIKKEISSLREKINGISQKIDQANKEI 216
                                       678899999999999999999999998876 PP

  == domain 6  score: 7.1 bits;  conditional E-value: 0.018
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100   9 lrqaaarfqkqaeeledelqrlkaevd 35 
                                       + q++ +++k+ +e++++l++lka++d
  gi|385806256|ref|YP_005842654.1| 205 ISQKIDQANKEITEISNRLNQLKASID 231
                                       456667777777777777777777776 PP

>> KASH_CCD  Coiled-coil region of CCDC155 or KASH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7  19.3   0.00013     0.042      63     165 ..      10     111 ..       4     125 .. 0.84
   2 ?   -1.6  33.3       6.1     2e+03      36     170 ..     131     276 ..     115     286 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00013
                          KASH_CCD  63 klleeEleelkalvkeleEkrarlkaqnkqlekenqsLiakiesLqeenikllaekdelkkklkeLlkekaeLkkql 139
                                       + ++e++ +lk+ + +l+E+r  l    k+++ e+  Li+  +s  ee+ k + ek++  + +k+L +ek+e+ k++
  gi|385806256|ref|YP_005842654.1|  10 EKISEDIYNLKQEIATLKEERIGLIEDLKKIKEEKRNLIESSKSVFEEINKKKDEKNAILEEIKKLKSEKDEIAKKI 86 
                                       67899999********************************************************************* PP

                          KASH_CCD 140 heleellaekealleektkqieeLkl 165
                                        el+ ++   e+ l++kt + ++L +
  gi|385806256|ref|YP_005842654.1|  87 EELKLVIKRYEE-LINKTPNGQSLSS 111
                                       888766655555.5556655555443 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 6.1
                          KASH_CCD  36 etnakLteei...eeLkkklkstQqalqkaklleeEleelkalvkeleEkrarlkaqnkqlekenqsLiakiesLqe 109
                                       ++ +kL++ei   ++L ++lk    a  k   ++ E   lk   k+++ + ++   + + ++ke  sL++ki+ + +
  gi|385806256|ref|YP_005842654.1| 131 DEEKKLMQEIdrlTQLYNRLKDARDAESKLMEVKAEYTSLKIKFKDIKNSMQEKIKKFESIKKEISSLREKINGISQ 207
                                       55689999982224556799999999999999999999999999999999999999999999999999999999999 PP

                          KASH_CCD 110 enikllaekdelkkklkeLlkekae....Lkkqlheleell....aekealleektkqieeLkltieEy 170
                                       ++ +   e+ e  ++l++L ++++e    Lkk   e  +++     +ke+++ ek+k+i e kl  +E 
  gi|385806256|ref|YP_005842654.1| 208 KIDQANKEITEISNRLNQLKASIDEkyehLKKLQEESAKIKeeesKKKESEILEKKKKIAEEKLKKKER 276
                                       999999999999999999988776522223333333333321111456777777777777766665554 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 ?    0.8  14.5      0.61     2e+02      28      86 ..      69     147 ..      60     166 .. 0.68
   2 ?    9.1  28.8    0.0018       0.6      39     147 ..     155     266 ..     141     285 .. 0.58

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.61
                             Atg14  28 rerlaklksekeslkkkie..kalegke..................eaeqledkiknkkakleelksliadlrerlq 84 
                                        e+++klksek+++ kkie  k++ +++                  + eql++k +++ ++++e k+l++++ + +q
  gi|385806256|ref|YP_005842654.1|  69 LEEIKKLKSEKDEIAKKIEelKLVIKRYeelinktpngqslsslkkRIEQLTWKQQTTPMSIDEEKKLMQEIDRLTQ 145
                                       57899**************6666777777888888777766666666666666666666666666666666555444 PP

                             Atg14  85 el 86 
                                       + 
  gi|385806256|ref|YP_005842654.1| 146 LY 147
                                       32 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0018
                             Atg14  39 eslkkkiekalegke...eaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklk 112
                                       ++  k +e + e ++   + ++ ++  + k +k e++k++i++lre+++ +++k++q +kei e +++l +l++++ 
  gi|385806256|ref|YP_005842654.1| 155 DAESKLMEVKAEYTSlkiKFKDIKNSMQEKIKKFESIKKEISSLREKINGISQKIDQANKEITEISNRLNQLKASID 231
                                       33333333333333333334455566667777777777777777777777777777777777777777777777777 PP

                             Atg14 113 kRrsdleslqneleerrkkqiaklqdaikrieqkl 147
                                       ++++ l++lq+e ++ ++++ +k  ++i ++++k+
  gi|385806256|ref|YP_005842654.1| 232 EKYEHLKKLQEESAKIKEEESKKKESEILEKKKKI 266
                                       77777777777766555555444444444333333 PP

>> COG2  COG (conserved oligomeric Golgi) complex component, COG2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.4      0.33   1.1e+02      70     113 ..       8      44 ..       3      56 .. 0.42
   2 ?    5.2   5.8     0.063        21      63     125 ..      36      99 ..      31     104 .. 0.59
   3 ?    3.5   1.5      0.22        73      62     122 ..     107     167 ..     105     178 .. 0.73
   4 ?   10.7   8.7    0.0012      0.41      50     117 ..     181     248 ..     173     284 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.33
                              COG2  70 eleevesplaaarkkvesvreklsereeeveskleeakeleekr 113
                                        l       +++ +++ +++++++  +ee  + +e+ k+++e++
  gi|385806256|ref|YP_005842654.1|   8 TL-------EKISEDIYNLKQEIATLKEERIGLIEDLKKIKEEK 44 
                                       33.......34444444444444444444444444444444443 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.063
                              COG2  63 hLvglqeeleevesplaaarkkvesvreklsereeeveskleeakeleekrellklllk.ldev 125
                                        L+ ++ee +++  + +++ +++++ +++ ++  ee+++  +e+ e+++k e lkl++k ++e+
  gi|385806256|ref|YP_005842654.1|  36 DLKKIKEEKRNLIESSKSVFEEINKKKDEKNAILEEIKKLKSEKDEIAKKIEELKLVIKrYEEL 99 
                                       4555556666666666666666677777777777777766667766666666666554314444 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.22
                              COG2  62 ghLvglqeeleevesplaaarkkvesvreklsereeeveskleeakeleekr.ellklllkl 122
                                       ++L +l++++e+++ + +++   +++ + kl + + ++++  +  k++++++ +l+++  ++
  gi|385806256|ref|YP_005842654.1| 107 QSLSSLKKRIEQLTWKQQTTPMSIDEEK-KLMQEIDRLTQLYNRLKDARDAEsKLMEVKAEY 167
                                       68999999********999999998876.566666777777777777766655555555555 PP

  == domain 4  score: 10.7 bits;  conditional E-value: 0.0012
                              COG2  50 vnedyadFvslSghLvglqeeleevesplaaarkkvesvreklsereeeveskleeakeleekrellk 117
                                         e ++ F s+ ++  +l+e+++ +++++ +a k+++++ + l++ ++ +++k e  k+l+e+++ +k
  gi|385806256|ref|YP_005842654.1| 181 MQEKIKKFESIKKEISSLREKINGISQKIDQANKEITEISNRLNQLKASIDEKYEHLKKLQEESAKIK 248
                                       5666778889999999********************************************99985444 PP

>> DegS  Sensor protein DegS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2  14.2     0.081        27      23     150 ..      10     124 ..       3     130 .. 0.67
   2 ?    2.4   1.1       0.3        98      37      74 ..     134     170 ..     128     183 .. 0.64
   3 ?    4.9  21.0      0.05        16      26     128 ..     178     278 ..     162     284 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.081
                              DegS  23 EsarkeverlkkeleelkeevsevikevdklekkerkarkrLaeVskdFkkyseeeikeaYeeakelqvelallrek 99 
                                       E++ +++ +lk+e+++lkee   +i              + L ++  + ++   e  k+++ee ++ + e     e+
  gi|385806256|ref|YP_005842654.1|  10 EKISEDIYNLKQEIATLKEERIGLI--------------EDLKKIKEEKRNLI-ESSKSVFEEINKKKDEKNAILEE 71 
                                       3333333333333333333333333..............33333333322222.33467899999999999999999 PP

                              DegS 100 EkqlrerRdelerrLkklketierAeklvsqv..gvvlnyLsgdlkqvsekle 150
                                        k+l++ +de+ +++++lk +i+r e+l+++   g  l+ L++ ++q+++k +
  gi|385806256|ref|YP_005842654.1|  72 IKKLKSEKDEIAKKIEELKLVIKRYEELINKTpnGQSLSSLKKRIEQLTWKQQ 124
                                       9****************************997546788888888888887765 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.3
                              DegS  37 eelkeevsevikevdklekkerkarkrLaeVskdFkky 74 
                                       ++l +e+ ++ +  ++l k+ r a  +L+eV  ++ + 
  gi|385806256|ref|YP_005842654.1| 134 KKLMQEIDRLTQLYNRL-KDARDAESKLMEVKAEYTSL 170
                                       45555555555555555.45677888999999888754 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.05
                              DegS  26 rkeverlkkeleelkeevsevikevdklekkerkarkrLaeVskdFkkyseeeikeaYeeakelqvelallrekEkq 102
                                       ++ +++  k+ e +k+e+s++ ++++ +++k  +a k+ +e+s + ++ + + i e Ye+ k+lq e a  +e+E++
  gi|385806256|ref|YP_005842654.1| 178 KNSMQEKIKKFESIKKEISSLREKINGISQKIDQANKEITEISNRLNQLK-ASIDEKYEHLKKLQEESAKIKEEESK 253
                                       56667777888899999999999999999999999999999999998875.68***************999999887 PP

                              DegS 103 lrerRdelerrLkklketierAeklv 128
                                        ++  + le++ k ++e +++ e+l+
  gi|385806256|ref|YP_005842654.1| 254 -KKESEILEKKKKIAEEKLKKKERLT 278
                                       .5556788999999999999988886 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   2.2      0.09        30     107     167 ..      35      74 ..       5     105 .. 0.62
   2 ?   10.8  10.8   0.00091       0.3      69     171 ..     151     253 ..     142     266 .. 0.94

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.09
                            DUF745 107 ealkallkaakenlenaeqvaagaqqelaektqlleaAkkRveeLkkqlkearkdlektkk 167
                                       e lk++ ++ ++ +e++++v ++ +++ +ek+++le+                      kk
  gi|385806256|ref|YP_005842654.1|  35 EDLKKIKEEKRNLIESSKSVFEEINKKKDEKNAILEEI---------------------KK 74 
                                       44444445555555555555555555555555555544.....................43 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00091
                            DUF745  69 qelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqlleaAk 145
                                       ++ r+ae+ + e+k++++s + + k  ++++++  +++e++k+ + + +e+++ + q  ++a++e+ e ++ l++ k
  gi|385806256|ref|YP_005842654.1| 151 KDARDAESKLMEVKAEYTSLKIKFKDIKNSMQEKIKKFESIKKEISSLREKINGISQKIDQANKEITEISNRLNQLK 227
                                       5789************************************************************************* PP

                            DUF745 146 kRveeLkkqlkearkdlektkkaAyk 171
                                       + ++e  ++lk+ +++ +k+k++ +k
  gi|385806256|ref|YP_005842654.1| 228 ASIDEKYEHLKKLQEESAKIKEEESK 253
                                       *******************9987555 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 ?    2.1  13.6      0.35   1.2e+02     143     251 ..      41     162 ..       5     173 .. 0.42
   2 ?   10.1  15.7    0.0013      0.44     143     256 ..     168     274 ..     156     287 .. 0.65

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.35
                      Exonuc_VII_L 143 aeleeqleelerrlekaikrlleekkqrleklasrlkspeellerkrqrldeleerleralkkq.....lkkkrerl 214
                                       +e +++l e ++++ ++i+++ +ek++ le++ ++lks ++ +++k ++l+ + +r e+ ++k+     l++ ++r+
  gi|385806256|ref|YP_005842654.1|  41 KEEKRNLIESSKSVFEEINKKKDEKNAILEEI-KKLKSEKDEIAKKIEELKLVIKRYEELINKTpngqsLSSLKKRI 116
                                       11133333333333333333334444444444.34555555555555555555555555443333333333333333 PP

                      Exonuc_VII_L 215 eelkerlk...........ekleekkerlkklkerlelleekkerlee 251
                                       e+l+   k           +kl ++ +rl++l +rl+ +++++++l e
  gi|385806256|ref|YP_005842654.1| 117 EQLTW--KqqttpmsideeKKLMQEIDRLTQLYNRLKDARDAESKLME 162
                                       33321..01223333433333444444455555555555555554444 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0013
                      Exonuc_VII_L 143 aeleeqleelerrlekaikrlleekkqrleklasrlkspeellerkrqrldeleerleralkkqlkkkrerleelke 219
                                       + l+ ++++++++++++ik ++e+ k+++++l+++++  ++++++++++++e+++rl++ lk ++++k e+l++l+e
  gi|385806256|ref|YP_005842654.1| 168 TSLKIKFKDIKNSMQEKIK-KFESIKKEISSLREKINGISQKIDQANKEITEISNRLNQ-LKASIDEKYEHLKKLQE 242
                                       4456666777777777775.567778899999999999999999999999999999999.99999999999999996 PP

                      Exonuc_VII_L 220 rl.k...ekleekkerlkklkerlelleekkerleeleekl 256
                                       +  k   e+ ++k+++         +le+kk+ +ee  +k 
  gi|385806256|ref|YP_005842654.1| 243 ESaKikeEESKKKESE---------ILEKKKKIAEEKLKKK 274
                                       6634422222222222.........2333333333333333 PP

>> Leu_zip  Leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1  14.3      0.36   1.2e+02     131     203 ..      19      92 ..       5     116 .. 0.52
   2 ?    8.8  29.3    0.0031         1     111     249 ..     117     256 ..      98     276 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.36
                           Leu_zip 131 LkkeierLkeenekLkerlkelEkqatsaleeksklekalkelqkelgek.kdekenskeiskleeklaelkld 203
                                       Lk+ei+ Lkee   L e lk++ ++  +++e ++ + ++++++++e ++  ++ k+ ++e  ++ +k++elkl 
  gi|385806256|ref|YP_005842654.1|  19 LKQEIATLKEERIGLIEDLKKIKEEKRNLIESSKSVFEEINKKKDEKNAIlEEIKKLKSEKDEIAKKIEELKLV 92 
                                       55566666666666666666665555555555555555555554444433222333333334444444444433 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0031
                           Leu_zip 111 seelkkkkLePlnegGgaeLLkkeierLkeenekLkerlkelEkqatsaleeksklekalkelqkelgek.kdeken 186
                                       ++ + k++ +P+      + L +ei+rL +  ++Lk+  ++ E++++++  e + l+ + k+++++++ek k+ ++ 
  gi|385806256|ref|YP_005842654.1| 117 EQLTWKQQTTPMSIDEEKK-LMQEIDRLTQLYNRLKD-ARDAESKLMEVKAEYTSLKIKFKDIKNSMQEKiKKFESI 191
                                       4444567788888765555.5679***********98.6899***********************999996777779 PP

                           Leu_zip 187 skeiskleeklaelkldlektleek...tasaksleedlastkhelLkvqeqLelaekeLekkfqq 249
                                       +keis+l+ek++ + +++++  +e    +++ ++l++ + +  ++l k+qe+ +  ++e  kk ++
  gi|385806256|ref|YP_005842654.1| 192 KKEISSLREKINGISQKIDQANKEIteiSNRLNQLKASIDEKYEHLKKLQEESAKIKEEESKK-KE 256
                                       9**************999996665511266777888899998889999999866554443333.33 PP

>> Lebercilin  Ciliary protein causing Leber congenital amaurosis disease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5  21.8     0.037        12      48     185 ..       9     146 ..       6     153 .. 0.86
   2 ?    7.0  25.0     0.013       4.2      64     173 ..     162     272 ..     148     282 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.037
                        Lebercilin  48 LskyedteaeLpqllarhneEvrvlrerlRksqekerelekklkekeaellrlkdklkklkkLsedknL.aereeLq 123
                                       L+k  ++  +L q +a  +eE   l e+l+k +e+ r+l ++ k+  +e+++ kd+ ++  +  e k+L  e++e++
  gi|385806256|ref|YP_005842654.1|   9 LEKISEDIYNLKQEIATLKEERIGLIEDLKKIKEEKRNLIESSKSVFEEINKKKDEKNAILE--EIKKLkSEKDEIA 83 
                                       7888888899*****************************************99998877544..33444259***** PP

                        Lebercilin 124 kkLeeleakleekeekikeLerkleleeksfrrqlaaekkktkeaq.eevkalqeeierlkqk 185
                                       kk+eel+  +++ ee i++  +   l++ + r ++ ++k++t  +  +e k+l +ei+rl+q 
  gi|385806256|ref|YP_005842654.1|  84 KKIEELKLVIKRYEELINKTPNGQSLSSLKKRIEQLTWKQQTTPMSiDEEKKLMQEIDRLTQL 146
                                       ********************99999999888888888888877765388999999****9985 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.013
                        Lebercilin  64 rhneEvrvlrerlRksqekerelekklkekeaellrlkdklkklkkLsedknLaereeLqkkLeeleakleekeeki 140
                                       + ++E   l+ ++++ +++ +e  kk  +  +e+ +l++k++  ++  + +  +e  e++++L++l+a ++ek e +
  gi|385806256|ref|YP_005842654.1| 162 EVKAEYTSLKIKFKDIKNSMQEKIKKFESIKKEISSLREKINGISQKID-QANKEITEISNRLNQLKASIDEKYEHL 237
                                       568999999***********************************99995.55579*********************9 PP

                        Lebercilin 141 keLerklel..eeksfrrqlaaekkktkeaqeevk 173
                                       k+L+ +     ee+s +++ +  +kk+k a+e++k
  gi|385806256|ref|YP_005842654.1| 238 KKLQEESAKikEEESKKKESEILEKKKKIAEEKLK 272
                                       99987654311333444445555555555555555 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4  48.6     0.035        12     282     499 ..      13     270 ..       3     279 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.035
                            AAA_13 282 eekqerLekliekveskkselleklkavsdeasensa.feedkeelkaeaealeeqLkglqraleaKrkepfksve. 356
                                        e++ +L++ i+++++++  l+e lk++ +e++  ++ +++  ee+++++++ ++ L+++++ l+  ++e++k++e 
  gi|385806256|ref|YP_005842654.1|  13 SEDIYNLKQEIATLKEERIGLIEDLKKIKEEKRNLIEsSKSVFEEINKKKDEKNAILEEIKK-LKSEKDEIAKKIEe 88 
                                       56677888888888888888888888888877766663555578888888888888777654.44445577776665 PP

                            AAA_13 357 lesvkakie..................................sikklvaeineliakhNekvanleeekeeakkkl 399
                                       l+ v ++ e                                  + kkl++ei +l + +N+  +  ++e + +++k 
  gi|385806256|ref|YP_005842654.1|  89 LKLVIKRYEelinktpngqslsslkkrieqltwkqqttpmsidEEKKLMQEIDRLTQLYNRLKDARDAESKLMEVKA 165
                                       55555555566778888888888888888***********999999******************************9 PP

                            AAA_13 400 elhlv....eeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeLkafGl 472
                                       e+  +    +++++ ++e  kk+++++k+i++l ++++ +++++ ++++ei e+ ++l++ k +++e  + Lk+   
  gi|385806256|ref|YP_005842654.1| 166 EYTSLkikfKDIKNSMQEKIKKFESIKKEISSLREKINGISQKIDQANKEITEISNRLNQLKASIDEKYEHLKKLQE 242
                                       999886667788888888889999***************************************************88 PP

                            AAA_13 473 geleLkfeee.kkgYrivrkggsqaaet 499
                                       +++++k ee  kk  +i+ k+++ a+e+
  gi|385806256|ref|YP_005842654.1| 243 ESAKIKEEESkKKESEILEKKKKIAEEK 270
                                       8888988887788999999877655555 PP

>> Laminin_I  Laminin Domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0  22.7       0.2        68      12     186 ..       7     189 ..       4     190 .. 0.76
   2 ?    9.8  16.9    0.0018      0.59      27     127 ..     166     266 ..     157     278 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.2
                         Laminin_I  12 eapykinanledltkeLqeklskesakkskieilekelesLaqeteeLqkkatqvlakaqkvnaesertlnnakeLa 88 
                                       e+++ki + +++l++e+    +++    ++++  ++e  +L +  ++  ++ ++  ++ + + +e+++  ++  e a
  gi|385806256|ref|YP_005842654.1|   7 ETLEKISEDIYNLKQEIATLKEERIGLIEDLKKIKEEKRNLIESSKSVFEEINKKKDEKNAILEEIKKLKSEKDEIA 83 
                                       57788999999999998887777766666666666777788888888888888888888888888888888888888 PP

                         Laminin_I  89 ekikkla...dnikeilekvatlne.........neealpssklseelaeaqrlLeelrsRdftkqleeaeaelkaA 153
                                       +ki++l+   +  +e+++k+ + ++         ++    +++      e ++l++e+   d  +ql +  ++++ A
  gi|385806256|ref|YP_005842654.1|  84 KKIEELKlviKRYEELINKTPN-GQslsslkkriEQLTWKQQTTPMSIDEEKKLMQEI---DRLTQLYNRLKDARDA 156
                                       8887765111444678887732.22355555555555555555666677889999999...989999999999**** PP

                         Laminin_I 154 qkLLsrvqtllqklqeenkaLkealrdsLaeye 186
                                       +  L +v+  + +l+ + k++k++++++++++e
  gi|385806256|ref|YP_005842654.1| 157 ESKLMEVKAEYTSLKIKFKDIKNSMQEKIKKFE 189
                                       ******************************998 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0018
                         Laminin_I  27 eLqeklskesakkskieilekelesLaqeteeLqkkatqvlakaqkvnaesertlnnakeLaekikkladnikeile 103
                                       e  +  +k +  k  ++ + k+ es+++e+ +L +k +  ++k  + n+e+ +++n+ ++L++ i +  + +k + e
  gi|385806256|ref|YP_005842654.1| 166 EYTSLKIKFKDIKNSMQEKIKKFESIKKEISSLREKINGISQKIDQANKEITEISNRLNQLKASIDEKYEHLKKLQE 242
                                       5555556666667777778889******************************************************* PP

                         Laminin_I 104 kvatlneneealpssklseelaea 127
                                         a++ e+e++  +s++ e+ +++
  gi|385806256|ref|YP_005842654.1| 243 ESAKIKEEESKKKESEILEKKKKI 266
                                       *******99999999999998876 PP

>> Jnk-SapK_ap_N  JNK_SAPK-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5  16.2      0.11        38      36     143 ..       7     119 ..       4     127 .. 0.73
   2 ?   10.9  11.3    0.0012       0.4      51     147 ..     132     223 ..     115     226 .. 0.78
   3 ?    4.4  12.5      0.12        39      89     152 ..     207     268 ..     204     276 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.11
                     Jnk-SapK_ap_N  36 ElLeslasrneeeeaeleelreeleqLeteyerekelrkrae....eeleeiedqweeerkelqekveqleeenrel 108
                                       E+Le++ ++  + ++e+  l+ee+  L +++++ ke++++        +eei ++ ++e++++ e++++l++e++e+
  gi|385806256|ref|YP_005842654.1|   7 ETLEKISEDIYNLKQEIATLKEERIGLIEDLKKIKEEKRNLIesskSVFEEINKK-KDEKNAILEEIKKLKSEKDEI 82 
                                       999***9*999***********987777766666666655441111444444443.56777899999********** PP

                     Jnk-SapK_ap_N 109 elkaknaadqlsrlee..keaelkkeysklheretel 143
                                        +k+++++  ++r ee  +++   ++ s+l++r ++l
  gi|385806256|ref|YP_005842654.1|  83 AKKIEELKLVIKRYEEliNKTPNGQSLSSLKKRIEQL 119
                                       ************9999333445556666777777766 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0012
                     Jnk-SapK_ap_N  51 eleelreeleqLeteyerekelrkraeeeleeiedqweeerkelqekveqleeenrelelkaknaadqlsrleekea 127
                                       e+++l +e+++L++ y+r k + ++ae +l+e+  ++ + + ++++  ++++e+++++e    ++++++s+l ek +
  gi|385806256|ref|YP_005842654.1| 132 EEKKLMQEIDRLTQLYNRLK-DARDAESKLMEVKAEYTSLKIKFKDIKNSMQEKIKKFE----SIKKEISSLREKIN 203
                                       6778999*****99888888.56677888999999988888888888888888888888....78888888888888 PP

                     Jnk-SapK_ap_N 128 elkkeysklheretellkkl 147
                                         +++ ++++++ te+ ++l
  gi|385806256|ref|YP_005842654.1| 204 GISQKIDQANKEITEISNRL 223
                                       88777777777777766655 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.12
                     Jnk-SapK_ap_N  89 eerkelqekveqleeenrelelkaknaadqlsrleekeaelkkeysklheretellkklkelve 152
                                       ++  + ++++++  ++ ++l++ +++  ++l++l+e++a+ k+e+sk+  +e+e+l+k k+  e
  gi|385806256|ref|YP_005842654.1| 207 QKIDQANKEITEISNRLNQLKASIDEKYEHLKKLQEESAKIKEEESKK--KESEILEKKKKIAE 268
                                       5556778888888888888888888888*************9999996..67777777776655 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8  16.6      0.29        96     233     344 ..       9     119 ..       3     130 .. 0.73
   2 ?    8.8  21.8    0.0022      0.72     226     324 ..     160     254 ..     122     268 .. 0.59

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.29
                             IFT57 233 kksieeslpetksqlkklhed...isktlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegvseltre 306
                                        ++i+e++ ++k++++ l+e+   + + l+ki++  ++l ++ ++  +e +++++e +++ e++k+l+++  e    
  gi|385806256|ref|YP_005842654.1|   9 LEKISEDIYNLKQEIATLKEErigLIEDLKKIKEEKRNLIESSKSVFEEINKKKDEKNAILEEIKKLKSEKDEI--- 82 
                                       46788888888888888888833345666777777777777777777777777777777777777766554444... PP

                             IFT57 307 laeiseelekvkqemeergssmtDgsplvkikkaltkl 344
                                        a+  eel+ v ++ ee  ++  +g++l ++kk +++l
  gi|385806256|ref|YP_005842654.1|  83 -AKKIEELKLVIKRYEELINKTPNGQSLSSLKKRIEQL 119
                                       .4445778888899999999999***********9998 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0022
                             IFT57 226 leqmkkhkksieeslpetksqlkklhedisktlekiesrEkyl...nsqleellqeyreaqeelsevkekykqlseg 299
                                       l        +++++++++k ++k++++ +++ ++k es  k +    ++++   q+  +a++e++e++++++ql+++
  gi|385806256|ref|YP_005842654.1| 160 LM-------EVKAEYTSLKIKFKDIKNSMQEKIKKFESIKKEIsslREKINGISQKIDQANKEITEISNRLNQLKAS 229
                                       33.......34444444444444444444444444444443331114555666667777777777777777777777 PP

                             IFT57 300 vseltrelaeiseelekvkqemeer 324
                                       + e+ ++l++++ee  k+k+e  ++
  gi|385806256|ref|YP_005842654.1| 230 IDEKYEHLKKLQEESAKIKEEESKK 254
                                       7777777777777777777665444 PP

>> TACC_C  Transforming acidic coiled-coil-containing protein (TACC), C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   3.2      0.77   2.6e+02      59     106 ..      12      59 ..       3      68 .. 0.61
   2 ?    8.5   6.4    0.0047       1.6       9      54 ..      57     102 ..      49     108 .. 0.75
   3 ?    2.5  33.0      0.32   1.1e+02      22     160 ..     114     253 ..     105     274 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.77
                            TACC_C  59 kqkqkelakkeiqkvleekeqlladlnsveksfsdlfkryekqkevle 106
                                         ++  + k+ei+ ++ee+  l++dl++++ +  +l++  +   e ++
  gi|385806256|ref|YP_005842654.1|  12 ISEDIYNLKQEIATLKEERIGLIEDLKKIKEEKRNLIESSKSVFEEIN 59 
                                       444445667777777777777777777777777777665554444444 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0047
                            TACC_C   9 alekvkeeveekeeeiqelkkkveelkkenqemkkivaefektiaq 54 
                                        ++k k e +   eei++lk++ +e  k+ +e+k +++++e+ i++
  gi|385806256|ref|YP_005842654.1|  57 EINKKKDEKNAILEEIKKLKSEKDEIAKKIEELKLVIKRYEELINK 102
                                       4455555555566788999999999999999999999999999876 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.32
                            TACC_C  22 eeiqelkkkveelkkenqemkkivaefektiaqlieekqkqkelakkeiqkvleekeqlladlnsveksfsdlfkry 98 
                                       ++i++l+ k +   +   e kk+++e ++  +ql +   k+++ a+ ++++v++e   l+ ++++++ s+++ +k++
  gi|385806256|ref|YP_005842654.1| 114 KRIEQLTWKQQTTPMSIDEEKKLMQEIDRL-TQLYNRL-KDARDAESKLMEVKAEYTSLKIKFKDIKNSMQEKIKKF 188
                                       455566666666666667778999999885.5555555.77788999****************************** PP

                            TACC_C  99 ekqkevlegykkneeslkkcaeeylarvkkeeqRYqaLkahaeek...LekAneeiaqvrskaka 160
                                       e  k+ ++ ++++ +   +++++  + +++  +R ++Lka  +ek   L+k +ee a+++++ ++
  gi|385806256|ref|YP_005842654.1| 189 ESIKKEISSLREKINGISQKIDQANKEITEISNRLNQLKASIDEKyehLKKLQEESAKIKEEESK 253
                                       *****************************************999844456666777766644322 PP

>> SpecificRecomb  Site-specific recombinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   1.9      0.66   2.2e+02     193     260 ..      71     151 ..       7     167 .. 0.49
   2 ?    6.5   3.4    0.0065       2.2     152     230 ..     160     238 ..     110     248 .. 0.54

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.66
                    SpecificRecomb 193 ayeaaledeeeaeedlkhlr................vlldqcreavdrvrkhleenGvsvslvfllerlrqrleRle 253
                                       ++++ +++++e +++ ++l+                + l+  ++ +++++ + +++ +s++   + ++l q+++Rl+
  gi|385806256|ref|YP_005842654.1|  71 EIKKLKSEKDEIAKKIEELKlvikryeelinktpngQSLSSLKKRIEQLTWKQQTTPMSID---EEKKLMQEIDRLT 144
                                       2222222222222222222233333334444444444444444555555555555555554...2344556666666 PP

                    SpecificRecomb 254 eLldlll 260
                                       +L + l+
  gi|385806256|ref|YP_005842654.1| 145 QLYNRLK 151
                                       6666664 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0065
                    SpecificRecomb 152 vlsvqiaalglepelrrrlpeleeeespFlalqrelealleayeaaledeeeaeedlkhlrvlldqcreavdrvrkh 228
                                       ++ v+   + l+ ++ +  ++++e+ + F ++++e+++l+e+++   ++ ++a+++ ++++  l+q ++ +d+ ++h
  gi|385806256|ref|YP_005842654.1| 160 LMEVKAEYTSLKIKFKDIKNSMQEKIKKFESIKKEISSLREKINGISQKIDQANKEITEISNRLNQLKASIDEKYEH 236
                                       22222333333444444445555555555555555555555555555555555555555555555555555555555 PP

                    SpecificRecomb 229 le 230
                                       l+
  gi|385806256|ref|YP_005842654.1| 237 LK 238
                                       44 PP

>> Mod_r  Modifier of rudimentary (Mod(r)) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9  16.3      0.08        27       6      92 ..       7      97 ..       6     125 .. 0.78
   2 ?    3.6  11.7       0.2        67      19      92 ..     134     210 ..      93     212 .. 0.76
   3 ?    7.7  10.7     0.011       3.7      16      83 ..     183     250 ..     180     254 .. 0.77
   4 ?    1.9   3.5      0.64   2.1e+02      30      57 ..     251     278 ..     247     282 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.08
                             Mod_r  6 eeLqelledeeklealvktl.pevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqe 83
                                      e L+++ ed   l++ + tl +e   l e+++++ +e ++l e+  s  +e++++++e ++ lee+k+l++e +e  ++
  gi|385806256|ref|YP_005842654.1|  7 ETLEKISEDIYNLKQEIATLkEERIGLIEDLKKIKEEKRNLIESSKSVFEEINKKKDEKNAILEEIKKLKSEKDEIAKK 85
                                      5688888888888888888878889999999999999999999999999999999999999999999999999988888 PP

                             Mod_r 84 ldell...qkfs 92
                                       +el    +++ 
  gi|385806256|ref|YP_005842654.1| 86 IEELKlviKRYE 97
                                      887765554443 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.2
                             Mod_r  19 ealvktlpevkqlkeekeellaeneslaeknlslep...eleelrselqekleelkelekefeekeqeldellqkfs 92 
                                       ++l+++++++ ql ++++++++++ +l e + +      ++++ ++++qek++++++++ke   + ++ + ++qk +
  gi|385806256|ref|YP_005842654.1| 134 KKLMQEIDRLTQLYNRLKDARDAESKLMEVKAEYTSlkiKFKDIKNSMQEKIKKFESIKKEISSLREKINGISQKID 210
                                       34556667777777777777777777776555443344488888888888888888888888888888888887765 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.011
                             Mod_r  16 eklealvktl.pevkqlkeekeellaeneslaeknlsl.epeleelrselqekleelkelekefeekeqe 83 
                                       ek++++  ++ +e+ +l+e+   +  + ++ a+k + +  ++l++l++++ ek+e+lk+l++e  + ++e
  gi|385806256|ref|YP_005842654.1| 183 EKIKKFE-SIkKEISSLREKINGI-SQKIDQANKEITEiSNRLNQLKASIDEKYEHLKKLQEESAKIKEE 250
                                       4555554.4447788888888888.6667777777777799********************998887765 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.64
                             Mod_r  30 qlkeekeellaeneslaeknlslepele 57 
                                       + k++ +e+l++ +++ae++l+++++l+
  gi|385806256|ref|YP_005842654.1| 251 ESKKKESEILEKKKKIAEEKLKKKERLT 278
                                       5678889999999**********99885 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8  11.6      0.35   1.2e+02       5      77 ..      18      90 ..       4      91 .. 0.68
   2 ?    2.4  10.5      0.47   1.6e+02       5      74 ..      53     124 ..      49     139 .. 0.71
   3 ?    2.0   7.1      0.63   2.1e+02      34      88 ..     133     189 ..     107     195 .. 0.33
   4 ?   11.1  17.3   0.00091       0.3      13     110 ..     149     246 ..     131     252 .. 0.87
   5 ?    5.2  22.4     0.063        21       4     112 ..     168     277 ..     166     284 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.35
                        TPR_MLP1_2  5 sleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelk 77
                                      +l++ei++lkee   + ++l+k++e+ ++  e+ k   +   +   ++++ ++e+++l++e +e+ ++i+elk
  gi|385806256|ref|YP_005842654.1| 18 NLKQEIATLKEERIGLIEDLKKIKEEKRNLIESSKSVFEEINKKKDEKNAILEEIKKLKSEKDEIAKKIEELK 90
                                      5666777777777777777777777777777777777777777777777777777777777777777777665 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.47
                        TPR_MLP1_2   5 sleeeikslkeekeeaeaklqklq...edlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeia 74 
                                       s+ eei+++k+ek++  ++++kl+   +++ k+ e++k   ++Ye el+++  + ++l++l++++++l+ + +
  gi|385806256|ref|YP_005842654.1|  53 SVFEEINKKKDEKNAILEEIKKLKsekDEIAKKIEELKLVIKRYE-ELINKTPNGQSLSSLKKRIEQLTWKQQ 124
                                       566788888888888888888776111456666666677778887.788889999999999999999876655 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.63
                        TPR_MLP1_2  34 qaeiakeaqq...kYerelvkhaedvkelqalreelnelkaeiaelkaeaesakaele 88 
                                       ++++++e  +    Y   l    ++  +l ++++e+ +lk + +++k++ ++  +++e
  gi|385806256|ref|YP_005842654.1| 133 EKKLMQEIDRltqLYN-RLKDARDAESKLMEVKAEYTSLKIKFKDIKNSMQEKIKKFE 189
                                       3333333322000111.11111222223333333333333333333333333322222 PP

  == domain 4  score: 11.1 bits;  conditional E-value: 0.00091
                        TPR_MLP1_2  13 lkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakaelee 89 
                                        ++++ +ae+kl +++ + ++ +   k+ +++ ++ + k ++  ke+++lre++n + ++i ++++e  + ++ l++
  gi|385806256|ref|YP_005842654.1| 149 RLKDARDAESKLMEVKAEYTSLKIKFKDIKNSMQEKIKKFESIKKEISSLREKINGISQKIDQANKEITEISNRLNQ 225
                                       456789999**********************99999999999999******************************** PP

                        TPR_MLP1_2  90 seesweeqkeelekelselek 110
                                        ++s++e+ e+l+k  +e+ k
  gi|385806256|ref|YP_005842654.1| 226 LKASIDEKYEHLKKLQEESAK 246
                                       ********9999987777655 PP

  == domain 5  score: 5.2 bits;  conditional E-value: 0.063
                        TPR_MLP1_2   4 ksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaea 80 
                                       +sl+ + k++k++ +e  +k++++++++ + +e  +   qk  +   +  e ++ l++l++ ++e  + +++l++e 
  gi|385806256|ref|YP_005842654.1| 168 TSLKIKFKDIKNSMQEKIKKFESIKKEISSLREKINGISQKIDQANKEITEISNRLNQLKASIDEKYEHLKKLQEES 244
                                       67788889999999999********************************************************9998 PP

                        TPR_MLP1_2  81 esakae.leeseesweeqkeelekelselekri 112
                                        + k+e  +++e+++ e+k+++ +e+ + ++r+
  gi|385806256|ref|YP_005842654.1| 245 AKIKEEeSKKKESEILEKKKKIAEEKLKKKERL 277
                                       887765166777789999999999999888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      4250  (0.237046); expected 358.6 (0.02)
Passed bias filter:                      758  (0.0422779); expected 358.6 (0.02)
Passed Vit filter:                       275  (0.0153383); expected 17.9 (0.001)
Passed Fwd filter:                       182  (0.0101512); 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: 2.51u 0.41s 00:00:02.92 Elapsed: 00:00:00.70
# Mc/sec: 1260.48
//
Query:       gi|385806257|ref|YP_005842655.1|  [L=443]
Description: glutamyl-tRNA(Gln) amidotransferase subunit D [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-58  197.4   0.0    3.2e-58  196.4   0.0    1.5  2  Asparaginase    Asparaginase, N-terminal
    1.5e-31  108.9   0.0    2.7e-31  108.1   0.0    1.4  1  Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
    1.4e-16   59.5   1.7    2.7e-16   58.6   1.7    1.5  1  GatD_N          GatD N-terminal domain
  ------ inclusion threshold ------
      0.029   14.0   0.0      0.058   13.0   0.0    1.4  1  Pox_VP8_L4R     Poxvirus nucleic acid binding protein VP8/L4R


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 !  196.4   0.0   7.1e-62   3.2e-58       2     187 ..      90     284 ..      89     288 .. 0.96
   2 ?   -3.9   0.0       1.8   8.3e+03      81      94 ..     386     399 ..     372     407 .. 0.79

  Alignments for each domain:
  == domain 1  score: 196.4 bits;  conditional E-value: 7.1e-62
                                       EEEEEEESGGGEEECTTS--CCEES-HHHHHCCTTTCCCCSEEEEEEEEEE-GGG--HHHHHHHHHHHHHHC.CT.- CS
                      Asparaginase   2 vlvlatGGTiasekdesggalapalsaeellealpelekiaeleseqlanidSsnmtpadwlklaeaieeal.ee.y 76 
                                       +++++tGGTias+ d+++g ++p l+a+el+e++pel+ ia+++se l++i S+nm+p+ w+k+ae+++e l +e  
  gi|385806257|ref|YP_005842655.1|  90 IHIISTGGTIASKIDYQTGGVKPVLTADELIEMIPELNSIAKFKSEILMSIFSENMNPKYWEKIAERVAEVLvKEpD 166
                                       89**********************************************************************97779 PP

                                       SEEEEE--STTHHHHHHHHHHHEES.SSEEEEE--SS-TTSTT-SHHHHHHHHHHHHHCGGTTSECEEEETTE.... CS
                      Asparaginase  77 dgfVvlhGTDTlaytAsaLslmlknldkpvvltGsqrplselrsDgpeNlldAllvaasseriagvlvvfngk.... 149
                                        g++++hGTDTlayt+saLs++l+n++ p+ l+Gsqr++++++sD+p Nl++A + a+s+  i + +vv++g+    
  gi|385806257|ref|YP_005842655.1| 167 TGVIITHGTDTLAYTSSALSFALRNIGSPIALVGSQRSSDRPSSDSPFNLIAASIYATSD--ICEPAVVMHGEtsds 241
                                       9********************************************************987..*************** PP

                                       ...EEETTTEEE-BSSSSS-EEETTT--SEEE..ETTEEEESE CS
                      Asparaginase 150 ...llranrvtKvhtssldaFespnlgplaev..egskvkvnk 187
                                           +r++rv+K+hts++daF+s++  pla++  +++k++v +
  gi|385806257|ref|YP_005842655.1| 242 yalAHRGTRVRKMHTSRRDAFQSISSLPLAKIfpAEKKIEVIR 284
                                       ******************************9977677777665 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 1.8
                                       EE--STTHHHHHHH CS
                      Asparaginase  81 vlhGTDTlaytAsa 94 
                                       +++G   l++tA++
  gi|385806257|ref|YP_005842655.1| 386 IISGENMLSETAFV 399
                                       88999999999986 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 !  108.1   0.0   6.1e-35   2.7e-31       1     114 []     305     418 ..     305     418 .. 0.99

  Alignments for each domain:
  == domain 1  score: 108.1 bits;  conditional E-value: 6.1e-35
                                       -EEEEE--TT--HHHHHHHHHTT--EEEEEEBTTTB--HHHHHHHHHHHTTT-EEEEEESSSBS-----H.....HH CS
                    Asparaginase_C   1 rVvvlklhpgmdtkvlkallkkgakGvvlegtGvGnlpsallealkeakargivvvatsqcpsgsvsnseyeagkel 77 
                                       +V +lk +pgm + +++ l +kg+kG+v+eg G G++++++++ +k++++rg++vv+tsqc++g+v++++y++g+ l
  gi|385806257|ref|YP_005842655.1| 305 NVSLLKYYPGMPGWIFEILAEKGIKGIVIEGSGLGHVSTEIIDSIKNVIDRGTIVVMTSQCIFGRVNMNVYSTGRLL 381
                                       799************************************************************************** PP

                                       HHHTEEE-TT--HHHHHHHHHHHCTT---HHHHHHHH CS
                    Asparaginase_C  78 erlgvisaddmtpeaarikLmlllgkgldpaevrklf 114
                                       ++ g+is+++m  e+a +kL +llg+ +d +e+ +lf
  gi|385806257|ref|YP_005842655.1| 382 KKIGIISGENMLSETAFVKLSWLLGNFKDEEEITRLF 418
                                       ***********************************98 PP

>> GatD_N  GatD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.6   1.7   6.1e-20   2.7e-16       2      55 .]       9      63 ..       8      63 .. 0.96

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 6.1e-20
                                      -TT-EEEEE-SS.-EEEEEE----TTS-SSEEEEEETTS-EEEEE-TT-.---EE CS
                            GatD_N  2 evGDlikvekkg.reyeGilmPrselsdddiivlKLdnGYNiGikieeiekiell 55
                                      ++G ++++++k+   +eG++  r+e+ d+ +i+lKL+nGYNiGi+i++ie++ell
  gi|385806257|ref|YP_005842655.1|  9 SPGIYVRIKTKDgAIIEGLIVQRYEIFDPGFITLKLKNGYNIGISIKKIESVELL 63
                                      57889*****999****************************************97 PP

>> Pox_VP8_L4R  Poxvirus nucleic acid binding protein VP8/L4R
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.3e-05     0.058     100     148 ..     262     315 ..     237     320 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.3e-05
                       Pox_VP8_L4R 100 frk.gsaPlllvfesrkkvdiykedk....keeesssyakieanvalvekyanl 148
                                       f++ +s Pl+ +f + kk++++++d     k+ +   y+k  +nv+l++ y ++
  gi|385806257|ref|YP_005842655.1| 262 FQSiSSLPLAKIFPAEKKIEVIRKDAkicsKSGNLEAYTKFSENVSLLKYYPGM 315
                                       4441689*****************9833222333457************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 2707.96
//
Query:       gi|385806258|ref|YP_005842656.1|  [L=643]
Description: glutamyl-tRNA(Gln) amidotransferase subunit E [Fervidicoccus fontis Kam940]
Scores for complete 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-69  234.7   0.1    1.7e-69  234.2   0.1    1.2  1  GatB_N        GatB/GatE catalytic domain
    1.6e-22   80.0   2.7    1.6e-22   80.0   2.7    2.7  3  GatB_Yqey     GatB domain
    9.1e-12   45.1   0.3    3.7e-11   43.1   0.0    2.1  2  GAD           GAD domain
    0.00053   20.1   0.7    0.00053   20.1   0.7    2.2  2  YqeY          Yqey-like protein
     0.0038   17.1   1.5      0.015   15.2   0.1    2.4  3  DUF4435       Protein of unknown function (DUF4435)
  ------ inclusion threshold ------
       0.11   11.9   0.0        0.2   11.0   0.0    1.4  1  Beta_protein  Beta protein
       0.27   11.3   2.6        3.7    7.6   0.2    2.9  3  EcoEI_R_C     EcoEI R protein C-terminal


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 !  234.2   0.1   6.7e-73   1.7e-69       2     272 ..      16     453 ..      15     454 .. 0.96

  Alignments for each domain:
  == domain 1  score: 234.2 bits;  conditional E-value: 6.7e-73
                                       EEEEEEEEEB--SB-SSSSSBSSSSCE.........S.TTSS--TTTTTS........................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx.........x.xxxxxxxxxxxx........................... RF
                            GatB_N   2 viGlEiHaqlktksKlFssasteeege.........e.pnsevsevdlal........................... 41 
                                       ++GlEiH+qlkt++KlF++++ ++e+          + ++se++evd+a+                           
  gi|385806258|ref|YP_005842656.1|  16 KVGLEIHQQLKTERKLFCNCPISSEEGreelferslRpTTSEFGEVDIAAyfewkkgrryryhaphpssclveadee 92 
                                       89*******************874222466788888548999********************************999 PP

                                       TT..--.EEHHHHHHHHHHHHHTTEEE-SEE-EEEEE-TCTTCTTSEEEEESSS.SE.EEEEEEE.TEEEEEEEEEE CS
                                       xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx.xxxxxxxxxxx RF
                            GatB_N  42 PGtlPv.lnkeavelaikaalalnceiaeeskfdRKnyfypdlpkgyQitqkeepla.keGslel.ekkvrierihl 115
                                       P   P+ +n+ea+e++i +++al++   +e++++RK+++++++++g+Q+t+    l+  +G++e+  k++ri++i+l
  gi|385806258|ref|YP_005842656.1|  93 P---PHeINREALEVVIGISKALGSIPVDEVHVMRKIVIDGSNTSGFQRTM----LVsIGGRIEVeGKSYRIQTICL 162
                                       8...999********************************************....554999**9966788******* PP

                                       EE---EEEEEETTEEEEETTSTT-EEEEEEE-STB-SHHHHHHHHHHHHHHHHHHTSB--SGGGTTEEEEEEEEECT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N 116 EeDaaksvheekeeslvdlnRaGvpLiEivtepdlrspeearavveklrellralgvsdgnmeeGslRcDvNvSvre 192
                                       EeDaa++ ++e + s + ++R+G+pLiEi+t+pd+++peea++v+  +++llr  g++++++  G++R+D+N+S++ 
  gi|385806258|ref|YP_005842656.1| 163 EEDAARKGEDEGNISHYIIDRLGIPLIEIATAPDIETPEEAQKVALYIGQLLRLSGKVKRGI--GTIRQDLNISIEG 237
                                       ************9*************************************************..************4 PP

                                       SETTSSS.--EEEEEE-SHHHHHHHHHHHHHHHHHHH........................................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................................ RF
                            GatB_N 193 eekgeeegtrvEiKnlnslksiekaieyeierqiell........................................ 229
                                              g++vEiK++++lk ++k++e e+ rq++ll                                        
  gi|385806258|ref|YP_005842656.1| 238 -------GEKVEIKGVQELKILAKTVELEAMRQLRLLeireelkkrglseqdvklspidvtdilkrsqskivranls 307
                                       .......49******************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                            GatB_N 230 ............................................................................. 229
                                                                                                                    
  gi|385806258|ref|YP_005842656.1| 308 kpkgkalaqilhrfkgilgtevqpnrrfgteladyarfygdvrglfhsdelpnygiskeevemiynalgadrekdaf 384
                                       ***************************************************************************** PP

                                       .............................-EEEEEETTTTEEEEECC----...-EEE-TTS--EE--HHHH CS
                                       .............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N 230 .............................qeTrkfdedkgetvslRskeeaedYryfpepdlppleiseeli 272
                                                                    +eTr + +d g+t+ lR+++ a   r++pe+d+pp+ i+ee++
  gi|385806258|ref|YP_005842656.1| 385 vlivdeeskalksmeavinrvkyafkgipKETRVAMPD-GTTKFLRPQPGA--ARMYPETDIPPIIITEEIM 453
                                       **************************************.**********77..5***************987 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.2     0.029        75      10      55 ..     255     300 ..     249     322 .. 0.76
   2 ?   -2.5   0.1       1.6   4.1e+03      57     105 ..     363     412 ..     360     420 .. 0.76
   3 !   80.0   2.7   6.2e-26   1.6e-22       1     148 []     492     636 ..     492     636 .. 0.97

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.029
                                       SS.HHHHHHHHHTCHHHHHHHHTXXTTCSSTTHHHHHHHHHHHHTT CS
                         GatB_Yqey  10 gadaklaanwllnellgelnkegleieelkltpeqlaellkliaeg 55 
                                       + + + + +  l e+ +el+k+gl+ +++kl+p +++++lk+ +++
  gi|385806258|ref|YP_005842656.1| 255 TVELEAMRQLRLLEIREELKKRGLSEQDVKLSPIDVTDILKRSQSK 300
                                       5556666677788999************************984443 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.6
                                       SGHHHHHHHHHHHHHH.TXXHHHHHHHCTXXXXXXSSXHHHHHHHHHHTX CS
                         GatB_Yqey  57 Iskkiakevleellee.gkspeeiieekgLkqisdeeeleklveeviaen 105
                                       Isk+ ++++ ++l ++ +k++  +i  ++ k++++ e++ + v+ +++  
  gi|385806258|ref|YP_005842656.1| 363 ISKEEVEMIYNALGADrEKDAFVLIVDEESKALKSMEAVINRVKYAFKGI 412
                                       78888888888887777888888888888888888888888887777665 PP

  == domain 3  score: 80.0 bits;  conditional E-value: 6.2e-26
                                       HHHHHHHHHSS...HHHHHHHHHTCHHHHHHHHTXXTTCSSTTHHHHHHHHHHHHTTSSGHHHHHHHHHHHHHH.TX CS
                         GatB_Yqey   1 dffeevvkegad..aklaanwllnellgelnkegleieelkltpeqlaellkliaegkIskkiakevleellee.gk 74 
                                       dff+e+v+e +   ++++++ ++  ++  l++egl++e   ++++++ e++ l+a+  I+ + ++e+l++l ++ ++
  gi|385806258|ref|YP_005842656.1| 492 DFFDELVEEFKGsiEPTTIASIMLVTMPALKREGLNVEL--IPERSIREIFSLFARRMITREGIEELLKQLSKKpEE 566
                                       79******995567999999*******************..9*********************************** PP

                                       XHHHHHHHCTXXXXXXSSXHHHHHHHHHHTXHHHHHHHTTXXTTSTHHHHHHHHHTTSSXSXHHHHHHHHHHHS CS
                         GatB_Yqey  75 speeiieekgLkqisdeeeleklveeviaenpkavedyksgkekalkflvGqvMkktkGkadpklvnellkekL 148
                                       +pe+i +e gL  + + ee++k++e+v++en   ++ ++++ eka ++l+G+ M+ ++Gka + lv++l++ekL
  gi|385806258|ref|YP_005842656.1| 567 KPEKIAKELGLLSLGE-EEVRKIIEKVVEEN---MNVIREKGEKAEGILMGKAMQILRGKAPGSLVSKLIREKL 636
                                       **************98.**************...999***********************************98 PP

>> GAD  GAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   0.0   1.4e-14   3.7e-11       4      95 .]     305     398 ..     302     398 .. 0.92
   2 ?   -1.3   0.1       1.1   2.7e+03      61      73 ..     580     592 ..     547     611 .. 0.61

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 1.4e-14
                                       HHHS.TEEEEEEEETTG-TTTSHHHHHHHHHHHHHTTHSHCEEEEESSGGEETTTCCC.S-HHHHHHHHHHCT--TT CS
                               GAD   4 alks.ggsvkalrvpggaaklsrkeideleefakelgakglawikvegegltgpiakf.lteeevkklleavgaeeg 78 
                                       +l++ +g+  a ++ + ++++ + e+++ ++f++el+++++++  v+g +++++++ + +++eev+ +++a+ga+ +
  gi|385806258|ref|YP_005842656.1| 305 NLSKpKGKALAQILHR-FKGILGTEVQPNRRFGTELADYARFYGDVRGLFHSDELPNYgISKEEVEMIYNALGADRE 380
                                       5566678888888889.7********************************************************998 PP

                                       .EEEEEEEEEHHHHHHHH CS
                               GAD  79 .DillfvAdkkktvnkal 95 
                                        D++++++d+++++ k++
  gi|385806258|ref|YP_005842656.1| 381 kDAFVLIVDEESKALKSM 398
                                       8************99986 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.1
                                       S-HHHHHHHHHHC CS
                               GAD  61 lteeevkklleav 73 
                                       l eeev+k++e+v
  gi|385806258|ref|YP_005842656.1| 580 LGEEEVRKIIEKV 592
                                       3444444444444 PP

>> YqeY  Yqey-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.8       1.6   4.2e+03      16      53 ..     257     297 ..     239     301 .. 0.68
   2 !   20.1   0.7   2.1e-07   0.00053      91     143 .]     580     636 ..     561     636 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.6
                                       -HHHHHHHHH..HHHHHHHHHHHTTS.S--HHHHHHHHHHH CS
                              YqeY  16 dkerlstlrl..lkaaikqeevderk.elsdeevlkvlake 53 
                                       + e +  lrl  ++ ++k++  +e+  +ls  +v+++l++ 
  gi|385806258|ref|YP_005842656.1| 257 ELEAMRQLRLleIREELKKRGLSEQDvKLSPIDVTDILKRS 297
                                       45555566652245778888888877788888888888875 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 2.1e-07
                                       --HHHHHHHHHHHHHHT....T--BGGGHHHHHHHHHHHHTTTS-HHHHHHHHHHH- CS
                              YqeY  91 lseeeiealvkeaiaev....gaesmkdmGkvmkalkpkvkGkaDgkkvsalvkekL 143
                                       l eee++++++++++e      +++ k+ G +m+++++ ++Gka g+ vs+l++ekL
  gi|385806258|ref|YP_005842656.1| 580 LGEEEVRKIIEKVVEENmnviREKGEKAEGILMGKAMQILRGKAPGSLVSKLIREKL 636
                                       889999999999999864444788******************************997 PP

>> DUF4435  Protein of unknown function (DUF4435)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0         3   7.6e+03     148     169 ..     275     296 ..     258     318 .. 0.50
   2 ?    0.1   0.0      0.25   6.3e+02      35      69 ..     364     398 ..     338     409 .. 0.76
   3 !   15.2   0.1   5.9e-06     0.015      88     201 ..     470     581 ..     469     640 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3
                           DUF4435 148 klslslqevdlssi.ekitleei 169
                                       k++ls q+v+ls i ++ +  ++
  gi|385806258|ref|YP_005842656.1| 275 KRGLSEQDVKLSPIdVT-DILKR 296
                                       34455555555333211.22222 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.25
                           DUF4435  35 gkkkvlkivkllekeelgrdvlaiVDrDfdylkqn 69 
                                       +k++v++i+++l  ++ ++  + iVD +   lk+ 
  gi|385806258|ref|YP_005842656.1| 364 SKEEVEMIYNALGADREKDAFVLIVDEESKALKSM 398
                                       699*********77778888999999998777764 PP

  == domain 3  score: 15.2 bits;  conditional E-value: 5.9e-06
                           DUF4435  88 flcyaesLhkvlvevltlndrdyktifdlfeqfleelseiiiplflwnvlfyrkklekdiklslsl.qevdlssiek 163
                                       +++++  L ++l e + +n+      fd f +  ee++ +i p ++ +++ +    +k   l ++l  e  +++i++
  gi|385806258|ref|YP_005842656.1| 470 YYIKELGLSRALAEQMVMNES-----FDFFDELVEEFKGSIEPTTIASIMLVTMPALKREGLNVELiPERSIREIFS 541
                                       8999999********999997.....9*******************9999999998885555555555556666666 PP

                           DUF4435 164 itleeikvenkieelkeefpdkieeekeeikkelrkl..n 201
                                           ++  ++ ieel +++++k ee+ e+i+kel+ l  +
  gi|385806258|ref|YP_005842656.1| 542 LFARRMITREGIEELLKQLSKKPEEKPEKIAKELGLLslG 581
                                       666677677*************************987554 PP

>> Beta_protein  Beta protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0     8e-05       0.2     131     190 ..     353     416 ..     327     425 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8e-05
                      Beta_protein 131 ldqddf.sae.iteeierllaalgleese..ldlilDlgavlkgssdaaeaalrellallpead 190
                                       +++d++ ++   +ee+e + +alg+++++  ++li+D +++  +s++a++++++ +++ +p++ 
  gi|385806258|ref|YP_005842656.1| 353 FHSDELpNYGiSKEEVEMIYNALGADREKdaFVLIVDEESKALKSMEAVINRVKYAFKGIPKET 416
                                       5678888888669***********9999999********9999999*****9999999998765 PP

>> EcoEI_R_C  EcoEI R protein C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.2       1.5   3.9e+03      23      54 ..     254     283 ..     243     297 .. 0.69
   2 ?    2.4   0.0     0.059   1.5e+02      45     104 ..     359     416 ..     355     454 .. 0.82
   3 ?    7.6   0.2    0.0015       3.7      17      61 ..     535     578 ..     530     600 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.5
                         EcoEI_R_C  23 iiwsdreltkellkeLeekLkepppgitpeal 54 
                                       +    + +++  l e++e+Lk++  g++++++
  gi|385806258|ref|YP_005842656.1| 254 KTVELEAMRQLRLLEIREELKKR--GLSEQDV 283
                                       33335566677777888888876..8888776 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.059
                         EcoEI_R_C  45 pppgitpealweayellek.kvspqltdlidlirkiagldeeletrserverafkrwikek 104
                                       p++gi++e+++  y+ l + ++      ++ ++ +     + +e   +rv+ afk + ke 
  gi|385806258|ref|YP_005842656.1| 359 PNYGISKEEVEMIYNALGAdRE---KDAFVLIVDEESKALKSMEAVINRVKYAFKGIPKET 416
                                       688***********99977554...448999999999999999999999999999887665 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0015
                         EcoEI_R_C  17 sidaLqiiwsdreltkellkeLeekLkepppgitpealweayell 61 
                                       si ++  ++ +r +t+e ++eL ++L+++ p  +pe++++++ ll
  gi|385806258|ref|YP_005842656.1| 535 SIREIFSLFARRMITREGIEELLKQLSKK-PEEKPEKIAKELGLL 578
                                       45555555669***************986.788999999998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (643 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       865  (0.0482459); expected 358.6 (0.02)
Passed bias filter:                      652  (0.0363657); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.74u 0.37s 00:00:01.10 Elapsed: 00:00:00.54
# Mc/sec: 3614.26
//
Query:       gi|385806259|ref|YP_005842657.1|  [L=424]
Description: Pre-mRNA processing ribonucleoprotein, binding region [Fervidicoccus fontis Kam940]
Scores for complete 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-72  241.7   0.0    9.7e-72  241.2   0.0    1.2  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 !  241.2   0.0   5.4e-76   9.7e-72       2     229 ..     150     375 ..     149     376 .. 0.94

  Alignments for each domain:
  == domain 1  score: 241.2 bits;  conditional E-value: 5.4e-76
                                       HHHHHHHHHHHHHHHHHHHTTTSTCHHHHS-SHHHHHHHHHHCCCCHCCT.HHTT...HHHHHHHHHHHHCHHHH-S CS
                               Nop   2 ldeidkeintlhkrvrewYswhFpELeslvkdnleYakvvkligneredlekkee..deelakevimaakvtastsm 76 
                                       +d++dk+ n ++ r+rewYs hFpEL++lv+++ +Y+++v+++g +r+++e + +  ++  ++++ + ++ +a++s 
  gi|385806259|ref|YP_005842657.1| 150 IDDLDKTYNLFVIRLREWYSVHFPELDNLVPNHEQYVRLVAELG-HRDNFEVS-SivNLGFSQDKAEKLTDAAKKSI 224
                                       799*****************************************.88999555.345455677777777777777** PP

                                       SS-S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHCHHHHHHHHHHHHSSHHHHHCS-HHHHTTT CS
                               Nop  77 gaelseedlknikelcdrvleleelrkelleYlesrmsaiAPNlsaLvGeevaarLishaGgLtnLakmPastiqil 153
                                       ga+ls+ d+k i+ l++++ + + lr++l+ Y+es m+++APN++aLvG+ ++arLis aG+L+nLak+Pastiq+l
  gi|385806259|ref|YP_005842657.1| 225 GADLSDFDIKPIQTLARMAWDTYVLREDLAGYIESVMKEVAPNITALVGSLLGARLISLAGSLENLAKLPASTIQVL 301
                                       ***************************************************************************** PP

                                       T-HHHHCCCHH.T---SSSCHHHCSHHHHHTS-CCCHHHHHHHHHHHHHHHHHHHHTT----SHHHHHHHHHHHHHH CS
                               Nop 154 Gaekalfralk.kkntpkyGliyhselvqkatppklkkkiaRllaaKvalaaRiDafsekdgslGkklreeiekklk 229
                                       Gaekalfralk +++ pk+G+i++ + ++ka p+++++k+aR+laaK+a+aa++Daf  +   +G+kl e+++k+l+
  gi|385806259|ref|YP_005842657.1| 302 GAEKALFRALKtGSRPPKHGIIFQYPEIHKA-PRWQRGKMARTLAAKLAIAAKVDAF--TGRWIGDKLVEDLQKRLE 375
                                       ***********888***************77.*************************..7899************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1168  (0.0651459); expected 358.6 (0.02)
Passed bias filter:                      782  (0.0436165); 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: 0.69u 0.33s 00:00:01.02 Elapsed: 00:00:00.51
# Mc/sec: 2499.17
//
Query:       gi|385806260|ref|YP_005842658.1|  [L=235]
Description: fibrillarin [Fervidicoccus fontis Kam940]
Scores for complete 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-101  337.1   0.1   3.9e-101  336.9   0.1    1.0  1  Fibrillarin      Fibrillarin
     0.0016   18.2   0.0      0.002   17.9   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
  ------ inclusion threshold ------
       0.01   15.6   0.0      0.014   15.1   0.0    1.3  1  GCD14            tRNA methyltransferase complex GCD14 subunit
      0.088   12.8   0.0       0.15   12.0   0.0    1.4  1  GP24_25          Tail assembly gene products 24 & 25
       0.14   11.7   0.0       0.23   11.1   0.0    1.3  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F


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 !  336.9   0.1  1.1e-104  3.9e-101       5     225 ..      11     232 ..       7     233 .. 0.98

  Alignments for each domain:
  == domain 1  score: 336.9 bits;  conditional E-value: 1.1e-104
                                       CSSTTEEEEE.TTSSEEEEEE-SSTT--SSSSEEEEETTEEEEEE-TTTSHHHHHHHTT-S--S--TTSEEEEESTT CS
                       Fibrillarin   5 eklegvyivk.ekgdarlatknlvpgekvYgEklikveeeEyRvWnpfrsKlaaailkglkelpikkgskvLYlGaa 80 
                                       e  e +++++ ++g+++lat nlvpg+kvYgE+l ++ ++EyR+W p+rsKla+ai+kg+k +pik+g+kvLYlGaa
  gi|385806260|ref|YP_005842658.1|  11 ELNERIFEIEfDDGSKKLATINLVPGKKVYGERLYRIAGTEYREWIPYRSKLAGAIMKGIKAVPIKEGEKVLYLGAA 87 
                                       567889*********************************************************************** PP

                                       TSHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHTTSTTEEEEES-TTSGGGGTTTS--EEEEEEESSSTTHHHHH CS
                       Fibrillarin  81 sGttvsHvsDivgeegvvyavefsprvlrelievakkRknivPileDArkPekYralvekvDvifaDvaqpdqaril 157
                                       sGtt+sH+sDivge+g++y+vef+prv+re++ va++Rkn++Pi+ DArkP+ Y+++ve vD+i+aDvaqp+qa+i+
  gi|385806260|ref|YP_005842658.1|  88 SGTTPSHISDIVGEKGIIYSVEFAPRVMREFLLVASDRKNLIPIMSDARKPQLYSHIVELVDIIYADVAQPEQASIV 164
                                       ***************************************************************************** PP

                                       HHHHHHHEEEEEEEEEEEEHHHHHSSSSHHHHHHHHHHHHHHTTEEEEEEEE-TTTSTTEEEEEEEEE CS
                       Fibrillarin 158 aknaklflkeggyllisikarsidvtkepeevfkeeveklkeeglkvleqvklepyekdhalvvgkyk 225
                                       ++nak+flk+ g+++++ikarsidvtkep+ev+k+e++ l+e++++++++v+l+py+kdha+v+++y+
  gi|385806260|ref|YP_005842658.1| 165 VENAKWFLKSRGKIFLAIKARSIDVTKEPTEVYKKEISILQENRFEIIDVVHLDPYDKDHAMVLASYE 232
                                       *****************************************************************986 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 !   17.9   0.0   5.5e-07     0.002      68     134 ..      72     136 ..      53     200 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 5.5e-07
                                       HTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GG CS
                              PCMT  68 llelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGr 134
                                        + +k+g++vL +G+ sG     ++ +vgekg + s+e  +++++e    l ++d++n+i +++D r
  gi|385806260|ref|YP_005842658.1|  72 AVPIKEGEKVLYLGAASGTTPSHISDIVGEKGIIYSVEFAPRVMREF--LLVASDRKNLIPIMSDAR 136
                                       3459*************************************998764..456667777777777665 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   3.9e-06     0.014      35     141 ..      72     178 ..      51     215 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.9e-06
                             GCD14  35 kLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsq.lvtvthrDvckeGfdeev 110
                                        + +k+G +v+  G+ sg+  + i+  v+ +G ++++ef  +     + ef     +  ++     D+ k  + +++
  gi|385806260|ref|YP_005842658.1|  72 AVPIKEGEKVLYLGAASGTTPSHISDIVGEKGIIYSVEFAPR----VMREFLLVASDRkNLIPIMSDARKPQLYSHI 144
                                       56799**********************************654....4556655554332444456799999998999 PP

                             GCD14 111 sgkvDavfLDlPaPwea...iphaakalkkeggr 141
                                        + vD ++ D+ +P +a   +++a+  lk++g  
  gi|385806260|ref|YP_005842658.1| 145 VELVDIIYADVAQPEQAsivVENAKWFLKSRGKI 178
                                       9*************99866567777777766655 PP

>> GP24_25  Tail assembly gene products 24 & 25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.2e-05      0.15      72     116 ..     106     146 ..      94     162 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.2e-05
                           GP24_25  72 ysdelekviakvfrliatdPkklidaldeeedPriraelyaavln 116
                                       ys e  + +   f+l+a d k+li  + +  +P++       +++
  gi|385806260|ref|YP_005842658.1| 106 YSVEFAPRVMREFLLVASDRKNLIPIMSDARKPQLYSH----IVE 146
                                       999**************************9***65544....443 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 ?   11.1   0.0   6.5e-05      0.23       7      86 ..      76     154 ..      71     178 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6.5e-05
                                       -TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHH.HHHHHHHTT--SEEEEES-CTCCHHHHCC...EE CS
                   Methyltr_RsmB-F   7 qeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkr.vaenlkrLgvtntivleaDarkidkvlgg.elfD 81 
                                       +e+e++l l aa G   +hi++++ +kg ++ v+   + +++ +     r   +n+i +  Dark++ ++   el+D
  gi|385806260|ref|YP_005842658.1|  76 KEGEKVLYLGAASGTTPSHISDIVGEKGIIYSVEFAPRVMREfLLVASDR---KNLIPIMSDARKPQLYSHIvELVD 149
                                       799******************************98876554412233333...455667777777766554456677 PP

                                       EEEEE CS
                   Methyltr_RsmB-F  82 riLlD 86 
                                        i  D
  gi|385806260|ref|YP_005842658.1| 150 IIYAD 154
                                       66666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 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:                        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 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1708.45
//
Query:       gi|385806261|ref|YP_005842659.1|  [L=141]
Description: hypothetical protein FFONT_1219 [Fervidicoccus fontis Kam940]
Scores for complete 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   79.7   3.8    2.3e-22   79.4   3.8    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 !   79.4   3.8   1.3e-26   2.3e-22       2     123 ..      13     133 ..      12     135 .. 0.95

  Alignments for each domain:
  == domain 1  score: 79.4 bits;  conditional E-value: 1.3e-26
                                       S---SHHHHHGGGSBSS-EEHHHHHHT--EEEB.TTS-EEE--HHHHHHHHTTS-GGGGGT-EESEEEEE-SSSSE. CS
                             DUF61   2 rilakeiksinkhlPaerktLkelLeeekptivtkdgsehrfdkeeleklkeilpeelwdklkLPIllemdpelges 78 
                                       +++  ++++in+  P+e+    + + +e+  ++tk++s+++++k+++ klke+lp++++++l LPI +++  + +++
  gi|385806261|ref|YP_005842659.1|  13 KKVILDLSAIND--PVEEYVRLNEVGNEDVLLKTKSKSFFILKKDDIAKLKENLPSYFHEMLALPIEINILVTPNNK 87 
                                       6788999*****..7788888888899999*********************************************** PP

                                       .EEEES-HH.HHHHHHHHT--...-SSEEEHH.HHHHHHHH-ST.. CS
                             DUF61  79 vylvrgkae.vkvvskilgkereeedelviykpevrelrrklptat 123
                                       +y+++++++  ++v++il+k+ e e + +i++ e+++l+  +p++ 
  gi|385806261|ref|YP_005842659.1|  88 IYMLNEDLWqRRAVRYILNKKLEYEPKKYITNDELNTLISLMPSVF 133
                                       *******************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); 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: 00:00:00.41
# Mc/sec: 1032.92
//
Query:       gi|385806262|ref|YP_005842660.1|  [L=329]
Description: helix-turn-helix domain-containing protein [Fervidicoccus fontis Kam940]
Scores for complete 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   39.5   0.1    2.4e-09   37.1   0.0    2.2  2  HTH_3      Helix-turn-helix
    3.1e-08   33.5   2.7      4e-08   33.1   0.2    2.6  4  HTH_19     Helix-turn-helix domain
    4.7e-06   26.9   0.0    1.9e-05   24.9   0.0    1.9  2  HTH_31     Helix-turn-helix domain
      0.003   17.4   0.1     0.0081   16.0   0.1    1.7  1  HTH_25     Helix-turn-helix domain
     0.0039   17.1   0.4       0.12   12.4   0.0    3.3  3  HTH_11     HTH domain
  ------ inclusion threshold ------
      0.014   15.5   2.7      0.037   14.1   2.7    1.7  1  DUF1542    Domain of Unknown Function (DUF1542)
      0.048   13.6   0.0        1.6    8.8   0.0    2.6  2  HTH_Crp_2  Crp-like helix-turn-helix domain
       0.11   12.8   0.1       0.11   12.8   0.1    3.5  4  UPF0122    Putative helix-turn-helix protein, YlxM / p13 like
       0.15   11.9   0.0       0.43   10.4   0.0    1.7  1  TetR_N     Bacterial regulatory proteins, tetR family
       0.16   11.9   2.0       0.35   10.8   2.0    1.6  1  TMCCDC2    Transmembrane and coiled-coil domain-containing pr
       0.48   10.6   4.6       0.91    9.6   0.0    3.3  4  HTH_22     HTH 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 ?   -0.9   0.0       1.1   1.7e+03      10      25 ..      69      84 ..      69      84 .. 0.85
   2 !   37.1   0.0   1.5e-12   2.4e-09       1      51 [.     147     197 ..     147     199 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.1
                                      HHHHHHHHHHTSSHHH CS
                             HTH_3 10 lsqeeLAeklGvsrst 25
                                      ls+ee+ +++G+++s+
  gi|385806262|ref|YP_005842660.1| 69 LSKEEIRDLIGITKSA 84
                                      6889999999999985 PP

  == domain 2  score: 37.1 bits;  conditional E-value: 1.5e-12
                                       HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSE CS
                             HTH_3   1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvs 51 
                                       ++e+R++lgls+ eLA +lGv+r +i+ +E++    +++ + kl ++Lg +
  gi|385806262|ref|YP_005842660.1| 147 MRERREKLGLSLGELANRLGVTRKSIYEYEKNTFDVRIDYADKLFDTLGEE 197
                                       59*********************************************9965 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0         4   6.5e+03      13      27 ..      69      83 ..      68      84 .. 0.80
   2 !   33.1   0.2   2.5e-11     4e-08       1      40 [.     144     182 ..     144     204 .. 0.85
   3 ?   -2.8   0.0       4.3     7e+03      12      18 ..     214     220 ..     207     239 .. 0.54
   4 ?   -3.7   0.0       7.6   1.2e+04      39      52 ..     312     325 ..     307     327 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 4
                            HTH_19 13 ltqeelaerlgisrs 27
                                      l++ee+ + +gi++s
  gi|385806262|ref|YP_005842660.1| 69 LSKEEIRDLIGITKS 83
                                      788999999998875 PP

  == domain 2  score: 33.1 bits;  conditional E-value: 2.5e-11
                            HTH_19   1 GerLkeaReelgltqeelaerlgisrskisaiEngkkdvp 40 
                                       Ge+ +e Re+lgl++ ela+rlg++r++i+++E++ +d  
  gi|385806262|ref|YP_005842660.1| 144 GEKMRERREKLGLSLGELANRLGVTRKSIYEYEKNTFD-V 182
                                       8999*******************************773.3 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 4.3
                            HTH_19  12 gltqeel 18 
                                       ++++ee+
  gi|385806262|ref|YP_005842660.1| 214 KMKKEEI 220
                                       4555554 PP

  == domain 4  score: -3.7 bits;  conditional E-value: 7.6
                            HTH_19  39 vpsaelllkiaeal 52 
                                        ++ ++++ i+++l
  gi|385806262|ref|YP_005842660.1| 312 IIPDDKINTISRIL 325
                                       56678888888776 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       2.2   3.6e+03      15      32 ..      69      86 ..      68      87 .. 0.86
   2 !   24.9   0.0   1.1e-08   1.9e-05       3      55 ..     144     195 ..     144     198 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.2
                            HTH_31 15 LsqeevAerlgvsestls 32
                                      Ls+ee  +++g+++s  s
  gi|385806262|ref|YP_005842660.1| 69 LSKEEIRDLIGITKSASS 86
                                      899*********999765 PP

  == domain 2  score: 24.9 bits;  conditional E-value: 1.1e-08
                            HTH_31   3 GalLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralg 55 
                                       G+  r++Re+ GLs+ e+A rlgv++  +  +E  + + ++ +  ++l + lg
  gi|385806262|ref|YP_005842660.1| 144 GEKMRERREKLGLSLGELANRLGVTRKSIYEYEKNTFD-VRIDYADKLFDTLG 195
                                       6778*****************************99986.88888888877776 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   4.9e-06    0.0081       2      36 ..     147     181 ..     146     182 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.9e-06
                                       HHHHHHTTT--HHHHHHHSS--HHHHHHHHCT--T CS
                            HTH_25   2 LraaRearglsleevaketkIrkdylealEeddfd 36 
                                       +r++Re++glsl e+a+++ +  + + + E++ fd
  gi|385806262|ref|YP_005842660.1| 147 MRERREKLGLSLGELANRLGVTRKSIYEYEKNTFD 181
                                       79*******************99998888887776 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       2.3   3.8e+03       4      30 ..      57      83 ..      54      84 .. 0.74
   2 ?    0.2   0.0      0.46   7.5e+02       6      29 ..     104     127 ..     100     128 .. 0.86
   3 !   12.4   0.0   7.1e-05      0.12      16      34 ..     156     174 ..     146     176 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.3
                            HTH_11  4 qilelLleargpisgeeLAeeLnvSrr 30
                                      +i   +   ++++s ee+ + ++++++
  gi|385806262|ref|YP_005842660.1| 57 KIHLKITLDTSFLSKEEIRDLIGITKS 83
                                      566666667778999999999999876 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.46
                            HTH_11   6 lelLleargpisgeeLAeeLnvSr 29 
                                       ++ L+e+ ++++  +L + L++S+
  gi|385806262|ref|YP_005842660.1| 104 VIYLKENVPTVNVTTLPKLLSCSK 127
                                       6789899999************95 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 7.1e-05
                            HTH_11  16 isgeeLAeeLnvSrrtvrr 34 
                                       +s  eLA +L+v+r+ ++ 
  gi|385806262|ref|YP_005842660.1| 156 LSLGELANRLGVTRKSIYE 174
                                       99***************96 PP

>> DUF1542  Domain of Unknown Function (DUF1542)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   2.7   2.3e-05     0.037      26      76 ..     270     320 ..     266     321 .. 0.96

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.3e-05
                           DUF1542  26 aTdeEKqaainkvnaalneaiknInqattnddVdtaknnginaIeniqpat 76 
                                       +T eEK+++++k++++++  +  + + ++++++++++++ i  I++ +++t
  gi|385806262|ref|YP_005842660.1| 270 LTLEEKAEQLSKIKKLKDVEKMIVAKKEKAKELKKEYSDEIRIIPDDKINT 320
                                       8********************************************999887 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 ?    1.6   0.0      0.17   2.7e+02      21      40 ..      68      87 ..      45      89 .. 0.73
   2 ?    8.8   0.0   0.00096       1.6      17      38 ..     151     172 ..     137     174 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.17
                                      EHHHHHHHHHTTSSHHHHHH CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsr 40
                                       l++ee+ +++G+t +  sr
  gi|385806262|ref|YP_005842660.1| 68 FLSKEEIRDLIGITKSASSR 87
                                      69************988777 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00096
                                       EEEEEHHHHHHHHHTTSSHHHH CS
                         HTH_Crp_2  17 eielpltqeelAsmlGltretv 38 
                                       + +l l+  elA++lG+tr ++
  gi|385806262|ref|YP_005842660.1| 151 REKLGLSLGELANRLGVTRKSI 172
                                       3469999************986 PP

>> UPF0122  Putative helix-turn-helix protein, YlxM / p13 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.2      0.42   6.9e+02      34      54 ..      69      89 ..      51     111 .. 0.64
   2 ?   12.8   0.1   6.5e-05      0.11      34      68 ..     156     190 ..     151     231 .. 0.88
   3 ?   -2.0   0.0       2.6   4.2e+03      38      56 ..     208     226 ..     196     254 .. 0.62
   4 ?   -0.1   2.9      0.69   1.1e+03      60      97 ..     268     305 ..     262     310 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.42
                           UPF0122 34 lSlsEiAeefnvsrqavydni 54
                                      lS +Ei +   ++++a +  i
  gi|385806262|ref|YP_005842660.1| 69 LSKEEIRDLIGITKSASSRPI 89
                                      455799999999998866544 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 6.5e-05
                           UPF0122  34 lSlsEiAeefnvsrqavydnikrtekllekyEekL 68 
                                       lSl+E+A++  v+r+++y+  k t ++  +y +kL
  gi|385806262|ref|YP_005842660.1| 156 LSLGELANRLGVTRKSIYEYEKNTFDVRIDYADKL 190
                                       8******************************9998 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 2.6
                           UPF0122  38 EiAeefnvsrqavydnikr 56 
                                       E+ e  +++++ + dn+  
  gi|385806262|ref|YP_005842660.1| 208 EVVEMVKMKKEEIPDNLFE 226
                                       5556666666666666532 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 0.69
                           UPF0122  60 llekyEekLkllekykkreellekikdkllkqkelekk 97 
                                       + +++Eek + l+k kk +++ + i  k+ k kel+k+
  gi|385806262|ref|YP_005842660.1| 268 MPLTLEEKAEQLSKIKKLKDVEKMIVAKKEKAKELKKE 305
                                       55678999999999999999999998888888877665 PP

>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00027      0.43      17      36 ..     156     175 ..     154     175 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00027
                                       --HHHHHHHHTSSHHHHHHH CS
                            TetR_N  17 ttvreIAkrAGvskgalYry 36 
                                       +++ e+A r+Gv++ ++Y y
  gi|385806262|ref|YP_005842660.1| 156 LSLGELANRLGVTRKSIYEY 175
                                       7899**************98 PP

>> TMCCDC2  Transmembrane and coiled-coil domain-containing protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   2.0   0.00021      0.35      85     147 ..     241     300 ..     225     311 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00021
                           TMCCDC2  85 kkGsdlfqallanpegaelki.qdnknlllslglqekilkklqmvenkvkdlegliiaqkpatk 147
                                           + f +++a++ ++ + i  d++++ l+l+ +   l k+    +k+kd+e++i+a+k ++k
  gi|385806262|ref|YP_005842660.1| 241 YHARKTFVDIIAKKGEEIFFIaIDHEHMPLTLEEKAEQLSKI----KKLKDVEKMIVAKKEKAK 300
                                       445556777777666555544378788777776555555555....59************7665 PP

>> HTH_22  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       4.9     8e+03      13      29 ..      42      58 ..      39      59 .. 0.70
   2 ?    9.6   0.0   0.00056      0.91      45      61 ..     159     175 ..     156     176 .. 0.90
   3 ?    0.8   0.0      0.32   5.3e+02      18      40 ..     210     232 ..     200     236 .. 0.87
   4 ?   -2.7   0.2       3.9   6.4e+03      17      31 ..     276     290 ..     266     299 .. 0.66

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 4.9
                            HTH_22 13 lgkpverltkeekieiv 29
                                      +++ + + +k+ek++ +
  gi|385806262|ref|YP_005842660.1| 42 RSIDILAWSKDEKKKKI 58
                                      55666678899998765 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00056
                            HTH_22  45 ekvAekLgiSraTvYry 61 
                                        ++A++Lg++r ++Y y
  gi|385806262|ref|YP_005842660.1| 159 GELANRLGVTRKSIYEY 175
                                       578************99 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.32
                            HTH_22  18 erltkeekieivraLdekGiFll 40 
                                        ++ k +k ei  +L e+ iF++
  gi|385806262|ref|YP_005842660.1| 210 VEMVKMKKEEIPDNLFEEKIFNI 232
                                       468899999************97 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 3.9
                            HTH_22  17 verltkeekieivra 31 
                                       +e+l+k +k++ v++
  gi|385806262|ref|YP_005842660.1| 276 AEQLSKIKKLKDVEK 290
                                       355666666555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1763  (0.0983323); expected 358.6 (0.02)
Passed bias filter:                      637  (0.035529); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 1945.00
//
Query:       gi|385806263|ref|YP_005842661.1|  [L=188]
Description: hypothetical protein FFONT_1221 [Fervidicoccus fontis Kam940]
Scores for complete 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-32  113.3   0.0    1.2e-32  113.1   0.0    1.0  1  NTPase_1      NTPase
    0.00051   20.5   0.0    0.00092   19.6   0.0    1.4  1  AAA_16        AAA ATPase domain
    0.00066   19.3   0.0     0.0022   17.6   0.1    1.7  2  AAA_25        AAA domain
      0.002   18.6   0.2     0.0043   17.5   0.1    1.7  2  AAA           ATPase family associated with various cellular 
     0.0027   17.4   0.0     0.0035   17.1   0.0    1.4  1  AAA_24        AAA domain
     0.0041   17.0   0.1     0.0072   16.3   0.1    1.4  1  NACHT         NACHT domain
     0.0077   16.0   0.0     0.0096   15.7   0.0    1.2  1  AAA_30        AAA domain
     0.0098   15.9   0.2      0.022   14.7   0.1    1.6  2  AAA_5         AAA domain (dynein-related subfamily)
  ------ inclusion threshold ------
      0.012   15.2   0.1      0.019   14.6   0.1    1.3  1  SRP54         SRP54-type protein, GTPase domain
       0.02   15.2   0.1      0.035   14.4   0.1    1.6  1  AAA_22        AAA domain
      0.024   13.8   0.0      0.045   12.9   0.0    1.5  1  NB-ARC        NB-ARC domain
      0.024   13.6   0.1      0.032   13.2   0.1    1.2  1  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
      0.038   14.0   0.1      0.068   13.2   0.1    1.4  1  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
      0.068   13.3   0.0       0.11   12.7   0.0    1.4  1  AAA_33        AAA domain
      0.079   12.1   0.0       0.13   11.4   0.0    1.4  1  DAP3          Mitochondrial ribosomal death-associated protei
      0.086   13.1   0.1       0.13   12.5   0.1    1.3  1  AAA_28        AAA domain
       0.11   12.9   0.0       0.26   11.7   0.0    1.7  1  RNA_helicase  RNA helicase
       0.11   12.4   0.0       0.19   11.6   0.0    1.4  1  AAA_3         ATPase family associated with various cellular 
       0.12   12.1   0.0       0.23   11.2   0.0    1.4  1  RuvB_N        Holliday junction DNA helicase RuvB P-loop doma
       0.13   12.6   0.2       0.17   12.2   0.2    1.3  1  AAA_19        AAA domain
       0.14   11.9   0.0       0.26   11.0   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
       0.16   12.5   1.2       0.26   11.8   0.2    1.7  2  AAA_18        AAA domain
       0.19   11.1   0.1       0.29   10.5   0.1    1.2  1  Mg_chelatase  Magnesium chelatase, subunit ChlI


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 !  113.1   0.0   1.6e-35   1.2e-32       1     167 [.       9     179 ..       9     180 .. 0.94

  Alignments for each domain:
  == domain 1  score: 113.1 bits;  conditional E-value: 1.6e-35
                                       EEEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE-------EEEEEET.T--EEEEEETT..---SSEETTEE CS
                          NTPase_1   1 kvfiTGppGvGKtTlvkkvlellkssgvkvgGfyteevreggrrigFkivdlasgeegiLarve..akreprvgkyv 75 
                                       ++f+TG+pG+GKtTlv k+++ l  + vk +Gf t+e r +  r gF+++   s+e ++La+++  +  ++++g+y+
  gi|385806263|ref|YP_005842661.1|   9 RIFLTGHPGIGKTTLVLKLASILTLEKVKFAGFATPEKRGKSGREGFELIIFPSNEVHELASKSieKGYKMKLGSYY 85 
                                       69*************************************************************987778889***** PP

                                       E-HHHHHHHHHHHHHHHHHHH-..EEEE---STTGGG-HHHHHHHHHHHT.TTSEEEEE--SS-...-SHHHHHHHT CS
                          NTPase_1  76 vdvesfeelalealrkalsead..viviDEiGkmElkskkfkeaveevLk.sekpvlavihrrk...dlalveeire 146
                                       v+ e++  ++l+++++ l++     ++ DE+G+mEl ++ ++e + ++Lk +ek +l+ +h +    d+++++ i++
  gi|385806263|ref|YP_005842661.1|  86 VN-ENMGAIILKIINEYLNDDSfkFFIGDEVGPMELMIPGIREGILKLLKaEEKSMLMSFHINLkqkDPEIYDLISK 161
                                       **.99*********99885555779999*********************************9987778888888886 PP

                                       -TT-EEEE--TTTTTTHHHHH CS
                          NTPase_1 147 rkdvkvfevteenrdalleei 167
                                          + v+ ++ enr+++l++i
  gi|385806263|ref|YP_005842661.1| 162 ---GDVYVLSTENRNQILNDI 179
                                       ...79**************99 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   0.00092      26      55 ..       9      38 ..       2      71 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.2e-06
                            AAA_16 26 lvllsGesGvGKsslvrellralekdggif 55
                                       ++l+G++G+GK++lv +l+  l+ +++ f
  gi|385806263|ref|YP_005842661.1|  9 RIFLTGHPGIGKTTLVLKLASILTLEKVKF 38
                                      689***************998877765555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   2.8e-06    0.0022      34      66 ..       8      42 ..       4      50 .. 0.80
   2 ?   -1.6   0.0       2.1   1.6e+03      71      88 ..     161     178 ..     148     187 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.8e-06
                            AAA_25 34 elallaGapgtGKttlaldlalava.tGkpwlg.p 66
                                        + l+G+pg GKttl+l la  ++ +  +++g  
  gi|385806263|ref|YP_005842661.1|  8 VRIFLTGHPGIGKTTLVLKLASILTlEKVKFAGfA 42
                                      6789******************9998888888853 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.1
                            AAA_25  71 qgkVlyvsaEdsedelrr 88 
                                       +g V ++s+E++++ l+ 
  gi|385806263|ref|YP_005842661.1| 161 KGDVYVLSTENRNQILND 178
                                       567777788877766654 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   5.5e-06    0.0043       2      37 ..      11      49 ..      10     101 .. 0.76
   2 ?   -1.8   0.0       4.9   3.8e+03     101     117 ..     162     178 ..     131     187 .. 0.55

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 5.5e-06
                                      EEESSTTSSHHHHHHHHHHHH...THEEEEEETTTCSSS CS
                               AAA  2 llyGppGtGKTllakavakel...gvefleisgsellsk 37
                                       l+G pG+GKT+l+  +a+ l   +v+f  +  +e + k
  gi|385806263|ref|YP_005842661.1| 11 FLTGHPGIGKTTLVLKLASILtleKVKFAGFATPEKRGK 49
                                      799*****************9444466666666666655 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.9
                                       STEEEEEEESSGGGSTH CS
                               AAA 101 skvivigatnrpdkldp 117
                                       ++v v+ + nr + l++
  gi|385806263|ref|YP_005842661.1| 162 GDVYVLSTENRNQILND 178
                                       33444444444322222 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   4.6e-06    0.0035       2      29 ..       7      33 ..       6     100 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.6e-06
                            AAA_24  2 klkiliyGpsgiGKTtlakelgpkplfi 29
                                      +++i+++G +giGKTtl+++l  ++l +
  gi|385806263|ref|YP_005842661.1|  7 SVRIFLTGHPGIGKTTLVLKL-ASILTL 33
                                      579*****************9.666655 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   9.3e-06    0.0072       3      27 ..      10      34 ..       8      43 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9.3e-06
                                      EEEEC-TTTCHHHHHHHHHHHHCTS CS
                             NACHT  3 vilqGeaGsGKTtLlqklalawaeg 27
                                      ++l+G +G+GKTtL+ kla+ +  +
  gi|385806263|ref|YP_005842661.1| 10 IFLTGHPGIGKTTLVLKLASILTLE 34
                                      899***************9987655 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   1.2e-05    0.0096      22      78 ..      11      70 ..       3     118 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.2e-05
                            AAA_30 22 vltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgi...eastiakllk 78
                                      +ltG +G GKtt++ +l+ +++ ++ + +g+A  +k  k  +e++++   +++ +++l +
  gi|385806263|ref|YP_005842661.1| 11 FLTGHPGIGKTTLVLKLASILTLEKVKFAGFATPEKRGKSGREGFELiifPSNEVHELAS 70
                                      79******************************9999999888877744458888887764 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 !   14.7   0.1   2.8e-05     0.022       2      24 ..      10      32 ..       9      43 .. 0.86
   2 ?   -2.9   0.0       7.9   6.1e+03     113     124 ..     161     174 ..     134     185 .. 0.55

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.8e-05
                                      EEEE--SSSSHHHHHHHGGGGBS CS
                             AAA_5  2 vlLvGppGtgKselaerlaaaln 24
                                      ++L G pG+gK++l+ +la+ l+
  gi|385806263|ref|YP_005842661.1| 10 IFLTGHPGIGKTTLVLKLASILT 32
                                      79*****************9994 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 7.9
                                       ...-EEEEEESS-- CS
                             AAA_5 113 r..frviatanpld 124
                                       +  ++v+ t n+++
  gi|385806263|ref|YP_005842661.1| 161 KgdVYVLSTENRNQ 174
                                       13455555555554 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   2.5e-05     0.019       4      33 ..      10      39 ..       7      47 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.5e-05
                                      EEEEESTTSSHHHHHHHHHHHHHHTTS-EE CS
                             SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvl 33
                                      i l G  G+GKTt + KLa +l+ e+ k +
  gi|385806263|ref|YP_005842661.1| 10 IFLTGHPGIGKTTLVLKLASILTLEKVKFA 39
                                      7899******************99987765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   4.5e-05     0.035       8      30 ..      10      32 ..       9     133 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.5e-05
                            AAA_22  8 lvvtGesGtGKTtllrrlleqld 30
                                      +++tG++G+GKTtl+ +l++ l+
  gi|385806263|ref|YP_005842661.1| 10 IFLTGHPGIGKTTLVLKLASILT 32
                                      689**************998875 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   5.8e-05     0.045      15      42 ..       2      29 ..       1      43 [. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.8e-05
                                      TTTSCSEEEEEEESTTSSHHHHHHHHCC CS
                            NB-ARC 15 kdelqslvvalvGmgGvGKttlakqiln 42
                                      k++ +s+ ++l G +G+GKttl+ +  +
  gi|385806263|ref|YP_005842661.1|  2 KENRESVRIFLTGHPGIGKTTLVLKLAS 29
                                      57788899**************987665 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 ?   13.2   0.1     4e-05     0.032      28      58 ..       6      36 ..       1      51 [. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4e-05
                                      -SEEEEEEE-TTSSHHHHHHHHHHHHHCTT- CS
                              MeaB 28 raqvvGltGvPGaGkstlvealglelrrrGk 58
                                      ++ ++ ltG PG Gk tlv +l+  l+ +  
  gi|385806263|ref|YP_005842661.1|  6 ESVRIFLTGHPGIGKTTLVLKLASILTLEKV 36
                                      577999****************988876555 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   8.7e-05     0.068      21      53 ..       9      41 ..       1      49 [. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.7e-05
                                      EEEEEESTTSSHHHHHHHHHHHTT------TTT CS
                              TsaE 21 vilLeGdLGaGKTtlvrglakalgveevkSPTF 53
                                       i+L+G  G GKTtlv +la+ l +e+vk   F
  gi|385806263|ref|YP_005842661.1|  9 RIFLTGHPGIGKTTLVLKLASILTLEKVKFAGF 41
                                      499********************9998886655 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   0.00014      0.11       2      23 ..      10      31 ..      10      78 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00014
                            AAA_33  2 vllvGlpGsGKstlaerllkkl 23
                                      ++l G+pG GK+tl+ +l+  l
  gi|385806263|ref|YP_005842661.1| 10 IFLTGHPGIGKTTLVLKLASIL 31
                                      6899***********9998544 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 ?   11.4   0.0   0.00017      0.13      19      43 ..       3      27 ..       1      36 [. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00017
                                      SSS---EEEEE-SSSSSTTTTHHHH CS
                              DAP3 19 kkkkvkrlvltGekgsGKSvlLlqa 43
                                      ++++ +r+ ltG +g GK++l+l++
  gi|385806263|ref|YP_005842661.1|  3 ENRESVRIFLTGHPGIGKTTLVLKL 27
                                      68999****************9976 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00016      0.13       1      21 [.       9      29 ..       9      44 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00016
                            AAA_28  1 kivitGgestGKTtlleaLaa 21
                                      +i +tG ++ GKTtl+ +La+
  gi|385806263|ref|YP_005842661.1|  9 RIFLTGHPGIGKTTLVLKLAS 29
                                      799**************9995 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   0.00033      0.26       1      23 [.      10      32 ..      10      51 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00033
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakall 23
                                      i+l+G++g+GK+tl+ +La+ l+
  gi|385806263|ref|YP_005842661.1| 10 IFLTGHPGIGKTTLVLKLASILT 32
                                      789**************999876 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 ?   11.6   0.0   0.00024      0.19       2      26 ..      10      34 ..       9      45 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00024
                             AAA_3  2 vllegvPGlaktllvkalakaldle 26
                                      ++l+g PG++kt+lv +la++l le
  gi|385806263|ref|YP_005842661.1| 10 IFLTGHPGIGKTTLVLKLASILTLE 34
                                      6899****************99875 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 ?   11.2   0.0   0.00029      0.23      35      58 ..       9      32 ..       2      48 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00029
                            RuvB_N 35 hvllyGpPGlGkttlakiiakelg 58
                                       ++l+G PG+Gkttl   +a+ l 
  gi|385806263|ref|YP_005842661.1|  9 RIFLTGHPGIGKTTLVLKLASILT 32
                                      689***********9988877655 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   0.00022      0.17      12      40 ..       9      36 ..       2     150 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00022
                            AAA_19 12 vllvtaGpGtGKTrvlkhivallvelggv 40
                                       +++t+ pG GKT+++ +  ++l  ++ v
  gi|385806263|ref|YP_005842661.1|  9 RIFLTGHPGIGKTTLVLKLASILTLEK-V 36
                                      5899*********99888777766555.3 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00034      0.26      24      53 ..       9      37 ..       2      43 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00034
                            AAA_29 24 atlltGpsGsGKSTllDAiqalLvpakkvr 53
                                       ++ltG+ G GK+Tl+  ++ +L+ +k v+
  gi|385806263|ref|YP_005842661.1|  9 RIFLTGHPGIGKTTLVLKLASILTLEK-VK 37
                                      578************988888887766.55 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   0.00034      0.26       1      21 [.      10      30 ..      10      53 .. 0.87
   2 ?   -2.0   0.0       6.5   5.1e+03      69      70 ..     153     158 ..     125     184 .. 0.49

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00034
                            AAA_18  1 IlltGtpGvGKttlakeLskr 21
                                      I+ltG pG GKttl   L++ 
  gi|385806263|ref|YP_005842661.1| 10 IFLTGHPGIGKTTLVLKLASI 30
                                      99************9999875 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 6.5
                            AAA_18  69 s....a 70 
                                             
  gi|385806263|ref|YP_005842661.1| 153 PeiydL 158
                                       222222 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00037      0.29      25      47 ..      10      32 ..       7      40 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00037
                      Mg_chelatase 25 lllvGppGsGKtmlakrlpsllp 47
                                      ++l+G pG GKt l  +l+s+l+
  gi|385806263|ref|YP_005842661.1| 10 IFLTGHPGIGKTTLVLKLASILT 32
                                      799******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); 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: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1219.39
//
Query:       gi|385806264|ref|YP_005842662.1|  [L=389]
Description: N2,N2-dimethylguanosine tRNA methyltransferase [Fervidicoccus fontis Kam940]
Scores for 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-79  266.2   0.1      8e-79  265.5   0.1    1.3  1  TRM       N2,N2-dimethylguanosine tRNA methyltransferase
    0.00045   20.0   0.1    0.00074   19.3   0.1    1.3  1  Met_10    Met-10+ like-protein
  ------ inclusion threshold ------
      0.033   13.6   0.5      0.043   13.2   0.0    1.4  2  PrmA      Ribosomal protein L11 methyltransferase (PrmA)
       0.05   13.2   0.3       0.05   13.2   0.3    2.0  2  DUF2067   Uncharacterized protein conserved in archaea (DUF20
      0.071   11.5   0.1       0.19   10.1   0.0    1.6  2  DUF3029   Protein of unknown function (DUF3029)


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 !  265.5   0.1   2.2e-82     8e-79      19     375 ..      38     386 ..      27     387 .. 0.88

  Alignments for each domain:
  == domain 1  score: 265.5 bits;  conditional E-value: 2.2e-82
                                       -SS--GGGHHHHHHHHHH...HHHHHHHH-S-EEEEESS-TTSHHHHHHHHH-S-EE.EEEEE-S-HHHHHHHHHHH CS
                               TRM  19 eVFYNPvqefnRDlsvlvirqlellkkklgekikvldaLsasGlRaiRfalEvpgvk.evlaNDisekAvelikeNv 94 
                                       ++FYNP   +nRDl+vl i+ ++ l +k+    + +++L++s +R+iR  lE +  + + +aNDis+ Ave   +N+
  gi|385806264|ref|YP_005842662.1|  38 PIFYNPYSSINRDLTVLGIKAFSSLFRKI---ENFIEPLAGSCVRTIRVVLENDDIEiNGYANDISKDAVEYCVKNI 111
                                       89******************666666775...3789****************666542459**************** PP

                                       HHTT--GGEEEE-S-HHHHHC...--SS-EEEEEE--SS--GGGHHHHHHHEEEEEEEEEEE--HHHHTTSSHHHHH CS
                               TRM  95 klneveeivvineddAnvlla...ekkkrfdviDlDPfGspapfldsavqsvkekglLlvTaTDtavLaGaspekcl 168
                                       +ln  ee +++ +++An++l+   +k  + d++D+DP+Gsp +fldsa ++++++glL vTaTD  +L G+++++ l
  gi|385806264|ref|YP_005842662.1| 112 SLNGLEEKIKVMNEEANFFLHfllKKGIKQDAVDIDPYGSPINFLDSASKAISNNGLLFVTATDIGTLMGKYKDTSL 188
                                       *******9999999*******9999999************************************************* PP

                                       HHHSSB---STTHHHHHHHHHHHHHHHHHHTTTEEEEEEEEEEETTEEEEEEEEEE-HHHHHHHHTTEEEEEEETTT CS
                               TRM 169 rkYgavalkselcHEvalRillkavareaakYekavepllslsadfYvrvfvkvktgaakvkkvleklglvlhCsgC 245
                                       r+Yg+   k+++  E+a R+l+++v r+ +  ek   pl++++++++++  + +k+      k ++k+g++     C
  gi|385806264|ref|YP_005842662.1| 189 RRYGSHVYKTDYGREIAARVLIYSVIRAFSSNEKNAYPLFTYYHEHFLKTGFLIKKE-----KQANKIGFL-----C 255
                                       ************************************************998887764.....345566665.....4 PP

                                       --EEEE--GGG--.SB-TTT-SBEEEEEEEE-S-S--HHHHHHHHHHHCT..-TTS-HHHHHHHHHHHHHH.S--SS CS
                               TRM 246 lseekvkglakfk.aecehcgaklhlaGPlwlgplkdkefveevleeaekekeeelkkrvkklLklikeEl.ldapl 320
                                       +++++ + + k+   +  + ++  + +GP+wlg+l++++f+ +v +  +k  +e+++ +++k ++++ +E+ +++p+
  gi|385806264|ref|YP_005842662.1| 256 IDSNSGYPFDKVIlGKDGFKSECSNYIGPIWLGELWNRDFLLKVEDFYRKG-KENYSIKLEKDINTMLAESeIENPF 331
                                       44444444544443455566666789***************9999998885.6667666666666555565599*** PP

                                       -EEHHHHHHHHT-SS---HHHHHHH....TT-EE-TTSTTEEE-SS-HHHHHHHH CS
                               TRM 321 yydlsqlasvlklsvpplkkvvsalkelgfevsrtHakpkaikTnapleavvevl 375
                                       yy+++++as+lk +vp+ +k+ ++lk+lg+  srtH+  k+ikTnap++ v +v+
  gi|385806264|ref|YP_005842662.1| 332 YYHIDKIASKLKKNVPKFEKIEEELKKLGYASSRTHFDAKGIKTNAPYDIVFNVI 386
                                       ***************************************************9997 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   2.1e-07   0.00074     128     195 ..      95     167 ..      60     171 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2.1e-07
                                       EEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---....TT-.EEEEEE--TTTGGGGHHHHHHHEEEEE CS
                            Met_10 128 laidlnPesvkylkeniklNkvekvvkpileDgrevir....eql.adrvvmnlpksaieFldkvlaalkdgg 195
                                       +a+d+  ++v+y  +ni lN +e+++k+++e+++ +++    + +  d v ++   s i+Fld++ +a+ ++g
  gi|385806264|ref|YP_005842662.1|  95 YANDISKDAVEYCVKNISLNGLEEKIKVMNEEANFFLHfllkKGIkQDAVDIDPYGSPINFLDSASKAISNNG 167
                                       9********************************9998766653330344546666788888888877776655 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.2e-05     0.043     148     219 ..      52     126 ..      48     146 .. 0.80
   2 ?   -3.8   0.1       1.8   6.5e+03      47      94 ..     307     354 ..     297     355 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.2e-05
                              PrmA 148 TklclealeklvkegeevlDvGtGSGiLaiaaakLga.kkv..vavDiDevAvkvakeNaelNkveaklevalse 219
                                       T l ++a+ +l ++ e+++   +GS + +i +++ +   ++  +a Di + Av+   +N++lN++e+k++v+++e
  gi|385806264|ref|YP_005842662.1|  52 TVLGIKAFSSLFRKIENFIEPLAGSCVRTIRVVLENDdIEIngYANDISKDAVEYCVKNISLNGLEEKIKVMNEE 126
                                       8888999999999999999999999999998765543134433778***********************996543 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 1.8
                              PrmA  47 leeeelkeevkvkalfkeeteakeliaqlkeselglekgkvkveevee 94 
                                       +e+ ++k e ++++++ e++  + +  ++++   +l+k+  k+e++ee
  gi|385806264|ref|YP_005842662.1| 307 KENYSIKLEKDINTMLAESEIENPFYYHIDKIASKLKKNVPKFEKIEE 354
                                       444455666777777776666666777777777777777777777776 PP

>> DUF2067  Uncharacterized protein conserved in archaea (DUF2067)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.2      0.31   1.1e+03       9      56 ..      66     111 ..      64     124 .. 0.63
   2 ?   13.2   0.3   1.4e-05      0.05      52     124 ..     317     389 .]     303     389 .] 0.79

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.31
                           DUF2067   9 leeflekisekiksaeevkievegnrllievyGtekeikdiirrikel 56 
                                       +e+f+e +  +  +++++ + +e++ + i+ y ++ +++   + +k++
  gi|385806264|ref|YP_005842662.1|  66 IENFIEPLAGS--CVRTIRVVLENDDIEINGYANDISKDAVEYCVKNI 111
                                       67777777764..36777777887776665555444445555566665 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1.4e-05
                           DUF2067  52 rikellreklkkekrglfkyslsdllreagapvpp.dvLvdaLkllGykaelre..envlktnapleevvelaerl 124
                                        i ++     ++e +  f y+++++ ++++++vp+ + + + Lk+lGy  +      + +ktnap++ v  +++ l
  gi|385806264|ref|YP_005842662.1| 317 DINTM---LAESEIENPFYYHIDKIASKLKKNVPKfEKIEEELKKLGYASSRTHfdAKGIKTNAPYDIVFNVIKSL 389
                                       34444...44588999******************659***********77666554789*******9999888765 PP

>> DUF3029  Protein of unknown function (DUF3029)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   5.3e-05      0.19     219     285 ..      72     139 ..      68     144 .. 0.82
   2 ?   -2.1   0.0      0.26   9.2e+02     273     297 ..     229     253 ..     197     257 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 5.3e-05
                           DUF3029 219 plgGgaytLvRlnLkevakkaks.vedfleevlpkvve.lmlelidaRikflveeskffessfLvkegl 285
                                       pl+G ++  +R+ L++   + ++ ++d+ + +++++v+ + l+ ++++ik + ee++ff  +fL k g+
  gi|385806264|ref|YP_005842662.1|  72 PLAGSCVRTIRVVLENDDIEINGyANDISKDAVEYCVKnISLNGLEEKIKVMNEEANFF-LHFLLKKGI 139
                                       67888888889999888777776478889999999886256899***************.99***9996 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.26
                           DUF3029 273 kffessfLvkegliekdrftamfgi 297
                                       ++++++fL +  li+k++ +  +g+
  gi|385806264|ref|YP_005842662.1| 229 TYYHEHFLKTGFLIKKEKQANKIGF 253
                                       5788888888888888887776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); 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: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.54
# Mc/sec: 2149.73
//
Query:       gi|385806265|ref|YP_005842663.1|  [L=137]
Description: hypothetical protein FFONT_1223 [Fervidicoccus fontis Kam940]
Scores for complete 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   19.9   7.2      0.038   13.4   0.1    2.0  2  RNA_pol_Rpc34   RNA polymerase Rpc34 subunit
     0.0023   17.8   0.2     0.0036   17.1   0.2    1.4  1  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0048   17.5   0.2       0.01   16.5   0.1    1.5  2  RPA_C           Replication protein A C terminal
     0.0057   16.8   1.3     0.0059   16.7   1.3    1.3  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
  ------ inclusion threshold ------
      0.037   13.3   0.1      0.052   12.8   0.1    1.2  1  FAM91_N         FAM91 N-terminus


Domain annotation for each model (and alignments):
>> RNA_pol_Rpc34  RNA polymerase Rpc34 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   3.5    0.0003       1.1      80     136 ..       7      64 ..       5      78 .. 0.89
   2 !   13.4   0.1   1.1e-05     0.038     301     336 .]      91     126 ..      67     126 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0003
                                       HHHTSXHHHH.HHHHHHHHHXSSXEEHHHHHHTTGXXHHHHHHHHHHHHHTTXXEEEE CS
                     RNA_pol_Rpc34  80 kktslsedes.lVysiIeesGneGIwsrtiksklnLhksvvkkcLksLeskkyiksvk 136
                                       k t+l++d +  + +i e+sGn+G    ++++ l++++  +k ++  L  k+ +k+ k
  gi|385806265|ref|YP_005842663.1|   7 KNTTLPKDIEnTIIKILESSGNSGMNLSELQKILKIKEDKLKLVVARLSRKGIVKKEK 64 
                                       6788888855599*****************************************9877 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1.1e-05
                                       SSTTXXSSXSSSSSXXTSSSSSSSSSSTTSSSSXXX CS
                     RNA_pol_Rpc34 301 sglveapcgecpvfdlceeggavspkncvYlkeWle 336
                                       s +++ pc +c  ++ c  g + sp nc+ lk+Wle
  gi|385806265|ref|YP_005842663.1|  91 STVIKIPCFTCKYIKECGIGREWSPANCEILKNWLE 126
                                       567899****************************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 !   17.1   0.2     1e-06    0.0036      21      58 ..      29      66 ..      20      83 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1e-06
                                      CCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB 21 gpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                        ++ +e+ ++l++ + k   v+ +L++kG+V++ek +
  gi|385806265|ref|YP_005842663.1| 29 SGMNLSELQKILKIKEDKLKLVVARLSRKGIVKKEKIK 66
                                      578999*****************************977 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 !   16.5   0.1   2.9e-06      0.01      49      97 ..      14      60 ..       2      61 .. 0.82
   2 ?   -2.9   0.0       3.2   1.1e+04      70      87 ..     118     135 ..     116     136 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.9e-06
                                      HHHHHHHHHHHH.SXSTTTEEHHHHHHHSTSXHHHHHHHHHHHHHTTSE CS
                             RPA_C 49 alaqqvlnlikqspeseeGvhvdeiaqklrlsvndvkqavdeLsneGii 97
                                      + +++++ ++ +   ++ G++++e+ + l++ + ++k +v  Ls +Gi+
  gi|385806265|ref|YP_005842663.1| 14 DIENTIIKILES--SGNSGMNLSELQKILKIKEDKLKLVVARLSRKGIV 60
                                      445555555555..9********************************97 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.2
                                       HHHHHHHSTSXHHHHHHH CS
                             RPA_C  70 vdeiaqklrlsvndvkqa 87 
                                       ++++++ l+ + n+++qa
  gi|385806265|ref|YP_005842663.1| 118 CEILKNWLESETNKIEQA 135
                                       677788888888888887 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   1.3   1.6e-06    0.0059      13      54 ..      25      66 ..      14     132 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.6e-06
                    B-block_TFIIIC 13 ssRysGitqsdLakeskqdprslfyrlksLekkgLIvkqsii 54
                                      ss+ sG++ s+L k++k++  +l  ++  L++kg ++k +i 
  gi|385806265|ref|YP_005842663.1| 25 SSGNSGMNLSELQKILKIKEDKLKLVVARLSRKGIVKKEKIK 66
                                      899************************************994 PP

>> FAM91_N  FAM91 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   1.5e-05     0.052     244     300 ..      11      68 ..       7      79 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.5e-05
                           FAM91_N 244 sgDylEtLLYkilvsi.dertsvkeLakvLqidlelvkqAvslycRLglakkkteeil 300
                                       +   +E+ + kil s  ++ ++++eL k+L+i+++++k  v  + R g+ kk++ +++
  gi|385806265|ref|YP_005842663.1|  11 LPKDIENTIIKILESSgNSGMNLSELQKILKIKEDKLKLVVARLSRKGIVKKEKIKKE 68 
                                       5566899999999776155689****************************99988743 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       853  (0.0475766); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); 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 0.34s 00:00:00.88 Elapsed: 00:00:00.54
# Mc/sec: 764.26
//
Query:       gi|385806266|ref|YP_005842664.1|  [L=267]
Description: undecaprenyl diphosphate synthase [Fervidicoccus fontis Kam940]
Scores for complete 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-73  246.1   0.3    3.6e-73  245.8   0.3    1.1  1  Prenyltransf  Putative undecaprenyl diphosphate synthase


Domain annotation for each model (and alignments):
>> Prenyltransf  Putative undecaprenyl diphosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  245.8   0.3     2e-77   3.6e-73       1     224 []      43     266 ..      43     266 .. 0.92

  Alignments for each domain:
  == domain 1  score: 245.8 bits;  conditional E-value: 2e-77
                                       EE--HHHHHHHTT.S-HHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEEGGGG.GS-HHHHHHHHHHHH...HHHHH CS
                      Prenyltransf   1 imDGNrRwAkkrgleereeGhkaGaealkeilelclelgvkvvtvYafSteNf.kRskeevdalmellk...eellk 73 
                                       i DGNrRwAk++g e  + Ghk+G+e+++++l+++ +l+vk+vt+Y++SteN+ kRs+ee +++++ll    e  l+
  gi|385806266|ref|YP_005842664.1|  43 IPDGNRRWAKRHGYE-YTFGHKMGYEKVSQVLDWIWNLNVKAVTLYVLSTENClKRSEEEKQNIFQLLYmglE-QLE 117
                                       78***********55.555*********************************77**************86644.454 PP

                                       HHHHHHHHTTEEEEEESSGGGS-HHHHHHHHHHHHHHT.TTTSEEEEEEEEE-HHHHHHHHHHHHHHTT..SSSG.G CS
                      Prenyltransf  74 eelkellkegvrvrviGdlellpedvlealekaeeatkknnkklvlniavnYgsrdeiveavrelvkekseekkk.e 149
                                       ++ +++ +++v+v++iG+ el+p+ + ++++++ee+t+kn+   +lniav+Yg+r+ei+ea++++++++++   + +
  gi|385806266|ref|YP_005842664.1| 118 ND-RRIYDSKVKVKIIGNFELIPDWIIKKAKEVEEKTEKNE-LRILNIAVCYGGRHEIIEAIKKIASDYKKGVISlN 192
                                       44.699999*****************************555.59*********************999977666667 PP

                                       GHSHHHHHCTSTT..TSSS-SEEEEESS--S-TTSSTTTTTT-EEEEESSSGGG--HHHHHHHHHHHHHCHHHTT CS
                      Prenyltransf 150 eideetlekhlytakalpdpDlliRtsGeeRlSnFllwqlayselyfldvlWPdfskedllealleyqkrerrfg 224
                                       eide++++++l t+++ pdpDl+iRtsGeeR+SnFllwq+aysel+f+dv+WP+f+k dl++a++++qkr+r+fg
  gi|385806266|ref|YP_005842664.1| 193 EIDENKVSSYLFTSDS-PDPDLIIRTSGEERISNFLLWQSAYSELFFTDVYWPEFRKIDLWRAIRSFQKRRRNFG 266
                                       789**********888.******************************************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       964  (0.0537676); expected 358.6 (0.02)
Passed bias filter:                      594  (0.0331307); 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: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1661.60
//
Query:       gi|385806267|ref|YP_005842665.1|  [L=129]
Description: 30S ribosomal protein S8e [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-26   93.3   4.3    1.5e-26   93.2   4.3    1.0  1  Ribosomal_S8e  Ribosomal protein S8e
  ------ inclusion threshold ------
      0.056   12.7   0.1      0.059   12.6   0.1    1.2  1  Lyx_isomer     D-lyxose isomerase
      0.079   12.6   0.1      0.091   12.4   0.1    1.1  1  EMG1           EMG1/NEP1 methyltransferase


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 !   93.2   4.3   2.6e-30   1.5e-26       1     137 []       1     127 [.       1     127 [. 0.95

  Alignments for each domain:
  == domain 1  score: 93.2 bits;  conditional E-value: 2.6e-30
                                       XXXBXXCCCSEESSTEEXXXSSXXXCCSBXXXXXXXEES.SHEEEEEEETTCEEEEEEESESEEEEEETTTTEEEEE CS
                     Ribosomal_S8e   1 mgisrdskhkrkltGgkakllrkkrkielgrkekatklg.aervkvvrvrgGkrkkralrlkkanvthpeekvtkkl 76 
                                       mgi +++  k++  G k ++++ krk   g   ++tk++ ++  + ++vrgG++k ++ +++ka ++ +  k++k  
  gi|385806267|ref|YP_005842665.1|   1 MGIYQENDLKKSSGGKKTRPYKVKRKALFGGYFTETKVHsEDEKEIIKVRGGNIKIKLKKASKAVIMSKDGKTVKVE 77 
                                       788888999999999999999*****************76778888899**************************** PP

                                       EEEEEECSSSTCHHHHTTC--TTEEEEEESHHHHHHHHTTEEEEEEESEHHHHSSEEEEEE CS
                     Ribosomal_S8e  77 kIlgVkknpsnneyvrlgvltKgaiievdvseLgevtqsgkvvAqvtsrPgqdGcvnavlL 137
                                       kI +V+++psn+e++r+g++tKg+iiev++++           A v srPgqdG++navl+
  gi|385806267|ref|YP_005842665.1|  78 KISRVVETPSNKEFARRGIITKGSIIEVESGK-----------ALVVSRPGQDGVINAVLI 127
                                       ********************************...........****************96 PP

>> Lyx_isomer  D-lyxose isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   9.8e-06     0.059      84     150 ..      19      85 ..       6     114 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.8e-06
                        Lyx_isomer  84 klYaekllivkegqvtpmHfHwskaeDiinRgGgklvielynsdedeklededvtvsvDGvkktvaa 150
                                       ++Y  k   +  g  t + +H +   +ii+  Gg++ i+l +++++  ++++  tv+v+ +++ v++
  gi|385806267|ref|YP_005842665.1|  19 RPYKVKRKALFGGYFTETKVHSEDEKEIIKVRGGNIKIKLKKASKAVIMSKDGKTVKVEKISRVVET 85 
                                       55555555555667788999************************99999999999999998888775 PP

>> EMG1  EMG1/NEP1 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   1.5e-05     0.091      96     147 ..      31      79 ..      20     117 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.5e-05
                                       HHHCCSEEEETTEE.SCEEEECS-HHHHCCC.SEEEEE-TTSEE-....... CS
                              EMG1  96 qLLkklsirategeekLlkviknpitdhlppgskiillsesaekklvdleef 147
                                         + + ++++++++ +++kv   +i+  l++ sk +++s+++++++  +e++
  gi|385806267|ref|YP_005842665.1|  31 GYFTETKVHSEDEK-EIIKVRGGNIKIKLKKASKAVIMSKDGKTVK--VEKI 79 
                                       5678899***9998.****************************554..3332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       840  (0.0468515); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 918.57
//
Query:       gi|385806268|ref|YP_005842666.1|  [L=102]
Description: signal recognition particle protein Srp19 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-18   67.0   0.1    2.4e-18   66.8   0.1    1.1  1  SRP19     SRP19 protein
  ------ inclusion threshold ------
      0.051   13.8   1.5       0.44   10.8   0.0    2.0  2  DUF1431   Protein of unknown function (DUF1431)


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 !   66.8   0.1   2.7e-22   2.4e-18       1      67 [.      12      78 ..      12     101 .. 0.85

  Alignments for each domain:
  == domain 1  score: 66.8 bits;  conditional E-value: 2.7e-22
                                      EEECCCCBTTS-CCCT--S-CCCSBSS--HHHHHHHHHHCTSCEEEEEEECTTSSTTCC.EEEEEC-. CS
                             SRP19  1 viYPvYldskktrkeGRrvpkelavenPtaqeiaealkalglevvvepeksyPrdwanp.GrVrvklk 67
                                      viYP Yld + +r +GR++pk+l+v++P+++ei e++k l l+ ++e +k++P++w++   rV v+++
  gi|385806268|ref|YP_005842666.1| 12 VIYPSYLDCTSSRTHGRKIPKSLCVQKPSISEILEVAKGLSLNPILE-DKKFPKKWWEIkQRVIVDKR 78
                                      7**********************************************.*******8865499*99985 PP

>> DUF1431  Protein of unknown function (DUF1431)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   4.9e-05      0.44     118     154 ..      12      48 ..       6      50 .. 0.89
   2 ?    2.1   0.7     0.024   2.2e+02      25      51 ..      59      85 ..      56     102 .] 0.70

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 4.9e-05
                           DUF1431 118 tpypsFSEckkeklpkarpveCeClkkpslCevwael 154
                                         yps+ +c++++++ ++  +  C++kps+ e+++++
  gi|385806268|ref|YP_005842666.1|  12 VIYPSYLDCTSSRTHGRKIPKSLCVQKPSISEILEVA 48 
                                       56****************************9998775 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.024
                           DUF1431 25 krkyqrtWvecppvkrkpkkvcclekk 51
                                      ++k+ ++W+e  +  +  k+   +e+ 
  gi|385806268|ref|YP_005842666.1| 59 DKKFPKKWWEIKQRVIVDKRWGKIETL 85
                                      6899******99988888876644444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); 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 0.29s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 639.74
//
Query:       gi|385806269|ref|YP_005842667.1|  [L=271]
Description: hypothetical protein FFONT_1227 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.011   15.8   0.3       0.06   13.4   0.1    2.3  2  CppA_N    CppA N-terminal
      0.012   15.2   0.0      0.021   14.4   0.0    1.5  1  FmrO      Ribosomal RNA methyltransferase (FmrO)


Domain annotation for each model (and alignments):
>> CppA_N  CppA N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   6.7e-06      0.06      43      98 ..     124     183 ..      83     187 .. 0.73
   2 ?   -1.3   0.0      0.24   2.2e+03      13      54 ..     203     247 ..     196     254 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.7e-06
                            CppA_N  43 eelfvieespslrtraveGtkkl.akiiikvenpke.iekllakga..qakklfkGqnGy 98 
                                        + f+ e sp+lr  a+e +kk+ + ++i ++++k  +  +la  +  + ++++k  n y
  gi|385806269|ref|YP_005842667.1| 124 FDAFLGEASPKLRYYAIEKNKKIyESLLIYSKKSKMlLTPILADADtdSLEEIYKNINNY 183
                                       468999****************94467888888776256799865434999****99998 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.24
                            CppA_N  13 lniafyqetlGlk..llseen.alavfsdwaeaeelfvieespsl 54 
                                       ln   + e++G k  l+se + +l+   d +++e+ f++  s +l
  gi|385806269|ref|YP_005842667.1| 203 LNLVEFVEKIGSKylLISEPKfSLVKKNDISKKEKAFLLRLSNKL 247
                                       666667777777732334432256666778888888887766655 PP

>> FmrO  Ribosomal RNA methyltransferase (FmrO)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   2.4e-06     0.021      82     217 ..      82     229 ..      52     249 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.4e-06
                              FmrO  82 rhastrer...LpfLrefyaavyaalPapasvlDvaCgLnpLavpw.lllaa.datylasDidsdlve...fldrfl 150
                                       +h+s  er   L+ ++ef   +  +   +++++D++ g  p+ +   l++a+ +  y+a + + ++ e   +  +  
  gi|385806269|ref|YP_005842667.1|  82 EHVSILERgknLTAILEFLKKL-MIEKNINTIVDIGSGTFPIYFDAfLGEASpKLRYYAIEKNKKIYEsllIYSKKS 157
                                       5777777633344445555554.355677888888888888887641455542456777777766665322222222 PP

                              FmrO 151 alveve..grve...vrDlvadvpapraDlaLvLktlpvLeqrrrGaglrLvetldapfvvvsfPtralggr 217
                                        ++  +    ++    +++  +       l+L+L++l+ L + +r   +++ve + +++ ++s P  +l ++
  gi|385806269|ref|YP_005842667.1| 158 KMLLTPilADADtdsLEEIYKNINNYDKSLTLLLRILHTLYRTKRLNLVEFVEKIGSKYLLISEPKFSLVKK 229
                                       23222200222200022333345666778***********************************99888665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1087  (0.060628); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); 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: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1647.45
//
Query:       gi|385806270|ref|YP_005842668.1|  [L=465]
Description: glutamine synthetase [Fervidicoccus fontis Kam940]
Scores for 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  388.8   0.0   2.3e-116  388.5   0.0    1.0  1  Gln-synt_C  Glutamine synthetase, catalytic domain
    9.2e-17   60.6   0.0    1.7e-16   59.7   0.0    1.5  1  Gln-synt_N  Glutamine synthetase, beta-Grasp 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 !  388.5   0.0  2.6e-120  2.3e-116       2     345 .]     103     462 ..     102     462 .. 0.96

  Alignments for each domain:
  == domain 1  score: 388.5 bits;  conditional E-value: 2.6e-120
                                       T-HHHHHHHHHHHHHHTTCEEEEEEEEEEEEESEECCCE.SSEEEEEEE.T.......B...B.TSS-TTBHCCCCC CS
                        Gln-synt_C   2 rdPRsvlkralarlaeeGltvvvgpElEFflfdkeedke.asksllevdse.......ekgrpaekggyfsvapvde 70 
                                       +dPR+v+++++a++++ G++ ++++ElEF++fd+ +    +  s +e++s        +++  + kggy+  +p+de
  gi|385806270|ref|YP_005842668.1| 103 TDPRYVAQKTIAYTSSFGYNSLTAAELEFYIFDEIRSWLrPLFSGFEIKSGsagydekTNHSLTIKGGYYVPPPFDE 179
                                       79*******************************9998665666666666668999998889999************* PP

                                       TCCHHHHHHHHHHHT.T--EECCEEECCCT.EEEEEE--EECHHHHHHHHHHHHHHHHHHHHTT-EEE-SSSSSTTS CS
                        Gln-synt_C  71 aedlrreivealeal.gieveashhEvatg.QvEinlkfadalkaaDnvvtfKrvvkevArkhgltatFmpKplegd 145
                                         ++r+ei + l+++ +i++e++hhEv+ + Q Ein++  d++++ Dn++ +K+v + vA+k+g+ +tFmpKp+++d
  gi|385806270|ref|YP_005842668.1| 180 SIKIRSEISDLLQDFyKITIESHHHEVGGAgQGEINMQALDPVSTSDNIQRIKYVSRFVAHKYGKIITFMPKPISDD 256
                                       ************87539**********9888********************************************** PP

                                       ---BEEEEEEEEECTTEESSB-TTSGGG.B-HHHHHHHHHHHHHHHHHHHHHS-SCCHHHHCSSSTTSSSBEEEESS CS
                        Gln-synt_C 146 nGsgmHvhlSlwdkdgknlfadeddeya.lselarhfigGllkhakaltaltaptvnSYkRlvpgyeaPvalawgar 221
                                       +G+gmHvh+Slw ++gkn+f+d +d+ya +s+ ar+figGll h kal+a+++ptvnSYkRl p+yeaP+ l+w++ 
  gi|385806270|ref|YP_005842668.1| 257 AGNGMHVHVSLW-NNGKNAFYDINDDYAgISQEARYFIGGLLSHGKALSAIVSPTVNSYKRLLPHYEAPIFLTWSKG 332
                                       ************.**************99************************************************ PP

                                       -TTCSEEEE-...TSGGCSTEEEECEBTTS-HHHHHHHHHHHHHHHHHTT--------S-SSSS-TTTH..TSS-B- CS
                        Gln-synt_C 222 NRsallRipa...skekakrvElRlpdasaNPYLalAallaAgldGienklepgepvekdlyelspeer..kgieel 293
                                       NRsa++Rip    + e+ krvE+R pd+s+NPYLa++a++ Ag+dGi +k++pg+p+++++y++++++   ++ie+l
  gi|385806270|ref|YP_005842668.1| 333 NRSAAVRIPSyhkNYERRKRVEYRPPDPSCNPYLAISAIILAGIDGIVKKIDPGDPIDENIYKMAESKLreLKIERL 409
                                       **********9877788999**********************************************998899***** PP

                                       -SSHHHHHHHHHCS.HHHCCSS-HHHHHHHHHHHHHCHHHHHCT--HHHHHHH CS
                        Gln-synt_C 294 PasleeAlealeed.ellkevlgeevieaylalkraEleeleeevsdwelery 345
                                       P+sl++Al++l +d e+l+ ++++++ie y++lkr+E+e++++++s+ e+  y
  gi|385806270|ref|YP_005842668.1| 410 PSSLDKALDELLNDnEFLRPAFSQSLIELYIELKRKEIEKINRTISPAEFYYY 462
                                       **************9**********************************9876 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 !   59.7   0.0   1.9e-20   1.7e-16       2      82 ..      15      94 ..      14      95 .. 0.95

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 1.9e-20
                                      --EEEEEEE-SSS-EEEEEEEHHHHHHHTTTT-E.EEETTSSTTT------EEEEEEEGGGEEE-SS-SS-.EEEEEEE CS
                        Gln-synt_N  2 vkfvdlqFtDikgklkhvtipadelsedaleegv.sFDGSsiegfaeieeSDmlLkPdlstavidPfreekktarvicd 79
                                       k+++lq tD+ g +++v i+++ ++eda++ g+ ++DGSs+ gf+ei eSD+ L+P+l+t+ + Pf+  + ta +i +
  gi|385806270|ref|YP_005842668.1| 15 LKWINLQLTDLLGIFRQVVISSKMFDEDAINLGIgKLDGSSVYGFKEIYESDLTLRPVLDTLRTNPFEI-N-TADIITE 91
                                      689******************9999******************************************96.4.7****** PP

                                      EE- CS
                        Gln-synt_N 80 vyd 82
                                      v+d
  gi|385806270|ref|YP_005842668.1| 92 VFD 94
                                      997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (465 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); 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: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 2900.01
//
Query:       gi|385806271|ref|YP_005842669.1|  [L=326]
Description: hypothetical protein FFONT_1229 [Fervidicoccus fontis Kam940]
Scores for complete 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   33.7   0.3    5.1e-08   32.7   0.3    1.5  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
  ------ inclusion threshold ------
      0.028   14.5   1.4          4    7.6   0.1    3.0  3  HHH_2           Helix-hairpin-helix motif
       0.12   12.5   1.6        0.5   10.5   0.0    2.8  3  DUF1296         Protein of unknown function (DUF1296)
       0.45   10.8   5.2       0.36   11.2   2.4    2.3  2  DUF1947         Domain of unknown function (DUF1947)


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 !   32.7   0.3   1.1e-11   5.1e-08       3      43 ..      10      50 ..       8      52 .. 0.89

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 1.1e-11
                                      ETTEEEEEE-CCCHHHCCEECTCEEEEEECTTCCCCCCCHH CS
                    MazE_antitoxin  3 vGnsgavriPkevrfelgireGdevelevdgdkiilrplks 43
                                      +++s+++++Pk ++ + gi++Gd+v +++ +  + ++ +++
  gi|385806271|ref|YP_005842669.1| 10 GSSSLIITLPKSWVNKVGIKAGDSVYIIEREKELRIIAFEN 50
                                      789**************************999888877765 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1    0.0009         4      23      56 ..     151     184 ..     146     189 .. 0.91
   2 ?    4.3   0.0    0.0093        42      13      57 ..     196     241 ..     196     242 .. 0.89
   3 ?   -1.8   0.0      0.77   3.5e+03      44      58 ..     272     286 ..     256     291 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0009
                             HHH_2  23 FksldaLkkasleeLlevddiGeeiAqsivefFe 56 
                                        +sl  + + s++eL +v++  e  A++i+ fF+
  gi|385806271|ref|YP_005842669.1| 151 LESLTSFNEKSFDELKKVKEAFELRASNIKHFFN 184
                                       5799999**************************7 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0093
                             HHH_2  13 ektAklLakrFksldaLkkasleeLlevddiGee.iAqsivefFen 57 
                                       ek Akl ++ + s+ ++ +  l++Ll + +iGee i+++ ve+F+n
  gi|385806271|ref|YP_005842669.1| 196 EKKAKLKMTIYYSIYNILRNLLDTLLVLIEIGEEdISKNEVEYFKN 241
                                       57788889999*********************86599999999986 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.77
                             HHH_2  44 GeeiAqsivefFene 58 
                                        + i+++i ef++n 
  gi|385806271|ref|YP_005842669.1| 272 FTNISNNISEFLANG 286
                                       567899999999875 PP

>> DUF1296  Protein of unknown function (DUF1296)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       1.2   5.3e+03      19      28 ..      48      57 ..      36      59 .. 0.71
   2 ?   -1.3   0.0      0.54   2.4e+03      41      59 ..      89     107 ..      87     108 .. 0.85
   3 ?   10.5   0.0   0.00011       0.5      16      44 ..     124     152 ..     121     170 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.2
                           DUF1296 19 hsdeeIyamL 28
                                       ++ee+ya+ 
  gi|385806271|ref|YP_005842669.1| 48 FENEEVYAVV 57
                                      6899999985 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.54
                           DUF1296  41 kLLsqDtfheVkskrdkkK 59 
                                        L+  D   eV s +d++K
  gi|385806271|ref|YP_005842669.1|  89 ELITDDIAREVMSVKDENK 107
                                       699999999**99999887 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.00011
                           DUF1296  16 vgkhsdeeIyamLkecnmDpneavqkLLs 44 
                                       v+k++de+I a+L+e+    + a++kLL 
  gi|385806271|ref|YP_005842669.1| 124 VSKMTDEDIDAILRESLISFEGAINKLLE 152
                                       6789***********************95 PP

>> DUF1947  Domain of unknown function (DUF1947)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   2.4   8.1e-05      0.36       7      57 ..      40      91 ..      38      92 .. 0.86
   2 ?   -2.4   0.0       1.4   6.3e+03      31      37 ..     224     230 ..     216     244 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 8.1e-05
                                      HHHHHHHHHHHHTTT---TT--...-EEEE-S.S-EEEEETTEEEEEE.SSSEE CS
                           DUF1947  7 kKeakeileklkekyisislesdk.iEieeek.keklYlingvpilfe.eekli 57
                                      +Ke + i  + +e y  +++e+++ iE  e k k+k++++ g+p+++  + +li
  gi|385806271|ref|YP_005842669.1| 40 EKELRIIAFENEEVYAVVEFEKNQlIE--EIKnKAKCLMYAGIPYFILkSNELI 91
                                      8999****9**************8555..555589***********98777776 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.4
                                       -EEEE-S CS
                           DUF1947  31 iEieeek 37 
                                       iEi+ee+
  gi|385806271|ref|YP_005842669.1| 224 IEIGEED 230
                                       5565553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1093  (0.0609627); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); 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: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2158.04
//
Query:       gi|385806272|ref|YP_005842670.1|  [L=299]
Description: transcription initiation factor IIB [Fervidicoccus fontis Kam940]
Scores for complete 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-19   69.1   0.4    6.8e-10   38.9   0.0    2.6  2  TFIIB         Transcription factor TFIIB repeat
    2.2e-05   23.8   0.1    4.1e-05   23.0   0.1    1.4  1  TF_Zn_Ribbon  TFIIB zinc-binding
  ------ inclusion threshold ------
      0.068   12.9   0.1       0.17   11.6   0.1    1.6  2  Cyclin_N      Cyclin, N-terminal 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 !   38.9   0.0   1.1e-13   6.8e-10       5      60 ..     119     174 ..     115     185 .. 0.93
   2 !   27.9   0.1   2.9e-10   1.7e-06       1      63 [.     211     273 ..     211     276 .. 0.95

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 1.1e-13
                                       HHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHH CS
                             TFIIB   5 adaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkei 60 
                                       a +l+Lp+kV++ A + +k+++e+++  G    +++AA+l++Acr+ +v rt+  +
  gi|385806272|ref|YP_005842670.1| 119 ARKLGLPQKVTETAAYYIKKVVEKGLGRGEMIRAYVAASLFMACRLMKVPRTFYSV 174
                                       789*************************************************9765 PP

  == domain 2  score: 27.9 bits;  conditional E-value: 2.9e-10
                                       HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHH CS
                             TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissv 63 
                                       i+++ ++l+L+ + ++    la+   + ++  G+sp+++aAA  yiA+  +++k+ qk+i+s 
  gi|385806272|ref|YP_005842670.1| 211 IPMITSKLGLSMQSENLMYRLANAIEKLNMDHGKSPIALAAATAYIASSIFGEKKNQKDIASA 273
                                       7899999999999999999*****************************************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 !   23.0   0.1   6.9e-09   4.1e-05       5      43 .]      11      46 ..      11      46 .. 0.95

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 6.9e-09
                                      TTTCEECHEETSTTCEEESSSSBEEEECCCCCCCHHHHH CS
                      TF_Zn_Ribbon  5 nCgstnlveDpergelvCtdCGlVlednsidegpewref 43
                                      nC +t  + D ergel+C d G+V+   +id+gpewr+f
  gi|385806272|ref|YP_005842670.1| 11 NCQHT--IADMERGELICLDTGEVIS-TIIDSGPEWRDF 46
                                      79987..9*****************8.9*********98 PP

>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   2.8e-05      0.17      33     102 ..     110     177 ..      72     196 .. 0.70
   2 ?   -2.2   0.0      0.53   3.2e+03      18      74 ..     209     267 ..     192     274 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.8e-05
                                       HHHHHHHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSSS---HHHHHHHT CS
                          Cyclin_N  33 ilidwlvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKveeisppkledlvyit 102
                                        +++ l + a+k+ l +++  +a+ y+ ++++k   + ++++  +a++L++A+++ ++  p+    v+i+
  gi|385806272|ref|YP_005842670.1| 110 KALQILNDEARKLGLPQKVTETAAYYIKKVVEKGLGRGEMIRAYVAASLFMACRLMKV--PRTFYSVIIS 177
                                       3567788889999*******************9999999***************9554..5555444444 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.53
                                       TCT.TCTSSS-HHHHHHHHHH.HHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHH CS
                          Cyclin_N  18 dyl.dqqpelnpemRailidw.lvevaekfkltpetlflavnyldRflskksvpkdklq 74 
                                       dy+ +  ++l  +m +  +++ l +  ek+++++    +a+     ++++ ++ ++k q
  gi|385806272|ref|YP_005842670.1| 209 DYIpMITSKLGLSMQSENLMYrLANAIEKLNMDHGKSPIALAAATAYIASSIFGEKKNQ 267
                                       44455555555555554444447777777777776666666666666666666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.50
# Mc/sec: 1803.18
//
Query:       gi|385806273|ref|YP_005842671.1|  [L=93]
Description: hypothetical protein FFONT_1231 [Fervidicoccus fontis Kam940]
Scores for complete 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-09   36.5   0.1    4.3e-09   36.3   0.1    1.1  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 !   36.3   0.1   2.4e-13   4.3e-09      20      85 ..       6      70 ..       3      91 .. 0.81

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 2.4e-13
                                      EEEEEEEEEEETTEE.EEEE---S--B--BTT-EEEETT--EEEE--EEES-SSS-EEEEE--GGHH CS
                              Gar1 20 vleiGtvssivenev.viksttsgekkvldfnsilflenktqiGkVdEifGpvnepyysVklnssee 85
                                      ++++G ++++  n++ ++k t  ++k++++++ ++ l + +  GkV +++G+vn+py ++k+ ++ee
  gi|385806273|ref|YP_005842671.1|  6 LKKLGVIEKVATNNLlLVKIT--DSKNIPNIGNRVLLPDFRGFGKVMDVIGNVNNPYAVIKPFKKEE 70
                                      5789****9998865156666..347***********************************875533 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); 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 0.26s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 640.18
//
Query:       gi|385806274|ref|YP_005842672.1|  [L=987]
Description: leucyl-tRNA synthetase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-52  178.1   5.1    2.9e-50  171.1   5.1    3.2  1  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    6.5e-24   84.4   4.0    1.3e-12   47.2   0.0    3.8  4  tRNA-synt_1g   tRNA synthetases class I (M)
    2.8e-17   63.1   4.3      1e-16   61.3   2.6    2.8  2  Anticodon_1    Anticodon-binding domain of tRNA
    1.1e-14   54.5   0.4    1.4e-08   34.5   0.0    3.0  3  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain
    4.7e-09   36.0   0.0    9.7e-09   35.0   0.0    1.4  1  tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2


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 !  171.1   5.1   8.1e-54   2.9e-50       2     601 ..      18     693 ..      16     694 .. 0.85

  Alignments for each domain:
  == domain 1  score: 171.1 bits;  conditional E-value: 8.1e-54
                       tRNA-synt_1   2 lyekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaiea 78 
                                       + e We+ ++ ++    e ++k+f l++  Py +G lH+Gha +  + d++ rykr++G++vl+ + +   G +i +
  gi|385806274|ref|YP_005842672.1|  18 WNEVWEKIKINEAD--PEPSRKKFYLTAAYPYPNGPLHLGHARTYLIPDVIARYKRLQGYNVLFPMAFHFTGTPILS 92 
                                       66788888887776..5666999***************************************************987 PP

                       tRNA-synt_1  79 kvek.....klgakekkerkklgreefrekvr..ewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfv 148
                                         e+     +  +ke +e +++++e+  +      ++++++e+ +k++k+   s+D+ re  T+d+e++  +++ f 
  gi|385806274|ref|YP_005842672.1|  93 SSEAiargeEHLIKEFRELYEVSEEDLEKLKTplGMANYFKERAKKDMKDYMLSIDWRREFTTIDPEYSSFITWQFL 169
                                       76541111122355556778888887755433225788999************************************ PP

                       tRNA-synt_1 149 rladkgliyrgkklvnwstklktalselEv..eykdkkdalihvafpladkeevklviaTTtPeTllgdtavavnpe 223
                                       +l ++g i +g+++v w++  + ++   ++  + + + +  + + f+ +d++      aT +PeT++g t + vn +
  gi|385806274|ref|YP_005842672.1| 170 KLKERGYIVQGTHPVGWCPYHQMPVGMHDTkgDVEPEIQEYTLILFEGEDGT--IYPTATLRPETIFGVTNLWVNED 244
                                       ********************99998776662233333344555666555554..4789******************* PP

                       tRNA-synt_1 224 ldyv...itkeklilaeallkslv.kkesekkiledergkeLegkevelplvnrkipiiaddyvdkeaGtGvVkiaP 296
                                        +yv   i+++k+ l ++   +++ +k++ + i++  +g ++ gk+v++p++++ + i+   +vd  +GtGvV   P
  gi|385806274|ref|YP_005842672.1| 245 AEYVianIDGKKYFLSKQAFYKITfQKKNVQLIKDAGKGVNVLGKKVRNPITGKVVSILPSSFVDPSTGTGVVMSVP 321
                                       ****999999999999877766651555778899999**************************************** PP

                       tRNA-synt_1 297 ahdedDyevgkkynlevinildedgtlteea.............................................. 327
                                        h + Dy + k  ++   n +++ g  +e++                                              
  gi|385806274|ref|YP_005842672.1| 322 SHAPYDYVALK--EIISSNEVKKFGLDEEKLkpvpviylkgyspnpaedvvqkykiksvkekenldkatkelyleef 396
                                       *******8755..5677788888887777778888888888888888999*************************** PP

                       tRNA-synt_1 328 ..........................aefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrate 378
                                                                 +  +g +v+d +k+v++ l  +       +i  +  +c  + ++++  + +
  gi|385806274|ref|YP_005842672.1| 397 sngviredliktiavdvadrkvieliEGIRGKNVKDVKKNVISFLLSNKIGDMFYEIANKPVYCRCGTEIVVKLLEN 473
                                       *************************999***************998887777777888887788888888889999* PP

                       tRNA-synt_1 379 qWfvrvke..ladaalkave.kvqfvpkskekryaswleniqdWciSRqrwWGhripl...fvsketeevvvreelk 449
                                       qWf+  ++   +d++ ka+e ++++vp+ +++ +++ +e  +  +  R+r  G+ +p    ++ ++  + ++     
  gi|385806274|ref|YP_005842672.1| 474 QWFIDYENqkWKDKVRKALEnRIEIVPEEYKEWFFNTIEWLKKRACARSRGLGTSLPWdknWIIESLSDSTIYMAFY 550
                                       ****998766889999999989***********************************65558888888877777788 PP

                       tRNA-synt_1 450 elvagreeeeaekkalekeakdklkkekgelekdedvlDvWFsSgswpfstlgypeedteelkkffpadmlleGlDi 526
                                        + +++   + ++++l++e+ d +  + g+ + +++ l +        + +l+   + ++e+   +p d   +G D 
  gi|385806274|ref|YP_005842672.1| 551 TVIKKIRDYKITSEKLTEEFWDYVFLGYGDEKEISEKLKI-------DTEVLK---SIRNEFLYWYPLDNRHSGKDL 617
                                       8888888888888888899999886666666666666543.......344555...33679999************* PP

                       tRNA-synt_1 527 irgWvarlillslaltgsePf.kevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltli.lsdvgrdinl 601
                                       +   ++ +++  +a++ ++ + k+++v+g ++  eG KmSKslgN i   + i+ +g + lR  l+ +++ g+d n 
  gi|385806274|ref|YP_005842672.1| 618 VPNHLSFMLFNHIAIFPENLWpKRIVVNGHIMV-EGVKMSKSLGNFIPMFKAIRDVGPNTLRVSLLySAEIGNDANY 693
                                       ****************99955489999**9985.7*******************************77888888775 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 !   47.2   0.0   3.5e-16   1.3e-12       2      73 ..      40     111 ..      39     124 .. 0.88
   2 ?    1.6   0.0     0.025        90      61     128 ..     123     192 ..     113     201 .. 0.80
   3 ?   -3.2   1.9      0.73   2.6e+03     181     256 ..     472     547 ..     452     581 .. 0.60
   4 !   34.2   0.0   3.2e-12   1.2e-08     289     379 ..     614     705 ..     599     713 .. 0.85

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 3.5e-16
                                       EEEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHH CS
                      tRNA-synt_1g   2 lvttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvhee 73 
                                       ++t+a pY+ng+lHlGh++++++ D++aRykrl+g++vlf  +    Gtpi  + e+     e+l+++++e 
  gi|385806274|ref|YP_005842672.1|  40 YLTAAYPYPNGPLHLGHARTYLIPDVIARYKRLQGYNVLFPMAFHFTGTPILSSSEAIARGEEHLIKEFREL 111
                                       79*************************************************999888877778888777655 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.025
                                       S-HHHHHHHHHHHHHHHHHHTT---S..EEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTE CS
                      tRNA-synt_1g  61 vtpeelvekvheeikelfkklnisfd..kygrttseehkelvqeifkklkekgliyekeieqlycpkder 128
                                        tp  +++ ++e+ k+++k++ +s d     +t + e +++    f klke+g+i +++  + +cp +++
  gi|385806274|ref|YP_005842672.1| 123 KTPLGMANYFKERAKKDMKDYMLSIDwrREFTTIDPEYSSFITWQFLKLKERGYIVQGTHPVGWCPYHQM 192
                                       67888899999999999999877777323335667777888888899************99999998775 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 0.73
                                       EEEEEE-G..GGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS-EETTECCEEE-HHHHHHHHH CS
                      tRNA-synt_1g 181 tehlffkl..skfekklkewieeeekeleenvkkivkewlkegLkdlaisrdldwGipvPgaekkvlYVWldAligY 255
                                       ++++f +   +k+++k+++ +e++ +  +e+ k+   ++++  Lk++a +r    G ++P +++ ++    d +i Y
  gi|385806274|ref|YP_005842672.1| 472 ENQWFIDYenQKWKDKVRKALENRIEIVPEEYKEWFFNTIEW-LKKRACARSRGLGTSLPWDKNWIIESLSDSTI-Y 546
                                       455664441156778888888555555888888888888877.99999999999999999555555544444444.3 PP

                                       H CS
                      tRNA-synt_1g 256 i 256
                                       +
  gi|385806274|ref|YP_005842672.1| 547 M 547
                                       3 PP

  == domain 4  score: 34.2 bits;  conditional E-value: 3.2e-12
                                       EGGGHHHHHTHHHHHHHH..TT----S-EEEE--EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS- CS
                      tRNA-synt_1g 289 gkdiikFHtifwPaillg..aelklpkkvvaheyltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkD 363
                                       gkd ++ H  f     ++   e   pk++v++++++veg K+SkS g+++ + +a+  + +++lR  l+++a+  +D
  gi|385806274|ref|YP_005842672.1| 614 GKDLVPNHLSFMLFNHIAifPENLWPKRIVVNGHIMVEGVKMSKSLGNFIPMFKAIRDVGPNTLRVSLLYSAEIGND 690
                                       8999999976655555554477779**************************************************** PP

                                       EEE-HHHHHHHHHHHC CS
                      tRNA-synt_1g 364 ldfswedfvervNseL 379
                                       +++s e +v+ v ++L
  gi|385806274|ref|YP_005842672.1| 691 ANYSKE-LVRVVQDKL 705
                                       ***965.566666665 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 !   61.3   2.6   2.8e-20     1e-16       1     145 [.     735     866 ..     735     872 .. 0.84
   2 ?   -1.2   0.0      0.51   1.8e+03       7      46 ..     896     936 ..     894     943 .. 0.83

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 2.8e-20
                       Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrll 77 
                                       d+w++s++ ++vk+vt+++e y +++a+ +++  + +++   y+ + ++  +           ++l e+++++++++
  gi|385806274|ref|YP_005842672.1| 735 DKWFISKFKRIVKRVTDDLEGYVLRDAVVQIFFETEQSI-EEYISIKQNPNS-----------KILNEIIHEWIIMM 799
                                       9*******************************9877776.99*999766642...........8************* PP

                       Anticodon_1  78 aPfmPfitEelwqreeeelgkk...esimlaewpekaeel..ekeleeeevellkeivkairklrselkikps 145
                                       +Pf+P ++E+lw    +++ k+   +s+++++wp +++e   +  + e ++ ++++i++ i+ +++ lk  p+
  gi|385806274|ref|YP_005842672.1| 800 SPFVPSFAEDLW----HLVTKDpieKSVFNNKWP-DYNEIssYSFE-ELAIIYMERIISDIEGIKKALKKTPN 866
                                       ************....55544446699*******.77666664444.56788888899999999998887766 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.51
                       Anticodon_1   7 elnklvkevteayee.yrfnkaasalyeffwndlcdwylel 46 
                                       el +++++    y++ y+ ++ +++ y+ + +d++d++l++
  gi|385806274|ref|YP_005842672.1| 896 ELTSAISKEIGGYANpYQVAEQFNEFYQSIPEDISDFILKS 936
                                       6777777777888888**************9***9999876 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 !   16.8   0.0     9e-07    0.0032      23      75 ..      52     104 ..      34     147 .. 0.75
   2 ?   -2.6   0.3      0.73   2.6e+03      97     144 ..     414     464 ..     367     487 .. 0.53
   3 !   34.5   0.0   3.9e-12   1.4e-08     209     299 ..     609     701 ..     597     703 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 9e-07
                                       -BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTTS-HHHH CS
                      tRNA-synt_1e  23 shlGhaRslvafDilrrilqalgYdvqfvqnvtDidDkiikrareeeksvkel 75 
                                        hlGhaR++++ D+++r+ + +gY+v f   +      i+  +++  +  ++l
  gi|385806274|ref|YP_005842672.1|  52 LHLGHARTYLIPDVIARYKRLQGYNVLFPMAFHFTGTPILSSSEAIARGEEHL 104
                                       7*************************997766655555555555554444444 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.73
                                       B--BGGGGHHHHHH.HHHHHHHTTSEEE-TT..S-EEE-GGG-TTTTTTTT CS
                      tRNA-synt_1e  97 leprvsekvdeiie.lvekliekgyaYavsd..gdvyfdvskkeeYgklsk 144
                                       +  +v e ++ i +  v+ + ++ +++  s+  gd+ ++  +k+ Y ++ +
  gi|385806274|ref|YP_005842672.1| 414 ADRKVIELIEGIRGkNVKDVKKNVISFLLSNkiGDMFYEIANKPVYCRCGT 464
                                       223344444444321344444445555555577888888888888888765 PP

  == domain 3  score: 34.5 bits;  conditional E-value: 3.9e-12
                                       EEEEEEGGGTTTHHHHHHHHHHHHSS.S--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHH.HHSS CS
                      tRNA-synt_1e 209 dihsGGiDLafPhhenelaqseaafd.kqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRll.llsa 283
                                       d    G+DL+  h    l  + a f  + + k  + ngh+++eg kmsksL+nfi + ++++ + p++lR+  l+sa
  gi|385806274|ref|YP_005842672.1| 609 DNRHSGKDLVPNHLSFMLFNHIAIFPeNLWPKRIVVNGHIMVEGVKMSKSLGNFIPMFKAIRDVGPNTLRVSlLYSA 685
                                       5556789999999999999999999867899***************************************8615688 PP

                                       -TTS-EEE-HHHHHHH CS
                      tRNA-synt_1e 284 hyrsqldfkeelleea 299
                                       +  +  ++++el++ +
  gi|385806274|ref|YP_005842672.1| 686 EIGNDANYSKELVRVV 701
                                       9999999999998766 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 !   35.0   0.0   2.7e-12   9.7e-09      27     126 ..     227     328 ..     214     341 .. 0.80

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 2.7e-12
                     tRNA-synt_1_2  27 ttrpdtlfGvtfvalapehplvekl.aekkkel..aafieevkkksesereletkekeGv.ftglkaihPitgekip 99 
                                       t rp+t+fGvt + +  + + v +    kk  l  +af + + +k++ +  + +   +Gv   g k+ +Pitg+ + 
  gi|385806274|ref|YP_005842672.1| 227 TLRPETIFGVTNLWVNEDAEYVIANiDGKKYFLskQAFYKITFQKKNVQL-I-KDAGKGVnVLGKKVRNPITGKVVS 301
                                       77***************999876653444444421567666666665553.4.4556788689************** PP

                     tRNA-synt_1_2 100 iwvanyvlmeygtgavmavPahdqrDf 126
                                       i  + +v  + gtg+vm+vP+h   D+
  gi|385806274|ref|YP_005842672.1| 302 ILPSSFVDPSTGTGVVMSVPSHAPYDY 328
                                       **********************98887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (987 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       833  (0.046461); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); 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: 0.88u 0.32s 00:00:01.20 Elapsed: 00:00:00.54
# Mc/sec: 5520.73
//
Query:       gi|385806275|ref|YP_005842673.1|  [L=378]
Description: diaminopimelate decarboxylase [Fervidicoccus fontis Kam940]
Scores for complete 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-46  157.4   0.0    5.2e-46  157.0   0.0    1.1  1  Orn_Arg_deC_N    Pyridoxal-dependent decarboxylase, pyridoxal
    1.3e-26   92.7   0.0    1.3e-26   92.7   0.0    1.2  1  Orn_DAP_Arg_deC  Pyridoxal-dependent decarboxylase, C-termina


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 !  157.0   0.0   5.8e-50   5.2e-46       8     247 .]       6     240 ..       2     240 .. 0.96

  Alignments for each domain:
  == domain 1  score: 157.0 bits;  conditional E-value: 5.8e-50
                                       HHHHHHHCT..CCEEEEEGGG---HHHHHHHHHTTEEEEESSHHHHHHHHHCTTTGGGEEEEESS--HHHHHHHHHC CS
                     Orn_Arg_deC_N   8 lkrwkkalp..rikvfYavKansdlavlellaelGlgldcaSkaElelvlaagvsperiifanpckqreelryalek 82 
                                       ++r kk+++  + +v Y  Kan+++ +l++l+e+G gld++S  E  l +++g++ ++i f++++ ++ee++ ++e 
  gi|385806275|ref|YP_005842673.1|   6 YERLKKSIKyrDLEVLYSCKANNNIDILKVLKEEGSGLDVVSPFEALLGVKLGFQKDKILFTGNNVSNEEMKFLKEL 82 
                                       5677777777799**************************************************************** PP

                                       THTEEEESSHHHHHHHHHHHCCEEEEEEEE-SCCSSSSTCCCSSSTTSSSSEEHCHHHHHHHHHHHHTTEEEEEEE- CS
                     Orn_Arg_deC_N  83 gvkvvtvdnveeleklaklapeakvllRiktdvsaatcelistggessKFGaaleeavealleaakeenlqlvGvsf 159
                                       g+  +++d+ ++l++   + p+ ++++Ri++++  +++e+  tgg  +KFG+ l +++ea++e   + nl + G+++
  gi|385806275|ref|YP_005842673.1|  83 GIL-INIDSISQLKRYGIMFPGTDISIRINPGIGYGHHEYAKTGG-LTKFGIYL-NEIEAAKEYVMKYNLRIRGIHI 156
                                       **9.************************************88887.69******.9********************* PP

                                       --BSSC-SCHHHHHHHHHHHHHHHHHHHHT---SEEE--S-BS-HCSTTSSSSTHHHHHHHHHHHHHHHHHTSSS-E CS
                     Orn_Arg_deC_N 160 HvGSgvsdleafvkavekalklfdelaelGvklkiLdvGGGfgveyeeeeeplkleeiaekirealeeafpgdkevt 236
                                       H+GSg+ ++ ++ +a++ +lk+ +e +    +l+++d+GGG+g+ y+ +ee+ +l +  ek++  le++ +++ +v+
  gi|385806275|ref|YP_005842673.1| 157 HIGSGILQTDPYISALNILLKIANEFK----DLEFIDLGGGLGIPYRPGEEKFDLGDFGEKVSSILEDFSRKHGHVK 229
                                       ****************99999999987....6799****************************************** PP

                                       EEE--SHHHHG CS
                     Orn_Arg_deC_N 237 iiaEpGRalva 247
                                       + +EpGR++v+
  gi|385806275|ref|YP_005842673.1| 230 LRIEPGRYIVG 240
                                       *********95 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 !   92.7   0.0   1.4e-30   1.3e-26       5      98 .]     237     334 ..      21     334 .. 0.79

  Alignments for each domain:
  == domain 1  score: 92.7 bits;  conditional E-value: 1.4e-30
                                       E...GGEEEEEEEEEEEEET.C...EEEEEES--TTTS-HHHHCTT-S-E.ESBTT-SCEEC.EEEEEEEE-SSSST CS
                                       x...xxxxxxxxxxxxxxxx.x...xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Orn_DAP_Arg_deC   5 d...eagvLvtrViavkese.k...kkfvivdaGmndllrpalygsfhei.pvkeeeaekeeeeeeevdvvGptCes 73 
                                           ++gvL++rV+++k+++ +   k f+ vd Gmn+l+rp+lygs+hei  v+    ++++e+e  +d+vG++Ce+
  gi|385806275|ref|YP_005842673.1| 237 YivgSCGVLLVRVVSIKDVSlNgkrKIFIGVDSGMNHLIRPSLYGSYHEIiDVT----KASDEKEIVADIVGNICET 309
                                       05559*************775577799***********************7775....345567789********** PP

                                       T-EEEEEEEEEE--TT-EEEESS-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Orn_DAP_Arg_deC  74 gDvlakdrelpelevGdllafedaG 98 
                                       gD+la dr +p++e+Gd+la++daG
  gi|385806275|ref|YP_005842673.1| 310 GDFLALDRPMPKVEEGDVLAVMDAG 334
                                       ************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2424.39
//
Query:       gi|385806276|ref|YP_005842674.1|  [L=147]
Description: YbaK/prolyl-tRNA synthetase associated domain-containing protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.4e-24   84.4   0.0      8e-24   84.1   0.0    1.0  1  tRNA_edit  Aminoacyl-tRNA editing domain


Domain annotation for each model (and alignments):
>> tRNA_edit  Aminoacyl-tRNA editing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.1   0.0   4.4e-28     8e-24       4     121 ..      20     135 ..      18     137 .. 0.96

  Alignments for each domain:
  == domain 1  score: 84.1 bits;  conditional E-value: 4.4e-28
                         tRNA_edit   4 tktieelaaalgvdpsaiaKtlvlkdkkgelvlvllpgdreldlkklakllgakklrlaseeelrellgvepGgvgP 80 
                                       ++t+e++    g + ++iaKtl++k  ++e+v+++++gdr++d+ k+   lg  k +las+e+++++lg epG+v+P
  gi|385806276|ref|YP_005842674.1|  20 VETVEKASLLSGEPREKIAKTLLFKL-NNEYVVFIVRGDRKVDYIKANDILG-TKPQLASPEDVKRILGTEPGAVSP 94 
                                       789999999999*************7.777**********************.************************ PP

                         tRNA_edit  81 lglkaagvpvllDeslkeyptvvvgagengatlelspedlr 121
                                       +  + ++++++lD++++e++ +++g+g+++++ ++++ dl+
  gi|385806276|ref|YP_005842674.1|  95 IDRQIKKLKIFLDPKILEEEYILCGGGSKNKLYKVKTSDLI 135
                                       **98**********************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 927.47
//
Query:       gi|385806277|ref|YP_005842675.1|  [L=175]
Description: hypothetical protein FFONT_1235 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-09   37.6   0.7    4.3e-09   36.9   0.7    1.4  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   0.7   2.4e-13   4.3e-09       1      73 [.       5      96 ..       5     118 .. 0.77

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 2.4e-13
                          CxxCxxCC  1 eCkeC.gaCCk....elkvklteedlerlkaaevaeeeeeskkiak..............adgrCvfldeetklCkiYe 60
                                      +C  C + CC+    e+++ + + + +rl++ ++  + +e   i+k               +grC fl++e ++C+i++
  gi|385806277|ref|YP_005842675.1|  5 NCLLCgAVCCTfkseEESPLVFPWEKRRLERLNK-SSMFEPYIIYKinneeigvlmyrwkIEGRCLFLNRE-GRCTIHN 81
                                      5999*6679*999996677777777777777777.33333333344678899*******************.6****** PP

                          CxxCxxCC 61 eRpkicrlfpas..e 73
                                      ++p+ c++fp     
  gi|385806277|ref|YP_005842675.1| 82 SKPLSCKMFPLIigL 96
                                      **********97653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); 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: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.40
# Mc/sec: 1329.09
//
Query:       gi|385806278|ref|YP_005842676.1|  [L=367]
Description: aspartate aminotransferase [Fervidicoccus fontis Kam940]
Scores for complete 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-127  425.9   0.1   1.7e-127  425.7   0.1    1.0  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    5.7e-07   29.0   0.1    8.3e-07   28.5   0.1    1.4  1  Aminotran_1_2    Aminotransferase class I and II
    1.9e-05   23.8   0.5    7.4e-05   21.9   0.1    1.8  2  Aminotran_5      Aminotransferase class-V
     0.0029   17.0   1.4      0.012   14.9   1.4    1.8  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
      0.051   13.5   0.2       0.18   11.8   0.1    2.1  2  DUF1967          Domain of unknown function (DUF1967)


Domain annotation for each model (and alignments):
>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  425.7   0.1  4.6e-131  1.7e-127       2     359 ..      12     359 ..      11     361 .. 0.97

  Alignments for each domain:
  == domain 1  score: 425.7 bits;  conditional E-value: 4.6e-131
                                       HHHHHHHHHHHHHTSS-SSSSHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHH CS
                   DegT_DnrJ_EryC1   2 ikeeeleaveevlksgwltsgpeveeFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatan 78 
                                       i+++e++av evlksg+lt+g+++e FEk+fa y+g+k+a++v++Gt Al+ aL+algvg+gdeVIvp +tF+atan
  gi|385806278|ref|YP_005842676.1|  12 IEQDEIDAVIEVLKSGMLTRGKNTELFEKEFASYIGTKYAVTVTNGTVALEAALKALGVGEGDEVIVPDFTFIATAN 88 
                                       6899************************************************************************* PP

                                       HHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEEEB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETT CS
                   DegT_DnrJ_EryC1  79 avlelgakpvfvDvdpdtynidpaaieaaitertkaIlpVhlyGqvadmdalkaiaakhglkvieDaAhAlGatykg 155
                                       av+++g +pvf+D+d+ ty+idp++++++it+rt+aI+pVhl+G++adm+++++ia + +l+v+eD+A+A+Ga+++g
  gi|385806278|ref|YP_005842676.1|  89 AVVNVGGRPVFADIDERTYCIDPESVNEKITNRTRAIIPVHLFGHMADMNSINEIAIDNKLVVLEDSAQAHGAEMNG 165
                                       ***************************************************************************** PP

                                       EECCCSSSEEEEE-BTTSSS-SSS-EEEEESTHHHHHHHHHHHBTTCECCTCSSCECCSS---B-B-BHHHHHHHHH CS
                   DegT_DnrJ_EryC1 156 kkvGalgdaavfSFyptKnlttGeGGavvtndeelaekarvlrnhGlkrkaekryvgevelGynyrlteiqAAigla 232
                                        k+G++g a++fSFy+tKn+ tGeGG+v+tn +++ e + + ++hG +    kry +++ lG+n+ +te+qAAig++
  gi|385806278|ref|YP_005842676.1| 166 VKAGSIGHASAFSFYATKNMMTGEGGMVTTNLDAVYEFLVKWKKHGEA----KRYLSDT-LGTNLSMTEMQAAIGRV 237
                                       **********************************************99....8******.***************** PP

                                       HHCTHHHHHHHHHHHHHHHHHHHHTCCCCEESCGGTTSSSEEESCEEEEEHCCHHHCHHHHHHHHHHCCEE-B-SGS CS
                   DegT_DnrJ_EryC1 233 qLerldelvarRreiaelykeeLaelegtaelttpketkkhawhlyavlveeeaevkrdelvealkeegigtrvhyp 309
                                       qL++ld++++ Rr++a+++++eL++++++ ++ + +  k h++h+y+++v+ e   +rd+l+e+l++ gigt +hyp
  gi|385806278|ref|YP_005842676.1| 238 QLKKLDRFNEIRRQNAAYFTKELSKVKEIKTPVELPGYK-HVYHQYVIRVPAE---DRDKLIEHLNKLGIGTAIHYP 310
                                       ***************************987777777777.***********98...9******************** PP

                                       CHGGGSCCHHHHHHCCCHC-HHHHHHHHHEEEEEGGTTGSHHHHHHHHHH CS
                   DegT_DnrJ_EryC1 310 nplhrqpvyaerkeeasgdlpnaerlaervlsLplypelteedvdrVvea 359
                                        plh qp+y+    + +++ p++ +++++vls+p++p l++ d++++v+ 
  gi|385806278|ref|YP_005842676.1| 311 YPLHIQPIYKAMG-YPEKQNPVSLEVSKEVLSIPVHPLLSKSDLEYIVKG 359
                                       ***********96.55679****************************986 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 !   28.5   0.1   2.3e-10   8.3e-07      43     194 ..      35     161 ..      14     270 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 2.3e-10
                                       TTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEE CS
                     Aminotran_1_2  43 idglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilrlsggevvr 119
                                       ++    +e++ a+++g        ++ av+v++G+ al +al++l  +  gde++vpd t+    n++ + gg  v 
  gi|385806278|ref|YP_005842676.1|  35 TE---LFEKEFASYIG--------TKYAVTVTNGTVALEAALKALG-VGEGDEVIVPDFTFIATANAVVNVGGRPVF 99 
                                       44...79*********........666*******************.9***************************** PP

                                       EEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCB CS
                     Aminotran_1_2 120 yplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfv 194
                                         ++ e ++ +d e++ e++++      +t+ i+   p +  G +a+ + + ++   a  ++l+++ D a a+++
  gi|385806278|ref|YP_005842676.1| 100 ADID-ERTYCIDPESVNEKITN------RTRAII---PVHLFGHMADMNSINEI---AIDNKLVVLEDSAQAHGA 161
                                       **66.99**************9......777777...55556777777777777...555677777776666665 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.1   2.1e-08   7.4e-05      46     187 ..      36     166 ..      25     191 .. 0.84
   2 ?    0.2   0.0     0.082   2.9e+02     258     299 ..     227     268 ..     194     300 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 2.1e-08
                                       HHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBE CS
                       Aminotran_5  46 eearekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipld 122
                                       e  ++++a  i+++    +  + ++t a+++++++l+  + +gde++v +    a+ ++ +++    g  v ++ +d
  gi|385806278|ref|YP_005842676.1|  36 ELFEKEFASYIGTKY--AVT-VTNGTVALEAALKALG--VGEGDEVIVPDFTFIATANAVVNVG---GRPV-FADID 103
                                       556788899999985..555.556666*********5..9*************99998888876...4455.77777 PP

                                       TT.SCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS---H CS
                       Aminotran_5 123 ee.geldldelekllnektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavghipidv 187
                                       e+   +d++ ++++++++t++++  h     G + ++++i+++a +++ +vl D+aqa g     v
  gi|385806278|ref|YP_005842676.1| 104 ERtYCIDPESVNEKITNRTRAIIPVH---LFGHMADMNSINEIAIDNKLVVLEDSAQAHGAEMNGV 166
                                       6515799***************9999...59***************************98876555 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.082
                                       HHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEE CS
                       Aminotran_5 258 iiglgaaleyleeigleaiekhekelaeyllerlkslpgvrl 299
                                       +  ++aa+  ++  +l++ ++  ++ a+y +++l++++++++
  gi|385806278|ref|YP_005842676.1| 227 MTEMQAAIGRVQLKKLDRFNEIRRQNAAYFTKELSKVKEIKT 268
                                       566899999999999999******************999987 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   1.4   3.4e-06     0.012      32     234 ..      33     222 ..      27     278 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.4e-06
                                       HHHHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH-.-TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTT. CS
                   Beta_elim_lyase  32 ktvnrLedavaelfgkeaalfvpqGtaAnsillkill.qrgeevivtepahihfdetgaiaelagvklrdlknkea. 106
                                       k+++ +e+++a ++g+++a+ v++Gt A + +lk+l    g+eviv +   ++  ++ a++ ++g +++ ++++e  
  gi|385806278|ref|YP_005842676.1|  33 KNTELFEKEFASYIGTKYAVTVTNGTVALEAALKALGvGEGDEVIVPD--FTFIATANAVVNVGG-RPVFADIDERt 106
                                       67788999**************************99968889998865..344555555555555.48888888775 PP

                                       TBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CH CS
                   Beta_elim_lyase 107 GkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslgeivk 183
                                         +d+e+++++i+++       ++i+              ++ ++ + +ia ++++ ++ D+A    a    g+++ 
  gi|385806278|ref|YP_005842676.1| 107 YCIDPESVNEKITNRT------RAIIPVHLFG-------HMADMNSINEIAIDNKLVVLEDSAQAHGAE-MNGVKAG 169
                                       789***********44......4444333222.......58999999999*************876655.6677766 PP

                                       HHHTTSSEEEEESSSTT--SS-EEEEE-HH....HHHHHHHH...HHHHT---S CS
                   Beta_elim_lyase 184 emfsyvDsvtmslkKdllanvGgvlafrddeledylaerveq...rkylggglr 234
                                       ++  ++  +++ ++K++++  Gg++ ++ d   ++l +  +    ++yl + l 
  gi|385806278|ref|YP_005842676.1| 170 SI-GHASAFSFYATKNMMTGEGGMVTTNLDAVYEFLVKWKKHgeaKRYLSDTLG 222
                                       65.56789**********************998887654443333444444433 PP

>> DUF1967  Domain of unknown function (DUF1967)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   5.1e-05      0.18      46      68 ..      61      83 ..      58      84 .. 0.93
   2 ?   -3.7   0.0       3.4   1.2e+04      38      46 ..     295     303 ..     289     306 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.1e-05
                                      HHHHHHTTT--TT-EEEETTEEE CS
                           DUF1967 46 vedaLrkaGakeGdtVrIgdveF 68
                                      +e aL+++G+ eGd+V + d++F
  gi|385806278|ref|YP_005842676.1| 61 LEAALKALGVGEGDEVIVPDFTF 83
                                      689******************99 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3.4
                                       HHHHHHTTH CS
                           DUF1967  38 arrLkklGv 46 
                                        + L+klG+
  gi|385806278|ref|YP_005842676.1| 295 IEHLNKLGI 303
                                       344555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); 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: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2502.25
//
Query:       gi|385806279|ref|YP_005842677.1|  [L=504]
Description: hypothetical protein FFONT_1237 [Fervidicoccus fontis Kam940]
Scores for 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-17   62.0   0.0    1.2e-16   60.8   0.0    1.7  2  SO_alpha_A3  Sarcosine oxidase A3 domain
    1.6e-08   34.7   0.7    3.5e-08   33.6   0.1    2.0  2  Fer2_BFD     BFD-like [2Fe-2S] binding domain


Domain annotation for each model (and alignments):
>> SO_alpha_A3  Sarcosine oxidase A3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       1.8   1.6e+04      11      23 ..     269     281 ..     268     291 .. 0.66
   2 !   60.8   0.0   1.3e-20   1.2e-16       2      83 ..     422     503 ..     421     504 .] 0.96

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 1.8
                       SO_alpha_A3  11 Dvtvkdielavre 23 
                                       D t+ d+++ v+e
  gi|385806279|ref|YP_005842677.1| 269 DTTIVDVKNNVKE 281
                                       6666777766665 PP

  == domain 2  score: 60.8 bits;  conditional E-value: 1.3e-20
                       SO_alpha_A3   2 krqFvdlqnDvtvkdielavregfesiehvKRYttlgmgtdQgklsavnaaaivaeltgkevaevgtttlRpPlapv 78 
                                       + +Fv+  +Dvt +d+ +a   gf ++e +KR+t+lg+gt Qg++  ++a++ ++   +  ++++g +++R+Pl+pv
  gi|385806279|ref|YP_005842677.1| 422 GMKFVCPCQDVTLEDLIKAFDMGFSNLEEIKRFTALGTGTCQGRICRIAALHALSYFRNVPIGSIGNFRQRAPLVPV 498
                                       679************************************************************************** PP

                       SO_alpha_A3  79 klaal 83 
                                       ++  l
  gi|385806279|ref|YP_005842677.1| 499 EIEYL 503
                                       99765 PP

>> Fer2_BFD  BFD-like [2Fe-2S] binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       1.3   1.2e+04      13      33 ..     260     280 ..     259     281 .. 0.69
   2 !   33.6   0.1     4e-12   3.5e-08       2      45 ..     426     471 ..     425     476 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.3
                          Fer2_BFD  13 Irdairraglttveevkrrtk 33 
                                       + + i + + tt+ +vk+ +k
  gi|385806279|ref|YP_005842677.1| 260 VANEISKYKDTTIVDVKNNVK 280
                                       556675655789999998765 PP

  == domain 2  score: 33.6 bits;  conditional E-value: 4e-12
                          Fer2_BFD   2 VCrCegvtegeIrdairraglttveevkrrtkagtg.Cgg..Crpai 45 
                                       VC C++vt +++++a    g +++ee+kr+t  gtg C+g  Cr a+
  gi|385806279|ref|YP_005842677.1| 426 VCPCQDVTLEDLIKAF-DMGFSNLEEIKRFTALGTGtCQGriCRIAA 471
                                       9***************.99************************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (504 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); 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: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 3140.04
//
Query:       gi|385806280|ref|YP_005842678.1|  [L=387]
Description: FAD dependent oxidoreductase [Fervidicoccus fontis Kam940]
Scores for complete 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-53  181.8   0.0    3.3e-53  181.5   0.0    1.0  1  DAO            FAD dependent oxidoreductase
    0.00015   20.7   0.2     0.0064   15.2   0.0    2.1  2  HI0933_like    HI0933-like protein
    0.00062   19.1   0.7      0.012   14.9   0.7    2.1  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
     0.0033   17.4   0.1       0.55   10.2   0.1    2.3  2  NAD_binding_9  FAD-NAD(P)-binding
     0.0088   15.3   0.7       0.22   10.7   0.0    2.2  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.022   15.0   0.1       0.19   12.0   0.2    2.4  3  NAD_binding_8  NAD(P)-binding Rossmann-like domain
       0.06   12.4   0.1        2.6    7.0   0.0    2.1  2  FAD_binding_2  FAD binding domain
       0.12   11.5   0.7         12    5.0   0.0    2.2  2  Thi4           Thi4 family
       0.13   12.9   1.9        2.8    8.6   0.2    2.5  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.5   0.0   1.6e-56   3.3e-53       4     351 ..      10     355 ..       9     356 .. 0.81

  Alignments for each domain:
  == domain 1  score: 181.5 bits;  conditional E-value: 1.6e-56
                                       EECTSHHHHHHHHHHH.HTT....EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHHHHHH CS
                               DAO   4 iiGGGiiGlstAyeLa.rrg....VtllekgdiagsgaSgrnsgllhsglrylpeaselarlslealeelreleeel 75 
                                       iiGGG++Gls+A+ La + g    ++l+e++  +g g+S rn+g ++ ++   +++  l +++ e+ ++l  l++ +
  gi|385806280|ref|YP_005842678.1|  10 IIGGGVVGLSVAMNLAiANGkgndICLFESK-YLGYGSSLRNAGRFRVHFG-DENN--L-EFAVESSKYLNSLSKIT 81 
                                       9**************9666677*********.****************886.5544..3.9**************** PP

                                       SSTTSEEEEEEEEEESSHHHHHHHHHHHHHH.HHTTTTEEEEEHHHHHHHSTTST...TTSEEEEETTEEEEEHHHH CS
                               DAO  76 gididyrrtGllslaadeeelealdkllall.leagldaelldaeevrelepalp...gllgalfypdtgqvdpakl 148
                                       g+++ + +tG+l++a+de++ + l k++ +  +++g++   + +ee+ +++  l+   ++  +++ +++g+++p  +
  gi|385806280|ref|YP_005842678.1|  82 GMNVLFAKTGYLWIASDEASYNIL-KNANSTfKKWGVPLTEIPSEELYKKYKFLRkrnEIISGFLGKEDGTIHPDSV 157
                                       ***************887555545.333333799***99668888899999883346788999999999******** PP

                                       HHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEEEEEEEEEE--GGGHHHH.HTT.CTTTSEEEEEEEE CS
                               DAO 149 taalaraaealGveilegtevtgleeedgkvwgverttpgendaadavVnaaGawsdll.gll.keldlpispvrgq 223
                                       + ++ar++++l v+i+e+++v++++ ++gkv  ++   +g++++ + v++a+Gaw +++ ++l  +l  pi+pvr +
  gi|385806280|ref|YP_005842678.1| 158 IFGMARKCKSLKVNIFEHSNVEDISIRSGKVESIK--VNGSKVETERVIIANGAWMTFFsEKLgLNL--PIEPVRKE 230
                                       ************************99999999994..3477744488**********5556665555..******** PP

                                       EEEEEECCTHSTGSGCSEEEEEEEETTTTEEEEEETTSEEEEEESSE..EETTCSSTSCSHHHHHHHHHHHHHHSGG CS
                               DAO 224 vlvlkplseklvspaailpvpetdddgrgvyvtprkdgrvlvGgtad..eesgdddpevdeedidellealrklfPq 298
                                       + v++p       ++ i p   ++d + ++yv ++++g+ ++G+t +  e++g  ++  +   + +l +++++l+  
  gi|385806280|ref|YP_005842678.1| 231 ISVTEPF------AYRIEPF--IVDSSLHTYVSQTLKGE-IIGSTSTgaEPKGLVELGNS---FLWLKKYAERLSRI 295
                                       ****884......4566665..8999**********996.55888744444444444444...44455555555544 PP

                                       G.....CGEEEEEEEEEE.ETTSSEEEEEEE.TEEEEEEEEECTTTHHHHHHHHHHHHHH CS
                               DAO 299 l.....gdvlrkwaGlrp.lpdglpligetp.gvkglylatGhsghGltlapatGkllae 351
                                       l      ++ r+w+G++  +pd+  ++g+++ + + ly+  G+sghG++l+p++Gkl+ae
  gi|385806280|ref|YP_005842678.1| 296 LagaerIRIIRAWSGYYEmTPDRSHVVGRSNdWPEELYVIGGFSGHGFMLGPLAGKLMAE 355
                                       33322355779*******559********885555************************8 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1     0.012        25       4      49 ..       9      58 ..       6      77 .. 0.76
   2 !   15.2   0.0   3.2e-06    0.0064     104     164 ..     155     209 ..     139     223 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.012
                                      EEE--SHHHHHHHHHH...HHTT--EEEE-SSS.SS-HHHHHCGGGT-EE CS
                       HI0933_like  4 iviGgGaAGlmaAisa...akrgkrVlllekak.klgrKilisGgGrcNv 49
                                       +iGgG  Gl  A+++   + +g+++ l+e++    g+ ++ +G+ r+ +
  gi|385806280|ref|YP_005842678.1|  9 SIIGGGVVGLSVAMNLaiaNGKGNDICLFESKYlGYGSSLRNAGRFRVHF 58
                                      59*********999975557789999999976425677777777666655 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 3.2e-06
                                       TT.-CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE---- CS
                       HI0933_like 104 vsdkaedivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGG 164
                                       +s     ++  + +++k+ +v++  +++v++++ +++++ ++k+ +++++e++++++A G 
  gi|385806280|ref|YP_005842678.1| 155 DS-----VIFGMARKCKSLKVNIFEHSNVEDISIRSGKVESIKV-NGSKVETERVIIANGA 209
                                       44.....888899*******************************.*************985 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.7   5.9e-06     0.012       5     111 ..      10     211 ..       7     221 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.9e-06
                                       EE--SHHHHHHHHHHHH...HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH..................... CS
                                       xxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..................... RF
                       Pyr_redox_2   5 viGgGpAGlaaaltlaq...agakvtlvelegtclnggcllskallgvaedaeias..................... 57 
                                       +iGgG+ Gl++a++la    +g ++ l+  e   l+ g +l +a +   +++++                       
  gi|385806280|ref|YP_005842678.1|  10 IIGGGVVGLSVAMNLAIangKGNDICLF--ESKYLGYGSSLRNAGRFRVHFGDENNlefavesskylnslskitgmn 84 
                                       9**************9987889999999..66677777777776666666655555666788888888888888888 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                       Pyr_redox_2  58 ............................................................................. 57 
                                                                                                                    
  gi|385806280|ref|YP_005842678.1|  85 vlfaktgylwiasdeasynilknanstfkkwgvplteipseelykkykflrkrneiisgflgkedgtihpdsvifgm 161
                                       ***************************************************************************** PP

                                       .HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE CS
                                       .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  58 .evvkklnqgielllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssp 111
                                        +++k+l+ +i    +  v +i   ++kv+  k    ++ k++ +++++A G++ 
  gi|385806280|ref|YP_005842678.1| 162 aRKCKSLKVNIFEHSN--VEDISIRSGKVESIK---VNGSKVETERVIIANGAWM 211
                                       9889999999999999..555555666777754...46789***********975 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.1   0.00028      0.55       2      41 ..      10      47 ..       9      57 .. 0.87
   2 ?    4.9   0.0     0.012        24     115     154 ..     168     208 ..     158     209 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00028
                     NAD_binding_9  2 ivGaGprGlavlerLlarakkkspleitlfdpsepgagrv 41
                                      i+G+G+ Gl+v+ +L+  +  ++  +i lf+ + +g g+ 
  gi|385806280|ref|YP_005842678.1| 10 IIGGGVVGLSVAMNLAIAN--GKGNDICLFESKYLGYGSS 47
                                      9**************9996..999*******998886765 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.012
                     NAD_binding_9 115 vtvevh.raevvdleeradgqavlladgaslaadaVvLAlG 154
                                       ++v+++ +++v+d++ r ++++ ++ +g++++ ++V++A G
  gi|385806280|ref|YP_005842678.1| 168 LKVNIFeHSNVEDISIRSGKVESIKVNGSKVETERVIIANG 208
                                       4566553779*****************************99 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.2     0.028        55       2      19 ..      10      27 ..       9      49 .. 0.83
   2 !   10.7   0.0   0.00011      0.22      91     135 ..     165     210 ..     160     246 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.028
                       Pyr_redox_3  2 IiGaGPaGlaaaielkka 19
                                      IiG+G  Gl++a++l  a
  gi|385806280|ref|YP_005842678.1| 10 IIGGGVVGLSVAMNLAIA 27
                                      9***********998755 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00011
                       Pyr_redox_3  91 aksfelpiklfeeVesvkk.edegfevetsketyeAkkviiAtGef 135
                                       +ks +++i ++++Ve+++  +++  +++ + +++e+++viiA G +
  gi|385806280|ref|YP_005842678.1| 165 CKSLKVNIFEHSNVEDISIrSGKVESIKVNGSKVETERVIIANGAW 210
                                       6788999***********84677899*****************974 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   9.6e-05      0.19       1      28 [.      10      40 ..      10      62 .. 0.80
   2 ?   -2.0   0.0       2.2   4.4e+03      20      46 ..     168     199 ..     161     214 .. 0.61
   3 ?   -1.3   0.0       1.3   2.7e+03      33      65 ..     264     296 ..     259     298 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.6e-05
                                      EE--SHHHHHHHHHHHCC...TEEEEEE-SS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLaka...gfdvlllekr 28
                                      I+G+G+ Gl+ A  La a   g d+ l+e+ 
  gi|385806280|ref|YP_005842678.1| 10 IIGGGVVGLSVAMNLAIAngkGNDICLFESK 40
                                      9**************97554477*****975 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.2
                                       EEEEEE-SSSS..SS...GGG-EECETTCEEC CS
                     NAD_binding_8  20 fdvlllekrdr..lG...Graasyevpgvrvd 46 
                                       ++v ++e+++   ++   G++ s++v+g +v+
  gi|385806280|ref|YP_005842678.1| 168 LKVNIFEHSNVedISirsGKVESIKVNGSKVE 199
                                       56777776642224433366666666665555 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.3
                                       GGG-EECETTCEECTS---EEETTHHHHCHHHH CS
                     NAD_binding_8  33 Graasyevpgvrvdygahifhgsgyypnvrrll 65 
                                       G  ++   p+  v++g + ++  +y ++++r+l
  gi|385806280|ref|YP_005842678.1| 264 GSTSTGAEPKGLVELGNSFLWLKKYAERLSRIL 296
                                       455666666678899999999877788888876 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.3      0.02        41       4      27 ..      10      36 ..      10      49 .. 0.75
   2 ?    7.0   0.0    0.0013       2.6     142     203 ..     156     211 ..     112     232 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.02
                                      EE--SHHHHHHHHHHHH...TTT-EEE CS
                     FAD_binding_2  4 ViGsGlAGLaAAleaae...aGlkvav 27
                                      +iG+G+ GL+ A+++a    +G ++++
  gi|385806280|ref|YP_005842678.1| 10 IIGGGVVGLSVAMNLAIangKGNDICL 36
                                      8************99873123335555 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0013
                                       HHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----G CS
                     FAD_binding_2 142 allarlvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfg 203
                                        ++  +++++++++v ++e+ +++++ +++g+v  + v+    g++v+    +v++a+g++ 
  gi|385806280|ref|YP_005842678.1| 156 SVIFGMARKCKSLKVNIFEHSNVEDISIRSGKVESIKVN----GSKVE--TERVIIANGAWM 211
                                       567789999999************************999....44443..558999998886 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1    0.0077        15      21      50 ..       9      40 ..       2      54 .. 0.79
   2 ?    5.0   0.0    0.0061        12     104     145 ..     161     201 ..     144     207 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0077
                                      EEE--SHHHHHHHHHHHHC..TTS-EEEEESS CS
                              Thi4 21 vivGaGssGLtaayylakk..pdlkvailers 50
                                       i+G+G  GL+ a  la +   +  ++++e++
  gi|385806280|ref|YP_005842678.1|  9 SIIGGGVVGLSVAMNLAIAngKGNDICLFESK 40
                                      599**********9998664578899999987 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0061
                                       HHHHHTSTTEEEEESEEEEEEEEETBTEEEEEEEEEHHHHTC CS
                              Thi4 104 lskvlqlanvkllnavaveDlivregegvaGvvinwtlvela 145
                                       +++ ++   v +++   veD+ +r   +v  + +n + ve++
  gi|385806280|ref|YP_005842678.1| 161 MARKCKSLKVNIFEHSNVEDISIRS-GKVESIKVNGSKVETE 201
                                       5677777789***************.7899999998888865 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.2    0.0014       2.8       4      25 ..      10      34 ..       7      41 .. 0.76
   2 ?    3.2   0.1     0.068   1.4e+02      46      79 ..     161     194 ..     156     200 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0014
                                      EECSSHHHHHHHHHH...HHTTSEE CS
                         Pyr_redox  4 vvGgGyiglElAgal...aelgkkV 25
                                      ++GgG++gl +A +l   +  g+++
  gi|385806280|ref|YP_005842678.1| 10 IIGGGVVGLSVAMNLaiaNGKGNDI 34
                                      9************995544455555 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.068
                                       HHHHHHHTTEEEECSEEEEEEEEETTSEEEEEEE CS
                         Pyr_redox  46 lqeklekngievllntkveeiegsedgvesvklk 79 
                                       +++k + +++++  +++ve i   + +ves+k++
  gi|385806280|ref|YP_005842678.1| 161 MARKCKSLKVNIFEHSNVEDISIRSGKVESIKVN 194
                                       57888999**************88877**99985 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:                      395  (0.0220313); 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: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 2352.50
//
Query:       gi|385806281|ref|YP_005842679.1|  [L=541]
Description: DNA polymerase B region [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.1e-12   45.0   0.1    2.2e-11   43.2   0.0    1.8  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 !   43.2   0.0   1.2e-15   2.2e-11      24     177 ..     246     384 ..     236     411 .. 0.70
   2 ?   -2.6   0.0      0.09   1.6e+03     283     328 ..     478     518 ..     476     535 .. 0.65

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 1.2e-15
                                       HHTTBE-B-....----.--SS...-S.----BE----EEESS-EEEEEETTHHHHHHHHTT-STTTCE-HCCHCC. CS
                         DNA_pol_B  24 keegfilpd....rtekkgkeee..gY.qGatVlePkkglydkpvlvlDFaSLYPsiiqahNlcyttlvaseeeak. 92 
                                        ++++++p+      e  ++ +e  +Y  G+++  P+ g+y+ +vl +DF+SLYPsii ++N++++t+++ + +++ 
  gi|385806281|ref|YP_005842679.1| 246 YRRKMVVPNiriyN-EGWRNVDEllTYdSGGLIGIPEAGVYE-NVLQIDFSSLYPSIISKFNISPETIDRPNCRNRl 320
                                       56777777754431.22222222544526888889******7.5999**********************99888665 PP

                                       T--BTT...TEEE-TCC-EEE-TTS---HHHHHHHHHHHHHHHHHHHHHCS--HHHHHHHHHHHHHHHHHHHHHHHH CS
                         DNA_pol_B  93 eleaedeyleveveprlvefvkksvregllpklLkdllakRkaikkelkeekdefekalldkqQlalKvtaNsvYGf 169
                                       +l++  + ++v                gl+++ Lk+l++ R +ik+     + +f k+    + +a+K ++ + +G+
  gi|385806281|ref|YP_005842679.1| 321 HLNDAPHEVCVD-------------FDGLVSSTLKKLIDLRSKIKE----INGPFSKT----MEKAVKWIMVASFGY 376
                                       666554444333.............368999999999998887764....45554443....457788888888888 PP

                                       HTSTTSTT CS
                         DNA_pol_B 170 tGvansrl 177
                                       +G++n r+
  gi|385806281|ref|YP_005842679.1| 377 LGYRNARF 384
                                       88888777 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.09
                                       EEEEEEEEESSTTSEEEEESSGGGSTTS-HHHHHHHHHHHHHHSSS CS
                         DNA_pol_B 283 kYaglkvektskanklliKGvdlvRrdncklvkevikkvlelllkd 328
                                       +Y+gl+++     ++l++KGv     +  k    v ++ +++ll +
  gi|385806281|ref|YP_005842679.1| 478 RYYGLTYD-----GELIVKGVKCEGIEGLKVNDSVLEEKMKKLLLK 518
                                       89999999.....667777776655555555555555544444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (541 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); 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: 0.63u 0.34s 00:00:00.97 Elapsed: 00:00:00.50
# Mc/sec: 3254.37
//
Query:       gi|385806282|ref|YP_005842680.1|  [L=62]
Description: hypothetical protein FFONT_1240 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); 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 0.30s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 402.34
//
Query:       gi|385806283|ref|YP_005842681.1|  [L=240]
Description: hypothetical protein FFONT_1241 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00055   19.5   0.0    0.00077   19.0   0.0    1.1  1  RecA      recA bacterial DNA recombination protein


Domain annotation for each model (and alignments):
>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   4.3e-08   0.00077      35     138 ..      25     131 ..       4     136 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 4.3e-08
                                       --S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EE......EEESS----HHHHHHTT--G CS
                              RecA  35 ssGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaa......fidaehaldpkyakklGvdi 105
                                        sG  ++d    +G +pkG i e yG         + ++ia+    +g+a+      +i+ +  +  +ya+ +G ++
  gi|385806283|ref|YP_005842681.1|  25 KSGIEGIDEL--VGCIPKGIIAEFYGDFQLVLQ-TSYKVIANFHCIDGTAVgimqneLINYDFYMLRMYARSFGCNT 98 
                                       4566666665..569***********7544333.3556666666666655511111266777778899********* PP

                                       GG-EEE--SSHHHHHHHHHHHHTTT--SEEEEE CS
                              RecA 106 dellvsqpdtGeqaleiadalvrsgaidlivvd 138
                                       +++lvs+  + e+a++++++  +  a ++ ++d
  gi|385806283|ref|YP_005842681.1|  99 NDMLVSRAFRLEDAINMLKSASNIDAENIAIID 131
                                       ****************99999888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        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: 00:00:00.45
# Mc/sec: 1602.18
//
Query:       gi|385806284|ref|YP_005842682.1|  [L=251]
Description: DNA polymerase sliding clamp subunit [Fervidicoccus fontis Kam940]
Scores for complete 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   60.0   0.2    3.8e-16   59.0   0.2    1.5  1  PCNA_N          Proliferating cell nuclear antigen, N-termina
    4.8e-09   36.5   0.6    6.1e-07   29.7   0.0    2.3  2  PCNA_C          Proliferating cell nuclear antigen, C-termina
    9.5e-09   35.1   0.4    2.1e-08   33.9   0.3    1.7  1  Rad9            Rad9
  ------ inclusion threshold ------
       0.02   15.4   1.3      0.092   13.3   0.1    2.5  2  Pih1_fungal_CS  Fungal Pih1 CS domain


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 !   59.0   0.2   8.5e-20   3.8e-16       8     117 ..      13     122 ..       7     128 .. 0.93

  Alignments for each domain:
  == domain 1  score: 59.0 bits;  conditional E-value: 8.5e-20
                                       SHHHHHHHHHHHTTTCSEEEEEEETTEEEEEEE-TTSSEEEEEEEEGGGSSEEEESS-EEEEEEHHHHHHHHTTSTT CS
                            PCNA_N   8 qasllkklleaikdlvneanfdcddsGislqalDsshvaLvslelrsegfekyrCDrnlalgvnlnslskilkcann 84 
                                       +a ++k l+e++  l++e+ ++++++G++++a+Ds+ vaL+s+++ +e+f+++  + + ++g+nl++l k++k + +
  gi|385806284|ref|YP_005842682.1|  13 DAKIFKSLFESMSKLIDEIRLEINENGLEIRAIDSANVALMSVSFPKESFSEFIINEKKSVGLNLSTLVKMMKRVRK 89 
                                       799************************************************************************** PP

                                       TSEEEEEEETTSSEEEEEEEECTSSEEEEEEEE CS
                            PCNA_N  85 edsvtlkaedeadtlalvfesekkdkiaeydlk 117
                                       ed   ++ ++++ +l l+  ++++ k+++ ++ 
  gi|385806284|ref|YP_005842682.1|  90 EDRFEIEINEDEISLRLIGTTKREFKVNNLEVA 122
                                       **********99999999999999898876665 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 !    5.1   0.2    0.0053        24      16      97 ..      15      91 ..       7     105 .. 0.76
   2 !   29.7   0.0   1.3e-10   6.1e-07      62     127 ..     183     248 ..     125     249 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0053
                                      HHHHHHHHHHTTT-SEEEEEEETTEEEEEEEETTEEEEEEE--BEESSSGGGCBEEEESS-EEEEEEHHHHHHHGGGGG CS
                            PCNA_C 16 sefaricrdlsqlsdsvvisvtkegvkfsasGdiGsasivlkqvkdvdkeeeavklelkepvtltfalkYlaeftkats 94
                                        f+ +   +s+l d++ + +  +g+  +a   i sa++ l  v+  +++ +  +++ k++v l  +   l++++k   
  gi|385806284|ref|YP_005842682.1| 15 KIFKSLFESMSKLIDEIRLEINENGLEIRA---IDSANVALMSVSFPKESFSEFIINEKKSVGLNLS--TLVKMMKRVR 88
                                      558888899*******************98...8999999999988887777778888888777654..4556655555 PP

                                      C-S CS
                            PCNA_C 95 Lse 97
                                        +
  gi|385806284|ref|YP_005842682.1| 89 KED 91
                                      555 PP

  == domain 2  score: 29.7 bits;  conditional E-value: 1.3e-10
                                       SSSGGGCBEEEESS-EEEEEEHHHHHHHGGGGGC-SEEEEEEETTSEEEEEEEETTCEEEEEEE-B CS
                            PCNA_C  62 vdkeeeavklelkepvtltfalkYlaeftkatsLservtlslssevPlvveykikdvgllayllak 127
                                        + + + +++   +p + t++++Yl+++   t +++++++s+ss++P+++e ++  +g + ylla+
  gi|385806284|ref|YP_005842682.1| 183 TKSSGSIIEVISGNPAKSTYSVEYLLNLLSLTKIADTISISFSSQMPIKLEIDLPTGGNISYLLAP 248
                                       344455667777899*************************************************98 PP

>> Rad9  Rad9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.3   4.7e-12   2.1e-08       4      77 ..      20     113 ..      17     189 .. 0.83

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 4.7e-12
                              Rad9   4 alqclsrigdelyleisedglelrtvnssrSayalvtlkksfFdky..ekevseqirckilvKsvlsvfr....... 71 
                                       +++++s++ de+ lei+e+gle+r+++s++ a  +v + k+ F+++  +++ s  +++++lvK +  v +       
  gi|385806284|ref|YP_005842682.1|  20 LFESMSKLIDEIRLEINENGLEIRAIDSANVALMSVSFPKESFSEFiiNEKKSVGLNLSTLVKMMKRVRKedrfeie 96 
                                       789*******************************************99899999999******99888764444444 PP

                              Rad9  72 ...........slsake 77 
                                                  ++ ++e
  gi|385806284|ref|YP_005842682.1|  97 inedeislrliGTTKRE 113
                                       44444444444444444 PP

>> Pih1_fungal_CS  Fungal Pih1 CS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   2.1e-05     0.092      20      69 ..      80     129 ..      63     148 .. 0.88
   2 ?    0.3   0.1      0.23     1e+03      21      64 ..     190     237 ..     175     242 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.1e-05
                    Pih1_fungal_CS  20 rieieselesskdlevsYdakeneLiiknlntqeykekklkipLPnifke 69 
                                        +++ +++ + + +e++ +++e +L +  + ++e+k ++l++++P+i ++
  gi|385806284|ref|YP_005842682.1|  80 LVKMMKRVRKEDRFEIEINEDEISLRLIGTTKREFKVNNLEVAIPEIPEG 129
                                       5777889999***********************************99665 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.23
                    Pih1_fungal_CS  21 ieieselesskdlevsYdakeneLi.iknlntqey...kekklkipLP 64 
                                       ie+ s +  ++ ++v+Y  +  +L  i  + +  +    + kl+i+LP
  gi|385806284|ref|YP_005842682.1| 190 IEVISGNPAKSTYSVEYLLNLLSLTkIADTISISFssqMPIKLEIDLP 237
                                       677777777777777777665555323333333334434457777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 1734.67
//
Query:       gi|385806285|ref|YP_005842683.1|  [L=353]
Description: phage integrase family protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-32  111.8   0.1    1.3e-31  109.6   0.1    2.2  2  Phage_integrase  Phage integrase family
    3.2e-09   36.2   7.4    5.8e-09   35.4   7.4    1.5  1  zinc_ribbon_2    zinc-ribbon domain
    9.8e-08   31.1   4.2    1.7e-07   30.4   4.2    1.3  1  zf-ribbon_3      zinc-ribbon domain
    3.8e-07   30.3   1.2    8.2e-06   26.0   1.1    2.9  2  Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
    6.2e-07   29.8   1.8    3.5e-05   24.2   0.1    3.2  4  Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
    6.4e-06   26.1   0.3    1.1e-05   25.4   0.3    1.3  1  DZR              Double zinc ribbon
    1.8e-05   25.4   0.8    3.5e-05   24.5   0.8    1.5  1  zinc_ribbon_15   zinc-ribbon family
    5.1e-05   23.3   4.5    8.9e-05   22.5   4.5    1.3  1  UPF0547          Uncharacterised protein family UPF0547
  ------ inclusion threshold ------
      0.027   14.4   4.0        1.5    8.8   0.6    2.4  2  Nudix_N_2        Nudix N-terminal
      0.053   13.9   0.0       0.15   12.5   0.0    1.8  1  NblA             Phycobilisome degradation protein nblA
      0.079   12.9   1.2         18    5.3   0.0    3.0  3  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.079   12.6   0.1       0.15   11.7   0.1    1.5  1  TackOD1          Thaumarchaeal output domain 1
       0.19   11.8   0.3       0.36   10.9   0.3    1.4  1  DHHC             DHHC palmitoyltransferase
       0.44   10.3   2.2         14    5.6   0.1    2.4  2  A2L_zn_ribbon    A2L zinc ribbon domain
       0.48   10.1   3.3        6.8    6.5   0.0    2.4  2  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
        1.7    8.5   4.3        3.5    7.4   4.3    1.5  1  YacG             DNA gyrase inhibitor YacG


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 ?   -3.6   0.0       7.4   8.3e+03     103     125 ..       9      31 ..       5      39 .. 0.72
   2 !  109.6   0.1   1.2e-34   1.3e-31       3     171 ..     125     279 ..     123     280 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 7.4
                                       SSB--HHHHHHHHHHHHHHCT-S CS
                   Phage_integrase 103 gkplsrqtvrkafkraveeagie 125
                                        k++s++++ ++f ++  ++g++
  gi|385806285|ref|YP_005842683.1|   9 IKEMSSEQAAEYFLSLLSASGLS 31 
                                       56788888888888888888776 PP

  == domain 2  score: 109.6 bits;  conditional E-value: 1.2e-34
                                       HHHHHHHHHHHCCGCHHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEEEEECSSSSEEEEECTHHHHHH CS
                   Phage_integrase   3 ltedeverllaaleeslkirdklllellyetGlRisEllsLrvkdldlengvilvheregKgskeravplseealel 79 
                                       lt++e+++l++ +++   + d l++ ll+etG+R++Ells++ +d+dl +g+i v  ++ K +k r+v l+e+   l
  gi|385806285|ref|YP_005842683.1| 125 LTKEEIDKLFSSSRD---LLDMLIISLLFETGMRANELLSITADDVDLTDGEISV--KNAKYGKVRTVFLGENSKFL 196
                                       89*************...*************************************..**************999999 PP

                                       HHHHHHHHCHCCTTTSBSSBETTSSB--HHHHHHHHHHHHHHCT-S.SC--TTHHHHHHHHHHHHHCTSHHHHHHHH CS
                   Phage_integrase  80 lkellskaleeaeksellfaskrgkplsrqtvrkafkraveeagie.kpltpHtlRhsfataLleagvdlrvvqkll 155
                                       l e +++     +        +r  pls + ++k++k+++++agi  ++++pH lRh+fat+ +++g++l ++qk+l
  gi|385806285|ref|YP_005842683.1| 197 LAERVKNI----S------SGERVIPLSYNGLYKRIKSLAKRAGIPlEKVRPHILRHTFATEAVRSGMSLPALQKIL 263
                                       98888887....3......334566889************************************************* PP

                                       T-SSCCHHHHHHCCCH CS
                   Phage_integrase 156 GHssisttqiYthvak 171
                                       GHs+i+ tqiYth++k
  gi|385806285|ref|YP_005842683.1| 264 GHSDIKVTQIYTHLLK 279
                                       *************976 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   7.4   5.2e-12   5.8e-09       1      23 []     318     340 ..     318     340 .. 0.96

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 5.2e-12
                     zinc_ribbon_2   1 fCpnCGaelqdnakFCpyCGtpl 23 
                                       fCpnCG++l++++kFCp CG+ l
  gi|385806285|ref|YP_005842683.1| 318 FCPNCGKKLPPGSKFCPFCGYRL 340
                                       9*******************976 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   4.2   1.6e-10   1.7e-07       3      26 .]     317     340 ..     317     340 .. 0.94

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 1.6e-10
                       zf-ribbon_3   3 vrCPnCGaplssddnvCpyCGtkl 26 
                                       ++CPnCG++l ++ ++Cp CG++l
  gi|385806285|ref|YP_005842683.1| 317 KFCPNCGKKLPPGSKFCPFCGYRL 340
                                       68******88************97 PP

>> Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   1.1   7.3e-09   8.2e-06       3      62 ..      19      75 ..      17     104 .. 0.90
   2 ?   -0.1   0.0       1.1   1.2e+03      30      61 ..     222     254 ..     214     263 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 7.3e-09
                                      HHHHHHHHTT-S-HHHHHHHHHHHHHHHHHHHH.TS--TTT--HHHHHHHHHS------- CS
                   Phage_int_SAM_1  3 qfleyLikerglspnTlraYrrdLrrflkflaergkesleqlttedvraflaeleeegls 62
                                      +++  L ++ gls++T+r+Yr ++ +fl+f +    + l++++++ +++++++++++g+ 
  gi|385806285|ref|YP_005842683.1| 19 EYFLSLLSASGLSEKTIRSYRAAIYDFLNFSKV---KRLNEISQNLILNWINYRLKNGFE 75
                                      799999***************************...********************9954 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.1
                                       HHHHHH.TS--TTT--HHHHH.HHHHS------ CS
                   Phage_int_SAM_1  30 lkflaergkesleqlttedvr.aflaeleeegl 61 
                                       +k la+r +  le+++++ +r +f  e +++g 
  gi|385806285|ref|YP_005842683.1| 222 IKSLAKRAGIPLEKVRPHILRhTFATEAVRSGM 254
                                       56778889999******9997699999999884 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 ?    2.6   0.0      0.17   1.9e+02      36      57 ..       7      28 ..       1      31 [. 0.81
   2 !   24.2   0.1   3.1e-08   3.5e-05       5      54 ..      21      70 ..      18      77 .. 0.89
   3 ?    2.9   0.0      0.14   1.6e+02      13      47 ..      84     131 ..      76     138 .. 0.80
   4 ?   -2.7   0.0       7.9   8.9e+03      73      84 ..     272     283 ..     270     284 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.17
                   Phage_int_SAM_4 36 kapeeltkedieaYlnyLaner 57
                                      ++++e++ e++ +Y+ +L+   
  gi|385806285|ref|YP_005842683.1|  7 DEIKEMSSEQAAEYFLSLLSAS 28
                                      799**************99655 PP

  == domain 2  score: 24.2 bits;  conditional E-value: 3.1e-08
                   Phage_int_SAM_4  5 frealrlaglserTiksYlsaikrflrflkkkapeeltkedieaYlnyLa 54
                                      f+  l ++glse+Ti+sY  ai++fl+f k k+ +e++++ i   +ny +
  gi|385806285|ref|YP_005842683.1| 21 FLSLLSASGLSEKTIRSYRAAIYDFLNFSKVKRLNEISQNLILNWINYRL 70
                                      56667889***********************************9999987 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.14
                   Phage_int_SAM_4  13 glserTiksYlsaikrflrflkkk.............apeeltkedie 47 
                                       ++ ++T+++Y+  ++  l +   +             +++ ltke+i 
  gi|385806285|ref|YP_005842683.1|  84 RKIQSTMHYYTLFLRKWLTWAGFDskivpivkkpqsgEISALTKEEID 131
                                       56689***************9633447777777888899999999986 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 7.9
                   Phage_int_SAM_4  73 ffykkvlerela 84 
                                       ++y+++l+++l+
  gi|385806285|ref|YP_005842683.1| 272 QIYTHLLKDDLK 283
                                       6899***99985 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.3   9.8e-09   1.1e-05       1      22 [.     319     340 ..     303     345 .. 0.72

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 9.8e-09
                               DZR   1 CpqCgeelppdarfCseCgtkl 22 
                                       Cp+Cg++lpp+++fC+ Cg +l
  gi|385806285|ref|YP_005842683.1| 319 CPNCGKKLPPGSKFCPFCGYRL 340
                                       6666666666666666666665 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.8   3.1e-08   3.5e-05      35      86 .]     285     337 ..     269     337 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 3.1e-08
                    zinc_ribbon_15  35 kpylacskCkslleaskelgkeiekkesse.kkeCknCgkeveeefkyCpkCg 86 
                                       ++y + ++ +++ ++++++++++++++ +e  k C+nCgk++ + +k+Cp+Cg
  gi|385806285|ref|YP_005842683.1| 285 EYYSKFTSSREKTMSKNDESSAFNDENIHEdIKFCPNCGKKLPPGSKFCPFCG 337
                                       56666666665555555555555555444469********************9 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   4.5   7.9e-08   8.9e-05       1      23 [.     317     339 ..     317     339 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 7.9e-08
                           UPF0547   1 KvCPeCeakvPvaaqfCphCGyv 23 
                                       K CP C  k+P   +fCp+CGy+
  gi|385806285|ref|YP_005842683.1| 317 KFCPNCGKKLPPGSKFCPFCGYR 339
                                       66********************5 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.6    0.0013       1.5       1      10 [.     317     326 ..     317     328 .. 0.91
   2 ?    6.4   0.2    0.0075       8.4       1      11 [.     331     341 ..     331     350 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0013
                                       -B-TTT--B- CS
                         Nudix_N_2   1 kFCsqCGtpv 10 
                                       kFC++CG+++
  gi|385806285|ref|YP_005842683.1| 317 KFCPNCGKKL 326
                                       9******986 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0075
                                       -B-TTT--B-E CS
                         Nudix_N_2   1 kFCsqCGtpve 11 
                                       kFC+ CG ++ 
  gi|385806285|ref|YP_005842683.1| 331 KFCPFCGYRLP 341
                                       8******8875 PP

>> NblA  Phycobilisome degradation protein nblA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00013      0.15      15      44 ..       7      36 ..       2      38 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                                      HHHCCS-CHHHHHHHHHHHHHHHHHHHHHH CS
                              NblA 15 dqvqqmSrEqaqelLlelyrqmmvkenlir 44
                                      d++++mS Eqa e++l l+    + e +ir
  gi|385806285|ref|YP_005842683.1|  7 DEIKEMSSEQAAEYFLSLLSASGLSEKTIR 36
                                      899*************99987777777666 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 ?    5.3   0.0     0.016        18       2      25 ..     216     239 ..     215     240 .. 0.89
   2 ?    4.3   0.8     0.034        38      31      55 ..     319     339 ..     317     341 .. 0.74
   3 ?    1.9   0.0       0.2   2.2e+02      28      38 ..     330     340 ..     327     346 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.016
                    OrfB_Zn_ribbon   2 rklkeqleykakeyGikveevnpa 25 
                                       + l ++++  ak++Gi++e+v p+
  gi|385806285|ref|YP_005842683.1| 216 NGLYKRIKSLAKRAGIPLEKVRPH 239
                                       568899***************996 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.034
                    OrfB_Zn_ribbon  31 CseCgsknkealsgrtfkCpnCgfe 55 
                                       C++Cg+k+ +        Cp Cg++
  gi|385806285|ref|YP_005842683.1| 319 CPNCGKKLPP----GSKFCPFCGYR 339
                                       9999998888....55568888875 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.2
                    OrfB_Zn_ribbon  28 SktCseCgskn 38 
                                       Sk C+ Cg+++
  gi|385806285|ref|YP_005842683.1| 330 SKFCPFCGYRL 340
                                       899*****986 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00013      0.15      44      94 ..     286     337 ..     242     339 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                           TackOD1  44 alskekeeseelleelvkrglle.eelvdrirlCpsCksghlnvrevCpkCk 94 
                                        +sk++++ e+++ +  ++ +++ e++++ i++Cp+C  +     + Cp C+
  gi|385806285|ref|YP_005842683.1| 286 YYSKFTSSREKTMSKNDESSAFNdENIHEDIKFCPNCGKKLPPGSKFCPFCG 337
                                       2333555777778888888888879**************99999******96 PP

>> DHHC  DHHC palmitoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.3   0.00032      0.36       4      26 ..     315     337 ..     312     341 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00032
                              DHHC   4 elkfCstcniykpprskHcrvCn 26 
                                       + kfC++c    pp sk+c +C+
  gi|385806285|ref|YP_005842683.1| 315 DIKFCPNCGKKLPPGSKFCPFCG 337
                                       679*******************7 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.2     0.034        38      20      28 ..     315     323 ..     311     324 .. 0.88
   2 ?    5.6   0.1     0.012        14      23      29 ..     332     338 ..     329     342 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.034
                     A2L_zn_ribbon  20 gylvCieCg 28 
                                       ++ +C++Cg
  gi|385806285|ref|YP_005842683.1| 315 DIKFCPNCG 323
                                       788*****9 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.012
                     A2L_zn_ribbon  23 vCieCga 29 
                                       +C++Cg+
  gi|385806285|ref|YP_005842683.1| 332 FCPFCGY 338
                                       9*****8 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 ?    6.5   0.0     0.006       6.8       4      12 ..     317     325 ..     315     327 .. 0.87
   2 ?    3.3   1.1     0.059        66       4      10 ..     331     337 ..     330     340 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.006
                     zf-NADH-PPase   4 rFCgrCGap 12 
                                       +FC+ CG +
  gi|385806285|ref|YP_005842683.1| 317 KFCPNCGKK 325
                                       6******76 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.059
                     zf-NADH-PPase   4 rFCgrCG 10 
                                       +FC+ CG
  gi|385806285|ref|YP_005842683.1| 331 KFCPFCG 337
                                       7*****9 PP

>> YacG  DNA gyrase inhibitor YacG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   4.3    0.0031       3.5       3      25 ..     319     339 ..     318     343 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0031
                              YacG   3 CPtCkkevewseenpfrPFCSeR 25 
                                       CP C+k+    +  +f PFC  R
  gi|385806285|ref|YP_005842683.1| 319 CPNCGKKLPPGS--KFCPFCGYR 339
                                       *******98776..9*****977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       764  (0.0426125); expected 358.6 (0.02)
Passed bias filter:                      597  (0.033298); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); 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: 0.64u 0.36s 00:00:01.00 Elapsed: 00:00:00.55
# Mc/sec: 1939.80
//
Query:       gi|385806286|ref|YP_005842684.1|  [L=255]
Description: putative signal transduction protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-31  108.3  10.4    1.6e-10   41.3   0.5    4.1  4  CBS       CBS domain
  ------ inclusion threshold ------
      0.025   14.1   0.1        6.9    6.3   0.1    2.4  2  DisA_N    DisA bacterial checkpoint controller nucleotide-bin


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 !   12.1   0.0   2.3e-05      0.21      25      53 ..      12      38 ..       1      41 [. 0.75
   2 !   25.1   0.2   1.9e-09   1.7e-05      17      54 ..      74     111 ..      60     113 .. 0.89
   3 !   41.3   0.5   1.8e-14   1.6e-10       3      55 ..     124     176 ..     122     178 .. 0.89
   4 !   34.2   0.3   2.8e-12   2.5e-08       4      54 ..     198     248 ..     195     251 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.3e-05
                                      HHHHTSSEE.EEEETTTBEEEEEEHHHHHH CS
                               CBS 25 mrekgvsrl.PVVdedgklvGivtlrDllr 53
                                      +r+  + r+ PV++edg++ G++ l  +++
  gi|385806286|ref|YP_005842684.1| 12 FRR--I-RYpPVIEEDGRYMGLLRLQNIIE 38
                                      433..8.9967*************999987 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 1.9e-09
                                       BHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS  17 tleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                                       ++ e+++lm++++v++l VV+++++++G +t++ l++ 
  gi|385806286|ref|YP_005842684.1|  74 SIDELIDLMTSHKVGALAVVNKNEEVIGEITEKNLIDT 111
                                       699*******999*********************9976 PP

  == domain 3  score: 41.3 bits;  conditional E-value: 1.8e-14
                                       HH.SBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   3 di.mtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       di   ++++ v  ++ l  a+elmr+++v rlPVV  +g+l+Gi+t rD+l++ 
  gi|385806286|ref|YP_005842684.1| 124 DIiSGKEIIKVEATDILISAVELMRKHKVKRLPVV-FQGELIGIITIRDVLKYF 176
                                       554567899***************9999******9.79**************97 PP

  == domain 4  score: 34.2 bits;  conditional E-value: 2.8e-12
                                       HSBSSCEEEETTSBHHHHHHHHHHHT.SSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS   4 imtrdvvtvppdttleealelmrekg.vsrlPVVdedgklvGivtlrDllra 54 
                                       i t++++t+  d+++ +a+el+ +++ v++l VVde+ +l G++t+ D+lr 
  gi|385806286|ref|YP_005842684.1| 198 ISTPKPITIGIDDDIVKAIELF-KTEdVGSLIVVDENYNLRGMLTEIDILRH 248
                                       6799******************.4446****99987779***********96 PP

>> DisA_N  DisA bacterial checkpoint controller nucleotide-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1   0.00077       6.9       7      24 ..      82     111 ..      77     151 .. 0.68
   2 ?    5.6   0.0    0.0013        11       2      28 ..     214     240 ..     213     254 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.00077
                                       HHHHT--EEEEEESSSC............C CS
                            DisA_N   7 lskkkiGaliviereee............l 24 
                                       + ++k+Gal v++++ee             
  gi|385806286|ref|YP_005842684.1|  82 MTSHKVGALAVVNKNEEvigeiteknlidT 111
                                       7899*************5555444444440 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0013
                                       HHHHHHHHHT--EEEEEESSSCCCTTC CS
                            DisA_N   2 eaveelskkkiGaliviereeelkeii 28 
                                       +a+e ++ + +G liv++++ +l+ ++
  gi|385806286|ref|YP_005842684.1| 214 KAIELFKTEDVGSLIVVDENYNLRGML 240
                                       7899999**************998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.54
# Mc/sec: 1420.57
//
Query:       gi|385806287|ref|YP_005842685.1|  [L=186]
Description: DNA-binding protein containing PIN domain-like protein [Fervidicoccus fontis Kam940]
Scores for complete 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-49  168.4   2.4    1.5e-49  168.2   2.4    1.0  1  PIN_5           PINc domain ribonuclease
  ------ inclusion threshold ------
      0.053   13.7   0.1       0.88    9.8   0.1    2.1  2  DUF5333         Family of unknown function (DUF5333)
      0.054   13.0   0.2      0.068   12.6   0.2    1.2  1  ComA            (2R)-phospho-3-sulfolactate synthase (ComA)
       0.27   11.1   4.4       0.23   11.4   1.9    1.8  2  DNA_pol3_a_NII  DNA polymerase III polC-type N-terminus II


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 !  168.2   2.4   3.4e-53   1.5e-49      25     204 ..       3     176 ..       1     178 [. 0.97

  Alignments for each domain:
  == domain 1  score: 168.2 bits;  conditional E-value: 3.4e-53
                             PIN_5  25 eavkklldliaearlklgiscyippsvykElkeflkreeveeeviakldtwlvkkspdryevkipaeilyeyveevr 101
                                       +++ kl +li++ +l+lg+s+++++s+ kE+k+++  ++vee++i+++ +w+++k p++ ++kipa i+ ey++e+r
  gi|385806287|ref|YP_005842685.1|   3 DVIIKLTQLISKLKLSLGVSFFVTNSIAKEMKNYMLANGVEESTINEFFMWVTVKMPEKLSIKIPAVIFSEYLKEMR 79 
                                       6778999********************************************************************** PP

                             PIN_5 102 erinkGlrvaEeavreaaeeseklekeeeeeevgelikklRekYrealRkGilDsaeDldvllLAkELdaavvssDe 178
                                        r  k l+++E+ +++a + ++      +e++++eli++lRek+rea+RkGi+Ds eD+d +lL +EL++++v++De
  gi|385806287|ref|YP_005842685.1|  80 MREIKALKISEDFIKKAYDLNY------DEKNISELIHDLREKFREAMRKGIIDSPEDFDAVLLSYELKGVLVTNDE 150
                                       *******************999......5689********************************************* PP

                             PIN_5 179 GikkwaeklGlrlveakkfpkvlkey 204
                                       G++k++e +G+ ++++  f + l+ +
  gi|385806287|ref|YP_005842685.1| 151 GMRKVSEIMGVITIDPLAFLENLRRL 176
                                       *******************9999877 PP

>> DUF5333  Family of unknown function (DUF5333)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.062   2.8e+02      37      59 ..      27      49 ..       7      53 .. 0.65
   2 ?    9.8   0.1    0.0002      0.88      28      69 ..      77     118 ..      62     127 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.062
                           DUF5333 37 lseleslkakarelGYseaeiea 59
                                       s ++++k+++ ++G +e+ i++
  gi|385806287|ref|YP_005842685.1| 27 NSIAKEMKNYMLANGVEESTINE 49
                                      44455555555555555555554 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0002
                           DUF5333  28 sisarllkalseleslkakarelGYseaeieayvddkaekar 69 
                                       +++ r +kal+  e+  +ka +l Y e++i+++++d  ek r
  gi|385806287|ref|YP_005842685.1|  77 EMRMREIKALKISEDFIKKAYDLNYDEKNISELIHDLREKFR 118
                                       6889********************************888754 PP

>> ComA  (2R)-phospho-3-sulfolactate synthase (ComA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   1.5e-05     0.068      26     120 ..       2     113 ..       1     142 [. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.5e-05
                                       HHHHHHHGGG-SEEEE-TTGGGGSTCHHHHHHHHHHHCTT-EEEE-HHHHHHHHHTT...........-HHHHHHHH CS
                              ComA  26 edlletageyiDglKlgggtsallpeeilrekielahehgvyvstGgtlfEaalaqg...........kvdeyleec 91 
                                       +d++  + ++i  lKl+ g s+++ ++i +e+ +++  +gv+ st   +f  + ++             ++eyl+e+
  gi|385806287|ref|YP_005842685.1|   2 NDVIIKLTQLISKLKLSLGVSFFVTNSIAKEMKNYMLANGVEESTINEFFMWVTVKMpeklsikipavIFSEYLKEM 78 
                                       5777788999***********************************9999999988888999999999999******* PP

                                       HHCT-SEEEE--SSS-......--HHHHHHHHHHH CS
                              ComA  92 kelgfdviEvsdgtle......lpeeeklrlieka 120
                                       +  ++++  +s+ +++       +e++  +li+++
  gi|385806287|ref|YP_005842685.1|  79 RMREIKALKISEDFIKkaydlnYDEKNISELIHDL 113
                                       **************985555333333344555555 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 ?   -0.7   0.0      0.27   1.2e+03      35      64 ..      23      52 ..      20      59 .. 0.79
   2 ?   11.4   1.9   5.1e-05      0.23      31      95 ..      60     123 ..      59     128 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.27
                    DNA_pol3_a_NII 35 ikvpneiiaealkkkkldklleeyikfgFg 64
                                      ++v n+i +e+ + +    ++e++i++ F 
  gi|385806287|ref|YP_005842685.1| 23 FFVTNSIAKEMKNYMLANGVEESTINEFFM 52
                                      688899999999999999999999998886 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 5.1e-05
                    DNA_pol3_a_NII  31 nkliikvpneiiaealkkkkldklleeyikfgFgklkidvevdedesseeeieefeeqkeeeeek 95 
                                       +kl ik+p  i+ e+lk++   ++ +  i++ F k  +d + de ++  e+i +++e+ +e ++k
  gi|385806287|ref|YP_005842685.1|  60 EKLSIKIPAVIFSEYLKEMRMREIKALKISEDFIKKAYDLNYDE-KNISELIHDLREKFREAMRK 123
                                       6999****************************************.88999999999998887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       879  (0.0490267); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); 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: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1101.71
//
Query:       gi|385806288|ref|YP_005842686.1|  [L=387]
Description: ATP dependent DNA ligase [Fervidicoccus fontis Kam940]
Scores for complete 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-22   78.4   4.4    1.2e-21   77.0   4.4    1.7  1  Lig_C       Ligase Pab1020 C-terminal region
    3.4e-16   60.0   1.7      7e-16   59.0   1.7    1.5  1  RNA_ligase  RNA ligase
  ------ inclusion threshold ------
      0.042   13.6   0.0       0.12   12.1   0.0    1.8  1  UPF0175     Uncharacterised protein family (UPF0175)


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 !   77.0   4.4     2e-25   1.2e-21       3     114 ..     261     371 ..     260     381 .. 0.93

  Alignments for each domain:
  == domain 1  score: 77.0 bits;  conditional E-value: 2e-25
                                       CCSCCGS-STSCHHHHHHHHHHHHHH--SHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---EEEEEEE-SSHHHHHH CS
                             Lig_C   3 fsylfelgrdFlfsRviReafqavefeeseeelrerakeLGesiLepmvetikkvkeeekvkeefrvrfkdeeniee 79 
                                       ++++f+ g+ ++f R++Re f++ e++ ++ el++r  eLG+++Le+ +e+i+++k++  ++eef++rfk+ ++++e
  gi|385806288|ref|YP_005842686.1| 261 MKFFFDEGKGYIFPRILREMFKIEEENLDKSELEKREIELGKALLESAIESINSFKKNGYLGEEFSLRFKNINEMNE 337
                                       589************************************************************************** PP

                                       HHHHHHCTT--EEEEEEE..TTEEEEE..EE-HHH CS
                             Lig_C  80 llehLrrlgvkaeveekekedgelvvkfkkiaqst 114
                                       ++++++++g  +e++e +ke+ge++ kf k  ++t
  gi|385806288|ref|YP_005842686.1| 338 FVSFMKKQGGLIEIREVKKENGEIIAKFLKR-KRT 371
                                       ***************************9874.344 PP

>> RNA_ligase  RNA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.0   1.7   1.2e-19     7e-16       2     149 ..      96     241 ..      95     248 .. 0.73

  Alignments for each domain:
  == domain 1  score: 59.0 bits;  conditional E-value: 1.2e-19
                                       EEEEEEE-SSEEEEEEEE..TTEEEEETTCEB.CTTTHHHHHHTHHHHHHHHHHHHH.....ECCEEEEEEEES... CS
                        RNA_ligase   2 evvvtEKlDGtnfriylv..kevgvasRsqil.pfgeekfkefkrwaaalrkklkekla...neelilyGElig..h 70 
                                        +vv+EKl+G+n+ri+    k +  ++R++++ p           + +++ k+l ekl+   n+  +++ E++g  +
  gi|385806288|ref|YP_005842686.1|  96 YIVVEEKLNGYNVRIVRYygK-ILTITRGGYIcP-----------YTTQKIKELLEKLGgkiNKGEVVFVEVVGdeN 160
                                       68**************99766.**********65...........333444556666666666889********543 PP

                                       SS...TTSS...EEEEEEEEEEECTTBECE--HHHHHHHHHCCTB..EEEEE.SSHHHHHCCC....H.HHHTC--E CS
                        RNA_ligase  71 si.kygglpk..efyvFdifdirdkeeqrylspdevealakglgtvpvlyegkflaaeellel...ll.skgnkrEG 140
                                       ++ +y+ +p+   f+ F i +++    +++l+ ++ e ++++    p ++++++ + +e ++l   +   ++  rEG
  gi|385806288|ref|YP_005842686.1| 161 PYtRYK-YPNcnGFCFFVIDVLK---GKKWLDVKQKERFCRER-NLPCVKQYGIVKKDETAKLweiIRkLEKDEREG 232
                                       333333.5667466655555544...9*********9999944.78999999998777777777542257788**** PP

                                       EEEEESSSS CS
                        RNA_ligase 141 lVikpesel 149
                                       +V+k+ +++
  gi|385806288|ref|YP_005842686.1| 233 IVLKDIKNR 241
                                       ****88875 PP

>> UPF0175  Uncharacterised protein family (UPF0175)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     2e-05      0.12      33      67 ..      10      44 ..       1      47 [. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2e-05
                           UPF0175 33 rlSlgkAaelaglsrveflelLarrgiplinydee 67
                                      ++S++  a+++++s +e +++L+++++  +ny++ 
  gi|385806288|ref|YP_005842686.1| 10 MISSSLMADVLNISENEARKILNSKNVRFLNYNDI 44
                                      69***************************9**875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       908  (0.0506442); expected 358.6 (0.02)
Passed bias filter:                      602  (0.0335769); 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: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.54
# Mc/sec: 2172.67
//
Query:       gi|385806289|ref|YP_005842687.1|  [L=209]
Description: hypothetical protein FFONT_1247 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.2e-33  114.2  26.5    5.2e-33  114.2  26.5    1.9  2  DUF996        Protein of unknown function (DUF996)
  ------ inclusion threshold ------
       0.16   12.1   0.1       0.16   12.1   0.1    2.9  3  DUF2371       Uncharacterised conserved protein (DUF2371)
        3.9    6.6  13.3        4.4    6.4  12.7    1.4  1  Bac_export_2  FlhB HrpN YscU SpaS Family


Domain annotation for each model (and alignments):
>> DUF996  Protein of unknown function (DUF996)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.4      0.28   1.7e+03      87      98 ..       6      17 ..       1      50 [. 0.47
   2 !  114.2  26.5   8.8e-37   5.2e-33       2     135 .]      56     185 ..      55     185 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.28
                            DUF996 87 savflkksyell 98
                                       ++f+  s+++l
  gi|385806289|ref|YP_005842687.1|  6 FGIFIIFSFYNL 17
                                      222222222222 PP

  == domain 2  score: 114.2 bits;  conditional E-value: 8.8e-37
                            DUF996   2 sivGliLvlvalkeiskavndekifsnaliafilsiialvvailalllvlgalatalelpgleeaaslilllllvli 78 
                                        ++Gl+L+ va+k is++++d++if+n+++ ++++ii+ +vai++ l+++   a+ + +     ++s+il+++++li
  gi|385806289|ref|YP_005842687.1|  56 LLIGLVLIGVAVKYISDETKDSTIFNNFMYFILITIIGSIVAIILGLGTFLLGAITIRRM----FFSAILTFIVALI 128
                                       79************************************************9999977766....4448********* PP

                            DUF996  79 iayvlliisavflkksyellgkrtgvklFetagllyfiGaiLtivlvGliilliaei 135
                                       i++v++ i++++l++s+e+++++t+v+lF+tag++yf+Ga+Lti+lvG+iilli+ i
  gi|385806289|ref|YP_005842687.1| 129 IVWVTFTIASTYLRRSFEQIKEKTNVNLFSTAGKFYFWGALLTIILVGFIILLIGII 185
                                       *******************************************************87 PP

>> DUF2371  Uncharacterised conserved protein (DUF2371)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.3      0.16   9.4e+02      41      63 ..      46      68 ..      35      83 .. 0.61
   2 ?   -0.5   0.9      0.22   1.3e+03      94     119 ..      79     107 ..      69     113 .. 0.67
   3 ?   12.1   0.1   2.7e-05      0.16      19      65 ..     148     194 ..     136     208 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.16
                           DUF2371 41 glvlllGllvllvGiamavlgyw 63
                                      + + + G ++ll+G+++  ++  
  gi|385806289|ref|YP_005842687.1| 46 TGFHFTGSILLLIGLVLIGVAVK 68
                                      44556677777777776554443 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.22
                           DUF2371  94 fleqylysdklkvlGP...limGiGiflf 119
                                       ++++++y   + ++G    +i+G+G fl+
  gi|385806289|ref|YP_005842687.1|  79 IFNNFMYFILITIIGSivaIILGLGTFLL 107
                                       55666666666666652115788888875 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 2.7e-05
                           DUF2371  19 akkkrkadvvvvkGklkLlsvsglvlllGllvllvGiamavlgywpk 65 
                                        k+k + ++    Gk+ +  +   ++l+G+++ll+Gi + v++++  
  gi|385806289|ref|YP_005842687.1| 148 IKEKTNVNLFSTAGKFYFWGALLTIILVGFIILLIGIIFMVVAFFSL 194
                                       4555555666778999999999999***************9999754 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 ?    6.4  12.7   0.00074       4.4      28     146 ..      51     182 ..      43     205 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.00074
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.............XXXXXXXXXXXXXXXXX............. CS
                      Bac_export_2  28 ssalvllaglllllllgpslveelaellrevlsa.............lelllelllallllllp............. 78 
                                       +  ++ll+gl+l+ ++++++ +e ++  ++++++             ++++           l              
  gi|385806289|ref|YP_005842687.1|  51 TGSILLLIGLVLIGVAVKYISDETKD--STIFNNfmyfilitiigsiVAII-----------LGlgtfllgaitirr 114
                                       667899999999*********99998..55556555446655544442222...........111111122222233 PP

                                       .XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      Bac_export_2  79 .lllvlllaallanllqvgflfstkalkpklsklnplkglkrifslrslvellksllkvvlvgavaylv 146
                                        ++ ++l + ++  ++ v f+++   l+  +++++  +++ ++fs+ + + +  +ll ++lvg+++ l+
  gi|385806289|ref|YP_005842687.1| 115 mFFSAILTFIVALIIVWVTFTIASTYLRRSFEQIKEKTNV-NLFSTAGKFYFWGALLTIILVGFIILLI 182
                                       2444444455555556668999999999999999997776.9999999999999999999999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1693  (0.094428); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); expected 358.6 (0.02)
Passed Vit filter:                       113  (0.00630264); expected 17.9 (0.001)
Passed Fwd filter:                        64  (0.00356964); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.91u 0.37s 00:00:01.28 Elapsed: 00:00:00.55
# Mc/sec: 1152.78
//
Query:       gi|385806290|ref|YP_005842688.1|  [L=324]
Description: D-3-phosphoglycerate dehydrogenase [Fervidicoccus fontis Kam940]
Scores for complete 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-61  205.3   0.0    6.8e-61  204.7   0.0    1.3  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    6.3e-25   87.4   0.0    7.3e-25   87.2   0.0    1.0  1  2-Hacid_dh      D-isomer specific 2-hydroxyacid dehydrogenase
    5.2e-10   39.7   0.2    4.6e-09   36.6   0.1    2.4  3  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
    1.7e-06   28.4   0.1      6e-06   26.6   0.1    1.8  2  NAD_binding_7   Putative NAD(P)-binding
    0.00098   19.7   0.5     0.0022   18.5   0.1    1.9  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
      0.002   17.7   0.1      0.035   13.7   0.1    2.3  2  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
     0.0064   15.8   0.7      0.016   14.5   0.2    2.0  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
     0.0095   16.0   0.7      0.032   14.3   0.7    1.9  1  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
  ------ inclusion threshold ------
      0.011   15.6   0.2      0.031   14.2   0.0    1.9  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
      0.025   14.6   0.4      0.078   12.9   0.1    2.1  2  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
      0.036   14.6   0.0       0.11   13.1   0.0    1.9  1  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
       0.13   11.6   0.8       0.52    9.6   0.7    1.8  2  ThiF            ThiF family
       0.16   12.8   1.3         11    6.9   0.8    2.9  2  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f


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 !  204.7   0.0   4.9e-64   6.8e-61       1     178 []     112     289 ..     112     289 .. 0.98

  Alignments for each domain:
  == domain 1  score: 204.7 bits;  conditional E-value: 4.9e-64
                                       HHHHHHHHTTHHHHHHHHHTTCC..HTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCH CS
                      2-Hacid_dh_C   1 lalllallrrlaeadeevregew..ksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeee 75 
                                       +al+la++r++ +++e++r+g+w  + +++l g++++gk++GiiG+GrIG ++akr+ afg++v ++dr+ k+e  e
  gi|385806290|ref|YP_005842688.1| 112 IALILAHYRNIIKGEEYLRSGKWvgRIPSELIGHTIHGKKIGIIGMGRIGAELAKRMIAFGAEVSYWDRKVKPEV-E 187
                                       689********************999999*******************************************998.8 PP

                                       HHHTCEECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCCEEEES CS
                      2-Hacid_dh_C  76 eelgvelvsleellaesDivslhlpltpetrhlinaeelakmkkgailiNtaRGglvdeeaLleaLksgkiagaalD 152
                                       +  +++  +l++ll+esDi+ +++ ltpet+hl+n+e++ k+kkga+++Nt+RG+++de+aL+e Lksg+i  aalD
  gi|385806290|ref|YP_005842688.1| 188 HLININRIELDKLLEESDIIAVTIALTPETKHLLNKERILKVKKGALIVNTSRGSIIDEQALIERLKSGEIY-AALD 263
                                       88999******************************************************************8.99** PP

                                       --SSSSSGTCHHHHHSTTEEE-SS-T CS
                      2-Hacid_dh_C 153 vfeeeplpedspllelpnviltPHia 178
                                       v+e+eplp++spll+++nviltPHi+
  gi|385806290|ref|YP_005842688.1| 264 VYETEPLPTSSPLLSMKNVILTPHIG 289
                                       ************************98 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 !   87.2   0.0   5.3e-28   7.3e-25       4     133 ..      10     320 ..       7     322 .. 0.95

  Alignments for each domain:
  == domain 1  score: 87.2 bits;  conditional E-value: 5.3e-28
                                       EST.CHHHHHHHHHTTEEEEEES..CSSHH.HCHHHHTTESEEEE-TTS-BSHHHHHHHTT--EEEESSSSCTTB-H CS
                                       xxxxxxxxxxxxxxxxxxxxxxx..xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        2-Hacid_dh   4 leplreeelellkeegvevevkd..ellte.ellekakdadalivrsntkvtaevlealpkLkviaragvGvDnvDl 77 
                                       +++ +e ele+lk+eg+ev++++  +++ e  l +++ +ad+++v    ++ +e++ ++++Lk+i+  g G D++D+
  gi|385806290|ref|YP_005842688.1|  10 IHKPNEVELEFLKKEGLEVSFHQhpQQTYEeWLEKEIINADIIVVPPAHPFGKEFIGKAKNLKLIMVSGSGLDKIDI 86 
                                       55558999******888******9966655156678999************************************** PP

                                       HHHHHTT-EEEE-TTTTHHHHHHHH.................................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.................................................... RF
                        2-Hacid_dh  78 daakerGilVtnvpgystesvAElt.................................................... 102
                                       + a++rGi V+n+p++ +e+vA++                                                     
  gi|385806290|ref|YP_005842688.1|  87 EEASKRGIYVANAPDSIAEAVADHIialilahyrniikgeeylrsgkwvgripselightihgkkigiigmgrigae 163
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                        2-Hacid_dh 103 ............................................................................. 102
                                                                                                                    
  gi|385806290|ref|YP_005842688.1| 164 lakrmiafgaevsywdrkvkpevehlininrieldklleesdiiavtialtpetkhllnkerilkvkkgalivntsr 240
                                       ***************************************************************************** PP

                                       .................................................T-BHHHHHHHHHHHHHHHHHHHTTCCGT CS
                                       .................................................xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        2-Hacid_dh 103 .................................................aaTeeaqeniaeeaaenlvaflkgespa 130
                                                                                        +++ ea ++  e +a ++v+f+k+++++
  gi|385806290|ref|YP_005842688.1| 241 gsiideqalierlksgeiyaaldvyeteplptsspllsmknviltphigGYSWEATKETSEYVARSIVEFAKEGKLP 317
                                       ***********************************************************************997765 PP

                                       TBC CS
                                       xxx RF
                        2-Hacid_dh 131 nav 133
                                         v
  gi|385806290|ref|YP_005842688.1| 318 KTV 320
                                       544 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 ?   -0.9   0.0       1.2   1.6e+03      18      46 ..      21      49 ..      18      78 .. 0.82
   2 ?   -0.7   0.0       1.1   1.5e+03      31      63 ..      82     115 ..      61     125 .. 0.72
   3 !   36.6   0.1   3.4e-12   4.6e-09       1     108 [.     151     257 ..     151     264 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.2
                                      HHHTT-EEEEE-SSHHHHHHHHHTTEEE- CS
                     NAD_binding_2 18 llkagykvavynrtkekveelvaegakaa 46
                                      l+k+g +v+++++ ++  ee++++++  a
  gi|385806290|ref|YP_005842688.1| 21 LKKEGLEVSFHQHPQQTYEEWLEKEIINA 49
                                      67899999999999999999999985443 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.1
                                       SHHHHHHHHHTTEEE-SSHHHHHHHC.SEEEE-S CS
                     NAD_binding_2  31 tkekveelvaegakaaesieelvasl.dvvitmv 63 
                                       +k  +ee+ ++g+ +a+ + ++++++ d +i ++
  gi|385806290|ref|YP_005842688.1|  82 DKIDIEEASKRGIYVANAPDSIAEAVaDHIIALI 115
                                       5556778888888888888888877775555544 PP

  == domain 3  score: 36.6 bits;  conditional E-value: 3.4e-12
                                       EEEEE--SHHHHHHHHHHHHTT-EEEEE-SS.HHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS. CS
                     NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrt.kekveelvaegakaaesieelvasldvvitmvkagkavdevieg. 75 
                                       kig+iG+G +G+++a+++++ g +v+ ++r+ k +ve+l++ +     ++ +l+++ d++ + +  ++++++++++ 
  gi|385806290|ref|YP_005842688.1| 151 KIGIIGMGRIGAELAKRMIAFGAEVSYWDRKvKPEVEHLININR---IELDKLLEESDIIAVTIALTPETKHLLNKe 224
                                       79***************************983567888886543...35567999********************99 PP

                                       HCCC--TT-EEEE-S---HHHHHHHHHHHHHTT CS
                     NAD_binding_2  76 llealkkgdilidgstsspedtrelakelkekg 108
                                        + ++kkg++++++s  s+ d + l ++lk+ +
  gi|385806290|ref|YP_005842688.1| 225 RILKVKKGALIVNTSRGSIIDEQALIERLKSGE 257
                                       66679********************99999766 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       2.4   3.4e+03      59      69 ..      46      56 ..      13     106 .. 0.66
   2 !   26.6   0.1   4.3e-09     6e-06       3      77 ..     145     219 ..     143     240 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.4
                     NAD_binding_7 59 legadlviaat 69
                                      + +ad++++ +
  gi|385806290|ref|YP_005842688.1| 46 IINADIIVVPP 56
                                      33466555543 PP

  == domain 2  score: 26.6 bits;  conditional E-value: 4.3e-09
                     NAD_binding_7   3 ldlkgkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvklaeeelekdlegadlviaatddrelner 77 
                                       + ++gkk+ ++G G+++a+ +++++++ga+v   + +vk+e+e l+++++ el+k le+ d++ +++  + + ++
  gi|385806290|ref|YP_005842688.1| 145 HTIHGKKIGIIGMGRIGAELAKRMIAFGAEVSYWDRKVKPEVEHLININRIELDKLLEESDIIAVTIALTPETKH 219
                                       7899*************************************************9999998866665544444333 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   0.1   1.6e-06    0.0022       1      69 [.     151     211 ..     151     241 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.6e-06
                                       EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S CS
                     F420_oxidored   1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlav 69 
                                       kigiiG+G++g+ la++++a g    e+    +r+ +   e +    +++   +  +++ee+d++ +++
  gi|385806290|ref|YP_005842688.1| 151 KIGIIGMGRIGAELAKRMIAFG---AEVSYW-DRKVKP--EVEHL--ININRIELDKLLEESDIIAVTI 211
                                       7*********************...999955.554442..22222..3444445677777777766554 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.13   1.8e+02      37      84 ..      82     115 ..      59     129 .. 0.57
   2 !   13.7   0.1   2.6e-05     0.035       2      90 ..     147     234 ..     146     255 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.13
                                       T-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHHHHHHHHTGGG CS
                              IlvN  37 gsksvkkAkeegfevltvaeavkkadvvmiliPDelqkevyeeeiepn 84 
                                       ++  +++A+++g+ v+++              PD++ ++v ++ i+  
  gi|385806290|ref|YP_005842688.1|  82 DKIDIEEASKRGIYVANA--------------PDSIAEAVADHIIALI 115
                                       233445555555555554..............5555555544444433 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 2.6e-05
                                       HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE...-S-HHHHHH CS
                              IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmi...liPDelqke 75 
                                       ++gkki +iG+G  G   a+ +   g +v +  r+ +  v++    +++ ++++++ +++d++++   l+P++  k+
  gi|385806290|ref|YP_005842688.1| 147 IHGKKIGIIGMGRIGAELAKRMIAFGAEVSYWDRKVKPEVEHLI--NINRIELDKLLEESDIIAVtiaLTPET--KH 219
                                       789****************************9999998777655..567788888888888886511144543..33 PP

                                       HHHHHTGGG--TT-E CS
                              IlvN  76 vyeeeiepnlkegka 90 
                                       ++++e   ++k+g+ 
  gi|385806290|ref|YP_005842688.1| 220 LLNKERILKVKKGAL 234
                                       444444445566554 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.4   1.9e+03      70      96 ..      21      53 ..       4      55 .. 0.66
   2 !   14.5   0.2   1.2e-05     0.016      27     126 ..     148     237 ..     135     309 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.4
                                      TTTCECEE......HCHHHHHHHHHHHH-SEEE CS
                       AlaDh_PNT_C 70 lgakfvev......lksqeellaeavkeadvvi 96
                                      l+++ +ev      ++  ee l++++ +ad+++
  gi|385806290|ref|YP_005842688.1| 21 LKKEGLEVsfhqhpQQTYEEWLEKEIINADIIV 53
                                      444444445555557777888999999999997 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 1.2e-05
                                       ---EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHHHHHH-SEEEE---BTT CS
                       AlaDh_PNT_C  27 epakvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeellaeavkeadvvigtvlipG 103
                                       +  k+ +iG G  G + ++   ++ga+V   D +  ++ ++e+l +        ++ +l++ ++e+d++  t++++ 
  gi|385806290|ref|YP_005842688.1| 148 HGKKIGIIGMGRIGAELAKRMIAFGAEVSYWDRK--VKPEVEHLINI-------NRIELDKLLEESDIIAVTIALTP 215
                                       466899*************************976..45667665444.......8999**********988877665 PP

                                       SS---SC-HHHHHTS-TTEEEEE CS
                       AlaDh_PNT_C 104 kkaPkLvteemvksMkpgsVivD 126
                                        ++ +L+++e + + k+g+ iv 
  gi|385806290|ref|YP_005842688.1| 216 -ETKHLLNKERILKVKKGALIVN 237
                                       .456899**************96 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.7   2.3e-05     0.032       9     100 ..     146     231 ..     140     245 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.3e-05
                                       ..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEE...EE- CS
                      Shikimate_DH   9 slkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvv...isa 82 
                                       ++++kk+ +iG G+++ ++ak ++a g++ v    R ++      e+l   +i+ ++l+   +ll+e+d++   i+ 
  gi|385806290|ref|YP_005842688.1| 146 TIHGKKIGIIGMGRIGAELAKRMIAFGAE-VSYWDRKVKPEV---EHL--ININRIELD---KLLEESDIIavtIAL 213
                                       6899************************9.999999776432...223..233445555...555666665211556 PP

                                       SSSSS-SB-HHHHHCCHH CS
                      Shikimate_DH  83 taseepilekeeveealk 100
                                       t  ++++l+ke++ +++k
  gi|385806290|ref|YP_005842688.1| 214 TPETKHLLNKERILKVKK 231
                                       677888888888877664 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.2e-05     0.031       1      38 [.     151     188 ..     151     239 .. 0.80
   2 ?   -1.8   0.1       1.8   2.5e+03     152     170 ..     296     314 ..     294     323 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.2e-05
                                       EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHH CS
                           3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvdiseealeka 38 
                                       k+++iG G +Ga++a+ +++ g eV   d++ +   + 
  gi|385806290|ref|YP_005842688.1| 151 KIGIIGMGRIGAELAKRMIAFGAEVSYWDRKVKPEVEH 188
                                       69**************************9976544444 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.8
                                       -TT--HHHHHHHHHHHHHT CS
                           3HCDH_N 152 gekTseetvatvvelakki 170
                                       +++Tse +   +ve+ak+ 
  gi|385806290|ref|YP_005842688.1| 296 TKETSEYVARSIVEFAKEG 314
                                       6789999999999998864 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 ?   -2.4   0.0         3   4.1e+03     134     152 ..     102     120 ..      84     124 .. 0.68
   2 ?   12.9   0.1   5.7e-05     0.078       1      42 [.     151     194 ..     151     229 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3
                                       --HHHHHTT--EEEEEEES CS
                    NAD_Gly3P_dh_N 134 slAeEvakgkptavviask 152
                                       s+Ae va++ ++ + +++ 
  gi|385806290|ref|YP_005842688.1| 102 SIAEAVADHIIALILAHYR 120
                                       6777777777777777665 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 5.7e-05
                                       -EEEE--SHHHHHHHHHHHTTT--EEEE-S-H..HHHHHHHHHS CS
                    NAD_Gly3P_dh_N   1 kiavlGaGswGtalAkvlaenghevrlwvree..elieeineeh 42 
                                       ki+++G+G  G  lAk +   g ev+ w r+   e+ + in ++
  gi|385806290|ref|YP_005842688.1| 151 KIGIIGMGRIGAELAKRMIAFGAEVSYWDRKVkpEVEHLININR 194
                                       79***************************987554555555555 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     8e-05      0.11       1      32 [.     151     182 ..     151     200 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8e-05
                                       EEEEECSSHHHHHHHHHHHHTTSEEEEEESSS CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversd 32 
                                       k+ ++G G ig ElA+ + ++g++V+  +r+ 
  gi|385806290|ref|YP_005842688.1| 151 KIGIIGMGRIGAELAKRMIAFGAEVSYWDRKV 182
                                       688**********************9877765 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.7   0.00038      0.52      15      41 ..     146     172 ..     140     176 .. 0.90
   2 ?   -1.1   0.0      0.69   9.5e+02     102     132 ..     196     230 ..     172     295 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00038
                                       HHHTSEEEEE--SHHHHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  15 kLrdskvllvGaGglGsellknLalsG 41 
                                        ++ +k+ ++G+G +G el+k +++ G
  gi|385806290|ref|YP_005842688.1| 146 TIHGKKIGIIGMGRIGAELAKRMIAFG 172
                                       57889*****************99998 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.69
                                       S-HHHHTT-SEEEEESSS.HHHHHHHHHHHH...H CS
                                       xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx...x RF
                              ThiF 102 vleellesvDlVvdalDn.iearrlvnracv...k 132
                                        l++lle+ D+++ ++    e+++l+n+  +   k
  gi|385806290|ref|YP_005842688.1| 196 ELDKLLEESDIIAVTIALtPETKHLLNKERIlkvK 230
                                       36889999999988887547888888876553333 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 ?    2.6   0.0      0.17   2.4e+02      43      79 ..      27      65 ..       4      74 .. 0.66
   2 ?    6.9   0.8    0.0078        11       2      63 ..     151     206 ..     150     237 .. 0.60

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.17
                                      HHHTTHEEESSHHHHHTCTTESEEEE-S-G..GGHHHHH CS
                      GFO_IDH_MocA 43 aesfgveaysdleelladpeidavivatpn..gtheela 79
                                        sf+ +  + +ee l+++ i+a i+++p+    ++e++
  gi|385806290|ref|YP_005842688.1| 27 EVSFHQHPQQTYEEWLEKEIINADIIVVPPahPFGKEFI 65
                                      445666677779*****9999999999999433365555 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0078
                                       EEEEETTSHHHHHHHHHHHHTTTTE.........EEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTE CS
                      GFO_IDH_MocA   2 rvaiiGaGkigskhlrplnesqrle.........evvalldpdaeraeavaesfgveaysdleelladpei 63 
                                       +++iiG+G+ig + ++ + +   +          ev +l++++  + +++               l++++i
  gi|385806290|ref|YP_005842688.1| 151 KIGIIGMGRIGAELAKRMIAFGAEVsywdrkvkpEVEHLININRIELDKL---------------LEESDI 206
                                       899*******9999977777633334445555555555554444444444...............443334 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); 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: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 1924.76
//
Query:       gi|385806291|ref|YP_005842689.1|  [L=382]
Description: malate dehydrogenase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.3e-110  369.7   0.1   1.5e-110  369.5   0.1    1.0  1  Ldh_2     Malate/L-lactate dehydrogenase


Domain annotation for each model (and alignments):
>> Ldh_2  Malate/L-lactate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  369.5   0.1  8.5e-115  1.5e-110       2     333 .]      25     367 ..      24     367 .. 0.96

  Alignments for each domain:
  == domain 1  score: 369.5 bits;  conditional E-value: 8.5e-115
                                       -HHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHTT-GGGTGGGHHHHHHHHHTTSSBSS---EEEEEETTEEEEE CS
                             Ldh_2   2 saeelralveavleaagvseedAeivadvlveadlrGvdsHGvarlpryverlkkgkinpkaepevvketpavavvD 78 
                                       + eelralve+++e+ g+s+e+++iv+dvlv+adl G++sHGv+r++ry+  lkk  +np++e++vv+e +a+av+D
  gi|385806291|ref|YP_005842689.1|  25 KEEELRALVENIFENNGLSKEHSKIVTDVLVSADLMGISSHGVQRVNRYIMGLKKCCVNPRPEIKVVREIGATAVID 101
                                       789************************************************************************** PP

                                       ETTE-HHHHHHHHHHHHHHHHHHHSEEEEEEEEEE--SSHHHHHHHHHHTTSEEEEEEEESSEB--TTBSS--BE-- CS
                             Ldh_2  79 gdnglGqvvakkamelaiekakehGigivavrnsnhfGaagyyaemaaeaGligiaftnssplvaptggkeavlGtN 155
                                       +d glG++++ kam+laiekak++G+++v v+ns+hfG+agyya +a+e+ lig+a+tns++lv  +++  ++lGtN
  gi|385806291|ref|YP_005842689.1| 102 ADAGLGHIAGLKAMDLAIEKAKTYGTSLVLVKNSQHFGIAGYYALKAIEKKLIGVAMTNSESLVSYVNTVGKTLGTN 178
                                       ***************************************************************************** PP

                                       EEEEEEEETTSSEEEEEEESBSS-HHHHHHHHHCT---STTSEEETTSS.EES-HHHHHCC.....CEE-BT..... CS
                             Ldh_2 156 PiafaaPakeeepfvlDmAtSvvargkievaarkgkpiPegwalDadGn.pttDPaaaleg.....gallpl..... 221
                                       Pia+a+P+++ +p+++D AtS++  gk+e++a+++k++P+gw+l +dG+  ++D ++ale      ++llpl     
  gi|385806291|ref|YP_005842689.1| 179 PIAIAIPKASLPPILFDAATSIIPVGKVEIYAKEEKELPHGWVLGDDGKvISKDSKKALEMiknnrASLLPLggige 255
                                       *************************************************6689*******9999********55555 PP

                                       ..TTHHHHHHHHHHHHHHTCTTTS-HGGGSSSSSSCTSS-SSEEEEEEEEEGGGTT.HHHHHHHHHHHHHHHHTS-B CS
                             Ldh_2 222 ..GghKGyglalmvelLagvLsgaatgkevsgsedeekkpaklghffiaidpeafgdaeefkervdalldelraspp 296
                                         GghKG+gla+++++++gvLsgaa+g +v    + ++kpa++gh f a+++e f++ +ef++r++++++e+++ ++
  gi|385806291|ref|YP_005842689.1| 256 efGGHKGSGLAFIIDIITGVLSGAAWGIHVGY--TVGEKPANVGHAFAAVNIESFMELAEFEKRLEKYIEEIKSLRK 330
                                       5556***********************66655..558889999********************************** PP

                                       STTTSS---TTHHHHHHHHHHHHH-EEEEHHHHHHHH CS
                             Ldh_2 297 aegadevllPGereaaaraerlkeGipldeavleelk 333
                                       +++ad++++PGe+ + ++++r+k Gipl+++v +el+
  gi|385806291|ref|YP_005842689.1| 331 IPNADSIWIPGEKAWYTMQTRKKIGIPLHKNVCNELN 367
                                       **********************************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      637  (0.035529); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2581.81
//
Query:       gi|385806292|ref|YP_005842690.1|  [L=269]
Description: hypothetical protein FFONT_1250 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.051   13.6   0.2      0.097   12.7   0.2    1.4  1  IL7       Interleukin 7/9 family


Domain annotation for each model (and alignments):
>> IL7  Interleukin 7/9 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   5.4e-06     0.097      15      58 ..      34      77 ..      29      78 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.4e-06
                               IL7 15 dvsidkLdkaiesksnCsanetsclkkiscDdckeacFlvraqe 58
                                      + s dk ++  e ++ Cs ne ++l +i+    k+  F+++++e
  gi|385806292|ref|YP_005842690.1| 34 NASFDKENRILEYDCRCSINEDKILSRIPNASEKTIKFIKKVSE 77
                                      5667777888999***************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); 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: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1588.13
//
Query:       gi|385806293|ref|YP_005842691.1|  [L=237]
Description: CopG family transcriptional regulator [Fervidicoccus fontis Kam940]
Scores for complete 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   1.0       0.25   11.3   0.4    2.8  2  TBD              TBD domain
     0.0064   16.8   0.6      0.019   15.3   0.0    2.0  1  RHH_7            Transcriptional regulator, RHH-like, CopG
     0.0076   15.6   4.3     0.0076   15.6   4.3    1.7  1  DUF3450          Protein of unknown function (DUF3450)
     0.0077   15.9   2.3     0.0077   15.9   2.3    2.0  2  RPW8             Arabidopsis broad-spectrum mildew resistance
  ------ inclusion threshold ------
      0.035   13.7   6.7      0.023   14.3   4.8    1.6  2  HAUS6_N          HAUS augmin-like complex subunit 6 N-terminu
      0.037   13.7   1.4      0.037   13.7   0.2    1.6  2  ATG2_CAD         Autophagy-related protein 2 CAD motif
      0.045   13.8   0.7       0.21   11.7   0.1    2.2  1  T2SSM            Type II secretion system (T2SS), protein M
      0.051   13.6   2.3       0.12   12.4   2.3    1.7  1  DUF1664          Protein of unknown function (DUF1664)
      0.051   13.6   7.0      0.029   14.4   4.3    1.9  2  Laminin_II       Laminin Domain II
       0.06   12.2  12.8      0.036   13.0  10.5    1.7  2  Spc7             Spc7 kinetochore protein
      0.079   12.7   6.6      0.038   13.7   3.7    1.9  2  LXG              LXG domain of WXG superfamily
       0.15   11.2   2.8       0.22   10.7   2.8    1.2  1  Med3             Mediator complex subunit 3 fungal
       0.23   12.0   9.6      0.094   13.2   6.8    1.8  2  APG6_N           Apg6 coiled-coil region
       0.23    9.4   5.3       0.36    8.7   5.3    1.2  1  Prominin         Prominin
       0.38   10.9   8.3       0.54   10.4   6.6    2.0  2  Med2             Mediator complex subunit 2
        0.4   10.9   6.1       0.25   11.5   4.0    1.7  2  STN1_2           CST, Suppressor of cdc thirteen homolog, com
       0.71   10.4   3.6       0.61   10.6   1.8    1.9  1  NPV_P10          Nucleopolyhedrovirus P10 protein
       0.82    9.8   7.5       0.49   10.5   0.9    2.9  2  bZIP_1           bZIP transcription factor
       0.83    8.7   5.7        1.3    8.0   5.7    1.4  1  Atg14            Vacuolar sorting 38 and autophagy-related su
       0.88    9.6  13.2      0.091   12.8   8.6    1.7  2  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
        1.1    9.4   3.8        2.1    8.5   3.9    1.4  2  DDHD             DDHD domain
        1.2    8.3   7.6       0.48    9.6   5.1    1.6  2  TMPIT            TMPIT-like protein
        1.2    8.6   3.4       0.95    8.9   2.2    1.4  1  Allexi_40kDa     Allexivirus 40kDa protein
          2    8.9   8.8       0.14   12.5   1.3    2.8  2  Snapin_Pallidin  Snapin/Pallidin
        2.1    9.0   9.0       0.57   10.8   2.8    2.7  3  YabA             Initiation control protein YabA
        2.2    8.1  13.0       0.64    9.8   8.9    2.1  2  DUF724           Protein of unknown function (DUF724)
        2.7    8.2   7.8        1.3    9.2   4.1    2.2  2  Fib_alpha        Fibrinogen alpha/beta chain family
        4.2    7.3   5.2        9.5    6.1   1.3    2.5  2  60KD_IMP         60Kd inner membrane protein
        4.7    7.3   7.8        2.3    8.3   0.4    2.7  3  Spore_III_AB     Stage III sporulation protein AB (spore_III_
        7.5    7.3   8.7        1.9    9.2   2.6    2.5  2  DUF2203          Uncharacterized conserved protein (DUF2203)
        7.5    6.6  15.0          2    8.5   3.1    2.5  2  ADIP             Afadin- and alpha -actinin-Binding


Domain annotation for each model (and alignments):
>> TBD  TBD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.4   0.00043      0.25       5      22 ..      85     102 ..      82     131 .. 0.80
   2 ?    3.2   0.0      0.14        82       3      22 ..     174     194 ..     172     206 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00043
                               TBD   5 vnlekaywELkeElsrlr 22 
                                       ++l + + ELkeE+ r+ 
  gi|385806293|ref|YP_005842691.1|  85 DELTRSFAELKEEMERIE 102
                                       79999***********95 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.14
                               TBD   3 ervnlekaywE.LkeElsrlr 22 
                                       e v + +++wE  k Els++ 
  gi|385806293|ref|YP_005842691.1| 174 EYVAIDRTFWEdFKNELSKIN 194
                                       5577899***889*****996 PP

>> RHH_7  Transcriptional regulator, RHH-like, CopG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   3.3e-05     0.019      35      66 ..       6      38 ..       3      41 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.3e-05
                                      EEEE-HHHHHHHHHHHHHTTS-.CCHHHHHHHH CS
                             RHH_7 35 sfYlSkeeydiLeklAneEaeS.VgsfiKRyiL 66
                                       f l +e+y++L++lAn    S Vg f+K  i 
  gi|385806293|ref|YP_005842691.1|  6 CFSLTEEQYKKLQNLANSMGYSdVGEFVKQNIF 38
                                      68899************976555******9875 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   4.3   1.3e-05    0.0076      31      93 ..      48     110 ..      41     117 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.3e-05
                           DUF3450  31 aaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeiee 93 
                                       +++++ + ++k++ e+++ ++ +r++++ ++  +++ ++l+r+ a++++e++++e +i+e+e 
  gi|385806293|ref|YP_005842691.1|  48 TQQEVKTAQEKIQLERDQFQNLIRTIQDLINPFTAKIDELTRSFAELKEEMERIESKISEVET 110
                                       57899999****************************************************986 PP

>> RPW8  Arabidopsis broad-spectrum mildew resistance protein RPW8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   2.3   1.3e-05    0.0077      19      74 ..      51     107 ..      45     113 .. 0.89
   2 ?   -1.1   0.1       2.3   1.3e+03      62      78 ..     206     223 ..     183     226 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.3e-05
                              RPW8  19 aileakkksldfksilkrLestler.itPvvkeieklnkeldrpreeieeLkklLek 74 
                                        ++ a++k    + ++++L +t+++ i+P+ ++i++l+  + + +ee+e++++++ +
  gi|385806293|ref|YP_005842691.1|  51 EVKTAQEKIQLERDQFQNLIRTIQDlINPFTAKIDELTRSFAELKEEMERIESKISE 107
                                       57889999999999*********98689***********************999876 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.3
                              RPW8  62 reei.eeLkklLekaekL 78 
                                        e++   +k+lLe+++ +
  gi|385806293|ref|YP_005842691.1| 206 SEKMaILFKRLLEEGKVM 223
                                       233304567888888876 PP

>> HAUS6_N  HAUS augmin-like complex subunit 6 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   4.8   3.9e-05     0.023     141     225 ..      48     130 ..      15     138 .. 0.74
   2 ?   -2.0   0.0       3.7   2.1e+03     143     164 ..     188     209 ..     170     221 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.9e-05
                           HAUS6_N 141 kaqdlsklvaahrvslrrflrekaaadrarqkyqenaqllekkerelraeleelqaelkaekeaakkekkeasedae 217
                                       ++q+++++++++++++ +f++ +++   +++ +  + ++l+ +  el++e+e+++++++  + + +ke  +++ +a+
  gi|385806293|ref|YP_005842691.1|  48 TQQEVKTAQEKIQLERDQFQNLIRTIQDLINPFTAKIDELTRSFAELKEEMERIESKIS--EVETRKELPKQKFQAK 122
                                       46778888888888888888888888888888888888888888888888888888776..3333333333334444 PP

                           HAUS6_N 218 eekikkvr 225
                                       e++++kv+
  gi|385806293|ref|YP_005842691.1| 123 ETQSQKVK 130
                                       44777765 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.7
                           HAUS6_N 143 qdlsklvaahrvslrrflreka 164
                                       ++lsk++++ + + +++l ek 
  gi|385806293|ref|YP_005842691.1| 188 NELSKINERNADKVSKMLSEKM 209
                                       3444444444444444444444 PP

>> ATG2_CAD  Autophagy-related protein 2 CAD motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   6.5e-05     0.037      74     150 ..      12      86 ..       8      90 .. 0.81
   2 ?   -3.1   0.1       9.9   5.8e+03      70      85 ..     122     139 ..     104     143 .. 0.46

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.5e-05
                          ATG2_CAD  74 sssssqvsylskrGyvsigsissakvgvtvnedkdgeksvdvevnddllvLelCADStqtLiqllndLkpPttpp.k 149
                                       ++++++ +   ++Gy+++g++ + ++  + + +k  +++ +v++ +++++Le   D +q Li +++dL  P t + +
  gi|385806293|ref|YP_005842691.1|  12 EQYKKLQNLANSMGYSDVGEFVKQNIF-NLQPSKLPLTQQEVKTAQEKIQLER--DQFQNLIRTIQDLINPFTAKiD 85 
                                       567777788899********9887764.6666645888889999999999996..****************988766 PP

                          ATG2_CAD 150 e 150
                                       e
  gi|385806293|ref|YP_005842691.1|  86 E 86 
                                       5 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 9.9
                          ATG2_CAD  70 e..rsssssssqvsylsk 85 
                                       +  +s++ + + +++l++
  gi|385806293|ref|YP_005842691.1| 122 KetQSQKVKPKAIERLKS 139
                                       123455555555555555 PP

>> T2SSM  Type II secretion system (T2SS), protein M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00036      0.21      35      81 ..      76     122 ..      73     135 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00036
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX- CS
                             T2SSM  35 lwqPlserieraqaelqklraqlawveeqaaevralraapasalsga 81 
                                       l+ P +++i+++ +++++l+++++++e++++ev++ ++ p+++ +++
  gi|385806293|ref|YP_005842691.1|  76 LINPFTAKIDELTRSFAELKEEMERIESKISEVETRKELPKQKFQAK 122
                                       799*******************************9999998877665 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   2.3    0.0002      0.12      57     122 ..      45     110 ..      17     130 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0002
                           DUF1664  57 laatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleriee 122
                                       l  t+++ +   ++++ + d+ +++++ i++ ++    +++e+ + + ++ke +e +esk++++e+
  gi|385806293|ref|YP_005842691.1|  45 LPLTQQEVKTAQEKIQLERDQFQNLIRTIQDLINPFTAKIDELTRSFAELKEEMERIESKISEVET 110
                                       444444555555555555566666666666667777777777777777777777777777766665 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   4.3     5e-05     0.029      15      83 ..      48     113 ..      34     130 .. 0.87
   2 ?   -1.4   0.0       3.9   2.2e+03      35      67 ..     192     208 ..     182     218 .. 0.44

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHH CS
                        Laminin_II  15 vleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqlee 83 
                                       +++ ++  +++++ ++++ +++ r+   ++++++ ++  i++  rs  +L+++++++++k++e+++++e
  gi|385806293|ref|YP_005842691.1|  48 TQQEVKTAQEKIQLERDQFQNLIRT---IQDLINPFTAKIDELTRSFAELKEEMERIESKISEVETRKE 113
                                       6777777788888888888888777...99***********************************9876 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.9
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--T CS
                        Laminin_II  35 einrsveetnekvkdankairdArrsvkkLekl 67 
                                       +in+                r A + +k L ++
  gi|385806293|ref|YP_005842691.1| 192 KINE----------------RNADKVSKMLSEK 208
                                       3332................2233333333333 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0  10.5   6.2e-05     0.036     179     284 ..      48     150 ..      28     155 .. 0.77
   2 ?   -1.8   0.0       1.9   1.1e+03     193     218 ..     175     200 ..     155     216 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.2e-05
                              Spc7 179 leeeleklqeaaeelesid.keeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeae 254
                                        ++e+++ qe + +le  + ++ ++++++ ++   a+i+e+ +  ael+e++e++e+ki+e++++k+  +++ +++e
  gi|385806293|ref|YP_005842691.1|  48 TQQEVKTAQE-KIQLERDQfQNLIRTIQDLINPFTAKIDELTRSFAELKEEMERIESKISEVETRKELPKQKFQAKE 123
                                       3555555555.44567766699999*************************************888877777777665 PP

                              Spc7 255 rvleeckgwsesevsrlkeevkaleeltgw 284
                                             ++++ + ++rlk+e   +++ + w
  gi|385806293|ref|YP_005842691.1| 124 TQS---QKVKPKAIERLKSEGVVFQKDLSW 150
                                       544...466777788888777766666666 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.9
                              Spc7 193 lesidkeeLeelreelaelkaeieek 218
                                         +id++  e +++el+++++  + k
  gi|385806293|ref|YP_005842691.1| 175 YVAIDRTFWEDFKNELSKINERNADK 200
                                       44555555666666666666655533 PP

>> LXG  LXG domain of WXG superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   3.7   6.6e-05     0.038     105     168 ..      49     112 ..       9     137 .. 0.88
   2 ?   -1.1   0.0       2.2   1.3e+03      95     116 ..     178     198 ..     172     209 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.6e-05
                               LXG 105 englkkakevteelkdeinkilasvsdivslpelddsevkdslqkakkkvqetiekledfdqeq 168
                                       ++++k a+e+++   d+ ++ +++++d+++    +++e++ s+++ k++++++  k+ + ++  
  gi|385806293|ref|YP_005842691.1|  49 QQEVKTAQEKIQLERDQFQNLIRTIQDLINPFTAKIDELTRSFAELKEEMERIESKISEVETRK 112
                                       6899*******************************************************99976 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.2
                               LXG  95 idedfLeqelenglkkakevte 116
                                       id+ f+e + +n+l+k  e  +
  gi|385806293|ref|YP_005842691.1| 178 IDRTFWE-DFKNELSKINERNA 198
                                       6666666.66666666555444 PP

>> Med3  Mediator complex subunit 3 fungal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   2.8   0.00037      0.22       4      67 ..      42     105 ..      39     132 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00037
                              Med3   4 taklkLdeLevklakeedskakdvvakrikeaedeiLPLrLqfnefiqimaslDeertkekskq 67 
                                       ++kl L++ evk a+e+    +d+ ++ i+  +d i P+  + +e++++ a+l ee  + +sk 
  gi|385806293|ref|YP_005842691.1|  42 PSKLPLTQQEVKTAQEKIQLERDQFQNLIRTIQDLINPFTAKIDELTRSFAELKEEMERIESKI 105
                                       78999************99**********************************99877666665 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   6.8   0.00016     0.094      12     101 ..      50     136 ..      46     156 .. 0.85
   2 ?   -2.1   0.0       9.3   5.4e+03      53      64 ..     187     198 ..     177     212 .. 0.51

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00016
                            APG6_N  12 eeldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaale 88 
                                       +e+++  e+ + erd++++  +++++  +  +    +++el +++++l++e e+ ++++ e+e+ +e  +++ +a e
  gi|385806293|ref|YP_005842691.1|  50 QEVKTAQEKIQLERDQFQNLIRTIQDLINPFT---AKIDELTRSFAELKEEMERIESKISEVETRKELPKQKFQAKE 123
                                       667788889999*************9966654...7***************************************** PP

                            APG6_N  89 eelealeeeeerf 101
                                        ++++++ +  + 
  gi|385806293|ref|YP_005842691.1| 124 TQSQKVKPKAIER 136
                                       *999988766555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 9.3
                            APG6_N  53 eeeleklekeee 64 
                                       ++el+k+++  +
  gi|385806293|ref|YP_005842691.1| 187 KNELSKINERNA 198
                                       233333333222 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   5.3   0.00063      0.36     589     690 ..       9     108 ..       6     140 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00063
                          Prominin 589 LteeerkdLeklresglskihsslyleqlckkltkvnletlaekleelanelsngkknlkqslkneaqdlraiqqel 665
                                       Ltee+ k+L++l++s     ++ ++++q   +l +  l+ +++++++ +++++ + ++  q+l ++ qdl +  + +
  gi|385806293|ref|YP_005842691.1|   9 LTEEQYKKLQNLANSM-GYSDVGEFVKQNIFNLQPSKLPLTQQEVKTAQEKIQLE-RDQFQNLIRTIQDLINPFTAK 83 
                                       8999999999999975.88899999999999999999999999988888888665.555555555555665556666 PP

                          Prominin 666 vlplessvkklkksvkkldeensdl 690
                                       +++l++s ++lk+++++++++ s+ 
  gi|385806293|ref|YP_005842691.1|  84 IDELTRSFAELKEEMERIESKISEV 108
                                       6667777777777777777733332 PP

>> Med2  Mediator complex subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   6.6   0.00093      0.54      21      97 ..      47     123 ..      38     130 .. 0.81
   2 ?   -0.7   0.0       2.8   1.6e+03      41      62 ..     199     221 ..     184     234 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00093
                              Med2  21 lvqeqlktiqldsnvvtGfnnqlqksLkekikkFhsiLDdleiklndaksyveqlveikkekeeekekeeeerqrke 97 
                                       l q+ +kt q + ++     ++l++++++ i+ F + +D+l+ ++++ k+ +e+++++  e e  ke  +++ q ke
  gi|385806293|ref|YP_005842691.1|  47 LTQQEVKTAQEKIQLERDQFQNLIRTIQDLINPFTAKIDELTRSFAELKEEMERIESKISEVETRKELPKQKFQAKE 123
                                       779********************************************999999887776666655554444444443 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.8
                              Med2  41 nqlqksLkekik.kFhsiLDdle 62 
                                        + +k+L+ek++  F  +L + +
  gi|385806293|ref|YP_005842691.1| 199 DKVSKMLSEKMAiLFKRLLEEGK 221
                                       34488999998745888887655 PP

>> STN1_2  CST, Suppressor of cdc thirteen homolog, complex subunit STN1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   4.0   0.00043      0.25      26     127 ..      43     147 ..      28     153 .. 0.53
   2 ?   -2.0   0.0       6.2   3.6e+03     100     119 ..     199     218 ..     182     228 .. 0.46

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00043
                                       XXXXXXXXXHHHHSCGGS.....HHHHHHHHHHHHHHHHHHCT-SEE......EHHHHHT-HHHHHHHSSHHCH-SS CS
                            STN1_2  26 fqlpeeekeesssdasel.....lkslvsllsekikefllekkvqtf......yqqeletveslvslaskpvkessa 91 
                                        +lp +++e  +++++ +     +++l+ ++++ i+ f    k+ ++       ++e+e +es +s +++       
  gi|385806293|ref|YP_005842691.1|  43 SKLPLTQQEVKTAQEKIQlerdqFQNLIRTIQDLINPFT--AKIDELtrsfaeLKEEMERIESKISEVET------R 111
                                       555555544444433333322234445555555555555..44555511112222333333333333333......2 PP

                                       ---SS----SCHHHHHHHHHHHHHHHHHCTSEE-SS CS
                            STN1_2  92 aeevevagesaskqirslfkealqllqeeGlvfqkk 127
                                       +e  +++ +++ +q +++  +a++ l++eG+vfqk+
  gi|385806293|ref|YP_005842691.1| 112 KELPKQKFQAKETQSQKVKPKAIERLKSEGVVFQKD 147
                                       233333444555566666789**************6 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 6.2
                                       -SCHHHHHHHHHHHHHHHHH CS
                            STN1_2 100 esaskqirslfkealqllqe 119
                                       + +sk++ + +    + l e
  gi|385806293|ref|YP_005842691.1| 199 DKVSKMLSEKMAILFKRLLE 218
                                       22333333333333333333 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.8     0.001      0.61      10      66 ..      49     106 ..      40     127 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.001
                           NPV_P10  10 radikavddkVdalqqqvddvqenlpd.vtelnekLdaqsaqLaeletkvenIqdiLn 66 
                                        +++k  ++k++   +q +++   ++d ++  ++k+d+++ + ael++++e I++  +
  gi|385806293|ref|YP_005842691.1|  49 QQEVKTAQEKIQLERDQFQNLIRTIQDlINPFTAKIDELTRSFAELKEEMERIESKIS 106
                                       6788999999987778888888888774567899******************998776 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.9   0.00085      0.49      26      55 ..      82     111 ..      81     120 .. 0.85
   2 ?    1.6   0.9       0.5   2.9e+02      42      64 .]     188     209 ..     185     209 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00085
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  26 aeieeLerrvkaLekeNksLkseleelkke 55 
                                       a+i+eL+r +++L++e++   s+++e +  
  gi|385806293|ref|YP_005842691.1|  82 AKIDELTRSFAELKEEMERIESKISEVETR 111
                                       6899********************998765 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.5
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  42 NksLkseleelkkevekLkskvk 64 
                                       N+ L++ +e+ +++v+k++s+++
  gi|385806293|ref|YP_005842691.1| 188 NE-LSKINERNADKVSKMLSEKM 209
                                       55.9999************9975 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   5.7    0.0023       1.3      56     131 ..      50     127 ..      11     149 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0023
                             Atg14  56 eqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklk..kRrsdleslqneleerrk 130
                                       ++ +++ ++ +   ++ ++li+ +++ ++   +k+++l+++ +e k+++++  +k++  + r++l + +++ +e + 
  gi|385806293|ref|YP_005842691.1|  50 QEVKTAQEKIQLERDQFQNLIRTIQDLINPFTAKIDELTRSFAELKEEMERIESKISevETRKELPKQKFQAKETQS 126
                                       44455555556667788888888899999999999999999999999999999999977555555555555555554 PP

                             Atg14 131 k 131
                                       +
  gi|385806293|ref|YP_005842691.1| 127 Q 127
                                       4 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   8.6   0.00016     0.091      39     123 ..      48     132 ..      12     152 .. 0.85
   2 ?   -2.0   0.1       5.8   3.3e+03      76      96 ..     191     201 ..     180     219 .. 0.46

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00016
                    CENP-F_leu_zip  39 nqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLeslnsslenlleekEq 115
                                        q++v++  E+ + e  ++++ i++++   + +++++++l++   eL++e++   +++se e++++  ++  + kE 
  gi|385806293|ref|YP_005842691.1|  48 TQQEVKTAQEKIQLERDQFQNLIRTIQDLINPFTAKIDELTRSFAELKEEMERIESKISEVETRKELPKQKFQAKET 124
                                       46789999999999999999999999999***********************************************9 PP

                    CENP-F_leu_zip 116 ekvqmkee 123
                                       +  ++k +
  gi|385806293|ref|YP_005842691.1| 125 QSQKVKPK 132
                                       97666643 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 5.8
                    CENP-F_leu_zip  76 valrsekeeLekelqkkqerv 96 
                                       +++           + + ++v
  gi|385806293|ref|YP_005842691.1| 191 SKIN----------ERNADKV 201
                                       2222..........2222222 PP

>> DDHD  DDHD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   3.9    0.0036       2.1      65     168 ..      33     140 ..      29     209 .. 0.69
   2 ?   -2.4   0.0       7.7   4.5e+03      89     113 ..     185     209 ..     172     225 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0036
                              DDHD  65 lepkfsklkPvsiprykrrkllh....lelkesltsigaalkqkvsglvsslsallnrslelaeeesaslaessksh 137
                                       +++++ +l+P ++p +++   ++    +  +++++++ +++++  + +++++  l +++ el+ee +  +++ s+ +
  gi|385806293|ref|YP_005842691.1|  33 VKQNIFNLQPSKLPLTQQEVKTAqekiQLERDQFQNLIRTIQDLINPFTAKIDELTRSFAELKEEMERIESKISEVE 109
                                       667778999****9999977555444433344444444444444444555555578888999999888888888888 PP

                              DDHD 138 erasesskasqeskaaesstasssaksskae 168
                                       +r++  +++ q +++++++ ++++ ++ k+e
  gi|385806293|ref|YP_005842691.1| 110 TRKELPKQKFQAKETQSQKVKPKAIERLKSE 140
                                       8888888888887777777766666555444 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 7.7
                              DDHD  89 elkesltsigaalkqkvsglvssls 113
                                       + k++l++i+++ ++kvs+++s+  
  gi|385806293|ref|YP_005842691.1| 185 DFKNELSKINERNADKVSKMLSEKM 209
                                       5667777777777777777766544 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   5.1   0.00083      0.48       5      83 ..      50     127 ..      47     155 .. 0.68
   2 ?   -1.9   0.0       2.6   1.5e+03       5      74 ..     184     204 ..     159     227 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00083
                             TMPIT   5 eelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelke.elkerkk 80 
                                       +e+++ +++++ + +++++ +++++ l++ ++ +i++ ++   elk+++++++++++  e e+ +el + +++ +++
  gi|385806293|ref|YP_005842691.1|  50 QEVKTAQEKIQLERDQFQNLIRTIQDLINPFTAKIDELTRSFAELKEEMERIESKIS--EVETRKELPKqKFQAKET 124
                                       567777888888888888888888888888888888888888888888888888854..333333333202333333 PP

                             TMPIT  81 vlk 83 
                                       + +
  gi|385806293|ref|YP_005842691.1| 125 QSQ 127
                                       333 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.6
                             TMPIT   5 eelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkee 74 
                                       e++++e+ +++e++                                                 +++++++
  gi|385806293|ref|YP_005842691.1| 184 EDFKNELSKINERN-------------------------------------------------ADKVSKM 204
                                       33333333333333.................................................2222222 PP

>> Allexi_40kDa  Allexivirus 40kDa protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   2.2    0.0016      0.95      61     161 ..      33     132 ..      10     143 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0016
                      Allexi_40kDa  61 vdsiinklnpvsllsqttlLselrdalrtltklldklksvekklelsaetasdskllkklesietsleelhakldel 137
                                       v + i +l+p++l  +++++   +++++  ++++++l ++ + l +  + + d +l+++++ +++++e++  k+ e+
  gi|385806293|ref|YP_005842691.1|  33 VKQNIFNLQPSKLPLTQQEVKTAQEKIQLERDQFQNLIRTIQDLINPFTAKID-ELTRSFAELKEEMERIESKISEV 108
                                       44555556666666566666666666666666666666666666665555544.45678888888888888888777 PP

                      Allexi_40kDa 138 sssetsesegPsssptkassaeaa 161
                                        + ++  +++ ++ +t++++ +++
  gi|385806293|ref|YP_005842691.1| 109 ETRKELPKQKFQAKETQSQKVKPK 132
                                       666665555555555555554444 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.3       1.8     1e+03      53      53 ..      28      28 ..       7      71 .. 0.53
   2 ?   12.5   1.3   0.00025      0.14       6      57 ..      68     116 ..      64     135 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.8
                   Snapin_Pallidin 53 e 53
                                      +
  gi|385806293|ref|YP_005842691.1| 28 D 28
                                      2 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00025
                   Snapin_Pallidin   6 gllellepkldeldeklkelrqsQeeLleqldrlnekLkeleeaqe.aevlpd 57 
                                        l+++++  ++ +++k+ el++s  eL+e+++r  +k+ e+e  +e      +
  gi|385806293|ref|YP_005842691.1|  68 NLIRTIQDLINPFTAKIDELTRSFAELKEEMERIESKISEVETRKElP----K 116
                                       588999999********************************9999943....3 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1       3.6   2.1e+03      32      44 ..      50      62 ..      10      73 .. 0.52
   2 ?   10.8   2.8   0.00099      0.57      10      77 ..      70     138 ..      61     144 .. 0.50
   3 ?    0.8   0.1       1.3   7.4e+02       8      46 ..     188     228 ..     180     231 .. 0.60

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 3.6
                                      HHHHHHHHHHHHH CS
                              YabA 32 aelleenaeLele 44
                                      +e+    ++++le
  gi|385806293|ref|YP_005842691.1| 50 QEVKTAQEKIQLE 62
                                      2222222233333 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00099
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXX.XXXXXXXXXXXX CS
                              YabA  10 leeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkke.lsegkenLarlY 77 
                                       ++++++ ++ ++++++el +++ael ee +++e   +++ +r e  ++k ++k+++ ++   + ++rl 
  gi|385806293|ref|YP_005842691.1|  70 IRTIQDLINPFTAKIDELTRSFAELKEEMERIESKISEVETRKELPKQKFQAKETQsQKVKPKAIERLK 138
                                       455555666666666677777777777766666665555444422222222222220222234455555 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHHHHHHHHHH CS
                              YabA   8 dkleeleeqleelleel..eelkeelaelleenaeLelene 46 
                                       ++l++++e+ ++ ++++  e++   +++llee + + +ene
  gi|385806293|ref|YP_005842691.1| 188 NELSKINERNADKVSKMlsEKMAILFKRLLEEGKVMYVENE 228
                                       45556655554444444112344445788888888888886 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   8.9    0.0011      0.64     105     184 ..      50     129 ..      33     133 .. 0.75
   2 ?   -1.9   0.1       4.3   2.5e+03      53      75 ..     188     210 ..     176     220 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0011
                            DUF724 105 tklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleeeledveqeF 181
                                       ++++++++k++ +  + ++  r +++ i+ +  ki el r  a lke++e+ +++i+++++ +e  +++ ++ e++ 
  gi|385806293|ref|YP_005842691.1|  50 QEVKTAQEKIQLERDQFQNLIRTIQDLINPFTAKIDELTRSFAELKEEMERIESKISEVETRKELPKQKFQAKETQS 126
                                       33333334444444444444566778888999999999999999999999999999999999999999999999887 PP

                            DUF724 182 eav 184
                                       ++v
  gi|385806293|ref|YP_005842691.1| 127 QKV 129
                                       776 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.3
                            DUF724  53 gllekvkklsiddsrseleslke 75 
                                       + l k+++ ++d+ +++l++++ 
  gi|385806293|ref|YP_005842691.1| 188 NELSKINERNADKVSKMLSEKMA 210
                                       44444555555555555554444 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 ?    9.2   4.1    0.0022       1.3      68     128 ..      48     108 ..       9     115 .. 0.73
   2 ?   -0.4   0.0       2.1   1.2e+03      72      93 ..     191     212 ..     173     223 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0022
                                       HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  68 kqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvlesneqkiqkLeqdidqk 128
                                       +q++ k  ++ i+  +++ ++ i ++++ i+    +i +L+  + +++++++++e++i++ 
  gi|385806293|ref|YP_005842691.1|  48 TQQEVKTAQEKIQLERDQFQNLIRTIQDLINPFTAKIDELTRSFAELKEEMERIESKISEV 108
                                       3444444577888888888888888888888888999999999999999999999998765 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2.1
                                       HHHHHHHHHHHHHHHHHCCCHH CS
                         Fib_alpha  72 kkdndnvikksskeleeeilrl 93 
                                       +k n++   k+sk+l e+++ l
  gi|385806293|ref|YP_005842691.1| 191 SKINERNADKVSKMLSEKMAIL 212
                                       2335667777777777665554 PP

>> 60KD_IMP  60Kd inner membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   1.3     0.016       9.5      12      60 ..      73     121 ..      66     133 .. 0.70
   2 ?    2.1   0.0      0.27   1.6e+02      32      60 ..     185     214 ..     180     216 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.016
                          60KD_IMP  12 vrlillpltlkqlkssakmqelqPelkeiqekyk.....kdkqklqqemmklYk 60 
                                       ++ ++ p+t+k  + ++  +el+ e+++i++k +     k     +   +k++ 
  gi|385806293|ref|YP_005842691.1|  73 IQDLINPFTAKIDELTRSFAELKEEMERIESKISevetrK-----ELPKQKFQA 121
                                       555788999999999999**************98544331.....333333332 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.27
                          60KD_IMP  32 elqPelkeiqekykkd.kqklqqemmklYk 60 
                                       +++ el +i+e+ +++  ++l+++m  l+k
  gi|385806293|ref|YP_005842691.1| 185 DFKNELSKINERNADKvSKMLSEKMAILFK 214
                                       57889********87744667788877776 PP

>> Spore_III_AB  Stage III sporulation protein AB (spore_III_AB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.4    0.0039       2.3     100     128 ..       7      35 ..       4      73 .. 0.68
   2 ?    0.7   3.4      0.86     5e+02      32      94 ..      65     120 ..      48     152 .. 0.47
   3 ?   -0.9   0.1       2.7   1.5e+03      75      75 ..     188     188 ..     119     222 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0039
                                       S---HHHHHHHHHHHHHHT--SHHHHHHH CS
                      Spore_III_AB 100 laLkkedkeilkelgeslgysdregqlka 128
                                       ++L++e+ + l++l++s+gysd+ +  k+
  gi|385806293|ref|YP_005842691.1|   7 FSLTEEQYKKLQNLANSMGYSDVGEFVKQ 35 
                                       589*******************9987665 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.86
                                       HHHHHHHHHHHHHHH-SS-HHHHHHHHHHCS-TTHHHHHHHHHHHHH.STSS-HHHHHHHHHH CS
                      Spore_III_AB  32 elkralellegeirygatpLpealeklaeksesplseffeevaerleekegesfeeaweeave 94 
                                       +++++++ ++  i+   + + e+ +++a     +l+e +e++ ++++  e e+ +e+ +++++
  gi|385806293|ref|YP_005842691.1|  65 QFQNLIRTIQDLINPFTAKIDELTRSFA-----ELKEEMERIESKIS--EVETRKELPKQKFQ 120
                                       3444444444444444444444444444.....33333333333332..33333333333333 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 2.7
                                       H CS
                      Spore_III_AB  75 e 75 
                                       +
  gi|385806293|ref|YP_005842691.1| 188 N 188
                                       2 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.2      0.78   4.5e+02      39      71 ..      43      75 ..      10      82 .. 0.65
   2 ?    9.2   2.6    0.0034       1.9      14      77 ..      83     145 ..      71     153 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.78
                           DUF2203 39 akaeaekseaaeleaeleeleaeieelveeiee 71
                                      +k   +++e ++++++++  ++++++l+++i++
  gi|385806293|ref|YP_005842691.1| 43 SKLPLTQQEVKTAQEKIQLERDQFQNLIRTIQD 75
                                      444444444666677777777777777777665 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0034
                           DUF2203  14 llkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvevk 77 
                                       +++el++ +++l++e+e++e++++e ++++e   +++ +a++++ ++   +++e++++ Gv+ +
  gi|385806293|ref|YP_005842691.1|  83 KIDELTRSFAELKEEMERIESKISEVETRKEL-PKQKFQAKETQSQKVKPKAIERLKSEGVVFQ 145
                                       45666666667777777777777776666543.3888888888888999999999999998764 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   2.3    0.0056       3.2      95     149 ..      43      97 ..      31      98 .. 0.84
   2 ?    8.5   3.1    0.0034         2      58     125 ..      87     151 ..      80     160 .. 0.60

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0056
                              ADIP  95 akerqlekklktleqklknekeelqrlknalqqiktqyahelkkkdreiekLkek 149
                                       +k+  +++++kt+++k++ e++++q l +++q++ + ++  +   +r+ ++Lke 
  gi|385806293|ref|YP_005842691.1|  43 SKLPLTQQEVKTAQEKIQLERDQFQNLIRTIQDLINPFTAKIDELTRSFAELKEE 97 
                                       5566678999***********************9999999999999999999986 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0034
                              ADIP  58 lnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlknal 125
                                       l++   +l+ e+er +ski+ ++t+ e  +++    qake+q +k   ++++ lk+e   +q+  ++l
  gi|385806293|ref|YP_005842691.1|  87 LTRSFAELKEEMERIESKISEVETRKELPKQKF---QAKETQSQKVKPKAIERLKSEGVVFQKDLSWL 151
                                       445555666666666666666666666665554...45566666666666666666666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2333  (0.130124); expected 358.6 (0.02)
Passed bias filter:                      931  (0.051927); expected 358.6 (0.02)
Passed Vit filter:                       165  (0.00920297); expected 17.9 (0.001)
Passed Fwd filter:                        40  (0.00223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              31  [number of targets reported over threshold]
# CPU time: 0.77u 0.30s 00:00:01.07 Elapsed: 00:00:00.50
# Mc/sec: 1421.08
//
Query:       gi|385806294|ref|YP_005842692.1|  [L=182]
Description: hypothetical protein FFONT_1252 [Fervidicoccus fontis Kam940]
Scores for 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-05   22.5   6.8    8.6e-05   22.2   6.8    1.1  1  Snf7      Snf7
  ------ inclusion threshold ------
      0.034   13.7   4.5      0.061   12.9   4.5    1.5  1  Filament  Intermediate filament protein
        1.5    8.9   5.5       0.52   10.4   2.3    1.8  2  Swi5      Swi5


Domain annotation for each model (and alignments):
>> Snf7  Snf7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   6.8   1.4e-08   8.6e-05       2     169 ..      14     182 .]      13     182 .] 0.90

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.4e-08
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              Snf7   2 airsLrkaerkldkkqeslekkikkleaelkklakkgnkdralllLKqkkryekqldqldnqlanleqvslaienlk 78 
                                       ai +Lr +e+kl   +++l++ i    +el k+++    d+a+ ++ ++ ++ k l ++ n++ ++e v+   e+ +
  gi|385806294|ref|YP_005842692.1|  14 AITQLRLMENKLRMIEDRLQNSIDSKMNELLKYNQLYGVDAAKMIAGEIAEQKKVLFNIRNMRTSVERVRIRFETVM 90 
                                       7899************************************************************************* PP

                                       HHHHHHHHHHHHHHHHHHHHHCT..CCHHHHHHHHHHHHHHHHHT.CH..HHHHHHHHTT-GGTTHHHHHHHHHHHH CS
                              Snf7  79 snkevlnamkqgakamkamnkkv..didkidklmdeiedqmekae.ei..sEalsrslddadeedEeeleaeLdaLe 150
                                       + +  ++ +k++    +  +k +   ++++  +  ++e+++ + + ei  sE l+++   ++e + e++ea+L + e
  gi|385806294|ref|YP_005842692.1|  91 DLNGSVEMLKDVVPLVNDLKKSIvkAYPDLSIMFNDFEEKLNQIGlEIdsSELLNNPQIPMSEGMNEDVEAILKEAE 167
                                       *************99999998874458**********99877654366447******9888************9977 PP

                                       HHHHHCSH.HHHHHHHTXX CS
                              Snf7 151 qelgdeelldesvklpevP 169
                                       +  +  e    ++ lp+ P
  gi|385806294|ref|YP_005842692.1| 168 EVAKTRE----KNRLPSPP 182
                                       7755555....89999876 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   4.5     1e-05     0.061      12     127 ..      10     132 ..       8     176 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          Filament  12 rlAsYidkVraLEqenkeLeakieeleekksaevsklkelyekeleelrkqldeltkerarlqleldnlreeledlr 88 
                                       ++A  i + r +E++ +++e ++++  + k +e  k ++ly     ++ k +    +e++++  +++n+r+++e++r
  gi|385806294|ref|YP_005842692.1|  10 KMAKAITQLRLMENKLRMIEDRLQNSIDSKMNELLKYNQLYGV---DAAKMIAGEIAEQKKVLFNIRNMRTSVERVR 83 
                                       678889999****************999999999999999975...67788999*********************** PP

                                       XXXXXXXXXXXXXX..XXXXXXX........XXXXXXXXXXXXXXXXXX CS
                          Filament  89 kkyekelnkreevE..aelkalr........kdldeatlarvdLekkve 127
                                        ++e+ + +  +vE  ++++ l         k   +++++  d e+k++
  gi|385806294|ref|YP_005842692.1|  84 IRFETVMDLNGSVEmlKDVVPLVndlkksivKAYPDLSIMFNDFEEKLN 132
                                       *****98887777733344433322223333333344444444444444 PP

>> Swi5  Swi5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   2.3   8.7e-05      0.52      17      66 ..      16      68 ..       4      72 .. 0.70
   2 ?   -1.7   0.1      0.52   3.1e+03      12      12 ..     159     159 ..     125     177 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 8.7e-05
                                      HHHHHHHHHHHHHH..HHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHCTS CS
                              Swi5 17 kelaelkeelkekk.dpeetvkrhIklLheYNEiK..DvgqgLigliAeargv 66
                                      ++l  ++++l+  +   ++ ++++ + L +YN +   D++ ++ g iAe+++v
  gi|385806294|ref|YP_005842692.1| 16 TQLRLMENKLRMIEdRLQNSIDSKMNELLKYNQLYgvDAAKMIAGEIAEQKKV 68
                                      333333333333224678999*************6559************998 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.52
                                       H CS
                              Swi5  12 l 12 
                                       +
  gi|385806294|ref|YP_005842692.1| 159 V 159
                                       2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1121  (0.0625244); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); 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: 0.58u 0.38s 00:00:00.96 Elapsed: 00:00:00.56
# Mc/sec: 970.11
//
Query:       gi|385806295|ref|YP_005842693.1|  [L=429]
Description: ABC-type sodium efflux pump system permease [Fervidicoccus fontis Kam940]
Scores for complete 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   92.1  54.6    4.3e-26   91.9  54.6    1.0  1  ABC2_membrane_3  ABC-2 family transporter protein
    7.8e-19   68.0  26.6    1.2e-18   67.4  26.6    1.2  1  ABC2_membrane_2  ABC-2 family transporter protein
    7.2e-06   25.6  46.9    0.00029   20.3  26.5    3.6  3  ABC2_membrane    ABC-2 type transporter
  ------ inclusion threshold ------
      0.011   15.7   1.9      0.038   14.0   1.9    2.0  1  TPPK_C           Thiamine pyrophosphokinase C terminal


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 !   91.9  54.6   9.5e-30   4.3e-26       2     342 ..      22     408 ..      21     411 .. 0.81

  Alignments for each domain:
  == domain 1  score: 91.9 bits;  conditional E-value: 9.5e-30
                   ABC2_membrane_3   2 sfliitlllPiilvlllglifsnsve......ddentpiavvdednsslsqqlvealeaspsvelvyevdseeeakk 72 
                                       +++i++l++Pi+++++lg ++++s +      + + ++iav+++dn + sq ++++++++ + + v+ +++ +   +
  gi|385806295|ref|YP_005842693.1|  22 KIIITMLVVPIVIFFILGEVMGYSISktseisNMTGVNIAVINYDNGTFSQYFINFIKNDLNSN-VKVFANGT-VYD 96 
                                       5688************99666655543333556999999********************55444.55999999.668 PP

                   ABC2_membrane_3  73 alkngdidgilvipkgfskdllkgesatvtvlinssnlnss.....kailnalns.llqqlnasalv.......... 133
                                       +++ng++  ++vip++f+++++ g sa+++ +++ +  ++s     +++ n + s + ++ + s+l+          
  gi|385806295|ref|YP_005842693.1|  97 LMRNGNYLIVFVIPNNFTYNIVNGVSANIESYTYIKEISISslsqvSLASNLIISsFNRMVLLSYLAkaypnmnatf 173
                                       ***************************99999999999999888874444443333555655555555554555555 PP

                   ABC2_membrane_3 134 .lqseatstsaninvestqleeelsnvasflvg.liliilifitasfiavsiveEkesrikelqlvsgvsplqywls 208
                                        l   ++++s  in ++++ +  +s +  + +  ++ i++++i +s+ a+s+ +Eke +++e+ l+ +v+++ ++ls
  gi|385806295|ref|YP_005842693.1| 174 fLNPVSANESVFINGNILPANTIESLTGPYTALiIAPILMFSIASSISASSMGTEKEEKTLEITLSLPVKRSYILLS 250
                                       533334467777777777777777777778777455566677777888889************************** PP

                   ABC2_membrane_3 209 kilgdflvyllqlllilllafgl.......................gipfgnlglllllfllfglayialgyllssl 262
                                       k+l++f+v+l+ l+ +   ++ +                        i+ + l+l+ l fl+ +++++ ++ + ssl
  gi|385806295|ref|YP_005842693.1| 251 KVLSSFVVSLIGLIGMSTAMLYYeykifsstgiseagglnissassIISPTVLFLFALGFLFAIFVILLISIVASSL 327
                                       **************9976433333577777*******99988877666666666666999999999*********** PP

                   ABC2_membrane_3 263 fknsetaqilifivilllsgffgglfp..ledlpsalkwifsiiPffapglgllrlitgdplweillsliilalfav 337
                                        +n ++aqi+++ ++l++++ +++l+   +++l s+ + i si+P ++p+ +++++  g+ ++ +l+s+i+ +l ++
  gi|385806295|ref|YP_005842693.1| 328 ANNIREAQIIASYIWLPFLIPYILLIYvnISQLGSFGAFIVSILPASTPIIAIKSVFLGN-YIYLLTSFIANILYIA 403
                                       ****************999999999664899999***********************999.6788899999988888 PP

                   ABC2_membrane_3 338 vylll 342
                                       + l +
  gi|385806295|ref|YP_005842693.1| 404 IILYI 408
                                       88766 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 !   67.4  26.6   2.7e-22   1.2e-18       1     283 [.       7     413 ..       7     416 .. 0.77

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 2.7e-22
                   ABC2_membrane_2   1 laiakkEfrdlvrsrrfllltvllpli......................................dvalaylkdlgs 39 
                                       l++akkE++dl r+++++++++++p++                                      ++++ ++k++ +
  gi|385806295|ref|YP_005842693.1|   7 LTLAKKEVKDLFRDPKIIITMLVVPIViffilgevmgysisktseisnmtgvniavinydngtfsQYFINFIKNDLN 83 
                                       589************************98887777777777777777777444444444444444333333333333 PP

                   ABC2_membrane_2  40 slqseakaikeatlaleyveaasasdeaedtdqdlkv........................................ 76 
                                       s+                                  v                                        
  gi|385806295|ref|YP_005842693.1|  84 SNVK--------------------------------Vfangtvydlmrngnylivfvipnnftynivngvsaniesy 128
                                       3333................................03333333333344445666666666666667********* PP

                   ABC2_membrane_2  77 ...........................................................................vs 78 
                                                                                                                    
  gi|385806295|ref|YP_005842693.1| 129 tyikeisisslsqvslasnliissfnrmvllsylakaypnmnatfflnpvsanesvfingnilpantiesltgpyTA 205
                                       ***********************************************************************977655 PP

                   ABC2_membrane_2  79 timavlipvi.aalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvll.......... 144
                                       +i+a ++ +  a  ++a +   Eke++Tl++ Ls+Pv R+ ill+K++++++++l++++ +  ++l           
  gi|385806295|ref|YP_005842693.1| 206 LIIAPILMFSiASSISASSMGTEKEEKTLEITLSLPVKRSYILLSKVLSSFVVSLIGLIGMSTAMLYyeykifsstg 282
                                       55555554425999***************************************9995444444434479*****766 PP

                   ABC2_membrane_2 145 .....alaiilalgivlaledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygv 216
                                            +l i+ a++i   ++  +l+++a  +l++++v l ++++ Ss+a + rea  +a  +++ ++i ++++ y  
  gi|385806295|ref|YP_005842693.1| 283 iseagGLNISSASSI---ISPTVLFLFALGFLFAIFVILLISIVASSLANNIREAQIIASYIWLPFLIPYILLIYVN 356
                                       664443433333333...3344556666666666668899*******************999999999999999885 PP

                   ABC2_membrane_2 217 aellagpavpqeindflsllsptsayntllneilagsdlnalgstatnllilllllavllvlgyvlF 283
                                       ++ l  + +      f+  + p+s   +++++++ g     +++  t++++ +l++a+ l +g+  F
  gi|385806295|ref|YP_005842693.1| 357 ISQLGSFGA------FIVSILPASTPIIAIKSVFLGN----YIYLLTSFIANILYIAIILYIGTKWF 413
                                       555554555......89999999999999999*9999....7*******************999877 PP

>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   9.1   3.7e-05      0.17       2     121 ..       5     167 ..       4     180 .. 0.80
   2 !   20.3  26.5   6.6e-08   0.00029      52     174 ..     195     347 ..     146     385 .. 0.75
   3 ?   -1.8   3.2      0.37   1.7e+03      89     127 ..     376     412 ..     368     419 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.7e-05
                     ABC2_membrane   2 qikallkreflqrwrdpslgllwrliqplllalvfgtvfgnlgnsedglnr.......................... 52 
                                       ++++l k+e++  +rdp ++ +++l+ p+++++++g v g   ++++++++                          
  gi|385806295|ref|YP_005842693.1|   5 EFLTLAKKEVKDLFRDPKII-ITMLVVPIVIFFILGEVMGYSISKTSEISNmtgvniavinydngtfsqyfinfikn 80 
                                       5899*************999.*******************7444444453336777788888999999999999999 PP

                     ABC2_membrane  53 .....................pgllffsvlflafsaltsvapvferergvlerelvsplyslsayvlakvlvelpvs 108
                                                             +l++f + +++++++ +  ++  +e  ++ +e +     ls + la+ l+   ++
  gi|385806295|ref|YP_005842693.1|  81 dlnsnvkvfangtvydlmrngNYLIVFVIPNNFTYNIVNG-VSANIESYTYIKEISISS--LSQVSLASNLIISSFN 154
                                       9999999999999999999999999999999997766666.899999999999987654..7777777777777777 PP

                     ABC2_membrane 109 llqalifllivyf 121
                                        ++ l +l+ +y+
  gi|385806295|ref|YP_005842693.1| 155 RMVLLSYLAKAYP 167
                                       7777777776666 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 6.6e-08
                     ABC2_membrane  52 r.........pgllffsvlflafsaltsvapvferergvlerelvsplyslsayvlakvlvelpvsllqalifll.i 118
                                                 + +++ +++f   s+++++++ +e+e+++le  l+ p+ ++s ++l+kvl++++vsl+  + +++ +
  gi|385806295|ref|YP_005842693.1| 195 TiesltgpytALIIAPILMFSIASSISASSMGTEKEEKTLEITLSLPV-KRSYILLSKVLSSFVVSLIGLIGMSTaM 270
                                       033444455566777788888889999999******************.************************9956 PP

                     ABC2_membrane 119 vyf...lv.........gldls......rf...flflllllltalaasslgllisalapsfedasqlaslvllplll 174
                                        y+   ++         gl++s      +    flf l +l+ +++++ ++++ s+la +++ a+++as + lp+l+
  gi|385806295|ref|YP_005842693.1| 271 LYYeykIFsstgiseagGLNISsassiiSPtvlFLFALGFLFAIFVILLISIVASSLANNIREAQIIASYIWLPFLI 347
                                       666555226667777779999998866622668************************************99999985 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.37
                     ABC2_membrane  89 plyslsayvlakvlvelpvsllqalifllivyflvgldl 127
                                       p+   ++++l+++ ++l+ s+++ +++++i++++ g ++
  gi|385806295|ref|YP_005842693.1| 376 PIIAIKSVFLGNY-IYLLTSFIANILYIAIILYI-GTKW 412
                                       5555566666666.56777777777777777776.6665 PP

>> TPPK_C  Thiamine pyrophosphokinase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.9   8.5e-06     0.038      11      44 ..     298     331 ..     295     334 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8.5e-06
                            TPPK_C  11 isggallllvlAaLvAvavallvspagqsfldll 44 
                                       is+  l l +l+ L+A++v+ll+s + +s+++++
  gi|385806295|ref|YP_005842693.1| 298 ISPTVLFLFALGFLFAIFVILLISIVASSLANNI 331
                                       89999********************999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1010  (0.0563333); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.66u 0.34s 00:00:01.00 Elapsed: 00:00:00.52
# Mc/sec: 2462.33
//
Query:       gi|385806296|ref|YP_005842694.1|  [L=236]
Description: daunorubicin resistance ATP-binding protein drrA [Fervidicoccus fontis Kam940]
Scores for complete 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-31  107.9   0.0    7.3e-31  107.5   0.0    1.2  1  ABC_tran      ABC transporter
    2.3e-10   40.8   0.2      9e-05   22.4   0.1    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    0.00014   21.7   0.1    0.00018   21.3   0.1    1.5  1  AAA_15        AAA ATPase domain
    0.00038   20.2   0.0    0.00066   19.4   0.0    1.3  1  AAA_29        P-loop containing region of AAA domain
     0.0024   18.1   0.0     0.0041   17.4   0.0    1.4  1  AAA_22        AAA domain
     0.0026   17.7   0.0     0.0048   16.8   0.0    1.4  1  Rad17         Rad17 P-loop domain
      0.003   18.1   1.1     0.0042   17.6   1.1    1.6  1  AAA_23        AAA domain
     0.0091   16.4   0.1      0.064   13.7   0.0    2.1  2  AAA           ATPase family associated with various cellular 
  ------ inclusion threshold ------
      0.017   14.7   0.0      0.029   13.9   0.0    1.3  1  AAA_27        AAA domain
      0.024   14.6   0.0      0.055   13.4   0.0    1.6  2  RsgA_GTPase   RsgA GTPase
      0.055   13.3   0.0      0.096   12.5   0.0    1.3  1  MukB          MukB N-terminal
      0.069   13.1   0.5       0.22   11.4   0.1    1.9  2  ATPase_2      ATPase domain predominantly from Archaea
      0.078   12.7   0.0       0.13   12.0   0.0    1.3  1  AAA_30        AAA domain
       0.11   12.0   0.6        1.5    8.2   0.1    2.2  2  SMC_N         RecF/RecN/SMC N terminal domain
       0.11   12.4   0.2       0.22   11.5   0.2    1.6  1  BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette 
       0.12   12.6   0.0       0.19   11.9   0.0    1.3  1  AAA_28        AAA domain
       0.13   12.9   0.0       0.34   11.5   0.0    1.8  2  AAA_18        AAA domain
       0.16   11.6   0.0       0.28   10.8   0.0    1.4  1  SRP54         SRP54-type protein, GTPase domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.5   0.0   7.4e-34   7.3e-31       1     137 []      18     158 ..      18     158 .. 0.84

  Alignments for each domain:
  == domain 1  score: 107.5 bits;  conditional E-value: 7.4e-34
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       lk +s+++ ege+++++G+nGaGKSt l++la llkpt+Ge+ +d+ ++ e e e++rk i++lp+e+   p++t  
  gi|385806296|ref|YP_005842694.1|  18 LKSISFNIDEGEIYGLIGPNGAGKSTTLRILATLLKPTSGEVYIDNINVAE-EPEKVRKIISYLPEEAGAYPNMTGI 93 
                                       789***********************************************9.9999******************955 PP

                                       HH.HHHTCHHHHHHHSTTGG....TTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xx.xxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.esdeeiekalsklglke....lkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       e  ++ +ei+ + +++  ++       + +k++ +++S+G+k+r+++ar+l+ kpkl +lDEpt+
  gi|385806296|ref|YP_005842694.1|  94 EYlKYIAEIYGVDESFIEVGkeisGLGDALKDKIKTYSKGMKRRLQVARTLMVKPKLAILDEPTS 158
                                       5555555544444444444433333445555555*****************************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 !   22.4   0.1   9.1e-08     9e-05       2      29 ..      31      61 ..      30     101 .. 0.71
   2 !   16.9   0.0   4.5e-06    0.0044     237     300 ..     130     191 ..      82     194 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 9.1e-08
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarl...drdv 29
                                       +liGpNg+GKS+ L++l  l        ++
  gi|385806296|ref|YP_005842694.1| 31 YGLIGPNGAGKSTTLRILATLLKPtsgEVYI 61
                                      68****************8886444443333 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 4.5e-06
                            AAA_21 237 lSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSpl 300
                                        S G+kr l ++  l   +   +l ++DEp +g++      l + +k+ s+ +++ +il++H+ l
  gi|385806296|ref|YP_005842694.1| 130 YSKGMKRRLQVARTLMVKP---KLAILDEPTSGIDVLYSLQLRRSIKDFSKvKRITIILSSHNML 191
                                       4999999966666666555...89************9999999999***99***********976 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.1   1.8e-07   0.00018      14      71 ..      18      72 ..      10     197 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.8e-07
                            AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifeni 71
                                      lk+++ +++e  +  liG+N++GKS+ l++l  +l+ +    + +++i++ ++ ++ ++
  gi|385806296|ref|YP_005842694.1| 18 LKSISFNIDEGeIYGLIGPNGAGKSTTLRILATLLKPT----SGEVYIDNINVAEEPEK 72
                                      566566666657999*********************98....66777777766665444 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 !   19.4   0.0   6.6e-07   0.00066      17      50 ..      23      56 ..      11      65 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 6.6e-07
                            AAA_29 17 ieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      ++id+ +++ l+Gp+G+GKST l  +++lL p++
  gi|385806296|ref|YP_005842694.1| 23 FNIDEGEIYGLIGPNGAGKSTTLRILATLLKPTS 56
                                      4556444999*************99999999986 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   4.2e-06    0.0041       7     127 ..      30     185 ..      25     196 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.2e-06
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaee..............erpevvfvtlpsst......sskdllrellra 63 
                                       i  ++G+ G+GK+t+lr l+  l+  +                  e+++ +  +lp++       +  + l+ ++++
  gi|385806296|ref|YP_005842694.1|  30 IYGLIGPNGAGKSTTLRILATLLK--PT--SgevyidninvaeepEKVRKIISYLPEEAgaypnmTGIEYLKYIAEI 102
                                       5669******************94..23..24477999999988866666644555444488867777779999999 PP

                            AAA_22  64 lglelka................erlsseellealeqalrarav...............ielliiDEaqh.lr...s 105
                                       +g++ +                 +              ++++++               ++l i+DE    ++   s
  gi|385806296|ref|YP_005842694.1| 103 YGVDESFievgkeisglgdalkdK--------------IKTYSKgmkrrlqvartlmvkPKLAILDEPTSgIDvlyS 165
                                       999999999666666666653333..............333333333333333335558889999997776655444 PP

                            AAA_22 106 eealeeLrsllnlsrkgvqliL 127
                                        ++ + ++++++   k +++iL
  gi|385806296|ref|YP_005842694.1| 166 LQLRRSIKDFSK--VKRITIIL 185
                                       555555555555..77777776 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   4.8e-06    0.0048      32      89 ..      15      73 ..       8     100 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.8e-06
                             Rad17 32 kewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklre.wlnpvslkepdnqk 89
                                      ke+lk+ + +  + +i  + GP G gkst++++L+  l +   e +++ +++ e + ++
  gi|385806296|ref|YP_005842694.1| 15 KEALKSISFNIDEGEIYGLIGPNGAGKSTTLRILATLLKPTSGEvYIDNINVAEEPEKV 73
                                      6788888888888889999****************998776544245555555555555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   1.1   4.2e-06    0.0042      15      44 ..      21      53 ..      10     230 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.2e-06
                            AAA_23 15 idF...skgltlItGpNGaGKTTildAiklaLy 44
                                      i F   +  ++ ++GpNGaGK+T l+ +   L 
  gi|385806296|ref|YP_005842694.1| 21 ISFnidEGEIYGLIGPNGAGKSTTLRILATLLK 53
                                      677776668999*************99987775 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   6.5e-05     0.064       3      55 ..      33      82 ..      31     102 .. 0.85
   2 ?    0.6   0.0      0.73   7.3e+02      88     116 ..     167     194 ..     115     203 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.5e-05
                                      EESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeake 55
                                      l+Gp G GK+++ + +a+ l+ +  e+   ++    v e ++k+r++++ + e
  gi|385806296|ref|YP_005842694.1| 33 LIGPNGAGKSTTLRILATLLKPTSGEVYIDNIN---VAEEPEKVRKIISYLPE 82
                                      89******************9888888777777...88888888888876655 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.73
                                       HHHHHHHHTTTSSSTEEEEEEESSGGGST CS
                               AAA  88 qLlteldgvkkkeskvivigatnrpdkld 116
                                       qL + +++++k  +++++i+ ++++ +++
  gi|385806296|ref|YP_005842694.1| 167 QLRRSIKDFSKV-KRITIILSSHNMLEVE 194
                                       788889999986.5599999888876665 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0     3e-05     0.029      17      50 ..      19      52 ..       6      53 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3e-05
                            AAA_27 17 rsldfsaeeadlhliyGpNEAGKstalrAisdll 50
                                      +s++f+ +e ++  ++GpN AGKst+lr +  ll
  gi|385806296|ref|YP_005842694.1| 19 KSISFNIDEGEIYGLIGPNGAGKSTTLRILATLL 52
                                      578899999999999************9988876 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   5.5e-05     0.055      85     124 ..      13      53 ..       4      65 .. 0.83
   2 ?   -2.9   0.0       5.5   5.5e+03      13      24 ..     175     186 ..     133     200 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.5e-05
                                       TTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-- CS
                       RsgA_GTPase  85 ktkegleelkellkd.ktsvlvGqSGvGKStLinallpele 124
                                        +ke+l++++ ++++ ++  l+G+ G+GKSt +  l+  l+
  gi|385806296|ref|YP_005842694.1|  13 GEKEALKSISFNIDEgEIYGLIGPNGAGKSTTLRILATLLK 53 
                                       57899999*****999***************9999887655 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.5
                                       EES--EEEEEEE CS
                       RsgA_GTPase  13 vaNvdqllivvs 24 
                                        + v ++ i++s
  gi|385806296|ref|YP_005842694.1| 175 FSKVKRITIILS 186
                                       333334444433 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   9.7e-05     0.096      22      62 ..      23      64 ..      17      75 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.7e-05
                                      E-HHH.HHHHHHS--SHHHHHHHHHHHHHHS--TTT------ CS
                              MukB 22 fdlde.lvttlsGgnGaGksttmaafvtaliPdlsllhfrnt 62
                                      f++de  +  l G nGaGkstt+  + t l P    +   n+
  gi|385806296|ref|YP_005842694.1| 23 FNIDEgEIYGLIGPNGAGKSTTLRILATLLKPTSGEVYIDNI 64
                                      7888745889**************999999998776666655 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00022      0.22      15      69 ..      25      76 ..      15     144 .. 0.76
   2 ?   -0.6   0.0         1     1e+03      45      84 ..     194     232 ..     181     235 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00022
                          ATPase_2 15 lerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefi 69
                                      +++   eiy + Gp g GK++ l+ +++ l+      +y+++++  ++ ++ ++i
  gi|385806296|ref|YP_005842694.1| 25 IDE--GEIYGLIGPNGAGKSTTLRILATLLKP-TSGEVYIDNINVAEEPEKVRKI 76
                                      444..7899999***********999988866.55899****9987777666654 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1
                          ATPase_2  45 edkdkyviyyialreesiskldefieeeeekkklekalgi 84 
                                       e++ ++v ++++ r + + + +e i+e++++k+le+a+  
  gi|385806296|ref|YP_005842694.1| 194 ENLCDRVSFLYDGRLIVEGTPEE-IKEKYDAKNLEEAFVR 232
                                       55677899999999998888888.5999999999998755 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00013      0.13      20      49 ..      30      59 ..      16      77 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                            AAA_30 20 vavltGpAGtGKttalkalreaweaaggrv 49
                                      +  l Gp G+GK+t+l+ l+ +++   g+v
  gi|385806296|ref|YP_005842694.1| 30 IYGLIGPNGAGKSTTLRILATLLKPTSGEV 59
                                      67799**************99988775454 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   0.1    0.0015       1.5      25      41 ..      29      45 ..       9      58 .. 0.75
   2 ?    1.7   0.0      0.14   1.4e+02     161     212 ..     150     201 ..     134     207 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0015
                                      SEEEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnll 41
                                      ++  ++GpNG+GKs  l
  gi|385806296|ref|YP_005842694.1| 29 EIYGLIGPNGAGKSTTL 45
                                      46679*********765 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.14
                                       EEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 161 lyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklvgvt 212
                                       l +lDe  + +D  +  ++ + +k  sk   + +i  +++mle  + + +v+
  gi|385806296|ref|YP_005842694.1| 150 LAILDEPTSGIDVLYSLQLRRSIKDFSKVKRITIILSSHNMLEVENLCDRVS 201
                                       789************************9999999999999999877766665 PP

>> BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   0.00022      0.22       1      12 [.     207     218 ..     207     219 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00022
                      BCA_ABC_TP_C   1 rvIAeGtPaEvr 12 
                                       r+I eGtP+E++
  gi|385806296|ref|YP_005842694.1| 207 RLIVEGTPEEIK 218
                                       79*********6 PP

>> AAA_28  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      0.19       4      35 ..      33      77 ..      31      99 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00019
                            AAA_28  4 itGgestGKTtlleaLaar...........gypvv..pEaareil 35
                                      ++G+ ++GK+t+l+ La             +++v   pE +r+i+
  gi|385806296|ref|YP_005842694.1| 33 LIGPNGAGKSTTLRILATLlkptsgevyidNINVAeePEKVRKII 77
                                      79***************5433333344555555665555555555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00034      0.34       3      31 ..      33      63 ..      32     130 .. 0.81
   2 ?   -1.6   0.0       3.8   3.8e+03      63      86 ..     192     217 ..     157     230 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00034
                            AAA_18  3 ltGtpGvGKttlakeLskrlgf..gvnlrdv 31
                                      l G+ G+GK+t  + L+ +l+   g++++d+
  gi|385806296|ref|YP_005842694.1| 33 LIGPNGAGKSTTLRILATLLKPtsGEVYIDN 63
                                      89**************999833464444433 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.8
                            AAA_18  63 aleenss...aleegknlvidghlael 86 
                                       ++e+ ++        + l+++g ++e 
  gi|385806296|ref|YP_005842694.1| 192 EVENLCDrvsF-LYDGRLIVEGTPEEI 217
                                       44443334421.112445666666554 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00028      0.28       6      32 ..      33      59 ..      29      65 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00028
                                      EEESTTSSHHHHHHHHHHHHHHTTS-E CS
                             SRP54  6 lvGlqGaGKTttlaKLaallkkegkkv 32
                                      l+G++GaGK ttl  La llk    +v
  gi|385806296|ref|YP_005842694.1| 33 LIGPNGAGKSTTLRILATLLKPTSGEV 59
                                      89****************999776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); 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: 0.64u 0.35s 00:00:00.99 Elapsed: 00:00:00.57
# Mc/sec: 1236.92
//
Query:       gi|385806297|ref|YP_005842695.1|  [L=152]
Description: 30S ribosomal protein S15 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-25   89.4   0.2    2.9e-25   88.1   0.1    1.8  2  Ribosomal_S13_N  Ribosomal S13/S15 N-terminal domain
    1.7e-15   57.0   0.2    2.4e-15   56.5   0.2    1.2  1  Ribosomal_S15    Ribosomal protein S15


Domain annotation for each model (and alignments):
>> Ribosomal_S13_N  Ribosomal S13/S15 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.1   0.1   3.3e-29   2.9e-25       5      60 .]       3      58 ..       1      58 [. 0.97
   2 ?   -2.1   0.0      0.46   4.2e+03      27      40 ..     110     123 ..     103     126 .. 0.69

  Alignments for each domain:
  == domain 1  score: 88.1 bits;  conditional E-value: 3.3e-29
                                      SSSSS--------S-SS--TTS---HHHHHHHHHHHHHTT--HHHHHHHHHHCCT- CS
                   Ribosomal_S13_N  5 hsrgkGkSgSarPyrreapsWlklskeeveelivklakkGltpSqIGviLRDqyGv 60
                                      ++r+kGkS+S+rP++  +p+Wl+l++ee+eel+v+lakkG++pS+IG+iLRDqyG+
  gi|385806297|ref|YP_005842695.1|  3 KKREKGKSHSTRPVSVGTPKWLRLEPEEIEELVVELAKKGYPPSMIGIILRDQYGI 58
                                      4899***************************************************9 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.46
                                       ---HHHHHHHHHHH CS
                   Ribosomal_S13_N  27 klskeeveelivkl 40 
                                       k   +e+e++i +l
  gi|385806297|ref|YP_005842695.1| 110 KKGLQEIESKIRRL 123
                                       55567888888665 PP

>> Ribosomal_S15  Ribosomal protein S15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.5   0.2   2.6e-19   2.4e-15       4      80 ..      72     146 ..      68     147 .. 0.93

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 2.6e-19
                                       HHHHHSSSTT-TSSHHHHHHHHHHHHHHHHHHHHCTTT-HHHHHHHHHHHHHHHHHHHHHHHH-H..HHHHHHHHHC CS
                     Ribosomal_S15   4 likefqrhekDtGspevqiallterInnltehlkenkkDkhsrrgLlklvskRrkllkYLkrkdv..erYkkliekl 78 
                                       ++ke +  +    ++++++++l++r++n+++hl+e++kD + ++gL++++sk+r+l++Y+kr  +  +++++  e++
  gi|385806297|ref|YP_005842695.1|  72 ILKERGLLP----QIPEDLYNLIRRAVNVRRHLSEHPKDENVKKGLQEIESKIRRLVRYYKRIGRlpPNWEYSPETA 144
                                       577777777....89************************************************9999********99 PP

                                       TS CS
                     Ribosomal_S15  79 gl 80 
                                       +l
  gi|385806297|ref|YP_005842695.1| 145 KL 146
                                       87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       792  (0.0441742); expected 358.6 (0.02)
Passed bias filter:                      682  (0.0380389); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 975.34
//
Query:       gi|385806298|ref|YP_005842696.1|  [L=154]
Description: 30S ribosomal protein S19e [Fervidicoccus fontis Kam940]
Scores for complete 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-49  165.9   0.0    4.3e-49  165.8   0.0    1.0  1  Ribosomal_S19e  Ribosomal protein S19e
  ------ inclusion threshold ------
      0.049   14.0   0.1       0.12   12.7   0.1    1.7  1  Rrf2            Transcriptional regulator
       0.05   13.5   0.0       0.28   11.1   0.0    2.3  3  MarR            MarR family
       0.06   13.3   0.0       0.91    9.5   0.0    2.5  3  HTH_12          Ribonuclease R winged-helix domain
       0.11   12.7   0.1        0.3   11.3   0.0    1.8  2  Ribosomal_S25   S25 ribosomal protein


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 !  165.8   0.0   1.2e-52   4.3e-49       3     136 ..       5     141 ..       3     142 .. 0.95

  Alignments for each domain:
  == domain 1  score: 165.8 bits;  conditional E-value: 1.2e-52
                                       SSHHHHHHHHHS--S--..-S-SSS-SSSS-SS-S-SS-SSTTTHHHHHHHHHHHTS--TTS.GGGGS----SS-SS CS
                    Ribosomal_S19e   3 kdVpaeelikalaeeLk..ksgklevPewadlvKtgsakelapededWfyvRaAsilRkvyl.rgpvGverlrkvYG 76 
                                        +Vp++ l+++la++Lk   s+ +++Pew ++ Ktgs ke+ p +edW+y+RaAsilRk+y  +gpvG+er+r +YG
  gi|385806298|ref|YP_005842696.1|   5 MQVPPSILVERLAKYLKenYSEVINPPEWSKFSKTGSYKEYIPLQEDWWYYRAASILRKLYKaKGPVGIERFRVIYG 81 
                                       68***************433467**************************************9466************ PP

                                       S-------THHHHHHHHHTTSSS--SSS---SS-HHHHHTHHHHH--SS--S--XXXXXX CS
                    Ribosomal_S19e  77 gkkrrgvrpshfvkasgsvirkilqqLeklglvkkekkkgrrltkkGqrlldriaeevak 136
                                       gkkr g++p hf+k+sg+++r+il+qLek+glv++ ++kgr+lt+++ +lldri++e+++
  gi|385806298|ref|YP_005842696.1|  82 GKKRFGSSPPHFRKGSGAIARNILKQLEKAGLVTRISGKGRTLTPNAVSLLDRISKEIMS 141
                                       *********************************************************986 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   3.5e-05      0.12      40      67 ..      99     124 ..      94     137 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.5e-05
                                       HHHHHHHHHHHHTTSEEEETTT-TCEEE CS
                              Rrf2  40 sylekilakLrkaglvksvrGkgGGyrL 67 
                                        +++ il++L+kaglv+ + Gk  G +L
  gi|385806298|ref|YP_005842696.1|  99 AIARNILKQLEKAGLVTRISGK--GRTL 124
                                       57899****************9..6666 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.82   2.9e+03       7      15 ..      59      67 ..      55      70 .. 0.67
   2 ?   11.1   0.0   7.8e-05      0.28      36      50 ..     103     117 ..      97     121 .. 0.87
   3 ?   -3.0   0.0         2   7.1e+03       1      13 [.     124     136 ..     124     139 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.82
                                      HHHHHHHHS CS
                              MarR  7 viLrilyeq 15
                                      +iLr+ly  
  gi|385806298|ref|YP_005842696.1| 59 SILRKLYKA 67
                                      567777755 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 7.8e-05
                                       HHHHHHHHTTSEEEE CS
                              MarR  36 rvldrLekkGlieRs 50 
                                       ++l++Lek+Gl++R 
  gi|385806298|ref|YP_005842696.1| 103 NILKQLEKAGLVTRI 117
                                       79***********95 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 2
                                       --HHHHHHHHHHH CS
                              MarR   1 ltltqfviLrily 13 
                                       lt++ +++L  ++
  gi|385806298|ref|YP_005842696.1| 124 LTPNAVSLLDRIS 136
                                       6888888888776 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.14   5.1e+02       2      17 ..      59      74 ..      58      77 .. 0.87
   2 ?    9.5   0.0   0.00025      0.91      36      61 ..     102     127 ..      96     132 .. 0.85
   3 ?   -3.0   0.0       2.1   7.4e+03       2      10 ..     138     146 ..     136     149 .. 0.57

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.14
                            HTH_12  2 eILkilaesdkpigak 17
                                       IL+ l +++ p+g +
  gi|385806298|ref|YP_005842696.1| 59 SILRKLYKAKGPVGIE 74
                                      59***********976 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00025
                            HTH_12  36 RyrLrkleergltrrvgyagreltEk 61 
                                       R  L+ le+ gl+ r +  gr+lt  
  gi|385806298|ref|YP_005842696.1| 102 RNILKQLEKAGLVTRISGKGRTLTPN 127
                                       6679*******************976 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 2.1
                            HTH_12   2 eILkilaes 10 
                                       eI++ lae+
  gi|385806298|ref|YP_005842696.1| 138 EIMSELAEQ 146
                                       455555554 PP

>> Ribosomal_S25  S25 ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   8.3e-05       0.3      69      94 ..      97     122 ..      94     125 .. 0.86
   2 ?   -3.3   0.0         3   1.1e+04      44      52 ..     132     140 ..     129     146 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.3e-05
                     Ribosomal_S25  69 ngslArraLreleekgliklvskhra 94 
                                       +g++Ar++L++le+ gl+ ++s + +
  gi|385806298|ref|YP_005842696.1|  97 SGAIARNILKQLEKAGLVTRISGKGR 122
                                       689*****************987655 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3
                     Ribosomal_S25  44 ydkllkevp 52 
                                       +d+++ke+ 
  gi|385806298|ref|YP_005842696.1| 132 LDRISKEIM 140
                                       667777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 992.34
//
Query:       gi|385806299|ref|YP_005842697.1|  [L=116]
Description: DNA-binding protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-26   92.7  16.2      2e-26   92.4  16.2    1.1  1  dsDNA_bind      Double-stranded DNA-binding domain
  ------ inclusion threshold ------
      0.063   12.6  12.4      0.069   12.4  12.4    1.1  1  Radial_spoke_3  Radial spoke protein 3
        8.4    5.9   6.7        3.2    7.3   2.0    2.0  2  MMTV_SAg        Mouse mammary tumour virus superantigen


Domain annotation for each model (and alignments):
>> dsDNA_bind  Double-stranded DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.4  16.2   3.4e-30     2e-26       1     110 [.      13     114 ..       8     115 .. 0.88

  Alignments for each domain:
  == domain 1  score: 92.4 bits;  conditional E-value: 3.4e-30
                                       XXXXXXXXXXXXXXXXXXXX...XXXX--SS..S--SSHHHHTTS--HHHHHHHHHHTTT-HHHHHHHHHHHHHHHH CS
                        dsDNA_bind   1 irkarlaelqaqagsssgsggaseqqeqqqeaseeeakqaiLsqiLepeAreRLsrirlvkperaeavenrLiqlaq 77 
                                       i +++l elq++++          ++++++++++e++kq+iL++iL+p+Ar+RL++++lv+pe aea+en+Li laq
  gi|385806299|ref|YP_005842697.1|  13 IEQRKLLELQRRMEM---------EERRRRATEAEAQKQEILRKILTPQARDRLNNVKLVRPELAEAIENQLIVLAQ 80 
                                       567778888877664.........344455556899***************************************** PP

                                       --SS-----HHHHHHHHHHHS-.--XXXXX..XX CS
                        dsDNA_bind  78 sGqlrskvteeqLkeLLeqvae.kkketkivisr 110
                                       sG++++ +teeq+keLL ++++ ++ke +i+i+ 
  gi|385806299|ref|YP_005842697.1|  81 SGRITEPITEEQIKELLAEITTrSRKEFNIKIRE 114
                                       **********************888889999975 PP

>> Radial_spoke_3  Radial spoke protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4  12.4   1.2e-05     0.069     166     263 ..      11     109 ..       4     116 .] 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.2e-05
                    Radial_spoke_3 166 eelRnaelaevq.rLeeqekrlreekerrlkqqkealkkeketaekiaaralakqylaellpsvlesLedsgyfydp 241
                                       +e  +  l e+q r+e +e+r+r+ + + +kq+  ++    +++ ++ + +l++  lae +++ l  L +sg +++p
  gi|385806299|ref|YP_005842697.1|  11 AEIEQRKLLELQrRMEMEERRRRATEAEAQKQEILRKILTPQARDRLNNVKLVRPELAEAIENQLIVLAQSGRITEP 87 
                                       45555556666526888888888888889999999999999************************************ PP

                    Radial_spoke_3 242 verdveteflpwLmeeveeele 263
                                       + ++  +e+l+ ++++  +e +
  gi|385806299|ref|YP_005842697.1|  88 ITEEQIKELLAEITTRSRKEFN 109
                                       ************9999998876 PP

>> MMTV_SAg  Mouse mammary tumour virus superantigen
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   2.0   0.00053       3.2      80     113 ..      18      49 ..       9      64 .. 0.79
   2 ?    1.0   0.2     0.045   2.7e+02      85     126 ..      74     112 ..      66     115 .. 0.55

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00053
                          MMTV_SAg  80 kleveqrmgiekskrksssveeqvrkLlrpttlL 113
                                        le+++rm +e+++r++++ e q +++l  ++ L
  gi|385806299|ref|YP_005842697.1|  18 LLELQRRMEMEERRRRATEAEAQKQEIL--RKIL 49 
                                       478999*****************88887..4444 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.045
                          MMTV_SAg  85 qrmgiekskrksssv.eeqvrkLlrpttlLevkkGkksvkyki 126
                                       q++   +s r +  + eeq+++Ll     + ++  +k  ++ki
  gi|385806299|ref|YP_005842697.1|  74 QLIVLAQSGRITEPItEEQIKELL---AEITTR-SRKEFNIKI 112
                                       455555555544443389999998...333333.444555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1738  (0.0969379); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); 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: 0.49u 0.35s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 681.50
//
Query:       gi|385806300|ref|YP_005842698.1|  [L=51]
Description: hypothetical protein FFONT_1258 [Fervidicoccus fontis Kam940]
Scores for complete 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   70.5  11.9    7.5e-20   70.3  11.9    1.1  1  Ribosomal_L39  Ribosomal L39 protein
  ------ inclusion threshold ------
      0.019   15.0   0.7       0.02   14.9   0.7    1.0  1  REV            REV protein (anti-repression trans-activator p


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 !   70.3  11.9   8.4e-24   7.5e-20       1      42 []       9      50 ..       9      50 .. 0.99

  Alignments for each domain:
  == domain 1  score: 70.3 bits;  conditional E-value: 8.4e-24
                     Ribosomal_L39  1 kKlrLaKalkqNrpvPaWvrlktdrkvrynpkrRhWRrtkLk 42
                                      +KlrL Kalk+N+p+P+Wv +kt+rkvr n+krR WRr+kLk
  gi|385806300|ref|YP_005842698.1|  9 RKLRLSKALKSNSPIPVWVAVKTKRKVRFNFKRRFWRRNKLK 50
                                      7****************************************8 PP

>> REV  REV protein (anti-repression trans-activator protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.7   2.2e-06      0.02      12      51 ..       7      50 ..       2      51 .] 0.73

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.2e-06
                               REV 12 lirklrllkllyqsnPyPqgeGtasarrnr....rrrrrerqlr 51
                                      l rklrl k l    P P     + +r+ r    rr +r+++l+
  gi|385806300|ref|YP_005842698.1|  7 LARKLRLSKALKSNSPIPVWVAVKTKRKVRfnfkRRFWRRNKLK 50
                                      89****************98777777765522225556766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 350.50
//
Query:       gi|385806301|ref|YP_005842699.1|  [L=114]
Description: hypothetical protein FFONT_1259 [Fervidicoccus fontis Kam940]
Scores for 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   47.1   1.2      2e-12   47.1   1.2    2.1  2  Ribosomal_L31e  Ribosomal protein L31e
  ------ inclusion threshold ------
       0.06   13.5   0.0      0.077   13.1   0.0    1.2  1  DUF3612         Protein of unknown function (DUF3612)


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 !   47.1   1.2   2.3e-16     2e-12       7      71 ..       8      71 ..       6      82 .. 0.89
   2 ?    1.4   0.3     0.042   3.8e+02      57      72 ..      83      98 ..      76     112 .. 0.75

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 2.3e-16
                    Ribosomal_L31e  7 ytInihkrihgvgfkkraprAlkeikkfamkemgtpdvridtrLnkavwakgirnvpyrirvrls 71
                                       +In  +++++ + + ra rA++ ik+++++ ++t++ +id ++nk +w++gi+++p+++rv++ 
  gi|385806301|ref|YP_005842699.1|  8 EVIN-LRKVYSSRKTSRAARAIRYIKDYIRRRFHTEEIKIDDSVNKLIWSRGIEKPPRKLRVKII 71
                                      5799.566778888999*********************************************985 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.042
                    Ribosomal_L31e 57 kgirnvpyrirvrlsr 72
                                        +r+ p++++v+l +
  gi|385806301|ref|YP_005842699.1| 83 GEVRKHPTKVKVELPK 98
                                      5699999999999975 PP

>> DUF3612  Protein of unknown function (DUF3612)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   8.6e-06     0.077      50     153 ..      13     112 ..       7     114 .] 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.6e-06
                           DUF3612  50 rkisepskgssaqisilnvgde.priyccesikvkdlagnnhvlcagidlnpaieaqgkdalslaeelkkacvkngg 125
                                       rk+ ++ k+s a  +i  ++d   r +  e ik+ d+  n+ +   gi+  p         + +aee+k++  k+g 
  gi|385806301|ref|YP_005842699.1|  13 RKVYSSRKTSRAARAIRYIKDYiRRRFHTEEIKIDDSV-NKLIWSRGIEKPPR----KLRVKIIAEEMKEIKTKSGE 84 
                                       66666777777777777666651456778888887765.56778888887774....3456789************* PP

                           DUF3612 126 saaipkaikkdlvsvakilninwvergi 153
                                         + p+++k +l +v k+ n n  e+g 
  gi|385806301|ref|YP_005842699.1|  85 VRKHPTKVKVELPKVEKVENKNKKEKGK 112
                                       **********************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1138  (0.0634726); 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:                         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: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 887.23
//
Query:       gi|385806302|ref|YP_005842700.1|  [L=228]
Description: translation initiation factor IF-6 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-60  203.2   7.2    3.4e-60  202.8   7.2    1.2  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 !  202.8   7.2   1.9e-64   3.4e-60       1     197 []       8     206 ..       8     225 .. 0.98

  Alignments for each domain:
  == domain 1  score: 202.8 bits;  conditional E-value: 1.9e-64
                                       .E-BTTB--HHHH-EE-SSEEEE-TTS-HHHHHHHHHHHT-EEEE--BTTBS-HHHH-EE-SSEEEEETT--HHHHH CS
                             eIF-6   1 rlsiegsseiGvfarltnkyalvpegveeefvkaieeeLkvevvettiagsrlvGslvvgNsngllvpstvtdeele 77 
                                       +ls++++++iGv+++ +nk+alvp+g+++  +k++ee+L+v+++etti+++r++G+lv gN++++l+p  v++ee++
  gi|385806302|ref|YP_005842700.1|   8 KLSVFRNHNIGVYIFSNNKFALVPNGISHGSKKVVEETLGVDAIETTIMDTRIIGVLVSGNDRAILLPYAVKSEEID 84 
                                       68999************************************************************************ PP

                                       HHHHHHH..---EEE--SS--HHHHEEE-SSEEEE-GGGGG.GHHHHHHHHTSEEEE--BTTBS-TTTSEEE-SSEE CS
                             eIF-6  78 klkeslk..leverleekltAlGNvilaNDkvAlvhpdlsketveiiadvLgvevvrgtiagiktvGsaavvtnkgl 152
                                       +lkes+   +++ ++++k+tAlGN i+aN+k+A+++p l++e +++i+d L+v+v +++  gi+++Gs++v ++  +
  gi|385806302|ref|YP_005842700.1|  85 RLKESIGgsVKIGIIDSKFTALGNYITANNKFAYISPLLEDEIARKISDLLDVKVSKKSYLGISIIGSIIVSNDYVA 161
                                       ******966777***************************************************************** PP

                                       EE-TT--HHHHHHHHHHHT-SEEE--BTTTBS-GGGTEEE-SS-E CS
                             eIF-6 153 lvhpkateeeleeleellkveveagTvNrGsklvgsglvaNdkga 197
                                       +vhp  ++++ +e+++ +kvev + TvN G+++v+sg+vaN++g+
  gi|385806302|ref|YP_005842700.1| 162 FVHPMLSDSDASEIKNDMKVEVVQTTVNEGVPFVKSGIVANNNGV 206
                                       ******************************************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1424.26
//
Query:       gi|385806303|ref|YP_005842701.1|  [L=71]
Description: hypothetical protein FFONT_1261 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 461.33
//
Query:       gi|385806304|ref|YP_005842702.1|  [L=86]
Description: 50S ribosomal protein LX [Fervidicoccus fontis Kam940]
Scores for complete 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   40.3   0.1    4.2e-10   39.8   0.1    1.3  1  Ribosomal_L18A  Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A


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 !   39.8   0.1   2.3e-14   4.2e-10      65     121 .]       3      63 ..       1      63 [. 0.87

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 2.3e-14
                                       ..................TEEEEEEEEEEESSHHHHHHHHHHHHHHHS---GGGEEEEEEE CS
                    Ribosomal_L18A  65 kvknygi....wlrydsrsgthnfykeyrdlteegaveqvYselgsrhrakrssIqIekve 121
                                       +vk y i    ++  d   ++++f  e+  ++e++a++++Ys lgs+h+++r +I+I kve
  gi|385806304|ref|YP_005842702.1|   3 QVKVYRIsgemLISHDHFPKWQKFNLELTGTSEKDAINKTYSLLGSKHKLRRFHIKINKVE 63 
                                       66777443333789999******************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); 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: 00:00:00.46
# Mc/sec: 559.43
//
Query:       gi|385806305|ref|YP_005842703.1|  [L=143]
Description: hypothetical protein FFONT_1263 [Fervidicoccus fontis Kam940]
Scores for 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   51.2   5.3    1.3e-13   50.9   5.3    1.2  1  Prefoldin       Prefoldin subunit
    3.6e-05   23.7   8.4    0.00058   19.8   2.1    2.2  2  Prefoldin_2     Prefoldin subunit
  ------ inclusion threshold ------
      0.023   15.0   6.0       0.11   12.8   2.0    2.2  2  OmpH            Outer membrane protein (OmpH-like)
      0.027   14.9   0.5      0.027   14.9   0.5    1.8  2  Cep57_MT_bd     Centrosome microtubule-binding domain of Cep5
      0.031   14.0   8.7       0.44   10.3   2.8    2.1  2  DUF4201         Domain of unknown function (DUF4201)
      0.036   14.3   8.6      0.065   13.5   0.6    2.1  2  MapZ_EC1        MapZ extracellular domain 1
      0.039   14.4   5.7        2.7    8.5   2.2    2.5  2  Enkurin         Calmodulin-binding
      0.062   12.4   0.3      0.071   12.2   0.3    1.1  1  NgoMIV_restric  NgoMIV restriction enzyme
      0.088   13.1   6.5        2.5    8.4   0.3    2.1  2  Spc24           Spc24 subunit of Ndc80
        0.1   12.8   0.1       0.26   11.6   0.1    1.7  2  HHH_6           Helix-hairpin-helix motif
       0.66   10.1   4.2         11    6.1   0.5    2.1  2  DUF848          Gammaherpesvirus protein of unknown function 
        1.5    9.4  10.0          4    8.0   0.6    2.1  2  APG6_N          Apg6 coiled-coil region
        1.5    9.5   5.4        7.2    7.3   0.4    2.1  2  YabA            Initiation control protein YabA
        2.2    8.4   9.2       0.23   11.7   0.7    2.2  2  CENP-Q          CENP-Q, a CENPA-CAD centromere complex subuni
        2.8    8.1   9.9        2.9    8.0   2.8    2.4  2  bZIP_1          bZIP transcription factor


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 !   50.9   5.3   1.1e-16   1.3e-13       2     119 ..      23     141 ..       9     142 .. 0.96

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 1.1e-16
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT..-TT-EEEEEEETTEEEEEE--STTEEEEEEETTEEEEEEHHH CS
                         Prefoldin   2 keeleslqaelaqlkeaieelektletlktlkk.edegkevlvplgaglyvkaevkdtdkvlvdlGagyyvekslee 77 
                                       +++lesl+  ++ l+e++ e++ ++e+lk++   ++ ++ v ++  ++l vk +  ++ + lv+lG ++y+e++++ 
  gi|385806305|ref|YP_005842703.1|  23 EKYLESLRNAIGLLNERLLEVKIAREALKRINSeNTSDIIVSMDKDSNLMVKLKANIDGNPLVHLGLDIYAELPYDR 99 
                                       789******************************888899999*********************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  78 Aiellkkkleelekqlekleeeleklkdqittleanlaqlyq 119
                                       A+ +l ++++++++ l+ + +e +++ +++++l+  + +l+q
  gi|385806305|ref|YP_005842703.1| 100 AESVLAERENSITEELKRMSKEYDEKNKEYQKLQSLIYALSQ 141
                                       *********************************998877766 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.5    0.0024       2.9       2      45 ..      14      57 ..      13      70 .. 0.90
   2 !   19.8   2.1   4.9e-07   0.00058      61     105 ..      98     142 ..      90     143 .] 0.91

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0024
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT- CS
                       Prefoldin_2  2 elinkfqqlqqqlqqlaqqikqletqlkelelvleelelldedt 45
                                      +l+   ++l++ l+ l + i  l+++l e++ + e+l+ + +++
  gi|385806305|ref|YP_005842703.1| 14 ALLQTVANLEKYLESLRNAIGLLNERLLEVKIAREALKRINSEN 57
                                      6778899*******************************999985 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 4.9e-07
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCTS- CS
                       Prefoldin_2  61 eevkeeLeerketlekeiktlekqleklekeleelkeelqkklqq 105
                                       + +++ L er++++++e+k+++k++++++ke+++l++ ++++ qq
  gi|385806305|ref|YP_005842703.1|  98 DRAESVLAERENSITEELKRMSKEYDEKNKEYQKLQSLIYALSQQ 142
                                       6788899*********************************99887 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1     0.042        50      87     121 ..      37      71 ..       3      85 .. 0.58
   2 ?   12.8   2.0   9.3e-05      0.11      17      52 ..      97     132 ..      90     143 .] 0.81

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.042
                                       HHHHHHHHHHHHHHHHHHHHHHTT-SEEEE....GGG- CS
                              OmpH  87 qqellkpildkinkaikevakekgydlvld...srgav 121
                                       ++ ll+  ++ +++a+k +++e+  d++++   + +++
  gi|385806305|ref|YP_005842703.1|  37 NERLLE--VKIAREALKRINSENTSDIIVSmdkD-SNL 71 
                                       222333..3667899999****999999987642.333 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 9.3e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH  17 gkaaqeqlekkfkklqaeleakekelqklqeelqkk 52 
                                       + +a++ l++ ++++ +el+++ ke++++ +e+qk 
  gi|385806305|ref|YP_005842703.1|  97 YDRAESVLAERENSITEELKRMSKEYDEKNKEYQKL 132
                                       667888899999*********************953 PP

>> Cep57_MT_bd  Centrosome microtubule-binding domain of Cep57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       2.8   3.3e+03      44      44 ..      32      32 ..       6      67 .. 0.60
   2 ?   14.9   0.5   2.3e-05     0.027      11      42 ..     102     133 ..      96     142 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.8
                       Cep57_MT_bd 44 s 44
                                      +
  gi|385806305|ref|YP_005842703.1| 32 A 32
                                      2 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 2.3e-05
                       Cep57_MT_bd  11 eaLaevlkeLedEfehlklelqelaaqynald 42 
                                        +Lae  + +++E++ +++e++e +++y++l+
  gi|385806305|ref|YP_005842703.1| 102 SVLAERENSITEELKRMSKEYDEKNKEYQKLQ 133
                                       57888888899*******************98 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.3    0.0029       3.4      88     130 ..      14      56 ..       6      61 .. 0.87
   2 ?   10.3   2.8   0.00037      0.44      84     121 ..     106     143 .]     100     143 .] 0.91

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0029
                           DUF4201  88 mleselselkkelkekeerlaklrkelykvklerdklrkqnek 130
                                       +l +++++l+k l+++ + +  l ++l +vk  r+ l++ n++
  gi|385806305|ref|YP_005842703.1|  14 ALLQTVANLEKYLESLRNAIGLLNERLLEVKIAREALKRINSE 56 
                                       567788999999999999******************9999986 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00037
                           DUF4201  84 eklhmleselselkkelkekeerlaklrkelykvkler 121
                                       e+++ +++el+++ ke++ek+++ +kl+  +y + ++r
  gi|385806305|ref|YP_005842703.1| 106 ERENSITEELKRMSKEYDEKNKEYQKLQSLIYALSQQR 143
                                       889999**************************999887 PP

>> MapZ_EC1  MapZ extracellular domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.6   5.4e-05     0.065      36     108 ..       9      80 ..       4      95 .. 0.88
   2 ?    5.2   2.0     0.019        23      53      78 ..     113     139 ..      90     142 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.4e-05
                          MapZ_EC1  36 flknsef.aklseLekkLeklkgskeYkklkkkldslkkqisaieavNsqFtkpiivdgklkeeatvkadanfd 108
                                       ++ ++   + + +Lek Le l +      l+++l ++k + +a++ +Ns  t++iiv  + + ++ vk +an+d
  gi|385806305|ref|YP_005842703.1|   9 QIDAEALlQTVANLEKYLESLRNAI--GLLNERLLEVKIAREALKRINSENTSDIIVSMDKDSNLMVKLKANID 80 
                                       5666666688999999999999877..88*****************************999*******999998 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.019
                          MapZ_EC1  53 eklk.gskeYkklkkkldslkkqisai 78 
                                       e+lk  skeY++ +k++++l++ i a+
  gi|385806305|ref|YP_005842703.1| 113 EELKrMSKEYDEKNKEYQKLQSLIYAL 139
                                       445555777888888888887766665 PP

>> Enkurin  Calmodulin-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1    0.0049       5.9      60      96 ..       2      38 ..       1      39 [. 0.93
   2 ?    8.5   2.2    0.0023       2.7      41      74 ..     109     142 ..      42     143 .] 0.80

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0049
                           Enkurin 60 eyqslpllidtlskrqrKeklEkeLkqlEkdikllek 96
                                      ey s +++id  +  q  ++lEk L+ l ++i ll++
  gi|385806305|ref|YP_005842703.1|  2 EYMSRTVQIDAEALLQTVANLEKYLESLRNAIGLLNE 38
                                      799999**************************99875 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0023
                           Enkurin  41 eerqellegLkkkweelnkeyqslpllidtlskr 74 
                                       +   e l+ + k+++e nkeyq+l  li  ls++
  gi|385806305|ref|YP_005842703.1| 109 NSITEELKRMSKEYDEKNKEYQKLQSLIYALSQQ 142
                                       33456788999999*********98887777665 PP

>> NgoMIV_restric  NgoMIV restriction enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.3   5.9e-05     0.071     115     197 ..      28     113 ..       4     120 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.9e-05
                    NgoMIV_restric 115 elaaalGsdylitPdivvlrelled.eeinraeflv..denvaklaslrkangekPllhasisckwtlrsdraqnar 188
                                        l  a+G       ++ + re l+  +  n ++++v  d+++  + +l+++  ++Pl+h  +     l  dra    
  gi|385806305|ref|YP_005842703.1|  28 SLRNAIGLLNERLLEVKIAREALKRiNSENTSDIIVsmDKDSNLMVKLKANIDGNPLVHLGLDIYAELPYDRAESVL 104
                                       555555544444456778888876525568889999899***********************************999 PP

                    NgoMIV_restric 189 aealnlirn 197
                                       ae  n i +
  gi|385806305|ref|YP_005842703.1| 105 AERENSITE 113
                                       999887765 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.3    0.0021       2.5      11      55 ..      17      75 ..      11      95 .. 0.68
   2 ?    7.6   1.3    0.0036       4.3       8      39 ..     103     134 ..      97     142 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0021
                             Spc24 11 kelsdleselesleselaelkeeleeleeesee.......keser......ve.detl...l 55
                                      + + +le+ lesl++    l+e+l e++  +e+       +   +       + d++l   l
  gi|385806305|ref|YP_005842703.1| 17 QTVANLEKYLESLRNAIGLLNERLLEVKIAREAlkrinseN---TsdiivsMDkDSNLmvkL 75
                                      67789999999999999999999999999888877665332...134577633355555332 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0036
                             Spc24   8 riakelsdleselesleselaelkeeleelee 39 
                                        +a+  +++++el+++++e +e+++e+++l++
  gi|385806305|ref|YP_005842703.1| 103 VLAERENSITEELKRMSKEYDEKNKEYQKLQS 134
                                       678889999*******************9997 PP

>> HHH_6  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       2.5     3e+03      59      83 ..      29      53 ..      12      59 .. 0.61
   2 ?   11.6   0.1   0.00022      0.26      20      76 ..      78     137 ..      42     139 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.5
                             HHH_6 59 larrvdslnkrqleaLakaGaldsl 83
                                      l + ++ ln+r le  ++  al+ +
  gi|385806305|ref|YP_005842703.1| 29 LRNAIGLLNERLLEVKIAREALKRI 53
                                      4444444666666665555555555 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00022
                             HHH_6  20 eedga..irlGLaaikglgeaaaerivaeRekegpfksledlarrvds..lnkrqleaLak 76 
                                       + dg+  + lGL+   +l  + ae+++aeRe +   ++l+ ++++ d+   + ++l++L++
  gi|385806305|ref|YP_005842703.1|  78 NIDGNplVHLGLDIYAELPYDRAESVLAERE-NSITEELKRMSKEYDEknKEYQKLQSLIY 137
                                       3456678***********************9.99999999999999976666667777776 PP

>> DUF848  Gammaherpesvirus protein of unknown function (DUF848)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.5    0.0091        11      41     109 ..      11      80 ..       6      83 .. 0.82
   2 ?    5.5   0.2     0.015        17      52      81 ..     105     134 ..      97     139 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0091
                            DUF848  41 darkalrsleqlkr.tkeikalveavdteieakkkelslLkklnrkkvarveeLtdkvlelkeevsleld 109
                                       da++ l+ + +l++  +++++ + ++++++ + k  ++ Lk++n ++  ++   +dk  +l   ++ ++d
  gi|385806305|ref|YP_005842703.1|  11 DAEALLQTVANLEKyLESLRNAIGLLNERLLEVKIAREALKRINSENTSDIIVSMDKDSNLMVKLKANID 80 
                                       5777788888887636889**************************9999888777877777666666665 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.015
                            DUF848  52 lkrtkeikalveavdteieakkkelslLkk 81 
                                       ++r+++i + ++ + +e ++k+ke ++L+ 
  gi|385806305|ref|YP_005842703.1| 105 AERENSITEELKRMSKEYDEKNKEYQKLQS 134
                                       68999*********************9986 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.6    0.0033         4      59     122 ..       8      71 ..       2      80 .. 0.81
   2 ?    6.0   3.0     0.014        16      59      96 ..     104     141 ..      94     143 .] 0.71

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0033
                            APG6_N  59 lekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlelleleeeldsl 122
                                       ++ + e+ll+  ++lek  e+l++++  l e l +++   e+  r  +e   + +   ++   l
  gi|385806305|ref|YP_005842703.1|   8 VQIDAEALLQTVANLEKYLESLRNAIGLLNERLLEVKIAREALKRINSENTSDIIVSMDKDSNL 71 
                                       67788999*******************9999999999999988888888777777666666655 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.014
                            APG6_N  59 lekeeeelleeLkelekereeleaelaaleeelealee 96 
                                       l + e++  eeLk++ ke +e ++e ++l++   al +
  gi|385806305|ref|YP_005842703.1| 104 LAERENSITEELKRMSKEYDEKNKEYQKLQSLIYALSQ 141
                                       55667777777777777777777777777776666665 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.4     0.006       7.2       2      47 ..      11      56 ..      10      81 .. 0.76
   2 ?    4.7   0.5     0.038        45       4      35 ..     109     140 ..     102     143 .] 0.77

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.006
                                      -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YabA  2 dkkelfdkleeleeqleelleeleelkeelaelleenaeLelenek 47
                                      d + l++++++le+ le+l + ++ l+e+l e+    ++L+  n++
  gi|385806305|ref|YP_005842703.1| 11 DAEALLQTVANLEKYLESLRNAIGLLNERLLEVKIAREALKRINSE 56
                                      6778899999999999999999999999999888777777655543 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.038
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YabA   4 kelfdkleeleeqleelleeleelkeelaell 35 
                                       ++++++l++++++ +e ++e ++l++ +++l 
  gi|385806305|ref|YP_005842703.1| 109 NSITEELKRMSKEYDEKNKEYQKLQSLIYALS 140
                                       56788888888888888888888888777765 PP

>> CENP-Q  CENP-Q, a CENPA-CAD centromere complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.7   0.00019      0.23      21      61 ..       6      46 ..       3      56 .. 0.85
   2 ?    1.1   2.2      0.33   3.9e+02      51      74 ..     111     134 ..      94     143 .] 0.64

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00019
                            CENP-Q 21 kekeldfeklldekaaleaqLspelhslelLeaeiekeera 61
                                      + ++ d e+ll+  a+le++L+ ++ ++ lL + + +++ a
  gi|385806305|ref|YP_005842703.1|  6 RTVQIDAEALLQTVANLEKYLESLRNAIGLLNERLLEVKIA 46
                                      67889**************************9977665555 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.33
                            CENP-Q  51 LeaeiekeeralerdyeaLreLek 74 
                                         +e++++ +++ +  ++ ++L+ 
  gi|385806305|ref|YP_005842703.1| 111 ITEELKRMSKEYDEKNKEYQKLQS 134
                                       456667666666666666666654 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.7      0.04        47      29      55 ..      13      39 ..       9      55 .. 0.77
   2 ?    8.0   2.8    0.0024       2.9      31      61 ..     104     134 ..     100     136 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.04
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1 29 eeLerrvkaLekeNksLkseleelkke 55
                                      e+L + v+ Lek  +sL++ ++ l++ 
  gi|385806305|ref|YP_005842703.1| 13 EALLQTVANLEKYLESLRNAIGLLNER 39
                                      677888888888888888888888775 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0024
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  31 LerrvkaLekeNksLkseleelkkevekLks 61 
                                       L++r   +++e k +++e +e +ke++kL+s
  gi|385806305|ref|YP_005842703.1| 104 LAERENSITEELKRMSKEYDEKNKEYQKLQS 134
                                       8899999*********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1670  (0.0931452); expected 358.6 (0.02)
Passed bias filter:                      689  (0.0384294); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 988.36
//
Query:       gi|385806306|ref|YP_005842704.1|  [L=307]
Description: putative signal recognition particle protein [Fervidicoccus fontis Kam940]
Scores for complete 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-69  231.2   0.0    1.1e-68  230.8   0.0    1.2  1  SRP54            SRP54-type protein, GTPase domain
    2.9e-09   37.0   1.9    2.9e-09   37.0   1.9    2.5  2  SRP54_N          SRP54-type protein, helical bundle domain
    0.00015   21.9   0.6    0.00067   19.7   0.1    2.2  2  MMR_HSR1         50S ribosome-binding GTPase
     0.0003   21.2   0.3     0.0013   19.1   0.1    2.2  2  AAA              ATPase family associated with various cellul
    0.00046   19.9   0.0       0.13   12.0   0.0    2.6  2  Thymidylate_kin  Thymidylate kinase
     0.0012   18.7   0.0     0.0017   18.1   0.0    1.2  1  AAA_30           AAA domain
     0.0012   18.6   0.0     0.0021   17.8   0.0    1.4  1  AAA_24           AAA domain
     0.0017   18.4   0.1      0.015   15.4   0.0    2.4  2  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
     0.0036   17.6   0.1      0.012   15.8   0.1    1.8  1  AAA_22           AAA domain
     0.0054   16.0   0.0     0.0085   15.4   0.0    1.5  1  Zeta_toxin       Zeta toxin
      0.007   16.8   4.3      0.018   15.5   4.3    1.7  1  CelTOS           Cell-traversal protein for ookinetes and spo
  ------ inclusion threshold ------
       0.01   16.3   0.0       0.02   15.3   0.0    1.6  1  AAA_16           AAA ATPase domain
      0.027   14.4   1.3      0.036   14.0   0.2    1.9  2  AAA_31           AAA domain
      0.037   13.8   0.1       0.23   11.2   0.0    2.2  2  CLP1_P           mRNA cleavage and polyadenylation factor CLP
      0.039   13.7   0.3       0.11   12.2   0.1    1.9  2  ATP_bind_1       Conserved hypothetical ATP binding protein
       0.04   13.1   0.1      0.092   11.9   0.1    1.5  1  ArsA_ATPase      Anion-transporting ATPase
      0.059   13.5   0.0      0.086   13.0   0.0    1.3  1  AAA_33           AAA domain
      0.067   13.1   0.0       0.49   10.3   0.0    2.2  2  RsgA_GTPase      RsgA GTPase
      0.075   12.3   0.0       0.11   11.7   0.0    1.5  1  6PF2K            6-phosphofructo-2-kinase
      0.081   12.9   0.1        0.2   11.6   0.1    1.6  1  ResIII           Type III restriction enzyme, res subunit
      0.082   12.8   0.0       0.14   12.0   0.0    1.3  1  APS_kinase       Adenylylsulphate kinase
       0.11   12.0   0.0       0.18   11.3   0.0    1.3  1  AAA_7            P-loop containing dynein motor region
       0.11   12.5   0.7       0.37   10.8   0.1    2.3  2  AAA_14           AAA domain
       0.11   12.7   0.0        0.2   11.9   0.0    1.5  1  AAA_28           AAA domain
       0.12   11.9   0.0       0.19   11.2   0.0    1.3  1  PPK2             Polyphosphate kinase 2 (PPK2)
       0.12   12.7   0.3       0.43   11.0   0.0    2.0  2  AAA_17           AAA domain
       0.14   12.1   0.2       0.14   12.1   0.2    2.6  3  NTPase_1         NTPase
       0.19   10.9   0.7       0.31   10.2   0.1    1.6  2  NB-ARC           NB-ARC domain
        0.2   11.8   0.1       0.76    9.9   0.1    1.9  1  Torsin           Torsin


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 !  230.8   0.0   1.7e-71   1.1e-68       2     196 .]     111     305 ..     110     305 .. 0.99

  Alignments for each domain:
  == domain 1  score: 230.8 bits;  conditional E-value: 1.7e-71
                                       EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHH CS
                             SRP54   2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeavek 78 
                                        +i+++G++G+GKTt++aKLa+++kk+g+++l+vaaDtfRa+ +eQL+++a++lgvp+i++k ++dpa++a++++  
  gi|385806306|ref|YP_005842704.1| 111 FIIIFMGINGVGKTTSIAKLANYIKKNGMTPLIVAADTFRAGSQEQLQVHADRLGVPIIRAKYNSDPASIAFDGIAY 187
                                       789************************************************************************** PP

                                       HHHTTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSSSS CS
                             SRP54  79 akeekidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltklDgdak 155
                                       a++++i vvl+DTaGr++ d++l++elkki +vv  d  llv+da++g++ v+qa a++++vg +g+ ltk D+d+k
  gi|385806306|ref|YP_005842704.1| 188 AEKKNIPVVLIDTAGRMHVDRDLINELKKIIDVVGYDLRLLVIDALSGNDSVEQAIAYEKNVGYEGFFLTKSDADTK 264
                                       ***************************************************************************** PP

                                       TTHHHHHHHHHTS-EEEEE-SSSTTGEEE--HHHHHHHHHT CS
                             SRP54 156 gGaalsiaaelklPikfigvGekiedleefdperlvsrllg 196
                                       gG alsi+ e+k+Pi+f+g+G++++d+ +f++e+l++ llg
  gi|385806306|ref|YP_005842704.1| 265 GGVALSISVETKKPIYFLGTGQNYDDIVPFNKEWLIKTLLG 305
                                       **************************************985 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 !   37.0   1.9   4.6e-12   2.9e-09       6      75 .]      13      81 ..       5      81 .. 0.85
   2 ?    0.7   0.0         1   6.4e+02      46      61 ..      95     114 ..      94     134 .. 0.73

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 4.6e-12
                                      HHHHHHHCCSSCGHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTSS-HHHHHHHHHHHHH CS
                           SRP54_N  6 nsalkklsgkskideedleealkeleeaLleaDVgvkvvkklienvkkkavgekklkpkqqvkkivkdeL 75
                                      ++ l+   + ++i+ ed++e+ ++    L+e+DV+++v++++i+ +k++ +g k++ + +++k+ +k++L
  gi|385806306|ref|YP_005842704.1| 13 SNSLAEKFKTKEIKPEDFDEIGNDFLLELVENDVAYSVAEEIINTLKNTIIG-KRVPKNSDIKESIKEAL 81
                                      333333334567************************************99**.99************987 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1
                                       HHHHHHHHHHHCTTS....S CS
                           SRP54_N  46 klienvkkkavgekk....l 61 
                                       ++ie +k+k+++ekk    +
  gi|385806306|ref|YP_005842704.1|  95 DIIEAIKNKQAKEKKpfiiI 114
                                       699*****999977666550 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0         2   1.2e+03      93     111 ..      96     114 ..      20     115 .. 0.62
   2 !   19.7   0.1   1.1e-06   0.00067       2      93 ..     113     239 ..     112     256 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 2
                                       HHHHHHHHHHHTTSEEEEE CS
                          MMR_HSR1  93 ldeeleelleeakkplilv 111
                                       + e +++ + ++kkp+i++
  gi|385806306|ref|YP_005842704.1|  96 IIEAIKNKQAKEKKPFIII 114
                                       1233333333466666665 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 1.1e-06
                                       EEEEESTTSSHHHHHHHHHT.......STEEESSSTTSSSSEEEEEEEETTEE........................ CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltg.......ekaivsdkpgtTrdinegrvklkgke........................ 47 
                                       ++++G   vGK+t i +l +       +  iv++  +     ++ +v+ +  +                        
  gi|385806306|ref|YP_005842704.1| 113 IIFMGINGVGKTTSIAKLANyikkngmTPLIVAADTFRAGSQEQLQVHAD--Rlgvpiirakynsdpasiafdgiay 187
                                       7899**************98555443324577777777777777777633..1234444444455555566666666 PP

                                       .......EEEEECGGCSSHHHHHHHHHHHHHHHHC...TSEEEEEEETT..TTCSHHH CS
                          MMR_HSR1  48 .......ielvDtpGliegaseekglgkaflalee...adlillvvdas..eeklkpl 93 
                                              ++l+Dt+G   + + +++l ++++++++    dl llv+da   +   + +
  gi|385806306|ref|YP_005842704.1| 188 aekknipVVLIDTAG---RMHVDRDLINELKKIIDvvgYDLRLLVIDALsgN---DSV 239
                                       6666666********...456888889998888876546********76332...222 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 ?   -2.0   0.0       7.2   4.5e+03      80      97 ..      49      66 ..      29      92 .. 0.62
   2 !   19.1   0.1   2.2e-06    0.0013       1     119 [.     113     243 ..     113     249 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 7.2
                                      HHHHHHHHHHHHHHHHTT CS
                               AAA 80 eeeervvnqLlteldgvk 97
                                      +++e+++n+L + + g +
  gi|385806306|ref|YP_005842704.1| 49 SVAEEIINTLKNTIIGKR 66
                                      455555555555554444 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 2.2e-06
                                       EEEESSTTSSHHHHHHHHHHHHT...HEEEEEETTTCSSS....................STTHHHHHHHHHHHHHH CS
                               AAA   1 vllyGppGtGKTllakavakelg...vefleisgsellsk....................yvgesekkirelfkeak 54 
                                       ++++G  G+GKT+ +  +a+ ++   ++ l + + +++                      y ++ ++   + ++ a+
  gi|385806306|ref|YP_005842704.1| 113 IIFMGINGVGKTTSIAKLANYIKkngMTPLIVAADTFRAGsqeqlqvhadrlgvpiirakYNSDPASIAFDGIAYAE 189
                                       5899*****************85333444444444444222455555555555555555488888888888888899 PP

                                       HTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHH CS
                               AAA  55 ekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpal 119
                                       +k+   +++iD + +++ +r         +++n+L + +d v  + + ++vi a    d++++a+
  gi|385806306|ref|YP_005842704.1| 190 KKN-IPVVLIDTAGRMHVDR---------DLINELKKIIDVVGYDLR-LLVIDALSGNDSVEQAI 243
                                       998.9***********9999.........99******9999988755.88877666666666665 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.024        15      56     133 ..      37     107 ..       7     110 .. 0.77
   2 !   12.0   0.0    0.0002      0.13       3      26 ..     117     140 ..     115     147 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.024
                                       HHHHHHHHHHHHTTHHHHHHHHHTT-EEEEES-HHHHHHHHHTTTTTTCHHHHHHGGGTTSE-SEEEEEESSHHHHH CS
                   Thymidylate_kin  56 teallfaadriehleekikpalkqgktvivdRylfSslaYqgakegvdldlvlslnedvllkPdltflldvdpeval 132
                                       +++ l   d++++++e+i+  lk+  t+i  R   +s + +++ke    +lv  ++++++ +Pdl ++  ++ + a 
  gi|385806306|ref|YP_005842704.1|  37 FLLELVENDVAYSVAEEIINTLKN--TIIGKRVPKNSDIKESIKE----ALVDFIKKNIP-EPDLDIIEAIKNKQAK 106
                                       377788899999999999999998..9999999999977676666....89999999*99.****999999888776 PP

                                       T CS
                   Thymidylate_kin 133 k 133
                                       +
  gi|385806306|ref|YP_005842704.1| 107 E 107
                                       6 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.0002
                                       ESTTSSHHHHHHHHHHHHHHTTE. CS
                   Thymidylate_kin   3 GlDGaGKttqaellkerlkeegik 26 
                                       G++G+GKtt +++l++++k++g  
  gi|385806306|ref|YP_005842704.1| 117 GINGVGKTTSIAKLANYIKKNGMT 140
                                       9*******************9965 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   2.7e-06    0.0017      19     108 ..     111     214 ..      99     229 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.7e-06
                            AAA_30  19 rvavltGpAGtGKttalkalreaweaag.grviglAptgkaAkvLaeelgieastiakllkrlk............. 81 
                                        + +  G  G GKtt++++l++ ++++g  ++i++A t +a  +  e+l+++a+++   + r k             
  gi|385806306|ref|YP_005842704.1| 111 FIIIFMGINGVGKTTSIAKLANYIKKNGmTPLIVAADTFRAGSQ--EQLQVHADRLGVPIIRAKynsdpasiafdgi 185
                                       567889*********************75789999999998764..5667777776666655556666667777654 PP

                            AAA_30  82 grarlepg.tllivDEagmv..dtkqlaal 108
                                       + a+ + +  ++++D ag +  d + +++l
  gi|385806306|ref|YP_005842704.1| 186 AYAEKK-NiPVVLIDTAGRMhvDRDLINEL 214
                                       222222.23677777777654455555555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   3.3e-06    0.0021       5      91 ..     113     216 ..     109     225 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.3e-06
                            AAA_24   5 iliyGpsgiGKTtlakel.......gpkplfi..dtek.Glksldadkfpdieswedfldevvel..........aa 61 
                                       i+ +G +g+GKTt++++l       g +pl++  dt++ G+++    + +++ +++ ++ +++++          +a
  gi|385806306|ref|YP_005842704.1| 113 IIFMGINGVGKTTSIAKLanyikknGMTPLIVaaDTFRaGSQEQLQVHADRL-GVPIIRAKYNSDpasiafdgiaYA 188
                                       6789*******************99777777755777778877666666766.9999******99**********99 PP

                            AAA_24  62 eladyktlviDtideleelclaevirqnek 91 
                                       e++++ ++ iDt++ +  ++++++i+  +k
  gi|385806306|ref|YP_005842704.1| 189 EKKNIPVVLIDTAGRM--HVDRDLINELKK 216
                                       *************998..777777766665 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 ?    0.3   0.1       1.1   6.6e+02      92     124 ..      50      79 ..       4     108 .. 0.73
   2 !   15.4   0.0   2.4e-05     0.015       6      87 ..     117     262 ..     112     298 .. 0.68

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.1
                                       TCHHHHHHHHHHCTS-EEE.EEE--CCHCCCCHH CS
                                       xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                              CbiA  92 llkealeelkqrygvpvlg.viprdeavaeapar 124
                                         +e + +l    ++ ++g  +p+++++ e++++
  gi|385806306|ref|YP_005842704.1|  50 VAEEIINTL----KNTIIGkRVPKNSDIKESIKE 79 
                                       333333333....677777788888888877765 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 2.4e-05
                                       SSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH............................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................ RF
                              CbiA   6 tkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep............................ 54 
                                       +  GvGKTt  a+La +++++g   l v aD+ +  +   e+l+                                 
  gi|385806306|ref|YP_005842704.1| 117 GINGVGKTTSIAKLANYIKKNGMTPLIVAADTFRAGSQ--EQLQ----Vhadrlgvpiirakynsdpasiafdgiay 187
                                       5569********************99999998855555..3333....23334677777777888888888888888 PP

                                       ...........................................CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS. CS
                                       ...........................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ...........................................dlkrllellealgkkkalllkiagvvlnrvdge 87 
                                                                                  d+ ++  ++e+    +++++ + g+ l++ d +
  gi|385806306|ref|YP_005842704.1| 188 aekknipvvlidtagrmhvdrdlinelkkiidvvgydlrllviDALSGNDSVEQAIA-YEKNVGYEGFFLTKSDAD 262
                                       888888888888777777777777777777777777777777766666666655543.344566666666666665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1     2e-05     0.012       7     126 ..     112     228 ..     105     231 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2e-05
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka..erlsseellea 81 
                                       i++ +G  G+GKTt++++l++  +     + + p +v  +    + s++ l+  +  lg++  +  ++ +   +   
  gi|385806306|ref|YP_005842704.1| 112 IIIFMGINGVGKTTSIAKLANYIK----KNGMTPLIVAADTFRAG-SQEQLQVHADRLGVPIIRakYNSDPASIAFD 183
                                       78899****************874....23355555566666666.5555688899999999994433333333344 PP

                            AAA_22  82 leqalraravielliiDEaqhlr.seealeeLrsllnlsrkgvqli 126
                                          +++++  i++++iD a ++    ++++eL+++ ++  ++++l+
  gi|385806306|ref|YP_005842704.1| 184 GIAYAEKKN-IPVVLIDTAGRMHvDRDLINELKKIIDVVGYDLRLL 228
                                       444444444.59*********9555999****99999767776665 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.4e-05    0.0085       6      56 ..     101     151 ..      95     232 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.4e-05
                        Zeta_toxin   6 kdkkypsqerPklillgGqpGAGKselaellkdele.rqgnvvrldpDdlRe 56 
                                       k+k+  ++++P +i+  G  G GK++ +++l+++++ ++   + + +D++R+
  gi|385806306|ref|YP_005842704.1| 101 KNKQ-AKEKKPFIIIFMGINGVGKTTSIAKLANYIKkNGMTPLIVAADTFRA 151
                                       3333.567***************************956667899999*9996 PP

>> CelTOS  Cell-traversal protein for ookinetes and sporozoites
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   4.3     3e-05     0.018       8      94 ..      11     102 ..       5     115 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3e-05
                            CelTOS   8 rlqkslsskl..seiiradldskgde.lvdliandlekelqknsl..vaasfLqsgfdvkkkaKeiiKkvllevlks 79 
                                          +sl +k+  +ei  +d+d++g++ l +l+ nd+  ++ ++ +  ++ + + +    ++++Ke iK+ l++ +k+
  gi|385806306|ref|YP_005842704.1|  11 SFSNSLAEKFktKEIKPEDFDEIGNDfLLELVENDVAYSVAEEIIntLKNTIIGKRVPKNSDIKESIKEALVDFIKK 87 
                                       4556666665224677899****99956899999999999988642145667777767779**************** PP

                            CelTOS  80 llpvvekivadavkP 94 
                                        +p  +  + +a+k 
  gi|385806306|ref|YP_005842704.1|  88 NIPEPDLDIIEAIKN 102
                                       ******999999995 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   3.2e-05      0.02      18      76 ..     104     164 ..      93     246 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.2e-05
                            AAA_16  18 rvrsgrpelvllsGesGvGKsslvrellralekdggif..lrgkcdqlesaipysalaqal 76 
                                       ++++  p ++++ G  GvGK++ + +l+++++k+g+    +++++ + +s+  +++ a+ l
  gi|385806306|ref|YP_005842704.1| 104 QAKEKKPFIIIFMGINGVGKTTSIAKLANYIKKNGMTPliVAADTFRAGSQEQLQVHADRL 164
                                       55666778999**********************9432222333333332332222233333 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       6.1   3.8e+03      65      71 ..      69      75 ..      35     106 .. 0.54
   2 ?   14.0   0.2   5.8e-05     0.036      12      46 ..     120     154 ..     111     233 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 6.1
                            AAA_31 65 eeknike 71
                                      ++++ike
  gi|385806306|ref|YP_005842704.1| 69 KNSDIKE 75
                                      2222222 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 5.8e-05
                            AAA_31  12 GvGKTTtsvnlaaalaklgkkvLlvDlDpQanatt 46 
                                       GvGKTT+  +la  + k+g+  L+v +D+  + ++
  gi|385806306|ref|YP_005842704.1| 120 GVGKTTSIAKLANYIKKNGMTPLIVAADTFRAGSQ 154
                                       9***************************9776665 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00038      0.23       3      31 ..     119     147 ..     117     153 .. 0.91
   2 ?   -0.7   0.0       1.7   1.1e+03      99     134 ..     189     226 ..     181     251 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00038
                            CLP1_P   3 kdsGKSTlarlLlNyalrkgrkpvyvDlD 31 
                                       + +GK+T ++ L+Ny+ ++g++p++v +D
  gi|385806306|ref|YP_005842704.1| 119 NGVGKTTSIAKLANYIKKNGMTPLIVAAD 147
                                       689**********************9988 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.7
                            CLP1_P  99 kkakasgliIntpGwvk..glgaellleliealepdvv 134
                                       +k +  +++I+t G ++     ++ l+++i+++  d+ 
  gi|385806306|ref|YP_005842704.1| 189 EKKNIPVVLIDTAGRMHvdRDLINELKKIIDVVGYDLR 226
                                       45667789999999765114455666667777666664 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 ?   -3.1   0.0       8.5   5.3e+03     204     228 ..      54      77 ..      28      89 .. 0.51
   2 ?   12.2   0.1   0.00018      0.11       2      33 ..     116     147 ..     115     152 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 8.5
                        ATP_bind_1 204 iaelleefalvlrflplssekeesi 228
                                       i ++l+++ +  + +p +s+ +esi
  gi|385806306|ref|YP_005842704.1|  54 IINTLKNTIIG-KRVPKNSDIKESI 77 
                                       34444433333.2222222222222 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00018
                        ATP_bind_1   2 vGpaGsGKttfvgalseilelrgrsvavvNLD 33 
                                       +G  G+GKtt + +l+++++++g ++ +v  D
  gi|385806306|ref|YP_005842704.1| 116 MGINGVGKTTSIAKLANYIKKNGMTPLIVAAD 147
                                       89************************999766 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00015     0.092       3      38 ..     112     147 ..     111     151 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00015
                                       EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                       ArsA_ATPase   3 vilvgGKGGVGKttvsaatavklsekgkkvllistD 38 
                                       +i++ G  GVGKtt+ a +a ++ ++g   l+++ D
  gi|385806306|ref|YP_005842704.1| 112 IIIFMGINGVGKTTSIAKLANYIKKNGMTPLIVAAD 147
                                       689999***************************998 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00014     0.086       1      37 [.     112     153 ..     112     229 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00014
                            AAA_33   1 lvllvGlpGsGKstlaerl...lkklg..avllssdtlrrrl 37 
                                       ++++ G +G+GK+t + +l   +kk+g    +++ dt+r   
  gi|385806306|ref|YP_005842704.1| 112 IIIFMGINGVGKTTSIAKLanyIKKNGmtPLIVAADTFRAGS 153
                                       589************999866678888888889999966544 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    0.0008      0.49      98     122 ..     109     133 ..      54     163 .. 0.82
   2 ?    0.3   0.0       0.9   5.5e+02      56      77 ..     230     251 ..     184     283 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0008
                                       TTSEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpe 122
                                       k  +++++G  GvGK+t i +l++ 
  gi|385806306|ref|YP_005842704.1| 109 KPFIIIFMGINGVGKTTSIAKLANY 133
                                       33689************99999874 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.9
                                       GGG--HHHHHHHHHHHHHHTTS CS
                       RsgA_GTPase  56 iDlleeeeeleelkeelealgy 77 
                                       iD l+ ++++e+  +  +++gy
  gi|385806306|ref|YP_005842704.1| 230 IDALSGNDSVEQAIAYEKNVGY 251
                                       3444444444555555555555 PP

>> 6PF2K  6-phosphofructo-2-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00019      0.11       8      44 ..     105     141 ..      98     243 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00019
                                       HT..S-EEEEEESSTTSSHHHHHHHHHHHHHHTT--E CS
                             6PF2K   8 nlknsklvivlvGLpargKtyiskkltrylkwlgvrt 44 
                                        +++++++i+++G+   gKt+   kl  y+k +g++ 
  gi|385806306|ref|YP_005842704.1| 105 AKEKKPFIIIFMGINGVGKTTSIAKLANYIKKNGMTP 141
                                       457899*************************998864 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00033       0.2       6      53 ..      91     139 ..      86     160 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00033
                                       HHHHHHHHHHT.......TTSEEEEEESTTSTHHHHHHHHHHHH-S... CS
                            ResIII   6 eyQeeaienlleklks.krdkrglikmaTGtGKTlvaaklierllkkgk 53 
                                       e   ++ie++++k  + k+   +++    G+GKT  +akl+ +++k+g 
  gi|385806306|ref|YP_005842704.1|  91 EPDLDIIEAIKNKQAKeKKPFIIIFMGINGVGKTTSIAKLANYIKKNGM 139
                                       55667788888776632344456677899************99999865 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00023      0.14       1      51 [.     109     159 ..     109     166 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00023
                                       S-EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT--S CS
                        APS_kinase   1 rgvvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLgf 51 
                                       +++++ + G+ g GK+t   +l+++++++g++  ++  d+ R g +++L  
  gi|385806306|ref|YP_005842704.1| 109 KPFIIIFMGINGVGKTTSIAKLANYIKKNGMTPLIVAADTFRAGSQEQLQV 159
                                       5799*************99************************99998865 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0    0.0003      0.18      23      68 ..      98     145 ..      80     161 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0003
                             AAA_7  23 syllelllknkkp..vllvGptGtGKtviikdllkkldkekylsltin 68 
                                       + + ++  k+kkp  ++++G  G+GKt+ i +l + ++k+ +++l++ 
  gi|385806306|ref|YP_005842704.1|  98 EAIKNKQAKEKKPfiIIFMGINGVGKTTSIAKLANYIKKNGMTPLIVA 145
                                       5566666777777224689*******************9999988775 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       3.8   2.4e+03     103     130 ..       6      33 ..       3      34 .. 0.77
   2 ?   10.8   0.1   0.00059      0.37       4      41 ..     112     149 ..     108     244 .. 0.65

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 3.8
                            AAA_14 103 kllskeiatslagrvaeielyplsfaEf 130
                                       k   +  ++sla++ ++ e+ p +f E+
  gi|385806306|ref|YP_005842704.1|   6 KKSIESFSNSLAEKFKTKEIKPEDFDEI 33 
                                       5555667889999999999999999986 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00059
                            AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldde 41 
                                       i++ +G+  vGKTt + +l++    +    l ++ d+ 
  gi|385806306|ref|YP_005842704.1| 112 IIIFMGINGVGKTTSIAKLANYIKKNGMTPLIVAADTF 149
                                       78999**************9544433333344444443 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00032       0.2       2      44 ..     113     162 ..     112     206 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00032
                            AAA_28   2 ivitGgestGKTtlleaLaar....gyp..vv.pEaareileeklakged 44 
                                       i+++G  + GKTt +++La+     g++  +v ++++r   +e+l+ + d
  gi|385806306|ref|YP_005842704.1| 113 IIFMGINGVGKTTSIAKLANYikknGMTplIVaADTFRAGSQEQLQVHAD 162
                                       8999***************7666666444533588888888887765555 PP

>> PPK2  Polyphosphate kinase 2 (PPK2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00031      0.19      19      79 ..      97     158 ..      85     167 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00031
                                       HHHH.HSGGGGG-EEEEEEEESTTS-HHHHHHHHHTTS-GGG-EEEE--S--HHHHTS-TTH CS
                              PPK2  19 vklq.ekvkaegkklvvifegrDaAGKgGaikrvtealnprvarvvalkaPteeEksqwylq 79 
                                       ++++ +k ++e+k  ++if g ++ GK   i+++ +++++ +++   ++a t +  sq+ lq
  gi|385806306|ref|YP_005842704.1|  97 IEAIkNKQAKEKKPFIIIFMGINGVGKTTSIAKLANYIKKNGMTPLIVAADTFRAGSQEQLQ 158
                                       55440555667777***********************9999888777777766666666555 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       4.6   2.9e+03      46      74 ..      85     111 ..      50     114 .. 0.68
   2 ?   11.0   0.0   0.00069      0.43       1      97 [.     116     218 ..     116     233 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 4.6
                                       HCTSHHHHHHHHHHHHHHHHHHHHHSSEE CS
                            AAA_17  46 mrklpleekkelqkeaaekiaeeakkkgv 74 
                                       ++k+  e++ ++ + +++k a+e  kk +
  gi|385806306|ref|YP_005842704.1|  85 IKKNIPEPDLDIIEAIKNKQAKE--KKPF 111
                                       45566666666666666655554..3445 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00069
                                       EE-TTSSHHHHHHHHHHHH....TEEEEEHHHHHHHHHHTTTSHSSHHHHC..TSHHHHHHHHHHHHHHHHHHHHHS CS
                            AAA_17   1 lGgPGsGKgtqceklveky....gfthlsaGdllreeakrgglakardemr..klpleekkelqkeaaekiaeeakk 71 
                                       +G+ G+GK+t ++kl+  +      + + a d +r+  ++++l+ + d++       + + +   +a + ia ++kk
  gi|385806306|ref|YP_005842704.1| 116 MGINGVGKTTSIAKLANYIkkngMTPLIVAADTFRAG-SQEQLQVHADRLGvpIIRAKYNSDPASIAFDGIAYAEKK 191
                                       599************9544333246789999999987.556665566666544445555556667777777665544 PP

                                       SE..EEEEE-SEEEETTEEEESSHHHHH CS
                            AAA_17  72 kg..vlvdghprikeqagfldglpkevl 97 
                                       +   vl+d+  r+  +++++ +l+k ++
  gi|385806306|ref|YP_005842704.1| 192 NIpvVLIDTAGRMHVDRDLINELKK-II 218
                                       4344888888888888888887775.44 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1       1.9   1.2e+03     102     146 ..      31      79 ..       6     101 .. 0.60
   2 ?   12.1   0.2   0.00023      0.14       3      29 ..     114     140 ..     112     156 .. 0.86
   3 ?   -0.5   0.0       1.6     1e+03      94     121 ..     191     217 ..     147     249 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.9
                                       ---ST...TGGG-HHHHHHH.HHHHTTTSEEEEE--SS--SHHHHHHHT CS
                          NTPase_1 102 DEiGk...mElkskkfkeav.eevLksekpvlavihrrkdlalveeire 146
                                       DEiG+   +El  + ++ +v ee++++ k+ ++  +++k++++ e+i+e
  gi|385806306|ref|YP_005842704.1|  31 DEIGNdflLELVENDVAYSVaEEIINTLKNTIIGKRVPKNSDIKESIKE 79 
                                       6666444456666555555523455555555554444444444444443 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00023
                                       EEE--TTSSHHHHHHHHHHHH...GGG CS
                          NTPase_1   3 fiTGppGvGKtTlvkkvlellkssgvk 29 
                                       +  G  GvGKtT + k+++ +k++g++
  gi|385806306|ref|YP_005842704.1| 114 IFMGINGVGKTTSIAKLANYIKKNGMT 140
                                       556889*****************9986 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1.6
                                       HHH-EEEE---STTGGG-HHHHHHHHHH CS
                          NTPase_1  94 seadviviDEiGkmElkskkfkeaveev 121
                                       ++  v++iD  G+m +    ++++++++
  gi|385806306|ref|YP_005842704.1| 191 KNIPVVLIDTAGRMHVDR-DLINELKKI 217
                                       333377788888886543.344444444 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       7.4   4.6e+03      66     100 ..      48      81 ..      40      83 .. 0.52
   2 ?   10.2   0.1   0.00051      0.31       5      42 ..      97     132 ..      94     140 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 7.4
                                       HHHHHXXHHHHHCCCTTSSSS-STTSHHHHHHHHC CS
                            NB-ARC  66 eeiletilkeLslseddleekeeveslkrklvrlL 100
                                       +++ e+i++ L+++       ++++ +k+ + ++L
  gi|385806306|ref|YP_005842704.1|  48 YSVAEEIINTLKNTIIGKRVPKNSD-IKESIKEAL 81 
                                       5566666666655543333333333.555555555 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00051
                                       HHHHHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCC CS
                            NB-ARC   5 vekviekLlekdelqslvvalvGmgGvGKttlakqiln 42 
                                       +e++++k  +++++  +++ ++G  GvGKtt +++  n
  gi|385806306|ref|YP_005842704.1|  97 IEAIKNKQAKEKKP--FIIIFMGINGVGKTTSIAKLAN 132
                                       67888887755544..6**************8777665 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1    0.0012      0.76      39      85 ..      98     142 ..      93     154 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0012
                                       HHHHHHHT-SS-SS-EEEEEEE-TTSSHHHHHHHHHHHHSTTGGGST CS
                            Torsin  39 ksvkaylenekpkkpLvlsfhGwtGtGknfvaeiiaenlyrdGlrsd 85 
                                       +++k   ++ k kkp+++ f G  G Gk      +a+ + ++G+   
  gi|385806306|ref|YP_005842704.1|  98 EAIKN--KQAKEKKPFIIIFMGINGVGKTTSIAKLANYIKKNGMTPL 142
                                       45544..455889****************999999999999999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       918  (0.051202); expected 358.6 (0.02)
Passed bias filter:                      705  (0.0393218); expected 358.6 (0.02)
Passed Vit filter:                       116  (0.00646996); 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: 0.67u 0.33s 00:00:01.00 Elapsed: 00:00:00.52
# Mc/sec: 1772.04
//
Query:       gi|385806307|ref|YP_005842705.1|  [L=181]
Description: Rpr2 multi-domain protein [Fervidicoccus fontis Kam940]
Scores for complete 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   49.8   0.0    5.6e-13   49.0   0.0    1.4  1  Rpr2             RNAse P Rpr2/Rpp21/SNM1 subunit domain
    1.6e-10   41.0   2.6    3.1e-10   40.1   2.6    1.5  1  CRS1_YhbY        CRS1 / YhbY (CRM) domain
  ------ inclusion threshold ------
      0.037   13.8   0.6       0.27   11.0   0.1    2.3  2  Ribosomal_S27e   Ribosomal protein S27
      0.084   13.3   0.1         13    6.3   0.0    2.3  2  Lar_restr_allev  Restriction alleviation protein Lar
       0.14   12.2   0.1       0.24   11.5   0.1    1.3  1  DZR              Double zinc ribbon
       0.16   11.5   0.4        4.5    6.9   0.0    2.4  2  TF_Zn_Ribbon     TFIIB zinc-binding
       0.17   12.1   1.3       0.47   10.7   0.1    2.1  2  zinc_ribbon_13   Nucleic-acid-binding protein containing Zn-r
       0.35   10.6   5.4        1.8    8.3   0.8    3.1  3  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
        3.7    7.8   5.6         77    3.6   5.6    2.2  1  Ribosomal_L37e   Ribosomal protein L37e


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 !   49.0   0.0   2.8e-16   5.6e-13      23      90 .]      30      89 ..      12      89 .. 0.89

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 2.8e-16
                                      HHHHHHHHHHHHCT---SSTCCCTB-TTT--B--CTTTEEEEEE-SSS-E.........EEEEETTTT CS
                              Rpr2 23 ylakqlrevskkaqlrlppsvkrtvCkkCgsvlipgvtcsvrvenkskkkkkkkkkadvlvvtClaCg 90
                                      y ++ ++++++k++l + +++k+ +Ck+Cg++lipgv++s r+++ks ++         l+v+Cl+Cg
  gi|385806307|ref|YP_005842705.1| 30 YGGRYIKSIAQKTNLPVRDDLKHFICKRCGAILIPGVNSSYRIHSKSGNSY--------LKVKCLNCG 89
                                      55667899***********************************98887654........78******7 PP

>> CRS1_YhbY  CRS1 / YhbY (CRM) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   2.6   1.6e-13   3.1e-10      18      82 ..     109     177 ..     100     179 .. 0.90

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 1.6e-13
                         CRS1_YhbY  18 pkvkiGkaGvtkevvdeiheklkteelvkvkc.....egppalnmkrmaeiLeektgglviqrsgtsivL 82 
                                       + ++iGk+G+++ +++ei+ +lk +++vk+++     e  + ++++++a+++   +++++++++g++++L
  gi|385806307|ref|YP_005842705.1| 109 ADINIGKNGINERIIKEIDTRLKVKKVVKIRInknfiE-SSGEEREEIAKKVSSLLNAELVEIRGNTFIL 177
                                       6689*****************************99976.44555************************98 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1       0.3   5.9e+02      28      36 ..      54      62 ..      51      64 .. 0.81
   2 ?   11.0   0.1   0.00014      0.27       4      28 ..      79     103 ..      76     107 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.3
                                      EESSSTCEE CS
                    Ribosomal_S27e 28 kCisCgkvL 36
                                       C  Cg +L
  gi|385806307|ref|YP_005842705.1| 54 ICKRCGAIL 62
                                      599999988 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00014
                                       -EEEEE-TTTS-EE.EEESS-SS-EE CS
                    Ribosomal_S27e   4 kFldvkCpdCenet.vvFshaatvvk 28 
                                        +l+vkC +C+  + ++F ++  vvk
  gi|385806307|ref|YP_005842705.1|  79 SYLKVKCLNCGYSKkIIF-KPRDVVK 103
                                       589*******86551555.5666665 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 ?    6.3   0.0    0.0065        13      17      37 ..      41      66 ..      18      79 .. 0.71
   2 ?    5.7   0.0    0.0098        20      26      37 ..      77      91 ..      64     110 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0065
                   Lar_restr_allev 17 rsqrvvaeigqcvyCadCga.....s 37
                                      +++++v +  + ++C+ Cga     +
  gi|385806307|ref|YP_005842705.1| 41 KTNLPVRDDLKHFICKRCGAilipgV 66
                                      4444555555599*******766553 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0098
                   Lar_restr_allev 26 gq...cvyCadCgas 37
                                      g     v C +Cg+s
  gi|385806307|ref|YP_005842705.1| 77 GNsylKVKCLNCGYS 91
                                      3344589******93 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00012      0.24      13      37 ..      53      91 ..      45      95 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                               DZR 13 rfCseCgtklkavaa..............edrCpsCgek 37
                                        C++Cg+ l +  +              + +C +Cg++
  gi|385806307|ref|YP_005842705.1| 53 FICKRCGAILIPGVNssyrihsksgnsylKVKCLNCGYS 91
                                      58*******98655589********************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 ?    6.9   0.0    0.0023       4.5      19      29 ..      52      62 ..      41      67 .. 0.84
   2 ?    2.3   0.1     0.062   1.2e+02       2      12 ..      84      95 ..      83     100 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0023
                                      CEEESSSSBEE CS
                      TF_Zn_Ribbon 19 elvCtdCGlVl 29
                                       ++C++CG++l
  gi|385806307|ref|YP_005842705.1| 52 HFICKRCGAIL 62
                                      59******986 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.062
                                      EETTTTCEE.CH CS
                      TF_Zn_Ribbon  2 kCPnCgstn.lv 12
                                      kC nCg ++ ++
  gi|385806307|ref|YP_005842705.1| 84 KCLNCGYSKkII 95
                                      8****9755455 PP

>> zinc_ribbon_13  Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1       0.7   1.4e+03      37      42 ..      54      59 ..      50      61 .. 0.74
   2 ?   10.7   0.1   0.00023      0.47      31      45 ..      78      92 ..      69     107 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.7
                    zinc_ribbon_13 37 sCknCg 42
                                      +Ck+Cg
  gi|385806307|ref|YP_005842705.1| 54 ICKRCG 59
                                      577776 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00023
                    zinc_ribbon_13 31 kkfitvsCknCgYte 45
                                      + ++ v C nCgY+ 
  gi|385806307|ref|YP_005842705.1| 78 NSYLKVKCLNCGYSK 92
                                      89***********85 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       0.9   1.8e+03      26      31 ..      10      15 ..       9      15 .. 0.87
   2 ?    2.8   0.0     0.047        94      19      24 ..      54      59 ..      40      62 .. 0.81
   3 ?    8.3   0.8    0.0009       1.8      18      32 .]      83      99 ..      79      99 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.9
                                      ---B-- CS
                    DNA_RNApol_7kD 26 RilYKk 31
                                      R++YK+
  gi|385806307|ref|YP_005842705.1| 10 RVFYKA 15
                                      9****5 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.047
                                      --SSS- CS
                    DNA_RNApol_7kD 19 RCkeCG 24
                                       Ck CG
  gi|385806307|ref|YP_005842705.1| 54 ICKRCG 59
                                      488898 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0009
                                      ---SSS--..---B--- CS
                    DNA_RNApol_7kD 18 iRCkeCGh..RilYKkR 32
                                      ++C +CG+  +i++K+R
  gi|385806307|ref|YP_005842705.1| 83 VKCLNCGYskKIIFKPR 99
                                      89*****9889****99 PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   5.6     0.039        77      15      32 ..      51      75 ..      46      97 .. 0.58

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.039
                    Ribosomal_L37e 15 tHilCrrCg.......krsyhvqkk 32
                                       H +C+rCg       ++sy ++ k
  gi|385806307|ref|YP_005842705.1| 51 KHFICKRCGailipgvNSSYRIHSK 75
                                      69******93333333356666544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       856  (0.0477439); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1133.31
//
Query:       gi|385806308|ref|YP_005842706.1|  [L=291]
Description: l-asparagine amidohydrolase [Fervidicoccus fontis Kam940]
Scores for complete 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-73  245.7   8.0    1.3e-72  244.4   8.0    1.5  1  Asparaginase_2  Asparaginase


Domain annotation for each model (and alignments):
>> Asparaginase_2  Asparaginase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  244.4   8.0   7.4e-77   1.3e-72       5     299 ..       2     281 ..       1     286 [. 0.88

  Alignments for each domain:
  == domain 1  score: 244.4 bits;  conditional E-value: 7.4e-77
                                       EEEEEESE-G.-HHHHHHHHHCHHHHHHHHHHHHHTT--HHHHHHHHHHHHHCTCCCSSSTTSS-BTTS---EEEEE CS
                    Asparaginase_2   5 ihGGAgsilk.tkereeavrkalkealeagykvLkeggsaldaVeaavrllEddplfnaGkGsvltedgeveldAsi 80 
                                       +hGGAgs +k +ke++ ++++alk+a++ g+++Lk+++sa++aV +a+r+lEd+ + naG Gsv +++g +eldA i
  gi|385806308|ref|YP_005842706.1|   2 VHGGAGSWSKiPKETKISAQQALKDAVTFGMEILKREKSAVEAVAEAIRILEDSGSLNAGLGSVTNSEGYMELDAGI 78 
                                       8*********999**************************************************************** PP

                                       EETTTTEEEEEEEESSBS-HHHHHHHHHHHCS-SEEEHHHHHHHHHHTT-----CGGG--HHHHHHHHHHHHCCCHS CS
                    Asparaginase_2  81 mdgktlraGaVagvkrvknpislArlvmeksehvlLvgegAeefareqglelvdeesllteerlkelekakkekaek 157
                                       mdgk+++aGaVa+++ ++npi +A +vm +++hv+LvgegA++fa ++g++   +e +  +++ k+++ + +++++ 
  gi|385806308|ref|YP_005842706.1|  79 MDGKKMDAGAVAAIRGIRNPILVAMKVMRETPHVILVGEGAQKFALSKGFK--IDERINVKKDVKDISINIEKRSN- 152
                                       **************************************************2..23333444444444444433333. PP

                                       ..B-S-BS-TTTTT---EEEEEE-TTS-EEEEEEE--STTB-TTEE-STTSTTTSEEEETTTEEEEEEE-HHHHCCT CS
                    Asparaginase_2 158 keaknvsekelkaklgTvGaValDsegnlAaaTSTgGltnklvGRvGDspiiGaGtYAdnkvgAvsaTGkGeeiire 234
                                                     + TvGa+a+ s+   Aa+ STgG++ k++GR+GD+pi+GaG YA n+++A++aTG Ge+ii +
  gi|385806308|ref|YP_005842706.1| 153 ------------WIHDTVGAIAISSDCDTAAGASTGGIRGKMPGRIGDTPIPGAGYYA-NHFAAAAATGIGEVIILT 216
                                       ............3456******************************************.****************** PP

                                       THHHHHHHHHHTTT--HHHHHH..HHHHCHHHHTTT-EEEEEEETTS-EEEEECSCCCEEEEEETTS CS
                    Asparaginase_2 235 llaadivalmeykglsleeAae..kvieeklkrvkgsgGviavdkkGevaaefnsegmlrayakede 299
                                        +++ iv++ + +g+ l    +  + ++++ +   +++G+i  d +G+++  fn+e + +++ +ed 
  gi|385806308|ref|YP_005842706.1| 217 GATRWIVERGTLAGNVLFVGKDliEYVNRMYST--NTIGIIMADIRGNYGRIFNTEALPYGVFTEDM 281
                                       ************998876554311444444443..69********************9999888764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); 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: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.54
# Mc/sec: 1616.80
//
Query:       gi|385806309|ref|YP_005842707.1|  [L=240]
Description: ribosome biogenesis protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-44  150.9   0.5    3.9e-44  150.6   0.5    1.0  1  EMG1      EMG1/NEP1 methyltransferase


Domain annotation for each model (and alignments):
>> EMG1  EMG1/NEP1 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.6   0.5   2.2e-48   3.9e-44       3     194 .]      24     237 ..      22     237 .. 0.90

  Alignments for each domain:
  == domain 1  score: 150.6 bits;  conditional E-value: 2.2e-48
                                       EEEES--B--GG................SCGGSB--HHHHCGG.TTSTTGGGSS-CHHHHHHHHHHHCSCHHCTT.E CS
                              EMG1   3 LeeasLelvkvk................kkseqLLnsddhkkilkklkreakeaRpDIvHqcLlalldspLnkagll 63 
                                       L e+sLe  +++                ++++ +L+++  ++ +k lk+++k++RpDI+Hq+Lla++ s Ln +g+l
  gi|385806309|ref|YP_005842707.1|  24 LVESSLEPLPKElvnskkavilsrrfniEPKYLILDKSLFYEEMKVLKEKEKRGRPDIIHQFLLATQYSYLNLKGKL 100
                                       67888998888888889999999999999************************************************ PP

                                       EEEEEETTSEEEEE-TT----SSHHHHHHHHHHHHCCSEEEETTEE.SCEEEECS.-HHHHCCC...SEEEEE-TTS CS
                              EMG1  64 qvyihttknvlIevnpqtRiPrtfkrFagLmvqLLkklsirategeekLlkvikn.pitdhlpp..gskiillsesa 137
                                       +v+iht +n +Ievnp tRiP+++ +F+ L+++L k ++++ +++   Ll + kn +++++l++   +k ill+e+a
  gi|385806309|ref|YP_005842707.1| 101 KVFIHTINNDIIEVNPITRIPKNYFQFVSLIQNLYKYKKVPRSGEA--LLILRKNvKLSEYLKEknIEKPILLHEKA 175
                                       ******************************************9987..666666439*****99666899******* PP

                                       EE-..............EEEE-SSSS....---HH.......EEESS.SS---HHHHHHHHHHHCH CS
                              EMG1 138 ekk.lvdleefvvkpvvfvigamskgsvkidykee.......eisis.nypLsaavvcskiltafE 194
                                       ek+   +le+f   p++f+ig++++g    d++++       +is+  +  ++a++v+ +i++++E
  gi|385806309|ref|YP_005842707.1| 176 EKVeYNELEKFYFPPCSFLIGGFPHG----DFSKDtkmvawrSISLKkDFIMDAWMVADRIICHLE 237
                                       *7743457777799************....666655566777****97899************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.34s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1359.92
//
Query:       gi|385806310|ref|YP_005842708.1|  [L=147]
Description: hypothetical protein FFONT_1268 [Fervidicoccus fontis Kam940]
Scores for complete 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  137.9   0.3    2.8e-40  137.8   0.3    1.0  1  Archease         Archease protein family (MTH1598/TM1083)
  ------ inclusion threshold ------
      0.029   14.2   0.2        5.5    6.8   0.0    2.2  2  DUF4494          Domain of unknown function (DUF4494)
      0.074   13.3   0.3      0.098   12.9   0.3    1.2  1  PcfK             PcfK-like protein
      0.078   13.0   0.0       0.12   12.3   0.0    1.4  1  tRNA_NucTran2_2  tRNA nucleotidyltransferase domain 2 putativ


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 !  137.8   0.3   6.2e-44   2.8e-40       1     138 []       9     147 .]       9     147 .] 0.98

  Alignments for each domain:
  == domain 1  score: 137.8 bits;  conditional E-value: 6.2e-44
                                       EEE---SSEEEEEEE-SSSHHHHHHHHHHHHHHHS--TT---S-EEEEEEEESSSHHHHHHHHHHHHHHHHHT--S- CS
                          Archease   1 yeyldhtADviieawGksleeafesaalalfeymtdlskvepkeekeieveaedledlLfdfLdellylfdteyfvf 77 
                                       y + +ht+Dvii a+Gk+le+afe +a++l+e+mt+ s+++ ke+ke++v++ dle+lL+++ +e+lylfd+e f++
  gi|385806310|ref|YP_005842708.1|   9 YSFEEHTSDVIIVARGKTLERAFEYIAKGLMEIMTNPSQIDIKEKKELKVNGFDLENLLYRWVEEFLYLFDAEGFLA 85 
                                       8899************************************************************************* PP

                                       ---EEEE..E-SSSEEEEEEEE----.-TT--------B--S---EEEEETTEEEEEEEEE- CS
                          Archease  78 kevkvde.eeeeeeleleaeargekfdkekhevqtevKAvTyhelrieeeddgweayvvvDi 138
                                       +e+kv++ e+ +ee+ ++++a+ge+++++khe +t+vKA Ty+++++++e+d w+++++vDi
  gi|385806310|ref|YP_005842708.1|  86 REIKVEKiEKLNEEYLVNGVAYGERYNERKHESRTHVKAPTYSQINVTRESDLWKLKITVDI 147
                                       *****77568899*******************99***************************9 PP

>> DUF4494  Domain of unknown function (DUF4494)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0    0.0028        13      91     136 ..      13      58 ..       3      61 .. 0.81
   2 ?    6.8   0.0    0.0012       5.5      15      41 ..      91     117 ..      76     143 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0028
                           DUF4494  91 ekktkstmlvqAedlkeAlerleeslkgtlvdyeiasvketkildv 136
                                       e ++ + ++ ++++l++A+e + + l + +++ +  ++ke k l v
  gi|385806310|ref|YP_005842708.1|  13 EHTSDVIIVARGKTLERAFEYIAKGLMEIMTNPSQIDIKEKKELKV 58 
                                       44455556667899*************9999998889999988776 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0012
                           DUF4494  15 gklkkvteeylvdAvsyteaEariyee 41 
                                        k+ k++eeylv+ v+y e  +   +e
  gi|385806310|ref|YP_005842708.1|  91 EKIEKLNEEYLVNGVAYGERYNERKHE 117
                                       678999***********9965544444 PP

>> PcfK  PcfK-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   2.2e-05     0.098      30      93 ..      22      99 ..       9     140 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.2e-05
                              PcfK 30 kekKtleeclkYileea............kklaesgcaavs.ddevyewaveYfeeddievtk......eeekaekrad 89
                                         Ktle++++Yi +              k+++e + ++++ ++ +y w++e+    d+e+        e     k ++
  gi|385806310|ref|YP_005842708.1| 22 ARGKTLERAFEYIAKGLmeimtnpsqidiKEKKELKVNGFDlENLLYRWVEEFLYLFDAEGFLareikvE-----KIEK 95
                                      568***********99977788888888877777777999845678*******98888887775444331.....2222 PP

                              PcfK 90 avsk 93
                                        ++
  gi|385806310|ref|YP_005842708.1| 96 LNEE 99
                                      2222 PP

>> tRNA_NucTran2_2  tRNA nucleotidyltransferase domain 2 putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.8e-05      0.12      87     112 ..      40      65 ..      15      76 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.8e-05
                   tRNA_NucTran2_2  87 aldeiyqaLpIkskkeLaitGkdLle 112
                                       ++ ++ ++  Ik+kkeL+++G dL +
  gi|385806310|ref|YP_005842708.1|  40 EIMTNPSQIDIKEKKELKVNGFDLEN 65 
                                       566777999**************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.36u 0.28s 00:00:00.64 Elapsed: 00:00:00.44
# Mc/sec: 1006.63
//
Query:       gi|385806311|ref|YP_005842709.1|  [L=95]
Description: hypothetical protein FFONT_1269 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.97   10.3   3.8        2.1    9.2   3.8    1.6  1  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
        1.3    9.4  14.8      0.075   13.3   3.8    2.1  2  Orf78            Orf78 (ac78)
        1.5    9.0   7.3        3.9    7.6   0.4    2.3  2  CBP_BcsF         Cellulose biosynthesis protein BcsF
        2.2    6.9   5.9        2.8    6.6   5.9    1.1  1  DUF2207          Predicted membrane protein (DUF2207)
        4.1    6.8   6.3        8.7    5.7   0.8    2.2  2  Rax2             Cortical protein marker for cell polarity


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 ?    9.2   3.8   0.00058       2.1       5      27 ..      25      75 ..      24      88 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00058
                                      HHHHHHHHHHHHHHHGGGS-H.............................. CS
                   CDP-OH_P_transf  5 aiTllrlllsvlailllltyyp............................l 27
                                      +iTll++l+++l++++++++                              +
  gi|385806311|ref|YP_005842709.1| 25 IITLLGILFILLNYIFIFSFPEnikiyplfiiethggysvisldfgqivaV 75
                                      79************8775555588888888888888888888777765532 PP

>> Orf78  Orf78 (ac78)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   4.0     0.086   3.1e+02      63      88 ..      18      41 ..      11      55 .. 0.59
   2 ?   13.3   3.8   2.1e-05     0.075      63      93 ..      62      92 ..      46      95 .] 0.85

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.086
                             Orf78 63 lnillisllavvcvlvllyviyYfvi 88
                                      ++ +++++++++ +l +l    Y++i
  gi|385806311|ref|YP_005842709.1| 18 YEKIFLTIITLLGILFILL--NYIFI 41
                                      5555556666555544442..23333 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 2.1e-05
                             Orf78 63 lnillisllavvcvlvllyviyYfvilrerq 93
                                      ++++ + +  +v+v+v++y+++Yf+i ++++
  gi|385806311|ref|YP_005842709.1| 62 YSVISLDFGQIVAVVVIIYLLLYFLIKKKNR 92
                                      66777778889***************99877 PP

>> CBP_BcsF  Cellulose biosynthesis protein BcsF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   1.5      0.01        36       7      33 ..      23      49 ..      21      57 .. 0.82
   2 ?    7.6   0.4    0.0011       3.9       5      25 ..      68      88 ..      66      94 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.01
                          CBP_BcsF  7 vqiiilcaLiflpLgyllarllrrlsd 33
                                      + ii l+ ++f++L y+   + +  ++
  gi|385806311|ref|YP_005842709.1| 23 LTIITLLGILFILLNYIFIFSFPENIK 49
                                      5699************99988887766 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0011
                          CBP_BcsF  5 DivqiiilcaLiflpLgylla 25
                                      D  qi++++++i l+L  l+ 
  gi|385806311|ref|YP_005842709.1| 68 DFGQIVAVVVIIYLLLYFLIK 88
                                      566999999999998877765 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   5.9   0.00077       2.8     372     429 ..      11      87 ..       8      94 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.00077
                           DUF2207 372 fdkkgkkklkklsalglgliilglilillallllvll...................lvfllilllillliaiivlll 429
                                       f+  g+k+ k++ +++++l+il+++l+ ++++++                      l f  i+++++++ +++++l+
  gi|385806311|ref|YP_005842709.1|  11 FQPSGQKYEKIFLTIITLLGILFILLNYIFIFSFPENikiyplfiiethggysvisLDFGQIVAVVVIIYLLLYFLI 87 
                                       6677888888888888888888888887777776665999************8774333333333333333333333 PP

>> Rax2  Cortical protein marker for cell polarity
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.8    0.0024       8.7     174     191 ..      23      40 ..      21      47 .. 0.91
   2 ?    4.0   0.5    0.0084        30     176     196 ..      72      92 ..      69      94 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0024
                              Rax2 174 Lgtvallgllgiilayir 191
                                       L +++llg+l+i+l+yi+
  gi|385806311|ref|YP_005842709.1|  23 LTIITLLGILFILLNYIF 40 
                                       7899************98 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.0084
                              Rax2 176 tvallgllgiilayirkkreg 196
                                       +va++++++++l+++ kk++ 
  gi|385806311|ref|YP_005842709.1|  72 IVAVVVIIYLLLYFLIKKKNR 92 
                                       589***********8888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1153  (0.0643092); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); 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):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 558.30
//
Query:       gi|385806312|ref|YP_005842710.1|  [L=66]
Description: hypothetical protein FFONT_1270 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      0.005   16.7   0.2     0.0071   16.3   0.2    1.2  1  SecE      SecE/Sec61-gamma subunits of protein translocation 
  ------ inclusion threshold ------
      0.064   13.0   0.3       0.13   12.0   0.3    1.5  1  RPEL      RPEL repeat


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 !   16.3   0.2   7.9e-07    0.0071       2      49 ..      13      60 ..      12      65 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 7.9e-07
                                      HCHHHHHHHHHCCCCCHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              SecE  2 kFfkevkaElkKVtWPtrkEllkttvvVlvfvvimglflflvDlvfsk 49
                                      + ++ +++ lk    P+++E+    +  +++++++g + +++  +++ 
  gi|385806312|ref|YP_005842710.1| 13 EMLSMWRKILKLSRRPDKEEFNLLLKLNIIGFTLVGTIAYIIHIMVTV 60
                                      5677889999********************************988754 PP

>> RPEL  RPEL repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.3   1.4e-05      0.13       5      14 ..      23      32 ..      21      32 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.4e-05
                              RPEL  5 KLshRPtreE 14
                                      KLs+RP++eE
  gi|385806312|ref|YP_005842710.1| 23 KLSRRPDKEE 32
                                      9********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       728  (0.0406046); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.33s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 393.98
//
Query:       gi|385806313|ref|YP_005842711.1|  [L=167]
Description: transcription antitermination protein NusG [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-16   60.6   0.0    1.9e-16   59.7   0.0    1.4  1  Spt5-NGN  Early transcription elongation factor of RNA pol II
    1.5e-06   28.0   0.4      3e-06   27.0   0.4    1.5  1  KOW       KOW motif
  ------ inclusion threshold ------
      0.055   13.4   0.0       0.32   10.9   0.0    2.0  2  CdiI_3    CDI immunity proteins
      0.071   13.0   0.1       0.14   12.1   0.1    1.5  1  YajC      Preprotein translocase subunit
       0.15   12.5   0.0       0.32   11.5   0.0    1.5  1  DUF1318   Protein of unknown function (DUF1318)


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 !   59.7   0.0   5.3e-20   1.9e-16       1      83 [.      22     100 ..      22     101 .. 0.93

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 5.3e-20
                          Spt5-NGN   1 siwavkctagqErevalslmkkilelakkenleIkSvfapdelkGyiyvEAdrkaaveralegipnvrgvvqglvpi 77 
                                       s++ +++ ++qE +val l++ki    +     I+S++ p++lkGy ++E+++++ave ++++++++r +v g++++
  gi|385806313|ref|YP_005842711.1|  22 SFYLIRTVSRQELNVALLLERKI----ALSHSPIYSIILPPKLKGYLVLESQKSSAVEAVIKDMQHLRKRVYGTLTV 94 
                                       69********************4....333459******************************************** PP

                          Spt5-NGN  78 kEvedl 83 
                                       ++ve++
  gi|385806313|ref|YP_005842711.1|  95 EDVERM 100
                                       ***986 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.4   8.5e-10     3e-06       1      30 [.     112     141 ..     112     143 .. 0.92

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 8.5e-10
                                       TTSEEEESSSTTTTCEEEEEEEETTTTEEE CS
                               KOW   1 pGdhVkVvsGphkGktGkVvkvdqhkvrVf 30 
                                       pGd+V+V++Gp+ G +++V ++d+ k  V+
  gi|385806313|ref|YP_005842711.1| 112 PGDTVEVIAGPFQGIKAQVIEIDKVKQEVV 141
                                       8***********************997665 PP

>> CdiI_3  CDI immunity proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.31   1.1e+03      37      55 ..      26      44 ..      15      50 .. 0.81
   2 ?   10.9   0.0   8.9e-05      0.32      12      50 ..      72     110 ..      65     119 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.31
                            CdiI_3 37 lrllirQeiglellvplAl 55
                                      +r+  rQe+ ++ll+++ +
  gi|385806313|ref|YP_005842711.1| 26 IRTVSRQELNVALLLERKI 44
                                      5666789999999998866 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 8.9e-05
                            CdiI_3  12 edasrlvekveelrkkpleeltveDlrllirQeiglell 50 
                                       +  +++ + +++lrk+  + ltveD+ ++ + +  +e+l
  gi|385806313|ref|YP_005842711.1|  72 SAVEAVIKDMQHLRKRVYGTLTVEDVERMTKPKATIETL 110
                                       3456788999*******************9988888877 PP

>> YajC  Preprotein translocase subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   3.9e-05      0.14      23      72 ..      98     154 ..      88     161 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.9e-05
                              YajC  23 kkqkehkemlasLkkGdeVvtig....GivGkvvkvd..ddevtveigesa.gvkik 72 
                                        ++ + k+++++L++Gd V  i     Gi ++v+++d  ++ev++ i esa   k++
  gi|385806313|ref|YP_005842711.1|  98 ERMTKPKATIETLNPGDTVEVIAgpfqGIKAQVIEIDkvKQEVVLNILESAyPLKVT 154
                                       5788899************887634446999****9965556888887666555555 PP

>> DUF1318  Protein of unknown function (DUF1318)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   8.9e-05      0.32      21      70 ..      60     103 ..      58     124 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.9e-05
                           DUF1318  21 adGylgvvkaaaaearalvkaiNakRkavYteiAaknglsleevaklaae 70 
                                        +Gyl + ++++++++a++k++ + Rk+vY ++      ++e+v++++  
  gi|385806313|ref|YP_005842711.1|  60 LKGYLVLESQKSSAVEAVIKDMQHLRKRVYGTL------TVEDVERMTKP 103
                                       58****************************876......44555554443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       788  (0.0439511); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); 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: 0.58u 0.34s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 944.05
//
Query:       gi|385806314|ref|YP_005842712.1|  [L=167]
Description: 50S ribosomal protein L11 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-14   53.2   0.2    3.2e-14   53.2   0.2    2.0  3  Ribosomal_L11  Ribosomal protein L11, RNA binding domain
  ------ inclusion threshold ------
      0.018   15.3   0.5        5.2    7.4   0.1    3.0  3  Poly_export    Polysaccharide biosynthesis/export protein
      0.061   13.1   0.0        1.8    8.4   0.0    2.3  2  CW_7           CW_7 repeat
       0.16   11.5   0.1       0.63    9.6   0.0    2.0  2  Phage_P2_GpE   Phage P2 GpE


Domain annotation for each model (and alignments):
>> Ribosomal_L11  Ribosomal protein L11, RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.88     4e+03      26      37 ..      12      23 ..       7      27 .. 0.78
   2 ?   -3.2   0.1       2.7   1.2e+04      35      43 ..      31      39 ..      30      50 .. 0.63
   3 !   53.2   0.2   7.2e-18   3.2e-14       1      70 []      68     136 ..      68     136 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.88
                                      XXEEEEHHHHHH CS
                     Ribosomal_L11 26 tvGtvslkqvye 37
                                      ++G+vs k++ e
  gi|385806314|ref|YP_005842712.1| 12 KTGNVSQKDLEE 23
                                      679999988776 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.7
                                      HHHHHHHHG CS
                     Ribosomal_L11 35 vyeIAkiKk 43
                                      v eIA+   
  gi|385806314|ref|YP_005842712.1| 31 VDEIAEKIN 39
                                      557776544 PP

  == domain 3  score: 53.2 bits;  conditional E-value: 7.2e-18
                                       ---SHHHHHHHHHTXSSXXSSTTTSXXEEEEHHHHHHHHHHHGGGHTXS.SHHHHHHHHHHHHCTTTEEE CS
                     Ribosomal_L11   1 ktPptsylLkkaagiekgsgkpgketvGtvslkqvyeIAkiKksdlnaalsleaavksilgtArsmGikV 70 
                                       k P+++ lL+  a++++ sg p +++vG+++++++ e+A i+k++l ++ +l++avk+ lg+Ars+G++V
  gi|385806314|ref|YP_005842712.1|  68 KPPTVTELLLWKAKAKEPSGDPAHKKVGDIKVADLAEVAIIMKNELLTR-DLKKAVKMLLGSARSIGLTV 136
                                       68999**************************************999988.******************98 PP

>> Poly_export  Polysaccharide biosynthesis/export protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1    0.0012       5.2      39      81 ..      13      54 ..       9      56 .. 0.80
   2 ?    0.2   0.0      0.19   8.7e+02      46      56 ..      93     103 ..      84     125 .. 0.65
   3 ?    4.1   0.0     0.012        53      50      69 ..     134     153 ..     132     163 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0012
                       Poly_export 39 dGtIslPllGkikvaGltveelreeieeklskylkdpqvtVrv 81
                                       G++s   l + k  G  v+e++e+i +++   lk+ +v++++
  gi|385806314|ref|YP_005842712.1| 13 TGNVSQKDLEEAKKYGFNVDEIAEKINKRIGA-LKEKEVKITI 54
                                      57777788888888899*************66.4776666654 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.19
                       Poly_export  46 llGkikvaGlt 56 
                                        +G+ikva+l 
  gi|385806314|ref|YP_005842712.1|  93 KVGDIKVADLA 103
                                       68999999874 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.012
                       Poly_export  50 ikvaGltveelreeieekls 69 
                                       + v+G+ ++++++e+e+  +
  gi|385806314|ref|YP_005842712.1| 134 LTVEGKDPKDVQKELESGTY 153
                                       679************99874 PP

>> CW_7  CW_7 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.032   1.4e+02      23      39 ..      25      41 ..      19      42 .. 0.87
   2 ?    8.4   0.0   0.00039       1.8      15      35 ..     127     147 ..     126     149 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.032
                              CW_7 23 taaGydYdaVQarVNel 39
                                      +++G++ d++ +++N++
  gi|385806314|ref|YP_005842712.1| 25 KKYGFNVDEIAEKINKR 41
                                      578**********9986 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00039
                              CW_7  15 GaeRkkrLtaaGydYdaVQar 35 
                                       G++R   Lt +G d ++VQ++
  gi|385806314|ref|YP_005842712.1| 127 GSARSIGLTVEGKDPKDVQKE 147
                                       899****************97 PP

>> Phage_P2_GpE  Phage P2 GpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00014      0.63      17      35 ..      69      87 ..      66      88 .. 0.84
   2 ?   -2.6   0.1      0.96   4.3e+03       1       7 [.      99     105 ..      99     105 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00014
                      Phage_P2_GpE 17 dmsLtELldWRerArrRsg 35
                                      + ++tELl W+ +A++ sg
  gi|385806314|ref|YP_005842712.1| 69 PPTVTELLLWKAKAKEPSG 87
                                      5589**********99776 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.96
                      Phage_P2_GpE   1 MADiAvv 7  
                                       +AD+A v
  gi|385806314|ref|YP_005842712.1|  99 VADLAEV 105
                                       5999965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       993  (0.0553851); expected 358.6 (0.02)
Passed bias filter:                      657  (0.0366445); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 944.04
//
Query:       gi|385806315|ref|YP_005842713.1|  [L=219]
Description: 50S ribosomal protein L1P [Fervidicoccus fontis Kam940]
Scores for complete 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-34  118.1   6.3    5.1e-34  117.8   6.3    1.1  1  Ribosomal_L1  Ribosomal protein L1p/L10e family
  ------ inclusion threshold ------
      0.044   14.0   0.8        0.6   10.3   0.1    2.4  2  SpmSyn_N      S-adenosylmethionine decarboxylase N -terminal


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 !  117.8   6.3   5.7e-38   5.1e-34       2     204 .]      20     212 ..      15     212 .. 0.95

  Alignments for each domain:
  == domain 1  score: 117.8 bits;  conditional E-value: 5.7e-38
                                       HHHS-SSS--EEEEEEEESSS-TTSGGG--EEEEE-STSTSSCS-EEEEE-HHHHH...HHHHTT..-SEEETCHHH CS
                      Ribosomal_L1   2 lkhakkkfdesveialnlttkkpkkadqrkpgkipLphplgkevkiclitkdpqaeyakeakeagriakviglkklk 78 
                                        k  k++f++s+e++++++ ++pkk++ ++++ + Lp+  +ke +ic++++++ a    +ak+ + +++vi+   l 
  gi|385806315|ref|YP_005842713.1|  20 EKSPKRNFKQSIEMIITFKEIDPKKPEFKIRENVFLPNAPKKEPEICIVADGDLAL---QAKNLN-VKQVIDKAILD 92 
                                       566699*************************************************9...999999.*********** PP

                                       HHHT-HHHHHHTCCH-SEEEEEGGGHHHHHHHCHHHHGGGT-S-ECC..CT.BTS-HHHHHHHHCTTEEEEE-TTTS CS
                      Ribosomal_L1  79 kkyksfeakrkllkefdlfladdrimpllpklLGkvfgkrkkmPipvltkgtvkedvkkevekalkstvvvrldkgt 155
                                       +  k++++ +k++k++d++l++ ++m +++++LG+ +g+r+k Pip       + d+++ +e+++k +  vr++++ 
  gi|385806315|ref|YP_005842713.1|  93 EISKDKKKAKKIAKNCDVILVQTDLMSQVGRTLGPALGPRGKAPIPLPP----RSDLQSILERYKKIA-IVRIKDQP 164
                                       ***********************************************44....469**********66.5566**** PP

                                       EEEEEEEETTSSHHHHHHHHHHHHHHHHHTSTTTSGSEEEEEEEETTS- CS
                      Ribosomal_L1 156 clsvkvGklsftaeelaeNieavvkalvekvpkkwkniksiylkttmsp 204
                                        ++vk+G+ + t +el+eN+ a+++ +++k  k  +n+ +iy k +m+p
  gi|385806315|ref|YP_005842713.1| 165 QIQVKIGTEDNTLKELTENAIAILNVIENK-LKTLSNVDAIYFKKAMGP 212
                                       ***************************999.7889************98 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 ?    1.7   0.1     0.033     3e+02      66      87 ..       5      26 ..       1      34 [. 0.83
   2 ?   10.3   0.1   6.7e-05       0.6      32      88 ..     149     207 ..     142     215 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.033
                          SpmSyn_N 66 dkllnkveerlkellegsikrv 87
                                       +l +k+e+ l+e+le+s kr 
  gi|385806315|ref|YP_005842713.1|  5 TTLTEKIENALREVLEKSPKRN 26
                                      578899*********9999884 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 6.7e-05
                          SpmSyn_N  32 igkngsfaslriyphGlvlldlqsyeedekaq..evdkllnkveerlkellegsikrvk 88 
                                       +++  ++a++ri     + + + + ++  k+   +   +ln +e++lk+l++ ++   k
  gi|385806315|ref|YP_005842713.1| 149 LERYKKIAIVRIKDQPQIQVKIGTEDNTLKELteNAIAILNVIENKLKTLSNVDAIYFK 207
                                       566778999*****999999999999877654337789************987665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1013  (0.0565006); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.50
# Mc/sec: 1307.54
//
Query:       gi|385806316|ref|YP_005842714.1|  [L=347]
Description: 50S ribosomal protein L10 [Fervidicoccus fontis Kam940]
Scores for 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-18   64.6   0.1    1.2e-17   63.7   0.1    1.5  1  RL10P_insert   Insertion domain in 60S ribosomal protein L10P
    8.5e-14   51.5   2.3    8.5e-14   51.5   2.3    1.9  2  Ribosomal_L10  Ribosomal protein L10
  ------ inclusion threshold ------
      0.058   14.0   3.3       0.12   13.0   3.3    1.5  1  U1snRNP70_N    U1 small nuclear ribonucleoprotein of 70kDa MW
       0.34   11.4   1.7       0.41   11.2   0.4    1.8  2  DUF4724        Domain of unknown function (DUF4724)


Domain annotation for each model (and alignments):
>> RL10P_insert  Insertion domain in 60S ribosomal protein L10P
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.7   0.1   2.6e-21   1.2e-17       1      71 []     120     190 ..     120     190 .. 0.99

  Alignments for each domain:
  == domain 1  score: 63.7 bits;  conditional E-value: 2.6e-21
                      RL10P_insert   1 AraGtiAtedviipagplelaPgsiepeLrklglptklkkGkivleedylvckkGetltseqaqlLklLgi 71 
                                       A+aG + ++++ +++++++l+Pg++ + + kl++ptk+++G+i++ ++++++k G++++++ a++L++Lgi
  gi|385806316|ref|YP_005842714.1| 120 AKAGMKVDREIAVEPMDTHLQPGPLLSAFGKLKIPTKVQNGTIWIAKRTVLAKPGDVISADLASMLQRLGI 190
                                       9*********************************************************************9 PP

>> Ribosomal_L10  Ribosomal protein L10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.5   2.3   1.9e-17   8.5e-14       4      97 ..      15     113 ..      13     115 .. 0.93
   2 ?   -7.3   5.2         4   1.8e+04       2      19 ..     318     335 ..     317     338 .. 0.75

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 1.9e-17
                                       CCHCCCCCCCCCCCTTSSEEEEEE-TTS-HHHHHHCCCHHHHH...GCEEEEESCCCCCCCCHCCTSS.S..SCGCC CS
                     Ribosomal_L10   4 ekKeelvkelkellkkyksvvvvdyegltvaqlqelRkklren...gaelkvvKntlmrrAleetgeeek..lkell 75 
                                        +Kee v+el +l+k+y ++ ++d ++++++ +q+++  lr++    + +k vKn+l+ +Ale+++ + k  lke +
  gi|385806316|ref|YP_005842714.1|  15 SWKEEEVNELVKLMKEYPVLGIIDAKDVPASLIQKIKVMLRDKvddAIVIKSVKNNLFLIALEKADVKGKekLKEVI 91 
                                       79***********************************99999998899****************98863356***** PP

                                       SSSEEEEEESS-TCHHHHCCCC CS
                     Ribosomal_L10  76 kgpvalvftnedpvalakvlee 97 
                                       k + ++vf++ +p+ la ++++
  gi|385806316|ref|YP_005842714.1|  92 KDQKIFVFSKLNPFMLAAMINR 113
                                       ***************9999876 PP

  == domain 2  score: -7.3 bits;  conditional E-value: 4
                                       SCCCHCCCCCCCCCCCTT CS
                     Ribosomal_L10   2 tkekKeelvkelkellkk 19 
                                       + ekKee  +e k+ l++
  gi|385806316|ref|YP_005842714.1| 318 KEEKKEEKAEEEKKELSE 335
                                       678888888888888776 PP

>> U1snRNP70_N  U1 small nuclear ribonucleoprotein of 70kDa MW N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   3.3   2.8e-05      0.12      34      84 ..     283     336 ..     266     340 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.8e-05
                       U1snRNP70_N  34 kkitGvaaflselke....deeeqeppektetkeekkererkekkekkeekleea 84 
                                       k+++ vaa+ ++ ke       + + p++ e keekke++++ek+e+++++l e+
  gi|385806316|ref|YP_005842714.1| 283 KAYSIVAAMGDKAKElgieG-VQLQRPPEGEKKEEKKEEKKEEKAEEEKKELSEE 336
                                       56777777777777777742.3334455589999999999999999999988765 PP

>> DUF4724  Domain of unknown function (DUF4724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0         2   8.8e+03      22      33 ..      91     102 ..      65     109 .. 0.68
   2 ?   11.2   0.4   9.1e-05      0.41      46      86 ..     287     327 ..     272     333 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2
                           DUF4724  22 vkvkPlfvqskt 33 
                                       +k + +fv sk+
  gi|385806316|ref|YP_005842714.1|  91 IKDQKIFVFSKL 102
                                       444445555555 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 9.1e-05
                           DUF4724  46 htssldskyvdvvsdqiflslspkgresekpkeekskekql 86 
                                         +++  k ++ + + + l+  p+g+++e++keek++ek  
  gi|385806316|ref|YP_005842714.1| 287 IVAAMGDKAKELGIEGVQLQRPPEGEKKEEKKEEKKEEKAE 327
                                       556677799999999999******************99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1525  (0.0850577); expected 358.6 (0.02)
Passed bias filter:                      821  (0.0457917); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.71u 0.38s 00:00:01.08 Elapsed: 00:00:00.54
# Mc/sec: 1921.29
//
Query:       gi|385806317|ref|YP_005842715.1|  [L=99]
Description: 50S ribosomal protein L12 [Fervidicoccus fontis Kam940]
Scores for complete 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   71.8  12.5    6.1e-20   71.6  12.5    1.0  1  Ribosomal_60s  60s Acidic ribosomal protein
    0.00035   20.5   3.3       0.29   11.1   0.8    2.2  2  PepSY_2        Peptidase propeptide and YPEB domain
      0.001   19.3   2.0     0.0016   18.8   0.0    1.9  2  EF-hand_14     EF-hand domain
     0.0034   17.3   0.1     0.0049   16.8   0.1    1.2  1  TFIID_30kDa    Transcription initiation factor TFIID 23-30kDa
  ------ inclusion threshold ------
      0.025   15.2   1.3      0.034   14.8   1.3    1.1  1  DUF3824        Domain of unknwon function (DUF3824)
      0.058   13.6   2.8      0.086   13.0   2.5    1.4  2  CPSF100_C      Cleavage and polyadenylation factor 2 C-termin


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 !   71.6  12.5     2e-23   6.1e-20       2      88 .]       9      98 ..       8      98 .. 0.90

  Alignments for each domain:
  == domain 1  score: 71.6 bits;  conditional E-value: 2e-23
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.X..X CS
                     Ribosomal_60s  2 ptaenikkvlkaagveveaarvkllvkalegkdieellangaaklaaaaaaaaaaaaaaaaaaaaeekkkeeeeeE..e 78
                                      +++enikkvl++ag++v+++rvk+lv+al++ +i+e+l+ +   +a a+aa+aaa a ++++++++e+k+eee++E  e
  gi|385806317|ref|YP_005842715.1|  9 INEENIKKVLESAGIQVDDVRVKALVAALQQINIDEVLKSALVTGAVAPAAPAAAPASEEKKEEKKEEKAEEEKKElsE 87
                                      89****************************************9999999999999999999999999999999996425 PP

                                      --SS--.STTT CS
                     Ribosomal_60s 79 edddmG.fgLF 88
                                      e+   G ++LF
  gi|385806317|ref|YP_005842715.1| 88 EELSSGlGALF 98
                                      55599999999 PP

>> PepSY_2  Peptidase propeptide and YPEB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.1   0.00025      0.75      27      51 ..       6      30 ..       3      35 .. 0.89
   2 !   11.1   0.8   9.8e-05      0.29       3      35 ..      49      82 ..      47      93 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00025
                           PepSY_2 27 adwlpreklvakleaqGykvkkiev 51
                                      ++++++e++++ le +G +v++++v
  gi|385806317|ref|YP_005842715.1|  6 KKDINEENIKKVLESAGIQVDDVRV 30
                                      67899******************98 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 9.8e-05
                           PepSY_2  3 alalalallaaaAlA.grrdtdspkadwlprekl 35
                                      al++ ++++aa+A A ++++++++k+++  +e+ 
  gi|385806317|ref|YP_005842715.1| 49 ALVTGAVAPAAPAAApASEEKKEEKKEEKAEEEK 82
                                      6777888899999995455555555555544443 PP

>> EF-hand_14  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   5.3e-07    0.0016      12      51 ..       4      43 ..       1      55 [. 0.85
   2 ?   -0.1   0.6       0.4   1.2e+03      48      66 ..      70      88 ..      64      94 .. 0.59

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 5.3e-07
                        EF-hand_14 12 eetdklsvakllkaLaetGirkdDpRLkellkklkkveke 51
                                      + +++++ +++ k+L+++Gi+ dD R+k l+ +l++++ +
  gi|385806317|ref|YP_005842715.1|  4 SAKKDINEENIKKVLESAGIQVDDVRVKALVAALQQINID 43
                                      5667899999*************************98765 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.4
                        EF-hand_14 48 vekekseaeesetleldre 66
                                       e++k+e+ e e++el+ e
  gi|385806317|ref|YP_005842715.1| 70 KEEKKEEKAEEEKKELSEE 88
                                      3333345566666777666 PP

>> TFIID_30kDa  Transcription initiation factor TFIID 23-30kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   1.6e-06    0.0049       8      44 ..      14      50 ..      11      53 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.6e-06
                       TFIID_30kDa  8 tayyLekaGletsDprlarlvsLaaqKFisdiaadAy 44
                                      ++ +Le+aG++ +D+r++ lv+   q  i +++++A+
  gi|385806317|ref|YP_005842715.1| 14 IKKVLESAGIQVDDVRVKALVAALQQINIDEVLKSAL 50
                                      5779**********************99999999996 PP

>> DUF3824  Domain of unknwon function (DUF3824)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   1.3   1.1e-05     0.034       9      55 ..      45      89 ..      40      93 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.1e-05
                           DUF3824  9 lAeaalaaggaglAaheyakrrerkkaerererrreedeardsyeee 55
                                      + + al++g+++ Aa  +a   e+kk+e+++e+ +ee+  ++ +eee
  gi|385806317|ref|YP_005842715.1| 45 VLKSALVTGAVAPAAPAAAPASEEKKEEKKEEKAEEEK--KELSEEE 89
                                      55788999999999999988888887777777664444..4666665 PP

>> CPSF100_C  Cleavage and polyadenylation factor 2 C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.8   5.3e+03     113     125 ..      13      25 ..       8      29 .. 0.78
   2 ?   13.0   2.5   2.9e-05     0.086       6      62 ..      32      83 ..      24      94 .. 0.58

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.8
                         CPSF100_C 113 dLkkallssgikA 125
                                       ++kk+l s+gi++
  gi|385806317|ref|YP_005842715.1|  13 NIKKVLESAGIQV 25 
                                       5788888888875 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 2.9e-05
                         CPSF100_C  6 sLvksLkwqkveg.levatvtgeleieeea....eeaeeeekeeeeeeeeeeeeeeeaskkq 62
                                      +Lv++L+  ++++ l+ a vtg + +++ a    +    eek+ee++ee++eee+      +
  gi|385806317|ref|YP_005842715.1| 32 ALVAALQQINIDEvLKSALVTGAVAPAAPAaapaS----EEKKEEKKEEKAEEEK------K 83
                                      799999999999999*********96554222211....1111111111111111......1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2552  (0.142339); expected 358.6 (0.02)
Passed bias filter:                     1208  (0.0673769); expected 358.6 (0.02)
Passed Vit filter:                       117  (0.00652574); expected 17.9 (0.001)
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 0.38s 00:00:00.97 Elapsed: 00:00:00.52
# Mc/sec: 573.91
//
Query:       gi|385806318|ref|YP_005842716.1|  [L=843]
Description: alanyl-tRNA synthetase [Fervidicoccus fontis Kam940]
Scores for complete 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-95  319.2   0.0    3.8e-94  316.2   0.0    2.3  1  tRNA-synt_2c  tRNA synthetases class II (A)
    6.9e-11   42.1   0.8    1.8e-10   40.8   0.8    1.8  1  tRNA_SAD      Threonyl and Alanyl tRNA synthetase second addi
    2.5e-09   37.7   0.7    2.5e-09   37.7   0.7    2.2  2  DHHA1         DHHA1 domain
     0.0032   16.8   0.0       0.01   15.1   0.0    1.9  1  tRNA-synt_2e  Glycyl-tRNA synthetase alpha subunit
  ------ inclusion threshold ------
      0.038   14.2   1.6       0.14   12.3   1.6    2.0  1  Med30         Mediator complex subunit 30
       0.11   12.4   0.2       0.32   10.9   0.2    1.8  1  Sec20         Sec20
       0.46   10.1   0.0       0.46   10.1   0.0    3.8  4  VASP_tetra    VASP tetramerisation domain


Domain annotation for each model (and alignments):
>> tRNA-synt_2c  tRNA synthetases class II (A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  316.2   0.0   1.5e-97   3.8e-94       7     550 ..       1     521 [.       1     523 [. 0.86

  Alignments for each domain:
  == domain 1  score: 316.2 bits;  conditional E-value: 1.5e-97
                                       HHHHHCTT-EEE----SS-SSSTTCSS--SGGGGGHHHHTTSSCGGSSSEEEEEEEEE-EETTEEGGGGTTTS.SS- CS
                      tRNA-synt_2c   7 ldfFekkgHtvvksssvvpendptllfvnAgmaqfkpiflgkeakpklkravnsQkciRagGkhnDlenVGkt.arH 82 
                                       ++fFek+gH+++   +vv++++++l++++A+++ f+p ++++   p+++++v sQ+ciR++    D++nVG t +rH
  gi|385806318|ref|YP_005842716.1|   1 MTFFEKRGHKILDPRPVVARWREDLYLTIASIVLFQPHVTSGLVPPPANPLVVSQPCIRLE----DIDNVGLTmGRH 73 
                                       68***********************************************************....******9967** PP

                                       -SEEEEEEEEESS......SS-HHHHHHHHHHHHHTTTT--GGGEEEEEETTEH..HHHHHHHHTTTTEGGGEEEE- CS
                      tRNA-synt_2c  83 hTfFeMlGnfsfg......dYfkeeaiefawelltkelgldkerlyvtvfeedd..eaveiweklvgvpeerilrfg 151
                                       +T+FeM G+++f+      +Y+k+e++ +++e++tke+g+++e l+++++++++  +a++ +e +vg+ e ++l+f 
  gi|385806318|ref|YP_005842716.1|  74 LTLFEMGGHHAFNerngkfIYWKDETVRYSFEFFTKEIGIPPELLVFKESWWEGggNAGPSFEVTVGGLEPATLVF- 149
                                       *****************************************************999********************. PP

                                       HHHHEEESSSSEEEEEEEEEEEECETTSHHCHCCCCTTCTCCHEEEEEEEEEEEEEESTTSHEEEEEEEEEEEEEEH CS
                      tRNA-synt_2c 152 ekdnfwemgdtgpcgpcseiyydrgeeigkrkaaseveadddrvleiwnlvfmqfnreedgtlkpLpkksidtGmgl 228
                                         +++++ g++ + +p +++++++g e+ ++  +++++a  +++ +++n   ++ + e      + pk+   +    
  gi|385806318|ref|YP_005842716.1| 150 --MQYKKNGNNLEPIPLQIVDTGYGIERIAWFTQKTPTAFHAIYGDLVNEFRKKLGLE------EPPKEYYKA---A 215
                                       ..************************************77777777777655555554......334444443...4 PP

                                       HHHHHHHTTHSSGGGSCCTHHHHHHHHHHHT--TCSTCCHHHHHHHHHHHHHHHHHHHHTT--SSSSHHHHHHHHHH CS
                      tRNA-synt_2c 229 erlvavLqevrsnydtdlfvpvieaieeisgatyedkdetdealrviaDHvralafaladGvvpsnegrgYvlRrll 305
                                        r v +L    ++   ++f++ i++ +   +++ ++  + d++l  i DH ++la++l+dG+vpsn+g+gY++R++l
  gi|385806318|ref|YP_005842716.1| 216 FRYVGLLDPSSEQ-SVSMFIKNISKHSGFDEESVKAFLQNDMKLFTILDHSKTLAYMLGDGIVPSNQGEGYLARLVL 291
                                       5666666554443.445555555555555555556667789************************************ PP

                                       HHHHHHHHHTT-SSTHHHHHHHHHHHHHTTTGCCHHCCHHHHHHHHHHHHHHHHCCHHHHH.HHHHHHHHHCCCCSE CS
                      tRNA-synt_2c 306 RravrhakkLglkekflaklvavvvevlgdvypelkekeekveeiieeEeerFakTlerGl.klleelikklkkkke 381
                                       Rra+r ++ ++ + + +++ ++ ++e  ++   +lke ++++ ++++ E+++F + +++   kll+ ++++      
  gi|385806318|ref|YP_005842716.1| 292 RRALRTLYLINPEID-FTDFIEKQIEYWKQDNYKLKEFHNYIINVVQYEQKKFYELVKEKIpKLLQTVVSN-P---- 362
                                       ***************.999***********999**********************9987651444444443.3.... PP

                                       EXHHHHHHHHHCHXXXHHHHHHHHHCTTXEEXHHHHHHHHHHHHHHHCCHHSXSSXXXXXXXXTTSHCHHCCTSTTT CS
                      tRNA-synt_2c 382 lsgedafkLydtyGfPvdltkeiaeekglkvdiegfekameeqrerskkekkekklikkdvealkelkkteeflgye 458
                                        + e+  k+y   G+P++l+ + a++k+++++++  ++++  +re+s+ +  +k+++++ +e l++++ te  l++ 
  gi|385806318|ref|YP_005842716.1| 363 -NFETFEKIYKEQGIPPELIVNEAKKKNISIEVPFDFYSKI-ARESSRPKLGKKQEVTTRLEWLNNIPPTEL-LFHV 436
                                       .35566689************************98777665.56677777777777999********99998.5555 PP

                                       XXXXXXTSXXXXXXSEEEEEEEEEETTEEEESEEXXXXSSSSCSXXXEEEEESSEEEEESEEEEETTEEEEEXSS.. CS
                      tRNA-synt_2c 459 eleaeakvlallkdkefveeveegeevgvvLdrTpfYaesGGqigDeGliekegaefrvkdvqkakgvvlhkgkl.. 533
                                       +             +e+ +++ + +e+++vLd+T fY+ +GGq +D+G ie +g+  +v++v+k+++ v+h  +   
  gi|385806318|ref|YP_005842716.1| 437 D----------PYLRESDAKILAAKENMLVLDKTIFYPLGGGQSSDKGSIEVDGKIYNVVNVEKYDEHVIHYLDKni 503
                                       5..........3458999************************************************99999876522 PP

                                       ..XSXXXTTSEEEEEEXH CS
                      tRNA-synt_2c 534 .eegklkvgdkvkaevde 550
                                        ++++  +g + k+++d+
  gi|385806318|ref|YP_005842716.1| 504 eKDAEKLIGSSCKLKIDW 521
                                       122234456666666666 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 !   40.8   0.8   6.9e-14   1.8e-10       1      43 [.     622     664 ..     622     665 .. 0.94

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 6.9e-14
                                       EEEEEETT.EEEEESS---SBGGGC-SEEEECCECCCTCEEEE CS
                          tRNA_SAD   1 vrvvsiGdisvelCgGtHvpnTgeIgafkilseesiakglrRI 43 
                                       +r+v+i  ++ve+C GtHv+nTge+g +ki++  + ++g+ R 
  gi|385806318|ref|YP_005842716.1| 622 IRIVEIPGHDVEACFGTHVSNTGEVGGIKIINVAKLQDGIIRF 664
                                       79****659******************************9996 PP

>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.2      0.82   2.1e+03      11      62 ..     311     361 ..     308     369 .. 0.70
   2 !   37.7   0.7   9.8e-13   2.5e-09       1     137 [.     701     838 ..     701     839 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.82
                                       HHHHHHCHHH.HHHHHHHHHHHHTCEEECTCEEEEEECHCCHHHHHHHHHHHH CS
                             DHHA1  11 lekeleelke.alaklkaeellekaeevkgvkvlvaevgeewdagalgiaadk 62 
                                       +ek++e +k+   + +++ +++ ++ ++ ++k ++  v +e+ ++ l++++++
  gi|385806318|ref|YP_005842716.1| 311 IEKQIEYWKQdNYKLKEFHNYIINVVQY-EQKKFYELV-KEKIPKLLQTVVSN 361
                                       6778876655145666788999999888.777777777.66667777777765 PP

  == domain 2  score: 37.7 bits;  conditional E-value: 9.8e-13
                                       HHHHCHHHHHHHHHHHCHHHHHHHHHHHHHHHTCEEECTCEEEEEECHCCHHHHHHHHHHHHHHTHGBTTCEEEEEE CS
                             DHHA1   1 leslneerkelekeleelkealaklkaeellekaeevkgvkvlvaevgeewdagalgiaadklksklkkpvivfvak 77 
                                       +++ln+e ++ ++ l+ +++  +++ +e+l +kae ++g  ++v ++ e  d   + ++  ++  ++ + +++ ++k
  gi|385806318|ref|YP_005842716.1| 701 VKKLNQEFEQMKNRLNLYRDIYSEVFRENLKSKAEVINGIRLFVYKD-EIDDEEFTTELLKEITREMREIIVIRIFK 776
                                       689********************************************.88888999999999999888888888888 PP

                                       EECT.EEEEEEEESSH.SS-HHHHHHHHHHHTTCCEEEE.TCEEEEEEEHCHHHHHHHHHHHH CS
                             DHHA1  78 eegd.kvkvsarskkd.gvdagelakeaaaklgggGGGH.dlAaGagipaekleealealeea 137
                                       + +   + vs +  ++ +++a e++k+  +  g +GGG+ d A++++ ++ +++++ + ++e+
  gi|385806318|ref|YP_005842716.1| 777 NAKGtSIEVSEGRESSeKLNATEIIKA-LSSYGCKGGGKkDHAQCTSEQEINVDDVWKMVKEL 838
                                       87778*****9988889**********.*****************************999997 PP

>> tRNA-synt_2e  Glycyl-tRNA synthetase alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   4.1e-06      0.01     113     179 ..     125     193 ..     109     233 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.1e-06
                                       EEEGGGTEEEEEEEEEETTCEEEEEEEEE.EETTEE-SS--EEE...EEEHHHHHHHHCT-SSGGG-ECCT CS
                      tRNA-synt_2e 113 WesptlGawGlGwevwldGmeitqftYfq.qvgglelkpvsvei...tyGleRlamylqevdnvydlewne 179
                                       We    G  G  +ev + G+e + + ++q +  g +l+p++  i    yG+eR+a + q++ + +   + +
  gi|385806318|ref|YP_005842716.1| 125 WE--GGGNAGPSFEVTVGGLEPATLVFMQyKKNGNNLEPIPLQIvdtGYGIERIAWFTQKTPTAFHAIYGD 193
                                       44..4589999*****************9557899*****98773336************98888777755 PP

>> Med30  Mediator complex subunit 30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.6   5.5e-05      0.14      41     125 ..     695     778 ..     672     784 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.5e-05
                             Med30  41 hqaqdrkkklqeqlrqlkvlfkkLrliYekckenc..qgleevpiesLipyvdeekskreerkkseevkqlkeerke 115
                                           +r kkl+ +++q+k++ +  r iY ++ ++   ++ e ++   L  y+de+    +e+ ++e +k+++ e++e
  gi|385806318|ref|YP_005842716.1| 695 PLLLNRVKKLNQEFEQMKNRLNLYRDIYSEVFRENlkSKAEVINGIRLFVYKDEI---DDEEFTTELLKEITREMRE 768
                                       5556799*********************998655448899999999*******88...6666778999********* PP

                             Med30 116 lleklkeknk 125
                                       ++     kn+
  gi|385806318|ref|YP_005842716.1| 769 IIVIRIFKNA 778
                                       *998888886 PP

>> Sec20  Sec20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2   0.00013      0.32      36      81 ..     699     744 ..     677     746 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00013
                             Sec20  36 kslekleeeykqvedvlsrskklvkklerrdktdkllvflalglfl 81 
                                       + ++kl++e+ q+++ l+  +++ + + r++++ k  v+ ++ lf+
  gi|385806318|ref|YP_005842716.1| 699 NRVKKLNQEFEQMKNRLNLYRDIYSEVFRENLKSKAEVINGIRLFV 744
                                       6799*****************************************8 PP

>> VASP_tetra  VASP tetramerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.3      0.41     1e+03      11      19 ..     682     690 ..     679     691 .. 0.87
   2 ?   10.1   0.0   0.00018      0.46       3      31 ..     707     741 ..     705     742 .. 0.80
   3 ?    0.7   2.8      0.15   3.8e+02       5      19 ..     752     766 ..     748     769 .. 0.84
   4 ?   -2.7   0.0       1.8   4.5e+03      25      30 ..     799     804 ..     798     806 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.41
                        VASP_tetra  11 ILeEvrkEL 19 
                                       IL Ev kE+
  gi|385806318|ref|YP_005842716.1| 682 ILNEVSKEV 690
                                       9*******6 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00018
                        VASP_tetra   3 DlErlK......qEILeEvrkELqKvKeEIIeAir 31 
                                       ++E++K      ++I +Ev +E  K K E+I+ ir
  gi|385806318|ref|YP_005842716.1| 707 EFEQMKnrlnlyRDIYSEVFRENLKSKAEVINGIR 741
                                       67777744433359******************998 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.15
                        VASP_tetra   5 ErlKqEILeEvrkEL 19 
                                       E +  E+L+E+ +E+
  gi|385806318|ref|YP_005842716.1| 752 EEFTTELLKEITREM 766
                                       78889*********8 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 1.8
                        VASP_tetra  25 EIIeAi 30 
                                       EII+A+
  gi|385806318|ref|YP_005842716.1| 799 EIIKAL 804
                                       9***98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (843 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1303  (0.0726756); expected 358.6 (0.02)
Passed bias filter:                      765  (0.0426683); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); 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: 0.92u 0.36s 00:00:01.28 Elapsed: 00:00:00.55
# Mc/sec: 4649.30
//
Query:       gi|385806319|ref|YP_005842717.1|  [L=238]
Description: hypothetical protein FFONT_1277 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-27   96.4   0.1    2.7e-27   95.8   0.1    1.2  1  DUF5616   Domain of unknown function (DUF5616)
    7.1e-16   57.6   0.3    1.2e-15   56.9   0.3    1.4  1  DUF434    Protein of unknown function (DUF434)
  ------ inclusion threshold ------
      0.019   14.9   0.0      0.031   14.2   0.0    1.4  1  DUF2621   Protein of unknown function (DUF2621)


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 !   95.8   0.1   4.5e-31   2.7e-27       2     138 ..      72     213 ..      71     215 .. 0.93

  Alignments for each domain:
  == domain 1  score: 95.8 bits;  conditional E-value: 4.5e-31
                           DUF5616   2 eelkgkelliDGfNvlitlesalsgevlllcdDgviRDlagvrgkyklveet.eealelilellkelkvkkvifllD 77 
                                       ++++gk+++iD +Nv+ t++ a++g  +++c Dg+iRDla+ +g+ k+  ++ e+++e + e l e+++++v+++ D
  gi|385806319|ref|YP_005842717.1|  72 SQVEGKKIAIDYYNVVTTISEAIEGYFVFRCTDGIIRDLAKTEGRSKREWQIhETVMEYVKESLYEISPEEVVLVAD 148
                                       5799****************************************9988777615678999***************** PP

                           DUF5616  78 kpvSnSgelaklireileeaglegevelvknvDkeLkesee....ivatsDsvildkvksvldla 138
                                       k+v+ Sge+ ++  ++++e+  +++  l + +D+ L++++     i+a+sDs i +k+ +++dl+
  gi|385806319|ref|YP_005842717.1| 149 KQVPFSGEYLSKASSLFSERLKNTKFYLDNMADSLLIKLSLegkyIIASSDSLIAEKALNIFDLS 213
                                       *************************************77766677******************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 !   56.9   0.3   2.1e-19   1.2e-15       1      56 []      12      67 ..      12      67 .. 0.98

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 2.1e-19
                            DUF434  1 kLkeAaeDlryLLnRGYpkksalelVgnhYqLskrqRlaLaRcvssdeeiearksK 56
                                      +LkeA++ + +LLn+++++++a+++ + +Y Ls ++R++L+Rc++s e  +++k+K
  gi|385806319|ref|YP_005842717.1| 12 RLKEAIKTYLFLLNNNFKSETAINIASSKYFLSIKERELLKRCFHSFEFNKMVKQK 67
                                      69****************************************************98 PP

>> DUF2621  Protein of unknown function (DUF2621)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   5.2e-06     0.031      10      67 ..      83     148 ..      76     204 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.2e-06
                           DUF2621  10 lwvvvlvsllaiGGffmfrk...flkrlpkedGkseldwqee.....yiektrhlwtdeekellee 67 
                                       ++ vv     ai G+f+fr     ++ l k +G+s+ +wq +     y+++++   + ee  l+ +
  gi|385806319|ref|YP_005842717.1|  83 YYNVVTTISEAIEGYFVFRCtdgIIRDLAKTEGRSKREWQIHetvmeYVKESLYEISPEEVVLVAD 148
                                       56677777789********644479**************953222226666666666666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       741  (0.0413297); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); 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: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.55
# Mc/sec: 1311.61
//
Query:       gi|385806320|ref|YP_005842718.1|  [L=275]
Description: ABC transporter [Fervidicoccus fontis Kam940]
Scores for complete 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  102.6   0.0    3.7e-29  102.0   0.0    1.3  1  ABC_tran     ABC transporter
    2.6e-16   60.3   2.0    1.4e-09   38.3   0.0    2.3  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    8.8e-09   35.1   0.3    3.9e-08   33.0   0.3    1.8  1  SMC_N        RecF/RecN/SMC N terminal domain
    0.00018   22.1   2.0     0.0003   21.3   1.6    1.7  1  AAA_23       AAA domain
      0.003   17.8   0.1       0.13   12.5   0.1    2.3  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
     0.0032   17.2   2.9      0.021   14.6   0.3    2.4  2  AAA_15       AAA ATPase domain
     0.0068   15.5   0.1      0.013   14.5   0.0    1.4  2  T2SSE        Type II/IV secretion system protein
     0.0077   15.9   0.0      0.015   15.0   0.0    1.5  1  AAA_29       P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.011   15.3   0.0      0.021   14.4   0.0    1.3  1  AAA_27       AAA domain
      0.019   15.1   0.1       0.14   12.3   0.1    2.2  1  AAA_33       AAA domain
      0.035   14.4   0.0       0.07   13.4   0.0    1.5  1  AAA_22       AAA domain
      0.039   13.9   0.0      0.077   12.9   0.0    1.5  1  RsgA_GTPase  RsgA GTPase
       0.05   12.8   0.1       0.37    9.9   0.0    2.0  2  NB-ARC       NB-ARC domain
      0.052   13.1   0.2      0.093   12.3   0.2    1.3  1  cobW         CobW/HypB/UreG, nucleotide-binding domain
      0.061   13.4   0.2       0.69    9.9   0.0    2.3  2  AAA_14       AAA domain
      0.079   12.7   0.0       0.14   11.9   0.0    1.3  1  AAA_30       AAA domain
       0.13    9.8   0.1       0.17    9.3   0.1    1.1  1  DUF3584      Protein of unknown function (DUF3584)
       0.15   12.4   0.0       0.21   11.9   0.0    1.4  1  AAA_16       AAA ATPase domain
       0.16   12.4   0.3       0.69   10.3   0.0    2.1  2  AAA          ATPase family associated with various cellular a
       0.17   11.5   0.0       0.28   10.8   0.0    1.3  1  SRP54        SRP54-type protein, GTPase domain
       0.21   10.9   0.0       0.37   10.1   0.0    1.4  1  Zeta_toxin   Zeta toxin


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.0   0.0   4.3e-32   3.7e-29       2     136 ..      35     187 ..      34     188 .. 0.87

  Alignments for each domain:
  == domain 1  score: 102.0 bits;  conditional E-value: 4.3e-32
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS....--S-TTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe....pqlfpel 74 
                                       +n+s++l +  ++++vG+nGaGK+tL+kll+gl++p+eG+i ++g+d++  + + ++k ++++pq     ++l+  +
  gi|385806320|ref|YP_005842718.1|  35 ENLSFSLPKKGLMQVVGPNGAGKTTLFKLLLGLYNPKEGKIIVNGEDITG-NPRLASKYFSYVPQLiissKSLNFPI 110
                                       79************************************************.88899999******966655555555 PP

                                       BHHHH...............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxx...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  75 tvren...............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       ++re                  ++  +++ ++l+ + l++t  ++++++LSgGqkq+v +a+allk+++++llDEp+
  gi|385806320|ref|YP_005842718.1| 111 SAREFlewelafeerwprfkINNNITNRIKNTLKFVRLEETAFEKDMRELSGGQKQKVFIAKALLKDKPVMLLDEPF 187
                                       56666**9998888887775333337777777888888889999999*****************************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 !   21.2   0.5   2.5e-07   0.00021       4      59 ..      49      96 ..      46     136 .. 0.61
   2 !   38.3   0.0   1.6e-12   1.4e-09     233     302 ..     156     221 ..     124     222 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 2.5e-07
                            AAA_21  4 liGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfe 59
                                      ++GpNg+GK++L+++l +l            e   +++  +i++ ++l ++  + +
  gi|385806320|ref|YP_005842718.1| 49 VVGPNGAGKTTLFKLLLGLYN--------PKEGKIIVNGEDITGNPRLASKYFSYV 96
                                      79**************99964........333333334444444444444444444 PP

  == domain 2  score: 38.3 bits;  conditional E-value: 1.6e-12
                            AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQv.iltTHSplll 302
                                       ++relS G+k+  +++ all +    ++ l+DEp ++++P+    l+e++ +lsr   ++ i+t+H+p ll
  gi|385806320|ref|YP_005842718.1| 156 DMRELSGGQKQKVFIAKALLKDK---PVMLLDEPFSSIDPATRIDLAEIIVKLSR--EKLvIITSHDPNLL 221
                                       789*****************988...************************99999..5666*******997 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.3   4.6e-11   3.9e-08      23     207 ..      43     226 ..      26     236 .. 0.77

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 4.6e-11
                                       TSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEE.EEEEEETTEESSSSSSCEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                             SMC_N  23 sksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaev.eitfdnedkklkiekeevs 98 
                                       +k++  +vGpNG+GK+ l+  +   LG  + k+ +     + i+ + + as  + +v +++++ ++ +++i++ e+ 
  gi|385806320|ref|YP_005842718.1|  43 KKGLMQVVGPNGAGKTTLFKLL---LGLYNPKEGKIIVNGEDITGNPRLASKYFSYVpQLIISSKSLNFPISAREFL 116
                                       678899*************988...99766655554433333333366666677777345557777789******99 PP

                                       EEEEEETTSEEEEEETTEEE-H.HHHHHH..HHCTT-STT..CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxx.xxxxxx..xxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  99 isrrvkrkgeseykingkevtk.kevsel..lesagiske..lLSgGektLvalaLlfAiqkvkpaplyllDeidaa 170
                                           ++++   ++kin++  ++ k+  ++  le++ ++k+  +LSgG+k+ v +    A    k +p++llDe  + 
  gi|385806320|ref|YP_005842718.1| 117 EWELAFEERWPRFKINNNITNRiKNTLKFvrLEETAFEKDmrELSGGQKQKVFI----AKALLKDKPVMLLDEPFSS 189
                                       9999999999******998765444444312555666554558*****986544....55567999*********** PP

                                       S-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 171 LDeknvkkvaellkeksknaQfivislreemlekadk 207
                                       +D + +  +ae++ + s +  +i++s++ ++l k  +
  gi|385806320|ref|YP_005842718.1| 190 IDPATRIDLAEIIVKLSREKLVIITSHDPNLLMKNTN 226
                                       ****************************999887655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   1.6   3.5e-07    0.0003      10      45 ..      34      69 ..      25     185 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 3.5e-07
                            AAA_23 10 frdqeidF.skgltlItGpNGaGKTTildAiklaLyg 45
                                      f++ ++ + +kgl  ++GpNGaGKTT++  + l+Ly+
  gi|385806320|ref|YP_005842718.1| 34 FENLSFSLpKKGLMQVVGPNGAGKTTLFKLL-LGLYN 69
                                      67777777999*****************855.55555 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 !   12.5   0.1   0.00015      0.13      23      87 ..     150     201 ..     126     204 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00015
                           SbcCD_C  23 ekelsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllel 87 
                                       e+ +++++++lSGG+kq+++    a    al++++        +++LDE Fs++D+ ++  l e+
  gi|385806320|ref|YP_005842718.1| 150 ETAFEKDMRELSGGQKQKVFI---A---KALLKDK-------PVMLLDEPFSSIDPATRIDLAEI 201
                                       556899999*******77653...3...4456675.......47999********9988777766 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.3   2.4e-05     0.021      23      55 ..      43      96 ..      33     167 .. 0.63
   2 ?    1.8   1.2      0.18   1.5e+02     325     368 ..     179     220 ..     128     221 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.4e-05
                            AAA_15 23 ee.ltvliGkNnsGKSsilealdlFlnnkekkn....................k 55
                                      ++ l+ ++G+N++GK+++ ++l  + n ke k                     +
  gi|385806320|ref|YP_005842718.1| 43 KKgLMQVVGPNGAGKTTLFKLLLGLYNPKEGKIivngeditgnprlaskyfsyV 96
                                      345999*********************995555666666666666666665551 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.18
                            AAA_15 325 villiEEPEahLHpqaqkvlikllkelandnktQviitTHSphi 368
                                        + l++EP  ++ p     l++ + +l++++   viit+H p +
  gi|385806320|ref|YP_005842718.1| 179 PVMLLDEPFSSIDPATRIDLAEIIVKLSREK--LVIITSHDPNL 220
                                       5677888888888999999999*******99..5******9986 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   1.6e-05     0.013     113     162 ..      28      77 ..       2      83 .. 0.75
   2 ?   -3.5   0.0       4.9   4.2e+03      93     125 ..     135     173 ..     127     183 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.6e-05
                             T2SSE 113 alkekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderivt 162
                                        ++e+i e l+ ++ ++gl+ v G+ g GKttl   ll   n ++ +i++
  gi|385806320|ref|YP_005842718.1|  28 YNSENIFENLSFSLPKKGLMQVVGPNGAGKTTLFKLLLGLYNPKEGKIIV 77 
                                       344777788899999**************************999887764 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4.9
                             T2SSE  93 lviR.kksakeltlddlgaeealk.....ekiaevlrka 125
                                       ++ R k++ k ++l++ ++e++++     +k++ +++ka
  gi|385806320|ref|YP_005842718.1| 135 ITNRiKNTLKFVRLEETAFEKDMRelsggQKQKVFIAKA 173
                                       555666666666777777776666555555555555555 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.7e-05     0.015      11      39 ..      33      61 ..      25      78 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.7e-05
                            AAA_29 11 tfdghtieidlkgatlltGpsGsGKSTll 39
                                       f++ ++++  kg + ++Gp+G+GK+Tl+
  gi|385806320|ref|YP_005842718.1| 33 IFENLSFSLPKKGLMQVVGPNGAGKTTLF 61
                                      57778889999999*************97 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   2.5e-05     0.021      18      45 ..      36      63 ..      33      69 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.5e-05
                            AAA_27 18 sldfsaeeadlhliyGpNEAGKstalrA 45
                                      +l+fs  +++l  ++GpN AGK+t+++ 
  gi|385806320|ref|YP_005842718.1| 36 NLSFSLPKKGLMQVVGPNGAGKTTLFKL 63
                                      57788889****************9875 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00016      0.14       3      20 ..      48      65 ..      46     226 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00016
                            AAA_33  3 llvGlpGsGKstlaerll 20
                                       +vG++G+GK+tl + ll
  gi|385806320|ref|YP_005842718.1| 48 QVVGPNGAGKTTLFKLLL 65
                                      589**********99885 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   8.2e-05      0.07       5      29 ..      44      68 ..      42     108 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.2e-05
                            AAA_22  5 agilvvtGesGtGKTtllrrlleql 29
                                      +g++ v+G+ G+GKTtl + ll  +
  gi|385806320|ref|YP_005842718.1| 44 KGLMQVVGPNGAGKTTLFKLLLGLY 68
                                      78899**************998776 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     9e-05     0.077      78     123 ..      22      68 ..       2      82 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9e-05
                                       EEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT- CS
                       RsgA_GTPase  78 evllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpel 123
                                       e +  s ++++ +e+l+  l +  ++ +vG+ G+GK+tL + ll+  
  gi|385806320|ref|YP_005842718.1|  22 EKIRFSYNSENIFENLSFSLPKkGLMQVVGPNGAGKTTLFKLLLGLY 68 
                                       455667778889999999998868999*************9998755 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   0.0   0.00043      0.37       6      38 ..      31      62 ..      26      70 .. 0.81
   2 ?    0.4   0.1      0.35     3e+02      81     117 ..     155     191 ..     130     227 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00043
                                      HHHHHHHHCTTTSCSEEEEEEESTTSSHHHHHH CS
                            NB-ARC  6 ekviekLlekdelqslvvalvGmgGvGKttlak 38
                                      e++ e+L+    +++ ++ +vG  G GKttl+k
  gi|385806320|ref|YP_005842718.1| 31 ENIFENLS-FSLPKKGLMQVVGPNGAGKTTLFK 62
                                      66777777.55566679**************97 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.35
                                       TTSSSS-STTSHHHHHHHHCCCTTEEEEEEEE-SHHH CS
                            NB-ARC  81 ddleekeeveslkrklvrlLltkrfllvlDDVweeed 117
                                       +d+ e + +++ k  + ++Ll+ + +++lD  + + d
  gi|385806320|ref|YP_005842718.1| 155 KDMRELSGGQKQKVFIAKALLKDKPVMLLDEPFSSID 191
                                       3333333344478889999999999999997665555 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   0.00011     0.093       4      34 ..      48      78 ..      46      85 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                                      EEEESTTCCHHHHHHHHHCT--SS-EEEEES CS
                              cobW  4 vltGflGsGKTtLlnhllenraglklavivN 34
                                       ++G+ G+GKTtL + ll   + ++  +ivN
  gi|385806320|ref|YP_005842718.1| 48 QVVGPNGAGKTTLFKLLLGLYNPKEGKIIVN 78
                                      689***************7777777777877 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00081      0.69       5      43 ..      47      84 ..      43     111 .. 0.76
   2 ?    1.1   0.1      0.43   3.7e+02      35      75 ..     145     188 ..     130     238 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00081
                            AAA_14  5 lvitGaRrvGKTtllkqlikellvkkesilyinldderd 43
                                      + ++G+  +GKTtl k l+  +  +ke  + +n +d + 
  gi|385806320|ref|YP_005842718.1| 47 MQVVGPNGAGKTTLFKLLLGLYN-PKEGKIIVNGEDITG 84
                                      6799**********988885555.999999999988654 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.43
                            AAA_14  35 yinldderdkk.ladpe..kllelilek.lkeekktylflDEiqe 75 
                                       ++ l++  ++k +++ +  +  +++ +k l + +k +++lDE   
  gi|385806320|ref|YP_005842718.1| 145 FVRLEETAFEKdMRELSggQKQKVFIAKaLLK-DKPVMLLDEPFS 188
                                       45555555543122222343344444443444.789999999554 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00016      0.14      19      51 ..      45      77 ..      39      89 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00016
                            AAA_30 19 rvavltGpAGtGKttalkalreaweaaggrvig 51
                                       ++ ++Gp G+GKtt+ k l  +++ ++g++i+
  gi|385806320|ref|YP_005842718.1| 45 GLMQVVGPNGAGKTTLFKLLLGLYNPKEGKIIV 77
                                      47889***************9999998777775 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1    0.0002      0.17      17      37 ..      44      64 ..      40      76 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0002
                           DUF3584 17 dghtnieGtNaaGKTtLlrLi 37
                                      +g  +++G N+aGKTtL +L+
  gi|385806320|ref|YP_005842718.1| 44 KGLMQVVGPNGAGKTTLFKLL 64
                                      57789*************997 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   0.00025      0.21      25      85 ..      45      99 ..      31     214 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00025
                            AAA_16 25 elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysa.laqalareellrql 85
                                      +l+ ++G+ G GK++l + ll  ++ +     +gk   ++++i+  + la+   + +++ ql
  gi|385806320|ref|YP_005842718.1| 45 GLMQVVGPNGAGKTTLFKLLLGLYNPK-----EGKIIVNGEDITGNPrLASKY-F-SYVPQL 99
                                      67779***************9888888.....344444433333333344444.3.333333 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 ?   10.3   0.0    0.0008      0.69       3      23 ..      49      69 ..      47     106 .. 0.74
   2 ?   -0.3   0.1       1.6   1.3e+03      26      66 ..     145     185 ..     131     226 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0008
                                      EESSTTSSHHHHHHHHHHHHT CS
                               AAA  3 lyGppGtGKTllakavakelg 23
                                      ++Gp G GKT+l k +    +
  gi|385806320|ref|YP_005842718.1| 49 VVGPNGAGKTTLFKLLLGLYN 69
                                      79************9987764 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.6
                                       EEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS.TSEEEEEET CS
                               AAA  26 fleisgsellskyvgesekkirelfkeakeka.kpsilfiDE 66 
                                       f++++ + + +++ + s  + +++f  ak+   ++ ++++DE
  gi|385806320|ref|YP_005842718.1| 145 FVRLEETAFEKDMRELSGGQKQKVFI-AKALLkDKPVMLLDE 185
                                       55555555554455555555555552.333333446777776 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00033      0.28       5      38 ..      48      81 ..      44      87 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00033
                                      EEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                             SRP54  5 llvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                       +vG++GaGKTt    L  l++ ++ k+++   D
  gi|385806320|ref|YP_005842718.1| 48 QVVGPNGAGKTTLFKLLLGLYNPKEGKIIVNGED 81
                                      58***********999999999988888877666 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00043      0.37      14      53 ..      42      81 ..      30      86 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00043
                        Zeta_toxin 14 erPklillgGqpGAGKselaellkdelerqgnvvrldpDd 53
                                       ++ l++++G  GAGK++l +ll    +++++ + +++ d
  gi|385806320|ref|YP_005842718.1| 42 PKKGLMQVVGPNGAGKTTLFKLLLGLYNPKEGKIIVNGED 81
                                      6777899***************999888777777666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); 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: 0.66u 0.38s 00:00:01.04 Elapsed: 00:00:00.57
# Mc/sec: 1440.92
//
Query:       gi|385806321|ref|YP_005842719.1|  [L=370]
Description: periplasmic solute binding protein [Fervidicoccus fontis Kam940]
Scores for complete 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-24   84.4   0.0    1.1e-23   83.9   0.0    1.1  1  ZnuA      Zinc-uptake complex component A periplasmic
  ------ inclusion threshold ------
      0.012   16.0   2.3      0.099   13.1   0.6    2.4  2  FtsX      FtsX-like permease family
      0.023   14.4   4.8       0.98    9.1   0.4    2.3  2  Yip1      Yip1 domain
       0.17   11.8   3.4        0.1   12.5   1.3    1.6  2  RIFIN     Rifin
       0.19   11.8   7.1      0.083   13.0   0.8    2.5  2  MpPF26    M penetrans paralogue family 26
       0.19   11.2   3.2       0.11   12.0   0.4    1.9  2  Stevor    Subtelomeric Variable Open Reading frame
       0.28   11.5   5.1       0.44   10.9   0.2    2.8  3  DUF4064   Protein of unknown function (DUF4064)
       0.64    9.6   4.6        2.4    7.7   0.6    2.3  2  Saf_2TM   SAVED-fused 2TM effector domain
        1.6    8.8   7.5       0.59   10.2   2.0    2.4  2  DUF3671   Protein of unknown function
        2.6    8.2   7.4        1.1    9.4   0.3    2.8  3  DUF5367   Family of unknown function (DUF5367)


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 !   83.9   0.0   6.4e-27   1.1e-23       1     205 [.      56     264 ..      56     273 .. 0.82

  Alignments for each domain:
  == domain 1  score: 83.9 bits;  conditional E-value: 6.4e-27
                                       EEESSHHHHHHHHHHHGGGCEEEECS-TTSTTTT----HHHHHHHHHSSEEEES.STTTSGTHHHHHHHH...TTCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx...xxxx RF
                              ZnuA   1 VvattsplgdlvrqvaGdrvevtvLvppgadpHsyeptprdvrklaeAdllvyn.glelEtwldkllass...sqat 73 
                                       +v+t++ l d v+ + G+ ++v ++vppg+dpH+y++tp+dv  l++A l++++ +  +E  +d+ ++s    s   
  gi|385806321|ref|YP_005842719.1|  56 IVTTFPSLVDDVKLITGNYFTVVSIVPPGVDPHDYSLTPQDVDILKNATLIISTlHTPMEVQIDNYFKSGllhS--Y 130
                                       8***************************************************8625789999999985553321..1 PP

                                       CEEEEETTTTCCSEBCSS....ESTG.GGSHHHHHHHHHHHHHHHHHHTGGGHHHHHHHHHHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxx....xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ZnuA  74 rvevidlsegveeeeeee....DpHi.WlspknaiamveniadaLveadpanadtyeanaaayiekLeeldaeiree 145
                                        +++ + + g+   ++ +    DpH+  ++p+n+ ++  n++ + +e+dp ++++y +n+++  +++e l ++++ +
  gi|385806321|ref|YP_005842719.1| 131 YIAIPNIT-GIVFVDNPNnglpDPHMpIYDPNNYLKFLYNLTLTVSEIDPSHKQYYMQNYENISNQVESLIEKYEGK 206
                                       22333333.4422222223456***7589************************************************ PP

                                       HTTSSGTEGEEEESSSTTHHHHHHTT-EEEEEESSSSS....HHHHHHHHHHHHHTT-SEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxx RF
                              ZnuA 146 laeipeekrklvtthdafgylarayglevagiagiste....aaqiaalieeikeagvkaifve 205
                                                + v + +   y  +  g++v  +   ++e    +++++ ++ +i++  ++a+ + 
  gi|385806321|ref|YP_005842719.1| 207 YR----G--TAVASTPEAVYAINWLGFNVTRLLLTEEEasvsPQDVNTITSMIENGTANAVAIL 264
                                       99....2..35777777778889*******99866666799**************999998765 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.16   2.9e+02      25      40 ..      24      39 ..      11      90 .. 0.68
   2 ?   13.1   0.6   5.5e-05     0.099      40      94 ..     313     367 ..     290     369 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.16
                              FtsX 25 illitlvalviGlglg 40
                                      +++itlv l++G+ l+
  gi|385806321|ref|YP_005842719.1| 24 LFFITLVFLFVGFSLS 39
                                      2344444444443332 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 5.5e-05
                              FtsX  40 gllaaqllsdvllssvfsselkisidlitvliiivlllllalla.gllsiskilkk 94 
                                        +++aql+s    s++  s+ +is ++ + ++ iv++++l++l+ +ll  ++ +++
  gi|385806321|ref|YP_005842719.1| 313 QFIVAQLSSYNNTSNYT-SNSSISESTASSYVYIVIAIILIVLItVLLYYWRSRRQ 367
                                       46677777777766666.77777777777777777777666666357777887776 PP

>> Yip1  Yip1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.5    0.0026       4.7       2      55 ..       7      49 ..       7      81 .. 0.58
   2 ?    9.1   0.4   0.00054      0.98      34      86 ..     314     362 ..     296     367 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0026
                              Yip1  2 lldPrevfrrlkkeppilrapdlallllalltlllgllaslnlgqtlasgeevq 55
                                      +++++++f++++k ++        +l++++l +l++ ++ ++  + la+    q
  gi|385806321|ref|YP_005842719.1|  7 FVHVKKFFAQVRKMKR--------ILFFITLVFLFVGFSLSIPNTALAET---Q 49
                                      6899************........45555444444444442222222222...2 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00054
                              Yip1  34 lllgllas.lnlgqtlasgeevqgltlssllgaiiggylglllgllllalllhl 86 
                                       ++++ l+s +n +++++++       + s +++ ++++++++l++l+  ll+++
  gi|385806321|ref|YP_005842719.1| 314 FIVAQLSSyNNTSNYTSNS-----SISESTASSYVYIVIAIILIVLITVLLYYW 362
                                       4555555555666666666.....444555555566666666666666666666 PP

>> RIFIN  Rifin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.2   2.1e+03     183     201 ..     187     205 ..     165     267 .. 0.54
   2 ?   12.5   1.3   5.6e-05       0.1     266     312 ..     328     370 .]     304     370 .] 0.58

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.2
                             RIFIN 183 tnyknvtslvkaikeeyee 201
                                       +ny+n ++ v+++ e+ye 
  gi|385806321|ref|YP_005842719.1| 187 QNYENISNQVESLIEKYEG 205
                                       3444443333333333332 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 5.6e-05
                             RIFIN 266 taaveattaslqtaiiasivaivvIvLimvIIYLiLRYrRKkKmkkK 312
                                        +  ++ + s+ ++ ++ ++ai+ IvLi v     L Y R ++ +kK
  gi|385806321|ref|YP_005842719.1| 328 YTSNSSISESTASSYVYIVIAIILIVLITVL----LYYWRSRRQNKK 370
                                       3333334444444555555555555555555....556666666665 PP

>> MpPF26  M penetrans paralogue family 26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.8      0.16   2.8e+02      16      31 ..      23      38 ..       4      80 .. 0.57
   2 ?   13.0   0.8   4.6e-05     0.083      26      83 ..     307     360 ..     299     370 .] 0.80

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.16
                            MpPF26 16 iilyllatvlllvsll 31
                                      i++++++++l++ + l
  gi|385806321|ref|YP_005842719.1| 23 ILFFITLVFLFVGFSL 38
                                      3333333333333333 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 4.6e-05
                            MpPF26  26 llvsllayivllskskllskeyeeesslleaelligvllillidifyivnfileiiLi 83 
                                       +++s l++iv+++ s+++ ++y  +ss++e     +++ ++ i i +i +++++++L 
  gi|385806321|ref|YP_005842719.1| 307 SILSKLQFIVAQLSSYNNTSNYTSNSSISES----TASSYVYIVIAIILIVLITVLLY 360
                                       67888999********************999....88888888886677777766664 PP

>> Stevor  Subtelomeric Variable Open Reading frame
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.68   1.2e+03      52      74 ..     187     209 ..     178     217 .. 0.55
   2 ?   12.0   0.4   6.1e-05      0.11     212     261 ..     318     367 ..     281     370 .] 0.59

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.68
                            Stevor  52 qqthdpykqLkevveKngtkstg 74 
                                       q+ ++  +q++ ++eK + k++g
  gi|385806321|ref|YP_005842719.1| 187 QNYENISNQVESLIEKYEGKYRG 209
                                       22233345555566666555555 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 6.1e-05
                            Stevor 212 avsaaaasdlagtaasaassafepygiaalvllilavvliiLYiwlyrRR 261
                                       ++s+   ++  ++ +s++ s+  +y   ++ +++++++ ++LY w  rR 
  gi|385806321|ref|YP_005842719.1| 318 QLSSYNNTSNYTSNSSISESTASSYVYIVIAIILIVLITVLLYYWRSRRQ 367
                                       22222222222333555566666666555556666666677888876665 PP

>> DUF4064  Protein of unknown function (DUF4064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.2      0.16   2.8e+02      17      46 ..      25      52 ..      18      82 .. 0.53
   2 ?   -2.7   0.0       4.1   7.3e+03      29      43 ..     174     197 ..     166     230 .. 0.56
   3 ?   10.9   0.2   0.00024      0.44      43      83 ..     323     363 ..     299     369 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.16
                           DUF4064 17 illglllllflfllssgefsqelteeqals 46
                                      ++++l+ l++ f ls+++++ + t++  ++
  gi|385806321|ref|YP_005842719.1| 25 FFITLVFLFVGFSLSIPNTALAETQN--QT 52
                                      45555566666666666655555443..22 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.1
                           DUF4064  29 llssgefsqeltee.........q 43 
                                       ++ ++++ ++++ +         +
  gi|385806321|ref|YP_005842719.1| 174 VSEIDPSHKQYYMQnyenisnqvE 197
                                       555555555555433432322220 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00024
                           DUF4064  43 qalsgedasavleflstllivlgvialiaivlgivgalllk 83 
                                       +++s + ++++ +  + + +v++via+i+ivl+ v +++ +
  gi|385806321|ref|YP_005842719.1| 323 NNTSNYTSNSSISESTASSYVYIVIAIILIVLITVLLYYWR 363
                                       45566667777788888999************999887755 PP

>> Saf_2TM  SAVED-fused 2TM effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.2     0.029        52      68      93 ..      21      46 ..       3      80 .. 0.69
   2 ?    7.7   0.6    0.0013       2.4      50     100 ..     320     370 .]     303     370 .] 0.55

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.029
                           Saf_2TM 68 laiilvigvllivvGavllilryvne 93
                                        i+++i+ +++ vG+ l+i + +  
  gi|385806321|ref|YP_005842719.1| 21 KRILFFITLVFLFVGFSLSIPNTALA 46
                                      45677888888888888887765332 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0013
                           Saf_2TM  50 aggslevsfssse.ipeiv..laiilvigvllivvGavllilryvneakrqskk 100
                                        +++ + ++ s++ i e +  +++ +vi+++liv+  vll++     ++rq+kk
  gi|385806321|ref|YP_005842719.1| 320 SSYNNTSNYTSNSsISESTasSYVYIVIAIILIVLITVLLYYWR---SRRQNKK 370
                                       34444444444443333331156777777777776666666544...5888887 PP

>> DUF3671  Protein of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.3      0.23   4.1e+02      41      57 ..      17      33 ..       6      82 .. 0.53
   2 ?   10.2   2.0   0.00033      0.59      56     109 ..     311     359 ..     276     362 .. 0.61

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.23
                           DUF3671 41 lkkyglllilpvllpli 57
                                      ++k+  +l+++ l++l 
  gi|385806321|ref|YP_005842719.1| 17 VRKMKRILFFITLVFLF 33
                                      33333333333333332 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00033
                           DUF3671  56 liglivpilfeakskkslkkkelevlatsieklytiffiilvviillvliYili 109
                                        + +iv+ l +     +++ ++     +  e++  ++++i++ iil+vli +l+
  gi|385806321|ref|YP_005842719.1| 311 KLQFIVAQLSS-----YNNTSNYTSNSSISESTASSYVYIVIAIILIVLITVLL 359
                                       33334444433.....33333333444567788888888888888888887764 PP

>> DUF5367  Family of unknown function (DUF5367)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.8      0.15   2.7e+02       8      58 ..      20      70 ..      13      83 .. 0.69
   2 ?   -1.7   0.0       1.8   3.2e+03      68      92 ..     114     140 ..     103     145 .. 0.66
   3 ?    9.4   0.3   0.00062       1.1       5      38 ..     336     369 ..     333     370 .] 0.80

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.15
                           DUF5367  8 llllvlfllviplllvlllpvykykklnkterlkaailialpgmllDvlil 58
                                      +  +++f++++ l++  +l + +    + ++++++ i+ + p ++ Dv  +
  gi|385806321|ref|YP_005842719.1| 20 MKRILFFITLVFLFVGFSLSIPNTALAETQNQTQGFIVTTFPSLVDDVKLI 70
                                      555667777777666666676677777888888999999999999999655 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.8
                           DUF5367  68 lqpeaaslFaswlLwayslvl..ltgv 92 
                                       ++ + +++F s lL  y + +  +tg+
  gi|385806321|ref|YP_005842719.1| 114 MEVQIDNYFKSGLLHSYYIAIpnITGI 140
                                       666778888888888775443115555 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.00062
                           DUF5367   5 eatllllvlfllviplllvlllpvykykklnkte 38 
                                       e+t    v ++++i+l++++++ +y+++   +++
  gi|385806321|ref|YP_005842719.1| 336 ESTASSYVYIVIAIILIVLITVLLYYWRSRRQNK 369
                                       5566667778899999999********9988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1401  (0.0781416); expected 358.6 (0.02)
Passed bias filter:                      784  (0.043728); 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):              10  [number of targets reported over threshold]
# CPU time: 0.72u 0.37s 00:00:01.08 Elapsed: 00:00:00.55
# Mc/sec: 2022.44
//
Query:       gi|385806322|ref|YP_005842720.1|  [L=294]
Description: Mn2+/Zn2+ ABC transporter permease [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      8e-22   78.0  26.3    9.8e-22   77.7  26.3    1.1  1  ABC-3     ABC 3 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 !   77.7  26.3   5.5e-26   9.8e-22       4     254 ..      27     285 ..      24     289 .. 0.88

  Alignments for each domain:
  == domain 1  score: 77.7 bits;  conditional E-value: 5.5e-26
                             ABC-3   4 flqrallasilvs..lacallgsfvvlrrqsllgdalsHaalpGvalayllgvn....lllgailvgliaavalell 74 
                                         ++ ++ ++l++  l+ +++g  +  +   +l++++ H+al    +++ll++      l+ +i++ +i+ ++++l+
  gi|385806322|ref|YP_005842720.1|  27 SYFNPIWMTVLLGsaLIYGIIGPILSAKNLLFLAGSIPHSALLSASMGILLSMMisgsNLVWSIIFNVILIFTIGLV 103
                                       567778888888633789************************87777777766644445555666666777777777 PP

                             ABC-3  75 krktklkedtaigivlsvflalglvlvslikk...skvdldsyLfGniltisqedliliaiieavvllllllfwkel 148
                                        ++   + +  + i + ++ +l ++++ +i +      +++s+L+G+ l  ++ d ili++++a++ll + l +ke 
  gi|385806322|ref|YP_005842720.1| 104 IHRG-GDPNKYTSIFIGTTASLTVIVLYYITNhfyLLTSVESILLGDPLLSTRSDAILIFVLTAITLLFFGLTYKEH 179
                                       6654.456678899999999999999999999898899*************************************** PP

                             ABC-3 149 llitfdeelAkveglsvkllkllllalialavvvalqavGviLvialliiPaatArrltrslesllivAillglvsv 225
                                       + i +  e Ak +gl+++++++ + + ++++ ++ +++vG iL    + iP+a+  +++r+ ++ +++++ +++ s+
  gi|385806322|ref|YP_005842720.1| 180 IYIGITGEEAKLAGLRTEIYEFFFYLFLGITSATLMKIVGFILTHVFILIPGAAGSLVARKSKEAIALSMNIAAYSA 256
                                       ***************************************************************************** PP

                             ABC-3 226 vaGlllSyyldlatGavivlvatllflla 254
                                       ++Gl+l ++++l+++++  ++++++++++
  gi|385806322|ref|YP_005842720.1| 257 IIGLFLGVFFNLSPSGTTGICMIAIYIVI 285
                                       ***********999999999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       822  (0.0458475); 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:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.55
# Mc/sec: 1619.32
//
Query:       gi|385806323|ref|YP_005842721.1|  [L=136]
Description: CopG family transcriptional regulator [Fervidicoccus fontis Kam940]
Scores for complete 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-08   32.3   0.1    3.9e-06   26.6   0.4    2.3  2  RHH_1     Ribbon-helix-helix protein, copG family
    6.2e-08   32.5   0.0      1e-07   31.8   0.0    1.4  1  RHH_3     Ribbon-helix-helix domain
    2.6e-06   27.5   0.3      7e-06   26.1   0.0    1.8  2  NikR_C    NikR C terminal nickel binding domain
  ------ inclusion threshold ------
      0.052   13.3   0.0      0.082   12.7   0.0    1.2  1  DUF126    Aconitase X swivel domain
       0.12   12.3   0.0        9.5    6.2   0.0    2.0  2  APAF1_C   APAF-1 helical 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 !   26.6   0.4   1.1e-09   3.9e-06       1      35 [.      10      44 ..      10      48 .. 0.95
   2 ?    3.4   0.0     0.023        81      21      37 ..      68      84 ..      64      86 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 1.1e-09
                                      EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHH CS
                             RHH_1  1 rvsirldeellerLdelarrrgrSrSelIReAlre 35
                                      r+ i++de l+++Ld+l +++   rS+++++A+r 
  gi|385806323|ref|YP_005842721.1| 10 RFGISIDEGLADKLDKLSKALSTDRSAIVEDAIRG 44
                                      899******************************95 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.023
                                      HTSSHHHHHHHHHHHHH CS
                             RHH_1 21 rgrSrSelIReAlreyl 37
                                      +g+  S ++R+++++++
  gi|385806323|ref|YP_005842721.1| 68 EGKGCSVFVRQLIEDFK 84
                                      6778899*******987 PP

>> RHH_3  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.0   2.8e-11     1e-07       2      43 ..       8      49 ..       7      50 .. 0.97

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 2.8e-11
                             RHH_3  2 ktrttvsidpelaekLkaLSekTrIprSklldeAiellLekY 43
                                      k+r+++sid+ la+kL+ LS++++  rS +++ Ai  +++++
  gi|385806323|ref|YP_005842721.1|  8 KKRFGISIDEGLADKLDKLSKALSTDRSAIVEDAIRGVIAEH 49
                                      89*************************************998 PP

>> 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 ?   -2.3   0.0       1.4   5.1e+03      50      65 ..      17      32 ..      13      38 .. 0.74
   2 !   26.1   0.0   1.9e-09     7e-06       2      69 ..      60     125 ..      59     130 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.4
                                      EE-HHHHHHHHHHHHT CS
                            NikR_C 50 kGeaeeikelaeklra 65
                                      +G a+++ +l+++l++
  gi|385806323|ref|YP_005842721.1| 17 EGLADKLDKLSKALST 32
                                      5667788888877765 PP

  == domain 2  score: 26.1 bits;  conditional E-value: 1.9e-09
                                       EEEEEEEETTSTTHHHHHHHHHHHHSSEEEEEEEEEESSSEEEEEEEEEE-HHHHHHHHHHHHTSTTE CS
                            NikR_C   2 GvitivydhhqrelserltdiqheyhdliisslhvhldhdncLevivlkGeaeeikelaeklralkgV 69 
                                       G++++vy +  ++ s  + ++  +++d+i+ s h+h + +nc ev+++ G++ +i++l  + ++ k +
  gi|385806323|ref|YP_005842721.1|  60 GIMILVYSE-GKGCSVFVRQLIEDFKDIIQFSSHYH-TGNNCTEVFFIAGNSLRIRDLHSEAKKRKDI 125
                                       566677766.6778888899999*************.9999*****************9988777765 PP

>> DUF126  Aconitase X swivel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.3e-05     0.082       8      41 ..      40      74 ..      37      83 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.3e-05
                                      -TTT-BB-S.-SSSTT-B-TT.SEEEES--S--SS CS
                            DUF126  8 dpetGkvidkghplegqsiag.kiLvlpsgkGStv 41
                                      d+ +G++ +++h l+ ++ +g  iLv+ +gkG +v
  gi|385806323|ref|YP_005842721.1| 40 DAIRGVIAEHSHYLYEHECKGiMILVYSEGKGCSV 74
                                      5678*****************66*********998 PP

>> APAF1_C  APAF-1 helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0    0.0099        36      68     116 ..      17      66 ..       8      76 .. 0.80
   2 ?    6.2   0.0    0.0026       9.5      87     131 ..      78     122 ..      73     124 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0099
                           APAF1_C  68 sslledyvkyrkileendeeeled.feeflsvnahlleekpfpdiiQlal 116
                                         l   + k  k l+ ++++ +ed +   + +++h l e+ +  i+ l  
  gi|385806323|ref|YP_005842721.1|  17 EGLADKLDKLSKALSTDRSAIVEDaIRGVIAEHSHYLYEHECKGIMILVY 66 
                                       557778899999999999999887578899*******9999999877655 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0026
                           APAF1_C  87 eeledfeeflsvnahlleekpfpdiiQlalsqpessevyqqAkkl 131
                                       + +edf+++++  +h  + + ++++  +a +  +   ++ +Akk+
  gi|385806323|ref|YP_005842721.1|  78 QLIEDFKDIIQFSSHYHTGNNCTEVFFIAGNSLRIRDLHSEAKKR 122
                                       7899***********9999**********9999999999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 785.47
//
Query:       gi|385806324|ref|YP_005842722.1|  [L=98]
Description: hypothetical protein FFONT_1282 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       740  (0.0412739); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); 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: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 568.67
//
Query:       gi|385806325|ref|YP_005842723.1|  [L=476]
Description: Component HyfD of membrane-bound [Ni,Fe]-hydrogenase [Fervidicoccus fontis Kam940]
Scores for complete 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-55  186.3  26.9    6.9e-55  186.3  26.9    2.4  2  Proton_antipo_M  Proton-conducting membrane transporter
     0.0021   18.1   0.3      0.016   15.2   0.3    2.7  1  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   1.9     0.033     3e+02     146     174 ..      30      58 ..       4     117 .. 0.70
   2 !  186.3  26.9   7.7e-59   6.9e-55       1     287 [.     130     413 ..     130     420 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.033
                   Proton_antipo_M 146 isqlllilaiismllgslvalaqtdiKrl 174
                                       ++   li +++s+l+++l  l+++d+ ++
  gi|385806325|ref|YP_005842723.1|  30 ATWSSLIASLLSILIAALTFLQKVDYEKV 58 
                                       333445678899*******9999999886 PP

  == domain 2  score: 186.3 bits;  conditional E-value: 7.7e-59
                   Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskalelgln 77 
                                       +++L  + +++El++l++  Li +++++ ++ +A+l++f +t ++ + L  +  ++y  tg++++++ls+       
  gi|385806325|ref|YP_005842723.1| 130 SSSLTFMIIFFELTSLCSWGLISFYETE-EAKSAGLIAFTITHIAAFGLYAATGIIYYETGSVDLRNLSSL-----P 200
                                       678999*******************777.9*****************************************.....8 PP

                   Proton_antipo_M  78 slelllllllllvgllvKsaqvplhlWlpdayveaPtpvsall.Aatlvkagvlllirlllllavssneisqlllil 153
                                       s   l+ l+ ll++   K aq+p+h+Wlp a + aPtpvsa l Aa lvk+g++l ir+++      n ++++ +i 
  gi|385806325|ref|YP_005842723.1| 201 SGLKLISLIGLLIASWGKGAQFPFHVWLPRA-MSAPTPVSAYLhAAALVKLGAFLAIRTMMWAGSIPNSVAYICAIF 276
                                       8999999999*********************.**************************9999999999********* PP

                   Proton_antipo_M 154 aiismllgslvalaqtdiKrllAySsishlGymlialav...atqygveaaiihllthalfkallFllagsviyere 227
                                       a+i+ml+  ++   qtdiK+llAyS+is+l y++ ++++   +++ ++ a+++++++h++ k l Fl ag+++ +  
  gi|385806325|ref|YP_005842723.1| 277 AVITMLYSLTLYFPQTDIKKLLAYSTISQLSYIFTGVSLiamGSKLAIIASVLYIFAHGFGKGLFFLTAGAISLSS- 352
                                       **********************************998775657788999999*****************9886665. PP

                   Proton_antipo_M 228 ktrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvla.v 287
                                        trd+r+++gL kk+    + ++v++ +++G+Pp+ +F++k+l++ +av+ ++il  ++ v
  gi|385806325|ref|YP_005842723.1| 353 GTRDLREIKGLIKKQKASGIGFTVATATITGVPPFGCFWGKLLLILSAVQLGSILSYTLaV 413
                                       9*************************************************99987766644 PP

>> Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.3   1.8e-06     0.016      11      57 ..      64     117 ..      58     118 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.8e-06
                   Proton_antipo_N  11 sieigfllDklsalmllvvtfvsllvhlYSigYMa.dde......gyqRFfayl 57 
                                        ieig ++D  sal+ +++ +v+++ ++ S+ Y + + +      +++R+++++
  gi|385806325|ref|YP_005842723.1|  64 PIEIGWYMDAASALVGMLIAIVGFCSIMESLNYISpNNKehpitsKFNRYYSLM 117
                                       589*******************************732223345557****9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (476 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       881  (0.0491383); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); 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):               2  [number of targets reported over threshold]
# CPU time: 0.71u 0.34s 00:00:01.05 Elapsed: 00:00:00.52
# Mc/sec: 2737.86
//
Query:       gi|385806326|ref|YP_005842724.1|  [L=251]
Description: Component HyfI of membrane-bound [Ni,Fe]-hydrogenase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.3e-28   97.2   0.6      1e-27   96.6   0.6    1.3  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 !   96.6   0.6   5.6e-32     1e-27       1     128 [.      32     140 ..      32     143 .. 0.94

  Alignments for each domain:
  == domain 1  score: 96.6 bits;  conditional E-value: 5.6e-32
                                       -SHHHHHHT-TTTTHHHHHHTEEEEEETTT-S--HHHHHHTHTTTSEEEEEESBE...EEEHHHHHHHHGGGSSEEE CS
                       Oxidored_q6   1 CtGcsisllaleedlldllelielryhetlladskeeeieakekeadvlvveGavtrkpkealellkelaekakavi 77 
                                       C+Gc+is+la+ ++l+d+     +r++ +++ +++         +adv++++G++tr+  +a+++++e ++k+ +v+
  gi|385806326|ref|YP_005842724.1|  32 CNGCDISVLASLTPLYDV-----ERFGVKVVYSPR---------QADVILITGPITRQFYPAMKIIYESTPKPCVVV 94 
                                       ******************.....************.........9******************************** PP

                                       EESHHHHH-TGGGSTT-TEE-HHHHHHHC.S-E.EEE-SSS--HHHHHHHH CS
                       Oxidored_q6  78 avGtCAafGGipaaannpsvgeevgellevvpvdinipGCPphpeailetl 128
                                       a+G+CA++GGi+  +n ++     g++++vvpvd++ipGCPp+p+ai++++
  gi|385806326|ref|YP_005842724.1|  95 ACGSCASSGGIW--YNTYD---TLGGADKVVPVDVYIPGCPPRPAAIIHGM 140
                                       ************..77443...4589*********************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       729  (0.0406604); expected 358.6 (0.02)
Passed bias filter:                      591  (0.0329634); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.34s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 1430.05
//
Query:       gi|385806327|ref|YP_005842725.1|  [L=179]
Description: Component HyfH of membrane-bound [Ni,Fe]-hydrogenase [Fervidicoccus fontis Kam940]
Scores for complete 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   55.6  12.9    8.6e-09   34.9   3.4    3.6  4  Fer4        4Fe-4S binding domain
    2.4e-13   50.5   7.6    2.4e-13   50.5   7.6    2.7  2  Fer4_7      4Fe-4S dicluster domain
    4.4e-13   49.2  33.5    1.1e-09   38.3   7.4    2.9  3  Fer4_9      4Fe-4S dicluster domain
      4e-12   46.0  20.6    5.1e-09   36.1   8.2    2.9  3  Fer4_10     4Fe-4S dicluster domain
    6.2e-11   42.3  11.2    3.3e-10   39.9   5.2    2.2  2  Fer4_21     4Fe-4S dicluster domain
    6.6e-09   36.6  14.8    0.00039   21.3   7.6    3.1  2  Fer4_16     4Fe-4S double cluster binding domain
      2e-08   34.6  12.3     0.0054   17.3   0.3    3.3  3  Fer4_17     4Fe-4S dicluster domain
    3.8e-07   29.8  17.5    3.2e-05   23.8   1.7    3.9  4  Fer4_2      4Fe-4S binding domain
    1.5e-06   28.0  23.7    0.00025   21.0   2.4    3.7  4  Fer4_6      4Fe-4S binding domain
    5.8e-06   26.7  16.4    0.00086   19.7   9.4    3.0  2  Fer4_8      4Fe-4S dicluster domain
    3.7e-05   24.4  17.4    0.00065   20.5   4.6    3.1  2  Fer4_3      4Fe-4S binding domain
     0.0015   18.9  10.5     0.0066   16.9   1.3    3.8  4  Fer4_4      4Fe-4S binding domain
  ------ inclusion threshold ------
      0.049   14.5  18.3       0.17   12.7   1.8    3.2  3  Fer4_22     4Fe-4S dicluster domain
       0.11   12.2   0.1       0.23   11.3   0.1    1.5  1  UVR         UvrB/uvrC motif
       0.12   12.6   0.7       0.12   12.6   0.7    3.1  3  Fer4_18     4Fe-4S dicluster domain
       0.13   12.4   0.0       0.13   12.4   0.0    2.0  1  HNH         HNH endonuclease
       0.38   11.3  13.3        0.3   11.7   0.8    2.9  3  Fer4_13     4Fe-4S single cluster domain of Ferredoxin I
        1.6    8.9   5.2        1.6    8.9   0.0    2.6  3  ETF_QO      Electron transfer flavoprotein-ubiquinone oxidore
        6.1    6.7  12.9        1.4    8.7   0.2    3.0  3  zf-CSL      CSL zinc finger
        6.8    7.5  16.8       0.85   10.4   1.5    3.4  3  Fer4_15     4Fe-4S single cluster domain
        7.3    7.1  11.5        8.7    6.8   7.3    2.3  2  E6          Early Protein (E6)
        8.6    6.5  10.7        1.2    9.2   2.1    2.5  2  zf-RRPl_C4  Putative ribonucleoprotein zinc-finger pf C4 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 !   32.8   2.0   4.7e-11   3.9e-08       1      24 []      35      58 ..      35      58 .. 0.94
   2 !   34.9   3.4   1.1e-11   8.6e-09       2      23 ..      69      90 ..      68      91 .. 0.92
   3 ?   -0.3   0.4       1.4   1.1e+03       7      12 ..     116     121 ..     114     122 .. 0.83
   4 ?   -1.4   0.2         3   2.4e+03       6      12 ..     155     161 ..     154     162 .. 0.69

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 4.7e-11
                                      EEEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  1 vvideekCigCGaCvevCPvgAIt 24
                                      +v + ++CigCG C  +CP +AIt
  gi|385806327|ref|YP_005842725.1| 35 PVLNFDLCIGCGSCSLACPPDAIT 58
                                      5789*******************7 PP

  == domain 2  score: 34.9 bits;  conditional E-value: 1.1e-11
                                      EEETTTSSS-THHHHHSTTTEE CS
                              Fer4  2 videekCigCGaCvevCPvgAI 23
                                      +i + +Ci+CG+C+evCPvgAI
  gi|385806327|ref|YP_005842725.1| 69 KIFYGRCIFCGRCEEVCPVGAI 90
                                      57899****************9 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.4
                                       TSSS-T CS
                              Fer4   7 kCigCG 12 
                                       kC  CG
  gi|385806327|ref|YP_005842725.1| 116 KCASCG 121
                                       899999 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 3
                                       TTSSS-T CS
                              Fer4   6 ekCigCG 12 
                                       ++C  C+
  gi|385806327|ref|YP_005842725.1| 155 SLCSECK 161
                                       5788885 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.5   7.6   2.9e-16   2.4e-13       2      52 .]      42      89 ..      41      89 .. 0.95
   2 ?    2.3   1.1      0.31   2.5e+02      30      45 ..     109     124 ..      92     162 .. 0.77

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 2.9e-16
                            Fer4_7  2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      CigCg C  aCp +ai+++ +en+++   ++i + +C++Cg+C++vCP+ga
  gi|385806327|ref|YP_005842725.1| 42 CIGCGSCSLACPPDAITFTRKENHAE---WKIFYGRCIFCGRCEEVCPVGA 89
                                      *******************9988877...********************98 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.31
                            Fer4_7  30 kveidpekClgCgaCv 45 
                                        ++++  kC +Cg+ +
  gi|385806327|ref|YP_005842725.1| 109 VANLKVAKCASCGKSM 124
                                       4566778899998755 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.9   1.6e-06    0.0013      33      51 .]      38      57 ..      22      57 .. 0.69
   2 !   38.3   7.4   1.4e-12   1.1e-09       2      51 .]      42      90 ..      41      90 .. 0.93
   3 !   16.3  10.3     1e-05    0.0081       1      41 [.      74     122 ..      74     163 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.6e-06
                            Fer4_9 33 e.eaCigCgaCveaCpkgai 51
                                      + + CigCg+C  aCp +ai
  gi|385806327|ref|YP_005842725.1| 38 NfDLCIGCGSCSLACPPDAI 57
                                      1467************9987 PP

  == domain 2  score: 38.3 bits;  conditional E-value: 1.4e-12
                            Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                      C+gCg+C  aCp ++++  ++e+ a+ +++   +Ci+Cg+C+e+Cp gai
  gi|385806327|ref|YP_005842725.1| 42 CIGCGSCSLACPPDAITFTRKENHAEWKIFYG-RCIFCGRCEEVCPVGAI 90
                                      ****************9999999999988866.9*************987 PP

  == domain 3  score: 16.3 bits;  conditional E-value: 1e-05
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase........eaCigCga 41 
                                       +C+ Cg+C+e+Cp g++++ +  + a+ ++++          +C +Cg+
  gi|385806327|ref|YP_005842725.1|  74 RCIFCGRCEEVCPVGAIIQNEEFELASKKKDDLevvanlkvAKCASCGK 122
                                       5****************99888888887776669*******99****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 !   36.1   8.2   6.3e-12   5.1e-09       2      56 .]      35      86 ..      34      86 .. 0.84
   2 !   22.5   4.5   1.1e-07     9e-05       6      51 ..      72     123 ..      67     126 .. 0.73
   3 ?   -0.8   0.1       2.1   1.7e+03       8      13 ..     156     161 ..     143     163 .. 0.57

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 6.3e-12
                           Fer4_10  2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrk..kvekCtgcgaCveaCP 56
                                      +v++ d Ci+Cg C  aCP      +a+ ++ +e++ +    +++C++cg C e+CP
  gi|385806327|ref|YP_005842725.1| 35 PVLNFDLCIGCGSCSLACPP-----DAITFTRKENHAEWkiFYGRCIFCGRCEEVCP 86
                                      68899***************.....6666666666666535899************9 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 1.1e-07
                           Fer4_10   6 ddtCirCgkCvkaCPadl.....tsvgakgeaseeeavrk.kvekCtgcgaC 51 
                                         +Ci Cg+C ++CP+ +     +   a++++++ e+v   kv kC  cg+ 
  gi|385806327|ref|YP_005842725.1|  72 YGRCIFCGRCEEVCPVGAiiqneEFELASKKKDDLEVVANlKVAKCASCGKS 123
                                       568*************99999984444445555545544459*******975 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 2.1
                           Fer4_10   8 tCirCg 13 
                                        C +C+
  gi|385806327|ref|YP_005842725.1| 156 LCSECK 161
                                       344443 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   5.2   4.1e-13   3.3e-10       4      57 ..      38      90 ..      35      93 .. 0.79
   2 ?    6.2   0.3     0.014        11       1      48 [.     110     161 ..     110     171 .. 0.74

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 4.1e-13
                           Fer4_21  4 dedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedci 57
                                      + d CigCg+C +aC+  +++  ++++++ +k+   +C+ C  C +vCPv ++i
  gi|385806327|ref|YP_005842725.1| 38 NFDLCIGCGSCSLACPPDAITFTRKENHAEWKIFYGRCIFCGRCEEVCPV-GAI 90
                                      6689************7444444555556668899**************9.544 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.014
                           Fer4_21   1 AridedkCigCgkCliaCedtshqai....eidaktvlkvvedeCvGCnlCs 48 
                                       A+++ +kC +Cgk + + e +    i    +  ++++++v+++    C  C 
  gi|385806327|ref|YP_005842725.1| 110 ANLKVAKCASCGKSMNVTEREVKYVIdvlrSSLPQSKAEVISELASLCSECK 161
                                       567789***********99999888844433335667788877766666664 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   0.7   3.8e-06    0.0031       2      23 ..      42      63 ..      41      71 .. 0.82
   2 !   21.3   7.6   4.7e-07   0.00039       1      33 [.      74     106 ..      74     163 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3.8e-06
                           Fer4_16  2 CgtCgkCaevCPtnaikekkek 23
                                      C++Cg C  +CP +ai+ ++++
  gi|385806327|ref|YP_005842725.1| 42 CIGCGSCSLACPPDAITFTRKE 63
                                      *****************88433 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 4.7e-07
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkekeiearecisy 33 
                                       rC+ Cg+C evCP++ai +++e+e++++++ + 
  gi|385806327|ref|YP_005842725.1|  74 RCIFCGRCEEVCPVGAIIQNEEFELASKKKDDL 106
                                       6*******************9998888875444 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.3   6.6e-06    0.0054      33      58 ..      26      54 ..      12      57 .. 0.74
   2 !   16.3   0.9   1.4e-05     0.011      38      58 ..      67      87 ..      54      89 .. 0.73
   3 !   14.7   7.2   4.1e-05     0.033       1      51 [.      74     122 ..      74     162 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 6.6e-06
                           Fer4_17 33 lleeaekee...kaslCieCgeCerkCPq 58
                                      ++ee  + +   +++lCi+Cg C+ +CP 
  gi|385806327|ref|YP_005842725.1| 26 KVEEDYRGKpvlNFDLCIGCGSCSLACPP 54
                                      55555555334489**************6 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 1.4e-05
                           Fer4_17 38 ekeekaslCieCgeCerkCPq 58
                                      e +   ++Ci Cg+Ce++CP 
  gi|385806327|ref|YP_005842725.1| 67 EWKIFYGRCIFCGRCEEVCPV 87
                                      4456789*************6 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 4.1e-05
                           Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCge 51 
                                       rCi Cg C+++Cp +++++ne+ +l+ + k  +le   ++ k+ +C++Cg+
  gi|385806327|ref|YP_005842725.1|  74 RCIFCGRCEEVCPVGAIIQNEEFELASKKKD-DLEV-VANLKVAKCASCGK 122
                                       7*******************99999999443.3433.46779999999986 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   1.7   3.9e-08   3.2e-05       2      21 ..      34      53 ..      33      54 .. 0.93
   2 !   12.6   1.3   0.00014      0.11       9      21 ..      74      86 ..      68      87 .. 0.86
   3 ?    2.3   0.1      0.27   2.2e+02       8      14 ..     115     121 ..     108     122 .. 0.83
   4 ?   -0.5   0.1       2.1   1.7e+03       9      14 ..     156     161 ..     149     162 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 3.9e-08
                            Fer4_2  2 pvvvdtdrCigCgaCvsaCP 21
                                      ++v + d CigCg+C  aCP
  gi|385806327|ref|YP_005842725.1| 34 KPVLNFDLCIGCGSCSLACP 53
                                      6899***************9 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00014
                            Fer4_2  9 rCigCgaCvsaCP 21
                                      rCi Cg C  +CP
  gi|385806327|ref|YP_005842725.1| 74 RCIFCGRCEEVCP 86
                                      8999********* PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.27
                            Fer4_2   8 drCigCg 14 
                                       ++C +Cg
  gi|385806327|ref|YP_005842725.1| 115 AKCASCG 121
                                       69****9 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 2.1
                            Fer4_2   9 rCigCg 14 
                                        C +C+
  gi|385806327|ref|YP_005842725.1| 156 LCSECK 161
                                       699996 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   3.1   1.4e-06    0.0011       7      24 .]      40      57 ..      38      57 .. 0.94
   2 !   21.0   2.4     3e-07   0.00025       6      24 .]      72      90 ..      69      90 .. 0.89
   3 ?    1.0   0.2      0.65   5.3e+02       7      14 ..     115     122 ..     113     122 .. 0.84
   4 ?   -1.3   0.2       3.3   2.7e+03       8      12 ..     156     160 ..     154     162 .. 0.58

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.4e-06
                            Fer4_6  7 dkCigCgdCvrvCPegai 24
                                      d+CigCg C  +CP +ai
  gi|385806327|ref|YP_005842725.1| 40 DLCIGCGSCSLACPPDAI 57
                                      89************9887 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 3e-07
                            Fer4_6  6 pdkCigCgdCvrvCPegai 24
                                      + +Ci Cg+C+ vCP gai
  gi|385806327|ref|YP_005842725.1| 72 YGRCIFCGRCEEVCPVGAI 90
                                      669***************8 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.65
                            Fer4_6   7 dkCigCgd 14 
                                        kC +Cg+
  gi|385806327|ref|YP_005842725.1| 115 AKCASCGK 122
                                       59****96 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 3.3
                            Fer4_6   8 kCigC 12 
                                       +C  C
  gi|385806327|ref|YP_005842725.1| 156 LCSEC 160
                                       66666 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   9.4   1.1e-06   0.00086       3      64 ..      40      88 ..      38      89 .. 0.71
   2 !   16.8   7.3   8.2e-06    0.0067       4      56 ..      74     122 ..      71     162 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.1e-06
                            Fer4_8  3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                                      + Ci+Cg C  aCp    t      +r+e+ +   e++        ++C  cg+C+evCpvg
  gi|385806327|ref|YP_005842725.1| 40 DLCIGCGSCSLACPPDAIT-----FTRKENHA---EWKI-----FYGRCIFCGRCEEVCPVG 88
                                      67***********933322.....33333333...3444.....369*************97 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 8.2e-06
                            Fer4_8   4 kCieCgaCqsaCp...vlrrtkkhlldargeaaedvqeeqvleeeealwsCttcga 56 
                                       +Ci Cg+C++ Cp   +++++  +l +++++  e v+ + +      + +C +cg+
  gi|385806327|ref|YP_005842725.1|  74 RCIFCGRCEEVCPvgaIIQNEEFELASKKKDDLE-VVANLK------VAKCASCGK 122
                                       8************443333333344444444444.666666......677777764 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   4.9   1.6e-05     0.013       1      15 []      42      56 ..      42      56 .. 0.97
   2 !   20.5   4.6   7.9e-07   0.00065       1      15 []      75      89 ..      75      89 .. 0.98

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.6e-05
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+gCg C  +CP++A
  gi|385806327|ref|YP_005842725.1| 42 CIGCGSCSLACPPDA 56
                                      *************98 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 7.9e-07
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+ Cg+C+evCPvgA
  gi|385806327|ref|YP_005842725.1| 75 CIFCGRCEEVCPVGA 89
                                      **************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 !   16.9   1.3   8.1e-06    0.0066       2      15 ..      40      53 ..      39      61 .. 0.90
   2 !   13.6   2.2     9e-05     0.073       3      17 .]      74      88 ..      72      93 .. 0.91
   3 ?   -0.4   0.5       2.7   2.2e+03       3       8 ..     116     121 ..     115     122 .. 0.71
   4 ?    0.0   0.2         2   1.7e+03       3       8 ..     156     161 ..     154     162 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 8.1e-06
                            Fer4_4  2 erCigCgsCvaaCP 15
                                      + CigCgsC  aCP
  gi|385806327|ref|YP_005842725.1| 40 DLCIGCGSCSLACP 53
                                      78***********9 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 9e-05
                            Fer4_4  3 rCigCgsCvaaCPqg 17
                                      rCi Cg+C+ +CP+g
  gi|385806327|ref|YP_005842725.1| 74 RCIFCGRCEEVCPVG 88
                                      9************75 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 2.7
                            Fer4_4   3 rCigCg 8  
                                       +C  Cg
  gi|385806327|ref|YP_005842725.1| 116 KCASCG 121
                                       688887 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 2
                            Fer4_4   3 rCigCg 8  
                                        C +C+
  gi|385806327|ref|YP_005842725.1| 156 LCSECK 161
                                       599998 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   2.1    0.0012      0.96      79      93 ..      39      53 ..      25      57 .. 0.78
   2 ?   12.7   1.8   0.00021      0.17      68      94 ..      61      87 ..      55      91 .. 0.77
   3 ?    1.2   0.1      0.83   6.8e+02      73      91 ..     108     126 ..      91     131 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0012
                           Fer4_22 79 esgCvGCgRCieacp 93
                                         C+GCg C+ acp
  gi|385806327|ref|YP_005842725.1| 39 FDLCIGCGSCSLACP 53
                                      567888888888887 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00021
                           Fer4_22 68 hklsefkekfgesgCvGCgRCieacpv 94
                                      +k ++ + k+    C+ CgRC+e+cpv
  gi|385806327|ref|YP_005842725.1| 61 RKENHAEWKIFYGRCIFCGRCEEVCPV 87
                                      56666666666778999******9997 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.83
                           Fer4_22  73 fkekfgesgCvGCgRCiea 91 
                                       ++++ +  +C  Cg+ +++
  gi|385806327|ref|YP_005842725.1| 108 VVANLKVAKCASCGKSMNV 126
                                       4556677888888887665 PP

>> UVR  UvrB/uvrC motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00028      0.23      15      32 ..      91     108 ..      90     112 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00028
                               UVR  15 aenedFEkAAklRDqina 32 
                                       ++ne+FE+A+k +D ++ 
  gi|385806327|ref|YP_005842725.1|  91 IQNEEFELASKKKDDLEV 108
                                       689***********9986 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   1.4      0.11        89      61      72 ..      42      53 ..      24      62 .. 0.78
   2 ?   12.6   0.7   0.00014      0.12      55      78 ..      69      92 ..      54      97 .. 0.75
   3 ?    1.4   0.3      0.45   3.6e+02      48      72 ..     104     128 ..      91     138 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.11
                           Fer4_18 61 cidcescvkvcP 72
                                      ci c+sc   cP
  gi|385806327|ref|YP_005842725.1| 42 CIGCGSCSLACP 53
                                      888888888887 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00014
                           Fer4_18 55 ekgagdcidcescvkvcPtgidir 78
                                      +   g ci c+ c +vcP+g  i+
  gi|385806327|ref|YP_005842725.1| 69 KIFYGRCIFCGRCEEVCPVGAIIQ 92
                                      445799*************98776 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.45
                           Fer4_18  48 kekeerkekgagdcidcescvkvcP 72 
                                        + e  ++ ++++c +c++ ++v  
  gi|385806327|ref|YP_005842725.1| 104 DDLEVVANLKVAKCASCGKSMNVTE 128
                                       3344555667888888888888765 PP

>> HNH  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00016      0.13       1      42 [.     117     162 ..     117     164 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00016
                               HNH   1 CeyCgrkfhksealevdHiipisq.....ggaddieNlqllCksCHn 42 
                                       C  Cg+   ++ + ev ++i + +     ++a  i+ l+ lC++C +
  gi|385806327|ref|YP_005842725.1| 117 CASCGKSMNVT-EREVKYVIDVLRsslpqSKAEVISELASLCSECKR 162
                                       999****9997.**********955455599999***********66 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 ?   11.7   0.8   0.00037       0.3       4      17 ..      40      53 ..      37      65 .. 0.91
   2 ?    7.2   1.4    0.0089       7.2       5      17 ..      74      86 ..      73      88 .. 0.94
   3 ?   -2.1   0.2       7.3     6e+03       5      10 ..     116     121 ..     115     126 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00037
                           Fer4_13  4 dtCiacgaCvelaP 17
                                      d Ci+cg+C  ++P
  gi|385806327|ref|YP_005842725.1| 40 DLCIGCGSCSLACP 53
                                      68***********9 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0089
                           Fer4_13  5 tCiacgaCvelaP 17
                                      +Ci cg C e++P
  gi|385806327|ref|YP_005842725.1| 74 RCIFCGRCEEVCP 86
                                      7***********9 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 7.3
                           Fer4_13   5 tCiacg 10 
                                       +C +cg
  gi|385806327|ref|YP_005842725.1| 116 KCASCG 121
                                       466665 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 ?    8.9   0.0     0.002       1.6      62      95 ..      29      62 ..       9      66 .. 0.77
   2 ?    1.0   1.2      0.55   4.5e+02      42      55 ..      77      90 ..      65     136 .. 0.57
   3 ?   -2.9   0.0       9.4   7.7e+03      78      98 ..     157     177 ..     143     178 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.002
                                      TTSSEEEEE-CCC--S--HHHHH-TT--EEE--- CS
                            ETF_QO 62 eakekklqinaqnCvhCktCdikdpsqniewvvP 95
                                      e    k ++n   C+ C +C++  p + i+++  
  gi|385806327|ref|YP_005842725.1| 29 EDYRGKPVLNFDLCIGCGSCSLACPPDAITFTRK 62
                                      33455678999******************99865 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.55
                                      HS-THHHH-TTS-E CS
                            ETF_QO 42 yagpeqryCPagvy 55
                                      + g ++ +CP g  
  gi|385806327|ref|YP_005842725.1| 77 FCGRCEEVCPVGAI 90
                                      44455556665543 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 9.4
                                       --HHHHH-TT--EEE---STT CS
                            ETF_QO  78 CktCdikdpsqniewvvPeGg 98 
                                       C  C  k   ++i  +  +Gg
  gi|385806327|ref|YP_005842725.1| 157 CSECKRKRFIEKIIKTYGKGG 177
                                       666766666666665555555 PP

>> zf-CSL  CSL zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.2    0.0017       1.4      39      52 ..      35      50 ..      19      52 .. 0.73
   2 ?    1.2   4.8      0.37     3e+02      31      56 ..      95     126 ..      57     129 .. 0.66
   3 ?    5.9   0.9     0.013        10      19      40 ..     115     146 ..      90     161 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0017
                                      .....--EEEETTSSE CS
                            zf-CSL 39 e..gaevvvqCssCSL 52
                                         ++++ ++C+sCSL
  gi|385806327|ref|YP_005842725.1| 35 PvlNFDLCIGCGSCSL 50
                                      15578999*******9 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.37
                                       HHHHHTT..........--EEEETTSSEEEEE CS
                            zf-CSL  31 eedleegae......gaevvvqCssCSLwikV 56 
                                       e +l ++++          v++C sC   + V
  gi|385806327|ref|YP_005842725.1|  95 EFELASKKKddlevvANLKVAKCASCGKSMNV 126
                                       33333332255555677889999999776666 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.013
                                       EEE.TTSSEEEEEHHHHHTT............ CS
                            zf-CSL  19 ypC.RCgdeFelteedleegae.........g 40 
                                        +C  Cg+ +++te++++   +         +
  gi|385806327|ref|YP_005842725.1| 115 AKCaSCGKSMNVTEREVKYVIDvlrsslpqsK 146
                                       46777888888877777665445555555553 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   0.0       5.3   4.3e+03      19      30 ..      24      35 ..       7      40 .. 0.70
   2 ?   10.4   1.5     0.001      0.85       4      23 ..      38      58 ..      35      67 .. 0.78
   3 ?    1.6   7.2       0.6   4.9e+02       7      25 ..      74      99 ..      72     159 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 5.3
                           Fer4_15 19 pevfeldedgla 30
                                      pe +e+d +g++
  gi|385806327|ref|YP_005842725.1| 24 PEKVEEDYRGKP 35
                                      566677777776 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.001
                           Fer4_15  4 DrdaCigcglCvaea.pevfe 23
                                      + d+Cigcg C  ++ p+ ++
  gi|385806327|ref|YP_005842725.1| 38 NFDLCIGCGSCSLACpPDAIT 58
                                      5699***********655555 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.6
                           Fer4_15  7 aCigcglCvaea.......pevfeld 25
                                      +Ci cg+C +++        e fel+
  gi|385806327|ref|YP_005842725.1| 74 RCIFCGRCEEVCpvgaiiqNEEFELA 99
                                      7*******999966555553333333 PP

>> E6  Early Protein (E6)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   1.4         3   2.5e+03      69      78 ..      40      49 ..      17      78 .. 0.53
   2 ?    6.8   7.3     0.011       8.7       9      79 ..      92     162 ..      75     172 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 3
                                      GSEEEETTT- CS
                                E6 69 dleiRCvvCl 78
                                      dl+i C +C+
  gi|385806327|ref|YP_005842725.1| 40 DLCIGCGSCS 49
                                      4555555553 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.011
                                       XHHHHHHHHHTTXBXEEETTEEEBXXHHHHHHHHHHHHHHHEEEEEEHHHHHHHHTSTGGGSEEEETTT-- CS
                                E6   9 skleallfkekklslvwreglpygvCkkClevlallelllhlerslkakeleelvgkslsdleiRCvvClk 79 
                                       ++ e  l ++kk  l    +l+++ C +C + + + e++  +  ++  ++l + + + +s+l   C  C +
  gi|385806327|ref|YP_005842725.1|  92 QNEEFELASKKKDDLEVVANLKVAKCASCGKSMNVTEREVKYVIDVLRSSLPQSKAEVISELASLCSECKR 162
                                       44444444444444445567888899999999999999999999999999999999999999999999876 PP

>> zf-RRPl_C4  Putative ribonucleoprotein zinc-finger pf C4 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   5.0       2.2   1.8e+03      53      90 ..      76     124 ..      41     140 .. 0.58
   2 ?    9.2   2.1    0.0015       1.2      38      69 ..     140     171 ..     117     174 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2.2
                        zf-RRPl_C4  53 kLCtkCkeknekekeircetfeeylkklk...........lCkeCkerv 90 
                                       + C  C+e      +i+ e+fe   kk              C +C ++ 
  gi|385806327|ref|YP_005842725.1|  76 IFCGRCEEVCPVGAIIQNEEFELASKKKDdlevvanlkvaKCASCGKSM 124
                                       3444444444444444444444444443344444444444444444433 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0015
                        zf-RRPl_C4  38 elvpikelekislrdkLCtkCkeknekekeir 69 
                                       +++p ++ e is+   LC++Ck+k   ek+i+
  gi|385806327|ref|YP_005842725.1| 140 SSLPQSKAEVISELASLCSECKRKRFIEKIIK 171
                                       567777899***************99998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       878  (0.0489709); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.62u 0.36s 00:00:00.98 Elapsed: 00:00:00.55
# Mc/sec: 983.38
//
Query:       gi|385806328|ref|YP_005842726.1|  [L=563]
Description: Component HyfG of membrane-bound [Ni,Fe]-hydrogenase [Fervidicoccus fontis Kam940]
Scores for complete 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-61  207.4   0.1    1.2e-45  155.8   0.1    2.3  2  Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd s
      2e-23   83.3   0.0    4.6e-23   82.2   0.0    1.6  1  Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd s
    6.3e-18   64.9   1.7    3.3e-14   52.7   0.0    2.9  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 !  155.8   0.1   1.9e-49   1.2e-45       8     171 ..     300     463 ..     295     469 .. 0.97
   2 !   49.7   0.0   4.2e-17   2.5e-13     204     271 .]     469     536 ..     460     536 .. 0.94

  Alignments for each domain:
  == domain 1  score: 155.8 bits;  conditional E-value: 1.9e-49
                                       HHHHHHHHHHHHHHHHHHHSSSSS-TTBESSBBSS---TTHHHHHHHHHHHHHHHHHHHHHHHHSSSSHHHHHSSSS CS
                    Complex1_49kDa   8 flyafreRekildlleevtGaRltasyiriGGvarDlpegllekikeflkelekkldeleklltknrifkkRtkgvg 84 
                                       f+ +++ Re++++l e +tGaR t+ +  +GGv+rD+ e+  +k  e+lk+ e +l+++ + + k +++ kR++g+g
  gi|385806328|ref|YP_005842726.1| 300 FMQLWKVRERLMNLAEVLTGARKTYGINVVGGVRRDIIEERRKKSLEILKKTEVELKDIGETVLKTSTLLKRMEGIG 376
                                       88999************************************************************************ PP

                                       -BSHHHHHHHTT-SSSSGGGT-TTTHHHHSS-SSGGGS-------SSBSHHHHHHHHHHHHHHHHHHHHHHHHT--. CS
                    Complex1_49kDa  85 vlskeealelgltGpvlRasGvkyDlRkaepYeaYdeldfdvpvgeegDvydRylvrveEmrqSlkIieqaleklpe 161
                                       vl k+ a  l ++Gpv+R+sG+  D+Rk++pY+aY el+f++p+ +egD+++R+lvr+eE  +Sl+Iieqal++lp+
  gi|385806328|ref|YP_005842726.1| 377 VLPKDVARTLNVVGPVARGSGLYRDVRKDHPYAAYRELSFKIPLYTEGDILARFLVRYEETFESLSIIEQALDRLPN 453
                                       ***************************************************************************** PP

                                       S-SB---TTT CS
                    Complex1_49kDa 162 gpvlaedkkv 171
                                       gp+  e k+v
  gi|385806328|ref|YP_005842726.1| 454 GPIFEEVKEV 463
                                       **99877665 PP

  == domain 2  score: 49.7 bits;  conditional E-value: 4.2e-17
                                       EEEEEEETTEEEEEEEEEESSSS-SEEEEE-HHHHTTTTHHHHTTTS-SGGGTHHHHTT---HHHHH- CS
                    Complex1_49kDa 204 vyaavEapkGelgvylvsdgsskpyrlkirapsfvnlqaleellkgellaDvvailgsldivlgevDR 271
                                       ++ avEap+Ge++++ +  ++sk yr+++rap++ n  +++++++g++laDv+ i++s+d++ ++++R
  gi|385806328|ref|YP_005842726.1| 469 AIGAVEAPRGEVVHFAIIGEDSKIYRWRVRAPTYSNWPSVPYMSRGYTLADVPLIVASIDPCYSCTER 536
                                       5679**********************************************************999877 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 !   82.2   0.0   7.6e-27   4.6e-23       3     118 ..      36     158 ..      34     162 .. 0.84

  Alignments for each domain:
  == domain 1  score: 82.2 bits;  conditional E-value: 7.6e-27
                                       --HHHHHHHHHHHHH...TT--EEEEEEEEETT..SSSEEEEEEEE--S-........-EEEEEE....-S-BEE-- CS
                    Complex1_30kDa   3 vepedllevakflkdeeelgfdvlsdltavDek..eerfevvyhllslekn.......erirvkvevdeeepevpSv 70 
                                       +++++ll++++++  e  lg  +ls+++  D +  +++f++ y+++ +e++         i v + ++ ++p+++Sv
  gi|385806328|ref|YP_005842726.1|  36 IRKDALLKICSYIFWE--LG-GFLSTMSVSDMRkiNGSFRLDYVFS-IEEKeessspkPWIIVYTMIPGNNPRFQSV 108
                                       5678888888888873..44.6888888889667799999999998.4333356777788999999999******** PP

                                       TTT-STHHHHHHHHHHHSHHBCTTSSTSS-SSSSTTS..SS-TTSTTS-- CS
                    Complex1_30kDa  71 tdlfpgadwyEREayDmfGivfeghpdlrrillpedf..eghPLRkdfpl 118
                                       t+  p+a+wyEREa D+fG+  eghpd+r+++lp+d+    +PLRkd++ 
  gi|385806328|ref|YP_005842726.1| 109 TPELPAANWYEREAKDLFGVIPEGHPDPRKLILPDDWpdGIYPLRKDMDY 158
                                       *************************************86567*****986 PP

>> NiFeSe_Hases  Nickel-dependent hydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.7   0.0   5.6e-18   3.3e-14       1      78 [.     217     298 ..     217     347 .. 0.92
   2 !    9.8   0.8   5.3e-05      0.32     419     456 ..     464     502 ..     388     535 .. 0.78

  Alignments for each domain:
  == domain 1  score: 52.7 bits;  conditional E-value: 5.6e-18
                                       --HHHHTTTS.-GGGHHHHHHTT-SSSTTHHHHHHHHHHHHHHT----HHHHHHHHHHHHHHHHHHHHHHH...HHT CS
                      NiFeSe_Hases   1 RGlElilkgr.dprdawalvqRiCGVCttvHalasvravedAlgikipknarlirnliaaalllhdhivhF...YhL 73 
                                       RG+E++ + r + +++ +l++RiCG+C  vH+++ v+a+e+A++i++p+ a++ir+++   +   +h++++    hL
  gi|385806328|ref|YP_005842726.1| 217 RGVEKLGEARlTYNQVPFLAERICGICGFVHSTSYVQAIEEAMKIDVPERAKYIRTIMLEIERATSHLLWLglaSHL 293
                                       7888887777356778899***************************************************855569* PP

                                       TGGGT CS
                      NiFeSe_Hases  74 halDw 78 
                                       +a+Dw
  gi|385806328|ref|YP_005842726.1| 294 AAFDW 298
                                       ****9 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 5.3e-05
                                       -SEEEEEEEEEETTEEEEEEEEE.ETTEEEEEEEE-HHH CS
                      NiFeSe_Hases 419 pkeakGvglveapRGaLsHwiki.kdgkienYqavvPsT 456
                                       ++    +g veapRG   H+  i +d+ki ++ +  P+ 
  gi|385806328|ref|YP_005842726.1| 464 EAYRPAIGAVEAPRGEVVHFAIIgEDSKIYRWRVRAPTY 502
                                       33345799***************88********999973 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (563 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.37s 00:00:01.04 Elapsed: 00:00:00.54
# Mc/sec: 3128.16
//
Query:       gi|385806329|ref|YP_005842727.1|  [L=486]
Description: Component HyfF of membrane-bound [Ni,Fe]-hydrogenase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-55  188.5  30.4    1.5e-55  188.5  30.4    2.2  2  Proton_antipo_M  Proton-conducting membrane transporter
    6.6e-05   22.9   0.7    6.6e-05   22.9   0.7    4.3  4  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   2.1      0.12   1.1e+03      46      88 ..      68     110 ..       8     123 .. 0.67
   2 !  188.5  30.4   1.6e-59   1.5e-55       2     288 ..     125     418 ..     124     427 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.12
                   Proton_antipo_M  46 sliLLlgilllynltgtlefeelskalelglnslellllllll 88 
                                       s i++++++lly +++  ++ ++   ++ g  s e+  l++ l
  gi|385806329|ref|YP_005842727.1|  68 SAIMIFALSLLYFAASIFSIGYIEHEITIGEISKERKRLFYSL 110
                                       4567777777777777666666655553333333333333333 PP

  == domain 2  score: 188.5 bits;  conditional E-value: 1.6e-59
                   Proton_antipo_M   2 ndLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskal...... 72 
                                       n+++ +++++E++ +++++L+g++ +kp+sleAs k+++l ++g ++ L+g +l+y+++ +  +++  ++       
  gi|385806329|ref|YP_005842727.1| 125 NNIVVMWIAIEATTIASTFLVGIY-NKPESLEASWKYLILCSVGLSFSLYGTVLFYSISYQAGLTKPWLYSsilnss 200
                                       7999*******************9.788******************************9988888877776667876 PP

                   Proton_antipo_M  73 .elglnslelllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla..vssnei 146
                                         +    +++ l++++llvg+ +K+++vplh Wlpda+ eaP+pvsal++++l + ++++l+r   ++     + ++
  gi|385806329|ref|YP_005842727.1| 201 nLFSNYISMIKLIFIFLLVGFGTKAGLVPLHAWLPDAHSEAPAPVSALFSGILIECSMYVLMRYYGIMVavGLGSFV 277
                                       33444456788999*****************************************************99888999** PP

                   Proton_antipo_M 147 sqlllilaiismllgslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallFllagsvi 223
                                       ++++li++++sm+++s++ ++ +d+KrllA+Ssi ++G++  +l+ ++++g+ +a+++l++h l+k +lFl +g++ 
  gi|385806329|ref|YP_005842727.1| 278 RYIFLIIGLLSMFIASMLMITARDVKRLLAFSSIEQMGIIACGLGFGSYIGIIGAVFQLISHTLIKGSLFLSSGAI- 353
                                       *************************************************************************766. PP

                   Proton_antipo_M 224 yerektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvlavv 288
                                        +  +tr+i++++g+ k+ P+l +++l+++l+++  Pp++ F+s + + ++  + + ++ +++++
  gi|385806329|ref|YP_005842727.1| 354 MNIYNTRNINRIRGIIKASPVLGTLVLLGMLGIVLCPPFSTFYSGLFVVMSGAEENNLAGIITMI 418
                                       7888****************************************999999888887777776644 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 !   22.9   0.7   7.4e-09   6.6e-05      15      58 .]      61     112 ..      52     112 .. 0.88
   2 ?   -1.4   1.4       0.3   2.6e+03      24      37 ..     117     130 ..     114     135 .. 0.78
   3 ?   -1.5   0.2       0.3   2.7e+03      36      43 ..     176     183 ..     170     197 .. 0.88
   4 ?   -0.1   0.4      0.11     1e+03      28      40 ..     414     426 ..     411     428 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 7.4e-09
                   Proton_antipo_N  15 gfllDklsalmllvvtfvsllvhlYSigYMadd........egyqRFfayls 58 
                                        f +D lsa+m++  +++ +   ++SigY +++        e+++ F+++l+
  gi|385806329|ref|YP_005842727.1|  61 EFAVDYLSAIMIFALSLLYFAASIFSIGYIEHEitigeiskERKRLFYSLLN 112
                                       699*****************************97777777557888998886 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.3
                   Proton_antipo_N  24 lmllvvtfvsllvh 37 
                                       +mllvvt+   +v+
  gi|385806329|ref|YP_005842727.1| 117 TMLLVVTTNNIVVM 130
                                       8******9777665 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.3
                   Proton_antipo_N  36 vhlYSigY 43 
                                       v++YSi+Y
  gi|385806329|ref|YP_005842727.1| 176 VLFYSISY 183
                                       899***99 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 0.11
                   Proton_antipo_N  28 vvtfvsllvhlYS 40 
                                       ++t+++llv+ ++
  gi|385806329|ref|YP_005842727.1| 414 IITMIALLVIAFA 426
                                       7899999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (486 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1075  (0.0599587); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); 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):               2  [number of targets reported over threshold]
# CPU time: 0.79u 0.37s 00:00:01.16 Elapsed: 00:00:00.57
# Mc/sec: 2564.62
//
Query:       gi|385806330|ref|YP_005842728.1|  [L=220]
Description: Component HyfE of membrane-bound [Ni,Fe]-hydrogenase [Fervidicoccus fontis Kam940]
Scores for complete 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   24.3   1.9    1.9e-05   24.3   1.9    3.1  3  Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase cha
  ------ inclusion threshold ------
        1.4    8.8   6.4        1.6    8.5   2.0    2.4  2  PGG          Domain of unknown function


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 ?   -2.6   0.2      0.48   4.3e+03      67      74 ..      19      26 ..       5      32 .. 0.55
   2 !    3.7   0.2     0.005        45      22      74 ..      46     109 ..      39     118 .. 0.70
   3 !   24.3   1.9   2.1e-09   1.9e-05       5     104 ..     134     216 ..     130     220 .] 0.94

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.48
                                      GHHHHHHH CS
                       Oxidored_q2 67 qalvLtai 74
                                       ++++tai
  gi|385806330|ref|YP_005842728.1| 19 ALMIFTAI 26
                                      23344444 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.005
                                       CCHHHHHHHHHHHHHHHHHHHHHHHHC........................TTSCGGHHHHHHH CS
                       Oxidored_q2  22 nllkvliglelisnavnlllvlagvftegtlvi...........tnpatefadplpqalvLtai 74 
                                        ll  ++++  i  + +l+ +l++  t++ +v+           + +  ++  p   ++v++ai
  gi|385806330|ref|YP_005842728.1|  46 FLLTLIFAMMSIRDSYFLIWALVAFVTKTLIVPwlviksleksgERKDIKTSIPSWLTMVIYAI 109
                                       5789999****************99997777779999998886633333333344444444444 PP

  == domain 3  score: 24.3 bits;  conditional E-value: 2.1e-09
                                       HHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHHHHHHHC.............TTSCGGHHHHHHHHHHHHHH CS
                       Oxidored_q2   5 liallfliGlygvllrrnllkvliglelisnavnlllvlagvftegtlvitnpatefadplpqalvLtaivigaaet 81 
                                       +++ lfliGl  ++++++++k+++gl+  +n+ +l+l+l+                 a  +p+++ +   + ++  +
  gi|385806330|ref|YP_005842728.1| 134 VSISLFLIGLKQMVTKKSIFKQILGLCHFENGSHLTLALL-----------------APGIPETIEIGCTTDAVFLI 193
                                       7899***********************************9.................7789**************** PP

                                       HHHHHHHHHHHHHSSS-BCCG-- CS
                       Oxidored_q2  82 avgLallvrlyreygtddvqelr 104
                                       av   l+v + + ++t+dv +l+
  gi|385806330|ref|YP_005842728.1| 194 AVCCILAVHIKKVNNTVDVTQLK 216
                                       *******************9985 PP

>> PGG  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   1.2     0.024   2.1e+02      66     105 ..      17      57 ..       6      61 .. 0.72
   2 ?    8.5   2.0   0.00018       1.6      54     112 ..      60     118 ..      49     121 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.024
                               PGG  66 aSlvvvvlllis.slvedeakslpkklrvllvllvlsllsl 105
                                       +S +++++ +++ + ++ ++ ++  +l+  l++l+++++s+
  gi|385806330|ref|YP_005842728.1|  17 LSALMIFTAIWIsETIDLRRAANIYRLQSFLLTLIFAMMSI 57 
                                       46777777776545567777777888888888888888876 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00018
                               PGG  54 kvFvisnaiAlvaSlvvvvlllisslvedeakslpkklrvllvllvlsllsllvaFaag 112
                                         F+i   +A+v+ +++v  l+i+sl+++ +++  k ++   +++v+  + l+++F +g
  gi|385806330|ref|YP_005842728.1|  60 SYFLIWALVAFVTKTLIVPWLVIKSLEKSGERKDIKTSIPSWLTMVIYAILLVFSFWTG 118
                                       67********************8888777777777888888889999999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.40s 00:00:01.01 Elapsed: 00:00:00.59
# Mc/sec: 1119.04
//
Query:       gi|385806331|ref|YP_005842729.1|  [L=310]
Description: Component HyfC of membrane-bound [Ni,Fe]-hydrogenase [Fervidicoccus fontis Kam940]
Scores for complete 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-50  170.6  19.0    5.8e-50  170.3  19.0    1.0  1  NADHdh           NADH dehydrogenase
  ------ inclusion threshold ------
      0.012   15.6   0.0       0.02   14.8   0.0    1.3  1  Pathogen_betaC1  Beta-satellite pathogenicity beta C1 protein
       0.11   12.8   2.4       0.19   12.0   0.0    2.7  2  TadE             TadE-like protein


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 !  170.3  19.0   9.7e-54   5.8e-50       5     297 ..      10     305 ..       5     307 .. 0.89

  Alignments for each domain:
  == domain 1  score: 170.3 bits;  conditional E-value: 9.7e-54
                                       HHHHHHHHHHHHHHHHHHHHHHHHTTS--S-SSTTTTTTHHHHHHHHHCCS-----TTS-HHHHHHHHHHHHHHHHC CS
                            NADHdh   5 lllvvlllvvalltlleRkvlAriqdRlGPnrvGplGllqplaDalKlllKediipkkadkllfllapvlalilall 81 
                                       l ++++l++ ++l ++ Rk++Ar+++R+GP      ++ qp+ D++Kl  K + i+ + ++++f  ap++al++ l+
  gi|385806331|ref|YP_005842729.1|  10 LQITIVLFMSLFLEGVRRKLIARLHSRIGP------PISQPFRDLVKLWRKREEIKPECSSWIFEKAPIIALAVLLT 80 
                                       33445666666*******************......9************99999999999***************** PP

                                       TTTTS-SSSSSS--TT.HHHHHHHHHHHCHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-SS CS
                            NADHdh  82 afaviPfgevladlnv.glllilalsslgvygillaGwasnskYallGalRsaaqmisyEvalglsllavvllagsl 157
                                       + ++iP+ +  + +++ +++li++ + +  +++ la++++ s+Y + +a R++   i  Eval+l +l++v+++g++
  gi|385806331|ref|YP_005842729.1|  81 LSIMIPIIS-SIGFSLrDIILIIYSLIIFRFILSLAAFDASSPYGIPSAWRETYLGILGEVALILPVLCLVVTTGTT 156
                                       ******773.33444469*********************************************************** PP

                                       -HHHHHHCCCTT...-CCCCHHHHHHHHHHHHHHCCTCTTBTTTTSTTSSSSCCCTT-HCHHHHHHHHHHHHHHHHH CS
                            NADHdh 158 slseiveaqeei...wfillqllafiifliallaetnraPFDlpeaesELvaGfhtEYsgmkfalfflaeyanmvlv 231
                                       +l +i  + e++     ++   la+i+ +iall et+  PFD++eae+EL +G+ +EYsg  +alf l ++++ v++
  gi|385806331|ref|YP_005842729.1| 157 DLGKISYYVESNlqlLSYPSFYLAAIAGFIALLLETGVQPFDVAEAEQELQEGISVEYSGKTLALFKLDQMLKRVVI 233
                                       *****76665544333377779******************************************************* PP

                                       HHHHHHHCT.SS-HCCS............HHHHHHHHHHHHHHHHHHHHHC----TCHHHHHHHCCTCHHHHHHHHH CS
                            NADHdh 232 salavllFlgGwllpfs............gllwfllKvllllflfiwiratlpRlRydqlmklgwkvllplalanll 296
                                        +l+  lF+  w    +            g+l f++K++++ ++f+ +  + +R+R+ ++ ++ ++v + l++++l+
  gi|385806331|ref|YP_005842729.1| 234 PSLFLSLFV-PW----GisstfslagllvGTLSFMAKIFIIHMIFLTLSVSNARIRFVEMPQY-FEVSIFLSIIALV 304
                                       ********9.34....2223355999999*****************************99886.7788888888887 PP

                                       H CS
                            NADHdh 297 l 297
                                       l
  gi|385806331|ref|YP_005842729.1| 305 L 305
                                       6 PP

>> Pathogen_betaC1  Beta-satellite pathogenicity beta C1 protein
   #    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      26      90 ..     167     231 ..     160     236 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.3e-06
                   Pathogen_betaC1  26 veiellsTrspvlakkkfiipYthegiipPfdfngleegiknilkimykdskieefkqedmveai 90 
                                        +++lls  s +la+    i    e  + Pfd+ ++e+++++ +++ y++ ++  fk ++m++++
  gi|385806331|ref|YP_005842729.1| 167 SNLQLLSYPSFYLAAIAGFIALLLETGVQPFDVAEAEQELQEGISVEYSGKTLALFKLDQMLKRV 231
                                       567888889999999999999999999**********************************9987 PP

>> TadE  TadE-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.2e-05      0.19       6      30 ..     139     164 ..     136     170 .. 0.90
   2 ?   -3.3   1.1         2   1.2e+04       9      18 ..     231     241 ..     231     242 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.2e-05
                              TadE   6 EFALvlPllll.lllgiiefgrylya 30 
                                       E AL+lP+l l + +g+ ++g++ y+
  gi|385806331|ref|YP_005842729.1| 139 EVALILPVLCLvVTTGTTDLGKISYY 164
                                       89******9999*********99875 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2
                              TadE   9 LvlPllll.ll 18 
                                       +v+P l+l l+
  gi|385806331|ref|YP_005842729.1| 231 VVIPSLFLsLF 241
                                       58996665254 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       806  (0.0449551); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.35s 00:00:00.98 Elapsed: 00:00:00.56
# Mc/sec: 1675.42
//
Query:       gi|385806332|ref|YP_005842730.1|  [L=698]
Description: Component HyfB of membrane-bound [Ni,Fe]-hydrogenase [Fervidicoccus fontis Kam940]
Scores for complete 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-51  173.3  33.9    2.9e-50  171.2  33.9    2.2  1  Proton_antipo_M  Proton-conducting membrane transporter
     0.0097   16.0   3.1     0.0097   16.0   3.1    4.5  6  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.2  33.9   3.2e-54   2.9e-50       1     291 [.     139     444 ..     139     446 .. 0.88

  Alignments for each domain:
  == domain 1  score: 171.2 bits;  conditional E-value: 3.2e-54
                   Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskalelgln 77 
                                       +nd+l++ + +El+ l +y+Li ++ ++ ++ +A++ +f+   lg l+ Ll++++l+ ++ +l+f++  ++ +  l 
  gi|385806332|ref|YP_005842730.1| 139 SNDVLSFMFYWELMTLISYFLIVYNHTDGSTRRAGMLYFIFAHLGGLLVLLSFAVLFINSRSLSFDYFQRF-SSYLP 214
                                       79********************************************************************9.99999 PP

                   Proton_antipo_M  78 slelllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla..vssneisqllli 152
                                       ++e++l+++l ++g+ +K+++vplh Wlp+ay  a+    a+l++ + k++++++ir+ l++       +i  + ++
  gi|385806332|ref|YP_005842730.1| 215 QIEASLAFILAFFGFGIKAGMVPLHAWLPEAYTVASSNTVAILSGAMEKMAIYGIIRFALFFLpiGRMSAIGAFAVA 291
                                       ************************************************************9998778889999**** PP

                   Proton_antipo_M 153 laiismllgslvalaqtdiKrllAySsishlGymlialav...atqygveaa........iihllthalfkallFll 218
                                       +++i+++ g ++a +q+d+Kr lAyS+i  +G++++++++    ++yg+++a        + + l h+l k+llFl 
  gi|385806332|ref|YP_005842730.1| 292 MGLITAITGIFLASVQSDLKRFLAYSTIENMGIIILGIGLtilFSSYGLASAatialvatLYQTLNHSLAKSLLFLG 368
                                       ***********************************9988744434455443311111111556789*********** PP

                   Proton_antipo_M 219 agsviyerektrdirayggLakkmPilalvllvlllslaGlPptagFlskfli....Leaavavslillvlavvasv 291
                                        g v  +  +tr+i+++ggL+k+ P++ ++++++ + +a++Pp+ +F s++l+    + +a++++++++ ++++ sv
  gi|385806332|ref|YP_005842730.1| 369 TGTV-TNIFNTRNIDQLGGLSKYLPVTTWTFFIASWCIAAIPPFGCFASEWLLyqslMFSAWSAQSFVVSIISILSV 444
                                       *777.7888******************************************97222245556666666666666665 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 !   16.0   3.1   1.1e-06    0.0097      14      43 ..      80     109 ..      75     127 .. 0.92
   2 ?   -2.6   0.1      0.67     6e+03      21      29 ..     131     139 ..     120     147 .. 0.77
   3 ?   -3.2   0.4         1   9.2e+03      49      57 ..     205     213 ..     195     213 .. 0.86
   4 ?   -3.8   0.4       1.6   1.5e+04      25      38 ..     322     335 ..     322     339 .. 0.76
   5 ?    1.7   1.3      0.03   2.7e+02      15      35 ..     433     453 ..     417     468 .. 0.75
   6 ?   -4.7   1.8         2   1.8e+04      21      33 ..     684     696 ..     680     697 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.1e-06
                   Proton_antipo_N  14 igfllDklsalmllvvtfvsllvhlYSigY 43 
                                       +++ +D+ls  +l+ +++v  +v +YSi Y
  gi|385806332|ref|YP_005842730.1|  80 FSVKIDPLSSFFLVCISLVYIFVSIYSIDY 109
                                       7899*************************9 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.67
                   Proton_antipo_N  21 lsalmllvv 29 
                                       l+++mll+ 
  gi|385806332|ref|YP_005842730.1| 131 LTMIMLLLS 139
                                       899999875 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 1
                   Proton_antipo_N  49 gyqRFfayl 57 
                                        +qRF +yl
  gi|385806332|ref|YP_005842730.1| 205 YFQRFSSYL 213
                                       6899*9998 PP

  == domain 4  score: -3.8 bits;  conditional E-value: 1.6
                   Proton_antipo_N  25 mllvvtfvsllvhl 38 
                                       m +++ +++l +++
  gi|385806332|ref|YP_005842730.1| 322 MGIIILGIGLTILF 335
                                       66899999999864 PP

  == domain 5  score: 1.7 bits;  conditional E-value: 0.03
                   Proton_antipo_N  15 gfllDklsalmllvvtfvsll 35 
                                       +f ++ +s+l +lv+ +v+++
  gi|385806332|ref|YP_005842730.1| 433 SFVVSIISILSVLVIAIVGAV 453
                                       577777777777777777764 PP

  == domain 6  score: -4.7 bits;  conditional E-value: 2
                   Proton_antipo_N  21 lsalmllvvtfvs 33 
                                       l+ ++l+++ +vs
  gi|385806332|ref|YP_005842730.1| 684 LTFIVLITIAVVS 696
                                       6777888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (698 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       977  (0.0544927); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.80u 0.34s 00:00:01.14 Elapsed: 00:00:00.53
# Mc/sec: 4000.69
//
Query:       gi|385806333|ref|YP_005842731.1|  [L=158]
Description: Component HyfA of membrane-bound [Ni,Fe]-hydrogenase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-22   77.8  11.3    5.5e-22   77.8  11.3    2.0  2  Fer4_11   4Fe-4S dicluster domain
    8.1e-13   48.8  53.1    1.2e-06   29.0  11.8    3.5  4  Fer4_7    4Fe-4S dicluster domain
    8.5e-13   47.5  41.7    2.3e-06   27.1   2.9    5.5  5  Fer4      4Fe-4S binding domain
    1.5e-12   47.0  39.5    2.2e-05   24.3   2.3    4.8  4  Fer4_6    4Fe-4S binding domain
      1e-11   44.7  51.2    1.6e-06   28.1  11.6    3.5  4  Fer4_10   4Fe-4S dicluster domain
      2e-11   43.9  51.0    2.8e-06   27.4  11.0    3.2  4  Fer4_9    4Fe-4S dicluster domain
    1.8e-10   40.2  32.1    6.6e-05   22.8   1.5    4.4  4  Fer4_2    4Fe-4S binding domain
    5.3e-09   35.9  34.7    0.00081   19.7   2.1    4.8  4  Fer4_4    4Fe-4S binding domain
    8.1e-07   29.1  34.6    0.00042   20.4  13.1    3.8  4  Fer4_21   4Fe-4S dicluster domain
    1.7e-06   28.6  40.2      0.074   14.0   4.9    4.3  4  Fer4_3    4Fe-4S binding domain
    3.7e-06   27.8  33.5      0.043   14.8   0.7    4.8  5  Fer4_16   4Fe-4S double cluster binding domain
     0.0055   17.1  33.1      0.054   13.9   2.3    4.4  4  Fer4_8    4Fe-4S dicluster domain
     0.0071   16.9  28.5      0.017   15.7   1.5    4.4  4  Fer4_17   4Fe-4S dicluster domain
  ------ inclusion threshold ------
       0.86   10.5  23.7       0.24   12.3   2.6    4.1  4  Fer4_22   4Fe-4S dicluster domain
        1.6    9.5  25.2         11    6.9   9.7    3.9  2  Fer4_15   4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.3      0.55   6.5e+02       5      18 ..       7      18 ..       3      36 .. 0.61
   2 !   77.8  11.3   4.6e-25   5.5e-22       6      96 ..      44     132 ..      40     136 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.55
                           Fer4_11  5 flpeqCrhCleppC 18
                                      + p++C  C   +C
  gi|385806333|ref|YP_005842731.1|  7 MDPKKCIGCR--AC 18
                                      5556655553..22 PP

  == domain 2  score: 77.8 bits;  conditional E-value: 4.6e-25
                           Fer4_11   6 lpeqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivrkneetgkvekCdmcldrveaGl 82 
                                       +p +C+hC +++C++++p++a+ +de +GaV +d+ ++  ++ +++ acP+ i++  +e +++ kCd+c+dr +aGl
  gi|385806333|ref|YP_005842731.1|  44 VPLTCMHCKDAQCINICPVGAMKRDE-DGAVYVDSLQCI-GCGMCTIACPFGIPMLYSELKVAVKCDLCMDRRKAGL 118
                                       7999***************9987776.***********7.************************************* PP

                           Fer4_11  83 lpacvescptgaln 96 
                                       +pac ++cp+ a++
  gi|385806333|ref|YP_005842731.1| 119 KPACATVCPADAIT 132
                                       *********99876 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8  13.1     2e-08   2.4e-05       1      52 []      11      64 ..      11      64 .. 0.80
   2 !   29.0  11.8     1e-09   1.2e-06       1      52 []      47      94 ..      47      94 .. 0.93
   3 !   19.9  12.2     7e-07   0.00084       1      52 []      79     130 ..      79     130 .. 0.80
   4 !   11.7   2.0   0.00025       0.3       2      28 ..     107     142 ..     105     153 .. 0.66

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 2e-08
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCga..CvavCPtga 52
                                      +CigC+aC++aC +    + + ++    ++++ +p +C++C+   C++ CP+ga
  gi|385806333|ref|YP_005842731.1| 11 KCIGCRACEVACETLHNGISNITVYTVEDSLVNVPLTCMHCKDaqCINICPVGA 64
                                      7***********9544444444444555779999*******9888*******98 PP

  == domain 2  score: 29.0 bits;  conditional E-value: 1e-09
                            Fer4_7  1 rCigCg..aCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      +C++C+  +C + Cpv+a++ de+        v++d+ +C+gCg+C  +CP+g+
  gi|385806333|ref|YP_005842731.1| 47 TCMHCKdaQCINICPVGAMKRDED------GAVYVDSLQCIGCGMCTIACPFGI 94
                                      5****888*************997......489*******************96 PP

  == domain 3  score: 19.9 bits;  conditional E-value: 7e-07
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       +CigCg C+ aCp +  +l  e + + + ++ +d +k     aC++vCP++a
  gi|385806333|ref|YP_005842731.1|  79 QCIGCGMCTIACPFGIPMLYSELKVAVKCDLCMDRRKAGLKPACATVCPADA 130
                                       6******************888655555556666666666779******987 PP

  == domain 4  score: 11.7 bits;  conditional E-value: 0.00025
                            Fer4_7   2 CigCg.........aCvaaCpvkaieldeeenekgt 28 
                                       C  C          aC+ +Cp++ai++++ e+ + +
  gi|385806333|ref|YP_005842731.1| 107 CDLCMdrrkaglkpACATVCPADAITYRKIEDVAAQ 142
                                       666744555556669***********9975544433 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   3.9   2.6e-07   0.00031       3      19 ..       7      23 ..       5      24 .. 0.89
   2 !    7.0   4.9    0.0045       5.4      13      23 ..      55      65 ..      44      66 .. 0.89
   3 !   27.1   2.9     2e-09   2.3e-06       1      22 [.      73      94 ..      73      96 .. 0.92
   4 ?    0.8   0.1      0.41   4.9e+02      10      16 ..     106     112 ..     105     113 .. 0.71
   5 !   12.4   2.2   9.2e-05      0.11      13      24 .]     121     132 ..     121     132 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.6e-07
                                      EETTTSSS-THHHHHST CS
                              Fer4  3 ideekCigCGaCvevCP 19
                                       d+ kCigC aC+ +C 
  gi|385806333|ref|YP_005842731.1|  7 MDPKKCIGCRACEVACE 23
                                      59**************6 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0045
                                      HHHHHSTTTEE CS
                              Fer4 13 aCvevCPvgAI 23
                                      +C+++CPvgA 
  gi|385806333|ref|YP_005842731.1| 55 QCINICPVGAM 65
                                      7*********7 PP

  == domain 3  score: 27.1 bits;  conditional E-value: 2e-09
                                      EEEETTTSSS-THHHHHSTTTE CS
                              Fer4  1 vvideekCigCGaCvevCPvgA 22
                                      v++d   CigCG C  +CP+g 
  gi|385806333|ref|YP_005842731.1| 73 VYVDSLQCIGCGMCTIACPFGI 94
                                      689999**************96 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 0.41
                                       S-THHHH CS
                              Fer4  10 gCGaCve 16 
                                       +C +C++
  gi|385806333|ref|YP_005842731.1| 106 KCDLCMD 112
                                       6888875 PP

  == domain 5  score: 12.4 bits;  conditional E-value: 9.2e-05
                                       HHHHHSTTTEEE CS
                              Fer4  13 aCvevCPvgAIt 24 
                                       aC+ vCP +AIt
  gi|385806333|ref|YP_005842731.1| 121 ACATVCPADAIT 132
                                       7**********7 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   2.4   6.9e-08   8.3e-05       5      21 ..       8      24 ..       6      29 .. 0.90
   2 !   10.5   3.4   0.00041      0.49       8      23 ..      47      64 ..      42      65 .. 0.89
   3 !   24.3   2.3   1.9e-08   2.2e-05       2      23 ..      73      94 ..      72      95 .. 0.90
   4 !    6.3   8.2    0.0088        11       8      24 .]     106     131 ..     104     131 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 6.9e-08
                            Fer4_6  5 dpdkCigCgdCvrvCPe 21
                                      dp kCigC++C+++C +
  gi|385806333|ref|YP_005842731.1|  8 DPKKCIGCRACEVACET 24
                                      99*************86 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00041
                            Fer4_6  8 kCigCgd..CvrvCPega 23
                                       C +C d  C+++CP ga
  gi|385806333|ref|YP_005842731.1| 47 TCMHCKDaqCINICPVGA 64
                                      699**999********98 PP

  == domain 3  score: 24.3 bits;  conditional E-value: 1.9e-08
                            Fer4_6  2 veidpdkCigCgdCvrvCPega 23
                                      v +d   CigCg C+++CP+g+
  gi|385806333|ref|YP_005842731.1| 73 VYVDSLQCIGCGMCTIACPFGI 94
                                      6789999************996 PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.0088
                            Fer4_6   8 kCigCgd.........CvrvCPegai 24 
                                       kC+ C+d         C++vCP++ai
  gi|385806333|ref|YP_005842731.1| 106 KCDLCMDrrkaglkpaCATVCPADAI 131
                                       8999999999999999********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 !   20.7  12.9   2.8e-07   0.00034       3      56 .]       6      61 ..       4      61 .. 0.90
   2 !   28.1  11.6   1.3e-09   1.6e-06       5      56 .]      44      91 ..      40      91 .. 0.94
   3 !   20.8  10.8   2.5e-07    0.0003       2      56 .]      73     127 ..      72     127 .. 0.75
   4 !    6.6   2.5    0.0071       8.5      14      24 ..     121     136 ..     105     153 .. 0.63

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.8e-07
                           Fer4_10  3 vidddtCirCgkCvkaCPadl.tsvgakgeaseeeavrkkvekCtgcg..aCveaCP 56
                                      + d+++Ci+C++C  aC + l ++ +++  ++ e+    ++  C++c   +C+ +CP
  gi|385806333|ref|YP_005842731.1|  6 IMDPKKCIGCRACEVACET-LhNGISNITVYTVEDSLVNVPLTCMHCKdaQCINICP 61
                                      789**************44.359999999999999************777******9 PP

  == domain 2  score: 28.1 bits;  conditional E-value: 1.3e-09
                           Fer4_10  5 dddtCirCg..kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                       + tC++C+  +C + CP+      +  +++e++av +++ +C+gcg+C+ aCP
  gi|385806333|ref|YP_005842731.1| 44 VPLTCMHCKdaQCINICPV------GAMKRDEDGAVYVDSLQCIGCGMCTIACP 91
                                      5679*****99********......999*************************9 PP

  == domain 3  score: 20.8 bits;  conditional E-value: 2.5e-07
                           Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgc...g...aCveaCP 56 
                                       v++d+ +Ci+Cg C+ aCP+      +++    e +v +k++ C++    g   aC+ +CP
  gi|385806333|ref|YP_005842731.1|  73 VYVDSLQCIGCGMCTIACPF------GIPMLYSELKVAVKCDLCMDRrkaGlkpACATVCP 127
                                       6789999*************......6666666666666666666634333678******9 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.0071
                           Fer4_10  14 kCvkaCPadl.....t 24 
                                       +C ++CPad+      
  gi|385806333|ref|YP_005842731.1| 121 ACATVCPADAityrkI 136
                                       69999**965333321 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0  12.5   4.9e-07   0.00059       1      51 []      11      65 ..      11      65 .. 0.80
   2 !   27.4  11.0   2.4e-09   2.8e-06       2      49 ..      48      93 ..      47      95 .. 0.88
   3 !   21.5  11.5   1.6e-07   0.00019       1      51 []      79     131 ..      79     131 .. 0.95
   4 !    9.6   1.7   0.00085         1       1      24 [.     106     138 ..     105     147 .. 0.52

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 4.9e-07
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase..eaCigCga..CveaCpkgai 51
                                      kC+gC+aC+ aC++ ++  ++ + +   +   +    C++C++  C+++Cp ga+
  gi|385806333|ref|YP_005842731.1| 11 KCIGCRACEVACETLHNGISNITVYTVEDSLVNvpLTCMHCKDaqCINICPVGAM 65
                                      7***********8888888877766665433337778****9999******9975 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 2.4e-09
                            Fer4_9  2 CtgCga..CveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49
                                      C+ C+   C++ Cp g++++d+ +           +CigCg C+ aCp g
  gi|385806333|ref|YP_005842731.1| 48 CMHCKDaqCINICPVGAMKRDEDGAVYVDSL----QCIGCGMCTIACPFG 93
                                      ****8555*************9999988765....6************87 PP

  == domain 3  score: 21.5 bits;  conditional E-value: 1.6e-07
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCga.........CveaCpkgai 51 
                                       +C+gCg C+ aCp+g+ +  +  + a        +C  C++         C+ +Cp +ai
  gi|385806333|ref|YP_005842731.1|  79 QCIGCGMCTIACPFGIPMLYSELKVAV-------KCDLCMDrrkaglkpaCATVCPADAI 131
                                       6******************99999988.......5**********************987 PP

  == domain 4  score: 9.6 bits;  conditional E-value: 0.00085
                            Fer4_9   1 kCtgC.........gaCveaCpagvvvedaaer 24 
                                       kC  C          aC ++Cpa+++++++ e 
  gi|385806333|ref|YP_005842731.1| 106 KCDLCmdrrkaglkPACATVCPADAITYRKIED 138
                                       455553333322222366666666666666555 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   1.8   1.2e-06    0.0014       5      20 ..       7      22 ..       4      24 .. 0.89
   2 !    9.8   2.3   0.00073      0.88       6      21 ..      44      61 ..      40      62 .. 0.86
   3 !   22.8   1.5   5.5e-08   6.6e-05       2      21 ..      72      91 ..      71      92 .. 0.92
   4 ?    6.1   4.0     0.011        13       9      22 .]     106     128 ..     101     128 .. 0.66

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.2e-06
                            Fer4_2  5 vdtdrCigCgaCvsaC 20
                                       d+ +CigC+aC  aC
  gi|385806333|ref|YP_005842731.1|  7 MDPKKCIGCRACEVAC 22
                                      6999************ PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00073
                            Fer4_2  6 dtdrCigCg..aCvsaCP 21
                                      ++ +C++C+   C++ CP
  gi|385806333|ref|YP_005842731.1| 44 VPLTCMHCKdaQCINICP 61
                                      4789****999******* PP

  == domain 3  score: 22.8 bits;  conditional E-value: 5.5e-08
                            Fer4_2  2 pvvvdtdrCigCgaCvsaCP 21
                                      +v+vd+  CigCg C+ aCP
  gi|385806333|ref|YP_005842731.1| 72 AVYVDSLQCIGCGMCTIACP 91
                                      5899**************** PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.011
                            Fer4_2   9 rCigCg.........aCvsaCPa 22 
                                       +C  C          aC ++CPa
  gi|385806333|ref|YP_005842731.1| 106 KCDLCMdrrkaglkpACATVCPA 128
                                       455552234455889*******8 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   1.9   1.1e-06    0.0014       1      15 [.       9      23 ..       9      31 .. 0.92
   2 !   13.6   3.0   6.1e-05     0.073       3      17 .]      47      63 ..      45      63 .. 0.91
   3 !   19.7   2.1   6.8e-07   0.00081       4      17 .]      80      93 ..      65      93 .. 0.92
   4 ?   -0.2   4.8       1.6   1.9e+03       8      16 ..     120     128 ..     101     134 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.1e-06
                            Fer4_4  1 qerCigCgsCvaaCP 15
                                      +++CigC++C+ aC+
  gi|385806333|ref|YP_005842731.1|  9 PKKCIGCRACEVACE 23
                                      589***********8 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 6.1e-05
                            Fer4_4  3 rCigCg..sCvaaCPqg 17
                                      +C +C+  +C+++CP+g
  gi|385806333|ref|YP_005842731.1| 47 TCMHCKdaQCINICPVG 63
                                      6*****999******86 PP

  == domain 3  score: 19.7 bits;  conditional E-value: 6.8e-07
                            Fer4_4  4 CigCgsCvaaCPqg 17
                                      CigCg C++aCP+g
  gi|385806333|ref|YP_005842731.1| 80 CIGCGMCTIACPFG 93
                                      ************86 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 1.6
                            Fer4_4   8 gsCvaaCPq 16 
                                       ++C  +CP 
  gi|385806333|ref|YP_005842731.1| 120 PACATVCPA 128
                                       479999995 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4  13.1   3.5e-07   0.00042       3      57 ..       7      65 ..       6      67 .. 0.75
   2 !   16.9  13.9   4.2e-06     0.005       7      53 ..      47      92 ..      42      96 .. 0.90
   3 !   10.4   8.1   0.00047      0.56       3      19 ..      75      91 ..      72     114 .. 0.75
   4 ?    5.2   0.3     0.019        23      47      58 ..     122     132 ..     119     133 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3.5e-07
                           Fer4_21  3 idedkCigCgkCliaCedtshqai....eidaktvlkvvedeCvGCn..lCssvCPvedci 57
                                      +d++kCigC  C +aCe t h+ i     ++ +  l  v  +C+ C+   C+++CPv +++
  gi|385806333|ref|YP_005842731.1|  7 MDPKKCIGCRACEVACE-TLHNGIsnitVYTVEDSLVNVPLTCMHCKdaQCINICPV-GAM 65
                                      6899*************.688888543333344455567889****6448******9.665 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 4.2e-06
                           Fer4_21  7 kCigCg..kCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPv 53
                                      +C++C+  +C+  C+   + a++ d++  + v + +C+GC +C++ CP 
  gi|385806333|ref|YP_005842731.1| 47 TCMHCKdaQCINICP---VGAMKRDEDGAVYVDSLQCIGCGMCTIACPF 92
                                      7****6448******...7999**************************5 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00047
                           Fer4_21  3 idedkCigCgkCliaCe 19
                                      +d+ +CigCg C+iaC+
  gi|385806333|ref|YP_005842731.1| 75 VDSLQCIGCGMCTIACP 91
                                      55667777777777776 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.019
                           Fer4_21  47 CssvCPvedcie 58 
                                       C++vCP  d+i+
  gi|385806333|ref|YP_005842731.1| 122 CATVCPA-DAIT 132
                                       ******5.9987 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   5.4     0.002       2.4       1      11 [.      12      22 ..      12      24 .. 0.97
   2 !   14.0   4.9   6.2e-05     0.074       1      15 []      48      64 ..      48      64 .. 0.90
   3 !   12.8   3.9   0.00016      0.19       1      14 [.      80      93 ..      80      94 .. 0.94
   4 !   11.1   2.5   0.00054      0.65       1      15 []     107     130 ..     107     130 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.002
                            Fer4_3  1 CtgCgaCvevC 11
                                      C+gC+aC+++C
  gi|385806333|ref|YP_005842731.1| 12 CIGCRACEVAC 22
                                      *********** PP

  == domain 2  score: 14.0 bits;  conditional E-value: 6.2e-05
                            Fer4_3  1 CtgCg..aCvevCPvgA 15
                                      C++C   +C + CPvgA
  gi|385806333|ref|YP_005842731.1| 48 CMHCKdaQCINICPVGA 64
                                      ****6669********9 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 0.00016
                            Fer4_3  1 CtgCgaCvevCPvg 14
                                      C+gCg C  +CP g
  gi|385806333|ref|YP_005842731.1| 80 CIGCGMCTIACPFG 93
                                      ************98 PP

  == domain 4  score: 11.1 bits;  conditional E-value: 0.00054
                            Fer4_3   1 CtgCg.........aCvevCPvgA 15 
                                       C+ C+         aC  vCP +A
  gi|385806333|ref|YP_005842731.1| 107 CDLCMdrrkaglkpACATVCPADA 130
                                       9***99999999999******887 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   1.6    0.0058       6.9       1      13 [.      11      23 ..       9      35 .. 0.83
   2 !   13.5   1.9   8.9e-05      0.11       2      22 ..      48      70 ..      47      77 .. 0.83
   3 !   11.0   3.7   0.00054      0.64      53      66 ..      79      92 ..      73      93 .. 0.81
   4 ?   -0.5   0.1       2.1   2.6e+03      55      62 ..     105     112 ..      98     113 .. 0.72
   5 !   14.8   0.7   3.6e-05     0.043       7      34 ..     121     148 ..     119     158 .] 0.79

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0058
                           Fer4_16  1 rCgtCgkCaevCP 13
                                      +C++C++C  +C 
  gi|385806333|ref|YP_005842731.1| 11 KCIGCRACEVACE 23
                                      5888888888885 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 8.9e-05
                           Fer4_16  2 CgtCgk..CaevCPtnaikekke 22
                                      C  C+   C+++CP++a+k +++
  gi|385806333|ref|YP_005842731.1| 48 CMHCKDaqCINICPVGAMKRDED 70
                                      99999777***********9965 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00054
                           Fer4_16 53 aitgCdiCqdvCPa 66
                                      +++gC++C+ +CP+
  gi|385806333|ref|YP_005842731.1| 79 QCIGCGMCTIACPF 92
                                      68899999999998 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 2.1
                           Fer4_16  55 tgCdiCqd 62 
                                         Cd C+d
  gi|385806333|ref|YP_005842731.1| 105 VKCDLCMD 112
                                       56888875 PP

  == domain 5  score: 14.8 bits;  conditional E-value: 3.6e-05
                           Fer4_16   7 kCaevCPtnaikekkekeiearecisyn 34 
                                       +Ca vCP++ai+ +k + ++a++ +++ 
  gi|385806333|ref|YP_005842731.1| 121 ACATVCPADAITYRKIEDVAAQKREATV 148
                                       6*************88888888877653 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7  13.0    0.0041       4.8       3      64 ..      10      63 ..       8      64 .. 0.72
   2 ?    5.1   2.5     0.027        32       4      19 ..      47      64 ..      45      76 .. 0.68
   3 !   13.9   2.3   4.5e-05     0.054       4      17 ..      79      92 ..      76     106 .. 0.71
   4 ?    2.4   2.6      0.18   2.2e+02      50      63 ..     106     128 ..      98     130 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0041
                            Fer4_8  3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcga..CtevCpvg 64
                                      +kCi+C aC+ aC +l++    +     e      ++ v    +   +C++c+   C + Cpvg
  gi|385806333|ref|YP_005842731.1| 10 KKCIGCRACEVACETLHNGISNITVYTVE------DSLV----NVPLTCMHCKDaqCINICPVG 63
                                      69***********9888774433333333......3333....3467899999888*****997 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.027
                            Fer4_8  4 kCieCg..aCqsaCpvlr 19
                                       C++C    C + Cpv  
  gi|385806333|ref|YP_005842731.1| 47 TCMHCKdaQCINICPVGA 64
                                      477775447777777654 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 4.5e-05
                            Fer4_8  4 kCieCgaCqsaCpv 17
                                      +Ci+Cg+C+ aCp+
  gi|385806333|ref|YP_005842731.1| 79 QCIGCGMCTIACPF 92
                                      67777777777774 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.18
                            Fer4_8  50 sCttcga.........CtevCpv 63 
                                       +C  c+          C++vCp 
  gi|385806333|ref|YP_005842731.1| 106 KCDLCMDrrkaglkpaCATVCPA 128
                                       56666666666666669999997 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   1.1   0.00032      0.38      45      57 ..      11      23 ..       7      35 .. 0.76
   2 ?    5.4   1.8     0.022        27       2      20 ..      48      68 ..      47      78 .. 0.78
   3 !   15.7   1.5   1.4e-05     0.017      45      60 ..      79      94 ..      65      95 .. 0.83
   4 ?    6.2  11.0     0.013        15      46      60 ..      80      94 ..      79     153 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00032
                           Fer4_17 45 lCieCgeCerkCP 57
                                      +Ci+C+ Ce +C 
  gi|385806333|ref|YP_005842731.1| 11 KCIGCRACEVACE 23
                                      6777777777774 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.022
                           Fer4_17  2 CiqCgy..ClpeCpsyeaydn 20
                                      C++C+   C++ Cp ++  ++
  gi|385806333|ref|YP_005842731.1| 48 CMHCKDaqCINICPVGAMKRD 68
                                      99**9667******9876555 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 1.4e-05
                           Fer4_17 45 lCieCgeCerkCPqgl 60
                                      +Ci+Cg+C+ +CP g+
  gi|385806333|ref|YP_005842731.1| 79 QCIGCGMCTIACPFGI 94
                                      8999999999999877 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.013
                           Fer4_17 46 CieCgeCerkCPqgl 60
                                      Ci+Cg+C+ +CP g+
  gi|385806333|ref|YP_005842731.1| 80 CIGCGMCTIACPFGI 94
                                      555555555555444 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   0.9    0.0029       3.4       1      14 [.      11      24 ..       6      38 .. 0.79
   2 ?    0.9   2.0       0.7   8.4e+02       2      14 ..      48      62 ..      47      76 .. 0.76
   3 ?   12.3   2.6    0.0002      0.24      78      95 ..      76      93 ..      64      94 .. 0.76
   4 ?    1.8   0.0      0.38   4.6e+02       7      25 ..     121     141 ..     117     154 .. 0.56

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0029
                           Fer4_22  1 rClsCgaCtlvCpt 14
                                      +C++C aC ++C t
  gi|385806333|ref|YP_005842731.1| 11 KCIGCRACEVACET 24
                                      57777777777766 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.7
                           Fer4_22  2 ClsC..gaCtlvCpt 14
                                      C++C  ++C  +Cp 
  gi|385806333|ref|YP_005842731.1| 48 CMHCkdAQCINICPV 62
                                      889944479999986 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.0002
                           Fer4_22 78 gesgCvGCgRCieacpvk 95
                                      ++ +C+GCg C+ acp +
  gi|385806333|ref|YP_005842731.1| 76 DSLQCIGCGMCTIACPFG 93
                                      677899999999999876 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.38
                           Fer4_22   7 aCtlvCptCsCf..dvedetk 25 
                                       aC++vCp+   +  ++ed+++
  gi|385806333|ref|YP_005842731.1| 121 ACATVCPADAITyrKIEDVAA 141
                                       699999974432114455553 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 ?    4.5   7.2      0.05        60       3      63 ..       7      64 ..       5      67 .. 0.66
   2 ?    6.9   9.7    0.0089        11       1      65 [.      73     132 ..      73     133 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.05
                           Fer4_15  3 vDrdaCigcglCvaeapevfeldedglasvllddgeiaegevpddeeeaaq.eAaraCPvdA 63
                                       D ++Cigc +C  +++   +l  +g++ +++ + e++   vp + + + + +    CPv+A
  gi|385806333|ref|YP_005842731.1|  7 MDPKKCIGCRACEVACE---TL-HNGISNITVYTVEDSLVNVPLTCMHCKDaQCINICPVGA 64
                                      5899***********96...33.367777776666655556666665554324456666666 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0089
                           Fer4_15   1 VvvDrdaCigcglCvaeapevfeldedglasvllddgeiaegevpddeeeaaqeA.araCPvdAIr 65 
                                       V+vD  +Cigcg+C  ++p  + +    l+ v ++      +   d +++  + A a +CP+dAI+
  gi|385806333|ref|YP_005842731.1|  73 VYVDSLQCIGCGMCTIACPFGIPMLYSELK-VAVK-----CDLCMDRRKAGLKPAcATVCPADAIT 132
                                       89****************988887766666.3333.....23444445555555536678888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); 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):              15  [number of targets reported over threshold]
# CPU time: 0.57u 0.35s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 934.22
//
Query:       gi|385806334|ref|YP_005842732.1|  [L=684]
Description: formate dehydrogenase [Fervidicoccus fontis Kam940]
Scores for 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-78  264.3   0.0    2.5e-78  264.0   0.0    1.1  1  Molybdopterin    Molybdopterin oxidoreductase
    1.1e-12   48.0   0.0    1.8e-12   47.2   0.0    1.4  1  Molydop_binding  Molydopterin dinucleotide binding domain
    0.00015   21.7   0.0    0.00031   20.7   0.0    1.6  1  Molybdop_Fe4S4   Molybdopterin oxidoreductase Fe4S4 domain
  ------ inclusion threshold ------
      0.046   14.0   0.0        2.8    8.3   0.0    2.6  2  PEX-2N           Peroxisome biogenesis factor 1, N-terminal
       0.12   12.2   0.0       0.34   10.7   0.0    1.8  1  Elong-fact-P_C   Elongation factor P, C-terminal


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 !  264.0   0.0     7e-82   2.5e-78       1     431 [.      62     483 ..      62     484 .. 0.90

  Alignments for each domain:
  == domain 1  score: 264.0 bits;  conditional E-value: 7e-82
                                       B--S-EEECTTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEEEEEBTSSCSHHHHHHHHHHHHHTT-EEE-BE CS
                     Molybdopterin   1 RlkyPmvRkqargeGkFvrvsWdeAleliaaslkytikkygpdrvagfssgplmsmeslaslkkllsllggknlsfy 77 
                                       Rl +Pm+R   + e++Fv++sW +A ++i++++k++ k  +p++  + +s + + +e  ++++k+++++g +n+   
  gi|385806334|ref|YP_005842732.1|  62 RLAHPMKR---K-ENGFVEISWGDAIKEISERIKEITKSDDPSSLGFLGSANCT-NEDNYVFQKFARAIGTNNIDHH 133
                                       9*******...6.899******************************99998888.****************877777 PP

                                       ECCGGGTTHHHHCHHCCCCCTTTS-SS-CCGGGG-SEEEEESS-HHHHSHHHHHHHHHHHHTTC-EEEEECSSB-HC CS
                     Molybdopterin  78 dwyadlppasaqqtigsdsrsnyessnpledlensdliilwGsNvreerpilnarirkaalkkkakvivigpryael 154
                                        ++  l+  +a     ++s   +++s++ e+l +s+++++wG N++e+ p+l ++ + +a++k+akv+v++pr++++
  gi|385806334|ref|YP_005842732.1| 134 ASFFALSEINA----MYKSLGIPSLSSTYEELLKSSVVLIWGFNPAETNPVLMGQYILKAKEKGAKVVVVDPRKTKT 206
                                       77777754333....4455566889999************************877777788888************9 PP

                                       GGGCSEEEEEHTTTHHHHHHHHHHHHHHCCCCTCHHHHHHEECHHHCCCCCCCEECCSHHHHHHCCHHHHHHHHHHH CS
                     Molybdopterin 155 lkfadewlaikpgtdaalalamghvilqelkvdkeflrkytygkeetdmpllvtleeetgkkkevvariarelarna 231
                                       + f d +l ++p+td alal++ +vi  e ++dk+  +++ +  ++  + +  +++e ++k++++ a+++r++a+  
  gi|385806334|ref|YP_005842732.1| 207 AWFSDIHLMLNPKTDYALALSLLNVIFNEKLYDKNYSERI-NLSQKSIEVINSYSPEVVEKICGIQANTIRQVAKL- 281
                                       99********************************554444.56677778899999999999999999999998875. PP

                                       HHHTSSEEEEECHHHHTSTTHHHHHHHHHHHHHHCTHCSSTTCEEEEESSCTTHHHCHHHHTCCTTCCCCCCCTT.. CS
                     Molybdopterin 232 aktagksmiivGaglnhrqdgdaiyravinLallvgnvgqpgGgwahlnGqlilagaaekvgalpvllsvkslke.. 306
                                       ++t gk+ i++G g++++ +gd+i++a++++ +l+g  g++g+ ++++  +++l+g a+++g lp  l+ +  ++  
  gi|385806334|ref|YP_005842732.1| 282 IATSGKASILWGLGILQQINGDDIIEALLTISALCGYLGKEGCVVGGIKNEVNLQG-ASDMGVLPNFLPGYIDVSnk 357
                                       667788*******************************************8888888.*******8887776555567 PP

                                       .HHHHHCCCTTTCSTSS--ECGGCHHHHHHTTSSSEEEEESH.HHHHSTTSCCCHCHHHCSSEEEEEESCSSHHHHT CS
                     Molybdopterin 307 .ekikfaaeqpgnlgnfprnlfversnllkssgkkvlyllgnnpevdhadenevekalekldlvvvldgrltstaly 382
                                        e +kf + +   ++ + + ++ e+    +s+++k ly++g np v  ++ n+++k le+ld++vv d + t+ta++
  gi|385806334|ref|YP_005842732.1| 358 nEIEKFSKIWGFYVPDKEGMNAFEMLYSSNSTKIKGLYIMGMNPLVLLPNMNLTKKILENLDFLVVQDSFFTETAEF 434
                                       77778888888888888888899999999************************************************ PP

                                       SSEEEEBE-CCGSEEEEE-TTSEEEEEEESSS-STT-BEHHHHHHHHHH CS
                     Molybdopterin 383 aDiiLPaatwyEkedlytndegrfqhlkqavsppgeaksdwkIlkaLak 431
                                       aDiiLPaat  Ek++++tn e+r+   ++av+p geak+dw I++++ak
  gi|385806334|ref|YP_005842732.1| 435 ADIILPAATLPEKDGTVTNFERRVRWNNKAVEPVGEAKPDWMIVREIAK 483
                                       ************************************************8 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.2   0.0   5.2e-16   1.8e-12       1     109 [.     571     672 ..     571     674 .. 0.88

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 5.2e-16
                                       EEEEEE-BTTBSTTTTTCGCCHHHHCSSS.-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-TTEEEE CS
                   Molydop_binding   1 lrLitgrsldqlhsqtrtrpvlrlakpep.evveinpedAaalGikdGdlVevesrrGsvevrakvtervrpGvvfm 76 
                                       + Lit  + +q+ + t tr+ + l k+ + +  e+n e+A+ lGi++Gd+V++++++G++ +++++t+++ ++v+++
  gi|385806334|ref|YP_005842732.1| 571 FLLITFEYAGQHGAATLTRNFSPLMKRWGeAIGELNVETAKSLGINEGDKVKIKTEYGEFSCKVHLTQNIVKDVIAV 647
                                       6899***99999999999999888888887899******************************************** PP

                                       ESSHCC.....S-GHCTS--SCSTTT--CSTT- CS
                   Molydop_binding  77 pfgwweagekggnaNaltddatdplsgtpefks 109
                                       p ++++        N++ + ++ +  + pe+k+
  gi|385806334|ref|YP_005842732.1| 648 PWHFGA--------NSIFSCEIAKKYRKPELKV 672
                                       ****88........7777666666666666665 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   8.6e-08   0.00031       7      49 ..      10      53 ..       4      59 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 8.6e-08
                                      E-SSBTT--EEEEEE.ETTEEEEEEE-TTSTTTTT---HHHHTC CS
                    Molybdop_Fe4S4  7 aCpyCgvgCglevhv.kdgkivkvegdpdhpvnegrlCvKGrtl 49
                                      +Cp+Cg gC ++++  + g+ ++v+  + + v++g++C+K  ++
  gi|385806334|ref|YP_005842732.1| 10 ICPFCGLGCAVTLKIdEFGRPYAVDAFEGDHVSKGKACPKPFSI 53
                                      8*************9788*********************96555 PP

>> PEX-2N  Peroxisome biogenesis factor 1, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0   0.00079       2.8      11      38 ..      55      82 ..      53      87 .. 0.93
   2 ?    2.6   0.0     0.046   1.7e+02      56      80 ..     600     624 ..     550     625 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00079
                                      S-EEE-HHHHHHTT--TT--EEEESSS. CS
                            PEX-2N 11 cFlhlpsklvsqLrlqenqalelswgds 38
                                       Fl+ +++l+  ++++en  +e+swgd+
  gi|385806334|ref|YP_005842732.1| 55 SFLNSSNRLAHPMKRKENGFVEISWGDA 82
                                      59999*********************85 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.046
                                       --EEEEEHHHHHHTT--TT-EEEEE CS
                            PEX-2N  56 eneveinrqlgeklGlkdGeqvfLr 80 
                                       e   e+n + ++ lG+++G++v ++
  gi|385806334|ref|YP_005842732.1| 600 EAIGELNVETAKSLGINEGDKVKIK 624
                                       556699999***********98665 PP

>> Elong-fact-P_C  Elongation factor P, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   9.5e-05      0.34      38      53 ..     615     630 ..     612     633 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 9.5e-05
                                       --TT-EEEEETTTTEE CS
                    Elong-fact-P_C  38 IneGdkIkvdTrtgeY 53 
                                       IneGdk+k++T+ ge+
  gi|385806334|ref|YP_005842732.1| 615 INEGDKVKIKTEYGEF 630
                                       9*************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (684 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); 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:                         5  (0.000278878); expected 0.2 (1e-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 0.34s 00:00:01.11 Elapsed: 00:00:00.55
# Mc/sec: 3722.59
//
Query:       gi|385806335|ref|YP_005842733.1|  [L=151]
Description: hydrogenase maturation protease [Fervidicoccus fontis Kam940]
Scores for complete 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-12   45.0   0.1    1.4e-11   44.3   0.1    1.3  1  HycI           Hydrogenase maturation protease
  ------ inclusion threshold ------
       0.02   14.4   0.0      0.031   13.8   0.0    1.2  1  FBP_C          FBP C-terminal treble-clef zinc-finger
      0.085   12.3   0.1       0.17   11.3   0.0    1.7  2  DUF1256        Protein of unknown function (DUF1256)
       0.12   11.2   0.1       0.24   10.3   0.1    1.4  1  Peptidase_A25  Germination protease


Domain annotation for each model (and alignments):
>> HycI  Hydrogenase maturation protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.1   3.1e-15   1.4e-11      35     129 ..      61     146 ..      49     147 .. 0.87

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 3.1e-15
                                       C-SEEEEEEE--SSS-TT-EEEEECCHHHHHHTTC.CGCCCHCHHHHHHHHHHCCS--SEEEEEEE--S-BST.CCS CS
                              HycI  35 eadkliivDavdfglepGevkiikddevpkklkakkmsaHqlplaevlklleekgeipkevillgvqpesledvgie 111
                                       ++d ++i+D vdfg  pG++ i   + +    k++ +s+H+lp+  + +++  k    +++ l+g+qp+sl++ g +
  gi|385806335|ref|YP_005842733.1|  61 QPDVIVIIDSVDFGASPGSILIT--EGISD--KTS-ISIHKLPIRLIFDAVGLKA---EKIFLIGIQPKSLNF-GEQ 128
                                       399****************9886..56885..555.99****************5...6**************.*** PP

                                       --HHHHCCHHHHHHHCCC CS
                              HycI 112 lseevkkavekavelile 129
                                       lseevk++ + ++e+i e
  gi|385806335|ref|YP_005842733.1| 129 LSEEVKNSADFLIEQIKE 146
                                       *************99965 PP

>> FBP_C  FBP C-terminal treble-clef zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   6.9e-06     0.031      97     127 ..      22      52 ..      18      62 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.9e-06
                             FBP_C  97 gaagrkgntvGtyiCadlaCslnvrgkkksa 127
                                       g++ r+ + vG yiC  l+C ++v    + +
  gi|385806335|ref|YP_005842733.1|  22 GNELREDDGVGPYICDKLNCKNTVSVDVPEN 52 
                                       6778999***************998776655 PP

>> DUF1256  Protein of unknown function (DUF1256)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   3.8e-05      0.17      18      61 ..       4      49 ..       1      73 [. 0.81
   2 ?   -2.3   0.0      0.56   2.5e+03      99     125 ..     109     135 ..      90     146 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.8e-05
                           DUF1256 18 sseikkv..keeivivciGtdrstgdsLgPlvGtllkekkipklnv 61
                                      ++++k++  +++ +i+c+G++  + d  gP +  +l+ k++ ++ v
  gi|385806335|ref|YP_005842733.1|  4 QEKLKNLlnEKKALIICLGNELREDDGVGPYICDKLNCKNTVSVDV 49
                                      3444444447999***********************9998877766 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.56
                           DUF1256  99 eeknigkiviknkplkpgkavnkkLpk 125
                                       + ++i  i i+ k+l+ g+ ++ ++++
  gi|385806335|ref|YP_005842733.1| 109 KAEKIFLIGIQPKSLNFGEQLSEEVKN 135
                                       445555555555555555555555444 PP

>> Peptidase_A25  Germination protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   5.3e-05      0.24      91     136 ..       8      53 ..       2      67 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 5.3e-05
                     Peptidase_A25  91 lgikeeasclvvGlGnwnvtPdalGPlvvenllvtrhlfelqpeev 136
                                       +++ +e+++l++ lGn     d +GP ++++l   + +    pe++
  gi|385806335|ref|YP_005842733.1|   8 KNLLNEKKALIICLGNELREDDGVGPYICDKLNCKNTVSVDVPENL 53 
                                       5677899************************987766666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); 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: 0.55u 0.41s 00:00:00.96 Elapsed: 00:00:00.57
# Mc/sec: 803.53
//
Query:       gi|385806336|ref|YP_005842734.1|  [L=77]
Description: hypothetical protein FFONT_1294 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score 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   15.3   0.0      0.021   15.3   0.0    1.2  1  Spaetzle  Spaetzle


Domain annotation for each model (and alignments):
>> Spaetzle  Spaetzle
   #    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      35      70 ..      24      59 ..       3      74 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.2e-06
                          Spaetzle 35 kvrietCknegkkCsllaelkegykskCkQkyvvrr 70
                                       v+ie C +e++k    ++l + y++ C+Qk +v +
  gi|385806336|ref|YP_005842734.1| 24 SVKIENCGEETSKIVAEDNLGNIYETPCEQKKIVSK 59
                                      699****************************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.37s 00:00:00.88 Elapsed: 00:00:00.56
# Mc/sec: 416.23
//
Query:       gi|385806337|ref|YP_005842735.1|  [L=121]
Description: hypothetical protein FFONT_1295 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); 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 0.30s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 719.81
//
Query:       gi|385806338|ref|YP_005842736.1|  [L=47]
Description: hypothetical protein FFONT_1296 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); 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: 0.49u 0.34s 00:00:00.83 Elapsed: 00:00:00.52
# Mc/sec: 273.09
//
Query:       gi|385806339|ref|YP_005842737.1|  [L=251]
Description: transcriptional regulator TrmB [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-19   68.8   0.1    6.4e-19   67.6   0.1    1.6  1  TrmB      Sugar-specific transcriptional regulator TrmB
    9.4e-07   28.3   0.0      2e-06   27.3   0.0    1.6  1  HTH_24    Winged helix-turn-helix DNA-binding
    0.00012   21.8   0.0    0.00018   21.2   0.0    1.3  1  HTH_IclR  IclR helix-turn-helix domain
    0.00013   21.8   0.0    0.00024   20.9   0.0    1.4  1  HTH_5     Bacterial regulatory protein, arsR family
    0.00022   21.7   0.0    0.00045   20.6   0.0    1.5  1  HTH_27    Winged helix DNA-binding domain
     0.0015   18.5   0.0     0.0035   17.4   0.0    1.6  1  HTH_9     RNA polymerase III subunit RPC82 helix-turn-helix d
     0.0029   17.5   0.0     0.0053   16.6   0.0    1.3  1  MarR_2    MarR family
  ------ inclusion threshold ------
      0.034   14.6   0.0      0.095   13.2   0.0    1.8  2  HTH_40    Helix-turn-helix domain
      0.085   12.8   0.0       0.18   11.8   0.0    1.5  1  MarR      MarR family


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.6   0.1   3.2e-22   6.4e-19       1      67 [.      22      88 ..      22      89 .. 0.98

  Alignments for each domain:
  == domain 1  score: 67.6 bits;  conditional E-value: 3.2e-22
                                      HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE--H CS
                              TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravdp 67
                                      L+++G+++ ++++Yl Ll++g +ta+e++ ++g+p+skvYe+L++L++kG+V+++  rp ++ +v++
  gi|385806339|ref|YP_005842737.1| 22 LKVYGMKKRDIEIYLRLLNSGGLTAKELSVMTGLPQSKVYESLSKLIEKGWVMKSSDRPSIFYPVNI 88
                                      899*************************************************************985 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   9.9e-10     2e-06       2      47 ..      28      73 ..      27      74 .. 0.95

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 9.9e-10
                            HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                       + d++I+  L   ++++ +eL+ ++gl++s v + l +L+e+G++
  gi|385806339|ref|YP_005842737.1| 28 KKRDIEIYLRLLNSGGLTAKELSVMTGLPQSKVYESLSKLIEKGWV 73
                                      5789****************************************98 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   9.2e-08   0.00018      17      48 ..      42      73 ..      36      77 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 9.2e-08
                                      SS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_IclR 17 qeltlselArrtglpkStvhRlLqtLvelGyv 48
                                      ++lt +el+  tglp S+v+  L+ L+e G+v
  gi|385806339|ref|YP_005842737.1| 42 GGLTAKELSVMTGLPQSKVYESLSKLIEKGWV 73
                                      6799***************************9 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   1.2e-07   0.00024       8      45 ..      36      73 ..      34      75 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.2e-07
                                      HHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  8 LklLaegelcvcelaeelglsqstvShHLkkLreaGLV 45
                                      L+lL++g l++ el+ ++gl+qs+v + L+kL e G V
  gi|385806339|ref|YP_005842737.1| 36 LRLLNSGGLTAKELSVMTGLPQSKVYESLSKLIEKGWV 73
                                      789******************************99966 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   2.3e-07   0.00045       5      54 ..      31      79 ..      27      83 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.3e-07
                            HTH_27  5 qalv.LhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgde 54
                                      ++ + L+l++   ++ ++++l+ ++ + +s + +sl+kL+ekG+v+++ d+
  gi|385806339|ref|YP_005842737.1| 31 DIEIyLRLLN--SGGLTAKELSVMTGLPQSKVYESLSKLIEKGWVMKSSDR 79
                                      5666699999..9********************************888774 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 !   17.4   0.0   1.8e-06    0.0035      18      54 ..      34      70 ..      32      74 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.8e-06
                                      HHHHHHHHSSBEHHHHHHHHSSTHHHHHHHHHHHHHT CS
                             HTH_9 18 VvetLlrkgrltlrelvkktkLsldqVkksLvvLiqh 54
                                      ++  Ll++g lt++el+  t+L+ ++V  sL+ Li  
  gi|385806339|ref|YP_005842737.1| 34 IYLRLLNSGGLTAKELSVMTGLPQSKVYESLSKLIEK 70
                                      6677******************************965 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   2.7e-06    0.0053      14      56 ..      38      78 ..      32      80 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.7e-06
                                      HHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2 14 LgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                      L +++g  lt++el   +gl++s v   l +L ++G+v ++++
  gi|385806339|ref|YP_005842737.1| 38 LLNSGG--LTAKELSVMTGLPQSKVYESLSKLIEKGWVMKSSD 78
                                      667888..******************************88764 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.8e-05     0.095       3      68 ..      33     110 ..      31     138 .. 0.85
   2 ?   -1.6   0.0       1.9   3.9e+03      46      46 ..     157     157 ..     127     193 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.8e-05
                            HTH_40   3 eetlell.eeglsieeIAkerglkesTIegHLaelieeg............eeidlerlvseeeekeIeeaiekvgs 66 
                                       e+ l+ll   gl+ +e +   gl +s +++ L +lie+g            +++++ ++   e++ eI + +e+v++
  gi|385806339|ref|YP_005842737.1|  33 EIYLRLLnSGGLTAKELSVMTGLPQSKVYESLSKLIEKGwvmkssdrpsifYPVNIAEV-WNETKHEISKKMEEVET 108
                                       67899997889***************************988888888888888999775.77888899999999986 PP

                            HTH_40  67 ek 68 
                                       + 
  gi|385806339|ref|YP_005842737.1| 109 KV 110
                                       65 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.9
                            HTH_40  46 e 46 
                                       +
  gi|385806339|ref|YP_005842737.1| 157 K 157
                                       2 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     9e-05      0.18      11      52 ..      37      78 ..      31      79 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9e-05
                                      HHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE CS
                              MarR 11 ilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsks 52
                                       l ++g+l+ +eL  + g+ +s v + l +L++kG++++s +
  gi|385806339|ref|YP_005842737.1| 37 RLLNSGGLTAKELSVMTGLPQSKVYESLSKLIEKGWVMKSSD 78
                                      57799*********************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       879  (0.0490267); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 1471.02
//
Query:       gi|385806340|ref|YP_005842738.1|  [L=69]
Description: hypothetical protein FFONT_1298 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-06   27.6   0.0    2.5e-06   27.2   0.0    1.2  1  RHH_1           Ribbon-helix-helix protein, copG family
     0.0071   16.2   0.2     0.0089   15.9   0.2    1.3  1  VapB_antitoxin  Bacterial antitoxin of type II TA system, Vap
  ------ inclusion threshold ------
      0.071   12.8   0.5       0.15   11.8   0.3    1.6  2  Fur_reg_FbpA    Fur-regulated basic protein A


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.0   4.2e-10   2.5e-06       2      39 .]      10      48 ..       9      48 .. 0.96

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 4.2e-10
                                      EEEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHHHHHHH CS
                             RHH_1  2 vsirldeellerLdelarrrg.rSrSelIReAlreyler 39
                                      +++++++++le++ el+r ++ ++r ++I  Al e+l++
  gi|385806340|ref|YP_005842738.1| 10 ITVKVSDDVLELIKELIRSGKyKNRNQIINKALDEFLAK 48
                                      9**********************************9975 PP

>> VapB_antitoxin  Bacterial antitoxin of type II TA system, VapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.2   1.5e-06    0.0089      10      39 ..      20      49 ..       6      57 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.5e-06
                                      XXXXXXXXXXXXXXXXXXXXXXXXX----- CS
                    VapB_antitoxin 10 eLlaeAirltglktKrEaVnlALreLiqrr 39
                                      eL++e ir +++k +  ++n+AL e+++++
  gi|385806340|ref|YP_005842738.1| 20 ELIKELIRSGKYKNRNQIINKALDEFLAKE 49
                                      89*************************986 PP

>> Fur_reg_FbpA  Fur-regulated basic protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.3   2.5e-05      0.15       5      19 ..      21      35 ..      20      37 .. 0.89
   2 ?   -2.7   0.0      0.83     5e+03      10      16 ..      46      52 ..      43      54 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.5e-05
                      Fur_reg_FbpA  5 LIekLIqsGiykkdg 19
                                      LI++LI+sG yk ++
  gi|385806340|ref|YP_005842738.1| 21 LIKELIRSGKYKNRN 35
                                      9***********877 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.83
                      Fur_reg_FbpA 10 IqsGiyk 16
                                      ++++i++
  gi|385806340|ref|YP_005842738.1| 46 LAKEIFS 52
                                      6778886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       957  (0.0533772); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); 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 0.36s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 389.89
//
Query:       gi|385806341|ref|YP_005842739.1|  [L=56]
Description: 50S ribosomal protein L40E [Fervidicoccus fontis Kam940]
Scores for complete 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   45.3   4.7    7.3e-12   45.0   4.7    1.1  1  Ribosomal_L40e  Ribosomal L40e family
      1e-05   25.1   5.0    1.5e-05   24.6   5.0    1.2  1  zinc_ribbon_2   zinc-ribbon domain
    0.00021   20.5   3.7    0.00027   20.2   3.7    1.2  1  zf-RanBP        Zn-finger in Ran binding protein and others
    0.00022   21.2   0.7    0.00025   21.0   0.7    1.1  1  DZR             Double zinc ribbon
    0.00027   20.7   0.8    0.00036   20.3   0.8    1.2  1  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
     0.0027   17.7   0.3     0.0028   17.7   0.3    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
     0.0049   16.2   3.9     0.0076   15.6   3.9    1.4  1  zf-ribbon_3     zinc-ribbon domain
  ------ inclusion threshold ------
      0.015   16.1   0.2      0.016   15.9   0.2    1.1  1  zinc_ribbon_15  zinc-ribbon family
      0.034   14.2   0.8        0.2   11.7   0.8    1.9  1  CpXC            CpXC protein
      0.039   14.6   3.2       0.62   10.8   0.8    2.2  2  zf-ISL3         zinc-finger of transposase IS204/IS1001/IS109
      0.051   14.0   0.8       0.17   12.4   0.1    1.8  2  hSH3            Helically-extended SH3 domain
      0.071   13.0   3.1        1.4    8.9   0.0    2.4  2  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
       0.13   12.4   3.1       0.96    9.6   3.1    2.1  1  Zn-ribbon_8     Zinc ribbon domain
       0.13   11.7   0.8       0.13   11.7   0.8    2.2  2  DUF2688         Protein of unknown function (DUF2688)
       0.21   11.7   5.5        2.8    8.2   0.2    2.2  2  zf-CCHC         Zinc knuckle
       0.28   10.7   3.9        5.5    6.6   0.3    2.3  2  TF_Zn_Ribbon    TFIIB zinc-binding
       0.34   11.1   6.3       0.25   11.5   0.7    2.1  2  Ribosomal_L37e  Ribosomal protein L37e
       0.39   10.4   3.4        7.1    6.4   0.0    2.1  2  zf-RRN7         Zinc-finger of RNA-polymerase I-specific TFII
        0.4   10.7   5.0        3.2    7.8   4.8    2.1  2  ADK_lid         Adenylate kinase, active site lid
       0.63    9.8   7.9        2.6    7.8   0.9    2.3  2  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
       0.84    9.4   5.1        2.5    7.9   5.2    1.7  1  Rubredoxin_2    Rubredoxin metal binding domain
        6.1    6.8   8.2        4.6    7.1   1.3    2.3  2  zf-CCHC_2       Zinc knuckle


Domain annotation for each model (and alignments):
>> Ribosomal_L40e  Ribosomal L40e family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   4.7     9e-15   7.3e-12       2      49 ..       5      49 ..       4      50 .. 0.96

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 9e-15
                    Ribosomal_L40e  2 epsLrqLAqKyncdKmiCrkCYArlpprAtnCrkkkCghsnnlrpKKk 49
                                      +p L+ +  K   dKmiCr C A  pp At+Cr  +Cg s+nlrpKKk
  gi|385806341|ref|YP_005842739.1|  5 DPELVEIVTKRVLDKMICRNCGAINPPNATKCR--RCG-SKNLRPKKK 49
                                      799******************************..9**.899*****8 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   5.0   1.8e-08   1.5e-05       2      22 ..      22      42 ..      21      43 .. 0.95

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.8e-08
                     zinc_ribbon_2  2 CpnCGaelqdnakFCpyCGtp 22
                                      C nCGa +++na+ C +CG++
  gi|385806341|ref|YP_005842739.1| 22 CRNCGAINPPNATKCRRCGSK 42
                                      *******************97 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 !   20.2   3.7   3.3e-07   0.00027       6      28 ..      21      43 ..      21      45 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 3.3e-07
                                      E-SSS--EEESSSSB-TTT--BT CS
                          zf-RanBP  6 dCskClvqNfawstkCvaCqapk 28
                                      +C  C++ N++ +tkC +C++++
  gi|385806341|ref|YP_005842739.1| 21 ICRNCGAINPPNATKCRRCGSKN 43
                                      5999****************986 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.7     3e-07   0.00025       1      21 [.      22      42 ..      13      53 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3e-07
                               DZR  1 CpqCgeelppdarfCseCgtk 21
                                      C +Cg+ +pp+a  C +Cg+k
  gi|385806341|ref|YP_005842739.1| 22 CRNCGAINPPNATKCRRCGSK 42
                                      888888888888888888876 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 !   20.3   0.8   4.5e-07   0.00036      14      36 ..      22      44 ..      18      45 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 4.5e-07
                           DUF35_N 14 CpdCGtvqfPPr.avCphCgsddl 36
                                      C++CG+   PP    C++Cgs++l
  gi|385806341|ref|YP_005842739.1| 22 CRNCGAIN-PPNaTKCRRCGSKNL 44
                                      *******9.***9*********98 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.3   3.4e-06    0.0028      61      99 ..      10      46 ..       3      53 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.4e-06
                                      EEEEEEE--EEEETTTS-EEECHHHHHS-TTTSSS-EEE CS
                              HypA 61 eLeieevpvkvrCreCgkefeleekalrCpkCgsadvei 99
                                      e+  ++v  k+ Cr+Cg+    +  a++C +Cgs++++ 
  gi|385806341|ref|YP_005842739.1| 10 EIVTKRVLDKMICRNCGAINPPN--ATKCRRCGSKNLRP 46
                                      56677888899******877766..469******99875 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   3.9   9.3e-06    0.0076       5      25 ..      22      42 ..      19      43 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 9.3e-06
                       zf-ribbon_3  5 CPnCGa.plssddnvCpyCGtk 25
                                      C nCGa +  + +++C  CG+k
  gi|385806341|ref|YP_005842739.1| 22 CRNCGAiN-PPNATKCRRCGSK 42
                                      89****99.***********97 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.9   0.2     2e-05     0.016      56      86 .]      10      40 ..       1      40 [. 0.79

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2e-05
                    zinc_ribbon_15 56 eiekkessekkeCknCgkeveeefkyCpkCg 86
                                      ei +k+  +k++C+nCg+   ++ + C +Cg
  gi|385806341|ref|YP_005842739.1| 10 EIVTKRVLDKMICRNCGAINPPNATKCRRCG 40
                                      44455556699*******************9 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.8   0.00024       0.2      22      51 ..       4      33 ..       1      49 [. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00024
                              CpXC 22 edpelkeklldgslfeatCpkCgataklea 51
                                      +dpel+e + +  l ++ C +Cga + ++a
  gi|385806341|ref|YP_005842739.1|  4 KDPELVEIVTKRVLDKMICRNCGAINPPNA 33
                                      79*********************9887765 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 ?    4.4   0.1     0.076        62       3      10 ..      20      27 ..      18      29 .. 0.77
   2 ?   10.8   0.8   0.00076      0.62       3      18 ..      34      49 ..      32      51 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.076
                           zf-ISL3  3 hrCPnCgs 10
                                      + C+nCg+
  gi|385806341|ref|YP_005842739.1| 20 MICRNCGA 27
                                      67999985 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00076
                           zf-ISL3  3 hrCPnCgsktvvkhgk 18
                                      ++C++Cgsk+++ + k
  gi|385806341|ref|YP_005842739.1| 34 TKCRRCGSKNLRPKKK 49
                                      68*******9987765 PP

>> hSH3  Helically-extended SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1    0.0002      0.17      34      56 ..       2      24 ..       1      28 [. 0.93
   2 ?    0.5   0.0       1.1   8.7e+02      23      36 ..      34      47 ..      26      54 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0002
                              hSH3 34 pvkrgeildviqktddkkvlcrn 56
                                      p+k  e +++++k   +k++crn
  gi|385806341|ref|YP_005842739.1|  2 PIKDPELVEIVTKRVLDKMICRN 24
                                      79999*****************9 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.1
                              hSH3 23 laskklggkdLpvk 36
                                      ++ ++ g+k+L+ k
  gi|385806341|ref|YP_005842739.1| 34 TKCRRCGSKNLRPK 47
                                      56788999998755 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0017       1.4      24      32 ..      22      30 ..      11      34 .. 0.80
   2 ?    4.7   0.6     0.035        28      23      30 ..      35      42 ..      31      43 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0017
                                      ESSSS-EEE CS
                    RNA_POL_M_15KD 24 CrqCgYeep 32
                                      Cr+Cg++ p
  gi|385806341|ref|YP_005842739.1| 22 CRNCGAINP 30
                                      ******998 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.035
                                      EESSSS-E CS
                    RNA_POL_M_15KD 23 eCrqCgYe 30
                                       Cr Cg++
  gi|385806341|ref|YP_005842739.1| 35 KCRRCGSK 42
                                      5****986 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   3.1    0.0012      0.96       8      37 ..      22      45 ..       7      46 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0012
                       Zn-ribbon_8  8 CeeCghefevlqsisdaplta.CPeCgs.evr 37
                                      C++Cg    ++     +p+ + C +Cgs ++r
  gi|385806341|ref|YP_005842739.1| 22 CRNCG----AI----NPPNATkCRRCGSkNLR 45
                                      88888....23....3444444******8876 PP

>> DUF2688  Protein of unknown function (DUF2688)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   1.1      0.39   3.2e+02      10      14 ..      22      26 ..       7      28 .. 0.73
   2 ?   11.7   0.8   0.00016      0.13       7      19 ..      33      45 ..      32      55 .. 0.64

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.39
                           DUF2688 10 CrRCG 14
                                      Cr CG
  gi|385806341|ref|YP_005842739.1| 22 CRNCG 26
                                      99998 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00016
                           DUF2688  7 tTqCrRCGkslst 19
                                      +T+CrRCG    +
  gi|385806341|ref|YP_005842739.1| 33 ATKCRRCGSKNLR 45
                                      69******64333 PP

>> zf-CCHC  Zinc knuckle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.2    0.0035       2.8       2       8 ..      21      27 ..      20      29 .. 0.82
   2 ?    6.0   1.1     0.017        13       2       8 ..      35      41 ..      35      43 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0035
                                      CTSSSSS CS
                           zf-CCHC  2 kCynCGe 8 
                                       C+nCG 
  gi|385806341|ref|YP_005842739.1| 21 ICRNCGA 27
                                      6*****7 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.017
                                      CTSSSSS CS
                           zf-CCHC  2 kCynCGe 8 
                                      kC++CG+
  gi|385806341|ref|YP_005842739.1| 35 KCRRCGS 41
                                      7*****8 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.2     0.013        10      20      27 ..      20      27 ..      12      32 .. 0.77
   2 ?    6.6   0.3    0.0068       5.5       2      11 ..      35      44 ..      34      49 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.013
                                      EEESSSSB CS
                      TF_Zn_Ribbon 20 lvCtdCGl 27
                                      ++C +CG+
  gi|385806341|ref|YP_005842739.1| 20 MICRNCGA 27
                                      46777765 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0068
                                      EETTTTCEEC CS
                      TF_Zn_Ribbon  2 kCPnCgstnl 11
                                      kC  Cgs+nl
  gi|385806341|ref|YP_005842739.1| 35 KCRRCGSKNL 44
                                      8******984 PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.5      0.14   1.1e+02      17      24 ..      20      27 ..      13      29 .. 0.80
   2 ?   11.5   0.7   0.00031      0.25      17      33 ..      34      50 ..      29      53 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.14
                    Ribosomal_L37e 17 ilCrrCgk 24
                                      ++Cr Cg 
  gi|385806341|ref|YP_005842739.1| 20 MICRNCGA 27
                                      78999995 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00031
                    Ribosomal_L37e 17 ilCrrCgkrsyhvqkkt 33
                                      ++CrrCg++    +kk+
  gi|385806341|ref|YP_005842739.1| 34 TKCRRCGSKNLRPKKKK 50
                                      79*******99999886 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0087       7.1      22      29 ..      20      27 ..      19      28 .. 0.80
   2 ?    4.2   1.2     0.044        36      24      29 ..      36      41 ..      36      42 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0087
                           zf-RRN7 22 yyCrrCht 29
                                      ++Cr+C+ 
  gi|385806341|ref|YP_005842739.1| 20 MICRNCGA 27
                                      79999996 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.044
                           zf-RRN7 24 CrrCht 29
                                      CrrC++
  gi|385806341|ref|YP_005842739.1| 36 CRRCGS 41
                                      *****7 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.4     0.014        12       2      10 ..      20      28 ..      13      28 .. 0.79
   2 ?    7.8   4.8    0.0039       3.2       3      30 ..      21      42 ..      19      48 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.014
                                      EE-TTT--E CS
                           ADK_lid  2 rvCpkCGrs 10
                                      ++C++CG++
  gi|385806341|ref|YP_005842739.1| 20 MICRNCGAI 28
                                      478888875 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0039
                                      E-TTT--EEETTTB--SSTTB-TTT--. CS
                           ADK_lid  3 vCpkCGrsYhvvfnpPkveglCDkCGep 30
                                      +C++CG++ +     P +  +C  CG++
  gi|385806341|ref|YP_005842739.1| 21 ICRNCGAI-N-----PPNATKCRRCGSK 42
                                      89999998.5.....559********95 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   1.0    0.0087       7.1      16      24 ..      18      26 ..      10      28 .. 0.83
   2 ?    7.8   0.9    0.0032       2.6      15      26 ..      31      42 ..      27      45 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0087
                                      S----SSS- CS
                    DNA_RNApol_7kD 16 dpiRCkeCG 24
                                      d   C++CG
  gi|385806341|ref|YP_005842739.1| 18 DKMICRNCG 26
                                      6678****9 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0032
                                      SS----SSS--- CS
                    DNA_RNApol_7kD 15 gdpiRCkeCGhR 26
                                        + +C+ CG++
  gi|385806341|ref|YP_005842739.1| 31 PNATKCRRCGSK 42
                                      56779*****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 ?    7.9   5.2    0.0031       2.5       2      22 ..      21      41 ..      21      43 .. 0.94

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0031
                      Rubredoxin_2  2 vCsqCGfesakwfGrCpsCgs 22
                                      +C++CG+  +    +C+ Cgs
  gi|385806341|ref|YP_005842739.1| 21 ICRNCGAINPPNATKCRRCGS 41
                                      5******************97 PP

>> zf-CCHC_2  Zinc knuckle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.8     0.079        65       5      10 ..      21      26 ..      21      27 .. 0.87
   2 ?    7.1   1.3    0.0057       4.6       5      12 ..      35      42 ..      35      42 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.079
                         zf-CCHC_2  5 vChiCg 10
                                      +C+ Cg
  gi|385806341|ref|YP_005842739.1| 21 ICRNCG 26
                                      8****9 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0057
                         zf-CCHC_2  5 vChiCgkk 12
                                      +C++Cg+k
  gi|385806341|ref|YP_005842739.1| 35 KCRRCGSK 42
                                      7*****87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); 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: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 361.55
//
Query:       gi|385806342|ref|YP_005842740.1|  [L=306]
Description: putative amidohydrolase [Fervidicoccus fontis Kam940]
Scores for complete 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   59.7   0.0    3.4e-16   59.4   0.0    1.2  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 !   59.4   0.0   1.9e-20   3.4e-16       1     231 [.       9     232 ..       9     265 .. 0.83

  Alignments for each domain:
  == domain 1  score: 59.4 bits;  conditional E-value: 1.9e-20
                                       EEEEEEBB-STTHHHHHHHHHHHHHHHHHHTTESEEEEETTTTTBS..............SSHHHHHHHHBHSSSHH CS
                      CN_hydrolase   1 rvAvvQlpqkaadleanlqklleliaeAarkgadLivlPElfitgy..............keeahfleaAeaglget 63 
                                       ++A++ ++ k  +++ n++++++ + eA++kga++++lP + + g               k++a+         g t
  gi|385806342|ref|YP_005842740.1|   9 KIAIAHMTLKLLSKKLNFERAKKVVHEAKQKGAKVVILPSMINLGPaisftspaqlksilKNHAER-----IPSGGT 80 
                                       5899999999999*******************************8865555555554444444444.....55677* PP

                                       HHHHHHHHHHHTEEEEEE.EEEEECCTTEEEEEEEEEEEETTSEEEEEEE-SS--EECTTSCECCGHHTSCS.-SSS CS
                      CN_hydrolase  64 lallaalarkngiavvig.liereltngklqayntavlldldgklvgkyrKlhLfpgeprpptaverelfep.gdgi 138
                                       + +l+ la +n i ++ g ++er  +++k+  + t + ++++g++vgkyrK+ L        ++   ++  + g+  
  gi|385806342|ref|YP_005842740.1|  81 AYFLSTLAVQNSIFIISGpILER--AGPKV--FLTSLAISPTGNIVGKYRKIVL--------SHSDISIGLSsGK-- 143
                                       ******************88888..9****..*********************8........4555666666266.. PP

                                       -EEEETTE....EEEEEEGGGGGSHHHHHHHHHTT-SEEEEBH.GCCCTCHHHHHHHHHHHHHHHHHHTSEEEEEEB CS
                      CN_hydrolase 139 pvfdtpvg....kiGaaiCyeigfpellralalkgaeilvnlserapvpksmgppqwellgraralengcfviaanq 211
                                          +++v+    k G++  ++ ++pe++r l   g  +l+n    +p  +    + +  + ++r++en ++++ +  
  gi|385806342|ref|YP_005842740.1| 144 ---SLEVVdmkeKYGIMAEWDSYHPEIARGLTILGSTVLIN----FPRIEPVFDKKLKKILETRSIENNVPIMSIGG 213
                                       ...44444445699***************************....566778889999999***********988877 PP

                                       EEEHCETTEEEE--EEEE-T CS
                      CN_hydrolase 212 vggyeqlilwpvghSaiidp 231
                                       +    q++      S i+dp
  gi|385806342|ref|YP_005842740.1| 214 IIK-SQDQFLAEFPSLIYDP 232
                                       777.6666666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       998  (0.055664); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.36s 00:00:01.02 Elapsed: 00:00:00.55
# Mc/sec: 1671.26
//
Query:       gi|385806343|ref|YP_005842741.1|  [L=1245]
Description: reverse gyrase [Fervidicoccus fontis Kam940]
Scores for complete 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-85  287.7   1.2    1.5e-85  287.7   1.2    1.7  2  Topoisom_bac    DNA topoisomerase
      4e-25   88.0   0.0      4e-25   88.0   0.0    3.1  2  Toprim          Toprim domain
    1.5e-13   50.9   0.0    7.6e-13   48.6   0.0    2.3  1  DEAD            DEAD/DEAH box helicase
    4.1e-13   48.5   1.2    4.1e-13   48.5   1.2    2.5  2  zf_Rg           Reverse gyrase zinc finger
    2.2e-09   37.7   0.2      0.071   13.5   0.0    5.0  4  Helicase_C      Helicase conserved C-terminal domain
    5.7e-06   26.4   0.1    3.5e-05   23.9   0.0    2.4  2  ResIII          Type III restriction enzyme, res subunit
     0.0034   16.2   0.1     0.0096   14.8   0.1    1.7  1  NRDD            Anaerobic ribonucleoside-triphosphate reducta
  ------ inclusion threshold ------
       0.05   13.6   4.6       0.28   11.2   0.6    2.4  2  DZR             Double zinc ribbon
      0.066   13.7   0.2       0.48   10.9   0.0    2.6  1  Toprim_4        Toprim domain
      0.085   13.1   0.0       0.28   11.4   0.0    1.9  1  DUF5433         Family of unknown function (DUF5433)
       0.09   12.9   7.0       0.19   11.8   0.9    2.7  2  Zn-ribbon_8     Zinc ribbon domain
      0.098   13.4   0.3      0.098   13.4   0.3    2.7  2  zinc_ribbon_15  zinc-ribbon family
       0.14   11.8   2.8       0.45   10.1   0.1    2.7  2  TackOD1         Thaumarchaeal output domain 1
       0.14   12.0   3.1       0.59   10.1   0.2    2.4  2  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
       0.16   12.0   3.7       0.13   12.3   0.3    2.3  2  HypA            Hydrogenase/urease nickel incorporation, meta
       0.17   12.6   0.8        3.2    8.5   0.0    2.7  2  zf-ISL3         zinc-finger of transposase IS204/IS1001/IS109
        0.9    9.3  10.2       0.69    9.7   3.1    2.5  2  zinc_ribbon_2   zinc-ribbon domain
          2    8.4   6.0       0.72    9.8   1.2    2.5  2  Prok-RING_1     Prokaryotic RING finger family 1
        2.1    8.6   4.6         12    6.2   0.7    2.6  2  IBR             IBR domain, a half RING-finger domain
        2.1    7.8   7.2         13    5.2   0.8    3.0  3  zf-TFIIB        Transcription factor zinc-finger
        2.9    7.8   7.0         37    4.3   0.2    3.8  3  zf-FPG_IleRS    Zinc finger found in FPG and IleRS
        3.6    7.3   6.4        5.2    6.8   0.1    2.8  3  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
        3.9    7.5   7.6         22    5.1   1.4    2.8  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
        3.9    7.0  11.2        5.5    6.6   0.5    3.0  3  zf-ribbon_3     zinc-ribbon domain
        4.8    6.8   7.1       0.78    9.4   0.9    2.6  2  RecR            RecR protein
        9.4    6.3   5.9         34    4.5   0.6    2.7  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain


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 ?   -2.8   0.3       3.3   2.3e+03     383     411 ..     254     282 ..     247     283 .. 0.80
   2 !  287.7   1.2   2.2e-88   1.5e-85       2     412 ..     818    1233 ..     817    1234 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.3
                      Topoisom_bac 383 kdlvspelTaeleekLdeIaegkadakev 411
                                       +d +s++l++el ekL++ ++ k++  +v
  gi|385806343|ref|YP_005842741.1| 254 EDNKSEKLRKELNEKLEKLKKEKEKIGAV 282
                                       56678999999999999999999886665 PP

  == domain 2  score: 287.7 bits;  conditional E-value: 2.2e-88
                      Topoisom_bac    2 inenlvdaaeaRrelDwliGinlsrlltk...............klkgkkvlsaGRVqtptLaliveRereienF 61  
                                        i+e+lvda+ +Rr+ D++iG++ls+ l+k               +++++k+lsaGRVqtp+L++i+eR++++ + 
  gi|385806343|ref|YP_005842741.1|  818 IDEKLVDAQITRRVEDRWIGFSLSQKLQKdfwkeycmkyvknesRCSENKNLSAGRVQTPVLGWIIERYHDHLKS 892 
                                        689**********************999989988877655433333359********************999887 PP

                      Topoisom_bac   62 vpeeyweveatlkkekkekekkkkkkkerikdkeeaeaileklkkkeakvesvekkekkk.ppplpfdtttLqke 135 
                                          ++  +++a+   +++    + + +ke ++ + + +a+ ek    ++ v+ v+++  +  p+p pf+t+tL+ e
  gi|385806343|ref|YP_005842741.1|  893 -EKTIISIQAK---NGGLI--ELSFAKEDYNRELDLDALKEK----KVIVKVVKEEDAEVfPRP-PFTTDTLLIE 956 
                                        .5667888876...44444..255666666655555555544....489999999999998999.********** PP

                      Topoisom_bac  136 asrklglsakktlsiaqkLYekaglitYpRTdstrlseeaelkailealakkygkeylefaekllkktkkksvvk 210 
                                         ++ lglsa++t+++aq+L+e  glitY+RTds r+s++  ++ ++++++++    + ++ ekl++ ++ +    
  gi|385806343|ref|YP_005842741.1|  957 SNKVLGLSASRTMQLAQDLFEA-GLITYHRTDSIRVSTTG-IEVAKDYIQRN----FVDSWEKLFT-PRIW---- 1020
                                        *********************5.*****************.9*********8....5555666887.6644.... PP

                      Topoisom_bac  211 nkkveaHeAIrPteelpklkels...............ddekklYelIvrrflaslmkdakyeettvkleveeee 270 
                                        +++ +aHeAIrPt+ l+k ++l+               + +  lY+lI+rrf+as+mk+++++++ +  e+e+  
  gi|385806343|ref|YP_005842741.1| 1021 GSE-GAHEAIRPTRPLSK-DDLIklidegeiivpkpltRTHFSLYDLIFRRFVASQMKPCVVSKQFIVYEIEGTG 1093
                                        667.9********99995.4555666999999**999988888**************************996655 PP

                      Topoisom_bac  271 fkas....gktilekGfkkvykeekkeeeeeelpelkegeevkvkeveleekkTkppkryteasLikamekagiG 341 
                                        +k+s    ++ i++kGf++vy + + +++      +keg    + +  +++ k +  + yt+a+L+++m+++g+G
  gi|385806343|ref|YP_005842741.1| 1094 IKISeeilTNNIKDKGFLTVYSYLELRQR------MKEGSYS-IVN--VNAIKKRVIQLYTQADLVSKMKERGLG 1159
                                        55541111677899********9988854......8999994.444..677888899****************** PP

                      Topoisom_bac  342 tpaTraeiieklvergYverk.k.kslvptelGkalvell.ekfkdlvspelTaeleekLdeIaegkadakevl 412 
                                        +p+T+a+ii+k+++r+Y+ ++ k +++vpt+lG+++++ l  +f++lvs+e T++leek++++a+g++d+++v+
  gi|385806343|ref|YP_005842741.1| 1160 RPSTYATIISKILTRRYALESgKyRKIVPTKLGINVYNYLsANFSKLVSEERTRSLEEKMSRVANGEEDYRNVI 1233
                                        *****************999977999**************8889**************************9998 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       2.9     2e+03      44      67 ..     585     616 ..     557     618 .. 0.73
   2 !   88.0   0.0   5.8e-28     4e-25       2     103 .]     632     803 ..     631     803 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.9
                                       E........ECTTTHHHHHHHHHHHHHHSEEE CS
                            Toprim  44 e........eiedkkkvlkalkelakradeii 67 
                                       +        ei d ++vlk+++e +k++ +ii
  gi|385806343|ref|YP_005842741.1| 585 IesadikplEIIDLNQVLKEIDEDRKKVLKII 616
                                       25666667788899999999999999999987 PP

  == domain 2  score: 88.0 bits;  conditional E-value: 5.8e-28
                                       EEEESSHHHHHHHHHTHT...................STEEEEEEESSSSEEEHS...................... CS
                            Toprim   2 lvivEgpsdaktiakalg...................sgfqavtaslGhildlet...................... 37 
                                       l+ivE+p++akti++++g                   +  + +t+s Ghi+d++t                      
  gi|385806343|ref|YP_005842741.1| 632 LMIVESPNKAKTISNFFGrpsvrilgenlkayevsigNLMLLITSSGGHIVDVVTnandnelkaysglkkelygily 708
                                       9**************************************************************************** PP

                                       .....TTEEEEE.........................ECTTTHHHHHHHHHHHHHHSEEEEECSSSHHHHHHHHHHH CS
                            Toprim  38 .....efkpvye.........................eiedkkkvlkalkelakradeiilatDpDreGeaiawell 84 
                                             f pvy                          ei+d ++v++al+ la ++d++++atDpD+eGe+i+w++ 
  gi|385806343|ref|YP_005842741.1| 709 dekrkTFVPVYStikkclncgnqfsdeidrcprcgsrEIKDSRNVINALRDLATEVDKVLIATDPDTEGEKIGWDIS 785
                                       ****9777777788888888888888888************************************************ PP

                                       HHHTHHHTTTEEEEEESSS CS
                            Toprim  85 evlkellenkigrvefsei 103
                                        +l+++++n i+rv f+e+
  gi|385806343|ref|YP_005842741.1| 786 VLLRPFTQN-IKRVLFHEV 803
                                       9999*****.*******95 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   0.0   1.1e-15   7.6e-13      14     149 ..      98     229 ..      86     297 .. 0.83

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 1.1e-15
                                       TCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST..SEEE..EEETTSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxx..xxxxxxx RF
                              DEAD  14 ggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyid..lrvl..liiggva 86 
                                       ++++ + a+TG GKT   +i +l  ++   +k++ k +iv Ptr+L+ q++++l++fk++++   ++l  +++    
  gi|385806343|ref|YP_005842741.1|  98 NKSFSIVAPTGVGKTVFGMITAL--FF---SKHKEKSMIVLPTRALVSQVCEKLERFKETLEidAKILcsSMLRAGI 169
                                       678889*****************..54...589999***********************855223333113444555 PP

                                       HHHHHHHHHTT.CSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHS CS
                                       xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  87 ardqlskldng.vdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnql 149
                                       +++ l+ l++g  di+v t + +++  ++  l+   +rf+ +D +d +l++  ++ i++++n++
  gi|385806343|ref|YP_005842741.1| 170 KSEVLEMLSKGdFDIFVCTSKFMIR--NSSILKRAGFRFFFVDDVDSVLKS--GKSIESLFNAM 229
                                       567777777778********99999..555777999*************98..67777777766 PP

>> zf_Rg  Reverse gyrase zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   1.2     6e-16   4.1e-13       2      36 ..       4      38 ..       3      49 .. 0.89
   2 ?   -2.6   0.3       5.3   3.6e+03       9      20 ..     738     750 ..     736     752 .. 0.68

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 6e-16
                             zf_Rg  2 ikavfeklCPNCgGdisdeRlekGLpCkrClPkeg 36
                                      +k ++ ++CPNCgG++sd Rl kGL C+rClP+ +
  gi|385806343|ref|YP_005842741.1|  4 VKGIYIRSCPNCGGPVSDLRLSKGLACERCLPDIN 38
                                      577999**************************964 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5.3
                             zf_Rg   9 lCPNCgG.disde 20 
                                        CP Cg  +i+d 
  gi|385806343|ref|YP_005842741.1| 738 RCPRCGSrEIKDS 750
                                       59***95356655 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 !   11.9   0.1   0.00031      0.21       6      74 ..     117     189 ..     113     253 .. 0.81
   2 !   13.5   0.0    0.0001     0.071      19      95 ..     345     424 ..     329     435 .. 0.77
   3 ?    3.1   0.0      0.17   1.2e+02      95     110 ..     537     552 ..     526     553 .. 0.86
   4 ?    2.1   0.0      0.34   2.4e+02      15      74 ..     711     772 ..     699     781 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00031
                                       HHHHHHHTTTTSEEEEEESSHH....HHHHHHHHHHHTTSTEEEESTT.STHHHHHHHHHHHHTTSSSEEEESG CS
                        Helicase_C   6 llellkleeeggkilifvntid....rlekvklllekkgikvavlhge.lpqnereeileqfnkgesdvLiatd 74 
                                       +++l+ ++++++k++i+++t+      +ek++ ++e+ +i + +l ++ l +  + e+le   kg++d+ ++t+
  gi|385806343|ref|YP_005842741.1| 117 ITALF-FSKHKEKSMIVLPTRAlvsqVCEKLERFKETLEIDAKILCSSmLRAGIKSEVLEMLSKGDFDIFVCTS 189
                                       66676.7899************65554455778877779999999886378899***************99997 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.0001
                                       EEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGG....GTSSSTST.TESEEEE CS
                        Helicase_C  19 ilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdv....aerGidip.kvnlVin 90 
                                        l+fv++    e +k +     ++++ + +e  ++++++++++f  ge+dvL+  ++    + rG+d+p +v++Vi+
  gi|385806343|ref|YP_005842741.1| 345 GLVFVPSDMGTEYAKKI--ADLLNYIGIKSEAISSKNIRSIKSFETGEIDVLVGVSIyygiLVRGLDLPhRVRYVIF 419
                                       57777777755333333..3356777778888888999*****************99888899*****9789****9 PP

                                       SSSSS CS
                        Helicase_C  91 fdlpr 95 
                                        +lpr
  gi|385806343|ref|YP_005842741.1| 420 AGLPR 424
                                       99984 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.17
                                       SSHHHHHHHHTTSSST CS
                        Helicase_C  95 rnvtsyiqriGRtgRa 110
                                        +++syiq++GR+ R 
  gi|385806343|ref|YP_005842741.1| 537 PDIKSYIQASGRCSRL 552
                                       5789*********996 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.34
                                       TTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHH..TTSSS.EEEESG CS
                        Helicase_C  15 eggkilifvntidrlek.vklllekkgikvavlhgelpqnereeileqfn..kgesd.vLiatd 74 
                                       ++++ + +  ti+++ +  + +  + +i  ++  g+ + ++ + ++++ +  + e+d vLiatd
  gi|385806343|ref|YP_005842741.1| 711 KRKTFVPVYSTIKKCLNcGNQF--SDEIDRCPRCGSREIKDSRNVINALRdlATEVDkVLIATD 772
                                       4444444555555552233344..448999999999999999999*999988899999*****9 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   5.1e-08   3.5e-05      21      82 ..      82     154 ..      58     214 .. 0.68
   2 ?   -3.0   0.0       9.3   6.4e+03      43      84 ..    1166    1213 ..    1134    1233 .. 0.56

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 5.1e-08
                                       ...............TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG.. CS
                            ResIII  21 s.............krdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseay 82 
                                       +               +k + i+++TG+GKT+    +i +l+ ++++ek +++ p+++l++q  e++++f+++  
  gi|385806343|ref|YP_005842741.1|  82 NppwsaqitwakrvFLNKSFSIVAPTGVGKTVF--GMITALFFSKHKEKSMIVLPTRALVSQVCEKLERFKETLE 154
                                       144444445554445788999**********75..5566666666778****************88888777654 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 9.3
                                        HHHHHH-S........-EEEEESSH...HHHHHHHHHGGGGTGG.... CS
                            ResIII   43 klierllkkgkee...kflflvprk...slleqtleefkkflseayke 84  
                                         +i ++l+ ++     k   +vp+k   ++++ +  +f+k+ se++++
  gi|385806343|ref|YP_005842741.1| 1166 TIISKILTRRYALesgKYRKIVPTKlgiNVYNYLSANFSKLVSEERTR 1213
                                        333333333322223333333444333377777777777777776655 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   1.4e-05    0.0096     466     531 ..     676     747 ..     669     756 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.4e-05
                                       GTT-S-EEEEBSS--SSHHHH....HHHHH.HHHHTT--EEEEE--EEEETT.--..EESSSB-TTT--BE.E CS
                              NRDD 466 ttGGailyieldeekknpeal....eklvk.iakktgigYfsinpkidvCnecgy..kgeiekCpkCgseeev 531
                                       ++GG+i+ +  + + ++++a+    ++l   ++++++  ++ +  +i+ C +cg   + ei++Cp+Cgs+e +
  gi|385806343|ref|YP_005842741.1| 676 SSGGHIVDVVTNANDNELKAYsglkKELYGiLYDEKRKTFVPVYSTIKKCLNCGNqfSDEIDRCPRCGSRE-I 747
                                       689999999999888999998222234455456778889999*************999999*******876.5 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.2      0.11        75      14      34 ..      11      33 ..       8      43 .. 0.62
   2 ?   11.2   0.6   0.00041      0.28      29      49 .]     723     743 ..     710     752 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.11
                               DZR 14 fCseCgtklkavaa..edrCpsC 34
                                       C++Cg +++        +C +C
  gi|385806343|ref|YP_005842741.1| 11 SCPNCGGPVSDLRLskGLACERC 33
                                      57777777653322445566666 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00041
                               DZR  29 drCpsCgekvdpearfCpeCG 49 
                                       ++C +Cg + + e   Cp CG
  gi|385806343|ref|YP_005842741.1| 723 KKCLNCGNQFSDEIDRCPRCG 743
                                       566666666666666666665 PP

>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00069      0.48      45      76 ..     755     786 ..     744     799 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00069
                          Toprim_4  45 enlveaekkvkevilaldgDaeGeataerlae 76 
                                       ++l++   +v++v++a+d+D eGe+    ++ 
  gi|385806343|ref|YP_005842741.1| 755 NALRDLATEVDKVLIATDPDTEGEKIGWDISV 786
                                       4555677789**************97655555 PP

>> DUF5433  Family of unknown function (DUF5433)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00041      0.28      19      59 ..     533     576 ..     531     583 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00041
                           DUF5433  19 iifvPtiklyiqiimrc..vyanginkr.stplshnrnpkilkv 59 
                                        i+vP ik yiq   rc  +ya g+ k  +  l+ ++ ++++ +
  gi|385806343|ref|YP_005842741.1| 533 FIYVPDIKSYIQASGRCsrLYAGGLTKGlAITLVPKSENRLFEI 576
                                       59***************6669*9999842556666666666665 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.7      0.12        83      29      37 ..      12      20 ..       6      33 .. 0.67
   2 ?   11.8   0.9   0.00028      0.19       7      35 ..     724     746 ..     718     749 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.12
                       Zn-ribbon_8 29 CPeCgsevr 37
                                      CP+Cg++v 
  gi|385806343|ref|YP_005842741.1| 12 CPNCGGPVS 20
                                      777777653 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00028
                       Zn-ribbon_8   7 rCeeCghefevlqsisdaplta.CPeCgs.e 35 
                                       +C +Cg++f       d  +++ CP+Cgs e
  gi|385806343|ref|YP_005842741.1| 724 KCLNCGNQFS------D--EIDrCPRCGSrE 746
                                       6*****9999......2..5566*****955 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.5         6   4.1e+03      45      45 ..      17      17 ..       3      43 .. 0.50
   2 ?   13.4   0.3   0.00014     0.098      64      86 .]     714     743 ..     685     743 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 6
                    zinc_ribbon_15 45 s 45
                                       
  gi|385806343|ref|YP_005842741.1| 17 G 17
                                      2 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00014
                    zinc_ribbon_15  64 e.......kkeCknCgkeveeefkyCpkCg 86 
                                       +        k+C nCg++ ++e++ Cp+Cg
  gi|385806343|ref|YP_005842741.1| 714 TfvpvystIKKCLNCGNQFSDEIDRCPRCG 743
                                       1444555589*******************9 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.58     4e+02      86     109 ..       8      33 ..       3      47 .. 0.68
   2 ?   10.1   0.1   0.00066      0.45      69     101 ..     718     750 ..     682     755 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.58
                           TackOD1  86 vrevCpkCkS..idieeqelihhftC 109
                                       ++ +Cp+C+   +d++ ++ + + +C
  gi|385806343|ref|YP_005842741.1|   8 YIRSCPNCGGpvSDLRLSKGLACERC 33 
                                       67788888753357777777777777 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00066
                           TackOD1  69 lvdrirlCpsCksghlnvrevCpkCkSidieeq 101
                                       ++ +i+ C +C  +    ++ Cp C+S +i+ +
  gi|385806343|ref|YP_005842741.1| 718 VYSTIKKCLNCGNQFSDEIDRCPRCGSREIKDS 750
                                       5678899*********************99875 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 ?    1.8   0.2      0.33   2.3e+02      27      33 ..      11      17 ..       9      22 .. 0.81
   2 ?   10.1   0.2   0.00085      0.59      11      35 ..     722     746 ..     721     747 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.33
                           DUF35_N 27 vCphCgs 33
                                      +Cp+Cg+
  gi|385806343|ref|YP_005842741.1| 11 SCPNCGG 17
                                      7999997 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00085
                           DUF35_N  11 gqrCpdCGtvqfPPr.avCphCgsdd 35 
                                       + +C +CG   f  +   Cp+Cgs++
  gi|385806343|ref|YP_005842741.1| 722 IKKCLNCGNQ-FSDEiDRCPRCGSRE 746
                                       569*******.78888********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 ?   -0.9   0.3       2.4   1.6e+03      72      91 ..      11      32 ..       3      36 .. 0.53
   2 ?   12.3   0.3   0.00018      0.13      71      98 ..     723     748 ..     706     753 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2.4
                                      EETTTS-EEECHH.H.HHS-TT CS
                              HypA 72 rCreCgkefelee.k.alrCpk 91
                                       C +Cg  ++  + +  l C++
  gi|385806343|ref|YP_005842741.1| 11 SCPNCGGPVSDLRlSkGLACER 32
                                      3555554444222222445555 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00018
                                       EEETTTS-EEECHHHHHS-TTTSSS-EE CS
                              HypA  71 vrCreCgkefeleekalrCpkCgsadve 98 
                                        +C +Cg++f+ e +  rCp+Cgs++++
  gi|385806343|ref|YP_005842741.1| 723 KKCLNCGNQFSDEID--RCPRCGSREIK 748
                                       58*********7756..9******9865 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 ?    1.2   0.4      0.87     6e+02       4      10 ..      11      17 ..       9      21 .. 0.82
   2 ?    8.5   0.0    0.0046       3.2       4      26 ..     738     760 ..     736     770 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.87
                           zf-ISL3  4 rCPnCgs 10
                                       CPnCg 
  gi|385806343|ref|YP_005842741.1| 11 SCPNCGG 17
                                      7****96 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0046
                           zf-ISL3   4 rCPnCgsktvvkhgkkerrvrhl 26 
                                       rCP+Cgs+  ++  ++    r+l
  gi|385806343|ref|YP_005842741.1| 738 RCPRCGSREIKDSRNVINALRDL 760
                                       8*******999888777777777 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.7      0.11        74      16      20 ..      12      16 ..      10      20 .. 0.69
   2 ?    9.7   3.1     0.001      0.69       1      21 [.     724     744 ..     724     745 .. 0.95

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.11
                     zinc_ribbon_2 16 CpyCG 20
                                      Cp+CG
  gi|385806343|ref|YP_005842741.1| 12 CPNCG 16
                                      77777 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.001
                     zinc_ribbon_2   1 fCpnCGaelqdnakFCpyCGt 21 
                                       +C nCG++ +d+   Cp+CG+
  gi|385806343|ref|YP_005842741.1| 724 KCLNCGNQFSDEIDRCPRCGS 744
                                       7*******************6 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.3       1.8   1.3e+03      23      29 ..      12      18 ..       8      20 .. 0.81
   2 ?    9.8   1.2     0.001      0.72       5      28 ..     723     744 ..     720     748 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.8
                       Prok-RING_1 23 CpeCgtp 29
                                      Cp+Cg p
  gi|385806343|ref|YP_005842741.1| 12 CPNCGGP 18
                                      9999987 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.001
                       Prok-RING_1   5 kkCpvCgkelkeedDiVvCpeCgt 28 
                                       kkC  Cg+++++e  i  Cp Cg+
  gi|385806343|ref|YP_005842741.1| 723 KKCLNCGNQFSDE--IDRCPRCGS 744
                                       79*********99..779****96 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 ?    3.3   0.2      0.14        98      18      44 ..       9      33 ..       3      38 .. 0.82
   2 ?    6.2   0.7     0.017        12       5      46 ..     709     744 ..     706     746 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.14
                               IBR 18 lkwCprpdCeaiieksegcksvtCskC 44
                                      ++ Cp  +C++++++   +k + C++C
  gi|385806343|ref|YP_005842741.1|  9 IRSCP--NCGGPVSDLRLSKGLACERC 33
                                      688**..******77777777889998 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.017
                               IBR   5 klklkkslesdpnlkwCprpdCeaiieksegcksvtCskCgf 46 
                                       + k+k+++   +++k+C   +C++ ++++ +    +C++Cg 
  gi|385806343|ref|YP_005842741.1| 709 DEKRKTFVPVYSTIKKCL--NCGNQFSDEID----RCPRCGS 744
                                       5678889999999*****..***99988888....5999985 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.8     0.019        13      19      27 ..       9      17 ..       1      33 [. 0.55
   2 ?   -2.5   0.0       4.8   3.3e+03       9      23 ..     174     188 ..     171     189 .. 0.85
   3 ?    4.9   0.3     0.023        16      18      26 ..     735     743 ..     731     744 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.019
                          zf-TFIIB 19 idyCpqCrG 27
                                      i  Cp+C+G
  gi|385806343|ref|YP_005842741.1|  9 IRSCPNCGG 17
                                      555555555 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.8
                          zf-TFIIB   9 leeserggveidyCp 23 
                                       le++ +g++ i++C+
  gi|385806343|ref|YP_005842741.1| 174 LEMLSKGDFDIFVCT 188
                                       7888999*******7 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.023
                          zf-TFIIB  18 eidyCpqCr 26 
                                       eid+Cp+C+
  gi|385806343|ref|YP_005842741.1| 735 EIDRCPRCG 743
                                       89******7 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 ?    4.3   0.2     0.054        37       4      27 ..      12      33 ..      12      35 .. 0.72
   2 ?    1.4   0.0      0.43     3e+02       2       9 ..     723     730 ..     723     735 .. 0.81
   3 ?    2.9   0.7      0.15     1e+02       3      10 ..     738     745 ..     737     751 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.054
                                      -TTT--BBEEEECTTEEEEE-TTT CS
                      zf-FPG_IleRS  4 CpRCwryiervgqagrstyfCprC 27
                                      Cp C++++++ ++       C+rC
  gi|385806343|ref|YP_005842741.1| 12 CPNCGGPVSDLRL--SKGLACERC 33
                                      ********99998..333336666 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.43
                                       SB-TTT-- CS
                      zf-FPG_IleRS   2 epCpRCwr 9  
                                       ++C  C++
  gi|385806343|ref|YP_005842741.1| 723 KKCLNCGN 730
                                       79*****9 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.15
                                       B-TTT--B CS
                      zf-FPG_IleRS   3 pCpRCwry 10 
                                       +CpRC+  
  gi|385806343|ref|YP_005842741.1| 738 RCPRCGSR 745
                                       6****965 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 ?    6.8   0.1    0.0075       5.2      13      28 ..       1      16 [.       1      19 [. 0.90
   2 ?   -2.6   0.1       6.5   4.5e+03      22      30 ..     723     731 ..     722     732 .. 0.80
   3 ?    3.0   0.6      0.12        80       6      12 ..     739     745 ..     738     747 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0075
                     zf-NADH-PPase 13 tepaeggwarvCpaCg 28
                                      +++++g + r Cp+Cg
  gi|385806343|ref|YP_005842741.1|  1 MQQVKGIYIRSCPNCG 16
                                      789999999******8 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6.5
                     zf-NADH-PPase  22 rvCpaCgle 30 
                                       + C +Cg+ 
  gi|385806343|ref|YP_005842741.1| 723 KKCLNCGNQ 731
                                       5799***85 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.12
                     zf-NADH-PPase   6 CgrCGap 12 
                                       C+rCG++
  gi|385806343|ref|YP_005842741.1| 739 CPRCGSR 745
                                       9999986 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 ?    4.8   0.5     0.039        27      30      53 ..      11      34 ..      10      40 .. 0.88
   2 ?    5.1   1.4     0.031        22      22      65 ..     715     755 ..     699     759 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.039
                    OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCg 53
                                      +C++Cg  +++ + ++ + C++C 
  gi|385806343|ref|YP_005842741.1| 11 SCPNCGGPVSDLRLSKGLACERCL 34
                                      7**********8889999*****6 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.031
                    OrfB_Zn_ribbon  22 vnpay.TSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiN 65 
                                         p y T k+C +Cg + ++    +  +Cp+Cg +   D   +iN
  gi|385806343|ref|YP_005842741.1| 715 FVPVYsTIKKCLNCGNQFSD----EIDRCPRCGSREIKDSRNVIN 755
                                       4566779999*****99888....666899999876666655555 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.5    0.0079       5.5       4      13 ..      11      20 ..      10      22 .. 0.68
   2 ?    2.0   4.7      0.22   1.5e+02       4      24 ..     724     744 ..     723     745 .. 0.75
   3 ?    5.7   0.3     0.014        10       4      15 ..     738     750 ..     735     753 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0079
                       zf-ribbon_3  4 rCPnCGapls 13
                                      +CPnCG p+s
  gi|385806343|ref|YP_005842741.1| 11 SCPNCGGPVS 20
                                      6888887665 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.22
                       zf-ribbon_3   4 rCPnCGa.plssddnvCpyCGt 24 
                                       +C nCG+   s++   Cp CG+
  gi|385806343|ref|YP_005842741.1| 724 KCLNCGNqF-SDEIDRCPRCGS 744
                                       677888855.888888888886 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.014
                       zf-ribbon_3   4 rCPnCGa.plssd 15 
                                       rCP+CG+  ++++
  gi|385806343|ref|YP_005842741.1| 738 RCPRCGSrEIKDS 750
                                       8*****9667776 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.7       1.2   8.2e+02      16      24 ..       9      17 ..       8      34 .. 0.70
   2 ?    9.4   0.9    0.0011      0.78      13      35 ..     719     743 ..     713     746 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.2
                                      -EE-TTT-- CS
                              RecR 16 vrhCsrCgn 24
                                      +r C++Cg 
  gi|385806343|ref|YP_005842741.1|  9 IRSCPNCGG 17
                                      899****96 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0011
                                       HHH-EE-TTT--E.ESS.SS-CCCC CS
                              RecR  13 kekvrhCsrCgnl.tee.dlCaICs 35 
                                        ++++ C +Cgn  ++e d C+ C 
  gi|385806343|ref|YP_005842741.1| 719 YSTIKKCLNCGNQfSDEiDRCPRCG 743
                                       578*********86555589****6 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       0.1        71      20      43 ..      11      33 ..       5      34 .. 0.77
   2 ?    4.5   0.6     0.049        34      20      28 ..     738     746 ..     724     754 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.1
                     Zn_Tnp_IS1595 20 vCPhCgsr.kayriktrglfqCkeC 43
                                       CP+Cg+  +  r+++   + C++C
  gi|385806343|ref|YP_005842741.1| 11 SCPNCGGPvSDLRLSK--GLACERC 33
                                      6*****8876666665..7888888 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.049
                     Zn_Tnp_IS1595  20 vCPhCgsrk 28 
                                       +CP+Cgsr+
  gi|385806343|ref|YP_005842741.1| 738 RCPRCGSRE 746
                                       6*****996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1564  (0.087233); expected 358.6 (0.02)
Passed bias filter:                      926  (0.0516482); expected 358.6 (0.02)
Passed Vit filter:                       112  (0.00624686); 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):              26  [number of targets reported over threshold]
# CPU time: 1.18u 0.37s 00:00:01.54 Elapsed: 00:00:00.59
# Mc/sec: 6400.38
//
Query:       gi|385806344|ref|YP_005842742.1|  [L=402]
Description: flavoprotein [Fervidicoccus fontis Kam940]
Scores for complete 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   38.7   0.0    2.3e-09   37.5   0.0    1.6  1  Lactamase_B    Metallo-beta-lactamase superfamily
     0.0018   18.5   0.0     0.0037   17.5   0.0    1.6  1  Flavodoxin_1   Flavodoxin
     0.0019   17.8   0.0     0.0032   17.0   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 !   37.5   0.0   3.9e-13   2.3e-09       5     154 ..      46     182 ..      43     234 .. 0.77

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 3.9e-13
                                       SSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHC CS
                       Lactamase_B   5 pvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapa 81 
                                       + nsyl+ g ++v LiDt  s  ++ +++      +++kd+++vi  H+ +DH G  + ++e++  ++ +  + +++
  gi|385806344|ref|YP_005842742.1|  46 SYNSYLVKGSTSVALIDTVESDFQSEFFE-KLESVVNIKDIKYVIMNHAEPDHSGSIPVVMEKASDAKLVTTAFGAK 121
                                       56*************************97.666779********************************999999999 PP

                                       CHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSS CS
                       Lactamase_B  82 lfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDalla 154
                                       l +       +               ++++++ +++ggr +  +    +h +  +  ++ +++vlf+ D++ a
  gi|385806344|ref|YP_005842742.1| 122 LAKVFYHVPDE------------RIKIVRDGDIIDLGGRTLKFIEAPMLHWPETMFTYLVEDGVLFSCDFFSA 182
                                       99999955444............455888888888888888888888899999999999**********9873 PP

>> Flavodoxin_1  Flavodoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   6.2e-07    0.0037       1      55 [.     262     318 ..     262     388 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 6.2e-07
                                       EEEETSSSHHHHHHHHHHHHHHHTTTEEEEEEEEGTTSC..GGGGGTHSEEEEEEEE CS
                      Flavodoxin_1   1 ilYgSetGnteklAkqlaeelgehgfnadvvslsdydes..lseieeealllvvtsT 55 
                                       ilY S++ +te++A+ l  e+ ++g+n+++++l +++ s   +++ +   +++ ++T
  gi|385806344|ref|YP_005842742.1| 262 ILYVSMYKHTESIARLLESEFFNRGINVKLYDLVQANLSevSKNMADSSAIVLAVPT 318
                                       89*******************************999977745555555555555555 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 !   17.0   0.0   5.3e-07    0.0032       4     131 ..      60     170 ..      59     183 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.3e-07
                                       EES--TTHHHH.HTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHC CS
                     Lactamase_B_2   4 LiDagpdlrqq.alralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylal 79 
                                       LiD++ + +q  +    ++ e + ++++i+ V++ ha+ DH   ++ + e +  +++l ++   +a+l++ f y++ 
  gi|385806344|ref|YP_005842742.1|  60 LIDTVESDFQSeFF---EKLESVVNIKDIKYVIMNHAEPDHSGSIPVVMEKAS-DAKL-VTTAFGAKLAKVF-YHV- 129
                                       78888884444222...3345566789***********************544.4555.79999*****996.333. PP

                                       HTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEE CS
                     Lactamase_B_2  80 eeepavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlrie 131
                                          p ++++ +  g+ ++lg  g ++++++a+  + +      ++++ +++e
  gi|385806344|ref|YP_005842742.1| 130 ---PDERIKIVRDGDIIDLG--GRTLKFIEAPMLHWP------ETMFTYLVE 170
                                       ...35679***********9..457888888888887......566666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       800  (0.0446204); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); 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: 0.66u 0.39s 00:00:01.05 Elapsed: 00:00:00.55
# Mc/sec: 2206.34
//
Query:       gi|385806345|ref|YP_005842743.1|  [L=196]
Description: Cluster: Integral membrane protein [Fervidicoccus fontis Kam940]
Scores for complete 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  103.2  19.2    1.7e-29  102.9  19.2    1.0  1  SpoIIM           Stage II sporulation protein M
  ------ inclusion threshold ------
        1.6    8.6  18.2        1.1    9.2  12.1    2.3  2  DUF4271          Domain of unknown function (DUF4271)


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 !  102.9  19.2   1.9e-33   1.7e-29       2     156 .]      13     181 ..      12     181 .. 0.85

  Alignments for each domain:
  == domain 1  score: 102.9 bits;  conditional E-value: 1.9e-33
                            SpoIIM   2 lllflvgillgallaa......snfaeqis...........seskensalslflaifanNlrvalllfllGllllgi 61 
                                       ++lfl+g +lg+l++              s            ++ +  ++s +laif+nNl+v+l+ +l+Gl ++ i
  gi|385806345|ref|YP_005842743.1|  13 IFLFLIGGILGYLIVLsgqsdlI------SqliggvgekakTINFKPFSPSSVLAIFVNNLTVSLISILSGL-TVVI 82 
                                       89**************5544330......2333466666657888888999********************7.6655 PP

                            SpoIIM  62 ptilvllinGfvlGavaalvaef.gglllflllilPhgilelpaiiiagaaglrlgkal....rsrrkalkeakrel 133
                                       p+ +++l+nG++ G+v +l+++   +++  +l+++Phgi+el+ai++++a+g  lg+++     +r +++ +  +++
  gi|385806345|ref|YP_005842743.1|  83 PS-FIVLANGIITGLVVGLLTQEgLSVFSGILSLMPHGIFELTAIFLSAAYGTSLGVNFwkfmFRRENNFFDVLKKM 158
                                       55.5667*******77555555536688999************************9999999*999*********** PP

                            SpoIIM 134 lklllllvpllliAaliEafvtp 156
                                        k++l +v+llliAa+iE+f++p
  gi|385806345|ref|YP_005842743.1| 159 PKYVLNIVILLLIAAVIEVFISP 181
                                       *********************98 PP

>> DUF4271  Domain of unknown function (DUF4271)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   3.1     0.063   5.6e+02       2      65 ..      14      75 ..      11      82 .. 0.67
   2 ?    9.2  12.1   0.00012       1.1      52     150 ..      84     182 ..      58     190 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.063
                           DUF4271  2 tillllcflllalaksrfrkffsrllklffnnkereslfkeetksesrfqlflllltclllgll 65
                                      ++ l++  +l  l+ +++++ +  +l   + +k +++ fk   +++s   +f + lt+ l+++l
  gi|385806345|ref|YP_005842743.1| 14 FLFLIGG-ILGYLIVLSGQSDLISQLIGGVGEKAKTINFKP-FSPSSVLAIFVNNLTVSLISIL 75
                                      3344444.444456666666666666677777778888888.8888888888888888888876 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00012
                           DUF4271  52 lflllltclllglllylllsefgslfgsylassllllliiflilllylllKlllykllgwlFfdkkkirqwifsyls 128
                                        f++l + ++ gl++ ll++e+ s+f+  l+     ++ +++i+l       l ++++ ++F  ++    +++++ +
  gi|385806345|ref|YP_005842743.1|  84 SFIVLANGIITGLVVGLLTQEGLSVFSGILSLMPHGIFELTAIFLSAAYGTSLGVNFWKFMFRRENNFFDVLKKMPK 160
                                       6999*********************998777889999999999********************************** PP

                           DUF4271 129 ylsllglllfplvlllvyfpls 150
                                       y++ +++ll++++++ v++++ 
  gi|385806345|ref|YP_005842743.1| 161 YVLNIVILLLIAAVIEVFISPL 182
                                       *************999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       939  (0.0523733); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); 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):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 1164.69
//
Query:       gi|385806346|ref|YP_005842744.1|  [L=210]
Description: hypothetical protein FFONT_1304 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.5e-07   29.0   1.2    7.5e-07   29.0   1.2    3.1  5  TM_helix      Conserved TM helix
  ------ inclusion threshold ------
       0.29   11.5   2.7        8.8    6.7   0.5    2.6  2  MMgT          Membrane magnesium transporter


Domain annotation for each model (and alignments):
>> TM_helix  Conserved TM helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   1.2   8.3e-11   7.5e-07       8      49 ..       5      46 ..       3      47 .. 0.93
   2 ?   -3.1   0.0      0.93   8.3e+03      37      46 ..      52      61 ..      50      62 .. 0.80
   3 ?   -2.8   1.5      0.74   6.7e+03      20      30 ..     115     125 ..     108     133 .. 0.64
   4 ?   -4.0   1.2       1.7   1.5e+04      10      20 ..     155     165 ..     154     166 .. 0.52
   5 ?   -3.4   0.5       1.1   9.9e+03      21      33 ..     191     203 ..     185     205 .. 0.58

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 8.3e-11
                                      HHHHTTHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS-H CS
                          TM_helix  8 nellsflPnLvgAilILlvGwiiAkfvsrlvtkllaktgidd 49
                                      +++   l  +v+A++I lvG++i+++ + l+   l++tg+d+
  gi|385806346|ref|YP_005842744.1|  5 SSFYDILFSVVIAVIIILVGYLIGRLMKYLIEASLKRTGFDN 46
                                      567778999********************************8 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.93
                                      HHHHHHHHHT CS
                          TM_helix 37 lvtkllaktg 46
                                       +++ l+k+g
  gi|385806346|ref|YP_005842744.1| 52 TIGRALDKAG 61
                                      5789999987 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 0.74
                                       HHHHHHHHHHH CS
                          TM_helix  20 AilILlvGwii 30 
                                        i+I + G+i+
  gi|385806346|ref|YP_005842744.1| 115 VIIIVIPGFIL 125
                                       56666666665 PP

  == domain 4  score: -4.0 bits;  conditional E-value: 1.7
                                       HHTTHSHHHHH CS
                          TM_helix  10 llsflPnLvgA 20 
                                       +l +++ ++ A
  gi|385806346|ref|YP_005842744.1| 155 ILLYIVIVIFA 165
                                       45555555555 PP

  == domain 5  score: -3.4 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHH CS
                          TM_helix  21 ilILlvGwiiAkf 33 
                                        +I  v  ii ++
  gi|385806346|ref|YP_005842744.1| 191 MIIVSVSIIISRM 203
                                       4555555555554 PP

>> MMgT  Membrane magnesium transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.5   0.00098       8.8      38      72 ..       9      50 ..       7      56 .. 0.84
   2 ?    4.0   0.1    0.0073        65       8      22 ..      57      71 ..      52      78 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.00098
                              MMgT 38 Ditletlvslvllilglvl.......saeeLkpIqlrkaagk 72
                                      Di + ++++++++++g ++        +  Lk    +++ +k
  gi|385806346|ref|YP_005842744.1|  9 DILFSVVIAVIIILVGYLIgrlmkylIEASLKRTGFDNWLKK 50
                                      9****************9988888887778888777777766 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.0073
                              MMgT  8 LlHagYSahehsall 22
                                      L  agYSa e+ al 
  gi|385806346|ref|YP_005842744.1| 57 LDKAGYSASEFFALV 71
                                      6689*******9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1189  (0.0663171); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); 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):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.38s 00:00:01.03 Elapsed: 00:00:00.55
# Mc/sec: 1148.95
//
Query:       gi|385806347|ref|YP_005842745.1|  [L=211]
Description: beta-lactamase [Fervidicoccus fontis Kam940]
Scores for complete 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-23   81.3   0.0    8.6e-23   80.9   0.0    1.2  1  Lactamase_B_2    Beta-lactamase superfamily domain
    5.6e-21   75.1   0.2    9.6e-21   74.4   0.2    1.3  1  Lactamase_B_3    Beta-lactamase superfamily domain
    5.5e-11   42.8   0.4    7.6e-11   42.4   0.4    1.4  1  Lactamase_B      Metallo-beta-lactamase superfamily
  ------ inclusion threshold ------
      0.078   12.5   0.0       0.12   11.8   0.0    1.2  1  Lactamase_B_5    Metallo-beta-lactamase superfamily
       0.13   12.0   0.1        6.9    6.5   0.0    2.4  2  Ribosomal_L7Ae   Ribosomal protein L7Ae/L30e/S12e/Gadd45 fami
       0.22   11.4   1.6        1.8    8.4   0.0    2.6  3  Transketolase_C  Transketolase, C-terminal 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 !   80.9   0.0   2.9e-26   8.6e-23       2     201 .]       9     175 ..       8     175 .. 0.86

  Alignments for each domain:
  == domain 1  score: 80.9 bits;  conditional E-value: 2.9e-26
                                       EEEES--TTHHHHHTCGG.S--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHH CS
                     Lactamase_B_2   2 riLiDagpdlrqqalral.qPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvyl 77 
                                        +LiD++     +   +   +ve  +  ++id +++th+H DHl ++ ++ ++++  +++++  +++++ e+n+   
  gi|385806347|ref|YP_005842745.1|   9 TVLIDPWIT--NP---LSkAKVEDFS-NKKIDYIIVTHDHSDHLGNAYDICKITG--AKMVGVYELAEEAEKNG--- 74 
                                       589999999..34...3323455344.47***********************766..56777788888888885... PP

                                       HCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HH.HHHH CS
                     Lactamase_B_2  78 aleeepavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipee.iger 153
                                              +++   + g++++++  +l+i ++pa h+s++         +G+++ g + ++y++gDtg ++++ i  +
  gi|385806347|ref|YP_005842745.1|  75 -------ISAIGGNVGGRLSID--DLDIVLVPAVHSSEK------AVPVGVVVSGRDFTFYHAGDTGVFTDMsIISE 136
                                       .......45566779******9..578************......9************************665999* PP

                                       HCT-SEEEEE-S-SSTTHHHHHHT---STSHHHHCTTSSSSEEEEESB CS
                     Lactamase_B_2 154 lggadllllditayeddemirhmgHltpeeaveaaadlgakrlvliHi 201
                                       l+ +dl++l+i+         +++++ ++eav+a++ +++k +v++H+
  gi|385806347|ref|YP_005842745.1| 137 LYSPDLAFLPIG---------GHFTMGIKEAVKAVQLIKPKMVVPMHY 175
                                       ************.........8899999*******************7 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.4   0.2   3.2e-24   9.6e-21      17     163 .]       8     174 ..       3     174 .. 0.79

  Alignments for each domain:
  == domain 1  score: 74.4 bits;  conditional E-value: 3.2e-24
                     Lactamase_B_3  17 arilvDPf......kanlgyeppaeeaDlvlisqaledHahlet.lkql......aenvkvlee............. 67 
                                       +++l+DP+      k  +  + +++++D ++++++++dH   +  + ++                            
  gi|385806347|ref|YP_005842745.1|   8 KTVLIDPWitnplsK-AKVEDFSNKKIDYIIVTHDHSDHLGNAYdICKItgakmvG-------Vyelaeeaekngis 76 
                                       79******8777532.44455677***************75543044434434330.......34455556666666 PP

                     Lactamase_B_3  68 ......geslevggleiravatshdavggsergenngflleqdgltiyhlGhlahelsseelkelgrvDvvltPvgg 138
                                             g+ l +++l+i  v++ h +++  +    +g +++ ++ t+yh G+++   +++ + el  +D+ ++P+gg
  gi|385806347|ref|YP_005842745.1|  77 aiggnvGGRLSIDDLDIVLVPAVHSSEKAVP----VGVVVSGRDFTFYHAGDTGVFTDMSIISELYSPDLAFLPIGG 149
                                       666677788***************6554444....5679999*********************************** PP

                     Lactamase_B_3 139 pltlgqeealelakrLkpklvlPmh 163
                                       ++t+g +ea+++++++kpk+v+Pmh
  gi|385806347|ref|YP_005842745.1| 150 HFTMGIKEAVKAVQLIKPKMVVPMH 174
                                       ************************9 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   0.4   2.5e-14   7.6e-11      16      87 ..       8      75 ..       4     174 .. 0.79

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 2.5e-14
                                      CEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHH CS
                       Lactamase_B 16 gviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeea 87
                                      +++LiD+ ++++ ++a+     +++  k++d++i+TH H+DH G++ ++++ t+++ + v+e a++ ++++ 
  gi|385806347|ref|YP_005842745.1|  8 KTVLIDPWITNPLSKAK----VEDFSNKKIDYIIVTHDHSDHLGNAYDICKITGAKMVGVYELAEEAEKNGI 75
                                      68*************96....7******************************************99988876 PP

>> Lactamase_B_5  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   4.1e-05      0.12      35      84 ..      10      63 ..       6      77 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.1e-05
                     Lactamase_B_5 35 ilidpvalsnhdwnhlesl..ggvawivltn..sdhlraakeiaeltyakiagp 84
                                      +lidp         ++e +    +++i++t   sdhl  a +i+++t+ak+ g 
  gi|385806347|ref|YP_005842745.1| 10 VLIDPWITNPLSKAKVEDFsnKKIDYIIVTHdhSDHLGNAYDICKITGAKMVGV 63
                                      7888875555555555544114689****95449****************9885 PP

>> 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 ?    3.4   0.0     0.021        64      50      89 ..      25      65 ..       4      71 .. 0.70
   2 ?    6.5   0.0    0.0023       6.9      15      36 ..     150     171 ..     145     203 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.021
                                      HHHHHHHTTEEEEEES..CHHHHHHHTTSSSECSEEEEEEST CS
                    Ribosomal_L7Ae 50 lealckekevpyvkvk..skkeLGelvgkkrpvsalaikdeg 89
                                      +e ++ +k++ y++v+      LG + + ++++ a ++ +++
  gi|385806347|ref|YP_005842745.1| 25 VEDFS-NKKIDYIIVThdHSDHLGNAYDICKITGAKMVGVYE 65
                                      55554.5789999998664589****9999999888876665 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0023
                                       EEEESHHHHHHHHHTTTESEEE CS
                    Ribosomal_L7Ae  15 klvlGlkevtkalergeaklvi 36 
                                       + ++G+ke++ka++  + k+v+
  gi|385806347|ref|YP_005842745.1| 150 HFTMGIKEAVKAVQLIKPKMVV 171
                                       5689****************98 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0   0.00061       1.8      36      83 ..       7      55 ..       3      63 .. 0.86
   2 ?    1.8   0.1     0.071   2.1e+02      17      38 ..      56      77 ..      55      78 .. 0.89
   3 ?   -1.7   0.0      0.82   2.4e+03      47      65 ..     184     202 ..     156     206 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00061
                                      TCEEEEE-SEEESHHHHHHH.HHHHHHSEEEEEEEEESTTSHHHHHHHH CS
                   Transketolase_C 36 isaeVvdlrtvkplDketil.esvkktgrlvvveeavkrgGigsevaaa 83
                                      +++ ++d+  ++pl k+ ++  s kk + ++v+++++   G + +++++
  gi|385806347|ref|YP_005842745.1|  7 VKTVLIDPWITNPLSKAKVEdFSNKKIDYIIVTHDHSDHLGNAYDICKI 55
                                      567789**************7899999************9999888876 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.071
                                      ETTHHHHHHHHHHHHHTTTTCE CS
                   Transketolase_C 17 yGsmveealeAaeeLekegisa 38
                                      +G+ +  + e aee+ek+gisa
  gi|385806347|ref|YP_005842745.1| 56 TGAKMVGVYELAEEAEKNGISA 77
                                      688888899***********97 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.82
                                       ESHHHHHHHHHHHHHSEEE CS
                   Transketolase_C  47 kplDketilesvkktgrlv 65 
                                       +pl ++ + es+ kt+ +v
  gi|385806347|ref|YP_005842745.1| 184 DPLAFKSLVESLTKTKVIV 202
                                       4666666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.61u 0.35s 00:00:00.96 Elapsed: 00:00:00.55
# Mc/sec: 1163.43
//
Query:       gi|385806348|ref|YP_005842746.1|  [L=323]
Description: putative phosphate regulatory protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-14   54.5   9.2    5.3e-14   52.5   1.4    2.8  2  PhoU            PhoU domain
    3.9e-07   29.9   0.0    1.1e-06   28.4   0.0    1.8  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
  ------ inclusion threshold ------
      0.014   15.2   0.0      0.033   14.0   0.0    1.6  1  Chalcone_2      Chalcone isomerase like


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 !   52.5   1.4   8.8e-18   5.3e-14       1      88 [.     135     222 ..     135     223 .. 0.91
   2 !    5.7   1.1    0.0035        21      14      68 ..     253     307 ..     235     315 .. 0.67

  Alignments for each domain:
  == domain 1  score: 52.5 bits;  conditional E-value: 8.8e-18
                                       HHHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHGG-SHHHHHHHHHHHHHHHHH CS
                              PhoU   1 lrrmaeiveemlddalealeekdtelarevierddeidrlekeierslleal.akrqplaedlrellsllriardlE 76 
                                       +++m +++  ml+d+   l+++d ++++++++rdd idrl+   +r+l++++ +  q+   +    +++  ++++lE
  gi|385806348|ref|YP_005842746.1| 135 INSMMKTIIYMLEDLAIGLRKNDLKIIKDIYQRDDYIDRLYLYSIRYLVNIYnMPTQERI-NPSSSVHYALATKSLE 210
                                       689*************************************************44444444.578889********** PP

                                       HHHHHHHHHHHH CS
                              PhoU  77 RigDhavniaer 88 
                                       RigDh+  i++ 
  gi|385806348|ref|YP_005842746.1| 211 RIGDHVSAISKN 222
                                       *******99985 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0035
                                       HHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHH CS
                              PhoU  14 dalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsl 68 
                                       + l+++ + d el++e+ e+   + + e e++ sll+   + + +ae lr+++++
  gi|385806348|ref|YP_005842746.1| 253 QILKLVLKFDGELLNEITEKAINLMNVESELRVSLLKYSVNLSYVAESLRRIIAY 307
                                       4456666677777777776666666667777777777666666666667776554 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 !   28.4   0.0   1.9e-10   1.1e-06       3      39 ..       5      42 ..       4      48 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 1.9e-10
                                      ETTEEEEEE-CCCHHHCCEECTCEEEEEECTT.CCCCC CS
                    MazE_antitoxin  3 vGnsgavriPkevrfelgireGdevelevdgd.kiilr 39
                                      +G++++ ++Pk ++++ +++eG e+ +e+ ++  ++++
  gi|385806348|ref|YP_005842746.1|  5 GGSTYILSLPKSWAEKVDLKEGEELFVEELSNqALLIY 42
                                      7******************************9777665 PP

>> Chalcone_2  Chalcone isomerase like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   5.5e-06     0.033     133     195 ..      15      81 ..       7      87 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.5e-06
                        Chalcone_2 133 slFnrkgsvpkgkeLlLerdangeLsvlyedkkkk....kleklGrvedervsrllwlnYLagkkva 195
                                       + +++k +++ g+eL++e+ +n++L ++  +++++    +++  ++ + +++ r+++ +YLagkk +
  gi|385806348|ref|YP_005842746.1|  15 KSWAEKVDLKEGEELFVEELSNQALLIYAPERREHfskaEISFTCKESRNFIERTIIAQYLAGKKEI 81 
                                       5567788999***************9999888877887788888888899**************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       925  (0.0515924); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); 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 0.34s 00:00:00.98 Elapsed: 00:00:00.55
# Mc/sec: 1778.68
//
Query:       gi|385806349|ref|YP_005842747.1|  [L=210]
Description: CRISPR-associated protein Cas4 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-06   26.6   0.4    9.8e-06   25.8   0.4    1.5  1  Cas_Cas4  Domain of unknown function DUF83
    5.4e-06   26.7   0.2    9.6e-06   25.9   0.2    1.3  1  PDDEXK_3  PD-(D/E)XK nuclease superfamily
     0.0043   17.0   2.7       0.23   11.3   1.2    2.8  2  PDDEXK_1  PD-(D/E)XK nuclease superfamily


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 !   25.8   0.4   1.6e-09   9.8e-06       2     160 ..      40     205 ..      39     207 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 1.6e-09
                          Cas_Cas4   2 gtkiqyyliCk..rklwlisheitleensetvelGkllhe...........esyerek...kevel.se....siki 57 
                                       ++ ++ +++C+  r + + + ei++  + + ++ G+l+h+           e    ek   +++ + se    ++++
  gi|385806349|ref|YP_005842747.1|  40 IIYVSDLVYCPlkRLFRMQYPEISFIFEPQAIQ-GELIHKglqlylkdlgyE---IEKeisEKIYInSEefvlKGRM 112
                                       577899999*73255555666999999999999.********9998885432...3333568899976689999*** PP

                          Cas_Cas4  58 DvvekekeklvvvEvKkskkk....eeaaklQllyYlllLekkgveikeGvleypkekkreevelteelreelekai 130
                                       D  +   e+ +v+E+K  k+     ++ + lQl+ Yl +      +i++G l y++  +  e  +++++     +  
  gi|385806349|ref|YP_005842747.1| 113 DAYK---EGEEVIEIKTAKSSlgipHDHHILQLKIYLSMT-----NISKGTLIYVSPDRIAEFPIKKDNL----DLS 177
                                       **99...6666666666666555556666******98764.....57889************99977775....556 PP

                          Cas_Cas4 131 keieeiissekppkvkkkkiCkkCayaelC 160
                                       k + +++s+++ p+      Ck+C +++lC
  gi|385806349|ref|YP_005842747.1| 178 KLVFDYLSKKYAPRWD--WECKNCIFSKLC 205
                                       6778889998888775..469999999999 PP

>> PDDEXK_3  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.2   1.6e-09   9.6e-06      28     106 ..      77     159 ..      71     169 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 1.6e-09
                          PDDEXK_3  28 ekaLaveLkkrglkveeqvelpvvYkgkevgeeyrlDllveekvivElKavee.l...keeheaqllnYlkltklkl 100
                                       +k L+  Lk+ g ++e++++ +++ + +e+  + r+D + e + ++E+K++++ l   +++h  ql+ Yl +t++  
  gi|385806349|ref|YP_005842747.1|  77 HKGLQLYLKDLGYEIEKEISEKIYINSEEFVLKGRMDAYKEGEEVIEIKTAKSsLgipHDHHILQLKIYLSMTNISK 153
                                       6789999************************99*****************87633334577889************* PP

                          PDDEXK_3 101 GlliNF 106
                                       G li  
  gi|385806349|ref|YP_005842747.1| 154 GTLIYV 159
                                       ***965 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 !    3.8   0.0    0.0075        45      15      54 ..      51      88 ..      43     102 .. 0.64
   2 !   11.3   1.2   3.9e-05      0.23     124     254 ..      96     205 ..      85     206 .. 0.62

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.0075
                          PDDEXK_1 15 lrfflryllglre...eeeleapdlGtlvHaaleefyewkkld 54
                                      l+  +r  ++++e   ++e +a   G+l+H+ l+ + +  +l 
  gi|385806349|ref|YP_005842747.1| 51 LKRLFR--MQYPEisfIFEPQA-IQGELIHKGLQLYLK--DLG 88
                                      444442..44466744555555.99********99988..333 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 3.9e-05
                          PDDEXK_1 124 g.....g.ekvrLkGriDrvddkegelriiDyKtgsappkskelaelkegl.QlllYllalaegeelkeegepagal 193
                                       +     + e++ LkGr+D   + e+   +i+ Kt +    s+      +++ Ql +Yl +            ++ ++
  gi|385806349|ref|YP_005842747.1|  96 SekiyiNsEEFVLKGRMDAYKEGEE---VIEIKTAK---SSLGIPHD-HHIlQLKIYLSMTNIS--------KGTLI 157
                                       233344337888*******987777...*****999...66664444.4446******999888........67777 PP

                          PDDEXK_1 194 ylrleepkvkdeevvkkmalteeeleallqeleelaeeilagefparpskkCeyCpyksvC 254
                                       y++          ++++ + ++++l+     l++l+  +l++++++r + +C++C ++++C
  gi|385806349|ref|YP_005842747.1| 158 YVSP--------DRIAEFPIKKDNLD-----LSKLVFDYLSKKYAPRWDWECKNCIFSKLC 205
                                       7776........33444444444442.....333333333445666666667777777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       843  (0.0470188); expected 358.6 (0.02)
Passed bias filter:                      616  (0.0343577); 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: 0.64u 0.36s 00:00:01.00 Elapsed: 00:00:00.55
# Mc/sec: 1145.36
//
Query:       gi|385806350|ref|YP_005842748.1|  [L=262]
Description: tRNA methyltransferase [Fervidicoccus fontis Kam940]
Scores for complete 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   70.8   0.0    1.8e-19   70.4   0.0    1.1  1  GCD14            tRNA methyltransferase complex GCD14 subunit
    8.3e-06   25.7   0.0    1.2e-05   25.2   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
      8e-05   22.4   0.0    0.00017   21.4   0.0    1.5  1  GCD14_N          tRNA methyltransferase complex GCD14 subunit
    0.00014   21.7   0.0    0.00019   21.2   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
     0.0072   17.0   0.0      0.011   16.4   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
  ------ inclusion threshold ------
      0.055   12.6   0.1       0.11   11.6   0.1    1.4  1  Fibrillarin      Fibrillarin
      0.068   13.9   0.0       0.22   12.3   0.0    1.8  1  Methyltransf_12  Methyltransferase domain
       0.13   12.9   0.0       0.25   12.0   0.0    1.5  1  Methyltransf_11  Methyltransferase domain


Domain annotation for each model (and alignments):
>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.4   0.0   8.1e-23   1.8e-19      17     184 ..      78     241 ..      63     250 .. 0.89

  Alignments for each domain:
  == domain 1  score: 70.4 bits;  conditional E-value: 8.1e-23
                             GCD14  17 LphrtqilytaDisliimkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsql 93 
                                       ++ + q++y +D   ii +  lk G +v e+G Gsg l+  i+  ++  G  + ++  ++ +e+a++++   + +  
  gi|385806350|ref|YP_005842748.1|  78 FKRKSQVIYPKDAYAIISEAGLKRGDKVGEAGVGSGFLAAHILSIIGNEGEYYGYDLRDDMIETAINNLSLLGYDVS 154
                                       45679************************************************************************ PP

                             GCD14  94 vtvthrDvckeGfdeevsgkvDavfLDlPaPweaiphaakalkkeggrlCsfsPCieqvqrtceaLrelgftei.et 169
                                        +++++Dv keG de   ++ +a fLDlP Pw+a++ +   l   ++r+  f P ++qv +    + ++   +i + 
  gi|385806350|ref|YP_005842748.1| 155 GKIRKKDV-KEGIDE---SDLNAFFLDLPDPWNAVNAIYPSL-APDARIVIFVPTLNQVIKFLASIDDSSKFKInRI 226
                                       *******9.789943...3569********************.999****************999988655555167 PP

                             GCD14 170 levllrtyevrkskl 184
                                       +e   r+y+v k  l
  gi|385806350|ref|YP_005842748.1| 227 FETFSREYAVSKDAL 241
                                       8********998776 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   5.2e-09   1.2e-05       3     127 ..     101     220 ..      99     246 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 5.2e-09
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdiee.leklledekfDl 77 
                                       +g +v ++G G+G+l+  + + +g ++e++G D   ++ie A +n++ lg+d   + ++ d+ e ++++      Dl
  gi|385806350|ref|YP_005842748.1| 101 RGDKVGEAGVGSGFLAAHILSIIGNEGEYYGYDLRDDMIETAINNLSLLGYDvSGKIRKKDVKEgIDES------DL 171
                                       67788899********************************************77788888888888854......66 PP

                   Methyltransf_31  78 ilsnevlnaladpdkileeiervlkpggilliedprllaelp...akveeesk 127
                                          n+++ +l+dp ++ + i   l p+ +++i  p  l +++   a++ ++sk
  gi|385806350|ref|YP_005842748.1| 172 ---NAFFLDLPDPWNAVNAIYPSLAPDARIVIFVPT-LNQVIkflASIDDSSK 220
                                       ...777889999999999999999999999998887.5555545566666555 PP

>> GCD14_N  tRNA methyltransferase complex GCD14 subunit N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   7.5e-08   0.00017      18      45 ..      21      48 ..       6      49 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 7.5e-08
                           GCD14_N 18 rkhtitLepGgefhthrGaieHDdlIGr 45
                                       k  ++L++G+ + ++ G i+HDd+IG+
  gi|385806350|ref|YP_005842748.1| 21 TKKLVVLKRGKYTESKYGRIKHDDIIGK 48
                                      56789**********************8 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   8.5e-08   0.00019      70     139 ..      98     168 ..      81     228 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 8.5e-08
                                       T--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC.SEEEEES-GGGTTGG CS
                              PCMT  70 elkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle.nvivvvgDGrkGyee 139
                                        lk+g++v e G GsG+l+a +  ++g++g   + +   +++e+a +nl  l+++ + +++  D ++G +e
  gi|385806350|ref|YP_005842748.1|  98 GLKRGDKVGEAGVGSGFLAAHILSIIGNEGEYYGYDLRDDMIETAINNLSLLGYDvSGKIRKKDVKEGIDE 168
                                       499***********************************************999987667777777777654 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   5.1e-06     0.011       3      55 ..     107     162 ..     105     191 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.1e-06
                                       EET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBC CS
                   Methyltransf_25   3 dlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeegl..nvefvqgda 55 
                                       ++G G+G l+++++  +g +++++g D+ ++m+e+a ++++  g+  + +++++d+
  gi|385806350|ref|YP_005842748.1| 107 EAGVGSGFLAAHILSIIGnEGEYYGYDLRDDMIETAINNLSLLGYdvSGKIRKKDV 162
                                       78************999559*****************9998766633444555555 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   4.9e-05      0.11      63     107 ..      94     138 ..      88     146 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.9e-05
                                       -S--S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHH CS
                       Fibrillarin  63 lkelpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprv 107
                                       ++e  +k+g+kv   G++sG  ++H+  i+g+eg  y+ +  + +
  gi|385806350|ref|YP_005842748.1|  94 ISEAGLKRGDKVGEAGVGSGFLAAHILSIIGNEGEYYGYDLRDDM 138
                                       567889*******************************98876655 PP

>> Methyltransf_12  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      0.22       2      52 ..     107     158 ..     107     198 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0001
                   Methyltransf_12   2 eiGcGtGsllrallekl.pdieytgvDispsaiedakeklakrennnnnnve 52 
                                       e G G+G l++++l  +  + ey+g+D+  ++ie a + l+  + +   +++
  gi|385806350|ref|YP_005842748.1| 107 EAGVGSGFLAAHILSIIgNEGEYYGYDLRDDMIETAINNLSLLGYDVSGKIR 158
                                       789**************9***************9998888777765544444 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00011      0.25       2      95 ..     107     199 ..     106     200 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                                       EET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-C CS
                   Methyltransf_11   2 dvGcGtGrlaealakrg...arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhve 75 
                                       ++G+G+G la+++ +     ++++g Dl + m+++a ++ s  g     v + ++k  +++  +D   ++ ++  ++
  gi|385806350|ref|YP_005842748.1| 107 EAGVGSGFLAAHILSIIgneGEYYGYDLRDDMIETAINNLSLLGYD---VSGKIRKKDVKE-GIDESDLNAFFLDLP 179
                                       589**********95555778***************9998888864...556666555554.566666667777777 PP

                                       CHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  76 dpekalkeiaRvLkpgGllv 95 
                                       dp  a++ i+  L p+ ++v
  gi|385806350|ref|YP_005842748.1| 180 DPWNAVNAIYPSLAPDARIV 199
                                       77777777777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.38s 00:00:01.00 Elapsed: 00:00:00.55
# Mc/sec: 1422.74
//
Query:       gi|385806351|ref|YP_005842749.1|  [L=111]
Description: hypothetical protein FFONT_1309 [Fervidicoccus fontis Kam940]
Scores for complete 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   22.4  10.6      0.001   19.5   9.5    1.9  2  V-ATPase_G_2    Vacuolar (H+)-ATPase G subunit
    0.00064   19.5   5.0     0.0017   18.1   4.3    1.9  2  DUF4456         Domain of unknown function (DUF4456)
  ------ inclusion threshold ------
      0.039   12.8  14.7      0.043   12.7  14.7    1.0  1  Mitofilin       Mitochondrial inner membrane protein
       0.06   11.8   4.7      0.068   11.6   4.7    1.0  1  DUF3160         Protein of unknown function (DUF3160)
      0.074   13.3   3.4      0.094   13.0   2.6    1.5  1  DUF1722         Protein of unknown function (DUF1722)
      0.081   12.8   2.0      0.099   12.5   2.0    1.1  1  DUF2797         Protein of unknown function (DUF2797)
      0.083   13.5   8.5       0.15   12.6   8.5    1.4  1  ING             Inhibitor of growth proteins N-terminal histo
      0.094   13.1   6.1       0.11   12.9   5.6    1.4  1  Syntaxin_2      Syntaxin-like protein
      0.099   12.1   1.0       0.13   11.7   1.0    1.2  1  GCP_C_terminal  Gamma tubulin complex component C-terminal
       0.18   11.4   2.6       0.22   11.1   2.6    1.1  1  Exonuc_VII_L    Exonuclease VII, large subunit
       0.18   10.8   8.6        0.2   10.6   8.6    1.0  1  BPS1            Protein BYPASS1-related
       0.25   10.5   7.6       0.39    9.9   7.5    1.3  1  RE_HindIII      HindIII restriction endonuclease
       0.26   11.5   4.6       0.39   11.0   0.7    2.0  2  M11L            Apoptosis regulator M11L like
       0.42   11.1  15.5       0.97    9.9   7.7    2.3  2  ZapB            Cell division protein ZapB
       0.43   11.1   5.9        2.1    8.8   5.8    1.8  1  DUF2115         Uncharacterized protein conserved in archaea 
       0.43    9.2   5.9       0.47    9.0   5.9    1.0  1  Peptidase_S46   Peptidase S46
       0.45   10.4   3.4        0.5   10.2   3.0    1.3  1  Folliculin      Vesicle coat protein involved in Golgi to pla
       0.77   10.1  10.4        1.2    9.4  10.4    1.5  1  TCTP            Translationally controlled tumour protein
        1.2    8.6  17.0        1.5    8.3  17.0    1.0  1  DUF2031         Protein of unknown function (DUF2031)
        1.5    9.3   7.7        2.8    8.5   0.2    2.8  3  YlbE            YlbE-like protein
        2.7    7.2   7.6          3    7.0   7.6    1.0  1  TMPIT           TMPIT-like protein
        4.5    6.9   8.9       0.85    9.3   2.2    2.0  2  DCB             Dimerisation and cyclophilin-binding domain o
        4.9    7.0   7.7        5.7    6.8   7.7    1.2  1  CemA            CemA family
        9.3    6.8   6.2         68    4.1   6.2    2.1  1  Arc_PepC_II     Archaeal Peptidase A24 C-terminus Type II


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 ?    3.2   0.0      0.16   1.2e+02      38      63 ..       6      31 ..       4      35 .. 0.85
   2 !   19.5   9.5   1.4e-06     0.001      31     102 ..      32     103 ..      27     105 .. 0.95

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.16
                                      HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      V-ATPase_G_2 38 eAarilreAeakakalqaeyeqelae 63
                                      e  +i+++ e+++++l++ ye++ ++
  gi|385806351|ref|YP_005842749.1|  6 ESIKIITDFEKDVEELKSTYEKKFSN 31
                                      6678999**************99876 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 1.4e-06
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHH CS
                      V-ATPase_G_2  31 eveaAeaeAarilreAeakakalqaeyeqelaeevarireeararaeaeaqavrkraearlqqAvelilkaV 102
                                        +e Ae +A+ + + A+a + + ++e +++l++e ++++ee++++ ++e  +++++ e + + Ave+ lk  
  gi|385806351|ref|YP_005842749.1|  32 LIEVAERNAKMLNEVANAIVISAKKEIDEKLKNESKEVEEEYNKKLKEELAKIEEAKERKFKLAVEEALKSF 103
                                       5899****************************************************************9975 PP

>> DUF4456  Domain of unknown function (DUF4456)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.084        62     137     165 ..       2      30 ..       1      31 [. 0.92
   2 !   18.1   4.3   2.3e-06    0.0017      47     104 ..      23      80 ..       9      91 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.084
                           DUF4456 137 kRqkevlaaieataealqeaakkvaseFv 165
                                       kR++e +++i ++++ ++e ++++ ++F 
  gi|385806351|ref|YP_005842749.1|   2 KRISESIKIITDFEKDVEELKSTYEKKFS 30 
                                       79******************999999886 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 2.3e-06
                           DUF4456  47 eyhnsalqelreqverleellakvpelvvesllkrhlqkleaarkdieaeFeqklkql 104
                                       + +++ + +l+e  er  ++l +v+ ++v s++k+  +kl+++ k++e+e+++klk+ 
  gi|385806351|ref|YP_005842749.1|  23 STYEKKFSNLIEVAERNAKMLNEVANAIVISAKKEIDEKLKNESKEVEEEYNKKLKEE 80 
                                       55789999**********************************************9975 PP

>> Mitofilin  Mitochondrial inner membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7  14.7   5.7e-05     0.043     269     361 ..       9     101 ..       2     110 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.7e-05
                         Mitofilin 269 siipeiitnlkednkklskddlnsliahAkteidqlskelaelkkeeekkieralekqkee.lekqeealsarleee 344
                                       +ii++    ++e ++  ++++++ li+ A+++ + l++  +++ ++++k+i+++l++  +e +e+  ++l+++l++ 
  gi|385806351|ref|YP_005842749.1|   9 KIITDFEKDVEELKS-TYEKKFSNLIEVAERNAKMLNEVANAIVISAKKEIDEKLKNESKEvEEEYNKKLKEELAKI 84 
                                       667777666667666.7777777777777777777777777777777777777777777665555555555555544 PP

                         Mitofilin 345 rakeerqlrlelerele 361
                                        +++er+++l  e++l+
  gi|385806351|ref|YP_005842749.1|  85 EEAKERKFKLAVEEALK 101
                                       44555555555555544 PP

>> DUF3160  Protein of unknown function (DUF3160)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   4.7   9.1e-05     0.068      78     139 ..      19      91 ..       4     103 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.1e-05
                           DUF3160  78 eelekqyesekseelkeaakrnvayfavArsLldekak...........evpeevkeeveeelelieaaegla 139
                                       eel+++ye++ s+ ++ a +++++   vA++ +  ++k           ev ee++++ +eel++ie+a++ +
  gi|385806351|ref|YP_005842749.1|  19 EELKSTYEKKFSNLIEVAERNAKMLNEVANAIVISAKKeideklkneskEVEEEYNKKLKEELAKIEEAKERK 91 
                                       56777788888888888888888888999988888877888889999999*******************9844 PP

>> DUF1722  Protein of unknown function (DUF1722)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   2.6   0.00013     0.094      21      85 ..      13      77 ..       2      85 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00013
                           DUF1722 21 nakkepleelaeeYeellmealskpatrkkhin.vlqhilgyfkkklsaeekqelleliekYregk 85
                                      + + +++eel ++Ye+++ ++++   + +k++n v++ i+   kk+++++ k+e  e+ e+Y++++
  gi|385806351|ref|YP_005842749.1| 13 DFE-KDVEELKSTYEKKFSNLIEVAERNAKMLNeVANAIVISAKKEIDEKLKNESKEVEEEYNKKL 77
                                      444.568*******************9999998678888999********************9875 PP

>> DUF2797  Protein of unknown function (DUF2797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   2.0   0.00013     0.099     103     165 ..      28      89 ..      26     108 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                           DUF2797 103 qaiplaevanRrlaglvevalketvaDktnwrkmlksevedvdlsaeaeelaeliaeeselga 165
                                       +++ l+eva+R    l eva +  ++ k +  ++lk+e+++v++ + +++l+e++a+ +e+++
  gi|385806351|ref|YP_005842749.1|  28 KFSNLIEVAERNAKMLNEVANAIVISAKKEIDEKLKNESKEVEE-EYNKKLKEELAKIEEAKE 89 
                                       57899*****************9*****************8865.566788888888333333 PP

>> ING  Inhibitor of growth proteins N-terminal histone-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   8.5    0.0002      0.15       3      80 ..      12      95 ..      10     101 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0002
                                      HHHHTSGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH......TS..S-HHHHHHHHHHHHHHHHHHHHHHHH CS
                               ING  3 edyldsvenLPlelqrnltelreiDakvqellkeidskiekfl......kngslqknekeeelsriqeelkeaqellde 75
                                       d+  +ve+L +  +++++ l e+  +  + l+e+ + i          k ++++k+ +ee  ++++eel +++e  + 
  gi|385806351|ref|YP_005842749.1| 12 TDFEKDVEELKSTYEKKFSNLIEVAERNAKMLNEVANAIVISAkkeideKLKNESKEVEEEYNKKLKEELAKIEEAKER 90
                                      68999*******************9999999999955443333344354335566666666666*************** PP

                                      HHHHH CS
                               ING 76 Kiqla 80
                                      K +la
  gi|385806351|ref|YP_005842749.1| 91 KFKLA 95
                                      **998 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   5.6   0.00015      0.11      22      90 ..      11      77 ..       1      88 [. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00015
                        Syntaxin_2 22 Lgtk.kdteelreklhelieeinelikktnellkklsqldnsssdsqqklqkekLkkdfkealqeFqkiq 90
                                      + +  kd eel++  ++  +++ e++++  + l+++++ +  s   ++k + ekLk++ ke+ +e++k  
  gi|385806351|ref|YP_005842749.1| 11 ITDFeKDVEELKSTYEKKFSNLIEVAERNAKMLNEVANAIVIS---AKKEIDEKLKNESKEVEEEYNKKL 77
                                      4444479999999999999999999999999999999988888...7899****************9754 PP

>> GCP_C_terminal  Gamma tubulin complex component C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.0   0.00018      0.13     221     298 ..       1     102 [.       1     109 [. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00018
                    GCP_C_terminal 221 lklleeilelileFakvldgly.lsvselt.......................aeeaeeeeleekleerleelekeF 273
                                       +k+++e +++i +F+k +++l     ++                         +    ++e++ekl+++ +e+e+e+
  gi|385806351|ref|YP_005842749.1|   1 MKRISESIKIITDFEKDVEELKsTYEKK-FsnlievaernakmlnevanaiviS---AKKEIDEKLKNESKEVEEEY 73 
                                       578999999*****99999977433333.25899************99997542...35689999999********* PP

                    GCP_C_terminal 274 rkkvslllkvlralkeqe....ededlrq 298
                                       +kk+++ l ++++ ke++     +e l++
  gi|385806351|ref|YP_005842749.1|  74 NKKLKEELAKIEEAKERKfklaVEEALKS 102
                                       *****999999887666555554445555 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   2.6   0.00029      0.22     143     220 ..      12      90 ..       3     110 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00029
                      Exonuc_VII_L 143 aeleeqleelerrlekaikrll...eekkqrleklasrlk.speellerk.rqrldeleerleralkkqlkkkrerl 214
                                       +++e+++eel++ +ek++++l+   e+++++l+++a+++  s+++ +++k +++ +e+ee+ ++    +lk++ +++
  gi|385806351|ref|YP_005842749.1|  12 TDFEKDVEELKSTYEKKFSNLIevaERNAKMLNEVANAIViSAKKEIDEKlKNESKEVEEEYNK----KLKEELAKI 84 
                                       5677788888888888888777444444455666666663233333332223333333333333....333333333 PP

                      Exonuc_VII_L 215 eelker 220
                                       ee+ker
  gi|385806351|ref|YP_005842749.1|  85 EEAKER 90 
                                       333322 PP

>> BPS1  Protein BYPASS1-related
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   8.6   0.00027       0.2     290     368 ..      10      86 ..       2     100 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00027
                              BPS1 290 lislhdrileeskkkekkkscGLlkeiqrieklsrslmeladsvefpleedkevevkerveelee.vcealkegLdp 365
                                       +i+ +++ +ee k   +kk + L+   +  e+++++l+e+a+++  +++++ +++ k++ +e+ee   ++lke+L +
  gi|385806351|ref|YP_005842749.1|  10 IITDFEKDVEELKSTYEKKFSNLI---EVAERNAKMLNEVANAIVISAKKEIDEKLKNESKEVEEeYNKKLKEELAK 83 
                                       677789999999999888888876...4679*******************************97527899*****99 PP

                              BPS1 366 ler 368
                                       +e 
  gi|385806351|ref|YP_005842749.1|  84 IEE 86 
                                       886 PP

>> RE_HindIII  HindIII restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   7.5   0.00053      0.39     184     268 ..      19     103 ..       7     108 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00053
                        RE_HindIII 184 erlLkeyakivaaldpaklkeakaYWskinqtilklaettkellreeklaasellkeakqeelarleaekerirgls 260
                                       e+l   y k + +l   + ++ak   +  n  ++  ++++ e+l++e +  +e  ++  +eela++e  ker  +l+
  gi|385806351|ref|YP_005842749.1|  19 EELKSTYEKKFSNLIEVAERNAKMLNEVANAIVISAKKEIDEKLKNESKEVEEEYNKKLKEELAKIEEAKERKFKLA 95 
                                       34445688999999998889999999999************************************************ PP

                        RE_HindIII 261 deealkel 268
                                        eealk  
  gi|385806351|ref|YP_005842749.1|  96 VEEALKSF 103
                                       ****9975 PP

>> M11L  Apoptosis regulator M11L like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.7   0.00052      0.39      25      70 ..       8      52 ..       2      57 .. 0.88
   2 ?    2.7   0.3      0.18   1.4e+02      25      70 ..      56      98 ..      52     105 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00052
                                      HHHHHHHHHHHHHHHHHTHHHHHHHHHHHSSST--HHH.HHHHHHH CS
                              M11L 25 rslldkikksCekinndYakdlnslydileveditvydniknevie 70
                                       ++++  +k  e ++ +Y+k + +l++++e ++ ++ +++ n++  
  gi|385806351|ref|YP_005842749.1|  8 IKIITDFEKDVEELKSTYEKKFSNLIEVAE-RNAKMLNEVANAIVI 52
                                      6899999***********************.889999989998865 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.18
                                      HHHHHHHHHHHHHHHHHTHHHHHHHHHHHSSST--HHH.HHHHHHH CS
                              M11L 25 rslldkikksCekinndYakdlnslydileveditvydniknevie 70
                                      +++ +k+k+    ++++Y+k l+   +++++e+ ++    k +v e
  gi|385806351|ref|YP_005842749.1| 56 KEIDEKLKNESKEVEEEYNKKLKE--ELAKIEEAKERK-FKLAVEE 98
                                      556678889999999999998875..334444555544.4445544 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.9     0.023        17      11      53 ..       2      44 ..       2      49 .. 0.89
   2 ?    9.9   7.7    0.0013      0.97      21      71 .]      60     109 ..      52     109 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.023
                              ZapB 11 skiqkaidtitlLqmeieeLkeeneelkeenreleeeneqlke 53
                                      ++i++ i  it   + +eeLk   e+  ++  e+ e n ++ +
  gi|385806351|ref|YP_005842749.1|  2 KRISESIKIITDFEKDVEELKSTYEKKFSNLIEVAERNAKMLN 44
                                      589999999*****************99999999999998755 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0013
                              ZapB  21 tlLqmeieeLkeen.eelkeenreleeeneqlkeereawqerlkkLLgklee 71 
                                       ++L++e +e++ee  ++lkee +++e    ++++ + a++e lk+ Lgk++e
  gi|385806351|ref|YP_005842749.1|  60 EKLKNESKEVEEEYnKKLKEELAKIE--EAKERKFKLAVEEALKSFLGKFDE 109
                                       58999999988885267888666654..467788899************997 PP

>> DUF2115  Uncharacterized protein conserved in archaea (DUF2115)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   5.8    0.0028       2.1      20     101 ..       6      92 ..       2      97 .. 0.51

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0028
                           DUF2115  20 Dlmkisarlekeikklpekyrkelsesl..teylfeaykelkn.krsgdkseykeevideeelkeflemleeqceee 93 
                                       +  ki + +ek++++l++ y k++s+ +  +e   + ++e+ n    ++k+e     ide +lk+  +++ee+++++
  gi|385806351|ref|YP_005842749.1|   6 ESIKIITDFEKDVEELKSTYEKKFSNLIevAERNAKMLNEVANaIVISAKKE-----IDE-KLKNESKEVEEEYNKK 76 
                                       5667888999999999999999998854114555555666555322222222.....222.2444444444444444 PP

                           DUF2115  94 keek........eerl 101
                                        +e+        e+++
  gi|385806351|ref|YP_005842749.1|  77 LKEElakieeakERKF 92 
                                       3333222221114444 PP

>> Peptidase_S46  Peptidase S46
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   5.9   0.00062      0.47     275     366 ..       2      94 ..       1     107 [. 0.79

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00062
                                       HHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHCT-H..HHHT CS
                     Peptidase_S46 275 evleeriallkeemkkdpeirikyasklagleNylKnliGmlealkkkkvlekkqaeeaalrawlkkdpek.kekyg 350
                                       ++ +e+i++++++ k+ +e + +y++k+ +l   + +   ml+ +++  v+  k++ +++l++  k+ +e+ ++k++
  gi|385806351|ref|YP_005842749.1|   2 KRISESIKIITDFEKDVEELKSTYEKKFSNLIEVAERNAKMLNEVANAIVISAKKEIDEKLKNESKEVEEEyNKKLK 78 
                                       5778999************************999999999*********************9999887764144555 PP

                                       THHHHHHHHHHHHHHH CS
                     Peptidase_S46 351 kalselealvkekrkl 366
                                       + l+++e++ ++k kl
  gi|385806351|ref|YP_005842749.1|  79 EELAKIEEAKERKFKL 94 
                                       5555555555555444 PP

>> Folliculin  Vesicle coat protein involved in Golgi to plasma membrane transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   3.0   0.00066       0.5      79     154 ..      30     105 ..      21     111 .] 0.81

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00066
                        Folliculin  79 rlllkawsfiveafeklaaeiqalaeaelereskeeeassaassssalkadgsglsrregssfslskekylrrsks 154
                                       + l++  +  +++++++a+ i  +a++e++++ k+e+++ +++ +++lk++  +++++++++f+l  e+ l++   
  gi|385806351|ref|YP_005842749.1|  30 SNLIEVAERNAKMLNEVANAIVISAKKEIDEKLKNESKEVEEEYNKKLKEELAKIEEAKERKFKLAVEEALKSFLG 105
                                       5566666666899*******************99999888888888899999999999999999988888876555 PP

>> TCTP  Translationally controlled tumour protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4  10.4    0.0016       1.2      56     129 ..      31     109 ..       3     111 .] 0.69

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0016
                                       S.SS.SCCCECCEEHHHHCCTEEEE.CC...HHHHHHHHHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHHHHCTCC CS
                              TCTP  56 e.eegvddevekvndivdnfrLqet.sf...dkksykaylkdYmkkvkkkleekkpeevkeFkkgaqeavkkilanf 127
                                       +  e+++ ++++ n++ ++   +   ++    k++ k+   +Y kk+k++l + ++ + ++Fk  ++ea+k+ l++f
  gi|385806351|ref|YP_005842749.1|  31 NlIEVAERNAKMLNEVANAIVISAKkEIdekLKNESKEVEEEYNKKLKEELAKIEEAKERKFKLAVEEALKSFLGKF 107
                                       25444555666666655555555443332225668999999**********999*********************** PP

                                       TT CS
                              TCTP 128 kd 129
                                       ++
  gi|385806351|ref|YP_005842749.1| 108 DE 109
                                       97 PP

>> DUF2031  Protein of unknown function (DUF2031)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3  17.0     0.002       1.5     111     199 ..       8      98 ..       2     106 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.002
                           DUF2031 111 kklinelrkeleevkkeldnkrnseLaiqpiedkritkkdenssvSeeedf.kqLeneenvleeeyneikssneykk 186
                                        k+i++++k++ee+k   + k ++ +++ + + k +++  + +++S +++  ++L+ne++ +eeeyn+   ++   k
  gi|385806351|ref|YP_005842749.1|   8 IKIITDFEKDVEELKSTYEKKFSNLIEVAERNAKMLNEVANAIVISAKKEIdEKLKNESKEVEEEYNKKLKEE-LAK 83 
                                       599****************************99***999999****98887368************9865544.445 PP

                           DUF2031 187 lkvkkklk..kaakk 199
                                       +++ k+ k   a+++
  gi|385806351|ref|YP_005842749.1|  84 IEEAKERKfkLAVEE 98 
                                       555444331044444 PP

>> YlbE  YlbE-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.2    0.0037       2.8      28      56 ..      18      46 ..       2      50 .. 0.82
   2 ?    3.6   1.1      0.12        89      22      47 ..      60      85 ..      58      87 .. 0.85
   3 ?    3.3   0.3      0.16   1.2e+02      21      46 ..      78     103 ..      75     108 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0037
                              YlbE 28 ekemkekYkktipdkvekisnslqmvsml 56
                                       +e k  Y+k++++ +e ++++ +m++  
  gi|385806351|ref|YP_005842749.1| 18 VEELKSTYEKKFSNLIEVAERNAKMLNEV 46
                                      467899*******************9876 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.12
                              YlbE 22 eelkelekemkekYkktipdkvekis 47
                                      e+lk+  ke+ e+Y+k++++ + ki+
  gi|385806351|ref|YP_005842749.1| 60 EKLKNESKEVEEEYNKKLKEELAKIE 85
                                      67888899**********99999886 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.16
                              YlbE  21 peelkelekemkekYkktipdkveki 46 
                                       +eel+++e++  +k+k+ +++ ++ +
  gi|385806351|ref|YP_005842749.1|  78 KEELAKIEEAKERKFKLAVEEALKSF 103
                                       58999************998877666 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   7.6     0.004         3       5      80 ..      12      89 ..       5     108 .. 0.54

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.004
                             TMPIT  5 eelekefkeleetakeykqkleelsklqskcskeikkqk..krlkelksslkklkksvkeeeeeeveelkeelkerkk 80
                                      +++ek+++el++t ++  ++l e+++ + k+ +e+++       ke++++lk+ +k+v+ee++++++e  ++++e+k+
  gi|385806351|ref|YP_005842749.1| 12 TDFEKDVEELKSTYEKKFSNLIEVAERNAKMLNEVANAIviSAKKEIDEKLKNESKEVEEEYNKKLKEELAKIEEAKE 89
                                      566777777777776666666666666666666665542113445556666665555554444444444444444433 PP

>> DCB  Dimerisation and cyclophilin-binding domain of Mon2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   2.2    0.0011      0.85       5      58 ..       9      67 ..       5      71 .. 0.81
   2 ?    1.4   0.8       0.3   2.2e+02       6      35 ..      73     103 ..      68     109 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0011
                               DCB  5 kllealqsdlkalsseskrkhskvkeasekgilkLktiksss.....eeeeqslaease 58
                                      k+++  ++d ++l+s  ++k+s++ e +e+    L++++++      +e +++l+++s+
  gi|385806351|ref|YP_005842749.1|  9 KIITDFEKDVEELKSTYEKKFSNLIEVAERNAKMLNEVANAIvisakKEIDEKLKNESK 67
                                      67788999*****************************9998766653333777777665 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.3
                               DCB   6 llealqsdlkalsseskrkhs.kvkeasekg 35 
                                         ++l+++l ++ ++ +rk++  v+ea +++
  gi|385806351|ref|YP_005842749.1|  73 YNKKLKEELAKIEEAKERKFKlAVEEALKSF 103
                                       5678888899988888888763456665555 PP

>> CemA  CemA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   7.7    0.0077       5.7      45     110 ..      18      84 ..       3      99 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0077
                              CemA  45 elflnkeleeealeelkefeekleleeligeapels.eeeieeelkekaeelakeyreesseaikni 110
                                          l+++ e++  + ++ +e + ++ + + +a  +s ++ei e+lk++ +e+++ey+++ +e +++i
  gi|385806351|ref|YP_005842749.1|  18 VEELKSTYEKKFSNLIEVAERNAKMLNEVANAIVISaKKEIDEKLKNESKEVEEEYNKKLKEELAKI 84 
                                       4456667777777777777888887777777766654889******************999888765 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 ?    4.1   6.2     0.091        68      18      59 ..      26      71 ..       4     102 .. 0.60

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.091
                       Arc_PepC_II 18 lkkflflleefeekdgk....ikrkfisvekeldeelrkelkkykk 59
                                      +kkf  l+e  e + +      +  +is +ke+de+l++e k++++
  gi|385806351|ref|YP_005842749.1| 26 EKKFSNLIEVAERNAKMlnevANAIVISAKKEIDEKLKNESKEVEE 71
                                      5666666666666555533323333344444444333333333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3444  (0.192091); expected 358.6 (0.02)
Passed bias filter:                      970  (0.0541023); expected 358.6 (0.02)
Passed Vit filter:                       129  (0.00719505); 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):              24  [number of targets reported over threshold]
# CPU time: 0.68u 0.38s 00:00:01.06 Elapsed: 00:00:00.54
# Mc/sec: 619.61
//
Query:       gi|385806352|ref|YP_005842750.1|  [L=345]
Description: hypothetical protein FFONT_1310 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-08   35.1  10.0    1.2e-08   34.8  10.0    1.1  1  vATP-synt_AC39  ATP synthase (C/AC39) subunit
  ------ inclusion threshold ------
      0.025   14.8   0.1      0.071   13.4   0.1    1.8  1  DUF3024         Protein of unknown function (DUF3024)
      0.064   13.3   0.8       0.21   11.7   0.8    1.9  1  Sigma70_r1_1    Sigma-70 factor, region 1.1


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 !   34.8  10.0     2e-12   1.2e-08       5     335 ..      13     341 ..       9     342 .. 0.84

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 2e-12
                                       HHHHGGGS--HHHHHHHTTS.-HHHHHHHHHTSGGGGG--.....SSSHHHHHHHHHHHHHHHTTTGGGGS-H..HH CS
                    vATP-synt_AC39   5 vramrsglLteedyenLlqcesledvkryLketdYgnfladelseplsrsdiekalreklarefnklreqapgp.sr 80 
                                       +   +s+lL+ + y+++++ + le ++++L++++ +   + e+s +++++ i   +++   + ++++ ++ap++ s 
  gi|385806352|ref|YP_005842750.1|  13 LYYWKSKLLNFNSYKSIIETNELEKIISILEQSGIKI--SGEKS-EINVDMIATQIEKFTLSMIEEIIKIAPEEtS- 85 
                                       56679****************************9998..88988.8****************************55. PP

                                       HHHHHHHHHHHHHHHHHHHHHHHH..T-......-GGGS-..--.SS.SS-HHHHHHHHHSSSHHHHHHHHHT-HHH CS
                    vATP-synt_AC39  81 efldyllyrydidNvklllrgklsg.dl......dleeleeklhplg.elsaldldklieaksveelyeallgtpya 149
                                        ++  +        +  +++   ++ ++        +e    + +l   +++ +++    ++s+  l +++ g ++ 
  gi|385806352|ref|YP_005842750.1|  86 SLVGSFYNWLNMSALLSVVKIYQNKkNIsyagfiLSDET---FSKLKkGIDSGSVTLNEDPNSIALLMKYFFGYEIV 159
                                       ************************877798877634454...44444466666665555677777777777755555 PP

                                       HHHHHHHCC...--SHHHHHHHHHHHHHHHHHHH.HHTSS-HH...HHHHHHHHHHHHHHHHHHHTTTSS......T CS
                    vATP-synt_AC39 150 kyleealdeleetgdleiienaLdkayledllkf.ckklggetaeilreilgfeiDlrniniilrskkygelskedr 225
                                       + l + +++l e+ + + +  +L  +++++ +k+  ++++  +  ++re+lg+ +D++++  ++++ k+ ++ k+ +
  gi|385806352|ref|YP_005842750.1| 160 AELGK-YKQLAEQSSCFSLYQILGTMFYAKKIKSaFSEIDTFNYMMVRELLGAYMDMKAVEEFINAHKMCNDKKS-I 234
                                       55555.7888888889999999999888887777566777778899**********************8877777.7 PP

                                       ...--SS-..S--HHHHHHHHTT-G.....GG..GGSSTSSTTGGGTT--S.HHHHHHHHHHHHHHHHHT.TTSSST CS
                    vATP-synt_AC39 226 kkllipgg..slypeglealaeaedveellaal.kyteygelleealeeagslksledaldealvkllkk.afrqqf 298
                                       ++  ++++  +++ ++++  + + ++e+  + l ++ ++++         +++k++   +++ + +l+++ + +++f
  gi|385806352|ref|YP_005842750.1| 235 EHIALEYNgfFINGKDISNSLISGSYESSFELLaSKLNIKSEK-------DEKKDVSFNIKRKIRNLAEHqFGKYPF 304
                                       7777777668999999998888889999999998888888853.......349999999***********999**** PP

                                       STHHHHHHHHHHHHHHHHHHHHHHHHHHT--SHHHHG CS
                    vATP-synt_AC39 299 svgvfyaYlklkeqEirnlrwIaegiaqglpkekIre 335
                                       s++  ++Y++l     +nl  I+ g++ ++++e I e
  gi|385806352|ref|YP_005842750.1| 305 SPALSLGYVLLLLIQRDNLMSILIGKSSNISEEIILE 341
                                       *******************************999965 PP

>> DUF3024  Protein of unknown function (DUF3024)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   1.2e-05     0.071      20      50 ..      15      45 ..      12      49 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.2e-05
                           DUF3024 20 YwadrdlkWhpYpplpkskdlealLeevekD 50
                                      Yw+++ l++ +Y+ + ++++le++++++e+ 
  gi|385806352|ref|YP_005842750.1| 15 YWKSKLLNFNSYKSIIETNELEKIISILEQS 45
                                      999*************************985 PP

>> Sigma70_r1_1  Sigma-70 factor, region 1.1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.8   3.5e-05      0.21      32      61 ..      28      57 ..      21      75 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.5e-05
                                      SS--HHHHHHHHHHHHCCT-EEE-SS-... CS
                      Sigma70_r1_1 32 deldseqiediiemLedmgIdvveeaeded 61
                                      +++++ ++e+ii++Le+ gI++  e+ + +
  gi|385806352|ref|YP_005842750.1| 28 SIIETNELEKIISILEQSGIKISGEKSEIN 57
                                      5788999***************99988544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.32s 00:00:00.96 Elapsed: 00:00:00.54
# Mc/sec: 1935.28
//
Query:       gi|385806353|ref|YP_005842751.1|  [L=258]
Description: Lipoate-protein ligase A (lplA-1) [Fervidicoccus fontis Kam940]
Scores for complete 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   24.1   0.3    6.3e-05   22.9   0.0    1.8  2  BPL_LplA_LipB   Biotin/lipoate A/B protein ligase family
  ------ inclusion threshold ------
       0.03   13.6   0.1      0.055   12.8   0.1    1.4  1  Porin_OmpG_1_2  OMPG-porin 1 family


Domain annotation for each model (and alignments):
>> BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0     7e-09   6.3e-05      14     131 .]      59     166 ..      51     166 .. 0.77
   2 ?   -3.0   0.1      0.71   6.3e+03     105     118 ..     183     196 ..     180     200 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 7e-09
                                       ..GCGGG--TT-EEEEEEESS-B-B--B-TTSEEEEEEEEE.SS...-CCGTHHHHHHHHHHHHHHH......HHTT CS
                     BPL_LplA_LipB  14 eslnsselesgglvvvrrqtgGrnvwhspkgeltyslllsp.eqktfqnrvlelyvsllvlavlealgyrdskpgie 89 
                                       e++ ++  ++ g+ ++rr tgG +v+h+  g++++++ +++ e ++   ++l  y    ++ +le+l       g++
  gi|385806353|ref|YP_005842751.1|  59 EEVDLEYAKNNGIAITRRFTGGGAVYHD-LGNINFAFSTKVpEGEKGGVDYLFNYLINGAIYALEKL-------GFS 127
                                       56667778999*****************.99999999999614444555566666777777777777.......444 PP

                                       -TTEEEETTTEEEETTEEEEEEEEEEEETTS-EEEEEEEEEE CS
                     BPL_LplA_LipB  90 gipvfikwpnDlyvngrKlaGiavtstrgktlhhivigvgvn 131
                                         + +    nD+ ++g+K++Gia   +r+    h++++ ++n
  gi|385806353|ref|YP_005842751.1| 128 PKKEN---YNDIIIDGKKIIGIAGSIRRNCAFIHGAMLYNTN 166
                                       44433...79*************9999988888888887776 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.71
                                       TEEEEEEEEEEEET CS
                     BPL_LplA_LipB 105 grKlaGiavtstrg 118
                                        +K+++++ ++t +
  gi|385806353|ref|YP_005842751.1| 183 EKKVSSVKYRVTTI 196
                                       68999999998864 PP

>> Porin_OmpG_1_2  OMPG-porin 1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   6.1e-06     0.055      34      84 ..     199     248 ..     182     254 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.1e-06
                    Porin_OmpG_1_2  34 wrnesvneGkvkltlvqgvlRhddLPgwdfGFyeaReenynGqlkkadYdg 84 
                                       +rn+ + e  v  +l+ g++R  dL g+++ F + +e++   +l k++Y+ 
  gi|385806353|ref|YP_005842751.1| 199 IRNDIR-ERDVVNALIYGFMRVKDLKGFYLDFLSEKEFDLSLELYKNKYST 248
                                       455544.4567779******************************9999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); 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: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1560.29
//
Query:       gi|385806354|ref|YP_005842752.1|  [L=92]
Description: hypothetical protein FFONT_1312 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.8e-10   39.6   0.3    4.2e-10   39.5   0.3    1.1  1  Lip_prot_lig_C  Bacterial lipoate protein ligase C-terminus


Domain annotation for each model (and alignments):
>> Lip_prot_lig_C  Bacterial lipoate protein ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.3   2.4e-14   4.2e-10      13      84 ..      11      87 ..       3      88 .. 0.84

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 2.4e-14
                                      TTEEEEEEEEE.ETTEEEEEEEEESBS..SSSHCHHHHHHHTTSBSSHHHHHHHHHTSC..HHHHCCTHHHHHHHHH CS
                    Lip_prot_lig_C 13 dwGtvevrldv.ekgiIkdikiyGDff..gpkdieeleekLigvkyekeaieealekid..lseyfggieleellel 84
                                      + G ++ r+ + ++ +I++i+i+GDff   ++ +  lee+L+g+k++++a++e++ k+   ls+ f g+++++l+  
  gi|385806354|ref|YP_005842752.1| 11 KKGLLKSRVLLsDDDKIEKIEITGDFFiyPEEFLWILEERLKGTKFDENAVKEVVTKLIdeLSAEFVGMTPDDLVRA 87
                                      567777777765788************6447777*********************9764489************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); 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: 0.55u 0.35s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 510.47
//
Query:       gi|385806355|ref|YP_005842753.1|  [L=456]
Description: hypothetical protein FFONT_1313 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.51
# Mc/sec: 2698.27
//
Query:       gi|385806356|ref|YP_005842754.1|  [L=121]
Description: hypothetical protein FFONT_1314 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.84    9.4   6.1          1    9.1   5.6    1.4  1  MNHE             Na+/H+ ion antiporter subunit
       0.94    9.5   5.0          5    7.2   0.2    2.4  2  Phage_holin_2_1  Bacteriophage P21 holin S
        5.6    5.4   5.2          7    5.1   5.2    1.1  1  FUSC             Fusaric acid resistance protein family


Domain annotation for each model (and alignments):
>> MNHE  Na+/H+ ion antiporter subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   5.6   0.00017         1      15      72 ..      41      99 ..      22     116 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00017
                              MNHE 15 lgelllGlllallvalllrrlllplrrv...llrllayllvflweivkanldVakrvlrpk 72
                                        ell+G ++ ++++++l+ ++  ++r+   ++ +  ++l+f++e++    +V++  l ++
  gi|385806356|ref|YP_005842754.1| 41 SYELLIGSIIIWMLTFFLKVFF-YPTRFvlsFV-ISGFFLLFVYEVLIGRTEVVYAFLLGS 99
                                      6799**************7665.4566635344.6679999*************9988655 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 ?    7.2   0.2   0.00083         5      40      56 ..      18      34 ..      14      41 .. 0.83
   2 ?    3.6   1.0     0.011        65      37      54 ..      45      62 ..      44      65 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00083
                   Phage_holin_2_1 40 glvigllTyltnlYFKr 56
                                      g++ g++ +++ lYFK 
  gi|385806356|ref|YP_005842754.1| 18 GILSGVILIIIDLYFKN 34
                                      678888888999***95 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.011
                   Phage_holin_2_1 37 vlgglvigllTyltnlYF 54
                                      ++g+++i +lT++   +F
  gi|385806356|ref|YP_005842754.1| 45 LIGSIIIWMLTFFLKVFF 62
                                      58**********999888 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   5.2    0.0012         7      48     105 ..      40      97 ..      36     103 .. 0.95

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0012
                              FUSC  48 KslyRllGTllGaaaavllvalfvqapllfllalalWiglclalslldrnfrsYafvL 105
                                       Ks   l+G+++  + + +l  +f+  +++++++++ ++ l ++  l+ r+   Yaf+L
  gi|385806356|ref|YP_005842754.1|  40 KSYELLIGSIIIWMLTFFLKVFFYPTRFVLSFVISGFFLLFVYEVLIGRTEVVYAFLL 97 
                                       888889**************************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       817  (0.0455686); 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:                         3  (0.000167327); expected 0.2 (1e-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 0.36s 00:00:00.91 Elapsed: 00:00:00.55
# Mc/sec: 665.32
//
Query:       gi|385806357|ref|YP_005842755.1|  [L=41]
Description: hypothetical protein FFONT_1315 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      199  (0.0110993); 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 0.34s 00:00:00.82 Elapsed: 00:00:00.52
# Mc/sec: 239.02
//
Query:       gi|385806358|ref|YP_005842756.1|  [L=311]
Description: anion-transporting ATPase [Fervidicoccus fontis Kam940]
Scores for complete 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  102.5   0.0    2.7e-29  102.3   0.0    1.0  1  ArsA_ATPase   Anion-transporting ATPase
    1.6e-07   31.4   0.0    5.4e-07   29.7   0.0    1.7  1  CbiA          CobQ/CobB/MinD/ParA nucleotide binding domain
    5.5e-06   26.4   1.2    1.5e-05   25.0   0.0    2.2  2  AAA_31        AAA domain
      3e-05   23.6   0.0    0.00066   19.2   0.0    2.1  2  ParA          NUBPL iron-transfer P-loop NTPase
     0.0018   17.8   0.1      0.005   16.3   0.0    1.7  2  Fer4_NifH     4Fe-4S iron sulfur cluster binding proteins, Ni
     0.0061   15.8   1.0       0.45    9.7   0.1    2.3  2  NB-ARC        NB-ARC domain
     0.0065   16.1   0.1      0.011   15.3   0.1    1.3  1  AAA_25        AAA domain
  ------ inclusion threshold ------
      0.024   13.6   0.0      0.041   12.8   0.0    1.4  1  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
       0.06   13.7   0.3       0.14   12.5   0.3    1.6  1  Ribosomal_L5  Ribosomal protein L5
      0.089   12.1   0.0       0.13   11.6   0.0    1.2  1  VirC1         VirC1 protein
        0.1   12.3   0.0       0.21   11.3   0.0    1.4  1  IstB_IS21     IstB-like ATP binding protein


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 !  102.3   0.0   1.7e-32   2.7e-29       3     291 ..       5     289 ..       3     304 .. 0.84

  Alignments for each domain:
  == domain 1  score: 102.3 bits;  conditional E-value: 1.7e-32
                                       EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHTS--BSS-EEET..SSEEEEE--HH....HHH CS
                       ArsA_ATPase   3 vilvgGKGGVGKttvsaatavklsekgkkvllistDPAhslsDsfdqklgkeptkvk..eNLsavEidpe....vel 73 
                                       v+ + GKGGVGKtt+  +++++l+  gkk++ ++tDP + l    +++    + k k  +NL+   +  +      +
  gi|385806358|ref|YP_005842756.1|   5 VLSFWGKGGVGKTTLTFSLSLELALRGKKTIYLTTDPTPPLPYWGSKDCDWREYKAKcgDNLELYLMSEKivreLWI 81 
                                       56789************************************987777776666666666**9988777665544556 PP

                                       HHHHCCHHGGGSCCHHHHHHHHHHHHHHTSSTTHHHHHHHHHHHHHHHCSSSSEEEEESBSCCHTCGGGGHHHHHHH CS
                       ArsA_ATPase  74 eeakqevqkeeeallgleeledvlaeelaslPGideilsfeellkyvkeeeydvvvlDtaPTGhtlrllslpevlek 150
                                       ++  +ev++ + +++    +++v++  + + PGi + + +  +++++++e  d++v Dt   G ++rl++l + + +
  gi|385806358|ref|YP_005842756.1|  82 KKFGEEVYEVASSIFP--VEREVIDYVAGA-PGIADEFLMYFVQNLCRNESADYIVWDTTAAGGSIRLIRLEKEFYE 155
                                       7777777777777766..788999999998.*****999999*******************************9999 PP

                                       HHHHHHHHHHHHHHHHHHHCCCSHCHHHHHHHHHHHHHHHHHHHHHHHHHHTSTTTEEEEEEEESSHHHHHHHHHHH CS
                       ArsA_ATPase 151 lleklvklkeklsplakqlvkllglggvsieealeeleetkeeikkveeiltdpertsfrlVvipEklslkEteRai 227
                                        l ++ k+  k++  ++++    + g+++  e +++ ++  ee+      l+  +     +V+ip+   l+ t    
  gi|385806358|ref|YP_005842756.1| 156 HLGQASKMYLKIKGTLEKI----RRGKKDPAELIDSWRKIAEEVL---SFLSSSSH-KAYIVSIPDYYGLQVTSSIY 224
                                       9998888888777777776....5588888899999999999888...44555444.5569**************** PP

                                       HHHHHTT-EEEEEEEEEE-TTCSSSTSHHHHHHHHHHHHHHHHHHHHTTTS.EEEEEE--SS-S- CS
                       ArsA_ATPase 228 keLkkygikvdavivNkllpeeeqenCeflearkkiqkkylkeieelfedl.evvklplleeEvv 291
                                       +eL+  +i+v++vi N ++ ee+q++C+ + +  + qkky++e  ++fe +  +  + ++ eE++
  gi|385806358|ref|YP_005842756.1| 225 EELTMNKINVEKVILNMVFGEEVQKECKEIGNMAREQKKYIQEFFKKFEGKaDICMVNYYFEELQ 289
                                       ************************************************96515677777777764 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 !   29.7   0.0   3.3e-10   5.4e-07       6      95 ..      10     253 ..       8     273 .. 0.85

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 3.3e-10
                                       SSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH....HTTEB-HHHH........................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxx........................ RF
                              CbiA   6 tkGGvGKTtlaanLaralarrglrVllvDaDpqannlai....leglendiep........................ 54 
                                       +kGGvGKTtl+ +L   la rg++++ + +Dp  ++        ++      +                        
  gi|385806358|ref|YP_005842756.1|  10 GKGGVGKTTLTFSLSLELALRGKKTIYLTTDPTPPLPYWgskdCDWR-----Eykakcgdnlelylmsekivrelwi 81 
                                       7********************************99987465543333.....144446999999************* PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|385806358|ref|YP_005842756.1|  82 kkfgeevyevassifpverevidyvagapgiadeflmyfvqnlcrnesadyivwdttaaggsirlirlekefyehlg 158
                                       *************************************************************9999999999999999 PP

                                       ......................................................CCHCCCHHHHHHCHCHHHH...E CS
                                       ......................................................xxxxxxxxxxxxxxxxxxx.xxx RF
                              CbiA  55 ......................................................dlkrllellealgkkkall.lki 76 
                                                                                             d    l++ +++++++  + +++
  gi|385806358|ref|YP_005842756.1| 159 qaskmylkikgtlekirrgkkdpaelidswrkiaeevlsflsssshkayivsipDYYG-LQVTSSIYEELTMNkINV 234
                                       9999999999999999999999999999999999999999999999999999995544.555555555555556999 PP

                                       EEEEEEEESS...-TTCHH CS
                                       xxxxxxxxxxxxxxxxxxx RF
                              CbiA  77 agvvlnrvdgeneetllke 95 
                                         v+ln+v ge+ +++ ke
  gi|385806358|ref|YP_005842756.1| 235 EKVILNMVFGEEVQKECKE 253
                                       9999999988866655544 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   9.3e-09   1.5e-05      10      41 ..      11      42 ..       4     138 .. 0.86
   2 ?   -0.4   0.3      0.57   9.2e+02      51      64 ..     230     243 ..     201     304 .. 0.52

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 9.3e-09
                            AAA_31 10 KGGvGKTTtsvnlaaalaklgkkvLlvDlDpQ 41
                                      KGGvGKTT ++ l+  la +gkk++    Dp 
  gi|385806358|ref|YP_005842756.1| 11 KGGVGKTTLTFSLSLELALRGKKTIYLTTDPT 42
                                      9************************9999995 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.57
                            AAA_31  51 ekneiektlyevli 64 
                                       +k ++ek ++++++
  gi|385806358|ref|YP_005842756.1| 230 NKINVEKVILNMVF 243
                                       33344444555442 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 !   19.2   0.0     4e-07   0.00066      11      40 ..      10      39 ..       3      44 .. 0.85
   2 ?    2.1   0.0     0.069   1.1e+02     131     188 ..     199     257 ..     184     297 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 4e-07
                              ParA 11 gKGGVGKStvavnlAlaLakkglkvgllDa 40
                                      gKGGVGK+t++ +l+l+La +g+k+  l +
  gi|385806358|ref|YP_005842756.1| 10 GKGGVGKTTLTFSLSLELALRGKKTIYLTT 39
                                      9*********************99876655 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.069
                              ParA 131 aqklplagaviVttpqevaladvkkaiemfkkvkvkvlGvveNmsgf..vcpkcgektei 188
                                       +++   ++a iV+ p    l++++   e ++  k++v  v+ Nm     v+++c+e  ++
  gi|385806358|ref|YP_005842756.1| 199 LSSS-SHKAYIVSIPDYYGLQVTSSIYEELTMNKINVEKVILNMVFGeeVQKECKEIGNM 257
                                       4444.467889************999999999************7641144455544443 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 !   16.3   0.0   3.1e-06     0.005       3      38 ..       6      41 ..       4      44 .. 0.94
   2 ?   -2.2   0.1       1.4   2.3e+03     215     246 ..     230     260 ..     202     269 .. 0.50

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.1e-06
                         Fer4_NifH  3 iaiyGkGGiGksttsqnlsaalaemgkkvlivGCDP 38
                                      ++++GkGG+Gk+t +  ls  la +gkk + +  DP
  gi|385806358|ref|YP_005842756.1|  6 LSFWGKGGVGKTTLTFSLSLELALRGKKTIYLTTDP 41
                                      5799***************************99999 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.4
                         Fer4_NifH 215 rkaelrkktvieyapeseqakeyrelarkile 246
                                       +k +++ k++ +++  +e+ ke +e+ +   e
  gi|385806358|ref|YP_005842756.1| 230 NKINVE-KVILNMVFGEEVQKECKEIGNMARE 260
                                       222222.2333444444444444444444444 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.1   0.00027      0.45      22      37 ..       5      20 ..       1      29 [. 0.87
   2 !    4.6   0.1    0.0096        16     169     196 ..     281     308 ..     251     309 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00027
                                      EEEEEESTTSSHHHHH CS
                            NB-ARC 22 vvalvGmgGvGKttla 37
                                      v+++ G+gGvGKttl 
  gi|385806358|ref|YP_005842756.1|  5 VLSFWGKGGVGKTTLT 20
                                      899***********96 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0096
                                       HHCCTS-GGCHH..CHHHHHHHHHHCTT CS
                            NB-ARC 169 enkvfekkleekesleevakeivekckG 196
                                        n+ fe+ ++e++ lee++k+i+e+c G
  gi|385806358|ref|YP_005842756.1| 281 VNYYFEELQKESHILEEIGKRIIESCIG 308
                                       46777777788888************88 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1     7e-06     0.011      37      63 ..       7      34 ..       3      48 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 7e-06
                            AAA_25 37 llaGapgtGKttlaldlalava.tGkpw 63
                                       ++G +g+GKttl+ +l+l++a +Gk+ 
  gi|385806358|ref|YP_005842756.1|  7 SFWGKGGVGKTTLTFSLSLELAlRGKKT 34
                                      578*******************988864 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 ?   12.8   0.0   2.5e-05     0.041      31      70 ..       5      44 ..       2      50 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.5e-05
                                      EEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE----- CS
                              MeaB 31 vvGltGvPGaGkstlvealglelrrrGkrvavlavDPssp 70
                                      v+ + G  G+Gk tl+  l lel+ rGk+   l  DP+ p
  gi|385806358|ref|YP_005842756.1|  5 VLSFWGKGGVGKTTLTFSLSLELALRGKKTIYLTTDPTPP 44
                                      6778899******************************976 PP

>> Ribosomal_L5  Ribosomal protein L5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.3   8.5e-05      0.14       3      23 ..     229     249 ..     228     268 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.5e-05
                                       TTS-EEEEEEEEEE-SSSSSC CS
                      Ribosomal_L5   3 MqvPrleKivinmgvGeaged 23 
                                       M+++ +eK+ +nm  Ge +++
  gi|385806358|ref|YP_005842756.1| 229 MNKINVEKVILNMVFGEEVQK 249
                                       99***************9997 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   7.7e-05      0.13       9      60 ..       8      61 ..       3      92 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.7e-05
                             VirC1  9 l..kGGaGkttalmglcsalasdgkrvalfeadenrPltkwkenalrkgawdda 60
                                      +  kGG Gktt   +l   la +gk+   + +d   Pl  w  +      ++ +
  gi|385806358|ref|YP_005842756.1|  8 FwgKGGVGKTTLTFSLSLELALRGKKTIYLTTDPTPPLPYWGSKDCDWREYKAK 61
                                      5449**********************************9997665555444444 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 ?   11.3   0.0   0.00013      0.21      51      83 ..       7      39 ..       3      42 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00013
                         IstB_IS21 51 vllGpsGvGKshlaialgveavraglsvlfvrv 83
                                       + G  GvGK+ l+ +l+ e + +g++++++++
  gi|385806358|ref|YP_005842756.1|  7 SFWGKGGVGKTTLTFSLSLELALRGKKTIYLTT 39
                                      5789**************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       955  (0.0532657); expected 358.6 (0.02)
Passed bias filter:                      664  (0.037035); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); 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: 0.66u 0.37s 00:00:01.03 Elapsed: 00:00:00.53
# Mc/sec: 1763.91
//
Query:       gi|385806359|ref|YP_005842757.1|  [L=167]
Description: hypothetical protein FFONT_1317 [Fervidicoccus fontis Kam940]
Scores for complete 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   29.2   0.0    1.1e-06   28.5   0.0    1.3  1  Thioredoxin    Thioredoxin
      7e-05   23.1   0.6    0.00016   21.9   0.3    1.5  1  Thioredoxin_4  Thioredoxin
     0.0027   18.0   0.0     0.0044   17.3   0.0    1.4  1  Thioredoxin_8  Thioredoxin-like
  ------ inclusion threshold ------
      0.022   15.2   0.6       0.12   12.8   0.6    1.9  1  Thioredoxin_2  Thioredoxin-like domain


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   2.5e-10   1.1e-06      18     102 ..      65     162 ..      61     163 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 2.5e-10
                                       SSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTT.........TSEEEEEETTTSHHHHHHTT-SSSSE..EEEEETTE CS
                       Thioredoxin  18 kklvlveFyApwCghCkalaPeleklaeelkd.........kvklakvdvdenedlakkyevegiPt..lklfkngk 83 
                                       +   +v F  + C  C+++ Pe+ ++ ee+kd         +    ++d ++ + +    ev++ Pt  + l+k+g 
  gi|385806359|ref|YP_005842757.1|  65 DGIYVVYFDNTQCSACRRFDPEWYSFVEEYKDrgkfyiilcDWFARECDSKAASRTFFINEVRASPTtmIFLVKEGA 141
                                       56789***************************99665444444445666666677777789*****94344568888 PP

                                       ..EEEEEESS-HHHHHHHHHH CS
                       Thioredoxin  84 ..evkkyegarekeklaaflk 102
                                         + +++eg+ +ke+la++ k
  gi|385806359|ref|YP_005842757.1| 142 ivKNERIEGSVKKEELASKFK 162
                                       888899**********98765 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.3   3.6e-08   0.00016      13      66 ..      65     117 ..      58     121 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 3.6e-08
                                       -SEEEEEEE-TT-HHHHHHHHHHHHHHHHHHHTTSEEEEEEE-..---STTTHH CS
                     Thioredoxin_4  13 ApvtvieyedlrCphCakfeeeveklleeyidtGkvkfiirdfpldkekeslka 66 
                                         + v+ + + +C+ C++f+ e + ++eey d Gk ++i  d +  +   s+ a
  gi|385806359|ref|YP_005842757.1|  65 DGIYVVYFDNTQCSACRRFDPEWYSFVEEYKDRGKFYIILCDWFARECD-SKAA 117
                                       5678999*******************************99988544443.5555 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   9.9e-07    0.0044       3      39 ..      67     103 ..      65     138 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 9.9e-07
                                       EEEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEE CS
                     Thioredoxin_8   3 vvlLyfgaswcppckaftpklkelyeklkkkkkveiv 39 
                                       ++++yf +++c+ c++f p+   + e++k++ k+ i+
  gi|385806359|ref|YP_005842757.1|  67 IYVVYFDNTQCSACRRFDPEWYSFVEEYKDRGKFYII 103
                                       789**************************88888777 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.6   2.8e-05      0.12       8     106 ..      68     158 ..      62     161 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.8e-05
                     Thioredoxin_2   8 vlvvftdpdCpyCkklkkelkel.ddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarky...gvrg 80 
                                        +v+f+ ++C  C+++  e  +  +++++r            k+  i c+    ++ +     ++ +r++   +vr+
  gi|385806359|ref|YP_005842757.1|  68 YVVYFDNTQCSACRRFDPEWYSFvEEYKDR-----------GKFYIILCDWFA-RECDS----KAASRTFfinEVRA 128
                                       689999************998884444444...........577777777777.44444....44444444559999 PP

                     Thioredoxin_2  81 tPt.ivfldgk...eivarlpGyvpaeele 106
                                        Pt ++fl ++    + +r++G v++eel+
  gi|385806359|ref|YP_005842757.1| 129 SPTtMIFLVKEgaiVKNERIEGSVKKEELA 158
                                       999877888888788888999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); 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: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 962.63
//
Query:       gi|385806360|ref|YP_005842758.1|  [L=40]
Description: hypothetical protein FFONT_1318 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       262  (0.0146132); expected 358.6 (0.02)
Passed bias filter:                      172  (0.0095934); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 235.11
//
Query:       gi|385806361|ref|YP_005842759.1|  [L=100]
Description: 4Fe-4S ferredoxin [Fervidicoccus fontis Kam940]
Scores for complete 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-08   33.8   5.1    3.9e-08   33.4   5.1    1.3  1  ETF_QO    Electron transfer flavoprotein-ubiquinone oxidoredu
    1.7e-07   31.7   7.6     0.0021   18.6   0.3    2.2  2  Fer4_7    4Fe-4S dicluster domain
    4.1e-07   29.7   9.8    0.00097   19.1   0.9    2.3  2  Fer4_2    4Fe-4S binding domain
    2.4e-06   27.6  11.9    3.9e-06   26.9  11.9    1.3  1  Fer4_9    4Fe-4S dicluster domain
    2.6e-05   24.2   5.8      4e-05   23.7   5.8    1.2  1  Fer4_11   4Fe-4S dicluster domain
     0.0001   22.3  22.3     0.0053   16.8  13.2    2.1  2  Fer4_10   4Fe-4S dicluster domain
    0.00043   20.0   1.7    0.00043   20.0   1.7    3.1  3  Fer4      4Fe-4S binding domain
     0.0047   17.3   1.4     0.0047   17.3   1.4    2.5  2  Fer4_4    4Fe-4S binding domain
     0.0065   16.6  12.4       0.11   12.6  12.8    2.1  2  Fer4_21   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.015   16.2   0.7      0.015   16.2   0.7    2.8  3  Fer4_16   4Fe-4S double cluster binding domain
       0.69   10.4  13.8       0.14   12.6   2.4    2.3  2  Fer4_8    4Fe-4S dicluster domain
        1.1    9.5  13.1        1.9    8.7   1.8    2.3  2  Fer4_6    4Fe-4S binding domain
        2.1    9.0  14.2    1.8e+02    2.8   4.5    2.2  2  Fer4_17   4Fe-4S dicluster domain
        5.2    8.3  18.9       0.26   12.3   3.6    2.4  2  Fer4_3    4Fe-4S binding domain
        5.6    7.6  11.4       0.94   10.1   2.4    2.4  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
        8.8    6.1  11.2        2.5    7.9   3.1    2.1  2  Fer4_20   Dihydroprymidine dehydrogenase domain II, 4Fe-4S cl


Domain annotation for each model (and alignments):
>> 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 !   33.4   5.1   3.5e-11   3.9e-08      36     103 ..      35      97 ..       9      98 .. 0.82

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 3.5e-11
                                       HTHHHHHS-THHHH-TTS-EEEEETTTTSSEEEEE-CCC--S--HHHHH-TT--EEE---STT-C--- CS
                            ETF_QO  36 kvnlekyagpeqryCPagvyeivedeeakekklqinaqnCvhCktCdikdpsqniewvvPeGggGPky 103
                                       +++ +  ++p+   CPag y + e+      k+  n + C+ C tC +  p + i+w+ Pe g+G +y
  gi|385806361|ref|YP_005842759.1|  35 EQCEKCQSKPCLYLCPAGCYTLSESG-----KIMFNHEGCLECGTCRVICPLKAIKWEYPEPGKGIHY 97 
                                       34444556799999*******99776.....7999******************************998 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   1.9   8.2e-06    0.0092      23      51 ..      22      52 ..       4      53 .. 0.81
   2 !   18.6   0.3   1.8e-06    0.0021       2      26 ..      69      93 ..      64      99 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 8.2e-06
                            Fer4_7 23 enekgtekveidpekClgCga..CvavCPtg 51
                                       + ++++++++d+e+C  C++  C   CP+g
  gi|385806361|ref|YP_005842759.1| 22 WEVDEKPHIVVDYEQCEKCQSkpCLYLCPAG 52
                                      34457899************999******98 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 1.8e-06
                            Fer4_7  2 CigCgaCvaaCpvkaieldeeenek 26
                                      C +Cg C + Cp kai++++ e  k
  gi|385806361|ref|YP_005842759.1| 69 CLECGTCRVICPLKAIKWEYPEPGK 93
                                      99***************99876555 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   2.2   1.5e-05     0.017       1      22 []      28      51 ..      28      51 .. 0.90
   2 !   19.1   0.9   8.7e-07   0.00097       2      21 ..      61      80 ..      60      81 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.5e-05
                            Fer4_2  1 apvvvdtdrCigCg..aCvsaCPa 22
                                      +++vvd + C  C   +C+  CPa
  gi|385806361|ref|YP_005842759.1| 28 PHIVVDYEQCEKCQskPCLYLCPA 51
                                      689**********556*******8 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 8.7e-07
                            Fer4_2  2 pvvvdtdrCigCgaCvsaCP 21
                                      ++ ++ + C++Cg+C+  CP
  gi|385806361|ref|YP_005842759.1| 61 KIMFNHEGCLECGTCRVICP 80
                                      57789999*********9*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 !   26.9  11.9   3.4e-09   3.9e-06       1      51 []      36      84 ..      36      84 .. 0.93

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 3.4e-09
                            Fer4_9  1 kCtgCga..CveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                      +C +C++  C + Cpag ++ +++++++ +++     C++Cg+C  +Cp +ai
  gi|385806361|ref|YP_005842759.1| 36 QCEKCQSkpCLYLCPAGCYTLSESGKIMFNHE----GCLECGTCRVICPLKAI 84
                                      6****8777********************987....5************9987 PP

>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   5.8   3.5e-08     4e-05       7      62 ..      34      87 ..      29      91 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 3.5e-08
                           Fer4_11  7 peqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivrkn 62
                                       eqC++C+++pC+  +p++  +   e G ++++++ +  e+ +++  cP+k+++++
  gi|385806361|ref|YP_005842759.1| 34 YEQCEKCQSKPCLYLCPAGC-YTLSESGKIMFNHEGCL-ECGTCRVICPLKAIKWE 87
                                      58***************965.555569**********7.************99986 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8  13.2   4.7e-06    0.0053       1      56 []      29      80 ..      29      80 .. 0.92
   2 !   16.7   1.6   5.2e-06    0.0058       2      22 ..      62      82 ..      61      97 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.7e-06
                           Fer4_10  1 kvvidddtCirCg..kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      ++v+d ++C +C+   C   CPa      + +  se++++  + e C +cg C  +CP
  gi|385806361|ref|YP_005842759.1| 29 HIVVDYEQCEKCQskPCLYLCPA------GCYTLSESGKIMFNHEGCLECGTCRVICP 80
                                      7899********9999*******......888888888888899*************9 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 5.2e-06
                           Fer4_10  2 vvidddtCirCgkCvkaCPad 22
                                      + ++ + C++Cg+C+  CP +
  gi|385806361|ref|YP_005842759.1| 62 IMFNHEGCLECGTCRVICPLK 82
                                      5678899************94 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.3    0.0088       9.9       1      11 [.      30      40 ..      30      42 .. 0.90
   2 ?    1.3   1.3       0.3   3.4e+02      14      23 ..      45      54 ..      44      55 .. 0.83
   3 !   20.0   1.7   3.9e-07   0.00043       3      24 .]      64      85 ..      62      85 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0088
                                      EEEETTTSSS- CS
                              Fer4  1 vvideekCigC 11
                                      +v+d+e C +C
  gi|385806361|ref|YP_005842759.1| 30 IVVDYEQCEKC 40
                                      69********* PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.3
                                      HHHHSTTTEE CS
                              Fer4 14 CvevCPvgAI 23
                                      C   CP g+ 
  gi|385806361|ref|YP_005842759.1| 45 CLYLCPAGCY 54
                                      7788***996 PP

  == domain 3  score: 20.0 bits;  conditional E-value: 3.9e-07
                                      EETTTSSS-THHHHHSTTTEEE CS
                              Fer4  3 ideekCigCGaCvevCPvgAIt 24
                                      ++ e C  CG+C  +CP  AI+
  gi|385806361|ref|YP_005842759.1| 64 FNHEGCLECGTCRVICPLKAIK 85
                                      78999***************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 ?   -1.6   6.1       4.8   5.4e+03       4      16 ..      37      51 ..      34      55 .. 0.72
   2 !   17.3   1.4   4.2e-06    0.0047       2      16 ..      67      81 ..      66      89 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 4.8
                            Fer4_4  4 CigCgs..CvaaCPq 16
                                      C  C s  C + CP 
  gi|385806361|ref|YP_005842759.1| 37 CEKCQSkpCLYLCPA 51
                                      666777778888886 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 4.2e-06
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      e C++Cg C+ +CP 
  gi|385806361|ref|YP_005842759.1| 67 EGCLECGTCRVICPL 81
                                      56************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 !    8.6   3.1    0.0018         2      27      57 ..      23      54 ..       4      56 .. 0.81
   2 !   12.6  12.8   9.8e-05      0.11       2      57 ..      31      84 ..      30      86 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0018
                           Fer4_21 27 eidaktvlkvvedeCvGCnl..CssvCPvedci 57
                                      e+d+k ++ v  ++C  C+   C+  CP  +c 
  gi|385806361|ref|YP_005842759.1| 23 EVDEKPHIVVDYEQCEKCQSkpCLYLCPA-GCY 54
                                      678889999999******7555******5.886 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 9.8e-05
                           Fer4_21  2 ridedkCigCgk..CliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedci 57
                                      ++d ++C +C++  Cl  C+     + +++++ ++   ++ C  C  C  +CP+ ++i
  gi|385806361|ref|YP_005842759.1| 31 VVDYEQCEKCQSkpCLYLCPA---GCYTLSESGKIMFNHEGCLECGTCRVICPL-KAI 84
                                      58999*****8556******5...56667777888899***************8.776 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   5.3      0.21   2.4e+02       1      65 [.      36      50 ..       2      52 .. 0.43
   2 ?    5.0   4.1     0.044        49       1      21 [.      36      58 ..      36      67 .. 0.80
   3 ?   16.2   0.7   1.3e-05     0.015       2      20 ..      69      87 ..      68      97 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.21
                           Fer4_16  1 rCgtCgk..CaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCP 65
                                      +C +C+   C+                                                      CP
  gi|385806361|ref|YP_005842759.1| 36 QCEKCQSkpCL----------------------------------------------------YLCP 50
                                      23333333333....................................................3444 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.044
                           Fer4_16  1 rCgtCgk..CaevCPtnaikekk 21
                                      +C +C+   C+  CP+++ +  +
  gi|385806361|ref|YP_005842759.1| 36 QCEKCQSkpCLYLCPAGCYTLSE 58
                                      5****9899*******9877664 PP

  == domain 3  score: 16.2 bits;  conditional E-value: 1.3e-05
                           Fer4_16  2 CgtCgkCaevCPtnaikek 20
                                      C +Cg C  +CP +aik +
  gi|385806361|ref|YP_005842759.1| 69 CLECGTCRVICPLKAIKWE 87
                                      99**************955 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   4.1      0.11   1.3e+02      27      64 ..      11      52 ..       1      53 [. 0.60
   2 ?   12.6   2.4   0.00012      0.14       4      17 ..      68      81 ..      65      97 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.11
                            Fer4_8 27 dargeaaedvqeeqvlee...eealwsCttcga..CtevCpvg 64
                                      ++ +e ++ + +++v e+       ++C  c++  C   Cp g
  gi|385806361|ref|YP_005842759.1| 11 KTLDEIMK-EDKWEVDEKphiVVDYEQCEKCQSkpCLYLCPAG 52
                                      44444455.5555555555554456778888888888889875 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00012
                            Fer4_8  4 kCieCgaCqsaCpv 17
                                       C eCg C+  Cp+
  gi|385806361|ref|YP_005842759.1| 68 GCLECGTCRVICPL 81
                                      47777777777763 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   3.8     0.013        14       2      23 ..      30      53 ..      29      54 .. 0.86
   2 ?    8.7   1.8    0.0017       1.9       9      20 ..      69      80 ..      63      84 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.013
                            Fer4_6  2 veidpdkCigC.gd.CvrvCPega 23
                                      +++d++ C  C  + C   CP+g 
  gi|385806361|ref|YP_005842759.1| 30 IVVDYEQCEKCqSKpCLYLCPAGC 53
                                      89*******998667******985 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0017
                            Fer4_6  9 CigCgdCvrvCP 20
                                      C+ Cg C ++CP
  gi|385806361|ref|YP_005842759.1| 69 CLECGTCRVICP 80
                                      ***********9 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   4.5      0.16   1.8e+02      41      59 ..      32      52 ..       3      54 .. 0.58
   2 ?   -0.4  15.0       1.6   1.8e+03      40      57 ..      63      80 ..      36      83 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.16
                           Fer4_17 41 ekaslCieCge..CerkCPqg 59
                                         ++C +C+   C + CP+g
  gi|385806361|ref|YP_005842759.1| 32 VDYEQCEKCQSkpCLYLCPAG 52
                                      467888888654599999976 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.6
                           Fer4_17 40 eekaslCieCgeCerkCP 57
                                      + + + C+eCg C+  CP
  gi|385806361|ref|YP_005842759.1| 63 MFNHEGCLECGTCRVICP 80
                                      457789*********999 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   7.4       0.6   6.7e+02       1      14 [.      37      52 ..      36      53 .. 0.84
   2 ?   12.3   3.6   0.00023      0.26       1      15 []      69      83 ..      69      83 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.6
                            Fer4_3  1 CtgCg..aCvevCPvg 14
                                      C  C+  +C+  CP g
  gi|385806361|ref|YP_005842759.1| 37 CEKCQskPCLYLCPAG 52
                                      88897778******76 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00023
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+ Cg+C + CP +A
  gi|385806361|ref|YP_005842759.1| 69 CLECGTCRVICPLKA 83
                                      9***********887 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 ?    2.9   1.6      0.15   1.6e+02       1      18 [.      32      51 ..      32      66 .. 0.82
   2 ?   10.1   2.4   0.00084      0.94       2      17 ..      65      80 ..      62      82 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.15
                           Fer4_13  1 VDrdtCiacga..CvelaPd 18
                                      VD ++C  c++  C  l+P 
  gi|385806361|ref|YP_005842759.1| 32 VDYEQCEKCQSkpCLYLCPA 51
                                      8999*****87779999996 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00084
                           Fer4_13  2 DrdtCiacgaCvelaP 17
                                      + + C +cg+C+ ++P
  gi|385806361|ref|YP_005842759.1| 65 NHEGCLECGTCRVICP 80
                                      5689***********9 PP

>> Fer4_20  Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   3.1    0.0022       2.5      16      39 ..      29      52 ..      10      57 .. 0.81
   2 ?    2.7   2.2     0.094   1.1e+02      17      39 ..      62      82 ..      53      88 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0022
                                      HHHHHHTT----TT-HHHHCSTT- CS
                           Fer4_20 16 ealeeAsRClqCkkapcvkgCPve 39
                                      +++ + + C +C+++pc   CP+ 
  gi|385806361|ref|YP_005842759.1| 29 HIVVDYEQCEKCQSKPCLYLCPAG 52
                                      56777899**************86 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.094
                                      HHHHHTT----TT-HHHHCSTT- CS
                           Fer4_20 17 aleeAsRClqCkkapcvkgCPve 39
                                      ++ + + Cl+C   +c   CP++
  gi|385806361|ref|YP_005842759.1| 62 IMFNHEGCLEC--GTCRVICPLK 82
                                      5556678****..789999**87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1126  (0.0628033); expected 358.6 (0.02)
Passed bias filter:                      587  (0.0327403); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); 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: 00:00:00.51
# Mc/sec: 588.14
//
Query:       gi|385806362|ref|YP_005842760.1|  [L=424]
Description: Electron-transferring-flavoproteindehydrogenase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.7e-18   65.4   0.1    2.9e-08   33.7   0.0    2.2  2  DAO             FAD dependent oxidoreductase
    3.2e-10   39.7   0.0    6.1e-10   38.8   0.0    1.5  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.3e-09   37.2   0.2    5.9e-06   25.2   0.1    2.2  2  HI0933_like     HI0933-like protein
    1.4e-09   37.6   0.2    2.1e-06   27.1   0.1    2.3  2  FAD_binding_2   FAD binding domain
    6.8e-09   35.6   0.0    1.2e-08   34.8   0.0    1.4  1  FAD_oxidored    FAD dependent oxidoreductase
    4.8e-08   33.1   0.0    1.3e-07   31.7   0.0    1.8  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    2.9e-07   30.0   0.0    4.9e-07   29.2   0.0    1.4  1  Thi4            Thi4 family
      3e-07   30.0   0.0    3.5e-05   23.2   0.0    2.5  3  FAD_binding_3   FAD binding domain
    3.1e-06   26.6   2.5    5.1e-05   22.5   2.5    2.5  2  GIDA            Glucose inhibited division protein A
    8.3e-06   24.9   0.7     0.0088   14.9   0.0    2.2  2  Trp_halogenase  Tryptophan halogenase
    6.4e-05   23.4   0.0      0.032   14.8   0.0    3.3  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    0.00017   21.0   0.5    0.00037   19.9   0.5    1.6  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    0.00021   21.3   0.3     0.0013   18.8   0.3    2.2  1  NAD_binding_9   FAD-NAD(P)-binding
    0.00057   19.3   0.0       0.11   11.9   0.0    2.2  2  GMC_oxred_N     GMC oxidoreductase
     0.0046   16.5   0.1       0.45   10.1   0.0    2.3  2  DUF2106         Predicted membrane protein (DUF2106)
  ------ inclusion threshold ------
        0.1   11.6   0.3       0.35    9.9   0.1    2.1  2  Lycopene_cycl   Lycopene cyclase protein


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.0   2.5e-10   2.8e-07       1      68 [.       8      72 ..       8      89 .. 0.77
   2 !   33.7   0.0   2.6e-11   2.9e-08     142     351 ..     100     327 ..      58     328 .. 0.63

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 2.5e-10
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSS..STHHSTHHHHHHHHHH.HHHH CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsgl..rylpeaselarlslea.leel 68
                                      d +++GGG +G+++Ay+La++g  ++lle+g++   g+    +g ++s++    +p      ++ +ea ++++
  gi|385806362|ref|YP_005842760.1|  8 DAIVVGGGPAGATAAYFLAKKGynTLLLERGKRY--GSKNVYGGKIYSYYvkKLFP------EFEKEApIQRW 72
                                      789****************************665..69999999999966332222......55555544555 PP

  == domain 2  score: 33.7 bits;  conditional E-value: 2.6e-11
                                       EEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEE.EEEEEEEE--GGGHH.HHHTT...CTT CS
                               DAO 142 qvdpakltaalaraaealGveilegtevtgleeedgkvwgverttpgen.daadavVnaaGawsd.llgll...kel 213
                                       ++    +t++l ++ae++G++++ ++++tgl +e++k++g+  ++ ge+ ++ad  ++a Ga  + ll+++   ++ 
  gi|385806362|ref|YP_005842760.1| 100 TAYLSDFTNWLCKKAEQQGATVISESKATGLIREGDKIVGI--EA-GEEkVKADVTIIAEGAN-RiLLEKAglvRPP 172
                                       446678************************988899*****..33.444467799******99.5455333223222 PP

                                       T.SEEEEEEEEEEEE..EECCTHSTGSGCSEEEEE...............EEETTTTEEEEEETTSEEEEEESSE.. CS
                               DAO 214 d.lpispvrgqvlvl..kplseklvspaailpvpe...............tdddgrgvyvtprkdgrvlvGgtad.. 270
                                       d  ++     + + l  k ++e +                          t+   +g +++  k + v vG+  +  
  gi|385806362|ref|YP_005842760.1| 173 DpMQVAVGIKETIKLdqKAINERF----------NigdneglswlflgdvTNGLPDGAFLYTFK-DAVSVGAVVTlg 238
                                       212222223333333112222222..........133344556555777766777777777766.558888877444 PP

                                       ..EETTCSSTSCSHHHHHHHHHHHHHHSGG...G...CGEEE.EEEEEEE..E.TTSSEEEEEEETEEEEEEEEECT CS
                               DAO 271 ..eesgdddpevdeedidellealrklfPq...l...gdvlr.kwaGlrp..l.pdglpligetpgvkglylatGhs 335
                                           ++ ++   + ++  ++ + +r+l+ +   +   ++++      + p  l  +g  +ig      gl+ ++G+ 
  gi|385806362|ref|YP_005842760.1| 239 taI-DSINEHIYNFAEKLRIHPVMRNLLKDgeiVeyaAHLTVvDVESFIPekLsGNGYMIIGD---AGGLLANMGYT 311
                                       422.22222355555555699999999977443133344333222247776433466888888...47********* PP

                                       TTHHHHHHHHHHHHHH CS
                               DAO 336 ghGltlapatGkllae 351
                                        +G+ +a+ +G l+ae
  gi|385806362|ref|YP_005842760.1| 312 FRGVDFAMYSGYLAAE 327
                                       ************9998 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.0   5.5e-13   6.1e-10       2     118 ..       8     167 ..       7     201 .. 0.83

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 5.5e-13
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEE....TTHCHHHCSHHH....HCHHHHHHHHHHHHH............. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxx....xxxxxxxxxxxxxxx............. RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlve....legtclnggcll....skallgvaedaeias............. 57 
                                       d +v+GgGpAG +aa +la++g++++l+e     +   ++gg ++    +k + +++++a i +             
  gi|385806362|ref|YP_005842760.1|   8 DAIVVGGGPAGATAAYFLAKKGYNTLLLErgkrYGSKNVYGGKIYsyyvKKLFPEFEKEAPIQRwvnrerysitynd 84 
                                       789*************************988887777788888885555566666666666666************* PP

                                       ...........................HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE-- CS
                                       ...........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  58 ...........................evvkklnqgielllgeevvkidpgkkkvklekkkegdeekiaydklvlAt 107
                                                                  ++    +qg +++ ++++++++++  k++     e  eek+++d  ++A 
  gi|385806362|ref|YP_005842760.1|  85 savtfeyfspqapsftaylsdftnwlcKK--AEQQGATVISESKATGLIREGDKIVGI---EAGEEKVKADVTIIAE 156
                                       ************************87632..3456788888888*****999888884...46689*********** PP

                                       -EEE-BCTCTT CS
                                       xxxxxxxxxxx RF
                       Pyr_redox_2 108 GssprdlgipG 118
                                       G++  +l   G
  gi|385806362|ref|YP_005842760.1| 157 GANRILLEKAG 167
                                       **988875555 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.1   5.3e-09   5.9e-06       2      43 ..       8      49 ..       7      50 .. 0.92
   2 !   10.1   0.0   0.00021      0.24     112     164 ..     107     158 ..      56     161 .. 0.92

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 5.3e-09
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHHHCG CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrKilisG 43
                                      d iv+GgG+AG  aA  +ak+g ++llle++k+ g+K    G
  gi|385806362|ref|YP_005842760.1|  8 DAIVVGGGPAGATAAYFLAKKGYNTLLLERGKRYGSKNVYGG 49
                                      89**********************************976655 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00021
                                       HHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE---- CS
                       HI0933_like 112 vdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGG 164
                                        + l k+++++g ++  e++ +++ +e d+++ +++ +ee+++ad +++A G 
  gi|385806362|ref|YP_005842760.1| 107 TNWLCKKAEQQGATVISESKATGLIREGDKIVGIEA-GEEKVKADVTIIAEGA 158
                                       678999******************************.*************996 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.1   1.8e-09   2.1e-06       1      38 [.       8      45 ..       8      50 .. 0.92
   2 !    8.3   0.0   0.00093         1     147     193 ..     110     156 ..     105     214 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 1.8e-09
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGG CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggat 38
                                      D+iV+G+G AG +AA+ +a++G +++++e +++ g+  
  gi|385806362|ref|YP_005842760.1|  8 DAIVVGGGPAGATAAYFLAKKGYNTLLLERGKRYGSKN 45
                                      89*****************************9988865 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00093
                                       HHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEES CS
                     FAD_binding_2 147 lvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirak 193
                                       l ++a++ g ++  + +a+ Li+e+++++G+++ +++ + +v+i a 
  gi|385806362|ref|YP_005842760.1| 110 LCKKAEQQGATVISESKATGLIREGDKIVGIEAGEEKVKADVTIIAE 156
                                       668899999**********************9998866666665554 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.0   1.1e-11   1.2e-08       1     140 [.       8     153 ..       8     167 .. 0.68

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 1.1e-11
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaee....qvvtgiareflerlrqrgga 73 
                                       D +VvGGgpaG +AA+  a++G ++lL+e+ ++ G     g+   +  ++ ++    +  +  ++++++r r   ++
  gi|385806362|ref|YP_005842760.1|   8 DAIVVGGGPAGATAAYFLAKKGYNTLLLERGKRYGSKNVYGG--KIYSYYVKKlfpeFEKEAPIQRWVNRERYSITY 82 
                                       779**************************9887775555444..444444333223222222233333333221111 PP

                      FAD_oxidored  74 rlkkrskwn........tfepevakavleeml....aeagvtvllntrlvevekegkriesvtveskegrktirAkv 138
                                           + + +        +   +++ + + ++l    +++g tv+ ++++++ ++eg++i ++++    g+++++A+v
  gi|385806362|ref|YP_005842760.1|  83 ----NDSAVtfeyfspqAPSFTAYLSDFTNWLckkaEQQGATVISESKATGLIREGDKIVGIEA----GEEKVKADV 151
                                       ....11111122333225666677777888889998889*****************9******9....578888888 PP

                      FAD_oxidored 139 fi 140
                                       +i
  gi|385806362|ref|YP_005842760.1| 152 TI 153
                                       87 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 !   31.7   0.0   1.2e-10   1.3e-07       1      38 [.      11      54 ..      11      75 .. 0.83

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 1.2e-10
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSS......GGG-EE CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlG......Graasy 38
                                      +vG+G +G++aAy+Lak+g++ llle++ r G      G+++sy
  gi|385806362|ref|YP_005842760.1| 11 VVGGGPAGATAAYFLAKKGYNTLLLERGKRYGsknvygGKIYSY 54
                                      8***************************9998555555666555 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   4.3e-10   4.9e-07      16      68 ..       5      56 ..       1      88 [. 0.86

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 4.3e-10
                                      TEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTBSEEE CS
                              Thi4 16 aesDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlfsaiv 68
                                       + D ++vG+G++G taay lakk + ++++ler   +G     GG+++s+ v
  gi|385806362|ref|YP_005842760.1|  5 LDFDAIVVGGGPAGATAAYFLAKK-GYNTLLLERGKRYGSKNVYGGKIYSYYV 56
                                      56799*******************.************************9976 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   3.1e-08   3.5e-05       2      33 ..       7      38 ..       6      45 .. 0.92
   2 ?    4.1   0.0     0.021        23     105     174 ..     104     168 ..      63     191 .. 0.84
   3 ?   -2.7   0.0       2.4   2.7e+03     256     292 ..     265     301 ..     252     302 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 3.1e-08
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekr 33
                                       d ++VG+GpaG+++a +L+++G +++l+e+ 
  gi|385806362|ref|YP_005842760.1|  7 FDAIVVGGGPAGATAAYFLAKKGYNTLLLERG 38
                                      5889**************************96 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.021
                                       HHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE--GTT-HHHHHHTG CS
                     FAD_binding_3 105 teleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrakYlvGaDGgrStvrktlgi 174
                                       +++++ L ++ae++g++v  + + ++l +++++    + + e+gee +v+a+ ++ a+G++ +  +++g+
  gi|385806362|ref|YP_005842760.1| 104 SDFTNWLCKKAEQQGATVISESKATGLIREGDK----IVGIEAGEE-KVKADVTIIAEGANRILLEKAGL 168
                                       678999*********99999999999****999....677788888.9**********999887777776 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 2.4
                                       HTTSSCEEEEEEEEEEEEEEEEESSSEETTEEE-GGG CS
                     FAD_binding_3 256 vgektldveieevsawtvaqrvaekyrkgrvflaGDA 292
                                        ++ ++       ++++v++++ ek++ +  +++GDA
  gi|385806362|ref|YP_005842760.1| 265 LKDGEIVEYAAHLTVVDVESFIPEKLSGNGYMIIGDA 301
                                       555555566667888999999999999999******9 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   2.5   4.6e-08   5.1e-05       1     150 [.       8     158 ..       8     193 .. 0.73
   2 ?   -1.9   0.0       1.2   1.4e+03      48      81 ..     233     266 ..     225     288 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 4.6e-08
                                       CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT--SSSSEEE-TTHHHHHHHHHHHT-SHHHHHHHHEEEEEEE CS
                              GIDA   1 dviViGgGhAGceAAlaaarlGakvlLithkldtiaelsCnpsiggiakgllvrEidalggliikaadkagiqfril 77 
                                       d iV+GgG AG  AA+ +a++G+++lL+        + ++   i++  + +l  E ++ +  i ++ ++ +  +   
  gi|385806362|ref|YP_005842760.1|   8 DAIVVGGGPAGATAAYFLAKKGYNTLLLERGKRYGSKNVYGGKIYSYYVKKLFPEFEK-EAPIQRWVNRERYSITYN 83 
                                       579*************************776666667777777777777777777777.666666666666544443 PP

                                       STT...S-CCC-EEEEEE-HHHHHHHHHHHHHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT CS
                              GIDA  78 Nrs...kGpavralraqvdrelyskevteklenepnleiieeeveeliveekkvkgvvtedgetikakavviatGt 150
                                        +      ++ +a+   +  + + +++ +k e++    i e +++ li e +k+ g+    +e++ka++++ia G+
  gi|385806362|ref|YP_005842760.1|  84 DSAvtfEYFSPQAPSFTAYLSDFTNWLCKKAEQQGATVISESKATGLIREGDKIVGIEA-GEEKVKADVTIIAEGA 158
                                       32211234666777777777888888888888888888888888888887788888754.5567788888888887 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.2
                                       THHHHHHHHHHHT-SHHHHHHHHEEEEEEESTTS CS
                              GIDA  48 akgllvrEidalggliikaadkagiqfrilNrsk 81 
                                       a+ +l + id ++  i ++a+k +i+  + N  k
  gi|385806362|ref|YP_005842760.1| 233 AVVTLGTAIDSINEHIYNFAEKLRIHPVMRNLLK 266
                                       7778889999999999999999999988888655 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.3   0.00082      0.91       3      22 ..      10      29 ..       8      40 .. 0.83
   2 !   14.9   0.0   7.8e-06    0.0088     129     217 ..      73     166 ..      39     173 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00082
                                      EEE--SHHHHHHHHHHHHHT CS
                    Trp_halogenase  3 vivGGGtaGwlaAaalakal 22
                                      ++vGGG+aG +aA  lak +
  gi|385806362|ref|YP_005842760.1| 10 IVVGGGPAGATAAYFLAKKG 29
                                      79***************988 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 7.8e-06
                                       HHHTTB-SB-TT......S-B-S--EEEE-HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE CS
                    Trp_halogenase 129 akakkfsprekd......glsalsyAyhldaalyakfLrrvaearGvtrvegkvvevqldedgrveslrledgreve 199
                                       +++++ s + +d      + s  + ++    + + ++L + ae++G t+++   ++  ++e +++ +++   +++v+
  gi|385806362|ref|YP_005842760.1|  73 VNRERYSITYNDsavtfeYFSPQAPSFTAYLSDFTNWLCKKAEQQGATVISESKATGLIREGDKIVGIEA-GEEKVK 148
                                       444555555555444444667777788888899***********************************99.6677** PP

                                       -SEEEE-SGGG-IIIIII CS
                    Trp_halogenase 200 adlfiDcsGfrgllieqa 217
                                       ad  i + G +++l+e+a
  gi|385806362|ref|YP_005842760.1| 149 ADVTIIAEGANRILLEKA 166
                                       ****************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 !   14.8   0.0   2.8e-05     0.032       2      48 ..       9      57 ..       8      88 .. 0.80
   2 ?    4.1   0.0     0.061        69      41      76 ..     105     140 ..      97     145 .. 0.87
   3 ?   -0.3   0.0       1.4   1.6e+03      23      50 ..     359     386 ..     349     413 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.8e-05
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS..TTSSHHHHHHHHH CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll..rllDeeaskilqe 48
                                      ++vvGgG  g  +A +la+ g ++ ++er+++    ++++ ++ ++  +
  gi|385806362|ref|YP_005842760.1|  9 AIVVGGGPAGATAAYFLAKKGYNTLLLERGKRYGskNVYGGKIYSYYVK 57
                                      58****************************9998555555544444444 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.061
                                       HHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEE CS
                         Pyr_redox  41 easkilqeklekngievllntkveeiegsedgvesv 76 
                                       ++ ++l +k e++g +v+ ++k++ +  ++d++ ++
  gi|385806362|ref|YP_005842760.1| 105 DFTNWLCKKAEQQGATVISESKATGLIREGDKIVGI 140
                                       778999********************9999995555 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.4
                                       SEEEEEESSSSSSTTSSHHHHHHHHHHH CS
                         Pyr_redox  23 kkVtvversdkllrllDeeaskilqekl 50 
                                        kV+ v+ ++kll  +++ +s++++ k+
  gi|385806362|ref|YP_005842760.1| 359 RKVHEVVKNPKLLTSYPKLLSDLMASKF 386
                                       4888899999999999999999888776 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 !   19.9   0.5   3.3e-07   0.00037       1     133 [.      10     157 ..      10     161 .. 0.63

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 3.3e-07
                       Pyr_redox_3   1 iIiGaGPaGlaaaielkkagledylilEkgn.......ignsiyrypkemtf..ispsftsekleipdlnaiseets 68 
                                       i++G+GPaG +aa+ l k+g  + l lE+g+        g  iy y+ ++ f  + ++ + +++   +  +i+ + s
  gi|385806362|ref|YP_005842760.1|  10 IVVGGGPAGATAAYFLAKKGY-NTLLLERGKrygsknvYGGKIYSYYVKKLFpeFEKEAPIQRWVNRERYSITYNDS 85 
                                       89*******************.689***9952222222345688888888876666666777777777777776666 PP

                       Pyr_redox_3  69 pafslkeeklsrkealeYlr.......evaksfelpiklfeeVesvkke.degfevetsketyeAkkviiAtG 133
                                        a++++   +++  +  Yl+       + a+++   +  +++ + + +e d+   +e+ +e+++A+  iiA G
  gi|385806362|ref|YP_005842760.1|  86 -AVTFEYFSPQAPSFTAYLSdftnwlcKKAEQQGATVISESKATGLIREgDKIVGIEAGEEKVKADVTIIAEG 157
                                       .445554444444444444300000004455666666666666666554145566777777777777777776 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 !   18.8   0.3   1.1e-06    0.0013       2     154 ..      11     157 ..      10     159 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.1e-06
                     NAD_binding_9   2 ivGaGprGlavlerLlarakkkspleitlfdp.sepgagrvwrtdqseelllNvpasemslftddpptfaeWlrerg 77 
                                       +vG+Gp+G++++  L+++       +  l ++ + +g++ v+  +        + ++++ +  +++   ++W+++++
  gi|385806362|ref|YP_005842760.1|  11 VVGGGPAGATAAYFLAKK-----GYNTLLLERgKRYGSKNVYGGKI-----YSYYVKKLFPEFEKEAPIQRWVNRER 77 
                                       89*********9999999.....4888999**7777*999999994.....33344444444456789********9 PP

                     NAD_binding_9  78 a....leeaeeldpddfvpRa.lyGrYlrdlfeellarlpegvtvevhraevvdleeradgqavlladgaslaadaV 149
                                            +    +++ + f p a  + +Yl+d+ + l+++++++    + +++++ l +++d+   ++a++++++ad  
  gi|385806362|ref|YP_005842760.1|  78 YsityN--DSAVTFEYFSPQApSFTAYLSDFTNWLCKKAEQQGATVISESKATGLIREGDKIVGIEAGEEKVKADVT 152
                                       986532..345555555555438****************99888888899***********99999999******** PP

                     NAD_binding_9 150 vLAlG 154
                                       ++A G
  gi|385806362|ref|YP_005842760.1| 153 IIAEG 157
                                       **988 PP

>> GMC_oxred_N  GMC oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.4   0.0    0.0093        10       1      40 [.       7      45 ..       7      78 .. 0.76
   2 !   11.9   0.0   9.4e-05      0.11     196     254 ..     107     156 ..     102     201 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0093
                       GMC_oxred_N  1 vdelveggGsagsvvAaRLsedpstsvlvleaggreknrl 40
                                      +d++v+ggG ag++ A+ L++++ +++ +le g r+ +++
  gi|385806362|ref|YP_005842760.1|  7 FDAIVVGGGPAGATAAYFLAKKGYNTL-LLERGKRYGSKN 45
                                      699***********9999998887765.677777766555 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 9.4e-05
                       GMC_oxred_N 196 rawLrpalerpnleiltgakaekiilegrkkravGVeasdkkgtvkrlvvaakevvvaa 254
                                       ++wL +  e+++++++++ ka+ +i e  ++++vG+ea ++k ++  +++a        
  gi|385806362|ref|YP_005842760.1| 107 TNWLCKKAEQQGATVISESKATGLIRE--GDKIVGIEAGEEKVKADVTIIA-------E 156
                                       68**********************878..*********9998884444443.......3 PP

>> DUF2106  Predicted membrane protein (DUF2106)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0    0.0004      0.45      78     118 ..      89     131 ..      53     137 .. 0.82
   2 ?    4.1   0.1     0.028        32      98     134 ..     285     321 ..     267     327 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0004
                           DUF2106  78 yPenepalGlvtayltPlsellaettlylGttivss..PGGii 118
                                       +  ++p++   tayl+ ++++l +++   G+t++s+    G+i
  gi|385806362|ref|YP_005842760.1|  89 FEYFSPQAPSFTAYLSDFTNWLCKKAEQQGATVISEskATGLI 131
                                       5568999999***********************9851145666 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.028
                           DUF2106  98 llaettlylGttivssPGGiideilyytrGldtvles 134
                                       ++ e+ +  G  i+   GG++ ++ y  rG+d  + s
  gi|385806362|ref|YP_005842760.1| 285 FIPEKLSGNGYMIIGDAGGLLANMGYTFRGVDFAMYS 321
                                       556666667889********************77655 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00031      0.35       1      36 [.       8      41 ..       8     188 .. 0.77
   2 ?   -1.8   0.0       1.1   1.2e+03      36      94 ..     332     387 ..     310     413 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00031
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieaspsl 36
                                      D +v+G+GpAg   A  l  ak+g + +l+e ++  
  gi|385806362|ref|YP_005842760.1|  8 DAIVVGGGPAGATAAYFL--AKKGYNTLLLERGKRY 41
                                      789***************..**********998766 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.1
                     Lycopene_cycl  36 llfpnnyvWsdefedlgaleecvehsWsgtivylddgkkillgraYgrvsskrlkeell 94 
                                       + + n+ +W  +++ +    ++ e   +   v+   ++++ll+  Y ++ s+ ++++ +
  gi|385806362|ref|YP_005842760.1| 332 I-RNNKESWNAFDSMVR-SSSMFEEIMRYRKVHEVVKNPKLLT-SYPKLLSDLMASKFH 387
                                       3.444558888887777.6777777777777777777777777.787777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      612  (0.0341346); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.77u 0.36s 00:00:01.12 Elapsed: 00:00:00.53
# Mc/sec: 2393.75
//
Query:       gi|385806363|ref|YP_005842761.1|  [L=386]
Description: acyl-CoA dehydrogenase family protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-46  158.8   0.1    1.6e-46  158.3   0.1    1.2  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    3.7e-26   91.1   0.0    6.3e-26   90.4   0.0    1.4  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    4.8e-18   65.7   0.0      7e-18   65.2   0.0    1.2  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
    8.2e-16   58.7   0.0    1.4e-15   57.9   0.0    1.4  1  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.3   0.1   3.5e-50   1.6e-46       1     149 [.     235     383 ..     235     384 .. 0.99

  Alignments for each domain:
  == domain 1  score: 158.3 bits;  conditional E-value: 3.5e-50
                                       TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH- CS
                     Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaea 77 
                                       ++Gf++am++l+ +R++    +lg+ +rale +l++a++r +f++p++d++ +++kla+m+a++ aa +l+y++ ++
  gi|385806363|ref|YP_005842761.1| 235 NEGFKIAMKSLDIGRIGASSISLGISKRALEVSLSFAKSRVQFNQPIADFEGIQFKLADMYAKMKAAEALTYHVSYM 311
                                       79*************************************************************************** PP

                                       -------HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHHH CS
                     Acyl-CoA_dh_1  78 ldagkpdraeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarrl 149
                                       ld+g+ ++ +++ aKlf se++++++++a+q++Gg Gy ++ +verlyrdar+l+igeGtseiq+ iiar l
  gi|385806363|ref|YP_005842761.1| 312 LDRGRAEPSDIATAKLFSSEAVNYIVSEALQIFGGFGYIRGAEVERLYRDARILSIGEGTSEIQKIIIARKL 383
                                       **********************************************************************87 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.4   0.0   1.4e-29   6.3e-26       1      97 []     128     223 ..     128     223 .. 0.93

  Alignments for each domain:
  == domain 1  score: 90.4 bits;  conditional E-value: 1.4e-29
                                       EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS---.----EEEEEEE..GGGEEE- CS
                     Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpd.rarglslflvprdapgvsvr 76 
                                       afal EpqaGsdv s++t+a+++ g +y++nGeK++itna i+++++++a+ ++p+ +++gls f+++++++gv+++
  gi|385806363|ref|YP_005842761.1| 128 AFALAEPQAGSDVSSIRTNAVKKGG-KYIINGEKRFITNAYISDYLILFAK-TDPErGNKGLSAFIIDSKRQGVKIS 202
                                       79****************7766555.9************************.555568******************* PP

                                       ----BSS-TTS-EEEEEEE.. CS
                     Acyl-CoA_dh_M  77 rieeklGlrglptgelvfedv 97 
                                       + ++k+G+rg+p +++ f+dv
  gi|385806363|ref|YP_005842761.1| 203 EPQPKMGMRGAPVSQISFKDV 223
                                       *******************97 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.2   0.0   1.6e-21     7e-18       2     128 ..     251     367 ..     250     373 .. 0.92

  Alignments for each domain:
  == domain 1  score: 65.2 bits;  conditional E-value: 1.6e-21
                                       HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HH CS
                     Acyl-CoA_dh_2   2 giaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtve 78 
                                       g + + lG+ ++al+  +++a+ rv+  +++++ad++ +q++la++ a+++AA+al++++ +      ++g++    
  gi|385806363|ref|YP_005842761.1| 251 GASSISLGISKRALEVSLSFAKSRVQ--FNQPIADFEGIQFKLADMYAKMKAAEALTYHVSYM----LDRGRA---- 317
                                       678899********************..**********************************9....677766.... PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHCT CS
                     Acyl-CoA_dh_2  79 draearraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaaa 128
                                       +  ++++a+++ +e    +v+++ +++Gg ++   ++++Rl+RDa+++++
  gi|385806363|ref|YP_005842761.1| 318 EPSDIATAKLFSSEAVNYIVSEALQIFGGFGYIRGAEVERLYRDARILSI 367
                                       35788999999999999*****************************9875 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.9   0.0   3.1e-19   1.4e-15      20     111 ..      31     123 ..      13     125 .. 0.80

  Alignments for each domain:
  == domain 1  score: 57.9 bits;  conditional E-value: 3.1e-19
                                       HHHHHHHHHHTSGH..HHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHHHHHHHHHHHTTHHHHH CS
                     Acyl-CoA_dh_N  20 aphaaewdeegefp..relwkklaelGllgitvpeeygGagldyleaaivaeelaradaglalllgvhsslvapail 94 
                                       + +  e+de++ +   +  + kl+e  llgi vpe ygG+gld+ +   ++eel+r+++++a ++ +h    +  il
  gi|385806363|ref|YP_005842761.1|  31 RRYSMEVDEKEDYNlvKRNLLKLGEDKLLGIFVPESYGGRGLDFRAFSFFTEELSRHCTSTAFSYIAHILS-ISSIL 106
                                       456777886665443244599****************************************9988887644.469** PP

                                       HHS-HHHHHHHHHHHHT CS
                     Acyl-CoA_dh_N  95 rfGteeqkrryLpklas 111
                                         G+eeqkr+ Lp + +
  gi|385806363|ref|YP_005842761.1| 107 FGGSEEQKRELLPVMSR 123
                                       *************8865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.52
# Mc/sec: 2223.32
//
Query:       gi|385806364|ref|YP_005842762.1|  [L=270]
Description: electron transfer flavoprotein subunit beta [Fervidicoccus fontis Kam940]
Scores for complete 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-41  141.3   2.6    3.5e-41  141.1   2.6    1.1  1  ETF       Electron transfer flavoprotein domain


Domain annotation for each model (and alignments):
>> ETF  Electron transfer flavoprotein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.1   2.6   1.9e-45   3.5e-41       2     181 ..      32     216 ..      31     217 .. 0.94

  Alignments for each domain:
  == domain 1  score: 141.1 bits;  conditional E-value: 1.9e-45
                                       EEEE-EC.CCCE-HHHHHHHHHHHHHHHHHT--EEEEEEES....S-CHHHHHHCT-SEEEEEE-GGGSS--CCHHH CS
                               ETF   2 lvlaehgvdgklnpvdlealeaArrlkekaggevtavvvGppeaeealrealaamGadkvilvddpalagydaeata 78 
                                       +++++++ + ++np+dl+ale A ++kek +g+vt +++ pp a++al+e +a +G d++il++d+++ g+d++ata
  gi|385806364|ref|YP_005842762.1|  32 GTIERESSELVINPFDLHALEVAAQIKEKVNGTVTTISMAPPHAADALKESIA-RGSDRAILLSDRKFGGADTLATA 107
                                       57889999*********************99**********************.*********************** PP

                                       HHHHHHHHHC-.-SEEEEESSCC.H..HHHHHHHHHHCT-EEEEEESE.EEEETCCEEEEEECCCCTEEEEEE-TSS CS
                               ETF  79 kalaalikked.pdlvlagatai.g..kqvaprlAalLgvplitdvte.leveggkltvtRpieggnglaevveadl 150
                                       +ala +i+k++ pdl++ag++++ g  +qv+p +A++Lg+p++++v++ ++++++ + v+ + e+   +   ve++l
  gi|385806364|ref|YP_005842762.1| 108 YALASAIRKLGiPDLIVAGEKSVdGdtAQVPPLVAEMLGIPHASYVSKvIDIKEKAIEVITEQEA--PY--RVELRL 180
                                       **********66***********98***********************66667555888888888..55..8999** PP

                                       SEEEEE-TTSS--.....--S-TT---EEEE--HHH CS
                               ETF 151 pavltvrpgafep.....aaimaakkkeveevevad 181
                                       pa++ v++++ +p     +++ +akk e+e++++++
  gi|385806364|ref|YP_005842762.1| 181 PALIQVTKEVAKPrvptlKDKLKAKKYEIEVWSADK 216
                                       ******************99*************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.55
# Mc/sec: 1484.29
//
Query:       gi|385806365|ref|YP_005842763.1|  [L=330]
Description: Electron transfer flavoprotein, alpha subunit-like protein [Fervidicoccus fontis Kam940]
Scores for complete 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-44  150.2   0.0    8.3e-44  149.6   0.0    1.2  1  ETF        Electron transfer flavoprotein domain
    1.2e-34  118.1   0.1    3.2e-34  116.8   0.0    1.7  2  ETF_alpha  Electron transfer flavoprotein FAD-binding domain


Domain annotation for each model (and alignments):
>> ETF  Electron transfer flavoprotein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.6   0.0   9.2e-48   8.3e-44       2     178 ..      10     184 ..       9     187 .. 0.96

  Alignments for each domain:
  == domain 1  score: 149.6 bits;  conditional E-value: 9.2e-48
                                       EEEE-EC.CCCE-HHHHHHHHHHHHHHHHHT--EEEEEEES....S-..CHHHHHHCT-SEEEEEE-GGGSS--CCH CS
                               ETF   2 lvlaehgvdgklnpvdlealeaArrlkekaggevtavvvGppeaeea..lrealaamGadkvilvddpalagydaea 76 
                                       +v+ae++ dg+++pv++e+l++Ar+l+ek+g +v a ++G     ++  l  +l  +Gad+v++vd+++l+ +d   
  gi|385806365|ref|YP_005842763.1|  10 MVFAEQH-DGVIHPVTFELLGKARELAEKKGSKVYAALLGY----NVgsLSSELIYYGADRVYVVDSEKLKVFDVMH 81 
                                       699***7.*********************************....5556**************************** PP

                                       HHHHHHHHHHHC--SEEEEESSCCHHHHHHHHHHHCT-EEEEEESEEEEETCC.EEEEEECCCCTEEEEEE-TSSSE CS
                               ETF  77 takalaalikkedpdlvlagataigkqvaprlAalLgvplitdvteleveggk.ltvtRpieggnglaevveadlpa 152
                                       + +a  ++i+k +p+ +l+gat +g+ +apr++a L+++l++d+t+l +++++  +++Rp+++gn++a++ + ++pa
  gi|385806365|ref|YP_005842763.1|  82 YKDAFLKVIEKAKPEAILMGATNTGRTLAPRISAALKTGLTADCTDLFIDEKGnFIQVRPAFSGNIFAHIGTKTKPA 158
                                       **********************************************88864446*********************** PP

                                       EEEE-TTSS----S-TT---EEEE-- CS
                               ETF 153 vltvrpgafepaaimaakkkeveeve 178
                                       ++tvr + f++ +++ ++k+eve+ve
  gi|385806365|ref|YP_005842763.1| 159 MATVRYRTFKAIEKDTSRKGEVEKVE 184
                                       ************************97 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 ?   -3.0   0.0      0.85   7.7e+03      56      66 ..     104     114 ..      97     117 .. 0.80
   2 !  116.8   0.0   3.6e-38   3.2e-34       1      84 []     204     287 ..     204     287 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.85
                                       SSS-----S-E CS
                         ETF_alpha  56 qtGktvaPkly 66 
                                        tG+t+aP++ 
  gi|385806365|ref|YP_005842763.1| 104 NTGRTLAPRIS 114
                                       58999999886 PP

  == domain 2  score: 116.8 bits;  conditional E-value: 3.6e-38
                                       .-TTT-S-EEEE-GGGSSGGGHHHHHHHHHHHT-EEEE-HHHHTTTSS-CCCB-SSSS-----S-EEEES----HHH CS
                         ETF_alpha   1 vdLeeakvvvsgGrGlkskenlelleelaealgaavgasRavvdagwipeerqvGqtGktvaPklyiavGisGaiqh 77 
                                       v++++a+v+v++G+Glk+ke+l+++e+la+ l+a+vgasR++vd++wi++++qvG +G++v+Pk+yia+GisG+ qh
  gi|385806365|ref|YP_005842763.1| 204 VNISDAEVIVAVGKGLKKKEDLKIIEDLAKLLNATVGASRPLVDDDWISRDHQVGFSGNIVKPKIYIAIGISGSPQH 280
                                       6899************************************************************************* PP

                                       HGGGTT- CS
                         ETF_alpha  78 laGmkes 84 
                                       ++Gmk+s
  gi|385806365|ref|YP_005842763.1| 281 TVGMKDS 287
                                       *****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2066.93
//
Query:       gi|385806366|ref|YP_005842764.1|  [L=92]
Description: hypothetical protein FFONT_1324 [Fervidicoccus fontis Kam940]
Scores for complete 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  124.6   2.7    1.4e-36  124.4   2.7    1.0  1  UPF0147   Uncharacterised protein family (UPF0147)
  ------ inclusion threshold ------
      0.033   14.4   1.0        4.3    7.7   0.2    2.2  2  UPF0253   Uncharacterised protein family (UPF0253)


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 !  124.4   2.7   1.5e-40   1.4e-36       1      81 []      10      90 ..      10      90 .. 0.99

  Alignments for each domain:
  == domain 1  score: 124.4 bits;  conditional E-value: 1.5e-40
                                      HHHHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHH CS
                           UPF0147  1 neekikevielLeeiiedtsvPrniRraakeakekLkdekeslavraataisiLdeisnDpnmPlhaRtliwevvskLE 79
                                      neekik++i +L+++++d svPrniRr+a++a++kLkd + s++vraa+ai++Ldeis+DpnmP+h+R++iw++vs LE
  gi|385806366|ref|YP_005842764.1| 10 NEEKIKNAIVMLTKVVNDVSVPRNIRRVATDAINKLKDPSLSPGVRAANAIQVLDEISQDPNMPVHTRITIWNIVSLLE 88
                                      689**************************************************************************** PP

                                      HH CS
                           UPF0147 80 ti 81
                                      t+
  gi|385806366|ref|YP_005842764.1| 89 TV 90
                                      97 PP

>> UPF0253  Uncharacterised protein family (UPF0253)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.2   0.00048       4.3      26      52 ..      13      39 ..       6      46 .. 0.86
   2 ?    5.6   0.0    0.0021        19      29      48 ..      58      77 ..      54      79 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00048
                           UPF0253 26 AiscalktLdevaanealpeevrekAA 52
                                       i+ a+  L +v+++ ++p+++r  A 
  gi|385806366|ref|YP_005842764.1| 13 KIKNAIVMLTKVVNDVSVPRNIRRVAT 39
                                      5889999****************8875 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0021
                           UPF0253 29 calktLdevaanealpeevr 48
                                       a+++Lde+ ++ ++p ++r
  gi|385806366|ref|YP_005842764.1| 58 NAIQVLDEISQDPNMPVHTR 77
                                      589************98877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 575.19
//
Query:       gi|385806367|ref|YP_005842765.1|  [L=466]
Description: citrate transporter [Fervidicoccus fontis Kam940]
Scores for 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   87.4  62.0    6.5e-23   81.4  37.1    1.9  2  CitMHS    Citrate transporter
  ------ inclusion threshold ------
       0.26   10.6  42.2        0.5    9.7  21.5    2.8  3  DUF1646   Protein of unknown function (DUF1646)


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 !   81.4  37.1   7.2e-27   6.5e-23      10     299 ..      51     397 ..      35     399 .. 0.72
   2 !   20.0  16.9   3.6e-08   0.00033      17     167 ..     283     457 ..     276     463 .. 0.68

  Alignments for each domain:
  == domain 1  score: 81.4 bits;  conditional E-value: 7.2e-27
                                       xxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                            CitMHS  10 rldvvallvlvll...vltieealsgiaspiillllgamiigaaleetGlfdrlaakllrlaggkrd.llvllvllt 82 
                                       r +++ l +++l+   vl+i+  ++   ++++ l++++mi+++ lee  +fd+l+a+++  +  +++ +++ll ll+
  gi|385806367|ref|YP_005842765.1|  51 RVAFAFLGITLLFvfnVLDIQHFINYSNIDVLTLIIAMMIVVGFLEEYKFFDWLTARIIVNFLDRPMvVIFLLLLLS 127
                                       4455555444444899*******************************************9999999*99999***** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxx RF
                            CitMHS  83 allsafvsndgvvlimipivlslakrlkklppllliplalaaniggaltpiGtpttraa..........arpglslp 149
                                       +++s++v+ ++ ++ m++i+++++k   ++p+ l i l++  n+g+++t iG+p+   +           ++ ++++
  gi|385806367|ref|YP_005842765.1| 128 FIMSSLVNEVASIIFMLAIAVRVCKYYEMNPIPLSIFLVFTTNLGSSATVIGNPIG--VliafkaglsfMDFMRWAF 202
                                       *******99****************99999999*********************33..2335555555544444444 PP

                                       xxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxx......xx RF
                            CitMHS 150 nllllalllvgl...........lplvllfmfgvalalpvnap.......kvkkqkaiieaiarsllpv......at 202
                                        + lla l++++                                      +vk+  +++++  ++l+ v      + 
  gi|385806367|ref|YP_005842765.1| 203 PISLLATLVTIAisryylegelkK------------------AktvkhpeEVKNEIKRMAKFHKKLI-VptivffG- 259
                                       444444444422222222222220..................1333333433333333333333333.22233331. PP

                                       xxxxx.............................................xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 203 illla.............................................ykkveWsvlllfaGvfllvgaleqtGi 234
                                           +                                              kkv+W  +l f  +f  vg le t +
  gi|385806367|ref|YP_005842765.1| 260 ----VilglalhhyieeylrletntmllgmsllgasaslfiahdraidivEKKVDWWSILYFLLLFASVGTLEYTHV 332
                                       ....13444455555555555555555555677777777777888888889*************************9 PP

                                       xxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 235 lealadllga...ggplvalalvlgliallsafisnvavaalmapialgmapalgllspsplalalav 299
                                       ++ + +++ +   g++l +++++ ++ ++++++++nv + a+++p++ ++  +++   + p+++a+++
  gi|385806367|ref|YP_005842765.1| 333 SDIITSAVMSvtkGNILYIMLILSAVAGAITSVMDNVLAIAIVIPVIDSLKGVIN---VFPIWWAILF 397
                                       99999888455544555555666777777*****************999777777...9999999876 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 3.6e-08
                                       xxxxxx..........xxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                            CitMHS  17 lvlvll..........vltiee....alsgiaspiillllgamiigaaleetGlfdrlaakllrlaggkrd.llvll 78 
                                       l+++ll                    + + +++  il +l+++  ++ le t + d ++  ++++++g+   ++++l
  gi|385806367|ref|YP_005842765.1| 283 LGMSLLgasaslfiahD----RaidiVEKKVDWWSILYFLLLFASVGTLEYTHVSDIITSAVMSVTKGNILyIMLIL 355
                                       44444444444533331....23333446677777899999999999999999999999999999999988889999 PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                            CitMHS  79 vlltallsafvsndgvvlimipivlslakrlkklppllliplalaaniggaltpiGtpttraaarpglslpnlll.. 153
                                       +++++ ++++++n+ +++i+ip++ sl   ++ +p+    ++ +a    g +t+iG               n+++  
  gi|385806367|ref|YP_005842765.1| 356 SAVAGAITSVMDNVLAIAIVIPVIDSLKGVINVFPIWW--AILFAGTYWGNATLIGST------------ANIVMag 418
                                       99999999999999999999999999988877777775..355666665669999988............7777766 PP

                                       .........................xxxxxxxxxxxxxx RF
                            CitMHS 154 .........................lalllvgllplvll 167
                                                                ++ +++++l+++ll
  gi|385806367|ref|YP_005842765.1| 419 ymdklkkrgelersvgmwewikigvPVSAITFFLAFLLL 457
                                       667777777777766666666655433344444444444 PP

>> DUF1646  Protein of unknown function (DUF1646)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7  21.5   5.6e-05       0.5      26     254 ..      51     275 ..      26     292 .. 0.63
   2 ?   -5.3  10.3         2   1.8e+04      18     132 ..     267     381 ..     251     388 .. 0.63
   3 ?    6.6  11.1   0.00047       4.2     257     345 ..     345     458 ..     318     460 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 5.6e-05
                           DUF1646  26 elfllimgvaavtvsglfslelliealktplailevgaipigitqavllaGlvfellkk.klkslla..evldklal 99 
                                        + +  +g+  ++v ++  ++ +            + +  i ++  ++++ +v+ +l++ k+   l+    ++ l +
  gi|385806367|ref|YP_005842765.1|  51 RVAFAFLGITLLFVFNVLDIQHF------------INYSNIDVLTLIIAMMIVVGFLEEyKFFDWLTarIIVNFLDR 115
                                       44444444444444444433333............333344444444444444443333133333320033455666 PP

                           DUF1646 100 kvfvfllivilG.lassvisaivaavilaei.vallplerkekvklvviasfaiGlGaaltPvGePlstiavsklne 174
                                       +++v+ l+++l  ++ss++  + + + +  i v + +    + + l ++  f+  lG++ t +G+P+  ++  k   
  gi|385806367|ref|YP_005842765.1| 116 PMVVIFLLLLLSfIMSSLVNEVASIIFMLAIaVRVCKYYEMNPIPLSIFLVFTTNLGSSATVIGNPIGVLIAFKAGL 192
                                       655554444554167777777666555555515667778889999******************************** PP

                           DUF1646 175 dflylidvlgeyiiiavlvlallaalslkrlskreelvevve.yeeelkev..liravkvfvfilalellGegfkPl 248
                                       +f+ +++  +   + a lv   ++ ++l+++ k+ ++v+++e  ++e+k++  + + + v   ++  ++lG +++  
  gi|385806367|ref|YP_005842765.1| 193 SFMDFMRWAFPISLLATLVTIAISRYYLEGELKKAKTVKHPEeVKNEIKRMakFHKKLIVPTIVFFGVILGLALHHY 269
                                       ***99999998888888888888999999999999999996515788998622455555666788888999888888 PP

                           DUF1646 249 ikayia 254
                                       i+ y+ 
  gi|385806367|ref|YP_005842765.1| 270 IEEYLR 275
                                       888875 PP

  == domain 2  score: -5.3 bits;  conditional E-value: 2
                           DUF1646  18 vrkveenl....elfllimgvaavtvsglfslelliealktplailevgaipigitqavllaGlvfellkkklksll 90 
                                        +++ee l    +++ll m++ ++  s   + +  i+++++++    + +      +    +G + ++  + + +  
  gi|385806367|ref|YP_005842765.1| 267 HHYIEEYLrletNTMLLGMSLLGASASLFIAHDRAIDIVEKKVDWWSILYFL----LLFASVGTLEYTHVSDIITSA 339
                                       3566665422213578888888888888888888888888888888554432....222234555454445555555 PP

                           DUF1646  91 aevldklalkvfvfllivilGlassvisaivaavilaeival 132
                                       +  + k  +  ++++l  + G ++sv+  ++a +i++ ++  
  gi|385806367|ref|YP_005842765.1| 340 VMSVTKGNILYIMLILSAVAGAITSVMDNVLAIAIVIPVIDS 381
                                       555556666667777778899999999999999888888765 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.00047
                           DUF1646 257 kseilywvnlisavvdnat......laaaeisPelteeq....irailmsllisG....GlliPGniPnivsaG... 316
                                       k +ily++ ++sav+   t      la a + P + + +    +  i  ++l +G      ++ G   niv+aG   
  gi|385806367|ref|YP_005842765.1| 345 KGNILYIMLILSAVAGAITsvmdnvLAIAIVIPVIDSLKgvinVFPIWWAILFAGtywgNATLIGSTANIVMAGymd 421
                                       45778887777776543332222227888888887654322113344556676652221568999********9444 PP

                           DUF1646 317 klk........ikskeWarvgvPlgiilliiyfivll 345
                                       klk        +++ eW+++gvP+++i++ + f++l+
  gi|385806367|ref|YP_005842765.1| 422 KLKkrgelersVGMWEWIKIGVPVSAITFFLAFLLLY 458
                                       333344444447899*************999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1226  (0.0683808); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.72u 0.36s 00:00:01.08 Elapsed: 00:00:00.54
# Mc/sec: 2596.27
//
Query:       gi|385806368|ref|YP_005842766.1|  [L=94]
Description: ArsR family transcriptional regulator [Fervidicoccus fontis Kam940]
Scores for 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   46.8   1.6    2.9e-12   46.3   0.1    2.0  3  HTH_5            Bacterial regulatory protein, arsR family
    0.00025   20.8   0.0    0.00067   19.5   0.0    1.6  2  TrmB             Sugar-specific transcriptional regulator Trm
    0.00053   19.8   0.0    0.00075   19.3   0.0    1.2  1  MarR_2           MarR family
     0.0037   17.3   0.0     0.0051   16.8   0.0    1.2  1  HTH_20           Helix-turn-helix domain
     0.0069   16.2   0.0      0.012   15.4   0.0    1.4  1  TFIIE_alpha      TFIIE alpha subunit
     0.0091   15.9   0.0      0.011   15.7   0.0    1.2  1  Phage_rep_org_N  N-terminal phage replisome organiser (Phage_
  ------ inclusion threshold ------
      0.022   14.7   0.1      0.046   13.7   0.1    1.6  2  HTH_45           Winged helix-turn-helix
      0.036   14.1   0.1      0.061   13.3   0.1    1.3  1  Cdc6_C           CDC6, C terminal winged helix domain
      0.037   14.1   0.1       0.15   12.1   0.0    1.9  2  DUF2250          Uncharacterized protein conserved in archaea
      0.059   13.5   0.0        0.1   12.7   0.0    1.4  1  DpnI_C           Dam-replacing HTH domain
      0.069   13.1   0.0       0.13   12.2   0.0    1.5  1  MarR             MarR family
      0.071   13.1   0.0      0.088   12.8   0.0    1.4  1  HTH_Crp_2        Crp-like helix-turn-helix domain
      0.075   12.9   0.0       0.15   11.9   0.0    1.6  1  HTH_IclR         IclR 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 ?   -3.0   0.0       5.1     7e+03      19      25 ..      14      20 ..      11      21 .. 0.68
   2 !   46.3   0.1   2.1e-15   2.9e-12       2      47 .]      26      71 ..      25      71 .. 0.97
   3 ?   -1.2   0.1       1.4   1.9e+03       8      21 ..      79      92 ..      79      94 .] 0.73

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 5.1
                                      HHHHHHH CS
                             HTH_5 19 celaeel 25
                                       e++++l
  gi|385806368|ref|YP_005842766.1| 14 NEISKIL 20
                                      5777776 PP

  == domain 2  score: 46.3 bits;  conditional E-value: 2.1e-15
                                      HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5  2 ptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                      p++lkIL+lL +g+l vc ++ +lgl q  +Sh Lk Lr++GL+e+
  gi|385806368|ref|YP_005842766.1| 26 PNKLKILFLLKNGPLPVCVISYILGLDQTLISHLLKTLRDLGLIEY 71
                                      99******************************************86 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.4
                                      HHHHTTSSEEHHHH CS
                             HTH_5  8 LklLaegelcvcel 21
                                      L++L++++ +v +l
  gi|385806368|ref|YP_005842766.1| 79 LYSLSDSSIKVLDL 92
                                      78888888777665 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       1.9   2.7e+03      32      47 ..       6      21 ..       4      24 .. 0.58
   2 !   19.5   0.0   4.9e-07   0.00067      17      64 ..      34      82 ..      31      86 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.9
                                      TTSSCHCHHHHHHHHH CS
                              TrmB 32 lgvprskvYevLrsLe 47
                                      ++vp  k +e+ + L 
  gi|385806368|ref|YP_005842766.1|  6 IEVPSEKLNEISKILR 21
                                      6677777666655554 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 4.9e-07
                                      HHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES.STTTEEEE CS
                              TrmB 17 LlklgpatadeiaeelgvprskvYevLrsLedkGlVerek.grpklYra 64
                                      Llk+gp+ +  i+ +lg++++ +   L+ L d Gl+e ++ g+ klY+ 
  gi|385806368|ref|YP_005842766.1| 34 LLKNGPLPVCVISYILGLDQTLISHLLKTLRDLGLIEYSRkGNFKLYSL 82
                                      9************************************887467888876 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   5.4e-07   0.00075       5      55 ..      26      73 ..      22      76 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 5.4e-07
                                      HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2  5 paqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                      p  + +L+ L ++p   l v  +   lgl++  +s +lk L + GL+e+++
  gi|385806368|ref|YP_005842766.1| 26 PNKLKILFLLKNGP---LPVCVISYILGLDQTLISHLLKTLRDLGLIEYSR 73
                                      56667889998888...9******************************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 !   16.8   0.0   3.7e-06    0.0051       4      60 ..      20      75 ..      17      76 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.7e-06
                                      HHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                            HTH_20  4 aeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                                      ++ +++P  ++il +L  +++l +  +   l+l+++ +s+ L++L++ gL+e  r g
  gi|385806368|ref|YP_005842766.1| 20 LRNIGEPNKLKILFLL-KNGPLPVCVISYILGLDQTLISHLLKTLRDLGLIEYSRKG 75
                                      55678999********.**************999999***************99876 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   8.9e-06     0.012       4      62 ..      17      74 ..      13      81 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.9e-06
                                      HHHHHHCS-HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEE CS
                       TFIIE_alpha  4 kevvrkfygeeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrr 62
                                        ++r++ + +  ++l+ L  +g +    ++  l++d++ + +lL  L++ +l++y r+
  gi|385806368|ref|YP_005842766.1| 17 SKILRNIGEPNKLKILFLLK-NGPLPVCVISYILGLDQTLISHLLKTLRDLGLIEYSRK 74
                                      67888998989999998766.9*99999****************************996 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 !   15.7   0.0     8e-06     0.011      38      96 ..      24      82 ..      13      89 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 8e-06
                   Phage_rep_org_N 38 GKlnenGelylsenipytaemlalifnreletvrlaLkvlkdlelieisedkvikiknw 96
                                      G  n+   l+l +n+p     ++ i+  +   +   Lk+l+dl+lie s ++ +k+  +
  gi|385806368|ref|YP_005842766.1| 24 GEPNKLKILFLLKNGPLPVCVISYILGLDQTLISHLLKTLRDLGLIEYSRKGNFKLYSL 82
                                      56666667999999*************************************99998765 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0      0.64   8.8e+02       8      26 ..      16      32 ..      11      36 .. 0.73
   2 ?   13.7   0.1   3.3e-05     0.046      10      60 ..      30      84 ..      28      94 .] 0.78

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.64
                            HTH_45  8 iadILeaisegeakkTkim 26
                                      i+ IL++i  ge +k ki+
  gi|385806368|ref|YP_005842766.1| 16 ISKILRNI--GEPNKLKIL 32
                                      78899988..777777775 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 3.3e-05
                            HTH_45 10 dILeaisegeakkTkimykanLsykllnkYLdmLvekgli....kkskekYvlTe 60
                                       IL  +++g      i y   L+  l++  L++L + gli    k + + Y+l +
  gi|385806368|ref|YP_005842766.1| 30 KILFLLKNGPLPVCVISYILGLDQTLISHLLKTLRDLGLIeysrKGNFKLYSLSD 84
                                      689999999999****************************544333445565555 PP

>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   4.4e-05     0.061      36      79 ..      50      87 ..      42      91 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.4e-05
                                      ---HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSSCH CS
                            Cdc6_C 36 pltqrevsdllseLemlgileleksskGrregrtrkisLnvdpd 79
                                       l+q+ +s+ll+ L +lg++e  +      +g+ +++sL+ ++ 
  gi|385806368|ref|YP_005842766.1| 50 GLDQTLISHLLKTLRDLGLIEYSR------KGNFKLYSLSDSSI 87
                                      689999****************74......59999999976655 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 ?    0.1   0.0      0.63   8.7e+02      31      50 ..       5      24 ..       2      30 .. 0.83
   2 ?   12.1   0.0   0.00011      0.15      28      61 ..      45      78 ..      23      88 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.63
                           DUF2250 31 eleipleevrellkkLeelG 50
                                      ++e+p e+ +e+ k L+++G
  gi|385806368|ref|YP_005842766.1|  5 KIEVPSEKLNEISKILRNIG 24
                                      57888999999999998887 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00011
                           DUF2250 28 iakeleipleevrellkkLeelGLlervegktik 61
                                      i+  l ++++ +++llk L++lGL+e+  +   k
  gi|385806368|ref|YP_005842766.1| 45 ISYILGLDQTLISHLLKTLRDLGLIEYSRKGNFK 78
                                      55667889999***************98876655 PP

>> DpnI_C  Dam-replacing HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   7.5e-05       0.1      47      69 ..      56      78 ..      53      79 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.5e-05
                                      HHHHHHHHHHTTSEEE-STTEEE CS
                            DpnI_C 47 irqqLqvlRDkglieFlgrGkYk 69
                                      i+  L++lRD glie+  +G++k
  gi|385806368|ref|YP_005842766.1| 56 ISHLLKTLRDLGLIEYSRKGNFK 78
                                      677799**************998 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   9.4e-05      0.13       4      51 ..      27      73 ..      25      76 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.4e-05
                                      HHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR  4 tqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsk 51
                                      + ++iL++l+ +gpl v  +   lg++++ ++ +l++L + Glie s+
  gi|385806368|ref|YP_005842766.1| 27 NKLKILFLLK-NGPLPVCVISYILGLDQTLISHLLKTLRDLGLIEYSR 73
                                      6678888886.49999999999**********************9776 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   6.4e-05     0.088      26      55 ..      44      74 ..      16      84 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.4e-05
                                      HHHHHTTSSHHHHHHHHHHHHHTTSEE.ETE CS
                         HTH_Crp_2 26 elAsmlGltretvsrilseLkreglis.rgr 55
                                       ++ +lGl +  +s +l+ L++ gli+  ++
  gi|385806368|ref|YP_005842766.1| 44 VISYILGLDQTLISHLLKTLRDLGLIEySRK 74
                                      678899*********************6343 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00011      0.15      16      50 ..      37      71 ..      29      73 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                                      BSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 16 pqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      +++l +  ++  +gl  +  ++lL+tL  lG++e+
  gi|385806368|ref|YP_005842766.1| 37 NGPLPVCVISYILGLDQTLISHLLKTLRDLGLIEY 71
                                      556667789999*********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.46u 0.33s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 597.95
//
Query:       gi|385806369|ref|YP_005842767.1|  [L=251]
Description: ABC transporter [Fervidicoccus fontis Kam940]
Scores for complete 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-35  120.8   0.0    8.2e-35  120.3   0.0    1.2  1  ABC_tran      ABC transporter
    6.2e-12   45.9   2.4    4.7e-05   23.4   0.1    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    8.9e-07   28.6   0.5      0.012   15.0   0.1    2.2  2  SMC_N         RecF/RecN/SMC N terminal domain
      2e-06   28.2   0.7    2.4e-05   24.6   0.7    2.0  1  AAA_22        AAA domain
    1.2e-05   25.2   0.5    0.00015   21.6   0.0    2.0  2  AAA_15        AAA ATPase domain
    5.9e-05   22.7   0.1    0.00014   21.5   0.1    1.6  1  AAA_29        P-loop containing region of AAA domain
    0.00015   21.7   0.3    0.00055   19.9   0.1    1.9  2  RsgA_GTPase   RsgA GTPase
    0.00072   20.1   0.0     0.0011   19.5   0.0    1.3  1  AAA_23        AAA domain
     0.0008   18.9   1.1     0.0044   16.5   0.2    2.0  2  TniB          Bacterial TniB protein
      0.002   17.0   1.0       0.01   14.7   0.2    2.1  2  ABC_ATPase    Predicted ATPase of the ABC class
     0.0033   17.8   0.2      0.014   15.8   0.2    1.9  1  AAA_16        AAA ATPase domain
      0.004   16.9   0.1      0.012   15.3   0.1    1.9  1  AAA_30        AAA domain
     0.0049   16.3   0.2     0.0088   15.5   0.2    1.3  1  HSM3_N        DNA mismatch repair protein HSM3, N terminal do
     0.0053   16.7   0.1      0.012   15.5   0.0    1.6  2  Rad17         Rad17 P-loop domain
     0.0094   15.7   0.3       0.48   10.1   0.0    2.2  2  IstB_IS21     IstB-like ATP binding protein
  ------ inclusion threshold ------
      0.013   15.4   0.1      0.027   14.4   0.1    1.7  1  ATPase_2      ATPase domain predominantly from Archaea
      0.015   14.7   0.0      0.022   14.1   0.0    1.4  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.021   14.5   0.0      0.038   13.6   0.0    1.4  1  AAA_27        AAA domain
      0.021   14.8   0.1       0.92    9.5   0.0    2.7  3  AAA_5         AAA domain (dynein-related subfamily)
      0.041   13.9   0.0       0.71    9.9   0.0    2.3  2  AAA_14        AAA domain
      0.045   13.9   0.0       0.14   12.3   0.0    1.8  1  AAA_33        AAA domain
      0.084   11.8   0.1       0.13   11.1   0.1    1.3  1  AAA_PrkA      PrkA AAA domain
      0.097   13.1   0.0       0.32   11.4   0.0    1.8  2  RNA_helicase  RNA helicase
      0.098   13.1   0.2       0.82   10.1   0.0    2.1  2  AAA           ATPase family associated with various cellular 
       0.12   12.3   0.0       0.25   11.2   0.0    1.5  1  NACHT         NACHT domain
       0.17   12.2   0.4       0.52   10.6   0.4    1.8  1  AAA_19        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 !  120.3   0.0   1.2e-37   8.2e-35       2     137 .]      21     167 ..      20     167 .. 0.98

  Alignments for each domain:
  == domain 1  score: 120.3 bits;  conditional E-value: 1.2e-37
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       + vsl++k+ge++ ++G+nGaGKStLl+++ g lkp+ G++ +d++++ e++++s+ k +g++pq+ + f  ++v++
  gi|385806369|ref|YP_005842767.1|  21 DGVSLHIKKGEVLCVIGPNGAGKSTLLRVINGILKPKIGTVYVDKRSIYEIPHKSAAKIFGYVPQKLHSFGMISVYD 97 
                                       789************************************************************************** PP

                                       H...............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       x...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n...............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                                       ++de++ kal+ +++++++++++    ++LSgG+ qrv +aral+ +p++l+lDEpt+
  gi|385806369|ref|YP_005842767.1|  98 FvmtgrkphiglvptkADDERVFKALKLVNMENFAERTL----EELSGGELQRVLIARALAGEPEVLILDEPTN 167
                                       ***************999999******************....******************************8 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.1   6.8e-08   4.7e-05       3      33 ..      34      63 ..      32     101 .. 0.65
   2 !   22.8   0.2     1e-07     7e-05     220     295 ..     122     194 ..      99     199 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 6.8e-08
                            AAA_21  3 vliGpNgsGKSnLLdaldllarldrdveglt 33
                                      ++iGpNg+GKS+LL+ + ++    + ++   
  gi|385806369|ref|YP_005842767.1| 34 CVIGPNGAGKSTLLRVINGILK-PKIGTVYV 63
                                      79***************99964.33333333 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 1e-07
                            AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQvilt 295
                                        + ++ +++  e+++ elS G ++   ++ al+  +    +l++DEp n+L+ k +++ll l+k ls++g  vi++
  gi|385806369|ref|YP_005842767.1| 122 ALKLVNMENFAERTLEELSGGELQRVLIARALAGEP---EVLILDEPTNNLDLKHQTELLNLVKVLSNEGLIVIMS 194
                                       677788999999**********99955555555544...9***************************988877776 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 !   15.0   0.1   1.8e-05     0.012       2      44 ..       2      50 ..       1      58 [. 0.69
   2 !   12.2   0.1   0.00013     0.089     134     199 ..     136     197 ..      58     215 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.8e-05
                                      EEEEEEESETTEECEEEEEE.....TTS.SEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxx.....xxx.xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  2 lkrleienFksyagktvilp.....fsk.sftaivGpNGSGKsnlldAi 44
                                      + ++e++++k y ++t+ ++     ++k ++ +++GpNG+GKs ll  i
  gi|385806369|ref|YP_005842767.1|  2 VIEIEVKDVKVYYKSTKAIDgvslhIKKgEVLCVIGPNGAGKSTLLRVI 50
                                      567888888888766655441111144325789***********99776 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00013
                                       TTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 134 kelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislre 199
                                        e+LSgGe + v +a  +A    +p+ + +lDe   +LD k+ +++ +l+k  s++  ++++sl++
  gi|385806369|ref|YP_005842767.1| 136 LEELSGGELQRVLIARALA---GEPE-VLILDEPTNNLDLKHQTELLNLVKVLSNEGLIVIMSLHD 197
                                       3489***988666665554...3444.679************************888888888765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.7   3.5e-08   2.4e-05       4     123 ..      29     190 ..      26     196 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 3.5e-08
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.....sskdllrellralglelka..... 70 
                                       +  +l+v+G+ G+GK+tllr +   l+        + ++v+v+  s       s ++++  + ++l+    +     
  gi|385806369|ref|YP_005842767.1|  29 KGEVLCVIGPNGAGKSTLLRVINGILKP-------KIGTVYVDKRSIYeiphkSAAKIFGYVPQKLH----Sfgmis 94 
                                       56789*******************9953.......55555444433333211124444444444444....334557 PP

                            AAA_22  71 .....................................erlsseell.ealeqalrarav...ielliiDEaqh.lr. 104
                                                                            ++ ++eel    l++ l ara    +e+li+DE  + l+ 
  gi|385806369|ref|YP_005842767.1|  95 vydfvmtgrkphiglvptkaddervfkalklvnmenfAERTLEELSgGELQRVLIARALagePEVLILDEPTNnLDl 171
                                       77888888888888888888888888999999999**9********9***********************9999*88 PP

                            AAA_22 105 ..seealeeLrsllnlsrkgv 123
                                         + e+l+ ++ l+n  + ++
  gi|385806369|ref|YP_005842767.1| 172 khQTELLNLVKVLSN--EGLI 190
                                       755999999999999..6655 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   2.2e-07   0.00015      13      64 ..      19      67 ..      14      90 .. 0.78
   2 ?    1.9   0.1      0.22   1.5e+02     323     355 ..     156     188 ..     145     198 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.2e-07
                            AAA_15 13 slkdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvikieked 64
                                      +++ v++++++  + ++iG+N++GKS++l++++ +l+ k      +++++k +
  gi|385806369|ref|YP_005842767.1| 19 AIDGVSLHIKKGeVLCVIGPNGAGKSTLLRVINGILKPK----IGTVYVDKRS 67
                                      56667888888889*******************999988....3444444444 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.22
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandn 355
                                       ++ +l+++EP ++L  ++q++l +l k l+n++
  gi|385806369|ref|YP_005842767.1| 156 EPEVLILDEPTNNLDLKHQTELLNLVKVLSNEG 188
                                       577899************************997 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.1     2e-07   0.00014      12      48 ..      20      56 ..      17      62 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2e-07
                            AAA_29 12 fdghtieidlkgatlltGpsGsGKSTllDAiqalLvp 48
                                      +dg +++i+  ++  ++Gp+G+GKSTll  i+ +L p
  gi|385806369|ref|YP_005842767.1| 20 IDGVSLHIKKGEVLCVIGPNGAGKSTLLRVINGILKP 56
                                      67889999966699*************9888777776 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1     8e-07   0.00055      77     130 ..       7      61 ..       2      67 .. 0.82
   2 ?   -0.6   0.0       1.6   1.1e+03      17      31 ..     187     201 ..     136     219 .. 0.55

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 8e-07
                                       SEEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                       RsgA_GTPase  77 yevllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpelelktgev 130
                                       ++ ++v  k++++++ ++ ++k+ ++ +++G+ G+GKStL+ ++++ l+ k+g v
  gi|385806369|ref|YP_005842767.1|   7 VKDVKVYYKSTKAIDGVSLHIKKgEVLCVIGPNGAGKSTLLRVINGILKPKIGTV 61 
                                       455556667778999999999988********************99888888876 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.6
                                       -EEEEEEESTTTT-- CS
                       RsgA_GTPase  17 dqllivvslkepels 31 
                                       + l++++sl++ +  
  gi|385806369|ref|YP_005842767.1| 187 EGLIVIMSLHDLTQA 201
                                       334455555544444 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.6e-06    0.0011      20      43 ..      31      54 ..       4      72 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.6e-06
                            AAA_23 20 gltlItGpNGaGKTTildAiklaL 43
                                       + +++GpNGaGK+T+l+ i  +L
  gi|385806369|ref|YP_005842767.1| 31 EVLCVIGPNGAGKSTLLRVINGIL 54
                                      57799*************998776 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.38   2.6e+02      37      53 ..      32      48 ..      24      56 .. 0.86
   2 !   16.5   0.2   6.3e-06    0.0044      78     157 ..     111     192 ..     107     204 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.38
                              TniB 37 nlllvGdsnnGKtmive 53
                                       l ++G+   GK+++++
  gi|385806369|ref|YP_005842767.1| 32 VLCVIGPNGAGKSTLLR 48
                                      5789**********986 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 6.3e-06
                              TniB  78 ppkpdekrlyaai....LealgaplkararvskleqqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLg 150
                                       p+k+d++r ++a+    +e++ +++ ++ +  +l++  ++   + +++vLi+DE  n l    ++q e+ln++k L+
  gi|385806369|ref|YP_005842767.1| 111 PTKADDERVFKALklvnMENFAERTLEELSGGELQRVLIARALAGEPEVLILDEPTNNL--DLKHQTELLNLVKVLS 185
                                       77888888888765444556666666666777788888888888899**********99..899************* PP

                              TniB 151 nelkipi 157
                                       ne  i i
  gi|385806369|ref|YP_005842767.1| 186 NEGLIVI 192
                                       *977655 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 !   14.7   0.2   1.5e-05      0.01     227     265 ..      10      51 ..       5      58 .. 0.85
   2 ?    0.5   0.0      0.29     2e+02     322     352 ..     138     168 ..     125     230 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.5e-05
                                       EEEEETTTEEEEEEE..E-SS.EEEEEE-TTSSHHHHHHHHH CS
                        ABC_ATPase 227 veielpngkkvsGmg..ipkG.vtlIvGggfhGKsTLLeAle 265
                                       v++  +++k++ G+   i+kG v  ++G++  GKsTLL+ ++
  gi|385806369|ref|YP_005842767.1|  10 VKVYYKSTKAIDGVSlhIKKGeVLCVIGPNGAGKSTLLRVIN 51 
                                       6777888999999653389*******************9886 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.29
                                       S--HHHHHHHHHHHHHHTT-SEEEEEGGGS- CS
                        ABC_ATPase 322 dASGStsqAanimealeagakllLiDEDtsA 352
                                       + SG   q + i++al  + ++l++DE t  
  gi|385806369|ref|YP_005842767.1| 138 ELSGGELQRVLIARALAGEPEVLILDEPTNN 168
                                       5566666667777777777777777775543 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   0.2     2e-05     0.014      23      52 ..      29      67 ..      16     192 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2e-05
                            AAA_16 23 rpelvllsGesGvGKsslvrellralekd.........g 52
                                       +e++ ++G+ G GKs+l+r +   l+ +          
  gi|385806369|ref|YP_005842767.1| 29 KGEVLCVIGPNGAGKSTLLRVINGILKPKigtvyvdkrS 67
                                      348899**************9997777775433333330 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   1.7e-05     0.012      17      46 ..      29      59 ..      21     194 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.7e-05
                            AAA_30 17 gdrvavltGpAGtGKttalkalreaweaa.g 46
                                      +  v ++ Gp G+GK+t+l++++ +++ + g
  gi|385806369|ref|YP_005842767.1| 29 KGEVLCVIGPNGAGKSTLLRVINGILKPKiG 59
                                      445999****************999987744 PP

>> HSM3_N  DNA mismatch repair protein HSM3, N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2   1.3e-05    0.0088      41     120 ..     148     226 ..     126     237 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.3e-05
                            HSM3_N  41 dakrllanikrllvenksedkldydlllelldklvkvssfedvlevysvddlvkalkseidslvvaackvieksyPk 117
                                        + r la    +l+ ++++++ld +   ell +lvkv s e ++ + s++dl++a + + + l +   kv++   P 
  gi|385806369|ref|YP_005842767.1| 148 LIARALAGEPEVLILDEPTNNLDLKHQTELL-NLVKVLSNEGLIVIMSLHDLTQAYRISDKVLLMNKGKVVAFGEPS 223
                                       567778888899999**************99.59*************************************999887 PP

                            HSM3_N 118 glf 120
                                        ++
  gi|385806369|ref|YP_005842767.1| 224 KVL 226
                                       665 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.8e-05     0.012      33      73 ..      18      58 ..       4     101 .. 0.88
   2 ?   -1.7   0.0       3.4   2.3e+03     106     147 ..     128     171 ..     108     201 .. 0.51

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.8e-05
                             Rad17 33 ewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgikl 73
                                      ++++  +L  +k ++L + GP G gkst ++v+  +l +k+
  gi|385806369|ref|YP_005842767.1| 18 KAIDGVSLHIKKGEVLCVIGPNGAGKSTLLRVINGILKPKI 58
                                      57788899999999******************999988876 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.4
                             Rad17 106 iesfkeleLkdakylklqk..lGddlrtdkklilvedlPnkfyr 147
                                       +e f e  L +     lq+      l ++ +++++++  n+   
  gi|385806369|ref|YP_005842767.1| 128 MENFAERTLEELSGGELQRvlIARALAGEPEVLILDEPTNNLDL 171
                                       55555555555444444431124455555555555554444433 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 !   10.1   0.0   0.00069      0.48      43      63 ..      26      46 ..       5      52 .. 0.79
   2 ?    3.7   0.1     0.066        45     106     148 ..     154     195 ..     122     209 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00069
                         IstB_IS21 43 fiekkenivllGpsGvGKshl 63
                                      +i+k e ++++Gp G+GKs l
  gi|385806369|ref|YP_005842767.1| 26 HIKKGEVLCVIGPNGAGKSTL 46
                                      6999**************987 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.066
                         IstB_IS21 106 llkvdllilDdlgllpldqaeaellfeviekryerrsiiitsn 148
                                         ++++lilD+  +++ld +++++l+++++   +   i+i s 
  gi|385806369|ref|YP_005842767.1| 154 AGEPEVLILDEP-TNNLDLKHQTELLNLVKVLSNEGLIVIMSL 195
                                       35679*****96.678999999999999999888888888775 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   3.9e-05     0.027      19      68 ..      29      77 ..      18     194 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.9e-05
                          ATPase_2 19 pneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldef 68
                                      + e++ + Gp g GK++Ll+ i    ++ +   +y+++ + ++i +++  
  gi|385806369|ref|YP_005842767.1| 29 KGEVLCVIGPNGAGKSTLLRVINGI-LKPKIGTVYVDKRSIYEIPHKSAA 77
                                      568999*************976555.5668899**999999988887665 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   3.2e-05     0.022      23     102 ..      31     110 ..       8     156 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.2e-05
                      Mg_chelatase  23 HnlllvGppGsGKtmlakrlpsllpplseeealevakiasvagkkeeekllkrrpfraphhsaskaalvGggskpkp 99 
                                         l ++Gp G+GK+ l + ++++l p   +  ++ ++i+ + +k++++     +   +    +s   +v  g+kp+ 
  gi|385806369|ref|YP_005842767.1|  31 EVLCVIGPNGAGKSTLLRVINGILKPKIGTVYVDKRSIYEIPHKSAAKIFGYVPQKLHSFGMISVYDFVMTGRKPHI 107
                                       56789*********************999999999999999885554443333333444455555556666666665 PP

                      Mg_chelatase 100 Gei 102
                                       G +
  gi|385806369|ref|YP_005842767.1| 108 GLV 110
                                       555 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   5.5e-05     0.038      24      49 ..      28      53 ..      19      55 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.5e-05
                            AAA_27 24 eeadlhliyGpNEAGKstalrAisdl 49
                                      ++ ++  ++GpN AGKst+lr i+ +
  gi|385806369|ref|YP_005842767.1| 28 KKGEVLCVIGPNGAGKSTLLRVINGI 53
                                      456677899***********998765 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 ?    9.5   0.0    0.0013      0.92       2      29 ..      33      60 ..      32      70 .. 0.81
   2 ?   -0.8   0.0         2   1.4e+03      64      74 ..     154     165 ..     127     190 .. 0.64
   3 ?    2.4   0.0      0.21   1.4e+02      37      72 ..     194     229 ..     148     243 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0013
                                      EEEE--SSSSHHHHHHHGGGGBS--EEE CS
                             AAA_5  2 vlLvGppGtgKselaerlaaalnrevey 29
                                      ++++Gp G gKs+l + +   l+ ++ +
  gi|385806369|ref|YP_005842767.1| 33 LCVIGPNGAGKSTLLRVINGILKPKIGT 60
                                      799*************999888655544 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2
                                       -.G-SEEEEESG CS
                             AAA_5  64 r.egeilvlDEv 74 
                                         e+e+l+lDE 
  gi|385806369|ref|YP_005842767.1| 154 AgEPEVLILDEP 165
                                       246677777763 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.21
                                       -HHHHH--B--.........--------G-SEEEEE CS
                             AAA_5  37 teedlkgrreikngttslvdsplvraaregeilvlD 72 
                                       +  dl++ ++i+++   + ++++v  ++ +++l+ D
  gi|385806369|ref|YP_005842767.1| 194 SLHDLTQAYRISDKVLLMNKGKVVAFGEPSKVLRAD 229
                                       445777777777777777777777666666666555 PP

>> AAA_14  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      0.71       2      39 ..      30      66 ..      29      92 .. 0.66
   2 ?    1.8   0.0      0.32   2.2e+02      40      76 ..     130     168 ..     116     236 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.001
                            AAA_14  2 rkilvitGaRrvGKTtllkqlikellvkkesilyinld 39
                                      +++l++ G+  +GK+tll+ + +  l +k  ++y++  
  gi|385806369|ref|YP_005842767.1| 30 GEVLCVIGPNGAGKSTLLRVI-NGILKPKIGTVYVDKR 66
                                      5799*************8655.4544233344444333 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.32
                            AAA_14  40 derdkkladpe..kllelilek.lkeekktylflDEiqev 76 
                                       +  +++l++ +  +l +++ ++ l + + ++l+lDE  + 
  gi|385806369|ref|YP_005842767.1| 130 NFAERTLEELSggELQRVLIARaLAG-EPEVLILDEPTNN 168
                                       33333333222345666666663445.8899999997665 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0    0.0002      0.14       1      19 [.      32      50 ..      32     209 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0002
                            AAA_33  1 lvllvGlpGsGKstlaerl 19
                                      ++ ++G++G+GKstl++ +
  gi|385806369|ref|YP_005842767.1| 32 VLCVIGPNGAGKSTLLRVI 50
                                      6789***********9865 PP

>> AAA_PrkA  PrkA AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1    0.0002      0.13      87     123 ..      29      67 ..       5      84 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0002
                          AAA_PrkA  87 rkqilyllGPvggGksslverlkklleaa..piyalegs 123
                                       + ++l ++GP g+Gks+l   +  +l+ +  ++y+ ++s
  gi|385806369|ref|YP_005842767.1|  29 KGEVLCVIGPNGAGKSTLLRVINGILKPKigTVYVDKRS 67 
                                       4479*******************9999887788876554 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00046      0.32       1      52 [.      33      87 ..      33      91 .. 0.68
   2 ?   -1.8   0.0       5.8     4e+03      51      86 ..     158     193 ..     152     210 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00046
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallkkl..klkkkdsvys.rnpeddfwdgYtgqev 52
                                      +++ Gp+g GKStl + +   l  k+   +  k s+y    ++     gY  q+ 
  gi|385806369|ref|YP_005842767.1| 33 LCVIGPNGAGKSTLLRVINGILKPKIgtVYVDKRSIYEiPHKSAAKIFGYVPQKL 87
                                      5899************955444444455445567777756666666677777665 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 5.8
                      RNA_helicase  51 evvvidDfgqvkdee.npsdlaelirlvsstpyplnm 86 
                                       ev++ d+ + ++ +  ++ +l +l+++ s+  +++ m
  gi|385806369|ref|YP_005842767.1| 158 EVLILDE-PTNNLDLkHQTELLNLVKVLSNEGLIVIM 193
                                       3444444.44444442444888888888887777766 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 ?   10.1   0.0    0.0012      0.82       1      25 [.      33      57 ..      33      94 .. 0.65
   2 ?    0.8   0.0      0.86   5.9e+02      49      66 ..     148     164 ..     117     208 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0012
                                      EEEESSTTSSHHHHHHHHHHHHTHE CS
                               AAA  1 vllyGppGtGKTllakavakelgve 25
                                      ++++Gp G GK++l + +   l+ +
  gi|385806369|ref|YP_005842767.1| 33 LCVIGPNGAGKSTLLRVINGILKPK 57
                                      589**************99998532 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.86
                                       HHHHHHHTS.TSEEEEEET CS
                               AAA  49 lfkeakeka.kpsilfiDE 66 
                                       l+  a++ a +p +l++DE
  gi|385806369|ref|YP_005842767.1| 148 LI--ARALAgEPEVLILDE 164
                                       33..344455689999998 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   0.00036      0.25       2      20 ..      32      50 ..      31      57 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00036
                                      CEEEEC-TTTCHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqkl 20
                                      ++++ G++G GK+tLl+ +
  gi|385806369|ref|YP_005842767.1| 32 VLCVIGPNGAGKSTLLRVI 50
                                      799*************977 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.4   0.00075      0.52       9     126 ..      29     182 ..      23     202 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00075
                            AAA_19   9 kekvllvtaGpGtGKTrvlkhivallv.elggvkpeeillvaftgrAakelrerlaalgaeatTiHrlal....... 77 
                                       k +vl+v+++ G GK+++l+ i  +l+ ++g+v +++  +    +++a ++   +       + +H++++       
  gi|385806369|ref|YP_005842767.1|  29 KGEVLCVIGPNGAGKSTLLRVINGILKpKIGTVYVDKRSIYEIPHKSAAKIFGYV------PQKLHSFGMisvydfv 99 
                                       57899***************99998873456666666666666666666655555......4455555555556666 PP

                            AAA_19  78 ..........................ldfddlltealelle.....eaeeekklqeee.llivDE.fqdvd.elqyr 120
                                                                 +++++  + +le l      +    + l  e  +li DE + ++d + q +
  gi|385806369|ref|YP_005842767.1| 100 mtgrkphiglvptkaddervfkalklVNMENFAERTLEELSggelqRVLIARALAGEPeVLILDEpTNNLDlKHQTE 176
                                       66666666666666666666655555222222222233333444443333344433334777777445667667777 PP

                            AAA_19 121 Llkall 126
                                       Ll+ ++
  gi|385806369|ref|YP_005842767.1| 177 LLNLVK 182
                                       766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.71u 0.36s 00:00:01.06 Elapsed: 00:00:00.55
# Mc/sec: 1382.78
//
Query:       gi|385806370|ref|YP_005842768.1|  [L=347]
Description: transport system permease [Fervidicoccus fontis Kam940]
Scores for complete 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  264.9  32.5    9.8e-79  264.6  32.5    1.0  1  FecCD           FecCD transport family
  ------ inclusion threshold ------
          1    9.4   6.1        2.9    7.9   6.1    1.9  1  SK_channel      Calcium-activated SK potassium channel
        1.1    7.8   6.5        1.8    7.1   6.5    1.3  1  Chitin_synth_2  Chitin synthase


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 !  264.6  32.5   1.6e-82   9.8e-79       2     312 .]      19     339 ..      15     339 .. 0.96

  Alignments for each domain:
  == domain 1  score: 264.6 bits;  conditional E-value: 1.6e-82
                             FecCD   2 lllllllslllgavkispsevfeallgkadsleaeivlelrlprvlaallvGaaLavaGallQtvtrNpLadPsilG 78 
                                       ++l++ l++ lg +k s+ e+ +++++ ++s+ + +v++lr+ r+laa+++Ga+L+ +G+ +Q+ +rNpLa+P +lG
  gi|385806370|ref|YP_005842768.1|  19 VFLSVPLCIYLGYYKASIFEITRVIFRPDNSQLSIVVWDLRIKRILAAIIIGAILGGSGTAVQASMRNPLASPFTLG 95 
                                       345566778******************************************************************** PP

                             FecCD  79 issgaalgavlallll.........lgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsallsa 146
                                       +s +a++g++++ll l         +  ++ f ++++af+++l+ +l++llla  ++g s+++l+L+ ia+s+  +a
  gi|385806370|ref|YP_005842768.1|  96 LSYAASVGVAVGLLALnegsilryqINIQNPFIIAFFAFIFSLIQVLIILLLA-YKAGLSSISLVLSSIAISFAYQA 171
                                       ************************99999************************.*********************** PP

                             FecCD 147 ltsllllll.neealesilfwllGslsgaswskvllllvllllllllll.llarkldllalgdetAkslGvnvervr 221
                                       l  l+++++ ne  +++++fw++G+l+++sw+++ l+++++ll+++ ++ + + ++d++  gd++Aks G+n++r+r
  gi|385806370|ref|YP_005842768.1| 172 LLYLIQYFFlNEIYVSTVVFWTFGDLERISWEELKLIAIVSLLIVIPYFvYRSIDYDVIIGGDDIAKSSGINPRRLR 248
                                       *******999************************999998877766555055679********************** PP

                             FecCD 222 llllllvalltavavalvGpigFvGLivPhiarllvgadhrkllplsallGallllladllarlllsptelpvgivt 298
                                       + +++++al +++a+++vG++gFv+L++Phi r+lvg  hr+l+p s+ +G+l+ll++d+l+r+++sp+++pvgi+t
  gi|385806370|ref|YP_005842768.1| 249 FETIFIAALGASLATSFVGVVGFVCLLAPHISRFLVGGGHRYLMPTSMAMGSLILLWSDTLGRIIISPVTIPVGIMT 325
                                       ***************************************************************************** PP

                             FecCD 299 aliGapffiylllr 312
                                       +l+G+p++i+ll++
  gi|385806370|ref|YP_005842768.1| 326 SLLGVPLLIFLLIK 339
                                       ***********986 PP

>> SK_channel  Calcium-activated SK potassium channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   6.1   0.00049       2.9      20      80 ..     127     189 ..     116     222 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00049
                        SK_channel  20 LvlalfGivlmvvetEllalavtek.lsivslalk.vlislsTviLLvlivlyhaaeiqlfli 80 
                                       +++a+f  ++ ++++ ++ l  ++  ls +sl+l  ++is++  +LL+li +++++ei +  +
  gi|385806370|ref|YP_005842768.1| 127 FIIAFFAFIFSLIQVLIILLLAYKAgLSSISLVLSsIAISFAYQALLYLIQYFFLNEIYVSTV 189
                                       788999999999999887776665415888888862679*******************98765 PP

>> Chitin_synth_2  Chitin synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   6.5   0.00031       1.8     422     493 ..     132     206 ..     110     210 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00031
                    Chitin_synth_2 422 asilksklvpviplvllaivlGlpailivltarkleyvawllvyllalPifn.fvlPlyafwhlddf...swGetr 493
                                       ++++  +l++v+ ++lla   Gl +i +vl +  +++    l+yl+ +   n   + +  fw + d+   sw e +
  gi|385806370|ref|YP_005842768.1| 132 FAFI-FSLIQVLIILLLAYKAGLSSISLVLSSIAISFAYQALLYLIQYFFLNeIYVSTVVFWTFGDLeriSWEELK 206
                                       3333.48999************************************998877245678899999885333777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       874  (0.0487478); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.58u 0.34s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 2079.70
//
Query:       gi|385806371|ref|YP_005842769.1|  [L=376]
Description: periplasmic binding protein [Fervidicoccus fontis Kam940]
Scores for complete 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   82.8   0.0    4.7e-23   82.0   0.0    1.3  1  Peripla_BP_2  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.0   0.0   2.6e-27   4.7e-23       8     234 ..      75     307 ..      70     309 .. 0.90

  Alignments for each domain:
  == domain 1  score: 82.0 bits;  conditional E-value: 2.6e-27
                                       HHHHHHHTT-GGGEEEB-GGG--GGGGGGT....TS-BSBESSSB-HHHHHHH--SEEEE-GGG....GGGHHHHHH CS
                      Peripla_BP_2   8 vteillalGatdkvvgvdtttsdpldadklee..aivevgadgeidvEklaalkPDlvilskgl.gltdedeellks 81 
                                        t++l+++ +++  +g  + ++ ++ +d+ ++   i   g ++ ++ E l+ +kPDl+i+s+ + +  d d  ++++
  gi|385806371|ref|YP_005842769.1|  75 ATDMLVGIEQSELQWGPTGRDYAMAYYDEFKNltVIGPGGPGKAPNPELLLSVKPDLIIMSEIYcQFIDPDTLQREV 151
                                       57888888888888888888888889998887755556777778888*****************99999999999** PP

                                       HS-EEE----TTS....HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT..-EEEEEEEETTE..EEE CS
                      Peripla_BP_2  82 giptvivessntg....eslkeqiralgellgledeaeklvaeidsklaaaksaidse.kpkpvlvfggadeggyvv 153
                                       ++ +++ +++++g     +l ++++ lg +l++ed+a+ l++ i+s +++++++++++  +++v v + +++g+  +
  gi|385806371|ref|YP_005842769.1| 152 NATVIVLDYGPAGyldfKELNNSLTILGIALNREDRAKSLINYIQSIVDDLNNRTNNItMRPKVYVGAVSYKGAQPF 228
                                       ***********99*********************************************7777788888999999*** PP

                                       E-TTSTTTHHHHTS--EESTTT--.STT-EEE-HHHHHHH--SEEEEEEHHHHT-S--HHHHT-SHH.HHTSHHHHT CS
                      Peripla_BP_2 154 agsnsyigdlldalgieniaaesk.kseyeeisaEqilasdpdvifvsgraeadnktgleflkenpl.laelpAvkn 228
                                       ++++s + +l   l+ ++ia+++  k ++ ++++E++ +++pdv+f++     + + +++ +++np  + +l+A++n
  gi|385806371|ref|YP_005842769.1| 229 TSTQSPFPPLSL-LNTKSIADNYSnKTGFVSLDFEYLISEQPDVVFIDEG---NLQLVKQSFESNPSpYLQLNAFRN 301
                                       *****9999865.******999989***********************99...************7536689***** PP

                                       T-EEEE CS
                      Peripla_BP_2 229 grVyal 234
                                       g Vy++
  gi|385806371|ref|YP_005842769.1| 302 GEVYGI 307
                                       ****86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); 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: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.53
# Mc/sec: 2125.25
//
Query:       gi|385806372|ref|YP_005842770.1|  [L=225]
Description: formylmethanofuran dehydrogenase subunit E region [Fervidicoccus fontis Kam940]
Scores for complete 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-39  135.3   0.0    1.8e-39  134.8   0.0    1.2  1  FmdE             FmdE, Molybdenum formylmethanofuran dehydrog
    7.9e-07   28.9   0.3    1.7e-06   27.9   0.3    1.6  1  zf-dskA_traR     Prokaryotic dksA/traR C4-type zinc finger
  ------ inclusion threshold ------
       0.79   10.1   5.8        3.2    8.2   0.9    2.9  3  Lar_restr_allev  Restriction alleviation protein Lar
        6.5    6.8  10.6       0.13   12.2   3.1    2.1  2  DUF4428          Domain of unknown function (DUF4428)


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 !  134.8   0.0     4e-43   1.8e-39       1     131 [.      13     156 ..      13     157 .. 0.97

  Alignments for each domain:
  == domain 1  score: 134.8 bits;  conditional E-value: 4e-43
                                       HHSS--CHHHHHHHHHHHHHHCC....-TT....SSSEEEEES-STCHHHHHHHHCS--TTTTSEEE--SS-SEEEE CS
                              FmdE   1 fHGHlCpglvlGyrmakaalkelgpkeeeg....deelvaivetdsCldDAiqvltgctlGkgnlivmdygkkaltf 73 
                                       fHGH+Cp++vlG+r++++a+++l++k++++    +e+++aive+++C++D++qv+tgct+G++ li+md+gk+a+t+
  gi|385806372|ref|YP_005842770.1|  13 FHGHICPYVVLGLRASEIAMQRLNIKKASEaetvNEDIIAIVECNNCFADGVQVATGCTFGNNGLIYMDTGKNAVTL 89 
                                       9************************999889********************************************** PP

                                       EETTT-EEEEEEE-..........CCTHHHHHHHCCT--GGGS-HHHHHHHHHHHHHHHHHS.HHHHE CS
                              FmdE  74 kkrktgkavrlklk..........eelpelreklakgkakeekeeeeleeeleeaikkilnapeeelf 131
                                       ++r++ k++r++++          ee+++l+ek++++++ +++++e+l+++++e++ ++++apee +f
  gi|385806372|ref|YP_005842770.1|  90 VRRRDWKGIRVYVDsekmkkryfsEEASRLFEKVIARREGTSEDQERLRKLWNEIGFALRDAPEE-IF 156
                                       ***************************************7777*******************966.44 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 !   27.9   0.3   3.8e-10   1.7e-06       1      32 [.     170     203 ..     170     204 .. 0.93

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 3.8e-10
                      zf-dskA_traR   1 giygs..CeeCGEpIpeaRlralPgarlCveCqe 32 
                                       +i+++  C+ CGE ++  R +++ g++lC  C++
  gi|385806372|ref|YP_005842770.1| 170 PIFETvkCDLCGELVMKTRAKVVNGKTLCQTCAG 203
                                       6788899**********************99996 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 ?    3.1   0.1     0.028   1.3e+02      21      37 ..      46      62 ..      24      76 .. 0.68
   2 ?   -1.1   0.0      0.57   2.5e+03      45      59 ..     128     142 ..     123     143 .. 0.78
   3 ?    8.2   0.9   0.00071       3.2       5      36 ..     176     207 ..     173     220 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.028
                   Lar_restr_allev 21 vvaeigqcvyCadCgas 37
                                      v ++i   v+C +C a 
  gi|385806372|ref|YP_005842770.1| 46 VNEDIIAIVECNNCFAD 62
                                      33333339******993 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.57
                   Lar_restr_allev  45 edeaeaekeaieaWN 59 
                                       e   e+++++ + WN
  gi|385806372|ref|YP_005842770.1| 128 EGTSEDQERLRKLWN 142
                                       556788899999**9 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.00071
                   Lar_restr_allev   5 pCPfCggravlersqrvvaeigqcvyCad.Cga 36 
                                        C+ Cg+   + r++ v  +   c +Ca  C+a
  gi|385806372|ref|YP_005842770.1| 176 KCDLCGELVMKTRAKVVNGKTL-CQTCAGsCNA 207
                                       6*****9988888866665444.9999778999 PP

>> DUF4428  Domain of unknown function (DUF4428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.8       1.9   8.7e+03      23      27 ..      56      60 ..      56      61 .. 0.88
   2 ?   12.2   3.1     3e-05      0.13       1      29 [.     176     204 ..     176     215 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.9
                           DUF4428 23 CkdCl 27
                                      C++C+
  gi|385806372|ref|YP_005842770.1| 56 CNNCF 60
                                      9***8 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 3e-05
                           DUF4428   1 iCaiCgkKigllkrlkleDg.yvCkdClkK 29 
                                       +C++Cg+ + + +r k+ +g ++C++C++ 
  gi|385806372|ref|YP_005842770.1| 176 KCDLCGELV-MKTRAKVVNGkTLCQTCAGS 204
                                       7****9755.666799999978*****986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); 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: 0.61u 0.34s 00:00:00.95 Elapsed: 00:00:00.56
# Mc/sec: 1218.08
//
Query:       gi|385806373|ref|YP_005842771.1|  [L=174]
Description: nucleoside-triphosphatase [Fervidicoccus fontis Kam940]
Scores for complete 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-43  147.7   0.0    3.9e-43  147.5   0.0    1.0  1  Ham1p_like  Ham1 family


Domain annotation for each model (and alignments):
>> Ham1p_like  Ham1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.5   0.0   2.2e-47   3.9e-43      13     187 .]       2     166 ..       1     166 [. 0.89

  Alignments for each domain:
  == domain 1  score: 147.5 bits;  conditional E-value: 2.2e-47
                                       HHHHHTTTECCCE.EECCCCEE----BS.SSHHHHHHHHHHHHH.HHTS-EEEEEEEEEEGGGTTTBGGGTTTTTHT CS
                        Ham1p_like  13 evkeilaeellevkslkelelpeveEtq.gtfeenalkKaraaa.eaglpvladDsgLevdaLnglPGvysarfage 87 
                                       e+++il+  +++v++l    + e +E+q +++ee+al   ++++ ++++p+l+dD+gL+++aLng+PG+y  +f++ 
  gi|385806373|ref|YP_005842771.1|   2 EISKILKAYGIHVEHL----EREKVEIQaESVEEIALFAGENLFlKEKKPILVDDTGLYIEALNGFPGPYAEYFLK- 73 
                                       7888998888888888....44557999999******9999988456888************************64. PP

                                       TCHHHHHHHHHHHHCTHTTS--EEEEEEEEEEEETTTTEEEEEEEEEEEEE-SS.--SSSSTTGGGEEETT-SSBTT CS
                        Ham1p_like  88 gaedeenlaklleeleeeeedrsArfvcvlaladpeeeeellfeGeveGeiveeprgeggfGyDpiFvpeegektfa 164
                                           + +l+ lle l+ ++e+r+A f+++++++    + +++f Ge+ Gei  e++g  gfGyDp+Fvp++ +kt+a
  gi|385806373|ref|YP_005842771.1|  74 ----TVGLDGLLELLK-NSENRKACFKTAICFCYY--DIKKIFVGELCGEIGMEKKGYFGFGYDPVFVPNGYSKTLA 143
                                       ....348999***998.4569************96..66689***************************76567*** PP

                                       TS.CHHHHHHSHHHHHHHHHHHH CS
                        Ham1p_like 165 elskeeknaiShRgkAlekllef 187
                                       e+s eekn+iShRg A +k++e+
  gi|385806373|ref|YP_005842771.1| 144 EMSIEEKNKISHRGIAARKFAEW 166
                                       ********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.36s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 977.13
//
Query:       gi|385806374|ref|YP_005842772.1|  [L=220]
Description: protein kinase RIO family [Fervidicoccus fontis Kam940]
Scores for 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-12   44.9   0.0    1.3e-11   44.5   0.0    1.1  1  RIO1            RIO1 family
    6.4e-11   42.1   0.1    8.1e-11   41.8   0.1    1.1  1  Pkinase         Protein kinase domain
    3.5e-08   33.1   0.0    2.3e-07   30.4   0.0    1.9  1  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
    6.8e-08   32.1   0.0    8.6e-08   31.8   0.0    1.1  1  Pkinase_Tyr     Protein tyrosine kinase
    5.2e-07   29.8   0.0    0.00011   22.2   0.0    2.3  2  APH             Phosphotransferase enzyme family
    1.4e-05   24.8   0.1    3.4e-05   23.6   0.1    1.6  2  WaaY            Lipopolysaccharide core biosynthesis protein 
  ------ inclusion threshold ------
      0.056   12.7   0.0      0.079   12.3   0.0    1.2  1  EcKinase        Ecdysteroid kinase
      0.062   12.1   0.0        0.1   11.5   0.0    1.3  1  DUF1679         Protein of unknown function (DUF1679)
      0.085   12.6   0.0      0.091   12.6   0.0    1.2  1  PI3_PI4_kinase  Phosphatidylinositol 3- and 4-kinase
       0.11   12.0   0.4       0.31   10.6   0.4    1.7  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 !   44.5   0.0   7.1e-15   1.3e-11      48     158 ..      46     156 ..      37     186 .. 0.80

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 7.1e-15
                                       HHHHHHHHHHHHHHHHHHHHTT--S--EEEE..ETTEEEEE--EETTEEGGBHHHCG-HHHHHHHHHHHHHHHHHHH CS
                              RIO1  48 rklvklwaekEfrnLkrleeagvpvPkpiel..krhvlvmefigedgvaapklkdveeeeeaeelyeevleemrkly 122
                                       ++l+   +  E r+L+   +ag++vP p+++  ++  l+ ++i+  +v    l++   +e a++++ ev +++ k+ 
  gi|385806374|ref|YP_005842772.1|  46 KSLISKRTSSEARILMDCIKAGIRVPYPLKVdaENGLLIISYIS-GEVFRDYLNEKGFDELAKNIVFEVANSISKMH 121
                                       5677888999******************876226789*******.34444455555568999999999999877776 PP

                                       HTSTEEESS-STTSEEEETTEEEE--GTTEEETTST CS
                              RIO1 123 keaglvHaDLSeyNvlvdedkvviIDvsQaveldhp 158
                                        +  ++H+DL   N+++++++ +iID++ +   + +
  gi|385806374|ref|YP_005842772.1| 122 -NLDIIHGDLTTSNIIIKDGNAFIIDFGLSFRSKRE 156
                                       .**************************988776544 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   0.1   4.5e-14   8.1e-11      43     153 ..      51     158 ..      31     176 .. 0.83

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 4.5e-14
                                       HHHHHHHHHHHHHSCTTB--EEEEEEESSEEEEEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTE CS
                           Pkinase  43 kkvlrEikilkklkhpnivrlyevfeekdelylvleyveggeladllerkgslseeeakkiakqilegleylHskgi 119
                                       k++ +E +il  +    i   y    + ++ +l+  y++g+ + d+l++ + + +e ak+i+ +++++++ +H+  i
  gi|385806374|ref|YP_005842772.1|  51 KRTSSEARILMDCIKAGIRVPYPLKVDAENGLLIISYISGEVFRDYLNE-KGF-DELAKNIVFEVANSISKMHNLDI 125
                                       56666777777777777766677777888999*********999***85.445.5689******************* PP

                                       E-SS-SGGGEEEETTTEEEE-SGTTSEESSSSCS CS
                           Pkinase 120 iHrDlKpeNiLidekgelKitDFGlakelesssk 153
                                       iH Dl ++Ni+i+ +g+  i+DFGl+ + +++++
  gi|385806374|ref|YP_005842772.1| 126 IHGDLTTSNIIIK-DGNAFIIDFGLSFRSKREED 158
                                       *************.************98888765 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.0   1.3e-10   2.3e-07      55     203 ..      50     185 ..      33     189 .. 0.77

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 1.3e-10
                               Kdo  55 rtravrEfrllkrLeeagvavpkpvaagavkvgleyrAlllterlegaqdLedllakwaelaeelkrallkavgrli 131
                                         r   E r+l    +ag++vp+p+   a+        ll++  + g     d+l++  +  +el ++++ +v+  i
  gi|385806374|ref|YP_005842772.1|  50 SKRTSSEARILMDCIKAGIRVPYPLKVDAEN------GLLIISYISGEV-FRDYLNE--KGFDELAKNIVFEVANSI 117
                                       5567778888888888888888888666553......466777776643.5666664..556789999********* PP

                               Kdo 132 aklhragvnHadlyaknillqqeeeeeaeiwliDldkarlrlradrwrekdLarLkrsfl..kielteadweal 203
                                       +k+h++++ H+dl   ni ++ ++     + +iD+  + +   ++ ++  dL+  +r ++  + e +e+  e +
  gi|385806374|ref|YP_005842772.1| 118 SKMHNLDIIHGDLTTSNIIIKDGN-----AFIIDFGLSFRSK-REEDKAMDLRIFERAVEstHPEYKEKILEPF 185
                                       *********************997.....9******998776.9999********9988755455555555555 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.0   4.8e-11   8.6e-08      48     158 ..      53     158 ..      35     179 .. 0.78

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 4.8e-11
                                       HHHHHHHHHTS-BTTB--EEEEEESSSSEEEEEE--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTE CS
                       Pkinase_Tyr  48 lleeakimkklkhpnivkllgvctkeepllivteyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskkl 124
                                         +ea+i++++ +  i   + + +++e+ l+++ y++g  ++++L++k  ++l      +++++vA+ ++ +++ ++
  gi|385806374|ref|YP_005842772.1|  53 TSSEARILMDCIKAGIRVPYPLKVDAENGLLIISYISGEVFRDYLNEKGFDELA----KNIVFEVANSISKMHNLDI 125
                                       556777777777777777777778889999*****************9333333....368899************* PP

                                       EEST-SGGGEEEEETTEEEE-STTTHEETTTSSE CS
                       Pkinase_Tyr 125 vHrdlaarNvLlsenkvvkisDfGLardiekdde 158
                                       +H dl++ N+++++++ + i DfGL+ + +++++
  gi|385806374|ref|YP_005842772.1| 126 IHGDLTTSNIIIKDGN-AFIIDFGLSFRSKREED 158
                                       ************9655.6688****987744443 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.0    0.0059        11      35     107 ..      51     122 ..       7     125 .. 0.77
   2 !   22.2   0.0   6.2e-08   0.00011     168     216 ..     125     169 ..     123     189 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0059
                                       HHHHHHHHHHHHHHHTT-B--B-CTTBS-EEETTEEEEEEE----EE-SS....HHHHHHHHHHHHHHHHHHCCHHC CS
                               APH  35 eeirrevallrlLakagvpvPevlagdtddeeigllfalieyvpgrsllr....klsaaqlpellealgeflaalhq 107
                                        ++++e+++l    kag++vP +l     d+e+g   ++i+y+ g+++++    k  ++ +++++ +++  + ++h+
  gi|385806374|ref|YP_005842772.1|  51 KRTSSEARILMDCIKAGIRVPYPLK---VDAENG--LLIISYISGEVFRDylneKGFDELAKNIVFEVANSISKMHN 122
                                       56789999**9999***********...778888..799*********99776666666666666666666666665 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 6.2e-08
                                       EE-SS-SGGGEEEC..TTEEEEE---TT-EEEECCHHHHCCHHHCSCHC CS
                               APH 168 llHgDlhpgNllvdpddgrvtGviDfedaglgpplyDlavllrswtsel 216
                                       ++HgDl + N++++ d++ +  +iDf+++  + +  D a+ l ++ +++
  gi|385806374|ref|YP_005842772.1| 125 IIHGDLTTSNIIIK-DGNAF--IIDFGLSFRSKREEDKAMDL-RIFERA 169
                                       79************.88999..***************99998.434444 PP

>> WaaY  Lipopolysaccharide core biosynthesis protein (WaaY)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.4   2.5e+03     119     139 ..      19      39 ..       7      53 .. 0.63
   2 !   23.6   0.1   1.9e-08   3.4e-05     120     197 ..      83     168 ..      77     191 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.4
                              WaaY 119 imiieyiegielvdmpeidde 139
                                       + +iey++ i +    +i+  
  gi|385806374|ref|YP_005842772.1|  19 LYLIEYLNDIAVLKERIIKPY 39 
                                       567777777766655555544 PP

  == domain 2  score: 23.6 bits;  conditional E-value: 1.9e-08
                              WaaY 120 miieyiegielvd......mpeiddevkakikqsieklhqlgmvsgdphrgnfivkkdevriid..lsgkrasaerk 188
                                       +ii yi g  + d      + e+ +++  ++ +si k+h+l+++ gd    n+i+k+++  iid  ls ++   e k
  gi|385806374|ref|YP_005842772.1|  83 LIISYISGEVFRDylnekgFDELAKNIVFEVANSISKMHNLDIIHGDLTTSNIIIKDGNAFIIDfgLSFRSKREEDK 159
                                       6788888765555211122457788888999********************************96668888888899 PP

                              WaaY 189 akdridler 197
                                       a d   +er
  gi|385806374|ref|YP_005842772.1| 160 AMDLRIFER 168
                                       998766676 PP

>> EcKinase  Ecdysteroid kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.4e-05     0.079     191     285 ..     101     193 ..      86     201 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.4e-05
                          EcKinase 191 kleklkenlferllelveekeeefnvlnHGDlwvnNimfkydeegepedvilvDFQlsrygS....palDLlyf..l 261
                                        +++l++n++ ++++++   + +   + HGDl ++Ni++k        ++ ++DF ls+ +      a+DL  f   
  gi|385806374|ref|YP_005842772.1| 101 GFDELAKNIVFEVANSI--SKMHNLDIIHGDLTTSNIIIKDG------NAFIIDFGLSFRSKreedKAMDLRIFerA 169
                                       55666666666666666..556666799***********886......5699**99997664222279999998556 PP

                          EcKinase 262 ytsteeelrkekfdellriYhesL 285
                                       + st++e++++ ++ ++ +Y+++ 
  gi|385806374|ref|YP_005842772.1| 170 VESTHPEYKEKILEPFFSTYFKNA 193
                                       789*****************9875 PP

>> DUF1679  Protein of unknown function (DUF1679)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   5.6e-05       0.1     267     353 ..     122     204 ..      91     209 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.6e-05
                           DUF1679 267 kkvlvhgDlwsaNiLfseeeegklklkkviDyQlvslgnpaeDlvrlllscLsgedRrarkeelLeqyyetflkale 343
                                       +  ++hgDl  +Ni+ +  +   + ++  + +        a+Dl r++  ++  +   + ke++Le +++t+ k+  
  gi|385806374|ref|YP_005842772.1| 122 NLDIIHGDLTTSNIIIKDGNA--FIIDFGLSFRSKREEDKAMDL-RIFERAVEST-HPEYKEKILEPFFSTYFKNAA 194
                                       44589************9666..544444555555555667776.7777776544.57899*********9999886 PP

                           DUF1679 344 dngeepytle 353
                                        ++++  +le
  gi|385806374|ref|YP_005842772.1| 195 GSEKIRKSLE 204
                                       5556665555 PP

>> PI3_PI4_kinase  Phosphatidylinositol 3- and 4-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.1e-05     0.091     139     189 ..     114     165 ..      22     199 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.1e-05
                                       HHHHHHHHHHHHHHT-TT--TTTEEEETTTSEEEESSTTTCC.....TCSHCSSSS CS
                    PI3_PI4_kinase 139 vrslaklsvldyilgngDRhldNilvdktsgklihIDfGlil.....pdewkllpf 189
                                       + s++k+  ld+i   gD + +Ni +  ++g+ + IDfGl++     +d+ ++l++
  gi|385806374|ref|YP_005842772.1| 114 ANSISKMHNLDII--HGDLTTSNIII--KDGNAFIIDFGLSFrskreEDKAMDLRI 165
                                       6677777777777..468899*****..9*************77666555555554 PP

>> Choline_kinase  Choline/ethanolamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.4   0.00018      0.31     141     179 ..     119     155 ..      94     182 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00018
                                       HGG-EEEE-S--SGGGEEE.-CTTEEEE--GTT-EEEEH CS
                    Choline_kinase 141 lespvvfcHnDlqegNillnkeekklvlIDFEYagynyr 179
                                       + +++   H Dl  +Ni+   ++++ ++IDF  +  + r
  gi|385806374|ref|YP_005842772.1| 119 KMHNLDIIHGDLTTSNIII--KDGNAFIIDFGLSFRSKR 155
                                       33457778***********..999*******77766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 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:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.64u 0.34s 00:00:00.98 Elapsed: 00:00:00.54
# Mc/sec: 1222.46
//
Query:       gi|385806375|ref|YP_005842773.1|  [L=345]
Description: endopeptidase, family M22 [Fervidicoccus fontis Kam940]
Scores for complete 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-76  255.2   0.0      1e-75  254.9   0.0    1.0  1  Peptidase_M22  Glycoprotease 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 !  254.9   0.0   5.8e-80     1e-75       4     271 .]      39     311 ..      36     311 .. 0.92

  Alignments for each domain:
  == domain 1  score: 254.9 bits;  conditional E-value: 5.8e-80
                                       XEEEEEEEEE....SSSSHHHHHHHHHHHHHHHHHHHHHHHTSTGGGEEEEEEEEESS-HHHHHHHHHHHHHHHHHC CS
                     Peptidase_M22   4 anvvasqkelhakyGGvvPelasraHserllplieealaeaglsledldaIavtkgPGlftgLrvGvsfAkglalal 80 
                                       an+    +++ +++GG++P++asr+H+e++ ++i +al++a+l+++d+da+av+ gPG++++LrvG+++A++++  +
  gi|385806375|ref|YP_005842773.1|  39 ANEK---DKYEPEKGGIHPRDASRHHAEKIGSIISRALKKANLKIDDIDAVAVALGPGMGPCLRVGATAARAISSYF 112
                                       4333...3455889*************************************************************** PP

                                       T--EEEEEHHHHHHHCCHCTSECSSCEEEEESSSTEEEEEECTTEEEEEEEESSSEHHHHHHHHHHHHT..S....S CS
                     Peptidase_M22  81 nkPlvgVnhleahalaarleekeefPvvllvsGghtqvylvkegryeilgetlddaagealdkvarllglpy....p 153
                                       +kPl++Vnh +ah++ ++l ++ ++P+v+++sGg+t+++++k++ry+++get d+a+g+ +d +ar  gl      +
  gi|385806375|ref|YP_005842773.1| 113 GKPLIPVNHAIAHIEIGNLLSGFSDPLVVYISGGNTSIIAYKQKRYRVFGETQDIALGNLIDTFAREAGLAPpyvvN 189
                                       ******************9976699****************99***************************9944544 PP

                                       CCHHHHHHHCTC..S........EETTEEE.CHHHHHHHHHH.STTHHHHHHHHHHHHHHHHHHHHHHHHHHCTBSE CS
                     Peptidase_M22 154 ggpkieklakeg..kk.iefprplkgldfsfsGlktavlkel.ekevedlaasfqeavvdhlvekteralklpkake 226
                                       g  ++e +a++   kk +++p+ +kg+d+s+ Gl t+ lk + +++  d+++s+ e   ++++e++er l+++++ke
  gi|385806375|ref|YP_005842773.1| 190 GRHVVELCAERSkeKKlLDLPYIVKGQDVSYGGLLTSSLKMIgKEDLGDVCYSLVEISYSMITEVAERGLAHTRKKE 266
                                       5557887777667544899***********************44469****************************** PP

                                       EEEESGGGGXHHHHHCHCCHHHHTTSEEEXXXHHHHSSXCHHHHH CS
                     Peptidase_M22 227 lvilGGvaankrLrealeeeaeelglkliiPplkyctdnaamiaw 271
                                       +++ GGv+a k L e+le++++ +g+k++  p+++  dn+amiaw
  gi|385806375|ref|YP_005842773.1| 267 VILTGGVSASKVLTEKLEKMSALHGAKFFSVPPAFAGDNGAMIAW 311
                                       ******************99999*********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 1970.32
//
Query:       gi|385806376|ref|YP_005842774.1|  [L=56]
Description: 30S ribosomal protein S27a [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.4e-15   55.0   5.4    7.4e-15   54.8   5.4    1.1  1  Ribosomal_S27    Ribosomal protein S27a
    0.00018   21.4   3.3    0.00022   21.1   3.3    1.2  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
    0.00037   20.3   2.9    0.00048   20.0   2.9    1.4  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
     0.0021   18.2   0.9     0.0026   17.9   0.9    1.2  1  Auto_anti-p27    Sjogren's syndrome/scleroderma autoantigen 1
     0.0063   16.4   1.0      0.011   15.6   1.0    1.5  1  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
  ------ inclusion threshold ------
      0.021   15.2   1.1      0.031   14.6   1.1    1.4  1  Lar_restr_allev  Restriction alleviation protein Lar
      0.029   14.5   0.2      0.029   14.5   0.2    1.1  1  zf-piccolo       Piccolo Zn-finger
      0.033   14.5   1.7          1    9.7   0.1    2.0  2  GFA              Glutathione-dependent formaldehyde-activatin
       0.04   14.1   4.0      0.068   13.3   3.9    1.5  1  Ribosomal_L37e   Ribosomal protein L37e
       0.04   14.1   0.7       0.06   13.5   0.7    1.3  1  DUF2387          Probable metal-binding protein (DUF2387)
      0.043   14.1   1.6       0.35   11.2   0.2    2.0  2  zf-LITAF-like    LITAF-like zinc ribbon domain
      0.049   13.7   2.0       0.14   12.2   2.0    1.8  1  DZR              Double zinc ribbon
      0.054   13.4   3.9       0.99    9.4   3.9    2.1  1  Nudix_N_2        Nudix N-terminal
      0.064   13.0   4.6       0.45   10.3   0.0    2.2  2  zinc_ribbon_2    zinc-ribbon domain
       0.15   12.1   0.5       0.15   12.1   0.5    2.2  2  YhfH             YhfH-like protein
       0.15   11.8   2.4       0.35   10.6   2.3    1.6  2  zinc_ribbon_10   Predicted integral membrane zinc-ribbon meta
       0.17   11.3   0.4       0.17   11.3   0.4    2.2  2  zf-ribbon_3      zinc-ribbon domain
       0.27   10.9   5.6       0.96    9.2   0.2    2.3  2  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
       0.34   11.1   0.5       0.34   11.1   0.5    2.3  3  zinc_ribbon_13   Nucleic-acid-binding protein containing Zn-r
        1.6    8.3   6.9        3.2    7.4   4.5    2.4  2  TF_Zn_Ribbon     TFIIB zinc-binding
        2.5    8.1  11.0        2.8    7.9   0.4    2.7  2  Zn_ribbon_SprT   SprT-like zinc ribbon domain


Domain annotation for each model (and alignments):
>> Ribosomal_S27  Ribosomal protein S27a
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.8   5.4   8.7e-18   7.4e-15       1      45 []       4      49 ..       4      49 .. 0.98

  Alignments for each domain:
  == domain 1  score: 54.8 bits;  conditional E-value: 8.7e-18
                                      SSSSCCESS.SSSEEESS-B-SS-S-TTSBEEECTT...EEEESSTTTE CS
                     Ribosomal_S27  1 vlkyYkvdd.sgkverlrkeCpreCGaGvfMAehkd...RkyCGkCglT 45
                                      v++yY++d+ +++++ ++k+Cpr C  G +M+++k+   R+yCG+Cg+T
  gi|385806376|ref|YP_005842774.1|  4 VHNYYEYDYkTKTIKLKNKRCPR-C--GSIMGHYKEpteRWYCGSCGYT 49
                                      89*******9*************.*..********9999*********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 !   21.1   3.3   2.6e-07   0.00022      17      46 .]      21      49 ..      14      49 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.6e-07
                     Zn_Tnp_IS1595 17 ngfvCPhCgsr.kayriktrglfqCkeCrkq 46
                                      n++ CP+Cgs   +y+  t +++ C +C+++
  gi|385806376|ref|YP_005842774.1| 21 NKR-CPRCGSImGHYKEPT-ERWYCGSCGYT 49
                                      555.********9999999.9*******985 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 !   20.0   2.9   5.6e-07   0.00048      29      55 ..      22      49 ..       2      51 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 5.6e-07
                    OrfB_Zn_ribbon 29 ktCseCgsknke.alsgrtfkCpnCgfe 55
                                      k+C++Cgs++ + +  +++++C +Cg++
  gi|385806376|ref|YP_005842774.1| 22 KRCPRCGSIMGHyKEPTERWYCGSCGYT 49
                                      89**********9*************97 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 !   17.9   0.9   3.1e-06    0.0026      12      40 .]      18      47 ..      15      47 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.1e-06
                     Auto_anti-p27 12 tMLaetCpvCgvPLmrdr.kggkvyCvaCd 40
                                      ++ ++ Cp+Cg+++  ++  ++++yC +C+
  gi|385806376|ref|YP_005842774.1| 18 KLKNKRCPRCGSIMGHYKePTERWYCGSCG 47
                                      577999***********98789*******6 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   1.0   1.3e-05     0.011       4      31 ..      24      50 ..      22      54 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.3e-05
                                      ESTTTSBE.EEEECSCCCEEEESSSS-EE CS
                    RNA_POL_M_15KD  4 CpkCgNlL.lpkedkegknfeCrqCgYee 31
                                      Cp Cg+ +  +ke  e ++  C +CgY e
  gi|385806376|ref|YP_005842774.1| 24 CPRCGSIMgHYKEPTERWY--CGSCGYTE 50
                                      ********6699999**99..******76 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 ?   14.6   1.1   3.7e-05     0.031       3      36 ..      21      48 ..      19      56 .] 0.74

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.7e-05
                   Lar_restr_allev  3 LkpCPfCggravlersqrvvaeigqcvyCadCga 36
                                       k CP Cg+   + +++  +       yC  Cg+
  gi|385806376|ref|YP_005842774.1| 21 NKRCPRCGSIMGHYKEPTER------WYCGSCGY 48
                                      589*****976666665555......69*****9 PP

>> zf-piccolo  Piccolo Zn-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.2   3.5e-05     0.029      25      54 ..      18      47 ..       2      52 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.5e-05
                        zf-piccolo 25 eCkkqvCnlCGFnptphlte.kkeWlclnCQ 54
                                      + k++ C  CG + + h +e ++ W c  C 
  gi|385806376|ref|YP_005842774.1| 18 KLKNKRCPRCG-SIMGHYKEpTERWYCGSCG 47
                                      678999*****.999*****8999*****95 PP

>> GFA  Glutathione-dependent formaldehyde-activating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1    0.0012         1      37      62 ..      10      34 ..       2      39 .. 0.71
   2 ?    6.2   0.1     0.015        13      44      61 ..      35      52 ..      30      56 .] 0.78

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0012
                               GFA 37 ykktadsgnkvtrsfCpeCgsplyse 62
                                      y++ + ++ k++++ Cp+Cgs + + 
  gi|385806376|ref|YP_005842774.1| 10 YDY-KTKTIKLKNKRCPRCGSIMGHY 34
                                      443.456778899*******988754 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.015
                               GFA 44 gnkvtrsfCpeCgsplys 61
                                      +++ +r+ C +Cg + + 
  gi|385806376|ref|YP_005842774.1| 35 KEPTERWYCGSCGYTEFL 52
                                      578899*******88776 PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   3.9     8e-05     0.068      17      40 ..      22      49 ..      13      55 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8e-05
                    Ribosomal_L37e 17 ilCrrCgkrsyhvqk....ktCascGyp 40
                                       +C rCg+   h+++     +C+scGy 
  gi|385806376|ref|YP_005842774.1| 22 KRCPRCGSIMGHYKEpterWYCGSCGYT 49
                                      58*******999875222278******6 PP

>> DUF2387  Probable metal-binding protein (DUF2387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.7     7e-05      0.06      11      45 ..      24      55 ..      21      56 .] 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7e-05
                           DUF2387 11 CPrCsemDkirmweedeveyrECvsCgftdelsek 45
                                      CPrC    +i+ + ++++e   C sCg+t+ l++k
  gi|385806376|ref|YP_005842774.1| 24 CPRCG---SIMGHYKEPTERWYCGSCGYTEFLEKK 55
                                      99997...5999999***************99876 PP

>> zf-LITAF-like  LITAF-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2    0.0004      0.35      50      70 .]      15      35 ..      11      35 .. 0.85
   2 ?    2.3   0.1      0.23     2e+02      57      63 ..      41      47 ..      38      51 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0004
                     zf-LITAF-like 50 dslkdvehyCpnCgallgtyk 70
                                      ++ k ++ +Cp+Cg+ +g+yk
  gi|385806376|ref|YP_005842774.1| 15 KTIKLKNKRCPRCGSIMGHYK 35
                                      66788899**********996 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.23
                     zf-LITAF-like 57 hyCpnCg 63
                                       yC++Cg
  gi|385806376|ref|YP_005842774.1| 41 WYCGSCG 47
                                      6899998 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   2.0   0.00017      0.14      11      49 .]      20      47 ..       3      54 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00017
                               DZR 11 darfCseCgtklkavaa...edrCpsCgekvdpearfCpeCG 49
                                      +++ C++Cg+ +  +++                    C++CG
  gi|385806376|ref|YP_005842774.1| 20 KNKRCPRCGSIMGHYKEpteRWY--------------CGSCG 47
                                      34444444444333333332334..............55554 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   3.9    0.0012      0.99       3      31 ..      24      49 ..      22      51 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0012
                                      -TTT--B-EEE--TT-SS-EEEETTTTEE CS
                         Nudix_N_2  3 CsqCGtpvelripdgDnreRlvCpaCgti 31
                                      C+ CG+ + +     +  eR  C +Cg++
  gi|385806376|ref|YP_005842774.1| 24 CPRCGSIMGHYK---EPTERWYCGSCGYT 49
                                      999999987544...4589********97 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00052      0.45       9      21 ..      17      29 ..      15      31 .. 0.74
   2 ?    3.5   1.9     0.072        61       1      21 [.      42      48 ..      42      49 .. 0.49

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00052
                     zinc_ribbon_2  9 lqdnakFCpyCGt 21
                                      ++ ++k Cp+CG+
  gi|385806376|ref|YP_005842774.1| 17 IKLKNKRCPRCGS 29
                                      6667888999985 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.072
                     zinc_ribbon_2  1 fCpnCGaelqdnakFCpyCGt 21
                                      +C +CG              +
  gi|385806376|ref|YP_005842774.1| 42 YCGSCG--------------Y 48
                                      455555..............4 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.5   0.00017      0.15      10      24 ..      18      32 ..      16      37 .. 0.84
   2 ?    0.3   1.1      0.81   6.9e+02      15      20 ..      42      47 ..      36      55 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00017
                              YhfH 10 nLPkKkCteCGkeie 24
                                      +L +K C+ CG+ + 
  gi|385806376|ref|YP_005842774.1| 18 KLKNKRCPRCGSIMG 32
                                      6899*******9885 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.81
                              YhfH 15 kCteCG 20
                                       C +CG
  gi|385806376|ref|YP_005842774.1| 42 YCGSCG 47
                                      599999 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1     0.054        46      46      53 ..      23      30 ..      10      31 .. 0.82
   2 ?   10.6   2.3   0.00041      0.35      25      52 ..      24      48 ..      23      50 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.054
                    zinc_ribbon_10 46 rCpkCgal 53
                                      rCp Cg++
  gi|385806376|ref|YP_005842774.1| 23 RCPRCGSI 30
                                      8****985 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00041
                    zinc_ribbon_10 25 CskChshnGlapkeeleev.kyrCpkCga 52
                                      C+ C s  G +    +e++ +++C +Cg 
  gi|385806376|ref|YP_005842774.1| 24 CPRCGSIMGHY----KEPTeRWYCGSCGY 48
                                      99*********....444549******97 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.4    0.0002      0.17       2      11 ..      21      30 ..      20      31 .. 0.85
   2 ?    2.4   1.2      0.13   1.1e+02      19      24 ..      43      48 ..      41      49 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0002
                       zf-ribbon_3  2 tvrCPnCGap 11
                                       +rCP+CG++
  gi|385806376|ref|YP_005842774.1| 21 NKRCPRCGSI 30
                                      589*****85 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.13
                       zf-ribbon_3 19 CpyCGt 24
                                      C +CG+
  gi|385806376|ref|YP_005842774.1| 43 CGSCGY 48
                                      888886 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.2    0.0011      0.96       4      11 ..      22      29 ..      19      33 .. 0.76
   2 ?    4.1   1.2     0.043        36       5      10 ..      42      47 ..      42      51 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0011
                     zf-NADH-PPase  4 rFCgrCGa 11
                                      + C+rCG+
  gi|385806376|ref|YP_005842774.1| 22 KRCPRCGS 29
                                      56999997 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.043
                     zf-NADH-PPase  5 FCgrCG 10
                                      +Cg CG
  gi|385806376|ref|YP_005842774.1| 42 YCGSCG 47
                                      677777 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 ?   -2.8   0.2       8.9   7.6e+03      47      53 ..      12      18 ..       6      21 .. 0.53
   2 ?    2.3   0.1      0.22   1.9e+02       1       7 [.      23      29 ..      23      38 .. 0.79
   3 ?   11.1   0.5    0.0004      0.34      37      50 ..      42      55 ..      40      56 .] 0.88

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 8.9
                    zinc_ribbon_13 47 Ykaetse 53
                                      Yk++t +
  gi|385806376|ref|YP_005842774.1| 12 YKTKTIK 18
                                      5555544 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.22
                    zinc_ribbon_13  1 kCpKCgn 7 
                                      +Cp+Cg+
  gi|385806376|ref|YP_005842774.1| 23 RCPRCGS 29
                                      5999997 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.0004
                    zinc_ribbon_13 37 sCknCgYtelYkae 50
                                      +C +CgYte+ +++
  gi|385806376|ref|YP_005842774.1| 42 YCGSCGYTEFLEKK 55
                                      6*********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 ?   -1.1   0.0       1.6   1.4e+03      10      18 ..       7      15 ..       4      17 .. 0.72
   2 ?    7.4   4.5    0.0037       3.2       2      27 ..      23      48 ..      22      50 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.6
                                      ECHEETSTT CS
                      TF_Zn_Ribbon 10 nlveDperg 18
                                      ++++D+++ 
  gi|385806376|ref|YP_005842774.1|  7 YYEYDYKTK 15
                                      478999875 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0037
                                      EETTTTCEECHEETSTTCEEESSSSB CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGl 27
                                      +CP Cgs +  + + +   +C++CG+
  gi|385806376|ref|YP_005842774.1| 23 RCPRCGSIMGHYKEPTERWYCGSCGY 48
                                      6*****97745555667779999996 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 ?    3.6   4.6     0.075        64      20      32 ..      17      29 ..       2      34 .. 0.73
   2 ?    7.9   0.4    0.0033       2.8       5      12 ..      41      48 ..      38      52 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.075
                    Zn_ribbon_SprT 20 irrhnYrCrrCkg 32
                                      i+  n rC+rC++
  gi|385806376|ref|YP_005842774.1| 17 IKLKNKRCPRCGS 29
                                      4555677888874 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0033
                    Zn_ribbon_SprT  5 YrCtgCgr 12
                                      ++C++Cg 
  gi|385806376|ref|YP_005842774.1| 41 WYCGSCGY 48
                                      89999993 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       776  (0.0432818); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); 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 0.36s 00:00:00.88 Elapsed: 00:00:00.54
# Mc/sec: 311.22
//
Query:       gi|385806377|ref|YP_005842775.1|  [L=138]
Description: 30S ribosomal protein S24 [Fervidicoccus fontis Kam940]
Scores for complete 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   64.1   2.4    1.7e-17   63.1   2.4    1.6  1  Ribosomal_S24e  Ribosomal protein S24e
  ------ inclusion threshold ------
       0.14   11.1   0.1       0.26   10.3   0.0    1.5  2  Gly_kinase      Glycerate kinase family


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 !   63.1   2.4   1.9e-21   1.7e-17       4      77 ..      40     113 ..      38     136 .. 0.97

  Alignments for each domain:
  == domain 1  score: 63.1 bits;  conditional E-value: 1.9e-21
                                       EE-SSS-S--HHHHHHHHHHHHTS-CTTEEEEEEEE-SSSSEEEEEEEEES-HHHHHHHS-HHHHHHTTSS--- CS
                    Ribosomal_S24e   4 vlHpgkatpskteireklakmykvdpdlvvvfgfrthfGggkttGfakiYdsleaakkfEpkhrlaRnglaekk 77 
                                       v+H+gk+tps   +r k+a+++kvd   ++v ++ t++G g++++ ++iY +++aa++f pk++++Rn+  +++
  gi|385806377|ref|YP_005842775.1|  40 VYHQGKGTPSLGVLRTKVAEKMKVDLGSIYVISLVTEYGIGRSKVLFHIYPNKKAAERFVPKYIIERNKTLQEE 113
                                       99******************************************************************988776 PP

>> Gly_kinase  Glycerate kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   2.9e-05      0.26     179     212 ..      13      47 ..       2      68 .. 0.81
   2 ?   -2.5   0.1      0.21   1.9e+03     336     355 ..     103     122 ..      91     127 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 2.9e-05
                        Gly_kinase 179 prlkdveitvacDvtnpLlGeeGaa.avFgpQKGa 212
                                       +  ++++++++ Dv+npL+G +  + +v+ + KG+
  gi|385806377|ref|YP_005842775.1|  13 DLGDQLSLEIVNDVKNPLIGRREISgYVYHQGKGT 47 
                                       45568899*************99875899999986 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.21
                        Gly_kinase 336 ildgpesleealeeaaelle 355
                                       i+++ ++l+e ++ea+e+ +
  gi|385806377|ref|YP_005842775.1| 103 IIERNKTLQEEMQEAEEKEK 122
                                       78888999999999888655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2748  (0.153271); expected 358.6 (0.02)
Passed bias filter:                      983  (0.0548274); expected 358.6 (0.02)
Passed Vit filter:                       137  (0.00764125); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.36s 00:00:01.00 Elapsed: 00:00:00.61
# Mc/sec: 681.29
//
Query:       gi|385806378|ref|YP_005842776.1|  [L=232]
Description: hypothetical protein FFONT_1336 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.7e-23   80.6   0.7    1.5e-22   79.5   0.7    1.6  1  SBDS      Shwachman-Bodian-Diamond syndrome (SBDS) protein
    1.1e-21   77.0   2.4    1.8e-21   76.3   2.4    1.3  1  SBDS_C    SBDS protein C-terminal domain
     0.0068   16.3   0.0      0.013   15.3   0.0    1.5  1  DUF1949   Domain of unknown function (DUF1949)
  ------ inclusion threshold ------
      0.016   15.2   0.0      0.035   14.1   0.0    1.5  1  EFG_C     Elongation factor G C-terminus


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 !   79.5   0.7   3.3e-26   1.5e-22       3      88 .]       7      92 ..       5      92 .. 0.97

  Alignments for each domain:
  == domain 1  score: 79.5 bits;  conditional E-value: 3.3e-26
                                      EEEEEEETTEEEEEEE-HHHHHHHHCTT---HHHHBSSSS-EEETTTTEE--HHHHHHHHS---HHHHHHHHHHHSEEE CS
                              SBDS  3 sivrykkgkkrFeiavyknklleyregkeidLsevlqsekiFtnaskGetaskselekafgteskdeiikeILkkGeiq 81
                                       i++y++++k+Fei+v+++ + ey+e  + +++ev++se i+++a+kG +as ++++++fgte+   ++++ILk Ge+q
  gi|385806378|ref|YP_005842776.1|  7 IIAKYESKGKHFEILVDPELVFEYKESGKPNIEEVVKSEFIYKDAKKGLKASPEDIKSVFGTEDFLAVAEKILKGGELQ 85
                                      5889*************************************************************************** PP

                                      --HHHHH CS
                              SBDS 82 vsaeerk 88
                                      +++e+r+
  gi|385806378|ref|YP_005842776.1| 86 LTTEQRR 92
                                      ****996 PP

>> SBDS_C  SBDS protein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.3   2.4     4e-25   1.8e-21       2     114 ..      99     215 ..      98     217 .. 0.84

  Alignments for each domain:
  == domain 1  score: 76.3 bits;  conditional E-value: 4e-25
                                       HHHHHHHHHHHEEBTTTTB---HHHHHHHHHHTT----TTS-CCCCHHHHHHHHTTTS--EE-EEEEEEEE-...CC CS
                            SBDS_C   2 ekeiieivaeklvnpqtkrpytttmIekalkelgtsvktnksaksQalevikaLiqeipiqrarmrlritcptsikd 78 
                                       +k ii+++++++++p+tk p+++++Ieka++e+++sv++n+s+++Qa +++ka+ ++ipi++a+  l++++p+s ++
  gi|385806378|ref|YP_005842776.1|  99 RKMIITYISRNAIDPTTKLPIPPQRIEKAMEEARVSVNLNESVEKQAINIVKAIARQIPIKMAKALLEVNIPSSYAS 175
                                       689*********************************************************************88877 PP

                                       CHHHHHHHH.HH.......S.EEEEEE.EEGGGHHHHHHH CS
                            SBDS_C  79 kilklieqv.esqk..vaekewevvvl.iePgaykeleef 114
                                       k+ +  +++  ++k  ++++   ++ l i++g+++e+ + 
  gi|385806378|ref|YP_005842776.1| 176 KAYSNAKTLgIVHKtnWNQDGSVTFELeIPAGMQEEVIDK 215
                                       7777776664443322333444466678999999887765 PP

>> DUF1949  Domain of unknown function (DUF1949)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0     3e-06     0.013      30      55 ..     197     222 ..     194     223 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3e-06
                           DUF1949  30 dVtltlavpeeeveafkaaLtdltsG 55 
                                       +Vt++l++p++ +e+++++L+ lt G
  gi|385806378|ref|YP_005842776.1| 197 SVTFELEIPAGMQEEVIDKLNKLTKG 222
                                       6***********************99 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 ?   14.1   0.0   7.8e-06     0.035       9      71 ..     165     226 ..     163     229 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.8e-06
                                       EEEEEECCCCCCHHHHHHHCT-EEEEEEEE.TTEEEEEEEEEGGG-TTHHHCHHHCTTTS-EE CS
                             EFG_C   9 veievpeeyvgkvisdlssrrGeiedmeqdasgrviieaeiPlaeligfateLrslTkGegsf 71 
                                       +e+++p++y +k++s+ ++  G++ +++ +++g v+ e eiP+    +  ++L++lTkGe s+
  gi|385806378|ref|YP_005842776.1| 165 LEVNIPSSYASKAYSN-AKTLGIVHKTNWNQDGSVTFELEIPAGMQEEVIDKLNKLTKGEVSV 226
                                       799***********65.56679999999999***********99999************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.55
# Mc/sec: 1269.48
//
Query:       gi|385806379|ref|YP_005842777.1|  [L=242]
Description: exosome complex RNA-binding protein Rrp4 [Fervidicoccus fontis Kam940]
Scores for 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-05   22.7   0.1    0.00017   21.8   0.1    1.5  1  KH_6      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 !   21.8   0.1   9.6e-09   0.00017       1      44 [.     150     196 ..     150     198 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 9.6e-09
                              KH_6   1 GmlfeVslslvrRll...nhvLeeLgkagpfeiavGlNGriWvkses 44 
                                       G ++++  + v +l+     + e + k+ + ei + +NGr+W+k+++
  gi|385806379|ref|YP_005842777.1| 150 GKVIDIAQHAVNSLInrkRALVEAIVKETKTEILISNNGRVWIKGTD 196
                                       678888889999999443333344445589**************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.55
# Mc/sec: 1334.71
//
Query:       gi|385806380|ref|YP_005842778.1|  [L=246]
Description: exosome complex exonuclease 1 [Fervidicoccus fontis Kam940]
Scores for complete 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  121.0   0.0    6.3e-35  120.6   0.0    1.2  1  RNase_PH    3' exoribonuclease family, domain 1
    1.4e-15   57.0   0.4    2.8e-15   56.1   0.4    1.5  1  RNase_PH_C  3' exoribonuclease family, domain 2


Domain annotation for each model (and alignments):
>> RNase_PH  3' exoribonuclease family, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.6   0.0     7e-39   6.3e-35       1     132 []      24     153 ..      24     153 .. 0.94

  Alignments for each domain:
  == domain 1  score: 120.6 bits;  conditional E-value: 7e-39
                                       EEEEEEEEESSSSTTSEEEEEEECCEEEEEEEEEEEEEE-TCCG..--CCEEEECCCCECCCCEC-C...S...HHH CS
                          RNase_PH   1 elRslsietgvlsqanGSaylelGdtkvlasvtgpieerpseer..ddaegaldveveyapfasgerrregrpsdee 75 
                                       +lR++s++ g+l++a GSa++++G+t+v+a+v+gp+e+ p+ ++  d+a   l +++ +apf++ er++   p+++e
  gi|385806380|ref|YP_005842778.1|  24 QLRPISMKVGILKNAQGSALVSYGKTQVMAAVYGPREALPRHMTlpDRA--ILRIRYHMAPFSTSERKS-PAPTRRE 97 
                                       69************************************67777663444..5***************66.78***** PP

                                       HHHHHHHHHHHCCTC-CCGCCTCEEEEEEEEEECCCS-CHHHCHHHHHHHHHCTCEE CS
                          RNase_PH  76 ielsrlleralrpsillekkpkstididitvlssdggslldalinaaslALadagip 132
                                       iels+++ +al++ +  e +p++tid++i+vl++dg ++   + +aaslALadagip
  gi|385806380|ref|YP_005842778.1|  98 IELSKVIREALEATVFSELFPRTTIDVFIEVLQADG-GTRTTSLTAASLALADAGIP 153
                                       ************************************.*******************9 PP

>> RNase_PH_C  3' exoribonuclease family, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.1   0.4   3.1e-19   2.8e-15       1      67 []     156     221 ..     156     221 .. 0.97

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 3.1e-19
                                       S--EEEEEEEETTEEEES--HHHHHHSSEEEEEEEETTSEEEEEEEECSSCEEHHHHHHHHHHHHHH CS
                        RNase_PH_C   1 apviavtvgkvddqfvlDptkeEedlsegdltlavagtkevvtlmkeggsqldeetlleaielAkkg 67 
                                       +++++v+vgkvd+ +vlD +  E++ +++d+++a+  + ++++l++++g  l+++++ ea+++A+k+
  gi|385806380|ref|YP_005842778.1| 156 DLIAGVAVGKVDGVLVLDINEIEDSTGQADMPVAIMPNLNKIVLLQLNGT-LTRDEFNEALKMAQKA 221
                                       5899**********************************************.*************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 1397.00
//
Query:       gi|385806381|ref|YP_005842779.1|  [L=274]
Description: exosome complex RNA-binding protein Rrp42 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.8e-24   86.1   0.0    5.2e-24   85.2   0.0    1.4  1  RNase_PH    3' exoribonuclease family, domain 1
      2e-11   43.7   0.0    1.3e-10   41.2   0.0    2.2  2  RNase_PH_C  3' exoribonuclease family, domain 2


Domain annotation for each model (and alignments):
>> RNase_PH  3' exoribonuclease family, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.2   0.0   5.7e-28   5.2e-24       1     132 []      36     171 ..      36     171 .. 0.96

  Alignments for each domain:
  == domain 1  score: 85.2 bits;  conditional E-value: 5.7e-28
                                       EEEEEEEEESSSSTTSEEEEEEECCEEEEEEEEEEEEEE-TCCG--CCEEEECCCCECCCCEC-C...S...HHHHH CS
                          RNase_PH   1 elRslsietgvlsqanGSaylelGdtkvlasvtgpieerpseerddaegaldveveyapfasgerrregrpsdeeie 77 
                                       e+R+++i  + +++++GSa++ lGdt vl++v+++  + p ++ +++eg+l+v+ e+ p+as++++  g p++ + e
  gi|385806381|ref|YP_005842779.1|  36 EVRKITIVPNYIEKSDGSALVYLGDTLVLVGVKVEPGA-PYPD-NPNEGVLMVNAEFVPLASPAFEP-GPPDENAYE 109
                                       68**********************************99.8899.77789****************77.9******** PP

                                       HHHHHHHHHCCTC-C........CGCCTCEEEEEEEEEECCCS-CHHHCHHHHHHHHHCTCEE CS
                          RNase_PH  78 lsrlleralrpsill........ekkpkstididitvlssdggslldalinaaslALadagip 132
                                       l+r+++r+ r+s  +        ++++ + +  di+vl+++g +l+da+ +a+ +AL++++ip
  gi|385806381|ref|YP_005842779.1| 110 LARIIDRSYRESKAIglgelalvPGQKVLVVWNDIYVLNHSG-NLIDASAIASLVALMNTRIP 171
                                       **************9999999999999***************.*******************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 ?   -0.8   0.0      0.18   1.6e+03      52      66 ..      14      28 ..      10      29 .. 0.86
   2 !   41.2   0.0   1.4e-14   1.3e-10       4      64 ..     199     259 ..     197     262 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.18
                                      EEHHHHHHHHHHHHH CS
                        RNase_PH_C 52 ldeetlleaielAkk 66
                                      +++et++ ++e++k+
  gi|385806381|ref|YP_005842779.1| 14 MKRETIISVLETGKR 28
                                      899********9996 PP

  == domain 2  score: 41.2 bits;  conditional E-value: 1.4e-14
                                       EEEEEEEETTEEEES--HHHHHHSSEEEEEEEETTSEEEEEEEECSSCEEHHHHHHHHHHH CS
                        RNase_PH_C   4 iavtvgkvddqfvlDptkeEedlsegdltlavagtkevvtlmkeggsqldeetlleaielA 64 
                                       i  t++k++++++ Dpt eEe +s+++l +  ++++ +  ++k+g + lde ++ ++i+lA
  gi|385806381|ref|YP_005842779.1| 199 ITATIAKIGNYYLADPTDEEEYVSDARLSVSFTEDGIIAGMQKMGIGYLDENDINQMIDLA 259
                                       678*********************************999999999999************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 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:                        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: 0.64u 0.34s 00:00:00.98 Elapsed: 00:00:00.57
# Mc/sec: 1439.15
//
Query:       gi|385806382|ref|YP_005842780.1|  [L=86]
Description: 50S ribosomal protein L37Ae [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-33  113.9   1.6    2.8e-33  113.8   1.6    1.0  1  Ribosomal_L37ae  Ribosomal L37ae protein family
    5.3e-07   29.5   1.3      8e-07   28.9   1.3    1.4  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
     0.0023   17.8   0.3      0.003   17.4   0.3    1.2  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
     0.0092   16.3   2.2       0.11   12.9   0.4    2.2  2  DUF4379          Probable Zinc-ribbon domain
  ------ inclusion threshold ------
       0.06   13.1   3.0        3.3    7.5   0.1    2.2  2  A2L_zn_ribbon    A2L zinc ribbon domain
      0.065   14.0   0.6       0.39   11.5   0.2    2.0  2  zf-3CxxC_2       Zinc-binding domain
      0.086   12.4   1.4        7.9    6.1   0.1    2.1  2  TF_Zn_Ribbon     TFIIB zinc-binding
        0.2   11.4   0.3       0.24   11.1   0.3    1.1  1  Rep_fac-A_C      Replication factor-A C terminal domain
       0.24   11.5   1.0        2.5    8.2   0.0    2.0  2  CpXC             CpXC protein
       0.39   11.6   2.5        1.5    9.7   0.3    2.0  2  Ima1_N           Ima1 N-terminal domain
       0.78   10.3   4.8        1.3    9.5   0.5    2.2  2  zf-H2C2_2        Zinc-finger double domain
        2.4    8.1   6.6       0.45   10.4   1.8    2.0  2  HalOD2           Halobacterial output domain 2


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 !  113.8   1.6   1.9e-36   2.8e-33       1      81 [.       3      84 ..       3      86 .] 0.98

  Alignments for each domain:
  == domain 1  score: 113.8 bits;  conditional E-value: 1.9e-36
                                      XXXXXX-GGGGTTSS-HHHHHHHHHHHHHHHS-BEESSSSSS.EEEEEETTEEEETTTTEEEE-BSSSSS-HHHHHHHH CS
                   Ribosomal_L37ae  1 rtkkvgiaGkygtrYGaslrkrvkkieisqhakytCpfcgkt.kvkRkavgiwkCkkcgktvaGgAytpettsaktvks 78
                                      rtk vgiaGk+g+rYG++lrk+ k+i+++++a + Cpfcg + kv R ++g+wkC+kcg+++aGgAy+p+t  +k++ +
  gi|385806382|ref|YP_005842780.1|  3 RTKIVGIAGKFGARYGSTLRKQYKEIMEKRYAPHVCPFCGMSgKVTRISIGLWKCEKCGNVWAGGAYVPRTGLNKMFPK 81
                                      79***************************************99***********************************9 PP

                                      -XX CS
                   Ribosomal_L37ae 79 air 81
                                      +i+
  gi|385806382|ref|YP_005842780.1| 82 SIN 84
                                      997 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   1.3   5.4e-10     8e-07      18      44 ..      35      61 ..      22      63 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 5.4e-10
                     Zn_Tnp_IS1595 18 gfvCPhCgsr.kayriktrglfqCkeCr 44
                                       +vCP+Cg + k++ri+  gl++C++C+
  gi|385806382|ref|YP_005842780.1| 35 PHVCPFCGMSgKVTRISI-GLWKCEKCG 61
                                      367**************9.********8 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.3     2e-06     0.003      23      56 ..      30      64 ..      17      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2e-06
                    OrfB_Zn_ribbon 23 npayTSktCseCgsknke.alsgrtfkCpnCgfea 56
                                      +++y    C+ Cg  +k  + s  ++kC++Cg ++
  gi|385806382|ref|YP_005842780.1| 30 EKRYAPHVCPFCGMSGKVtRISIGLWKCEKCGNVW 64
                                      56678889*********999************986 PP

>> DUF4379  Probable Zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1     0.081   1.2e+02      37      56 .]      23      41 ..      17      41 .. 0.81
   2 !   12.9   0.4   7.3e-05      0.11      29      40 ..      54      65 ..      49      70 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.081
                           DUF4379 37 heWeasvsnrtkgsskCpkC 56
                                      +++++ +++r + +  Cp C
  gi|385806382|ref|YP_005842780.1| 23 KQYKEIMEKRYAPHV-CPFC 41
                                      578888899997776.***9 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 7.3e-05
                           DUF4379 29 wWkCakCgheWe 40
                                      +WkC+kCg+ W 
  gi|385806382|ref|YP_005842780.1| 54 LWKCEKCGNVWA 65
                                      6**********5 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1    0.0022       3.3      23      30 ..      37      44 ..      34      46 .. 0.90
   2 ?    5.8   0.6    0.0076        11       3      11 ..      54      62 ..      53      63 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0022
                     A2L_zn_ribbon 23 vCieCgas 30
                                      vC++Cg s
  gi|385806382|ref|YP_005842780.1| 37 VCPFCGMS 44
                                      9*****86 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0076
                     A2L_zn_ribbon  3 lkvCsvCgg 11
                                      l++C++Cg+
  gi|385806382|ref|YP_005842780.1| 54 LWKCEKCGN 62
                                      699****96 PP

>> zf-3CxxC_2  Zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.57   8.5e+02      47      66 ..      23      42 ..      15      44 .. 0.65
   2 ?   11.5   0.2   0.00026      0.39       6      20 ..      53      67 ..      49      73 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.57
                        zf-3CxxC_2 47 kkkgaakkesdkeHesrlCe 66
                                      k+ ++  +++ ++H   +C+
  gi|385806382|ref|YP_005842780.1| 23 KQYKEIMEKRYAPHVCPFCG 42
                                      44444555577888888885 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00026
                        zf-3CxxC_2  6 GefkCekCgkeWsSa 20
                                      G +kCekCg+ W  +
  gi|385806382|ref|YP_005842780.1| 53 GLWKCEKCGNVWAGG 67
                                      889*********865 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.2    0.0081        12      21      26 ..      37      42 ..      35      50 .. 0.75
   2 ?    6.1   0.1    0.0053       7.9      22      29 ..      57      64 ..      53      72 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0081
                                      EESSSS CS
                      TF_Zn_Ribbon 21 vCtdCG 26
                                      vC++CG
  gi|385806382|ref|YP_005842780.1| 37 VCPFCG 42
                                      555555 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0053
                                      ESSSSBEE CS
                      TF_Zn_Ribbon 22 CtdCGlVl 29
                                      C++CG+V+
  gi|385806382|ref|YP_005842780.1| 57 CEKCGNVW 64
                                      ******98 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 ?   11.1   0.3   0.00016      0.24      13      45 ..      30      62 ..      19      69 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00016
                                      TTTTEEEB--STT---B-EEETTTEEEETTTTE CS
                       Rep_fac-A_C 13 kdnlvYkACpsedCnkKvveeedgewrCekCdk 45
                                      +++ + + Cp  +   Kv++ + g w+CekC +
  gi|385806382|ref|YP_005842780.1| 30 EKRYAPHVCPFCGMSGKVTRISIGLWKCEKCGN 62
                                      5566667899777789***************76 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0017       2.5      27      50 ..      25      48 ..      19      52 .. 0.87
   2 ?    2.6   0.2     0.088   1.3e+02      36      45 ..      53      62 ..      46      65 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0017
                              CpXC 27 keklldgslfeatCpkCgatakle 50
                                       ++++++++  ++Cp Cg ++k++
  gi|385806382|ref|YP_005842780.1| 25 YKEIMEKRYAPHVCPFCGMSGKVT 48
                                      5789***************99876 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.088
                              CpXC 36 featCpkCga 45
                                        ++C+kCg+
  gi|385806382|ref|YP_005842780.1| 53 GLWKCEKCGN 62
                                      5689999996 PP

>> Ima1_N  Ima1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.8    0.0055       8.2     114     132 ..      23      42 ..      14      44 .. 0.86
   2 ?    9.7   0.3   0.00098       1.5       3      27 ..      38      62 ..      36      66 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0055
                            Ima1_N 114 eeykkeleerY.pqlCesCe 132
                                       ++yk+ +e+rY p++C  C 
  gi|385806382|ref|YP_005842780.1|  23 KQYKEIMEKRYaPHVCPFCG 42 
                                       79*********989***996 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00098
                            Ima1_N  3 CffCnkkskvkyeeknsfeCpsCea 27
                                      C fC+ + kv++ +   ++C++C  
  gi|385806382|ref|YP_005842780.1| 38 CPFCGMSGKVTRISIGLWKCEKCGN 62
                                      99************999******75 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.5    0.0009       1.3      14      23 ..      35      44 ..      24      47 .. 0.74
   2 ?    2.9   0.3      0.11   1.6e+02      15      21 ..      55      61 ..      44      63 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0009
                         zf-H2C2_2 14 pyeCplCdka 23
                                      p+ Cp+C+ +
  gi|385806382|ref|YP_005842780.1| 35 PHVCPFCGMS 44
                                      79*****976 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.11
                         zf-H2C2_2 15 yeCplCd 21
                                      ++C++C+
  gi|385806382|ref|YP_005842780.1| 55 WKCEKCG 61
                                      79****7 PP

>> HalOD2  Halobacterial output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.2      0.53   7.9e+02       2      10 ..      35      43 ..      34      49 .. 0.79
   2 ?   10.4   1.8    0.0003      0.45      30      43 ..      53      66 ..      42      70 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.53
                            HalOD2  2 PekCseCsl 10
                                      P+ C+ C++
  gi|385806382|ref|YP_005842780.1| 35 PHVCPFCGM 43
                                      788999986 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0003
                            HalOD2 30 yvWkCtrCGevqaa 43
                                        WkC +CG+v a+
  gi|385806382|ref|YP_005842780.1| 53 GLWKCEKCGNVWAG 66
                                      57********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); 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: 0.50u 0.33s 00:00:00.83 Elapsed: 00:00:00.53
# Mc/sec: 491.12
//
Query:       gi|385806383|ref|YP_005842781.1|  [L=207]
Description: hypothetical protein FFONT_1341 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score 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   0.0      0.038   14.1   0.0    1.2  1  Brix      Brix domain


Domain annotation for each model (and alignments):
>> Brix  Brix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.1e-06     0.038       1      60 [.      13      75 ..      13     163 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.1e-06
                                      BTT--HHHHHHHHHHHHHCTTSEEEEEEECT-TTTHHHHHHH...-HHHHHHHHHCTC..SEEEE CS
                              Brix  1 grktssrlrqllkdlrslmkphtasflkrnsnklkdlvelag...vthlellsekndc..slfvf 60
                                      +r +s r+r++lkd+ sl  p  ++ + r++  +kdlv ++     t ++++ ekn +   +++ 
  gi|385806383|ref|YP_005842781.1| 13 SREPSLRVRSFLKDIISLA-PWLVKVN-RGKLTFKDLVDITIsekSTTFVIIGEKNGNpsIMRIY 75
                                      678999*************.8787744.67779**997777666999999999955433145554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.34s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 1191.89
//
Query:       gi|385806384|ref|YP_005842782.1|  [L=95]
Description: hypothetical protein FFONT_1342 [Fervidicoccus fontis Kam940]
Scores for complete 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   0.0    0.00015   21.9   0.0    1.1  1  Pcc1      Transcription factor Pcc1
  ------ inclusion threshold ------
      0.031   14.5   2.1       0.06   13.6   0.1    2.4  3  HALZ      Homeobox associated leucine zipper


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 !   21.9   0.0   1.6e-08   0.00015       1      69 [.      11      83 ..      11      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.6e-08
                                      EEEEEEE-SSHHHHHHHHHHHHHH....CHC-TTE.CEEEEEEETTEEEEEEEESSHHHHHHHHHHHHHHHHHH CS
                              Pcc1  1 sltisvpfpterlAsialrtLqvD....kelspla.vkrslslegnvLqveykAttnrmLRvavngfleslglv 69
                                      s+++++  ++e+l ++ +++L+++       +++  v +++  e+++L ++++++t   +++ +n++l +++ +
  gi|385806384|ref|YP_005842782.1| 11 SFSLEIHHENEKLLKAYFESLKPEadslVN-QKKGkVFVEYNAEEKKLILKMETETISDFKALMNSYLYLIKAI 83
                                      6899********************876422.33334999*****************************999977 PP

>> HALZ  Homeobox associated leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1     0.052   4.6e+02      25      33 ..      17      25 ..      15      25 .. 0.80
   2 ?   13.6   0.1   6.7e-06      0.06       9      29 ..      23      43 ..      22      44 .. 0.92
   3 ?   -1.2   0.1      0.27   2.5e+03       6      15 ..      68      77 ..      67      90 .. 0.48

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.052
                              HALZ 25 kkenekLka 33
                                      ++enekL++
  gi|385806384|ref|YP_005842782.1| 17 HHENEKLLK 25
                                      789**9985 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 6.7e-06
                              HALZ  9 vLKasYdaLksdydsLkkene 29
                                       LKa +++Lk + dsL ++++
  gi|385806384|ref|YP_005842782.1| 23 LLKAYFESLKPEADSLVNQKK 43
                                      69**************99996 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.27
                              HALZ  6 DYdvLKasYd 15
                                      D+++L  sY 
  gi|385806384|ref|YP_005842782.1| 68 DFKALMNSYL 77
                                      5555555553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1159  (0.0646439); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); 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: 0.54u 0.34s 00:00:00.88 Elapsed: 00:00:00.54
# Mc/sec: 527.70
//
Query:       gi|385806385|ref|YP_005842783.1|  [L=51]
Description: hypothetical protein FFONT_1343 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       199  (0.0110993); expected 358.6 (0.02)
Passed bias filter:                      172  (0.0095934); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.33s 00:00:00.78 Elapsed: 00:00:00.52
# Mc/sec: 295.87
//
Query:       gi|385806386|ref|YP_005842784.1|  [L=131]
Description: prefoldin subunit beta [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-18   66.4  12.7    2.3e-18   66.1  12.7    1.1  1  Prefoldin_2      Prefoldin subunit
  ------ inclusion threshold ------
      0.013   15.6   4.3       0.33   11.0   0.2    2.1  2  Med28            Mediator complex subunit 28
      0.014   15.1   4.4       0.34   10.6   0.2    2.0  2  BCAS2            Breast carcinoma amplified sequence 2 (BCAS2
      0.015   14.9   1.3      0.018   14.6   1.3    1.1  1  Exonuc_VII_L     Exonuclease VII, large subunit
      0.016   15.4   7.7       0.39   10.9   0.5    2.2  2  K-box            K-box region
      0.019   15.2   2.0        3.1    8.2   0.1    2.2  2  KxDL             Uncharacterized conserved protein
      0.044   13.9   7.8       0.69   10.0   1.0    2.3  2  DivIVA           DivIVA protein
      0.054   14.0   1.7       0.52   10.8   0.2    2.3  2  NPV_P10          Nucleopolyhedrovirus P10 protein
      0.054   13.6   1.2      0.054   13.6   1.2    2.7  2  NYD-SP28_assoc   Sperm tail C-terminal domain
      0.064   13.6   9.0       0.91    9.9   1.1    3.2  2  Syntaxin_2       Syntaxin-like protein
      0.064   12.8   9.6       0.46   10.0   9.7    1.8  1  Filament         Intermediate filament protein
      0.066   13.0  10.7       0.16   11.7   2.2    2.1  2  KASH_CCD         Coiled-coil region of CCDC155 or KASH
      0.089   12.8   2.4        1.2    9.2   0.2    2.1  2  Laminin_II       Laminin Domain II
      0.093   13.0   7.6       0.31   11.3   1.3    2.1  2  Jnk-SapK_ap_N    JNK_SAPK-associated protein-1
      0.096   12.1   0.1       0.12   11.8   0.1    1.2  1  eIF-6            eIF-6 family
       0.11   12.6   3.3       0.14   12.3   0.1    2.2  2  T3SchapCesA      Type III secretion system filament chaperone
       0.11   11.7   4.1       0.37   10.0   0.6    2.0  2  Vps54_N          Vacuolar-sorting protein 54, of GARP complex
       0.13   12.8   1.0         12    6.5   1.1    2.6  2  YtxH             YtxH-like protein
       0.13   12.3   8.6       0.35   10.9   0.6    2.2  2  FlxA             FlxA-like protein
       0.13   12.3   3.2       0.84    9.7   0.3    2.4  2  Cullin_Nedd8     Cullin protein neddylation domain
       0.14   11.8   3.4       0.12   12.0   0.9    1.8  2  RlaP             RNA repair pathway DNA polymerase beta famil
       0.15   12.4   0.8        0.8   10.1   0.0    2.3  2  TraC             TraC-like protein
       0.15   12.1   1.2        5.8    7.0   0.1    2.2  2  DUF1664          Protein of unknown function (DUF1664)
       0.17   11.9  11.7        1.6    8.7   1.2    2.3  2  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
       0.17   12.5   4.0       0.79   10.4   3.9    1.8  1  AATF-Che1        Apoptosis antagonizing transcription factor
       0.17   11.7   5.1       0.37   10.7   1.1    2.1  2  ACCA             Acetyl co-enzyme A carboxylase carboxyltrans
       0.19   10.4   8.0       0.23   10.2   8.0    1.0  1  HlyD_2           HlyD family secretion protein
       0.21   11.9   8.0        1.2    9.5   1.6    2.1  2  OmpH             Outer membrane protein (OmpH-like)
       0.22   12.0   8.3        0.2   12.1   1.7    2.3  2  Snapin_Pallidin  Snapin/Pallidin
       0.29   11.4   1.1        2.8    8.3   0.2    2.3  2  DUF948           Bacterial protein of unknown function (DUF94
       0.38    9.3   6.4       0.56    8.7   6.4    1.3  1  FapA             Flagellar Assembly Protein A
       0.43   11.3  13.1        2.4    9.0   4.4    2.1  2  RecG_N           RecG N-terminal helical domain
       0.47   10.3   4.8       0.56   10.0   0.2    2.1  2  DUF2570          Protein of unknown function (DUF2570)
       0.48    9.8   6.6        1.2    8.4   3.2    2.1  2  FliD_C           Flagellar hook-associated protein 2 C-termin
       0.56   10.0   7.8       0.87    9.4   3.1    1.9  2  PCRF             PCRF domain
       0.64   10.5  13.3          1    9.9   2.2    2.1  2  APG6_N           Apg6 coiled-coil region
       0.68   10.4  13.9        3.7    8.1   1.7    2.7  2  ZapB             Cell division protein ZapB
       0.93    9.9  10.6        2.7    8.4   1.9    2.5  2  CLZ              C-terminal leucine zipper domain of cyclic n
       0.99    9.5  13.9       0.19   11.7   3.2    2.7  2  Bap31_Bap29_C    Bap31/Bap29 cytoplasmic coiled-coil domain
        1.1    8.8   9.0        1.7    8.1   1.5    2.4  2  4HB_MCP_1        Four helix bundle sensory module for signal 
        1.3    8.9  14.6        1.1    9.1   4.3    2.8  3  CdvA             CdvA-like coiled-coil domain
        1.4    8.7   7.3        1.4    8.7   0.6    2.5  2  IL31             Interleukin 31
        1.5    9.3  11.0        3.4    8.1   0.9    2.8  3  FlaC_arch        Flagella accessory protein C (FlaC)
        1.6    8.0   6.4         28    3.9   6.4    2.1  1  CorA             CorA-like Mg2+ transporter protein
        2.2    9.2   6.0       0.65   10.9   1.0    2.2  2  DUF5339          Family of unknown function (DUF5339)
        2.3    7.8  11.1        7.6    6.1  11.1    1.7  1  DUF4795          Domain of unknown function (DUF4795)
        2.5    7.4   4.7        1.2    8.5   0.6    1.9  2  TraF_2           F plasmid transfer operon, TraF, protein
        3.2    8.5   8.1         11    6.7   0.2    2.7  3  Sas10_Utp3       Sas10/Utp3/C1D family
        3.5    8.4   7.3        2.6    8.8   1.0    2.4  2  FliD_N           Flagellar hook-associated protein 2 N-termin
        3.8    7.8  12.1        2.1    8.7   0.3    3.2  4  Osmo_CC          Osmosensory transporter coiled coil
        4.2    7.5   8.1        5.1    7.2   1.4    2.1  2  GvpK             Gas vesicle protein K
        5.1    7.0  13.7        2.4    8.1   1.0    3.1  2  Prefoldin        Prefoldin subunit
        5.6    7.1  15.5        1.9    8.6   3.8    2.4  2  DHR10            Designed helical repeat protein 10 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 !   66.1  12.7   6.9e-21   2.3e-18       2     105 ..      11     114 ..      10     115 .. 0.97

  Alignments for each domain:
  == domain 1  score: 66.1 bits;  conditional E-value: 6.9e-21
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT--EEEEETTEEEEE-HHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2   2 elinkfqqlqqqlqqlaqqikqletqlkelelvleelelldedtkvyklvGdvlvkqdkeevkeeLeerketlekei 78 
                                       + + ++ +lq++  +l +q+  +e +lke+++ le+l++++++tk+y++vG++++ +d++++ +eL e+ket e  +
  gi|385806386|ref|YP_005842784.1|  11 QVAQQLDELQEKYNNLLNQRLIVESELKEINKLLETLNNIPPETKIYRSVGNIFFAEDRDKLVKELTEKKETDELIY 87 
                                       667899*********************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHCCTS- CS
                       Prefoldin_2  79 ktlekqleklekeleelkeelqkklqq 105
                                       ++ +k +e+l+k+++ l+e+l+ +l +
  gi|385806386|ref|YP_005842784.1|  88 ERFKKDEEDLKKQISTLQEKLRGLLSK 114
                                       *********************998865 PP

>> Med28  Mediator complex subunit 28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2   0.00098      0.33      68     117 ..      10      59 ..       3      73 .. 0.85
   2 ?    6.3   0.7     0.028       9.5      52      83 ..      79     110 ..      64     123 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00098
                             Med28  68 eqlatqlkalrekgqnvfgdgtkidstidyleklkqvlsdaedvykvrde 117
                                       eq+a ql  l+ek +n++ +   ++s +  ++kl ++l+++    k   +
  gi|385806386|ref|YP_005842784.1|  10 EQVAQQLDELQEKYNNLLNQRLIVESELKEINKLLETLNNIPPETKIYRS 59 
                                       89********************************9999988655555444 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.028
                             Med28  52 kvapeellmkHlqktseqlatqlkalrekgqn 83 
                                       k   +el+   ++k  e+l  q+ +l+ek + 
  gi|385806386|ref|YP_005842784.1|  79 KKETDELIYERFKKDEEDLKKQISTLQEKLRG 110
                                       456799**********************9665 PP

>> BCAS2  Breast carcinoma amplified sequence 2 (BCAS2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.5      0.02       6.9     162     200 ..      10      48 ..       8      53 .. 0.89
   2 ?   10.6   0.2     0.001      0.34     134     184 ..      67     117 ..      57     121 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.02
                             BCAS2 162 eeageeLksleekWrelvsknleieaaceeleaeieelk 200
                                       e+++++L +l+ek+ +l ++ l +e + +e+++ +e l+
  gi|385806386|ref|YP_005842784.1|  10 EQVAQQLDELQEKYNNLLNQRLIVESELKEINKLLETLN 48 
                                       68999**********************999998877765 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.001
                             BCAS2 134 aelkklekeleetkeeieevnrqRkseQeeageeLksleekWrelvsknle 184
                                       ++ +kl kel+e+ke  e +  + k++ e++++++++l+ek r l sk ++
  gi|385806386|ref|YP_005842784.1|  67 EDRDKLVKELTEKKETDELIYERFKKDEEDLKKQISTLQEKLRGLLSKYYQ 117
                                       566788999999887777777777**********************99886 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   1.3   5.3e-05     0.018     135     244 ..       2     114 ..       1     127 [. 0.53

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.3e-05
                      Exonuc_VII_L 135 Aelvvpdkaeleeqleelerrlekaikrll..eekkqrleklasrlk..speellerkrqrldeleerleralkkql 207
                                       Ae+v p+++++++ql+el++++++ ++++l  e++ ++++kl ++l+   pe+++ r+  ++  +e+r +  l k+l
  gi|385806386|ref|YP_005842784.1|   2 AEKVPPEIEQVAQQLDELQEKYNNLLNQRLivESELKEINKLLETLNniPPETKIYRSVGNIFFAEDRDK--LVKEL 76 
                                       99999**********************9997744556666666666312344444444333332222211..22233 PP

                      Exonuc_VII_L 208 kkkrerleelkerlkekleekkerlkklkerle.llee 244
                                       ++k+e+ e + er+k++ e+ k+++++l+e+l+ ll++
  gi|385806386|ref|YP_005842784.1|  77 TEKKETDELIYERFKKDEEDLKKQISTLQEKLRgLLSK 114
                                       33333333333344333344444444444444433333 PP

>> K-box  K-box region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   1.6    0.0083       2.8      10      53 ..       4      48 ..       1      51 [. 0.84
   2 ?   10.9   0.5    0.0012      0.39       7      40 ..      86     119 ..      73     122 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0083
                             K-box 10 elkqEvskLkkeieklqrsqRkllGedl.eslslkeLqqLEqqLe 53
                                      ++  E++++ +++++lq++  +ll + l  + +lke ++L ++L+
  gi|385806386|ref|YP_005842784.1|  4 KVPPEIEQVAQQLDELQEKYNNLLNQRLiVESELKEINKLLETLN 48
                                      566799********************9977888888888877776 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0012
                             K-box   7 eeeelkqEvskLkkeieklqrsqRkllGedlesl 40 
                                        +e++k++ + Lkk+i  lq+++R ll + ++++
  gi|385806386|ref|YP_005842784.1|  86 IYERFKKDEEDLKKQISTLQEKLRGLLSKYYQKV 119
                                       6889999******************998776665 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1     0.009       3.1      37      75 ..      10      48 ..       7      53 .. 0.75
   2 ?    6.7   0.3     0.026       8.7      21      52 ..      86     117 ..      71     123 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.009
                              KxDL 37 alsqerlaklrarfkqgtkllkevkkdLesifkkirslk 75
                                      +++ ++l +l++++++  +    v ++L+ i+k +++l+
  gi|385806386|ref|YP_005842784.1| 10 EQVAQQLDELQEKYNNLLNQRLIVESELKEINKLLETLN 48
                                      566777888888888888888888888888888777776 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.026
                              KxDL  21 tsgrlnkknreLlelnalsqerlaklrarfkq 52 
                                       +  r++k ++ L++++  +qe+l  l +++ q
  gi|385806386|ref|YP_005842784.1|  86 IYERFKKDEEDLKKQISTLQEKLRGLLSKYYQ 117
                                       45677777777777777777777776666655 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.0    0.0021      0.69      27      67 ..       9      49 ..       2      54 .. 0.78
   2 ?    8.0   0.5    0.0087         3      34      56 ..      87     109 ..      82     120 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0021
                                      HHHHHHHHHHHHHHHHHHHHHHHCCCCTXXXXXXXXXXXXX CS
                            DivIVA 27 LdqvakdyeallkeneelkekvkeleeklkeykeleetLkk 67
                                      ++qva+++ +l ++ ++l ++    e++lke ++l etL++
  gi|385806386|ref|YP_005842784.1|  9 IEQVAQQLDELQEKYNNLLNQRLIVESELKEINKLLETLNN 49
                                      67888888888888888888888888888888888888876 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0087
                                       HHHHHHHHHHHHHHHHCCCCTXX CS
                            DivIVA  34 yeallkeneelkekvkeleeklk 56 
                                       ye++ k+ e+lk+++++l+ekl 
  gi|385806386|ref|YP_005842784.1|  87 YERFKKDEEDLKKQISTLQEKLR 109
                                       99*******************95 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2    0.0015      0.52      12      56 ..       8      49 ..       3      64 .. 0.62
   2 ?    2.5   0.1       0.6     2e+02      14      30 ..      95     111 ..      70     125 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0015
                           NPV_P10 12 dikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaelet 56
                                      +i++v +++d lq++ +++ ++   v   +++L ++++ L++l++
  gi|385806386|ref|YP_005842784.1|  8 EIEQVAQQLDELQEKYNNLLNQRLIV---ESELKEINKLLETLNN 49
                                      46667777777777776666555443...3556666666666655 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.6
                           NPV_P10  14 kavddkVdalqqqvddv 30 
                                       ++++++++ lq+++  +
  gi|385806386|ref|YP_005842784.1|  95 EDLKKQISTLQEKLRGL 111
                                       44555555565555444 PP

>> NYD-SP28_assoc  Sperm tail C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.2   0.00016     0.054       6      53 ..       1      48 [.       1      50 [. 0.85
   2 ?    1.9   1.4      0.71   2.4e+02      41      57 ..      93     109 ..      66     116 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00016
                    NYD-SP28_assoc  6 lanvipeeklklWdalekaLekYhevLteRaklieetesLekqNeeLr 53
                                      +a+ +p+e +++ ++l++  ekY+++L++R  + +e +++ k  e L 
  gi|385806386|ref|YP_005842784.1|  1 MAEKVPPEIEQVAQQLDELQEKYNNLLNQRLIVESELKEINKLLETLN 48
                                      5777999999999*****************999999988887666665 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.71
                    NYD-SP28_assoc  41 etesLekqNeeLrnlLk 57 
                                       + e L+kq + L++ L+
  gi|385806386|ref|YP_005842784.1|  93 DEEDLKKQISTLQEKLR 109
                                       23777888777777664 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   3.5      0.15        52      29      65 ..      10      49 ..       3      81 .. 0.60
   2 ?    9.9   1.1    0.0027      0.91      25      54 ..      91     120 ..      68     128 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.15
                        Syntaxin_2 29 eelreklhelieeinelikk...tnellkklsqldnsssd 65
                                      e++ ++l+el+e+ n+l+++   +++ lk++++l +++++
  gi|385806386|ref|YP_005842784.1| 10 EQVAQQLDELQEKYNNLLNQrliVESELKEINKLLETLNN 49
                                      6777788888888887776544346666666666665543 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0027
                        Syntaxin_2  25 kkdteelreklhelieeinelikktnellk 54 
                                       kkd e+l++++ +l+e+++ l++k  ++++
  gi|385806386|ref|YP_005842784.1|  91 KKDEEDLKKQISTLQEKLRGLLSKYYQKVS 120
                                       37899999*************999877776 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   9.7    0.0014      0.46      72     137 ..       4     112 ..       2     121 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0014
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX......................................X CS
                          Filament  72 rlqleldnlreeledlrkkyekelnkreevEaelkalr......................................k 110
                                       ++  e+++++++l++l++ky++ ln+r  vE+elk+++                                      k
  gi|385806386|ref|YP_005842784.1|   4 KVPPEIEQVAQQLDELQEKYNNLLNQRLIVESELKEINklletlnnippetkiyrsvgniffaedrdklvkeltekK 80 
                                       566799********************************566666666666666666666666666666666666655 PP

                                       XXXXXXXXXX.....XXXXXXXXXXXXXXXXX CS
                          Filament 111 dldeatlarv.....dLekkvesLkeelaflk 137
                                       + de+  +r      dL k++ +L+e l+ l 
  gi|385806386|ref|YP_005842784.1|  81 ETDELIYERFkkdeeDLKKQISTLQEKLRGLL 112
                                       55555555433333355566666666555443 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 ?    6.6   1.5     0.018       6.2      64     108 ..       4      48 ..       1      60 [. 0.78
   2 ?   11.7   2.2   0.00048      0.16      70     113 ..      67     110 ..      65     118 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.018
                          KASH_CCD  64 lleeEleelkalvkeleEkrarlkaqnkqlekenqsLiakiesLq 108
                                        +  E+e++ + + el+Ek ++l +q+  +e e + +++ +e+L+
  gi|385806386|ref|YP_005842784.1|   4 KVPPEIEQVAQQLDELQEKYNNLLNQRLIVESELKEINKLLETLN 48 
                                       566688888888888888888888888888888877777777776 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00048
                          KASH_CCD  70 eelkalvkeleEkrarlkaqnkqlekenqsLiakiesLqeenik 113
                                       e+  +lvkel Ek++  +   ++ +k+++ L+++i +Lqe+++ 
  gi|385806386|ref|YP_005842784.1|  67 EDRDKLVKELTEKKETDELIYERFKKDEEDLKKQISTLQEKLRG 110
                                       667789**********************************9875 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.2    0.0034       1.2      12      51 ..       9      48 ..       1      63 [. 0.61
   2 ?    4.1   0.2      0.13        45      38      74 ..      78     114 ..      65     124 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0034
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II 12 akevleqlaplsqnlentkeklseinrsveetnekvkdan 51
                                      +++v +ql +l+++ +n+ ++   ++++++e+n++++ +n
  gi|385806386|ref|YP_005842784.1|  9 IEQVAQQLDELQEKYNNLLNQRLIVESELKEINKLLETLN 48
                                      4455555555555555555555556666666666655544 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.13
                                       XXXXXXXXXXX.XXXXXXXXXXXXXXXX--TTTTTGGG CS
                        Laminin_II  38 rsveetnekvk.dankairdArrsvkkLeklapqLldk 74 
                                       ++ +et+e++   ++k  +d ++++++L++++  Ll+k
  gi|385806386|ref|YP_005842784.1|  78 EK-KETDELIYeRFKKDEEDLKKQISTLQEKLRGLLSK 114
                                       44.66666665467777777777777777777777776 PP

>> Jnk-SapK_ap_N  JNK_SAPK-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.6     0.052        18      50      88 ..       7      45 ..       2      57 .. 0.78
   2 ?   11.3   1.3    0.0009      0.31      63     111 ..      73     114 ..      63     126 .. 0.60

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.052
                     Jnk-SapK_ap_N 50 aeleelreeleqLeteyerekelrkraeeeleeiedqwe 88
                                       e+e++ ++l++L+++y++  ++r   e el ei + +e
  gi|385806386|ref|YP_005842784.1|  7 PEIEQVAQQLDELQEKYNNLLNQRLIVESELKEINKLLE 45
                                      578888888888888888888888888888888776555 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0009
                     Jnk-SapK_ap_N  63 eteyerekelrkraeeeleeiedqweeerkelqekveqleeenrelelk 111
                                        +e++++ke         e+i + +++++++l+++++ l+e+ r l  k
  gi|385806386|ref|YP_005842784.1|  73 VKELTEKKET-------DELIYERFKKDEEDLKKQISTLQEKLRGLLSK 114
                                       4444433333.......34556667777777777777777777777733 PP

>> eIF-6  eIF-6 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00035      0.12      63     120 ..      24      83 ..      19     108 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00035
                                       SEEEEETT--HHHHHHHHHHHH..---EEE--SS--HHHHEEE-SSEEEE-GGGGG.GHH CS
                             eIF-6  63 ngllvpstvtdeeleklkeslk..leverleekltAlGNvilaNDkvAlvhpdlsketve 120
                                       n ll  +++ ++el+++++ l+   ++    + +  +GN++ a+D+  lv++  +k++ +
  gi|385806386|ref|YP_005842784.1|  24 NNLLNQRLIVESELKEINKLLEtlNNIPPETKIYRSVGNIFFAEDRDKLVKELTEKKETD 83 
                                       6677788999*********9988778866667889***************9999877654 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 ?   12.3   0.1    0.0004      0.14      49      87 ..      10      49 ..       1      57 [. 0.82
   2 ?    0.9   0.5       1.5   5.2e+02      39      57 ..      74      92 ..      65     117 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0004
                       T3SchapCesA 49 pqaaeklnkliegytyg.eerklydsalskieklietlkp 87
                                       q a++l+ l e y    ++r + +s l  i+kl+etl+ 
  gi|385806386|ref|YP_005842784.1| 10 EQVAQQLDELQEKYNNLlNQRLIVESELKEINKLLETLNN 49
                                      4899**********87615666789************975 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 1.5
                       T3SchapCesA 39 nilsekaktdpqaaeklnk 57
                                      ++l+ek  td    e+++k
  gi|385806386|ref|YP_005842784.1| 74 KELTEKKETDELIYERFKK 92
                                      4444444444433333333 PP

>> Vps54_N  Vacuolar-sorting protein 54, of GARP complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.2      0.14        46      36      77 ..       8      48 ..       2      55 .. 0.79
   2 ?   10.0   0.6    0.0011      0.37       3      63 ..      59     120 ..      57     126 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.14
                           Vps54_N 36 evkklksqhdvvskklsqlilekreefvkelseveeiekelk 77
                                      e++++ +q+d +++k + + l++r  + +el+e++++ + l+
  gi|385806386|ref|YP_005842784.1|  8 EIEQVAQQLDELQEKYN-NLLNQRLIVESELKEINKLLETLN 48
                                      67788899999999965.557888899999999999888776 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0011
                           Vps54_N   3 sieevyFdeefdpikyeLkklpdde.lsyesiekevkklksqhdvvskklsqlilekreefv 63 
                                       s+ +++F e+ d    eL +  +++ l ye + k  + lk+q   +++kl  l  + +++++
  gi|385806386|ref|YP_005842784.1|  59 SVGNIFFAEDRDKLVKELTEKKETDeLIYERFKKDEEDLKKQISTLQEKLRGLLSKYYQKVS 120
                                       67789*********99**98888888************************999988887765 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1       0.2        68      29      66 ..      11      79 ..       3      88 .. 0.57
   2 ?    6.5   1.1     0.036        12      28      52 ..      95     119 ..      66     130 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.2
                              YtxH 29 dlkekaddlkekakelleeakeka..................................kekaedlkekvkek 66
                                      ++++++d+l+ek ++ll++   +                                   +e  ++l+++++ek
  gi|385806386|ref|YP_005842784.1| 11 QVAQQLDELQEKYNNLLNQ---RLiveselkeinklletlnnippetkiyrsvgniffAEDRDKLVKELTEK 79
                                      4455556666665555432...22454555555555555555555555666666666656666666666655 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.036
                              YtxH  28 kdlkekaddlkekakelleeakeka 52 
                                       +dlk++ ++l+ek+  ll + ++k+
  gi|385806386|ref|YP_005842784.1|  95 EDLKKQISTLQEKLRGLLSKYYQKV 119
                                       6788888888888888887777766 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   1.9     0.046        15      17      54 ..       7      44 ..       1      50 [. 0.74
   2 ?   10.9   0.6     0.001      0.35      28      67 ..      71     110 ..      66     124 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.046
                              FlxA 17 sqiasLqkQiknlqkqLkelsesdeltkeekkkqqqli 54
                                       +i++  +Q+++lq++ ++l ++    + e k+  +l+
  gi|385806386|ref|YP_005842784.1|  7 PEIEQVAQQLDELQEKYNNLLNQRLIVESELKEINKLL 44
                                      57999999999999999999998555555555555555 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.001
                              FlxA  28 nlqkqLkelsesdeltkeekkkqqqliqaQIqqlqaQIaq 67 
                                       +l k+L e +e+del  e  kk ++ +++QI+ lq  ++ 
  gi|385806386|ref|YP_005842784.1|  71 KLVKELTEKKETDELIYERFKKDEEDLKKQISTLQEKLRG 110
                                       6677777778888888888888899999999999988875 PP

>> Cullin_Nedd8  Cullin protein neddylation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.2       0.3     1e+02      36      54 ..       4      22 ..       1      48 [. 0.83
   2 ?    9.7   0.3    0.0025      0.84      23      54 ..      70     107 ..      68     119 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.3
                      Cullin_Nedd8 36 rftpsiadikkrIesLiek 54
                                      +++p+i+++ +++++L ek
  gi|385806386|ref|YP_005842784.1|  4 KVPPEIEQVAQQLDELQEK 22
                                      6788899999999999887 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0025
                      Cullin_Nedd8  23 neLvsevieqlsk......rftpsiadikkrIesLiek 54 
                                       ++Lv+e +e+ +       rf+ + +d kk+I  L ek
  gi|385806386|ref|YP_005842784.1|  70 DKLVKELTEKKETdeliyeRFKKDEEDLKKQISTLQEK 107
                                       5677777777666777777****************998 PP

>> RlaP  RNA repair pathway DNA polymerase beta family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1       1.9   6.3e+02     177     196 ..      25      45 ..       9      63 .. 0.55
   2 ?   12.0   0.9   0.00035      0.12     175     232 ..      65     123 ..      55     129 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.9
                              RlaP 177 sllaalv.dasleaeieeLla 196
                                       +ll++    +s  +ei++Ll+
  gi|385806386|ref|YP_005842784.1|  25 NLLNQRLiVESELKEINKLLE 45 
                                       333333334444455555555 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00035
                              RlaP 175 fesllaalv.dasleaeieeLlaikkggeekeagkrvpeldafiereLesaeeesklpe 232
                                       f++ +++lv + + ++e++eL+  + +++e + +k++  l++ ++  L+++++++++p 
  gi|385806386|ref|YP_005842784.1|  65 FAEDRDKLVkELTEKKETDELIYERFKKDEEDLKKQISTLQEKLRGLLSKYYQKVSTPV 123
                                       7888899999999****************************************999886 PP

>> TraC  TraC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1       3.1     1e+03       4      21 ..       9      26 ..       4      36 .. 0.79
   2 ?   10.1   0.0    0.0024       0.8       1      38 [.      91     128 ..      91     130 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 3.1
                              TraC  4 isdirdeiakLqerlkqa 21
                                      i ++ ++++ Lqe+  ++
  gi|385806386|ref|YP_005842784.1|  9 IEQVAQQLDELQEKYNNL 26
                                      667888888899887665 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0024
                              TraC   1 KkpisdirdeiakLqerlkqaevreAeRigRiAlkaGL 38 
                                       Kk   d++++i  Lqe+l+ ++ +  ++++   +k+G 
  gi|385806386|ref|YP_005842784.1|  91 KKDEEDLKKQISTLQEKLRGLLSKYYQKVSTPVTKTGS 128
                                       788899******************99999999999885 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1     0.017       5.8      67     108 ..       8      49 ..       3      57 .. 0.77
   2 ?    4.2   0.1      0.13        42      97     118 ..      88     109 ..      64     126 .. 0.58

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.017
                           DUF1664  67 ridrvdkkldeqkeiskeikeevtevredlseigedvesvke 108
                                       +i++v ++lde +e  +++ ++   v+++l+ei++ +e++++
  gi|385806386|ref|YP_005842784.1|   8 EIEQVAQQLDELQEKYNNLLNQRLIVESELKEINKLLETLNN 49 
                                       688888888888888888888888888888888877777665 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.13
                           DUF1664  97 seigedvesvkeavegleskle 118
                                       +++++d e +k+ +++l++kl+
  gi|385806386|ref|YP_005842784.1|  88 ERFKKDEEDLKKQISTLQEKLR 109
                                       3444444444444444444444 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   1.2    0.0047       1.6      55     100 ..       3      48 ..       1      57 [. 0.75
   2 ?    7.9   3.6    0.0085       2.9      35      71 ..      75     111 ..      67     118 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0047
                    CENP-F_leu_zip  55 etlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLe 100
                                       e++  eie+ a++l el+ + ++l +++  +e el++ ++  ++L+
  gi|385806386|ref|YP_005842784.1|   3 EKVPPEIEQVAQQLDELQEKYNNLLNQRLIVESELKEINKLLETLN 48 
                                       6666788888888888888888888888888888888777777765 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0085
                    CENP-F_leu_zip  35 mseenqekvileaEtskaevetlkeeieelaeelrel 71 
                                       ++ e++e  +l  E  k+  e lk++i +l+e+lr l
  gi|385806386|ref|YP_005842784.1|  75 ELTEKKETDELIYERFKKDEEDLKKQISTLQEKLRGL 111
                                       4566777777888999999999999999999999988 PP

>> AATF-Che1  Apoptosis antagonizing transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   3.9    0.0023      0.79      49     137 ..      10     116 ..       2     118 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0023
                         AATF-Che1  49 eefeealeeaekalkklleslleLreelleqne.ikkla....................eskeeeekkkskrkrkkk 104
                                       e+++++l+e+++++++ll++ l + +el e n+ +++l+                    +   ++  k+ ++k++++
  gi|385806386|ref|YP_005842784.1|  10 EQVAQQLDELQEKYNNLLNQRLIVESELKEINKlLETLNnippetkiyrsvgniffaedR---DKLVKELTEKKETD 83 
                                       466778888888888888888888888855566555555888888888888888885431...22222222333222 PP

                         AATF-Che1 105 kkeetsleelwkeleklekalkpfrnatldkWs 137
                                       +   + +++ +++l+k+ ++l++  +  l+k++
  gi|385806386|ref|YP_005842784.1|  84 ELIYERFKKDEEDLKKQISTLQEKLRGLLSKYY 116
                                       222223333345555555555555555555555 PP

>> ACCA  Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.2      0.24        82      10      42 ..      11      46 ..       3      61 .. 0.50
   2 ?   10.7   1.1    0.0011      0.37       3      52 ..      68     120 ..      66     127 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.24
                              ACCA 10 eleekieelkklaee...sevdlseeieklekklek 42
                                      ++ ++++el++  ++   +++ +++e+++++k le+
  gi|385806386|ref|YP_005842784.1| 11 QVAQQLDELQEKYNNllnQRLIVESELKEINKLLET 46
                                      344444444333332222333344444444444444 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0011
                              ACCA   3 dfekpiaeleekiee...lkklaeesevdlseeieklekkleklkkeiyknlt 52 
                                       d +k ++el+ek e+   + +  +++e dl+++i++l++kl+ l +++y++++
  gi|385806386|ref|YP_005842784.1|  68 DRDKLVKELTEKKETdelIYERFKKDEEDLKKQISTLQEKLRGLLSKYYQKVS 120
                                       55677888888855511333445668999********************9974 PP

>> HlyD_2  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   8.0   0.00067      0.23     101     209 ..      10     119 ..       3     124 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00067
                            HlyD_2 101 eklkekletlnerikeienneaieni.ekdiekldreInvlekdikesiknedikki...eelKeelnalldkKkll 173
                                       e+ +++l++l+e+ +++ n+  i +   k+i+kl + +n    + k +   ++i      ++l +el+ + +  +l+
  gi|385806386|ref|YP_005842784.1|  10 EQVAQQLDELQEKYNNLLNQRLIVESeLKEINKLLETLNNIPPETKIYRSVGNIFFAedrDKLVKELTEKKETDELI 86 
                                       4567888888888888888887777768899999999999999999999999986651115678899999999999* PP

                            HlyD_2 174 ygskslsgkdleqlkkkkkeienklesskevikake 209
                                       y+    + kd e lkk+ +++++kl      ++ k 
  gi|385806386|ref|YP_005842784.1|  87 YER---FKKDEEDLKKQISTLQEKLRGLLSKYYQKV 119
                                       **9...99*****************98777666655 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.6     0.028       9.4      34      66 ..       8      41 ..       1      58 [. 0.47
   2 ?    9.5   1.6    0.0036       1.2       6      49 ..      68     111 ..      64     126 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.028
                                      HHHHHHHHHHHHHHHHHHHTTTS.....-HHHHHHHH CS
                              OmpH 34 eleakekelqklqeelqkkakkle....keekeqelq 66
                                      e+e+ +++l++lqe++++     +     e + +e++
  gi|385806386|ref|YP_005842784.1|  8 EIEQVAQQLDELQEKYNNLL---NqrliVESELKEIN 41
                                      34444444444444443111...11222333333333 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0036
                                       -HHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH   6 dvqkileespegkaaqeqlekkfkklqaeleakekelqklqeel 49 
                                       d +k+++e +e k+ +e + + fkk +++l+++   lq++ + l
  gi|385806386|ref|YP_005842784.1|  68 DRDKLVKELTEKKETDELIYERFKKDEEDLKKQISTLQEKLRGL 111
                                       67899999999999999777777777777776666666665544 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.7    0.0006       0.2      12      61 ..       6      57 ..       1      60 [. 0.79
   2 ?    4.1   0.6      0.19        64      27      47 ..      92     112 ..      70     125 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0006
                   Snapin_Pallidin 12 epkldeldeklkelrqsQeeLleqldrlnekLkeleeaqe..aevlpdlkey 61
                                       p+++++ ++l el+++ + Ll+q     ++Lke++++ e  ++++p++k y
  gi|385806386|ref|YP_005842784.1|  6 PPEIEQVAQQLDELQEKYNNLLNQRLIVESELKEINKLLEtlNNIPPETKIY 57
                                      599*****************99998788888888888877444666666655 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.19
                   Snapin_Pallidin  27 qsQeeLleqldrlnekLkele 47 
                                       +  e+L++q+++l+ekL+ l 
  gi|385806386|ref|YP_005842784.1|  92 KDEEDLKKQISTLQEKLRGLL 112
                                       556789999999999998665 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 ?    8.3   0.2    0.0083       2.8      41      80 ..       8      50 ..       1      56 [. 0.62
   2 ?    1.9   0.1      0.78   2.6e+02      35      56 ..      94     115 ..      68     126 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0083
                            DUF948 41 qvdpilkevedllakvnelled...vneklekvdplteavadl 80
                                      +++++ +++++l +k n+ll++   v+++l+++++l e ++++
  gi|385806386|ref|YP_005842784.1|  8 EIEQVAQQLDELQEKYNNLLNQrliVESELKEINKLLETLNNI 50
                                      4555555555555555555554444888888888888887776 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.78
                            DUF948  35 ieelekqvdpilkevedllakv 56 
                                        e+l+kq+  + +++++ll+k 
  gi|385806386|ref|YP_005842784.1|  94 EEDLKKQISTLQEKLRGLLSKY 115
                                       4566666666666666666654 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   6.4    0.0017      0.56     328     414 ..      11      95 ..       4     126 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0017
                              FapA 328 v.gldepelkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkk.lletkeklkeeleeleeelk 402
                                       + + +  el+ek+++l ++   +e+el++++k ++ l+++   ++ ++  ++  +    e++ kl++el+e +e  +
  gi|385806386|ref|YP_005842784.1|  11 QvAQQLDELQEKYNNLLNQRLIVESELKEINKLLETLNNIP--PE-TKIYRSVGNIfFAEDRDKLVKELTEKKETDE 84 
                                       44666678999999999999999*********966666532..22.1112222222123444667777777777666 PP

                              FapA 403 elkeeleskkee 414
                                        + e++++ + e
  gi|385806386|ref|YP_005842784.1|  85 LIYERFKKDE-E 95 
                                       6666666662.2 PP

>> RecG_N  RecG N-terminal helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   1.5     0.015         5      24      73 ..      10      58 ..       2      64 .. 0.78
   2 ?    9.0   4.4     0.007       2.4      10      62 ..      70     119 ..      62     122 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.015
                                      ......HHHHHHH---GGGG-HHHH.HHHHHHHHHHTTSSSS-HHHHHHH CS
                            RecG_N 24 eelieeikkkleliddplleneevlkeklskfldYikpiasLpeeRkikR 73
                                      e++ + + + l++ +++ll++  + +  l+++ + ++ ++++p+e ki+R
  gi|385806386|ref|YP_005842784.1| 10 EQVAQQLDE-LQEKYNNLLNQRLIVESELKEINKLLETLNNIPPETKIYR 58
                                      455555555.6667788888888888899999999999999999999998 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.007
                                       HHHHTS---TTT........HHHHHHH---GGGG-HHHH.HHHHHHHH.HHTTS CS
                            RecG_N  10 ekllkkvlsgkleteelieeikkkleliddplleneevlkeklskfld.Yikpi 62 
                                       +kl+k+ l +k+et+el   i++++++ +++l+++ + l+ekl  +l+ Y++++
  gi|385806386|ref|YP_005842784.1|  70 DKLVKE-LTEKKETDEL---IYERFKKDEEDLKKQISTLQEKLRGLLSkYYQKV 119
                                       444444.4666667877...678999*****************99875488876 PP

>> DUF2570  Protein of unknown function (DUF2570)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.7      0.42   1.4e+02      57      83 ..      13      39 ..       3      55 .. 0.54
   2 ?   10.0   0.2    0.0017      0.56      41      87 ..      68     114 ..      62     124 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.42
                           DUF2570 57 rqavekqqkianelkakveeekeevkt 83
                                       q  ++ q++ n+l ++  + + e+k 
  gi|385806386|ref|YP_005842784.1| 13 AQQLDELQEKYNNLLNQRLIVESELKE 39
                                      344444444444444443333333333 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0017
                           DUF2570  41 eqqkanqrLteqLeqerqavekqqkianelkakveeekeevktilkq 87 
                                       +++k  ++Lte+ e++    e+ +k  ++lk+++++ +e+++ +l +
  gi|385806386|ref|YP_005842784.1|  68 DRDKLVKELTEKKETDELIYERFKKDEEDLKKQISTLQEKLRGLLSK 114
                                       6778899**********************************999876 PP

>> FliD_C  Flagellar hook-associated protein 2 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.3      0.17        57      49      69 ..       9      29 ..       3      49 .. 0.51
   2 ?    8.4   3.2    0.0037       1.2     173     229 ..      65     120 ..      32     126 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.17
                                      SCCCCCCHCHHHHHHHHCCCC CS
                            FliD_C 49 tdkikealkeFVdaYNalvte 69
                                      ++++ ++l e  ++YN+l+++
  gi|385806386|ref|YP_005842784.1|  9 IEQVAQQLDELQEKYNNLLNQ 29
                                      455555555555555555543 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0037
                                       HHHHHHHHHHHHHSTT.SHHHHHHHHXXXXHHHHHHHHHHHHHCHHHHHHHHHHHHH CS
                            FliD_C 173 latrlenllksyvkssngtlqtasknltkqikdldkkiedldkrletleerlkkqfa 229
                                       +a++ ++l+k++++ + +t +   ++ +k+ +dl+k+i +l+++l+ l ++++++ +
  gi|385806386|ref|YP_005842784.1|  65 FAEDRDKLVKELTEKK-ETDELIYERFKKDEEDLKKQISTLQEKLRGLLSKYYQKVS 120
                                       6777889999999888.88889999999************************99976 PP

>> PCRF  PCRF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.2      0.25        85      67      91 ..       4      28 ..       1      33 [. 0.78
   2 ?    9.4   3.1    0.0026      0.87      22      92 ..      38     114 ..      29     126 .. 0.61

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.25
                                      .-GGGTHHHHHHHHHH..HHHHHT- CS
                              PCRF 67 laeeeleelekeleeleeelkklLl 91
                                       +  e+e+++++l+el+e+ ++lL 
  gi|385806386|ref|YP_005842784.1|  4 KVPPEIEQVAQQLDELQEKYNNLLN 28
                                      3444899999999999999999987 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0026
                                       GGSSSTTHHHHHTHHHHHHHHHHHHH...TTTHHH...HT.......-S-..-GGGTHHHHHHHHHH..HHHHHT-. CS
                              PCRF  22 ekakklskelaeleeivealeeleea...ledleeakelle...edeelaelaeeeleelekeleeleeelkklLlp 92 
                                       ++++kl ++l+++ + ++ ++++ +    ++  + +kel e   +de + e  +++ e+l+k++++l+e+l+ lL+ 
  gi|385806386|ref|YP_005842784.1|  38 KEINKLLETLNNIPPETKIYRSVGNIffaEDRDKLVKELTEkkeTDELIYERFKKDEEDLKKQISTLQEKLRGLLSK 114
                                       455666666666666666666555541113333334444423333444445556689*****************983 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   2.2     0.003         1      54      95 ..       7      48 ..       2      53 .. 0.71
   2 ?    6.3   3.6      0.04        13      84     122 ..      73     111 ..      65     120 .. 0.43

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.003
                            APG6_N 54 eeleklekeeeelleeLkelekereeleaelaaleeeleale 95
                                       e+e++ ++ +el+e+ ++l ++r  +e+el+++ + le l+
  gi|385806386|ref|YP_005842784.1|  7 PEIEQVAQQLDELQEKYNNLLNQRLIVESELKEINKLLETLN 48
                                      567777777777777777777777777777777777776665 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.04
                            APG6_N  84 laaleeelealeeeeerfwreynelqlelleleeeldsl 122
                                       +++l+e++e  e   erf ++  +l+ + + l+e+l+ l
  gi|385806386|ref|YP_005842784.1|  73 VKELTEKKETDELIYERFKKDEEDLKKQISTLQEKLRGL 111
                                       333333333333333444444444444444444444433 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   4.8     0.024       8.3       3      20 ..      13      30 ..       9      51 .. 0.70
   2 ?    8.1   1.7     0.011       3.7      29      68 ..      75     114 ..      65     117 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.024
                              ZapB  3 lelLeqLEskiqkaidti 20
                                       ++L++L++k+++++++ 
  gi|385806386|ref|YP_005842784.1| 13 AQQLDELQEKYNNLLNQR 30
                                      589999999999998864 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.011
                              ZapB  29 eLkeeneelkeenrele.......eeneqlkeereawqerlkkLLgk 68 
                                       eL e++e+        e       +  e lk++ + +qe+l++LL k
  gi|385806386|ref|YP_005842784.1|  75 ELTEKKETD-------EliyerfkKDEEDLKKQISTLQEKLRGLLSK 114
                                       333333333.......3334444488999999999999999999987 PP

>> CLZ  C-terminal leucine zipper domain of cyclic nucleotide-gated channels
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   1.9     0.008       2.7      31      63 ..       7      39 ..       2      47 .. 0.82
   2 ?    6.2   1.6     0.041        14      28      54 ..      89     115 ..      68     121 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.008
                               CLZ 31 ekverLessLeaLqtrlarLlaeyessqrkLkq 63
                                        +e++ ++L+ Lq +++ Ll++   ++++Lk+
  gi|385806386|ref|YP_005842784.1|  7 PEIEQVAQQLDELQEKYNNLLNQRLIVESELKE 39
                                      578999****************98888888876 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.041
                               CLZ  28 eleekverLessLeaLqtrlarLlaey 54 
                                        +++  e L++++ +Lq +l+ Ll++y
  gi|385806386|ref|YP_005842784.1|  89 RFKKDEEDLKKQISTLQEKLRGLLSKY 115
                                       444555778889999999999998887 PP

>> Bap31_Bap29_C  Bap31/Bap29 cytoplasmic coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   1.4      0.13        45      17      37 ..       9      29 ..       2      38 .. 0.72
   2 ?   11.7   3.2   0.00058      0.19       5      36 ..      71     113 ..      67     129 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.13
                     Bap31_Bap29_C 17 lealKkQaeglakEYDrLade 37
                                      +e + +Q + l+  Y+ L+++
  gi|385806386|ref|YP_005842784.1|  9 IEQVAQQLDELQEKYNNLLNQ 29
                                      566667777777777777765 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00058
                     Bap31_Bap29_C   5 kLkkeLkkkk...........kDlealKkQaeglakEYDrLad 36 
                                       kL keL +kk           kD e lKkQ+  l+     L+ 
  gi|385806386|ref|YP_005842784.1|  71 KLVKELTEKKetdeliyerfkKDEEDLKKQISTLQEKLRGLLS 113
                                       89999999999999*****************999976555555 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 ?    5.0   1.0     0.047        16      72      97 ..       4      29 ..       1      55 [. 0.63
   2 ?    8.1   1.5    0.0051       1.7      67     105 ..      84     122 ..      65     126 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.047
                         4HB_MCP_1 72 kdkaekdellkdieeleaeidkllek 97
                                      k ++e ++++++++el+++ ++ll++
  gi|385806386|ref|YP_005842784.1|  4 KVPPEIEQVAQQLDELQEKYNNLLNQ 29
                                      55677777777777777777777764 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0051
                         4HB_MCP_1  67 eliltkdkaekdellkdieeleaeidkllekyektilte 105
                                       eli+++ k++ ++l+k+i +l++++  ll+ky +   t+
  gi|385806386|ref|YP_005842784.1|  84 ELIYERFKKDEEDLKKQISTLQEKLRGLLSKYYQKVSTP 122
                                       8999*9**************************9887775 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   2.5      0.31     1e+02      27      60 ..       9      41 ..       1      47 [. 0.45
   2 ?    3.7   0.3      0.16        53      94     114 ..      33      53 ..      31      59 .. 0.84
   3 ?    9.1   4.3    0.0033       1.1       7      50 ..      70     113 ..      69     121 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.31
                              CdvA 27 leealkklkekakelkeklkkrlkeledqiksle 60
                                      +e+  ++l+e +++ ++ l++rl  +e+++k+++
  gi|385806386|ref|YP_005842784.1|  9 IEQVAQQLDELQEKYNNLLNQRLI-VESELKEIN 41
                                      444444444444444444444442.344444443 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.16
                              CdvA  94 aleekeeikklleklsklele 114
                                       +++e++ei+klle+l+++  e
  gi|385806386|ref|YP_005842784.1|  33 VESELKEINKLLETLNNIPPE 53 
                                       57899*********9998666 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0033
                              CdvA   7 eeLvsegdipkstyeeikekleealkklkekakelkeklkkrlk 50 
                                       ++Lv+e    k+t e i e++++  ++lk++ ++l+ekl+  l+
  gi|385806386|ref|YP_005842784.1|  70 DKLVKELTEKKETDELIYERFKKDEEDLKKQISTLQEKLRGLLS 113
                                       67888888888888888888888888888888888888887665 PP

>> IL31  Interleukin 31
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   1.2      0.18        60       7      43 ..       5      41 ..       1      89 [. 0.73
   2 ?    8.7   0.6    0.0041       1.4       8      35 ..      91     118 ..      85     126 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.18
                              IL31  7 lrpskedlkkiikeLkslskklledyekkekGvsese 43
                                      ++p+ e++ + ++eL+++ ++ll++    e+ ++e +
  gi|385806386|ref|YP_005842784.1|  5 VPPEIEQVAQQLDELQEKYNNLLNQRLIVESELKEIN 41
                                      5778888999999999999999998777666665544 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0041
                              IL31   8 rpskedlkkiikeLkslskklledyekk 35 
                                       ++++edlkk i+ L+++ + ll  y +k
  gi|385806386|ref|YP_005842784.1|  91 KKDEEDLKKQISTLQEKLRGLLSKYYQK 118
                                       57899******************99876 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.2      0.24        80      21      41 ..       7      27 ..       2      29 .. 0.77
   2 ?    5.8   2.2     0.053        18       2      34 ..      16      48 ..      15      50 .. 0.93
   3 ?    8.1   0.9      0.01       3.4      17      44 ..      88     115 ..      72     123 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.24
                         FlaC_arch 21 keneelsksveelkenVkdll 41
                                       e+e++ ++++el+e+ ++ll
  gi|385806386|ref|YP_005842784.1|  7 PEIEQVAQQLDELQEKYNNLL 27
                                      578999999999998877776 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.053
                         FlaC_arch  2 idelEnklsklsteletvkkeneelsksveelk 34
                                      +del++k ++l  +   v++e++e++k +e+l+
  gi|385806386|ref|YP_005842784.1| 16 LDELQEKYNNLLNQRLIVESELKEINKLLETLN 48
                                      79***********999**************998 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.01
                         FlaC_arch  17 etvkkeneelsksveelkenVkdllsLY 44 
                                       e  kk+ e+l+k++ +l+e+ + lls Y
  gi|385806386|ref|YP_005842784.1|  88 ERFKKDEEDLKKQISTLQEKLRGLLSKY 115
                                       6779999*****************9855 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   6.4     0.084        28     126     225 ..       8     118 ..       3     122 .. 0.54

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.084
                              CorA 126 llekleeeldeledel.....edstkkeilrelaqlrrrlvkl...rralapnrevlk........rllakaddkll 186
                                       ++e++ ++ldel++       ++ + +++l+e+ +l ++l ++       +  r v +        +l++  +  + 
  gi|385806386|ref|YP_005842784.1|   8 EIEQVAQQLDELQEKYnnllnQRLIVESELKEINKLLETLNNIppeT---KIYRSVGNiffaedrdKLVK--ELTEK 79 
                                       56777777777777777667767777777777777777777774442...33333332111222212222..22222 PP

                              CorA 187 ddedkeylrdlldelerllemlealrerleslqdtyssl 225
                                       +++d++ +++   + e l +++++l+e+l+ l + y + 
  gi|385806386|ref|YP_005842784.1|  80 KETDELIYERFKKDEEDLKKQISTLQEKLRGLLSKYYQK 118
                                       333334455566666667788888888888777777655 PP

>> DUF5339  Family of unknown function (DUF5339)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.3       2.7   9.1e+02      24      36 ..      11      23 ..       1      48 [. 0.66
   2 ?   10.9   1.0    0.0019      0.65      12      49 ..      69     107 ..      64     110 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 2.7
                           DUF5339 24 gtktqadaikkql 36
                                      + ++q+d+++ ++
  gi|385806386|ref|YP_005842784.1| 11 QVAQQLDELQEKY 23
                                      3344444444444 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0019
                           DUF5339  12 vdkliakaekqpgtkt.qadaikkqleqsKkqilalpke 49 
                                        dkl+++++++++t++   + +kk  e  Kkqi++l ++
  gi|385806386|ref|YP_005842784.1|  69 RDKLVKELTEKKETDElIYERFKKDEEDLKKQISTLQEK 107
                                       699***998886666515689***************987 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1  11.1     0.023       7.6      16     155 ..       9     114 ..       2     125 .. 0.48

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.023
                           DUF4795  16 ieklqeelekleekvkelekrledkekklealkkqieelekvkadkeeveeelaekadkeaLatkvsrdqfDeakke 92 
                                       ie++ ++l                                                                   +e
  gi|385806386|ref|YP_005842784.1|   9 IEQVAQQL-------------------------------------------------------------------DE 18 
                                       44444444...................................................................44 PP

                           DUF4795  93 Lekmleellek...leeqeealkkaldtLq.........................eelkekldrlel..epLkeqle 139
                                       L+++ + ll++   +e++ ++++k+l+tL+                         +el+ek + +el  e++k+  e
  gi|385806386|ref|YP_005842784.1|  19 LQEKYNNLLNQrliVESELKEINKLLETLNnippetkiyrsvgniffaedrdklvKELTEKKETDELiyERFKKDEE 95 
                                       44444555444444444445555555555555555555555555555555555555555555533322244443322 PP

                           DUF4795 140 ...erlkelqkelqeamek 155
                                          +++  lq++l+  ++k
  gi|385806386|ref|YP_005842784.1|  96 dlkKQISTLQEKLRGLLSK 114
                                       2224444444444443333 PP

>> TraF_2  F plasmid transfer operon, TraF, protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.6    0.0035       1.2      39      80 ..       8      49 ..       3      69 .. 0.83
   2 ?    1.1   0.3      0.62   2.1e+02      42      81 ..      71     107 ..      56     124 .. 0.55

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0035
                            TraF_2 39 kiDdlsdildgleaavnaasadetqvdeaaddlnalLedlgg 80
                                      +i+++ ++ld+l++  n++  ++  v+++++++n+lLe+l++
  gi|385806386|ref|YP_005842784.1|  8 EIEQVAQQLDELQEKYNNLLNQRLIVESELKEINKLLETLNN 49
                                      5677777788777777788877777*************9986 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.62
                            TraF_2  42 dlsdildgleaavnaasadetqvdeaaddlnalLedlggd 81 
                                       +l ++l   ++ ++++++++  ++++ +dl++++++l+++
  gi|385806386|ref|YP_005842784.1|  71 KLVKELT-EKKETDELIYER--FKKDEEDLKKQISTLQEK 107
                                       4444444.223333334432..555555555555555543 PP

>> Sas10_Utp3  Sas10/Utp3/C1D family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   1.1      0.11        36       2      22 ..      10      33 ..       9      51 .. 0.63
   2 ?    6.1   1.0     0.049        17       2      20 ..      95     113 ..      66     121 .. 0.61
   3 ?    6.7   0.2     0.033        11       2      21 ..      95     114 ..      94     129 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.11
                        Sas10_Utp3  2 eslsksldelqeslepllsk...a 22
                                      e+ +++ldelqe+  +ll++   +
  gi|385806386|ref|YP_005842784.1| 10 EQVAQQLDELQEKYNNLLNQrliV 33
                                      6788999*********99953321 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.049
                        Sas10_Utp3   2 eslsksldelqesleplls 20 
                                       e+l+k++++lqe+l+ lls
  gi|385806386|ref|YP_005842784.1|  95 EDLKKQISTLQEKLRGLLS 113
                                       4555666666666655555 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.033
                        Sas10_Utp3   2 eslsksldelqeslepllsk 21 
                                       e+l+k++++lqe+l+ llsk
  gi|385806386|ref|YP_005842784.1|  95 EDLKKQISTLQEKLRGLLSK 114
                                       79****************96 PP

>> FliD_N  Flagellar hook-associated protein 2 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.7      0.49   1.6e+02      27      43 ..      13      29 ..       2      62 .. 0.50
   2 ?    8.8   1.0    0.0076       2.6       4      56 ..      68     118 ..      66     131 .] 0.60

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.49
                                      XXXXXXXHHHHHHHHHH CS
                            FliD_N 27 ktklewkqsayrelnsk 43
                                       ++l++ q++y++l ++
  gi|385806386|ref|YP_005842784.1| 13 AQQLDELQEKYNNLLNQ 29
                                      33333333333333222 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0076
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXHHHHHHHHHHHHHHHHHHHHHXX CS
                            FliD_N   4 Dtdslvkqlmkaerakldkleqkktklewkqsayrelnsklsnlksalsalsk 56 
                                       D d+lvk+l++ +++    +e+ k++ e  ++ +++l+ kl+ l s++   +k
  gi|385806386|ref|YP_005842784.1|  68 DRDKLVKELTEKKETDELIYERFKKDEEDLKKQISTLQEKLRGLLSKYY--QK 118
                                       6688899998877776444666666666666666667777777777663..22 PP

>> Osmo_CC  Osmosensory transporter coiled coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.3    0.0061       2.1      20      41 ..       8      29 ..       3      30 .. 0.91
   2 ?   -1.1   0.1       7.1   2.4e+03      28      30 ..      44      46 ..      33      75 .. 0.52
   3 ?   -0.9   0.1       5.8     2e+03      22      36 ..      67      81 ..      56      86 .. 0.80
   4 ?    4.7   2.5      0.11        37       4      38 ..      80     111 ..      77     117 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0061
                                      HHHHHHHHHHHHHHHHHHHHHH CS
                           Osmo_CC 20 kvedideeIaaLeekRqrLvdq 41
                                      ++e++ +++ +L+ek ++L +q
  gi|385806386|ref|YP_005842784.1|  8 EIEQVAQQLDELQEKYNNLLNQ 29
                                      69****************9988 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 7.1
                                      HHH CS
                           Osmo_CC 28 Iaa 30
                                      ++ 
  gi|385806386|ref|YP_005842784.1| 44 LET 46
                                      322 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 5.8
                                      HHHHHHHHHHHHHHH CS
                           Osmo_CC 22 edideeIaaLeekRq 36
                                      ed d+ +++L ek++
  gi|385806386|ref|YP_005842784.1| 67 EDRDKLVKELTEKKE 81
                                      555677778888876 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.11
                                       XXXXXXXXXXXTHHHHHHHHHHHHHHHHHHHHHHH CS
                           Osmo_CC   4 eEAkelLqehYdnIEqkvedideeIaaLeekRqrL 38 
                                       +E  el  e++ + E   ed+ ++I  L+ek   L
  gi|385806386|ref|YP_005842784.1|  80 KETDELIYERFKKDE---EDLKKQISTLQEKLRGL 111
                                       566666666666555...899*********97666 PP

>> GvpK  Gas vesicle protein K
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   1.4     0.015       5.1      45      75 ..       8      38 ..       3      50 .. 0.83
   2 ?    4.3   1.2      0.12        41      43      83 ..      66     106 ..      40     108 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.015
                              GvpK 45 eierlgetLmkleeeleelkesfgleeedLn 75
                                      eie+++++L +l+e+ ++l ++  + e++L+
  gi|385806386|ref|YP_005842784.1|  8 EIEQVAQQLDELQEKYNNLLNQRLIVESELK 38
                                      89****************9988887777665 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.12
                              GvpK  43 deeierlgetLmkleeeleelkesfgleeedLnldLgplgt 83 
                                       +e+ ++l ++L + +e  e + e+f+ +eedL+ ++ +l++
  gi|385806386|ref|YP_005842784.1|  66 AEDRDKLVKELTEKKETDELIYERFKKDEEDLKKQISTLQE 106
                                       6889999999**999999999************99988875 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   3.2      0.17        58       2      31 ..      20      49 ..       8      63 .. 0.58
   2 ?    8.1   1.0     0.007       2.4      80     107 ..      88     115 ..      87     121 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.17
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  2 keeleslqaelaqlkeaieelektletlkt 31
                                      +e+ ++l  ++  ++++++e++k+letl++
  gi|385806386|ref|YP_005842784.1| 20 QEKYNNLLNQRLIVESELKEINKLLETLNN 49
                                      344444455555555555555555555555 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.007
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  80 ellkkkleelekqlekleeeleklkdqi 107
                                       e +kk +e+l+kq+ +l+e+l+ l +++
  gi|385806386|ref|YP_005842784.1|  88 ERFKKDEEDLKKQISTLQEKLRGLLSKY 115
                                       67899***************99887776 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   4.0      0.22        74       8      96 ..      13      46 ..       7      54 .. 0.43
   2 ?    8.6   3.8    0.0055       1.9      54      97 ..      68     111 ..      66     120 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.22
                             DHR10  8 keelaelErkarelqakidalqvvekdlrsciklleeieaelakleeakkklkelrdaleekeielrelerkeerlqrq 86
                                       ++l+el++k++                                                        l +++  ++  
  gi|385806386|ref|YP_005842784.1| 13 AQQLDELQEKYN-------------------------------------------------------NLLNQRLIVESE 36
                                      333344444443.......................................................333333333333 PP

                             DHR10 87 lenaeekler 96
                                      l+  ++ le 
  gi|385806386|ref|YP_005842784.1| 37 LKEINKLLET 46
                                      3333333333 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0055
                             DHR10  54 eakkklkelrdaleekeielrelerkeerlqrqlenaeeklerl 97 
                                       + +k +kel ++ e+ e   +  ++ ee l++q++  +ekl  l
  gi|385806386|ref|YP_005842784.1|  68 DRDKLVKELTEKKETDELIYERFKKDEEDLKKQISTLQEKLRGL 111
                                       6678899*********************************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2701  (0.15065); expected 358.6 (0.02)
Passed bias filter:                     1217  (0.0678789); expected 358.6 (0.02)
Passed Vit filter:                       158  (0.00881254); expected 17.9 (0.001)
Passed Fwd filter:                        59  (0.00329076); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              53  [number of targets reported over threshold]
# CPU time: 0.81u 0.44s 00:00:01.25 Elapsed: 00:00:00.58
# Mc/sec: 677.04
//
Query:       gi|385806387|ref|YP_005842785.1|  [L=100]
Description: hypothetical protein FFONT_1345 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); 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 0.32s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 600.44
//
Query:       gi|385806388|ref|YP_005842786.1|  [L=314]
Description: phosphoesterase, RecJ domain protein [Fervidicoccus fontis Kam940]
Scores for complete 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   41.5   0.2    3.3e-09   36.9   0.2    2.3  2  DHH           DHH family
  ------ inclusion threshold ------
      0.017   15.4   2.3      0.024   14.9   0.1    2.4  2  Lzipper-MIP1  Leucine-zipper of ternary complex factor MIP1
      0.084   12.7   0.0       0.26   11.1   0.0    1.8  1  DUF4651       Domain of unknown function (DUF4651)
       0.37   10.8   1.7        1.6    8.7   0.2    2.4  2  YpjP          YpjP-like protein
       0.41   11.1   4.5       0.15   12.4   0.8    2.2  2  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 !   36.9   0.2   9.2e-13   3.3e-09       3     101 .]       1     148 [.       1     148 [. 0.78
   2 !    5.1   0.0    0.0074        27      13      38 ..     137     162 ..     135     189 .. 0.86

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 9.2e-13
                                       EEE-ECSSSHHHHHHHHHHHH.....................................................CEC CS
                                       xxxxxxxxxxxxxxxxxxxxx.....................................................xxx RF
                               DHH   3 livghknpDtDsigSaialan.....................................................llv 26 
                                       +iv+hk+ D+D++ Sa+al++                                                     +++
  gi|385806388|ref|YP_005842786.1|   1 MIVTHKQADVDAFSSALALKRlivrefgsqsgeikvvfpesisseaerlekvllskqenfeylneinevngetiIIL 77 
                                       5899*****************777777777777777777777777777666666666666666666666666666** PP

                                       S--TCGGCGCCHHCCCSEEEEEEE-S---SS---SS--EEEE-SSS-HHHHHHHHHHHTT----HHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DHH  27 DhneksqavegeakeeaedviiiDHHrlgeefetlapilflnepvgstaeivaelleekkeeiskeiaellllgi 101
                                       D+ ++sq  +   +  +  +  iDHH  + +++++   ++++ ++ st+e++a ++ e   +  +++  lll+gi
  gi|385806388|ref|YP_005842786.1|  78 DTASESQLPNF-QEILKGYTFLIDHHYYN-SIKKFVSEYYIDRTAYSTSELIASIFPEGLLD--EATSCLLLAGI 148
                                       *******9987.4556777899******9.*************************9764333..44455666666 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0074
                                       HHHHHHHHHHHCECS--TCGGCGCCH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DHH  13 DsigSaialanllvDhneksqavege 38 
                                       D ++S+++la ++ D+n+ +++ e +
  gi|385806388|ref|YP_005842786.1| 137 DEATSCLLLAGIVFDTNRFKRSSEST 162
                                       999***************99998876 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 ?   14.9   0.1   6.8e-06     0.024      35      79 ..     156     201 ..     137     204 .. 0.82
   2 ?   -1.8   0.5       1.1     4e+03      71      82 ..     293     304 ..     280     308 .. 0.46

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6.8e-06
                      Lzipper-MIP1  35 ssssdgsllslstllpk.kakellkeiallEeevvkLEqkllsLyr 79 
                                       ++ss++++++ s+l+ + + ++l++ei++ Ee+v+k+  kl+ L+r
  gi|385806388|ref|YP_005842786.1| 156 KRSSESTFICASKLSSRcNYNKLISEIETREEDVSKRMAKLKALQR 201
                                       55667788888885553499**********************9998 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.1
                      Lzipper-MIP1  71 EqkllsLyrklf 82 
                                       +++++sL  k+ 
  gi|385806388|ref|YP_005842786.1| 293 KREIESLMKKIK 304
                                       344444433333 PP

>> DUF4651  Domain of unknown function (DUF4651)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   7.2e-05      0.26      10      50 ..      24      63 ..      19      70 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 7.2e-05
                           DUF4651 10 vReffsqlGeIavlYvnetesdqeelsGGvvledgrvysFv 50
                                      vRef sq GeI+v++ + + s++e+l   v l+    +++ 
  gi|385806388|ref|YP_005842786.1| 24 VREFGSQSGEIKVVFPESISSEAERLE-KVLLSKQENFEYL 63
                                      9********************999986.3566666666655 PP

>> YpjP  YpjP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.11   4.1e+02      61     116 ..      64     111 ..      18     122 .. 0.57
   2 ?    8.7   0.2   0.00046       1.6      20      53 ..     242     275 ..     220     308 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.11
                              YpjP  61 leisekpasgkgEkifhiynkktkedllrfhvrrdkrpkeGywf..nFHyHtaeDnfe 116
                                       +ei+e     +gE i+ i ++ ++++l  f+     +  +Gy f  + Hy ++  +f 
  gi|385806388|ref|YP_005842786.1|  64 NEINE----VNGETII-ILDTASESQLPNFQ-----EILKGYTFliDHHYYNSIKKFV 111
                                       33444....6677765.66777777777664.....3446665433778877777775 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00046
                              YpjP  20 lKlGkkiaekiedefeeeilpkieevieellekv 53 
                                       + +G +i  + ++e+e+e+l ki+ev+e+l+e  
  gi|385806388|ref|YP_005842786.1| 242 KDFGLRIVLRSKSEVEDEVLRKIREVVERLAEGK 275
                                       469**************************99876 PP

>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1      0.77   2.8e+03       8      44 ..      46      76 ..      40      85 .. 0.57
   2 ?   12.4   0.8   4.3e-05      0.15      59     135 ..     224     304 ..     175     307 .. 0.59

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.77
                                      HHHHHHHHHCHHHHHHHHHHHHHHHTCEEECTCEEEE CS
                             DHHA1  8 rkelekeleelkealaklkaeellekaeevkgvkvlv 44
                                       + lek l      l+k+++ e+l+++ ev+g ++++
  gi|385806388|ref|YP_005842786.1| 46 AERLEKVL------LSKQENFEYLNEINEVNGETIII 76
                                      44455555......33344445666666666666655 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 4.3e-05
                                       HHHHHHTHGBT.TCEEEEEEEECTEEEEEEEESSH.....SS-HHHHHHHHHHHTTCCEEEE..TCEEEEEEEHCH. CS
                             DHHA1  59 aadklksklkk.pvivfvakeegdkvkvsarskkd.....gvdagelakeaaaklgggGGGH..dlAaGagipaek. 126
                                       +a+ ++    + + i +v+++++   ++++rsk++       +++e++++      g++GGH   +   ++i +ek 
  gi|385806388|ref|YP_005842786.1| 224 VASSILR---EgADISLVISDKDFGLRIVLRSKSEvedevLRKIREVVER---LAEGKFGGHreSMVLESNIRIEKr 294
                                       3444444...336777777776448********99997555567777777...777******854544444443332 PP

                                       .HHHHHHHHH CS
                             DHHA1 127 .leealeale 135
                                        +e + ++++
  gi|385806388|ref|YP_005842786.1| 295 eIESLMKKIK 304
                                       2666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1041  (0.0580624); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.66u 0.35s 00:00:01.01 Elapsed: 00:00:00.56
# Mc/sec: 1687.51
//
Query:       gi|385806389|ref|YP_005842787.1|  [L=736]
Description: elongation factor EF-2 [Fervidicoccus fontis Kam940]
Scores for 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-66  221.0   0.5    1.3e-65  220.6   0.5    1.2  1  GTP_EFTU         Elongation factor Tu GTP binding domain
    8.5e-31  106.3   0.0      3e-30  104.5   0.0    2.0  2  EFG_IV           Elongation factor G, domain IV
    7.5e-24   83.6   0.0    1.7e-23   82.5   0.0    1.7  1  EFG_II           Elongation Factor G, domain II
    7.4e-22   77.2   0.0    1.9e-21   75.9   0.0    1.8  1  EFG_C            Elongation factor G C-terminus
    3.1e-11   43.5   0.1    9.8e-11   41.9   0.1    1.9  1  GTP_EFTU_D2      Elongation factor Tu domain 2
    2.4e-05   24.4   0.3    7.5e-05   22.8   0.3    1.9  1  MMR_HSR1         50S ribosome-binding GTPase
  ------ inclusion threshold ------
      0.019   14.9   0.5      0.059   13.4   0.0    2.0  2  HIGH_NTase1_ass  Cytidyltransferase-related C-terminal region
      0.028   14.1   0.0      0.096   12.4   0.0    1.9  1  TFA2_Winged_2    TFA2 Winged helix domain 2
      0.034   14.0   0.0       0.13   12.1   0.0    2.0  2  RF3_C            Class II release factor RF3, C-terminal doma


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 !  220.6   0.5   6.7e-69   1.3e-65       2     193 ..      19     258 ..      18     259 .. 0.96

  Alignments for each domain:
  == domain 1  score: 220.6 bits;  conditional E-value: 6.7e-69
                                       CEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEET..TCSSEEEEEEE CS
                          GTP_EFTU   2 rirnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaislek..etkkylinliD 76 
                                       ++rnigii+hvDhGKtT++d+Ll+++g+is+  ++a+e+ ++D l+ E++rgiT+k+a++sl++  ++k+y inliD
  gi|385806389|ref|YP_005842787.1|  19 QVRNIGIIAHVDHGKTTTSDTLLAAAGIISQ--KVAGEALATDYLEVEQKRGITVKAANVSLYHevDGKSYVINLID 93 
                                       68*****************************..9999999***********************5579********** PP

                                       ESSSGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHH CS
                          GTP_EFTU  77 tPGHvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrlkaelkeiveevkqklsrk 153
                                       tPGHvdF+ +v+r+lrvlDga++vvdaveG+++qte+vlr+al+e+v++ +fiNK+Drl++elk ++++++q++ + 
  gi|385806389|ref|YP_005842787.1|  94 TPGHVDFTGKVTRSLRVLDGAIVVVDAVEGIMTQTETVLRQALEERVRPLLFINKVDRLIKELKYTPQQMQQRFVEI 170
                                       **************************************************************************999 PP

                                       HHHHHHHHHTTT............TTEEEEEEBTTTTBTHH.................................... CS
                          GTP_EFTU 154 eeklekygekge............kevpvvfgSalkgegvk.................................... 182
                                        ++++k  +++              + +v+fgSa++++g++                                    
  gi|385806389|ref|YP_005842787.1| 171 IKDINKLIMNQAepefrdkwlldpAKGQVAFGSAKEKWGFTipvsakkginlshvidaynkgkeaieelakevpian 247
                                       9999988777667999999999999*************999999999*****************************9 PP

                                       HHHHHHHHHSH CS
                          GTP_EFTU 183 tllealvellp 193
                                       +ll+++++++p
  gi|385806389|ref|YP_005842787.1| 248 SLLDMVIKYVP 258
                                       9********98 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 ?   -2.6   0.0       2.2   4.3e+03       3      20 ..     468     485 ..     466     509 .. 0.65
   2 !  104.5   0.0   1.5e-33     3e-30      11     121 .]     516     624 ..     510     624 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.2
                                       CESCEE.SS-CCHCCCCC CS
                            EFG_IV   3 VayrEtirkpvkereekl 20 
                                       + yrE+ir+ ++ +e+k 
  gi|385806389|ref|YP_005842787.1| 468 IVYRESIRTTSDVFEGKS 485
                                       678998888887666554 PP

  == domain 2  score: 104.5 bits;  conditional E-value: 1.5e-33
                                       S-CCHCCCCCCCHTSSSHCCCCCEEEECCTTTTSSEEEEE--STCCCHCCCCHHHHCCCCCCTTS-TTTS--EESEE CS
                            EFG_IV  11 kpvkereeklkkqsggdgqyakvileiePleegsgnefvdetkggqvpkeyieavekGfqealkeGplagepvtdvk 87 
                                       ++  +r+++l +++g+d ++a++i+ +e +     n+fvd+t+g q+++e+++++ ++f+ a+keGpla+epv++vk
  gi|385806389|ref|YP_005842787.1| 516 QDFRDRAKILRDKAGWDYDEARKIWLVEDN----INIFVDKTSGLQYLREVKDTILQAFRLAMKEGPLANEPVRGVK 588
                                       66778999*********************7....8****************************************** PP

                                       EEEEEEE--T..TTC-HHHHHHHHCHHHHHHHHCC- CS
                            EFG_IV  88 vtLldgslhe..vdsseaafkpaarralkeallkAs 121
                                       v+L+d+++he   ++++a++ pa+r+a+ +++l+A+
  gi|385806389|ref|YP_005842787.1| 589 VVLHDAVIHEdpAHRGPAQIYPAVRNAIFAGMLSAK 624
                                       *********************************995 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 !   82.5   0.0   8.7e-27   1.7e-23       1      74 [.     391     464 ..     391     465 .. 0.98

  Alignments for each domain:
  == domain 1  score: 82.5 bits;  conditional E-value: 8.7e-27
                            EFG_II   1 fPePvislaiepkskadedklskaLarlleEDptlrverdeeTketilsGmGelHleivverlkreykvevelg 74 
                                       ++ePv+++a+epk+ +d  kl ++L rl+ EDp l v+ +eeT+e++lsGmG lHlei+++ lk +y+vev+++
  gi|385806389|ref|YP_005842787.1| 391 VSEPVVTVAVEPKNTKDLPKLIESLYRLSIEDPNLVVKINEETGEYLLSGMGPLHLEIAMTFLKDNYGVEVTTS 464
                                       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 !   75.9   0.0   9.7e-25   1.9e-21       2      86 ..     627     710 ..     626     713 .. 0.97

  Alignments for each domain:
  == domain 1  score: 75.9 bits;  conditional E-value: 9.7e-25
                                       EEEEEEEEEEEEECCCCCCHHHHHHHCT-EEEEEEEE.TTEEEEEEEEEGGG-TTHHHCHHHCTTTS-EEEEEEEEE CS
                             EFG_C   2 llEPivkveievpeeyvgkvisdlssrrGeiedmeqdasgrviieaeiPlaeligfateLrslTkGegsfsmefsgY 78 
                                       llEPi+k++i+ p +y++ v+  ++++rG+i+++ +  ++ +++ aeiP+ae++++a+eLrs+T+G++ + +efs++
  gi|385806389|ref|YP_005842787.1| 627 LLEPIQKLDIRLPMDYLSGVTAIITKKRGKILTVAEA-GDLTRVIAEIPVAESFDLASELRSVTAGKAFWGLEFSRW 702
                                       8************************************.*************************************** PP

                                       EE--HHHH CS
                             EFG_C  79 eevpgdkl 86 
                                       ++vp ++l
  gi|385806389|ref|YP_005842787.1| 703 SPVPDSLL 710
                                       ****9865 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 !   41.9   0.1   4.9e-14   9.8e-11       1      73 [.     307     373 ..     307     374 .. 0.92

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 4.9e-14
                                       EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEE CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtl 73 
                                       G va+gr++sG l+ G ev++  + +   +   +i ++   +++ +e+ + ++aG+i+a+ gl++a ++G+t+
  gi|385806389|ref|YP_005842787.1| 307 GLVATGRLFSGYLESGKEVWL--VNS---KVPQKILQVSLYMGPTREVADRVVAGNILAVLGLDKA-RAGETV 373
                                       679******************..766...44588*******************************8.****98 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.3   3.8e-08   7.5e-05       2     112 ..      23     146 ..      22     148 .. 0.68

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 3.8e-08
                                       EEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEEETTEE.....................EEEEECGGC CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvklkgke.....................ielvDtpGl 56 
                                       ++i+ +   GK+t   +l+ +   i ++ +g  + + + +v+ k  +                     i+l+DtpG 
  gi|385806389|ref|YP_005842787.1|  23 IGIIAHVDHGKTTTSDTLLAAaGIISQKVAGEALATDYLEVEQK--RgitvkaanvslyhevdgksyvINLIDTPGH 97 
                                       788889999**********9834566888899999999999833..2344556666666677777777********6 PP

                                       SSHHHHHHHHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEE CS
                          MMR_HSR1  57 iegaseekglgkaflaleeadlillvvdaseeklkpldeeleelleeakkplilvl 112
                                       ++        gk  ++l+  d +++vvda e+ +++ +  l + lee+ +p +l +
  gi|385806389|ref|YP_005842787.1|  98 VD------FTGKVTRSLRVLDGAIVVVDAVEGIMTQTETVLRQALEERVRP-LLFI 146
                                       66......344445544557********99555555555555555555555.4444 PP

>> HIGH_NTase1_ass  Cytidyltransferase-related C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       2.8   5.6e+03     120     142 ..     129     151 ..     108     184 .. 0.45
   2 ?   13.4   0.0     3e-05     0.059      92     174 ..     496     576 ..     483     590 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.8
                   HIGH_NTase1_ass 120 ekiletvneldldelldlnllde 142
                                       e++l+++ e  ++ ll +n +d 
  gi|385806389|ref|YP_005842787.1| 129 ETVLRQALEERVRPLLFINKVDR 151
                                       33333333333333333333322 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 3e-05
                   HIGH_NTase1_ass  92 kdmlPeetievlkeelendnpledirdeekiletvneldldelldlnlldeklankliekrpyesieeikeaiprgf 168
                                        + l eeti++++e    ++  +d rd  kil+    +d+de  ++ l+++++   + ++   + ++e+k++i ++f
  gi|385806389|ref|YP_005842787.1| 496 VEPLNEETIKLIQEGQVFND--QDFRDRAKILRDKAGWDYDEARKIWLVEDNINIFVDKTSGLQYLREVKDTILQAF 570
                                       55678999999988765555..799****************************9999*******************9 PP

                   HIGH_NTase1_ass 169 skhyke 174
                                          +ke
  gi|385806389|ref|YP_005842787.1| 571 RLAMKE 576
                                       877766 PP

>> TFA2_Winged_2  TFA2 Winged helix domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   4.8e-05     0.096      16      41 ..     217     242 ..     192     257 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.8e-05
                     TFA2_Winged_2  16 aeGikvkdLkdswpdveealeeLeae 41 
                                       ++Gi ++ + d++ + +ea+eeL++e
  gi|385806389|ref|YP_005842787.1| 217 KKGINLSHVIDAYNKGKEAIEELAKE 242
                                       79**********************95 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 ?   -2.4   0.0       1.9   3.8e+03      30      72 ..      17      60 ..      12      77 .. 0.76
   2 ?   12.1   0.0   6.4e-05      0.13      14      86 ..     399     471 ..     392     518 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.9
                                      HHHHHHCTSSEEEEET.TS.S-EEEEESSTHHHHHHHHHHHHHH CS
                             RF3_C 30 leqLaeEGavqvfkeeeag.eelilgaVGqLQfeVveeRlknEY 72
                                      l+q+ + G++    + +++ ++++l+a G +   V  e l++ Y
  gi|385806389|ref|YP_005842787.1| 17 LDQVRNIGIIAHVDHGKTTtSDTLLAAAGIISQKVAGEALATDY 60
                                      67788888888876655554889999999998888888888877 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 6.4e-05
                                       EEEESSGGGHHHHHHHHHHHHHCTSSEEEEET.TSS-EEEEESSTHHHHHHHHHHHHHH---EEEEE-S--EE CS
                             RF3_C  14 rvrlkdplkrkqlrkgleqLaeEGavqvfkeeeageelilgaVGqLQfeVveeRlknEYgvevrleslpysla 86 
                                        v+ k++    +l + l  L+ E    v k +e++ e++l+ +G L +e+  + lk+ Ygvev++++  + + 
  gi|385806389|ref|YP_005842787.1| 399 AVEPKNTKDLPKLIESLYRLSIEDPNLVVKINEETGEYLLSGMGPLHLEIAMTFLKDNYGVEVTTSPPVIVYR 471
                                       56677777777788888888999999999999999****************************9887555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (736 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); 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: 0.84u 0.35s 00:00:01.19 Elapsed: 00:00:00.58
# Mc/sec: 3830.39
//
Query:       gi|385806390|ref|YP_005842788.1|  [L=128]
Description: hypothetical protein FFONT_1348 [Fervidicoccus fontis Kam940]
Scores for complete 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   25.4   2.0    1.2e-05   25.4   2.0    1.6  2  Oxidored_q4  NADH-ubiquinone/plastoquinone oxidoreductase, ch
  ------ inclusion threshold ------
       0.02   14.2   0.5       0.02   14.2   0.5    1.8  2  S_4TM        SMODS-associating 4TM effector domain
      0.031   14.7   5.9      0.038   14.5   5.9    1.1  1  SNARE_assoc  SNARE associated Golgi protein
       0.13   11.9   0.9       0.16   11.7   0.9    1.1  1  GET2         GET complex subunit GET2
       0.44   10.7   7.1       0.49   10.5   0.4    2.7  3  Insulin_TMD  Insulin receptor trans-membrane segment


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 ?    2.0   0.2     0.066   2.4e+02      77      92 ..      15      30 ..       2      36 .. 0.52
   2 !   25.4   2.0   3.4e-09   1.2e-05       4      86 ..      24     107 ..      19     118 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.066
                                      HHHHHHHHHHHHHHHH CS
                       Oxidored_q4 77 mllFllillvglvYew 92
                                      +llF+l+ ++ l+Y +
  gi|385806390|ref|YP_005842788.1| 15 LLLFFLLAVISLLYFV 30
                                      3444444444554433 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 3.4e-09
                                       HHHHHCHSS-----HH..HHS-SSSS--SS---.--HHCHHHHHHHHHHHHHHHHHHHHHHHHSST..HHHHHHHHH CS
                       Oxidored_q4   4 llllsallgpkkpnke..klspYEcGfepvgearlrfsvkfylvallFliFDvevvflfpwavslkelglfglieml 78 
                                       + ll ++l++++++ +  k++ YE+G  p  +ar+r+ +++  + +lF  F+  vv ++  ++s   + + +l+e++
  gi|385806390|ref|YP_005842788.1|  24 ISLLYFVLRKEEKTITglKDERYEAGNPPKYKARVRVGFQYLGFFILFASFESVVVTFLLLSLSSG-AYINKLAEFF 99 
                                       445556666555444488*********************************988877777777644.3455555555 PP

                                       HHHHHHHH CS
                       Oxidored_q4  79 lFllillv 86 
                                       l ++++ v
  gi|385806390|ref|YP_005842788.1| 100 LSIVLVSV 107
                                       54444433 PP

>> S_4TM  SMODS-associating 4TM effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.3      0.12   4.5e+02     184     213 ..       4      33 ..       1      43 [. 0.66
   2 ?   14.2   0.5   5.5e-06      0.02     158     218 ..      54     121 ..      52     125 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.12
                             S_4TM 184 vgliknlslsdlllsvivpllpllllalke 213
                                       +++++   +  lll++++ +++ll ++l++
  gi|385806390|ref|YP_005842788.1|   4 TAIFSYGVVPALLLFFLLAVISLLYFVLRK 33 
                                       555566666677777777777777777664 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 5.5e-06
                             S_4TM 158 Wdsrlrrryaklllfalvlwillvlvvgliknls.......lsdlllsvivpllpllllalkeyreqr 218
                                       + +r+r  ++ l +f+l++ + +v+v++l+ +ls       l++++ls+++ ++p+ll+++ke+ + +
  gi|385806390|ref|YP_005842788.1|  54 YKARVRVGFQYLGFFILFASFESVVVTFLLLSLSsgayinkLAEFFLSIVLVSVPILLYGIKEAEKVE 121
                                       6677777777777777777777777777766665333333378888*****************99876 PP

>> SNARE_assoc  SNARE associated Golgi protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   5.9   1.1e-05     0.038       6     110 ..       1     109 [.       1     114 [. 0.92

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.1e-05
                       SNARE_assoc   6 llvaaGvlfglllgtlvtslgallGaslayllgrylgr.....kalrrkllsekrvka.lerlverygflallllrl 76 
                                       ++++a + +g++ ++l+ +l a+++  l y++ r+  +     k+ r  ++++ ++ka +   ++  gf++l+ +  
  gi|385806390|ref|YP_005842788.1|   1 MTITAIFSYGVVPALLLFFLLAVIS--LLYFVLRKEEKtitglKDERYEAGNPPKYKArVRVGFQYLGFFILFASFE 75 
                                       578899999**************95..889999999999***999999999999999999***************** PP

                       SNARE_assoc  77 lpivPrdlvnyvaGltrvsfkrFflatfiGsipw 110
                                       + +v + l+++  G+   ++++Ffl  ++ s+p 
  gi|385806390|ref|YP_005842788.1|  76 SVVVTFLLLSLSSGAYINKLAEFFLSIVLVSVPI 109
                                       *****************************99885 PP

>> GET2  GET complex subunit GET2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.9   4.3e-05      0.16     189     253 ..      16      94 ..      12     116 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.3e-05
                              GET2 189 lvrllllllnfvYhvfrssks...................alvralteasvrnFftvFltfEvvllsiyylllkkie 246
                                       l+ +ll ++ ++Y+v+r++++                   a vr+  +    +Ff +F++fE v+++  +l l   +
  gi|385806390|ref|YP_005842788.1|  16 LLFFLLAVISLLYFVLRKEEKtitglkderyeagnppkykARVRVGFQYL--GFFILFASFESVVVTFLLLSL---S 87 
                                       45566666788899988777778888888999999987555555555555..**************9998888...4 PP

                              GET2 247 kenkvkt 253
                                       +  ++++
  gi|385806390|ref|YP_005842788.1|  88 SGAYINK 94 
                                       4444444 PP

>> Insulin_TMD  Insulin receptor trans-membrane segment
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.4   0.00014      0.49      20      41 ..      12      33 ..       4      36 .. 0.90
   2 ?    3.6   0.0      0.02        71      21      37 ..      76      92 ..      73      93 .. 0.91
   3 ?   -2.3   0.2       1.4   4.9e+03      17      20 ..     104     107 ..      98     113 .. 0.47

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00014
                       Insulin_TMD 20 gPviciillllvigavfvvvkK 41
                                      +P  ++++ll vi+ ++ v++K
  gi|385806390|ref|YP_005842788.1| 12 VPALLLFFLLAVISLLYFVLRK 33
                                      788999***************9 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.02
                       Insulin_TMD 21 Pviciillllvigavfv 37
                                      +v++ +lll + +++++
  gi|385806390|ref|YP_005842788.1| 76 SVVVTFLLLSLSSGAYI 92
                                      699*********99996 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1.4
                       Insulin_TMD  17 Ivig 20 
                                        v +
  gi|385806390|ref|YP_005842788.1| 104 LVSV 107
                                       2222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       958  (0.053433); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); 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: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.52
# Mc/sec: 746.27
//
Query:       gi|385806391|ref|YP_005842789.1|  [L=175]
Description: Membrane-bound oxidoreductase, subunit MbxJ [Fervidicoccus fontis Kam940]
Scores for complete 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   0.1      2e-22   79.4   0.1    1.2  1  Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit
      0.009   16.0   0.0      0.016   15.2   0.0    1.4  1  US6          Viral unique short region 6


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 !   79.4   0.1   2.3e-26     2e-22       1     129 [.      51     157 ..      50     159 .. 0.84

  Alignments for each domain:
  == domain 1  score: 79.4 bits;  conditional E-value: 2.3e-26
                                       -SHHHHHHT-TTTTHHHHHHTEEEEEETTT-S--HHHHHHTHTTTSEEEEEESBE...EEEHHHHHHHHGGGSSEEE CS
                       Oxidored_q6   1 CtGcsisllaleedlldllelielryhetlladskeeeieakekeadvlvveGavtrkpkealellkelaekakavi 77 
                                       C  c  +++a++++ +d      +ry++   +  +         + + +++eG++++k+++al++++++++++k+vi
  gi|385806391|ref|YP_005842789.1|  51 C--CGCEFAATYDPRFDS-----ERYGSLPFTHVR---------DTNTIIIEGTISKKMAKALKVVYDQMPSPKYVI 111
                                       4..555677778888888.....888777777777.........7899***************************** PP

                                       EESHHHHH-TGGGSTT-TEE-HHHHHHHC.S-E.EEE-SSS--HHHHHHHHH CS
                       Oxidored_q6  78 avGtCAafGGipaaannpsvgeevgellevvpvdinipGCPphpeailetll 129
                                       a+G+CA++GGi+  +n+++v+    +  + +pv+++ipGCPp+pea+ +++l
  gi|385806391|ref|YP_005842789.1| 112 AMGACAIDGGIF--YNSYNVV----KPRDFLPVEVYIPGCPPRPEAVENAIL 157
                                       ************..7744444....557789***************999886 PP

>> US6  Viral unique short region 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.8e-06     0.016      61     130 ..      73     142 ..      66     157 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.8e-06
                               US6  61 pkthksrpndrnlegrltcqrvrrllpcdldihpshrlltlmnncvcdgav.wnafrlierhgffavtlyl 130
                                       p th    n   +eg ++ +++ + l +  d  ps + +  m  c  dg + +n++ +++ + f+ v +y+
  gi|385806391|ref|YP_005842789.1|  73 PFTHVRDTNTIIIEGTIS-KKMAKALKVVYDQMPSPKYVIAMGACAIDGGIfYNSYNVVKPRDFLPVEVYI 142
                                       778888889999999886.6677888999*******************876379*************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.34s 00:00:00.85 Elapsed: 00:00:00.53
# Mc/sec: 1000.35
//
Query:       gi|385806392|ref|YP_005842790.1|  [L=138]
Description: Membrane-bound oxidoreductase, subunit MbxK [Fervidicoccus fontis Kam940]
Scores for complete 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-32  110.6   0.1    8.4e-32  110.4   0.1    1.0  1  Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd s


Domain annotation for each model (and alignments):
>> Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.4   0.1   4.7e-36   8.4e-32       1     118 [.       8     129 ..       8     132 .. 0.92

  Alignments for each domain:
  == domain 1  score: 110.4 bits;  conditional E-value: 4.7e-36
                                       EE--HHHHHHHHHHHHH...TT--EEEEEEEEETT.SSSEEEEEEEE--S-.....-EEEEEE....-S-BEE--TT CS
                    Complex1_30kDa   1 lvvepedllevakflkdeeelgfdvlsdltavDek.eerfevvyhllslekn....erirvkvevdeeepevpSvtd 72 
                                       ++v++e+ll+ a+ l++    g+d++++++avD++ ++++e+v+h++s++++    + + +++++d+++p+v+S+t+
  gi|385806392|ref|YP_005842790.1|   8 IYVSKEELLKKAEELYK---SGYDHVISISAVDYPeRNEIELVVHVSSYTRKdispKILEIRTKLDRSSPRVNSLTK 81 
                                       57999***********9...8************9999************8777898777788888999********* PP

                                       T-STHHHHHHHHHHHSHHBCTTSSTSS-SSS.STTS.SS-TTSTTS-- CS
                    Complex1_30kDa  73 lfpgadwyEREayDmfGivfeghpdlrrill.pedf.eghPLRkdfpl 118
                                       ++++a+++EREa++mfGi fegh dl+ +ll pe+f  ++PLRkdf++
  gi|385806392|ref|YP_005842790.1|  82 VWRSAEFQEREAHEMFGIFFEGHSDLKYLLLdPEEFrFKYPLRKDFKV 129
                                       *******************************667786677******86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 804.92
//
Query:       gi|385806393|ref|YP_005842791.1|  [L=405]
Description: Membrane-bound oxidoreductase, subunit MbxL [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-88  295.9   0.1    2.7e-88  295.6   0.1    1.1  1  Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd s
  ------ inclusion threshold ------
      0.093   11.6   0.0         10    4.8   0.0    2.2  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 !  295.6   0.1     3e-92   2.7e-88       2     271 .]     137     405 .]     136     405 .] 0.96

  Alignments for each domain:
  == domain 1  score: 295.6 bits;  conditional E-value: 3e-92
                                       TT-HHHHHHHHHHHHHHHHHHHHHHSSSSS-TTBESSBBSS---TTHHHHHHHHHHHHHHHHHHHHHHHHSSSSHHH CS
                    Complex1_49kDa   2 lGaltvflyafreRekildlleevtGaRltasyiriGGvarDlpegllekikeflkelekkldeleklltknrifkk 78 
                                       lG+ t +++ f +Re  ++l e+++GaRlt+sy ++GGv+rD+p+++++++++ ++++e++l+e+e ++++n+++++
  gi|385806393|ref|YP_005842791.1| 137 LGSSTGYMWFFGDREVPIELAERMSGARLTHSYHIPGGVRRDVPKDFFDELERGISYIERRLKEYEIMFVNNPVIRS 213
                                       699************************************************************************** PP

                                       HHSSSS-BSHHHHHHHTT-SSSSGGGT-TTTHHHHSS-SSGGGS-------SSBSHHHHHHHHHHHHHHHHHHHHHH CS
                    Complex1_49kDa  79 RtkgvgvlskeealelgltGpvlRasGvkyDlRkaepYeaYdeldfdvpvgeegDvydRylvrveEmrqSlkIieqa 155
                                       R+++vgv+ske a++lg++Gp+lRasGv+yD+R +epY+aY e+df+vp+ +egD+++R++ rv+E+rqS+++++q+
  gi|385806393|ref|YP_005842791.1| 214 RLENVGVMSKEMAVSLGVVGPNLRASGVSYDVRVEEPYNAYTEIDFEVPIYKEGDCLARVMQRVDEIRQSISMLRQL 290
                                       ***************************************************************************** PP

                                       HHT--.S-SB---TTTS---GGGGGT-HHHHHHHHHHHH..S-----SEEEEEEEEETTEEEEEEEEEESSSS-SEE CS
                    Complex1_49kDa 156 leklpegpvlaedkkvalpkkeevkksmealihhfklvt..egfkvpkgevyaavEapkGelgvylvsdgsskpyrl 230
                                        +k+p+gp+ +e+   ++   ++++k++ +  ++ kl     ++k +kg +y+++Ea++Gel +y+ s g+ kpyr+
  gi|385806393|ref|YP_005842791.1| 291 SKKIPDGPIFNEKYMKQF---TKIMKDIYDAEKRVKLPAsfLNLKPQKGTAYSRIEASRGELFYYIESSGDLKPYRV 364
                                       *********998766655...557777777777778776346788999***************************** PP

                                       EEE-HHHHTTTTHHHHTTTS-SGGGTHHHHTT---HHHHH- CS
                    Complex1_49kDa 231 kirapsfvnlqaleellkgellaDvvailgsldivlgevDR 271
                                       ++ +psf n  +l++l  g++laD+vai+gs+d++ +e+DR
  gi|385806393|ref|YP_005842791.1| 365 RVVTPSFRNSIILKYLPVGYRLADLVAIYGSIDYFPPEADR 405
                                       ****************************************9 PP

>> NiFeSe_Hases  Nickel-dependent hydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0    0.0012        10      35      67 ..      95     127 ..      59     131 .. 0.91
   2 ?    4.6   0.0    0.0014        12     383     449 ..     298     362 ..     268     374 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0012
                                       HHHHHHHHT----HHHHHHHHHHHHHHHHHHHH CS
                      NiFeSe_Hases  35 vravedAlgikipknarlirnliaaalllhdhi 67 
                                       v a+e+ lgi++p  a ++r++++  + + +h+
  gi|385806393|ref|YP_005842791.1|  95 VLALEKLLGIDVPPRALYLRTILSEINRIASHL 127
                                       789************************999997 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0014
                                       HHHHHHHHHHHHHHHHHHHTTB---B--TT-SGGGS-SEEEEEEEEEETTEEEEEEEEEETTEEEEE CS
                      NiFeSe_Hases 383 kliaellkewldelvenikkgdtetaneekldkkevpkeakGvglveapRGaLsHwikikdgkienY 449
                                        ++ e+ ++++++++++i   ++++   +++ + + p++ + +  +ea+RG L  +i+ + g ++ Y
  gi|385806393|ref|YP_005842791.1| 298 PIFNEKYMKQFTKIMKDIYDAEKRVKLPASFLNLK-PQKGTAYSRIEASRGELFYYIESS-GDLKPY 362
                                       5677889999999*****99999888888777775.67799999***********99854.334444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      598  (0.0333538); 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: 0.66u 0.35s 00:00:01.01 Elapsed: 00:00:00.54
# Mc/sec: 2270.19
//
Query:       gi|385806394|ref|YP_005842792.1|  [L=342]
Description: Membrane-bound oxidoreductase, subunit MbxM [Fervidicoccus fontis Kam940]
Scores for complete 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-78  263.8  24.8    2.3e-78  263.6  24.8    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 !  263.6  24.8   1.3e-82   2.3e-78       7     297 ..      25     330 ..      18     332 .. 0.95

  Alignments for each domain:
  == domain 1  score: 263.6 bits;  conditional E-value: 1.3e-82
                                       HHHHHHHHHHHHHHHHHHHHHHTTS--S-SSTTT..TTTHHHHHHHHHCCS-----TTS-HHHHHHHHHHHHHHHHC CS
                            NADHdh   7 lvvlllvvalltlleRkvlAriqdRlGPnrvGpl..GllqplaDalKlllKediipkkadkllfllapvlalilall 81 
                                       l++++ ++++l+++eRk+++riq+R+GP +++p   G +q+laD+++++++e iip+++d l +++ap+l +++all
  gi|385806394|ref|YP_005842792.1|  25 LITVMGALIFLIWAERKIAGRIQMRYGPLEISPKigGAIQLLADLMRYMFQEIIIPRNVDLLPYFIAPILGFVVALL 101
                                       345777777***********************9667***************************************** PP

                                       TTTTS-SSS..SSS--TTHHHHHHHHHHHCHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-S CS
                            NADHdh  82 afaviPfge..vladlnvglllilalsslgvygillaGwasnskYallGalRsaaqmisyEvalglsllavvllags 156
                                        +a iP+++  + ++ + ++l+++ l++l ++ ++laGw+sn+k++llG+ R+a  + +yE+ ++ls+++ v+++++
  gi|385806394|ref|YP_005842792.1| 102 PIASIPISPyyYPSPTSNSILVAVGLTTLPPLLTILAGWSSNNKFSLLGSTREAFLISAYELLIILSAVSAVIIYST 178
                                       ********8445555566*********************************************************** PP

                                       S-HHHHHHCCCTT-CCCCHHHHHHHHHHHHHHCCTCTTBTTTTSTTSSSSCCCTT-HCHHHHHHHHHHHHHHHHHHH CS
                            NADHdh 157 lslseiveaqeeiwfillqllafiifliallaetnraPFDlpeaesELvaGfhtEYsgmkfalfflaeyanmvlvsa 233
                                        +++  v++q+ iw i+l+++++i+f++++l+ t+r+PF+++ea+sE+v G +tEYsg+ ++l +   y++m+++ +
  gi|385806394|ref|YP_005842792.1| 179 PDFTVAVQEQH-IWGIVLNPISAITFYVSVLMATGRFPFEIAEADSEIVMGAYTEYSGLMYGLSMGIPYTRMFVYNL 254
                                       ********996.9**************************************************************** PP

                                       HHHHHCT.SS-HCCS............HHHHHHHHHHHHHHHHHHHHHC----TCHHHHHHHCCTCHHHHHHHHHH CS
                            NADHdh 234 lavllFlgGwllpfs............gllwfllKvllllflfiwiratlpRlRydqlmklgwkvllplalanlll 297
                                       +++llFlgGw++ +             +++++++K+l++ +++++ ra++ RlR+dq++  +wk+ + ++++ + +
  gi|385806394|ref|YP_005842792.1| 255 IFTLLFLGGWSPLIVipghafisfvliPAIIVVVKALIVSLTMVFTRAIYGRLRIDQALGGAWKFWFVVTMVGIAW 330
                                       **********8766689999999****99******************************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 2032.39
//
Query:       gi|385806395|ref|YP_005842793.1|  [L=169]
Description: Membrane-bound oxidoreductase, subunit MbxN [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-16   57.3  14.1    2.8e-08   33.2   3.7    2.3  2  Fer4      4Fe-4S binding domain
    1.8e-13   50.8  21.7    1.1e-10   41.9  11.4    1.6  2  Fer4_7    4Fe-4S dicluster domain
    4.2e-11   42.4  14.3    5.6e-06   26.2   3.0    2.3  2  Fer4_6    4Fe-4S binding domain
    5.6e-11   43.2   4.8    0.00018   22.3   0.1    2.3  2  Fer4_16   4Fe-4S double cluster binding domain
    5.6e-10   39.2  11.0    1.2e-09   38.2  11.2    1.4  1  Fer4_10   4Fe-4S dicluster domain
    9.2e-10   38.5   9.9    1.4e-09   37.9   9.9    1.3  1  Fer4_9    4Fe-4S dicluster domain
    5.8e-09   36.0   8.3    9.1e-09   35.3   8.3    1.3  1  Fer4_21   4Fe-4S dicluster domain
    9.1e-09   34.9  14.1    5.6e-05   23.0   1.4    2.8  3  Fer4_2    4Fe-4S binding domain
      1e-07   32.3   2.9     0.0084   16.5   0.1    2.2  2  Fer4_8    4Fe-4S dicluster domain
    4.6e-06   26.7  10.6     0.0043   17.4   1.3    2.2  2  Fer4_4    4Fe-4S binding domain
    6.8e-05   23.3  11.1      0.057   14.0   3.5    2.3  3  Fer4_17   4Fe-4S dicluster domain
    0.00015   22.4   3.8       0.23   12.2   0.5    2.3  2  Fer4_15   4Fe-4S single cluster domain
     0.0021   18.6  12.3      0.029   14.9   1.4    2.6  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
     0.0029   17.8   9.8      0.097   12.9   0.6    2.2  2  Fer4_18   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.031   15.2  18.0       0.58   11.2   4.3    2.3  2  Fer4_3    4Fe-4S binding domain
      0.039   14.1   6.9       0.46   10.6   7.6    2.2  2  ETF_QO    Electron transfer flavoprotein-ubiquinone oxidoredu
      0.061   14.2  12.3       0.56   11.1   1.0    2.4  2  Fer4_22   4Fe-4S dicluster domain
        6.7    6.5  10.8        8.7    6.2   1.5    2.2  2  Fer4_20   Dihydroprymidine dehydrogenase domain II, 4Fe-4S cl


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   3.5e-10   3.5e-07       1      23 [.      60      82 ..      60      83 .. 0.92
   2 !   33.2   3.7   2.8e-11   2.8e-08       2      23 ..      95     116 ..      94     117 .. 0.93

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 3.5e-10
                                      EEEETTTSSS-THHHHHSTTTEE CS
                              Fer4  1 vvideekCigCGaCvevCPvgAI 23
                                      +++++ekCi C  C+ vCP +A 
  gi|385806395|ref|YP_005842793.1| 60 IIYNKEKCISCSMCARVCPANAM 82
                                      579******************97 PP

  == domain 2  score: 33.2 bits;  conditional E-value: 2.8e-11
                                       EEETTTSSS-THHHHHSTTTEE CS
                              Fer4   2 videekCigCGaCvevCPvgAI 23 
                                        i++e+C++CG+Cv++CP +A+
  gi|385806395|ref|YP_005842793.1|  95 AINYERCVFCGYCVDICPAEAL 116
                                       69*******************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 !   41.9  11.4   1.1e-13   1.1e-10       1      52 []      66     115 ..      66     115 .. 0.93
   2 !   21.2   2.5   3.2e-07   0.00032       1      24 [.     100     123 ..     100     145 .. 0.76

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 1.1e-13
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       +Ci C  C+++Cp++a+++ +++++k   +++i++e+C++Cg Cv+ CP++a
  gi|385806395|ref|YP_005842793.1|  66 KCISCSMCARVCPANAMKMFQDTDKKL--RPAINYERCVFCGYCVDICPAEA 115
                                       7******************99987765..89******************986 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 3.2e-07
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeen 24 
                                       rC+ Cg+Cv+ Cp++a++  + ++
  gi|385806395|ref|YP_005842793.1| 100 RCVFCGYCVDICPAEALRHAKTHD 123
                                       8****************9987644 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   3.0   5.6e-09   5.6e-06       2      23 ..      60      81 ..      59      82 .. 0.91
   2 !   21.8   3.6   1.4e-07   0.00014       2      24 .]      94     116 ..      93     116 .. 0.94

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 5.6e-09
                            Fer4_6  2 veidpdkCigCgdCvrvCPega 23
                                      + ++++kCi+C  C+rvCP++a
  gi|385806395|ref|YP_005842793.1| 60 IIYNKEKCISCSMCARVCPANA 81
                                      6689****************98 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 1.4e-07
                            Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                       ++i++++C+ Cg Cv++CP+ a+
  gi|385806395|ref|YP_005842793.1|  94 PAINYERCVFCGYCVDICPAEAL 116
                                       78******************996 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 !   21.8   1.7   2.7e-07   0.00027       1      31 [.      66      96 ..      66      99 .. 0.79
   2 !   22.3   0.1   1.8e-07   0.00018       1      33 [.     100     134 ..     100     157 .. 0.68

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 2.7e-07
                           Fer4_16  1 rCgtCgkCaevCPtnaikekkekeieareci 31
                                      +C++C  Ca vCP+na+k+ +++  + r  i
  gi|385806395|ref|YP_005842793.1| 66 KCISCSMCARVCPANAMKMFQDTDKKLRPAI 96
                                      6*****************9866655555555 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 1.8e-07
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkeke..iearecisy 33 
                                       rC+ Cg C+++CP++a+++ k     +e+ e++ y
  gi|385806395|ref|YP_005842793.1| 100 RCVFCGYCVDICPAEALRHAKTHDivFEKGEEMLY 134
                                       6*****************98554400455555544 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2  11.2   1.2e-12   1.2e-09       2      56 .]      60     112 ..      59     112 .. 0.92

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 1.2e-12
                           Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       +++++++Ci C  C ++CPa  ++++  + ++++ +  +++e+C +cg+Cv++CP
  gi|385806395|ref|YP_005842793.1|  60 IIYNKEKCISCSMCARVCPA--NAMKMFQDTDKKLRPAINYERCVFCGYCVDICP 112
                                       6899****************..88888888888888889***************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 !   37.9   9.9   1.4e-12   1.4e-09       1      50 [.      66     115 ..      66     116 .. 0.95

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 1.4e-12
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                       kC++C  C ++Cpa+++++ + + k    a ++e+C++Cg Cv++Cp +a
  gi|385806395|ref|YP_005842793.1|  66 KCISCSMCARVCPANAMKMFQDTDKKLRPAINYERCVFCGYCVDICPAEA 115
                                       7******************99999999999999**************976 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   8.3   9.1e-12   9.1e-09       4      55 ..      63     114 ..      60     118 .. 0.85

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 9.1e-12
                           Fer4_21   4 dedkCigCgkCliaCedtshqaieidaktvlkvv.edeCvGCnlCssvCPved 55 
                                       +++kCi+C  C+ +C+ ++++  + ++k+  + +  ++Cv C  C+++CP  +
  gi|385806395|ref|YP_005842793.1|  63 NKEKCISCSMCARVCPANAMKMFQDTDKKLRPAInYERCVFCGYCVDICPA-E 114
                                       789*******************98777776666538**************6.4 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   1.4   5.6e-08   5.6e-05       3      22 .]      60      79 ..      58      79 .. 0.93
   2 !   18.5   3.1   1.5e-06    0.0015       2      22 .]      93     113 ..      92     113 .. 0.94
   3 ?   -2.3   0.0       6.3   6.3e+03       2       8 ..     138     144 ..     137     145 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 5.6e-08
                            Fer4_2  3 vvvdtdrCigCgaCvsaCPa 22
                                      + ++ ++Ci+C+ C  +CPa
  gi|385806395|ref|YP_005842793.1| 60 IIYNKEKCISCSMCARVCPA 79
                                      679****************8 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 1.5e-06
                            Fer4_2   2 pvvvdtdrCigCgaCvsaCPa 22 
                                       +++++ +rC+ Cg Cv+ CPa
  gi|385806395|ref|YP_005842793.1|  93 RPAINYERCVFCGYCVDICPA 113
                                       689*****************8 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 6.3
                            Fer4_2   2 pvvvdtd 8  
                                       ++++d+d
  gi|385806395|ref|YP_005842793.1| 138 KFQYDPD 144
                                       789**99 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.3     1e-05    0.0099       3      19 ..      65      86 ..      47      96 .. 0.73
   2 !   16.5   0.1   8.4e-06    0.0084       3      34 ..      99     133 ..      97     161 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1e-05
                            Fer4_8  3 ekCieCgaCqsaCp.....vlr 19
                                      ekCi C++C   Cp     +++
  gi|385806395|ref|YP_005842793.1| 65 EKCISCSMCARVCPanamkMFQ 86
                                      5788888888888744444444 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 8.4e-06
                            Fer4_8   3 ekCieCgaCqsaCp..vlrrtk.khlldargeaae 34 
                                       e+C+ Cg+C + Cp  +lr+ k +++   +ge + 
  gi|385806395|ref|YP_005842793.1|  99 ERCVFCGYCVDICPaeALRHAKtHDIVFEKGEEML 133
                                       79***********9776666665555555665555 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   2.4   4.9e-05     0.049       1      16 [.      64      79 ..      64      86 .. 0.92
   2 !   17.4   1.3   4.4e-06    0.0043       1      16 [.      98     113 ..      98     123 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.9e-05
                            Fer4_4  1 qerCigCgsCvaaCPq 16
                                      +e+Ci C  C ++CP 
  gi|385806395|ref|YP_005842793.1| 64 KEKCISCSMCARVCPA 79
                                      69*************6 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 4.4e-06
                            Fer4_4   1 qerCigCgsCvaaCPq 16 
                                       +erC+ Cg Cv++CP 
  gi|385806395|ref|YP_005842793.1|  98 YERCVFCGYCVDICPA 113
                                       59*************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 !   14.0   3.5   5.7e-05     0.057      42      59 ..      63      80 ..      35      82 .. 0.76
   2 !   12.1  12.4   0.00022      0.22       1      59 [.      66     114 ..      66     116 .. 0.74
   3 !   12.9   1.1   0.00012      0.12       1      22 [.     100     121 ..     100     154 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.7e-05
                           Fer4_17 42 kaslCieCgeCerkCPqg 59
                                      + ++Ci+C +C+r+CP++
  gi|385806395|ref|YP_005842793.1| 63 NKEKCISCSMCARVCPAN 80
                                      567899999999999976 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00022
                           Fer4_17   1 rCiqCgyClpeCpsyea..ydnepkkllraaklglleeaekeekaslCieCgeCerkCPqg 59 
                                       +Ci+C++C+++Cp ++    ++  kkl+ a             + ++C+ Cg C+  CP++
  gi|385806395|ref|YP_005842793.1|  66 KCISCSMCARVCPANAMkmFQDTDKKLRPA------------INYERCVFCGYCVDICPAE 114
                                       6************97762233333344443............46689************86 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 0.00012
                           Fer4_17   1 rCiqCgyClpeCpsyeaydnep 22 
                                       rC  CgyC++ Cp  + +  + 
  gi|385806395|ref|YP_005842793.1| 100 RCVFCGYCVDICPAEALRHAKT 121
                                       6999*********876644433 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 !   12.2   0.5   0.00023      0.23       2      20 ..      61      79 ..      60      91 .. 0.84
   2 !   11.3   0.2   0.00044      0.43       3      21 ..      96     113 ..      95     145 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00023
                           Fer4_15  2 vvDrdaCigcglCvaeape 20
                                       +++++Ci+c +C++++p 
  gi|385806395|ref|YP_005842793.1| 61 IYNKEKCISCSMCARVCPA 79
                                      6789*************85 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00044
                           Fer4_15   3 vDrdaCigcglCvaeapev 21 
                                       ++ ++C  cg Cv+ +p  
  gi|385806395|ref|YP_005842793.1|  96 INYERCVFCGYCVDICP-A 113
                                       6789************9.3 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 !   14.9   1.4   2.9e-05     0.029       2      18 ..      63      79 ..      62      91 .. 0.92
   2 !   10.1   1.7   0.00094      0.94       1      18 [.      96     113 ..      96     114 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.9e-05
                           Fer4_13  2 DrdtCiacgaCvelaPd 18
                                      ++++Ci+c  C+ ++P 
  gi|385806395|ref|YP_005842793.1| 63 NKEKCISCSMCARVCPA 79
                                      689*************6 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00094
                           Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                       ++ ++C+ cg Cv+++P 
  gi|385806395|ref|YP_005842793.1|  96 INYERCVFCGYCVDICPA 113
                                       6789*************5 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   2.7    0.0012       1.1      58      73 ..      64      79 ..      49      82 .. 0.88
   2 !   12.9   0.6   9.7e-05     0.097      49      74 ..      89     114 ..      79     120 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0012
                           Fer4_18 58 agdcidcescvkvcPt 73
                                      + +ci+c++c +vcP 
  gi|385806395|ref|YP_005842793.1| 64 KEKCISCSMCARVCPA 79
                                      678************7 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 9.7e-05
                           Fer4_18  49 ekeerkekgagdcidcescvkvcPtg 74 
                                       +k++r + +   c+ c++cv++cP +
  gi|385806395|ref|YP_005842793.1|  89 DKKLRPAINYERCVFCGYCVDICPAE 114
                                       455566667789************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 ?    9.9   5.9    0.0016       1.6       1      15 []      67      81 ..      67      81 .. 0.95
   2 ?   11.2   4.3   0.00058      0.58       1      13 [.     101     113 ..     101     115 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0016
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+ C+ C +vCP +A
  gi|385806395|ref|YP_005842793.1| 67 CISCSMCARVCPANA 81
                                      ************987 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00058
                            Fer4_3   1 CtgCgaCvevCPv 13 
                                       C+ Cg Cv+ CP 
  gi|385806395|ref|YP_005842793.1| 101 CVFCGYCVDICPA 113
                                       ************5 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 ?    2.1   0.4       0.2     2e+02      67      81 ..      59      73 ..      39      74 .. 0.71
   2 ?   10.6   7.6   0.00046      0.46      45      84 ..      72     110 ..      61     122 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.2
                                      EEEE-CCC--S--HH CS
                            ETF_QO 67 klqinaqnCvhCktC 81
                                       +  n + C+ C  C
  gi|385806395|ref|YP_005842793.1| 59 FIIYNKEKCISCSMC 73
                                      3456999******99 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00046
                                       THHHH-TTS-EEEEETTTTSSEEEEE-CCC--S--HHHHH CS
                            ETF_QO  45 peqryCPagvyeivedeeakekklqinaqnCvhCktCdik 84 
                                       +++r+CPa+  ++ +d++ k+ +  in + Cv C  C   
  gi|385806395|ref|YP_005842793.1|  72 MCARVCPANAMKMFQDTD-KKLRPAINYERCVFCGYCVDI 110
                                       689***********9996.899999*********999444 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   3.5    0.0018       1.7       1      23 [.      66      88 ..      66      94 .. 0.79
   2 ?   11.1   1.0   0.00057      0.56      72      95 ..      91     114 ..      79     115 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0018
                           Fer4_22  1 rClsCgaCtlvCptCsCfdvede 23
                                      +C+sC+ C+ vCp+     ++d+
  gi|385806395|ref|YP_005842793.1| 66 KCISCSMCARVCPANAMKMFQDT 88
                                      7************9766666555 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00057
                           Fer4_22  72 efkekfgesgCvGCgRCieacpvk 95 
                                       +++  ++ + Cv Cg C++ cp++
  gi|385806395|ref|YP_005842793.1|  91 KLRPAINYERCVFCGYCVDICPAE 114
                                       4455568999***********975 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 ?    5.6   2.3     0.013        13      21      39 ..      64      80 ..      47      85 .. 0.58
   2 ?    6.2   1.5    0.0087       8.7      21      39 ..      98     114 ..      81     138 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.013
                                      HTT----TT-HHHHCSTT- CS
                           Fer4_20 21 AsRClqCkkapcvkgCPve 39
                                       ++C++C  ++c + CP++
  gi|385806395|ref|YP_005842793.1| 64 KEKCISC--SMCARVCPAN 80
                                      3455555..4555555544 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0087
                                       HTT----TT-HHHHCSTT- CS
                           Fer4_20  21 AsRClqCkkapcvkgCPve 39 
                                        +RC+ C   +cv+ CP+e
  gi|385806395|ref|YP_005842793.1|  98 YERCVFC--GYCVDICPAE 114
                                       58*****..89******87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1054.64
//
Query:       gi|385806396|ref|YP_005842794.1|  [L=174]
Description: hypothetical protein FFONT_1354 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.6e-17   61.8  18.6    5.6e-17   61.8  18.6    1.4  1  Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase cha


Domain annotation for each model (and alignments):
>> Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase chain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.8  18.6   3.1e-21   5.6e-17       2     144 .]      27     163 ..      26     163 .. 0.91

  Alignments for each domain:
  == domain 1  score: 61.8 bits;  conditional E-value: 3.1e-21
                                       HHHHHH-SBHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHIIIIIHHHHHHHHHHHSSTTS----TTCHHHHHHH CS
                       Oxidored_q3   2 allvitsknpvysalfLilsfvgvaglfillgaeFlallqilvYvGAilvlflFvimllesaeeeepeslsrslala 78 
                                       +ll+i +k +vy a+ L+   ++v++l+ +lg + +a++qi+vYvGA + +f+ ++++    +e+++es  ++++++
  gi|385806396|ref|YP_005842794.1|  27 SLLIIKTKTLVYNAFILAGIALSVSALIAMLGFQVIAAIQIIVYVGAAVLFFIISLSM---IGESKAESVDPAIPAV 100
                                       7899******************************************************...5778899999999999 PP

                                       HHHHHHHHHHHHTT--......--------TT-HHHHHHHHTTTTHHHHHHHHHHHHHHHHHHHHC CS
                       Oxidored_q3  79 alligllllalllllllessssavdaqvadvsnieaigsllftkyllpfelasllLLvaligaivl 144
                                       + ++++++++l+++++++   s+ ++  ++  n + ++s l++++ +p+++as  +++a   +i+l
  gi|385806396|ref|YP_005842794.1| 101 IGIVSFVVFYLVIYTVSS---SMPAQPSPTILNGSDLSSYLLNEFAFPLIIASCGIIIASAFSIYL 163
                                       999999999998888764...55567788999************************9999888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1124  (0.0626917); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1075.01
//
Query:       gi|385806397|ref|YP_005842795.1|  [L=98]
Description: hypothetical protein FFONT_1355 [Fervidicoccus fontis Kam940]
Scores for complete 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   45.2   9.7    7.6e-12   44.8   9.7    1.2  1  Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase cha
  ------ inclusion threshold ------
       0.33   10.5   4.0       0.77    9.3   4.0    1.6  1  TM140        TM140 protein family
        3.5    7.0   6.1          4    6.8   6.1    1.1  1  TMEM43       Transmembrane protein 43


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 !   44.8   9.7   1.3e-15   7.6e-12       2     101 ..       4      89 ..       3      93 .. 0.96

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 1.3e-15
                                       HHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHHHHHHHC.............TTSCGGHHHHHHHHHHH CS
                       Oxidored_q2   2 lllliallfliGlygvllrrnllkvliglelisnavnlllvlagvftegtlvitnpatefadplpqalvLtaiviga 78 
                                       + l+ia+l + Gl ++l +++l+++lig e++ n++ l+l  ++++              + + + +  ++ai i+ 
  gi|385806397|ref|YP_005842795.1|   4 YKLVIAALLATGLTVILSSKSLVRMLIGAEVMFNGALLYLTYIASL--------------VPVQGAVYSFFAIIIAS 66 
                                       789****************************************886..............7999************* PP

                                       HHHHHHHHHHHHHHHHSSS-BCC CS
                       Oxidored_q2  79 aetavgLallvrlyreygtddvq 101
                                       +e+ +++++++  yr+++t++++
  gi|385806397|ref|YP_005842795.1|  67 SELLIAVSIVILYYRTHKTLEIN 89 
                                       ********************986 PP

>> TM140  TM140 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   4.0   0.00013      0.77     111     174 ..      25      87 ..       3      93 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00013
                             TM140 111 avgflaassvllagGlglflsyvwkWvrlsllGpgflalvlaqallillllaivlfparakkdk 174
                                        v +l  + v++  G  l+l+y++  v +     +f a+ +a   l++ + +++l+   +k+ +
  gi|385806397|ref|YP_005842795.1|  25 LVRMLIGAEVMF-NGALLYLTYIASLVPVQGAVYSFFAIIIASSELLIAVSIVILYYRTHKTLE 87 
                                       455665566665.56669*************************999999999998887776655 PP

>> TMEM43  Transmembrane protein 43
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   6.1   0.00066         4     190     250 ..      27      81 ..       9      82 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.00066
                            TMEM43 190 R.llGfllmflglllllsplsvlvslipllgelvglglalvalllslslsllvialawllyR 250
                                       R l+G  +mf g ll+l+ +   +sl+p+     g++ +++a++++ s  l+ +++  l+yR
  gi|385806397|ref|YP_005842795.1|  27 RmLIGAEVMFNGALLYLTYI---ASLVPV----QGAVYSFFAIIIASSELLIAVSIVILYYR 81 
                                       32455555555555555554...444444....88899999999999999999999999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       815  (0.0454571); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.56
# Mc/sec: 528.34
//
Query:       gi|385806398|ref|YP_005842796.1|  [L=505]
Description: Membrane-bound oxidoreductase, subunit MbxH [Fervidicoccus fontis Kam940]
Scores for complete 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  207.9  27.5    1.8e-61  207.9  27.5    1.8  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   0.5      0.29   5.2e+03     140     140 ..      27      27 ..       7      57 .. 0.45
   2 !  207.9  27.5     1e-65   1.8e-61       1     282 [.     139     423 ..     139     438 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 0.29
                   Proton_antipo_M 140 a 140
                                       +
  gi|385806398|ref|YP_005842796.1|  27 K 27 
                                       2 PP

  == domain 2  score: 207.9 bits;  conditional E-value: 1e-65
                   Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgil..llynltg.....tlefeelsk 70 
                                       +++Ll +yl+lE+ l+ +++L++ ++++ ++ + sl++++ t +g +++L+g l   +y++t        ++++++ 
  gi|385806398|ref|YP_005842796.1| 139 STNLLEFYLFLEISLITSFILVNNYGYN-DKRKVSLIYLVWTHVGAVLFLVGSLilGIYAATFdvysgYASLKNIA- 213
                                       78***********************999.88899******************772255654432111144444444. PP

                   Proton_antipo_M  71 alelglnslelllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla.vssnei 146
                                          + + s+ l + ++l+++gllvKsa + +hlWlp ay eaPtpvs+ ++a+   ++ ++++r++ +++  +    
  gi|385806398|ref|YP_005842796.1| 214 ---QYIPSSVLAWSFYLIMIGLLVKSASFGFHLWLPYAYAEAPTPVSMAMSALFTGIAPYAIFRFVIPVFpSMFASF 287
                                       ...45899999******************************************************999887899999 PP

                   Proton_antipo_M 147 sqlllilaiismllgslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallFllagsvi 223
                                       s++l++ a++sm++g+l al ++d +r l ySsis++Gy+l+a++++++yg+ ++++h ++ha+ k llF  +gs++
  gi|385806398|ref|YP_005842796.1| 288 SKYLALWAAVSMIYGGLNALYESDFRRFLSYSSISQMGYLLLAVSTNSIYGYVGLLLHYISHAFGKELLFGSSGSMM 364
                                       ***************************************************************************** PP

                   Proton_antipo_M 224 yerektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslil 282
                                        +   +rd+r++gg++k+mPi+a + l++++s++G+Ppt gF+s++ iL +av++ + +
  gi|385806398|ref|YP_005842796.1| 365 LSLDGARDMRKMGGFSKVMPITANMALIGFFSISGMPPTIGFWSELFILRGAVDAFWEM 423
                                       ****************************************************9987755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (505 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1053  (0.0587317); 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:                         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: 0.69u 0.39s 00:00:01.08 Elapsed: 00:00:00.56
# Mc/sec: 2691.57
//
Query:       gi|385806399|ref|YP_005842797.1|  [L=665]
Description: Membrane-bound oxidoreductase, subunit MbxH' [Fervidicoccus fontis Kam940]
Scores for 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-47  160.5  29.8    4.9e-43  147.4  28.4    5.4  4  Proton_antipo_M  Proton-conducting membrane transporter
    1.1e-16   60.7   5.1    1.4e-15   57.1   5.1    3.1  1  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -6.5   7.0         2   1.8e+04     141     167 ..      28      54 ..       3     118 .. 0.61
   2 !   21.0   0.0   1.8e-08   0.00016       1      30 [.     133     162 ..     133     167 .. 0.93
   3 !  147.4  28.4   5.5e-47   4.9e-43      34     291 ..     185     468 ..     179     470 .. 0.84
   4 ?    1.6   1.4     0.015   1.3e+02      37     101 ..     498     566 ..     476     572 .. 0.66

  Alignments for each domain:
  == domain 1  score: -6.5 bits;  conditional E-value: 2
                   Proton_antipo_M 141 vssneisqlllilaiismllgslvala 167
                                       +  +++++ l i++++  +l+sl+ l+
  gi|385806399|ref|YP_005842797.1|  28 KRFEKVNSSLSIISLTISFLASLALLV 54 
                                       333344444444444444444444333 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 1.8e-08
                   Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpk 30 
                                       an+L+ll++g+E+++l++y Lig w+++++
  gi|385806399|ref|YP_005842797.1| 133 ANNLILLFFGWEGTGLASYALIGHWRNDEE 162
                                       89***********************99876 PP

  == domain 3  score: 147.4 bits;  conditional E-value: 5.5e-47
                   Proton_antipo_M  34 AslklflltllgsliLLlgilllynltgtlefeelskal....elglnslelllllllllvgllvKsaqvplhlWlp 106
                                       ++l ++l t++ ++++L++i++ly + g+ e++ l++ +    +  + s  l l +++l +g l+Ksaq+plh Wl+
  gi|385806399|ref|YP_005842797.1| 185 SALRAILFTRVPDILMLIAIFILYLYGGSFEINVLMNKAphilSSLYTSGILGLTMFMLSMGSLAKSAQFPLHEWLV 261
                                       788999*******************************997776666666666677888899**************** PP

                   Proton_antipo_M 107 dayveaPtpvsall.Aatlvkagvlllirllllla..................vssneisqlllilaiismllgslv 164
                                        a + +Ptpvsal+ Aat+vkagv+ ++r+++l++                   +  + ++ ++++++++++  + +
  gi|385806399|ref|YP_005842797.1| 262 TA-MTGPTPVSALIhAATMVKAGVYFMLRISPLFIygsselislgapnsagvlSAVHAFYYAIFLIGAVTAFALGSM 337
                                       **.******************************9874333222211111111111234568899************* PP

                   Proton_antipo_M 165 alaqtdiKrllAySsishlGymlialavatqyg.....veaaiihllthalfkallFllagsviyerektrdirayg 236
                                       al+ ++ K +lAyS+ s+lGym+ ++++a + +     ++ +++hl++ha+fka+lFl ag +i+e   +r i++  
  gi|385806399|ref|YP_005842797.1| 338 ALVAREAKLILAYSTASQLGYMFAGIGAAAFSSepsiiLTFVLAHLIAHAVFKAGLFLGAGTFIHEG-GSRFIDEWP 413
                                       *************************9996555411111455678*******************9998.99******* PP

                   Proton_antipo_M 237 gLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvla.vvasv 291
                                       +L+  +  +++++l l+lslaG+Pp++gF+ k+++ e+ ++ +l++ v++ +++++
  gi|385806399|ref|YP_005842797.1| 414 NLYRLKGSMSMMWL-LVLSLAGIPPFLGFWTKDALVEGYLSTGLYIPVILlMTTIL 468
                                       ****9999998776.579****************************9999555555 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.015
                   Proton_antipo_M  37 klflltllgsliLLlgilllynltg.....tlefeelskal.....elglnslelllllllllvgllvKsaqvpl 101
                                        l  ++ l+ l++Llgi++ + + g     t +f ++s+               + + l +++++ll+ ++++++
  gi|385806399|ref|YP_005842797.1| 498 VLSTYSILALLSILLGIAWPFIVRGfstfvTASFSAISSSYsieigL------PMYVSLTIVVIALLLSLSAYLF 566
                                       556788999999*************8666666666666664333222......2333333444555555555555 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 !   57.1   5.1   1.5e-19   1.4e-15      11      57 ..      74     120 ..      67     121 .. 0.95

  Alignments for each domain:
  == domain 1  score: 57.1 bits;  conditional E-value: 1.5e-19
                   Proton_antipo_N  11 sieigfllDklsalmllvvtfvsllvhlYSigYMaddegyqRFfayl 57 
                                        ++++f  D+ls++m+++v+f+sll+ +YS+ YM++degy+R+f+y+
  gi|385806399|ref|YP_005842797.1|  74 GFSLSFIYDPLSVIMMALVSFLSLLIAIYSTNYMKGDEGYNRYFVYF 120
                                       5899*****************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (665 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1057  (0.0589548); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.78u 0.35s 00:00:01.12 Elapsed: 00:00:00.52
# Mc/sec: 3867.11
//
Query:       gi|385806400|ref|YP_005842798.1|  [L=480]
Description: Membrane-bound oxidoreductase, subunit MbxH'' [Fervidicoccus fontis Kam940]
Scores for complete 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  34.8    1.3e-30  106.7  34.8    2.7  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 ?   -4.7   5.7      0.58     1e+04       4      57 ..       7      54 ..       4     100 .. 0.68
   2 !  106.7  34.8   7.1e-35   1.3e-30       5     293 .]     130     422 ..     127     422 .. 0.81

  Alignments for each domain:
  == domain 1  score: -4.7 bits;  conditional E-value: 0.58
                   Proton_antipo_M  4 LlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgillly 57
                                      L+l+ ++++ ++  + l+  + +k+ k      ++ +lt+l+s  L++ i+ll 
  gi|385806400|ref|YP_005842798.1|  7 LFLITIAIGFIGALSPLILSYSYKE-K-----SYFGVLTALSSAYLFVQIILLS 54
                                      5555555555554444444433333.2.....3677888888888888887765 PP

  == domain 2  score: 106.7 bits;  conditional E-value: 7.1e-35
                   Proton_antipo_M   5 lllyl.glElvllplylLiglwkkkpksleAslklflltllgsliLLlgil.llynltgtlefeelskalelglnsl 79 
                                       ++++l ++ l+ +++y+ i+  k+k  s+ A+lk+ l++ ++  +++l +   +y + g    +e+       l s 
  gi|385806400|ref|YP_005842798.1| 130 ISMFLsSWILIVISSYIAIASEKSK-LSSDAALKYSLMGVVSTAFIVLWLGsGIY-FGG----DEIYGG-VYPLTSK 199
                                       4555526999999999999998665.9***************9877665542444.344....344444.4456899 PP

                   Proton_antipo_M  80 elllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla...vssneisqlllil 153
                                        +++++++l++g+ +K++ +p++ W++d+y  a      l+ + + k+gv+  ++++l +      s  +  ++ il
  gi|385806400|ref|YP_005842798.1| 200 LAMIAIVMLTAGIGFKLGIFPFQWWMVDVYSFADGKSVSLITG-VIKVGVIFAFTRMLYYTfylSPSSVALLMISIL 275
                                       99****************************9998766666647.899999988888888875545566778888999 PP

                   Proton_antipo_M 154 aiismllgslvalaqtdiKrllAySsishlGymlialav......atqy.....gveaaiihllthalfkallFlla 219
                                       +i++m +g+++a +     r+lAySsi+++Gy++++++       ++++     + +a+ ++ l++al+k+l Fl++
  gi|385806400|ref|YP_005842798.1| 276 SILTMTFGNFAAFTSKVFPRILAYSSIAQIGYIMVGMVGllngaiTGNQtlvlfSSAAIAVQGLSYALSKSLSFLVS 352
                                       9*********************************99864342222333312222345566789************** PP

                   Proton_antipo_M 220 gsviyerektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvlavvasvlt 293
                                       g       +  ++ +++gL+ ++P++a  ++v++l l GlPp++gF++k+++++a + +s +l+v+a++ s+++
  gi|385806400|ref|YP_005842798.1| 353 GRY----GSMVELSQLKGLYRRDPVVAFSIIVAMLNLLGLPPLLGFWGKVYLFQAGLTYSIWLVVIAIINSGIS 422
                                       777....67789******************************************************99999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (480 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       990  (0.0552178); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.71u 0.37s 00:00:01.08 Elapsed: 00:00:00.54
# Mc/sec: 2665.36
//
Query:       gi|385806401|ref|YP_005842799.1|  [L=458]
Description: replication factor C large subunit [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      6e-14   52.6   0.0    1.6e-13   51.3   0.0    1.7  1  AAA              ATPase family associated with various cellul
    2.2e-11   43.7   0.0    6.4e-11   42.2   0.0    1.8  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    9.2e-07   29.0   0.5    7.3e-06   26.0   0.1    2.6  2  Rad17            Rad17 P-loop domain
    1.2e-06   28.9   0.1    0.00077   19.8   0.0    3.4  4  AAA_22           AAA domain
    1.5e-06   28.3   0.0    4.3e-06   26.8   0.0    1.8  1  AAA_14           AAA domain
    1.7e-06   28.5   0.0    7.4e-06   26.5   0.0    2.1  1  AAA_16           AAA ATPase domain
    1.4e-05   25.3   0.4    2.4e-05   24.6   0.4    1.4  1  RFC1             Replication factor RFC1 C terminal domain
    3.2e-05   23.9   0.0    7.1e-05   22.8   0.0    1.6  1  AAA_5            AAA domain (dynein-related subfamily)
    4.2e-05   23.7   0.1    0.00014   22.1   0.0    1.9  1  AAA_33           AAA domain
    9.9e-05   22.6   0.1    0.00031   21.0   0.0    1.8  1  AAA_28           AAA domain
    0.00016   21.5   0.0    0.00034   20.4   0.0    1.5  1  IstB_IS21        IstB-like ATP binding protein
    0.00031   21.3   0.6    0.00085   19.9   0.0    2.1  1  AAA_18           AAA domain
    0.00041   20.2   0.4     0.0011   18.8   0.0    1.9  1  DNA_pol3_delta   DNA polymerase III, delta subunit
    0.00058   19.2   0.0     0.0014   17.9   0.0    1.6  1  Zeta_toxin       Zeta toxin
    0.00063   20.1   0.0     0.0015   18.9   0.0    1.7  1  RNA_helicase     RNA helicase
     0.0007   19.5   0.2       0.68    9.8   0.0    3.1  3  NACHT            NACHT domain
    0.00098   19.6   0.1     0.0051   17.2   0.0    2.1  2  AAA_17           AAA domain
     0.0013   17.9   0.0     0.0041   16.3   0.0    1.8  1  DUF815           Protein of unknown function (DUF815)
      0.003   16.8   0.0       0.86    8.7   0.0    3.0  3  NB-ARC           NB-ARC domain
     0.0045   16.9   0.0       0.01   15.7   0.0    1.6  1  RsgA_GTPase      RsgA GTPase
     0.0047   16.7   0.0      0.014   15.1   0.0    1.9  2  AAA_24           AAA domain
     0.0076   16.0   0.1       0.39   10.4   0.0    2.3  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
     0.0088   16.1   0.0      0.019   15.1   0.0    1.7  1  MMR_HSR1         50S ribosome-binding GTPase
  ------ inclusion threshold ------
      0.012   15.1   0.0      0.028   13.9   0.0    1.6  1  AAA_7            P-loop containing dynein motor region
      0.013   15.4   0.2      0.052   13.5   0.0    2.3  1  ATPase_2         ATPase domain predominantly from Archaea
      0.015   14.4   0.2      0.083   12.0   0.0    2.1  2  Parvo_NS1        Parvovirus non-structural protein NS1
      0.017   15.1   0.0      0.063   13.3   0.0    1.9  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.02   14.1   0.1      0.062   12.5   0.0    1.8  2  KAP_NTPase       KAP family P-loop domain
      0.022   15.3   0.2        0.2   12.2   0.0    2.6  3  ABC_tran         ABC transporter
      0.023   15.0   0.0       0.13   12.6   0.0    2.1  2  RsdA_SigD_bd     Anti-sigma-D factor RsdA to sigma factor bin
      0.046   12.9   0.0      0.093   11.9   0.0    1.5  1  TIP49            TIP49 P-loop domain
      0.047   13.5   0.0       0.16   11.8   0.0    1.9  1  dNK              Deoxynucleoside kinase
      0.052   13.1   0.0       0.14   11.7   0.0    1.7  1  AAA_25           AAA domain
      0.065   13.0   0.0       0.15   11.8   0.0    1.5  1  AAA_29           P-loop containing region of AAA domain
      0.073   13.1   0.0       0.26   11.3   0.0    2.0  1  Band_7           SPFH domain / Band 7 family
      0.077   12.4   0.0       0.43   10.0   0.0    2.2  2  SRPRB            Signal recognition particle receptor beta su
      0.093   12.8   0.2       0.24   11.5   0.0    1.8  1  AAA_2            AAA domain (Cdc48 subfamily)
      0.099   12.9   0.1       0.54   10.5   0.0    2.3  2  Roc              Ras of Complex, Roc, domain of DAPkinase
        0.1   12.8   0.6       0.24   11.6   0.0    1.9  1  DUF2774          Protein of unknown function (DUF2774)
       0.11   11.9   0.5       0.83    9.0   0.0    2.5  2  TniB             Bacterial TniB protein
       0.12   12.7   0.0       0.52   10.6   0.0    2.0  2  AAA_19           AAA domain
       0.12   12.1   0.0        2.1    8.1   0.0    2.3  2  DEAD             DEAD/DEAH box helicase
       0.15   11.9   4.7       0.45   10.3   0.0    2.5  2  AAA_11           AAA domain
       0.22   12.0   0.0       0.22   12.0   0.0    2.6  2  AAA_23           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 !   51.3   0.0   3.8e-16   1.6e-13       1      95 [.      48     136 ..      48     161 .. 0.75

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 3.8e-16
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS...STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellsk...yvgesekkirelfkeakekakpsilfiDEidalaksr 74 
                                       vllyGppG+GKT+l++a+a++ g e++e+++s+ +     y +  ++ i+++++      +++ +++DE+d l ++ 
  gi|385806401|ref|YP_005842799.1|  48 VLLYGPPGVGKTSLIEALANDYGYEIVETNASDYRRRddiYRKVYNSAIQGTLTG-----RKKLILLDEVDGLSSTG 119
                                       79*********************************33455555556666666544.....4578*********9998 PP

                                       TTCCCHHHHHHHHHHHHHHHH CS
                               AAA  75 sgseseeeervvnqLlteldg 95 
                                           ++ + +++ qL+t+ ++
  gi|385806401|ref|YP_005842799.1| 120 ----DKGGIEAIVQLITQTKN 136
                                       ....55555555566555443 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 !   42.2   0.0   1.6e-13   6.4e-11       2      96 ..      14     115 ..      13     127 .. 0.83
   2 ?   -2.2   0.0       7.7   3.1e+03      66      91 ..     147     174 ..     123     186 .. 0.74

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 1.6e-13
                            RuvB_N   2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvklkitsgPvlekagdl... 75 
                                       rPksl+ey+ qe+  + ++  i+  +kr  +   vllyGpPG+Gkt+l + +a++ g ++  t +    +  d+   
  gi|385806401|ref|YP_005842799.1|  14 RPKSLKEYVNQETAVAIITSWIKDWEKRAPTKKAVLLYGPPGVGKTSLIEALANDYGYEIVETNASDYRRRDDIyrk 90 
                                       9***************************************************************9999999998332 PP

                            RuvB_N  76 ...aalltnle.ekdvlfideihrl 96 
                                          +a+  +l+ +k+++++de+  l
  gi|385806401|ref|YP_005842799.1|  91 vynSAIQGTLTgRKKLILLDEVDGL 115
                                       2223444444423456666666655 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 7.7
                            RuvB_N  66 gPvlekagdlaal..ltnleekdvlfid 91 
                                        P l+  +dla +  l+nl++k+vl + 
  gi|385806401|ref|YP_005842799.1| 147 HPDLKPIRDLAVMieLKNLNQKHVLTVL 174
                                       5667777888877445788888888765 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.1   1.8e-08   7.3e-06       4      79 ..       4      78 ..       1     184 [. 0.88
   2 ?   -2.2   0.0       7.9   3.2e+03     105     159 ..     344     398 ..     313     409 .. 0.58

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 1.8e-08
                             Rad17  4 denelWfekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklrewlnp 79
                                      +++ +W+ ky+P+ ++e       +  +  w+k        k+ +L+ GP+G gk+  ++ L+  +g+++ e  n+
  gi|385806401|ref|YP_005842799.1|  4 EKGLPWIIKYRPKSLKEYVNQETAVAIITSWIKDWEKRAPTKKAVLLYGPPGVGKTSLIEALANDYGYEIVET-NA 78
                                      56679**************9************9988887788999***********************99885.43 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 7.9
                             Rad17 105 qiesfkeleLkdakylklqklGddlrtdkklilvedlPnkfyrdsdalrevirky 159
                                       + e+ +  eL ++  +kl+k+  +  ++ k  l+  l + +  +   + ++ r y
  gi|385806401|ref|YP_005842799.1| 344 LSETKRSRELLNSSLQKLSKRLSQSTSKSKKDLLPYLRSIYRLSPPHFVQICRSY 398
                                       3333333444555555777776666666666666666666666666666666655 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   1.9e-06   0.00077       4      62 ..      44      93 ..      41     100 .. 0.89
   2 ?    5.2   0.0      0.06        24      80     128 ..      94     141 ..      90     148 .. 0.73
   3 ?   -1.5   0.0       6.7   2.7e+03      45      87 ..     203     245 ..     163     257 .. 0.74
   4 ?   -1.3   0.0         6   2.5e+03      60      89 ..     333     365 ..     303     387 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.9e-06
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellr 62
                                      t++ ++++G++G+GKT l++ l++ +         + e+v+ +++    ++d++r++ +
  gi|385806401|ref|YP_005842799.1| 44 TKKAVLLYGPPGVGKTSLIEALANDY---------GYEIVETNASDYRRRDDIYRKVYN 93
                                      57889********************9.........999999999999999999988865 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.06
                            AAA_22  80 ealeqalraravielliiDEaqhlrs...eealeeLrsllnlsrkgvqliLv 128
                                       +a++  l  r++  l+++DE++ l+s   +  +e +++l    +++ ++iL 
  gi|385806401|ref|YP_005842799.1|  94 SAIQGTLTGRKK--LILLDEVDGLSStgdKGGIEAIVQLIT--QTKNPIILT 141
                                       566667777777..**********62566778888877777..777777775 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 6.7
                            AAA_22  45 vtlpsstsskdllrellralglelkaerlsseellealeqalr 87 
                                        +++ + s ++++ ++ ++l  el ++r+++   +++l++ + 
  gi|385806401|ref|YP_005842799.1| 203 ACINDLQSIAEVYGKVNEELATELTYYRDRELNPFDTLRNIFT 245
                                       4555666777888888888888887777777666666666655 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 6
                            AAA_22  60 llralglelka..erlsseell.ealeqalrar 89 
                                       l  ++ ++lk   e+++s+ell + l++ +++ 
  gi|385806401|ref|YP_005842799.1| 333 LKYNYPSKLKMlsETKRSRELLnSSLQKLSKRL 365
                                       444444444445556666666645555444443 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0   1.1e-08   4.3e-06       2      98 ..      45     141 ..      44     156 .. 0.73

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 1.1e-08
                            AAA_14   2 rkilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelilek.lkeekktylflDEiqev. 76 
                                       +k++++ G+  vGKT l++ l++++     +i++ n  d r ++   ++k+++   +  l++ +k++++lDE+  + 
  gi|385806401|ref|YP_005842799.1|  45 KKAVLLYGPPGVGKTSLIEALANDYG---YEIVETNASDYRRRDDI-YRKVYNSAIQGtLTG-RKKLILLDEVDGLs 116
                                       689*******************9999...9********98887644.434554444443777.9*********9875 PP

                            AAA_14  77 ....pewekalkslvdegknldvivt 98 
                                           ++  +a+ +l+ ++kn  +i+t
  gi|385806401|ref|YP_005842799.1| 117 stgdKGGIEAIVQLITQTKN-PIILT 141
                                       55554444444444444434.55555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   1.8e-08   7.4e-06      10      63 ..      29      81 ..      21     140 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1.8e-08
                            AAA_16 10 eqLlsalervrsgrp..elvllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                      + ++s ++++ +  p   +vll+G++GvGK+sl+++l++ +  +    +++++ ++
  gi|385806401|ref|YP_005842799.1| 29 AIITSWIKDWEKRAPtkKAVLLYGPPGVGKTSLIEALANDYGYE---IVETNASDY 81
                                      556666676666666779********************988777...456655555 PP

>> RFC1  Replication factor RFC1 C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.4   5.8e-08   2.4e-05       1     126 [.     291     410 ..     291     441 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 5.8e-08
                                       HHHHHHHHHHHTTSS-GGGHHHHHHHHTHHHHHTT-EE-SS....-----SHHHHHHHHHHHHHHHHHHHTTTTT-- CS
                              RFC1   1 isdgDlvdkkirseqnWsLlpthavlssvlPaslvrgsleg....risFpswLGknSktnKnkRllqelqshlrlkt 73 
                                       +s++D+    i+++ n++ l +  +  ++ Pa   + + ++    ++++ps L   S+t++++ ll+   ++l+ ++
  gi|385806401|ref|YP_005842799.1| 291 LSRADVYRGIIKKTGNYDFLAY--ITEMIGPAISFSRKKTKfkwlKYNYPSKLKMLSETKRSRELLNSSLQKLSKRL 365
                                       599*******************..9999***86666555557999******************************** PP

                                       ----HHHHHTTTHHHHHHHHS---------HHHHHHTTT--SHHHHHHHHHH- CS
                              RFC1  74 saskselrldylpllkkklvkpLkeegkdgveevielmdeysLtkedvdslve 126
                                       s s+s+ + d lp+l+ +   +L        + ++++  +y++t e+   +v 
  gi|385806401|ref|YP_005842799.1| 366 SQSTSKSKKDLLPYLRSI--YRLSP------PHFVQICRSYGITVEEAAVIVG 410
                                       ***************875..45666......6667777777777666666655 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 !   22.8   0.0   1.8e-07   7.1e-05       2      76 ..      48     114 ..      47     119 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.8e-07
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEver 76 
                                       vlL GppG+gK++l+e la  ++ e+++ + +++ +++d+  ++       s  ++ l+    ++++++lDEv+ 
  gi|385806401|ref|YP_005842799.1|  48 VLLYGPPGVGKTSLIEALANDYGYEIVETNASDYRRRDDIYRKVY-----NSAIQGTLT---GRKKLILLDEVDG 114
                                       8**************************************998877.....466677777...6778888888875 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   3.4e-07   0.00014       2      93 ..      48     158 ..      48     173 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 3.4e-07
                            AAA_33   2 vllvGlpGsGKstlaerllkklgavllssdt........lrrrlfg.......tdqqskt......dytrvldr..l 55 
                                       vll G+pG+GK+ l+e l++  g++++++++        ++r++++       t+    +      d  + l++   
  gi|385806401|ref|YP_005842799.1|  48 VLLYGPPGVGKTSLIEALANDYGYEIVETNAsdyrrrddIYRKVYNsaiqgtlTG----RkklillDEVDGLSStgD 120
                                       7899**************************9999999996666666433333322....122333333333333223 PP

                            AAA_33  56 yqilnelarkalsagrnvildatnlsrrerarflklar 93 
                                       ++ ++++++   + ++++il a n+++ + + ++ la 
  gi|385806401|ref|YP_005842799.1| 121 KGGIEAIVQLITQTKNPIILTANNAFHPDLKPIRDLAV 158
                                       44888899999999999999999999999988888875 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   7.7e-07   0.00031       2      34 ..      48      81 ..      47      91 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 7.7e-07
                            AAA_28  2 ivitGgestGKTtlleaLaar.gypvvpEaarei 34
                                      + + G+++ GKT+l+eaLa++ gy++v+  a ++
  gi|385806401|ref|YP_005842799.1| 48 VLLYGPPGVGKTSLIEALANDyGYEIVETNASDY 81
                                      7899***************988*****8877776 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 !   20.4   0.0   8.4e-07   0.00034      46     151 ..      44     146 ..      17     157 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 8.4e-07
                         IstB_IS21  46 kkenivllGpsGvGKshlaialgve....avraglsvlfvrvedLveelkrarrdgklaralkrllkvdllilDdl. 117
                                       +k++++l Gp+GvGK+ l  al+ +     v+   +  + r +d+ +++     +g l        + +l++lD++ 
  gi|385806401|ref|YP_005842799.1|  44 TKKAVLLYGPPGVGKTSLIEALANDygyeIVE-TNASDYRRRDDIYRKVYNSAIQGTL------TGRKKLILLDEVd 113
                                       57899****************97651110333.3344677777777777766666655......567899999*994 PP

                         IstB_IS21 118 gllpl.dqaeaellfeviekryerrsiiitsnlpf 151
                                       gl    d+   e + ++i +   +++ii+t+n  f
  gi|385806401|ref|YP_005842799.1| 114 GLSSTgDKGGIEAIVQLITQ--TKNPIILTANNAF 146
                                       45433155567889999987..5899999999877 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   2.1e-06   0.00085       1      40 [.      48      90 ..      48     134 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.1e-06
                            AAA_18  1 IlltGtpGvGKttlakeLskrlgf...gvnlrdvakengllle 40
                                      +ll G+pGvGKt+l ++L++  g+    +n +d+ + ++++  
  gi|385806401|ref|YP_005842799.1| 48 VLLYGPPGVGKTSLIEALANDYGYeivETNASDYRRRDDIYRK 90
                                      799***************9998888898888888877777765 PP

>> DNA_pol3_delta  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   2.6e-06    0.0011      20     172 ..      67     211 ..      58     212 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.6e-06
                                       HHHHTTTEEEEEEEE-STTS-HHH.HTTTSTTTTSSSSEEEEEEE--.....TT-S-TTHHHHHHHHTTT--SSEEE CS
                    DNA_pol3_delta  20 kqalkqgfedlnyikfdlnedwiddvleecetlpffsdkrivvlknpklltkesklnekllkeLeeylsnlpedtlL 96 
                                       +  +  ++ ++n +++   +d + +v++++ +  + + k++++l+    l  +s  ++  ++++ +++++  +++ +
  gi|385806401|ref|YP_005842799.1|  67 ND-YGYEIVETNASDYRRRDDIYRKVYNSAIQGTLTGRKKLILLDEVDGL--SSTGDKGGIEAIVQLITQ--TKNPI 138
                                       44.778999**************************************777..777788888888888888..78889 PP

                                       EEEES.S--HHHHHHHHHTTTEEEEEE----TTTHHHHHHHHHHHTT-EE-HHHHHHHHHHHTT-HHHHHHHHHHH CS
                    DNA_pol3_delta  97 iliapkklderkklvklLkkkatvveaktlkeeelkkwiqkraqelglkiekealelLlelvennlsaikqelekL 172
                                       il+a+   +     +k +   a+++e k l+++ + + ++ +++++g++ e+  l++++e+  ++l+a  + l+ +
  gi|385806401|ref|YP_005842799.1| 139 ILTAN---NAFHPDLKPIRDLAVMIELKNLNQKHVLTVLKIICEREGVECEDAGLKVIYEKNRGDLRACINDLQSI 211
                                       99999...44455788899999*************************************************99865 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   3.4e-06    0.0014       7      65 ..      37      92 ..      31     100 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.4e-06
                        Zeta_toxin  7 dkkypsqerPklillgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPeyeeil 65
                                      d + ++  ++k++ll G pG GK++l+e+l+++   + ++v+ ++ d+R++   y++++
  gi|385806401|ref|YP_005842799.1| 37 DWE-KRAPTKKAVLLYGPPGVGKTSLIEALANDY--GYEIVETNASDYRRRDDIYRKVY 92
                                      444.566899***********************9..99***********9876666655 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   3.8e-06    0.0015       1      81 [.      48     135 ..      48     144 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 3.8e-06
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl......klkkkdsvysrnpeddfwdgYt.gqevvvidDfgqvkdeenpsdl 70 
                                       ++lyGp+g+GK++l++ La++   ++      ++ ++d++y +  ++ +    t +++ ++ d++   +++ ++  +
  gi|385806401|ref|YP_005842799.1|  48 VLLYGPPGVGKTSLIEALANDYGYEIvetnasDYRRRDDIYRKVYNSAIQGTLTgRKKLILLDEVDGLSSTGDKGGI 124
                                       689********************888777777888888999888888888888866666677777766655344466 PP

                      RNA_helicase  71 aelirlvsstp 81 
                                       + +++l++ t+
  gi|385806401|ref|YP_005842799.1| 125 EAIVQLITQTK 135
                                       66777766655 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0    0.0017      0.68       3      23 ..      48      68 ..      46      78 .. 0.89
   2 ?    5.9   0.0     0.027        11      83     158 ..     105     173 ..      95     179 .. 0.88
   3 ?   -1.3   0.0       4.4   1.8e+03      17      32 ..     358     373 ..     336     396 .. 0.53

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0017
                                      EEEEC-TTTCHHHHHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqklala 23
                                      v+l G++G+GKT L++ la +
  gi|385806401|ref|YP_005842799.1| 48 VLLYGPPGVGKTSLIEALAND 68
                                      899************999875 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.027
                                       EEEEEE-STT-SS-TCH.........HHHHHCTTTTT--EEEEEEECCCHHHHCTTSSCE..EEEE--TCCHHHHH CS
                             NACHT  83 lLlilDglDelvtdlgqkekqpvrtlLselirkkllpeasllltvrpralrdleeqleeaivlevegfsesrrkql 158
                                        L++lD +D l++  ++       + + +li++   ++++++lt+ +   +dl+     a ++e++ ++++++ ++
  gi|385806401|ref|YP_005842799.1| 105 KLILLDEVDGLSSTGDK----GGIEAIVQLITQ---TKNPIILTANNAFHPDLKPIRDLAVMIELKNLNQKHVLTV 173
                                       5899********95555....788888899999...******************99999999*******9998766 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 4.4
                                       HHHHHHHHCTS-SCCC CS
                             NACHT  17 lqklalawaegklpqg 32 
                                       lqkl   + +++ +++
  gi|385806401|ref|YP_005842799.1| 358 LQKLSKRLSQSTSKSK 373
                                       3333444444444433 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.2e-05    0.0051       1      26 [.      51      76 ..      51      87 .. 0.91
   2 ?   -1.4   0.2       7.3     3e+03      49      70 ..     410     431 ..     392     452 .. 0.51

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.2e-05
                                      EE-TTSSHHHHHHHHHHHHTEEEEEH CS
                            AAA_17  1 lGgPGsGKgtqceklvekygfthlsa 26
                                      +G+PG+GK+ ++e l+ +yg++++++
  gi|385806401|ref|YP_005842799.1| 51 YGPPGVGKTSLIEALANDYGYEIVET 76
                                      7*********************9975 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 7.3
                                       SHHHHHHHHHHHHHHHHHHHHH CS
                            AAA_17  49 lpleekkelqkeaaekiaeeak 70 
                                       ++++++k++ ++aae+ ++ a+
  gi|385806401|ref|YP_005842799.1| 410 GDKQVEKAFAEMAAERQEKSAE 431
                                       3444444444444444333322 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0     1e-05    0.0041      23     100 ..      14      89 ..       2     102 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1e-05
                            DUF815  23 devklddLvgidkqkealventeqfleglpan.nvLLwGarGtGKSslvkallneyaeegLrlievekedlkelpkl 98 
                                       ++ +l++ v+ ++  + +++ ++ + + +p++  vLL+G  G+GK sl+ al n+y      ++e + +d +  +++
  gi|385806401|ref|YP_005842799.1|  14 RPKSLKEYVNQETAVAIITSWIKDWEKRAPTKkAVLLYGPPGVGKTSLIEALANDYGY---EIVETNASDYRRRDDI 87 
                                       55566666777777777777778888888775258******************99865...4666666666655555 PP

                            DUF815  99 ve 100
                                       ++
  gi|385806401|ref|YP_005842799.1|  88 YR 89 
                                       55 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0021      0.86      15      43 ..      40      68 ..      25      74 .. 0.83
   2 ?   -0.6   0.0       1.5   5.9e+02      92     112 ..      92     112 ..      72     116 .. 0.77
   3 ?    3.8   0.0     0.066        27      41      90 ..     297     375 ..     293     386 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0021
                                      TTTSCSEEEEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC 15 kdelqslvvalvGmgGvGKttlakqilnk 43
                                      k  + +  v l+G +GvGKt l++   n+
  gi|385806401|ref|YP_005842799.1| 40 KRAPTKKAVLLYGPPGVGKTSLIEALAND 68
                                      5556667899************9988887 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.5
                                       HHHHHHHHCCCTTEEEEEEEE CS
                            NB-ARC  92 lkrklvrlLltkrfllvlDDV 112
                                        +  ++  L +++ l++lD V
  gi|385806401|ref|YP_005842799.1|  92 YNSAIQGTLTGRKKLILLDEV 112
                                       46789999***********98 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.066
                                       CCSHCCCCCCBTEEEEE.............................EEESXXHHHHHHHXXHHHHHCCCTTSSSS-S CS
                            NB-ARC  41 lnksdevegrFdsvawv.............................vvsktdkseeiletilkeLslseddleekee 88 
                                       ++   + +g++d +a++                             ++s+t  s+e+l++ l++Ls++ ++  +k++
  gi|385806401|ref|YP_005842799.1| 297 YRGIIKKTGNYDFLAYItemigpaisfsrkktkfkwlkynypsklkMLSETKRSRELLNSSLQKLSKRLSQSTSKSK 373
                                       555666788899999999999999999999999999999999999999999*******9999999999888777775 PP

                                       TT CS
                            NB-ARC  89 ve 90 
                                       ++
  gi|385806401|ref|YP_005842799.1| 374 KD 375
                                       54 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.5e-05      0.01      98     133 ..      44      79 ..      16      91 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.5e-05
                                       TTSEEEEECSTTSSHHHHHHHHCTT-----S----- CS
                       RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpelelktgevsek 133
                                       ++k ++l G+ GvGK++Li+al+++   ++ e+ ++
  gi|385806401|ref|YP_005842799.1|  44 TKKAVLLYGPPGVGKTSLIEALANDYGYEIVETNAS 79 
                                       468899*****************9987777776655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   3.5e-05     0.014       2      23 ..      45      68 ..      44     114 .. 0.81
   2 ?   -2.5   0.0       8.9   3.6e+03      33      68 ..     187     239 ..     183     240 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.5e-05
                            AAA_24  2 klkiliyGpsgiGKTtlakel..g 23
                                      k+ +l+yGp+g+GKT+l+  l   
  gi|385806401|ref|YP_005842799.1| 45 KKAVLLYGPPGVGKTSLIEALanD 68
                                      7889*************9988543 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 8.9
                            AAA_24  33 k.Glksldadkfpdie.......swedfldevvel.........aaeladykt 68 
                                       + Glk ++ ++  d++       s+++++ +v+e          ++el++++t
  gi|385806401|ref|YP_005842799.1| 187 DaGLKVIYEKNRGDLRacindlqSIAEVYGKVNEElateltyyrDRELNPFDT 239
                                       44888888888877775444444445554444444766666666666666666 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 !   10.4   0.0   0.00097      0.39       5      71 ..      52     112 ..      48     118 .. 0.67
   2 ?    3.0   0.1      0.17        70      99     163 ..     367     426 ..     366     450 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00097
                   Viral_helicase1   5 GvpGcGKStlirkllrtsliltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                       G pG GK++li  l+++ +   ++  +a +++++      ++v+  +s+ +  + + ++k+++lDE 
  gi|385806401|ref|YP_005842799.1|  52 GPPGVGKTSLIEALAND-YGYEIVETNASDYRRRD--DIYRKVY--NSAIQGTLTG-RKKLILLDEV 112
                                       78***************.44444555566777764..3333333..4444444443.5789999985 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.17
                   Viral_helicase1  99 Qipfhsrnasfllahlpsslshrvgrrttyllpsdvaeilsakvgteveversgel.kvetepkgq 163
                                       Q++++s+++  ll+ l s + ++++++ +++++s+++ +++a     +++++++e  + e++ + q
  gi|385806401|ref|YP_005842799.1| 367 QSTSKSKKD--LLPYLRSIY-RLSPPHFVQICRSYGITVEEAA---VIVGDKQVEKaFAEMAAERQ 426
                                       888888888..999999999.********************99...34444444444333333333 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   4.6e-05     0.019       2      42 ..      48      92 ..      47     175 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.6e-05
                                      EEEEESTTSSHHHHHHHHHTS....TEEESSSTTSSSSEEEEEEE CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltge....kaivsdkpgtTrdinegrvk 42
                                      v+++G p vGK++Li al ++     +++++     rd ++++v 
  gi|385806401|ref|YP_005842799.1| 48 VLLYGPPGVGKTSLIEALANDygyeIVETNASDYRRRDDIYRKVY 92
                                      789****************96543345555555555555555555 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 ?   13.9   0.0   6.8e-05     0.028      32      58 ..      44      70 ..      31      94 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.8e-05
                             AAA_7 32 nkkpvllvGptGtGKtviikdllkkld 58
                                       kk vll+Gp G+GKt++i+ l + + 
  gi|385806401|ref|YP_005842799.1| 44 TKKAVLLYGPPGVGKTSLIEALANDYG 70
                                      689*****************9998776 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   0.00013     0.052      18      43 ..      43      68 ..      21     140 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00013
                          ATPase_2 18 epneiyfiYGpegsGKtaLlkeiien 43
                                       +++ +++YGp g+GKt+L+  +++ 
  gi|385806401|ref|YP_005842799.1| 43 PTKKAVLLYGPPGVGKTSLIEALAND 68
                                      3567899*************998875 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0    0.0002     0.083     101     138 ..      33      69 ..      16      91 .. 0.71
   2 ?   -0.7   0.1       1.4   5.9e+02      20      62 ..     325     368 ..     312     374 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0002
                         Parvo_NS1 101 qvllawlskqlgkrntvwfyGpantGktnlaeaIakav 138
                                       +++  w ++    + +v++yGp+  Gkt l ea+a+  
  gi|385806401|ref|YP_005842799.1|  33 SWIKDWEKRA-PTKKAVLLYGPPGVGKTSLIEALANDY 69 
                                       3333443333.66789******************9864 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.4
                         Parvo_NS1  20 givteedWaaid.sesYlrlsrsragrrqienaleqakirmfst 62 
                                       ++ t+ +W++ + +++  +ls ++++r+ +++ l+  ++r++++
  gi|385806401|ref|YP_005842799.1| 325 RKKTKFKWLKYNyPSKLKMLSETKRSRELLNSSLQKLSKRLSQS 368
                                       66788888877757888899999999999999999999998776 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   0.00015     0.063      18      46 ..      42      72 ..      22      82 .. 0.77
   2 ?   -2.1   0.0       9.2   3.7e+03      94     102 ..     264     272 ..     233     298 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00015
                                      H..TEEEEEEESTTSSHHHHHHHHHHHTT-- CS
                              TsaE 18 l..gdvilLeGdLGaGKTtlvrglakalgve 46
                                      +  ++++lL+G+ G+GKT l+ +la+ +g+e
  gi|385806401|ref|YP_005842799.1| 42 AptKKAVLLYGPPGVGKTSLIEALANDYGYE 72
                                      244678********************99987 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 9.2
                                       EEEEETGGG CS
                              TsaE  94 vvlvEWpek 102
                                        +l+EW ++
  gi|385806401|ref|YP_005842799.1| 264 DTLIEWLSE 272
                                       478899766 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 ?   12.5   0.0   0.00015     0.062      18      76 ..      43      94 ..      17     175 .. 0.86
   2 ?   -1.2   0.0       2.2     9e+02     279     295 ..     360     376 ..     286     445 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00015
                        KAP_NTPase 18 atpivvgLygkWGsGKssllnkledelkefakpvrflfaefnawsfkggddavaellaa 76
                                       t+ +v Lyg+ G+GK+sl++ l +++  +       ++e na  +  +dd+ ++++++
  gi|385806401|ref|YP_005842799.1| 43 PTKKAVLLYGPPGVGKTSLIEALANDYGYE-------IVETNASDYRRRDDIYRKVYNS 94
                                      567789********************9999.......8888888888888877777654 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.2
                        KAP_NTPase 279 tlgnsasksnlqlaldl 295
                                       +l++ +s+s+++ ++dl
  gi|385806401|ref|YP_005842799.1| 360 KLSKRLSQSTSKSKKDL 376
                                       22333333333333333 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00049       0.2      11      36 ..      45      70 ..      36      99 .. 0.82
   2 ?   -1.4   0.0       7.7   3.1e+03     119     134 ..      96     111 ..      92     113 .. 0.84
   3 ?   -1.3   0.1       7.2   2.9e+03      79     100 ..     405     441 ..     338     457 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00049
                                      TSEEEEEESTTSSHHHHHHHHTTSS- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 11 gekvaivGenGaGKStLlkllagllk 36
                                       + v + G+ G GK++L+++la+ + 
  gi|385806401|ref|YP_005842799.1| 45 KKAVLLYGPPGVGKTSLIEALANDYG 70
                                      678999***************99875 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 7.7
                                       HHHHHHHTSSEEEEES CS
                                       xxxxxxxxxxxxxxxx RF
                          ABC_tran 119 larallkkpkllllDE 134
                                       +  +l  ++kl+llDE
  gi|385806401|ref|YP_005842799.1|  96 IQGTLTGRKKLILLDE 111
                                       66788999*******9 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 7.2
                                       H...............HHHTCHHHHHHHSTTGGTTCB CS
                                       x...............xxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n...............esdeeiekalsklglkelkdt 100
                                                        + e+ ek ++k +++ ++++
  gi|385806401|ref|YP_005842799.1| 405 AavivgdkqvekafaeMAAERQEKSAEKAEISRTQAK 441
                                       3555332222222332222223333333343334444 PP

>> RsdA_SigD_bd  Anti-sigma-D factor RsdA to sigma factor binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       6.9   2.8e+03      11      18 ..      61      68 ..      60      77 .. 0.88
   2 ?   12.6   0.0   0.00032      0.13       8      32 ..     263     287 ..     260     289 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 6.9
                                      HHHHHHTT CS
                      RsdA_SigD_bd 11 LLDALAgr 18
                                      L++ALA +
  gi|385806401|ref|YP_005842799.1| 61 LIEALAND 68
                                      9*****87 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00032
                                       HHHHHHHHHTT-----SSHHHHHHH CS
                      RsdA_SigD_bd   8 dDaLLDALAgrgpvdtddpdeyeLA 32 
                                       +D L++ L+++ pv+ +dp+++ LA
  gi|385806401|ref|YP_005842799.1| 263 TDTLIEWLSENIPVQLTDPEDAYLA 287
                                       9*********************999 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00023     0.093      34      78 ..      26      73 ..      12      85 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00023
                                      XXXXXXXXXXXX..XXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 34 eaagvivelike..kkl.aGravLlaGpsgtGktalaiaiskelgedv 78
                                       a+++i++ ik+  k+  + +avLl Gp+g Gkt+l  a++++ g ++
  gi|385806401|ref|YP_005842799.1| 26 TAVAIITSWIKDweKRApTKKAVLLYGPPGVGKTSLIEALANDYGYEI 73
                                      578888888885323332579******************999988665 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00039      0.16       5      47 ..      52      93 ..      48     100 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00039
                                      ESTTSSHHHHHHHHHCCSTCEEEE-HHHHCCSSSSHHHHHHHH CS
                               dNK  5 GnIgaGKstlvklLskklgvkvfeEpvdkwtnvqknlLekfYk 47
                                      G+ g+GK++l++ L++ +g++++e   +++   +  + +k+Y+
  gi|385806401|ref|YP_005842799.1| 52 GPPGVGKTSLIEALANDYGYEIVETNASDY-RRRDDIYRKVYN 93
                                      888**************************9.445566677775 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00035      0.14      28      54 ..      40      66 ..      31      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00035
                            AAA_25 28 gllpagelallaGapgtGKttlaldla 54
                                         p ++ +ll+G+pg+GKt l   la
  gi|385806401|ref|YP_005842799.1| 40 KRAPTKKAVLLYGPPGVGKTSLIEALA 66
                                      5679999*************9986665 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   0.00037      0.15      22      43 ..      45      66 ..      34      67 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00037
                            AAA_29 22 kgatlltGpsGsGKSTllDAiq 43
                                      k a+ll Gp G+GK++l+ A++
  gi|385806401|ref|YP_005842799.1| 45 KKAVLLYGPPGVGKTSLIEALA 66
                                      3479**************9986 PP

>> Band_7  SPFH domain / Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00063      0.26     129     177 ..     354     441 ..     187     446 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00063
                            Band_7 129 n......................................eqlrkyGvevldvritdidpppevaqalaakqaaeaea 167
                                                                              + +r yG++v+++ +  i+  ++v++a+a+ +a ++e+
  gi|385806401|ref|YP_005842799.1| 354 LnsslqklskrlsqstskskkdllpylrsiyrlspphfvQICRSYGITVEEAAV--IVGDKQVEKAFAEMAAERQEK 428
                                       033333333444444445555555777777777777777779********8763..444455555555555555555 PP

                            Band_7 168 ...qaeiaraeae 177
                                          +aei+r +a+
  gi|385806401|ref|YP_005842799.1| 429 saeKAEISRTQAK 441
                                       5557777777765 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 ?   -1.7   0.0         4   1.6e+03     138     167 ..       4      33 ..       2      39 .. 0.80
   2 ?   10.0   0.0     0.001      0.43       3      34 ..      45      79 ..      43      96 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 4
                                       HHHHHHHHHCHHHHHH------T....T-- CS
                             SRPRB 138 EkElnkiierrskalkeldeeedksavlak 167
                                       Ek l  ii+ r k+lke  ++e+++a +++
  gi|385806401|ref|YP_005842799.1|   4 EKGLPWIIKYRPKSLKEYVNQETAVAIITS 33 
                                       88899999********99888888877765 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.001
                                      --EEEEE-STTSSHHHHHHHHHHS...S---B--- CS
                             SRPRB  3 kpavllvGlsdsGKTslftrLttd...svkktvtS 34
                                      k+avll G+   GKTsl++ L +d   ++ +t +S
  gi|385806401|ref|YP_005842799.1| 45 KKAVLLYGPPGVGKTSLIEALANDygyEIVETNAS 79
                                      789*******************9977766677666 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00059      0.24       5      82 ..      47     117 ..      44     133 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00059
                                       -EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTSEEEEETGGG-- CS
                             AAA_2   5 silllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegGivllDEidKih 81 
                                        +ll gp gvGkt l +ala+        +++  +as++  ++++ + v +  ++ +   +   +  +llDE+d  +
  gi|385806401|ref|YP_005842799.1|  47 AVLLYGPPGVGKTSLIEALANDYGY----EIVETNASDYRRRDDIYRKVYNSAIQGTLTGR---KKLILLDEVDGLS 116
                                       57899****************9997....9***********66666666555554443332...339******9887 PP

                                       - CS
                             AAA_2  82 p 82 
                                       +
  gi|385806401|ref|YP_005842799.1| 117 S 117
                                       7 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 ?   -0.4   0.0       3.2   1.3e+03      89     113 ..      25      49 ..      16      51 .. 0.75
   2 ?   10.5   0.0    0.0013      0.54       2      22 ..      48      68 ..      46      95 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 3.2
                                       GHHHHCHHHHHHHHHHHCSSS-EEE CS
                               Roc  89 srssenlkeWlkelkkvagkspvil 113
                                       ++  + + +W+k+ +k+a++++++l
  gi|385806401|ref|YP_005842799.1|  25 ETAVAIITSWIKDWEKRAPTKKAVL 49 
                                       344567789*******999887765 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0013
                                      EEEESSTTSSHHHHHHCHCT- CS
                               Roc  2 vvlvGdsgvGKtsllkrfved 22
                                      v+l G  gvGKtsl++ + +d
  gi|385806401|ref|YP_005842799.1| 48 VLLYGPPGVGKTSLIEALAND 68
                                      6789************99976 PP

>> DUF2774  Protein of unknown function (DUF2774)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00059      0.24      15      42 ..     390     419 ..     385     429 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00059
                           DUF2774  15 nFveIAkkldirakdvaklw..veveeare 42 
                                        Fv+I + ++i+ +++a ++  ++ve+a +
  gi|385806401|ref|YP_005842799.1| 390 HFVQICRSYGITVEEAAVIVgdKQVEKAFA 419
                                       6******************95556777653 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0     0.002      0.83      28      59 ..      37      69 ..      16      81 .. 0.70
   2 ?   -1.1   0.0       2.6   1.1e+03      98     133 ..      81     117 ..      71     141 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.002
                              TniB 28 eypkrkrm.pnlllvGdsnnGKtmivekFarlh 59
                                      ++ kr  + + +ll+G++ +GKt+++e  a+++
  gi|385806401|ref|YP_005842799.1| 37 DWEKRAPTkKAVLLYGPPGVGKTSLIEALANDY 69
                                      444443332789***************998876 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.6
                              TniB  98 lkararvs.kleqqvlrllrelkvrvLiiDEihnlla 133
                                       ++ r+++  k ++ +++   + + +++++DE++ l +
  gi|385806401|ref|YP_005842799.1|  81 YRRRDDIYrKVYNSAIQGTLTGRKKLILLDEVDGLSS 117
                                       5555554436667777777777889999***998763 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0    0.0013      0.52       9      31 ..      44      66 ..      39     117 .. 0.90
   2 ?   -1.4   0.0       6.5   2.6e+03      42      69 ..     338     380 ..     327     436 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0013
                            AAA_19  9 kekvllvtaGpGtGKTrvlkhiv 31
                                      ++k +l+ ++pG GKT ++++  
  gi|385806401|ref|YP_005842799.1| 44 TKKAVLLYGPPGVGKTSLIEALA 66
                                      67899*************99876 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 6.5
                            AAA_19  42 peeillvaftgrAakelrerlaalgae...............a 69 
                                       p ++ +++ t+r+ + l+ +l++l ++                
  gi|385806401|ref|YP_005842799.1| 338 PSKLKMLSETKRSRELLNSSLQKLSKRlsqstskskkdllpyL 380
                                       5666777777777777777776666554444444444444441 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.75   3.1e+02      13      31 ..      44      62 ..      23      83 .. 0.79
   2 ?    8.1   0.0    0.0052       2.1     122     154 ..     104     136 ..      82     148 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.75
                                      TTCEEEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxxxxxx RF
                              DEAD 13 gggdvlvaaeTGsGKTlaf 31
                                      +++ vl+ ++ G GKT   
  gi|385806401|ref|YP_005842799.1| 44 TKKAVLLYGPPGVGKTSLI 62
                                      56899***********875 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0052
                                       EEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 122 vrflVlDEadrlldqgfsdfinrilnqlpqitc 154
                                        +++ lDE+d+l++ g +  i++i++ + q+++
  gi|385806401|ref|YP_005842799.1| 104 KKLILLDEVDGLSSTGDKGGIEAIVQLITQTKN 136
                                       57899********************99955433 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0    0.0011      0.45      13      41 ..      42      69 ..      23     103 .. 0.79
   2 ?   -1.4   5.1       4.1   1.7e+03     129     167 ..     354     437 ..     317     456 .. 0.47

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0011
                            AAA_11 13 alseseitliqGPPGtgKTktivellsql 41
                                      a +++  +l+ GPPG gKT+ i +l +  
  gi|385806401|ref|YP_005842799.1| 42 APTKK-AVLLYGPPGVGKTSLIEALANDY 69
                                      44444.59*************99888765 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.1
                            AAA_11 129 iskeleklakelrafeeeeek.............................................eklkkskeksk 160
                                       ++++l+kl+k l++++++++k                                             e  ++ +eks+
  gi|385806401|ref|YP_005842799.1| 354 LNSSLQKLSKRLSQSTSKSKKdllpylrsiyrlspphfvqicrsygitveeaavivgdkqvekafaEMAAERQEKSA 430
                                       23333333333333333333355555555566666666667777777777776655543333333322222222222 PP

                            AAA_11 161 skleqer 167
                                       +k+e +r
  gi|385806401|ref|YP_005842799.1| 431 EKAEISR 437
                                       2222222 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00054      0.22      19      39 ..      45      65 ..      34     136 .. 0.94
   2 ?   -1.0   4.2       5.3   2.1e+03     114     154 ..     346     410 ..     190     451 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00054
                            AAA_23 19 kgltlItGpNGaGKTTildAi 39
                                      k+ +l++Gp G GKT++++A+
  gi|385806401|ref|YP_005842799.1| 45 KKAVLLYGPPGVGKTSLIEAL 65
                                      56789***************9 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 5.3
                            AAA_23 114 i.deleqfisellgskkiilnlilflgqerfeefelkdkke..................................r 154
                                       + + ++++++++l++  ++l+++  + ++           +                                   
  gi|385806401|ref|YP_005842799.1| 346 EtKRSRELLNSSLQKLSKRLSQSTSKSKK-----------DllpylrsiyrlspphfvqicrsygitveeaavivG 410
                                       11333333333333333333333333333...........122233333333444444555555553333333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (458 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1274  (0.0710581); expected 358.6 (0.02)
Passed bias filter:                      716  (0.0399353); expected 358.6 (0.02)
Passed Vit filter:                       120  (0.00669307); expected 17.9 (0.001)
Passed Fwd filter:                        44  (0.00245412); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              44  [number of targets reported over threshold]
# CPU time: 0.74u 0.36s 00:00:01.10 Elapsed: 00:00:00.50
# Mc/sec: 2752.46
//
Query:       gi|385806402|ref|YP_005842800.1|  [L=326]
Description: replication factor C small subunit [Fervidicoccus fontis Kam940]
Scores for complete 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   77.6   0.1    1.6e-21   76.5   0.1    1.6  1  Rep_fac_C        Replication factor C C-terminal domain
    1.8e-14   53.9   0.1    4.8e-10   39.5   0.1    2.3  2  DNA_pol3_delta2  DNA polymerase III, delta subunit
    2.4e-14   53.9   0.0    4.5e-14   53.0   0.0    1.5  1  AAA              ATPase family associated with various cellul
    4.3e-06   26.5   0.0    2.7e-05   24.0   0.0    2.1  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    8.6e-06   26.1   0.1      0.029   14.6   0.0    2.7  3  AAA_22           AAA domain
    1.2e-05   25.2   0.0    2.4e-05   24.2   0.0    1.5  1  AAA_3            ATPase family associated with various cellul
    2.4e-05   24.4   0.0    6.7e-05   22.9   0.0    1.7  1  Rad17            Rad17 P-loop domain
    4.9e-05   23.8   0.0     0.0099   16.3   0.0    2.3  2  AAA_16           AAA ATPase domain
    7.1e-05   22.9   0.0    0.00038   20.5   0.0    2.0  1  ResIII           Type III restriction enzyme, res subunit
    7.4e-05   22.8   0.1    0.00055   19.9   0.0    2.4  3  AAA_5            AAA domain (dynein-related subfamily)
    0.00015   22.0   0.0    0.00033   20.9   0.0    1.6  1  AAA_assoc_2      AAA C-terminal domain
    0.00046   20.0   0.6     0.0023   17.7   0.2    2.2  3  DNA_pol3_delta   DNA polymerase III, delta subunit
    0.00049   20.1   0.0     0.0019   18.2   0.0    2.0  2  AAA_14           AAA domain
    0.00062   19.3   0.3      0.059   12.8   0.0    2.4  2  PhoH             PhoH-like protein
    0.00067   19.5   0.0    0.00084   19.2   0.0    1.3  1  AAA_11           AAA domain
    0.00072   19.3   0.0     0.0018   18.1   0.0    1.6  1  IstB_IS21        IstB-like ATP binding protein
     0.0011   18.5   0.0     0.0018   17.8   0.0    1.3  1  AAA_7            P-loop containing dynein motor region
     0.0016   17.8   0.0       0.15   11.4   0.0    2.3  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0023   17.7   0.0     0.0043   16.8   0.0    1.4  1  AAA_24           AAA domain
     0.0038   16.8   0.7      0.037   13.6   0.2    2.5  3  AAA_25           AAA domain
      0.004   17.7   0.2      0.071   13.7   0.0    2.7  3  AAA_18           AAA domain
     0.0046   16.4   0.0       0.19   11.1   0.0    2.5  2  TniB             Bacterial TniB protein
     0.0049   16.8   0.1      0.008   16.1   0.1    1.5  1  ATPase_2         ATPase domain predominantly from Archaea
     0.0055   16.5   0.4        1.8    8.3   0.0    2.5  2  DEAD             DEAD/DEAH box helicase
     0.0057   15.9   0.0      0.009   15.2   0.0    1.4  1  DUF815           Protein of unknown function (DUF815)
     0.0061   15.8   0.0      0.013   14.7   0.0    1.6  1  TIP49            TIP49 P-loop domain
  ------ inclusion threshold ------
      0.028   14.3   0.1       0.35   10.8   0.1    2.2  1  NACHT            NACHT domain
       0.03   14.7   0.6       0.46   10.8   0.1    2.6  3  AAA_19           AAA domain
      0.032   14.0   0.3       0.41   10.4   0.1    2.5  2  AAA_30           AAA domain
      0.073   12.4   0.0       0.23   10.8   0.0    1.8  2  FtsK_SpoIIIE     FtsK/SpoIIIE family
      0.086   12.5   0.0        1.3    8.7   0.0    2.2  2  Sigma54_activat  Sigma-54 interaction domain
      0.091   12.1   0.7       0.55    9.5   0.0    2.4  3  ATPase           KaiC
      0.091   11.8   0.0       0.19   10.8   0.0    1.5  1  T2SSE            Type II/IV secretion system protein
       0.11   11.2   0.0        1.1    8.0   0.0    2.0  2  SNF2_N           SNF2 family N-terminal domain
       0.18   12.0   0.2        0.4   10.8   0.2    1.8  1  AAA_33           AAA domain


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 !   76.5   0.1   3.1e-24   1.6e-21       2      87 ..     231     317 ..     230     318 .. 0.98

  Alignments for each domain:
  == domain 1  score: 76.5 bits;  conditional E-value: 3.1e-24
                                       -HHHHHHHHHHHHHT-HHHHHHHHHHHHHHC---HHHHHHHHHHHGCCS...S-HHHHHHHHHHHHHHHHHHHCTH- CS
                         Rep_fac_C   2 hpteieeileaclngdfeeaykklrellvekGysaediltqlhrvvkeq.eelpeaqkleilellgeiekrlveGas 77 
                                       hp+ei+e+l+ +l+gdf+ a++ lr+l++++G+s+ d+++q+h+ ++++  +l+e++kl i ++ gei +r++eG++
  gi|385806402|ref|YP_005842800.1| 231 HPKEIREMLNLALSGDFNGARERLRKLMMDYGLSGVDVIKQIHKEIFSNeIDLSEEMKLMIADYTGEILFRITEGSD 307
                                       9***********************************************9988************************* PP

                                       HHHHHHHHHH CS
                         Rep_fac_C  78 ehlqlsalla 87 
                                       +++ql+++la
  gi|385806402|ref|YP_005842800.1| 308 DEIQLNSFLA 317
                                       ********98 PP

>> DNA_pol3_delta2  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   0.00022      0.11       2      48 ..      27      72 ..      26      76 .. 0.85
   2 !   39.5   0.1   9.3e-13   4.8e-10      84     162 ..      86     166 ..      72     167 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00022
                   DNA_pol3_delta2  2 qeealkilskalksgrlahayLfeGdegigkkelalnlakallceek 48
                                      qee++  l+k +k+++  h +Lf+G+ g+gk ++al++a+ l  ++ 
  gi|385806402|ref|YP_005842800.1| 27 QEETIIRLKKFVKEKNAPH-MLFAGPPGTGKTTAALAFAHDLYGKNY 72
                                      6778888999888887777.7*******************9988775 PP

  == domain 2  score: 39.5 bits;  conditional E-value: 9.3e-13
                   DNA_pol3_delta2  84 kldqirelieelsrkpres..kkkiiiiedaekmtksAaNalLktlEEPsenaifiLitsdtnklLktirSRcqelk 158
                                        +d ir  i+e+ r+++ +    k+ii+++ +++t+ A+ al +++E+    + fiLi++ ++k++++i+SR+  ++
  gi|385806402|ref|YP_005842800.1|  86 GIDVIRGKIKEFARTSVVGgvPFKLIILDESDNLTSDAQQALRRMMENFTLTSRFILIANYPSKIIEPIQSRTALFR 162
                                       7999**99999999999962257****************************************************** PP

                   DNA_pol3_delta2 159 fspl 162
                                       fspl
  gi|385806402|ref|YP_005842800.1| 163 FSPL 166
                                       **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 !   53.0   0.0   8.8e-17   4.5e-14       1     125 [.      46     159 ..      46     166 .. 0.86

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 8.8e-17
                                       EEEESSTTSSHHHHHHHHHHHH.....THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTS.EEEEEETGGGHH CS
                               AAA   1 vllyGppGtGKTllakavakel.....gvefleisgsellskyvgesekkirelfkeakekakp.silfiDEidala 71 
                                       +l+ GppGtGKT++a a a++l     ++ +le+++s+ +   +     ki+e+ ++      p + +++DE d+l+
  gi|385806402|ref|YP_005842800.1|  46 MLFAGPPGTGKTTAALAFAHDLygknyQQFVLELNASDER--GIDVIRGKIKEFARTSVVGGVPfKLIILDESDNLT 120
                                       89*******************9554433668*********..88888888888887755555788***********9 PP

                                       HHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSS CS
                               AAA  72 ksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfd 125
                                       ++            +++L +++++++       +i+++n+p+k+ +++  +R  
  gi|385806402|ref|YP_005842800.1| 121 SDA-----------QQALRRMMENFTLT---SRFILIANYPSKIIEPIQ-SRTA 159
                                       999...........*************4...68***************9.8865 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 !   24.0   0.0   5.3e-08   2.7e-05       2      58 ..      17      68 ..      16      82 .. 0.89
   2 ?   -0.5   0.0       1.7   8.9e+02      87     113 ..     110     136 ..     102     150 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 5.3e-08
                            RuvB_N  2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelg 58
                                      rP+sl+e + qe+   +lk f++     e++  h+l++GpPG Gktt a   a++l 
  gi|385806402|ref|YP_005842800.1| 17 RPRSLDEIVDQEETIIRLKKFVK-----EKNAPHMLFAGPPGTGKTTAALAFAHDLY 68
                                      9*************999999986.....56678*****************9999985 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.7
                            RuvB_N  87 vlfideihrlsraveevlysamedfrl 113
                                       ++ +de   l++ +++ l   me+f+l
  gi|385806402|ref|YP_005842800.1| 110 LIILDESDNLTSDAQQALRRMMENFTL 136
                                       67899999999999*********9987 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   5.7e-05     0.029       3      51 ..      41      85 ..      38     104 .. 0.71
   2 !    9.4   0.1    0.0023       1.2      81     120 ..      93     135 ..      66     149 .. 0.64
   3 ?   -2.0   0.0       7.9   4.1e+03      51      85 ..     230     261 ..     209     271 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.7e-05
                            AAA_22  3 ktagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst 51
                                      k+a +++  G++GtGKTt +  +++ l      ++ +  v++ +++ + 
  gi|385806402|ref|YP_005842800.1| 41 KNAPHMLFAGPPGTGKTTAALAFAHDLY----GKNYQQFVLELNASDER 85
                                      5788999***************999883....33345555555555554 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0023
                            AAA_22  81 aleqalrarav....ielliiDEaqhlrseealeeLrsllnlsr 120
                                       ++ + +r+  v     +l+i+DE ++l + +a + Lr+++++ +
  gi|385806402|ref|YP_005842800.1|  93 KIKEFARTSVVggvpFKLIILDESDNL-TSDAQQALRRMMENFT 135
                                       44444444444666779**********.8888888877776433 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 7.9
                            AAA_22  51 tsskdllrellralglelkaerlsseellealeqa 85 
                                         +k+++++l  al  + ++    +e+l++++ ++
  gi|385806402|ref|YP_005842800.1| 230 AHPKEIREMLNLALSGDFNG---ARERLRKLMMDY 261
                                       46778888888877766555...667777666665 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 !   24.2   0.0   4.6e-08   2.4e-05       1      92 [.      45     137 ..      45     145 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 4.6e-08
                             AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkk..Gpvfanllladeinrap 75 
                                       h+l+ g PG++kt+++ a+a+ l  +    qf  +l  sd  G++v++ k kef  ++  G v  +l++ de +  +
  gi|385806402|ref|YP_005842800.1|  45 HMLFAGPPGTGKTTAALAFAHDLYGKN-YQQFVLELNASDERGIDVIRGKIKEFARTSvvGGVPFKLIILDESDNLT 120
                                       99******************9997664.459*********************99765333999999*********** PP

                             AAA_3  76 pktqsalleameerqvt 92 
                                       + +q al  +me+ ++t
  gi|385806402|ref|YP_005842800.1| 121 SDAQQALRRMMENFTLT 137
                                       ***********987776 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   1.3e-07   6.7e-05       4     144 ..       7     149 ..       4     162 .. 0.69

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.3e-07
                             Rad17   4 denelWfekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskel.giklrewlnp 79 
                                       ++  lW eky+P  ++e+    + i  +k+++k +  ++      L +GP+G gk+t+    +  l g ++++++  
  gi|385806402|ref|YP_005842800.1|   7 ENYLLWAEKYRPRSLDEIVDQEETIIRLKKFVKEKNAPHM-----LFAGPPGTGKTTAALAFAHDLyGKNYQQFVLE 78 
                                       55668*************9999999999999988766655.....99**********98888876438999999987 PP

                             Rad17  80 vslkepdnqksdfkgltekesrf.......lsqiesfkeleLkdakyl......klqklGddlrtdkklilvedlPn 143
                                       ++  + +   + ++g+++ + r               k + L ++ +l       l+++ ++     ++il+ + P+
  gi|385806402|ref|YP_005842800.1|  79 LN-ASDERGIDVIRGKIKEFARTsvvggvpF------KLIILDESDNLtsdaqqALRRMMENFTLTSRFILIANYPS 148
                                       77.4444456667888887776544444331......3333333333211111156666777777778888888777 PP

                             Rad17 144 k 144
                                       k
  gi|385806402|ref|YP_005842800.1| 149 K 149
                                       6 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.9e-05    0.0099      17      51 ..      36      70 ..      25     100 .. 0.71
   2 ?    5.5   0.0      0.04        20     122     168 ..      93     141 ..      78     143 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.9e-05
                            AAA_16 17 ervrsgrpelvllsGesGvGKsslvrellralekd 51
                                      + v++   + +l+ G++G+GK++ + ++++ l ++
  gi|385806402|ref|YP_005842800.1| 36 KFVKEKNAPHMLFAGPPGTGKTTAALAFAHDLYGK 70
                                      3455666689*****************99988877 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.04
                            AAA_16 122 llkrllallsrderp.lvlvlDdlqwadeaslqllaaLlrllesk.pll 168
                                       ++k++++ +  ++ p  +++lD+ + + ++ +q+l+ ++++ +   +++
  gi|385806402|ref|YP_005842800.1|  93 KIKEFARTSVVGGVPfKLIILDESDNLTSDAQQALRRMMENFTLTsRFI 141
                                       4555554444445565699*******************99877643444 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 !   20.5   0.0   7.3e-07   0.00038       8      58 ..      27      76 ..      22     133 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 7.3e-07
                                      HHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EE CS
                            ResIII  8 QeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekfl 58
                                      Qee i +l++ +k+k+  ++l++ + GtGKT  a++++  l+ k++++ f+
  gi|385806402|ref|YP_005842800.1| 27 QEETIIRLKKFVKEKNAPHMLFAGPPGTGKTTAALAFAHDLYGKNYQQ-FV 76
                                      999999***999999999*************************98865.33 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 !   19.9   0.0   1.1e-06   0.00055       1      93 [.      45     135 ..      45     152 .. 0.85
   2 ?   -1.0   0.0       3.1   1.6e+03      79     109 ..     169     199 ..     166     243 .. 0.63
   3 ?   -2.4   0.0       8.7   4.4e+03      74     104 ..     269     299 ..     266     304 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.1e-06
                                       EEEEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaal.nreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEver 76 
                                       ++l  GppGtgK++ a  +a+ l +++++   l  + + e  +  ++  ++ +++   ++v  +   ++++lDE ++
  gi|385806402|ref|YP_005842800.1|  45 HMLFAGPPGTGKTTAALAFAHDLyGKNYQQFVLELNASDERGIDVIR--GKIKEFARTSVV-GGVPFKLIILDESDN 118
                                       68999****************99988888888877666665444444..788899999999.7889999******** PP

                                       --HHHHHHHHHHHHSSE CS
                             AAA_5  77 aesevlnsLlslleerr 93 
                                       + s+++++L +++e+ +
  gi|385806402|ref|YP_005842800.1| 119 LTSDAQQALRRMMENFT 135
                                       *********99999865 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.1
                                       HHHHHHHHHHHHSSEEE..-SSSEEE---.. CS
                             AAA_5  79 sevlnsLlslleerrllleeggelvkakndd 109
                                        +v+++L  +le++ ++ ee+  +  ++  +
  gi|385806402|ref|YP_005842800.1| 169 EDVIKRLKWILENESVSYEESALEAVFEISE 199
                                       5788888888888888877776666555444 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 8.7
                                       GGG--HHHHHHHHHHHHSSEEE..-SSSEEE CS
                             AAA_5  74 veraesevlnsLlslleerrllleeggelvk 104
                                       ++++++e+++  + l ee +l++++ ++++ 
  gi|385806402|ref|YP_005842800.1| 269 IKQIHKEIFSNEIDLSEEMKLMIADYTGEIL 299
                                       7788899999888999999999888888775 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   6.4e-07   0.00033       2      37 ..     181     216 ..     180     246 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 6.4e-07
                                       XX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       AAA_assoc_2   2 ekklkleddalealaeladGDaRkaLnlLElaaeaa 37 
                                       ++++++e++alea+ e+++GD+Rka+n+L+ a +  
  gi|385806402|ref|YP_005842800.1| 181 NESVSYEESALEAVFEISEGDMRKAINVLQSASAIG 216
                                       578999************************776544 PP

>> DNA_pol3_delta  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.2   4.5e-06    0.0023      61     170 ..     111     210 ..     106     211 .. 0.90
   2 ?   -2.1   0.0       5.6   2.9e+03     141     173 ..     226     258 ..     219     259 .. 0.82
   3 ?   -1.5   0.0       3.7   1.9e+03     130     163 ..     267     300 ..     263     304 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.5e-06
                                       EEEE--.....TT-S-TTHHHHHHHHTTT--SSEEEEEEES.S--HHHHHHHHHTTTEEEEEE----TTTHHHHHHH CS
                    DNA_pol3_delta  61 vvlknpklltkesklnekllkeLeeylsnlpedtlLiliapkklderkklvklLkkkatvveaktlkeeelkkwiqk 137
                                       ++l+       +++l+ + +++L ++++n   ++ +ilia+       k++  +++++ ++++++lk+e+++k ++ 
  gi|385806402|ref|YP_005842800.1| 111 IILD------ESDNLTSDAQQALRRMMENFTLTSRFILIAN-Y---PSKIIEPIQSRTALFRFSPLKKEDVIKRLKW 177
                                       3444......5578999************************.4...458999************************* PP

                                       HHHHTT-EE-HHHHHHHHHHHTT-HHHHHHHHH CS
                    DNA_pol3_delta 138 raqelglkiekealelLlelvennlsaikqele 170
                                       +++++ +  e+ ale   e +e++++ + + l+
  gi|385806402|ref|YP_005842800.1| 178 ILENESVSYEESALEAVFEISEGDMRKAINVLQ 210
                                       **************************9988776 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5.6
                                       HTT-EE-HHHHHHHHHHHTT-HHHHHHHHHHHH CS
                    DNA_pol3_delta 141 elglkiekealelLlelvennlsaikqelekLa 173
                                         gl   ke  e+L  +++++++ +   l kL+
  gi|385806402|ref|YP_005842800.1| 226 VVGLAHPKEIREMLNLALSGDFNGARERLRKLM 258
                                       567777888999999999999999999999997 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 3.7
                                       THHHHHHHHHHHTT-EE-HHHHHHHHHHHTT-HH CS
                    DNA_pol3_delta 130 elkkwiqkraqelglkiekealelLlelvennls 163
                                       +++k+i k + ++ +++++e   +++++++  l+
  gi|385806402|ref|YP_005842800.1| 267 DVIKQIHKEIFSNEIDLSEEMKLMIADYTGEILF 300
                                       5788999999999999999988888888876555 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0       1.6   8.4e+02      69      98 ..      20      49 ..       3      51 .. 0.75
   2 !   18.2   0.0   3.7e-06    0.0019       6      90 ..      47     134 ..      42     167 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 1.6
                            AAA_14 69 flDEiqevpewekalkslvdegknldvivt 98
                                       lDEi   +e    lk++v+e++  +++++
  gi|385806402|ref|YP_005842800.1| 20 SLDEIVDQEETIIRLKKFVKEKNAPHMLFA 49
                                      699999999999999999999855566655 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 3.7e-06
                            AAA_14   6 vitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe.kllelilek.lke.ekktylflDEiqev.pe 78 
                                       +  G+  +GKTt +  ++++l+ k+ + + ++l+  +++ ++  + k+ e+ + + + +    ++++lDE  ++ ++
  gi|385806402|ref|YP_005842800.1|  47 LFAGPPGTGKTTAALAFAHDLYGKNYQQFVLELNASDERGIDVIRgKIKEFARTSvV-GgVPFKLIILDESDNLtSD 122
                                       6679999***************44444444444444444444333256666666633.3445678******998467 PP

                            AAA_14  79 wekalkslvdeg 90 
                                       +++al++++++ 
  gi|385806402|ref|YP_005842800.1| 123 AQQALRRMMENF 134
                                       ********9987 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   0.00012     0.059      21      55 ..      45      78 ..      24      97 .. 0.73
   2 ?    4.2   0.1     0.049        25     121     146 ..     109     133 ..      84     148 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00012
                                      EEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEE CS
                              PhoH 21 ivfaiGpaGtGKtylavalavealkkkkvkriilt 55
                                       +  +Gp GtGKt  a+a a +++  k++++++l 
  gi|385806402|ref|YP_005842800.1| 45 HMLFAGPPGTGKTTAALAFAHDLYG-KNYQQFVLE 78
                                      56678**************988765.567777775 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.049
                                       EEEEE-SGGG--HHHHHHHHTTB-TT CS
                              PhoH 121 afvilDEAQnttkeqmkmfltRlGen 146
                                       +++ilDE+ n+t+   +  l R+ en
  gi|385806402|ref|YP_005842800.1| 109 KLIILDESDNLTSDA-QQALRRMMEN 133
                                       58*********9875.5566676555 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.6e-06   0.00084      11      75 ..      35      95 ..      24     213 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.6e-06
                            AAA_11 11 ksalsese..itliqGPPGtgKTktivellsqllsrrkseeeksakpriL.vCapSNaAvDellerll 75
                                      k++++e++    l+ GPPGtgKT++ +++ + l+        k++++ +L + a+ +  +D++  ++ 
  gi|385806402|ref|YP_005842800.1| 35 KKFVKEKNapHMLFAGPPGTGKTTAALAFAHDLY-------GKNYQQFVLeLNASDERGIDVIRGKIK 95
                                      556666555668*********************3.......234444444244444455555555555 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 !   18.1   0.0   3.4e-06    0.0018      40     127 ..      34     126 ..      19     149 .. 0.66

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.4e-06
                         IstB_IS21  40 tlsfiekken..ivllGpsGvGKshlaialgveavraglsvlfvrvedLvee.lkrarrd..gklaralkrllkvdl 111
                                         +f+++k++  +++ Gp+G+GK+  a a++++   ++++ + + +++  e+ + + r++  + + + +   + ++l
  gi|385806402|ref|YP_005842800.1|  34 LKKFVKEKNAphMLFAGPPGTGKTTAALAFAHDLYGKNYQQFVLELNASDERgIDVIRGKikEFARTSVVGGVPFKL 110
                                       4567776654338999******************9999986655554432221333333200223333444556799 PP

                         IstB_IS21 112 lilDdlgllpldqaea 127
                                       +ilD+   l+ d ++a
  gi|385806402|ref|YP_005842800.1| 111 IILDESDNLTSDAQQA 126
                                       9999987777665554 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   3.5e-06    0.0018      26      72 ..      34      82 ..      22     104 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.5e-06
                             AAA_7 26 lelllk..nkkpvllvGptGtGKtviikdllkkldkekylsltinfsaq 72
                                      l++++k  n  ++l+ Gp GtGKt+ +  + + l  ++y+  +++++a+
  gi|385806402|ref|YP_005842800.1| 34 LKKFVKekNAPHMLFAGPPGTGKTTAALAFAHDLYGKNYQQFVLELNAS 82
                                      4555541045589*****************************9999985 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   0.00029      0.15      23      43 ..      44      64 ..      21      84 .. 0.76
   2 ?    4.0   0.0     0.057        29     110     149 ..     111     149 ..     105     156 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00029
                      Mg_chelatase 23 HnlllvGppGsGKtmlakrlp 43
                                       ++l++GppG+GKt  a +++
  gi|385806402|ref|YP_005842800.1| 44 PHMLFAGPPGTGKTTAALAFA 64
                                      589***********9997765 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.057
                      Mg_chelatase 110 LfLDElpefkrkvlevLRePledgevtisrakakvefpar 149
                                       ++LDE  ++++++ ++LR+ +e+ ++t sr    +++p++
  gi|385806402|ref|YP_005842800.1| 111 IILDESDNLTSDAQQALRRMMENFTLT-SRFILIANYPSK 149
                                       78********************99876.666666667665 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   8.5e-06    0.0043       4      91 ..      45     133 ..      42     140 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 8.5e-06
                            AAA_24   4 kiliyGpsgiGKTtlakel.......gpkplfidtekGlks.ldadkfpdieswedfldevvelaaeladyktlviD 72 
                                        +l  Gp+g+GKTt a+ +        ++ +++ ++++  + +d+++++       +++++ +      ++k +++D
  gi|385806402|ref|YP_005842800.1|  45 HMLFAGPPGTGKTTAALAFahdlygkNYQQFVLELNASDERgIDVIRGK-------IKEFARTSVVGGVPFKLIILD 114
                                       68899**************999999888888888888765436666655.......56666666888999******* PP

                            AAA_24  73 tideleelclaevirqnek 91 
                                         d l + + + ++r+ e+
  gi|385806402|ref|YP_005842800.1| 115 ESDNLTSDAQQALRRMMEN 133
                                       *******999999999876 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.2   7.2e-05     0.037      37      57 ..      47      67 ..      40     132 .. 0.92
   2 ?    0.3   0.0      0.86   4.4e+02     124     157 ..     196     229 ..     170     245 .. 0.81
   3 ?    0.0   0.0       1.1   5.4e+02     130     157 ..     202     229 ..     196     295 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.2e-05
                            AAA_25 37 llaGapgtGKttlaldlalav 57
                                      l+aG+pgtGKtt+al  a+++
  gi|385806402|ref|YP_005842800.1| 47 LFAGPPGTGKTTAALAFAHDL 67
                                      789*************99986 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.86
                            AAA_25 124 tlltadvdaleaaieevegvrlvviDplsralgg 157
                                       ++ ++d+++ +++++++  ++ v +D++++++g 
  gi|385806402|ref|YP_005842800.1| 196 EISEGDMRKAINVLQSASAIGKVTVDTVYKVVGL 229
                                       4567899999999999888999999999998876 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 1.1
                            AAA_25 130 vdaleaaieevegvrlvviDplsralgg 157
                                       +++ +++++++  ++ v +D++++++g 
  gi|385806402|ref|YP_005842800.1| 202 MRKAINVLQSASAIGKVTVDTVYKVVGL 229
                                       5555555555555555555555555543 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   0.00014     0.071       3      41 ..      48      85 ..      46     103 .. 0.79
   2 ?   -0.0   0.0       2.4   1.2e+03      25      69 ..     135     183 ..     120     278 .. 0.58
   3 ?   -0.0   0.0       2.4   1.2e+03      28      86 ..     254     319 ..     230     325 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00014
                            AAA_18  3 ltGtpGvGKttlakeLskrlgfgvnlrdvakenglllev 41
                                       +G+pG+GKtt a + +  l +g n+++ + e + ++e+
  gi|385806402|ref|YP_005842800.1| 48 FAGPPGTGKTTAALAFAHDL-YGKNYQQFVLELNASDER 85
                                      79***********9998886.788888888887766665 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 2.4
                            AAA_18  25 gvnlrdvakenglllevdpe....aldeskrldedkldklldaleenss 69 
                                          +r+++  n+++   +p     al ++  l+++ + k l+ + en s
  gi|385806402|ref|YP_005842800.1| 135 TLTSRFILIANYPSKIIEPIqsrtALFRFSPLKKEDVIKRLKWILENES 183
                                       5555555555555544444444444444444444444444444444433 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 2.4
                            AAA_18  28 lrdvakenglllevdpe.........aldeskrldedkldklldaleenssaleegknlvidghlael 86 
                                       lr++  + gl+  +  +         ++d s++++ +  d+  ++l ++   +++ + + + ++la+l
  gi|385806402|ref|YP_005842800.1| 254 LRKLMMDYGLSGVDVIKqihkeifsnEIDLSEEMKLMIADYTGEILFRIT--EGSDDEIQLNSFLAWL 319
                                       33333333333333333333333333557777777777777777777775..4777777777777776 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00038      0.19      22      58 ..      30      66 ..      20      78 .. 0.85
   2 ?    2.3   0.0      0.18        94     114     143 ..     102     131 ..      91     137 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00038
                              TniB 22 rLeeLleypkrkrmpnlllvGdsnnGKtmivekFarl 58
                                      ++ +L ++ k+k  p++l++G++ +GKt+ +  Fa++
  gi|385806402|ref|YP_005842800.1| 30 TIIRLKKFVKEKNAPHMLFAGPPGTGKTTAALAFAHD 66
                                      56678889999*******************9999865 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.18
                              TniB 114 llrelkvrvLiiDEihnllagsarkqrefl 143
                                       +   +  +++i+DE +nl +  +++ r+++
  gi|385806402|ref|YP_005842800.1| 102 VVGGVPFKLIILDESDNLTSDAQQALRRMM 131
                                       55567789*********9976666655554 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   1.6e-05     0.008       2     125 ..      25     145 ..      24     239 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.6e-05
                          ATPase_2   2 fdRekelkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkkl 78 
                                       +d e+ + +l++ +++++++ ++  Gp g GKt+    ++  l  k+ y  ++ +l+ +++  +d      + k+++
  gi|385806402|ref|YP_005842800.1|  25 VDQEETIIRLKKFVKEKNAPHMLFAGPPGTGKTTAALAFAHDLYGKN-YQQFVLELNASDERGIDVI--RGKIKEFA 98 
                                       7999************999999999******************8866.799*************999..22222222 PP

                          ATPase_2  79 ekalgiavpkaeleeilk...eksklvfkaielllekikkkgkkiiiiiD 125
                                       +  +   vp + +  il+   + + ++++a+ +++e+ + +  + i+i+ 
  gi|385806402|ref|YP_005842800.1|  99 RTSVVGGVPFKLI--ILDesdNLTSDAQQALRRMMENFTLTS-RFILIAN 145
                                       3333223332222..233333667777777777777666553.3555555 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.018       9.3      15      36 ..      44      65 ..      25      84 .. 0.76
   2 !    8.3   0.0    0.0036       1.8     122     149 ..     108     134 ..      78     143 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.018
                                      CEEEEEESTTSSHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 15 gdvlvaaeTGsGKTlaflipvl 36
                                       ++l a++ G+GKT+a+l  + 
  gi|385806402|ref|YP_005842800.1| 44 PHMLFAGPPGTGKTTAALAFAH 65
                                      47899***********987654 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0036
                                       EEEEEEETHHHHHHTTTHHHHHHHHHHS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 122 vrflVlDEadrlldqgfsdfinrilnql 149
                                       +++++lDE d+l ++  ++ ++r+++++
  gi|385806402|ref|YP_005842800.1| 108 FKLIILDESDNLTSD-AQQALRRMMENF 134
                                       489***********8.9999***99987 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.8e-05     0.009      28     107 ..      19      99 ..       3     143 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.8e-05
                            DUF815  28 ddLvgidkqkealventeqfleglpannvLLwGarGtGKSslvkallneyaeeg..Lrlievekedlkelpklvell 102
                                       ++L +i +q+e++++  ++f++ ++a ++L+ G  GtGK +   a  +++  ++    ++e++ +d + ++ +  ++
  gi|385806402|ref|YP_005842800.1|  19 RSLDEIVDQEETIIR-LKKFVKEKNAPHMLFAGPPGTGKTTAALAFAHDLYGKNyqQFVLELNASDERGIDVIRGKI 94 
                                       455555566666665.689*********************9999998888777644345666666666666666666 PP

                            DUF815 103 rerpe 107
                                       +e ++
  gi|385806402|ref|YP_005842800.1|  95 KEFAR 99 
                                       65544 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   2.6e-05     0.013      40      75 ..      35      68 ..      24     102 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.6e-05
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 40 velikekklaGravLlaGpsgtGktalaiaiskelg 75
                                       +++kek+     +L+aGp+gtGkt  a+a +++l 
  gi|385806402|ref|YP_005842800.1| 35 KKFVKEKNAP--HMLFAGPPGTGKTTAALAFAHDLY 68
                                      5678888844..89*******************995 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00068      0.35       3     129 ..      46     147 ..      45     177 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00068
                                       EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-...-HCHHHCCCCTS--SSS-CCHHHHCCS CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgnarsladllfsqlpepaapvsevwavllel 79 
                                       ++  G++G GKTt +  +a+++  ++++q      F+l+l +  ++g     +d+++ + +e a+++      ++  
  gi|385806402|ref|YP_005842800.1|  46 MLFAGPPGTGKTTAALAFAHDLYGKNYQQ------FVLELNASDERG-----IDVIRGKIKEFARTS------VVGG 105
                                       5778******************9999777......777777777765.....677777777777666......4455 PP

                                       CCCEEEEEE-STT-SS-TCH.........HHHHHCTTTTT--EEEEEEEC CS
                             NACHT  80 perlLlilDglDelvtdlgqkekqpvrtlLselirkkllpeasllltvrp 129
                                           L+ilD  D l +d +q         L+++++   l++  +l++  p
  gi|385806402|ref|YP_005842800.1| 106 VPFKLIILDESDNLTSDAQQ--------ALRRMMENFTLTSRFILIANYP 147
                                       55567777777777777777........5555556555556566555555 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1    0.0009      0.46       5      27 ..      38      60 ..      35      81 .. 0.81
   2 ?    0.3   0.0       1.6     8e+02     105     126 ..     110     131 ..     105     143 .. 0.75
   3 ?   -1.0   0.0         4     2e+03      73      73 ..     224     224 ..     169     310 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0009
                            AAA_19  5 vealkekvllvtaGpGtGKTrvl 27
                                      v++ +++++l  ++pGtGKT+  
  gi|385806402|ref|YP_005842800.1| 38 VKEKNAPHMLFAGPPGTGKTTAA 60
                                      557788999999********965 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.6
                            AAA_19 105 llivDEfqdvdelqyrLlkall 126
                                       l+i DE+ +++  +++ l++++
  gi|385806402|ref|YP_005842800.1| 110 LIILDESDNLTSDAQQALRRMM 131
                                       7999*****9966666666666 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 4
                            AAA_19  73 H 73 
                                        
  gi|385806402|ref|YP_005842800.1| 224 Y 224
                                       2 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00079      0.41      20      42 ..      45      68 ..      32     136 .. 0.75
   2 ?    0.8   0.0      0.67   3.4e+02     168     187 ..     196     215 ..     174     257 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00079
                            AAA_30 20 vavltGpAGtGKttalkal.reaw 42
                                       ++  Gp+GtGKtta  a   +++
  gi|385806402|ref|YP_005842800.1| 45 HMLFAGPPGTGKTTAALAFaHDLY 68
                                      56789*********8655424444 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.67
                            AAA_30 168 alregdaeealealadrgri 187
                                       +++egd+++a++ l++ ++i
  gi|385806402|ref|YP_005842800.1| 196 EISEGDMRKAINVLQSASAI 215
                                       55555555555555544444 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00044      0.23      24      55 ..      29      59 ..      10      65 .. 0.73
   2 ?   -2.7   0.0       5.9     3e+03     115     147 ..     250     285 ..     220     295 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00044
                                      EETTS-EEEEEGGGS-.SEEEE--TTSSHHHH CS
                      FtsK_SpoIIIE 24 keisgnplvldlkkmashllvaGatgsGKSta 55
                                      + i++ +  + +k+++ h+l aG +g+GK+ta
  gi|385806402|ref|YP_005842800.1| 29 ETIIRLKKFVKEKNAP-HMLFAGPPGTGKTTA 59
                                      5556666666777777.*************98 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.9
                                       HHHHHHHHHHHTT-SSHHH...HHHHHHHHHHTT-- CS
                      FtsK_SpoIIIE 115 emeeryalfreagvrsiaa...ydgeiaedpldifg 147
                                       ++e+  +l+ + g   +++    ++ei + + d+ +
  gi|385806402|ref|YP_005842800.1| 250 ARERLRKLMMDYGLSGVDVikqIHKEIFSNEIDLSE 285
                                       344444666666555555544455555555555544 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    0.0025       1.3      14      54 ..      33      76 ..      23      86 .. 0.69
   2 ?    1.1   0.0      0.54   2.7e+02      97     120 ..     111     134 ..     105     138 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0025
                                      HHHHHCTSS..S-EEEECSTTSSHHHHHHHH.HHHSTTTTS-EE CS
                   Sigma54_activat 14 qikkvaktd..lsvlitGesGtGKellarai.heaskrkekpfv 54
                                      ++kk++k +   ++l  G  GtGK++ a a  h+   ++ ++fv
  gi|385806402|ref|YP_005842800.1| 33 RLKKFVKEKnaPHMLFAGPPGTGKTTAALAFaHDLYGKNYQQFV 76
                                      4455554443468999**********997754777777777776 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.54
                                       EEEETGGGS-HHHHHHHHHHHHHS CS
                   Sigma54_activat  97 lfLDeigelplelQekLlrvlqeg 120
                                       + LDe  +l+ ++Q+ L r++++ 
  gi|385806402|ref|YP_005842800.1| 111 IILDESDNLTSDAQQALRRMMENF 134
                                       78*****************99975 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0    0.0011      0.55      21      41 ..      45      65 ..      21      84 .. 0.88
   2 ?   -1.5   0.0       2.6   1.3e+03     117     147 ..     105     134 ..      68     141 .. 0.71
   3 ?   -0.6   0.0       1.4   7.1e+02     109     145 ..     200     240 ..     163     244 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0011
                            ATPase 21 vvlitGepGtGKtifalqFli 41
                                       +l +G pGtGKt+ al F+ 
  gi|385806402|ref|YP_005842800.1| 45 HMLFAGPPGTGKTTAALAFAH 65
                                      5899***************86 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.6
                            ATPase 117 eikakrvviDsitglayeekeavaReilrql 147
                                        +  k +++D  ++l +++ ++ +R+ + ++
  gi|385806402|ref|YP_005842800.1| 105 GVPFKLIILDESDNL-TSDAQQALRRMMENF 134
                                       445577888888888.777777788777665 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.4
                            ATPase 109 eelaeaikeika....krvviDsitglayeekeavaReilr 145
                                        ++++ai+ ++      +v +D++  +   ++++++Re l 
  gi|385806402|ref|YP_005842800.1| 200 GDMRKAINVLQSasaiGKVTVDTVYKVVGLAHPKEIREMLN 240
                                       33444444443322237888999999989999999998875 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00036      0.19     104     151 ..      20      65 ..       5      78 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00036
                             T2SSE 104 tlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallk 151
                                       +ld+++ +e++  ++++++++   +   +l++G+ g+GKtt + a  +
  gi|385806402|ref|YP_005842800.1|  20 SLDEIVDQEETIIRLKKFVKEK--NAPHMLFAGPPGTGKTTAALAFAH 65 
                                       6788888888888899999998..8889*************9877665 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 ?    0.7   0.0      0.34   1.8e+02      41      77 ..      29      65 ..      21      75 .. 0.80
   2 ?    8.0   0.0    0.0021       1.1     165     211 ..      95     142 ..      70     145 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.34
                                      ........HHHHHTT--EEE---TTS--HHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 41 tgevveesaeakqsvrGGiLaDemGLGKTvqvlalil 77
                                      ++++  +++ ++++ +  ++a  +G GKT  +la+ +
  gi|385806402|ref|YP_005842800.1| 29 ETIIRLKKFVKEKNAPHMLFAGPPGTGKTTAALAFAH 65
                                      56666677888888889999************99865 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0021
                                       ......TTS-S-S-SEEEES-GGGT--T.TSHHHHHHHH---S-EEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 165 elqkkrsvlkqvewkrvvlDEghtlkns.tskaaeavskLstsnrwil 211
                                       + +++ sv+  v  k ++lDE  +l +  ++ ++ +++++    r il
  gi|385806402|ref|YP_005842800.1|  95 KEFARTSVVGGVPFKLIILDESDNLTSDaQQALRRMMENFTLTSRFIL 142
                                       34478899999999**************8999999**99999999887 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   0.00078       0.4       3      18 ..      47      62 ..      46     159 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00078
                            AAA_33  3 llvGlpGsGKstlaer 18
                                      l+ G+pG+GK+t a  
  gi|385806402|ref|YP_005842800.1| 47 LFAGPPGTGKTTAALA 62
                                      799*********9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       869  (0.048469); expected 358.6 (0.02)
Passed bias filter:                      712  (0.0397122); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); 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):              35  [number of targets reported over threshold]
# CPU time: 0.71u 0.32s 00:00:01.03 Elapsed: 00:00:00.48
# Mc/sec: 2034.87
//
Query:       gi|385806403|ref|YP_005842801.1|  [L=169]
Description: Adenosine_kin domain containing protein [Fervidicoccus fontis Kam940]
Scores for complete 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-75  250.6   0.3    5.4e-75  250.4   0.3    1.0  1  Adenosine_kin  Adenosine specific kinase
  ------ inclusion threshold ------
      0.056   13.8   0.0       0.38   11.2   0.0    2.1  2  DUF2122        RecB-family nuclease (DUF2122)


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 !  250.4   0.3     6e-79   5.4e-75       1     154 []      12     165 ..      12     165 .. 0.99

  Alignments for each domain:
  == domain 1  score: 250.4 bits;  conditional E-value: 6e-79
                                       EEE---TTEEEEEEEESSTTHHHHHHHHHHCCSTTSEEEEEEE--STT-EEEEEESSHHHHHHHHHHHHHH--TTEE CS
                     Adenosine_kin   1 vkiekpeevnvilgqshfiktvedlyealvtsvpgikfglafcEasgkrLvrvegndeelvelavknalaigaghvf 77 
                                       v+i +pe+vnvi+gqshfiktvedlye+l+ts++ ikfg+af+EasgkrL+r++gndeel+++av++a++igaghvf
  gi|385806403|ref|YP_005842801.1|  12 VNIPVPEDVNVIIGQSHFIKTVEDLYEVLTTSSTCIKFGIAFNEASGKRLIRYDGNDEELTQMAVDAAKSIGAGHVF 88 
                                       7899************************************************************************* PP

                                       EEEEEST-HHHHHHHHHHCTTCEEEEEEESSSEEEEEEEETTEEEEEEEEES---SEE--HHHHHHHHHHHHHTTS- CS
                     Adenosine_kin  78 villknafPinvlnaiksvpevvkifaAtanplevivaeteqgrgvlgvvDGfspkgveeeedkkerkellrkigYk 154
                                       vi+++n++Pinvlnaik+v+ev +i++At+np++vi+ et+qgr+vlgvvDG++p+gve eedkker e+lrkigYk
  gi|385806403|ref|YP_005842801.1|  89 VIYIRNGWPINVLNAIKHVQEVLNIYVATSNPVQVIIGETDQGRSVLGVVDGYTPLGVEGEEDKKERIEFLRKIGYK 165
                                       ****************************************************************************9 PP

>> DUF2122  RecB-family nuclease (DUF2122)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.05   4.5e+02      29      81 ..      34      78 ..      26      82 .. 0.57
   2 ?   11.2   0.0   4.2e-05      0.38       3      69 ..      79     140 ..      77     165 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.05
                           DUF2122 29 kDalellkpekvlllskeegeelleeeeleekgrvllvfsgadegfskkelel 81
                                      +D +e+l+ +++        +  + ++e   +g+ l+  +g+de++++  ++ 
  gi|385806403|ref|YP_005842801.1| 34 EDLYEVLTTSSTC------IKFGIAFNE--ASGKRLIRYDGNDEELTQMAVDA 78
                                      5555555332221......222233333..47888888888888888776665 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 4.2e-05
                           DUF2122   3 AAqsGipevlklalklgksllvlpdlkDalellkpekvlllskeegeelleeeeleekgrvllvfsg 69 
                                       A  +G   v+ + +++g ++ vl+ +k + e+l   ++++++++  + ++ e +  + ++vl v++g
  gi|385806403|ref|YP_005842801.1|  79 AKSIGAGHVFVIYIRNGWPINVLNAIKHVQEVL---NIYVATSNPVQVIIGETD--QGRSVLGVVDG 140
                                       5567999**************************...999999985555554443..35556656655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.49
# Mc/sec: 1034.38
//
Query:       gi|385806404|ref|YP_005842802.1|  [L=186]
Description: hypothetical protein FFONT_1362 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.34s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 1047.54
//
Query:       gi|385806405|ref|YP_005842803.1|  [L=239]
Description: hypothetical protein FFONT_1363 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.015   15.0   0.0      0.072   12.9   0.0    1.9  2  Prok-JAB  Prokaryotic homologs of the JAB domain
      0.041   13.8   0.0      0.081   12.9   0.0    1.5  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 ?   -0.5   0.0      0.11     1e+03       8      40 ..       6      38 ..       3      62 .. 0.76
   2 ?   12.9   0.0   8.1e-06     0.072      73      95 ..     143     165 ..     122     188 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.11
                          Prok-JAB  8 lvaharrahpeEtcGlllgkeseseevivvplv 40
                                       ++  r +  +E c l+l +e+ +ee+ v p +
  gi|385806405|ref|YP_005842803.1|  6 VIRNSRTEGLAEKCMLILASEDVAEETGVQPHL 38
                                      566667777789999999999888888777755 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 8.1e-06
                          Prok-JAB  73 iwHSHpggsarPSetDrrdaaal 95 
                                         H+Hp+g   PS+ D+++a+  
  gi|385806405|ref|YP_005842803.1| 143 FLHTHPNGVCLPSKRDIQSASSF 165
                                       57*****************9874 PP

>> RadC  RadC-like JAB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   9.1e-06     0.081      67      88 ..     141     162 ..     131     173 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.1e-06
                                       EEEEEE-TTS--S--HHHHHHH CS
                              RadC  67 vilaHnhPsgdlepSeeDielt 88 
                                        +++H hP+g + pS++Di+  
  gi|385806405|ref|YP_005842803.1| 141 CLFLHTHPNGVCLPSKRDIQSA 162
                                       5789***************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.34s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 1364.22
//
Query:       gi|385806406|ref|YP_005842804.1|  [L=559]
Description: cobalamin B12-binding domain-containing protein [Fervidicoccus fontis Kam940]
Scores for complete 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   43.2   0.0    8.1e-11   42.0   0.0    1.6  1  B12-binding  B12 binding domain
    1.3e-05   25.6   0.0    2.9e-05   24.5   0.0    1.6  1  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
       0.06   13.4   0.1       0.14   12.2   0.1    1.6  1  DUF2680      Protein of unknown function (DUF2680)


Domain annotation for each model (and alignments):
>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   0.0   1.4e-14   8.1e-11       8     114 ..      35     146 ..      29     151 .. 0.94

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 1.4e-14
                       B12-binding   8 vggdlhplGlavlaaalrdagfeVqllganven.....edivaairaekpdvvglSalltsqleavkelvellkrir 79 
                                         +d++p+G+ ++a +l ++g++V + +a + +       + + i++ +  + g+ +++  +  ++ e ++ +k+ +
  gi|385806406|ref|YP_005842804.1|  35 PVFDMYPYGFLSIATYLIKRGYSVGIHNAAALMilnesYSFSDYIKSSDSLLYGIDLHWLVHAHGAIESARIIKELN 111
                                       5689***************************99***9999************************************* PP

                       B12-binding  80 prvkvvvGGahpsldpeetleaklgiddvvvgege 114
                                       p++k+v+GG  +++ ++e++e+ + id+v++g+  
  gi|385806406|ref|YP_005842804.1| 112 PNAKIVLGGFSATIFHREIMEKYPWIDYVILGDTS 146
                                       ********************977********9865 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   4.9e-09   2.9e-05       2     159 ..     228     388 ..     227     392 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 4.9e-09
                                       EEESEESS--TTTSCCTT....HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC CS
                                       xxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpet....vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla 74 
                                       + ++gC++ C+ C  +         +g    +s+  +++ev  + +++ +  v++ g+  ++  +f+e l r+    
  gi|385806406|ref|YP_005842804.1| 228 ISFKGCRYSCVTCGGSNYtfkkYLGRGELGKKSLKTVMNEVATMQEYM-KIPVFFIGDMSFMGMNFTENLVRELNDS 303
                                       6789************999*99888999999*************7666.77777777779999*********99995 PP

                                       CCTEEEEEEECSSCHG.HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET.EEEE CS
                                       xxxxxxxxxxxxxxxx.xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                       Radical_SAM  75 vpgiritvetngtlpd.eeklerllelg.vdrvslgleaaddekvlklmnrghtfeevlealeklreagikr.vvdr 148
                                         +i   v    ++p   e l+ l++l    +++++ e+ ++  v+ +++r+++++++ + ++   +  + r   ++
  gi|385806406|ref|YP_005842804.1| 304 --KIDSGVFFEFFRPPsIELLKILDNLKtDVYLQISPETHNEH-VRARFGRPYSNKQLEDFIRSTVSMHFSRlDLYF 377
                                       ..44444444444444478999999999899************.***********99999999999999999989** PP

                                       EEEBTTTSHHH CS
                                       xxxxxxxxxxx RF
                       Radical_SAM 149 ivglpGendee 159
                                       ++glp +++e+
  gi|385806406|ref|YP_005842804.1| 378 MIGLPEQTFED 388
                                       ********997 PP

>> DUF2680  Protein of unknown function (DUF2680)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   2.4e-05      0.14      17      50 ..     479     512 ..     472     516 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.4e-05
                           DUF2680  17 aelrKqivdKyVeaGllTkeqgekikkniDkrlk 50 
                                        +  K+++   +++Gl+ +e   ki+++iD +++
  gi|385806406|ref|YP_005842804.1| 479 YQNAKEMIRLKASFGLIGEEASRKIIERIDSAYS 512
                                       5667**************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (559 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); 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:                         3  (0.000167327); expected 0.2 (1e-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: 3273.67
//
Query:       gi|385806407|ref|YP_005842805.1|  [L=407]
Description: cell division control protein 6 [Fervidicoccus fontis Kam940]
Scores for complete 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   54.1   0.0    5.7e-14   51.8   0.0    2.1  2  Cdc6_C           CDC6, C terminal winged helix domain
      2e-09   37.8   0.0    7.1e-09   36.1   0.0    1.9  1  AAA_22           AAA domain
    5.2e-05   23.7   0.0    0.00023   21.6   0.0    2.0  2  AAA              ATPase family associated with various cellul
    0.00016   22.1   0.1     0.0029   18.0   0.0    2.6  2  AAA_16           AAA ATPase domain
     0.0098   15.3   0.0      0.016   14.6   0.0    1.2  1  TniB             Bacterial TniB protein
  ------ inclusion threshold ------
      0.021   14.8   0.0        2.2    8.3   0.0    2.5  2  AAA_5            AAA domain (dynein-related subfamily)
      0.025   14.5   0.3       0.05   13.5   0.3    1.6  1  ATPase_2         ATPase domain predominantly from Archaea
      0.056   12.6   0.0       0.11   11.6   0.0    1.4  1  DUF815           Protein of unknown function (DUF815)
      0.069   13.1   0.0       0.93    9.5   0.0    2.1  2  ResIII           Type III restriction enzyme, res subunit
        0.1   12.6   0.0       0.25   11.4   0.0    1.7  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.12   12.1   0.0       0.43   10.3   0.0    1.8  2  Sigma54_activat  Sigma-54 interaction domain
       0.12   12.4   0.1       0.68   10.0   0.0    2.2  2  DUF61            Protein of unknown function DUF61
       0.14   11.7   0.0       0.28   10.7   0.0    1.4  1  AAA_7            P-loop containing dynein motor region


Domain annotation for each model (and alignments):
>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0         2   2.7e+03      34      48 ..     213     227 ..     209     232 .. 0.83
   2 !   51.8   0.0   4.2e-17   5.7e-14       3      82 ..     318     396 ..     317     398 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2
                                       -----HHHHHHHHHH CS
                            Cdc6_C  34 vdpltqrevsdllse 48 
                                       ++p t +e +d+l+e
  gi|385806407|ref|YP_005842805.1| 213 FSPYTYSELYDILKE 227
                                       5799999****9998 PP

  == domain 2  score: 51.8 bits;  conditional E-value: 4.2e-17
                                       HHHHHHCHCSSS-EEHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSSCH CS
                            Cdc6_C   3 alvlllrksgkeevttgevyevYkslCesegvdpltqrevsdllseLemlgileleksskGrregrtrkisLnvdpd 79 
                                       ++++ l+ sg+  v++g+v++ Y+ lCe ++++p+ +++v+ ++ eL ++g++++++s+kG r g++++i ++  p 
  gi|385806407|ref|YP_005842805.1| 318 SVIKALKGSGSGFVRIGDVEKIYRVLCEAYNLQPRRHTQVYTHILELRSMGFIQTKSSGKGFR-GKSTLIGISAAPL 393
                                       78999999******************************************************7.9999999988777 PP

                                       HHH CS
                            Cdc6_C  80 dvl 82 
                                        vl
  gi|385806407|ref|YP_005842805.1| 394 YVL 396
                                       665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.0   5.1e-12   7.1e-09       9     128 ..      62     188 ..      57     193 .. 0.87

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 5.1e-12
                            AAA_22   9 vvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseellealeqa 85 
                                       +++G  GtGKT++ + +  ++   a+ +  r ++v+v++ +s ++ ++  ++  +lg  l  ++ls +el++ l + 
  gi|385806407|ref|YP_005842805.1|  62 MLVGSFGTGKTVTSKLFGASASSLASRNGIRLKYVHVNCYKSRTLPQIIYNISLDLGITLPQRGLSAQELMRGLIEE 138
                                       799******************9888888899********************************************** PP

                            AAA_22  86 lraravielliiDEaqhlr...s.eealeeLrsllnl...srkgvqliLv 128
                                       l++r + +++ +DE++++    s  + +  L++ ++    ++k +++i++
  gi|385806407|ref|YP_005842805.1| 139 LERRNTYAIVALDEFDYFAlmsSgLNSIYVLVRAYDEyvnKKKRLHFIFI 188
                                       ******9**********966432455555555544448889999999987 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   1.6e-07   0.00023       1     117 [.      61     197 ..      61     210 .. 0.81
   2 ?   -1.2   0.0       1.8   2.5e+03      56      99 ..     231     277 ..     202     294 .. 0.67

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.6e-07
                                       EEEESSTTSSHHHHHHHHHHHH.........THEEEEEETTTCSSS..................STTHHHHHHHHHH CS
                               AAA   1 vllyGppGtGKTllakavakel.........gvefleisgsellsk..................yvgesekkirelf 50 
                                       v+l+G  GtGKT + k    ++           +++ +++ + +                        +++ +r+l+
  gi|385806407|ref|YP_005842805.1|  61 VMLVGSFGTGKTVTSKLFGASAsslasrngiRLKYVHVNCYKSR-TlpqiiynisldlgitlpqRGLSAQELMRGLI 136
                                       689***************99974444433223667777777777.346788888999998888555566778899** PP

                                       HHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTH CS
                               AAA  51 keakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldp 117
                                       +e+++ ++  i+ +DE+d +a  +      ++ + + +L+++ d++ +k++++ +i ++ ++++l++
  gi|385806407|ref|YP_005842805.1| 137 EELERRNTYAIVALDEFDYFALMS------SGLNSIYVLVRAYDEYVNKKKRLHFIFISRSISTLEN 197
                                       **9999956***********9999......7788899************999*****9999777654 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.8
                                       TS.TSEEEEEETGGGHHHHH..TTCCCHHHHHHHHHHHHHHHHTTTS CS
                               AAA  56 ka.kpsilfiDEidalaksr..sgseseeeervvnqLlteldgvkkk 99 
                                       +a  p ++  DE+  +   +  +++ s++++++++ L+++ +  +++
  gi|385806407|ref|YP_005842805.1| 231 EAlYPGVISDDELKYISMIEgyDKGGSGSARTALEILVRAGESADSE 277
                                       23567888888888887777776677777777777777766655554 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.1e-06    0.0029       2      49 ..      33      83 ..      32     188 .. 0.72
   2 ?   -2.1   0.0       3.2   4.4e+03     142     144 ..     285     287 ..     223     343 .. 0.64

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.1e-06
                            AAA_16  2 lvGReeeleqLlsalervrsgrp...elvllsGesGvGKsslvrellrale 49
                                      l+ Re++l+qL++++++  s+ +   + v+l+G  G+GK+   + +  +++
  gi|385806407|ref|YP_005842805.1| 33 LPHREKQLKQLAQLFKSFFSSPGeemQRVMLVGSFGTGKTVTSKLFGASAS 83
                                      789*************5544433469**************99877765443 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.2
                            AAA_16 142 Ddl 144
                                       Dd+
  gi|385806407|ref|YP_005842805.1| 285 DDI 287
                                       332 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.2e-05     0.016      18     129 ..      38     154 ..      31     162 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.2e-05
                              TniB  18 eilerLeeLley...pkrkrmpnlllvGdsnnGKtmivekFarlhppekdedaekvpvlvvqappkpdekrlyaaiL 91 
                                       + l++L++L++     + ++m+ ++lvG   +GKt+  + F ++ ++  + +  +++ ++v++ ++ +  ++  +i 
  gi|385806407|ref|YP_005842805.1|  38 KQLKQLAQLFKSffsSPGEEMQRVMLVGSFGTGKTVTSKLFGASASSLASRNGIRLKYVHVNCYKSRTLPQIIYNIS 114
                                       445555555554332456789************************99999999999999999999999999999999 PP

                              TniB  92 ealgaplkara.rvskleqqvlrllrelkv.rvLiiDEih 129
                                         lg  l +r  ++++l +  ++ l++ ++  ++ +DE++
  gi|385806407|ref|YP_005842805.1| 115 LDLGITLPQRGlSAQELMRGLIEELERRNTyAIVALDEFD 154
                                       9999998777646667777777777666551555688887 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 ?    8.3   0.0    0.0016       2.2       2     118 ..      61     187 ..      60     210 .. 0.75
   2 ?    4.3   0.0     0.026        36      40      90 ..     242     303 ..     215     324 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0016
                                       EEEE--SSSSHHHHHHHGGGGB.........S--EEEEE--TT--HHHHH--B--.............--------. CS
                             AAA_5   2 vlLvGppGtgKselaerlaaal.........nreveyvqltrdtteedlkgrreik....ngttslvdsplvraar. 64 
                                       v+LvG  GtgK+  ++ + a           + +++ v+++++ t  ++++ ++++      ++ l+ ++l+r    
  gi|385806407|ref|YP_005842805.1|  61 VMLVGSFGTGKTVTSKLFGASAsslasrngiRLKYVHVNCYKSRTLPQIIYNISLDlgitLPQRGLSAQELMRGLIe 137
                                       89**********99988865555667888888899999999999999999999998766655566677777776668 PP

                                       ......G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEE CS
                             AAA_5  65 ......egeilvlDEveraesevlnsLlslleerrllleeggelvkaknddllerfrvia 118
                                             + +i+ lDE++      ++ + s l+  ++l+   +e+v++k+      +++i+
  gi|385806407|ref|YP_005842805.1| 138 elerrnTYAIVALDEFD-----YFALMSSGLNSIYVLVRAYDEYVNKKKR-----LHFIF 187
                                       88888888888888888.....6777777777777777777777766664.....45555 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.026
                                       HHH--B--...............--------.....G-SEEEEESGGG--HHHHHHHHHHHH CS
                             AAA_5  40 dlkgrreik......ngttslvdsplvraar.....egeilvlDEveraesevlnsLlslle 90 
                                       +lk+   i+      +g ++    +lvra++     + + + lD++ +a+  v ++L +l +
  gi|385806407|ref|YP_005842805.1| 242 ELKYISMIEgydkggSGSARTALEILVRAGEsadseKRSSITLDDIRKAHVIVKPELAMLQD 303
                                       55555555555555677788888999***9999998888999********999999988755 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.3   3.6e-05      0.05     101     209 ..     127     234 ..      35     251 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.6e-05
                          ATPase_2 101 lvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLlnlie.sltkekhlcvviclsSeglfiervyn 176
                                        +++ +  l+e+++++ +  i+ +De+ +   +   +  + ++ L+++++ +  k+k+l +++++ S + + + ++ 
  gi|385806407|ref|YP_005842805.1| 127 SAQELMRGLIEELERRNTYAIVALDEFDYFALM--SSGLNSIYVLVRAYDeYVNKKKRLHFIFISRSISTLEN-IDP 200
                                       5677888999*****************998833..33345566666666515556777777888889988877.999 PP

                          ATPase_2 177 eselegrhkyilvddldketalnflkegfkel.e 209
                                       +s  +  ++ ++  + ++ +  ++lke + e  +
  gi|385806407|ref|YP_005842805.1| 201 SSSTYFLKNIVEFSPYTYSELYDILKERADEAlY 234
                                       9999988888888888888888888888877654 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   7.9e-05      0.11      30     102 ..      33     113 ..      23     118 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.9e-05
                            DUF815  30 Lvgidkqkealventeqfle..glpannvLLwGarGtGKSslvk...allneyaeeg...Lrlievekedlkelpkl 98 
                                       L   +kq ++l +  + f +  g++ + v+L+G+ GtGK  + k   a  +++a+++   L+ + v+  + ++lp++
  gi|385806407|ref|YP_005842805.1|  33 LPHREKQLKQLAQLFKSFFSspGEEMQRVMLVGSFGTGKTVTSKlfgASASSLASRNgirLKYVHVNCYKSRTLPQI 109
                                       56668888999999998875458999*************66555221666666666588889999999999999999 PP

                            DUF815  99 vell 102
                                       + ++
  gi|385806407|ref|YP_005842805.1| 110 IYNI 113
                                       8776 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00067      0.93       5      42 ..      36      76 ..      32      91 .. 0.75
   2 ?    1.3   0.0      0.22     3e+02      39      96 ..     167     232 ..     142     313 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00067
                                      -HHHHHHHHHHT.........TTSEEEEEESTTSTHHHHHH CS
                            ResIII  5 reyQeeaienlleklks...krdkrglikmaTGtGKTlvaa 42
                                      re Q + + +l +++ s   ++ +r++++   GtGKT+++ 
  gi|385806407|ref|YP_005842805.1| 36 REKQLKQLAQLFKSFFSspgEEMQRVMLVGSFGTGKTVTSK 76
                                      555555555655555559888889**************984 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.22
                                       HHHHHHHHHH-S.....-EEEEESSHHHHHHHH........HHGGGGTGG....GEEEESSS-B-- CS
                            ResIII  39 lvaaklierllkkgkeekflflvprkslleqtl........eefkkflseaykeigkkvsgdkkka 96 
                                       +v++++ +++ +k+k+ +f+f+  ++s le           +++ +f++ +y+e   +++++ ++a
  gi|385806407|ref|YP_005842805.1| 167 YVLVRAYDEYVNKKKRLHFIFISRSISTLENIDpssstyflKNIVEFSPYTYSELYDILKERADEA 232
                                       567788889999999889999999998888777666555555555555555555444444444444 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00018      0.25       3      41 ..      36      80 ..      34     107 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00018
                                      SHHHHHHHHHHHHHCH......TEEEEEEESTTSSHHHHHHHHHH CS
                              TsaE  3 seeetealgkklakal......gdvilLeGdLGaGKTtlvrglak 41
                                      +e+++++l++ +++ +       + ++L G  G+GKT+ ++ + +
  gi|385806407|ref|YP_005842805.1| 36 REKQLKQLAQLFKSFFsspgeeMQRVMLVGSFGTGKTVTSKLFGA 80
                                      5677888888887765777644445************99987765 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00031      0.43       5      59 ..      37     101 ..      33     110 .. 0.72
   2 ?   -1.6   0.0       1.3   1.8e+03      95     121 ..     203     229 ..     199     233 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00031
                                       SHHHHHHHHHHHHHCTSS....S-EEEECSTTSSHHHHHHHHHH......HSTTTTS-EEEEETT CS
                   Sigma54_activat   5 sealkelleqikkvaktd....lsvlitGesGtGKellaraihe......askrkekpfvavnca 59 
                                       +++lk+l +  k++ +++     +v+++G  GtGK++ +++  +      +++  + ++v+vnc 
  gi|385806407|ref|YP_005842805.1|  37 EKQLKQLAQLFKSFFSSPgeemQRVMLVGSFGTGKTVTSKLFGAsasslaSRNGIRLKYVHVNCY 101
                                       677888888888888777777789************99998865443321112223478888885 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.3
                                       SEEEEETGGGS-HHHHHHHHHHHHHSE CS
                   Sigma54_activat  95 GtlfLDeigelplelQekLlrvlqege 121
                                       +t fL +i e+++ + ++L  +l+e+ 
  gi|385806407|ref|YP_005842805.1| 203 STYFLKNIVEFSPYTYSELYDILKERA 229
                                       688*******************99985 PP

>> DUF61  Protein of unknown function DUF61
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0         2   2.7e+03      13      26 ..      31      44 ..      28      51 .. 0.84
   2 ?   10.0   0.0   0.00049      0.68      30     114 ..     279     366 ..     272     368 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2
                                      GGSBSS-EEHHHHH CS
                             DUF61 13 khlPaerktLkelL 26
                                      ++lP ++k+Lk+l 
  gi|385806407|ref|YP_005842805.1| 31 SSLPHREKQLKQLA 44
                                      68999999999986 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00049
                                       -EEEB.TT.S-EEE--HHHHHHHHTTS-GGGGGT-EESEEEEE-SSS.SE..EEEES-HH.HHHHHHHHT--...-S CS
                             DUF61  30 kptivtkd.gsehrfdkeeleklkeilpeelwdklkLPIllemdpel.gesvylvrgkae.vkvvskilgkereeed 103
                                       +++i + d  + h++ k el +l++ ++   ++ l L + + +  +  g++++++ + +   +v++++ +++ ++ +
  gi|385806407|ref|YP_005842805.1| 279 RSSITLDDiRKAHVIVKPELAMLQDQVSALDRHELVLYLSVIKALKGsGSGFVRIGDVEKiYRVLCEAYNLQPRRHT 355
                                       334433332367********************99999997666665538888888888889***********88888 PP

                                       SEEEHH.HHHH CS
                             DUF61 104 elviykpevre 114
                                       +++ +  e+r+
  gi|385806407|ref|YP_005842805.1| 356 QVYTHILELRS 366
                                       88888777776 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    0.0002      0.28      31      52 ..      56      77 ..      46      96 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0002
                             AAA_7 31 knkkpvllvGptGtGKtviikd 52
                                      ++ + v+lvG+ GtGKtv+ k 
  gi|385806407|ref|YP_005842805.1| 56 EEMQRVMLVGSFGTGKTVTSKL 77
                                      56789*************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      572  (0.0319036); 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: 0.68u 0.33s 00:00:01.01 Elapsed: 00:00:00.53
# Mc/sec: 2313.85
//
Query:       gi|385806408|ref|YP_005842806.1|  [L=85]
Description: hypothetical protein FFONT_1366 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-07   30.3   0.2    5.8e-07   29.3   0.2    1.5  1  HTH_5           Bacterial regulatory protein, arsR family
    1.1e-05   24.8   0.2    1.6e-05   24.3   0.2    1.3  1  HTH_24          Winged helix-turn-helix DNA-binding
      0.001   18.9   0.2     0.0012   18.7   0.2    1.2  1  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0025   17.7   0.0     0.0036   17.1   0.0    1.2  1  MarR_2          MarR family
  ------ inclusion threshold ------
      0.011   15.7   0.1      0.014   15.3   0.1    1.3  1  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.015   15.2   0.1      0.022   14.7   0.1    1.2  1  MarR            MarR family
      0.017   15.1   0.0       0.03   14.3   0.0    1.4  1  HTH_45          Winged helix-turn-helix
      0.026   14.7   0.1      0.042   14.1   0.1    1.3  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.044   14.1   0.0      0.062   13.7   0.0    1.3  1  Rrf2            Transcriptional regulator
      0.071   12.9   0.0        0.1   12.4   0.0    1.3  1  HTH_IclR        IclR helix-turn-helix domain
      0.087   13.3   0.2       0.12   12.9   0.2    1.2  1  HTH_27          Winged helix DNA-binding domain
      0.094   12.8   0.0       0.13   12.4   0.0    1.2  1  HTH_20          Helix-turn-helix domain
       0.11   11.4   0.0       0.12   11.3   0.0    1.1  1  Tfb2            Transcription factor Tfb2


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 !   29.3   0.2   4.2e-10   5.8e-07       4      46 ..      10      53 ..       8      54 .. 0.96

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 4.2e-10
                                      HHHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  4 RlkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      ++kILk   + ge  ++ +++e+gl+   vS HL  L+++G+V+
  gi|385806408|ref|YP_005842806.1| 10 KVKILKVIYKlGEVNITRISRETGLNHKSVSIHLEELKKMGIVY 53
                                      89*****************************************6 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.2   1.2e-08   1.6e-05       7      47 ..      12      52 ..      10      53 .. 0.97

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1.2e-08
                            HTH_24  7 kILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      kIL++++k +  +++ +++++gl    v+ +l++L+++G++
  gi|385806408|ref|YP_005842806.1| 12 KILKVIYKLGEVNITRISRETGLNHKSVSIHLEELKKMGIV 52
                                      9***************************************8 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.2   8.5e-07    0.0012      12      56 ..      12      56 ..      10      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 8.5e-07
                                      CHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB 12 kvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                                      k+ +++ klg+ +++ i++e+g+ + +v   L++L+++G+V+ ++
  gi|385806408|ref|YP_005842806.1| 12 KILKVIYKLGEVNITRISRETGLNHKSVSIHLEELKKMGIVYERR 56
                                      66777789*********************************9887 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   2.6e-06    0.0036      10      55 ..      13      56 ..       7      59 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.6e-06
                                      HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                      +L +++  ++  ++++ + r++gl + +vs +l++L + G v +r+
  gi|385806408|ref|YP_005842806.1| 13 ILKVIYKLGE--VNITRISRETGLNHKSVSIHLEELKKMGIVYERR 56
                                      6777888888..99****************************8774 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.1     1e-05     0.014      26      66 ..      27      69 ..      12      70 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1e-05
                                      HHHHHTTSSHHHHHHHHHHHHHTTSEE.ET.EEEEES-HHHHH CS
                         HTH_Crp_2 26 elAsmlGltretvsrilseLkreglis.rg.rririldleaLr 66
                                       +++  Gl+  +vs  l eLk+ g++  r+ +r+r l+l++L+
  gi|385806408|ref|YP_005842806.1| 27 RISRETGLNHKSVSIHLEELKKMGIVYeRRfGRVRMLSLNYLN 69
                                      578889*********************765545****999985 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   1.6e-05     0.022       5      48 ..      10      53 ..       7      56 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.6e-05
                                      HHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR  5 qfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlie 48
                                       ++iL  +y  g+ +++ + +  g++  +v+  l +L k G ++
  gi|385806408|ref|YP_005842806.1| 10 KVKILKVIYKLGEVNITRISRETGLNHKSVSIHLEELKKMGIVY 53
                                      679**************************************997 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   2.2e-05      0.03      10      51 ..      12      54 ..      10      61 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.2e-05
                            HTH_45 10 dILeais.egeakkTkimykanLsykllnkYLdmLvekglikk 51
                                       IL++i   ge + T+i  +  L+ k ++  L+ L + g++ +
  gi|385806408|ref|YP_005842806.1| 12 KILKVIYkLGEVNITRISRETGLNHKSVSIHLEELKKMGIVYE 54
                                      79999975899****************************9954 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1     3e-05     0.042      10      52 ..      14      52 ..      11      58 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3e-05
                                      HHHHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                    Fe_dep_repress 10 LetIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyv 52
                                      L++IY+l      v  ++++++ +    sVs  l++L+k+G v
  gi|385806408|ref|YP_005842806.1| 14 LKVIYKLG----EVNITRISRETGLNHKSVSIHLEELKKMGIV 52
                                      89999988....5899*************************87 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.5e-05     0.062      24      59 ..      21      56 ..       8      59 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.5e-05
                                      C-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                              Rrf2 24 epvsseeiaerqnispsylekilakLrkaglvksvr 59
                                      + v+++ i+++++++++ ++  l++L+k g+v  +r
  gi|385806408|ref|YP_005842806.1| 21 GEVNITRISRETGLNHKSVSIHLEELKKMGIVYERR 56
                                      3499****************************8776 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   7.5e-05       0.1       8      49 ..      13      53 ..      11      56 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.5e-05
                                      HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR  8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      iL+ + + ++ ++++ ++r+tgl+  +v+ +L  L ++G+v 
  gi|385806408|ref|YP_005842806.1| 13 ILKVIYKLGE-VNITRISRETGLNHKSVSIHLEELKKMGIVY 53
                                      5556666666.79**************************997 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   8.5e-05      0.12       8      62 ..      13      60 ..      10      62 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.5e-05
                            HTH_27  8 vLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrv 62
                                      +L +i+  ++++ ++++++ + ++  ++s  l++L ++G v       +rr  rv
  gi|385806408|ref|YP_005842806.1| 13 ILKVIY-KLGEVNITRISRETGLNHKSVSIHLEELKKMGIV------YERRFGRV 60
                                      899999.9********************************9......55666665 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   9.2e-05      0.13      23      61 .]      21      59 ..      11      59 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.2e-05
                                      TTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                            HTH_20 23 egltaselaerldlskntlsyHLrvLeeagLvevvregr 61
                                      +++  + + ++ +l  +++s HL++L + g+v  +r gr
  gi|385806408|ref|YP_005842806.1| 21 GEVNITRISRETGLNHKSVSIHLEELKKMGIVYERRFGR 59
                                      5566677889999*******************9999987 PP

>> Tfb2  Transcription factor Tfb2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0     9e-05      0.12     210     256 ..       9      56 ..       2      68 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9e-05
                              Tfb2 210 dlvevlsflfqLsslelgkaYsvealset.qkemledLrdlGLvyqrk 256
                                        +v++l+++++L+++++++    + l+++  +  le+L+++G+vy+r+
  gi|385806408|ref|YP_005842806.1|   9 GKVKILKVIYKLGEVNITRISRETGLNHKsVSIHLEELKKMGIVYERR 56 
                                       5799***************999999766505677***********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); 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):              13  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 518.86
//
Query:       gi|385806409|ref|YP_005842807.1|  [L=281]
Description: putative ATPase [Fervidicoccus fontis Kam940]
Scores for 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  192.0   1.0    1.1e-56  191.8   1.0    1.0  1  ATPase        KaiC
    3.9e-07   29.1   0.0    5.9e-07   28.5   0.0    1.2  1  GvpD          GvpD gas vesicle protein
    7.8e-07   28.6   0.1    1.3e-06   27.9   0.1    1.5  1  Rad51         Rad51
    1.2e-06   28.3   0.0    2.3e-06   27.3   0.0    1.5  1  AAA_25        AAA domain
    2.1e-05   24.4   0.0    3.6e-05   23.6   0.0    1.4  1  IstB_IS21     IstB-like ATP binding protein
    2.4e-05   23.8   0.0    5.8e-05   22.6   0.0    1.6  1  DnaB_C        DnaB-like helicase C terminal domain
    0.00012   21.6   0.1    0.00018   21.1   0.1    1.3  1  RecA          recA bacterial DNA recombination protein
     0.0013   18.7   0.1     0.0022   18.0   0.1    1.4  1  ResIII        Type III restriction enzyme, res subunit
     0.0022   17.8   0.1     0.0048   16.7   0.1    1.5  1  AAA_24        AAA domain
     0.0077   16.7   0.0      0.017   15.6   0.0    1.7  1  ABC_tran      ABC transporter
  ------ inclusion threshold ------
      0.011   15.7   0.1       0.02   14.9   0.1    1.3  1  AAA_14        AAA domain
      0.015   15.1   0.0      0.024   14.5   0.0    1.3  1  MEDS          MEDS: MEthanogen/methylotroph, DcmR Sensory dom
      0.026   14.8   0.0      0.045   14.0   0.0    1.4  1  AAA_22        AAA domain
      0.048   14.1   0.0      0.088   13.2   0.0    1.4  1  RNA_helicase  RNA helicase
      0.069   13.6   0.1       0.14   12.6   0.1    1.6  1  DUF4174       Domain of unknown function (DUF4174)
      0.069   12.4   0.0      0.088   12.0   0.0    1.3  1  DUF2075       Uncharacterized conserved protein (DUF2075)
      0.098   12.1   0.1       0.16   11.4   0.1    1.3  1  DUF1571       Protein of unknown function (DUF1571)
       0.12   11.4   0.0       0.17   10.9   0.0    1.2  1  T2SSE         Type II/IV secretion system protein


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.8   1.0   1.1e-59   1.1e-56       2     229 ..      14     241 ..      13     243 .. 0.97

  Alignments for each domain:
  == domain 1  score: 191.8 bits;  conditional E-value: 1.1e-59
                            ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekle 78 
                                       ktg++g+De+++gGip+g  + i+GepGtGKtif+ +F+++g+++  +++++vt+ee++e++ ++a+++G++++k  
  gi|385806409|ref|YP_005842807.1|  14 KTGVKGFDELIEGGIPRGFFISIVGEPGTGKTIFSIHFAWEGIKE-SDRVIYVTTEESKESIVQQASQFGMNFRKGL 89 
                                       9********************************************.9****************************** PP

                            ATPase  79 eegklaiidasesaeesaeekdkedleelieelaeaikeika..krvviDsitglayeekeavaReilrqlvrvlkk 153
                                       +e k++iida ++++e++   +  ++eel++++ ea k+++   +r+viDs +++  ++k+a+aR+    ++rvl k
  gi|385806409|ref|YP_005842807.1|  90 NEKKMIIIDALMKSKEEEWTLNDLNIEELVSKVIEAKKALGYgrTRLVIDSMSAF-WIDKPAMARKMSYYIKRVLYK 165
                                       *************99988889999************99988777***********.********************* PP

                            ATPase 154 lgvTailvsekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIte.egikvlee 229
                                       ++vTa l+s+  ++ + a g+g+e+ i+dg+i+ ++ + ++ l+R++ + kmR+t+h+   h+  I++  g ++ + 
  gi|385806409|ref|YP_005842807.1| 166 WDVTAYLISQYAVTTDLAYGFGLEH-IADGIIRFKKILSRGVLKRYVLVEKMRQTNHDLTSHEVYIKPgIGMEIGPG 241
                                       *************************.******************************************889999875 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0     6e-10   5.9e-07      13     193 ..      34     218 ..      23     223 .. 0.69

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 6e-10
                              GvpD  13 llikGaPGtGktlftlrg.ldvlrresdvlyvstrvddetvseay....fsgeaeldktalldllkdpleldldvdv 84 
                                       + i G+PGtGkt+f +++  + +++ + v+yv+t   +e++ +      ++ +  l++ ++  ++ d+l    + + 
  gi|385806409|ref|YP_005842807.1|  34 ISIVGEPGTGKTIFSIHFaWEGIKESDRVIYVTTEESKESIVQQAsqfgMNFRKGLNEKKM--IIIDALMKSKEEEW 108
                                       5688*************94589************988887766553544444444554444..57799999999999 PP

                              GvpD  85 Piekldlesllefvdeiaaiatkliialdswelvyeylaery.dsPediktvkndl..vvlaresgvrlvl....vl 154
                                        ++ l++e l++ v        k  + +   +lv++ +++ + d+P   + +   +  v    +  + l++     +
  gi|385806409|ref|YP_005842807.1| 109 TLNDLNIEELVSKVI-----EAKKALGYGRTRLVIDSMSAFWiDKPAMARKMSYYIkrVLYKWDVTAYLISqyavTT 180
                                       9******99988665.....456667777777777777554425565544444443112233344444444111134 PP

                              GvpD 155 etaansrleyivdGvvtlnvkeddrgrlrrdlrleklrG 193
                                       + a    le+i+dG++ ++     rg l+r + +ek+r 
  gi|385806409|ref|YP_005842807.1| 181 DLAYGFGLEHIADGIIRFKKILS-RGVLKRYVLVEKMRQ 218
                                       4555667999*******964444.8************95 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.1   1.3e-09   1.3e-06      12     104 ..       6      90 ..       1     145 [. 0.80

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1.3e-09
                                       HHHSS-EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEESSS---GGGG CS
                             Rad51  12 krsellqlttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyidtegtfrperl 88 
                                       ++  + +l tG k +Del++GGi+ g    i+Ge ++Gkt ++  ++             ++++y+ te +   e +
  gi|385806409|ref|YP_005842807.1|   6 QQAAVERLKTGVKGFDELIEGGIPRGFFISIVGEPGTGKTIFSIHFAWE------GIKESDRVIYVTTEES--KESI 74 
                                       6788899**********************************99887653......3334678899999886..4568 PP

                                       HHHHHHTT--HHHHGG CS
                             Rad51  89 veiaerykldkeevle 104
                                       v+ a +++++ ++ l+
  gi|385806409|ref|YP_005842807.1|  75 VQQASQFGMNFRKGLN 90 
                                       8888888887665554 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   2.3e-09   2.3e-06      23     169 ..      21     163 ..       6     172 .. 0.71

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 2.3e-09
                            AAA_25  23 rwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal.. 97 
                                       + l++g +p+g ++ ++G pgtGKt + ++ a +  +          e  +V+yv +E+s + + + +++ g ++  
  gi|385806409|ref|YP_005842807.1|  21 DELIEGGIPRGFFISIVGEPGTGKTIFSIHFAWEGIK----------ESDRVIYVTTEESKESIVQQASQFGMNFrk 87 
                                       679****************************998885..........5669******************99988866 PP

                            AAA_25  98 ..rddarllvldlagv.eslpLfakdrggtlltadvdaleaaieeveg..vrlvviDplsralggdensnsdv.... 165
                                         ++++   +  l+++ e+   +    ++  +++ v ++++a ++  g     +viD++s+++   +  ++++    
  gi|385806409|ref|YP_005842807.1|  88 glNEKKMIIIDALMKSkEE-EWT---LNDLNIEELVSKVIEAKKAL-GygRTRLVIDSMSAFWIDKPAMARKMsyyi 159
                                       5555555555544444222.111...12233667777777666665.234677899999999988888777752223 PP

                            AAA_25 166 galv 169
                                       ++++
  gi|385806409|ref|YP_005842807.1| 160 KRVL 163
                                       5555 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   3.6e-08   3.6e-05      50     121 ..      34     104 ..      28     147 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 3.6e-08
                         IstB_IS21  50 ivllGpsGvGKshlaialgveavraglsvlfvrvedLveelkrarrdgklaralkr.llkvdllilDdlgllp 121
                                       i ++G +G+GK+ ++i ++ e++++  +v++v++e+  e++ ++ +  ++  + ++ l + +++i+D l   +
  gi|385806409|ref|YP_005842807.1|  34 ISIVGEPGTGKTIFSIHFAWEGIKESDRVIYVTTEESKESIVQQAS--QFGMNFRKgLNEKKMIIIDALMKSK 104
                                       679********************************99888765444..4444444415666899999775544 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 !   22.6   0.0   5.8e-08   5.8e-05       2      67 ..      13      78 ..      12     142 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 5.8e-08
                                      BXSSTHHHHHHCT.SBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHHH CS
                                      xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  2 lstgfkdLDklts.GlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqRl 67
                                      l+tg k +D+l++ G+ +g +i i + p++Gkt + +++a +  + e+ +v+++  e s+e++vq+ 
  gi|385806409|ref|YP_005842807.1| 13 LKTGVKGFDELIEgGIPRGFFISIVGEPGTGKTIFSIHFAWEGIK-ESDRVIYVTTEESKESIVQQA 78
                                      68999****99862688999999*****************88765.5668*************9975 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.1   1.8e-07   0.00018      26     105 ..       5      85 ..       1     106 [. 0.84

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.8e-07
                                       -.-----EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEESS----H..HHHHH CS
                              RecA  26 keklkvetissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafidaehaldp..kyakk 100
                                        ++  ve + +G  ++d  +  GG+p+G  i i G   +Gkt +++h   e  k++  + ++ +e + ++  + a +
  gi|385806409|ref|YP_005842807.1|   5 GQQAAVERLKTGVKGFDELIE-GGIPRGFFISIVGEPGTGKTIFSIHFAWEGIKESDRVIYVTTEESKESivQQASQ 80 
                                       456789***********9886.*****************************************99987752245666 PP

                                       TT--G CS
                              RecA 101 lGvdi 105
                                       +G++ 
  gi|385806409|ref|YP_005842807.1|  81 FGMNF 85 
                                       66665 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   2.3e-06    0.0022       7     111 ..       5     115 ..       2     142 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.3e-06
                                       HHHHHHHHHT...............TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSH...HHHHHHH CS
                            ResIII   7 yQeeaienlleklks.........krdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprk...slleqtl 71 
                                        Q+ a+e+l+  +k           r   + i+ + GtGKT+ +++++++  k+ +  +++ +  ++   s+++q+ 
  gi|385806409|ref|YP_005842807.1|   5 GQQAAVERLKTGVKGfdelieggiPRGFFISIVGEPGTGKTIFSIHFAWEGIKESD--RVIYVTTEEskeSIVQQAS 79 
                                       689999999977776667887777777788899********************866..8999987765557888888 PP

                                       ...HHGGGGTGG....GEEEESSS-B--.......-SEEEEEH CS
                            ResIII  72 ...eefkkflseaykeigkkvsgdkkkakekdstnkkilvtti 111
                                           +f+k l+e+   ++ +++   k++    ++++ +   +i
  gi|385806409|ref|YP_005842807.1|  80 qfgMNFRKGLNEK---KMIIIDALMKSK----EEEWTLNDLNI 115
                                       3434444444444...333333333333....44444444444 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   4.8e-06    0.0048       5      86 ..      34     153 ..      31     161 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.8e-06
                            AAA_24   5 iliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdie........................... 47 
                                       i i+G++g+GKT +  ++        ++++++ te++  s+     +                              
  gi|385806409|ref|YP_005842807.1|  34 ISIVGEPGTGKTIFSIHFawegikeSDRVIYVTTEESKESIVQQASQF-Gmnfrkglnekkmiiidalmkskeeewt 109
                                       569*********************99******9998776665555432.2344455555555444444455555555 PP

                            AAA_24  48 ....swedfldevvel.aaeladyktlviDtideleelclaevi 86 
                                           ++e+++++v e  +a   +   lviD+ + ++  + a+++
  gi|385806409|ref|YP_005842807.1| 110 lndlNIEELVSKVIEAkKALGYGRTRLVIDSMSAFWIDKPAMAR 153
                                       55555555555555546666677788999999988866655555 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.7e-05     0.017       7     116 ..      27     136 ..      23     221 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.7e-05
                                       EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHH.HH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx.xx RF
                          ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvren.es 81 
                                        + +g  + ivGe G+GK+ +   +a +  ++++++ +  ++ +++++ +  +++g+ + +  + ++ + + +   +
  gi|385806409|ref|YP_005842807.1|  27 GIPRGFFISIVGEPGTGKTIFSIHFAWEGIKESDRVIYVTTEESKESIVQQASQFGMNFRKgLNEKKMI-IIDAlMK 102
                                       57788899****************************999777777799999999999999944444444.4444588 PP

                                       HTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  82 deeiekalsklglkelkdtvvksspssLSgGqkqr 116
                                       ++e e  l+ l+++el  +v+ + ++ L +G  + 
  gi|385806409|ref|YP_005842807.1| 103 SKEEEWTLNDLNIEELVSKVI-EAKKALGYGRTRL 136
                                       888888999999999888887.6667787776654 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1     2e-05      0.02       5      87 ..      34     114 ..      31     125 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2e-05
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevpewek 81 
                                       + i+G   +GKT +  +++ e + ++++++y++ ++ +++  ++ +++   +++ l  ++k+++++D   +++e e 
  gi|385806409|ref|YP_005842807.1|  34 ISIVGEPGTGKTIFSIHFAWEGIKESDRVIYVTTEESKESIVQQASQFGMNFRKGL--NEKKMIIIDALMKSKEEEW 108
                                       568888899**********999999***********99987776655555666654..58999****9999988888 PP

                            AAA_14  82 alkslv 87 
                                       +l++l 
  gi|385806409|ref|YP_005842807.1| 109 TLNDLN 114
                                       877765 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 ?   14.5   0.0   2.4e-05     0.024      20     108 ..      51     140 ..      47     180 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.4e-05
                              MEDS  20 fikaglargekvlyvasastldelrealrkagldvdaalesgqleildaeetylrgggfdp...ermlealrralak 93 
                                       f  +g+++ ++v+yv+++++ + + ++ ++ g++  + l+++++ i+da    +++ + ++   +  +e+l +++ +
  gi|385806409|ref|YP_005842807.1|  51 FAWEGIKESDRVIYVTTEESKESIVQQASQFGMNFRKGLNEKKMIIIDAL---MKSKEEEWtlnDLNIEELVSKVIE 124
                                       6679*********************************9999999999965...777777776679999999999999 PP

                              MEDS  94 al.adgyaglrvigem 108
                                       a  a gy + r++++ 
  gi|385806409|ref|YP_005842807.1| 125 AKkALGYGRTRLVIDS 140
                                       99666***99998874 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   4.5e-05     0.045       7      98 ..      33     139 ..      30     163 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.5e-05
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllrellralglelka............ 70 
                                       ++ ++Ge+GtGKT     ++ +        +e+++v++vt  +s+ s  + ++++  ++  +l++            
  gi|385806409|ref|YP_005842807.1|  33 FISIVGEPGTGKTIFSIHFAWEGI------KESDRVIYVTTEESKeSIVQQASQFGMNFRKGLNEkkmiiidalmks 103
                                       689**********98877776542......25999999999999988888888888888888887777888888888 PP

                            AAA_22  71 .......erlsseellealeqalrarav.ielliiD 98 
                                              + l+ eel++++ +a +a +  +  l+iD
  gi|385806409|ref|YP_005842807.1| 104 keeewtlNDLNIEELVSKVIEAKKALGYgRTRLVID 139
                                       887777777777777777777666666666777777 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   8.9e-05     0.088       2      70 ..      35     113 ..      34     126 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.9e-05
                      RNA_helicase   2 wlyGpsgeGKStlakeLakallkkl.......klkkkdsvys..rnpeddfwdgYtgqevvvidDfgqvkdee.nps 68 
                                        ++G++g+GK+ ++ ++a +  k++        +++k+s++    +   +f +g +++++++id ++++k+ee + +
  gi|385806409|ref|YP_005842807.1|  35 SIVGEPGTGKTIFSIHFAWEGIKESdrviyvtTEESKESIVQqaSQFGMNFRKGLNEKKMIIIDALMKSKEEEwTLN 111
                                       689***************99999999999*99666667776634555678999***************999966655 PP

                      RNA_helicase  69 dl 70 
                                       dl
  gi|385806409|ref|YP_005842807.1| 112 DL 113
                                       44 PP

>> DUF4174  Domain of unknown function (DUF4174)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00014      0.14       6      73 ..      57     119 ..      53     140 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00014
                           DUF4174   6 kwkrRlLlisapseedekykqqreel.eeqecelaeRklvvltivgsgaketgkieeeqlsaeliselr 73 
                                       k+  R++ +++ +e++e++ qq +++  + +++l+e k++++  + ++++e     e++l+  +i+el 
  gi|385806409|ref|YP_005842807.1|  57 KESDRVIYVTT-EESKESIVQQASQFgMNFRKGLNEKKMIIIDALMKSKEE-----EWTLNDLNIEELV 119
                                       67788888887.777788888888895699*************55444443.....3556555555554 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   8.9e-05     0.088       6      52 ..      36      80 ..      32     167 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.9e-05
                           DUF2075  6 VtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlreala 52
                                      + G++GtGKt+  ++++ e    +e  +++y++  ++   ++++a +
  gi|385806409|ref|YP_005842807.1| 36 IVGEPGTGKTIFSIHFAWEG--IKESDRVIYVTTEESKESIVQQASQ 80
                                      78**************9999..8999999999999999888888754 PP

>> DUF1571  Protein of unknown function (DUF1571)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00016      0.16      33     108 ..      47     127 ..      42     166 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00016
                           DUF1571  33 lsvYlkflepkkGrevlYvegenenkllaheggvlgall.....ptlkldpdgplAmaesrypvtdlGlenliekli 104
                                       +s+ + ++  k+  +v+Yv++e+ ++ ++++++  g+        +  + +d+ +  +e+ ++ +dl +e+l++k+i
  gi|385806409|ref|YP_005842807.1|  47 FSIHFAWEGIKESDRVIYVTTEESKESIVQQASQFGMNFrkglnEKKMIIIDALMKSKEEEWTLNDLNIEELVSKVI 123
                                       899999999999999**************99987665432111145568899999999******************* PP

                           DUF1571 105 eere 108
                                       e  +
  gi|385806409|ref|YP_005842807.1| 124 EAKK 127
                                       9765 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00018      0.17     116     183 ..      18      91 ..       3     104 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00018
                             T2SSE 116 ekiaevlrkavrerglilvsGgTgsGKttll.yallkeinksderi.vtvEDpvEiqleganqvqlnak....k 183
                                       + ++e+++  + +   i + G  g+GKt++    + + i++sd+ i vt E + E  +++a q  +n +    +
  gi|385806409|ref|YP_005842807.1|  18 KGFDELIEGGIPRGFFISIVGEPGTGKTIFSiHFAWEGIKESDRVIyVTTEESKESIVQQASQFGMNFRkglnE 91 
                                       5678888888888888999**********875788899999966655799**************9999833332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.65u 0.33s 00:00:00.98 Elapsed: 00:00:00.53
# Mc/sec: 1583.28
//
Query:       gi|385806410|ref|YP_005842808.1|  [L=525]
Description: radical SAM protein [Fervidicoccus fontis Kam940]
Scores for complete 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-16   59.2   0.0    2.5e-14   54.0   0.0    2.7  3  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 ?   -1.3   0.0      0.14   2.6e+03      28      67 ..      46      95 ..      41     155 .. 0.51
   2 !   54.0   0.0   1.4e-18   2.5e-14       4     167 .]     196     391 ..     193     391 .. 0.89
   3 ?    2.3   0.0     0.011     2e+02      63     121 ..     394     452 ..     387     462 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.14
                                      HHHHHHHHHHHHHHHHHTTSEEEEEE...........SSTGGGSTTHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxx RF
                       Radical_SAM 28 slsveeileevkelkaekgvkevilg...........ggepllypdfvell 67
                                      + +++++ + v+++ +e +   ++             ggep+    + +ll
  gi|385806410|ref|YP_005842808.1| 46 YYTIDQVRKDVDSFVKEANSSDLTAIvagvvvpgkyiGGEPISAE-ELKLL 95
                                      556666666666664222233333334556666666666666633.22333 PP

  == domain 2  score: 54.0 bits;  conditional E-value: 1.4e-18
                                       ESEESS-....-TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEE...............SSTGGGST CS
                                       xxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...............xxxxxxxx RF
                       Radical_SAM   4 trgCnlr....CsfCarpetvrregrgrslsveeileevkelkaekgvkevilg...............ggepllyp 61 
                                       +rgC++     CsfC+ p     +gr+  + +e+++ e++el ++ g++ + lg                  p  +p
  gi|385806410|ref|YP_005842808.1| 196 YRGCSRWisggCSFCIEP----LYGRPVQRNPEDVILEMREL-YRLGARAFRLGrqsdilvygskelgeKELPRPNP 267
                                       56665544444*******....79******************.8**********9777777777777666667777* PP

                                       THHHHHHHHHHTC.......CCTEEEEEEECSSCHGHHHHHHHHHTT..-SEEEEEEBSSSHHHHHHHHTCTSHHHH CS
                                       xxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  62 dfvellerlakla.......vpgiritvetngtlpdeeklerllelg..vdrvslgleaaddekvlklmnrghtfee 129
                                       +f+e  ++la+ a       v++ + +v++ ++  +++ + ++ e++   d +++gle +d+e v +++n + + e 
  gi|385806410|ref|YP_005842808.1| 268 EFIERFFQLARDAiegsvlhVDNSNPAVIAKYPEESKKAMLAMIEYHtpGDILAFGLENLDEE-VAEINNLNSNEEV 343
                                       ************999999999999999999999988***************************.******99***** PP

                                       HHHHHHHHHHTTSET..........EEEEEEEBTTTSHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 130 vlealeklreagikr..........vvdrivglpGendeeleellell 167
                                        +ea+++ +e+g+ r            ++i+glpGe ++ +e+ +++l
  gi|385806410|ref|YP_005842808.1| 344 AYEAVKAVNEVGLLRgdngmphllpGLNFIIGLPGERKASFEKNISFL 391
                                       ************8888889999999****************9988875 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.011
                                       HHHHHHHHHHTCCCTEEEEEEECSSCHG....HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  63 fvellerlaklavpgiritvetngtlpd....eeklerllelgvdrvslgleaaddekvlklm 121
                                       ++e+ ++ +++   +ir +++++gt+++    +e+ler  e    r++  + ++ d k+lk++
  gi|385806410|ref|YP_005842808.1| 394 IYEDGFAVRRI---NIRKVLVIPGTRLSvmwrREYLERNEEEA-ERFEWIVRHVYDVKFLKRI 452
                                       66777888888...9*************999999999888854.7777777777776666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (525 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); 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: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.52
# Mc/sec: 3053.71
//
Query:       gi|385806411|ref|YP_005842809.1|  [L=708]
Description: DEAD/DEAH box helicase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-26   93.7   0.0      2e-25   89.6   0.0    2.5  2  DEAD             DEAD/DEAH box helicase
      8e-13   48.7   0.1    2.4e-11   44.0   0.1    2.6  1  Helicase_C       Helicase conserved C-terminal domain
    8.4e-13   48.7   0.0    5.1e-12   46.2   0.0    2.3  1  HHH_5            Helix-hairpin-helix domain
    8.6e-10   38.9   0.0    1.6e-09   38.0   0.0    1.5  1  ResIII           Type III restriction enzyme, res subunit
    2.8e-09   36.9   0.0    8.4e-09   35.4   0.0    1.8  1  HHH_2            Helix-hairpin-helix motif
    1.8e-06   27.5   0.0     0.0026   17.6   0.0    2.8  2  HHH              Helix-hairpin-helix motif
    2.5e-06   27.2   0.0    2.9e-05   23.8   0.0    2.7  3  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
    0.00015   22.0   0.1     0.0053   17.0   0.0    2.8  2  HHH_3            Helix-hairpin-helix motif
     0.0061   16.8   0.0      0.015   15.5   0.0    1.7  1  Cdd1             Pathogenicity locus
  ------ inclusion threshold ------
       0.02   13.6   0.0      0.031   13.0   0.0    1.3  1  SNF2_N           SNF2 family N-terminal domain
      0.062   13.2   1.8       0.37   10.7   0.0    2.9  3  ATPase_2         ATPase domain predominantly from Archaea
       0.07   12.6   0.0        1.8    8.0   0.0    2.5  2  PhoH             PhoH-like protein
      0.078   13.4   0.1        1.1    9.7   0.1    2.6  2  HHH_8            Helix-hairpin-helix domain
       0.11   12.2   0.2          6    6.6   0.0    2.4  2  IstB_IS21        IstB-like ATP binding protein
       0.18   12.1   0.1          1    9.6   0.1    2.4  1  AAA_22           AAA domain
        1.7    9.4   4.7        3.1    8.6   0.2    3.2  3  CsgA             Minor curli fiber component A


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 !   89.6   0.0   1.7e-28     2e-25       2     170 ..      26     183 ..      25     188 .. 0.87
   2 ?    1.2   0.0      0.24   2.7e+02      31      94 ..     230     297 ..     227     350 .. 0.64

  Alignments for each domain:
  == domain 1  score: 89.6 bits;  conditional E-value: 1.7e-28
                                       HHHHHHHHH.HHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSE CS
                                       xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   2 diQaeaipl.ilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlr 77 
                                       + Q+eai   il+g++vl+  +T+sGKT  + + ++++v+    + + k+++++P+++La + ++++ ++   i++r
  gi|385806411|ref|YP_005842809.1|  26 PPQEEAIRKgILDGKNVLMVTQTASGKTFLAELIAVNNVL----SGRGKTVYLTPLKALAIEKYSDFIEYER-IGIR 97 
                                       669999976366***************************6....57889********************999.8999 PP

                                       EEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  78 vlliiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitc 154
                                       + +++g+  +++    l +++di+v+t +++d++l+ +   ls+v+++++DE++ l d+++++ +++++++l+++++
  gi|385806411|ref|YP_005842809.1|  98 TIATMGD--YDSSEPML-ERYDIIVATYEKMDSILRHRPSWLSRVSLVIIDEIHYLDDEKRGPVLESLIAKLKSMKS 171
                                       9988884..33344444.678**************888878*******************************76666 PP

                                       TSTTTSEEEEEESSBS CS
                                       xxxxxxxxxxxxxxxx RF
                              DEAD 155 dgklqrqvivlSATlp 170
                                       d     q++ lSAT+ 
  gi|385806411|ref|YP_005842809.1| 172 D----AQILGLSATVG 183
                                       6....45*******86 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.24
                                       HHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST...SEEE..EEETTSSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxx..xxxxxxxxxxxxxxx RF
                              DEAD  31 flipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyid...lrvl..liiggvaardqlskl 94 
                                       f+ pvl+ + +   ++g +a++ + +r  a   ++++ k++k  +    ++l  lii++++ ++  ++l
  gi|385806411|ref|YP_005842809.1| 230 FSSPVLDLIND-VISDGGQAIVFVNSRRRAVSLAQTVAKRLKMNKsseAEELskLIIESSEVQSLNEVL 297
                                       66777766644.667777888888888777777777777777322223222223445554444444444 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 !   44.0   0.1   2.1e-14   2.4e-11      14     111 .]     243     382 ..     232     382 .. 0.66

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 2.1e-14
                                       TTTSEEEEEESSHHHH........................HHHHHH......HHHT.........TSTEEEESTTST CS
                        Helicase_C  14 eeggkilifvntidrl........................ekvkll......lekk.........gikvavlhgelp 51 
                                       ++gg++++fvn+++r+                             +      +  +         + +v  +h+ l+
  gi|385806411|ref|YP_005842809.1| 243 SDGGQAIVFVNSRRRAvslaqtvakrlkmnksseaeelskL----IiessevQ--SlnevlsemiKNRVSFHHAGLT 313
                                       67888888888888554444555555555444444333320....13333220..022233444599999******* PP

                                       HHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEESSSS.......SSH....HHHHHHHTTSSSTT CS
                        Helicase_C  52 qnereeileqfnkgesdvLiatdvaerGidipkvnlVinfdlp.......rnv....tsyiqriGRtgRag 111
                                        ++r+ i e f+kg ++v++at  ++ G+++p  +++i  +                 +y+q +GR+gR g
  gi|385806411|ref|YP_005842809.1| 314 VEQRRMIEEGFRKGAINVIVATPTLAAGVNLPARRVII-ESSEryvagegN-SpikvLEYKQFAGRAGRPG 382
                                       ********************************655555.555525555542.04444************75 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.0   4.6e-15   5.1e-12       3      53 ..     651     701 ..     650     704 .. 0.96

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 4.6e-15
                                       HHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHH CS
                             HHH_5   3 eLlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriil 53 
                                       eL s++ iG+++A++l+s G++s+ed+ +a+v+eL ++ GiG+++A ri++
  gi|385806411|ref|YP_005842809.1| 651 ELVSIPEIGRVRARNLYSSGFRSIEDIRKASVNELMRVRGIGERLAYRIKE 701
                                       689**********************************************87 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.0   1.4e-12   1.6e-09       3     169 ..      23     182 ..      21     184 .. 0.79

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 1.4e-12
                                       EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGT CS
                            ResIII   3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkkfl 78 
                                       ++++ Qeeai++ +      + k++l++  T +GKT++a + ++ ++l+ ++  k++ l p k+l    +++f ++ 
  gi|385806411|ref|YP_005842809.1|  23 SFYPPQEEAIRKGI-----LDGKNVLMVTQTASGKTFLAeLIAVNNVLSGRG--KTVYLTPLKALAIEKYSDFIEYE 92 
                                       68999******999.....4688****************7777788887655..9******9999766666666555 PP

                                       GG....GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T....... CS
                            ResIII  79 seaykeigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk....... 148
                                             i ++ +   ++++e   +  +i+v+t++++d+++      +     +r  ++iiDE H l ++k       
  gi|385806411|ref|YP_005842809.1|  93 RIG---IRTIATMGDYDSSEPMLERYDIIVATYEKMDSIL-----RHRPSWLSRVSLVIIDEIHYLDDEKrgpvles 161
                                       555...66665555555558899*****************.....78888899999************856663333 PP

                                       TTHHHHHT---SEEEEEESS- CS
                            ResIII 149 swreilekfkeavllglTATp 169
                                        + +++ + ++a +lgl+AT 
  gi|385806411|ref|YP_005842809.1| 162 LIAKLKSMKSDAQILGLSATV 182
                                       44444555567*********6 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.0   7.5e-12   8.4e-09       6      54 ..     653     702 ..     648     706 .. 0.92

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 7.5e-12
                             HHH_2   6 LGIrhVGektAklLakr.FksldaLkkasleeLlevddiGeeiAqsivef 54 
                                        +I+++G   A++L ++ F+s++ ++kas++eL  v++iGe+ A  i+e+
  gi|385806411|ref|YP_005842809.1| 653 VSIPEIGRVRARNLYSSgFRSIEDIRKASVNELMRVRGIGERLAYRIKEY 702
                                       58************8755*****************************998 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0048       5.4      12      28 ..     651     667 ..     650     669 .. 0.89
   2 !   17.6   0.0   2.3e-06    0.0026       1      30 []     673     702 ..     673     702 .. 0.95

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0048
                                       HHHTSTT-SHHHHHHHH CS
                               HHH  12 eLlalPGVGpktAeaIl 28 
                                       eL+++P +G+ +A+  +
  gi|385806411|ref|YP_005842809.1| 651 ELVSIPEIGRVRARNLY 667
                                       8************9766 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 2.3e-06
                                       SHHHHHTSSHHHHHTSTT-SHHHHHHHHHH CS
                               HHH   1 sleglipasreeLlalPGVGpktAeaIlsy 30 
                                       s+e ++ as+ eL+ + G+G+  A +I +y
  gi|385806411|ref|YP_005842809.1| 673 SIEDIRKASVNELMRVRGIGERLAYRIKEY 702
                                       6899***********************998 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 ?   -2.1   0.0       3.2   3.6e+03      17      44 ..     612     646 ..     609     646 .. 0.65
   2 !   23.8   0.0   2.6e-08   2.9e-05       3      37 ..     652     687 ..     651     695 .. 0.81
   3 ?    0.4   0.0      0.51   5.7e+02       2      14 ..     684     696 ..     683     699 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.2
                   DNA_pol_lambd_f  17 wyakGirtledlra.......krakLtreqqiGlk 44 
                                       w+a  i  l d+++       k + L+  +++G+k
  gi|385806411|ref|YP_005842809.1| 612 WIAYAIYKLSDVLEqakqyskKLEALSYRVKYGIK 646
                                       77777777888887666666433667777777765 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 2.6e-08
                   DNA_pol_lambd_f   3 FtkvyGVGpktAkkwyakGirtledlra.krakLtr 37 
                                       + ++  +G+++A+++y+ G+r++ed+r+   ++L r
  gi|385806411|ref|YP_005842809.1| 652 LVSIPEIGRVRARNLYSSGFRSIEDIRKaSVNELMR 687
                                       678999**********************43355555 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.51
                   DNA_pol_lambd_f   2 lFtkvyGVGpktA 14 
                                       ++++v G+G + A
  gi|385806411|ref|YP_005842809.1| 684 ELMRVRGIGERLA 696
                                       79*******9988 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.34   3.8e+02      31      54 ..     637     660 ..     635     666 .. 0.86
   2 !   17.0   0.0   4.7e-06    0.0053       7      33 ..     676     702 ..     673     707 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.34
                             HHH_3  31 vayReknGpfksreeLlkvkglgp 54 
                                       + yR k+G  + + eL++++++g 
  gi|385806411|ref|YP_005842809.1| 637 LSYRVKYGIKEELYELVSIPEIGR 660
                                       579999999999********9996 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 4.7e-06
                             HHH_3   7 diNtAsaeeLqklpGlgpklAknIvay 33 
                                       di +As+ eL+++ G+g++lA +I +y
  gi|385806411|ref|YP_005842809.1| 676 DIRKASVNELMRVRGIGERLAYRIKEY 702
                                       899*********************998 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.3e-05     0.015       3      42 ..     647     686 ..     645     697 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.3e-05
                              Cdd1   3 kalkelqdiPniGkalaedlvelGirsveelkgedpeely 42 
                                       ++l el +iP+iG+  a++l++ G+rs+e++++ + +el+
  gi|385806411|ref|YP_005842809.1| 647 EELYELVSIPEIGRVRARNLYSSGFRSIEDIRKASVNELM 686
                                       68999***************************99988876 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 ?   13.0   0.0   2.7e-05     0.031     143     193 ..     108     154 ..      63     181 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.7e-05
                                       ---------EEEE-HHHHHHHT......TTS-S-S-SEEEES-GGGT--TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 143 apklladydvvittYdvlsreaelqkkrsvlkqvewkrvvlDEghtlknst 193
                                       ++ +l+ yd+++ tY+++   + l++++s l++v+   v++DE h l  ++
  gi|385806411|ref|YP_005842809.1| 108 SEPMLERYDIIVATYEKMD--SILRHRPSWLSRVS--LVIIDEIHYLDDEK 154
                                       66799**************..54589*****9875..7********99886 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 ?   10.7   0.0   0.00033      0.37      30      80 ..      49     101 ..      39     172 .. 0.62
   2 ?   -0.2   0.1      0.69   7.8e+02      48     101 ..     246     303 ..     234     319 .. 0.64
   3 ?   -1.5   0.0       1.8     2e+03     174     208 ..     483     514 ..     427     533 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00033
                          ATPase_2  30 gsGKtaLlkeiienl.edkdkyviyyialreesiskldefie.eeeekkklek 80 
                                        sGKt L   i+ n  ++   + +y+++l+  +i+k+++fie e    + ++ 
  gi|385806411|ref|YP_005842809.1|  49 ASGKTFLAELIAVNNvLSGRGKTVYLTPLKALAIEKYSDFIEyERIGIRTIAT 101
                                       69******99977774666669******************8753333333333 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.69
                          ATPase_2  48 dkyviyyialreesiskldefie.....eeeekkklekalgiavpkaeleeilkekskl 101
                                       ++ ++++++ r+  +   +   +     +++e+++l+k + +  + ++l+e+l+e +k+
  gi|385806411|ref|YP_005842809.1| 246 GQAIVFVNSRRRAVSLAQTVA-KrlkmnKSSEAEELSKLIIESSEVQSLNEVLSEMIKN 303
                                       556677766665443322222.2244667888888899998888888888888855544 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.8
                          ATPase_2 174 vyneselegrhky.ilvddldketalnflkegfkel 208
                                        y++++ +g+    +++d+l    + +++ke f + 
  gi|385806411|ref|YP_005842809.1| 483 KYYKATSYGKYVSdLYIDPL----SAELVKEAFSKK 514
                                       35555555554444555555....455555555544 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0016       1.8      16      52 ..      36      72 ..      25      87 .. 0.79
   2 ?    1.7   0.0      0.13   1.5e+02      63      93 ..     214     244 ..     202     296 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0016
                                      HHH-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEE CS
                              PhoH 16 lkkndivfaiGpaGtGKtylavalavealkkkkvkri 52
                                      + + + v ++ ++ +GKt+la  +av+ + +++ k +
  gi|385806411|ref|YP_005842809.1| 36 ILDGKNVLMVTQTASGKTFLAELIAVNNVLSGRGKTV 72
                                      44566788899999*************9998876665 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.13
                                       ----SS---------TTTHHHHHHHTTTS-T CS
                              PhoH  63 eelGflpgdleekvdpylrplydaLkdllga 93 
                                        ++ f +g++++  +p+ +p+ d ++d++++
  gi|385806411|ref|YP_005842809.1| 214 GKIKFSDGEEKKISEPFSSPVLDLINDVISD 244
                                       5788999*999999*************9943 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.66   7.4e+02      34      57 ..     633     660 ..     631     666 .. 0.84
   2 ?    9.7   0.1   0.00099       1.1      28      66 ..     667     702 ..     647     703 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.66
                                       CCCC-SS-HHHH.TT...HCTTSTT--H CS
                             HHH_8  34 aiealpeeitsl.ee...eltklpgiGk 57 
                                        +eal+++++ + +e   el ++p iG 
  gi|385806411|ref|YP_005842809.1| 633 KLEALSYRVKYGiKEelyELVSIPEIGR 660
                                       6999******9995559999******95 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00099
                                       HHHHHCCCCC-SS.-HHHHTTHCTTSTT--HHHHHHHHHH CS
                             HHH_8  28 YrrAaraiealpe.eitsleeeltklpgiGkkiaakieei 66 
                                       Y+   r+ie+  +  +++    l +++giG+++a +i+e+
  gi|385806411|ref|YP_005842809.1| 667 YSSGFRSIEDIRKaSVNE----LMRVRGIGERLAYRIKEY 702
                                       666666777776644444....9***************98 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0054         6      46      82 ..      38      76 ..      31      85 .. 0.79
   2 ?    3.1   0.0     0.062        69      99     124 ..     129     154 ..     118     175 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0054
                         IstB_IS21 46 kkenivllGpsGvGKshlaialgveavr..aglsvlfvr 82
                                      + +n++++ ++  GK++la  ++v+ v   +g+ v+ + 
  gi|385806411|ref|YP_005842809.1| 38 DGKNVLMVTQTASGKTFLAELIAVNNVLsgRGKTVYLTP 76
                                      5789*******************9999733455665555 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.062
                         IstB_IS21  99 laralkrllkvdllilDdlgllpldq 124
                                       l ++ + l +v+l+i+D++ +l+ ++
  gi|385806411|ref|YP_005842809.1| 129 LRHRPSWLSRVSLVIIDEIHYLDDEK 154
                                       4555567899*********9987443 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1   0.00091         1      82     113 ..     125     163 ..      38     186 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00091
                            AAA_22  82 leqalrarav....ielliiDEaqhlr...seealeeLr 113
                                       +   lr+r      ++l+iiDE+++l+   +  +le L 
  gi|385806411|ref|YP_005842809.1| 125 MDSILRHRPSwlsrVSLVIIDEIHYLDdekRGPVLESLI 163
                                       4445555555778889**********9865466666663 PP

>> CsgA  Minor curli fiber component A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.2    0.0028       3.1      21      61 ..     261     302 ..     254     310 .. 0.85
   2 ?    0.8   0.0      0.78   8.7e+02       8      33 ..     399     422 ..     398     467 .. 0.73
   3 ?   -2.3   0.1         7   7.8e+03      52      66 ..     620     634 ..     616     652 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0028
                              CsgA  21 vgkeiykkleekeykseeefvkd.LseeEiefLnkiLeeeik 61 
                                        ++++ k+l+ ++ ++ ee+ k  ++++E++ Ln++L+e ik
  gi|385806411|ref|YP_005842809.1| 261 LAQTVAKRLKMNKSSEAEELSKLiIESSEVQSLNEVLSEMIK 302
                                       578999*****99888888887625889**********9997 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.78
                              CsgA   8 LrEvlsnyteesevgkeiykkleeke 33 
                                       +rE+ s+y++   + ++iy+k+ +++
  gi|385806411|ref|YP_005842809.1| 399 VREMFSQYIN--GKPESIYSKMGSSS 422
                                       69******98..77889999997653 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 7
                              CsgA  52 LnkiLeeeikyakee 66 
                                       L ++Le++ +y+k+ 
  gi|385806411|ref|YP_005842809.1| 620 LSDVLEQAKQYSKKL 634
                                       667777777777653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (708 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.78u 0.35s 00:00:01.12 Elapsed: 00:00:00.51
# Mc/sec: 4187.53
//
Query:       gi|385806412|ref|YP_005842810.1|  [L=696]
Description: MCM family protein [Fervidicoccus fontis Kam940]
Scores for 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-101  335.6   0.1   1.6e-100  334.8   0.1    1.4  1  MCM              MCM P-loop domain
    1.8e-34  118.3   0.1    3.3e-34  117.4   0.1    1.4  1  MCM_OB           MCM OB domain
    6.7e-29  100.2   0.6      2e-28   98.6   0.6    1.9  1  MCM_lid          MCM AAA-lid domain
    2.9e-16   59.9   3.0    3.4e-16   59.7   1.6    1.9  1  MCM_N            MCM N-terminal domain
    1.5e-08   34.3   0.1    6.2e-05   22.5   0.0    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    7.1e-08   32.5   0.0    2.1e-07   31.0   0.0    1.8  1  AAA_5            AAA domain (dynein-related subfamily)
    2.6e-07   30.6   0.0    5.3e-07   29.6   0.0    1.5  1  AAA_3            ATPase family associated with various cellul
    7.7e-05   22.5   0.4    0.00061   19.5   0.1    2.5  2  Sigma54_activat  Sigma-54 interaction domain
    0.00088   18.4   0.1       0.15   11.0   0.2    2.6  2  DUF3987          Protein of unknown function (DUF3987)
     0.0099   16.2   0.1      0.061   13.6   0.2    2.4  2  Mnd1             Mnd1 HTH domain
  ------ inclusion threshold ------
      0.028   14.8   0.0      0.079   13.3   0.0    1.8  1  AAA_16           AAA ATPase domain
      0.029   14.4   1.4       0.28   11.3   0.1    3.2  3  Sigma70_r1_1     Sigma-70 factor, region 1.1
      0.045   13.5   0.4       0.16   11.7   0.4    1.9  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
       0.27   11.3   2.4       0.21   11.7   0.2    2.0  2  HAD_2            Haloacid dehalogenase-like hydrolase


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 !  334.8   0.1  1.3e-103  1.6e-100       2     224 .]     284     506 ..     283     506 .. 0.99

  Alignments for each domain:
  == domain 1  score: 334.8 bits;  conditional E-value: 1.3e-103
                                       HHHHHHHHTSSTHHHHHHHHSSTTSSS-HHHHHHHHHHHH---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHH CS
                               MCM   2 veeikelakekdiieklvksiapsiyghedvkkaillqlfggvkkkledktklrgdinvllvgdpgtaKsqlLkyve 78 
                                       +e+i +l+k++ i +k+v+siap+iygh dvk+ai+l+lfggv+k+++dkt++rgdi++llvgdpgtaKsqlL++++
  gi|385806412|ref|YP_005842810.1| 284 EERILQLSKDPWIRKKIVASIAPAIYGHWDVKEAIALALFGGVQKETKDKTRIRGDIHILLVGDPGTAKSQLLQFLS 360
                                       789************************************************************************** PP

                                       HHSSSEEEEESSSSSSSHSSSEEEEESSSSSEEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESS CS
                               MCM  79 klapravytsgkgssaagLtaavvrdeetgefvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKa 155
                                       ++apravyt+gkgssaagLtaav rd+++g+f+leaGa+vlad+Gv+++De+dkm+eedr+a+hEamEqqt+siaKa
  gi|385806412|ref|YP_005842810.1| 361 RIAPRAVYTTGKGSSAAGLTAAVIRDKKSGDFYLEAGAMVLADGGVALVDEIDKMREEDRVAIHEAMEQQTVSIAKA 437
                                       ***************************************************************************** PP

                                       SCEEEEE--EEEEEEE--SSSSCCTTS-HHHHSSSSHHHHHHSSEEEEE-SSTTHHHHHHHHHHHHHHH CS
                               MCM 156 GivatLnartsvlaAanpkagrydkkksvaeninlsaalLsrFDlifvllDkvdeekDeelaehivslh 224
                                       Giva+Lnar++v+aA npk+gry +++sva+ninl+ ++LsrFDlif+l+Dk+++e D++la+h++++h
  gi|385806412|ref|YP_005842810.1| 438 GIVAKLNARATVIAAGNPKYGRYVEERSVADNINLPVTILSRFDLIFILKDKPSAEYDTMLASHMIHVH 506
                                       *****************************************************************9987 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.4   0.1   2.6e-37   3.3e-34       2     125 ..     116     248 ..     115     249 .. 0.91

  Alignments for each domain:
  == domain 1  score: 117.4 bits;  conditional E-value: 2.6e-37
                                       XGG--GGGTTSEEEEEEEEEEE---EEEEEEEEEEE..TTT-.-EEE.......S---....-SB-..TTT-HHH-E CS
                            MCM_OB   2 lRdlrsehigklvkveGivtrasevkpklkkavfec..kkcgktvev.......elee....PrkCeekeCeskdpf 65 
                                       +R+++s++i+kl++++Gi +r++ +k+k+ ka+f++  ++c++t  +       +  +    P+ C  + C++ +++
  gi|385806412|ref|YP_005842810.1| 116 IRSIKSDYINKLIMIDGILVRVTPIKEKMFKAKFRHniEECNQTFYWppageeiK--DviepPQVC--PICGKPGNL 188
                                       8*******************************99885578998777688777550..25556****..99******* PP

                                       EE-GGGSEEEEEEEEEEE-------------EEEEEEEGGGTT---TT-EEEEEEEEEEE CS
                            MCM_OB  66 kletekskfvdfqklklQEspeevpaGelPrslevileddlvdkvkPGdrvevtGiyral 125
                                       +l  e+s+f+d+q+  +QE+pee+p+G++Prs+ev+l++dlvd+++PGdrv+++Gi+r++
  gi|385806412|ref|YP_005842810.1| 189 RLIYEESQFIDYQRTVVQERPEEIPPGQIPRSIEVVLTRDLVDQARPGDRVSIVGILRVV 248
                                       *********************************************************987 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.6   0.6   1.6e-31     2e-28       1      86 [.     519     604 ..     519     605 .. 0.96

  Alignments for each domain:
  == domain 1  score: 98.6 bits;  conditional E-value: 1.6e-31
                                       HHHHHHHHHHHHTT--BETCHHHHHHHHHHHHHHHHHTSSTSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHHHH CS
                           MCM_lid   1 ellrkYiayarekikPklseeakeklseaYvelRkeeedskrksipitvRqLesliRLseAlAklrlsevvteedve 77 
                                       +ll+kYi+ya++ ++P+l+eea + l++++ve+R+  ++s+++ ++it+RqLe+liRL+eA+Ak+ l+++vteed+ 
  gi|385806412|ref|YP_005842810.1| 519 DLLKKYISYAKRYYRPVLTEEAGNLLRDFFVEMRRIGSESQSNVVSITPRQLEALIRLAEAHAKMALKTEVTEEDAL 595
                                       58*********************************99888999********************************** PP

                                       HHHHHHHHH CS
                           MCM_lid  78 eairllkes 86 
                                       eairl+k +
  gi|385806412|ref|YP_005842810.1| 596 EAIRLMKVF 604
                                       ******976 PP

>> MCM_N  MCM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.7   1.6   2.7e-19   3.4e-16       3     100 ..      20     105 ..      18     127 .. 0.91

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 2.7e-19
                             MCM_N   3 kFedFLeefkddsededgekkYrdqlqemaerekttLevdlddLaafdeeLaeailenpkeylplleealkevvkkl 79 
                                       + ++FL+ef     ++++e+kY ++++em +++++ ++vd++dL+ +d++La a++++p e+l +l++a+   v ++
  gi|385806412|ref|YP_005842810.1|  20 RLRKFLKEF----YTREKEYKYKAEIKEMVNEGRNWMYVDWNDLYIYDRQLATALQNKPDEMLSYLNAAIYSSVLDF 92 
                                       6799*****....67889*********************************************************** PP

                             MCM_N  80 epsykddakefpaeltrrfqv 100
                                        p+y+++        +++f  
  gi|385806412|ref|YP_005842810.1|  93 SPDYAEE--------KKEFFA 105
                                       ***9998........555544 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0   0.00061      0.78      20      49 ..     337     366 ..     322     378 .. 0.87
   2 !   22.5   0.0   4.8e-08   6.2e-05      96     162 ..     393     459 ..     388     470 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00061
                      Mg_chelatase  20 aGgHnlllvGppGsGKtmlakrlpsllppl 49 
                                        G  ++llvG pG+ K+ l + l+ + p+ 
  gi|385806412|ref|YP_005842810.1| 337 RGDIHILLVGDPGTAKSQLLQFLSRIAPRA 366
                                       6889*********************99976 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 4.8e-08
                      Mg_chelatase  96 kpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpcpcg 162
                                         + G++ la  Gv ++DE+ +++++   ++ e +e+++v+i++a   ++  ar +++aa Np    
  gi|385806412|ref|YP_005842810.1| 393 YLEAGAMVLADGGVALVDEIDKMREEDRVAIHEAMEQQTVSIAKAGIVAKLNARATVIAAGNPKYGR 459
                                       6788**********************************************************96544 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 !   31.0   0.0   1.7e-10   2.1e-07       1     125 [.     341     459 ..     341     468 .. 0.83

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 1.7e-10
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--...........--------G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik..ngttslvdsplvraaregeilvlDEve 75 
                                       ++lLvG+pGt+Ks+l + l++   r v +    ++ +++ l+  +  +  +g+  l+ +++v     g ++++DE++
  gi|385806412|ref|YP_005842810.1| 341 HILLVGDPGTAKSQLLQFLSRIAPRAVYT--TGKGSSAAGLTAAVIRDkkSGDFYLEAGAMV--LADGGVALVDEID 413
                                       79*******************98554433..3455556666665554445899999999999..88*********** PP

                                       G--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.. CS
                             AAA_5  76 raesevlnsLlslleerrllleeggelvkaknddllerfrviatanpld.r 125
                                       +++ e   + +  +e++++++++ g + k ++       +via++np + r
  gi|385806412|ref|YP_005842810.1| 414 KMREEDRVAIHEAMEQQTVSIAKAGIVAKLNAR-----ATVIAAGNPKYgR 459
                                       ********************9999999999886.....9********9843 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 !   29.6   0.0   4.1e-10   5.3e-07       1     112 [.     341     455 ..     341     472 .. 0.84

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 4.1e-10
                             AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftp.dllPsdilGtevfeekekefefkkGpvf.an..llladeinr 73 
                                       h+ll g PG+ak +l + l+++    +     t      + ++ + + ++k+ +f +++G+++ a+  + l+dei++
  gi|385806412|ref|YP_005842810.1| 341 HILLVGDPGTAKSQLLQFLSRIAPRAV---YTTGkGSSAAGLTAAVIRDKKSGDFYLEAGAMVlADggVALVDEIDK 414
                                       9******************99876444...33431345688999999999**********976243559******** PP

                             AAA_3  74 appktqsalleameerqvtvege..thklpepflvlatqnP 112
                                            + a+ eame+++v+++++    kl+   +v+a+ nP
  gi|385806412|ref|YP_005842810.1| 415 MREEDRVAIHEAMEQQTVSIAKAgiVAKLNARATVIAAGNP 455
                                       ******************9986522689************9 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1   4.8e-07   0.00061      18     154 ..     335     466 ..     326     476 .. 0.84
   2 ?   -1.4   0.0       1.3   1.6e+03     124     163 ..     623     663 ..     600     668 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 4.8e-07
                                       HCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BEHHHHHTTT CS
                   Sigma54_activat  18 vaktdlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFtGAekekkGlfekadg 94 
                                        ++ d+++l++G+ Gt K+ l + + +  +r+   + +   ++ ++ l ++ +   ++G F      ++G++  adg
  gi|385806412|ref|YP_005842810.1| 335 RIRGDIHILLVGDPGTAKSQLLQFLSRIAPRA---VYTTGKGSSAAGLTAAVIRDKKSGDFY----LEAGAMVLADG 404
                                       56678999999999999999988888777755...557777888888888888889999885....578******** PP

                                       SEEEEETGGGS-HHHHHHHHHHHHHSE..EESBTSSSEEE--EEEEEEESS-HHHHHHTTSS CS
                   Sigma54_activat  95 GtlfLDeigelplelQekLlrvlqege..vervGsskeikvdvriiaatnedleeaveegkf 154
                                       G+ ++Dei ++  e  + + +++++++  + + G  ++ ++   +iaa n +  + vee+++
  gi|385806412|ref|YP_005842810.1| 405 GVALVDEIDKMREEDRVAIHEAMEQQTvsIAKAGIVAKLNARATVIAAGNPKYGRYVEERSV 466
                                       ***********************9997225799*****************999999988766 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.3
                                       SBTSSSEEE--EEEEEEESS-HHHHHHTTSS-.HHHHHHHT CS
                   Sigma54_activat 124 rvGsskeikvdvriiaatnedleeaveegkfr.edLyyrln 163
                                        vG+sk+++ ++++i  t +d+ ++  e+  r +d++ rl+
  gi|385806412|ref|YP_005842810.1| 623 MVGKSKSKREKMMLIEDTIRDILNETGEKCARiKDIMERLK 663
                                       5899999999999**99999988777666554378888876 PP

>> DUF3987  Protein of unknown function (DUF3987)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.013        17      14      58 ..     317     361 ..     315     366 .. 0.84
   2 !   11.0   0.2   0.00012      0.15     279     359 ..     535     608 ..     493     613 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.013
                           DUF3987  14 alsaalqgrvrvepkrgyteplnLytlvvapsGerKSpvdklvlr 58 
                                       a+++al g v+ e k++++    +++l v+++G+ KS++++++ r
  gi|385806412|ref|YP_005842810.1| 317 AIALALFGGVQKETKDKTRIRGDIHILLVGDPGTAKSQLLQFLSR 361
                                       57778888888888888899999***************9977665 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00012
                           DUF3987 279 rlsdeAkerfneffnelesrlrpggdledirdwasKlagnvaRiAgilhllredgigeateisaetlqaAialaeyl 355
                                        l++eA  ++++ff e+ + ++++ + + + ++  +  ++++R+A   + +       +te+++e+   Ai+l++++
  gi|385806412|ref|YP_005842810.1| 535 VLTEEAGNLLRDFFVEMRR-IGSESQSN-VVSITPRQLEALIRLAEAHAKM-----ALKTEVTEEDALEAIRLMKVF 604
                                       5899999999999888754.45555544.9999999999999999888777.....7899***************** PP

                           DUF3987 356 leha 359
                                       +++a
  gi|385806412|ref|YP_005842810.1| 605 MQQA 608
                                       **98 PP

>> Mnd1  Mnd1 HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0         5   6.5e+03      38      52 ..     542     556 ..     536     558 .. 0.87
   2 !   13.6   0.2   4.7e-05     0.061       4      51 ..     644     691 ..     641     695 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 5
                              Mnd1  38 sLvdDglveveKiGs 52 
                                       +L+ D  ve+ +iGs
  gi|385806412|ref|YP_005842810.1| 542 NLLRDFFVEMRRIGS 556
                                       6899999*******8 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 4.7e-05
                              Mnd1   4 ifqes.kefytlKeleklapkekgivsqsVkdvlqsLvdDglveveKiG 51 
                                       i++e+ +++  +K++  +++   +i++++ +d++ ++ +Dg++ +++ G
  gi|385806412|ref|YP_005842810.1| 644 ILNETgEKCARIKDIMERLKG-ENISQKELEDLISKMYKDGIIVQDRFG 691
                                       666665677789*********.9***********************988 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   6.1e-05     0.079      26     105 ..     341     427 ..     332     493 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.1e-05
                            AAA_16  26 lvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqllde.............. 88 
                                        +ll+G++G+ Ks l++ l r + ++  ++++gk  +             l++  ++r+ ++               
  gi|385806412|ref|YP_005842810.1| 341 HILLVGDPGTAKSQLLQFLSRIAPRA--VYTTGKGSSA----------AGLTA-AVIRDKKSGdfyleagamvladg 404
                                       689*************8888655555..6666666666..........22222.22222222222222222333333 PP

                            AAA_16  89 ......aesaeleawrekleeal 105
                                             + ++ +e++r +++ea+
  gi|385806412|ref|YP_005842810.1| 405 gvalvdEIDKMREEDRVAIHEAM 427
                                       33333333334444444444444 PP

>> Sigma70_r1_1  Sigma-70 factor, region 1.1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       2.7   3.5e+03       3      20 ..      37      54 ..      36      59 .. 0.79
   2 ?   -1.1   0.2       1.6     2e+03      45      62 ..     400     420 ..     394     432 .. 0.63
   3 ?   11.3   0.1   0.00022      0.28      23      55 ..     656     688 ..     653     691 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.7
                                      HHHHHHHHHHHHHHHSCE CS
                      Sigma70_r1_1  3 qkaavkeLikkgKkkGyL 20
                                      +ka++ke++++g+   y+
  gi|385806412|ref|YP_005842810.1| 37 YKAEIKEMVNEGRNWMYV 54
                                      799*********976665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.6
                                       HHHCCT-EEE-SS-....... CS
                      Sigma70_r1_1  45 mLedmgIdvveeae...dede 62 
                                        L d g+++v+e +   +ed 
  gi|385806412|ref|YP_005842810.1| 400 VLADGGVALVDEIDkmrEEDR 420
                                       688999999999994322222 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.00022
                                       HHHHHHGCCSS--HHHHHHHHHHHHCCT-EEE- CS
                      Sigma70_r1_1  23 eEindaLpddeldseqiediiemLedmgIdvve 55 
                                       ++i++ L+ +++++ ++ed+i+++ + gI v++
  gi|385806412|ref|YP_005842810.1| 656 KDIMERLKGENISQKELEDLISKMYKDGIIVQD 688
                                       79***************************9998 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.4   0.00013      0.16      29     116 ..     335     435 ..     310     452 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                            RuvB_N  29 reealdhvllyGpPGlGkttlakiiakelgvklkit....sg.....Pvl..ekagd..laalltnleekdvlfide 92 
                                       r +   h+ll+G PG  k+ l + +++     + +t    s+      v+  +k+gd  l a  + l ++ v ++de
  gi|385806412|ref|YP_005842810.1| 335 RIRGDIHILLVGDPGTAKSQLLQFLSRIAPRAVYTTgkgsSAagltaAVIrdKKSGDfyLEAGAMVLADGGVALVDE 411
                                       445556*************9877766544333333211113311111344334567755678888999********* PP

                            RuvB_N  93 ihrlsraveevlysamedfrldiv 116
                                       i +++++    ++ ame  ++ i 
  gi|385806412|ref|YP_005842810.1| 412 IDKMREEDRVAIHEAMEQQTVSIA 435
                                       ******************999874 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1         7     9e+03      61      89 ..      20      46 ..       6      48 .. 0.55
   2 ?   11.7   0.2   0.00016      0.21      64     166 ..     550     645 ..     494     655 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 7
                             HAD_2 61 kieellrkyneekkkkevkpydgvkelLe 89
                                       + ++l+++++++k+   k   ++ke+++
  gi|385806412|ref|YP_005842810.1| 20 RLRKFLKEFYTREKE--YKYKAEIKEMVN 46
                                      344444555555555..666777777765 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00016
                             HAD_2  64 ellrkyneekkkkevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpev 140
                                       e++r+  e++ +  v++ +   e+L  L+ea  k+++ T  ++e + e ++   + ++F +  +  + ++     ++
  gi|385806412|ref|YP_005842810.1| 550 EMRRIGSESQSN-VVSITPRQLEALIRLAEAHAKMALKTEVTEEDALEAIR---LMKVFMQQAGLMTESGV---VDI 619
                                       443444455555.99999*******************99998887755555...55566666666666666...699 PP

                             HAD_2 141 iekaleklklkkeeviyvGDsptDie 166
                                        + ++ k k k+e+++ ++D+++Di 
  gi|385806412|ref|YP_005842810.1| 620 DALMVGKSKSKREKMMLIEDTIRDIL 645
                                       999*********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (696 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       932  (0.0519828); expected 358.6 (0.02)
Passed bias filter:                      655  (0.036533); 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: 0.75u 0.32s 00:00:01.07 Elapsed: 00:00:00.51
# Mc/sec: 4122.14
//
Query:       gi|385806413|ref|YP_005842811.1|  [L=186]
Description: hypothetical protein FFONT_1371 [Fervidicoccus fontis Kam940]
Scores for complete 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   25.1   1.0    2.8e-05   24.5   1.0    1.2  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 !   24.5   1.0   1.6e-09   2.8e-05       1     109 []      44     162 ..      44     162 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.6e-09
                                       EEEEHHHHHHHHHTTSCCCHHCHHHCHHHHHHCCCHHTTS...SSSTTTTTTHHHHHHHHHHHHT............ CS
                              Sld5   1 veLPlWlaelLkrqrrveieppewlspesleailedetks...sdlpslpphflelavkllelard........... 63 
                                       veLP W a  L++++ v+ +  e +s +++++i+ +e +    +d ++lp +f+ l   +l+  +            
  gi|385806413|ref|YP_005842811.1|  44 VELPRWIANFLEERGLVKRKWDE-ISVQEVSKIHYREMSRravKDIEQLPSNFYWLVQEYLDYLEKkirseadpsfi 119
                                       69***************988655.59********************************9999998544445556665 PP

                                       ..HCHHHHHHHHHHHHHHHHHHHTHCHHHHHHHTS-TCCHCCS-HHHH CS
                              Sld5  64 ..ldelkrllrdllevRlakirkfaenledaagggggellsglseeEk 109
                                          ++l + l +++e R++ +  ++ +++d       e+ ++l++eE+
  gi|385806413|ref|YP_005842811.1| 120 edRQNLLEFLSEIVEKRMRAVITYVFSYGDYT-----EISQKLTQEEI 162
                                       555555599********************999.....99999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       955  (0.0532657); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); 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: 0.54u 0.36s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 1031.57
//
Query:       gi|385806414|ref|YP_005842812.1|  [L=170]
Description: phosphoesterase [Fervidicoccus fontis Kam940]
Scores for complete 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  107.9   0.0    6.6e-31  107.7   0.0    1.0  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    5.6e-09   36.8   0.3    1.8e-06   28.6   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 !  107.7   0.0   7.3e-35   6.6e-31       1     164 [.       1     162 [.       1     163 [. 0.91

  Alignments for each domain:
  == domain 1  score: 107.7 bits;  conditional E-value: 7.3e-35
                     Metallophos_2   1 MklaiiSDlHsnldaleavlealkevgvdaiihaGDleeeepevleellela..pvlaVrGNnD.eev.veedvlre 73 
                                       Mk++iiSD+H+n++ +  +le++k+++v+++ih+GD+  ++p + + +++ +  + +aV+GNnD ++v + ++ +r 
  gi|385806414|ref|YP_005842812.1|   1 MKIGIISDTHDNMKNISMFLEIMKSHEVELLIHLGDF--SSPFAFKSIFSSYqnRGYAVFGNNDgDRVvLTKMAMRM 75 
                                       *************************************..***999999998899**********6555799999999 PP

                     Metallophos_2  74 aaelgtdlpeeaelelagekvlliHgdpl.gvkdalaellkeaeegsd.vvvcGHtHvpevekeggvlvvnPGsvge 148
                                         e+++++     ++++g++++l+Hg  + +++ ++ae++ +  +g++ +v++GHtH  ++++ +  l++nPG++++
  gi|385806414|ref|YP_005842812.1|  76 GIEVAESV---NPVSIGGRRFFLMHGFGSpELTSEIAEAVAR--SGKYdYVLFGHTHSLRISQMERALLINPGEASG 147
                                       99999999...99*************9778888888888888..55555**************************** PP

                     Metallophos_2 149 prdgdpetyaildtde 164
                                       + +++  t++il++ e
  gi|385806414|ref|YP_005842812.1| 148 ALTQKA-TAVILEIPE 162
                                       977776.****99865 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0     2e-10   1.8e-06       1     127 [.       1     104 [.       1     114 [. 0.79
   2 !    7.5   0.1    0.0006       5.4     182     203 ..     107     128 ..     100     129 .. 0.78

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 2e-10
                                       EEEEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTSCH CS
                       Metallophos   1 lrilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvkypipvylllGNHegf 77 
                                       ++i +i+D+H      ++ ++  +l+  +++ ++ l++++GD+     + + +  +     +   + y++ GN +  
  gi|385806414|ref|YP_005842812.1|   1 MKIGIISDTH-----DNMKNISMFLEIMKSH-EVELLIHLGDFSSPFAFKSIFSSY----QN---RGYAVFGNND-- 62 
                                       89********.....**********888777.**********99999555533333....33...6789******.. PP

                                       HHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESE.CEEE CS
                       Metallophos  78 eeellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGg.spel 127
                                         +         ++++  r+  ev + ++ +s+g+   +++l+hG  spel
  gi|385806414|ref|YP_005842812.1|  63 --GDRVV-----LTKMAMRMGIEVAESVNPVSIGGR--RFFLMHGFgSPEL 104
                                       ..33333.....236778888999999999999999..*******876666 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0006
                                       HHHHHHHHHTTESEEEEESSSS CS
                       Metallophos 182 ealedllkkygvdlvisGHtHv 203
                                       e +e + + ++ d+v++GHtH 
  gi|385806414|ref|YP_005842812.1| 107 EIAEAVARSGKYDYVLFGHTHS 128
                                       55666778899**********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.35s 00:00:00.92 Elapsed: 00:00:00.57
# Mc/sec: 896.61
//
Query:       gi|385806415|ref|YP_005842813.1|  [L=182]
Description: putative Acetyltransferase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-20   73.9   0.3    2.1e-20   73.1   0.2    1.5  2  Acetyltransf_1   Acetyltransferase (GNAT) family
    2.1e-14   53.7   0.2    4.4e-14   52.7   0.2    1.5  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    6.9e-13   48.7   0.2    1.2e-12   47.8   0.2    1.5  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    4.3e-09   36.2   0.1    7.4e-09   35.5   0.1    1.4  1  FR47             FR47-like protein
    2.3e-08   33.8   0.0      1e-07   31.7   0.0    1.8  1  Acetyltransf_8   Acetyltransferase (GNAT) domain
    8.5e-06   26.0   0.2    1.9e-05   24.9   0.2    1.6  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    6.5e-05   23.6   0.0    9.2e-05   23.1   0.0    1.2  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
    7.2e-05   22.9   0.1    0.00015   21.8   0.1    1.6  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.023   14.3   0.0      0.054   13.1   0.0    1.5  1  GNAT_acetyltran  GNAT acetyltransferase
      0.028   13.9   0.3      0.032   13.7   0.3    1.3  1  Acetyltransf_15  Putative 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 ?   -1.1   0.0       1.2   2.1e+03      36      66 ..      16      48 ..       3      54 .. 0.54
   2 !   73.1   0.2   1.2e-23   2.1e-20      14     117 .]      52     159 ..      31     159 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.2
                                      EEEEETTEEEEEEEEEEEET...TSTTEEEEEEE CS
                    Acetyltransf_1 36 lvaeedgeliGfisllkipd...ekggvayiesl 66
                                      ++ + +g+++G   +  +       ++v+yi+++
  gi|385806415|ref|YP_005842813.1| 16 WLSSNEGTIVGRGFIIRN-VkkeDLPKVIYINEV 48
                                      444566777776622222.134423566666655 PP

  == domain 2  score: 73.1 bits;  conditional E-value: 1.2e-23
                                       HHHHHHHHHHHHHHHHSTTC.EEEEEEETTEEEEEEEEEEEET......TSTTEEEEEEEEESGGGTTSSHHHHHHH CS
                    Acetyltransf_1  14 ppnedaseeefeesfsleae.gllvaeedgeliGfisllkipd......ekggvayieslaVspeyrgkGlGsaLle 83 
                                       +++++     f+e++ ++ +  +++ae dg+ +G+i+ ++ +         ++++++ s+aV + yr++G+G aL++
  gi|385806415|ref|YP_005842813.1|  52 ENYPEY----FYEYHLDNWGrAFFLAEVDGRAVGYIMNRIETVmglsrsFFQKKGHVVSIAVLEGYRRRGIGEALMR 124
                                       333333....555655556647777***********555555555555536799*********************** PP

                                       HHHHHHHHT.TESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  84 aleeraree.gikkivlaveedndaairlYeklGF 117
                                       a ++ +++  g+k ++l+v+++nd+ai+lYeklGF
  gi|385806415|ref|YP_005842813.1| 125 AGMKSMKDVyGAKSVYLEVRVSNDPAIKLYEKLGF 159
                                       **********************************9 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.7   0.2   2.4e-17   4.4e-14       4      76 .]      69     161 ..      66     161 .. 0.74

  Alignments for each domain:
  == domain 1  score: 52.7 bits;  conditional E-value: 2.4e-17
                                       EEEEEEETTEEEEEEEEEEES............TCTEE...EEE-GGGTTSSHHHHHHHH.....TT.SEEE.EE.E CS
                    Acetyltransf_7   4 evfVaeddgkivGfialslld............aeitr...laVdpeyrgkGiGraLlea.....ae.kgii.le.q 57 
                                        +f+ae dg+ vG+i   ++             +   +   +aV++ yr++GiG aL++a     +   g + ++ +
  gi|385806415|ref|YP_005842813.1|  69 AFFLAEVDGRAVGYIMNRIETvmglsrsffqkkG---HvvsIAVLEGYRRRGIGEALMRAgmksmKDvYGAKsVYlE 142
                                       5899**********9988888*999988875544...1456******************965443114442222223 PP

                                       EEETHHHHHHHHHHTTEEE CS
                    Acetyltransf_7  58 lelnaekaikfYeklGFee 76 
                                       +++++++aik+YeklGF++
  gi|385806415|ref|YP_005842813.1| 143 VRVSNDPAIKLYEKLGFKK 161
                                       4444459**********95 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   0.2   6.9e-16   1.2e-12      28     126 ..      65     181 ..      36     182 .] 0.80

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 6.9e-16
                   Acetyltransf_10  28 egealllvaeeggkivGvi..elrdgs.............hisllfVdpeyrgqGigkaLleaveeeaekdgikl.. 87 
                                       +    +++ae++g+ vG+i  +++                h+  ++V + yr++Gig+aL+ a  + +++  +++  
  gi|385806415|ref|YP_005842813.1|  65 NWGRAFFLAEVDGRAVGYImnRIE--TvmglsrsffqkkgHVVSIAVLEGYRRRGIGEALMRAGMKSMKDVYGAKsv 139
                                       4456789999999****9966442..12356777788889***********************99998887777779 PP

                   Acetyltransf_10  88 eltvnasp.yavpfYeklGFkav..geeqeenGirfvpMeke 126
                                        l+v+ s+  a+++YeklGFk+v   e  + +G   + Me+e
  gi|385806415|ref|YP_005842813.1| 140 YLEVRVSNdPAIKLYEKLGFKKVrvIEGYYSDGENAYVMERE 181
                                       **********************95445566777777777765 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.1   4.1e-12   7.4e-09      20      81 ..     100     163 ..      83     168 .. 0.88

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 4.1e-12
                                       TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHH..S-S-EEEEEETT-HHHHHHHHHHT-EEEE CS
                              FR47  20 dggelgalqvlpehrrrGlgsrlvkalakeiae..rgktvllvvvasNtpsirlyeklGfekie 81 
                                       + g + ++ vl+  rrrG g  l +a  k +      k v l v+ sN+p+i+lyeklGf+k +
  gi|385806415|ref|YP_005842813.1| 100 KKGHVVSIAVLEGYRRRGIGEALMRAGMKSMKDvyGAKSVYLEVRVSNDPAIKLYEKLGFKKVR 163
                                       5689999************************998445678899*****************9974 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.0   5.8e-11     1e-07      16     143 ..      40     165 ..      38     166 .. 0.75

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 5.8e-11
                                       CCCHHHH-----HHHHHHHHHHHC.STTEEEEEEEETTEEEEEEEEEEGGGCGGGGCS....---TT-EEEEEEESS CS
                    Acetyltransf_8  16 prvaewweeagtleevrellakldadphsepliglldgepvgyfeiYwakedelaeyy....daepgdrGiHllige 88 
                                       p+v ++ e + +++  ++++++  ++  +  +++++dg+ vgy+   +++     +      + + + + i +l g 
  gi|385806415|ref|YP_005842813.1|  40 PKVIYINEVTLPENYPEYFYEYHLDNWGRAFFLAEVDGRAVGYIMN-RIETV--MGLSrsffQKKGHVVSIAVLEG- 112
                                       6666777777777777788884444666777899999999999754.44444..3333122344555555555554. PP

                                       HHHCTTTCHHHHHHHHHHHHHCCTT--EEEE--BTT-HHHHHHHHHTT-EEEEEE CS
                    Acetyltransf_8  89 aeargkglttallralvhylfadprtrrvvvEPdvrNerairllekaGfekekev 143
                                         +r++g++ al+ra ++ + +  ++++v +E +v+N  ai+l+ek+Gf+k++ +
  gi|385806415|ref|YP_005842813.1| 113 --YRRRGIGEALMRAGMKSMKDVYGAKSVYLEVRVSNDPAIKLYEKLGFKKVRVI 165
                                       ..999**********************************************9876 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.2   1.1e-08   1.9e-05      45     151 ..      64     176 ..      31     178 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.1e-08
                    Acetyltransf_4  45 dsekeyvflvaesdrivGyaylg.....qfkkr.akdwkaelsvylaerdnnkeglgrelidaleqvl.keqnienl 114
                                       d  ++ +fl++ ++r vGy   +     ++     +++   +s+ +  +  + +g+g +l+ a ++ +   ++ ++ 
  gi|385806415|ref|YP_005842813.1|  64 DNWGRAFFLAEVDGRAVGYIMNRietvmGLSRSfFQKKGHVVSIAVL-EGYRRRGIGEALMRAGMKSMkDVYGAKSV 139
                                       34467778877799999997554211114444456777888899998.569*****************899****** PP

                    Acetyltransf_4 115 laeiaspnensiqfhkalGFelvgifkkcikkngrwi 151
                                       + e+ ++n+++i+++++lGF++v+  ++++ ++   +
  gi|385806415|ref|YP_005842813.1| 140 YLEVRVSNDPAIKLYEKLGFKKVRVIEGYYSDGENAY 176
                                       ***************************9998877665 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   5.1e-08   9.2e-05       3     138 .]      30     160 ..      29     160 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 5.1e-08
                    Acetyltransf_3   3 lLrplteeDlealfelrsdpevmrylpepltleeaeewlerawaeeseeegygwaivlkdtgviGsv.glrdleeed 78 
                                       ++r++++eDl+++    ++ ++ + +pe   +   + w + ++ +e +++++g++++  +t v+G   ++++ ++  
  gi|385806415|ref|YP_005842813.1|  30 IIRNVKKEDLPKVIY-INEVTLPENYPEYFYEYHLDNWGRAFFLAEVDGRAVGYIMNRIET-VMGLSrSFFQKKG-- 102
                                       789999999999953.333333333444333333444555444455667889999988888.8888844443333.. PP

                    Acetyltransf_3  79 eeaelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGfe 138
                                           +++ + + ++++G++   +ra ++ + +  g++ ++ ++  +N   i+++eklGf+
  gi|385806415|ref|YP_005842813.1| 103 --HVVSIAVLEGYRRRGIGEALMRAGMKSMKDVYGAKSVYLEVRVSNDPAIKLYEKLGFK 160
                                       ..57999999********************9999*************************7 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.1   8.4e-08   0.00015       2     127 ..      31     161 ..      30     162 .. 0.68

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 8.4e-08
                                       EEEE-GGGHHHHHHHHHHHTT----H..HHHHHHHHHHTT..SEEEEEEETTEEEEEEEE.EEEEEEETTEEE.EEE CS
                    Acetyltransf_9   2 irelteedldevlellkyaFqdeespleeireyfrkllee..srvlgaedngelvgqlal.lplelnvpGktl.kaa 74 
                                       ir++++edl++v+ + +    ++ ++     +++++ l++    +++ae +g+ vg ++  +   + +  + + k +
  gi|385806415|ref|YP_005842813.1|  31 IRNVKKEDLPKVIYINEVTLPENYPE-----YFYEYHLDNwgRAFFLAEVDGRAVGYIMNrIETVMGLSRSFFqKKG 102
                                       67777777777776655555555554.....3455555554335666677777777554303333333223332459 PP

                                       EEEEEEE-CCGTTS-HHHHHHHHHHHHHHHT.T--EEEE--.....SSHHHHHTTT-EE CS
                    Acetyltransf_9  75 gvtgVavapehrgrgvlskLlaraleemree.gqplsllfP.....ssipiYrrfGyei 127
                                        v+++av   +r+rg+ ++L+++ ++ m++  g++ ++l        +i++Y+++G+++
  gi|385806415|ref|YP_005842813.1| 103 HVVSIAVLEGYRRRGIGEALMRAGMKSMKDVyGAKSVYLEVrvsndPAIKLYEKLGFKK 161
                                       9****************************988999999988776554579999999976 PP

>> GNAT_acetyltran  GNAT acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     3e-05     0.054     162     238 ..      83     163 ..      76     168 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3e-05
                   GNAT_acetyltran 162 ilkngeivsgasSysvyekgieieidTkedyrrkgLAtivaaalileclk....rglyPsWDaaneaSvaLaekLGY 234
                                       i+++ e v g s  +  +kg+ ++i+  e yrr+g  +++  a  +   +    +++y +    n ++++L+ekLG+
  gi|385806415|ref|YP_005842813.1|  83 IMNRIETVMGLSRSFFQKKGHVVSIAVLEGYRRRGIGEALMRAGMKSMKDvygaKSVYLEVRVSNDPAIKLYEKLGF 159
                                       455556677778888899******************9998877776654322114455555555************* PP

                   GNAT_acetyltran 235 efek 238
                                       + ++
  gi|385806415|ref|YP_005842813.1| 160 KKVR 163
                                       9876 PP

>> Acetyltransf_15  Putative acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.3   1.8e-05     0.032      65     141 ..      96     164 ..       5     178 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.8e-05
                   Acetyltransf_15  65 silieknvleiYtlyvsekyrgkGlakklLeeslkelkknYkvdnelllaLHlnpkDksMnisfalYyslgFrkglf 141
                                       s+ ++k    + ++ v e yr++G+   l+   +k++k  Y ++   +l   ++  D     +  lY +lgF+k+  
  gi|385806415|ref|YP_005842813.1|  96 SFFQKKGH--VVSIAVLEGYRRRGIGEALMRAGMKSMKDVYGAK-SVYLEVRVSN-DP----AIKLYEKLGFKKVRV 164
                                       55555544..66899***************************99.8999999985.44....7789******99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.58u 0.35s 00:00:00.93 Elapsed: 00:00:00.55
# Mc/sec: 1000.17
//
Query:       gi|385806416|ref|YP_005842814.1|  [L=293]
Description: beta-lactamase [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-09   38.0   0.3      6e-09   36.2   0.3    1.9  1  Lactamase_B    Metallo-beta-lactamase superfamily
    1.1e-08   34.8   0.7    2.3e-08   33.8   0.7    1.8  1  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.019   14.4   0.0      0.031   13.7   0.0    1.3  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.3     1e-12     6e-09       7     197 .]      33     264 ..      29     264 .. 0.71

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 1e-12
                                       EEEEEE....ETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHH CS
                       Lactamase_B   7 nsylie....gdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeea 79 
                                        s++++     +  ++L+D G  t a +    + +  ++   +da++lTH H+DH+ g +++ ++ +     v ++ 
  gi|385806416|ref|YP_005842814.1|  33 VSFFVQtysgSERANVLVDVGQNTYALMHN--MELMNIDSSTIDAIVLTHCHYDHTRGIAEVLRKIGKRDLPVIAHP 107
                                       67888888888999*******999999985..8*******************************9999998888888 PP

                                       HCCHCHHHHHHHHHCCHH.................TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEE CS
                       Lactamase_B  80 palfmeeaddaasrkgll.................lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvve 139
                                         ++ +  +d   r+ +                  la+++ +     +  +++ +  + ++  +  ++ +  +gvve
  gi|385806416|ref|YP_005842814.1| 108 DIFRLNLSNDPVLRHVGMtledsrekieesggrliLARDPLMVFPGLITTGEVRRQTDFEGRGYRLFTVTDNGGVVE 184
                                       88888888887777777677777777777777766555555555555555555666666666666666666666666 PP

                                       ETTCCEEEECTTTSSHHCCCCCC........................TTCEEE-SHCHHHHHHHHHHHHHHHCHSEE CS
                       Lactamase_B 140 ygggkvlftGDallagetgridl.......................tlrgaevrdpsdaekyldsllklaglkaevl 193
                                       +++ + + +   + +g  +++++                        ++g++ +d+sd +    +++ l ++k++++
  gi|385806416|ref|YP_005842814.1| 185 DRMMDDISVVGITNSGIVILTGCshagivniikhsaelakedrvlaVIGGFHLIDASDERIEK-TVRALSQMKIDRI 260
                                       666666666666666666666666666666666666666666666666666666666666655.6666666666666 PP

                                       EESS CS
                       Lactamase_B 194 vpgH 197
                                       ++gH
  gi|385806416|ref|YP_005842814.1| 261 YAGH 264
                                       6666 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 !   33.8   0.7   3.8e-12   2.3e-08       3      68 ..      48     111 ..      46     265 .. 0.84

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 3.8e-12
                                       EEES--TTHHHHHTCGG.S--S.SS--..SEEEEE-SS--HHHHGGGGCCCC.C--EEEEEEEEHHHHH CS
                     Lactamase_B_2   3 iLiDagpdlrqqalral.qPve.lrdelppidaVllthaHyDHlaglltlre.lrpkklplyapkgvla 68 
                                       +L+D g ++ +     l ++ e    + + ida++lth+HyDH+ g+  + + + +++lp++a++++ +
  gi|385806416|ref|YP_005842814.1|  48 VLVDVGQNTYA-----LmHNMElMNIDSSTIDAIVLTHCHYDHTRGIAEVLRkIGKRDLPVIAHPDIFR 111
                                       55555555433.....33444554455589*****************98877555566******98765 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.2e-06     0.031       6      71 ..      45     105 ..      42     116 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.2e-06
                     Lactamase_B_6   6 nvkiLlDvGwdeskvslesalkelekviptvdliLLshatlehlGayallyakfksklllnipvya 71 
                                        +++L+DvG++ + +   + ++ ++   +t+d+i+L+h   +h  + a ++ k+++    ++pv a
  gi|385806416|ref|YP_005842814.1|  45 RANVLVDVGQNTYAL--MHNMELMNIDSSTIDAIVLTHCHYDHTRGIAEVLRKIGK---RDLPVIA 105
                                       578********9865..356676666789**************9998777766653...4555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 1670.05
//
Query:       gi|385806417|ref|YP_005842815.1|  [L=229]
Description: PHP C-terminal domain-containing protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.1e-10   40.6   0.0    3.2e-10   40.5   0.0    1.2  1  PHP           PHP domain
    5.7e-10   38.8   0.0    1.1e-09   37.9   0.0    1.5  1  PHP_C         PHP-associated
  ------ inclusion threshold ------
       0.11   12.2   0.1       0.22   11.3   0.1    1.4  1  Importin_rep  Importin 13 repeat


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 !   40.5   0.0   5.4e-14   3.2e-10       1      68 [.       9      73 ..       9     202 .. 0.77

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 5.4e-14
                                      EEEE--CCC--.S-H..HHHHHHHHHCT-SEEEEEEEEBTTHHHHHHHHHHHHTTTTSEEEEEEE... CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               PHP  1 dlHvHteyslldgalsieelvkkakelglkaiaiTDhgnlfgyvefykaakkkykagikpiiGleayv 68
                                      d+H+H+++s  ++ +  e ++  a++ gl a+ iTDh+ ++g +++ k ak+k   gi++++G e+  
  gi|385806417|ref|YP_005842815.1|  9 DMHMHSNFSDGESDV--ESILLHAERIGLNAVSITDHNTFQGSFHASKVAKEKG-IGIHVVMGSEVRT 73
                                      79*******444777..*********************************7666.8*********433 PP

>> PHP_C  PHP-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.0   1.8e-13   1.1e-09       4      46 ..     148     188 ..     146     202 .. 0.77

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 1.8e-13
                             PHP_C   4 NrrArrfAeklglpgtgGSDAHrleeVGrayTefeepiatpde 46 
                                       N +A rfA+++ +p+ ++SDAH+l+++G     ++ ++   ++
  gi|385806417|ref|YP_005842815.1| 148 NSKAYRFAREHSIPCMASSDAHTLKNIGIFRMIVSLESS--ED 188
                                       99**************************99999843333..33 PP

>> Importin_rep  Importin 13 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   3.7e-05      0.22      23      33 ..      72      82 ..      71      84 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.7e-05
                      Importin_rep 23 RqDIsDTlmyl 33
                                      R D++DTl+y+
  gi|385806417|ref|YP_005842815.1| 72 RTDVGDTLVYC 82
                                      99********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1367.73
//
Query:       gi|385806418|ref|YP_005842816.1|  [L=90]
Description: hypothetical protein FFONT_1376 [Fervidicoccus fontis Kam940]
Scores for complete 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   58.3  15.1    5.9e-09   35.4   2.7    2.2  2  Fer4      4Fe-4S binding domain
    3.8e-13   48.9  14.7      7e-07   29.1   4.8    2.2  2  Fer4_6    4Fe-4S binding domain
    2.3e-11   44.1   7.7    9.1e-06   26.2   0.8    2.1  2  Fer4_7    4Fe-4S dicluster domain
    7.1e-10   38.9  24.4    5.6e-07   29.6  14.0    2.0  2  Fer4_21   4Fe-4S dicluster domain
    1.5e-09   37.9   8.4    2.1e-09   37.4   8.4    1.3  1  Fer4_9    4Fe-4S dicluster domain
      2e-09   37.4  10.3    2.9e-09   36.9  10.3    1.3  1  Fer4_10   4Fe-4S dicluster domain
    1.5e-08   35.4   7.7    0.00047   21.0   1.3    2.2  2  Fer4_16   4Fe-4S double cluster binding domain
      3e-08   33.3  11.5    0.00051   20.0   1.7    2.2  2  Fer4_2    4Fe-4S binding domain
    3.8e-07   30.1  12.4    0.00091   19.6   1.3    2.2  2  Fer4_4    4Fe-4S binding domain
    1.9e-06   28.2   5.8      0.002   18.6   0.7    2.1  2  Fer4_8    4Fe-4S dicluster domain
    1.8e-05   25.2  12.9      0.012   16.2   3.8    2.4  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
    2.3e-05   24.8   6.5      0.007   16.9   0.6    2.1  2  Fer4_17   4Fe-4S dicluster domain
    0.00062   20.5  15.6      0.021   15.8   4.0    2.2  2  Fer4_3    4Fe-4S binding domain
      0.002   18.2   7.8     0.0031   17.6   1.2    2.1  2  ETF_QO    Electron transfer flavoprotein-ubiquinone oxidoredu
     0.0023   18.1  10.9       0.02   15.1  10.9    1.9  1  Fer4_18   4Fe-4S dicluster domain
     0.0042   17.9   5.6       0.57   11.1   0.3    2.1  2  Fer4_22   4Fe-4S dicluster domain
     0.0071   17.1  15.6       0.52   11.1   2.4    3.4  4  Fer4_15   4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   2.7   5.6e-12   5.9e-09       1      24 []      22      45 ..      22      45 .. 0.95
   2 !   28.8   4.7   6.5e-10   6.9e-07       2      24 .]      52      74 ..      51      74 .. 0.94

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 5.6e-12
                                      EEEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  1 vvideekCigCGaCvevCPvgAIt 24
                                      v++d+ekC+ C++C+e CPvgAI+
  gi|385806418|ref|YP_005842816.1| 22 VIVDQEKCTLCKKCEELCPVGAIS 45
                                      689*******************96 PP

  == domain 2  score: 28.8 bits;  conditional E-value: 6.5e-10
                                      EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  2 videekCigCGaCvevCPvgAIt 24
                                       +d e Ci+C  C+ +CP gAI+
  gi|385806418|ref|YP_005842816.1| 52 RVDSENCIACYSCAIICPEGAIS 74
                                      79*******************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 !   25.7   2.2   7.8e-09   8.3e-06       2      24 .]      22      44 ..      21      44 .. 0.94
   2 !   29.1   4.8   6.6e-10     7e-07       1      24 []      50      73 ..      50      73 .. 0.97

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 7.8e-09
                            Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                      v +d++kC+ C +C+  CP gai
  gi|385806418|ref|YP_005842816.1| 22 VIVDQEKCTLCKKCEELCPVGAI 44
                                      679*******************8 PP

  == domain 2  score: 29.1 bits;  conditional E-value: 6.6e-10
                            Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                      +v++d ++Ci C+ C+++CPegai
  gi|385806418|ref|YP_005842816.1| 50 KVRVDSENCIACYSCAIICPEGAI 73
                                      699********************8 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.8   8.7e-09   9.1e-06      28      52 .]      19      43 ..       2      43 .. 0.80
   2 !   22.0   1.1   1.7e-07   0.00018      29      52 .]      49      72 ..      45      72 .. 0.92

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 8.7e-09
                            Fer4_7 28 tekveidpekClgCgaCvavCPtga 52
                                      +e+v +d+ekC+ C++C++ CP+ga
  gi|385806418|ref|YP_005842816.1| 19 KEEVIVDQEKCTLCKKCEELCPVGA 43
                                      4778899****************98 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 1.7e-07
                            Fer4_7 29 ekveidpekClgCgaCvavCPtga 52
                                       kv++d+e+C+ C++C+  CP ga
  gi|385806418|ref|YP_005842816.1| 49 GKVRVDSENCIACYSCAIICPEGA 72
                                      5899*****************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 !   20.7   2.6   3.2e-07   0.00033      29      58 ..      17      45 ..       7      46 .. 0.80
   2 !   29.6  14.0   5.3e-10   5.6e-07       3      58 ..      24      74 ..      23      75 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 3.2e-07
                           Fer4_21 29 daktvlkvvedeCvGCnlCssvCPvedcie 58
                                      + k+ + v +++C+ C+ C + CPv ++i+
  gi|385806418|ref|YP_005842816.1| 17 KLKEEVIVDQEKCTLCKKCEELCPV-GAIS 45
                                      4456667889**************9.9986 PP

  == domain 2  score: 29.6 bits;  conditional E-value: 5.3e-10
                           Fer4_21  3 idedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58
                                      +d++kC  C+kC   C+   + ai+i++ + ++v +++C++C  C+++CP e++i+
  gi|385806418|ref|YP_005842816.1| 24 VDQEKCTLCKKCEELCP---VGAISIEDGK-VRVDSENCIACYSCAIICP-EGAIS 74
                                      89***************...899**98655.59*****************.79996 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   8.4     2e-12   2.1e-09       1      51 []      28      73 ..      15      73 .. 0.95

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 2e-12
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                      kCt C++C+e Cp g+++ ++++  +  +     +Ci C +C+ +Cp+gai
  gi|385806418|ref|YP_005842816.1| 28 KCTLCKKCEELCPVGAISIEDGKVRVDSE-----NCIACYSCAIICPEGAI 73
                                      7******************9999998874.....6*************997 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9  10.3   2.8e-12   2.9e-09       2      56 .]      22      69 ..      21      75 .. 0.95

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 2.8e-12
                           Fer4_10  2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      v++d+++C+ C+kC + CP+        ++  e+++vr+++e+C++c +C+ +CP
  gi|385806418|ref|YP_005842816.1| 22 VIVDQEKCTLCKKCEELCPV-------GAISIEDGKVRVDSENCIACYSCAIICP 69
                                      789*****************.......888889999999***************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 !   21.0   1.3   4.4e-07   0.00047       1      20 [.      28      47 ..      28      56 .. 0.83
   2 !   18.2   0.6   3.5e-06    0.0037       1      20 [.      57      76 ..      57      87 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 4.4e-07
                           Fer4_16  1 rCgtCgkCaevCPtnaikek 20
                                      +C+ C+kC e CP++ai+ +
  gi|385806418|ref|YP_005842816.1| 28 KCTLCKKCEELCPVGAISIE 47
                                      5****************966 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 3.5e-06
                           Fer4_16  1 rCgtCgkCaevCPtnaikek 20
                                      +C+ C  Ca +CP++ai+ k
  gi|385806418|ref|YP_005842816.1| 57 NCIACYSCAIICPEGAISIK 76
                                      6****************977 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   1.7   4.8e-07   0.00051       3      21 ..      22      40 ..      20      41 .. 0.91
   2 !   18.7   2.7   1.3e-06    0.0013       2      22 .]      50      70 ..      49      70 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 4.8e-07
                            Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                      v vd ++C+ C++C   CP
  gi|385806418|ref|YP_005842816.1| 22 VIVDQEKCTLCKKCEELCP 40
                                      789**************** PP

  == domain 2  score: 18.7 bits;  conditional E-value: 1.3e-06
                            Fer4_2  2 pvvvdtdrCigCgaCvsaCPa 22
                                      +v vd+++Ci+C +C   CP+
  gi|385806418|ref|YP_005842816.1| 50 KVRVDSENCIACYSCAIICPE 70
                                      5789****************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 !   15.8   3.9   1.4e-05     0.015       1      17 []      26      42 ..      26      42 .. 0.94
   2 !   19.6   1.3   8.6e-07   0.00091       1      16 [.      55      70 ..      55      79 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.4e-05
                            Fer4_4  1 qerCigCgsCvaaCPqg 17
                                      qe+C+ C++C+  CP+g
  gi|385806418|ref|YP_005842816.1| 26 QEKCTLCKKCEELCPVG 42
                                      79*************86 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 8.6e-07
                            Fer4_4  1 qerCigCgsCvaaCPq 16
                                      +e+Ci C sC ++CP 
  gi|385806418|ref|YP_005842816.1| 55 SENCIACYSCAIICPE 70
                                      699************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 !   18.6   0.7   1.9e-06     0.002      48      64 ..      26      42 ..       3      43 .. 0.76
   2 !   12.7   0.4   0.00012      0.13      49      64 ..      56      71 ..      47      81 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.9e-06
                            Fer4_8 48 lwsCttcgaCtevCpvg 64
                                       ++Ct c++C+e Cpvg
  gi|385806418|ref|YP_005842816.1| 26 QEKCTLCKKCEELCPVG 42
                                      579************97 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00012
                            Fer4_8 49 wsCttcgaCtevCpvg 64
                                      ++C +c +C+  Cp+g
  gi|385806418|ref|YP_005842816.1| 56 ENCIACYSCAIICPEG 71
                                      5788888888888875 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   1.8   4.4e-05     0.046       1      17 [.      24      40 ..      24      46 .. 0.97
   2 !   16.2   3.8   1.1e-05     0.012       1      18 [.      53      70 ..      53      71 .. 0.97

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.4e-05
                           Fer4_13  1 VDrdtCiacgaCvelaP 17
                                      VD+++C+ c++C el+P
  gi|385806418|ref|YP_005842816.1| 24 VDQEKCTLCKKCEELCP 40
                                      9***************9 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.1e-05
                           Fer4_13  1 VDrdtCiacgaCvelaPd 18
                                      VD ++Ciac +C+ ++P+
  gi|385806418|ref|YP_005842816.1| 53 VDSENCIACYSCAIICPE 70
                                      9****************8 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   0.6   6.6e-06     0.007      43      58 ..      26      41 ..       3      43 .. 0.74
   2 !   11.4   0.7   0.00034      0.36      44      59 ..      56      71 ..      45      74 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.6e-06
                           Fer4_17 43 aslCieCgeCerkCPq 58
                                       ++C+ C++Ce+ CP 
  gi|385806418|ref|YP_005842816.1| 26 QEKCTLCKKCEELCPV 41
                                      589************6 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00034
                           Fer4_17 44 slCieCgeCerkCPqg 59
                                      ++Ci C  C+  CP+g
  gi|385806418|ref|YP_005842816.1| 56 ENCIACYSCAIICPEG 71
                                      7899999999999986 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   4.0   1.9e-05     0.021       1      15 []      29      43 ..      29      43 .. 0.98
   2 !   10.7   3.8   0.00081      0.85       1      15 []      58      72 ..      58      72 .. 0.97

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.9e-05
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      Ct C  C+e CPvgA
  gi|385806418|ref|YP_005842816.1| 29 CTLCKKCEELCPVGA 43
                                      **************9 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00081
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+ C+ C   CP+gA
  gi|385806418|ref|YP_005842816.1| 58 CIACYSCAIICPEGA 72
                                      9*************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 ?    5.2   1.1     0.022        23      63      90 ..      17      44 ..       3      47 .. 0.72
   2 !   17.6   1.2   2.9e-06    0.0031      64      93 ..      47      78 ..      37      83 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.022
                                      TSSEEEEE-CCC--S--HHHHH-TT--E CS
                            ETF_QO 63 akekklqinaqnCvhCktCdikdpsqni 90
                                      + ++++ ++ + C  Ck C+   p   i
  gi|385806418|ref|YP_005842816.1| 17 KLKEEVIVDQEKCTLCKKCEELCPVGAI 44
                                      34566889999********977776665 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 2.9e-06
                                      SSEEEEE-CCC--S--HHHHH-TT--E..EE- CS
                            ETF_QO 64 kekklqinaqnCvhCktCdikdpsqni..ewv 93
                                      ++ k++++++nC+ C +C i  p+  i  +w+
  gi|385806418|ref|YP_005842816.1| 47 EDGKVRVDSENCIACYSCAIICPEGAIsiKWK 78
                                      466899*****************986511565 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1  10.9   1.9e-05      0.02      50      97 ..      18      70 ..       3      80 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.9e-05
                           Fer4_18 50 keerkekgagdcidcescvkvcPtg.idirkGl....qleciscllcidacdk 97
                                       +e+   ++ +c+ c++c ++cP+g i i +G       +ci+c  c   c +
  gi|385806418|ref|YP_005842816.1| 18 LKEEVIVDQEKCTLCKKCEELCPVGaISIEDGKvrvdSENCIACYSCAIICPE 70
                                      44445667889************9769*****63222347*******988865 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.3   0.00054      0.57      66      94 ..      11      41 ..       2      43 .. 0.71
   2 !    9.6   0.8    0.0016       1.6       1      14 [.      57      70 ..      50      78 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00054
                           Fer4_22 66 llhklsefkekf..gesgCvGCgRCieacpv 94
                                      +   ++++ke++  ++++C+ C +C+e cpv
  gi|385806418|ref|YP_005842816.1| 11 VGAVFEKLKEEVivDQEKCTLCKKCEELCPV 41
                                      555555666655559999***********97 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0016
                           Fer4_22  1 rClsCgaCtlvCpt 14
                                      +C++C +C+++Cp 
  gi|385806418|ref|YP_005842816.1| 57 NCIACYSCAIICPE 70
                                      59999999999985 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 !    9.8   3.7    0.0012       1.3       1      19 [.      22      40 ..      22      41 .. 0.94
   2 ?    4.8   0.1     0.045        48      58      66 .]      38      46 ..      36      46 .. 0.87
   3 !   11.1   2.4   0.00049      0.52       1      20 [.      51      70 ..      51      72 .. 0.94
   4 ?    2.7   0.1      0.21   2.2e+02      59      66 .]      68      75 ..      65      75 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0012
                           Fer4_15  1 VvvDrdaCigcglCvaeap 19
                                      V vD+++C+ c  C +++p
  gi|385806418|ref|YP_005842816.1| 22 VIVDQEKCTLCKKCEELCP 40
                                      78**************998 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.045
                           Fer4_15 58 aCPvdAIrv 66
                                       CPv+AI++
  gi|385806418|ref|YP_005842816.1| 38 LCPVGAISI 46
                                      6******97 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00049
                           Fer4_15  1 VvvDrdaCigcglCvaeape 20
                                      V+vD ++Ci c  C+  +pe
  gi|385806418|ref|YP_005842816.1| 51 VRVDSENCIACYSCAIICPE 70
                                      89*************99997 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.21
                           Fer4_15 59 CPvdAIrv 66
                                      CP++AI++
  gi|385806418|ref|YP_005842816.1| 68 CPEGAISI 75
                                      ******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       816  (0.0455129); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 521.38
//
Query:       gi|385806419|ref|YP_005842817.1|  [L=91]
Description: hypothetical protein FFONT_1377 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-14   53.3  13.5    1.6e-14   53.3  13.5    1.8  2  DUF131         Protein of unknown function DUF131
  ------ inclusion threshold ------
       0.17   10.1   7.4        0.2    9.9   7.4    1.0  1  DUF2070        Predicted membrane protein (DUF2070)
        0.2   12.0   4.2        8.6    6.7   2.7    2.1  2  Orf78          Orf78 (ac78)
       0.31   10.6   6.2        5.3    6.7   2.0    2.1  2  Baculo_11_kDa  Baculovirus 11 kDa family
       0.38   10.9   0.1       0.38   10.9   0.1    1.8  2  TssO           Type VI secretion system, TssO
       0.46   10.4   4.0        1.1    9.2   4.0    1.6  1  DUF1461        Protein of unknown function (DUF1461)
        5.2    7.4   8.3          4    7.8   0.5    2.2  2  Sigma_reg_N    Sigma factor regulator N-terminal
          8    6.5  10.6         12    5.9   0.7    2.3  2  DUF4083        Domain of unknown function (DUF4083)
        9.2    6.5  16.5          1    9.6   5.4    2.1  2  DUF3784        Domain of unknown function (DUF3784)
         10    6.2  10.5       0.92    9.5   0.2    2.5  2  FixQ           Cbb3-type cytochrome oxidase component FixQ


Domain annotation for each model (and alignments):
>> DUF131  Protein of unknown function DUF131
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   2.0      0.49   8.8e+02      46      60 ..      13      27 ..       6      30 .. 0.71
   2 !   53.3  13.5   8.8e-18   1.6e-14       2      61 ..      24      79 ..      19      84 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.49
                            DUF131 46 taiiLaIilmillli 60
                                      ++++++Ii+++ +++
  gi|385806419|ref|YP_005842817.1| 13 LLVFIGIIVIMGAFL 27
                                      467888887765555 PP

  == domain 2  score: 53.3 bits;  conditional E-value: 8.8e-18
                            DUF131  2 gvvlkalekeeeeaekeesrvkgGGVvliGPIPIiFGsdkrlaktaiiLaIilmilllil 61
                                      g++l +     +++ +++s+v+gGG+++iGPIPIiFGs+k+++k ++i+a+++ ++l+++
  gi|385806419|ref|YP_005842817.1| 24 GAFLYMF----MKSPSSSSEVQGGGIIFIGPIPIIFGSSKNITKSLLIVAMVISLVLIVV 79
                                      4445555....4899*************************99999999999988887775 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   7.4   0.00011       0.2      70     148 ..       5      83 ..       2      90 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00011
                           DUF2070  70 rslflalltelivviisllaillsallqalvllalvlslalvfalrllvlvavsdesllkavlpaliqpllailllv 146
                                       rsl+   + ++++ ii++++++l++++++ ++ + v +  ++f+ ++ +++  s++ ++  +++a++++l++i++++
  gi|385806419|ref|YP_005842817.1|   5 RSLLSIGFLLVFIGIIVIMGAFLYMFMKSPSSSSEVQGGGIIFIGPIPIIFGSSKNITKSLLIVAMVISLVLIVVYI 81 
                                       677777788889999999999999888888888889999***********************************999 PP

                           DUF2070 147 ly 148
                                       l 
  gi|385806419|ref|YP_005842817.1|  82 LS 83 
                                       86 PP

>> Orf78  Orf78 (ac78)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.015        28      69      89 ..      12      32 ..       3      44 .. 0.74
   2 ?    6.7   2.7    0.0048       8.6      59      85 ..      58      84 ..      54      86 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.015
                             Orf78 69 sllavvcvlvllyviyYfvil 89
                                       ll+++ ++v++ + +Y ++ 
  gi|385806419|ref|YP_005842817.1| 12 FLLVFIGIIVIMGAFLYMFMK 32
                                      367888999999999998765 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0048
                             Orf78 59 kaqalnillisllavvcvlvllyviyY 85
                                      ++++++ lli+++++  vl+++y++++
  gi|385806419|ref|YP_005842817.1| 58 SKNITKSLLIVAMVISLVLIVVYILSF 84
                                      467788899999999999999999987 PP

>> Baculo_11_kDa  Baculovirus 11 kDa family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1    0.0044       7.9      38      61 ..       8      32 ..       3      41 .. 0.54
   2 ?    6.7   2.0     0.003       5.3      35      54 ..      63      82 ..      57      86 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0044
                     Baculo_11_kDa 38 Lvicglvvfvvivlfi.lLlvvilk 61
                                      L i+ l+vf+ i++ +  +l++ +k
  gi|385806419|ref|YP_005842817.1|  8 LSIGFLLVFIGIIVIMgAFLYMFMK 32
                                      4455556666333333145555554 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.003
                     Baculo_11_kDa 35 dFvLvicglvvfvvivlfil 54
                                        +L+++ ++ +v+iv++il
  gi|385806419|ref|YP_005842817.1| 63 KSLLIVAMVISLVLIVVYIL 82
                                      55788888888888888875 PP

>> TssO  Type VI secretion system, TssO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00021      0.38       4      43 ..       3      41 ..       2      43 .. 0.88
   2 ?   -0.5   0.5      0.67   1.2e+03      17      30 ..      66      79 ..      57      88 .. 0.46

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00021
                              TssO  4 kErrsgflyflllFlvtvlllflivffffkssplqekeil 43
                                      +Er    + fll+F+ ++++++ ++++f k sp +++e++
  gi|385806419|ref|YP_005842817.1|  3 DERSLLSIGFLLVFIGIIVIMGAFLYMFMK-SPSSSSEVQ 41
                                      678888899*******************99.999988875 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.67
                              TssO 17 Flvtvlllflivff 30
                                      ++v+++++ +++  
  gi|385806419|ref|YP_005842817.1| 66 LIVAMVISLVLIVV 79
                                      23333333222222 PP

>> DUF1461  Protein of unknown function (DUF1461)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   4.0   0.00059       1.1      86     150 ..       1      78 [.       1      87 [. 0.63

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00059
                           DUF1461  86 maDVkkLfllglivrlvtlillvllllllivlkkkkkkir..............llk.skslllavilllliliilg 147
                                       m D + L++ g++++++ +i+++ ++l++++++ ++++ +              ++  sk+++ ++++ ++++i l+
  gi|385806419|ref|YP_005842817.1|   1 MIDERSLLSIGFLLVFIGIIVIMGAFLYMFMKSPSSSS-EvqgggiifigpipiIFGsSKNITKSLLI-VAMVISLV 75 
                                       677899***********999998888888877777333.23688888777777533344444444444.33333333 PP

                           DUF1461 148 lla 150
                                       l++
  gi|385806419|ref|YP_005842817.1|  76 LIV 78 
                                       322 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 ?    7.8   0.5    0.0022         4      17      38 ..       7      33 ..       5      41 .. 0.64
   2 ?    3.7   1.9     0.043        76      10      31 ..      63      84 ..      58      91 .] 0.46

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0022
                       Sigma_reg_N 17 lislivlllifvilvvtllyl.....a 38
                                      l+s+++ll+++ i+v+ +++l     +
  gi|385806419|ref|YP_005842817.1|  7 LLSIGFLLVFIGIIVIMGAFLymfmkS 33
                                      789999999999995444443345443 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.043
                       Sigma_reg_N 10 ksilrivlislivlllifvilv 31
                                      ks+l +++++ +vl++++++++
  gi|385806419|ref|YP_005842817.1| 63 KSLLIVAMVISLVLIVVYILSF 84
                                      4444444433333333333333 PP

>> DUF4083  Domain of unknown function (DUF4083)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.7    0.0068        12       7      33 ..      12      38 ..       8      42 .. 0.57
   2 ?    4.9   3.4     0.014        24      13      31 ..      65      83 ..      60      87 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0068
                           DUF4083  7 yliivivLilllvfsftlfiRrvvsrs 33
                                      +l++ i++i+ +   +++f+ + +s+s
  gi|385806419|ref|YP_005842817.1| 12 FLLVFIGIIVIMGAFLYMFMKSPSSSS 38
                                      344445555444444467777766665 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.014
                           DUF4083 13 vLilllvfsftlfiRrvvs 31
                                      +Li+++v+s++l++ +++s
  gi|385806419|ref|YP_005842817.1| 65 LLIVAMVISLVLIVVYILS 83
                                      4677777777776666654 PP

>> DUF3784  Domain of unknown function (DUF3784)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   3.1     0.045        81      46      65 ..      10      29 ..       2      40 .. 0.65
   2 ?    9.6   5.4   0.00056         1      45      89 ..      40      84 ..      35      88 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.045
                           DUF3784 46 mgivllligilflllgllsa 65
                                      +g +l++igi+ ++ ++l +
  gi|385806419|ref|YP_005842817.1| 10 IGFLLVFIGIIVIMGAFLYM 29
                                      57777778866666666633 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00056
                           DUF3784 45 fmgivllligilflllgllsaiesealliiali.viiiiviylivy 89
                                        g ++++ig + +++g  ++  +++lli+a++  +++iv+y++ +
  gi|385806419|ref|YP_005842817.1| 40 VQGGGIIFIGPIPIIFGSSKN-ITKSLLIVAMViSLVLIVVYILSF 84
                                      568899*************55.555555555551555555555544 PP

>> FixQ  Cbb3-type cytochrome oxidase component FixQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   5.1      0.71   1.3e+03      17      27 ..      11      21 ..       5      35 .. 0.57
   2 ?    9.5   0.2   0.00051      0.92      11      30 ..      63      82 ..      59      83 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.71
                              FixQ 17 flvllfygvvi 27
                                       ++l+f+g+++
  gi|385806419|ref|YP_005842817.1| 11 GFLLVFIGIIV 21
                                      34455555443 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00051
                              FixQ 11 dswgllflvllfygvviyaf 30
                                      +s++++++v+ ++ +v+y++
  gi|385806419|ref|YP_005842817.1| 63 KSLLIVAMVISLVLIVVYIL 82
                                      7999**************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1339  (0.0746835); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.48u 0.33s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 587.27
//
Query:       gi|385806420|ref|YP_005842818.1|  [L=215]
Description: hypothetical protein FFONT_1378 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.074   12.9   0.0       0.15   11.9   0.0    1.5  1  DAO_C     C-terminal domain of alpha-glycerophosphate oxidase


Domain annotation for each model (and alignments):
>> DAO_C  C-terminal domain of alpha-glycerophosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   8.4e-06      0.15      30      75 ..      17      72 ..       5      76 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.4e-06
                                      HHHHHHHHHHHGGGHHHHHHHHHHTH.............HHHHHTTS-HHHHHHHH CS
                             DAO_C 30 eevaehLaerYGsraeevlelakedekp..........elaerlspelpyieaevv 75
                                       ++++ L+ +YGs+aeev+  a++++++             +    +++ +e ev+
  gi|385806420|ref|YP_005842818.1| 17 YDRVKMLLLNYGSKAEEVMLAALKRAEEldangngfrfGDFDFKGLKEKLTEMEVK 72
                                      57899*************95555554446666666655444444445555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.49
# Mc/sec: 1309.29
//
Query:       gi|385806421|ref|YP_005842819.1|  [L=98]
Description: hypothetical protein FFONT_1379 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-07   29.6   1.3    6.3e-07   29.3   1.3    1.1  1  TRAM      TRAM domain
     0.0035   17.1   0.0     0.0039   16.9   0.0    1.2  1  DUF3016   Protein of unknown function (DUF3016)
  ------ inclusion threshold ------
      0.016   15.6   0.7        2.8    8.3   0.2    2.3  2  S1        S1 RNA binding domain
      0.021   15.0   0.2      0.063   13.5   0.1    1.8  2  CSD2      Cold shock 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 !   29.3   1.3   1.4e-10   6.3e-07       3      62 .]      37      93 ..      35      93 .. 0.92

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 1.4e-10
                                      XXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T...TEEEEEEEEEE-SSEEEEEEE CS
                              TRAM  3 yvGstqeVlveglsksegegiGrtdngkvvfvpgdlpg.IGdfVeVkItkvkrqyLrGell 62
                                        Gs++++++ + +  +g g+G+ +   v+ v+g+  g +Gd+V VkIt+ + + + ++++
  gi|385806421|ref|YP_005842819.1| 37 RPGSEITIEIRDID-EKGRGVGYYN-RTVIRVNGG--GtVGDKVRVKITERRDNEAYADIV 93
                                      57************.**********.********8..337**************9999986 PP

>> DUF3016  Protein of unknown function (DUF3016)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   8.8e-07    0.0039      11      64 ..       2      54 ..       1      82 [. 0.90

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 8.8e-07
                           DUF3016 11 ekfrDvkesnesrerarervlaeLeealeklaekaLpegqkLevevtDvdlAGd 64
                                       k+rD k +  +r+ +r++v  ++ +  e +a++ L++g ++++e+ D+d  G+
  gi|385806421|ref|YP_005842819.1|  2 TKYRDHK-EVYTRDYSRWSVYPKIPKPEEYQAQEKLRPGSEITIEIRDIDEKGR 54
                                      689**99.8889999***********************************8876 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0    0.0044        20      44      70 ..      30      56 ..      18      59 .. 0.87
   2 ?    8.3   0.2   0.00063       2.8      51      70 ..      71      90 ..      60      92 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0044
                                      SCHHHCEETTEEEEEEEEEEETTTTEE CS
                                S1 44 edpdevlkvGdevkvkvlkvdkdrrri 70
                                      ++  e+l++G e+  ++ ++d++ r++
  gi|385806421|ref|YP_005842819.1| 30 YQAQEKLRPGSEITIEIRDIDEKGRGV 56
                                      577899****************98865 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00063
                                      ETTEEEEEEEEEEETTTTEE CS
                                S1 51 kvGdevkvkvlkvdkdrrri 70
                                      +vGd+v+vk+++ +++++++
  gi|385806421|ref|YP_005842819.1| 71 TVGDKVRVKITERRDNEAYA 90
                                      69*********998888766 PP

>> CSD2  Cold shock domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.29   1.3e+03      21      38 ..      34      51 ..      20      66 .. 0.69
   2 ?   13.5   0.1   1.4e-05     0.063      21      50 ..      68      96 ..      57      98 .] 0.81

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.29
                              CSD2 21 kgakdGdkVvveiteypd 38
                                      ++++ G  + +ei + ++
  gi|385806421|ref|YP_005842819.1| 34 EKLRPGSEITIEIRDIDE 51
                                      346667777777777654 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 1.4e-05
                              CSD2 21 kgakdGdkVvveiteypdkknpeGevievL 50
                                      +g   GdkV v+ite+ d +++ + ++e L
  gi|385806421|ref|YP_005842819.1| 68 GGGTVGDKVRVKITERRD-NEAYADIVEWL 96
                                      56788**********977.4599*999977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.35s 00:00:00.89 Elapsed: 00:00:00.55
# Mc/sec: 531.90
//
Query:       gi|385806422|ref|YP_005842820.1|  [L=260]
Description: hypothetical protein FFONT_1380 [Fervidicoccus fontis Kam940]
Scores for complete 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-88  294.4   6.2    6.1e-88  294.2   6.2    1.0  1  DUF2192        Uncharacterized protein conserved in archaea (
  ------ inclusion threshold ------
      0.037   13.9   0.2       0.25   11.2   0.0    2.1  2  HEPN-like_int  HEPN-like integron domain
      0.037   13.8   0.6       0.16   11.8   0.6    2.1  1  SHOCT          Short C-terminal domain
      0.088   12.9   0.1       0.34   11.0   0.1    2.0  1  DUF1707        Domain of unknown function (DUF1707)
       0.19   12.0   0.8        1.3    9.3   0.1    2.3  2  CdiA_C         Contact-dependent growth inhibition CdiA C-ter


Domain annotation for each model (and alignments):
>> DUF2192  Uncharacterized protein conserved in archaea (DUF2192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  294.2   6.2   1.7e-91   6.1e-88       1     229 []       9     239 ..       9     239 .. 0.98

  Alignments for each domain:
  == domain 1  score: 294.2 bits;  conditional E-value: 1.7e-91
                           DUF2192   1 kelykkrievlvdllsklleeekltReelvellkkvYeekgiePlrGlskPediYdkElatlYvvgkyGlgleeelk 77 
                                       k++y+k+++v++d+ls++le+ +++Ree++ell+k+Y+e++i+P+rG++ P+diYdkElatlYv+gkyG+g++ +++
  gi|385806422|ref|YP_005842820.1|   9 KKVYRKKVSVAIDVLSEALERGEISREEMAELLRKKYRENKISPFRGIALPSDIYDKELATLYVIGKYGMGVMYDYP 85 
                                       689************************************************************************** PP

                           DUF2192  78 elfdkifsvEekleealeiilskkkeeavekvkevl..gkidenkvarvlrlvltkvvlgfadeeelikllrkleea 152
                                       e+f+++fs+E+++e+a+e++ s+ ++e+++k+++ +  g  ++n+var+lr+++tkv++gfa+e+el++l++++++a
  gi|385806422|ref|YP_005842820.1|  86 EFFESVFSKEMEYERAIEVLSSDASDEEKRKIVSGIfgGIPSSNDVARMLRIAFTKVIFGFAEEKELLDLFSAIKRA 162
                                       ***********************9999999999888889999*********************************** PP

                           DUF2192 153 fpelektvkkyarfyiAfkiaekiaegeirnrlekealkkalalrlgiekalPsdeyiaeiakevfkvpkkvlkkvl 229
                                       +pe+ek+v+++arfyi+fkiaeki+ gei++r+ekea+k+a++l++++ +++P+d+yi++ia++vfkvp+++l++vl
  gi|385806422|ref|YP_005842820.1| 163 LPECEKDVSNFARFYIGFKIAEKITIGEIKSRVEKEATKQAMNLSVNLGMNMPDDKYIYVIARKVFKVPEEILERVL 239
                                       ***************************************************************************97 PP

>> HEPN-like_int  HEPN-like integron domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1      0.19   6.8e+02      68     107 ..      15      54 ..      10      66 .. 0.65
   2 ?   11.2   0.0   6.9e-05      0.25      48      98 ..     128     177 ..     116     187 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.19
                     HEPN-like_int  68 klsEliEkkdrlltslpiElakelke.lkkkffledikeyR 107
                                       k+s +i++    l+   i +++e+ e l+kk+  + i  +R
  gi|385806422|ref|YP_005842820.1|  15 KVSVAIDVLSEALERGEI-SREEMAElLRKKYRENKISPFR 54 
                                       555555555555554443.4666665257888888888887 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 6.9e-05
                     HEPN-like_int  48 lvayvalsrvalsnliigifklsEliEkkdrlltslpiElakelkelkkkf 98 
                                        + ++ + r+a+ ++i g     El++ +  +   lp E +k++ ++ + +
  gi|385806422|ref|YP_005842820.1| 128 SNDVARMLRIAFTKVIFGFAEEKELLDLFSAIKRALP-ECEKDVSNFARFY 177
                                       56667788*****************************.*********9877 PP

>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.6   4.3e-05      0.16       2      19 ..      19      36 ..      19      36 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.3e-05
                             SHOCT  2 aLekLkeLyarGeIteEE 19
                                      a++ L e ++rGeI++EE
  gi|385806422|ref|YP_005842820.1| 19 AIDVLSEALERGEISREE 36
                                      6899*************9 PP

>> DUF1707  Domain of unknown function (DUF1707)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   9.4e-05      0.34      11      34 ..      19      42 ..      17      46 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9.4e-05
                           DUF1707 11 avelLrealaeGrLtldEfdeRle 34
                                      a+++L+eal++G ++ +E+ e l 
  gi|385806422|ref|YP_005842820.1| 19 AIDVLSEALERGEISREEMAELLR 42
                                      899****************99776 PP

>> CdiA_C  Contact-dependent growth inhibition CdiA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0       0.2   7.1e+02      44      66 ..      27      49 ..       2      57 .. 0.71
   2 ?    9.3   0.1   0.00036       1.3      25      78 ..     191     244 ..     180     246 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.2
                            CdiA_C 44 lrdsdlsieeikegieralkwpk 66
                                      l++ ++s ee++e ++++++ +k
  gi|385806422|ref|YP_005842820.1| 27 LERGEISREEMAELLRKKYRENK 49
                                      45778889999999999877655 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00036
                            CdiA_C  25 iisnilkkakkQaknivlnlrdsdls.ieeikegieralkwpkkglkeliiikkd 78 
                                       i s++ k a kQa n  +nl   +++ ++ i  ++++++k p+++l++++ +k  
  gi|385806422|ref|YP_005842820.1| 191 IKSRVEKEATKQAMNLSVNLG-MNMPdDKYIYVIARKVFKVPEEILERVLSVKER 244
                                       55677788888**********.777746777777777788888999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       887  (0.0494729); expected 358.6 (0.02)
Passed bias filter:                      641  (0.0357521); 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: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 1495.47
//
Query:       gi|385806423|ref|YP_005842821.1|  [L=293]
Description: hypothetical protein FFONT_1381 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       219  (0.0122148); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.59u 0.34s 00:00:00.93 Elapsed: 00:00:00.56
# Mc/sec: 1573.47
//
Query:       gi|385806424|ref|YP_005842822.1|  [L=140]
Description: hypothetical protein FFONT_1382 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------

   [No hits detected that satisfy 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:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); 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):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.34s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 779.59
//
Query:       gi|385806425|ref|YP_005842823.1|  [L=419]
Description: asparaginyl-tRNA synthetase [Fervidicoccus fontis Kam940]
Scores for 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-89  298.8   0.1    4.8e-89  298.5   0.1    1.0  1  tRNA-synt_2      tRNA synthetases class II (D, K and N)
    8.6e-12   44.9   2.1    1.5e-11   44.1   2.1    1.4  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
     0.0042   16.6   0.2       0.25   10.8   0.0    2.3  2  tRNA-synt_2d     tRNA synthetases class II core domain (F)


Domain annotation for each model (and alignments):
>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  298.5   0.1     8e-93   4.8e-89       3     313 ..     101     413 ..      99     414 .. 0.95

  Alignments for each domain:
  == domain 1  score: 298.5 bits;  conditional E-value: 8e-93
                                       CHHHHTHHHHCCSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE....-E CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xx RF
                       tRNA-synt_2   3 elrlknryldlrtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeff....aL 75 
                                       e++l+nr+l lr+  + +v+++++t++k++r++ +++g+ e+++Pi+++s++e+ga+lFkv       ++f    +L
  gi|385806425|ref|YP_005842823.1| 101 EFLLDNRHLWLRSTYLTNVMKVKHTALKLLREFHTQEGWWEVTPPIITSSAVEGGATLFKV-------DYFgepaYL 170
                                       7899*********************************************************.......78888889* PP

                                       -S-SHHHHHHHHHCTHSEEEEEEEEE--S--BTTB-S-CEEEEEEEEET-SCHHHHHHHHHHHHHHHHHHHHCSCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  76 tqspqlylellivagidrvfqiaraFRaEdsrtdrhlaEFtqieaemsfieeedimqvleelikslvkevlessakd 152
                                        qs q+yle+li + +++vf ++++FRaE+srt+rhl+E++++e+e +++++e++m+++e+ ++++v++++++ +k+
  gi|385806425|ref|YP_005842823.1| 171 SQSAQFYLEVLIYS-LEKVFALTPSFRAEKSRTRRHLSEYYHFEIEGAWMDMEELMKFTERTVEYVVQNLIDERQKE 246
                                       **************.*********************************************************99999 PP

                                       CCHTTTTTS..EE-SSS-EEEEHHHHHHHHHTS......-SS--HHHHHHHHHHS--SEEEEEEEBGGGSTTCBBBS CS
                                       xxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 153 iefvirrns..kdlkkpfkrltykeaieklnei......gkdldkaderalvkkeknepvfvtdfPaelkpFyarke 221
                                       +e   r  +  k +k+pf+r+ty++aie l+++      g+d   ade a+++k   +p+fvt+fP+++kpFy++ +
  gi|385806425|ref|YP_005842823.1| 247 LEDLGRDIEslKRVKAPFERITYTKAIEFLKQNgvniewGNDY-GADEEAMLTKLFDRPFFVTHFPKTIKPFYMKVD 322
                                       999988877889******************9997777663333.4677778888*********************** PP

                                       TTSTTBBSEEEEEET.TE.EEEEEEEB--SHHHHHHHHHHCCHHSSSGGGGHHHHHHHHCT--SEEEEEEEHHHHHH CS
                                       xxxxxxxxxxxxxxx.xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 222 eddkkltesyDllin.gv.ElvgGslRiedpeeleeklkskgldeeaeekfswylealeyGapphgGlglGldRlvm 296
                                       e+d+++++++Dll + g+ E++gGs+R++++++l +++ ++g+d   ++ ++wyl++++yG++ph+G+glG++Rlvm
  gi|385806425|ref|YP_005842823.1| 323 ENDERVVKGFDLLAPeGYgEIIGGSQREDSYDVLLKRIVEQGYD---PKDYYWYLDLRKYGSVPHSGYGLGIERLVM 396
                                       **************9889**************************...****************************** PP

                                       HHCT-SSGGGCSSS-XX CS
                                       xxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 297 lllgsesIrdviaFPkl 313
                                       +++g+e+Ird+i+FP+ 
  gi|385806425|ref|YP_005842823.1| 397 WVAGLEHIRDAIPFPRF 413
                                       ***************95 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   2.1   2.6e-15   1.5e-11       1      73 [.       7      83 ..       7      86 .. 0.95

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 2.6e-15
                                      EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET....HHHHHHHTTS-TTSEEEEEEEEEEC...TTSSEEEEEEE CS
                   tRNA_anti-codon  1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfr....eeatklaenlkeGdvvrvtGrvkrr...pggelelkvee 72
                                      V+++G+++++   + gk ifi +rD +g iq+v+      +e+++ +e  k+++ v v+G+++++   pgg  e++v+e
  gi|385806425|ref|YP_005842823.1|  7 VSIRGWIHRK--FQVGKKIFIRVRDSSGVIQCVIEEgvvgKEKFNEFEGAKRESSVVVSGKLRTDeraPGG-KEMYVSE 82
                                      89********..*****************************************************999999.9999987 PP

                                      E CS
                   tRNA_anti-codon 73 i 73
                                       
  gi|385806425|ref|YP_005842823.1| 83 G 83
                                      5 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 !    3.2   0.1    0.0084        50     103     155 ..     187     242 ..     184     247 .. 0.81
   2 !   10.8   0.0   4.2e-05      0.25     209     233 ..     382     406 ..     375     410 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.0084
                                       EEEEEEEEEBSST.-SSSB-SEEE..EEEEEEEETT--HHHHHHHHHHHHHHHCTS CS
                      tRNA-synt_2d 103 kiisigrvfRrda.vDathlaeFh..qveglvvdenvsladlkgvleellkklfga 155
                                       k++++   fR ++   ++hl e++   +eg ++d +  ++    ++e ++++l ++
  gi|385806425|ref|YP_005842823.1| 187 KVFALTPSFRAEKsRTRRHLSEYYhfEIEGAWMDMEELMKFTERTVEYVVQNLIDE 242
                                       78899999****978899999986336999***99988888888888888888655 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 4.2e-05
                                       SEEEEEEEEHHHHHHHHHT-SSGHH CS
                      tRNA-synt_2d 209 vsgfafGlGveRlamlkygieDiRe 233
                                       v+  ++GlG+eRl m   g+e iR+
  gi|385806425|ref|YP_005842823.1| 382 VPHSGYGLGIERLVMWVAGLEHIRD 406
                                       566789******************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); expected 358.6 (0.02)
Passed bias filter:                      660  (0.0368119); 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: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.49
# Mc/sec: 2588.55
//
Query:       gi|385806426|ref|YP_005842824.1|  [L=211]
Description: putative ATP binding protein [Fervidicoccus fontis Kam940]
Scores for complete 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-47  160.1   0.0    6.6e-47  159.8   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 !  159.8   0.0   3.7e-51   6.6e-47      23     218 ..       8     203 ..       2     204 .. 0.97

  Alignments for each domain:
  == domain 1  score: 159.8 bits;  conditional E-value: 3.7e-51
                   Diphthami_syn_2  23 esevesLvsvisenkesymfhvvnvhlvellaesvGiplikletaGeeekevedLkgtlkkldveavviGaieseyq 99 
                                        +e++s+ s+ +++++s  fh +  +++++  e+ Gipl  le +G+e ++ ++L  + k  ++e vv+Ga++s+yq
  gi|385806426|ref|YP_005842824.1|   8 GFEISSFCSIAPKEEDSMLFHYPATRFLKVFEEAYGIPLLLLEGSGDEMEDLRNLLSECKSEGIEYVVSGALASDYQ 84 
                                       5899*******************************************999999999999999*************** PP

                   Diphthami_syn_2 100 ksriervCrelGlksvaPLWkkdpeelleeiveekfevivvavkaegldeslLGrridkklidelkklsekygidka 176
                                       + r   v +elGlk++ PLW+kd +e+++  +e +fe i+v ++  gl  +lLG+ i+ +    + +l+ekyg ++a
  gi|385806426|ref|YP_005842824.1|  85 RIRYSIVAEELGLKTLNPLWRKDQKEYMKWLIEGGFEYIIVKISSFGLPFDLLGKTITYEDTLRIISLAEKYGFNPA 161
                                       ***************************************************************************** PP

                   Diphthami_syn_2 177 gegGeaetlvlDaPlfkkrlevkelekkwderrgyldierak 218
                                       +egGeaetlvlDaPl kkrlev+  ++ +++   y+di+ +k
  gi|385806426|ref|YP_005842824.1| 162 FEGGEAETLVLDAPLMKKRLEVEGERRIEGNYVAYYDIRNIK 203
                                       *************************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.52
# Mc/sec: 1218.12
//
Query:       gi|385806427|ref|YP_005842825.1|  [L=142]
Description: S-adenosylmethionine decarboxylase [Fervidicoccus fontis Kam940]
Scores for complete 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  108.7   0.0      2e-31  108.4   0.0    1.1  1  AdoMet_dc  S-adenosylmethionine decarboxylase


Domain annotation for each model (and alignments):
>> AdoMet_dc  S-adenosylmethionine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.4   0.0   1.1e-35     2e-31       1     105 [.      23     130 ..      23     131 .. 0.97

  Alignments for each domain:
  == domain 1  score: 108.4 bits;  conditional E-value: 1.1e-35
                                       EEEEEEES--HHHCTSHHHHHHHHHHHHHHCT-EEEEEEEEE-..SSS-EEEEEEETTEEEEEEEEGGGTEEEEEEE CS
                         AdoMet_dc   1 hllvdlygcdpelledaelleqilteaaeaigatvlsvafhkf..epeGvsvvvliaeShlsiHtwpetgyaaiDvf 75 
                                       h++ +ly++dp++l d+e +++i+ ea+++++at+ +v +++f  +++Gvsv++l+ eShl+iHtw e++ya++D++
  gi|385806427|ref|YP_005842825.1|  23 HVYGNLYDMDPKILGDEEYIRNIMLEAVKKANATLFDVRSWSFpgKKGGVSVLILVLESHLAIHTWTEYRYATLDIY 99 
                                       999****************************************87778***************************** PP

                                       EEST.HHHHHHHHHHHHHHT-SEEEEEEEEE CS
                         AdoMet_dc  76 tcge.ispekaleylieafkadrvtvdelkR 105
                                       tcg  ++pe+a+++++e++++++v  +++ R
  gi|385806427|ref|YP_005842825.1| 100 TCGPhTHPEAAFDFVVEKLNPKKVVKHKTFR 130
                                       ************************9988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); 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 0.30s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 851.04
//
Query:       gi|385806428|ref|YP_005842826.1|  [L=195]
Description: Rossmann fold nucleotide-binding protein-like protein [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.7e-15   55.5   0.0    5.9e-15   55.2   0.0    1.1  1  LDcluster4  SLOG cluster4 family


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 !   55.2   0.0   3.3e-19   5.9e-15      16     156 ..      16     166 ..       2     167 .. 0.70

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 3.3e-19
                        LDcluster4  16 eealelaeelGrliAke......gavlltGgrtGvmeaaskGakeagGltvGilpa.ssekehsnkyvdiiiyTGlg 85 
                                       e+++++a e   ++ ++      ++ ll Gg  G+m++a   a ++ Gl v + p  + e++   +   i+i TG+ 
  gi|385806428|ref|YP_005842826.1|  16 EDHRKKAIEFVDEVYQRsvsegiEVYLLLGGYWGIMKVAVDEAIRK-GLKVILFPPlERESDVDYPKEAILIRTGMS 91 
                                       444555555555555542222224689*************998766.5555555551555554555779******** PP

                        LDcluster4  86 lagRnlilvlssdvviaiggrsGTlsEialaleegkpvivlkgt...dellseiiek.kekderkvivaespkel 156
                                       + gR++  v+ss+v+ ++gg+sGT  E  +a+ eg pv vl++    +++l+ +     e++++++ + e+pk++
  gi|385806428|ref|YP_005842826.1|  92 MRGRSIPFVRSSEVLAVLGGSSGTFLEAIVAYAEGIPVFVLSNLglpTDELKALSPYiDERRSTEIKIFEEPKKM 166
                                       ******************************************768884444444333033333378888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); 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: 0.59u 0.38s 00:00:00.97 Elapsed: 00:00:00.58
# Mc/sec: 1005.70
//
Query:       gi|385806429|ref|YP_005842827.1|  [L=81]
Description: hypothetical protein FFONT_1387 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 476.84
//
Query:       gi|385806430|ref|YP_005842828.1|  [L=40]
Description: hypothetical protein FFONT_1388 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                        83  (0.00462937); expected 358.6 (0.02)
Passed bias filter:                       79  (0.00440627); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.32s 00:00:00.78 Elapsed: 00:00:00.50
# Mc/sec: 239.88
//
Query:       gi|385806431|ref|YP_005842829.1|  [L=45]
Description: hypothetical protein FFONT_1389 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.024   13.7   0.0      0.024   13.7   0.0    1.0  1  DUF4071   Domain of unknown function (DUF4071)


Domain annotation for each model (and alignments):
>> DUF4071  Domain of unknown function (DUF4071)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.3e-06     0.024     276     306 ..       9      39 ..       3      42 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.3e-06
                           DUF4071 276 rkigvvLnnllgrkgsleslqdYWdvatfle 306
                                       ++i   L+nl+ +k+++  +++YW  a +++
  gi|385806431|ref|YP_005842829.1|   9 QEIINFLKNLISKKIRVCFISSYWRLALYMQ 39 
                                       678889***********************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); 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: 0.50u 0.33s 00:00:00.83 Elapsed: 00:00:00.52
# Mc/sec: 259.10
//
Query:       gi|385806432|ref|YP_005842830.1|  [L=98]
Description: hypothetical protein FFONT_1390 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       972  (0.0542138); 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:                         0  (0); expected 0.2 (1e-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 0.35s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 542.62
//
Query:       gi|385806433|ref|YP_005842831.1|  [L=262]
Description: silent information regulator protein Sir2 [Fervidicoccus fontis Kam940]
Scores for complete 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-49  168.0   0.0    2.8e-49  167.4   0.0    1.2  1  SIR2           Sir2 family
     0.0064   16.6   2.0      0.008   16.3   0.3    2.0  2  zf-RING_7      C4-type zinc ribbon domain
  ------ inclusion threshold ------
      0.012   15.7   0.1      0.027   14.6   0.1    1.6  1  CxC7           CxC7 like cysteine cluster associated with KDZ
      0.083   12.9   0.0       0.17   11.9   0.0    1.5  1  HypA           Hydrogenase/urease nickel incorporation, metal
       0.11   12.7   0.6       0.19   11.9   0.1    1.6  2  DUF2250        Uncharacterized protein conserved in archaea (
       0.13   12.0   0.9        1.1    9.1   0.0    2.2  2  zinc_ribbon_2  zinc-ribbon domain


Domain annotation for each model (and alignments):
>> SIR2  Sir2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.4   0.0   9.4e-53   2.8e-49       1     177 []      23     199 ..      23     199 .. 0.94

  Alignments for each domain:
  == domain 1  score: 167.4 bits;  conditional E-value: 9.4e-53
                                       -GGGGGGGT---SSSTTSHHHHSCHHHHSSHHHHHHHHHHHHHHHHHHHHHHHCCTSS--HHHHHHHHHHHTTCEEE CS
                              SIR2   1 GAGiStesGipdfRskeGlyaklakeelaspealfskkllveevfyniarellaeeaepnaaHkalkklekkgkllr 77 
                                       GAG StesG+pdfR+ +Gl++++ +e + + + + ++++  ++++ + + ++++ +a pn aH ++++le+ g + +
  gi|385806433|ref|YP_005842831.1|  23 GAGASTESGVPDFRGPQGLWKRIPPE-VFDIDLFYRDPEYSWRIYAEYVYSQIS-RASPNRAHIVIAELESLGLVEA 97 
                                       9*********************9876.6999************88888877777.7********************* PP

                                       EEES-SSSHHHHTT-SSEEETTEEEEEEEETTTSBEEECCGG.HCHHHCCTT.B-TTTCCBEEEEE--CTSB-S.HH CS
                              SIR2  78 liTQNiDgLekkaGskkvvelHGslakakcvkcekkldkeel.qeeieaekvpecekcgkllkpdvvfFGealp.dk 152
                                       +iTQNiD+L++kaGskkv+elHG+  k++c +c+ + d ++  ++ i++++vp+c+kcg++lkp vv+FGe lp ++
  gi|385806433|ref|YP_005842831.1|  98 VITQNIDKLHQKAGSKKVIELHGTYDKVQCLRCGFHGDIKDFiEDFIREKRVPRCPKCGRILKPAVVYFGEPLPsEE 174
                                       ************************************99877615568999*************************** PP

                                       HHHHHHHHHH-SEEEEES--STSTT CS
                              SIR2 153 lkkliekveeadlllviGtSlkVap 177
                                       l+++++ +++  l++v+G+Sl+V+p
  gi|385806433|ref|YP_005842831.1| 175 LSSAFSLAKSSKLIIVVGSSLSVYP 199
                                       ***********************98 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       1.7     5e+03      16      30 ..     117     131 ..     113     131 .. 0.70
   2 !   16.3   0.3   2.7e-06     0.008      18      33 .]     145     159 ..     139     159 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.7
                                       HHCCS.TB-EE-TTT- CS
                         zf-RING_7  16 elrag.devvtCpeCG 30 
                                       el+++ d+ v+C  CG
  gi|385806433|ref|YP_005842831.1| 117 ELHGTyDK-VQCLRCG 131
                                       66666666.8888887 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 2.7e-06
                                       CCSTB-EE-TTT--EE CS
                         zf-RING_7  18 ragdevvtCpeCGRIL 33 
                                       r +  v++Cp CGRIL
  gi|385806433|ref|YP_005842831.1| 145 REK-RVPRCPKCGRIL 159
                                       555.79*********9 PP

>> CxC7  CxC7 like cysteine cluster associated with KDZ transposases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   9.2e-06     0.027       3      38 ..     137     167 ..     135     171 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.2e-06
                              CxC7   3 srfsedykkefrvPfsliecsecgdifkdspvGyvG 38 
                                       + f ed+ +e rvP    +c++cg+i k + v y G
  gi|385806433|ref|YP_005842831.1| 137 KDFIEDFIREKRVP----RCPKCGRILKPA-VVYFG 167
                                       5799**********....7*********98.66766 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   5.8e-05      0.17      43      94 ..      98     157 ..      67     164 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.8e-05
                                       HHHHHHHHHHCC.TTTT-EEEEEEE--EEEETTTS-EEECHHHHH..........S-TTTSS CS
                              HypA  43 aLefafellaegtvlegaeLeieevpvkvrCreCgkefeleekal..........rCpkCgs 94 
                                       ++++  + l+++   +++++e++ +  kv+C +Cg ++++++  +          rCpkCg+
  gi|385806433|ref|YP_005842831.1|  98 VITQNIDKLHQKA-GSKKVIELHGTYDKVQCLRCGFHGDIKDF-IedfirekrvpRCPKCGR 157
                                       4555555554443.33477888899999**********98863.12358899999*****97 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   6.2e-05      0.19      33      79 ..      76     122 ..      64     127 .. 0.85
   2 ?   -2.7   0.0       2.2   6.7e+03      37      38 ..     241     242 ..     224     259 .. 0.49

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.2e-05
                           DUF2250  33 eipleevrellkkLeelGLlervegktikrteaklKkksevhkhHtY 79 
                                       +++ ++++ ++ +Le+lGL+e v  + i + ++k+  k++   h tY
  gi|385806433|ref|YP_005842831.1|  76 RASPNRAHIVIAELESLGLVEAVITQNIDKLHQKAGSKKVIELHGTY 122
                                       556667788999************************99999999999 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.2
                           DUF2250  37 ee 38 
                                       e+
  gi|385806433|ref|YP_005842831.1| 241 EK 242
                                       22 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.2      0.12   3.6e+02      15      22 ..     126     133 ..     123     134 .. 0.76
   2 ?    9.1   0.0   0.00036       1.1       1      11 [.     151     161 ..     148     165 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.12
                     zinc_ribbon_2  15 FCpyCGtp 22 
                                        C +CG++
  gi|385806433|ref|YP_005842831.1| 126 QCLRCGFH 133
                                       58999976 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00036
                     zinc_ribbon_2   1 fCpnCGaelqd 11 
                                       +Cp+CG+ l++
  gi|385806433|ref|YP_005842831.1| 151 RCPKCGRILKP 161
                                       69999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       875  (0.0488036); expected 358.6 (0.02)
Passed bias filter:                      801  (0.0446762); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
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 0.32s 00:00:00.93 Elapsed: 00:00:00.56
# Mc/sec: 1405.64
//
Query:       gi|385806434|ref|YP_005842832.1|  [L=47]
Description: hypothetical protein FFONT_1392 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.34s 00:00:00.83 Elapsed: 00:00:00.53
# Mc/sec: 267.52
//
Query:       gi|385806435|ref|YP_005842833.1|  [L=226]
Description: hypothetical protein FFONT_1393 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.5e-07   29.1   0.2    9.8e-07   28.2   0.2    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
      1e-05   25.4   0.1    2.3e-05   24.2   0.1    1.6  1  HTH_11          HTH domain
      2e-05   24.4   0.0    8.7e-05   22.3   0.0    1.8  2  TrmB            Sugar-specific transcriptional regulator TrmB
    5.2e-05   23.7   0.0    0.00011   22.6   0.0    1.6  1  HTH_27          Winged helix DNA-binding domain
     0.0001   22.1   0.0    0.00018   21.4   0.0    1.3  1  MarR_2          MarR family
    0.00024   20.9   0.0    0.00045   20.1   0.0    1.3  1  MarR            MarR family
     0.0016   18.4   0.0     0.0044   17.1   0.0    1.7  2  HTH_20          Helix-turn-helix domain
     0.0043   17.2   0.0     0.0089   16.1   0.0    1.5  1  Mrr_N           Mrr N-terminal domain
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.026   14.4   0.0    1.7  1  HTH_5           Bacterial regulatory protein, arsR family
      0.012   15.8   0.0      0.022   14.9   0.0    1.4  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.017   14.7   0.0       0.04   13.5   0.0    1.6  1  GerE            Bacterial regulatory proteins, luxR family
       0.02   14.6   0.0      0.032   13.9   0.0    1.2  1  DUF4423         Domain of unknown function (DUF4423)
      0.024   14.5   0.3       0.16   11.9   0.0    2.4  3  RuvB_C          RuvB C-terminal winged helix domain
      0.025   14.6   0.0       0.05   13.6   0.0    1.4  1  HTH_Mga         M protein trans-acting positive regulator (MG
      0.026   14.5   0.0      0.065   13.2   0.0    1.6  1  HTH_12          Ribonuclease R winged-helix domain
       0.15   12.1   0.1       0.33   10.9   0.1    1.7  1  HTH_36          Helix-turn-helix domain
       0.15   12.2   0.0       0.28   11.4   0.0    1.4  1  HTH_34          Winged helix DNA-binding domain


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.2   9.3e-10   9.8e-07       5      48 .]     150     193 ..     148     193 .. 0.97

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 9.3e-10
                            HTH_24   5 drkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                       d +ILe+L+ n + + +++++ l++   t+  r+ +L+++G+I+
  gi|385806435|ref|YP_005842833.1| 150 DGDILEALYNNRGSTPKDISRILNIGEKTIVNRITKLKKMGFIE 193
                                       789***************************************97 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.1   2.2e-08   2.3e-05       4      48 ..     152     194 ..     149     199 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 2.2e-08
                            HTH_11   4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpIes 48 
                                       +ile L+++rg  + +++++ Ln+ ++t++++I +L+++g  Ie+
  gi|385806435|ref|YP_005842833.1| 152 DILEALYNNRG-STPKDISRILNIGEKTIVNRITKLKKMG-FIEK 194
                                       7**********.8***************************.4554 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.9     2e+03       3      14 ..      55      66 ..      53      68 .. 0.85
   2 !   22.3   0.0   8.2e-08   8.7e-05       5      56 ..     145     196 ..     142     203 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.9
                                      HCHHHHHCCCHC CS
                              TrmB  3 klGLseyEakvY 14
                                      k G++e ++kv 
  gi|385806435|ref|YP_005842833.1| 55 KAGIKESDIKVL 66
                                      679******995 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 8.2e-08
                                       HHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB   5 GLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerek 56 
                                       G+ + + ++  aL ++  +t ++i+++l++ + ++ + + +L+++G++e++ 
  gi|385806435|ref|YP_005842833.1| 145 GIGSRDGDILEALYNNRGSTPKDISRILNIGEKTIVNRITKLKKMGFIEKRG 196
                                       7888899999***************************************984 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   1.1e-07   0.00011       8      66 ..     153     204 ..     152     206 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.1e-07
                            HTH_27   8 vLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTd 66 
                                       +L+ ++ ++r+++ +d+++ ln++  +i++ + kL ++G++e       r++ + +lT+
  gi|385806435|ref|YP_005842833.1| 153 ILEALY-NNRGSTPKDISRILNIGEKTIVNRITKLKKMGFIE------KRGRGLPSLTP 204
                                       678888.7888888***************************4......45555666665 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   1.7e-07   0.00018       6      54 ..     149     195 ..     144     201 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.7e-07
                                       HHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2   6 aqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54 
                                        + ++L aL+++ g   t++++ r l++   ++ +++ +L + G++e+r
  gi|385806435|ref|YP_005842833.1| 149 RDGDILEALYNNRG--STPKDISRILNIGEKTIVNRITKLKKMGFIEKR 195
                                       6679**********..8******************************98 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   4.2e-07   0.00045       7      50 ..     152     195 ..     148     196 .. 0.95

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4.2e-07
                                       HHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR   7 viLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50 
                                       +iL+ ly++ + + +++ + l++   t+ + +++L k G+ie++
  gi|385806435|ref|YP_005842833.1| 152 DILEALYNNRGSTPKDISRILNIGEKTIVNRITKLKKMGFIEKR 195
                                       79***************************************985 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       6.5   6.8e+03       4      19 ..     110     125 ..     108     132 .. 0.69
   2 !   17.1   0.0   4.1e-06    0.0044      14      59 ..     152     197 ..     151     198 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 6.5
                                       HHHHS-HHHHHHHHHH CS
                            HTH_20   4 aeALahPvRrrilraL 19 
                                       ++A+a+  R  i+  +
  gi|385806435|ref|YP_005842833.1| 110 LSAIASGKRVSIETTI 125
                                       6788888888887666 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 4.1e-06
                                       HHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                            HTH_20  14 rilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvre 59 
                                       +il aL  ++g t++++ + l +  +t+ +++ +L + g++e ++ 
  gi|385806435|ref|YP_005842833.1| 152 DILEALYNNRGSTPKDISRILNIGEKTIVNRITKLKKMGFIEKRGR 197
                                       79****************************************9986 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   8.5e-06    0.0089       8      84 ..     138     209 ..     133     211 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.5e-06
                             Mrr_N   8 lLealadgsehrlkeirervaerfglseeeraellpsgkqtrfknrvgWartyLkkagllespkrgvwkiTekGrev 84 
                                       +L+++ +g ++r  +i e++ ++ g ++++ ++ l+ g++ ++ nr+    t+Lkk+g++e+  rg  ++T+ G ++
  gi|385806435|ref|YP_005842833.1| 138 FLRFVISGIGSRDGDILEALYNNRGSTPKDISRILNIGEK-TIVNRI----TKLKKMGFIEKRGRGLPSLTPWGEAA 209
                                       67777777777778999999999999*********99965.777886....9********************99876 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   2.5e-05     0.026       7      47 .]     153     194 ..     152     194 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.5e-05
                                       HHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5   7 ILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVek 47 
                                       IL +L + +  +  +++++l++ + t+     kL+++G++ek
  gi|385806435|ref|YP_005842833.1| 153 ILEALYNnRGSTPKDISRILNIGEKTIVNRITKLKKMGFIEK 194
                                       8888888455999***************************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 ?   14.9   0.0   2.1e-05     0.022       8      54 ..     152     194 ..     147     198 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.1e-05
                                       HHHHHHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                    Fe_dep_repress   8 dYLetIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyvey 54 
                                       d Le++Y + ++    ++kd++++Ln+   ++   + kL+k+G++e 
  gi|385806435|ref|YP_005842833.1| 152 DILEALYNNRGS----TPKDISRILNIGEKTIVNRITKLKKMGFIEK 194
                                       567777777743....799************************9986 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.8e-05      0.04      16      42 ..     161     187 ..     148     192 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.8e-05
                                       TTS-HHHHHHHHTS-HHHHHHHHHHHH CS
                              GerE  16 eGksnkeIAeelniSekTVkvhksnim 42 
                                        G + k+I+++lni ekT+ + ++ + 
  gi|385806435|ref|YP_005842833.1| 161 RGSTPKDISRILNIGEKTIVNRITKLK 187
                                       49999**************99888763 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0     3e-05     0.032      33      74 ..     160     198 ..     153     203 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3e-05
                           DUF4423  33 kdfkadpeelakrlrpkisaeevekalefLlklgllkkdedg 74 
                                       + + ++p+ ++++l+  i ++ + + +  L+k+g+++k + g
  gi|385806435|ref|YP_005842833.1| 160 NRG-STPKDISRILN--IGEKTIVNRITKLKKMGFIEKRGRG 198
                                       455.89*********..*********************9875 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 ?   -1.9   0.0         3   3.2e+03       2      13 ..      56      67 ..      55      75 .. 0.86
   2 ?   -2.1   0.0       3.3   3.5e+03      29      45 ..     110     126 ..     103     127 .. 0.65
   3 ?   11.9   0.0   0.00015      0.16       3      60 ..     145     198 ..     144     208 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3
                                      T---HHHHHHHH CS
                            RuvB_C  2 lGLdeldikyLk 13
                                       G++e dik+L+
  gi|385806435|ref|YP_005842833.1| 56 AGIKESDIKVLH 67
                                      69999***9997 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.3
                                       HHHHTT--HHHHHHTTH CS
                            RuvB_C  29 laailgeeketiedviE 45 
                                       l+ai++ ++  ie+ iE
  gi|385806435|ref|YP_005842833.1| 110 LSAIASGKRVSIETTIE 126
                                       56666666667777766 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00015
                                       ---HHHHHHHHHHHHT.TT--B-HHHHHHHTT--HHHHHHTTHHHHHHTTSEEEETTE CS
                            RuvB_C   3 GLdeldikyLkllkekfkggpvglktlaailgeeketiedviEPyLlkeglIertsrG 60 
                                       G+ + d ++L++l+   +++    k ++ il++ ++ti + i   L k+g+Ie+  rG
  gi|385806435|ref|YP_005842833.1| 145 GIGSRDGDILEALY---NNRGSTPKDISRILNIGEKTIVNRIT-KLKKMGFIEKRGRG 198
                                       77889999999997...677778899****************5.799******98888 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   4.8e-05      0.05       6      51 ..     149     194 ..     147     197 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.8e-05
                           HTH_Mga   6 rklkLlelLteneksltldelakeLglseltlqsdiseLnel.Fpee 51 
                                       r+ ++le+L+  ++  t ++++  L++ e+t+ ++i++L+   F+e+
  gi|385806435|ref|YP_005842833.1| 149 RDGDILEALYN-NRGSTPKDISRILNIGEKTIVNRITKLKKMgFIEK 194
                                       56689******.5556679*********************9888876 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   6.2e-05     0.065      29      63 ..     173     207 ..     169     210 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.2e-05
                            HTH_12  29 digeravRyrLrkleergltrrvgyagreltEkGl 63 
                                       +ige+++  r+ kl ++g++++ g++   lt +G+
  gi|385806435|ref|YP_005842833.1| 173 NIGEKTIVNRITKLKKMGFIEKRGRGLPSLTPWGE 207
                                       89******************************997 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00031      0.33      29      55 .]     166     192 ..     153     192 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00031
                            HTH_36  29 etlakrlglsknTvsraikeLeqlGyi 55 
                                       +++++ l++ ++T+++ i +L + G+i
  gi|385806435|ref|YP_005842833.1| 166 KDISRILNIGEKTIVNRITKLKKMGFI 192
                                       799**********************98 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00027      0.28       5      45 ..     153     193 ..     152     210 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00027
                            HTH_34   5 vlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYie 45 
                                       +l  L+ ++  ++++++  l++ +  +   ++kL+k g+ie
  gi|385806435|ref|YP_005842833.1| 153 ILEALYNNRGSTPKDISRILNIGEKTIVNRITKLKKMGFIE 193
                                       8999***********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); 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 0.34s 00:00:00.93 Elapsed: 00:00:00.54
# Mc/sec: 1255.76
//
Query:       gi|385806436|ref|YP_005842834.1|  [L=57]
Description: hypothetical protein FFONT_1394 [Fervidicoccus fontis Kam940]
Scores for complete sequence (score 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   12.9   0.0      0.093   12.5   0.0    1.3  1  Cecropin  Cecropin family


Domain annotation for each model (and alignments):
>> Cecropin  Cecropin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.2e-06     0.093       6      21 ..      31      46 ..      28      47 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.2e-06
                          Cecropin  6 LEnaGkrirdAaIkgg 21
                                      LE++Gk+i+d aI ++
  gi|385806436|ref|YP_005842834.1| 31 LEKMGKNISDLAIFAI 46
                                      9********9777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); 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 0.29s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 376.14
//
[ok]
